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= 030532
(175 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 32.3 bits (72), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 23/51 (45%)
Query: 115 KSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSF 165
K I W + ++ + LF GDL V+D+ L AF FPS+
Sbjct: 64 KQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSY 114
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 31.6 bits (70), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 139 YRLFCGDLGNEVNDDVLSKAFSRFPSF 165
+ LF GDL V+D+ L AF FPS+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSY 28
>pdb|2ED8|A Chain A, Solution Structure Of The Second Fibronectin Type Iii
Domain Of Human Netrin Receptor Dcc
Length = 106
Score = 30.8 bits (68), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 125 TWEDPTLAEWPENDYRLFCGDL--GNEVNDDV 154
TWE P A P YRLFC ++ G E N +V
Sbjct: 27 TWEPPAYANGPVQGYRLFCTEVSTGKEQNIEV 58
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 123 GQTWEDPTLAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV 170
GQ L+E P N + LF +L E N+ +LS F++FP F ++
Sbjct: 193 GQMPPAQPLSENPPN-HILFLTNLPEETNELMLSMLFNQFPGFKEVRL 239
>pdb|4GA7|A Chain A, Crystal Structure Of Human Serpinb1 Mutant
pdb|4GA7|B Chain B, Crystal Structure Of Human Serpinb1 Mutant
Length = 389
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 78 AQQLFQRDAQTITPEALESVK----AALASSDIEHKAETKKKSIPRKAAGQT 125
A +L+ PE L S + A LAS D +H +E +K+I + GQT
Sbjct: 99 ANRLYGEKTYNFLPEFLVSTQKTYGADLASVDFQHASEDARKTINQWVKGQT 150
>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 1003
Score = 28.5 bits (62), Expect = 1.8, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 82 FQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPE 136
F RD TI E+ +A L D+E++ +KK A G W+ PT + PE
Sbjct: 469 FVRDLGTIESAQAET-EALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPE 522
>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
Length = 977
Score = 28.5 bits (62), Expect = 1.9, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 82 FQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPE 136
F RD TI E+ +A L D+E++ +KK A G W+ PT + PE
Sbjct: 443 FVRDLGTIESAQAET-EALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPE 496
>pdb|2VNU|D Chain D, Crystal Structure Of Sc Rrp44
Length = 760
Score = 28.5 bits (62), Expect = 2.1, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 82 FQRDAQTITPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPE 136
F RD TI E+ +A L D+E++ +KK A G W+ PT + PE
Sbjct: 226 FVRDLGTIESAQAET-EALLLEHDVEYRPFSKKVLECLPAEGHDWKAPTKLDDPE 279
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 141 LFCGDLGNEVNDDVLSKAFSRFPSFNMAK 169
LF +L N V +++L KAFS+F K
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVK 42
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 131 LAEWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV 170
L+E P N + LF +L E N+ +LS F++FP F ++
Sbjct: 7 LSENPPN-HILFLTNLPEETNELMLSMLFNQFPGFKEVRL 45
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 27.7 bits (60), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 135 PENDYRLFCGDLGNEVNDDVLSKAFSRFP---SFNMAK 169
P++ ++LF G L N +NDD + + + F +FN+ K
Sbjct: 111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK 148
>pdb|2B0G|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
pdb|2AYM|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd2
Length = 83
Score = 27.3 bits (59), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 133 EWPENDYRLFCGDLGNEVNDDVLSKAFSRFPSFNMAKV 170
E P N LF +L E N+ +LS F++FP F ++
Sbjct: 4 EQPPNQI-LFLTNLPEETNEMMLSMLFNQFPGFKEVRL 40
>pdb|2YLK|A Chain A, Carbohydrate-Binding Module Cbm3b From The Cellulosomal
Cellobiohydrolase 9a From Clostridium Thermocellum
pdb|2YLK|B Chain B, Carbohydrate-Binding Module Cbm3b From The Cellulosomal
Cellobiohydrolase 9a From Clostridium Thermocellum
pdb|2YLK|C Chain C, Carbohydrate-Binding Module Cbm3b From The Cellulosomal
Cellobiohydrolase 9a From Clostridium Thermocellum
pdb|2YLK|D Chain D, Carbohydrate-Binding Module Cbm3b From The Cellulosomal
Cellobiohydrolase 9a From Clostridium Thermocellum
Length = 145
Score = 26.2 bits (56), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 4/80 (5%)
Query: 90 TPEALESVKAALASSDIEHKAETKKKSIPRKAAGQTWEDPTLAEWPENDYRLFCGDLGNE 149
TP ++ + S EH + + K + A GQT E + + +N + D N+
Sbjct: 59 TPIGSGNLIPSFGGSGDEHYLQLEFKDVKLPAGGQTGEIQFVIRYADNSFH----DQSND 114
Query: 150 VNDDVLSKAFSRFPSFNMAK 169
+ D KAF + + K
Sbjct: 115 YSFDPTIKAFQDYGKVTLYK 134
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
0.316 0.129 0.393
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,753,543
Number of Sequences: 62578
Number of extensions: 113644
Number of successful extensions: 312
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 307
Number of HSP's gapped (non-prelim): 14
length of query: 175
length of database: 14,973,337
effective HSP length: 92
effective length of query: 83
effective length of database: 9,216,161
effective search space: 764941363
effective search space used: 764941363
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)