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= psy16349
(351 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2FTC|A Chain A, Structural Model For The Large Subunit Of The Mammalian
Mitochondrial Ribosome
Length = 189
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 42/179 (23%), Positives = 83/179 (46%), Gaps = 11/179 (6%)
Query: 135 KVKYMDPWTHIVEVEHSFDHGEDRSIIAFCSQHETAAQLQDMGVALVGDSDTIKGIERGL 194
K K ++P+T ++ + + F E + F ++ G A G + I+ I
Sbjct: 11 KKKNVEPFTSVLSLPYPF-ASEINKVAVFTENASEVKIAEENGAAFAGGTSLIQKIWDDE 69
Query: 195 VTMPTFQFVICNPKILADLMRIRGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKD 254
+ F + P+I+ +L R+R L K+ P L ++G D+ + + + G + +K D
Sbjct: 70 IVA---DFYVAVPEIMPELNRLRKKLNKKYPKLSRNSIGRDIPKMLELFKNG--HEIKVD 124
Query: 255 PQEQDFGYSDFHIGRLDMSQEQLEDNLKRILADISTMKPPSKPEDEDFITRILLWSEPS 313
+ ++F + I LDMS +Q+ NL+ ++ ++ +P + F+ R L S S
Sbjct: 125 EERENFLQT--KIATLDMSSDQIAANLQAVINEVCRHRPLNLGP---FVVRAFLRSSTS 178
>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 = 35.8 bits (81), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 40/148 (27%), Positives = 67/148 (45%), Gaps = 21/148 (14%)
Query: 154 HGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKILAD 212
HG RS+ +A +Q A + G LVG D I++G + F VI +P D
Sbjct: 62 HGTGRSVRVAVFTQGANAEAAKAAGAELVGMEDLADQIKKGEMN---FDVVIASP----D 114
Query: 213 LMRIRGLL------KKRIPTLKSQTLGVDLIGIAKRLQTG-IKYSMKKDPQEQDFGYSDF 265
MR+ G L + +P K T+ ++ K + G ++Y K+ G
Sbjct: 115 AMRVVGQLGQVLGPRGLMPNPKVGTVTPNVAEAVKNAKAGQVRYRNDKN------GIIHT 168
Query: 266 HIGRLDMSQEQLEDNLKRILADISTMKP 293
IG++D ++L++NL+ +L + KP
Sbjct: 169 TIGKVDFDADKLKENLEALLVALKKAKP 196
>pdb|2RDO|9 Chain 9, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
Length = 233
Score = 35.8 bits (81), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 40/148 (27%), Positives = 67/148 (45%), Gaps = 21/148 (14%)
Query: 154 HGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKILAD 212
HG RS+ +A +Q A + G LVG D I++G + F VI +P D
Sbjct: 66 HGTGRSVRVAVFTQGANAEAAKAAGAELVGMEDLADQIKKGEMN---FDVVIASP----D 118
Query: 213 LMRIRGLL------KKRIPTLKSQTLGVDLIGIAKRLQTG-IKYSMKKDPQEQDFGYSDF 265
MR+ G L + +P K T+ ++ K + G ++Y K+ G
Sbjct: 119 AMRVVGQLGQVLGPRGLMPNPKVGTVTPNVAEAVKNAKAGQVRYRNDKN------GIIHT 172
Query: 266 HIGRLDMSQEQLEDNLKRILADISTMKP 293
IG++D ++L++NL+ +L + KP
Sbjct: 173 TIGKVDFDADKLKENLEALLVALKKAKP 200
>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 = 35.4 bits (80), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 40/148 (27%), Positives = 67/148 (45%), Gaps = 21/148 (14%)
Query: 154 HGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKILAD 212
HG RS+ +A +Q A + G LVG D I++G + F VI +P D
Sbjct: 67 HGTGRSVRVAVFTQGANAEAAKAAGAELVGMEDLADQIKKGEMN---FDVVIASP----D 119
Query: 213 LMRIRGLL------KKRIPTLKSQTLGVDLIGIAKRLQTG-IKYSMKKDPQEQDFGYSDF 265
MR+ G L + +P K T+ ++ K + G ++Y K+ G
Sbjct: 120 AMRVVGQLGQVLGPRGLMPNPKVGTVTPNVAEAVKNAKAGQVRYRNDKN------GIIHT 173
Query: 266 HIGRLDMSQEQLEDNLKRILADISTMKP 293
IG++D ++L++NL+ +L + KP
Sbjct: 174 TIGKVDFDADKLKENLEALLVALKKAKP 201
>pdb|3TG8|A Chain A, Mutant Ribosomal Protein L1 Lacking Ala158 From Thermus
Thermophilus
Length = 228
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 35/151 (23%), Positives = 65/151 (43%), Gaps = 21/151 (13%)
Query: 151 SFDHGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI 209
S HG + + + ++ E + ++ G VG + I+ I G + F V+ P +
Sbjct: 64 SLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMD---FDAVVATPDV 120
Query: 210 LA----DLMRI---RGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGY 262
+ L RI RGLL P K+ T+G ++ I + ++ I++ K G
Sbjct: 121 MGAVGSKLGRILGPRGLL----PNPKAGTVGFNIGEIIREIKGRIEFRNDKT------GA 170
Query: 263 SDFHIGRLDMSQEQLEDNLKRILADISTMKP 293
+G+ E+L DN++ + + KP
Sbjct: 171 IHAPVGKASFPPEKLADNIRAFIRALEAHKP 201
>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 = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 35/151 (23%), Positives = 65/151 (43%), Gaps = 20/151 (13%)
Query: 151 SFDHGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI 209
S HG + + + ++ E + ++ G VG + I+ I G + F V+ P +
Sbjct: 64 SLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMD---FDAVVATPDV 120
Query: 210 LA----DLMRI---RGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGY 262
+ L RI RGLL P K+ T+G ++ I + ++ G + + D G
Sbjct: 121 MGAVGSKLGRILGPRGLL----PNPKAGTVGFNIGEIIREIKAG-RIEFRNDKT----GA 171
Query: 263 SDFHIGRLDMSQEQLEDNLKRILADISTMKP 293
+G+ E+L DN++ + + KP
Sbjct: 172 IHAPVGKASFPPEKLADNIRAFIRALEAHKP 202
>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 = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 35/151 (23%), Positives = 65/151 (43%), Gaps = 20/151 (13%)
Query: 151 SFDHGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI 209
S HG + + + ++ E + ++ G VG + I+ I G + F V+ P +
Sbjct: 63 SLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMD---FDAVVATPDV 119
Query: 210 LA----DLMRI---RGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGY 262
+ L RI RGLL P K+ T+G ++ I + ++ G + + D G
Sbjct: 120 MGAVGSKLGRILGPRGLL----PNPKAGTVGFNIGEIIREIKAG-RIEFRNDKT----GA 170
Query: 263 SDFHIGRLDMSQEQLEDNLKRILADISTMKP 293
+G+ E+L DN++ + + KP
Sbjct: 171 IHAPVGKASFPPEKLADNIRAFIRALEAHKP 201
>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 = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 35/151 (23%), Positives = 65/151 (43%), Gaps = 20/151 (13%)
Query: 151 SFDHGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI 209
S HG + + + ++ E + ++ G VG + I+ I G + F V+ P +
Sbjct: 63 SLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMD---FDAVVATPDV 119
Query: 210 LA----DLMRI---RGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGY 262
+ L RI RGLL P K+ T+G ++ I + ++ G + + D G
Sbjct: 120 MGAVGSKLGRILGPRGLL----PNPKAGTVGFNIGEIIREIKAG-RIEFRNDKT----GA 170
Query: 263 SDFHIGRLDMSQEQLEDNLKRILADISTMKP 293
+G+ E+L DN++ + + KP
Sbjct: 171 IHAPVGKASFPPEKLADNIRAFIRALEAHKP 201
>pdb|4F9T|A Chain A, Ribosomal Protein L1 From Thermus Thermophilus With
Substitution Thr217ala
Length = 229
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 35/151 (23%), Positives = 65/151 (43%), Gaps = 20/151 (13%)
Query: 151 SFDHGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI 209
S HG + + + ++ E + ++ G VG + I+ I G + F V+ P +
Sbjct: 64 SLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMD---FDAVVATPDV 120
Query: 210 LA----DLMRI---RGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGY 262
+ L RI RGLL P K+ T+G ++ I + ++ G + + D G
Sbjct: 121 MGAVGSKLGRILGPRGLL----PNPKAGTVGFNIGEIIREIKAG-RIEFRNDKT----GA 171
Query: 263 SDFHIGRLDMSQEQLEDNLKRILADISTMKP 293
+G+ E+L DN++ + + KP
Sbjct: 172 IHAPVGKASFPPEKLADNIRAFIRALEAHKP 202
>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 = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 35/151 (23%), Positives = 65/151 (43%), Gaps = 20/151 (13%)
Query: 151 SFDHGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI 209
S HG + + + ++ E + ++ G VG + I+ I G + F V+ P +
Sbjct: 64 SLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMD---FDAVVATPDV 120
Query: 210 LA----DLMRI---RGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGY 262
+ L RI RGLL P K+ T+G ++ I + ++ G + + D G
Sbjct: 121 MGAVGSKLGRILGPRGLL----PNPKAGTVGFNIGEIIREIKAG-RIEFRNDKT----GA 171
Query: 263 SDFHIGRLDMSQEQLEDNLKRILADISTMKP 293
+G+ E+L DN++ + + KP
Sbjct: 172 IHAPVGKASFPPEKLADNIRAFIRALEAHKP 202
>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 = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 35/151 (23%), Positives = 65/151 (43%), Gaps = 20/151 (13%)
Query: 151 SFDHGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI 209
S HG + + + ++ E + ++ G VG + I+ I G + F V+ P +
Sbjct: 64 SLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMD---FDAVVATPDV 120
Query: 210 LA----DLMRI---RGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGY 262
+ L RI RGLL P K+ T+G ++ I + ++ G + + D G
Sbjct: 121 MGAVGSKLGRILGPRGLL----PNPKAGTVGFNIGEIIREIKAG-RIEFRNDKT----GA 171
Query: 263 SDFHIGRLDMSQEQLEDNLKRILADISTMKP 293
+G+ E+L DN++ + + KP
Sbjct: 172 IHAPVGKASFPPEKLADNIRAFIRALEAHKP 202
>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 = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 33/151 (21%), Positives = 63/151 (41%), Gaps = 20/151 (13%)
Query: 151 SFDHGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI 209
S HG + + + ++ E + ++ G VG + I+ I G F V+ P +
Sbjct: 63 SLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWXD---FDAVVATPDV 119
Query: 210 -------LADLMRIRGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGY 262
L ++ RGLL P K+ T+G ++ I + ++ G + + D G
Sbjct: 120 XGAVGSKLGRILGPRGLL----PNPKAGTVGFNIGEIIREIKAG-RIEFRNDKT----GA 170
Query: 263 SDFHIGRLDMSQEQLEDNLKRILADISTMKP 293
+G+ E+L DN++ + + KP
Sbjct: 171 IHAPVGKASFPPEKLADNIRAFIRALEAHKP 201
>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 = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 34/151 (22%), Positives = 65/151 (43%), Gaps = 20/151 (13%)
Query: 151 SFDHGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI 209
S HG + + + ++ E + ++ G VG + I+ I G + F V+ P +
Sbjct: 64 SLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMD---FDAVVATPDV 120
Query: 210 LA----DLMRI---RGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGY 262
+ + RI RGLL P K+ T+G ++ I + ++ G + + D G
Sbjct: 121 MGAVGSKMGRILGPRGLL----PNPKAGTVGFNIGEIIREIKAG-RIEFRNDKT----GA 171
Query: 263 SDFHIGRLDMSQEQLEDNLKRILADISTMKP 293
+G+ E+L DN++ + + KP
Sbjct: 172 IHAPVGKASFPPEKLADNIRAFIRALEAHKP 202
>pdb|3QOY|A Chain A, Crystal Structure Of Ribosomal Protein L1 From Aquifex
Aeolicus
Length = 242
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 39/178 (21%), Positives = 81/178 (45%), Gaps = 15/178 (8%)
Query: 154 HGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKILAD 212
HG + I + ++ E A + ++ G VG + I I + T F I P+++
Sbjct: 70 HGLGKPIKVVVFAEGEYAKKAEEAGADYVGGDELINKILKEEWT--DFDVAIATPEMMPK 127
Query: 213 LMRIRGLLKKR--IPTLKSQTLGVDLIGIAKRLQTG-IKYSMKKDPQEQDFGYSDFHIGR 269
+ ++ +L R +P+ K+ T+ ++ K + G +++ + K G +G+
Sbjct: 128 VAKLGRILGPRGLMPSPKTGTVTTNVEQAIKDAKRGRVEFKVDK------AGNVHMPVGK 181
Query: 270 LDMSQEQLEDNLKRILADISTMKPPSKPEDEDFITRILLWSEPSPEKFKLDLSGLIEK 327
+ +E+L DNL + + KPP +I + + SP KLD++ +++K
Sbjct: 182 ISFEKEKLIDNLYAAIDAVVRAKPPG--AKGQYIKNMAVSLTMSPS-VKLDINEVLKK 236
>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 = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 35/151 (23%), Positives = 64/151 (42%), Gaps = 20/151 (13%)
Query: 151 SFDHGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI 209
S HG + + + ++ E + ++ G VG + I+ I L F V+ P +
Sbjct: 64 SLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKI---LDAWMDFDAVVATPDV 120
Query: 210 LA----DLMRI---RGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGY 262
+ L RI RGLL P K+ T+G ++ I + ++ G + + D G
Sbjct: 121 MGAVGSKLGRILAPRGLL----PNPKAGTVGFNIGEIIREIKAG-RIEFRNDKT----GA 171
Query: 263 SDFHIGRLDMSQEQLEDNLKRILADISTMKP 293
+G+ E+L DN++ + + KP
Sbjct: 172 IHAPVGKASFPPEKLADNIRAFIRALEAHKP 202
>pdb|1XDV|A Chain A, Experimentally Phased Structure Of Human The Son Of
Sevenless Protein At 4.1 Ang.
pdb|1XDV|B Chain B, Experimentally Phased Structure Of Human The Son Of
Sevenless Protein At 4.1 Ang
Length = 847
Score = 31.6 bits (70), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 270 LDMSQEQLEDNLKRILADISTMKPPSKPEDEDFITRILLWSEPSPEKFKLDLSGLIEKPK 329
L+ + E ED+ K+ LA + ++ PP P ++T IL E +PE K LI K
Sbjct: 704 LEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSK 763
Query: 330 AKELD--TGE 337
+++ TGE
Sbjct: 764 RRKVAEITGE 773
>pdb|1XD4|A Chain A, Crystal Structure Of The Dh-Ph-Cat Module Of Son Of
Sevenless (Sos)
pdb|1XD4|B Chain B, Crystal Structure Of The Dh-Ph-Cat Module Of Son Of
Sevenless (Sos)
Length = 852
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 270 LDMSQEQLEDNLKRILADISTMKPPSKPEDEDFITRILLWSEPSPEKFKLDLSGLIEKPK 329
L+ + E ED+ K+ LA + ++ PP P ++T IL E +PE K LI K
Sbjct: 704 LEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSK 763
Query: 330 AKELD--TGE 337
+++ TGE
Sbjct: 764 RRKVAEITGE 773
>pdb|2HW8|A Chain A, Structure Of Ribosomal Protein L1-Mrna Complex At 2.1
Resolution
Length = 228
Score = 31.6 bits (70), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 32/151 (21%), Positives = 63/151 (41%), Gaps = 20/151 (13%)
Query: 151 SFDHGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI 209
S HG + + + ++ E + ++ G VG + I+ I G + F V+ P +
Sbjct: 63 SLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMD---FDAVVATPDV 119
Query: 210 LAD-------LMRIRGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGY 262
++ RGLL P K+ T+G ++ I + ++ G + + D G
Sbjct: 120 XGAVGSKXGRILGPRGLL----PNPKAGTVGFNIGEIIREIKAG-RIEFRNDKT----GA 170
Query: 263 SDFHIGRLDMSQEQLEDNLKRILADISTMKP 293
+G+ E+L DN++ + + KP
Sbjct: 171 IHAPVGKASFPPEKLADNIRAFIRALEAHKP 201
>pdb|3KSY|A Chain A, Crystal Structure Of The Histone Domain, Dh-Ph Unit, And
Catalytic Unit Of The Ras Activator Son Of Sevenless
(Sos)
Length = 1049
Score = 31.6 bits (70), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 270 LDMSQEQLEDNLKRILADISTMKPPSKPEDEDFITRILLWSEPSPEKFKLDLSGLIEKPK 329
L+ + E ED+ K+ LA + ++ PP P ++T IL E +PE K LI K
Sbjct: 901 LEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSK 960
Query: 330 AKELD--TGE 337
+++ TGE
Sbjct: 961 RRKVAEITGE 970
>pdb|1BKD|S Chain S, Complex Of Human H-Ras With Human Sos-1
Length = 477
Score = 31.2 bits (69), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 270 LDMSQEQLEDNLKRILADISTMKPPSKPEDEDFITRILLWSEPSPEKFKLDLSGLIEKPK 329
L+ + E ED+ K+ LA + ++ PP P ++T IL E +PE K LI K
Sbjct: 334 LEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSK 393
Query: 330 AKELD--TGE 337
+++ TGE
Sbjct: 394 RRKVAEITGE 403
>pdb|1XD2|C Chain C, Crystal Structure Of A Ternary Ras:sos:ras*gdp Complex
Length = 484
Score = 31.2 bits (69), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 270 LDMSQEQLEDNLKRILADISTMKPPSKPEDEDFITRILLWSEPSPEKFKLDLSGLIEKPK 329
L+ + E ED+ K+ LA + ++ PP P ++T IL E +PE K LI K
Sbjct: 336 LEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSK 395
Query: 330 AKELD--TGE 337
+++ TGE
Sbjct: 396 RRKVAEITGE 405
>pdb|1NVU|S Chain S, Structural Evidence For Feedback Activation By Rasgtp Of
The Ras-Specific Nucleotide Exchange Factor Sos
pdb|1NVV|S Chain S, Structural Evidence For Feedback Activation By Rasgtp Of
The Ras-specific Nucleotide Exchange Factor Sos
pdb|1NVW|S Chain S, Structural Evidence For Feedback Activation By Rasgtp Of
The Ras-specific Nucleotide Exchange Factor Sos
pdb|1NVX|S Chain S, Structural Evidence For Feedback Activation By Rasgtp Of
The Ras-Specific Nucleotide Exchange Factor Sos
Length = 481
Score = 31.2 bits (69), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 270 LDMSQEQLEDNLKRILADISTMKPPSKPEDEDFITRILLWSEPSPEKFKLDLSGLIEKPK 329
L+ + E ED+ K+ LA + ++ PP P ++T IL E +PE K LI K
Sbjct: 336 LEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSK 395
Query: 330 AKELD--TGE 337
+++ TGE
Sbjct: 396 RRKVAEITGE 405
>pdb|2II0|A Chain A, Crystal Structure Of Catalytic Domain Of Son Of Sevenless
(Rem-Cdc25) In The Absence Of Ras
Length = 490
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 270 LDMSQEQLEDNLKRILADISTMKPPSKPEDEDFITRILLWSEPSPEKFKLDLSGLIEKPK 329
L+ + E ED+ K+ LA + ++ PP P ++T IL E +PE K LI K
Sbjct: 342 LEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSK 401
Query: 330 AKELD--TGE 337
+++ TGE
Sbjct: 402 RRKVAEITGE 411
>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 = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 32/147 (21%), Positives = 66/147 (44%), Gaps = 13/147 (8%)
Query: 151 SFDHGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI 209
S G +++ IA +Q + + + G +VG + I+ I+ G + F +I +
Sbjct: 178 SLPKGTGKTVKIAVLAQGDKIDEAKAAGADIVGGEELIEQIKGGFMD---FDKLIATSDM 234
Query: 210 LADLMRIRGLLKKR--IPTLKSQTLGVDLIGIAKRLQTG-IKYSMKKDPQEQDFGYSDFH 266
+A + + +L R +PT K+ T+ ++ + + G +++ + K G
Sbjct: 235 MAKVASLGRILGPRGLMPTPKAGTVTPNVAQAVEEFKKGKVEFRVDKT------GIVHIP 288
Query: 267 IGRLDMSQEQLEDNLKRILADISTMKP 293
G+L+ +E L NL + + T KP
Sbjct: 289 FGKLNFEEEDLLINLFATIKSVETNKP 315
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 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,187,009
Number of Sequences: 62578
Number of extensions: 418105
Number of successful extensions: 1047
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 1038
Number of HSP's gapped (non-prelim): 31
length of query: 351
length of database: 14,973,337
effective HSP length: 100
effective length of query: 251
effective length of database: 8,715,537
effective search space: 2187599787
effective search space used: 2187599787
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: 52 (24.6 bits)