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= 027876
(217 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|A Chain A, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 216
Score = 355 bits (911), Expect = 1e-98, Method: Compositional matrix adjust.
Identities = 170/217 (78%), Positives = 190/217 (87%), Gaps = 1/217 (0%)
Query: 1 MSKLQSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPR 60
MSKLQSDA+++A++ IV ++E KKR FTET+ELQIGLKNYDPQKDKRFSGSVKLPHIPR
Sbjct: 1 MSKLQSDAVKDAITQIVGEARE-KKRKFTETVELQIGLKNYDPQKDKRFSGSVKLPHIPR 59
Query: 61 PKMKVCMLGDAQHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQI 120
PKM+VCMLGDAQHV++AEK+GLDYMDVE YHAFLASE++IKQI
Sbjct: 60 PKMRVCMLGDAQHVDQAEKMGLDYMDVESLKKMNKNKKLVKKLAKKYHAFLASEAIIKQI 119
Query: 121 PRLLGPGLNKAGKFPTLVTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIF 180
PRLLGPGLNKAGKFPTLV+HQESLE+KVNETKATVKFQLKKVLCMGVAVGNLSM+EKQI
Sbjct: 120 PRLLGPGLNKAGKFPTLVSHQESLEAKVNETKATVKFQLKKVLCMGVAVGNLSMDEKQIQ 179
Query: 181 QNVQMSVNFLVSLLKKNWQNVRCLYLKSTMGPSNRIF 217
QN+QMSVNFLVSLLKKNWQNVRCLY+KSTMG R+F
Sbjct: 180 QNIQMSVNFLVSLLKKNWQNVRCLYVKSTMGKRVRVF 216
>pdb|1S1I|A Chain A, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h.
pdb|3IZS|A Chain A, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O58|A Chain A, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|A Chain A, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit
Length = 217
Score = 260 bits (665), Expect = 3e-70, Method: Compositional matrix adjust.
Identities = 122/217 (56%), Positives = 158/217 (72%)
Query: 1 MSKLQSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPR 60
MSK+ S +RE V +++YS ETKKRNF ET+ELQ+GLKNYDPQ+DKRFSGS+KLP+ PR
Sbjct: 1 MSKITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPR 60
Query: 61 PKMKVCMLGDAQHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQI 120
P M +C+ GDA V+ A+ G+D M V+ Y+AF+ASE +IKQ+
Sbjct: 61 PNMSICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQV 120
Query: 121 PRLLGPGLNKAGKFPTLVTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIF 180
PRLLGP L+KAGKFPT V+H + L KV + ++T+KFQLKKVLC+ VAVGN+ MEE +
Sbjct: 121 PRLLGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKFQLKKVLCLAVAVGNVEMEEDVLV 180
Query: 181 QNVQMSVNFLVSLLKKNWQNVRCLYLKSTMGPSNRIF 217
+ MSVNF VSLLKKNWQNV L +KS+MGP+ R++
Sbjct: 181 NQILMSVNFFVSLLKKNWQNVGSLVVKSSMGPAFRLY 217
>pdb|2NOQ|G Chain G, Structure Of Ribosome-Bound Cricket Paralysis Virus Ires
Rna
pdb|3JYW|A Chain A, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
pdb|3J0L|B Chain B, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 9.8a Cryo-Em Map: Classic Pre State 1
pdb|3J0O|B Chain B, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 9a Cryo-Em Map: Classic Pre State 2
pdb|3J0P|B Chain B, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 10.6a Cryo-Em Map: Rotated Pre State 1
pdb|3J0Q|B Chain B, Core Of Mammalian 80s Pre-Ribosome In Complex With Trnas
Fitted To A 10.6a Cryo-Em Map: Rotated Pre State 2
Length = 213
Score = 254 bits (648), Expect = 3e-68, Method: Compositional matrix adjust.
Identities = 119/213 (55%), Positives = 154/213 (72%)
Query: 4 LQSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKM 63
+ S +RE V +++YS ETKKRNF ET+ELQ+GLKNYDPQ+DKRFSGS+KLP+ PRP M
Sbjct: 1 ITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPRPNM 60
Query: 64 KVCMLGDAQHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRL 123
+C+ GDA V+ A+ G+D M V+ Y+AF+ASE +IKQ+PRL
Sbjct: 61 SICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQVPRL 120
Query: 124 LGPGLNKAGKFPTLVTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNV 183
LGP L+KAGKFPT V+H + L KV + ++T+KFQLKKVLC+ VAVGN+ MEE + +
Sbjct: 121 LGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKFQLKKVLCLAVAVGNVEMEEDVLVNQI 180
Query: 184 QMSVNFLVSLLKKNWQNVRCLYLKSTMGPSNRI 216
MSVNF VSLLKKNWQNV L +KS+MGP+ R+
Sbjct: 181 LMSVNFFVSLLKKNWQNVGSLVVKSSMGPAFRL 213
>pdb|3ZF7|J Chain J, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 214
Score = 230 bits (586), Expect = 6e-61, Method: Compositional matrix adjust.
Identities = 113/217 (52%), Positives = 150/217 (69%), Gaps = 3/217 (1%)
Query: 1 MSKLQSDALREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPR 60
MSK+ L EA+ +++ K+ K+R F E+I+LQ+ LKNYDPQKDKRFSGSV+LPH+ R
Sbjct: 1 MSKIPPALLSEAIQNVL---KDRKERKFKESIDLQVNLKNYDPQKDKRFSGSVRLPHVCR 57
Query: 61 PKMKVCMLGDAQHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQI 120
P+M VC+L D H + A+K + M+ E Y AFL SES+IK +
Sbjct: 58 PRMTVCLLCDLVHEDIAKKNDVPTMNQEELKKLNKNKKLVKKMCNQYDAFLCSESIIKTV 117
Query: 121 PRLLGPGLNKAGKFPTLVTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIF 180
PRL+GP +++ GKFPT+ ESL KV E ++TVKFQLKKVLC+G VG++ M E Q+
Sbjct: 118 PRLVGPHMHRVGKFPTVCAQNESLPDKVLELQSTVKFQLKKVLCLGTCVGHVDMTEDQVR 177
Query: 181 QNVQMSVNFLVSLLKKNWQNVRCLYLKSTMGPSNRIF 217
QNV M++NFLVSLLKKNWQN++ Y+KSTMG S RI+
Sbjct: 178 QNVVMAINFLVSLLKKNWQNLKSAYIKSTMGKSQRIY 214
>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 = 93.2 bits (230), Expect = 9e-20, Method: Compositional matrix adjust.
Identities = 58/206 (28%), Positives = 101/206 (49%), Gaps = 2/206 (0%)
Query: 13 VSSIVQYSKETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDA 71
V ++ + K RNFT+++E+ + LK+ D ++ + RF V LPH +K+ ++ D
Sbjct: 9 VKAVKEAKARAKPRNFTQSVEVAVNLKDIDLKRPENRFKLEVVLPHGRGKDVKIAVIADG 68
Query: 72 QHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKA 131
E A K+GLD + Y F+A ++ +I R LG L
Sbjct: 69 AVAEAARKLGLDVISSAELEEIASSPRQARKLAKKYDFFIAEAPLMPKIGRYLGRYLGPR 128
Query: 132 GKFPTLVTHQ-ESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
K P +V L V + K TV+ QLK + VG M +++I +N++ +N +
Sbjct: 129 NKMPVVVPPTLTDLTPIVEKLKKTVRIQLKNNPVVHAPVGTEKMSDEEIAENIEAVLNAI 188
Query: 191 VSLLKKNWQNVRCLYLKSTMGPSNRI 216
+ L++ V+ +Y+K+TMGP+ +I
Sbjct: 189 IGKLERGESQVKSVYVKTTMGPAVKI 214
>pdb|1CJS|A Chain A, Crystal Structure Of Ribosomal Protein L1 From
Methanococcus Jannaschii
pdb|1I2A|A Chain A, Crystal Structure Of L1 Ribosomal Protein From
Methanococcus Jannaschii With 1.85a Resolution
Length = 219
Score = 77.0 bits (188), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 57/205 (27%), Positives = 94/205 (45%), Gaps = 2/205 (0%)
Query: 10 REAVSSIVQYSKE-TKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCM 67
REA+ V+ ++E K RNFT++ E LK D +K + R V LPH + K+ +
Sbjct: 3 REALLQAVKEARELAKPRNFTQSFEFIATLKEIDMRKPENRIKTEVVLPHGRGKEAKIAV 62
Query: 68 LGDAQHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPG 127
+G ++AE++GL + E + F+A ++ I R +G
Sbjct: 63 IGTGDLAKQAEELGLTVIRKEEIEELGKNKRKLRKIAKAHDFFIAQADLMPLIGRYMGVI 122
Query: 128 LNKAGKFPTLVTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSV 187
L GK P V +++ V K TV + V VGN M ++QI N++ +
Sbjct: 123 LGPRGKMPKPVPANANIKPLVERLKKTVVINTRDKPYFQVLVGNEKMTDEQIVDNIEAVL 182
Query: 188 NFLVSLLKKNWQNVRCLYLKSTMGP 212
N + +K +++ Y+K TMGP
Sbjct: 183 NVVAKKYEKGLYHIKDAYVKLTMGP 207
>pdb|1U63|A Chain A, The Structure Of A Ribosomal Protein L1-Mrna Complex
pdb|1U63|C Chain C, The Structure Of A Ribosomal Protein L1-Mrna Complex
Length = 219
Score = 69.7 bits (169), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 55/205 (26%), Positives = 90/205 (43%), Gaps = 2/205 (0%)
Query: 10 REAVSSIVQYSKE-TKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCM 67
REA+ V+ ++E K RNFT++ E LK D +K + R V LPH + K+ +
Sbjct: 3 REALLQAVKEARELAKPRNFTQSFEFIATLKEIDXRKPENRIKTEVVLPHGRGKEAKIAV 62
Query: 68 LGDAQHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPG 127
+G ++AE++GL + E + F+A + I R G
Sbjct: 63 IGTGDLAKQAEELGLTVIRKEEIEELGKNKRKLRKIAKAHDFFIAQADLXPLIGRYXGVI 122
Query: 128 LNKAGKFPTLVTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSV 187
L GK P V +++ V K TV + V VGN ++QI N++ +
Sbjct: 123 LGPRGKXPKPVPANANIKPLVERLKKTVVINTRDKPYFQVLVGNEKXTDEQIVDNIEAVL 182
Query: 188 NFLVSLLKKNWQNVRCLYLKSTMGP 212
N + +K +++ Y+K T GP
Sbjct: 183 NVVAKKYEKGLYHIKDAYVKLTXGP 207
>pdb|1DWU|A Chain A, Ribosomal Protein L1
pdb|1DWU|B Chain B, Ribosomal Protein L1
Length = 213
Score = 68.6 bits (166), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 53/209 (25%), Positives = 94/209 (44%), Gaps = 2/209 (0%)
Query: 10 REAVSSIVQYSKE-TKKRNFTETIELQIGLKNYD-PQKDKRFSGSVKLPHIPRPKMKVCM 67
RE + V+ ++ K RNFT++++L I LK D + + R V LP+ + K+ +
Sbjct: 3 RENILKAVKEARSLAKPRNFTQSLDLIINLKELDLSRPENRLKEQVVLPNGRGKEPKIAV 62
Query: 68 LGDAQHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPG 127
+ +AE++GL + + + F+A ++ + + LGP
Sbjct: 63 IAKGDLAAQAEEMGLTVIRQDELEELGKNKKMAKKIANEHDFFIAQADMMPLVGKTLGPV 122
Query: 128 LNKAGKFPTLVTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSV 187
L GK P V +L V K TV + V VGN M ++++ +N++ +
Sbjct: 123 LGPRGKMPQPVPANANLTPLVERLKKTVLINTRDKPLFHVLVGNEKMSDEELAENIEAIL 182
Query: 188 NFLVSLLKKNWQNVRCLYLKSTMGPSNRI 216
N + +K +V+ Y K TMGP +I
Sbjct: 183 NTVSRKYEKGLYHVKSAYTKLTMGPPAQI 211
>pdb|2ZKR|5 Chain 5, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 212
Score = 65.9 bits (159), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 47/207 (22%), Positives = 92/207 (44%), Gaps = 1/207 (0%)
Query: 8 ALREAVSSIVQYSKETKKRNFTETIELQIGLKNYD-PQKDKRFSGSVKLPHIPRPKMKVC 66
A +E +++ + ++ +RNF ET++L + L++ D R SV LP + +
Sbjct: 2 ADQEIENAVSRALEDAPERNFRETVDLAVNLRDLDLNDPSNRVDESVVLPAGTGQETTIV 61
Query: 67 MLGDAQHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGP 126
+ + + AE++ D +D + F+A + +++ I R LG
Sbjct: 62 VFAEGETALRAEEVADDVLDEDELEELGGDDDAAKDLADDTDFFIAEKGLMQDIGRYLGT 121
Query: 127 GLNKAGKFPTLVTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMS 186
L GK P + + + + K TV+ + + VG M + I N+ +
Sbjct: 122 VLGPRGKMPEPLDPDDDVVEVIERMKNTVQLRSGERRTFHTRVGAEDMSAENIADNIDVI 181
Query: 187 VNFLVSLLKKNWQNVRCLYLKSTMGPS 213
+ L + L+K N+ +Y+K+TMGP+
Sbjct: 182 LRRLHADLEKGPLNIDTVYVKTTMGPA 208
>pdb|3QOY|A Chain A, Crystal Structure Of Ribosomal Protein L1 From Aquifex
Aeolicus
Length = 242
Score = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 54/215 (25%), Positives = 109/215 (50%), Gaps = 16/215 (7%)
Query: 9 LREAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQ-KDKRFSGSVKLPHIPRPKMKVCM 67
L EAV +++ +E +R F ET+EL + L N DP+ D+ GSV LPH +KV +
Sbjct: 23 LEEAVD-LLKKMEEVLQRRFDETVELAMRL-NVDPRYADQMVRGSVVLPHGLGKPIKVVV 80
Query: 68 LGDAQHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIP---RLL 124
+ ++ ++AE+ G DY+ + + +A+ ++ ++ R+L
Sbjct: 81 FAEGEYAKKAEEAGADYVGGD-----ELINKILKEEWTDFDVAIATPEMMPKVAKLGRIL 135
Query: 125 GP-GLNKAGKFPTLVTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNV 183
GP GL + K T+ T+ E ++ + + V+F++ K + + VG +S E++++ N+
Sbjct: 136 GPRGLMPSPKTGTVTTNVE--QAIKDAKRGRVEFKVDKAGNVHMPVGKISFEKEKLIDNL 193
Query: 184 QMSVNFLVSLLKKN--WQNVRCLYLKSTMGPSNRI 216
+++ +V Q ++ + + TM PS ++
Sbjct: 194 YAAIDAVVRAKPPGAKGQYIKNMAVSLTMSPSVKL 228
>pdb|3TG8|A Chain A, Mutant Ribosomal Protein L1 Lacking Ala158 From Thermus
Thermophilus
Length = 228
Score = 58.5 bits (140), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 50/201 (24%), Positives = 90/201 (44%), Gaps = 12/201 (5%)
Query: 21 KETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEK 79
KE F ET+E+ L DP++ D+ G+V LPH +++V + + ++EAE+
Sbjct: 31 KELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEE 89
Query: 80 IGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKAGKFPT--L 137
G DY+ E + A +A+ V+ + LG L G P
Sbjct: 90 AGADYVGGE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKA 143
Query: 138 VTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKKN 197
T ++ + E K ++F+ K + VG S +++ N++ + L + +
Sbjct: 144 GTVGFNIGEIIREIKGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEG 203
Query: 198 WQN--VRCLYLKSTMGPSNRI 216
+ +R +Y+ +TMGPS RI
Sbjct: 204 AKGTFLRSVYVTTTMGPSVRI 224
>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 = 56.6 bits (135), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 51/194 (26%), Positives = 92/194 (47%), Gaps = 21/194 (10%)
Query: 28 FTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLDYMD 86
F ET+E+ L DP++ D+ G+V LPH +++V + + ++EAE+ G DY+
Sbjct: 14 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 72
Query: 87 VEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGP-GLNKAGKFPTLVTHQESLE 145
E + F+ +V ++ R+LGP GLN P T ++
Sbjct: 73 GE---------EIIQKILDGWMDFVMG-AVGSKLGRILGPRGLN-----PKAGTVGFNIG 117
Query: 146 SKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNWQN--VR 202
+ E KA ++F+ K + VG S +++ N++ + L + + + +R
Sbjct: 118 EIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLR 177
Query: 203 CLYLKSTMGPSNRI 216
+Y+ +TMGPS RI
Sbjct: 178 SVYVTTTMGPSVRI 191
>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 = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 51/210 (24%), Positives = 93/210 (44%), Gaps = 13/210 (6%)
Query: 13 VSSIVQYSKETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDA 71
+ + KE F ET+E+ L DP++ D+ G+V LPH +++V +
Sbjct: 23 IDEAARLVKELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKG 81
Query: 72 QHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKA 131
+ ++EAE+ G DY+ E + A +A+ V+ + LG L
Sbjct: 82 EKIKEAEEAGADYVGGE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPR 135
Query: 132 GKFPT--LVTHQESLESKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVN 188
G P T ++ + E KA ++F+ K + VG S +++ N++ +
Sbjct: 136 GLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIR 195
Query: 189 FLVSLLKKNWQN--VRCLYLKSTMGPSNRI 216
L + + + +R +Y+ +TMGPS RI
Sbjct: 196 ALEAHKPEGAKGTFLRSVYVTTTMGPSVRI 225
>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 = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 51/202 (25%), Positives = 91/202 (45%), Gaps = 13/202 (6%)
Query: 21 KETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEK 79
KE F ET+E+ L DP++ D+ G+V LPH +++V + + ++EAE+
Sbjct: 31 KELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEE 89
Query: 80 IGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKAGKFPT--L 137
G DY+ E + A +A+ V+ + LG L G P
Sbjct: 90 AGADYVGGE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKA 143
Query: 138 VTHQESLESKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKK 196
T ++ + E KA ++F+ K + VG S +++ N++ + L + +
Sbjct: 144 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPE 203
Query: 197 NWQN--VRCLYLKSTMGPSNRI 216
+ +R +Y+ +TMGPS RI
Sbjct: 204 GAKGTFLRSVYVTTTMGPSVRI 225
>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 = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 51/202 (25%), Positives = 91/202 (45%), Gaps = 13/202 (6%)
Query: 21 KETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEK 79
KE F ET+E+ L DP++ D+ G+V LPH +++V + + ++EAE+
Sbjct: 30 KELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEE 88
Query: 80 IGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKAGKFPT--L 137
G DY+ E + A +A+ V+ + LG L G P
Sbjct: 89 AGADYVGGE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKA 142
Query: 138 VTHQESLESKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKK 196
T ++ + E KA ++F+ K + VG S +++ N++ + L + +
Sbjct: 143 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPE 202
Query: 197 NWQN--VRCLYLKSTMGPSNRI 216
+ +R +Y+ +TMGPS RI
Sbjct: 203 GAKGTFLRSVYVTTTMGPSVRI 224
>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 = 55.5 bits (132), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 51/210 (24%), Positives = 93/210 (44%), Gaps = 13/210 (6%)
Query: 13 VSSIVQYSKETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDA 71
+ + KE F ET+E+ L DP++ D+ G+V LPH +++V +
Sbjct: 23 IDEAARLVKELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKG 81
Query: 72 QHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKA 131
+ ++EAE+ G DY+ E + A +A+ V+ + LG L
Sbjct: 82 EKIKEAEEAGADYVGGE------EIIQKILDAWMDFDAVVATPDVMGAVGSKLGRILAPR 135
Query: 132 GKFPT--LVTHQESLESKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVN 188
G P T ++ + E KA ++F+ K + VG S +++ N++ +
Sbjct: 136 GLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIR 195
Query: 189 FLVSLLKKNWQN--VRCLYLKSTMGPSNRI 216
L + + + +R +Y+ +TMGPS RI
Sbjct: 196 ALEAHKPEGAKGTFLRSVYVTTTMGPSVRI 225
>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 = 54.7 bits (130), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 50/202 (24%), Positives = 91/202 (45%), Gaps = 13/202 (6%)
Query: 21 KETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEK 79
KE F ET+E+ L DP++ D+ G+V LPH +++V + + ++EAE+
Sbjct: 31 KELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEE 89
Query: 80 IGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKAGKFPT--L 137
G DY+ E + A +A+ V+ + +G L G P
Sbjct: 90 AGADYVGGE------EIIQKILDGWMDFDAVVATPDVMGAVGSKMGRILGPRGLLPNPKA 143
Query: 138 VTHQESLESKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKK 196
T ++ + E KA ++F+ K + VG S +++ N++ + L + +
Sbjct: 144 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPE 203
Query: 197 NWQN--VRCLYLKSTMGPSNRI 216
+ +R +Y+ +TMGPS RI
Sbjct: 204 GAKGTFLRSVYVTTTMGPSVRI 225
>pdb|4F9T|A Chain A, Ribosomal Protein L1 From Thermus Thermophilus With
Substitution Thr217ala
Length = 229
Score = 53.9 bits (128), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 50/202 (24%), Positives = 90/202 (44%), Gaps = 13/202 (6%)
Query: 21 KETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEK 79
KE F ET+E+ L DP++ D+ G+V LPH +++V + + ++EAE+
Sbjct: 31 KELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEE 89
Query: 80 IGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKAGKFPT--L 137
G DY+ E + A +A+ V+ + LG L G P
Sbjct: 90 AGADYVGGE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKA 143
Query: 138 VTHQESLESKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKK 196
T ++ + E KA ++F+ K + VG S +++ N++ + L + +
Sbjct: 144 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPE 203
Query: 197 NWQN--VRCLYLKSTMGPSNRI 216
+ +R +Y+ + MGPS RI
Sbjct: 204 GAKGTFLRSVYVTTAMGPSVRI 225
>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 = 53.5 bits (127), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 50/202 (24%), Positives = 90/202 (44%), Gaps = 13/202 (6%)
Query: 21 KETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEK 79
KE F ET+E+ L DP++ D+ G+V LPH +++V + + ++EAE+
Sbjct: 26 KELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEE 84
Query: 80 IGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKAGKFPT--L 137
G DY+ E + A +A+ V+ + LG L G P
Sbjct: 85 AGADYVGGE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKA 138
Query: 138 VTHQESLESKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKK 196
T ++ + E KA ++F+ K + VG +++ N++ + L + +
Sbjct: 139 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKACFPPEKLADNIRAFIRALEAHKPE 198
Query: 197 NWQN--VRCLYLKSTMGPSNRI 216
+ +R +Y+ +TMGPS RI
Sbjct: 199 GAKGTFLRSVYVTTTMGPSVRI 220
>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 = 53.5 bits (127), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 50/202 (24%), Positives = 90/202 (44%), Gaps = 13/202 (6%)
Query: 21 KETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEK 79
KE F ET+E+ L DP++ D+ G+V LPH +++V + + ++EAE+
Sbjct: 30 KELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEE 88
Query: 80 IGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKAGKFPT--L 137
G DY+ E + A +A+ V+ + LG L G P
Sbjct: 89 AGADYVGGE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKA 142
Query: 138 VTHQESLESKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKK 196
T ++ + E KA ++F+ K + VG S +++ N++ + L + +
Sbjct: 143 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPE 202
Query: 197 NWQN--VRCLYLKSTMGPSNRI 216
+ +R +Y+ + MGPS RI
Sbjct: 203 GAKGTFLRSVYVTTAMGPSVRI 224
>pdb|1AD2|A Chain A, Ribosomal Protein L1 Mutant With Serine 179 Replaced By
Cysteine
Length = 228
Score = 53.5 bits (127), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 50/202 (24%), Positives = 90/202 (44%), Gaps = 13/202 (6%)
Query: 21 KETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEK 79
KE F ET+E+ L DP++ D+ G+V LPH +++V + + ++EAE+
Sbjct: 30 KELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEE 88
Query: 80 IGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKAGKFPT--L 137
G DY+ E + A +A+ V+ + LG L G P
Sbjct: 89 AGADYVGGE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKA 142
Query: 138 VTHQESLESKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKK 196
T ++ + E KA ++F+ K + VG +++ N++ + L + +
Sbjct: 143 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKACFPPEKLADNIRAFIRALEAHKPE 202
Query: 197 NWQN--VRCLYLKSTMGPSNRI 216
+ +R +Y+ +TMGPS RI
Sbjct: 203 GAKGTFLRSVYVTTTMGPSVRI 224
>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 = 53.5 bits (127), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 50/202 (24%), Positives = 90/202 (44%), Gaps = 13/202 (6%)
Query: 21 KETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEK 79
KE F ET+E+ L DP++ D+ G+V LPH +++V + + ++EAE+
Sbjct: 31 KELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEE 89
Query: 80 IGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKAGKFPT--L 137
G DY+ E + A +A+ V+ + LG L G P
Sbjct: 90 AGADYVGGE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKA 143
Query: 138 VTHQESLESKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKK 196
T ++ + E KA ++F+ K + VG S +++ N++ + L + +
Sbjct: 144 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPE 203
Query: 197 NWQN--VRCLYLKSTMGPSNRI 216
+ +R +Y+ + MGPS RI
Sbjct: 204 GAKGTFLRSVYVTTVMGPSVRI 225
>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 = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 51/202 (25%), Positives = 90/202 (44%), Gaps = 13/202 (6%)
Query: 21 KETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEK 79
KE F ET+E+ L DP++ D+ G+V LPH +++V + + ++EAE+
Sbjct: 30 KELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEE 88
Query: 80 IGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKAGKFPT--L 137
G DY+ E + A +A+ V + LG L G P
Sbjct: 89 AGADYVGGE------EIIQKILDGWXDFDAVVATPDVXGAVGSKLGRILGPRGLLPNPKA 142
Query: 138 VTHQESLESKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKK 196
T ++ + E KA ++F+ K + VG S +++ N++ + L + +
Sbjct: 143 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPE 202
Query: 197 NWQN--VRCLYLKSTMGPSNRI 216
+ +R +Y+ +T GPS RI
Sbjct: 203 GAKGTFLRSVYVTTTXGPSVRI 224
>pdb|1MZP|A Chain A, Structure Of The L1 Protuberance In The Ribosome
pdb|1PNU|5 Chain 5, Crystal Structure Of A Streptomycin Dependent Ribosome
From Escherichia Coli, 50s Subunit Of 70s Ribosome. This
File, 1pnu, Contains Only Molecules Of The 50s Ribosomal
Subunit. The 30s Subunit, Mrna, P-Site Trna, And A-Site
Trna Are In The Pdb File 1pns.
pdb|1PNY|5 Chain 5, Crystal Structure Of The Wild Type Ribosome From E. Coli,
50s Subunit Of 70s Ribosome. This File, 1pny, Contains
Only Molecules Of The 50s Ribosomal Subunit. The 30s
Subunit Is In The Pdb File 1pnx.
pdb|1VOR|7 Chain 7, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOU|7 Chain 7, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOW|7 Chain 7, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOY|7 Chain 7, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VP0|7 Chain 7, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400
Length = 217
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 46/189 (24%), Positives = 83/189 (43%), Gaps = 3/189 (1%)
Query: 25 KRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLD 83
KRNFT+++E+ + K D +K D + V LP P +V ++ ++ +E A+K
Sbjct: 23 KRNFTQSVEIILTFKGIDXKKGDLKLREIVPLPKQPSKAKRVLVVPSSEQLEYAKKASPK 82
Query: 84 Y-MDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIPRLLGPGLNKAGKFPTLVTHQE 142
+ E FL ++ R+LGP L GKFPT + +
Sbjct: 83 VVITREELQKLQGQKRPVKKLARQNEWFLINQESXALAGRILGPALGPRGKFPTPLPNTA 142
Query: 143 SLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNWQNVR 202
+ +N K +V + K + V +G + + + +N +N + + K N+R
Sbjct: 143 DISEYINRFKRSVLVKTKDQPQVQVFIGTEDXKPEDLAENAIAVLNAIENKAKVE-TNLR 201
Query: 203 CLYLKSTMG 211
+Y+K+T G
Sbjct: 202 NIYVKTTXG 210
>pdb|2HW8|A Chain A, Structure Of Ribosomal Protein L1-Mrna Complex At 2.1
Resolution
Length = 228
Score = 51.2 bits (121), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 54/208 (25%), Positives = 94/208 (45%), Gaps = 25/208 (12%)
Query: 21 KETKKRNFTETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEK 79
KE F ET+E+ L DP++ D+ G+V LPH +++V + + ++EAE+
Sbjct: 30 KELATAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEE 88
Query: 80 IGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQI----PRLLGP-GL---NKA 131
G DY+ E + A +A+ V + R+LGP GL KA
Sbjct: 89 AGADYVGGE------EIIQKILDGWMDFDAVVATPDVXGAVGSKXGRILGPRGLLPNPKA 142
Query: 132 GKFPTLVTHQESLESKVNETKAT-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
G T ++ + E KA ++F+ K + VG S +++ N++ + L
Sbjct: 143 G------TVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRAL 196
Query: 191 VSLLKKNWQN--VRCLYLKSTMGPSNRI 216
+ + + +R +Y+ +T GPS RI
Sbjct: 197 EAHKPEGAKGTFLRSVYVTTTXGPSVRI 224
>pdb|3E1B|Z Chain Z, Structure Of The 50s Subunit Of E. Coli Ribosome In
Pre-Accommodation State
pdb|3E1D|Z Chain Z, Structure Of The 50s Subunit Of E. Coli Ribosome In
Post-Accommodation State
Length = 213
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 47/187 (25%), Positives = 82/187 (43%), Gaps = 6/187 (3%)
Query: 25 KRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLDY 84
KRNFT+++E+ + K D + D + V LP P +V ++ ++ +E A+K
Sbjct: 23 KRNFTQSVEIILTFKGIDKKGDLKLREIVPLPKQPSKAKRVLVVPSSEQLEYAKKASPKV 82
Query: 85 -MDVEGXXXXXXXXXXXXXXXXXYHAFLAS-ESVIKQIPRLLGPGLNKAGKFPTLVTHQE 142
+ E FL + ES + R+LGP L GKFPT + +
Sbjct: 83 VITREELQKLQGQKRPVKKLARQNEWFLINQESALAG--RILGPALGPRGKFPTPLPNTA 140
Query: 143 SLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLLKKNWQNVR 202
+ +N K +V + K + V +G E + +N +N + + K N+R
Sbjct: 141 DISEYINRFKRSVLVKTKDQPQVQVFIGTEDKPE-DLAENAIAVLNAIENKAKVE-TNLR 198
Query: 203 CLYLKST 209
+Y+K+T
Sbjct: 199 NIYVKTT 205
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 47/204 (23%), Positives = 89/204 (43%), Gaps = 18/204 (8%)
Query: 21 KETKKRNFTETIELQIGLKNYDPQ-KDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEK 79
K+ F ET E L N DP+ D++ +V LP +K+ +L ++EA+
Sbjct: 145 KQMSSTKFVETAEAHFRL-NIDPKYNDQQLRATVSLPKGTGKTVKIAVLAQGDKIDEAKA 203
Query: 80 IGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASESVIKQIP---RLLGP-GLNKAGKFP 135
G D + E + +A+ ++ ++ R+LGP GL K
Sbjct: 204 AGADIVGGE------ELIEQIKGGFMDFDKLIATSDMMAKVASLGRILGPRGLMPTPKAG 257
Query: 136 TLVTHQESLESKVNE-TKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFLVSLL 194
T+ + + V E K V+F++ K + + G L+ EE+ + N+ ++ + +
Sbjct: 258 TVTPN---VAQAVEEFKKGKVEFRVDKTGIVHIPFGKLNFEEEDLLINLFATIKSVETNK 314
Query: 195 KKNWQNV--RCLYLKSTMGPSNRI 216
+ V + ++ S+MGPS R+
Sbjct: 315 PTGAKGVYWKSAHISSSMGPSIRL 338
>pdb|4B4T|N Chain N, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 945
Score = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 11 EAVSSIVQYSKETKKRNFTETIELQIGLKNYDPQK 45
EA+ + YS+ET+ N T + + + L NY Q+
Sbjct: 496 EAIHDMFTYSQETQHGNITRGLAVGLALINYGRQE 530
>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 = 26.9 bits (58), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 46/220 (20%), Positives = 90/220 (40%), Gaps = 28/220 (12%)
Query: 9 LREAVSSIVQYS--------KETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPR 60
+RE V + QY KE F E++++ + L + D+ G+ LPH
Sbjct: 6 IREKVDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRGATVLPHGTG 65
Query: 61 PKMKVCMLGDAQHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASES---VI 117
++V + + E A+ G + + +E + +AS V+
Sbjct: 66 RSVRVAVFTQGANAEAAKAAGAELVGME------DLADQIKKGEMNFDVVIASPDAMRVV 119
Query: 118 KQIPRLLGP-GLNKAGKFPTLVTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEE 176
Q+ ++LGP GL K T+ + E+ N V+++ K + +G + +
Sbjct: 120 GQLGQVLGPRGLMPNPKVGTVTPN--VAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDFDA 177
Query: 177 KQIFQNVQMSVNFLVSLLKKNWQNVRCLYLK-----STMG 211
++ +N++ LV+L K + +Y+K +TMG
Sbjct: 178 DKLKENLEA---LLVALKKAKPTQAKGVYIKKVSISTTMG 214
>pdb|3H9Y|A Chain A, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|3H9Y|B Chain B, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|3H9Y|E Chain E, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|3H9Z|A Chain A, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|3H9Z|B Chain B, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|3H9Z|C Chain C, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|3H9Z|D Chain D, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|3HA0|A Chain A, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|3HA0|B Chain B, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|3HA0|C Chain C, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|3HA0|D Chain D, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|3HA0|E Chain E, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|3HA0|F Chain F, Crystal Structure Of The Ige-Fc3-4 Domains
pdb|4EZM|A Chain A, Crystal Structure Of The Human Ige-Fc(Epsilon)3-4 Bound To
Its B Cell Receptor Dercd23
pdb|4EZM|B Chain B, Crystal Structure Of The Human Ige-Fc(Epsilon)3-4 Bound To
Its B Cell Receptor Dercd23
pdb|4EZM|C Chain C, Crystal Structure Of The Human Ige-Fc(Epsilon)3-4 Bound To
Its B Cell Receptor Dercd23
pdb|4EZM|D Chain D, Crystal Structure Of The Human Ige-Fc(Epsilon)3-4 Bound To
Its B Cell Receptor Dercd23
pdb|4EZM|E Chain E, Crystal Structure Of The Human Ige-Fc(Epsilon)3-4 Bound To
Its B Cell Receptor Dercd23
pdb|4EZM|F Chain F, Crystal Structure Of The Human Ige-Fc(Epsilon)3-4 Bound To
Its B Cell Receptor Dercd23
Length = 223
Score = 26.9 bits (58), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 17 VQYS--KETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMK 64
VQ+S KE K+RN T T+ + + D + + + V PH+PR M+
Sbjct: 58 VQHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMR 107
>pdb|2RDO|9 Chain 9, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
Length = 233
Score = 26.9 bits (58), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 46/220 (20%), Positives = 90/220 (40%), Gaps = 28/220 (12%)
Query: 9 LREAVSSIVQYS--------KETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPR 60
+RE V + QY KE F E++++ + L + D+ G+ LPH
Sbjct: 10 IREKVDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRGATVLPHGTG 69
Query: 61 PKMKVCMLGDAQHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASES---VI 117
++V + + E A+ G + + +E + +AS V+
Sbjct: 70 RSVRVAVFTQGANAEAAKAAGAELVGME------DLADQIKKGEMNFDVVIASPDAMRVV 123
Query: 118 KQIPRLLGP-GLNKAGKFPTLVTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEE 176
Q+ ++LGP GL K T+ + E+ N V+++ K + +G + +
Sbjct: 124 GQLGQVLGPRGLMPNPKVGTVTPN--VAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDFDA 181
Query: 177 KQIFQNVQMSVNFLVSLLKKNWQNVRCLYLK-----STMG 211
++ +N++ LV+L K + +Y+K +TMG
Sbjct: 182 DKLKENLEA---LLVALKKAKPTQAKGVYIKKVSISTTMG 218
>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 = 26.9 bits (58), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 46/220 (20%), Positives = 90/220 (40%), Gaps = 28/220 (12%)
Query: 9 LREAVSSIVQYS--------KETKKRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPR 60
+RE V + QY KE F E++++ + L + D+ G+ LPH
Sbjct: 11 IREKVDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRGATVLPHGTG 70
Query: 61 PKMKVCMLGDAQHVEEAEKIGLDYMDVEGXXXXXXXXXXXXXXXXXYHAFLASES---VI 117
++V + + E A+ G + + +E + +AS V+
Sbjct: 71 RSVRVAVFTQGANAEAAKAAGAELVGME------DLADQIKKGEMNFDVVIASPDAMRVV 124
Query: 118 KQIPRLLGP-GLNKAGKFPTLVTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEE 176
Q+ ++LGP GL K T+ + E+ N V+++ K + +G + +
Sbjct: 125 GQLGQVLGPRGLMPNPKVGTVTPN--VAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDFDA 182
Query: 177 KQIFQNVQMSVNFLVSLLKKNWQNVRCLYLK-----STMG 211
++ +N++ LV+L K + +Y+K +TMG
Sbjct: 183 DKLKENLEA---LLVALKKAKPTQAKGVYIKKVSISTTMG 219
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 0.132 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,180,248
Number of Sequences: 62578
Number of extensions: 172680
Number of successful extensions: 443
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 389
Number of HSP's gapped (non-prelim): 35
length of query: 217
length of database: 14,973,337
effective HSP length: 95
effective length of query: 122
effective length of database: 9,028,427
effective search space: 1101468094
effective search space used: 1101468094
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: 49 (23.5 bits)