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= 036232
(259 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 = 340 bits (872), Expect = 5e-94, Method: Compositional matrix adjust.
Identities = 159/215 (73%), Positives = 184/215 (85%)
Query: 45 SKLSSEVLREAVSTICGDAKEKNRNFVETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPM 104
SKL S+ +++A++ I G+A+EK R F ET+ELQIGLKNYDPQKDKRFSGSVKLPHIPRP
Sbjct: 2 SKLQSDAVKDAITQIVGEAREKKRKFTETVELQIGLKNYDPQKDKRFSGSVKLPHIPRPK 61
Query: 105 MKVCMLGDAQHVEQAEKIGMDYMDVEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPR 164
M+VCMLGDAQHV+QAEK+G+DYMDVE YHAFLASEA+IKQIPR
Sbjct: 62 MRVCMLGDAQHVDQAEKMGLDYMDVESLKKMNKNKKLVKKLAKKYHAFLASEAIIKQIPR 121
Query: 165 LLGPGLNKAGKFPTLVTHQESLEAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQN 224
LLGPGLNKAGKFPTLV+HQESLEAKVNETKA VKFQLKKVLCMGVAVGN SM+EKQ+ QN
Sbjct: 122 LLGPGLNKAGKFPTLVSHQESLEAKVNETKATVKFQLKKVLCMGVAVGNLSMDEKQIQQN 181
Query: 225 VQLSVNFLVSLLKKSWQNVRCLHLKSTMGRPQRIY 259
+Q+SVNFLVSLLKK+WQNVRCL++KSTMG+ R++
Sbjct: 182 IQMSVNFLVSLLKKNWQNVRCLYVKSTMGKRVRVF 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 = 233 bits (593), Expect = 9e-62, Method: Compositional matrix adjust.
Identities = 114/216 (52%), Positives = 151/216 (69%), Gaps = 1/216 (0%)
Query: 45 SKLSSEVLREAVSTICGDAKE-KNRNFVETIELQIGLKNYDPQKDKRFSGSVKLPHIPRP 103
SK++S +RE V + + E K RNF+ET+ELQ+GLKNYDPQ+DKRFSGS+KLP+ PRP
Sbjct: 2 SKITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPRP 61
Query: 104 MMKVCMLGDAQHVEQAEKIGMDYMDVEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIP 163
M +C+ GDA V++A+ G+D M V+ Y+AF+ASE +IKQ+P
Sbjct: 62 NMSICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQVP 121
Query: 164 RLLGPGLNKAGKFPTLVTHQESLEAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQ 223
RLLGP L+KAGKFPT V+H + L KV + ++ +KFQLKKVLC+ VAVGN MEE +
Sbjct: 122 RLLGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKFQLKKVLCLAVAVGNVEMEEDVLVN 181
Query: 224 NVQLSVNFLVSLLKKSWQNVRCLHLKSTMGRPQRIY 259
+ +SVNF VSLLKK+WQNV L +KS+MG R+Y
Sbjct: 182 QILMSVNFFVSLLKKNWQNVGSLVVKSSMGPAFRLY 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 = 227 bits (578), Expect = 6e-60, Method: Compositional matrix adjust.
Identities = 111/213 (52%), Positives = 148/213 (69%), Gaps = 1/213 (0%)
Query: 47 LSSEVLREAVSTICGDAKE-KNRNFVETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPMM 105
++S +RE V + + E K RNF+ET+ELQ+GLKNYDPQ+DKRFSGS+KLP+ PRP M
Sbjct: 1 ITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPRPNM 60
Query: 106 KVCMLGDAQHVEQAEKIGMDYMDVEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPRL 165
+C+ GDA V++A+ G+D M V+ Y+AF+ASE +IKQ+PRL
Sbjct: 61 SICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQVPRL 120
Query: 166 LGPGLNKAGKFPTLVTHQESLEAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQNV 225
LGP L+KAGKFPT V+H + L KV + ++ +KFQLKKVLC+ VAVGN MEE + +
Sbjct: 121 LGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKFQLKKVLCLAVAVGNVEMEEDVLVNQI 180
Query: 226 QLSVNFLVSLLKKSWQNVRCLHLKSTMGRPQRI 258
+SVNF VSLLKK+WQNV L +KS+MG R+
Sbjct: 181 LMSVNFFVSLLKKNWQNVGSLVVKSSMGPAFRL 213
>pdb|3ZF7|J Chain J, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 214
Score = 219 bits (559), Expect = 9e-58, Method: Compositional matrix adjust.
Identities = 110/215 (51%), Positives = 145/215 (67%), Gaps = 2/215 (0%)
Query: 45 SKLSSEVLREAVSTICGDAKEKNRNFVETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPM 104
SK+ +L EA+ + D KE R F E+I+LQ+ LKNYDPQKDKRFSGSV+LPH+ RP
Sbjct: 2 SKIPPALLSEAIQNVLKDRKE--RKFKESIDLQVNLKNYDPQKDKRFSGSVRLPHVCRPR 59
Query: 105 MKVCMLGDAQHVEQAEKIGMDYMDVEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPR 164
M VC+L D H + A+K + M+ E Y AFL SE++IK +PR
Sbjct: 60 MTVCLLCDLVHEDIAKKNDVPTMNQEELKKLNKNKKLVKKMCNQYDAFLCSESIIKTVPR 119
Query: 165 LLGPGLNKAGKFPTLVTHQESLEAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQN 224
L+GP +++ GKFPT+ ESL KV E ++ VKFQLKKVLC+G VG+ M E QV QN
Sbjct: 120 LVGPHMHRVGKFPTVCAQNESLPDKVLELQSTVKFQLKKVLCLGTCVGHVDMTEDQVRQN 179
Query: 225 VQLSVNFLVSLLKKSWQNVRCLHLKSTMGRPQRIY 259
V +++NFLVSLLKK+WQN++ ++KSTMG+ QRIY
Sbjct: 180 VVMAINFLVSLLKKNWQNLKSAYIKSTMGKSQRIY 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 = 81.3 bits (199), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 51/193 (26%), Positives = 93/193 (48%), Gaps = 2/193 (1%)
Query: 63 AKEKNRNFVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEK 121
A+ K RNF +++E+ + LK+ D ++ + RF V LPH +K+ ++ D E A K
Sbjct: 17 ARAKPRNFTQSVEVAVNLKDIDLKRPENRFKLEVVLPHGRGKDVKIAVIADGAVAEAARK 76
Query: 122 IGMDYMDVEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPRLLGPGLNKAGKFPTLVT 181
+G+D + Y F+A ++ +I R LG L K P +V
Sbjct: 77 LGLDVISSAELEEIASSPRQARKLAKKYDFFIAEAPLMPKIGRYLGRYLGPRNKMPVVVP 136
Query: 182 HQ-ESLEAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSW 240
L V + K V+ QLK + VG M ++++ +N++ +N ++ L++
Sbjct: 137 PTLTDLTPIVEKLKKTVRIQLKNNPVVHAPVGTEKMSDEEIAENIEAVLNAIIGKLERGE 196
Query: 241 QNVRCLHLKSTMG 253
V+ +++K+TMG
Sbjct: 197 SQVKSVYVKTTMG 209
>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 = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 52/204 (25%), Positives = 89/204 (43%), Gaps = 3/204 (1%)
Query: 53 REAVSTICGDAKE--KNRNFVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCM 109
REA+ +A+E K RNF ++ E LK D +K + R V LPH K+ +
Sbjct: 3 REALLQAVKEARELAKPRNFTQSFEFIATLKEIDMRKPENRIKTEVVLPHGRGKEAKIAV 62
Query: 110 LGDAQHVEQAEKIGMDYMDVEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPRLLGPG 169
+G +QAE++G+ + E + F+A ++ I R +G
Sbjct: 63 IGTGDLAKQAEELGLTVIRKEEIEELGKNKRKLRKIAKAHDFFIAQADLMPLIGRYMGVI 122
Query: 170 LNKAGKFPTLVTHQESLEAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSV 229
L GK P V +++ V K V + V VGN M ++Q+ N++ +
Sbjct: 123 LGPRGKMPKPVPANANIKPLVERLKKTVVINTRDKPYFQVLVGNEKMTDEQIVDNIEAVL 182
Query: 230 NFLVSLLKKSWQNVRCLHLKSTMG 253
N + +K +++ ++K TMG
Sbjct: 183 NVVAKKYEKGLYHIKDAYVKLTMG 206
>pdb|1DWU|A Chain A, Ribosomal Protein L1
pdb|1DWU|B Chain B, Ribosomal Protein L1
Length = 213
Score = 60.8 bits (146), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 47/194 (24%), Positives = 84/194 (43%), Gaps = 1/194 (0%)
Query: 66 KNRNFVETIELQIGLKNYD-PQKDKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGM 124
K RNF ++++L I LK D + + R V LP+ K+ ++ QAE++G+
Sbjct: 18 KPRNFTQSLDLIINLKELDLSRPENRLKEQVVLPNGRGKEPKIAVIAKGDLAAQAEEMGL 77
Query: 125 DYMDVEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPRLLGPGLNKAGKFPTLVTHQE 184
+ + + F+A ++ + + LGP L GK P V
Sbjct: 78 TVIRQDELEELGKNKKMAKKIANEHDFFIAQADMMPLVGKTLGPVLGPRGKMPQPVPANA 137
Query: 185 SLEAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQNVR 244
+L V K V + V VGN M ++++ +N++ +N + +K +V+
Sbjct: 138 NLTPLVERLKKTVLINTRDKPLFHVLVGNEKMSDEELAENIEAILNTVSRKYEKGLYHVK 197
Query: 245 CLHLKSTMGRPQRI 258
+ K TMG P +I
Sbjct: 198 SAYTKLTMGPPAQI 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 = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 47/208 (22%), Positives = 89/208 (42%), Gaps = 3/208 (1%)
Query: 47 LSSEVLREAVSTICGDAKEKNRNFVETIELQIGLKNYD-PQKDKRFSGSVKLPHIPRPMM 105
++ + + AVS DA E RNF ET++L + L++ D R SV LP
Sbjct: 1 MADQEIENAVSRALEDAPE--RNFRETVDLAVNLRDLDLNDPSNRVDESVVLPAGTGQET 58
Query: 106 KVCMLGDAQHVEQAEKIGMDYMDVEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPRL 165
+ + + + +AE++ D +D + F+A + +++ I R
Sbjct: 59 TIVVFAEGETALRAEEVADDVLDEDELEELGGDDDAAKDLADDTDFFIAEKGLMQDIGRY 118
Query: 166 LGPGLNKAGKFPTLVTHQESLEAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQNV 225
LG L GK P + + + + K V+ + + VG M + + N+
Sbjct: 119 LGTVLGPRGKMPEPLDPDDDVVEVIERMKNTVQLRSGERRTFHTRVGAEDMSAENIADNI 178
Query: 226 QLSVNFLVSLLKKSWQNVRCLHLKSTMG 253
+ + L + L+K N+ +++K+TMG
Sbjct: 179 DVILRRLHADLEKGPLNIDTVYVKTTMG 206
>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 = 3e-09, Method: Compositional matrix adjust.
Identities = 50/204 (24%), Positives = 85/204 (41%), Gaps = 3/204 (1%)
Query: 53 REAVSTICGDAKE--KNRNFVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCM 109
REA+ +A+E K RNF ++ E LK D +K + R V LPH K+ +
Sbjct: 3 REALLQAVKEARELAKPRNFTQSFEFIATLKEIDXRKPENRIKTEVVLPHGRGKEAKIAV 62
Query: 110 LGDAQHVEQAEKIGMDYMDVEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPRLLGPG 169
+G +QAE++G+ + E + F+A + I R G
Sbjct: 63 IGTGDLAKQAEELGLTVIRKEEIEELGKNKRKLRKIAKAHDFFIAQADLXPLIGRYXGVI 122
Query: 170 LNKAGKFPTLVTHQESLEAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSV 229
L GK P V +++ V K V + V VGN ++Q+ N++ +
Sbjct: 123 LGPRGKXPKPVPANANIKPLVERLKKTVVINTRDKPYFQVLVGNEKXTDEQIVDNIEAVL 182
Query: 230 NFLVSLLKKSWQNVRCLHLKSTMG 253
N + +K +++ ++K T G
Sbjct: 183 NVVAKKYEKGLYHIKDAYVKLTXG 206
>pdb|3QOY|A Chain A, Crystal Structure Of Ribosomal Protein L1 From Aquifex
Aeolicus
Length = 242
Score = 54.3 bits (129), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 55/206 (26%), Positives = 100/206 (48%), Gaps = 17/206 (8%)
Query: 37 KDKSEIENSKLSSE----VLREAVSTICGDAKEKNRNFVETIELQIGLKNYDPQ-KDKRF 91
+ K IE SKL L EAV + + R F ET+EL + L N DP+ D+
Sbjct: 4 RGKKYIEASKLVDRNKRYTLEEAVDLLKKMEEVLQRRFDETVELAMRL-NVDPRYADQMV 62
Query: 92 SGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMDVEXXXXXXXXXXXXXXXXXXYHA 151
GSV LPH +KV + + ++ ++AE+ G DY+ + +
Sbjct: 63 RGSVVLPHGLGKPIKVVVFAEGEYAKKAEEAGADYVGGD-----ELINKILKEEWTDFDV 117
Query: 152 FLASEAVIKQIP---RLLGP-GLNKAGKFPTLVTHQESLEAKVNETKAVVKFQLKKVLCM 207
+A+ ++ ++ R+LGP GL + K T+ T+ E +A + + V+F++ K +
Sbjct: 118 AIATPEMMPKVAKLGRILGPRGLMPSPKTGTVTTNVE--QAIKDAKRGRVEFKVDKAGNV 175
Query: 208 GVAVGNCSMEEKQVFQNVQLSVNFLV 233
+ VG S E++++ N+ +++ +V
Sbjct: 176 HMPVGKISFEKEKLIDNLYAAIDAVV 201
>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 = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 49/202 (24%), Positives = 91/202 (45%), Gaps = 21/202 (10%)
Query: 62 DAKEKNRNFVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAE 120
D + F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE
Sbjct: 6 DEAARTAKFDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAE 64
Query: 121 KIGMDYMDVEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPRLLGP-GLNKAGKFPTL 179
+ G DY+ E + F+ AV ++ R+LGP GLN P
Sbjct: 65 EAGADYVGGE---------EIIQKILDGWMDFVMG-AVGSKLGRILGPRGLN-----PKA 109
Query: 180 VTHQESLEAKVNETKAV-VKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKK 238
T ++ + E KA ++F+ K + VG S +++ N++ + L + +
Sbjct: 110 GTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPE 169
Query: 239 SWQN--VRCLHLKSTMGRPQRI 258
+ +R +++ +TMG RI
Sbjct: 170 GAKGTFLRSVYVTTTMGPSVRI 191
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 47/207 (22%), Positives = 86/207 (41%), Gaps = 3/207 (1%)
Query: 50 EVLREAVSTICGDAKEKNRNFVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVC 108
E L EA+ RNF +++E+ + K D +K D + V LP P +V
Sbjct: 6 ESLIEALKLALSTEYNVKRNFTQSVEIILTFKGIDXKKGDLKLREIVPLPKQPSKAKRVL 65
Query: 109 MLGDAQHVEQAEKIGMDY-MDVEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPRLLG 167
++ ++ +E A+K + E FL ++ R+LG
Sbjct: 66 VVPSSEQLEYAKKASPKVVITREELQKLQGQKRPVKKLARQNEWFLINQESXALAGRILG 125
Query: 168 PGLNKAGKFPTLVTHQESLEAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQNVQL 227
P L GKFPT + + + +N K V + K + V +G + + + +N
Sbjct: 126 PALGPRGKFPTPLPNTADISEYINRFKRSVLVKTKDQPQVQVFIGTEDXKPEDLAENAIA 185
Query: 228 SVNFLVSLLKKSWQNVRCLHLKSTMGR 254
+N + + K N+R +++K+T G+
Sbjct: 186 VLNAIENKAKVE-TNLRNIYVKTTXGK 211
>pdb|3TG8|A Chain A, Mutant Ribosomal Protein L1 Lacking Ala158 From Thermus
Thermophilus
Length = 228
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 90/197 (45%), Gaps = 18/197 (9%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 38 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 96
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASE----AVIKQIPRLLGP-GLNKAGKFPTLVTHQ 183
E + A +A+ AV ++ R+LGP GL K T+ +
Sbjct: 97 GE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNI 150
Query: 184 ESLEAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN- 242
+ + E K ++F+ K + VG S +++ N++ + L + + +
Sbjct: 151 GEI---IREIKGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGT 207
Query: 243 -VRCLHLKSTMGRPQRI 258
+R +++ +TMG RI
Sbjct: 208 FLRSVYVTTTMGPSVRI 224
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 48/198 (24%), Positives = 91/198 (45%), Gaps = 19/198 (9%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 37 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 95
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASE----AVIKQIPRLLGP-GLNKAGKFPTLVTHQ 183
E + A +A+ AV ++ R+LGP GL K T+ +
Sbjct: 96 GE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNI 149
Query: 184 ESLEAKVNETKAV-VKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN 242
+ + E KA ++F+ K + VG S +++ N++ + L + + +
Sbjct: 150 GEI---IREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKG 206
Query: 243 --VRCLHLKSTMGRPQRI 258
+R +++ +TMG RI
Sbjct: 207 TFLRSVYVTTTMGPSVRI 224
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 48/198 (24%), Positives = 91/198 (45%), Gaps = 19/198 (9%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 38 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 96
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASE----AVIKQIPRLLGP-GLNKAGKFPTLVTHQ 183
E + A +A+ AV ++ R+LGP GL K T+ +
Sbjct: 97 GE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNI 150
Query: 184 ESLEAKVNETKAV-VKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN 242
+ + E KA ++F+ K + VG S +++ N++ + L + + +
Sbjct: 151 GEI---IREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKG 207
Query: 243 --VRCLHLKSTMGRPQRI 258
+R +++ +TMG RI
Sbjct: 208 TFLRSVYVTTTMGPSVRI 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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 48/198 (24%), Positives = 91/198 (45%), Gaps = 19/198 (9%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 38 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 96
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASE----AVIKQIPRLLGP-GLNKAGKFPTLVTHQ 183
E + A +A+ AV ++ R+LGP GL K T+ +
Sbjct: 97 GE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNI 150
Query: 184 ESLEAKVNETKAV-VKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN 242
+ + E KA ++F+ K + VG S +++ N++ + L + + +
Sbjct: 151 GEI---IREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKG 207
Query: 243 --VRCLHLKSTMGRPQRI 258
+R +++ +TMG RI
Sbjct: 208 TFLRSVYVTTTMGPSVRI 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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 48/198 (24%), Positives = 91/198 (45%), Gaps = 19/198 (9%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 38 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 96
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASE----AVIKQIPRLLGP-GLNKAGKFPTLVTHQ 183
E + A +A+ AV ++ R+LGP GL K T+ +
Sbjct: 97 GE------EIIQKILDGWMDFDAVVATPDVMGAVGSKMGRILGPRGLLPNPKAGTVGFNI 150
Query: 184 ESLEAKVNETKAV-VKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN 242
+ + E KA ++F+ K + VG S +++ N++ + L + + +
Sbjct: 151 GEI---IREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKG 207
Query: 243 --VRCLHLKSTMGRPQRI 258
+R +++ +TMG RI
Sbjct: 208 TFLRSVYVTTTMGPSVRI 225
>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 = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 45/195 (23%), Positives = 86/195 (44%), Gaps = 13/195 (6%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 38 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 96
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPRLLGPGLNKAGKFPT--LVTHQESL 186
E + A +A+ V+ + LG L G P T ++
Sbjct: 97 GE------EIIQKILDAWMDFDAVVATPDVMGAVGSKLGRILAPRGLLPNPKAGTVGFNI 150
Query: 187 EAKVNETKA-VVKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN--V 243
+ E KA ++F+ K + VG S +++ N++ + L + + + +
Sbjct: 151 GEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFL 210
Query: 244 RCLHLKSTMGRPQRI 258
R +++ +TMG RI
Sbjct: 211 RSVYVTTTMGPSVRI 225
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 47/198 (23%), Positives = 90/198 (45%), Gaps = 19/198 (9%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 37 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 95
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASE----AVIKQIPRLLGP-GLNKAGKFPTLVTHQ 183
E + A +A+ AV ++ R+LGP GL K T+ +
Sbjct: 96 GE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNI 149
Query: 184 ESLEAKVNETKAV-VKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN 242
+ + E KA ++F+ K + VG S +++ N++ + L + + +
Sbjct: 150 GEI---IREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKG 206
Query: 243 --VRCLHLKSTMGRPQRI 258
+R +++ + MG RI
Sbjct: 207 TFLRSVYVTTAMGPSVRI 224
>pdb|4F9T|A Chain A, Ribosomal Protein L1 From Thermus Thermophilus With
Substitution Thr217ala
Length = 229
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 47/198 (23%), Positives = 90/198 (45%), Gaps = 19/198 (9%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 38 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 96
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASE----AVIKQIPRLLGP-GLNKAGKFPTLVTHQ 183
E + A +A+ AV ++ R+LGP GL K T+ +
Sbjct: 97 GE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNI 150
Query: 184 ESLEAKVNETKAV-VKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN 242
+ + E KA ++F+ K + VG S +++ N++ + L + + +
Sbjct: 151 GEI---IREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKG 207
Query: 243 --VRCLHLKSTMGRPQRI 258
+R +++ + MG RI
Sbjct: 208 TFLRSVYVTTAMGPSVRI 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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 44/195 (22%), Positives = 85/195 (43%), Gaps = 13/195 (6%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 33 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 91
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPRLLGPGLNKAGKFPT--LVTHQESL 186
E + A +A+ V+ + LG L G P T ++
Sbjct: 92 GE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNI 145
Query: 187 EAKVNETKAV-VKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN--V 243
+ E KA ++F+ K + VG +++ N++ + L + + + +
Sbjct: 146 GEIIREIKAGRIEFRNDKTGAIHAPVGKACFPPEKLADNIRAFIRALEAHKPEGAKGTFL 205
Query: 244 RCLHLKSTMGRPQRI 258
R +++ +TMG RI
Sbjct: 206 RSVYVTTTMGPSVRI 220
>pdb|1AD2|A Chain A, Ribosomal Protein L1 Mutant With Serine 179 Replaced By
Cysteine
Length = 228
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 44/195 (22%), Positives = 85/195 (43%), Gaps = 13/195 (6%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 37 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 95
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPRLLGPGLNKAGKFPT--LVTHQESL 186
E + A +A+ V+ + LG L G P T ++
Sbjct: 96 GE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNI 149
Query: 187 EAKVNETKAV-VKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN--V 243
+ E KA ++F+ K + VG +++ N++ + L + + + +
Sbjct: 150 GEIIREIKAGRIEFRNDKTGAIHAPVGKACFPPEKLADNIRAFIRALEAHKPEGAKGTFL 209
Query: 244 RCLHLKSTMGRPQRI 258
R +++ +TMG RI
Sbjct: 210 RSVYVTTTMGPSVRI 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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 47/198 (23%), Positives = 90/198 (45%), Gaps = 19/198 (9%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 38 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 96
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASE----AVIKQIPRLLGP-GLNKAGKFPTLVTHQ 183
E + A +A+ AV ++ R+LGP GL K T+ +
Sbjct: 97 GE------EIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNI 150
Query: 184 ESLEAKVNETKAV-VKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN 242
+ + E KA ++F+ K + VG S +++ N++ + L + + +
Sbjct: 151 GEI---IREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKG 207
Query: 243 --VRCLHLKSTMGRPQRI 258
+R +++ + MG RI
Sbjct: 208 TFLRSVYVTTVMGPSVRI 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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 48/198 (24%), Positives = 91/198 (45%), Gaps = 19/198 (9%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 37 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 95
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASE----AVIKQIPRLLGP-GLNKAGKFPTLVTHQ 183
E + A +A+ AV ++ R+LGP GL K T+ +
Sbjct: 96 GE------EIIQKILDGWXDFDAVVATPDVXGAVGSKLGRILGPRGLLPNPKAGTVGFNI 149
Query: 184 ESLEAKVNETKAV-VKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN 242
+ + E KA ++F+ K + VG S +++ N++ + L + + +
Sbjct: 150 GEI---IREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKG 206
Query: 243 --VRCLHLKSTMGRPQRI 258
+R +++ +T G RI
Sbjct: 207 TFLRSVYVTTTXGPSVRI 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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 43/202 (21%), Positives = 79/202 (39%), Gaps = 2/202 (0%)
Query: 50 EVLREAVSTICGDAKEKNRNFVETIELQIGLKNYDPQKDKRFSGSVKLPHIPRPMMKVCM 109
E L EA+ RNF +++E+ + K D + D + V LP P +V +
Sbjct: 6 ESLIEALKLALSTEYNVKRNFTQSVEIILTFKGIDKKGDLKLREIVPLPKQPSKAKRVLV 65
Query: 110 LGDAQHVEQAEKIGMDYMDVEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQIPRLLGPG 169
+ ++ +E A+K + + + R+LGP
Sbjct: 66 VPSSEQLEYAKKASPKVVITREELQKLQGQKRPVKKLARQNEWFLINQESALAGRILGPA 125
Query: 170 LNKAGKFPTLVTHQESLEAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSV 229
L GKFPT + + + +N K V + K + V +G E + +N +
Sbjct: 126 LGPRGKFPTPLPNTADISEYINRFKRSVLVKTKDQPQVQVFIGTEDKPE-DLAENAIAVL 184
Query: 230 NFLVSLLKKSWQNVRCLHLKST 251
N + + K N+R +++K+T
Sbjct: 185 NAIENKAKVE-TNLRNIYVKTT 205
>pdb|2HW8|A Chain A, Structure Of Ribosomal Protein L1-Mrna Complex At 2.1
Resolution
Length = 228
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 47/198 (23%), Positives = 89/198 (44%), Gaps = 19/198 (9%)
Query: 70 FVETIELQIGLKNYDPQK-DKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
F ET+E+ L DP++ D+ G+V LPH ++V + + +++AE+ G DY+
Sbjct: 37 FDETVEVHAKL-GIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVG 95
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASE----AVIKQIPRLLGP-GLNKAGKFPTLVTHQ 183
E + A +A+ AV + R+LGP GL K T+ +
Sbjct: 96 GE------EIIQKILDGWMDFDAVVATPDVXGAVGSKXGRILGPRGLLPNPKAGTVGFNI 149
Query: 184 ESLEAKVNETKAV-VKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQN 242
+ + E KA ++F+ K + VG S +++ N++ + L + + +
Sbjct: 150 GEI---IREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKG 206
Query: 243 --VRCLHLKSTMGRPQRI 258
+R +++ +T G RI
Sbjct: 207 TFLRSVYVTTTXGPSVRI 224
>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 = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 42/194 (21%), Positives = 77/194 (39%), Gaps = 12/194 (6%)
Query: 70 FVETIELQIGLKNYDPQ-KDKRFSGSVKLPHIPRPMMKVCMLGDAQHVEQAEKIGMDYMD 128
FVET E L N DP+ D++ +V LP +K+ +L +++A+ G D +
Sbjct: 152 FVETAEAHFRL-NIDPKYNDQQLRATVSLPKGTGKTVKIAVLAQGDKIDEAKAAGADIVG 210
Query: 129 VEXXXXXXXXXXXXXXXXXXYHAFLASEAVIKQI--PRLLGPGLNKAGKFPTLVTHQESL 186
E +A A + +I PR L P P + E
Sbjct: 211 GEELIEQIKGGFMDFDKLIATSDMMAKVASLGRILGPRGLMPTPKAGTVTPNVAQAVEEF 270
Query: 187 EAKVNETKAVVKFQLKKVLCMGVAVGNCSMEEKQVFQNVQLSVNFLVSLLKKSWQNV--R 244
+ K V+F++ K + + G + EE+ + N+ ++ + + + V +
Sbjct: 271 K------KGKVEFRVDKTGIVHIPFGKLNFEEEDLLINLFATIKSVETNKPTGAKGVYWK 324
Query: 245 CLHLKSTMGRPQRI 258
H+ S+MG R+
Sbjct: 325 SAHISSSMGPSIRL 338
>pdb|1SCI|A Chain A, K236l Mutant Of Hydroxynitrile Lyase From Hevea
Brasiliensis
pdb|1SCK|A Chain A, K236l Mutant Of Hydroxynitrile Lyase From Hevea
Brasiliensis In Complex With Acetone
pdb|1SCQ|A Chain A, K236l Mutant Of Hydroxynitrile Lyase From Hevea
Brasiliensis In Complex With Acetonecyanohydrin
Length = 257
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 26 TTRFNWVGGNTKDKSEIENSKLSSEVLREAVSTICG 61
TT F + TKD EI KL +LRE + T+CG
Sbjct: 131 TTYFTY----TKDGKEITGLKLGFTLLRENLYTLCG 162
>pdb|2G4L|A Chain A, Anomalous Substructure Of Hydroxynitrile Lyase
Length = 257
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 26 TTRFNWVGGNTKDKSEIENSKLSSEVLREAVSTICG 61
TT F + TKD EI KL +LRE + T+CG
Sbjct: 131 TTYFTY----TKDGKEITGLKLGFTLLRENLYTLCG 162
>pdb|1YAS|A Chain A, Hydroxynitrile Lyase Complexed With Histidine
pdb|7YAS|A Chain A, Hydroxynitrile Lyase, Low Temperature Native Structure
pdb|2YAS|A Chain A, Hydroxynitrile Lyase From Hevea Brasiliensis Complexed
With Rhodanide
pdb|3YAS|A Chain A, Hydroxynitrile Lyase Complexed With Acetone
pdb|4YAS|A Chain A, Hydroxynitrile Lyase Complexed With Chloralhydrate
pdb|5YAS|A Chain A, Hydroxynitrile Lyase Complexed With Hexafluoroacetone
pdb|6YAS|A Chain A, Hydroxynitrile Lyase From Hevea Brasiliensis, Room
Temperature Structure
pdb|1QJ4|A Chain A, Hydroxynitrile-lyase From Hevea Brasiliensis At Atomic
Resolution
pdb|1SC9|A Chain A, Hydroxynitrile Lyase From Hevea Brasiliensis In Complex
With The Natural Substrate Acetone Cyanohydrin
pdb|3C6X|A Chain A, Hnl From Hevea Brasiliensis To Atomic Resolution
pdb|3C6Y|A Chain A, Hnl From Hevea Brasiliensis To Atomic Resolution
pdb|3C6Z|A Chain A, Hnl From Hevea Brasiliensis To Atomic Resolution
pdb|3C70|A Chain A, Hnl From Hevea Brasiliensis To Atomic Resolution
Length = 257
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 26 TTRFNWVGGNTKDKSEIENSKLSSEVLREAVSTICG 61
TT F + TKD EI KL +LRE + T+CG
Sbjct: 131 TTYFTY----TKDGKEITGLKLGFTLLRENLYTLCG 162
>pdb|1YB6|A Chain A, Hydroxynitrile Lyase From Hevea Brasiliensis In Complex
With Mandelonitrile
pdb|1YB7|A Chain A, Hydroxynitrile Lyase From Hevea Brasiliensis In Complex
With 2,3- Dimethyl-2-Hydroxy-Butyronitrile
Length = 256
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 26 TTRFNWVGGNTKDKSEIENSKLSSEVLREAVSTICG 61
TT F + TKD EI KL +LRE + T+CG
Sbjct: 130 TTYFTY----TKDGKEITGLKLGFTLLRENLYTLCG 161
>pdb|1PX8|A Chain A, Crystal Structure Of Beta-D-Xylosidase From
Thermoanaerobacterium Saccharolyticum, A Family 39
Glycoside Hydrolase
pdb|1PX8|B Chain B, Crystal Structure Of Beta-D-Xylosidase From
Thermoanaerobacterium Saccharolyticum, A Family 39
Glycoside Hydrolase
pdb|1UHV|A Chain A, Crystal Structure Of Beta-D-Xylosidase From
Thermoanaerobacterium Saccharolyticum, A Family 39
Glycoside Hydrolase
pdb|1UHV|B Chain B, Crystal Structure Of Beta-D-Xylosidase From
Thermoanaerobacterium Saccharolyticum, A Family 39
Glycoside Hydrolase
pdb|1UHV|C Chain C, Crystal Structure Of Beta-D-Xylosidase From
Thermoanaerobacterium Saccharolyticum, A Family 39
Glycoside Hydrolase
pdb|1UHV|D Chain D, Crystal Structure Of Beta-D-Xylosidase From
Thermoanaerobacterium Saccharolyticum, A Family 39
Glycoside Hydrolase
Length = 500
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 19/42 (45%)
Query: 16 FQRKKLKKGTTTRFNWVGGNTKDKSEIENSKLSSEVLREAVS 57
F KKL GT T F W G T K + S L VL +S
Sbjct: 102 FMPKKLASGTQTVFYWEGNVTPPKDYEKWSDLVKAVLHHFIS 143
>pdb|2JG6|A Chain A, Crystal Structure Of A 3-Methyladenine Dna Glycosylase I
From Staphylococcus Aureus
Length = 186
Score = 27.3 bits (59), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 10/41 (24%), Positives = 25/41 (60%)
Query: 160 KQIPRLLGPGLNKAGKFPTLVTHQESLEAKVNETKAVVKFQ 200
+++ ++ +++ FP +V H++ LEA VN+ + +K +
Sbjct: 66 EKVAQMTAQDIDRLMTFPNIVHHRKKLEAIVNQAQGYLKIE 106
>pdb|4AIA|A Chain A, The Structural Basis Of 3-Methyladenine Recognition By
3-Methyladenine Dna Glycosylase I (Tag) From
Staphylococcus Aureus
pdb|4AIA|B Chain B, The Structural Basis Of 3-Methyladenine Recognition By
3-Methyladenine Dna Glycosylase I (Tag) From
Staphylococcus Aureus
pdb|4AIA|C Chain C, The Structural Basis Of 3-Methyladenine Recognition By
3-Methyladenine Dna Glycosylase I (Tag) From
Staphylococcus Aureus
pdb|4AIA|D Chain D, The Structural Basis Of 3-Methyladenine Recognition By
3-Methyladenine Dna Glycosylase I (Tag) From
Staphylococcus Aureus
pdb|4AIA|E Chain E, The Structural Basis Of 3-Methyladenine Recognition By
3-Methyladenine Dna Glycosylase I (Tag) From
Staphylococcus Aureus
Length = 188
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 10/41 (24%), Positives = 25/41 (60%)
Query: 160 KQIPRLLGPGLNKAGKFPTLVTHQESLEAKVNETKAVVKFQ 200
+++ ++ +++ FP +V H++ LEA VN+ + +K +
Sbjct: 68 EKVAQMTAQDIDRLMTFPNIVHHRKKLEAIVNQAQGYLKIE 108
>pdb|4AI5|A Chain A, Crystal Structure Of Y16f Of 3-Methyladenine Dna
Glycosylase I (Tag) In Complex With 3-Methyladenine
pdb|4AI5|B Chain B, Crystal Structure Of Y16f Of 3-Methyladenine Dna
Glycosylase I (Tag) In Complex With 3-Methyladenine
pdb|4AI5|C Chain C, Crystal Structure Of Y16f Of 3-Methyladenine Dna
Glycosylase I (Tag) In Complex With 3-Methyladenine
pdb|4AI5|D Chain D, Crystal Structure Of Y16f Of 3-Methyladenine Dna
Glycosylase I (Tag) In Complex With 3-Methyladenine
pdb|4AI5|E Chain E, Crystal Structure Of Y16f Of 3-Methyladenine Dna
Glycosylase I (Tag) In Complex With 3-Methyladenine
Length = 188
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 10/41 (24%), Positives = 25/41 (60%)
Query: 160 KQIPRLLGPGLNKAGKFPTLVTHQESLEAKVNETKAVVKFQ 200
+++ ++ +++ FP +V H++ LEA VN+ + +K +
Sbjct: 68 EKVAQMTAQDIDRLMTFPNIVHHRKKLEAIVNQAQGYLKIE 108
>pdb|4AI4|A Chain A, Crystal Structure Of E38q Mutant Of 3-Methyladenine Dna
Glycosylase I From Staphylococcus Aureus
Length = 188
Score = 26.9 bits (58), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 10/41 (24%), Positives = 25/41 (60%)
Query: 160 KQIPRLLGPGLNKAGKFPTLVTHQESLEAKVNETKAVVKFQ 200
+++ ++ +++ FP +V H++ LEA VN+ + +K +
Sbjct: 68 EKVAQMTAQDIDRLMTFPNIVHHRKKLEAIVNQAQGYLKIE 108
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
0.318 0.133 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,231,035
Number of Sequences: 62578
Number of extensions: 210811
Number of successful extensions: 564
Number of sequences better than 100.0: 42
Number of HSP's better than 100.0 without gapping: 39
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 515
Number of HSP's gapped (non-prelim): 42
length of query: 259
length of database: 14,973,337
effective HSP length: 97
effective length of query: 162
effective length of database: 8,903,271
effective search space: 1442329902
effective search space used: 1442329902
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: 50 (23.9 bits)