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= 003862
(790 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2R17|C Chain C, Functional Architecture Of The Retromer Cargo-Recognition
Complex
pdb|2R17|D Chain D, Functional Architecture Of The Retromer Cargo-Recognition
Complex
Length = 298
Score = 211 bits (536), Expect = 1e-54, Method: Compositional matrix adjust.
Identities = 121/307 (39%), Positives = 181/307 (58%), Gaps = 18/307 (5%)
Query: 477 DFKEEQNSVARLIQMLQNDDTEEMFKIICTVRKHILTGGPKRLPFTVPPLVFSSLKLVRQ 536
DF +EQ+ V R I +L+++D ++ + I+ T RKH GG +R+ FT+PPLVF++ +L
Sbjct: 1 DFADEQSLVGRFIHLLRSEDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVFAAYQLA-- 58
Query: 537 LQGPEENPFGEEGSTTPKKVFQLLNQTIETLYGVPAPELALRLYLQCAEAAND---SDLE 593
+ E + ++ +K+F +QTI L EL LRL+LQ A AA + + E
Sbjct: 59 FRYKENSKVDDKWEKKCQKIFSFAHQTISALIKAELAELPLRLFLQGALAAGEIGFENHE 118
Query: 594 PVAYEFFTQAYILYEEEISDSRAQVTAIHLIIGTLQRMHVFGVENRDTLTHKATGYSAKL 653
VAYEF +QA+ LYE+EISDS+AQ+ AI LIIGT +R F EN + L + ++KL
Sbjct: 119 TVAYEFXSQAFSLYEDEISDSKAQLAAITLIIGTFERXKCFSEENHEPLRTQCALAASKL 178
Query: 654 LKKPDQCRAVYACSHLFWV-----DDQDNMKDGERVLLCLKRALRIANAAQQMSNATRGS 708
LKKPDQ RAV C+HLFW + + + G+RV CLK+AL+IAN S
Sbjct: 179 LKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVXECLKKALKIANQCXDPS------ 232
Query: 709 TGSVTLFVEILNKYLYFFEKGNTQINAAAIQSLIELITAEMQS-ESNSPDPAADAFFAST 767
V LF+EILN+Y+YF+EK N + + LI+ I ++ + ES+ + F +T
Sbjct: 233 -LQVQLFIEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHFHNT 291
Query: 768 LRYIQFQ 774
L +++ +
Sbjct: 292 LEHLRLR 298
>pdb|1WN1|A Chain A, Crystal Structure Of Dipeptiase From Pyrococcus Horikoshii
Ot3
pdb|1WN1|B Chain B, Crystal Structure Of Dipeptiase From Pyrococcus Horikoshii
Ot3
pdb|2HOW|A Chain A, Dipeptidase (Ph0974) From Pyrococcus Horikoshii Ot3
pdb|2HOW|B Chain B, Dipeptidase (Ph0974) From Pyrococcus Horikoshii Ot3
Length = 356
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 34/119 (28%), Positives = 56/119 (47%), Gaps = 4/119 (3%)
Query: 478 FKEEQNSVARLIQMLQNDDTEEMFKII-CTVRKHILTGGPKRLPFTVPPLVFSSLKLVRQ 536
+ + +N A+L ++L+ + +I T+R L G K FT PL S +K +R
Sbjct: 72 WHDGENPYAKLREILEELGISKGRILIEDTMRADWLIGIMKLGKFTFQPLS-SLIKELRM 130
Query: 537 LQGPEENPFGEEGSTTPKKVFQLLNQTIETLYGVPAPELALRLYLQCAEAANDSDLEPV 595
++ EE E S KVF+ + L G+ ELAL++ L E ++ EP+
Sbjct: 131 IKDKEEVKMMEHASRIADKVFEEI--LTWDLIGMKERELALKIELLIRELSDGIAFEPI 187
>pdb|3UIT|A Chain A, Overall Structure Of PatjPALS1MALS COMPLEX
pdb|3UIT|B Chain B, Overall Structure Of PatjPALS1MALS COMPLEX
pdb|3UIT|C Chain C, Overall Structure Of PatjPALS1MALS COMPLEX
pdb|3UIT|D Chain D, Overall Structure Of PatjPALS1MALS COMPLEX
Length = 265
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 10/81 (12%)
Query: 458 IKGLIRDLDGAAHDQVDEDDFKEEQNSVARLIQMLQNDDTEEMFKIICTVRKHILTGGPK 517
I+ L L H VD + Q ++ L+Q++QN D + FKI + H+ P
Sbjct: 82 IEDLFSSLKHIQHTLVD----SQSQEDISLLLQLVQNKDFQNAFKIHNAITVHMNKASP- 136
Query: 518 RLPFTVPPLVFSSLKLVRQLQ 538
PF PL+ ++ L +++Q
Sbjct: 137 --PF---PLISNAQDLAQEVQ 152
>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 = 30.8 bits (68), Expect = 3.0, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 9/90 (10%)
Query: 93 ELVQHAGNILPRLYLLCTVGSVYIKSKEAPAKDVLKDLVEMCRGIQHPVR---GLFLRSY 149
E AG ILP + + S K PA +LK + +G P R G R
Sbjct: 38 ETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQ 97
Query: 150 LSQISRDKLPDIGSEYEGDADTVNDAMEFV 179
+ +I++ K+PD+ +A+++ AM+ +
Sbjct: 98 IEEIAKTKMPDL------NANSLEAAMKII 121
>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 = 30.8 bits (68), Expect = 3.3, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 9/90 (10%)
Query: 93 ELVQHAGNILPRLYLLCTVGSVYIKSKEAPAKDVLKDLVEMCRGIQHPVR---GLFLRSY 149
E AG ILP + + S K PA +LK + +G P R G R
Sbjct: 44 ETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQ 103
Query: 150 LSQISRDKLPDIGSEYEGDADTVNDAMEFV 179
+ +I++ K+PD+ +A+++ AM+ +
Sbjct: 104 IEEIAKTKMPDL------NANSLEAAMKII 127
>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 = 30.8 bits (68), Expect = 3.3, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 9/90 (10%)
Query: 93 ELVQHAGNILPRLYLLCTVGSVYIKSKEAPAKDVLKDLVEMCRGIQHPVR---GLFLRSY 149
E AG ILP + + S K PA +LK + +G P R G R
Sbjct: 45 ETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQ 104
Query: 150 LSQISRDKLPDIGSEYEGDADTVNDAMEFV 179
+ +I++ K+PD+ +A+++ AM+ +
Sbjct: 105 IEEIAKTKMPDL------NANSLEAAMKII 128
>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 = 30.8 bits (68), Expect = 3.4, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 9/90 (10%)
Query: 93 ELVQHAGNILPRLYLLCTVGSVYIKSKEAPAKDVLKDLVEMCRGIQHPVR---GLFLRSY 149
E AG ILP + + S K PA +LK + +G P R G R
Sbjct: 44 ETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQ 103
Query: 150 LSQISRDKLPDIGSEYEGDADTVNDAMEFV 179
+ +I++ K+PD+ +A+++ AM+ +
Sbjct: 104 IEEIAKTKMPDL------NANSLEAAMKII 127
>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 = 30.8 bits (68), Expect = 3.4, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 9/90 (10%)
Query: 93 ELVQHAGNILPRLYLLCTVGSVYIKSKEAPAKDVLKDLVEMCRGIQHPVR---GLFLRSY 149
E AG ILP + + S K PA +LK + +G P R G R
Sbjct: 45 ETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQ 104
Query: 150 LSQISRDKLPDIGSEYEGDADTVNDAMEFV 179
+ +I++ K+PD+ +A+++ AM+ +
Sbjct: 105 IEEIAKTKMPDL------NANSLEAAMKII 128
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 0.135 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,716,396
Number of Sequences: 62578
Number of extensions: 867531
Number of successful extensions: 1989
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1982
Number of HSP's gapped (non-prelim): 13
length of query: 790
length of database: 14,973,337
effective HSP length: 107
effective length of query: 683
effective length of database: 8,277,491
effective search space: 5653526353
effective search space used: 5653526353
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)