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= 021488
(311 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 51/86 (59%), Gaps = 1/86 (1%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALKLD 124
+Y+GN+ + T +DL+ FS C I+ + +K +G +GYA+++F++ S+ A+ +D
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD 98
Query: 125 QEVVRGRPVKISCAVPPKKGINSKSR 150
+ V RGR +K+ GI+S R
Sbjct: 99 ETVFRGRTIKVLPKRTNMPGISSTDR 124
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALKLD 124
IY+GN+ + T E+L+ F C ++ + +K +G +G+A+++FSD S+ +L LD
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 68
Query: 125 QEVVRGRPVKI 135
+ + RGR +K+
Sbjct: 69 ESLFRGRQIKV 79
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 45/71 (63%), Gaps = 1/71 (1%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALKLD 124
IY+GN+ + T E+L+ F C ++ + +K +G +G+A+++FSD S+ +L LD
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 67
Query: 125 QEVVRGRPVKI 135
+ + RGR +K+
Sbjct: 68 ESLFRGRQIKV 78
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 43/72 (59%)
Query: 67 YIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALKLDQE 126
Y+GNL ++ + D+ +F D I S+R +K+T +F+G+ +V+F + SL AL D
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGA 78
Query: 127 VVRGRPVKISCA 138
++ R +++ A
Sbjct: 79 LLGDRSLRVDIA 90
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 47/76 (61%), Gaps = 2/76 (2%)
Query: 62 GYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMA 120
G R+Y+G+L ++ITE+ L+ +F +I S++ + ETG +GY + FSDS A
Sbjct: 25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 121 L-KLDQEVVRGRPVKI 135
L +L+ + GRP+K+
Sbjct: 85 LEQLNGFELAGRPMKV 100
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 57 PKIVEGYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDS- 114
P + +++GN+ ++ TEE LK +FS+ + S R ++ETG+ +GY ++ D
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 115 LSLSMALKLDQEVVRGRPVKISCA 138
+LS L+ GR +++ A
Sbjct: 62 TALSAMRNLNGREFSGRALRVDNA 85
>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 = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 58/114 (50%), Gaps = 3/114 (2%)
Query: 6 TGKFRGIAIINFRTEGAVKRAL-ALDGSEMDGLFLKI-QPYKATKAKRTSDFTPKIVEGY 63
T K +G A + + A + AL ++ + G +K+ +P +A+ D + +
Sbjct: 66 TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF 125
Query: 64 NRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLS 116
NRIY+ ++ D++++D+K +F KI S + TG+ +GY +++ + S
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQS 179
>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 = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 29/114 (25%), Positives = 57/114 (50%), Gaps = 3/114 (2%)
Query: 6 TGKFRGIAIINFRTEGAVKRALALDGS-EMDGLFLKI-QPYKATKAKRTSDFTPKIVEGY 63
T K +G A + + A + AL S + G +K+ +P +A+ D + +
Sbjct: 50 TXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF 109
Query: 64 NRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLS 116
NRIY+ ++ D++++D+K +F KI S + TG+ +GY +++ + S
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQS 163
>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 = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 58/114 (50%), Gaps = 3/114 (2%)
Query: 6 TGKFRGIAIINFRTEGAVKRAL-ALDGSEMDGLFLKI-QPYKATKAKRTSDFTPKIVEGY 63
T K +G A + + A + AL ++ + G +K+ +P +A+ D + +
Sbjct: 51 TMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF 110
Query: 64 NRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLS 116
NRIY+ ++ D++++D+K +F KI S + TG+ +GY +++ + S
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQS 164
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 46/76 (60%), Gaps = 2/76 (2%)
Query: 62 GYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMA 120
G + +Y+G+L ++ITE+ L+ +F KI ++ + +TG +GY + FSDS A
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 121 L-KLDQEVVRGRPVKI 135
L +L+ + GRP+++
Sbjct: 64 LEQLNGFELAGRPMRV 79
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 10/77 (12%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKET--GEFRGYAHVDF-SDSLSLSMAL 121
R+++GNL DITEED K+LF R+G E RG+ + S +L+
Sbjct: 24 RLFVGNLPTDITEEDFKRLFE-------RYGEPSEVFINRDRGFGFIRLESRTLAEIAKA 76
Query: 122 KLDQEVVRGRPVKISCA 138
+LD +++ RP++I A
Sbjct: 77 ELDGTILKSRPLRIRFA 93
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALKLD 124
IY+GNL + T E +K+LFS K+ +++ ++ET + +G+ V+ + KLD
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 125 QEVVRGRPVKISCAVPPK 142
GR ++++ A P K
Sbjct: 64 NTDFMGRTIRVTEANPKK 81
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 44/81 (54%), Gaps = 4/81 (4%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMAL-K 122
+++G+LS +IT ED+K F+ KIS R + TG+ +GY V F + L A+
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 123 LDQEVVRGRPVKISCAV--PP 141
+ + + GR ++ + A PP
Sbjct: 77 MGGQWLGGRQIRTNWATRKPP 97
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 44/91 (48%), Gaps = 6/91 (6%)
Query: 63 YNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMAL 121
+ +I++G L + T+ L+K F I T+++TG+ RGY V +D + A
Sbjct: 17 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76
Query: 122 KLDQEVVRGRPVKISCAVPPKKGINSKSRSL 152
K ++ GR ++ A + +K RSL
Sbjct: 77 KDPNPIIDGRKANVNLAY-----LGAKPRSL 102
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 60/140 (42%), Gaps = 5/140 (3%)
Query: 1 MTFPDTGKFRGIAIINFRTEGAVKRALALDGSEMDGLFLKIQPYKATKAKRTSDFTPKIV 60
M P+T + RG + + T V A+ ++DG ++P +A R P
Sbjct: 47 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRV--VEPKRA--VSREDSQRPGAH 102
Query: 61 EGYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSM 119
+I++G + D E L+ F KI + T++ +G+ RG+A V F D S+
Sbjct: 103 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 162
Query: 120 ALKLDQEVVRGRPVKISCAV 139
+ V G ++ A+
Sbjct: 163 IVIQKYHTVNGHNCEVRKAL 182
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 27/113 (23%), Positives = 49/113 (43%), Gaps = 17/113 (15%)
Query: 56 TPKIVEGYNRIYIGNLSWDITEEDLKKLF------SDCKISSLRFGTNKETGEFRGYAHV 109
+PK E +++IG LS++ T+E L+ F +DC + +R K + RG+ V
Sbjct: 7 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV--MRDPNTKRS---RGFGFV 61
Query: 110 DFSDSLSLSMALKLDQEVVRGRPVKISCAVPPKKGINSKSRSLPSNKRATSKV 162
++ + A+ V GR V PK+ ++ + P K+
Sbjct: 62 TYATVEEVDAAMNARPHKVDGR------VVEPKRAVSREDSQRPGAHLTVKKI 108
>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 = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-L 123
+Y+G+L D+TE L + FS I S+R + T GYA+V+F AL +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 124 DQEVVRGRPVKI 135
+ +V++G+PV+I
Sbjct: 78 NFDVIKGKPVRI 89
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALKL 123
+++IG L+WD TE++L++ F ++ L+ + TG RG+ + F S+ +K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 124 DQEVVRGRPVKISCAVP 140
Q ++ G+ + A+P
Sbjct: 65 -QHILDGKVIDPKRAIP 80
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 60/140 (42%), Gaps = 5/140 (3%)
Query: 1 MTFPDTGKFRGIAIINFRTEGAVKRALALDGSEMDGLFLKIQPYKATKAKRTSDFTPKIV 60
M P+T + RG + + T V A+ ++DG ++P +A R P
Sbjct: 45 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRV--VEPKRA--VSREDSQRPGAH 100
Query: 61 EGYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSM 119
+I++G + D E L+ F KI + T++ +G+ RG+A V F D S+
Sbjct: 101 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 160
Query: 120 ALKLDQEVVRGRPVKISCAV 139
+ V G ++ A+
Sbjct: 161 IVIQKYHTVNGHNCEVRKAL 180
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 27/113 (23%), Positives = 49/113 (43%), Gaps = 17/113 (15%)
Query: 56 TPKIVEGYNRIYIGNLSWDITEEDLKKLF------SDCKISSLRFGTNKETGEFRGYAHV 109
+PK E +++IG LS++ T+E L+ F +DC + +R K + RG+ V
Sbjct: 5 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV--MRDPNTKRS---RGFGFV 59
Query: 110 DFSDSLSLSMALKLDQEVVRGRPVKISCAVPPKKGINSKSRSLPSNKRATSKV 162
++ + A+ V GR V PK+ ++ + P K+
Sbjct: 60 TYATVEEVDAAMNARPHKVDGR------VVEPKRAVSREDSQRPGAHLTVKKI 106
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 60/140 (42%), Gaps = 5/140 (3%)
Query: 1 MTFPDTGKFRGIAIINFRTEGAVKRALALDGSEMDGLFLKIQPYKATKAKRTSDFTPKIV 60
M P+T + RG + + T V A+ ++DG ++P +A R P
Sbjct: 46 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRV--VEPKRA--VSREDSQRPGAH 101
Query: 61 EGYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSM 119
+I++G + D E L+ F KI + T++ +G+ RG+A V F D S+
Sbjct: 102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 161
Query: 120 ALKLDQEVVRGRPVKISCAV 139
+ V G ++ A+
Sbjct: 162 IVIQKYHTVNGHNCEVRKAL 181
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 27/113 (23%), Positives = 49/113 (43%), Gaps = 17/113 (15%)
Query: 56 TPKIVEGYNRIYIGNLSWDITEEDLKKLF------SDCKISSLRFGTNKETGEFRGYAHV 109
+PK E +++IG LS++ T+E L+ F +DC + +R K + RG+ V
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVV--MRDPNTKRS---RGFGFV 60
Query: 110 DFSDSLSLSMALKLDQEVVRGRPVKISCAVPPKKGINSKSRSLPSNKRATSKV 162
++ + A+ V GR V PK+ ++ + P K+
Sbjct: 61 TYATVEEVDAAMNARPHKVDGR------VVEPKRAVSREDSQRPGAHLTVKKI 107
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-L 123
+Y+G+L D+TE L + FS I S+R + T GYA+V+F AL +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 124 DQEVVRGRPVKI 135
+ +V++G+PV+I
Sbjct: 73 NFDVIKGKPVRI 84
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 60/140 (42%), Gaps = 5/140 (3%)
Query: 1 MTFPDTGKFRGIAIINFRTEGAVKRALALDGSEMDGLFLKIQPYKATKAKRTSDFTPKIV 60
M P+T + RG + + T V A+ ++DG ++P +A R P
Sbjct: 39 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRV--VEPKRA--VSREDSQRPGAH 94
Query: 61 EGYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSM 119
+I++G + D E L+ F KI + T++ +G+ RG+A V F D S+
Sbjct: 95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 154
Query: 120 ALKLDQEVVRGRPVKISCAV 139
+ V G ++ A+
Sbjct: 155 IVIQKYHTVNGHNCEVRKAL 174
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 24/108 (22%), Positives = 44/108 (40%), Gaps = 17/108 (15%)
Query: 61 EGYNRIYIGNLSWDITEEDLKKLF------SDCKISSLRFGTNKETGEFRGYAHVDFSDS 114
E +++IG LS++ T+E L+ F +DC + + T RG+ V ++
Sbjct: 4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR-----DPNTKRSRGFGFVTYATV 58
Query: 115 LSLSMALKLDQEVVRGRPVKISCAVPPKKGINSKSRSLPSNKRATSKV 162
+ A+ V GR V PK+ ++ + P K+
Sbjct: 59 EEVDAAMNARPHKVDGR------VVEPKRAVSREDSQRPGAHLTVKKI 100
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 60/140 (42%), Gaps = 5/140 (3%)
Query: 1 MTFPDTGKFRGIAIINFRTEGAVKRALALDGSEMDGLFLKIQPYKATKAKRTSDFTPKIV 60
M P+T + RG + + T V A+ ++DG ++P +A R P
Sbjct: 46 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRV--VEPKRA--VSREDSQRPGAH 101
Query: 61 EGYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSM 119
+I++G + D E L+ F KI + T++ +G+ RG+A V F D S+
Sbjct: 102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 161
Query: 120 ALKLDQEVVRGRPVKISCAV 139
+ V G ++ A+
Sbjct: 162 IVIQKYHTVNGHNCEVRKAL 181
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 26/113 (23%), Positives = 47/113 (41%), Gaps = 17/113 (15%)
Query: 56 TPKIVEGYNRIYIGNLSWDITEEDLKKLF------SDCKISSLRFGTNKETGEFRGYAHV 109
+PK E +++IG LS++ T+E L+ F +DC + + T RG+ V
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR-----DPNTKRSRGFGFV 60
Query: 110 DFSDSLSLSMALKLDQEVVRGRPVKISCAVPPKKGINSKSRSLPSNKRATSKV 162
++ + A+ V GR V PK+ ++ + P K+
Sbjct: 61 TYATVEEVDAAMNARPHKVDGR------VVEPKRAVSREDSQRPGAHLTVKKI 107
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 60/140 (42%), Gaps = 5/140 (3%)
Query: 1 MTFPDTGKFRGIAIINFRTEGAVKRALALDGSEMDGLFLKIQPYKATKAKRTSDFTPKIV 60
M P+T + RG + + T V A+ ++DG ++P +A R P
Sbjct: 44 MRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRV--VEPKRA--VSREDSQRPGAH 99
Query: 61 EGYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSM 119
+I++G + D E L+ F KI + T++ +G+ RG+A V F D S+
Sbjct: 100 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 159
Query: 120 ALKLDQEVVRGRPVKISCAV 139
+ V G ++ A+
Sbjct: 160 IVIQKYHTVNGHNCEVRKAL 179
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 26/113 (23%), Positives = 47/113 (41%), Gaps = 17/113 (15%)
Query: 56 TPKIVEGYNRIYIGNLSWDITEEDLKKLF------SDCKISSLRFGTNKETGEFRGYAHV 109
+PK E +++IG LS++ T+E L+ F +DC + + T RG+ V
Sbjct: 4 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR-----DPNTKRSRGFGFV 58
Query: 110 DFSDSLSLSMALKLDQEVVRGRPVKISCAVPPKKGINSKSRSLPSNKRATSKV 162
++ + A+ V GR V PK+ ++ + P K+
Sbjct: 59 TYATVEEVDAAMNARPHKVDGR------VVEPKRAVSREDSQRPGAHLTVKKI 105
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 45/91 (49%), Gaps = 10/91 (10%)
Query: 43 PYKATKAKRTSDFTPKIVEGY----NR---IYIGNLSWDITEEDLKKLFSDC---KISSL 92
P + + + ++ TP I+ Y NR +Y+G+ SW T++ L ++ + L
Sbjct: 28 PVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVEL 87
Query: 93 RFGTNKETGEFRGYAHVDFSDSLSLSMALKL 123
+F N+ G+ +GYA V + S+ L+L
Sbjct: 88 KFAENRANGQSKGYAEVVVASENSVHKLLEL 118
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 41/89 (46%), Gaps = 17/89 (19%)
Query: 61 EGYNRIYIGNLSWDITEEDLKKLFS------DCKISSLRFGTNKETGEFRGYAHVDFSDS 114
E + ++G LSWD +++DLK F+ DC I + TG RG+ + F D+
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKX-----DPNTGRSRGFGFILFKDA 63
Query: 115 LSLSMALKLDQEVVRGRPVKISCAVPPKK 143
S+ L + + GR + PKK
Sbjct: 64 ASVEKVLDQKEHRLDGR------VIDPKK 86
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 5/52 (9%)
Query: 62 GYNRIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSD 113
G N++YIGNLS +T +DL++LF D K+ + GYA VD+ D
Sbjct: 7 GMNKLYIGNLSPAVTADDLRQLFGDRKLP-----LAGQVLLKSGYAFVDYPD 53
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic
Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 44/81 (54%), Gaps = 4/81 (4%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMAL-K 122
+++G+LS +IT ED+K F+ +IS R + TG+ +GY V F + A+ +
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 123 LDQEVVRGRPVKISCAV--PP 141
+ + + GR ++ + A PP
Sbjct: 77 MGGQWLGGRQIRTNWATRKPP 97
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 67 YIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGE-FRGYAHVDFSDSLSLSMALKLDQ 125
++GNL +D+TEE +K+ F IS++R E +G+ + +F D SL AL L++
Sbjct: 19 FLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNE 78
Query: 126 EVVRGRPVKISCA 138
E + + +++ A
Sbjct: 79 ESLGNKRIRVDVA 91
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 50/105 (47%), Gaps = 11/105 (10%)
Query: 10 RGIAIINFRTEGAVKRALALDGSEMDGLFLKIQPYKATKAKRTSDFTPKIVEGYNRIYIG 69
+ A + FR+ +A+A DG G LKI +R D+ P + G ++++IG
Sbjct: 53 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKI--------RRPHDYQP--LPGAHKLFIG 102
Query: 70 NLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSD 113
L + ++ +K+L + + + + TG +GYA ++ D
Sbjct: 103 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 147
Score = 30.8 bits (68), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 14/81 (17%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDCKISSLRFG----------TNKETGEFRGYAHVDFSDS 114
R+Y+GN+ + ITEE + F+ + +R G + + + +A ++F
Sbjct: 8 RLYVGNIPFGITEEAMMDFFN----AQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63
Query: 115 LSLSMALKLDQEVVRGRPVKI 135
+ A+ D + +G+ +KI
Sbjct: 64 DETTQAMAFDGIIFQGQSLKI 84
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 52/94 (55%), Gaps = 11/94 (11%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFS---DSLSLSMA 120
++++G LS+D E+ L+++FS +IS + ++ET RG+ V F D+ MA
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 121 LKLDQEVVRGRPVKISCAVPPKKGINSKSRSLPS 154
++ + V GR +++ A G +S +RS PS
Sbjct: 74 --MNGKSVDGRQIRVDQA-----GKSSDNRSGPS 100
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/105 (24%), Positives = 50/105 (47%), Gaps = 11/105 (10%)
Query: 10 RGIAIINFRTEGAVKRALALDGSEMDGLFLKIQPYKATKAKRTSDFTPKIVEGYNRIYIG 69
+ A + FR+ +A+A DG G LKI +R D+ P + G ++++IG
Sbjct: 51 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKI--------RRPHDYQP--LPGAHKLFIG 100
Query: 70 NLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSD 113
L + ++ +K+L + + + + TG +GYA ++ D
Sbjct: 101 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 145
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 14/81 (17%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDCKISSLRFG----------TNKETGEFRGYAHVDFSDS 114
R+Y+GN+ + ITEE + F+ + +R G + + + +A ++F
Sbjct: 6 RLYVGNIPFGITEEAMMDFFN----AQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 115 LSLSMALKLDQEVVRGRPVKI 135
+ A+ D + +G+ +KI
Sbjct: 62 DETTQAMAFDGIIFQGQSLKI 82
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 28/106 (26%), Positives = 54/106 (50%), Gaps = 12/106 (11%)
Query: 6 TGKFRGIAIINFRTEGAVKRALALDGSEMDGLFLKIQPYKATKAKRTSDFTPKIVEGYNR 65
TG R ++F + +++AL L G ++ G +K++ K +K+ V
Sbjct: 50 TGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKK--------VRAART 101
Query: 66 IYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDF 111
+ NLS++ITE++LK++F D L + G+ +G A+++F
Sbjct: 102 LLAKNLSFNITEDELKEVFEDA----LEIRLVSQDGKSKGIAYIEF 143
>pdb|2LXU|A Chain A, Solution Nmr Structure Of The Eukaryotic Rna Recognition
Motif, Rrm1, From The Heterogeneous Nuclear
Ribonucleoprotein H From Homo Sapiens, Northeast
Structural Genomics Consortium (Nesg) Target Hr8614a
Length = 108
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 66 IYIGNLSWDITEEDLKKLFSDCKISS----LRFGTNKETGEFRGYAHVDFSDSLSLSMAL 121
+ + L W + +++++ FSDCKI + +RF +E G G A V+ + +AL
Sbjct: 10 VKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTRE-GRPSGEAFVELESEDEVKLAL 68
Query: 122 KLDQEVVRGRPVKI 135
K D+E + R V++
Sbjct: 69 KKDRETMGHRYVEV 82
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-L 123
+ + L D+T+ +L LF I++ R + +TG GYA VDF+ + A+K L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 124 DQEVVRGRPVKISCAVP 140
+ VR + +K+S A P
Sbjct: 66 NGITVRNKRLKVSYARP 82
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 68 IGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-LDQ 125
+ L D+T+ +L LF I++ R + +TG GYA VDF+ + A+K L+
Sbjct: 8 VNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNG 67
Query: 126 EVVRGRPVKISCAVP 140
VR + +K+S A P
Sbjct: 68 ITVRNKRLKVSYARP 82
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 67 YIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGE-FRGYAHVDFSDSLSLSMALKLDQ 125
++GNL +D+TEE +K+ F IS++R E +G+ + +F D SL AL L++
Sbjct: 23 FLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNE 82
Query: 126 EVVRGRPVKISCA 138
E + R +++ A
Sbjct: 83 ESLGNRRIRVDVA 95
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 2/84 (2%)
Query: 57 PKIVEGYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSL 115
P VEG + + NL++ + + L+++F ++ + ++ T E RG+A V F D
Sbjct: 41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR 100
Query: 116 SLSMALK-LDQEVVRGRPVKISCA 138
A+ +D V+ GR +++ A
Sbjct: 101 DAEDAMDAMDGAVLDGRELRVQMA 124
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 37.4 bits (85), Expect = 0.010, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALKLD 124
++IG LSWD T++DLK FS ++ + TG RG+ V F +S S+ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 125 QEVVRGRPV 133
+ + G+ +
Sbjct: 62 EHKLNGKVI 70
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 28/93 (30%), Positives = 52/93 (55%), Gaps = 6/93 (6%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFS-DSLSLSMALK 122
R+++ NLS+ +EEDL+KLFS +S L + + T + +G+A V F ++ +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 123 LDQEVVRGRPVKISCAVPPKKGINSKSRSLPSN 155
+D +V +GR + + + K+ S+S PS+
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKEA----SQSGPSS 98
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 73 WDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALKLDQEVVRGRP 132
+++TE+++ + + K ++R N G GY VDFS+ + ALK ++E + GR
Sbjct: 20 FNVTEKNVMEFLAPLKPVAIRIVRNAH-GNKTGYIFVDFSNEEEVKQALKCNREYMGGRY 78
Query: 133 VKI 135
+++
Sbjct: 79 IEV 81
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 45/75 (60%), Gaps = 4/75 (5%)
Query: 64 NRIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALKL 123
+R+++GNL DITEE+++KLF + F +K+ G G+ ++ + +L+ ++L
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKG--FGFIRLE-TRTLAEIAKVEL 71
Query: 124 DQEVVRGRPVKISCA 138
D +RG+ +++ A
Sbjct: 72 DNMPLRGKQLRVRFA 86
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 57 PKIVEGYN----RIYIGNLSWDITEEDLKKLFSDCKIS---SLRFGTNKETGEFRGYAHV 109
P +V Y +YIGNL+W T+EDL + ++ ++F N+ G+ +G+A V
Sbjct: 58 PNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 117
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 34/82 (41%), Gaps = 11/82 (13%)
Query: 65 RIYIGNLSWDITEEDLKKLFS------DCKISSLRFGTNKETGEFRGYAHVDFSDSLSLS 118
++++G L W T+E L+ FS DC I +K T + RG+ V F D +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMK-----DKTTNQSRGFGFVKFKDPNCVG 72
Query: 119 MALKLDQEVVRGRPVKISCAVP 140
L + GR + P
Sbjct: 73 TVLASRPHTLDGRNIDPKPCTP 94
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 35.4 bits (80), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 11/85 (12%)
Query: 61 EGYNRIYIGNLSWDITEEDLKKLF------SDCKISSLRFGTNKETGEFRGYAHVDFSDS 114
E + +++IG LS++ TEE L+ + +DC + +R +K + RG+ V FS
Sbjct: 25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVV--MRDPASKRS---RGFGFVTFSSM 79
Query: 115 LSLSMALKLDQEVVRGRPVKISCAV 139
+ A+ + GR V+ AV
Sbjct: 80 AEVDAAMAARPHSIDGRVVEPKRAV 104
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 45/75 (60%), Gaps = 4/75 (5%)
Query: 64 NRIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALKL 123
+R+++GNL DITEE+++KLF + F +K+ G G+ ++ + +L+ ++L
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVF-IHKDKG--FGFIRLE-TRTLAEIAKVEL 78
Query: 124 DQEVVRGRPVKISCA 138
D +RG+ +++ A
Sbjct: 79 DNMPLRGKQLRVRFA 93
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 35.4 bits (80), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-L 123
+ + L D T+ +L LF I++ R + +TG GYA VDF+ A+K L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 124 DQEVVRGRPVKISCAVP 140
+ VR + +K+S A P
Sbjct: 77 NGITVRNKRLKVSYARP 93
>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 = 35.4 bits (80), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 27/116 (23%), Positives = 53/116 (45%), Gaps = 13/116 (11%)
Query: 10 RGIAIINFRTEGAVKRALALDGSEMDGLFLKI------QPYKATKAKRTSDFTPKIV--- 60
+ A + FR+ +A+A DG G LKI QP ++ S + P +V
Sbjct: 51 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGM-SENPSVYVPGVVSTV 109
Query: 61 --EGYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSD 113
+ ++++IG L + ++ +K+L + + + + TG +GYA ++ D
Sbjct: 110 VPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 165
Score = 31.2 bits (69), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 14/81 (17%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDCKISSLRFG----------TNKETGEFRGYAHVDFSDS 114
R+Y+GN+ + ITEE + F+ + +R G + + + +A ++F
Sbjct: 6 RLYVGNIPFGITEEAMMDFFN----AQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 115 LSLSMALKLDQEVVRGRPVKI 135
+ A+ D + +G+ +KI
Sbjct: 62 DETTQAMAFDGIIFQGQSLKI 82
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 35.0 bits (79), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 66 IYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-LD 124
+++ LS D TEE LK+ F D + + R T++ETG +G+ VDF+ A + ++
Sbjct: 18 LFVKGLSEDTTEETLKESF-DGSVRA-RIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 125 QEVVRGRPVKISCAVP 140
+ G V + A P
Sbjct: 76 DGEIDGNKVTLDWAKP 91
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 35.0 bits (79), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 64 NRIYIGNLSWDITEEDLKKLFSDCKI---------SSLRFGTNKETGEFRGYAHVDFSDS 114
N I++ L ++T E + F I + T++ETG+ +G A V F D
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 115 LSLSMALK-LDQEVVRGRPVKISCA 138
S A+ D + G P+K+S A
Sbjct: 74 PSAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 35.0 bits (79), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 66 IYIGNLSWDITE----EDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMAL 121
+++G+L+ D+ + E K++ C+ + +TG +GY V F+D L AL
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVL---DQTGVSKGYGFVKFTDELEQKRAL 68
Query: 122 KLDQEVV--RGRPVKISCAVP 140
Q V +PV++S A+P
Sbjct: 69 TECQGAVGLGSKPVRLSVAIP 89
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 35.0 bits (79), Expect = 0.058, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK 122
+Y+G++ +D TEE + L S+ + +L+ + +TG +GYA ++F D S + A++
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 34.7 bits (78), Expect = 0.068, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK 122
+Y+G++ +D TEE + L S+ + +L+ + +TG +GYA ++F D S + A++
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 34.7 bits (78), Expect = 0.075, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK 122
+Y+G++ +D TEE + L S+ + +L+ + +TG +GYA ++F D S + A++
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 34.7 bits (78), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-L 123
+Y+G L ++E L +LF + + ++ TG+ +GY V+F A+K +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 124 DQEVVRGRPVKISCA 138
D + G+P++++ A
Sbjct: 78 DMIKLYGKPIRVNKA 92
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 34.3 bits (77), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 64 NRIYIGNLSWDITEEDLKKLFSDCKI---------SSLRFGTNKETGEFRGYAHVDFSDS 114
N I++ L ++T E + F I + T++ETG+ +G A V F D
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 115 LSLSMALK-LDQEVVRGRPVKISCA 138
S A+ D + G P+K+S A
Sbjct: 68 PSAKAAIDWFDGKEFSGNPIKVSFA 92
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 3/47 (6%)
Query: 66 IYIGNLSWDITEEDLKKLFSDCKIS---SLRFGTNKETGEFRGYAHV 109
+YIGNL+W T+EDL + ++ ++F N+ G+ +G+A V
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALV 50
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 11/82 (13%)
Query: 62 GYNRIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKET---GEFRGYAHVDFSDSLSLS 118
G + +++G + D+TE++L++ FS ++G + FR +A V F+D ++
Sbjct: 4 GSSGVFVGRCTGDMTEDELREFFS-------QYGDVMDVFIPKPFRAFAFVTFADD-QIA 55
Query: 119 MALKLDQEVVRGRPVKISCAVP 140
+L + +++G V IS A P
Sbjct: 56 QSLCGEDLIIKGISVHISNAEP 77
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDF 111
I + NLS D E DL++LF IS + +K TG+ +G+A + F
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 62 GYNRIYIGNLSWDITEEDLKKLFS--DCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSM 119
G + I+IGNL +I E+ L FS + + + + +TG +GYA ++F+ +
Sbjct: 4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63
Query: 120 ALK-LDQEVVRGRPVKISCAV 139
A++ ++ + + RP+ +S A
Sbjct: 64 AIEAMNGQYLCNRPITVSYAF 84
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 2/76 (2%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-L 123
+Y+ NL + +T DL ++FS K+ + +K+T + +G A + F D S + +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 124 DQEVVRGRPVKISCAV 139
+ + + GR +K S A+
Sbjct: 79 NNKQLFGRVIKASIAI 94
>pdb|2DB1|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein F Homolog
Length = 118
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 57 PKIVEGYNRIYIGNLSWDITEEDLKKLFSDCKI----SSLRFGTNKETGEFRGYAHVDFS 112
P+ EGY + + L W + ED++ SDC I + + F +E G G A V+
Sbjct: 12 PEGGEGY-VVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELE 69
Query: 113 DSLSLSMALKLDQEVVRGRPVKI 135
+ +ALK D+E + R +++
Sbjct: 70 SEDDVKLALKKDRESMGHRYIEV 92
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 66 IYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-LD 124
+ + NLS+ TEE L+++F K + ++ N + G+ +GYA ++F+ AL +
Sbjct: 18 LVLSNLSYSATEETLQEVFE--KATFIKVPQN-QNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 125 QEVVRGRPVKISCAVP 140
+ + GR +++ P
Sbjct: 75 KREIEGRAIRLELQGP 90
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 35/84 (41%), Gaps = 15/84 (17%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKE--------TGEFRGYAHVDFSDSLS 116
+++IG LSW T+E L++ F +FG KE T RG+ V F D
Sbjct: 27 KMFIGGLSWQTTQEGLREYFG-------QFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 79
Query: 117 LSMALKLDQEVVRGRPVKISCAVP 140
+ L + + + + A P
Sbjct: 80 VDKVLAQSRHELDSKTIDPKVAFP 103
>pdb|2HGL|A Chain A, Nmr Structure Of The First Qrrm Domain Of Human Hnrnp F
pdb|2KFY|A Chain A, Nmr Structure Of The First Qrrm Of Hnrnp F In Complex With
Agggau G- Tract Rna
Length = 136
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 57 PKIVEGYNRIYIGNLSWDITEEDLKKLFSDCKI----SSLRFGTNKETGEFRGYAHVDFS 112
P+ EG+ + + L W + ED++ SDC I + + F +E G G A V+
Sbjct: 39 PEGGEGFV-VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELG 96
Query: 113 DSLSLSMALKLDQEVVRGRPVKI 135
+ MALK D+E + R +++
Sbjct: 97 SEDDVKMALKKDRESMGHRYIEV 119
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 57 PKIVEGYNRIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSD 113
P+++ +++ NL+ +TEE L+K FS+ FG + + + YA V F D
Sbjct: 9 PEVMAKVKVLFVRNLATTVTEEILEKSFSE-------FGKLERVKKLKDYAFVHFED 58
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 29/137 (21%), Positives = 62/137 (45%), Gaps = 13/137 (9%)
Query: 7 GKFRGIAIINFRTEGAVKRALALDGSEMDGLFLKIQPYKATKAKRTSDFTPKIVEGYNRI 66
G R ++F + +++AL L G ++ G +K++ K +K+ D +
Sbjct: 45 GMTRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGKDSKKERD--------ARTL 96
Query: 67 YIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALKLDQE 126
NL + +T+++LK++F D + +R + G+ +G A+++F + Q
Sbjct: 97 LAKNLPYKVTQDELKEVFEDA--AEIRLVSK--DGKSKGIAYIEFKTEADAEKTFEEKQG 152
Query: 127 V-VRGRPVKISCAVPPK 142
+ GR + + PK
Sbjct: 153 TEIDGRSISLYYTGEPK 169
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 32.7 bits (73), Expect = 0.30, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 276 RRRTCYECGEKGHLSSACPKKTA 298
RR+ C++CG+ GH+ + CP++ A
Sbjct: 26 RRQGCWKCGKTGHVMAKCPERQA 48
Score = 28.5 bits (62), Expect = 4.8, Method: Composition-based stats.
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 209 RRRTCYECGEKGHLSSACLKKTA 231
RR+ C++CG+ GH+ + C ++ A
Sbjct: 26 RRQGCWKCGKTGHVMAKCPERQA 48
>pdb|2E1X|A Chain A, Nmr Structure Of The Hiv-2 Nucleocapsid Protein
pdb|2IWJ|A Chain A, Solution Structure Of The Zn Complex Of Hiv-2 Ncp(23-49)
Peptide, Encompassing Protein Cchc-Linker, Distal Cchc
Zn- Binding Motif And C-Terminal Tail
Length = 27
Score = 32.3 bits (72), Expect = 0.33, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 276 RRRTCYECGEKGHLSSACPKKTA 298
RR+ C++CG+ GH+ + CP++ A
Sbjct: 4 RRQGCWKCGKTGHVMAKCPERQA 26
Score = 28.5 bits (62), Expect = 5.3, Method: Composition-based stats.
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 209 RRRTCYECGEKGHLSSACLKKTA 231
RR+ C++CG+ GH+ + C ++ A
Sbjct: 4 RRQGCWKCGKTGHVMAKCPERQA 26
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 10/83 (12%)
Query: 66 IYIGNLSWDITEEDLKKLFSDCKISSL--RFGT-------NKETGEFRGYAHVDFSDSLS 116
IY+ L+ +T +DL F C + + R G +KETG+ +G A V + D +
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 117 LSMALK-LDQEVVRGRPVKISCA 138
A++ D + +G +K+S A
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLA 100
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 32.3 bits (72), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 56 TPKIVEGYNRIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDF 111
T K V + NLS++ITE++LK++F D +L + G+ +G A+++F
Sbjct: 9 TSKKVRAARTLLAKNLSFNITEDELKEVFED----ALEIRLVSQDGKSKGIAYIEF 60
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 32.3 bits (72), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 40/77 (51%), Gaps = 12/77 (15%)
Query: 66 IYIGNLSWDITEEDLK----KLFS--DCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSM 119
++IGNL+ + + +LK +LF+ D + +R GTN R + +VDF + L
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTN------RKFGYVDFESAEDLEK 73
Query: 120 ALKLDQEVVRGRPVKIS 136
AL+L V G +K+
Sbjct: 74 ALELTGLKVFGNEIKLE 90
>pdb|3OS4|A Chain A, The Crystal Structure Of Nicotinate
Phosphoribosyltransferase From Yersinia Pestis
pdb|3OS4|B Chain B, The Crystal Structure Of Nicotinate
Phosphoribosyltransferase From Yersinia Pestis
Length = 407
Score = 32.0 bits (71), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 111 FSDSLSLSMALKLDQE------VVRGRPVKISCAVPPKKGINSKSRSLPSNKRATSKVTD 164
FSD+L L AL L + +V G +++C +P K +N + + N + +K++D
Sbjct: 313 FSDNLDLEKALFLYRHFYQRIKLVFGIGTRLTCDIPDVKPLNIVIKLVECNDKPVAKLSD 372
Query: 165 SAG 167
S G
Sbjct: 373 SPG 375
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 32.0 bits (71), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 66 IYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMAL-KLD 124
+++ NL+ +TEE L+K FS +FG + + + YA + F + A+ +++
Sbjct: 14 LFVRNLANTVTEEILEKAFS-------QFGKLERVKKLKDYAFIHFDERDGAVKAMEEMN 66
Query: 125 QEVVRGRPVKISCAVPP 141
+ + G ++I A PP
Sbjct: 67 GKDLEGENIEIVFAKPP 83
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 32.0 bits (71), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-L 123
+++G+L+ ++ +E L+ F D S + +TG RGY V F+ A+ +
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 124 DQEVVRGRPVKISCA 138
+ + GRP++I+ A
Sbjct: 150 QGQDLNGRPLRINWA 164
Score = 31.6 bits (70), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 3/80 (3%)
Query: 66 IYIGNLSWDITEEDLKKLFS-DCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-L 123
+Y+GNL ITE+ LK+ F I++++ +K YA V++ S ++AL+ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNV-NYAFVEYHQSHDANIALQTL 61
Query: 124 DQEVVRGRPVKISCAVPPKK 143
+ + + VKI+ A ++
Sbjct: 62 NGKQIENNIVKINWAFQSQQ 81
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSD---SLSLSMA 120
+++IG + ++ E+DLK LF + KI L ++ TG +G A + + + +L A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 121 LKLDQEVVRG--RPVKISCA 138
L +Q+ + G RP+++ A
Sbjct: 75 LH-EQKTLPGMNRPIQVKPA 93
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 31.6 bits (70), Expect = 0.61, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 15/65 (23%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKE--------TGEFRGYAHVDFSDSLS 116
+++IG LSW T+E L++ F +FG KE T RG+ V F D
Sbjct: 2 KMFIGGLSWQTTQEGLREYFG-------QFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 54
Query: 117 LSMAL 121
+ L
Sbjct: 55 VDKVL 59
>pdb|1Z6Z|A Chain A, Crystal Structure Of Human Sepiapterin Reductase In
Complex With Nadp+
pdb|1Z6Z|B Chain B, Crystal Structure Of Human Sepiapterin Reductase In
Complex With Nadp+
pdb|1Z6Z|C Chain C, Crystal Structure Of Human Sepiapterin Reductase In
Complex With Nadp+
pdb|1Z6Z|D Chain D, Crystal Structure Of Human Sepiapterin Reductase In
Complex With Nadp+
pdb|1Z6Z|E Chain E, Crystal Structure Of Human Sepiapterin Reductase In
Complex With Nadp+
pdb|1Z6Z|F Chain F, Crystal Structure Of Human Sepiapterin Reductase In
Complex With Nadp+
Length = 282
Score = 31.6 bits (70), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 86 DCKISSLRFGTNKETGEFRGYAHVDFSD 113
DCK+S+ + + E EF+ AHVDF D
Sbjct: 252 DCKVSAQKLLSLLEKDEFKSGAHVDFYD 279
>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 = 31.2 bits (69), Expect = 0.73, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMAL-KL 123
+++G+L+ ++ +E L+ F D S + +TG RGY V F+ A+ +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 124 DQEVVRGRPVKISCA 138
+ + GRP++I+ A
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 31.2 bits (69), Expect = 0.75, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 44/86 (51%), Gaps = 11/86 (12%)
Query: 64 NRIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKET---GEFRGYAHVDFSDSLSLSMA 120
+++++G + D+T E+L++ F ++G + FR +A V F+D ++ +
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFC-------QYGEVVDVFIPKPFRAFAFVTFADD-KVAQS 63
Query: 121 LKLDQEVVRGRPVKISCAVPPKKGIN 146
L + +++G V IS A P +N
Sbjct: 64 LCGEDLIIKGISVHISNAEPKHNKLN 89
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 31.2 bits (69), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 66 IYIGNLSWDITEEDLKKLF-SDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-L 123
+ + L ++T+++ K LF S I S + +K TG+ GY V++SD A+ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 124 DQEVVRGRPVKISCAVP 140
+ ++ + +K+S A P
Sbjct: 67 NGLKLQTKTIKVSYARP 83
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 31.2 bits (69), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 66 IYIGNLSWDITEEDLKKLF-SDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-L 123
+ + L ++T+++ K LF S I S + +K TG+ GY V++SD A+ L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 124 DQEVVRGRPVKISCAVPPKKGI 145
+ ++ + +K+S A P I
Sbjct: 67 NGLKLQTKTIKVSYARPSSASI 88
>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58)
Peptide, Including Two Cchc Zn-Binding Motifs
Length = 37
Score = 30.8 bits (68), Expect = 0.98, Method: Composition-based stats.
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 211 RTCYECGEKGHLSSAC 226
+TCY CG+ GHLSS C
Sbjct: 1 QTCYNCGKPGHLSSQC 16
Score = 30.8 bits (68), Expect = 0.98, Method: Composition-based stats.
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 278 RTCYECGEKGHLSSAC 293
+TCY CG+ GHLSS C
Sbjct: 1 QTCYNCGKPGHLSSQC 16
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK 122
R+++ D+ E +L ++F FG KE G+A V+F ++ S + A++
Sbjct: 33 RLFVRPFPLDVQESELNEIFGP-------FGPMKEVKILNGFAFVEFEEAESAAKAIE 83
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 66 IYIGNLSWDITEEDLKKLF-SDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK-L 123
+ + L ++T+E+ + LF S +I S + +K TG+ GY V++ D A+ L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 124 DQEVVRGRPVKISCAVP 140
+ ++ + +K+S A P
Sbjct: 65 NGLRLQTKTIKVSYARP 81
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 28/118 (23%), Positives = 58/118 (49%), Gaps = 10/118 (8%)
Query: 6 TGKFRGIAIINFRTEGAVKRALALDGSEMDGLFLKIQPYKATKAKRTSDFTPKIVEGYNR 65
TG+ G +N+ ++A+ + ++GL L+ + K + A+ +S + N
Sbjct: 40 TGQSLGYGFVNYIDPKDAEKAI----NTLNGLRLQTKTIKVSYARPSS----ASIRDAN- 90
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK 122
+Y+ L +T+++L++LFS +I + R ++ TG RG + F + A+K
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 66 IYIGNLSWDITEEDLKKLFS---DCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK 122
+Y+ NLS +TE DL LF+ + K ++F TG RG A + F + AL
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQF--RMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 123 L 123
L
Sbjct: 86 L 86
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 30.4 bits (67), Expect = 1.4, Method: Composition-based stats.
Identities = 17/78 (21%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 64 NRIYIGNLSWDITEEDLKKLFSDCKI-SSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK 122
N+I++G + + E +L++ F + + + + E RG+ + F D S+ A+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 123 LDQEVVRGRPVKISCAVP 140
+ + G+ V++ A P
Sbjct: 71 MHFHDIMGKKVEVKRAEP 88
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 71 LSWDITEEDLKKLFSDCKISS----LRFGTNKETGEFRGYAHVDFSDSLSLSMALKLDQE 126
L W T ED+ FSDC+I + + F N++ G+ RG A ++ + AL+ +
Sbjct: 19 LPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRM 77
Query: 127 VVRGRPVKI 135
+ R V++
Sbjct: 78 YMGQRYVEV 86
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 62 GYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDF 111
G + +YI L T++DL KL KI S + +K T + +GY VDF
Sbjct: 4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 54
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 22/99 (22%), Positives = 47/99 (47%), Gaps = 7/99 (7%)
Query: 38 FLKIQPYKATKAKRTSDFTPKIVEGYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGT 96
++++ Y+ + ++ K+++ +Y+GNLS+ TEE + +LFS I + G
Sbjct: 14 YVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGL 73
Query: 97 NKETGEFRGYAHVDFSDSLSLSMAL------KLDQEVVR 129
+K G+ V++ A+ +LD ++R
Sbjct: 74 DKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIR 112
>pdb|1KSF|X Chain X, Crystal Structure Of Clpa, An Hsp100 Chaperone And
Regulator Of Clpap Protease: Structural Basis Of
Differences In Function Of The Two Aaa+ Atpase Domains
pdb|1R6B|X Chain X, High Resolution Crystal Structure Of Clpa
Length = 758
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 71 LSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRG 105
L+W I + D+ ++ +DC I SL G+ ++RG
Sbjct: 227 LAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRG 261
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 42/79 (53%), Gaps = 5/79 (6%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDF--SDSLSLSMAL 121
++++G + + E+DLK LF + +I L ++ TG +G A + + DS + +
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 122 KLDQEVVRG--RPVKISCA 138
+Q+ + G RP+++ A
Sbjct: 77 LHEQKTLPGMNRPIQVKPA 95
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 29.6 bits (65), Expect = 2.0, Method: Composition-based stats.
Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 14/81 (17%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKET----------GEFRGYAHVDFSDS 114
R+Y+GN+ + ITEE + F+ + +R G + + + +A ++F
Sbjct: 3 RLYVGNIPFGITEEAMMDFFN----AQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 58
Query: 115 LSLSMALKLDQEVVRGRPVKI 135
+ A+ D + +G+ +KI
Sbjct: 59 DETTQAMAFDGIIFQGQSLKI 79
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 14/81 (17%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKET----------GEFRGYAHVDFSDS 114
R+Y+GN+ + ITEE + F+ + +R G + + + +A ++F
Sbjct: 8 RLYVGNIPFGITEEAMMDFFN----AQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63
Query: 115 LSLSMALKLDQEVVRGRPVKI 135
+ A+ D + +G+ +KI
Sbjct: 64 DETTQAMAFDGIIFQGQSLKI 84
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus Nucleocapsid
Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 29.3 bits (64), Expect = 2.8, Method: Composition-based stats.
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 277 RRTCYECGEKGHLSSACPKK 296
R CY CG GH + CPKK
Sbjct: 4 RGLCYTCGSPGHYQAQCPKK 23
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 28.9 bits (63), Expect = 3.3, Method: Composition-based stats.
Identities = 19/80 (23%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEF-RGYAHVDFSDSLSLSMALK 122
+++IG L+ ++T++ + ++FS KI + + +GYA+V+F + ALK
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 123 -LDQEVVRGRPVKISCAVPP 141
+D + G+ + + + P
Sbjct: 66 HMDGGQIDGQEITATAVLAP 85
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 28.9 bits (63), Expect = 3.6, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 57 PKIVEGYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDFSDSL 115
P E +++GNL + EE L +LF ++ + ++E G+ + + V F
Sbjct: 10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPE 68
Query: 116 SLSMALKLDQEV-VRGRPVKIS 136
S+S A+ L + + GRP+ +S
Sbjct: 69 SVSYAIALLNGIRLYGRPINVS 90
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 28.9 bits (63), Expect = 4.2, Method: Composition-based stats.
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 7/58 (12%)
Query: 65 RIYIGNLSWDITEEDLKKLFSDCKISSLRFGTNKETGEFRGYAHVDFSDSLSLSMALK 122
R+++ D+ E +L ++F FG KE G+A V+F ++ S + A++
Sbjct: 6 RLFVRPFPLDVQESELNEIFGP-------FGPMKEVKILNGFAFVEFEEAESAAKAIE 56
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 28.5 bits (62), Expect = 4.7, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 58 KIVEGYNRIYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGE-----FRGYAHVDF 111
K+++ +Y+GNLS+ TEE + +LFS I + G +K Y+ D
Sbjct: 13 KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADA 72
Query: 112 SDSLSLSMALKLDQEVVR 129
+++ +LD ++R
Sbjct: 73 ENAMRYINGTRLDDRIIR 90
>pdb|1U6P|A Chain A, Nmr Structure Of The Mlv Encapsidation Signal Bound To The
Nucleocapsid Protein
pdb|1WWD|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Aacagu
pdb|1WWE|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uuuugcu
pdb|1WWF|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Ccuccgu
pdb|1WWG|A Chain A, Nmr Structure Determined For Mlv Nc Complex With Rna
Sequence Uaucug
Length = 56
Score = 28.5 bits (62), Expect = 4.7, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 16/33 (48%)
Query: 264 DNAGLSAVSGKIRRRTCYECGEKGHLSSACPKK 296
D G ++ R C C EKGH + CPKK
Sbjct: 10 DRQGGERRRSQLDRDQCAYCKEKGHWAKDCPKK 42
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 28.5 bits (62), Expect = 4.7, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 66 IYIGNLSWDITEEDLKKLFSDC-KISSLRFGTNKETGEFRGYAHVDF 111
I++G LS + T ED+K F K+ +K T RG+ V F
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
>pdb|1A6B|B Chain B, Nmr Structure Of The Complex Between The Zinc Finger
Protein Ncp10 Of Moloney Murine Leukemia Virus And A
Sequence Of The Psi-Packaging Domain Of Hiv-1, 20
Structures
Length = 40
Score = 28.5 bits (62), Expect = 5.1, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 274 KIRRRTCYECGEKGHLSSACPKK 296
++ R C C EKGH + CPKK
Sbjct: 7 QLDRDQCAYCKEKGHWAKDCPKK 29
>pdb|1AAF|A Chain A, Nucleocapsid Zinc Fingers Detected In Retroviruses: Exafs
Studies On Intact Viruses And The Solution-State
Structure Of The Nucleocapsid Protein From Hiv-1
Length = 55
Score = 28.1 bits (61), Expect = 5.8, Method: Composition-based stats.
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 276 RRRTCYECGEKGHLSSACPKKTAD 299
R+R C++CG++GH C ++ A+
Sbjct: 32 RKRGCWKCGKEGHQMKDCTERQAN 55
Score = 28.1 bits (61), Expect = 6.0, Method: Composition-based stats.
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 209 RRRTCYECGEKGHLSSACLKKTAD 232
R+R C++CG++GH C ++ A+
Sbjct: 32 RKRGCWKCGKEGHQMKDCTERQAN 55
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 28.1 bits (61), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 66 IYIGNLSWDITEEDLKKLFSD---CKISSLRFGTNKETGEFRGYAHVDFSDSL-SLSMAL 121
+Y+GNLS D+TE + +LFS CK S + T + + Y V+F + + +
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCK--SCKMITEHTSND--PYCFVEFYEHRDAAAALA 73
Query: 122 KLDQEVVRGRPVKISCAVPP 141
++ + G+ VK++ A P
Sbjct: 74 AMNGRKILGKEVKVNWATTP 93
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 27.3 bits (59), Expect = 9.9, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 76 TEEDLKKLFSDCKISS--LRFGTNKETGEFRGYAHVDFSDSLSLSMALKLDQEVVRGRPV 133
TE+D++ + + +R NK +G+ RG+A V+FS + ++ +Q +
Sbjct: 14 TEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQ 73
Query: 134 KISCAVP-PKKGIN 146
K+S PK IN
Sbjct: 74 KVSMHYSDPKPKIN 87
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
0.312 0.128 0.363
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,816,339
Number of Sequences: 62578
Number of extensions: 352599
Number of successful extensions: 883
Number of sequences better than 100.0: 125
Number of HSP's better than 100.0 without gapping: 43
Number of HSP's successfully gapped in prelim test: 82
Number of HSP's that attempted gapping in prelim test: 746
Number of HSP's gapped (non-prelim): 184
length of query: 311
length of database: 14,973,337
effective HSP length: 99
effective length of query: 212
effective length of database: 8,778,115
effective search space: 1860960380
effective search space used: 1860960380
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)