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= 030925
(169 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XTG|L Chain L, Trna Tranlocation On The 70s Ribosome: The Pre-
Translocational Translocation Intermediate Ti(Pre)
pdb|2XUX|L Chain L, Trna Translocation On The 70s Ribosome: The Post-
Translocational Translocation Intermediate Ti(Post)
pdb|3SGF|J Chain J, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3SGF|K Chain K, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3SGF|L Chain L, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3SGF|M Chain M, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3UOS|J Chain J, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
pdb|3UOS|K Chain K, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
pdb|3UOS|L Chain L, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
pdb|3UOS|M Chain M, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
Length = 121
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/63 (52%), Positives = 46/63 (73%), Gaps = 1/63 (1%)
Query: 102 FDVKLEKYDQAAKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKE 161
FDV L K A K+ +IK V+ TGLGLKE+KDLVE APA +K+GV+K++A+ + + L+E
Sbjct: 55 FDVIL-KAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEE 113
Query: 162 LNA 164
A
Sbjct: 114 AGA 116
>pdb|1RQU|A Chain A, Nmr Structure Of L7 Dimer From E.Coli
pdb|1RQU|B Chain B, Nmr Structure Of L7 Dimer From E.Coli
pdb|1RQV|A Chain A, Spatial Model Of L7 Dimer From E.Coli With One Hinge
Region In Helical State
pdb|1RQV|B Chain B, Spatial Model Of L7 Dimer From E.Coli With One Hinge
Region In Helical State
Length = 120
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/63 (52%), Positives = 46/63 (73%), Gaps = 1/63 (1%)
Query: 102 FDVKLEKYDQAAKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKE 161
FDV L K A K+ +IK V+ TGLGLKE+KDLVE APA +K+GV+K++A+ + + L+E
Sbjct: 54 FDVIL-KAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEE 112
Query: 162 LNA 164
A
Sbjct: 113 AGA 115
>pdb|2BCW|B Chain B, 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 = 68
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 34/65 (52%), Positives = 47/65 (72%), Gaps = 1/65 (1%)
Query: 102 FDVKLEKYDQAAKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKE 161
FDV L K A K+ +IK V+ TGLGLKE+KDLVE APA +K+GV+K++A+ + + L+E
Sbjct: 2 FDVIL-KAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEE 60
Query: 162 LNAIV 166
A V
Sbjct: 61 AGAEV 65
>pdb|1RQS|A Chain A, Nmr Structure Of C-Terminal Domain Of Ribosomal Protein L7
From E.Coli
pdb|1CTF|A Chain A, Structure Of The C-Terminal Domain Of The Ribosomal
Protein L7L12 FROM ESCHERICHIA COLI AT 1.7 ANGSTROMS
Length = 74
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 34/65 (52%), Positives = 47/65 (72%), Gaps = 1/65 (1%)
Query: 102 FDVKLEKYDQAAKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKE 161
FDV L K A K+ +IK V+ TGLGLKE+KDLVE APA +K+GV+K++A+ + + L+E
Sbjct: 8 FDVIL-KAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEE 66
Query: 162 LNAIV 166
A V
Sbjct: 67 AGAEV 71
>pdb|2GYA|3 Chain 3, Structure Of The 50s Subunit Of A Pre-Translocational E.
Coli Ribosome Obtained By Fitting Atomic Models For Rna
And Protein Components Into Cryo-Em Map Emd-1056
pdb|2GYA|5 Chain 5, Structure Of The 50s Subunit Of A Pre-Translocational E.
Coli Ribosome Obtained By Fitting Atomic Models For Rna
And Protein Components Into Cryo-Em Map Emd-1056
pdb|2GYC|3 Chain 3, Structure Of The 50s Subunit Of A Secm-Stalled E. Coli
Ribosome Complex Obtained By Fitting Atomic Models For
Rna And Protein Components Into Cryo-Em Map Emd-1143
pdb|2GYC|5 Chain 5, Structure Of The 50s Subunit Of A Secm-Stalled E. Coli
Ribosome Complex Obtained By Fitting Atomic Models For
Rna And Protein Components Into Cryo-Em Map Emd-1143
Length = 119
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/63 (52%), Positives = 46/63 (73%), Gaps = 1/63 (1%)
Query: 102 FDVKLEKYDQAAKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKE 161
FDV L K A K+ +IK V+ TGLGLKE+KDLVE APA +K+GV+K++A+ + + L+E
Sbjct: 53 FDVIL-KAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEE 111
Query: 162 LNA 164
A
Sbjct: 112 AGA 114
>pdb|2J01|L Chain L, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4).
This File Contains The 50s Subunit From Molecule I.
pdb|2J01|M Chain M, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4).
This File Contains The 50s Subunit From Molecule I.
pdb|2J03|L Chain L, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 4 Of 4).
This File Contains The 50s Subunit From Molecule Ii.
pdb|2J03|M Chain M, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 4 Of 4).
This File Contains The 50s Subunit From Molecule Ii.
pdb|3I8I|I Chain I, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8i Contains 50s Ribosomal Subnit. The 30s
Ribosomal Can Be Found In Pdb Entry 3i8h. Molecule A In
The Same Asym Unit Is Deposited As 3i8f (50s) And 3i8g
(30s).
pdb|3I8I|J Chain J, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8i Contains 50s Ribosomal Subnit. The 30s
Ribosomal Can Be Found In Pdb Entry 3i8h. Molecule A In
The Same Asym Unit Is Deposited As 3i8f (50s) And 3i8g
(30s)
Length = 125
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 35/67 (52%), Positives = 50/67 (74%), Gaps = 2/67 (2%)
Query: 102 FDVKLEKYDQAAKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKE 161
FDV L K A K+++IKE++ TGLGLKE+KDL EK V K+GV+K+EA++I +KL+
Sbjct: 60 FDVIL-KEAGAKKLEVIKELRAITGLGLKEAKDLAEKGGPV-KEGVSKQEAEEIKKKLEA 117
Query: 162 LNAIVVL 168
+ A+V L
Sbjct: 118 VGAVVEL 124
>pdb|2ZJQ|5 Chain 5, Interaction Of L7 With L11 Induced By Microccocin Binding
To The Deinococcus Radiodurans 50s Subunit
Length = 122
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/57 (50%), Positives = 42/57 (73%), Gaps = 1/57 (1%)
Query: 112 AAKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIVVL 168
A+KI +IKE++ TGLGLKE+KD+ EK V+K+GV K+EA+K+ +L+ A V L
Sbjct: 66 ASKINVIKEIRGITGLGLKEAKDMSEKG-GVLKEGVAKDEAEKMKAQLEAAGARVEL 121
>pdb|1DD3|A Chain A, Crystal Structure Of Ribosomal Protein L12 From Thermotoga
Maritima
pdb|1DD3|B Chain B, Crystal Structure Of Ribosomal Protein L12 From Thermotoga
Maritima
pdb|1DD4|A Chain A, Crystal Structure Of Ribosomal Protein L12 From Thermotoga
Maritim
pdb|1DD4|B Chain B, Crystal Structure Of Ribosomal Protein L12 From Thermotoga
Maritim
pdb|1GIY|I Chain I, 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|1GIY|J Chain J, 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|1YL3|I Chain I, 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|1YL3|J Chain J, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. Large Subunit. The Coordinates For The Small
Subunit Are In The Pdb Entry 1yl4
Length = 128
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/50 (60%), Positives = 37/50 (74%), Gaps = 4/50 (8%)
Query: 102 FDVKLEKYDQAAKIKIIKEVKTFTGLGLKESKDLVEKAP---AVIKKGVT 148
FDV L+ + Q KI++IK V+ TGLGLKE+KDLVEKA AVIK GV+
Sbjct: 59 FDVVLKSFGQN-KIQVIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVS 107
>pdb|2FTC|E Chain E, Structural Model For The Large Subunit Of The Mammalian
Mitochondrial Ribosome
pdb|2FTC|F Chain F, Structural Model For The Large Subunit Of The Mammalian
Mitochondrial Ribosome
Length = 137
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/69 (42%), Positives = 41/69 (59%), Gaps = 1/69 (1%)
Query: 102 FDVKLEKYDQAAKIKIIKEVKTFT-GLGLKESKDLVEKAPAVIKKGVTKEEADKIVEKLK 160
F V+L + K+K+IKE+K + G+ L ++K LVE P IK V K EA+KI L+
Sbjct: 69 FTVRLTEAKPVDKVKLIKEIKNYVQGINLVQAKKLVESLPQEIKANVAKAEAEKIKAALE 128
Query: 161 ELNAIVVLE 169
+ VVLE
Sbjct: 129 AVGGTVVLE 137
>pdb|2Y8K|A Chain A, Structure Of Ctgh5-Cbm6, An Arabinoxylan-Specific Xylanase
Length = 491
Score = 29.6 bits (65), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 108 KYDQAAKIKIIKEVKTFTGLGL-KESKDLVEKAPAVIKKGVTKEEADKIVEKLKELNAIV 166
YDQ A++K + F + L E D AP G E DKIVE+ +EL +
Sbjct: 41 PYDQIARVKELG----FNAVHLYAECFDPRYPAPGSKAPGYAVNEIDKIVERTRELGLYL 96
Query: 167 VL 168
V+
Sbjct: 97 VI 98
>pdb|2PZI|A Chain A, Crystal Structure Of Protein Kinase Pkng From
Mycobacterium Tuberculosis In Complex With
Tetrahydrobenzothiophene Ax20017
pdb|2PZI|B Chain B, Crystal Structure Of Protein Kinase Pkng From
Mycobacterium Tuberculosis In Complex With
Tetrahydrobenzothiophene Ax20017
Length = 681
Score = 27.3 bits (59), Expect = 4.4, Method: Composition-based stats.
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 9 PRLGRVFTTLKVTEAVT--SSRSLCTVTESRTQKLER 43
P R FTT ++T AVT S RS VTE + + R
Sbjct: 561 PPTSRHFTTARLTSAVTLLSGRSTSEVTEEQIRDAAR 597
>pdb|4FUK|A Chain A, Aminopeptidase From Trypanosoma Brucei
pdb|4FUK|B Chain B, Aminopeptidase From Trypanosoma Brucei
Length = 337
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 109 YDQAAKIKIIKEVKTFTGLGLKESKDLVEKAPAVIKKGVTKEEADKIVEK 158
+D + K I+ +KT L S+++++ A A K G+T +E D+IV +
Sbjct: 60 HDDSKKTAEIQRIKTVCQL----SREVLDIATAAAKPGITTDELDRIVHE 105
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
0.317 0.134 0.355
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,499,113
Number of Sequences: 62578
Number of extensions: 106096
Number of successful extensions: 579
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 563
Number of HSP's gapped (non-prelim): 19
length of query: 169
length of database: 14,973,337
effective HSP length: 92
effective length of query: 77
effective length of database: 9,216,161
effective search space: 709644397
effective search space used: 709644397
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)