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= 021890
(306 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 77.8 bits (190), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 50/167 (29%), Positives = 80/167 (47%), Gaps = 8/167 (4%)
Query: 103 LVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLE 162
L N+ T + ++ F+ G + +I++ + N+N AFV +A AL L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 163 SYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDV 222
+ E +K+N+A F Q TFNLF+ +L+ + LR F +
Sbjct: 63 GKQIENNIVKINWA-------FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAF-KDFPSY 114
Query: 223 VSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQGKLFMGRPLRV 269
+S V++ S GYGFVSF S+ A+ A+ + QG+ GRPLR+
Sbjct: 115 LSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161
Score = 35.4 bits (80), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%)
Query: 141 RGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYA 176
RG FV+ S D+A A+++++ + GR L++N+A
Sbjct: 129 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 62.8 bits (151), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 45/176 (25%), Positives = 83/176 (47%), Gaps = 21/176 (11%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNR----NRGLAFVTMGSPDEA 154
SKT L+ +P T ++ ++LF G++ DIE +++ + G FV P++A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLF---GSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDA 59
Query: 155 TAALNNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREF 214
A+N L + + +T+KV+YA+ P NL+++ L K++ +
Sbjct: 60 DKAINTLNGLKLQTKTIKVSYAR-----P----SSASIRDANLYVSGLPKTMSQKEMEQL 110
Query: 215 FISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQGKLFMGRPLRVA 270
F S+ ++++ ++ S G GF+ F + AE AI G+ +PL A
Sbjct: 111 F-SQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ----KPLGAA 161
Score = 31.2 bits (69), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
NL + L + + F S G D+ S +++ +S GYGFV++ A+ AI+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIG-DIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 256 AFQGKLFMGRPLRVAPSR 273
G + ++V+ +R
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
>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 = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 43/163 (26%), Positives = 73/163 (44%), Gaps = 11/163 (6%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHS-KNRNRGLAFVTMGSPDEATAA 157
SKT L+ +P T E+ R+LF G + +L ++ G FV P +A A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 158 LNNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFIS 217
+N L + +T+KV+YA+ P NL+++ L K+L + F S
Sbjct: 61 INTLNGLRLQTKTIKVSYAR-----P----SSASIRDANLYVSGLPKTMTQKELEQLF-S 110
Query: 218 EGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQGK 260
+ ++++ ++ S G GF+ F + AE AI G+
Sbjct: 111 QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
NL + L ++ R F S G ++ S +++ +S GYGFV++ K AE AI+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIG-EIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 256 AFQGKLFMGRPLRVAPSR 273
G + ++V+ +R
Sbjct: 63 TLNGLRLQTKTIKVSYAR 80
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 43/162 (26%), Positives = 73/162 (45%), Gaps = 11/162 (6%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHS-KNRNRGLAFVTMGSPDEATAA 157
+T L+ +P T +++R+LF G V +L + G FV + +A A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 158 LNNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFIS 217
+N L + +T+KV+YA+ P V NL+I+ L KD+ + F S
Sbjct: 61 INTLNGLRLQSKTIKVSYAR-----PSSEV----IKDANLYISGLPRTMTQKDVEDMF-S 110
Query: 218 EGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQG 259
++++ V+ S G F+ F + AE AI++F G
Sbjct: 111 RFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
NL + L +LR F S G +V SA++I S GYGFV++ + K AE AI+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIG-EVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 256 AFQGKLFMGRPLRVAPSR 273
G + ++V+ +R
Sbjct: 63 TLNGLRLQSKTIKVSYAR 80
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 58.2 bits (139), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 43/162 (26%), Positives = 73/162 (45%), Gaps = 11/162 (6%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHS-KNRNRGLAFVTMGSPDEATAA 157
+T L+ +P T +++R+LF G V +L + G FV + +A A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 158 LNNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFIS 217
+N L + +T+KV+YA+ P V NL+I+ L KD+ + F S
Sbjct: 61 INTLNGLRLQSKTIKVSYAR-----PSSEV----IKDANLYISGLPRTMTQKDVEDMF-S 110
Query: 218 EGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQG 259
++++ V+ S G F+ F + AE AI++F G
Sbjct: 111 RFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
NL + L +LR F S G +V SA++I S GYGFV++ + K AE AI+
Sbjct: 4 NLIVNYLPQNMTQDELRSLFSSIG-EVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 256 AFQGKLFMGRPLRVAPSR 273
G + ++V+ +R
Sbjct: 63 TLNGLRLQSKTIKVSYAR 80
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 52/182 (28%), Positives = 77/182 (42%), Gaps = 30/182 (16%)
Query: 100 KTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALN 159
+ RL N+P T ED + LFE++G ++ + NR+RG F+ + S L
Sbjct: 22 RCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI-----NRDRGFGFIRLES-----RTLA 71
Query: 160 NLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFN--LFIANLSFEARAKDLREFFIS 217
+ E +G LK +I+ FAT L + NLS + L + F
Sbjct: 72 EIAKAELDGTILKSRPLRIR------------FATHGAALTVKNLSPVVSNELLEQAFSQ 119
Query: 218 EGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQGKLFM----GRPLRVAPSR 273
G V V+ D+ R+ G GFV F +K A A+ F+ RP+ V P
Sbjct: 120 FG--PVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPME 177
Query: 274 QF 275
QF
Sbjct: 178 QF 179
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 48/162 (29%), Positives = 78/162 (48%), Gaps = 16/162 (9%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIE-LSMHSKN--RNRGLAFVTM---GSPDEAT 155
++ VP T + +D+R LFEQ+G V +I L S+N +++G FVT + EA
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 156 AALNNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFF 215
AL+N++ +++ A +K N V+ + LFI +S + D+R F
Sbjct: 77 NALHNMKVLPGMHHPIQMKPADSEKNN---AVEDR-----KLFIGMISKKCTENDIRVMF 128
Query: 216 ISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAF 257
S G + I S G FV+F ++ +A+TAI A
Sbjct: 129 SSFGQ--IEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 168
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 48/162 (29%), Positives = 78/162 (48%), Gaps = 16/162 (9%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIE-LSMHSKN--RNRGLAFVTM---GSPDEAT 155
++ VP T + +D+R LFEQ+G V +I L S+N +++G FVT + EA
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 156 AALNNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFF 215
AL+N++ +++ A +K N V+ + LFI +S + D+R F
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNN---AVEDR-----KLFIGMISKKCTENDIRVMF 116
Query: 216 ISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAF 257
S G + I S G FV+F ++ +A+TAI A
Sbjct: 117 SSFGQ--IEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 156
>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 = 51.6 bits (122), Expect = 6e-07, Method: Composition-based stats.
Identities = 29/76 (38%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 194 TFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETA 253
TFNLF+ +L+ + LR F + +S V++ S GYGFVSF S+ A+ A
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAF-KDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 59
Query: 254 ISAFQGKLFMGRPLRV 269
+ + QG+ GRPLR+
Sbjct: 60 MDSMQGQDLNGRPLRI 75
Score = 34.7 bits (78), Expect = 0.077, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 25/37 (67%)
Query: 140 NRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYA 176
+RG FV+ S D+A A+++++ + GR L++N+A
Sbjct: 42 SRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 78
>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 = 51.2 bits (121), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 42/152 (27%), Positives = 75/152 (49%), Gaps = 17/152 (11%)
Query: 121 FEQHGTVLDIELSMHS-KNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYAKIK 179
F G +L I + R+ G A+V P +A AL+ + +G+ +++ +++
Sbjct: 36 FSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ-- 93
Query: 180 KKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGY 239
++P + N+FI NL K L + F + G +++S +V+ +N S GY
Sbjct: 94 -RDP----SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG-NILSCKVVCDENG--SKGY 145
Query: 240 GFVSFKSKKVAETAISAFQG------KLFMGR 265
GFV F++++ AE AI G K+F+GR
Sbjct: 146 GFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 5/93 (5%)
Query: 182 NPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGF 241
NP P P +L++ +L + L E F G ++S V RRS GY +
Sbjct: 7 NPSAPSYPMA----SLYVGDLHPDVTEAMLYEKFSPAG-PILSIRVCRDMITRRSLGYAY 61
Query: 242 VSFKSKKVAETAISAFQGKLFMGRPLRVAPSRQ 274
V+F+ AE A+ + G+P+R+ S++
Sbjct: 62 VNFQQPADAERALDTMNFDVIKGKPVRIMWSQR 94
>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 = 51.2 bits (121), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 32/147 (21%), Positives = 70/147 (47%), Gaps = 13/147 (8%)
Query: 101 TRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMH-SKNRNRGLAFVTMGSPDEATAALN 159
++ + W +T +++R F ++GTV D+++ + R+RG F++ P +
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 160 NLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEG 219
+ +G+ I K P + + T +F+ + + R K+ EFF S+
Sbjct: 64 T--QHILDGKV-------IDPKRAIP--RDEQDKTGKIFVGGIGPDVRPKEFEEFF-SQW 111
Query: 220 WDVVSAEVIFHDNPRRSAGYGFVSFKS 246
++ A+++ + +S G+GFV++ S
Sbjct: 112 GTIIDAQLMLDKDTGQSRGFGFVTYDS 138
>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 = 51.2 bits (121), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 42/152 (27%), Positives = 75/152 (49%), Gaps = 17/152 (11%)
Query: 121 FEQHGTVLDIELSMHS-KNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYAKIK 179
F G +L I + R+ G A+V P +A AL+ + +G+ +++ +++
Sbjct: 31 FSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ-- 88
Query: 180 KKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGY 239
++P + N+FI NL K L + F + G +++S +V+ +N S GY
Sbjct: 89 -RDP----SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG-NILSCKVVCDENG--SKGY 140
Query: 240 GFVSFKSKKVAETAISAFQG------KLFMGR 265
GFV F++++ AE AI G K+F+GR
Sbjct: 141 GFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 172
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 5/93 (5%)
Query: 182 NPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGF 241
NP P P +L++ +L + L E F G ++S V RRS GY +
Sbjct: 2 NPSAPSYPMA----SLYVGDLHPDVTEAMLYEKFSPAG-PILSIRVCRDMITRRSLGYAY 56
Query: 242 VSFKSKKVAETAISAFQGKLFMGRPLRVAPSRQ 274
V+F+ AE A+ + G+P+R+ S++
Sbjct: 57 VNFQQPADAERALDTMNFDVIKGKPVRIMWSQR 89
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRN-RGLAFVTMGSPDEATAALNN 160
RL +N+ +TS+ ED+ LF +G + ++ + S + +G AFVT P+ A A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 161 LESYEFEGRTLKVNYAKIKKK 181
++ F+GR L V + IKK+
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKE 90
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
LF+ NLS+ + +DL + F + G + ++ G+ FV+F + A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYG-PLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 257 FQGKLFMGRPLRVAPS 272
G++F GR L V PS
Sbjct: 70 VDGQVFQGRMLHVLPS 85
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 47/152 (30%), Positives = 70/152 (46%), Gaps = 10/152 (6%)
Query: 108 VPWTSTHEDIRALFEQHGTVLDIE-LSMHSKN--RNRGLAFVTMGSPDEATAALNNLESY 164
VP T + +D+R LFEQ+G V +I L S+N +++G FVT + A A N L +
Sbjct: 11 VPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNX 70
Query: 165 EFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVS 224
+ L + I+ K P + LFI +S + D+R F S G +
Sbjct: 71 ----KVLPGXHHPIQXK-PADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQ--IE 123
Query: 225 AEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
I S G FV+F ++ A+TAI A
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAXAQTAIKA 155
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 48/204 (23%), Positives = 92/204 (45%), Gaps = 10/204 (4%)
Query: 71 HFSATTQDPFVDSSSAAAVNTEQREEEYS-KTRLVAQNVPWTSTHEDIRALFEQHGTVLD 129
H ++ T + SAA QR+ + +R+ ++ + + IR F G +
Sbjct: 3 HMASMTGGQQMGRGSAA-----QRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKS 57
Query: 130 IELSMHSKN-RNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNY-AKIKKKNPFPPV 187
I++S S +++G AFV P+ A AL + S GR +KV + I + P
Sbjct: 58 IDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQ 117
Query: 188 QPKPFATFN-LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKS 246
+ FN +++A++ + D++ F + G + SA + + GYGF+ ++
Sbjct: 118 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG-KIKSATLARDPTTGKHKGYGFIEYEK 176
Query: 247 KKVAETAISAFQGKLFMGRPLRVA 270
+ ++ A+S+ G+ LRV
Sbjct: 177 AQSSQDAVSSMNLFDLGGQYLRVG 200
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 20/96 (20%), Positives = 45/96 (46%), Gaps = 4/96 (4%)
Query: 95 EEEYSKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMH-SKNRNRGLAFVTMGSPDE 153
EE + R+ +V + +DI+++FE G + L+ + +++G F+
Sbjct: 120 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQS 179
Query: 154 ATAALNNLESYEFEGRTLKVNYAKIKKKNPFPPVQP 189
+ A++++ ++ G+ L+V A P P + P
Sbjct: 180 SQDAVSSMNLFDLGGQYLRVGKAVTP---PMPLLTP 212
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 36/145 (24%), Positives = 68/145 (46%), Gaps = 8/145 (5%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKN--RNRGLAFVTMGSPDEATAALN 159
+L + + +T E +R+ FEQ GT+ D + M N R+RG FVT + +E AA+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDC-VVMRDPNTKRSRGFGFVTYATVEEVDAAM- 72
Query: 160 NLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEG 219
N ++ +GR ++ A ++ + P +F+ + + LR++F G
Sbjct: 73 NARPHKVDGRVVEPKRAVSREDSQRPGAH---LTVKKIFVGGIKEDTEEHHLRDYFEQYG 129
Query: 220 WDVVSAEVIFHDNPRRSAGYGFVSF 244
+ E++ + G+ FV+F
Sbjct: 130 -KIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 34/100 (34%), Positives = 52/100 (52%), Gaps = 11/100 (11%)
Query: 179 KKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHD-NPRRSA 237
K ++P P Q + LFI LSFE + LR F E W ++ V+ D N +RS
Sbjct: 3 KSESPKEPEQLR-----KLFIGGLSFETTDESLRSHF--EQWGTLTDCVVMRDPNTKRSR 55
Query: 238 GYGFVSFKSKKVAETAISAFQGKLFMGRPLRVAPSRQFAR 277
G+GFV++ + + + A++A K+ GR V P R +R
Sbjct: 56 GFGFVTYATVEEVDAAMNARPHKV-DGRV--VEPKRAVSR 92
>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 = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 36/145 (24%), Positives = 68/145 (46%), Gaps = 8/145 (5%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKN--RNRGLAFVTMGSPDEATAALN 159
+L + + +T E +R+ FEQ GT+ D + M N R+RG FVT + +E AA+
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDC-VVMRDPNTKRSRGFGFVTYATVEEVDAAM- 71
Query: 160 NLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEG 219
N ++ +GR ++ A ++ + P +F+ + + LR++F G
Sbjct: 72 NARPHKVDGRVVEPKRAVSREDSQRPGAH---LTVKKIFVGGIKEDTEEHHLRDYFEQYG 128
Query: 220 WDVVSAEVIFHDNPRRSAGYGFVSF 244
+ E++ + G+ FV+F
Sbjct: 129 -KIEVIEIMTDRGSGKKRGFAFVTF 152
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 34/100 (34%), Positives = 52/100 (52%), Gaps = 11/100 (11%)
Query: 179 KKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHD-NPRRSA 237
K ++P P Q + LFI LSFE + LR F E W ++ V+ D N +RS
Sbjct: 2 KSESPKEPEQLR-----KLFIGGLSFETTDESLRSHF--EQWGTLTDCVVMRDPNTKRSR 54
Query: 238 GYGFVSFKSKKVAETAISAFQGKLFMGRPLRVAPSRQFAR 277
G+GFV++ + + + A++A K+ GR V P R +R
Sbjct: 55 GFGFVTYATVEEVDAAMNARPHKV-DGRV--VEPKRAVSR 91
>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 = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 36/145 (24%), Positives = 68/145 (46%), Gaps = 8/145 (5%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKN--RNRGLAFVTMGSPDEATAALN 159
+L + + +T E +R+ FEQ GT+ D + M N R+RG FVT + +E AA+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDC-VVMRDPNTKRSRGFGFVTYATVEEVDAAM- 72
Query: 160 NLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEG 219
N ++ +GR ++ A ++ + P +F+ + + LR++F G
Sbjct: 73 NARPHKVDGRVVEPKRAVSREDSQRPGAH---LTVKKIFVGGIKEDTEEHHLRDYFEQYG 129
Query: 220 WDVVSAEVIFHDNPRRSAGYGFVSF 244
+ E++ + G+ FV+F
Sbjct: 130 -KIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 34/100 (34%), Positives = 52/100 (52%), Gaps = 11/100 (11%)
Query: 179 KKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHD-NPRRSA 237
K ++P P Q + LFI LSFE + LR F E W ++ V+ D N +RS
Sbjct: 3 KSESPKEPEQLR-----KLFIGGLSFETTDESLRSHF--EQWGTLTDCVVMRDPNTKRSR 55
Query: 238 GYGFVSFKSKKVAETAISAFQGKLFMGRPLRVAPSRQFAR 277
G+GFV++ + + + A++A K+ GR V P R +R
Sbjct: 56 GFGFVTYATVEEVDAAMNARPHKV-DGRV--VEPKRAVSR 92
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 36/145 (24%), Positives = 68/145 (46%), Gaps = 8/145 (5%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKN--RNRGLAFVTMGSPDEATAALN 159
+L + + +T E +R+ FEQ GT+ D + M N R+RG FVT + +E AA+
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDC-VVMRDPNTKRSRGFGFVTYATVEEVDAAM- 70
Query: 160 NLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEG 219
N ++ +GR ++ A ++ + P +F+ + + LR++F G
Sbjct: 71 NARPHKVDGRVVEPKRAVSREDSQRPGAH---LTVKKIFVGGIKEDTEEHHLRDYFEQYG 127
Query: 220 WDVVSAEVIFHDNPRRSAGYGFVSF 244
+ E++ + G+ FV+F
Sbjct: 128 -KIEVIEIMTDRGSGKKRGFAFVTF 151
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 34/100 (34%), Positives = 52/100 (52%), Gaps = 11/100 (11%)
Query: 179 KKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHD-NPRRSA 237
K ++P P Q + LFI LSFE + LR F E W ++ V+ D N +RS
Sbjct: 1 KSESPKEPEQLR-----KLFIGGLSFETTDESLRSHF--EQWGTLTDCVVMRDPNTKRSR 53
Query: 238 GYGFVSFKSKKVAETAISAFQGKLFMGRPLRVAPSRQFAR 277
G+GFV++ + + + A++A K+ GR V P R +R
Sbjct: 54 GFGFVTYATVEEVDAAMNARPHKV-DGRV--VEPKRAVSR 90
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 36/145 (24%), Positives = 68/145 (46%), Gaps = 8/145 (5%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKN--RNRGLAFVTMGSPDEATAALN 159
+L + + +T E +R+ FEQ GT+ D + M N R+RG FVT + +E AA+
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDC-VVMRDPNTKRSRGFGFVTYATVEEVDAAM- 73
Query: 160 NLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEG 219
N ++ +GR ++ A ++ + P +F+ + + LR++F G
Sbjct: 74 NARPHKVDGRVVEPKRAVSREDSQRPGAH---LTVKKIFVGGIKEDTEEHHLRDYFEQYG 130
Query: 220 WDVVSAEVIFHDNPRRSAGYGFVSF 244
+ E++ + G+ FV+F
Sbjct: 131 -KIEVIEIMTDRGSGKKRGFAFVTF 154
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 34/100 (34%), Positives = 52/100 (52%), Gaps = 11/100 (11%)
Query: 179 KKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHD-NPRRSA 237
K ++P P Q + LFI LSFE + LR F E W ++ V+ D N +RS
Sbjct: 4 KSESPKEPEQLR-----KLFIGGLSFETTDESLRSHF--EQWGTLTDCVVMRDPNTKRSR 56
Query: 238 GYGFVSFKSKKVAETAISAFQGKLFMGRPLRVAPSRQFAR 277
G+GFV++ + + + A++A K+ GR V P R +R
Sbjct: 57 GFGFVTYATVEEVDAAMNARPHKV-DGRV--VEPKRAVSR 93
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 48/189 (25%), Positives = 82/189 (43%), Gaps = 29/189 (15%)
Query: 100 KTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALN 159
++RL N+P T E++R LFE++G ++ + ++++G F+ + + A A
Sbjct: 22 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-----HKDKGFGFIRLETRTLAEIAKV 76
Query: 160 NLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEG 219
L++ G+ L+V +A + +L + NL + L E F G
Sbjct: 77 ELDNMPLRGKQLRVRFA---------------CHSASLTVRNLPQYVSNELLEEAFSVFG 121
Query: 220 WDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS-AFQGKLFMG---RPLRVAPSRQF 275
V V+ D+ R +G G V F K A A+ +G + RP+ V P Q
Sbjct: 122 Q--VERAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEGSFLLTTFPRPVTVEPMDQ- 178
Query: 276 ARLQTKEGL 284
L +EGL
Sbjct: 179 --LDDEEGL 185
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
++F+ N+ +EA + L++ F SE VVS +++ + GYGF ++ ++ A +A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIF-SEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 256 AFQGKLFMGRPLRV 269
G+ F GR LRV
Sbjct: 69 NLNGREFSGRALRV 82
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 107 NVPWTSTHEDIRALFEQHGTVLDIELSMHSK-NRNRGLAFVTMGSPDEATAALNNLESYE 165
N+P+ +T E ++ +F + G V+ L + + +G F + A +A+ NL E
Sbjct: 15 NIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGRE 74
Query: 166 FEGRTLKVNYAKIKK 180
F GR L+V+ A +K
Sbjct: 75 FSGRALRVDNAASEK 89
>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 = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 36/145 (24%), Positives = 68/145 (46%), Gaps = 8/145 (5%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKN--RNRGLAFVTMGSPDEATAALN 159
+L + + +T E +R+ FEQ GT+ D + M N R+RG FVT + +E AA+
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDC-VVMRDPNTKRSRGFGFVTYATVEEVDAAM- 65
Query: 160 NLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEG 219
N ++ +GR ++ A ++ + P +F+ + + LR++F G
Sbjct: 66 NARPHKVDGRVVEPKRAVSREDSQRPGAH---LTVKKIFVGGIKEDTEEHHLRDYFEQYG 122
Query: 220 WDVVSAEVIFHDNPRRSAGYGFVSF 244
+ E++ + G+ FV+F
Sbjct: 123 -KIEVIEIMTDRGSGKKRGFAFVTF 146
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 45/82 (54%), Gaps = 6/82 (7%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHD-NPRRSAGYGFVSFKSKKVAETAIS 255
LFI LSFE + LR F E W ++ V+ D N +RS G+GFV++ + + + A++
Sbjct: 9 LFIGGLSFETTDESLRSHF--EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 256 AFQGKLFMGRPLRVAPSRQFAR 277
A K+ GR V P R +R
Sbjct: 67 ARPHKV-DGRV--VEPKRAVSR 85
>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 = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 40/174 (22%), Positives = 79/174 (45%), Gaps = 6/174 (3%)
Query: 101 TRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKN-RNRGLAFVTMGSPDEATAALN 159
R+ ++ + + IR F G + I++S S +++G AFV P+ A AL
Sbjct: 14 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 73
Query: 160 NLESYEFEGRTLKVNY-AKIKKKNPFPPVQPKPFATFN-LFIANLSFEARAKDLREFFIS 217
+ S GR +KV + I + P + FN +++A++ + D++ F
Sbjct: 74 QMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVF-- 131
Query: 218 EGWDVVSAEVIFHD-NPRRSAGYGFVSFKSKKVAETAISAFQGKLFMGRPLRVA 270
E + + + + D + GYGF+ ++ + ++ A+S+ G+ LRV
Sbjct: 132 EAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVG 185
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 20/96 (20%), Positives = 45/96 (46%), Gaps = 4/96 (4%)
Query: 95 EEEYSKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMH-SKNRNRGLAFVTMGSPDE 153
EE + R+ +V + +DI+++FE G + L+ + +++G F+
Sbjct: 105 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQS 164
Query: 154 ATAALNNLESYEFEGRTLKVNYAKIKKKNPFPPVQP 189
+ A++++ ++ G+ L+V A P P + P
Sbjct: 165 SQDAVSSMNLFDLGGQYLRVGKAVTP---PMPLLTP 197
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 4/91 (4%)
Query: 86 AAAVNTEQREEEYSKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAF 145
+ +NTE + + RL N+P+ D+R +F Q G +LD+E+ + + ++G F
Sbjct: 18 GSHMNTENKSQ---PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGF 73
Query: 146 VTMGSPDEATAALNNLESYEFEGRTLKVNYA 176
VT + +A A L EGR ++VN A
Sbjct: 74 VTFENSADADRAREKLHGTVVEGRKIEVNNA 104
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 8/82 (9%)
Query: 188 QPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSK 247
QPK L ++N+ F R DLR+ F G ++ E+IF N R S G+GFV+F++
Sbjct: 28 QPK-----RLHVSNIPFRFRDPDLRQMFGQFG-KILDVEIIF--NERGSKGFGFVTFENS 79
Query: 248 KVAETAISAFQGKLFMGRPLRV 269
A+ A G + GR + V
Sbjct: 80 ADADRAREKLHGTVVEGRKIEV 101
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNL 161
RL N+P+ D+R +F Q G +LD+E+ + + ++G FVT + +A A L
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKL 75
Query: 162 ESYEFEGRTLKVNYA 176
EGR ++VN A
Sbjct: 76 HGTVVEGRKIEVNNA 90
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 46/87 (52%), Gaps = 5/87 (5%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
L ++N+ F R DLR+ F G ++ E+IF N R S G+GFV+F++ A+ A
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFG-KILDVEIIF--NERGSKGFGFVTFENSADADRAREK 74
Query: 257 FQGKLFMGRPLRVAPSRQFARLQTKEG 283
G + GR + V + AR+ T G
Sbjct: 75 LHGTVVEGRKIEV--NNATARVMTNSG 99
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
+F+ANL ++ K L+E F G VV I D +S G G V+F+ A AIS
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAG--VVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 257 FQGKLFMGRPLRV 269
F G+L RP+ V
Sbjct: 76 FNGQLLFDRPMHV 88
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 45/77 (58%), Gaps = 2/77 (2%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
N+++ NL + A ++ ++E F S+ V + ++I+ ++ G+GFV + + V+E AI+
Sbjct: 3 NIYVGNLVYSATSEQVKELF-SQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIA 60
Query: 256 AFQGKLFMGRPLRVAPS 272
FMGR +RV +
Sbjct: 61 KLDNTDFMGRTIRVTEA 77
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSK-NRNRGLAFVTMGSPDEATAALNN 160
RL ++ + T + +R +FE G + I+L M S+ R++G F+T + A AL
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 161 LESYEFEGRTLKVNYA 176
L +E GR +KV +
Sbjct: 88 LNGFELAGRPMKVGHV 103
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 1/84 (1%)
Query: 187 VQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKS 246
+Q L++ +L F LR F G + S +++ RS GYGF++F
Sbjct: 19 LQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGR-IESIQLMMDSETGRSKGYGFITFSD 77
Query: 247 KKVAETAISAFQGKLFMGRPLRVA 270
+ A+ A+ G GRP++V
Sbjct: 78 SECAKKALEQLNGFELAGRPMKVG 101
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDN-PRRSAGYGFVSFKSKKVAETAIS 255
LF+ LSF+ + L + F G +S V+ D +RS G+GFV+F++ A+ A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQ--ISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Query: 256 AFQGKLFMGRPLRV 269
A GK GR +RV
Sbjct: 73 AMNGKSVDGRQIRV 86
Score = 34.7 bits (78), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 41/86 (47%), Gaps = 1/86 (1%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSK-NRNRGLAFVTMGSPDEATAALNN 160
+L + + + + + +F ++G + ++ + + R+RG FVT + D+A A+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 161 LESYEFEGRTLKVNYAKIKKKNPFPP 186
+ +GR ++V+ A N P
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNRSGP 99
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic
Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 195 FNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAI 254
F++F+ +LS E +D++ F G + A V+ +S GYGFVSF +K AE AI
Sbjct: 16 FHVFVGDLSPEITTEDIKAAFAPFG-RISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 74
Query: 255 SAFQGKLFMGRPLRV 269
G+ GR +R
Sbjct: 75 QQMGGQWLGGRQIRT 89
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 113 THEDIRALFEQHGTVLDIELSMH-SKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTL 171
T EDI+A F G + D + + +++G FV+ + +A A+ + GR +
Sbjct: 28 TTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87
Query: 172 KVNYAKIKKKNP 183
+ N+A K P
Sbjct: 88 RTNWATRKPPAP 99
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 45.1 bits (105), Expect = 5e-05, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 46/83 (55%), Gaps = 7/83 (8%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNR----NRGLAFVTMGSPDEA 154
SKT L+ +P T ++ ++LF G++ DIE +++ + G FV P++A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLF---GSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDA 59
Query: 155 TAALNNLESYEFEGRTLKVNYAK 177
A+N L + + +T+KV+YA+
Sbjct: 60 DKAINTLNGLKLQTKTIKVSYAR 82
Score = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
NL + L + + F S G D+ S +++ +S GYGFV++ A+ AI+
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIG-DIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 256 AFQGKLFMGRPLRVAPSR 273
G + ++V+ +R
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 195 FNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAI 254
F++F+ +LS E +D++ F G + A V+ +S GYGFVSF +K AE AI
Sbjct: 16 FHVFVGDLSPEITTEDIKSAFAPFG-KISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 74
Query: 255 SAFQGKLFMGRPLRV 269
G+ GR +R
Sbjct: 75 VHMGGQWLGGRQIRT 89
Score = 31.2 bits (69), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 113 THEDIRALFEQHGTVLDIELSMH-SKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTL 171
T EDI++ F G + D + + +++G FV+ + +A A+ ++ GR +
Sbjct: 28 TTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 87
Query: 172 KVNYAKIKKKNPFPP 186
+ N+A K P P
Sbjct: 88 RTNWATRKPPAPSGP 102
>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 = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 40/174 (22%), Positives = 77/174 (44%), Gaps = 6/174 (3%)
Query: 101 TRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHS-KNRNRGLAFVTMGSPDEATAALN 159
R+ ++ + + IR F G + I+ S S +++G AFV P+ A AL
Sbjct: 13 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
Query: 160 NLESYEFEGRTLKVNY-AKIKKKNPFPPVQPKPFATFN-LFIANLSFEARAKDLREFFIS 217
S GR +KV + I + P + FN +++A++ + D++ F
Sbjct: 73 QXNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVF-- 130
Query: 218 EGWDVVSAEVIFHD-NPRRSAGYGFVSFKSKKVAETAISAFQGKLFMGRPLRVA 270
E + + + + D + GYGF+ ++ + ++ A+S+ G+ LRV
Sbjct: 131 EAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVG 184
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/83 (20%), Positives = 40/83 (48%), Gaps = 1/83 (1%)
Query: 95 EEEYSKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMH-SKNRNRGLAFVTMGSPDE 153
EE + R+ +V + +DI+++FE G + L+ + +++G F+
Sbjct: 104 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQS 163
Query: 154 ATAALNNLESYEFEGRTLKVNYA 176
+ A+++ ++ G+ L+V A
Sbjct: 164 SQDAVSSXNLFDLGGQYLRVGKA 186
>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 = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 9/81 (11%)
Query: 191 PFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVA 250
P + N+FI NL K L + F + G +++S +V+ +N S GYGFV F++++ A
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFG-NILSCKVVCDENG--SKGYGFVHFETQEAA 58
Query: 251 ETAISAFQG------KLFMGR 265
E AI G K+F+GR
Sbjct: 59 ERAIEKMNGMLLNDRKVFVGR 79
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 184 FPPVQ--PKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGF 241
PP Q P+P NL + + LR+ F G + S +++ R+S GYGF
Sbjct: 30 IPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYG-PIESVKIVCDRETRQSRGYGF 88
Query: 242 VSFKSKKVAETAISAFQGKLFMGRPLRVA 270
V F+S A+ AI+ G + + L+VA
Sbjct: 89 VKFQSGSSAQQAIAGLNGFNILNKRLKVA 117
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 103 LVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNR-NRGLAFVTMGSPDEATAALNNL 161
L+ +P T +R LFE++G + +++ + R +RG FV S A A+ L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 162 ESYEFEGRTLKVNYAKIKKKNP 183
+ + LKV A + P
Sbjct: 105 NGFNILNKRLKVALAASGHQRP 126
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 4/71 (5%)
Query: 117 IRALFEQHGTVLDIELSM-HSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNY 175
+ A F G + DI++ + + ++RG AFV ++A AA++N+ E GRT++VN
Sbjct: 29 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 88
Query: 176 AK---IKKKNP 183
AK IK+ P
Sbjct: 89 AKPMRIKESGP 99
Score = 27.7 bits (60), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
L++ L+ E K L FI G D+ ++ + G+ FV F+ + A AI
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFG-DITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 257 FQGKLFMGRPLRV 269
GR +RV
Sbjct: 74 MNESELFGRTIRV 86
>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 = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 117 IRALFEQHGTVLDIELSM-HSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNY 175
+ A F G + DI++ + + ++RG AFV ++A AA++N+ E GRT++VN
Sbjct: 24 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 83
Query: 176 AK 177
AK
Sbjct: 84 AK 85
Score = 29.6 bits (65), Expect = 2.0, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
L++ L+ E K L FI G D+ ++ + G+ FV F+ + A AI
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFG-DITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 257 FQGKLFMGRPLRV 269
GR +RV
Sbjct: 69 MNESELFGRTIRV 81
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 30/93 (32%), Positives = 46/93 (49%), Gaps = 14/93 (15%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHD-NPRRSAGYGFVSFKSKKVAETAI 254
LFI LSFE + LR ++ E W ++ V+ D +RS G+GFV+F S + A+
Sbjct: 29 KLFIGGLSFETTEESLRNYY--EQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Query: 255 SA----FQGKLFMGRPLRVAPSRQFARLQTKEG 283
+A G++ V P R AR ++ G
Sbjct: 87 AARPHSIDGRV-------VEPKRAVAREESGSG 112
Score = 32.7 bits (73), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 49/96 (51%), Gaps = 3/96 (3%)
Query: 92 EQREEEYSKTRLVAQNVPWTSTHEDIRALFEQHGTVLD-IELSMHSKNRNRGLAFVTMGS 150
++RE+E + +L + + +T E +R +EQ G + D + + + R+RG FVT S
Sbjct: 20 KKREKEQFR-KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 78
Query: 151 PDEATAALNNLESYEFEGRTLKVNYAKIKKKNPFPP 186
E AA+ + +GR ++ A ++++ P
Sbjct: 79 MAEVDAAM-AARPHSIDGRVVEPKRAVAREESGSGP 113
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 117 IRALFEQHGTVLDIELSM-HSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNY 175
+ A F G + DI++ + + ++RG AFV ++A AA++N+ E GRT++VN
Sbjct: 22 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 81
Query: 176 AK 177
AK
Sbjct: 82 AK 83
Score = 29.6 bits (65), Expect = 2.0, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
L++ L+ E K L FI G D+ ++ + G+ FV F+ + A AI
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFG-DITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 257 FQGKLFMGRPLRV 269
GR +RV
Sbjct: 67 MNESELFGRTIRV 79
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 48/88 (54%), Gaps = 7/88 (7%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAAL 158
+ T+L N+ T T++++RA FE++G V++ ++ + AFV M ++A A+
Sbjct: 9 ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAI 61
Query: 159 NNLESYEFEGRTLKVNYAKIKKKNPFPP 186
L++ EF+G+ + V + + + P
Sbjct: 62 RGLDNTEFQGKRMHVQLSTSRLRTASGP 89
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 28/85 (32%), Positives = 44/85 (51%), Gaps = 7/85 (8%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNL 161
+L N+P +T ++IR+LFEQ+G VL+ ++ +N G FV + A A+ NL
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII-----KNYG--FVHIEDKTAAEDAIRNL 62
Query: 162 ESYEFEGRTLKVNYAKIKKKNPFPP 186
Y+ G + V +K K K P
Sbjct: 63 HHYKLHGVNINVEASKNKSKASSGP 87
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 6/81 (7%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRG--LAFVTMGSPDEATA 156
+ R+ N+P +DI +F ++G + DI+L KNR G AFV P +A
Sbjct: 21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL----KNRRGGPPFAFVEFEDPRDAED 76
Query: 157 ALNNLESYEFEGRTLKVNYAK 177
A+ + Y+++G L+V + +
Sbjct: 77 AVYGRDGYDYDGYRLRVEFPR 97
>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 = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 5/86 (5%)
Query: 100 KTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALN 159
K +L +P++ T E++ + + HGTV D+ L + + +GLA+V + +A+ A+
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAV- 75
Query: 160 NLESYEFEGRTLKVNYAKIKKKNPFP 185
+ +G T+K N K+ N P
Sbjct: 76 ----MKMDGMTIKENIIKVAISNSGP 97
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 112 STHEDIRALFEQHGTVLDIELSMHSKNR-NRGLAFVTMGSPDEATAALNNLESYEFEGRT 170
+T D+R +F ++G + D+ + ++R +RG AFV + D+A A E +GR
Sbjct: 24 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 83
Query: 171 LKVNYAKIKK 180
++V+++ K+
Sbjct: 84 IRVDFSITKR 93
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 3/81 (3%)
Query: 189 PKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKK 248
P P +F LS +DLRE F G + +++ RRS G+ FV F++
Sbjct: 9 PDPNCCLGVF--GLSLYTTERDLREVFSKYG-PIADVSIVYDQQSRRSRGFAFVYFENVD 65
Query: 249 VAETAISAFQGKLFMGRPLRV 269
A+ A G GR +RV
Sbjct: 66 DAKEAKERANGMELDGRRIRV 86
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 112 STHEDIRALFEQHGTVLDIELSMHSKNR-NRGLAFVTMGSPDEATAALNNLESYEFEGRT 170
+T D+R +F ++G + D+ + ++R +RG AFV + D+A A E +GR
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 171 LKVNYAKIKK 180
++V+++ K+
Sbjct: 87 IRVDFSITKR 96
Score = 37.4 bits (85), Expect = 0.010, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 3/81 (3%)
Query: 189 PKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKK 248
P P +F LS +DLRE F G + +++ RRS G+ FV F++
Sbjct: 12 PDPNCCLGVF--GLSLYTTERDLREVFSKYG-PIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 249 VAETAISAFQGKLFMGRPLRV 269
A+ A G GR +RV
Sbjct: 69 DAKEAKERANGMELDGRRIRV 89
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 1/70 (1%)
Query: 112 STHEDIRALFEQHGTVLDIELSMHSKNR-NRGLAFVTMGSPDEATAALNNLESYEFEGRT 170
+T D+R +F ++G + D+ + ++R +RG AFV + D+A A E +GR
Sbjct: 58 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 117
Query: 171 LKVNYAKIKK 180
++V+++ K+
Sbjct: 118 IRVDFSITKR 127
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 3/81 (3%)
Query: 189 PKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKK 248
P P +F LS +DLRE F G + +++ RRS G+ FV F++
Sbjct: 43 PDPNCCLGVF--GLSLYTTERDLREVFSKYG-PIADVSIVYDQQSRRSRGFAFVYFENVD 99
Query: 249 VAETAISAFQGKLFMGRPLRV 269
A+ A G GR +RV
Sbjct: 100 DAKEAKERANGMELDGRRIRV 120
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 9/76 (11%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
N+FI NL K L + F + G +++S +V+ +N S GYGFV F++++ AE AI
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFG-NILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 69
Query: 256 AFQG------KLFMGR 265
G K+F+GR
Sbjct: 70 KMNGMLLNDRKVFVGR 85
>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 = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 117 IRALFEQHGTVLDIELSM-HSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNY 175
+ A F G + DI++ + + ++RG AFV ++A AA++N+ E GRT++VN
Sbjct: 19 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 78
Query: 176 A 176
A
Sbjct: 79 A 79
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
L++ L+ E K L FI G D+ ++ + G+ FV F+ + A AI
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFG-DITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 257 FQGKLFMGRPLRV 269
GR +RV
Sbjct: 64 MNESELFGRTIRV 76
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 35/61 (57%)
Query: 117 IRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYA 176
++A+F +HG + ++ L +++RG AF+T +P +A A ++ G+ +KV A
Sbjct: 24 LKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA 83
Query: 177 K 177
K
Sbjct: 84 K 84
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPR-RSAGYGFVSFKSKKVAETAIS 255
L++ +L F LR F E + + V+ D+ RS GYGF++F + A A+
Sbjct: 8 LYVGSLHFNITEDMLRGIF--EPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 256 AFQGKLFMGRPLRVA 270
G GRP+RV
Sbjct: 66 QLNGFELAGRPMRVG 80
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 192 FATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAE 251
+ NL++ NL + LR+ F G + SA+V+ RS G+GFV F S + A
Sbjct: 13 YQVVNLYVKNLDDGIDDERLRKAFSPFGT-ITSAKVMMEGG--RSKGFGFVCFSSPEEAT 69
Query: 252 TAISAFQGKLFMGRPLRVA 270
A++ G++ +PL VA
Sbjct: 70 KAVTEMNGRIVATKPLYVA 88
Score = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 25/101 (24%), Positives = 44/101 (43%), Gaps = 1/101 (0%)
Query: 86 AAAVNTEQREEEYSKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAF 145
++ ++ R Y L +N+ E +R F GT+ ++ M R++G F
Sbjct: 1 GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGF 59
Query: 146 VTMGSPDEATAALNNLESYEFEGRTLKVNYAKIKKKNPFPP 186
V SP+EAT A+ + + L V A+ K++ P
Sbjct: 60 VCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGP 100
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 117 IRALFEQHGTVLDIELSM-HSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNY 175
+ A F G + DI++ + + ++RG AFV ++A AA++N+ E GRT++VN
Sbjct: 80 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
Query: 176 A 176
A
Sbjct: 140 A 140
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
L++ L+ E K L FI G D+ ++ + G+ FV F+ + A AI
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFG-DITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 257 FQGKLFMGRPLRV 269
GR +RV
Sbjct: 125 MNESELFGRTIRV 137
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 119 ALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYAK 177
A+F Q G +LDI +S K R G AFV AT AL +++ + F + +++ YAK
Sbjct: 31 AIFSQFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 119 ALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYAK 177
A+F Q G +LDI +S K R G AFV AT AL +++ + F + +++ YAK
Sbjct: 32 AIFSQFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 88
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 44/75 (58%), Gaps = 4/75 (5%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAAL 158
SKT LV N+ +++T E ++ +FE+ I++ + +++G AF+ S ++A AL
Sbjct: 15 SKT-LVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 159 NNLESYEFEGRTLKV 173
N+ E EGR +++
Sbjct: 71 NSCNKREIEGRAIRL 85
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 119 ALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYAK 177
A+F Q G +LDI +S K R G AFV AT AL +++ + F + +++ YAK
Sbjct: 32 AIFSQFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 88
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 4/72 (5%)
Query: 107 NVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEF 166
N+P + + ED++ LF +G V+ ++R +A + MGS +EA AL +L +++
Sbjct: 127 NIPPSVSEEDLKVLFSSNGGVVK---GFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL 183
Query: 167 -EGRTLKVNYAK 177
E L+V+++K
Sbjct: 184 GENHHLRVSFSK 195
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 112 STHEDIRALFEQHGTVLDIELSMHSKNR-NRGLAFVTMGSPDEATAALNNLESYEFEGRT 170
+T D+R +F ++G + D+ + ++R +RG AFV + D+A A E +GR
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 171 LKVN 174
++V+
Sbjct: 87 IRVS 90
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 189 PKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKK 248
P P +F LS +DLRE F G + +++ RRS G+ FV F++
Sbjct: 12 PDPNCCLGVF--GLSLYTTERDLREVFSKYG-PIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 249 VAETAISAFQGKLFMGRPLRVA 270
A+ A G GR +RV+
Sbjct: 69 DAKEAKERANGMELDGRRIRVS 90
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 3/82 (3%)
Query: 103 LVAQNVPWTSTHEDIRALFEQHGTVLDIELSM--HSKNRNRGLAFVTMGSPDEATAALNN 160
L N+ + ++ + +R +FE++G V D+ + H+K RG AFV +A A
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKA-PRGFAFVRFHDRRDAQDAEAA 74
Query: 161 LESYEFEGRTLKVNYAKIKKKN 182
++ E +GR L+V A+ +++
Sbjct: 75 MDGAELDGRELRVQVARYGRRD 96
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 4/72 (5%)
Query: 107 NVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEF 166
N+P + + ED++ LF +G V+ ++R +A + MGS +EA AL +L +++
Sbjct: 158 NIPPSVSEEDLKVLFSSNGGVVK---GFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL 214
Query: 167 -EGRTLKVNYAK 177
E L+V+++K
Sbjct: 215 GENHHLRVSFSK 226
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 43/174 (24%), Positives = 69/174 (39%), Gaps = 13/174 (7%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNR-NRGLAFVTMGSPDEATAA 157
S T L+ +P T ++ ALF G + + K + G AFV S ++ A
Sbjct: 13 SNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRA 72
Query: 158 LNNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFIS 217
+ L + LKV+YA+ ++ NL++ NL L F
Sbjct: 73 IKVLNGITVRNKRLKVSYARPGGES---------IKDTNLYVTNLPRTITDDQLDTIFGK 123
Query: 218 EGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQGKLFMG--RPLRV 269
G +V ++ R G FV + ++ A+ AISA + G +PL V
Sbjct: 124 YG-SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 176
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 101 TRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNR-NRGLAFVTMGSPDEATAALN 159
T L N+ + ++ + +R +FE++G V D+ + + +RG AFV +A A++
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 160 NLESYEFEGRTLKVNYAKIKK 180
++ +GR L+V A+ +
Sbjct: 108 AMDGAVLDGRELRVQMARYGR 128
>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 = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 100 KTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHS-KNRNRGLAFVTMGSPDEATAAL 158
+T L+ +P T +++R+LF G V +L + G FV + +A A+
Sbjct: 4 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 159 NNLESYEFEGRTLKVNYAK 177
N L + +T+KV+YA+
Sbjct: 64 NTLNGLRLQSKTIKVSYAR 82
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
NL + L +LR F S G +V SA++I S GYGFV++ + K AE AI+
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIG-EVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 256 AFQGKLFMGRPLRVAPSR 273
G + ++V+ +R
Sbjct: 65 TLNGLRLQSKTIKVSYAR 82
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLD-IELSMHSKNRNRGLAFVTMGSPDEATAALNN 160
+L + W++T E +R+ F Q+G V+D + + + N++RG FV P+ L +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 161 LESYEFEGRTL 171
+ +GR +
Sbjct: 78 -RPHTLDGRNI 87
Score = 34.3 bits (77), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
LF+ L + + LR +F G +VV ++ +S G+GFV FK T +++
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYG-EVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
>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 = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 1/81 (1%)
Query: 98 YSKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHS-KNRNRGLAFVTMGSPDEATA 156
+ T L+ +P T +++R+LF G V +L + G FV + +A
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 157 ALNNLESYEFEGRTLKVNYAK 177
A+N L + +T+KV+YA+
Sbjct: 77 AINTLNGLRLQSKTIKVSYAR 97
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 41/82 (50%), Gaps = 1/82 (1%)
Query: 192 FATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAE 251
F NL + L +LR F S G +V SA++I S GYGFV++ + K AE
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIG-EVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 75
Query: 252 TAISAFQGKLFMGRPLRVAPSR 273
AI+ G + ++V+ +R
Sbjct: 76 RAINTLNGLRLQSKTIKVSYAR 97
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 100 KTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALN 159
++RL N+P T E++R LFE++G ++ + ++++G F+ + + A A
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI-----HKDKGFGFIRLETRTLAEIAKV 69
Query: 160 NLESYEFEGRTLKVNYA 176
L++ G+ L+V +A
Sbjct: 70 ELDNMPLRGKQLRVRFA 86
Score = 32.3 bits (72), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
LF+ NL + +++R+ F G + EV H + G+GF+ +++ +AE A
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGK---AGEVFIH----KDKGFGFIRLETRTLAEIAKVE 70
Query: 257 FQGKLFMGRPLRV 269
G+ LRV
Sbjct: 71 LDNMPLRGKQLRV 83
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 115 EDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVN 174
+ + A+F + G +LDI +S K R G AFV AT AL +++ + F + +++
Sbjct: 27 KSLHAIFSRFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 84
Query: 175 YAK 177
YAK
Sbjct: 85 YAK 87
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 40/171 (23%), Positives = 70/171 (40%), Gaps = 22/171 (12%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAAL 158
++ +++ + +P T++++ H + D EL ++ +G AFVT+ + ++A AA+
Sbjct: 21 NRRKILIRGLPGDVTNQEV------HDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAI 74
Query: 159 NNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISE 218
N R L V +QP L +ANL + E
Sbjct: 75 NAFHQSRLRERELSVQ------------LQPTDAL---LCVANLPPSLTQQQFEELVRPF 119
Query: 219 GWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQGKLFMGRPLRV 269
G + +++ + +S GYGF + K A A S GK R L V
Sbjct: 120 G-SLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 115 EDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVN 174
+ + A+F + G +LDI +S K R G AFV AT AL +++ + F + +++
Sbjct: 27 KSLHAIFSRFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 84
Query: 175 YAK 177
YAK
Sbjct: 85 YAK 87
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 115 EDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVN 174
+ + A+F + G +LDI +S K R G AFV AT AL +++ + F + +++
Sbjct: 25 KSLHAIFSRFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 82
Query: 175 YAK 177
YAK
Sbjct: 83 YAK 85
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 115 EDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVN 174
+ + A+F + G +LDI +S K R G AFV AT AL +++ + F + +++
Sbjct: 28 KSLHAIFSRFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 85
Query: 175 YAK 177
YAK
Sbjct: 86 YAK 88
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 115 EDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVN 174
+ + A+F + G +LDI +S K R G AFV AT AL +++ + F + +++
Sbjct: 27 KSLHAIFSRFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 84
Query: 175 YAK 177
YAK
Sbjct: 85 YAK 87
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 40/171 (23%), Positives = 70/171 (40%), Gaps = 22/171 (12%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAAL 158
++ +++ + +P T++++ H + D EL ++ +G AFVT+ + ++A AA+
Sbjct: 19 NRRKILIRGLPGDVTNQEV------HDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAI 72
Query: 159 NNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISE 218
N R L V +QP L +ANL + E
Sbjct: 73 NAFHQSRLRERELSVQ------------LQPTDAL---LCVANLPPSLTQQQFEELVRPF 117
Query: 219 GWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQGKLFMGRPLRV 269
G + +++ + +S GYGF + K A A S GK R L V
Sbjct: 118 G-SLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 115 EDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVN 174
+ + A+F + G +LDI +S K R G AFV AT AL +++ + F + +++
Sbjct: 23 KSLHAIFSRFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 80
Query: 175 YAK 177
YAK
Sbjct: 81 YAK 83
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 115 EDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVN 174
+ + A+F + G +LDI +S K R G AFV AT AL +++ + F + +++
Sbjct: 22 KSLHAIFSRFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 79
Query: 175 YAK 177
YAK
Sbjct: 80 YAK 82
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 40/171 (23%), Positives = 70/171 (40%), Gaps = 22/171 (12%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAAL 158
++ +++ + +P T++++ H + D EL ++ +G AFVT+ + ++A AA+
Sbjct: 21 NRRKILIRGLPGDVTNQEV------HDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAI 74
Query: 159 NNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISE 218
N R L V +QP L +ANL + E
Sbjct: 75 NAFHQSRLRERELSVQ------------LQPTDAL---LCVANLPPSLTQQQFEELVRPF 119
Query: 219 GWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQGKLFMGRPLRV 269
G + +++ + +S GYGF + K A A S GK R L V
Sbjct: 120 G-SLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 45/87 (51%), Gaps = 5/87 (5%)
Query: 101 TRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNR-NRGLAFVTMGSPDEATAALN 159
T L N+ + ++ + +R +FE++G V D+ + + +RG AFV +A A++
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 160 NLESYEFEGRTLKVNYAKIKKKNPFPP 186
++ +GR L+V A+ + PP
Sbjct: 131 AMDGAVLDGRELRVQMARYGR----PP 153
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 115 EDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVN 174
+ + A+F + G +LDI +S K R G AFV AT AL +++ + F + +++
Sbjct: 24 KSLHAIFSRFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 81
Query: 175 YAK 177
YAK
Sbjct: 82 YAK 84
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 115 EDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVN 174
+ + A+F + G +LDI +S K R G AFV AT AL +++ + F + +++
Sbjct: 28 KSLHAIFSRFGQILDILVSRSLKMR--GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ 85
Query: 175 YAK 177
YAK
Sbjct: 86 YAK 88
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 119 ALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYAK 177
ALF Q G V+DI +++ + + RG AFV +T AL L+ + F G+ +++ YAK
Sbjct: 29 ALFSQFGHVVDI-VALKTM-KMRGQAFVIFKELGSSTNALRQLQGFPFYGKPMRIQYAK 85
>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 = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 198 FIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAF 257
F+ LS++ KDL+++F G +VV + N RS G+GF+ FK E +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFG-EVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQK 73
Query: 258 QGKL 261
+ +L
Sbjct: 74 EHRL 77
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 38/74 (51%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
+FI NL E K L + F + G + + +++ + S GY F++F S ++ AI A
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 257 FQGKLFMGRPLRVA 270
G+ RP+ V+
Sbjct: 68 MNGQYLCNRPITVS 81
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 39/160 (24%), Positives = 63/160 (39%), Gaps = 11/160 (6%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSK-NRNRGLAFVTMGSPDEATAA 157
S T L+ +P T ++ ALF G + + K + G AFV S ++ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 158 LNNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFIS 217
+ L + LKV+YA+ ++ NL++ NL L F
Sbjct: 62 IKVLNGITVRNKRLKVSYARPGGES---------IKDTNLYVTNLPRTITDDQLDTIFGK 112
Query: 218 EGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAF 257
G +V ++ R G FV + ++ A+ AISA
Sbjct: 113 YG-SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
+F+ NL R + L E F+ G ++ I D + +GFV FK + AI+
Sbjct: 19 VFVGNLEARVREEILYELFLQAGP--LTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76
Query: 257 FQGKLFMGRPLRVA 270
G GRP+ V+
Sbjct: 77 LNGIRLYGRPINVS 90
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/94 (24%), Positives = 46/94 (48%), Gaps = 3/94 (3%)
Query: 86 AAAVNTEQREEEYSKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIEL--SMHSKNRNRGL 143
++ ++ Q ++ + ++++ +N+P+ + +IR LF G + + L M +RG
Sbjct: 1 GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 144 AFVTMGSPDEATAALNNL-ESYEFEGRTLKVNYA 176
FV + +A A N L S GR L + +A
Sbjct: 61 GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWA 94
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 12/75 (16%)
Query: 189 PKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSA------GYGFV 242
PK T + + N+ F+A +++RE F + G E+ P++ G+GFV
Sbjct: 10 PKKQTTSKILVRNIPFQANQREIRELFSTFG------ELKTVRLPKKMTGTGAHRGFGFV 63
Query: 243 SFKSKKVAETAISAF 257
F +K+ A+ A +A
Sbjct: 64 DFITKQDAKKAFNAL 78
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 37.4 bits (85), Expect = 0.010, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNR-NRGLAFVTMGSPDEATAA 157
SK+ + N+P++ T+ D+ +F ++G V+ + + R ++G+AF+ D A
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 158 LNNLESYEFEGRTLKVNYA 176
+ + + GR +K + A
Sbjct: 75 TRAINNKQLFGRVIKASIA 93
Score = 35.4 bits (80), Expect = 0.041, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 1/74 (1%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
++++NL F DL F G VV ++ + R+S G F+ F K A+ A
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYG-KVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 257 FQGKLFMGRPLRVA 270
K GR ++ +
Sbjct: 78 INNKQLFGRVIKAS 91
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
NLFI +L E DL F+ G +V+SA+V S +GFVSF + A+ AI
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFG-NVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 256 AFQG 259
A G
Sbjct: 101 AMNG 104
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 101 TRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNR-NRGLAFVTMGSPDEATAALN 159
L ++P T D+ + F G V+ ++ + + ++ FV+ +PD A A+
Sbjct: 41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 160 NLESYEFEGRTLKVNYAK 177
+ ++ + LKV K
Sbjct: 101 AMNGFQVGTKRLKVQLKK 118
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 40/92 (43%), Gaps = 2/92 (2%)
Query: 181 KNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYG 240
+ P + P+ +F L+ R +DL +FF + G V +I N RRS G
Sbjct: 12 REPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVG-KVRDVRIISDRNSRRSKGIA 70
Query: 241 FVSFKSKKVAETAISAFQGKLFMGRPLRVAPS 272
+V F + AI G+ +G P+ V S
Sbjct: 71 YVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS 101
>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 = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 37/128 (28%), Positives = 53/128 (41%), Gaps = 14/128 (10%)
Query: 140 NRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFI 199
NR +V S ++ AL E G LKV +IK + P K A L
Sbjct: 53 NRKFGYVDFESAEDLEKAL------ELTG--LKVFGNEIKLEKPKGRDSKKVRAARTLLA 104
Query: 200 ANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQG 259
NLSF +L+E F D + ++ D +S G ++ FKS+ AE + QG
Sbjct: 105 KNLSFNITEDELKEVF----EDALEIRLVSQDG--KSKGIAYIEFKSEADAEKNLEEKQG 158
Query: 260 KLFMGRPL 267
GR +
Sbjct: 159 AEIDGRSV 166
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 103 LVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLE 162
L+A+N+ + T ++++ +FE L+I L + +++G+A++ S +A L +
Sbjct: 102 LLAKNLSFNITEDELKEVFED---ALEIRL-VSQDGKSKGIAYIEFKSEADAEKNLEEKQ 157
Query: 163 SYEFEGRTLKVNY 175
E +GR++ + Y
Sbjct: 158 GAEIDGRSVSLYY 170
>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 = 36.6 bits (83), Expect = 0.019, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
+FI LS++ KDL+++F G +VV + RS G+GFV FK + + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFG-EVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60
Query: 257 FQGKL 261
+ KL
Sbjct: 61 KEHKL 65
Score = 30.4 bits (67), Expect = 1.4, Method: Composition-based stats.
Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 110 WTSTHEDIRALFEQHGTVLDIELSMHS-KNRNRGLAFVTMGSPDEATAALNNLESYEFEG 168
W +T +D++ F + G V+D L + R+RG FV + ++ E ++ G
Sbjct: 9 WDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKE-HKLNG 67
Query: 169 RTL 171
+ +
Sbjct: 68 KVI 70
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 28/51 (54%)
Query: 113 THEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLES 163
T ED+R +FE GT+ + + ++G AFV + EA AA+N L S
Sbjct: 25 TDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLHS 75
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 115 EDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVN 174
+ + A+F + G +LDI +S K R G AFV AT AL + + + F + ++
Sbjct: 27 KSLHAIFSRFGQILDILVSRSLKXR--GQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQ 84
Query: 175 YAK 177
YAK
Sbjct: 85 YAK 87
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 115 EDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVN 174
+ + A+F + G +LDI +S K R G AFV AT AL + + + F + ++
Sbjct: 28 KSLHAIFSRFGQILDILVSRSLKXR--GQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQ 85
Query: 175 YAK 177
YAK
Sbjct: 86 YAK 88
>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 = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 24/102 (23%), Positives = 48/102 (47%), Gaps = 8/102 (7%)
Query: 171 LKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFH 230
++ +Y +++ P Q + + LF+ + EA +D+ + F G + I
Sbjct: 1 MREDYDSVEQDGDEPGPQ-RSVEGWILFVTGVHEEATEEDIHDKFAEYG----EIKNIHL 55
Query: 231 DNPRRSA---GYGFVSFKSKKVAETAISAFQGKLFMGRPLRV 269
+ RR+ GY V +++ K A+ A+ G+ MG+P+ V
Sbjct: 56 NLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 97
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 115 EDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVN 174
+ + A+F + G +LDI +S K R G AFV AT AL + + + F + ++
Sbjct: 25 KSLHAIFSRFGQILDILVSRSLKXR--GQAFVIFKEVSSATNALRSXQGFPFYDKPXRIQ 82
Query: 175 YAK 177
YAK
Sbjct: 83 YAK 85
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 36.2 bits (82), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 195 FNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAI 254
++LF+ +L+ + L EFF+ +V+ D S GYGFV F + + A+
Sbjct: 10 YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVL-DQTGVSKGYGFVKFTDELEQKRAL 68
Query: 255 SAFQGKLFMG-RPLRVA 270
+ QG + +G +P+R++
Sbjct: 69 TECQGAVGLGSKPVRLS 85
>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 = 36.2 bits (82), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIE-LSMHSKN--RNRGLAFVTMGSPDEATAAL 158
++ VP T + +D+R LFEQ+G V +I L S+N +++G FVT + A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 159 NNLES 163
N L +
Sbjct: 65 NALHN 69
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 8/84 (9%)
Query: 195 FNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHD---NPRRSAGYGFVSFKSKKVAE 251
+F+ + KDLRE F E + V + D NP +S G FV+F ++K A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELF--EQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 252 TAISAFQG-KLF--MGRPLRVAPS 272
A +A K+ M P+++ P+
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPA 85
>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 = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
NLFI +L E +DL + F+ G +VVSA+V S +GFVS+ + A+ AI
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFG-NVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 256 AFQGKLFMGRPLRVAPSR 273
+ G + L+V R
Sbjct: 86 SMNGFQIGMKRLKVQLKR 103
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 17/80 (21%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 108 VPWTSTHEDIRALFEQHGTVLDIELSMHSK-NRNRGLAFVTMGSPDEATAALNNLESYEF 166
+P +D+ +F G V+ ++ + + N ++ FV+ +P A AA+ ++ ++
Sbjct: 33 LPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQI 92
Query: 167 EGRTLKVNYAKIKKKNPFPP 186
+ LKV + K + P
Sbjct: 93 GMKRLKVQLKRSKNDSKSGP 112
>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 = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 46/99 (46%), Gaps = 8/99 (8%)
Query: 174 NYAKIKKKNPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNP 233
+Y +++ P Q + + LF+ + EA +D+ + F G + I +
Sbjct: 3 DYDSVEQDGDEPGPQ-RSVEGWILFVTGVHEEATEEDIHDKFAEYG----EIKNIHLNLD 57
Query: 234 RRSA---GYGFVSFKSKKVAETAISAFQGKLFMGRPLRV 269
RR+ GY V +++ K A+ A+ G+ MG+P+ V
Sbjct: 58 RRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 96
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 35.4 bits (80), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 17/74 (22%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 103 LVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKN-RNRGLAFVTMGSPDEATAALNNL 161
L+A+N+P+ T ++++ +FE E+ + SK+ +++G+A++ + +A
Sbjct: 96 LLAKNLPYKVTQDELKEVFEDAA-----EIRLVSKDGKSKGIAYIEFKTEADAEKTFEEK 150
Query: 162 ESYEFEGRTLKVNY 175
+ E +GR++ + Y
Sbjct: 151 QGTEIDGRSISLYY 164
Score = 30.8 bits (68), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 35/141 (24%), Positives = 55/141 (39%), Gaps = 19/141 (13%)
Query: 127 VLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYAKIKKKNPFPP 186
V+D+ + M R +V S ++ AL E G LKV +IK + P
Sbjct: 39 VVDVRIGM-----TRKFGYVDFESAEDLEKAL------ELTG--LKVFGNEIKLEKPKGK 85
Query: 187 VQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKS 246
K L NL ++ +L+E F +AE+ +S G ++ FK+
Sbjct: 86 DSKKERDARTLLAKNLPYKVTQDELKEVFED------AAEIRLVSKDGKSKGIAYIEFKT 139
Query: 247 KKVAETAISAFQGKLFMGRPL 267
+ AE QG GR +
Sbjct: 140 EADAEKTFEEKQGTEIDGRSI 160
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 10/76 (13%)
Query: 191 PFATFNLFIANLSFEARAKDLR----EFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKS 246
P FNLF+ NL+F A +L+ + F VV + + +G+V F+S
Sbjct: 4 PTTAFNLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGM------TRKFGYVDFES 57
Query: 247 KKVAETAISAFQGKLF 262
+ E A+ K+F
Sbjct: 58 AEDLEKALELTGLKVF 73
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 35.4 bits (80), Expect = 0.043, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 107 NVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEF 166
N+P +T D+ LF+ G +LD + +G F+ + ++A + L ++ F
Sbjct: 34 NIPHFATEADLIPLFQNFGFILDFK-----HYPEKGCCFIKYDTHEQAAVCIVALANFPF 88
Query: 167 EGRTLKVNYAK 177
+GR L+ + K
Sbjct: 89 QGRNLRTGWGK 99
>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 = 35.0 bits (79), Expect = 0.050, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 195 FNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAI 254
F++F+ +LS E + F G + A V+ +S GYGFVSF +K AE AI
Sbjct: 7 FHVFVGDLSPEITTAAIAAAFAPFG-RISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 65
Query: 255 SAFQGKLFMGRPLR 268
G+ GR +R
Sbjct: 66 QQMGGQWLGGRQIR 79
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 35.0 bits (79), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 44/182 (24%), Positives = 73/182 (40%), Gaps = 27/182 (14%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQH-----------GTVLDIELSMHSKNRNRGLAFVT 147
S RL N+P+ T E + F VL +++ N+++ AF+
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-----NQDKNFAFLE 57
Query: 148 MGSPDEATAALNNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEAR 207
S DE T A+ + F+G++L KI++ + + QP P A LFI L
Sbjct: 58 FRSVDETTQAM-AFDGIIFQGQSL-----KIRRPHDY---QPLPGA-HKLFIGGLPNYLN 107
Query: 208 AKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQGKLFMGRPL 267
++E S G + + ++ S GY F + V + AI+ G + L
Sbjct: 108 DDQVKELLTSFG-PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 166
Query: 268 RV 269
V
Sbjct: 167 LV 168
>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 = 35.0 bits (79), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 44/182 (24%), Positives = 73/182 (40%), Gaps = 27/182 (14%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQH-----------GTVLDIELSMHSKNRNRGLAFVT 147
S RL N+P+ T E + F VL +++ N+++ AF+
Sbjct: 5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-----NQDKNFAFLE 59
Query: 148 MGSPDEATAALNNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKPFATFNLFIANLSFEAR 207
S DE T A+ + F+G++L KI++ + + QP P A LFI L
Sbjct: 60 FRSVDETTQAM-AFDGIIFQGQSL-----KIRRPHDY---QPLPGA-HKLFIGGLPNYLN 109
Query: 208 AKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQGKLFMGRPL 267
++E S G + + ++ S GY F + V + AI+ G + L
Sbjct: 110 DDQVKELLTSFG-PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 168
Query: 268 RV 269
V
Sbjct: 169 LV 170
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 35.0 bits (79), Expect = 0.052, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAE 251
+F+ LS +D++ +F G V A ++F R G+GFV+F+S+ + E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFG-KVDDAMLMFDKTTNRHRGFGFVTFESEDIVE 55
Score = 34.7 bits (78), Expect = 0.065, Method: Composition-based stats.
Identities = 19/42 (45%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 112 STHEDIRALFEQHGTVLDIELSM-HSKNRNRGLAFVTMGSPD 152
+T ED++ FEQ G V D L + NR+RG FVT S D
Sbjct: 11 TTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 34.7 bits (78), Expect = 0.070, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
+F+ NL F+ K L++ F +E V+ A++ + +S G G V F+S +VAE A
Sbjct: 8 IFVRNLPFDFTWKMLKDKF-NECGHVLYADIKMENG--KSKGCGVVKFESPEVAERACRM 64
Query: 257 FQGKLFMGRPLRVAPSR 273
G GR + V R
Sbjct: 65 MNGMKLSGREIDVRIDR 81
Score = 29.3 bits (64), Expect = 2.7, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 103 LVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLE 162
+ +N+P+ T + ++ F + G VL ++ M + +++G V SP+ A A +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERACRMMN 66
Query: 163 SYEFEGRTLKV 173
+ GR + V
Sbjct: 67 GMKLSGREIDV 77
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 34.7 bits (78), Expect = 0.070, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
+F+ NL F+ K L++ F +E V+ A++ + +S G G V F+S +VAE A
Sbjct: 11 IFVRNLPFDFTWKMLKDKF-NECGHVLYADIKMENG--KSKGCGVVKFESPEVAERACRM 67
Query: 257 FQGKLFMGRPLRVAPSR 273
G GR + V R
Sbjct: 68 MNGMKLSGREIDVRIDR 84
Score = 29.6 bits (65), Expect = 2.0, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNL 161
++ +N+P+ T + ++ F + G VL ++ M + +++G V SP+ A A +
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN-GKSKGCGVVKFESPEVAERACRMM 68
Query: 162 ESYEFEGRTLKV 173
+ GR + V
Sbjct: 69 NGMKLSGREIDV 80
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 33/77 (42%), Gaps = 2/77 (2%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
NL+I+NL ++L G V+S I D+ S G GF +S + E I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFG-QVISTR-ILRDSSGTSRGVGFARMESTEKCEAVIG 84
Query: 256 AFQGKLFMGRPLRVAPS 272
F GK P AP+
Sbjct: 85 HFNGKFIKTPPGVSAPT 101
Score = 32.0 bits (71), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 17/80 (21%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 94 REEEYSKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDE 153
+++E T L N+P + +++ + + G V+ + S +RG+ F M S ++
Sbjct: 19 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEK 78
Query: 154 ATAALNNLESYEFEGRTLKV 173
A + + F G+ +K
Sbjct: 79 CEAVIGH-----FNGKFIKT 93
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 197 LFIANLSFEARAKDLREFFISEGW-DVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETA 253
+F+ L + LR++F EG+ D+ A VI +S GYGFV+ + AE A
Sbjct: 20 IFVGGLPYHTTDASLRKYF--EGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
>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 = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSA---GYGFVSFKSKKVAETA 253
LF+ + EA +D+ + F G + I + RR+ GY V +++ K A+ A
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYG----EIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 254 ISAFQGKLFMGRPLRV 269
+ G+ MG+P+ V
Sbjct: 66 MEGLNGQDLMGQPISV 81
>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
Growth Factor 2 Mrna Binding Protein 3
Length = 96
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNL 161
+L +N+P E + +L Q+G V E + + + VT S D+A AL+ L
Sbjct: 17 KLQIRNIPPHLQWEVLDSLLVQYGVVESCE--QVNTDSETAVVNVTYSSKDQARQALDKL 74
Query: 162 ESYEFEGRTLKVNY 175
++ E TLKV Y
Sbjct: 75 NGFQLENFTLKVAY 88
>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 = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 40/88 (45%), Gaps = 12/88 (13%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKS----KKVAET 252
+F+ + ++R FF G V I D S GYGFVSF + +K+ E+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGS--VKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 253 AISAFQGKLFMGRPLRVAPSRQFARLQT 280
I+ F G+ L++ P+ + L T
Sbjct: 70 QIN------FHGKKLKLGPAIRKQNLST 91
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 2/77 (2%)
Query: 116 DIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNY 175
+IR+ F ++G+V ++++ ++G FV+ + + + + F G+ LK+
Sbjct: 25 EIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES--QINFHGKKLKLGP 82
Query: 176 AKIKKKNPFPPVQPKPF 192
A K+ VQP+P
Sbjct: 83 AIRKQNLSTYHVQPRPL 99
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAIS 255
+FI LS++ + LRE+F G +V V+ +RS G+GFV+F + + ++
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFG-EVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 85
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 113 THEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYE 165
+ +D+R LFE G + + + ++G AFV S EA AA+N L +
Sbjct: 28 SEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALHGSQ 80
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 119 ALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYAK 177
A+F Q G +LDI +++ + + RG AFV A+ AL ++ + F + +++ Y+K
Sbjct: 29 AIFSQFGQILDI-VALKTL-KMRGQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAYSK 85
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 33.1 bits (74), Expect = 0.19, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 12/80 (15%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKS----KKVAET 252
+F+ + ++R FF G V I D S GYGFVSF + +K+ E+
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYG--SVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 70
Query: 253 AISAFQGKLFMGRPLRVAPS 272
I+ F G+ L++ P+
Sbjct: 71 QIN------FHGKKLKLGPA 84
>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 = 33.1 bits (74), Expect = 0.20, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 96 EEYSKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIE-LSMHSKNRNRGLAFVTMGSPDEA 154
E T L N+P T T + + +F ++G+++ L R RG+AFV +EA
Sbjct: 9 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 68
Query: 155 TAALNNLESYEFEG 168
A++ L + EG
Sbjct: 69 QEAISALNNVIPEG 82
>pdb|1WG1|A Chain A, Solution Structure Of Rna Binding Domain In
Bab13405(Homolog Exc-7)
Length = 88
Score = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 103 LVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLE 162
++ +N+P S +++ H + D +L +RN+ AFVT+ + ++A A+
Sbjct: 8 ILVKNLPQDSNCQEV------HDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFH 61
Query: 163 SYEFEGRTLKV 173
Y F G+ L V
Sbjct: 62 QYSFRGKDLIV 72
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 32.7 bits (73), Expect = 0.26, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 103 LVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLE 162
L+A+N+ + T ++++ +FE L+I L + +++G+A++ S +A L +
Sbjct: 19 LLAKNLSFNITEDELKEVFED---ALEIRL-VSQDGKSKGIAYIEFKSEADAEKNLEEKQ 74
Query: 163 SYEFEGRTLKVNY 175
E +GR++ + Y
Sbjct: 75 GAEIDGRSVSLYY 87
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 32.7 bits (73), Expect = 0.29, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSA---GYGFVSFKSKKVAETA 253
LF+ + EA +D+ + F G + I + RR+ GY V +++ K A+ A
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYG----EIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 254 ISAFQGKLFMGRPLRV 269
+ G+ MG+P+ V
Sbjct: 66 MEGLNGQDLMGQPISV 81
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 21/98 (21%), Positives = 46/98 (46%), Gaps = 3/98 (3%)
Query: 174 NYAKIKKKN--PFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHD 231
+Y +++ ++ P + + LF+ ++ EA+ +++E F G ++ + +
Sbjct: 4 SYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYG-EIKNIHLNLDR 62
Query: 232 NPRRSAGYGFVSFKSKKVAETAISAFQGKLFMGRPLRV 269
S GY V +++ K A A A G MG+ ++V
Sbjct: 63 RTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100
>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 = 32.3 bits (72), Expect = 0.30, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSA---GYGFVSFKSKKVAETA 253
LF+ + EA +D+ + F G + I + RR+ GY V +++ K A+ A
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYG----EIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 67
Query: 254 ISAFQGKLFMGRPLRV 269
+ G+ MG+P+ V
Sbjct: 68 MEGLNGQDLMGQPISV 83
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 103 LVAQNVPWTSTHEDIRALF----EQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAAL 158
L +N+ T D+ +LF E+ G I+ M + R RG AF+T + + A AL
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGP--PIQFRMMT-GRMRGQAFITFPNKEIAWQAL 84
Query: 159 NNLESYEFEGRTLKVNYAKIKKK 181
+ + Y+ G+ L + + K KK+
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQ 107
>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 = 32.3 bits (72), Expect = 0.32, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 12/80 (15%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKS----KKVAET 252
+F+ + ++R FF G V I D S GYGFVSF + +K+ E+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYG--SVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 253 AISAFQGKLFMGRPLRVAPS 272
I+ F G+ L++ P+
Sbjct: 70 QIN------FHGKKLKLGPA 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 = 32.3 bits (72), Expect = 0.34, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSA---GYGFVSFKSKKVAETA 253
LF+ + EA +D+ + F G + I + RR+ GY V +++ K A+ A
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYG----EIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 65
Query: 254 ISAFQGKLFMGRPLRV 269
+ G+ MG+P+ V
Sbjct: 66 MEGLNGQDLMGQPISV 81
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.3 bits (72), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 4/77 (5%)
Query: 196 NLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRR---SAGYGFVSFKSKKVAET 252
LFI NL+F + L+ F G + S + N S G+GFV +K + A+
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKVGA-IKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 253 AISAFQGKLFMGRPLRV 269
A+ QG G L V
Sbjct: 66 ALKQLQGHTVDGHKLEV 82
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 32.3 bits (72), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 108 VPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFE 167
VP + AL G +LDI + + + N G A++ + + A A + + Y F+
Sbjct: 41 VPKEKLQALLYALASSQGDILDIVVDL--SDDNSGKAYIVFATQESAQAFVEAFQGYPFQ 98
Query: 168 GRTLKVNYAK 177
G L + +++
Sbjct: 99 GNPLVITFSE 108
Score = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 6/76 (7%)
Query: 197 LFIANLSFEARAKDLREFF---ISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETA 253
+ I N++ E + L+ S D++ V D+ ++G ++ F +++ A+
Sbjct: 32 VLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDD---NSGKAYIVFATQESAQAF 88
Query: 254 ISAFQGKLFMGRPLRV 269
+ AFQG F G PL +
Sbjct: 89 VEAFQGYPFQGNPLVI 104
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 32.0 bits (71), Expect = 0.40, Method: Composition-based stats.
Identities = 26/84 (30%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 191 PFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVA 250
P A ++++ NL +AR DL+ G V + + PRR A F+ + A
Sbjct: 17 PLAA-DVYVGNLPRDARVSDLKRALRELG--SVPLRLTWQ-GPRRRA---FLHYPDSAAA 69
Query: 251 ETAISAFQGKLFMGRPLRVAPSRQ 274
+ A+S QG LRVA +RQ
Sbjct: 70 QQAVSCLQGLRLGTDTLRVALARQ 93
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 32.0 bits (71), Expect = 0.43, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSF 244
+FI LS++ + LRE+F G +V V+ +RS G+GFV+F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFG-EVKECLVMRDPLTKRSRGFGFVTF 49
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 32.0 bits (71), Expect = 0.47, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 9/81 (11%)
Query: 194 TFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETA 253
T+ +F+ N+S +++LR F G V+ +V+ Y FV + + A+ A
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRG-RVIECDVV--------KDYAFVHMEKEADAKAA 59
Query: 254 ISAFQGKLFMGRPLRVAPSRQ 274
I+ GK G+ + V S +
Sbjct: 60 IAQLNGKEVKGKRINVELSTK 80
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 31.6 bits (70), Expect = 0.57, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 222 VVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQG 259
+VS + I + GYGFV F S A+ A++A +
Sbjct: 32 IVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKA 69
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 31.6 bits (70), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 27/107 (25%), Positives = 48/107 (44%), Gaps = 16/107 (14%)
Query: 95 EEEYSKTRLVAQNVPWTSTHEDIRALFEQHGTV----------LDIELSMHSKNRNRGLA 144
+E+ + + Q + + T +D+ F+Q G V + I L + + +G A
Sbjct: 10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET-GKPKGDA 68
Query: 145 FVTMGSPDEATAALNNLESYEFEGRTLKVNYAKIKKKNPFPPVQPKP 191
V+ P A AA+ + +F+G LKV+ A+ K PP+ P
Sbjct: 69 TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK-----PPMNSGP 110
>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 = 31.6 bits (70), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 7/87 (8%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
L++ NLSF + + E F G D+ + + + G+ FV + S+ AE A+
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSG-DIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 257 FQGKLFMGRPLRV------APSRQFAR 277
G R +R RQ+ R
Sbjct: 101 INGTRLDDRIIRTDWDAGFKEGRQYGR 127
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 31.2 bits (69), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 42/190 (22%), Positives = 72/190 (37%), Gaps = 29/190 (15%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQH-----------GTVLDIELSMHSKNRNRGLAFVTMGS 150
RL N+P+ T E + F VL +++ N+++ AF+ S
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-----NQDKNFAFLEFRS 60
Query: 151 PDEATAALNNLESYEFEGRTLKV----NYAKIKKKNPFPPV-------QPKPFATFNLFI 199
DE T A+ + F+G++LK+ +Y + + P V P + LFI
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 200 ANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISAFQG 259
L ++E S G + + ++ S GY F + V + AI+ G
Sbjct: 120 GGLPNYLNDDQVKELLTSFG-PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 178
Query: 260 KLFMGRPLRV 269
+ L V
Sbjct: 179 MQLGDKKLLV 188
>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 = 31.2 bits (69), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 7/91 (7%)
Query: 182 NPFPPVQPKPFATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRR---SAG 238
+ P + + LF+ ++ EA+ +++E F G + I + RR S G
Sbjct: 60 DELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYG----EIKNIHLNLDRRTGFSKG 115
Query: 239 YGFVSFKSKKVAETAISAFQGKLFMGRPLRV 269
Y V +++ K A A A G MG+ ++V
Sbjct: 116 YALVEYETHKQALAAKEALNGAEIMGQTIQV 146
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 31.2 bits (69), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
+++ L + L E F+ G VV+ + + GYGFV F S++ A+ AI
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAG-PVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 257 FQGKLFMGRPLRV 269
G+P+RV
Sbjct: 77 MDMIKLYGKPIRV 89
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 31.2 bits (69), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 103 LVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLE 162
L +N+P+ T E++ +F ++G + I + + RG A+V +A A+++L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG--NTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 163 SYEFEGRTLKVNY 175
+ R L V Y
Sbjct: 69 GFNVSNRYLVVLY 81
>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 = 31.2 bits (69), Expect = 0.73, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
L++ NLSF + + E F G + ++ D + + G+ FV + S+ AE A+
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSG--DIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRY 78
Query: 257 FQGKLFMGRPLR 268
G R +R
Sbjct: 79 INGTRLDDRIIR 90
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 31.2 bits (69), Expect = 0.77, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 113 THEDIRALFEQHGTV--LDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRT 170
T + I +F +G + +D+ + + ++G A+V +PDEA AL +++ + +G+
Sbjct: 17 TKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQE 76
Query: 171 L 171
+
Sbjct: 77 I 77
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 31.2 bits (69), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 193 ATFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPR-RSAGYGFVSFKSKKVAE 251
A F +++ L FEA K + +FF + D+V + P ++ G GFV F+++ +
Sbjct: 24 AGFCVYLKGLPFEAENKHVIDFF--KKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK 81
Query: 252 TAISAFQGKLFMG-RPLRVAP 271
A+ + K +MG R ++V P
Sbjct: 82 AALC--RHKQYMGNRFIQVHP 100
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.8 bits (68), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 7/89 (7%)
Query: 93 QREEEYSKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPD 152
++E E S TRL + P ++ +F G + ++++ G AFV +
Sbjct: 24 RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAE 76
Query: 153 EATAALNNLESYEFEGRTLKVNYAKIKKK 181
A A+ + F + L+V Y+K+ K
Sbjct: 77 SAAKAIEEVHGKSFANQPLEVVYSKLPAK 105
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 238 GYGFVSFKSKKVAETAISAFQGKLFMGRPLRVAPSR 273
G+ FV F+ + A AI GK F +PL V S+
Sbjct: 66 GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK 101
>pdb|1WI6|A Chain A, Solution Structure Of The Rna Binding Domain From Mouse
Hypothetical Protein Bab23670
Length = 88
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 122 EQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKV 173
E H + D EL ++ +G AFVT+ + ++A AA+N R L V
Sbjct: 21 EVHDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSV 72
>pdb|2DGX|A Chain A, Solution Structure Of The Rna Recognition Motif In
Kiaa0430 Protein
Length = 96
Score = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 117 IRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYA 176
++ F +HG V +ELS H+ + + A V M + +A A+N+L Y+ + + V+ A
Sbjct: 30 LQEAFARHGKVKSVELSPHTDYQLK--AVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA 87
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 27/43 (62%), Gaps = 4/43 (9%)
Query: 139 RNRGLAFVTMGSPDEATAALNNLES----YEFEGRTLKVNYAK 177
+NRG AFV + S +A+ L L+S + +G+T+ V++AK
Sbjct: 51 QNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAK 93
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 30.0 bits (66), Expect = 1.6, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 1/80 (1%)
Query: 99 SKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKN-RNRGLAFVTMGSPDEATAA 157
S T L+ +P T ++ ALF G + + K + G AFV S ++ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 158 LNNLESYEFEGRTLKVNYAK 177
+ L + LKV+YA+
Sbjct: 62 IKVLNGITVRNKRLKVSYAR 81
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 12/72 (16%)
Query: 95 EEEYSKTRLV-AQNVPWTSTHEDIRALFE-------QHGTVLDIELSMHSKNRNRGLAFV 146
EEE L+ AQ +PW+ T ED+ F ++G I ++ + RG A +
Sbjct: 5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENG----IHFLLNRDGKRRGDALI 60
Query: 147 TMGSPDEATAAL 158
M S + AL
Sbjct: 61 EMESEQDVQKAL 72
>pdb|2EK6|A Chain A, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|B Chain B, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|C Chain C, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|D Chain D, Crystal Structure Of Human Rna-Binding Protein 12
Length = 95
Score = 30.0 bits (66), Expect = 1.8, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 101 TRLVAQNVPWTSTHEDIRALFEQHGTVL-DIELSMHSKNRNRGLAFVTMGSPDEATAALN 159
T + QN+P+T + ++I F + + + L + K G A V S DEATAA+
Sbjct: 16 TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 160 NLESYEFEGRTLKVN 174
+L R +K++
Sbjct: 76 DLNDRPIGSRKVKLS 90
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 30.0 bits (66), Expect = 1.9, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 101 TRLVAQNVPWTSTHEDIRALFEQHGTVL-DIELSMHSKNRNRGLAFVTMGSPDEATAALN 159
T + QN+P+T + ++I F + + + L + K G A V S DEATAA+
Sbjct: 16 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 160 NLESYEFEGRTLKV 173
+L R +K+
Sbjct: 76 DLNDRPIGSRKVKL 89
>pdb|2HGL|A Chain A, Nmr Structure Of The First Qrrm Domain Of Human Hnrnp F
pdb|2KFY|A Chain A, Nmr Structure Of The First Qrrm Of Hnrnp F In Complex With
Agggau G- Tract Rna
Length = 136
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 106 QNVPWTSTHEDIRALFEQHGTVLDIELSMH----SKNRNRGLAFVTMGSPDEATAALNN 160
+ +PW+ + ED++ F T+ D +H + R G AFV +GS D+ AL
Sbjct: 50 RGLPWSCSVEDVQN-FLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKK 107
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 29.6 bits (65), Expect = 2.0, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
L+I NLS A DLR+ F ++ +V+ +GY FV + + A AI
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLP-LAGQVLL------KSGYAFVDYPDQNWAIRAIET 63
Query: 257 FQGKL 261
GK+
Sbjct: 64 LSGKV 68
>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 = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 108 VPWTSTHEDIRALFEQHGT-VLDIELSMH-SKNRNRGLAFVTMGSPDEATAALN-NLESY 164
+P +T +DIR + HG ++ L + S ++RG AFV +AT + N S
Sbjct: 9 LPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSL 68
Query: 165 EFEGRTLKVNYAKIKKK 181
G+ + ++Y+ K K
Sbjct: 69 NILGQKVSMHYSDPKPK 85
>pdb|3H2V|E Chain E, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|F Chain F, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|G Chain G, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
pdb|3H2V|H Chain H, Human Raver1 Rrm1 Domain In Complex With Human Vinculin
Tail Domain Vt
Length = 74
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNL 161
+++ + +P T++++ H + D EL ++ +G AFVT+ + ++A AA+N
Sbjct: 4 KILIRGLPGDVTNQEV------HDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINAF 57
Query: 162 ESYEFEGRTLKV 173
R L V
Sbjct: 58 HQSRLRERELSV 69
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 31/64 (48%), Gaps = 11/64 (17%)
Query: 117 IRALFEQHGTVLDIELSMHSKNRNRGLAFVT---MGSPDEATAALNNLESYEFEGRTLKV 173
+R F G ++D LSM R AFVT M S D+A A LN + E LKV
Sbjct: 30 LRGAFSPFGNIID--LSMDPP---RNCAFVTYEKMESADQAVAELNGTQ---VESVQLKV 81
Query: 174 NYAK 177
N A+
Sbjct: 82 NIAR 85
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 31/64 (48%), Gaps = 11/64 (17%)
Query: 117 IRALFEQHGTVLDIELSMHSKNRNRGLAFVT---MGSPDEATAALNNLESYEFEGRTLKV 173
+R F G ++D+ S + R AFVT M S D+A A LN + E LKV
Sbjct: 54 LRGAFSPFGNIIDL-----SMDPPRNCAFVTYEKMESADQAVAELNGTQ---VESVQLKV 105
Query: 174 NYAK 177
N A+
Sbjct: 106 NIAR 109
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 194 TFNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSF 244
T +L + L ++ +DL+E+F + G +V+ +V S G+GFV F
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFG-EVLMVQVKKDLKTGHSKGFGFVRF 64
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 238 GYGFVSFKSKKVAETAISAFQGKLFMGRPLRVAPSR 273
G+ FV F+ + A AI GK F +PL V S+
Sbjct: 39 GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK 74
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 7/81 (8%)
Query: 97 EYSKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATA 156
E S TRL + P ++ +F G + ++++ G AFV + A
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAK 53
Query: 157 ALNNLESYEFEGRTLKVNYAK 177
A+ + F + L+V Y+K
Sbjct: 54 AIEEVHGKSFANQPLEVVYSK 74
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 19/95 (20%), Positives = 47/95 (49%), Gaps = 3/95 (3%)
Query: 84 SSAAAVNTEQREEEYSKTRLVAQNVPWTSTHEDIRALFEQHGTVLDIELSM-HSKNRNRG 142
S+ + +R ++ + R+ N+ + D++ LF G++ I L+ + +++G
Sbjct: 1 GSSGSSGPNRRADDNATIRVT--NLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKG 58
Query: 143 LAFVTMGSPDEATAALNNLESYEFEGRTLKVNYAK 177
AF++ ++A A+ + + ++ L V +AK
Sbjct: 59 FAFISFHRREDAARAIAGVSGFGYDHLILNVEWAK 93
>pdb|3IPK|A Chain A, Crystal Structure Of A3vp1 Of AgiII OF STREPTOCOCCUS
MUTANS
pdb|3IPK|B Chain B, Crystal Structure Of A3vp1 Of AgiII OF STREPTOCOCCUS
MUTANS
pdb|3IOX|A Chain A, Crystal Structure Of A3vp1 Of AgiII OF STREPTOCOCCUS
MUTANS
Length = 497
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 164 YEFEGRTLKVNYAKIKKKNPFPPVQP 189
Y G+ VN K+ K+ P PPV+P
Sbjct: 432 YSLNGKIRAVNVPKVTKEKPTPPVKP 457
>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 = 28.5 bits (62), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 197 LFIANLSFEARAKDLREFFISEGWDVVSAEVIFHDNPRRSAGYGFVSFKSKKVAETAISA 256
LF+A ++++ LR F G + +++ + GY F+ ++ ++ +A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYG-PIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 257 FQGKLFMGR 265
GK GR
Sbjct: 164 ADGKKIDGR 172
>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 = 28.5 bits (62), Expect = 5.1, Method: Composition-based stats.
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 238 GYGFVSFKSKKVAETAISAFQGKLFMGRPLRVA 270
G VSF A+ AI F GK F G P++V+
Sbjct: 64 GEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS 96
Score = 28.1 bits (61), Expect = 6.4, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 141 RGLAFVTMGSPDEATAALNNLESYEFEGRTLKVNYA 176
+G A V+ P A AA++ + EF G +KV++A
Sbjct: 63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|2EK1|A Chain A, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|B Chain B, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|C Chain C, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|D Chain D, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|E Chain E, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|F Chain F, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|G Chain G, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|H Chain H, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
Length = 95
Score = 28.5 bits (62), Expect = 5.2, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 101 TRLVAQNVPWTSTHEDIRALFEQHGTVL-DIELSMHSKNRNRGLAFVTMGSPDEATAALN 159
T + QN P+T + ++I F + + + L + K G A V S DEATAA+
Sbjct: 16 TVIKVQNXPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGXPTGEAXVAFESRDEATAAVI 75
Query: 160 NLESYEFEGRTLKVN 174
+L R +K++
Sbjct: 76 DLNDRPIGSRKVKLS 90
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 238 GYGFVSFKSKKVAETAISAFQGKLFMGRPLRVA 270
G VSF A+ AI F GK F G P++V+
Sbjct: 58 GEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVS 90
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 28.1 bits (61), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 31/72 (43%)
Query: 102 RLVAQNVPWTSTHEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNL 161
+L+ N+ + + DI+ LF + GT+ + R+ G A V +A A+
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 162 ESYEFEGRTLKV 173
+GR + +
Sbjct: 90 NGVPLDGRPMNI 101
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 27.7 bits (60), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 113 THEDIRALFEQHGTVLDIELSMHSKNRNRGLAFVTMGSPDEATAALNNLESYE 165
+ ED+ LF+ G + + + ++G AFV S EA AA++ L +
Sbjct: 28 SEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQ 80
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 195 FNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFH-DNPRRSAGYGFVSFK 245
+ F+ NL ++ + ++EFF G ++ + + NP R G+G+ F+
Sbjct: 16 YTAFLGNLPYDVTEESIKEFF--RGLNISAVRLPREPSNPERLKGFGYAEFE 65
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 27.7 bits (60), Expect = 8.7, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 239 YGFVSFKSKKVAETAISAFQGKLFMGRPLRVAPSR 273
Y FV F +++ A A+ A GK+ G P+ V ++
Sbjct: 53 YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 87
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 27.3 bits (59), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 195 FNLFIANLSFEARAKDLREFFISEGWDVVSAEVIFH-DNPRRSAGYGFVSFK 245
+ F+ NL ++ + ++EFF G ++ + + NP R G+G+ F+
Sbjct: 20 YTAFLGNLPYDVTEESIKEFF--RGLNISAVRLPREPSNPERLKGFGYAEFE 69
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 0.131 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,603,549
Number of Sequences: 62578
Number of extensions: 332942
Number of successful extensions: 1251
Number of sequences better than 100.0: 177
Number of HSP's better than 100.0 without gapping: 94
Number of HSP's successfully gapped in prelim test: 83
Number of HSP's that attempted gapping in prelim test: 988
Number of HSP's gapped (non-prelim): 268
length of query: 306
length of database: 14,973,337
effective HSP length: 98
effective length of query: 208
effective length of database: 8,840,693
effective search space: 1838864144
effective search space used: 1838864144
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: 51 (24.3 bits)