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= 040735
(779 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Z6T|A Chain A, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|B Chain B, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|C Chain C, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
pdb|1Z6T|D Chain D, Structure Of The Apoptotic Protease-activating Factor 1
Bound To Adp
Length = 591
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 62/235 (26%), Positives = 104/235 (44%), Gaps = 43/235 (18%)
Query: 296 VVLDDVWNENYNSWRALSCPFGAGAFGSK--IVVTHRNQGVAETMRAVSTKTLKE--LSD 351
++LDDVW+ SW AF S+ I++T R++ V +++ E L
Sbjct: 240 LILDDVWD----SWVL-------KAFDSQCQILLTTRDKSVTDSVMGPKYVVPVESSLGK 288
Query: 352 DDCLRVLIQHSLGARDFNIPQSLKEVAEKIVKKCKGLPLAAKTLGGLLRGKDDLNDWEFV 411
+ L +L + + ++P E A I+K+CKG PL +G LLR D N WE+
Sbjct: 289 EKGLEIL-SLFVNMKKADLP----EQAHSIIKECKGSPLVVSLIGALLR--DFPNRWEYY 341
Query: 412 L----NANIWDLQE----DKCDIVPALRVSYHFLPPQLKQCFAYFSLFPKDYDFQEEEII 463
L N +++ D + A+ +S L +K + S+ KD + +
Sbjct: 342 LKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLC 401
Query: 464 LLWTAEGFLDQEYNGRKMEDLGREFVRELHSRSLVQQSSKNAS-RFVMHDLINDL 517
+LW E ++ED+ +EFV ++SL+ S R+ +HDL D
Sbjct: 402 ILWDME--------TEEVEDILQEFV----NKSLLFCDRNGKSFRYYLHDLQVDF 444
>pdb|3IZA|A Chain A, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|B Chain B, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|C Chain C, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|D Chain D, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|E Chain E, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|F Chain F, Structure Of An Apoptosome-Procaspase-9 Card Complex
pdb|3IZA|G Chain G, Structure Of An Apoptosome-Procaspase-9 Card Complex
Length = 1263
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 62/246 (25%), Positives = 104/246 (42%), Gaps = 65/246 (26%)
Query: 296 VVLDDVWNENYNSWRALSCPFGAGAFGSK--IVVTHRNQGVAETMRAVSTKTLKELSDDD 353
++LDDVW+ SW AF S+ I++T R++ V +++
Sbjct: 246 LILDDVWD----SWVL-------KAFDSQCQILLTTRDKSVTDSVMGPK----------- 283
Query: 354 CLRVLIQHSLGARD--------FNIPQS-LKEVAEKIVKKCKGLPLAAKTLGGLLRGKDD 404
V ++ SLG N+ ++ L E A I+K+CKG PL +G LLR D
Sbjct: 284 -YVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKGSPLVVSLIGALLR--DF 340
Query: 405 LNDWEFVL------------NANIWDLQEDKCDIVPALRVSYHFLPPQLKQCFAYFSLFP 452
N WE+ L ++ +D + + A+ +S L +K + S+
Sbjct: 341 PNRWEYYLKQLQNKQFKRIRKSSSYDYEA----LDEAMSISVEMLREDIKDYYTDLSILQ 396
Query: 453 KDYDFQEEEIILLWTAEGFLDQEYNGRKMEDLGREFVRELHSRSLVQQSSKNAS-RFVMH 511
KD + + +LW E ++ED+ +EFV ++SL+ S R+ +H
Sbjct: 397 KDVKVPTKVLCILWDME--------TEEVEDILQEFV----NKSLLFCDRNGKSFRYYLH 444
Query: 512 DLINDL 517
DL D
Sbjct: 445 DLQVDF 450
>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
Length = 1249
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 57/240 (23%), Positives = 103/240 (42%), Gaps = 53/240 (22%)
Query: 296 VVLDDVWNENYNSWRALSCPFGAGAFGSK--IVVTHRNQGVAETMRAVSTKTLKE--LSD 351
++LDDVW+ P+ AF ++ I++T R++ V +++ E L
Sbjct: 240 LILDDVWD-----------PWVLKAFDNQCQILLTTRDKSVTDSVMGPKHVVPVESGLGR 288
Query: 352 DDCLRVLIQHSLGARDFNIPQSLKEVAEKIVKKCKGLPLAAKTLGGLLRGKDDLNDWEFV 411
+ L +L + + ++P A I+K+CKG PL +G LLR D N W +
Sbjct: 289 EKGLEIL-SLFVNMKKEDLPAE----AHSIIKECKGSPLVVSLIGALLR--DFPNRWAYY 341
Query: 412 L------------NANIWDLQEDKCDIVPALRVSYHFLPPQLKQCFAYFSLFPKDYDFQE 459
L ++ +D + + A+ +S L +K + S+ KD
Sbjct: 342 LRQLQNKQFKRIRKSSSYDYEA----LDEAMSISVEMLREDIKDYYTDLSILQKDVKVPT 397
Query: 460 EEIILLWTAEGFLDQEYNGRKMEDLGREFVRELHSRSLVQQSSKNASRFV--MHDLINDL 517
+ + +LW E ++ED+ +EFV ++SL+ ++N F +HDL D
Sbjct: 398 KVLCVLWDLE--------TEEVEDILQEFV----NKSLL-FCNRNGKSFCYYLHDLQVDF 444
>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
Murine Apaf-1
Length = 1256
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 41/160 (25%), Positives = 69/160 (43%), Gaps = 33/160 (20%)
Query: 372 QSLKEVAEKIVKKCKGLPLAAKTLGGLLRGKDDLNDWEFVL------------NANIWDL 419
+ L A I+K+CKG PL +G LLR D N W + L ++ +D
Sbjct: 311 EDLPAEAHSIIKECKGSPLVVSLIGALLR--DFPNRWAYYLRQLQNKQFKRIRKSSSYDY 368
Query: 420 QEDKCDIVPALRVSYHFLPPQLKQCFAYFSLFPKDYDFQEEEIILLWTAEGFLDQEYNGR 479
+ + A+ +S L +K + S+ KD + + +LW E
Sbjct: 369 EA----LDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWDLE--------TE 416
Query: 480 KMEDLGREFVRELHSRSLVQQSSKNASRFV--MHDLINDL 517
++ED+ +EFV ++SL+ ++N F +HDL D
Sbjct: 417 EVEDILQEFV----NKSLL-FCNRNGKSFCYYLHDLQVDF 451
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 37.4 bits (85), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 605 LHGYHISKLPNEIGNLKHLRFLNLSRTNIQILPESINSLYNLHTILLEDCRRLKKLCKNM 664
L+G +++LP EI NL +LR L+LS + LP + S + L D + L
Sbjct: 254 LNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFD-NMVTTLPWEF 312
Query: 665 GNLMKLHHL 673
GNL L L
Sbjct: 313 GNLCNLQFL 321
Score = 30.4 bits (67), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 27/57 (47%)
Query: 596 NLPRLRVFSLHGYHISKLPNEIGNLKHLRFLNLSRTNIQILPESINSLYNLHTILLE 652
NL LRV L ++ LP E+G+ L++ + LP +L NL + +E
Sbjct: 268 NLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYFFDNMVTTLPWEFGNLCNLQFLGVE 324
>pdb|2Z7X|B Chain B, Crystal Structure Of The Tlr1-Tlr2 Heterodimer Induced By
Binding Of A Tri-Acylated Lipopeptide
Length = 520
Score = 33.9 bits (76), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 10/86 (11%)
Query: 555 YDGKKRLKSVSDVERLRTFLPVNLSDYRRNYLAWSVLQRLLNLPRLRVFSLHGYHISKLP 614
YD KK D ++ L +N+S N L ++ + L PR++V LH I +P
Sbjct: 388 YDEKK-----GDCSWTKSLLSLNMSS---NILTDTIFRCLP--PRIKVLDLHSNKIKSIP 437
Query: 615 NEIGNLKHLRFLNLSRTNIQILPESI 640
++ L+ L+ LN++ ++ +P+ I
Sbjct: 438 KQVVKLEALQELNVASNQLKSVPDGI 463
>pdb|3A79|B Chain B, Crystal Structure Of Tlr2-Tlr6-Pam2csk4 Complex
Length = 562
Score = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 46/83 (55%), Gaps = 6/83 (7%)
Query: 572 TFLPVNLSDYRRNYLAWSVLQRLLNLPRLRVFSLHGYHISKLPNEIGNLKHLRFLNLSRT 631
+ L +NLS N L SV + L P+++V LH I +P ++ +L+ L+ LN++
Sbjct: 429 SILVLNLSS---NMLTGSVFRCLP--PKVKVLDLHNNRIMSIPKDVTHLQALQELNVASN 483
Query: 632 NIQILPESI-NSLYNLHTILLED 653
++ +P+ + + L +L I L D
Sbjct: 484 QLKSVPDGVFDRLTSLQYIWLHD 506
>pdb|1MJI|A Chain A, Detailed Analysis Of Rna-Protein Interactions Within The
Bacterial Ribosomal Protein L55S RRNA COMPLEX
pdb|1MJI|B Chain B, Detailed Analysis Of Rna-Protein Interactions Within The
Bacterial Ribosomal Protein L55S RRNA COMPLEX
Length = 182
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 534 AGENRQKFSQSLRHFSYIHGEYDGKKRLKSVSDVERLRTFLPVNLSDYRRNYLAWSVLQR 593
A E+ + ++ + + I G+ R K +LR +P+ L R W L++
Sbjct: 46 AKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRXWIFLEK 105
Query: 594 LLN--LPRLRVF 603
LLN LPR+R F
Sbjct: 106 LLNVALPRIRDF 117
>pdb|2J01|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|2WH4|G Chain G, Insights Into Translational Termination From The Structure
Of Rf2 Bound To The Ribosome
pdb|3HUX|G Chain G, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 50s Subunit For Molecule I.
pdb|3HUZ|G Chain G, Structure Of Ef-P Bound To The 70s Ribosome; This File
Contains The 50s Subunit For Molecule Ii.
pdb|2WRJ|G Chain G, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State (Part 2 Of 4).
pdb|2WRL|G Chain G, The Structure Of The Ribosome With Elongation Factor G
Trapped In The Post-Translocational State. (Part 4 Of
4).
pdb|2WRO|G Chain G, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 2 Of 4).
pdb|2WRR|G Chain G, The Crystal Structure Of The 70s Ribosome Bound To Ef-Tu
And Trna (Part 4 Of 4).
pdb|3KIR|G Chain G, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 2 Of 4)
pdb|3KIT|G Chain G, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Precleavage State; Part 4 Of 4)
pdb|3KIW|G Chain G, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 2 Of 4)
pdb|3KIY|G Chain G, Structure Of Rele Nuclease Bound To The 70s Ribosome
(Postcleavage State; Part 4 Of 4)
pdb|3KNI|G Chain G, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 50s Subunit For Molecule I
pdb|3KNK|G Chain G, The Structures Of Viomycin Bound To The 70s Ribosome. This
File Contains The 50s Subunit For Molecule Ii.
pdb|3KNM|G Chain G, The Structures Of Capreomycin Bound To The 70s Ribosome.
Thi Contains The 50s Subunit For Molecule I.
pdb|3KNO|G Chain G, The Structures Of Capreomycin Bound To The 70s Ribosome.
Thi Contains The 50s Subunit For Molecule Ii
pdb|3I8F|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2X9U|G Chain G, Structure Of The 70s Ribosome Bound To Release Factor 2
And A Substrate Analog Provides Insights Into Catalysis
Of Peptide Release
pdb|2XG0|G Chain G, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 2 Of 4)
pdb|2XG2|G Chain G, Structure Of Cytotoxic Domain Of Colicin E3 Bound To The
70s Ribosome (Part 4 Of 4)
pdb|3OH5|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, The Structure Of Ef-Tu And Aminoacyl-Trna Bound To The 70s
Ribosome With A Gtp Analog
pdb|2XTG|G Chain G, Trna Tranlocation On The 70s Ribosome: The Pre-
Translocational Translocation Intermediate Ti(Pre)
pdb|2XUX|G Chain G, Trna Translocation On The 70s Ribosome: The Post-
Translocational Translocation Intermediate Ti(Post)
pdb|2Y0V|G Chain G, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0X|G Chain G, The Crystal Structure Of Ef-Tu And A9c-Trna-Trp Bound To A
Near-Cognate Codon On The 70s Ribosome
pdb|2Y0Z|G Chain G, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y11|G Chain G, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome.
pdb|2Y13|G Chain G, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Near-Cognate Codon On The 70s Ribosome
pdb|2Y15|G Chain G, The Crystal Structure Of Ef-Tu And G24a-Trna-Trp Bound To
A Cognate Codon On The 70s Ribosome.
pdb|2Y17|G Chain G, Ef-Tu Complex 3
pdb|2Y19|G Chain G, The Crystal Structure Of Ef-Tu And Trp-Trna-Trp Bound To A
Cognate Codon On The 70s Ribosome.
pdb|3ZVP|G Chain G, Crystal Structure Of The Hybrid State Of Ribosome In
Complex With The Guanosine Triphosphatase Release Factor
3
pdb|3UXQ|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, Complex Of Smpb, A Tmrna Fragment And Ef-Tu-Gdp-Kirromycin
With The 70s Ribosome
pdb|4DHA|G Chain G, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|4DHC|G Chain G, Crystal Structure Of Yaej Bound To The 70s Ribosome
pdb|3V23|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, Crystal Structure Of Hpf Bound To The 70s Ribosome. This
Entry Contains The 50s Subunit Of The 2nd Molecule In
The Asu.
pdb|3V2D|G Chain G, 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|G Chain G, 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|G Chain G, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 50s Subunit Of Molecule A.
pdb|4G5N|G Chain G, Crystal Structure Of The 70s Ribosome With Tetracycline.
This Entry Contains The 50s Subunit Of Molecule B.
pdb|4G5U|G Chain G, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 50s Subunit Of Molecule A.
pdb|4G5W|G Chain G, Crystal Structure Of The 70s Ribosome With Tigecycline.
This Entry Contains The 50s Subunit Of Molecule B
Length = 182
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 534 AGENRQKFSQSLRHFSYIHGEYDGKKRLKSVSDVERLRTFLPVNLSDYRRNYLAWSVLQR 593
A E+ + ++ + + I G+ R K +LR +P+ L R W L++
Sbjct: 46 AKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEK 105
Query: 594 LLN--LPRLRVF 603
LLN LPR+R F
Sbjct: 106 LLNVALPRIRDF 117
>pdb|1VSA|E Chain E, 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|E Chain E, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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|G Chain G, 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 = 182
Score = 31.6 bits (70), Expect = 1.8, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 534 AGENRQKFSQSLRHFSYIHGEYDGKKRLKSVSDVERLRTFLPVNLSDYRRNYLAWSVLQR 593
A E+ + ++ + + I G+ R K +LR +P+ L R W L++
Sbjct: 46 AKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEK 105
Query: 594 LLN--LPRLRVF 603
LLN LPR+R F
Sbjct: 106 LLNVALPRIRDF 117
>pdb|3MRZ|F Chain F, 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|F Chain F, 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|3PYO|F Chain F, 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|F Chain F, 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|F Chain F, 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|F Chain F, 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 = 181
Score = 31.6 bits (70), Expect = 1.8, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 534 AGENRQKFSQSLRHFSYIHGEYDGKKRLKSVSDVERLRTFLPVNLSDYRRNYLAWSVLQR 593
A E+ + ++ + + I G+ R K +LR +P+ L R W L++
Sbjct: 45 AKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEK 104
Query: 594 LLN--LPRLRVF 603
LLN LPR+R F
Sbjct: 105 LLNVALPRIRDF 116
>pdb|3FIN|G Chain G, 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.
pdb|3TVE|G Chain G, 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|G Chain G, 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 = 181
Score = 31.6 bits (70), Expect = 1.8, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 534 AGENRQKFSQSLRHFSYIHGEYDGKKRLKSVSDVERLRTFLPVNLSDYRRNYLAWSVLQR 593
A E+ + ++ + + I G+ R K +LR +P+ L R W L++
Sbjct: 45 AKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEK 104
Query: 594 LLN--LPRLRVF 603
LLN LPR+R F
Sbjct: 105 LLNVALPRIRDF 116
>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 = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 42/171 (24%), Positives = 79/171 (46%), Gaps = 11/171 (6%)
Query: 529 IEDTLAGENRQKFSQSLRHFSYIHGEYDGKKRLKSVSDVERLRTFLPVNLSDYRRNYLAW 588
I+ +A + K Q +++ + G +L +S ++ L + L+ + L
Sbjct: 43 IDQIIANNSDIKSVQGIQYLPNVRYLALGGNKLHDISALKELTNLTYLILTGNQLQSLPN 102
Query: 589 SVLQRLLNLPRLRVFSLHGYHISKLPNEI-GNLKHLRFLNLSRTNIQILPESI-NSLYNL 646
V +L NL L + + LP+ + L +L +LNL+ +Q LP+ + + L NL
Sbjct: 103 GVFDKLTNLKELVLVE---NQLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNL 159
Query: 647 HTILLEDCRRLKKLCKNMGNLMKLHHLRNPNVH--SLEEMPKG-FGKLTCL 694
+ L +L+ L + G KL L++ ++ L+ +P G F +LT L
Sbjct: 160 TELDLS-YNQLQSLPE--GVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSL 207
>pdb|3RGX|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
pdb|3RGZ|A Chain A, Structural Insight Into Brassinosteroid Perception By Bri1
Length = 768
Score = 30.4 bits (67), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
Query: 580 DYRRNYLAWSVLQRLLNLPRLRVFSLHGYHIS-KLPNEIGNLKHLRFLNLSRTNIQI-LP 637
D N L+ + + + ++P L + +L IS +P+E+G+L+ L L+LS + +P
Sbjct: 638 DMSYNMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIP 697
Query: 638 ESINSLYNLHTILLED 653
+++++L L I L +
Sbjct: 698 QAMSALTMLTEIDLSN 713
>pdb|3RIZ|A Chain A, Crystal Structure Of The Plant Steroid Receptor Bri1
Ectodomain
pdb|3RJ0|A Chain A, Plant Steroid Receptor Bri1 Ectodomain In Complex With
Brassinolide
Length = 772
Score = 30.4 bits (67), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
Query: 580 DYRRNYLAWSVLQRLLNLPRLRVFSLHGYHIS-KLPNEIGNLKHLRFLNLSRTNIQI-LP 637
D N L+ + + + ++P L + +L IS +P+E+G+L+ L L+LS + +P
Sbjct: 635 DMSYNMLSGYIPKEIGSMPYLFILNLGHNDISGSIPDEVGDLRGLNILDLSSNKLDGRIP 694
Query: 638 ESINSLYNLHTILLED 653
+++++L L I L +
Sbjct: 695 QAMSALTMLTEIDLSN 710
>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
Iii Effector Xcv3220 (Xopl)
Length = 328
Score = 30.0 bits (66), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 30/103 (29%), Positives = 45/103 (43%), Gaps = 3/103 (2%)
Query: 592 QRLLNLPRLRVFSLHGYHISKLPNEIGNLKHLRFLNLSRTNIQILPESINSLYNLHTILL 651
Q L+NL LR L I LP I NL++L+ L + + + L +I+ L L + L
Sbjct: 180 QGLVNLQSLR---LEWTGIRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDL 236
Query: 652 EDCRRLKKLCKNMGNLMKLHHLRNPNVHSLEEMPKGFGKLTCL 694
C L+ G L L + +L +P +LT L
Sbjct: 237 RGCTALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQL 279
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 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,409,989
Number of Sequences: 62578
Number of extensions: 845836
Number of successful extensions: 2313
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 2288
Number of HSP's gapped (non-prelim): 42
length of query: 779
length of database: 14,973,337
effective HSP length: 106
effective length of query: 673
effective length of database: 8,340,069
effective search space: 5612866437
effective search space used: 5612866437
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: 55 (25.8 bits)