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= 015333
(409 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 129 bits (324), Expect = 3e-30, Method: Compositional matrix adjust.
Identities = 78/223 (34%), Positives = 117/223 (52%), Gaps = 6/223 (2%)
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 NQHGLMPNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGA 354
GLMP PK GTVT +VA+AV+E K+G ++F++D T VH GK++ +EE L N+ A
Sbjct: 246 GPRGLMPTPKAGTVTPNVAQAVEEFKKGKVEFRVDKTGIVHIPFGKLNFEEEDLLINLFA 305
Query: 355 FVNXXXXXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQSL 397
+ T Y S H+ S+MGPS ++I+ +
Sbjct: 306 TIK-----SVETNKPTGAKGVYWKSAHISSSMGPSIRLNIREM 343
>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 = 125 bits (315), Expect = 4e-29, Method: Compositional matrix adjust.
Identities = 76/216 (35%), Positives = 113/216 (52%), Gaps = 7/216 (3%)
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 KGEKIKEAEEAGADYVGGEEIIQKILD-GWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 138
Query: 301 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK S E L +N+ AF+
Sbjct: 139 PNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALE 198
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ +TMGPS ++ S
Sbjct: 199 AHKPEGAKGT-----FLRSVYVTTTMGPSVRINPHS 229
>pdb|3QOY|A Chain A, Crystal Structure Of Ribosomal Protein L1 From Aquifex
Aeolicus
Length = 242
Score = 125 bits (314), Expect = 4e-29, Method: Compositional matrix adjust.
Identities = 70/218 (32%), Positives = 117/218 (53%), Gaps = 5/218 (2%)
Query: 186 MDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXXXXXX 245
+D +K+++ + FDETVE +RL + PR + +VRG++ LPHG K ++V
Sbjct: 27 VDLLKKMEEVLQRRFDETVELAMRLNVDPRYADQMVRGSVVLPHGLGKPIKVVVFAEGEY 86
Query: 246 XXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNPKQ 305
VGG ELI +I D + +T + MP++ K+ +IL GLMP+PK
Sbjct: 87 AKKAEEAGADYVGGDELINKILKEEWTDFDVAIATPEMMPKVAKLGRILGPRGLMPSPKT 146
Query: 306 GTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXXXXXXX 365
GTVT +V +A+++AK+G ++FK+D NVH +GK+S ++E L +N+ A ++
Sbjct: 147 GTVTTNVEQAIKDAKRGRVEFKVDKAGNVHMPVGKISFEKEKLIDNLYAAIDAVVRAKPP 206
Query: 366 XXXXTSKFAGYVNSFHMCSTMGPSFPVSIQSLSRALDQ 403
Y+ + + TM PS + I + + L +
Sbjct: 207 GAK-----GQYIKNMAVSLTMSPSVKLDINEVLKKLQE 239
>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 = 124 bits (310), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 75/216 (34%), Positives = 112/216 (51%), Gaps = 7/216 (3%)
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 KGEKIKEAEEAGADYVGGEEIIQKILD-GWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 137
Query: 301 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK S E L +N+ AF+
Sbjct: 138 PNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALE 197
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ +TMGPS ++ S
Sbjct: 198 AHKPEGAKGT-----FLRSVYVTTTMGPSVRINPHS 228
>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 = 124 bits (310), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 75/216 (34%), Positives = 112/216 (51%), Gaps = 7/216 (3%)
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 KGEKIKEAEEAGADYVGGEEIIQKILD-GWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 138
Query: 301 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK S E L +N+ AF+
Sbjct: 139 PNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALE 198
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ +TMGPS ++ S
Sbjct: 199 AHKPEGAKGT-----FLRSVYVTTTMGPSVRINPHS 229
>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 = 123 bits (309), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 75/216 (34%), Positives = 112/216 (51%), Gaps = 7/216 (3%)
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 KGEKIKEAEEAGADYVGGEEIIQKILD-GWMDFDAVVATPDVMGAVGSKMGRILGPRGLL 138
Query: 301 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK S E L +N+ AF+
Sbjct: 139 PNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALE 198
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ +TMGPS ++ S
Sbjct: 199 AHKPEGAKGT-----FLRSVYVTTTMGPSVRINPHS 229
>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 = 123 bits (309), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 75/216 (34%), Positives = 113/216 (52%), Gaps = 7/216 (3%)
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 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK S E L +N+ AF+
Sbjct: 139 PNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALE 198
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ +TMGPS ++ S
Sbjct: 199 AHKPEGAKGT-----FLRSVYVTTTMGPSVRINPHS 229
>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 = 122 bits (305), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 74/216 (34%), Positives = 111/216 (51%), Gaps = 7/216 (3%)
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 KGEKIKEAEEAGADYVGGEEIIQKILD-GWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 137
Query: 301 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK S E L +N+ AF+
Sbjct: 138 PNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALE 197
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ + MGPS ++ S
Sbjct: 198 AHKPEGAKGT-----FLRSVYVTTAMGPSVRINPHS 228
>pdb|1AD2|A Chain A, Ribosomal Protein L1 Mutant With Serine 179 Replaced By
Cysteine
Length = 228
Score = 122 bits (305), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 74/216 (34%), Positives = 111/216 (51%), Gaps = 7/216 (3%)
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 KGEKIKEAEEAGADYVGGEEIIQKILD-GWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 137
Query: 301 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK E L +N+ AF+
Sbjct: 138 PNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKACFPPEKLADNIRAFIRALE 197
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ +TMGPS ++ S
Sbjct: 198 AHKPEGAKGT-----FLRSVYVTTTMGPSVRINPHS 228
>pdb|4F9T|A Chain A, Ribosomal Protein L1 From Thermus Thermophilus With
Substitution Thr217ala
Length = 229
Score = 122 bits (305), Expect = 5e-28, Method: Compositional matrix adjust.
Identities = 74/216 (34%), Positives = 111/216 (51%), Gaps = 7/216 (3%)
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 KGEKIKEAEEAGADYVGGEEIIQKILD-GWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 138
Query: 301 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK S E L +N+ AF+
Sbjct: 139 PNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALE 198
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ + MGPS ++ S
Sbjct: 199 AHKPEGAKGT-----FLRSVYVTTAMGPSVRINPHS 229
>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 = 122 bits (305), Expect = 5e-28, Method: Compositional matrix adjust.
Identities = 74/216 (34%), Positives = 111/216 (51%), Gaps = 7/216 (3%)
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 KGEKIKEAEEAGADYVGGEEIIQKILD-GWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 138
Query: 301 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK S E L +N+ AF+
Sbjct: 139 PNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALE 198
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ + MGPS ++ S
Sbjct: 199 AHKPEGAKGT-----FLRSVYVTTVMGPSVRINPHS 229
>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 = 121 bits (304), Expect = 5e-28, Method: Compositional matrix adjust.
Identities = 74/216 (34%), Positives = 111/216 (51%), Gaps = 7/216 (3%)
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 KGEKIKEAEEAGADYVGGEEIIQKILD-GWMDFDAVVATPDVMGAVGSKLGRILGPRGLL 133
Query: 301 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK E L +N+ AF+
Sbjct: 134 PNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKACFPPEKLADNIRAFIRALE 193
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ +TMGPS ++ S
Sbjct: 194 AHKPEGAKGT-----FLRSVYVTTTMGPSVRINPHS 224
>pdb|3TG8|A Chain A, Mutant Ribosomal Protein L1 Lacking Ala158 From Thermus
Thermophilus
Length = 228
Score = 119 bits (298), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 75/216 (34%), Positives = 112/216 (51%), Gaps = 8/216 (3%)
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 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK S E L +N+ AF+
Sbjct: 139 PNPKAGTVGFNIGEIIREIK-GRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALE 197
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ +TMGPS ++ S
Sbjct: 198 AHKPEGAKGT-----FLRSVYVTTTMGPSVRINPHS 228
>pdb|2HW8|A Chain A, Structure Of Ribosomal Protein L1-Mrna Complex At 2.1
Resolution
Length = 228
Score = 117 bits (294), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 73/216 (33%), Positives = 109/216 (50%), Gaps = 7/216 (3%)
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 KGEKIKEAEEAGADYVGGEEIIQKILD-GWMDFDAVVATPDVXGAVGSKXGRILGPRGLL 137
Query: 301 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK S E L +N+ AF+
Sbjct: 138 PNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALE 197
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ +T GPS ++ S
Sbjct: 198 AHKPEGAKGT-----FLRSVYVTTTXGPSVRINPHS 228
>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 = 117 bits (293), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 73/216 (33%), Positives = 109/216 (50%), Gaps = 7/216 (3%)
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 KGEKIKEAEEAGADYVGGEEIIQKILD-GWXDFDAVVATPDVXGAVGSKLGRILGPRGLL 137
Query: 301 PNPKQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXX 360
PNPK GTV ++ ++E K G I+F+ D T +HA +GK S E L +N+ AF+
Sbjct: 138 PNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALE 197
Query: 361 XXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQS 396
T ++ S ++ +T GPS ++ S
Sbjct: 198 AHKPEGAKGT-----FLRSVYVTTTXGPSVRINPHS 228
>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 = 104 bits (259), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 68/192 (35%), Positives = 95/192 (49%), Gaps = 15/192 (7%)
Query: 198 ATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVXXXXXXXXXXXXXXXXXXIV 257
A FDETVE H +L I PR+++ VRGT++LPHG K VRV V
Sbjct: 12 AKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYV 71
Query: 258 GGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNPKQGTVTNDVARAVQ 317
GG E+I++I LD F +L +IL GL NPK GTV ++ ++
Sbjct: 72 GGEEIIQKI-----LDGWMDFVMGAVGSKL---GRILGPRGL--NPKAGTVGFNIGEIIR 121
Query: 318 EAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXXXXXXXXXXXTSKFAGYV 377
E K G I+F+ D T +HA +GK S E L +N+ AF+ T ++
Sbjct: 122 EIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGT-----FL 176
Query: 378 NSFHMCSTMGPS 389
S ++ +TMGPS
Sbjct: 177 RSVYVTTTMGPS 188
>pdb|2RDO|9 Chain 9, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
Length = 233
Score = 102 bits (254), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 66/219 (30%), Positives = 108/219 (49%), Gaps = 6/219 (2%)
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 KQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXXXXX 363
K GTVT +VA AV+ AK G ++++ D +H +GKV + L+EN+ A +
Sbjct: 140 KVGTVTPNVAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDFDADKLKENLEALL-----VA 194
Query: 364 XXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQSLSRALD 402
T Y+ + +TMG V LS +++
Sbjct: 195 LKKAKPTQAKGVYIKKVSISTTMGAGVAVDQAGLSASVN 233
>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 = 102 bits (254), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 66/219 (30%), Positives = 108/219 (49%), Gaps = 6/219 (2%)
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 KQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXXXXX 363
K GTVT +VA AV+ AK G ++++ D +H +GKV + L+EN+ A +
Sbjct: 141 KVGTVTPNVAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDFDADKLKENLEALL-----VA 195
Query: 364 XXXXXXTSKFAGYVNSFHMCSTMGPSFPVSIQSLSRALD 402
T Y+ + +TMG V LS +++
Sbjct: 196 LKKAKPTQAKGVYIKKVSISTTMGAGVAVDQAGLSASVN 234
>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 = 100 bits (250), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 64/209 (30%), Positives = 103/209 (49%), Gaps = 6/209 (2%)
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 KQGTVTNDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXXXXX 363
K GTVT +VA AV+ AK G ++++ D +H +GKV + L+EN+ A +
Sbjct: 136 KVGTVTPNVAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDFDADKLKENLEALL-----VA 190
Query: 364 XXXXXXTSKFAGYVNSFHMCSTMGPSFPV 392
T Y+ + +TMG V
Sbjct: 191 LKKAKPTQAKGVYIKKVSISTTMGAGVAV 219
>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 = 51.2 bits (121), Expect = 9e-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
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 322 GHIKFKMDNTSNVHAGLGKVSLKEELLRENVGAFVNXXXXXXXXXXXXTSKFAGYVNSFH 381
G I+F+ D T +HA +GK S E L +N+ AF+ T ++ S +
Sbjct: 68 GRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGT-----FLRSVY 122
Query: 382 MCSTMGPSFPVSIQS 396
+ +TMGPS ++ S
Sbjct: 123 VTTTMGPSVRINPHS 137
>pdb|3J21|A Chain A, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 216
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 56/218 (25%), Positives = 95/218 (43%), Gaps = 21/218 (9%)
Query: 185 LMDAIKQVKANAKA-TFDETVEAHVRLA-IPPRKTELIVRGTMNLPHGDKKAVRVXXXXX 242
++ A+K+ KA AK F ++VE V L I ++ E + + LPHG K V++
Sbjct: 8 IVKAVKEAKARAKPRNFTQSVEVAVNLKDIDLKRPENRFKLEVVLPHGRGKDVKIAVIAD 67
Query: 243 XXXXXXXXXXXXXIVGGLELIEEIASSGKLDVEKCFSTRQFM----PRLFKISKILNQHG 298
++ EL EEIASS + K F P + KI + L ++
Sbjct: 68 GAVAEAARKLGLDVISSAEL-EEIASSPR-QARKLAKKYDFFIAEAPLMPKIGRYLGRY- 124
Query: 299 LMPNPKQGTVT----NDVARAVQEAKQGHIKFKMDNTSNVHAGLGKVSLKEELLRENVGA 354
L P K V D+ V++ K+ ++ ++ N VHA +G + +E + EN+ A
Sbjct: 125 LGPRNKMPVVVPPTLTDLTPIVEKLKK-TVRIQLKNNPVVHAPVGTEKMSDEEIAENIEA 183
Query: 355 FVNXXXXXXXXXXXXTSKFAGYVNSFHMCSTMGPSFPV 392
+N + V S ++ +TMGP+ +
Sbjct: 184 VLN-------AIIGKLERGESQVKSVYVKTTMGPAVKI 214
>pdb|3HAG|A Chain A, Crystal Structure Of The Hepatitis E Virus-Like Particle
Length = 504
Score = 30.4 bits (67), Expect = 2.0, 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|2ZZQ|A Chain A, Crystal Structure Analysis Of The Hev Capsid Protein,
Porf2
Length = 552
Score = 30.0 bits (66), Expect = 2.5, 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 = 30.0 bits (66), 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|2ZTN|A Chain A, Hepatitis E Virus Orf2 (Genotype 3)
Length = 478
Score = 29.3 bits (64), Expect = 3.9, 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 0.365
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,601,011
Number of Sequences: 62578
Number of extensions: 325053
Number of successful extensions: 772
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 726
Number of HSP's gapped (non-prelim): 27
length of query: 409
length of database: 14,973,337
effective HSP length: 101
effective length of query: 308
effective length of database: 8,652,959
effective search space: 2665111372
effective search space used: 2665111372
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: 53 (25.0 bits)