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= 031165
(164 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|U Chain U, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 164
Score = 311 bits (798), Expect = 8e-86, Method: Compositional matrix adjust.
Identities = 150/164 (91%), Positives = 157/164 (95%)
Query: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60
MPAGHGLRSRTRDLFARPFRKKGYIPL+TYLRTYK+G++VDVKVNGAVHKGMPHKFYHGR
Sbjct: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLTTYLRTYKVGEHVDVKVNGAVHKGMPHKFYHGR 60
Query: 61 TGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSRCTEEFKLRKKKNDELKADAK 120
TGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSRC EEF RK ND+LKA+AK
Sbjct: 61 TGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSRCNEEFLQRKLNNDKLKAEAK 120
Query: 121 ARGEVISTKRQPKGPKPGFMVEGATLETVTPIPYDVVNDLKGGY 164
ARGEVISTKRQP GPKPGFMVEG T+ETVTPIPYDVVNDLKGGY
Sbjct: 121 ARGEVISTKRQPAGPKPGFMVEGTTIETVTPIPYDVVNDLKGGY 164
>pdb|3IZS|U Chain U, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|T Chain T, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|T Chain T, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|T Chain T, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|T Chain T, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|T Chain T, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 160
Score = 174 bits (441), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 83/157 (52%), Positives = 113/157 (71%), Gaps = 2/157 (1%)
Query: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60
M HG RSRTR +F R FRK G + LSTYL+ YK+GD VD+K NG++ KGMPHKFY G+
Sbjct: 1 MGKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKGMPHKFYQGK 60
Query: 61 TGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSRCTEEFKLRKKKNDELKADAK 120
TG V+NVTK ++GV INK VGNR ++KR+++RVEH++ S+C +EF R K N +A+AK
Sbjct: 61 TGVVYNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSKCRQEFLERVKANAAKRAEAK 120
Query: 121 ARGEVISTKRQPKGPKPGFMV--EGATLETVTPIPYD 155
A+G + KRQP P+ +V EG +T+ P+PY+
Sbjct: 121 AQGVAVQLKRQPAQPRESRIVSTEGNVPQTLAPVPYE 157
>pdb|2ZKR|QQ Chain q, 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 = 160
Score = 150 bits (378), Expect = 4e-37, Method: Compositional matrix adjust.
Identities = 76/159 (47%), Positives = 105/159 (66%), Gaps = 2/159 (1%)
Query: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60
M G R TR +F+RPFRK G +PL+TY+R YK GD VD+K G V KGMPHK YHG+
Sbjct: 1 MTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKGMPHKCYHGK 60
Query: 61 TGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSRCTEEFKLRKKKNDELKADAK 120
TGRV+NVT+ A+G+ +NKQV +I+ KRI+VR+EH++ S+ + F R K+ND+ K +AK
Sbjct: 61 TGRVYNVTQHAVGIIVNKQVKGKILAKRINVRIEHIKHSKSRDSFLKRVKENDQKKKEAK 120
Query: 121 ARGEVISTKRQPKGPKPGFMV--EGATLETVTPIPYDVV 157
+G + KR P+ V G E + PIPY+ +
Sbjct: 121 EKGTWVQLKRHAAPPREAHFVRTNGKEPELLEPIPYEFM 159
>pdb|4A17|P Chain P, 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|P Chain P, 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|P Chain P, 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|P Chain P, 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 = 157
Score = 141 bits (356), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 67/144 (46%), Positives = 98/144 (68%)
Query: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60
M +G R +TR FA+ ++ KG++ +S YL TYK+G+YVD+ V+G+ HKGMP+K YHGR
Sbjct: 1 MTHSYGYRRQTRKKFAKAYKTKGHVRISRYLTTYKVGEYVDIMVDGSQHKGMPYKLYHGR 60
Query: 61 TGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSRCTEEFKLRKKKNDELKADAK 120
TG+V+NV R+IGV +++ V R I+KR+HV++EHV+PS R + ND+ KA+
Sbjct: 61 TGKVFNVNPRSIGVIVHRIVNGRYIEKRLHVKIEHVRPSNVKTALSKRYQANDQAKAEGN 120
Query: 121 ARGEVISTKRQPKGPKPGFMVEGA 144
G+ +STKR P P V+GA
Sbjct: 121 KAGKRVSTKRNPGQPLEAVQVQGA 144
>pdb|3ZF7|U Chain U, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 159
Score = 132 bits (331), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 67/121 (55%), Positives = 81/121 (66%)
Query: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60
M HG + TR LFA+ FRK G +ST L +K+GDYVDV + AV GMPHK+YHGR
Sbjct: 1 MVHSHGYKCGTRHLFAKKFRKHGVPSVSTILTNFKVGDYVDVVADAAVRAGMPHKYYHGR 60
Query: 61 TGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSRCTEEFKLRKKKNDELKADAK 120
TG VWNVT R +GV INK V NR ++KRI VR EHV+ SRC E FK + K + +A K
Sbjct: 61 TGIVWNVTPRGVGVIINKPVRNRTVRKRICVRFEHVRKSRCQEAFKQKLKDLEAFRAAKK 120
Query: 121 A 121
A
Sbjct: 121 A 121
>pdb|1S1I|Q Chain Q, 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 = 100
Score = 132 bits (331), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 60/100 (60%), Positives = 79/100 (79%)
Query: 1 MPAGHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGR 60
M HG RSRTR +F R FRK G + LSTYL+ YK+GD VD+K NG++ KGMPHKFY G+
Sbjct: 1 MGKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKGMPHKFYQGK 60
Query: 61 TGRVWNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSR 100
TG V+NVTK ++GV INK VGNR ++KR+++RVEH++ S+
Sbjct: 61 TGVVYNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSK 100
>pdb|3JYW|Q Chain Q, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 116
Score = 130 bits (327), Expect = 4e-31, Method: Compositional matrix adjust.
Identities = 59/96 (61%), Positives = 78/96 (81%)
Query: 5 HGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGRV 64
HG RSRTR +F R FRK G + LSTYL+ YK+GD VD+K NG++ KGMPHKFY G+TG V
Sbjct: 4 HGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKGMPHKFYQGKTGVV 63
Query: 65 WNVTKRAIGVEINKQVGNRIIKKRIHVRVEHVQPSR 100
+NVTK ++GV INK VGNR ++KR+++RVEH++ S+
Sbjct: 64 YNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSK 99
>pdb|3J21|R Chain R, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 97
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 41/74 (55%)
Query: 4 GHGLRSRTRDLFARPFRKKGYIPLSTYLRTYKIGDYVDVKVNGAVHKGMPHKFYHGRTGR 63
H R +TR ++ R++G PL+ +L+ +++G V + + + HKGMP +HGRTG
Sbjct: 5 AHSFRRKTRKKLSKHPRRRGLPPLTRFLQEFEVGQRVHIVIEPSYHKGMPDPRFHGRTGT 64
Query: 64 VWNVTKRAIGVEIN 77
V A VEI
Sbjct: 65 VVGKRGEAYIVEIK 78
>pdb|2G02|A Chain A, Nisin Cyclase
pdb|2G0D|A Chain A, Nisin Cyclase
Length = 409
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 141 VEGATLETVTPIPYDVVNDLKG 162
+EG LE +TP YDV+ L G
Sbjct: 121 IEGFNLENITPPDYDVIEGLSG 142
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
0.319 0.139 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,227,738
Number of Sequences: 62578
Number of extensions: 210165
Number of successful extensions: 392
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 381
Number of HSP's gapped (non-prelim): 13
length of query: 164
length of database: 14,973,337
effective HSP length: 91
effective length of query: 73
effective length of database: 9,278,739
effective search space: 677347947
effective search space used: 677347947
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)