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= 002280
(943 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 107 bits (266), Expect = 4e-23, Method: Composition-based stats.
Identities = 61/168 (36%), Positives = 98/168 (58%), Gaps = 7/168 (4%)
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 ASAALCCDGCSFSGSILKIKRPKEFVEV----AIFIGGISRTLSSKMVMEIVCAFGPLKA 579
+ A+ DG F G LKI+RP ++ + +FIGG+ L+ V E++ +FGPLKA
Sbjct: 64 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKA 123
Query: 580 YHF--EVNEDHEEPCAFIEYVDQLVTPKAIAGLNGLKVGGQVLTAVQA 625
++ + + AF EYVD VT +AIAGLNG+++G + L +A
Sbjct: 124 FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 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 = 107 bits (266), Expect = 4e-23, Method: Composition-based stats.
Identities = 61/168 (36%), Positives = 98/168 (58%), Gaps = 7/168 (4%)
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 ASAALCCDGCSFSGSILKIKRPKEFVEV----AIFIGGISRTLSSKMVMEIVCAFGPLKA 579
+ A+ DG F G LKI+RP ++ + +FIGG+ L+ V E++ +FGPLKA
Sbjct: 66 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKA 125
Query: 580 YHF--EVNEDHEEPCAFIEYVDQLVTPKAIAGLNGLKVGGQVLTAVQA 625
++ + + AF EYVD VT +AIAGLNG+++G + L +A
Sbjct: 126 FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 173
>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 = 97.8 bits (242), Expect = 2e-20, Method: Composition-based stats.
Identities = 61/188 (32%), Positives = 98/188 (52%), Gaps = 27/188 (14%)
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 ASAALCCDGCSFSGSILKIKRPKEFVEV------------------------AIFIGGIS 559
+ A+ DG F G LKI+RP ++ + +FIGG+
Sbjct: 64 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLP 123
Query: 560 RTLSSKMVMEIVCAFGPLKAYHF--EVNEDHEEPCAFIEYVDQLVTPKAIAGLNGLKVGG 617
L+ V E++ +FGPLKA++ + + AF EYVD VT +AIAGLNG+++G
Sbjct: 124 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD 183
Query: 618 QVLTAVQA 625
+ L +A
Sbjct: 184 KKLLVQRA 191
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 62.8 bits (151), Expect = 9e-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 = 3e-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 = 55.8 bits (133), Expect = 1e-07, Method: Composition-based stats.
Identities = 31/75 (41%), Positives = 47/75 (62%), Gaps = 2/75 (2%)
Query: 553 IFIGGISRTLSSKMVMEIVCAFGPLKAYHF--EVNEDHEEPCAFIEYVDQLVTPKAIAGL 610
+FIGG+ L+ V E++ +FGPLKA++ + + AF EYVD VT +AIAGL
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 611 NGLKVGGQVLTAVQA 625
NG+++G + L +A
Sbjct: 64 NGMQLGDKKLLVQRA 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 = 37.4 bits (85), Expect = 0.037, Method: Composition-based stats.
Identities = 36/139 (25%), Positives = 58/139 (41%), Gaps = 18/139 (12%)
Query: 506 VIQREKGQAFVEFLTAEDASAAL-CCDGCSFSGSILKIKRPK----------EFVEVA-- 552
V + KG AFVE+ E A AL + G +K+ RP + E A
Sbjct: 65 VTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124
Query: 553 ---IFIGGISRTLSSKMVMEIVCAFGPLKAYHF--EVNEDHEEPCAFIEYVDQLVTPKAI 607
I++ + + LS + + AFG +K+ + + FIEY + A+
Sbjct: 125 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
Query: 608 AGLNGLKVGGQVLTAVQAV 626
+ +N +GGQ L +AV
Sbjct: 185 SSMNLFDLGGQYLRVGKAV 203
>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 = 37.4 bits (85), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 50/110 (45%), Gaps = 7/110 (6%)
Query: 512 GQAFVEFLTAEDASAAL-CCDGCSFSGSILKIKRPKEFVEVA----IFIGGISRTLSSKM 566
G FV ++TA+DA A+ +G +K+ + EV ++I G+ RT++ K
Sbjct: 45 GYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKD 104
Query: 567 VMEIVCAFGPLKAYHFEVNEDH--EEPCAFIEYVDQLVTPKAIAGLNGLK 614
V ++ FG + V++ AFI + + +AI NG K
Sbjct: 105 VEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHK 154
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 37.4 bits (85), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 50/110 (45%), Gaps = 7/110 (6%)
Query: 512 GQAFVEFLTAEDASAAL-CCDGCSFSGSILKIKRPKEFVEVA----IFIGGISRTLSSKM 566
G FV ++TA+DA A+ +G +K+ + EV ++I G+ RT++ K
Sbjct: 45 GYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKD 104
Query: 567 VMEIVCAFGPLKAYHFEVNEDH--EEPCAFIEYVDQLVTPKAIAGLNGLK 614
V ++ FG + V++ AFI + + +AI NG K
Sbjct: 105 VEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHK 154
>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 = 35.8 bits (81), Expect = 0.10, Method: Composition-based stats.
Identities = 36/139 (25%), Positives = 57/139 (41%), Gaps = 18/139 (12%)
Query: 506 VIQREKGQAFVEFLTAEDASAAL-CCDGCSFSGSILKIKRPK----------EFVEVA-- 552
V + KG AFVE+ E A AL + G +K+ RP + E A
Sbjct: 49 VTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 108
Query: 553 ---IFIGGISRTLSSKMVMEIVCAFGPLKAYHF--EVNEDHEEPCAFIEYVDQLVTPKAI 607
I++ + + LS + + AFG +K+ + + FIEY + A+
Sbjct: 109 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Query: 608 AGLNGLKVGGQVLTAVQAV 626
+ N +GGQ L +AV
Sbjct: 169 SSXNLFDLGGQYLRVGKAV 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 = 34.3 bits (77), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 36/139 (25%), Positives = 58/139 (41%), Gaps = 18/139 (12%)
Query: 506 VIQREKGQAFVEFLTAEDASAAL-CCDGCSFSGSILKIKRPK----------EFVEVA-- 552
V + KG AFVE+ E A AL + G +K+ RP + E A
Sbjct: 50 VTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 109
Query: 553 ---IFIGGISRTLSSKMVMEIVCAFGPLKAYHF--EVNEDHEEPCAFIEYVDQLVTPKAI 607
I++ + + LS + + AFG +K+ + + FIEY + A+
Sbjct: 110 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 169
Query: 608 AGLNGLKVGGQVLTAVQAV 626
+ +N +GGQ L +AV
Sbjct: 170 SSMNLFDLGGQYLRVGKAV 188
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 34.3 bits (77), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 35/67 (52%)
Query: 552 AIFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDHEEPCAFIEYVDQLVTPKAIAGLN 611
+++G +SR ++ +++++ GP K+ +P F+E+ + A+A +N
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 76
Query: 612 GLKVGGQ 618
G K+ G+
Sbjct: 77 GRKILGK 83
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 33.5 bits (75), Expect = 0.57, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 553 IFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDH---EEPCAFIEYVDQLVTPKAIAG 609
+ IG ++R ++ +MEI +G +K V H + A++E+ + KA+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 610 LNGLKVGGQVLTA 622
++G ++ GQ +TA
Sbjct: 67 MDGGQIDGQEITA 79
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 33.5 bits (75), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 552 AIFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDHEEP--CAFIEYVDQLVTPKAIAG 609
++F+G I + + + +I GP+ ++ + + +P F EY DQ A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 610 LNGLKVGGQVL 620
LNG + G+ L
Sbjct: 70 LNGREFSGRAL 80
>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 = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 38/172 (22%), Positives = 72/172 (41%), Gaps = 17/172 (9%)
Query: 451 MDSVQLTQSNRPMRRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQRE 510
+ S+ + + PM L V +L +E L E F + + + C + +R
Sbjct: 3 LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYE---KFSPAGPILSIR---VCRDMITRRS 56
Query: 511 KGQAFVEFLTAEDASAALCCDGCSF---SGSILKIKRPKEFVEVA------IFIGGISRT 561
G A+V F DA AL D +F G ++I + + IFI + ++
Sbjct: 57 LGYAYVNFQQPADAERAL--DTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKS 114
Query: 562 LSSKMVMEIVCAFGPLKAYHFEVNEDHEEPCAFIEYVDQLVTPKAIAGLNGL 613
+ +K + + AFG + + +E+ + F+ + Q +AI +NG+
Sbjct: 115 IDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGM 166
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 35/165 (21%), Positives = 69/165 (41%), Gaps = 22/165 (13%)
Query: 461 RPMRRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQREKGQAFVEFLT 520
R R++ + LP + + + + L+++ L C + + KG AFV L
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLSDYELKY-------------CFVDKYKGTAFVTLLN 66
Query: 521 AEDASAALCCDGCSFSGSILKIKRPK---EFVEVAIFIGGISRTLSSKMVMEIVCAFGPL 577
E A AA+ +F S L+ + + + + + + +L+ + E+V FG L
Sbjct: 67 GEQAEAAI----NAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSL 122
Query: 578 KAYHFEVNE--DHEEPCAFIEYVDQLVTPKAIAGLNGLKVGGQVL 620
+ +E + F EY+ + +A + L G +G + L
Sbjct: 123 ERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL 167
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 35/165 (21%), Positives = 69/165 (41%), Gaps = 22/165 (13%)
Query: 461 RPMRRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQREKGQAFVEFLT 520
R R++ + LP + + + + L+++ L C + + KG AFV L
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLSDYELKY-------------CFVDKYKGTAFVTLLN 66
Query: 521 AEDASAALCCDGCSFSGSILKIKRPK---EFVEVAIFIGGISRTLSSKMVMEIVCAFGPL 577
E A AA+ +F S L+ + + + + + + +L+ + E+V FG L
Sbjct: 67 GEQAEAAI----NAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSL 122
Query: 578 KAYHFEVNE--DHEEPCAFIEYVDQLVTPKAIAGLNGLKVGGQVL 620
+ +E + F EY+ + +A + L G +G + L
Sbjct: 123 ERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL 167
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 32.3 bits (72), Expect = 1.3, Method: Composition-based stats.
Identities = 35/165 (21%), Positives = 69/165 (41%), Gaps = 22/165 (13%)
Query: 461 RPMRRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVIQREKGQAFVEFLT 520
R R++ + LP + + + + L+++ L C + + KG AFV L
Sbjct: 18 RNRRKILIRGLPGDVTNQEVHDLLSDYELKY-------------CFVDKYKGTAFVTLLN 64
Query: 521 AEDASAALCCDGCSFSGSILKIKRPK---EFVEVAIFIGGISRTLSSKMVMEIVCAFGPL 577
E A AA+ +F S L+ + + + + + + +L+ + E+V FG L
Sbjct: 65 GEQAEAAI----NAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSL 120
Query: 578 KAYHFEVNE--DHEEPCAFIEYVDQLVTPKAIAGLNGLKVGGQVL 620
+ +E + F EY+ + +A + L G +G + L
Sbjct: 121 ERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL 165
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 32.0 bits (71), Expect = 1.6, 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 = 31.6 bits (70), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 28/121 (23%), Positives = 53/121 (43%), Gaps = 11/121 (9%)
Query: 502 CIGCVIQREKGQAFVEFLTAEDASAALCCDGCSF---SGSILKIKRPKEFVEVA------ 552
C + +R G A+V F DA AL D +F G ++I + +
Sbjct: 43 CRDMITRRSLGYAYVNFQQPADAERAL--DTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 100
Query: 553 IFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDHEEPCAFIEYVDQLVTPKAIAGLNG 612
IFI + +++ +K + + AFG + + +E+ + F+ + Q +AI +NG
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 160
Query: 613 L 613
+
Sbjct: 161 M 161
>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 = 3.6, 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|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 = 4.1, 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|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 30.0 bits (66), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 553 IFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDHEEP--CAFIEYVDQLVTPKAIAGL 610
+F+ +S T S + + ++ A+GPL H+ ++ ++P AF+ ++ KA A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 611 NGLKVGGQVLTAVQAVL 627
+G G++L + + +
Sbjct: 71 DGQVFQGRMLHVLPSTI 87
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 30.0 bits (66), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 31/61 (50%)
Query: 553 IFIGGISRTLSSKMVMEIVCAFGPLKAYHFEVNEDHEEPCAFIEYVDQLVTPKAIAGLNG 612
IFI + +++ +K + + AFG + + +E+ + F+ + Q +AI +NG
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 613 L 613
+
Sbjct: 74 M 74
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 29.6 bits (65), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 14/94 (14%)
Query: 464 RRLCVENLPLSASEKALMEFLNNFLLSSGVQHVHGSLPCIGCVI----QREKGQAFVEFL 519
+ + + NL + E+AL E L F G L + V+ + KG AF +F+
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQF----------GDLKYVRVVLHPDTEHSKGCAFAQFM 65
Query: 520 TAEDASAALCCDGCSFSGSILKIKRPKEFVEVAI 553
T E A L G LK+ + V++A+
Sbjct: 66 TQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAV 99
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
0.310 0.127 0.356
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,895,687
Number of Sequences: 62578
Number of extensions: 983182
Number of successful extensions: 1913
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 1847
Number of HSP's gapped (non-prelim): 67
length of query: 943
length of database: 14,973,337
effective HSP length: 108
effective length of query: 835
effective length of database: 8,214,913
effective search space: 6859452355
effective search space used: 6859452355
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)