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= psy17712
(293 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LCK|A Chain A, Structure Of The Mitochondrial Uncoupling Protein 2
Determined By Nmr Molecular Fragment Replacement
Length = 303
Score = 92.8 bits (229), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 76/268 (28%), Positives = 112/268 (41%), Gaps = 17/268 (6%)
Query: 25 PFDTVKVRLQTMSTEK--------PQYKGTFDCFTKIVRNESAVGLYKGMGAPITGVAPI 76
P DT KVRLQ + QY+G +VR E LY G+ A +
Sbjct: 21 PLDTAKVRLQIQGESQGLVRTAASAQYRGVLGTILTMVRTEGPRSLYNGLVAGLQRQMS- 79
Query: 77 FALSFLGYGAGKKVLTNENNDKLAHWQYFVAGSFSGITTAAITAPGERIKCLLQIQSNET 136
FA +G K + ++ +AGS +G A+ P + +K Q Q+
Sbjct: 80 FASVRIGLYDSVKQFYTKGSEHAGIGSRLLAGSTTGALAVAVAQPTDVVKVRFQAQARAG 139
Query: 137 A-KVYSGPVDVVRKLVRQHGVTSVFKGLCATLLRDIPANGAYFVTYETIKNFLADRSTSP 195
+ Y V+ + + R+ G+ ++KG + R+ N A VTY+ IK+ L +
Sbjct: 140 GGRRYQSTVEAYKTIAREEGIRGLWKGTSPNVARNAIVNCAELVTYDLIKDTLLKANLMT 199
Query: 196 SGEKKSVSMLSTIFAGGCAGIMYWVVGMPADVLKSRLQTAPEGTYPNGVRSVLSTTLRNE 255
+ S AG C V+ P DV+K+R + G Y + L T LR E
Sbjct: 200 --DDLPCHFTSAFGAGFCTT----VIASPVDVVKTRYMNSALGQYHSAGHCAL-TMLRKE 252
Query: 256 GPGALYKGAIPVFLRAFPANAACFLGVE 283
GP A YKG +P FLR N F+ E
Sbjct: 253 GPRAFYKGFMPSFLRLGSWNVVMFVTYE 280
Score = 50.8 bits (120), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 45/170 (26%), Positives = 67/170 (39%), Gaps = 11/170 (6%)
Query: 24 HPFDTVKVRLQTMSTEK--PQYKGTFDCFTKIVRNESAVGLYKGMGAPITGVAPIFALSF 81
P D VKVR Q + +Y+ T + + I R E GL+KG + A +
Sbjct: 123 QPTDVVKVRFQAQARAGGGRRYQSTVEAYKTIAREEGIRGLWKGTSPNVARNAIVNCAEL 182
Query: 82 LGYGAGKKVLTNEN---NDKLAHWQYFVAGSFSGITTAAITAPGERIKCLLQIQSNETAK 138
+ Y K L N +D H F + +G T I +P + +K N
Sbjct: 183 VTYDLIKDTLLKANLMTDDLPCH---FTSAFGAGFCTTVIASPVDVVKTRYM---NSALG 236
Query: 139 VYSGPVDVVRKLVRQHGVTSVFKGLCATLLRDIPANGAYFVTYETIKNFL 188
Y ++R+ G + +KG + LR N FVTYE +K L
Sbjct: 237 QYHSAGHCALTMLRKEGPRAFYKGFMPSFLRLGSWNVVMFVTYEQLKRAL 286
>pdb|1OKC|A Chain A, Structure Of Mitochondrial AdpATP CARRIER IN COMPLEX WITH
Carboxyatractyloside
pdb|2C3E|A Chain A, The Bovine Mitochondrial Adp-Atp Carrier
Length = 297
Score = 69.3 bits (168), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 65/280 (23%), Positives = 110/280 (39%), Gaps = 23/280 (8%)
Query: 6 VKYFFAXXXXXXXXXXXXHPFDTVKVRLQTMSTEK-----PQYKGTFDCFTKIVRNESAV 60
+K F A P + VK+ LQ K QYKG DC +I + + +
Sbjct: 8 LKDFLAGGVAAAISKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFL 67
Query: 61 GLYKGMGAPITGVAPIFALSFLGYGAGKKVLTNENNDKLAHWQYF----VAGSFSGITTA 116
++G A + P AL+F K++ + W+YF +G +G T+
Sbjct: 68 SFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDRHKQFWRYFAGNLASGGAAGATSL 127
Query: 117 AITAPGE--RIKCLLQIQSNETAKVYSGPVDVVRKLVRQHGVTSVFKGLCATLLRDIPAN 174
P + R + + + ++G + + K+ + G+ +++G ++ I
Sbjct: 128 CFVYPLDFARTRLAADVGKGAAQREFTGLGNCITKIFKSDGLRGLYQGFNVSVQGIIIYR 187
Query: 175 GAYFVTYETIKNFLADRSTSPSGEKKSVSMLSTIFAGGCAGIMYWVVGMPADVLKSR--L 232
AYF Y+T K L D P VS + AG+ V P D ++ R +
Sbjct: 188 AAYFGVYDTAKGMLPD----PKNVHIIVSWMIAQTVTAVAGL----VSYPFDTVRRRMMM 239
Query: 233 QTAPEGT--YPNGVRSVLSTTLRNEGPGALYKGAIPVFLR 270
Q+ +G G ++EGP A +KGA LR
Sbjct: 240 QSGRKGADIMYTGTVDCWRKIAKDEGPKAFFKGAWSNVLR 279
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 43/179 (24%), Positives = 78/179 (43%), Gaps = 14/179 (7%)
Query: 95 NNDKLAHWQYFVAGSFSGITTAAITAPGERIKCLLQIQSN----ETAKVYSGPVDVVRKL 150
++ L+ + F+AG + + AP ER+K LLQ+Q K Y G +D V ++
Sbjct: 1 SDQALSFLKDFLAGGVAAAISKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRI 60
Query: 151 VRQHGVTSVFKGLCATLLRDIPANGAYFVTYETIKN-FLADRSTSPSGEKKSVSMLSTIF 209
++ G S ++G A ++R P F + K FL + L++
Sbjct: 61 PKEQGFLSFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDRHKQFWRYFAGNLAS-- 118
Query: 210 AGGCAGIMYWVVGMPADVLKSRL-----QTAPEGTYPNGVRSVLSTTLRNEGPGALYKG 263
GG AG P D ++RL + A + + G+ + ++ +++G LY+G
Sbjct: 119 -GGAAGATSLCFVYPLDFARTRLAADVGKGAAQREF-TGLGNCITKIFKSDGLRGLYQG 175
>pdb|3UXQ|I Chain I, The Structure Of Thermorubin In Complex With The 70s
Ribosome From Thermus Thermophilus. This File Contains
The 50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3UXR|I Chain I, The Structure Of Thermorubin In Complex With The 70s
Ribosome From Thermus Thermophilus. This File Contains
The 50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes
Length = 148
Score = 31.2 bits (69), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 38/122 (31%), Positives = 54/122 (44%), Gaps = 19/122 (15%)
Query: 70 ITGVAPIFALSFLGYGAGKKVLTNENNDKLAHWQYFVAGSFSGITTAAITAPGERIKCLL 129
+ V P +A ++L G VL E+N K + A A ER+K +L
Sbjct: 18 VVDVKPGYARNYL-LPRGLAVLATESNLKALEARIRAQAK----RLAERKAEAERLKEIL 72
Query: 130 Q-------IQSNETAKVYSGPV---DVVRKLVRQHGVTSVFKGLCATLLRDIPANGAYFV 179
+ +++ ET K+Y G V D+ L RQHGVT K L L + I G Y +
Sbjct: 73 ENLTLTIPVRAGET-KIY-GSVTAKDIAEALSRQHGVTIEPKRLA--LEKPIKELGEYVL 128
Query: 180 TY 181
TY
Sbjct: 129 TY 130
>pdb|2HGJ|K Chain K, 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|K Chain K, 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|K Chain K, 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
Length = 148
Score = 30.8 bits (68), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 38/123 (30%), Positives = 55/123 (44%), Gaps = 19/123 (15%)
Query: 70 ITGVAPIFALSFLGYGAGKKVLTNENNDKLAHWQYFVAGSFSGITTAAITAPGERIKCLL 129
+ V P +A ++L G VL E+N K + A A ER+K +L
Sbjct: 18 VVDVKPGYARNYL-LPRGLAVLATESNLKALEARIRAQAK----RLAERKAEAERLKKIL 72
Query: 130 Q-------IQSNETAKVYSGPV---DVVRKLVRQHGVTSVFKGLCATLLRDIPANGAYFV 179
+ +++ ET K+Y G V D+ L RQHGVT K L L + I G Y +
Sbjct: 73 ENLTLTIPVRAGET-KIY-GSVTAKDIAEALSRQHGVTIDPKRLA--LEKPIKELGEYVL 128
Query: 180 TYE 182
TY+
Sbjct: 129 TYK 131
>pdb|3TVE|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Leu Complex
pdb|3TVH|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Leu Complex
Length = 146
Score = 30.8 bits (68), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 38/123 (30%), Positives = 55/123 (44%), Gaps = 19/123 (15%)
Query: 70 ITGVAPIFALSFLGYGAGKKVLTNENNDKLAHWQYFVAGSFSGITTAAITAPGERIKCLL 129
+ V P +A ++L G VL E+N K + A A ER+K +L
Sbjct: 18 VVDVKPGYARNYL-LPRGLAVLATESNLKALEARIRAQAK----RLAERKAEAERLKEIL 72
Query: 130 Q-------IQSNETAKVYSGPV---DVVRKLVRQHGVTSVFKGLCATLLRDIPANGAYFV 179
+ +++ ET K+Y G V D+ L RQHGVT K L L + I G Y +
Sbjct: 73 ENLTLTIPVRAGET-KIY-GSVTAKDIAEALSRQHGVTIDPKRLA--LEKPIKELGEYVL 128
Query: 180 TYE 182
TY+
Sbjct: 129 TYK 131
>pdb|2V47|I Chain I, 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|2V49|I Chain I, 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.
pdb|2WDI|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A-Site Trna,
Deacylated P-Site Trna, And E-Site Trna. This File
Contains The 50s Subunit For Molecule I.
pdb|2WDJ|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A-Site Trna,
Deacylated P-Site Trna, And E-Site Trna. This File
Contains The 50s Subunit For Molecule Ii.
pdb|2WDL|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A- And P-Site
Trnas, And E-Site Trna. This File Contains The 50s
Subunit For Molecule I.
pdb|2WDN|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome In
Complex With Mrna, Paromomycin, Acylated A- And P-Site
Trnas, And E-Site Trna. This File Contains The 50s
Subunit For Molecule Ii.
pdb|2WH2|I Chain I, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|3HUX|I Chain I, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 50s Subunit For Molecule I.
pdb|3HUZ|I Chain I, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 50s Subunit For Molecule Ii.
pdb|3KIR|I Chain I, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 2 Of 4)
pdb|3KIT|I Chain I, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 4 Of 4)
pdb|3KIW|I Chain I, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 2 Of 4)
pdb|3KIY|I Chain I, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 4 Of 4)
pdb|3KNI|I Chain I, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 50s Subunit For Molecule I
pdb|3KNK|I Chain I, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 50s Subunit For Molecule Ii.
pdb|3KNM|I Chain I, The Structures Of Capreomycin Bound To The 70s Ribosome.
Thi Contains The 50s Subunit For Molecule I.
pdb|3KNO|I Chain I, The Structures Of Capreomycin Bound To The 70s Ribosome.
Thi Contains The 50s Subunit For Molecule Ii
pdb|3I8F|K Chain K, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8f Contains 50s Ribosomal Subunit. The 30s
Ribosoma Can Be Found In Pdb Entry 3i8g. Molecule B In
The Same Asym Unit Is Deposited As 3i8g (30s) And 3i8f
(50s).
pdb|3I8I|K Chain K, Elongation Complex Of The 70s Ribosome With Three Trnas
And Entry 3i8i Contains 50s Ribosomal Subnit. The 30s
Ribosomal Can Be Found In Pdb Entry 3i8h. Molecule A In
The Same Asym Unit Is Deposited As 3i8f (50s) And 3i8g
(30s).
pdb|3I9C|K Chain K, Initiation Complex Of 70s Ribosome With Two Trnas And
Mrna. 3i9c Contains 50s Ribosomal Subunit Of Molecule B.
The 30s Subunit Can Be Found In Pdb Entry 3i9b. Molecule
A In The S Asymmetric Unit Is Deposited As 3i9d (30s)
And 3i9e (50s)
pdb|3I9E|K Chain K, Initiation Complex Of 70s Ribosome With Two Trnas And
Mrna. 3i9e Contains 50s Ribosomal Subunit Of Molecule A.
The 30s Subunit Can Be Found In Pdb Entry 3i9d. Molecule
B In The S Asymmetric Unit Is Deposited As 3i9b (30s)
And 3i9c (50s)
pdb|2X9S|I Chain I, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9U|I Chain I, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2XG0|I Chain I, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 2 Of 4)
pdb|2XG2|I Chain I, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 4 Of 4)
pdb|3OH5|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Chloramphenicol. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OH7|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Chloramphenicol. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OHJ|I Chain I, Structure Of The Thermus Thermophilus Ribosome Complexed
With Erythromycin. This File Contains The 50s Subunit Of
One 70s Ribosome. The Entire Crystal Structure Contains
Two 70s Ribosomes.
pdb|3OHK|I Chain I, Structure Of The Thermus Thermophilus Ribosome Complexed
With Erythromycin. This File Contains The 50s Subunit Of
One 70s Ribosome. The Entire Crystal Structure Contains
Two 70s Ribosomes.
pdb|3OHZ|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Azithromycin. This File Contains The 50s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI1|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Azithromycin. This File Contains The 50s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI3|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Telithromycin. This File Contains The 50s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3OI5|I Chain I, Structure Of The Thermus Thermophilus 70s Ribosome
Complexed With Telithromycin. This File Contains The 50s
Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes.
pdb|3UYE|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Leu Complex
pdb|3UYG|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Leu Complex
pdb|3UZ1|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Leu Complex With Paromomycin
pdb|3UZ2|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Leu Complex With Paromomycin.
pdb|3UZ8|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Tyr Complex.
pdb|3UZ9|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Cognate
Trna-Tyr Complex.
pdb|3UZF|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Tyr Complex
pdb|3UZH|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Tyr Complex.
pdb|3UZK|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The First
70s Molecule In The Asymmetric Unit For The Near-Cognate
Trna-Tyr Complex With Paromomycin
pdb|3UZN|K Chain K, Crystal Structure Analysis Of Ribosomal Decoding. This
Entry Contains The 50s Ribosomal Subunit Of The Second
70s Molecule In The Asymmetric Unit For The Near-cognate
Trna-tyr Complex With Paromomycin
pdb|4DHA|I Chain I, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|4DHC|I Chain I, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|3V23|I Chain I, Crystal Structure Of Rmf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 50s Subunit Of
The 1st Ribosome In The Asu
pdb|3V25|I Chain I, Crystal Structure Of Rmf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 50s Subunit Of
The 2nd Ribosome In The Asu
pdb|3V27|I Chain I, Crystal Structure Of Hpf Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 50s Subunit Of
The 1st Ribosome In The Asu
pdb|3V29|I Chain I, Crystal Structure Of Hpf Bound To The 70s Ribosome. This
Entry Contains The 50s Subunit Of The 2nd Molecule In
The Asu.
pdb|3V2D|I Chain I, Crystal Structure Of Yfia Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 50s Subunit Of
The 1st Ribosome In The Asu
pdb|3V2F|I Chain I, Crystal Structure Of Yfia Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 50s Subunit Of
The 2nd Ribosome In The Asu
pdb|2J01|I Chain I, 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|I Chain I, 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|4G5L|K Chain K, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 50s Subunit Of Molecule A.
pdb|4G5N|K Chain K, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 50s Subunit Of Molecule B.
pdb|4G5U|K Chain K, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 50s Subunit Of Molecule A.
pdb|4G5W|K Chain K, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 50s Subunit Of Molecule B
Length = 148
Score = 30.8 bits (68), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 38/122 (31%), Positives = 54/122 (44%), Gaps = 19/122 (15%)
Query: 70 ITGVAPIFALSFLGYGAGKKVLTNENNDKLAHWQYFVAGSFSGITTAAITAPGERIKCLL 129
+ V P +A ++L G VL E+N K + A A ER+K +L
Sbjct: 18 VVDVKPGYARNYL-LPRGLAVLATESNLKALEARIRAQAK----RLAERKAEAERLKEIL 72
Query: 130 Q-------IQSNETAKVYSGPV---DVVRKLVRQHGVTSVFKGLCATLLRDIPANGAYFV 179
+ +++ ET K+Y G V D+ L RQHGVT K L L + I G Y +
Sbjct: 73 ENLTLTIPVRAGET-KIY-GSVTAKDIAEALSRQHGVTIDPKRLA--LEKPIKELGEYVL 128
Query: 180 TY 181
TY
Sbjct: 129 TY 130
>pdb|3FIN|I Chain I, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas
And Ef- Tu.Gdp.Kirromycin Ternary Complex, Fitted To A
6.4 A Cryo-Em Map. This File Contains The 50s Subunit
Length = 146
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 38/123 (30%), Positives = 55/123 (44%), Gaps = 19/123 (15%)
Query: 70 ITGVAPIFALSFLGYGAGKKVLTNENNDKLAHWQYFVAGSFSGITTAAITAPGERIKCLL 129
+ V P +A ++L G VL E+N K + A A ER+K +L
Sbjct: 18 VVDVKPGYARNYL-LPRGLAVLATESNLKALEARIRAQAK----RLAERKAEAERLKEIL 72
Query: 130 Q-------IQSNETAKVYSGPV---DVVRKLVRQHGVTSVFKGLCATLLRDIPANGAYFV 179
+ +++ ET K+Y G V D+ L RQHGVT K L L + I G Y +
Sbjct: 73 ENLTLTIPVRAGET-KIY-GSVTAKDIAEALSRQHGVTIDPKRLA--LEKPIKELGEYVL 128
Query: 180 TYE 182
TY+
Sbjct: 129 TYK 131
>pdb|1VSA|G Chain G, 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|G Chain G, 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|3D5B|I Chain I, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 50s Subunit Of One 70s
Ribosome. The Entire Crystal Structure Contains Two 70s
Ribosomes As Described In Remark 400.
pdb|3D5D|I Chain I, Structural Basis For Translation Termination On The 70s
Ribosome. This File Contains The 50s Subunit Of The
Second 70s Ribosome. The Entire Crystal Structure
Contains Two 70s Ribosomes As Described In Remark 400.
pdb|3F1F|I Chain I, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
50s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Two 70s Ribosomes As Described In
Remark 400.
pdb|3F1H|I Chain I, Crystal Structure Of A Translation Termination Complex
Formed With Release Factor Rf2. This File Contains The
50s Subunit Of The Second 70s Ribosome. The Entire
Crystal Structure Contains Two 70s Ribosomes As
Described In Remark 400.
pdb|2WH4|I Chain I, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|3MRZ|H Chain H, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3mrz Contains 50s Ribosomal Subunit. The 30s
Ribosomal Subunit Can Be Found In Pdb Entry 3ms0.
Molecule A In The Same Asymmetric Unit Is Deposited As
3mr8 (50s) And 3ms1 (30s).
pdb|3MS1|H Chain H, Recognition Of The Amber Stop Codon By Release Factor Rf1.
This Entry 3ms1 Contains 50s Ribosomal Subunit. The 30s
Ribosomal Subunit Can Be Found In Pdb Entry 3mr8.
Molecule B In The Same Asymmetric Unit Is Deposited As
3mrz (50s) And 3ms0 (30s)
Length = 148
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 37/122 (30%), Positives = 54/122 (44%), Gaps = 19/122 (15%)
Query: 70 ITGVAPIFALSFLGYGAGKKVLTNENNDKLAHWQYFVAGSFSGITTAAITAPGERIKCLL 129
+ V P +A ++L G VL E+N K + A A ER+K +L
Sbjct: 18 VVDVKPGYARNYL-LPRGLAVLATESNLKALEARIRAQAK----RLAERKAEAERLKEIL 72
Query: 130 Q-------IQSNETAKVYSGPV---DVVRKLVRQHGVTSVFKGLCATLLRDIPANGAYFV 179
+ +++ ET K+Y G V D+ L RQHG+T K L L + I G Y +
Sbjct: 73 ENLTLTIPVRAGET-KIY-GSVTAKDIAEALSRQHGITIDPKRLA--LEKPIKELGEYVL 128
Query: 180 TY 181
TY
Sbjct: 129 TY 130
>pdb|3PYO|H Chain H, Crystal Structure Of A Complex Containing Domain 3 From
The Psiv Igr Ires Rna Bound To The 70s Ribosome. This
File Contains The 50s Subunit Of The First 70s Ribosome.
pdb|3PYR|H Chain H, Crystal Structure Of A Complex Containing Domain 3 From
The Psiv Igr Ires Rna Bound To The 70s Ribosome. This
File Contains The 50s Subunit Of The Second 70s
Ribosome.
pdb|3PYT|H Chain H, Crystal Structure Of A Complex Containing Domain 3 Of Crpv
Igr Ires Rna Bound To The 70s Ribosome. This File
Contains The 50s Subunit Of The First 70s Ribosome.
pdb|3PYV|H Chain H, Crystal Structure Of A Complex Containing Domain 3 Of Crpv
Igr Ires Rna Bound To The 70s Ribosome. This File
Contains The 50s Subunit Of The Second 70s Ribosome
Length = 145
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 37/123 (30%), Positives = 55/123 (44%), Gaps = 19/123 (15%)
Query: 70 ITGVAPIFALSFLGYGAGKKVLTNENNDKLAHWQYFVAGSFSGITTAAITAPGERIKCLL 129
+ V P +A ++L G VL E+N K + A A ER+K +L
Sbjct: 18 VVDVKPGYARNYL-LPRGLAVLATESNLKALEARIRAQAK----RLAERKAEAERLKEIL 72
Query: 130 Q-------IQSNETAKVYSGPV---DVVRKLVRQHGVTSVFKGLCATLLRDIPANGAYFV 179
+ +++ ET K+Y G V D+ L RQHG+T K L L + I G Y +
Sbjct: 73 ENLTLTIPVRAGET-KIY-GSVTAKDIAEALSRQHGITIDPKRLA--LEKPIKELGEYVL 128
Query: 180 TYE 182
TY+
Sbjct: 129 TYK 131
>pdb|2YEE|A Chain A, Hsp90 Inhibitors And Drugs From Fragment And Virtual
Screening
Length = 252
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 7/79 (8%)
Query: 90 VLTNENNDKLAHWQYFVAGSFSGITTAAITAPGERIKCLLQIQSNETAKVYSGPVDVVRK 149
V+T N+D+ W+ GSF+ + T G K +L ++ ++T + +++
Sbjct: 166 VITKHNDDEQYAWESSAGGSFT-VRTDTGEPMGRGTKVILHLKEDQTEYLEERR---IKE 221
Query: 150 LVRQHGVTSVFKGLCATLL 168
+V++H S F+G TL
Sbjct: 222 IVKKH---SQFQGYPITLF 237
>pdb|2A5L|A Chain A, The Crystal Structure Of The Trp Repressor Binding Protein
Wrba From Pseudomonas Aeruginosa
pdb|2A5L|B Chain B, The Crystal Structure Of The Trp Repressor Binding Protein
Wrba From Pseudomonas Aeruginosa
Length = 200
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 29/71 (40%), Gaps = 7/71 (9%)
Query: 164 CATLLRDIPANGAYFVTYETIKNFLADRSTSPSGEKKSVSMLSTIFAGGCAGIMYW---- 219
C + DIPA GA + T E +KN SP+ S L G + W
Sbjct: 49 CEAVAPDIPAEGALYATLEDLKNCAGLALGSPTRFGNXASPLKYFLDGTSS---LWLTGS 105
Query: 220 VVGMPADVLKS 230
+VG PA V S
Sbjct: 106 LVGKPAAVFTS 116
>pdb|1ZWK|A Chain A, Structure Of Wrba From Pseudomonas Aeruginosa
pdb|1ZWK|B Chain B, Structure Of Wrba From Pseudomonas Aeruginosa
pdb|1ZWL|A Chain A, Structure Of Wrba From Pseudomonas Aeruginosa In Complex
With Fmn
Length = 207
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 29/71 (40%), Gaps = 7/71 (9%)
Query: 164 CATLLRDIPANGAYFVTYETIKNFLADRSTSPSGEKKSVSMLSTIFAGGCAGIMYW---- 219
C + DIPA GA + T E +KN SP+ S L G + W
Sbjct: 56 CEAVAPDIPAEGALYATLEDLKNCAGLALGSPTRFGNMASPLKYFLDGTSS---LWLTGS 112
Query: 220 VVGMPADVLKS 230
+VG PA V S
Sbjct: 113 LVGKPAAVFTS 123
>pdb|2XAA|A Chain A, Alcohol Dehydrogenase Adh-'a' From Rhodococcus Ruber Dsm
44541 At Ph 8.5 In Complex With Nad And Butane-1,4-Diol
pdb|2XAA|B Chain B, Alcohol Dehydrogenase Adh-'a' From Rhodococcus Ruber Dsm
44541 At Ph 8.5 In Complex With Nad And Butane-1,4-Diol
pdb|2XAA|C Chain C, Alcohol Dehydrogenase Adh-'a' From Rhodococcus Ruber Dsm
44541 At Ph 8.5 In Complex With Nad And Butane-1,4-Diol
pdb|2XAA|D Chain D, Alcohol Dehydrogenase Adh-'a' From Rhodococcus Ruber Dsm
44541 At Ph 8.5 In Complex With Nad And Butane-1,4-Diol
pdb|3JV7|A Chain A, Structure Of Adh-A From Rhodococcus Ruber
pdb|3JV7|B Chain B, Structure Of Adh-A From Rhodococcus Ruber
pdb|3JV7|C Chain C, Structure Of Adh-A From Rhodococcus Ruber
pdb|3JV7|D Chain D, Structure Of Adh-A From Rhodococcus Ruber
Length = 345
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 9/100 (9%)
Query: 68 APIT--GVAPIFALS----FLGYGAGKKVLTNENNDKLAHWQYFVAGSFSGITTAAITAP 121
AP+T G+ P A+S LG G+ V+ L H + + S A+
Sbjct: 149 APLTDAGLTPYHAISRVLPLLGPGSTAVVI---GVGGLGHVGIQILRAVSAARVIAVDLD 205
Query: 122 GERIKCLLQIQSNETAKVYSGPVDVVRKLVRQHGVTSVFK 161
+R+ ++ ++ K +G D +R+L G T+VF
Sbjct: 206 DDRLALAREVGADAAVKSGAGAADAIRELTGGQGATAVFD 245
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
0.320 0.136 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,271,133
Number of Sequences: 62578
Number of extensions: 333354
Number of successful extensions: 657
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 638
Number of HSP's gapped (non-prelim): 16
length of query: 293
length of database: 14,973,337
effective HSP length: 98
effective length of query: 195
effective length of database: 8,840,693
effective search space: 1723935135
effective search space used: 1723935135
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: 51 (24.3 bits)