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= 033200
(125 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A5N|A Chain A, Redoxregulator Hypr In Its Reduced Form
pdb|4A5N|B Chain B, Redoxregulator Hypr In Its Reduced Form
pdb|4A5N|C Chain C, Redoxregulator Hypr In Its Reduced Form
pdb|4A5N|D Chain D, Redoxregulator Hypr In Its Reduced Form
Length = 131
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 66 VVLTRNIIGKKRFNQFRGKAIALHSQVITEFCKSIGAD 103
++ I GKKRFN+FR ++ +++T + + AD
Sbjct: 30 ILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEAD 67
>pdb|4A5M|A Chain A, Redox Regulator Hypr In Its Oxidized Form
pdb|4A5M|B Chain B, Redox Regulator Hypr In Its Oxidized Form
pdb|4A5M|C Chain C, Redox Regulator Hypr In Its Oxidized Form
pdb|4A5M|D Chain D, Redox Regulator Hypr In Its Oxidized Form
pdb|4A5M|E Chain E, Redox Regulator Hypr In Its Oxidized Form
pdb|4A5M|F Chain F, Redox Regulator Hypr In Its Oxidized Form
pdb|4A5M|G Chain G, Redox Regulator Hypr In Its Oxidized Form
pdb|4A5M|H Chain H, Redox Regulator Hypr In Its Oxidized Form
Length = 131
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 66 VVLTRNIIGKKRFNQFRGKAIALHSQVITEFCKSIGAD 103
++ I GKKRFN+FR ++ +++T + + AD
Sbjct: 30 ILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEAD 67
>pdb|2BCW|A Chain A, Coordinates Of The N-Terminal Domain Of Ribosomal Protein
L11,C-Terminal Domain Of Ribosomal Protein L7L12 AND A
Portion Of The G' Domain Of Elongation Factor G, As
Fitted Into Cryo-Em Map Of An Escherichia Coli 70sEf-
GGdpFusidic Acid Complex
Length = 65
Score = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 83 GKAIALHSQVITEFCKSIGADAKQRQGLI 111
G A+ H I EFCK A+ + G+I
Sbjct: 18 GPALGQHGVNIMEFCKRFNAETADKAGMI 46
>pdb|487D|L Chain L, Seven Ribosomal Proteins Fitted To A Cryo-Electron
Microscopic Map Of The Large 50s Subunit At 7.5
Angstroms Resolution
pdb|1PN7|L Chain L, Coordinates Of S12, L11 Proteins And P-Trna, From The 70s
X- Ray Structure Aligned To The 70s Cryo-Em Map Of
E.Coli Ribosome
pdb|1PN8|L Chain L, Coordinates Of S12, L11 Proteins And E-Site Trna From 70s
Crystal Structure Separately Fitted Into The Cryo-Em Map
Of E.Coli 70s.Ef-G.Gdpnp Complex. The Atomic Coordinates
Originally From The E-Site Trna Were Fitted In The
Position Of The Hybrid PE-Site Trna
Length = 133
Score = 25.4 bits (54), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 83 GKAIALHSQVITEFCKSIGADAKQRQGLI 111
G A+ H I EFCK A+ + G+I
Sbjct: 18 GPALGQHGVNIMEFCKRFNAETADKAGMI 46
>pdb|1JQM|A Chain A, Fitting Of L11 Protein And Elongation Factor G (Ef-G) In
The Cryo-Em Map Of E. Coli 70s Ribosome Bound With Ef-G,
Gdp And Fusidic Acid
pdb|1JQS|A Chain A, Fitting Of L11 Protein And Elongation Factor G (Domain G'
And V) In The Cryo-Em Map Of E. Coli 70s Ribosome Bound
With Ef-G And Gmppcp, A Nonhydrolysable Gtp Analog
pdb|1JQT|A Chain A, Fitting Of L11 Protein In The Low Resolution Cryo-Em Map
Of E.Coli 70s Ribosome
Length = 139
Score = 25.4 bits (54), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 83 GKAIALHSQVITEFCKSIGADAKQRQGLI 111
G A+ H I EFCK A+ + G+I
Sbjct: 24 GPALGQHGVNIMEFCKRFNAETADKAGMI 52
>pdb|1GIY|L Chain L, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1giy, Contains The 50s Ribosome Subunit. The
30s Ribosome Subunit, Three Trna, And Mrna Molecules Are
In The File 1gix
pdb|1MJ1|L Chain L, Fitting The Ternary Complex Of Ef-TuTRNAGTP AND RIBOSOMAL
PROTEINS Into A 13 A Cryo-Em Map Of The Coli 70s
Ribosome
pdb|1ML5|LL Chain l, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1YL3|L Chain L, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. Large Subunit. The Coordinates For The Small
Subunit Are In The Pdb Entry 1yl4.
pdb|2B66|K Chain K, 50s Ribosomal Subunit From A Crystal Structure Of Release
Factor Rf1, Trnas And Mrna Bound To The Ribosome. This
File Contains The 50s Subunit From A Crystal Structure
Of Release Factor Rf1, Trnas And Mrna Bound To The
Ribosome And Is Described In Remark 400
pdb|2B9N|K Chain K, 50s Ribosomal Subunit From A Crystal Structure Of Release
Factor Rf2, Trnas And Mrna Bound To The Ribosome. This
File Contains The 50s Subunit From A Crystal Structure
Of Release Factor Rf1, Trnas And Mrna Bound To The
Ribosome And Is Described In Remark 400.
pdb|2B9P|K Chain K, 50s Ribosomal Subunit From A Crystal Structure Of The
Ribosome In Complex With Trnas And Mrna With A Stop
Codon In The A-Site. This File Contains The 50s Subunit
From A Crystal Structure Of The Ribosome In Complex With
Trnas And Mrna With A Stop Codon In The A-Site And Is
Described In Remark 400.
pdb|2JQ7|A Chain A, Model For Thiostrepton Binding To The Ribosomal L11-Rna
pdb|2K3F|A Chain A, Ribosomal Protein L11 From Thermotoga Maritima
Length = 141
Score = 25.4 bits (54), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 83 GKAIALHSQVITEFCKSIGADAKQRQGLI 111
G A+ H I EFCK A+ + G+I
Sbjct: 25 GPALGQHGVNIMEFCKRFNAETADKAGMI 53
>pdb|1EG0|K Chain K, Fitting Of Components With Known Structure Into An 11.5 A
Cryo-Em Map Of The E.Coli 70s Ribosome
Length = 140
Score = 25.4 bits (54), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 83 GKAIALHSQVITEFCKSIGADAKQRQGLI 111
G A+ H I EFCK A+ + G+I
Sbjct: 25 GPALGQHGVNIMEFCKRFNAETADKAGMI 53
>pdb|1R2W|A Chain A, Coordinates Of L11 With 58nts Of 23s Rrna Fitted Into The
Cryo-Em Map Of The 70s Ribosome
pdb|1R2X|A Chain A, Coordinates Of L11 With 58nts Of 23s Rrna Fitted Into The
Cryo-Em Map Of Ef-Tu Ternary Complex (Gdp.Kirromycin)
Bound 70s Ribosome
Length = 141
Score = 25.4 bits (54), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 83 GKAIALHSQVITEFCKSIGADAKQRQGLI 111
G A+ H I EFCK A+ + G+I
Sbjct: 24 GPALGQHGVNIMEFCKRFNAETADKAGMI 52
>pdb|1MMS|A Chain A, Crystal Structure Of The Ribosomal Protein L11-Rna Complex
pdb|1MMS|B Chain B, Crystal Structure Of The Ribosomal Protein L11-Rna Complex
pdb|1MVR|L Chain L, Decoding Center & Peptidyl Transferase Center From The
X-Ray Structure Of The Thermus Thermophilus 70s
Ribosome, Aligned To The Low Resolution Cryo-Em Map Of
E.Coli 70s Ribosome
pdb|1OLN|A Chain A, Model For Thiostrepton Antibiotic Binding To L11 Substrate
From 50s Ribosomal Rna
Length = 140
Score = 25.4 bits (54), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 83 GKAIALHSQVITEFCKSIGADAKQRQGLI 111
G A+ H I EFCK A+ + G+I
Sbjct: 24 GPALGQHGVNIMEFCKRFNAETADKAGMI 52
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
0.323 0.136 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,466,310
Number of Sequences: 62578
Number of extensions: 122200
Number of successful extensions: 230
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 221
Number of HSP's gapped (non-prelim): 9
length of query: 125
length of database: 14,973,337
effective HSP length: 86
effective length of query: 39
effective length of database: 9,591,629
effective search space: 374073531
effective search space used: 374073531
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)