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= 043596
(96 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 = 112 bits (279), Expect = 7e-26, Method: Compositional matrix adjust.
Identities = 53/79 (67%), Positives = 63/79 (79%)
Query: 18 DSNSHHAQEALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKSENRIVPDGVNAKLFE 77
+SN+ HA+EALRRAKFKFP RQKII SRKWGFTKF+R Y++ K+E RI+ DGVNA+L
Sbjct: 142 ESNAKHAEEALRRAKFKFPGRQKIIHSRKWGFTKFTREEYVKLKAEGRIMSDGVNAQLLG 201
Query: 78 CHGPLANRQPGRAFLEATI 96
HG LA R PG+AFL TI
Sbjct: 202 SHGRLAKRAPGKAFLAETI 220
>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 = 71.6 bits (174), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 34/63 (53%), Positives = 41/63 (65%)
Query: 20 NSHHAQEALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKSENRIVPDGVNAKLFECH 79
N H EALRRAKFKFP RQKI +S+KWGFTKF+ + +E R++PDG K
Sbjct: 144 NKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFNADEFENMVAEKRLIPDGCGVKYIPNR 203
Query: 80 GPL 82
GPL
Sbjct: 204 GPL 206
>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 = 69.3 bits (168), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 31/61 (50%), Positives = 44/61 (72%)
Query: 23 HAQEALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKSENRIVPDGVNAKLFECHGPL 82
+A +AL RAK KFP RQK++ S+KWGFTK +RA Y R +++ ++V DG N K+ GPL
Sbjct: 147 YAIDALTRAKAKFPGRQKVVTSQKWGFTKLTRAQYSRLRNQKKLVTDGSNVKVIGERGPL 206
Query: 83 A 83
+
Sbjct: 207 S 207
>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 = 63.2 bits (152), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 30/67 (44%), Positives = 38/67 (56%)
Query: 18 DSNSHHAQEALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKSENRIVPDGVNAKLFE 77
DSN E LRRA++KFP +QKII+S+KWGFT R YL+ + + DG K
Sbjct: 142 DSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPEYLKKREAGEVKDDGAFVKFLS 201
Query: 78 CHGPLAN 84
G L N
Sbjct: 202 KKGSLEN 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 = 63.2 bits (152), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 30/67 (44%), Positives = 38/67 (56%)
Query: 18 DSNSHHAQEALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKSENRIVPDGVNAKLFE 77
DSN E LRRA++KFP +QKII+S+KWGFT R YL+ + + DG K
Sbjct: 140 DSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPEYLKKREAGEVKDDGAFVKFLS 199
Query: 78 CHGPLAN 84
G L N
Sbjct: 200 KKGSLEN 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 = 55.5 bits (132), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 25/34 (73%), Positives = 28/34 (82%)
Query: 20 NSHHAQEALRRAKFKFPVRQKIIVSRKWGFTKFS 53
N H EALRRAKFKFP RQKI +S+KWGFTKF+
Sbjct: 113 NKEHVIEALRRAKFKFPGRQKIHISKKWGFTKFN 146
>pdb|3ZF7|K Chain K, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 213
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 36/66 (54%)
Query: 18 DSNSHHAQEALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKSENRIVPDGVNAKLFE 77
D+ A E+LRRAK KFP RQ I++S+ WGFT R Y + ++ G++ KL
Sbjct: 142 DTYVPQALESLRRAKMKFPGRQIIVISKYWGFTNILRNEYEELRDAGKLQQRGLHVKLIT 201
Query: 78 CHGPLA 83
G +
Sbjct: 202 PKGKIT 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 = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/27 (59%), Positives = 20/27 (74%)
Query: 18 DSNSHHAQEALRRAKFKFPVRQKIIVS 44
DSN E LRRA++KFP +QKII+S
Sbjct: 139 DSNKDVVVEGLRRARYKFPGQQKIILS 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 = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/27 (59%), Positives = 20/27 (74%)
Query: 18 DSNSHHAQEALRRAKFKFPVRQKIIVS 44
DSN E LRRA++KFP +QKII+S
Sbjct: 142 DSNKDVVVEGLRRARYKFPGQQKIILS 168
>pdb|2CR2|A Chain A, Solution Structure Of N-Terminal Domain Of Speckle-Type
Poz Protein
Length = 159
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 16/55 (29%)
Query: 30 RAKFKFPVRQ---------------KIIVSRKWGFTKFSRANYLRCKSENRIVPD 69
RAKFKF + + + + WGF KF R ++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 = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 16/55 (29%)
Query: 30 RAKFKFPVRQ---------------KIIVSRKWGFTKFSRANYLRCKSENRIVPD 69
RAKFKF + + + + WGF KF R ++L N ++PD
Sbjct: 78 RAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFL-LDEANGLLPD 131
>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 = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 16/55 (29%)
Query: 30 RAKFKFPVRQ---------------KIIVSRKWGFTKFSRANYLRCKSENRIVPD 69
RAKFKF + + + + WGF KF R +L ++ N ++PD
Sbjct: 74 RAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRGFLLDEA-NGLLPD 127
>pdb|3HQH|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmathx-Macroh2asbcpep1
pdb|3HQL|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin
Ligases:spopmathx-Pucsbc1_pep2
pdb|3HQL|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin
Ligases:spopmathx-Pucsbc1_pep2
pdb|3HQM|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmathx-Cisbc2
pdb|3HQM|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmathx-Cisbc2
pdb|3HSV|A Chain A, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmathx-Macroh2asbcpep2
pdb|3HSV|B Chain B, Structures Of Spop-Substrate Complexes: Insights Into
Molecular Architectures Of Btb-Cul3 Ubiquitin Ligases:
Spopmathx-Macroh2asbcpep2
Length = 145
Score = 25.8 bits (55), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 16/55 (29%)
Query: 30 RAKFKFPVRQ---------------KIIVSRKWGFTKFSRANYLRCKSENRIVPD 69
RAKFKF + + + + WGF KF R +L N ++PD
Sbjct: 78 RAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRGFL-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
0.321 0.134 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,909,334
Number of Sequences: 62578
Number of extensions: 88751
Number of successful extensions: 161
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: 152
Number of HSP's gapped (non-prelim): 13
length of query: 96
length of database: 14,973,337
effective HSP length: 62
effective length of query: 34
effective length of database: 11,093,501
effective search space: 377179034
effective search space used: 377179034
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: 45 (21.9 bits)