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= psy2919
(158 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TGX|A Chain A, Il-21:il21r Complex
pdb|3TGX|C Chain C, Il-21:il21r Complex
pdb|3TGX|E Chain E, Il-21:il21r Complex
pdb|3TGX|G Chain G, Il-21:il21r Complex
pdb|3TGX|I Chain I, Il-21:il21r Complex
pdb|3TGX|K Chain K, Il-21:il21r Complex
pdb|3TGX|M Chain M, Il-21:il21r Complex
pdb|3TGX|O Chain O, Il-21:il21r Complex
Length = 219
Score = 32.0 bits (71), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 68 GAYSGAWHYGFEVSGVYIWPSGSAYEGQWQN--------GKRHGLGVESRGRWIYRGEWT 119
G Y +W +E Y+ YE Q++N +R + V+SR + E+
Sbjct: 113 GQYQISWRSDYEDPAFYMLKGKLQYELQYRNRGDPWAVSPRRKLISVDSRSVSLLPLEFR 172
Query: 120 QGFKGRYGVRQSSTSNAKYEGTWAN 144
+ VR + Y+GTW+
Sbjct: 173 KDSSYELQVRAGPMPGSSYQGTWSE 197
>pdb|3C67|A Chain A, Escherichia Coli K12 Ygjk In A Complexed With Glucose
pdb|3C67|B Chain B, Escherichia Coli K12 Ygjk In A Complexed With Glucose
pdb|3C68|A Chain A, Escherichia Coli K12 Ygjk In A Complexed With Mannose
pdb|3C68|B Chain B, Escherichia Coli K12 Ygjk In A Complexed With Mannose
pdb|3C69|A Chain A, Escherichia Coli K12 Ygjk In A Complexed With Galactose
pdb|3C69|B Chain B, Escherichia Coli K12 Ygjk In A Complexed With Galactose
Length = 761
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 38 FDFDDGGTYCGGWEDGKAHGHGVCTGPKGQGAYSGAWHYGFEVSGVYIWPSGSAYE--GQ 95
+D+DD + ++ G HGH + GP G + G E YI S ++
Sbjct: 22 YDYDDHQRFNPFFDLGAWHGHLLPDGPNTMGGFPGVALLTEE----YINFMASNFDRLTV 77
Query: 96 WQNGKRHGLGVES 108
WQ+GK+ +E+
Sbjct: 78 WQDGKKVDFTLEA 90
>pdb|1FR5|A Chain A, Phage Fr Capsids With A Four Residue Deletion In The Coat
Protein Fg Loop
pdb|1FR5|B Chain B, Phage Fr Capsids With A Four Residue Deletion In The Coat
Protein Fg Loop
pdb|1FR5|C Chain C, Phage Fr Capsids With A Four Residue Deletion In The Coat
Protein Fg Loop
Length = 125
Score = 27.7 bits (60), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS +N KY
Sbjct: 30 AEWISSNSRSQAYKVTCSVRQSSANNRKY 58
>pdb|1FRS|A Chain A, Crystal Structure Of Bacteriophage Fr Capsids At 3.5
Angstroms Resolution
pdb|1FRS|B Chain B, Crystal Structure Of Bacteriophage Fr Capsids At 3.5
Angstroms Resolution
pdb|1FRS|C Chain C, Crystal Structure Of Bacteriophage Fr Capsids At 3.5
Angstroms Resolution
Length = 129
Score = 27.3 bits (59), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS +N KY
Sbjct: 30 AEWISSNSRSQAYKVTCSVRQSSANNRKY 58
>pdb|1MVB|A Chain A, Structure Of A Protein Capsid Of The T59s Mutant Of Phage
Ms2
pdb|1MVB|B Chain B, Structure Of A Protein Capsid Of The T59s Mutant Of Phage
Ms2
pdb|1MVB|C Chain C, Structure Of A Protein Capsid Of The T59s Mutant Of Phage
Ms2
pdb|1AQ3|A Chain A, Bacteriophage Ms2 Capsid ProteinRNA COMPLEX
pdb|1AQ3|B Chain B, Bacteriophage Ms2 Capsid ProteinRNA COMPLEX
pdb|1AQ3|C Chain C, Bacteriophage Ms2 Capsid ProteinRNA COMPLEX
Length = 129
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS N KY
Sbjct: 30 AEWISSNSRSQAYKVTCSVRQSSAQNRKY 58
>pdb|1MST|A Chain A, Crystal Structure Of Ms2 Capsids With Mutations In The
Subunit Fg Loop
pdb|1MST|B Chain B, Crystal Structure Of Ms2 Capsids With Mutations In The
Subunit Fg Loop
pdb|1MST|C Chain C, Crystal Structure Of Ms2 Capsids With Mutations In The
Subunit Fg Loop
Length = 129
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS N KY
Sbjct: 30 AEWISSNSRSQAYKVTCSVRQSSAQNRKY 58
>pdb|2BNY|A Chain A, Ms2 (N87a Mutant) - Rna Hairpin Complex
pdb|2BNY|B Chain B, Ms2 (N87a Mutant) - Rna Hairpin Complex
pdb|2BNY|C Chain C, Ms2 (N87a Mutant) - Rna Hairpin Complex
Length = 129
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS N KY
Sbjct: 30 AEWISSNSRSQAYKVTCSVRQSSAQNRKY 58
>pdb|1MSC|A Chain A, Crystal Structure Of Ms2 Coat Protein Dimer
Length = 129
Score = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS N KY
Sbjct: 30 AEWISSNSRSQAYKVTCSVRQSSAQNRKY 58
>pdb|2MS2|A Chain A, The Refined Structure Of Bacteriophage Ms2 At 2.8
Angstroms Resolution
pdb|2MS2|B Chain B, The Refined Structure Of Bacteriophage Ms2 At 2.8
Angstroms Resolution
pdb|2MS2|C Chain C, The Refined Structure Of Bacteriophage Ms2 At 2.8
Angstroms Resolution
pdb|1ZDH|A Chain A, Ms2 Coat ProteinRNA COMPLEX
pdb|1ZDH|B Chain B, Ms2 Coat ProteinRNA COMPLEX
pdb|1ZDH|C Chain C, Ms2 Coat ProteinRNA COMPLEX
pdb|1ZDI|A Chain A, Rna Bacteriophage Ms2 Coat ProteinRNA COMPLEX
pdb|1ZDI|B Chain B, Rna Bacteriophage Ms2 Coat ProteinRNA COMPLEX
pdb|1ZDI|C Chain C, Rna Bacteriophage Ms2 Coat ProteinRNA COMPLEX
pdb|1ZDJ|A Chain A, Structure Of Bacteriophage Coat Protein-Loop Rna Complex
pdb|1ZDJ|B Chain B, Structure Of Bacteriophage Coat Protein-Loop Rna Complex
pdb|1ZDJ|C Chain C, Structure Of Bacteriophage Coat Protein-Loop Rna Complex
pdb|6MSF|A Chain A, F6 Aptamer Ms2 Coat Protein Complex
pdb|6MSF|B Chain B, F6 Aptamer Ms2 Coat Protein Complex
pdb|6MSF|C Chain C, F6 Aptamer Ms2 Coat Protein Complex
pdb|5MSF|A Chain A, Ms2 Protein CapsidRNA COMPLEX
pdb|5MSF|B Chain B, Ms2 Protein CapsidRNA COMPLEX
pdb|5MSF|C Chain C, Ms2 Protein CapsidRNA COMPLEX
pdb|7MSF|A Chain A, Ms2 Protein CapsidRNA COMPLEX
pdb|7MSF|B Chain B, Ms2 Protein CapsidRNA COMPLEX
pdb|7MSF|C Chain C, Ms2 Protein CapsidRNA COMPLEX
pdb|1ZDK|A Chain A, Structure Of Bacteriophage Coat Protein-Loop Rna Complex
pdb|1ZDK|B Chain B, Structure Of Bacteriophage Coat Protein-Loop Rna Complex
pdb|1ZDK|C Chain C, Structure Of Bacteriophage Coat Protein-Loop Rna Complex
pdb|1U1Y|A Chain A, Crystal Structure Of A Complex Between Wt Bacteriophage
Ms2 Coat Protein And An F5 Aptamer Rna Stemloop With
2aminopurine Substituted At The-10 Position
pdb|1U1Y|B Chain B, Crystal Structure Of A Complex Between Wt Bacteriophage
Ms2 Coat Protein And An F5 Aptamer Rna Stemloop With
2aminopurine Substituted At The-10 Position
pdb|1U1Y|C Chain C, Crystal Structure Of A Complex Between Wt Bacteriophage
Ms2 Coat Protein And An F5 Aptamer Rna Stemloop With
2aminopurine Substituted At The-10 Position
pdb|2BU1|A Chain A, Ms2-Rna Hairpin (5bru-5) Complex
pdb|2BU1|B Chain B, Ms2-Rna Hairpin (5bru-5) Complex
pdb|2BU1|C Chain C, Ms2-Rna Hairpin (5bru-5) Complex
pdb|2C4Q|A Chain A, Ms2-Rna Hairpin (2one -5) Complex Virus
pdb|2C4Q|B Chain B, Ms2-Rna Hairpin (2one -5) Complex Virus
pdb|2C4Q|C Chain C, Ms2-Rna Hairpin (2one -5) Complex Virus
pdb|2C4Y|A Chain A, Ms2-Rna Hairpin (2thiouracil-5) Complex
pdb|2C4Y|B Chain B, Ms2-Rna Hairpin (2thiouracil-5) Complex
pdb|2C4Y|C Chain C, Ms2-Rna Hairpin (2thiouracil-5) Complex
pdb|2C4Z|A Chain A, Ms2-Rna Hairpin (2su -5-6) Complex
pdb|2C4Z|B Chain B, Ms2-Rna Hairpin (2su -5-6) Complex
pdb|2C4Z|C Chain C, Ms2-Rna Hairpin (2su -5-6) Complex
pdb|2C50|A Chain A, Ms2-rna Hairpin (a -5) Complex
pdb|2C50|B Chain B, Ms2-rna Hairpin (a -5) Complex
pdb|2C50|C Chain C, Ms2-rna Hairpin (a -5) Complex
pdb|2C51|A Chain A, Ms2-Rna Hairpin (G -5) Complex
pdb|2C51|B Chain B, Ms2-Rna Hairpin (G -5) Complex
pdb|2C51|C Chain C, Ms2-Rna Hairpin (G -5) Complex
pdb|2IZ8|A Chain A, Ms2-Rna Hairpin (C-7) Complex
pdb|2IZ8|B Chain B, Ms2-Rna Hairpin (C-7) Complex
pdb|2IZ8|C Chain C, Ms2-Rna Hairpin (C-7) Complex
pdb|2IZ9|A Chain A, Ms2-Rna Hairpin (4one-5) Complex
pdb|2IZ9|B Chain B, Ms2-Rna Hairpin (4one-5) Complex
pdb|2IZ9|C Chain C, Ms2-Rna Hairpin (4one-5) Complex
pdb|2IZN|A Chain A, Ms2-rna Hairpin (g-10) Complex
pdb|2IZN|B Chain B, Ms2-rna Hairpin (g-10) Complex
pdb|2IZN|C Chain C, Ms2-rna Hairpin (g-10) Complex
pdb|2IZM|A Chain A, Ms2-rna Hairpin (c-10) Complex
pdb|2IZM|B Chain B, Ms2-rna Hairpin (c-10) Complex
pdb|2IZM|C Chain C, Ms2-rna Hairpin (c-10) Complex
Length = 129
Score = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS N KY
Sbjct: 30 AEWISSNSRSQAYKVTCSVRQSSAQNRKY 58
>pdb|1BMS|A Chain A, Crystal Structure Of Ms2 Capsids With Mutations In The
Subunit Fg Loop
pdb|1BMS|B Chain B, Crystal Structure Of Ms2 Capsids With Mutations In The
Subunit Fg Loop
pdb|1BMS|C Chain C, Crystal Structure Of Ms2 Capsids With Mutations In The
Subunit Fg Loop
Length = 129
Score = 26.9 bits (58), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS N KY
Sbjct: 30 AEWISSNSRSQAYKVTCSVRQSSAQNRKY 58
>pdb|2VTU|J Chain J, Crystal Structure Of Bacteriophage Ms2 Covalent Coat
Protein Dimer
pdb|2VTU|L Chain L, Crystal Structure Of Bacteriophage Ms2 Covalent Coat
Protein Dimer
pdb|2WBH|A Chain A, Icosahedral Particle Of Covalent Coat Protein Dimer Of
Bacteriophage Ms2
pdb|2WBH|B Chain B, Icosahedral Particle Of Covalent Coat Protein Dimer Of
Bacteriophage Ms2
pdb|2WBH|C Chain C, Icosahedral Particle Of Covalent Coat Protein Dimer Of
Bacteriophage Ms2
Length = 257
Score = 26.9 bits (58), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS N KY
Sbjct: 30 AEWISSNSRSQAYKVTCSVRQSSAQNRKY 58
Score = 26.9 bits (58), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS N KY
Sbjct: 158 AEWISSNSRSQAYKVTCSVRQSSAQNRKY 186
>pdb|1ZSE|A Chain A, Rna Stemloop From Bacteriophage Qbeta Complexed With An
N87s Mutant Ms2 Capsid
pdb|1ZSE|B Chain B, Rna Stemloop From Bacteriophage Qbeta Complexed With An
N87s Mutant Ms2 Capsid
pdb|1ZSE|C Chain C, Rna Stemloop From Bacteriophage Qbeta Complexed With An
N87s Mutant Ms2 Capsid
pdb|2B2G|A Chain A, Ms2 Wild-Type Rna Stemloop Complexed With An N87s Mutant
Ms2 Capsid
pdb|2B2G|B Chain B, Ms2 Wild-Type Rna Stemloop Complexed With An N87s Mutant
Ms2 Capsid
pdb|2B2G|C Chain C, Ms2 Wild-Type Rna Stemloop Complexed With An N87s Mutant
Ms2 Capsid
Length = 129
Score = 26.9 bits (58), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS N KY
Sbjct: 30 AEWISSNSRSQAYKVTCSVRQSSAQNRKY 58
>pdb|2B2D|A Chain A, Rna Stemloop Operator From Bacteriophage Qbeta Complexed
With An N87s, E89k Mutant Ms2 Capsid
pdb|2B2D|B Chain B, Rna Stemloop Operator From Bacteriophage Qbeta Complexed
With An N87s, E89k Mutant Ms2 Capsid
pdb|2B2D|C Chain C, Rna Stemloop Operator From Bacteriophage Qbeta Complexed
With An N87s, E89k Mutant Ms2 Capsid
pdb|2B2E|A Chain A, Rna Stemloop From Bacteriophage Ms2 Complexed With An
N87s, E89k Mutant Ms2 Capsid
pdb|2B2E|B Chain B, Rna Stemloop From Bacteriophage Ms2 Complexed With An
N87s, E89k Mutant Ms2 Capsid
pdb|2B2E|C Chain C, Rna Stemloop From Bacteriophage Ms2 Complexed With An
N87s, E89k Mutant Ms2 Capsid
Length = 129
Score = 26.9 bits (58), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS N KY
Sbjct: 30 AEWISSNSRSQAYKVTCSVRQSSAQNRKY 58
>pdb|2BQ5|A Chain A, Ms2 (N87ae89k Mutant) - Rna Hairpin Complex
pdb|2BQ5|B Chain B, Ms2 (N87ae89k Mutant) - Rna Hairpin Complex
pdb|2BQ5|C Chain C, Ms2 (N87ae89k Mutant) - Rna Hairpin Complex
pdb|2BS0|A Chain A, Ms2 (N87ae89k Mutant) - Variant Qbeta Rna Hairpin Complex
pdb|2BS0|B Chain B, Ms2 (N87ae89k Mutant) - Variant Qbeta Rna Hairpin Complex
pdb|2BS0|C Chain C, Ms2 (N87ae89k Mutant) - Variant Qbeta Rna Hairpin Complex
pdb|2BS1|A Chain A, Ms2 (N87ae89k Mutant) - Qbeta Rna Hairpin Complex
pdb|2BS1|B Chain B, Ms2 (N87ae89k Mutant) - Qbeta Rna Hairpin Complex
pdb|2BS1|C Chain C, Ms2 (N87ae89k Mutant) - Qbeta Rna Hairpin Complex
Length = 129
Score = 26.9 bits (58), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS N KY
Sbjct: 30 AEWISSNSRSQAYKVTCSVRQSSAQNRKY 58
>pdb|1MVA|A Chain A, Structure Of A Protein Capsid Of The T45a Mutant Of Phage
Ms2
pdb|1MVA|B Chain B, Structure Of A Protein Capsid Of The T45a Mutant Of Phage
Ms2
pdb|1MVA|C Chain C, Structure Of A Protein Capsid Of The T45a Mutant Of Phage
Ms2
pdb|1AQ4|A Chain A, Structure Of A Ms2 Coat Protein Mutant In Complex With An
Rna Operator
pdb|1AQ4|B Chain B, Structure Of A Ms2 Coat Protein Mutant In Complex With An
Rna Operator
pdb|1AQ4|C Chain C, Structure Of A Ms2 Coat Protein Mutant In Complex With An
Rna Operator
Length = 129
Score = 26.9 bits (58), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 110 GRWIYRGEWTQGFKGRYGVRQSSTSNAKY 138
WI +Q +K VRQSS N KY
Sbjct: 30 AEWISSNSRSQAYKVACSVRQSSAQNRKY 58
>pdb|4B3N|A Chain A, Crystal Structure Of Rhesus Trim5alpha PrySPRY DOMAIN
pdb|4B3N|B Chain B, Crystal Structure Of Rhesus Trim5alpha PrySPRY DOMAIN
Length = 602
Score = 26.2 bits (56), Expect = 9.3, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 126 YGVRQSSTSNAKYEGTWANGLQDGYGSETYADG 158
Y + Q+ KY G W GLQ+G + DG
Sbjct: 498 YNIEQNENYQPKY-GYWVIGLQEGVKYSVFQDG 529
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
0.314 0.136 0.459
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,188,327
Number of Sequences: 62578
Number of extensions: 310503
Number of successful extensions: 497
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 481
Number of HSP's gapped (non-prelim): 29
length of query: 158
length of database: 14,973,337
effective HSP length: 91
effective length of query: 67
effective length of database: 9,278,739
effective search space: 621675513
effective search space used: 621675513
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)