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= 030388
(178 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TVE|4 Chain 4, 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
Length = 66
Score = 29.6 bits (65), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 110 MKKGLHPQMQWISYVTQSGRLMHVMMTK----IHNVGKVYHFRARRQ-MAQSIGQVAKFR 164
MK+G+HP++ + G ++ TK + K + F +Q + G+V +F+
Sbjct: 1 MKEGIHPKLVPARIICGCGNVIETYSTKPEIYVEVCSKCHPFYTGQQRFVDTEGRVERFQ 60
Query: 165 RRY 167
RRY
Sbjct: 61 RRY 63
>pdb|3TVH|4 Chain 4, 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 = 63
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 110 MKKGLHPQMQWISYVTQSGRLMHVMMTK----IHNVGKVYHFRARRQ-MAQSIGQVAKFR 164
MK+G+HP++ + G ++ TK + K + F +Q + G+V +F+
Sbjct: 1 MKEGIHPKLVPARIICGCGNVIETYSTKPEIYVEVCSKCHPFYTGQQRFVDTEGRVERFQ 60
Query: 165 RRY 167
RRY
Sbjct: 61 RRY 63
>pdb|2J01|4 Chain 4, 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|4 Chain 4, 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|2HGJ|3 Chain 3, 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|3 Chain 3, 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|3 Chain 3, 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|2V47|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|3HUX|4 Chain 4, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 50s Subunit For Molecule I.
pdb|3HUZ|4 Chain 4, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 50s Subunit For Molecule Ii.
pdb|2WRJ|4 Chain 4, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State (Part 2 Of 4).
pdb|2WRL|4 Chain 4, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State. (Part 4 Of
4).
pdb|2WRO|4 Chain 4, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 2 Of 4).
pdb|2WRR|4 Chain 4, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 4 Of 4).
pdb|3KIR|4 Chain 4, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 2 Of 4)
pdb|3KIT|4 Chain 4, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 4 Of 4)
pdb|3KIW|4 Chain 4, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 2 Of 4)
pdb|3KIY|4 Chain 4, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 4 Of 4)
pdb|3KNI|4 Chain 4, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 50s Subunit For Molecule I
pdb|3KNK|4 Chain 4, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 50s Subunit For Molecule Ii.
pdb|3KNM|4 Chain 4, The Structures Of Capreomycin Bound To The 70s Ribosome.
Thi Contains The 50s Subunit For Molecule I.
pdb|3KNO|4 Chain 4, The Structures Of Capreomycin Bound To The 70s Ribosome.
Thi Contains The 50s Subunit For Molecule Ii
pdb|3I8F|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9U|4 Chain 4, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|3MRZ|1 Chain 1, 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|1 Chain 1, 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).
pdb|2XG0|4 Chain 4, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 2 Of 4)
pdb|2XG2|4 Chain 4, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 4 Of 4)
pdb|3OH5|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|2XQE|4 Chain 4, The Structure Of Ef-Tu And Aminoacyl-Trna Bound To The 70s
Ribosome With A Gtp Analog
pdb|2XTG|4 Chain 4, Trna Tranlocation On The 70s Ribosome: The Pre-
Translocational Translocation Intermediate Ti(Pre)
pdb|2XUX|4 Chain 4, Trna Translocation On The 70s Ribosome: The Post-
Translocational Translocation Intermediate Ti(Post)
pdb|2Y0V|4 Chain 4, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0X|4 Chain 4, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0Z|4 Chain 4, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y11|4 Chain 4, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome.
pdb|2Y13|4 Chain 4, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y15|4 Chain 4, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Cognate Codon On The 70s Ribosome.
pdb|2Y17|4 Chain 4, Ef-Tu Complex 3
pdb|2Y19|4 Chain 4, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome.
pdb|3ZVP|4 Chain 4, Crystal Structure Of The Hybrid State Of Ribosome In
Complex With The Guanosine Triphosphatase Release Factor
3
pdb|3UXQ|4 Chain 4, 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|4 Chain 4, 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|3UYE|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4ABS|4 Chain 4, Complex Of Smpb, A Tmrna Fragment And Ef-Tu-Gdp-Kirromycin
With The 70s Ribosome
pdb|4DHA|4 Chain 4, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|4DHC|4 Chain 4, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|3V23|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, 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|4 Chain 4, Crystal Structure Of Hpf Bound To The 70s Ribosome. This
Entry Contains The 50s Subunit Of The 2nd Molecule In
The Asu.
pdb|3V2D|4 Chain 4, 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|4 Chain 4, 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|4G5L|4 Chain 4, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 50s Subunit Of Molecule A.
pdb|4G5N|4 Chain 4, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 50s Subunit Of Molecule B.
pdb|4G5U|4 Chain 4, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 50s Subunit Of Molecule A.
pdb|4G5W|4 Chain 4, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 50s Subunit Of Molecule B
Length = 71
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 110 MKKGLHPQMQWISYVTQSGRLMHVMMTK----IHNVGKVYHFRARRQ-MAQSIGQVAKFR 164
MK+G+HP++ + G ++ TK + K + F +Q + G+V +F+
Sbjct: 1 MKEGIHPKLVPARIICGCGNVIETYSTKPEIYVEVCSKCHPFYTGQQRFVDTEGRVERFQ 60
Query: 165 RRY 167
RRY
Sbjct: 61 RRY 63
>pdb|2W0M|A Chain A, Crystal Structure Of Sso2452 From Sulfolobus Solfataricus
P2
Length = 235
Score = 26.9 bits (58), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 86 HVRSSLKTFRQRLRNSVLGHY--LEKMKKGLHPQMQW-ISYVTQSGRLM 131
HV + FR+ +RN L Y +EKM++ H + W I V G ++
Sbjct: 181 HVADGIIRFRRMIRNGELHRYILIEKMRQTDHDKHVWEIDIVNGKGIVL 229
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 0.133 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,240,538
Number of Sequences: 62578
Number of extensions: 196628
Number of successful extensions: 368
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 367
Number of HSP's gapped (non-prelim): 5
length of query: 178
length of database: 14,973,337
effective HSP length: 92
effective length of query: 86
effective length of database: 9,216,161
effective search space: 792589846
effective search space used: 792589846
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)