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= 043054
(90 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|I Chain I, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 224
Score = 104 bits (259), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 49/76 (64%), Positives = 59/76 (77%)
Query: 15 ANPTQEALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNSENRIVPDGMNAKLFGCHG 74
A +EALRRAKFKFP RQKII SRKWGFTKF+R +Y++ +E RI+ DG+NA+L G HG
Sbjct: 145 AKHAEEALRRAKFKFPGRQKIIHSRKWGFTKFTREEYVKLKAEGRIMSDGVNAQLLGSHG 204
Query: 75 PLADRQPGRAFLEATI 90
LA R PG+AFL TI
Sbjct: 205 RLAKRAPGKAFLAETI 220
>pdb|4A17|H Chain H, 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|H Chain H, 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|H Chain H, 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|H Chain H, 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 = 215
Score = 69.7 bits (169), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 31/58 (53%), Positives = 42/58 (72%)
Query: 20 EALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNSENRIVPDGMNAKLFGCHGPLA 77
+AL RAK KFP RQK++ S+KWGFTK +RA Y R ++ ++V DG N K+ G GPL+
Sbjct: 150 DALTRAKAKFPGRQKVVTSQKWGFTKLTRAQYSRLRNQKKLVTDGSNVKVIGERGPLS 207
>pdb|2ZKR|HH Chain h, 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 = 214
Score = 67.0 bits (162), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 32/57 (56%), Positives = 40/57 (70%)
Query: 20 EALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNSENRIVPDGMNAKLFGCHGPL 76
EALRRAKFKFP RQKI +S+KWGFTKF+ ++ +E R++PDG K GPL
Sbjct: 150 EALRRAKFKFPGRQKIHISKKWGFTKFNADEFENMVAEKRLIPDGCGVKYIPNRGPL 206
>pdb|3IZS|I Chain I, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|J Chain J, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|J Chain J, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|I Chain I, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|I Chain I, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|I Chain I, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 221
Score = 56.6 bits (135), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 35/59 (59%)
Query: 20 EALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNSENRIVPDGMNAKLFGCHGPLAD 78
E LRRA++KFP +QKII+S+KWGFT R +YL+ + DG K G L +
Sbjct: 150 EGLRRARYKFPGQQKIILSKKWGFTNLDRPEYLKKREAGEVKDDGAFVKFLSKKGSLEN 208
>pdb|3J0L|J Chain J, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 9.8a Cryo-Em Map: Classic Pre State 1
pdb|3J0Q|J Chain J, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 10.6a Cryo-Em Map: Rotated Pre State 2
Length = 219
Score = 56.2 bits (134), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 35/59 (59%)
Query: 20 EALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNSENRIVPDGMNAKLFGCHGPLAD 78
E LRRA++KFP +QKII+S+KWGFT R +YL+ + DG K G L +
Sbjct: 148 EGLRRARYKFPGQQKIILSKKWGFTNLDRPEYLKKREAGEVKDDGAFVKFLSKKGSLEN 206
>pdb|2PA2|A Chain A, Crystal Structure Of Human Ribosomal Protein L10 Core
Domain
pdb|2PA2|B Chain B, Crystal Structure Of Human Ribosomal Protein L10 Core
Domain
Length = 151
Score = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 23/32 (71%), Positives = 28/32 (87%)
Query: 20 EALRRAKFKFPVRQKIIVSRKWGFTKFSRADY 51
EALRRAKFKFP RQKI +S+KWGFTKF+ ++
Sbjct: 119 EALRRAKFKFPGRQKIHISKKWGFTKFNADEF 150
>pdb|3ZF7|K Chain K, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 213
Score = 48.9 bits (115), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%)
Query: 20 EALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNSENRIVPDGMNAKLFGCHGPLA 77
E+LRRAK KFP RQ I++S+ WGFT R +Y ++ G++ KL G +
Sbjct: 150 ESLRRAKMKFPGRQIIVISKYWGFTNILRNEYEELRDAGKLQQRGLHVKLITPKGKIT 207
>pdb|3JYW|I Chain I, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 165
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 13/19 (68%), Positives = 17/19 (89%)
Query: 20 EALRRAKFKFPVRQKIIVS 38
E LRRA++KFP +QKII+S
Sbjct: 147 EGLRRARYKFPGQQKIILS 165
>pdb|1S1I|I Chain I, 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 = 168
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 13/19 (68%), Positives = 17/19 (89%)
Query: 20 EALRRAKFKFPVRQKIIVS 38
E LRRA++KFP +QKII+S
Sbjct: 150 EGLRRARYKFPGQQKIILS 168
>pdb|3HQI|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
SpopmathxBTB3-Box-Pucsbc1
pdb|3HQI|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
SpopmathxBTB3-Box-Pucsbc1
pdb|3HU6|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
SpopmathxBTB3-Box-Pucsbc1
pdb|3HU6|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
SpopmathxBTB3-Box-Pucsbc1
Length = 312
Score = 27.7 bits (60), Expect = 1.6, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 16/55 (29%)
Query: 24 RAKFKFPVRQ---------------KIIVSRKWGFTKFSRADYLRWNSENRIVPD 63
RAKFKF + + + + WGF KF R +L + N ++PD
Sbjct: 74 RAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRGFL-LDEANGLLPD 127
>pdb|2CR2|A Chain A, Solution Structure Of N-Terminal Domain Of Speckle-Type
Poz Protein
Length = 159
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 16/55 (29%)
Query: 24 RAKFKFPVRQ---------------KIIVSRKWGFTKFSRADYLRWNSENRIVPD 63
RAKFKF + + + + WGF KF R D+L + N ++PD
Sbjct: 79 RAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFL-LDEANGLLPD 132
>pdb|3IVB|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Architectures Of Btb-Cul3 Ubiquitin Ligases: Spopmath-
Macroh2asbcpep1
pdb|3IVQ|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmath-Cisbc2
pdb|3IVQ|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmath-Cisbc2
pdb|3IVV|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmath-Pucsbc1_pep1
Length = 145
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 16/55 (29%)
Query: 24 RAKFKFPVRQ---------------KIIVSRKWGFTKFSRADYLRWNSENRIVPD 63
RAKFKF + + + + WGF KF R D+L + N ++PD
Sbjct: 78 RAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFL-LDEANGLLPD 131
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
0.324 0.140 0.446
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,785,617
Number of Sequences: 62578
Number of extensions: 93209
Number of successful extensions: 180
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 171
Number of HSP's gapped (non-prelim): 13
length of query: 90
length of database: 14,973,337
effective HSP length: 57
effective length of query: 33
effective length of database: 11,406,391
effective search space: 376410903
effective search space used: 376410903
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 45 (21.9 bits)