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= 046577
(878 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2O6Q|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors A29
Length = 270
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 39/116 (33%), Positives = 55/116 (47%), Gaps = 6/116 (5%)
Query: 245 VSIPENFFVGMRKLKVVDFTGMQLFSLPS-SIDLLVKLKTLCLDESILRDIDIAIIGKLE 303
+IP N +KL D +L SLPS + L KL+ L L+++ L+ + I +L+
Sbjct: 29 TAIPSNIPADTKKL---DLQSNKLSSLPSKAFHRLTKLRLLYLNDNKLQTLPAGIFKELK 85
Query: 304 NLEILSFVRSDTVQLP-KALGQLTKLRLLDLTDCFHLKVIAPNVISSLIRLEELYM 358
NLE L + LP QL L L L D LK + P V SL +L L +
Sbjct: 86 NLETLWVTDNKLQALPIGVFDQLVNLAELRL-DRNQLKSLPPRVFDSLTKLTYLSL 140
>pdb|3M18|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R2.1 In Complex With Hen Egg Lysozyme
Length = 251
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 46/91 (50%), Gaps = 2/91 (2%)
Query: 245 VSIPENFFVGMRKLKVVDFTGMQLFSLPSSI-DLLVKLKTLCLDESILRDIDIAIIGKLE 303
S+P F + +L + G QL SLPS + D L KLK L L+ + L+ I KL
Sbjct: 96 ASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFDKLT 155
Query: 304 NLEILSFVRSDTVQLP-KALGQLTKLRLLDL 333
NL+ LS + +P A +L KL+ + L
Sbjct: 156 NLQTLSLSTNQLQSVPHGAFDRLGKLQTITL 186
>pdb|3M19|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R5.1
pdb|3M19|B Chain B, Crystal Structure Of Variable Lymphocyte Receptor
Vlra.R5.1
Length = 251
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 32/91 (35%), Positives = 46/91 (50%), Gaps = 2/91 (2%)
Query: 245 VSIPENFFVGMRKLKVVDFTGMQLFSLPSSI-DLLVKLKTLCLDESILRDIDIAIIGKLE 303
S+P F + +L + G QL SLPS + D L KLK L L+ + L+ I KL
Sbjct: 96 ASLPLGVFDHLTQLDKLYLGGNQLKSLPSGVFDRLTKLKELRLNTNQLQSIPAGAFDKLT 155
Query: 304 NLEILSFVRSDTVQLP-KALGQLTKLRLLDL 333
NL+ LS + +P A +L KL+ + L
Sbjct: 156 NLQTLSLSTNQLQSVPHGAFDRLGKLQTITL 186
>pdb|3ZYJ|A Chain A, Netring1 In Complex With Ngl1
pdb|3ZYJ|C Chain C, Netring1 In Complex With Ngl1
Length = 440
Score = 37.7 bits (86), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 37/122 (30%), Positives = 56/122 (45%), Gaps = 4/122 (3%)
Query: 245 VSIPENFFVGMRKLKVVDFTGMQLFSLPS-SIDLLVKLKTLCLDE-SILRDIDIAIIGKL 302
+IP FV + KLK + + S+PS + + + L+ L L E L I L
Sbjct: 125 TTIPNGAFVYLSKLKELWLRNNPIESIPSYAFNRIPSLRRLDLGELKRLSYISEGAFEGL 184
Query: 303 ENLEILSFVRSDTVQLPKALGQLTKLRLLDLTDCFHLKVIAPNVISSLIRLEELYMCNCS 362
NL L+ + ++P L L KL LDL+ HL I P L+ L++L+M
Sbjct: 185 SNLRYLNLAMCNLREIPN-LTPLIKLDELDLSG-NHLSAIRPGSFQGLMHLQKLWMIQSQ 242
Query: 363 IE 364
I+
Sbjct: 243 IQ 244
Score = 30.4 bits (67), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 45/91 (49%), Gaps = 8/91 (8%)
Query: 430 LDTSTLLFNEKVALPNLEALEISEINVDKIWHYNQ----IPAAVFPHFQSLTRLIVWRCH 485
L+T L N +PN + +S++ ++W N IP+ F SL RL +
Sbjct: 114 LNTLELFDNRLTTIPNGAFVYLSKL--KELWLRNNPIESIPSYAFNRIPSLRRLDLGELK 171
Query: 486 KLKYIFSASMIGSLKQLQHLDIRDCKDLQEI 516
+L YI + G L L++L++ C +L+EI
Sbjct: 172 RLSYISEGAFEG-LSNLRYLNLAMC-NLREI 200
>pdb|1VSA|H Chain H, 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|3D5B|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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
Length = 163
Score = 35.8 bits (81), Expect = 0.12, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 544 KLRCLYPGMHTPEW---LAL-EMLFVYRCDKLKIFAADLLQKNENDQLGIPVQQPPLPLE 599
K+ L G H P+W +A+ + + V DK+++ L QK G P +PLE
Sbjct: 52 KIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLE 111
Query: 600 KILPNLTELSLSGKDAKMILQADFPQHLFGSLK 632
K+L E L M+ + + LF LK
Sbjct: 112 KMLATHPERVLEHAVKGMLPKGPLGRRLFKRLK 144
>pdb|2J01|N Chain N, 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|N Chain N, 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|M Chain M, 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|M Chain M, 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|M Chain M, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|2WH4|N Chain N, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|3HUX|N Chain N, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 50s Subunit For Molecule I.
pdb|3HUZ|N Chain N, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 50s Subunit For Molecule Ii.
pdb|2WRJ|N Chain N, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State (Part 2 Of 4).
pdb|2WRL|N Chain N, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State. (Part 4 Of
4).
pdb|2WRO|N Chain N, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 2 Of 4).
pdb|2WRR|N Chain N, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 4 Of 4).
pdb|3KIR|N Chain N, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 2 Of 4)
pdb|3KIT|N Chain N, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 4 Of 4)
pdb|3KIW|N Chain N, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 2 Of 4)
pdb|3KIY|N Chain N, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 4 Of 4)
pdb|3KNI|N Chain N, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 50s Subunit For Molecule I
pdb|3KNK|N Chain N, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 50s Subunit For Molecule Ii.
pdb|3KNM|N Chain N, The Structures Of Capreomycin Bound To The 70s Ribosome.
Thi Contains The 50s Subunit For Molecule I.
pdb|3KNO|N Chain N, The Structures Of Capreomycin Bound To The 70s Ribosome.
Thi Contains The 50s Subunit For Molecule Ii
pdb|3I8F|M Chain M, 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|M Chain M, 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|M Chain M, 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|M Chain M, 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|N Chain N, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9U|N Chain N, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2XG0|N Chain N, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 2 Of 4)
pdb|2XG2|N Chain N, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 4 Of 4)
pdb|3OH5|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, The Structure Of Ef-Tu And Aminoacyl-Trna Bound To The 70s
Ribosome With A Gtp Analog
pdb|2XTG|N Chain N, Trna Tranlocation On The 70s Ribosome: The Pre-
Translocational Translocation Intermediate Ti(Pre)
pdb|2XUX|N Chain N, Trna Translocation On The 70s Ribosome: The Post-
Translocational Translocation Intermediate Ti(Post)
pdb|2Y0V|N Chain N, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0X|N Chain N, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0Z|N Chain N, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y11|N Chain N, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome.
pdb|2Y13|N Chain N, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y15|N Chain N, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Cognate Codon On The 70s Ribosome.
pdb|2Y17|N Chain N, Ef-Tu Complex 3
pdb|2Y19|N Chain N, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome.
pdb|3ZVP|N Chain N, Crystal Structure Of The Hybrid State Of Ribosome In
Complex With The Guanosine Triphosphatase Release Factor
3
pdb|3UXQ|N Chain N, 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|N Chain N, 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|M Chain M, 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|M Chain M, 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|M Chain M, 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|M Chain M, 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|M Chain M, 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|M Chain M, 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|M Chain M, 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|M Chain M, 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|M Chain M, 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|M Chain M, 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|N Chain N, Complex Of Smpb, A Tmrna Fragment And Ef-Tu-Gdp-Kirromycin
With The 70s Ribosome
pdb|4DHA|N Chain N, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|4DHC|N Chain N, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|3V23|N Chain N, 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|N Chain N, 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|N Chain N, 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|N Chain N, Crystal Structure Of Hpf Bound To The 70s Ribosome. This
Entry Contains The 50s Subunit Of The 2nd Molecule In
The Asu.
pdb|3V2D|N Chain N, 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|N Chain N, 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|M Chain M, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 50s Subunit Of Molecule A.
pdb|4G5N|M Chain M, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 50s Subunit Of Molecule B.
pdb|4G5U|M Chain M, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 50s Subunit Of Molecule A.
pdb|4G5W|M Chain M, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 50s Subunit Of Molecule B
Length = 140
Score = 35.8 bits (81), Expect = 0.12, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 544 KLRCLYPGMHTPEW---LAL-EMLFVYRCDKLKIFAADLLQKNENDQLGIPVQQPPLPLE 599
K+ L G H P+W +A+ + + V DK+++ L QK G P +PLE
Sbjct: 29 KIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLE 88
Query: 600 KILPNLTELSLSGKDAKMILQADFPQHLFGSLK 632
K+L E L M+ + + LF LK
Sbjct: 89 KMLATHPERVLEHAVKGMLPKGPLGRRLFKRLK 121
>pdb|3TVE|M Chain M, 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|M Chain M, 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 = 138
Score = 35.8 bits (81), Expect = 0.12, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 544 KLRCLYPGMHTPEW---LAL-EMLFVYRCDKLKIFAADLLQKNENDQLGIPVQQPPLPLE 599
K+ L G H P+W +A+ + + V DK+++ L QK G P +PLE
Sbjct: 29 KIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLE 88
Query: 600 KILPNLTELSLSGKDAKMILQADFPQHLFGSLK 632
K+L E L M+ + + LF LK
Sbjct: 89 KMLATHPERVLEHAVKGMLPKGPLGRRLFKRLK 121
>pdb|3PYO|J Chain J, 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|J Chain J, 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|J Chain J, 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|J Chain J, 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 = 137
Score = 35.8 bits (81), Expect = 0.12, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 544 KLRCLYPGMHTPEW---LAL-EMLFVYRCDKLKIFAADLLQKNENDQLGIPVQQPPLPLE 599
K+ L G H P+W +A+ + + V DK+++ L QK G P +PLE
Sbjct: 28 KIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLE 87
Query: 600 KILPNLTELSLSGKDAKMILQADFPQHLFGSLK 632
K+L E L M+ + + LF LK
Sbjct: 88 KMLATHPERVLEHAVKGMLPKGPLGRRLFKRLK 120
>pdb|3MRZ|J Chain J, 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|J Chain J, 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 = 139
Score = 35.8 bits (81), Expect = 0.12, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 544 KLRCLYPGMHTPEW---LAL-EMLFVYRCDKLKIFAADLLQKNENDQLGIPVQQPPLPLE 599
K+ L G H P+W +A+ + + V DK+++ L QK G P +PLE
Sbjct: 28 KIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLE 87
Query: 600 KILPNLTELSLSGKDAKMILQADFPQHLFGSLK 632
K+L E L M+ + + LF LK
Sbjct: 88 KMLATHPERVLEHAVKGMLPKGPLGRRLFKRLK 120
>pdb|3FIN|N Chain N, 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 = 139
Score = 35.8 bits (81), Expect = 0.12, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 544 KLRCLYPGMHTPEW---LAL-EMLFVYRCDKLKIFAADLLQKNENDQLGIPVQQPPLPLE 599
K+ L G H P+W +A+ + + V DK+++ L QK G P +PLE
Sbjct: 29 KIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLE 88
Query: 600 KILPNLTELSLSGKDAKMILQADFPQHLFGSLK 632
K+L E L M+ + + LF LK
Sbjct: 89 KMLATHPERVLEHAVKGMLPKGPLGRRLFKRLK 121
>pdb|1VSP|H Chain H, 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
Length = 140
Score = 35.8 bits (81), Expect = 0.12, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 544 KLRCLYPGMHTPEW---LAL-EMLFVYRCDKLKIFAADLLQKNENDQLGIPVQQPPLPLE 599
K+ L G H P+W +A+ + + V DK+++ L QK G P +PLE
Sbjct: 29 KIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIYTRYSGYPGGLKKIPLE 88
Query: 600 KILPNLTELSLSGKDAKMILQADFPQHLFGSLK 632
K+L E L M+ + + LF LK
Sbjct: 89 KMLATHPERVLEHAVKGMLPKGPLGRRLFKRLK 121
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 278 LVKLKTLCLDESILRDIDIAIIGKLENLEILSFVRSDTVQLPKALGQLTKLRLLDLTDCF 337
LV L++L L+ + +R + A I L+NL+ L S L A+ L KL LDL C
Sbjct: 182 LVNLQSLRLEWTGIRSLP-ASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCT 240
Query: 338 HLKVIAPNVISSLIRLEELYMCNCS 362
L+ P + L+ L + +CS
Sbjct: 241 ALRNYPP-IFGGRAPLKRLILKDCS 264
>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
Rbc36 In Complex With H-Trisaccharide
Length = 229
Score = 33.9 bits (76), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 43/187 (22%), Positives = 66/187 (35%), Gaps = 44/187 (23%)
Query: 223 PNALECPQLEFLCMSPEDSSLEVSIPENFFVGMRKLKVVDFTGMQLFSL-PSSIDLLVKL 281
P+ C C S +S+ IP N +++ Q+ L P D L+ L
Sbjct: 14 PSQCSCSGTTVDCRSKRHASVPAGIPTN-------AQILYLHDNQITKLEPGVFDSLINL 66
Query: 282 KTLCLDESILRDIDIAIIGKLENLEILSFVRSDTVQLPKALGQLTKLRLLDLTDCFHLKV 341
K L L + L + + + L L +L + LP A
Sbjct: 67 KELYLGSNQLGALPVGVFDSLTQLTVLDLGTNQLTVLPSA-------------------- 106
Query: 342 IAPNVISSLIRLEELYMCNCSIEWEVERANSKRSNASLDELMHLRWLTTLEIDVKNESML 401
V L+ L+EL+MC C+ E+ R ++ L H LT L +D +
Sbjct: 107 ----VFDRLVHLKELFMC-CNKLTELPRG--------IERLTH---LTHLALDQNQLKSI 150
Query: 402 PAGFLAR 408
P G R
Sbjct: 151 PHGAFDR 157
>pdb|3RFJ|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 279
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 246 SIPENFFVGMRKLKVVDFTGMQLFSLPSSI-DLLVKLKTLCLDESILRDIDIAIIGKLEN 304
S+P+ F + L +D QL SLP + D L +LK L L+++ L+ + + +L +
Sbjct: 147 SLPKGVFDKLTNLTRLDLDNNQLQSLPEGVFDKLTQLKQLSLNDNQLKSVPDGVFDRLTS 206
Query: 305 L 305
L
Sbjct: 207 L 207
>pdb|1PUT|A Chain A, An Nmr-Derived Model For The Solution Structure Of
Oxidized Putidaredoxin, A 2fe, 2-S Ferredoxin From
Pseudomonas
Length = 106
Score = 32.0 bits (71), Expect = 1.5, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 9/80 (11%)
Query: 171 MHDVVRDVARSIACRDQHVFVVENEDVWELPDKESLKKCYAISIRYCCIHEL-PNALECP 229
++D+V D S +C HV+V E DK I + C EL PN+ C
Sbjct: 32 IYDIVGDCGGSASCATCHVYVNE-----AFTDKVPAANEREIGMLECVTAELKPNSRLCC 86
Query: 230 QLEFLCMSPEDSSLEVSIPE 249
Q + M+PE + V +P+
Sbjct: 87 Q---IIMTPELDGIVVDVPD 103
>pdb|1PDX|A Chain A, Putidaredoxin
pdb|1YJI|A Chain A, Rdc-Refined Solution Nmr Structure Of Reduced
Putidaredoxin
pdb|1YJJ|A Chain A, Rdc-Refined Solution Nmr Structure Of Oxidized
Putidaredoxin
Length = 106
Score = 32.0 bits (71), Expect = 1.5, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 9/80 (11%)
Query: 171 MHDVVRDVARSIACRDQHVFVVENEDVWELPDKESLKKCYAISIRYCCIHEL-PNALECP 229
++D+V D S +C HV+V E DK I + C EL PN+ C
Sbjct: 32 IYDIVGDCGGSASCATCHVYVNE-----AFTDKVPAANEREIGMLECVTAELKPNSRLCC 86
Query: 230 QLEFLCMSPEDSSLEVSIPE 249
Q + M+PE + V +P+
Sbjct: 87 Q---IIMTPELDGIVVDVPD 103
>pdb|2O6S|A Chain A, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
pdb|2O6S|B Chain B, Structural Diversity Of The Hagfish Variable Lymphocyte
Receptors B59
Length = 208
Score = 30.4 bits (67), Expect = 4.3, Method: Composition-based stats.
Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 219 IHELPNAL--ECPQLEFLCMSPEDSSLEVSIPENFFVGMRKLKVVDFTGMQLFSLPSSI- 275
+ LPN + + L +L +S S+P F + +LK + QL SLP +
Sbjct: 64 LQSLPNGVFNKLTSLTYLNLSTNQLQ---SLPNGVFDKLTQLKELALNTNQLQSLPDGVF 120
Query: 276 DLLVKLKTLCLDESILRDIDIAIIGKLENLEIL 308
D L +LK L L ++ L+ + + +L +L+ +
Sbjct: 121 DKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYI 153
>pdb|2OMX|A Chain A, Crystal Structure Of Inla S192n G194s+sHEC1 COMPLEX
Length = 462
Score = 30.4 bits (67), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 36/112 (32%), Positives = 54/112 (48%), Gaps = 9/112 (8%)
Query: 254 GMRKLKVVDFTGMQLFSLPSSIDLLVKLKTL-CLDESILRDIDIAIIGKLENLEILSFVR 312
G+ L+ ++F+ Q+ L L L TL LD S + DI+++ KL NLE L
Sbjct: 149 GLTSLQQLNFSSNQVTDLKP----LANLTTLERLDISSNKVSDISVLAKLTNLESL-IAT 203
Query: 313 SDTVQLPKALGQLTKLRLLDLTDCFHLKVIAPNVISSLIRLEELYMCNCSIE 364
++ + LG LT L L L + LK I ++SL L +L + N I
Sbjct: 204 NNQISDITPLGILTNLDELSL-NGNQLKDIG--TLASLTNLTDLDLANNQIS 252
>pdb|3ZYO|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
And Immunoglobulin Domain Of Netrin-G Ligand-3
Length = 411
Score = 30.0 bits (66), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 36/126 (28%), Positives = 58/126 (46%), Gaps = 20/126 (15%)
Query: 429 TLDTSTLLFNEKVALPNLEALEISEINVDKIWHYNQ----IPAAVFPHFQSLTRLIVWRC 484
+L+T L N +P +S++ ++W N IP+ F SL RL +
Sbjct: 84 SLNTLELFDNRLTTVPTQAFEYLSKLR--ELWLRNNPIESIPSYAFNRVPSLRRLDLGEL 141
Query: 485 HKLKYIFSASMIGSLKQLQHLDIRDC--KDLQEI----------ISENRADQVIPYFVFP 532
+L+YI A+ G L L++L++ C KD+ + +S NR D + P F
Sbjct: 142 KRLEYISEAAFEG-LVNLRYLNLGMCNLKDIPNLTALVRLEELELSGNRLDLIRP-GSFQ 199
Query: 533 QLTTLR 538
LT+LR
Sbjct: 200 GLTSLR 205
>pdb|3ZYN|A Chain A, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
pdb|3ZYN|B Chain B, Crystal Structure Of The N-Terminal Leucine Rich Repeats
Of Netrin-G Ligand-3
Length = 321
Score = 30.0 bits (66), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 36/126 (28%), Positives = 58/126 (46%), Gaps = 20/126 (15%)
Query: 429 TLDTSTLLFNEKVALPNLEALEISEINVDKIWHYNQ----IPAAVFPHFQSLTRLIVWRC 484
+L+T L N +P +S++ ++W N IP+ F SL RL +
Sbjct: 84 SLNTLELFDNRLTTVPTQAFEYLSKLR--ELWLRNNPIESIPSYAFNRVPSLRRLDLGEL 141
Query: 485 HKLKYIFSASMIGSLKQLQHLDIRDC--KDLQEI----------ISENRADQVIPYFVFP 532
+L+YI A+ G L L++L++ C KD+ + +S NR D + P F
Sbjct: 142 KRLEYISEAAFEG-LVNLRYLNLGMCNLKDIPNLTALVRLEELELSGNRLDLIRP-GSFQ 199
Query: 533 QLTTLR 538
LT+LR
Sbjct: 200 GLTSLR 205
>pdb|3RFS|A Chain A, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
pdb|3RFS|B Chain B, Design Of A Binding Scaffold Based On Variable Lymphocyte
Receptors Of Jawless Vertebrates By Module Engineering
Length = 272
Score = 30.0 bits (66), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 246 SIPENFFVGMRKLKVVDFTGMQLFSLPSSI-DLLVKLKTLCLDESILRDIDIAIIGKLEN 304
S+P+ F + L +D + QL SLP + D L +LK L L ++ L+ + + +L +
Sbjct: 147 SLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTS 206
Query: 305 LEIL 308
L+ +
Sbjct: 207 LQYI 210
>pdb|2OMT|A Chain A, Crystal Structure Of Inla G194s+sHEC1 COMPLEX
Length = 462
Score = 29.6 bits (65), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 36/112 (32%), Positives = 53/112 (47%), Gaps = 9/112 (8%)
Query: 254 GMRKLKVVDFTGMQLFSLPSSIDLLVKLKTL-CLDESILRDIDIAIIGKLENLEILSFVR 312
G+ L+ + F+ Q+ L L L TL LD S + DI+++ KL NLE L
Sbjct: 149 GLTSLQQLSFSSNQVTDLKP----LANLTTLERLDISSNKVSDISVLAKLTNLESL-IAT 203
Query: 313 SDTVQLPKALGQLTKLRLLDLTDCFHLKVIAPNVISSLIRLEELYMCNCSIE 364
++ + LG LT L L L + LK I ++SL L +L + N I
Sbjct: 204 NNQISDITPLGILTNLDELSL-NGNQLKDIG--TLASLTNLTDLDLANNQIS 252
>pdb|3A79|B Chain B, Crystal Structure Of Tlr2-Tlr6-Pam2csk4 Complex
Length = 562
Score = 29.6 bits (65), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 49/188 (26%), Positives = 93/188 (49%), Gaps = 24/188 (12%)
Query: 229 PQLEFLCMSPEDSSLEVSIPENFFVGMRKLKVVDFTGMQLFSLPSSIDLLVK-LKTLCLD 287
P+ + L +S ++S E+ +P+ F+ +L+V+ + ++ SL + L + L+ L +
Sbjct: 52 PRTKALSLS-QNSISELRMPDISFLS--ELRVLRLSHNRIRSLDFHVFLFNQDLEYLDVS 108
Query: 288 ESILRDIDIAIIGKLENLEILSFVRSDTVQLPKALGQLTKLRLLDLTDC----------- 336
+ L++I + L +L+ LSF D + + K G LTKL L L+
Sbjct: 109 HNRLQNISCCPMASLRHLD-LSFNDFDVLPVCKEFGNLTKLTFLGLSAAKFRQLDLLPVA 167
Query: 337 -FHLKVIAPNVISSLIR---LEELYMCNCSIEWEVERANSKRS---NASLDELMHLRWLT 389
HL I +++S I+ E L + N ++ V NS S N S++ L HL+ L+
Sbjct: 168 HLHLSCILLDLVSYHIKGGETESLQIPNTTVLHLVFHPNSLFSVQVNMSVNALGHLQ-LS 226
Query: 390 TLEIDVKN 397
++++ +N
Sbjct: 227 NIKLNDEN 234
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
0.322 0.137 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,421,501
Number of Sequences: 62578
Number of extensions: 985428
Number of successful extensions: 2239
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 40
Number of HSP's that attempted gapping in prelim test: 2211
Number of HSP's gapped (non-prelim): 69
length of query: 878
length of database: 14,973,337
effective HSP length: 107
effective length of query: 771
effective length of database: 8,277,491
effective search space: 6381945561
effective search space used: 6381945561
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: 56 (26.2 bits)