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= 027063
(229 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 = 329 bits (844), Expect = 6e-91, Method: Compositional matrix adjust.
Identities = 159/201 (79%), Positives = 177/201 (88%), Gaps = 1/201 (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 QNVQMSVNFLVSLLKKNWQNV 201
QN+QMSVNFLVSLLKKNWQNV
Sbjct: 180 QNIQMSVNFLVSLLKKNWQNV 200
>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 = 245 bits (625), Expect = 2e-65, Method: Compositional matrix adjust.
Identities = 115/201 (57%), Positives = 146/201 (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 QNVQMSVNFLVSLLKKNWQNV 201
+ MSVNF VSLLKKNWQNV
Sbjct: 181 NQILMSVNFFVSLLKKNWQNV 201
>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 = 240 bits (612), Expect = 6e-64, Method: Compositional matrix adjust.
Identities = 112/198 (56%), Positives = 143/198 (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 QMSVNFLVSLLKKNWQNV 201
MSVNF VSLLKKNWQNV
Sbjct: 181 LMSVNFFVSLLKKNWQNV 198
>pdb|3ZF7|J Chain J, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 214
Score = 211 bits (537), Expect = 3e-55, Method: Compositional matrix adjust.
Identities = 104/201 (51%), Positives = 138/201 (68%), Gaps = 3/201 (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 QNVQMSVNFLVSLLKKNWQNV 201
QNV M++NFLVSLLKKNWQN+
Sbjct: 178 QNVVMAINFLVSLLKKNWQNL 198
>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 = 75.1 bits (183), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 51/191 (26%), Positives = 88/191 (46%), Gaps = 2/191 (1%)
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 VSLLKKNWQNV 201
+ L++ V
Sbjct: 189 IGKLERGESQV 199
>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 = 63.9 bits (154), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 51/194 (26%), Positives = 86/194 (44%), Gaps = 2/194 (1%)
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 NFLVSLLKKNWQNV 201
N + +K ++
Sbjct: 183 NVVAKKYEKGLYHI 196
>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 = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 50/194 (25%), Positives = 83/194 (42%), Gaps = 2/194 (1%)
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 NFLVSLLKKNWQNV 201
N + +K ++
Sbjct: 183 NVVAKKYEKGLYHI 196
>pdb|3QOY|A Chain A, Crystal Structure Of Ribosomal Protein L1 From Aquifex
Aeolicus
Length = 242
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 49/188 (26%), Positives = 98/188 (52%), Gaps = 14/188 (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 QMSVNFLV 191
+++ +V
Sbjct: 194 YAAIDAVV 201
>pdb|1DWU|A Chain A, Ribosomal Protein L1
pdb|1DWU|B Chain B, Ribosomal Protein L1
Length = 213
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 44/181 (24%), Positives = 80/181 (44%), Gaps = 2/181 (1%)
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 N 188
N
Sbjct: 183 N 183
>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 = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 41/195 (21%), Positives = 82/195 (42%), Gaps = 1/195 (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 VNFLVSLLKKNWQNV 201
+ L + L+K N+
Sbjct: 182 LRRLHADLEKGPLNI 196
>pdb|3TG8|A Chain A, Mutant Ribosomal Protein L1 Lacking Ala158 From Thermus
Thermophilus
Length = 228
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 41/173 (23%), Positives = 74/173 (42%), Gaps = 10/173 (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 VTHQESLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
T ++ + E K ++F+ K + VG S +++ N++ + L
Sbjct: 144 GTVGFNIGEIIREIKGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRAL 196
>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 = 44.3 bits (103), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 39/168 (23%), Positives = 71/168 (42%), Gaps = 2/168 (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 SLESKVNETKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
+ +N K +V + K + V +G + + + +N +N +
Sbjct: 143 DISEYINRFKRSVLVKTKDQPQVQVFIGTEDXKPEDLAENAIAVLNAI 190
>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 = 43.5 bits (101), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 42/166 (25%), Positives = 76/166 (45%), Gaps = 19/166 (11%)
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-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
+ E KA ++F+ K + VG S +++ N++ + L
Sbjct: 118 EIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRAL 163
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 42/182 (23%), Positives = 77/182 (42%), Gaps = 11/182 (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 FL 190
L
Sbjct: 196 AL 197
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 42/174 (24%), Positives = 75/174 (43%), Gaps = 11/174 (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-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
T ++ + E KA ++F+ K + VG S +++ N++ + L
Sbjct: 143 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRAL 196
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/148 (25%), Positives = 64/148 (43%), Gaps = 4/148 (2%)
Query: 25 KRNFTETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPKMKVCMLGDAQHVEEAEKIGLD- 83
KRNFT+++E+ + K D + D + V LP P +V ++ ++ +E A+K
Sbjct: 23 KRNFTQSVEIILTFKGIDKKGDLKLREIVPLPKQPSKAKRVLVVPSSEQLEYAKKASPKV 82
Query: 84 YMDVEGXXXXXXXXXXXXXXXXXYHAFLAS-ESVIKQIPRLLGPGLNKAGKFPTLVTHQE 142
+ E FL + ES + R+LGP L GKFPT + +
Sbjct: 83 VITREELQKLQGQKRPVKKLARQNEWFLINQESALAG--RILGPALGPRGKFPTPLPNTA 140
Query: 143 SLESKVNETKATVKFQLKKVLCMGVAVG 170
+ +N K +V + K + V +G
Sbjct: 141 DISEYINRFKRSVLVKTKDQPQVQVFIG 168
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 42/174 (24%), Positives = 75/174 (43%), Gaps = 11/174 (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-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
T ++ + E KA ++F+ K + VG S +++ N++ + L
Sbjct: 143 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRAL 196
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 42/174 (24%), Positives = 75/174 (43%), Gaps = 11/174 (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-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
T ++ + E KA ++F+ K + VG S +++ N++ + L
Sbjct: 144 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRAL 197
>pdb|4F9T|A Chain A, Ribosomal Protein L1 From Thermus Thermophilus With
Substitution Thr217ala
Length = 229
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 42/174 (24%), Positives = 75/174 (43%), Gaps = 11/174 (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-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
T ++ + E KA ++F+ K + VG S +++ N++ + L
Sbjct: 144 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRAL 197
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 42/174 (24%), Positives = 75/174 (43%), Gaps = 11/174 (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-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
T ++ + E KA ++F+ K + VG S +++ N++ + L
Sbjct: 144 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRAL 197
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 42/182 (23%), Positives = 77/182 (42%), Gaps = 11/182 (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--LVTHQESLESKVNETKA-TVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVN 188
G P T ++ + E KA ++F+ K + VG S +++ N++ +
Sbjct: 136 GLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIR 195
Query: 189 FL 190
L
Sbjct: 196 AL 197
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 43/174 (24%), Positives = 75/174 (43%), Gaps = 11/174 (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-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
T ++ + E KA ++F+ K + VG S +++ N++ + L
Sbjct: 143 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRAL 196
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 41/174 (23%), Positives = 75/174 (43%), Gaps = 11/174 (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-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
T ++ + E KA ++F+ K + VG S +++ N++ + L
Sbjct: 144 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRAL 197
>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 = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 41/174 (23%), Positives = 74/174 (42%), Gaps = 11/174 (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-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
T ++ + E KA ++F+ K + VG +++ N++ + L
Sbjct: 139 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKACFPPEKLADNIRAFIRAL 192
>pdb|1AD2|A Chain A, Ribosomal Protein L1 Mutant With Serine 179 Replaced By
Cysteine
Length = 228
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 41/174 (23%), Positives = 74/174 (42%), Gaps = 11/174 (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-VKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSVNFL 190
T ++ + E KA ++F+ K + VG +++ N++ + L
Sbjct: 143 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKACFPPEKLADNIRAFIRAL 196
>pdb|2HW8|A Chain A, Structure Of Ribosomal Protein L1-Mrna Complex At 2.1
Resolution
Length = 228
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 46/180 (25%), Positives = 79/180 (43%), Gaps = 23/180 (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
>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 = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 40/173 (23%), Positives = 74/173 (42%), Gaps = 16/173 (9%)
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-TKATVKFQLKKVLCMGVAVGNLSMEEKQIFQNVQMSV 187
T+ + + V E K V+F++ K + + G L+ EE+ + N+ ++
Sbjct: 258 TVTPN---VAQAVEEFKKGKVEFRVDKTGIVHIPFGKLNFEEEDLLINLFATI 307
>pdb|4B4T|N Chain N, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 945
Score = 27.3 bits (59), Expect = 6.4, 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|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 = 9.5, 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
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
0.316 0.131 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,742,966
Number of Sequences: 62578
Number of extensions: 199220
Number of successful extensions: 525
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: 480
Number of HSP's gapped (non-prelim): 35
length of query: 229
length of database: 14,973,337
effective HSP length: 95
effective length of query: 134
effective length of database: 9,028,427
effective search space: 1209809218
effective search space used: 1209809218
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: 50 (23.9 bits)