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= 016540
(387 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
L++ GLS T L HF G + D ++ DP T+ SRGFGFVT ATVEE D +
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 105 LDRSVLEGRIITVERA 120
V +GR++ +RA
Sbjct: 76 RPHKV-DGRVVEPKRA 90
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 38 DAENPGNNL-----YVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTM 92
D++ PG +L +V G+ + L +F GK+ + ++ D + + RGF FVT
Sbjct: 95 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
Query: 93 ATVEEADRCI 102
+ D+ +
Sbjct: 155 DDHDSVDKIV 164
>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 = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 49/85 (57%), Gaps = 5/85 (5%)
Query: 38 DAENPGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEE 97
D ++ ++V G+ P + +E E+ F+ G +ID L++D T +SRGFGFVT + +
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141
Query: 98 ADRCI--KYLDRSVLEGRIITVERA 120
DR K++D + R I ++RA
Sbjct: 142 VDRVCQNKFID---FKDRKIEIKRA 163
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
+++ GL+ T+ L ++F G V D+ ++ DP T SRGFGF++ D +K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 105 LDRSVLEGRIITVERA 120
+ +L+G++I +RA
Sbjct: 65 --QHILDGKVIDPKRA 78
>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 = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
L++ GLS T L HF G + D ++ DP T+ SRGFGFVT ATVEE D +
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 105 LDRSVLEGRIITVERA 120
V +GR++ +RA
Sbjct: 75 RPHKV-DGRVVEPKRA 89
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 38 DAENPGNNL-----YVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTM 92
D++ PG +L +V G+ + L +F GK+ + ++ D + + RGF FVT
Sbjct: 94 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Query: 93 ATVEEADRCI 102
+ D+ +
Sbjct: 154 DDHDSVDKIV 163
>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 = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
L++ GLS T L HF G + D ++ DP T+ SRGFGFVT ATVEE D +
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 105 LDRSVLEGRIITVERA 120
V +GR++ +RA
Sbjct: 74 RPHKV-DGRVVEPKRA 88
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 38 DAENPGNNL-----YVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTM 92
D++ PG +L +V G+ + L +F GK+ + ++ D + + RGF FVT
Sbjct: 93 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
Query: 93 ATVEEADRCI 102
+ D+ +
Sbjct: 153 DDHDSVDKIV 162
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
L++ GLS T L HF G + D ++ DP T+ SRGFGFVT ATVEE D +
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 105 LDRSVLEGRIITVERA 120
V +GR++ +RA
Sbjct: 75 RPHKV-DGRVVEPKRA 89
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 38 DAENPGNNL-----YVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTM 92
D++ PG +L +V G+ + L +F GK+ + ++ D + + RGF FVT
Sbjct: 94 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Query: 93 ATVEEADRCI 102
+ D+ +
Sbjct: 154 DDHDSVDKIV 163
>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 = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
L++ GLS T L HF G + D ++ DP T+ SRGFGFVT ATVEE D +
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 105 LDRSVLEGRIITVERA 120
V +GR++ +RA
Sbjct: 68 RPHKV-DGRVVEPKRA 82
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 38 DAENPGNNL-----YVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTM 92
D++ PG +L +V G+ + L +F GK+ + ++ D + + RGF FVT
Sbjct: 87 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
Query: 93 ATVEEADRCI 102
+ D+ +
Sbjct: 147 DDHDSVDKIV 156
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
L++ GLS T L HF G + D ++ DP T+ SRGFGFVT ATVEE D +
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 105 LDRSVLEGRIITVERA 120
V +GR++ +RA
Sbjct: 73 RPHKV-DGRVVEPKRA 87
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 38 DAENPGNNL-----YVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTM 92
D++ PG +L +V G+ + L +F GK+ + ++ D + + RGF FVT
Sbjct: 92 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
Query: 93 ATVEEADRCI 102
+ D+ +
Sbjct: 152 DDHDSVDKIV 161
>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 = 55.5 bits (132), Expect = 6e-08, Method: Composition-based stats.
Identities = 28/75 (37%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
+++ GLS TK++L+ +F+ G+V+D L +DP T SRGFGFV E D+ +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 106 DRSVLEGRIITVERA 120
+ L G++I +RA
Sbjct: 62 EHK-LNGKVIDPKRA 75
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 52.8 bits (125), Expect = 4e-07, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 47/75 (62%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+V GLS ++ LE+ F+ G++ +V +V D T+ SRGFGFVT +++A + +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 106 DRSVLEGRIITVERA 120
+ ++GR I V++A
Sbjct: 75 NGKSVDGRQIRVDQA 89
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 43/78 (55%)
Query: 41 NPGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADR 100
+P L V GLS T+R+L + F+ G + DV +V D +R SRGF FV V++A
Sbjct: 44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 103
Query: 101 CIKYLDRSVLEGRIITVE 118
+ + L+GR I V+
Sbjct: 104 AKERANGMELDGRRIRVD 121
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 44/77 (57%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
+L V L+ R + L + F G+V DV++ D +T+ESRGF FV +A+ +
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 104 YLDRSVLEGRIITVERA 120
+D +VL+GR + V+ A
Sbjct: 108 AMDGAVLDGRELRVQMA 124
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 39/62 (62%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
NLYV+GL +T++ELE+ F+ G++I ++VD T SRG GF+ EA+ IK
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
Query: 105 LD 106
L+
Sbjct: 150 LN 151
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 50.8 bits (120), Expect = 1e-06, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L++ GLS T+ L ++ GK+ D ++ DP ++ SRGFGFVT +++ E D +
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 106 DRSVLEGRIITVERA 120
S+ +GR++ +RA
Sbjct: 90 PHSI-DGRVVEPKRA 103
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 49.3 bits (116), Expect = 4e-06, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 42/72 (58%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+V LS ++ +LEK F+A G + ++H +D T++ +GF FVT E A + +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 106 DRSVLEGRIITV 117
D V +GR++ V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 31/80 (38%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 41 NPGNN--LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEA 98
NP N L V GLS T+R+L + F+ G + DV +V D +R SRGF FV V++A
Sbjct: 8 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 67
Query: 99 DRCIKYLDRSVLEGRIITVE 118
+ + L+GR I V+
Sbjct: 68 KEAKERANGMELDGRRIRVD 87
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 48.9 bits (115), Expect = 4e-06, Method: Composition-based stats.
Identities = 31/80 (38%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 41 NPGNN--LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEA 98
NP N L V GLS T+R+L + F+ G + DV +V D +R SRGF FV V++A
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 99 DRCIKYLDRSVLEGRIITVE 118
+ + L+GR I V+
Sbjct: 71 KEAKERANGMELDGRRIRVD 90
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 48.9 bits (115), Expect = 5e-06, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 44/80 (55%)
Query: 41 NPGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADR 100
N +YV GL ++++ L + F G V++ H+ D T + +G+GFV + E+AD
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 101 CIKYLDRSVLEGRIITVERA 120
IK +D L G+ I V +A
Sbjct: 73 AIKIMDMIKLYGKPIRVNKA 92
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 48.9 bits (115), Expect = 5e-06, Method: Composition-based stats.
Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+V+ + R +L + F GK++DV ++ + R S+GFGFVT +ADR + L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKL 75
Query: 106 DRSVLEGRIITVERA 120
+V+EGR I V A
Sbjct: 76 HGTVVEGRKIEVNNA 90
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 44/76 (57%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
+L V L+ R + L + F G+V DV++ D +T+ESRGF FV +A+ +
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 105 LDRSVLEGRIITVERA 120
+D +VL+GR + V+ A
Sbjct: 132 MDGAVLDGRELRVQMA 147
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 48.5 bits (114), Expect = 7e-06, Method: Composition-based stats.
Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+V+ + R +L + F GK++DV ++ + R S+GFGFVT +ADR + L
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKL 89
Query: 106 DRSVLEGRIITVERA 120
+V+EGR I V A
Sbjct: 90 HGTVVEGRKIEVNNA 104
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 48.5 bits (114), Expect = 7e-06, Method: Composition-based stats.
Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
N+YV L T ++++ F+ GKV +V L+ D T++ +GFGFV M E I
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 105 LDRSVLEGRIITVERA 120
LD + GR I V A
Sbjct: 62 LDNTDFMGRTIRVTEA 77
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 48.1 bits (113), Expect = 9e-06, Method: Composition-based stats.
Identities = 31/79 (39%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 41 NPGNN--LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEA 98
NP N L V GLS T+R+L + F+ G + DV +V D +R SRGF FV V++A
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 99 DRCIKYLDRSVLEGRIITV 117
+ + L+GR I V
Sbjct: 71 KEAKERANGMELDGRRIRV 89
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 47.8 bits (112), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 39/62 (62%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
NLYV+GL ++++E+E+ F+ G++I +++D T SRG GF+ EA+ IK
Sbjct: 92 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 151
Query: 105 LD 106
L+
Sbjct: 152 LN 153
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
NL V L +T+ E + F + G + LV D T +S G+GFV + +AD+ I
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 105 LDRSVLEGRIITVERA 120
L+ L+ + I V A
Sbjct: 66 LNGLKLQTKTIKVSYA 81
>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 = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 29/83 (34%), Positives = 46/83 (55%), Gaps = 5/83 (6%)
Query: 40 ENPGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEAD 99
E +V GLS +K++L+ +F G+V+D + DP T SRGFGF+ ++A
Sbjct: 8 EEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF---KDAA 64
Query: 100 RCIKYLDRSV--LEGRIITVERA 120
K LD+ L+GR+I ++A
Sbjct: 65 SVEKVLDQKEHRLDGRVIDPKKA 87
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 39/62 (62%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
NLYV+GL ++++E+E+ F+ G++I +++D T SRG GF+ EA+ IK
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 105 LD 106
L+
Sbjct: 63 LN 64
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 37/75 (49%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
LYV GL+ + + L F G + D+ + +D T + RGF FV E+A I +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 106 DRSVLEGRIITVERA 120
+ S L GR I V A
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 37/75 (49%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
LYV GL+ + + L F G + D+ + +D T + RGF FV E+A I +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 106 DRSVLEGRIITVERA 120
+ S L GR I V A
Sbjct: 70 NESELFGRTIRVNLA 84
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 37/75 (49%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
LYV GL+ + + L F G + D+ + +D T + RGF FV E+A I +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 106 DRSVLEGRIITVERA 120
+ S L GR I V A
Sbjct: 68 NESELFGRTIRVNLA 82
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 45.8 bits (107), Expect = 4e-05, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 41/71 (57%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
+++V LSP IT +++ FA GK+ D +V D T +S+G+GFV+ +A+ I +
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 105 LDRSVLEGRII 115
+ L GR I
Sbjct: 77 MGGQWLGGRQI 87
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 37/75 (49%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
LYV GL+ + + L F G + D+ + +D T + RGF FV E+A I +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 106 DRSVLEGRIITVERA 120
+ S L GR I V A
Sbjct: 75 NESELFGRTIRVNLA 89
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 45.4 bits (106), Expect = 6e-05, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 40/72 (55%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
+ +YV+ L +T +L + F+ GKV+ V ++ D TR+S+G F+ + A C +
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 104 YLDRSVLEGRII 115
++ L GR+I
Sbjct: 77 AINNKQLFGRVI 88
>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 = 45.4 bits (106), Expect = 6e-05, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 41/71 (57%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
+++V LSP IT +++ FA G++ D +V D T +S+G+GFV+ +A+ I+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 105 LDRSVLEGRII 115
+ L GR I
Sbjct: 77 MGGQWLGGRQI 87
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 37/75 (49%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
LYV GL+ + + L F G + D+ + +D T + RGF FV E+A I +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 106 DRSVLEGRIITVERA 120
+ S L GR I V A
Sbjct: 126 NESELFGRTIRVNLA 140
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 39/78 (50%)
Query: 43 GNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCI 102
G NL V L T+ EL F++ G+V L+ D S G+GFV T ++A+R I
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 78
Query: 103 KYLDRSVLEGRIITVERA 120
L+ L+ + I V A
Sbjct: 79 NTLNGLRLQSKTIKVSYA 96
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 27/83 (32%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 38 DAENPGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEE 97
+A++PG L++ GL+ ++ L+ F G + +V L+ D T +SRGF F+T +
Sbjct: 3 EADHPGK-LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPAD 60
Query: 98 ADRCIKYLDRSVLEGRIITVERA 120
A K ++ L G+ I VE+A
Sbjct: 61 AKNAAKDMNGKSLHGKAIKVEQA 83
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 36/62 (58%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
NLY++GL +T++++E F+ G++I+ ++VD T SRG F+ EA+ I
Sbjct: 90 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITS 149
Query: 105 LD 106
+
Sbjct: 150 FN 151
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 39/76 (51%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
NL V L +T+ EL F++ G+V L+ D S G+GFV T ++A+R I
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 105 LDRSVLEGRIITVERA 120
L+ L+ + I V A
Sbjct: 64 LNGLRLQSKTIKVSYA 79
>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 = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 35/58 (60%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCI 102
NLY++GL +T++++E F+ G++I+ ++VD T SRG F+ EA+ I
Sbjct: 90 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 39/76 (51%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
NL V L +T+ EL F++ G+V L+ D S G+GFV T ++A+R I
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 105 LDRSVLEGRIITVERA 120
L+ L+ + I V A
Sbjct: 64 LNGLRLQSKTIKVSYA 79
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 4/82 (4%)
Query: 43 GNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCI 102
G +++ GLS + T+ L ++F G+V + ++ DP T+ SRGFGFVT D+ +
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 103 KY----LDRSVLEGRIITVERA 120
LD ++ ++ RA
Sbjct: 85 AQSRHELDSKTIDPKVAFPRRA 106
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 42 PG-NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADR 100
PG NL V L +T+ EL F++ G+V L+ D S G+GFV T ++A+R
Sbjct: 2 PGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 61
Query: 101 CIKYLDRSVLEGRIITVERA 120
I L+ L+ + I V A
Sbjct: 62 AINTLNGLRLQSKTIKVSYA 81
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 34/57 (59%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCI 102
+++ GLS + T+ L ++F G+V + ++ DP T+ SRGFGFVT D+ +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>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 = 5e-04, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
++V GL T L K+F G + + ++ D T +SRG+GFVTMA A+R K
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 106 DRSVLEGRIITVERA 120
+ +++GR V A
Sbjct: 80 N-PIIDGRKANVNLA 93
>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 = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
N+++ L I + L F+A G ++ +V D S+G+GFV T E A+R I+
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 162
Query: 105 LDRSVLEGRIITVER 119
++ +L R + V R
Sbjct: 163 MNGMLLNDRKVFVGR 177
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
N+++ L I + L F+A G ++ +V D S+G+GFV T E A+R I+
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 157
Query: 105 LDRSVLEGRIITVER 119
++ +L R + V R
Sbjct: 158 MNGMLLNDRKVFVGR 172
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
N+++ L I + L F+A G ++ +V D S+G+GFV T E A+R I+
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 70
Query: 105 LDRSVLEGRIITVER 119
++ +L R + V R
Sbjct: 71 MNGMLLNDRKVFVGR 85
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 38/76 (50%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
NL V L +T+ E + F + G + LV D T +S G+GFV + +AD+ I
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 105 LDRSVLEGRIITVERA 120
L+ L+ + I V A
Sbjct: 66 LNGLKLQTKTIKVSYA 81
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
N+++ L I + L F+A G ++ +V D S+G+GFV T E A+R I+
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 64
Query: 105 LDRSVLEGRIITVER 119
++ +L R + V R
Sbjct: 65 MNGMLLNDRKVFVGR 79
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 37/71 (52%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
+ LY+ GL P T ++L K GK++ ++D T + +G+GFV + A + +
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 104 YLDRSVLEGRI 114
L S ++ ++
Sbjct: 66 ALKASGVQAQM 76
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 20/49 (40%), Positives = 28/49 (57%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMAT 94
++V GLS T +++ +F GKV D L+ D T RGFGFVT +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES 50
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDV-HLVVDPWTRESRGFGFVTMATVEEADRCI 102
+ +++ L P I ++ L F+A G ++ ++ DP T S+G+ F+ A+ + +D I
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 103 KYLDRSVLEGRIITVERA 120
+ ++ L R ITV A
Sbjct: 66 EAMNGQYLCNRPITVSYA 83
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 38 DAENPGNN-------LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFV 90
D + PG L+VTG+ T+ ++ FA G++ ++HL +D T +G+ V
Sbjct: 10 DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 69
Query: 91 TMATVEEADRCIKYLDRSVLEGRIITVE 118
T +EA ++ L+ L G+ I+V+
Sbjct: 70 EYETYKEAQAAMEGLNGQDLMGQPISVD 97
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 19/45 (42%), Positives = 28/45 (62%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFV 90
L+V GL T+ L +F+ G+V+D ++ D T +SRGFGFV
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 39/72 (54%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
LYV L IT+ L F G++ + L++D T S+G+GF+T + E A + ++ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 106 DRSVLEGRIITV 117
+ L GR + V
Sbjct: 89 NGFELAGRPMKV 100
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 31/57 (54%)
Query: 40 ENPGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVE 96
E ++ L+ RI R+LE F+A GKV DV ++ D +R S+G +V ++
Sbjct: 22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 78
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L V L+ R + L + F G+V DV++ +P T+ RGF FV +A +
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 106 DRSVLEGRIITVERA 120
D + L+GR + V+ A
Sbjct: 76 DGAELDGRELRVQVA 90
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 38 DAENPGNN-------LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFV 90
D + PG L+VTG+ T+ ++ FA G++ ++HL +D T +G+ V
Sbjct: 11 DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 70
Query: 91 TMATVEEADRCIKYLDRSVLEGRIITVE 118
T +EA ++ L+ L G+ I+V+
Sbjct: 71 EYETYKEAQAAMEGLNGQDLMGQPISVD 98
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 41/73 (56%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+VTG+ T+ ++ FA G++ ++HL +D T +G+ V T +EA ++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 106 DRSVLEGRIITVE 118
+ L G+ I+V+
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 42 PGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRC 101
P L+V GLS T+ L++ F + +V D T S+GFGFV + E+A
Sbjct: 14 PSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
Query: 102 IKYLDRSVLEGRIITVERA 120
+ ++ ++G +T++ A
Sbjct: 71 KEAMEDGEIDGNKVTLDWA 89
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 41/73 (56%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+VTG+ T+ ++ FA G++ ++HL +D T +G+ V T +EA ++ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 106 DRSVLEGRIITVE 118
+ L G+ I+V+
Sbjct: 72 NGQDLMGQPISVD 84
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
N ++V G+ + EL ++F G V +V ++ D + RGFGF+T + D+ +
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 104 YLDRSVLEGRIITVERA 120
++ G+ + V+RA
Sbjct: 71 MHFHDIM-GKKVEVKRA 86
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 41/73 (56%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+VTG+ T+ ++ FA G++ ++HL +D T +G+ V T +EA ++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 106 DRSVLEGRIITVE 118
+ L G+ I+V+
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 41/73 (56%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+VTG+ T+ ++ FA G++ ++HL +D T +G+ V T +EA ++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 106 DRSVLEGRIITVE 118
+ L G+ I+V+
Sbjct: 70 NGQDLMGQPISVD 82
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 2/70 (2%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
++L V GL + T+++L+++F+ G+V+ V + D T S+GFGFV E + +
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
Query: 104 YLDRSVLEGR 113
R +++GR
Sbjct: 76 --QRHMIDGR 83
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 40/74 (54%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
+ LYV L IT+ L F GK+ ++ L+ D T S+G+GF+T + E A R ++
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 104 YLDRSVLEGRIITV 117
L+ L GR + V
Sbjct: 66 QLNGFELAGRPMRV 79
>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 = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 40 ENPGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEAD 99
E ++YV + T ELE HF G V V ++ D ++ +GF ++ + +E+
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESV 61
Query: 100 RCIKYLDRSVLEGRIITV 117
R LD S+ GR I V
Sbjct: 62 RTSLALDESLFRGRQIKV 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 = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 40 ENPGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEAD 99
E ++YV + T ELE HF G V V ++ D ++ +GF ++ + +E+
Sbjct: 2 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESV 60
Query: 100 RCIKYLDRSVLEGRIITV 117
R LD S+ GR I V
Sbjct: 61 RTSLALDESLFRGRQIKV 78
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
NL V + + + +L + F G + V +V D TR+SRG+GFV + A + I
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 105 LD 106
L+
Sbjct: 104 LN 105
>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 = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 38/77 (49%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
N +YV + ++ +++ F A GK+ L DP T + +G+GF+ + + +
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Query: 104 YLDRSVLEGRIITVERA 120
++ L G+ + V +A
Sbjct: 186 SMNLFDLGGQYLRVGKA 202
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 36/76 (47%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
+ +YV + + + + + FA G + + + D T + +GF FV E A ++
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 104 YLDRSVLEGRIITVER 119
++ +L GR I V R
Sbjct: 89 QMNSVMLGGRNIKVGR 104
>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 = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 40/73 (54%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
LYV LS T+ ++ + F+ G + + + +D + + GF FV + +A+ ++Y+
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 106 DRSVLEGRIITVE 118
+ + L+ RII +
Sbjct: 102 NGTRLDDRIIRTD 114
>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 = 37.0 bits (84), Expect = 0.016, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
++YV + T ++LE HF++ G + + ++ D ++ +G+ ++ A D +
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA- 96
Query: 105 LDRSVLEGRIITV 117
+D +V GR I V
Sbjct: 97 MDETVFRGRTIKV 109
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 37.0 bits (84), Expect = 0.017, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 32/58 (55%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
++V GLSP + ++ ++F G+V + L +D T + RGF F+T E + ++
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 37.0 bits (84), Expect = 0.020, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 32/58 (55%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
++V GLSP + ++ ++F G+V + L +D T + RGF F+T E + ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>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 = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 38/77 (49%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
N +YV + ++ +++ F A GK+ L DP T + +G+GF+ + + +
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 170
Query: 104 YLDRSVLEGRIITVERA 120
++ L G+ + V +A
Sbjct: 171 SMNLFDLGGQYLRVGKA 187
Score = 32.0 bits (71), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 35/74 (47%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
+YV + + + + + FA G + + + D T + +GF FV E A ++ +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 106 DRSVLEGRIITVER 119
+ +L GR I V R
Sbjct: 76 NSVMLGGRNIKVGR 89
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 36.6 bits (83), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 35/76 (46%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
NL+V L+ + L F + H++ D T SRG+GFV+ + ++A +
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 105 LDRSVLEGRIITVERA 120
+ L GR + + A
Sbjct: 149 MQGQDLNGRPLRINWA 164
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 35.8 bits (81), Expect = 0.037, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 40 ENPGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEAD 99
E NLY++ L + ++ELE G+VI ++ D + SRG GF M + E+ +
Sbjct: 22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCE 80
Query: 100 RCIKYLD 106
I + +
Sbjct: 81 AVIGHFN 87
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 35.8 bits (81), Expect = 0.046, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 42 PGNNLYVTGLSPRITKRELEKHFA----AEGKVIDVHLVVDPWTRESRGFGFVTMATVEE 97
P LY+ LSPR+T+R+L FA +G I ++ T RG F+T E
Sbjct: 24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM----TGRMRGQAFITFPNKEI 79
Query: 98 ADRCIKYLDRSVLEGRIITVE 118
A + + ++ L G+I+ +E
Sbjct: 80 AWQALHLVNGYKLYGKILVIE 100
>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 = 35.4 bits (80), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 37/77 (48%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
N +YV + ++ +++ F A GK+ L DP T + +G+GF+ + + +
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 169
Query: 104 YLDRSVLEGRIITVERA 120
+ L G+ + V +A
Sbjct: 170 SXNLFDLGGQYLRVGKA 186
Score = 28.9 bits (63), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 32/74 (43%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
+YV + + + + + FA G + + D T + +GF FV E A ++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 106 DRSVLEGRIITVER 119
+ L GR I V R
Sbjct: 75 NSVXLGGRNIKVGR 88
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 35.4 bits (80), Expect = 0.058, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 7/74 (9%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
NLYV L I L K F+ G + ++++ S+GFGFV ++ EEA + +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAV-- 72
Query: 105 LDRSVLEGRIITVE 118
+ + GRI+ +
Sbjct: 73 ---TEMNGRIVATK 83
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 34.7 bits (78), Expect = 0.085, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 29/49 (59%)
Query: 55 ITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
+ K+ L F+ GKV+++ +D T +++GF FV ++ +A + IK
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 34.7 bits (78), Expect = 0.085, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 29/49 (59%)
Query: 55 ITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
+ K+ L F+ GKV+++ +D T +++GF FV ++ +A + IK
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
>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 = 34.7 bits (78), Expect = 0.092, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 35/76 (46%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
NL+V L+ + L F + H++ D T SRG+GFV+ + ++A +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 105 LDRSVLEGRIITVERA 120
+ L GR + + A
Sbjct: 63 MQGQDLNGRPLRINWA 78
>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 = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 6/77 (7%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
+ L+V L P IT+ E+ K F GK +V + D +GFGF+ + T A+
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 69
Query: 104 YLDRSVLEGRIITVERA 120
LD L G+ + V A
Sbjct: 70 ELDNMPLRGKQLRVRFA 86
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
+ L+V L P IT+ E+ K F GK +V + D +GFGF+ + T A+
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 76
Query: 104 YLDRSVLEGRIITV 117
LD L G+ + V
Sbjct: 77 ELDNMPLRGKQLRV 90
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 37/73 (50%)
Query: 48 VTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYLDR 107
VT LS + +L++ F G + ++L D T +S+GF F++ E+A R I +
Sbjct: 20 VTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
Query: 108 SVLEGRIITVERA 120
+ I+ VE A
Sbjct: 80 FGYDHLILNVEWA 92
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 40/73 (54%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+VT + + E+++ F G++ ++HL +D T S+G+ V T ++A + L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 106 DRSVLEGRIITVE 118
+ + + G+ I V+
Sbjct: 89 NGAEIMGQTIQVD 101
>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 = 0.16, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 37/76 (48%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
+++V + T+ +L+ F+ G V+ LV D T + +G+GF E A ++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 105 LDRSVLEGRIITVERA 120
L+ GR + V+ A
Sbjct: 70 LNGREFSGRALRVDNA 85
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIK 103
+ L+++GL TK ELE+ A G V D+ LV + + +G +V +A + +
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVM 76
Query: 104 YLDRSVLEGRIITV 117
+D ++ II V
Sbjct: 77 KMDGMTIKENIIKV 90
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 33.1 bits (74), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 40/73 (54%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+VT + + E+++ F G++ ++HL +D T S+G+ V T ++A + L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 106 DRSVLEGRIITVE 118
+ + + G+ I V+
Sbjct: 135 NGAEIMGQTIQVD 147
>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 = 32.3 bits (72), Expect = 0.41, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
LYV LS T+ ++ + F+ G + + + +D + + GF FV + +A+ ++Y+
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYYSRADAENAMRYI 79
Query: 106 DRSVLEGRIITVE 118
+ + L+ RII +
Sbjct: 80 NGTRLDDRIIRTD 92
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 32.3 bits (72), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+V ++ T+ +L + F G + +H+V + + RG+ F+ + K+
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 106 DRSVLEGR--IITVER 119
D ++GR ++ VER
Sbjct: 165 DGKKIDGRRVLVDVER 180
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 32.0 bits (71), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 45/87 (51%), Gaps = 5/87 (5%)
Query: 39 AENPGNNLYVTGLSPRITKRELEKHFA--AEGKVIDVHLVVDPWTRESRGFGFVTMATVE 96
+EN + + + L+P T + A A +V ++ D T+ +RGF F+ ++T+E
Sbjct: 19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIE 78
Query: 97 EAD--RCIKYLDRSV-LEGRIITVERA 120
A + ++ L + ++G+ I VE A
Sbjct: 79 AAQLLQILQALHPPLTIDGKTINVEFA 105
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 32.0 bits (71), Expect = 0.59, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 39/71 (54%)
Query: 45 NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKY 104
+++V LSP IT + FA G++ D +V D T +S+G+GFV+ +A+ I+
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 105 LDRSVLEGRII 115
+ L GR I
Sbjct: 68 MGGQWLGGRQI 78
>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 = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 36/75 (48%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L++ GL + ++++ + G + +LV D T S+G+ F + D+ I L
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 106 DRSVLEGRIITVERA 120
+ L + + V+RA
Sbjct: 159 NGMQLGDKKLLVQRA 173
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 31.6 bits (70), Expect = 0.76, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRE-SRGFGFVTMATVEEADRCIKY 104
+++ L+ +TK + + F+ GK+ + + V+ S+G+ +V +EA++ +K+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 105 LDRSVLEGRIIT 116
+D ++G+ IT
Sbjct: 67 MDGGQIDGQEIT 78
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 31.6 bits (70), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+V ++ T+ +L + F G + +H+V + + RG+ F+ + K+
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 106 DRSVLEGR--IITVER 119
D ++GR ++ VER
Sbjct: 165 DGKKIDGRRVLVDVER 180
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 31.6 bits (70), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 36/75 (48%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L++ GL + ++++ + G + +LV D T S+G+ F + D+ I L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 106 DRSVLEGRIITVERA 120
+ L + + V+RA
Sbjct: 157 NGMQLGDKKLLVQRA 171
>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 = 31.2 bits (69), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 36/75 (48%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L++ GL + ++++ + G + +LV D T S+G+ F + D+ I L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 106 DRSVLEGRIITVERA 120
+ L + + V+RA
Sbjct: 177 NGMQLGDKKLLVQRA 191
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 39 AENPGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEA 98
A GN LYV G +T L F+ G +ID L +DP R FVT +E A
Sbjct: 11 APRKGNTLYVYG--EDMTPTLLRGAFSPFGNIID--LSMDP----PRNCAFVTYEKMESA 62
Query: 99 DRCIKYLDRSVLE 111
D+ + L+ + +E
Sbjct: 63 DQAVAELNGTQVE 75
>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 = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 16/74 (21%), Positives = 36/74 (48%)
Query: 42 PGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRC 101
P +Y+ + T+ ++ + G VI++ ++ DP T S+G+ F+ +E +
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 62
Query: 102 IKYLDRSVLEGRII 115
++ L+ L R +
Sbjct: 63 VRNLNGYQLGSRFL 76
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 16/74 (21%), Positives = 36/74 (48%)
Query: 42 PGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRC 101
P +Y+ + T+ ++ + G VI++ ++ DP T S+G+ F+ +E +
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 102 IKYLDRSVLEGRII 115
++ L+ L R +
Sbjct: 61 VRNLNGYQLGSRFL 74
>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 = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 16/74 (21%), Positives = 36/74 (48%)
Query: 42 PGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRC 101
P +Y+ + T+ ++ + G VI++ ++ DP T S+G+ F+ +E +
Sbjct: 2 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 61
Query: 102 IKYLDRSVLEGRII 115
++ L+ L R +
Sbjct: 62 VRNLNGYQLGSRFL 75
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 39 AENPGNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEA 98
A GN LYV G +T L F+ G +ID L +DP R FVT +E A
Sbjct: 35 APRKGNTLYVYG--EDMTPTLLRGAFSPFGNIID--LSMDP----PRNCAFVTYEKMESA 86
Query: 99 DRCIKYLDRSVLE 111
D+ + L+ + +E
Sbjct: 87 DQAVAELNGTQVE 99
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 30.4 bits (67), Expect = 1.9, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 5/51 (9%)
Query: 43 GNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMA 93
G+ ++V + +T EL++ F G+V+DV + P+ R F FVT A
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDV-FIPKPF----RAFAFVTFA 56
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 30.0 bits (66), Expect = 2.1, Method: Composition-based stats.
Identities = 16/79 (20%), Positives = 42/79 (53%), Gaps = 7/79 (8%)
Query: 38 DAENPGN-NLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVE 96
+ +P N +Y G++ +T + + + F+ G+++++ + + +G+ FV +T E
Sbjct: 19 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHE 72
Query: 97 EADRCIKYLDRSVLEGRII 115
A I ++ + +EG ++
Sbjct: 73 SAAHAIVSVNGTTIEGHVV 91
>pdb|4AYJ|A Chain A, Molecular Structure Of A Metal-Independent Bacterial
Glycosyltransferase That Catalyzes The Synthesis Of
Histo- Blood Group A Antigen
pdb|4AYJ|B Chain B, Molecular Structure Of A Metal-Independent Bacterial
Glycosyltransferase That Catalyzes The Synthesis Of
Histo- Blood Group A Antigen
pdb|4AYJ|C Chain C, Molecular Structure Of A Metal-Independent Bacterial
Glycosyltransferase That Catalyzes The Synthesis Of
Histo- Blood Group A Antigen
pdb|4AYJ|D Chain D, Molecular Structure Of A Metal-Independent Bacterial
Glycosyltransferase That Catalyzes The Synthesis Of
Histo- Blood Group A Antigen
pdb|4AYL|A Chain A, Molecular Structure Of A Metal-Independent Bacterial
Glycosyltransferase That Catalyzes The Synthesis Of
Histo- Blood Group A Antigen
Length = 246
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 292 EVLHRHEGEALGGAIH--VVLAPNGGLTQEARGGATLRVYPQGLGRVFPVGGHPSGVT 347
E+L + L G +H PN T E R +T + P+G GR + GG G T
Sbjct: 107 EILPPSDSNGLLGTMHPGFYNKPNSEFTYERRDASTAYI-PEGEGRYYYAGGLSGGCT 163
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 11/36 (30%), Positives = 22/36 (61%)
Query: 83 ESRGFGFVTMATVEEADRCIKYLDRSVLEGRIITVE 118
+S+G+ F+ A+ E+A + ++ +EGR I +E
Sbjct: 51 KSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE 86
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 26/55 (47%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADR 100
L V L P +T+++ E+ G + LV T +S+G+GF + A R
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 26/55 (47%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADR 100
L V L P +T+++ E+ G + LV T +S+G+GF + A R
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152
>pdb|4A0C|C Chain C, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0C|E Chain E, Structure Of The Cand1-Cul4b-Rbx1 Complex
Length = 741
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 96 EEADRCIKYLDRSVLEGRIITVER 119
EEADR I YLD++ + I TVE+
Sbjct: 251 EEADRLITYLDQTTQKSLIATVEK 274
>pdb|4A0L|E Chain E, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
pdb|4A0L|H Chain H, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 726
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 96 EEADRCIKYLDRSVLEGRIITVER 119
EEADR I YLD++ + I TVE+
Sbjct: 236 EEADRLITYLDQTTQKSLIATVEK 259
>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 = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 26/55 (47%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADR 100
L V L P +T+++ E+ G + LV T +S+G+GF + A R
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 150
>pdb|4A64|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Cul4b
At 2.57a Resolution
pdb|4A64|B Chain B, Crystal Structure Of The N-Terminal Domain Of Human Cul4b
At 2.57a Resolution
pdb|4A64|C Chain C, Crystal Structure Of The N-Terminal Domain Of Human Cul4b
At 2.57a Resolution
pdb|4A64|D Chain D, Crystal Structure Of The N-Terminal Domain Of Human Cul4b
At 2.57a Resolution
Length = 354
Score = 29.3 bits (64), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 96 EEADRCIKYLDRSVLEGRIITVER 119
EEADR I YLD++ + I TVE+
Sbjct: 220 EEADRLITYLDQTTQKSLIATVEK 243
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 28.9 bits (63), Expect = 4.8, Method: Composition-based stats.
Identities = 11/36 (30%), Positives = 24/36 (66%)
Query: 70 VIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
V ++ L+ D T+++RGF FV +++ +A + ++ L
Sbjct: 38 VNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQIL 73
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 28.9 bits (63), Expect = 5.4, Method: Composition-based stats.
Identities = 18/78 (23%), Positives = 37/78 (47%)
Query: 43 GNNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCI 102
+ L++ GL + ++++ + G + +LV D T S+G+ F + D+ I
Sbjct: 1 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Query: 103 KYLDRSVLEGRIITVERA 120
L+ L + + V+RA
Sbjct: 61 AGLNGMQLGDKKLLVQRA 78
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 28.5 bits (62), Expect = 7.1, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 44 NNLYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGF------GFVTMATVEE 97
N ++V GLS R+ E+ K GK +H VV + G +VT E+
Sbjct: 16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75
Query: 98 ADRCIKYLDRSVLEGRII 115
A R I+ ++ V++GR +
Sbjct: 76 ALRAIQCVNNVVVDGRTL 93
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 28.5 bits (62), Expect = 7.3, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 7/74 (9%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCI-KY 104
LYV GL IT+ +L HF G++ + +V + + F+ AT + A+ K
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQAAEVAAEKS 68
Query: 105 LDRSVLEGRIITVE 118
++ ++ GR + V+
Sbjct: 69 FNKLIVNGRRLNVK 82
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 46 LYVTGLSPRITKRELEKHFAAEGKVIDVHLVVDPWTRESRGFGFVTMATVEEADRCIKYL 105
L+V L IT+ + ++ F G+ +V + D RGFGF+ + + A+ L
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAEL 78
Query: 106 DRSVLEGRIITV 117
D ++L+ R + +
Sbjct: 79 DGTILKSRPLRI 90
>pdb|3IYD|C Chain C, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
pdb|4IGC|C Chain C, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|H Chain H, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1342
Score = 28.1 bits (61), Expect = 9.8, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 27/63 (42%), Gaps = 15/63 (23%)
Query: 292 EVLHRHEGEALGGAIHVVLAPNGGLTQEARGGATLRVYPQGLGRVFPVGGHPSGVTLEGA 351
E+ H+ ALG GGLT+E G V+P GRV P+ T EG
Sbjct: 523 EITHKRRISALG---------PGGLTRERAGFEVRDVHPTHYGRVCPIE------TPEGP 567
Query: 352 TLG 354
+G
Sbjct: 568 NIG 570
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 27.7 bits (60), Expect = 9.9, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 27/63 (42%), Gaps = 15/63 (23%)
Query: 292 EVLHRHEGEALGGAIHVVLAPNGGLTQEARGGATLRVYPQGLGRVFPVGGHPSGVTLEGA 351
E+ H+ ALG GGLT+E G V+P GRV P+ T EG
Sbjct: 523 EITHKRRISALG---------PGGLTRERAGFEVRDVHPTHYGRVCPIE------TPEGP 567
Query: 352 TLG 354
+G
Sbjct: 568 NIG 570
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
0.322 0.141 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,766,139
Number of Sequences: 62578
Number of extensions: 198982
Number of successful extensions: 596
Number of sequences better than 100.0: 123
Number of HSP's better than 100.0 without gapping: 101
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 468
Number of HSP's gapped (non-prelim): 140
length of query: 387
length of database: 14,973,337
effective HSP length: 101
effective length of query: 286
effective length of database: 8,652,959
effective search space: 2474746274
effective search space used: 2474746274
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)