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= psy2134
(104 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 71.6 bits (174), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 39/84 (46%), Positives = 51/84 (60%), Gaps = 15/84 (17%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+G V +V+IY EKQ ++E +E+IVKIFV FS +E A ALNG
Sbjct: 153 FGAVNRVIIYQEKQGEEEDAEIIVKIFVEFS---------------IASETHKAIQALNG 197
Query: 80 RFFAGRMVRAELYDQSLFDHNDFS 103
R+FAGR V AE+YDQ FD++D S
Sbjct: 198 RWFAGRKVVAEVYDQERFDNSDLS 221
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 71.6 bits (174), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 39/84 (46%), Positives = 51/84 (60%), Gaps = 15/84 (17%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+G V +V+IY EKQ ++E +E+IVKIFV FS +E A ALNG
Sbjct: 44 FGAVNRVIIYQEKQGEEEDAEIIVKIFVEFS---------------IASETHKAIQALNG 88
Query: 80 RFFAGRMVRAELYDQSLFDHNDFS 103
R+FAGR V AE+YDQ FD++D S
Sbjct: 89 RWFAGRKVVAEVYDQERFDNSDLS 112
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 71.2 bits (173), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 39/84 (46%), Positives = 51/84 (60%), Gaps = 15/84 (17%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+G V +V+IY EKQ ++E +E+IVKIFV FS +E A ALNG
Sbjct: 49 FGAVNRVIIYQEKQGEEEDAEIIVKIFVEFS---------------IASETHKAIQALNG 93
Query: 80 RFFAGRMVRAELYDQSLFDHNDFS 103
R+FAGR V AE+YDQ FD++D S
Sbjct: 94 RWFAGRKVVAEVYDQERFDNSDLS 117
>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 = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 31/93 (33%), Positives = 45/93 (48%), Gaps = 20/93 (21%)
Query: 12 EKQSDDEAYGQVEKVVIYN-EKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEA 70
E + + E YG+V K VI+ DDEA V+IF+ F +++ A A
Sbjct: 29 ETKEECEKYGKVGKCVIFEIPGAPDDEA----VRIFLEFERVESAIKA------------ 72
Query: 71 EYARDALNGRFFAGRMVRAELYDQSLFDHNDFS 103
D LNGR+F GR+V+A Y+ F D +
Sbjct: 73 --VVD-LNGRYFGGRVVKACFYNLDKFRVLDLA 102
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 33.1 bits (74), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 8/60 (13%)
Query: 20 YGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYARDALNG 79
+GQ+ K+++++ + D AS VSF +EA+Y L+GR+F + A +G
Sbjct: 50 FGQIRKLLLFD-RHPDGVAS-------VSFRDPEEADYCIQTLDGRWFGGRQITAQAWDG 101
>pdb|1U5W|A Chain A, Crystal Structure Of Hypothetical Protein Yjjx From
Escherichia Coli
pdb|1U5W|B Chain B, Crystal Structure Of Hypothetical Protein Yjjx From
Escherichia Coli
pdb|1U5W|C Chain C, Crystal Structure Of Hypothetical Protein Yjjx From
Escherichia Coli
pdb|1U5W|D Chain D, Crystal Structure Of Hypothetical Protein Yjjx From
Escherichia Coli
pdb|1U5W|E Chain E, Crystal Structure Of Hypothetical Protein Yjjx From
Escherichia Coli
pdb|1U5W|F Chain F, Crystal Structure Of Hypothetical Protein Yjjx From
Escherichia Coli
pdb|1U5W|G Chain G, Crystal Structure Of Hypothetical Protein Yjjx From
Escherichia Coli
pdb|1U5W|H Chain H, Crystal Structure Of Hypothetical Protein Yjjx From
Escherichia Coli
Length = 184
Score = 29.3 bits (64), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 26 VVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFFAEAEYAR-DALNGRFFAG 84
VVI N Q + S + V K++E E A + R+ E R + G F AG
Sbjct: 91 VVIENASQRGEARSATLPLPAVILEKVREGE-ALGPVMSRYTGIDEIGRKEGAIGVFTAG 149
Query: 85 RMVRAELYDQSLF 97
++ RA +Y Q++
Sbjct: 150 KLTRASVYHQAVI 162
>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From Mus
Musculus
Length = 113
Score = 28.9 bits (63), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 75 DALNGRFFAGRMVRAELYDQSLFDHNDFS 103
+AL+GR+FAG+M+ A + HN F
Sbjct: 72 NALHGRWFAGKMITAAYVPLPTY-HNLFP 99
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 17 DEAYGQVEKVVIYNEKQSDDEASEVIVKIFVSFSKMQEAEYARDALNGRFF 67
+E YG+VE++ + D+ ++ ++V F + ++AE A LN R+F
Sbjct: 48 EEKYGEVEEMNV-----CDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWF 93
>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 = 25.8 bits (55), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 75 DALNGRFFAGRMVRAELYDQSLFDHNDFS 103
+AL+GR+FAG+ + A + HN F
Sbjct: 73 NALHGRWFAGKXITAAYVPLPTY-HNLFP 100
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
0.317 0.133 0.364
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,886,937
Number of Sequences: 62578
Number of extensions: 96665
Number of successful extensions: 283
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 267
Number of HSP's gapped (non-prelim): 22
length of query: 104
length of database: 14,973,337
effective HSP length: 69
effective length of query: 35
effective length of database: 10,655,455
effective search space: 372940925
effective search space used: 372940925
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)