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= 006608
(639 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 109 bits (272), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 51/84 (60%), Positives = 65/84 (77%)
Query: 246 RDQRTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPM 305
RD RTVF Q+ + RD+ +FFS GKVRDVR+I DRNSRRSKG+ YVEF ++ SVP+
Sbjct: 23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 82
Query: 306 AIALSGQPLLGQPVMVKPSEAEKN 329
AI L+GQ LLG P++V+ S+AEKN
Sbjct: 83 AIGLTGQRLLGVPIIVQASQAEKN 106
>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From Mus
Musculus
Length = 113
Score = 94.0 bits (232), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 48/97 (49%), Positives = 67/97 (69%), Gaps = 1/97 (1%)
Query: 544 SECLLLKNMFDPKNETYEEFDMDIKEDVEGECSKFGKLKHIFVEKDSA-GFVYLRFENTQ 602
++C L NMF+P+ E +D +IK+DV EC+K G + HI+V+K+SA G VY++ +
Sbjct: 6 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIA 65
Query: 603 SAFAAQRALHGRWFAGKMITATFMVPQTYEAKFPDSI 639
+A AA ALHGRWFAGKMITA ++ TY FPDS+
Sbjct: 66 AAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSM 102
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 87.8 bits (216), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 45/81 (55%), Positives = 60/81 (74%), Gaps = 3/81 (3%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNAL-N 411
RLYVG+LHFN+TED LR +FEPFG +E +QL +D ETG KG+GF+ F+ E A+ AL
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 412 LNGQLEIVGRAIKVSAVTDQS 432
LNG E+ GR +KV VT+++
Sbjct: 88 LNG-FELAGRPMKVGHVTERT 107
Score = 37.7 bits (86), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 4/60 (6%)
Query: 263 RDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQPVMV 321
R ++E F G++ ++L+MD + RSKG G++ F D A+ L+G L G+P+ V
Sbjct: 44 RGIFEPF---GRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100
>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 = 86.7 bits (213), Expect = 4e-17, Method: Composition-based stats.
Identities = 46/96 (47%), Positives = 64/96 (66%), Gaps = 1/96 (1%)
Query: 544 SECLLLKNMFDPKNETYEEFDMDIKEDVEGECSKFGKLKHIFVEKDSA-GFVYLRFENTQ 602
++C L N F+P+ E +D +IK+DV EC+K G + HI+V+K+SA G VY++ +
Sbjct: 7 TQCFQLSNXFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIA 66
Query: 603 SAFAAQRALHGRWFAGKMITATFMVPQTYEAKFPDS 638
+A AA ALHGRWFAGK ITA ++ TY FPDS
Sbjct: 67 AAIAAVNALHGRWFAGKXITAAYVPLPTYHNLFPDS 102
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 78.2 bits (191), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 41/79 (51%), Positives = 56/79 (70%), Gaps = 3/79 (3%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNAL-NL 412
LYVG+LHFN+TED LR +FEPFG ++ + L D +TG KG+GF+ F+ E AR AL L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 413 NGQLEIVGRAIKVSAVTDQ 431
NG E+ GR ++V VT++
Sbjct: 68 NG-FELAGRPMRVGHVTER 85
Score = 34.7 bits (78), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 4/60 (6%)
Query: 263 RDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQPVMV 321
R ++E F GK+ ++ L+ D ++ RSKG G++ F D A+ L+G L G+P+ V
Sbjct: 23 RGIFEPF---GKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRV 79
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 47/73 (64%), Gaps = 3/73 (4%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNL 412
+ L + NL ++ TE+ L++VFE +++P ++ G KG+ F++FA EDA+ ALN
Sbjct: 16 KTLVLSNLSYSATEETLQEVFE---KATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 413 NGQLEIVGRAIKV 425
+ EI GRAI++
Sbjct: 73 CNKREIEGRAIRL 85
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 58.9 bits (141), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 46/184 (25%), Positives = 79/184 (42%), Gaps = 34/184 (18%)
Query: 247 DQRTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDR--NSRRSKGVGYVEFYDVMSVP 304
D +F Q+ E+D+ E F + G V ++ ++ DR N +SKG +V FY +
Sbjct: 14 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA-- 71
Query: 305 MAIALSGQ---------PLLGQPVMVKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRL 355
AL Q P + P+ +KP+++EKN R+L
Sbjct: 72 ---ALEAQNALHNMKVLPGMHHPIQMKPADSEKN------------------NAVEDRKL 110
Query: 356 YVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLNGQ 415
++G + TE+ +R +F FG +E ++ G +G FV F A+ A+ Q
Sbjct: 111 FIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQ 170
Query: 416 LEIV 419
+ +
Sbjct: 171 AQTM 174
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 58.9 bits (141), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 46/184 (25%), Positives = 79/184 (42%), Gaps = 34/184 (18%)
Query: 247 DQRTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDR--NSRRSKGVGYVEFYDVMSVP 304
D +F Q+ E+D+ E F + G V ++ ++ DR N +SKG +V FY +
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA-- 59
Query: 305 MAIALSGQ---------PLLGQPVMVKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRL 355
AL Q P + P+ +KP+++EKN R+L
Sbjct: 60 ---ALEAQNALHNMKVLPGMHHPIQMKPADSEKN------------------NAVEDRKL 98
Query: 356 YVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLNGQ 415
++G + TE+ +R +F FG +E ++ G +G FV F A+ A+ Q
Sbjct: 99 FIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQ 158
Query: 416 LEIV 419
+ +
Sbjct: 159 AQTM 162
>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 = 58.2 bits (139), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 45/172 (26%), Positives = 74/172 (43%), Gaps = 24/172 (13%)
Query: 252 FAYQICLKADERDVYEFFSRAGKVRDVRLIMDR--NSRRSKGVGYVEFYDVMSVPMAI-A 308
F Q+ E+D+ E F + G V ++ ++ DR N +SKG +V FY + A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 309 LSGQPLL---GQPVMVKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMT 365
L +L P+ KP+++EKN R+L++G + T
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKN------------------NAVEDRKLFIGXISKKCT 108
Query: 366 EDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLNGQLE 417
E+ +R F FG +E ++ G +G FV F A+ A+ Q +
Sbjct: 109 ENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQAQ 160
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 33/82 (40%), Positives = 51/82 (62%), Gaps = 7/82 (8%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTV-ELVQLPLDETGHCKGFGFVQFARLEDARNA-LN 411
+L+VG L F+ E L QVF +G + E+V + ET +GFGFV F ++DA++A +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 412 LNGQLEIVGRAIKVSAVTDQSG 433
+NG+ + GR I+V DQ+G
Sbjct: 74 MNGK-SVDGRQIRV----DQAG 90
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 247 DQRTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMA 306
D+ +F + +E+ + + FS+ G++ +V ++ DR ++RS+G G+V F ++ A
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 307 -IALSGQPLLGQPVMV 321
+A++G+ + G+ + V
Sbjct: 71 MMAMNGKSVDGRQIRV 86
Score = 33.1 bits (74), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 5/51 (9%)
Query: 576 SKFGKLKHIFVEKD-----SAGFVYLRFENTQSAFAAQRALHGRWFAGKMI 621
SK+G++ + V KD S GF ++ FEN A A A++G+ G+ I
Sbjct: 34 SKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQI 84
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 57.0 bits (136), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN 411
R LYVG L + + L F PFG + +Q+PLD ET +GF FV+F EDA A++
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 412 LNGQLEIVGRAIKVS 426
+ E+ GR I+V+
Sbjct: 73 NMNESELFGRTIRVN 87
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 56.6 bits (135), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 33/87 (37%), Positives = 52/87 (59%), Gaps = 3/87 (3%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNAL- 410
R ++VGN+ + TE+QL+ +F G V +L D ETG KG+GF ++ E A +A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 411 NLNGQLEIVGRAIKVSAVTDQSGLQDL 437
NLNG+ E GRA++V + ++L
Sbjct: 69 NLNGR-EFSGRALRVDNAASEKNKEEL 94
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 45/85 (52%), Gaps = 1/85 (1%)
Query: 246 RDQRTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPM 305
R R+VF I +A E + + FS G V RL+ DR + + KG G+ E+ D +
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 306 AI-ALSGQPLLGQPVMVKPSEAEKN 329
A+ L+G+ G+ + V + +EKN
Sbjct: 66 AMRNLNGREFSGRALRVDNAASEKN 90
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN 411
R LYVG L + + L F PFG + +Q+PLD ET +GF FV+F EDA A++
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 412 LNGQLEIVGRAIKVS 426
+ E+ GR I+V+
Sbjct: 124 NMNESELFGRTIRVN 138
>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 = 56.2 bits (134), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNL 412
R+YVG++++ + ED +RQ F PFG ++ + + D T KGF FV++ E A+ AL
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 413 NGQLEIVGRAIKV 425
+ + GR IKV
Sbjct: 90 MNSVMLGGRNIKV 102
Score = 54.7 bits (130), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 41/195 (21%), Positives = 87/195 (44%), Gaps = 44/195 (22%)
Query: 251 VFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALS 310
V+ I + E + + F+ G ++ + + D + + KG +VE+ + +A+
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 311 GQPLLG---------------QPVMVKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRL 355
+LG QP++ + +E + R+
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF----------------------NRI 128
Query: 356 YVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNAL---- 410
YV ++H ++++D ++ VFE FG ++ L D TG KG+GF+++ + + +++A+
Sbjct: 129 YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Query: 411 --NLNGQLEIVGRAI 423
+L GQ VG+A+
Sbjct: 189 LFDLGGQYLRVGKAV 203
>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 = 56.2 bits (134), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNL 412
R+YVG++++ + ED +RQ F PFG ++ + D T KGF FV++ E A+ AL
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 413 NGQLEIVGRAIKV 425
+ + GR IKV
Sbjct: 74 XNSVXLGGRNIKV 86
Score = 53.5 bits (127), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 46/186 (24%), Positives = 88/186 (47%), Gaps = 26/186 (13%)
Query: 251 VFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALS 310
V+ I + E + + F+ G ++ + D + + KG +VE+ VP A L+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEY----EVPEAAQLA 70
Query: 311 GQ-----PLLGQPVMV-KPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNM 364
+ L G+ + V +PS N+ Q R+YV ++H ++
Sbjct: 71 LEQXNSVXLGGRNIKVGRPS----NIGQAQPIIDQLAEEARAF-----NRIYVASVHQDL 121
Query: 365 TEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNAL------NLNGQLE 417
++D ++ VFE FG ++ L D TG KG+GF+++ + + +++A+ +L GQ
Sbjct: 122 SDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYL 181
Query: 418 IVGRAI 423
VG+A+
Sbjct: 182 RVGKAV 187
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 55.8 bits (133), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNL 412
R+YVG++++ + ED +RQ F PFG ++ + + D T KGF FV++ E A+ AL
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 413 NGQLEIVGRAIKV 425
+ + GR IKV
Sbjct: 75 MNSVMLGGRNIKV 87
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 41/195 (21%), Positives = 87/195 (44%), Gaps = 44/195 (22%)
Query: 251 VFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALS 310
V+ I + E + + F+ G ++ + + D + + KG +VE+ + +A+
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 311 GQPLLG---------------QPVMVKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRL 355
+LG QP++ + +E + R+
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAF----------------------NRI 113
Query: 356 YVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNAL---- 410
YV ++H ++++D ++ VFE FG ++ L D TG KG+GF+++ + + +++A+
Sbjct: 114 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
Query: 411 --NLNGQLEIVGRAI 423
+L GQ VG+A+
Sbjct: 174 LFDLGGQYLRVGKAV 188
>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 = 55.1 bits (131), Expect = 1e-07, Method: Composition-based stats.
Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN 411
R LYVG L + + L F PFG + +Q+PLD ET +GF FV+F EDA A++
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 412 LNGQLEIVGRAIKVS 426
+ E+ GR I+V+
Sbjct: 68 NMNESELFGRTIRVN 82
>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 = 55.1 bits (131), Expect = 1e-07, Method: Composition-based stats.
Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN 411
R LYVG L + + L F PFG + +Q+PLD ET +GF FV+F EDA A++
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 412 LNGQLEIVGRAIKVS 426
+ E+ GR I+V+
Sbjct: 63 NMNESELFGRTIRVN 77
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 55.1 bits (131), Expect = 1e-07, Method: Composition-based stats.
Identities = 31/75 (41%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN 411
R LYVG L + + L F PFG + +Q+PLD ET +GF FV+F EDA A++
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 412 LNGQLEIVGRAIKVS 426
+ E+ GR I+V+
Sbjct: 66 NMNESELFGRTIRVN 80
>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 = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDET-GHCKGFGFVQFARLEDARNALNLN 413
L V L NMT+D+LR +F G VE +L D+ GH G+GFV + +DA A+N
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 414 GQLEIVGRAIKVS 426
L + + IKVS
Sbjct: 65 NGLRLQSKTIKVS 77
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 35/151 (23%), Positives = 64/151 (42%), Gaps = 22/151 (14%)
Query: 268 FFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQPVMVKPSEA 326
FS G+V +LI D+ + S G G+V + AI L+G L + + V +
Sbjct: 22 LFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP 81
Query: 327 EKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPL 386
+++ LY+ L MT+ + +F FG + ++ +
Sbjct: 82 SSEVIKDA-------------------NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV 122
Query: 387 DE-TGHCKGFGFVQFARLEDARNAL-NLNGQ 415
D+ TG +G F++F + +A A+ + NG
Sbjct: 123 DQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
Score = 33.5 bits (75), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 26/36 (72%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEF 297
++DV + FSR G++ + R+++D+ + S+GV ++ F
Sbjct: 102 QKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRF 137
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDET-GHCKGFGFVQFARLEDARNALNLN 413
L V L NMT+D+LR +F G VE +L D+ GH G+GFV + +DA A+N
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 414 GQLEIVGRAIKVS 426
L + + IKVS
Sbjct: 65 NGLRLQSKTIKVS 77
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 35/151 (23%), Positives = 64/151 (42%), Gaps = 22/151 (14%)
Query: 268 FFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQPVMVKPSEA 326
FS G+V +LI D+ + S G G+V + AI L+G L + + V +
Sbjct: 22 LFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP 81
Query: 327 EKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPL 386
+++ LY+ L MT+ + +F FG + ++ +
Sbjct: 82 SSEVIKDA-------------------NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV 122
Query: 387 DE-TGHCKGFGFVQFARLEDARNAL-NLNGQ 415
D+ TG +G F++F + +A A+ + NG
Sbjct: 123 DQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
Score = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 26/36 (72%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEF 297
++DV + FSR G++ + R+++D+ + S+GV ++ F
Sbjct: 102 QKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRF 137
>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 = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 33/74 (44%), Positives = 44/74 (59%), Gaps = 3/74 (4%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDET-GHCKGFGFVQFARLEDARNALN-L 412
L V L NMT+D+LR +F G VE +L D+ GH G+GFV + +DA A+N L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 413 NGQLEIVGRAIKVS 426
NG L + + IKVS
Sbjct: 67 NG-LRLQSKTIKVS 79
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 53.1 bits (126), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 46/89 (51%), Gaps = 14/89 (15%)
Query: 544 SECLLLKNMFDPKNETYEEFDMDIKEDVEGECSKFGKLKHIFVEKDSAG---------FV 594
S ++L+NM DPK+ D D++ +V EC KFG + + + ++ G +
Sbjct: 15 STVMVLRNMVDPKD-----IDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 69
Query: 595 YLRFENTQSAFAAQRALHGRWFAGKMITA 623
++ F A +AL+GRWFAG+ + A
Sbjct: 70 FVEFSIASETHKAIQALNGRWFAGRKVVA 98
>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 = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 43/157 (27%), Positives = 69/157 (43%), Gaps = 20/157 (12%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQPVM 320
E +YE FS AG + +R+ D +RRS G YV F A+ ++ + G+PV
Sbjct: 24 EAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVR 83
Query: 321 VKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQLRQVFEPFGTVE 380
+ S+ + +L + +++ NL ++ L F FG +
Sbjct: 84 IMWSQRDPSLRKSGVG-----------------NIFIKNLDKSIDNKALYDTFSAFGNIL 126
Query: 381 LVQLPLDETGHCKGFGFVQFARLEDARNAL-NLNGQL 416
++ DE G KG+GFV F E A A+ +NG L
Sbjct: 127 SCKVVCDENGS-KGYGFVHFETQEAAERAIEKMNGML 162
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNLN 413
LYVG+LH ++TE L + F P G + +++ D T G+ +V F + DA AL+
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 414 GQLEIVGRAIKV 425
I G+ +++
Sbjct: 73 NFDVIKGKPVRI 84
>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 = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 43/157 (27%), Positives = 69/157 (43%), Gaps = 20/157 (12%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQPVM 320
E +YE FS AG + +R+ D +RRS G YV F A+ ++ + G+PV
Sbjct: 29 EAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVR 88
Query: 321 VKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQLRQVFEPFGTVE 380
+ S+ + +L + +++ NL ++ L F FG +
Sbjct: 89 IMWSQRDPSLRKSGVG-----------------NIFIKNLDKSIDNKALYDTFSAFGNIL 131
Query: 381 LVQLPLDETGHCKGFGFVQFARLEDARNAL-NLNGQL 416
++ DE G KG+GFV F E A A+ +NG L
Sbjct: 132 SCKVVCDENGS-KGYGFVHFETQEAAERAIEKMNGML 167
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNLN 413
LYVG+LH ++TE L + F P G + +++ D T G+ +V F + DA AL+
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 414 GQLEIVGRAIKV 425
I G+ +++
Sbjct: 78 NFDVIKGKPVRI 89
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 47/79 (59%), Gaps = 2/79 (2%)
Query: 547 LLLKNMFDPKNETYEEFDMD-IKEDVEGECSKFGKLKHIFV-EKDSAGFVYLRFENTQSA 604
+++KNMF P + + ++ I+ED+ ECSKFG+++ + + ++ G + F + + A
Sbjct: 18 VIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEA 77
Query: 605 FAAQRALHGRWFAGKMITA 623
+ L GRWF G+ ITA
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 = 52.4 bits (124), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 35/153 (22%), Positives = 68/153 (44%), Gaps = 14/153 (9%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
R +F + + + + F + G + D ++ D N++RS+G G+V + V V A+
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 309 LSGQPLLGQPVMVKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQ 368
+ G+ +V+P A ++++VG + + E
Sbjct: 73 ARPHKVDGR--VVEPKRA-----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 119
Query: 369 LRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQF 400
LR FE +G +E++++ D +G +GF FV F
Sbjct: 120 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
Score = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 49/91 (53%), Gaps = 2/91 (2%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTV-ELVQLPLDETGHCKGFGFVQFARLEDARNALN 411
R+L++G L F T++ LR FE +GT+ + V + T +GFGFV +A +E+ A+N
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 412 LNGQLEIVGRAIKVSAVTDQSGLQDLGANTT 442
++ GR ++ + Q GA+ T
Sbjct: 73 ARPH-KVDGRVVEPKRAVSREDSQRPGAHLT 102
Score = 32.3 bits (72), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 17/82 (20%), Positives = 39/82 (47%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
+ +F I +E + ++F + GK+ + ++ DR S + +G +V F D SV +
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 163
Query: 309 LSGQPLLGQPVMVKPSEAEKNL 330
+ G V+ + +++ +
Sbjct: 164 QKYHTVNGHNCEVRKALSKQEM 185
>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 = 52.4 bits (124), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 35/153 (22%), Positives = 68/153 (44%), Gaps = 14/153 (9%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
R +F + + + + F + G + D ++ D N++RS+G G+V + V V A+
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 309 LSGQPLLGQPVMVKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQ 368
+ G+ +V+P A ++++VG + + E
Sbjct: 74 ARPHKVDGR--VVEPKRA-----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 120
Query: 369 LRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQF 400
LR FE +G +E++++ D +G +GF FV F
Sbjct: 121 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 49/91 (53%), Gaps = 2/91 (2%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTV-ELVQLPLDETGHCKGFGFVQFARLEDARNALN 411
R+L++G L F T++ LR FE +GT+ + V + T +GFGFV +A +E+ A+N
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 412 LNGQLEIVGRAIKVSAVTDQSGLQDLGANTT 442
++ GR ++ + Q GA+ T
Sbjct: 74 ARPH-KVDGRVVEPKRAVSREDSQRPGAHLT 103
Score = 32.3 bits (72), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 17/82 (20%), Positives = 39/82 (47%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
+ +F I +E + ++F + GK+ + ++ DR S + +G +V F D SV +
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164
Query: 309 LSGQPLLGQPVMVKPSEAEKNL 330
+ G V+ + +++ +
Sbjct: 165 QKYHTVNGHNCEVRKALSKQEM 186
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 52.4 bits (124), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 35/153 (22%), Positives = 68/153 (44%), Gaps = 14/153 (9%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
R +F + + + + F + G + D ++ D N++RS+G G+V + V V A+
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 309 LSGQPLLGQPVMVKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQ 368
+ G+ +V+P A ++++VG + + E
Sbjct: 75 ARPHKVDGR--VVEPKRA-----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 121
Query: 369 LRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQF 400
LR FE +G +E++++ D +G +GF FV F
Sbjct: 122 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 49/91 (53%), Gaps = 2/91 (2%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTV-ELVQLPLDETGHCKGFGFVQFARLEDARNALN 411
R+L++G L F T++ LR FE +GT+ + V + T +GFGFV +A +E+ A+N
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 412 LNGQLEIVGRAIKVSAVTDQSGLQDLGANTT 442
++ GR ++ + Q GA+ T
Sbjct: 75 ARPH-KVDGRVVEPKRAVSREDSQRPGAHLT 104
Score = 32.3 bits (72), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 17/82 (20%), Positives = 39/82 (47%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
+ +F I +E + ++F + GK+ + ++ DR S + +G +V F D SV +
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 165
Query: 309 LSGQPLLGQPVMVKPSEAEKNL 330
+ G V+ + +++ +
Sbjct: 166 QKYHTVNGHNCEVRKALSKQEM 187
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 35/153 (22%), Positives = 68/153 (44%), Gaps = 14/153 (9%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
R +F + + + + F + G + D ++ D N++RS+G G+V + V V A+
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 309 LSGQPLLGQPVMVKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQ 368
+ G+ +V+P A ++++VG + + E
Sbjct: 74 ARPHKVDGR--VVEPKRA-----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 120
Query: 369 LRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQF 400
LR FE +G +E++++ D +G +GF FV F
Sbjct: 121 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 48.9 bits (115), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 49/91 (53%), Gaps = 2/91 (2%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTV-ELVQLPLDETGHCKGFGFVQFARLEDARNALN 411
R+L++G L F T++ LR FE +GT+ + V + T +GFGFV +A +E+ A+N
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 412 LNGQLEIVGRAIKVSAVTDQSGLQDLGANTT 442
++ GR ++ + Q GA+ T
Sbjct: 74 ARPH-KVDGRVVEPKRAVSREDSQRPGAHLT 103
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 35/76 (46%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
+ +F I +E + ++F + GK+ + ++ DR S + +G +V F D SV +
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164
Query: 309 LSGQPLLGQPVMVKPS 324
+ G V+ +
Sbjct: 165 QKYHTVNGHNCEVRKA 180
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 35/153 (22%), Positives = 68/153 (44%), Gaps = 14/153 (9%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
R +F + + + + F + G + D ++ D N++RS+G G+V + V V A+
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 309 LSGQPLLGQPVMVKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQ 368
+ G+ +V+P A ++++VG + + E
Sbjct: 72 ARPHKVDGR--VVEPKRA-----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 118
Query: 369 LRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQF 400
LR FE +G +E++++ D +G +GF FV F
Sbjct: 119 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
Score = 48.9 bits (115), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 49/91 (53%), Gaps = 2/91 (2%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTV-ELVQLPLDETGHCKGFGFVQFARLEDARNALN 411
R+L++G L F T++ LR FE +GT+ + V + T +GFGFV +A +E+ A+N
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 412 LNGQLEIVGRAIKVSAVTDQSGLQDLGANTT 442
++ GR ++ + Q GA+ T
Sbjct: 72 ARPH-KVDGRVVEPKRAVSREDSQRPGAHLT 101
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 35/76 (46%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
+ +F I +E + ++F + GK+ + ++ DR S + +G +V F D SV +
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 162
Query: 309 LSGQPLLGQPVMVKPS 324
+ G V+ +
Sbjct: 163 QKYHTVNGHNCEVRKA 178
>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 = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 35/153 (22%), Positives = 68/153 (44%), Gaps = 14/153 (9%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
R +F + + + + F + G + D ++ D N++RS+G G+V + V V A+
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 309 LSGQPLLGQPVMVKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQ 368
+ G+ +V+P A ++++VG + + E
Sbjct: 67 ARPHKVDGR--VVEPKRA-----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 113
Query: 369 LRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQF 400
LR FE +G +E++++ D +G +GF FV F
Sbjct: 114 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 49/91 (53%), Gaps = 2/91 (2%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTV-ELVQLPLDETGHCKGFGFVQFARLEDARNALN 411
R+L++G L F T++ LR FE +GT+ + V + T +GFGFV +A +E+ A+N
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 412 LNGQLEIVGRAIKVSAVTDQSGLQDLGANTT 442
++ GR ++ + Q GA+ T
Sbjct: 67 ARPH-KVDGRVVEPKRAVSREDSQRPGAHLT 96
Score = 32.3 bits (72), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 17/82 (20%), Positives = 39/82 (47%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
+ +F I +E + ++F + GK+ + ++ DR S + +G +V F D SV +
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 157
Query: 309 LSGQPLLGQPVMVKPSEAEKNL 330
+ G V+ + +++ +
Sbjct: 158 QKYHTVNGHNCEVRKALSKQEM 179
>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 = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 46/89 (51%), Gaps = 14/89 (15%)
Query: 544 SECLLLKNMFDPKNETYEEFDMDIKEDVEGECSKFGKLKHIFVEKDSAG---------FV 594
S ++L+NM DPK+ D D++ +V EC KFG + + + ++ G +
Sbjct: 124 STVMVLRNMVDPKD-----IDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 178
Query: 595 YLRFENTQSAFAAQRALHGRWFAGKMITA 623
++ F A +AL+GRWFAG+ + A
Sbjct: 179 FVEFSIASETHKAIQALNGRWFAGRKVVA 207
>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 = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 38/146 (26%), Positives = 64/146 (43%), Gaps = 23/146 (15%)
Query: 281 IMDRNSRRSKGVGYVEFYDVMSVPMAIALSGQPLLGQPV-MVKPSEAEKNLVQXXXXXXX 339
++D + ++ GYV+F + A+ L+G + G + + KP + V+
Sbjct: 45 VVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAA----- 99
Query: 340 XXXXXXXXXXXXXRRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQ 399
R L NL FN+TED+L++VFE + LV + G KG +++
Sbjct: 100 -------------RTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIE 142
Query: 400 FARLEDARNALNLNGQLEIVGRAIKV 425
F DA L EI GR++ +
Sbjct: 143 FKSEADAEKNLEEKQGAEIDGRSVSL 168
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 41/63 (65%), Gaps = 2/63 (3%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALN-LN 413
LYV NL + +++LR+ F PFGT+ ++ + E G KGFGFV F+ E+A A+ +N
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-EGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 414 GQL 416
G++
Sbjct: 77 GRI 79
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 41/171 (23%), Positives = 87/171 (50%), Gaps = 21/171 (12%)
Query: 259 KADERDVY-EFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALSGQPLLGQ 317
KA D+ ++F G + ++++++D+N++ + +VE++ +A+ Q L G+
Sbjct: 10 KAITEDILKQYFQVGGPIANIKIMIDKNNK-NVNYAFVEYHQSHDANIAL----QTLNGK 64
Query: 318 PVMVKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQLRQVFEPFG 377
+ E N+V+ L+VG+L+ N+ ++ LR F+ F
Sbjct: 65 QI-------ENNIVKINWAFQSQQSSSDDTF-----NLFVGDLNVNVDDETLRNAFKDFP 112
Query: 378 TVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN-LNGQLEIVGRAIKVS 426
+ + D +TG +G+GFV F +DA+NA++ + GQ ++ GR ++++
Sbjct: 113 SYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ-DLNGRPLRIN 162
Score = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 2/75 (2%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALN- 411
R LYVGNL +TED L+Q F+ G + +++ +D+ + FV++ + DA AL
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 412 LNGQLEIVGRAIKVS 426
LNG+ +I +K++
Sbjct: 61 LNGK-QIENNIVKIN 74
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 47/84 (55%), Gaps = 2/84 (2%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN 411
R +YVGNL ++ T +Q++++F FG V V+L D ET KGFGFV+ E A+
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60
Query: 412 LNGQLEIVGRAIKVSAVTDQSGLQ 435
+ +GR I+V+ + L+
Sbjct: 61 KLDNTDFMGRTIRVTEANPKKSLE 84
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
R ++ + A V E FS+ GKV +V+LI DR +++ KG G+VE + SV AIA
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60
Query: 309 -LSGQPLLGQPVMVKPSEAEKNL 330
L +G+ + V + +K+L
Sbjct: 61 KLDNTDFMGRTIRVTEANPKKSL 83
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 31/87 (35%), Positives = 49/87 (56%), Gaps = 7/87 (8%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLP--LDETGHCKGFGFVQFARLEDARNALN 411
++ V N+ F + ++R++F FG ++ V+LP + TG +GFGFV F +DA+ A N
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76
Query: 412 -LNGQLEIVGRAIKV----SAVTDQSG 433
L + GR + + S VT QSG
Sbjct: 77 ALCHSTHLYGRRLVLEWADSEVTVQSG 103
>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 = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 2/74 (2%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALN 411
R +YVGN+ + T ++L F G+V V + D+ +GH KGF +++F+ E R +L
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 65
Query: 412 LNGQLEIVGRAIKV 425
L+ L GR IKV
Sbjct: 66 LDESL-FRGRQIKV 78
>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 = 49.7 bits (117), Expect = 5e-06, Method: Composition-based stats.
Identities = 29/73 (39%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDET-GHCKGFGFVQFARLEDARNALNLN 413
L V L N T+D+LR +F G VE +L D+ GH G+GFV + +DA A+N
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 414 GQLEIVGRAIKVS 426
L + + IKVS
Sbjct: 82 NGLRLQSKTIKVS 94
>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 = 5e-06, Method: Composition-based stats.
Identities = 32/101 (31%), Positives = 49/101 (48%), Gaps = 7/101 (6%)
Query: 541 GVPSECLLLKNMFDPKNETYEEFDMDIKEDVEGECSKFGKLKHI-------FVEKDSAGF 593
G P+E L L NM P+ +E +I EDV ECSK+G +K I VE G
Sbjct: 1 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGK 60
Query: 594 VYLRFENTQSAFAAQRALHGRWFAGKMITATFMVPQTYEAK 634
+++ F + A + L GR FA +++ + P +Y +
Sbjct: 61 IFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRR 101
>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 = 49.3 bits (116), Expect = 7e-06, Method: Composition-based stats.
Identities = 30/89 (33%), Positives = 49/89 (55%), Gaps = 11/89 (12%)
Query: 543 PSECLLLKNMFDPKNETYEEFDMDIKEDVEGECSKFGKL-KHIFVE-----KDSAGFVYL 596
P++ +LL+NM E D D++ + + EC K+GK+ K + E D A ++L
Sbjct: 7 PTKVVLLRNMVGAG-----EVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFL 61
Query: 597 RFENTQSAFAAQRALHGRWFAGKMITATF 625
FE +SA A L+GR+F G+++ A F
Sbjct: 62 EFERVESAIKAVVDLNGRYFGGRVVKACF 90
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 48.9 bits (115), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL-NL 412
+L++G L+ E L+ VF G + V L D T +GF F+ F DA+NA ++
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 413 NGQLEIVGRAIKV 425
NG+ + G+AIKV
Sbjct: 69 NGK-SLHGKAIKV 80
Score = 29.3 bits (64), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 577 KFGKLKHIFVEKD----SAGFVYLRFENTQSAFAAQRALHGRWFAGKMI 621
K G + + + KD S GF ++ FEN A A + ++G+ GK I
Sbjct: 30 KHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAI 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 = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 14/89 (15%)
Query: 544 SECLLLKNMFDPKNETYEEFDMDIKEDVEGECSKFGKLKHIFVEKDSAG---------FV 594
S +L+N DPK+ D D++ +V EC KFG + + + ++ G +
Sbjct: 20 STVXVLRNXVDPKD-----IDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 74
Query: 595 YLRFENTQSAFAAQRALHGRWFAGKMITA 623
++ F A +AL+GRWFAG+ + A
Sbjct: 75 FVEFSIASETHKAIQALNGRWFAGRKVVA 103
>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 = 48.5 bits (114), Expect = 1e-05, Method: Composition-based stats.
Identities = 31/99 (31%), Positives = 48/99 (48%), Gaps = 7/99 (7%)
Query: 543 PSECLLLKNMFDPKNETYEEFDMDIKEDVEGECSKFGKLKHI-------FVEKDSAGFVY 595
P+E L L NM P+ +E +I EDV ECSK+G +K I VE G ++
Sbjct: 3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 62
Query: 596 LRFENTQSAFAAQRALHGRWFAGKMITATFMVPQTYEAK 634
+ F + A + L GR FA +++ + P +Y +
Sbjct: 63 VEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRR 101
>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 = 48.1 bits (113), Expect = 2e-05, Method: Composition-based stats.
Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 2/74 (2%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALN 411
R +YVGN+ + T ++L F G+V V + D+ +GH KGF +++F+ E R +L
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 412 LNGQLEIVGRAIKV 425
L+ L GR IKV
Sbjct: 67 LDESL-FRGRQIKV 79
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 4/81 (4%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNL 412
R L NL FN+TED+L++VFE + LV + G KG +++F DA L
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEADAEKNLEE 72
Query: 413 NGQLEIVGRAIKVSAVTDQSG 433
EI GR++ + ++ G
Sbjct: 73 KQGAEIDGRSVSLYYTGEKGG 93
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNLN 413
L V NL + + D LR+VFE +G V V +P D T +GF FV+F DA +A++
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 414 GQLEIVGRAIKV 425
+ GR ++V
Sbjct: 133 DGAVLDGRELRV 144
Score = 32.3 bits (72), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 269 FSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQPVMVK 322
F + G+V DV + DR ++ S+G +V F+D A+ A+ G L G+ + V+
Sbjct: 91 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ 145
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 37/151 (24%), Positives = 62/151 (41%), Gaps = 27/151 (17%)
Query: 275 VRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALSGQPLLGQPVMVKPSEAEKNLVQXX 334
V DVR+ M R GYV+F + A+ L+G + G + ++ + + +
Sbjct: 39 VVDVRIGMTRK------FGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGKDS----- 87
Query: 335 XXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKG 394
R L NL + +T+D+L++VFE + LV + G KG
Sbjct: 88 ------------KKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVS----KDGKSKG 131
Query: 395 FGFVQFARLEDARNALNLNGQLEIVGRAIKV 425
+++F DA EI GR+I +
Sbjct: 132 IAYIEFKTEADAEKTFEEKQGTEIDGRSISL 162
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 355 LYVGNLHFNMTEDQLRQ-VFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLN 413
L+VGNL+FN + +L+ + + F +L + + G + FG+V F ED AL L
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDV-RIGMTRKFGYVDFESAEDLEKALELT 68
Query: 414 GQLEIVGRAIKV 425
G L++ G IK+
Sbjct: 69 G-LKVFGNEIKL 79
>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 = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNLN 413
L V NL + + D LR+VFE +G V V +P D T +GF FV+F DA +A++
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 414 GQLEIVGRAIKV 425
+ GR ++V
Sbjct: 110 DGAVLDGRELRV 121
Score = 29.3 bits (64), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 269 FSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQPVMVK 322
F + G+V DV + DR ++ S+G +V F+D A+ A+ G L G+ + V+
Sbjct: 68 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ 122
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDET-GHCKGFGFVQFARLEDARNAL 410
+ V NL + E L+++F PFG++ + L D+T G KGF F+ F R EDA A+
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 27/62 (43%)
Query: 247 DQRTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMA 306
D T+ + E D+ E F G + + L D+ + +SKG ++ F+ A
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 307 IA 308
IA
Sbjct: 74 IA 75
>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 = 3e-05, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALN- 411
R+L+VG L+ +ED +R++FE FG +E + G+ KG FV+++ +A+ A+N
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINA 75
Query: 412 LNGQLEIVG 420
L+G + G
Sbjct: 76 LHGSQTMPG 84
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL-N 411
+RL+V N+ F + LRQ+F FG + V++ +E G KGFGFV F DA A
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREK 74
Query: 412 LNGQLEIVGRAIKVSAVT 429
L+G + + GR I+V+ T
Sbjct: 75 LHGTV-VEGRKIEVNNAT 91
Score = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 564 DMDIKEDVEGECSKFGKLKHIFVEKDSAGFVYLRFENTQSAFAAQRALHGRWFAGKMI 621
D D+++ + G+ K ++ IF E+ S GF ++ FEN+ A A+ LHG G+ I
Sbjct: 29 DPDLRQ-MFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKI 85
Score = 30.8 bits (68), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 255 QICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEF 297
I + + D+ + F + GK+ DV +I N R SKG G+V F
Sbjct: 22 NIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTF 62
>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 = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 41/160 (25%), Positives = 71/160 (44%), Gaps = 28/160 (17%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQPVM 320
+ + F G++ +L+ D+ + +S G G+V + D AI L+G L + +
Sbjct: 16 QEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIK 75
Query: 321 V---KPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQLRQVFEPFG 377
V +PS A LYV L MT+ +L Q+F +G
Sbjct: 76 VSYARPSSAS----------------------IRDANLYVSGLPKTMTQKELEQLFSQYG 113
Query: 378 TVELVQLPLDE-TGHCKGFGFVQFARLEDARNALN-LNGQ 415
+ ++ +D+ TG +G GF++F + +A A+ LNGQ
Sbjct: 114 RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 27/73 (36%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNLN 413
L V L NMT+++ R +F G +E +L D+ TG G+GFV + +DA A+N
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 414 GQLEIVGRAIKVS 426
L + + IKVS
Sbjct: 65 NGLRLQTKTIKVS 77
Score = 33.5 bits (75), Expect = 0.38, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 39/64 (60%), Gaps = 3/64 (4%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLG--QP 318
++++ + FS+ G++ R+++D+ + S+GVG++ F + AI L+GQ G +P
Sbjct: 102 QKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEP 161
Query: 319 VMVK 322
+ VK
Sbjct: 162 ITVK 165
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDA-RNALN 411
+RL+V N+ F + LRQ+F FG + V++ +E G KGFGFV F DA R
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREK 88
Query: 412 LNGQLEIVGRAIKVSAVT 429
L+G + + GR I+V+ T
Sbjct: 89 LHGTV-VEGRKIEVNNAT 105
Score = 33.9 bits (76), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 570 DVEGECSKFGKL---KHIFVEKDSAGFVYLRFENTQSAFAAQRALHGRWFAGKMI 621
D+ +FGK+ + IF E+ S GF ++ FEN+ A A+ LHG G+ I
Sbjct: 45 DLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKI 99
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 255 QICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEF 297
I + + D+ + F + GK+ DV +I N R SKG G+V F
Sbjct: 36 NIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTF 76
>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 = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 47/81 (58%), Gaps = 2/81 (2%)
Query: 250 TVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIAL 309
TVF I ++ DE ++ FF+R G V++V++I DR SKG G+V FY+ + V I
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYGFVSFYNDVDV-QKIVE 68
Query: 310 SGQPLLGQPVMVKPSEAEKNL 330
S G+ + + P+ ++NL
Sbjct: 69 SQINFHGKKLKLGPAIRKQNL 89
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDAR----NAL 410
++VG + M E ++R F +G+V+ V++ D TG KG+GFV F D + + +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 71
Query: 411 NLNGQLEIVGRAIK 424
N +G+ +G AI+
Sbjct: 72 NFHGKKLKLGPAIR 85
>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 = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 48/74 (64%), Gaps = 3/74 (4%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN-L 412
L+VG+L+ N+ ++ LR F+ F + + D +TG +G+GFV F +DA+NA++ +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 413 NGQLEIVGRAIKVS 426
GQ ++ GR ++++
Sbjct: 64 QGQ-DLNGRPLRIN 76
>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 = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 41/165 (24%), Positives = 75/165 (45%), Gaps = 22/165 (13%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALSGQPLLGQPVMV 321
E ++ E+F + G V D++++ D + RS+G G++ F SV + Q +L V +
Sbjct: 17 EDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKV-I 73
Query: 322 KPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQLRQVFEPFGTVEL 381
P A Q +++VG + ++ + + F +GT+
Sbjct: 74 DPKRAIPRDEQDKTG-----------------KIFVGGIGPDVRPKEFEEFFSQWGTIID 116
Query: 382 VQLPLD-ETGHCKGFGFVQFARLEDARNALNLNGQLEIVGRAIKV 425
QL LD +TG +GFGFV + DA + + N ++ R I++
Sbjct: 117 AQLMLDKDTGQSRGFGFVTYDSA-DAVDRVCQNKFIDFKDRKIEI 160
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFAR 402
++++G L+++ TED LR+ F +GTV +++ D TG +GFGF+ F +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEK 54
>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 = 46.6 bits (109), Expect = 4e-05, Method: Composition-based stats.
Identities = 31/101 (30%), Positives = 48/101 (47%), Gaps = 7/101 (6%)
Query: 541 GVPSECLLLKNMFDPKNETYEEFDMDIKEDVEGECSKFGKLKHI-------FVEKDSAGF 593
G P+E L L N P+ +E +I EDV ECSK+G +K I VE G
Sbjct: 2 GHPTEVLCLXNXVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGK 61
Query: 594 VYLRFENTQSAFAAQRALHGRWFAGKMITATFMVPQTYEAK 634
+++ F + A + L GR FA +++ + P +Y +
Sbjct: 62 IFVEFTSVFDCQKAXQGLTGRKFANRVVVTKYCDPDSYHRR 102
>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 = 22/59 (37%), Positives = 36/59 (61%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALN 411
R+L+VG L T++ +R++FEPFGT++ + G KG FV+F +A+ A+N
Sbjct: 13 RKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAIN 71
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLE 404
L V L + TE L++ F FG V +VQ+ D +TGH KGFGFV+F E
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
Score = 33.1 bits (74), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 258 LKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEF 297
K E+D+ E+FS G+V V++ D + SKG G+V F
Sbjct: 25 WKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 47/89 (52%), Gaps = 3/89 (3%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALNLN 413
L V NL + + D LR+VFE +G V V +P + T +GF FV+F DA++A
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 414 GQLEIVGRAIKVSAVTDQSGLQDLGANTT 442
E+ GR ++V + G +DL ++
Sbjct: 76 DGAELDGRELRVQVA--RYGRRDLSGPSS 102
>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 = 45.8 bits (107), Expect = 8e-05, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALN-LN 413
LYVGNL F TE+Q+ ++F G ++ + + LD+ GF FV++ DA NA+ +N
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 414 G 414
G
Sbjct: 81 G 81
Score = 29.6 bits (65), Expect = 6.0, Method: Composition-based stats.
Identities = 12/49 (24%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 250 TVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFY 298
T++ + E +YE FS++G ++ + + +D+ + + G +VE+Y
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYY 67
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNLN 413
+YVG L ++E L ++F G V +P D TG +G+GFV+F EDA A+ +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 414 GQLEIVGRAIKVSAVT 429
+++ G+ I+V+ +
Sbjct: 78 DMIKLYGKPIRVNKAS 93
Score = 37.0 bits (84), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 250 TVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIAL 309
TV+ + K E ++E F +AG V + + DR + + +G G+VEF AI +
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 310 SGQ-PLLGQPVMV-KPSEAEKNL 330
L G+P+ V K S KNL
Sbjct: 77 MDMIKLYGKPIRVNKASAHNKNL 99
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 23/54 (42%), Positives = 35/54 (64%), Gaps = 1/54 (1%)
Query: 250 TVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSV 303
TVF I ++ DE ++ FF+R G V++V++I DR SKG G+V FY+ + V
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYGFVSFYNDVDV 64
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDAR----NAL 410
++VG + M E ++R F +G+V+ V++ D TG KG+GFV F D + + +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 72
Query: 411 NLNGQLEIVGRAIK 424
N +G+ +G AI+
Sbjct: 73 NFHGKKLKLGPAIR 86
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNLN 413
L V L NMT+D+ + +F G +E +L D+ TG G+GFV ++ DA A+N
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 414 GQLEIVGRAIKVS 426
L++ + IKVS
Sbjct: 67 NGLKLQTKTIKVS 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 = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 33/50 (66%), Gaps = 1/50 (2%)
Query: 250 TVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYD 299
TVF I ++ DE ++ FF+R G V++V++I DR SKG G+V FY+
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYGFVSFYN 59
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDAR----NAL 410
++VG + M E ++R F +G+V+ V++ D TG KG+GFV F D + + +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 71
Query: 411 NLNGQLEIVGRAIK 424
N +G+ +G AI+
Sbjct: 72 NFHGKKLKLGPAIR 85
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 45/76 (59%), Gaps = 3/76 (3%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNAL- 410
R L V + + E QLRQ+FE +G +E V++ D ET +G+GFV+F A+ A+
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 411 NLNGQLEIVGRAIKVS 426
LNG I+ + +KV+
Sbjct: 103 GLNG-FNILNKRLKVA 117
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
R + I DE + + F R G + V+++ DR +R+S+G G+V+F S AIA
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNLN 413
L V L NMT+D+ + +F G +E +L D+ TG G+GFV ++ DA A+N
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 414 GQLEIVGRAIKVS 426
L++ + IKVS
Sbjct: 67 NGLKLQTKTIKVS 79
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 40/154 (25%), Positives = 68/154 (44%), Gaps = 28/154 (18%)
Query: 268 FFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQPVMV---KP 323
F G + +L+ D+ + +S G G+V + D AI L+G L + + V +P
Sbjct: 24 LFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARP 83
Query: 324 SEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQLRQVFEPFGTVELVQ 383
S A LYV L M++ ++ Q+F +G + +
Sbjct: 84 SSAS----------------------IRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSR 121
Query: 384 LPLDE-TGHCKGFGFVQFARLEDARNALN-LNGQ 415
+ LD+ TG +G GF++F + +A A+ LNGQ
Sbjct: 122 ILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 155
Score = 37.0 bits (84), Expect = 0.037, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 40/64 (62%), Gaps = 3/64 (4%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLG--QP 318
++++ + FS+ G++ R+++D+ + S+GVG++ F + AI L+GQ LG +P
Sbjct: 104 QKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEP 163
Query: 319 VMVK 322
+ VK
Sbjct: 164 ITVK 167
>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 = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALNLN 413
++VG+L +T + ++ F PFG + ++ D TG KG+GFV F DA NA+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 414 GQLEIVGRAIKVSAVT 429
G + GR I+ + T
Sbjct: 78 GGQWLGGRQIRTNWAT 93
Score = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 32/66 (48%)
Query: 251 VFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALS 310
VF + + D+ F+ G++ D R++ D + +SKG G+V F++ AI
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 311 GQPLLG 316
G LG
Sbjct: 78 GGQWLG 83
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALNLN 413
++VG+L +T + ++ F PFG + ++ D TG KG+GFV F DA NA+
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 414 GQLEIVGRAIKVSAVT 429
G + GR I+ + T
Sbjct: 78 GGQWLGGRQIRTNWAT 93
Score = 39.3 bits (90), Expect = 0.007, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 33/66 (50%)
Query: 251 VFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALS 310
VF + + D+ F+ GK+ D R++ D + +SKG G+V FY+ + AI
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 311 GQPLLG 316
G LG
Sbjct: 78 GGQWLG 83
Score = 29.6 bits (65), Expect = 5.3, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 569 EDVEGECSKFGKLKHIFVEKD-----SAGFVYLRFENTQSAFAAQRALHGRWFAGKMI 621
ED++ + FGK+ V KD S G+ ++ F N A A + G+W G+ I
Sbjct: 30 EDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 87
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNLN 413
L V L TE LR+VF +G + V + D+ + +GF FV F ++DA+ A
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 414 GQLEIVGRAIKVSA 427
+E+ GR I+VS
Sbjct: 78 NGMELDGRRIRVSG 91
Score = 42.4 bits (98), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 254 YQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDV 300
+ + L ERD+ E FS+ G + DV ++ D+ SRRS+G +V F +V
Sbjct: 21 FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%)
Query: 251 VFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALS 310
+F I E ++ E+F + G V +V +I D +R +G G++ F D SV A+ +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 311 GQPLLGQPVMVKPSE 325
++G+ V VK +E
Sbjct: 73 FHDIMGKKVEVKRAE 87
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 2/73 (2%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTV-ELVQLPLDETGHCKGFGFVQFARLEDARNALNL 412
+++VG + N E +LR+ F+ FG V E+V + E +GFGF+ F + A+N+
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 413 NGQLEIVGRAIKV 425
+ +I+G+ ++V
Sbjct: 72 HFH-DIMGKKVEV 83
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 36/152 (23%), Positives = 68/152 (44%), Gaps = 21/152 (13%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQPVM 320
+R++Y F G + R++ D + S G +V+F M AI L+G + + +
Sbjct: 17 DRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLK 76
Query: 321 VKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQLRQVFEPFGTVE 380
V + ++ LYV NL +T+DQL +F +G++
Sbjct: 77 VSYARPGGESIKDT-------------------NLYVTNLPRTITDDQLDTIFGKYGSIV 117
Query: 381 LVQLPLDE-TGHCKGFGFVQFARLEDARNALN 411
+ D+ TG +G FV++ + E+A+ A++
Sbjct: 118 QKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Score = 33.1 bits (74), Expect = 0.53, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALNLN 413
L V L +MT+ +L +F G + ++ D +TG+ G+ FV F D++ A+ +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 414 GQLEIVGRAIKVS 426
+ + + +KVS
Sbjct: 66 NGITVRNKRLKVS 78
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 20/77 (25%), Positives = 45/77 (58%), Gaps = 2/77 (2%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGH--CKGFGFVQFARLEDARNALN 411
++++G L N+T+D + ++F +G ++++ +P++ KG+ +V+F ++A AL
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 412 LNGQLEIVGRAIKVSAV 428
+I G+ I +AV
Sbjct: 66 HMDGGQIDGQEITATAV 82
Score = 30.0 bits (66), Expect = 4.6, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 576 SKFGKLKHIFVEKD------SAGFVYLRFENTQSAFAAQRALHGRWFAGKMITAT 624
S +GK+K I + + S G+ Y+ FEN A A + + G G+ ITAT
Sbjct: 26 STYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITAT 80
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNLN 413
L V L TE LR+VF +G + V + D+ + +GF FV F ++DA+ A
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 414 GQLEIVGRAIKV 425
+E+ GR I+V
Sbjct: 78 NGMELDGRRIRV 89
Score = 42.4 bits (98), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 254 YQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDV 300
+ + L ERD+ E FS+ G + DV ++ D+ SRRS+G +V F +V
Sbjct: 21 FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 31/52 (59%)
Query: 248 QRTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYD 299
+ TV+ + D+Y FS+ GKV V ++ D+++R+SKGV ++ F D
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLD 67
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALNLN 413
+YV NL F++T + L ++F +G V V + D +T KG F+ F + A+N
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 414 GQLEIVGRAIKVS 426
++ GR IK S
Sbjct: 79 NNKQLFGRVIKAS 91
>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 = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALN 411
R +YVGN+ + T L F G++ + + D+ +GH KG+ +++FA A+
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Query: 412 LNGQLEIVGRAIKV 425
++ + GR IKV
Sbjct: 97 MD-ETVFRGRTIKV 109
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 39/77 (50%)
Query: 247 DQRTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMA 306
D+R+V+ + + +D+ FS G + + ++ D+ S KG Y+EF + SV A
Sbjct: 35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 94
Query: 307 IALSGQPLLGQPVMVKP 323
+A+ G+ + V P
Sbjct: 95 VAMDETVFRGRTIKVLP 111
>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 = 42.7 bits (99), Expect = 7e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 248 QRTV-----FAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMS 302
QR+V F + +A E D+++ F+ G+++++ L +DR + KG VE+
Sbjct: 2 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 303 VPMAI-ALSGQPLLGQPVMV 321
A+ L+GQ L+GQP+ V
Sbjct: 62 AQAAMEGLNGQDLMGQPISV 81
Score = 42.4 bits (98), Expect = 9e-04, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 44/73 (60%), Gaps = 3/73 (4%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN-L 412
L+V +H TE+ + F +G ++ + L LD TG+ KG+ V++ ++A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 413 NGQLEIVGRAIKV 425
NGQ +++G+ I V
Sbjct: 70 NGQ-DLMGQPISV 81
>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 = 42.7 bits (99), Expect = 7e-04, Method: Composition-based stats.
Identities = 29/98 (29%), Positives = 46/98 (46%), Gaps = 7/98 (7%)
Query: 544 SECLLLKNMFDPKNETYEEFDMDIKEDVEGECSKFGKLKHI-------FVEKDSAGFVYL 596
+E L L N P+ +E +I EDV ECSK+G +K I VE G +++
Sbjct: 6 TEVLCLXNXVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFV 65
Query: 597 RFENTQSAFAAQRALHGRWFAGKMITATFMVPQTYEAK 634
F + A + L GR FA +++ + P +Y +
Sbjct: 66 EFTSVFDCQKAXQGLTGRKFANRVVVTKYCDPDSYHRR 103
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 53/86 (61%), Gaps = 5/86 (5%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNAL- 410
R +Y+G++ ++ TE+Q+ + G V +++ D +TG KG+ F++F LE + +A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 411 NLNGQLEIVGRAIKV--SAVTDQSGL 434
NLNG ++ R +K S+ +D SG+
Sbjct: 63 NLNG-YQLGSRFLKCGYSSNSDISGV 87
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 30/59 (50%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI 307
R V+ I E + + S G V +++++ D + RSKG ++EF D+ S A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
>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 = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 53/86 (61%), Gaps = 5/86 (5%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNAL- 410
R +Y+G++ ++ TE+Q+ + G V +++ D +TG KG+ F++F LE + +A+
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 411 NLNGQLEIVGRAIKV--SAVTDQSGL 434
NLNG ++ R +K S+ +D SG+
Sbjct: 64 NLNG-YQLGSRFLKCGYSSNSDISGV 88
Score = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 30/59 (50%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI 307
R V+ I E + + S G V +++++ D + RSKG ++EF D+ S A+
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 254 YQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDV 300
+ + L ERD+ E FS+ G + DV ++ D+ SRRS+G +V F +V
Sbjct: 52 FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 98
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNLN 413
L V L TE LR+VF +G + V + D+ + +GF FV F ++DA+ A
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 414 GQLEIVGRAIKV 425
+E+ GR I+V
Sbjct: 109 NGMELDGRRIRV 120
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 37/75 (49%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNL 412
R ++VGNL + E+ L ++F G + V + D G K FGFV F E A+ L
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76
Query: 413 NGQLEIVGRAIKVSA 427
+ + GR I VS
Sbjct: 77 LNGIRLYGRPINVSG 91
Score = 39.3 bits (90), Expect = 0.006, Method: Composition-based stats.
Identities = 28/74 (37%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
RTVF + + E +YE F +AG + V + DR + K G+V F SV AIA
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPESVSYAIA 75
Query: 309 -LSGQPLLGQPVMV 321
L+G L G+P+ V
Sbjct: 76 LLNGIRLYGRPINV 89
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 248 QRTV-----FAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMS 302
QR+V F + +A E D+++ F+ G+++++ L +DR + KG VE+
Sbjct: 2 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 303 VPMAI-ALSGQPLLGQPVMV 321
A+ L+GQ L+GQP+ V
Sbjct: 62 AQAAMEGLNGQDLMGQPISV 81
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 44/73 (60%), Gaps = 3/73 (4%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN-L 412
L+V +H TE+ + F +G ++ + L LD TG+ KG+ V++ ++A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 413 NGQLEIVGRAIKV 425
NGQ +++G+ I V
Sbjct: 70 NGQ-DLMGQPISV 81
>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 = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 248 QRTV-----FAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMS 302
QR+V F + +A E D+++ F+ G+++++ L +DR + KG VE+
Sbjct: 4 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 63
Query: 303 VPMAI-ALSGQPLLGQPVMV 321
A+ L+GQ L+GQP+ V
Sbjct: 64 AQAAMEGLNGQDLMGQPISV 83
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 44/73 (60%), Gaps = 3/73 (4%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN-L 412
L+V +H TE+ + F +G ++ + L LD TG+ KG+ V++ ++A+ A+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 413 NGQLEIVGRAIKV 425
NGQ +++G+ I V
Sbjct: 72 NGQ-DLMGQPISV 83
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 42.4 bits (98), Expect = 8e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 248 QRTV-----FAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMS 302
QR+V F + +A E D+++ F+ G+++++ L +DR + KG VE+
Sbjct: 2 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 303 VPMAI-ALSGQPLLGQPVMV 321
A+ L+GQ L+GQP+ V
Sbjct: 62 AQAAMEGLNGQDLMGQPISV 81
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 44/73 (60%), Gaps = 3/73 (4%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN-L 412
L+V +H TE+ + F +G ++ + L LD TG+ KG+ V++ ++A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 413 NGQLEIVGRAIKV 425
NGQ +++G+ I V
Sbjct: 70 NGQ-DLMGQPISV 81
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALNLN 413
L V L TE LR+VF +G + V + D+ + +GF FV F ++DA+ A
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 414 GQLEIVGRAIKV 425
+E+ GR I+V
Sbjct: 75 NGMELDGRRIRV 86
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 30/48 (62%)
Query: 253 AYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDV 300
+ + L ERD+ E FS+ G + DV ++ D+ SRRS+G +V F +V
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 64
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 42.4 bits (98), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNL 412
+ L+V L + TE+ L++ F+ G+V + ETG KGFGFV F EDA+ A
Sbjct: 16 KTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 413 NGQLEIVGRAIKV 425
EI G + +
Sbjct: 74 MEDGEIDGNKVTL 86
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 46/85 (54%), Gaps = 8/85 (9%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN 411
+ +++ NL F+ E+ L +V + FG ++ V++ L +T H KG F QF E A+ L
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 412 L------NGQLEIVGRAIKVS-AVT 429
G L++ GR +KV AVT
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLAVT 100
>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 = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 41/64 (64%), Gaps = 2/64 (3%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNAL- 410
R +Y+G++ ++ TE+Q+ + G V +++ D +TG KG+ F++F LE + +A+
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 411 NLNG 414
NLNG
Sbjct: 65 NLNG 68
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 30/59 (50%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI 307
R V+ I E + + S G V +++++ D + RSKG ++EF D+ S A+
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNAL-N 411
RL+V NL + +E+ L ++F +G + + P+D T KGF FV F E A A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 412 LNGQLEIVGRAIKV 425
++GQ+ GR + V
Sbjct: 70 VDGQV-FQGRMLHV 82
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFA 401
+++VG L ++ T+ LR+ FE FG +E + D +TG +G+GFV A
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA 67
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTV-ELVQLPLDETGHCKGFGFVQFARLEDARNAL 410
R+L++G L F TE+ LR +E +G + + V + + +GFGFV F+ + + A+
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Score = 37.0 bits (84), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 249 RTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIA 308
R +F + + E + ++ + GK+ D ++ D S+RS+G G+V F + V A+A
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 309 LSGQPLLGQPVMVKPSEA 326
+ G+ +V+P A
Sbjct: 88 ARPHSIDGR--VVEPKRA 103
>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 = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 259 KADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQ 317
+A E D+++ F+ G+++++ L +DR + KG VE+ A+ L+GQ L+GQ
Sbjct: 33 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ 92
Query: 318 PVMV 321
P+ V
Sbjct: 93 PISV 96
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 44/73 (60%), Gaps = 3/73 (4%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN-L 412
L+V +H TE+ + F +G ++ + L LD TG+ KG+ V++ ++A+ A+ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 413 NGQLEIVGRAIKV 425
NGQ +++G+ I V
Sbjct: 85 NGQ-DLMGQPISV 96
>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 = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 259 KADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQ 317
+A E D+++ F+ G+++++ L +DR + KG VE+ A+ L+GQ L+GQ
Sbjct: 34 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ 93
Query: 318 PVMV 321
P+ V
Sbjct: 94 PISV 97
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 44/73 (60%), Gaps = 3/73 (4%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN-L 412
L+V +H TE+ + F +G ++ + L LD TG+ KG+ V++ ++A+ A+ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 413 NGQLEIVGRAIKV 425
NGQ +++G+ I V
Sbjct: 86 NGQ-DLMGQPISV 97
>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 = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 2/62 (3%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCK-GFGFVQFARLEDARNALN-L 412
LYVGNL F TE+Q+ ++F G ++ + + LD+ GF FV++ DA NA+ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 413 NG 414
NG
Sbjct: 102 NG 103
Score = 33.1 bits (74), Expect = 0.50, Method: Composition-based stats.
Identities = 12/49 (24%), Positives = 28/49 (57%)
Query: 250 TVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFY 298
T++ + E +YE FS++G ++ + + +D+ + + G +VE+Y
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYY 89
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 43/73 (58%), Gaps = 3/73 (4%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALN-L 412
L+V ++H ED++++ F +G ++ + L LD TG KG+ V++ + A A L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 413 NGQLEIVGRAIKV 425
NG EI+G+ I+V
Sbjct: 135 NG-AEIMGQTIQV 146
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 3/73 (4%)
Query: 251 VFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI--A 308
+F I +A E ++ E F G+++++ L +DR + SKG VE Y+ +A A
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE-YETHKQALAAKEA 133
Query: 309 LSGQPLLGQPVMV 321
L+G ++GQ + V
Sbjct: 134 LNGAEIMGQTIQV 146
>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 = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNAL 410
++++VG L + E+++R+ F FG VE ++LP+D +T +GF F+ F E + +
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 35/151 (23%), Positives = 65/151 (43%), Gaps = 21/151 (13%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLGQPVM 320
+R++Y F G + R+ D + S G +V+F AI L+G + + +
Sbjct: 28 DRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRLK 87
Query: 321 VKPSEAEKNLVQXXXXXXXXXXXXXXXXXXXXRRLYVGNLHFNMTEDQLRQVFEPFGTVE 380
V + ++ LYV NL +T+DQL +F +G++
Sbjct: 88 VSYARPGGESIKDTN-------------------LYVTNLPRTITDDQLDTIFGKYGSIV 128
Query: 381 LVQLPLDE-TGHCKGFGFVQFARLEDARNAL 410
+ D+ TG +G FV++ + E+A+ A+
Sbjct: 129 QKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
Score = 32.3 bits (72), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALNLN 413
L V L + T+ +L +F G + ++ D +TG+ G+ FV F D++ A+ +
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 414 GQLEIVGRAIKVS 426
+ + + +KVS
Sbjct: 77 NGITVRNKRLKVS 89
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNAL-NL 412
LYV L M++ ++ Q+F +G + ++ LD+ TG +G GF++F + +A A+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 413 NGQ 415
NGQ
Sbjct: 64 NGQ 66
Score = 37.4 bits (85), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 40/64 (62%), Gaps = 3/64 (4%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI-ALSGQPLLG--QP 318
++++ + FS+ G++ R+++D+ + S+GVG++ F + AI L+GQ LG +P
Sbjct: 15 QKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEP 74
Query: 319 VMVK 322
+ VK
Sbjct: 75 ITVK 78
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 41/69 (59%), Gaps = 1/69 (1%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALN- 411
R+L+VG L+ +E+ + ++F+PFG ++ + G KG FV+F+ +A+ A++
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 412 LNGQLEIVG 420
L+G + G
Sbjct: 76 LHGSQTMPG 84
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 40/80 (50%), Gaps = 9/80 (11%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLNG 414
LY+ NL +M E +L + +PFG V ++ D +G +G G FAR+E + G
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVG---FARMESTEKCEAVIG 84
Query: 415 QLEIVGRAIK----VSAVTD 430
G+ IK VSA T+
Sbjct: 85 HFN--GKFIKTPPGVSAPTE 102
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 31/60 (51%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLNG 414
L V NL ++ + L Q F FG VE + +D+ G G GFV+FA AR AL G
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCG 158
Score = 33.9 bits (76), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%), Gaps = 5/47 (10%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQF 400
RL+VGNL ++TE+ +++FE +G V + D +GFGF++
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRL 65
>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 = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALN 411
LYV NL +T+DQL +F +G++ + D+ TG +G FV++ + E+A+ A++
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 39.3 bits (90), Expect = 0.006, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNAL 410
++VG L + E+++R+ F FG VE ++LP+D +T +GF F+ F E + +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 3/71 (4%)
Query: 356 YVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALNLNG 414
YVGNL FN + + +F+ ++ V+L D +T KGF +V+F ++ + AL +G
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDG 77
Query: 415 QLEIVGRAIKV 425
L + R+++V
Sbjct: 78 AL-LGDRSLRV 87
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 31/54 (57%)
Query: 275 VRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALSGQPLLGQPVMVKPSEAEK 328
+R VRL+ D+++ + KG YVEF +V S+ A+ G L + + V +E K
Sbjct: 41 IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRK 94
>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 = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNA 409
L V NL ++T+ Q ++ PFG++E L E TG KG+GF ++ + + A A
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 151
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNA 409
L V NL ++T+ Q ++ PFG++E L E TG KG+GF ++ + + A A
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNA 409
L V NL ++T+ Q ++ PFG++E L E TG KG+GF ++ + + A A
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
>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 = 38.1 bits (87), Expect = 0.013, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNALN-- 411
+++G L ++ T+ L+ F FG V L LD TG +GFGFV F E ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 412 ---LNGQL 416
LNG++
Sbjct: 62 EHKLNGKV 69
Score = 33.5 bits (75), Expect = 0.42, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 28/42 (66%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSV 303
++D+ ++FS+ G+V D L +D + RS+G G+V F + SV
Sbjct: 13 KKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESV 54
>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 = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 31/47 (65%), Gaps = 5/47 (10%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQF 400
RL+VGNL ++TE+++R++FE +G V + D KGFGF++
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRL 58
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.1 bits (87), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 31/47 (65%), Gaps = 5/47 (10%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQF 400
RL+VGNL ++TE+++R++FE +G V + D KGFGF++
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRL 65
Score = 32.3 bits (72), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALN 411
L V NL ++ + L + F FG VE + +D+ G G G V+F+ AR AL+
Sbjct: 99 LTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALD 155
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 37/86 (43%), Gaps = 10/86 (11%)
Query: 549 LKNMFDPKNETYEE----FDMDIKEDVEGE-----CSKFGKLKHIFVEKDSAGFVYLRFE 599
LKN P +T+ + F ++ D+ E K+GK +F+ KD GF ++R E
Sbjct: 8 LKNFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-GFGFIRLE 66
Query: 600 NTQSAFAAQRALHGRWFAGKMITATF 625
A A+ L GK + F
Sbjct: 67 TRTLAEIAKVELDNMPLRGKQLRVRF 92
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 38.1 bits (87), Expect = 0.016, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALNLN 413
L+V ++H ED++++ F +G ++ + L LD TG KG+ V++ + A A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 414 GQLEIVGRAIKV 425
EI+G+ I+V
Sbjct: 89 NGAEIMGQTIQV 100
Score = 35.4 bits (80), Expect = 0.099, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 3/73 (4%)
Query: 251 VFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI--A 308
+F I +A E ++ E F G+++++ L +DR + SKG VE Y+ +A A
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE-YETHKQALAAKEA 87
Query: 309 LSGQPLLGQPVMV 321
L+G ++GQ + V
Sbjct: 88 LNGAEIMGQTIQV 100
>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 = 38.1 bits (87), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 16/92 (17%)
Query: 247 DQRTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDR--NSRRSKGVGYVEFYDVMSVP 304
D +F Q+ E+D+ E F + G V ++ ++ DR N +SKG +V FY +
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA-- 59
Query: 305 MAIALSGQ---------PLLGQPVMVKPSEAE 327
AL Q P + P+ +KP+++E
Sbjct: 60 ---ALEAQNALHNMKVLPGMHHPIQMKPADSE 88
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGH---CKGFGFVQF----ARLEDA 406
+++VG + +E LR++FE +G V + + D + + KG FV F A LE A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE-A 63
Query: 407 RNALN 411
+NAL+
Sbjct: 64 QNALH 68
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 37.7 bits (86), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFG-TVELVQLPLDETGHCKGFGFVQF 400
+L+VG L ++ T++ LR F +G V+ V + T +GFGFV+F
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
Score = 35.4 bits (80), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%)
Query: 268 FFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALSGQPLLGQPVMVKP 323
+FS+ G+V D ++ D+ + +S+G G+V+F D V +A L G+ + KP
Sbjct: 36 YFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKP 91
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 37.4 bits (85), Expect = 0.025, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQF 400
++VG L N T + ++ FE FG V+ L D+ T +GFGFV F
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
Score = 35.4 bits (80), Expect = 0.093, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 251 VFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEF 297
+F + + DV +F + GKV D L+ D+ + R +G G+V F
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLN 413
+L+VGN+ T +LR FE +G P+ E K + FV R EDA A+
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYG-------PVIECDIVKDYAFVHMERAEDAVEAIRGL 64
Query: 414 GQLEIVGRAIKVSAVTDQ 431
E G+ + V T +
Sbjct: 65 DNTEFQGKRMHVQLSTSR 82
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 7/57 (12%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL 410
RL+V ++ E +L ++F PFG P+ E GF FV+F E A A+
Sbjct: 6 RLFVRPFPLDVQESELNEIFGPFG-------PMKEVKILNGFAFVEFEEAESAAKAI 55
Score = 33.1 bits (74), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
Query: 563 FDMDIKEDVEGEC-SKFGKLKHIFVEKDSAGFVYLRFENTQSAFAAQRALHGRWFAGKMI 621
F +D++E E FG +K + K GF ++ FE +SA A +HG+ FA + +
Sbjct: 12 FPLDVQESELNEIFGPFGPMKEV---KILNGFAFVEFEEAESAAKAIEEVHGKSFANQPL 68
Query: 622 TATF 625
+
Sbjct: 69 EVVY 72
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 37.0 bits (84), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNL 412
R LYVGNL ++TE + Q+F G + ++ + T + + FV+F DA AL
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAA 74
Query: 413 NGQLEIVGRAIKVSAVTDQS 432
+I+G+ +KV+ T S
Sbjct: 75 MNGRKILGKEVKVNWATTPS 94
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 37.0 bits (84), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL-NLN 413
+++ NL ++ L F FG + ++ DE G KG+GFV F E A A+ +N
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAIEKMN 72
Query: 414 GQL 416
G L
Sbjct: 73 GML 75
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 36.6 bits (83), Expect = 0.040, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 354 RLYVGNLHF-NMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNL 412
RL++GNL N++++ L ++F P+G + + + FGF+QF + R+A+
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEC 76
Query: 413 NGQ 415
Q
Sbjct: 77 ESQ 79
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 36.6 bits (83), Expect = 0.047, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 354 RLYVGNLHF-NMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNL 412
RL++GNL N++++ L ++F P+G + + + FGF+QF + R+A+
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEX 76
Query: 413 NGQ 415
Q
Sbjct: 77 ESQ 79
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 36.6 bits (83), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 4/84 (4%)
Query: 246 RDQRTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPM 305
D +F QI DE+D+ F GK+ ++ ++ DR + KG ++ + + S
Sbjct: 11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALK 70
Query: 306 A-IALSGQ---PLLGQPVMVKPSE 325
A AL Q P + +P+ VKP++
Sbjct: 71 AQSALHEQKTLPGMNRPIQVKPAD 94
Score = 36.2 bits (82), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTV-ELVQLPLDETGHCKGFGFVQFARLED---ARNA 409
+L++G + N+ E L+ +FE FG + EL L TG KG F+ + E A++A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 410 LNLNGQLEIVGRAIKV 425
L+ L + R I+V
Sbjct: 75 LHEQKTLPGMNRPIQV 90
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 36.6 bits (83), Expect = 0.049, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLN 413
+++V NL F+ T L+ F G V + + E G KG G V+F E A A +
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSKGCGVVKFESPEVAERACRMM 68
Query: 414 GQLEIVGRAIKVSAVTDQSG 433
+++ GR I V + SG
Sbjct: 69 NGMKLSGREIDVRIDRNASG 88
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 36.2 bits (82), Expect = 0.050, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 354 RLYVGNLHF-NMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNL 412
RL++GNL N++++ L ++F P+G + + + FGF+QF + R+A+
Sbjct: 4 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEC 56
Query: 413 NGQ 415
Q
Sbjct: 57 ESQ 59
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 36.2 bits (82), Expect = 0.052, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 8/63 (12%)
Query: 354 RLYVGNLHF-NMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNL 412
RL++GNL N++++ L ++F P+G + + + FGF+QF + R+A+
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEC 64
Query: 413 NGQ 415
Q
Sbjct: 65 ESQ 67
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 36.2 bits (82), Expect = 0.054, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPL----DETGHCKGFGFVQFARLEDARNAL 410
+++GNL + E L F FG + +Q P +TG+ KG+ F+ FA + + A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 411 N-LNGQLEIVGRAIKVS 426
+NGQ + R I VS
Sbjct: 66 EAMNGQY-LCNRPITVS 81
>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 = 36.2 bits (82), Expect = 0.058, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALNLN 413
++VG+L +T + F PFG + ++ D TG KG+GFV F DA NA+
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 414 GQLEIVGRAIKVSAVT 429
G + GR I+ + T
Sbjct: 69 GGQWLGGRQIRTNWAT 84
Score = 32.7 bits (73), Expect = 0.61, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 273 GKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALSGQPLLG 316
G++ D R++ D + +SKG G+V F++ AI G LG
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG 74
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 36.2 bits (82), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 7/57 (12%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL 410
RL+V ++ E +L ++F PFG P+ E GF FV+F E A A+
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFG-------PMKEVKILNGFAFVEFEEAESAAKAI 82
Score = 32.7 bits (73), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
Query: 563 FDMDIKEDVEGEC-SKFGKLKHIFVEKDSAGFVYLRFENTQSAFAAQRALHGRWFAGKMI 621
F +D++E E FG +K + K GF ++ FE +SA A +HG+ FA + +
Sbjct: 39 FPLDVQESELNEIFGPFGPMKEV---KILNGFAFVEFEEAESAAKAIEEVHGKSFANQPL 95
Query: 622 TATF 625
+
Sbjct: 96 EVVY 99
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 36.2 bits (82), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 355 LYVGNLHFNMTEDQLR-QVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLN 413
L++GNL+ N + +L+ + E F +L + + TG + FG+V F ED AL L
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALELT 78
Query: 414 GQLEIVGRAIKV 425
G L++ G IK+
Sbjct: 79 G-LKVFGNEIKL 89
>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 = 0.070, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLNG 414
++V NL F+ T L+ F G V + + E G KG G V+F E A A +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKM-ENGKSKGCGVVKFESPEVAERACRMMN 66
Query: 415 QLEIVGRAIKVSAVTDQSG 433
+++ GR I V + SG
Sbjct: 67 GMKLSGREIDVRIDRNASG 85
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 35.8 bits (81), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNL-N 413
++V NL + + +L++VF G V + D+ G +G G V F + +A A+++ N
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFN 77
Query: 414 GQL 416
GQL
Sbjct: 78 GQL 80
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 35.8 bits (81), Expect = 0.083, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 11/82 (13%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGH-CKGFGFVQFARLEDARNALNLN 413
LY+ L T+ L ++ +P+G + + LD+T + CKG+GFV F A+ A+
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT-- 65
Query: 414 GQLEIVGRAIKVSAVTDQSGLQ 435
A+K S V Q Q
Sbjct: 66 --------ALKASGVQAQMAKQ 79
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 35.4 bits (80), Expect = 0.095, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 7/71 (9%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL-NLN 413
+Y G + +T+ +RQ F PFG + +++ + KG+ FV+F+ E A +A+ ++N
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVN 82
Query: 414 GQLEIVGRAIK 424
G I G +K
Sbjct: 83 GT-TIEGHVVK 92
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 35.4 bits (80), Expect = 0.099, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGH----CKGFGFVQFARLEDARNAL 410
L++ NL+F+ TE+ L+ VF G ++ + + GFGFV++ + E A+ AL
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
>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 = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 262 ERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSV 303
++D+ ++F++ G+V D + D N+ RS+G G++ F D SV
Sbjct: 25 KKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASV 66
Score = 31.2 bits (69), Expect = 2.1, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQF 400
+ +VG L ++ ++ L+ F FG V + D TG +GFGF+ F
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF 60
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 568 KEDVEGECSKFGKLKHIFVEKDSAGFVYLRFENTQSAFAAQRALHGRWFAGKMI 621
K DVE SK+GK+ V K GF ++++ N ++A AA GR AG+++
Sbjct: 30 KSDVEAIFSKYGKIVGCSVHK---GFAFVQYVNERNARAAVAGEDGRMIAGQVL 80
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 17/84 (20%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFE-----------PFGTVELVQLPLDETGHCKGFGFVQFA 401
RRLYVGN+ F +TE+ + F P V VQ+ D K F F++F
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFR 61
Query: 402 RLEDARNALNLNGQLEIVGRAIKV 425
+++ A+ +G + G+++K+
Sbjct: 62 SVDETTQAMAFDGII-FQGQSLKI 84
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 34.7 bits (78), Expect = 0.15, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 39/73 (53%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLN 413
+L++ L F+ T+++L ++ + GTV+ ++L + G KG +V++ A A+
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKM 78
Query: 414 GQLEIVGRAIKVS 426
+ I IKV+
Sbjct: 79 DGMTIKENIIKVA 91
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 34.7 bits (78), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 43/80 (53%), Gaps = 2/80 (2%)
Query: 355 LYVGNLHFNMTEDQLRQVF-EPFGTVELVQLPLDETGHCKGFGFVQFA-RLEDARNALNL 412
L+VG+L ++ + L + F + + + ++ LD+TG KG+GFV+F LE R
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 413 NGQLEIVGRAIKVSAVTDQS 432
G + + + +++S ++
Sbjct: 72 QGAVGLGSKPVRLSVAIPKA 91
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 34.7 bits (78), Expect = 0.16, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 17/84 (20%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFE-----------PFGTVELVQLPLDETGHCKGFGFVQFA 401
RRLYVGN+ F +TE+ + F P V VQ+ D K F F++F
Sbjct: 2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFR 56
Query: 402 RLEDARNALNLNGQLEIVGRAIKV 425
+++ A+ +G + G+++K+
Sbjct: 57 SVDETTQAMAFDGII-FQGQSLKI 79
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 34.7 bits (78), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 30/54 (55%)
Query: 568 KEDVEGECSKFGKLKHIFVEKDSAGFVYLRFENTQSAFAAQRALHGRWFAGKMI 621
K ++E S +G L+ +++ ++ GF ++ FE+ + A A R L G+ G +
Sbjct: 14 KGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRV 67
Score = 33.5 bits (75), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 6/77 (7%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL-NL 412
++YVGNL + +L + F +G + V + + GF FV+F DA +A+ L
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP----GFAFVEFEDPRDAEDAVRGL 57
Query: 413 NGQLEIVGRAIKVSAVT 429
+G++ I G ++V T
Sbjct: 58 DGKV-ICGSRVRVELST 73
>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 = 0.18, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL-NLN 413
+++ NL ++ L F FG + ++ DE G KG+GFV F E A A+ +N
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAIEKMN 66
Query: 414 GQL 416
G L
Sbjct: 67 GML 69
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 33/60 (55%)
Query: 251 VFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALS 310
+F + + + + E+F + G+V++ ++ D ++RS+G G+V F D V +A S
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Score = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 5/50 (10%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVE---LVQLPLDETGHCKGFGFVQF 400
++++G L + T++ LR+ F FG V+ +++ PL T +GFGFV F
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL--TKRSRGFGFVTF 74
>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 = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 17/84 (20%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFE-----------PFGTVELVQLPLDETGHCKGFGFVQFA 401
RRLYVGN+ F +TE+ + F P V VQ+ D K F F++F
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFR 59
Query: 402 RLEDARNALNLNGQLEIVGRAIKV 425
+++ A+ +G + G+++K+
Sbjct: 60 SVDETTQAMAFDG-IIFQGQSLKI 82
Score = 33.1 bits (74), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNAL- 410
+L++G L + +DQ++++ FG ++ L D TG KG+ F ++ + A+
Sbjct: 115 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 174
Query: 411 NLNG 414
LNG
Sbjct: 175 GLNG 178
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 8/73 (10%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLNG 414
++VG +MTED+LR+ F +G V V +P + F FV FA D + A +L G
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFA---DDQIAQSLCG 60
Query: 415 Q-LEIVGRAIKVS 426
+ L I G ++ +S
Sbjct: 61 EDLIIKGISVHIS 73
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 568 KEDVEGECSKFGKLKHIFVEKDSAGFVYLRFENTQSAFAAQRALHGRWFAG 618
K ++E +G L+ ++V ++ GF ++ FE+ + A A R L GR G
Sbjct: 87 KTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCG 137
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL 410
++YVGNL N + +L + F +G + V + + GF FV+F DA +A+
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP----PGFAFVEFEDPRDAADAV 127
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 33.9 bits (76), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 568 KEDVEGECSKFGKLKHIFVEKDSAGFVYLRFENTQSAFAAQRALHGRWFAG 618
K ++E +G L+ ++V ++ GF ++ FE+ + A A R L GR G
Sbjct: 87 KTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTLCG 137
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL-NL 412
++YVGNL N + +L + F +G + V + + GF FV+F DA +A+ +L
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP----PGFAFVEFEDPRDAADAVRDL 130
Query: 413 NGQLEIVGRAIKV 425
+G+ + G ++V
Sbjct: 131 DGRT-LCGCRVRV 142
>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 = 0.29, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALN 411
R LY+ NL + +T +++ +F +G + Q+ + T +G +V + + DA+NA++
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIR--QIRVGNTPETRGTAYVVYEDIFDAKNAVD 65
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 33.9 bits (76), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 4/85 (4%)
Query: 247 DQRTVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMA 306
D +F QI DE+D+ F G++ ++ ++ DR + KG ++ + S A
Sbjct: 14 DAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
Query: 307 -IALSGQ---PLLGQPVMVKPSEAE 327
AL Q P + +P+ VKP+ +E
Sbjct: 74 QSALHEQKTLPGMNRPIQVKPAASE 98
Score = 32.3 bits (72), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTV-ELVQLPLDETGHCKGFGFVQFARLED---ARNA 409
+L+VG + + E L+ +FE FG + EL L TG KG F+ + + A++A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 410 LNLNGQLEIVGRAIKVSAVTDQ 431
L+ L + R I+V +
Sbjct: 77 LHEQKTLPGMNRPIQVKPAASE 98
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 33.9 bits (76), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 5/50 (10%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVE---LVQLPLDETGHCKGFGFVQF 400
++++G L + T++ LR+ F FG V+ +++ PL T +GFGFV F
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL--TKRSRGFGFVTF 49
Score = 33.5 bits (75), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 34/64 (53%)
Query: 251 VFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAIALS 310
+F + + + + E+F + G+V++ ++ D ++RS+G G+V F D V +A S
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 311 GQPL 314
L
Sbjct: 63 RHEL 66
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 33.9 bits (76), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE---TGHCKGFGFVQFARLEDARNALN 411
LY+GNL + T++ L + G +++++ E G KGF V ++ ++
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 412 LNGQLEIVGRAIKVSAVTDQ 431
L + E+ G+ V+ V Q
Sbjct: 131 LLPKRELHGQNPVVTPVNKQ 150
>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 = 33.9 bits (76), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 17/84 (20%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFE-----------PFGTVELVQLPLDETGHCKGFGFVQFA 401
RRLYVGN+ F +TE+ + F P V VQ+ D K F F++F
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFR 61
Query: 402 RLEDARNALNLNGQLEIVGRAIKV 425
+++ A+ +G + G+++K+
Sbjct: 62 SVDETTQAMAFDG-IIFQGQSLKI 84
Score = 32.3 bits (72), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNAL- 410
+L++G L + +DQ++++ FG ++ L D TG KG+ F ++ + A+
Sbjct: 97 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 156
Query: 411 NLNG 414
LNG
Sbjct: 157 GLNG 160
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 33.5 bits (75), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 17/84 (20%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFE-----------PFGTVELVQLPLDETGHCKGFGFVQFA 401
RRLYVGN+ F +TE+ + F P V VQ+ D K F F++F
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFR 59
Query: 402 RLEDARNALNLNGQLEIVGRAIKV 425
+++ A+ +G + G+++K+
Sbjct: 60 SVDETTQAMAFDG-IIFQGQSLKI 82
Score = 32.3 bits (72), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 353 RRLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNAL- 410
+L++G L + +DQ++++ FG ++ L D TG KG+ F ++ + A+
Sbjct: 95 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154
Query: 411 NLNG 414
LNG
Sbjct: 155 GLNG 158
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 33.5 bits (75), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 9/73 (12%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL-NL 412
+++VGN+ T +LR +FE G V + D + FV + DA+ A+ L
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQL 63
Query: 413 NGQLEIVGRAIKV 425
NG+ E+ G+ I V
Sbjct: 64 NGK-EVKGKRINV 75
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 33.5 bits (75), Expect = 0.40, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALNLN 413
L V L +MT+ +L +F G + ++ D +TG+ G+ FV F D++ A+ +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 414 GQLEIVGRAIKVS 426
+ + + +KVS
Sbjct: 66 NGITVRNKRLKVS 78
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 33.1 bits (74), Expect = 0.43, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNAL-N 411
+L++G L + +DQ++++ FG ++ L D TG KG+ F ++ + A+
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 412 LNG 414
LNG
Sbjct: 63 LNG 65
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 33.1 bits (74), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 7/66 (10%)
Query: 363 NMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL-NLNG-QLEIVG 420
+MT LR F PFG + + L +D +C FV + ++E A A+ LNG Q+E V
Sbjct: 24 DMTPTLLRGAFSPFGNI--IDLSMDPPRNC---AFVTYEKMESADQAVAELNGTQVESVQ 78
Query: 421 RAIKVS 426
+ ++
Sbjct: 79 LKVNIA 84
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 33.1 bits (74), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 9/79 (11%)
Query: 549 LKNMFDPKNETYEEFDMDI------KEDVEGECSKFGKLKHIFVEKDSAGFVYLRFENTQ 602
+ N DPK+ F ++ K DVE SK+G++ V K G+ ++++ N +
Sbjct: 17 VTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK---GYAFVQYSNER 73
Query: 603 SAFAAQRALHGRWFAGKMI 621
A AA +GR AG+ +
Sbjct: 74 HARAAVLGENGRVLAGQTL 92
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 33.1 bits (74), Expect = 0.50, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALNLN 413
+L++GNL TE ++R +FE +G V E K +GFV A +A+
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVL-------ECDIIKNYGFVHIEDKTAAEDAIRNL 62
Query: 414 GQLEIVGRAIKVSAVTDQS 432
++ G I V A ++S
Sbjct: 63 HHYKLHGVNINVEASKNKS 81
>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 = 32.7 bits (73), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 7/66 (10%)
Query: 363 NMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL-NLNG-QLEIVG 420
+MT LR F PFG + + L +D +C FV + ++E A A+ LNG Q+E V
Sbjct: 48 DMTPTLLRGAFSPFGNI--IDLSMDPPRNC---AFVTYEKMESADQAVAELNGTQVESVQ 102
Query: 421 RAIKVS 426
+ ++
Sbjct: 103 LKVNIA 108
>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 = 32.7 bits (73), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 365 TEDQLRQVFEPFGTV--ELVQLPLDETGHCKGFGFVQFARLEDARNALNLNGQ-LEIVGR 421
TED +R + G E+ + +G +GF FV+F+ L+DA + N L I+G+
Sbjct: 14 TEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQ 73
Query: 422 AIKV 425
+ +
Sbjct: 74 KVSM 77
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 32.3 bits (72), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 356 YVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETG--HCKGFGFVQF 400
++GNL +++TE+ +++ F + V+LP + + KGFG+ +F
Sbjct: 23 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEF 68
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 32.3 bits (72), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 356 YVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETG--HCKGFGFVQF 400
++GNL +++TE+ +++ F + V+LP + + KGFG+ +F
Sbjct: 19 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEF 64
>pdb|2HGM|A Chain A, Nmr Structure Of The Second Qrrm Domain Of Human Hnrnp F
pdb|2KG0|A Chain A, Structure Of The Second Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 126
Score = 32.3 bits (72), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 359 NLHFNMTEDQLRQVFEPFGTV-ELVQLPLDETGHCKGFGFVQFARLEDARNALN 411
L F T++++ Q F V + LP+D G G FVQFA E A AL
Sbjct: 49 GLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG 102
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALNLN 413
L++ +L T+ L F PFG V ++ +D +T K FGFV F + A+ A+
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 414 GQLEIVGRAIKV 425
++ + +KV
Sbjct: 103 NGFQVGTKRLKV 114
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 353 RRLYVGNLHFNMT-EDQLRQVFEPFGTVELVQLPLDETGHC--KGFGFVQFARLEDARNA 409
R + + NL + E+ LR+ FE FG++E + +P + H F F + A A
Sbjct: 211 REIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAERA 270
Query: 410 LNLNGQLEIVGRAIKVS 426
L N L + R I VS
Sbjct: 271 LQXNRSL-LGNREISVS 286
>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 = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 369 LRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNAL 410
L +F G V ++ P+DE TG KGF FV+ + DA+ +
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKII 71
>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 = 31.2 bits (69), Expect = 1.9, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 369 LRQVFEPFGTVELVQLPLDE-TGHCKGFGFVQFARLEDARNAL 410
L +F G V ++ P+DE TG KGF FV+ + DA+ +
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKII 71
>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 = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 30/58 (51%)
Query: 250 TVFAYQICLKADERDVYEFFSRAGKVRDVRLIMDRNSRRSKGVGYVEFYDVMSVPMAI 307
+F Y + + ++D+ + F G V ++ +D+ + SK G+V + + +S AI
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 84
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLD-ETGHCKGFGFVQFARLEDARNALNLN 413
L++ +L + L Q+F PFG V ++ +D +T K FGFV + A+ A+
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 414 GQLEIVGRAIKV 425
+I + +KV
Sbjct: 88 NGFQIGMKRLKV 99
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 31.2 bits (69), Expect = 2.0, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCK-GFGFVQFARLEDARNAL-N 411
+LY+GNL +T D LRQ+F +LPL K G+ FV + A A+
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGD------RKLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63
Query: 412 LNGQLEIVGRAIKV 425
L+G++E+ G+ ++V
Sbjct: 64 LSGKVELHGKIMEV 77
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 30.4 bits (67), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 22/46 (47%)
Query: 593 FVYLRFENTQSAFAAQRALHGRWFAGKMITATFMVPQTYEAKFPDS 638
+ ++ F N + A A +AL+G+ G I T P ++ P S
Sbjct: 53 YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSS 98
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 30.0 bits (66), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL-NLN 413
L+V NL +TE+ L + F FG +E V+ K + F+ F + A A+ +N
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMN 66
Query: 414 GQ 415
G+
Sbjct: 67 GK 68
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 30.0 bits (66), Expect = 4.4, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDE---TGHCKGFGFVQFARLEDARNALN 411
LY+GNL + T++ L + G +++++ E G KGF V ++ ++
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 412 LNGQLEIVGR 421
L + E+ G+
Sbjct: 64 LLPKRELHGQ 73
>pdb|3ZZY|A Chain A, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZY|B Chain B, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|A Chain A, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|B Chain B, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
Length = 130
Score = 30.0 bits (66), Expect = 4.5, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 4/63 (6%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNA-LNL 412
R+ V NL + +T D L Q+F FGTV + + T + + +Q+A A++A L+L
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKI---ITFTKNNQFQALLQYADPVSAQHAKLSL 86
Query: 413 NGQ 415
+GQ
Sbjct: 87 DGQ 89
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 30.0 bits (66), Expect = 4.6, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 4/63 (6%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNA-LNL 412
R+ V NL + +T D L Q+F FGTV + + T + + +Q+A A++A L+L
Sbjct: 35 RIIVENLFYPVTLDVLHQIFSKFGTVLKI---ITFTKNNQFQALLQYADPVSAQHAKLSL 91
Query: 413 NGQ 415
+GQ
Sbjct: 92 DGQ 94
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 29.6 bits (65), Expect = 4.8, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 4/63 (6%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNA-LNL 412
R+ V NL + +T D L Q+F FGTV + + T + + +Q+A A++A L+L
Sbjct: 48 RIIVENLFYPVTLDVLHQIFSKFGTVLKI---ITFTKNNQFQALLQYADPVSAQHAKLSL 104
Query: 413 NGQ 415
+GQ
Sbjct: 105 DGQ 107
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 355 LYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNALN-LN 413
L+V NL +TE+ L + F FG +E V+ K + FV F A A++ +N
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVK-------KLKDYAFVHFEDRGAAVKAMDEMN 70
Query: 414 GQ 415
G+
Sbjct: 71 GK 72
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 29.6 bits (65), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 558 ETYEEFDMDIKEDVEGECSKFGKLKHIFVEKDSA----GFVYLRFENTQSAFAAQRALHG 613
E Y+EF ++ ++E K+G+++ + V + G VY++F + A A L+
Sbjct: 34 EHYDEFFEEVFTEME---EKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNN 90
Query: 614 RWFAGKMITA 623
RWF G+ I A
Sbjct: 91 RWFNGQPIHA 100
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 29.6 bits (65), Expect = 5.7, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 354 RLYVGNLHFNMTEDQLRQVFEPFGTVELVQLPLDETGHCKGFGFVQFARLEDARNAL 410
R+YVGNL ++ + VF +G + + L G F FV+F DA +A+
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG--PPFAFVEFEDPRDAEDAV 78
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
0.316 0.133 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,750,268
Number of Sequences: 62578
Number of extensions: 453129
Number of successful extensions: 1321
Number of sequences better than 100.0: 186
Number of HSP's better than 100.0 without gapping: 122
Number of HSP's successfully gapped in prelim test: 64
Number of HSP's that attempted gapping in prelim test: 928
Number of HSP's gapped (non-prelim): 346
length of query: 639
length of database: 14,973,337
effective HSP length: 105
effective length of query: 534
effective length of database: 8,402,647
effective search space: 4487013498
effective search space used: 4487013498
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)