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= 004362
(759 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 517 ETFKTMIEKRCVPNIITYSILGESLCKAHKITE-AFNLLEEMENKGLTLDTVAFGTLING 575
+ FK MI + VPN T++ G L A E AF+++++M+ G+ ++G + G
Sbjct: 91 DIFKQMIVDKVVPNEATFTN-GARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFG 149
Query: 576 FCNSGDLDGAYQL 588
FC GD D AY++
Sbjct: 150 FCRKGDADKAYEV 162
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 32/149 (21%), Positives = 69/149 (46%), Gaps = 14/149 (9%)
Query: 381 KALEKGLKPSI-VLYNTLIKGLSQQGLILQALQLMNEMSESGCCPDMWTYNIVINGLCKM 439
KA +K ++ S L + S++G +L+AL+L +E +G + YN+++ +C +
Sbjct: 15 KAKKKAIQQSPEALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSL 73
Query: 440 GCVSDANNLVNDAISKGY-----------IPDIFTFNTLIDGYCKQLKMEIAIEILNTMW 488
+ ++ N +S+G+ +P+ TF + E+A +++ M
Sbjct: 74 AEAATESS-PNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMK 132
Query: 489 SHGVTPDVITYNSLLNGLCKAAKSEDVME 517
+ G+ P + +Y L G C+ ++ E
Sbjct: 133 AFGIQPRLRSYGPALFGFCRKGDADKAYE 161
Score = 34.3 bits (77), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 26/115 (22%), Positives = 47/115 (40%), Gaps = 9/115 (7%)
Query: 165 ALRLLKNMPSQGFEPNAVAY------CTLIAGFYEENHN---VEAYELFDEMLGMGISPD 215
ALRL G + + Y C+L E + N +++F +M+ + P+
Sbjct: 45 ALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPN 104
Query: 216 IATFNKLIHTLCKKGNVRESEKLFNKVLKRGVSPNLFTFNMFIQGLCRKGAISEA 270
ATF K + + + ++ G+ P L ++ + G CRKG +A
Sbjct: 105 EATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKA 159
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 26/126 (20%), Positives = 54/126 (42%), Gaps = 9/126 (7%)
Query: 87 GRRGKVQEAVDVFERMDFYNCEPTVLSYNTIMNI--LVEYGY-------FSQVHKVYMRM 137
++G V EA+ +++ + + YN ++ + L E S+ ++ +M
Sbjct: 37 SKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQM 96
Query: 138 RNKGIVPDVYTFVIRIKSFCRTRRPHVALRLLKNMPSQGFEPNAVAYCTLIAGFYEENHN 197
+VP+ TF + P +A ++K M + G +P +Y + GF +
Sbjct: 97 IVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDA 156
Query: 198 VEAYEL 203
+AYE+
Sbjct: 157 DKAYEV 162
Score = 29.3 bits (64), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 29/140 (20%), Positives = 63/140 (45%), Gaps = 15/140 (10%)
Query: 213 SPDIATFNKLIHTLCKKGNVRESEKLFNKVLKRGVSPNLFTFN--MFIQGLCRKG----- 265
SP+ A + + KKG+V E+ +L+++ + GV + + +N +++ L
Sbjct: 24 SPE-ALLKQKLDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSP 82
Query: 266 --AISEAISLLDSLGREDLTPDVVTY-NTLMCGLCKNSKVVEAEYYLHKMVNEGLEPDGF 322
+S + + + + P+ T+ N + K+ + + + +M G++P
Sbjct: 83 NPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDM-VKQMKAFGIQPRLR 141
Query: 323 SYNAVIDGYCKAGMISSADK 342
SY + G+C+ G ADK
Sbjct: 142 SYGPALFGFCRKG---DADK 158
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 38.1 bits (87), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 516 METFKTMIEKRCVPNIITYSILGESLCKAHKITE-AFNLLEEMENKGLTLDTVAFGTLIN 574
+ FK I + VPN T++ G L A E AF+ +++ + G+ ++G +
Sbjct: 90 FDIFKQXIVDKVVPNEATFTN-GARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALF 148
Query: 575 GFCNSGDLDGAYQL 588
GFC GD D AY++
Sbjct: 149 GFCRKGDADKAYEV 162
Score = 36.2 bits (82), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 31/149 (20%), Positives = 66/149 (44%), Gaps = 14/149 (9%)
Query: 381 KALEKGLKPSI-VLYNTLIKGLSQQGLILQALQLMNEMSESGCCPDMWTYNIVINGLCKM 439
KA +K ++ S L + S++G +L+AL+L +E +G + YN+++ +C +
Sbjct: 15 KAKKKAIQQSPEALLKQKLDXCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCSL 73
Query: 440 GCVSDANNLVNDAISKGY-----------IPDIFTFNTLIDGYCKQLKMEIAIEILNTMW 488
+ ++ N +S+G+ +P+ TF + E A + +
Sbjct: 74 AEAATESS-PNPGLSRGFDIFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXK 132
Query: 489 SHGVTPDVITYNSLLNGLCKAAKSEDVME 517
+ G+ P + +Y L G C+ ++ E
Sbjct: 133 AFGIQPRLRSYGPALFGFCRKGDADKAYE 161
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 27/122 (22%), Positives = 51/122 (41%), Gaps = 2/122 (1%)
Query: 254 FNMFIQGLCRKGAISEAISLLDSLGREDLTPDVVTY-NTLMCGLCKNSKVVEAEYYLHKM 312
+N + G R+GA E + +L + LTPD+++Y L C ++ E L +M
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQM 227
Query: 313 VNEGLEPDGFSYNAVIDGYCKAGMISSADKILNDAIFKGFVPDEFTYCSLINGL-CQDGD 371
EGL+ ++ +A ++ + K+ +P L+ + +DG
Sbjct: 228 SQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKDGR 287
Query: 372 VD 373
V
Sbjct: 288 VS 289
Score = 29.6 bits (65), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 279 REDLTPDVVTYNTLMCGLCKNSKVVEAEYYLHKMVNEGLEPDGFSYNAVID 329
R+ LT D+ YN +M G + E Y L + + GL PD SY A +
Sbjct: 160 RKLLTLDM--YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQ 208
>pdb|2Y5W|A Chain A, Crystal Structure Of Drosophila Melanogaster Kinesin-1
Motor Domain Dimer
pdb|2Y5W|B Chain B, Crystal Structure Of Drosophila Melanogaster Kinesin-1
Motor Domain Dimer
pdb|2Y65|A Chain A, Crystal Structure Of Drosophila Melanogaster Kinesin-1
Motor Domain Dimer-Tail Complex
pdb|2Y65|B Chain B, Crystal Structure Of Drosophila Melanogaster Kinesin-1
Motor Domain Dimer-Tail Complex
pdb|2Y65|C Chain C, Crystal Structure Of Drosophila Melanogaster Kinesin-1
Motor Domain Dimer-Tail Complex
pdb|2Y65|D Chain D, Crystal Structure Of Drosophila Melanogaster Kinesin-1
Motor Domain Dimer-Tail Complex
Length = 365
Score = 30.4 bits (67), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 9/63 (14%)
Query: 687 RVHEAVGFVHLMVQKGIVPEVVNTIFEADKREVASPKIVVEDLLKKSHITYYAYELLFDG 746
+ H G + V++GI+P +VN IF I ++ + HI YE+ D
Sbjct: 98 KTHTMEGVIGDSVKQGIIPRIVNDIFN---------HIYAMEVNLEFHIKVSYYEIYMDK 148
Query: 747 IRD 749
IRD
Sbjct: 149 IRD 151
>pdb|1PNS|I Chain I, Crystal Structure Of A Streptomycin Dependent Ribosome
From E. Coli, 30s Subunit Of 70s Ribosome. This File,
1pns, Contains The 30s Subunit, Two Trnas, And One Mrna
Molecule. The 50s Ribosomal Subunit Is In File 1pnu.
pdb|1PNX|I Chain I, Crystal Structure Of The Wild Type Ribosome From E. Coli,
30s Subunit Of 70s Ribosome. This File, 1pnx, Contains
Only Molecules Of The 30s Ribosomal Subunit. The 50s
Subunit Is In The Pdb File 1pny.
pdb|1VOQ|I Chain I, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOS|I Chain I, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOV|I Chain I, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOX|I Chain I, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOZ|I Chain I, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|2R1G|G Chain G, Coordinates Of The Thermus Thermophilus 30s Components
Neighboring Rbfa As Obtained By Fitting Into The Cryo-em
Map Of A 30s-rbfa Complex
pdb|3FIC|I Chain I, 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 30s Subunit
And The Ligands
pdb|3MR8|I Chain I, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3mr8 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3ms1.
Molecule B In The Same Asymmetric Unit Is Deposited As
3mrz (50s) And 3ms0 (30s).
pdb|3MS0|I Chain I, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3ms0 Contains 30s Ribosomal Subunit. The 50s
Ribosomal Subunit Can Be Found In Pdb Entry 3mrz.
Molecule A In The Same Asymmetric Unit Is Deposited As
3mr8 (30s) And 3ms1 (50s).
pdb|3PYN|I Chain I, Crystal Structure Of A Complex Containing Domain 3 From
The Psiv Igr Ires Rna Bound To The 70s Ribosome. This
File Contains The 30s Subunit Of The First 70s Ribosome.
pdb|3PYQ|I Chain I, Crystal Structure Of A Complex Containing Domain 3 From
The Psiv Igr Ires Rna Bound To The 70s Ribosome. This
File Contains The 30s Subunit Of The Second 70s
Ribosome.
pdb|3PYS|I Chain I, Crystal Structure Of A Complex Containing Domain 3 Of Crpv
Igr Ires Rna Bound To The 70s Ribosome. This File
Contains The 30s Subunit Of The First 70s Ribosome.
pdb|3PYU|I Chain I, Crystal Structure Of A Complex Containing Domain 3 Of Crpv
Igr Ires Rna Bound To The 70s Ribosome. This File
Contains The 30s Subunit Of The Second 70s Ribosome
Length = 127
Score = 30.0 bits (66), Expect = 4.9, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 230 GNVRESEKLFNKVLKRG---VSPNLFTFNMFIQGLCRKGAISEAISLLDSLGRED 281
G R E + L+ G V+ N FN + QGL R A E + +D+LGR D
Sbjct: 5 GTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFD 59
>pdb|1FJG|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotics Streptomycin,
Spectinomycin, And Paromomycin
pdb|1HR0|I Chain I, Crystal Structure Of Initiation Factor If1 Bound To The
30s Ribosomal Subunit
pdb|1HNW|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Tetracycline
pdb|1HNX|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Pactamycin
pdb|1HNZ|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
pdb|1GIX|L Chain L, Crystal Structure Of The Ribosome At 5.5 A Resolution.
This File, 1gix, Contains The 30s Ribosome Subunit,
Three Trna, And Mrna Molecules. 50s Ribosome Subunit Is
In The File 1giy
pdb|1IBK|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With The Antibiotic Paromomycin
pdb|1IBL|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site And With The Antibiotic Paromomycin
pdb|1IBM|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site
pdb|1I94|I Chain I, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3
pdb|1I95|I Chain I, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Edeine
pdb|1I96|I Chain I, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With The Translation
Initiation Factor If3 (C-Terminal Domain)
pdb|1I97|I Chain I, Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
pdb|1JGO|L Chain L, The Path Of Messenger Rna Through The Ribosome. This File,
1jgo, Contains The 30s Ribosome Subunit, Three Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
pdb|1JGP|L Chain L, The Path Of Messenger Rna Through The Ribosome. This File,
1jgp, Contains The 30s Ribosome Subunit, Three Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
pdb|1JGQ|L Chain L, The Path Of Messenger Rna Through The Ribosome. This File,
1jgq, Contains The 30s Ribosome Subunit, Three Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File 1giy
pdb|1J5E|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit
pdb|1N32|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Bound To Codon And Near-Cognate Transfer Rna
Anticodon Stem-Loop Mismatched At The First Codon
Position At The A Site With Paromomycin
pdb|1N33|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Bound To Codon And Near-Cognate Transfer Rna
Anticodon Stem-Loop Mismatched At The Second Codon
Position At The A Site With Paromomycin
pdb|1N34|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In The Presence Of Codon And
Crystallographically Disordered Near-Cognate Transfer
Rna Anticodon Stem-Loop Mismatched At The First Codon
Position
pdb|1N36|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In The Presence Of Crystallographically
Disordered Codon And Near-cognate Transfer Rna Anticodon
Stem-loop Mismatched At The Second Codon Position
pdb|1ML5|L Chain L, Structure Of The E. Coli Ribosomal Termination Complex
With Release Factor 2
pdb|1XMO|I Chain I, Crystal Structure Of Mnm5u34t6a37-Trnalysuuu Complexed
With Aag-Mrna In The Decoding Center
pdb|1XMQ|I Chain I, Crystal Structure Of T6a37-Asllysuuu Aaa-Mrna Bound To The
Decoding Center
pdb|1XNQ|I Chain I, Structure Of An Inosine-Adenine Wobble Base Pair Complex
In The Context Of The Decoding Center
pdb|1XNR|I Chain I, Crystal Structure Of An Inosine-Cytosine Wobble Base Pair
In The Context Of The Decoding Center
pdb|1YL4|L Chain L, Crystal Structure Of 70s Ribosome With Thrs Operator And
Trnas. 30s Subunit. The Coordinates For The 50s Subunit
Are In The Pdb Entry 1yl3
pdb|2B64|I Chain I, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf1
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Subunit, Trnas, Mrna And
Release Factor Rf1 From A Crystal Structure Of The Whole
Ribosomal Complex". The Entire Crystal Structure
Contains One 70s Ribosome, Trnas, Mrna And Release
Factor Rf1 And Is Described In Remark 400.
pdb|2B9M|I Chain I, 30s Ribosomal Subunit, Trnas, Mrna And Release Factor Rf2
From A Crystal Structure Of The Whole Ribosomal Complex.
This File Contains The 30s Ribosomal Subunit, Trnas,
Mrna And Release Factor Rf2 From A Crystal Structure Of
The Whole Ribosomal Complex". The Entire Crystal
Structure Contains One 70s Ribosome, Trnas, Mrna And
Release Factor Rf2 And Is Described In Remark 400.
pdb|2B9O|I Chain I, 30s Ribosomal Subunit, Trnas And Mrna From A Crystal
Structure Of The Whole Ribosomal Complex With A Stop
Codon In The A-Site. This File Contains The 30s Subunit,
Trnas And Mrna From A Crystal Structure Of The Whole
Ribosomal Complex With A Stop Codon In The A-Site And Is
Described In Remark 400.
pdb|2F4V|I Chain I, 30s Ribosome + Designer Antibiotic
pdb|2HHH|I Chain I, Crystal Structure Of Kasugamycin Bound To The 30s
Ribosomal Subunit
pdb|2J00|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 1 Of 4).
This File Contains The 30s Subunit, Mrna, A-, P- And
E-Site Trnas And Paromomycin For Molecule I.
pdb|2J02|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Mrna, Trna And Paromomycin (Part 3 Of 4)
This File Contains The 30s Subunit, Mrna, A-, P- And
E-Site Trnas And Paromomycin For Molecule Ii.
pdb|2E5L|I Chain I, A Snapshot Of The 30s Ribosomal Subunit Capturing Mrna Via
The Shine- Dalgarno Interaction
pdb|2OW8|JJ Chain j, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals
Functional Interactions And Rearrangements. This File,
2ow8, Contains The 30s Ribosome Subunit, Two Trna, And
Mrna Molecules. 50s Ribosome Subunit Is In The File
1vsa.
pdb|2UXC|I Chain I, Crystal Structure Of An Extended Trna Anticodon Stem Loop
In Complex With Its Cognate Mrna Ucgu In The Context Of
The Thermus Thermophilus 30s Subunit.
pdb|2UXB|I Chain I, Crystal Structure Of An Extended Trna Anticodon Stem Loop
In Complex With Its Cognate Mrna Gggu In The Context Of
The Thermus Thermophilus 30s Subunit.
pdb|2V46|I Chain I, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 1 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 1.
pdb|2V48|I Chain I, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 3 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 2.
pdb|2UXD|I Chain I, Crystal Structure Of An Extended Trna Anticodon Stem Loop
In Complex With Its Cognate Mrna Cggg In The Context Of
The Thermus Thermophilus 30s Subunit.
pdb|2QNH|JJ Chain j, Interactions And Dynamics Of The Shine-Dalgarno Helix In
The 70s Ribosome. This File, 2qnh, Contains The 30s
Ribosome Subunit, Two Trna, And Mrna Molecules. 50s
Ribosome Subunit Is In The File 1vsp.
pdb|2VQE|I Chain I, Modified Uridines With C5-methylene Substituents At The
First Position Of The Trna Anticodon Stabilize U-g
Wobble Pairing During Decoding
pdb|2VQF|I Chain I, Modified Uridines With C5-Methylene Substituents At The
First Position Of The Trna Anticodon Stabilize U-G
Wobble Pairing During Decoding
pdb|3D5A|I Chain I, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of One 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes As Described In Remark 400.
pdb|3D5C|I Chain I, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 30s Subunit, Release
Factor 1 (Rf1), Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|3F1E|I Chain I, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of One
70s Ribosome. The Entire Crystal Structure Contains Two
70s Ribosomes As Described In Remark 400.
pdb|3F1G|I Chain I, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
30s Subunit, Rf2, Two Trna, And Mrna Molecules Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|2WDG|I Chain I, 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 30s Subunit A-,P-, And E-Site Trnas And
Paromomycin For Molecule I.
pdb|2WDH|I Chain I, 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 30s Subunit A-,P-, And E-Site Trnas And
Paromomycin For Molecule Ii.
pdb|2WDK|I Chain I, 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 30s
Subunit A-,P-, And E-Site Trnas And Paromomycin For
Molecule I.
pdb|2WDM|I Chain I, 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 30s
Subunit A-,P-, And E-Site Trnas And Paromomycin For
Molecule Ii.
pdb|2ZM6|I Chain I, Crystal Structure Of The Thermus Thermophilus 30s
Ribosomal Subunit
pdb|2WH1|I Chain I, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|2WH3|I Chain I, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome). This File Contains The
30s Subunit.
pdb|2X9R|I Chain I, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9T|I Chain I, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2XFZ|I Chain I, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 1 Of 4)
pdb|2XG1|I Chain I, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 3 Of 4)
pdb|3OTO|I Chain I, Crystal Structure Of The 30s Ribosomal Subunit From A Ksga
Mutant Of Thermus Thermophilus (Hb8)
pdb|3OGE|I Chain I, Structure Of The Thermus Thermophilus Ribosome Complexed
With Chloramphenicol. This File Contains The 30s Subunit
Of One 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3OGY|I Chain I, Structure Of The Thermus Thermophilus Ribosome Complexed
With Chloramphenicol. This File Contains The 30s Subunit
Of One 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3OHC|I Chain I, Structure Of The Thermus Thermophilus Ribosome Complexed
With Erythromycin. This File Contains The 30s Subunit Of
One 70s Ribosome. The Entire Crystal Structure Contains
Two 70s Ribosomes.
pdb|3OHD|I Chain I, Structure Of The Thermus Thermophilus Ribosome Complexed
With Erythromycin. This File Contains The 30s Subunit Of
One 70s Ribosome. The Entire Crystal Structure Contains
Two 70s Ribosomes.
pdb|3OHY|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Azithromycin. This File Contains The 30s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI0|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Azithromycin. This File Contains The 30s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI2|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Telithromycin. This File Contains The 30s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI4|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Telithromycin. This File Contains The 30s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|2XQD|I Chain I, The Structure Of Ef-Tu And Aminoacyl-Trna Bound To The 70s
Ribosome With A Gtp Analog
pdb|3ZVO|I Chain I, Crystal Structure Of The Hybrid State Of Ribosome In
Complex With The Guanosine Triphosphatase Release Factor
3
pdb|3T1H|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Human Anti-Codon Stem Loop
(Hasl) Of Transfer Rna Lysine 3 (Trnalys3) Bound To An
Mrna With An Aaa-Codon In The A-Site And Paromomycin
pdb|3T1Y|I Chain I, Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit Complexed With A Human Anti-Codon Stem Loop
(Hasl) Of Transfer Rna Lysine 3 (Trnalys3) Bound To An
Mrna With An Aag-Codon In The A-Site And Paromomycin
pdb|3UXS|I Chain I, The Structure Of Thermorubin In Complex With The 70s
Ribosome From Thermus Thermophilus. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3UXT|I Chain I, The Structure Of Thermorubin In Complex With The 70s
Ribosome From Thermus Thermophilus. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.'
pdb|4ABR|I Chain I, Complex Of Smpb, A Tmrna Fragment And Ef-Tu-Gdp-Kirromycin
With The 70s Ribosome
pdb|4AQY|I Chain I, Structure Of Ribosome-Apramycin Complexes
Length = 128
Score = 30.0 bits (66), Expect = 4.9, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 230 GNVRESEKLFNKVLKRG---VSPNLFTFNMFIQGLCRKGAISEAISLLDSLGRED 281
G R E + L+ G V+ N FN + QGL R A E + +D+LGR D
Sbjct: 6 GTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFD 60
>pdb|3PDK|A Chain A, Crystal Structure Of Phosphoglucosamine Mutase From B.
Anthracis
pdb|3PDK|B Chain B, Crystal Structure Of Phosphoglucosamine Mutase From B.
Anthracis
Length = 469
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 38/89 (42%), Gaps = 8/89 (8%)
Query: 582 LDGAYQLF---RRMEDQYKISHTTATYNIMINAFSEKLNFYMAEKLFYEMSEKGCPPDNY 638
+DG +F + M++ ++ H T +M N L FY A + S+K D Y
Sbjct: 277 VDGDQIMFICAKYMKETGQLKHNTVVSTVMSN-----LGFYKALEANGITSDKTAVGDRY 331
Query: 639 TYRIMIDSFCKTGGINSGYCLLLENIDKG 667
M GG SG+ +LL+ I G
Sbjct: 332 VMEEMKRGGYNLGGEQSGHIILLDYITTG 360
>pdb|3LKE|A Chain A, Crystal Structure Of Enoyl-Coa Hydratase From Bacillus
Halodurans
pdb|3LKE|B Chain B, Crystal Structure Of Enoyl-Coa Hydratase From Bacillus
Halodurans
pdb|3LKE|C Chain C, Crystal Structure Of Enoyl-Coa Hydratase From Bacillus
Halodurans
Length = 263
Score = 29.6 bits (65), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 350 KGFVPDEFTYCSLINGLCQDG-DVDRAMAVYVKALEKGLKPSIVLYNTLIKGLSQQGLIL 408
K F +E LI +C++ ++ + Y+KA+ +G P+I L+KG + + L
Sbjct: 170 KLFTSEEALRLGLIQEICENKQELQERVKNYLKAVSEGYVPAIAATKKLLKGKAAEELKQ 229
Query: 409 QALQLMNEM 417
Q Q E+
Sbjct: 230 QLEQETEEL 238
>pdb|1W3B|A Chain A, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha.
pdb|1W3B|B Chain B, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha
Length = 388
Score = 29.6 bits (65), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 49/188 (26%), Positives = 84/188 (44%), Gaps = 13/188 (6%)
Query: 358 TYCSLINGLCQDGDVDRAMAVYVKALEKGLKPS-IVLYNTLIKGLSQQGLILQALQLMNE 416
Y +L N L + DRA+A Y++AL L P+ V++ L +QGLI A+
Sbjct: 205 AYINLGNVLKEARIFDRAVAAYLRAL--SLSPNHAVVHGNLACVYYEQGLIDLAIDTYRR 262
Query: 417 MSE-SGCCPDMWTYNIVINGLCKMGCVSDANNLVNDAISKGYIPDIFTFNTLIDGYCKQL 475
E PD Y + N L + G V++A + N A+ + + N L + +Q
Sbjct: 263 AIELQPHFPD--AYCNLANALKEKGSVAEAEDCYNTAL-RLCPTHADSLNNLANIKREQG 319
Query: 476 KMEIAIEILNTMWSHGVTPD-VITYNSLLNGLCKAAKSEDVMETFKTMIEKRCVPNII-T 533
+E A+ + V P+ +++L + L + K ++ + +K I R P
Sbjct: 320 NIEEAVRLYRKALE--VFPEFAAAHSNLASVLQQQGKLQEALMHYKEAI--RISPTFADA 375
Query: 534 YSILGESL 541
YS +G +L
Sbjct: 376 YSNMGNTL 383
>pdb|1ZBP|A Chain A, X-Ray Crystal Structure Of Protein Vpa1032 From Vibrio
Parahaemolyticus. Northeast Structural Genomics
Consortium Target Vpr44
Length = 273
Score = 29.6 bits (65), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 40/89 (44%), Gaps = 9/89 (10%)
Query: 335 GMISSADKILNDAIFKGFVPDEFTYCSLINGLCQDGDVDRAMAVYVKALEKGLKPSIVLY 394
G + A ++L +AI K D S I LC DGD +RA ++ L SI L+
Sbjct: 11 GQLQQALELLIEAI-KASPKDASLRSSFIELLCIDGDFERA--------DEQLXQSIKLF 61
Query: 395 NTLIKGLSQQGLILQALQLMNEMSESGCC 423
+ G SQ +++A Q + ++
Sbjct: 62 PEYLPGASQLRHLVKAAQARKDFAQGAAT 90
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
0.323 0.139 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,992,679
Number of Sequences: 62578
Number of extensions: 926912
Number of successful extensions: 1867
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1838
Number of HSP's gapped (non-prelim): 33
length of query: 759
length of database: 14,973,337
effective HSP length: 106
effective length of query: 653
effective length of database: 8,340,069
effective search space: 5446065057
effective search space used: 5446065057
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)