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= 026156
(242 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 34.7 bits (78), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 5 GYVAEVVGLSPNATEKDIHEFFSHCGD--PVHVEI-IRSGECGGTAYVTFSNAYALETAV 61
G++ V G+ ATE+DIH+ F+ G+ +H+ + R+G G V + + A+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 62 L-LSGATIVDQPV----CIIR 77
L+G ++ QP+ C +R
Sbjct: 67 EGLNGQDLMGQPISVDWCFVR 87
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 34.7 bits (78), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 5 GYVAEVVGLSPNATEKDIHEFFSHCGD--PVHVEI-IRSGECGGTAYVTFSNAYALETAV 61
G++ V G+ ATE+DIH+ F+ G+ +H+ + R+G G V + + A+
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
Query: 62 L-LSGATIVDQPV----CIIR 77
L+G ++ QP+ C +R
Sbjct: 83 EGLNGQDLMGQPISVDWCFVR 103
>pdb|2XB2|D Chain D, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 90
Score = 34.3 bits (77), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 5 GYVAEVVGLSPNATEKDIHEFFSHCGD--PVHVEI-IRSGECGGTAYVTFSNAYALETAV 61
G++ V G+ ATE+DIH+ F+ G+ +H+ + R+G G V + + A+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 62 L-LSGATIVDQPV----CIIR 77
L+G ++ QP+ C +R
Sbjct: 67 EGLNGQDLMGQPISVDWCFVR 87
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 34.3 bits (77), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 5 GYVAEVVGLSPNATEKDIHEFFSHCGD--PVHVEI-IRSGECGGTAYVTFSNAYALETAV 61
G++ V G+ ATE+DIH+ F+ G+ +H+ + R+G G V + + A+
Sbjct: 9 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 68
Query: 62 L-LSGATIVDQPV----CIIR 77
L+G ++ QP+ C +R
Sbjct: 69 EGLNGQDLMGQPISVDWCFVR 89
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 33.9 bits (76), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 5 GYVAEVVGLSPNATEKDIHEFFSHCGD--PVHVEI-IRSGECGGTAYVTFSNAYALETAV 61
G++ V G+ ATE+DIH+ F+ G+ +H+ + R+G G V + + A+
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 62 L-LSGATIVDQPVCI 75
L+G ++ QP+ +
Sbjct: 82 EGLNGQDLMGQPISV 96
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
Length = 109
Score = 33.5 bits (75), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 5 GYVAEVVGLSPNATEKDIHEFFSHCGD--PVHVEI-IRSGECGGTAYVTFSNAYALETAV 61
G++ V G+ ATE+DIH+ F+ G+ +H+ + R+G G V + + A+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 62 L-LSGATIVDQPVCI 75
L+G ++ QP+ +
Sbjct: 67 EGLNGQDLMGQPISV 81
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 7/69 (10%)
Query: 10 VVGLSPNATEKDIHEFFSHCGDPVHVEI---IRSGECGGTAYVTFSNAYALETAV-LLSG 65
V+GL TE+D+ E+FS G+ + V++ +++G G +V F+ ET V ++S
Sbjct: 20 VLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE---YETQVKVMSQ 76
Query: 66 ATIVDQPVC 74
++D C
Sbjct: 77 RHMIDGRWC 85
>pdb|2HGN|A Chain A, Nmr Structure Of The Third Qrrm Domain Of Human Hnrnp F
pdb|2KG1|A Chain A, Structure Of The Third Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 139
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 5 GYVAEVVGLSPNATEKDIHEFFSHCGDP--VHVEIIRSGECGGTAYVTFS 52
G+ + GL ATE DI+ FFS +P VH+EI G G A V F+
Sbjct: 46 GHCVHMRGLPYKATENDIYNFFSPL-NPVRVHIEIGPDGRVTGEADVEFA 94
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein H'
Length = 102
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 27/50 (54%), Gaps = 3/50 (6%)
Query: 5 GYVAEVVGLSPNATEKDIHEFFSHCGDP--VHVEIIRSGECGGTAYVTFS 52
G+ + GL ATE DI+ FFS +P VH+EI G G A V F+
Sbjct: 15 GHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEADVEFA 63
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 3/66 (4%)
Query: 13 LSPNATEKDIHEFFSHCGDPVHVEII---RSGECGGTAYVTFSNAYALETAVLLSGATIV 69
L+ +D+ +FFS G V II S G AYV F ++ A+ L+G ++
Sbjct: 33 LAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLL 92
Query: 70 DQPVCI 75
P+ +
Sbjct: 93 GVPIIV 98
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 10 VVGLSPNATEKDIHEFFSHCGDPVHVEII---RSGECGGTAYVTFSN 53
V GLS TE+D+ E FS G V I+ +S G A+V F N
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 10 VVGLSPNATEKDIHEFFSHCGDPVHVEII---RSGECGGTAYVTFSN 53
V GLS TE+D+ E FS G V I+ +S G A+V F N
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 10 VVGLSPNATEKDIHEFFSHCGDPVHVEII---RSGECGGTAYVTFSN 53
V GLS TE+D+ E FS G V I+ +S G A+V F N
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 10 VVGLSPNATEKDIHEFFSHCGDPVHVEII---RSGECGGTAYVTFSN 53
V GLS TE+D+ E FS G V I+ +S G A+V F N
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 97
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 27.3 bits (59), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 10 VVGLSPNATEKDIHEFFSHCGDPVHVEI 37
V L + + ++++F HCG +HV++
Sbjct: 9 VKNLPKSYNQNKVYKYFKHCGPIIHVDV 36
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding
Domains Of The Yeast Splicing Factor Prp24
Length = 292
Score = 26.9 bits (58), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 10 VVGLSPNATEKDIHEFFSHCGDPVHVEI 37
V L + + ++++F HCG +HV++
Sbjct: 46 VKNLPKSYNQNKVYKYFKHCGPIIHVDV 73
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 0.129 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,307,115
Number of Sequences: 62578
Number of extensions: 245388
Number of successful extensions: 610
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 601
Number of HSP's gapped (non-prelim): 22
length of query: 242
length of database: 14,973,337
effective HSP length: 96
effective length of query: 146
effective length of database: 8,965,849
effective search space: 1309013954
effective search space used: 1309013954
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)