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= 032380
(142 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|Z Chain Z, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 162
Score = 174 bits (440), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 88/113 (77%), Positives = 95/113 (84%)
Query: 8 KVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAEAVKKKRRSTKKPYSRSIVGA 67
+VFLFANSKCKRYFHNRLKP+KLTWT+MYRKQHKKDI AEAVKK+RR+TKKPYSRSIVGA
Sbjct: 29 QVFLFANSKCKRYFHNRLKPAKLTWTAMYRKQHKKDIHAEAVKKRRRTTKKPYSRSIVGA 88
Query: 68 TLEVIQKRRTEKPEVRDAAREAALREIKERIXXXXXXXXXXXXXVTSKSKTQS 120
TLEVIQK+R+EKPEVRDAAREAALREIKERI V KTQS
Sbjct: 89 TLEVIQKKRSEKPEVRDAAREAALREIKERIKKTKDEKKAKKAEVAKSQKTQS 141
>pdb|2ZKR|UU Chain u, 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 = 157
Score = 72.4 bits (176), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 39/86 (45%), Positives = 57/86 (66%), Gaps = 3/86 (3%)
Query: 8 KVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAEAVKKK-RRSTKKPYSRSIVG 66
KVF F N+KC+ F ++ P ++ WT +YR++HKK + E KK+ RR+ K + R+I G
Sbjct: 27 KVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHKKGQSEEIQKKRTRRAVK--FQRAITG 84
Query: 67 ATLEVIQKRRTEKPEVRDAAREAALR 92
A+L I +R +KPEVR A RE A+R
Sbjct: 85 ASLADIMAKRNQKPEVRKAQREQAIR 110
>pdb|3IZS|Z Chain Z, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|V Chain V, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|V Chain V, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|W Chain W, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|W Chain W, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|W Chain W, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 155
Score = 71.2 bits (173), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 38/80 (47%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 8 KVFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAEAVKKKRRSTKKPYSRSIVGA 67
K+F F NSK F R P ++ WT ++RK HKK I E KK+ R T K R I GA
Sbjct: 27 KIFRFQNSKSASLFKQRKNPRRIAWTVLFRKHHKKGITEEVAKKRSRKTVKA-QRPITGA 85
Query: 68 TLEVIQKRRTEKPEVRDAAR 87
+L++I++RR+ KPEVR A R
Sbjct: 86 SLDLIKERRSLKPEVRKANR 105
>pdb|4A17|T Chain T, 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|T Chain T, 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|T Chain T, 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|T Chain T, 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 = 158
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 49/89 (55%), Gaps = 3/89 (3%)
Query: 10 FLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAE-AVKKKRRSTKKPYSRSIVGAT 68
F F K K ++K K+TWT R+ KK A + A KKK+R+ +R+IVG +
Sbjct: 31 FFFLTKKAKCLSLRKVKAQKITWTIARRRLWKKVKATDIAQKKKKRNV--TVARAIVGIS 88
Query: 69 LEVIQKRRTEKPEVRDAAREAALREIKER 97
LE I +R+ + A E A+RE+K++
Sbjct: 89 LEEINRRKNLDASHKKAEAEKAVRELKQK 117
>pdb|3ZF7|Y Chain Y, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 125
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 29/95 (30%), Positives = 48/95 (50%), Gaps = 4/95 (4%)
Query: 2 LPWLWVK---VFLFANSKCKRYFHNRLKPSKLTWTSMYRKQHKKDIAAEAVKKKRRSTKK 58
+P+ ++ V FA KC + + P + WT YR+ H+K + V ++R +
Sbjct: 22 VPFAFLSTKPVLTFARPKCFAMYMRKKNPRFIAWTRTYRRIHRK-TTTDRVGRRRAARTV 80
Query: 59 PYSRSIVGATLEVIQKRRTEKPEVRDAAREAALRE 93
R+IVGA L IQ+ R + +V A+ A+RE
Sbjct: 81 RAERAIVGAELSYIQEVRAKAKKVDRTAKGKAVRE 115
>pdb|3J21|V Chain V, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 66
Score = 30.0 bits (66), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 8 KVFLFANSKCKRYFHNRLKPSKLTWTSMYRK 38
+V F + KC+RY+ P KL WT Y++
Sbjct: 28 RVLFFCSRKCERYYFMGRNPRKLKWTKAYQE 58
>pdb|1S1I|S Chain S, 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|2X7N|D Chain D, Mechanism Of Eif6s Anti-Association Activity
Length = 56
Score = 29.6 bits (65), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 8 KVFLFANSKCKRYFHNRLKPSKLTWTSMYR 37
K+F F NSK F R P ++ WT ++R
Sbjct: 27 KIFRFQNSKSASLFKQRKNPRRIAWTVLFR 56
>pdb|2KKM|A Chain A, Solution Nmr Structure Of Yeast Protein Yor252w [residues
38-178]: Northeast Structural Genomics Consortium Target
Yt654
Length = 144
Score = 25.8 bits (55), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 16/62 (25%)
Query: 41 KKDIAAEAVKKKRRSTKKPYSRSIVGATLEVIQKRRTEK----------PEVRDAAREAA 90
+ D + +KKKRRS + P +R + ++Q+RR ++ P++ DA
Sbjct: 60 RDDTELDELKKKRRSNRPPSNRQV------LLQQRRDQELKEFKAGFLCPDLSDAKNMEF 113
Query: 91 LR 92
LR
Sbjct: 114 LR 115
>pdb|3JYW|S Chain S, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus
Ribosome At 8.9a Resolution
Length = 45
Score = 25.8 bits (55), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 8 KVFLFANSKCKRYFHNRLKPSKLTWT 33
K+F F NSK F R P ++ WT
Sbjct: 20 KIFRFQNSKSASLFKQRKNPRRIAWT 45
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 0.127 0.368
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,624,122
Number of Sequences: 62578
Number of extensions: 78021
Number of successful extensions: 205
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 193
Number of HSP's gapped (non-prelim): 10
length of query: 142
length of database: 14,973,337
effective HSP length: 89
effective length of query: 53
effective length of database: 9,403,895
effective search space: 498406435
effective search space used: 498406435
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)