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= 022012
(304 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2J01|C Chain C, 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|C Chain C, 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|2V47|C Chain C, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 2 Of 4). This File Contains The 50s
Subunit For Molecule 1.
pdb|2OM7|K Chain K, Structural Basis For Interaction Of The Ribosome With The
Switch Regions Of Gtp-Bound Elongation Factors
pdb|2WDI|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A-Site Trna,
Deacylated P-Site Trna, And E-Site Trna. This File
Contains The 50s Subunit For Molecule I.
pdb|2WDJ|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A-Site Trna,
Deacylated P-Site Trna, And E-Site Trna. This File
Contains The 50s Subunit For Molecule Ii.
pdb|2WDL|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A- And P-Site
Trnas, And E-Site Trna. This File Contains The 50s
Subunit For Molecule I.
pdb|2WDN|C Chain C, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A- And P-Site
Trnas, And E-Site Trna. This File Contains The 50s
Subunit For Molecule Ii.
pdb|2WH2|C Chain C, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|2WH4|C Chain C, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|3HUX|C Chain C, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 50s Subunit For Molecule I.
pdb|3HUZ|C Chain C, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 50s Subunit For Molecule Ii.
pdb|2WRJ|C Chain C, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State (Part 2 Of 4).
pdb|2WRL|C Chain C, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State. (Part 4 Of
4).
pdb|2WRO|C Chain C, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 2 Of 4).
pdb|2WRR|C Chain C, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 4 Of 4).
pdb|3KIR|C Chain C, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 2 Of 4)
pdb|3KIT|C Chain C, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 4 Of 4)
pdb|3KIW|C Chain C, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 2 Of 4)
pdb|3KIY|C Chain C, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 4 Of 4)
pdb|3KNI|C Chain C, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 50s Subunit For Molecule I
pdb|3KNK|C Chain C, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 50s Subunit For Molecule Ii.
pdb|3KNM|C Chain C, The Structures Of Capreomycin Bound To The 70s Ribosome.
Thi Contains The 50s Subunit For Molecule I.
pdb|3KNO|C Chain C, The Structures Of Capreomycin Bound To The 70s Ribosome.
Thi Contains The 50s Subunit For Molecule Ii
pdb|2X9S|C Chain C, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9U|C Chain C, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2XG0|C Chain C, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 2 Of 4)
pdb|2XG2|C Chain C, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 4 Of 4)
pdb|2XQE|C Chain C, The Structure Of Ef-Tu And Aminoacyl-Trna Bound To The 70s
Ribosome With A Gtp Analog
pdb|2XTG|C Chain C, Trna Tranlocation On The 70s Ribosome: The Pre-
Translocational Translocation Intermediate Ti(Pre)
pdb|2XUX|C Chain C, Trna Translocation On The 70s Ribosome: The Post-
Translocational Translocation Intermediate Ti(Post)
pdb|2Y0V|C Chain C, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0X|C Chain C, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0Z|C Chain C, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y11|C Chain C, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome.
pdb|2Y13|C Chain C, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y15|C Chain C, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Cognate Codon On The 70s Ribosome.
pdb|2Y17|C Chain C, Ef-Tu Complex 3
pdb|2Y19|C Chain C, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome
Length = 229
Score = 79.3 bits (194), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 48/124 (38%), Positives = 67/124 (54%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
V + +A + VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 20 VYTIDEAARLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 79
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I G +D + +T M + K+ +IL GL+
Sbjct: 80 KGEKIKEAEEAGADYVGGEEIIQKIL-DGWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 138
Query: 301 PNPK 304
PNPK
Sbjct: 139 PNPK 142
>pdb|1GIY|C Chain C, 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|1ML5|CC Chain c, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1YL3|C Chain C, 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 = 228
Score = 77.8 bits (190), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 47/124 (37%), Positives = 66/124 (53%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
+ + +A VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 19 IYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 78
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I G +D + +T M + K+ +IL GL+
Sbjct: 79 KGEKIKEAEEAGADYVGGEEIIQKIL-DGWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 137
Query: 301 PNPK 304
PNPK
Sbjct: 138 PNPK 141
>pdb|3UMY|A Chain A, Crystal Structure Of Mutant Ribosomal Protein T217a Tthl1
In Complex With 80nt 23s Rna From Thermus Thermophilus
Length = 228
Score = 77.8 bits (190), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 47/124 (37%), Positives = 66/124 (53%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
+ + +A VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 19 IYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 78
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I G +D + +T M + K+ +IL GL+
Sbjct: 79 KGEKIKEAEEAGADYVGGEEIIQKIL-DGWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 137
Query: 301 PNPK 304
PNPK
Sbjct: 138 PNPK 141
>pdb|4F9T|A Chain A, Ribosomal Protein L1 From Thermus Thermophilus With
Substitution Thr217ala
Length = 229
Score = 77.8 bits (190), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 47/124 (37%), Positives = 66/124 (53%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
+ + +A VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 20 IYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 79
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I G +D + +T M + K+ +IL GL+
Sbjct: 80 KGEKIKEAEEAGADYVGGEEIIQKIL-DGWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 138
Query: 301 PNPK 304
PNPK
Sbjct: 139 PNPK 142
>pdb|3TG8|A Chain A, Mutant Ribosomal Protein L1 Lacking Ala158 From Thermus
Thermophilus
Length = 228
Score = 77.8 bits (190), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 47/124 (37%), Positives = 66/124 (53%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
+ + +A VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 20 IYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 79
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I G +D + +T M + K+ +IL GL+
Sbjct: 80 KGEKIKEAEEAGADYVGGEEIIQKIL-DGWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 138
Query: 301 PNPK 304
PNPK
Sbjct: 139 PNPK 142
>pdb|1EG0|N Chain N, Fitting Of Components With Known Structure Into An 11.5 A
Cryo-Em Map Of The E.Coli 70s Ribosome
pdb|2HGJ|C Chain C, Crystal Structure Of The 70s Thermus Thermophilus Ribosome
Showing How The 16s 3'-End Mimicks Mrna E And P Codons.
This Entry 2hgj Contains 50s Ribosomal Subunit. The 30s
Ribosomal Subunit Can Be Found In Pdb Entry 2hgi.
pdb|2HGQ|C Chain C, Crystal Structure Of The 70s Thermus Thermophilus Ribosome
With Translocated And Rotated Shine-Dalgarno Duplex.
This Entry 2hgq Contains 50s Ribosomal Subunit. The 30s
Ribosomal Subunit Can Be Found In Pdb Entry 2hgp.
pdb|2HGU|C Chain C, 70s T.Th. Ribosome Functional Complex With Mrna And E- And
P-Site Trnas At 4.5a. This Entry 2hgu Contains 50s
Ribosomal Subunit. The 30s Ribosomal Subunit Can Be
Found In Pdb Entry 2hgr.
pdb|1VSA|A Chain A, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals
Functional Interactions And Rearrangements. This File,
1vsa, Contains The 50s Ribosome Subunit. 30s Ribosome
Subunit Is In The File 2ow8
pdb|1VSP|A Chain A, Interactions And Dynamics Of The Shine-Dalgarno Helix In
The 70s Ribosome. This File, 1vsp, Contains The 50s
Ribosome Subunit. 30s Ribosome Subunit Is In The File
2qnh
pdb|3U4M|A Chain A, Crystal Structure Of Ribosomal Protein Tthl1 In Complex
With 80nt 23s Rna From Thermus Thermophilus
Length = 229
Score = 77.8 bits (190), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 47/124 (37%), Positives = 66/124 (53%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
+ + +A VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 20 IYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 79
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I G +D + +T M + K+ +IL GL+
Sbjct: 80 KGEKIKEAEEAGADYVGGEEIIQKIL-DGWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 138
Query: 301 PNPK 304
PNPK
Sbjct: 139 PNPK 142
>pdb|3U42|A Chain A, Mutant Ribosomal Protein L1 From Thermus Thermophilus With
Threonine 217 Replaced By Valine
pdb|3U56|A Chain A, Crystal Structure Of Mutant Ribosomal Protein T217v Tthl1
In Complex With 80nt 23s Rna From Thermus Thermophilus
Length = 229
Score = 77.4 bits (189), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 47/124 (37%), Positives = 66/124 (53%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
+ + +A VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 20 IYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 79
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I G +D + +T M + K+ +IL GL+
Sbjct: 80 KGEKIKEAEEAGADYVGGEEIIQKIL-DGWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 138
Query: 301 PNPK 304
PNPK
Sbjct: 139 PNPK 142
>pdb|487D|H Chain H, Seven Ribosomal Proteins Fitted To A Cryo-Electron
Microscopic Map Of The Large 50s Subunit At 7.5
Angstroms Resolution
Length = 224
Score = 77.4 bits (189), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 47/124 (37%), Positives = 66/124 (53%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
+ + +A VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 15 IYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 74
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I G +D + +T M + K+ +IL GL+
Sbjct: 75 KGEKIKEAEEAGADYVGGEEIIQKIL-DGWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 133
Query: 301 PNPK 304
PNPK
Sbjct: 134 PNPK 137
>pdb|1AD2|A Chain A, Ribosomal Protein L1 Mutant With Serine 179 Replaced By
Cysteine
Length = 228
Score = 77.4 bits (189), Expect = 8e-15, Method: Compositional matrix adjust.
Identities = 47/124 (37%), Positives = 66/124 (53%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
+ + +A VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 19 IYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 78
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I G +D + +T M + K+ +IL GL+
Sbjct: 79 KGEKIKEAEEAGADYVGGEEIIQKIL-DGWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 137
Query: 301 PNPK 304
PNPK
Sbjct: 138 PNPK 141
>pdb|3ZVP|C Chain C, Crystal Structure Of The Hybrid State Of Ribosome In
Complex With The Guanosine Triphosphatase Release Factor
3
pdb|4ABS|C Chain C, Complex Of Smpb, A Tmrna Fragment And Ef-Tu-Gdp-Kirromycin
With The 70s Ribosome
Length = 229
Score = 77.4 bits (189), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 47/124 (37%), Positives = 66/124 (53%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
+ + +A VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 20 IYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 79
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I G +D + +T M + K+ +IL GL+
Sbjct: 80 KGEKIKEAEEAGADYVGGEEIIQKIL-DGWMDFDAVVATPDVMGAVGSKMGRILGPRGLL 138
Query: 301 PNPK 304
PNPK
Sbjct: 139 PNPK 142
>pdb|3BBO|D Chain D, Homology Model For The Spinach Chloroplast 50s Subunit
Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
Length = 352
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 45/130 (34%), Positives = 65/130 (50%), Gaps = 1/130 (0%)
Query: 175 KKKESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKA 234
K +E + DL A+ +K + F ET EAH RL I P+ + +R T++LP G K
Sbjct: 127 KLREIKQEYDLKTALSLMKQMSSTKFVETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKT 186
Query: 235 VRVXXXXXXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKIL 294
V++ IVGG ELIE+I G +D +K +T M ++ + +IL
Sbjct: 187 VKIAVLAQGDKIDEAKAAGADIVGGEELIEQI-KGGFMDFDKLIATSDMMAKVASLGRIL 245
Query: 295 NQHGLMPNPK 304
GLMP PK
Sbjct: 246 GPRGLMPTPK 255
>pdb|2V49|C Chain C, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 4 Of 4). This File Contains The 50s
Subunit Of Molecule 2
Length = 229
Score = 76.6 bits (187), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 47/124 (37%), Positives = 67/124 (54%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
V + +A + VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 20 VYTIDEAARLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 79
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I + +D + +T M + K+ +IL GL+
Sbjct: 80 KGEKIKEAEEAGADYVGGEEIIQKILDA-WMDFDAVVATPDVMGAVGSKLGRILAPRGLL 138
Query: 301 PNPK 304
PNPK
Sbjct: 139 PNPK 142
>pdb|3QOY|A Chain A, Crystal Structure Of Ribosomal Protein L1 From Aquifex
Aeolicus
Length = 242
Score = 74.7 bits (182), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 41/119 (34%), Positives = 64/119 (53%)
Query: 186 MDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXXXXXX 245
+D +K+++ + FDETVE +RL + PR + +VRG++ LPHG K ++V
Sbjct: 27 VDLLKKMEEVLQRRFDETVELAMRLNVDPRYADQMVRGSVVLPHGLGKPIKVVVFAEGEY 86
Query: 246 XXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNPK 304
VGG ELI +I D + +T + MP++ K+ +IL GLMP+PK
Sbjct: 87 AKKAEEAGADYVGGDELINKILKEEWTDFDVAIATPEMMPKVAKLGRILGPRGLMPSPK 145
>pdb|2HW8|A Chain A, Structure Of Ribosomal Protein L1-Mrna Complex At 2.1
Resolution
Length = 228
Score = 73.9 bits (180), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 46/124 (37%), Positives = 64/124 (51%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
+ + +A VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 19 IYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 78
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I G +D + +T + K +IL GL+
Sbjct: 79 KGEKIKEAEEAGADYVGGEEIIQKIL-DGWMDFDAVVATPDVXGAVGSKXGRILGPRGLL 137
Query: 301 PNPK 304
PNPK
Sbjct: 138 PNPK 141
>pdb|1ZHO|A Chain A, The Structure Of A Ribosomal Protein L1 In Complex With
Mrna
pdb|1ZHO|C Chain C, The Structure Of A Ribosomal Protein L1 In Complex With
Mrna
pdb|1ZHO|E Chain E, The Structure Of A Ribosomal Protein L1 In Complex With
Mrna
pdb|1ZHO|G Chain G, The Structure Of A Ribosomal Protein L1 In Complex With
Mrna
Length = 228
Score = 73.9 bits (180), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 46/124 (37%), Positives = 64/124 (51%), Gaps = 2/124 (1%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXX 241
+ + +A VK A A FDETVE H +L I PR+++ VRGT++LPHG K VRV
Sbjct: 19 IYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIA 78
Query: 242 XXXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLF-KISKILNQHGLM 300
VGG E+I++I G D + +T + K+ +IL GL+
Sbjct: 79 KGEKIKEAEEAGADYVGGEEIIQKIL-DGWXDFDAVVATPDVXGAVGSKLGRILGPRGLL 137
Query: 301 PNPK 304
PNPK
Sbjct: 138 PNPK 141
>pdb|2GYA|2 Chain 2, 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|2 Chain 2, 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 = 222
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 38/121 (31%), Positives = 62/121 (51%), Gaps = 1/121 (0%)
Query: 184 DLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXXXX 243
D+ +AI +K A A F E+V+ V L I RK++ VRG LPHG ++VRV
Sbjct: 17 DINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRGATVLPHGTGRSVRVAVFTQG 76
Query: 244 XXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNP 303
+VG +L ++I G+++ + ++ M + ++ ++L GLMPNP
Sbjct: 77 ANAEAAKAAGAELVGMEDLADQI-KKGEMNFDVVIASPDAMRVVGQLGQVLGPRGLMPNP 135
Query: 304 K 304
K
Sbjct: 136 K 136
>pdb|2RDO|9 Chain 9, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
Length = 233
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 38/121 (31%), Positives = 62/121 (51%), Gaps = 1/121 (0%)
Query: 184 DLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXXXX 243
D+ +AI +K A A F E+V+ V L I RK++ VRG LPHG ++VRV
Sbjct: 21 DINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRGATVLPHGTGRSVRVAVFTQG 80
Query: 244 XXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNP 303
+VG +L ++I G+++ + ++ M + ++ ++L GLMPNP
Sbjct: 81 ANAEAAKAAGAELVGMEDLADQI-KKGEMNFDVVIASPDAMRVVGQLGQVLGPRGLMPNP 139
Query: 304 K 304
K
Sbjct: 140 K 140
>pdb|3FIK|5 Chain 5, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
Consists Of The 50s Subunit.
pdb|3KCR|5 Chain 5, Ribosome-Secy Complex. This Entry 3kcr Contains 50s
Ribosomal Subnit. The 30s Ribosomal Subunit Can Be Found
In Pdb Entry 3kc4
pdb|2WWQ|5 Chain 5, E.Coli 70s Ribosome Stalled During Translation Of Tnac
Leader Peptide. This File Contains The 50s, The P-Site
Trna And The Tnac Leader Peptide (Part 2 Of 2).
pdb|3IZT|C Chain C, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Large Subunit Of A Ribosome Programmed With A
Near-Cognate Codon.
pdb|3IZU|C Chain C, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Large Subunit Of A Ribosome Programmed With A Cognate
Codon
pdb|3J01|5 Chain 5, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|3J0T|C Chain C, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0W|C Chain C, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0Y|C Chain C, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J11|C Chain C, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 3 Of The Six
Classes)
pdb|3J12|C Chain C, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J14|C Chain C, Structural Characterization Of Mrna-Trna Translocation
Intermediates (50s Ribosome Of Class 6 Of The Six
Classes)
Length = 234
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 38/121 (31%), Positives = 62/121 (51%), Gaps = 1/121 (0%)
Query: 184 DLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXXXX 243
D+ +AI +K A A F E+V+ V L I RK++ VRG LPHG ++VRV
Sbjct: 22 DINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRGATVLPHGTGRSVRVAVFTQG 81
Query: 244 XXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNP 303
+VG +L ++I G+++ + ++ M + ++ ++L GLMPNP
Sbjct: 82 ANAEAAKAAGAELVGMEDLADQI-KKGEMNFDVVIASPDAMRVVGQLGQVLGPRGLMPNP 140
Query: 304 K 304
K
Sbjct: 141 K 141
>pdb|3FIN|C Chain C, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas
And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A
6.4 A Cryo-Em Map. This File Contains The 50s Subunit
Length = 191
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 41/107 (38%), Positives = 52/107 (48%), Gaps = 10/107 (9%)
Query: 198 ATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXXXXXXXXXXXXXXXXIV 257
A FDETVE H +L I PR+++ VRGT++LPHG K VRV V
Sbjct: 12 AKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYV 71
Query: 258 GGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNPK 304
GG E+I++I LD F +L +IL GL NPK
Sbjct: 72 GGEEIIQKI-----LDGWMDFVMGAVGSKL---GRILGPRGL--NPK 108
>pdb|2OV7|A Chain A, The First Domain Of The Ribosomal Protein L1 From Thermus
Thermophilus
pdb|2OV7|B Chain B, The First Domain Of The Ribosomal Protein L1 From Thermus
Thermophilus
pdb|2OV7|C Chain C, The First Domain Of The Ribosomal Protein L1 From Thermus
Thermophilus
pdb|2OUM|A Chain A, The First Domain Of L1 From Thermus Thermophilus
pdb|2VPL|A Chain A, The Structure Of The Complex Between The First Domain Of
L1 Protein From Thermus Thermophilus And Mrna From
Methanococcus Jannaschii
pdb|2VPL|C Chain C, The Structure Of The Complex Between The First Domain Of
L1 Protein From Thermus Thermophilus And Mrna From
Methanococcus Jannaschii
Length = 137
Score = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/55 (45%), Positives = 35/55 (63%)
Query: 182 VLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVR 236
+ + +A VK A A FDETVE H +L I PR+++ VRGT++LPHG + R
Sbjct: 19 IYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGGRIEFR 73
>pdb|2ZZQ|A Chain A, Crystal Structure Analysis Of The Hev Capsid Protein,
Porf2
Length = 552
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 52 PVVSYASKPKDESNAPIENAQQQQNELQSDNPPHDFQAEEARTGLTREDIRYLKDVPTIT 111
PVVS +P + +ENAQQ + PHD E+R + D ++ +D PT +
Sbjct: 344 PVVSANGEPTVKLYTSVENAQQDKGIAI----PHDIDLGESRVVIQDYDNQHEQDRPTPS 399
Query: 112 PVSYPSR 118
P PSR
Sbjct: 400 PA--PSR 404
>pdb|3IYO|A Chain A, Cryo-Em Model Of Virion-Sized Hev Virion-Sized Capsid
pdb|3IYO|B Chain B, Cryo-Em Model Of Virion-Sized Hev Virion-Sized Capsid
pdb|3IYO|D Chain D, Cryo-Em Model Of Virion-Sized Hev Virion-Sized Capsid
Length = 660
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 52 PVVSYASKPKDESNAPIENAQQQQNELQSDNPPHDFQAEEARTGLTREDIRYLKDVPTIT 111
PVVS +P + +ENAQQ + PHD E+R + D ++ +D PT +
Sbjct: 400 PVVSANGEPTVKLYTSVENAQQDKGIAI----PHDIDLGESRVVIQDYDNQHEQDRPTPS 455
Query: 112 PVSYPSR 118
P PSR
Sbjct: 456 PA--PSR 460
>pdb|3HAG|A Chain A, Crystal Structure Of The Hepatitis E Virus-Like Particle
Length = 504
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 52 PVVSYASKPKDESNAPIENAQQQQNELQSDNPPHDFQAEEARTGLTREDIRYLKDVPTIT 111
PVVS +P + +ENAQQ + PHD E+R + D ++ +D PT +
Sbjct: 290 PVVSANGEPTVKLYTSVENAQQDKGIAI----PHDIDLGESRVVIQDYDNQHEQDRPTPS 345
Query: 112 PVSYPSR 118
P PSR
Sbjct: 346 PA--PSR 350
>pdb|2ZTN|A Chain A, Hepatitis E Virus Orf2 (Genotype 3)
Length = 478
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 52 PVVSYASKPKDESNAPIENAQQQQNELQSDNPPHDFQAEEARTGLTREDIRYLKDVPTIT 111
PVVS +P + +ENAQQ + PHD ++R + D ++ +D PT +
Sbjct: 272 PVVSANGEPTVKLYTSVENAQQDKGI----TIPHDIDLGDSRVVIQDYDNQHEQDRPTPS 327
Query: 112 PVSYPSR 118
P PSR
Sbjct: 328 PA--PSR 332
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
0.315 0.130 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,172,440
Number of Sequences: 62578
Number of extensions: 238568
Number of successful extensions: 580
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 537
Number of HSP's gapped (non-prelim): 26
length of query: 304
length of database: 14,973,337
effective HSP length: 98
effective length of query: 206
effective length of database: 8,840,693
effective search space: 1821182758
effective search space used: 1821182758
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)