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= 006380
(647 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 90.5 bits (223), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 43/81 (53%), Positives = 57/81 (70%), Gaps = 1/81 (1%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
+LYVG+LHFN+TE LR +FEPFG +E +QL +D ETG+ KG+GF+ F+ E AK A
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 439 LNGKLEIVGRTLKVSSVTDHV 459
LNG E+ GR +KV VT+
Sbjct: 88 LNG-FELAGRPMKVGHVTERT 107
>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From Mus
Musculus
Length = 113
Score = 83.2 bits (204), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 43/93 (46%), Positives = 60/93 (64%), Gaps = 1/93 (1%)
Query: 554 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTE 612
++C L NMF+P E + +D EI+ DV EEC+K+G V HIYVDK SA G VY++ S
Sbjct: 6 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIA 65
Query: 613 AAASAQRAMHMRWFARRLISAIFMKPEDYEAKF 645
AA +A A+H RWFA ++I+A ++ Y F
Sbjct: 66 AAIAAVNALHGRWFAGKMITAAYVPLPTYHNLF 98
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 80.1 bits (196), Expect = 4e-15, Method: Composition-based stats.
Identities = 38/80 (47%), Positives = 55/80 (68%), Gaps = 1/80 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
LYVG+LHFN+TE LR +FEPFG ++ + L D +TG+ KG+GF+ F+ E A+ A L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 440 NGKLEIVGRTLKVSSVTDHV 459
NG E+ GR ++V VT+ +
Sbjct: 68 NG-FELAGRPMRVGHVTERL 86
>pdb|3S6E|A Chain A, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
pdb|3S6E|B Chain B, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
Length = 114
Score = 76.6 bits (187), Expect = 4e-14, Method: Composition-based stats.
Identities = 42/93 (45%), Positives = 58/93 (62%), Gaps = 1/93 (1%)
Query: 554 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTE 612
++C L N F+P E + +D EI+ DV EEC+K+G V HIYVDK SA G VY++ S
Sbjct: 7 TQCFQLSNXFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIA 66
Query: 613 AAASAQRAMHMRWFARRLISAIFMKPEDYEAKF 645
AA +A A+H RWFA + I+A ++ Y F
Sbjct: 67 AAIAAVNALHGRWFAGKXITAAYVPLPTYHNLF 99
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 67.4 bits (163), Expect = 3e-11, Method: Composition-based stats.
Identities = 32/59 (54%), Positives = 41/59 (69%)
Query: 207 KEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
+E V+ + ERD RTVF Q+ + RD+ +FFS GKVRDVR+I DRNSRRSKG+
Sbjct: 12 REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIA 70
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 22/44 (50%), Positives = 33/44 (75%)
Query: 322 YIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSA 365
Y+EF ++ SVP+AI L+GQ LLG P++V+ S+AEKN + +S
Sbjct: 71 YVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGPSSG 114
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 35/83 (42%), Positives = 50/83 (60%), Gaps = 4/83 (4%)
Query: 375 AIDRKL---YVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH 431
A+DR L +VGN+ + TE QL+ +F GPV +L D ETG+ KG+GF ++ E
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 432 AKAAQSALNGKLEIVGRTLKVSS 454
A +A LNG+ E GR L+V +
Sbjct: 63 ALSAMRNLNGR-EFSGRALRVDN 84
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 29/49 (59%)
Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
+R R+VF +P +ATE + + FS+ G V RL+ DR + + KG G
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYG 53
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 1/74 (1%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
KL+VG L F+ E L ++F +G + V + D ET + +GFGFV F ++ AK A A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 439 LNGKLEIVGRTLKV 452
+NGK + GR ++V
Sbjct: 74 MNGK-SVDGRQIRV 86
Score = 33.1 bits (74), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 28/47 (59%)
Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
D+ +F + E+ + + FSK G++ +V ++ DR ++RS+G G
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFG 57
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 573 FDLEIQGDVEEECSKYGRVKHIYVDK-----RSAGFVYLRFESTEAAASAQRAMHMRWFA 627
FD Q +E+ SKYG++ + V K RS GF ++ FE+ + A A AM+ +
Sbjct: 22 FDTNEQ-SLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD 80
Query: 628 RRLI 631
R I
Sbjct: 81 GRQI 84
>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 = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/83 (39%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 371 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 430
G R LYVG L + + L F PFG + +Q+PLD ET + +GF FV+F E
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 431 HAKAAQSALNGKLEIVGRTLKVS 453
A AA +N + E+ GRT++V+
Sbjct: 61 DAAAAIDNMN-ESELFGRTIRVN 82
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 33/88 (37%), Positives = 49/88 (55%), Gaps = 1/88 (1%)
Query: 366 GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 425
G + + R LYVG L + + L F PFG + +Q+PLD ET + +GF FV+
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 426 FAQLEHAKAAQSALNGKLEIVGRTLKVS 453
F E A AA +N + E+ GRT++V+
Sbjct: 61 FELAEDAAAAIDNMN-ESELFGRTIRVN 87
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 34/86 (39%), Positives = 50/86 (58%), Gaps = 1/86 (1%)
Query: 368 TATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFA 427
T P + R L V + + E QLR+LFE +GP+E V++ D ET Q +G+GFV+F
Sbjct: 33 TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ 92
Query: 428 QLEHAKAAQSALNGKLEIVGRTLKVS 453
A+ A + LNG I+ + LKV+
Sbjct: 93 SGSSAQQAIAGLNG-FNILNKRLKVA 117
Score = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 213 EADPERD-QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
+ +PE D R + +P E + + F + G + V+++ DR +R+S+G G
Sbjct: 34 QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYG 87
>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 = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R LYVG L + + L F PFG + +Q+PLD ET + +GF FV+F E A AA
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 438 ALNGKLEIVGRTLKVS 453
+N + E+ GRT++V+
Sbjct: 63 NMN-ESELFGRTIRVN 77
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R LYVG L + + L F PFG + +Q+PLD ET + +GF FV+F E A AA
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 438 ALNGKLEIVGRTLKVS 453
+N + E+ GRT++V+
Sbjct: 66 NMN-ESELFGRTIRVN 80
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R LYVG L + + L F PFG + +Q+PLD ET + +GF FV+F E A AA
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 438 ALNGKLEIVGRTLKVS 453
+N + E+ GRT++V+
Sbjct: 124 NMN-ESELFGRTIRVN 138
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 55.8 bits (133), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 48/76 (63%), Gaps = 2/76 (2%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R +YVGNL ++ T Q+++LF FG V V+L D ET + KGFGFV+ Q E A +
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIA 60
Query: 438 ALNGKLEIVGRTLKVS 453
L+ + +GRT++V+
Sbjct: 61 KLDN-TDFMGRTIRVT 75
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 27/45 (60%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
R ++ + AT V E FS+ GKV +V+LI DR +++ KG G
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFG 46
>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 = 55.8 bits (133), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 48/78 (61%), Gaps = 1/78 (1%)
Query: 375 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 434
AI ++YVG++++ + E +R+ F PFGP++ + + D T + KGF FV++ E A+
Sbjct: 26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL 85
Query: 435 AQSALNGKLEIVGRTLKV 452
A +N + + GR +KV
Sbjct: 86 ALEQMNSVM-LGGRNIKV 102
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 49/74 (66%), Gaps = 1/74 (1%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
++YV ++H ++++ ++ +FE FG ++ L D TG+ KG+GF+++ + + ++ A S+
Sbjct: 127 RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
Query: 439 LNGKLEIVGRTLKV 452
+N ++ G+ L+V
Sbjct: 187 MN-LFDLGGQYLRV 199
>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 = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 48/78 (61%), Gaps = 1/78 (1%)
Query: 375 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 434
AI ++YVG++++ + E +R+ F PFGP++ + + D T + KGF FV++ E A+
Sbjct: 11 AIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL 70
Query: 435 AQSALNGKLEIVGRTLKV 452
A +N + + GR +KV
Sbjct: 71 ALEQMNSVM-LGGRNIKV 87
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 49/74 (66%), Gaps = 1/74 (1%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
++YV ++H ++++ ++ +FE FG ++ L D TG+ KG+GF+++ + + ++ A S+
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 439 LNGKLEIVGRTLKV 452
+N ++ G+ L+V
Sbjct: 172 MN-LFDLGGQYLRV 184
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
+L+V NL + +E L KLF +GP+ + P+D T + KGF FV F EHA A +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 439 LNGKLEIVGRTLKV 452
++G++ GR L V
Sbjct: 70 VDGQV-FQGRMLHV 82
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 54.3 bits (129), Expect = 2e-07, Method: Composition-based stats.
Identities = 33/100 (33%), Positives = 50/100 (50%), Gaps = 1/100 (1%)
Query: 364 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIE-TGQCKGFG 422
S+G + P K+ V N+ F + ++R+LF FG ++ V+LP + TG +GFG
Sbjct: 2 SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61
Query: 423 FVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQ 462
FV F + AK A +AL + GR L + V Q
Sbjct: 62 FVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101
>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 = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 375 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 434
AI ++YVG++++ + E +R+ F PFGP++ + D T + KGF FV++ E A+
Sbjct: 10 AIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQL 69
Query: 435 AQSALNGKLEIVGRTLKV 452
A N + + GR +KV
Sbjct: 70 ALEQXN-SVXLGGRNIKV 86
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 48/74 (64%), Gaps = 1/74 (1%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
++YV ++H ++++ ++ +FE FG ++ L D TG+ KG+GF+++ + + ++ A S+
Sbjct: 111 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170
Query: 439 LNGKLEIVGRTLKV 452
N ++ G+ L+V
Sbjct: 171 XN-LFDLGGQYLRV 183
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 52.4 bits (124), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
LYV NL + + +LRK F PFG + ++ + E G+ KGFGFV F+ E A A + +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 440 NGKL 443
NG++
Sbjct: 76 NGRI 79
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V NL + + LR++FE +G V V +P + T +GF FV+F A+ A++A+
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 440 NGKLEIVGRTLKV 452
+G E+ GR L+V
Sbjct: 76 DG-AELDGRELRV 87
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V NL + + LR++FE +G V V +P D T + +GF FV+F A+ A A+
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 440 NGKLEIVGRTLKV 452
+G + + GR L+V
Sbjct: 133 DGAV-LDGRELRV 144
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 587 KYGRVKHIYV-----DKRSAGFVYLRFESTEAAASAQRAM 621
KYGRV +Y+ K S GF ++RF A A AM
Sbjct: 93 KYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V L TE LR++F +GP+ V + D ++ + +GF FV F ++ AK A+
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 440 NGKLEIVGRTLKVS 453
NG +E+ GR ++VS
Sbjct: 78 NG-MELDGRRIRVS 90
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 26/38 (68%)
Query: 226 YQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
+ + L TERD+ E FSK G + DV ++ D+ SRRS+G
Sbjct: 21 FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG 58
Score = 30.4 bits (67), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 580 DVEEECSKYGRVKHIYV-----DKRSAGFVYLRFESTEAAASA-QRAMHMRWFARRL 630
D+ E SKYG + + + +RS GF ++ FE+ + A A +RA M RR+
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V L NMT+ +LR LF G VE +L D G G+GFV + + A+ A + L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 440 NGKLEIVGRTLKVS 453
NG L + +T+KVS
Sbjct: 65 NG-LRLQSKTIKVS 77
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
D LY+ L MT+ + +F FG + ++ +D TG +G F++F + A+ A
Sbjct: 88 DANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Query: 437 SALNG 441
++ NG
Sbjct: 148 TSFNG 152
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 26/37 (70%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGV 264
+P T++DV + FS+ G++ + R+++D+ + S+GV
Sbjct: 96 LPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGV 132
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
L V L NMT+ +LR LF G VE +L D G G+GFV + + A+ A +
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 439 LNGKLEIVGRTLKVS 453
LNG L + +T+KVS
Sbjct: 64 LNG-LRLQSKTIKVS 77
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
D LY+ L MT+ + +F FG + ++ +D TG +G F++F + A+ A
Sbjct: 88 DANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Query: 437 SALNG 441
++ NG
Sbjct: 148 TSFNG 152
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 26/37 (70%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGV 264
+P T++DV + FS+ G++ + R+++D+ + S+GV
Sbjct: 96 LPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGV 132
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 50.8 bits (120), Expect = 3e-06, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 41/78 (52%)
Query: 364 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 423
S+G + + + V NL + ET L++LF PFG + + L D TGQ KGF F
Sbjct: 2 SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61
Query: 424 VQFAQLEHAKAAQSALNG 441
+ F + E A A + ++G
Sbjct: 62 ISFHRREDAARAIAGVSG 79
>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 = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 40/64 (62%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R +Y+G++ ++ TE Q+ L GPV +++ D +TG+ KG+ F++F LE + +A
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 438 ALNG 441
LNG
Sbjct: 64 NLNG 67
>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 = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V L NMT+ +LR LF G VE +L D G G+GFV + + A+ A + L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 440 NGKLEIVGRTLKVS 453
NG L + +T+KVS
Sbjct: 67 NG-LRLQSKTIKVS 79
>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 = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 40/64 (62%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R +Y+G++ ++ TE Q+ L GPV +++ D +TG+ KG+ F++F LE + +A
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 438 ALNG 441
LNG
Sbjct: 65 NLNG 68
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 50.1 bits (118), Expect = 4e-06, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 40/64 (62%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R +Y+G++ ++ TE Q+ L GPV +++ D +TG+ KG+ F++F LE + +A
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 438 ALNG 441
LNG
Sbjct: 63 NLNG 66
>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 = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V NL + + LR++FE +G V V +P D T + +GF FV+F A+ A A+
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 440 NGKLEIVGRTLKV 452
+G + + GR L+V
Sbjct: 110 DGAV-LDGRELRV 121
Score = 29.6 bits (65), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 587 KYGRVKHIYVD-----KRSAGFVYLRFESTEAAASAQRAM 621
KYGRV +Y+ K S GF ++RF A A AM
Sbjct: 70 KYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 51/227 (22%), Positives = 86/227 (37%), Gaps = 70/227 (30%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKGVGNAIMMRDD 273
P+ D +F Q+P +E+D+ E F + G V ++ ++ DR N +SKG
Sbjct: 11 PDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG---------- 60
Query: 274 GNTLHSCLINSCCVIKFFLVAEVGMVFFLLGDETYTVLDPATVLVSYRYIEFYDVMSVPM 333
CC + F+ L+ L + +
Sbjct: 61 -----------CCFVTFYT--------------RKAALEAQNALHNMK------------ 83
Query: 334 AIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQ 393
L G + P+ +KP+++EKN DRKL++G + TE
Sbjct: 84 --VLPG---MHHPIQMKPADSEKN---------------NAVEDRKLFIGMISKKCTEND 123
Query: 394 LRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 440
+R +F FG +E ++ L G +G FV F A+ A A++
Sbjct: 124 IRVMFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG--QCKGFGFVQFAQLEHAKAAQ 436
K++VG + +E LR+LFE +G V + + D Q KG FV F + A AQ
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 437 SALNG 441
+AL+
Sbjct: 77 NALHN 81
Score = 29.3 bits (64), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 580 DVEEECSKYGRVKHIYVDK-------RSAGFVYLRFESTEAAASAQRAMHMRWFARRLIS 632
D+ E +YG V I V + +S G ++ F + +AA AQ A+H +
Sbjct: 31 DLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHH 90
Query: 633 AIFMKPEDYE 642
I MKP D E
Sbjct: 91 PIQMKPADSE 100
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 50.1 bits (118), Expect = 4e-06, Method: Composition-based stats.
Identities = 34/136 (25%), Positives = 69/136 (50%), Gaps = 14/136 (10%)
Query: 318 VSYRYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAID 377
V+Y ++E++ +A+ Q L G+ + E N+V+ N + + +
Sbjct: 41 VNYAFVEYHQSHDANIAL----QTLNGKQI-------ENNIVKINWAFQSQQSSSDDTFN 89
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
L+VG+L+ N+ + LR F+ F + D++TG +G+GFV F + A+ A
Sbjct: 90 --LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 147
Query: 438 ALNGKLEIVGRTLKVS 453
++ G+ ++ GR L+++
Sbjct: 148 SMQGQ-DLNGRPLRIN 162
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R LYVGNL +TE L++ F+ GP+ +++ +D + + + FV++ Q A A
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQ 59
Query: 438 ALNGK 442
LNGK
Sbjct: 60 TLNGK 64
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
D +YVG L ++E L +LF GPV +P D TGQ +G+GFV+F E A A
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 437 SALNGKLEIVGRTLKVSSVTDH 458
++ +++ G+ ++V+ + H
Sbjct: 75 KIMD-MIKLYGKPIRVNKASAH 95
>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 = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V L NMT+ + R LF G +E +L D TGQ G+GFV + + A+ A + L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 440 NGKLEIVGRTLKVS 453
NG L + +T+KVS
Sbjct: 65 NG-LRLQTKTIKVS 77
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 37/66 (56%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
D LYV L MT+ +L +LF +G + ++ +D TG +G GF++F + A+ A
Sbjct: 88 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
Query: 437 SALNGK 442
LNG+
Sbjct: 148 KGLNGQ 153
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
P + RD ++ +P T++++ + FS+ G++ R+++D+ + S+GVG
Sbjct: 81 PSSASIRDA-NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVG 133
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 49.7 bits (117), Expect = 5e-06, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 46/73 (63%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L+V ++H E ++++ F +G ++ + L LD TG KG+ V++ + A AA+ AL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 440 NGKLEIVGRTLKV 452
NG EI+G+T++V
Sbjct: 89 NGA-EIMGQTIQV 100
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 49.7 bits (117), Expect = 5e-06, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 557 LLLKNMFDPA-METDPDFDLEIQGDVEEECSKYGRVKHIYV-DKRSAGFVYLRFESTEAA 614
+++KNMF P E DP EI+ D+ ECSK+G+++ + + D+ G + F E A
Sbjct: 18 VIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEA 77
Query: 615 ASAQRAMHMRWFARRLISA 633
+ + RWF R I+A
Sbjct: 78 DYCIQTLDGRWFGGRQITA 96
>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 = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
RKL++G L F T+ LR FE +G + + D T + +GFGFV +A +E AA +
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 438 ALNGKLE 444
A K++
Sbjct: 73 ARPHKVD 79
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 426
+K++VG + + E LR FE +G +E++++ D +G+ +GF FV F
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
>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 = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
RKL++G L F T+ LR FE +G + + D T + +GFGFV +A +E AA +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 438 ALNGKLE 444
A K++
Sbjct: 74 ARPHKVD 80
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 426
+K++VG + + E LR FE +G +E++++ D +G+ +GF FV F
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V L NMT+ + + LF G +E +L D TGQ G+GFV ++ A A + L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 440 NGKLEIVGRTLKVS 453
NG L++ +T+KVS
Sbjct: 67 NG-LKLQTKTIKVS 79
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 37/66 (56%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
D LYV L M++ ++ +LF +G + ++ LD TG +G GF++F + A+ A
Sbjct: 90 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Query: 437 SALNGK 442
LNG+
Sbjct: 150 KGLNGQ 155
Score = 29.3 bits (64), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 212 PEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
P + RD ++ +P +++++ + FS+ G++ R+++D+ + S+GVG
Sbjct: 83 PSSASIRDA-NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVG 135
>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
pdb|2M0G|B Chain B, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 104
Score = 49.7 bits (117), Expect = 6e-06, Method: Composition-based stats.
Identities = 32/101 (31%), Positives = 47/101 (46%), Gaps = 7/101 (6%)
Query: 551 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-------RSAGF 603
G P+E L L NM P D + EI DV +ECSKYG VK I + + G
Sbjct: 1 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGK 60
Query: 604 VYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 644
+++ F S A + + R FA R++ + P+ Y +
Sbjct: 61 IFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRR 101
>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 = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
RKL++G L F T+ LR FE +G + + D T + +GFGFV +A +E AA +
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 438 ALNGKLE 444
A K++
Sbjct: 67 ARPHKVD 73
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 426
+K++VG + + E LR FE +G +E++++ D +G+ +GF FV F
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V L TE LR++F +GP+ V + D ++ + +GF FV F ++ AK A+
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 440 NGKLEIVGRTLKV 452
NG +E+ GR ++V
Sbjct: 75 NG-MELDGRRIRV 86
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 26/38 (68%)
Query: 226 YQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
+ + L TERD+ E FSK G + DV ++ D+ SRRS+G
Sbjct: 18 FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG 55
Score = 30.0 bits (66), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 580 DVEEECSKYGRVKHIYV-----DKRSAGFVYLRFESTEAAASA-QRAMHMRWFARRL 630
D+ E SKYG + + + +RS GF ++ FE+ + A A +RA M RR+
Sbjct: 28 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 84
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
RKL++G L F T+ LR FE +G + + D T + +GFGFV +A +E AA +
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 438 ALNGKLE 444
A K++
Sbjct: 75 ARPHKVD 81
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 426
+K++VG + + E LR FE +G +E++++ D +G+ +GF FV F
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
RKL++G L F T+ LR FE +G + + D T + +GFGFV +A +E AA +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 438 ALNGKLE 444
A K++
Sbjct: 74 ARPHKVD 80
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 426
+K++VG + + E LR FE +G +E++++ D +G+ +GF FV F
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 35/57 (61%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 435
K++VG L ++ T+ LRK FE FG +E + D +TG+ +G+GFV A A+ A
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
Score = 29.3 bits (64), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 24/47 (51%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGNAIM 269
+F +P T+ + ++F G + + +I DR + +S+G G M
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTM 66
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
RKL++G L F T+ LR FE +G + + D T + +GFGFV +A +E AA +
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 438 ALNGKLE 444
A K++
Sbjct: 72 ARPHKVD 78
Score = 43.1 bits (100), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 426
+K++VG + + E LR FE +G +E++++ D +G+ +GF FV F
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
>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 = 48.9 bits (115), Expect = 8e-06, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 46/73 (63%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L+V ++H E ++++ F +G ++ + L LD TG KG+ V++ + A AA+ AL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 440 NGKLEIVGRTLKV 452
NG EI+G+T++V
Sbjct: 135 NGA-EIMGQTIQV 146
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 48.9 bits (115), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V L TE LR++F +GP+ V + D ++ + +GF FV F ++ AK A+
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 440 NGKLEIVGRTLKV 452
NG +E+ GR ++V
Sbjct: 109 NG-MELDGRRIRV 120
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 26/38 (68%)
Query: 226 YQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
+ + L TERD+ E FSK G + DV ++ D+ SRRS+G
Sbjct: 52 FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG 89
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 580 DVEEECSKYGRVKHIYV-----DKRSAGFVYLRFESTEAAASA-QRAMHMRWFARRL 630
D+ E SKYG + + + +RS GF ++ FE+ + A A +RA M RR+
Sbjct: 62 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 118
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 48.1 bits (113), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V L TE LR++F +GP+ V + D ++ + +GF FV F ++ AK A+
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 440 NGKLEIVGRTLKV 452
NG +E+ GR ++V
Sbjct: 78 NG-MELDGRRIRV 89
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 18/38 (47%), Positives = 26/38 (68%)
Query: 226 YQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
+ + L TERD+ E FSK G + DV ++ D+ SRRS+G
Sbjct: 21 FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG 58
Score = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 580 DVEEECSKYGRVKHIYV-----DKRSAGFVYLRFESTEAAASA-QRAMHMRWFARRL 630
D+ E SKYG + + + +RS GF ++ FE+ + A A +RA M RR+
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 48/92 (52%), Gaps = 15/92 (16%)
Query: 554 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAG---------FV 604
S ++L+NM DP D D +++G+V EEC K+G V + + + G +
Sbjct: 15 STVMVLRNMVDP-----KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 69
Query: 605 YLRFESTEAAASAQRAMHMRWFA-RRLISAIF 635
++ F A +A++ RWFA R++++ ++
Sbjct: 70 FVEFSIASETHKAIQALNGRWFAGRKVVAEVY 101
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 14/89 (15%)
Query: 554 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAG---------FV 604
S ++L+NM DP D D +++G+V EEC K+G V + + + G +
Sbjct: 124 STVMVLRNMVDPK-----DIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 178
Query: 605 YLRFESTEAAASAQRAMHMRWFARRLISA 633
++ F A +A++ RWFA R + A
Sbjct: 179 FVEFSIASETHKAIQALNGRWFAGRKVVA 207
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 48.1 bits (113), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/51 (45%), Positives = 32/51 (62%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 430
L V L + TE L++ F FG V +VQ+ D++TG KGFGFV+F + E
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
Score = 33.5 bits (75), Expect = 0.39, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 24/38 (63%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
+P K TE+D+ E+FS G+V V++ D + SKG G
Sbjct: 23 LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V L NMT+ + + LF G +E +L D TGQ G+GFV ++ A A + L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 440 NGKLEIVGRTLKVS 453
NG L++ +T+KVS
Sbjct: 67 NG-LKLQTKTIKVS 79
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 31/99 (31%), Positives = 46/99 (46%), Gaps = 7/99 (7%)
Query: 553 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-------RSAGFVY 605
P+E L L NM P D + EI DV +ECSKYG VK I + + G ++
Sbjct: 3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 62
Query: 606 LRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 644
+ F S A + + R FA R++ + P+ Y +
Sbjct: 63 VEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRR 101
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 50/224 (22%), Positives = 84/224 (37%), Gaps = 70/224 (31%)
Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKGVGNAIMMRDDGNT 276
D +F Q+P +E+D+ E F + G V ++ ++ DR N +SKG
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG------------- 48
Query: 277 LHSCLINSCCVIKFFLVAEVGMVFFLLGDETYTVLDPATVLVSYRYIEFYDVMSVPMAIA 336
CC + F+ L+ L + +
Sbjct: 49 --------CCFVTFYT--------------RKAALEAQNALHNMK--------------V 72
Query: 337 LSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRK 396
L G + P+ +KP+++EKN DRKL++G + TE +R
Sbjct: 73 LPG---MHHPIQMKPADSEKN---------------NAVEDRKLFIGMISKKCTENDIRV 114
Query: 397 LFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 440
+F FG +E ++ L G +G FV F A+ A A++
Sbjct: 115 MFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 35.4 bits (80), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG--QCKGFGFVQFAQLEHAKAAQ 436
K++VG + +E LR+LFE +G V + + D Q KG FV F + A AQ
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 437 SALNG 441
+AL+
Sbjct: 65 NALHN 69
>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 = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L+VG+L+ N+ + LR F+ F + D++TG +G+GFV F + A+ A ++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 440 NGKLEIVGRTLKVS 453
G+ ++ GR L+++
Sbjct: 64 QGQ-DLNGRPLRIN 76
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
RKL+VG L+ +E +R+LFE FG +E + L G KG FV+++ A+AA +
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTI-LRGPDGNSKGCAFVKYSSHAEAQAAIN 74
Query: 438 ALNGKLEIVG 447
AL+G + G
Sbjct: 75 ALHGSQTMPG 84
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
DRKL+VG L+ +E + +LF+PFG ++ + L G KG FV+F+ A+AA
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTV-LRGPDGSSKGCAFVKFSSHTEAQAAI 73
Query: 437 SALNGKLEIVG 447
AL+G + G
Sbjct: 74 HALHGSQTMPG 84
>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
pdb|3V4M|B Chain B, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
Length = 105
Score = 47.0 bits (110), Expect = 4e-05, Method: Composition-based stats.
Identities = 31/101 (30%), Positives = 46/101 (45%), Gaps = 7/101 (6%)
Query: 551 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-------RSAGF 603
G P+E L L N P D + EI DV +ECSKYG VK I + + G
Sbjct: 2 GHPTEVLCLXNXVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGK 61
Query: 604 VYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 644
+++ F S A + + R FA R++ + P+ Y +
Sbjct: 62 IFVEFTSVFDCQKAXQGLTGRKFANRVVVTKYCDPDSYHRR 102
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 11/90 (12%)
Query: 552 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYV------DKRSAGFVY 605
P++ +LL+NM A E D D ++E + EEC KYG+V + A ++
Sbjct: 6 CPTKVVLLRNMVG-AGEVDEDLEVETK----EECEKYGKVGKCVIFEIPGAPDDEAVRIF 60
Query: 606 LRFESTEAAASAQRAMHMRWFARRLISAIF 635
L FE E+A A ++ R+F R++ A F
Sbjct: 61 LEFERVESAIKAVVDLNGRYFGGRVVKACF 90
>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 = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
D L V NL ++T+ Q +L PFG +E L TGQ KG+GF ++ + + A A+
Sbjct: 93 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 152
Query: 437 SALNGKLEIVGRTLKV 452
S L GK + RTL V
Sbjct: 153 SDLLGK-PLGPRTLYV 167
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
D L V NL ++T+ Q +L PFG +E L TGQ KG+GF ++ + + A A+
Sbjct: 95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 437 SALNGKLEIVGRTLKV 452
S L GK + RTL V
Sbjct: 155 SDLLGK-PLGPRTLYV 169
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
D L V NL ++T+ Q +L PFG +E L TGQ KG+GF ++ + + A A+
Sbjct: 95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 437 SALNGKLEIVGRTLKV 452
S L GK + RTL V
Sbjct: 155 SDLLGK-PLGPRTLYV 169
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
DRKL+VG L T+ +RK+FEPFG ++ + L G KG FV+F A+AA
Sbjct: 12 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTV-LRGPDGTSKGCAFVKFQTHAEAQAAI 70
Query: 437 SALNGKLEIVG 447
+ L+ + G
Sbjct: 71 NTLHSSRTLPG 81
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 34/61 (55%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
RKL++G L F TE LR +E +G + + D + + +GFGFV F+ + AA +
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 438 A 438
A
Sbjct: 88 A 88
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 217 ERDQ-RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
E++Q R +F + + TE + ++ + GK+ D ++ D S+RS+G G
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 72
>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 = 46.6 bits (109), Expect = 4e-05, Method: Composition-based stats.
Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L V L N T+ +LR LF G VE +L D G G+GFV + + A+ A + L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 440 NGKLEIVGRTLKVS 453
NG L + +T+KVS
Sbjct: 82 NG-LRLQSKTIKVS 94
>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 = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 9/90 (10%)
Query: 371 GPYGAID--------RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFG 422
GP G+++ LYVG+LH ++TE L + F P GP+ +++ D+ T + G+
Sbjct: 1 GPLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYA 60
Query: 423 FVQFAQLEHAKAAQSALNGKLEIVGRTLKV 452
+V F Q A+ A +N + I G+ +++
Sbjct: 61 YVNFQQPADAERALDTMNFDV-IKGKPVRI 89
Score = 36.6 bits (83), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 55/127 (43%), Gaps = 17/127 (13%)
Query: 318 VSYRYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI 376
+ Y Y+ F A+ ++ ++ G+PV + S+ + +L +S
Sbjct: 57 LGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG------------ 104
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
+++ NL ++ L F FG + ++ D E G KG+GFV F E A+ A
Sbjct: 105 --NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQEAAERAI 160
Query: 437 SALNGKL 443
+NG L
Sbjct: 161 EKMNGML 167
>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 = 46.6 bits (109), Expect = 5e-05, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 36/56 (64%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 433
+K++VG L + E ++R+ F FG VE ++LP+D +T + +GF F+ F + E K
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 57
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 46.6 bits (109), Expect = 5e-05, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 37/61 (60%), Gaps = 2/61 (3%)
Query: 220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGNAIMMRDDGNTLHS 279
+ TV+ +P T D+Y FSK GKV V ++ D+++R+SKGV A ++ D ++ +
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGV--AFILFLDKDSAQN 73
Query: 280 C 280
C
Sbjct: 74 C 74
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 46/84 (54%), Gaps = 2/84 (2%)
Query: 364 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 423
S+G + + AI KL++G + N+ E L+ LFE FG + + + D TG KG F
Sbjct: 2 SSGSSGMKDHDAI--KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAF 59
Query: 424 VQFAQLEHAKAAQSALNGKLEIVG 447
+ + + E A AQSAL+ + + G
Sbjct: 60 LTYCERESALKAQSALHEQKTLPG 83
>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 = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
+ L+V ++++ TE++LR+ FE +GP++ + + +G+ +G+ F+++ +A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 438 ALNGKLEIVGRTLKVS 453
+GK +I GR + V
Sbjct: 163 HADGK-KIDGRRVLVD 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 = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
LYVG+LH ++TE L + F P GP+ +++ D+ T + G+ +V F Q A+ A +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 440 NGKLEIVGRTLKV 452
N + I G+ +++
Sbjct: 73 NFDV-IKGKPVRI 84
Score = 37.0 bits (84), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 55/127 (43%), Gaps = 17/127 (13%)
Query: 318 VSYRYIEFYDVMSVPMAI-ALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI 376
+ Y Y+ F A+ ++ ++ G+PV + S+ + +L +S
Sbjct: 52 LGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG------------ 99
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
+++ NL ++ L F FG + ++ D E G KG+GFV F E A+ A
Sbjct: 100 --NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQEAAERAI 155
Query: 437 SALNGKL 443
+NG L
Sbjct: 156 EKMNGML 162
>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 = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L+V +H TE + F +G ++ + L LD TG KG+ V++ + A+AA L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 440 NGKLEIVGRTLKV 452
NG+ +++G+ + V
Sbjct: 72 NGQ-DLMGQPISV 83
Score = 30.4 bits (67), Expect = 3.4, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 24/33 (72%)
Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
+ATE D+++ F++ G+++++ L +DR + KG
Sbjct: 20 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 52
>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 = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L+V +H TE + F +G ++ + L LD TG KG+ V++ + A+AA L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 440 NGKLEIVGRTLKV 452
NG+ +++G+ + V
Sbjct: 70 NGQ-DLMGQPISV 81
Score = 30.4 bits (67), Expect = 3.5, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 24/33 (72%)
Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
+ATE D+++ F++ G+++++ L +DR + KG
Sbjct: 18 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 50
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L+V +H TE + F +G ++ + L LD TG KG+ V++ + A+AA L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 440 NGKLEIVGRTLKV 452
NG+ +++G+ + V
Sbjct: 70 NGQ-DLMGQPISV 81
Score = 30.4 bits (67), Expect = 3.5, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 24/33 (72%)
Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
+ATE D+++ F++ G+++++ L +DR + KG
Sbjct: 18 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 50
>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 = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L+V +H TE + F +G ++ + L LD TG KG+ V++ + A+AA L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 440 NGKLEIVGRTLKV 452
NG+ +++G+ + V
Sbjct: 70 NGQ-DLMGQPISV 81
Score = 30.4 bits (67), Expect = 3.6, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 24/33 (72%)
Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
+ATE D+++ F++ G+++++ L +DR + KG
Sbjct: 18 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 50
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 31/77 (40%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
DR ++VGNL + E L +LF GP+ V + D E G+ K FGFV F E A
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAI 74
Query: 437 SALNGKLEIVGRTLKVS 453
+ LNG + + GR + VS
Sbjct: 75 ALLNG-IRLYGRPINVS 90
Score = 29.6 bits (65), Expect = 5.9, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSR 259
E RTVF + + E +YE F +AG + V + DR +
Sbjct: 13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK 55
>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 = 45.8 bits (107), Expect = 7e-05, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 47/87 (54%), Gaps = 2/87 (2%)
Query: 367 GTATGPYGAIDR-KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 425
G GP +++ L+V +H TE + F +G ++ + L LD TG KG+ V+
Sbjct: 12 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71
Query: 426 FAQLEHAKAAQSALNGKLEIVGRTLKV 452
+ + A+AA LNG+ +++G+ + V
Sbjct: 72 YETYKEAQAAMEGLNGQ-DLMGQPISV 97
Score = 35.0 bits (79), Expect = 0.12, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 204 KEKKEVVEPEADPERDQRTV-----FAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS 258
+E + VE + D QR+V F + +ATE D+++ F++ G+++++ L +DR +
Sbjct: 2 REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 61
Query: 259 RRSKG 263
KG
Sbjct: 62 GYLKG 66
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 46/76 (60%), Gaps = 5/76 (6%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
+ L + NL ++ TE L+++FE +++P + + G+ KG+ F++FA E AK A
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQN-QNGKSKGYAFIEFASFEDAKEAL 70
Query: 437 SALNGKLEIVGRTLKV 452
++ N K EI GR +++
Sbjct: 71 NSCN-KREIEGRAIRL 85
>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 = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/127 (23%), Positives = 57/127 (44%), Gaps = 4/127 (3%)
Query: 319 SYRYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI-- 376
++ ++EF V A+A G + GQ + ++ + L + + G +
Sbjct: 52 NFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVP 111
Query: 377 --DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 434
KL++G L + + Q+++L FGP++ L D TG KG+ F ++ +
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Query: 435 AQSALNG 441
A + LNG
Sbjct: 172 AIAGLNG 178
Score = 37.7 bits (86), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 45/96 (46%), Gaps = 19/96 (19%)
Query: 374 GAIDRKLYVGNLHFNMTETQLRKLFE-----------PFGPVELVQLPLDIETGQCKGFG 422
GA+ R+LYVGN+ F +TE + F P PV VQ+ Q K F
Sbjct: 1 GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFA 54
Query: 423 FVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH 458
F++F ++ A A +G + G++LK+ D+
Sbjct: 55 FLEFRSVDETTQAM-AFDGII-FQGQSLKIRRPHDY 88
>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 = 45.8 bits (107), Expect = 8e-05, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 47/87 (54%), Gaps = 2/87 (2%)
Query: 367 GTATGPYGAIDR-KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 425
G GP +++ L+V +H TE + F +G ++ + L LD TG KG+ V+
Sbjct: 11 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70
Query: 426 FAQLEHAKAAQSALNGKLEIVGRTLKV 452
+ + A+AA LNG+ +++G+ + V
Sbjct: 71 YETYKEAQAAMEGLNGQ-DLMGQPISV 96
Score = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 204 KEKKEVVEPEADPERDQRTV-----FAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS 258
+E + VE + D QR+V F + +ATE D+++ F++ G+++++ L +DR +
Sbjct: 1 REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 60
Query: 259 RRSKG 263
KG
Sbjct: 61 GYLKG 65
>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 = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 3/68 (4%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF---AQLEHAKAA 435
K+++G L+++ TE LR+ F +G V +++ D TG+ +GFGF+ F + ++
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 436 QSALNGKL 443
Q L+GK+
Sbjct: 65 QHILDGKV 72
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 8/84 (9%)
Query: 350 KPSEAEKNLVQSNTSAGGTATGPYGAIDR-------KLYVGNLHFNMTETQLRKLFEPFG 402
KPS ++ +V++ G P AI R K++VG + ++ + + F +G
Sbjct: 54 KPSSVDE-VVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWG 112
Query: 403 PVELVQLPLDIETGQCKGFGFVQF 426
+ QL LD +TGQ +GFGFV +
Sbjct: 113 TIIDAQLMLDKDTGQSRGFGFVTY 136
Score = 33.5 bits (75), Expect = 0.41, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 208 EVVEPEADPERDQR----TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
+V++P+ RD++ +F + ++ EFFS+ G + D +L++D+++ +S+G
Sbjct: 71 KVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRG 130
Query: 264 VG 265
G
Sbjct: 131 FG 132
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
TE ++ E+F K G V D++++ D + RS+G G
Sbjct: 16 TEDNLREYFGKYGTVTDLKIMKDPATGRSRGFG 48
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/123 (23%), Positives = 55/123 (44%), Gaps = 16/123 (13%)
Query: 319 SYRYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDR 378
++ ++EF V A+A G + GQ + ++ + L ++
Sbjct: 52 NFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAH---------------- 95
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
KL++G L + + Q+++L FGP++ L D TG KG+ F ++ + A +
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 439 LNG 441
LNG
Sbjct: 156 LNG 158
Score = 33.9 bits (76), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 19/92 (20%)
Query: 378 RKLYVGNLHFNMTETQLRKLFE-----------PFGPVELVQLPLDIETGQCKGFGFVQF 426
R+LYVGN+ F +TE + F P PV VQ+ Q K F F++F
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEF 58
Query: 427 AQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH 458
++ A A +G + G++LK+ D+
Sbjct: 59 RSVDETTQAM-AFDGII-FQGQSLKIRRPHDY 88
>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-04, Method: Composition-based stats.
Identities = 29/84 (34%), Positives = 48/84 (57%), Gaps = 3/84 (3%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
++L+V N+ F + LR++F FG + V++ + E G KGFGFV F A A+
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGS-KGFGFVTFENSADADRARE 73
Query: 438 ALNGKLEIVGRTLKVSSVTDHVGT 461
L+G + + GR ++V++ T V T
Sbjct: 74 KLHGTV-VEGRKIEVNNATARVMT 96
>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 = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
+ L+V ++++ TE++LR+ FE +GP++ + + +G+ +G+ F+++ +A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 438 ALNGKLEIVGRTLKVS 453
+GK +I GR + V
Sbjct: 163 HADGK-KIDGRRVLVD 177
>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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/123 (23%), Positives = 55/123 (44%), Gaps = 16/123 (13%)
Query: 319 SYRYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDR 378
++ ++EF V A+A G + GQ + ++ + L ++
Sbjct: 54 NFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAH---------------- 97
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
KL++G L + + Q+++L FGP++ L D TG KG+ F ++ + A +
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 439 LNG 441
LNG
Sbjct: 158 LNG 160
Score = 35.8 bits (81), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 46/99 (46%), Gaps = 20/99 (20%)
Query: 371 GPYGAIDRKLYVGNLHFNMTETQLRKLFE-----------PFGPVELVQLPLDIETGQCK 419
GP G+ R+LYVGN+ F +TE + F P PV VQ+ Q K
Sbjct: 1 GPLGSA-RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDK 53
Query: 420 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH 458
F F++F ++ A A +G + G++LK+ D+
Sbjct: 54 NFAFLEFRSVDETTQAM-AFDGII-FQGQSLKIRRPHDY 90
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 4/75 (5%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
K++VG + N ET+LR+ F+ FG V V + D E + +GFGF+ F E ++ A
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF---EDEQSVDQA 68
Query: 439 LNGKL-EIVGRTLKV 452
+N +I+G+ ++V
Sbjct: 69 VNMHFHDIMGKKVEV 83
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
+F +P E ++ E+F K G V +V +I D +R +G G
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFG 55
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
+ L+V L + TE L++ F+ G V ++ D ETG KGFGFV F E AKAA+
Sbjct: 16 KTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 438 AL 439
A+
Sbjct: 73 AM 74
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 28/82 (34%), Positives = 47/82 (57%), Gaps = 3/82 (3%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
++L+V N+ F + LR++F FG + V++ + E G KGFGFV F A A+
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGS-KGFGFVTFENSADADRARE 87
Query: 438 ALNGKLEIVGRTLKVSSVTDHV 459
L+G + + GR ++V++ T V
Sbjct: 88 KLHGTV-VEGRKIEVNNATARV 108
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 49/219 (22%), Positives = 78/219 (35%), Gaps = 70/219 (31%)
Query: 224 FAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKGVGNAIMMRDDGNTLHSCL 281
F Q+P +E+D+ E F + G V ++ ++ DR N +SKG
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG------------------ 48
Query: 282 INSCCVIKFFLVAEVGMVFFLLGDETYTVLDPATVLVSYRYIEFYDVMSVPMAIALSGQL 341
CC + F+ + + E L VL +
Sbjct: 49 ---CCFVTFY-TRKAAL-------EAQNALHNXKVLPGXHH------------------- 78
Query: 342 LLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPF 401
P+ KP+++EKN DRKL++G + TE +R F F
Sbjct: 79 ----PIQXKPADSEKN---------------NAVEDRKLFIGXISKKCTENDIRVXFSSF 119
Query: 402 GPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 440
G +E ++ L G +G FV F A+ A A +
Sbjct: 120 GQIEECRI-LRGPDGLSRGCAFVTFTTRAXAQTAIKAXH 157
Score = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG--QCKGFGFVQFAQLEHAKAAQ 436
K +VG + +E LR+LFE +G V + + D Q KG FV F + A AQ
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 437 SALNGKLEIVG 447
+AL+ + G
Sbjct: 65 NALHNXKVLPG 75
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 34/54 (62%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 433
++VG L + E ++R+ F FG VE ++LP+D +T + +GF F+ F + E K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 55
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 33/60 (55%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
LY+ L T+ L KL +P+G + + LD T +CKG+GFV F A+ A +AL
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 37/66 (56%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
D LYV L M++ ++ +LF +G + ++ LD TG +G GF++F + A+ A
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 437 SALNGK 442
LNG+
Sbjct: 61 KGLNGQ 66
>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 = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA---- 435
+++G L ++ T+ L+ F FG V L LD TG+ +GFGFV F + E
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 436 QSALNGKL 443
+ LNGK+
Sbjct: 62 EHKLNGKV 69
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 23/33 (69%)
Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
T++D+ ++FSK G+V D L +D + RS+G G
Sbjct: 12 TKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFG 44
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 30/87 (34%), Positives = 44/87 (50%), Gaps = 4/87 (4%)
Query: 366 GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 425
G GP G L++ +L T+T L F PFG V ++ +D +T K FGFV
Sbjct: 32 GKQIEGPEGC---NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVS 88
Query: 426 FAQLEHAKAAQSALNGKLEIVGRTLKV 452
F + A+ A A+NG ++ + LKV
Sbjct: 89 FDNPDSAQVAIKAMNG-FQVGTKRLKV 114
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 24/64 (37%), Positives = 36/64 (56%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
D LYV NL +T+ QL +F +G + + D TG+ +G FV++ + E A+ A
Sbjct: 89 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Query: 437 SALN 440
SALN
Sbjct: 149 SALN 152
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 375 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 434
A + L V L +MT+ +L LF GP+ ++ D +TG G+ FV F ++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 435 AQSALNGKLEIVGRTLKVS 453
A LNG + + + LKVS
Sbjct: 61 AIKVLNG-ITVRNKRLKVS 78
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 34/63 (53%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
KL++G L + + Q+++L FGP++ L D TG KG+ F ++ + A +
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 439 LNG 441
LNG
Sbjct: 63 LNG 65
>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 = 5e-04, Method: Composition-based stats.
Identities = 24/64 (37%), Positives = 36/64 (56%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
D LYV NL +T+ QL +F +G + + D TG+ +G FV++ + E A+ A
Sbjct: 100 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
Query: 437 SALN 440
SALN
Sbjct: 160 SALN 163
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 375 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 434
A + L V L + T+ +L LF GP+ ++ D +TG G+ FV F ++
Sbjct: 12 ASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQR 71
Query: 435 AQSALNGKLEIVGRTLKVS 453
A LNG + + + LKVS
Sbjct: 72 AIKVLNG-ITVRNKRLKVS 89
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
KL++G L+ E L+ +F GP+ V L D T + +GF F+ F AK A
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKD 67
Query: 439 LNGKLEIVGRTLKV 452
+NGK + G+ +KV
Sbjct: 68 MNGK-SLHGKAIKV 80
>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-04, Method: Composition-based stats.
Identities = 24/64 (37%), Positives = 36/64 (56%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
D LYV NL +T+ QL +F +G + + D TG+ +G FV++ + E A+ A
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 437 SALN 440
SALN
Sbjct: 73 SALN 76
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
++VG+L +T ++ F PFG + ++ D+ TG+ KG+GFV F A+ A +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 440 NGKLEIVGRTLKVSSVT 456
G+ + GR ++ + T
Sbjct: 78 GGQW-LGGRQIRTNWAT 93
Score = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
VF + + T D+ F+ GK+ D R++ D + +SKG G
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYG 60
>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 = 42.7 bits (99), Expect = 7e-04, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
++VG+L +T ++ F PFG + ++ D+ TG+ KG+GFV F A+ A +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 440 NGKLEIVGRTLKVSSVT 456
G+ + GR ++ + T
Sbjct: 78 GGQW-LGGRQIRTNWAT 93
Score = 29.3 bits (64), Expect = 6.5, Method: Composition-based stats.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
VF + + T D+ F+ G++ D R++ D + +SKG G
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPV-ELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
+++GNL + E L F FG + + ++ D +TG KG+ F+ FA + + AA A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 439 LNGKLEIVGRTLKVS 453
+NG+ + R + VS
Sbjct: 68 MNGQY-LCNRPITVS 81
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 31/94 (32%), Positives = 49/94 (52%), Gaps = 9/94 (9%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK---- 433
+ +++ NL F+ E L ++ + FG ++ V++ L +T KG F QF E A+
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 434 -AAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAA 466
A+ A G L++ GR LKV D T+D AA
Sbjct: 76 AASLEAEGGGLKLDGRQLKV----DLAVTRDEAA 105
>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 = 42.4 bits (98), Expect = 9e-04, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
LYVGNL F TE Q+ +LF G ++ + + LD C GF FV++ A+ A +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC-GFCFVEYYSRADAENAMRYI 79
Query: 440 NG 441
NG
Sbjct: 80 NG 81
Score = 29.6 bits (65), Expect = 6.1, Method: Composition-based stats.
Identities = 10/35 (28%), Positives = 21/35 (60%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR 256
T++ + TE +YE FSK+G ++ + + +D+
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK 54
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 375 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 434
A + L V L +MT+ +L LF GP+ ++ D +TG G+ FV F ++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 435 AQSALNGKLEIVGRTLKVS 453
A LNG + + + LKVS
Sbjct: 61 AIKVLNG-ITVRNKRLKVS 78
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 26/98 (26%), Positives = 45/98 (45%), Gaps = 14/98 (14%)
Query: 554 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAG---------FV 604
S +L+N DP D D +++G+V EEC K+G V + + + G +
Sbjct: 20 STVXVLRNXVDPK-----DIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 74
Query: 605 YLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYE 642
++ F A +A++ RWFA R + A E ++
Sbjct: 75 FVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFD 112
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 32/93 (34%), Positives = 49/93 (52%), Gaps = 4/93 (4%)
Query: 360 QSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK 419
QS +AG GP GA L++ +L + L ++F PFG V ++ +D +T K
Sbjct: 11 QSIGAAGSQKEGPEGA---NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67
Query: 420 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 452
FGFV + A+AA ++NG +I + LKV
Sbjct: 68 CFGFVSYDNPVSAQAAIQSMNG-FQIGMKRLKV 99
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 7/78 (8%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
+L+VGNL ++TE ++LFE +G P ++ + +GFGF++ A+ A++
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGE------PSEVFINRDRGFGFIRLESRTLAEIAKAE 77
Query: 439 LNGKLEIVGRTLKVSSVT 456
L+G + + R L++ T
Sbjct: 78 LDGTI-LKSRPLRIRFAT 94
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 435
L V NL ++ L + F FGPVE + +D + G+ G GFV+FA A+ A
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKA 153
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 5/74 (6%)
Query: 371 GPYGA---IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFA 427
GP G+ + ++VG + M ET++R F +G V+ V++ D TG KG+GFV F
Sbjct: 1 GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFY 59
Query: 428 Q-LEHAKAAQSALN 440
++ K +S +N
Sbjct: 60 NDVDVQKIVESQIN 73
Score = 33.1 bits (74), Expect = 0.54, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
TVF + ++ E ++ FF++ G V++V++I DR SKG G
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYG 54
>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|C Chain C, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 106
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 29/98 (29%), Positives = 44/98 (44%), Gaps = 7/98 (7%)
Query: 554 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-------RSAGFVYL 606
+E L L N P D + EI DV +ECSKYG VK I + + G +++
Sbjct: 6 TEVLCLXNXVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFV 65
Query: 607 RFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 644
F S A + + R FA R++ + P+ Y +
Sbjct: 66 EFTSVFDCQKAXQGLTGRKFANRVVVTKYCDPDSYHRR 103
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
LYVG L +TET LR F FG + + + ++ QC F+QFA + A+ A
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITV---VQRQQC---AFIQFATRQAAEVAAEKS 68
Query: 440 NGKLEIVGRTLKV 452
KL + GR L V
Sbjct: 69 FNKLIVNGRRLNV 81
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 7/74 (9%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
+L+VGNL ++TE ++RKLFE +G V + D KGFGF++ A+ A+
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 439 LNGKLEIVGRTLKV 452
L+ + + G+ L+V
Sbjct: 78 LDN-MPLRGKQLRV 90
>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 = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 33/62 (53%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
LYVGNL F TE Q+ +LF G ++ + + LD GF FV++ A+ A +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 440 NG 441
NG
Sbjct: 102 NG 103
Score = 30.0 bits (66), Expect = 3.7, Method: Composition-based stats.
Identities = 11/42 (26%), Positives = 24/42 (57%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
T++ + TE +YE FSK+G ++ + + +D+ + + G
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R +YVGN+ + T +L F G V V + D +G KGF +++F+ E + +
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 64
Query: 438 ALNGKLEIVGRTLKV 452
AL+ L GR +KV
Sbjct: 65 ALDESL-FRGRQIKV 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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 7/74 (9%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
+L+VGNL ++TE ++RKLFE +G V + D KGFGF++ A+ A+
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 439 LNGKLEIVGRTLKV 452
L+ + + G+ L+V
Sbjct: 71 LD-NMPLRGKQLRV 83
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 426
KL+VG L ++ T+ LR F +G V + D T Q +GFGFV+F
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R +YVGN+ + T L F G + + + D +G KG+ +++FA+ AA
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA-V 95
Query: 438 ALNGKLEIVGRTLKV 452
A++ + GRT+KV
Sbjct: 96 AMDETV-FRGRTIKV 109
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 372 PYGAI-DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ-L 429
P G I ++VG + M ET++R F +G V+ V++ D TG KG+GFV F +
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDV 61
Query: 430 EHAKAAQSALN 440
+ K +S +N
Sbjct: 62 DVQKIVESQIN 72
Score = 33.1 bits (74), Expect = 0.54, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
TVF + ++ E ++ FF++ G V++V++I DR SKG G
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYG 53
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 29/78 (37%), Positives = 39/78 (50%), Gaps = 9/78 (11%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
K++VGN+ T +LR LFE G V IE K + FV + AKAA +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRV--------IECDVVKDYAFVHMEKEADAKAAIAQ 62
Query: 439 LNGKLEIVGRTLKVSSVT 456
LNGK E+ G+ + V T
Sbjct: 63 LNGK-EVKGKRINVELST 79
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 372 PYGAI-DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ-L 429
P G I ++VG + M ET++R F +G V+ V++ D TG KG+GFV F +
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDV 61
Query: 430 EHAKAAQSALN 440
+ K +S +N
Sbjct: 62 DVQKIVESQIN 72
Score = 32.7 bits (73), Expect = 0.65, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVG 265
TVF + ++ E ++ FF++ G V++V++I DR SKG G
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYG 53
>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 = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R +YVGN+ + T +L F G V V + D +G KGF +++F+ E + +
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 65
Query: 438 ALNGKLEIVGRTLKV 452
AL+ L GR +KV
Sbjct: 66 ALDESL-FRGRQIKV 79
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
LY+ NL +M E +L + +PFG V ++ L +G +G GF + E +A
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRI-LRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 440 NGKL 443
NGK
Sbjct: 87 NGKF 90
Score = 29.3 bits (64), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGNAIM 269
E+D ++ +PL E+++ G+V R++ D +S S+GVG A M
Sbjct: 22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARM 73
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 26/47 (55%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 426
++VG L N T ++ FE FG V+ L D T + +GFGFV F
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
Score = 34.7 bits (78), Expect = 0.19, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 7/68 (10%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGNAIMMRDDGNTLHSCLI 282
+F + + T DV +F + GKV D L+ D+ + R +G G +D ++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED-------IV 54
Query: 283 NSCCVIKF 290
C I F
Sbjct: 55 EKVCEIHF 62
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 18/78 (23%), Positives = 47/78 (60%), Gaps = 2/78 (2%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLD-IETGQCKGFGFVQFAQLEHAKAAQS 437
K+++G L N+T+ + ++F +G ++++ +P++ + KG+ +V+F + A+ A
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 438 ALNGKLEIVGRTLKVSSV 455
++G +I G+ + ++V
Sbjct: 66 HMDGG-QIDGQEITATAV 82
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 32/134 (23%), Positives = 59/134 (44%), Gaps = 22/134 (16%)
Query: 320 YRYIEFYDVMSVPMAIALSGQLLLGQPVMV-KPSEAEKNLVQSNTSAGGTATGPYGAIDR 378
+ Y++F + A+ L+G + G + + KP + V++ R
Sbjct: 56 FGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAA---------------R 100
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
L NL FN+TE +L+++FE + LV + G+ KG +++F A+
Sbjct: 101 TLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEE 155
Query: 439 LNGKLEIVGRTLKV 452
G EI GR++ +
Sbjct: 156 KQG-AEIDGRSVSL 168
Score = 32.3 bits (72), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 45/88 (51%), Gaps = 10/88 (11%)
Query: 366 GGTATGPYGAIDRKLYVGNLHFNMTETQLR-KLFEPFGPVELVQLPLDIETGQCKGFGFV 424
G +T P+ L++GNL+ N + +L+ + E F +L +D+ TG + FG+V
Sbjct: 7 GSESTTPFN-----LFIGNLNPNKSVAELKVAISELFAKNDLA--VVDVRTGTNRKFGYV 59
Query: 425 QFAQLEHAKAAQSALNGKLEIVGRTLKV 452
F E + A L G L++ G +K+
Sbjct: 60 DFESAEDLEKALE-LTG-LKVFGNEIKL 85
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 38.9 bits (89), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 8/66 (12%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
+ +L+V ++ E++L ++F PFGP++ V++ GF FV+F + E A A
Sbjct: 4 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAI 55
Query: 437 SALNGK 442
++GK
Sbjct: 56 EEVHGK 61
Score = 32.7 bits (73), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 573 FDLEIQ-GDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI 631
F L++Q ++ E +G +K + K GF ++ FE E+AA A +H + FA + +
Sbjct: 12 FPLDVQESELNEIFGPFGPMKEV---KILNGFAFVEFEEAESAAKAIEEVHGKSFANQPL 68
Query: 632 SAIFMK 637
++ K
Sbjct: 69 EVVYSK 74
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 34/62 (54%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
KL+VG + + E L+ LFE FG + + + D TG KG F+ + + A AQSA
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 439 LN 440
L+
Sbjct: 77 LH 78
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 38.1 bits (87), Expect = 0.014, Method: Composition-based stats.
Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 3/79 (3%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R LYVGNL ++TE + +LF GP + ++ E + FV+F + A AA +
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMI--TEHTSNDPYCFVEFYEHRDAAAALA 73
Query: 438 ALNGKLEIVGRTLKVSSVT 456
A+NG+ +I+G+ +KV+ T
Sbjct: 74 AMNGR-KILGKEVKVNWAT 91
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
R L NL FN+TE +L+++FE + LV + G+ KG +++F A+
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLE 71
Query: 438 ALNGKLEIVGRTLKVSSVTDHVGTQ 462
G EI GR++ + + GT+
Sbjct: 72 EKQG-AEIDGRSVSLYYTGEKGGTR 95
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 8/66 (12%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 436
+ +L+V ++ E++L ++F PFGP++ V++ GF FV+F + E A A
Sbjct: 31 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAI 82
Query: 437 SALNGK 442
++GK
Sbjct: 83 EEVHGK 88
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 573 FDLEIQ-GDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI 631
F L++Q ++ E +G +K + + GF ++ FE E+AA A +H + FA + +
Sbjct: 39 FPLDVQESELNEIFGPFGPMKEVKILN---GFAFVEFEEAESAAKAIEEVHGKSFANQPL 95
Query: 632 SAIFMK 637
++ K
Sbjct: 96 EVVYSK 101
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 37.7 bits (86), Expect = 0.021, Method: Composition-based stats.
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 376 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 435
+D K+YVGNL N +T+L + F +GP+ V + + GF FV+F A A
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADA 126
Query: 436 QSALNGK 442
L+G+
Sbjct: 127 VRELDGR 133
Score = 29.6 bits (65), Expect = 4.8, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 580 DVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMR 624
++E YG ++ ++V + GF ++ FE AA A R + R
Sbjct: 89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGR 133
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 37.7 bits (86), Expect = 0.022, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
KLY+GNL +T LR+LF +LPL + G+ FV + A A
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGD------RKLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63
Query: 439 LNGKLEIVGRTLKV 452
L+GK+E+ G+ ++V
Sbjct: 64 LSGKVELHGKIMEV 77
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 37.4 bits (85), Expect = 0.024, Method: Composition-based stats.
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 376 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 435
+D K+YVGNL N +T+L + F +GP+ V + + GF FV+F A A
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADA 126
Query: 436 QSALNGK 442
L+G+
Sbjct: 127 VRDLDGR 133
Score = 29.6 bits (65), Expect = 6.0, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 580 DVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMR 624
++E YG ++ ++V + GF ++ FE AA A R + R
Sbjct: 89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGR 133
>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 = 37.4 bits (85), Expect = 0.027, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
K +VG L ++ ++ L+ F FG V + D TG+ +GFGF+ F + A + +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF---KDAASVEKV 69
Query: 439 LNGK 442
L+ K
Sbjct: 70 LDQK 73
Score = 32.7 bits (73), Expect = 0.63, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGNAIMMRD 272
E D F + +++D+ ++F+K G+V D + D N+ RS+G G I+ +D
Sbjct: 8 EEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFG-FILFKD 62
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 37.0 bits (84), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 45/80 (56%), Gaps = 10/80 (12%)
Query: 375 AIDRKLYVGNLHFNMTE-TQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 433
+I+ ++++GNL+ + + + + +F +G V + KG+ FVQ++ HA+
Sbjct: 25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHAR 76
Query: 434 AAQSALNGKLEIVGRTLKVS 453
AA NG++ + G+TL ++
Sbjct: 77 AAVLGENGRV-LAGQTLDIN 95
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 37.0 bits (84), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%)
Query: 374 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 426
G+ K+++G L + T+ LR+ F FG V+ + D T + +GFGFV F
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 37.0 bits (84), Expect = 0.034, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 369 ATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ 428
++G GA +++V NL F+ T L+ F G V + + +E G+ KG G V+F
Sbjct: 2 SSGSSGAC--QIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFES 57
Query: 429 LEHAKAAQSALNGKLEIVGRTLKV 452
E A+ A +NG +++ GR + V
Sbjct: 58 PEVAERACRMMNG-MKLSGREIDV 80
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 37.0 bits (84), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 28/48 (58%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 426
K+++G L + T+ LR+ F FG V+ + D T + +GFGFV F
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 36.6 bits (83), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 37/83 (44%), Gaps = 9/83 (10%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
KL+VGN+ T +LR FE +GPV IE K + FV + E A A
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPV--------IECDIVKDYAFVHMERAEDAVEAIRG 63
Query: 439 LNGKLEIVGRTLKVSSVTDHVGT 461
L+ E G+ + V T + T
Sbjct: 64 LD-NTEFQGKRMHVQLSTSRLRT 85
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 36.6 bits (83), Expect = 0.045, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 6/62 (9%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
+Y G + +T+ +R+ F PFG + ++I KG+ FV+F+ E A A ++
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQI------MEIRVFPEKGYSFVRFSTHESAAHAIVSV 81
Query: 440 NG 441
NG
Sbjct: 82 NG 83
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 36.6 bits (83), Expect = 0.047, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
K+YVGNL + +L + F +GP+ V + + GF FV+F A+ A
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56
Query: 439 LNGKLEIVGRTLKVSSVT 456
L+GK+ I G ++V T
Sbjct: 57 LDGKV-ICGSRVRVELST 73
Score = 31.2 bits (69), Expect = 1.8, Method: Composition-based stats.
Identities = 12/44 (27%), Positives = 24/44 (54%)
Query: 578 QGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAM 621
+G++E S YG ++ +++ + GF ++ FE A A R +
Sbjct: 14 KGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGL 57
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 36.2 bits (82), Expect = 0.056, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 13/71 (18%)
Query: 369 ATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ 428
++G G + KL++GNL TE ++R LFE +G V +E K +GFV
Sbjct: 2 SSGSSGMV--KLFIGNLPREATEQEIRSLFEQYGKV--------LECDIIKNYGFV---H 48
Query: 429 LEHAKAAQSAL 439
+E AA+ A+
Sbjct: 49 IEDKTAAEDAI 59
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 36.2 bits (82), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 30/117 (25%), Positives = 51/117 (43%), Gaps = 9/117 (7%)
Query: 344 GQPVMVKPSEAEKNLVQSNTSAG-GTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG 402
GQ + P + + +L S G G TG KL V NL F +++ +++LF FG
Sbjct: 7 GQQMGRDPDKWQHDLFDSGCGGGEGVETGA------KLLVSNLDFGVSDADIQELFAEFG 60
Query: 403 PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHV 459
++ + D +G+ G V F + A A G + + GR + + V +
Sbjct: 61 TLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQYKG-VPLDGRPMDIQLVASQI 115
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 35.8 bits (81), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGP--VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 437
LYV NL + +E + K F P VE V+ + + + FV F+ E A A
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVK--------KIRDYAFVHFSNREDAVEAMK 69
Query: 438 ALNGKL 443
ALNGK+
Sbjct: 70 ALNGKV 75
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 35.8 bits (81), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 30/117 (25%), Positives = 51/117 (43%), Gaps = 9/117 (7%)
Query: 344 GQPVMVKPSEAEKNLVQSNTSAG-GTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG 402
GQ + P + + +L S G G TG KL V NL F +++ +++LF FG
Sbjct: 7 GQQMGRDPDKWQHDLFDSGCGGGEGVETGA------KLLVSNLDFGVSDADIQELFAEFG 60
Query: 403 PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHV 459
++ + D +G+ G V F + A A G + + GR + + V +
Sbjct: 61 TLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQYKG-VPLDGRPMDIQLVASQI 115
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 35.8 bits (81), Expect = 0.074, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 6/64 (9%)
Query: 372 PYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH 431
PY A YVGNL FN + + +F+ + V+L D +T + KGF +V+F +++
Sbjct: 15 PYTA-----YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDS 68
Query: 432 AKAA 435
K A
Sbjct: 69 LKEA 72
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 35.8 bits (81), Expect = 0.086, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
++V NL F+ T L+ F G V + + +E G+ KG G V+F E A+ A +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERACRMM 65
Query: 440 NGKLEIVGRTLKV 452
NG +++ GR + V
Sbjct: 66 NG-MKLSGREIDV 77
>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 = 35.4 bits (80), Expect = 0.096, Method: Composition-based stats.
Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 2/86 (2%)
Query: 371 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 430
GP G+ ++VG+L +T + F PFG + ++ D+ TG+ KG+GFV F
Sbjct: 1 GPLGS-HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW 59
Query: 431 HAKAAQSALNGKLEIVGRTLKVSSVT 456
A+ A + G+ + GR ++ + T
Sbjct: 60 DAENAIQQMGGQW-LGGRQIRTNWAT 84
>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 = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 394 LRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK 442
L LF G V ++ P+D TG+ KGF FV+ + AK + +GK
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
>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 = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 394 LRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK 442
L LF G V ++ P+D TG+ KGF FV+ + AK + +GK
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG--QCKGFGFVQFAQLEHAKAAQ 436
K++VG + +E LR+LFE +G V + + D Q KG FV F + A AQ
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 437 SALNG 441
+AL+
Sbjct: 65 NALHN 69
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKGV 264
D +F Q+P +E+D+ E F + G V ++ ++ DR N +SKG
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGC 49
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 44/93 (47%), Gaps = 20/93 (21%)
Query: 371 GPYGAIDRKLYVGNLHFNMTETQLRKLFE-----------PFGPVELVQLPLDIETGQCK 419
GP G+ R+LYVGN+ F +TE + F P PV VQ+ Q K
Sbjct: 1 GPLGSA-RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDK 53
Query: 420 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 452
F F++F ++ A A +G + G++LK+
Sbjct: 54 NFAFLEFRSVDETTQAM-AFDGII-FQGQSLKI 84
>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 = 34.7 bits (78), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 371 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 430
GP G+ + +++ NL ++ L F FG + ++ D E G KG+GFV F E
Sbjct: 1 GPLGSGN--IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQE 56
Query: 431 HAKAAQSALNGKL 443
A+ A +NG L
Sbjct: 57 AAERAIEKMNGML 69
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 376 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 435
++R LY+ NL + +T ++ +F +GP+ +++ T + +G +V + + AK A
Sbjct: 11 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNA 67
Query: 436 QSALNG 441
L+G
Sbjct: 68 CDHLSG 73
Score = 31.2 bits (69), Expect = 1.9, Method: Composition-based stats.
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRL 252
P R ++ +P K T ++Y+ F K G +R +R+
Sbjct: 8 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV 44
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 19/92 (20%)
Query: 378 RKLYVGNLHFNMTETQLRKLFE-----------PFGPVELVQLPLDIETGQCKGFGFVQF 426
R+LYVGN+ F +TE + F P PV VQ+ Q K F F++F
Sbjct: 2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEF 55
Query: 427 AQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH 458
++ A A +G + G++LK+ D+
Sbjct: 56 RSVDETTQAM-AFDGII-FQGQSLKIRRPHDY 85
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 33.9 bits (76), Expect = 0.26, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 376 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 435
++R LY+ NL + +T ++ +F +GP+ +++ T + +G +V + + AK A
Sbjct: 7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNA 63
Query: 436 QSALNG 441
L+G
Sbjct: 64 VDHLSG 69
Score = 30.8 bits (68), Expect = 2.8, Method: Composition-based stats.
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRL 252
P R ++ +P K T ++Y+ F K G +R +R+
Sbjct: 4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV 40
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 33.9 bits (76), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L+V NL +TE L K F FG +E V+ + K + F+ F + + A A +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEEM 65
Query: 440 NGK 442
NGK
Sbjct: 66 NGK 68
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 33.9 bits (76), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
KL V NL F +++ +++LF FG ++ + D +G+ G V F + A A
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 88
Query: 439 LNGKLEIVGRTLKVSSVT 456
NG + + GR + + VT
Sbjct: 89 YNG-VPLDGRPMNIQLVT 105
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 33.9 bits (76), Expect = 0.32, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 376 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 435
++R LY+ NL + +T ++ +F +GP+ +++ T + +G +V + + AK A
Sbjct: 17 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNA 73
Query: 436 QSALNG 441
L+G
Sbjct: 74 CDHLSG 79
Score = 30.8 bits (68), Expect = 2.8, Method: Composition-based stats.
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRL 252
P R ++ +P K T ++Y+ F K G +R +R+
Sbjct: 14 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV 50
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 33.5 bits (75), Expect = 0.36, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQC---KGFGFVQFAQLEHAKAAQ 436
L++ NL+F+ TE L+ +F G ++ + GFGFV++ + E A+ A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 437 SALNG 441
L G
Sbjct: 68 KQLQG 72
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 33.1 bits (74), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 28/110 (25%), Positives = 48/110 (43%), Gaps = 9/110 (8%)
Query: 351 PSEAEKNLVQSNTSAG-GTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQL 409
P + + +L S G G TG KL V NL F +++ +++LF FG ++ +
Sbjct: 67 PDKWQHDLFDSGCGGGEGVETGA------KLLVSNLDFGVSDADIQELFAEFGTLKKAAV 120
Query: 410 PLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHV 459
D +G+ G V F + A A G + + GR + + V +
Sbjct: 121 DYD-RSGRSLGTADVHFERRADALKAMKQYKG-VPLDGRPMDIQLVASQI 168
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 33.1 bits (74), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 364 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 423
S+G + G + ++V NL + + +L+++F G V + L+ + G+ +G G
Sbjct: 2 SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADI-LEDKDGKSRGIGT 60
Query: 424 VQFAQLEHAKAAQSALNGKL 443
V F Q A A S NG+L
Sbjct: 61 VTFEQSIEAVQAISMFNGQL 80
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.1 bits (74), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
L+V NL +TE L K F FG +E V+ + K + FV F A A +
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEDRGAAVKAMDEM 69
Query: 440 NGK 442
NGK
Sbjct: 70 NGK 72
>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 = 33.1 bits (74), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 15/84 (17%)
Query: 367 GTATGPYGAID-----RKLYVGNLHF----NMTETQLRKLFEPFGPVELVQLPLDIETGQ 417
G+ GP+ D R GN + +MT T LR F PFG + +D+
Sbjct: 18 GSHMGPFRRSDSFPERRAPRKGNTLYVYGEDMTPTLLRGAFSPFGNI------IDLSMDP 71
Query: 418 CKGFGFVQFAQLEHAKAAQSALNG 441
+ FV + ++E A A + LNG
Sbjct: 72 PRNCAFVTYEKMESADQAVAELNG 95
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 32.7 bits (73), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 388 NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 441
+MT T LR F PFG + +D+ + FV + ++E A A + LNG
Sbjct: 24 DMTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVAELNG 71
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 32.7 bits (73), Expect = 0.66, Method: Composition-based stats.
Identities = 20/91 (21%), Positives = 48/91 (52%), Gaps = 10/91 (10%)
Query: 364 SAGGTATGPYGAIDRKLYVGNLH-FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFG 422
S+G + +++ ++++GNL+ + ++ + +F +G + + KGF
Sbjct: 2 SSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKI--------VGCSVHKGFA 53
Query: 423 FVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 453
FVQ+ +A+AA + +G++ I G+ L ++
Sbjct: 54 FVQYVNERNARAAVAGEDGRM-IAGQVLDIN 83
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 32.7 bits (73), Expect = 0.70, Method: Composition-based stats.
Identities = 29/98 (29%), Positives = 46/98 (46%), Gaps = 9/98 (9%)
Query: 364 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVEL--------VQLPLDIET 415
S+G + + + +YV L+ ++T L F+ G V++ + + LD ET
Sbjct: 2 SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61
Query: 416 GQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 453
G+ KG V + AKAA +GK + G LKVS
Sbjct: 62 GKPKGDATVSYEDPPTAKAAVEWFDGK-DFQGSKLKVS 98
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 32.3 bits (72), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 380 LYVGNLHFNMTETQLRK-LFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
L+VGNL+FN + +L+ + + F +L +D+ G + FG+V F E + A
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKNDLA--VVDVRIGMTRKFGYVDFESAEDLEKALE- 66
Query: 439 LNGKLEIVGRTLKV 452
L G L++ G +K+
Sbjct: 67 LTG-LKVFGNEIKL 79
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVR 248
ERD RT+ A +P K T+ ++ E F A ++R
Sbjct: 90 ERDARTLLAKNLPYKVTQDELKEVFEDAAEIR 121
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 32.3 bits (72), Expect = 0.84, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
KL V NL F +++ +++LF FG ++ + D +G+ G V F + A A
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAXKQ 89
Query: 439 LNGKLEIVGRTLKVSSVT 456
NG + + GR + VT
Sbjct: 90 YNG-VPLDGRPXNIQLVT 106
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 32.3 bits (72), Expect = 0.88, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
++VG +MTE +LR+ F +G V V +P + F FV FA + AQS
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFAD---DQIAQSLC 59
Query: 440 NGKLEIVGRTLKVSS 454
L I G ++ +S+
Sbjct: 60 GEDLIIKGISVHISN 74
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 32.3 bits (72), Expect = 0.90, Method: Composition-based stats.
Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 9/88 (10%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVE--------LVQLPLDIETGQCKGFGFVQFAQ 428
+ ++V L N+T + F+ G ++ ++ L D ETG+ KG V F
Sbjct: 13 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 72
Query: 429 LEHAKAAQSALNGKLEIVGRTLKVSSVT 456
AKAA +GK E G +KVS T
Sbjct: 73 PPSAKAAIDWFDGK-EFSGNPIKVSFAT 99
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 28/98 (28%), Positives = 48/98 (48%), Gaps = 10/98 (10%)
Query: 366 GGTATGPYGAIDRKLYVGNLHFNMTETQLR-KLFEPFGPVELVQLPLDIETGQCKGFGFV 424
G +T P+ L++GNL+ N + +L+ + E F +L + D+ TG + FG+V
Sbjct: 11 GSESTTPF-----NLFIGNLNPNKSVAELKVAISELFAKNDLAVV--DVRTGTNRKFGYV 63
Query: 425 QFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQ 462
F E + A L G L++ G +K+ GT+
Sbjct: 64 DFESAEDLEKALE-LTG-LKVFGNEIKLEKPKGRDGTR 99
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 439
+++ NL ++ L F FG + ++ D E G KG+GFV F E A+ A +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQEAAERAIEKM 71
Query: 440 NGKL 443
NG L
Sbjct: 72 NGML 75
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 9/88 (10%)
Query: 377 DRKLYVGNLHFNMTETQLRKLFEPFGPVE--------LVQLPLDIETGQCKGFGFVQFAQ 428
+ ++V L N+T + F+ G ++ ++ L D ETG+ KG V F
Sbjct: 7 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 66
Query: 429 LEHAKAAQSALNGKLEIVGRTLKVSSVT 456
AKAA +GK E G +KVS T
Sbjct: 67 PPSAKAAIDWFDGK-EFSGNPIKVSFAT 93
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 390 TETQLRKLFEPFG-PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGR 448
TE +R + G V+L + +GQ +GF FV+F+ L+ A A L I+G+
Sbjct: 14 TEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQ 73
Query: 449 TLKV 452
+ +
Sbjct: 74 KVSM 77
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 12/76 (15%)
Query: 370 TGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKG---FGFVQF 426
GP G D ++YVGNL ++ + +F +G + DI+ +G F FV+F
Sbjct: 15 RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIR------DIDLKNRRGGPPFAFVEF 68
Query: 427 AQLEHAKAAQSALNGK 442
E + A+ A+ G+
Sbjct: 69 ---EDPRDAEDAVYGR 81
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 31.2 bits (69), Expect = 1.7, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 32/68 (47%)
Query: 374 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 433
G ++ LY+ NL +TE L LF F + + + TG+ +G F+ F E A
Sbjct: 22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAW 81
Query: 434 AAQSALNG 441
A +NG
Sbjct: 82 QALHLVNG 89
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
K++VG +MT +L++ F +G V V +P + F FV FA K AQS
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFAD---DKVAQSL 64
Query: 439 LNGKLEIVGRTLKVSS 454
L I G ++ +S+
Sbjct: 65 CGEDLIIKGISVHISN 80
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 7/56 (12%)
Query: 372 PYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQ-CKGFGFVQF 426
PY A ++GNL +++TE +++ F + V+LP + + KGFG+ +F
Sbjct: 19 PYTA-----FLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 68
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 381 YVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQ-CKGFGFVQF 426
++GNL +++TE +++ F + V+LP + + KGFG+ +F
Sbjct: 19 FLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 64
>pdb|2HGN|A Chain A, Nmr Structure Of The Third Qrrm Domain Of Human Hnrnp F
pdb|2KG1|A Chain A, Structure Of The Third Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 139
Score = 30.4 bits (67), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 228 MPLKATERDVYEFFSKAGKVR 248
+P KATE D+Y FFS VR
Sbjct: 54 LPYKATENDIYNFFSPLNPVR 74
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 30.4 bits (67), Expect = 3.2, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 380 LYVGNLHFNMTETQLRKLFEPFGPVEL-VQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
L++G+L M E + + F G + V++ + TG G+ FV+FA L A+
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 439 LNGK 442
+NGK
Sbjct: 72 INGK 75
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 30.0 bits (66), Expect = 4.2, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 378 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQC---KGFGFVQFAQLEHAKA 434
RK++VG L ++ E ++ F FGP+ +V P E+ KG+ F+ F + +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPL-VVDWPHKAESKSYFPPKGYAFLLF---QEESS 64
Query: 435 AQSALNGKLEIVGRT-LKVSSVT 456
Q+ ++ LE G+ L VSS T
Sbjct: 65 VQALIDACLEEDGKLYLCVSSPT 87
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 29.6 bits (65), Expect = 6.1, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 379 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 438
+L+VG L N + L + F+ FG + I+ + F ++Q+ L+ A+AA +
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIR------TIDHVKGDSFAYIQYESLDAAQAACAK 72
Query: 439 LNG 441
+ G
Sbjct: 73 MRG 75
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 29.3 bits (64), Expect = 6.5, Method: Composition-based stats.
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRL 252
P R + +P K T ++Y+ F K G +R +R+
Sbjct: 14 PPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRV 50
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
0.319 0.134 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,668,439
Number of Sequences: 62578
Number of extensions: 415240
Number of successful extensions: 1126
Number of sequences better than 100.0: 188
Number of HSP's better than 100.0 without gapping: 142
Number of HSP's successfully gapped in prelim test: 46
Number of HSP's that attempted gapping in prelim test: 772
Number of HSP's gapped (non-prelim): 371
length of query: 647
length of database: 14,973,337
effective HSP length: 105
effective length of query: 542
effective length of database: 8,402,647
effective search space: 4554234674
effective search space used: 4554234674
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)