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= 027939
(216 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 = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 19/37 (51%), Positives = 27/37 (72%)
Query: 3 VGNVYVQFREEEQAARALKSLSGRFYAGRPIIVDFSP 39
VGNVYV+FR EE A +A+ L+ R++ G+PI + SP
Sbjct: 68 VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP 104
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 7 YVQFREEEQAARALKSLSGRFYAGRPIIVDFSPVTD 42
+V F E A A+K+L+G+ G PI V + D
Sbjct: 55 FVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD 90
>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 = 30.0 bits (66), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 24/35 (68%)
Query: 3 VGNVYVQFREEEQAARALKSLSGRFYAGRPIIVDF 37
+ ++V+F + +A+++L+GR++AGR ++ +
Sbjct: 71 IVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105
>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 = 30.0 bits (66), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 9/32 (28%), Positives = 23/32 (71%)
Query: 3 VGNVYVQFREEEQAARALKSLSGRFYAGRPII 34
+ ++V+F + +A+++L+GR++AGR ++
Sbjct: 175 IVKIFVEFSIASETHKAIQALNGRWFAGRKVV 206
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 30.0 bits (66), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 9/35 (25%), Positives = 24/35 (68%)
Query: 3 VGNVYVQFREEEQAARALKSLSGRFYAGRPIIVDF 37
+ ++V+F + +A+++L+GR++AGR ++ +
Sbjct: 66 IVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 100
>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 = 30.0 bits (66), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 4 GNVYVQFREEEQAARALKSLSGRFYAGRPIIVDFSPVTDF 43
GNVYV+ A A+ +L GR++AG+ I + P+ +
Sbjct: 56 GNVYVKCPSIAAAIAAVNALHGRWFAGKXITAAYVPLPTY 95
>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From
Mus Musculus
Length = 113
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 4 GNVYVQFREEEQAARALKSLSGRFYAGRPIIVDFSPVTDF 43
GNVYV+ A A+ +L GR++AG+ I + P+ +
Sbjct: 55 GNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTY 94
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat
Specific Factor 1 Variant
Length = 112
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 4 GNVYVQFREEEQAARALKSLSGRFYAGRPI 33
G V FR+ E+A +++L GR++ GR I
Sbjct: 65 GVASVSFRDPEEADYCIQTLDGRWFGGRQI 94
>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 = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 6 VYVQFREEEQAARALKSLSGRFYAGRPIIVDFSPVTDFR 44
++++F E A +A+ L+GR++ GR + F + FR
Sbjct: 59 IFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNLDKFR 97
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 7 YVQFREEEQAARALKSLSGRFYAGRPIIV 35
++ F + E A RAL+ L+G AGRP+ V
Sbjct: 51 FITFSDSECARRALEQLNGFELAGRPMRV 79
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 26.6 bits (57), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 23/30 (76%)
Query: 7 YVQFREEEQAARALKSLSGRFYAGRPIIVD 36
+ +++++E A A+++L+GR ++GR + VD
Sbjct: 54 FCEYQDQETALSAMRNLNGREFSGRALRVD 83
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 0.134 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,366,872
Number of Sequences: 62578
Number of extensions: 102123
Number of successful extensions: 284
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 271
Number of HSP's gapped (non-prelim): 14
length of query: 216
length of database: 14,973,337
effective HSP length: 95
effective length of query: 121
effective length of database: 9,028,427
effective search space: 1092439667
effective search space used: 1092439667
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: 49 (23.5 bits)