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= 044692
(61 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|JJ Chain j, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 111
Score = 74.3 bits (181), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 45/93 (48%), Positives = 51/93 (54%), Gaps = 36/93 (38%)
Query: 1 SKSNQYPNTSLIHIEGVNTKEEV--------------------------------PHGNS 28
SKSNQY NTSL+ IEGVNTKEEV PHGNS
Sbjct: 23 SKSNQYENTSLLQIEGVNTKEEVGWYAGKRIAYVYKAKTKSNDSTIRCIWGKVTRPHGNS 82
Query: 29 GVVRAKFKSNLPPSPWYLNHGDRVRVVMYPGNI 61
GVVRAKF+SNLPP+ + G +VRV MYP +I
Sbjct: 83 GVVRAKFRSNLPPT----SMGKKVRVFMYPSSI 111
>pdb|3IZS|JJ Chain j, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3U5E|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|FF Chain f, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|FF Chain f, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 107
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 37/87 (42%), Gaps = 36/87 (41%)
Query: 7 PNTSLIHIEGVNTKEEV--------------------------------PHGNSGVVRAK 34
PN SLI IEGV T ++ HGNSGVVRA
Sbjct: 25 PNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVRGSKIRVMWGKVTRTHGNSGVVRAT 84
Query: 35 FKSNLPPSPWYLNHGDRVRVVMYPGNI 61
F++NLP + G VR+ +YP NI
Sbjct: 85 FRNNLPAKTF----GASVRIFLYPSNI 107
>pdb|4A18|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 1
pdb|4A1B|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 3.
pdb|4A1D|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 4.
pdb|4A19|H Chain H, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 26s Rrna And
Proteins Of Molecule 2
Length = 113
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 37/89 (41%), Gaps = 35/89 (39%)
Query: 1 SKSNQYPNTSLIHIEGVNTKEEVP-------------------------------HGNSG 29
SK Q N +L+ ++ VNTKE+V HGN+G
Sbjct: 26 SKHTQNSNQALLKLQNVNTKEDVAFYQGKRVVYIYKGQKKNGSNYRTIWGRIGKAHGNNG 85
Query: 30 VVRAKFKSNLPPSPWYLNHGDRVRVVMYP 58
V A+F NLPP G +RV++YP
Sbjct: 86 VAVARFAHNLPPQAI----GSVLRVMLYP 110
>pdb|3ZF7|LL Chain l, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 149
Score = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/39 (48%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 24 PHGNSGVVRAKFK-SNLPPSPWYLNHGDRVRVVMYPGNI 61
PHG SG VR KF S++P S G R+RV +YP I
Sbjct: 115 PHGTSGTVRVKFNGSSVPASA----IGRRIRVYLYPSRI 149
>pdb|1SQR|A Chain A, Solution Structure Of The 50s Ribosomal Protein L35ae
From Pyrococcus Furiosus. Northeast Structural Genomics
Consortium Target Pfr48.
pdb|2LP6|A Chain A, Refined Solution Nmr Structure Of The 50s Ribosomal
Protein L35ae From Pyrococcus Furiosus, Northeast
Structural Genomics Consortium Target (Nesg) Pfr48
Length = 95
Score = 30.0 bits (66), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 31/80 (38%), Gaps = 28/80 (35%)
Query: 1 SKSNQYPNTSLIHIEGVNTKEEVP------------------------HGNSGVVRAKFK 36
SK NQ+ N +I VN++EE HG G VRA+F+
Sbjct: 13 SKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSGKILKGKIVRVHGTKGAVRARFE 72
Query: 37 SNLPPSPWYLNHGDRVRVVM 56
LP GD V +V+
Sbjct: 73 KGLPGQAL----GDYVEIVL 88
>pdb|3J21|CC Chain c, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 87
Score = 28.9 bits (63), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 30/79 (37%), Gaps = 28/79 (35%)
Query: 1 SKSNQYPNTSLIHIEGVNTKEEVP------------------------HGNSGVVRAKFK 36
SK NQ+ N +I VN++EE HG G VRA+F+
Sbjct: 13 SKENQHNNVMIIKPLDVNSREEASKLIGRLVLWKSPSGKILKGKIVRVHGTKGAVRARFE 72
Query: 37 SNLPPSPWYLNHGDRVRVV 55
LP GD V +V
Sbjct: 73 KGLPGQAL----GDYVEIV 87
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
0.312 0.133 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,053,145
Number of Sequences: 62578
Number of extensions: 63478
Number of successful extensions: 86
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 75
Number of HSP's gapped (non-prelim): 10
length of query: 61
length of database: 14,973,337
effective HSP length: 32
effective length of query: 29
effective length of database: 12,970,841
effective search space: 376154389
effective search space used: 376154389
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 45 (21.9 bits)