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= 002093
(967 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 122 bits (305), Expect = 1e-27, Method: Composition-based stats.
Identities = 70/188 (37%), Positives = 108/188 (57%), Gaps = 3/188 (1%)
Query: 464 RRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQREKGQAFVEFLTAED 523
RRL V N+P +E+A+M+F N + G+ G+ P + I ++K AF+EF + ++
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN-PVLAVQINQDKNFAFLEFRSVDE 63
Query: 524 ASAALCCDGCSFSGSILKIKRPKEFVEVASGEAEKSVASVDSVSGIVKDSPHKIFIGGIS 583
+ A+ DG F G LKI+RP ++ + SV VS +V DS HK+FIGG+
Sbjct: 64 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLP 123
Query: 584 RTLSSKMVMEIVCAFGPLKAYHF--EVNEDHEEPCAFIEYVDQLVTPKAIAGLNGLKVGG 641
L+ V E++ +FGPLKA++ + + AF EYVD VT +AIAGLNG+++G
Sbjct: 124 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 183
Query: 642 QVLTAVQA 649
+ L +A
Sbjct: 184 KKLLVQRA 191
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 105 bits (263), Expect = 9e-23, Method: Composition-based stats.
Identities = 63/188 (33%), Positives = 100/188 (53%), Gaps = 23/188 (12%)
Query: 464 RRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQREKGQAFVEFLTAED 523
RRL V N+P +E+A+M+F N + G+ G+ P + I ++K AF+EF + ++
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN-PVLAVQINQDKNFAFLEFRSVDE 63
Query: 524 ASAALCCDGCSFSGSILKIKRPKEFVEVASGEAEKSVASVDSVSGIVKDSPHKIFIGGIS 583
+ A+ DG F G LKI+RP ++ + HK+FIGG+
Sbjct: 64 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGA--------------------HKLFIGGLP 103
Query: 584 RTLSSKMVMEIVCAFGPLKAYHF--EVNEDHEEPCAFIEYVDQLVTPKAIAGLNGLKVGG 641
L+ V E++ +FGPLKA++ + + AF EYVD VT +AIAGLNG+++G
Sbjct: 104 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 163
Query: 642 QVLTAVQA 649
+ L +A
Sbjct: 164 KKLLVQRA 171
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 105 bits (263), Expect = 1e-22, Method: Composition-based stats.
Identities = 63/188 (33%), Positives = 100/188 (53%), Gaps = 23/188 (12%)
Query: 464 RRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQREKGQAFVEFLTAED 523
RRL V N+P +E+A+M+F N + G+ G+ P + I ++K AF+EF + ++
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN-PVLAVQINQDKNFAFLEFRSVDE 65
Query: 524 ASAALCCDGCSFSGSILKIKRPKEFVEVASGEAEKSVASVDSVSGIVKDSPHKIFIGGIS 583
+ A+ DG F G LKI+RP ++ + HK+FIGG+
Sbjct: 66 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGA--------------------HKLFIGGLP 105
Query: 584 RTLSSKMVMEIVCAFGPLKAYHF--EVNEDHEEPCAFIEYVDQLVTPKAIAGLNGLKVGG 641
L+ V E++ +FGPLKA++ + + AF EYVD VT +AIAGLNG+++G
Sbjct: 106 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 165
Query: 642 QVLTAVQA 649
+ L +A
Sbjct: 166 KKLLVQRA 173
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 62.8 bits (151), Expect = 8e-10, Method: Composition-based stats.
Identities = 30/85 (35%), Positives = 50/85 (58%), Gaps = 1/85 (1%)
Query: 464 RRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQREKGQAFVEFLTAED 523
RRL V N+P +E+A+M+F N + G+ G+ P + I ++K AF+EF + ++
Sbjct: 2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN-PVLAVQINQDKNFAFLEFRSVDE 60
Query: 524 ASAALCCDGCSFSGSILKIKRPKEF 548
+ A+ DG F G LKI+RP ++
Sbjct: 61 TTQAMAFDGIIFQGQSLKIRRPHDY 85
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 61.2 bits (147), Expect = 2e-09, Method: Composition-based stats.
Identities = 30/82 (36%), Positives = 48/82 (58%), Gaps = 1/82 (1%)
Query: 464 RRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQREKGQAFVEFLTAED 523
RRL V N+P +E+A+M+F N + G+ G+ P + I ++K AF+EF + ++
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN-PVLAVQINQDKNFAFLEFRSVDE 65
Query: 524 ASAALCCDGCSFSGSILKIKRP 545
+ A+ DG F G LKI+RP
Sbjct: 66 TTQAMAFDGIIFQGQSLKIRRP 87
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 60.5 bits (145), Expect = 4e-09, Method: Composition-based stats.
Identities = 33/77 (42%), Positives = 49/77 (63%), Gaps = 2/77 (2%)
Query: 575 HKIFIGGISRTLSSKMVMEIVCAFGPLKAYHF--EVNEDHEEPCAFIEYVDQLVTPKAIA 632
HK+FIGG+ L+ V E++ +FGPLKA++ + + AF EYVD VT +AIA
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
Query: 633 GLNGLKVGGQVLTAVQA 649
GLNG+++G + L +A
Sbjct: 62 GLNGMQLGDKKLLVQRA 78
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 38.5 bits (88), Expect = 0.016, Method: Composition-based stats.
Identities = 36/148 (24%), Positives = 65/148 (43%), Gaps = 12/148 (8%)
Query: 506 VIQREKGQAFVEFLTAEDASAAL-CCDGCSFSGSILKIKRPKEFVEVASGEAEKSVASVD 564
V + KG AFVE+ E A AL + G +K+ RP G+A+ + +
Sbjct: 65 VTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI-----GQAQPIIDQLA 119
Query: 565 SVSGIVKDSPHKIFIGGISRTLSSKMVMEIVCAFGPLKAYHF--EVNEDHEEPCAFIEYV 622
+ + ++I++ + + LS + + AFG +K+ + + FIEY
Sbjct: 120 EEA----RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE 175
Query: 623 DQLVTPKAIAGLNGLKVGGQVLTAVQAV 650
+ A++ +N +GGQ L +AV
Sbjct: 176 KAQSSQDAVSSMNLFDLGGQYLRVGKAV 203
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 38.5 bits (88), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 567 SGIVKD--SPHKIFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDHEEPCAFIEYVDQ 624
SG+++D P +++G +SR ++ +++++ GP K+ +P F+E+ +
Sbjct: 6 SGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEH 65
Query: 625 LVTPKAIAGLNGLKVGGQ 642
A+A +NG K+ G+
Sbjct: 66 RDAAAALAAMNGRKILGK 83
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.7 bits (86), Expect = 0.035, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 574 PHKIFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDH---EEPCAFIEYVDQLVTPKA 630
P K+ IG ++R ++ +MEI +G +K V H + A++E+ + KA
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63
Query: 631 IAGLNGLKVGGQVLTA 646
+ ++G ++ GQ +TA
Sbjct: 64 LKHMDGGQIDGQEITA 79
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 37.4 bits (85), Expect = 0.041, Method: Composition-based stats.
Identities = 36/148 (24%), Positives = 64/148 (43%), Gaps = 12/148 (8%)
Query: 506 VIQREKGQAFVEFLTAEDASAAL-CCDGCSFSGSILKIKRPKEFVEVASGEAEKSVASVD 564
V + KG AFVE+ E A AL + G +K+ RP G+A+ + +
Sbjct: 49 VTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNI-----GQAQPIIDQLA 103
Query: 565 SVSGIVKDSPHKIFIGGISRTLSSKMVMEIVCAFGPLKAYHF--EVNEDHEEPCAFIEYV 622
+ + ++I++ + + LS + + AFG +K+ + + FIEY
Sbjct: 104 EEA----RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 159
Query: 623 DQLVTPKAIAGLNGLKVGGQVLTAVQAV 650
+ A++ N +GGQ L +AV
Sbjct: 160 KAQSSQDAVSSXNLFDLGGQYLRVGKAV 187
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 35.4 bits (80), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 36/148 (24%), Positives = 65/148 (43%), Gaps = 12/148 (8%)
Query: 506 VIQREKGQAFVEFLTAEDASAAL-CCDGCSFSGSILKIKRPKEFVEVASGEAEKSVASVD 564
V + KG AFVE+ E A AL + G +K+ RP G+A+ + +
Sbjct: 50 VTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI-----GQAQPIIDQLA 104
Query: 565 SVSGIVKDSPHKIFIGGISRTLSSKMVMEIVCAFGPLKAYHF--EVNEDHEEPCAFIEYV 622
+ + ++I++ + + LS + + AFG +K+ + + FIEY
Sbjct: 105 EEA----RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 160
Query: 623 DQLVTPKAIAGLNGLKVGGQVLTAVQAV 650
+ A++ +N +GGQ L +AV
Sbjct: 161 KAQSSQDAVSSMNLFDLGGQYLRVGKAV 188
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 34.3 bits (77), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 572 DSPHKIFIGGISRTLSSKMVMEIVCAFGPL-KAYHFEVNEDHEEPCAFIEYVDQLVTPKA 630
D P K+FIGG++R + KM+ + GP+ + + AFI + + A
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNA 64
Query: 631 IAGLNGLKVGGQVLTAVQA 649
+NG + G+ + QA
Sbjct: 65 AKDMNGKSLHGKAIKVEQA 83
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 33.9 bits (76), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 2/77 (2%)
Query: 570 VKDSPHKIFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDHEEP--CAFIEYVDQLVT 627
V S +F+G I + + + +I GP+ ++ + + +P F EY DQ
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 628 PKAIAGLNGLKVGGQVL 644
A+ LNG + G+ L
Sbjct: 64 LSAMRNLNGREFSGRAL 80
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 32.7 bits (73), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 32/132 (24%), Positives = 55/132 (41%), Gaps = 27/132 (20%)
Query: 512 GQAFVEFLTAEDASAAL-CCDGCSFSGSILKIK--RPKEFVEVASGEAEKSVASVDSVSG 568
G FV ++TA+DA A+ +G +K+ RP S
Sbjct: 45 GYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS--------------------SE 84
Query: 569 IVKDSPHKIFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDH--EEPCAFIEYVDQLV 626
++KD+ ++I G+ RT++ K V ++ FG + V++ AFI + +
Sbjct: 85 VIKDA--NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSE 142
Query: 627 TPKAIAGLNGLK 638
+AI NG K
Sbjct: 143 AEEAITSFNGHK 154
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 32.7 bits (73), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 32/132 (24%), Positives = 55/132 (41%), Gaps = 27/132 (20%)
Query: 512 GQAFVEFLTAEDASAAL-CCDGCSFSGSILKIK--RPKEFVEVASGEAEKSVASVDSVSG 568
G FV ++TA+DA A+ +G +K+ RP S
Sbjct: 45 GYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPS--------------------SE 84
Query: 569 IVKDSPHKIFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDH--EEPCAFIEYVDQLV 626
++KD+ ++I G+ RT++ K V ++ FG + V++ AFI + +
Sbjct: 85 VIKDA--NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSE 142
Query: 627 TPKAIAGLNGLK 638
+AI NG K
Sbjct: 143 AEEAITSFNGHK 154
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 41/187 (21%), Positives = 76/187 (40%), Gaps = 23/187 (12%)
Query: 451 MDSVQLTQSNRPMRRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQRE 510
+ S+ + + PM L V +L +E L E F + + + C + +R
Sbjct: 3 LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYE---KFSPAGPILSIR---VCRDMITRRS 56
Query: 511 KGQAFVEFLTAEDASAALCCDGCSFSGSILKIKRPKEFVEVASGEAEKSVASVDSVSGIV 570
G A+V F DA AL D +F +V G+ + + S S +
Sbjct: 57 LGYAYVNFQQPADAERAL--DTMNF--------------DVIKGKPVRIMWSQRDPS-LR 99
Query: 571 KDSPHKIFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDHEEPCAFIEYVDQLVTPKA 630
K IFI + +++ +K + + AFG + + +E+ + F+ + Q +A
Sbjct: 100 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERA 159
Query: 631 IAGLNGL 637
I +NG+
Sbjct: 160 IEKMNGM 166
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 11/81 (13%)
Query: 464 RRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQREKGQAFVEFLTAED 523
+ L + NL SA+E+ L E Q+ +G + KG AF+EF + ED
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNG----------KSKGYAFIEFASFED 65
Query: 524 ASAAL-CCDGCSFSGSILKIK 543
A AL C+ G ++++
Sbjct: 66 AKEALNSCNKREIEGRAIRLE 86
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 31/136 (22%), Positives = 57/136 (41%), Gaps = 17/136 (12%)
Query: 502 CIGCVIQREKGQAFVEFLTAEDASAALCCDGCSFSGSILKIKRPKEFVEVASGEAEKSVA 561
C + +R G A+V F DA AL D +F +V G+ + +
Sbjct: 43 CRDMITRRSLGYAYVNFQQPADAERAL--DTMNF--------------DVIKGKPVRIMW 86
Query: 562 SVDSVSGIVKDSPHKIFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDHEEPCAFIEY 621
S S + K IFI + +++ +K + + AFG + + +E+ + F+ +
Sbjct: 87 SQRDPS-LRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHF 145
Query: 622 VDQLVTPKAIAGLNGL 637
Q +AI +NG+
Sbjct: 146 ETQEAAERAIEKMNGM 161
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 31.2 bits (69), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 11/91 (12%)
Query: 489 LSSGVQHVHGS--LPCIGCVIQREKGQAFVEFLTAEDASAALCCDGCSFSGSILKIKRPK 546
L +G+ V L + I + +V+F +AED AL G G+ +K+++PK
Sbjct: 24 LKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK 83
Query: 547 EFVEVASGEAEKSVASVDSVSGIVKDSPHKI 577
+ S D+ + + K+ P+K+
Sbjct: 84 ---------GKDSKKERDARTLLAKNLPYKV 105
>pdb|3H2V|E Chain E, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|F Chain F, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|G Chain G, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|H Chain H, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
Length = 74
Score = 30.8 bits (68), Expect = 3.5, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 13/66 (19%)
Query: 463 MRRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQREKGQAFVEFLTAE 522
MR++ + LP + + + + L+++ L C + + KG AFV L E
Sbjct: 2 MRKILIRGLPGDVTNQEVHDLLSDYELKY-------------CFVDKYKGTAFVTLLNGE 48
Query: 523 DASAAL 528
A AA+
Sbjct: 49 QAEAAI 54
>pdb|1X4F|A Chain A, Solution Structure Of The Second Rrm Domain In Matrin 3
Length = 112
Score = 30.8 bits (68), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 7/54 (12%)
Query: 506 VIQREKGQAFVEFLTAEDASAALCCDGC-----SFSGSILKIKRPKEFVEVASG 554
++ R K QAF+E T EDA A + D C F G +K+ +++ ++ SG
Sbjct: 57 ILMRMKSQAFIEMETREDAMAMV--DHCLKKALWFQGRCVKVDLSEKYKKLVSG 108
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 30.8 bits (68), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 576 KIFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDHEEP--CAFIEYVDQLVTPKAIAG 633
++F+ +S T S + + ++ A+GPL H+ ++ ++P AF+ ++ KA A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 634 LNGLKVGGQVLTAVQAVL 651
++G G++L + + +
Sbjct: 70 VDGQVFQGRMLHVLPSTI 87
>pdb|2DB1|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein F Homolog
Length = 118
Score = 30.8 bits (68), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 468 VENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQREKGQAFVEFLTAEDASAA 527
+ LP S S + + FL++ + GV VH I R+ G+AFVE + +D A
Sbjct: 22 LRGLPWSCSIEDVQNFLSDCTIHDGVAGVH----FIYTREGRQSGEAFVELESEDDVKLA 77
Query: 528 L 528
L
Sbjct: 78 L 78
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 30.0 bits (66), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 576 KIFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDHEEPCAFIEYVDQLVTPKAIAGLN 635
++FIG ++ + K +E + Y V + AF++YV++ A+AG +
Sbjct: 17 RVFIGNLNTLVVKKSDVEAI-----FSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGED 71
Query: 636 GLKVGGQVL 644
G + GQVL
Sbjct: 72 GRMIAGQVL 80
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 30.0 bits (66), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 31/61 (50%)
Query: 577 IFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDHEEPCAFIEYVDQLVTPKAIAGLNG 636
IFI + +++ +K + + AFG + + +E+ + F+ + Q +AI +NG
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 637 L 637
+
Sbjct: 74 M 74
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 29.6 bits (65), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 567 SGIVKDSPHKIFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDH----EEPCAFIEYV 622
SG+ K+FIG I R L K + + FG K Y V +D + CAF+ Y
Sbjct: 6 SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFG--KIYELTVLKDRFTGMHKGCAFLTYC 63
Query: 623 DQLVTPKAIAGLN 635
++ KA + L+
Sbjct: 64 ERESALKAQSALH 76
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
0.309 0.127 0.354
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,556,488
Number of Sequences: 62578
Number of extensions: 1011362
Number of successful extensions: 1988
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 1927
Number of HSP's gapped (non-prelim): 69
length of query: 967
length of database: 14,973,337
effective HSP length: 108
effective length of query: 859
effective length of database: 8,214,913
effective search space: 7056610267
effective search space used: 7056610267
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 56 (26.2 bits)