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= psy16559
(207 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 54.3 bits (129), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 30/107 (28%), Positives = 56/107 (52%), Gaps = 5/107 (4%)
Query: 92 SKTLLLNNFFTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRS-LGQVTQ 150
S+T+ L N + + ++S + ++ + EM +++ EF+++V E+ G+V +
Sbjct: 1 SQTIALLNIYRNPQNSSQSADGLRSAVS----DVEMQEHYDEFFEEVFTEMEEKYGEVEE 56
Query: 151 FKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQIRGQFC 197
VC N HL GNVYV + E +A +A L R++ G+ I +
Sbjct: 57 MNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103
>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From Mus
Musculus
Length = 113
Score = 36.2 bits (82), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 133 EFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQI 192
E DDV+ E G V V N + +GNVYV + A+ A AL GR++ GK I
Sbjct: 28 EIKDDVIEECNKHGGVIHIYVDKNSA---QGNVYVKCPSIAAAIAAVNALHGRWFAGKMI 84
Query: 193 RGQFCNVPLW 202
+ +P +
Sbjct: 85 TAAYVPLPTY 94
>pdb|3S6E|A Chain A, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
pdb|3S6E|B Chain B, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
Length = 114
Score = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 132 VEFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQ 191
E DDV+ E G V V N + +GNVYV + A+ A AL GR++ GK
Sbjct: 28 TEIKDDVIEECNKHGGVIHIYVDKNSA---QGNVYVKCPSIAAAIAAVNALHGRWFAGKX 84
Query: 192 IRGQFCNVPLW 202
I + +P +
Sbjct: 85 ITAAYVPLPTY 95
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 30.8 bits (68), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 133 EFYDDVLPELRSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAFYALTGRFYGGKQI 192
E +D+ E GQ+ + + H G VS+ + EA L GR++GG+QI
Sbjct: 38 EIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQI 94
Query: 193 RGQ 195
Q
Sbjct: 95 TAQ 97
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 30.4 bits (67), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 10/74 (13%)
Query: 130 YFVEFYDDVLPELRS---------LGQVTQFKVCCN-KSPHLRGNVYVSYSNEREALRAF 179
+F F D+ PE+ + G+++ +V + + +G +VS+ N+ +A A
Sbjct: 15 HFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 74
Query: 180 YALTGRFYGGKQIR 193
+ G++ GG+QIR
Sbjct: 75 VHMGGQWLGGRQIR 88
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic
Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 30.4 bits (67), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 126 EMHKYFVEFYDDVLPELRS---------LGQVTQFKVCCN-KSPHLRGNVYVSYSNEREA 175
+ +F F D+ PE+ + G+++ +V + + +G +VS+ N+ +A
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70
Query: 176 LRAFYALTGRFYGGKQIR 193
A + G++ GG+QIR
Sbjct: 71 ENAIQQMGGQWLGGRQIR 88
>pdb|2P0T|A Chain A, Structural Genomics, The Crystal Structure Of A Conserved
Putative Protein From Pseudomonas Syringae Pv. Tomato
Str. Dc3000
Length = 176
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 123 DETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNKSP 159
D+ ++ K+ +E+ D +LRSL + Q +V NK P
Sbjct: 119 DDADLEKFVIEYPDADRQQLRSLIRQAQHEVARNKPP 155
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 126 EMHKYFVEFY-----DDVLPEL-RSLGQVTQFKVCCNKSPHLRGNVYVSYSNEREALRAF 179
E HK F+ + L E+ ++ G V ++ N++ +G YV Y NE +A +A
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAV 75
Query: 180 YALTG 184
+ G
Sbjct: 76 MKMDG 80
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 10/77 (12%)
Query: 127 MHKYFVEFYDDVLPELRS---------LGQVTQFKVCCN-KSPHLRGNVYVSYSNEREAL 176
+ +F F D+ PE+ + G+++ +V + + +G +VS+ N+ +A
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
Query: 177 RAFYALTGRFYGGKQIR 193
A + G++ GG+QIR
Sbjct: 63 NAIQQMGGQWLGGRQIR 79
>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 = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 116 TDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNERE 174
T ++ E E ++H F E+ G++ + ++ + +L+G V Y +E
Sbjct: 29 TGVHEEATEEDIHDKFAEY-----------GEIKNIHLNLDRRTGYLKGYTLVEYETYKE 77
Query: 175 ALRAFYALTGRFYGGKQIRGQFCNV 199
A A L G+ G+ I +C V
Sbjct: 78 AQAAMEGLNGQDLMGQPISVDWCFV 102
>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 = 27.7 bits (60), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 116 TDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNERE 174
T ++ E E ++H F E+ G++ + ++ + +L+G V Y +E
Sbjct: 28 TGVHEEATEEDIHDKFAEY-----------GEIKNIHLNLDRRTGYLKGYTLVEYETYKE 76
Query: 175 ALRAFYALTGRFYGGKQIRGQFCNV 199
A A L G+ G+ I +C V
Sbjct: 77 AQAAMEGLNGQDLMGQPISVDWCFV 101
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 27.3 bits (59), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 21/35 (60%)
Query: 165 VYVSYSNEREALRAFYALTGRFYGGKQIRGQFCNV 199
+++ + A++A L GR++GG+ ++ F N+
Sbjct: 59 IFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNL 93
>pdb|2HZ7|A Chain A, Crystal Structure Of The Glutaminyl-Trna Synthetase From
Deinococcus Radiodurans
Length = 851
Score = 27.3 bits (59), Expect = 6.7, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 89 PSVSKTLLLNNFFTHLSMDNKSVREYDTDINLEFDETEMHKYFVEFYDDVLPELRSLG 146
P S L + F L +D + R+Y NL D+T E+ D + +L+ LG
Sbjct: 73 PDPSGYAHLGHVFASL-LDFNTARQYGGQFNLRMDDTNPELARQEYVDSIADDLKWLG 129
>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 = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 116 TDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNERE 174
T ++ E E ++H F E+ G++ + ++ + +L+G V Y +E
Sbjct: 13 TGVHEEATEEDIHDKFAEY-----------GEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 175 ALRAFYALTGRFYGGKQIRGQFCNV 199
A A L G+ G+ I +C V
Sbjct: 62 AQAAMEGLNGQDLMGQPISVDWCFV 86
>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 = 26.9 bits (58), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 116 TDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNERE 174
T ++ E E ++H F E+ G++ + ++ + +L+G V Y +E
Sbjct: 13 TGVHEEATEEDIHDKFAEY-----------GEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 175 ALRAFYALTGRFYGGKQIRGQFCNV 199
A A L G+ G+ I +C V
Sbjct: 62 AQAAMEGLNGQDLMGQPISVDWCFV 86
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 26.9 bits (58), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 116 TDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNERE 174
T ++ E E ++H F E+ G++ + ++ + +L+G V Y +E
Sbjct: 13 TGVHEEATEEDIHDKFAEY-----------GEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 175 ALRAFYALTGRFYGGKQIRGQFCNV 199
A A L G+ G+ I +C V
Sbjct: 62 AQAAMEGLNGQDLMGQPISVDWCFV 86
>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 = 26.9 bits (58), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 116 TDINLEFDETEMHKYFVEFYDDVLPELRSLGQVTQFKVCCNK-SPHLRGNVYVSYSNERE 174
T ++ E E ++H F E+ G++ + ++ + +L+G V Y +E
Sbjct: 15 TGVHEEATEEDIHDKFAEY-----------GEIKNIHLNLDRRTGYLKGYTLVEYETYKE 63
Query: 175 ALRAFYALTGRFYGGKQIRGQFCNV 199
A A L G+ G+ I +C V
Sbjct: 64 AQAAMEGLNGQDLMGQPISVDWCFV 88
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
0.323 0.139 0.435
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,953,820
Number of Sequences: 62578
Number of extensions: 226142
Number of successful extensions: 567
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 555
Number of HSP's gapped (non-prelim): 22
length of query: 207
length of database: 14,973,337
effective HSP length: 94
effective length of query: 113
effective length of database: 9,091,005
effective search space: 1027283565
effective search space used: 1027283565
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: 49 (23.5 bits)