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= psy8115
(218 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZKQ|CC Chain c, Structure Of A Mammalian Ribosomal 40s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 243
Score = 194 bits (493), Expect = 3e-50, Method: Compositional matrix adjust.
Identities = 93/116 (80%), Positives = 107/116 (92%)
Query: 77 SLSICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGD 136
++ I +FVADG+F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+
Sbjct: 2 AVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGE 61
Query: 137 KGRRIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
KGRRIRELT+VVQKRF F +G++ELYAEKVATRGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 62 KGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRR 117
>pdb|3IZ6|B Chain B, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 227
Score = 182 bits (462), Expect = 1e-46, Method: Compositional matrix adjust.
Identities = 89/108 (82%), Positives = 97/108 (89%)
Query: 85 QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
+FV+DGVF AEL+E LTRELAEDGYSGVE+R TP RTEIII ATRTQNVLG+KGRRIREL
Sbjct: 10 KFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIREL 69
Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRR 192
TSVVQKRF F + +ELYAEKV RGLCAIAQAESLRYKL+GGLAVRR
Sbjct: 70 TSVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRR 117
>pdb|3IZB|B Chain B, Localization Of The Small Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
pdb|3O2Z|C Chain C, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O30|C Chain C, Yeast 80s Ribosome. This Entry Consists Of The 40s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5C|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|D Chain D, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
Length = 240
Score = 159 bits (402), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 78/125 (62%), Positives = 96/125 (76%)
Query: 80 ICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGR 139
I + VADGVF AEL+EF TRELAE+GYSGVE+R TP +TE+II ATRTQ+VLG+ GR
Sbjct: 5 ISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGR 64
Query: 140 RIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSL 199
RI ELT +VQKRFK+A G I LYAE+V RGL A+AQAES+++KL+ GLA+RR V
Sbjct: 65 RINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVR 124
Query: 200 YCLNC 204
Y +
Sbjct: 125 YVMES 129
>pdb|1S1H|C Chain C, 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,
1s1h, Contains 40s Subunit. The 60s Ribosomal Subunit Is
In File 1s1i
Length = 192
Score = 158 bits (400), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 77/120 (64%), Positives = 95/120 (79%)
Query: 85 QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
+ VADGVF AEL+EF TRELAE+GYSGVE+R TP +TE+II ATRTQ+VLG+ GRRI EL
Sbjct: 9 KLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGRRINEL 68
Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNC 204
T +VQKRFK+A G I LYAE+V RGL A+AQAES+++KL+ GLA+RR V Y +
Sbjct: 69 TLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMES 128
>pdb|3JYV|C Chain C, Structure Of The 40s Rrna And Proteins And PE TRNA FOR
EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces
Lanuginosus Ribosome At 8.9a Resolution
Length = 188
Score = 158 bits (400), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 77/120 (64%), Positives = 95/120 (79%)
Query: 85 QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
+ VADGVF AEL+EF TRELAE+GYSGVE+R TP +TE+II ATRTQ+VLG+ GRRI EL
Sbjct: 5 KLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENGRRINEL 64
Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLNC 204
T +VQKRFK+A G I LYAE+V RGL A+AQAES+++KL+ GLA+RR V Y +
Sbjct: 65 TLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMES 124
>pdb|3ZEY|X Chain X, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 214
Score = 142 bits (357), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 68/118 (57%), Positives = 90/118 (76%)
Query: 86 FVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELT 145
V DGVF AEL EFL RELA+DG++GVE R TP RTEI+I +T+T+ VLG+KGRRIRELT
Sbjct: 10 MVRDGVFYAELFEFLKRELADDGFAGVEHRVTPTRTEIVIRSTKTREVLGEKGRRIRELT 69
Query: 146 SVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVRRYNSDVSLYCLN 203
+ +Q+RF + +G ++L+AE+V RGL A+AQAESLR+KL+ L VRR + Y +
Sbjct: 70 ACLQQRFNYKEGKLQLFAERVEVRGLSAMAQAESLRFKLLSNLQVRRAAMGIIRYVME 127
>pdb|1WH9|A Chain A, Solution Structure Of The Kh Domain Of Human Ribosomal
Protein S3
Length = 92
Score = 140 bits (352), Expect = 7e-34, Method: Compositional matrix adjust.
Identities = 66/79 (83%), Positives = 75/79 (94%)
Query: 92 FRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKR 151
F+AEL+EFLTRELAEDGYSGVE+R TP RTEIII+ATRTQNVLG+KGRRIRELT+VVQKR
Sbjct: 8 FKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKR 67
Query: 152 FKFADGAIELYAEKVATRG 170
F F +G++ELYAEKVATRG
Sbjct: 68 FGFPEGSVELYAEKVATRG 86
>pdb|2XZM|C Chain C, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 1
pdb|2XZN|C Chain C, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 2
Length = 243
Score = 116 bits (291), Expect = 7e-27, Method: Compositional matrix adjust.
Identities = 52/107 (48%), Positives = 78/107 (72%)
Query: 85 QFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIREL 144
+FVADGVF AEL F ++ L + GY+G+E+R TP +TEI I AT+ Q V+G +G++ +EL
Sbjct: 13 KFVADGVFNAELHSFFSKSLQDAGYAGIEVRRTPTKTEIRIKATKPQQVIGVEGKKHKEL 72
Query: 145 TSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGLAVR 191
T +QKRF ++D I+++AE + +GLCA AQ E++ YKL+ + VR
Sbjct: 73 TQFLQKRFGYSDDQIQIWAEPIKFKGLCASAQVEAMNYKLLKDVPVR 119
>pdb|3J20|C Chain C, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (30s Ribosomal Subunit)
Length = 210
Score = 65.1 bits (157), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 40/109 (36%), Positives = 61/109 (55%), Gaps = 2/109 (1%)
Query: 80 ICVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGR 139
+ + F+ + V +DEFL +EL GY G++I+ TP T++II A V+G GR
Sbjct: 1 MAIERYFIREAVREMLIDEFLEKELRRAGYGGLDIKKTPLGTKVIIFAANPGYVIGRGGR 60
Query: 140 RIRELTSVVQKRFKFADGAIELYAEKVATRGLCAIAQAESLRYKLIGGL 188
RIRELT +++K+F + IE+ E++ L A QA L L G+
Sbjct: 61 RIRELTRILEKQFGLENPQIEV--EEIKNPYLNAKVQAVRLAQALERGI 107
>pdb|3OGK|B Chain B, Structure Of Coi1-Ask1 In Complex With Coronatine And An
Incomplete Jaz1 Degron
pdb|3OGK|D Chain D, Structure Of Coi1-Ask1 In Complex With Coronatine And An
Incomplete Jaz1 Degron
pdb|3OGK|F Chain F, Structure Of Coi1-Ask1 In Complex With Coronatine And An
Incomplete Jaz1 Degron
pdb|3OGK|H Chain H, Structure Of Coi1-Ask1 In Complex With Coronatine And An
Incomplete Jaz1 Degron
pdb|3OGK|J Chain J, Structure Of Coi1-Ask1 In Complex With Coronatine And An
Incomplete Jaz1 Degron
pdb|3OGK|L Chain L, Structure Of Coi1-Ask1 In Complex With Coronatine And An
Incomplete Jaz1 Degron
pdb|3OGK|N Chain N, Structure Of Coi1-Ask1 In Complex With Coronatine And An
Incomplete Jaz1 Degron
pdb|3OGK|P Chain P, Structure Of Coi1-Ask1 In Complex With Coronatine And An
Incomplete Jaz1 Degron
pdb|3OGL|B Chain B, Structure Of Coi1-Ask1 In Complex With Ja-Isoleucine And
The Jaz1 Degron
pdb|3OGL|D Chain D, Structure Of Coi1-Ask1 In Complex With Ja-Isoleucine And
The Jaz1 Degron
pdb|3OGL|F Chain F, Structure Of Coi1-Ask1 In Complex With Ja-Isoleucine And
The Jaz1 Degron
pdb|3OGL|H Chain H, Structure Of Coi1-Ask1 In Complex With Ja-Isoleucine And
The Jaz1 Degron
pdb|3OGL|J Chain J, Structure Of Coi1-Ask1 In Complex With Ja-Isoleucine And
The Jaz1 Degron
pdb|3OGL|L Chain L, Structure Of Coi1-Ask1 In Complex With Ja-Isoleucine And
The Jaz1 Degron
pdb|3OGL|N Chain N, Structure Of Coi1-Ask1 In Complex With Ja-Isoleucine And
The Jaz1 Degron
pdb|3OGL|P Chain P, Structure Of Coi1-Ask1 In Complex With Ja-Isoleucine And
The Jaz1 Degron
pdb|3OGM|B Chain B, Structure Of Coi1-Ask1 In Complex With Coronatine And The
Jaz1 Degron
pdb|3OGM|D Chain D, Structure Of Coi1-Ask1 In Complex With Coronatine And The
Jaz1 Degron
pdb|3OGM|F Chain F, Structure Of Coi1-Ask1 In Complex With Coronatine And The
Jaz1 Degron
pdb|3OGM|H Chain H, Structure Of Coi1-Ask1 In Complex With Coronatine And The
Jaz1 Degron
pdb|3OGM|J Chain J, Structure Of Coi1-Ask1 In Complex With Coronatine And The
Jaz1 Degron
pdb|3OGM|L Chain L, Structure Of Coi1-Ask1 In Complex With Coronatine And The
Jaz1 Degron
pdb|3OGM|N Chain N, Structure Of Coi1-Ask1 In Complex With Coronatine And The
Jaz1 Degron
pdb|3OGM|P Chain P, Structure Of Coi1-Ask1 In Complex With Coronatine And The
Jaz1 Degron
Length = 592
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 130 TQNVLGDKGRRIRELTSVVQKRFKFADGAIELYAEK----VATRGLCAIAQ-AESLRY 182
T+NV+GD+G + KR + GA E E V+ RGL A+AQ + L Y
Sbjct: 325 TRNVIGDRGLEVLAQYCKQLKRLRIERGADEQGMEDEEGLVSQRGLIALAQGCQELEY 382
>pdb|2EZ2|A Chain A, Apo Tyrosine Phenol-Lyase From Citrobacter Freundii At Ph
8.0
pdb|2EZ2|B Chain B, Apo Tyrosine Phenol-Lyase From Citrobacter Freundii At Ph
8.0
pdb|2VLF|A Chain A, Quinonoid Intermediate Of Citrobacter Freundii Tyrosine
Phenol-Lyase Formed With Alanine
pdb|2VLF|B Chain B, Quinonoid Intermediate Of Citrobacter Freundii Tyrosine
Phenol-Lyase Formed With Alanine
pdb|2VLH|A Chain A, Quinonoid Intermediate Of Citrobacter Freundii Tyrosine
Phenol-Lyase Formed With Methionine
pdb|2YCT|A Chain A, Tyrosine Phenol-Lyase From Citrobacter Freundii In Complex
With Pyridine N-Oxide And The Quinonoid Intermediate
Formed With L-Alanine
pdb|2YCT|B Chain B, Tyrosine Phenol-Lyase From Citrobacter Freundii In Complex
With Pyridine N-Oxide And The Quinonoid Intermediate
Formed With L-Alanine
Length = 456
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 30/94 (31%), Positives = 40/94 (42%), Gaps = 12/94 (12%)
Query: 97 DEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF-- 154
DEF + LA Y +R + II A R NV G+ R E + R +
Sbjct: 359 DEFPAQSLAASIYVETGVR---SMERGIISAGRN-NVTGEHHRPKLETVRLTIPRRVYTY 414
Query: 155 ------ADGAIELYAEKVATRGLCAIAQAESLRY 182
ADG I+LY K RGL I + + LR+
Sbjct: 415 AHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRF 448
>pdb|2TPL|A Chain A, Tyrosine Phenol-lyase From Citrobacter Intermedius Complex
With 3-(4'- Hydroxyphenyl)propionic Acid,
Pyridoxal-5'-phosphate And Cs+ Ion
pdb|2TPL|B Chain B, Tyrosine Phenol-lyase From Citrobacter Intermedius Complex
With 3-(4'- Hydroxyphenyl)propionic Acid,
Pyridoxal-5'-phosphate And Cs+ Ion
Length = 456
Score = 28.1 bits (61), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 39/94 (41%), Gaps = 12/94 (12%)
Query: 97 DEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF-- 154
DEF + LA Y +R E I++ NV G+ R E + R +
Sbjct: 359 DEFPAQSLAASIYVETGVR----SMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTY 414
Query: 155 ------ADGAIELYAEKVATRGLCAIAQAESLRY 182
ADG I+LY K RGL I + + LR+
Sbjct: 415 AHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRF 448
>pdb|1TPL|A Chain A, The Three-Dimensional Structure Of Tyrosine Phenol-Lyase
pdb|1TPL|B Chain B, The Three-Dimensional Structure Of Tyrosine Phenol-Lyase
Length = 456
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 39/94 (41%), Gaps = 12/94 (12%)
Query: 97 DEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF-- 154
DEF + LA Y +R E I++ NV G+ R E + R +
Sbjct: 359 DEFPAQSLAASIYVETGVR----SMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTY 414
Query: 155 ------ADGAIELYAEKVATRGLCAIAQAESLRY 182
ADG I+LY K RGL I + + LR+
Sbjct: 415 AHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRF 448
>pdb|2YHK|A Chain A, D214a Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii
pdb|2YHK|B Chain B, D214a Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii
Length = 456
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 39/94 (41%), Gaps = 12/94 (12%)
Query: 97 DEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF-- 154
DEF + LA Y +R E I++ NV G+ R E + R +
Sbjct: 359 DEFPAQSLAASIYVETGVR----SMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTY 414
Query: 155 ------ADGAIELYAEKVATRGLCAIAQAESLRY 182
ADG I+LY K RGL I + + LR+
Sbjct: 415 AHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRF 448
>pdb|2YCN|A Chain A, Y71f Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii In Complex With Quinonoid Intermediate Formed
With 3-Fluoro-L-Tyrosine
pdb|2YCN|B Chain B, Y71f Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii In Complex With Quinonoid Intermediate Formed
With 3-Fluoro-L-Tyrosine
Length = 456
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 39/94 (41%), Gaps = 12/94 (12%)
Query: 97 DEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF-- 154
DEF + LA Y +R E I++ NV G+ R E + R +
Sbjct: 359 DEFPAQSLAASIYVETGVR----SMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTY 414
Query: 155 ------ADGAIELYAEKVATRGLCAIAQAESLRY 182
ADG I+LY K RGL I + + LR+
Sbjct: 415 AHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRF 448
>pdb|2EZ1|A Chain A, Holo Tyrosine Phenol-Lyase From Citrobacter Freundii At Ph
8.0
pdb|2EZ1|B Chain B, Holo Tyrosine Phenol-Lyase From Citrobacter Freundii At Ph
8.0
pdb|2VLH|B Chain B, Quinonoid Intermediate Of Citrobacter Freundii Tyrosine
Phenol-Lyase Formed With Methionine
Length = 456
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 39/94 (41%), Gaps = 12/94 (12%)
Query: 97 DEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF-- 154
DEF + LA Y +R E I++ NV G+ R E + R +
Sbjct: 359 DEFPAQSLAASIYVETGVR----SMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTY 414
Query: 155 ------ADGAIELYAEKVATRGLCAIAQAESLRY 182
ADG I+LY K RGL I + + LR+
Sbjct: 415 AHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRF 448
>pdb|1VS5|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|1VS7|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With The Antibiotic
Kasugamyin At 3.5a Resolution. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|3E1A|O Chain O, Structure Of The 30s Subunit And The Trnas Of E. Coli
Ribosome In Pre- Accommodation State
pdb|3E1C|O Chain O, Structure Of The 30s Subunit And The Trnas Of E. Coli
Ribosome In Post-Accommodation State
pdb|3I1M|C Chain C, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1O|C Chain C, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1Q|C Chain C, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1S|C Chain C, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I1Z|C Chain C, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3I21|C Chain C, Crystal Structure Of The E. Coli 70s Ribosome In An
Intermediate State Of Ratcheting
pdb|3KC4|C Chain C, Ribosome-Secy Complex. This Entry 3kc4 Contains 30s
Ribosomal Subnit. The 50s Ribosomal Subunit Can Be Found
In Pdb Entry 3kcr
pdb|3OR9|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 30s Subunit Of The First
70s Ribosome.
pdb|3ORA|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Cem-101. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|3IZV|G Chain G, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding. This Entry Contains The
Small Subunit Of A Ribosome Programmed With A
Near-Cognate Codon, AT-Site Trna, P-Site Trna, Mrna And
Ef-Tu
pdb|3IZW|G Chain G, Structural Insights Into Cognate Vs. Near-Cognate
Discrimination During Decoding.This Entry Contains The
Small Subunit Of A Ribosome Programmed With A Cognate
Codon, AT-Site Trna, P-Site Trna, Mrna And Ef-Tu
pdb|3SFS|C Chain C, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome
pdb|3UOQ|C Chain C, Crystal Structure Of Release Factor Rf3 Trapped In The Gtp
State On A Rotated Conformation Of The Ribosome (Without
Viomycin)
pdb|4GAQ|C Chain C, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
pdb|4GAS|C Chain C, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 233
Score = 27.7 bits (60), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 95 ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVV 148
++ ++LT+ELA+ S + I + I R V+G KG + +L VV
Sbjct: 38 KVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVV 91
>pdb|1P6G|C Chain C, Real Space Refined Coordinates Of The 30s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp
State Of E. Coli 70s Ribosome
pdb|1P87|C Chain C, Real Space Refined Coordinates Of The 30s Subunit Fitted
Into The Low Resolution Cryo-Em Map Of The
Initiation-Like State Of E. Coli 70s Ribosome
pdb|2AVY|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2AW7|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli At 3.5 A Resolution. This File Contains
The 30s Subunit Of The Second 70s Ribosome. The Entire
Crystal Structure Contains Two 70s Ribosomes And Is
Described In Remark 400.
pdb|2I2P|C Chain C, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2I2U|C Chain C, Crystal Structure Of Ribosome With Messenger Rna And The
Anticodon Stem-Loop Of P-Site Trna. This File Contains
The 30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QOU|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 30s Subunit Of The First 70s Ribosome,
With Spectinomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|2QOW|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin. This
File Contains The 30s Subunit Of The Second 70s
Ribosome, With Spectinomycin Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|2QOY|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 30s Subunit Of The
First 70s Ribosome, With Spectinomycin And Neomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QP0|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Spectinomycin And
Neomycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome, With Spectinomycin And Neomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes.
pdb|2QAL|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 30s Subunit Of The First 70s Ribosome, With
Neomycin Bound. The Entire Crystal Structure Contains
Two 70s Ribosomes And Is Described In Remark 400.
pdb|2QAN|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Neomycin. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Neomycin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QB9|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 30s Subunit Of The First 70s Ribosome, With
Gentamicin Bound. The Entire Crystal Structure Contains
Two 70s Ribosomes And Is Described In Remark 400.
pdb|2QBB|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Gentamicin Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBD|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 30s Subunit Of The
First 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBF|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 30s Subunit Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes And Is Described In Remark
400.
pdb|2QBH|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 30s
Subunit Of The First 70s Ribosome, With Gentamicin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2QBJ|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 30s
Subunit Of The Second 70s Ribosome, With Gentamicin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4K|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
30s Subunit Of The First 70s Ribosome, With Paromomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4M|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
30s Subunit Of The Second 70s Ribosome, With Paromomycin
Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2VHO|C Chain C, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 3 Of 4)
pdb|2VHP|C Chain C, Structure Of Pdf Binding Helix In Complex With The
Ribosome (Part 4 Of 4)
pdb|3DF1|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This File
Contains The 30s Subunit Of The First 70s Ribosome, With
Hygromycin B Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3DF3|C Chain C, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Hygromycin B. This File
Contains The 30s Subunit Of The Second 70s Ribosome,
With Hygromycin B Bound. The Entire Crystal Structure
Contains Two 70s Ribosomes.
pdb|3J00|C Chain C, Structure Of The Ribosome-Secye Complex In The Membrane
Environment
pdb|4ADV|C Chain C, Structure Of The E. Coli Methyltransferase Ksga Bound To
The E. Coli 30s Ribosomal Subunit
pdb|3J0U|F Chain F, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class2 Of The Six
Classes)
pdb|3J0V|F Chain F, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 4a Of The Six
Classes)
pdb|3J0X|F Chain F, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 4b Of The Six
Classes)
pdb|3J0Z|F Chain F, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 5 Of The Six
Classes)
pdb|3J10|F Chain F, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 6 Of The Six
Classes)
pdb|3J13|E Chain E, Structural Characterization Of Mrna-Trna Translocation
Intermediates (30s Ribosome Of Class 3 Of The Six
Classes)
Length = 232
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 95 ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVV 148
++ ++LT+ELA+ S + I + I R V+G KG + +L VV
Sbjct: 37 KVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVV 90
>pdb|2YCP|A Chain A, F448h Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii In Complex With Quinonoid Intermediate Formed
With 3-Fluoro-L-Tyrosine
pdb|2YCP|B Chain B, F448h Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii In Complex With Quinonoid Intermediate Formed
With 3-Fluoro-L-Tyrosine
pdb|2YCP|C Chain C, F448h Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii In Complex With Quinonoid Intermediate Formed
With 3-Fluoro-L-Tyrosine
pdb|2YCP|D Chain D, F448h Mutant Of Tyrosine Phenol-Lyase From Citrobacter
Freundii In Complex With Quinonoid Intermediate Formed
With 3-Fluoro-L-Tyrosine
Length = 456
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 39/94 (41%), Gaps = 12/94 (12%)
Query: 97 DEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVVQKRFKF-- 154
DEF + LA Y +R E I++ NV G+ R E + R +
Sbjct: 359 DEFPAQSLAASIYVETGVR----SMERGIISAGRNNVTGEHHRPKLETVRLTIPRRVYTY 414
Query: 155 ------ADGAIELYAEKVATRGLCAIAQAESLRY 182
ADG I+LY K RGL I + + LR+
Sbjct: 415 AHMDVVADGIIKLYQHKEDIRGLKFIYEPKQLRH 448
>pdb|3GVP|A Chain A, Human Sahh-Like Domain Of Human Adenosylhomocysteinase 3
pdb|3GVP|B Chain B, Human Sahh-Like Domain Of Human Adenosylhomocysteinase 3
pdb|3GVP|C Chain C, Human Sahh-Like Domain Of Human Adenosylhomocysteinase 3
pdb|3GVP|D Chain D, Human Sahh-Like Domain Of Human Adenosylhomocysteinase 3
Length = 435
Score = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 27/54 (50%)
Query: 81 CVSLQFVADGVFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVL 134
C +L+ + V+ E+D + DG+ V++ + +I+I T +NV+
Sbjct: 236 CAALKAMGSIVYVTEIDPICALQACMDGFRLVKLNEVIRQVDIVITCTGNKNVV 289
>pdb|1VIQ|A Chain A, Crystal Structure Of Putative Adp Ribose Pyrophosphatase
pdb|1VIQ|B Chain B, Crystal Structure Of Putative Adp Ribose Pyrophosphatase
pdb|1VIQ|C Chain C, Crystal Structure Of Putative Adp Ribose Pyrophosphatase
Length = 220
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 22/36 (61%)
Query: 91 VFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIM 126
+F ++ + RE+ E G++ V + F P R E++++
Sbjct: 41 LFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLI 76
>pdb|2GY9|C Chain C, Structure Of The 30s 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|2GYB|C Chain C, Structure Of The 30s 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
pdb|3FIH|C Chain C, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry
Consists Of The 30s Subunit, Trnas And The Ternary
Complex.
pdb|2WWL|C Chain C, E.Coli 70s Ribosome Stalled During Translation Of Tnac
Leader Peptide. This File Contains The 30s, The P-Site
Trna And The Tnac Leader Peptide (Part 1 Of 2).
pdb|3OFO|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OFP|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Erythromycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|3OFA|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 30s Subunit Of
The First 70s Ribosome.
pdb|3OFB|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Chloramphenicol. This File Contains The 30s Subunit Of
The Second 70s Ribosome.
pdb|3OFX|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OFY|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Clindamycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome
pdb|3OAQ|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 30s Subunit Of The
First 70s Ribosome.
pdb|3OAR|C Chain C, Crystal Structure Of The E. Coli Ribosome Bound To
Telithromycin. This File Contains The 30s Subunit Of The
Second 70s Ribosome.
pdb|2YKR|C Chain C, 30s Ribosomal Subunit With Rsga Bound In The Presence Of
Gmppnp
pdb|4A2I|C Chain C, Cryo-Electron Microscopy Structure Of The 30s Subunit In
Complex With The Yjeq Biogenesis Factor
pdb|3J18|C Chain C, Structure Of The Bacterial Ribosome Complexed By
Tmrna-Smpb And Ef-G During Translocation And Mld-Loading
(30s Subunit)
pdb|4GD1|C Chain C, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
pdb|4GD2|C Chain C, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
Length = 206
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 95 ELDEFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRRIRELTSVV 148
++ ++LT+ELA+ S + I + I R V+G KG + +L VV
Sbjct: 37 KVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVV 90
>pdb|1G0S|A Chain A, The Crystal Structure Of The E.Coli Adp-Ribose
Pyrophosphatase
pdb|1G0S|B Chain B, The Crystal Structure Of The E.Coli Adp-Ribose
Pyrophosphatase
pdb|1G9Q|A Chain A, Complex Structure Of The Adpr-Ase And Its Substrate Adp-
Ribose
pdb|1G9Q|B Chain B, Complex Structure Of The Adpr-Ase And Its Substrate Adp-
Ribose
pdb|1GA7|A Chain A, Crystal Structure Of The Adp-Ribose Pyrophosphatase In
Complex With Gd+3
pdb|1GA7|B Chain B, Crystal Structure Of The Adp-Ribose Pyrophosphatase In
Complex With Gd+3
pdb|1KHZ|A Chain A, Structure Of The Adpr-Ase In Complex With Ampcpr And Mg
pdb|1KHZ|B Chain B, Structure Of The Adpr-Ase In Complex With Ampcpr And Mg
Length = 209
Score = 27.7 bits (60), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 22/36 (61%)
Query: 91 VFRAELDEFLTRELAEDGYSGVEIRFTPARTEIIIM 126
+F ++ + RE+ E G++ V + F P R E++++
Sbjct: 40 LFNGQMSHEVRREIFERGHAAVLLPFDPVRDEVVLI 75
>pdb|3A8R|A Chain A, The Structure Of The N-Terminal Regulatory Domain Of A
Plant Nadph Oxidase
pdb|3A8R|B Chain B, The Structure Of The N-Terminal Regulatory Domain Of A
Plant Nadph Oxidase
Length = 179
Score = 26.9 bits (58), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 98 EFLTRELAEDGYSGVEIRFTPARTEIIIMATRTQNVLGDKGRR---IRELTSVVQKR 151
+F+T ++ DG++ VE RF + + +++ +R +G G ++ S+ +KR
Sbjct: 16 QFVTAKVGNDGWAAVEKRFNQLQVDGVLLRSRFGKCIGMDGSDEFAVQMFDSLARKR 72
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
0.321 0.136 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,214,158
Number of Sequences: 62578
Number of extensions: 237412
Number of successful extensions: 454
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 437
Number of HSP's gapped (non-prelim): 25
length of query: 218
length of database: 14,973,337
effective HSP length: 95
effective length of query: 123
effective length of database: 9,028,427
effective search space: 1110496521
effective search space used: 1110496521
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)