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= psy9313
(356 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 232 bits (591), Expect = 3e-61, Method: Compositional matrix adjust.
Identities = 112/180 (62%), Positives = 137/180 (76%), Gaps = 15/180 (8%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NLIVNY+PQ MTQEE + LF S+GE+ESCKL+RDK T QSLGYGFVNY +DAE+AI
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 87 ELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILC 146
LNGL+LQ K+IKVSYARPSS +I+ ANLYVSGLPK MTQ++LE LF YG IITSRIL
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILV 122
Query: 147 DKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
D ++ +S+G+GF+RF++ IEAE A++ LNG P GA+EPITVKFA
Sbjct: 123 D---------------QVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 48/73 (65%)
Query: 20 SDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTE 79
S + +++NL V+ +P+TMTQ+EL+ LFS G + + +++ D+ T S G GF+ + +
Sbjct: 82 SSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 141
Query: 80 DAERAIIELNGLK 92
+AE AI LNG K
Sbjct: 142 EAEEAIKGLNGQK 154
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 35/57 (61%)
Query: 291 LFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
LFG G +++ K+VRD T + G+GFV + +A AI +LNG L + ++VS+
Sbjct: 22 LFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSY 78
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 15/80 (18%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
+ NL V+ LP++MTQE+ +LF G I + +++ DK+ +++ G
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSL---------------GY 46
Query: 172 GFVRFNQHIEAEHAMQELNG 191
GFV + +AE A+ LNG
Sbjct: 47 GFVNYIDPKDAEKAINTLNG 66
Score = 33.9 bits (76), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 29/62 (46%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L L QLF +G + +++ D T +G GF+ EA AI+ L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 334 NG 335
NG
Sbjct: 151 NG 152
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 230 bits (586), Expect = 1e-60, Method: Compositional matrix adjust.
Identities = 110/186 (59%), Positives = 139/186 (74%), Gaps = 15/186 (8%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+ +NLIVNY+PQ MTQ+E + LF S+G++ESCKL+RDK T QSLGYGFVNY DA++
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 84 AIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSR 143
AI LNGLKLQ K+IKVSYARPSS +I+ ANLYVSGLPK M+Q+++E LF YG IITSR
Sbjct: 62 AINTLNGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSR 121
Query: 144 ILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITV 203
IL D+ +S+G+GF+RF++ IEAE A++ LNG P GA+EPITV
Sbjct: 122 ILLDQATG---------------VSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITV 166
Query: 204 KFANSP 209
KFAN+P
Sbjct: 167 KFANNP 172
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 3/75 (4%)
Query: 275 FVYNLAPE--TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ N P+ T+D LFG G +++ K+VRD T + G+GFV ++ ++A AI +
Sbjct: 7 LIVNYLPQNMTQDE-FKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 333 LNGYALGDRLLQVSF 347
LNG L + ++VS+
Sbjct: 66 LNGLKLQTKTIKVSY 80
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 29/62 (46%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L + QLF +G + +++ D T +G GF+ EA AI+ L
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 334 NG 335
NG
Sbjct: 153 NG 154
>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 = 219 bits (557), Expect = 2e-57, Method: Compositional matrix adjust.
Identities = 106/180 (58%), Positives = 132/180 (73%), Gaps = 15/180 (8%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NLIVNY+PQ MTQ+EL+ LFSS+GEVES KLIRDK SLGYGFVNY +DAERAI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 87 ELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILC 146
LNGL+LQ+K+IKVSYARPSSE IK ANLY+SGLP+ MTQ+D+E++F +G II SR+L
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV 122
Query: 147 DKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
D+ +S+G+ F+RF++ EAE A+ NG P G+SEPITVKFA
Sbjct: 123 DQTTG---------------LSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVKFA 167
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 45/68 (66%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+++NL ++ +P+TMTQ++++ +FS G + + +++ D+TT S G F+ + + +AE A
Sbjct: 87 KDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEA 146
Query: 85 IIELNGLK 92
I NG K
Sbjct: 147 ITSFNGHK 154
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 15/80 (18%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
R NL V+ LP++MTQ++L +LF G + +++++ DK+A ++ G
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSL---------------GY 46
Query: 172 GFVRFNQHIEAEHAMQELNG 191
GFV + +AE A+ LNG
Sbjct: 47 GFVNYVTAKDAERAINTLNG 66
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 271 GWCIFVYNLAPE--TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF 328
G + N P+ T+D L LF G V++ K++RD G+GFV +A
Sbjct: 1 GRTNLIVNYLPQNMTQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 59
Query: 329 AIQSLNGYALGDRLLQVSF 347
AI +LNG L + ++VS+
Sbjct: 60 AINTLNGLRLQSKTIKVSY 78
Score = 32.7 bits (73), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 291 LFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGY 336
+F FG + N +V+ D T +G F+ EA AI S NG+
Sbjct: 108 MFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 216 bits (551), Expect = 1e-56, Method: Compositional matrix adjust.
Identities = 105/180 (58%), Positives = 131/180 (72%), Gaps = 15/180 (8%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NLIVNY+PQ MTQ+EL+ LFSS+GEVES KLIRDK SLGYGFVNY +DAERAI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 87 ELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILC 146
LNGL+LQ+K+IKVSYARPSSE IK ANLY+SGLP+ MTQ+D+E++F +G II SR+L
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV 122
Query: 147 DKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
D+ +S+G+ F+RF++ EAE A+ NG P G+SEPITV FA
Sbjct: 123 DQTTG---------------LSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITVXFA 167
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 45/68 (66%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+++NL ++ +P+TMTQ++++ +FS G + + +++ D+TT S G F+ + + +AE A
Sbjct: 87 KDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEA 146
Query: 85 IIELNGLK 92
I NG K
Sbjct: 147 ITSFNGHK 154
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 44/80 (55%), Gaps = 15/80 (18%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
R NL V+ LP++MTQ++L +LF G + +++++ DK+A ++ G
Sbjct: 2 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSL---------------GY 46
Query: 172 GFVRFNQHIEAEHAMQELNG 191
GFV + +AE A+ LNG
Sbjct: 47 GFVNYVTAKDAERAINTLNG 66
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 271 GWCIFVYNLAPE--TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF 328
G + N P+ T+D L LF G V++ K++RD G+GFV +A
Sbjct: 1 GRTNLIVNYLPQNMTQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 59
Query: 329 AIQSLNGYALGDRLLQVSF 347
AI +LNG L + ++VS+
Sbjct: 60 AINTLNGLRLQSKTIKVSY 78
Score = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 290 QLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGY 336
+F FG + N +V+ D T +G F+ EA AI S NG+
Sbjct: 107 DMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGH 153
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 169 bits (427), Expect = 3e-42, Method: Compositional matrix adjust.
Identities = 80/181 (44%), Positives = 118/181 (65%), Gaps = 15/181 (8%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
N+NLIVNY+PQ MT EL LF ++G + +C+++RD T S GY FV++ D++RAI
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 86 IELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRIL 145
LNG+ ++NK +KVSYARP E+IK NLYV+ LP+ +T + L+ +F YG+I+ IL
Sbjct: 63 KVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 122
Query: 146 CDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKF 205
DK+ +G P +G+ FVR+N+ EA+ A+ LN IPEG S+P++V+
Sbjct: 123 RDKL---------TGRP------RGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL 167
Query: 206 A 206
A
Sbjct: 168 A 168
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 40/67 (59%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+++NL V +P+T+T ++L +F G + ++RDK T + G FV Y + E+A+ A
Sbjct: 88 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 147
Query: 85 IIELNGL 91
I LN +
Sbjct: 148 ISALNNV 154
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 41/79 (51%)
Query: 269 GSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF 328
S + V L + D L+ LF G + +++RD +T G+ FV T+ ++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 329 AIQSLNGYALGDRLLQVSF 347
AI+ LNG + ++ L+VS+
Sbjct: 61 AIKVLNGITVRNKRLKVSY 79
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL D+ L +FG +G++ ++RD T + +G FV +EA AI +L
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 334 N 334
N
Sbjct: 152 N 152
>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 = 166 bits (420), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 80/187 (42%), Positives = 118/187 (63%), Gaps = 15/187 (8%)
Query: 20 SDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTE 79
+D N+NLIVNY+PQ T EL LF ++G + +C++ RD T S GY FV++
Sbjct: 8 NDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEX 67
Query: 80 DAERAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTI 139
D++RAI LNG+ ++NK +KVSYARP E+IK NLYV+ LP+ +T + L+ +F YG+I
Sbjct: 68 DSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSI 127
Query: 140 ITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASE 199
+ IL DK+ +G P +G+ FVR+N+ EA+ A+ LN IPEG S+
Sbjct: 128 VQKNILRDKL---------TGRP------RGVAFVRYNKREEAQEAISALNNVIPEGGSQ 172
Query: 200 PITVKFA 206
P++V+ A
Sbjct: 173 PLSVRLA 179
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 48/93 (51%), Gaps = 7/93 (7%)
Query: 255 DLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKG 314
DL+N+ P++ S + V L + D L+ LF G + ++ RD +T G
Sbjct: 5 DLMND----PRA---SNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFG 57
Query: 315 FGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
+ FV T+ ++ AI+ LNG + ++ L+VS+
Sbjct: 58 YAFVDFTSEXDSQRAIKVLNGITVRNKRLKVSY 90
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL D+ L +FG +G++ ++RD T + +G FV +EA AI +L
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 334 N 334
N
Sbjct: 163 N 163
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 126 bits (316), Expect = 2e-29, Method: Composition-based stats.
Identities = 58/88 (65%), Positives = 72/88 (81%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+ +NLIVNY+PQ MTQ+E + LF S+G++ESCKL+RDK T QSLGYGFVNY DA++
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 84 AIIELNGLKLQNKSIKVSYARPSSEAIK 111
AI LNGLKLQ K+IKVSYARPSS +I+
Sbjct: 62 AINTLNGLKLQTKTIKVSYARPSSASIR 89
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 37/57 (64%)
Query: 291 LFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
LFG G +++ K+VRD T + G+GFV ++ ++A AI +LNG L + ++VS+
Sbjct: 24 LFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSY 80
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 15/80 (18%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
+ NL V+ LP++MTQ++ ++LF G I + +++ DK+ + S G
Sbjct: 4 KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQ---------------SLGY 48
Query: 172 GFVRFNQHIEAEHAMQELNG 191
GFV ++ +A+ A+ LNG
Sbjct: 49 GFVNYSDPNDADKAINTLNG 68
>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 = 125 bits (314), Expect = 4e-29, Method: Compositional matrix adjust.
Identities = 59/80 (73%), Positives = 68/80 (85%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NLIVNY+PQ MTQ+EL+ LFSS+GEVES KLIRDK SLGYGFVNY +DAERAI
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 87 ELNGLKLQNKSIKVSYARPS 106
LNGL+LQ+K+IKVSYARPS
Sbjct: 65 TLNGLRLQSKTIKVSYARPS 84
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 51/95 (53%), Gaps = 17/95 (17%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
R NL V+ LP++MTQ++L +LF G + +++++ DK+A ++ G
Sbjct: 4 RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSL---------------GY 48
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
GFV + +AE A+ LNG + S+ I V +A
Sbjct: 49 GFVNYVTAKDAERAINTLNGLRLQ--SKTIKVSYA 81
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 41/81 (50%), Gaps = 3/81 (3%)
Query: 269 GSGWCIFVYNLAPE--TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA 326
G G + N P+ T+D L LF G V++ K++RD G+GFV +A
Sbjct: 1 GPGRTNLIVNYLPQNMTQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDA 59
Query: 327 VFAIQSLNGYALGDRLLQVSF 347
AI +LNG L + ++VS+
Sbjct: 60 ERAINTLNGLRLQSKTIKVSY 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 = 124 bits (311), Expect = 7e-29, Method: Compositional matrix adjust.
Identities = 59/82 (71%), Positives = 68/82 (82%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
Q +NLIVNY+PQ TQ+EL+ LFSS+GEVES KLIRDK SLGYGFVNY +DAERA
Sbjct: 18 QGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 77
Query: 85 IIELNGLKLQNKSIKVSYARPS 106
I LNGL+LQ+K+IKVSYARPS
Sbjct: 78 INTLNGLRLQSKTIKVSYARPS 99
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 41/83 (49%)
Query: 265 KSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
++L+ G + V L + L LF G V++ K++RD G+GFV
Sbjct: 13 ENLYFQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAK 72
Query: 325 EAVFAIQSLNGYALGDRLLQVSF 347
+A AI +LNG L + ++VS+
Sbjct: 73 DAERAINTLNGLRLQSKTIKVSY 95
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 48/93 (51%), Gaps = 17/93 (18%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NL V+ LP++ TQ++L +LF G + +++++ DK+A S G GF
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGH---------------SLGYGF 65
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
V + +AE A+ LNG + S+ I V +A
Sbjct: 66 VNYVTAKDAERAINTLNGLRLQ--SKTIKVSYA 96
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 106 bits (265), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 52/97 (53%), Positives = 67/97 (69%), Gaps = 15/97 (15%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
ANLYVSGLPK M+Q+++E LF YG IITSRIL D+ +S+G+G
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATG---------------VSRGVG 46
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
F+RF++ IEAE A++ LNG P GA+EPITVKFAN+P
Sbjct: 47 FIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFANNP 83
Score = 57.8 bits (138), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 45/67 (67%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
++NL V+ +P+TM+Q+E++ LFS G + + +++ D+ T S G GF+ + + +AE AI
Sbjct: 1 DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 86 IELNGLK 92
LNG K
Sbjct: 61 KGLNGQK 67
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 29/62 (46%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L + QLF +G + +++ D T +G GF+ EA AI+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 334 NG 335
NG
Sbjct: 64 NG 65
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 99.4 bits (246), Expect = 3e-21, Method: Composition-based stats.
Identities = 44/86 (51%), Positives = 62/86 (72%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
N+NLIVNY+PQ MT EL LF ++G + +C+++RD T S GY FV++ D++RAI
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 86 IELNGLKLQNKSIKVSYARPSSEAIK 111
LNG+ ++NK +KVSYARP E+IK
Sbjct: 63 KVLNGITVRNKRLKVSYARPGGESIK 88
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 27/78 (34%), Positives = 39/78 (50%), Gaps = 15/78 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NL V+ LP+ MT +L LFR G I T RI+ R + +G S G F
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIM---------RDYKTG------YSYGYAF 49
Query: 174 VRFNQHIEAEHAMQELNG 191
V F ++++ A++ LNG
Sbjct: 50 VDFTSEMDSQRAIKVLNG 67
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 40/74 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V L + D L+ LF G + +++RD +T G+ FV T+ ++ AI+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 334 NGYALGDRLLQVSF 347
NG + ++ L+VS+
Sbjct: 66 NGITVRNKRLKVSY 79
>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 = 90.5 bits (223), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 44/107 (41%), Positives = 66/107 (61%), Gaps = 15/107 (14%)
Query: 100 VSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVS 159
+SYARP E+IK NLYV+ LP+ +T + L+ +F YG+I+ IL DK+ +
Sbjct: 1 MSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL---------T 51
Query: 160 GTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
G P +G+ FVR+N+ EA+ A+ LN IPEG S+P++V+ A
Sbjct: 52 GRP------RGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 92
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 39/65 (60%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+++NL V +P+T+T ++L +F G + ++RDK T + G FV Y + E+A+ A
Sbjct: 12 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
Query: 85 IIELN 89
I LN
Sbjct: 72 ISALN 76
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL D+ L +FG +G++ ++RD T + +G FV +EA AI +L
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 334 N 334
N
Sbjct: 76 N 76
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 82.4 bits (202), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 47/169 (27%), Positives = 87/169 (51%), Gaps = 19/169 (11%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
++L V + +T+ L FS G + S ++ RD T +SLGY +VN+ + DAERA+
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 87 ELNGLKLQNKSIKVSYAR--PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
+N ++ K +++ +++ PS N+++ L K + + L + F +G I++ ++
Sbjct: 76 TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKV 135
Query: 145 LCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTI 193
+CD+ SKG GFV F AE A++++NG +
Sbjct: 136 VCDENG-----------------SKGYGFVHFETQEAAERAIEKMNGML 167
Score = 51.2 bits (121), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 46/73 (63%), Gaps = 2/73 (2%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
N+ + + +++ + L FS+ G + SCK++ D+ ++ GYGFV++ E AERAI +
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEK 162
Query: 88 LNGLKLQNKSIKV 100
+NG+ L ++ + V
Sbjct: 163 MNGMLLNDRKVFV 175
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 33/88 (37%), Positives = 45/88 (51%), Gaps = 4/88 (4%)
Query: 266 SLHGSGWC-IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
SL SG IF+ NL ++ L+ F FG + + KVV D KG+GFV +
Sbjct: 97 SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQE 154
Query: 325 EAVFAIQSLNGYALGDRLLQVS-FKTHK 351
A AI+ +NG L DR + V FK+ K
Sbjct: 155 AAERAIEKMNGMLLNDRKVFVGRFKSRK 182
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 48/102 (47%), Gaps = 17/102 (16%)
Query: 105 PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEI 164
PS+ + A+LYV L +T+ L F P G I++ R+ C M I
Sbjct: 8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRV-CRDM--------------I 52
Query: 165 PQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
+ S G +V F Q +AE A+ +N + +G +P+ + ++
Sbjct: 53 TRRSLGYAYVNFQQPADAERALDTMNFDVIKG--KPVRIMWS 92
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 82.0 bits (201), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 47/169 (27%), Positives = 87/169 (51%), Gaps = 19/169 (11%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
++L V + +T+ L FS G + S ++ RD T +SLGY +VN+ + DAERA+
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 87 ELNGLKLQNKSIKVSYAR--PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
+N ++ K +++ +++ PS N+++ L K + + L + F +G I++ ++
Sbjct: 71 TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKV 130
Query: 145 LCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTI 193
+CD+ SKG GFV F AE A++++NG +
Sbjct: 131 VCDENG-----------------SKGYGFVHFETQEAAERAIEKMNGML 162
Score = 51.2 bits (121), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 48/81 (59%), Gaps = 2/81 (2%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
N+ + + +++ + L FS+ G + SCK++ D+ ++ GYGFV++ E AERAI +
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEK 157
Query: 88 LNGLKLQNKSIKVSYARPSSE 108
+NG+ L ++ + V + E
Sbjct: 158 MNGMLLNDRKVFVGRFKSRKE 178
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 33/88 (37%), Positives = 45/88 (51%), Gaps = 4/88 (4%)
Query: 266 SLHGSGWC-IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
SL SG IF+ NL ++ L+ F FG + + KVV D KG+GFV +
Sbjct: 92 SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQE 149
Query: 325 EAVFAIQSLNGYALGDRLLQVS-FKTHK 351
A AI+ +NG L DR + V FK+ K
Sbjct: 150 AAERAIEKMNGMLLNDRKVFVGRFKSRK 177
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 48/102 (47%), Gaps = 17/102 (16%)
Query: 105 PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEI 164
PS+ + A+LYV L +T+ L F P G I++ R+ C M I
Sbjct: 3 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRV-CRDM--------------I 47
Query: 165 PQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
+ S G +V F Q +AE A+ +N + +G +P+ + ++
Sbjct: 48 TRRSLGYAYVNFQQPADAERALDTMNFDVIKG--KPVRIMWS 87
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 73.9 bits (180), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 39/96 (40%), Positives = 58/96 (60%), Gaps = 6/96 (6%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
NL+VNY+P T+ + +L+ LF G +ES K++ D+ T QS GYGFV + A++AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 88 LNGLKLQNKSIKVSYA-----RPS-SEAIKRANLYV 117
LNG + NK +KV+ A RP + A+ N Y+
Sbjct: 104 LNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 275 FVYNLAPETEDNV-LWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ N P T D V L QLF +G +++VK+V D +T + +G+GFV + A AI L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 334 NGYALGDRLLQVSF 347
NG+ + ++ L+V+
Sbjct: 105 NGFNILNKRLKVAL 118
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 15/78 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NL V+ +P + + L LF YG I + +I+CD+ + S+G GF
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQ---------------SRGYGF 88
Query: 174 VRFNQHIEAEHAMQELNG 191
V+F A+ A+ LNG
Sbjct: 89 VKFQSGSSAQQAIAGLNG 106
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 72.8 bits (177), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 46/180 (25%), Positives = 89/180 (49%), Gaps = 20/180 (11%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + +T++ L+ F G + + K++ DK +++ Y FV Y+++ DA A+ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQTL 61
Query: 89 NGLKLQNKSIKVSYARPS--SEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILC 146
NG +++N +K+++A S S + NL+V L ++ E L N F+ + + ++ ++
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 147 DKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
D S+G GFV F +A++AM + G G P+ + +A
Sbjct: 122 DMQTGS---------------SRGYGFVSFTSQDDAQNAMDSMQGQDLNG--RPLRINWA 164
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 40/74 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV +L +D L F F + + V+ D QT +G+GFV T+ D+A A+ S+
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 334 NGYALGDRLLQVSF 347
G L R L++++
Sbjct: 150 QGQDLNGRPLRINW 163
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 39/76 (51%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
NL V + + E L++ F S ++ D T S GYGFV++ +DA+ A+
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 88 LNGLKLQNKSIKVSYA 103
+ G L + +++++A
Sbjct: 149 MQGQDLNGRPLRINWA 164
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
++V NL +++L Q F G + N+K++ D K + FV +A A+Q+
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNN-KNVNYAFVEYHQSHDANIALQT 60
Query: 333 LNGYALGDRLLQVSF 347
LNG + + ++++++
Sbjct: 61 LNGKQIENNIVKINW 75
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 50/186 (26%), Positives = 89/186 (47%), Gaps = 23/186 (12%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTT--AQSLGYGFVNYYRTEDAERAII 86
+ V VP+T ++++L+ LF G V ++RD++ QS G FV +Y + A A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 87 ELNGLKL---QNKSIKVSYA-RPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITS 142
L+ +K+ + I++ A + A++ L++ + K T+ D+ +F +G I
Sbjct: 78 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 137
Query: 143 RILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELN-GTIPEGASEPI 201
RIL P+ +S+G FV F A+ A++ ++ EG S P+
Sbjct: 138 RIL--------------RGPD--GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPM 181
Query: 202 TVKFAN 207
VKFA+
Sbjct: 182 VVKFAD 187
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 33/108 (30%), Positives = 53/108 (49%), Gaps = 21/108 (19%)
Query: 104 RPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPE 163
+P +AIK ++V +P+ +++DL LF YG + +L D+ S+N
Sbjct: 10 QPDLDAIK---MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDR--SQN---------- 54
Query: 164 IPQISKGIGFVRF---NQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
P SKG FV F +EA++A+ N + G PI +K A+S
Sbjct: 55 -PPQSKGCCFVTFYTRKAALEAQNALH--NMKVLPGMHHPIQMKPADS 99
Score = 35.4 bits (80), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
++ L + + + T+ +++ +FSS G++E C+++R S G FV + A+ A
Sbjct: 106 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTA 164
Query: 85 I 85
I
Sbjct: 165 I 165
>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 = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 36/81 (44%), Positives = 46/81 (56%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
G +F+Y+L E D L Q+F PFG V + KV D QT K FGFV N A AI
Sbjct: 25 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 84
Query: 331 QSLNGYALGDRLLQVSFKTHK 351
QS+NG+ +G + L+V K K
Sbjct: 85 QSMNGFQIGMKRLKVQLKRSK 105
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 50/100 (50%)
Query: 10 TTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLG 69
T QS + + +NL + ++PQ ++L +F G V S K+ DK T S
Sbjct: 9 TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 68
Query: 70 YGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEA 109
+GFV+Y A+ AI +NG ++ K +KV R +++
Sbjct: 69 FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 108
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/92 (26%), Positives = 46/92 (50%), Gaps = 15/92 (16%)
Query: 100 VSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVS 159
+ A E + ANL++ LP+ +DL +F P+G ++++++ DK +
Sbjct: 13 IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN-------- 64
Query: 160 GTPEIPQISKGIGFVRFNQHIEAEHAMQELNG 191
+SK GFV ++ + A+ A+Q +NG
Sbjct: 65 -------LSKCFGFVSYDNPVSAQAAIQSMNG 89
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 63.5 bits (153), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 50/186 (26%), Positives = 89/186 (47%), Gaps = 23/186 (12%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTT--AQSLGYGFVNYYRTEDAERAII 86
+ V VP+T ++++L+ LF G V ++RD++ QS G FV +Y + A A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 87 ELNGLKL---QNKSIKVSYA-RPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITS 142
L+ +K+ + I++ A + A++ L++ + K T+ D+ +F +G I
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEEC 125
Query: 143 RILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELN-GTIPEGASEPI 201
RIL P+ +S+G FV F A+ A++ ++ EG S P+
Sbjct: 126 RIL--------------RGPD--GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPM 169
Query: 202 TVKFAN 207
VKFA+
Sbjct: 170 VVKFAD 175
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 48/231 (20%), Positives = 88/231 (38%), Gaps = 77/231 (33%)
Query: 107 SEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ 166
S+AIK ++V +P+ +++DL LF YG + +L D+ S+N P
Sbjct: 1 SDAIK---MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDR--SQN-----------PP 44
Query: 167 ISKGIGFVRF---NQHIEAEHAMQELNGTIPEGASEPITVKFANSPXXXXXXXXXXXXXX 223
SKG FV F +EA++A+ + +P
Sbjct: 45 QSKGCCFVTFYTRKAALEAQNALHNMK-VLP----------------------------- 74
Query: 224 XXXXXXXXXXXXXXGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPET 283
+HH + K AD N+ + + L F+ ++ +
Sbjct: 75 ----------------GMHHPIQMK----PADSEKNNAVEDRKL-------FIGMISKKC 107
Query: 284 EDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLN 334
+N + +F FG ++ +++R P +G FV T A AI++++
Sbjct: 108 TENDIRVMFSSFGQIEECRILRGPDGLS-RGCAFVTFTTRAMAQTAIKAMH 157
Score = 35.4 bits (80), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
++ L + + + T+ +++ +FSS G++E C+++R S G FV + A+ A
Sbjct: 94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTA 152
Query: 85 I 85
I
Sbjct: 153 I 153
>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 = 61.6 bits (148), Expect = 6e-10, Method: Composition-based stats.
Identities = 32/82 (39%), Positives = 47/82 (57%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV +L+PE + F PFG + + +VV+D T K KG+GFV N +A AIQ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 334 NGYALGDRLLQVSFKTHKPLPP 355
G LG R ++ ++ T KP P
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAP 99
Score = 52.4 bits (124), Expect = 4e-07, Method: Composition-based stats.
Identities = 29/110 (26%), Positives = 58/110 (52%), Gaps = 3/110 (2%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ Q + ++ V + +T E+++ F+ G + ++++D T +S GYGF
Sbjct: 2 SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGF 61
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYAR---PSSEAIKRANLYVSG 119
V+++ DAE AI ++ G L + I+ ++A P+ ++ +N SG
Sbjct: 62 VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSG 111
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 15/78 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+++V L +T ED++ F P+G I +R++ D + SKG GF
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGK---------------SKGYGF 61
Query: 174 VRFNQHIEAEHAMQELNG 191
V F +AE+A+Q++ G
Sbjct: 62 VSFFNKWDAENAIQQMGG 79
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 61.6 bits (148), Expect = 7e-10, Method: Composition-based stats.
Identities = 28/86 (32%), Positives = 50/86 (58%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+ N+ + V + + + +LQ LF G + L +DKTT QS G+ F++++R EDA R
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72
Query: 84 AIIELNGLKLQNKSIKVSYARPSSEA 109
AI ++G + + V +A+PS+ +
Sbjct: 73 AIAGVSGFGYDHLILNVEWAKPSTNS 98
Score = 47.8 bits (112), Expect = 9e-06, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 41/74 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I V NL+ +T + L +LF PFG++ + + +D T + KGF F+ ++A AI +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 334 NGYALGDRLLQVSF 347
+G+ +L V +
Sbjct: 78 SGFGYDHLILNVEW 91
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 15/87 (17%)
Query: 105 PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEI 164
P+ A A + V+ L + + DL+ LFRP+G+I + DK +
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQ------------ 55
Query: 165 PQISKGIGFVRFNQHIEAEHAMQELNG 191
SKG F+ F++ +A A+ ++G
Sbjct: 56 ---SKGFAFISFHRREDAARAIAGVSG 79
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 35/85 (41%), Positives = 47/85 (55%), Gaps = 1/85 (1%)
Query: 265 KSLHGSGWC-IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNY 323
K + G C +F+Y+L E D L F PFG V + KV D QT K FGFV N
Sbjct: 33 KQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNP 92
Query: 324 DEAVFAIQSLNGYALGDRLLQVSFK 348
D A AI+++NG+ +G + L+V K
Sbjct: 93 DSAQVAIKAMNGFQVGTKRLKVQLK 117
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 26/80 (32%), Positives = 43/80 (53%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+ NL + ++PQ T +L F G V S K+ DK T+ S +GFV++ + A+ A
Sbjct: 39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 85 IIELNGLKLQNKSIKVSYAR 104
I +NG ++ K +KV +
Sbjct: 99 IKAMNGFQVGTKRLKVQLKK 118
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 15/84 (17%)
Query: 108 EAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQI 167
E + NL++ LP+ T DL + F P+G +I++++ DK S +
Sbjct: 36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTS---------------L 80
Query: 168 SKGIGFVRFNQHIEAEHAMQELNG 191
SK GFV F+ A+ A++ +NG
Sbjct: 81 SKCFGFVSFDNPDSAQVAIKAMNG 104
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 60.5 bits (145), Expect = 2e-09, Method: Composition-based stats.
Identities = 29/79 (36%), Positives = 48/79 (60%), Gaps = 1/79 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAV-QNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
IF+ NL PE ++ +L+ F FG + Q K++RDP T KG+ F+ ++D + AI++
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 333 LNGYALGDRLLQVSFKTHK 351
+NG L +R + VS+ K
Sbjct: 68 MNGQYLCNRPITVSYAFKK 86
Score = 45.1 bits (105), Expect = 6e-05, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 45/79 (56%), Gaps = 1/79 (1%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEV-ESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+S + + + + ++ L FS+ G + ++ K++RD T S GY F+N+ + ++ A
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 85 IIELNGLKLQNKSIKVSYA 103
I +NG L N+ I VSYA
Sbjct: 65 IEAMNGQYLCNRPITVSYA 83
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 60.5 bits (145), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 41/140 (29%), Positives = 70/140 (50%), Gaps = 14/140 (10%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
Q S L V +P +T+EE++ LF G+ + +DK G+GF+ AE A
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIA 74
Query: 85 IIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
+EL+ + L+ K ++V +A S A+L V LP++++ E LE F +G + + +
Sbjct: 75 KVELDNMPLRGKQLRVRFACHS------ASLTVRNLPQYVSNELLEEAFSVFGQVERAVV 128
Query: 145 LCDKMASENVRSFV--SGTP 162
+ D + + V SG P
Sbjct: 129 IVDDRGRPSGKGIVEFSGKP 148
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 43/99 (43%), Gaps = 7/99 (7%)
Query: 252 LTADLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYK 311
LT DL N P + +FV NL P+ + + +LF +G V + +D
Sbjct: 4 LTIDL-KNFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD----- 57
Query: 312 CKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSFKTH 350
KGFGF+ + A A L+ L + L+V F H
Sbjct: 58 -KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH 95
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 38/96 (39%), Gaps = 23/96 (23%)
Query: 111 KRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKG 170
+R+ L+V LP +T+E++ LF YG I D KG
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD---------------------KG 59
Query: 171 IGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
GF+R AE A EL+ G + V+FA
Sbjct: 60 FGFIRLETRTLAEIAKVELDNMPLRGKQ--LRVRFA 93
>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 = 60.1 bits (144), Expect = 2e-09, Method: Composition-based stats.
Identities = 33/84 (39%), Positives = 49/84 (58%)
Query: 269 GSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF 328
GS + +FV +L+PE + F PFG + + +VV+D T K KG+GFV N +A
Sbjct: 4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63
Query: 329 AIQSLNGYALGDRLLQVSFKTHKP 352
AIQ + G LG R ++ ++ T KP
Sbjct: 64 AIQQMGGQWLGGRQIRTNWATRKP 87
Score = 45.1 bits (105), Expect = 6e-05, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 33/53 (62%)
Query: 51 GEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYA 103
G + ++++D T +S GYGFV+++ DAE AI ++ G L + I+ ++A
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83
Score = 29.6 bits (65), Expect = 2.7, Method: Composition-based stats.
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 15/57 (26%)
Query: 135 PYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNG 191
P+G I +R++ D MA+ SKG GFV F +AE+A+Q++ G
Sbjct: 29 PFGRISDARVVKD-MATGK--------------SKGYGFVSFFNKWDAENAIQQMGG 70
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 59.7 bits (143), Expect = 2e-09, Method: Composition-based stats.
Identities = 31/82 (37%), Positives = 46/82 (56%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV +L+PE + F PFG + + +VV+D T K KG+GFV N +A AI +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 334 NGYALGDRLLQVSFKTHKPLPP 355
G LG R ++ ++ T KP P
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAP 99
Score = 55.1 bits (131), Expect = 6e-08, Method: Composition-based stats.
Identities = 26/91 (28%), Positives = 51/91 (56%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ Q + ++ V + +T E+++ F+ G++ ++++D T +S GYGF
Sbjct: 2 SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGF 61
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYA 103
V++Y DAE AI+ + G L + I+ ++A
Sbjct: 62 VSFYNKLDAENAIVHMGGQWLGGRQIRTNWA 92
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 15/78 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+++V L +T ED+++ F P+G I +R++ D + SKG GF
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGK---------------SKGYGF 61
Query: 174 VRFNQHIEAEHAMQELNG 191
V F ++AE+A+ + G
Sbjct: 62 VSFYNKLDAENAIVHMGG 79
>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 = 58.9 bits (141), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 49/185 (26%), Positives = 81/185 (43%), Gaps = 23/185 (12%)
Query: 30 IVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTT--AQSLGYGFVNYYRTEDAERAIIE 87
V VP+T ++++L+ LF G V ++RD++ QS G FV +Y + A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 88 LNGLKLQNKSIKVSYARPSSE----AIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSR 143
L+ K+ +P+ A++ L++ + K T+ D+ F +G I R
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECR 126
Query: 144 ILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELN-GTIPEGASEPIT 202
IL P+ +S+G FV F A+ A++ + EG S P
Sbjct: 127 IL--------------RGPD--GLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEGCSSPXV 170
Query: 203 VKFAN 207
VKFA+
Sbjct: 171 VKFAD 175
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 33/105 (31%), Positives = 50/105 (47%), Gaps = 21/105 (20%)
Query: 107 SEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ 166
S+AIK +V +P+ +++DL LF YG + +L D+ S+N P
Sbjct: 1 SDAIK---XFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDR--SQN-----------PP 44
Query: 167 ISKGIGFVRF---NQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
SKG FV F +EA++A+ N + G PI K A+S
Sbjct: 45 QSKGCCFVTFYTRKAALEAQNALH--NXKVLPGXHHPIQXKPADS 87
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
++ L + + + T+ +++ FSS G++E C+++R S G FV + A+ A
Sbjct: 94 EDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAXAQTA 152
Query: 85 I 85
I
Sbjct: 153 I 153
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 35/100 (35%), Positives = 51/100 (51%), Gaps = 22/100 (22%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NLY+S LP M +++LEN+ +P+G +I++RIL D SGT S+G+GF
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDS----------SGT------SRGVGF 70
Query: 174 VRFNQHIEAEHAMQELNGTI---PEGAS---EPITVKFAN 207
R + E + NG P G S EP+ KF+
Sbjct: 71 ARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSG 110
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+NL ++ +P +M ++EL+++ G+V S +++RD ++ S G GF TE E I
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIG 84
Query: 87 ELNG 90
NG
Sbjct: 85 HFNG 88
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ NL ++ L + PFG V + +++RD + +G GF M + ++ I
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 334 NG 335
NG
Sbjct: 87 NG 88
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 54.7 bits (130), Expect = 7e-08, Method: Composition-based stats.
Identities = 28/82 (34%), Positives = 46/82 (56%)
Query: 22 VNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDA 81
V+ ++ V +P T+E+L+ +FS VG V S +L+ D+ T + GYGF Y E A
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 82 ERAIIELNGLKLQNKSIKVSYA 103
A+ LNG + ++++V A
Sbjct: 64 LSAMRNLNGREFSGRALRVDNA 85
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 40/72 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV N+ E + L +F G V + ++V D +T K KG+GF + + A+ A+++L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 334 NGYALGDRLLQV 345
NG R L+V
Sbjct: 71 NGREFSGRALRV 82
Score = 35.8 bits (81), Expect = 0.035, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 17/85 (20%)
Query: 109 AIKRA--NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ 166
A+ R+ +++V +P T+E L+++F G +++ R++ D+ +G P
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE---------TGKP---- 49
Query: 167 ISKGIGFVRFNQHIEAEHAMQELNG 191
KG GF + A AM+ LNG
Sbjct: 50 --KGYGFCEYQDQETALSAMRNLNG 72
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 54.7 bits (130), Expect = 8e-08, Method: Composition-based stats.
Identities = 26/72 (36%), Positives = 45/72 (62%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV L+ +T + L Q+F +G + V VV+D +T + +GFGFV N D+A A+ ++
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 334 NGYALGDRLLQV 345
NG ++ R ++V
Sbjct: 75 NGKSVDGRQIRV 86
Score = 52.0 bits (123), Expect = 4e-07, Method: Composition-based stats.
Identities = 21/69 (30%), Positives = 43/69 (62%)
Query: 40 QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIK 99
++ L+ +FS G++ +++D+ T +S G+GFV + +DA+ A++ +NG + + I+
Sbjct: 26 EQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIR 85
Query: 100 VSYARPSSE 108
V A SS+
Sbjct: 86 VDQAGKSSD 94
Score = 36.6 bits (83), Expect = 0.019, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 37/88 (42%), Gaps = 15/88 (17%)
Query: 109 AIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQIS 168
A L+V GL ++ LE +F YG I ++ D+ Q S
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRET---------------QRS 53
Query: 169 KGIGFVRFNQHIEAEHAMQELNGTIPEG 196
+G GFV F +A+ AM +NG +G
Sbjct: 54 RGFGFVTFENIDDAKDAMMAMNGKSVDG 81
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 46/74 (62%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + +T++ L+ +F G +ES +L+ D T +S GYGF+ + +E A++A+ +L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 89 NGLKLQNKSIKVSY 102
NG +L + +KV +
Sbjct: 89 NGFELAGRPMKVGH 102
Score = 52.0 bits (123), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 49/78 (62%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V +L +++L +F PFG +++++++ D +T + KG+GF+ ++ + A A++ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 334 NGYALGDRLLQVSFKTHK 351
NG+ L R ++V T +
Sbjct: 89 NGFELAGRPMKVGHVTER 106
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 46/89 (51%), Gaps = 17/89 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV L ++T++ L +F P+G I + +++ D SE R SKG GF+
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMD---SETGR------------SKGYGFI 73
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITV 203
F+ A+ A+++LNG E A P+ V
Sbjct: 74 TFSDSECAKKALEQLNGF--ELAGRPMKV 100
>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 = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 45/76 (59%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
+ V V Q ++ ++++ +F + G+++SC L RD TT + GYGF+ Y + + ++ A+
Sbjct: 112 RIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171
Query: 88 LNGLKLQNKSIKVSYA 103
+N L + ++V A
Sbjct: 172 MNLFDLGGQYLRVGKA 187
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 35/166 (21%), Positives = 77/166 (46%), Gaps = 30/166 (18%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKS 97
+ ++ ++ F+ G ++S + D T + G+ FV Y E A+ A+ ++N + L ++
Sbjct: 25 LGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRN 84
Query: 98 IKVSYARPSS-------------EAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
IKV RPS+ EA +YV+ + + ++ +D++++F +G I + +
Sbjct: 85 IKV--GRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTL 142
Query: 145 LCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELN 190
D ++ KG GF+ + + ++ A+ +N
Sbjct: 143 ARDPTTGKH---------------KGYGFIEYEKAQSSQDAVSSMN 173
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 44/81 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I+V ++ + D+ + +F FG +++ + RDP T K KG+GF+ + A+ S+
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 334 NGYALGDRLLQVSFKTHKPLP 354
N + LG + L+V P+P
Sbjct: 173 NLFDLGGQYLRVGKAVTPPMP 193
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 40/72 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V ++ E ++ + Q F PFG ++++ + D T K KGF FV + A A++ +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 334 NGYALGDRLLQV 345
N LG R ++V
Sbjct: 76 NSVMLGGRNIKV 87
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 43/79 (54%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
C+ V+ L+ T + L ++F +G + +V +V D Q+ + +GF FV N D+A A +
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 333 LNGYALGDRLLQVSFKTHK 351
NG L R ++V F K
Sbjct: 108 ANGMELDGRRIRVDFSITK 126
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 38/65 (58%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+ +L+ +FS G + ++ D+ + +S G+ FV + +DA+ A NG++L + I
Sbjct: 59 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 118
Query: 99 KVSYA 103
+V ++
Sbjct: 119 RVDFS 123
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 31/110 (28%), Positives = 43/110 (39%), Gaps = 23/110 (20%)
Query: 103 ARPSSEAIKRAN------LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRS 156
R S RAN L V GL + T+ DL +F YG I I+ D+ +
Sbjct: 31 GRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR---- 86
Query: 157 FVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
S+G FV F +A+ A + NG +G I V F+
Sbjct: 87 -----------SRGFAFVYFENVDDAKEAKERANGMELDG--RRIRVDFS 123
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 37/177 (20%), Positives = 82/177 (46%), Gaps = 30/177 (16%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
S + V + + ++ ++ F+ G ++S + D T + G+ FV Y E A+ A+
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
Query: 87 ELNGLKLQNKSIKVSYARPSS-------------EAIKRANLYVSGLPKHMTQEDLENLF 133
++N + L ++IKV RPS+ EA +YV+ + + ++ +D++++F
Sbjct: 89 QMNSVMLGGRNIKV--GRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVF 146
Query: 134 RPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELN 190
+G I ++ + D ++ KG GF+ + + ++ A+ +N
Sbjct: 147 EAFGKIKSATLARDPTTGKH---------------KGYGFIEYEKAQSSQDAVSSMN 188
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 44/75 (58%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V V Q ++ ++++ +F + G+++S L RD TT + GYGF+ Y + + ++ A+ +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 89 NGLKLQNKSIKVSYA 103
N L + ++V A
Sbjct: 188 NLFDLGGQYLRVGKA 202
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 44/81 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I+V ++ + D+ + +F FG +++ + RDP T K KG+GF+ + A+ S+
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 334 NGYALGDRLLQVSFKTHKPLP 354
N + LG + L+V P+P
Sbjct: 188 NLFDLGGQYLRVGKAVTPPMP 208
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 40/72 (55%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V ++ E ++ + Q F PFG ++++ + D T K KGF FV + A A++ +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 334 NGYALGDRLLQV 345
N LG R ++V
Sbjct: 91 NSVMLGGRNIKV 102
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 53.5 bits (127), Expect = 2e-07, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 48/77 (62%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+S L V + +T++ L+ +F G++++ L++D T +S GYGF+ + +E A RA+
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 86 IELNGLKLQNKSIKVSY 102
+LNG +L + ++V +
Sbjct: 65 EQLNGFELAGRPMRVGH 81
Score = 51.2 bits (121), Expect = 8e-07, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 47/78 (60%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V +L +++L +F PFG + N+ +++D T + KG+GF+ ++ + A A++ L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 334 NGYALGDRLLQVSFKTHK 351
NG+ L R ++V T +
Sbjct: 68 NGFELAGRPMRVGHVTER 85
Score = 36.6 bits (83), Expect = 0.024, Method: Composition-based stats.
Identities = 28/91 (30%), Positives = 44/91 (48%), Gaps = 17/91 (18%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+ LYV L ++T++ L +F P+G I ++ D S+ RS KG G
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKD---SDTGRS------------KGYG 50
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITV 203
F+ F+ A A+++LNG E A P+ V
Sbjct: 51 FITFSDSECARRALEQLNGF--ELAGRPMRV 79
>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 = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 44/75 (58%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V V Q ++ ++++ +F + G+++SC L RD TT + GYGF+ Y + + ++ A+
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 89 NGLKLQNKSIKVSYA 103
N L + ++V A
Sbjct: 172 NLFDLGGQYLRVGKA 186
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 35/166 (21%), Positives = 74/166 (44%), Gaps = 30/166 (18%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKS 97
+ ++ ++ F+ G ++S D T + G+ FV Y E A+ A+ + N + L ++
Sbjct: 24 LGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRN 83
Query: 98 IKVSYARPSS-------------EAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
IKV RPS+ EA +YV+ + + ++ +D++++F +G I + +
Sbjct: 84 IKV--GRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTL 141
Query: 145 LCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELN 190
D ++ KG GF+ + + ++ A+ N
Sbjct: 142 ARDPTTGKH---------------KGYGFIEYEKAQSSQDAVSSXN 172
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 42/81 (51%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I+V ++ + D+ + +F FG +++ + RDP T K KG+GF+ + A+ S
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 334 NGYALGDRLLQVSFKTHKPLP 354
N + LG + L+V P P
Sbjct: 172 NLFDLGGQYLRVGKAVTPPXP 192
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 38/72 (52%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V ++ E ++ + Q F PFG ++++ D T K KGF FV + A A++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 334 NGYALGDRLLQV 345
N LG R ++V
Sbjct: 75 NSVXLGGRNIKV 86
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 51.6 bits (122), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 282 ETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDR 341
+TE+ +L L G V N+K++ DPQT + KG+ F+ + + + A+++LNGY LG R
Sbjct: 14 QTEEQIL-DLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR 72
Query: 342 LLQVSFKTHKPLPPV 356
L+ + ++ + V
Sbjct: 73 FLKCGYSSNSDISGV 87
Score = 47.8 bits (112), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 42/73 (57%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P T+E++ L S+VG V + K++ D T +S GY F+ + E + A+ LNG +L
Sbjct: 10 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 69
Query: 94 QNKSIKVSYARPS 106
++ +K Y+ S
Sbjct: 70 GSRFLKCGYSSNS 82
>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 = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 282 ETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDR 341
+TE+ +L L G V N+K++ DPQT + KG+ F+ + + + A+++LNGY LG R
Sbjct: 15 QTEEQIL-DLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR 73
Query: 342 LLQVSFKTHKPLPPV 356
L+ + ++ + V
Sbjct: 74 FLKCGYSSNSDISGV 88
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 42/73 (57%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P T+E++ L S+VG V + K++ D T +S GY F+ + E + A+ LNG +L
Sbjct: 11 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 70
Query: 94 QNKSIKVSYARPS 106
++ +K Y+ S
Sbjct: 71 GSRFLKCGYSSNS 83
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 32/97 (32%), Positives = 54/97 (55%), Gaps = 6/97 (6%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQ---SLGYGFVNYYRTEDAE 82
+S L + + + T+E L+ +FS VG ++SC + + K A S+G+GFV Y + E A+
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 83 RAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSG 119
+A+ +L G + ++V R S A K A+ SG
Sbjct: 65 KALKQLQGHTVDGHKLEV---RISERATKPASGPSSG 98
Score = 31.6 bits (70), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 5/84 (5%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKC---KGFGFVCMTNYDEAVFAI 330
+F+ NL T + L +F GA+++ + + GFGFV ++A A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 331 QSLNGYAL-GDRL-LQVSFKTHKP 352
+ L G+ + G +L +++S + KP
Sbjct: 68 KQLQGHTVDGHKLEVRISERATKP 91
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
++ L V +P ++TQ++ + L G +E C L+ + T QS GYGF Y + + A RA
Sbjct: 95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 86 IELNGLKLQNKSIKVSY 102
+L G L +++ V +
Sbjct: 155 SDLLGKPLGPRTLYVHW 171
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 44/164 (26%), Positives = 73/164 (44%), Gaps = 28/164 (17%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
+++ +P +T +E+ L S E++ C + + K TA FV E AE AI
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDY-ELKYCFVDKYKGTA------FVTLLNGEQAEAAINA 76
Query: 88 LNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCD 147
+ +L+ + + V +P+ A L V+ LP +TQ+ E L RP+G++
Sbjct: 77 FHQSRLRERELSVQL-QPTD-----ALLCVANLPPSLTQQQFEELVRPFGSL-------- 122
Query: 148 KMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNG 191
R F+ + Q SKG GF + + A A +L G
Sbjct: 123 ------ERCFLVYSERTGQ-SKGYGFAEYMKKDSAARAKSDLLG 159
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 36/83 (43%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V NL P +L PFG+++ +V +T + KG+GF D A A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 334 NGYALGDRLLQVSFKTHKPLPPV 356
G LG R L V + L P
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPA 180
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 51.6 bits (122), Expect = 7e-07, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
C+ V+ L+ T + L ++F +G + +V +V D Q+ + +GF FV N D+A A +
Sbjct: 14 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 333 LNGYALGDRLLQVSFK-THKP 352
NG L R ++V F T +P
Sbjct: 74 ANGMELDGRRIRVDFSITKRP 94
Score = 44.3 bits (103), Expect = 9e-05, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+ +L+ +FS G + ++ D+ + +S G+ FV + +DA+ A NG++L + I
Sbjct: 25 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 84
Query: 99 KVSYA---RPSS 107
+V ++ RP +
Sbjct: 85 RVDFSITKRPHT 96
Score = 31.6 bits (70), Expect = 0.64, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 15/82 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L V GL + T+ DL +F YG I I+ D+ + S+G FV
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR---------------SRGFAFV 59
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F +A+ A + NG +G
Sbjct: 60 YFENVDDAKEAKERANGMELDG 81
>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 = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
++ L V +P ++TQ++ + L G +E C L+ + T QS GYGF Y + + A RA
Sbjct: 93 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 152
Query: 86 IELNGLKLQNKSIKVSY 102
+L G L +++ V +
Sbjct: 153 SDLLGKPLGPRTLYVHW 169
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 44/164 (26%), Positives = 73/164 (44%), Gaps = 28/164 (17%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
+++ +P +T +E+ L S E++ C + + K TA FV E AE AI
Sbjct: 22 KILIRGLPGDVTNQEVHDLLSDY-ELKYCFVDKYKGTA------FVTLLNGEQAEAAINA 74
Query: 88 LNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCD 147
+ +L+ + + V +P+ A L V+ LP +TQ+ E L RP+G++
Sbjct: 75 FHQSRLRERELSVQL-QPTD-----ALLCVANLPPSLTQQQFEELVRPFGSL-------- 120
Query: 148 KMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNG 191
R F+ + Q SKG GF + + A A +L G
Sbjct: 121 ------ERCFLVYSERTGQ-SKGYGFAEYMKKDSAARAKSDLLG 157
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 36/83 (43%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V NL P +L PFG+++ +V +T + KG+GF D A A L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 334 NGYALGDRLLQVSFKTHKPLPPV 356
G LG R L V + L P
Sbjct: 156 LGKPLGPRTLYVHWTDAGQLTPA 178
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
++ L V +P ++TQ++ + L G +E C L+ + T QS GYGF Y + + A RA
Sbjct: 95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 86 IELNGLKLQNKSIKVSY 102
+L G L +++ V +
Sbjct: 155 SDLLGKPLGPRTLYVHW 171
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 44/164 (26%), Positives = 73/164 (44%), Gaps = 28/164 (17%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
+++ +P +T +E+ L S E++ C + + K TA FV E AE AI
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDY-ELKYCFVDKYKGTA------FVTLLNGEQAEAAINA 76
Query: 88 LNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCD 147
+ +L+ + + V +P+ A L V+ LP +TQ+ E L RP+G++
Sbjct: 77 FHQSRLRERELSVQL-QPTD-----ALLCVANLPPSLTQQQFEELVRPFGSL-------- 122
Query: 148 KMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNG 191
R F+ + Q SKG GF + + A A +L G
Sbjct: 123 ------ERCFLVYSERTGQ-SKGYGFAEYMKKDSAARAKSDLLG 159
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 36/83 (43%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V NL P +L PFG+++ +V +T + KG+GF D A A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 334 NGYALGDRLLQVSFKTHKPLPPV 356
G LG R L V + L P
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPA 180
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 51.2 bits (121), Expect = 8e-07, Method: Composition-based stats.
Identities = 27/81 (33%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
C+ V+ L+ T + L ++F +G + +V +V D Q+ + +GF FV N D+A A +
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 333 LNGYALGDRLLQVSFK-THKP 352
NG L R ++V F T +P
Sbjct: 77 ANGMELDGRRIRVDFSITKRP 97
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 41/72 (56%), Gaps = 3/72 (4%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+ +L+ +FS G + ++ D+ + +S G+ FV + +DA+ A NG++L + I
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 99 KVSYA---RPSS 107
+V ++ RP +
Sbjct: 88 RVDFSITKRPHT 99
Score = 31.6 bits (70), Expect = 0.66, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 15/82 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L V GL + T+ DL +F YG I I+ D+ + S+G FV
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR---------------SRGFAFV 62
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F +A+ A + NG +G
Sbjct: 63 YFENVDDAKEAKERANGMELDG 84
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 51.2 bits (121), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 69/162 (42%), Gaps = 22/162 (13%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
EQ L + + T E L+ F G + C ++RD T +S G+GFV Y E+ +
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70
Query: 84 AI----IELNGLKLQNKSI--KVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYG 137
A+ +++G ++ K + RP + + ++V G+ + + L + F YG
Sbjct: 71 AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-KIFVGGIKEDTEEHHLRDYFEQYG 129
Query: 138 TIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQH 179
I I+ D+ + + +G FV F+ H
Sbjct: 130 KIEVIEIMTDRGSGKK---------------RGFAFVTFDDH 156
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+F+ L+ ET D L F +G + + V+RDP T + +GFGFV +E A+ +
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 30/51 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
IFV + +TE++ L F +G ++ ++++ D + K +GF FV ++D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 157
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 69/162 (42%), Gaps = 22/162 (13%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
EQ L + + T E L+ F G + C ++RD T +S G+GFV Y E+ +
Sbjct: 9 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 68
Query: 84 AI----IELNGLKLQNKSI--KVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYG 137
A+ +++G ++ K + RP + + ++V G+ + + L + F YG
Sbjct: 69 AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-KIFVGGIKEDTEEHHLRDYFEQYG 127
Query: 138 TIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQH 179
I I+ D+ + + +G FV F+ H
Sbjct: 128 KIEVIEIMTDRGSGKK---------------RGFAFVTFDDH 154
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+F+ L+ ET D L F +G + + V+RDP T + +GFGFV +E A+ +
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Score = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 30/51 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
IFV + +TE++ L F +G ++ ++++ D + K +GF FV ++D
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 155
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 51.2 bits (121), Expect = 9e-07, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 48/81 (59%), Gaps = 2/81 (2%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
N+ + + +++ + L FS+ G + SCK++ D+ ++ GYGFV++ E AERAI +
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAIEK 70
Query: 88 LNGLKLQNKSIKVSYARPSSE 108
+NG+ L ++ + V + E
Sbjct: 71 MNGMLLNDRKVFVGRFKSRKE 91
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 29/79 (36%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IF+ NL ++ L+ F FG + + KVV D KG+GFV + A AI+ +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKM 71
Query: 334 NGYALGDRLLQVS-FKTHK 351
NG L DR + V FK+ K
Sbjct: 72 NGMLLNDRKVFVGRFKSRK 90
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 17/91 (18%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTP 162
A PS N+++ L K + + L + F +G I++ +++CD+
Sbjct: 2 ADPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG------------ 49
Query: 163 EIPQISKGIGFVRFNQHIEAEHAMQELNGTI 193
SKG GFV F AE A++++NG +
Sbjct: 50 -----SKGYGFVHFETQEAAERAIEKMNGML 75
>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 = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 69/162 (42%), Gaps = 22/162 (13%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
EQ L + + T E L+ F G + C ++RD T +S G+GFV Y E+ +
Sbjct: 4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63
Query: 84 AI----IELNGLKLQNKSI--KVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYG 137
A+ +++G ++ K + RP + + ++V G+ + + L + F YG
Sbjct: 64 AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-KIFVGGIKEDTEEHHLRDYFEQYG 122
Query: 138 TIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQH 179
I I+ D+ + + +G FV F+ H
Sbjct: 123 KIEVIEIMTDRGSGKK---------------RGFAFVTFDDH 149
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+F+ L+ ET D L F +G + + V+RDP T + +GFGFV +E A+ +
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Score = 36.6 bits (83), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 30/51 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
IFV + +TE++ L F +G ++ ++++ D + K +GF FV ++D
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 150
>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 = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 69/162 (42%), Gaps = 22/162 (13%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
EQ L + + T E L+ F G + C ++RD T +S G+GFV Y E+ +
Sbjct: 10 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 69
Query: 84 AI----IELNGLKLQNKSI--KVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYG 137
A+ +++G ++ K + RP + + ++V G+ + + L + F YG
Sbjct: 70 AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-KIFVGGIKEDTEEHHLRDYFEQYG 128
Query: 138 TIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQH 179
I I+ D+ + + +G FV F+ H
Sbjct: 129 KIEVIEIMTDRGSGKK---------------RGFAFVTFDDH 155
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+F+ L+ ET D L F +G + + V+RDP T + +GFGFV +E A+ +
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 30/51 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
IFV + +TE++ L F +G ++ ++++ D + K +GF FV ++D
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 156
>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 = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 69/162 (42%), Gaps = 22/162 (13%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
EQ L + + T E L+ F G + C ++RD T +S G+GFV Y E+ +
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70
Query: 84 AI----IELNGLKLQNKSI--KVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYG 137
A+ +++G ++ K + RP + + ++V G+ + + L + F YG
Sbjct: 71 AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-KIFVGGIKEDTEEHHLRDYFEQYG 129
Query: 138 TIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQH 179
I I+ D+ + + +G FV F+ H
Sbjct: 130 KIEVIEIMTDRGSGKK---------------RGFAFVTFDDH 156
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+F+ L+ ET D L F +G + + V+RDP T + +GFGFV +E A+ +
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 30/51 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
IFV + +TE++ L F +G ++ ++++ D + K +GF FV ++D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 157
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 38/162 (23%), Positives = 69/162 (42%), Gaps = 22/162 (13%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
EQ L + + T E L+ F G + C ++RD T +S G+GFV Y E+ +
Sbjct: 12 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 71
Query: 84 AI----IELNGLKLQNKSI--KVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYG 137
A+ +++G ++ K + RP + + ++V G+ + + L + F YG
Sbjct: 72 AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVK-KIFVGGIKEDTEEHHLRDYFEQYG 130
Query: 138 TIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQH 179
I I+ D+ + + +G FV F+ H
Sbjct: 131 KIEVIEIMTDRGSGKK---------------RGFAFVTFDDH 157
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 32/59 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+F+ L+ ET D L F +G + + V+RDP T + +GFGFV +E A+ +
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 30/51 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
IFV + +TE++ L F +G ++ ++++ D + K +GF FV ++D
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 158
>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 = 50.8 bits (120), Expect = 1e-06, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 49/83 (59%), Gaps = 2/83 (2%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+ N+ + + +++ + L FS+ G + SCK++ D+ ++ GYGFV++ E AERAI
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERAI 62
Query: 86 IELNGLKLQNKSIKVSYARPSSE 108
++NG+ L ++ + V + E
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKE 85
Score = 46.2 bits (108), Expect = 3e-05, Method: Composition-based stats.
Identities = 32/84 (38%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 269 GSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF 328
GSG IF+ NL ++ L+ F FG + + KVV D KG+GFV + A
Sbjct: 4 GSG-NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAER 60
Query: 329 AIQSLNGYALGDRLLQVS-FKTHK 351
AI+ +NG L DR + V FK+ K
Sbjct: 61 AIEKMNGMLLNDRKVFVGRFKSRK 84
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 39/81 (48%), Gaps = 17/81 (20%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
N+++ L K + + L + F +G I++ +++CD+ SKG G
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-----------------SKGYG 48
Query: 173 FVRFNQHIEAEHAMQELNGTI 193
FV F AE A++++NG +
Sbjct: 49 FVHFETQEAAERAIEKMNGML 69
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 43/69 (62%), Gaps = 1/69 (1%)
Query: 282 ETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDR 341
+TE+ +L L G V N+K++ DPQT + KG+ F+ + + + A+++LNGY LG R
Sbjct: 16 QTEEQIL-DLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSR 74
Query: 342 LLQVSFKTH 350
L+ + ++
Sbjct: 75 FLKCGYSSN 83
Score = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 41/70 (58%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P T+E++ L S+VG V + K++ D T +S GY F+ + E + A+ LNG +L
Sbjct: 12 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL 71
Query: 94 QNKSIKVSYA 103
++ +K Y+
Sbjct: 72 GSRFLKCGYS 81
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 50.8 bits (120), Expect = 1e-06, Method: Composition-based stats.
Identities = 34/96 (35%), Positives = 50/96 (52%), Gaps = 19/96 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L K ++ED+ LF+P+G I +L S SKG FV
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGS----------------SKGCAFV 61
Query: 175 RFNQHIEAEHAMQELNG--TIPEGASEPITVKFANS 208
+F+ H EA+ A+ L+G T+P GAS + VKFA++
Sbjct: 62 KFSSHTEAQAAIHALHGSQTMP-GASSSLVVKFADT 96
Score = 37.0 bits (84), Expect = 0.017, Method: Composition-based stats.
Identities = 21/54 (38%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 282 ETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
++E++VL +LF PFG + V+R P KG FV +++ EA AI +L+G
Sbjct: 27 QSEEDVL-RLFQPFGVIDECTVLRGPDG-SSKGCAFVKFSSHTEAQAAIHALHG 78
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 35/135 (25%), Positives = 60/135 (44%), Gaps = 12/135 (8%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
Q L V +P +T+E+ + LF GE + RD+ G+GF+ AE A
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIA 74
Query: 85 IIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
EL+G L+++ +++ + A A L V L ++ E LE F +G + + +
Sbjct: 75 KAELDGTILKSRPLRIRF------ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVV 128
Query: 145 LCDKMASENVRSFVS 159
+ D + FV
Sbjct: 129 VVDDRGRATGKGFVE 143
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 31/108 (28%), Positives = 49/108 (45%), Gaps = 24/108 (22%)
Query: 101 SYARPSSEA-IKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVS 159
S+ +P + +R L+V LP +T+ED + LF YG S + ++
Sbjct: 10 SFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGE--PSEVFINR----------- 56
Query: 160 GTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
+G GF+R AE A EL+GTI + S P+ ++FA
Sbjct: 57 --------DRGFGFIRLESRTLAEIAKAELDGTILK--SRPLRIRFAT 94
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 42/93 (45%), Gaps = 7/93 (7%)
Query: 259 NSMLPPKSLHGSGWC-IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGF 317
S L P + C +FV NL + + +LF +G V + RD +GFGF
Sbjct: 9 KSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGF 62
Query: 318 VCMTNYDEAVFAIQSLNGYALGDRLLQVSFKTH 350
+ + + A A L+G L R L++ F TH
Sbjct: 63 IRLESRTLAEIAKAELDGTILKSRPLRIRFATH 95
Score = 31.2 bits (69), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
G + V NL+P + +L Q F FG V+ VV D + + G GFV
Sbjct: 96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRG-RATGKGFV 142
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 45/79 (56%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
Q++ + V + + +++ L LF G V + + +D+ T Q GYGFV + EDA+ A
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73
Query: 85 IIELNGLKLQNKSIKVSYA 103
I ++ +KL K I+V+ A
Sbjct: 74 IKIMDMIKLYGKPIRVNKA 92
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 42/74 (56%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
++V L + + +LW+LF G V N + +D T + +G+GFV + ++A +AI+
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 333 LNGYALGDRLLQVS 346
++ L + ++V+
Sbjct: 77 MDMIKLYGKPIRVN 90
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 35/96 (36%), Positives = 48/96 (50%), Gaps = 19/96 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L K T ED+ +F P+GTI +L GT SKG FV
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP----------DGT------SKGCAFV 58
Query: 175 RFNQHIEAEHAMQELNG--TIPEGASEPITVKFANS 208
+F H EA+ A+ L+ T+P GAS + VKFA++
Sbjct: 59 KFQTHAEAQAAINTLHSSRTLP-GASSSLVVKFADT 93
Score = 33.5 bits (75), Expect = 0.20, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV L + D + ++F PFG + V+R P KG FV + EA AI +L
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDG-TSKGCAFVKFQTHAEAQAAINTL 73
Query: 334 N 334
+
Sbjct: 74 H 74
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 42/74 (56%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
C+ V+ L+ T + L ++F +G + +V +V D Q+ + +GF FV N D+A A +
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 333 LNGYALGDRLLQVS 346
NG L R ++VS
Sbjct: 77 ANGMELDGRRIRVS 90
Score = 44.7 bits (104), Expect = 9e-05, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+ +L+ +FS G + ++ D+ + +S G+ FV + +DA+ A NG++L + I
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 99 KVSYARPSS 107
+VS PSS
Sbjct: 88 RVS--GPSS 94
Score = 31.6 bits (70), Expect = 0.70, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 15/82 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L V GL + T+ DL +F YG I I+ D+ + S+G FV
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR---------------SRGFAFV 62
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F +A+ A + NG +G
Sbjct: 63 YFENVDDAKEAKERANGMELDG 84
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL +D L + F PFG + + KV+ + + KGFGFVC ++ +EA A+ +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTEM 75
Query: 334 NGYALGDRLLQVSFKTHK 351
NG + + L V+ K
Sbjct: 76 NGRIVATKPLYVALAQRK 93
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 32/93 (34%), Positives = 45/93 (48%), Gaps = 19/93 (20%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NLYV L + E L F P+GTI +++++ E R SKG GF
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM-----EGGR------------SKGFGF 59
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
V F+ EA A+ E+NG I A++P+ V A
Sbjct: 60 VCFSSPEEATKAVTEMNGRIV--ATKPLYVALA 90
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 2/84 (2%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
Q NL V + + E L+ FS G + S K++ + +S G+GFV + E+A +A
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKA 71
Query: 85 IIELNGLKLQNKSIKVSYARPSSE 108
+ E+NG + K + V+ A+ E
Sbjct: 72 VTEMNGRIVATKPLYVALAQRKEE 95
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 41/75 (54%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + +P + ++++ L +S G +++ L++D T S GY F Y ++AI L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 89 NGLKLQNKSIKVSYA 103
NG++L +K + V A
Sbjct: 177 NGMQLGDKKLLVQRA 191
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 4/86 (4%)
Query: 260 SMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVC 319
S + P S H +F+ L D+ + +L FG ++ +V+D T KG+ F
Sbjct: 107 STVVPDSAH----KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 162
Query: 320 MTNYDEAVFAIQSLNGYALGDRLLQV 345
+ + AI LNG LGD+ L V
Sbjct: 163 YVDINVTDQAIAGLNGMQLGDKKLLV 188
>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 = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 41/75 (54%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + +P + ++++ L +S G +++ L++D T S GY F Y ++AI L
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 89 NGLKLQNKSIKVSYA 103
NG++L +K + V A
Sbjct: 159 NGMQLGDKKLLVQRA 173
Score = 36.6 bits (83), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ L D+ + +L FG ++ +V+D T KG+ F + + AI L
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 334 NGYALGDRLLQV 345
NG LGD+ L V
Sbjct: 159 NGMQLGDKKLLV 170
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 41/75 (54%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + +P + ++++ L +S G +++ L++D T S GY F Y ++AI L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 89 NGLKLQNKSIKVSYA 103
NG++L +K + V A
Sbjct: 157 NGMQLGDKKLLVQRA 171
Score = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ L D+ + +L FG ++ +V+D T KG+ F + + AI L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 334 NGYALGDRLLQV 345
NG LGD+ L V
Sbjct: 157 NGMQLGDKKLLV 168
>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 = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 43/81 (53%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E ++L V+ + + + L+ +F G V + RD+ T +S G+ FV ++ DAE
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104
Query: 84 AIIELNGLKLQNKSIKVSYAR 104
A+ ++G L + ++V AR
Sbjct: 105 AMDAMDGAVLDGRELRVQMAR 125
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 41/97 (42%), Gaps = 15/97 (15%)
Query: 100 VSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVS 159
+SY RP + +L V L + + L +F YG + I D+ E
Sbjct: 35 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE------- 87
Query: 160 GTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEG 196
S+G FVRF+ +AE AM ++G + +G
Sbjct: 88 --------SRGFAFVRFHDKRDAEDAMDAMDGAVLDG 116
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 41/75 (54%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + +P + ++++ L +S G +++ L++D T S GY F Y ++AI L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 89 NGLKLQNKSIKVSYA 103
NG++L +K + V A
Sbjct: 64 NGMQLGDKKLLVQRA 78
Score = 37.0 bits (84), Expect = 0.019, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 35/72 (48%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ L D+ + +L FG ++ +V+D T KG+ F + + AI L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 334 NGYALGDRLLQV 345
NG LGD+ L V
Sbjct: 64 NGMQLGDKKLLV 75
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 37/142 (26%), Positives = 65/142 (45%), Gaps = 25/142 (17%)
Query: 70 YGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKR--ANLYVSGLPKHMTQE 127
+G+V++ ED E+A+ EL GLK+ IK+ + +R L LP +TQ+
Sbjct: 50 FGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQD 108
Query: 128 DLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQ 187
+L+ +F I ++ S++ +S KGI ++ F +AE +
Sbjct: 109 ELKEVFEDAAEI--------RLVSKDGKS------------KGIAYIEFKTEADAEKTFE 148
Query: 188 ELNGTIPEGASEPITVKFANSP 209
E GT +G S I++ + P
Sbjct: 149 EKQGTEIDGRS--ISLYYTGEP 168
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 42/74 (56%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V LA E +D VL F PFG + ++++ D +T K +GF FV ++A AI ++
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 334 NGYALGDRLLQVSF 347
N L R ++V+
Sbjct: 126 NESELFGRTIRVNL 139
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 37/75 (49%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + + + L F G++ ++ D T + G+ FV + EDA AI +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 89 NGLKLQNKSIKVSYA 103
N +L ++I+V+ A
Sbjct: 126 NESELFGRTIRVNLA 140
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
N+ V + + T E+++ LFS G+V + KLI D+ T + G+GFV + E AI +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAK 61
Query: 88 LNGLKLQNKSIKVSYARP 105
L+ ++I+V+ A P
Sbjct: 62 LDNTDFMGRTIRVTEANP 79
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF-AIQS 332
I+V NL + +LF FG V NVK++ D +T K KGFGFV M +E+V AI
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ--EESVSEAIAK 61
Query: 333 LNGYALGDRLLQVS 346
L+ R ++V+
Sbjct: 62 LDNTDFMGRTIRVT 75
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 30/85 (35%), Positives = 48/85 (56%), Gaps = 3/85 (3%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
Q L V + + +T+ + LFS +G +SCK+I + T+ Y FV +Y DA A
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAA 71
Query: 85 IIELNGLKLQNKSIKVSYA-RPSSE 108
+ +NG K+ K +KV++A PSS+
Sbjct: 72 LAAMNGRKILGKEVKVNWATTPSSQ 96
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 42/74 (56%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V LA E +D VL F PFG + ++++ D +T K +GF FV ++A AI ++
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 334 NGYALGDRLLQVSF 347
N L R ++V+
Sbjct: 68 NESELFGRTIRVNL 81
Score = 34.7 bits (78), Expect = 0.074, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 38/76 (50%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + + + L F G++ ++ D T + G+ FV + EDA AI +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 89 NGLKLQNKSIKVSYAR 104
N +L ++I+V+ A+
Sbjct: 68 NESELFGRTIRVNLAK 83
>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 = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 42/74 (56%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V LA E +D VL F PFG + ++++ D +T K +GF FV ++A AI ++
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 334 NGYALGDRLLQVSF 347
N L R ++V+
Sbjct: 65 NESELFGRTIRVNL 78
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 37/75 (49%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + + + L F G++ ++ D T + G+ FV + EDA AI +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 89 NGLKLQNKSIKVSYA 103
N +L ++I+V+ A
Sbjct: 65 NESELFGRTIRVNLA 79
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 42/74 (56%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V LA E +D VL F PFG + ++++ D +T K +GF FV ++A AI ++
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 334 NGYALGDRLLQVSF 347
N L R ++V+
Sbjct: 70 NESELFGRTIRVNL 83
Score = 34.7 bits (78), Expect = 0.074, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 38/76 (50%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + + + L F G++ ++ D T + G+ FV + EDA AI +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 89 NGLKLQNKSIKVSYAR 104
N +L ++I+V+ A+
Sbjct: 70 NESELFGRTIRVNLAK 85
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 2/80 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V LA E +D VL F PFG + ++++ D +T K +GF FV ++A AI ++
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 334 NGYALGDRLLQVSFKTHKPL 353
N L R ++V+ KP+
Sbjct: 75 NESELFGRTIRVNLA--KPM 92
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 39/77 (50%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + + + L F G++ ++ D T + G+ FV + EDA AI +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 89 NGLKLQNKSIKVSYARP 105
N +L ++I+V+ A+P
Sbjct: 75 NESELFGRTIRVNLAKP 91
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/121 (23%), Positives = 56/121 (46%)
Query: 19 QSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRT 78
Q + +++ L V + T+E++ LFS G+++ + DK + G+ FV YY
Sbjct: 32 QEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSR 91
Query: 79 EDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGT 138
DAE A+ +NG +L ++ I+ + E + G + ++D + YG
Sbjct: 92 ADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRGGYGK 151
Query: 139 I 139
+
Sbjct: 152 L 152
Score = 35.4 bits (80), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 15/82 (18%)
Query: 111 KRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKG 170
K LYV L + T+E + LF G +++ + G ++ + + G
Sbjct: 38 KSCTLYVGNLSFYTTEEQIYELFSKSG---------------DIKKIIMGLDKMKKTACG 82
Query: 171 IGFVRFNQHIEAEHAMQELNGT 192
FV + +AE+AM+ +NGT
Sbjct: 83 FCFVEYYSRADAENAMRYINGT 104
Score = 33.1 bits (74), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 39/74 (52%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL+ T + +++LF G ++ + + D GF FV + +A A++ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 334 NGYALGDRLLQVSF 347
NG L DR+++ +
Sbjct: 102 NGTRLDDRIIRTDW 115
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 22/47 (46%), Positives = 30/47 (63%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
L V + + TQE L+ FS GEV C +++DKTT QS G+GFV +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
Score = 34.3 bits (77), Expect = 0.10, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 15/62 (24%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V GL TQE L + F YG ++ I+ DK ++ S+G GFV
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQ---------------SRGFGFV 63
Query: 175 RF 176
+F
Sbjct: 64 KF 65
Score = 30.4 bits (67), Expect = 1.6, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 23/45 (51%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+FV L T L F +G V + +++D T + +GFGFV
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 48/85 (56%), Gaps = 2/85 (2%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
P +S+ GW +FV ++ E +++ + + F +G ++N+ + D +T KG+ V
Sbjct: 66 PQRSV--EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 123
Query: 323 YDEAVFAIQSLNGYALGDRLLQVSF 347
+ +A+ A ++LNG + + +QV +
Sbjct: 124 HKQALAAKEALNGAEIMGQTIQVDW 148
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 38/74 (51%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + ++E+Q F GE+++ L D+ T S GY V Y + A A L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 89 NGLKLQNKSIKVSY 102
NG ++ ++I+V +
Sbjct: 135 NGAEIMGQTIQVDW 148
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 43/81 (53%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E ++L V+ + + + L+ +F G V + RD+ T +S G+ FV ++ DAE
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 84 AIIELNGLKLQNKSIKVSYAR 104
A+ ++G L + ++V AR
Sbjct: 128 AMDAMDGAVLDGRELRVQMAR 148
Score = 35.8 bits (81), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 15/83 (18%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+L V L + + L +F YG + I D+ E S+G F
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE---------------SRGFAF 116
Query: 174 VRFNQHIEAEHAMQELNGTIPEG 196
VRF+ +AE AM ++G + +G
Sbjct: 117 VRFHDKRDAEDAMDAMDGAVLDG 139
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 45.8 bits (107), Expect = 4e-05, Method: Composition-based stats.
Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 3/67 (4%)
Query: 261 MLPPKSLHGSGWC-IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVC 319
++P S GS C +F+ L+ +T L + FG FG V+ V+RDP T + +GFGFV
Sbjct: 14 LVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV- 72
Query: 320 MTNYDEA 326
T D+A
Sbjct: 73 -TFMDQA 78
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
TQE L+ F GEV+ C ++RD T +S G+GFV + ++ + + + +L +K+I
Sbjct: 38 TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTI 96
Query: 99 --KVSYAR 104
KV++ R
Sbjct: 97 DPKVAFPR 104
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
Identities = 24/83 (28%), Positives = 47/83 (56%), Gaps = 8/83 (9%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + T+T+E L+ FS G++E K ++D Y F+++ + A +A+ E+
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 89 NGLKLQNKSIKVSYARPSSEAIK 111
NG L+ ++I++ +A+P + K
Sbjct: 66 NGKDLEGENIEIVFAKPPDQKRK 88
Score = 35.4 bits (80), Expect = 0.043, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 8/74 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NLA + +L + F FG ++ VK K K + F+ D AV A++ +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEEM 65
Query: 334 NGYALGDRLLQVSF 347
NG L +++ F
Sbjct: 66 NGKDLEGENIEIVF 79
Score = 32.3 bits (72), Expect = 0.39, Method: Composition-based stats.
Identities = 30/104 (28%), Positives = 42/104 (40%), Gaps = 25/104 (24%)
Query: 106 SSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIP 165
SS K L+V L +T+E LE F +G + E V+
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKL------------ERVKKL-------- 44
Query: 166 QISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
K F+ F++ A AM+E+NG EG E I + FA P
Sbjct: 45 ---KDYAFIHFDERDGAVKAMEEMNGKDLEG--ENIEIVFAKPP 83
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL + +L++LF G + V + +D + K K FGFVC + + +AI L
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPESVSYAIALL 77
Query: 334 NGYALGDRLLQVS 346
NG L R + VS
Sbjct: 78 NGIRLYGRPINVS 90
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 3/84 (3%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E + + V + + +E L LF G + + +D+ + +GFV + E
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSY 72
Query: 84 AIIELNGLKLQNKSIKVSYARPSS 107
AI LNG++L + I VS PSS
Sbjct: 73 AIALLNGIRLYGRPINVS--GPSS 94
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 44.7 bits (104), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 1/77 (1%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKT-TAQSLGYG 71
S S+ Q + S ++V +P Q E++ LFS+ GE+++ +L + T T G+G
Sbjct: 2 SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61
Query: 72 FVNYYRTEDAERAIIEL 88
FV++ +DA++A L
Sbjct: 62 FVDFITKQDAKKAFNAL 78
>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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/79 (31%), Positives = 42/79 (53%), Gaps = 6/79 (7%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
Q S L V +P +T+EE++ LF G+ + +DK G+GF+ AE A
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIA 67
Query: 85 IIELNGLKLQNKSIKVSYA 103
+EL+ + L+ K ++V +A
Sbjct: 68 KVELDNMPLRGKQLRVRFA 86
Score = 34.7 bits (78), Expect = 0.074, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 6/77 (7%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL P+ + + +LF +G V + +D KGFGF+ + A A L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 334 NGYALGDRLLQVSFKTH 350
+ L + L+V F H
Sbjct: 72 DNMPLRGKQLRVRFACH 88
Score = 33.1 bits (74), Expect = 0.22, Method: Composition-based stats.
Identities = 26/96 (27%), Positives = 39/96 (40%), Gaps = 23/96 (23%)
Query: 111 KRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKG 170
+R+ L+V LP +T+E++ LF YG + K KG
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEKYGK--AGEVFIHK-------------------DKG 52
Query: 171 IGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
GF+R AE A EL+ G + + V+FA
Sbjct: 53 FGFIRLETRTLAEIAKVELDNMPLRG--KQLRVRFA 86
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 37/86 (43%), Gaps = 21/86 (24%)
Query: 111 KRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKG 170
K +Y G+ +T + + F P+G I+ R+ PE KG
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF----------------PE-----KG 62
Query: 171 IGFVRFNQHIEAEHAMQELNGTIPEG 196
FVRF+ H A HA+ +NGT EG
Sbjct: 63 YSFVRFSTHESAAHAIVSVNGTTIEG 88
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++ +A D ++ Q F PFG + ++V + KG+ FV + ++ A AI S+
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 334 NGYALGDRLLQVSFKTHKP 352
NG + +++ + P
Sbjct: 82 NGTTIEGHVVKCYWGKESP 100
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+N + + +T + ++ FS G++ ++ +K GY FV + E A A
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHA 77
Query: 85 IIELNGLKLQNKSIKVSYARPS 106
I+ +NG ++ +K + + S
Sbjct: 78 IVSVNGTTIEGHVVKCYWGKES 99
>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 = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 21 DVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTED 80
D ++ + V + + +E + FS G + +L+ DK T QS G+GFV Y + D
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVT-YDSAD 140
Query: 81 AERAIIELNGLKLQNKSIKVSYARP 105
A + + + +++ I++ A P
Sbjct: 141 AVDRVCQNKFIDFKDRKIEIKRAEP 165
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCM---TNYDEAVFAI 330
+F+ L +T ++ L + FG +G V ++K+++DP T + +GFGF+ ++ DE V
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 331 QSLNGYAL 338
L+G +
Sbjct: 66 HILDGKVI 73
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 32/73 (43%)
Query: 252 LTADLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYK 311
L +++ P+ IFV + P+ + F +G + + +++ D T +
Sbjct: 68 LDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQ 127
Query: 312 CKGFGFVCMTNYD 324
+GFGFV + D
Sbjct: 128 SRGFGFVTYDSAD 140
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 45/84 (53%), Gaps = 1/84 (1%)
Query: 19 QSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRT 78
Q + +++ L V + T+E++ LFS G+++ + DK + G+ FV YY
Sbjct: 11 QEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT-ACGFCFVEYYSR 69
Query: 79 EDAERAIIELNGLKLQNKSIKVSY 102
DAE A+ +NG +L ++ I+ +
Sbjct: 70 ADAENAMRYINGTRLDDRIIRTDW 93
Score = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL+ T + +++LF G ++ + + D C GF FV + +A A++ +
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC-GFCFVEYYSRADAENAMRYI 79
Query: 334 NGYALGDRLLQVSF 347
NG L DR+++ +
Sbjct: 80 NGTRLDDRIIRTDW 93
Score = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 16/82 (19%)
Query: 111 KRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKG 170
K LYV L + T+E + LF G I + DKM + + G
Sbjct: 17 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT----------------ACG 60
Query: 171 IGFVRFNQHIEAEHAMQELNGT 192
FV + +AE+AM+ +NGT
Sbjct: 61 FCFVEYYSRADAENAMRYINGT 82
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 31/96 (32%), Positives = 48/96 (50%), Gaps = 19/96 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L K +++D+ LF +G I IL + SKG FV
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGN----------------SKGCAFV 61
Query: 175 RFNQHIEAEHAMQELNG--TIPEGASEPITVKFANS 208
+++ H EA+ A+ L+G T+P GAS + VKFA++
Sbjct: 62 KYSSHAEAQAAINALHGSQTMP-GASSSLVVKFADT 96
Score = 31.6 bits (70), Expect = 0.68, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV L + ++ + +LF FG ++ ++R P KG FV +++ EA AI +L
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDG-NSKGCAFVKYSSHAEAQAAINAL 76
Query: 334 NG 335
+G
Sbjct: 77 HG 78
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 48/85 (56%), Gaps = 2/85 (2%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
P +S+ G W +FV ++ E +++ + + F +G ++N+ + D +T KG+ V
Sbjct: 20 PQRSVEG--WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 77
Query: 323 YDEAVFAIQSLNGYALGDRLLQVSF 347
+ +A+ A ++LNG + + +QV +
Sbjct: 78 HKQALAAKEALNGAEIMGQTIQVDW 102
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 38/74 (51%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + + ++E+Q F GE+++ L D+ T S GY V Y + A A L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 89 NGLKLQNKSIKVSY 102
NG ++ ++I+V +
Sbjct: 89 NGAEIMGQTIQVDW 102
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T E+++H F G+V+ L+ DKTT + G+GFV + +ED + E++ ++ NK +
Sbjct: 12 TVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVT-FESEDIVEKVCEIHFHEINNKMV 70
Query: 99 KVSYA 103
+ A
Sbjct: 71 ECKKA 75
Score = 29.6 bits (65), Expect = 2.7, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 25/51 (49%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
IFV L+ T + F FG V + ++ D T + +GFGFV + D
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESED 52
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 8/72 (11%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V V T +EL+ LF G V C +++D Y FV+ + DA+ AI +L
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63
Query: 89 NGLKLQNKSIKV 100
NG +++ K I V
Sbjct: 64 NGKEVKGKRINV 75
Score = 33.1 bits (74), Expect = 0.24, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 34/81 (41%), Gaps = 8/81 (9%)
Query: 269 GSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF 328
G+ W IFV N++ L LF G V VV+D + FV M +A
Sbjct: 7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKA 58
Query: 329 AIQSLNGYALGDRLLQVSFKT 349
AI LNG + + + V T
Sbjct: 59 AIAQLNGKEVKGKRINVELST 79
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ L P T D L +L P+G + + K + D T KCKG+GFV + A A+ +L
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 334 NGYALGDRLLQVS 346
+ ++ + S
Sbjct: 68 KASGVQAQMAKQS 80
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+S L + + T ++L L G++ S K I DKTT + GYGFV++ A++A+
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 86 IELNGLKLQNKSIKVSYARPSS 107
L +Q + K S PSS
Sbjct: 65 TALKASGVQAQMAKQS--GPSS 84
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 15/80 (18%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+ LY+ GL T +DL L +PYG I++++ + DK ++ KG G
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNK---------------CKGYG 50
Query: 173 FVRFNQHIEAEHAMQELNGT 192
FV F+ A+ A+ L +
Sbjct: 51 FVDFDSPSAAQKAVTALKAS 70
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
P +S+ GW +FV + E + + F +G ++N+ + D +T KG+ V
Sbjct: 16 PQRSV--EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 73
Query: 323 YDEAVFAIQSLNGYALGDRLLQVSF 347
Y EA A++ LNG L + + V +
Sbjct: 74 YKEAQAAMEGLNGQDLMGQPISVDW 98
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 38/74 (51%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V V + T+E++ F+ GE+++ L D+ T GY V Y ++A+ A+ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 89 NGLKLQNKSIKVSY 102
NG L + I V +
Sbjct: 85 NGQDLMGQPISVDW 98
Score = 34.7 bits (78), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 41/91 (45%), Gaps = 17/91 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V+G+ + T+ED+ + F YG I + D+ KG V
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTG---------------YLKGYTLV 69
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKF 205
+ + EA+ AM+ LNG G +PI+V +
Sbjct: 70 EYETYKEAQAAMEGLNGQDLMG--QPISVDW 98
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 34/56 (60%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTE 79
++ S+LIV +P T+++L+ FS+ GEV ++ +D T S G+GFV + E
Sbjct: 13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
Score = 37.0 bits (84), Expect = 0.019, Method: Composition-based stats.
Identities = 21/54 (38%), Positives = 29/54 (53%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAV 327
+ V L +T + L + F FG V V+V +D +T KGFGFV T Y+ V
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 71
Score = 35.0 bits (79), Expect = 0.064, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 20/78 (25%)
Query: 107 SEAIKRA-----NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGT 161
S +KRA +L V GLP T++DL+ F +G ++ ++ D
Sbjct: 5 SSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGH--------- 55
Query: 162 PEIPQISKGIGFVRFNQH 179
SKG GFVRF ++
Sbjct: 56 ------SKGFGFVRFTEY 67
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 41/77 (53%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
S + V+ +P ++T +L +FS G+V +++DK T +S G F+ + + A+
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 87 ELNGLKLQNKSIKVSYA 103
+N +L + IK S A
Sbjct: 77 AINNKQLFGRVIKASIA 93
Score = 37.4 bits (85), Expect = 0.013, Method: Composition-based stats.
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 15/82 (18%)
Query: 109 AIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQIS 168
A ++ +YVS LP +T DL +F YG ++ I+ DK + S
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRK---------------S 57
Query: 169 KGIGFVRFNQHIEAEHAMQELN 190
KG+ F+ F A++ + +N
Sbjct: 58 KGVAFILFLDKDSAQNCTRAIN 79
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 1/79 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + + + ++ L+ +F G + LI+D+T+ +S G+ F+ + DA+ A ++
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKNAAKDM 68
Query: 89 NGLKLQNKSIKVSYARPSS 107
NG L K+IKV A+ S
Sbjct: 69 NGKSLHGKAIKVEQAKKPS 87
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ L ET + +L +FG G + V +++D +T K +GF F+ N +A A + +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDM 68
Query: 334 NGYALGDRLLQVSFKTHKP 352
NG +L + ++V + KP
Sbjct: 69 NGKSLHGKAIKVE-QAKKP 86
Score = 29.6 bits (65), Expect = 2.6, Method: Composition-based stats.
Identities = 23/102 (22%), Positives = 45/102 (44%), Gaps = 18/102 (17%)
Query: 108 EAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQI 167
EA L++ GL + ++ L+ +F +G I ++ D+ +
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSK---------------- 46
Query: 168 SKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
S+G F+ F +A++A +++NG G + I V+ A P
Sbjct: 47 SRGFAFITFENPADAKNAAKDMNGKSLHGKA--IKVEQAKKP 86
>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 = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 40/74 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV +L +D L F F + + V+ D QT +G+GFV T+ D+A A+ S+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 334 NGYALGDRLLQVSF 347
G L R L++++
Sbjct: 64 QGQDLNGRPLRINW 77
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 39/76 (51%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
NL V + + E L++ F S ++ D T S GYGFV++ +DA+ A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 88 LNGLKLQNKSIKVSYA 103
+ G L + +++++A
Sbjct: 63 MQGQDLNGRPLRINWA 78
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 17/93 (18%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
NL+V L ++ E L N F+ + + ++ ++ D S+G GF
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGS---------------SRGYGF 47
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
V F +A++AM + G G P+ + +A
Sbjct: 48 VSFTSQDDAQNAMDSMQGQDLNG--RPLRINWA 78
>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 = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
P +S+ GW +FV + E + + F +G ++N+ + D +T KG+ V
Sbjct: 1 PQRSV--EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 58
Query: 323 YDEAVFAIQSLNGYALGDRLLQVSF 347
Y EA A++ LNG L + + V +
Sbjct: 59 YKEAQAAMEGLNGQDLMGQPISVDW 83
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V V + T+E++ F+ GE+++ L D+ T GY V Y ++A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 89 NGLKLQNKSIKVSYA 103
NG L + I V +
Sbjct: 70 NGQDLMGQPISVDWC 84
Score = 34.3 bits (77), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 41/92 (44%), Gaps = 17/92 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V+G+ + T+ED+ + F YG I + D+ KG V
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTG---------------YLKGYTLV 54
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
+ + EA+ AM+ LNG G +PI+V +
Sbjct: 55 EYETYKEAQAAMEGLNGQDLMG--QPISVDWC 84
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 41.6 bits (96), Expect = 7e-04, Method: Composition-based stats.
Identities = 22/53 (41%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA 326
+F+ L+ +T L + FG FG V+ V+RDP T + +GFGFV T D+A
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFV--TFMDQA 53
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 17/37 (45%), Positives = 24/37 (64%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
TQE L+ F GEV+ C ++RD T +S G+GFV +
Sbjct: 13 TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>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 = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 54/103 (52%), Gaps = 20/103 (19%)
Query: 107 SEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ 166
S ++++ L++SGLP T+E+LE + + +GT+ R++ ++ +G P
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR----------AGKP---- 57
Query: 167 ISKGIGFVRFNQHIEAEHAMQELNG-TIPEGASEPITVKFANS 208
KG+ +V + +A A+ +++G TI E I V +NS
Sbjct: 58 --KGLAYVEYENESQASQAVMKMDGMTIKENI---IKVAISNS 95
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 47/81 (58%), Gaps = 3/81 (3%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L ++ +P + T+EEL+ + + G V+ +L+ ++ + G +V Y A +A++++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAVMKM 78
Query: 89 NGLKLQNKSIKV--SYARPSS 107
+G+ ++ IKV S + PSS
Sbjct: 79 DGMTIKENIIKVAISNSGPSS 99
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 35/142 (24%), Positives = 64/142 (45%), Gaps = 23/142 (16%)
Query: 59 IRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSY--ARPSSEAIKRANLY 116
+ D T + +G+V++ ED E+A+ EL GLK+ IK+ R S + L
Sbjct: 45 VVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLL 103
Query: 117 VSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRF 176
L ++T+++L+ +F I ++ S++ +S KGI ++ F
Sbjct: 104 AKNLSFNITEDELKEVFEDALEI--------RLVSQDGKS------------KGIAYIEF 143
Query: 177 NQHIEAEHAMQELNGTIPEGAS 198
+AE ++E G +G S
Sbjct: 144 KSEADAEKNLEEKQGAEIDGRS 165
>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 = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 4/71 (5%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI- 85
+ + V + M + E++ F+ G V+ K+I D+T S GYGFV++Y D ++ +
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGV-SKGYGFVSFYNDVDVQKIVE 68
Query: 86 --IELNGLKLQ 94
I +G KL+
Sbjct: 69 SQINFHGKKLK 79
Score = 32.0 bits (71), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
+FV + ++ + F +G+V+ VK++ D +T KG+GFV N
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYN 59
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 16/73 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V G+ M + ++ + F YG++ +I+ D+ +SKG GFV
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG----------------VSKGYGFV 55
Query: 175 RFNQHIEAEHAMQ 187
F ++ + ++
Sbjct: 56 SFYNDVDVQKIVE 68
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 8/81 (9%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + +P+ T++E++ LF G+V C +I++ YGFV+ AE AI L
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRNL 62
Query: 89 NGLKLQNKSIKVSYARPSSEA 109
+ KL +I V ++ S+A
Sbjct: 63 HHYKLHGVNINVEASKNKSKA 83
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 23/76 (30%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L++ LP+ T++++ +LF YG ++ CD I K GFV
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLE----CD-------------------IIKNYGFV 47
Query: 175 RFNQHIEAEHAMQELN 190
AE A++ L+
Sbjct: 48 HIEDKTAAEDAIRNLH 63
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 3/84 (3%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+ + V +P T L+ F G++E +I D+ T +S GYGFV AERA
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Query: 87 ELNGLKLQNKS-IKVSY--ARPSS 107
+ N + K+ + ++Y A+P S
Sbjct: 78 DPNPIIDGRKANVNLAYLGAKPRS 101
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 31/61 (50%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV L T D L + F FG ++ V+ D QT K +G+GFV M + A A +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 334 N 334
N
Sbjct: 80 N 80
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 32/79 (40%), Gaps = 15/79 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V GLP H T L F +G I + ++ D+ + S+G GFV
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGK---------------SRGYGFV 64
Query: 175 RFNQHIEAEHAMQELNGTI 193
AE A ++ N I
Sbjct: 65 TMADRAAAERACKDPNPII 83
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
P +S+ G W +FV + E + + F +G ++N+ + D +T KG+ V
Sbjct: 1 PQRSVEG--WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 58
Query: 323 YDEAVFAIQSLNGYAL 338
Y EA A++ LNG L
Sbjct: 59 YKEAQAAMEGLNGQDL 74
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 38/74 (51%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V V + T+E++ F+ GE+++ L D+ T GY V Y ++A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 89 NGLKLQNKSIKVSY 102
NG L + I V +
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 34.3 bits (77), Expect = 0.12, Method: Composition-based stats.
Identities = 25/91 (27%), Positives = 41/91 (45%), Gaps = 17/91 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V+G+ + T+ED+ + F YG I + D+ KG V
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTG---------------YLKGYTLV 54
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKF 205
+ + EA+ AM+ LNG G +PI+V +
Sbjct: 55 EYETYKEAQAAMEGLNGQDLMG--QPISVDW 83
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
P +S+ G W +FV + E + + F +G ++N+ + D +T KG+ V
Sbjct: 1 PQRSVEG--WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 58
Query: 323 YDEAVFAIQSLNGYAL 338
Y EA A++ LNG L
Sbjct: 59 YKEAQAAMEGLNGQDL 74
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 38/74 (51%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V V + T+E++ F+ GE+++ L D+ T GY V Y ++A+ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 89 NGLKLQNKSIKVSY 102
NG L + I V +
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 25/91 (27%), Positives = 41/91 (45%), Gaps = 17/91 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V+G+ + T+ED+ + F YG I + D+ KG V
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTG---------------YLKGYTLV 54
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKF 205
+ + EA+ AM+ LNG G +PI+V +
Sbjct: 55 EYETYKEAQAAMEGLNGQDLMG--QPISVDW 83
>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 = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 38/74 (51%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V V + T+E++ F+ GE+++ L D+ T GY V Y ++A+ A+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 89 NGLKLQNKSIKVSY 102
NG L + I V +
Sbjct: 72 NGQDLMGQPISVDW 85
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
P +S+ G W +FV + E + + F +G ++N+ + D +T KG+ V
Sbjct: 3 PQRSVEG--WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 323 YDEAVFAIQSLNGYALGDRLLQVSF 347
Y EA A++ LNG L + + V +
Sbjct: 61 YKEAQAAMEGLNGQDLMGQPISVDW 85
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 25/91 (27%), Positives = 41/91 (45%), Gaps = 17/91 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V+G+ + T+ED+ + F YG I + D+ KG V
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTG---------------YLKGYTLV 56
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKF 205
+ + EA+ AM+ LNG G +PI+V +
Sbjct: 57 EYETYKEAQAAMEGLNGQDLMG--QPISVDW 85
>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 = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 38/74 (51%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V V + T+E++ F+ GE+++ L D+ T GY V Y ++A+ A+ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 89 NGLKLQNKSIKVSY 102
NG L + I V +
Sbjct: 86 NGQDLMGQPISVDW 99
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
P +S+ G W +FV + E + + F +G ++N+ + D +T KG+ V
Sbjct: 17 PQRSVEG--WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 74
Query: 323 YDEAVFAIQSLNGYAL 338
Y EA A++ LNG L
Sbjct: 75 YKEAQAAMEGLNGQDL 90
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 25/91 (27%), Positives = 41/91 (45%), Gaps = 17/91 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V+G+ + T+ED+ + F YG I + D+ KG V
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTG---------------YLKGYTLV 70
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKF 205
+ + EA+ AM+ LNG G +PI+V +
Sbjct: 71 EYETYKEAQAAMEGLNGQDLMG--QPISVDW 99
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 266 SLHGSG-WCIFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNY 323
L G+G + V NL PE L+ LFG +G VQ VK++ + K V M +
Sbjct: 28 GLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADG 82
Query: 324 DEAVFAIQSLNGYALGDRLLQVSFKTHK 351
++A A+ LNG+ L + ++++ H+
Sbjct: 83 NQAQLAMSHLNGHKLHGKPIRITLSKHQ 110
Score = 31.2 bits (69), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 54/105 (51%), Gaps = 14/105 (13%)
Query: 8 YNTTQSHRSTYQSDVNEQN-----SNLIVNYVPQTMTQEELQHLFSSVGE-VESCKLI-R 60
Y + HR N QN + L ++ +P ++++E+L+ LFSS G V+ K +
Sbjct: 128 YGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK 187
Query: 61 DKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL-QNKSIKVSYAR 104
D+ A + E+A +A+I+L+ L +N ++VS+++
Sbjct: 188 DRKMA------LIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK 226
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 4/60 (6%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI---IELNGLKLQ 94
M + E++ F+ G V+ K+I D+T S GYGFV++Y D ++ + I +G KL+
Sbjct: 22 MDETEIRSFFARYGSVKEVKIITDRTGV-SKGYGFVSFYNDVDVQKIVESQINFHGKKLK 80
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
+FV + ++ + F +G+V+ VK++ D +T KG+GFV N
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYN 60
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 16/81 (19%)
Query: 107 SEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ 166
S I ++V G+ M + ++ + F YG++ +I+ D+
Sbjct: 5 SGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG---------------- 48
Query: 167 ISKGIGFVRFNQHIEAEHAMQ 187
+SKG GFV F ++ + ++
Sbjct: 49 VSKGYGFVSFYNDVDVQKIVE 69
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 4/60 (6%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI---IELNGLKLQ 94
M + E++ F+ G V+ K+I D+T S GYGFV++Y D ++ + I +G KL+
Sbjct: 21 MDETEIRSFFARYGSVKEVKIITDRTGV-SKGYGFVSFYNDVDVQKIVESQINFHGKKLK 79
Score = 30.0 bits (66), Expect = 1.8, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
+FV + ++ + F +G+V+ VK++ D +T KG+GFV N
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYN 59
Score = 30.0 bits (66), Expect = 2.1, Method: Composition-based stats.
Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 16/73 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V G+ M + ++ + F YG++ +I+ D+ +SKG GFV
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG----------------VSKGYGFV 55
Query: 175 RFNQHIEAEHAMQ 187
F ++ + ++
Sbjct: 56 SFYNDVDVQKIVE 68
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 17/82 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+VS +P DL +F +G I+ I+ ++ S KG GFV
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-----------------KGFGFV 74
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F +A+ A ++L+GT+ EG
Sbjct: 75 TFENSADADRAREKLHGTVVEG 96
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 9/88 (10%)
Query: 264 PKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNY 323
PK LH V N+ D L Q+FG FG + +V+++ + + KGFGFV N
Sbjct: 29 PKRLH-------VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENS 79
Query: 324 DEAVFAIQSLNGYALGDRLLQVSFKTHK 351
+A A + L+G + R ++V+ T +
Sbjct: 80 ADADRAREKLHGTVVEGRKIEVNNATAR 107
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 22/88 (25%), Positives = 48/88 (54%), Gaps = 2/88 (2%)
Query: 16 STYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
S ++ Q L V+ +P +L+ +F G++ ++I ++ ++ G+GFV +
Sbjct: 19 SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTF 76
Query: 76 YRTEDAERAIIELNGLKLQNKSIKVSYA 103
+ DA+RA +L+G ++ + I+V+ A
Sbjct: 77 ENSADADRAREKLHGTVVEGRKIEVNNA 104
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 17/82 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+VS +P DL +F +G I+ I+ ++ S KG GFV
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-----------------KGFGFV 60
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F +A+ A ++L+GT+ EG
Sbjct: 61 TFENSADADRAREKLHGTVVEG 82
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 9/88 (10%)
Query: 264 PKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNY 323
PK LH V N+ D L Q+FG FG + +V+++ + + KGFGFV N
Sbjct: 15 PKRLH-------VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENS 65
Query: 324 DEAVFAIQSLNGYALGDRLLQVSFKTHK 351
+A A + L+G + R ++V+ T +
Sbjct: 66 ADADRAREKLHGTVVEGRKIEVNNATAR 93
Score = 37.0 bits (84), Expect = 0.016, Method: Composition-based stats.
Identities = 20/75 (26%), Positives = 44/75 (58%), Gaps = 2/75 (2%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V+ +P +L+ +F G++ ++I ++ ++ G+GFV + + DA+RA +L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRAREKL 75
Query: 89 NGLKLQNKSIKVSYA 103
+G ++ + I+V+ A
Sbjct: 76 HGTVVEGRKIEVNNA 90
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 273 CIFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
+ V NL PE L+ LFG +G VQ VK++ + K V M + ++A A+
Sbjct: 5 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQAQLAMS 59
Query: 332 SLNGYALGDRLLQVSFKTHK 351
LNG+ L + ++++ H+
Sbjct: 60 HLNGHKLHGKPIRITLSKHQ 79
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 54/105 (51%), Gaps = 14/105 (13%)
Query: 8 YNTTQSHRSTYQSDVNEQN-----SNLIVNYVPQTMTQEELQHLFSSVGE-VESCKLI-R 60
Y + HR N QN + L ++ +P ++++E+L+ LFSS G V+ K +
Sbjct: 97 YGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK 156
Query: 61 DKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL-QNKSIKVSYAR 104
D+ A + E+A +A+I+L+ L +N ++VS+++
Sbjct: 157 DRKMA------LIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSK 195
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 33/105 (31%), Positives = 52/105 (49%), Gaps = 21/105 (20%)
Query: 107 SEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ 166
S+AIK ++V +P+ +++DL LF YG + +L D+ S+N P
Sbjct: 1 SDAIK---MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDR--SQN-----------PP 44
Query: 167 ISKGIGFVRF---NQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
SKG FV F +EA++A+ N + G PI +K A+S
Sbjct: 45 QSKGCCFVTFYTRKAALEAQNALH--NMKVLPGMHHPIQMKPADS 87
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTT--AQSLGYGFVNYYRTEDAERAII 86
+ V VP+T ++++L+ LF G V ++RD++ QS G FV +Y + A A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 87 ELNGLKL 93
L+ +K+
Sbjct: 66 ALHNMKV 72
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 35/72 (48%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL+ + + L +LF +G + + D T K KGF FV + AV A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 334 NGYALGDRLLQV 345
+G R+L V
Sbjct: 71 DGQVFQGRMLHV 82
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 36/73 (49%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
L V + T ++E+L+ LFS+ G + D T + G+ FV + E A +A E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 88 LNGLKLQNKSIKV 100
++G Q + + V
Sbjct: 70 VDGQVFQGRMLHV 82
Score = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 32/83 (38%), Gaps = 15/83 (18%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L+V L ++EDLE LF YG + D + + KG F
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKK---------------PKGFAF 54
Query: 174 VRFNQHIEAEHAMQELNGTIPEG 196
V F A A E++G + +G
Sbjct: 55 VTFMFPEHAVKAYAEVDGQVFQG 77
>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 = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+++L+ FS GEV C L D T +S G+GFV + +E ++ +++ KL K I
Sbjct: 12 TKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDK-VMDQKEHKLNGKVI 70
Score = 31.6 bits (70), Expect = 0.80, Method: Composition-based stats.
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
+F+ L+ +T L F FG V + + DP T + +GFGFV
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFV 46
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 8/75 (10%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
++ L V + T T +EL+ F G V C +++D Y FV+ R EDA AI
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAI 61
Query: 86 IELNGLKLQNKSIKV 100
L+ + Q K + V
Sbjct: 62 RGLDNTEFQGKRMHV 76
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 46/82 (56%), Gaps = 3/82 (3%)
Query: 27 SNLI-VNYVPQTMTQEELQHLFSSVG-EVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
SN++ + +PQ T+++++ S G + +L+R+K++ QS G+ FV + +DA R
Sbjct: 1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRW 60
Query: 85 I-IELNGLKLQNKSIKVSYARP 105
+ + L + + + + Y+ P
Sbjct: 61 MEANQHSLNILGQKVSMHYSDP 82
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV + +++ L ++FGPFG ++ VK++ GF FV + A AI+ +
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEV 85
Query: 334 NGYALGDRLLQVSF 347
+G + ++ L+V +
Sbjct: 86 HGKSFANQPLEVVY 99
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 38.1 bits (87), Expect = 0.008, Method: Composition-based stats.
Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 15/82 (18%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFG--AVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
I + N+AP T + + P+ AV N+++++D QT + +GF FV +++ +A
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDA----- 66
Query: 332 SLNGYALGDRLLQVSFKTHKPL 353
+LLQ+ H PL
Sbjct: 67 --------SQLLQILQSLHPPL 80
>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 = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 30/45 (66%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
IFV L+P+T + + + FG FG V+++++ D +T K +GF F+
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFI 48
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 37.7 bits (86), Expect = 0.009, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 30/45 (66%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
IFV L+P+T + + + FG FG V+++++ D +T K +GF F+
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFI 46
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 44/83 (53%), Gaps = 3/83 (3%)
Query: 23 NEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAE 82
++ + L V + + T+E L+ F G V + +++ D+ T S G+GFV++ EDA+
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKESFD--GSVRA-RIVTDRETGSSKGFGFVDFNSEEDAK 68
Query: 83 RAIIELNGLKLQNKSIKVSYARP 105
A + ++ + + +A+P
Sbjct: 69 AAKEAMEDGEIDGNKVTLDWAKP 91
Score = 29.6 bits (65), Expect = 2.4, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 18/85 (21%)
Query: 105 PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEI 164
P++ + L+V GL + T+E L+ F G++ +RI+ D+
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESFD--GSV-RARIVTDRETGS------------ 52
Query: 165 PQISKGIGFVRFNQHIEAEHAMQEL 189
SKG GFV FN +A+ A + +
Sbjct: 53 ---SKGFGFVDFNSEEDAKAAKEAM 74
Score = 29.3 bits (64), Expect = 3.1, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV L+ +T + L + F G+V+ ++V D +T KGFGFV + ++A A +++
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVR-ARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 13/84 (15%)
Query: 27 SNLIVNYVPQTM---TQEELQHLFSSV--GEVESCKLIRDKTTAQSLGYGFVNYYRTEDA 81
S++ + YV M ++E ++ F+++ G VE K IRD Y FV++ EDA
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD--------YAFVHFSNREDA 64
Query: 82 ERAIIELNGLKLQNKSIKVSYARP 105
A+ LNG L I+V+ A+P
Sbjct: 65 VEAMKALNGKVLDGSPIEVTLAKP 88
Score = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 10/76 (13%)
Query: 274 IFVYNLAPETEDNVLWQLFGPF--GAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
++V NL T + ++ + F GAV+ VK +RD + FV +N ++AV A++
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD--------YAFVHFSNREDAVEAMK 69
Query: 332 SLNGYALGDRLLQVSF 347
+LNG L ++V+
Sbjct: 70 ALNGKVLDGSPIEVTL 85
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 18/84 (21%)
Query: 273 CIFVYNLAP-ETEDNVLWQLFGPFGAVQ--NVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
I + NL P T D++L L P+ + NV+V++D QT +GF F+ ++ + A
Sbjct: 25 TIILRNLNPHSTMDSILGAL-APYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAA--- 80
Query: 330 IQSLNGYALGDRLLQVSFKTHKPL 353
+LLQ+ H PL
Sbjct: 81 -----------QLLQILQALHPPL 93
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 37.4 bits (85), Expect = 0.013, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 37/70 (52%)
Query: 276 VYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
V NL T + L ++F +G V +V + R+P T +GF FV + +A A +++G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 336 YALGDRLLQV 345
L R L+V
Sbjct: 78 AELDGRELRV 87
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV + +++ L ++FGPFG ++ VK++ GF FV + A AI+ +
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEEV 58
Query: 334 NGYALGDRLLQVSF 347
+G + ++ L+V +
Sbjct: 59 HGKSFANQPLEVVY 72
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 37.0 bits (84), Expect = 0.016, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E N L + +P +T EE+ +F G + + IR T ++ G +V Y DA+
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYEDIFDAKN 62
Query: 84 AIIELNGLKLQNKSIKVSY 102
A+ L+G + N+ + V Y
Sbjct: 63 AVDHLSGFNVSNRYLVVLY 81
Score = 33.9 bits (76), Expect = 0.16, Method: Composition-based stats.
Identities = 17/74 (22%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ NL + ++ +FG +G ++ ++V P+T +G +V + +A A+ L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFDAKNAVDHL 67
Query: 334 NGYALGDRLLQVSF 347
+G+ + +R L V +
Sbjct: 68 SGFNVSNRYLVVLY 81
Score = 31.2 bits (69), Expect = 0.94, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 18/77 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LY+ LP +T E++ ++F YG I R V TPE ++G +V
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIR--------------VGNTPE----TRGTAYV 52
Query: 175 RFNQHIEAEHAMQELNG 191
+ +A++A+ L+G
Sbjct: 53 VYEDIFDAKNAVDHLSG 69
>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
Growth Factor 2 Mrna Binding Protein 3
Length = 96
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L + +P + E L L G VESC+ + T V Y + A +A+ +L
Sbjct: 18 LQIRNIPPHLQWEVLDSLLVQYGVVESCEQV---NTDSETAVVNVTYSSKDQARQALDKL 74
Query: 89 NGLKLQNKSIKVSY 102
NG +L+N ++KV+Y
Sbjct: 75 NGFQLENFTLKVAY 88
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 36.2 bits (82), Expect = 0.027, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 8/78 (10%)
Query: 38 MTQEELQHLFSSVGE-VESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQN- 95
M + + F+++GE V S K+IR++ T GY FV + AE+ + ++NG L
Sbjct: 21 MDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGA 80
Query: 96 ---KSIKVSYAR---PSS 107
K K++YA PSS
Sbjct: 81 TPAKRFKLNYATYSGPSS 98
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 36 QTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQN 95
+ MT L+ FS G + + + A FV Y + E A++A+ ELNG ++++
Sbjct: 47 EDMTPTLLRGAFSPFGNIIDLSMDPPRNCA------FVTYEKMESADQAVAELNGTQVES 100
Query: 96 KSIKVSYAR 104
+KV+ AR
Sbjct: 101 VQLKVNIAR 109
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 35.8 bits (81), Expect = 0.033, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 33/62 (53%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
EQ L + + T+E L++ + G++ C ++RD + +S G+GFV + + +
Sbjct: 25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 84
Query: 84 AI 85
A+
Sbjct: 85 AM 86
Score = 35.4 bits (80), Expect = 0.050, Method: Composition-based stats.
Identities = 16/52 (30%), Positives = 30/52 (57%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDE 325
+F+ L+ ET + L + +G + + V+RDP + + +GFGFV ++ E
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 81
Score = 32.0 bits (71), Expect = 0.50, Method: Composition-based stats.
Identities = 24/101 (23%), Positives = 38/101 (37%), Gaps = 15/101 (14%)
Query: 100 VSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVS 159
V R E + L++ GL T+E L N + +G + ++ D +
Sbjct: 15 VPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKR------- 67
Query: 160 GTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEP 200
S+G GFV F+ E + AM +I EP
Sbjct: 68 --------SRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEP 100
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 35.8 bits (81), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 6/69 (8%)
Query: 36 QTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQN 95
+ MT L+ FS G + + + A FV Y + E A++A+ ELNG ++++
Sbjct: 23 EDMTPTLLRGAFSPFGNIIDLSMDPPRNCA------FVTYEKMESADQAVAELNGTQVES 76
Query: 96 KSIKVSYAR 104
+KV+ AR
Sbjct: 77 VQLKVNIAR 85
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 35.8 bits (81), Expect = 0.034, Method: Composition-based stats.
Identities = 27/85 (31%), Positives = 45/85 (52%), Gaps = 3/85 (3%)
Query: 269 GSGWCIFVYNLAPETEDNVLWQLF-GPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAV 327
G + +FV +L P+ +D +L++ F + + + KVV D QT KG+GFV T+ E
Sbjct: 7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQK 65
Query: 328 FAIQSLNG-YALGDRLLQVSFKTHK 351
A+ G LG + +++S K
Sbjct: 66 RALTECQGAVGLGSKPVRLSVAIPK 90
Score = 32.7 bits (73), Expect = 0.32, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 167 ISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
+SKG GFV+F +E + A+ E G + G S+P+ + A
Sbjct: 49 VSKGYGFVKFTDELEQKRALTECQGAVGLG-SKPVRLSVA 87
Score = 32.3 bits (72), Expect = 0.37, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 57 KLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG-LKLQNKSIKVSYARPSSEAIK 111
K++ D+T S GYGFV + + +RA+ E G + L +K +++S A P + +K
Sbjct: 41 KVVLDQTGV-SKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVK 95
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 35.8 bits (81), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E N L++ +P +T EE+ +F G + IR T ++ G +V Y DA+
Sbjct: 16 EVNRILMIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKN 72
Query: 84 AIIELNGLKLQNKSIKVSY 102
A L+G + N+ + V Y
Sbjct: 73 ACDHLSGFNVCNRYLVVLY 91
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 259 NSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
N LPP+ + + NL + ++ +FG +G ++ ++V P+T +G +V
Sbjct: 10 NIRLPPEV----NRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYV 62
Query: 319 CMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
+ +A A L+G+ + +R L V +
Sbjct: 63 VYEDIFDAKNACDHLSGFNVCNRYLVVLY 91
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 41/96 (42%), Gaps = 28/96 (29%)
Query: 106 SSEAIKRAN----------LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVR 155
+ +A KRAN L + LP +T E++ ++F YG I R
Sbjct: 2 AMQAAKRANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIRQIR------------ 49
Query: 156 SFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNG 191
V TPE ++G +V + +A++A L+G
Sbjct: 50 --VGNTPE----TRGTAYVVYEDIFDAKNACDHLSG 79
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 35.4 bits (80), Expect = 0.043, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 2/82 (2%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+S + V +P T + L+ F+ G V + + +S G G V + E AERA
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERAC 62
Query: 86 IELNGLKLQNKSIKVSYARPSS 107
+NG+KL + I V R +S
Sbjct: 63 RMMNGMKLSGREIDVRIDRNAS 84
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.0 bits (79), Expect = 0.062, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E N L + +P +T EE+ +F G + + IR T ++ G +V Y DA+
Sbjct: 10 EVNRILYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYEDIFDAKN 66
Query: 84 AIIELNGLKLQNKSIKVSY 102
A L+G + N+ + V Y
Sbjct: 67 ACDHLSGFNVCNRYLVVLY 85
Score = 32.3 bits (72), Expect = 0.37, Method: Composition-based stats.
Identities = 21/89 (23%), Positives = 44/89 (49%), Gaps = 7/89 (7%)
Query: 259 NSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
N LPP+ +++ NL + ++ +FG +G ++ ++V P+T +G +V
Sbjct: 4 NIRLPPEV----NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYV 56
Query: 319 CMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
+ +A A L+G+ + +R L V +
Sbjct: 57 VYEDIFDAKNACDHLSGFNVCNRYLVVLY 85
Score = 31.2 bits (69), Expect = 0.92, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 18/77 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LY+ LP +T E++ ++F YG I R V TPE ++G +V
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIR--------------VGNTPE----TRGTAYV 56
Query: 175 RFNQHIEAEHAMQELNG 191
+ +A++A L+G
Sbjct: 57 VYEDIFDAKNACDHLSG 73
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 35.0 bits (79), Expect = 0.071, Method: Composition-based stats.
Identities = 29/104 (27%), Positives = 51/104 (49%), Gaps = 23/104 (22%)
Query: 108 EAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQI 167
+AIK L+V +P+ + ++DL+ LF +G I +L D++ +
Sbjct: 14 DAIK---LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTG---------------L 55
Query: 168 SKGIGFVRF---NQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
KG F+ + + ++A+ A+ E T+P G + PI VK A S
Sbjct: 56 HKGCAFLTYCARDSALKAQSALHE-QKTLP-GMNRPIQVKPAAS 97
>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 = 34.7 bits (78), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 3/79 (3%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E N L + +P +T EE+ +F G + IR T ++ G +V Y DA+
Sbjct: 16 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKN 72
Query: 84 AIIELNGLKLQNKSIKVSY 102
A L+G + N+ + V Y
Sbjct: 73 ACDHLSGFNVCNRYLVVLY 91
Score = 34.7 bits (78), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 21/89 (23%), Positives = 44/89 (49%), Gaps = 7/89 (7%)
Query: 259 NSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
N LPP+ +++ NL + ++ +FG +G ++ ++V P+T +G +V
Sbjct: 10 NIRLPPEV----NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYV 62
Query: 319 CMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
+ +A A L+G+ + +R L V +
Sbjct: 63 VYEDIFDAKNACDHLSGFNVCNRYLVVLY 91
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 42/96 (43%), Gaps = 28/96 (29%)
Query: 106 SSEAIKRAN----------LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVR 155
+ +A KRAN LY+ LP +T E++ ++F YG I R
Sbjct: 2 AMQAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIR------------ 49
Query: 156 SFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNG 191
V TPE ++G +V + +A++A L+G
Sbjct: 50 --VGNTPE----TRGTAYVVYEDIFDAKNACDHLSG 79
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 34.7 bits (78), Expect = 0.078, Method: Composition-based stats.
Identities = 23/101 (22%), Positives = 45/101 (44%), Gaps = 14/101 (13%)
Query: 109 AIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQIS 168
++K +++ L +++T++ + +F YG I + ++M P +S
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMH--------------PHLS 46
Query: 169 KGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
KG +V F EAE A++ ++G +G T A P
Sbjct: 47 KGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAPWP 87
Score = 30.4 bits (67), Expect = 1.7, Method: Composition-based stats.
Identities = 13/72 (18%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 31 VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQ-SLGYGFVNYYRTEDAERAIIELN 89
+ + + +T++ + +FS+ G+++ + ++ S GY +V + ++AE+A+ ++
Sbjct: 9 IGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMD 68
Query: 90 GLKLQNKSIKVS 101
G ++ + I +
Sbjct: 69 GGQIDGQEITAT 80
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGF 317
G +F+ NL+ ++E+ L ++ FG ++ V+VV P T KG F
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L+V+ + ++ ++Q LF+ G ++ + D++ +SLG V++ R DA +A+ +
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMKQY 89
Query: 89 NGLKLQNKSIKV 100
NG+ L + + +
Sbjct: 90 NGVPLDGRPMNI 101
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ V +P T + L+ F+ G V + + +S G G V + E AERA +
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 68
Query: 89 NGLKLQNKSIKVSYARPSS 107
NG+KL + I V R +S
Sbjct: 69 NGMKLSGREIDVRIDRNAS 87
>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 = 33.9 bits (76), Expect = 0.14, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
++++L+ F+ GEV C + D T +S G+GF+ + E+ +
Sbjct: 24 SKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL 70
Score = 33.1 bits (74), Expect = 0.24, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 23/44 (52%)
Query: 275 FVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFV 318
FV L+ +T L F FG V + + DP T + +GFGF+
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFI 58
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 33.5 bits (75), Expect = 0.18, Method: Composition-based stats.
Identities = 27/103 (26%), Positives = 51/103 (49%), Gaps = 23/103 (22%)
Query: 108 EAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQI 167
+AIK L++ +P+++ ++DL+ LF +G I +L D+ +
Sbjct: 12 DAIK---LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTG---------------M 53
Query: 168 SKGIGFVRFNQH---IEAEHAMQELNGTIPEGASEPITVKFAN 207
KG F+ + + ++A+ A+ E T+P G + PI VK A+
Sbjct: 54 HKGCAFLTYCERESALKAQSALHE-QKTLP-GMNRPIQVKPAD 94
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 5/51 (9%)
Query: 297 AVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL--NGYALGDRLLQV 345
++++V++VRD T K KGF C +DE ++L +G LGDR L+V
Sbjct: 40 SIRSVRLVRDKDTDKFKGF---CYVEFDEVDSLKEALTYDGALLGDRSLRV 87
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 8/77 (10%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V + T+T+E L+ FS G++E K ++D Y FV++ A +A+ E+
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEM 69
Query: 89 NGLKLQNKSIKVSYARP 105
NG +++ + I++ A+P
Sbjct: 70 NGKEIEGEEIEIVLAKP 86
Score = 32.3 bits (72), Expect = 0.43, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 8/62 (12%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NLA + +L + F FG ++ VK K K + FV + AV A+ +
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEDRGAAVKAMDEM 69
Query: 334 NG 335
NG
Sbjct: 70 NG 71
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 33.1 bits (74), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIR--DKTTAQSLGYGFVNYYRTEDAE 82
++ L+++ + + T+E LQ +F E I+ +S GY F+ + EDA+
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVF------EKATFIKVPQNQNGKSKGYAFIEFASFEDAK 67
Query: 83 RAIIELNGLKLQNKSIKVSYARP 105
A+ N +++ ++I++ P
Sbjct: 68 EALNSCNKREIEGRAIRLELQGP 90
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 32.7 bits (73), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 21/93 (22%), Positives = 43/93 (46%), Gaps = 9/93 (9%)
Query: 12 QSHRSTYQSDVNEQNSNLIVNYVPQTMTQE-ELQHLFSSVGEVESCKLIRDKTTAQSLGY 70
Q+ T ++D NS + + + + ++ +++ +FS G V C + + GY
Sbjct: 13 QASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GY 64
Query: 71 GFVNYYRTEDAERAIIELNGLKLQNKSIKVSYA 103
FV Y A A++ NG L +++ ++ A
Sbjct: 65 AFVQYSNERHARAAVLGENGRVLAGQTLDINMA 97
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 32.3 bits (72), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 30/102 (29%), Positives = 44/102 (43%), Gaps = 20/102 (19%)
Query: 110 IKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISK 169
I + ++YV + T +DLE F G+I ILCDK SG P K
Sbjct: 34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKF---------SGHP------K 78
Query: 170 GIGFVRFNQH--IEAEHAMQELNGTIPEGASEPITVKFANSP 209
G ++ F + ++A AM E T+ G + + K N P
Sbjct: 79 GYAYIEFAERNSVDAAVAMDE---TVFRGRTIKVLPKRTNMP 117
Score = 30.0 bits (66), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/73 (21%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIE 87
++ V V T ++L+ FSS G + ++ DK + GY ++ + + A +
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVD-AAVA 96
Query: 88 LNGLKLQNKSIKV 100
++ + ++IKV
Sbjct: 97 MDETVFRGRTIKV 109
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 32.3 bits (72), Expect = 0.42, Method: Composition-based stats.
Identities = 27/100 (27%), Positives = 43/100 (43%), Gaps = 8/100 (8%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCK--------LIRDKTT 64
S S+ D + NS + V + ++T ++L F G V+ K + DK T
Sbjct: 2 SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61
Query: 65 AQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYAR 104
+ G V+Y A+ A+ +G Q +KVS AR
Sbjct: 62 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 101
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 32.3 bits (72), Expect = 0.42, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 37/84 (44%), Gaps = 2/84 (2%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
G +FV NL + L ++F G V ++ D + K +G G V EAV AI
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQAI 73
Query: 331 QSLNGYALGDRLLQVSFKTHKPLP 354
NG L DR + V + LP
Sbjct: 74 SMFNGQLLFDRPMHVKMD-ERALP 96
Score = 32.0 bits (71), Expect = 0.53, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 16/81 (19%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+ ++V+ L + + L+ +F G ++ + IL DK S+GIG
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGK----------------SRGIG 59
Query: 173 FVRFNQHIEAEHAMQELNGTI 193
V F Q IEA A+ NG +
Sbjct: 60 TVTFEQSIEAVQAISMFNGQL 80
Score = 27.7 bits (60), Expect = 9.4, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 41 EELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKV 100
++L+ +FS G V ++ DK +S G G V + ++ +A +AI NG L ++ + V
Sbjct: 30 KKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV 88
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 32.0 bits (71), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 5/65 (7%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL L + FG +G +++V V R+P GF FV + +A A++ L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVRDL 130
Query: 334 NGYAL 338
+G L
Sbjct: 131 DGRTL 135
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 32.0 bits (71), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 5/65 (7%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL L + FG +G +++V V R+P GF FV + +A A++ L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAADAVREL 130
Query: 334 NGYAL 338
+G L
Sbjct: 131 DGRTL 135
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 31.6 bits (70), Expect = 0.63, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
++V+ +P + + ++L+ G+V + +D G G V Y R ED E A+ +L
Sbjct: 18 VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-------GMGMVEYLRKEDMEYALRKL 70
Query: 89 NGLKLQNKSIKVSYARPSSE 108
+ K ++ + SY R E
Sbjct: 71 DDTKFRSHEGETSYIRVYPE 90
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 31.6 bits (70), Expect = 0.66, Method: Composition-based stats.
Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L+V+ + ++ ++Q LF+ G ++ + D++ +SLG V++ R DA +A +
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAXKQY 90
Query: 89 NGLKLQNK 96
NG+ L +
Sbjct: 91 NGVPLDGR 98
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 31.2 bits (69), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 4/48 (8%)
Query: 42 ELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
E++ + V E+ C + D +G +V + R EDAE+A+I+LN
Sbjct: 46 EMEEKYGEVEEMNVCDNLGDHL----VGNVYVKFRREEDAEKAVIDLN 89
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 31.2 bits (69), Expect = 0.94, Method: Composition-based stats.
Identities = 13/44 (29%), Positives = 25/44 (56%)
Query: 42 ELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+L+ FS+VG+V ++I D+ + +S G +V + + AI
Sbjct: 41 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 84
>pdb|2YYY|A Chain A, Crystal Structure Of Glyceraldehyde-3-Phosphate
Dehydrogenase
pdb|2YYY|B Chain B, Crystal Structure Of Glyceraldehyde-3-Phosphate
Dehydrogenase
Length = 343
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 22/29 (75%)
Query: 108 EAIKRANLYVSGLPKHMTQEDLENLFRPY 136
+ I+ A++ V G PK + +++LEN+++P+
Sbjct: 77 DIIEDADIVVDGAPKKIGKQNLENIYKPH 105
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 30/57 (52%)
Query: 40 QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNK 96
++ L LFS G+V + + D+ T ++ G+ FV DA++ I +G +L K
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK 82
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 23 NEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCK--------LIRDKTTAQSLGYGFVN 74
N N+ + V + + +T E + F +G +++ K L D+ T + G V+
Sbjct: 4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63
Query: 75 YYRTEDAERAIIELNGLKLQNKSIKVSYA 103
+ A+ AI +G + IKVS+A
Sbjct: 64 FDDPPSAKAAIDWFDGKEFSGNPIKVSFA 92
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 30/57 (52%)
Query: 40 QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNK 96
++ L LFS G+V + + D+ T ++ G+ FV DA++ I +G +L K
Sbjct: 26 KKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK 82
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 112 RANLYVSGLP-KHMTQEDLENLFRPYGTIITSRI 144
++ L++ LP K++++EDL +F PYG I+ I
Sbjct: 2 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 35
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 112 RANLYVSGLP-KHMTQEDLENLFRPYGTIITSRI 144
++ L++ LP K++++EDL +F PYG I+ I
Sbjct: 22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 55
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 112 RANLYVSGLP-KHMTQEDLENLFRPYGTIITSRI 144
++ L++ LP K++++EDL +F PYG I+ I
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 43
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 112 RANLYVSGLP-KHMTQEDLENLFRPYGTIITSRI 144
++ L++ LP K++++EDL +F PYG I+ I
Sbjct: 22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI 55
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 29.6 bits (65), Expect = 2.8, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 14/84 (16%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLG---YGFVNYYRTEDAERAIIELNGL 91
P+ + + E F G++ + + A S G +V Y R+EDA RAI +N +
Sbjct: 30 PEVLKRPEY---FGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNV 86
Query: 92 KLQNKSIKV--------SYARPSS 107
+ +++K SY+ PSS
Sbjct: 87 VVDGRTLKASLGTTKYCSYSGPSS 110
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL L + F +G ++ V + R+P GF FV + +A A++ L
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 57
Query: 334 NGYALGDRLLQVSFKTHKP 352
+G + ++V T P
Sbjct: 58 DGKVICGSRVRVELSTGMP 76
>pdb|2DNR|A Chain A, Solution Structure Of Rna Binding Domain In Synaptojanin 1
Length = 91
Score = 29.3 bits (64), Expect = 3.9, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 10/75 (13%)
Query: 32 NYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGL 91
N+ + E LQ F+S GEV + + DK +V + A ++ LNG
Sbjct: 22 NFFDDALIDELLQQ-FASFGEVILIRFVEDKM--------WVTFLEGSSALN-VLSLNGK 71
Query: 92 KLQNKSIKVSYARPS 106
+L N++I ++ PS
Sbjct: 72 ELLNRTITIALKSPS 86
>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 = 4.3, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN---YDEAV 327
IFV + + L + F FG V V ++ D + + +GFGF+ + D+AV
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 28.9 bits (63), Expect = 4.3, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 59 IRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKV 100
+ D T + +G+V++ ED E+A +EL GLK+ IK+
Sbjct: 49 VVDVRTGTNRKFGYVDFESAEDLEKA-LELTGLKVFGNEIKL 89
>pdb|1F48|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1IHU|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase In Complex With
Mg-Adp-Alf3
pdb|1II0|A Chain A, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1II0|B Chain B, Crystal Structure Of The Escherichia Coli
Arsenite-Translocating Atpase
pdb|1II9|A Chain A, Crystal Structure Of The Escherichia Coli Arsenite-
Translocating Atpase In Complex With Amp-Pnp
pdb|1II9|B Chain B, Crystal Structure Of The Escherichia Coli Arsenite-
Translocating Atpase In Complex With Amp-Pnp
Length = 589
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 26/115 (22%), Positives = 53/115 (46%), Gaps = 14/115 (12%)
Query: 79 EDAERAIIELNGLKLQNKSIKVSYARPSSEAI---------KRANLYVSGLPKHMTQEDL 129
++ R +EL + L+N+ + ++ P +EA +R ++ LP +
Sbjct: 213 QEVARTHLELAAIGLKNQYLVINGVLPKTEAANDTLAAAIWEREQEALANLPADLAGLPT 272
Query: 130 ENLF-RPY---GTIITSRILCDK-MASENVRSFVSGTPEIPQISKGIGFVRFNQH 179
+ LF +P G SR+L + +AS + ++ P+IP +S + + N+H
Sbjct: 273 DTLFLQPVNMVGVSALSRLLSTQPVASPSSDEYLQQRPDIPSLSALVDDIARNEH 327
>pdb|3THT|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing
Trna Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|B Chain B, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing
Trna Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|C Chain C, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing
Trna Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
pdb|3THT|D Chain D, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing
Trna Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 28.5 bits (62), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 53 VESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
+E C L+ + Y F Y TE+++RA + LNG
Sbjct: 41 LEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNG 78
>pdb|3THP|A Chain A, Crystal Structure And Rna Binding Properties Of The
RrmALKB DOMAINS In Human Abh8, An Enzyme Catalyzing
Trna Hypermodification, Northeast Structural Genomics
Consortium Target Hr5601b
Length = 345
Score = 28.5 bits (62), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 53 VESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
+E C L+ + Y F Y TE+++RA + LNG
Sbjct: 41 LEKCGLVDALLXPPNKPYSFARYRTTEESKRAYVTLNG 78
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 28.1 bits (61), Expect = 7.5, Method: Composition-based stats.
Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 16/96 (16%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++YV + T E+LE F G++ ILCDK SG P KG +
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF---------SGHP------KGFAY 52
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
+ F+ E+ L+ ++ G + K N P
Sbjct: 53 IEFSDK-ESVRTSLALDESLFRGRQIKVIPKRTNRP 87
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 28.1 bits (61), Expect = 7.7, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 8/86 (9%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCK--------LIRDKTTAQSLGYGFVNYYR 77
N+ + V + + +T E + F +G +++ K L D+ T + G V++
Sbjct: 13 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDD 72
Query: 78 TEDAERAIIELNGLKLQNKSIKVSYA 103
A+ AI +G + IKVS+A
Sbjct: 73 PPSAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 28.1 bits (61), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 16/96 (16%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++YV + T E+LE F G++ ILCDK SG P KG +
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF---------SGHP------KGFAY 51
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
+ F+ E+ L+ ++ G + K N P
Sbjct: 52 IEFSDK-ESVRTSLALDESLFRGRQIKVIPKRTNRP 86
>pdb|2CQ2|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Loc91801
Length = 114
Score = 27.7 bits (60), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 53 VESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNG 90
+E C L+ + Y F Y TE+++RA + LNG
Sbjct: 48 LEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNG 85
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.133 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,842,027
Number of Sequences: 62578
Number of extensions: 377751
Number of successful extensions: 1483
Number of sequences better than 100.0: 182
Number of HSP's better than 100.0 without gapping: 140
Number of HSP's successfully gapped in prelim test: 42
Number of HSP's that attempted gapping in prelim test: 973
Number of HSP's gapped (non-prelim): 448
length of query: 356
length of database: 14,973,337
effective HSP length: 100
effective length of query: 256
effective length of database: 8,715,537
effective search space: 2231177472
effective search space used: 2231177472
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)