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= 032211
(145 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 5/73 (6%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
MF +GKI+ + +++ RG K GF F+ + +A A+EK+HG + GR + V
Sbjct: 35 MFGQFGKILDVEIIFNERGSK-----GFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 89
Query: 61 ASEKYLEDAAQNS 73
A+ + + ++ +S
Sbjct: 90 ATARVMTNSGPSS 102
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 34/63 (53%), Gaps = 5/63 (7%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
FSP+G I S + G +GF F+ +S+ EEA A +M+GR+ +PL V LA
Sbjct: 36 FSPFGTITSAKVMMEG-----GRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA 90
Query: 62 SEK 64
K
Sbjct: 91 QRK 93
>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 = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
F+P+G I S D W + K +GFAF+EY E A+LA E+M+ + GR + V
Sbjct: 49 FAPFGPIKSIDMSWDSVTMKH---KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 102
Score = 26.6 bits (57), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMH 47
+F +GKI S R P G +G+ FIEY + ++ A M+
Sbjct: 145 VFEAFGKIKSATL---ARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
>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 = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
F+P+G I S D W + K +GFAF+EY E A+LA E+M+ + GR + V
Sbjct: 34 FAPFGPIKSIDMSWDSVTMKH---KGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 87
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
MF +GKI+ + +++ RG K GF F+ + +A A+EK+HG + GR + V
Sbjct: 49 MFGQFGKILDVEIIFNERGSK-----GFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 103
Query: 61 ASEKYL 66
A+ + +
Sbjct: 104 ATARVM 109
>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 = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACG--RPLVV 58
+F YG IV ++ L R G PRG AF+ Y+ +EEA+ A ++ + G +PL V
Sbjct: 120 IFGKYGSIVQKNIL---RDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 176
Query: 59 RLASE 63
RLA E
Sbjct: 177 RLAEE 181
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The
Second Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACG--RPLVV 58
+F YG IV ++ L R G PRG AF+ Y+ +EEA+ A ++ + G +PL V
Sbjct: 33 IFGKYGSIVQKNIL---RDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 89
Query: 59 RLASE 63
RLA E
Sbjct: 90 RLAEE 94
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 42.7 bits (99), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
FS +G I+ + R P G +G+AFI +++ + + A E M+G+ C RP+ V A
Sbjct: 26 FSAFGVILQTPKIM--RDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYA 83
Query: 62 SEK 64
+K
Sbjct: 84 FKK 86
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 36/63 (57%), Gaps = 5/63 (7%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACG--RPLVV 58
+F YG IV ++ L R G PRG AF+ Y+ +EEA+ A ++ + G +PL V
Sbjct: 109 IFGKYGSIVQKNIL---RDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165
Query: 59 RLA 61
RLA
Sbjct: 166 RLA 168
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 7/64 (10%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLA---CGRPLV 57
MFS +G+I L RGP G+ RG AF+ ++T+ A+ A + MH C P+V
Sbjct: 115 MFSSFGQIEECRIL---RGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 170
Query: 58 VRLA 61
V+ A
Sbjct: 171 VKFA 174
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 7/64 (10%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLA---CGRPLV 57
MFS +G+I L RGP G+ RG AF+ ++T+ A+ A + MH C P+V
Sbjct: 127 MFSSFGQIEECRIL---RGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 182
Query: 58 VRLA 61
V+ A
Sbjct: 183 VKFA 186
>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 = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 33/60 (55%), Gaps = 9/60 (15%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEK-----MHGR-LACGRP 55
F+P+G I S D W + K +GFAF+EY E A+LA E+ + GR + GRP
Sbjct: 33 FAPFGPIKSIDXSWDSVTXKH---KGFAFVEYEVPEAAQLALEQXNSVXLGGRNIKVGRP 89
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+F P+G+I S + + + G +G+ FI +S E AK A E+++G GRP+ V
Sbjct: 46 IFEPFGRIESIQLMMDS---ETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH 102
Query: 61 ASEK 64
+E+
Sbjct: 103 VTER 106
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+F P+GKI D + + G +G+ FI +S E A+ A E+++G GRP+ V
Sbjct: 25 IFEPFGKI---DNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH 81
Query: 61 ASEK 64
+E+
Sbjct: 82 VTER 85
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 11/63 (17%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+FS YGKIV V +GFAF++Y + A+ A GR+ G+ L + L
Sbjct: 36 IFSKYGKIVGCS-----------VHKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL 84
Query: 61 ASE 63
A+E
Sbjct: 85 AAE 87
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
F + +S +W + G RG+ F+ ++++++A+ A + M G+ GRPL + A
Sbjct: 108 FKDFPSYLSGHVMWDM---QTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
Query: 62 SE 63
++
Sbjct: 165 AK 166
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+F YG++ ++ R P PRGFAF+ + + +A+ A+ M G GR L V++
Sbjct: 33 VFEKYGRVGD---VYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV 89
Query: 61 A 61
A
Sbjct: 90 A 90
>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 = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
F + +S +W + G RG+ F+ ++++++A+ A + M G+ GRPL + A
Sbjct: 22 FKDFPSYLSGHVMWDM---QTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78
Query: 62 SE 63
++
Sbjct: 79 AK 80
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV-RL 60
FS +G I+S + G K G+ F+ + T+E A+ A EKM+G L R + V R
Sbjct: 32 FSAFGNILSCKVVCDENGSK-----GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 86
Query: 61 ASEK 64
S K
Sbjct: 87 KSRK 90
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 35.4 bits (80), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+FS YG+I SE + R +R RGF F+ + ++AK A M+G+ GR + V
Sbjct: 32 VFSKYGQI-SEVVVVKDRETQR--SRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ 88
Query: 61 A 61
A
Sbjct: 89 A 89
>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 = 35.4 bits (80), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV-RL 60
FS +G I+S + G K G+ F+ + T+E A+ A EKM+G L R + V R
Sbjct: 26 FSAFGNILSCKVVCDENGSK-----GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 80
Query: 61 ASEK 64
S K
Sbjct: 81 KSRK 84
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 35.0 bits (79), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV-R 59
+FS G +VS ++ + G P+G+ F EY +E A A ++GR GR L V
Sbjct: 28 IFSEVGPVVSFRLVYDR---ETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN 84
Query: 60 LASEK 64
ASEK
Sbjct: 85 AASEK 89
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 34.3 bits (77), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+F YG+ V + ++ R K RGFAF+ + K +A+ A + M G + GR L V++
Sbjct: 90 VFEKYGR-VGDVYIPRDRYTKES--RGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 146
Query: 61 A 61
A
Sbjct: 147 A 147
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 34.3 bits (77), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
F YG + S +W R P GFAF+E+ +A A ++ GR CG + V L+
Sbjct: 94 FGYYGPLRS---VWVARNPP-----GFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145
Query: 62 S 62
+
Sbjct: 146 N 146
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 33.9 bits (76), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
F YG + S +W R P GFAF+E+ +A A + GR CG + V L+
Sbjct: 94 FGYYGPLRS---VWVARNPP-----GFAFVEFEDPRDAADAVRDLDGRTLCGCRVRVELS 145
Query: 62 S 62
+
Sbjct: 146 N 146
>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 = 33.9 bits (76), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV-RL 60
FS +G I+S + G K G+ F+ + T+E A+ A EKM+G L R + V R
Sbjct: 119 FSAFGNILSCKVVCDENGSK-----GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 173
Query: 61 ASEK 64
S K
Sbjct: 174 KSRK 177
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 33.9 bits (76), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 4/48 (8%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHG 48
+F P+G I D RGP G +G AF+++S+ EA+ A +HG
Sbjct: 35 LFQPFGVI---DECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHALHG 78
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 33.5 bits (75), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+FS YG I ++ + + RGFAF+ + ++AK AKE+ +G GR + V
Sbjct: 35 VFSKYGPIADVSIVYDQQSRR---SRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 91
Query: 61 ASEK 64
+ K
Sbjct: 92 SITK 95
>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 = 33.5 bits (75), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV-RL 60
FS +G I+S + G K G+ F+ + T+E A+ A EKM+G L R + V R
Sbjct: 124 FSAFGNILSCKVVCDENGSK-----GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 178
Query: 61 ASEK 64
S K
Sbjct: 179 KSRK 182
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 33.5 bits (75), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
+FS YG I ++ + + RGFAF+ + ++AK AKE+ +G GR + V
Sbjct: 35 VFSKYGPIADVSIVYDQQSRR---SRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 33.5 bits (75), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 11/63 (17%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+FS YG++ V +G+AF++YS + A+ A +GR+ G+ L + +
Sbjct: 48 IFSKYGRVAGCS-----------VHKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM 96
Query: 61 ASE 63
A E
Sbjct: 97 AGE 99
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 33.1 bits (74), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 26 RGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLAS 62
RGF FI ++ A++AK ++ G + RPL +R A+
Sbjct: 58 RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT 94
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 33.1 bits (74), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+FS YG I ++ + + RGFAF+ + ++AK AKE+ +G GR + V
Sbjct: 66 VFSKYGPIADVSIVYDQQSRR---SRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
Query: 61 ASEK 64
+ K
Sbjct: 123 SITK 126
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 33.1 bits (74), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
FS YG + + +W R P GFAF+E+ +A+ A + G++ CG + V L+
Sbjct: 21 FSYYGPLRT---VWIARNPP-----GFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS 72
Query: 62 S 62
+
Sbjct: 73 T 73
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 32.7 bits (73), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
F P+G I K RGFAF+E+ E+A A + M+ GR + V LA
Sbjct: 33 FIPFGDITDIQIPLDYETEKH---RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 89
Query: 62 SEKYLEDAAQNS 73
++++ +S
Sbjct: 90 KPMRIKESGPSS 101
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 32.7 bits (73), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+FS YG I ++ + + RGFAF+ + ++AK AKE+ +G GR + V
Sbjct: 32 VFSKYGPIADVSIVYDQQSRR---SRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 88
Query: 61 ASEK 64
+ K
Sbjct: 89 SITK 92
>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 = 32.3 bits (72), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 2 FSPYGKIVSEDFLWHTRGPKR-GVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
F+ YG+I + H +R G +G+ +EY T +EA+ A E ++G+ G+P+ V
Sbjct: 43 FAEYGEIKN----IHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 96
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 32.3 bits (72), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 26 RGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
R +AF+ +S +E+A A + ++G++ G P+ V LA
Sbjct: 51 RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86
>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 = 32.3 bits (72), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 26 RGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
RGFAF+ + K +A+ A + M G + GR L V++A
Sbjct: 89 RGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
F P+G I K RGFAF+E+ E+A A + M+ GR + V LA
Sbjct: 26 FIPFGDITDIQIPLDYETEKH---RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 82
>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 = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
F P+G I K RGFAF+E+ E+A A + M+ GR + V LA
Sbjct: 28 FIPFGDITDIQIPLDYETEKH---RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84
>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 = 32.0 bits (71), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 2 FSPYGKIVSEDFLWHTRGPKR-GVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
F+ YG+I + H +R G +G+ +EY T +EA+ A E ++G+ G+P+ V
Sbjct: 28 FAEYGEIKNI----HLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 81
>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 = 32.0 bits (71), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
F P+G I K RGFAF+E+ E+A A + M+ GR + V LA
Sbjct: 23 FIPFGDITDIQIPLDYETEKH---RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 79
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 31.6 bits (70), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 11/66 (16%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKR----GVPRGFAFIEYSTKEEAKLAKEKM-HGRLACGRP 55
+FS +G++ + R PK+ G RGF F+++ TK++AK A + H GR
Sbjct: 35 LFSTFGELKT------VRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRR 88
Query: 56 LVVRLA 61
LV+ A
Sbjct: 89 LVLEWA 94
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 31.6 bits (70), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
F P+G I K RGFAF+E+ E+A A + M+ GR + V LA
Sbjct: 84 FIPFGDITDIQIPLDYETEKH---RGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 31.6 bits (70), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKL 41
M P+G+++S L + G RGV GFA +E + K EA +
Sbjct: 45 MLKPFGQVISTRILRDSSGTSRGV--GFARMESTEKCEAVI 83
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 31.6 bits (70), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHG 48
+F +G I L RGP G +G AF++YS+ EA+ A +HG
Sbjct: 35 LFEAFGNIEECTIL---RGPD-GNSKGCAFVKYSSHAEAQAAINALHG 78
>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 = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 2 FSPYGKIVSEDFLWHTRGPKR-GVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
F+ YG+I + H +R G +G+ +EY T +EA+ A E ++G+ G+P+ V
Sbjct: 44 FAEYGEIKN----IHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 97
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 31.6 bits (70), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 2 FSPYGKIVSEDFLWHTRGPKR-GVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
F+ YG+I + H +R G +G+ +EY T +EA+ A E ++G+ G+P+ V
Sbjct: 28 FAEYGEIKNI----HLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 81
>pdb|2LT7|A Chain A, Solution Nmr Structure Of Kaiso Zinc Finger Dna Binding
Domain In Complex With Kaiso Binding Site Dna
pdb|4F6M|A Chain A, Crystal Structure Of Kaiso Zinc Finger Dna Binding
Domain In Complex With Kaiso Binding Site Dna
pdb|4F6N|A Chain A, Crystal Structure Of Kaiso Zinc Finger Dna Binding
Protein In Complex With Methylated Cpg Site Dna
Length = 133
Score = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 20/43 (46%)
Query: 15 WHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLV 57
W + P R + F EY TK E E+ + LACG+ +
Sbjct: 47 WEKKYPCRYCEKVFPLAEYRTKHEIHHTGERRYQCLACGKSFI 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 = 31.2 bits (69), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 21 KRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
+ G +G+ +EY T +EA+ A E ++G+ G+P+ V
Sbjct: 46 RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 83
>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 = 31.2 bits (69), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 21 KRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
+ G +G+ +EY T +EA+ A E ++G+ G+P+ V
Sbjct: 44 RTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 81
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 31.2 bits (69), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 26/42 (61%), Gaps = 3/42 (7%)
Query: 27 GFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV---RLASEKY 65
GFAF+E+ E A A E++HG+ +PL V +L +++Y
Sbjct: 66 GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 30.8 bits (68), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 5/60 (8%)
Query: 4 PYGKIVSEDFLWHTRGP-----KRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
P+ V E L GP + + GFAF+E+ E A A E++HG+ +PL V
Sbjct: 11 PFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEV 70
>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 = 30.8 bits (68), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 2 FSPYGKIVSEDFLWHTRGPKR-GVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
F YG+I + H +R G +G+A +EY T ++A AKE ++G G+ + V
Sbjct: 93 FCDYGEIKN----IHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 146
>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 = 30.8 bits (68), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
F YG I ++ R G PRG+AFIEY + + A + G+ GR ++V
Sbjct: 123 FEVYGPIKRIHMVYSKRS---GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 30.4 bits (67), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 23 GVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLASEK 64
G +GF F++++++E+AK AKE M G + + A K
Sbjct: 51 GSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPK 92
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 30.4 bits (67), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 27 GFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLASEKYLEDAAQNSS 74
GF F+EY E+A+ A +++ G G L VR+ SE+ + A+ SS
Sbjct: 51 GFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRI-SERATKPASGPSS 97
>pdb|2KH9|A Chain A, Solution Structure Of Yeast Prp24-Rrm2 Bound To A
Fragment Of U6 Rna
Length = 92
Score = 30.0 bits (66), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 26 RGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLASEKYLE 67
R FA+I+ ++KE+A+ EK++G G LV ++++ LE
Sbjct: 45 RRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLELE 86
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 30.0 bits (66), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 2 FSPYGKIVSEDFLWHTRGPKR-GVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
F YG+I + H +R G +G+A +EY T ++A AKE ++G G+ + V
Sbjct: 47 FCDYGEIKN----IHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100
>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 = 30.0 bits (66), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
F YG I ++ R G PRG+AFIEY + + A + G+ GR ++V
Sbjct: 123 FEVYGPIKRIHMVYSKRS---GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 29.6 bits (65), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+F +G I SE L R K RGFAFI + +AK A + M+G+ G+ + V
Sbjct: 27 VFGKHGPI-SEVLLIKDRTSKS---RGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ 82
Query: 61 A 61
A
Sbjct: 83 A 83
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 29.3 bits (64), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 4/63 (6%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAK--EKMHGRLAC-GRPLVV 58
+PY ++S + + + + RGFAFI+ ST E A+L + + +H L G+ + V
Sbjct: 44 LAPYA-VLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQALHPPLTIDGKTINV 102
Query: 59 RLA 61
A
Sbjct: 103 EFA 105
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 29.3 bits (64), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 25/37 (67%)
Query: 26 RGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLAS 62
R FA+I+ ++KE+A+ EK++G G LV ++++
Sbjct: 159 RRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN 195
>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 = 29.3 bits (64), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 9/73 (12%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
FSP+G I+ PR AF+ Y E A A +++G L V +A
Sbjct: 58 FSPFGNIIDLSM---------DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 108
Query: 62 SEKYLEDAAQNSS 74
++ + DAA S
Sbjct: 109 RKQPMLDAATGKS 121
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 29.3 bits (64), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 25/37 (67%)
Query: 26 RGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLAS 62
R FA+I+ ++KE+A+ EK++G G LV ++++
Sbjct: 122 RRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN 158
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 28.9 bits (63), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 13/67 (19%)
Query: 9 VSEDFLW----------HTRGPK---RGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRP 55
VSE LW +T PK G +G+ F+E+ ++E+A A + M G+P
Sbjct: 27 VSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKP 86
Query: 56 LVVRLAS 62
+ V AS
Sbjct: 87 IRVNKAS 93
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 26 RGFAFIEYSTKEEAKLAKEK-MHGRL 50
RGFAF+EY + A +A+ K M GR+
Sbjct: 52 RGFAFVEYESHRAAAMARRKLMPGRI 77
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 27.7 bits (60), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 9/72 (12%)
Query: 2 FSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRLA 61
FSP+G I+ D PR AF+ Y E A A +++G L V +A
Sbjct: 34 FSPFGNII--DLSMDP-------PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 84
Query: 62 SEKYLEDAAQNS 73
++ + D+ +S
Sbjct: 85 RKQPMLDSGPSS 96
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 27.7 bits (60), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHG 48
+FS YGKI D P + +G+A++E+ +EA+ A + M G
Sbjct: 24 IFSTYGKIKMIDMPVERMHPH--LSKGYAYVEFENPDEAEKALKHMDG 69
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 26.9 bits (58), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 24/40 (60%)
Query: 21 KRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+ G +G+AFIE+++ E+AK A + R GR + + L
Sbjct: 48 QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL 87
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 26.9 bits (58), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHG 48
+F P+G I ++ + G +GFAFI + +E+A A + G
Sbjct: 35 LFRPFGSISR---IYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSG 79
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 26.9 bits (58), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVV 58
+FS YG + + + K P+GFAF+ + E A A ++ G++ GR L V
Sbjct: 28 LFSAYGPLSELHYPIDSLTKK---PKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHV 82
>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 = 26.9 bits (58), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 23 GVPRGFAFIEYSTKEEAK 40
G P+GFA+IE+S KE +
Sbjct: 44 GHPKGFAYIEFSDKESVR 61
>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 = 26.9 bits (58), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 23 GVPRGFAFIEYSTKEEAK 40
G P+GFA+IE+S KE +
Sbjct: 45 GHPKGFAYIEFSDKESVR 62
>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 = 26.9 bits (58), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 21 KRGVPRGFAFIEYSTKEEAKLAKEKMHG 48
+ G P+G A++EY + +A A KM G
Sbjct: 53 RAGKPKGLAYVEYENESQASQAVMKMDG 80
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 26.2 bits (56), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 18 RGPKRGVPRGFAFIEYSTKEEAKLA----KEKMHGRLACGRPLVVRLASEK 64
R P RGF F+ Y+T EE A K+ GR+ + V R S++
Sbjct: 48 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQR 98
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 26.2 bits (56), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 1 MFSPYGKIVSEDFLWHTRGPKRGVPRGFAFIEYSTKEEAKLAKEKMHGRLACGRPLVVRL 60
+FS G +V D L K G RG + + EA A +G+L RP+ V++
Sbjct: 35 VFSMAGVVVRADILED----KDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM 90
>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 = 26.2 bits (56), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 18 RGPKRGVPRGFAFIEYSTKEEAKLA----KEKMHGRLACGRPLVVRLASEK 64
R P RGF F+ Y+T EE A K+ GR+ + V R S++
Sbjct: 46 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQR 96
>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 = 26.2 bits (56), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 18 RGPKRGVPRGFAFIEYSTKEEAKLA----KEKMHGRLACGRPLVVRLASEK 64
R P RGF F+ Y+T EE A K+ GR+ + V R S++
Sbjct: 47 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQR 97
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 26.2 bits (56), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 18 RGPKRGVPRGFAFIEYSTKEEAKLA----KEKMHGRLACGRPLVVRLASEK 64
R P RGF F+ Y+T EE A K+ GR+ + V R S++
Sbjct: 47 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQR 97
>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 = 26.2 bits (56), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 18 RGPKRGVPRGFAFIEYSTKEEAKLAK----EKMHGRLACGRPLVVRLASEK 64
R P RGF F+ Y+T EE A K+ GR+ + V R S++
Sbjct: 40 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQR 90
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 26.2 bits (56), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 18 RGPKRGVPRGFAFIEYSTKEEAKLA----KEKMHGRLACGRPLVVRLASEK 64
R P RGF F+ Y+T EE A K+ GR+ + V R S++
Sbjct: 45 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQR 95
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.310 0.127 0.359
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,222,390
Number of Sequences: 62578
Number of extensions: 99458
Number of successful extensions: 277
Number of sequences better than 100.0: 93
Number of HSP's better than 100.0 without gapping: 74
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 191
Number of HSP's gapped (non-prelim): 103
length of query: 145
length of database: 14,973,337
effective HSP length: 89
effective length of query: 56
effective length of database: 9,403,895
effective search space: 526618120
effective search space used: 526618120
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 47 (22.7 bits)