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= 032208
(145 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|H Chain H, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 258
Score = 202 bits (515), Expect = 4e-53, Method: Compositional matrix adjust.
Identities = 99/120 (82%), Positives = 105/120 (87%)
Query: 23 NPLFEKRPKQFGIGGALPPKKDLHRYVKWPKAXXXXXXXXXXXXXXKVPPALNQFTKTLD 82
NPLFEKRPKQFGIGGALPPKKDLHR+VKWPK KVPPALNQFT+TLD
Sbjct: 22 NPLFEKRPKQFGIGGALPPKKDLHRFVKWPKVVRIQRQRRILKQRLKVPPALNQFTRTLD 81
Query: 83 KNLASSLFKLLLKYRPEDRAAKKERLLKRAQAEAEGKTVEAKKPIVVKYGLNHVTYLIEQ 142
KNLA++LFK+LLKYRPED+AAKKERLLKRAQAEAEGKTVEAKKPIVVKYGLNHVTYLIEQ
Sbjct: 82 KNLATNLFKMLLKYRPEDKAAKKERLLKRAQAEAEGKTVEAKKPIVVKYGLNHVTYLIEQ 141
>pdb|4A17|F Chain F, 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|F Chain F, 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|F Chain F, 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|F Chain F, 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 = 255
Score = 134 bits (338), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 64/119 (53%), Positives = 85/119 (71%)
Query: 23 NPLFEKRPKQFGIGGALPPKKDLHRYVKWPKAXXXXXXXXXXXXXXKVPPALNQFTKTLD 82
NPLF+ +P+ F +GG + PK+DL R+V+WP+ KVPP ++QFTKTLD
Sbjct: 19 NPLFQAKPRSFRVGGDIQPKRDLTRFVRWPRYITLQRQKRVLLQRLKVPPQIHQFTKTLD 78
Query: 83 KNLASSLFKLLLKYRPEDRAAKKERLLKRAQAEAEGKTVEAKKPIVVKYGLNHVTYLIE 141
KN +S+LFKLL Y PE A KK+RL+ +A+A+ +GK VE KKPIV+KYGLNH+T LIE
Sbjct: 79 KNQSSNLFKLLASYAPEKPAEKKQRLVAQAEAKKDGKQVETKKPIVLKYGLNHITTLIE 137
>pdb|2ZKR|FF Chain f, 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 = 266
Score = 119 bits (299), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 62/120 (51%), Positives = 79/120 (65%), Gaps = 1/120 (0%)
Query: 23 NPLFEKRPKQFGIGGALPPKKDLHRYVKWPKAXXXXXXXXXXXXXXKVPPALNQFTKTLD 82
NPLFEKRPK FGIG + PK+DL R+VKWP+ KVPPA+NQFT+ LD
Sbjct: 29 NPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFTQALD 88
Query: 83 KNLASSLFKLLLKYRPEDRAAKKERLLKRAQAEAEGK-TVEAKKPIVVKYGLNHVTYLIE 141
+ A+ L KL KYRPE + KK+RLL RA+ +A GK V K+P V++ G+N VT L+E
Sbjct: 89 RQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTTLVE 148
>pdb|3IZS|H Chain H, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|H Chain H, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|H Chain H, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|G Chain G, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 256
Score = 118 bits (296), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 64/122 (52%), Positives = 74/122 (60%), Gaps = 2/122 (1%)
Query: 23 NPLFEKRPKQFGIGGALPPKKDLHRYVKWPKAXXXXXXXXXXXXXXKVPPALNQFTKTLD 82
NPL PK FGIG A+ PK++L RYVKWP+ KVPP + QF TLD
Sbjct: 24 NPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPPTIAQFQYTLD 83
Query: 83 KNLASSLFKLLLKYRPEDRAAKKERLLKRAQAEAEGKTVE--AKKPIVVKYGLNHVTYLI 140
+N A+ FKL KYRPE A KKERL K A A AEGK+ + + KP VKYGLNHV LI
Sbjct: 84 RNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQDASPKPYAVKYGLNHVVALI 143
Query: 141 EQ 142
E
Sbjct: 144 EN 145
>pdb|3ZF7|XX Chain x, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 276
Score = 94.0 bits (232), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 51/119 (42%), Positives = 68/119 (57%), Gaps = 2/119 (1%)
Query: 26 FEKRPKQFGIGGALPPKKDLHRYVKWPKAXXXXXXXXXXXXXXKVPPALNQFTKTLDKNL 85
F RPK FGIG +P +DL R+++WP KVPPALNQFTK LD++
Sbjct: 40 FVARPKDFGIGRDVPYARDLSRFMRWPTFVTMQRKKRVLQRRLKVPPALNQFTKVLDRSS 99
Query: 86 ASSLFKLLLKYRPEDRAAKKERLLKRAQAEAEG--KTVEAKKPIVVKYGLNHVTYLIEQ 142
+ L KL+ KY PE R A+++RL K A+ + + TV K P+ V GL VT IE+
Sbjct: 100 RNELLKLVKKYAPETRKARRDRLTKVAEEKKKNPKGTVSTKAPLCVVSGLQEVTRTIEK 158
>pdb|1S1I|G Chain G, 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 = 119
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/43 (60%), Positives = 29/43 (67%), Gaps = 2/43 (4%)
Query: 102 AAKKERLLKRAQAEAEGKTVE--AKKPIVVKYGLNHVTYLIEQ 142
A KKERL K A A AEGK+ + + KP VKYGLNHV LIE
Sbjct: 2 AEKKERLTKEAAAVAEGKSKQDASPKPYAVKYGLNHVVALIEN 44
>pdb|3JYW|G Chain G, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 113
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/39 (58%), Positives = 26/39 (66%), Gaps = 2/39 (5%)
Query: 106 ERLLKRAQAEAEGKTVE--AKKPIVVKYGLNHVTYLIEQ 142
ERL K A A AEGK+ + + KP VKYGLNHV LIE
Sbjct: 1 ERLTKEAAAVAEGKSKQDASPKPYAVKYGLNHVVALIEN 39
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
0.318 0.136 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,080,748
Number of Sequences: 62578
Number of extensions: 87893
Number of successful extensions: 234
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 216
Number of HSP's gapped (non-prelim): 10
length of query: 145
length of database: 14,973,337
effective HSP length: 89
effective length of query: 56
effective length of database: 9,403,895
effective search space: 526618120
effective search space used: 526618120
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: 47 (22.7 bits)