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= 007742
(591 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 = 113 bits (283), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 54/103 (52%), Positives = 74/103 (71%)
Query: 207 KEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGY 266
+E V+ + ERD RTVF Q+ + RD+ +FFS GKVRDVR+I DRNSRRSKG+ Y
Sbjct: 12 REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 71
Query: 267 IEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSA 309
+EF ++ SVP+AI L+GQ LLG P++V+ S+AEKN + +S
Sbjct: 72 VEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGPSSG 114
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 43/79 (54%), Positives = 57/79 (72%), Gaps = 1/79 (1%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
+LYVG+LHFN+TE LR +FEPFG +E +QL +D ETG+ KG+GF+ F+ E AK A
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 383 LNGKLEIVGRTLKVSSVTD 401
LNG E+ GR +KV VT+
Sbjct: 88 LNG-FELAGRPMKVGHVTE 105
Score = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
++ + TE + F G++ ++L+MD + RSKG G+I F D A+ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 282 SGQLLLGQPVMV 293
+G L G+P+ V
Sbjct: 89 NGFELAGRPMKV 100
>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From Mus
Musculus
Length = 113
Score = 83.2 bits (204), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 43/93 (46%), Positives = 60/93 (64%), Gaps = 1/93 (1%)
Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTE 556
++C L NMF+P E + +D EI+ DV EEC+K+G V HIYVDK SA G VY++ S
Sbjct: 6 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIA 65
Query: 557 AAASAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
AA +A A+H RWFA ++I+A ++ Y F
Sbjct: 66 AAIAAVNALHGRWFAGKMITAAYVPLPTYHNLF 98
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 79.3 bits (194), Expect = 5e-15, Method: Composition-based stats.
Identities = 38/80 (47%), Positives = 55/80 (68%), Gaps = 1/80 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
LYVG+LHFN+TE LR +FEPFG ++ + L D +TG+ KG+GF+ F+ E A+ A L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 384 NGKLEIVGRTLKVSSVTDHV 403
NG E+ GR ++V VT+ +
Sbjct: 68 NG-FELAGRPMRVGHVTERL 86
Score = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
TE + F GK+ ++ L+ D ++ RSKG G+I F D A+ L+G L G+P+
Sbjct: 18 TEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPM 77
Query: 292 MV 293
V
Sbjct: 78 RV 79
>pdb|3S6E|A Chain A, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
pdb|3S6E|B Chain B, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
Length = 114
Score = 76.6 bits (187), Expect = 4e-14, Method: Composition-based stats.
Identities = 42/93 (45%), Positives = 58/93 (62%), Gaps = 1/93 (1%)
Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSA-GFVYLRFESTE 556
++C L N F+P E + +D EI+ DV EEC+K+G V HIYVDK SA G VY++ S
Sbjct: 7 TQCFQLSNXFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIA 66
Query: 557 AAASAQRAMHMRWFARRLISAIFMKPEDYEAKF 589
AA +A A+H RWFA + I+A ++ Y F
Sbjct: 67 AAIAAVNALHGRWFAGKXITAAYVPLPTYHNLF 99
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 50/175 (28%), Positives = 83/175 (47%), Gaps = 22/175 (12%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKGVGYIEFYDVM 273
P+ D +F Q+P +E+D+ E F + G V ++ ++ DR N +SKG ++ FY
Sbjct: 11 PDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRK 70
Query: 274 SVPMA-IALSGQLLL---GQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNL 329
+ A AL +L P+ +KP+++EKN DRKL++G +
Sbjct: 71 AALEAQNALHNMKVLPGMHHPIQMKPADSEKN---------------NAVEDRKLFIGMI 115
Query: 330 HFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
TE +R +F FG +E ++ L G +G FV F A+ A A++
Sbjct: 116 SKKCTENDIRVMFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
Score = 29.3 bits (64), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 524 DVEEECSKYGRVKHIYVDK-------RSAGFVYLRFESTEAAASAQRAMHMRWFARRLIS 576
D+ E +YG V I V + +S G ++ F + +AA AQ A+H +
Sbjct: 31 DLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHH 90
Query: 577 AIFMKPEDYE 586
I MKP D E
Sbjct: 91 PIQMKPADSE 100
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 65.1 bits (157), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 49/172 (28%), Positives = 81/172 (47%), Gaps = 22/172 (12%)
Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKGVGYIEFYDVMSVP 276
D +F Q+P +E+D+ E F + G V ++ ++ DR N +SKG ++ FY +
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 277 MA-IALSGQLLL---GQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFN 332
A AL +L P+ +KP+++EKN DRKL++G +
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPADSEKN---------------NAVEDRKLFIGMISKK 106
Query: 333 MTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
TE +R +F FG +E ++ L G +G FV F A+ A A++
Sbjct: 107 CTENDIRVMFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 524 DVEEECSKYGRVKHIYVDK-------RSAGFVYLRFESTEAAASAQRAMHMRWFARRLIS 576
D+ E +YG V I V + +S G ++ F + +AA AQ A+H +
Sbjct: 19 DLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHH 78
Query: 577 AIFMKPEDYE 586
I MKP D E
Sbjct: 79 PIQMKPADSE 88
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 64.3 bits (155), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 35/83 (42%), Positives = 50/83 (60%), Gaps = 4/83 (4%)
Query: 319 AIDRKL---YVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH 375
A+DR L +VGN+ + TE QL+ +F GPV +L D ETG+ KG+GF ++ E
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 376 AKAAQSALNGKLEIVGRTLKVSS 398
A +A LNG+ E GR L+V +
Sbjct: 63 ALSAMRNLNGR-EFSGRALRVDN 84
Score = 52.0 bits (123), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 49/86 (56%), Gaps = 1/86 (1%)
Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVP 276
+R R+VF +P +ATE + + FS+ G V RL+ DR + + KG G+ E+ D +
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 277 MAI-ALSGQLLLGQPVMVKPSEAEKN 301
A+ L+G+ G+ + V + +EKN
Sbjct: 65 SAMRNLNGREFSGRALRVDNAASEKN 90
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 41/160 (25%), Positives = 77/160 (48%), Gaps = 11/160 (6%)
Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
E +PE+ R +F + + T+ + F + G + D ++ D N++RS+G G++ +
Sbjct: 6 ESPKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 64
Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLH 330
V V A+ + G+ +V+P A A T +K++VG +
Sbjct: 65 TVEEVDAAMNARPHKVDGR--VVEPKRAVSREDSQRPGAHLTV--------KKIFVGGIK 114
Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
+ E LR FE +G +E++++ D +G+ +GF FV F
Sbjct: 115 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
RKL++G L F T+ LR FE +G + + D T + +GFGFV +A +E AA +
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 382 ALNGKLE 388
A K++
Sbjct: 75 ARPHKVD 81
Score = 33.9 bits (76), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/91 (18%), Positives = 43/91 (47%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
+ +F + E + ++F + GK+ + ++ DR S + +G ++ F D SV +
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 165
Query: 281 LSGQLLLGQPVMVKPSEAEKNLVQSNTSAGG 311
+ G V+ + +++ + +++S G
Sbjct: 166 QKYHTVNGHNCEVRKALSKQEMASASSSQRG 196
>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 = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 41/160 (25%), Positives = 77/160 (48%), Gaps = 11/160 (6%)
Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
E +PE+ R +F + + T+ + F + G + D ++ D N++RS+G G++ +
Sbjct: 4 ESPKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 62
Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLH 330
V V A+ + G+ +V+P A A T +K++VG +
Sbjct: 63 TVEEVDAAMNARPHKVDGR--VVEPKRAVSREDSQRPGAHLTV--------KKIFVGGIK 112
Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
+ E LR FE +G +E++++ D +G+ +GF FV F
Sbjct: 113 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
RKL++G L F T+ LR FE +G + + D T + +GFGFV +A +E AA +
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 382 ALNGKLE 388
A K++
Sbjct: 73 ARPHKVD 79
Score = 33.9 bits (76), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 17/91 (18%), Positives = 43/91 (47%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
+ +F + E + ++F + GK+ + ++ DR S + +G ++ F D SV +
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 163
Query: 281 LSGQLLLGQPVMVKPSEAEKNLVQSNTSAGG 311
+ G V+ + +++ + +++S G
Sbjct: 164 QKYHTVNGHNCEVRKALSKQEMASASSSQRG 194
>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 = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 41/160 (25%), Positives = 77/160 (48%), Gaps = 11/160 (6%)
Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
E +PE+ R +F + + T+ + F + G + D ++ D N++RS+G G++ +
Sbjct: 5 ESPKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLH 330
V V A+ + G+ +V+P A A T +K++VG +
Sbjct: 64 TVEEVDAAMNARPHKVDGR--VVEPKRAVSREDSQRPGAHLTV--------KKIFVGGIK 113
Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
+ E LR FE +G +E++++ D +G+ +GF FV F
Sbjct: 114 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
RKL++G L F T+ LR FE +G + + D T + +GFGFV +A +E AA +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 382 ALNGKLE 388
A K++
Sbjct: 74 ARPHKVD 80
Score = 33.9 bits (76), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/91 (18%), Positives = 43/91 (47%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
+ +F + E + ++F + GK+ + ++ DR S + +G ++ F D SV +
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164
Query: 281 LSGQLLLGQPVMVKPSEAEKNLVQSNTSAGG 311
+ G V+ + +++ + +++S G
Sbjct: 165 QKYHTVNGHNCEVRKALSKQEMASASSSQRG 195
>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 = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 38/150 (25%), Positives = 72/150 (48%), Gaps = 10/150 (6%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
R +F + + T+ + F + G + D ++ D N++RS+G G++ + V V A+
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 281 LSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRK 340
+ G+ +V+P A A T +K++VG + + E LR
Sbjct: 67 ARPHKVDGR--VVEPKRAVSREDSQRPGAHLTV--------KKIFVGGIKEDTEEHHLRD 116
Query: 341 LFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
FE +G +E++++ D +G+ +GF FV F
Sbjct: 117 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
RKL++G L F T+ LR FE +G + + D T + +GFGFV +A +E AA +
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 382 ALNGKLEIVGRTLK 395
A K++ GR ++
Sbjct: 67 ARPHKVD--GRVVE 78
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 15/86 (17%), Positives = 40/86 (46%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
+ +F + E + ++F + GK+ + ++ DR S + +G ++ F D SV +
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 157
Query: 281 LSGQLLLGQPVMVKPSEAEKNLVQSN 306
+ G V+ + +++ + ++
Sbjct: 158 QKYHTVNGHNCEVRKALSKQEMASAS 183
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 41/160 (25%), Positives = 77/160 (48%), Gaps = 11/160 (6%)
Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
E +PE+ R +F + + T+ + F + G + D ++ D N++RS+G G++ +
Sbjct: 5 ESPKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLH 330
V V A+ + G+ +V+P A A T +K++VG +
Sbjct: 64 TVEEVDAAMNARPHKVDGR--VVEPKRAVSREDSQRPGAHLTV--------KKIFVGGIK 113
Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
+ E LR FE +G +E++++ D +G+ +GF FV F
Sbjct: 114 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
RKL++G L F T+ LR FE +G + + D T + +GFGFV +A +E AA +
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 382 ALNGKLE 388
A K++
Sbjct: 74 ARPHKVD 80
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/74 (20%), Positives = 33/74 (44%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
+ +F + E + ++F + GK+ + ++ DR S + +G ++ F D SV +
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164
Query: 281 LSGQLLLGQPVMVK 294
+ G V+
Sbjct: 165 QKYHTVNGHNCEVR 178
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 41/160 (25%), Positives = 77/160 (48%), Gaps = 11/160 (6%)
Query: 211 EPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
E +PE+ R +F + + T+ + F + G + D ++ D N++RS+G G++ +
Sbjct: 3 ESPKEPEQ-LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 61
Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLH 330
V V A+ + G+ +V+P A A T +K++VG +
Sbjct: 62 TVEEVDAAMNARPHKVDGR--VVEPKRAVSREDSQRPGAHLTV--------KKIFVGGIK 111
Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
+ E LR FE +G +E++++ D +G+ +GF FV F
Sbjct: 112 EDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
Score = 49.7 bits (117), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 38/67 (56%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
RKL++G L F T+ LR FE +G + + D T + +GFGFV +A +E AA +
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 382 ALNGKLE 388
A K++
Sbjct: 72 ARPHKVD 78
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/74 (20%), Positives = 33/74 (44%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
+ +F + E + ++F + GK+ + ++ DR S + +G ++ F D SV +
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 162
Query: 281 LSGQLLLGQPVMVK 294
+ G V+
Sbjct: 163 QKYHTVNGHNCEVR 176
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 45/74 (60%), Gaps = 1/74 (1%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
KL+VG L F+ E L ++F +G + V + D ET + +GFGFV F ++ AK A A
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 383 LNGKLEIVGRTLKV 396
+NGK + GR ++V
Sbjct: 74 MNGK-SVDGRQIRV 86
Score = 42.0 bits (97), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
D+ +F + E+ + + FSK G++ +V ++ DR ++RS+G G++ F ++ A
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 279 -IALSGQLLLGQPVMV 293
+A++G+ + G+ + V
Sbjct: 71 MMAMNGKSVDGRQIRV 86
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 517 FDLEIQGDVEEECSKYGRVKHIYVDK-----RSAGFVYLRFESTEAAASAQRAMHMRWFA 571
FD Q +E+ SKYG++ + V K RS GF ++ FE+ + A A AM+ +
Sbjct: 22 FDTNEQ-SLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD 80
Query: 572 RRLI 575
R I
Sbjct: 81 GRQI 84
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/83 (39%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
G R LYVG L + + L F PFG + +Q+PLD ET + +GF FV+F E
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 375 HAKAAQSALNGKLEIVGRTLKVS 397
A AA +N + E+ GRT++V+
Sbjct: 61 DAAAAIDNMN-ESELFGRTIRVN 82
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 33/88 (37%), Positives = 49/88 (55%), Gaps = 1/88 (1%)
Query: 310 GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 369
G + + R LYVG L + + L F PFG + +Q+PLD ET + +GF FV+
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKVS 397
F E A AA +N + E+ GRT++V+
Sbjct: 61 FELAEDAAAAIDNMN-ESELFGRTIRVN 87
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 60.1 bits (144), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 34/86 (39%), Positives = 50/86 (58%), Gaps = 1/86 (1%)
Query: 312 TATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFA 371
T P + R L V + + E QLR+LFE +GP+E V++ D ET Q +G+GFV+F
Sbjct: 33 TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ 92
Query: 372 QLEHAKAAQSALNGKLEIVGRTLKVS 397
A+ A + LNG I+ + LKV+
Sbjct: 93 SGSSAQQAIAGLNG-FNILNKRLKVA 117
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 213 EADPERD-QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
+ +PE D R + +P E + + F + G + V+++ DR +R+S+G G+++F
Sbjct: 34 QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
Query: 272 VMSVPMAIA 280
S AIA
Sbjct: 94 GSSAQQAIA 102
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
R LYVG L + + L F PFG + +Q+PLD ET + +GF FV+F E A AA
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 382 ALNGKLEIVGRTLKVS 397
+N + E+ GRT++V+
Sbjct: 63 NMN-ESELFGRTIRVN 77
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
R LYVG L + + L F PFG + +Q+PLD ET + +GF FV+F E A AA
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 382 ALNGKLEIVGRTLKVS 397
+N + E+ GRT++V+
Sbjct: 66 NMN-ESELFGRTIRVN 80
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
R LYVG L + + L F PFG + +Q+PLD ET + +GF FV+F E A AA
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 382 ALNGKLEIVGRTLKVS 397
+N + E+ GRT++V+
Sbjct: 124 NMN-ESELFGRTIRVN 138
>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 = 59.3 bits (142), Expect = 6e-09, Method: Composition-based stats.
Identities = 49/170 (28%), Positives = 76/170 (44%), Gaps = 22/170 (12%)
Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKGVGYIEFYDVMSVP 276
D F Q+P +E+D+ E F + G V ++ ++ DR N +SKG ++ FY +
Sbjct: 2 DAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 277 MAI-ALSGQLLL---GQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFN 332
A AL +L P+ KP+++EKN DRKL++G +
Sbjct: 62 EAQNALHNXKVLPGXHHPIQXKPADSEKN---------------NAVEDRKLFIGXISKK 106
Query: 333 MTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
TE +R F FG +E ++ L G +G FV F A+ A A
Sbjct: 107 CTENDIRVXFSSFGQIEECRI-LRGPDGLSRGCAFVTFTTRAXAQTAIKA 155
Score = 33.5 bits (75), Expect = 0.33, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG--QCKGFGFVQFAQLEHAKAAQ 380
K +VG + +E LR+LFE +G V + + D Q KG FV F + A AQ
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 381 SALN 384
+AL+
Sbjct: 65 NALH 68
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 58.9 bits (141), Expect = 7e-09, Method: Composition-based stats.
Identities = 46/157 (29%), Positives = 72/157 (45%), Gaps = 15/157 (9%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLL 287
+P T+R++Y F G + R++ D + S G +++F M AI ++L
Sbjct: 11 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI----KVLN 66
Query: 288 GQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGP 347
G V K L S GG + D LYV NL +T+ QL +F +G
Sbjct: 67 GITVR------NKRLKVSYARPGGESIK-----DTNLYVTNLPRTITDDQLDTIFGKYGS 115
Query: 348 VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
+ + D TG+ +G FV++ + E A+ A SALN
Sbjct: 116 IVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
A + L V L +MT+ +L LF GP+ ++ D +TG G+ FV F ++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 379 AQSALNGKLEIVGRTLKVS 397
A LNG + + + LKVS
Sbjct: 61 AIKVLNG-ITVRNKRLKVS 78
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 58.9 bits (141), Expect = 8e-09, Method: Composition-based stats.
Identities = 39/177 (22%), Positives = 90/177 (50%), Gaps = 15/177 (8%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
R ++ + TE + ++F G + ++++++D+N++ + ++E++ +A+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNK-NVNYAFVEYHQSHDANIAL- 58
Query: 281 LSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRK 340
Q L G+ + E N+V+ N + + + L+VG+L+ N+ + LR
Sbjct: 59 ---QTLNGKQI-------ENNIVKINWAFQSQQSSSDDTFN--LFVGDLNVNVDDETLRN 106
Query: 341 LFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVS 397
F+ F + D++TG +G+GFV F + A+ A ++ G+ ++ GR L+++
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ-DLNGRPLRIN 162
>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 = 58.2 bits (139), Expect = 1e-08, Method: Composition-based stats.
Identities = 40/145 (27%), Positives = 68/145 (46%), Gaps = 31/145 (21%)
Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVM 292
TE ++ E+F K G V D++++ D + RS+G G++ F
Sbjct: 16 TEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFE---------------------- 53
Query: 293 VKPSEAEKNLVQSNTSAGGTATGPYGAIDR-------KLYVGNLHFNMTETQLRKLFEPF 345
KPS ++ +V++ G P AI R K++VG + ++ + + F +
Sbjct: 54 -KPSSVDE-VVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQW 111
Query: 346 GPVELVQLPLDIETGQCKGFGFVQF 370
G + QL LD +TGQ +GFGFV +
Sbjct: 112 GTIIDAQLMLDKDTGQSRGFGFVTY 136
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 41/68 (60%), Gaps = 3/68 (4%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF---AQLEHAKAA 379
K+++G L+++ TE LR+ F +G V +++ D TG+ +GFGF+ F + ++
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 380 QSALNGKL 387
Q L+GK+
Sbjct: 65 QHILDGKV 72
>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 = 57.8 bits (138), Expect = 2e-08, Method: Composition-based stats.
Identities = 47/170 (27%), Positives = 73/170 (42%), Gaps = 15/170 (8%)
Query: 215 DPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMS 274
DP + +P T+R++Y F G + R+ D + S G +++F
Sbjct: 9 DPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXD 68
Query: 275 VPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMT 334
AI ++L G V K L S GG + D LYV NL +T
Sbjct: 69 SQRAI----KVLNGITVR------NKRLKVSYARPGGESIK-----DTNLYVTNLPRTIT 113
Query: 335 ETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALN 384
+ QL +F +G + + D TG+ +G FV++ + E A+ A SALN
Sbjct: 114 DDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
>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 = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/163 (25%), Positives = 73/163 (44%), Gaps = 23/163 (14%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
+P T+ + F G++ +L+ D+ + +S G G++ + D AI L+G L
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL 69
Query: 287 LGQPVMV---KPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFE 343
+ + V +PS A D LYV L MT+ +L +LF
Sbjct: 70 QTKTIKVSYARPSSASIR-------------------DANLYVSGLPKTMTQKELEQLFS 110
Query: 344 PFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK 386
+G + ++ +D TG +G GF++F + A+ A LNG+
Sbjct: 111 QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L V L NMT+ + R LF G +E +L D TGQ G+GFV + + A+ A + L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 384 NGKLEIVGRTLKVS 397
NG L + +T+KVS
Sbjct: 65 NG-LRLQTKTIKVS 77
>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 = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 44/156 (28%), Positives = 72/156 (46%), Gaps = 17/156 (10%)
Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
TE +YE FS AG + +R+ D +RRS G Y+ F A+ ++ ++ G+PV
Sbjct: 23 TEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 82
Query: 292 MVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELV 351
+ S+ + +L +S +++ NL ++ L F FG +
Sbjct: 83 RIMWSQRDPSLRKSGVG--------------NIFIKNLDKSIDNKALYDTFSAFGNILSC 128
Query: 352 QLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKL 387
++ D E G KG+GFV F E A+ A +NG L
Sbjct: 129 KVVCD-ENGS-KGYGFVHFETQEAAERAIEKMNGML 162
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
LYVG+LH ++TE L + F P GP+ +++ D+ T + G+ +V F Q A+ A +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 384 NGKLEIVGRTLKV 396
N + I G+ +++
Sbjct: 73 NFDV-IKGKPVRI 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 = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 44/156 (28%), Positives = 72/156 (46%), Gaps = 17/156 (10%)
Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
TE +YE FS AG + +R+ D +RRS G Y+ F A+ ++ ++ G+PV
Sbjct: 28 TEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 87
Query: 292 MVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELV 351
+ S+ + +L +S +++ NL ++ L F FG +
Sbjct: 88 RIMWSQRDPSLRKSGVG--------------NIFIKNLDKSIDNKALYDTFSAFGNILSC 133
Query: 352 QLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKL 387
++ D E G KG+GFV F E A+ A +NG L
Sbjct: 134 KVVCD-ENGS-KGYGFVHFETQEAAERAIEKMNGML 167
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 9/90 (10%)
Query: 315 GPYGAID--------RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFG 366
GP G+++ LYVG+LH ++TE L + F P GP+ +++ D+ T + G+
Sbjct: 1 GPLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYA 60
Query: 367 FVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
+V F Q A+ A +N + I G+ +++
Sbjct: 61 YVNFQQPADAERALDTMNFDV-IKGKPVRI 89
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 55.8 bits (133), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 48/78 (61%), Gaps = 1/78 (1%)
Query: 319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
AI ++YVG++++ + E +R+ F PFGP++ + + D T + KGF FV++ E A+
Sbjct: 26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL 85
Query: 379 AQSALNGKLEIVGRTLKV 396
A +N + + GR +KV
Sbjct: 86 ALEQMNSVM-LGGRNIKV 102
Score = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 38/172 (22%), Positives = 86/172 (50%), Gaps = 23/172 (13%)
Query: 234 ERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMV 293
E + + F+ G ++ + + D + + KG ++E+ + +A+ ++LG
Sbjct: 42 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLG----- 96
Query: 294 KPSEAEKNLVQSNTSAGGTATGPYGAIDR---------KLYVGNLHFNMTETQLRKLFEP 344
+N+ S G A P ID+ ++YV ++H ++++ ++ +FE
Sbjct: 97 -----GRNIKVGRPSNIGQAQ-PI--IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 148
Query: 345 FGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
FG ++ L D TG+ KG+GF+++ + + ++ A S++N ++ G+ L+V
Sbjct: 149 FGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN-LFDLGGQYLRV 199
Score = 29.3 bits (64), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 19/88 (21%), Positives = 39/88 (44%), Gaps = 6/88 (6%)
Query: 205 EKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGV 264
+ + +++ A+ R ++ + ++ D+ F GK++ L D + + KG
Sbjct: 110 QAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGY 169
Query: 265 GYIEFYDVMSVPMAIA------LSGQLL 286
G+IE+ S A++ L GQ L
Sbjct: 170 GFIEYEKAQSSQDAVSSMNLFDLGGQYL 197
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 55.8 bits (133), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 72/163 (44%), Gaps = 23/163 (14%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
+P T+ + F G + +L+ D+ + +S G G++ + D AI L+G L
Sbjct: 12 LPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKL 71
Query: 287 LGQPVMV---KPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFE 343
+ + V +PS A D LYV L M++ ++ +LF
Sbjct: 72 QTKTIKVSYARPSSASIR-------------------DANLYVSGLPKTMSQKEMEQLFS 112
Query: 344 PFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK 386
+G + ++ LD TG +G GF++F + A+ A LNG+
Sbjct: 113 QYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 155
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L V L NMT+ + + LF G +E +L D TGQ G+GFV ++ A A + L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 384 NGKLEIVGRTLKVS 397
NG L++ +T+KVS
Sbjct: 67 NG-LKLQTKTIKVS 79
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 55.5 bits (132), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 32/76 (42%), Positives = 48/76 (63%), Gaps = 2/76 (2%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
R +YVGNL ++ T Q+++LF FG V V+L D ET + KGFGFV+ Q E A +
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIA 60
Query: 382 ALNGKLEIVGRTLKVS 397
L+ + +GRT++V+
Sbjct: 61 KLDN-TDFMGRTIRVT 75
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 47/83 (56%), Gaps = 2/83 (2%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA 280
R ++ + AT V E FS+ GKV +V+LI DR +++ KG G++E + SV AIA
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIA 60
Query: 281 -LSGQLLLGQPVMVKPSEAEKNL 302
L +G+ + V + +K+L
Sbjct: 61 KLDNTDFMGRTIRVTEANPKKSL 83
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 48/78 (61%), Gaps = 1/78 (1%)
Query: 319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
AI ++YVG++++ + E +R+ F PFGP++ + + D T + KGF FV++ E A+
Sbjct: 11 AIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL 70
Query: 379 AQSALNGKLEIVGRTLKV 396
A +N + + GR +KV
Sbjct: 71 ALEQMNSVM-LGGRNIKV 87
Score = 53.1 bits (126), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 39/165 (23%), Positives = 90/165 (54%), Gaps = 9/165 (5%)
Query: 234 ERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVM 292
E + + F+ G ++ + + D + + KG ++E+ + +A+ ++ +L G+ +
Sbjct: 27 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIK 86
Query: 293 V-KPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELV 351
V +PS N+ Q+ A A +R +YV ++H ++++ ++ +FE FG ++
Sbjct: 87 VGRPS----NIGQAQPIIDQLAEEAR-AFNR-IYVASVHQDLSDDDIKSVFEAFGKIKSC 140
Query: 352 QLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
L D TG+ KG+GF+++ + + ++ A S++N ++ G+ L+V
Sbjct: 141 TLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN-LFDLGGQYLRV 184
Score = 29.3 bits (64), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 19/88 (21%), Positives = 39/88 (44%), Gaps = 6/88 (6%)
Query: 205 EKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGV 264
+ + +++ A+ R ++ + ++ D+ F GK++ L D + + KG
Sbjct: 95 QAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGY 154
Query: 265 GYIEFYDVMSVPMAIA------LSGQLL 286
G+IE+ S A++ L GQ L
Sbjct: 155 GFIEYEKAQSSQDAVSSMNLFDLGGQYL 182
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
+L+V NL + +E L KLF +GP+ + P+D T + KGF FV F EHA A +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 383 LNGKLEIVGRTLKV 396
++G++ GR L V
Sbjct: 70 VDGQV-FQGRMLHV 82
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 45/89 (50%), Gaps = 1/89 (1%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF-YDVMSVPMAIAL 281
+F + ++E D+ + FS G + ++ +D +++ KG ++ F + +V +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 282 SGQLLLGQPVMVKPSEAEKNLVQSNTSAG 310
GQ+ G+ + V PS +K QS S+G
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEASQSGPSSG 99
>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 = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 37/159 (23%), Positives = 70/159 (44%), Gaps = 17/159 (10%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
+P T+ ++ FS G+V +LI D+ + S G G++ + AI L+G L
Sbjct: 10 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 69
Query: 287 LGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG 346
+ + V + +++ D LY+ L MT+ + +F FG
Sbjct: 70 QSKTIKVSYARPSSEVIK----------------DANLYISGLPRTMTQKDVEDMFSRFG 113
Query: 347 PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
+ ++ +D TG +G F++F + A+ A ++ NG
Sbjct: 114 RIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
L V L NMT+ +LR LF G VE +L D G G+GFV + + A+ A +
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 383 LNGKLEIVGRTLKVS 397
LNG L + +T+KVS
Sbjct: 64 LNG-LRLQSKTIKVS 77
>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 = 37/159 (23%), Positives = 70/159 (44%), Gaps = 17/159 (10%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
+P T+ ++ FS G+V +LI D+ + S G G++ + AI L+G L
Sbjct: 10 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 69
Query: 287 LGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG 346
+ + V + +++ D LY+ L MT+ + +F FG
Sbjct: 70 QSKTIKVSYARPSSEVIK----------------DANLYISGLPRTMTQKDVEDMFSRFG 113
Query: 347 PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
+ ++ +D TG +G F++F + A+ A ++ NG
Sbjct: 114 RIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
L V L NMT+ +LR LF G VE +L D G G+GFV + + A+ A +
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 63
Query: 383 LNGKLEIVGRTLKVS 397
LNG L + +T+KVS
Sbjct: 64 LNG-LRLQSKTIKVS 77
>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 = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
AI ++YVG++++ + E +R+ F PFGP++ + D T + KGF FV++ E A+
Sbjct: 10 AIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQL 69
Query: 379 AQSALNGKLEIVGRTLKV 396
A N + + GR +KV
Sbjct: 70 ALEQXN-SVXLGGRNIKV 86
Score = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 37/172 (21%), Positives = 82/172 (47%), Gaps = 23/172 (13%)
Query: 234 ERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMV 293
E + + F+ G ++ + D + + KG ++E+ + +A+ + LG
Sbjct: 26 EDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGG---- 81
Query: 294 KPSEAEKNLVQSNTSAGGTATGPYGAIDR---------KLYVGNLHFNMTETQLRKLFEP 344
+N+ S G A ID+ ++YV ++H ++++ ++ +FE
Sbjct: 82 ------RNIKVGRPSNIGQAQP---IIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 132
Query: 345 FGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
FG ++ L D TG+ KG+GF+++ + + ++ A S+ N ++ G+ L+V
Sbjct: 133 FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN-LFDLGGQYLRV 183
Score = 29.6 bits (65), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 6/60 (10%)
Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA------LSGQLL 286
++ D+ F GK++ L D + + KG G+IE+ S A++ L GQ L
Sbjct: 122 SDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYL 181
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 53.1 bits (126), Expect = 4e-07, Method: Composition-based stats.
Identities = 33/100 (33%), Positives = 50/100 (50%), Gaps = 1/100 (1%)
Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIE-TGQCKGFG 366
S+G + P K+ V N+ F + ++R+LF FG ++ V+LP + TG +GFG
Sbjct: 2 SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61
Query: 367 FVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQ 406
FV F + AK A +AL + GR L + V Q
Sbjct: 62 FVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101
Score = 30.8 bits (68), Expect = 2.5, Method: Composition-based stats.
Identities = 24/92 (26%), Positives = 48/92 (52%), Gaps = 6/92 (6%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRS-KGVGYIEFY---DVMSVPMA 278
+ +P +A +R++ E FS G+++ VRL + +G G+++F D A
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 77
Query: 279 IALSGQLLLGQPVMVKPSEAEKNLVQSNTSAG 310
+ S L G+ ++++ +++E VQS S+G
Sbjct: 78 LCHSTH-LYGRRLVLEWADSEVT-VQSGPSSG 107
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
LYV NL + + +LRK F PFG + ++ + E G+ KGFGFV F+ E A A + +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 384 NGKL 387
NG++
Sbjct: 76 NGRI 79
>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 = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L+V ++H E ++++ F +G ++ + L LD TG KG+ V++ + A AA+ AL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 384 NGKLEIVGRTLKVS 397
NG EI+G+T++V
Sbjct: 135 NG-AEIMGQTIQVD 147
Score = 36.2 bits (82), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 3/73 (4%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI--A 280
+F + +A E ++ E F G+++++ L +DR + SKG +E Y+ +A A
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE-YETHKQALAAKEA 133
Query: 281 LSGQLLLGQPVMV 293
L+G ++GQ + V
Sbjct: 134 LNGAEIMGQTIQV 146
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L V NL + + LR++FE +G V V +P + T +GF FV+F A+ A++A+
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 384 NGKLEIVGRTLKV 396
+G E+ GR L+V
Sbjct: 76 DG-AELDGRELRV 87
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L V NL + + LR++FE +G V V +P D T + +GF FV+F A+ A A+
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 384 NGKLEIVGRTLKV 396
+G + + GR L+V
Sbjct: 133 DGAV-LDGRELRV 144
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 241 FSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK 294
F K G+V DV + DR ++ S+G ++ F+D A+ A+ G +L G+ + V+
Sbjct: 91 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ 145
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 531 KYGRVKHIYV-----DKRSAGFVYLRFESTEAAASAQRAM 565
KYGRV +Y+ K S GF ++RF A A AM
Sbjct: 93 KYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 22/52 (42%), Positives = 33/52 (63%)
Query: 220 QRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
+ TV+ +P T D+Y FSK GKV V ++ D+++R+SKGV +I F D
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLD 67
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L V L TE LR++F +GP+ V + D ++ + +GF FV F ++ AK A+
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 384 NGKLEIVGRTLKVS 397
NG +E+ GR ++VS
Sbjct: 78 NG-MELDGRRIRVS 90
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 31/47 (65%)
Query: 226 YQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
+ + L TERD+ E FSK G + DV ++ D+ SRRS+G ++ F +V
Sbjct: 21 FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
Score = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 524 DVEEECSKYGRVKHIYV-----DKRSAGFVYLRFESTEAAASA-QRAMHMRWFARRL 574
D+ E SKYG + + + +RS GF ++ FE+ + A A +RA M RR+
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
L V L NMT+ +LR LF G VE +L D G G+GFV + + A+ A +
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 383 LNGKLEIVGRTLKVS 397
LNG L + +T+KVS
Sbjct: 66 LNG-LRLQSKTIKVS 79
Score = 30.0 bits (66), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
+P T+ ++ FS G+V +LI D+ + S G G++ + AI L+G L
Sbjct: 12 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 71
Query: 287 LGQPVMV---KPS 296
+ + V +PS
Sbjct: 72 QSKTIKVSYARPS 84
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 40/64 (62%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
R +Y+G++ ++ TE Q+ L GPV +++ D +TG+ KG+ F++F LE + +A
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 382 ALNG 385
LNG
Sbjct: 64 NLNG 67
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 32/59 (54%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
R V+ +P TE + + S G V +++++ D + RSKG +IEF D+ S A+
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 46/74 (62%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L+V ++H E ++++ F +G ++ + L LD TG KG+ V++ + A AA+ AL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 384 NGKLEIVGRTLKVS 397
NG EI+G+T++V
Sbjct: 89 NGA-EIMGQTIQVD 101
Score = 37.0 bits (84), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 5/87 (5%)
Query: 211 EPEADPER--DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIE 268
E E P+R + +F + +A E ++ E F G+++++ L +DR + SKG +E
Sbjct: 15 ELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE 74
Query: 269 FYDVMSVPMAI--ALSGQLLLGQPVMV 293
Y+ +A AL+G ++GQ + V
Sbjct: 75 -YETHKQALAAKEALNGAEIMGQTIQV 100
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L V NL + + LR++FE +G V V +P D T + +GF FV+F A+ A A+
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 384 NGKLEIVGRTLKV 396
+G + + GR L+V
Sbjct: 110 DGAV-LDGRELRV 121
Score = 32.3 bits (72), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 241 FSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMVK 294
F K G+V DV + DR ++ S+G ++ F+D A+ A+ G +L G+ + V+
Sbjct: 68 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ 122
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 531 KYGRVKHIYV-----DKRSAGFVYLRFESTEAAASAQRAM 565
KYGRV +Y+ K S GF ++RF A A AM
Sbjct: 70 KYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 50.1 bits (118), Expect = 3e-06, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 40/64 (62%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
R +Y+G++ ++ TE Q+ L GPV +++ D +TG+ KG+ F++F LE + +A
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 382 ALNG 385
LNG
Sbjct: 65 NLNG 68
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 32/59 (54%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
R V+ +P TE + + S G V +++++ D + RSKG +IEF D+ S A+
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 50.1 bits (118), Expect = 3e-06, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 40/64 (62%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
R +Y+G++ ++ TE Q+ L GPV +++ D +TG+ KG+ F++F LE + +A
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 382 ALNG 385
LNG
Sbjct: 63 NLNG 66
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 32/59 (54%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI 279
R V+ +P TE + + S G V +++++ D + RSKG +IEF D+ S A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
>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 = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 37/174 (21%), Positives = 74/174 (42%), Gaps = 9/174 (5%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDV-----RLIMDRNSRRSKGVGYIEFYDVMSV 275
R ++ +P TE + +FF+ ++ + ++ + K ++EF V
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 276 PMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAI----DRKLYVGNLHF 331
A+A G + GQ + ++ + L + + G + KL++G L
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 332 NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
+ + Q+++L FGP++ L D TG KG+ F ++ + A + LNG
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 178
Score = 37.7 bits (86), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 45/96 (46%), Gaps = 19/96 (19%)
Query: 318 GAIDRKLYVGNLHFNMTETQLRKLFE-----------PFGPVELVQLPLDIETGQCKGFG 366
GA+ R+LYVGN+ F +TE + F P PV VQ+ Q K F
Sbjct: 1 GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFA 54
Query: 367 FVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH 402
F++F ++ A A +G + G++LK+ D+
Sbjct: 55 FLEFRSVDETTQAM-AFDGII-FQGQSLKIRRPHDY 88
Score = 28.5 bits (62), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L 281
+F +P + V E + G ++ L+ D + SKG + E+ D+ AIA L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 282 SGQLLLGQPVMVK 294
+G L + ++V+
Sbjct: 177 NGMQLGDKKLLVQ 189
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 50.1 bits (118), Expect = 4e-06, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 41/78 (52%)
Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
S+G + + + V NL + ET L++LF PFG + + L D TGQ KGF F
Sbjct: 2 SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61
Query: 368 VQFAQLEHAKAAQSALNG 385
+ F + E A A + ++G
Sbjct: 62 ISFHRREDAARAIAGVSG 79
Score = 31.2 bits (69), Expect = 1.6, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 27/62 (43%)
Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
D T+ + E D+ E F G + + L D+ + +SKG +I F+ A
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 279 IA 280
IA
Sbjct: 74 IA 75
>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 = 50.1 bits (118), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 37/175 (21%), Positives = 73/175 (41%), Gaps = 21/175 (12%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDV-----RLIMDRNSRRSKGVGYIEFY 270
P R ++ +P TE + +FF+ ++ + ++ + K ++EF
Sbjct: 2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR 61
Query: 271 DVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLH 330
V A+A G + GQ + ++ + L ++ KL++G L
Sbjct: 62 SVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAH----------------KLFIGGLP 105
Query: 331 FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
+ + Q+++L FGP++ L D TG KG+ F ++ + A + LNG
Sbjct: 106 NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 160
Score = 28.9 bits (63), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 1/80 (1%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
P +F +P + V E + G ++ L+ D + SKG + E+ D+
Sbjct: 92 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 151
Query: 276 PMAIA-LSGQLLLGQPVMVK 294
AIA L+G L + ++V+
Sbjct: 152 DQAIAGLNGMQLGDKKLLVQ 171
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/82 (34%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
D +YVG L ++E L +LF GPV +P D TGQ +G+GFV+F E A A
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 381 SALNGKLEIVGRTLKVSSVTDH 402
++ +++ G+ ++V+ + H
Sbjct: 75 KIMD-MIKLYGKPIRVNKASAH 95
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 32/97 (32%), Positives = 51/97 (52%), Gaps = 5/97 (5%)
Query: 217 ERDQR-TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
ER+Q TV+ + K +E ++E F +AG V + + DR + + +G G++EF
Sbjct: 11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70
Query: 276 PMAIALSGQL-LLGQPVMV-KPSEAEKNLVQSNTSAG 310
AI + + L G+P+ V K S KNL S S+G
Sbjct: 71 DYAIKIMDMIKLYGKPIRVNKASAHNKNL--SGPSSG 105
>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 = 47/101 (46%), Gaps = 7/101 (6%)
Query: 495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-------RSAGF 547
G P+E L L NM P D + EI DV +ECSKYG VK I + + G
Sbjct: 1 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGK 60
Query: 548 VYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 588
+++ F S A + + R FA R++ + P+ Y +
Sbjct: 61 IFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRR 101
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 36/170 (21%), Positives = 72/170 (42%), Gaps = 21/170 (12%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDV-----RLIMDRNSRRSKGVGYIEFYDVMSV 275
R ++ +P TE + +FF+ ++ + ++ + K ++EF V
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 276 PMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTE 335
A+A G + GQ + ++ + L ++ KL++G L + +
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGAH----------------KLFIGGLPNYLND 108
Query: 336 TQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
Q+++L FGP++ L D TG KG+ F ++ + A + LNG
Sbjct: 109 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 158
Score = 28.9 bits (63), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L 281
+F +P + V E + G ++ L+ D + SKG + E+ D+ AIA L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 282 SGQLLLGQPVMVK 294
+G L + ++V+
Sbjct: 157 NGMQLGDKKLLVQ 169
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 49.3 bits (116), Expect = 6e-06, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 501 LLLKNMFDPA-METDPDFDLEIQGDVEEECSKYGRVKHIYV-DKRSAGFVYLRFESTEAA 558
+++KNMF P E DP EI+ D+ ECSK+G+++ + + D+ G + F E A
Sbjct: 18 VIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEA 77
Query: 559 ASAQRAMHMRWFARRLISA 577
+ + RWF R I+A
Sbjct: 78 DYCIQTLDGRWFGGRQITA 96
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 49.3 bits (116), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L V L TE LR++F +GP+ V + D ++ + +GF FV F ++ AK A+
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 384 NGKLEIVGRTLKV 396
NG +E+ GR ++V
Sbjct: 75 NG-MELDGRRIRV 86
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 31/47 (65%)
Query: 226 YQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
+ + L TERD+ E FSK G + DV ++ D+ SRRS+G ++ F +V
Sbjct: 18 FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 64
Score = 30.0 bits (66), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 524 DVEEECSKYGRVKHIYV-----DKRSAGFVYLRFESTEAAASA-QRAMHMRWFARRL 574
D+ E SKYG + + + +RS GF ++ FE+ + A A +RA M RR+
Sbjct: 28 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 84
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 48.9 bits (115), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
K++VG L ++ T+ LRK FE FG +E + D +TG+ +G+GFV A + A A ++
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA--DRAAAERAC 76
Query: 383 LNGKLEIVGRTLKVS 397
+ I GR V+
Sbjct: 77 KDPNPIIDGRKANVN 91
Score = 32.3 bits (72), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 26/49 (53%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYD 271
+F +P T+ + ++F G + + +I DR + +S+G G++ D
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 68
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L V L TE LR++F +GP+ V + D ++ + +GF FV F ++ AK A+
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 384 NGKLEIVGRTLKV 396
NG +E+ GR ++V
Sbjct: 109 NG-MELDGRRIRV 120
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 31/47 (65%)
Query: 226 YQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
+ + L TERD+ E FSK G + DV ++ D+ SRRS+G ++ F +V
Sbjct: 52 FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 98
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 524 DVEEECSKYGRVKHIYV-----DKRSAGFVYLRFESTEAAASA-QRAMHMRWFARRL 574
D+ E SKYG + + + +RS GF ++ FE+ + A A +RA M RR+
Sbjct: 62 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 118
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 48/92 (52%), Gaps = 15/92 (16%)
Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAG---------FV 548
S ++L+NM DP D D +++G+V EEC K+G V + + + G +
Sbjct: 15 STVMVLRNMVDP-----KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 69
Query: 549 YLRFESTEAAASAQRAMHMRWFA-RRLISAIF 579
++ F A +A++ RWFA R++++ ++
Sbjct: 70 FVEFSIASETHKAIQALNGRWFAGRKVVAEVY 101
>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 = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 47/92 (51%), Gaps = 9/92 (9%)
Query: 204 KEKKEVVEPEADPERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKG 263
+EKKE+ D+R+V+ + +T +D+ FS G + + ++ D+ S KG
Sbjct: 29 EEKKEI---------DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKG 79
Query: 264 VGYIEFYDVMSVPMAIALSGQLLLGQPVMVKP 295
YIEF + SV A+A+ + G+ + V P
Sbjct: 80 YAYIEFAERNSVDAAVAMDETVFRGRTIKVLP 111
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
R +YVGN+ + T L F G + + + D +G KG+ +++FA+ AA
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA-V 95
Query: 382 ALNGKLEIVGRTLKV 396
A++ + GRT+KV
Sbjct: 96 AMDETV-FRGRTIKV 109
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 14/89 (15%)
Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAG---------FV 548
S ++L+NM DP D D +++G+V EEC K+G V + + + G +
Sbjct: 124 STVMVLRNMVDP-----KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 178
Query: 549 YLRFESTEAAASAQRAMHMRWFARRLISA 577
++ F A +A++ RWFA R + A
Sbjct: 179 FVEFSIASETHKAIQALNGRWFAGRKVVA 207
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 41/75 (54%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
+F +P E ++ E+F K G V +V +I D +R +G G+I F D SV A+ +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 283 GQLLLGQPVMVKPSE 297
++G+ V VK +E
Sbjct: 73 FHDIMGKKVEVKRAE 87
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 4/75 (5%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
K++VG + N ET+LR+ F+ FG V V + D E + +GFGF+ F E ++ A
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF---EDEQSVDQA 68
Query: 383 LNGKL-EIVGRTLKV 396
+N +I+G+ ++V
Sbjct: 69 VNMHFHDIMGKKVEV 83
>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 = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 29/96 (30%), Positives = 53/96 (55%), Gaps = 6/96 (6%)
Query: 204 KEKKEVVEPEADPERDQRTV-----FAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS 258
+E + VE + D QR+V F + +ATE D+++ F++ G+++++ L +DR +
Sbjct: 2 REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 61
Query: 259 RRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
KG +E+ A+ L+GQ L+GQP+ V
Sbjct: 62 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 97
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 47/87 (54%), Gaps = 2/87 (2%)
Query: 311 GTATGPYGAIDR-KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 369
G GP +++ L+V +H TE + F +G ++ + L LD TG KG+ V+
Sbjct: 12 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71
Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKV 396
+ + A+AA LNG+ +++G+ + V
Sbjct: 72 YETYKEAQAAMEGLNGQ-DLMGQPISV 97
>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 = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 29/96 (30%), Positives = 53/96 (55%), Gaps = 6/96 (6%)
Query: 204 KEKKEVVEPEADPERDQRTV-----FAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNS 258
+E + VE + D QR+V F + +ATE D+++ F++ G+++++ L +DR +
Sbjct: 1 REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 60
Query: 259 RRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPVMV 293
KG +E+ A+ L+GQ L+GQP+ V
Sbjct: 61 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 96
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 47/87 (54%), Gaps = 2/87 (2%)
Query: 311 GTATGPYGAIDR-KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 369
G GP +++ L+V +H TE + F +G ++ + L LD TG KG+ V+
Sbjct: 11 GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70
Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKV 396
+ + A+AA LNG+ +++G+ + V
Sbjct: 71 YETYKEAQAAMEGLNGQ-DLMGQPISV 96
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 29/74 (39%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L V L NMT+ + + LF G +E +L D TGQ G+GFV ++ A A + L
Sbjct: 7 LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 384 NGKLEIVGRTLKVS 397
NG L++ +T+KVS
Sbjct: 67 NG-LKLQTKTIKVS 79
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L V L TE LR++F +GP+ V + D ++ + +GF FV F ++ AK A+
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 384 NGKLEIVGRTLKV 396
NG +E+ GR ++V
Sbjct: 78 NG-MELDGRRIRV 89
Score = 46.6 bits (109), Expect = 4e-05, Method: Composition-based stats.
Identities = 20/47 (42%), Positives = 31/47 (65%)
Query: 226 YQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDV 272
+ + L TERD+ E FSK G + DV ++ D+ SRRS+G ++ F +V
Sbjct: 21 FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67
Score = 30.4 bits (67), Expect = 2.7, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 524 DVEEECSKYGRVKHIYV-----DKRSAGFVYLRFESTEAAASA-QRAMHMRWFARRL 574
D+ E SKYG + + + +RS GF ++ FE+ + A A +RA M RR+
Sbjct: 31 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 31/99 (31%), Positives = 46/99 (46%), Gaps = 7/99 (7%)
Query: 497 PSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-------RSAGFVY 549
P+E L L NM P D + EI DV +ECSKYG VK I + + G ++
Sbjct: 3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIF 62
Query: 550 LRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 588
+ F S A + + R FA R++ + P+ Y +
Sbjct: 63 VEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRR 101
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L+VG+L+ N+ + LR F+ F + D++TG +G+GFV F + A+ A ++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 384 NGKLEIVGRTLKVS 397
G+ ++ GR L+++
Sbjct: 64 QGQ-DLNGRPLRIN 76
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/51 (45%), Positives = 32/51 (62%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
L V L + TE L++ F FG V +VQ+ D++TG KGFGFV+F + E
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
Score = 37.7 bits (86), Expect = 0.018, Method: Composition-based stats.
Identities = 17/42 (40%), Positives = 27/42 (64%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
+P K TE+D+ E+FS G+V V++ D + SKG G++ F
Sbjct: 23 LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
RKL+VG L+ +E +R+LFE FG +E + L G KG FV+++ A+AA +
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTI-LRGPDGNSKGCAFVKYSSHAEAQAAIN 74
Query: 382 ALNGKLEIVG 391
AL+G + G
Sbjct: 75 ALHGSQTMPG 84
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 34/61 (55%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
RKL++G L F TE LR +E +G + + D + + +GFGFV F+ + AA +
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 382 A 382
A
Sbjct: 88 A 88
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 51/100 (51%), Gaps = 7/100 (7%)
Query: 217 ERDQ-RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
E++Q R +F + + TE + ++ + GK+ D ++ D S+RS+G G++ F + V
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 276 PMAIALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATG 315
A+A + G+ +V+P K V S G ++G
Sbjct: 83 DAAMAARPHSIDGR--VVEP----KRAVAREESGSGPSSG 116
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
DRKL+VG L+ +E + +LF+PFG ++ + L G KG FV+F+ A+AA
Sbjct: 15 DRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTV-LRGPDGSSKGCAFVKFSSHTEAQAAI 73
Query: 381 SALNGKLEIVG 391
AL+G + G
Sbjct: 74 HALHGSQTMPG 84
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 11/90 (12%)
Query: 496 SPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYV------DKRSAGFVY 549
P++ +LL+NM A E D D ++E + EEC KYG+V + A ++
Sbjct: 6 CPTKVVLLRNMVG-AGEVDEDLEVETK----EECEKYGKVGKCVIFEIPGAPDDEAVRIF 60
Query: 550 LRFESTEAAASAQRAMHMRWFARRLISAIF 579
L FE E+A A ++ R+F R++ A F
Sbjct: 61 LEFERVESAIKAVVDLNGRYFGGRVVKACF 90
>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
pdb|3V4M|B Chain B, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
Length = 105
Score = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 31/101 (30%), Positives = 46/101 (45%), Gaps = 7/101 (6%)
Query: 495 GSPSECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-------RSAGF 547
G P+E L L N P D + EI DV +ECSKYG VK I + + G
Sbjct: 2 GHPTEVLCLXNXVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGK 61
Query: 548 VYLRFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 588
+++ F S A + + R FA R++ + 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 = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
DRKL+VG L T+ +RK+FEPFG ++ + L G KG FV+F A+AA
Sbjct: 12 DRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTV-LRGPDGTSKGCAFVKFQTHAEAQAAI 70
Query: 381 SALNGKLEIVG 391
+ L+ + G
Sbjct: 71 NTLHSSRTLPG 81
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
D L V NL ++T+ Q +L PFG +E L TGQ KG+GF ++ + + A A+
Sbjct: 95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 381 SALNGKLEIVGRTLKV 396
S L GK + RTL V
Sbjct: 155 SDLLGK-PLGPRTLYV 169
>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 = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
D L V NL ++T+ Q +L PFG +E L TGQ KG+GF ++ + + A A+
Sbjct: 93 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 152
Query: 381 SALNGKLEIVGRTLKV 396
S L GK + RTL V
Sbjct: 153 SDLLGK-PLGPRTLYV 167
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
D L V NL ++T+ Q +L PFG +E L TGQ KG+GF ++ + + A A+
Sbjct: 95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 381 SALNGKLEIVGRTLKV 396
S L GK + RTL V
Sbjct: 155 SDLLGK-PLGPRTLYV 169
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
+ L+V ++++ TE++LR+ FE +GP++ + + +G+ +G+ F+++ +A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 382 ALNGKLEIVGRTLKVS 397
+GK +I GR + V
Sbjct: 163 HADGK-KIDGRRVLVD 177
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 46.2 bits (108), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 46/84 (54%), Gaps = 2/84 (2%)
Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
S+G + + AI KL++G + N+ E L+ LFE FG + + + D TG KG F
Sbjct: 2 SSGSSGMKDHDAI--KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAF 59
Query: 368 VQFAQLEHAKAAQSALNGKLEIVG 391
+ + + E A AQSAL+ + + G
Sbjct: 60 LTYCERESALKAQSALHEQKTLPG 83
Score = 35.4 bits (80), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 4/85 (4%)
Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVP 276
+ D +F Q+P E+D+ F + GK+ ++ ++ DR + KG ++ + + S
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69
Query: 277 MA-IALSGQLLL---GQPVMVKPSE 297
A AL Q L +P+ VKP++
Sbjct: 70 KAQSALHEQKTLPGMNRPIQVKPAD 94
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 46.2 bits (108), Expect = 5e-05, Method: Composition-based stats.
Identities = 29/74 (39%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L V L N T+ +LR LF G VE +L D G G+GFV + + A+ A + L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 384 NGKLEIVGRTLKVS 397
NG L + +T+KVS
Sbjct: 82 NG-LRLQSKTIKVS 94
Score = 30.4 bits (67), Expect = 2.6, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 4/73 (5%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLL 286
+P T+ ++ FS G+V +LI D+ + S G G++ + AI L+G L
Sbjct: 27 LPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL 86
Query: 287 LGQPVMV---KPS 296
+ + V +PS
Sbjct: 87 QSKTIKVSYARPS 99
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 46/76 (60%), Gaps = 5/76 (6%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
+ L + NL ++ TE L+++FE +++P + + G+ KG+ F++FA E AK A
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQN-QNGKSKGYAFIEFASFEDAKEAL 70
Query: 381 SALNGKLEIVGRTLKV 396
++ N K EI GR +++
Sbjct: 71 NSCN-KREIEGRAIRL 85
>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 = 45.8 bits (107), Expect = 6e-05, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 36/56 (64%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
+K++VG L + E ++R+ F FG VE ++LP+D +T + +GF F+ F + E K
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 57
>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 = 45.4 bits (106), Expect = 8e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L+V +H TE + F +G ++ + L LD TG KG+ V++ + A+AA L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 384 NGKLEIVGRTLKV 396
NG+ +++G+ + V
Sbjct: 70 NGQ-DLMGQPISV 81
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 40/64 (62%), Gaps = 1/64 (1%)
Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQ 289
+ATE D+++ F++ G+++++ L +DR + KG +E+ A+ L+GQ L+GQ
Sbjct: 18 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ 77
Query: 290 PVMV 293
P+ V
Sbjct: 78 PISV 81
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 45.4 bits (106), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
+ L+V ++++ TE++LR+ FE +GP++ + + +G+ +G+ F+++ +A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 382 ALNGKLEIVGRTLKVS 397
+GK +I GR + V
Sbjct: 163 HADGK-KIDGRRVLVD 177
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 45.4 bits (106), Expect = 8e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L+V +H TE + F +G ++ + L LD TG KG+ V++ + A+AA L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 384 NGKLEIVGRTLKV 396
NG+ +++G+ + V
Sbjct: 70 NGQ-DLMGQPISV 81
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 40/64 (62%), Gaps = 1/64 (1%)
Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQ 289
+ATE D+++ F++ G+++++ L +DR + KG +E+ A+ L+GQ L+GQ
Sbjct: 18 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ 77
Query: 290 PVMV 293
P+ V
Sbjct: 78 PISV 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 = 45.4 bits (106), Expect = 8e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L+V +H TE + F +G ++ + L LD TG KG+ V++ + A+AA L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 384 NGKLEIVGRTLKV 396
NG+ +++G+ + V
Sbjct: 72 NGQ-DLMGQPISV 83
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 40/64 (62%), Gaps = 1/64 (1%)
Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQ 289
+ATE D+++ F++ G+++++ L +DR + KG +E+ A+ L+GQ L+GQ
Sbjct: 20 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ 79
Query: 290 PVMV 293
P+ V
Sbjct: 80 PISV 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 = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L+V +H TE + F +G ++ + L LD TG KG+ V++ + A+AA L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 384 NGKLEIVGRTLKV 396
NG+ +++G+ + V
Sbjct: 70 NGQ-DLMGQPISV 81
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 40/64 (62%), Gaps = 1/64 (1%)
Query: 231 KATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQ 289
+ATE D+++ F++ G+++++ L +DR + KG +E+ A+ L+GQ L+GQ
Sbjct: 18 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ 77
Query: 290 PVMV 293
P+ V
Sbjct: 78 PISV 81
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 31/77 (40%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
DR ++VGNL + E L +LF GP+ V + D E G+ K FGFV F E A
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAI 74
Query: 381 SALNGKLEIVGRTLKVS 397
+ LNG + + GR + VS
Sbjct: 75 ALLNG-IRLYGRPINVS 90
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVP 276
E RTVF + + E +YE F +AG + V + DR + K G++ F SV
Sbjct: 13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPESVS 71
Query: 277 MAIA-LSGQLLLGQPVMV 293
AIA L+G L G+P+ V
Sbjct: 72 YAIALLNGIRLYGRPINV 89
>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 = 27/98 (27%), Positives = 49/98 (50%), Gaps = 5/98 (5%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-AL 281
VF + + T D+ F+ G++ D R++ D + +SKG G++ F++ AI +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 282 SGQLLLGQPV----MVKPSEAEKNLVQSNTSAGGTATG 315
GQ L G+ + + A K+ +SNT G ++G
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
++VG+L +T ++ F PFG + ++ D+ TG+ KG+GFV F A+ A +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 384 NGKLEIVGRTLKVSSVT 400
G+ + GR ++ + T
Sbjct: 78 GGQW-LGGRQIRTNWAT 93
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 29/84 (34%), Positives = 48/84 (57%), Gaps = 3/84 (3%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
++L+V N+ F + LR++F FG + V++ + E G KGFGFV F A A+
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGS-KGFGFVTFENSADADRARE 73
Query: 382 ALNGKLEIVGRTLKVSSVTDHVGT 405
L+G + + GR ++V++ T V T
Sbjct: 74 KLHGTV-VEGRKIEVNNATARVMT 96
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
+ L+V L + TE L++ F+ G V ++ D ETG KGFGFV F E AKAA+
Sbjct: 16 KTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 382 AL 383
A+
Sbjct: 73 AM 74
Score = 32.3 bits (72), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 221 RTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
+T+F + TE + E F G VR R++ DR + SKG G+++F
Sbjct: 16 KTLFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDF 61
>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 = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 36/64 (56%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
D LYV NL +T+ QL +F +G + + D TG+ +G FV++ + E A+ A
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 381 SALN 384
SALN
Sbjct: 73 SALN 76
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
KL++G L+ E L+ +F GP+ V L D T + +GF F+ F AK A
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKD 67
Query: 383 LNGKLEIVGRTLKV 396
+NGK + G+ +KV
Sbjct: 68 MNGK-SLHGKAIKV 80
Score = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 8/101 (7%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L 281
+F + + E+ + F K G + +V LI DR S +S+G +I F + A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKDM 68
Query: 282 SGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDR 322
+G+ L G+ + V+ +A+K QS GG P + +R
Sbjct: 69 NGKSLHGKAIKVE--QAKKPSFQS----GGRRRPPASSRNR 103
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 28/82 (34%), Positives = 47/82 (57%), Gaps = 3/82 (3%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
++L+V N+ F + LR++F FG + V++ + E G KGFGFV F A A+
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-ERGS-KGFGFVTFENSADADRARE 87
Query: 382 ALNGKLEIVGRTLKVSSVTDHV 403
L+G + + GR ++V++ T V
Sbjct: 88 KLHGTV-VEGRKIEVNNATARV 108
>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 = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 46/92 (50%), Gaps = 15/92 (16%)
Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDKRSAG---------FV 548
S +L+N DP D D +++G+V EEC K+G V + + + G +
Sbjct: 20 STVXVLRNXVDP-----KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKI 74
Query: 549 YLRFESTEAAASAQRAMHMRWFA-RRLISAIF 579
++ F A +A++ RWFA R++++ ++
Sbjct: 75 FVEFSIASETHKAIQALNGRWFAGRKVVAEVY 106
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 37/66 (56%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
D LYV L M++ ++ +LF +G + ++ LD TG +G GF++F + A+ A
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 381 SALNGK 386
LNG+
Sbjct: 61 KGLNGQ 66
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 45/76 (59%), Gaps = 3/76 (3%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-A 280
++ +P +++++ + FS+ G++ R+++D+ + S+GVG+I F + AI
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 281 LSGQLLLG--QPVMVK 294
L+GQ LG +P+ VK
Sbjct: 63 LNGQKPLGAAEPITVK 78
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 34/54 (62%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
++VG L + E ++R+ F FG VE ++LP+D +T + +GF F+ F + E K
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK 55
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA---- 379
+++G L ++ T+ L+ F FG V L LD TG+ +GFGFV F + E
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 380 QSALNGKL 387
+ LNGK+
Sbjct: 62 EHKLNGKV 69
Score = 36.6 bits (83), Expect = 0.045, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 29/43 (67%)
Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
T++D+ ++FSK G+V D L +D + RS+G G++ F + SV
Sbjct: 12 TKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESV 54
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 43.1 bits (100), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 33/60 (55%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
LY+ L T+ L KL +P+G + + LD T +CKG+GFV F A+ A +AL
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Score = 29.6 bits (65), Expect = 5.5, Method: Composition-based stats.
Identities = 10/37 (27%), Positives = 23/37 (62%)
Query: 233 TERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
T++D+ + GK+ + I+D+ + + KG G+++F
Sbjct: 18 TDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDF 54
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 34/63 (53%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
KL++G L + + Q+++L FGP++ L D TG KG+ F ++ + A +
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 383 LNG 385
LNG
Sbjct: 63 LNG 65
Score = 28.5 bits (62), Expect = 9.6, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L 281
+F +P + V E + G ++ L+ D + SKG + E+ D+ AIA L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 282 SGQLLLGQPVMVK 294
+G L + ++V+
Sbjct: 64 NGMQLGDKKLLVQ 76
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 30/87 (34%), Positives = 44/87 (50%), Gaps = 4/87 (4%)
Query: 310 GGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQ 369
G GP G L++ +L T+T L F PFG V ++ +D +T K FGFV
Sbjct: 32 GKQIEGPEGC---NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVS 88
Query: 370 FAQLEHAKAAQSALNGKLEIVGRTLKV 396
F + A+ A A+NG ++ + LKV
Sbjct: 89 FDNPDSAQVAIKAMNG-FQVGTKRLKV 114
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 42.7 bits (99), Expect = 5e-04, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L 281
VF + + T D+ F+ GK+ D R++ D + +SKG G++ FY+ + AI +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 282 SGQLLLGQPV 291
GQ L G+ +
Sbjct: 78 GGQWLGGRQI 87
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
++VG+L +T ++ F PFG + ++ D+ TG+ KG+GFV F A+ A +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 384 NGKLEIVGRTLKVSSVT 400
G+ + GR ++ + T
Sbjct: 78 GGQW-LGGRQIRTNWAT 93
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 42.4 bits (98), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 32/93 (34%), Positives = 49/93 (52%), Gaps = 4/93 (4%)
Query: 304 QSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCK 363
QS +AG GP GA L++ +L + L ++F PFG V ++ +D +T K
Sbjct: 11 QSIGAAGSQKEGPEGA---NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 67
Query: 364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
FGFV + A+AA ++NG +I + LKV
Sbjct: 68 CFGFVSYDNPVSAQAAIQSMNG-FQIGMKRLKV 99
Score = 34.7 bits (78), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 20/89 (22%), Positives = 42/89 (47%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
+F Y +P + ++D+ + F G V ++ +D+ + SK G++ + + +S AI
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 282 SGQLLLGQPVMVKPSEAEKNLVQSNTSAG 310
+G + + KN +S S+G
Sbjct: 87 MNGFQIGMKRLKVQLKRSKNDSKSGPSSG 115
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 32/94 (34%), Positives = 49/94 (52%), Gaps = 9/94 (9%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF-----AQLEHA 376
+ +++ NL F+ E L ++ + FG ++ V++ L +T KG F QF AQ A
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 377 KAAQSALNGKLEIVGRTLKVSSVTDHVGTQDTAA 410
A+ A G L++ GR LKV D T+D AA
Sbjct: 76 AASLEAEGGGLKLDGRQLKV----DLAVTRDEAA 105
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 42.0 bits (97), Expect = 9e-04, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
LYVGNL F TE Q+ +LF G ++ + + LD C GF FV++ A+ A +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC-GFCFVEYYSRADAENAMRYI 79
Query: 384 NG 385
NG
Sbjct: 80 NG 81
Score = 33.1 bits (74), Expect = 0.49, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
T++ + TE +YE FSK+G ++ + + +D+ + + G ++E+Y
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYY 67
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 7/78 (8%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
+L+VGNL ++TE ++LFE +G P ++ + +GFGF++ A+ A++
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGE------PSEVFINRDRGFGFIRLESRTLAEIAKAE 77
Query: 383 LNGKLEIVGRTLKVSSVT 400
L+G + + R L++ T
Sbjct: 78 LDGTI-LKSRPLRIRFAT 94
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 42/158 (26%), Positives = 65/158 (41%), Gaps = 30/158 (18%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIA-L 281
+F +P TE D F + G+ +V + DR G G+I +A A L
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 282 SGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKL 341
G +L +P+ ++ +GA L V NL ++ L +
Sbjct: 79 DGTILKSRPLRIR-------------------FATHGAA---LTVKNLSPVVSNELLEQA 116
Query: 342 FEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
F FGPVE + +D + G+ G GFV+FA A+ A
Sbjct: 117 FSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKA 153
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
P T + +P + D+ F K +R VRL+ D+++ + KG Y+EF +V S+
Sbjct: 11 PTEPPYTAYVGNLPFNTVQGDIDAIF-KDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSL 69
Query: 276 PMAIALSGQLLLGQPVMVKPSEAEK 300
A+ G LL + + V +E K
Sbjct: 70 KEALTYDGALLGDRSLRVDIAEGRK 94
Score = 35.4 bits (80), Expect = 0.092, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 6/64 (9%)
Query: 316 PYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEH 375
PY A YVGNL FN + + +F+ + V+L D +T + KGF +V+F +++
Sbjct: 15 PYTA-----YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDS 68
Query: 376 AKAA 379
K A
Sbjct: 69 LKEA 72
>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 = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 46/81 (56%), Gaps = 2/81 (2%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
TVF + ++ E ++ FF++ G V++V++I DR SKG G++ FY+ + V I
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYGFVSFYNDVDV-QKIVE 68
Query: 282 SGQLLLGQPVMVKPSEAEKNL 302
S G+ + + P+ ++NL
Sbjct: 69 SQINFHGKKLKLGPAIRKQNL 89
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 316 PYGAI-DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ-L 373
P G I ++VG + M ET++R F +G V+ V++ D TG KG+GFV F +
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDV 61
Query: 374 EHAKAAQSALN 384
+ K +S +N
Sbjct: 62 DVQKIVESQIN 72
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 319 AIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKA 378
A + L V L +MT+ +L LF GP+ ++ D +TG G+ FV F ++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 379 AQSALNGKLEIVGRTLKVS 397
A LNG + + + LKVS
Sbjct: 61 AIKVLNG-ITVRNKRLKVS 78
Score = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 14/54 (25%), Positives = 26/54 (48%)
Query: 228 MPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
+P T+R++Y F G + R++ D + S G +++F M AI +
Sbjct: 11 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPV-ELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
+++GNL + E L F FG + + ++ D +TG KG+ F+ FA + + AA A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 383 LNGKLEIVGRTLKVS 397
+NG+ + R + VS
Sbjct: 68 MNGQY-LCNRPITVS 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 = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 29/98 (29%), Positives = 44/98 (44%), Gaps = 7/98 (7%)
Query: 498 SECLLLKNMFDPAMETDPDFDLEIQGDVEEECSKYGRVKHIYVDK-------RSAGFVYL 550
+E L L N P D + EI DV +ECSKYG VK I + + G +++
Sbjct: 6 TEVLCLXNXVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFV 65
Query: 551 RFESTEAAASAQRAMHMRWFARRLISAIFMKPEDYEAK 588
F S A + + R FA R++ + P+ Y +
Sbjct: 66 EFTSVFDCQKAXQGLTGRKFANRVVVTKYCDPDSYHRR 103
>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 = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 41/162 (25%), Positives = 70/162 (43%), Gaps = 29/162 (17%)
Query: 237 VYEFFSKAG-KVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMV-K 294
+ E F+K V DVR +R GY++F + A+ L+G + G + + K
Sbjct: 34 ISELFAKNDLAVVDVRTGTNRK------FGYVDFESAEDLEKALELTGLKVFGNEIKLEK 87
Query: 295 PSEAEKNLVQSNTSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLP 354
P + V++ R L NL FN+TE +L+++FE + LV
Sbjct: 88 PKGRDSKKVRAA---------------RTLLAKNLSFNITEDELKEVFEDALEIRLVS-- 130
Query: 355 LDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
+ G+ KG +++F A+ G EI GR++ +
Sbjct: 131 ---QDGKSKGIAYIEFKSEADAEKNLEEKQGA-EIDGRSVSL 168
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 5/74 (6%)
Query: 315 GPYGA---IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFA 371
GP G+ + ++VG + M ET++R F +G V+ V++ D TG KG+GFV F
Sbjct: 1 GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFY 59
Query: 372 Q-LEHAKAAQSALN 384
++ K +S +N
Sbjct: 60 NDVDVQKIVESQIN 73
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
TVF + ++ E ++ FF++ G V++V++I DR SKG G++ FY+ + V
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYGFVSFYNDVDV 64
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 7/74 (9%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
+L+VGNL ++TE ++RKLFE +G V + D KGFGF++ A+ A+
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 383 LNGKLEIVGRTLKV 396
L+ + + G+ L+V
Sbjct: 78 LDN-MPLRGKQLRV 90
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
R +YVGN+ + T +L F G V V + D +G KGF +++F+ E + +
Sbjct: 6 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 64
Query: 382 ALNGKLEIVGRTLKV 396
AL+ L GR +KV
Sbjct: 65 ALDESL-FRGRQIKV 78
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
LYVG L +TET LR F FG + + + ++ QC F+QFA + A+ A
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITV---VQRQQC---AFIQFATRQAAEVAAEKS 68
Query: 384 NGKLEIVGRTLKV 396
KL + GR L V
Sbjct: 69 FNKLIVNGRRLNV 81
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
KL+VG L ++ T+ LR F +G V + D T Q +GFGFV+F
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
Score = 37.7 bits (86), Expect = 0.018, Method: Composition-based stats.
Identities = 22/88 (25%), Positives = 44/88 (50%), Gaps = 1/88 (1%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
+F + T+ + +FS+ G+V D ++ D+ + +S+G G+++F D V +A
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 283 GQLLLGQPVMVKPSEAEKNLVQSNTSAG 310
L G+ + KP + + S S+G
Sbjct: 79 PHTLDGRNIDPKPC-TPRGMQPSGPSSG 105
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 7/74 (9%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
+L+VGNL ++TE ++RKLFE +G V + D KGFGF++ A+ A+
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 383 LNGKLEIVGRTLKV 396
L+ + + G+ L+V
Sbjct: 71 LD-NMPLRGKQLRV 83
>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 = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 33/62 (53%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
LYVGNL F TE Q+ +LF G ++ + + LD GF FV++ A+ A +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 384 NG 385
NG
Sbjct: 102 NG 103
Score = 36.6 bits (83), Expect = 0.043, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 29/49 (59%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFY 270
T++ + TE +YE FSK+G ++ + + +D+ + + G ++E+Y
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYY 89
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 33/59 (55%)
Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
E D F + +++D+ ++F+K G+V D + D N+ RS+G G+I F D SV
Sbjct: 8 EEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASV 66
Score = 37.0 bits (84), Expect = 0.033, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
K +VG L ++ ++ L+ F FG V + D TG+ +GFGF+ F
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF 60
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 34/54 (62%), Gaps = 1/54 (1%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
TVF + ++ E ++ FF++ G V++V++I DR SKG G++ FY+ + V
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG-VSKGYGFVSFYNDVDV 63
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 316 PYGAI-DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ-L 373
P G I ++VG + M ET++R F +G V+ V++ D TG KG+GFV F +
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDV 61
Query: 374 EHAKAAQSALN 384
+ K +S +N
Sbjct: 62 DVQKIVESQIN 72
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 30/53 (56%), Gaps = 5/53 (9%)
Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
ERD RT+ A +P K T+ ++ E F A ++R V +SKG+ YIEF
Sbjct: 90 ERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLV-----SKDGKSKGIAYIEF 137
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 33/150 (22%), Positives = 65/150 (43%), Gaps = 26/150 (17%)
Query: 247 VRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQLLLGQPVMVKPSEAEKNLVQSN 306
V DVR+ M R GY++F + A+ L+G + G + ++ + + + + +
Sbjct: 39 VVDVRIGMTRK------FGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGKDSKKERD 92
Query: 307 TSAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFG 366
R L NL + +T+ +L+++FE + LV + G+ KG
Sbjct: 93 A--------------RTLLAKNLPYKVTQDELKEVFEDAAEIRLVS-----KDGKSKGIA 133
Query: 367 FVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
+++F A+ G EI GR++ +
Sbjct: 134 YIEFKTEADAEKTFEEKQG-TEIDGRSISL 162
Score = 33.1 bits (74), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 324 LYVGNLHFNMTETQLRK-LFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
L+VGNL+FN + +L+ + + F +L +D+ G + FG+V F E + A
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKNDLA--VVDVRIGMTRKFGYVDFESAEDLEKALE- 66
Query: 383 LNGKLEIVGRTLKV 396
L G L++ G +K+
Sbjct: 67 LTG-LKVFGNEIKL 79
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
LY+ NL +M E +L + +PFG V ++ L +G +G GF + E +A
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRI-LRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 384 NGKL 387
NGK
Sbjct: 87 NGKF 90
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 2/82 (2%)
Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVP 276
E+D ++ +PL E+++ G+V R++ D +S S+GVG+
Sbjct: 22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCE 80
Query: 277 MAIA-LSGQLLLGQPVMVKPSE 297
I +G+ + P + P+E
Sbjct: 81 AVIGHFNGKFIKTPPGVSAPTE 102
>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 = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 46/87 (52%), Gaps = 6/87 (6%)
Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDR--NSRRSKGVGYIEFYDVMSVP 276
D +F Q+P +E+D+ E F + G V ++ ++ DR N +SKG ++ FY +
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 277 MA-IALSGQLLL---GQPVMVKPSEAE 299
A AL +L P+ +KP+++E
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPADSE 88
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETG--QCKGFGFVQFAQLEHAKAAQ 380
K++VG + +E LR+LFE +G V + + D Q KG FV F + A AQ
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 381 SALNG 385
+AL+
Sbjct: 65 NALHN 69
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 26/47 (55%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
++VG L N T ++ FE FG V+ L D T + +GFGFV F
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
Score = 38.1 bits (87), Expect = 0.013, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
+F + + T DV +F + GKV D L+ D+ + R +G G++ F
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
>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 = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
R +YVGN+ + T +L F G V V + D +G KGF +++F+ E + +
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 65
Query: 382 ALNGKLEIVGRTLKV 396
AL+ L GR +KV
Sbjct: 66 ALDESL-FRGRQIKV 79
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 29/78 (37%), Positives = 39/78 (50%), Gaps = 9/78 (11%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
K++VGN+ T +LR LFE G V IE K + FV + AKAA +
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRV--------IECDVVKDYAFVHMEKEADAKAAIAQ 62
Query: 383 LNGKLEIVGRTLKVSSVT 400
LNGK E+ G+ + V T
Sbjct: 63 LNGK-EVKGKRINVELST 79
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 38.9 bits (89), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 34/62 (54%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
KL+VG + + E L+ LFE FG + + + D TG KG F+ + + A AQSA
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 383 LN 384
L+
Sbjct: 77 LH 78
Score = 32.3 bits (72), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 4/87 (4%)
Query: 217 ERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVP 276
+ D +F Q+P E+D+ F + G++ ++ ++ DR + KG ++ + S
Sbjct: 12 DHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSAL 71
Query: 277 MA-IALSGQLLL---GQPVMVKPSEAE 299
A AL Q L +P+ VKP+ +E
Sbjct: 72 KAQSALHEQKTLPGMNRPIQVKPAASE 98
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 8/66 (12%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
+ +L+V ++ E++L ++F PFGP++ V++ GF FV+F + E A A
Sbjct: 4 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAI 55
Query: 381 SALNGK 386
++GK
Sbjct: 56 EEVHGK 61
Score = 32.3 bits (72), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 517 FDLEIQ-GDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI 575
F L++Q ++ E +G +K + K GF ++ FE E+AA A +H + FA + +
Sbjct: 12 FPLDVQESELNEIFGPFGPMKEV---KILNGFAFVEFEEAESAAKAIEEVHGKSFANQPL 68
Query: 576 SAIFMK 581
++ K
Sbjct: 69 EVVYSK 74
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 18/78 (23%), Positives = 47/78 (60%), Gaps = 2/78 (2%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLD-IETGQCKGFGFVQFAQLEHAKAAQS 381
K+++G L N+T+ + ++F +G ++++ +P++ + KG+ +V+F + A+ A
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 382 ALNGKLEIVGRTLKVSSV 399
++G +I G+ + ++V
Sbjct: 66 HMDGG-QIDGQEITATAV 82
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 3/79 (3%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
R LYVGNL ++TE + +LF GP + ++ E + FV+F + A AA +
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMI--TEHTSNDPYCFVEFYEHRDAAAALA 73
Query: 382 ALNGKLEIVGRTLKVSSVT 400
A+NG+ +I+G+ +KV+ T
Sbjct: 74 AMNGR-KILGKEVKVNWAT 91
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 38.1 bits (87), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 8/66 (12%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQ 380
+ +L+V ++ E++L ++F PFGP++ V++ GF FV+F + E A A
Sbjct: 31 NTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAI 82
Query: 381 SALNGK 386
++GK
Sbjct: 83 EEVHGK 88
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 517 FDLEIQ-GDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMRWFARRLI 575
F L++Q ++ E +G +K + + GF ++ FE E+AA A +H + FA + +
Sbjct: 39 FPLDVQESELNEIFGPFGPMKEVKILN---GFAFVEFEEAESAAKAIEEVHGKSFANQPL 95
Query: 576 SAIFMK 581
++ K
Sbjct: 96 EVVYSK 101
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 6/85 (7%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
R L NL FN+TE +L+++FE + LV + G+ KG +++F A+
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLE 71
Query: 382 ALNGKLEIVGRTLKVSSVTDHVGTQ 406
G EI GR++ + + GT+
Sbjct: 72 EKQG-AEIDGRSVSLYYTGEKGGTR 95
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 5/52 (9%)
Query: 218 RDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
R RT+ A + TE ++ E F A ++R V +SKG+ YIEF
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEF 60
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 37.4 bits (85), Expect = 0.021, Method: Composition-based stats.
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
P R ++ +P K T ++Y+ F K G +R +R+ N+ ++G Y+ + D+
Sbjct: 8 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDA 64
Query: 276 PMA 278
A
Sbjct: 65 KNA 67
Score = 34.7 bits (78), Expect = 0.17, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
++R LY+ NL + +T ++ +F +GP+ +++ T + +G +V + + AK A
Sbjct: 11 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNA 67
Query: 380 QSALNG 385
L+G
Sbjct: 68 CDHLSG 73
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 37.4 bits (85), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 45/80 (56%), Gaps = 10/80 (12%)
Query: 319 AIDRKLYVGNLHFNMTE-TQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
+I+ ++++GNL+ + + + + +F +G V + KG+ FVQ++ HA+
Sbjct: 25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHAR 76
Query: 378 AAQSALNGKLEIVGRTLKVS 397
AA NG++ + G+TL ++
Sbjct: 77 AAVLGENGRV-LAGQTLDIN 95
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 37.4 bits (85), Expect = 0.022, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
P R ++ +P K T ++Y+ F K G +R +R+ N+ ++G Y+ + D+
Sbjct: 4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDA 60
Query: 276 PMAI-ALSG 283
A+ LSG
Sbjct: 61 KNAVDHLSG 69
Score = 33.5 bits (75), Expect = 0.30, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
++R LY+ NL + +T ++ +F +GP+ +++ T + +G +V + + AK A
Sbjct: 7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNA 63
Query: 380 QSALNG 385
L+G
Sbjct: 64 VDHLSG 69
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 37.4 bits (85), Expect = 0.023, Method: Composition-based stats.
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
+D K+YVGNL N +T+L + F +GP+ V + + GF FV+F A A
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADA 126
Query: 380 QSALNGK 386
L+G+
Sbjct: 127 VRELDGR 133
Score = 29.6 bits (65), Expect = 4.9, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 524 DVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMR 568
++E YG ++ ++V + GF ++ FE AA A R + R
Sbjct: 89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGR 133
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 37.0 bits (84), Expect = 0.028, Method: Composition-based stats.
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
+D K+YVGNL N +T+L + F +GP+ V + + GF FV+F A A
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADA 126
Query: 380 QSALNGK 386
L+G+
Sbjct: 127 VRDLDGR 133
Score = 29.3 bits (64), Expect = 6.1, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 23/45 (51%)
Query: 524 DVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAMHMR 568
++E YG ++ ++V + GF ++ FE AA A R + R
Sbjct: 89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGR 133
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 37.0 bits (84), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%)
Query: 318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
G+ K+++G L + T+ LR+ F FG V+ + D T + +GFGFV F
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
Score = 35.8 bits (81), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 34/60 (56%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
+F + + T+ + E+F + G+V++ ++ D ++RS+G G++ F D V +A S
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 37.0 bits (84), Expect = 0.032, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
KLY+GNL +T LR+LF +LPL + G+ FV + A A
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGD------RKLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63
Query: 383 LNGKLEIVGRTLKV 396
L+GK+E+ G+ ++V
Sbjct: 64 LSGKVELHGKIMEV 77
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 36.6 bits (83), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 37/83 (44%), Gaps = 9/83 (10%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
KL+VGN+ T +LR FE +GPV IE K + FV + E A A
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPV--------IECDIVKDYAFVHMERAEDAVEAIRG 63
Query: 383 LNGKLEIVGRTLKVSSVTDHVGT 405
L+ E G+ + V T + T
Sbjct: 64 LD-NTEFQGKRMHVQLSTSRLRT 85
>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 = 0.036, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 313 ATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ 372
++G GA +++V NL F+ T L+ F G V + + +E G+ KG G V+F
Sbjct: 2 SSGSSGAC--QIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFES 57
Query: 373 LEHAKAAQSALNGKLEIVGRTLKV 396
E A+ A +NG +++ GR + V
Sbjct: 58 PEVAERACRMMNG-MKLSGREIDV 80
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 36.6 bits (83), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 28/48 (58%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQF 370
K+++G L + T+ LR+ F FG V+ + D T + +GFGFV F
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 35.8 bits (81), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 34/60 (56%)
Query: 223 VFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIALS 282
+F + + T+ + E+F + G+V++ ++ D ++RS+G G++ F D V +A S
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 36.2 bits (82), Expect = 0.049, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 6/62 (9%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
+Y G + +T+ +R+ F PFG + ++I KG+ FV+F+ E A A ++
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQI------MEIRVFPEKGYSFVRFSTHESAAHAIVSV 81
Query: 384 NG 385
NG
Sbjct: 82 NG 83
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 36.2 bits (82), Expect = 0.049, Method: Composition-based stats.
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
P R ++ +P K T ++Y+ F K G +R +R+ N+ ++G Y+ + D+
Sbjct: 14 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDA 70
Query: 276 PMA 278
A
Sbjct: 71 KNA 73
Score = 33.5 bits (75), Expect = 0.37, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 320 IDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAA 379
++R LY+ NL + +T ++ +F +GP+ +++ T + +G +V + + AK A
Sbjct: 17 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNA 73
Query: 380 QSALNG 385
L+G
Sbjct: 74 CDHLSG 79
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 35.8 bits (81), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 30/117 (25%), Positives = 51/117 (43%), Gaps = 9/117 (7%)
Query: 288 GQPVMVKPSEAEKNLVQSNTSAG-GTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG 346
GQ + P + + +L S G G TG KL V NL F +++ +++LF FG
Sbjct: 7 GQQMGRDPDKWQHDLFDSGCGGGEGVETGA------KLLVSNLDFGVSDADIQELFAEFG 60
Query: 347 PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHV 403
++ + D +G+ G V F + A A G + + GR + + V +
Sbjct: 61 TLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQYKG-VPLDGRPMDIQLVASQI 115
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 35.8 bits (81), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGP--VELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQS 381
LYV NL + +E + K F P VE V+ + + + FV F+ E A A
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVK--------KIRDYAFVHFSNREDAVEAMK 69
Query: 382 ALNGKL 387
ALNGK+
Sbjct: 70 ALNGKV 75
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 35.8 bits (81), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 30/117 (25%), Positives = 51/117 (43%), Gaps = 9/117 (7%)
Query: 288 GQPVMVKPSEAEKNLVQSNTSAG-GTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFG 346
GQ + P + + +L S G G TG KL V NL F +++ +++LF FG
Sbjct: 7 GQQMGRDPDKWQHDLFDSGCGGGEGVETGA------KLLVSNLDFGVSDADIQELFAEFG 60
Query: 347 PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHV 403
++ + D +G+ G V F + A A G + + GR + + V +
Sbjct: 61 TLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQYKG-VPLDGRPMDIQLVASQI 115
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 35.8 bits (81), Expect = 0.064, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
K+YVGNL + +L + F +GP+ V + + GF FV+F A+ A
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56
Query: 383 LNGKLEIVGRTLKVSSVT 400
L+GK+ I G ++V T
Sbjct: 57 LDGKV-ICGSRVRVELST 73
Score = 30.8 bits (68), Expect = 2.1, Method: Composition-based stats.
Identities = 12/44 (27%), Positives = 24/44 (54%)
Query: 522 QGDVEEECSKYGRVKHIYVDKRSAGFVYLRFESTEAAASAQRAM 565
+G++E S YG ++ +++ + GF ++ FE A A R +
Sbjct: 14 KGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGL 57
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 35.4 bits (80), Expect = 0.084, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 13/71 (18%)
Query: 313 ATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQ 372
++G G + KL++GNL TE ++R LFE +G V +E K +GFV
Sbjct: 2 SSGSSGMV--KLFIGNLPREATEQEIRSLFEQYGKV--------LECDIIKNYGFV---H 48
Query: 373 LEHAKAAQSAL 383
+E AA+ A+
Sbjct: 49 IEDKTAAEDAI 59
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 35.4 bits (80), Expect = 0.089, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
++V NL F+ T L+ F G V + + +E G+ KG G V+F E A+ A +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERACRMM 65
Query: 384 NGKLEIVGRTLKV 396
NG +++ GR + V
Sbjct: 66 NG-MKLSGREIDV 77
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 35.4 bits (80), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
GP G+ + +++ NL ++ L F FG + ++ D E G KG+GFV F E
Sbjct: 1 GPLGSGN--IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQE 56
Query: 375 HAKAAQSALNGKL 387
A+ A +NG L
Sbjct: 57 AAERAIEKMNGML 69
>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 = 35.4 bits (80), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
++ +F +P T+ ++ E G V+D+RL+ +R + + KG+ Y+E+
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEY 65
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 35.4 bits (80), Expect = 0.098, Method: Composition-based stats.
Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 2/86 (2%)
Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLE 374
GP G+ ++VG+L +T + F PFG + ++ D+ TG+ KG+GFV F
Sbjct: 1 GPLGS-HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW 59
Query: 375 HAKAAQSALNGKLEIVGRTLKVSSVT 400
A+ A + G+ + GR ++ + T
Sbjct: 60 DAENAIQQMGGQW-LGGRQIRTNWAT 84
Score = 33.1 bits (74), Expect = 0.46, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 245 GKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAI-ALSGQLLLGQPV 291
G++ D R++ D + +SKG G++ F++ AI + GQ L G+ +
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 338 LRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK 386
L LF G V ++ P+D TG+ KGF FV+ + AK + +GK
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSV 275
P R + +P K T ++Y+ F K G +R +R+ N+ ++G Y+ + D+
Sbjct: 14 PPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDA 70
Query: 276 PMA 278
A
Sbjct: 71 KNA 73
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 35.0 bits (79), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 44/93 (47%), Gaps = 20/93 (21%)
Query: 315 GPYGAIDRKLYVGNLHFNMTETQLRKLFE-----------PFGPVELVQLPLDIETGQCK 363
GP G+ R+LYVGN+ F +TE + F P PV L ++ Q K
Sbjct: 1 GPLGSA-RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPV------LAVQINQDK 53
Query: 364 GFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKV 396
F F++F ++ A A +G + G++LK+
Sbjct: 54 NFAFLEFRSVDETTQAM-AFDGII-FQGQSLKI 84
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 338 LRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGK 386
L LF G V ++ P+D TG+ KGF FV+ + AK + +GK
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGK 77
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 34.7 bits (78), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 9/82 (10%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVEL--------VQLPLDIETGQCKGFGFVQFAQLEH 375
+YV L+ ++T L F+ G V++ + + LD ETG+ KG V +
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 376 AKAAQSALNGKLEIVGRTLKVS 397
AKAA +GK + G LKVS
Sbjct: 78 AKAAVEWFDGK-DFQGSKLKVS 98
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 19/92 (20%)
Query: 322 RKLYVGNLHFNMTETQLRKLFE-----------PFGPVELVQLPLDIETGQCKGFGFVQF 370
R+LYVGN+ F +TE + F P PV VQ+ Q K F F++F
Sbjct: 2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEF 55
Query: 371 AQLEHAKAAQSALNGKLEIVGRTLKVSSVTDH 402
++ A A +G + G++LK+ D+
Sbjct: 56 RSVDETTQAM-AFDGII-FQGQSLKIRRPHDY 85
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L+V NL +TE L K F FG +E V+ + K + F+ F + + A A +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEEM 65
Query: 384 NGK 386
NGK
Sbjct: 66 NGK 68
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 33.9 bits (76), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
KL V NL F +++ +++LF FG ++ + D +G+ G V F + A A
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 88
Query: 383 LNGKLEIVGRTLKVSSVT 400
NG + + GR + + VT
Sbjct: 89 YNG-VPLDGRPMNIQLVT 105
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 33.9 bits (76), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 28/110 (25%), Positives = 48/110 (43%), Gaps = 9/110 (8%)
Query: 295 PSEAEKNLVQSNTSAG-GTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQL 353
P + + +L S G G TG KL V NL F +++ +++LF FG ++ +
Sbjct: 67 PDKWQHDLFDSGCGGGEGVETGA------KLLVSNLDFGVSDADIQELFAEFGTLKKAAV 120
Query: 354 PLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHV 403
D +G+ G V F + A A G + + GR + + V +
Sbjct: 121 DYD-RSGRSLGTADVHFERRADALKAMKQYKG-VPLDGRPMDIQLVASQI 168
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 33.5 bits (75), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 9/75 (12%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQC---KGFGFVQFAQLEHAKAAQ 380
L++ NL+F+ TE L+ +F G ++ + GFGFV++ + E A+ A
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 381 SALNG------KLEI 389
L G KLE+
Sbjct: 68 KQLQGHTVDGHKLEV 82
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 33.5 bits (75), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 308 SAGGTATGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGF 367
S+G + G + ++V NL + + +L+++F G V + L+ + G+ +G G
Sbjct: 2 SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADI-LEDKDGKSRGIGT 60
Query: 368 VQFAQLEHAKAAQSALNGKL 387
V F Q A A S NG+L
Sbjct: 61 VTFEQSIEAVQAISMFNGQL 80
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.1 bits (74), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
L+V NL +TE L K F FG +E V+ + K + FV F A A +
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEDRGAAVKAMDEM 69
Query: 384 NGK 386
NGK
Sbjct: 70 NGK 72
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 33.1 bits (74), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 332 NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
+MT T LR F PFG + +D+ + FV + ++E A A + LNG
Sbjct: 48 DMTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVAELNG 95
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 33.1 bits (74), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 332 NMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNG 385
+MT T LR F PFG + +D+ + FV + ++E A A + LNG
Sbjct: 24 DMTPTLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVAELNG 71
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 32.7 bits (73), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 44/80 (55%), Gaps = 10/80 (12%)
Query: 319 AIDRKLYVGNLH-FNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
+++ ++++GNL+ + ++ + +F +G + + KGF FVQ+ +A+
Sbjct: 13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKI--------VGCSVHKGFAFVQYVNERNAR 64
Query: 378 AAQSALNGKLEIVGRTLKVS 397
AA + +G++ I G+ L ++
Sbjct: 65 AAVAGEDGRM-IAGQVLDIN 83
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 32.0 bits (71), Expect = 0.92, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
++VG +MTE +LR+ F +G V V +P + F FV FA + AQS
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFAD---DQIAQSLC 59
Query: 384 NGKLEIVGRTLKVSS 398
L I G ++ +S+
Sbjct: 60 GEDLIIKGISVHISN 74
>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 = 32.0 bits (71), Expect = 0.93, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 223 VFAYQMPLKATERDVY-EFFSKAGKVRDVRLIMDRNSRRSKGVGYIEF 269
V +P ATE D+ + S + R+VRL+ +++S +S+G ++EF
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEF 51
Score = 31.2 bits (69), Expect = 1.9, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 334 TETQLRKLFEPFG-PVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSALNGKLEIVGR 392
TE +R + G V+L + +GQ +GF FV+F+ L+ A A L I+G+
Sbjct: 14 TEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQ 73
Query: 393 TLKV 396
+ +
Sbjct: 74 KVSM 77
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
KL V NL F +++ +++LF FG ++ + D +G+ G V F + A A
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAXKQ 89
Query: 383 LNGKLEIVGRTLKVSSVT 400
NG + + GR + VT
Sbjct: 90 YNG-VPLDGRPXNIQLVT 106
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 9/88 (10%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVE--------LVQLPLDIETGQCKGFGFVQFAQ 372
+ ++V L N+T + F+ G ++ ++ L D ETG+ KG V F
Sbjct: 13 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 72
Query: 373 LEHAKAAQSALNGKLEIVGRTLKVSSVT 400
AKAA +GK E G +KVS T
Sbjct: 73 PPSAKAAIDWFDGK-EFSGNPIKVSFAT 99
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 31/99 (31%), Positives = 47/99 (47%), Gaps = 8/99 (8%)
Query: 219 DQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMA 278
D V + MP A E DV +FF +V V L+ D + R+ G G ++F A
Sbjct: 15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKD-HVGRNNGNGLVKFLSPQDTFEA 72
Query: 279 IALSGQLLLGQPVMVKPSEAEKNLVQSNTSAGGTAT-GP 316
+ + L++ + V V P+ E+ V +AGG T GP
Sbjct: 73 LKRNRMLMIQRYVEVSPA-TERQWV----AAGGHITSGP 106
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 2/64 (3%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSAL 383
+++ NL ++ L F FG + ++ D E G KG+GFV F E A+ A +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQEAAERAIEKM 71
Query: 384 NGKL 387
NG L
Sbjct: 72 NGML 75
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 31.6 bits (70), Expect = 1.4, Method: Composition-based stats.
Identities = 28/98 (28%), Positives = 48/98 (48%), Gaps = 10/98 (10%)
Query: 310 GGTATGPYGAIDRKLYVGNLHFNMTETQLR-KLFEPFGPVELVQLPLDIETGQCKGFGFV 368
G +T P+ L++GNL+ N + +L+ + E F +L + D+ TG + FG+V
Sbjct: 11 GSESTTPF-----NLFIGNLNPNKSVAELKVAISELFAKNDLAVV--DVRTGTNRKFGYV 63
Query: 369 QFAQLEHAKAAQSALNGKLEIVGRTLKVSSVTDHVGTQ 406
F E + A L G L++ G +K+ GT+
Sbjct: 64 DFESAEDLEKALE-LTG-LKVFGNEIKLEKPKGRDGTR 99
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
K++VG +MT +L++ F +G V V +P + F FV FA K AQS
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFAD---DKVAQSL 64
Query: 383 LNGKLEIVGRTLKVSS 398
L I G ++ +S+
Sbjct: 65 CGEDLIIKGISVHISN 80
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 318 GAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAK 377
G ++ LY+ NL +TE L LF F + + + TG+ +G F+ F E A
Sbjct: 22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAW 81
Query: 378 AAQSALNGKLEIVGRTLKV 396
A +NG ++ G+ L +
Sbjct: 82 QALHLVNG-YKLYGKILVI 99
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 31.2 bits (69), Expect = 1.6, Method: Composition-based stats.
Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 9/88 (10%)
Query: 321 DRKLYVGNLHFNMTETQLRKLFEPFGPVE--------LVQLPLDIETGQCKGFGFVQFAQ 372
+ ++V L N+T + F+ G ++ ++ L D ETG+ KG V F
Sbjct: 7 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 66
Query: 373 LEHAKAAQSALNGKLEIVGRTLKVSSVT 400
AKAA +GK E G +KVS T
Sbjct: 67 PPSAKAAIDWFDGK-EFSGNPIKVSFAT 93
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMD-RNSRRSKGVGYIEF 269
P+ T F +P TE + EFF + + VRL + N R KG GY EF
Sbjct: 11 PKSPPYTAFLGNLPYDVTEESIKEFF-RGLNISAVRLPREPSNPERLKGFGYAEF 64
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 7/56 (12%)
Query: 316 PYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQ-CKGFGFVQF 370
PY A ++GNL +++TE +++ F + V+LP + + KGFG+ +F
Sbjct: 15 PYTA-----FLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 64
>pdb|2O8H|A Chain A, Crystal Structure Of The Catalytic Domain Of Rat
Phosphodiesterase 10a
pdb|2OVV|A Chain A, Crystal Structure Of The Catalytic Domain Of Rat
Phosphodiesterase 10a
pdb|2OVY|A Chain A, Crystal Structure Of The Catalytic Domain Of Rat
Phosphodiesterase 10a
pdb|3QPN|A Chain A, Structure Of Pde10-Inhibitor Complex
pdb|3QPO|A Chain A, Structure Of Pde10-Inhibitor Complex
pdb|3QPP|A Chain A, Structure Of Pde10-Inhibitor Complex
Length = 362
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 231 KATERDVY-EFFSKAGKVRDVRL----IMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQL 285
K T D+Y EF+++ +++ + + +MDR+ R G + FY+ +++P L+ L
Sbjct: 254 KLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKRDEVPQGQLGFYNAVAIPCYTTLTQIL 313
Query: 286 LLGQPVM 292
+P++
Sbjct: 314 PPTEPLL 320
>pdb|3HQW|A Chain A, Discovery Of Novel Inhibitors Of Pde10a
Length = 376
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 231 KATERDVY-EFFSKAGKVRDVRL----IMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQL 285
K T D+Y EF+++ +++ + + +MDR+ R G + FY+ +++P L+ L
Sbjct: 268 KLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKRDEVPQGQLGFYNAVAIPCYTTLTQIL 327
Query: 286 LLGQPVM 292
+P++
Sbjct: 328 PPTEPLL 334
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.8 bits (68), Expect = 1.9, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 314 TGPYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQL 373
GP G D ++YVGNL ++ + +F +G + DI+ +G F +
Sbjct: 15 RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIR------DIDLKNRRGGPPFAFVEF 68
Query: 374 EHAKAAQSALNGK 386
E + A+ A+ G+
Sbjct: 69 EDPRDAEDAVYGR 81
>pdb|3HQY|A Chain A, Discovery Of Novel Inhibitors Of Pde10a
pdb|3HQZ|A Chain A, Discovery Of Novel Inhibitors Of Pde10a
pdb|3HR1|A Chain A, Discovery Of Novel Inhibitors Of Pde10a
Length = 380
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 231 KATERDVY-EFFSKAGKVRDVRL----IMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQL 285
K T D+Y EF+++ +++ + + +MDR+ R G + FY+ +++P L+ L
Sbjct: 272 KLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKRDEVPQGQLGFYNAVAIPCYTTLTQIL 331
Query: 286 LLGQPVM 292
+P++
Sbjct: 332 PPTEPLL 338
>pdb|3LXG|A Chain A, Crystal Structure Of Rat Phosphodiesterase 10a In Complex
Wi Web-3
Length = 308
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 5/67 (7%)
Query: 231 KATERDVY-EFFSKAGKVRDVRL----IMDRNSRRSKGVGYIEFYDVMSVPMAIALSGQL 285
K T D+Y EF+++ +++ + + +MDR+ R G + FY+ +++P L+ L
Sbjct: 224 KLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKRDEVPQGQLGFYNAVAIPCYTTLTQIL 283
Query: 286 LLGQPVM 292
+P++
Sbjct: 284 PPTEPLL 290
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 7/56 (12%)
Query: 316 PYGAIDRKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQ-CKGFGFVQF 370
PY A ++GNL +++TE +++ F + V+LP + + KGFG+ +F
Sbjct: 19 PYTA-----FLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 68
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 216 PERDQRTVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMD-RNSRRSKGVGYIEF 269
P+ T F +P TE + EFF + + VRL + N R KG GY EF
Sbjct: 15 PKSPPYTAFLGNLPYDVTEESIKEFF-RGLNISAVRLPREPSNPERLKGFGYAEF 68
>pdb|2HGN|A Chain A, Nmr Structure Of The Third Qrrm Domain Of Human Hnrnp F
pdb|2KG1|A Chain A, Structure Of The Third Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 139
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 228 MPLKATERDVYEFFSKAGKVR 248
+P KATE D+Y FFS VR
Sbjct: 54 LPYKATENDIYNFFSPLNPVR 74
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 33/74 (44%)
Query: 222 TVFAYQMPLKATERDVYEFFSKAGKVRDVRLIMDRNSRRSKGVGYIEFYDVMSVPMAIAL 281
V+ +P +A + V +FF K V D I + ++ G G++EF + A+
Sbjct: 27 CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR 86
Query: 282 SGQLLLGQPVMVKP 295
Q + + + V P
Sbjct: 87 HKQYMGNRFIQVHP 100
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 30.4 bits (67), Expect = 3.3, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 324 LYVGNLHFNMTETQLRKLFEPFGPVEL-VQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
L++G+L M E + + F G + V++ + TG G+ FV+FA L A+
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 383 LNGK 386
+NGK
Sbjct: 72 INGK 75
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 29.6 bits (65), Expect = 5.4, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 322 RKLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQC---KGFGFVQFAQLEHAKA 378
RK++VG L ++ E ++ F FGP+ +V P E+ KG+ F+ F + +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPL-VVDWPHKAESKSYFPPKGYAFLLF---QEESS 64
Query: 379 AQSALNGKLEIVGRT-LKVSSVT 400
Q+ ++ LE G+ L VSS T
Sbjct: 65 VQALIDACLEEDGKLYLCVSSPT 87
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 28.9 bits (63), Expect = 7.6, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 323 KLYVGNLHFNMTETQLRKLFEPFGPVELVQLPLDIETGQCKGFGFVQFAQLEHAKAAQSA 382
+L+VG L N + L + F+ FG + I+ + F ++Q+ L+ A+AA +
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIR------TIDHVKGDSFAYIQYESLDAAQAACAK 72
Query: 383 LNG 385
+ G
Sbjct: 73 MRG 75
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
0.317 0.132 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,091,121
Number of Sequences: 62578
Number of extensions: 348177
Number of successful extensions: 1153
Number of sequences better than 100.0: 196
Number of HSP's better than 100.0 without gapping: 145
Number of HSP's successfully gapped in prelim test: 51
Number of HSP's that attempted gapping in prelim test: 768
Number of HSP's gapped (non-prelim): 358
length of query: 591
length of database: 14,973,337
effective HSP length: 104
effective length of query: 487
effective length of database: 8,465,225
effective search space: 4122564575
effective search space used: 4122564575
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)