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= 014513
(423 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 97.4 bits (241), Expect = 1e-20, Method: Composition-based stats.
Identities = 51/88 (57%), Positives = 62/88 (70%), Gaps = 2/88 (2%)
Query: 113 AGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENER 172
+GPE+S+FVGDL PDV D +L E F YPS RG KVV D TG SKGYGFVKF DE E+
Sbjct: 6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQ 64
Query: 173 NRAMTEMNG-VFCSTRPMRISAATPKKT 199
RA+TE G V ++P+R+S A PK +
Sbjct: 65 KRALTECQGAVGLGSKPVRLSVAIPKAS 92
Score = 34.7 bits (78), Expect = 0.096, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 7/75 (9%)
Query: 235 TIFVGNLDPNVTEEELKQTFLHF------GEIVNVKIPMGRGCGFVQFAARASAEEAILR 288
++FVG+L P+V + L + F+ G++V + + +G GFV+F + A+
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 289 MQGHM-IGQQQVRIS 302
QG + +G + VR+S
Sbjct: 71 CQGAVGLGSKPVRLS 85
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 89.7 bits (221), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 58/172 (33%), Positives = 88/172 (51%), Gaps = 9/172 (5%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
R L++G+L E+ L F G + +IKI+ +K + Y FVE+ A LQ
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 84 TYNGTPMPGTEQNF-RLNWASFGIGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYP 142
T NG + E N ++NWA ++ + ++FVGDL +V D L+ F+ +P
Sbjct: 60 TLNGKQI---ENNIVKINWA---FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKD-FP 112
Query: 143 SVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRPMRISAA 194
S V+ D TG S+GYGFV F +++ AM M G + RP+RI+ A
Sbjct: 113 SYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 67.0 bits (162), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 49/194 (25%), Positives = 93/194 (47%), Gaps = 36/194 (18%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
++VG+L +T+ +L++ F+ P + K++ D N ++ Y FV++ ++ N A+
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGP-IANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQT 60
Query: 179 MNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFV 238
+NG ++I+ A FQ Q ++ T+ +FV
Sbjct: 61 LNGKQIENNIVKINWA-------FQSQQSSSDDTF---------------------NLFV 92
Query: 239 GNLDPNVTEEELKQTFLHF-----GEIV-NVKIPMGRGCGFVQFAARASAEEAILRMQGH 292
G+L+ NV +E L+ F F G ++ +++ RG GFV F ++ A+ A+ MQG
Sbjct: 93 GDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQ 152
Query: 293 MIGQQQVRISWGRK 306
+ + +RI+W K
Sbjct: 153 DLNGRPLRINWAAK 166
Score = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 2/83 (2%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
++ L++GDL D+ L + F +S ++ + TG GYGFV F S A+
Sbjct: 85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Query: 81 VLQTYNGTPMPGTEQNFRLNWAS 103
+ + G + G R+NWA+
Sbjct: 145 AMDSMQGQDLNGRP--LRINWAA 165
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 235 TIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR-----GCGFVQFAARASAEEAILRM 289
++VGNLD +TE+ LKQ F G I N+KI + + FV++ A A+ +
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 290 QGHMIGQQQVRISW 303
G I V+I+W
Sbjct: 62 NGKQIENNIVKINW 75
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 89.0 bits (219), Expect = 4e-18, Method: Composition-based stats.
Identities = 42/83 (50%), Positives = 59/83 (71%), Gaps = 3/83 (3%)
Query: 25 TLWIGDLQYWFDENYLSSCFAHTGE-VVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
+LW+GDL+ + DEN++S FA GE V+S+KIIRN++TG P GY FVEF A AE+ L
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 84 TYNGTPMPGT--EQNFRLNWASF 104
NG P+PG + F+LN+A++
Sbjct: 71 KINGKPLPGATPAKRFKLNYATY 93
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 45/90 (50%), Gaps = 9/90 (10%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
S+++GDL P + + + F + +V K++ + TG GY FV+F D + +
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 178 EMNGVFCSTRPMRISAATPKKTTGFQQQYA 207
++NG +P+ ATP K F+ YA
Sbjct: 71 KING-----KPL--PGATPAKR--FKLNYA 91
Score = 32.7 bits (73), Expect = 0.38, Method: Composition-based stats.
Identities = 20/64 (31%), Positives = 38/64 (59%), Gaps = 7/64 (10%)
Query: 235 TIFVGNLDPNVTEEELKQTFLHFGE-IVNVKIPMGRGCG------FVQFAARASAEEAIL 287
++++G+L+P + E + + F GE +++VKI R G FV+FA A+AE+ +
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 288 RMQG 291
++ G
Sbjct: 71 KING 74
>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 = 82.4 bits (202), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 55/174 (31%), Positives = 89/174 (51%), Gaps = 8/174 (4%)
Query: 25 TLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQT 84
+L++GDL E L F+ G ++SI++ R+ IT + GY +V F A AER L T
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 85 YNGTPMPGTEQNFRLNWASFGIGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSV 144
N + G + R+ W+ ++ G +IF+ +L + + L +TF S + ++
Sbjct: 72 MNFDVIKG--KPVRIMWSQRDPSLRKSGVG---NIFIKNLDKSIDNKALYDTF-SAFGNI 125
Query: 145 RGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRPMRISAATPKK 198
KVV D N SKGYGFV F + RA+ +MNG+ + R + + +K
Sbjct: 126 LSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 177
Score = 77.0 bits (188), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 56/189 (29%), Positives = 84/189 (44%), Gaps = 33/189 (17%)
Query: 115 PEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNR 174
P S++VGDL PDVT+ +L E F P + +V D T RS GY +V F + R
Sbjct: 9 PMASLYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRDMITRRSLGYAYVNFQQPADAER 67
Query: 175 AMTEMNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNT 234
A+ MN +P+RI + Q P+
Sbjct: 68 ALDTMNFDVIKGKPVRIMWS----------------------------QRDPSLRKSGVG 99
Query: 235 TIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM----GRGCGFVQFAARASAEEAILRMQ 290
IF+ NLD ++ + L TF FG I++ K+ +G GFV F + +AE AI +M
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 159
Query: 291 GHMIGQQQV 299
G ++ ++V
Sbjct: 160 GMLLNDRKV 168
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIP------MGRGCGFVQFAARASAEEAIL 287
+++VG+L P+VTE L + F G I+++++ G +V F A AE A+
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 288 RMQGHMIGQQQVRISWGRK 306
M +I + VRI W ++
Sbjct: 71 TMNFDVIKGKPVRIMWSQR 89
>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 = 82.0 bits (201), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 55/174 (31%), Positives = 89/174 (51%), Gaps = 8/174 (4%)
Query: 25 TLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQT 84
+L++GDL E L F+ G ++SI++ R+ IT + GY +V F A AER L T
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 85 YNGTPMPGTEQNFRLNWASFGIGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSV 144
N + G + R+ W+ ++ G +IF+ +L + + L +TF S + ++
Sbjct: 77 MNFDVIKG--KPVRIMWSQRDPSLRKSGVG---NIFIKNLDKSIDNKALYDTF-SAFGNI 130
Query: 145 RGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRPMRISAATPKK 198
KVV D N SKGYGFV F + RA+ +MNG+ + R + + +K
Sbjct: 131 LSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 182
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 56/189 (29%), Positives = 84/189 (44%), Gaps = 33/189 (17%)
Query: 115 PEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNR 174
P S++VGDL PDVT+ +L E F P + +V D T RS GY +V F + R
Sbjct: 14 PMASLYVGDLHPDVTEAMLYEKFSPAGP-ILSIRVCRDMITRRSLGYAYVNFQQPADAER 72
Query: 175 AMTEMNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNT 234
A+ MN +P+RI + Q P+
Sbjct: 73 ALDTMNFDVIKGKPVRIMWS----------------------------QRDPSLRKSGVG 104
Query: 235 TIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM----GRGCGFVQFAARASAEEAILRMQ 290
IF+ NLD ++ + L TF FG I++ K+ +G GFV F + +AE AI +M
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164
Query: 291 GHMIGQQQV 299
G ++ ++V
Sbjct: 165 GMLLNDRKV 173
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIP------MGRGCGFVQFAARASAEEAIL 287
+++VG+L P+VTE L + F G I+++++ G +V F A AE A+
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 288 RMQGHMIGQQQVRISWGRKQ 307
M +I + VRI W ++
Sbjct: 76 TMNFDVIKGKPVRIMWSQRD 95
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 46/142 (32%), Positives = 74/142 (52%), Gaps = 12/142 (8%)
Query: 42 SCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQNFRLNW 101
S F GE+ S K++R+KITGQ GYGFV ++ AE+ + T NG RL
Sbjct: 21 SLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG---------LRLQT 71
Query: 102 ASFGIGEKRPDAGP--EHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSK 159
+ + RP + + +++V L +T L++ F SQY + ++++ D TG S+
Sbjct: 72 KTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLF-SQYGRIITSRILVDQVTGVSR 130
Query: 160 GYGFVKFLDENERNRAMTEMNG 181
G GF++F E A+ +NG
Sbjct: 131 GVGFIRFDKRIEAEEAIKGLNG 152
Score = 77.4 bits (189), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 48/170 (28%), Positives = 79/170 (46%), Gaps = 39/170 (22%)
Query: 132 LLQETFRSQYPSV---RGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRP 188
+ QE FRS + S+ K+V D TG+S GYGFV ++D + +A+ +NG+ T+
Sbjct: 14 MTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKT 73
Query: 189 MRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFVGNLDPNVTEE 248
+++S A P + I + ++V L +T++
Sbjct: 74 IKVSYARPSSAS------------------------------IRDANLYVSGLPKTMTQK 103
Query: 249 ELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEAILRMQGH 292
EL+Q F +G I+ +I + RG GF++F R AEEAI + G
Sbjct: 104 ELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR------GCGFVQFAARASAEEA 285
+ T + V L N+T+EE + F GEI + K+ + G GFV + AE+A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 286 ILRMQGHMIGQQQVRISWGR 305
I + G + + +++S+ R
Sbjct: 61 INTLNGLRLQTKTIKVSYAR 80
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 36/77 (46%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L++ L + L F+ G +++ +I+ +++TG G GF+ F AE ++
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 86 NGTPMPGTEQNFRLNWA 102
NG G + + +A
Sbjct: 151 NGQKPSGATEPITVKFA 167
>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 = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 47/158 (29%), Positives = 80/158 (50%), Gaps = 12/158 (7%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L + L ++ L S F+ GEV S K+IR+K+ G GYGFV +V+ AER + T
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 86 NGTPMPGTEQNFRLNWASFGIGEKRPDAG--PEHSIFVGDLAPDVTDYLLQETFRSQYPS 143
NG RL + + RP + + ++++ L +T +++ F S++
Sbjct: 65 NG---------LRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMF-SRFGR 114
Query: 144 VRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNG 181
+ ++V+ D TG S+G F++F +E A+T NG
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 69.7 bits (169), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 42/170 (24%), Positives = 75/170 (44%), Gaps = 39/170 (22%)
Query: 132 LLQETFRSQYPS---VRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRP 188
+ Q+ RS + S V AK++ D G S GYGFV ++ + RA+ +NG+ ++
Sbjct: 14 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 73
Query: 189 MRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFVGNLDPNVTEE 248
+++S A P I + +++ L +T++
Sbjct: 74 IKVSYARPSSEV------------------------------IKDANLYISGLPRTMTQK 103
Query: 249 ELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEAILRMQGH 292
+++ F FG I+N ++ + RG F++F R+ AEEAI GH
Sbjct: 104 DVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR------GCGFVQFAARASAEEAIL 287
T + V L N+T++EL+ F GE+ + K+ + G GFV + AE AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 288 RMQGHMIGQQQVRISWGR 305
+ G + + +++S+ R
Sbjct: 63 TLNGLRLQSKTIKVSYAR 80
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 39/78 (50%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L+I L + + F+ G +++ +++ ++ TG G F+ F + AE + ++
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 86 NGTPMPGTEQNFRLNWAS 103
NG PG+ + + +A+
Sbjct: 151 NGHKPPGSSEPITVKFAA 168
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 47/158 (29%), Positives = 80/158 (50%), Gaps = 12/158 (7%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L + L ++ L S F+ GEV S K+IR+K+ G GYGFV +V+ AER + T
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 86 NGTPMPGTEQNFRLNWASFGIGEKRPDAG--PEHSIFVGDLAPDVTDYLLQETFRSQYPS 143
NG RL + + RP + + ++++ L +T +++ F S++
Sbjct: 65 NG---------LRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMF-SRFGR 114
Query: 144 VRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNG 181
+ ++V+ D TG S+G F++F +E A+T NG
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 69.7 bits (169), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 42/170 (24%), Positives = 75/170 (44%), Gaps = 39/170 (22%)
Query: 132 LLQETFRSQYPS---VRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRP 188
+ Q+ RS + S V AK++ D G S GYGFV ++ + RA+ +NG+ ++
Sbjct: 14 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 73
Query: 189 MRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFVGNLDPNVTEE 248
+++S A P I + +++ L +T++
Sbjct: 74 IKVSYARPSSEV------------------------------IKDANLYISGLPRTMTQK 103
Query: 249 ELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEAILRMQGH 292
+++ F FG I+N ++ + RG F++F R+ AEEAI GH
Sbjct: 104 DVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR------GCGFVQFAARASAEEAIL 287
T + V L N+T++EL+ F GE+ + K+ + G GFV + AE AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 288 RMQGHMIGQQQVRISWGR 305
+ G + + +++S+ R
Sbjct: 63 TLNGLRLQSKTIKVSYAR 80
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 39/78 (50%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L+I L + + F+ G +++ +++ ++ TG G F+ F + AE + ++
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 86 NGTPMPGTEQNFRLNWAS 103
NG PG+ + + +A+
Sbjct: 151 NGHKPPGSSEPITVXFAA 168
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 74.7 bits (182), Expect = 9e-14, Method: Compositional matrix adjust.
Identities = 45/170 (26%), Positives = 80/170 (47%), Gaps = 39/170 (22%)
Query: 132 LLQETFRSQYPSV---RGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRP 188
+ Q+ F+S + S+ K+V D TG+S GYGFV + D N+ ++A+ +NG+ T+
Sbjct: 16 MTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKT 75
Query: 189 MRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFVGNLDPNVTEE 248
+++S A P + I + ++V L ++++
Sbjct: 76 IKVSYARPSSAS------------------------------IRDANLYVSGLPKTMSQK 105
Query: 249 ELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAILRMQGH 292
E++Q F +G I+ +I + RG GF++F R AEEAI + G
Sbjct: 106 EMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 155
Score = 72.0 bits (175), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 41/147 (27%), Positives = 75/147 (51%), Gaps = 12/147 (8%)
Query: 37 ENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQN 96
++ S F G++ S K++R+KITGQ GYGFV + A++ + T NG
Sbjct: 18 QDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNG--------- 68
Query: 97 FRLNWASFGIGEKRPDAGP--EHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPN 154
+L + + RP + + +++V L ++ +++ F SQY + ++++ D
Sbjct: 69 LKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLF-SQYGRIITSRILLDQA 127
Query: 155 TGRSKGYGFVKFLDENERNRAMTEMNG 181
TG S+G GF++F E A+ +NG
Sbjct: 128 TGVSRGVGFIRFDKRIEAEEAIKGLNG 154
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR------GCGFVQFAARASAEEA 285
+ T + V L N+T++E K F G+I + K+ + G GFV ++ A++A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 286 ILRMQGHMIGQQQVRISWGR 305
I + G + + +++S+ R
Sbjct: 63 INTLNGLKLQTKTIKVSYAR 82
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 36/78 (46%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L++ L + + F+ G +++ +I+ ++ TG G GF+ F AE ++
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 86 NGTPMPGTEQNFRLNWAS 103
NG G + + +A+
Sbjct: 153 NGQKPLGAAEPITVKFAN 170
>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 = 68.6 bits (166), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 46/179 (25%), Positives = 90/179 (50%), Gaps = 12/179 (6%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
+++G + Y E+ + FA G + SI + + +T + +G+ FVE+ AA+ L+
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 86 NGTPMPGTEQNFRLNWASFGIGEKRP-------DAGPEHSIFVGDLAPDVTDYLLQETFR 138
N + G +N ++ S IG+ +P +A + I+V + D++D ++ F
Sbjct: 91 NSVMLGG--RNIKVGRPS-NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 147
Query: 139 SQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRPMRI-SAATP 196
+ + ++ A + DP TG+ KGYGF+++ A++ MN + +R+ A TP
Sbjct: 148 A-FGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 34/189 (17%), Positives = 83/189 (43%), Gaps = 26/189 (13%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
++VG + ++ + +++ F + + ++ + D T + KG+ FV++ A+ +
Sbjct: 31 VYVGSIYYELGEDTIRQAF-APFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 179 MNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFV 238
MN V R +++ P Q P+ A+ I+V
Sbjct: 90 MNSVMLGGRNIKV--GRPSNIGQAQ-----------------PIIDQLAEEARAFNRIYV 130
Query: 239 GNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEAILRMQGH 292
++ +++++++K F FG+I + + +G GF+++ S+++A+ M
Sbjct: 131 ASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF 190
Query: 293 MIGQQQVRI 301
+G Q +R+
Sbjct: 191 DLGGQYLRV 199
Score = 32.3 bits (72), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 44/82 (53%), Gaps = 8/82 (9%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIP------MGRGCGFVQFAARASAEEAIL 287
+ ++VG++ + E+ ++Q F FG I ++ + +G FV++ +A+ A+
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 288 RMQGHMIGQQQVRISWGRKQDV 309
+M M+G + +++ GR ++
Sbjct: 89 QMNSVMLGGRNIKV--GRPSNI 108
>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 = 67.4 bits (163), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 45/179 (25%), Positives = 89/179 (49%), Gaps = 12/179 (6%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
+++G + Y E+ + FA G + SI + + +T + +G+ FVE+ AA+ L+
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 86 NGTPMPGTEQNFRLNWASFGIGEKRP-------DAGPEHSIFVGDLAPDVTDYLLQETFR 138
N + G +N ++ S IG+ +P +A + I+V + D++D ++ F
Sbjct: 76 NSVMLGG--RNIKVGRPS-NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 132
Query: 139 SQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRPMRI-SAATP 196
+ + ++ + DP TG+ KGYGF+++ A++ MN + +R+ A TP
Sbjct: 133 A-FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 190
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 34/189 (17%), Positives = 83/189 (43%), Gaps = 26/189 (13%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
++VG + ++ + +++ F + + ++ + D T + KG+ FV++ A+ +
Sbjct: 16 VYVGSIYYELGEDTIRQAF-APFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 179 MNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFV 238
MN V R +++ P Q P+ A+ I+V
Sbjct: 75 MNSVMLGGRNIKV--GRPSNIGQAQ-----------------PIIDQLAEEARAFNRIYV 115
Query: 239 GNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEAILRMQGH 292
++ +++++++K F FG+I + + +G GF+++ S+++A+ M
Sbjct: 116 ASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF 175
Query: 293 MIGQQQVRI 301
+G Q +R+
Sbjct: 176 DLGGQYLRV 184
Score = 32.3 bits (72), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 43/80 (53%), Gaps = 8/80 (10%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIP------MGRGCGFVQFAARASAEEAILRM 289
++VG++ + E+ ++Q F FG I ++ + +G FV++ +A+ A+ +M
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 290 QGHMIGQQQVRISWGRKQDV 309
M+G + +++ GR ++
Sbjct: 76 NSVMLGGRNIKV--GRPSNI 93
>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 = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 44/179 (24%), Positives = 87/179 (48%), Gaps = 12/179 (6%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
+++G + Y E+ + FA G + SI + +T + +G+ FVE+ AA+ L+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 86 NGTPMPGTEQNFRLNWASFGIGEKRP-------DAGPEHSIFVGDLAPDVTDYLLQETFR 138
N + G +N ++ S IG+ +P +A + I+V + D++D ++ F
Sbjct: 75 NSVXLGG--RNIKVGRPS-NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE 131
Query: 139 SQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRPMRI-SAATP 196
+ + ++ + DP TG+ KGYGF+++ A++ N + +R+ A TP
Sbjct: 132 A-FGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKAVTP 189
Score = 35.4 bits (80), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 21 EEVRT---LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAA 77
EE R +++ + ++ + S F G++ S + R+ TG+ +GYGF+E+ +
Sbjct: 104 EEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQS 163
Query: 78 AERVLQTYN 86
++ + + N
Sbjct: 164 SQDAVSSXN 172
Score = 33.5 bits (75), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 32/189 (16%), Positives = 80/189 (42%), Gaps = 26/189 (13%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
++VG + ++ + +++ F + + ++ D T + KG+ FV++ A+ +
Sbjct: 15 VYVGSIYYELGEDTIRQAF-APFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 179 MNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFV 238
N V R +++ P Q P+ A+ I+V
Sbjct: 74 XNSVXLGGRNIKV--GRPSNIGQAQ-----------------PIIDQLAEEARAFNRIYV 114
Query: 239 GNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEAILRMQGH 292
++ +++++++K F FG+I + + +G GF+++ S+++A+
Sbjct: 115 ASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLF 174
Query: 293 MIGQQQVRI 301
+G Q +R+
Sbjct: 175 DLGGQYLRV 183
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 63.9 bits (154), Expect = 1e-10, Method: Composition-based stats.
Identities = 30/83 (36%), Positives = 50/83 (60%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
IF+G+L P++ + LL +TF + ++ K++ DP+TG SKGY F+ F + + A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 179 MNGVFCSTRPMRISAATPKKTTG 201
MNG + RP+ +S A K + G
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSKG 90
Score = 50.1 bits (118), Expect = 3e-06, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 7/87 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM-------GRGCGFVQFAARASAEEA 285
++ IF+GNLDP + E+ L TF FG I+ M +G F+ FA+ +++ A
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 286 ILRMQGHMIGQQQVRISWGRKQDVTGS 312
I M G + + + +S+ K+D GS
Sbjct: 65 IEAMNGQYLCNRPITVSYAFKKDSKGS 91
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSI-KIIRNKITGQPEGYGFVEFVSHAAAERVLQT 84
++IG+L DE L F+ G ++ KI+R+ TG +GY F+ F S A++ ++
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 85 YNG 87
NG
Sbjct: 68 MNG 70
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 63.9 bits (154), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 47/175 (26%), Positives = 74/175 (42%), Gaps = 37/175 (21%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
++ V L D+TD L FR+ P + +++ D TG S GY FV F E + RA+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGP-INTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 178 EMNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIF 237
+NG+ + +++S A P I +T ++
Sbjct: 64 VLNGITVRNKRLKVSYAR------------------------------PGGESIKDTNLY 93
Query: 238 VGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEAI 286
V NL +T+++L F +G IV I RG FV++ R A+EAI
Sbjct: 94 VTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 40/144 (27%), Positives = 72/144 (50%), Gaps = 8/144 (5%)
Query: 40 LSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQNFRL 99
L + F G + + +I+R+ TG GY FV+F S ++R ++ NG + + ++
Sbjct: 20 LYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV--RNKRLKV 77
Query: 100 NWASFGIGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSK 159
++A G GE D +++V +L +TD L F +Y S+ ++ D TGR +
Sbjct: 78 SYARPG-GESIKDT----NLYVTNLPRTITDDQLDTIF-GKYGSIVQKNILRDKLTGRPR 131
Query: 160 GYGFVKFLDENERNRAMTEMNGVF 183
G FV++ E A++ +N V
Sbjct: 132 GVAFVRYNKREEAQEAISALNNVI 155
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 35/77 (45%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L++ +L ++ L + F G +V I+R+K+TG+P G FV + A+ +
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 86 NGTPMPGTEQNFRLNWA 102
N G Q + A
Sbjct: 152 NNVIPEGGSQPLSVRLA 168
>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 = 63.2 bits (152), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 47/186 (25%), Positives = 87/186 (46%), Gaps = 29/186 (15%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
+E ++IG L + E+ L F G V +KI+++ TG+ G+GF+ F ++ +
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 81 VLQTYN---------GTPMPGTEQNFRLNWASFGIGEKRPDAGPEHSIFVGDLAPDVTDY 131
V++T + +P EQ+ IFVG + PDV
Sbjct: 61 VVKTQHILDGKVIDPKRAIPRDEQD------------------KTGKIFVGGIGPDVRPK 102
Query: 132 LLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRPMRI 191
+E F SQ+ ++ A+++ D +TG+S+G+GFV + + +R + + + R + I
Sbjct: 103 EFEEFF-SQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR-VCQNKFIDFKDRKIEI 160
Query: 192 SAATPK 197
A P+
Sbjct: 161 KRAEPR 166
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 43/168 (25%), Positives = 74/168 (44%), Gaps = 41/168 (24%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
+F+G L D T+ L+E F +Y +V K++ DP TGRS+G+GF+ F E+ ++
Sbjct: 5 KMFIGGLNWDTTEDNLREYF-GKYGTVTDLKIMKDPATGRSRGFGFLSF----EKPSSVD 59
Query: 178 EMNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPV-AAYTTPVQVFPADNDITNTTI 236
E+ VK + + P + P D I
Sbjct: 60 EV-----------------------------VKTQHILDGKVIDPKRAIPRDEQDKTGKI 90
Query: 237 FVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAA 278
FVG + P+V +E ++ F +G I++ ++ + RG GFV + +
Sbjct: 91 FVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS 138
Score = 35.4 bits (80), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 6/60 (10%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEAI 286
+ +F+G L+ + TE+ L++ F +G + ++KI RG GF+ F +S +E +
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
>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 = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 80/172 (46%), Gaps = 9/172 (5%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
E++R L+IG L + + L S F G + ++R+ T + G+G FV++A E
Sbjct: 4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG---FVTYATVEE 60
Query: 81 VLQTYNGTPMPGTEQNFRLNWASFGIGEKRPDAG-PEHSIFVGDLAPDVTDYLLQETFRS 139
V N P + A +RP A IFVG + D ++ L++ F
Sbjct: 61 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF-E 119
Query: 140 QYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE----MNGVFCSTR 187
QY + +++TD +G+ +G+ FV F D + ++ + + +NG C R
Sbjct: 120 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 171
Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/176 (26%), Positives = 76/176 (43%), Gaps = 32/176 (18%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+F+G L+ + TD L+ F Q+ ++ V+ DPNT RS+G+GFV + E + AM
Sbjct: 9 LFIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 66
Query: 179 MNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFV 238
A P K G + P A + P + +T IFV
Sbjct: 67 ---------------ARPHKVDG--------RVVEPKRAVSREDSQRPGAH-LTVKKIFV 102
Query: 239 GNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCG------FVQFAARASAEEAILR 288
G + + E L+ F +G+I ++I RG G FV F S ++ +++
Sbjct: 103 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158
>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 = 62.4 bits (150), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 80/172 (46%), Gaps = 9/172 (5%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
E++R L+IG L + + L S F G + ++R+ T + G+G FV++A E
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG---FVTYATVEE 67
Query: 81 VLQTYNGTPMPGTEQNFRLNWASFGIGEKRPDAG-PEHSIFVGDLAPDVTDYLLQETFRS 139
V N P + A +RP A IFVG + D ++ L++ F
Sbjct: 68 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF-E 126
Query: 140 QYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE----MNGVFCSTR 187
QY + +++TD +G+ +G+ FV F D + ++ + + +NG C R
Sbjct: 127 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 178
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 47/176 (26%), Positives = 76/176 (43%), Gaps = 32/176 (18%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+F+G L+ + TD L+ F Q+ ++ V+ DPNT RS+G+GFV + E + AM
Sbjct: 16 LFIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 73
Query: 179 MNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFV 238
A P K G + P A + P + +T IFV
Sbjct: 74 ---------------ARPHKVDG--------RVVEPKRAVSREDSQRPGAH-LTVKKIFV 109
Query: 239 GNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCG------FVQFAARASAEEAILR 288
G + + E L+ F +G+I ++I RG G FV F S ++ +++
Sbjct: 110 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 62.4 bits (150), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 80/172 (46%), Gaps = 9/172 (5%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
E++R L+IG L + + L S F G + ++R+ T + G+G FV++A E
Sbjct: 9 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG---FVTYATVEE 65
Query: 81 VLQTYNGTPMPGTEQNFRLNWASFGIGEKRPDAG-PEHSIFVGDLAPDVTDYLLQETFRS 139
V N P + A +RP A IFVG + D ++ L++ F
Sbjct: 66 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF-E 124
Query: 140 QYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE----MNGVFCSTR 187
QY + +++TD +G+ +G+ FV F D + ++ + + +NG C R
Sbjct: 125 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 176
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/177 (26%), Positives = 76/177 (42%), Gaps = 32/177 (18%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
+F+G L+ + TD L+ F Q+ ++ V+ DPNT RS+G+GFV + E + AM
Sbjct: 13 KLFIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 178 EMNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIF 237
A P K G + P A + P + +T IF
Sbjct: 72 ----------------ARPHKVDG--------RVVEPKRAVSREDSQRPGAH-LTVKKIF 106
Query: 238 VGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCG------FVQFAARASAEEAILR 288
VG + + E L+ F +G+I ++I RG G FV F S ++ +++
Sbjct: 107 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163
>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 = 62.4 bits (150), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 80/172 (46%), Gaps = 9/172 (5%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
E++R L+IG L + + L S F G + ++R+ T + G+G FV++A E
Sbjct: 10 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG---FVTYATVEE 66
Query: 81 VLQTYNGTPMPGTEQNFRLNWASFGIGEKRPDAG-PEHSIFVGDLAPDVTDYLLQETFRS 139
V N P + A +RP A IFVG + D ++ L++ F
Sbjct: 67 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF-E 125
Query: 140 QYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE----MNGVFCSTR 187
QY + +++TD +G+ +G+ FV F D + ++ + + +NG C R
Sbjct: 126 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 177
Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/176 (26%), Positives = 76/176 (43%), Gaps = 32/176 (18%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+F+G L+ + TD L+ F Q+ ++ V+ DPNT RS+G+GFV + E + AM
Sbjct: 15 LFIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 72
Query: 179 MNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFV 238
A P K G + P A + P + +T IFV
Sbjct: 73 ---------------ARPHKVDG--------RVVEPKRAVSREDSQRPGAH-LTVKKIFV 108
Query: 239 GNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCG------FVQFAARASAEEAILR 288
G + + E L+ F +G+I ++I RG G FV F S ++ +++
Sbjct: 109 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 62.4 bits (150), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 80/172 (46%), Gaps = 9/172 (5%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
E++R L+IG L + + L S F G + ++R+ T + G+G FV++A E
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG---FVTYATVEE 67
Query: 81 VLQTYNGTPMPGTEQNFRLNWASFGIGEKRPDAG-PEHSIFVGDLAPDVTDYLLQETFRS 139
V N P + A +RP A IFVG + D ++ L++ F
Sbjct: 68 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF-E 126
Query: 140 QYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE----MNGVFCSTR 187
QY + +++TD +G+ +G+ FV F D + ++ + + +NG C R
Sbjct: 127 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 178
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/176 (26%), Positives = 76/176 (43%), Gaps = 32/176 (18%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+F+G L+ + TD L+ F Q+ ++ V+ DPNT RS+G+GFV + E + AM
Sbjct: 16 LFIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 73
Query: 179 MNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFV 238
A P K G + P A + P + +T IFV
Sbjct: 74 ---------------ARPHKVDG--------RVVEPKRAVSREDSQRPGAH-LTVKKIFV 109
Query: 239 GNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCG------FVQFAARASAEEAILR 288
G + + E L+ F +G+I ++I RG G FV F S ++ +++
Sbjct: 110 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 62.0 bits (149), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 46/172 (26%), Positives = 80/172 (46%), Gaps = 9/172 (5%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
E++R L+IG L + + L S F G + ++R+ T + G+G FV++A E
Sbjct: 12 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFG---FVTYATVEE 68
Query: 81 VLQTYNGTPMPGTEQNFRLNWASFGIGEKRPDAG-PEHSIFVGDLAPDVTDYLLQETFRS 139
V N P + A +RP A IFVG + D ++ L++ F
Sbjct: 69 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF-E 127
Query: 140 QYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE----MNGVFCSTR 187
QY + +++TD +G+ +G+ FV F D + ++ + + +NG C R
Sbjct: 128 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 179
Score = 56.6 bits (135), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 47/176 (26%), Positives = 76/176 (43%), Gaps = 32/176 (18%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+F+G L+ + TD L+ F Q+ ++ V+ DPNT RS+G+GFV + E + AM
Sbjct: 17 LFIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 74
Query: 179 MNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFV 238
A P K G + P A + P + +T IFV
Sbjct: 75 ---------------ARPHKVDG--------RVVEPKRAVSREDSQRPGAH-LTVKKIFV 110
Query: 239 GNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCG------FVQFAARASAEEAILR 288
G + + E L+ F +G+I ++I RG G FV F S ++ +++
Sbjct: 111 GGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166
>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 = 62.0 bits (149), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 47/175 (26%), Positives = 72/175 (41%), Gaps = 37/175 (21%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
++ V L D TD L FR+ P + ++ D TG S GY FV F E + RA+
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGP-INTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 178 EMNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIF 237
+NG+ + +++S A P I +T ++
Sbjct: 75 VLNGITVRNKRLKVSYAR------------------------------PGGESIKDTNLY 104
Query: 238 VGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEAI 286
V NL +T+++L F +G IV I RG FV++ R A+EAI
Sbjct: 105 VTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
Score = 58.9 bits (141), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 42/157 (26%), Positives = 77/157 (49%), Gaps = 10/157 (6%)
Query: 40 LSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQNFRL 99
L + F G + + +I R+ TG GY FV+F S ++R ++ NG + + ++
Sbjct: 31 LYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITV--RNKRLKV 88
Query: 100 NWASFGIGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSK 159
++A G GE D +++V +L +TD L F +Y S+ ++ D TGR +
Sbjct: 89 SYARPG-GESIKDT----NLYVTNLPRTITDDQLDTIF-GKYGSIVQKNILRDKLTGRPR 142
Query: 160 GYGFVKFLDENERNRAMTEMNGVF--CSTRPMRISAA 194
G FV++ E A++ +N V ++P+ + A
Sbjct: 143 GVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 179
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 35/77 (45%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L++ +L ++ L + F G +V I+R+K+TG+P G FV + A+ +
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 86 NGTPMPGTEQNFRLNWA 102
N G Q + A
Sbjct: 163 NNVIPEGGSQPLSVRLA 179
>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 = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/96 (34%), Positives = 54/96 (56%), Gaps = 1/96 (1%)
Query: 102 ASFGIGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGY 161
S G ++ D +FVGDL+P++T ++ F + + + A+VV D TG+SKGY
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAF-APFGRISDARVVKDMATGKSKGY 59
Query: 162 GFVKFLDENERNRAMTEMNGVFCSTRPMRISAATPK 197
GFV F ++ + A+ +M G + R +R + AT K
Sbjct: 60 GFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 95
Score = 58.2 bits (139), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 44/78 (56%), Gaps = 6/78 (7%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEAILRM 289
+FVG+L P +T E++K F FG I + ++ +G GFV F + AE AI +M
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 290 QGHMIGQQQVRISWGRKQ 307
G +G +Q+R +W ++
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
+++GDL + + FA G + +++++ TG+ +GYGFV F + AE +Q
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 86 NGTPMPGTEQNFRLNWAS 103
G + G + R NWA+
Sbjct: 78 GGQWLGGRQ--IRTNWAT 93
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 45/78 (57%), Gaps = 6/78 (7%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEAILRM 289
+FVG+L P +T E++K F FG+I + ++ +G GFV F + AE AI+ M
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 290 QGHMIGQQQVRISWGRKQ 307
G +G +Q+R +W ++
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
Score = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 33/96 (34%), Positives = 53/96 (55%), Gaps = 1/96 (1%)
Query: 102 ASFGIGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGY 161
S G ++ D +FVGDL+P++T ++ F + + + A+VV D TG+SKGY
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAF-APFGKISDARVVKDMATGKSKGY 59
Query: 162 GFVKFLDENERNRAMTEMNGVFCSTRPMRISAATPK 197
GFV F ++ + A+ M G + R +R + AT K
Sbjct: 60 GFVSFYNKLDAENAIVHMGGQWLGGRQIRTNWATRK 95
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
+++GDL + S FA G++ +++++ TG+ +GYGFV F + AE +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 86 NGTPMPGTEQNFRLNWAS 103
G + G + R NWA+
Sbjct: 78 GGQWLGG--RQIRTNWAT 93
>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 = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 31/77 (40%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
++FVGDL +V D L+ F+ +PS V+ D TG S+GYGFV F +++ AM
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKD-FPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 178 EMNGVFCSTRPMRISAA 194
M G + RP+RI+ A
Sbjct: 62 SMQGQDLNGRPLRINWA 78
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 6/78 (7%)
Query: 235 TIFVGNLDPNVTEEELKQTFLHF-----GEIV-NVKIPMGRGCGFVQFAARASAEEAILR 288
+FVG+L+ NV +E L+ F F G ++ +++ RG GFV F ++ A+ A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 289 MQGHMIGQQQVRISWGRK 306
MQG + + +RI+W K
Sbjct: 63 MQGQDLNGRPLRINWAAK 80
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 25 TLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQT 84
L++GDL D+ L + F +S ++ + TG GYGFV F S A+ + +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 85 YNGTPMPGTEQNFRLNWAS 103
G + G + R+NWA+
Sbjct: 63 MQGQDLNG--RPLRINWAA 79
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 56.6 bits (135), Expect = 3e-08, Method: Composition-based stats.
Identities = 28/83 (33%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
++VG L ++T+ +L+ F + + ++ D +TGRSKGYGF+ F D RA+ +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEP-FGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 179 MNGVFCSTRPMRISAATPKKTTG 201
+NG + RPMR+ T + G
Sbjct: 67 LNGFELAGRPMRVGHVTERLDGG 89
Score = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 37/67 (55%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L++G L + E+ L F G++ +I ++++ TG+ +GYGF+ F A R L+
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 86 NGTPMPG 92
NG + G
Sbjct: 68 NGFELAG 74
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 6/75 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKI----PMGR--GCGFVQFAARASAEEAI 286
++ ++VG+L N+TE+ L+ F FG+I N+ + GR G GF+ F+ A A+
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 287 LRMQGHMIGQQQVRI 301
++ G + + +R+
Sbjct: 65 EQLNGFELAGRPMRV 79
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 56.2 bits (134), Expect = 3e-08, Method: Composition-based stats.
Identities = 28/89 (31%), Positives = 51/89 (57%), Gaps = 2/89 (2%)
Query: 109 KRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLD 168
++ AGP ++VG L ++T+ +L+ F + + +++ D TGRSKGYGF+ F D
Sbjct: 20 QKGSAGPMR-LYVGSLHFNITEDMLRGIFEP-FGRIESIQLMMDSETGRSKGYGFITFSD 77
Query: 169 ENERNRAMTEMNGVFCSTRPMRISAATPK 197
+A+ ++NG + RPM++ T +
Sbjct: 78 SECAKKALEQLNGFELAGRPMKVGHVTER 106
Score = 46.6 bits (109), Expect = 3e-05, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 37/67 (55%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L++G L + E+ L F G + SI+++ + TG+ +GYGF+ F A++ L+
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 86 NGTPMPG 92
NG + G
Sbjct: 89 NGFELAG 95
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 42/72 (58%), Gaps = 6/72 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAILRM 289
++VG+L N+TE+ L+ F FG I ++++ M +G GF+ F+ A++A+ ++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 290 QGHMIGQQQVRI 301
G + + +++
Sbjct: 89 NGFELAGRPMKV 100
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 226 PADNDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEA 285
+ D T TT++VG L +TE +L+ F FGEI + + + C F+QFA R +AE A
Sbjct: 5 SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVA 64
Query: 286 ILRMQGHMI-GQQQVRISWGR 305
+ +I +++ + WGR
Sbjct: 65 AEKSFNKLIVNGRRLNVKWGR 85
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 44/74 (59%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQGH 292
N T++ G + +T++ ++QTF FG+I+ +++ +G FV+F+ SA AI+ + G
Sbjct: 25 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGT 84
Query: 293 MIGQQQVRISWGRK 306
I V+ WG++
Sbjct: 85 TIEGHVVKCYWGKE 98
Score = 35.0 bits (79), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 15/93 (16%)
Query: 25 TLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQT 84
T++ G + + + F+ G+++ I++ K GY FV F +H +A + +
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVS 80
Query: 85 YNGTPMPGTEQNFRLNWASFGIGEKRPD--AGP 115
NGT + G + W G++ PD +GP
Sbjct: 81 VNGTTIEG--HVVKCYW-----GKESPDMTSGP 106
Score = 32.3 bits (72), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 7/64 (10%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
+++ G +A +TD L+++TF S + + +V + KGY FV+F A+
Sbjct: 27 TVYCGGIASGLTDQLMRQTF-SPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIV 79
Query: 178 EMNG 181
+NG
Sbjct: 80 SVNG 83
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 48/84 (57%), Gaps = 1/84 (1%)
Query: 114 GPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERN 173
G +FVGDL+P++T + + + + A+VV D TG+SKGYGFV F ++ +
Sbjct: 4 GSHFHVFVGDLSPEITTAAIAAA-FAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
Query: 174 RAMTEMNGVFCSTRPMRISAATPK 197
A+ +M G + R +R + AT K
Sbjct: 63 NAIQQMGGQWLGGRQIRTNWATRK 86
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEAILRM 289
+FVG+L P +T + F FG I + ++ +G GFV F + AE AI +M
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 290 QGHMIGQQQVRISWGRKQ 307
G +G +Q+R +W ++
Sbjct: 69 GGQWLGGRQIRTNWATRK 86
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 48 GEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQNFRLNWAS 103
G + +++++ TG+ +GYGFV F + AE +Q G + G + R NWA+
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ--IRTNWAT 84
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 50/183 (27%), Positives = 76/183 (41%), Gaps = 42/183 (22%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTD--PNTGRSKGYGFVKFLDENERNRAM 176
+FVG + ++ L+E F QY +V V+ D N +SKG FV F R A+
Sbjct: 6 MFVGQVPRTWSEKDLRELF-EQYGAVYEINVLRDRSQNPPQSKGCCFVTFYT---RKAAL 61
Query: 177 TEMNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPAD----NDIT 232
N + M++ + P+Q+ PAD N +
Sbjct: 62 EAQNAL----HNMKV-----------------------LPGMHHPIQMKPADSEKNNAVE 94
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG-----RGCGFVQFAARASAEEAIL 287
+ +F+G + TE +++ F FG+I +I G RGC FV F RA A+ AI
Sbjct: 95 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 154
Query: 288 RMQ 290
M
Sbjct: 155 AMH 157
Score = 31.6 bits (70), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 7/76 (9%)
Query: 22 EVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERV 81
E R L+IG + EN + F+ G++ +I+R G G FV F + A A+
Sbjct: 94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTA 152
Query: 82 L------QTYNGTPMP 91
+ QT G P
Sbjct: 153 IKAMHQAQTMEGCSSP 168
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 50/183 (27%), Positives = 76/183 (41%), Gaps = 42/183 (22%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTD--PNTGRSKGYGFVKFLDENERNRAM 176
+FVG + ++ L+E F QY +V V+ D N +SKG FV F R A+
Sbjct: 18 MFVGQVPRTWSEKDLRELF-EQYGAVYEINVLRDRSQNPPQSKGCCFVTFY---TRKAAL 73
Query: 177 TEMNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPAD----NDIT 232
N + M++ + P+Q+ PAD N +
Sbjct: 74 EAQNAL----HNMKV-----------------------LPGMHHPIQMKPADSEKNNAVE 106
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG-----RGCGFVQFAARASAEEAIL 287
+ +F+G + TE +++ F FG+I +I G RGC FV F RA A+ AI
Sbjct: 107 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 166
Query: 288 RMQ 290
M
Sbjct: 167 AMH 169
Score = 31.6 bits (70), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 7/76 (9%)
Query: 22 EVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERV 81
E R L+IG + EN + F+ G++ +I+R G G FV F + A A+
Sbjct: 106 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTA 164
Query: 82 L------QTYNGTPMP 91
+ QT G P
Sbjct: 165 IKAMHQAQTMEGCSSP 180
>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 = 52.0 bits (123), Expect = 7e-07, Method: Composition-based stats.
Identities = 24/51 (47%), Positives = 33/51 (64%)
Query: 37 ENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNG 87
++ L S F+ GEV S K+IR+K+ G GYGFV +V+ AER + T NG
Sbjct: 33 QDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 83
Score = 45.1 bits (105), Expect = 8e-05, Method: Composition-based stats.
Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 134 QETFRSQYPS---VRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRPMR 190
Q+ RS + S V AK++ D G S GYGFV ++ + RA+ +NG+ ++ ++
Sbjct: 33 QDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIK 92
Query: 191 ISAATP 196
+S A P
Sbjct: 93 VSYARP 98
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR------GCGFVQFAARASAEEAIL 287
T + V L N T++EL+ F GE+ + K+ + G GFV + AE AI
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 288 RMQGHMIGQQQVRISWGR 305
+ G + + +++S+ R
Sbjct: 80 TLNGLRLQSKTIKVSYAR 97
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 51.6 bits (122), Expect = 9e-07, Method: Composition-based stats.
Identities = 30/82 (36%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 113 AGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENER 172
A E +FVG L+ D + L++ F S+Y + VV D T RS+G+GFV F + ++
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVF-SKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 173 NRAMTEMNGVFCSTRPMRISAA 194
AM MNG R +R+ A
Sbjct: 68 KDAMMAMNGKSVDGRQIRVDQA 89
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 6/77 (7%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEAILRM 289
+FVG L + E+ L+Q F +G+I V + RG GFV F A++A++ M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 290 QGHMIGQQQVRISWGRK 306
G + +Q+R+ K
Sbjct: 75 NGKSVDGRQIRVDQAGK 91
Score = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 17/69 (24%), Positives = 37/69 (53%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L++G L + +E L F+ G++ + +++++ T + G+GFV F + A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 86 NGTPMPGTE 94
NG + G +
Sbjct: 75 NGKSVDGRQ 83
>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 = 51.6 bits (122), Expect = 9e-07, Method: Composition-based stats.
Identities = 24/51 (47%), Positives = 33/51 (64%)
Query: 37 ENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNG 87
++ L S F+ GEV S K+IR+K+ G GYGFV +V+ AER + T NG
Sbjct: 18 QDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 68
Score = 45.1 bits (105), Expect = 8e-05, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 132 LLQETFRSQYPS---VRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRP 188
+ Q+ RS + S V AK++ D G S GYGFV ++ + RA+ +NG+ ++
Sbjct: 16 MTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 75
Query: 189 MRISAATP 196
+++S A P
Sbjct: 76 IKVSYARP 83
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR------GCGFVQFAARASAEEAIL 287
T + V L N+T++EL+ F GE+ + K+ + G GFV + AE AI
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 288 RMQGHMIGQQQVRISWGR 305
+ G + + +++S+ R
Sbjct: 65 TLNGLRLQSKTIKVSYAR 82
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 45/162 (27%), Positives = 75/162 (46%), Gaps = 22/162 (13%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L++G+L E F GE + I R++ G+GF+ S AE
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 86 NGTPMPGTEQNFRLNWASFGIGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVR 145
+GT + + R+ +A+ G ++ V +L+P V++ LL++ F SQ+ V
Sbjct: 79 DGTILKS--RPLRIRFATHGA-----------ALTVKNLSPVVSNELLEQAF-SQFGPVE 124
Query: 146 GAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEM-NGVFCST 186
A VV D + GR+ G GFV+F + +A+ +G F T
Sbjct: 125 KAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLT 165
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/91 (31%), Positives = 48/91 (52%), Gaps = 3/91 (3%)
Query: 217 AYTTPVQVFPADNDITNTT---IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGF 273
+T ++ F + T T +FVGNL ++TEE+ K+ F +GE V I RG GF
Sbjct: 3 GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGF 62
Query: 274 VQFAARASAEEAILRMQGHMIGQQQVRISWG 304
++ +R AE A + G ++ + +RI +
Sbjct: 63 IRLESRTLAEIAKAELDGTILKSRPLRIRFA 93
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 48/176 (27%), Positives = 70/176 (39%), Gaps = 50/176 (28%)
Query: 119 IFVGDLAPDVTDYLLQETF-RSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
+FVG+L D+T+ + F R PS + R +G+GF++ A
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPS--------EVFINRDRGFGFIRLESRTLAEIAKA 76
Query: 178 EMNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIF 237
E++G +RP+RI AT +
Sbjct: 77 ELDGTILKSRPLRIRFAT------------------------------------HGAALT 100
Query: 238 VGNLDPNVTEEELKQTFLHFGEI---VNVKIPMGR--GCGFVQFAARASAEEAILR 288
V NL P V+ E L+Q F FG + V V GR G GFV+FAA+ A +A+ R
Sbjct: 101 VKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER 156
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 51.2 bits (121), Expect = 1e-06, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 40/70 (57%)
Query: 23 VRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVL 82
+R++++G++ Y E L F+ G VVS +++ ++ TG+P+GYGF E+ A +
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 83 QTYNGTPMPG 92
+ NG G
Sbjct: 68 RNLNGREFSG 77
Score = 50.1 bits (118), Expect = 3e-06, Method: Composition-based stats.
Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
S+FVG++ + T+ L++ F P V ++V D TG+ KGYGF ++ D+ AM
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVV-SFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 178 EMNGVFCSTRPMRISAATPKK 198
+NG S R +R+ A +K
Sbjct: 69 NLNGREFSGRALRVDNAASEK 89
Score = 37.0 bits (84), Expect = 0.022, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 235 TIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR------GCGFVQFAARASAEEAILR 288
++FVGN+ TEE+LK F G +V+ ++ R G GF ++ + +A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 289 MQGHMIGQQQVRI 301
+ G + +R+
Sbjct: 70 LNGREFSGRALRV 82
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 9/75 (12%)
Query: 221 PVQVFPAD----NDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG-----RGC 271
P+Q PAD N + + +F+G + TE +++ F FG+I +I G RGC
Sbjct: 79 PIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGC 138
Query: 272 GFVQFAARASAEEAI 286
FV F RA A+ AI
Sbjct: 139 AFVTFTTRAXAQTAI 153
Score = 32.0 bits (71), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 7/76 (9%)
Query: 22 EVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERV 81
E R L+IG + EN + F+ G++ +I+R G G FV F + A A+
Sbjct: 94 EDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAXAQTA 152
Query: 82 L------QTYNGTPMP 91
+ QT G P
Sbjct: 153 IKAXHQAQTXEGCSSP 168
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 50/81 (61%), Gaps = 3/81 (3%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
+++V +L + D L++ F S + ++ AKV+ + GRSKG+GFV F E +A+T
Sbjct: 17 NLYVKNLDDGIDDERLRKAF-SPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVT 73
Query: 178 EMNGVFCSTRPMRISAATPKK 198
EMNG +T+P+ ++ A K+
Sbjct: 74 EMNGRIVATKPLYVALAQRKE 94
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 44/77 (57%), Gaps = 4/77 (5%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM----GRGCGFVQFAARASAEEAILRMQG 291
++V NLD + +E L++ F FG I + K+ M +G GFV F++ A +A+ M G
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 292 HMIGQQQVRISWGRKQD 308
++ + + ++ ++++
Sbjct: 78 RIVATKPLYVALAQRKE 94
Score = 35.0 bits (79), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 18 MTLEEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAA 77
+T +V L++ +L D+ L F+ G + S K++ G+ +G+GFV F S
Sbjct: 10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEE 67
Query: 78 AERVLQTYNG 87
A + + NG
Sbjct: 68 ATKAVTEMNG 77
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 50.8 bits (120), Expect = 1e-06, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 132 LLQETFRSQYPSV---RGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRP 188
+ Q+ F+S + S+ K+V D TG+S GYGFV + D N+ ++A+ +NG+ T+
Sbjct: 16 MTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKT 75
Query: 189 MRISAATPKKTT 200
+++S A P +
Sbjct: 76 IKVSYARPSSAS 87
Score = 46.2 bits (108), Expect = 4e-05, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 31/51 (60%)
Query: 37 ENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNG 87
++ S F G++ S K++R+KITGQ GYGFV + A++ + T NG
Sbjct: 18 QDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNG 68
Score = 36.6 bits (83), Expect = 0.025, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR------GCGFVQFAARASAEEA 285
+ T + V L N+T++E K F G+I + K+ + G GFV ++ A++A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 286 ILRMQGHMIGQQQVRISWGR 305
I + G + + +++S+ R
Sbjct: 63 INTLNGLKLQTKTIKVSYAR 82
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 226 PADNDITNTT-IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEE 284
P + T + +FVGNL P++TEEE+++ F +G+ V I +G GF++ R AE
Sbjct: 14 PGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEI 73
Query: 285 AILRMQGHMIGQQQVRISWG 304
A + + + +Q+R+ +
Sbjct: 74 AKVELDNMPLRGKQLRVRFA 93
Score = 32.3 bits (72), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 40/175 (22%), Positives = 72/175 (41%), Gaps = 48/175 (27%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+FVG+L PD+T+ +++ F +Y + D KG+GF++ R + E
Sbjct: 25 LFVGNLPPDITEEEMRKLF-EKYGKAGEVFIHKD------KGFGFIRL-----ETRTLAE 72
Query: 179 MNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFV 238
+ V P+R + ++A A ++ V
Sbjct: 73 IAKVELDNMPLR--------GKQLRVRFACHSA-----------------------SLTV 101
Query: 239 GNLDPNVTEEELKQTFLHFGEI---VNVKIPMGR--GCGFVQFAARASAEEAILR 288
NL V+ E L++ F FG++ V + GR G G V+F+ + +A +A+ R
Sbjct: 102 RNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKALDR 156
>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 = 48.9 bits (115), Expect = 5e-06, Method: Composition-based stats.
Identities = 23/71 (32%), Positives = 42/71 (59%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQGHM 293
+ +FVGNL P++TEEE+++ F +G+ V I +G GF++ R AE A + +
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMP 75
Query: 294 IGQQQVRISWG 304
+ +Q+R+ +
Sbjct: 76 LRGKQLRVRFA 86
Score = 28.9 bits (63), Expect = 5.3, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 12/72 (16%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+FVG+L PD+T+ +++ F +Y + D KG+GF++ R + E
Sbjct: 18 LFVGNLPPDITEEEMRKLFE-KYGKAGEVFIHKD------KGFGFIRL-----ETRTLAE 65
Query: 179 MNGVFCSTRPMR 190
+ V P+R
Sbjct: 66 IAKVELDNMPLR 77
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 50/90 (55%), Gaps = 5/90 (5%)
Query: 106 IGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVK 165
I E+ DA +++VG L V++ LL E F P V + D TG+ +GYGFV+
Sbjct: 9 ISERNQDA----TVYVGGLDEKVSEPLLWELFLQAGPVVN-THMPKDRVTGQHQGYGFVE 63
Query: 166 FLDENERNRAMTEMNGVFCSTRPMRISAAT 195
FL E + + A+ M+ + +P+R++ A+
Sbjct: 64 FLSEEDADYAIKIMDMIKLYGKPIRVNKAS 93
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 25 TLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQT 84
T+++G L E L F G VV+ + ++++TGQ +GYGFVEF+S A+ ++
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 85 YNGTPMPGTEQNFRLNWAS 103
+ + G + R+N AS
Sbjct: 77 MDMIKLYG--KPIRVNKAS 93
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 6/76 (7%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR------GCGFVQFAARASAEEAI 286
+ T++VG LD V+E L + FL G +VN +P R G GFV+F + A+ AI
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 287 LRMQGHMIGQQQVRIS 302
M + + +R++
Sbjct: 75 KIMDMIKLYGKPIRVN 90
>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 = 48.9 bits (115), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 42/198 (21%), Positives = 88/198 (44%), Gaps = 36/198 (18%)
Query: 24 RTLWIGDLQYWFDENYLSSCF-----------AHTGEVVSIKIIRNKITGQPEGYGFVEF 72
R L++G++ + E + F A V++++I ++K + F+EF
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK------NFAFLEF 58
Query: 73 VS---------------HAAAERVLQTYNGTPMPGTEQNFRLNWASFGIGEKRPDAGPEH 117
S + ++ + ++ P+PG +N + + + PD+ H
Sbjct: 59 RSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSV-YVPGVVSTVVPDSA--H 115
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
+F+G L + D ++E S P ++ +V D TG SKGY F +++D N ++A+
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGP-LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 174
Query: 178 EMNGVFCSTRPMRISAAT 195
+NG+ + + + A+
Sbjct: 175 GLNGMQLGDKKLLVQRAS 192
Score = 36.2 bits (82), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 32/67 (47%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
+ L+IG L + +++ + G + + ++++ TG +GY F E+V ++
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Query: 81 VLQTYNG 87
+ NG
Sbjct: 172 AIAGLNG 178
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
++ V L D+TD L FR+ P + +++ D TG S GY FV F E + RA+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGP-INTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 178 EMNGVFCSTRPMRISAATP 196
+NG+ + +++S A P
Sbjct: 64 VLNGITVRNKRLKVSYARP 82
Score = 35.8 bits (81), Expect = 0.041, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 40 LSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQNFRL 99
L + F G + + +I+R+ TG GY FV+F S ++R ++ NG T +N RL
Sbjct: 20 LYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGI----TVRNKRL 75
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM----GRGCGFVQFAARASAEEAILRMQG 291
IF+ NLD ++ + L TF FG I++ K+ +G GFV F + +AE AI +M G
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 73
Query: 292 HMIGQQQV 299
++ ++V
Sbjct: 74 MLLNDRKV 81
Score = 45.8 bits (107), Expect = 5e-05, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
+IF+ +L + + L +TF S + ++ KVV D N SKGYGFV F + RA+
Sbjct: 13 NIFIKNLDKSIDNKALYDTF-SAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 69
Query: 178 EMNGVFCSTRPMRISAATPKK 198
+MNG+ + R + + +K
Sbjct: 70 KMNGMLLNDRKVFVGRFKSRK 90
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 23 VRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVL 82
V ++I +L D L F+ G ++S K++ ++ +GYGFV F + AAER +
Sbjct: 11 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAI 68
Query: 83 QTYNG 87
+ NG
Sbjct: 69 EKMNG 73
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 39/68 (57%), Gaps = 4/68 (5%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM----GRGCGFVQFAARASAEEAILRMQG 291
IF+ NLD ++ + L TF FG I++ K+ +G GFV F + +AE AI +M G
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 292 HMIGQQQV 299
++ ++V
Sbjct: 68 MLLNDRKV 75
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 3/81 (3%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
+IF+ +L + + L +TF S + ++ KVV D N SKGYGFV F + RA+
Sbjct: 7 NIFIKNLDKSIDNKALYDTF-SAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 63
Query: 178 EMNGVFCSTRPMRISAATPKK 198
+MNG+ + R + + +K
Sbjct: 64 KMNGMLLNDRKVFVGRFKSRK 84
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
++I +L D L F+ G ++S K++ ++ +GYGFV F + AAER ++
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65
Query: 86 NG 87
NG
Sbjct: 66 NG 67
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 45/89 (50%), Gaps = 4/89 (4%)
Query: 23 VRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVL 82
+R L + + DE L F G + S+KI+ ++ T Q GYGFV+F S ++A++ +
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 83 QTYNGTPMPGTEQNFRLNWASFGIGEKRP 111
NG + N RL A G +RP
Sbjct: 102 AGLNGFNI----LNKRLKVALAASGHQRP 126
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 49/92 (53%), Gaps = 8/92 (8%)
Query: 218 YTTPVQVFPADNDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKI------PMGRGC 271
+ P Q+ P + + N + V + V E +L+Q F +G I +VKI RG
Sbjct: 29 HIPPTQMNPEPDVLRN--LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGY 86
Query: 272 GFVQFAARASAEEAILRMQGHMIGQQQVRISW 303
GFV+F + +SA++AI + G I ++++++
Sbjct: 87 GFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL 118
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 117 HSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAM 176
++ V + V + L++ F +Y + K+V D T +S+GYGFVKF + +A+
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLF-ERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 177 TEMNGVFCSTRPMRISAA 194
+NG + ++++ A
Sbjct: 102 AGLNGFNILNKRLKVALA 119
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 34/93 (36%), Positives = 47/93 (50%), Gaps = 6/93 (6%)
Query: 107 GEKRPDA--GPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFV 164
G P+A P ++FV L+ D T+ L+E+F SVR A++VTD TG SKG+GFV
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDG---SVR-ARIVTDRETGSSKGFGFV 59
Query: 165 KFLDENERNRAMTEMNGVFCSTRPMRISAATPK 197
F E + A M + + A PK
Sbjct: 60 DFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPK 92
Score = 33.1 bits (74), Expect = 0.33, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 235 TIFVGNLDPNVTEEELKQTF---LHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQG 291
T+FV L + TEE LK++F + + + + +G GFV F + A+ A M+
Sbjct: 17 TLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMED 76
Query: 292 HMIGQQQVRISWGRKQ 307
I +V + W + +
Sbjct: 77 GEIDGNKVTLDWAKPK 92
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 45.8 bits (107), Expect = 5e-05, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 1/88 (1%)
Query: 114 GPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERN 173
GP +++G + D T+ + + + P + K++ DP TGRSKGY F++F D
Sbjct: 1 GPSRVVYLGSIPYDQTEEQILDLCSNVGPVIN-LKMMFDPQTGRSKGYAFIEFRDLESSA 59
Query: 174 RAMTEMNGVFCSTRPMRISAATPKKTTG 201
A+ +NG +R ++ ++ +G
Sbjct: 60 SAVRNLNGYQLGSRFLKCGYSSNSDISG 87
Score = 36.6 bits (83), Expect = 0.030, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 36/64 (56%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
R +++G + Y E + ++ G V+++K++ + TG+ +GY F+EF ++ ++
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 84 TYNG 87
NG
Sbjct: 64 NLNG 67
Score = 35.8 bits (81), Expect = 0.046, Method: Composition-based stats.
Identities = 16/82 (19%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAILRM 289
+++G++ + TEE++ + G ++N+K+ +G F++F S+ A+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 290 QGHMIGQQQVRISWGRKQDVTG 311
G+ +G + ++ + D++G
Sbjct: 66 NGYQLGSRFLKCGYSSNSDISG 87
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 44/191 (23%), Positives = 81/191 (42%), Gaps = 34/191 (17%)
Query: 20 LEEVRTLWIGDLQYWFDENYLSSCF-----------AHTGEVVSIKIIRNKITGQPEGYG 68
L R L++G++ + E + F A V++++I Q + +
Sbjct: 1 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFA 54
Query: 69 FVEFVSHAAAERVLQTYNGTPMPGTEQNFRLNWASFGIGEKRP-DAGP---EHSIFVGDL 124
F+EF S + + ++G G R RP D P H +F+G L
Sbjct: 55 FLEFRSVDETTQAM-AFDGIIFQGQSLKIR-----------RPHDYQPLPGAHKLFIGGL 102
Query: 125 APDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFC 184
+ D ++E S P ++ +V D TG SKGY F +++D N ++A+ +NG+
Sbjct: 103 PNYLNDDQVKELLTSFGP-LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 161
Query: 185 STRPMRISAAT 195
+ + + A+
Sbjct: 162 GDKKLLVQRAS 172
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 44/191 (23%), Positives = 82/191 (42%), Gaps = 34/191 (17%)
Query: 20 LEEVRTLWIGDLQYWFDENYLSSCF-----------AHTGEVVSIKIIRNKITGQPEGYG 68
L R L++G++ + E + F A V++++I ++K +
Sbjct: 3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK------NFA 56
Query: 69 FVEFVSHAAAERVLQTYNGTPMPGTEQNFRLNWASFGIGEKRP-DAGP---EHSIFVGDL 124
F+EF S + + ++G G R RP D P H +F+G L
Sbjct: 57 FLEFRSVDETTQAM-AFDGIIFQGQSLKIR-----------RPHDYQPLPGAHKLFIGGL 104
Query: 125 APDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFC 184
+ D ++E S P ++ +V D TG SKGY F +++D N ++A+ +NG+
Sbjct: 105 PNYLNDDQVKELLTSFGP-LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 163
Query: 185 STRPMRISAAT 195
+ + + A+
Sbjct: 164 GDKKLLVQRAS 174
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 26/82 (31%), Positives = 47/82 (57%), Gaps = 2/82 (2%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
+I+VG+L T ++E F SQ+ V K++ D T + KG+GFV+ + E + A+
Sbjct: 3 NIYVGNLVYSATSEQVKELF-SQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIA 60
Query: 178 EMNGVFCSTRPMRISAATPKKT 199
+++ R +R++ A PKK+
Sbjct: 61 KLDNTDFMGRTIRVTEANPKKS 82
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 38/64 (59%)
Query: 23 VRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVL 82
+R +++G+L Y + F+ G+V ++K+I ++ T +P+G+GFVE + +E +
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIA 60
Query: 83 QTYN 86
+ N
Sbjct: 61 KLDN 64
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 7/73 (9%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR------GCGFVQFAARASAEEAILRM 289
I+VGNL + T E++K+ F FG++ NVK+ R G GFV+ S EAI ++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAKL 62
Query: 290 QGHMIGQQQVRIS 302
+ +R++
Sbjct: 63 DNTDFMGRTIRVT 75
>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 = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 47/93 (50%), Gaps = 12/93 (12%)
Query: 223 QVFPADND------ITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR----GCG 272
Q F DN+ + T++VGNL TEE++ + F G+I + + + + CG
Sbjct: 23 QHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 273 --FVQFAARASAEEAILRMQGHMIGQQQVRISW 303
FV++ +RA AE A+ + G + + +R W
Sbjct: 83 FCFVEYYSRADAENAMRYINGTRLDDRIIRTDW 115
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 20 LEEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAE 79
L++ TL++G+L ++ E + F+ +G++ I + +K+ G+ FVE+ S A AE
Sbjct: 36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
Query: 80 RVLQTYNGTPMPGTEQNFRLNW 101
++ NGT + ++ R +W
Sbjct: 96 NAMRYINGTRLD--DRIIRTDW 115
>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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ MQG + +RI + +
Sbjct: 69 LRSMQGFPFYDKPMRIQYAK 88
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/84 (21%), Positives = 37/84 (44%)
Query: 111 PDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDEN 170
P+ P H+I++ +L + L+++ + + + + + +G FV F + +
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVS 63
Query: 171 ERNRAMTEMNGVFCSTRPMRISAA 194
A+ M G +PMRI A
Sbjct: 64 SATNALRSMQGFPFYDKPMRIQYA 87
>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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ MQG + +RI + +
Sbjct: 63 LRSMQGFPFYDKPMRIQYAK 82
Score = 29.6 bits (65), Expect = 3.0, Method: Composition-based stats.
Identities = 17/80 (21%), Positives = 35/80 (43%)
Query: 115 PEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNR 174
P H+I++ +L + L+++ + + + + + +G FV F + +
Sbjct: 2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61
Query: 175 AMTEMNGVFCSTRPMRISAA 194
A+ M G +PMRI A
Sbjct: 62 ALRSMQGFPFYDKPMRIQYA 81
>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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 4 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 63
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ MQG + +RI + +
Sbjct: 64 LRSMQGFPFYDKPMRIQYAK 83
Score = 29.6 bits (65), Expect = 3.1, Method: Composition-based stats.
Identities = 17/80 (21%), Positives = 35/80 (43%)
Query: 115 PEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNR 174
P H+I++ +L + L+++ + + + + + +G FV F + +
Sbjct: 3 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 62
Query: 175 AMTEMNGVFCSTRPMRISAA 194
A+ M G +PMRI A
Sbjct: 63 ALRSMQGFPFYDKPMRIQYA 82
>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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 5 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 64
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ MQG + +RI + +
Sbjct: 65 LRSMQGFPFYDKPMRIQYAK 84
Score = 29.6 bits (65), Expect = 3.1, Method: Composition-based stats.
Identities = 17/80 (21%), Positives = 35/80 (43%)
Query: 115 PEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNR 174
P H+I++ +L + L+++ + + + + + +G FV F + +
Sbjct: 4 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 63
Query: 175 AMTEMNGVFCSTRPMRISAA 194
A+ M G +PMRI A
Sbjct: 64 ALRSMQGFPFYDKPMRIQYA 83
>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 = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 6 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 65
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ MQG + +RI + +
Sbjct: 66 LRSMQGFPFYDKPMRIQYAK 85
Score = 32.3 bits (72), Expect = 0.52, Method: Composition-based stats.
Identities = 18/84 (21%), Positives = 37/84 (44%)
Query: 111 PDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDEN 170
P+ P H+I++ +L + L+++ + + + + + +G FV F + +
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 60
Query: 171 ERNRAMTEMNGVFCSTRPMRISAA 194
A+ M G +PMRI A
Sbjct: 61 SATNALRSMQGFPFYDKPMRIQYA 84
>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 = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ MQG + +RI + +
Sbjct: 69 LRSMQGFPFYDKPMRIQYAK 88
Score = 32.3 bits (72), Expect = 0.52, Method: Composition-based stats.
Identities = 18/84 (21%), Positives = 37/84 (44%)
Query: 111 PDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDEN 170
P+ P H+I++ +L + L+++ + + + + + +G FV F + +
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 63
Query: 171 ERNRAMTEMNGVFCSTRPMRISAA 194
A+ M G +PMRI A
Sbjct: 64 SATNALRSMQGFPFYDKPMRIQYA 87
>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 = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ MQG + +RI + +
Sbjct: 68 LRSMQGFPFYDKPMRIQYAK 87
Score = 32.3 bits (72), Expect = 0.51, Method: Composition-based stats.
Identities = 18/84 (21%), Positives = 37/84 (44%)
Query: 111 PDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDEN 170
P+ P H+I++ +L + L+++ + + + + + +G FV F + +
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 171 ERNRAMTEMNGVFCSTRPMRISAA 194
A+ M G +PMRI A
Sbjct: 63 SATNALRSMQGFPFYDKPMRIQYA 86
>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 = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ MQG + +RI + +
Sbjct: 68 LRSMQGFPFYDKPMRIQYAK 87
Score = 32.3 bits (72), Expect = 0.53, Method: Composition-based stats.
Identities = 18/84 (21%), Positives = 37/84 (44%)
Query: 111 PDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDEN 170
P+ P H+I++ +L + L+++ + + + + + +G FV F + +
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 171 ERNRAMTEMNGVFCSTRPMRISAA 194
A+ M G +PMRI A
Sbjct: 63 SATNALRSMQGFPFYDKPMRIQYA 86
>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 = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ MQG + +RI + +
Sbjct: 68 LRSMQGFPFYDKPMRIQYAK 87
Score = 32.3 bits (72), Expect = 0.52, Method: Composition-based stats.
Identities = 18/84 (21%), Positives = 37/84 (44%)
Query: 111 PDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDEN 170
P+ P H+I++ +L + L+++ + + + + + +G FV F + +
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 171 ERNRAMTEMNGVFCSTRPMRISAA 194
A+ M G +PMRI A
Sbjct: 63 SATNALRSMQGFPFYDKPMRIQYA 86
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ MQG + +RI + +
Sbjct: 69 LRSMQGFPFYDKPMRIQYAK 88
Score = 31.6 bits (70), Expect = 0.80, Method: Composition-based stats.
Identities = 18/84 (21%), Positives = 37/84 (44%)
Query: 111 PDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDEN 170
P+ P H+I++ +L + L+++ + + + + + +G FV F + +
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVS 63
Query: 171 ERNRAMTEMNGVFCSTRPMRISAA 194
A+ M G +PMRI A
Sbjct: 64 SATNALRSMQGFPFYDKPMRIQYA 87
>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 = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ MQG + +RI + +
Sbjct: 69 LRSMQGFPFYDKPMRIQYAK 88
Score = 32.3 bits (72), Expect = 0.54, Method: Composition-based stats.
Identities = 18/84 (21%), Positives = 37/84 (44%)
Query: 111 PDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDEN 170
P+ P H+I++ +L + L+++ + + + + + +G FV F + +
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 63
Query: 171 ERNRAMTEMNGVFCSTRPMRISAA 194
A+ M G +PMRI A
Sbjct: 64 SATNALRSMQGFPFYDKPMRIQYA 87
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/87 (26%), Positives = 44/87 (50%), Gaps = 1/87 (1%)
Query: 115 PEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNR 174
P +++G + D T+ + + + P + K++ DP TGRSKGY F++F D
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVIN-LKMMFDPQTGRSKGYAFIEFRDLESSAS 59
Query: 175 AMTEMNGVFCSTRPMRISAATPKKTTG 201
A+ +NG +R ++ ++ +G
Sbjct: 60 AVRNLNGYQLGSRFLKCGYSSNSDISG 86
Score = 36.6 bits (83), Expect = 0.028, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 36/64 (56%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
R +++G + Y E + ++ G V+++K++ + TG+ +GY F+EF ++ ++
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 84 TYNG 87
NG
Sbjct: 63 NLNG 66
Score = 35.8 bits (81), Expect = 0.044, Method: Composition-based stats.
Identities = 16/82 (19%), Positives = 43/82 (52%), Gaps = 6/82 (7%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAILRM 289
+++G++ + TEE++ + G ++N+K+ +G F++F S+ A+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 290 QGHMIGQQQVRISWGRKQDVTG 311
G+ +G + ++ + D++G
Sbjct: 65 NGYQLGSRFLKCGYSSNSDISG 86
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ MQG + +RI + +
Sbjct: 68 LRSMQGFPFYDKPMRIQYAK 87
Score = 31.6 bits (70), Expect = 0.89, Method: Composition-based stats.
Identities = 18/84 (21%), Positives = 37/84 (44%)
Query: 111 PDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDEN 170
P+ P H+I++ +L + L+++ + + + + + +G FV F + +
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 171 ERNRAMTEMNGVFCSTRPMRISAA 194
A+ M G +PMRI A
Sbjct: 63 SATNALRSMQGFPFYDKPMRIQYA 86
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
IFVG L TD L++ F + + A V+TD TG+S+GYGFV D RA +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEG-FGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 179 MN 180
N
Sbjct: 79 PN 80
Score = 41.6 bits (96), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 28/98 (28%), Positives = 43/98 (43%), Gaps = 10/98 (10%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
+++G L Y + L F G++ +I ++ TG+ GYGFV AAAER +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 86 NGTPMPGTEQNFRLNW---------ASFGIGEKRPDAG 114
N + G + N L + F IG P +G
Sbjct: 80 NPI-IDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSSG 116
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 229 NDITNTTIFVGNLDPNVTEEELKQTFLHFGE------IVNVKIPMGRGCGFVQFAARASA 282
D T T IFVG L + T+ L++ F FG+ I + + RG GFV A RA+A
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 283 EEA 285
E A
Sbjct: 73 ERA 75
>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 = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 28/92 (30%), Positives = 46/92 (50%), Gaps = 11/92 (11%)
Query: 223 QVFPADND------ITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKI---PMGRGCG- 272
Q F DN+ + T++VGNL TEE++ + F G+I + + M CG
Sbjct: 2 QHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGF 61
Query: 273 -FVQFAARASAEEAILRMQGHMIGQQQVRISW 303
FV++ +RA AE A+ + G + + +R W
Sbjct: 62 CFVEYYSRADAENAMRYINGTRLDDRIIRTDW 93
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 46/82 (56%), Gaps = 3/82 (3%)
Query: 20 LEEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAE 79
L++ TL++G+L ++ E + F+ +G++ I + +K+ G+ FVE+ S A AE
Sbjct: 15 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK-TACGFCFVEYYSRADAE 73
Query: 80 RVLQTYNGTPMPGTEQNFRLNW 101
++ NGT + ++ R +W
Sbjct: 74 NAMRYINGTRL--DDRIIRTDW 93
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 36/164 (21%), Positives = 69/164 (42%), Gaps = 26/164 (15%)
Query: 159 KGYGFVKFLDENERNRAMTEMNGVFCSTRPMRISAATPKKTT---------GFQQQYAAV 209
K V+ D N+ AM+ +NG +P+RI+ + + G + Y
Sbjct: 41 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYG-- 98
Query: 210 KATYPVAAYTTP-----VQVFPADNDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVN-- 262
P+ + P +FP + T+ + N+ P+V+EE+LK F G +V
Sbjct: 99 --NSPLHRFKKPGSKNFQNIFPP-----SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF 151
Query: 263 VKIPMGRGCGFVQFAARASAEEAILRMQGHMIGQ-QQVRISWGR 305
R +Q + A +A++ + H +G+ +R+S+ +
Sbjct: 152 KFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK 195
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 233 NTTIFVGNLDPN-VTEEELKQTFLHFGEIVNVKIPMGRG-CGFVQFAARASAEEAILRMQ 290
N+ + V NL+P VT + L F +G++ VKI + VQ A A+ A+ +
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62
Query: 291 GHMIGQQQVRISWGRKQDV 309
GH + + +RI+ + Q+V
Sbjct: 63 GHKLHGKPIRITLSKHQNV 81
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 117 HSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAM 176
H +F+G L + D ++E S P ++ +V D TG SKGY F +++D N ++A+
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGP-LKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Query: 177 TEMNGVFCSTRPMRISAAT 195
+NG+ + + + A+
Sbjct: 61 AGLNGMQLGDKKLLVQRAS 79
Score = 33.5 bits (75), Expect = 0.26, Method: Composition-based stats.
Identities = 14/65 (21%), Positives = 32/65 (49%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L+IG L + +++ + G + + ++++ TG +GY F E+V ++ +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 86 NGTPM 90
NG +
Sbjct: 64 NGMQL 68
>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 = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 35/160 (21%), Positives = 68/160 (42%), Gaps = 26/160 (16%)
Query: 163 FVKFLDENERNRAMTEMNGVFCSTRPMRISAATPKKTT---------GFQQQYAAVKATY 213
V+ D N+ AM+ +NG +P+RI+ + + G + Y
Sbjct: 76 LVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYG----NS 131
Query: 214 PVAAYTTP-----VQVFPADNDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVN--VKIP 266
P+ + P +FP + T+ + N+ P+V+EE+LK F G +V
Sbjct: 132 PLHRFKKPGSKNFQNIFPP-----SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ 186
Query: 267 MGRGCGFVQFAARASAEEAILRMQGHMIGQ-QQVRISWGR 305
R +Q + A +A++ + H +G+ +R+S+ +
Sbjct: 187 KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK 226
Score = 37.0 bits (84), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 233 NTTIFVGNLDP-NVTEEELKQTFLHFGEIVNVKIPMGRG-CGFVQFAARASAEEAILRMQ 290
N+ + V NL+P VT + L F +G++ VKI + VQ A A+ A+ +
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 93
Query: 291 GHMIGQQQVRISWGRKQDV 309
GH + + +RI+ + Q+V
Sbjct: 94 GHKLHGKPIRITLSKHQNV 112
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 6/66 (9%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAI 286
+ ++V L ++++E++Q F +G I+ +I + RG GF++F R AEEAI
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 287 LRMQGH 292
+ G
Sbjct: 61 KGLNGQ 66
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 36/78 (46%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L++ L + + F+ G +++ +I+ ++ TG G GF+ F AE ++
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 86 NGTPMPGTEQNFRLNWAS 103
NG G + + +A+
Sbjct: 64 NGQKPLGAAEPITVKFAN 81
Score = 35.8 bits (81), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 116 EHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRA 175
+ +++V L ++ +++ F SQY + ++++ D TG S+G GF++F E A
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLF-SQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEA 59
Query: 176 MTEMNG 181
+ +NG
Sbjct: 60 IKGLNG 65
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 30/92 (32%), Positives = 45/92 (48%), Gaps = 7/92 (7%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEF-----VSH 75
+E+ L++G L + + L S F+ GEVV I+++K T Q G+GFV+F V
Sbjct: 14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGT 73
Query: 76 AAAER--VLQTYNGTPMPGTEQNFRLNWASFG 105
A R L N P P T + + + S G
Sbjct: 74 VLASRPHTLDGRNIDPKPCTPRGMQPSGPSSG 105
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 22/52 (42%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDEN 170
+FVG L T L+ F SQY V ++ D T +S+G+GFVKF D N
Sbjct: 19 LFVGGLDWSTTQETLRSYF-SQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPN 69
Score = 35.4 bits (80), Expect = 0.063, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 6/47 (12%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKI------PMGRGCGFVQF 276
+FVG LD + T+E L+ F +GE+V+ I RG GFV+F
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 47/90 (52%), Gaps = 5/90 (5%)
Query: 226 PADNDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRG---CGFVQFAARASA 282
PA N+ + I+VGNL P++ ++++ F +G I ++ + RG FV+F A
Sbjct: 17 PAGNN--DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDA 74
Query: 283 EEAILRMQGHMIGQQQVRISWGRKQDVTGS 312
E+A+ G+ ++R+ + R TGS
Sbjct: 75 EDAVYGRDGYDYDGYRLRVEFPRSGRGTGS 104
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAIL 287
T++ V NL + + L++ F +G + +V IP RG FV+F + AE+A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 288 RMQGHMIGQQQVRISWGR 305
M G ++ +++R+ R
Sbjct: 131 AMDGAVLDGRELRVQMAR 148
Score = 35.4 bits (80), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 33/130 (25%), Positives = 52/130 (40%), Gaps = 7/130 (5%)
Query: 71 EFVSHAAAERVLQTYNGTPMPGTEQNFRLNWASFGIGE------KRPDAGPEHSIFVGDL 124
E V A AE+V + Y E + +F + E D S+ V +L
Sbjct: 19 EAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNL 78
Query: 125 APDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFC 184
+ L+ F +Y V + D T S+G+ FV+F D+ + AM M+G
Sbjct: 79 TYRTSPDTLRRVF-EKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 137
Query: 185 STRPMRISAA 194
R +R+ A
Sbjct: 138 DGRELRVQMA 147
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 35/78 (44%)
Query: 25 TLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQT 84
L++ +L ++ L + F G +V I+R+K+TG+P G FV + A+ +
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 85 YNGTPMPGTEQNFRLNWA 102
N G Q + A
Sbjct: 75 LNNVIPEGGSQPLSVRLA 92
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 226 PADNDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAAR 279
P I +T ++V NL +T+++L F +G IV I RG FV++ R
Sbjct: 6 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR 65
Query: 280 ASAEEAI 286
A+EAI
Sbjct: 66 EEAQEAI 72
Score = 35.0 bits (79), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
+++V +L +TD L F +Y S+ ++ D TGR +G FV++ E A++
Sbjct: 15 NLYVTNLPRTITDDQLDTIF-GKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 178 EMNGVF--CSTRPMRISAA 194
+N V ++P+ + A
Sbjct: 74 ALNNVIPEGGSQPLSVRLA 92
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 115 PEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNR 174
P +++G + D T+ + + + P + K++ DP TGRSKGY F++F D
Sbjct: 3 PSRVVYLGSIPYDQTEEQILDLCSNVGPVI-NLKMMFDPQTGRSKGYAFIEFRDLESSAS 61
Query: 175 AMTEMNGVFCSTRPMR 190
A+ +NG +R ++
Sbjct: 62 AVRNLNGYQLGSRFLK 77
Score = 36.2 bits (82), Expect = 0.033, Method: Composition-based stats.
Identities = 16/64 (25%), Positives = 36/64 (56%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
R +++G + Y E + ++ G V+++K++ + TG+ +GY F+EF ++ ++
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 84 TYNG 87
NG
Sbjct: 65 NLNG 68
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 14/74 (18%), Positives = 39/74 (52%), Gaps = 6/74 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAILRM 289
+++G++ + TEE++ + G ++N+K+ +G F++F S+ A+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 290 QGHMIGQQQVRISW 303
G+ +G + ++ +
Sbjct: 67 NGYQLGSRFLKCGY 80
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain
Of Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain
Of Xenopus Laevis Epabp2
Length = 124
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 30/49 (61%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEF 72
R++++G++ Y L + F+ G + I I+ +K +G P+GY ++EF
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF 85
Score = 32.7 bits (73), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 9/79 (11%)
Query: 217 AYTT-PVQVFPAD--NDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG----- 268
AYT P Q A+ +I +++VGN+D T ++L+ F G I + I
Sbjct: 17 AYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGH 76
Query: 269 -RGCGFVQFAARASAEEAI 286
+G +++FA R S + A+
Sbjct: 77 PKGYAYIEFAERNSVDAAV 95
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+F+G L+ T L+E F Q+ V+ V+ DP T RS+G+GFV F+D+ ++ + +
Sbjct: 3 MFIGGLSWQTTQEGLREYF-GQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVL 82
++IG L + + L F GEV ++R+ +T + G+GFV F+ A ++VL
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
Score = 32.7 bits (73), Expect = 0.42, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 6/57 (10%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEI---VNVKIPM---GRGCGFVQFAARASAEEAI 286
+F+G L T+E L++ F FGE+ + ++ P+ RG GFV F +A ++ +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 59
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 25 TLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQT 84
T+++G + DE + S FA G V +KII ++ TG +GYGFV F + ++++++
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 70
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 23/55 (41%), Positives = 36/55 (65%), Gaps = 6/55 (10%)
Query: 117 HSIFVG--DLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDE 169
+++FVG D+ D T+ +F ++Y SV+ K++TD TG SKGYGFV F ++
Sbjct: 11 NTVFVGGIDVRMDETEI---RSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYND 61
Score = 35.0 bits (79), Expect = 0.083, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 231 ITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR-----GCGFVQF 276
I T+FVG +D + E E++ F +G + VKI R G GFV F
Sbjct: 8 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 58
>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 = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 25 TLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQT 84
T+++G + DE + S FA G V +KII ++ TG +GYGFV F + ++++++
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 23/55 (41%), Positives = 36/55 (65%), Gaps = 6/55 (10%)
Query: 117 HSIFVG--DLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDE 169
+++FVG D+ D T+ +F ++Y SV+ K++TD TG SKGYGFV F ++
Sbjct: 10 NTVFVGGIDVRMDETEI---RSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYND 60
Score = 35.0 bits (79), Expect = 0.074, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 228 DNDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR-----GCGFVQF 276
+ I T+FVG +D + E E++ F +G + VKI R G GFV F
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
>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 = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 4/57 (7%)
Query: 112 DAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLD 168
DAG FVG L+ D + L++ F +++ V + DPNTGRS+G+GF+ F D
Sbjct: 10 DAGKX---FVGGLSWDTSKKDLKDYF-TKFGEVVDCTIKXDPNTGRSRGFGFILFKD 62
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 6/66 (9%)
Query: 237 FVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAILRMQ 290
FVG L + ++++LK F FGE+V+ I RG GF+ F AS E+ + + +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 291 GHMIGQ 296
+ G+
Sbjct: 75 HRLDGR 80
Score = 36.2 bits (82), Expect = 0.038, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 31/62 (50%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
E+ ++G L + + L F GEVV I + TG+ G+GF+ F A+ E+
Sbjct: 9 EDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEK 68
Query: 81 VL 82
VL
Sbjct: 69 VL 70
>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 = 42.0 bits (97), Expect = 7e-04, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNV---KIPMGRGCGFVQFAARASAEEA 285
N TI++ N++ + +EELK++ F FG +V++ K RG FV F S+ A
Sbjct: 6 NHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNA 65
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ ++QG + +RI + +
Sbjct: 66 LRQLQGFPFYGKPMRIQYAK 85
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 42.0 bits (97), Expect = 7e-04, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 25 TLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQT 84
T+++G + DE + S FA G V +KII ++ TG +GYGFV F + ++++++
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 23/55 (41%), Positives = 36/55 (65%), Gaps = 6/55 (10%)
Query: 117 HSIFVG--DLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDE 169
+++FVG D+ D T+ +F ++Y SV+ K++TD TG SKGYGFV F ++
Sbjct: 10 NTVFVGGIDVRMDETEI---RSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYND 60
Score = 35.0 bits (79), Expect = 0.087, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 228 DNDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR-----GCGFVQF 276
+ I T+FVG +D + E E++ F +G + VKI R G GFV F
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 41.6 bits (96), Expect = 8e-04, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 7/72 (9%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEAILRM 289
IFVG L P+ EE++++ F FGE+ ++++PM RG F+ F ++ I+
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK-IMEK 62
Query: 290 QGHMIGQQQVRI 301
+ H +G + I
Sbjct: 63 KYHNVGLSKCEI 74
Score = 33.9 bits (76), Expect = 0.19, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAM 176
IFVG L+PD + ++E F + V ++ D T + +G+ F+ F +E + M
Sbjct: 4 IFVGGLSPDTPEEKIREYF-GGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 41.6 bits (96), Expect = 8e-04, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 7/72 (9%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEAILRM 289
IFVG L P+ EE++++ F FGE+ ++++PM RG F+ F ++ I+
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKK-IMEK 60
Query: 290 QGHMIGQQQVRI 301
+ H +G + I
Sbjct: 61 KYHNVGLSKCEI 72
Score = 33.9 bits (76), Expect = 0.20, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAM 176
IFVG L+PD + ++E F + V ++ D T + +G+ F+ F +E + M
Sbjct: 2 IFVGGLSPDTPEEKIREYF-GGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 35/64 (54%)
Query: 244 NVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQGHMIGQQQVRISW 303
++T L+ F FG I+++ + R C FV + SA++A+ + G + Q++++
Sbjct: 24 DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 83
Query: 304 GRKQ 307
RKQ
Sbjct: 84 ARKQ 87
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 41.6 bits (96), Expect = 9e-04, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+F+G L+ T L+E F Q+ V+ V+ DP T RS+G+GFV F+D+ ++ + +
Sbjct: 28 MFIGGLSWQTTQEGLREYF-GQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVL 82
++IG L + + L F GEV ++R+ +T + G+GFV F+ A ++VL
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Score = 32.0 bits (71), Expect = 0.60, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 6/57 (10%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEI---VNVKIPM---GRGCGFVQFAARASAEEAI 286
+F+G L T+E L++ F FGE+ + ++ P+ RG GFV F +A ++ +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
>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 = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 35/64 (54%)
Query: 244 NVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQGHMIGQQQVRISW 303
++T L+ F FG I+++ + R C FV + SA++A+ + G + Q++++
Sbjct: 48 DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI 107
Query: 304 GRKQ 307
RKQ
Sbjct: 108 ARKQ 111
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAIL 287
T++ V NL + + L++ F +G + +V IP RG FV+F + AE+A+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 288 RMQGHMIGQQQVRISWGR 305
M G ++ +++R+ R
Sbjct: 108 AMDGAVLDGRELRVQMAR 125
Score = 37.0 bits (84), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 45/105 (42%), Gaps = 4/105 (3%)
Query: 90 MPGTEQNFRLNWASFGIGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKV 149
M G +Q + S G PD S+ V +L + L+ F +Y V +
Sbjct: 24 MTGGQQ---MGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVF-EKYGRVGDVYI 79
Query: 150 VTDPNTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRPMRISAA 194
D T S+G+ FV+F D+ + AM M+G R +R+ A
Sbjct: 80 PRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
>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 = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+F+G L+ D T L++ F S++ V + DP TGRS+G+GFV F + ++ M +
Sbjct: 2 MFIGGLSWDTTKKDLKDYF-SKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60
Score = 35.8 bits (81), Expect = 0.043, Method: Composition-based stats.
Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 6/67 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAILRM 289
+F+G L + T+++LK F FGE+V+ + + RG GFV F S ++ + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 290 QGHMIGQ 296
+ + G+
Sbjct: 62 EHKLNGK 68
Score = 35.0 bits (79), Expect = 0.071, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVL 82
++IG L + + L F+ GEVV + + ITG+ G+GFV F + ++V+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM 58
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNA 67
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ QG + RI + +
Sbjct: 68 LRSXQGFPFYDKPXRIQYAK 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 = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNA 68
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ QG + RI + +
Sbjct: 69 LRSXQGFPFYDKPXRIQYAK 88
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 233 NTTIFVGNLDPNVTEEELKQT----FLHFGEIVNVKIPMG---RGCGFVQFAARASAEEA 285
N TI++ NL+ + ++ELK++ F FG+I+++ + RG FV F +SA A
Sbjct: 6 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNA 65
Query: 286 ILRMQGHMIGQQQVRISWGR 305
+ QG + RI + +
Sbjct: 66 LRSXQGFPFYDKPXRIQYAK 85
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 21/51 (41%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG-RGCGFVQFAARASAE 283
+ +FVG ++T EEL+Q F +GE+V+V IP R FV FA A+
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQ 62
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 114 GPEH-SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENER 172
GPE ++F+ L + TD L TF + +V AKV D T SK +GFV F + +
Sbjct: 37 GPEGCNLFIYHLPQEFTDTDLASTFLP-FGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 173 NRAMTEMNGVFCSTRPMRI 191
A+ MNG T+ +++
Sbjct: 96 QVAIKAMNGFQVGTKRLKV 114
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEAILRM 289
+F+ +L T+ +L TFL FG +++ K+ + + GFV F SA+ AI M
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 290 QGHMIGQQQVRI 301
G +G +++++
Sbjct: 103 NGFQVGTKRLKV 114
Score = 33.1 bits (74), Expect = 0.29, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 33/62 (53%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L+I L F + L+S F G V+S K+ +K T + +GFV F + +A+ ++
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 86 NG 87
NG
Sbjct: 103 NG 104
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 38/74 (51%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQGHM 293
TT ++GN+ TE +L F +FG I++ K +GC F+++ A I+ +
Sbjct: 28 TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFP 87
Query: 294 IGQQQVRISWGRKQ 307
+ +R WG+++
Sbjct: 88 FQGRNLRTGWGKER 101
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 228 DNDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAIL 287
+ +++NT +FV +V E EL + F FG + VKI G FV+F SA +AI
Sbjct: 26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKAIE 83
Query: 288 RMQGHMIGQQQVRISWGR 305
+ G Q + + + +
Sbjct: 84 EVHGKSFANQPLEVVYSK 101
>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 = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 6/83 (7%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEAILRM 289
+F+ +L +++L Q F+ FG +V+ K+ + + GFV + SA+ AI M
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 290 QGHMIGQQQVRISWGRKQDVTGS 312
G IG +++++ R ++ + S
Sbjct: 88 NGFQIGMKRLKVQLKRSKNDSKS 110
Score = 32.3 bits (72), Expect = 0.47, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 33/66 (50%)
Query: 22 EVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERV 81
E L+I L F + L F G VVS K+ +K T + +GFV + + +A+
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 82 LQTYNG 87
+Q+ NG
Sbjct: 84 IQSMNG 89
Score = 32.0 bits (71), Expect = 0.70, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 2/88 (2%)
Query: 114 GPEHS-IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENER 172
GPE + +F+ L + D L + F + +V AKV D T SK +GFV + +
Sbjct: 22 GPEGANLFIYHLPQEFGDQDLLQMFMP-FGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 80
Query: 173 NRAMTEMNGVFCSTRPMRISAATPKKTT 200
A+ MNG + +++ K +
Sbjct: 81 QAAIQSMNGFQIGMKRLKVQLKRSKNDS 108
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 40/187 (21%), Positives = 76/187 (40%), Gaps = 32/187 (17%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
++F+G+L P+ + L+ + + V D TG ++ +G+V F + +A+
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFA--KNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL- 71
Query: 178 EMNGVFCSTRPMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIF 237
+ TG + +K P + V+ T+
Sbjct: 72 --------------------ELTGLKVFGNEIKLEKPKGRDSKKVR--------AARTLL 103
Query: 238 VGNLDPNVTEEELKQTFLHFGEIVNV-KIPMGRGCGFVQFAARASAEEAILRMQGHMIGQ 296
NL N+TE+ELK+ F EI V + +G +++F + A AE+ + QG I
Sbjct: 104 AKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG 163
Query: 297 QQVRISW 303
+ V + +
Sbjct: 164 RSVSLYY 170
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
RTL +L + E+ L F + + I+++ G+ +G ++EF S A AE+ L+
Sbjct: 100 RTLLAKNLSFNITEDELKEVFE---DALEIRLVSQ--DGKSKGIAYIEFKSEADAEKNLE 154
Query: 84 TYNGTPMPG 92
G + G
Sbjct: 155 EKQGAEIDG 163
Score = 32.0 bits (71), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 6/87 (6%)
Query: 235 TIFVGNLDPNVTEEELKQTFLH-FGE----IVNVKIPMGRGCGFVQFAARASAEEAILRM 289
+F+GNL+PN + ELK F + +V+V+ R G+V F + E+A L +
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA-LEL 73
Query: 290 QGHMIGQQQVRISWGRKQDVTGSVAAQ 316
G + ++++ + +D AA+
Sbjct: 74 TGLKVFGNEIKLEKPKGRDSKKVRAAR 100
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 32/92 (34%), Positives = 44/92 (47%), Gaps = 14/92 (15%)
Query: 225 FPADNDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR-----GCGFVQFAAR 279
FPA + + T+FVGNL+ V EE L + FL G + V I R GFV F
Sbjct: 9 FPAQEE-ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHP 67
Query: 280 ASAEEAILRMQGHMIGQQQVRISWGRKQDVTG 311
S AI + G +R+ +GR +V+G
Sbjct: 68 ESVSYAIALLNG-------IRL-YGRPINVSG 91
Score = 36.6 bits (83), Expect = 0.026, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 116 EHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRA 175
+ ++FVG+L V + +L E F P + + G+ K +GFV F + A
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTK--VTICKDREGKPKSFGFVCFKHPESVSYA 73
Query: 176 MTEMNGVFCSTRPMRISAAT 195
+ +NG+ RP+ +S +
Sbjct: 74 IALLNGIRLYGRPINVSGPS 93
Score = 34.7 bits (78), Expect = 0.092, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 1/76 (1%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
E RT+++G+L+ E L F G + + I +++ G+P+ +GFV F +
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSY 72
Query: 81 VLQTYNGTPMPGTEQN 96
+ NG + G N
Sbjct: 73 AIALLNGIRLYGRPIN 88
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 11/81 (13%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIP---------MGRGCGFVQFAARASAE 283
++ +F+ NL+ + TEE LK F G I + I + G GFV++ A+
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 284 EAILRMQGHMIG--QQQVRIS 302
+A+ ++QGH + + +VRIS
Sbjct: 65 KALKQLQGHTVDGHKLEVRIS 85
Score = 31.2 bits (69), Expect = 1.0, Method: Composition-based stats.
Identities = 23/93 (24%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQ---PEGYGFVEFVSHAAAERVL 82
L+I +L + E L F+ G + S I + K G+GFVE+ A++ L
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 83 QTYNGTPMPGTEQNFRLNWASFGIGEKRPDAGP 115
+ G + G + R++ + +P +GP
Sbjct: 68 KQLQGHTVDGHKLEVRISERA-----TKPASGP 95
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEA 285
T ++VG L V ++ L F+ FG+I +++IP+ RG FV+F A A
Sbjct: 62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121
Query: 286 ILRMQGHMIGQQQVRIS 302
I M + + +R++
Sbjct: 122 IDNMNESELFGRTIRVN 138
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
R L++G L D+ L + F G++ I+I + T + G+ FVEF A +
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 84 TYNGTPMPGTEQNFRLNWA 102
N + + G + R+N A
Sbjct: 124 NMNESELFG--RTIRVNLA 140
Score = 32.0 bits (71), Expect = 0.65, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 113 AGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENER 172
A + ++VG LA +V D +L F + + ++ D T + +G+ FV+F +
Sbjct: 60 ATTKRVLYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 118
Query: 173 NRAMTEMNGVFCSTRPMRISAA 194
A+ MN R +R++ A
Sbjct: 119 AAAIDNMNESELFGRTIRVNLA 140
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 30/92 (32%), Positives = 43/92 (46%), Gaps = 5/92 (5%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
RTL++G+L E + F+ G S K+I + P Y FVEF H A L
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALA 73
Query: 84 TYNGTPMPGTEQNFRLNWASFGIGEKR-PDAG 114
NG + G E ++NWA+ +K P +G
Sbjct: 74 AMNGRKILGKE--VKVNWATTPSSQKSGPSSG 103
Score = 37.0 bits (84), Expect = 0.023, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 47/84 (55%), Gaps = 3/84 (3%)
Query: 112 DAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENE 171
D G +++VG+L+ DVT+ L+ + F SQ + K++T+ + + Y FV+F + +
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLF-SQIGPCKSCKMITEHTS--NDPYCFVEFYEHRD 67
Query: 172 RNRAMTEMNGVFCSTRPMRISAAT 195
A+ MNG + ++++ AT
Sbjct: 68 AAAALAAMNGRKILGKEVKVNWAT 91
Score = 30.8 bits (68), Expect = 1.7, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 4/81 (4%)
Query: 228 DNDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCG----FVQFAARASAE 283
++D T++VGNL +VTE + Q F G + K+ FV+F A
Sbjct: 10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAA 69
Query: 284 EAILRMQGHMIGQQQVRISWG 304
A+ M G I ++V+++W
Sbjct: 70 AALAAMNGRKILGKEVKVNWA 90
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 230 DITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRM 289
+++NT +FV +V E EL + F FG + VKI G FV+F SA +AI +
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKAIEEV 58
Query: 290 QGHMIGQQQVRISWGR 305
G Q + + + +
Sbjct: 59 HGKSFANQPLEVVYSK 74
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG-----RGCGFVQFAARASAEEAI 286
++ +FVG L+ +E+++++ F FG I I G +GC FV++++ A A+ AI
Sbjct: 14 SHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAI 73
Query: 287 LRMQG 291
+ G
Sbjct: 74 NALHG 78
Score = 33.9 bits (76), Expect = 0.19, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
R L++G L E+ + F G + I+R G +G FV++ SHA A+ +
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYSSHAEAQAAIN 74
Query: 84 TYNGT-PMPGTEQNFRLNWA 102
+G+ MPG + + +A
Sbjct: 75 ALHGSQTMPGASSSLVVKFA 94
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEA 285
T ++VG L V ++ L F+ FG+I +++IP+ RG FV+F A A
Sbjct: 4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63
Query: 286 ILRMQGHMIGQQQVRISWGR 305
I M + + +R++ +
Sbjct: 64 IDNMNESELFGRTIRVNLAK 83
Score = 33.5 bits (75), Expect = 0.26, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
R L++G L D+ L + F G++ I+I + T + G+ FVEF A +
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 84 TYNGTPMPGTEQNFRLNWA 102
N + + G + R+N A
Sbjct: 66 NMNESELFG--RTIRVNLA 82
Score = 31.6 bits (70), Expect = 0.97, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
++VG LA +V D +L F + + ++ D T + +G+ FV+F + A+
Sbjct: 8 LYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 179 MNGVFCSTRPMRISAA 194
MN R +R++ A
Sbjct: 67 MNESELFGRTIRVNLA 82
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEA 285
T ++VG L V ++ L F+ FG+I +++IP+ RG FV+F A A
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65
Query: 286 ILRMQGHMIGQQQVRISWGR 305
I M + + +R++ +
Sbjct: 66 IDNMNESELFGRTIRVNLAK 85
Score = 33.1 bits (74), Expect = 0.26, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
R L++G L D+ L + F G++ I+I + T + G+ FVEF A +
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 84 TYNGTPMPGTEQNFRLNWA 102
N + + G + R+N A
Sbjct: 68 NMNESELFG--RTIRVNLA 84
Score = 31.6 bits (70), Expect = 0.98, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 113 AGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENER 172
A + ++VG LA +V D +L F + + ++ D T + +G+ FV+F +
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62
Query: 173 NRAMTEMNGVFCSTRPMRISAA 194
A+ MN R +R++ A
Sbjct: 63 AAAIDNMNESELFGRTIRVNLA 84
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
+I V +L+ D + LQE FR + S+ + D TG+SKG+ F+ F + RA+
Sbjct: 17 TIRVTNLSEDTRETDLQELFRP-FGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75
Query: 178 EMNGVFCSTRPMRISAATPKKTTG 201
++G + + A P +G
Sbjct: 76 GVSGFGYDHLILNVEWAKPSTNSG 99
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 35/85 (41%), Gaps = 6/85 (7%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIP------MGRGCGFVQFAARASAEEAI 286
N TI V NL + E +L++ F FG I + + +G F+ F R A AI
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
Query: 287 LRMQGHMIGQQQVRISWGRKQDVTG 311
+ G + + W + +G
Sbjct: 75 AGVSGFGYDHLILNVEWAKPSTNSG 99
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 6/87 (6%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEA 285
T ++VG L V ++ L F+ FG+I +++IP+ RG FV+F A A
Sbjct: 11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 70
Query: 286 ILRMQGHMIGQQQVRISWGRKQDVTGS 312
I M + + +R++ + + S
Sbjct: 71 IDNMNESELFGRTIRVNLAKPMRIKES 97
Score = 34.7 bits (78), Expect = 0.096, Method: Composition-based stats.
Identities = 26/92 (28%), Positives = 42/92 (45%), Gaps = 3/92 (3%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
R L++G L D+ L + F G++ I+I + T + G+ FVEF A +
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 84 TYNGTPMPGTEQNFRLNWAS-FGIGEKRPDAG 114
N + + G + R+N A I E P +G
Sbjct: 73 NMNESELFG--RTIRVNLAKPMRIKESGPSSG 102
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 1/86 (1%)
Query: 113 AGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENER 172
A + ++VG LA +V D +L F + + ++ D T + +G+ FV+F +
Sbjct: 9 ATTKRVLYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67
Query: 173 NRAMTEMNGVFCSTRPMRISAATPKK 198
A+ MN R +R++ A P +
Sbjct: 68 AAAIDNMNESELFGRTIRVNLAKPMR 93
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 38.5 bits (88), Expect = 0.008, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 1/94 (1%)
Query: 102 ASFGIGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGY 161
S G R + P + V L+ T+ L+E F S+Y + +V D + RS+G+
Sbjct: 1 GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVF-SKYGPIADVSIVYDQQSRRSRGF 59
Query: 162 GFVKFLDENERNRAMTEMNGVFCSTRPMRISAAT 195
FV F + ++ A NG+ R +R+S +
Sbjct: 60 AFVYFENVDDAKEAKERANGMELDGRRIRVSGPS 93
Score = 32.7 bits (73), Expect = 0.35, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 6/76 (7%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAI 286
N + V L TE +L++ F +G I +V I RG FV F A+EA
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 287 LRMQGHMIGQQQVRIS 302
R G + +++R+S
Sbjct: 75 ERANGMELDGRRIRVS 90
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 26/97 (26%), Positives = 45/97 (46%), Gaps = 1/97 (1%)
Query: 102 ASFGIGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGY 161
S G R + P + V L+ T+ L+E F S+Y + +V D + RS+G+
Sbjct: 1 GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVF-SKYGPIADVSIVYDQQSRRSRGF 59
Query: 162 GFVKFLDENERNRAMTEMNGVFCSTRPMRISAATPKK 198
FV F + ++ A NG+ R +R+ + K+
Sbjct: 60 AFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 96
Score = 31.6 bits (70), Expect = 0.81, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 6/77 (7%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAI 286
N + V L TE +L++ F +G I +V I RG FV F A+EA
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 287 LRMQGHMIGQQQVRISW 303
R G + +++R+ +
Sbjct: 75 ERANGMELDGRRIRVDF 91
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 9/80 (11%)
Query: 236 IFVGNLDPNVTEEEL-KQTFLHFGEIVNVKIPMGRG-------CGFVQFAARASAEEAIL 287
I + NL + +E L +++F FG I + IP G+ C F F + SAE A L
Sbjct: 213 IXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAERA-L 271
Query: 288 RMQGHMIGQQQVRISWGRKQ 307
+ ++G +++ +S K+
Sbjct: 272 QXNRSLLGNREISVSLADKK 291
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGF----VQFAARASAEEAILRM 289
TT+ V NL + + ++ + F H G I++V + F ++FA A AI +
Sbjct: 42 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 101
Query: 290 QGHMIGQQQVRIS 302
++GQ ++ +S
Sbjct: 102 H-KVVGQNEIIVS 113
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 7/73 (9%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR-------GCGFVQFAARASAEEAI 286
T + +G L NVT++ + + F +G+I + +P+ R G +V+F AE+A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 287 LRMQGHMIGQQQV 299
M G I Q++
Sbjct: 65 KHMDGGQIDGQEI 77
Score = 28.5 bits (62), Expect = 7.3, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKV-VTDPNTGRSKGYGFVKFLDENERNRAMT 177
+ +G L +VT + E F S Y ++ + V + SKGY +V+F + +E +A+
Sbjct: 7 VHIGRLTRNVTKDHIMEIF-STYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 178 EMNG 181
M+G
Sbjct: 66 HMDG 69
>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 = 37.7 bits (86), Expect = 0.013, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEA 285
+ ++VG L V ++ L F+ FG+I +++IP+ RG FV+F A A
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 286 ILRMQGHMIGQQQVRIS 302
I M + + +R++
Sbjct: 61 IDNMNESELFGRTIRVN 77
Score = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
R L++G L D+ L + F G++ I+I + T + G+ FVEF A +
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 84 TYNGTPMPGTEQNFRLNWA 102
N + + G + R+N A
Sbjct: 63 NMNESELFG--RTIRVNLA 79
Score = 31.6 bits (70), Expect = 0.79, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
++VG LA +V D +L F + + ++ D T + +G+ FV+F + A+
Sbjct: 5 LYVGGLAEEVDDKVLHAAF-IPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 179 MNGVFCSTRPMRISAA 194
MN R +R++ A
Sbjct: 64 MNESELFGRTIRVNLA 79
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 37.7 bits (86), Expect = 0.014, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 30/51 (58%)
Query: 22 EVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEF 72
+ R++++G++ Y L + F G V + I+ +K +G P+G+ ++EF
Sbjct: 4 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 54
Score = 28.5 bits (62), Expect = 7.2, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 235 TIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEAILR 288
+I+VGN+D T EEL+ F G + V I +G +++F+ + S ++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 66
Query: 289 MQGHMIGQQ 297
+ G+Q
Sbjct: 67 DESLFRGRQ 75
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG-------RGCGFVQFAARASAEE 284
T + I V N+ + E+++ F FGE+ V++P RG GFV F + A++
Sbjct: 14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 73
Query: 285 AI--LRMQGHMIGQQQVRISW 303
A L H+ G++ V + W
Sbjct: 74 AFNALCHSTHLYGRRLV-LEW 93
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
Hypothetical Polyadenylate-Binding Protein (Pabpn1)
From Homo Sapiens At 1.95 A Resolution
Length = 89
Score = 37.4 bits (85), Expect = 0.015, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 30/51 (58%)
Query: 22 EVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEF 72
+ R++++G++ Y L + F G V + I+ +K +G P+G+ ++EF
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEF 55
Score = 28.5 bits (62), Expect = 7.8, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 235 TIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEAILR 288
+I+VGN+D T EEL+ F G + V I +G +++F+ + S ++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 67
Query: 289 MQGHMIGQQ 297
+ G+Q
Sbjct: 68 DESLFRGRQ 76
>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 = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+ V +L P +T +E R + S+ +V TG+SKGYGF +++ ++ RA ++
Sbjct: 96 LCVANLPPSLTQQQFEELVRP-FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 154
Query: 179 MNG 181
+ G
Sbjct: 155 LLG 157
Score = 32.7 bits (73), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNV------KIPMGRGCGFVQFAARASAEEA 285
T+ + V NL P++T+++ ++ FG + + +G GF ++ + SA A
Sbjct: 92 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 151
Query: 286 ILRMQGHMIGQQQVRISW 303
+ G +G + + + W
Sbjct: 152 KSDLLGKPLGPRTLYVHW 169
Score = 32.3 bits (72), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 31/151 (20%), Positives = 58/151 (38%), Gaps = 9/151 (5%)
Query: 48 GEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQNFRLNWASFGIG 107
G + ++ ++ TGQ +GYGF E++ +A R G P+ + ++W G
Sbjct: 118 GSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL--GPRTLYVHWTD--AG 173
Query: 108 EKRPDAGPEHSIFVGDLAPDVTDY--LLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVK 165
+ P + V L P D L + P+ D G+ KG+ ++
Sbjct: 174 QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQD---GQLKGFAVLE 230
Query: 166 FLDENERNRAMTEMNGVFCSTRPMRISAATP 196
+ A + +G+ +R+S P
Sbjct: 231 YETAEMAEEAQQQADGLSLGGSHLRVSFCAP 261
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+ V +L P +T +E R + S+ +V TG+SKGYGF +++ ++ RA ++
Sbjct: 98 LCVANLPPSLTQQQFEELVRP-FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 179 MNG 181
+ G
Sbjct: 157 LLG 159
Score = 32.7 bits (73), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNV------KIPMGRGCGFVQFAARASAEEA 285
T+ + V NL P++T+++ ++ FG + + +G GF ++ + SA A
Sbjct: 94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Query: 286 ILRMQGHMIGQQQVRISW 303
+ G +G + + + W
Sbjct: 154 KSDLLGKPLGPRTLYVHW 171
Score = 32.3 bits (72), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 31/151 (20%), Positives = 58/151 (38%), Gaps = 9/151 (5%)
Query: 48 GEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQNFRLNWASFGIG 107
G + ++ ++ TGQ +GYGF E++ +A R G P+ + ++W G
Sbjct: 120 GSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL--GPRTLYVHWTD--AG 175
Query: 108 EKRPDAGPEHSIFVGDLAPDVTDY--LLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVK 165
+ P + V L P D L + P+ D G+ KG+ ++
Sbjct: 176 QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQD---GQLKGFAVLE 232
Query: 166 FLDENERNRAMTEMNGVFCSTRPMRISAATP 196
+ A + +G+ +R+S P
Sbjct: 233 YETAEMAEEAQQQADGLSLGGSHLRVSFCAP 263
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+ V +L P +T +E R + S+ +V TG+SKGYGF +++ ++ RA ++
Sbjct: 98 LCVANLPPSLTQQQFEELVRP-FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 179 MNG 181
+ G
Sbjct: 157 LLG 159
Score = 32.7 bits (73), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNV------KIPMGRGCGFVQFAARASAEEA 285
T+ + V NL P++T+++ ++ FG + + +G GF ++ + SA A
Sbjct: 94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Query: 286 ILRMQGHMIGQQQVRISW 303
+ G +G + + + W
Sbjct: 154 KSDLLGKPLGPRTLYVHW 171
Score = 32.0 bits (71), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 31/151 (20%), Positives = 58/151 (38%), Gaps = 9/151 (5%)
Query: 48 GEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQNFRLNWASFGIG 107
G + ++ ++ TGQ +GYGF E++ +A R G P+ + ++W G
Sbjct: 120 GSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL--GPRTLYVHWTD--AG 175
Query: 108 EKRPDAGPEHSIFVGDLAPDVTDY--LLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVK 165
+ P + V L P D L + P+ D G+ KG+ ++
Sbjct: 176 QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQD---GQLKGFAVLE 232
Query: 166 FLDENERNRAMTEMNGVFCSTRPMRISAATP 196
+ A + +G+ +R+S P
Sbjct: 233 YETAEMAEEAQQQADGLSLGGSHLRVSFCAP 263
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 37.4 bits (85), Expect = 0.017, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 1/89 (1%)
Query: 110 RPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDE 169
R + P + V L+ T+ L+E F S+Y + +V D + RS+G+ FV F +
Sbjct: 6 RANPDPNCCLGVFGLSLYTTERDLREVF-SKYGPIADVSIVYDQQSRRSRGFAFVYFENV 64
Query: 170 NERNRAMTEMNGVFCSTRPMRISAATPKK 198
++ A NG+ R +R+ + K+
Sbjct: 65 DDAKEAKERANGMELDGRRIRVDFSITKR 93
Score = 31.6 bits (70), Expect = 0.78, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 17/82 (20%)
Query: 239 GNLDPN-----------VTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARAS 281
N DPN TE +L++ F +G I +V I RG FV F
Sbjct: 7 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 66
Query: 282 AEEAILRMQGHMIGQQQVRISW 303
A+EA R G + +++R+ +
Sbjct: 67 AKEAKERANGMELDGRRIRVDF 88
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 37.4 bits (85), Expect = 0.017, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 1/89 (1%)
Query: 110 RPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDE 169
R + P + V L+ T+ L+E F S+Y + +V D + RS+G+ FV F +
Sbjct: 40 RANPDPNCCLGVFGLSLYTTERDLREVF-SKYGPIADVSIVYDQQSRRSRGFAFVYFENV 98
Query: 170 NERNRAMTEMNGVFCSTRPMRISAATPKK 198
++ A NG+ R +R+ + K+
Sbjct: 99 DDAKEAKERANGMELDGRRIRVDFSITKR 127
Score = 31.6 bits (70), Expect = 0.78, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 17/82 (20%)
Query: 239 GNLDPN-----------VTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARAS 281
N DPN TE +L++ F +G I +V I RG FV F
Sbjct: 41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 100
Query: 282 AEEAILRMQGHMIGQQQVRISW 303
A+EA R G + +++R+ +
Sbjct: 101 AKEAKERANGMELDGRRIRVDF 122
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 37.0 bits (84), Expect = 0.019, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAI 286
+F+GNL TE+E++ F +G+++ I + GFV + +AE+AI
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAI 59
Score = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 8/71 (11%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L+IG+L E + S F G+V+ II+N YGFV AAE ++
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRNL 62
Query: 86 NGTPMPGTEQN 96
+ + G N
Sbjct: 63 HHYKLHGVNIN 73
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 37.0 bits (84), Expect = 0.022, Method: Composition-based stats.
Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 2/80 (2%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQGHM 293
T ++VG L PN + L + F FG I + G ++Q+ + +A+ A +M+G
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFP 77
Query: 294 IG--QQQVRISWGRKQDVTG 311
+G +++R+ + + +G
Sbjct: 78 LGGPDRRLRVDFAKSGPSSG 97
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 37.0 bits (84), Expect = 0.022, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 44/85 (51%), Gaps = 8/85 (9%)
Query: 235 TIFVGNLDPNVTEEELKQTFLHFGEIVNVKIP------MGRGCGFVQFAARASAEEAILR 288
T+ V NL + + L++ F +G + +V IP RG FV+F R A++A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 289 MQGHMIGQQQVRISWGR--KQDVTG 311
M G + +++R+ R ++D++G
Sbjct: 75 MDGAELDGRELRVQVARYGRRDLSG 99
Score = 33.1 bits (74), Expect = 0.31, Method: Composition-based stats.
Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 1/88 (1%)
Query: 107 GEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKF 166
G PD ++ V +L + L+ F +Y V + +P+T +G+ FV+F
Sbjct: 4 GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFE-KYGRVGDVYIPREPHTKAPRGFAFVRF 62
Query: 167 LDENERNRAMTEMNGVFCSTRPMRISAA 194
D + A M+G R +R+ A
Sbjct: 63 HDRRDAQDAEAAMDGAELDGRELRVQVA 90
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 36.6 bits (83), Expect = 0.025, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG-----RGCGFVQFAARASAEEAILRMQ 290
+FVG L+ +EE++ + F FG I + G +GC FV+F++ A+ AI +
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 291 G 291
G
Sbjct: 78 G 78
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 2/80 (2%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
R L++G L E + F G + ++R G +G FV+F SH A+ +
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIH 74
Query: 84 TYNGT-PMPGTEQNFRLNWA 102
+G+ MPG + + +A
Sbjct: 75 ALHGSQTMPGASSSLVVKFA 94
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 36.6 bits (83), Expect = 0.025, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEA 285
+F+G + N+ E++LK F FG+I + + M +GC F+ + R SA +A
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Score = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 13/53 (24%), Positives = 27/53 (50%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAA 78
L+IG + DE L F G++ + +++++ TG +G F+ + +A
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 36.6 bits (83), Expect = 0.025, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+ V +L V+D +QE F +++ +++ A V D +GRS G V F + + +AM +
Sbjct: 31 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 88
Query: 179 MNGVFCSTRPMRISAAT 195
NGV RPM I T
Sbjct: 89 YNGVPLDGRPMNIQLVT 105
Score = 30.0 bits (66), Expect = 2.5, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L + +L + + + FA G + + ++ +G+ G V F A A + ++ Y
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 89
Query: 86 NGTPMPGTEQNFRL 99
NG P+ G N +L
Sbjct: 90 NGVPLDGRPMNIQL 103
>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 = 0.026, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGF------VQFAARASAEEAILRM 289
+FV + TEE++ F +GEI N+ + + R G+ V++ A+ A+ +
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 290 QGHMIGQQQVRISW 303
G + Q + + W
Sbjct: 86 NGQDLMGQPISVDW 99
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 37 ENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQN 96
E + FA GE+ +I + ++ TG +GY VE+ ++ A+ ++ NG + G Q
Sbjct: 37 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QP 94
Query: 97 FRLNWA 102
++W
Sbjct: 95 ISVDWC 100
Score = 31.6 bits (70), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 114 GPEHSI-----FVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLD 168
GP+ S+ FV + + T+ + + F ++Y ++ + D TG KGY V++
Sbjct: 16 GPQRSVEGWILFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYET 74
Query: 169 ENERNRAMTEMNGVFCSTRPMRIS 192
E AM +NG +P+ +
Sbjct: 75 YKEAQAAMEGLNGQDLMGQPISVD 98
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 36.6 bits (83), Expect = 0.026, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQGHMIG 295
+FV NL VTEE L++ F FG++ VK + F+ F R A +A+ M G +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVK--KLKDYAFIHFDERDGAVKAMEEMNGKDLE 71
Query: 296 QQQVRISWGRKQD 308
+ + I + + D
Sbjct: 72 GENIEIVFAKPPD 84
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 13/94 (13%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+FV +LA VT+ +L++ F SQ+ + K + D Y F+ F + + +AM E
Sbjct: 14 LFVRNLANTVTEEILEKAF-SQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEE 64
Query: 179 MNGVFCSTRPMRISAATP----KKTTGFQQQYAA 208
MNG + I A P +K Q+Q A+
Sbjct: 65 MNGKDLEGENIEIVFAKPPDQKRKERKAQRQAAS 98
>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 = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L++ + E+ + F GE+ +I + ++ TG +GY VE+ +H A +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 86 NGTPMPGTEQNFRLNWASFGIGEKR 110
NG + G Q +++W F G KR
Sbjct: 135 NGAEIMG--QTIQVDWC-FVKGPKR 156
Score = 36.6 bits (83), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGF------VQFAARASAEEAILRM 289
+FV ++ E+E+++ F +GEI N+ + + R GF V++ A A +
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 290 QGHMIGQQQVRISW 303
G I Q +++ W
Sbjct: 135 NGAEIMGQTIQVDW 148
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 114 GPEHSI-----FVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLD 168
GP+ S+ FV + + + +QE F Y ++ + D TG SKGY V++
Sbjct: 65 GPQRSVEGWILFVTSIHEEAQEDEIQEKF-CDYGEIKNIHLNLDRRTGFSKGYALVEYET 123
Query: 169 ENERNRAMTEMNG 181
+ A +NG
Sbjct: 124 HKQALAAKEALNG 136
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 36.6 bits (83), Expect = 0.029, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEAILRM 289
IFVG + N E EL++ F FG + V + RG GF+ F S ++A+ M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71
Query: 290 QGHMIGQQQVRISWGRKQDVTGS 312
H I ++V + +D S
Sbjct: 72 HFHDIMGKKVEVKRAEPRDSKSS 94
Score = 32.3 bits (72), Expect = 0.57, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 117 HSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAM 176
+ IFVG + + + L+E F+ ++ V ++ D R +G+GF+ F DE ++A+
Sbjct: 11 NKIFVGGIPHNCGETELREYFK-KFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|3U1L|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
pdb|3U1M|A Chain A, Structure Of The Mrna Splicing Complex Component Cwc2
Length = 240
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 9/62 (14%)
Query: 233 NTTIFVGNLD---------PNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAE 283
N T++VG +D P E ++ F G+I ++ + CGFV+F +A+AE
Sbjct: 134 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 193
Query: 284 EA 285
A
Sbjct: 194 FA 195
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 36.2 bits (82), Expect = 0.033, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 6/74 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGF------VQFAARASAEEAILRM 289
+FV ++ E+E+++ F +GEI N+ + + R GF V++ A A +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 290 QGHMIGQQQVRISW 303
G I Q +++ W
Sbjct: 89 NGAEIMGQTIQVDW 102
Score = 35.4 bits (80), Expect = 0.063, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L++ + E+ + F GE+ +I + ++ TG +GY VE+ +H A +
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 86 NGTPMPGTEQNFRLNWASFGIGEKR 110
NG + G Q +++W F G KR
Sbjct: 89 NGAEIMG--QTIQVDWC-FVKGPKR 110
Score = 30.4 bits (67), Expect = 1.9, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 112 DAGPEHSI-----FVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKF 166
+ GP+ S+ FV + + + +QE F Y ++ + D TG SKGY V++
Sbjct: 17 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKF-CDYGEIKNIHLNLDRRTGFSKGYALVEY 75
Query: 167 LDENERNRAMTEMNG 181
+ A +NG
Sbjct: 76 ETHKQALAAKEALNG 90
>pdb|3TP2|A Chain A, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
pdb|3TP2|B Chain B, Crystal Structure Of The Splicing Factor Cwc2 From Yeast
Length = 229
Score = 36.2 bits (82), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 9/62 (14%)
Query: 233 NTTIFVGNLD---------PNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAE 283
N T++VG +D P E ++ F G+I ++ + CGFV+F +A+AE
Sbjct: 136 NKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAE 195
Query: 284 EA 285
A
Sbjct: 196 FA 197
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 36.2 bits (82), Expect = 0.034, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG-----RGCGFVQFAARASAEEAI 286
+FVG L T+E++++ F FG I + G +GC FV+F A A+ AI
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI 70
Score = 28.5 bits (62), Expect = 6.7, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 114 GPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERN 173
G + +FVG L TD +++ F + ++ V+ P+ G SKG FVKF E
Sbjct: 10 GEDRKLFVGMLGKQQTDEDVRKMFEP-FGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQ 67
Query: 174 RAMTEMN 180
A+ ++
Sbjct: 68 AAINTLH 74
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 36.2 bits (82), Expect = 0.036, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM----GRGCGFVQFAARASAEEAILR 288
++ IFV NL + T + LK F G ++ I M +GCG V+F + AE A
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRM 64
Query: 289 MQGHMIGQQQVRISWGR 305
M G + +++ + R
Sbjct: 65 MNGMKLSGREIDVRIDR 81
Score = 32.3 bits (72), Expect = 0.54, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 2/80 (2%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
+++ +L + F L F G V+ I G+ +G G V+F S AER +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 65
Query: 86 NGTPMPGTEQNFRLNWASFG 105
NG + G E + R++ + G
Sbjct: 66 NGMKLSGREIDVRIDRNASG 85
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
IFV +L D T +L++ F ++ V A + + G+SKG G VKF RA
Sbjct: 8 IFVRNLPFDFTWKMLKDKF-NECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRM 64
Query: 179 MNGVFCSTRPMRI 191
MNG+ S R + +
Sbjct: 65 MNGMKLSGREIDV 77
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 36.2 bits (82), Expect = 0.038, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 3/81 (3%)
Query: 233 NTTIFVGNLDPNVTEE-ELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQG 291
N+ +F+GNL+ V ++ +++ F +G+IV + +G FVQ+ +A A+ G
Sbjct: 15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--HKGFAFVQYVNERNARAAVAGEDG 72
Query: 292 HMIGQQQVRISWGRKQDVTGS 312
MI Q + I+ + V S
Sbjct: 73 RMIAGQVLDINLAAEPKVNRS 93
>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 = 36.2 bits (82), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGF------VQFAARASAEEAILRM 289
+FV + TEE++ F +GEI N+ + + R G+ V++ A+ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 290 QGHMIGQQQVRISW 303
G + Q + + W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 37 ENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQN 96
E + FA GE+ +I + ++ TG +GY VE+ ++ A+ ++ NG + G Q
Sbjct: 21 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QP 78
Query: 97 FRLNWA 102
++W
Sbjct: 79 ISVDWC 84
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+FV + + T+ + + F ++Y ++ + D TG KGY V++ E AM
Sbjct: 10 LFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 179 MNGVFCSTRPMRIS 192
+NG +P+ +
Sbjct: 69 LNGQDLMGQPISVD 82
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 36.2 bits (82), Expect = 0.040, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQG 291
+FV NL VTEE L+++F FG++ VK + FV F R +A +A+ M G
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVK--KLKDYAFVHFEDRGAAVKAMDEMNG 71
Score = 34.7 bits (78), Expect = 0.100, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 9/63 (14%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+FV +LA VT+ +L+++F S++ + K + D Y FV F D +AM E
Sbjct: 18 LFVRNLATTVTEEILEKSF-SEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDE 68
Query: 179 MNG 181
MNG
Sbjct: 69 MNG 71
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 36.2 bits (82), Expect = 0.040, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM----GRGCGFVQFAARASAEEAILRMQG 291
IFV NL + T + LK F G ++ I M +GCG V+F + AE A M G
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 70
Query: 292 HMIGQQQVRISWGR 305
+ +++ + R
Sbjct: 71 MKLSGREIDVRIDR 84
Score = 32.3 bits (72), Expect = 0.54, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 37/80 (46%), Gaps = 2/80 (2%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
+++ +L + F L F G V+ I G+ +G G V+F S AER +
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 68
Query: 86 NGTPMPGTEQNFRLNWASFG 105
NG + G E + R++ + G
Sbjct: 69 NGMKLSGREIDVRIDRNASG 88
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
IFV +L D T +L++ F ++ V A + + G+SKG G VKF RA
Sbjct: 11 IFVRNLPFDFTWKMLKDKF-NECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRM 67
Query: 179 MNGVFCSTRPMRI 191
MNG+ S R + +
Sbjct: 68 MNGMKLSGREIDV 80
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 35.8 bits (81), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG-RGCGFVQFAARASAEEAILRMQG 291
+ ++VGNL N + EL++ F ++G + +V + G FV+F A +A+ + G
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDG 132
Query: 292 HMIGQQQVRI 301
+ +VR+
Sbjct: 133 RTLCGCRVRV 142
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
+++G+L ++ L F + G + S+ + RN P G+ FVEF A ++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 130
Query: 86 NGTPMPGTEQNFRLNWASFGIGEKR 110
+G + G L+ GEKR
Sbjct: 131 DGRTLCGCRVRVELS-----NGEKR 150
>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 = 35.8 bits (81), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGF------VQFAARASAEEAILRM 289
+FV + TEE++ F +GEI N+ + + R G+ V++ A+ A+ +
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 290 QGHMIGQQQVRISW 303
G + Q + + W
Sbjct: 72 NGQDLMGQPISVDW 85
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 37 ENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQN 96
E + FA GE+ +I + ++ TG +GY VE+ ++ A+ ++ NG + G Q
Sbjct: 23 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QP 80
Query: 97 FRLNWA 102
++W
Sbjct: 81 ISVDWC 86
Score = 32.3 bits (72), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 114 GPEHSI-----FVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLD 168
GP+ S+ FV + + T+ + + F ++Y ++ + D TG KGY V++
Sbjct: 2 GPQRSVEGWILFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 169 ENERNRAMTEMNGVFCSTRPMRIS 192
E AM +NG +P+ +
Sbjct: 61 YKEAQAAMEGLNGQDLMGQPISVD 84
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 35.8 bits (81), Expect = 0.043, Method: Composition-based stats.
Identities = 24/97 (24%), Positives = 46/97 (47%), Gaps = 3/97 (3%)
Query: 102 ASFGIGEKRPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGY 161
S G K P ++ +VG+L + + F+ S+R ++V D +T + KG+
Sbjct: 1 GSSGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDL--SIRSVRLVRDKDTDKFKGF 58
Query: 162 GFVKFLDENERNRAMTEMNGVFCSTRPMRISAATPKK 198
+V+F + + A+T +G R +R+ A +K
Sbjct: 59 CYVEFDEVDSLKEALT-YDGALLGDRSLRVDIAEGRK 94
Score = 28.5 bits (62), Expect = 7.1, Method: Composition-based stats.
Identities = 22/91 (24%), Positives = 50/91 (54%), Gaps = 7/91 (7%)
Query: 25 TLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQT 84
T ++G+L + + + + F + S++++R+K T + +G+ +VEF + + L T
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-T 74
Query: 85 YNGTPMPGTEQNFRLNWASFGIGEKRPDAGP 115
Y+G + +++ R++ A G K+ +GP
Sbjct: 75 YDGALL--GDRSLRVDIAE---GRKQDKSGP 100
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 35.8 bits (81), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGF------VQFAARASAEEAILRM 289
+FV + TEE++ F +GEI N+ + + R G+ V++ A+ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 290 QGHMIGQQQVRISW 303
G + Q + + W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 37 ENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQN 96
E + FA GE+ +I + ++ TG +GY VE+ ++ A+ ++ NG + G Q
Sbjct: 21 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QP 78
Query: 97 FRLNWA 102
++W
Sbjct: 79 ISVDWC 84
Score = 31.6 bits (70), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+FV + + T+ + + F ++Y ++ + D TG KGY V++ E AM
Sbjct: 10 LFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 179 MNGVFCSTRPMRIS 192
+NG +P+ +
Sbjct: 69 LNGQDLMGQPISVD 82
>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 = 35.8 bits (81), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGF------VQFAARASAEEAILRM 289
+FV + TEE++ F +GEI N+ + + R G+ V++ A+ A+ +
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 290 QGHMIGQQQVRISW 303
G + Q + + W
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 37 ENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQN 96
E + FA GE+ +I + ++ TG +GY VE+ ++ A+ ++ NG + G Q
Sbjct: 21 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QP 78
Query: 97 FRLNWA 102
++W
Sbjct: 79 ISVDWC 84
Score = 31.6 bits (70), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+FV + + T+ + + F ++Y ++ + D TG KGY V++ E AM
Sbjct: 10 LFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 179 MNGVFCSTRPMRIS 192
+NG +P+ +
Sbjct: 69 LNGQDLMGQPISVD 82
>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 = 35.8 bits (81), Expect = 0.052, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGF------VQFAARASAEEAILRM 289
+FV + TEE++ F +GEI N+ + + R G+ V++ A+ A+ +
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 290 QGHMIGQQQVRISW 303
G + Q + + W
Sbjct: 85 NGQDLMGQPISVDW 98
Score = 33.5 bits (75), Expect = 0.26, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 44 FAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNGTPMPGTEQNFRLNW 101
FA GE+ +I + ++ TG +GY VE+ ++ A+ ++ NG + G Q ++W
Sbjct: 43 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG--QPISVDW 98
Score = 31.6 bits (70), Expect = 0.81, Method: Composition-based stats.
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 6/85 (7%)
Query: 112 DAGPEHSI-----FVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKF 166
+ GP+ S+ FV + + T+ + + F ++Y ++ + D TG KGY V++
Sbjct: 13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKF-AEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
Query: 167 LDENERNRAMTEMNGVFCSTRPMRI 191
E AM +NG +P+ +
Sbjct: 72 ETYKEAQAAMEGLNGQDLMGQPISV 96
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 35.8 bits (81), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG-RGCGFVQFAARASAEEAILRMQG 291
+ ++VGNL N + EL++ F ++G + +V + G FV+F A +A+ + G
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDG 132
Query: 292 HMIGQQQVRI 301
+ +VR+
Sbjct: 133 RTLCGCRVRV 142
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
+++G+L ++ L F + G + S+ + RN P G+ FVEF A ++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRDL 130
Query: 86 NGTPMPGTEQNFRLNWASFGIGEKR 110
+G + G L+ GEKR
Sbjct: 131 DGRTLCGCRVRVELS-----NGEKR 150
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 35.8 bits (81), Expect = 0.053, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG-RGCGFVQFA 277
++ +FVG ++TE+EL++ F +G++++V IP R FV FA
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFA 50
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 35.4 bits (80), Expect = 0.054, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG-RGCGFVQFAARASAEEAILRMQGHMI 294
++VGNL + EL++ F ++G + V I G FV+F AE+A+ + G +I
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 295 GQQQVRI 301
+VR+
Sbjct: 63 CGSRVRV 69
Score = 29.3 bits (64), Expect = 3.8, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
+++G+L + L F++ G + ++ I RN P G+ FVEF AE ++
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 86 NGTPMPGTEQNFRLN 100
+G + G+ L+
Sbjct: 58 DGKVICGSRVRVELS 72
>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 = 35.4 bits (80), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 28/49 (57%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEF 72
+TL++ + Y E+ L F G + I ++ +K +G+P GY F+E+
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 35.4 bits (80), Expect = 0.058, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 36 DENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVL 82
D++ + C + G++VS K I +K T + +GYGFV+F S +AA++ +
Sbjct: 19 DQDLVKLCQPY-GKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Score = 32.0 bits (71), Expect = 0.74, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+++ L P TD L + + Y + K + D T + KGYGFV F + +A+T
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQP-YGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66
Query: 179 M 179
+
Sbjct: 67 L 67
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 17/76 (22%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEAI 286
++ +++ L P T+++L + +G+IV+ K + +G GFV F + ++A++A+
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 287 LRMQGHMIGQQQVRIS 302
++ + Q + S
Sbjct: 65 TALKASGVQAQMAKQS 80
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 35.4 bits (80), Expect = 0.060, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 44/85 (51%), Gaps = 4/85 (4%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM----GRGCGFVQFAARASAEEAIL 287
T + V N+ + +L+Q F FG+I++V+I +G GFV F A A+ A
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRARE 73
Query: 288 RMQGHMIGQQQVRISWGRKQDVTGS 312
++ G ++ +++ ++ + +T S
Sbjct: 74 KLHGTVVEGRKIEVNNATARVMTNS 98
Score = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
+ L + ++ + F + L F G+++ ++II N+ + G+GFV F + A A+R +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRARE 73
Query: 84 TYNGTPMPG 92
+GT + G
Sbjct: 74 KLHGTVVEG 82
Score = 32.0 bits (71), Expect = 0.71, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 154 NTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRPMRISAATPKKTT 200
N SKG+GFV F + + +RA +++G R + ++ AT + T
Sbjct: 50 NERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVMT 96
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 35.4 bits (80), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 235 TIFVGNLDPNVTEEELKQTFLHFGEIVNV-KIPMGRGCGFVQFAARASAEEAILRMQGHM 293
T+ NL VT++ELK+ F EI V K +G +++F A AE+ QG
Sbjct: 95 TLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTE 154
Query: 294 IGQQQVRISW 303
I + + + +
Sbjct: 155 IDGRSISLYY 164
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 22 EVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERV 81
+ RTL +L Y ++ L F E I+++ G+ +G ++EF + A AE+
Sbjct: 92 DARTLLAKNLPYKVTQDELKEVFEDAAE---IRLVSK--DGKSKGIAYIEFKTEADAEKT 146
Query: 82 LQTYNGTPMPG 92
+ GT + G
Sbjct: 147 FEEKQGTEIDG 157
Score = 32.7 bits (73), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 6/78 (7%)
Query: 236 IFVGNLDPNVTEEELKQTFLH-FGE----IVNVKIPMGRGCGFVQFAARASAEEAILRMQ 290
+FVGNL+ N + ELK F + +V+V+I M R G+V F + E+A L +
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKA-LELT 68
Query: 291 GHMIGQQQVRISWGRKQD 308
G + ++++ + +D
Sbjct: 69 GLKVFGNEIKLEKPKGKD 86
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 35.4 bits (80), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 28/49 (57%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEF 72
+TL++ + Y E+ L F G + I ++ +K +G+P GY F+E+
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEY 151
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 35.4 bits (80), Expect = 0.063, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 235 TIFVGNLDPNVTEEELKQTFLHFGEIVNV-KIPMGRGCGFVQFAARASAEEAILRMQGHM 293
T+ NL N+TE+ELK+ F EI V + +G +++F + A AE+ + QG
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 294 IGQQQVRISW-GRKQDVTG 311
I + V + + G K G
Sbjct: 78 IDGRSVSLYYTGEKGGTRG 96
Score = 30.4 bits (67), Expect = 2.0, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 5/69 (7%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
RTL +L + E+ L F + + I+++ G+ +G ++EF S A AE+ L+
Sbjct: 17 RTLLAKNLSFNITEDELKEVFE---DALEIRLVSQD--GKSKGIAYIEFKSEADAEKNLE 71
Query: 84 TYNGTPMPG 92
G + G
Sbjct: 72 EKQGAEIDG 80
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 35.4 bits (80), Expect = 0.065, Method: Composition-based stats.
Identities = 21/91 (23%), Positives = 44/91 (48%), Gaps = 2/91 (2%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQT- 84
L++G + DE L F G + + ++++++TG +G F+ + + +A +
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSAL 77
Query: 85 YNGTPMPGTEQNFRLN-WASFGIGEKRPDAG 114
+ +PG + ++ AS G GE P +G
Sbjct: 78 HEQKTLPGMNRPIQVKPAASEGRGESGPSSG 108
Score = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR------GCGFVQFAARASAEEA 285
+FVG + + E++LK F FG I + + R GC F+ + AR SA +A
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 35.0 bits (79), Expect = 0.075, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 7/65 (10%)
Query: 229 NDITN-TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARAS 281
+D+T T+F+ NL + EE L + FG++ V++ + +GC F QF + +
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69
Query: 282 AEEAI 286
A++ +
Sbjct: 70 AQKCL 74
Score = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 112 DAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENE 171
D ++F+ +L+ D + L E + Q+ ++ +VV P+T SKG F +F+ +
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQ-QFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69
Query: 172 RNRAM 176
+ +
Sbjct: 70 AQKCL 74
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 35.0 bits (79), Expect = 0.075, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPM----GRGCGFVQFAARASAEEAILRMQG 291
+ V N+ + +L+Q F FG+I++V+I +G GFV F A A+ A ++ G
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 91
Query: 292 HMIGQQQVRIS 302
++ +++ ++
Sbjct: 92 TVVEGRKIEVN 102
Score = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 24 RTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
+ L + ++ + F + L F G+++ ++II N+ + G+GFV F + A A+R +
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRARE 87
Query: 84 TYNGTPMPG 92
+GT + G
Sbjct: 88 KLHGTVVEG 96
Score = 31.6 bits (70), Expect = 0.93, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 154 NTGRSKGYGFVKFLDENERNRAMTEMNGVFCSTRPMRISAATPK 197
N SKG+GFV F + + +RA +++G R + ++ AT +
Sbjct: 64 NERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 35.0 bits (79), Expect = 0.084, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 34/48 (70%)
Query: 40 LSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNG 87
L+S F+ G+VV+++ ++ TG+ +G+ FVE S A++++++++G
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 35.0 bits (79), Expect = 0.084, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 34/48 (70%)
Query: 40 LSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNG 87
L+S F+ G+VV+++ ++ TG+ +G+ FVE S A++++++++G
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 2/75 (2%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTG--EVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
+++G +W + L G +VV +K N+ GQ +GY V S + ++L+
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 84 TYNGTPMPGTEQNFR 98
G + G + + R
Sbjct: 118 LLPGKVLNGEKVDVR 132
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAM 176
+F+G L+ + T+ L+ + Q+ + V+ DP + RS+G+GFV F E + AM
Sbjct: 30 LFIGGLSFETTEESLR-NYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 32/62 (51%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
E+ R L+IG L + E L + + G++ ++R+ + + G+GFV F S A +
Sbjct: 25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 84
Query: 81 VL 82
+
Sbjct: 85 AM 86
Score = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 6/57 (10%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKI------PMGRGCGFVQFAARASAEEAI 286
+F+G L TEE L+ + +G++ + + RG GFV F++ A + A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L+I +L DE L + G+V+S +I+R+ +G G GF S E V+ +
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86
Query: 86 NG 87
NG
Sbjct: 87 NG 88
Score = 31.6 bits (70), Expect = 0.90, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 5/66 (7%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKI-----PMGRGCGFVQFAARASAEEAILR 288
T +++ NL ++ E+EL+ FG++++ +I RG GF + + E I
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 85
Query: 289 MQGHMI 294
G I
Sbjct: 86 FNGKFI 91
>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 = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 17/84 (20%), Positives = 42/84 (50%), Gaps = 5/84 (5%)
Query: 224 VFPADNDITNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR-----GCGFVQFAA 278
VF + +F+ L + T+EEL++ G + ++++ R G +V++
Sbjct: 8 VFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYEN 67
Query: 279 RASAEEAILRMQGHMIGQQQVRIS 302
+ A +A+++M G I + ++++
Sbjct: 68 ESQASQAVMKMDGMTIKENIIKVA 91
Score = 28.5 bits (62), Expect = 8.3, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 43 CFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTYNG 87
C AH G V ++++ N+ G+P+G +VE+ + + A + + +G
Sbjct: 38 CKAH-GTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDG 80
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKI-----PMGRGCGFVQFAARASAEEAIL 287
+T+FV NLD V ++LK+ F G +V I RG G V F A +AI
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74
Query: 288 RMQGHMI 294
G ++
Sbjct: 75 MFNGQLL 81
Score = 32.3 bits (72), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
++FV +L V L+E F VR A ++ D + G+S+G G V F E +A++
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVR-ADILEDKD-GKSRGIGTVTFEQSIEAVQAIS 74
Query: 178 EMNGVFCSTRPMRI 191
NG RPM +
Sbjct: 75 MFNGQLLFDRPMHV 88
Score = 31.6 bits (70), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 1/94 (1%)
Query: 25 TLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQT 84
T+++ +L Y L F+ G VV I+ +K G+ G G V F A + +
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISM 75
Query: 85 YNGTPMPGTEQNFRLNWASFGIGEKRPDAGPEHS 118
+NG + + +++ + G+ P P+ S
Sbjct: 76 FNGQLLFDRPMHVKMDERALPKGDFFPPERPQQS 109
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDEN 170
IFVG L+ + T ++ F Q+ V A ++ D T R +G+GFV F E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFE-QFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
Score = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMG------RGCGFVQFAARASAEEAILRM 289
IFVG L N T E++K F FG++ + + RG GFV F + E+ + +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK-VCEI 60
Query: 290 QGHMIGQQQV 299
H I + V
Sbjct: 61 HFHEINNKMV 70
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 113 AGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENER 172
A + +++V +L +T+ L F S+Y V ++ D +T +SKG F+ FLD++
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIF-SKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 173 NRAMTEMNGVFCSTRPMRISAA 194
+N R ++ S A
Sbjct: 72 QNCTRAINNKQLFGRVIKASIA 93
>pdb|3DQQ|A Chain A, The Crystal Structure Of The Putative Trna Synthase From
Salmonella Typhimurium Lt2
pdb|3DQQ|B Chain B, The Crystal Structure Of The Putative Trna Synthase From
Salmonella Typhimurium Lt2
Length = 421
Score = 33.9 bits (76), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 1/79 (1%)
Query: 188 PMRISAATPKKTTGFQQQYAAVKATYPVAAYTTPVQVFPADNDITNTTIFVGNLDPNVTE 247
PM + A+ + QQQY A +A++ V A + + A+ IT I G V
Sbjct: 311 PMISATASTQALAAIQQQYGATEASHAVEALFSLLAARLAEGGITR-FIVAGGETSGVVT 369
Query: 248 EELKQTFLHFGEIVNVKIP 266
+ L T H G ++ +P
Sbjct: 370 QSLGITGFHIGPCISPGVP 388
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 234 TTIFVGNLD-PNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAI 286
+ +F+GNL NV++E+L + F +G I+ + I GF+QF S +AI
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAI 74
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 33.5 bits (75), Expect = 0.24, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 129 TDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE---MNGVFCS 185
T+ L+E F S + V +V D TG SKG+GFV+F + + + M++ ++G +C
Sbjct: 28 TEQDLKEYF-STFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCD 86
Query: 186 TR 187
+
Sbjct: 87 CK 88
Score = 32.0 bits (71), Expect = 0.60, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 26/46 (56%)
Query: 37 ENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVL 82
E L F+ GEV+ +++ ++ TG +G+GFV F + +V+
Sbjct: 29 EQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74
Score = 29.3 bits (64), Expect = 4.6, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 8/55 (14%)
Query: 246 TEEELKQTFLHFGEIVNVKIPM------GRGCGFVQFAARASAEEAILRMQGHMI 294
TE++LK+ F FGE++ V++ +G GFV+F + + + Q HMI
Sbjct: 28 TEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM--SQRHMI 80
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 33.5 bits (75), Expect = 0.25, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 234 TTIFVGNLD-PNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAI 286
+ +F+GNL NV++E+L + F +G I+ + I GF+QF S +AI
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAI 54
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 33.5 bits (75), Expect = 0.26, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEI-VNVKIPMGRGCGFVQFAARASAEEAILRMQGHMI 294
++VGNL + +LK+ G + + + R F+ + A+A++A+ +QG +
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRL 81
Query: 295 GQQQVRISWGRKQ 307
G +R++ R+Q
Sbjct: 82 GTDTLRVALARQQ 94
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 33.5 bits (75), Expect = 0.26, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 234 TTIFVGNLD-PNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAI 286
+ +F+GNL NV++E+L + F +G I+ + I GF+QF S +AI
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAI 74
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 33.1 bits (74), Expect = 0.27, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQGHMIG 295
IFVGN+ T +EL+ F G ++ + + FV A A+ AI ++ G +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVV--KDYAFVHMEKEADAKAAIAQLNGKEVK 69
Query: 296 QQQVRISWGRK 306
+++ + K
Sbjct: 70 GKRINVELSTK 80
>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 21
Length = 94
Score = 33.1 bits (74), Expect = 0.30, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 31/67 (46%)
Query: 235 TIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQGHMI 294
++FV V +L + FL FG + +V + +G + A EA+L H +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHSL 69
Query: 295 GQQQVRI 301
G ++R+
Sbjct: 70 GGHRLRV 76
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 33.1 bits (74), Expect = 0.31, Method: Composition-based stats.
Identities = 26/94 (27%), Positives = 41/94 (43%), Gaps = 9/94 (9%)
Query: 22 EVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERV 81
E +TL + +L Y E L F + IK+ +N+ G+ +GY F+EF S A+
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFE---KATFIKVPQNQ-NGKSKGYAFIEFASFEDAKEA 69
Query: 82 LQTYNGTPMPGTEQNFRLNWASFGIGEKRPDAGP 115
L + N + G L P++GP
Sbjct: 70 LNSCNKREIEGRAIRLELQGP-----RGSPNSGP 98
Score = 29.6 bits (65), Expect = 3.0, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 5/80 (6%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
++ + +L+ T+ LQE F KV + N G+SKGY F++F + A+
Sbjct: 17 TLVLSNLSYSATEETLQEVFEK----ATFIKVPQNQN-GKSKGYAFIEFASFEDAKEALN 71
Query: 178 EMNGVFCSTRPMRISAATPK 197
N R +R+ P+
Sbjct: 72 SCNKREIEGRAIRLELQGPR 91
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 33.1 bits (74), Expect = 0.33, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 233 NTTIFVGNLDPN-VTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAILRMQG 291
N+ +F+GNL+ V + +++ F +G + + +G FVQ++ A A+L G
Sbjct: 27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--HKGYAFVQYSNERHARAAVLGENG 84
Query: 292 HMIGQQQVRIS 302
++ Q + I+
Sbjct: 85 RVLAGQTLDIN 95
Score = 29.3 bits (64), Expect = 4.8, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 9/80 (11%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+F+G+L + ET S+Y V G V KGY FV++ +E A+
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLG 81
Query: 179 MNGVFCSTRPMRIS-AATPK 197
NG + + + I+ A PK
Sbjct: 82 ENGRVLAGQTLDINMAGEPK 101
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 33.1 bits (74), Expect = 0.34, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 234 TTIFVGNLD-PNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAI 286
+ +F+GNL NV++E+L + F +G I+ + I GF+QF S +AI
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAI 62
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 32.3 bits (72), Expect = 0.52, Method: Composition-based stats.
Identities = 24/87 (27%), Positives = 43/87 (49%), Gaps = 8/87 (9%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHF----GEIVNVKIPMG--RGCGFVQFAARASAEEAI 286
N +++ NL P VTE +L F F G + ++ G RG F+ F + A +A+
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
Query: 287 LRMQGHMIGQQQVRISWG--RKQDVTG 311
+ G+ + + + I +G +KQ +G
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQRSSG 111
Score = 28.5 bits (62), Expect = 7.8, Method: Composition-based stats.
Identities = 25/95 (26%), Positives = 40/95 (42%), Gaps = 5/95 (5%)
Query: 21 EEVRTLWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAER 80
E + L++ +L E L S FA E I +TG+ G F+ F + A +
Sbjct: 23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 81 VLQTYNGTPMPGTEQNFRLNWASFGIGEKRPDAGP 115
L NG + G ++ FG +K+ +GP
Sbjct: 83 ALHLVNGYKLYG-----KILVIEFGKNKKQRSSGP 112
Score = 28.5 bits (62), Expect = 8.3, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 115 PEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNR 174
P +++ +L+P VT+ L F +++ +G + TGR +G F+ F ++ +
Sbjct: 24 PNKVLYLKNLSPRVTERDLVSLF-ARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 175 AMTEMNG 181
A+ +NG
Sbjct: 83 ALHLVNG 89
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 32.0 bits (71), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 14/92 (15%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR-----GCGFVQFAARASAEEAI 286
T + V NLD V++ ++++ F FG + + R G V F RA A +A+
Sbjct: 87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAM 146
Query: 287 LRMQGHMIGQQQVRISWGRKQDVTGSVAAQVD 318
+ +G + GR D+ VA+Q+D
Sbjct: 147 KQYKGVPLD--------GRPMDIQ-LVASQID 169
Score = 31.6 bits (70), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 118 SIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
+ V +L V+D +QE F +++ +++ A V D +GRS G V F + +AM
Sbjct: 90 KLLVSNLDFGVSDADIQELF-AEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMK 147
Query: 178 EMNGVFCSTRPMRI 191
+ GV RPM I
Sbjct: 148 QYKGVPLDGRPMDI 161
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 32.0 bits (71), Expect = 0.61, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+ V +L V+D +QE F +++ +++ A V D +GRS G V F + +AM +
Sbjct: 38 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 95
Query: 179 MNGVFCSTRPMRI 191
GV RPM I
Sbjct: 96 YKGVPLDGRPMDI 108
Score = 32.0 bits (71), Expect = 0.67, Method: Composition-based stats.
Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 14/92 (15%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR-----GCGFVQFAARASAEEAI 286
T + V NLD V++ ++++ F FG + + R G V F RA A +A+
Sbjct: 34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAM 93
Query: 287 LRMQGHMIGQQQVRISWGRKQDVTGSVAAQVD 318
+ +G + GR D+ VA+Q+D
Sbjct: 94 KQYKGVPLD--------GRPMDIQ-LVASQID 116
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 32.0 bits (71), Expect = 0.63, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+ V +L V+D +QE F +++ +++ A V D +GRS G V F + +AM +
Sbjct: 38 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 95
Query: 179 MNGVFCSTRPMRI 191
GV RPM I
Sbjct: 96 YKGVPLDGRPMDI 108
Score = 32.0 bits (71), Expect = 0.70, Method: Composition-based stats.
Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 14/92 (15%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGR-----GCGFVQFAARASAEEAI 286
T + V NLD V++ ++++ F FG + + R G V F RA A +A+
Sbjct: 34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAM 93
Query: 287 LRMQGHMIGQQQVRISWGRKQDVTGSVAAQVD 318
+ +G + GR D+ VA+Q+D
Sbjct: 94 KQYKGVPLD--------GRPMDIQ-LVASQID 116
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 32.0 bits (71), Expect = 0.63, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 7/82 (8%)
Query: 231 ITNTTIFVGNLD----PNVTEEELKQTFLHFGEIVNV---KIPMGRGCGFVQFAARASAE 283
+ N TI++ NL+ ++ L F FG+I+++ K RG FV F SA
Sbjct: 4 LPNQTIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSAS 63
Query: 284 EAILRMQGHMIGQQQVRISWGR 305
A+ MQG + ++I++ +
Sbjct: 64 NALRTMQGFPFYDKPMQIAYSK 85
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 32.0 bits (71), Expect = 0.73, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIVNV-----KIPMGRGCGFVQFAARASAEEAILRMQ 290
+F+G L+ E+ LK F G I V + RG F+ F A A+ A M
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 291 GHMIGQQQVRISWGRK 306
G + + +++ +K
Sbjct: 70 GKSLHGKAIKVEQAKK 85
Score = 31.2 bits (69), Expect = 1.3, Method: Composition-based stats.
Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+F+G L + + +L+ F P + ++ D T +S+G+ F+ F + + A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGP-ISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKD 67
Query: 179 MNGVFCSTRPMRISAATPKKTTGFQ 203
MNG + +++ A K FQ
Sbjct: 68 MNGKSLHGKAIKVEQA---KKPSFQ 89
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 32.0 bits (71), Expect = 0.76, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 110 RPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDP-NTGRSKGYGFVKF 166
R P ++ F+G+L DVT+ ++E FR ++ ++ +P N R KG+G+ +F
Sbjct: 13 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGL--NISAVRLPREPSNPERLKGFGYAEF 68
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 32.0 bits (71), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 233 NTTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEAI 286
+T + VGN+ P T +EL+ F +G ++ I + FV A EAI
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--KDYAFVHMERAEDAVEAI 61
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 31.6 bits (70), Expect = 0.87, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 6/84 (7%)
Query: 232 TNTTIFVGNLDPNVTEEELKQTFLH-FGE----IVNVKIPMGRGCGFVQFAARASAEEAI 286
T +F+GNL+PN + ELK F + +V+V+ R G+V F + E+A
Sbjct: 16 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA- 74
Query: 287 LRMQGHMIGQQQVRISWGRKQDVT 310
L + G + ++++ + +D T
Sbjct: 75 LELTGLKVFGNEIKLEKPKGRDGT 98
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 31.6 bits (70), Expect = 0.87, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 110 RPDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDP-NTGRSKGYGFVKF 166
R P ++ F+G+L DVT+ ++E FR ++ ++ +P N R KG+G+ +F
Sbjct: 9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGL--NISAVRLPREPSNPERLKGFGYAEF 64
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 31.6 bits (70), Expect = 0.87, Method: Composition-based stats.
Identities = 13/39 (33%), Positives = 23/39 (58%)
Query: 45 AHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQ 83
+H + ++++RNK +GQ G+ FVEF A R ++
Sbjct: 24 SHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWME 62
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 31.6 bits (70), Expect = 0.97, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 111 PDAGPEHSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLD 168
P+ ++F LA + L++ F S VR ++++D N+ RSKG +V+F +
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFF-SAVGKVRDVRIISDRNSRRSKGIAYVEFCE 76
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMTE 178
+ V +L V+D +QE F +++ +++ A V D +GRS G V F + + +A +
Sbjct: 32 LLVSNLDFGVSDADIQELF-AEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAXKQ 89
Query: 179 MNGVFCSTRPMRISAAT 195
NGV RP I T
Sbjct: 90 YNGVPLDGRPXNIQLVT 106
Score = 28.5 bits (62), Expect = 7.1, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 1/74 (1%)
Query: 26 LWIGDLQYWFDENYLSSCFAHTGEVVSIKIIRNKITGQPEGYGFVEFVSHAAAERVLQTY 85
L + +L + + + FA G + + ++ +G+ G V F A A + + Y
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQY 90
Query: 86 NGTPMPGTEQNFRL 99
NG P+ G N +L
Sbjct: 91 NGVPLDGRPXNIQL 104
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 30.0 bits (66), Expect = 2.6, Method: Composition-based stats.
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 236 IFVGNLDPNVTEEELKQTFLHFGEIV 261
+FVG L P++ E+E+ +F FG +V
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLV 36
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGF----VQFAARASAEEAILRM 289
TT+ V NL + + ++ + F H G I++V + F ++FA A AI +
Sbjct: 5 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 64
Query: 290 QGHMIGQQQVRIS 302
++GQ ++ +S
Sbjct: 65 HK-VVGQNEIIVS 76
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 29.3 bits (64), Expect = 4.3, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 7/65 (10%)
Query: 117 HSIFVGDLAPDVTDYLLQETFRSQYPSVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAM 176
+ +++G+L+P VT L++ F + + G ++ GY FV + D+N RA+
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAI 61
Query: 177 TEMNG 181
++G
Sbjct: 62 ETLSG 66
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 28.1 bits (61), Expect = 9.2, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 23/52 (44%)
Query: 234 TTIFVGNLDPNVTEEELKQTFLHFGEIVNVKIPMGRGCGFVQFAARASAEEA 285
T I NL E+++TF FG + V +P G V+F A +A
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKA 62
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 28.1 bits (61), Expect = 9.5, Method: Composition-based stats.
Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 9/79 (11%)
Query: 119 IFVGDLAPDVTDYLLQETFRSQYP-SVRGAKVVTDPNTGRSKGYGFVKFLDENERNRAMT 177
++V +L ++ ++++ F + P +V K + D Y FV F + + AM
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD--------YAFVHFSNREDAVEAMK 69
Query: 178 EMNGVFCSTRPMRISAATP 196
+NG P+ ++ A P
Sbjct: 70 ALNGKVLDGSPIEVTLAKP 88
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.132 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,439,652
Number of Sequences: 62578
Number of extensions: 453811
Number of successful extensions: 1599
Number of sequences better than 100.0: 200
Number of HSP's better than 100.0 without gapping: 138
Number of HSP's successfully gapped in prelim test: 62
Number of HSP's that attempted gapping in prelim test: 1062
Number of HSP's gapped (non-prelim): 492
length of query: 423
length of database: 14,973,337
effective HSP length: 101
effective length of query: 322
effective length of database: 8,652,959
effective search space: 2786252798
effective search space used: 2786252798
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: 53 (25.0 bits)