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= psy4086
(305 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 116 bits (290), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 58/103 (56%), Positives = 76/103 (73%), Gaps = 6/103 (5%)
Query: 119 ALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSK 178
L+ G+ AQMA+QQEQDPTNLYI+NLPL+ E +LE++L + V+STRILRD++ TS+
Sbjct: 7 GLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSR 66
Query: 179 GVGFARLESKDKCDQMIQLFNG---STLPGSK---EPLLVKFA 215
GVGFAR+ES +KC+ +I FNG T PG EPLL KF+
Sbjct: 67 GVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFS 109
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
TNLYI L +++L NM +G +IST+ IL ++ RG GF ES A +
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTR-ILRDSSGTSRGVGFARMESTEKCEAVIG 84
Query: 119 ALQDKGI 125
K I
Sbjct: 85 HFNGKFI 91
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 101 bits (251), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 47/74 (63%), Positives = 57/74 (77%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
+ LYIRGL TTD+DL+ +C YG I+STKAILDKTTNKC+GYGFVDF+S A AV
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 119 ALQDKGIHAQMARQ 132
AL+ G+ AQMA+Q
Sbjct: 66 ALKASGVQAQMAKQ 79
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 27/65 (41%), Gaps = 1/65 (1%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTR-ILRDNNNTSKGVGFARLESKDKCDQMIQ 196
+ LYI L + DL L Y +VST+ IL N KG GF +S + +
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 197 LFNGS 201
S
Sbjct: 66 ALKAS 70
>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 = 96.7 bits (239), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 56/166 (33%), Positives = 87/166 (52%), Gaps = 8/166 (4%)
Query: 58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
+TNL + L Q+ T +L ++ S G + S K I DK GYGFV++ + A A+
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 118 KA-----LQDKGIHAQMARQQEQ--DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRIL 170
LQ K I AR + NLYI+ LP + D+E + +++ ++++R+L
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVL 121
Query: 171 RDNNN-TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
D S+GV F R + + + ++ I FNG PGS EP+ VKFA
Sbjct: 122 VDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFA 167
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 40/67 (59%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
E + NLYI GL + T KD+ +M S++G II+++ ++D+TT RG F+ F+ A
Sbjct: 84 EVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEA 143
Query: 114 LAAVKAL 120
A+ +
Sbjct: 144 EEAITSF 150
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 94.4 bits (233), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 55/166 (33%), Positives = 86/166 (51%), Gaps = 8/166 (4%)
Query: 58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
+TNL + L Q+ T +L ++ S G + S K I DK GYGFV++ + A A+
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 118 KA-----LQDKGIHAQMARQQEQ--DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRIL 170
LQ K I AR + NLYI+ LP + D+E + +++ ++++R+L
Sbjct: 62 NTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVL 121
Query: 171 RDNNN-TSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
D S+GV F R + + + ++ I FNG PGS EP+ V FA
Sbjct: 122 VDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVXFA 167
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 40/67 (59%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
E + NLYI GL + T KD+ +M S++G II+++ ++D+TT RG F+ F+ A
Sbjct: 84 EVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEA 143
Query: 114 LAAVKAL 120
A+ +
Sbjct: 144 EEAITSF 150
>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 = 90.5 bits (223), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 57/167 (34%), Positives = 87/167 (52%), Gaps = 8/167 (4%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
SKTNL + L Q+ T ++ ++ G I S K + DK T + GYGFV++ A A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 117 VKA-----LQDKGIHAQMARQQEQD--PTNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
+ LQ K I AR NLY++ LP + +LE L ++Y ++++RI
Sbjct: 61 INTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 170 LRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
L D S+GVGF R + + + ++ I+ NG G+ EP+ VKFA
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 89.7 bits (221), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 56/169 (33%), Positives = 88/169 (52%), Gaps = 8/169 (4%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
SKTNL + L Q+ T + ++ G I S K + DK T + GYGFV++ A A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 117 VKA-----LQDKGIHAQMARQQEQD--PTNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
+ LQ K I AR NLY++ LP + ++E L ++Y ++++RI
Sbjct: 63 INTLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
Query: 170 LRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
L D S+GVGF R + + + ++ I+ NG G+ EP+ VKFA++
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFANN 171
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 84.7 bits (208), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 54/167 (32%), Positives = 81/167 (48%), Gaps = 8/167 (4%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
S TNL + L QD TD++L + GPI + + + D T GY FVDF S + A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 117 VKAL-----QDKGIHAQMAR--QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
+K L ++K + AR + TNLY+ NLP + L+++ KY ++V I
Sbjct: 62 IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 170 LRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
LRD +GV F R +++ + I N G +PL V+ A
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 41/87 (47%), Gaps = 1/87 (1%)
Query: 36 ITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT 95
IT N + S P G E + TNLY+ L + TD L + +YG I+ + DK
Sbjct: 68 ITVRNKRLKVSYARP-GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL 126
Query: 96 TNKCRGYGFVDFESGGYALAAVKALQD 122
T + RG FV + A A+ AL +
Sbjct: 127 TGRPRGVAFVRYNKREEAQEAISALNN 153
>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 = 84.3 bits (207), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 54/168 (32%), Positives = 81/168 (48%), Gaps = 8/168 (4%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
S TNL + L QD TD++L + GPI + + D T GY FVDF S + A
Sbjct: 13 SNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRA 72
Query: 117 VKAL-----QDKGIHAQMAR--QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRI 169
+K L ++K + AR + TNLY+ NLP + L+++ KY ++V I
Sbjct: 73 IKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 170 LRDN-NNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD 216
LRD +GV F R +++ + I N G +PL V+ A+
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLAE 180
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 41/87 (47%), Gaps = 1/87 (1%)
Query: 36 ITTNNVQHNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT 95
IT N + S P G E + TNLY+ L + TD L + +YG I+ + DK
Sbjct: 79 ITVRNKRLKVSYARPGG-ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL 137
Query: 96 TNKCRGYGFVDFESGGYALAAVKALQD 122
T + RG FV + A A+ AL +
Sbjct: 138 TGRPRGVAFVRYNKREEAQEAISALNN 164
>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 = 62.4 bits (150), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 48/196 (24%), Positives = 87/196 (44%), Gaps = 15/196 (7%)
Query: 46 SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
+P P+ P +LY+ L D T+ L S GPI+S + D T + GY +V
Sbjct: 7 NPSAPSYP----MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62
Query: 106 DFESGGYALAAVKALQDKGIHAQMAR--QQEQDPT-------NLYIANLPLNFKECDLES 156
+F+ A A+ + I + R ++DP+ N++I NL + L
Sbjct: 63 NFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 122
Query: 157 LLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFAD 216
+ + ++S +++ D N SKG GF E+++ ++ I+ NG L ++ + +F
Sbjct: 123 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLL-NDRKVFVGRFKS 180
Query: 217 SGLKKRGAGAGGPNIY 232
++ GA Y
Sbjct: 181 RKEREAELGARAKEFY 196
>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 = 62.0 bits (149), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 39/143 (27%), Positives = 71/143 (49%), Gaps = 6/143 (4%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
++I GL DTT+ +L +YG + K + D T + RG+GF+ FE VK
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 120 ---LQDKGIHAQMAR-QQEQDPT-NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN 174
L K I + A + EQD T +++ + + + + E +++ T++ +++ D +
Sbjct: 65 QHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKD 124
Query: 175 N-TSKGVGFARLESKDKCDQMIQ 196
S+G GF +S D D++ Q
Sbjct: 125 TGQSRGFGFVTYDSADAVDRVCQ 147
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
EQ +++ G+ D K+ SQ+G II + +LDK T + RG+GFV ++S A
Sbjct: 83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS---A 139
Query: 114 LAAVKALQDKGI 125
A + Q+K I
Sbjct: 140 DAVDRVCQNKFI 151
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 62.0 bits (149), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 45/187 (24%), Positives = 82/187 (43%), Gaps = 15/187 (8%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN--KCRG 101
NG+ P P+ L +++ + + ++KDL + QYG + + D++ N + +G
Sbjct: 2 NGTLDHPDQPD-LDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG 60
Query: 102 YGFVDFESGGYALAAVKALQDK----GIH-------AQMARQQEQDPTNLYIANLPLNFK 150
FV F + AL A AL + G+H A + + L+I +
Sbjct: 61 CCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCT 120
Query: 151 ECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ-LFNGSTLPGSKEP 209
E D+ + + + + RILR + S+G F ++ I+ + T+ G P
Sbjct: 121 ENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP 180
Query: 210 LLVKFAD 216
++VKFAD
Sbjct: 181 MVVKFAD 187
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 40/90 (44%), Gaps = 4/90 (4%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT---SKGVGFARLES- 187
Q + D +++ +P + E DL L +Y V +LRD + SKG F +
Sbjct: 10 QPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR 69
Query: 188 KDKCDQMIQLFNGSTLPGSKEPLLVKFADS 217
K + L N LPG P+ +K ADS
Sbjct: 70 KAALEAQNALHNMKVLPGMHHPIQMKPADS 99
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 61.6 bits (148), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 50/80 (62%), Gaps = 1/80 (1%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQL 197
NLY++ LP + ++E L ++Y ++++RIL D S+GVGF R + + + ++ I+
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 198 FNGSTLPGSKEPLLVKFADS 217
NG G+ EP+ VKFA++
Sbjct: 63 LNGQKPLGAAEPITVKFANN 82
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 38/61 (62%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
NLY+ GL + + K++ + SQYG II+++ +LD+ T RG GF+ F+ A A+K
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 120 L 120
L
Sbjct: 63 L 63
>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 = 61.2 bits (147), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 45/171 (26%), Positives = 78/171 (45%), Gaps = 14/171 (8%)
Query: 46 SPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
+P P+ P +LY+ L D T+ L S GPI+S + D T + GY +V
Sbjct: 2 NPSAPSYP----MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 57
Query: 106 DFESGGYALAAVKALQDKGIHAQMAR--QQEQDPT-------NLYIANLPLNFKECDLES 156
+F+ A A+ + I + R ++DP+ N++I NL + L
Sbjct: 58 NFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 117
Query: 157 LLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSK 207
+ + ++S +++ D N SKG GF E+++ ++ I+ NG L K
Sbjct: 118 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRK 167
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 57.4 bits (137), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 40/170 (23%), Positives = 75/170 (44%), Gaps = 14/170 (8%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN--KCRGYGFVDFESGGYALAAVK 118
+++ + + ++KDL + QYG + + D++ N + +G FV F + AL A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 119 ALQDK----GIH-------AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVST 167
AL + G+H A + + L+I + E D+ + + + +
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 125
Query: 168 RILRDNNNTSKGVGFARLESKDKCDQMIQ-LFNGSTLPGSKEPLLVKFAD 216
RILR + S+G F ++ I+ + T+ G P++VKFAD
Sbjct: 126 RILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 4/86 (4%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT---SKGVGFARLES-KDKC 191
D +++ +P + E DL L +Y V +LRD + SKG F + K
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADS 217
+ L N LPG P+ +K ADS
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPADS 87
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 54.7 bits (130), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 73/160 (45%), Gaps = 15/160 (9%)
Query: 49 TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
+P PEQL K L+I GL+ +TTD+ L + Q+G + + D T + RG+GFV +
Sbjct: 7 SPKEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 64
Query: 109 SGGYALAAVKA----LQDKGIHAQMA--RQQEQDP------TNLYIANLPLNFKECDLES 156
+ AA+ A + + + + A R+ Q P +++ + + +E L
Sbjct: 65 TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 124
Query: 157 LLAKYVTVVSTRILRDNNNTSK-GVGFARLESKDKCDQMI 195
+Y + I+ D + K G F + D D+++
Sbjct: 125 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
>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 = 54.3 bits (129), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 73/160 (45%), Gaps = 15/160 (9%)
Query: 49 TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
+P PEQL K L+I GL+ +TTD+ L + Q+G + + D T + RG+GFV +
Sbjct: 6 SPKEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 109 SGGYALAAVKA----LQDKGIHAQMA--RQQEQDP------TNLYIANLPLNFKECDLES 156
+ AA+ A + + + + A R+ Q P +++ + + +E L
Sbjct: 64 TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 123
Query: 157 LLAKYVTVVSTRILRDNNNTSK-GVGFARLESKDKCDQMI 195
+Y + I+ D + K G F + D D+++
Sbjct: 124 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 54.3 bits (129), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 73/160 (45%), Gaps = 15/160 (9%)
Query: 49 TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
+P PEQL K L+I GL+ +TTD+ L + Q+G + + D T + RG+GFV +
Sbjct: 6 SPKEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 63
Query: 109 SGGYALAAVKA----LQDKGIHAQMA--RQQEQDP------TNLYIANLPLNFKECDLES 156
+ AA+ A + + + + A R+ Q P +++ + + +E L
Sbjct: 64 TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 123
Query: 157 LLAKYVTVVSTRILRDNNNTSK-GVGFARLESKDKCDQMI 195
+Y + I+ D + K G F + D D+++
Sbjct: 124 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 54.3 bits (129), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 73/160 (45%), Gaps = 15/160 (9%)
Query: 49 TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
+P PEQL K L+I GL+ +TTD+ L + Q+G + + D T + RG+GFV +
Sbjct: 5 SPKEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 62
Query: 109 SGGYALAAVKA----LQDKGIHAQMA--RQQEQDP------TNLYIANLPLNFKECDLES 156
+ AA+ A + + + + A R+ Q P +++ + + +E L
Sbjct: 63 TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 122
Query: 157 LLAKYVTVVSTRILRDNNNTSK-GVGFARLESKDKCDQMI 195
+Y + I+ D + K G F + D D+++
Sbjct: 123 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 54.3 bits (129), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 73/160 (45%), Gaps = 15/160 (9%)
Query: 49 TPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
+P PEQL K L+I GL+ +TTD+ L + Q+G + + D T + RG+GFV +
Sbjct: 4 SPKEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYA 61
Query: 109 SGGYALAAVKA----LQDKGIHAQMA--RQQEQDP------TNLYIANLPLNFKECDLES 156
+ AA+ A + + + + A R+ Q P +++ + + +E L
Sbjct: 62 TVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRD 121
Query: 157 LLAKYVTVVSTRILRDNNNTSK-GVGFARLESKDKCDQMI 195
+Y + I+ D + K G F + D D+++
Sbjct: 122 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQ 196
TNLY+ NLP + L+++ KY ++V ILRD +GV F R +++ + I
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 197 LFNGSTLPGSKEPLLVKFAD 216
N G +PL V+ A+
Sbjct: 74 ALNNVIPEGGSQPLSVRLAE 93
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 35/71 (49%)
Query: 52 GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
G E + TNLY+ L + TD L + +YG I+ + DK T + RG FV +
Sbjct: 7 GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 66
Query: 112 YALAAVKALQD 122
A A+ AL +
Sbjct: 67 EAQEAISALNN 77
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 43/165 (26%), Positives = 73/165 (44%), Gaps = 13/165 (7%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
LY+ L + T+ L GPI + K ++DK NK Y FV++ A A++ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTL 61
Query: 121 QDKGIHAQMAR-----QQEQ----DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILR 171
K I + + Q +Q D NL++ +L +N + L + + + +S ++
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 172 D-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
D +S+G GF S+D + G L G PL + +A
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG--RPLRINWA 164
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 35/72 (48%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
NL++ L + D+ L N + +S + D T RGYGFV F S A A+ +
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 120 LQDKGIHAQMAR 131
+Q + ++ + R
Sbjct: 149 MQGQDLNGRPLR 160
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 39/156 (25%), Positives = 71/156 (45%), Gaps = 15/156 (9%)
Query: 53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
PEQL K L+I GL+ +TTD+ L + Q+G + + D T + RG+GFV + +
Sbjct: 3 PEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60
Query: 113 ALAAVKA----LQDKGIHAQMA--RQQEQDP------TNLYIANLPLNFKECDLESLLAK 160
AA+ A + + + + A R+ Q P +++ + + +E L +
Sbjct: 61 VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 120
Query: 161 YVTVVSTRILRDNNNTSK-GVGFARLESKDKCDQMI 195
Y + I+ D + K G F + D D+++
Sbjct: 121 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 66/160 (41%), Gaps = 14/160 (8%)
Query: 71 TDKDLINMCSQYGPIISTKAILDKTTN--KCRGYGFVDFESGGYALAAVKALQDK----G 124
++KDL + QYG + + D++ N + +G FV F + AL A AL + G
Sbjct: 16 SEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNXKVLPG 75
Query: 125 IH-------AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTS 177
H A + + L+I + E D+ + + + RILR + S
Sbjct: 76 XHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLS 135
Query: 178 KGVGFARLESKDKCDQMIQLFN-GSTLPGSKEPLLVKFAD 216
+G F ++ I+ + T G P +VKFAD
Sbjct: 136 RGCAFVTFTTRAXAQTAIKAXHQAQTXEGCSSPXVVKFAD 175
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 36/86 (41%), Gaps = 4/86 (4%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT---SKGVGFARLES-KDKC 191
D ++ +P + E DL L +Y V +LRD + SKG F + K
Sbjct: 2 DAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADS 217
+ L N LPG P+ K ADS
Sbjct: 62 EAQNALHNXKVLPGXHHPIQXKPADS 87
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 51.2 bits (121), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 37/74 (50%)
Query: 47 PGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVD 106
P T PE NL + + + L + +YGPI S K + D+ T + RGYGFV
Sbjct: 31 PPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVK 90
Query: 107 FESGGYALAAVKAL 120
F+SG A A+ L
Sbjct: 91 FQSGSSAQQAIAGL 104
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 42/92 (45%), Gaps = 4/92 (4%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDKCDQMIQL 197
NL + +P E L L +Y + S +I+ D S+G GF + +S Q I
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 198 FNGSTLPGSKEPLLVKFADSGLKKRG-AGAGG 228
NG + + L V A SG ++ G AGA G
Sbjct: 104 LNGFNILNKR--LKVALAASGHQRPGIAGAVG 133
>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 = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 5/84 (5%)
Query: 52 GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
GPE NL+I L Q+ D+DL+ M +G ++S K +DK TN + +GFV +++
Sbjct: 22 GPE---GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78
Query: 112 YALAAVKALQDKGIHAQMARQQEQ 135
A AA++++ G M R + Q
Sbjct: 79 SAQAAIQSM--NGFQIGMKRLKVQ 100
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 119 ALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTS 177
L + I A ++++ + NL+I +LP F + DL + + VVS ++ D N S
Sbjct: 7 GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS 66
Query: 178 KGVGFARLESKDKCDQMIQLFNG 200
K GF ++ IQ NG
Sbjct: 67 KCFGFVSYDNPVSAQAAIQSMNG 89
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 48/84 (57%), Gaps = 5/84 (5%)
Query: 43 HNGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
+GS G P Q SKT L+++GL++DTT++ L + + + + D+ T +G+
Sbjct: 2 SSGSSG-PNARSQPSKT-LFVKGLSEDTTEETLKE---SFDGSVRARIVTDRETGSSKGF 56
Query: 103 GFVDFESGGYALAAVKALQDKGIH 126
GFVDF S A AA +A++D I
Sbjct: 57 GFVDFNSEEDAKAAKEAMEDGEID 80
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 52 GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
GPE NL+I L Q+ TD DL + +G +IS K +DK T+ + +GFV F++
Sbjct: 37 GPE---GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPD 93
Query: 112 YALAAVKAL 120
A A+KA+
Sbjct: 94 SAQVAIKAM 102
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT-SKGVGFARLESKDKCDQMIQL 197
NL+I +LP F + DL S + V+S ++ D + SK GF ++ D I+
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 198 FNG 200
NG
Sbjct: 102 MNG 104
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 40/71 (56%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ GL+ DT ++ L + S+YG I + D+ T + RG+GFV FE+ A A+ A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 121 QDKGIHAQMAR 131
K + + R
Sbjct: 75 NGKSVDGRQIR 85
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNN-NTSKGVGFARLESKDKCDQM 194
D L++ L + E LE + +KY + +++D S+G GF E+ D
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 195 IQLFNGSTLPG 205
+ NG ++ G
Sbjct: 71 MMAMNGKSVDG 81
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L+I GL ++T +K L + ++GPI I D+T+ K RG+ F+ FE+ A A K +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKDM 68
Query: 121 QDKGIHAQMAR-QQEQDPT 138
K +H + + +Q + P+
Sbjct: 69 NGKSLHGKAIKVEQAKKPS 87
Score = 30.8 bits (68), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 30/69 (43%)
Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
P L+I L E L+++ K+ + +++D + S+G F E+ +
Sbjct: 7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAK 66
Query: 197 LFNGSTLPG 205
NG +L G
Sbjct: 67 DMNGKSLHG 75
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 47.0 bits (110), Expect = 1e-05, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 37/60 (61%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
+Y+ + D T++ ++++CS GP+I+ K + D T + +GY F++F + +AV+ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
>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 = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 4/69 (5%)
Query: 52 GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
GP ++ +Y+ + D T++ ++++CS GP+I+ K + D T + +GY F++F
Sbjct: 1 GPSRV----VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 56
Query: 112 YALAAVKAL 120
+ +AV+ L
Sbjct: 57 SSASAVRNL 65
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 20/49 (40%), Positives = 33/49 (67%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
+++ GL+ +TT +D+ + Q+G + + DKTTN+ RG+GFV FES
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFES 50
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 127 AQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLE 186
+ M + + P L+++N+P F++ DL + ++ ++ I+ N SKG GF E
Sbjct: 19 SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF-NERGSKGFGFVTFE 77
Query: 187 SKDKCDQMIQLFNGSTLPGSK 207
+ D+ + +G+ + G K
Sbjct: 78 NSADADRAREKLHGTVVEGRK 98
Score = 35.0 bits (79), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 7/69 (10%)
Query: 53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
P++L +N+ R D DL M Q+G I+ + I ++ +K G+GFV FE+
Sbjct: 29 PKRLHVSNIPFR-----FRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSAD 81
Query: 113 ALAAVKALQ 121
A A + L
Sbjct: 82 ADRAREKLH 90
>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 = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 37/60 (61%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
+Y+ + D T++ ++++CS GP+I+ K + D T + +GY F++F + +AV+ L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 31/48 (64%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
L++ GL TT + L + SQYG ++ + DKTTN+ RG+GFV F+
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 44/75 (58%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
S ++++ + + T++ L ++ S+ GP++S + + D+ T K +GYGF +++ AL+A
Sbjct: 7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66
Query: 117 VKALQDKGIHAQMAR 131
++ L + + R
Sbjct: 67 MRNLNGREFSGRALR 81
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTS-KGVGFARLESKDKCDQMIQL 197
++++ N+P E L+ + ++ VVS R++ D KG GF + ++ ++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 198 FNGSTLPG 205
NG G
Sbjct: 70 LNGREFSG 77
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 53/105 (50%), Gaps = 17/105 (16%)
Query: 56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALA 115
L N++I+ L + +K L + S +G I+S K + D+ N +GYGFV FE+ A
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAER 60
Query: 116 AVKA-----LQDKGIH-----AQMARQQE-----QDPTNLYIANL 145
A++ L D+ + ++ R+ E ++ TN+YI N
Sbjct: 61 AIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNF 105
Score = 35.0 bits (79), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
N++I NL + L + + ++S +++ D N SKG GF E+++ ++ I+
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 199 NGSTLPGSK 207
NG L K
Sbjct: 66 NGMLLNDRK 74
>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 = 45.1 bits (105), Expect = 5e-05, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 31/48 (64%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
++I GL+ DTT KDL + S++G ++ LD T + RG+GFV F+
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFK 49
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 45.1 bits (105), Expect = 5e-05, Method: Composition-based stats.
Identities = 25/64 (39%), Positives = 34/64 (53%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
S TNL + L QD TD++L + GPI + + + D T GY FVDF S + A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 117 VKAL 120
+K L
Sbjct: 62 IKVL 65
Score = 30.4 bits (67), Expect = 1.4, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 3/82 (3%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQ 196
TNL + LP + + +L +L + + RI+RD S G F S+ + I+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 197 LFNGSTLPGSKEPLLVKFADSG 218
+ NG T+ + L V +A G
Sbjct: 64 VLNGITVRNKR--LKVSYARPG 83
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 29/97 (29%), Positives = 44/97 (45%), Gaps = 5/97 (5%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+GS G T +K LY+ GL ++ DK L +G I + LD T K RG+
Sbjct: 3 SGSSGMAT-----TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 57
Query: 104 FVDFESGGYALAAVKALQDKGIHAQMARQQEQDPTNL 140
FV+FE A AA+ + + + + R P +
Sbjct: 58 FVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI 94
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
P L+++N+P F++ DL + ++ ++ I+ N SKG GF E+ D+ +
Sbjct: 15 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF-NERGSKGFGFVTFENSADADRARE 73
Query: 197 LFNGSTLPGSK 207
+G+ + G K
Sbjct: 74 KLHGTVVEGRK 84
Score = 34.7 bits (78), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 7/69 (10%)
Query: 53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
P++L +N+ R D DL M Q+G I+ + I ++ +K G+GFV FE+
Sbjct: 15 PKRLHVSNIPFR-----FRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSAD 67
Query: 113 ALAAVKALQ 121
A A + L
Sbjct: 68 ADRAREKLH 76
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
L++ L E D+ L + + ILR + SKG F + S + I +
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 200 GS-TLPGSKEPLLVKFADS 217
GS T+PG+ L+VKFAD+
Sbjct: 78 GSQTMPGASSSLVVKFADT 96
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
EQ K L+I GL+ +TT++ L N Q+G + + D + + RG+GFV F S
Sbjct: 25 EQFRK--LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 114 LAAVKA 119
AA+ A
Sbjct: 83 DAAMAA 88
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+GS G P+ L + GL+ TT++DL + S+YGPI + D+ + + RG+
Sbjct: 3 SGSSGNRANPD--PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 104 FVDFES 109
FV FE+
Sbjct: 61 FVYFEN 66
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 36/67 (53%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
E + +Y+ + QD +D D+ ++ +G I S D TT K +GYGF+++E +
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180
Query: 114 LAAVKAL 120
AV ++
Sbjct: 181 QDAVSSM 187
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 31/166 (18%), Positives = 67/166 (40%), Gaps = 19/166 (11%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF---ESGGYALA 115
+ +Y+ + + + + + +GPI S D T K +G+ FV++ E+ AL
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 116 AVKALQDKGIHAQMAR---------------QQEQDPTNLYIANLPLNFKECDLESLLAK 160
+ ++ G + ++ R ++ + +Y+A++ + + D++S+
Sbjct: 89 QMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEA 148
Query: 161 YVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG 205
+ + S + RD KG GF E + N L G
Sbjct: 149 FGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGG 194
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+GS G P+ L + GL+ TT++DL + S+YGPI + D+ + + RG+
Sbjct: 3 SGSSGNRANPD--PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 104 FVDFES 109
FV FE+
Sbjct: 61 FVYFEN 66
>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 = 19/49 (38%), Positives = 31/49 (63%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
L + GL+ TT++DL + S+YGPI + D+ + + RG+ FV FE+
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 97
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 2/90 (2%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
L++ L E D+ L + + +LR + +SKG F + S + I
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 199 NGS-TLPGSKEPLLVKFADSGLKKRGAGAG 227
+GS T+PG+ L+VKFAD+ K+ G +G
Sbjct: 77 HGSQTMPGASSSLVVKFADTD-KESGPSSG 105
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
N+Y+ L T + + + SQ+G + + K I D+ T K +G+GFV+ + + A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVS-EAIAK 61
Query: 120 LQDKGIHAQMARQQEQDP 137
L + + R E +P
Sbjct: 62 LDNTDFMGRTIRVTEANP 79
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
L++ L + D+ + + T+ +LR + TSKG F + ++ + I
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 199 NGS-TLPGSKEPLLVKFADS 217
+ S TLPG+ L+VKFAD+
Sbjct: 74 HSSRTLPGASSSLVVKFADT 93
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 37/75 (49%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
SK LY+ GL ++ DK L +G I + LD T K RG+ FV+FE A AA
Sbjct: 1 SKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 60
Query: 117 VKALQDKGIHAQMAR 131
+ + + + + R
Sbjct: 61 IDNMNESELFGRTIR 75
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 36/67 (53%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
E + +Y+ + QD +D D+ ++ +G I S D TT K +GYGF+++E +
Sbjct: 106 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 165
Query: 114 LAAVKAL 120
AV ++
Sbjct: 166 QDAVSSM 172
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 31/165 (18%), Positives = 66/165 (40%), Gaps = 19/165 (11%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF---ESGGYALAA 116
+Y+ + + + + + +GPI S D T K +G+ FV++ E+ AL
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 117 VKALQDKGIHAQMAR---------------QQEQDPTNLYIANLPLNFKECDLESLLAKY 161
+ ++ G + ++ R ++ + +Y+A++ + + D++S+ +
Sbjct: 75 MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 134
Query: 162 VTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG 205
+ S + RD KG GF E + N L G
Sbjct: 135 GKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGG 179
>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 = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
+TNL + L Q+ T +L ++ S G + S K I DK GYGFV++ + A A+
Sbjct: 4 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 63
Query: 118 KA-----LQDKGIHAQMAR 131
LQ K I AR
Sbjct: 64 NTLNGLRLQSKTIKVSYAR 82
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQ 196
TNL + LP N + +L SL + V S +++RD S G GF + ++ I
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 197 LFNGSTL 203
NG L
Sbjct: 65 TLNGLRL 71
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 19/49 (38%), Positives = 31/49 (63%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
L + GL+ TT++DL + S+YGPI + D+ + + RG+ FV FE+
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
>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 = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 38/80 (47%)
Query: 52 GPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGG 111
G +K LY+ GL ++ DK L +G I + LD T K RG+ FV+FE
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 112 YALAAVKALQDKGIHAQMAR 131
A AA+ + + + + R
Sbjct: 61 DAAAAIDNMNESELFGRTIR 80
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 37/136 (27%), Positives = 63/136 (46%), Gaps = 11/136 (8%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
++ + IRGL D T++++ ++ S Y K +K +G FV +G A AA
Sbjct: 21 NRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCF---VDKYKGTAFVTLLNGEQAEAA 73
Query: 117 VKALQDKGIHAQMARQQEQDPTN--LYIANLPLNFKECDLESLLAKYVTVVSTRIL-RDN 173
+ A + + Q Q PT+ L +ANLP + + E L+ + ++ ++ +
Sbjct: 74 INAFHQSRLRERELSVQLQ-PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER 132
Query: 174 NNTSKGVGFARLESKD 189
SKG GFA KD
Sbjct: 133 TGQSKGYGFAEYMKKD 148
>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 = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 35/66 (53%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
E + +Y+ + QD +D D+ ++ +G I S D TT K +GYGF+++E +
Sbjct: 105 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSS 164
Query: 114 LAAVKA 119
AV +
Sbjct: 165 QDAVSS 170
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 31/164 (18%), Positives = 65/164 (39%), Gaps = 19/164 (11%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF---ESGGYALAAV 117
+Y+ + + + + + +GPI S D T K +G+ FV++ E+ AL
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 118 KALQDKGIHAQMAR---------------QQEQDPTNLYIANLPLNFKECDLESLLAKYV 162
++ G + ++ R ++ + +Y+A++ + + D++S+ +
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 163 TVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQLFNGSTLPG 205
+ S + RD KG GF E + N L G
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGG 178
>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 = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 37/136 (27%), Positives = 63/136 (46%), Gaps = 11/136 (8%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
++ + IRGL D T++++ ++ S Y K +K +G FV +G A AA
Sbjct: 19 NRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCF---VDKYKGTAFVTLLNGEQAEAA 71
Query: 117 VKALQDKGIHAQMARQQEQDPTN--LYIANLPLNFKECDLESLLAKYVTVVSTRIL-RDN 173
+ A + + Q Q PT+ L +ANLP + + E L+ + ++ ++ +
Sbjct: 72 INAFHQSRLRERELSVQLQ-PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER 130
Query: 174 NNTSKGVGFARLESKD 189
SKG GFA KD
Sbjct: 131 TGQSKGYGFAEYMKKD 146
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 37/75 (49%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
+K LY+ GL ++ DK L +G I + LD T K RG+ FV+FE A AA
Sbjct: 4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63
Query: 117 VKALQDKGIHAQMAR 131
+ + + + + R
Sbjct: 64 IDNMNESELFGRTIR 78
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 37/136 (27%), Positives = 63/136 (46%), Gaps = 11/136 (8%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
++ + IRGL D T++++ ++ S Y K +K +G FV +G A AA
Sbjct: 21 NRRKILIRGLPGDVTNQEVHDLLSDY----ELKYCF---VDKYKGTAFVTLLNGEQAEAA 73
Query: 117 VKALQDKGIHAQMARQQEQDPTN--LYIANLPLNFKECDLESLLAKYVTVVSTRIL-RDN 173
+ A + + Q Q PT+ L +ANLP + + E L+ + ++ ++ +
Sbjct: 74 INAFHQSRLRERELSVQLQ-PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER 132
Query: 174 NNTSKGVGFARLESKD 189
SKG GFA KD
Sbjct: 133 TGQSKGYGFAEYMKKD 148
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARLESKDKCDQMIQ 196
+ +Y++NLP + DL + +KY VV I++D + SKGV F KD +
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 197 LFNGSTLPG 205
N L G
Sbjct: 77 AINNKQLFG 85
Score = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 38/75 (50%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
SK+ +Y+ L T+ DL + S+YG ++ + DK T K +G F+ F A
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 117 VKALQDKGIHAQMAR 131
+A+ +K + ++ +
Sbjct: 75 TRAINNKQLFGRVIK 89
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 40/68 (58%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ G+ ++ T++D+ + ++YG I + LD+ T +GY V++E+ A AA++ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 121 QDKGIHAQ 128
+ + Q
Sbjct: 86 NGQDLMGQ 93
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 37/67 (55%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
E+ +Y+ GL + ++ L + Q GP+++T D+ T + +GYGFV+F S A
Sbjct: 11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 70
Query: 114 LAAVKAL 120
A+K +
Sbjct: 71 DYAIKIM 77
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 37/75 (49%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
+K LY+ GL ++ DK L +G I + LD T K RG+ FV+FE A AA
Sbjct: 62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121
Query: 117 VKALQDKGIHAQMAR 131
+ + + + + R
Sbjct: 122 IDNMNESELFGRTIR 136
>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 = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 4/86 (4%)
Query: 136 DPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT---SKGVGFARLES-KDKC 191
D +++ +P + E DL L +Y V +LRD + SKG F + K
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADS 217
+ L N LPG P+ +K ADS
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPADS 87
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTN--KCRGYGFVDFESGGYALAAVK 118
+++ + + ++KDL + QYG + + D++ N + +G FV F + AL A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 119 ALQDKGI 125
AL + +
Sbjct: 66 ALHNMKV 72
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
N++I+ L + +K L + S +G I+S K + D+ N +GYGFV FE+ A A++
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 70
Query: 120 L 120
+
Sbjct: 71 M 71
Score = 35.0 bits (79), Expect = 0.049, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
N++I NL + L + + ++S +++ D N SKG GF E+++ ++ I+
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 71
Query: 199 NGSTLPGSK 207
NG L K
Sbjct: 72 NGMLLNDRK 80
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
SKTNL + L Q+ T + ++ G I S K + DK T + GYGFV++ A A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 117 VKA-----LQDKGIHAQMAR 131
+ LQ K I AR
Sbjct: 63 INTLNGLKLQTKTIKVSYAR 82
Score = 31.6 bits (70), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 1/67 (1%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQ 196
TNL + LP N + + +SL + S +++RD S G GF + D+ I
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 197 LFNGSTL 203
NG L
Sbjct: 65 TLNGLKL 71
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 40/68 (58%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ G+ ++ T++D+ + ++YG I + LD+ T +GY V++E+ A AA++ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 121 QDKGIHAQ 128
+ + Q
Sbjct: 85 NGQDLMGQ 92
>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 = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 40/68 (58%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ G+ ++ T++D+ + ++YG I + LD+ T +GY V++E+ A AA++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 121 QDKGIHAQ 128
+ + Q
Sbjct: 70 NGQDLMGQ 77
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 45 GSPGTPTGPEQLSKTNLYIR--GLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGY 102
GS G+ +GP + + N IR L++DT + DL + +G I DKTT + +G+
Sbjct: 1 GSSGS-SGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGF 59
Query: 103 GFVDF---ESGGYALAAVKAL 120
F+ F E A+A V
Sbjct: 60 AFISFHRREDAARAIAGVSGF 80
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
TNL + L Q+ T +L ++ S G + S K I DK GYGFV++ + A A+
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 119 A-----LQDKGIHAQMAR 131
LQ K I AR
Sbjct: 80 TLNGLRLQSKTIKVSYAR 97
Score = 32.0 bits (71), Expect = 0.50, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 1/67 (1%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQ 196
TNL + LP N + +L SL + V S +++RD S G GF + ++ I
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 197 LFNGSTL 203
NG L
Sbjct: 80 TLNGLRL 86
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 40/68 (58%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ G+ ++ T++D+ + ++YG I + LD+ T +GY V++E+ A AA++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 121 QDKGIHAQ 128
+ + Q
Sbjct: 70 NGQDLMGQ 77
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 2/84 (2%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
+ +++ANL L+ + + VV IL D + S+G+G E + Q I +
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 198 FNGSTLPGSKEPLLVKFADSGLKK 221
FNG L P+ VK + L K
Sbjct: 76 FNGQLL--FDRPMHVKMDERALPK 97
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 4/65 (6%)
Query: 62 YIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKALQ 121
++ GL+ DT+ KDL + +++G ++ D T + RG+GF+ F+ A+V+ +
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDA----ASVEKVL 70
Query: 122 DKGIH 126
D+ H
Sbjct: 71 DQKEH 75
Score = 28.1 bits (61), Expect = 6.8, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 130 ARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGF 182
A + E+D ++ L + + DL+ K+ VV I D N S+G GF
Sbjct: 4 ASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGF 57
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 40/68 (58%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ G+ ++ T++D+ + ++YG I + LD+ T +GY V++E+ A AA++ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 121 QDKGIHAQ 128
+ + Q
Sbjct: 70 NGQDLMGQ 77
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 7/80 (8%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
L++ NLP + E D + L +Y I RD +G GF RLES+ +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAEL 78
Query: 199 NGSTLPGSKEPLLVKFADSG 218
+G+ L PL ++FA G
Sbjct: 79 DGTILKSR--PLRIRFATHG 96
Score = 32.3 bits (72), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 29/132 (21%), Positives = 52/132 (39%), Gaps = 7/132 (5%)
Query: 58 KTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAV 117
+ L++ L D T++D + +YG N+ RG+GF+ ES A A
Sbjct: 22 RCRLFVGNLPTDITEEDFKRLFERYGEPSEV------FINRDRGFGFIRLESRTLAEIAK 75
Query: 118 KALQDKGIHAQMARQQ-EQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNT 176
L + ++ R + L + NL LE +++ V ++ D+
Sbjct: 76 AELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGR 135
Query: 177 SKGVGFARLESK 188
+ G GF +K
Sbjct: 136 ATGKGFVEFAAK 147
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 40/68 (58%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ G+ ++ T++D+ + ++YG I + LD+ T +GY V++E+ A AA++ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 121 QDKGIHAQ 128
+ + Q
Sbjct: 72 NGQDLMGQ 79
>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 = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 30/65 (46%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ + DTT+ L YGPI + K + K RGY F+++E +A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 121 QDKGI 125
K I
Sbjct: 165 DGKKI 169
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 37/86 (43%), Gaps = 2/86 (2%)
Query: 133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGF-ARLESKDK 190
++ D L+I +P N E DL+ L ++ + +L+D KG F E +
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
Query: 191 CDQMIQLFNGSTLPGSKEPLLVKFAD 216
L TLPG P+ VK AD
Sbjct: 69 LKAQSALHEQKTLPGMNRPIQVKPAD 94
Score = 31.2 bits (69), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 1/95 (1%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS G+ +G + L+I + ++ +KDL + ++G I + D+ T +G F
Sbjct: 1 GSSGS-SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAF 59
Query: 105 VDFESGGYALAAVKALQDKGIHAQMARQQEQDPTN 139
+ + AL A AL ++ M R + P +
Sbjct: 60 LTYCERESALKAQSALHEQKTLPGMNRPIQVKPAD 94
>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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 31/68 (45%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ + DTT+ L YGPI + K + K RGY F+++E +A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 121 QDKGIHAQ 128
K I +
Sbjct: 165 DGKKIDGR 172
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 24/47 (51%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFV 105
T +++ GL TTD L +G I I D+ T K RGYGFV
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFV 64
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 36/69 (52%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++R L+ ++++DL + S YGP+ +D T K +G+ FV F +A+ A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 121 QDKGIHAQM 129
+ +M
Sbjct: 71 DGQVFQGRM 79
>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 = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 35/72 (48%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
NL++ L + D+ L N + +S + D T RGYGFV F S A A+ +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 120 LQDKGIHAQMAR 131
+Q + ++ + R
Sbjct: 63 MQGQDLNGRPLR 74
Score = 32.0 bits (71), Expect = 0.45, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 3/78 (3%)
Query: 139 NLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESKDKCDQMIQL 197
NL++ +L +N + L + + + +S ++ D +S+G GF S+D +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 198 FNGSTLPGSKEPLLVKFA 215
G L G PL + +A
Sbjct: 63 MQGQDLNG--RPLRINWA 78
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 42/100 (42%), Gaps = 6/100 (6%)
Query: 133 QEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKC 191
++ D L++ +P E DL+ L ++ + +L+D KG F ++D
Sbjct: 11 KDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSA 70
Query: 192 -DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPN 230
L TLPG P+ VK A S G G GP+
Sbjct: 71 LKAQSALHEQKTLPGMNRPIQVKPAAS----EGRGESGPS 106
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 2/88 (2%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+GS G P K L++ + + ++DL + ++G I + D+ T +G
Sbjct: 3 SGSSGVPMKDHDAIK--LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCA 60
Query: 104 FVDFESGGYALAAVKALQDKGIHAQMAR 131
F+ + + AL A AL ++ M R
Sbjct: 61 FLTYCARDSALKAQSALHEQKTLPGMNR 88
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYAL 114
+LS T L++R D + +L + +GP+ K IL+ G+ FV+FE A
Sbjct: 28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK-ILN-------GFAFVEFEEAESAA 79
Query: 115 AAVKALQDKGIHAQ 128
A++ + K Q
Sbjct: 80 KAIEEVHGKSFANQ 93
Score = 32.0 bits (71), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 20/96 (20%), Positives = 41/96 (42%), Gaps = 9/96 (9%)
Query: 120 LQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKG 179
L +G H ++ E T L++ PL+ +E +L + + + +IL G
Sbjct: 14 LVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NG 66
Query: 180 VGFARLESKDKCDQMIQLFNGSTLPGSKEPLLVKFA 215
F E + + I+ +G + + +PL V ++
Sbjct: 67 FAFVEFEEAESAAKAIEEVHGKSF--ANQPLEVVYS 100
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 26/51 (50%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
S ++I GL+ TT + L Q+G + + D T + RG+GFV F
Sbjct: 24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ + ++ + ++ YG I + LD+ T +GY V++E+ ALAA +AL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 121 QDKGIHAQ 128
I Q
Sbjct: 89 NGAEIMGQ 96
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 45 GSPGTPTGPEQLSKT-NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS G+ + KT +L + GL TT++DL S +G ++ + D T +G+G
Sbjct: 1 GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Query: 104 FVDF 107
FV F
Sbjct: 61 FVRF 64
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 135 QDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARL 185
Q ++L + LP E DL+ + + V+ ++ +D SKG GF R
Sbjct: 13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 28/48 (58%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
++++ L+ + T +D+ + + +G I + + D T K +GYGFV F
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 36.2 bits (82), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++ + ++ + ++ YG I + LD+ T +GY V++E+ ALAA +AL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 121 QDKGIHAQ 128
I Q
Sbjct: 135 NGAEIMGQ 142
>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 = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 13/60 (21%), Positives = 29/60 (48%)
Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
P +++ + + E ++ S A+Y +V +I+ D SKG GF + ++++
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68
Score = 29.3 bits (64), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
+++ G+ + ++ + ++YG + K I D+ T +GYGFV F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 35.4 bits (80), Expect = 0.035, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 9/80 (11%)
Query: 45 GSPGTPTGPEQLSKTN-LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
GS G+ PE ++K L++R L T++ L S++G + K + D Y
Sbjct: 1 GSSGSSGDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YA 52
Query: 104 FVDFESGGYALAAVKALQDK 123
FV FE G A+ A+ + K
Sbjct: 53 FVHFEDRGAAVKAMDEMNGK 72
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 35.4 bits (80), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 31/60 (51%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
LY+ L + T+ L + +G I S + ++D T + +GYGF+ F A A++ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARLESKDKCDQMI 195
P LY+ +L N E L + + + S +++ D+ SKG GF + + +
Sbjct: 26 PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKAL 85
Query: 196 QLFNGSTLPG 205
+ NG L G
Sbjct: 86 EQLNGFELAG 95
>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 = 35.0 bits (79), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 43/90 (47%), Gaps = 5/90 (5%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKA 119
++++ L+ + T +D+ + +G I + + D T K +GYGFV F + A A++
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 120 -----LQDKGIHAQMARQQEQDPTNLYIAN 144
L + I A ++ P + Y +N
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPKSTYESN 106
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 133 QEQDPTN---LYIANLPLNFKECDLESLLAKYVTVVSTRILRD-NNNTSKGVGFARLESK 188
Q++D +N +++ +L D+++ A + + R+++D SKG GF +K
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 67
Query: 189 DKCDQMIQLFNGSTLPG 205
+ IQ G L G
Sbjct: 68 WDAENAIQQMGGQWLGG 84
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 34.7 bits (78), Expect = 0.062, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
++I GL+ TT + L Q+G + + D T + RG+GFV F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>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 = 34.7 bits (78), Expect = 0.068, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
P +++ + + E ++ S A+Y +V +I+ D SKG GF
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGF 54
Score = 28.5 bits (62), Expect = 5.5, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 53 PE-QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
PE ++ +++ G+ + ++ + ++YG + K I D+ T +GYGFV F
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 34.7 bits (78), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
LY+ L++D T+ ++ + SQ GP S K I + T+N Y FV+F
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND--PYCFVEF 62
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 34.7 bits (78), Expect = 0.077, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 55 QLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYAL 114
+LS T L++R D + +L + +GP+ K + G+ FV+FE A
Sbjct: 1 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAA 52
Query: 115 AAVKALQDKGIHAQ 128
A++ + K Q
Sbjct: 53 KAIEEVHGKSFANQ 66
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 34.3 bits (77), Expect = 0.080, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 137 PTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGF 182
P +++ + + E ++ S A+Y +V +I+ D SKG GF
Sbjct: 10 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGF 55
Score = 31.2 bits (69), Expect = 0.72, Method: Composition-based stats.
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 50 PTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF 107
P G ++ +++ G+ + ++ + ++YG + K I D+ T +GYGFV F
Sbjct: 2 PLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 58
>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 = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
+++ GL+ DT ++ + +G + S + +D TNK RG+ F+ F+ VK +
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE----EPVKKI 59
Query: 121 QDKGIH 126
+K H
Sbjct: 60 MEKKYH 65
>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 = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 37/84 (44%), Gaps = 5/84 (5%)
Query: 53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY 112
P+ T+L + LT T+ L + +YG + D+ T + RG+ FV F
Sbjct: 42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 101
Query: 113 ALAAVKA-----LQDKGIHAQMAR 131
A A+ A L + + QMAR
Sbjct: 102 AEDAMDAMDGAVLDGRELRVQMAR 125
Score = 32.3 bits (72), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 3/82 (3%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQ 196
T+L + NL L + KY V I RD S+G F R K + +
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 197 LFNGSTLPGSKEPLLVKFADSG 218
+G+ L G + L V+ A G
Sbjct: 108 AMDGAVLDGRE--LRVQMARYG 127
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 30/103 (29%), Positives = 45/103 (43%), Gaps = 14/103 (13%)
Query: 45 GSPGTPTGPEQLSKTN-LYIRGLTQDTTDKDLINMCSQYGPIISTKAI--------LDKT 95
GS G+ P++ S + +Y++GL T DL + Q G + K LDK
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 96 TNKCRGYGFVDFESGGYALAAV-----KALQDKGIHAQMARQQ 133
T K +G V +E A AAV K Q + +AR++
Sbjct: 61 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 103
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
+++ GL+ DT ++ + +G + S + +D TNK RG+ F+ F+ VK +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE----EPVKKI 57
Query: 121 QDKGIH 126
+K H
Sbjct: 58 MEKKYH 63
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 13/79 (16%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
+ T L++ ++ T+++L +YGP+I + D Y FV E A+ A
Sbjct: 9 ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEA 60
Query: 117 VKAL-----QDKGIHAQMA 130
++ L Q K +H Q++
Sbjct: 61 IRGLDNTEFQGKRMHVQLS 79
>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 = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 57 SKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF---VDFESGGYA 113
S L+I GL D + + + +GP+ + + D T +GY F VD A
Sbjct: 113 SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 172
Query: 114 LAAVKALQ--DKGIHAQMA 130
+A + +Q DK + Q A
Sbjct: 173 IAGLNGMQLGDKKLLVQRA 191
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 7/78 (8%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
+ L++ NLP + E ++ L KY I +D KG GF RLE++ + I
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAE--IAK 75
Query: 198 FNGSTLPGSKEPLLVKFA 215
+P + L V+FA
Sbjct: 76 VELDNMPLRGKQLRVRFA 93
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 33.1 bits (74), Expect = 0.20, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAIL-DKTTNKCRGYGFVDFESGGYALAAV 117
+ ++I L + +K L + S +G I+ T I+ D T +GY F++F S + AA+
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 118 KAL 120
+A+
Sbjct: 66 EAM 68
Score = 32.7 bits (73), Expect = 0.24, Method: Composition-based stats.
Identities = 27/92 (29%), Positives = 41/92 (44%), Gaps = 7/92 (7%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVST-RILRD-NNNTSKGVGFARLESKDKCDQMI 195
+ ++I NL E L + + ++ T +I+RD + SKG F S D D I
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 196 QLFNGSTLPGSKEPLLVKFADSGLKKRGAGAG 227
+ NG L P+ V +A KK G+G
Sbjct: 66 EAMNGQYL--CNRPITVSYA---FKKDSKGSG 92
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 38/88 (43%), Gaps = 7/88 (7%)
Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
+Y+ NLP + + D+E + KY + D N G FA +E +D D ++
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDI----DLKNRRGGPPFAFVEFEDPRDAEDAVYG 80
Query: 200 GSTLPGSKEPLLVKFADSGLKKRGAGAG 227
L V+F SG RG G+G
Sbjct: 81 RDGYDYDGYRLRVEFPRSG---RGTGSG 105
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 32.7 bits (73), Expect = 0.26, Method: Composition-based stats.
Identities = 20/80 (25%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
L+I+ LP + + +LE + + TV R++ + KG+ + E++ + Q + +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 200 GSTLPGSKEPLL-VKFADSG 218
G T+ KE ++ V ++SG
Sbjct: 80 GMTI---KENIIKVAISNSG 96
Score = 32.3 bits (72), Expect = 0.30, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 44 NGSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYG 103
+GS G L K L+I GL T ++L +C +G + + + ++ K +G
Sbjct: 3 SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLA 61
Query: 104 FVDFESGGYALAAV 117
+V++E+ A AV
Sbjct: 62 YVEYENESQASQAV 75
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 32.7 bits (73), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF---VDFESGGYALAAV 117
L+I GL D + + + +GP+ + + D T +GY F VD A+A +
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 118 KALQ--DKGIHAQMA 130
+Q DK + Q A
Sbjct: 159 NGMQLGDKKLLVQRA 173
>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 = 32.3 bits (72), Expect = 0.34, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 9/79 (11%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCD-QMIQ 196
+ L++ NLP + E ++ L KY I +D KG GF RLE++ + ++
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVE 70
Query: 197 LFNGSTLPGSKEPLLVKFA 215
L N +P + L V+FA
Sbjct: 71 LDN---MPLRGKQLRVRFA 86
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF---VDFESGGYALAAV 117
L+I GL D + + + +GP+ + + D T +GY F VD A+A +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 118 KALQ--DKGIHAQMA 130
+Q DK + Q A
Sbjct: 157 NGMQLGDKKLLVQRA 171
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 32.0 bits (71), Expect = 0.42, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF---VDFESGGYALAAV 117
L+I GL D + + + +GP+ + + D T +GY F VD A+A +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 118 KALQ--DKGIHAQMA 130
+Q DK + Q A
Sbjct: 64 NGMQLGDKKLLVQRA 78
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 29/129 (22%), Positives = 58/129 (44%), Gaps = 22/129 (17%)
Query: 90 AILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA-----QMAR------QQEQDPT 138
A++D R +G+VDFES A KAL+ G+ ++ + ++E+D
Sbjct: 38 AVVDVRIGMTRKFGYVDFES---AEDLEKALELTGLKVFGNEIKLEKPKGKDSKKERDAR 94
Query: 139 NLYIANLPLNFKECDLESLL--AKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQ 196
L NLP + +L+ + A + +VS + SKG+ + +++ ++ +
Sbjct: 95 TLLAKNLPYKVTQDELKEVFEDAAEIRLVS------KDGKSKGIAYIEFKTEADAEKTFE 148
Query: 197 LFNGSTLPG 205
G+ + G
Sbjct: 149 EKQGTEIDG 157
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 31.6 bits (70), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 5/78 (6%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
T+L + LT T+ L + +YG + D+ T + RG+ FV F A A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 119 A-----LQDKGIHAQMAR 131
A L + + QMAR
Sbjct: 131 AMDGAVLDGRELRVQMAR 148
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 3/82 (3%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDN-NNTSKGVGFARLESKDKCDQMIQ 196
T+L + NL L + KY V I RD S+G F R K + +
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 197 LFNGSTLPGSKEPLLVKFADSG 218
+G+ L G + L V+ A G
Sbjct: 131 AMDGAVLDGRE--LRVQMARYG 150
>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 = 31.2 bits (69), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 29/127 (22%), Positives = 57/127 (44%), Gaps = 18/127 (14%)
Query: 90 AILDKTTNKCRGYGFVDFESGGYALAAVKALQDKGIHA-----QMARQQEQDPTNLYIA- 143
A++D T R +G+VDFES A KAL+ G+ ++ + + +D + A
Sbjct: 44 AVVDVRTGTNRKFGYVDFES---AEDLEKALELTGLKVFGNEIKLEKPKGRDSKKVRAAR 100
Query: 144 -----NLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLF 198
NL N E +L+ + + + L + SKG+ + +S+ ++ ++
Sbjct: 101 TLLAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEK 156
Query: 199 NGSTLPG 205
G+ + G
Sbjct: 157 QGAEIDG 163
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 31.2 bits (69), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 45/96 (46%), Gaps = 8/96 (8%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVST--RILRD----NNNTSKGVGFARLESKDKC 191
+Y+ NL + +E DL+ + +YV S RI+ D KG F L ++
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSGLKKRGAGAG 227
+ ++ NG L G +P++V+FA S K+ G
Sbjct: 106 AKALKEANGYVLFG--KPMVVQFARSARPKQDPKEG 139
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 61 LYIRGLTQDTTDKDLINMCSQY----GPIISTKAILDKTTNKCRGYGFVDFESGGYALAA 116
LY++ L+ T++DL+++ +++ GP I + + T + RG F+ F + A A
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM----TGRMRGQAFITFPNKEIAWQA 83
Query: 117 VKALQDKGIHAQM 129
+ + ++ ++
Sbjct: 84 LHLVNGYKLYGKI 96
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 30.4 bits (67), Expect = 1.5, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L+I L ++ T++++ ++ QYG ++ I + YGFV E A A++ L
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNL 62
Query: 121 QDKGIHA 127
+H
Sbjct: 63 HHYKLHG 69
Score = 28.5 bits (62), Expect = 4.7, Method: Composition-based stats.
Identities = 23/91 (25%), Positives = 36/91 (39%), Gaps = 13/91 (14%)
Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
L+I NLP E ++ SL +Y V+ I+ K GF +E K + I+ +
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLH 63
Query: 200 GSTLPGSKEPLLVKFADSGLKKRGAGAGGPN 230
L G V K + + GP+
Sbjct: 64 HYKLHG------VNINVEASKNKSKASSGPS 88
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 30.0 bits (66), Expect = 1.5, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQL 197
+ +++ NLP +F L+ + V+ I + N SKG G + ES + ++ ++
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCGVVKFESPEVAERACRM 64
Query: 198 FNGSTLPG 205
NG L G
Sbjct: 65 MNGMKLSG 72
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 8/68 (11%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
L++R L T++ L SQ+G + K + D Y F+ F+ A+ A++ +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 121 QDKGIHAQ 128
K + +
Sbjct: 66 NGKDLEGE 73
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 29.6 bits (65), Expect = 2.0, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 140 LYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKCDQMIQLFN 199
+++ NLP +F L+ + V+ I + N SKG G + ES + ++ ++ N
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCGVVKFESPEVAERACRMMN 69
Query: 200 GSTLPG 205
G L G
Sbjct: 70 GMKLSG 75
>pdb|3Q2S|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2S|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25 COMPLEX
pdb|3Q2T|C Chain C, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
pdb|3Q2T|D Chain D, Crystal Structure Of Cfim68 RrmCFIM25RNA COMPLEX
Length = 229
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 2/70 (2%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYG--PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
LYI LT TTD+DL G I+ K ++ + +G+ V S + +
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 119 ALQDKGIHAQ 128
L + +H Q
Sbjct: 131 LLPKRELHGQ 140
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 29.6 bits (65), Expect = 2.4, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 7/68 (10%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKC-----RGYGFVDFESGGYA 113
+ L+I+ L TT++ L + S+ G I S + K NK G+GFV+++ A
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKS--CTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 114 LAAVKALQ 121
A+K LQ
Sbjct: 64 QKALKQLQ 71
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 29.6 bits (65), Expect = 2.4, Method: Composition-based stats.
Identities = 17/62 (27%), Positives = 30/62 (48%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
+ LY+ L + T+ L + +G I + + D T + +GYGF+ F A A++
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 119 AL 120
L
Sbjct: 66 QL 67
Score = 28.5 bits (62), Expect = 5.2, Method: Composition-based stats.
Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 7/94 (7%)
Query: 138 TNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNN-TSKGVGFARLESKDKCDQMIQ 196
+ LY+ +L N E L + + + + +++D++ SKG GF + + ++
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 197 LFNGSTLPGSKEPLLVKFADSGLKKRGAGAGGPN 230
NG L G P+ V + +R G GP+
Sbjct: 66 QLNGFELAG--RPMRV----GHVTERLDGGSGPS 93
>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 = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 31/64 (48%)
Query: 54 EQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYA 113
+++ K ++Y+ + +T +DL S G I + DK + +GY +++F
Sbjct: 32 KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSV 91
Query: 114 LAAV 117
AAV
Sbjct: 92 DAAV 95
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 3/60 (5%)
Query: 60 NLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDF---ESGGYALAA 116
++IR L+ D+ ++ L + Q+G + + +L T +G F F E+ LAA
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 29.3 bits (64), Expect = 3.0, Method: Composition-based stats.
Identities = 24/87 (27%), Positives = 35/87 (40%), Gaps = 3/87 (3%)
Query: 132 QQEQDPTNLYIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFARLESKDKC 191
Q+E D T +++ NL +E L L + + I +D K GF + +
Sbjct: 12 QEEADRT-VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESV 70
Query: 192 DQMIQLFNGSTLPGSKEPLLVKFADSG 218
I L NG L G P+ V SG
Sbjct: 71 SYAIALLNGIRLYG--RPINVSGPSSG 95
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGYALAAVKAL 120
LYIR L T +++ ++ +YGPI + I T + RG +V +E A AV L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 28.9 bits (63), Expect = 3.5, Method: Composition-based stats.
Identities = 11/48 (22%), Positives = 24/48 (50%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
+++ G+ + + +L ++G + I D + RG+GF+ FE
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 53 PEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT-TNKCRGYGFVDFESGG 111
P++ + + + +R + +++ + S +G + + + T T RG+GFVDF +
Sbjct: 10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 69
Query: 112 YALAAVKAL 120
A A AL
Sbjct: 70 DAKKAFNAL 78
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 28.9 bits (63), Expect = 4.0, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFE 108
LYIR L T +++ ++ +YGPI + I T + RG +V +E
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYE 59
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 28.9 bits (63), Expect = 4.1, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 56 LSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKT-TNKCRGYGFVDFESGGYAL 114
+ T ++I LT++ T ++ + S YG I +++ + +GY +V+FE+ A
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61
Query: 115 AAVKALQDKGIHAQ 128
A+K + I Q
Sbjct: 62 KALKHMDGGQIDGQ 75
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 28.5 bits (62), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 31/150 (20%), Positives = 60/150 (40%), Gaps = 8/150 (5%)
Query: 59 TNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFESGGY--ALAA 116
T + ++ L + + GPII +D + + + F E Y ALAA
Sbjct: 5 TTVLVKNLPKSYNQNKVYKYFKHCGPIIH----VDVADSLKKNFRFARIEFARYDGALAA 60
Query: 117 VKALQDKGIHAQMARQQEQDPTNLYIANLPLNFKECDLESLLAKY-VTVVSTRILRDNNN 175
+ ++ + T L++ N P ++ + ++ LL V +S R+ N
Sbjct: 61 ITKTHKVVGQNEIIVSHLTECT-LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFN 119
Query: 176 TSKGVGFARLESKDKCDQMIQLFNGSTLPG 205
TS+ + + SK+ ++ NG + G
Sbjct: 120 TSRRFAYIDVTSKEDARYCVEKLNGLKIEG 149
>pdb|3LCA|A Chain A, Structure Of Tom71 Complexed With Hsp70 Ssa1 C Terminal
Tail Indicating Conformational Plasticity
Length = 533
Score = 28.5 bits (62), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 22/80 (27%)
Query: 129 MARQQEQDPTNL----YIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFAR 184
+ARQ QDPT L + A + L K C+L D + +G A+
Sbjct: 424 LARQSSQDPTQLDEEKFNAAIKLLTKACEL-----------------DPRSEQAKIGLAQ 466
Query: 185 LESK-DKCDQMIQLFNGSTL 203
L+ + +K D+ I+LF S +
Sbjct: 467 LKLQMEKIDEAIELFEDSAI 486
>pdb|3FP2|A Chain A, Crystal Structure Of Tom71 Complexed With Hsp82 C-Terminal
Fragment
pdb|3FP3|A Chain A, Crystal Structure Of Tom71
pdb|3FP4|A Chain A, Crystal Structure Of Tom71 Complexed With Ssa1 C-Terminal
Fragment
Length = 537
Score = 28.1 bits (61), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 22/80 (27%)
Query: 129 MARQQEQDPTNL----YIANLPLNFKECDLESLLAKYVTVVSTRILRDNNNTSKGVGFAR 184
+ARQ QDPT L + A + L K C+L D + +G A+
Sbjct: 428 LARQSSQDPTQLDEEKFNAAIKLLTKACEL-----------------DPRSEQAKIGLAQ 470
Query: 185 LESK-DKCDQMIQLFNGSTL 203
L+ + +K D+ I+LF S +
Sbjct: 471 LKLQMEKIDEAIELFEDSAI 490
>pdb|3P5T|L Chain L, Cfim25-Cfim68 Complex
pdb|3P5T|M Chain M, Cfim25-Cfim68 Complex
pdb|3P5T|N Chain N, Cfim25-Cfim68 Complex
pdb|3P5T|O Chain O, Cfim25-Cfim68 Complex
pdb|3P5T|P Chain P, Cfim25-Cfim68 Complex
pdb|3P5T|Q Chain Q, Cfim25-Cfim68 Complex
pdb|3P6Y|C Chain C, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|D Chain D, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|G Chain G, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|H Chain H, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|K Chain K, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|L Chain L, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|O Chain O, Cf Im25-Cf Im68-Uguaa Complex
pdb|3P6Y|P Chain P, Cf Im25-Cf Im68-Uguaa Complex
Length = 90
Score = 27.7 bits (60), Expect = 7.4, Method: Composition-based stats.
Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 2/70 (2%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYG--PIISTKAILDKTTNKCRGYGFVDFESGGYALAAVK 118
LYI LT TTD+DL G I+ K ++ + +G+ V S + +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 119 ALQDKGIHAQ 128
L + +H Q
Sbjct: 64 LLPKRELHGQ 73
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS G+ +GPE +L++ LT D D L + P ++ T +GYGF
Sbjct: 1 GSSGS-SGPEY----SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGF 55
Query: 105 VDF 107
V F
Sbjct: 56 VKF 58
>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 = 27.7 bits (60), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 61 LYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGFVDFES 109
LYIR L T +++ ++ +YGPI + I T + RG +V +E
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYED 66
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 27.7 bits (60), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 40/97 (41%), Gaps = 6/97 (6%)
Query: 45 GSPGTPTGPEQLSKTNLYIRGLTQDTTDKDLINMCSQYGPIISTKAILDKTTNKCRGYGF 104
GS G+ +GP+ L + LT T+ L + +YG + + T RG+ F
Sbjct: 1 GSSGS-SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAF 59
Query: 105 VDFESGGYALAAVKA-----LQDKGIHAQMARQQEQD 136
V F A A A L + + Q+AR +D
Sbjct: 60 VRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRD 96
>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 = 27.7 bits (60), Expect = 8.6, Method: Composition-based stats.
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 82 YGPIISTKAILDKTTNKCRGYGFVDF 107
+G I + + D T K +GYGFV F
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSF 55
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 27.7 bits (60), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 85 IISTKAILDKTTNKCRGYGFVDFESGGYALAAV----KALQDKGIHAQMARQQEQDPT 138
I S + + DK T+K +G+ +V+F+ A+ L D+ + +A ++QD +
Sbjct: 41 IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKS 98
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.134 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,074,279
Number of Sequences: 62578
Number of extensions: 396019
Number of successful extensions: 967
Number of sequences better than 100.0: 146
Number of HSP's better than 100.0 without gapping: 99
Number of HSP's successfully gapped in prelim test: 47
Number of HSP's that attempted gapping in prelim test: 756
Number of HSP's gapped (non-prelim): 212
length of query: 305
length of database: 14,973,337
effective HSP length: 98
effective length of query: 207
effective length of database: 8,840,693
effective search space: 1830023451
effective search space used: 1830023451
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)