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= 016857
(381 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 97.8 bits (242), Expect = 9e-21, Method: Composition-based stats.
Identities = 48/98 (48%), Positives = 63/98 (64%), Gaps = 2/98 (2%)
Query: 274 PTRVLLLRNMXXXXXXXXXXXXXXXXXCAKYGTVTRVLIFEITEPNFPVDEAVRIFVQFE 333
PT+V+LLRNM C KYG V + +IFEI P P DEAVRIF++FE
Sbjct: 7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEI--PGAPDDEAVRIFLEFE 64
Query: 334 RSEQTTKALIDLDGRFFGGRVVRATFYDEERFSKNELA 371
R E KA++DL+GR+FGGRVV+A FY+ ++F +LA
Sbjct: 65 RVESAIKAVVDLNGRYFGGRVVKACFYNLDKFRVLDLA 102
>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 = 65.1 bits (157), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 36/100 (36%), Positives = 56/100 (56%), Gaps = 5/100 (5%)
Query: 275 TRVLLLRNMXXXXXXXXXXXXXXXXXCAKYGTVTRVLIFEITEPNFPVDEA---VRIFVQ 331
+ V++LRNM C K+G V RV+I++ E ++A V+IFV+
Sbjct: 124 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQ--EKQGEEEDAEIIVKIFVE 181
Query: 332 FERSEQTTKALIDLDGRFFGGRVVRATFYDEERFSKNELA 371
F + +T KA+ L+GR+F GR V A YD+ERF ++L+
Sbjct: 182 FSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSDLS 221
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 62.0 bits (149), Expect = 5e-10, Method: Composition-based stats.
Identities = 35/98 (35%), Positives = 54/98 (55%), Gaps = 1/98 (1%)
Query: 275 TRVLLLRNMXXXXXXXXXXXXXXXXXCAKYGTVTRVLIFEITEPNFPVDEA-VRIFVQFE 333
+ V++LRNM C K+G V RV+I++ + E V+IFV+F
Sbjct: 15 STVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFS 74
Query: 334 RSEQTTKALIDLDGRFFGGRVVRATFYDEERFSKNELA 371
+ +T KA+ L+GR+F GR V A YD+ERF ++L+
Sbjct: 75 IASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSDLS 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 = 59.7 bits (143), Expect = 3e-09, Method: Composition-based stats.
Identities = 35/100 (35%), Positives = 54/100 (54%), Gaps = 5/100 (5%)
Query: 275 TRVLLLRNMXXXXXXXXXXXXXXXXXCAKYGTVTRVLIFEITEPNFPVDEA---VRIFVQ 331
+ V +LRN C K+G V RV+I++ E ++A V+IFV+
Sbjct: 20 STVXVLRNXVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQ--EKQGEEEDAEIIVKIFVE 77
Query: 332 FERSEQTTKALIDLDGRFFGGRVVRATFYDEERFSKNELA 371
F + +T KA+ L+GR+F GR V A YD+ERF ++L+
Sbjct: 78 FSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNSDLS 117
>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
pdb|2M0G|B Chain B, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 104
Score = 36.6 bits (83), Expect = 0.022, Method: Composition-based stats.
Identities = 31/106 (29%), Positives = 41/106 (38%), Gaps = 10/106 (9%)
Query: 272 GPPTRVLLLRNMXXXXXXXXXXX-----XXXXXXCAKYGTVTRVLIFEITEP--NFPVDE 324
G PT VL L NM C+KYG V + EI P V
Sbjct: 1 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSI---EIPRPVDGVEVPG 57
Query: 325 AVRIFVQFERSEQTTKALIDLDGRFFGGRVVRATFYDEERFSKNEL 370
+IFV+F KA+ L GR F RVV + D + + + +
Sbjct: 58 CGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDF 103
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 35.8 bits (81), Expect = 0.045, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 5/72 (6%)
Query: 301 CAKYGTVTRVLIFEITEP--NFPVDEAVRIFVQFERSEQTTKALIDLDGRFFGGRVVRAT 358
C+KYG V + EI P V +IFV+F KA+ L GR F RVV
Sbjct: 35 CSKYGLVKSI---EIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTK 91
Query: 359 FYDEERFSKNEL 370
+ D + + + +
Sbjct: 92 YCDPDSYHRRDF 103
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 34.3 bits (77), Expect = 0.10, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 328 IFVQFERSEQTTKALIDLDGRFFGGRVVRA 357
++V+F R E KA+IDL+ R+F G+ + A
Sbjct: 71 VYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 301 CAKYGTVTRVLIFEITEPNFPVDEAVRIFVQFERSEQTTKALIDLDGRFFGGRVVRATFY 360
C+K+G + ++L+F+ P+ V F E+ + LDGR+FGGR + A +
Sbjct: 47 CSKFGQIRKLLLFD-RHPDGVAS------VSFRDPEEADYCIQTLDGRWFGGRQITAQAW 99
Query: 361 D 361
D
Sbjct: 100 D 100
>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
pdb|3V4M|B Chain B, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
Length = 105
Score = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 301 CAKYGTVTRVLIFEITEP--NFPVDEAVRIFVQFERSEQTTKALIDLDGRFFGGRVVRAT 358
C+KYG V + EI P V +IFV+F KA L GR F RVV
Sbjct: 36 CSKYGLVKSI---EIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVVVTK 92
Query: 359 FYDEERFSKNEL 370
+ D + + + +
Sbjct: 93 YCDPDSYHRRDF 104
>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|C Chain C, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 106
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 301 CAKYGTVTRVLIFEITEP--NFPVDEAVRIFVQFERSEQTTKALIDLDGRFFGGRVVRAT 358
C+KYG V + EI P V +IFV+F KA L GR F RVV
Sbjct: 37 CSKYGLVKSI---EIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVVVTK 93
Query: 359 FYDEERFSKNEL 370
+ D + + + +
Sbjct: 94 YCDPDSYHRRDF 105
>pdb|2EK6|A Chain A, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|B Chain B, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|C Chain C, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|D Chain D, Crystal Structure Of Human Rna-Binding Protein 12
Length = 95
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 304 YGTVTRVLIFEITEPNFPVDEAVRIFVQFERSEQTTKALIDLDGRFFGGRVVRAT 358
Y + + + E P EA+ V FE ++ T A+IDL+ R G R V+ +
Sbjct: 39 YQVIPGSVCLKYNEKGMPTGEAM---VAFESRDEATAAVIDLNDRPIGSRKVKLS 90
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 28.9 bits (63), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 304 YGTVTRVLIFEITEPNFPVDEAVRIFVQFERSEQTTKALIDLDGRFFGGRVVRATF 359
Y + + + E P EA+ V FE ++ T A+IDL+ R G R V+
Sbjct: 39 YQVIPGSVCLKYNEKGMPTGEAM---VAFESRDEATAAVIDLNDRPIGSRKVKLVL 91
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 27.7 bits (60), Expect = 9.9, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 315 ITEPNFPVDEAVR-----IFVQFERSEQTTKALIDLDGRFFGGRVV 355
++E ++P+D + FV F E KA ++DG+ F GR++
Sbjct: 35 LSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRML 80
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
0.315 0.132 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,347,988
Number of Sequences: 62578
Number of extensions: 245821
Number of successful extensions: 688
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 673
Number of HSP's gapped (non-prelim): 16
length of query: 381
length of database: 14,973,337
effective HSP length: 101
effective length of query: 280
effective length of database: 8,652,959
effective search space: 2422828520
effective search space used: 2422828520
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: 52 (24.6 bits)