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= 017119
(377 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 149 bits (377), Expect = 2e-36, Method: Compositional matrix adjust.
Identities = 67/85 (78%), Positives = 79/85 (92%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+ +FIGNLDP++DEKLLYDTFSAFGVI+ PKIMRDPDTGNS+G+ FI++ SF+ASDAAI
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 172 EAMNGQYLCNRQITVSYAYKKDTKG 196
EAMNGQYLCNR ITVSYA+KKD+KG
Sbjct: 66 EAMNGQYLCNRPITVSYAFKKDSKG 90
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNV-YVPKDRVTNLHQGYGFVEFRSEEDADYAIKVL 86
++GNLDP++ E+LL++ F G ++ + +D T +GY F+ F S + +D AI+ +
Sbjct: 9 FIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAM 68
Query: 87 NMIKLYGKPIRVNKA 101
N L +PI V+ A
Sbjct: 69 NGQYLCNRPITVSYA 83
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 149 bits (375), Expect = 3e-36, Method: Compositional matrix adjust.
Identities = 69/90 (76%), Positives = 79/90 (87%)
Query: 19 AERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEED 78
+ERNQDAT YVG LD +V+E LLWELF+QAGPVVN ++PKDRVT HQGYGFVEF SEED
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69
Query: 79 ADYAIKVLNMIKLYGKPIRVNKASQDKKSL 108
ADYAIK+++MIKLYGKPIRVNKAS K+L
Sbjct: 70 ADYAIKIMDMIKLYGKPIRVNKASAHNKNL 99
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
A +++G LD V E LL++ F G +V N + +D TG +G+GF+ + S E +D AI
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVV-NTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 172 EAMNGQYLCNRQITVSYA 189
+ M+ L + I V+ A
Sbjct: 75 KIMDMIKLYGKPIRVNKA 92
>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 = 130 bits (327), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 68/175 (38%), Positives = 108/175 (61%), Gaps = 5/175 (2%)
Query: 25 ATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
A+ YVG+L P VTE +L+E F AGP++++ V +D +T GY +V F+ DA+ A+
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 85 VLNMIKLYGKPIRVNKASQDKKSLDVGA-NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPK 143
+N + GKP+R+ + +D G N+FI NLD +D K LYDTFSAFG I++
Sbjct: 71 TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKV 130
Query: 144 IMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQITV-SYAYKKDTKGE 197
+ D S+G+GF+ +++ EA++ AIE MNG L +R++ V + +K+ + E
Sbjct: 131 VC---DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 182
>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 = 130 bits (327), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 68/175 (38%), Positives = 108/175 (61%), Gaps = 5/175 (2%)
Query: 25 ATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
A+ YVG+L P VTE +L+E F AGP++++ V +D +T GY +V F+ DA+ A+
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 85 VLNMIKLYGKPIRVNKASQDKKSLDVGA-NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPK 143
+N + GKP+R+ + +D G N+FI NLD +D K LYDTFSAFG I++
Sbjct: 76 TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKV 135
Query: 144 IMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQITV-SYAYKKDTKGE 197
+ D S+G+GF+ +++ EA++ AIE MNG L +R++ V + +K+ + E
Sbjct: 136 VC---DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 187
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 103 bits (257), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 58/165 (35%), Positives = 101/165 (61%), Gaps = 3/165 (1%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YVGNLD +TE++L + F GP+ N+ + D+ N + Y FVE+ DA+ A++ LN
Sbjct: 4 YVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 88 MIKLYGKPIRVNKASQDKKSL-DVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMR 146
++ +++N A Q ++S D NLF+G+L+ +VD++ L + F F ++ +M
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLS-GHVMW 121
Query: 147 DPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQITVSYAYK 191
D TG+SRG+GF+S+ S + + A+++M GQ L R + +++A K
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
L++GNLD + E +L F G I N KIM D + N + F+ Y ++ A++
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPI-ANIKIMIDKNNKNV-NYAFVEYHQSHDANIALQT 60
Query: 174 MNGQYLCNRQITVSYAYK 191
+NG+ + N + +++A++
Sbjct: 61 LNGKQIENNIVKINWAFQ 78
>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 = 90.1 bits (222), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 59/197 (29%), Positives = 104/197 (52%), Gaps = 21/197 (10%)
Query: 3 TRIAPGVGANLLGQHSAERNQDATA-----YVGNLDPQVTEELLWELFVQAGPVVNVYVP 57
+ +A G +G+ SA + Q A A YVG++ ++ E+ + + F GP+ ++ +
Sbjct: 2 SHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMS 61
Query: 58 KDRVTNLHQGYGFVEFRSEEDADYAIKVLNMIKLYGKPIRVNKAS---QDKKSLDVGAN- 113
D VT H+G+ FVE+ E A A++ +N + L G+ I+V + S Q + +D A
Sbjct: 62 WDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEE 121
Query: 114 ------LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEAS 167
+++ ++ D+ + + F AFG I + + RDP TG +G+GFI Y+ ++S
Sbjct: 122 ARAFNRIYVASVHQDLSDDDIKSVFEAFGKI-KSATLARDPTTGKHKGYGFIEYEKAQSS 180
Query: 168 DAAIEAMN-----GQYL 179
A+ +MN GQYL
Sbjct: 181 QDAVSSMNLFDLGGQYL 197
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 42/74 (56%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YV ++ ++++ + +F G + + + +D T H+GYGF+E+ + + A+ +N
Sbjct: 129 YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Query: 88 MIKLYGKPIRVNKA 101
+ L G+ +RV KA
Sbjct: 189 LFDLGGQYLRVGKA 202
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 49/94 (52%), Gaps = 1/94 (1%)
Query: 93 GKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGN 152
G+ + A+Q + +L + + +++G++ ++ E + F+ FG I + + D T
Sbjct: 10 GQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPI-KSIDMSWDSVTMK 68
Query: 153 SRGFGFISYDSFEASDAAIEAMNGQYLCNRQITV 186
+GF F+ Y+ EA+ A+E MN L R I V
Sbjct: 69 HKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 102
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 87.8 bits (216), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 85/153 (55%), Gaps = 3/153 (1%)
Query: 26 TAYVGNLDPQ-VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
T + N PQ +T++ LF G + + + +D++T GYGFV + DAD AI
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 85 VLNMIKLYGKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKI 144
LN +KL K I+V+ A S+ ANL++ L + +K + FS +G I+T+ +I
Sbjct: 65 TLNGLKLQTKTIKVSYARPSSASIR-DANLYVSGLPKTMSQKEMEQLFSQYGRIITS-RI 122
Query: 145 MRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQ 177
+ D TG SRG GFI +D ++ AI+ +NGQ
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQ 155
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 36/121 (29%), Positives = 52/121 (42%), Gaps = 22/121 (18%)
Query: 108 LDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEAS 167
+D NL + L ++ + F + G I + K++RD TG S G+GF++Y +
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDI-ESCKLVRDKITGQSLGYGFVNYSDPNDA 59
Query: 168 DAAIEAMNGQYLCNRQITVSYAYKKDTKGERHGTPAERILAANNPSSQKSRPHTLFASGP 227
D AI +NG L + I VSYA PSS R L+ SG
Sbjct: 60 DKAINTLNGLKLQTKTIKVSYA---------------------RPSSASIRDANLYVSGL 98
Query: 228 P 228
P
Sbjct: 99 P 99
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 23 QDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYA 82
+DA YV L ++++ + +LF Q G ++ + D+ T + +G GF+ F +A+ A
Sbjct: 89 RDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEA 148
Query: 83 IKVLNMIKLYG--KPIRVNKAS 102
IK LN K G +PI V A+
Sbjct: 149 IKGLNGQKPLGAAEPITVKFAN 170
>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 = 87.4 bits (215), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 55/153 (35%), Positives = 86/153 (56%), Gaps = 3/153 (1%)
Query: 26 TAYVGNLDPQ-VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
T + N PQ +T+E LF G + + + +D++T GYGFV + +DA+ AI
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 85 VLNMIKLYGKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKI 144
LN ++L K I+V+ A S+ ANL++ L + +K L FS +G I+T+ +I
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSASIR-DANLYVSGLPKTMTQKELEQLFSQYGRIITS-RI 120
Query: 145 MRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQ 177
+ D TG SRG GFI +D ++ AI+ +NGQ
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 153
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 38/65 (58%)
Query: 23 QDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYA 82
+DA YV L +T++ L +LF Q G ++ + D+VT + +G GF+ F +A+ A
Sbjct: 87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 146
Query: 83 IKVLN 87
IK LN
Sbjct: 147 IKGLN 151
>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 = 85.9 bits (211), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 54/153 (35%), Positives = 84/153 (54%), Gaps = 3/153 (1%)
Query: 26 TAYVGNLDPQ-VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
T + N PQ +T++ L LF G V + + +D+V GYGFV + + +DA+ AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 85 VLNMIKLYGKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKI 144
LN ++L K I+V+ A + + ANL+I L + +K + D FS FG I+ N ++
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIK-DANLYISGLPRTMTQKDVEDMFSRFGRII-NSRV 120
Query: 145 MRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQ 177
+ D TG SRG FI +D ++ AI + NG
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 38/70 (54%)
Query: 18 SAERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEE 77
S+E +DA Y+ L +T++ + ++F + G ++N V D+ T L +G F+ F
Sbjct: 82 SSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRS 141
Query: 78 DADYAIKVLN 87
+A+ AI N
Sbjct: 142 EAEEAITSFN 151
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 85.9 bits (211), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 54/153 (35%), Positives = 84/153 (54%), Gaps = 3/153 (1%)
Query: 26 TAYVGNLDPQ-VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
T + N PQ +T++ L LF G V + + +D+V GYGFV + + +DA+ AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 85 VLNMIKLYGKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKI 144
LN ++L K I+V+ A + + ANL+I L + +K + D FS FG I+ N ++
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIK-DANLYISGLPRTMTQKDVEDMFSRFGRII-NSRV 120
Query: 145 MRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQ 177
+ D TG SRG FI +D ++ AI + NG
Sbjct: 121 LVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 38/70 (54%)
Query: 18 SAERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEE 77
S+E +DA Y+ L +T++ + ++F + G ++N V D+ T L +G F+ F
Sbjct: 82 SSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRS 141
Query: 78 DADYAIKVLN 87
+A+ AI N
Sbjct: 142 EAEEAITSFN 151
>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 = 83.6 bits (205), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 51/167 (30%), Positives = 91/167 (54%), Gaps = 16/167 (9%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YVG++ ++ E+ + + F GP+ ++ + D VT H+G+ FVE+ E A A++ +N
Sbjct: 17 YVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMN 76
Query: 88 MIKLYGKPIRVNKAS---QDKKSLDVGAN-------LFIGNLDPDVDEKLLYDTFSAFGV 137
+ L G+ I+V + S Q + +D A +++ ++ D+ + + F AFG
Sbjct: 77 SVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGK 136
Query: 138 IVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMN-----GQYL 179
I + + RDP TG +G+GFI Y+ ++S A+ +MN GQYL
Sbjct: 137 I-KSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 182
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 47/89 (52%)
Query: 13 LLGQHSAERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVE 72
++ Q + E YV ++ ++++ + +F G + + + +D T H+GYGF+E
Sbjct: 99 IIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIE 158
Query: 73 FRSEEDADYAIKVLNMIKLYGKPIRVNKA 101
+ + + A+ +N+ L G+ +RV KA
Sbjct: 159 YEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 1/85 (1%)
Query: 102 SQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISY 161
+Q +++L + +++G++ ++ E + F+ FG I + + D T +GF F+ Y
Sbjct: 4 AQRQRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPI-KSIDMSWDSVTMKHKGFAFVEY 62
Query: 162 DSFEASDAAIEAMNGQYLCNRQITV 186
+ EA+ A+E MN L R I V
Sbjct: 63 EVPEAAQLALEQMNSVMLGGRNIKV 87
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 83.6 bits (205), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 54/151 (35%), Positives = 79/151 (52%), Gaps = 3/151 (1%)
Query: 26 TAYVGNLDPQ-VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
T + N PQ +T+ L+ LF GP+ + +D T GY FV+F SE D+ AIK
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 85 VLNMIKLYGKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKI 144
VLN I + K ++V+ A +S+ NL++ NL + + L F +G IV I
Sbjct: 64 VLNGITVRNKRLKVSYARPGGESIK-DTNLYVTNLPRTITDDQLDTIFGKYGSIV-QKNI 121
Query: 145 MRDPDTGNSRGFGFISYDSFEASDAAIEAMN 175
+RD TG RG F+ Y+ E + AI A+N
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
NL + L D+ ++ LY F A G I T +IMRD TG S G+ F+ + S S AI
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINT-CRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 172 EAMNGQYLCNRQITVSYA 189
+ +NG + N+++ VSYA
Sbjct: 63 KVLNGITVRNKRLKVSYA 80
>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 = 82.8 bits (203), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 50/151 (33%), Positives = 80/151 (52%), Gaps = 4/151 (2%)
Query: 22 NQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADY 81
+ ++G L+ TE+ L E F + G V ++ + KD T +G+GF+ F D
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 82 AIKVLNMIKLYGKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTN 141
+K ++ L GK I +A + D +F+G + PDV K + FS +G I+ +
Sbjct: 61 VVKTQHI--LDGKVIDPKRAIP-RDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTII-D 116
Query: 142 PKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
++M D DTG SRGFGF++YDS +A D +
Sbjct: 117 AQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ 147
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 43/73 (58%), Gaps = 4/73 (5%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+FIG L+ D E L + F +G VT+ KIM+DP TG SRGFGF+ SFE +
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGT-VTDLKIMKDPATGRSRGFGFL---SFEKPSSVD 59
Query: 172 EAMNGQYLCNRQI 184
E + Q++ + ++
Sbjct: 60 EVVKTQHILDGKV 72
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 20 ERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDA 79
E+++ +VG + P V + E F Q G +++ + D+ T +G+GFV + S +
Sbjct: 83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142
Query: 80 DYAIKVLNMIKLYGKPIRVNKAS 102
D + I + I + +A
Sbjct: 143 DRVCQN-KFIDFKDRKIEIKRAE 164
>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 = 82.0 bits (201), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 54/151 (35%), Positives = 78/151 (51%), Gaps = 3/151 (1%)
Query: 26 TAYVGNLDPQ-VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
T + N PQ T+ L+ LF GP+ + +D T GY FV+F SE D+ AIK
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 85 VLNMIKLYGKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKI 144
VLN I + K ++V+ A +S+ NL++ NL + + L F +G IV I
Sbjct: 75 VLNGITVRNKRLKVSYARPGGESIK-DTNLYVTNLPRTITDDQLDTIFGKYGSIV-QKNI 132
Query: 145 MRDPDTGNSRGFGFISYDSFEASDAAIEAMN 175
+RD TG RG F+ Y+ E + AI A+N
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/78 (38%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
NL + L D ++ LY F A G I T +I RD TG S G+ F+ + S S AI
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINT-CRIXRDYKTGYSFGYAFVDFTSEXDSQRAI 73
Query: 172 EAMNGQYLCNRQITVSYA 189
+ +NG + N+++ VSYA
Sbjct: 74 KVLNGITVRNKRLKVSYA 91
>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 = 79.3 bits (194), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 50/167 (29%), Positives = 88/167 (52%), Gaps = 16/167 (9%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YVG++ ++ E+ + + F GP+ ++ D VT H+G+ FVE+ E A A++ N
Sbjct: 16 YVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXN 75
Query: 88 MIKLYGKPIRVNKAS---QDKKSLDVGAN-------LFIGNLDPDVDEKLLYDTFSAFGV 137
+ L G+ I+V + S Q + +D A +++ ++ D+ + + F AFG
Sbjct: 76 SVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGK 135
Query: 138 IVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMN-----GQYL 179
I + + RDP TG +G+GFI Y+ ++S A+ + N GQYL
Sbjct: 136 I-KSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYL 181
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 41/74 (55%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YV ++ ++++ + +F G + + + +D T H+GYGF+E+ + + A+ N
Sbjct: 113 YVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
Query: 88 MIKLYGKPIRVNKA 101
+ L G+ +RV KA
Sbjct: 173 LFDLGGQYLRVGKA 186
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 1/86 (1%)
Query: 101 ASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFIS 160
A+Q +++L + +++G++ ++ E + F+ FG I + D T +GF F+
Sbjct: 2 AAQRQRALAIXCRVYVGSIYYELGEDTIRQAFAPFGPI-KSIDXSWDSVTXKHKGFAFVE 60
Query: 161 YDSFEASDAAIEAMNGQYLCNRQITV 186
Y+ EA+ A+E N L R I V
Sbjct: 61 YEVPEAAQLALEQXNSVXLGGRNIKV 86
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 79.3 bits (194), Expect = 3e-15, Method: Composition-based stats.
Identities = 40/84 (47%), Positives = 56/84 (66%), Gaps = 1/84 (1%)
Query: 19 AERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEED 78
A+ D T +VGNL+ +V EE+L+ELF+QAGP+ V + KDR + +GFV F+ E
Sbjct: 11 AQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPES 69
Query: 79 ADYAIKVLNMIKLYGKPIRVNKAS 102
YAI +LN I+LYG+PI V+ S
Sbjct: 70 VSYAIALLNGIRLYGRPINVSGPS 93
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 27/74 (36%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
+F+GNL+ V E++LY+ F G + T I +D + G + FGF+ + E+ AI
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPL-TKVTICKDRE-GKPKSFGFVCFKHPESVSYAIAL 76
Query: 174 MNGQYLCNRQITVS 187
+NG L R I VS
Sbjct: 77 LNGIRLYGRPINVS 90
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 70.9 bits (172), Expect = 1e-12, Method: Composition-based stats.
Identities = 36/87 (41%), Positives = 56/87 (64%), Gaps = 4/87 (4%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
N+FI NLD +D K LYDTFSAFG I++ + D S+G+GF+ +++ EA++ AI
Sbjct: 12 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC---DENGSKGYGFVHFETQEAAERAI 68
Query: 172 EAMNGQYLCNRQITVS-YAYKKDTKGE 197
E MNG L +R++ V + +K+ + E
Sbjct: 69 EKMNGMLLNDRKVFVGRFKSRKEREAE 95
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++ NLD + + L++ F G +++ V D N +GYGFV F ++E A+ AI+ +N
Sbjct: 15 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMN 72
Query: 88 MIKLYGKPIRVNKASQDKK 106
+ L + + V + K+
Sbjct: 73 GMLLNDRKVFVGRFKSRKE 91
>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 = 69.3 bits (168), Expect = 3e-12, Method: Composition-based stats.
Identities = 36/87 (41%), Positives = 56/87 (64%), Gaps = 4/87 (4%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
N+FI NLD +D K LYDTFSAFG I++ + D S+G+GF+ +++ EA++ AI
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC---DENGSKGYGFVHFETQEAAERAI 62
Query: 172 EAMNGQYLCNRQITVS-YAYKKDTKGE 197
E MNG L +R++ V + +K+ + E
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKEREAE 89
Score = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 29/101 (28%), Positives = 55/101 (54%), Gaps = 9/101 (8%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++ NLD + + L++ F G +++ V D N +GYGFV F ++E A+ AI+ +N
Sbjct: 9 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMN 66
Query: 88 MIKLYGKPIRVNK-ASQDKKSLDVGA------NLFIGNLDP 121
+ L + + V + S+ ++ ++GA N++I N P
Sbjct: 67 GMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGP 107
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 69.3 bits (168), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 44/149 (29%), Positives = 75/149 (50%), Gaps = 7/149 (4%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++G L + T+E L F Q G + + V +D T +G+GFV + + E+ D A+
Sbjct: 18 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 77
Query: 88 MIKLYGKPIRVNKASQDKKSLDVGANL-----FIGNLDPDVDEKLLYDTFSAFGVIVTNP 142
K+ G+ + +A + S GA+L F+G + D +E L D F +G I
Sbjct: 78 H-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV-I 135
Query: 143 KIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+IM D +G RGF F+++D ++ D +
Sbjct: 136 EIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
LFIG L + ++ L F +G + T+ +MRDP+T SRGFGF++Y + E DAA+
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTL-TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 173 A 173
A
Sbjct: 75 A 75
>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 = 68.9 bits (167), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 44/149 (29%), Positives = 75/149 (50%), Gaps = 7/149 (4%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++G L + T+E L F Q G + + V +D T +G+GFV + + E+ D A+
Sbjct: 17 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 76
Query: 88 MIKLYGKPIRVNKASQDKKSLDVGANL-----FIGNLDPDVDEKLLYDTFSAFGVIVTNP 142
K+ G+ + +A + S GA+L F+G + D +E L D F +G I
Sbjct: 77 H-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV-I 134
Query: 143 KIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+IM D +G RGF F+++D ++ D +
Sbjct: 135 EIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
LFIG L + ++ L F +G + T+ +MRDP+T SRGFGF++Y + E DAA+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTL-TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 173 A 173
A
Sbjct: 74 A 74
>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 = 68.9 bits (167), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 44/149 (29%), Positives = 75/149 (50%), Gaps = 7/149 (4%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++G L + T+E L F Q G + + V +D T +G+GFV + + E+ D A+
Sbjct: 16 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 75
Query: 88 MIKLYGKPIRVNKASQDKKSLDVGANL-----FIGNLDPDVDEKLLYDTFSAFGVIVTNP 142
K+ G+ + +A + S GA+L F+G + D +E L D F +G I
Sbjct: 76 H-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV-I 133
Query: 143 KIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+IM D +G RGF F+++D ++ D +
Sbjct: 134 EIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
LFIG L + ++ L F +G + T+ +MRDP+T SRGFGF++Y + E DAA+
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTL-TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 173 A 173
A
Sbjct: 73 A 73
>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 = 68.2 bits (165), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 44/149 (29%), Positives = 75/149 (50%), Gaps = 7/149 (4%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++G L + T+E L F Q G + + V +D T +G+GFV + + E+ D A+
Sbjct: 10 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 69
Query: 88 MIKLYGKPIRVNKASQDKKSLDVGANL-----FIGNLDPDVDEKLLYDTFSAFGVIVTNP 142
K+ G+ + +A + S GA+L F+G + D +E L D F +G I
Sbjct: 70 H-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV-I 127
Query: 143 KIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+IM D +G RGF F+++D ++ D +
Sbjct: 128 EIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
LFIG L + ++ L F +G + T+ +MRDP+T SRGFGF++Y + E DAA+
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTL-TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 173 A 173
A
Sbjct: 67 A 67
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 68.2 bits (165), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 44/149 (29%), Positives = 75/149 (50%), Gaps = 7/149 (4%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++G L + T+E L F Q G + + V +D T +G+GFV + + E+ D A+
Sbjct: 17 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 76
Query: 88 MIKLYGKPIRVNKASQDKKSLDVGANL-----FIGNLDPDVDEKLLYDTFSAFGVIVTNP 142
K+ G+ + +A + S GA+L F+G + D +E L D F +G I
Sbjct: 77 H-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV-I 134
Query: 143 KIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+IM D +G RGF F+++D ++ D +
Sbjct: 135 EIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
LFIG L + ++ L F +G + T+ +MRDP+T SRGFGF++Y + E DAA+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTL-TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 173 A 173
A
Sbjct: 74 A 74
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 67.8 bits (164), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 44/149 (29%), Positives = 75/149 (50%), Gaps = 7/149 (4%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++G L + T+E L F Q G + + V +D T +G+GFV + + E+ D A+
Sbjct: 15 FIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARP 74
Query: 88 MIKLYGKPIRVNKASQDKKSLDVGANL-----FIGNLDPDVDEKLLYDTFSAFGVIVTNP 142
K+ G+ + +A + S GA+L F+G + D +E L D F +G I
Sbjct: 75 H-KVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV-I 132
Query: 143 KIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+IM D +G RGF F+++D ++ D +
Sbjct: 133 EIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
LFIG L + ++ L F +G + T+ +MRDP+T SRGFGF++Y + E DAA+
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTL-TDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 173 A 173
A
Sbjct: 72 A 72
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 65.1 bits (157), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 53/170 (31%), Positives = 85/170 (50%), Gaps = 10/170 (5%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTN--LHQGYGFVEFRSEEDADYAIKV 85
+VG + +E+ L ELF Q G V + V +DR N +G FV F + + A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 86 LNMIKLY---GKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNP 142
L+ +K+ PI++ A +K + LFIG + E + FS+FG I
Sbjct: 67 LHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI-EEC 125
Query: 143 KIMRDPDTGNSRGFGFISYDSFEASDAAIEAMN-GQYL--CNRQITVSYA 189
+I+R PD G SRG F+++ + + AI+AM+ Q + C+ + V +A
Sbjct: 126 RILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 65.1 bits (157), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 54/170 (31%), Positives = 85/170 (50%), Gaps = 10/170 (5%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQ--GYGFVEFRSEEDADYAIKV 85
+VG + +E+ L ELF Q G V + V +DR N Q G FV F + + A A
Sbjct: 19 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 78
Query: 86 LNMIKL---YGKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNP 142
L+ +K+ PI++ A +K + LFIG + E + FS+FG I
Sbjct: 79 LHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI-EEC 137
Query: 143 KIMRDPDTGNSRGFGFISYDSFEASDAAIEAMN-GQYL--CNRQITVSYA 189
+I+R PD G SRG F+++ + + AI+AM+ Q + C+ + V +A
Sbjct: 138 RILRGPD-GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 186
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 49/166 (29%), Positives = 75/166 (45%), Gaps = 26/166 (15%)
Query: 22 NQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADY 81
Q +VGNL +TEE LF + G V++ +DR G+GF+ S A+
Sbjct: 20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEI 73
Query: 82 AIKVLNMIKLYGKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFG----- 136
A L+ L +P+R+ A+ GA L + NL P V +LL FS FG
Sbjct: 74 AKAELDGTILKSRPLRIRFATH-------GAALTVKNLSPVVSNELLEQAFSQFGPVEKA 126
Query: 137 VIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAM-NGQYLCN 181
V+V + D G + G GF+ + + + A+E +G +L
Sbjct: 127 VVVVD-------DRGRATGKGFVEFAAKPPARKALERCGDGAFLLT 165
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 105 KKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSF 164
+K+ LF+GNL D+ E+ F +G + I RD RGFGFI +S
Sbjct: 16 EKTYTQRCRLFVGNLPTDITEEDFKRLFERYGE-PSEVFINRD------RGFGFIRLESR 68
Query: 165 EASDAAIEAMNGQYLCNRQITVSYA 189
++ A ++G L +R + + +A
Sbjct: 69 TLAEIAKAELDGTILKSRPLRIRFA 93
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 63.2 bits (152), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 35/92 (38%), Positives = 56/92 (60%), Gaps = 5/92 (5%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKV 85
+ +VGN+ + TEE L ++F + GPVV+ + DR T +GYGF E++ +E A A++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 86 LNMIKLYGKPIRVNKASQDK-----KSLDVGA 112
LN + G+ +RV+ A+ +K KSL GA
Sbjct: 70 LNGREFSGRALRVDNAASEKNKEELKSLGTGA 101
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 1/85 (1%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
++F+GN+ + E+ L D FS G +V+ +++ D +TG +G+GF Y E + +A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSF-RLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 173 AMNGQYLCNRQITVSYAYKKDTKGE 197
+NG+ R + V A + K E
Sbjct: 69 NLNGREFSGRALRVDNAASEKNKEE 93
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 54/202 (26%), Positives = 91/202 (45%), Gaps = 22/202 (10%)
Query: 22 NQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADY 81
Q + +VGNL P +TEE + +LF + G V++ KD+ G+GF+ + A+
Sbjct: 20 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEI 73
Query: 82 AIKVLNMIKLYGKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTN 141
A L+ + L GK +RV A A+L + NL V +LL + FS FG +
Sbjct: 74 AKVELDNMPLRGKQLRVRFACH-------SASLTVRNLPQYVSNELLEEAFSVFGQVERA 126
Query: 142 PKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMN-GQYLCN---RQITVSYAYKKDTKGE 197
I+ D G G G + + A+ A++ + G +L R +TV D +
Sbjct: 127 VVIV--DDRGRPSGKGIVEFSGKPAARKALDRCSEGSFLLTTFPRPVTVEPM---DQLDD 181
Query: 198 RHGTPAERILAANNPSSQKSRP 219
G P + ++ ++ +P
Sbjct: 182 EEGLPEKLVIKNQQFHKEREQP 203
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 15/89 (16%)
Query: 105 KKSLDVGANLFIGNLDPDVDEKLLYDTFSAFG----VIVTNPKIMRDPDTGNSRGFGFIS 160
+K+ + LF+GNL PD+ E+ + F +G V + K GFGFI
Sbjct: 16 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-----------GFGFIR 64
Query: 161 YDSFEASDAAIEAMNGQYLCNRQITVSYA 189
++ ++ A ++ L +Q+ V +A
Sbjct: 65 LETRTLAEIAKVELDNMPLRGKQLRVRFA 93
>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 = 62.0 bits (149), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 58/92 (63%), Gaps = 1/92 (1%)
Query: 101 ASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFIS 160
+S KK ++F+G+L P++ + + F+ FG I ++ ++++D TG S+G+GF+S
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRI-SDARVVKDMATGKSKGYGFVS 63
Query: 161 YDSFEASDAAIEAMNGQYLCNRQITVSYAYKK 192
+ + ++ AI+ M GQ+L RQI ++A +K
Sbjct: 64 FFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 95
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 44/76 (57%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+VG+L P++T E + F G + + V KD T +GYGFV F ++ DA+ AI+ +
Sbjct: 19 FVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMG 78
Query: 88 MIKLYGKPIRVNKASQ 103
L G+ IR N A++
Sbjct: 79 GQWLGGRQIRTNWATR 94
>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 = 61.2 bits (147), Expect = 9e-10, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 45/74 (60%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YVG L +V +++L F+ G + ++ +P D T H+G+ FVEF EDA AI +N
Sbjct: 6 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 65
Query: 88 MIKLYGKPIRVNKA 101
+L+G+ IRVN A
Sbjct: 66 ESELFGRTIRVNLA 79
Score = 51.6 bits (122), Expect = 7e-07, Method: Composition-based stats.
Identities = 30/76 (39%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
L++G L +VD+K+L+ F FG I T+ +I D +T RGF F+ ++ E + AAI+
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDI-TDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 174 MNGQYLCNRQITVSYA 189
MN L R I V+ A
Sbjct: 64 MNESELFGRTIRVNLA 79
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 60.8 bits (146), Expect = 1e-09, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 45/74 (60%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YVG L +V +++L F+ G + ++ +P D T H+G+ FVEF EDA AI +N
Sbjct: 11 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 70
Query: 88 MIKLYGKPIRVNKA 101
+L+G+ IRVN A
Sbjct: 71 ESELFGRTIRVNLA 84
Score = 51.6 bits (122), Expect = 8e-07, Method: Composition-based stats.
Identities = 30/76 (39%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
L++G L +VD+K+L+ F FG I T+ +I D +T RGF F+ ++ E + AAI+
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDI-TDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 174 MNGQYLCNRQITVSYA 189
MN L R I V+ A
Sbjct: 69 MNESELFGRTIRVNLA 84
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 60.8 bits (146), Expect = 1e-09, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 45/74 (60%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YVG L +V +++L F+ G + ++ +P D T H+G+ FVEF EDA AI +N
Sbjct: 9 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 68
Query: 88 MIKLYGKPIRVNKA 101
+L+G+ IRVN A
Sbjct: 69 ESELFGRTIRVNLA 82
Score = 51.6 bits (122), Expect = 8e-07, Method: Composition-based stats.
Identities = 30/76 (39%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
L++G L +VD+K+L+ F FG I T+ +I D +T RGF F+ ++ E + AAI+
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDI-TDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 174 MNGQYLCNRQITVSYA 189
MN L R I V+ A
Sbjct: 67 MNESELFGRTIRVNLA 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 = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 49/153 (32%), Positives = 74/153 (48%), Gaps = 7/153 (4%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQ--GYGFVEFRSEEDADYAIKV 85
+VG + +E+ L ELF Q G V + V +DR N Q G FV F + + A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 86 LNMIKLY---GKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNP 142
L+ K+ PI+ A +K + LFIG + E + FS+FG I
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQI-EEC 125
Query: 143 KIMRDPDTGNSRGFGFISYDSFEASDAAIEAMN 175
+I+R PD G SRG F+++ + + AI+A +
Sbjct: 126 RILRGPD-GLSRGCAFVTFTTRAXAQTAIKAXH 157
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 45/74 (60%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YVG L +V +++L F+ G + ++ +P D T H+G+ FVEF EDA AI +N
Sbjct: 67 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 126
Query: 88 MIKLYGKPIRVNKA 101
+L+G+ IRVN A
Sbjct: 127 ESELFGRTIRVNLA 140
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
L++G L +VD+K+L+ F FG I T+ +I D +T RGF F+ ++ E + AAI+
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDI-TDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 174 MNGQYLCNRQITVSYA 189
MN L R I V+ A
Sbjct: 125 MNESELFGRTIRVNLA 140
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/91 (36%), Positives = 54/91 (59%), Gaps = 6/91 (6%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
NL++ NLD +D++ L FS FG I T+ K+M + G S+GFGF+ + S E + A+
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTI-TSAKVMMEG--GRSKGFGFVCFSSPEEATKAVT 73
Query: 173 AMNGQYLCNRQITVSYAYKKDTKGERHGTPA 203
MNG+ + + + V+ A +K+ ER P+
Sbjct: 74 EMNGRIVATKPLYVALAQRKE---ERQSGPS 101
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 2/86 (2%)
Query: 21 RNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDAD 80
R Q YV NLD + +E L + F G + + V + +G+GFV F S E+A
Sbjct: 12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEAT 69
Query: 81 YAIKVLNMIKLYGKPIRVNKASQDKK 106
A+ +N + KP+ V A + ++
Sbjct: 70 KAVTEMNGRIVATKPLYVALAQRKEE 95
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 57/92 (61%), Gaps = 1/92 (1%)
Query: 101 ASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFIS 160
+S KK ++F+G+L P++ + + F+ FG I ++ ++++D TG S+G+GF+S
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKI-SDARVVKDMATGKSKGYGFVS 63
Query: 161 YDSFEASDAAIEAMNGQYLCNRQITVSYAYKK 192
+ + ++ AI M GQ+L RQI ++A +K
Sbjct: 64 FYNKLDAENAIVHMGGQWLGGRQIRTNWATRK 95
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 43/76 (56%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+VG+L P++T E + F G + + V KD T +GYGFV F ++ DA+ AI +
Sbjct: 19 FVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMG 78
Query: 88 MIKLYGKPIRVNKASQ 103
L G+ IR N A++
Sbjct: 79 GQWLGGRQIRTNWATR 94
>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 = 59.7 bits (143), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 46/173 (26%), Positives = 85/173 (49%), Gaps = 20/173 (11%)
Query: 28 YVGNLDPQVTEELLWELF---------VQA--GPVVNVYVPKDRVTNLHQGYGFVEFRSE 76
YVGN+ +TEE + + F QA PV+ V + +D+ + F+EFRS
Sbjct: 10 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK------NFAFLEFRSV 63
Query: 77 EDADYAIKVLNMIKLYGKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFG 136
++ A+ + I G+ +++ + D + L LFIG L +++ + + ++FG
Sbjct: 64 DETTQAM-AFDGIIFQGQSLKIRR-PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFG 121
Query: 137 VIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQITVSYA 189
+ +++D TG S+G+ F Y +D AI +NG L ++++ V A
Sbjct: 122 PLKAF-NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 173
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++G L + ++ + EL GP+ + KD T L +GY F E+ D AI LN
Sbjct: 100 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 159
Query: 88 MIKLYGKPIRVNKAS 102
++L K + V +AS
Sbjct: 160 GMQLGDKKLLVQRAS 174
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 58.9 bits (141), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 46/173 (26%), Positives = 85/173 (49%), Gaps = 20/173 (11%)
Query: 28 YVGNLDPQVTEELLWELF---------VQA--GPVVNVYVPKDRVTNLHQGYGFVEFRSE 76
YVGN+ +TEE + + F QA PV+ V + +D+ + F+EFRS
Sbjct: 8 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK------NFAFLEFRSV 61
Query: 77 EDADYAIKVLNMIKLYGKPIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFG 136
++ A+ + I G+ +++ + D + L LFIG L +++ + + ++FG
Sbjct: 62 DETTQAM-AFDGIIFQGQSLKIRR-PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFG 119
Query: 137 VIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQITVSYA 189
+ +++D TG S+G+ F Y +D AI +NG L ++++ V A
Sbjct: 120 PLKAF-NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++G L + ++ + EL GP+ + KD T L +GY F E+ D AI LN
Sbjct: 98 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 157
Query: 88 MIKLYGKPIRVNKAS 102
++L K + V +AS
Sbjct: 158 GMQLGDKKLLVQRAS 172
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 58.9 bits (141), Expect = 4e-09, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 45/74 (60%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YVG L +V +++L F+ G + ++ +P D T H+G+ FVEF EDA AI +N
Sbjct: 16 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 75
Query: 88 MIKLYGKPIRVNKA 101
+L+G+ IRVN A
Sbjct: 76 ESELFGRTIRVNLA 89
Score = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 30/76 (39%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
L++G L +VD+K+L+ F FG I T+ +I D +T RGF F+ ++ E + AAI+
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDI-TDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 174 MNGQYLCNRQITVSYA 189
MN L R I V+ A
Sbjct: 74 MNESELFGRTIRVNLA 89
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 58.2 bits (139), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 30/78 (38%), Positives = 49/78 (62%), Gaps = 1/78 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+G L D +E+ L FS +G I + +++D +T SRGFGF+++++ + + A+ A
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQI-SEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 174 MNGQYLCNRQITVSYAYK 191
MNG+ + RQI V A K
Sbjct: 74 MNGKSVDGRQIRVDQAGK 91
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 47/82 (57%), Gaps = 2/82 (2%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+VG L E+ L ++F + G + V V KDR T +G+GFV F + +DA A+ +N
Sbjct: 16 FVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMN 75
Query: 88 MIKLYGKPIRVNKA--SQDKKS 107
+ G+ IRV++A S D +S
Sbjct: 76 GKSVDGRQIRVDQAGKSSDNRS 97
>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 = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 52/79 (65%), Gaps = 1/79 (1%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
NLF+G+L+ +VD++ L + F F ++ +M D TG+SRG+GF+S+ S + + A++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSG-HVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 173 AMNGQYLCNRQITVSYAYK 191
+M GQ L R + +++A K
Sbjct: 62 SMQGQDLNGRPLRINWAAK 80
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 43/76 (56%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+VG+L+ V +E L F ++ +V D T +GYGFV F S++DA A+ +
Sbjct: 5 FVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ 64
Query: 88 MIKLYGKPIRVNKASQ 103
L G+P+R+N A++
Sbjct: 65 GQDLNGRPLRINWAAK 80
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 55.8 bits (133), Expect = 4e-08, Method: Composition-based stats.
Identities = 37/82 (45%), Positives = 47/82 (57%), Gaps = 2/82 (2%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YVGNL T E + ELF Q G V NV + DR T +G+GFVE + EE AI L+
Sbjct: 5 YVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKLD 63
Query: 88 MIKLYGKPIRVNKASQDKKSLD 109
G+ IRV +A+ KKSL+
Sbjct: 64 NTDFMGRTIRVTEANP-KKSLE 84
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
N+++GNL + + + FS FG + N K++ D +T +GFGF+ S+A +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVF-NVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 173 AMNGQYLCNRQITVSYAYKKDT 194
N ++ R I V+ A K +
Sbjct: 62 LDNTDFM-GRTIRVTEANPKKS 82
>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 = 55.5 bits (132), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 44/75 (58%)
Query: 25 ATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
T YVGNL TEE ++ELF ++G + + + D++ G+ FVE+ S DA+ A++
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 85 VLNMIKLYGKPIRVN 99
+N +L + IR +
Sbjct: 100 YINGTRLDDRIIRTD 114
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 5/88 (5%)
Query: 103 QDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMR--DPDTGNSRGFGFIS 160
+ +K L L++GNL E+ +Y+ FS G I KI+ D + GF F+
Sbjct: 31 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI---KKIIMGLDKMKKTACGFCFVE 87
Query: 161 YDSFEASDAAIEAMNGQYLCNRQITVSY 188
Y S ++ A+ +NG L +R I +
Sbjct: 88 YYSRADAENAMRYINGTRLDDRIIRTDW 115
>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 = 54.7 bits (130), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 53/80 (66%), Gaps = 1/80 (1%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
++F+G+L P++ + F+ FG I ++ ++++D TG S+G+GF+S+ + ++ AI+
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRI-SDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
Query: 173 AMNGQYLCNRQITVSYAYKK 192
M GQ+L RQI ++A +K
Sbjct: 67 QMGGQWLGGRQIRTNWATRK 86
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 43/76 (56%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+VG+L P++T + F G + + V KD T +GYGFV F ++ DA+ AI+ +
Sbjct: 10 FVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMG 69
Query: 88 MIKLYGKPIRVNKASQ 103
L G+ IR N A++
Sbjct: 70 GQWLGGRQIRTNWATR 85
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 54.7 bits (130), Expect = 8e-08, Method: Composition-based stats.
Identities = 28/81 (34%), Positives = 48/81 (59%), Gaps = 1/81 (1%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+ L++G+L ++ E +L F FG I N +M+D DTG S+G+GFI++ E + A+
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKI-DNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 172 EAMNGQYLCNRQITVSYAYKK 192
E +NG L R + V + ++
Sbjct: 65 EQLNGFELAGRPMRVGHVTER 85
Score = 53.9 bits (128), Expect = 1e-07, Method: Composition-based stats.
Identities = 28/76 (36%), Positives = 45/76 (59%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YVG+L +TE++L +F G + N+ + KD T +GYGF+ F E A A++ LN
Sbjct: 9 YVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLN 68
Query: 88 MIKLYGKPIRVNKASQ 103
+L G+P+RV ++
Sbjct: 69 GFELAGRPMRVGHVTE 84
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 48/84 (57%), Gaps = 1/84 (1%)
Query: 20 ERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDA 79
E + ++G L+ + E++L +F + GP+ V + KDR T+ +G+ F+ F + DA
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61
Query: 80 DYAIKVLNMIKLYGKPIRVNKASQ 103
A K +N L+GK I+V +A +
Sbjct: 62 KNAAKDMNGKSLHGKAIKVEQAKK 85
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LFIG L+ + +EK+L F G I + +++D T SRGF FI++++ + A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPI-SEVLLIKD-RTSKSRGFAFITFENPADAKNAAKD 67
Query: 174 MNGQYLCNRQITVSYAYK 191
MNG+ L + I V A K
Sbjct: 68 MNGKSLHGKAIKVEQAKK 85
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 52.8 bits (125), Expect = 3e-07, Method: Composition-based stats.
Identities = 31/77 (40%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
NL + L D+ ++ LY F A G I T +IMRD TG S G+ F+ + S S AI+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTC-RIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 173 AMNGQYLCNRQITVSYA 189
+NG + N+++ VSYA
Sbjct: 64 VLNGITVRNKRLKVSYA 80
Score = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 31/84 (36%), Positives = 46/84 (54%), Gaps = 1/84 (1%)
Query: 26 TAYVGNLDPQ-VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
T + N PQ +T+ L+ LF GP+ + +D T GY FV+F SE D+ AIK
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 85 VLNMIKLYGKPIRVNKASQDKKSL 108
VLN I + K ++V+ A +S+
Sbjct: 64 VLNGITVRNKRLKVSYARPGGESI 87
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 52.8 bits (125), Expect = 3e-07, Method: Composition-based stats.
Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
+++G++ D E+ + D S G ++ N K+M DP TG S+G+ FI + E+S +A+
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVI-NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 174 MNGQYLCNRQITVSYAYKKDTKG 196
+NG L +R + Y+ D G
Sbjct: 64 LNGYQLGSRFLKCGYSSNSDISG 86
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 43/80 (53%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
Y+G++ TEE + +L GPV+N+ + D T +GY F+EFR E + A++ LN
Sbjct: 6 YLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLN 65
Query: 88 MIKLYGKPIRVNKASQDKKS 107
+L + ++ +S S
Sbjct: 66 GYQLGSRFLKCGYSSNSDIS 85
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 52.8 bits (125), Expect = 3e-07, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 47/79 (59%), Gaps = 1/79 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
L++G+L ++ E +L F FG I + ++M D +TG S+G+GFI++ E + A+E
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRI-ESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 174 MNGQYLCNRQITVSYAYKK 192
+NG L R + V + ++
Sbjct: 88 LNGFELAGRPMKVGHVTER 106
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 44/76 (57%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YVG+L +TE++L +F G + ++ + D T +GYGF+ F E A A++ LN
Sbjct: 30 YVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLN 89
Query: 88 MIKLYGKPIRVNKASQ 103
+L G+P++V ++
Sbjct: 90 GFELAGRPMKVGHVTE 105
>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 = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
+++G++ D E+ + D S G ++ N K+M DP TG S+G+ FI + E+S +A+
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVI-NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 174 MNGQYLCNRQITVSYAYKKDTKG 196
+NG L +R + Y+ D G
Sbjct: 65 LNGYQLGSRFLKCGYSSNSDISG 87
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKV 85
Y+G++ TEE + +L GPV+N+ + D T +GY F+EFR E + A++
Sbjct: 5 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 64
Query: 86 LNMIKLYGKPIRVNKAS 102
LN +L + ++ +S
Sbjct: 65 LNGYQLGSRFLKCGYSS 81
>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 = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 30/83 (36%), Positives = 49/83 (59%), Gaps = 1/83 (1%)
Query: 111 GANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAA 170
GANLFI +L + ++ L F FG +V+ K+ D T S+ FGF+SYD+ ++ AA
Sbjct: 25 GANLFIYHLPQEFGDQDLLQMFMPFGNVVS-AKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 171 IEAMNGQYLCNRQITVSYAYKKD 193
I++MNG + +++ V K+
Sbjct: 84 IQSMNGFQIGMKRLKVQLKRSKN 106
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 47/85 (55%), Gaps = 2/85 (2%)
Query: 25 ATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
A ++ +L + ++ L ++F+ G VV+ V D+ TNL + +GFV + + A AI+
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 85 VLNMIKLYGKPIRV--NKASQDKKS 107
+N ++ K ++V ++ D KS
Sbjct: 86 SMNGFQIGMKRLKVQLKRSKNDSKS 110
>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 = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 42/73 (57%)
Query: 29 VGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLNM 88
V NL + + + L +F + G V +VY+P+DR T +G+ FV F + DA+ A+ ++
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 89 IKLYGKPIRVNKA 101
L G+ +RV A
Sbjct: 112 AVLDGRELRVQMA 124
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+L + NL L F +G V + I RD T SRGF F+ + ++ A+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGR-VGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 172 EAMNGQYLCNRQITVSYA 189
+AM+G L R++ V A
Sbjct: 107 DAMDGAVLDGRELRVQMA 124
>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 = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 47/193 (24%), Positives = 86/193 (44%), Gaps = 40/193 (20%)
Query: 28 YVGNLDPQVTEELLWELF---------VQA--GPVVNVYVPKDRVTNLHQGYGFVEFRSE 76
YVGN+ +TEE + + F QA PV+ V + +D+ + F+EFRS
Sbjct: 8 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK------NFAFLEFRSV 61
Query: 77 EDADYAIKVLNMIKLYGKPIRVNKASQDKKSL--------------------DVGANLFI 116
++ A+ + I G+ +++ + D + L D LFI
Sbjct: 62 DETTQAM-AFDGIIFQGQSLKIRR-PHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 117 GNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNG 176
G L +++ + + ++FG + +++D TG S+G+ F Y +D AI +NG
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAF-NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 178
Query: 177 QYLCNRQITVSYA 189
L ++++ V A
Sbjct: 179 MQLGDKKLLVQRA 191
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 40/80 (50%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++G L + ++ + EL GP+ + KD T L +GY F E+ D AI LN
Sbjct: 118 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 177
Query: 88 MIKLYGKPIRVNKASQDKKS 107
++L K + V +AS K+
Sbjct: 178 GMQLGDKKLLVQRASVGAKN 197
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 26/66 (39%), Positives = 41/66 (62%), Gaps = 1/66 (1%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
ANL++ L + +K + FS +G I+T+ +I+ D TG SRG GFI +D ++ AI
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITS-RILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 172 EAMNGQ 177
+ +NGQ
Sbjct: 61 KGLNGQ 66
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 2/81 (2%)
Query: 24 DATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAI 83
DA YV L ++++ + +LF Q G ++ + D+ T + +G GF+ F +A+ AI
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 84 KVLNMIKLYG--KPIRVNKAS 102
K LN K G +PI V A+
Sbjct: 61 KGLNGQKPLGAAEPITVKFAN 81
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 42/73 (57%)
Query: 29 VGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLNM 88
V NL + + + L +F + G V +VY+P+DR T +G+ FV F + DA+ A+ ++
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 89 IKLYGKPIRVNKA 101
L G+ +RV A
Sbjct: 135 AVLDGRELRVQMA 147
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 41/91 (45%), Gaps = 9/91 (9%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+L + NL L F +G V + I RD T SRGF F+ + ++ A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGR-VGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
Query: 172 EAMNGQYLCNRQITVSYAYKKDTKGERHGTP 202
+AM+G L R++ V A R+G P
Sbjct: 130 DAMDGAVLDGRELRVQMA--------RYGRP 152
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 40/67 (59%), Gaps = 2/67 (2%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
NL+I NL +DE+ L + FG +++ +I+RD +G SRG GF +S E +A I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVIST-RILRD-SSGTSRGVGFARMESTEKCEAVIG 84
Query: 173 AMNGQYL 179
NG+++
Sbjct: 85 HFNGKFI 91
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 46/76 (60%), Gaps = 1/76 (1%)
Query: 111 GANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAA 170
G NLFI +L + + L TF FG +++ K+ D T S+ FGF+S+D+ +++ A
Sbjct: 40 GCNLFIYHLPQEFTDTDLASTFLPFGNVIS-AKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 171 IEAMNGQYLCNRQITV 186
I+AMNG + +++ V
Sbjct: 99 IKAMNGFQVGTKRLKV 114
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 40/71 (56%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++ +L + T+ L F+ G V++ V D+ T+L + +GFV F + + A AIK +N
Sbjct: 44 FIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMN 103
Query: 88 MIKLYGKPIRV 98
++ K ++V
Sbjct: 104 GFQVGTKRLKV 114
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 109 DVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASD 168
DV NL + + VDE L F +G I + KI+ D +T SRG+GF+ + S ++
Sbjct: 40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPI-ESVKIVCDRETRQSRGYGFVKFQSGSSAQ 98
Query: 169 AAIEAMNGQYLCNRQITVSYA 189
AI +NG + N+++ V+ A
Sbjct: 99 QAIAGLNGFNILNKRLKVALA 119
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 31 NLDPQVTEEL-LWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLNMI 89
N P +E+ L +LF + GP+ +V + DR T +GYGFV+F+S A AI LN
Sbjct: 48 NYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGF 107
Query: 90 KLYGKPIRVNKAS 102
+ K ++V A+
Sbjct: 108 NILNKRLKVALAA 120
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 34/96 (35%), Positives = 50/96 (52%), Gaps = 4/96 (4%)
Query: 110 VGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDA 169
+G+ +F+ NLD V K L + FS GV+V I+ D D G SRG G ++++ +
Sbjct: 14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVV-RADILEDKD-GKSRGIGTVTFEQSIEAVQ 71
Query: 170 AIEAMNGQYLCNRQITVSYAYKKDTKGERHGTPAER 205
AI NGQ L +R + V + KG+ P ER
Sbjct: 72 AISMFNGQLLFDRPMHVKMDERALPKGDFF--PPER 105
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 45/87 (51%), Gaps = 4/87 (4%)
Query: 25 ATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
+T +V NLD +V + L E+F AG VV + +D+ +G G V F +A AI
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAIS 74
Query: 85 VLNMIKLYGKPIRVNKASQDKKSLDVG 111
+ N L+ +P+ V D+++L G
Sbjct: 75 MFNGQLLFDRPMHVK---MDERALPKG 98
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 47/186 (25%), Positives = 85/186 (45%), Gaps = 20/186 (10%)
Query: 15 GQHSAERNQDAT---AYVGNLDP-QVTEEL---LWELFVQAGPVVNVYVPKDRVTNLHQG 67
G H E ++ T ++GNL+P + EL + ELF + N D T ++
Sbjct: 1 GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAK-----NDLAVVDVRTGTNRK 55
Query: 68 YGFVEFRSEEDADYAIKVLNMIKLYGKPIRVNK-ASQDKKSLDVGANLFIGNLDPDVDEK 126
+G+V+F S ED + A++ L +K++G I++ K +D K + L NL ++ E
Sbjct: 56 FGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITED 114
Query: 127 LLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQITV 186
L + F +I G S+G +I + S ++ +E G + R +++
Sbjct: 115 ELKEVFE------DALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL 168
Query: 187 SYAYKK 192
Y +K
Sbjct: 169 YYTGEK 174
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 32/101 (31%), Positives = 49/101 (48%), Gaps = 7/101 (6%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
NLFIGNL+P+ L S + N + D TG +R FG++ ++S E + A+E
Sbjct: 15 NLFIGNLNPNKSVAELKVAISE--LFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE 72
Query: 173 AMNGQYLCNRQITVSYAYKKDTKGERHGTPAERILAANNPS 213
+ G + +I + +D+K R A R L A N S
Sbjct: 73 -LTGLKVFGNEIKLEKPKGRDSKKVR----AARTLLAKNLS 108
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
+++G++ D E+ + D S G ++ N K+M DP TG S+G+ FI + E+S +A+
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVI-NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 174 MNGQYLCNRQITVSYA 189
+NG L +R + Y+
Sbjct: 66 LNGYQLGSRFLKCGYS 81
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 42/77 (54%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKV 85
Y+G++ TEE + +L GPV+N+ + D T +GY F+EFR E + A++
Sbjct: 6 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 65
Query: 86 LNMIKLYGKPIRVNKAS 102
LN +L + ++ +S
Sbjct: 66 LNGYQLGSRFLKCGYSS 82
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 111 GANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAA 170
G NL + L + + L FS+ G V + K++RD G+S G+GF++Y + + ++ A
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGE-VESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 171 IEAMNGQYLCNRQITVSYA 189
I +NG L ++ I VSYA
Sbjct: 78 INTLNGLRLQSKTIKVSYA 96
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 26 TAYVGNLDPQ-VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
T + N PQ T++ L LF G V + + +D+V GYGFV + + +DA+ AI
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 85 VLNMIKLYGKPIRVNKA 101
LN ++L K I+V+ A
Sbjct: 80 TLNGLRLQSKTIKVSYA 96
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
NL + L ++ + L FS+ G V + K++RD G+S G+GF++Y + + ++ AI
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGE-VESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 172 EAMNGQYLCNRQITVSYA 189
+NG L ++ I VSYA
Sbjct: 64 NTLNGLRLQSKTIKVSYA 81
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 26 TAYVGNLDPQ-VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
T + N PQ +T++ L LF G V + + +D+V GYGFV + + +DA+ AI
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 85 VLNMIKLYGKPIRVNKA 101
LN ++L K I+V+ A
Sbjct: 65 TLNGLRLQSKTIKVSYA 81
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 32/80 (40%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 23 QDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYA 82
Q T YVGNL VTE L+ +LF Q GP + + + +N Y FVEF DA A
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAA 71
Query: 83 IKVLNMIKLYGKPIRVNKAS 102
+ +N K+ GK ++VN A+
Sbjct: 72 LAAMNGRKILGKEVKVNWAT 91
>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 = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 26/77 (33%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 23 QDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYA 82
+ T YVGNL TEE ++ELF ++G + + + D++ G+ FVE+ S DA+ A
Sbjct: 17 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTA-CGFCFVEYYSRADAENA 75
Query: 83 IKVLNMIKLYGKPIRVN 99
++ +N +L + IR +
Sbjct: 76 MRYINGTRLDDRIIRTD 92
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 42/87 (48%), Gaps = 4/87 (4%)
Query: 103 QDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSR-GFGFISY 161
+ +K L L++GNL E+ +Y+ FS G I KI+ D + GF F+ Y
Sbjct: 10 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI---KKIIMGLDKMKTACGFCFVEY 66
Query: 162 DSFEASDAAIEAMNGQYLCNRQITVSY 188
S ++ A+ +NG L +R I +
Sbjct: 67 YSRADAENAMRYINGTRLDDRIIRTDW 93
>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 = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 111 GANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAA 170
G LF+ + + E+ ++D F+ +G I N + D TG +G+ + Y++++ + AA
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEI-KNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 80
Query: 171 IEAMNGQYLCNRQITVSYAY 190
+E +NGQ L + I+V + +
Sbjct: 81 MEGLNGQDLMGQPISVDWCF 100
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 42/72 (58%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+V + + TEE + + F + G + N+++ DR T +GY VE+ + ++A A++ LN
Sbjct: 26 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 85
Query: 88 MIKLYGKPIRVN 99
L G+PI V+
Sbjct: 86 GQDLMGQPISVD 97
>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 = 48.1 bits (113), Expect = 8e-06, Method: Composition-based stats.
Identities = 27/70 (38%), Positives = 40/70 (57%), Gaps = 5/70 (7%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE- 172
+FIG L D +K L D FS FG +V + + DP TG SRGFGF+ + E+ D ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVV-DCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60
Query: 173 ---AMNGQYL 179
+NG+ +
Sbjct: 61 KEHKLNGKVI 70
Score = 37.0 bits (84), Expect = 0.020, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++G L T++ L + F + G VV+ + D +T +G+GFV F+ E D KV++
Sbjct: 3 FIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVD---KVMD 59
Query: 88 MI--KLYGKPIRVNKA 101
KL GK I +A
Sbjct: 60 QKEHKLNGKVIDPKRA 75
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 32/62 (51%)
Query: 22 NQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADY 81
+ +AT V NL E L ELF G + +Y+ KD+ T +G+ F+ F EDA
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
Query: 82 AI 83
AI
Sbjct: 73 AI 74
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 109 DVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASD 168
D A + + NL D E L + F FG I + + +D TG S+GF FIS+ E +
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSI-SRIYLAKDKTTGQSKGFAFISFHRREDAA 71
Query: 169 AAIEAMNG 176
AI ++G
Sbjct: 72 RAIAGVSG 79
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 47.4 bits (111), Expect = 1e-05, Method: Composition-based stats.
Identities = 28/82 (34%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 108 LDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEAS 167
+D NL + L ++ + F + G I + K++RD TG S G+GF++Y +
Sbjct: 1 MDSKTNLIVNYLPQNMTQDEFKSLFGSIGDI-ESCKLVRDKITGQSLGYGFVNYSDPNDA 59
Query: 168 DAAIEAMNGQYLCNRQITVSYA 189
D AI +NG L + I VSYA
Sbjct: 60 DKAINTLNGLKLQTKTIKVSYA 81
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 29/84 (34%), Positives = 44/84 (52%), Gaps = 1/84 (1%)
Query: 26 TAYVGNLDPQ-VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
T + N PQ +T++ LF G + + + +D++T GYGFV + DAD AI
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 85 VLNMIKLYGKPIRVNKASQDKKSL 108
LN +KL K I+V+ A S+
Sbjct: 65 TLNGLKLQTKTIKVSYARPSSASI 88
>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 = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+ + + E+ ++D F+ +G I N + D TG +G+ + Y++++ + AA+E
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEI-KNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 174 MNGQYLCNRQITVSYAY 190
+NGQ L + I+V + +
Sbjct: 69 LNGQDLMGQPISVDWCF 85
Score = 45.8 bits (107), Expect = 4e-05, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 42/72 (58%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+V + + TEE + + F + G + N+++ DR T +GY VE+ + ++A A++ LN
Sbjct: 11 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 70
Query: 88 MIKLYGKPIRVN 99
L G+PI V+
Sbjct: 71 GQDLMGQPISVD 82
>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 = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 6/79 (7%)
Query: 23 QDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYA 82
Q + +VGNL P +TEE + +LF + G V++ KD+ G+GF+ + A+ A
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIA 67
Query: 83 IKVLNMIKLYGKPIRVNKA 101
L+ + L GK +RV A
Sbjct: 68 KVELDNMPLRGKQLRVRFA 86
Score = 35.0 bits (79), Expect = 0.071, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 7/85 (8%)
Query: 105 KKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSF 164
+K+ + LF+GNL PD+ E+ + F +G I +D +GFGFI ++
Sbjct: 9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGK-AGEVFIHKD------KGFGFIRLETR 61
Query: 165 EASDAAIEAMNGQYLCNRQITVSYA 189
++ A ++ L +Q+ V +A
Sbjct: 62 TLAEIAKVELDNMPLRGKQLRVRFA 86
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 42/77 (54%)
Query: 25 ATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
+T YV NL +T L+ +F + G VV V + KD+ T +G F+ F ++ A +
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 85 VLNMIKLYGKPIRVNKA 101
+N +L+G+ I+ + A
Sbjct: 77 AINNKQLFGRVIKASIA 93
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+ +++ NL + LY FS +G +V IM+D DT S+G FI + +++
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVV-KVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Query: 172 EAMNGQYLCNRQITVSYA 189
A+N + L R I S A
Sbjct: 76 RAINNKQLFGRVIKASIA 93
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+ + + E+ ++D F+ +G I N + D TG +G+ + Y++++ + AA+E
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEI-KNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 174 MNGQYLCNRQITVSYAY 190
+NGQ L + I+V + +
Sbjct: 69 LNGQDLMGQPISVDWCF 85
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 42/72 (58%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+V + + TEE + + F + G + N+++ DR T +GY VE+ + ++A A++ LN
Sbjct: 11 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 70
Query: 88 MIKLYGKPIRVN 99
L G+PI V+
Sbjct: 71 GQDLMGQPISVD 82
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 45.8 bits (107), Expect = 3e-05, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+ + + E+ ++D F+ +G I N + D TG +G+ + Y++++ + AA+E
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEI-KNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 68
Query: 174 MNGQYLCNRQITVSYAY 190
+NGQ L + I+V + +
Sbjct: 69 LNGQDLMGQPISVDWCF 85
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 42/72 (58%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+V + + TEE + + F + G + N+++ DR T +GY VE+ + ++A A++ LN
Sbjct: 11 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 70
Query: 88 MIKLYGKPIRVN 99
L G+PI V+
Sbjct: 71 GQDLMGQPISVD 82
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 45.8 bits (107), Expect = 4e-05, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+ + + E+ ++D F+ +G I N + D TG +G+ + Y++++ + AA+E
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEI-KNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 70
Query: 174 MNGQYLCNRQITVSYAY 190
+NGQ L + I+V + +
Sbjct: 71 LNGQDLMGQPISVDWCF 87
Score = 44.7 bits (104), Expect = 8e-05, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 42/72 (58%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+V + + TEE + + F + G + N+++ DR T +GY VE+ + ++A A++ LN
Sbjct: 13 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 72
Query: 88 MIKLYGKPIRVN 99
L G+PI V+
Sbjct: 73 GQDLMGQPISVD 84
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 43/83 (51%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKV 85
T V NL + + + L +F + G V +VY+P++ T +G+ FV F DA A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 86 LNMIKLYGKPIRVNKASQDKKSL 108
++ +L G+ +RV A ++ L
Sbjct: 75 MDGAELDGRELRVQVARYGRRDL 97
Score = 31.6 bits (70), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 37/86 (43%), Gaps = 3/86 (3%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
L + NL L F +G V + I R+P T RGF F+ + + A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGR-VGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA 73
Query: 173 AMNGQYLCNRQITVSYAY--KKDTKG 196
AM+G L R++ V A ++D G
Sbjct: 74 AMDGAELDGRELRVQVARYGRRDLSG 99
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 1/60 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LFIG L + E+ L + + +G + T+ +MRDP + SRGFGF+++ S DAA+ A
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKL-TDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Score = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 35/70 (50%)
Query: 14 LGQHSAERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEF 73
L + E+ Q ++G L + TEE L + Q G + + V +D + +G+GFV F
Sbjct: 17 LERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76
Query: 74 RSEEDADYAI 83
S + D A+
Sbjct: 77 SSMAEVDAAM 86
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+ + + E+ ++D F+ +G I N + D TG +G+ + Y++++ + AA+E
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEI-KNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 174 MNGQYLCNRQITVSYAY 190
+NGQ L + I+V + +
Sbjct: 85 LNGQDLMGQPISVDWCF 101
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 42/72 (58%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+V + + TEE + + F + G + N+++ DR T +GY VE+ + ++A A++ LN
Sbjct: 27 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 86
Query: 88 MIKLYGKPIRVN 99
L G+PI V+
Sbjct: 87 GQDLMGQPISVD 98
>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 = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 23/47 (48%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 115 FIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISY 161
F+G L D +K L D F+ FG +V + I DP+TG SRGFGFI +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVV-DCTIKXDPNTGRSRGFGFILF 60
Score = 32.7 bits (73), Expect = 0.31, Method: Composition-based stats.
Identities = 27/90 (30%), Positives = 47/90 (52%), Gaps = 6/90 (6%)
Query: 15 GQHSAERNQDA-TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEF 73
G ++++ +DA +VG L +++ L + F + G VV+ + D T +G+GF+ F
Sbjct: 1 GINASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF 60
Query: 74 RSEEDADYAIKVLNMI--KLYGKPIRVNKA 101
+ DA KVL+ +L G+ I KA
Sbjct: 61 K---DAASVEKVLDQKEHRLDGRVIDPKKA 87
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 45.1 bits (105), Expect = 7e-05, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 4/79 (5%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+ L D E+ L ++F +I+ D +TG+S+GFGF+ ++S E + AA EA
Sbjct: 18 LFVKGLSEDTTEETLKESFDG----SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 174 MNGQYLCNRQITVSYAYKK 192
M + ++T+ +A K
Sbjct: 74 MEDGEIDGNKVTLDWAKPK 92
Score = 37.4 bits (85), Expect = 0.014, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 3/84 (3%)
Query: 18 SAERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEE 77
+A T +V L TEE L E F + V + DR T +G+GFV+F SEE
Sbjct: 9 NARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEE 65
Query: 78 DADYAIKVLNMIKLYGKPIRVNKA 101
DA A + + ++ G + ++ A
Sbjct: 66 DAKAAKEAMEDGEIDGNKVTLDWA 89
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+G L+ E + F AFG I I+R PD GNS+G F+ Y S + AAI A
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNI-EECTILRGPD-GNSKGCAFVKYSSHAEAQAAINA 75
Query: 174 MNG 176
++G
Sbjct: 76 LHG 78
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 12/101 (11%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+ NL V E++L FS FG + K+ + + FI +D + + A+E
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKL---------KDYAFIHFDERDGAVKAMEE 64
Query: 174 MNGQYLCNRQITVSYAYKKDTKGERHGTPAERILAANNPSS 214
MNG+ L I + +A D K R A+R AA+ PSS
Sbjct: 65 MNGKDLEGENIEIVFAKPPDQK--RKERKAQR-QAASGPSS 102
Score = 34.7 bits (78), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+V NL VTEE+L + F Q G + V KD Y F+ F + A A++ +N
Sbjct: 15 FVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEMN 66
Query: 88 MIKLYGKPIRV 98
L G+ I +
Sbjct: 67 GKDLEGENIEI 77
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/47 (44%), Positives = 30/47 (63%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFR 74
+VG LD T+E L F Q G VV+ + KD+ TN +G+GFV+F+
Sbjct: 20 FVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISY 161
LF+G LD ++ L FS +G +V + IM+D T SRGFGF+ +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVV-DCVIMKDKTTNQSRGFGFVKF 65
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 39/68 (57%)
Query: 32 LDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLNMIKL 91
L TE L E+F + GP+ +V + D+ + +G+ FV F + +DA A + N ++L
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 82
Query: 92 YGKPIRVN 99
G+ IRV+
Sbjct: 83 DGRRIRVS 90
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 125 EKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQI 184
E+ L + FS +G I + I+ D + SRGF F+ +++ + + A E NG L R+I
Sbjct: 29 ERDLREVFSKYGPI-ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 185 TVS 187
VS
Sbjct: 88 RVS 90
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 3/87 (3%)
Query: 16 QHSAER-NQDATAYVG--NLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVE 72
+H R N D +G L TE L E+F + GP+ +V + D+ + +G+ FV
Sbjct: 35 RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 94
Query: 73 FRSEEDADYAIKVLNMIKLYGKPIRVN 99
F + +DA A + N ++L G+ IRV+
Sbjct: 95 FENVDDAKEAKERANGMELDGRRIRVD 121
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 125 EKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQI 184
E+ L + FS +G I + I+ D + SRGF F+ +++ + + A E NG L R+I
Sbjct: 60 ERDLREVFSKYGPI-ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 118
Query: 185 TVSYAYKK 192
V ++ K
Sbjct: 119 RVDFSITK 126
>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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
NL++ NL + + L F +G IV I+RD TG RG F+ Y+ E + AI
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIV-QKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 172 EAMN 175
A+N
Sbjct: 73 SALN 76
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 40/70 (57%)
Query: 110 VGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDA 169
+ A+L++G+L+P +DE + F+ G V + KI+R+ TG G+ F+ + ++
Sbjct: 8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEK 67
Query: 170 AIEAMNGQYL 179
+ +NG+ L
Sbjct: 68 CLHKINGKPL 77
Score = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 25 ATAYVGNLDPQVTEELLWELFVQAG-PVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAI 83
A+ ++G+L+P + E + F G V++V + ++R+T + GY FVEF AD A
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEF-----ADLAT 64
Query: 84 KVLNMIKLYGKPI 96
+ K+ GKP+
Sbjct: 65 AEKCLHKINGKPL 77
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 111 GANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAA 170
G LF+ ++ + E + + F +G I N + D TG S+G+ + Y++ + + AA
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEI-KNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 171 IEAMNGQYLCNRQITVSYAYKK 192
EA+NG + + I V + + K
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVK 152
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+V ++ + E+ + E F G + N+++ DR T +GY VE+ + + A A + LN
Sbjct: 76 FVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN 135
Query: 88 MIKLYGKPIRVN 99
++ G+ I+V+
Sbjct: 136 GAEIMGQTIQVD 147
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISY-DSFEASDAAI 171
+LF+G+L PDVD+ +LY+ F K++ D TG S+G+GF+ + D E A
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRALT 69
Query: 172 EAMNGQYLCNRQITVSYAYKKDTK 195
E L ++ + +S A K ++
Sbjct: 70 ECQGAVGLGSKPVRLSVAIPKASR 93
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 18 SAERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEE 77
S + + +VG+L P V + +L+E FV+ P T + +GYGFV+F E
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDEL 62
Query: 78 DADYAI-KVLNMIKLYGKPIRVNKA 101
+ A+ + + L KP+R++ A
Sbjct: 63 EQKRALTECQGAVGLGSKPVRLSVA 87
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
Y+ L P T++ L +L G +V+ D+ TN +GYGFV+F S A A+ L
Sbjct: 9 YIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALK 68
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+ L+I L P ++ L +G IV+ I+ D T +G+GF+ +DS A+ A+
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAIL-DKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 172 EAMN 175
A+
Sbjct: 65 TALK 68
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 46/178 (25%), Positives = 71/178 (39%), Gaps = 23/178 (12%)
Query: 24 DATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAI 83
DA V NL P +T++ EL G + ++ T +GYGF E+ ++ A A
Sbjct: 95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 84 KVLNMIKLYGKP-------IRVNKASQDKKSLDVGANLFIGNLDP---DVDEKLLYDTFS 133
L GKP + A Q +L L + L P DVD L S
Sbjct: 155 S-----DLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDA--LCRALS 207
Query: 134 AFGVIVTNPKIMRDP--DTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQITVSYA 189
A V +P + G +GF + Y++ E ++ A + +G L + VS+
Sbjct: 208 A----VHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
>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 = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 46/178 (25%), Positives = 71/178 (39%), Gaps = 23/178 (12%)
Query: 24 DATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAI 83
DA V NL P +T++ EL G + ++ T +GYGF E+ ++ A A
Sbjct: 93 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 152
Query: 84 KVLNMIKLYGKP-------IRVNKASQDKKSLDVGANLFIGNLDP---DVDEKLLYDTFS 133
L GKP + A Q +L L + L P DVD L S
Sbjct: 153 S-----DLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDA--LCRALS 205
Query: 134 AFGVIVTNPKIMRDP--DTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQITVSYA 189
A V +P + G +GF + Y++ E ++ A + +G L + VS+
Sbjct: 206 A----VHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 259
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++G L + ++ + EL GP+ + KD T L +GY F E+ D AI LN
Sbjct: 5 FIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 64
Query: 88 MIKLYGKPIRVNKAS 102
++L K + V +AS
Sbjct: 65 GMQLGDKKLLVQRAS 79
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LFIG L +++ + + ++FG + +++D TG S+G+ F Y +D AI
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKA-FNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 174 MNGQYLCNRQITVSYA 189
+NG L ++++ V A
Sbjct: 63 LNGMQLGDKKLLVQRA 78
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 46/178 (25%), Positives = 71/178 (39%), Gaps = 23/178 (12%)
Query: 24 DATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAI 83
DA V NL P +T++ EL G + ++ T +GYGF E+ ++ A A
Sbjct: 95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 84 KVLNMIKLYGKP-------IRVNKASQDKKSLDVGANLFIGNLDP---DVDEKLLYDTFS 133
L GKP + A Q +L L + L P DVD L S
Sbjct: 155 S-----DLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDA--LCRALS 207
Query: 134 AFGVIVTNPKIMRDP--DTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQITVSYA 189
A V +P + G +GF + Y++ E ++ A + +G L + VS+
Sbjct: 208 A----VHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 41.2 bits (95), Expect = 9e-04, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+V ++ + E+ + E F G + N+++ DR T +GY VE+ + + A A + LN
Sbjct: 30 FVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN 89
Query: 88 MIKLYGKPIRVN 99
++ G+ I+V+
Sbjct: 90 GAEIMGQTIQVD 101
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+ ++ + E + + F +G I N + D TG S+G+ + Y++ + + AA EA
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEI-KNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 174 MNGQYLCNRQITVSYAYKKDTK 195
+NG + + I V + + K K
Sbjct: 88 LNGAEIMGQTIQVDWCFVKGPK 109
>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 = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 28/50 (56%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEE 77
+VG L P EE + E F G V ++ +P D TN +G+ F+ F+ EE
Sbjct: 5 FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 54
Score = 35.4 bits (80), Expect = 0.049, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
+F+G L PD E+ + + F FG V + ++ D T RGF FI++ E +E
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGE-VESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 19/50 (38%), Positives = 28/50 (56%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEE 77
+VG L P EE + E F G V ++ +P D TN +G+ F+ F+ EE
Sbjct: 3 FVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
Score = 35.4 bits (80), Expect = 0.047, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
+F+G L PD E+ + + F FG V + ++ D T RGF FI++ E +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGE-VESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>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 = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 7/83 (8%)
Query: 26 TAYVGNLDPQVT-EEL---LWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADY 81
T Y+ N++ ++ EEL L+ LF Q G VV++ K T +G FV F+ +
Sbjct: 8 TIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKELGSSTN 64
Query: 82 AIKVLNMIKLYGKPIRVNKASQD 104
A++ L YGKP+R+ A D
Sbjct: 65 ALRQLQGFPFYGKPMRIQYAKTD 87
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 2/87 (2%)
Query: 15 GQHSAERNQDATAYVG--NLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVE 72
G + N D +G L TE L E+F + GP+ +V + D+ + +G+ FV
Sbjct: 1 GPLGSRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 60
Query: 73 FRSEEDADYAIKVLNMIKLYGKPIRVN 99
F + +DA A + N ++L G+ IRV+
Sbjct: 61 FENVDDAKEAKERANGMELDGRRIRVD 87
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 125 EKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQI 184
E+ L + FS +G I + I+ D + SRGF F+ +++ + + A E NG L R+I
Sbjct: 26 ERDLREVFSKYGPI-ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 84
Query: 185 TVSYAYKK 192
V ++ K
Sbjct: 85 RVDFSITK 92
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 27/87 (31%), Positives = 44/87 (50%), Gaps = 2/87 (2%)
Query: 15 GQHSAERNQDATAYVG--NLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVE 72
G N D +G L TE L E+F + GP+ +V + D+ + +G+ FV
Sbjct: 4 GSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 63
Query: 73 FRSEEDADYAIKVLNMIKLYGKPIRVN 99
F + +DA A + N ++L G+ IRV+
Sbjct: 64 FENVDDAKEAKERANGMELDGRRIRVD 90
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 125 EKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQI 184
E+ L + FS +G I + I+ D + SRGF F+ +++ + + A E NG L R+I
Sbjct: 29 ERDLREVFSKYGPI-ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 185 TVSYAYKK 192
V ++ K
Sbjct: 88 RVDFSITK 95
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
+F+G + + E L + F FGV VT ++ D + RGFGFI+++ ++ D A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGV-VTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN- 70
Query: 174 MNGQYLCNRQITVSYAYKKDTK 195
M+ + +++ V A +D+K
Sbjct: 71 MHFHDIMGKKVEVKRAEPRDSK 92
Score = 35.4 bits (80), Expect = 0.051, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 2/81 (2%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+VG + E L E F + G V V + D +G+GF+ F E+ D A+ ++
Sbjct: 14 FVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MH 72
Query: 88 MIKLYGKPIRVNKAS-QDKKS 107
+ GK + V +A +D KS
Sbjct: 73 FHDIMGKKVEVKRAEPRDSKS 93
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 47/92 (51%), Gaps = 9/92 (9%)
Query: 24 DATAYVGNLDPQVTEELLWELFV----QAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDA 79
+ Y+ NL P+VTE L LF + GP + + +T +G F+ F ++E A
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM----MTGRMRGQAFITFPNKEIA 80
Query: 80 DYAIKVLNMIKLYGKPIRVNKASQDKKSLDVG 111
A+ ++N KLYGK I V + ++KK G
Sbjct: 81 WQALHLVNGYKLYGK-ILVIEFGKNKKQRSSG 111
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
L++ NL P V E+ L F+ F P I TG RG FI++ + E + A+
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQE-KKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 174 MNGQYLCNRQITVSYAYKKDTK 195
+NG L + + + + K +
Sbjct: 87 VNGYKLYGKILVIEFGKNKKQR 108
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKV 85
T +VG +D ++ E + F + G V V + DR T + +GYGFV F + D D V
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYN--DVDVQKIV 67
Query: 86 LNMIKLYGKPIRVNKA 101
+ I +GK +++ A
Sbjct: 68 ESQINFHGKKLKLGPA 83
Score = 32.7 bits (73), Expect = 0.32, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISY 161
+F+G +D +DE + F+ +G V KI+ D TG S+G+GF+S+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGS-VKEVKIITD-RTGVSKGYGFVSF 57
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 111 GANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISY 161
G +FIG L ++ L + F FG V +MRDP T SRGFGF+++
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGE-VKECLVMRDPLTKRSRGFGFVTF 74
Score = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 20/53 (37%), Positives = 28/53 (52%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDAD 80
++G L Q T+E L E F Q G V V +D +T +G+GFV F + D
Sbjct: 29 FIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD 81
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFG-VIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAA 170
+ +F+ NL D K+L D F+ G V+ + K+ + G S+G G + ++S E ++ A
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM----ENGKSKGCGVVKFESPEVAERA 61
Query: 171 IEAMNGQYLCNRQITV 186
MNG L R+I V
Sbjct: 62 CRMMNGMKLSGREIDV 77
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 20/50 (40%), Positives = 28/50 (56%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEE 77
+VG L T E + F Q G V + + D+ TN H+G+GFV F SE+
Sbjct: 3 FVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
Score = 31.6 bits (70), Expect = 0.69, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDS 163
+F+G L + + + F FG V + +M D T RGFGF++++S
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGK-VDDAMLMFDKTTNRHRGFGFVTFES 50
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 5/74 (6%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFG-VIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
+F+ NL D K+L D F+ G V+ + K+ + G S+G G + ++S E ++ A
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKM----ENGKSKGCGVVKFESPEVAERACR 66
Query: 173 AMNGQYLCNRQITV 186
MNG L R+I V
Sbjct: 67 MMNGMKLSGREIDV 80
>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 = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKV 85
T +VG +D ++ E + F + G V V + DR T + +GYGFV F + D D V
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYN--DVDVQKIV 67
Query: 86 LNMIKLYGKPIRVNKA 101
+ I +GK +++ A
Sbjct: 68 ESQINFHGKKLKLGPA 83
Score = 32.7 bits (73), Expect = 0.37, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISY 161
+F+G +D +DE + F+ +G V KI+ D TG S+G+GF+S+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGS-VKEVKIITD-RTGVSKGYGFVSF 57
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKV 85
T +VG +D ++ E + F + G V V + DR T + +GYGFV F + D D V
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYN--DVDVQKIV 68
Query: 86 LNMIKLYGKPIRVNKA 101
+ I +GK +++ A
Sbjct: 69 ESQINFHGKKLKLGPA 84
Score = 32.3 bits (72), Expect = 0.42, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISY 161
+F+G +D +DE + F+ +G V KI+ D TG S+G+GF+S+
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGS-VKEVKIITD-RTGVSKGYGFVSF 58
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISY 161
+FIG L ++ L + F FG V +MRDP T SRGFGF+++
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGE-VKECLVMRDPLTKRSRGFGFVTF 49
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 20/53 (37%), Positives = 28/53 (52%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDAD 80
++G L Q T+E L E F Q G V V +D +T +G+GFV F + D
Sbjct: 4 FIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVD 56
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+G L+ E+ + F FGVI ++R PD G+S+G F+ + S + AAI A
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVI-DECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIHA 75
Query: 174 MNG 176
++G
Sbjct: 76 LHG 78
>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 = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 52/202 (25%), Positives = 78/202 (38%), Gaps = 46/202 (22%)
Query: 24 DATAYVGNLDPQ-VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYA 82
++ V NL+P+ VT + L+ LF G V V + ++ N V+ A A
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLA 88
Query: 83 IKVLNMIKLYGKPIRVN----------KASQDKKSL--DVG------------------- 111
+ LN KL+GKPIR+ + Q+ + L D G
Sbjct: 89 MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 148
Query: 112 ---ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSF-EAS 167
A L + N+ P V E+ L FS+ G +V K + R I S EA
Sbjct: 149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAV 203
Query: 168 DAAIEAMNGQYLCNRQITVSYA 189
A I+ N N + VS++
Sbjct: 204 QALIDLHNHDLGENHHLRVSFS 225
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 9/84 (10%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
++GNL + TE+ + LF Q G V+ + K+ YGFV + A+ AI+ L+
Sbjct: 12 FIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRNLH 63
Query: 88 MIKLYGKPIRVNKASQDKKSLDVG 111
KL+G I V +AS++K G
Sbjct: 64 HYKLHGVNINV-EASKNKSKASSG 86
>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 = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 49/98 (50%), Gaps = 9/98 (9%)
Query: 95 PIRVNKASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSR 154
P R + + ++++ G L++ D+ LL FS FG I+ + DP R
Sbjct: 23 PFRRSDSFPERRAPRKGNTLYV--YGEDMTPTLLRGAFSPFGNII---DLSMDP----PR 73
Query: 155 GFGFISYDSFEASDAAIEAMNGQYLCNRQITVSYAYKK 192
F++Y+ E++D A+ +NG + + Q+ V+ A K+
Sbjct: 74 NCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ 111
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 24 DATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAI 83
D YVGNL + L F GP+ +V+V ++ G+ FVEF DA A+
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAV 127
Query: 84 KVLNMIKLYGKPIRVNKASQDKK 106
+ L+ L G +RV ++ +K+
Sbjct: 128 RELDGRTLCGCRVRVELSNGEKR 150
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 23 QDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYA 82
+ T + NL TEE L E+F +A + VP+++ +GY F+EF S EDA A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEKA---TFIKVPQNQ-NGKSKGYAFIEFASFEDAKEA 69
Query: 83 IKVLNMIKLYGKPIRV 98
+ N ++ G+ IR+
Sbjct: 70 LNSCNKREIEGRAIRL 85
Score = 28.5 bits (62), Expect = 6.5, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 44/89 (49%), Gaps = 12/89 (13%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
L + NL E+ L + F I K+ ++ + G S+G+ FI + SFE A EA
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFI----KVPQNQN-GKSKGYAFIEFASFE---DAKEA 69
Query: 174 MNGQYLCNRQITVSYAYKKDTKGERHGTP 202
+N CN++ A + + +G R G+P
Sbjct: 70 LNS---CNKREIEGRAIRLELQGPR-GSP 94
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 44/70 (62%), Gaps = 1/70 (1%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRV-TNLHQGYGFVEFRSEEDADYAIKVL 86
++G L VT++ + E+F G + + +P +R+ +L +GY +VEF + ++A+ A+K +
Sbjct: 8 HIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHM 67
Query: 87 NMIKLYGKPI 96
+ ++ G+ I
Sbjct: 68 DGGQIDGQEI 77
Score = 28.1 bits (61), Expect = 8.0, Method: Composition-based stats.
Identities = 17/74 (22%), Positives = 40/74 (54%), Gaps = 4/74 (5%)
Query: 116 IGNLDPDVDEKLLYDTFSAFGVI--VTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
IG L +V + + + FS +G I + P P S+G+ ++ +++ + ++ A++
Sbjct: 9 IGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHL--SKGYAYVEFENPDEAEKALKH 66
Query: 174 MNGQYLCNRQITVS 187
M+G + ++IT +
Sbjct: 67 MDGGQIDGQEITAT 80
>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 = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 44/89 (49%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVT-EEL---LWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ +EL L+ +F Q G ++++ V + +G FV F+
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM---RGQAFVIFKE 61
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ + Y KP+R+ A D
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYAKTD 90
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 24 DATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAI 83
D YVGNL + L F GP+ +V+V ++ G+ FVEF DA A+
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAV 127
Query: 84 KVLNMIKLYGKPIRVNKASQDKK 106
+ L+ L G +RV ++ +K+
Sbjct: 128 RDLDGRTLCGCRVRVELSNGEKR 150
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 31/127 (24%), Positives = 56/127 (44%), Gaps = 8/127 (6%)
Query: 64 LHQGYGFVEFRSEEDADYAIKVLNMIKLYGKPIRVNK-ASQDKKSLDVGANLFIGNLDPD 122
+ + +G+V+F S ED + A++ L +K++G I++ K +D K L NL
Sbjct: 46 MTRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYK 104
Query: 123 VDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNR 182
V + L + F I K G S+G +I + + ++ E G + R
Sbjct: 105 VTQDELKEVFEDAAEIRLVSK------DGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGR 158
Query: 183 QITVSYA 189
I++ Y
Sbjct: 159 SISLYYT 165
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 31/100 (31%), Positives = 48/100 (48%), Gaps = 6/100 (6%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
NLF+GNL+ + L S V N + D G +R FG++ ++S E + A+E
Sbjct: 9 NLFVGNLNFNKSAPELKTGIS--DVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALE 66
Query: 173 AMNGQYLCNRQITVSYAYKKDTKGERHGTPAERILAANNP 212
+ G + +I + KD+K ER A +LA N P
Sbjct: 67 -LTGLKVFGNEIKLEKPKGKDSKKERD---ARTLLAKNLP 102
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 15 GQHSAERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFR 74
G+ S + T NL +VT++ L E+F A + V KD +G ++EF+
Sbjct: 84 GKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIR--LVSKD---GKSKGIAYIEFK 138
Query: 75 SEEDADYAIKVLNMIKLYGKPIRV 98
+E DA+ + ++ G+ I +
Sbjct: 139 TEADAEKTFEEKQGTEIDGRSISL 162
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+VGN+ P T + L F + GPV+ + KD Y FV EDA AI+ L+
Sbjct: 14 HVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLD 65
Query: 88 MIKLYGKPIRVNKAS 102
+ GK + V ++
Sbjct: 66 NTEFQGKRMHVQLST 80
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 38.1 bits (87), Expect = 0.009, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 29 VGNLDPQVTEELLWELFVQAGPVVNVYVPKDRV-TNLHQGYGFVEFRSEEDADYAIKVL- 86
V N+ Q + + ELF G + V +PK T H+G+GFV+F +++DA A L
Sbjct: 20 VRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALC 79
Query: 87 NMIKLYGK 94
+ LYG+
Sbjct: 80 HSTHLYGR 87
Score = 31.6 bits (70), Expect = 0.84, Method: Composition-based stats.
Identities = 18/79 (22%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAI 171
+ + + N+ +++ + + FS FG + T + TG RGFGF+ + + + + A
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Query: 172 EAM-NGQYLCNRQITVSYA 189
A+ + +L R++ + +A
Sbjct: 76 NALCHSTHLYGRRLVLEWA 94
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 109 DVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASD 168
+V L+I NL + + +YD F +G I + +R +T +RG ++ Y+ +
Sbjct: 10 EVNRILYIRNLPYKITAEEMYDIFGKYGPI----RQIRVGNTPETRGTAYVVYEDIFDAK 65
Query: 169 AAIEAMNGQYLCNRQITVSY 188
A + ++G +CNR + V Y
Sbjct: 66 NACDHLSGFNVCNRYLVVLY 85
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 37.7 bits (86), Expect = 0.012, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 48/93 (51%), Gaps = 10/93 (10%)
Query: 109 DVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASD 168
+V L+I NL + + +YD F +G I + +R +T +RG ++ Y+ +
Sbjct: 16 EVNRILYIRNLPYKITAEEMYDIFGKYGPI----RQIRVGNTPETRGTAYVVYEDIFDAK 71
Query: 169 AAIEAMNGQYLCNRQITVSY-----AYKK-DTK 195
A + ++G +CNR + V Y A++K DTK
Sbjct: 72 NACDHLSGFNVCNRYLVVLYYNANRAFQKMDTK 104
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 51/202 (25%), Positives = 75/202 (37%), Gaps = 46/202 (22%)
Query: 24 DATAYVGNLDPQ-VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYA 82
++ V NL+P+ VT + L+ LF G V V + ++ N V+ A A
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLA 57
Query: 83 IKVLNMIKLYGKPIRVNKASQDKKSL------------DVG------------------- 111
+ LN KL+GKPIR+ + L D G
Sbjct: 58 MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117
Query: 112 ---ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSF-EAS 167
A L + N+ P V E+ L FS+ G +V K + R I S EA
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAV 172
Query: 168 DAAIEAMNGQYLCNRQITVSYA 189
A I+ N N + VS++
Sbjct: 173 QALIDLHNHDLGENHHLRVSFS 194
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPK-------IMRDPDTGNSRGFGFISYDSFEA 166
+F+ L +V + + D F G+I TN K + D +TG +G +S+D +
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 167 SDAAIEAMNGQYLCNRQITVSYAYKK 192
+ AAI+ +G+ I VS+A ++
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRR 95
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 12/88 (13%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAG----------PVVNVYVPKDRVTNLHQGYGFVEFRS 75
T +V L VT E + + F Q G P++N+Y DR T +G V F
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYT--DRETGKLKGEATVSFDD 66
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQ 103
A AI + + G PI+V+ A++
Sbjct: 67 PPSAKAAIDWFDGKEFSGNPIKVSFATR 94
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 44/89 (49%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVT-EEL---LWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ +EL L+ +F Q G ++++ V + +G FV F+
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM---RGQAFVIFKE 61
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ + Y KP+R+ A D
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYAKTD 90
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 122 DVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCN 181
D+ LL FS FG I+ + DP R F++Y+ E++D A+ +NG + +
Sbjct: 24 DMTPTLLRGAFSPFGNII---DLSMDP----PRNCAFVTYEKMESADQAVAELNGTQVES 76
Query: 182 RQITVSYAYKK 192
Q+ V+ A K+
Sbjct: 77 VQLKVNIARKQ 87
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 37.0 bits (84), Expect = 0.018, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 44/89 (49%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVT-EEL---LWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ +EL L+ +F Q G ++++ V + +G FV F+
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM---RGQAFVIFKE 60
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ + Y KP+R+ A D
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAKTD 89
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPK-------IMRDPDTGNSRGFGFISYDSFEA 166
+F+ L +V + + D F G+I TN K + D +TG +G +S+D +
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 75
Query: 167 SDAAIEAMNGQYLCNRQITVSYA 189
+ AAI+ +G+ I VS+A
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFA 98
>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 = 0.024, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 43/88 (48%), Gaps = 4/88 (4%)
Query: 18 SAERNQDATA-YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSE 76
S ++ DA ++G + + E+ L LF + G + + V KDR T +H+G F+ +
Sbjct: 6 SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCER 65
Query: 77 EDADYAIKVLNMIKL---YGKPIRVNKA 101
E A A L+ K +PI+V A
Sbjct: 66 ESALKAQSALHEQKTLPGMNRPIQVKPA 93
Score = 35.4 bits (80), Expect = 0.057, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LFIG + ++DEK L F FG I +++D TG +G F++Y E++ A A
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIY-ELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 174 MNGQYLC---NRQITVSYA 189
++ Q NR I V A
Sbjct: 75 LHEQKTLPGMNRPIQVKPA 93
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 36.6 bits (83), Expect = 0.026, Method: Composition-based stats.
Identities = 27/93 (29%), Positives = 47/93 (50%), Gaps = 10/93 (10%)
Query: 109 DVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASD 168
+V L I NL + + +YD F +G I + +R +T +RG ++ Y+ +
Sbjct: 16 EVNRILMIRNLPYKITAEEMYDIFGKYGPI----RQIRVGNTPETRGTAYVVYEDIFDAK 71
Query: 169 AAIEAMNGQYLCNRQITVSY-----AYKK-DTK 195
A + ++G +CNR + V Y A++K DTK
Sbjct: 72 NACDHLSGFNVCNRYLVVLYYNANRAFQKMDTK 104
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 36.2 bits (82), Expect = 0.035, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 101 ASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFIS 160
+S K+++ ++L + L E+ L + FS FG ++ ++ +D TG+S+GFGF+
Sbjct: 5 SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLM-VQVKKDLKTGHSKGFGFVR 63
Query: 161 YDSFE 165
+ +E
Sbjct: 64 FTEYE 68
Score = 31.6 bits (70), Expect = 0.67, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 23/43 (53%)
Query: 35 QVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEE 77
+ TE+ L E F G V+ V V KD T +G+GFV F E
Sbjct: 26 KTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
>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 = 35.8 bits (81), Expect = 0.044, Method: Composition-based stats.
Identities = 21/49 (42%), Positives = 27/49 (55%)
Query: 36 VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
V ++ L LF +AG VVN+ P D T +G+ FVE S DA IK
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 35.8 bits (81), Expect = 0.045, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 47/90 (52%), Gaps = 4/90 (4%)
Query: 21 RNQDATA-YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDA 79
++ DA +VG + + E+ L LF + G + + V KDR+T LH+G F+ + + + A
Sbjct: 11 KDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSA 70
Query: 80 DYAIKVLNMIKL---YGKPIRVNKASQDKK 106
A L+ K +PI+V A+ + +
Sbjct: 71 LKAQSALHEQKTLPGMNRPIQVKPAASEGR 100
Score = 29.6 bits (65), Expect = 3.3, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+G + +DE+ L F FG I +++D TG +G F++Y + +++ A A
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIY-ELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 174 MNGQ 177
++ Q
Sbjct: 77 LHEQ 80
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 35.4 bits (80), Expect = 0.048, Method: Composition-based stats.
Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 7/89 (7%)
Query: 111 GANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASD-- 168
G +FI NL D +E+ L + FG + +++ PDT +S+G F + + EA+
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDL-KYVRVVLHPDTEHSKGCAFAQFMTQEAAQKC 73
Query: 169 ---AAIEAMNGQY-LCNRQITVSYAYKKD 193
A++EA G L RQ+ V A +D
Sbjct: 74 LAAASLEAEGGGLKLDGRQLKVDLAVTRD 102
>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 = 0.049, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 36/74 (48%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKV 85
T +V ++ TE L F GP+ +++ + + +GY F+E+ E D A K
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 86 LNMIKLYGKPIRVN 99
+ K+ G+ + V+
Sbjct: 164 ADGKKIDGRRVLVD 177
Score = 34.7 bits (78), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 1/88 (1%)
Query: 109 DVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASD 168
D LF+ ++ D E L F +G I ++ +G RG+ FI Y+
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPI-KRIHMVYSKRSGKPRGYAFIEYEHERDMH 158
Query: 169 AAIEAMNGQYLCNRQITVSYAYKKDTKG 196
+A + +G+ + R++ V + KG
Sbjct: 159 SAYKHADGKKIDGRRVLVDVERGRTVKG 186
>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 = 35.4 bits (80), Expect = 0.051, Method: Composition-based stats.
Identities = 21/49 (42%), Positives = 27/49 (55%)
Query: 36 VTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
V ++ L LF +AG VVN+ P D T +G+ FVE S DA IK
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 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 = 0.053, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 1/88 (1%)
Query: 109 DVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASD 168
D LF+ ++ D E L F +G I ++ +G RG+ FI Y+
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEVYGPI-KRIHMVYSKRSGKPRGYAFIEYEHERDMH 158
Query: 169 AAIEAMNGQYLCNRQITVSYAYKKDTKG 196
+A + +G+ + R++ V + KG
Sbjct: 159 SAYKHADGKKIDGRRVLVDVERGRTVKG 186
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 36/74 (48%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKV 85
T +V ++ TE L F GP+ +++ + + +GY F+E+ E D A K
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 86 LNMIKLYGKPIRVN 99
+ K+ G+ + V+
Sbjct: 164 ADGKKIDGRRVLVD 177
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 35.4 bits (80), Expect = 0.054, Method: Composition-based stats.
Identities = 23/86 (26%), Positives = 47/86 (54%), Gaps = 2/86 (2%)
Query: 17 HSAERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSE 76
++ ++Q +V N+ + + L ++F Q G +++V + + + +G+GFV F +
Sbjct: 22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENS 79
Query: 77 EDADYAIKVLNMIKLYGKPIRVNKAS 102
DAD A + L+ + G+ I VN A+
Sbjct: 80 ADADRAREKLHGTVVEGRKIEVNNAT 105
Score = 32.0 bits (71), Expect = 0.55, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 120 DPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYL 179
DPD L F FG I+ I + S+GFGF+++++ +D A E ++G +
Sbjct: 43 DPD-----LRQMFGQFGKILDVEIIFNER---GSKGFGFVTFENSADADRAREKLHGTVV 94
Query: 180 CNRQITVSYA 189
R+I V+ A
Sbjct: 95 EGRKIEVNNA 104
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 35.0 bits (79), Expect = 0.068, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
NLFIGNL+P+ L S + N + D TG +R FG++ ++S E + A+E
Sbjct: 19 NLFIGNLNPNKSVAELKVAISE--LFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE 76
Score = 32.0 bits (71), Expect = 0.54, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 10/77 (12%)
Query: 28 YVGNLDP-QVTEEL---LWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAI 83
++GNL+P + EL + ELF + N D T ++ +G+V+F S ED + A+
Sbjct: 21 FIGNLNPNKSVAELKVAISELFAK-----NDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 75
Query: 84 KVLNMIKLYGKPIRVNK 100
+ L +K++G I++ K
Sbjct: 76 E-LTGLKVFGNEIKLEK 91
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 35.0 bits (79), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 7/86 (8%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPK-------IMRDPDTGNSRGFGFISYDSFEA 166
+++ L+ V L D F GV+ N + I D +TG +G +SY+
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 167 SDAAIEAMNGQYLCNRQITVSYAYKK 192
+ AA+E +G+ ++ VS A KK
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 35.0 bits (79), Expect = 0.078, Method: Composition-based stats.
Identities = 26/93 (27%), Positives = 48/93 (51%), Gaps = 10/93 (10%)
Query: 109 DVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASD 168
+V L+I NL + + +YD F +G I + +R +T +RG ++ Y+ +
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPI----RQIRVGNTPETRGTAYVVYEDIFDAK 61
Query: 169 AAIEAMNGQYLCNRQITVSY-----AYKK-DTK 195
A++ ++G + NR + V Y A++K DTK
Sbjct: 62 NAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTK 94
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 34.7 bits (78), Expect = 0.087, Method: Composition-based stats.
Identities = 31/81 (38%), Positives = 37/81 (45%), Gaps = 7/81 (8%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YV NL +EE++ + F P V K R Y FV F + EDA A+K LN
Sbjct: 19 YVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR------DYAFVHFSNREDAVEAMKALN 72
Query: 88 MIKLYGKPIRVNKASQ-DKKS 107
L G PI V A DK S
Sbjct: 73 GKVLDGSPIEVTLAKPVDKDS 93
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 34.7 bits (78), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 9/79 (11%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
L++G L P+ L F FG I T + D F +I Y+S +A+ AA
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS-------FAYIQYESLDAAQAACA 71
Query: 173 AMNGQYLC--NRQITVSYA 189
M G L +R++ V +A
Sbjct: 72 KMRGFPLGGPDRRLRVDFA 90
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 34.7 bits (78), Expect = 0.095, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 41/84 (48%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+V NL +EE L +LF GP+ ++ P D +T +G+ FV F E A A ++
Sbjct: 12 FVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVD 71
Query: 88 MIKLYGKPIRVNKASQDKKSLDVG 111
G+ + V ++ K++ G
Sbjct: 72 GQVFQGRMLHVLPSTIKKEASQSG 95
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 34.7 bits (78), Expect = 0.097, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTN---LHQGYGFVEFRSEEDADYAIK 84
++ NL+ TEE L +F + G + + + K + L G+GFVE++ E A A+K
Sbjct: 9 FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 68
Query: 85 VLNMIKLYGKPIRVNKASQDKK 106
L + G + V + + K
Sbjct: 69 QLQGHTVDGHKLEVRISERATK 90
Score = 31.6 bits (70), Expect = 0.74, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 2/77 (2%)
Query: 112 ANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGN--SRGFGFISYDSFEASDA 169
+ LFI NL+ E+ L FS G I + + G S GFGF+ Y E +
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 170 AIEAMNGQYLCNRQITV 186
A++ + G + ++ V
Sbjct: 66 ALKQLQGHTVDGHKLEV 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 = 34.3 bits (77), Expect = 0.10, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVTEELLWE----LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ ++ L + +F + G ++++ V + +G FV F+
Sbjct: 1 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKE 57
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ + Y KP+R+ A D
Sbjct: 58 VSSATNALRSMQGFPFYDKPMRIQYAKTD 86
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
Y+GNL P VT + L +LF + +P L GY FV++ + A AI+ L+
Sbjct: 12 YIGNLSPAVTADDLRQLF------GDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLS 65
Query: 88 -MIKLYGKPIRVNKASQDK 105
++L+GK + V+ + K
Sbjct: 66 GKVELHGKIMEVDYSVSKK 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 = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVTEELLWE----LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ ++ L + +F + G ++++ V + +G FV F+
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKE 61
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ + Y KP+R+ A D
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYAKTD 90
>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 = 34.3 bits (77), Expect = 0.13, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVTEELLWE----LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ ++ L + +F + G ++++ V + +G FV F+
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKE 58
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ + Y KP+R+ A D
Sbjct: 59 VSSATNALRSMQGFPFYDKPMRIQYAKTD 87
>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 = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVTEELLWE----LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ ++ L + +F + G ++++ V + +G FV F+
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKE 60
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ + Y KP+R+ A D
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAKTD 89
>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 = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVTEELLWE----LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ ++ L + +F + G ++++ V + +G FV F+
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKE 60
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ + Y KP+R+ A D
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAKTD 89
>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 = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVTEELLWE----LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ ++ L + +F + G ++++ V + +G FV F+
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKE 60
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ + Y KP+R+ A D
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQYAKTD 89
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 46/86 (53%), Gaps = 9/86 (10%)
Query: 21 RNQDATAYVGNLDPQVTEELLWE-LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDA 79
R+ ++ ++GNL+ V ++ E +F + G +V V H+G+ FV++ +E +A
Sbjct: 12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNA 63
Query: 80 DYAIKVLNMIKLYGKPIRVNKASQDK 105
A+ + + G+ + +N A++ K
Sbjct: 64 RAAVAGEDGRMIAGQVLDINLAAEPK 89
>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 = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVTEELLWE----LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ ++ L + +F + G ++++ V + +G FV F+
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKE 61
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ + Y KP+R+ A D
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQYAKTD 90
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 29/94 (30%), Positives = 38/94 (40%), Gaps = 1/94 (1%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+VG L T+ L + F G + V DR T +GYGFV A+ A K N
Sbjct: 21 FVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN 80
Query: 88 MIKLYGKPIRVNKASQDKKSLDVGANLFIGNLDP 121
I + G+ VN A K + IG P
Sbjct: 81 PI-IDGRKANVNLAYLGAKPRSLQTGFAIGVSGP 113
Score = 32.3 bits (72), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 2/78 (2%)
Query: 113 NLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIE 172
+F+G L + L F FG I ++ D TG SRG+GF++ A++ A +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDI-EEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 173 AMNGQYLCNRQITVSYAY 190
N + R+ V+ AY
Sbjct: 78 DPN-PIIDGRKANVNLAY 94
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 33.5 bits (75), Expect = 0.18, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRG---FGFISYDSFEASDAA 170
+++GNL PD+ K + D F +G I RD D N RG F F+ ++ ++ A
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAI-------RDIDLKNRRGGPPFAFVEFEDPRDAEDA 77
Query: 171 IEAMNG 176
+ +G
Sbjct: 78 VYGRDG 83
Score = 30.0 bits (66), Expect = 2.1, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 22 NQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADY 81
N D YVGNL P + + + ++F + G + ++ + R + FVEF DA+
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAED 76
Query: 82 AI 83
A+
Sbjct: 77 AV 78
>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 = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 26 TAYVGNLDPQVTEELLWE----LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADY 81
T Y+ NL+ ++ ++ L + +F + G ++++ V + +G FV F+ A
Sbjct: 5 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATN 61
Query: 82 AIKVLNMIKLYGKPIRVNKASQD 104
A++ + Y KP+R+ A D
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAKTD 84
>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 = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 26 TAYVGNLDPQVTEELLWE----LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADY 81
T Y+ NL+ ++ ++ L + +F + G ++++ V + +G FV F+ A
Sbjct: 6 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATN 62
Query: 82 AIKVLNMIKLYGKPIRVNKASQD 104
A++ + Y KP+R+ A D
Sbjct: 63 ALRSMQGFPFYDKPMRIQYAKTD 85
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
+V N+ + + L ++F Q G +++V + + + +G+GFV F + DAD A + L+
Sbjct: 19 HVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADADRAREKLH 76
Query: 88 MIKLYGKPIRVNKAS 102
+ G+ I VN A+
Sbjct: 77 GTVVEGRKIEVNNAT 91
Score = 31.6 bits (70), Expect = 0.72, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 120 DPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYL 179
DPD L F FG I+ I + S+GFGF+++++ +D A E ++G +
Sbjct: 29 DPD-----LRQMFGQFGKILDVEIIFNER---GSKGFGFVTFENSADADRAREKLHGTVV 80
Query: 180 CNRQITVSYA 189
R+I V+ A
Sbjct: 81 EGRKIEVNNA 90
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLN 87
YVGNL + L F GP+ V++ ++ G+ FVEF DA+ A++ L+
Sbjct: 4 YVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGLD 58
Query: 88 MIKLYGKPIRV 98
+ G +RV
Sbjct: 59 GKVICGSRVRV 69
Score = 32.3 bits (72), Expect = 0.51, Method: Composition-based stats.
Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 6/94 (6%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
+++GNL + L FS +G + T I R+P GF F+ ++ ++ A+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRT-VWIARNPP-----GFAFVEFEDPRDAEDAVRG 56
Query: 174 MNGQYLCNRQITVSYAYKKDTKGERHGTPAERIL 207
++G+ +C ++ V + + PA R L
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRSRFDRPPARRKL 90
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+ DV E L + F FG + KI+ GF F+ ++ E++ AIE
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPM-KEVKILN--------GFAFVEFEEAESAAKAIEE 57
Query: 174 MNGQYLCNRQITVSYA 189
++G+ N+ + V Y+
Sbjct: 58 VHGKSFANQPLEVVYS 73
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 33.1 bits (74), Expect = 0.25, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+ DV E L + F FG + KI+ GF F+ ++ E++ AIE
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPM-KEVKILN--------GFAFVEFEEAESAAKAIEE 84
Query: 174 MNGQYLCNRQITVSYA 189
++G+ N+ + V Y+
Sbjct: 85 VHGKSFANQPLEVVYS 100
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 25 ATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
A V NLD V++ + ELF + G + V DR + G V F DA A+K
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMK 147
Query: 85 VLNMIKLYGKPIRV 98
+ L G+P+ +
Sbjct: 148 QYKGVPLDGRPMDI 161
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 132 FSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
+ GV ++MR+ +G SRGF F+ + + + +EA
Sbjct: 22 LQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
>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 = 32.7 bits (73), Expect = 0.34, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 18 SAERNQDA---TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFR 74
SAE ++ + YVGN+D T + L F G + + + D+ + +GY ++EF
Sbjct: 27 SAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA 86
Query: 75 SEEDADYAIKVLNMIKLYGKPIRV 98
D A+ ++ G+ I+V
Sbjct: 87 ERNSVDAAV-AMDETVFRGRTIKV 109
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 101 ASQDKKSLDVGANLFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFIS 160
++++KK +D ++++GN+D + L FS+ G I I+ D +G+ +G+ +I
Sbjct: 27 SAEEKKEID-KRSVYVGNVDYGSTAQDLEAHFSSCGSI-NRITILCDKFSGHPKGYAYIE 84
Query: 161 YDSFEASDAAIEAMNGQYLCNRQITV 186
+ + DAA+ AM+ R I V
Sbjct: 85 FAERNSVDAAV-AMDETVFRGRTIKV 109
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 32.7 bits (73), Expect = 0.38, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 7/79 (8%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTN-PKIMRDPDTGNSRGFGFISYDSFEAS----- 167
+F+G L PD+DE + +F FG +V + P +G+ F+ + E+S
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE-ESSVQALI 69
Query: 168 DAAIEAMNGQYLCNRQITV 186
DA +E YLC T+
Sbjct: 70 DACLEEDGKLYLCVSSPTI 88
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 32.3 bits (72), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 29 VGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLNM 88
V NLD V++ + ELF + G + V DR + G V F + DA A+K N
Sbjct: 33 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNG 91
Query: 89 IKLYGKPIRV 98
+ L G+P+ +
Sbjct: 92 VPLDGRPMNI 101
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 32.3 bits (72), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 49/105 (46%), Gaps = 9/105 (8%)
Query: 15 GQHSAERNQDATAYVGNLDPQVTEELLWELFVQAGPVV--NVYVPKDRVTNLHQGYGFVE 72
G + N + T + NL+P T + + + NV V KD+ T L++G+ F++
Sbjct: 14 GSEPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQ 73
Query: 73 FRSEEDADYAIKVLNM----IKLYGKPIRVNKASQDKKSLDVGAN 113
+ E A +++L + + GK I V A K+ D+ +N
Sbjct: 74 LSTIEAAQL-LQILQALHPPLTIDGKTINVEFAKGSKR--DMASN 115
Score = 32.3 bits (72), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 23/104 (22%), Positives = 51/104 (49%), Gaps = 4/104 (3%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVT-NPKIMRDPDTGNSRGFGFISYDSFEASDA--A 170
+ + NL+P + + + V+ + N ++++D T +RGF FI + EA+
Sbjct: 26 IILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQI 85
Query: 171 IEAMNGQYLCNRQITVSYAYKKDTKGERHGTPAERILAANNPSS 214
++A++ + + T++ + K +K + RI AA+ S+
Sbjct: 86 LQALHPPLTIDGK-TINVEFAKGSKRDMASNEGSRISAASVAST 128
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 32.0 bits (71), Expect = 0.53, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 25 ATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDA 79
+ +VG +T E L + F Q G VV+V++PK + + FV F ++ A
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVA 61
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 32.0 bits (71), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 9/83 (10%)
Query: 24 DATAYVGNLDPQVTEELLWE-LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYA 82
++ ++GNL+ + ++ E +F + G V V H+GY FV++ +E A A
Sbjct: 27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAA 78
Query: 83 IKVLNMIKLYGKPIRVNKASQDK 105
+ N L G+ + +N A + K
Sbjct: 79 VLGENGRVLAGQTLDINMAGEPK 101
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 12/87 (13%)
Query: 104 DKKSLDVGANLFIGNLDPDVDEKLLYDT-FSAFGVIVTNPKIMRDPDTGNSRGFGFISYD 162
D KS++ + +FIGNL+ + +K +T FS +G R +G+ F+ Y
Sbjct: 22 DPKSIN--SRVFIGNLNTALVKKSDVETIFSKYG---------RVAGCSVHKGYAFVQYS 70
Query: 163 SFEASDAAIEAMNGQYLCNRQITVSYA 189
+ + AA+ NG+ L + + ++ A
Sbjct: 71 NERHARAAVLGENGRVLAGQTLDINMA 97
>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 = 32.0 bits (71), Expect = 0.55, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKV 85
+ YVGN+D T E L F G V V + D+ + +G+ ++EF +E ++
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 65
Query: 86 LNMIKLYGKPIRV 98
L+ G+ I+V
Sbjct: 66 LDESLFRGRQIKV 78
>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 = 31.6 bits (70), Expect = 0.73, Method: Composition-based stats.
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKV 85
+ YVGN+D T E L F G V V + D+ + +G+ ++EF +E ++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66
Query: 86 LNMIKLYGKPIRV 98
L+ G+ I+V
Sbjct: 67 LDESLFRGRQIKV 79
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 31.6 bits (70), Expect = 0.86, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVTEELLWE----LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ ++ L + +F + G ++++ V + +G FV F+
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKX---RGQAFVIFKE 60
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ Y KP R+ A D
Sbjct: 61 VSSATNALRSXQGFPFYDKPXRIQYAKTD 89
>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 = 31.6 bits (70), Expect = 0.86, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVTEELLWE----LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ ++ L + +F + G ++++ V + +G FV F+
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKX---RGQAFVIFKE 61
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ Y KP R+ A D
Sbjct: 62 VSSATNALRSXQGFPFYDKPXRIQYAKTD 90
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 31.2 bits (69), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 26 TAYVGNLDPQ-VTEELLWELFVQAGPVVN-VYVPKDRVTNLHQGYGFVEFRSEEDADYAI 83
T + N+ P V + ++ L A VN + + KD+ T ++G+ FV+ S DA +
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70
Query: 84 KVLNM----IKLYGKPIRVNKA 101
++L +K+ GK I V+ A
Sbjct: 71 QILQSLHPPLKIDGKTIGVDFA 92
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 31.2 bits (69), Expect = 0.93, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 7/89 (7%)
Query: 20 ERNQDATAYVGNLDPQVTEELLWE----LFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRS 75
E + T Y+ NL+ ++ ++ L + +F + G ++++ V + +G FV F+
Sbjct: 2 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKX---RGQAFVIFKE 58
Query: 76 EEDADYAIKVLNMIKLYGKPIRVNKASQD 104
A A++ Y KP R+ A D
Sbjct: 59 VSSATNALRSXQGFPFYDKPXRIQYAKTD 87
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 24/91 (26%), Positives = 38/91 (41%), Gaps = 1/91 (1%)
Query: 18 SAERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEE 77
S E T + L ++ L + F G V +V + DR + +G +VEF +
Sbjct: 19 SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQ 78
Query: 78 DADYAIKVLNMIKLYGKPIRVNKASQDKKSL 108
AI + +L G PI V + +K L
Sbjct: 79 SVPLAIGLTGQ-RLLGVPIIVQASQAEKNRL 108
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
Length = 88
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQ--GYGFVEFRSEEDADYAIKV 85
+VG + +E+ L ELF Q G V + V +DR N Q G FV F + + A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 86 LNMIKL 91
L+ +K+
Sbjct: 67 LHNMKV 72
>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 = 30.8 bits (68), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 29 VGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLNM 88
V NLD V++ + ELF + G + V DR + G V F + DA A K N
Sbjct: 34 VSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQYNG 92
Query: 89 IKLYGKPIRV 98
+ L G+P +
Sbjct: 93 VPLDGRPXNI 102
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 28 YVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDA 79
+VG +TE+ L E F Q G V++V++PK + + FV F ++ A
Sbjct: 9 FVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIA 55
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 30.0 bits (66), Expect = 2.2, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+G L ++ + F FG I ++R PD G S+G F+ + + + AAI
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTI-DECTVLRGPD-GTSKGCAFVKFQTHAEAQAAINT 72
Query: 174 MN 175
++
Sbjct: 73 LH 74
>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 = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 44/97 (45%), Gaps = 2/97 (2%)
Query: 13 LLGQHSAERNQDATAYVGNLDPQVTEELLWELFVQAG--PVVNVYVPKDRVTNLHQGYGF 70
+L +S RN+ A YVG+ T++ L ++ G VV + ++R +GY
Sbjct: 44 ILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAE 103
Query: 71 VEFRSEEDADYAIKVLNMIKLYGKPIRVNKASQDKKS 107
V SE +++L L G+ + V A++ S
Sbjct: 104 VVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 29.6 bits (65), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 41/84 (48%), Gaps = 18/84 (21%)
Query: 28 YVGNLDPQVTEELLWELF---------VQA--GPVVNVYVPKDRVTNLHQGYGFVEFRSE 76
YVGN+ +TEE + + F QA PV+ V + +D+ + F+EFRS
Sbjct: 10 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK------NFAFLEFRSV 63
Query: 77 EDADYAIKVLNMIKLYGKPIRVNK 100
++ A+ + I G+ +++ +
Sbjct: 64 DETTQAM-AFDGIIFQGQSLKIRR 86
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 25 ATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
A V NLD V++ + ELF + G + V DR + G V F DA A+K
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMK 94
Query: 85 VLNMIKLYGKPIRV 98
+ L G+P+ +
Sbjct: 95 QYKGVPLDGRPMDI 108
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 9/64 (14%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
LF+ NL V E++L +FS FG + K+ + + F+ ++ A+ A++
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKL---------KDYAFVHFEDRGAAVKAMDE 68
Query: 174 MNGQ 177
MNG+
Sbjct: 69 MNGK 72
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 29.6 bits (65), Expect = 3.1, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 25 ATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIK 84
A V NLD V++ + ELF + G + V DR + G V F DA A+K
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMK 94
Query: 85 VLNMIKLYGKPIRV 98
+ L G+P+ +
Sbjct: 95 QYKGVPLDGRPMDI 108
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 44/85 (51%), Gaps = 5/85 (5%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVT-NLHQGYGFVEFRSEEDADYAIK 84
TA++GNL VTEE + E F + + V +P++ +G+G+ EF + +
Sbjct: 17 TAFLGNLPYDVTEESIKEFF-RGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLL-SAL 74
Query: 85 VLNMIKLYGKPIRVNKA--SQDKKS 107
LN L K IRV+ A +QDK S
Sbjct: 75 SLNEESLGNKRIRVDVADQAQDKDS 99
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 41/84 (48%), Gaps = 18/84 (21%)
Query: 28 YVGNLDPQVTEELLWELF---------VQA--GPVVNVYVPKDRVTNLHQGYGFVEFRSE 76
YVGN+ +TEE + + F QA PV+ V + +D+ + F+EFRS
Sbjct: 5 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK------NFAFLEFRSV 58
Query: 77 EDADYAIKVLNMIKLYGKPIRVNK 100
++ A+ + I G+ +++ +
Sbjct: 59 DETTQAM-AFDGIIFQGQSLKIRR 81
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 29.3 bits (64), Expect = 4.3, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 7/71 (9%)
Query: 21 RNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDAD 80
R D V L P + + L + +AG V V KD G G VE+ +ED +
Sbjct: 12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-------GMGMVEYLRKEDME 64
Query: 81 YAIKVLNMIKL 91
YA++ L+ K
Sbjct: 65 YALRKLDDTKF 75
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 28.9 bits (63), Expect = 5.5, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 7/63 (11%)
Query: 114 LFIGNLDPDVDEKLLYDTFSAFGVIVTNPKIMRDPDTGNSRGFGFISYDSFEASDAAIEA 173
++ G + + ++L+ TFS FG I+ +I P+ +G+ F+ + + E++ AI +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIM---EIRVFPE----KGYSFVRFSTHESAAHAIVS 80
Query: 174 MNG 176
+NG
Sbjct: 81 VNG 83
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 28.9 bits (63), Expect = 5.5, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 143 KIMRDPDTGNSRGFGFISYDSFEASDAAIEAMNGQYLCNRQITVSYA--YKKDTKGERHG 200
+++RD DT +GF ++ +D ++ A+ +G L +R + V A K+D G G
Sbjct: 45 RLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQDKSGPSSG 103
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 28.1 bits (61), Expect = 8.6, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 38 EELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEEDADYAIKVLNMIKLYGKPI 96
EE+ E+ + G V + V D + + G +V+FR EEDA+ A+ LN G+PI
Sbjct: 41 EEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI 98
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 28.1 bits (61), Expect = 9.2, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 7/82 (8%)
Query: 18 SAERNQDATAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVTNLHQGYGFVEFRSEE 77
S E T YVG L +TE L F Q G + + V + Q F++F + +
Sbjct: 6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFATRQ 59
Query: 78 DADYAI-KVLNMIKLYGKPIRV 98
A+ A K N + + G+ + V
Sbjct: 60 AAEVAAEKSFNKLIVNGRRLNV 81
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation
Initiation Factor 4b
Length = 100
Score = 27.7 bits (60), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 26 TAYVGNLDPQVTEELLWELFVQAGPVVNVYVPKDRVT-NLHQGYGFVEF 73
TA++GNL VTEE + E F + + V +P++ +G+G+ EF
Sbjct: 21 TAFLGNLPYDVTEESIKEFF-RGLNISAVRLPREPSNPERLKGFGYAEF 68
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
0.314 0.133 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,061,253
Number of Sequences: 62578
Number of extensions: 378790
Number of successful extensions: 1028
Number of sequences better than 100.0: 198
Number of HSP's better than 100.0 without gapping: 134
Number of HSP's successfully gapped in prelim test: 64
Number of HSP's that attempted gapping in prelim test: 642
Number of HSP's gapped (non-prelim): 340
length of query: 377
length of database: 14,973,337
effective HSP length: 100
effective length of query: 277
effective length of database: 8,715,537
effective search space: 2414203749
effective search space used: 2414203749
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)