RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9313
(356 letters)
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex,
AU-rich element, transcription/RNA complex; 1.80A {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H
1d8z_A 1d9a_A 3hi9_A
Length = 167
Score = 234 bits (599), Expect = 2e-77
Identities = 113/181 (62%), Positives = 138/181 (76%), Gaps = 15/181 (8%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+NLIVNY+PQ MTQEE + LF S+GE+ESCKL+RDK T QSLGYGFVNY +DAE+AI
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 86 IELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRIL 145
LNGL+LQ K+IKVSYARPSS +I+ ANLYVSGLPK MTQ++LE LF YG IITSRIL
Sbjct: 62 NTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRIL 121
Query: 146 CDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKF 205
D++ +G S+G+GF+RF++ IEAE A++ LNG P GA+EPITVKF
Sbjct: 122 VDQV---------TGV------SRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF 166
Query: 206 A 206
A
Sbjct: 167 A 167
Score = 84.5 bits (210), Expect = 7e-20
Identities = 31/88 (35%), Positives = 52/88 (59%), Gaps = 2/88 (2%)
Query: 18 YQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYR 77
S + +++NL V+ +P+TMTQ+EL+ LFS G + + +++ D+ T S G GF+ + +
Sbjct: 80 RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDK 139
Query: 78 TEDAERAIIELNG--LKLQNKSIKVSYA 103
+AE AI LNG + I V +A
Sbjct: 140 RIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 82.2 bits (204), Expect = 5e-19
Identities = 24/74 (32%), Positives = 38/74 (51%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V L LFG G +++ K+VRD T + G+GFV + +A AI +L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 334 NGYALGDRLLQVSF 347
NG L + ++VS+
Sbjct: 65 NGLRLQTKTIKVSY 78
Score = 79.5 bits (197), Expect = 4e-18
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 2/76 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V L L QLF +G + +++ D T +G GF+ EA AI+ L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 334 NGYAL--GDRLLQVSF 347
NG + V F
Sbjct: 151 NGQKPSGATEPITVKF 166
>1b7f_A Protein (SXL-lethal protein), RNA
(5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing
regulation, RNP domain, RNA complex; 2.60A {Drosophila
melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A*
1sxl_A 2sxl_A
Length = 168
Score = 230 bits (590), Expect = 4e-76
Identities = 79/181 (43%), Positives = 117/181 (64%), 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 +G+ FVR+N+ EA+ A+ LN IPEG S+P++V+
Sbjct: 123 RDKL---------TGR------PRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL 167
Query: 206 A 206
A
Sbjct: 168 A 168
Score = 86.9 bits (216), Expect = 1e-20
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
Score = 84.5 bits (210), Expect = 8e-20
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 2/76 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL D+ L +FG +G++ ++RD T + +G FV +EA AI +L
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 334 NGYAL--GDRLLQVSF 347
N G + L V
Sbjct: 152 NNVIPEGGSQPLSVRL 167
Score = 83.4 bits (207), Expect = 2e-19
Identities = 25/88 (28%), Positives = 47/88 (53%), Gaps = 2/88 (2%)
Query: 18 YQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYR 77
+ +++NL V +P+T+T ++L +F G + ++RDK T + G FV Y +
Sbjct: 81 RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 140
Query: 78 TEDAERAIIELNGLKLQ--NKSIKVSYA 103
E+A+ AI LN + + ++ + V A
Sbjct: 141 REEAQEAISALNNVIPEGGSQPLSVRLA 168
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 229 bits (586), Expect = 7e-74
Identities = 60/329 (18%), Positives = 107/329 (32%), Gaps = 85/329 (25%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+++ +P +T +E+ L S ++ C + + K G FV E AE A
Sbjct: 21 NRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYK------GTAFVTLLNGEQAEAA 73
Query: 85 IIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
I + +L+ + + V A L V+ LP +TQ+ E L RP+G++ +
Sbjct: 74 INAFHQSRLRERELSVQLQPTD------ALLCVANLPPSLTQQQFEELVRPFGSLERCFL 127
Query: 145 LCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVK 204
+ + +G SKG GF + + A A +L G + V
Sbjct: 128 VYSE---------RTGQ------SKGYGFAEYMKKDSAARAKSDLLGKPLGP--RTLYVH 170
Query: 205 FANSPAGRAKALAANLNAQAAAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPP 264
+ ++ L +
Sbjct: 171 WTDAGQLTPALLHSR--------------------------------------------- 185
Query: 265 KSLHGSGWCIFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNY 323
C+ V L P + + L + + ++ + KGF +
Sbjct: 186 --------CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETA 236
Query: 324 DEAVFAIQSLNGYALGDRLLQVSFKTHKP 352
+ A A Q +G +LG L+VSF P
Sbjct: 237 EMAEEAQQQADGLSLGGSHLRVSFCAPGP 265
Score = 191 bits (487), Expect = 5e-59
Identities = 49/208 (23%), Positives = 81/208 (38%), Gaps = 22/208 (10%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
++ L V +P ++TQ++ + L G +E C L+ + T QS GYGF Y + + A R
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152
Query: 84 AIIELNGLKLQNKSIKVSYA---RPSSEAIKRANLYVSGLPKHMTQED-LENLFRPYGTI 139
A +L G L +++ V + + + + L V LP D L +
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSP 212
Query: 140 ITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASE 199
++ C + KG + + AE A Q+ +G G
Sbjct: 213 TFCQLACGQ----------------DGQLKGFAVLEYETAEMAEEAQQQADGLSLGG--S 254
Query: 200 PITVKFANSPAGRAKALAANLNAQAAAM 227
+ V F LAA + AQA A+
Sbjct: 255 HLRVSFCAPGPPGRSMLAALIAAQATAL 282
Score = 91.2 bits (227), Expect = 3e-21
Identities = 26/82 (31%), Positives = 36/82 (43%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V NL P +L PFG+++ +V +T + KG+GF D A A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 334 NGYALGDRLLQVSFKTHKPLPP 355
G LG R L V + L P
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTP 179
Score = 85.4 bits (212), Expect = 3e-19
Identities = 21/109 (19%), Positives = 40/109 (36%), Gaps = 2/109 (1%)
Query: 19 QSDVNEQNSNLIVNYVPQTMTQEE-LQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYR 77
+ + L V+ +P + L S+V C+L + Q G+ + Y
Sbjct: 177 LTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQD-GQLKGFAVLEYET 235
Query: 78 TEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQ 126
E AE A + +GL L ++VS+ P ++ + +
Sbjct: 236 AEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATALNR 284
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA
binding protein-RNA complex; 1.85A {Homo sapiens} PDB:
3nna_A 3nnc_A 2dhs_A 3nnh_A
Length = 175
Score = 209 bits (535), Expect = 1e-67
Identities = 48/187 (25%), Positives = 84/187 (44%), Gaps = 23/187 (12%)
Query: 28 NLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTT--AQSLGYGFVNYYRTEDAERAI 85
+ V VP+T ++++L+ LF G V ++RD++ QS G FV +Y + A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 86 IELNGLKLQNKSIKVSYARPSS----EAIKRANLYVSGLPKHMTQEDLENLFRPYGTIIT 141
L+ +K+ +P+ A++ L++ + K T+ D+ +F +G I
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 124
Query: 142 SRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGT-IPEGASEP 200
RIL +S+G FV F A+ A++ ++ EG S P
Sbjct: 125 CRILRGPD----------------GLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP 168
Query: 201 ITVKFAN 207
+ VKFA+
Sbjct: 169 MVVKFAD 175
Score = 100 bits (251), Expect = 1e-25
Identities = 41/237 (17%), Positives = 77/237 (32%), Gaps = 71/237 (29%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++V +P+ +++DL LF YG + +L D+ P+ SKG F
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDR---------SQNPPQ----SKGCCF 51
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAA 233
V F + +A A L+
Sbjct: 52 -----------------------------VTFY-TRKAALEAQNA-LH------------ 68
Query: 234 MRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFG 293
+HH + K A K+ +F+ ++ + +N + +F
Sbjct: 69 NMKVLPGMHHPIQMKPAD-----------SEKNNAVEDRKLFIGMISKKCTENDIRVMFS 117
Query: 294 PFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGY---ALGDRLLQVSF 347
FG ++ +++R P +G FV T A AI++++ + V F
Sbjct: 118 SFGQIEECRILRGPDG-LSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKF 173
Score = 81.5 bits (202), Expect = 1e-18
Identities = 18/82 (21%), Positives = 42/82 (51%), Gaps = 4/82 (4%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
++ L + + + T+ +++ +FSS G++E C+++R S G FV + A+ A
Sbjct: 94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDG-LSRGCAFVTFTTRAMAQTA 152
Query: 85 IIELNG---LKLQNKSIKVSYA 103
I ++ ++ + + V +A
Sbjct: 153 IKAMHQAQTMEGCSSPMVVKFA 174
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 198 bits (506), Expect = 8e-63
Identities = 51/196 (26%), Positives = 92/196 (46%), Gaps = 21/196 (10%)
Query: 19 QSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRT 78
S + ++L V + +T+ L FS G + S ++ RD T +SLGY +VN+ +
Sbjct: 8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 67
Query: 79 EDAERAIIELNGLKLQNKSIKVSYAR--PSSEAIKRANLYVSGLPKHMTQEDLENLFRPY 136
DAERA+ +N ++ K +++ +++ PS N+++ L K + + L + F +
Sbjct: 68 ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAF 127
Query: 137 GTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEG 196
G I++ +++CD SKG GFV F AE A++++NG +
Sbjct: 128 GNILSCKVVCD-----------------ENGSKGYGFVHFETQEAAERAIEKMNGMLLND 170
Query: 197 ASEPITVKFANSPAGR 212
+ V S R
Sbjct: 171 --RKVFVGRFKSRKER 184
Score = 115 bits (289), Expect = 1e-30
Identities = 53/253 (20%), Positives = 88/253 (34%), Gaps = 73/253 (28%)
Query: 100 VSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVS 159
+ PS+ + A+LYV L +T+ L F P G I++ R+ D ++
Sbjct: 3 LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDM---------IT 53
Query: 160 GTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAAN 219
S G +V F Q +AE A+ +N + +G +P+ + ++ K+ N
Sbjct: 54 RR------SLGYAYVNFQQPADAERALDTMNFDVIKG--KPVRIMWSQRDPSLRKSGVGN 105
Query: 220 LNAQAAAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNL 279
+ F N L
Sbjct: 106 I---------F------IKN----------------------LDK--------------- 113
Query: 280 APETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALG 339
++ L+ F FG + + KVV D KG+GFV + A AI+ +NG L
Sbjct: 114 --SIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLN 169
Query: 340 DRLLQVSFKTHKP 352
DR + V +
Sbjct: 170 DRKVFVGRFKSRK 182
Score = 95.4 bits (238), Expect = 2e-23
Identities = 33/129 (25%), Positives = 56/129 (43%), Gaps = 8/129 (6%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S R N+ + + +++ + L FS+ G + SCK++ D S GYGF
Sbjct: 92 SQRDPSLRKSG--VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGF 147
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENL 132
V++ E AERAI ++NG+ L ++ + V + E K D+ +
Sbjct: 148 VHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG----ARAKEFYPYDVPDY 203
Query: 133 FRPYGTIIT 141
G I+T
Sbjct: 204 AGSSGRIVT 212
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA
binding domain, RNA recognition motif, SP factor, snRNP,
spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP:
d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A
Length = 292
Score = 194 bits (495), Expect = 3e-60
Identities = 60/332 (18%), Positives = 116/332 (34%), Gaps = 79/332 (23%)
Query: 23 NEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAE 82
N + + ++V +P++ Q ++ F G + + ++ + + + R + A
Sbjct: 38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGAL 95
Query: 83 RAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITS 142
AI + + + I VS+ L+++ P TQ ++ +L + + S
Sbjct: 96 AAITKTHK-VVGQNEIIVSHL-------TECTLWMTNFPPSYTQRNIRDLLQDINVVALS 147
Query: 143 RILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPIT 202
L T S+ ++ +A + +++LNG EG +
Sbjct: 148 IRLPSLR---------FNT------SRRFAYIDVTSKEDARYCVEKLNGLKIEG--YTLV 190
Query: 203 VKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSML 262
K + NPL S R A L
Sbjct: 191 TKVS--------------------------------NPLEKSKRTDSATL---------- 208
Query: 263 PPKSLHGSGWCIFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVVRD-PQTYKCKGFGFVCM 320
G I + NL+ E ++N+L + F FG+++ + + + F+
Sbjct: 209 -------EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVF 261
Query: 321 TNYDEAVFAIQSLNGYALGDRLLQVSFKTHKP 352
N D A A+Q +N LG+R + VS KP
Sbjct: 262 ENKDSAERALQ-MNRSLLGNREISVSLADKKP 292
Score = 77.3 bits (191), Expect = 3e-16
Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 3/96 (3%)
Query: 12 QSHRSTYQSDVNEQNSNLIVNYVPQTMTQEE-LQHLFSSVGEVESCKLIRD-KTTAQSLG 69
+S + +++ + + E L+ F G +E + K + +
Sbjct: 196 PLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNC 255
Query: 70 YGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
F+ + + AERA+ ++N L N+ I VS A
Sbjct: 256 CAFMVFENKDSAERAL-QMNRSLLGNREISVSLADK 290
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 174 bits (443), Expect = 1e-52
Identities = 49/230 (21%), Positives = 84/230 (36%), Gaps = 35/230 (15%)
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 KAELDGTILKSRPLRIRFATHG------AALTVKNLSPVVSNELLEQAFSQFGPVEKAVV 128
Query: 145 LCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGT--IPEGASEPIT 202
+ D G + G GFV F A A++ + P+
Sbjct: 129 VVDD----------RGR------ATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVI 172
Query: 203 VKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFGNP----LHHSARFK 248
V+ L L + F P +++R+K
Sbjct: 173 VEPMEQF-DDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRWK 221
Score = 77.0 bits (190), Expect = 2e-16
Identities = 21/120 (17%), Positives = 41/120 (34%), Gaps = 5/120 (4%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+ L V + ++ E L+ FS G VE ++ D ++ G GFV + A +
Sbjct: 94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRG-RATGKGFVEFAAKPPARK 152
Query: 84 AIIELNGLK-LQNKSIKVSYARP---SSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTI 139
A+ L + + P + + ++ + + F GT
Sbjct: 153 ALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTF 212
Score = 77.0 bits (190), Expect = 2e-16
Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 6/96 (6%)
Query: 257 LNNSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFG 316
+ + + P + + +FV NL + + +LF +G V + RD +GFG
Sbjct: 8 IKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFG 61
Query: 317 FVCMTNYDEAVFAIQSLNGYALGDRLLQVSFKTHKP 352
F+ + + A A L+G L R L++ F TH
Sbjct: 62 FIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGA 97
Score = 72.0 bits (177), Expect = 1e-14
Identities = 31/118 (26%), Positives = 45/118 (38%), Gaps = 25/118 (21%)
Query: 95 NKSIKVSYA--RPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASE 152
+I + +R L+V LP +T+ED + LF YG I D
Sbjct: 3 GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD----- 57
Query: 153 NVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPA 210
+G GF+R AE A EL+GTI + P+ ++FA A
Sbjct: 58 ----------------RGFGFIRLESRTLAEIAKAELDGTILKS--RPLRIRFATHGA 97
Score = 70.9 bits (174), Expect = 3e-14
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 257 LNNSMLPPKSL----HGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKC 312
L+ ++L + L G + V NL+P + +L Q F FG V+ VV D + +
Sbjct: 78 LDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRG-RA 136
Query: 313 KGFGFVCMTNYDEAVFAIQSLNG 335
G GFV A A++
Sbjct: 137 TGKGFVEFAAKPPARKALERCGD 159
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP,
RBD, poly(U) binding, tandem, acetylation, cytopla
nucleus; 2.70A {Saccharomyces cerevisiae}
Length = 166
Score = 168 bits (428), Expect = 1e-51
Identities = 46/180 (25%), Positives = 91/180 (50%), 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 NGLKLQNKSIKVSYARPSSEAIK--RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILC 146
NG +++N +K+++A S ++ NL+V L ++ E L N F+ + + ++ ++
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 147 DKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
D +G S+G GFV F +A++AM + G G P+ + +A
Sbjct: 122 DMQ---------TG------SSRGYGFVSFTSQDDAQNAMDSMQGQDLNG--RPLRINWA 164
Score = 98.8 bits (247), Expect = 4e-25
Identities = 48/233 (20%), Positives = 80/233 (34%), Gaps = 72/233 (30%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV L K +T++ L+ F+ G I +I+ DK + FV
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNK----------------NVNYAFV 46
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAM 234
++Q A AL LN +
Sbjct: 47 EYHQ---------------SHDA---------------NIALQT-LN-----GKQI---- 66
Query: 235 RHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGP 294
N + +N + +S + +FV +L +D L F
Sbjct: 67 --ENNIVK--------------INWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKD 110
Query: 295 FGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
F + + V+ D QT +G+GFV T+ D+A A+ S+ G L R L++++
Sbjct: 111 FPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW 163
Score = 81.0 bits (201), Expect = 1e-18
Identities = 22/85 (25%), Positives = 42/85 (49%)
Query: 19 QSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRT 78
Q ++ NL V + + E L++ F S ++ D T S GYGFV++
Sbjct: 80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ 139
Query: 79 EDAERAIIELNGLKLQNKSIKVSYA 103
+DA+ A+ + G L + +++++A
Sbjct: 140 DDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 73.7 bits (182), Expect = 5e-16
Identities = 19/79 (24%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL +++L Q F G + N+K++ D + K + FV +A A+Q+L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 334 NGYALGDRLLQVSFKTHKP 352
NG + + ++++++
Sbjct: 62 NGKQIENNIVKINWAFQSQ 80
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 145 bits (367), Expect = 1e-42
Identities = 40/197 (20%), Positives = 82/197 (41%), Gaps = 28/197 (14%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
SH + + NL + + + EL+ S + ++ +T + +G+
Sbjct: 2 SHMV--EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-GTNRKFGY 58
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRA--NLYVSGLPKHMTQEDLE 130
V++ ED E+A+ EL GLK+ IK+ + RA L L ++T+++L+
Sbjct: 59 VDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELK 117
Query: 131 NLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELN 190
+F I ++ S++ + SKGI ++ F +AE ++E
Sbjct: 118 EVFEDALEI--------RLVSQDGK------------SKGIAYIEFKSEADAEKNLEEKQ 157
Query: 191 GTIPEGASEPITVKFAN 207
G +G +++ +
Sbjct: 158 GAEIDG--RSVSLYYTG 172
Score = 101 bits (254), Expect = 5e-26
Identities = 35/251 (13%), Positives = 69/251 (27%), Gaps = 78/251 (31%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
S+ SE+ NL++ L + + +L+ ++ + +G
Sbjct: 2 SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR----------TG 51
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANL 220
T ++ G+V F + E A+ EL G G I ++ + A L
Sbjct: 52 T------NRKFGYVDFESAEDLEKAL-ELTGLKVFG--NEIKLEKPKGRDSKKVRAARTL 102
Query: 221 NAQAAAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLA 280
N L + T D L
Sbjct: 103 ---------------LAKN-LSFNI-------TEDELKE--------------------- 118
Query: 281 PETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGD 340
+F ++ Q K KG ++ + +A ++ G +
Sbjct: 119 ----------VFEDAL-----EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG 163
Query: 341 RLLQVSFKTHK 351
R + + + K
Sbjct: 164 RSVSLYYTGEK 174
Score = 74.2 bits (183), Expect = 4e-16
Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 5/82 (6%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
L+ + +T++EL+ +F E+ +S G ++ + DAE+
Sbjct: 97 RAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYIEFKSEADAEK 151
Query: 84 AIIELNGLKLQNKSIKVSYARP 105
+ E G ++ +S+ + Y
Sbjct: 152 NLEEKQGAEIDGRSVSLYYTGE 173
Score = 71.1 bits (175), Expect = 5e-15
Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 2/79 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ NL P L A ++ VV D +T + FG+V + ++ A++ L
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 334 NGYALGDRLLQVSFKTHKP 352
G + +++ +
Sbjct: 74 TGLKVFGNEIKLEKPKGRD 92
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 143 bits (362), Expect = 2e-41
Identities = 37/209 (17%), Positives = 86/209 (41%), Gaps = 28/209 (13%)
Query: 12 QSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYG 71
+ + S + V + + ++ ++ F+ G ++S + D T + G+
Sbjct: 14 GRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFA 73
Query: 72 FVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRA-----------NLYVSGL 120
FV Y E A+ A+ ++N + L ++IKV +A +YV+ +
Sbjct: 74 FVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASV 133
Query: 121 PKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHI 180
+ ++ +D++++F +G I ++ + D + KG GF+ + +
Sbjct: 134 HQDLSDDDIKSVFEAFGKIKSATLARDP---TTGK------------HKGYGFIEYEKAQ 178
Query: 181 EAEHAMQELNGTIPEGASEPITVKFANSP 209
++ A+ +N G + + V A +P
Sbjct: 179 SSQDAVSSMNLFDLGG--QYLRVGKAVTP 205
Score = 137 bits (347), Expect = 4e-39
Identities = 46/253 (18%), Positives = 88/253 (34%), Gaps = 62/253 (24%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTP 162
A+ + +YV + + ++ + F P+G I + + D V+
Sbjct: 19 AQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDS---------VTMK- 68
Query: 163 EIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNA 222
KG FV + A+ A++++N + G I V ++
Sbjct: 69 -----HKGFAFVEYEVPEAAQLALEQMNSVMLGG--RNIKVGRPSNIGQAQ--------- 112
Query: 223 QAAAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPE 282
+ A R F I+V ++ +
Sbjct: 113 --PIIDQLAEEARAFNR----------------------------------IYVASVHQD 136
Query: 283 TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRL 342
D+ + +F FG +++ + RDP T K KG+GF+ + A+ S+N + LG +
Sbjct: 137 LSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQY 196
Query: 343 LQVSFKTHKPLPP 355
L+V P+P
Sbjct: 197 LRVGKAVTPPMPL 209
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 134 bits (338), Expect = 1e-37
Identities = 53/251 (21%), Positives = 83/251 (33%), Gaps = 49/251 (19%)
Query: 103 ARPSSEAIKRANLYVSGL-PKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGT 161
A P + L VS L P+ +T + L LF YG + +IL +K
Sbjct: 25 AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK------------- 71
Query: 162 PEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLN 221
K V+ +A+ AM LNG G PI + + +
Sbjct: 72 -------KENALVQMADGNQAQLAMSHLNGHKLHGK--PIRITLSKHQNVQLPREGQEDQ 122
Query: 222 AQAAAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAP 281
+ +GN H +F + N P + + N+ P
Sbjct: 123 GL----------TKDYGNSPLH----RFKKPGSKNFQNIFPP-------SATLHLSNIPP 161
Query: 282 ETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGD- 340
+ L LF G V K + + M + +EAV A+ L+ + LG+
Sbjct: 162 SVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGEN 217
Query: 341 RLLQVSFKTHK 351
L+VSF
Sbjct: 218 HHLRVSFSKST 228
Score = 103 bits (258), Expect = 4e-26
Identities = 44/232 (18%), Positives = 81/232 (34%), Gaps = 63/232 (27%)
Query: 15 RSTYQSDVNEQNSNLIV-NYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFV 73
R NS L+V N P+ +T + L LF G+V+ K++ +K V
Sbjct: 23 RIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK-----ENALV 77
Query: 74 NYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRAN------------------- 114
A+ A+ LNG KL K I+++ ++ + + R
Sbjct: 78 QMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFK 137
Query: 115 ----------------LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFV 158
L++S +P +++EDL+ LF G ++ K
Sbjct: 138 KPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK---------- 187
Query: 159 SGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGT-IPEGASEPITVKFANSP 209
+ + ++ EA A+ +L+ + E + V F+ S
Sbjct: 188 ---------DRKMALIQMGSVEEAVQALIDLHNHDLGEN--HHLRVSFSKST 228
Score = 72.0 bits (176), Expect = 9e-15
Identities = 27/115 (23%), Positives = 47/115 (40%), Gaps = 6/115 (5%)
Query: 242 HHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPET-EDNVLWQLFGPFGAVQN 300
HH + + P + V NL PE L+ LFG +G VQ
Sbjct: 5 HHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQR 64
Query: 301 VKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSFKTHKPLPP 355
VK++ + K V M + ++A A+ LNG+ L + ++++ H+ +
Sbjct: 65 VKIL-----FNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQL 114
Score = 63.9 bits (155), Expect = 5e-12
Identities = 24/110 (21%), Positives = 52/110 (47%), Gaps = 10/110 (9%)
Query: 3 KHEEMYNTTQSHR-----STYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCK 57
+ Y + HR S ++ ++ L ++ +P ++++E+L+ LFSS G V
Sbjct: 123 GLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF 182
Query: 58 LIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL-QNKSIKVSYARPS 106
K + E+A +A+I+L+ L +N ++VS+++ +
Sbjct: 183 KFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi}
SCOP: d.58.7.1
Length = 139
Score = 131 bits (330), Expect = 1e-37
Identities = 39/115 (33%), Positives = 60/115 (52%), Gaps = 6/115 (5%)
Query: 9 NTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSL 68
Q T + + NL+VNY+P T+ + +L+ LF G +ES K++ D+ T QS
Sbjct: 25 QQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSR 84
Query: 69 GYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE------AIKRANLYV 117
GYGFV + A++AI LNG + NK +KV+ A + A+ N Y+
Sbjct: 85 GYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGYL 139
Score = 89.8 bits (223), Expect = 4e-22
Identities = 24/82 (29%), Positives = 44/82 (53%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V + ++ L QLF +G +++VK+V D +T + +G+GFV + A AI L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 334 NGYALGDRLLQVSFKTHKPLPP 355
NG+ + ++ L+V+ P
Sbjct: 105 NGFNILNKRLKVALAASGHQRP 126
Score = 80.6 bits (199), Expect = 1e-18
Identities = 34/141 (24%), Positives = 57/141 (40%), Gaps = 20/141 (14%)
Query: 73 VNYYRTEDAERAIIELNGL-KLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLEN 131
+ D +L L + Q + I + P + ++ NL V+ +P + + L
Sbjct: 4 IPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLR--NLMVNYIPTTVDEVQLRQ 61
Query: 132 LFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNG 191
LF YG I + +I+CD+ + S+G GFV+F A+ A+ LNG
Sbjct: 62 LFERYGPIESVKIVCDR---------ETR------QSRGYGFVKFQSGSSAQQAIAGLNG 106
Query: 192 TIPEGASEPITVKFANSPAGR 212
+ + V A S R
Sbjct: 107 FNILN--KRLKVALAASGHQR 125
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA,
spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1
d.58.7.1
Length = 198
Score = 128 bits (322), Expect = 9e-36
Identities = 51/241 (21%), Positives = 81/241 (33%), Gaps = 49/241 (20%)
Query: 113 ANLYVSGL-PKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
+ L VS L P+ +T + L LF YG + +IL +K K
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK--------------------KEN 43
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFA 231
V+ +A+ AM LNG G PI + + +
Sbjct: 44 ALVQMADGNQAQLAMSHLNGHKLHGK--PIRITLSKHQNVQLPREGQEDQGLT------- 94
Query: 232 AAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQL 291
+ +GN H +F + N P + + N+ P + L L
Sbjct: 95 ---KDYGNSPLH----RFKKPGSKNFQNIFPP-------SATLHLSNIPPSVSEEDLKVL 140
Query: 292 FGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGD-RLLQVSFKTH 350
F G V K + + M + +EAV A+ L+ + LG+ L+VSF
Sbjct: 141 FSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS 196
Query: 351 K 351
Sbjct: 197 T 197
Score = 111 bits (279), Expect = 2e-29
Identities = 43/220 (19%), Positives = 80/220 (36%), Gaps = 61/220 (27%)
Query: 26 NSNLIV-NYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
NS L+V N P+ +T + L LF G+V+ K++ +K V A+ A
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK-----ENALVQMADGNQAQLA 57
Query: 85 IIELNGLKLQNKSIKVSYARPSSEAIKRA------------------------------- 113
+ LNG KL K I+++ ++ + + R
Sbjct: 58 MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 117
Query: 114 ----NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISK 169
L++S +P +++EDL+ LF G ++ K +
Sbjct: 118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-------------------DR 158
Query: 170 GIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
+ ++ EA A+ +L+ G + + V F+ S
Sbjct: 159 KMALIQMGSVEEAVQALIDLHNH-DLGENHHLRVSFSKST 197
Score = 71.9 bits (176), Expect = 4e-15
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 6/83 (7%)
Query: 274 IFVYNLAPET-EDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ V NL PE L+ LFG +G VQ VK++ + K V M + ++A A+
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 60
Query: 333 LNGYALGDRLLQVSFKTHKPLPP 355
LNG+ L + ++++ H+ +
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQL 83
Score = 63.8 bits (155), Expect = 3e-12
Identities = 21/102 (20%), Positives = 49/102 (48%), Gaps = 5/102 (4%)
Query: 6 EMYNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTA 65
+ + S ++ ++ L ++ +P ++++E+L+ LFSS G V K
Sbjct: 100 SPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--- 156
Query: 66 QSLGYGFVNYYRTEDAERAIIELNGLKL-QNKSIKVSYARPS 106
+ E+A +A+I+L+ L +N ++VS+++ +
Sbjct: 157 -DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 197
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA
splicing factor, RNA recognition motif, RNA binding
protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A
Length = 172
Score = 126 bits (319), Expect = 2e-35
Identities = 30/183 (16%), Positives = 68/183 (37%), Gaps = 26/183 (14%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKL-----IRDKTTAQSLGYGFVNYYRTEDAERA 84
YV P +T+E + F++ + + Q + F+ + ++ +A
Sbjct: 8 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 67
Query: 85 IIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
+ +G+ Q +S+K+ L++ GLP ++ + ++ L +G + +
Sbjct: 68 M-AFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNL 126
Query: 145 LCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVK 204
+ D SKG F + + A+ LNG + + + V+
Sbjct: 127 VKDSATGL---------------SKGYAFCEYVDINVTDQAIAGLNGM--QLGDKKLLVQ 169
Query: 205 FAN 207
A+
Sbjct: 170 RAS 172
Score = 88.1 bits (219), Expect = 4e-21
Identities = 22/73 (30%), Positives = 35/73 (47%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ L D+ + +L FG ++ +V+D T KG+ F + + AI L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 334 NGYALGDRLLQVS 346
NG LGD+ L V
Sbjct: 157 NGMQLGDKKLLVQ 169
Score = 85.0 bits (211), Expect = 6e-20
Identities = 23/89 (25%), Positives = 43/89 (48%)
Query: 15 RSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVN 74
R + L + +P + ++++ L +S G +++ L++D T S GY F
Sbjct: 83 RRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCE 142
Query: 75 YYRTEDAERAIIELNGLKLQNKSIKVSYA 103
Y ++AI LNG++L +K + V A
Sbjct: 143 YVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 63.8 bits (156), Expect = 2e-12
Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 6/77 (7%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVK-----VVRDPQTYKCKGFGFVCMTNYDEAVF 328
++V N+ + + F + + V Q + K F F+ + DE
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 329 AIQSLNGYALGDRLLQV 345
A+ +G + L++
Sbjct: 67 AMA-FDGIIFQGQSLKI 82
Score = 52.2 bits (126), Expect = 2e-08
Identities = 17/95 (17%), Positives = 33/95 (34%), Gaps = 13/95 (13%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV +P +T+E + + F + + V + K F+
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGG----LTQAPGNPVLAVQINQ------DKNFAFL 56
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
F E AM +G I +G + + ++ +
Sbjct: 57 EFRSVDETTQAM-AFDGIIFQG--QSLKIRRPHDY 88
>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure
genomics, RRM domain, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 122 bits (308), Expect = 1e-34
Identities = 35/125 (28%), Positives = 59/125 (47%), Gaps = 24/125 (19%)
Query: 93 LQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASE 152
L+ ++ A+ + NLY+S LP M +++LEN+ +P+G +I++RIL D
Sbjct: 8 LKASGVQAQMAKQQEQ--DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS---- 61
Query: 153 NVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEG------ASEPITVKFA 206
SGT S+G+GF R + E + NG + +EP+ KF+
Sbjct: 62 ------SGT------SRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFS 109
Query: 207 NSPAG 211
+G
Sbjct: 110 GPSSG 114
Score = 93.5 bits (233), Expect = 1e-23
Identities = 23/91 (25%), Positives = 43/91 (47%), Gaps = 3/91 (3%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+ +NL ++ +P +M ++EL+++ G+V S +++RD + S G GF TE E
Sbjct: 23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS-GTSRGVGFARMESTEKCEA 81
Query: 84 AIIELNGLKLQNKSIKVSYARPSSEAIKRAN 114
I NG ++ + P K +
Sbjct: 82 VIGHFNGKFIKTPPGVSAPTEP--LLCKFSG 110
Score = 83.5 bits (207), Expect = 5e-20
Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 3/80 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ NL ++ L + PFG V + +++RD + +G GF M + ++ I
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86
Query: 334 NGYALGDRLLQVSFKTHKPL 353
NG + + +PL
Sbjct: 87 NGKFIKTPPGVSAP--TEPL 104
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 125 bits (314), Expect = 2e-34
Identities = 29/238 (12%), Positives = 60/238 (25%), Gaps = 42/238 (17%)
Query: 111 KRANLYVSGL-PKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISK 169
L V GL M + + N+F YG + + + K
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK--------------------P 42
Query: 170 GIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRH 229
G V + A+ LN + + V + PA + +
Sbjct: 43 GAAMVEMADGYAVDRAITHLNNNFMF--GQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDF 100
Query: 230 FAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNVLW 289
+ F P + + +N E + +
Sbjct: 101 SESRNNRFSTPEQA-------------------AKNRIQHPSNVLHFFNAPLEVTEENFF 141
Query: 290 QLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
++ G + V + G + + +A+ + LN Y + + +
Sbjct: 142 EICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 199
Score = 105 bits (262), Expect = 4e-27
Identities = 31/222 (13%), Positives = 62/222 (27%), Gaps = 60/222 (27%)
Query: 25 QNSNLIV-NYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+ L+V M + + ++F G VE K ++ K G V +R
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP-----GAAMVEMADGYAVDR 57
Query: 84 AIIELNGLKLQNKSIKVSYARPSSEAIKRA------------------------------ 113
AI LN + + + V ++ + ++
Sbjct: 58 AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117
Query: 114 -------NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ 166
L+ P +T+E+ + G + + SE
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSE-------------- 163
Query: 167 ISKGIGFVRFNQHIEAEHAMQELNGTIPEG--ASEPITVKFA 206
G + ++ +A + LN + P T+K
Sbjct: 164 -RSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC 204
Score = 71.3 bits (174), Expect = 1e-14
Identities = 14/102 (13%), Positives = 34/102 (33%)
Query: 1 MMKHEEMYNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIR 60
E N + ++ + ++ L P +T+E + +G +
Sbjct: 98 KDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKV 157
Query: 61 DKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSY 102
++ G + + DA + LN +++N + Y
Sbjct: 158 FSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 199
Score = 66.3 bits (161), Expect = 5e-13
Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 6/83 (7%)
Query: 274 IFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ VY L + ++ +F +G V+ VK ++ G V M + AI
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITH 61
Query: 333 LNGYALGDRLLQVSFKTHKPLPP 355
LN + + + V + P
Sbjct: 62 LNNNFMFGQKMNVCVSKQPAIMP 84
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 122 bits (307), Expect = 2e-33
Identities = 40/238 (16%), Positives = 75/238 (31%), Gaps = 49/238 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV +P +T+E + + F + + V + K F+
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGG----LTQAPGNPVLAVQINQ------DKNFAFL 56
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAM 234
F E AM +G I +G + + ++ + ++ ++
Sbjct: 57 EFRSVDETTQAMA-FDGIIFQG--QSLKIRRPHDYQPLPGM------SENPSVYVPGVVS 107
Query: 235 RHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGP 294
+ H +F+ L D+ + +L
Sbjct: 108 TVVPDSAHK------------------------------LFIGGLPNYLNDDQVKELLTS 137
Query: 295 FGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSFKTHKP 352
FG ++ +V+D T KG+ F + + AI LNG LGD+ L V +
Sbjct: 138 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGA 195
Score = 118 bits (298), Expect = 3e-32
Identities = 32/209 (15%), Positives = 70/209 (33%), Gaps = 46/209 (22%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKL-----IRDKTTAQSLGYGFVNYYRTEDAERA 84
YV P +T+E + F++ + + Q + F+ + ++ +A
Sbjct: 8 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 67
Query: 85 IIELNGLKLQNKSIKVSYARPSSEAIKRA--------------------NLYVSGLPKHM 124
+ +G+ Q +S+K+ + L++ GLP ++
Sbjct: 68 M-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYL 126
Query: 125 TQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEH 184
+ ++ L +G + ++ D SKG F + +
Sbjct: 127 NDDQVKELLTSFGPLKAFNLVKDSATGL---------------SKGYAFCEYVDINVTDQ 171
Query: 185 AMQELNGTIPEGASEPITVKFANSPAGRA 213
A+ LNG + + V+ A+ A A
Sbjct: 172 AIAGLNGMQLGD--KKLLVQRASVGAKNA 198
Score = 89.7 bits (223), Expect = 2e-21
Identities = 24/100 (24%), Positives = 48/100 (48%)
Query: 9 NTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSL 68
N + + V + L + +P + ++++ L +S G +++ L++D T S
Sbjct: 97 NPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK 156
Query: 69 GYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
GY F Y ++AI LNG++L +K + V A ++
Sbjct: 157 GYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK 196
Score = 67.0 bits (164), Expect = 2e-13
Identities = 14/87 (16%), Positives = 29/87 (33%), Gaps = 6/87 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVK-----VVRDPQTYKCKGFGFVCMTNYDEAVF 328
++V N+ + + F + + V Q + K F F+ + DE
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 329 AIQSLNGYALGDRLLQVSFKTHKPLPP 355
A+ +G + L++ P
Sbjct: 67 AMA-FDGIIFQGQSLKIRRPHDYQPLP 92
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 117 bits (296), Expect = 6e-33
Identities = 41/115 (35%), Positives = 58/115 (50%), Gaps = 4/115 (3%)
Query: 238 GNPLHHS-ARFKFAPLTADLLNNS--MLPPKSLHG-SGWCIFVYNLAPETEDNVLWQLFG 293
G P S + +PL + L+ + K + G G +F+Y+L E D L F
Sbjct: 3 GLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFL 62
Query: 294 PFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSFK 348
PFG V + KV D QT K FGFV N D A AI+++NG+ +G + L+V K
Sbjct: 63 PFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117
Score = 107 bits (269), Expect = 6e-29
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 = 79.0 bits (195), Expect = 2e-18
Identities = 28/126 (22%), Positives = 57/126 (45%), Gaps = 20/126 (15%)
Query: 84 AIIELNGLKLQNKSIKVSYARPSSEAIKR---ANLYVSGLPKHMTQEDLENLFRPYGTII 140
+ L+ L + ++ + A + + I+ NL++ LP+ T DL + F P+G +I
Sbjct: 9 SASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVI 68
Query: 141 TSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEP 200
++++ DK + +SK GFV F+ A+ A++ +NG +
Sbjct: 69 SAKVFIDK---------QTS------LSKCFGFVSFDNPDSAQVAIKAMNGFQVGT--KR 111
Query: 201 ITVKFA 206
+ V+
Sbjct: 112 LKVQLK 117
>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1 PDB: 2rq4_A 2rqc_A
Length = 115
Score = 115 bits (290), Expect = 5e-32
Identities = 36/82 (43%), Positives = 46/82 (56%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
G +F+Y+L E D L Q+F PFG V + KV D QT K FGFV N A A
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 330 IQSLNGYALGDRLLQVSFKTHK 351
IQS+NG+ +G + L+V K K
Sbjct: 84 IQSMNGFQIGMKRLKVQLKRSK 105
Score = 112 bits (281), Expect = 1e-30
Identities = 30/99 (30%), Positives = 49/99 (49%)
Query: 10 TTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLG 69
T QS + + +NL + ++PQ ++L +F G V S K+ DK T S
Sbjct: 9 TQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKC 68
Query: 70 YGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
+GFV+Y A+ AI +NG ++ K +KV R ++
Sbjct: 69 FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND 107
Score = 82.0 bits (203), Expect = 2e-19
Identities = 29/130 (22%), Positives = 58/130 (44%), Gaps = 21/130 (16%)
Query: 89 NGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDK 148
+GL Q+ + A E + ANL++ LP+ +DL +F P+G ++++++ DK
Sbjct: 6 SGLTQQS----IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK 61
Query: 149 MASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
+ +SK GFV ++ + A+ A+Q +NG + + V+ S
Sbjct: 62 Q---------TN------LSKCFGFVSYDNPVSAQAAIQSMNGFQIGM--KRLKVQLKRS 104
Query: 209 PAGRAKALAA 218
++
Sbjct: 105 KNDSKSGPSS 114
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 113 bits (284), Expect = 3e-31
Identities = 32/111 (28%), Positives = 50/111 (45%), Gaps = 17/111 (15%)
Query: 106 SSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIP 165
S + L+V L K ++ED+ LF+P+G I +L
Sbjct: 9 ESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD---------------- 52
Query: 166 QISKGIGFVRFNQHIEAEHAMQELNGT-IPEGASEPITVKFANSPAGRAKA 215
SKG FV+F+ H EA+ A+ L+G+ GAS + VKFA++ +
Sbjct: 53 GSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESGPS 103
Score = 88.9 bits (221), Expect = 4e-22
Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 4/99 (4%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ ++ L V + + ++E++ LF G ++ C ++R S G F
Sbjct: 2 SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDG-SSKGCAF 60
Query: 73 VNYYRTEDAERAIIELNG---LKLQNKSIKVSYARPSSE 108
V + +A+ AI L+G + + S+ V +A E
Sbjct: 61 VKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKE 99
Score = 76.2 bits (188), Expect = 2e-17
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV L + + + +LF PFG + V+R P KG FV +++ EA AI +L
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDG-SSKGCAFVKFSSHTEAQAAIHAL 76
Query: 334 NG---YALGDRLLQVSF 347
+G L V F
Sbjct: 77 HGSQTMPGASSSLVVKF 93
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding,
RNA processing, mRNA processing, nonsense-mediated mRNA
decay, cleavage; NMR {Saccharomyces cerevisiae} PDB:
2km8_C
Length = 167
Score = 112 bits (283), Expect = 2e-30
Identities = 37/189 (19%), Positives = 76/189 (40%), Gaps = 28/189 (14%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+++ + + + T++ L+ F G V K+++D T +S G+GF+++ + +
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 84 AIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSR 143
+ + L K I A P E K ++V G+ + ++ E F +GTII ++
Sbjct: 61 VVKTQH--ILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQ 118
Query: 144 ILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAM----QELNGTIPEGASE 199
++ DK +G +G GFV ++ + +
Sbjct: 119 LMLDKD---------TGQS------RGFGFVTYDSADAVDRVCQNKFIDFKDR------- 156
Query: 200 PITVKFANS 208
I +K A
Sbjct: 157 KIEIKRAEP 165
Score = 66.4 bits (163), Expect = 2e-13
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV + P+ + F +G + + +++ D T + +GFGFV + D AV +
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD-AVDRVCQN 148
Query: 334 NGYALGDRLLQVSF 347
DR +++
Sbjct: 149 KFIDFKDRKIEIKR 162
Score = 65.6 bits (161), Expect = 4e-13
Identities = 16/59 (27%), Positives = 34/59 (57%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+F+ L +T ++ L + FG +G V ++K+++DP T + +GFGF+ +++
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A
Length = 282
Score = 115 bits (288), Expect = 4e-30
Identities = 48/327 (14%), Positives = 93/327 (28%), Gaps = 61/327 (18%)
Query: 26 NSNLIVNYVPQTMTQEEL----QHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDA 81
N + +N + + + ++EL +FS G++ + R + G FV + A
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSSA 65
Query: 82 ERAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIIT 141
A+ + G +K +++ YA+ S+ I + + +
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKR-------------- 111
Query: 142 SRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPI 201
+ TP + +G G ++ P
Sbjct: 112 -------------KPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHM- 157
Query: 202 TVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSM 261
Q M P
Sbjct: 158 -------------------PGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPA 198
Query: 262 LPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMT 321
P + +F+ NL ET + +L LF F + V++V FV
Sbjct: 199 QPLSE-NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFD 252
Query: 322 NYDEAVFAIQSLNGYAL-GDRLLQVSF 347
N +A A +L G+ + + +++SF
Sbjct: 253 NEVQAGAARDALQGFKITQNNAMKISF 279
Score = 65.3 bits (158), Expect = 3e-12
Identities = 20/105 (19%), Positives = 36/105 (34%), Gaps = 6/105 (5%)
Query: 1 MMKHEEMYNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIR 60
N N L + +P+ + L LF+ + +L+
Sbjct: 182 PGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP 241
Query: 61 DKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL-QNKSIKVSYAR 104
+ FV + A A L G K+ QN ++K+S+A+
Sbjct: 242 GRH-----DIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 281
Score = 64.9 bits (157), Expect = 4e-12
Identities = 22/242 (9%), Positives = 63/242 (26%), Gaps = 24/242 (9%)
Query: 113 ANLYVSGLPKHMTQEDLE----NLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQIS 168
+Y++ L + + +++L+ +F +G I+ +
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK------------------M 51
Query: 169 KGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMR 228
+G FV F + A +A++ + G +P+ +++A + + + +
Sbjct: 52 RGQAFVIFKEVSSATNALRSMQGF--PFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKRE 109
Query: 229 HFAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNVL 288
+ P+ + P + P +
Sbjct: 110 KRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGM 169
Query: 289 WQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSFK 348
G + Q + ++ + + +L + F
Sbjct: 170 IPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFN 229
Query: 349 TH 350
Sbjct: 230 QF 231
Score = 64.1 bits (155), Expect = 8e-12
Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 274 IFVYNLAPETEDNVLWQ----LFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
I++ NL + + + L + +F FG + ++ V R K +G FV A A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSSATNA 68
Query: 330 IQSLNGYALGDRLLQVSFKTHKP 352
++S+ G+ D+ +++ +
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDS 91
Score = 57.2 bits (137), Expect = 2e-09
Identities = 17/93 (18%), Positives = 32/93 (34%), Gaps = 21/93 (22%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L+++ LP+ + L LF + R++ + I F
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR--------------------HDIAF 248
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
V F+ ++A A L G + + + FA
Sbjct: 249 VEFDNEVQAGAARDALQGF-KITQNNAMKISFA 280
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 106 bits (266), Expect = 1e-28
Identities = 24/89 (26%), Positives = 42/89 (47%)
Query: 264 PKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNY 323
P I V NL+ +T + L +LF PFG++ + + +D T + KGF F+
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 324 DEAVFAIQSLNGYALGDRLLQVSFKTHKP 352
++A AI ++G+ +L V +
Sbjct: 68 EDAARAIAGVSGFGYDHLILNVEWAKPST 96
Score = 101 bits (254), Expect = 5e-27
Identities = 30/97 (30%), Positives = 54/97 (55%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ + + N+ + V + + + +LQ LF G + L +DKTT QS G+ F
Sbjct: 2 SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEA 109
++++R EDA RAI ++G + + V +A+PS+ +
Sbjct: 62 ISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS 98
Score = 68.0 bits (167), Expect = 1e-14
Identities = 25/103 (24%), Positives = 46/103 (44%), Gaps = 17/103 (16%)
Query: 104 RPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPE 163
P+ A A + V+ L + + DL+ LFRP+G+I + DK +
Sbjct: 7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQ----------- 55
Query: 164 IPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
SKG F+ F++ +A A+ ++G + + V++A
Sbjct: 56 ----SKGFAFISFHRREDAARAIAGVSGFGYDH--LILNVEWA 92
>1x4e_A RNA binding motif, single-stranded interacting protein 2;
structural genomics, RRM domain, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 85
Score = 101 bits (254), Expect = 4e-27
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 = 97.2 bits (243), Expect = 2e-25
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 = 74.9 bits (185), Expect = 2e-17
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 15/84 (17%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+ LY+ GL T +DL L +PYG I++++ + DK + KG G
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT---------TNK------CKGYG 50
Query: 173 FVRFNQHIEAEHAMQELNGTIPEG 196
FV F+ A+ A+ L + +
Sbjct: 51 FVDFDSPSAAQKAVTALKASGVQA 74
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA
binding domain, RBD, RNA splicing, apoptosis,
phosphoprotein, RNA-binding; 1.95A {Homo sapiens}
Length = 87
Score = 99 bits (250), Expect = 1e-26
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 = 85.7 bits (213), Expect = 3e-21
Identities = 20/67 (29%), Positives = 37/67 (55%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T + F+ G + ++++D T +S GYGFV+++ DAE AI ++ G L + I
Sbjct: 19 TTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
Query: 99 KVSYARP 105
+ ++A
Sbjct: 79 RTNWATR 85
Score = 65.7 bits (161), Expect = 6e-14
Identities = 25/95 (26%), Positives = 41/95 (43%), Gaps = 17/95 (17%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+++V L +T + F P+G I +R++ D +G SKG G
Sbjct: 7 FHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDM---------ATGK------SKGYG 51
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
FV F +AE+A+Q++ G G I +A
Sbjct: 52 FVSFFNKWDAENAIQQMGGQWLGG--RQIRTNWAT 84
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 103 bits (259), Expect = 2e-26
Identities = 43/195 (22%), Positives = 75/195 (38%), Gaps = 33/195 (16%)
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 AIIELNGLKLQNKSIKVSYARPSSEAIKRAN------LYVSGLPKHMTQEDLENLFRPYG 137
A + K+ + ++ A ++ + ++V G+ + + L + F YG
Sbjct: 71 A-MNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYG 129
Query: 138 TIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAM----QELNGTI 193
I I+ D+ SG +G FV F+ H + + +NG
Sbjct: 130 KIEVIEIMTDRG---------SGKK------RGFAFVTFDDHDSVDKIVIQKYHTVNGH- 173
Query: 194 PEGASEPITVKFANS 208
V+ A S
Sbjct: 174 ------NCEVRKALS 182
Score = 86.6 bits (215), Expect = 3e-20
Identities = 46/257 (17%), Positives = 84/257 (32%), Gaps = 77/257 (29%)
Query: 100 VSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVS 159
+S + E + L++ GL T E L + F +GT+ ++ D +
Sbjct: 1 MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN---------T 51
Query: 160 GTPEIPQISKGIGFVRFNQHIEAEHAMQ----ELNGTIPEGASEPITVKFANSPAGRAKA 215
S+G GFV + E + AM +++G + K A S +
Sbjct: 52 KR------SRGFGFVTYATVEEVDAAMNARPHKVDGR-------VVEPKRAVSREDSQR- 97
Query: 216 LAANLNAQAAAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIF 275
P H K IF
Sbjct: 98 ------------------------PGAHLTVKK-------------------------IF 108
Query: 276 VYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNG 335
V + +TE++ L F +G ++ ++++ D + K +GF FV ++D +V I
Sbjct: 109 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHD-SVDKIVIQKY 167
Query: 336 YALGDRLLQVSFKTHKP 352
+ + +V K
Sbjct: 168 HTVNGHNCEVRKALSKQ 184
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} PDB: 2dgq_A
Length = 106
Score = 100 bits (251), Expect = 2e-26
Identities = 25/110 (22%), Positives = 45/110 (40%), Gaps = 16/110 (14%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
S + L++ +P+++ ++DL+ LF +G I +L D+ +G
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF---------TG 52
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQELNG-TIPEGASEPITVKFANSP 209
KG F+ + + A A L+ G + PI VK A+S
Sbjct: 53 M------HKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSE 96
Score = 87.8 bits (218), Expect = 1e-21
Identities = 22/96 (22%), Positives = 42/96 (43%), Gaps = 3/96 (3%)
Query: 16 STYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
S + L + +P+ + +++L+ LF G++ +++D+ T G F+ Y
Sbjct: 3 SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62
Query: 76 YRTEDAERAIIELNG---LKLQNKSIKVSYARPSSE 108
E A +A L+ L N+ I+V A S
Sbjct: 63 CERESALKAQSALHEQKTLPGMNRPIQVKPADSESR 98
Score = 77.4 bits (191), Expect = 6e-18
Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 3/77 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ + ++ L LF FG + + V++D T KG F+ + A+ A +L
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 334 NGYAL---GDRLLQVSF 347
+ +R +QV
Sbjct: 76 HEQKTLPGMNRPIQVKP 92
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation,
RNA-binding, EIF4G-binding translation; 1.90A {Homo
sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 99.6 bits (249), Expect = 5e-26
Identities = 30/109 (27%), Positives = 55/109 (50%), Gaps = 10/109 (9%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
N+ + + +++ + L FS+ G + SCK++ D+ S GYGFV++ E AERAI
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 63
Query: 87 ELNGLKLQNKSIKVSYARPSSE--------AIKRANLYVSGLPKHMTQE 127
++NG+ L ++ + V + E A + N+Y+ T+
Sbjct: 64 KMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRA 112
Score = 88.1 bits (219), Expect = 9e-22
Identities = 26/79 (32%), Positives = 38/79 (48%), Gaps = 2/79 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IF+ NL ++ L+ F FG + + KVV D KG+GFV + A AI+ +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 65
Query: 334 NGYALGDRLLQVSFKTHKP 352
NG L DR + V +
Sbjct: 66 NGMLLNDRKVFVGRFKSRK 84
Score = 68.8 bits (169), Expect = 1e-14
Identities = 26/107 (24%), Positives = 45/107 (42%), Gaps = 19/107 (17%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
N+++ L K + + L + F +G I++ +++CD+ SKG G
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-----------NG------SKGYG 48
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAAN 219
FV F AE A++++NG + + V S R L A
Sbjct: 49 FVHFETQEAAERAIEKMNGMLLND--RKVFVGRFKSRKEREAELGAR 93
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA
splicing, mRNA transport, nonsense-mediated mRNA decay,
nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*
Length = 126
Score = 98.2 bits (245), Expect = 2e-25
Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 2/93 (2%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
P +S+ GW +FV + E + + F +G ++N+ + D +T KG+ V
Sbjct: 16 PQRSV--EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 73
Query: 323 YDEAVFAIQSLNGYALGDRLLQVSFKTHKPLPP 355
Y EA A++ LNG L + + V + + P
Sbjct: 74 YKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPK 106
Score = 83.2 bits (206), Expect = 7e-20
Identities = 24/98 (24%), Positives = 44/98 (44%)
Query: 8 YNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQS 67
Y++ + + + L V V + T+E++ F+ GE+++ L D+ T
Sbjct: 4 YDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 63
Query: 68 LGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
GY V Y ++A+ A+ LNG L + I V +
Sbjct: 64 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 101
Score = 61.2 bits (149), Expect = 7e-12
Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 17/94 (18%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
L+V+G+ + T+ED+ + F YG I + D+ +G KG
Sbjct: 23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR---------TGY------LKGYT 67
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
V + + EA+ AM+ LNG G +PI+V +
Sbjct: 68 LVEYETYKEAQAAMEGLNGQDLMG--QPISVDWC 99
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 97.3 bits (243), Expect = 2e-25
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 1/86 (1%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
GW +FV + E + + F +G ++N+ + D +T KG+ V Y EA A
Sbjct: 22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAA 81
Query: 330 IQSLNGYALGDRLLQVSFKTHKPLPP 355
++ LNG L + + V + + PP
Sbjct: 82 MEGLNGQDLMGQPISVDWCFVRG-PP 106
Score = 84.6 bits (210), Expect = 1e-20
Identities = 24/98 (24%), Positives = 44/98 (44%)
Query: 8 YNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQS 67
Y++ + + + L V V + T+E++ F+ GE+++ L D+ T
Sbjct: 5 YDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYL 64
Query: 68 LGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
GY V Y ++A+ A+ LNG L + I V +
Sbjct: 65 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 102
Score = 60.3 bits (147), Expect = 9e-12
Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 17/94 (18%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
L+V+G+ + T+ED+ + F YG I + D+ +G KG
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR---------TGY------LKGYT 68
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
V + + EA+ AM+ LNG + +PI+V +
Sbjct: 69 LVEYETYKEAQAAMEGLNGQ--DLMGQPISVDWC 100
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 95.6 bits (239), Expect = 6e-25
Identities = 24/79 (30%), Positives = 40/79 (50%)
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 NGYALGDRLLQVSFKTHKP 352
G L R L++++
Sbjct: 64 QGQDLNGRPLRINWAAKLE 82
Score = 82.9 bits (206), Expect = 3e-20
Identities = 18/68 (26%), Positives = 35/68 (51%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKS 97
+ E L++ F S ++ D T S GYGFV++ +DA+ A+ + G L +
Sbjct: 13 VDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP 72
Query: 98 IKVSYARP 105
+++++A
Sbjct: 73 LRINWAAK 80
Score = 68.3 bits (168), Expect = 6e-15
Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 17/95 (17%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
NL+V L ++ E L N F+ + + ++ ++ D +G+ S+G G
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQ---------TGS------SRGYG 46
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
FV F +A++AM + G G P+ + +A
Sbjct: 47 FVSFTSQDDAQNAMDSMQGQDLNG--RPLRINWAA 79
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain,
RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 95.4 bits (238), Expect = 1e-24
Identities = 30/96 (31%), Positives = 50/96 (52%), Gaps = 2/96 (2%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ + + Q L V + + +T+ + LFS +G +SCK+I + T+ Y F
Sbjct: 2 SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCF 59
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
V +Y DA A+ +NG K+ K +KV++A S
Sbjct: 60 VEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS 95
Score = 78.1 bits (193), Expect = 3e-18
Identities = 15/75 (20%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
++V NL+ + + ++ QLF G ++ K++ + + + FV + +A A+ +
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAA 74
Query: 333 LNGYALGDRLLQVSF 347
+NG + + ++V++
Sbjct: 75 MNGRKILGKEVKVNW 89
Score = 65.3 bits (160), Expect = 1e-13
Identities = 20/110 (18%), Positives = 44/110 (40%), Gaps = 19/110 (17%)
Query: 105 PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEI 164
+ + LYV L + +T+ + LF G + +++ + ++ +
Sbjct: 8 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN---DPY------- 57
Query: 165 PQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAK 214
FV F +H +A A+ +NG G + + V +A +P+ +
Sbjct: 58 -------CFVEFYEHRDAAAALAAMNGRKILG--KEVKVNWATTPSSQKS 98
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain,
structural genomics, NPPSFA; NMR {Mus musculus} PDB:
2rne_A 2dh7_A
Length = 115
Score = 95.9 bits (239), Expect = 1e-24
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 = 87.0 bits (216), Expect = 2e-21
Identities = 27/100 (27%), Positives = 52/100 (52%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ Q + ++ V + +T E+++ F+ G + ++++D T +S GYGF
Sbjct: 2 SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGF 61
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKR 112
V+++ DAE AI ++ G L + I+ ++A A K
Sbjct: 62 VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKS 101
Score = 68.5 bits (168), Expect = 1e-14
Identities = 28/112 (25%), Positives = 48/112 (42%), Gaps = 17/112 (15%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+++V L +T ED++ F P+G I +R++ D +G SKG GF
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA---------TGK------SKGYGF 61
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAA 225
V F +AE+A+Q++ G I +A K+ + Q+
Sbjct: 62 VSFFNKWDAENAIQQMGGQ--WLGGRQIRTNWATRKPPAPKSTYESNTKQSG 111
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar
mRNA localization, translation; 1.90A {Drosophila
melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A
Length = 165
Score = 97.6 bits (243), Expect = 1e-24
Identities = 21/83 (25%), Positives = 45/83 (54%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
GW +FV ++ E +++ + + F +G ++N+ + D +T KG+ V + +A+ A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 330 IQSLNGYALGDRLLQVSFKTHKP 352
++LNG + + +QV + K
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVKG 153
Score = 84.9 bits (210), Expect = 5e-20
Identities = 22/79 (27%), Positives = 38/79 (48%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
L V + + ++E+Q F GE+++ L D+ T S GY V Y + A A
Sbjct: 73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132
Query: 87 ELNGLKLQNKSIKVSYARP 105
LNG ++ ++I+V +
Sbjct: 133 ALNGAEIMGQTIQVDWCFV 151
Score = 63.3 bits (154), Expect = 2e-12
Identities = 28/147 (19%), Positives = 52/147 (35%), Gaps = 28/147 (19%)
Query: 77 RTEDAERAIIELNGLKLQNKSIKVSYARPSSE-----------AIKRANLYVSGLPKHMT 125
E A+ G + SY R +E +++ L+V+ + +
Sbjct: 26 LKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQ 85
Query: 126 QEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHA 185
+++++ F YG I + D+ +G SKG V + H +A A
Sbjct: 86 EDEIQEKFCDYGEIKNIHLNLDRR---------TGF------SKGYALVEYETHKQALAA 130
Query: 186 MQELNGTIPEGASEPITVKFANSPAGR 212
+ LNG G + I V + +
Sbjct: 131 KEALNGAEIMG--QTIQVDWCFVKGPK 155
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 94.1 bits (234), Expect = 4e-24
Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 3/86 (3%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
++ L + +P + E L L G VESC+ + + V Y + A +
Sbjct: 13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQ 69
Query: 84 AIIELNGLKLQNKSIKVSYARPSSEA 109
A+ +LNG +L+N ++KV+Y A
Sbjct: 70 ALDKLNGFQLENFTLKVAYIPDEMAA 95
Score = 74.8 bits (184), Expect = 4e-17
Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 3/78 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ + N+ P + VL L +G V++ + V V ++ D+A A+ L
Sbjct: 18 LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKL 74
Query: 334 NGYALGDRLLQVSFKTHK 351
NG+ L + L+V++ +
Sbjct: 75 NGFQLENFTLKVAYIPDE 92
Score = 63.2 bits (154), Expect = 7e-13
Identities = 16/99 (16%), Positives = 33/99 (33%), Gaps = 20/99 (20%)
Query: 111 KRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKG 170
+ L + +P H+ E L++L YG + + +
Sbjct: 14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS------------------ETA 55
Query: 171 IGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
+ V ++ +A A+ +LNG E + V +
Sbjct: 56 VVNVTYSSKDQARQALDKLNGFQLEN--FTLKVAYIPDE 92
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein
complex, EXON junct complex, signaling protein; 1.85A
{Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B*
2j0s_D* 2xb2_D*
Length = 110
Score = 93.9 bits (234), Expect = 5e-24
Identities = 22/95 (23%), Positives = 49/95 (51%)
Query: 258 NNSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGF 317
++ + P GW +FV ++ E +++ + + F +G ++N+ + D +T KG+
Sbjct: 13 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 72
Query: 318 VCMTNYDEAVFAIQSLNGYALGDRLLQVSFKTHKP 352
V + +A+ A ++LNG + + +QV + K
Sbjct: 73 VEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 107
Score = 81.2 bits (201), Expect = 3e-19
Identities = 22/77 (28%), Positives = 38/77 (49%)
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 NGLKLQNKSIKVSYARP 105
NG ++ ++I+V +
Sbjct: 89 NGAEIMGQTIQVDWCFV 105
Score = 57.3 bits (139), Expect = 1e-10
Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 17/94 (18%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
L+V+ + + +++++ F YG I + D+ +G SKG
Sbjct: 27 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR---------TGF------SKGYA 71
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
V + H +A A + LNG G + I V +
Sbjct: 72 LVEYETHKQALAAKEALNGAEIMG--QTIQVDWC 103
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 92.7 bits (231), Expect = 1e-23
Identities = 28/100 (28%), Positives = 51/100 (51%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ Q++ + V + + +++ L LF G V + + +D+ T Q GYGF
Sbjct: 2 SSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGF 61
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKR 112
V + EDA+ AI ++ +KL K I+V+ A ++ +
Sbjct: 62 VEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101
Score = 83.1 bits (206), Expect = 4e-20
Identities = 20/80 (25%), Positives = 43/80 (53%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
++V L + + +LW+LF G V N + +D T + +G+GFV + ++A +AI+
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 333 LNGYALGDRLLQVSFKTHKP 352
++ L + ++V+ +
Sbjct: 77 MDMIKLYGKPIRVNKASAHN 96
Score = 65.0 bits (159), Expect = 2e-13
Identities = 27/112 (24%), Positives = 51/112 (45%), Gaps = 17/112 (15%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTP 162
+ P SE + A +YV GL + +++ L LF G ++ + + D+ V+G
Sbjct: 6 SGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR---------VTGQ- 55
Query: 163 EIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAK 214
+G GFV F +A++A++ ++ G +PI V A++
Sbjct: 56 -----HQGYGFVEFLSEEDADYAIKIMDMIKLYG--KPIRVNKASAHNKNLS 100
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 91.6 bits (228), Expect = 3e-23
Identities = 26/93 (27%), Positives = 46/93 (49%), Gaps = 5/93 (5%)
Query: 20 SDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGE-VESCKLIRDKTTAQSLGYGFVNYYRT 78
S + ++L + + M + + F+++GE V S K+IR++ T GY FV +
Sbjct: 3 SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62
Query: 79 EDAERAIIELNGLKLQN----KSIKVSYARPSS 107
AE+ + ++NG L K K++YA S
Sbjct: 63 ATAEKCLHKINGKPLPGATPAKRFKLNYATYSG 95
Score = 81.6 bits (202), Expect = 1e-19
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 1/81 (1%)
Query: 269 GSGWCIFVYNLAPETEDNVLWQLFGPFG-AVQNVKVVRDPQTYKCKGFGFVCMTNYDEAV 327
G +++ +L P ++N + + F G V +VK++R+ T G+ FV + A
Sbjct: 7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAE 66
Query: 328 FAIQSLNGYALGDRLLQVSFK 348
+ +NG L FK
Sbjct: 67 KCLHKINGKPLPGATPAKRFK 87
Score = 58.1 bits (141), Expect = 4e-11
Identities = 21/101 (20%), Positives = 39/101 (38%), Gaps = 16/101 (15%)
Query: 105 PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITS-RILCDKMASENVRSFVSGTPE 163
S + A+L++ L +M + + F G + S +I+ ++ ++G
Sbjct: 2 SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNR---------LTGI-- 50
Query: 164 IPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVK 204
G FV F AE + ++NG GA+ K
Sbjct: 51 ----PAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFK 87
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 90.8 bits (226), Expect = 6e-23
Identities = 21/82 (25%), Positives = 46/82 (56%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ ++ + + + L G V N+K++ DPQT + KG+ F+ + + + A+++L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 334 NGYALGDRLLQVSFKTHKPLPP 355
NGY LG R L+ + ++ +
Sbjct: 65 NGYQLGSRFLKCGYSSNSDISG 86
Score = 82.3 bits (204), Expect = 8e-20
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
Y+ P T+E++ L S+VG V + K++ D T +S GY F+ + E + A+ LN
Sbjct: 6 YLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLN 65
Query: 90 GLKLQNKSIKVSYARP 105
G +L ++ +K Y+
Sbjct: 66 GYQLGSRFLKCGYSSN 81
Score = 59.6 bits (145), Expect = 1e-11
Identities = 19/95 (20%), Positives = 39/95 (41%), Gaps = 17/95 (17%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+Y+ +P T+E + +L G +I +++ D +G SKG
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ---------TGR------SKGYA 47
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
F+ F + A++ LNG + S + +++
Sbjct: 48 FIEFRDLESSASAVRNLNGY--QLGSRFLKCGYSS 80
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 90.4 bits (225), Expect = 1e-22
Identities = 26/95 (27%), Positives = 50/95 (52%), Gaps = 2/95 (2%)
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-NGLKLQNKSIKVSYARP 105
FV++ +DA++A L + L + + + +A
Sbjct: 62 FVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96
Score = 78.1 bits (193), Expect = 4e-18
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 2/85 (2%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDP-QTYKCKGFGFVCMTNYDEAVF 328
+ I V N+ + + +LF FG ++ V++ + T +GFGFV +A
Sbjct: 14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 73
Query: 329 AIQSL-NGYALGDRLLQVSFKTHKP 352
A +L + L R L + + +
Sbjct: 74 AFNALCHSTHLYGRRLVLEWADSEV 98
Score = 64.6 bits (158), Expect = 3e-13
Identities = 20/111 (18%), Positives = 39/111 (35%), Gaps = 17/111 (15%)
Query: 106 SSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIP 165
+ + + V +P Q ++ LF +G + T R+ +
Sbjct: 9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGA------------ 56
Query: 166 QISKGIGFVRFNQHIEAEHAMQEL-NGTIPEGASEPITVKFANSPAGRAKA 215
+G GFV F +A+ A L + T G + +++A+S
Sbjct: 57 --HRGFGFVDFITKQDAKKAFNALCHSTHLYG--RRLVLEWADSEVTVQSG 103
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 91.4 bits (227), Expect = 1e-22
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 = 79.1 bits (195), Expect = 4e-18
Identities = 23/101 (22%), Positives = 41/101 (40%)
Query: 3 KHEEMYNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDK 62
E + S S L V + + + + L F G++ ++ D
Sbjct: 40 NCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY 99
Query: 63 TTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYA 103
T + G+ FV + EDA AI +N +L ++I+V+ A
Sbjct: 100 ETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
Score = 66.0 bits (161), Expect = 2e-13
Identities = 25/120 (20%), Positives = 39/120 (32%), Gaps = 17/120 (14%)
Query: 87 ELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILC 146
+N + A + LYV GL + + + L F P+G I +I
Sbjct: 38 CVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 97
Query: 147 DKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
D + +G FV F +A A+ +N + E I V A
Sbjct: 98 DY---------ETEK------HRGFAFVEFELAEDAAAAIDNMNES--ELFGRTIRVNLA 140
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 90.0 bits (224), Expect = 1e-22
Identities = 22/105 (20%), Positives = 46/105 (43%), Gaps = 8/105 (7%)
Query: 4 HEEMYNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKT 63
H + ++ + N+ L V P + + EL +F G ++ K++
Sbjct: 9 HHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--- 65
Query: 64 TAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
G+ FV + E A +AI E++G N+ ++V Y++ ++
Sbjct: 66 -----GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105
Score = 73.5 bits (181), Expect = 1e-16
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
Score = 71.9 bits (177), Expect = 6e-16
Identities = 22/112 (19%), Positives = 41/112 (36%), Gaps = 25/112 (22%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTP 162
+ L+V P + + +L +F P+G + +IL
Sbjct: 22 HHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL----------------- 64
Query: 163 EIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAK 214
G FV F + A A++E++G +P+ V ++ PA R +
Sbjct: 65 ------NGFAFVEFEEAESAAKAIEEVHGKSFAN--QPLEVVYSKLPAKRYR 108
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 115
Score = 90.0 bits (224), Expect = 2e-22
Identities = 20/79 (25%), Positives = 37/79 (46%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+++ NL+P + L LF F + + T + +G F+ N + A A+
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 333 LNGYALGDRLLQVSFKTHK 351
+NGY L ++L + F +K
Sbjct: 87 VNGYKLYGKILVIEFGKNK 105
Score = 84.6 bits (210), Expect = 1e-20
Identities = 19/89 (21%), Positives = 39/89 (43%)
Query: 21 DVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTED 80
+ E N L + + +T+ +L LF+ E + + T + G F+ + E
Sbjct: 20 NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 79
Query: 81 AERAIIELNGLKLQNKSIKVSYARPSSEA 109
A +A+ +NG KL K + + + + +
Sbjct: 80 AWQALHLVNGYKLYGKILVIEFGKNKKQR 108
Score = 63.1 bits (154), Expect = 1e-12
Identities = 20/99 (20%), Positives = 34/99 (34%), Gaps = 17/99 (17%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
LY+ L +T+ DL +LF + I M +G F
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGR---------------MRGQAF 71
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
+ F A A+ +NG G + + ++F + R
Sbjct: 72 ITFPNKEIAWQALHLVNGYKLYG--KILVIEFGKNKKQR 108
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 89.8 bits (223), Expect = 2e-22
Identities = 17/95 (17%), Positives = 35/95 (36%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+ + + + L+ + GEVE +++ T + LG V + T A+ +
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65
Query: 86 IELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGL 120
L+ + I + +K L V+G
Sbjct: 66 KNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGS 100
Score = 85.1 bits (211), Expect = 9e-21
Identities = 13/74 (17%), Positives = 31/74 (41%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ L + L + +G V+ V+++ P+T K G V T+ A +++L
Sbjct: 9 VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68
Query: 334 NGYALGDRLLQVSF 347
+ ++ ++
Sbjct: 69 HLTSVMGNIIHAQL 82
Score = 75.1 bits (185), Expect = 5e-17
Identities = 18/112 (16%), Positives = 35/112 (31%), Gaps = 17/112 (15%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+ + L ++ + L+++ R YG + IL + G+
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRK---------------HLGLAR 52
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAA 225
V F A+ ++ L+ T G I + R K +N
Sbjct: 53 VLFTSTRGAKETVKNLHLTSVMG--NIIHAQLDIKGQQRMKYYELIVNGSYT 102
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 88.7 bits (221), Expect = 2e-22
Identities = 25/73 (34%), Positives = 42/73 (57%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V LA E +D VL F PFG + ++++ D +T K +GF FV ++A AI ++
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 334 NGYALGDRLLQVS 346
N L R ++V+
Sbjct: 70 NESELFGRTIRVN 82
Score = 80.7 bits (200), Expect = 2e-19
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
YV + + + L F G++ ++ D T + G+ FV + EDA AI +N
Sbjct: 11 YVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMN 70
Query: 90 GLKLQNKSIKVSYAR 104
+L ++I+V+ A+
Sbjct: 71 ESELFGRTIRVNLAK 85
Score = 61.4 bits (150), Expect = 2e-12
Identities = 23/94 (24%), Positives = 34/94 (36%), Gaps = 17/94 (18%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
LYV GL + + + L F P+G I +I D + +G
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY---------ETEK------HRGFA 52
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
FV F +A A+ +N + E I V A
Sbjct: 53 FVEFELAEDAAAAIDNMNES--ELFGRTIRVNLA 84
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 88.8 bits (221), Expect = 3e-22
Identities = 23/79 (29%), Positives = 47/79 (59%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V +L +++L +F PFG + N+ +++D T + KG+GF+ ++ + A A++ L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 334 NGYALGDRLLQVSFKTHKP 352
NG+ L R ++V T +
Sbjct: 68 NGFELAGRPMRVGHVTERL 86
Score = 81.4 bits (202), Expect = 1e-19
Identities = 24/87 (27%), Positives = 50/87 (57%)
Query: 23 NEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAE 82
+ +S L V + +T++ L+ +F G++++ L++D T +S GYGF+ + +E A
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 83 RAIIELNGLKLQNKSIKVSYARPSSEA 109
RA+ +LNG +L + ++V + +
Sbjct: 62 RALEQLNGFELAGRPMRVGHVTERLDG 88
Score = 66.4 bits (163), Expect = 4e-14
Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 17/95 (17%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+ LYV L ++T++ L +F P+G I ++ D +G SKG G
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSD---------TGR------SKGYG 50
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
F+ F+ A A+++LNG G P+ V
Sbjct: 51 FITFSDSECARRALEQLNGFELAG--RPMRVGHVT 83
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1;
RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 94
Score = 88.4 bits (220), Expect = 4e-22
Identities = 22/78 (28%), Positives = 40/78 (51%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
S ++V NL +N L+++F +G V V +++D T K KG F+ + D A
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNC 74
Query: 330 IQSLNGYALGDRLLQVSF 347
+++N L R+++ S
Sbjct: 75 TRAINNKQLFGRVIKASI 92
Score = 84.2 bits (209), Expect = 1e-20
Identities = 22/83 (26%), Positives = 42/83 (50%)
Query: 21 DVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTED 80
+ S + V+ +P ++T +L +FS G+V +++DK T +S G F+ + +
Sbjct: 11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70
Query: 81 AERAIIELNGLKLQNKSIKVSYA 103
A+ +N +L + IK S A
Sbjct: 71 AQNCTRAINNKQLFGRVIKASIA 93
Score = 69.9 bits (172), Expect = 2e-15
Identities = 26/106 (24%), Positives = 42/106 (39%), Gaps = 17/106 (16%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
S A ++ +YVS LP +T DL +F YG ++ I+ DK + +
Sbjct: 5 SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK---DTRK----- 56
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
SKG+ F+ F A++ + +N G I A
Sbjct: 57 -------SKGVAFILFLDKDSAQNCTRAINNKQLFG--RVIKASIA 93
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 88.8 bits (221), Expect = 4e-22
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL +D L + F PFG + + KV+ + + KGFGFVC ++ +EA A+ +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 334 NGYALGDRLLQVSFKTHKP 352
NG + + L V+ K
Sbjct: 76 NGRIVATKPLYVALAQRKE 94
Score = 86.1 bits (214), Expect = 4e-21
Identities = 28/96 (29%), Positives = 47/96 (48%), Gaps = 2/96 (2%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ Q NL V + + E L+ FS G + S K++ + +S G+GF
Sbjct: 2 SSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGF 59
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
V + E+A +A+ E+NG + K + V+ A+ E
Sbjct: 60 VCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEE 95
Score = 69.5 bits (171), Expect = 4e-15
Identities = 34/116 (29%), Positives = 49/116 (42%), Gaps = 22/116 (18%)
Query: 105 PSSEAIKR---ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGT 161
S + I R NLYV L + E L F P+GTI +++++ + G
Sbjct: 5 SSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-----------GG- 52
Query: 162 PEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALA 217
SKG GFV F+ EA A+ E+NG I +P+ V A R +
Sbjct: 53 -----RSKGFGFVCFSSPEEATKAVTEMNGRIVAT--KPLYVALAQRKEERQSGPS 101
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 88.0 bits (219), Expect = 6e-22
Identities = 25/75 (33%), Positives = 42/75 (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 LNGYALGDRLLQVSF 347
NG L R ++VS
Sbjct: 77 ANGMELDGRRIRVSG 91
Score = 82.6 bits (205), Expect = 5e-20
Identities = 24/92 (26%), Positives = 45/92 (48%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ + N L V + T+ +L+ +FS G + ++ D+ + +S G+ F
Sbjct: 2 SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 61
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYAR 104
V + +DA+ A NG++L + I+VS
Sbjct: 62 VYFENVDDAKEAKERANGMELDGRRIRVSGPS 93
Score = 70.7 bits (174), Expect = 1e-15
Identities = 28/108 (25%), Positives = 42/108 (38%), Gaps = 19/108 (17%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
S R + + L V GL + T+ DL +F YG I I+ D+ +
Sbjct: 6 SGNRANPDPNCC--LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR-------- 55
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
S+G FV F +A+ A + NG +G I V +S
Sbjct: 56 -------SRGFAFVYFENVDDAKEAKERANGMELDG--RRIRVSGPSS 94
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.54A {Homo sapiens}
Length = 95
Score = 86.9 bits (216), Expect = 1e-21
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV NL + +L++LF G + V + +D + K K FGFVC + + +AI
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPESVSYAIAL 76
Query: 333 LNGYALGDRLLQVSF 347
LNG L R + VS
Sbjct: 77 LNGIRLYGRPINVSG 91
Score = 85.4 bits (212), Expect = 5e-21
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 1/80 (1%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E + + V + + +E L LF G + + +D+ + +GFV + E
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPESVSY 72
Query: 84 AIIELNGLKLQNKSIKVSYA 103
AI LNG++L + I VS
Sbjct: 73 AIALLNGIRLYGRPINVSGP 92
Score = 72.7 bits (179), Expect = 2e-16
Identities = 25/108 (23%), Positives = 36/108 (33%), Gaps = 18/108 (16%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
S ++ ++V L + +E L LF G + I D+ G
Sbjct: 5 SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR----------EG 54
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
K GFV F +A+ LNG G PI V +S
Sbjct: 55 K------PKSFGFVCFKHPESVSYAIALLNGIRLYG--RPINVSGPSS 94
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 96
Score = 86.5 bits (215), Expect = 2e-21
Identities = 29/80 (36%), Positives = 48/80 (60%), Gaps = 1/80 (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 LNGYALGDRLLQVSFKTHKP 352
+NG L +R + VS+ K
Sbjct: 68 MNGQYLCNRPITVSYAFKKD 87
Score = 76.9 bits (190), Expect = 7e-18
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 1/84 (1%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESC-KLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+S + + + + ++ L FS+ G + K++RD T S GY F+N+ + ++ A
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 85 IIELNGLKLQNKSIKVSYARPSSE 108
I +NG L N+ I VSYA
Sbjct: 65 IEAMNGQYLCNRPITVSYAFKKDS 88
Score = 56.4 bits (137), Expect = 1e-10
Identities = 20/106 (18%), Positives = 43/106 (40%), Gaps = 18/106 (16%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITS-RILCDKMASENVRSFVSGTPEIPQISKGI 171
+ +++ L + ++ L + F +G I+ + +I+ D + S KG
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDP---DTGNS------------KGY 50
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALA 217
F+ F ++ A++ +NG PITV +A + +
Sbjct: 51 AFINFASFDASDAAIEAMNGQYLCN--RPITVSYAFKKDSKGSGPS 94
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 86.5 bits (215), Expect = 2e-21
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: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 334 NGYALGDRLLQVSF 347
N L R ++V+
Sbjct: 75 NESELFGRTIRVNL 88
Score = 86.1 bits (214), Expect = 4e-21
Identities = 23/93 (24%), Positives = 43/93 (46%)
Query: 16 STYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
S+ S + L V + + + + L F G++ ++ D T + G+ FV +
Sbjct: 2 SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 61
Query: 76 YRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
EDA AI +N +L ++I+V+ A+P
Sbjct: 62 ELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI 94
Score = 68.4 bits (168), Expect = 8e-15
Identities = 25/110 (22%), Positives = 39/110 (35%), Gaps = 17/110 (15%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTP 162
+ S A + LYV GL + + + L F P+G I +I D +
Sbjct: 3 SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY---------ETEK- 52
Query: 163 EIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
+G FV F +A A+ +N + G I V A +
Sbjct: 53 -----HRGFAFVEFELAEDAAAAIDNMNESELFG--RTIRVNLAKPMRIK 95
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT
arginine/serine-rich 2, S35, splicing factor SC35,; RRM
domain, cell WALL; NMR {Streptococcus SP}
Length = 158
Score = 88.4 bits (219), Expect = 2e-21
Identities = 24/83 (28%), Positives = 41/83 (49%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ V NL T + L ++F +G V +V + RD T + +GF FV + +A A+ +
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 131
Query: 333 LNGYALGDRLLQVSFKTHKPLPP 355
++G L R L+V + P
Sbjct: 132 MDGAVLDGRELRVQMARYGRPPD 154
Score = 80.7 bits (199), Expect = 2e-18
Identities = 23/82 (28%), Positives = 43/82 (52%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E ++L V+ + + + L+ +F G V + RD+ T +S G+ FV ++ DAE
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 84 AIIELNGLKLQNKSIKVSYARP 105
A+ ++G L + ++V AR
Sbjct: 128 AMDAMDGAVLDGRELRVQMARY 149
Score = 67.6 bits (165), Expect = 6e-14
Identities = 33/161 (20%), Positives = 56/161 (34%), Gaps = 28/161 (17%)
Query: 57 KLIRDKTTAQSLGYG-FVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRA-- 113
KLI + T + V+ E + NG+ + + +E
Sbjct: 4 KLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHH 63
Query: 114 --------NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIP 165
+L V L + + L +F YG + I D+ E
Sbjct: 64 HMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE------------- 110
Query: 166 QISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
S+G FVRF+ +AE AM ++G + +G + V+ A
Sbjct: 111 --SRGFAFVRFHDKRDAEDAMDAMDGAVLDG--RELRVQMA 147
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition
motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 99
Score = 85.8 bits (213), Expect = 4e-21
Identities = 28/96 (29%), Positives = 47/96 (48%), Gaps = 6/96 (6%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ Q S L V +P +T+EE++ LF G+ + +DK G+GF
Sbjct: 2 SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGF 55
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
+ AE A +EL+ + L+ K ++V +A S+
Sbjct: 56 IRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS 91
Score = 83.5 bits (207), Expect = 3e-20
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 6/79 (7%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL P+ + + +LF +G V + +D KGFGF+ + A A L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 334 NGYALGDRLLQVSFKTHKP 352
+ L + L+V F H
Sbjct: 72 DNMPLRGKQLRVRFACHSA 90
Score = 71.9 bits (177), Expect = 4e-16
Identities = 27/104 (25%), Positives = 38/104 (36%), Gaps = 23/104 (22%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
R+ L+V LP +T+E++ LF YG I KG
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI---------------------HKDKGF 53
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKA 215
GF+R AE A EL+ G + + V+FA A
Sbjct: 54 GFIRLETRTLAEIAKVELDNMPLRG--KQLRVRFACHSASLTSG 95
>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing
factor, RNA protein complex, SMN, binding protein-RNA
complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A
Length = 129
Score = 86.7 bits (215), Expect = 4e-21
Identities = 27/91 (29%), Positives = 47/91 (51%), Gaps = 1/91 (1%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
++ C+ V+ L+ T + L ++F +G + +V +V D Q+ + +GF FV N
Sbjct: 38 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 97
Query: 323 YDEAVFAIQSLNGYALGDRLLQVSF-KTHKP 352
D+A A + NG L R ++V F T +P
Sbjct: 98 VDDAKEAKERANGMELDGRRIRVDFSITKRP 128
Score = 84.8 bits (210), Expect = 2e-20
Identities = 22/97 (22%), Positives = 45/97 (46%)
Query: 9 NTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSL 68
+ R + N L V + T+ +L+ +FS G + ++ D+ + +S
Sbjct: 29 QMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 88
Query: 69 GYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
G+ FV + +DA+ A NG++L + I+V ++
Sbjct: 89 GFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSIT 125
Score = 67.1 bits (164), Expect = 6e-14
Identities = 26/106 (24%), Positives = 40/106 (37%), Gaps = 17/106 (16%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
+ + L V GL + T+ DL +F YG I I+ D+ +
Sbjct: 35 RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR-------- 86
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
S+G FV F +A+ A + NG +G I V F+
Sbjct: 87 -------SRGFAFVYFENVDDAKEAKERANGMELDG--RRIRVDFS 123
>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP
domain, MIF4G domain, RNA maturation, RNA export,
nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP:
d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B
3fey_B 1h6k_X
Length = 156
Score = 87.6 bits (217), Expect = 4e-21
Identities = 27/99 (27%), Positives = 48/99 (48%), Gaps = 2/99 (2%)
Query: 12 QSHRSTY--QSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLG 69
Q R Q + +++ L V + T+E++ LFS G+++ + DK + G
Sbjct: 23 QHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 70 YGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
+ FV YY DAE A+ +NG +L ++ I+ + E
Sbjct: 83 FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE 121
Score = 85.6 bits (212), Expect = 2e-20
Identities = 19/75 (25%), Positives = 39/75 (52%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
++V NL+ T + +++LF G ++ + + D GF FV + +A A++
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 333 LNGYALGDRLLQVSF 347
+NG L DR+++ +
Sbjct: 101 INGTRLDDRIIRTDW 115
Score = 66.4 bits (162), Expect = 2e-13
Identities = 28/120 (23%), Positives = 43/120 (35%), Gaps = 18/120 (15%)
Query: 94 QNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASEN 153
+++ + K LYV L + T+E + LF G I + DKM
Sbjct: 21 RDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM---- 76
Query: 154 VRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS-PAGR 212
T G FV + +AE+AM+ +NGT + I + GR
Sbjct: 77 -----KKTA------CGFCFVEYYSRADAENAMRYINGTRLDD--RIIRTDWDAGFKEGR 123
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 85.7 bits (213), Expect = 4e-21
Identities = 25/79 (31%), Positives = 37/79 (46%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL+ + + L +LF +G + + D T K KGF FV + AV A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 334 NGYALGDRLLQVSFKTHKP 352
+G R+L V T K
Sbjct: 71 DGQVFQGRMLHVLPSTIKK 89
Score = 84.2 bits (209), Expect = 2e-20
Identities = 21/77 (27%), Positives = 37/77 (48%)
Query: 37 TMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNK 96
T ++E+L+ LFS+ G + D T + G+ FV + E A +A E++G Q +
Sbjct: 19 TSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGR 78
Query: 97 SIKVSYARPSSEAIKRA 113
+ V + EA +
Sbjct: 79 MLHVLPSTIKKEASQSG 95
Score = 64.9 bits (159), Expect = 1e-13
Identities = 23/101 (22%), Positives = 38/101 (37%), Gaps = 17/101 (16%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V L ++EDLE LF YG + D + + KG FV
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL---------TKK------PKGFAFV 55
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKA 215
F A A E++G + +G + V + +++
Sbjct: 56 TFMFPEHAVKAYAEVDGQVFQG--RMLHVLPSTIKKEASQS 94
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A
Length = 103
Score = 85.8 bits (213), Expect = 5e-21
Identities = 25/94 (26%), Positives = 49/94 (52%), Gaps = 8/94 (8%)
Query: 19 QSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRT 78
S + L V + T+T+E L+ FS G++E K ++D Y F+++
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDER 55
Query: 79 EDAERAIIELNGLKLQNKSIKVSYARPSSEAIKR 112
+ A +A+ E+NG L+ ++I++ +A+P + K
Sbjct: 56 DGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKE 89
Score = 76.6 bits (189), Expect = 1e-17
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NLA + +L + F FG ++ VK ++D + F+ D AV A++ +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 334 NGYALGDRLLQVSF 347
NG L +++ F
Sbjct: 66 NGKDLEGENIEIVF 79
Score = 72.7 bits (179), Expect = 2e-16
Identities = 33/120 (27%), Positives = 47/120 (39%), Gaps = 25/120 (20%)
Query: 106 SSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIP 165
SS K L+V L +T+E LE F +G + E V+
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKL------------ERVK---------- 42
Query: 166 QISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAA 225
K F+ F++ A AM+E+NG EG E I + FA P + K A A +
Sbjct: 43 -KLKDYAFIHFDERDGAVKAMEEMNGKDLEG--ENIEIVFAKPPDQKRKERKAQRQAASG 99
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 99
Score = 85.8 bits (213), Expect = 5e-21
Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 6/96 (6%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ D L V + + ++E ++ F+++ ++ + + Y F
Sbjct: 2 SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR------DYAF 55
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
V++ EDA A+ LNG L I+V+ A+P +
Sbjct: 56 VHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK 91
Score = 74.6 bits (184), Expect = 5e-17
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
++V NL T + ++ + F +V K + + FV +N ++AV A+++
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKA 70
Query: 333 LNGYALGDRLLQVSF 347
LNG L ++V+
Sbjct: 71 LNGKVLDGSPIEVTL 85
Score = 68.5 bits (168), Expect = 7e-15
Identities = 22/93 (23%), Positives = 33/93 (35%), Gaps = 23/93 (24%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
LYV L ++E +E F R+ + + F
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV---------------------KKIRDYAF 55
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
V F+ +A AM+ LNG + +G PI V A
Sbjct: 56 VHFSNREDAVEAMKALNGKVLDG--SPIEVTLA 86
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 85.8 bits (213), Expect = 5e-21
Identities = 22/79 (27%), Positives = 49/79 (62%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V +L +++L +F PFG +++++++ D +T + KG+GF+ ++ + A A++ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 334 NGYALGDRLLQVSFKTHKP 352
NG+ L R ++V T +
Sbjct: 89 NGFELAGRPMKVGHVTERT 107
Score = 82.0 bits (203), Expect = 1e-19
Identities = 27/108 (25%), Positives = 55/108 (50%)
Query: 1 MMKHEEMYNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIR 60
M H ++ + + + L V + +T++ L+ +F G +ES +L+
Sbjct: 1 MGHHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMM 60
Query: 61 DKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
D T +S GYGF+ + +E A++A+ +LNG +L + +KV + ++
Sbjct: 61 DSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108
Score = 66.9 bits (164), Expect = 4e-14
Identities = 29/119 (24%), Positives = 51/119 (42%), Gaps = 22/119 (18%)
Query: 94 QNKSIKVSYARPSSEAIKRA-----NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDK 148
+ A + +++ LYV L ++T++ L +F P+G I + +++ D
Sbjct: 3 HHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDS 62
Query: 149 MASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
E R SKG GF+ F+ A+ A+++LNG E A P+ V
Sbjct: 63 ---ETGR------------SKGYGFITFSDSECAKKALEQLNGF--ELAGRPMKVGHVT 104
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif,
C-terminal helix, N-terminal helix, RNA binding protein;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 85.4 bits (212), Expect = 8e-21
Identities = 24/82 (29%), Positives = 41/82 (50%)
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 NGYALGDRLLQVSFKTHKPLPP 355
NG R L+V +
Sbjct: 71 NGREFSGRALRVDNAASEKNKE 92
Score = 82.7 bits (205), Expect = 6e-20
Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
+V P T+E+L+ +FS VG V S +L+ D+ T + GYGF Y E A A+ LN
Sbjct: 12 FVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLN 71
Query: 90 GLKLQNKSIKVSYARP 105
G + ++++V A
Sbjct: 72 GREFSGRALRVDNAAS 87
Score = 61.9 bits (151), Expect = 2e-12
Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 17/100 (17%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+++V +P T+E L+++F G +++ R++ D+ +G KG G
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE---------TGK------PKGYG 53
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
F + A AM+ LNG G + V A S +
Sbjct: 54 FCEYQDQETALSAMRNLNGREFSG--RALRVDNAASEKNK 91
>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 85.0 bits (211), Expect = 9e-21
Identities = 23/83 (27%), Positives = 39/83 (46%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ V NL T + L ++F +G V +V + R+P T +GF FV + +A A +
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 333 LNGYALGDRLLQVSFKTHKPLPP 355
++G L R L+V +
Sbjct: 75 MDGAELDGRELRVQVARYGRRDL 97
Score = 80.7 bits (200), Expect = 3e-19
Identities = 19/82 (23%), Positives = 38/82 (46%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+ L V+ + + + L+ +F G V + R+ T G+ FV ++ DA+
Sbjct: 11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQD 70
Query: 84 AIIELNGLKLQNKSIKVSYARP 105
A ++G +L + ++V AR
Sbjct: 71 AEAAMDGAELDGRELRVQVARY 92
Score = 69.6 bits (171), Expect = 3e-15
Identities = 20/112 (17%), Positives = 35/112 (31%), Gaps = 17/112 (15%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
S + L V L + + L +F YG + I +
Sbjct: 2 SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKA-------- 53
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
+G FVRF+ +A+ A ++G +G + V+ A
Sbjct: 54 -------PRGFAFVRFHDRRDAQDAEAAMDGAELDG--RELRVQVARYGRRD 96
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 84.6 bits (210), Expect = 1e-20
Identities = 26/80 (32%), Positives = 45/80 (56%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV L+ +T + L Q+F +G + V VV+D +T + +GFGFV N D+A A+ +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 333 LNGYALGDRLLQVSFKTHKP 352
+NG ++ R ++V
Sbjct: 74 MNGKSVDGRQIRVDQAGKSS 93
Score = 84.2 bits (209), Expect = 2e-20
Identities = 25/93 (26%), Positives = 50/93 (53%)
Query: 16 STYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
S+ S + L V + ++ L+ +FS G++ +++D+ T +S G+GFV +
Sbjct: 2 SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61
Query: 76 YRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
+DA+ A++ +NG + + I+V A SS+
Sbjct: 62 ENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD 94
Score = 70.7 bits (174), Expect = 2e-15
Identities = 30/108 (27%), Positives = 43/108 (39%), Gaps = 17/108 (15%)
Query: 105 PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEI 164
S A L+V GL ++ LE +F YG I ++ D+ E R
Sbjct: 5 SSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR---ETQR--------- 52
Query: 165 PQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
S+G GFV F +A+ AM +NG +G I V A +
Sbjct: 53 ---SRGFGFVTFENIDDAKDAMMAMNGKSVDG--RQIRVDQAGKSSDN 95
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 98
Score = 84.6 bits (210), Expect = 1e-20
Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 3/82 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKC---KGFGFVCMTNYDEAVFAI 330
+F+ NL T + L +F GA+++ + + GFGFV ++A A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 331 QSLNGYALGDRLLQVSFKTHKP 352
+ L G+ + L+V
Sbjct: 68 KQLQGHTVDGHKLEVRISERAT 89
Score = 82.7 bits (205), Expect = 5e-20
Identities = 25/87 (28%), Positives = 50/87 (57%), Gaps = 3/87 (3%)
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 RAIIELNGLKLQNKSIKVSYARPSSEA 109
+A+ +L G + ++V + +++
Sbjct: 65 KALKQLQGHTVDGHKLEVRISERATKP 91
Score = 76.5 bits (189), Expect = 1e-17
Identities = 22/106 (20%), Positives = 44/106 (41%), Gaps = 14/106 (13%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+ L++ L T+E L+ +F G I + I K + + S G G
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLL------------SMGFG 53
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAA 218
FV + + +A+ A+++L G +G + V+ + A ++
Sbjct: 54 FVEYKKPEQAQKALKQLQGHTVDG--HKLEVRISERATKPASGPSS 97
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 84.3 bits (209), Expect = 2e-20
Identities = 16/81 (19%), Positives = 33/81 (40%), Gaps = 6/81 (7%)
Query: 25 QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
+ + + +P T+ +L LF + G + K +K G F+ Y E A
Sbjct: 26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDTHEQAAVC 79
Query: 85 IIELNGLKLQNKSIKVSYARP 105
I+ L Q ++++ + +
Sbjct: 80 IVALANFPFQGRNLRTGWGKE 100
Score = 79.3 bits (196), Expect = 1e-18
Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 6/74 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++ N+ + L LF FG + + K + KG F+ +++A I +L
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVAL 83
Query: 334 NGYALGDRLLQVSF 347
+ R L+ +
Sbjct: 84 ANFPFQGRNLRTGW 97
Score = 68.1 bits (167), Expect = 1e-14
Identities = 16/95 (16%), Positives = 33/95 (34%), Gaps = 23/95 (24%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
Y+ +P T+ DL LF+ +G I+ + + KG F
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE---------------------KGCCF 67
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
++++ H +A + L +G + +
Sbjct: 68 IKYDTHEQAAVCIVALANFPFQG--RNLRTGWGKE 100
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 83.9 bits (208), Expect = 2e-20
Identities = 24/96 (25%), Positives = 48/96 (50%), Gaps = 2/96 (2%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ S+ L V+ +P +L+ +F G++ ++I ++ S G+GF
Sbjct: 2 SSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGF 59
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
V + + DA+RA +L+G ++ + I+V+ A
Sbjct: 60 VTFENSADADRAREKLHGTVVEGRKIEVNNATARVM 95
Score = 82.3 bits (204), Expect = 9e-20
Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 2/79 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V N+ D L Q+FG FG + +V+++ + + KGFGFV N +A A + L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 75
Query: 334 NGYALGDRLLQVSFKTHKP 352
+G + R ++V+ T +
Sbjct: 76 HGTVVEGRKIEVNNATARV 94
Score = 73.5 bits (181), Expect = 1e-16
Identities = 27/102 (26%), Positives = 43/102 (42%), Gaps = 19/102 (18%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L+VS +P DL +F +G I+ I+ ++ + SKG GF
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-----------------RGSKGFGF 59
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKA 215
V F +A+ A ++L+GT+ EG I V A +
Sbjct: 60 VTFENSADADRAREKLHGTVVEG--RKIEVNNATARVMTNSG 99
>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 83.9 bits (208), Expect = 2e-20
Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 6/86 (6%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+F+ NL+ ++E+ L ++ FG ++ V+VV P T KG F + A + +
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 333 LN------GYALGDRLLQVSFKTHKP 352
+ G L R L+V +
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDLAVTRD 102
Score = 82.4 bits (204), Expect = 1e-19
Identities = 21/108 (19%), Positives = 41/108 (37%), Gaps = 6/108 (5%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ + + + + +E L + G+++ +++ T S G F
Sbjct: 2 SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61
Query: 73 VNYYRTEDAERAI------IELNGLKLQNKSIKVSYARPSSEAIKRAN 114
+ E A++ + E GLKL + +KV A EA +
Sbjct: 62 AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109
Score = 61.6 bits (150), Expect = 3e-12
Identities = 16/116 (13%), Positives = 37/116 (31%), Gaps = 19/116 (16%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTP 162
+ S+ + +++ L +E L + + +G + R++ +
Sbjct: 6 SGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHP---------DTEH- 55
Query: 163 EIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASE----PITVKFANSPAGRAK 214
SKG F +F A+ + + G + + V A + A
Sbjct: 56 -----SKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 83.5 bits (207), Expect = 3e-20
Identities = 18/95 (18%), Positives = 49/95 (51%), Gaps = 1/95 (1%)
Query: 11 TQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGY 70
+ ++ + + L ++ +P + T+EEL+ + + G V+ +L+ ++ + G
Sbjct: 2 SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGL 60
Query: 71 GFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
+V Y A +A+++++G+ ++ IKV+ +
Sbjct: 61 AYVEYENESQASQAVMKMDGMTIKENIIKVAISNS 95
Score = 81.2 bits (201), Expect = 2e-19
Identities = 16/79 (20%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ L L ++ G V+++++V + + K KG +V N +A A+ +
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVMKM 78
Query: 334 NGYALGDRLLQVSFKTHKP 352
+G + + +++V+ P
Sbjct: 79 DGMTIKENIIKVAISNSGP 97
Score = 72.7 bits (179), Expect = 3e-16
Identities = 24/106 (22%), Positives = 51/106 (48%), Gaps = 18/106 (16%)
Query: 107 SEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ 166
S ++++ L++SGLP T+E+LE + + +GT+ R++ ++ +G
Sbjct: 12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR----------AGK----- 56
Query: 167 ISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
KG+ +V + +A A+ +++G + I V +NS
Sbjct: 57 -PKGLAYVEYENESQASQAVMKMDGMTIKE--NIIKVAISNSGPSS 99
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 84.8 bits (210), Expect = 3e-20
Identities = 24/83 (28%), Positives = 41/83 (49%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ V NL T + L ++F +G V +V + RD T + +GF FV + +A A+ +
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 333 LNGYALGDRLLQVSFKTHKPLPP 355
++G L R L+V + P
Sbjct: 109 MDGAVLDGRELRVQMARYGRPPD 131
Score = 80.9 bits (200), Expect = 6e-19
Identities = 23/82 (28%), Positives = 43/82 (52%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E ++L V+ + + + L+ +F G V + RD+ T +S G+ FV ++ DAE
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104
Query: 84 AIIELNGLKLQNKSIKVSYARP 105
A+ ++G L + ++V AR
Sbjct: 105 AMDAMDGAVLDGRELRVQMARY 126
Score = 65.9 bits (161), Expect = 1e-13
Identities = 28/106 (26%), Positives = 44/106 (41%), Gaps = 17/106 (16%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
SY RP + +L V L + + L +F YG + I D+ E
Sbjct: 36 SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE-------- 87
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
S+G FVRF+ +AE AM ++G + +G + V+ A
Sbjct: 88 -------SRGFAFVRFHDKRDAEDAMDAMDGAVLDG--RELRVQMA 124
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition
motif, RRM, RNA binding domain, RBD, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 83.9 bits (208), Expect = 3e-20
Identities = 22/96 (22%), Positives = 42/96 (43%), Gaps = 1/96 (1%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ S + V + + ++L+ +FS G V ++ DK +S G G
Sbjct: 2 SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGT 60
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
V + ++ +A +AI NG L ++ + V +
Sbjct: 61 VTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALP 96
Score = 83.5 bits (207), Expect = 5e-20
Identities = 24/79 (30%), Positives = 32/79 (40%), Gaps = 1/79 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV NL + L ++F G V ++ D K +G G V EAV AI
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDG-KSRGIGTVTFEQSIEAVQAISMF 76
Query: 334 NGYALGDRLLQVSFKTHKP 352
NG L DR + V
Sbjct: 77 NGQLLFDRPMHVKMDERAL 95
Score = 77.0 bits (190), Expect = 1e-17
Identities = 27/113 (23%), Positives = 44/113 (38%), Gaps = 18/113 (15%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
+ ++V+ L + + L+ +F G ++ + IL DK G S+GIG
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK----------DG------KSRGIG 59
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAA 225
V F Q IEA A+ NG + P+ VK + Q+
Sbjct: 60 TVTFEQSIEAVQAISMFNGQLLFD--RPMHVKMDERALPKGDFFPPERPQQSG 110
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA
processing, mRNA splicing, transport, nucleus,
RNA-binding, spliceosome, transport; NMR {Mus musculus}
Length = 124
Score = 84.3 bits (209), Expect = 3e-20
Identities = 18/85 (21%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E + L+V+ + ++ ++Q LF+ G ++ + D++ +SLG V++ R DA +
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALK 91
Query: 84 AIIELNGLKLQNKSIKVSYARPSSE 108
A+ + G+ L + + + +
Sbjct: 92 AMKQYKGVPLDGRPMDIQLVASQID 116
Score = 77.0 bits (190), Expect = 1e-17
Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 1/83 (1%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
+G + V NL D + +LF FG ++ V D + + G V +A+ A
Sbjct: 34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKA 92
Query: 330 IQSLNGYALGDRLLQVSFKTHKP 352
++ G L R + + +
Sbjct: 93 MKQYKGVPLDGRPMDIQLVASQI 115
Score = 75.1 bits (185), Expect = 6e-17
Identities = 24/117 (20%), Positives = 42/117 (35%), Gaps = 18/117 (15%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTP 162
A L VS L ++ D++ LF +GT+ + + D+ SG
Sbjct: 26 CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR----------SGR- 74
Query: 163 EIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAAN 219
S G V F + +A AM++ G +G P+ ++ S +
Sbjct: 75 -----SLGTADVHFERRADALKAMKQYKGVPLDG--RPMDIQLVASQIDLEHHHHHH 124
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related
protein, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 83.5 bits (207), Expect = 3e-20
Identities = 20/103 (19%), Positives = 48/103 (46%), Gaps = 9/103 (8%)
Query: 9 NTTQSHRSTYQSDVNE---QNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTA 65
++ + + ++ VN+ +N + + +T + ++ FS G++ ++ +K
Sbjct: 5 SSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK--- 61
Query: 66 QSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
GY FV + E A AI+ +NG ++ +K + + S +
Sbjct: 62 ---GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD 101
Score = 78.9 bits (195), Expect = 2e-18
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 = 69.7 bits (171), Expect = 4e-15
Identities = 24/108 (22%), Positives = 40/108 (37%), Gaps = 23/108 (21%)
Query: 111 KRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKG 170
K +Y G+ +T + + F P+G I+ R+ + KG
Sbjct: 24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---------------------KG 62
Query: 171 IGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAA 218
FVRF+ H A HA+ +NGT EG + + ++
Sbjct: 63 YSFVRFSTHESAAHAIVSVNGTTIEG--HVVKCYWGKESPDMTSGPSS 108
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 83.5 bits (207), Expect = 5e-20
Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 1/82 (1%)
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 NGYALGDRLLQVSFKTHKPLPP 355
NG +L + ++V
Sbjct: 69 NGKSLHGKAIKVEQAKKPSFQS 90
Score = 78.5 bits (194), Expect = 3e-18
Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 1/85 (1%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+ L + + + ++ L+ +F G + LI+D+T+ +S G+ F+ + DA+
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS-KSRGFAFITFENPADAKN 63
Query: 84 AIIELNGLKLQNKSIKVSYARPSSE 108
A ++NG L K+IKV A+ S
Sbjct: 64 AAKDMNGKSLHGKAIKVEQAKKPSF 88
Score = 68.9 bits (169), Expect = 8e-15
Identities = 23/105 (21%), Positives = 47/105 (44%), Gaps = 18/105 (17%)
Query: 108 EAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQI 167
EA L++ GL + ++ L+ +F +G I ++ D+ +
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR----------TSK------ 46
Query: 168 SKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
S+G F+ F +A++A +++NG G + I V+ A P+ +
Sbjct: 47 SRGFAFITFENPADAKNAAKDMNGKSLHG--KAIKVEQAKKPSFQ 89
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 83.2 bits (206), Expect = 7e-20
Identities = 29/114 (25%), Positives = 47/114 (41%), Gaps = 11/114 (9%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E N L + +P +T EE+ +F G + IR T ++ G +V Y DA+
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKN 62
Query: 84 AIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYG 137
A+ L+G + N+ + V Y + K +E L+ L YG
Sbjct: 63 AVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKK--------KEEQLKLLKEKYG 108
Score = 77.4 bits (191), Expect = 9e-18
Identities = 20/91 (21%), Positives = 44/91 (48%), Gaps = 7/91 (7%)
Query: 262 LPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMT 321
LPP+ +++ NL + ++ +FG +G ++ ++V P+T +G +V
Sbjct: 3 LPPEV----NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYE 55
Query: 322 NYDEAVFAIQSLNGYALGDRLLQVSFKTHKP 352
+ +A A+ L+G+ + +R L V +
Sbjct: 56 DIFDAKNAVDHLSGFNVSNRYLVVLYYNANR 86
Score = 62.8 bits (153), Expect = 1e-12
Identities = 21/115 (18%), Positives = 42/115 (36%), Gaps = 20/115 (17%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
LY+ LP +T E++ ++F YG I R+ ++G +
Sbjct: 10 ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE------------------TRGTAY 51
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMR 228
V + +A++A+ L+G + V + N+ K Q ++
Sbjct: 52 VVYEDIFDAKNAVDHLSGFNVSN--RYLVVLYYNANRAFQKMDTKKKEEQLKLLK 104
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 84.9 bits (210), Expect = 7e-20
Identities = 18/85 (21%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E + L+V+ + ++ ++Q LF+ G ++ + D++ +SLG V++ R DA +
Sbjct: 86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALK 144
Query: 84 AIIELNGLKLQNKSIKVSYARPSSE 108
A+ + G+ L + + + +
Sbjct: 145 AMKQYKGVPLDGRPMDIQLVASQID 169
Score = 76.8 bits (189), Expect = 5e-17
Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 1/78 (1%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
+G + V NL D + +LF FG ++ V D + + G V +A+ A
Sbjct: 87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKA 145
Query: 330 IQSLNGYALGDRLLQVSF 347
++ G L R + +
Sbjct: 146 MKQYKGVPLDGRPMDIQL 163
Score = 74.1 bits (182), Expect = 5e-16
Identities = 24/117 (20%), Positives = 42/117 (35%), Gaps = 18/117 (15%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTP 162
A L VS L ++ D++ LF +GT+ + + D+ SG
Sbjct: 79 CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR----------SGR- 127
Query: 163 EIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAAN 219
S G V F + +A AM++ G +G P+ ++ S +
Sbjct: 128 -----SLGTADVHFERRADALKAMKQYKGVPLDG--RPMDIQLVASQIDLEHHHHHH 177
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 82.3 bits (204), Expect = 9e-20
Identities = 19/80 (23%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
E L+V+ + ++ ++Q LF+ G ++ + D++ +SLG V++ R DA +
Sbjct: 27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALK 85
Query: 84 AIIELNGLKLQNKSIKVSYA 103
A+ + NG+ L + + +
Sbjct: 86 AMKQYNGVPLDGRPMNIQLV 105
Score = 77.7 bits (192), Expect = 4e-18
Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 1/78 (1%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
+G + V NL D + +LF FG ++ V D + + G V +A+ A
Sbjct: 28 TGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKA 86
Query: 330 IQSLNGYALGDRLLQVSF 347
++ NG L R + +
Sbjct: 87 MKQYNGVPLDGRPMNIQL 104
Score = 76.2 bits (188), Expect = 2e-17
Identities = 24/105 (22%), Positives = 42/105 (40%), Gaps = 18/105 (17%)
Query: 104 RPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPE 163
+ L VS L ++ D++ LF +GT+ + + D+ SG
Sbjct: 21 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR----------SGR-- 68
Query: 164 IPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
S G V F + +A AM++ NG +G P+ ++ S
Sbjct: 69 ----SLGTADVHFERKADALKAMKQYNGVPLDG--RPMNIQLVTS 107
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 82.0 bits (203), Expect = 1e-19
Identities = 24/104 (23%), Positives = 49/104 (47%), Gaps = 2/104 (1%)
Query: 2 MKHEEMYNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRD 61
H + S ++ Q L V+ +P +L+ +F G++ ++I +
Sbjct: 5 HHHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN 64
Query: 62 KTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
+ S G+GFV + + DA+RA +L+G ++ + I+V+ A
Sbjct: 65 ERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA 106
Score = 80.1 bits (198), Expect = 6e-19
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ V N+ D L Q+FG FG + +V+++ + + KGFGFV N +A A +
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 88
Query: 333 LNGYALGDRLLQVSFKTHKPL 353
L+G + R ++V+ T + +
Sbjct: 89 LHGTVVEGRKIEVNNATARVM 109
Score = 72.4 bits (178), Expect = 5e-16
Identities = 27/94 (28%), Positives = 42/94 (44%), Gaps = 19/94 (20%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L+VS +P DL +F +G I+ I+ ++ + SKG GF
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-----------------RGSKGFGF 73
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
V F +A+ A ++L+GT+ EG I V A
Sbjct: 74 VTFENSADADRAREKLHGTVVEG--RKIEVNNAT 105
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 80.7 bits (200), Expect = 2e-19
Identities = 26/91 (28%), Positives = 36/91 (39%), Gaps = 3/91 (3%)
Query: 266 SLHGSGWC-IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
S SG C IFV NL + +L F G V + + K KG G V + +
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPE 59
Query: 325 EAVFAIQSLNGYALGDRLLQVSFKTHKPLPP 355
A A + +NG L R + V + P
Sbjct: 60 VAERACRMMNGMKLSGREIDVRIDRNASGPS 90
Score = 78.8 bits (195), Expect = 1e-18
Identities = 24/84 (28%), Positives = 37/84 (44%), Gaps = 2/84 (2%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAER 83
+ V +P T + L+ F+ G V + + +S G G V + E AER
Sbjct: 6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAER 63
Query: 84 AIIELNGLKLQNKSIKVSYARPSS 107
A +NG+KL + I V R +S
Sbjct: 64 ACRMMNGMKLSGREIDVRIDRNAS 87
Score = 69.5 bits (171), Expect = 3e-15
Identities = 26/108 (24%), Positives = 44/108 (40%), Gaps = 19/108 (17%)
Query: 106 SSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIP 165
SS + ++V LP T + L++ F G ++ + I + +G
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-----------NGK---- 46
Query: 166 QISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRA 213
SKG G V+F AE A + +NG G I V+ + +G +
Sbjct: 47 --SKGCGVVKFESPEVAERACRMMNGMKLSG--REIDVRIDRNASGPS 90
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 80.4 bits (199), Expect = 4e-19
Identities = 24/96 (25%), Positives = 43/96 (44%), Gaps = 8/96 (8%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ + + + L V + MT L+ FS G + + + F
Sbjct: 2 SSGSSGERRAPRKGNTLYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPR------NCAF 53
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
V Y + E A++A+ ELNG ++++ +KV+ AR
Sbjct: 54 VTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM 89
Score = 76.6 bits (189), Expect = 9e-18
Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 8/83 (9%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
G ++VY + +L F PFG + ++ + + FV + A A
Sbjct: 14 KGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQA 65
Query: 330 IQSLNGYALGDRLLQVSFKTHKP 352
+ LNG + L+V+ +P
Sbjct: 66 VAELNGTQVESVQLKVNIARKQP 88
Score = 61.9 bits (151), Expect = 2e-12
Identities = 24/106 (22%), Positives = 34/106 (32%), Gaps = 25/106 (23%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
LYV G MT L F P+G II + +
Sbjct: 16 NTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM---------------------DPPRNCA 52
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAA 218
FV + + A+ A+ ELNGT E + V A ++
Sbjct: 53 FVTYEKMESADQAVAELNGTQVES--VQLKVNIARKQPMLDSGPSS 96
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 80.0 bits (198), Expect = 4e-19
Identities = 18/90 (20%), Positives = 42/90 (46%), Gaps = 7/90 (7%)
Query: 16 STYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
S+ S ++ + L V + T+T+ +L++ F GE+ + +++ + F+ +
Sbjct: 2 SSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQF 55
Query: 76 YRTEDAERAIIE-LNGLKLQNKSIKVSYAR 104
+ AE A + N L + + + V + R
Sbjct: 56 ATRQAAEVAAEKSFNKLIVNGRRLNVKWGR 85
Score = 66.1 bits (162), Expect = 4e-14
Identities = 23/94 (24%), Positives = 35/94 (37%), Gaps = 24/94 (25%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
LYV GL +T+ DL N F +G I T ++ + F
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR---------------------QQCAF 52
Query: 174 VRFNQHIEAEHAMQE-LNGTIPEGASEPITVKFA 206
++F AE A ++ N I G + VK+
Sbjct: 53 IQFATRQAAEVAAEKSFNKLIVNG--RRLNVKWG 84
Score = 65.8 bits (161), Expect = 5e-14
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 7/75 (9%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ-S 332
++V L + L F FG ++ + VV+ + F+ A A + S
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68
Query: 333 LNGYALGDRLLQVSF 347
N + R L V +
Sbjct: 69 FNKLIVNGRRLNVKW 83
>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A)
binding, structural genomics, protein structure
initiative, PSI-2; NMR {Xenopus laevis}
Length = 124
Score = 80.5 bits (199), Expect = 6e-19
Identities = 19/110 (17%), Positives = 43/110 (39%), Gaps = 1/110 (0%)
Query: 5 EEMYNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTT 64
Y + + ++ V V T ++L+ FSS G + ++ DK +
Sbjct: 15 AGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFS 74
Query: 65 AQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRAN 114
GY ++ + ++ A + ++ + ++IKV R + I +
Sbjct: 75 GHPKGYAYIE-FAERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGISSTD 123
Score = 76.3 bits (188), Expect = 3e-17
Identities = 13/75 (17%), Positives = 32/75 (42%), Gaps = 1/75 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V N+ + L F G++ + ++ D + KG+ ++ +V A ++
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAVAM 97
Query: 334 NGYALGDRLLQVSFK 348
+ R ++V K
Sbjct: 98 DETVFRGRTIKVLPK 112
Score = 59.3 bits (144), Expect = 2e-11
Identities = 28/120 (23%), Positives = 45/120 (37%), Gaps = 20/120 (16%)
Query: 81 AERAIIELNGLKLQNKSIKVSYARPSSEAIKRA----NLYVSGLPKHMTQEDLENLFRPY 136
A ++ K+ + +P S K+ ++YV + T +DLE F
Sbjct: 1 AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60
Query: 137 GTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEG 196
G+I ILCDK SG P KG ++ F + A ++ T+ G
Sbjct: 61 GSINRITILCDKF---------SGHP------KGYAYIEF-AERNSVDAAVAMDETVFRG 104
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 79.7 bits (197), Expect = 7e-19
Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 6/90 (6%)
Query: 23 NEQNSNLIVNYVPQTMTQEELQHLFSSVG--EVESCKLIRDKTTAQSLGYGFVNYYRTED 80
+ +I+ + + + S V + +LI+DK T Q+ G+ FV D
Sbjct: 6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMD 65
Query: 81 AERAIIELNG----LKLQNKSIKVSYARPS 106
A + + L LK+ K+I V +A+ +
Sbjct: 66 ASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95
Score = 78.1 bits (193), Expect = 2e-18
Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 6/80 (7%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGA--VQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
I + N+AP T + + P+ + V N+++++D QT + +GF FV +++ +A +Q
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 332 SLNG----YALGDRLLQVSF 347
L + + + V F
Sbjct: 72 ILQSLHPPLKIDGKTIGVDF 91
Score = 63.1 bits (154), Expect = 7e-13
Identities = 19/99 (19%), Positives = 36/99 (36%), Gaps = 19/99 (19%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGT--IITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
+ + + H + + PY + + R++ DK Q ++G
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQ---------------TQQNRGF 55
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASE--PITVKFANS 208
FV+ + ++A +Q L P + I V FA S
Sbjct: 56 AFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 79.1 bits (196), Expect = 8e-19
Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 4/76 (5%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
YV + T E+++ LFS G+V + KLI D+ T + G+GFV + E AI +L+
Sbjct: 5 YVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAKLD 63
Query: 90 GLKLQNKSIKVSYARP 105
++I+V+ A P
Sbjct: 64 NTDFMGRTIRVTEANP 79
Score = 77.6 bits (192), Expect = 3e-18
Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I+V NL + +LF FG V NVK++ D +T K KGFGFV M + AI L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 334 NGYALGDRLLQVS 346
+ R ++V+
Sbjct: 63 DNTDFMGRTIRVT 75
Score = 62.6 bits (153), Expect = 7e-13
Identities = 23/99 (23%), Positives = 37/99 (37%), Gaps = 18/99 (18%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
N+YV L T E ++ LF +G + +++ D+ + KG GF
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRE---------TKK------PKGFGF 47
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
V + A+ +L+ T G I V AN
Sbjct: 48 VEMQEE-SVSEAIAKLDNTDFMG--RTIRVTEANPKKSL 83
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG, protein
structure initiative; HET: PGE; 1.95A {Homo sapiens}
PDB: 3b4d_A 3b4m_A
Length = 89
Score = 78.3 bits (194), Expect = 2e-18
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
V T EEL+ F G V ++ DK + G+ ++ + +++ R + L+
Sbjct: 14 VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIE-FSDKESVRTSLALDESLF 72
Query: 94 QNKSIKVSYARP 105
+ + IKV R
Sbjct: 73 RGRQIKVIPKRT 84
Score = 74.5 bits (184), Expect = 4e-17
Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 2/80 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I+V N+ L F G+V V ++ D + KGF ++ ++ E+V +L
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSLAL 67
Query: 334 NGYALGDRLLQVSFK-THKP 352
+ R ++V K T++P
Sbjct: 68 DESLFRGRQIKVIPKRTNRP 87
Score = 57.5 bits (140), Expect = 5e-11
Identities = 25/99 (25%), Positives = 39/99 (39%), Gaps = 20/99 (20%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++YV + T E+LE F G++ ILCDK SG P KG +
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF---------SGHP------KGFAY 52
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFA--NSPA 210
+ F+ ++ L+ ++ G I V N P
Sbjct: 53 IEFSDKESVRTSL-ALDESLFRG--RQIKVIPKRTNRPG 88
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 78.9 bits (195), Expect = 2e-18
Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 3/81 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFG-PFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV +L P+ +D +L++ F + + + KVV D QT KG+GFV T+ E A+
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRALTE 70
Query: 333 LNG-YALGDRLLQVSFKTHKP 352
G LG + +++S K
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKA 91
Score = 71.9 bits (177), Expect = 5e-16
Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 3/96 (3%)
Query: 19 QSDVNEQNSNLIVNYVPQTMTQEELQHLFSSV-GEVESCKLIRDKTTAQSLGYGFVNYYR 77
S + +L V + + L F V K++ D+T S GYGFV +
Sbjct: 2 SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTG-VSKGYGFVKFTD 60
Query: 78 TEDAERAIIELNG-LKLQNKSIKVSYARPSSEAIKR 112
+ +RA+ E G + L +K +++S A P + +K
Sbjct: 61 ELEQKRALTECQGAVGLGSKPVRLSVAIPKASRVKP 96
Score = 65.8 bits (161), Expect = 9e-14
Identities = 27/114 (23%), Positives = 49/114 (42%), Gaps = 18/114 (15%)
Query: 106 SSEAIKRANLYVSGLPKHMTQEDLENLF-RPYGTIITSRILCDKMASENVRSFVSGTPEI 164
S + +L+V L + L F + Y + +++ D+ +G
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ----------TG---- 48
Query: 165 PQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAA 218
+SKG GFV+F +E + A+ E G + G S+P+ + A A R K + +
Sbjct: 49 --VSKGYGFVKFTDELEQKRALTECQGAVGLG-SKPVRLSVAIPKASRVKPVES 99
>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 78.9 bits (195), Expect = 2e-18
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+ + +L+ FS+VG+V ++I D+ + +S G +V + + A I L G +L
Sbjct: 33 LAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA-IGLTGQRL 91
Query: 94 QNKSIKVSYARP 105
I V ++
Sbjct: 92 LGVPIIVQASQA 103
Score = 72.0 bits (177), Expect = 6e-16
Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 1/75 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F LA L F G V++V+++ D + + KG +V AI L
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GL 86
Query: 334 NGYALGDRLLQVSFK 348
G L + V
Sbjct: 87 TGQRLLGVPIIVQAS 101
Score = 58.9 bits (143), Expect = 3e-11
Identities = 26/111 (23%), Positives = 39/111 (35%), Gaps = 18/111 (16%)
Query: 105 PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEI 164
S E ++ L + DLE+ F G + RI+ D+ S
Sbjct: 18 LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN---------SRR--- 65
Query: 165 PQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKA 215
SKGI +V F + A+ L G G PI V+ + + R
Sbjct: 66 ---SKGIAYVEFCEIQSVPLAI-GLTGQRLLGV--PIIVQASQAEKNRLSG 110
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 113
Score = 78.6 bits (194), Expect = 3e-18
Identities = 26/104 (25%), Positives = 42/104 (40%), Gaps = 8/104 (7%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVES--------CKLIRDKTT 64
S S+ D + NS + V + ++T ++L F G V+ + DK T
Sbjct: 2 SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61
Query: 65 AQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
+ G V+Y A+ A+ +G Q +KVS AR
Sbjct: 62 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105
Score = 76.7 bits (189), Expect = 1e-17
Identities = 21/91 (23%), Positives = 32/91 (35%), Gaps = 8/91 (8%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQN--------VKVVRDPQTYKCKGFGFVCMT 321
I+V L + L F G V+ + + D +T K KG V
Sbjct: 14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73
Query: 322 NYDEAVFAIQSLNGYALGDRLLQVSFKTHKP 352
+ A A++ +G L+VS KP
Sbjct: 74 DPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 104
Score = 58.2 bits (141), Expect = 5e-11
Identities = 24/121 (19%), Positives = 41/121 (33%), Gaps = 25/121 (20%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITS--------RILCDKMASENV 154
+ E + +YV GL +T +DL + F+ G + + I DK
Sbjct: 6 SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE----- 60
Query: 155 RSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAK 214
+G P KG V + A+ A++ +G +G + V A
Sbjct: 61 ----TGKP------KGDATVSYEDPPTAKAAVEWFDGKDFQG--SKLKVSLARKKPPMNS 108
Query: 215 A 215
Sbjct: 109 G 109
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 78.6 bits (194), Expect = 3e-18
Identities = 24/109 (22%), Positives = 45/109 (41%), Gaps = 8/109 (7%)
Query: 23 NEQNSNLIVNYVPQTMTQEELQHLFSSVGEVES--------CKLIRDKTTAQSLGYGFVN 74
N N+ + V + + +T E + F +G +++ L D+ T + G V+
Sbjct: 4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63
Query: 75 YYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKH 123
+ A+ AI +G + IKVS+A ++ + GL H
Sbjct: 64 FDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRGGLEHH 112
Score = 75.9 bits (187), Expect = 3e-17
Identities = 20/87 (22%), Positives = 31/87 (35%), Gaps = 8/87 (9%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQN--------VKVVRDPQTYKCKGFGFVCMTNYDE 325
IFV L + F G ++ + + D +T K KG V +
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 326 AVFAIQSLNGYALGDRLLQVSFKTHKP 352
A AI +G ++VSF T +
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRRA 96
Score = 57.0 bits (138), Expect = 2e-10
Identities = 25/109 (22%), Positives = 40/109 (36%), Gaps = 23/109 (21%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQI------ 167
++V GL +++T E + + F+ G I + +G P I
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGII--------------KTNKKTGQPMINLYTDRETG 54
Query: 168 -SKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKA 215
KG V F+ A+ A+ +G G PI V FA A +
Sbjct: 55 KLKGEATVSFDDPPSAKAAIDWFDGKEFSG--NPIKVSFATRRADFNRG 101
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 102
Score = 77.3 bits (191), Expect = 6e-18
Identities = 22/96 (22%), Positives = 46/96 (47%), Gaps = 3/96 (3%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ + ++ + L V + + T+E L+ F +++ D+ T S G+GF
Sbjct: 2 SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFGF 58
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
V++ EDA+ A + ++ + + +A+P E
Sbjct: 59 VDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGE 94
Score = 77.3 bits (191), Expect = 6e-18
Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 3/80 (3%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV L+ +T + L + F ++V D +T KGFGFV + ++A A ++
Sbjct: 17 TLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 333 LNGYALGDRLLQVSFKTHKP 352
+ + + + + K
Sbjct: 74 MEDGEIDGNKVTLDWAKPKG 93
Score = 60.0 bits (146), Expect = 9e-12
Identities = 26/105 (24%), Positives = 48/105 (45%), Gaps = 20/105 (19%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTP 162
+ P++ + L+V GL + T+E L+ F + +RI+ D+ +G+
Sbjct: 6 SGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRE---------TGS- 52
Query: 163 EIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
SKG GFV FN +A+ A + + +G +T+ +A
Sbjct: 53 -----SKGFGFVDFNSEEDAKAAKEAMEDGEIDG--NKVTLDWAK 90
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 77.1 bits (190), Expect = 1e-17
Identities = 24/95 (25%), Positives = 43/95 (45%), Gaps = 10/95 (10%)
Query: 12 QSHRSTYQSDVNEQNSNLIVNYV-PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGY 70
+ S + + + L YV + MT L+ FS G + + +
Sbjct: 25 RRSDSFPERRAPRKGNTL---YVYGEDMTPTLLRGAFSPFGNIIDLSMDPPR------NC 75
Query: 71 GFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
FV Y + E A++A+ ELNG ++++ +KV+ AR
Sbjct: 76 AFVTYEKMESADQAVAELNGTQVESVQLKVNIARK 110
Score = 74.0 bits (182), Expect = 1e-16
Identities = 21/114 (18%), Positives = 39/114 (34%), Gaps = 8/114 (7%)
Query: 239 NPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAV 298
+ H S + P + G ++VY + +L F PFG +
Sbjct: 7 HHHHSSGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNI 64
Query: 299 QNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSFKTHKP 352
++ + + FV + A A+ LNG + L+V+ +P
Sbjct: 65 IDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP 112
Score = 60.9 bits (148), Expect = 6e-12
Identities = 25/102 (24%), Positives = 33/102 (32%), Gaps = 25/102 (24%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
LYV G MT L F P+G II + + F
Sbjct: 41 TLYVYGED--MTPTLLRGAFSPFGNIIDLSM---------------------DPPRNCAF 77
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKA 215
V + + A+ A+ ELNGT E + V A A
Sbjct: 78 VTYEKMESADQAVAELNGTQVES--VQLKVNIARKQPMLDAA 117
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription,
splicing, RNA processing, nonsense mediated D NMD, HDAC,
histone deacetylation; 1.90A {Homo sapiens}
Length = 88
Score = 75.7 bits (187), Expect = 1e-17
Identities = 12/75 (16%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRD-PQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ + L + + ++F +G ++ + + + + KG+ +V N DEA A++
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 333 LNGYALGDRLLQVSF 347
++G + + + +
Sbjct: 67 MDGGQIDGQEITATA 81
Score = 75.7 bits (187), Expect = 1e-17
Identities = 13/77 (16%), Positives = 40/77 (51%), Gaps = 4/77 (5%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKLIRDK-TTAQSLGYGFVNYYRTEDAERAIIEL 88
++ + +T++ + +FS+ G+++ + ++ S GY +V + ++AE+A+ +
Sbjct: 8 HIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHM 67
Query: 89 NGLKLQNKSIKVSYARP 105
+G ++ + I +
Sbjct: 68 DGGQIDGQEITATAVLA 84
Score = 67.6 bits (166), Expect = 1e-14
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 16/104 (15%)
Query: 109 AIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQIS 168
++K +++ L +++T++ + +F YG I + ++M +S
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHP--------------HLS 46
Query: 169 KGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
KG +V F EAE A++ ++G +G IT +P R
Sbjct: 47 KGYAYVEFENPDEAEKALKHMDGGQIDGQ--EITATAVLAPWPR 88
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein;
2.50A {Homo sapiens}
Length = 143
Score = 76.8 bits (189), Expect = 2e-17
Identities = 20/95 (21%), Positives = 39/95 (41%), Gaps = 5/95 (5%)
Query: 23 NEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKL-----IRDKTTAQSLGYGFVNYYR 77
E N + V + + + +++L+++F + S IR + G F+
Sbjct: 42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPN 101
Query: 78 TEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKR 112
+ A +A+ E NG L K + V +AR +
Sbjct: 102 EKAAAKALKEANGYVLFGKPMVVQFARSARPKQDP 136
Score = 68.3 bits (167), Expect = 3e-14
Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKV-----VRDPQTYKCKGFGFVCMTNYDEAVF 328
I+V NLA ++ L +FG + + +R + + KG F+ + N A
Sbjct: 48 IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107
Query: 329 AIQSLNGYALGDRLLQVSF 347
A++ NGY L + + V F
Sbjct: 108 ALKEANGYVLFGKPMVVQF 126
Score = 66.0 bits (161), Expect = 2e-13
Identities = 29/145 (20%), Positives = 50/145 (34%), Gaps = 27/145 (18%)
Query: 81 AERAIIELNGLKLQNKSIKVSYARPSSEAIKRA-----------NLYVSGLPKHMTQEDL 129
E+ + + ++ +YV L KH+ ++DL
Sbjct: 3 LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDL 62
Query: 130 ENLFRPYGTI--ITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQ 187
+ +F Y T RI+ D + R KG F+ A A++
Sbjct: 63 KYIFGRYVDFSSETQRIMFDIRLMKEGR------------MKGQAFIGLPNEKAAAKALK 110
Query: 188 ELNGTIPEGASEPITVKFANSPAGR 212
E NG + G +P+ V+FA S +
Sbjct: 111 EANGYVLFG--KPMVVQFARSARPK 133
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 75.4 bits (186), Expect = 2e-17
Identities = 20/93 (21%), Positives = 46/93 (49%), Gaps = 4/93 (4%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ S + ++ L+++ + + T+E LQ +F ++ + +S GY F
Sbjct: 2 SSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAF 57
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
+ + EDA+ A+ N +++ ++I++ P
Sbjct: 58 IEFASFEDAKEALNSCNKREIEGRAIRLELQGP 90
Score = 74.2 bits (183), Expect = 8e-17
Identities = 16/83 (19%), Positives = 36/83 (43%), Gaps = 4/83 (4%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ + NL+ + L ++F + V Q K KG+ F+ ++++A A+ S
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 333 LNGYALGDRLLQVSFKTHKPLPP 355
N + R +++ + + P
Sbjct: 73 CNKREIEGRAIRLELQGPRGSPN 95
Score = 56.9 bits (138), Expect = 1e-10
Identities = 23/112 (20%), Positives = 36/112 (32%), Gaps = 23/112 (20%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
S S K L +S L T+E L+ +F I + +N +S
Sbjct: 6 SGNSTWSGESKT--LVLSNLSYSATEETLQEVFEKATFIK----VPQN---QNGKS---- 52
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
KG F+ F +A+ A+ N EG I ++
Sbjct: 53 --------KGYAFIEFASFEDAKEALNSCNKREIEG--RAIRLELQGPRGSP 94
>2la6_A RNA-binding protein FUS; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative, RNA recognition; NMR {Homo sapiens}
Length = 99
Score = 74.6 bits (184), Expect = 5e-17
Identities = 20/85 (23%), Positives = 30/85 (35%), Gaps = 8/85 (9%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQ--------NVKVVRDPQTYKCKGFGFVCMTNYD 324
IFV L + F G ++ + + D +T K KG V +
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74
Query: 325 EAVFAIQSLNGYALGDRLLQVSFKT 349
A AI +G ++VSF T
Sbjct: 75 SAKAAIDWFDGKEFSGNPIKVSFAT 99
Score = 73.5 bits (181), Expect = 1e-16
Identities = 20/96 (20%), Positives = 40/96 (41%), Gaps = 8/96 (8%)
Query: 16 STYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVES--------CKLIRDKTTAQS 67
+ + N+ + V + + +T E + F +G +++ L D+ T +
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62
Query: 68 LGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYA 103
G V++ A+ AI +G + IKVS+A
Sbjct: 63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
Score = 54.2 bits (131), Expect = 1e-09
Identities = 24/110 (21%), Positives = 40/110 (36%), Gaps = 25/110 (22%)
Query: 105 PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITS--------RILCDKMASENVRS 156
++V GL +++T E + + F+ G I T+ + D+ E +
Sbjct: 6 HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR---ETGK- 61
Query: 157 FVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
KG V F+ A+ A+ +G G PI V FA
Sbjct: 62 -----------LKGEATVSFDDPPSAKAAIDWFDGKEFSG--NPIKVSFA 98
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 78.2 bits (192), Expect = 5e-17
Identities = 16/90 (17%), Positives = 31/90 (34%), Gaps = 2/90 (2%)
Query: 268 HGSGWCIFVYNLAPETEDNVLWQLFGPFGA--VQNVKVVRDPQTYKCKGFGFVCMTNYDE 325
G +++ NL T D L + G + +K + + KGF V + +
Sbjct: 65 TGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEAS 124
Query: 326 AVFAIQSLNGYALGDRLLQVSFKTHKPLPP 355
+ + L L + V+ + L
Sbjct: 125 SKKLMDLLPKRELHGQNPVVTPVNKQFLSQ 154
Score = 73.6 bits (180), Expect = 2e-15
Identities = 14/108 (12%), Positives = 35/108 (32%), Gaps = 2/108 (1%)
Query: 9 NTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVG--EVESCKLIRDKTTAQ 66
+ + + L + + T E+L S+G ++ K ++ Q
Sbjct: 51 DVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQ 110
Query: 67 SLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRAN 114
S G+ V +++ + L +L ++ V+ +
Sbjct: 111 SKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQ 158
Score = 70.5 bits (172), Expect = 2e-14
Identities = 25/140 (17%), Positives = 39/140 (27%), Gaps = 19/140 (13%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGT--IITSRILCDKMASENVRSFVSG 160
+ KR LY+ L T EDL G I+ + ++ N +
Sbjct: 59 NVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR---ANGQ----- 110
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANL 220
SKG V ++ M L G + V N + +
Sbjct: 111 -------SKGFALVGVGSEASSKKLMDLLPKRELHG--QNPVVTPVNKQFLSQFEMQSRK 161
Query: 221 NAQAAAMRHFAAAMRHFGNP 240
Q+ M A G+
Sbjct: 162 TTQSGQMSGEGKAGPPGGSS 181
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 73.8 bits (182), Expect = 8e-17
Identities = 25/88 (28%), Positives = 33/88 (37%), Gaps = 8/88 (9%)
Query: 268 HGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAV 327
G+ W IFV N++ L LF G V VV K + FV M +A
Sbjct: 6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAK 57
Query: 328 FAIQSLNGYALGDRLLQVSFKTHKPLPP 355
AI LNG + + + V T
Sbjct: 58 AAIAQLNGKEVKGKRINVELSTKGQKKS 85
Score = 71.5 bits (176), Expect = 5e-16
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 11/79 (13%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
+V T +EL+ LF G V C +++ Y FV+ + DA+ AI +LN
Sbjct: 13 FVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLN 64
Query: 90 GLKLQNKSIKVSYARPSSE 108
G +++ K I V + +
Sbjct: 65 GKEVKGKRINVELSTKGQK 83
Score = 64.2 bits (157), Expect = 2e-13
Identities = 20/109 (18%), Positives = 40/109 (36%), Gaps = 27/109 (24%)
Query: 104 RPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPE 163
SS + ++V + T ++L +LF G +I ++
Sbjct: 3 SGSSGNTWK--IFVGNVSAACTSQELRSLFERRGRVIECDVV------------------ 42
Query: 164 IPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
K FV + +A+ A+ +LNG +G + I V+ + +
Sbjct: 43 -----KDYAFVHMEKEADAKAAIAQLNGKEVKG--KRINVELSTKGQKK 84
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain,
poly(A) site recognition, RNA, nuclear, RNA BIND
protein; 2.70A {Homo sapiens} PDB: 3p6y_C
Length = 90
Score = 73.8 bits (182), Expect = 9e-17
Identities = 13/73 (17%), Positives = 29/73 (39%), Gaps = 2/73 (2%)
Query: 38 MTQEELQHLFSSVG--EVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQN 95
T E+L S+G ++ K ++ QS G+ V +++ + L +L
Sbjct: 13 TTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHG 72
Query: 96 KSIKVSYARPSSE 108
++ V+ +
Sbjct: 73 QNPVVTPSNKLEH 85
Score = 71.1 bits (175), Expect = 8e-16
Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 2/76 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGA--VQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
+++ NL T D L + G + +K + + KGF V + + + +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 332 SLNGYALGDRLLQVSF 347
L L + V+
Sbjct: 64 LLPKRELHGQNPVVTP 79
Score = 68.8 bits (169), Expect = 5e-15
Identities = 20/103 (19%), Positives = 30/103 (29%), Gaps = 19/103 (18%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGT--IITSRILCDKMASENVRSFVSGTPEIPQISK 169
R LY+ L T EDL G I+ + ++ N + SK
Sbjct: 1 RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR---ANGQ------------SK 45
Query: 170 GIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
G V ++ M L G + V +N
Sbjct: 46 GFALVGVGSEASSKKLMDLLPKRELHG--QNPVVTPSNKLEHH 86
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 93
Score = 73.4 bits (181), Expect = 1e-16
Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 10/80 (12%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
Y+ +T ++L+ LF + +++ GY FV+Y A RAI L+
Sbjct: 12 YIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS------GYAFVDYPDQNWAIRAIETLS 65
Query: 90 G-LKLQNKSIKVSYARPSSE 108
G ++L K ++V Y+
Sbjct: 66 GKVELHGKIMEVDYSVSKKL 85
Score = 68.8 bits (169), Expect = 5e-15
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 7/80 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ NL+P + L QLFG + Q G+ FV + + A+ AI++L
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIETL 64
Query: 334 NGYA-LGDRLLQVSFKTHKP 352
+G L ++++V + K
Sbjct: 65 SGKVELHGKIMEVDYSVSKK 84
Score = 62.3 bits (152), Expect = 1e-12
Identities = 20/98 (20%), Positives = 36/98 (36%), Gaps = 22/98 (22%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LY+ L +T +DL LF + ++L + G FV
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPLAGQVL---------------------LKSGYAFV 49
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
+ A A++ L+G + E + + V ++ S R
Sbjct: 50 DYPDQNWAIRAIETLSGKV-ELHGKIMEVDYSVSKKLR 86
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 101
Score = 73.4 bits (181), Expect = 1e-16
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKS 97
+ EL+ S + + D T + +G+V++ ED E+A +EL GLK+
Sbjct: 29 KSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFESAEDLEKA-LELTGLKVFGNE 86
Query: 98 IKVSYARP 105
IK+ +
Sbjct: 87 IKLEKPKG 94
Score = 71.5 bits (176), Expect = 7e-16
Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 2/79 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ NL P L A ++ V D +T + FG+V + ++ A++ L
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALE-L 77
Query: 334 NGYALGDRLLQVSFKTHKP 352
G + +++ +
Sbjct: 78 TGLKVFGNEIKLEKPKGRD 96
Score = 56.1 bits (136), Expect = 2e-10
Identities = 16/110 (14%), Positives = 34/110 (30%), Gaps = 19/110 (17%)
Query: 99 KVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFV 158
+ SE+ NL++ L + + +L+ ++ D
Sbjct: 4 MLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DV---RTGT--- 56
Query: 159 SGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
++ G+V F + E A+ EL G + I ++
Sbjct: 57 ---------NRKFGYVDFESAEDLEKAL-ELTGL--KVFGNEIKLEKPKG 94
>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 92
Score = 73.0 bits (180), Expect = 2e-16
Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 8/82 (9%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V N++P + L F +G V +V+ + FV M ++AV AI+ L
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGL 64
Query: 334 NGYALGDRLLQVSFKTHKPLPP 355
+ + + V T +
Sbjct: 65 DNTEFQGKRMHVQLSTSRLRTA 86
Score = 71.5 bits (176), Expect = 6e-16
Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 8/86 (9%)
Query: 23 NEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAE 82
+ ++ L V + T T +EL+ F G V C +++ Y FV+ R EDA
Sbjct: 7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAV 58
Query: 83 RAIIELNGLKLQNKSIKVSYARPSSE 108
AI L+ + Q K + V +
Sbjct: 59 EAIRGLDNTEFQGKRMHVQLSTSRLR 84
Score = 63.0 bits (154), Expect = 6e-13
Identities = 23/111 (20%), Positives = 41/111 (36%), Gaps = 27/111 (24%)
Query: 104 RPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPE 163
S +A + L+V + T ++L F YG +I CD +
Sbjct: 4 GSSGKASTK--LHVGNISPTCTNQELRAKFEEYGPVIE----CDIV-------------- 43
Query: 164 IPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAK 214
K FV + +A A++ L+ T +G + + V+ + S A
Sbjct: 44 -----KDYAFVHMERAEDAVEAIRGLDNTEFQG--KRMHVQLSTSRLRTAS 87
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 72.5 bits (178), Expect = 4e-16
Identities = 16/111 (14%), Positives = 37/111 (33%), Gaps = 13/111 (11%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L++ G+PK +E++ + I+ ++G FV
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYAS-------------AADKMKNRGFAFV 57
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAA 225
+ H A A ++L + I V +A + + ++ ++
Sbjct: 58 EYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGPSS 108
Score = 70.2 bits (172), Expect = 3e-15
Identities = 20/89 (22%), Positives = 35/89 (39%), Gaps = 4/89 (4%)
Query: 24 EQNSNLIVNYVPQTMTQEELQHLFSSVGE-VESCKLIRD-KTTAQSLGYGFVNYYRTEDA 81
N L + +P+ +EE+ + V E V + ++ G+ FV Y A
Sbjct: 6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAA 65
Query: 82 ERAIIELN--GLKLQNKSIKVSYARPSSE 108
A +L ++L I V +A P +
Sbjct: 66 AMARRKLMPGRIQLWGHQIAVDWAEPEID 94
Score = 57.5 bits (139), Expect = 8e-11
Identities = 14/78 (17%), Positives = 27/78 (34%), Gaps = 4/78 (5%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGA-VQNVKVVRDPQ-TYKCKGFGFVCMTNYDEAVFAIQ 331
+F+ + + + + V +V V K +GF FV ++ A A +
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70
Query: 332 SLN--GYALGDRLLQVSF 347
L L + V +
Sbjct: 71 KLMPGRIQLWGHQIAVDW 88
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 72.6 bits (178), Expect = 4e-16
Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 6/84 (7%)
Query: 274 IFVYNLAPETEDNVLW---QLFGPFGAVQNVKVVRDPQTYKCK---GFGFVCMTNYDEAV 327
+FV L+ D + + FG FG + V + + +V ++A+
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 328 FAIQSLNGYALGDRLLQVSFKTHK 351
AIQ +N + R L+ S T K
Sbjct: 78 RAIQCVNNVVVDGRTLKASLGTTK 101
Score = 66.4 bits (162), Expect = 6e-14
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 7/83 (8%)
Query: 28 NLI-VNYVPQTMTQEEL---QHLFSSVGEVESCKLIRDKTTAQS---LGYGFVNYYRTED 80
NL+ V + Q + E+ F G++ + + A S +V Y R+ED
Sbjct: 16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75
Query: 81 AERAIIELNGLKLQNKSIKVSYA 103
A RAI +N + + +++K S
Sbjct: 76 ALRAIQCVNNVVVDGRTLKASLG 98
Score = 53.7 bits (129), Expect = 2e-09
Identities = 14/90 (15%), Positives = 33/90 (36%), Gaps = 15/90 (16%)
Query: 110 IKRANLYVSGLPKHMTQEDL---ENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQ 166
+++ ++V GL + + ++ F +G I I + Q
Sbjct: 13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAG------------SQ 60
Query: 167 ISKGIGFVRFNQHIEAEHAMQELNGTIPEG 196
+V + + +A A+Q +N + +G
Sbjct: 61 GPSASAYVTYIRSEDALRAIQCVNNVVVDG 90
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 71.8 bits (177), Expect = 4e-16
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 11/80 (13%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
++ P+ T++E++ LF G+V C +I+ YGFV+ AE AI L+
Sbjct: 12 FIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDKTAAEDAIRNLH 63
Query: 90 GLKLQNKSIKVSYARPSSEA 109
KL +I V ++ S+A
Sbjct: 64 HYKLHGVNINVEASKNKSKA 83
Score = 68.8 bits (169), Expect = 4e-15
Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 8/82 (9%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+F+ NL E + + LF +G V ++ K +GFV + + A AI++L
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNL 62
Query: 334 NGYALGDRLLQVSFKTHKPLPP 355
+ Y L + V +K
Sbjct: 63 HHYKLHGVNINVEASKNKSKAS 84
Score = 63.4 bits (155), Expect = 4e-13
Identities = 22/110 (20%), Positives = 42/110 (38%), Gaps = 25/110 (22%)
Query: 106 SSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIP 165
SS + L++ LP+ T++++ +LF YG ++ I+
Sbjct: 2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------------------- 41
Query: 166 QISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKA 215
K GFV AE A++ L+ G I V+ + + + +
Sbjct: 42 ---KNYGFVHIEDKTAAEDAIRNLHHYKLHG--VNINVEASKNKSKASSG 86
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 71.5 bits (176), Expect = 7e-16
Identities = 19/91 (20%), Positives = 42/91 (46%), Gaps = 7/91 (7%)
Query: 26 NSNLIVNYVPQTMTQEELQH----LFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDA 81
N + +N + + + ++EL+ +FS G++ + R + G FV + A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSSA 64
Query: 82 ERAIIELNGLKLQNKSIKVSYARPSSEAIKR 112
A+ + G +K +++ YA+ S+ I +
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95
Score = 67.3 bits (165), Expect = 2e-14
Identities = 17/78 (21%), Positives = 38/78 (48%), Gaps = 7/78 (8%)
Query: 274 IFVYNLAPETEDNVL----WQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
I++ NL + + + L +F FG + ++ V ++ K +G FV A A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATNA 67
Query: 330 IQSLNGYALGDRLLQVSF 347
++S+ G+ D+ +++ +
Sbjct: 68 LRSMQGFPFYDKPMRIQY 85
Score = 51.1 bits (123), Expect = 1e-08
Identities = 17/112 (15%), Positives = 44/112 (39%), Gaps = 26/112 (23%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLE----NLFRPYGTIITSRILCDKMASENVRSFV 158
A P + +Y++ L + + +++L+ +F +G I+ +
Sbjct: 1 AVPETRPNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--------- 49
Query: 159 SGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPA 210
+G FV F + A +A++ + G +P+ +++A + +
Sbjct: 50 ---------MRGQAFVIFKEVSSATNALRSMQGFPFYD--KPMRIQYAKTDS 90
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 71.1 bits (175), Expect = 9e-16
Identities = 20/120 (16%), Positives = 37/120 (30%), Gaps = 25/120 (20%)
Query: 94 QNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASEN 153
S K+ Y + + L+V GL + + L F +G+I T +
Sbjct: 3 SGSSGKIGYGKANPTT----RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD----- 53
Query: 154 VRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRA 213
++++ A+ A ++ G G + V FA S
Sbjct: 54 ----------------SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSSG 97
Score = 71.1 bits (175), Expect = 9e-16
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
++V L P T L + F FG+++ + V+ F ++ + D A A
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72
Query: 333 LNGYALG--DRLLQVSF 347
+ G+ LG DR L+V F
Sbjct: 73 MRGFPLGGPDRRLRVDF 89
Score = 70.7 bits (174), Expect = 1e-15
Identities = 12/82 (14%), Positives = 32/82 (39%), Gaps = 8/82 (9%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+ L V + + L F G + + ++ + ++ Y + A+ A
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQAAC 70
Query: 86 IELNGLKL--QNKSIKVSYARP 105
++ G L ++ ++V +A+
Sbjct: 71 AKMRGFPLGGPDRRLRVDFAKS 92
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 71.1 bits (175), Expect = 9e-16
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 2/79 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+V NL T + +F +++V++VRD T K KGF +V D A+ +
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TY 75
Query: 334 NGYALGDRLLQVSFKTHKP 352
+G LGDR L+V +
Sbjct: 76 DGALLGDRSLRVDIAEGRK 94
Score = 68.8 bits (169), Expect = 7e-15
Identities = 19/79 (24%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
YV P Q ++ +F + + S +L+RDK T + G+ +V + D+ + + +
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVE-FDEVDSLKEALTYD 76
Query: 90 GLKLQNKSIKVSYARPSSE 108
G L ++S++V A +
Sbjct: 77 GALLGDRSLRVDIAEGRKQ 95
Score = 48.8 bits (117), Expect = 1e-07
Identities = 19/98 (19%), Positives = 36/98 (36%), Gaps = 19/98 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
YV LP + Q D++ +F+ I + R++ DK + KG +V
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKD---------TDKF------KGFCYV 61
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
F++ + A+ +G + + V A
Sbjct: 62 EFDEVDSLKEAL-TYDGALLGD--RSLRVDIAEGRKQD 96
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 72.6 bits (178), Expect = 1e-15
Identities = 18/95 (18%), Positives = 34/95 (35%), Gaps = 2/95 (2%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGA--VQNVKVVRDPQTYKCKGFGFVCM 320
L ++V + + T D L Q+ G V +K + + KG+ V +
Sbjct: 47 TYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVV 106
Query: 321 TNYDEAVFAIQSLNGYALGDRLLQVSFKTHKPLPP 355
+ + ++ L G L + V T + L
Sbjct: 107 ASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQ 141
Score = 70.7 bits (173), Expect = 5e-15
Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 2/79 (2%)
Query: 38 MTQEELQHLFSSVG--EVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQN 95
T ++L + S+G +V K ++ QS GY V + + L G L
Sbjct: 67 TTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNG 126
Query: 96 KSIKVSYARPSSEAIKRAN 114
+ + V A + + A
Sbjct: 127 EKVDVRPATRQNLSQFEAQ 145
Score = 67.3 bits (164), Expect = 1e-13
Identities = 21/121 (17%), Positives = 36/121 (29%), Gaps = 19/121 (15%)
Query: 94 QNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGT--IITSRILCDKMAS 151
N S +RA +YV T + L + R G ++ + ++
Sbjct: 37 PNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENR--- 93
Query: 152 ENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAG 211
N + SKG V ++ L G + G E + V+ A
Sbjct: 94 ANGQ------------SKGYAEVVVASENSVHKLLELLPGKVLNG--EKVDVRPATRQNL 139
Query: 212 R 212
Sbjct: 140 S 140
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 108
Score = 71.0 bits (174), Expect = 1e-15
Identities = 18/84 (21%), Positives = 39/84 (46%), Gaps = 7/84 (8%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
++V+ +P + + ++L+ G+V + RD G G V + R ED A+ +L
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKL 70
Query: 89 NGLKLQNKSIKVSYARPSSEAIKR 112
+ K ++ + +Y R + +
Sbjct: 71 DNTKFRSHEGETAYIRVKVDGPRS 94
Score = 66.0 bits (161), Expect = 1e-13
Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 7/78 (8%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
S + V L P L G V V RD G G V ++ +A
Sbjct: 14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA 66
Query: 330 IQSLNGYALGDRLLQVSF 347
++ L+ + ++
Sbjct: 67 VRKLDNTKFRSHEGETAY 84
Score = 52.5 bits (126), Expect = 5e-09
Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 24/92 (26%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
S PS + R + VSGLP + +DL++ R G + + +
Sbjct: 6 SGGPPSRRSENR--VVVSGLPPSGSWQDLKDHMREAGDVCYADV---------------- 47
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQELNGT 192
G G V F + + +A+++L+ T
Sbjct: 48 ------YRDGTGVVEFVRKEDMTYAVRKLDNT 73
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A
{Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A
Length = 102
Score = 70.7 bits (174), Expect = 1e-15
Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV + ++ + F +G+V+ VK++ D +T KG+GFV N + ++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVE-- 68
Query: 334 NGYALGDRLLQV 345
+ + L++
Sbjct: 69 SQINFHGKKLKL 80
Score = 68.0 bits (167), Expect = 1e-14
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
+ + V + M + E++ F+ G V+ K+I D+ T S GYGFV++Y D ++ +
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV- 67
Query: 87 ELNGLKLQNKSIKVSYARPSSE 108
+ + K +K+ A
Sbjct: 68 -ESQINFHGKKLKLGPAIRKQN 88
Score = 56.9 bits (138), Expect = 1e-10
Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 19/81 (23%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++V G+ M + ++ + F YG++ +I+ D+ +G SKG GF
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR----------TGV------SKGYGF 54
Query: 174 VRFNQHIEAEHAMQ---ELNG 191
V F ++ + ++ +G
Sbjct: 55 VSFYNDVDVQKIVESQINFHG 75
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein
biosynthesis, RNA recognition motif, RNA binding domain,
RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 70.0 bits (172), Expect = 2e-15
Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTY-KCKGFGFVCMTNYDEAVFAIQS 332
F+ NL + + + + F + V++ R+P + KGFG+ + D + A+
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS- 79
Query: 333 LNGYALGDRLLQVSF 347
LN +LG+R ++V
Sbjct: 80 LNEESLGNRRIRVDV 94
Score = 66.5 bits (163), Expect = 5e-14
Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDK-TTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
P +T+E ++ F + + +L R+ + G+G+ + + A + LN L
Sbjct: 28 PYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-LSLNEESL 85
Query: 94 QNKSIKVSYARPSSE 108
N+ I+V A + +
Sbjct: 86 GNRRIRVDVADQAQD 100
Score = 48.0 bits (115), Expect = 2e-07
Identities = 19/95 (20%), Positives = 31/95 (32%), Gaps = 18/95 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++ LP +T+E ++ FR I R+ + P+ KG G+
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREP--------------SNPERLKGFGYA 66
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
F A+ LN I V A+
Sbjct: 67 EFEDLDSLLSAL-SLNEESLGNR--RIRVDVADQA 98
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 69.6 bits (171), Expect = 6e-15
Identities = 27/114 (23%), Positives = 46/114 (40%), Gaps = 4/114 (3%)
Query: 11 TQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGY 70
+ + S + + + V +P T L+ F G++E +I D+ T +S GY
Sbjct: 2 SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGY 61
Query: 71 GFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE---AIKRANLYVSGLP 121
GFV AERA + N + + V+ A ++ + VSG
Sbjct: 62 GFVTMADRAAAERACKDPNP-IIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPS 114
Score = 67.3 bits (165), Expect = 3e-14
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 = 53.1 bits (128), Expect = 4e-09
Identities = 26/96 (27%), Positives = 38/96 (39%), Gaps = 18/96 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V GLP H T L F +G I + ++ D+ +G S+G GFV
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQ---------TGK------SRGYGFV 64
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPA 210
AE A ++ N I +G V A A
Sbjct: 65 TMADRAAAERACKDPNPII-DG--RKANVNLAYLGA 97
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 68.6 bits (168), Expect = 1e-14
Identities = 23/100 (23%), Positives = 43/100 (43%), Gaps = 9/100 (9%)
Query: 7 MYNTTQSHRSTYQSDVNEQNSNLIV-NYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTA 65
M Q+ T ++D NS + + N + + +++ +FS G V C + +
Sbjct: 8 MSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK----- 62
Query: 66 QSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
GY FV Y A A++ NG L +++ ++ A
Sbjct: 63 ---GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE 99
Score = 60.1 bits (146), Expect = 1e-11
Identities = 20/129 (15%), Positives = 44/129 (34%), Gaps = 27/129 (20%)
Query: 89 NGLKLQNKSIKVSYARPSSEAIKRAN-LYVSGLPKH-MTQEDLENLFRPYGTIITSRILC 146
+G + ++ S ++ + +++ L + + D+E +F YG + C
Sbjct: 3 SGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAG----C 58
Query: 147 DKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFA 206
+ KG FV+++ A A+ NG + G + + + A
Sbjct: 59 S-------------------VHKGYAFVQYSNERHARAAVLGENGRVLAG--QTLDINMA 97
Query: 207 NSPAGRAKA 215
P
Sbjct: 98 GEPKPDRSG 106
Score = 57.8 bits (140), Expect = 7e-11
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 274 IFVYNLAPE-TEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+F+ NL + + + +F +G V V KG+ FV +N A A+
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVLG 81
Query: 333 LNGYALGDRLLQVSF 347
NG L + L ++
Sbjct: 82 ENGRVLAGQTLDINM 96
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 68.4 bits (168), Expect = 1e-14
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTY-KCKGFGFVCMTNYDEAVFAIQS 332
F+ NL + + + + F + V++ R+P + KGFG+ + D + A+ S
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75
Query: 333 LNGYALGDRLLQVSFKTHKP 352
LN +LG++ ++V
Sbjct: 76 LNEESLGNKRIRVDVADQAQ 95
Score = 66.5 bits (163), Expect = 5e-14
Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDK-TTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
P +T+E ++ F + + + +L R+ + G+G+ + + A + LN L
Sbjct: 24 PYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-LSLNEESL 81
Query: 94 QNKSIKVSYARPSSE 108
NK I+V A + +
Sbjct: 82 GNKRIRVDVADQAQD 96
Score = 50.7 bits (122), Expect = 2e-08
Identities = 20/98 (20%), Positives = 32/98 (32%), Gaps = 18/98 (18%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++ LP +T+E ++ FR I R+ + S R KG G+
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREP--SNPER------------LKGFGYA 62
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
F A+ LN I V A+ +
Sbjct: 63 EFEDLDSLLSAL-SLNEESLGNK--RIRVDVADQAQDK 97
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 68.1 bits (167), Expect = 1e-14
Identities = 14/68 (20%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKS 97
+T++EL+ +F E+ +S G ++ + DAE+ + E G ++ +S
Sbjct: 28 ITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRS 82
Query: 98 IKVSYARP 105
+ + Y
Sbjct: 83 VSLYYTGE 90
Score = 66.1 bits (162), Expect = 6e-14
Identities = 12/79 (15%), Positives = 31/79 (39%), Gaps = 5/79 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ NL+ ++ L ++F +++V K KG ++ + +A ++
Sbjct: 19 LLAKNLSFNITEDELKEVFEDAL---EIRLVSQ--DGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 334 NGYALGDRLLQVSFKTHKP 352
G + R + + + K
Sbjct: 74 QGAEIDGRSVSLYYTGEKG 92
Score = 63.8 bits (156), Expect = 3e-13
Identities = 18/109 (16%), Positives = 39/109 (35%), Gaps = 22/109 (20%)
Query: 104 RPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPE 163
S + L L ++T+++L+ +F I ++ +
Sbjct: 8 CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS--------QDGK-------- 51
Query: 164 IPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
SKGI ++ F +AE ++E G +G +++ + G
Sbjct: 52 ----SKGIAYIEFKSEADAEKNLEEKQGAEIDG--RSVSLYYTGEKGGT 94
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 68.7 bits (168), Expect = 1e-14
Identities = 20/96 (20%), Positives = 42/96 (43%), Gaps = 7/96 (7%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
+ R Y + ++V+ +P + + ++L+ G+V + RD G G
Sbjct: 3 APRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 55
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
V + R ED A+ +L+ K ++ + +Y R +
Sbjct: 56 VEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVD 91
Score = 62.1 bits (151), Expect = 2e-12
Identities = 17/86 (19%), Positives = 27/86 (31%), Gaps = 7/86 (8%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
S + V L P L G V V RD G G V ++ +A
Sbjct: 15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYA 67
Query: 330 IQSLNGYALGDRLLQVSFKTHKPLPP 355
++ L+ + ++ K P
Sbjct: 68 VRKLDNTKFRSHEGETAYIRVKVDGP 93
Score = 52.1 bits (125), Expect = 7e-09
Identities = 25/117 (21%), Positives = 43/117 (36%), Gaps = 27/117 (23%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
Y PS + R + VSGLP + +DL++ R G + + +
Sbjct: 7 RYGPPSRRSENR--VVVSGLPPSGSWQDLKDHMREAGDVCYADV---------------- 48
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQELNGTI---PEGASEPITVKFANSPAGRAK 214
G G V F + + +A+++L+ T EG + I VK +
Sbjct: 49 ------YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYG 99
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 68.4 bits (167), Expect = 2e-14
Identities = 14/98 (14%), Positives = 37/98 (37%), Gaps = 7/98 (7%)
Query: 19 QSDVNEQNSNLIVNYVPQTMTQEELQH----LFSSVGEVESCKLIRDKTTAQSLGYGFVN 74
E + +++ + + +E+LQ L SS G++ I + + G ++
Sbjct: 22 TPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLSDDNSGKAYIV 78
Query: 75 YYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKR 112
+ E A+ + G Q + ++++ +
Sbjct: 79 FATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAE 116
Score = 60.3 bits (146), Expect = 2e-11
Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 7/82 (8%)
Query: 274 IFVYNLAPETEDNVLWQ----LFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
+ + N+ PE L L G + ++ V + G ++ + A
Sbjct: 32 VLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAF 88
Query: 330 IQSLNGYALGDRLLQVSFKTHK 351
+++ GY L ++F
Sbjct: 89 VEAFQGYPFQGNPLVITFSETP 110
Score = 51.4 bits (123), Expect = 2e-08
Identities = 17/136 (12%), Positives = 41/136 (30%), Gaps = 30/136 (22%)
Query: 79 EDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDL----ENLFR 134
++ A E + + + PS + ++ + + +E L L
Sbjct: 2 KETAAAKFERQHMDSPDLGSTPPHTEPSQ------VVLITNINPEVPKEKLQALLYALAS 55
Query: 135 PYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIP 194
G I+ + + G ++ F A+ ++ G
Sbjct: 56 SQGDILDIVVDLSDD------------------NSGKAYIVFATQESAQAFVEAFQGYPF 97
Query: 195 EGASEPITVKFANSPA 210
+G P+ + F+ +P
Sbjct: 98 QGN--PLVITFSETPQ 111
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 66.7 bits (163), Expect = 4e-14
Identities = 23/79 (29%), Positives = 31/79 (39%), Gaps = 6/79 (7%)
Query: 269 GSGWCIFVYNL------APETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
GS I V L LF G V N++ D T K KGF FV +
Sbjct: 4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGS 63
Query: 323 YDEAVFAIQSLNGYALGDR 341
++A I+S +G L +
Sbjct: 64 MNDAKKIIKSFHGKRLDLK 82
Score = 61.7 bits (150), Expect = 3e-12
Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 7/86 (8%)
Query: 26 NSNLIVNYVPQ------TMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTE 79
+ ++VN P + ++ L LFS G+V + + D+ T ++ G+ FV
Sbjct: 6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMN 65
Query: 80 DAERAIIELNGLKL-QNKSIKVSYAR 104
DA++ I +G +L + + +
Sbjct: 66 DAKKIIKSFHGKRLDLKHRLFLYTMK 91
Score = 44.7 bits (106), Expect = 2e-06
Identities = 12/77 (15%), Positives = 27/77 (35%), Gaps = 15/77 (19%)
Query: 116 YVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVR 175
+ + ++ L +LF G ++ D+ +G +KG FV
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDE---------ATGK------TKGFLFVE 60
Query: 176 FNQHIEAEHAMQELNGT 192
+A+ ++ +G
Sbjct: 61 CGSMNDAKKIIKSFHGK 77
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 66.6 bits (163), Expect = 5e-14
Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
YV P + ++++ +F G + L + + FV + DAE A+ +
Sbjct: 26 YVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GPPFAFVEFEDPRDAEDAVYGRD 82
Query: 90 GLKLQNKSIKVSYARPS 106
G ++V + R
Sbjct: 83 GYDYDGYRLRVEFPRSG 99
Score = 65.4 bits (160), Expect = 1e-13
Identities = 22/98 (22%), Positives = 36/98 (36%), Gaps = 20/98 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+YV LP + +D+E++F YG I + + FV
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR------------------GGPPFAFV 66
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
F +AE A+ +G +G + V+F S G
Sbjct: 67 EFEDPRDAEDAVYGRDGYDYDG--YRLRVEFPRSGRGT 102
Score = 64.6 bits (158), Expect = 2e-13
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 3/78 (3%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
+ I+V NL P+ + +F +GA++++ + F FV + +A A
Sbjct: 21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAEDA 77
Query: 330 IQSLNGYALGDRLLQVSF 347
+ +GY L+V F
Sbjct: 78 VYGRDGYDYDGYRLRVEF 95
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; 2.00A {Homo sapiens} PDB:
2ek6_A
Length = 95
Score = 66.2 bits (162), Expect = 5e-14
Identities = 15/78 (19%), Positives = 30/78 (38%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
I V N+ + + F + + ++ + G V + DEA A+
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 333 LNGYALGDRLLQVSFKTH 350
LN +G R +++S +
Sbjct: 77 LNDRPIGSRKVKLSGPSS 94
Score = 57.3 bits (139), Expect = 7e-11
Identities = 13/70 (18%), Positives = 31/70 (44%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P T++ +E+ F + ++ G V + ++A A+I+LN +
Sbjct: 23 MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI 82
Query: 94 QNKSIKVSYA 103
++ +K+S
Sbjct: 83 GSRKVKLSGP 92
Score = 52.7 bits (127), Expect = 3e-09
Identities = 17/77 (22%), Positives = 27/77 (35%), Gaps = 15/77 (19%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+ V +P ++ +++ + F Y I S L G P G V
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE---------KGMP------TGEAMV 62
Query: 175 RFNQHIEAEHAMQELNG 191
F EA A+ +LN
Sbjct: 63 AFESRDEATAAVIDLND 79
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 99
Score = 65.7 bits (161), Expect = 1e-13
Identities = 16/72 (22%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
IFV + + L + F FG V V ++ D + + +GFGF+ + +++V ++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED-EQSVDQAVNM 71
Query: 334 NGYALGDRLLQV 345
+ + + + ++V
Sbjct: 72 HFHDIMGKKVEV 83
Score = 63.0 bits (154), Expect = 7e-13
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 1/71 (1%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQ 94
P + EL+ F G V +I D + G+GF+ + E + + ++ +
Sbjct: 19 PHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFI-TFEDEQSVDQAVNMHFHDIM 77
Query: 95 NKSIKVSYARP 105
K ++V A P
Sbjct: 78 GKKVEVKRAEP 88
Score = 49.5 bits (119), Expect = 4e-08
Identities = 20/115 (17%), Positives = 40/115 (34%), Gaps = 26/115 (22%)
Query: 105 PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEI 164
S K ++V G+P + + +L F+ +G + ++ D E R
Sbjct: 3 SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDA---EKQR--------- 50
Query: 165 PQISKGIGFVRFNQHIEAEHAM----QELNGTIPEGASEPITVKFANSPAGRAKA 215
+G GF+ F + A+ ++ G + VK A ++
Sbjct: 51 ---PRGFGFITFEDEQSVDQAVNMHFHDIMGK-------KVEVKRAEPRDSKSSG 95
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 66.8 bits (163), Expect = 1e-13
Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 5/79 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
++V NL L + FG +G +++V V R+P GF FV + +A A++ L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVREL 130
Query: 334 NGYALGDRLLQVSFKTHKP 352
+G L ++V +
Sbjct: 131 DGRTLCGCRVRVELSNGEK 149
Score = 64.5 bits (157), Expect = 7e-13
Identities = 21/103 (20%), Positives = 38/103 (36%), Gaps = 5/103 (4%)
Query: 3 KHEEMYNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDK 62
K + + H D + + V + + EL+ F G + S + R+
Sbjct: 50 KTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP 109
Query: 63 TTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
G+ FV + DA A+ EL+G L ++V +
Sbjct: 110 P-----GFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG 147
Score = 62.2 bits (151), Expect = 6e-12
Identities = 25/139 (17%), Positives = 44/139 (31%), Gaps = 27/139 (19%)
Query: 71 GFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLE 130
V+ T D + + + P +YV L + + +LE
Sbjct: 37 NGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLD-----CKVYVGNLGNNGNKTELE 91
Query: 131 NLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELN 190
F YG + +V + + G FV F +A A++EL+
Sbjct: 92 RAFGYYGPL------------RSVW--------VARNPPGFAFVEFEDPRDAADAVRELD 131
Query: 191 GTIPEGASEPITVKFANSP 209
G G + V+ +N
Sbjct: 132 GRTLCG--CRVRVELSNGE 148
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 64.8 bits (158), Expect = 2e-13
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 8/84 (9%)
Query: 264 PKSLHGSGWCIFVYNLAPETED------NVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGF 317
P+ G I V N+ D NV+ ++F FG + + K KG+ F
Sbjct: 8 PQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKI--TNDFYPEEDGKTKGYIF 65
Query: 318 VCMTNYDEAVFAIQSLNGYALGDR 341
+ + AV A+++ +GY L +
Sbjct: 66 LEYASPAHAVDAVKNADGYKLDKQ 89
Score = 50.1 bits (120), Expect = 3e-08
Identities = 18/85 (21%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 26 NSNLIVNYVPQT------MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTE 79
+S ++V+ VPQ + + +FS G++ + + ++ GY F+ Y
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 72
Query: 80 DAERAIIELNGLKL-QNKSIKVSYA 103
A A+ +G KL + + +V+
Sbjct: 73 HAVDAVKNADGYKLDKQHTFRVNLF 97
Score = 43.6 bits (103), Expect = 5e-06
Identities = 15/95 (15%), Positives = 31/95 (32%), Gaps = 23/95 (24%)
Query: 104 RPSSEAIKRANLYVSGLPK------HMTQEDLENLFRPYGTIITSRILCDKMASENVRSF 157
RP + + V +P+ + + +F +G I D E+ ++
Sbjct: 7 RPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN-----DFYPEEDGKT- 60
Query: 158 VSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNGT 192
KG F+ + A A++ +G
Sbjct: 61 -----------KGYIFLEYASPAHAVDAVKNADGY 84
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 64.2 bits (157), Expect = 3e-13
Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 8/76 (10%)
Query: 33 YV---PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELN 89
YV + EL+ FS G + + + R+ G+ FV + DAE A+ L+
Sbjct: 4 YVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLD 58
Query: 90 GLKLQNKSIKVSYARP 105
G + ++V +
Sbjct: 59 GKVICGSRVRVELSTG 74
Score = 64.2 bits (157), Expect = 3e-13
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
Score = 61.2 bits (149), Expect = 4e-12
Identities = 22/99 (22%), Positives = 35/99 (35%), Gaps = 22/99 (22%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+YV L + +LE F YG + V I + G F
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPL------------RTVW--------IARNPPGFAF 41
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
V F +AE A++ L+G + G + V+ + R
Sbjct: 42 VEFEDPRDAEDAVRGLDGKVICG--SRVRVELSTGMPRR 78
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 64.8 bits (158), Expect = 3e-13
Identities = 15/78 (19%), Positives = 24/78 (30%), Gaps = 6/78 (7%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
S I NL T + + F FG++ V + + V EA A
Sbjct: 9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKA 62
Query: 330 IQSLNGYALGDRLLQVSF 347
+ L L + +
Sbjct: 63 FRHLAYSKFHHVPLYLEW 80
Score = 61.8 bits (150), Expect = 3e-12
Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 6/78 (7%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+ ++ +P E+Q FS G + L TA V + +A +A
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITA------IVEFLEPLEARKAF 63
Query: 86 IELNGLKLQNKSIKVSYA 103
L K + + + +A
Sbjct: 64 RHLAYSKFHHVPLYLEWA 81
Score = 53.7 bits (129), Expect = 2e-09
Identities = 13/89 (14%), Positives = 27/89 (30%), Gaps = 23/89 (25%)
Query: 106 SSEAIKRAN--LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPE 163
SS + R+ + LP +++ F +G++ +
Sbjct: 2 SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE----------------- 44
Query: 164 IPQISKGIGFVRFNQHIEAEHAMQELNGT 192
V F + +EA A + L +
Sbjct: 45 ----GGITAIVEFLEPLEARKAFRHLAYS 69
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding
domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 98
Score = 64.2 bits (157), Expect = 3e-13
Identities = 14/75 (18%), Positives = 28/75 (37%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
I V N+ + + F + + ++ + G V + DEA A+
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 333 LNGYALGDRLLQVSF 347
LN +G R +++
Sbjct: 77 LNDRPIGSRKVKLVL 91
Score = 60.0 bits (146), Expect = 8e-12
Identities = 13/76 (17%), Positives = 31/76 (40%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P T++ +E+ F + ++ G V + ++A A+I+LN +
Sbjct: 23 MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI 82
Query: 94 QNKSIKVSYARPSSEA 109
++ +K+ S
Sbjct: 83 GSRKVKLVLGSGPSSG 98
Score = 55.8 bits (135), Expect = 3e-10
Identities = 18/96 (18%), Positives = 32/96 (33%), Gaps = 17/96 (17%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+ V +P ++ +++ + F Y I S L G P G V
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE---------KGMP------TGEAMV 62
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPA 210
F EA A+ +LN + + + P+
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSR--KVKLVLGSGPS 96
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 63.8 bits (155), Expect = 6e-13
Identities = 20/110 (18%), Positives = 48/110 (43%), Gaps = 21/110 (19%)
Query: 1 MMKHEEMYNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIR 60
+++HE + + + +S + N L +++ +L + G V++ +
Sbjct: 12 LLRHEGIETVSYATQSLVVA-----NGGL-----GNGVSRNQLLPVLEKCGLVDALLMPP 61
Query: 61 DKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL-----QNKSIKVSYARP 105
+K Y F Y TE+++RA + LNG ++ Q ++ +++
Sbjct: 62 NK------PYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105
Score = 52.2 bits (125), Expect = 7e-09
Identities = 14/97 (14%), Positives = 27/97 (27%), Gaps = 24/97 (24%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+ GL +++ L + G + + +K F
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK---------------------PYSFA 68
Query: 175 RFNQHIEAEHAMQELNGTIP---EGASEPITVKFANS 208
R+ E++ A LNG G + + F
Sbjct: 69 RYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK 105
Score = 50.7 bits (121), Expect = 2e-08
Identities = 17/74 (22%), Positives = 27/74 (36%), Gaps = 8/74 (10%)
Query: 273 CIFVYN--LAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
+ V N L N L + G V + + + K + F +E+ A
Sbjct: 27 SLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAY 80
Query: 331 QSLNGYALGDRLLQ 344
+LNG + D L Q
Sbjct: 81 VTLNGKEVVDDLGQ 94
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 62.0 bits (151), Expect = 1e-12
Identities = 18/80 (22%), Positives = 31/80 (38%), Gaps = 7/80 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
I V NL ++ + L + +K + K FV + N ++A AIQ
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKDYD----LKYCY---VDRNKRTAFVTLLNGEQAQNAIQMF 60
Query: 334 NGYALGDRLLQVSFKTHKPL 353
+ Y+ + L V + L
Sbjct: 61 HQYSFRGKDLIVQLQPTDAL 80
Score = 59.7 bits (145), Expect = 8e-12
Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 7/85 (8%)
Query: 23 NEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAE 82
+ +S ++V +PQ +E+ L ++ C + R+K FV E A+
Sbjct: 2 SSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNK------RTAFVTLLNGEQAQ 54
Query: 83 RAIIELNGLKLQNKSIKVSYARPSS 107
AI + + K + V +
Sbjct: 55 NAIQMFHQYSFRGKDLIVQLQPTDA 79
Score = 58.2 bits (141), Expect = 3e-11
Identities = 15/99 (15%), Positives = 34/99 (34%), Gaps = 24/99 (24%)
Query: 112 RANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
+ + V LP+ +++ +L + Y D+ +K
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYDLKYCY---VDR-------------------NKRT 42
Query: 172 GFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPA 210
FV +A++A+Q + G + + V+ + A
Sbjct: 43 AFVTLLNGEQAQNAIQMFHQYSFRG--KDLIVQLQPTDA 79
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 62.4 bits (152), Expect = 1e-12
Identities = 16/86 (18%), Positives = 37/86 (43%), Gaps = 4/86 (4%)
Query: 15 RSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVN 74
R ++DV ++ + + P T ++++ G+V + ++ R G FV
Sbjct: 2 RWILKNDVKNRS--VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVV 58
Query: 75 YYRTEDAERAIIELNGLKLQNKSIKV 100
+ E A++ +E G K + + +
Sbjct: 59 FDSIESAKKF-VETPGQKYKETDLLI 83
Score = 60.9 bits (148), Expect = 5e-12
Identities = 13/86 (15%), Positives = 29/86 (33%), Gaps = 16/86 (18%)
Query: 108 EAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQI 167
+K ++Y+ G P T +D++ G ++ ++ +
Sbjct: 7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL----------------HKA 50
Query: 168 SKGIGFVRFNQHIEAEHAMQELNGTI 193
KG FV F+ A+ ++
Sbjct: 51 FKGSIFVVFDSIESAKKFVETPGQKY 76
Score = 55.9 bits (135), Expect = 3e-10
Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 2/75 (2%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+++ + + + + G V N+++ R KG FV + + A ++
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHK-AFKGSIFVVFDSIESAKKFVE-T 71
Query: 334 NGYALGDRLLQVSFK 348
G + L + FK
Sbjct: 72 PGQKYKETDLLILFK 86
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 66.0 bits (160), Expect = 4e-12
Identities = 22/107 (20%), Positives = 38/107 (35%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
L V V T+ +L+ F G ++ ++ K + + GY F+ Y D A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 89 NGLKLQNKSIKVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRP 135
+G K+ + + V R + R GL N+
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHS 211
Score = 61.4 bits (148), Expect = 1e-10
Identities = 14/76 (18%), Positives = 37/76 (48%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV + +T ++ L + F +G ++ + +V ++ K +G+ F+ + + A +
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 333 LNGYALGDRLLQVSFK 348
+G + R + V +
Sbjct: 164 ADGKKIDGRRVLVDVE 179
Score = 51.8 bits (123), Expect = 2e-07
Identities = 15/95 (15%), Positives = 33/95 (34%), Gaps = 15/95 (15%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L+V+ + T+ L F YG I ++ K + + +G F+
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGK---------------PRGYAFI 149
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANSP 209
+ + A + +G +G + V+ +
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV 184
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 60.7 bits (148), Expect = 4e-12
Identities = 10/73 (13%), Positives = 28/73 (38%), Gaps = 8/73 (10%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQ 94
+ +++E+L +FS G + + +GF+ + + AI +
Sbjct: 20 LKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIECESQEMNF 71
Query: 95 NKSIKVSYARPSS 107
K + + + ++
Sbjct: 72 GKKLILEVSSSNA 84
Score = 58.4 bits (142), Expect = 3e-11
Identities = 20/101 (19%), Positives = 42/101 (41%), Gaps = 26/101 (25%)
Query: 115 LYVSGLP-KHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L++ LP K++++EDL +F PYG I+ + I GF
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIM------------QIN-----------IKNAFGF 49
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAK 214
++F+ A++ + + G + + ++ ++S A
Sbjct: 50 IQFDNPQSVRDAIECESQEMNFG--KKLILEVSSSNARPQF 88
Score = 51.8 bits (125), Expect = 6e-09
Identities = 16/75 (21%), Positives = 31/75 (41%), Gaps = 13/75 (17%)
Query: 274 IFVYNLAPET---EDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
+F+ NL + ED L+++F P+G + + + FGF+ N AI
Sbjct: 13 LFIGNLPLKNVSKED--LFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAI 62
Query: 331 QSLNGYALGDRLLQV 345
+ + + L +
Sbjct: 63 ECESQEMNFGKKLIL 77
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 61.5 bits (149), Expect = 5e-12
Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 8/84 (9%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ-- 331
I + L + + + L PFG V N+ +++ K F+ M + A +
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 87
Query: 332 SLNGYALGDRLLQVSFKTHKPLPP 355
+ L + + + F HK L
Sbjct: 88 TSVTPVLRGQPIYIQFSNHKELKT 111
Score = 54.5 bits (131), Expect = 1e-09
Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 21/94 (22%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+++ LP +T+ ++ +L P+G + +L K F+
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---------------------KNQAFI 72
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
N A + P +PI ++F+N
Sbjct: 73 EMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106
Score = 53.8 bits (129), Expect = 2e-09
Identities = 14/107 (13%), Positives = 35/107 (32%), Gaps = 10/107 (9%)
Query: 4 HEEMYNTTQSHRSTYQSDVNEQNSN--LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRD 61
H + S + + + + +P +T+ E+ L G+V + +++
Sbjct: 7 HHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG 66
Query: 62 KTTAQSLGYGFVNYYRTEDAERAI--IELNGLKLQNKSIKVSYARPS 106
K F+ E A + L+ + I + ++
Sbjct: 67 K------NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK 107
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 60.1 bits (146), Expect = 5e-12
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 273 CIFVYNLAPETED------NVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA 326
I V N+ D NV+ ++F FG + N + K KG+ F+ + A
Sbjct: 3 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHA 60
Query: 327 VFAIQSLNGYALGDR 341
V A+++ +GY L +
Sbjct: 61 VDAVKNADGYKLDKQ 75
Score = 50.9 bits (122), Expect = 1e-08
Identities = 13/63 (20%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL-QNKS 97
+ + +FS G++ + + ++ GY F+ Y A A+ +G KL + +
Sbjct: 20 LKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT 77
Query: 98 IKV 100
+V
Sbjct: 78 FRV 80
Score = 42.0 bits (99), Expect = 1e-05
Identities = 13/84 (15%), Positives = 28/84 (33%), Gaps = 23/84 (27%)
Query: 115 LYVSGLPKH------MTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQIS 168
+ V +P+ + + +F +G I D E+ ++
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN-----DFYPEEDGKT------------ 46
Query: 169 KGIGFVRFNQHIEAEHAMQELNGT 192
KG F+ + A A++ +G
Sbjct: 47 KGYIFLEYASPAHAVDAVKNADGY 70
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 60.8 bits (148), Expect = 5e-12
Identities = 15/95 (15%), Positives = 35/95 (36%), Gaps = 9/95 (9%)
Query: 14 HRSTYQSDVNEQNSNLIV-NYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
H S + S L + N + +++E+L +FS G + + +GF
Sbjct: 10 HSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGF 61
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSS 107
+ + + AI + K + + + ++
Sbjct: 62 IQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSNA 96
Score = 55.4 bits (134), Expect = 4e-10
Identities = 21/97 (21%), Positives = 43/97 (44%), Gaps = 26/97 (26%)
Query: 115 LYVSGLP-KHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
L++ LP K++++EDL +F PYG I+ +I I GF
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIM----------------------QI-NIKNAFGF 61
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPA 210
++F+ A++ + + G + + ++ ++S A
Sbjct: 62 IQFDNPQSVRDAIEXESQEMNFG--KKLILEVSSSNA 96
Score = 51.2 bits (123), Expect = 1e-08
Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 13/82 (15%)
Query: 274 IFVYNLAPET---EDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI 330
+F+ NL + ED L+++F P+G + + + FGF+ N AI
Sbjct: 25 LFIGNLPLKNVSKED--LFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAI 74
Query: 331 QSLNGYALGDRLLQVSFKTHKP 352
+ + + L + +
Sbjct: 75 EXESQEMNFGKKLILEVSSSNA 96
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 60.7 bits (148), Expect = 5e-12
Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 2/96 (2%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ ++ S+LIV +P T+++L+ FS+ GEV ++ +D T S G+GF
Sbjct: 2 SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSE 108
V + E + + + + + +
Sbjct: 62 VRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQS 95
Score = 60.3 bits (147), Expect = 8e-12
Identities = 21/61 (34%), Positives = 31/61 (50%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+ V L +T + L + F FG V V+V +D +T KGFGFV T Y+ V +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 334 N 334
+
Sbjct: 78 H 78
Score = 48.8 bits (117), Expect = 8e-08
Identities = 26/111 (23%), Positives = 42/111 (37%), Gaps = 25/111 (22%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
+ K ++L V GLP T++DL+ F +G ++ ++ D +G
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK---------TG 54
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAMQ---ELNGTIPEGASEPITVKFANS 208
SKG GFVRF ++ M ++G K NS
Sbjct: 55 ------HSKGFGFVRFTEYETQVKVMSQRHMIDGRW-------CDCKLPNS 92
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 59.4 bits (145), Expect = 8e-12
Identities = 17/53 (32%), Positives = 31/53 (58%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA 326
IFV L+P+T + + + FG FG V+++++ D +T K +GF F+ +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPV 54
Score = 52.9 bits (128), Expect = 2e-09
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+ +E+++ F GEVES +L D T + G+ F+ ++ E+ + I+E +
Sbjct: 7 LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFIT-FKEEEPVKKIMEKKYHNV 65
Query: 94 QNKSIKVSYA 103
++ A
Sbjct: 66 GLSKCEIKVA 75
Score = 46.0 bits (110), Expect = 5e-07
Identities = 11/81 (13%), Positives = 25/81 (30%), Gaps = 19/81 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V GL +E + F +G + + + D + +G F+
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNK---------TNK------RRGFCFI 46
Query: 175 RFNQHIEAEHAM----QELNG 191
F + + M +
Sbjct: 47 TFKEEEPVKKIMEKKYHNVGL 67
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 60.3 bits (146), Expect = 9e-12
Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 8/84 (9%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ-- 331
I + L + + + L PFG V N+ +++ K F+ M + A +
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 72
Query: 332 SLNGYALGDRLLQVSFKTHKPLPP 355
+ L + + + F HK L
Sbjct: 73 TSVTPVLRGQPIYIQFSNHKELKT 96
Score = 55.2 bits (133), Expect = 6e-10
Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 21/94 (22%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+++ LP +T+ ++ +L P+G + +L K F+
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLML---------------------KGKNQAFI 57
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
N A + P +PI ++F+N
Sbjct: 58 EMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 91
Score = 52.6 bits (126), Expect = 5e-09
Identities = 12/74 (16%), Positives = 28/74 (37%), Gaps = 8/74 (10%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI--IELNGL 91
+P +T+ E+ L G+V + +++ K F+ E A +
Sbjct: 24 LPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANTMVNYYTSVTP 77
Query: 92 KLQNKSIKVSYARP 105
L+ + I + ++
Sbjct: 78 VLRGQPIYIQFSNH 91
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 58.7 bits (143), Expect = 1e-11
Identities = 19/58 (32%), Positives = 30/58 (51%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
+F+ L+ +T L + FG FG V+ V+RDP T + +GFGFV + +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Score = 54.4 bits (132), Expect = 4e-10
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
TQE L+ F GEV+ C ++RD T +S G+GFV + ++ + + +L +K+I
Sbjct: 13 TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQSRHELDSKTI 71
Query: 99 KVSYA 103
A
Sbjct: 72 DPKVA 76
Score = 43.6 bits (104), Expect = 3e-06
Identities = 20/96 (20%), Positives = 33/96 (34%), Gaps = 26/96 (27%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+++ GL TQE L F +G + ++ D + + S+G GFV
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLT---------------KRSRGFGFV 47
Query: 175 RFNQHIEAEHAM----QELNGTIPEGASEPITVKFA 206
F + + EL+ I K A
Sbjct: 48 TFMDQAGVDKVLAQSRHELDSKT-------IDPKVA 76
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 58.6 bits (143), Expect = 1e-11
Identities = 18/66 (27%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAI--- 330
IFV L+ T + F FG V + ++ D T + +GFGFV + D
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 331 -QSLNG 335
+N
Sbjct: 62 FHEINN 67
Score = 54.8 bits (133), Expect = 3e-10
Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 35 PQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQ 94
T E+++H F G+V+ L+ DKTT + G+GFV + +ED + E++ ++
Sbjct: 8 SVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFV-TFESEDIVEKVCEIHFHEIN 66
Query: 95 NKSIKVSYA 103
NK ++ A
Sbjct: 67 NKMVECKKA 75
Score = 46.7 bits (112), Expect = 2e-07
Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 19/81 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V GL + T ED+++ F +G + + ++ DK + +G GFV
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKT---------TNR------HRGFGFV 46
Query: 175 RFNQHIEAEHAM----QELNG 191
F E E+N
Sbjct: 47 TFESEDIVEKVCEIHFHEINN 67
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 58.6 bits (142), Expect = 3e-11
Identities = 12/83 (14%), Positives = 25/83 (30%), Gaps = 8/83 (9%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ + L + L + FG + V V+ K V + A A+
Sbjct: 23 VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNY 76
Query: 333 LNGYA--LGDRLLQVSFKTHKPL 353
+ V++ T + +
Sbjct: 77 AADNQIYIAGHPAFVNYSTSQKI 99
Score = 54.4 bits (131), Expect = 1e-09
Identities = 13/101 (12%), Positives = 30/101 (29%), Gaps = 9/101 (8%)
Query: 7 MYNTTQSHRSTYQSDVNEQNSNLI-VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTA 65
M + H Y S ++ + + + + +L G + ++ K
Sbjct: 1 MGHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK--- 57
Query: 66 QSLGYGFVNYYRTEDAERAI--IELNGLKLQNKSIKVSYAR 104
V + A A+ N + + V+Y+
Sbjct: 58 ---RQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYST 95
Score = 50.5 bits (121), Expect = 2e-08
Identities = 15/94 (15%), Positives = 29/94 (30%), Gaps = 21/94 (22%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+++ GL + + DL + +G I ++ K V
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVM---------------------PKKRQALV 62
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
F + A +A+ A P V ++ S
Sbjct: 63 EFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTS 96
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 58.7 bits (142), Expect = 3e-11
Identities = 18/85 (21%), Positives = 31/85 (36%), Gaps = 5/85 (5%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
PP ++V NL + + L + G+V + P + F+ +
Sbjct: 11 PPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP-----RRRAFLHYPD 65
Query: 323 YDEAVFAIQSLNGYALGDRLLQVSF 347
A A+ L G LG L+V+
Sbjct: 66 SAAAQQAVSCLQGLRLGTDTLRVAL 90
Score = 55.6 bits (134), Expect = 3e-10
Identities = 18/97 (18%), Positives = 41/97 (42%), Gaps = 5/97 (5%)
Query: 9 NTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSL 68
++ S + + +++ V +P+ +L+ +G V T
Sbjct: 2 SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPL-----RLTWQGPR 56
Query: 69 GYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
F++Y + A++A+ L GL+L +++V+ AR
Sbjct: 57 RRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ 93
Score = 54.5 bits (131), Expect = 8e-10
Identities = 18/100 (18%), Positives = 31/100 (31%), Gaps = 22/100 (22%)
Query: 113 ANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIG 172
A++YV LP+ DL+ R G + R+ Q +
Sbjct: 20 ADVYVGNLPRDARVSDLKRALRELG-SVPLRL-------------------TWQGPRRRA 59
Query: 173 FVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
F+ + A+ A+ L G + V A +
Sbjct: 60 FLHYPDSAAAQQAVSCLQGLRLGTD--TLRVALARQQRDK 97
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 58.3 bits (141), Expect = 4e-11
Identities = 16/83 (19%), Positives = 34/83 (40%), Gaps = 8/83 (9%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ-- 331
+ + L E + + L PFG V N+ +++ K F+ + + A+ +
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYY 71
Query: 332 SLNGYALGDRLLQVSFKTHKPLP 354
S L ++ + + + HK L
Sbjct: 72 SAVTPHLRNQPIYIQYSNHKELK 94
Score = 53.7 bits (129), Expect = 2e-09
Identities = 15/94 (15%), Positives = 33/94 (35%), Gaps = 21/94 (22%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L++ LP +T+ ++ L P+G + +L K F+
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILML---------------------KGKNQAFL 56
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
A + + P ++PI ++++N
Sbjct: 57 ELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNH 90
Score = 52.1 bits (125), Expect = 6e-09
Identities = 15/93 (16%), Positives = 36/93 (38%), Gaps = 9/93 (9%)
Query: 15 RSTYQSDVNEQNSNLI-VNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFV 73
+ ++ S ++ + +P +T+ E+ L G+V + +++ K F+
Sbjct: 3 SGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFL 56
Query: 74 NYYRTEDAERAI--IELNGLKLQNKSIKVSYAR 104
E A + L+N+ I + Y+
Sbjct: 57 ELATEEAAITMVNYYSAVTPHLRNQPIYIQYSN 89
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 57.9 bits (140), Expect = 5e-11
Identities = 13/83 (15%), Positives = 26/83 (31%), Gaps = 8/83 (9%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ- 331
+ V L + L + FG + V ++ K V N D A +
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTF 70
Query: 332 -SLNGYALGDRLLQVSFKTHKPL 353
+ + + ++ T K +
Sbjct: 71 AADVPVYIAGQQAFFNYSTSKRI 93
Score = 53.6 bits (129), Expect = 2e-09
Identities = 11/101 (10%), Positives = 33/101 (32%), Gaps = 10/101 (9%)
Query: 16 STYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNY 75
S+ + + V + +++ + +L G + ++ K V +
Sbjct: 5 SSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEF 58
Query: 76 YRTEDAERAI--IELNGLKLQNKSIKVSYARPSSEAIKRAN 114
+ A+ + + + + +Y+ S+ I R
Sbjct: 59 ENIDSAKECVTFAADVPVYIAGQQAFFNYST--SKRITRPG 97
Score = 52.1 bits (125), Expect = 6e-09
Identities = 14/95 (14%), Positives = 27/95 (28%), Gaps = 21/95 (22%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++V GL + + + DL +GTI ++ K
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPF---------------------KRQAL 55
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
V F A+ + A + ++ S
Sbjct: 56 VEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTS 90
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 58.4 bits (142), Expect = 5e-11
Identities = 16/53 (30%), Positives = 30/53 (56%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA 326
+F+ L+ ET + L + +G + + V+RDP + + +GFGFV ++ E
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Score = 55.7 bits (135), Expect = 4e-10
Identities = 14/67 (20%), Positives = 33/67 (49%), Gaps = 1/67 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
T+E L++ + G++ C ++RD + +S G+GFV + + + A + + + +
Sbjct: 40 TEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA-MAARPHSIDGRVV 98
Query: 99 KVSYARP 105
+ A
Sbjct: 99 EPKRAVA 105
Score = 45.0 bits (107), Expect = 2e-06
Identities = 24/113 (21%), Positives = 43/113 (38%), Gaps = 26/113 (23%)
Query: 100 VSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVS 159
V R E + L++ GL T+E L N + +G + ++ D
Sbjct: 15 VPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA---------- 64
Query: 160 GTPEIPQISKGIGFVRFNQHIEAEHAMQ----ELNGTIPEGASEPITVKFANS 208
+ + S+G GFV F+ E + AM ++G + + K A +
Sbjct: 65 -S----KRSRGFGFVTFSSMAEVDAAMAARPHSIDGRV-------VEPKRAVA 105
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 56.8 bits (138), Expect = 1e-10
Identities = 16/59 (27%), Positives = 26/59 (44%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV L+ +T L F FG V + + DP T + +GFGF+ + +
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Score = 53.3 bits (129), Expect = 1e-09
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
++++L+ F+ GEV C + D T +S G+GF+ + E+ + + +L + I
Sbjct: 24 SKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEH-RLDGRVI 82
Query: 99 KVSYA 103
A
Sbjct: 83 DPKKA 87
Score = 44.9 bits (107), Expect = 1e-06
Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 15/89 (16%)
Query: 105 PSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEI 164
S ++V GL +++DL++ F +G ++ I D +G
Sbjct: 4 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDP---------NTGR--- 51
Query: 165 PQISKGIGFVRFNQHIEAEHAMQELNGTI 193
S+G GF+ F E + + +
Sbjct: 52 ---SRGFGFILFKDAASVEKVLDQKEHRL 77
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 57.3 bits (139), Expect = 1e-10
Identities = 19/53 (35%), Positives = 29/53 (54%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA 326
+F+ L+ +T L + FG FG V+ V+RDP T + +GFGFV +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 80
Score = 55.3 bits (134), Expect = 4e-10
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 39 TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
TQE L+ F GEV+ C ++RD T +S G+GFV + ++ + + +L +K+I
Sbjct: 38 TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQSRHELDSKTI 96
Query: 99 KVSYARP 105
A P
Sbjct: 97 DPKVAFP 103
Score = 45.3 bits (108), Expect = 2e-06
Identities = 24/120 (20%), Positives = 38/120 (31%), Gaps = 26/120 (21%)
Query: 99 KVSYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFV 158
R S +++ GL TQE L F +G + ++ D +
Sbjct: 12 SGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL--------- 62
Query: 159 SGTPEIPQISKGIGFVRFNQHIEAEHAM----QELNGTIPEGASEPITVKFANSPAGRAK 214
T + S+G GFV F + + EL+ I K A + K
Sbjct: 63 --T----KRSRGFGFVTFMDQAGVDKVLAQSRHELDSKT-------IDPKVAFPRRAQPK 109
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 57.1 bits (138), Expect = 1e-10
Identities = 14/86 (16%), Positives = 24/86 (27%), Gaps = 3/86 (3%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
+ I + NL L L T G G + + + V A
Sbjct: 27 KRYRITMKNLPEGCSWQDLKDLARENSLET---TFSSVNTRDFDGTGALEFPSEEILVEA 83
Query: 330 IQSLNGYALGDRLLQVSFKTHKPLPP 355
++ LN ++ V + P
Sbjct: 84 LERLNNIEFRGSVITVERDDNPPPIR 109
Score = 53.3 bits (128), Expect = 3e-09
Identities = 22/112 (19%), Positives = 39/112 (34%), Gaps = 22/112 (19%)
Query: 104 RPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPE 163
S KR + + LP+ + +DL++L R T + +
Sbjct: 20 HMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRD-------------- 65
Query: 164 IPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS--PAGRA 213
G G + F A++ LN G+ ITV+ ++ P R+
Sbjct: 66 ----FDGTGALEFPSEEILVEALERLNNIEFRGS--VITVERDDNPPPIRRS 111
Score = 52.9 bits (127), Expect = 4e-09
Identities = 14/85 (16%), Positives = 32/85 (37%), Gaps = 4/85 (4%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ + +P+ + ++L+ L + T G G + + E A+ L
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTF---SSVNTRDFDGTGALEFPSEEILVEALERL 87
Query: 89 NGLKLQNKSIKVSYARPSSEAIKRA 113
N ++ + I V + I+R+
Sbjct: 88 NNIEFRGSVITVERDD-NPPPIRRS 111
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 56.9 bits (138), Expect = 1e-10
Identities = 27/93 (29%), Positives = 41/93 (44%), Gaps = 1/93 (1%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S + ++ L V + + TQE L+ FS GEV C +++DKTT QS G+GF
Sbjct: 3 SGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGF 62
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARP 105
V + + L ++I P
Sbjct: 63 VKFKDPNCVGTV-LASRPHTLDGRNIDPKPCTP 94
Score = 56.5 bits (137), Expect = 2e-10
Identities = 16/59 (27%), Positives = 27/59 (45%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+FV L T L F +G V + +++D T + +GFGFV + + + S
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Score = 44.5 bits (106), Expect = 3e-06
Identities = 28/112 (25%), Positives = 39/112 (34%), Gaps = 26/112 (23%)
Query: 101 SYARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSG 160
S +S A + L+V GL TQE L + F YG ++ I+ DK
Sbjct: 5 SSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKT----------- 53
Query: 161 TPEIPQISKGIGFVRFNQHIEAEHAM----QELNGTIPEGASEPITVKFANS 208
T S+G GFV+F + L+G I K
Sbjct: 54 T----NQSRGFGFVKFKDPNCVGTVLASRPHTLDGRN-------IDPKPCTP 94
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 55.1 bits (133), Expect = 4e-10
Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 11/81 (13%)
Query: 33 YV---PQTMTQEELQHLFSSVGE-----VESCKLIRDKTTAQSLGYGFVNYYRTEDAERA 84
YV P +T+E + F++ + Q + F+ + ++ +A
Sbjct: 10 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 69
Query: 85 IIELNGLKLQNKSIKVSYARP 105
+ +G+ Q +S+K+ RP
Sbjct: 70 -MAFDGIIFQGQSLKIR--RP 87
Score = 53.2 bits (128), Expect = 2e-09
Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 6/77 (7%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKV-----VRDPQTYKCKGFGFVCMTNYDEAVF 328
++V N+ + + F + + V Q + K F F+ + DE
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 329 AIQSLNGYALGDRLLQV 345
A+ +G + L++
Sbjct: 69 AMA-FDGIIFQGQSLKI 84
Score = 45.1 bits (107), Expect = 1e-06
Identities = 19/82 (23%), Positives = 28/82 (34%), Gaps = 11/82 (13%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
LYV +P +T+E + + F + A N V K F+
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLG-----GLTQAPGNPVLAVQINQ-----DKNFAFL 58
Query: 175 RFNQHIEAEHAMQELNGTIPEG 196
F E AM +G I +G
Sbjct: 59 EFRSVDETTQAMA-FDGIIFQG 79
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 58.3 bits (140), Expect = 4e-10
Identities = 15/86 (17%), Positives = 33/86 (38%), Gaps = 6/86 (6%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+ L ++ + ++ +FS +G+++ + + K GFV + +AE A
Sbjct: 143 DGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------NCGFVKFKYQANAEFAK 196
Query: 86 IELNGLKLQNKSIKVSYARPSSEAIK 111
++ L S K R +
Sbjct: 197 EAMSNQTLLLPSDKEWDDRREGTGLL 222
Score = 52.1 bits (124), Expect = 5e-08
Identities = 19/127 (14%), Positives = 40/127 (31%), Gaps = 9/127 (7%)
Query: 225 AAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPETE 284
+ + FG R + + N L + G+ + +L P
Sbjct: 100 GKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGA---LNSKHLKPAQI 156
Query: 285 DNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQ 344
++ + +F G + ++ V K GFV A FA ++++ L +
Sbjct: 157 ESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTLLLPSDK 210
Query: 345 VSFKTHK 351
+
Sbjct: 211 EWDDRRE 217
Score = 45.9 bits (108), Expect = 7e-06
Identities = 22/114 (19%), Positives = 33/114 (28%), Gaps = 40/114 (35%)
Query: 114 NLYVSGLP---------KHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEI 164
LYV G+ + + +F G I R +
Sbjct: 136 TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------------------- 176
Query: 165 PQISKGIGFVRFNQHIEAEHAMQELNGTIPEGAS----------EPITVKFANS 208
SK GFV+F AE A + ++ S + VK+AN
Sbjct: 177 --ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANE 228
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 53.5 bits (129), Expect = 1e-09
Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 6/82 (7%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSL 333
+FV + L + F FG V +V + +D F V M + A A+ S
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDVG-AREAVLSQ 64
Query: 334 NGYALGDRLLQVSFKTHKPLPP 355
+ ++LG L+V + K
Sbjct: 65 SQHSLGGHRLRVRPREQKEFQS 86
Score = 50.0 bits (120), Expect = 2e-08
Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 6/72 (8%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
P+ + +L F + G V S + +DK + V A A++ + L
Sbjct: 16 FPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVE-MGDVGAREAVLSQSQHSL 69
Query: 94 QNKSIKVSYARP 105
++V
Sbjct: 70 GGHRLRVRPREQ 81
Score = 41.9 bits (99), Expect = 2e-05
Identities = 12/88 (13%), Positives = 27/88 (30%), Gaps = 20/88 (22%)
Query: 106 SSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIP 165
SS + +++VSG P+ + L F +G + +V +
Sbjct: 2 SSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPV------------ASVV--------MD 41
Query: 166 QISKGIGFVRFNQHIEAEHAMQELNGTI 193
+ V E + + ++
Sbjct: 42 KDKGVFAIVEMGDVGAREAVLSQSQHSL 69
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 54.1 bits (130), Expect = 2e-09
Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 3/90 (3%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQN-VKVVRDPQTYKCKGFGFVCMT 321
+S H +G+C+++ L E E+ + F V++ + + P K G GFV
Sbjct: 17 RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNG-KATGEGFVEFR 75
Query: 322 NYDEAVFAIQSLNGYALGDRLLQVSFKTHK 351
N + A+ + +G+R +QV T K
Sbjct: 76 NEADYKAALC-RHKQYMGNRFIQVHPITKK 104
Score = 49.1 bits (117), Expect = 1e-07
Identities = 15/93 (16%), Positives = 33/93 (35%), Gaps = 1/93 (1%)
Query: 14 HRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFV 73
+ + +E + + +P + + F + VE I ++ G GFV
Sbjct: 13 QKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFV 72
Query: 74 NYYRTEDAERAIIELNGLKLQNKSIKVSYARPS 106
+ D + A + + + N+ I+V
Sbjct: 73 EFRNEADYKAA-LCRHKQYMGNRFIQVHPITKK 104
Score = 43.7 bits (103), Expect = 8e-06
Identities = 15/90 (16%), Positives = 29/90 (32%), Gaps = 16/90 (17%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTP 162
+R S +Y+ GLP + + + F+ + S + +G
Sbjct: 16 SRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP---------NGKA 66
Query: 163 EIPQISKGIGFVRFNQHIEAEHAMQELNGT 192
G GFV F + + A+ +
Sbjct: 67 ------TGEGFVEFRNEADYKAAL-CRHKQ 89
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 52.8 bits (127), Expect = 3e-09
Identities = 14/83 (16%), Positives = 33/83 (39%), Gaps = 3/83 (3%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
+G C+ + L +N ++ F P V + P + G V +++AV A
Sbjct: 14 TGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDG-RVTGEADVEFATHEDAVAA 71
Query: 330 IQSLNGYALGDRLLQVSFKTHKP 352
+ + + + R +++ +
Sbjct: 72 M-AKDKANMQHRYVELFLNSTAG 93
Score = 42.4 bits (100), Expect = 2e-05
Identities = 18/107 (16%), Positives = 41/107 (38%), Gaps = 6/107 (5%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ S + + + +P T+ ++ + FS + + + G
Sbjct: 2 SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDG-RVTGEAD 59
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSG 119
V + EDA A + + +Q++ +++ +S A + SG
Sbjct: 60 VEFATHEDAVAA-MAKDKANMQHRYVELF---LNSTAGTSGSGPSSG 102
Score = 38.9 bits (91), Expect = 2e-04
Identities = 17/73 (23%), Positives = 24/73 (32%), Gaps = 17/73 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+++ GLP T+ D+ N F P + I G G V
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP----------DGRV------TGEADV 60
Query: 175 RFNQHIEAEHAMQ 187
F H +A AM
Sbjct: 61 EFATHEDAVAAMA 73
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 53.2 bits (128), Expect = 3e-09
Identities = 17/94 (18%), Positives = 33/94 (35%), Gaps = 3/94 (3%)
Query: 264 PKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQN-VKVVRDPQTYKCKGFGFVCMTN 322
++ + C + N+ + Q +N V V+ D + G V N
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNG-QGLGQALVQFKN 66
Query: 323 YDEAVFAIQSLNGYALGDRLLQVSFKTHKPLPPV 356
D+A + + L+ L R V T + + +
Sbjct: 67 EDDARKSER-LHRKKLNGREAFVHVVTLEDMREI 99
Score = 53.2 bits (128), Expect = 3e-09
Identities = 19/101 (18%), Positives = 38/101 (37%), Gaps = 4/101 (3%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ + DVN + +P ++T+ ++ + E+ + Q LG
Sbjct: 2 SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRA 113
V + +DA ++ L+ KL + V + R
Sbjct: 62 VQFKNEDDARKS-ERLHRKKLNGREAFV---HVVTLEDMRE 98
Score = 44.3 bits (105), Expect = 3e-06
Identities = 11/91 (12%), Positives = 27/91 (29%), Gaps = 18/91 (19%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITS-RILCDKMASENVRSFVSGT 161
+ + +++ +P +T+ D+ + +L D +G
Sbjct: 6 SGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN----------NGQ 55
Query: 162 PEIPQISKGIGFVRFNQHIEAEHAMQELNGT 192
G V+F +A + L+
Sbjct: 56 G------LGQALVQFKNEDDARKSE-RLHRK 79
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 54.5 bits (130), Expect = 5e-09
Identities = 16/100 (16%), Positives = 38/100 (38%), Gaps = 2/100 (2%)
Query: 1 MMKHEEMYNTTQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIR 60
+ T + + +N ++ + P T ++++ G+V + ++ R
Sbjct: 84 DKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR 143
Query: 61 DKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKV 100
A G FV + E A++ +E G K + + +
Sbjct: 144 TLHKAFK-GSIFVVFDSIESAKKF-VETPGQKYKETDLLI 181
Score = 45.2 bits (106), Expect = 6e-06
Identities = 15/94 (15%), Positives = 34/94 (36%), Gaps = 19/94 (20%)
Query: 114 NLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
++Y+ G P T +D++ G ++ ++ ++F KG F
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-----HKAF-----------KGSIF 154
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
V F+ A+ ++ E + + F +
Sbjct: 155 VVFDSIESAKKFVETPGQKYKE---TDLLILFKD 185
Score = 42.5 bits (99), Expect = 7e-05
Identities = 12/76 (15%), Positives = 29/76 (38%), Gaps = 2/76 (2%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+++ + + + + G V N+++ R KG FV + + A +++
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHK-AFKGSIFVVFDSIESAKKFVET 169
Query: 333 LNGYALGDRLLQVSFK 348
+ L + FK
Sbjct: 170 PGQK-YKETDLLILFK 184
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 52.4 bits (126), Expect = 6e-09
Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 3/84 (3%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
P ++ + V+ + +N + F V V +++D + G G V +
Sbjct: 8 KPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVG-RNNGNGLVKFLS 65
Query: 323 YDEAVFAIQSLNGYALGDRLLQVS 346
+ A++ N + R ++VS
Sbjct: 66 PQDTFEALK-RNRMLMIQRYVEVS 88
Score = 49.0 bits (117), Expect = 8e-08
Identities = 18/98 (18%), Positives = 46/98 (46%), Gaps = 4/98 (4%)
Query: 22 VNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDA 81
+N + + V+ +P + + +++ F + V++ L++D ++ G G V + +D
Sbjct: 12 INPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVG-RNNGNGLVKFLSPQDT 69
Query: 82 ERAIIELNGLKLQNKSIKVSYARPSSEAIKRANLYVSG 119
A ++ N + + + ++VS A + + SG
Sbjct: 70 FEA-LKRNRMLMIQRYVEVSPATE-RQWVAAGGHITSG 105
Score = 39.3 bits (92), Expect = 2e-04
Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 18/78 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+ V G+P + D+ + F + +L D + + G G V
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGR----------------NNGNGLV 61
Query: 175 RFNQHIEAEHAMQELNGT 192
+F + A+ + N
Sbjct: 62 KFLSPQDTFEAL-KRNRM 78
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 51.5 bits (124), Expect = 8e-09
Identities = 14/83 (16%), Positives = 33/83 (39%), Gaps = 3/83 (3%)
Query: 270 SGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFA 329
+ + + + + + P +++VR+ G+ FV +N +E A
Sbjct: 9 TCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHG-NKTGYIFVDFSNEEEVKQA 66
Query: 330 IQSLNGYALGDRLLQVSFKTHKP 352
++ N +G R ++V + P
Sbjct: 67 LK-CNREYMGGRYIEVFREKSGP 88
Score = 43.1 bits (102), Expect = 7e-06
Identities = 13/78 (16%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+ + P +T++ + + + V + +++R+ GY FV++ E+ ++A ++
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHG-NKTGYIFVDFSNEEEVKQA-LKC 69
Query: 89 NGLKLQNKSIKVSYARPS 106
N + + I+V +
Sbjct: 70 NREYMGGRYIEVFREKSG 87
Score = 39.2 bits (92), Expect = 1e-04
Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 17/85 (20%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTP 162
S + + G P ++T++++ P + RI+ + G
Sbjct: 1 GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA----------HGNK 49
Query: 163 EIPQISKGIGFVRFNQHIEAEHAMQ 187
G FV F+ E + A++
Sbjct: 50 ------TGYIFVDFSNEEEVKQALK 68
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 52.3 bits (125), Expect = 9e-09
Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 6/88 (6%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+IV + +T + L +FS G V Q + Y A+ A + L
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLSL 86
Query: 89 NGLKLQNKS--IKVSYARPSSEAIKRAN 114
+G + N +++ +++ +S +K N
Sbjct: 87 DGQNIYNACCTLRIDFSKLTSLNVKYNN 114
Score = 45.4 bits (107), Expect = 2e-06
Identities = 19/83 (22%), Positives = 30/83 (36%), Gaps = 6/83 (7%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
I V NL +VL Q+F FG V + ++ + + A A S
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLS 85
Query: 333 LNGYAL--GDRLLQVSFKTHKPL 353
L+G + L++ F L
Sbjct: 86 LDGQNIYNACCTLRIDFSKLTSL 108
Score = 37.3 bits (86), Expect = 0.002
Identities = 14/93 (15%), Positives = 31/93 (33%), Gaps = 19/93 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+ V L +T + L +F +GT++ + +
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ-------------------ALL 71
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
++ + A+HA L+G A + + F+
Sbjct: 72 QYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 104
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 52.8 bits (126), Expect = 1e-08
Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 6/88 (6%)
Query: 29 LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIEL 88
+IV + +T + L +FS G V Q + Y A+ A + L
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLSL 104
Query: 89 NGLKLQNKS--IKVSYARPSSEAIKRAN 114
+G + N +++ +++ +S +K N
Sbjct: 105 DGQNIYNACCTLRIDFSKLTSLNVKYNN 132
Score = 46.6 bits (110), Expect = 2e-06
Identities = 24/124 (19%), Positives = 39/124 (31%), Gaps = 16/124 (12%)
Query: 242 HHSARFKFAPLTADLLNNSMLPPKSLHGSG----------WCIFVYNLAPETEDNVLWQL 291
H SA+ + + N L + I V NL +VL Q+
Sbjct: 7 HGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQI 66
Query: 292 FGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYAL--GDRLLQVSFKT 349
F FG V + ++ + + A A SL+G + L++ F
Sbjct: 67 FSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 122
Query: 350 HKPL 353
L
Sbjct: 123 LTSL 126
Score = 40.5 bits (94), Expect = 2e-04
Identities = 21/139 (15%), Positives = 51/139 (36%), Gaps = 24/139 (17%)
Query: 74 NYYRTEDAERAIIELNGLKLQNKSIKVSYA-RPSSEAIKRAN----LYVSGLPKHMTQED 128
+++ A+ A+ +N ++ N ++ S A + A+ + + V L +T +
Sbjct: 3 HHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDV 62
Query: 129 LENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQE 188
L +F +GT++ + +++ + A+HA
Sbjct: 63 LHQIFSKFGTVLKIITFTKNNQFQ-------------------ALLQYADPVSAQHAKLS 103
Query: 189 LNGTIPEGASEPITVKFAN 207
L+G A + + F+
Sbjct: 104 LDGQNIYNACCTLRIDFSK 122
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions,
RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus
musculus}
Length = 89
Score = 49.9 bits (120), Expect = 3e-08
Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 7/87 (8%)
Query: 19 QSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRT 78
+ S + V + MT EELQ F GEV + + + FV +
Sbjct: 4 SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADD 58
Query: 79 EDAERAIIELNGLKLQNKSIKVSYARP 105
+ A+ E L ++ S+ +S A P
Sbjct: 59 KVAQSLCGE--DLIIKGISVHISNAEP 83
Score = 46.1 bits (110), Expect = 5e-07
Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 5/58 (8%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
+FV + L Q F +G V +V + + + F FV + A
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSLCG 66
Score = 42.2 bits (100), Expect = 1e-05
Identities = 14/74 (18%), Positives = 23/74 (31%), Gaps = 20/74 (27%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V + MT E+L+ F YG ++ I + FV
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP--------------------FRAFAFV 53
Query: 175 RFNQHIEAEHAMQE 188
F A+ E
Sbjct: 54 TFADDKVAQSLCGE 67
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 49.1 bits (118), Expect = 4e-08
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
MT++EL+ FS G+V + + + FV + + A+ E L +
Sbjct: 13 CTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLII 65
Query: 94 QNKSIKVSYARPSSEA 109
+ S+ +S A P +
Sbjct: 66 KGISVHISNAEPKHNS 81
Score = 48.4 bits (116), Expect = 9e-08
Identities = 11/53 (20%), Positives = 22/53 (41%), Gaps = 5/53 (9%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEA 326
+FV + ++ L + F +G V +V + + + F FV + A
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIA 55
Score = 42.6 bits (101), Expect = 1e-05
Identities = 14/74 (18%), Positives = 24/74 (32%), Gaps = 20/74 (27%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V MT+++L F YG ++ IP+ + FV
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDV--------------------FIPKPFRAFAFV 47
Query: 175 RFNQHIEAEHAMQE 188
F A+ E
Sbjct: 48 TFADDQIAQSLCGE 61
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 50.1 bits (119), Expect = 5e-08
Identities = 21/110 (19%), Positives = 42/110 (38%), Gaps = 9/110 (8%)
Query: 9 NTTQSHRSTYQSDVNEQNSNL--IVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQ 66
+ + R D + N L + +T + L + + VG+V+ + +
Sbjct: 6 SGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGI-- 63
Query: 67 SLGYGFVNYYRTEDAERAIIELNGLKLQNKS--IKVSYARPSSEAIKRAN 114
V + A++A LNG + +K+ YARP+ + R +
Sbjct: 64 ---QAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVIRND 110
Score = 38.5 bits (89), Expect = 6e-04
Identities = 16/83 (19%), Positives = 28/83 (33%), Gaps = 7/83 (8%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ + N +VL+ + P G VQ R + V + A A +
Sbjct: 27 LLSIQNPLYPITVDVLYTVCNPVGKVQ-----RIVIFKRNGIQAMVEFESVLCAQKAKAA 81
Query: 333 LNGYALGDR--LLQVSFKTHKPL 353
LNG + L++ + L
Sbjct: 82 LNGADIYAGCCTLKIEYARPTRL 104
Score = 31.6 bits (71), Expect = 0.15
Identities = 14/93 (15%), Positives = 25/93 (26%), Gaps = 20/93 (21%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
L + +T + L + P G + I V
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN--------------------GIQAMV 67
Query: 175 RFNQHIEAEHAMQELNGTIPEGASEPITVKFAN 207
F + A+ A LNG + +++A
Sbjct: 68 EFESVLCAQKAKAALNGADIYAGCCTLKIEYAR 100
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 50.2 bits (120), Expect = 6e-08
Identities = 17/90 (18%), Positives = 35/90 (38%), Gaps = 3/90 (3%)
Query: 263 PPKSLHGSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
+G C+ + L + +N ++ F P V V + P + G V
Sbjct: 38 EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPDG-RVTGEADVEFAT 95
Query: 323 YDEAVFAIQSLNGYALGDRLLQVSFKTHKP 352
++EAV A+ S + + R +++ +
Sbjct: 96 HEEAVAAM-SKDRANMQHRYIELFLNSTTG 124
Score = 39.8 bits (93), Expect = 3e-04
Identities = 18/73 (24%), Positives = 24/73 (32%), Gaps = 17/73 (23%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+++ GLP T+ D+ N F P + I G G V
Sbjct: 49 VHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP----------DGRV------TGEADV 91
Query: 175 RFNQHIEAEHAMQ 187
F H EA AM
Sbjct: 92 EFATHEEAVAAMS 104
Score = 36.7 bits (85), Expect = 0.002
Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 5/82 (6%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL 93
+P T+ ++ + FS + V + + G V + E+A A + + +
Sbjct: 54 LPYKATENDIYNFFSPLNPV-RVHIEIGPDG-RVTGEADVEFATHEEAVAA-MSKDRANM 110
Query: 94 QNKSIKV--SYARPSSEAIKRA 113
Q++ I++ + +S +
Sbjct: 111 QHRYIELFLNSTTGASNGAYSS 132
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM
domain, riken structural genomics/proteomics initiative,
RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 49.0 bits (117), Expect = 8e-08
Identities = 18/94 (19%), Positives = 43/94 (45%), Gaps = 1/94 (1%)
Query: 13 SHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGF 72
S S+ S + + + +P ++EE+ FS + V + + +S G F
Sbjct: 2 SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61
Query: 73 VNYYRTEDAERAIIELNGLKLQNKSIKVSYARPS 106
V + E AE+A ++ + ++ ++ I++ + +
Sbjct: 62 VQFASQEIAEKA-LKKHKERIGHRYIEIFKSSRA 94
Score = 47.4 bits (113), Expect = 2e-07
Identities = 12/81 (14%), Positives = 28/81 (34%), Gaps = 1/81 (1%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ + L + Q F V N + + G FV + + A A++
Sbjct: 17 FVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK- 75
Query: 333 LNGYALGDRLLQVSFKTHKPL 353
+ +G R +++ + +
Sbjct: 76 KHKERIGHRYIEIFKSSRAEV 96
Score = 38.6 bits (90), Expect = 3e-04
Identities = 18/89 (20%), Positives = 30/89 (33%), Gaps = 18/89 (20%)
Query: 102 YARPSSEAIKRAN---LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFV 158
+ S + AN + + GLP ++E++ F + L R
Sbjct: 2 SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD---FQGR--- 55
Query: 159 SGTPEIPQISKGIGFVRFNQHIEAEHAMQ 187
S G FV+F AE A++
Sbjct: 56 ---------STGEAFVQFASQEIAEKALK 75
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kg0_A
Length = 126
Score = 49.1 bits (117), Expect = 1e-07
Identities = 21/107 (19%), Positives = 46/107 (42%), Gaps = 6/107 (5%)
Query: 5 EEMYNTTQSHRSTYQSDVNEQNSN--LIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDK 62
M + T + S+ + ++ + + +P T+EE+ FS + V + +
Sbjct: 19 SHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVD 78
Query: 63 TTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEA 109
+ G FV + E AE+A + + ++ ++ I+V SS+
Sbjct: 79 PEGKITGEAFVQFASQELAEKA-LGKHKERIGHRYIEVF---KSSQE 121
Score = 45.6 bits (108), Expect = 2e-06
Identities = 14/74 (18%), Positives = 25/74 (33%), Gaps = 1/74 (1%)
Query: 273 CIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQS 332
+ + L + Q F V N + K G FV + + A A+
Sbjct: 44 FVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG- 102
Query: 333 LNGYALGDRLLQVS 346
+ +G R ++V
Sbjct: 103 KHKERIGHRYIEVF 116
Score = 39.1 bits (91), Expect = 3e-04
Identities = 15/73 (20%), Positives = 23/73 (31%), Gaps = 15/73 (20%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+ + GLP T+E++ F + L G G FV
Sbjct: 45 VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDP---------EGKI------TGEAFV 89
Query: 175 RFNQHIEAEHAMQ 187
+F AE A+
Sbjct: 90 QFASQELAEKALG 102
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 47.7 bits (113), Expect = 2e-07
Identities = 22/91 (24%), Positives = 39/91 (42%), Gaps = 7/91 (7%)
Query: 269 GSGWCIFVYNLAPETED----NVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYD 324
G+G + V N+ +L + F G V++V++ + V M N
Sbjct: 7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQ 63
Query: 325 EAVFAIQSLNGYALGDRLLQVSFKTHKPLPP 355
+A+ A+ SL+ Y +G + + VS T P
Sbjct: 64 DAIGAVNSLHRYKIGSKKILVSLATGASGPS 94
Score = 45.0 bits (106), Expect = 2e-06
Identities = 24/95 (25%), Positives = 40/95 (42%), Gaps = 5/95 (5%)
Query: 16 STYQSD-VNEQNSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVN 74
S + + Q SN+ + + Q+ LQ F+ G+V+S +L V
Sbjct: 3 SGSSGNGADVQVSNIDYRLSRKEL-QQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQ 58
Query: 75 YYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEA 109
+DA A+ L+ K+ +K I VS A +S
Sbjct: 59 MENLQDAIGAVNSLHRYKIGSKKILVSLATGASGP 93
Score = 29.6 bits (66), Expect = 0.44
Identities = 16/104 (15%), Positives = 35/104 (33%), Gaps = 24/104 (23%)
Query: 113 ANLYVSGLPKHMT----QEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQIS 168
A++ VS + ++ Q+ L+ F +G + + +
Sbjct: 10 ADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD------------------Y 51
Query: 169 KGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGR 212
+ V+ +A A+ L+ + S+ I V A +G
Sbjct: 52 QLKAVVQMENLQDAIGAVNSLHRY--KIGSKKILVSLATGASGP 93
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 46.5 bits (110), Expect = 7e-07
Identities = 13/79 (16%), Positives = 29/79 (36%), Gaps = 3/79 (3%)
Query: 269 GSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDP--QTYKCKGFGFVCMTNYDEA 326
G G+ + + L + V V + + G FV + + D+
Sbjct: 15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDV 74
Query: 327 VFAIQSLNGYALGDRLLQV 345
A++ + ++G R ++V
Sbjct: 75 KLALK-KDRESMGHRYIEV 92
Score = 41.4 bits (97), Expect = 5e-05
Identities = 17/116 (14%), Positives = 42/116 (36%), Gaps = 7/116 (6%)
Query: 11 TQSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSS---VGEVESCKLIRDKTTAQS 67
+ + + + +P + + E++Q+ S V I + QS
Sbjct: 2 SSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQS 61
Query: 68 LGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPS--SEAIKRANLYVSGLP 121
G FV +D + A ++ + + ++ I+V + + +K + + P
Sbjct: 62 -GEAFVELESEDDVKLA-LKKDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGP 115
Score = 36.8 bits (85), Expect = 0.002
Identities = 16/130 (12%), Positives = 35/130 (26%), Gaps = 23/130 (17%)
Query: 103 ARPSSEAIKRANLYVSGLPKHMTQEDLENLFRPY---GTIITSRILCDKMASENVRSFVS 159
E + + + GLP + ED++N + + +
Sbjct: 8 MMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR-------- 59
Query: 160 GTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPAGRAKALAAN 219
G FV + + A+++ ++ I V F + L +
Sbjct: 60 --------QSGEAFVELESEDDVKLALKKDRESM---GHRYIEV-FKSHRTEMDWVLKHS 107
Query: 220 LNAQAAAMRH 229
A+
Sbjct: 108 GPNSASGPSS 117
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 45.4 bits (107), Expect = 2e-06
Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 3/81 (3%)
Query: 274 IFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRD--PQTYKCKGFGFVCMTNYDEAVFAIQ 331
+FV L P+ +++ + F FG + + + KG+ F+ + +V A+
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLF-QEESSVQALI 69
Query: 332 SLNGYALGDRLLQVSFKTHKP 352
G L VS T K
Sbjct: 70 DACLEEDGKLYLCVSSPTIKD 90
Score = 38.8 bits (90), Expect = 3e-04
Identities = 11/80 (13%), Positives = 28/80 (35%), Gaps = 8/80 (10%)
Query: 34 VPQTMTQEELQHLFSSVGEVESCKLIRDKTTA--QSLGYGFVNYYRTEDAERAI------ 85
+P + ++E+ F G + + ++ + GY F+ + + I
Sbjct: 16 LPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEE 75
Query: 86 IELNGLKLQNKSIKVSYARP 105
L + + +IK +
Sbjct: 76 DGKLYLCVSSPTIKDKPVQI 95
Score = 38.4 bits (89), Expect = 4e-04
Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 13/74 (17%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
++V GLP + ++++ FR +G ++ + S KG F+
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFP-------------PKGYAFL 57
Query: 175 RFNQHIEAEHAMQE 188
F + + +
Sbjct: 58 LFQEESSVQALIDA 71
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 45.8 bits (108), Expect = 2e-06
Identities = 16/123 (13%), Positives = 36/123 (29%), Gaps = 7/123 (5%)
Query: 225 AAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVYNLAPETE 284
+ H H + L + + + G G+ + + L
Sbjct: 2 GSSHH----HHHHSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCS 57
Query: 285 DNVLWQLFGPFGAVQNVKVVRDPQTY--KCKGFGFVCMTNYDEAVFAIQSLNGYALGDRL 342
+ V T + G FV + + D+ A++ + ++G R
Sbjct: 58 VEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRY 116
Query: 343 LQV 345
++V
Sbjct: 117 IEV 119
Score = 41.9 bits (98), Expect = 4e-05
Identities = 14/107 (13%), Positives = 38/107 (35%), Gaps = 7/107 (6%)
Query: 12 QSHRSTYQSDVNEQNSNLIVNYVPQTMTQEELQHLFSS---VGEVESCKLIRDKTTAQSL 68
S + + + +P + + E++Q+ S I + +
Sbjct: 30 MGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREG-RQS 88
Query: 69 GYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPS--SEAIKRA 113
G FV +D + A ++ + + ++ I+V + + +K +
Sbjct: 89 GEAFVELGSEDDVKMA-LKKDRESMGHRYIEVFKSHRTEMDWVLKHS 134
Score = 32.3 bits (73), Expect = 0.084
Identities = 11/79 (13%), Positives = 25/79 (31%), Gaps = 13/79 (16%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+ + GLP + ED++N + + V G FV
Sbjct: 47 VKLRGLPWSCSVEDVQNFLSDCTIH-------------DGAAGVHFIYTREGRQSGEAFV 93
Query: 175 RFNQHIEAEHAMQELNGTI 193
+ + A+++ ++
Sbjct: 94 ELGSEDDVKMALKKDRESM 112
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 44.1 bits (104), Expect = 5e-06
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 1/63 (1%)
Query: 40 QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIK 99
+E + GEVE + D +G +V + R EDAE+A+I+LN + I
Sbjct: 41 EEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
Query: 100 VSY 102
Sbjct: 100 AEL 102
Score = 43.3 bits (102), Expect = 7e-06
Identities = 12/66 (18%), Positives = 24/66 (36%), Gaps = 1/66 (1%)
Query: 282 ETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDR 341
E + V ++ +G V+ + V D G +V ++A A+ LN +
Sbjct: 38 EFFEEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96
Query: 342 LLQVSF 347
+
Sbjct: 97 PIHAEL 102
Score = 29.1 bits (65), Expect = 0.66
Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 16/66 (24%)
Query: 126 QEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHA 185
+E + YG + + CD + G +V+F + +AE A
Sbjct: 41 EEVFTEMEEKYGEVEEMNV-CDNLGDH---------------LVGNVYVKFRREEDAEKA 84
Query: 186 MQELNG 191
+ +LN
Sbjct: 85 VIDLNN 90
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 43.7 bits (103), Expect = 6e-06
Identities = 10/77 (12%), Positives = 23/77 (29%), Gaps = 3/77 (3%)
Query: 271 GWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTY--KCKGFGFVCMTNYDEAVF 328
+ I L + F + K +G + M + +
Sbjct: 11 VFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQK 70
Query: 329 AIQSLNGYALGDRLLQV 345
A++ + +G R ++V
Sbjct: 71 ALE-KHRMYMGQRYVEV 86
Score = 40.6 bits (95), Expect = 7e-05
Identities = 13/104 (12%), Positives = 39/104 (37%), Gaps = 10/104 (9%)
Query: 20 SDVNEQNSNLIVNYV---PQTMTQEELQHLFSS---VGEVESCKLIRDKTTAQSLGYGFV 73
S + E+ ++ + P + T E++ + FS + ++ + G +
Sbjct: 2 SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDG-KRRGDALI 60
Query: 74 NYYRTEDAERAIIELNGLKLQNKSIKVSYARPS--SEAIKRANL 115
+D ++A +E + + + + ++V +K +
Sbjct: 61 EMESEQDVQKA-LEKHRMYMGQRYVEVYEINNEDVDALMKSLQV 103
Score = 34.8 bits (80), Expect = 0.007
Identities = 11/76 (14%), Positives = 21/76 (27%), Gaps = 19/76 (25%)
Query: 115 LYVSGLPKHMTQEDLENLFRPY---GTIITSRILCDKMASENVRSFVSGTPEIPQISKGI 171
+ GLP T ED+ N F L ++ +G
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGK----------------RRGD 57
Query: 172 GFVRFNQHIEAEHAMQ 187
+ + + A++
Sbjct: 58 ALIEMESEQDVQKALE 73
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 43.3 bits (102), Expect = 1e-05
Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 8/78 (10%)
Query: 273 CIFVYNLAPE-TEDNVLWQLFGPFGAVQN----VKVVRDPQTYKCKGFGFVCMTNYDEAV 327
+ + L T + V+ FG + + V P + G FV + A
Sbjct: 25 IVRMRGLPFTATAEEVV-AFFGQHCPITGGKEGILFVTYPDG-RPTGDAFVLFACEEYAQ 82
Query: 328 FAIQSLNGYALGDRLLQV 345
A++ + LG R +++
Sbjct: 83 NALR-KHKDLLGKRYIEL 99
Score = 39.9 bits (93), Expect = 2e-04
Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 6/84 (7%)
Query: 35 PQTMTQEELQHLFSSVGEVESCK---LIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGL 91
P T T EE+ F + K L + G FV + E A+ A + +
Sbjct: 32 PFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNA-LRKHKD 90
Query: 92 KLQNKSIKVSYARPS--SEAIKRA 113
L + I++ + + + + R
Sbjct: 91 LLGKRYIELFRSTAAEVQQVLNRF 114
Score = 37.9 bits (88), Expect = 7e-04
Identities = 14/73 (19%), Positives = 26/73 (35%), Gaps = 12/73 (16%)
Query: 115 LYVSGLPKHMTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFV 174
+ + GLP T E++ F + I + + + R G FV
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR------------PTGDAFV 73
Query: 175 RFNQHIEAEHAMQ 187
F A++A++
Sbjct: 74 LFACEEYAQNALR 86
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 45.6 bits (107), Expect = 2e-05
Identities = 39/244 (15%), Positives = 63/244 (25%), Gaps = 80/244 (32%)
Query: 18 YQSDVN-EQNSNLIVNY-VPQTMTQEELQHLFSS------------VGEVE-------SC 56
YQ D N S+ N + Q EL+ L S V + SC
Sbjct: 207 YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSC 266
Query: 57 K-LI--RDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSSEAIKRA 113
K L+ R K L + + + L K + E +
Sbjct: 267 KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN 326
Query: 114 NLYVSGLP-------------KHMTQEDLEN----------------LFR-----PYGTI 139
+S + KH+ + L +F P
Sbjct: 327 PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH 386
Query: 140 ITSRILC---DKMASENVRSFV--------------SGTPEIPQISKGIGFVRFNQHIEA 182
I + +L + +V V T IP I ++ +E
Sbjct: 387 IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI-----YLELKVKLEN 441
Query: 183 EHAM 186
E+A+
Sbjct: 442 EYAL 445
Score = 44.1 bits (103), Expect = 6e-05
Identities = 36/221 (16%), Positives = 73/221 (33%), Gaps = 55/221 (24%)
Query: 4 HEEMYNTTQSHRSTYQS--DVNEQN--SNLIVNYVP----QTMTQEELQHLFSSVGEVES 55
H M T H+ Y+ V E N V +++EE+ H+ S V
Sbjct: 4 HHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSG 63
Query: 56 CKLIRD--KTTAQSLGYGFV------NY------YRTEDAERAIIELNGL----KLQNKS 97
+ + + + FV NY +TE + +++ + +L N
Sbjct: 64 TLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN-- 121
Query: 98 IKVSYARPSSEAIKRANLYVSGLPKHMT-QEDLENLFRPYGTIITSRIL-----CDK--M 149
++ + N VS L ++ ++ L L RP + ++ K +
Sbjct: 122 --------DNQVFAKYN--VSRLQPYLKLRQALLEL-RPAKNV----LIDGVLGSGKTWV 166
Query: 150 ASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHAMQELN 190
A + S+ ++ I ++ E ++ L
Sbjct: 167 ALDVCLSY----KVQCKMDFKIFWLNLKNCNSPETVLEMLQ 203
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 41.2 bits (96), Expect = 3e-05
Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 7/81 (8%)
Query: 269 GSGWCIFVYNLAPETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVF 328
GS W + + NL + + L L G + + Y +G T +EA
Sbjct: 6 GSSW-LLLKNLTAQIDGPTLRTLCMQHGPLVSF------HPYLNQGIALCKYTTREEANK 58
Query: 329 AIQSLNGYALGDRLLQVSFKT 349
A +LN L + + +
Sbjct: 59 AQMALNNCVLANTTIFAESPS 79
Score = 31.6 bits (71), Expect = 0.075
Identities = 16/78 (20%), Positives = 29/78 (37%), Gaps = 6/78 (7%)
Query: 26 NSNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI 85
+S L++ + + L+ L G + S ++ G Y E+A +A
Sbjct: 7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ------GIALCKYTTREEANKAQ 60
Query: 86 IELNGLKLQNKSIKVSYA 103
+ LN L N +I
Sbjct: 61 MALNNCVLANTTIFAESP 78
>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 40.4 bits (94), Expect = 8e-05
Identities = 14/89 (15%), Positives = 33/89 (37%), Gaps = 11/89 (12%)
Query: 24 EQNSNLIVNYVPQTM-----TQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRT 78
+S LI + T+ + + LF + + + + + S +N+
Sbjct: 3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNP 56
Query: 79 EDAERAIIELNGLKLQNKSIKVSYARPSS 107
A A + L+ + K +K+ +A+
Sbjct: 57 LSAADARLRLHKTEFLGKEMKLYFAQTLH 85
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 42.7 bits (100), Expect = 2e-04
Identities = 56/322 (17%), Positives = 106/322 (32%), Gaps = 85/322 (26%)
Query: 10 TTQSHRSTYQSDVNEQNSNLIV---------NYVPQTMTQEELQHLFSS----VGE-VES 55
+ S V E N+ L+ +Y EEL+ L+ + VG+ ++
Sbjct: 137 FDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYF------EELRDLYQTYHVLVGDLIKF 190
Query: 56 C-----KLIRDKTTAQSL---GYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSYARPSS 107
+LIR A+ + G + + L SI +S P
Sbjct: 191 SAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLL-------SIPISC--PLI 241
Query: 108 EAIKRANLYVSGLPKHMTQEDLENLFRPYGT------IITSRILCDKMASENVRSFVSGT 161
I+ A+ V+ T +L + + G ++T+ + +++ SF
Sbjct: 242 GVIQLAHYVVTAKLLGFTPGELRSYLK--GATGHSQGLVTAVAIA---ETDSWESFFVSV 296
Query: 162 PEIPQISKGIGFVRFNQ---HIEAEHAMQELNGTIPEGASEP-ITVKFANSPAGRAKALA 217
+ + IG VR + + ++ E + EG P +++ N + +
Sbjct: 297 RKAITVLFFIG-VRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSIS--NLTQEQVQDYV 353
Query: 218 ANLNAQAAAMRHFAAAMRHFGNPLHHSARFKFAPLTADLLNNSMLPPKSLHGSGWCIFVY 277
N+ A + + L + A+ ++ PP+SL+G
Sbjct: 354 NKTNSHLPAGKQVEIS-------LVNGAK-NLV-VSG--------PPQSLYG-----LNL 391
Query: 278 NL----APETEDNVLWQLFGPF 295
L AP D Q PF
Sbjct: 392 TLRKAKAPSGLD----QSRIPF 409
Score = 30.0 bits (67), Expect = 1.5
Identities = 28/145 (19%), Positives = 43/145 (29%), Gaps = 61/145 (42%)
Query: 14 HRSTYQSDVNEQNSNLIVNY-----VPQTM----TQEELQHLFSSVGE-----VESCKLI 59
+R ++ NY P + +QE LQ++ VG+ VE I
Sbjct: 1788 YRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVE----I 1843
Query: 60 RDKTTAQSLGYGFVNY------Y----RTEDAERAIIELNGLKLQNKSIKVSYARPSSEA 109
VNY Y + LN +KLQ
Sbjct: 1844 -------------VNYNVENQQYVAAGDLRALDTVTNVLNFIKLQK-------------- 1876
Query: 110 IKRANLYVSGLPKHMTQEDL-ENLF 133
I L S ++ E++ +LF
Sbjct: 1877 IDIIELQKS-----LSLEEVEGHLF 1896
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 39.5 bits (92), Expect = 2e-04
Identities = 14/87 (16%), Positives = 30/87 (34%), Gaps = 8/87 (9%)
Query: 30 IVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAI--IE 87
+ N + + L G++++ L+R K F+ EDA +
Sbjct: 30 LSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK------SQAFIEMETREDAMAMVDHCL 83
Query: 88 LNGLKLQNKSIKVSYARPSSEAIKRAN 114
L Q + +KV + + + +
Sbjct: 84 KKALWFQGRCVKVDLSEKYKKLVSGPS 110
Score = 38.4 bits (89), Expect = 5e-04
Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 9/81 (11%)
Query: 274 IFVYNL-APETEDNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ- 331
I + NL D+ + +L P+G ++N ++R K F+ M ++A+ +
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDH 81
Query: 332 -SLNGYALGDRLLQVSFKTHK 351
R ++V
Sbjct: 82 CLKKALWFQGRCVKVDLSEKY 102
Score = 37.2 bits (86), Expect = 0.001
Identities = 12/95 (12%), Positives = 24/95 (25%), Gaps = 22/95 (23%)
Query: 115 LYVSGLPKH-MTQEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+++S LP + + L PYG I ++ K F
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM---------------------RMKSQAF 66
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
+ +A + + V +
Sbjct: 67 IEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEK 101
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 38.2 bits (89), Expect = 4e-04
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 40 QEELQHLFSSVGEVESCKLIR--DKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKS 97
E+++ S G V+S ++ R D G FV + D ++A+ L G K N+
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRV 88
Query: 98 IKVSY 102
+ Y
Sbjct: 89 VVTKY 93
Score = 38.2 bits (89), Expect = 5e-04
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 2/55 (3%)
Query: 295 FGAVQNVKVVRDPQ--TYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
+G V+++++ R G FV T+ + A+Q L G +R++ +
Sbjct: 39 YGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 93
Score = 32.5 bits (74), Expect = 0.045
Identities = 14/66 (21%), Positives = 21/66 (31%), Gaps = 13/66 (19%)
Query: 126 QEDLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGFVRFNQHIEAEHA 185
ED+ + YG + I + + G FV F + + A
Sbjct: 29 VEDVRDECSKYGLVK--SIEIPRP-----------VDGVEVPGCGKIFVEFTSVFDCQKA 75
Query: 186 MQELNG 191
MQ L G
Sbjct: 76 MQGLTG 81
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 39.0 bits (90), Expect = 0.001
Identities = 20/105 (19%), Positives = 45/105 (42%), Gaps = 14/105 (13%)
Query: 38 MTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKL---- 93
+++ +L + G V++ + +K Y F Y TE+++RA + LNG ++
Sbjct: 32 VSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTLNGKEVVDDL 85
Query: 94 -QNKSIKVSYARPSSEAIKRANLYVSGL---PKHMTQEDLENLFR 134
Q ++ +++ R GL + ++ E+ + L
Sbjct: 86 GQKITLYLNFVEKVQWKELRPQALPPGLMVVEEIISSEEEKMLLE 130
Score = 31.7 bits (71), Expect = 0.31
Identities = 13/86 (15%), Positives = 27/86 (31%), Gaps = 11/86 (12%)
Query: 274 IFVYNLAPETE--DNVLWQLFGPFGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQ 331
+ V N N L + G V + + + K + F +E+ A
Sbjct: 21 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYV 74
Query: 332 SLNG---YALGDRLLQVSFKTHKPLP 354
+LNG + + + + +
Sbjct: 75 TLNGKEVVDDLGQKITLYLNFVEKVQ 100
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 36.6 bits (85), Expect = 0.002
Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 4/66 (6%)
Query: 40 QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIK 99
+E+L+ S G++ L G V++ E+A+ I L+G + I
Sbjct: 40 REDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 95
Query: 100 VSYARP 105
Sbjct: 96 AQAWDG 101
Score = 35.1 bits (81), Expect = 0.007
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 295 FGAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
FG ++ + + G V + +EA + IQ+L+G G R +
Sbjct: 50 FGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 98
Score = 28.5 bits (64), Expect = 1.3
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 168 SKGIGFVRFNQHIEAEHAMQELNG 191
G+ V F EA++ +Q L+G
Sbjct: 63 PDGVASVSFRDPEEADYCIQTLDG 86
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 36.3 bits (84), Expect = 0.003
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 4/57 (7%)
Query: 295 FGAVQNVKVVRDPQTYKCKGFG----FVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
FGAV V + ++ Q + FV + E AIQ+LNG R +
Sbjct: 49 FGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105
Score = 35.9 bits (83), Expect = 0.004
Identities = 10/56 (17%), Positives = 21/56 (37%), Gaps = 4/56 (7%)
Query: 51 GEVESCKLIR----DKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVSY 102
G V + + ++ A+ + FV + + +AI LNG + +
Sbjct: 50 GAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105
Score = 28.2 bits (63), Expect = 2.0
Identities = 10/34 (29%), Positives = 12/34 (35%)
Query: 158 VSGTPEIPQISKGIGFVRFNQHIEAEHAMQELNG 191
E FV F+ E A+Q LNG
Sbjct: 60 EKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG 93
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint
center for struc genomics, JCSG, protein structure
initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus
musculus} PDB: 2lq5_A
Length = 114
Score = 34.6 bits (80), Expect = 0.009
Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 14/85 (16%)
Query: 273 CIFVYNL-APETEDNVLWQL---------FGPFGAVQNVKVVRDPQTYKCKGFGFVCMTN 322
C + N+ P+TE+ V W G V ++ V ++ G +V +
Sbjct: 9 CFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQ----GNVYVKCPS 64
Query: 323 YDEAVFAIQSLNGYALGDRLLQVSF 347
A+ A+ +L+G +++ ++
Sbjct: 65 IAAAIAAVNALHGRWFAGKMITAAY 89
Score = 33.1 bits (76), Expect = 0.036
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 4/63 (6%)
Query: 40 QEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIK 99
++++ + G V + DK +AQ G +V A A+ L+G K I
Sbjct: 31 KDDVIEECNKHGGVIHIYV--DKNSAQ--GNVYVKCPSIAAAIAAVNALHGRWFAGKMIT 86
Query: 100 VSY 102
+Y
Sbjct: 87 AAY 89
Score = 26.9 bits (60), Expect = 5.2
Identities = 7/30 (23%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 163 EIPQISK-GIGFVRFNQHIEAEHAMQELNG 191
+ + S G +V+ A A+ L+G
Sbjct: 48 YVDKNSAQGNVYVKCPSIAAAIAAVNALHG 77
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 32.1 bits (73), Expect = 0.054
Identities = 13/95 (13%), Positives = 25/95 (26%), Gaps = 22/95 (23%)
Query: 115 LYVSGLPKHMTQE-DLENLFRPYGTIITSRILCDKMASENVRSFVSGTPEIPQISKGIGF 173
+++ + L L P+G I IL F
Sbjct: 18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL---------------------NKINEAF 56
Query: 174 VRFNQHIEAEHAMQELNGTIPEGASEPITVKFANS 208
+ +A+ A+ T +P+ V +
Sbjct: 57 IEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQK 91
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 32.1 bits (73), Expect = 0.057
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 1/54 (1%)
Query: 295 FGAVQNVKVVRDPQTYKC-KGFGFVCMTNYDEAVFAIQSLNGYALGDRLLQVSF 347
+G V + P F+ + A+ A+ LNG G R+++ F
Sbjct: 37 YGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACF 90
Score = 31.7 bits (72), Expect = 0.093
Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 1/64 (1%)
Query: 40 QEELQHLFSSVGEVESCKLIRDK-TTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSI 98
+ E + G+V C + F+ + R E A +A+++LNG + +
Sbjct: 27 EVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV 86
Query: 99 KVSY 102
K +
Sbjct: 87 KACF 90
>2c42_A Pyruvate-ferredoxin oxidoreductase; 4Fe-4S, iron, iron-sulfur,
iron-sulfur cluster, pyruvate catabolism, TPP-dependent
enzyme; HET: TPP; 1.78A {Desulfovibrio africanus} SCOP:
c.36.1.8 c.36.1.12 c.48.1.3 c.64.1.1 d.58.1.5 PDB:
1b0p_A* 1kek_A* 2c3o_A* 2c3p_A* 2c3u_A* 2c3y_A* 2c3m_A*
2pda_A* 2uza_A*
Length = 1231
Score = 34.1 bits (78), Expect = 0.088
Identities = 17/59 (28%), Positives = 20/59 (33%), Gaps = 15/59 (25%)
Query: 70 YGFVNYYRTEDAERAII--------------ELNGLKLQNKSIKVSYARP-SSEAIKRA 113
Y +Y DAER I+ L + IKV RP SEA A
Sbjct: 257 YKLFDYVGAPDAERVIVSMGSSCETIEEVINHLAAKGEKIGLIKVRLYRPFVSEAFFAA 315
>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, PARN, structural genomics; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*
Length = 100
Score = 29.7 bits (66), Expect = 0.44
Identities = 12/34 (35%), Positives = 15/34 (44%)
Query: 111 KRANLYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
KR ++ PK DL LF +G I S I
Sbjct: 14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI 47
>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle
structural genomics center for infectious electron
transport, iron; NMR {Mycobacterium tuberculosis}
Length = 81
Score = 29.3 bits (66), Expect = 0.46
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 4/32 (12%)
Query: 296 GAVQNVKVVRDPQTYKCKGFGFVCMTNYDEAV 327
Q + D + ++C GF YDEA+
Sbjct: 14 AQTQGPGSMNDYKLFRCIQCGFE----YDEAL 41
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 29.5 bits (66), Expect = 0.56
Identities = 16/92 (17%), Positives = 28/92 (30%), Gaps = 19/92 (20%)
Query: 269 GSGWCIFVYNLAPETEDNVLWQLFGPF-----GAVQNVKVVRDPQTYKCKGFGFVCMTNY 323
G + V L P D +L F G V + + + G +
Sbjct: 6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREP 57
Query: 324 DEAVFAIQSLNGYALGDRLLQVSFKTHKPLPP 355
+A + + + L L + +P PP
Sbjct: 58 ADAERVLAQAD-HELHGAQLSL-----RPAPP 83
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 28.9 bits (64), Expect = 0.78
Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 10/85 (11%)
Query: 27 SNLIVNYVPQTMTQEELQHLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTEDAERAII 86
NL N ++++ L+ L + G K + + + + + AERA
Sbjct: 15 YNLPANKDGKSVSNR-LRRLSDNCG---------GKVLSITGCSAILRFINQDSAERAQK 64
Query: 87 ELNGLKLQNKSIKVSYARPSSEAIK 111
+ + I VS+ + E +
Sbjct: 65 RMENEDVFGNRIIVSFTPKNRELCE 89
Score = 28.9 bits (64), Expect = 0.78
Identities = 10/45 (22%), Positives = 14/45 (31%), Gaps = 2/45 (4%)
Query: 166 QISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPITVKFANSPA 210
I+ +RF AE A + + G I V F
Sbjct: 43 SITGCSAILRFINQDSAERAQKRMENEDVFG--NRIIVSFTPKNR 85
>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP,
M7GTP, RNA recognition motif, RRM, cytoplasm,
exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo
sapiens}
Length = 101
Score = 28.8 bits (64), Expect = 0.85
Identities = 10/35 (28%), Positives = 14/35 (40%)
Query: 110 IKRANLYVSGLPKHMTQEDLENLFRPYGTIITSRI 144
+ ++ PK DL LF +G I S I
Sbjct: 3 LGSDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI 37
>1ja9_A 4HNR, 1,3,6,8-tetrahydroxynaphthalene reductase;
protein-NADPH-active site inhibitor complex,
oxidoreductase, chain dehydrogenase; HET: NDP PYQ; 1.50A
{Magnaporthe grisea} SCOP: c.2.1.2
Length = 274
Score = 29.5 bits (67), Expect = 1.6
Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 194 PEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFG 238
+ A E V + A+ A+++ + + F A+ HFG
Sbjct: 56 SKAAEE--VVAELKKLGAQGVAIQADISKPSEVVALFDKAVSHFG 98
>3u5t_A 3-oxoacyl-[acyl-carrier-protein] reductase; structural genomics,
PSI-biology, NEW YORK structural genomi research
consortium, nysgrc; 2.40A {Sinorhizobium meliloti}
Length = 267
Score = 29.4 bits (67), Expect = 1.7
Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 194 PEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFG 238
A E + G+A A+++ AA R FA A FG
Sbjct: 62 AAAAEE--VAGKIEAAGGKALTAQADVSDPAAVRRLFATAEEAFG 104
>3is3_A 17BETA-hydroxysteroid dehydrogenase; short chain dehydrogenase/REDU
SDR, fungi, oxidoreductase; HET: GOL; 1.48A
{Cochliobolus lunatus} PDB: 3qwf_A* 3qwh_A* 3qwi_A*
3itd_A
Length = 270
Score = 28.7 bits (65), Expect = 2.3
Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 194 PEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFG 238
+ A + V + A A+ A++ ++ F A+ HFG
Sbjct: 53 TKDAEK--VVSEIKALGSDAIAIKADIRQVPEIVKLFDQAVAHFG 95
>3ksu_A 3-oxoacyl-acyl carrier protein reductase; structural genomics,
PSI-2, dehydrogenase, protein structure initiative;
2.30A {Oenococcus oeni psu-1}
Length = 262
Score = 28.6 bits (65), Expect = 2.6
Identities = 6/45 (13%), Positives = 16/45 (35%), Gaps = 2/45 (4%)
Query: 194 PEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFG 238
+ A++ + ++L+ + + F A + FG
Sbjct: 48 SDTANK--LKDELEDQGAKVALYQSDLSNEEEVAKLFDFAEKEFG 90
>3v2g_A 3-oxoacyl-[acyl-carrier-protein] reductase; structural genomics,
PSI-biology, protein structure initiati nysgrc; 2.30A
{Sinorhizobium meliloti}
Length = 271
Score = 28.7 bits (65), Expect = 2.8
Identities = 7/28 (25%), Positives = 11/28 (39%)
Query: 211 GRAKALAANLNAQAAAMRHFAAAMRHFG 238
GRA A+ A+ A + + G
Sbjct: 81 GRAVAIRADNRDAEAIEQAIRETVEALG 108
>3zxs_A Cryptochrome B, rscryb; lyase, cryPro, lumazine,
iron-sulfur-cluster; HET: FAD DLZ; 2.70A {Rhodobacter
sphaeroides}
Length = 522
Score = 29.0 bits (65), Expect = 2.8
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 225 AAMRHFAAAMRHFGNPLHH 243
AAMR FA ++ G + +
Sbjct: 67 AAMRKFARRLQERGFRVAY 85
>1g0o_A Trihydroxynaphthalene reductase; protein-NADPH-active site
inhibitor complex, dinucleotide binding fold,
oxidoreductase; HET: NDP PYQ; 1.70A {Magnaporthe grisea}
SCOP: c.2.1.2 PDB: 1doh_A* 1g0n_A* 1ybv_A*
Length = 283
Score = 28.7 bits (65), Expect = 3.1
Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 2/45 (4%)
Query: 194 PEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFG 238
E A E V A + AN+ +R F A++ FG
Sbjct: 64 TESAEE--VVAAIKKNGSDAACVKANVGVVEDIVRMFEEAVKIFG 106
>4e3z_A Putative oxidoreductase protein; PSI-biology, structural genomics,
protein structure initiati nysgrc,oxidoreductase; 2.00A
{Rhizobium etli}
Length = 272
Score = 28.3 bits (64), Expect = 3.2
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 211 GRAKALAANLNAQAAAMRHFAAAMRHFG 238
G A A+ ++ A F+A R FG
Sbjct: 76 GEAVAIPGDVGNAADIAAMFSAVDRQFG 103
>3cam_A Cold-shock domain family protein; cold shock protein, chain SWAP,
STRU genomics, oxford protein production facility, OPPF,
gene RE; 2.60A {Neisseria meningitidis MC58}
Length = 67
Score = 26.4 bits (59), Expect = 3.4
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 5/28 (17%)
Query: 313 KGFGFVCMTNYDEAVF----AIQSLNGY 336
KGFGF+ E +F AI G+
Sbjct: 13 KGFGFITPDEGGEDLFAHFSAINM-EGF 39
>2x31_A Magnesium-chelatase 60 kDa subunit; ligase, bacteriochlorophyll
biosynthesis, photosynthesis; 7.50A {Rhodobacter
capsulatus}
Length = 189
Score = 28.0 bits (62), Expect = 4.0
Identities = 14/77 (18%), Positives = 26/77 (33%), Gaps = 3/77 (3%)
Query: 160 GTPEIPQISKGIGFVRFNQHIEAEHAMQELNGTIPEGASEPIT---VKFANSPAGRAKAL 216
TP I ++ G G + + E A ++ + + + A P L
Sbjct: 101 MTPTIALLTDGRGNIALDGTANRELAGEQATKVARAIRASGMPAVIIDTAMRPNPALVDL 160
Query: 217 AANLNAQAAAMRHFAAA 233
A ++A A+ A
Sbjct: 161 ARTMDAHYIALPRATAH 177
>1i39_A Ribonuclease HII, RNAse HII; mixed beta sheet, helix-loop-helix,
hydrolase; 1.95A {Archaeoglobus fulgidus} SCOP: c.55.3.1
PDB: 1i3a_A 3p83_D*
Length = 225
Score = 28.0 bits (63), Expect = 4.4
Identities = 3/33 (9%), Positives = 11/33 (33%), Gaps = 3/33 (9%)
Query: 229 HFAAAMRHFGNPLHHSARFKFAPLTADLLNNSM 261
+ P R ++ + ++L ++
Sbjct: 193 VLKEWIASGRIPSCV--RMRWKTV-SNLRQKTL 222
>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA
binding protein; NMR {Saccharomyces cerevisiae}
Length = 117
Score = 26.6 bits (58), Expect = 5.7
Identities = 14/101 (13%), Positives = 37/101 (36%), Gaps = 12/101 (11%)
Query: 7 MYNTTQSHRSTYQSDVNEQNSNLIVNY-VPQTMTQEELQHLFS-----SVGEVESCKLIR 60
M+ + S +++ LI + + ++ + + ++ L+
Sbjct: 1 MFLERNEVKRLLASRNSKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVS 60
Query: 61 DKTTAQSLGYGFVNYYRTEDAERAIIELNGLKLQNKSIKVS 101
D A + + ++ A + ++ LNG + Q K I+
Sbjct: 61 DFNGA------IIIFRDSKFAAKMLMILNGSQFQGKVIRSG 95
>3gem_A Short chain dehydrogenase; structural genomics, APC65077,
oxidoreductase, PSI-2, protein structure initiative;
1.83A {Pseudomonas syringae PV}
Length = 260
Score = 27.5 bits (62), Expect = 5.9
Identities = 4/29 (13%), Positives = 7/29 (24%)
Query: 210 AGRAKALAANLNAQAAAMRHFAAAMRHFG 238
A AL + + + M
Sbjct: 70 QAGAVALYGDFSCETGIMAFIDLLKTQTS 98
>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural
genomics, PSI-2, prote structure initiative; HET: ATP;
2.20A {Chlorobium tepidum}
Length = 245
Score = 27.6 bits (62), Expect = 6.4
Identities = 5/43 (11%), Positives = 12/43 (27%), Gaps = 10/43 (23%)
Query: 188 ELNGTIPEGAS---------EPITVKFANSPAGRA-KALAANL 220
++ IP+ + + S + A +L
Sbjct: 200 PISKRIPQDEDAMQESLLSGQSVLKVAPKSQLSKTIVDWALHL 242
>3lf2_A Short chain oxidoreductase Q9HYA2; SDR, SCOR, rossmann fold; HET:
NAP; 2.30A {Pseudomonas aeruginosa} PDB: 3lf1_A*
Length = 265
Score = 27.5 bits (62), Expect = 6.8
Identities = 7/50 (14%), Positives = 10/50 (20%)
Query: 189 LNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFG 238
E + P R A ++ A R G
Sbjct: 37 FCARDGERLRAAESALRQRFPGARLFASVCDVLDALQVRAFAEACERTLG 86
>3pk0_A Short-chain dehydrogenase/reductase SDR; ssgcid, structural
genomics, seattle structural genomics CEN infectious
disease; 1.75A {Mycobacterium smegmatis}
Length = 262
Score = 27.5 bits (62), Expect = 6.9
Identities = 6/50 (12%), Positives = 15/50 (30%), Gaps = 1/50 (2%)
Query: 189 LNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFG 238
+ G +G+ + +++ +A A+ FG
Sbjct: 39 VAGRSTADIDA-CVADLDQLGSGKVIGVQTDVSDRAQCDALAGRAVEEFG 87
>3rih_A Short chain dehydrogenase or reductase; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; HET: PG5; 2.15A {Mycobacterium
abscessus}
Length = 293
Score = 27.6 bits (62), Expect = 7.1
Identities = 7/50 (14%), Positives = 16/50 (32%), Gaps = 1/50 (2%)
Query: 189 LNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFG 238
+ P S +T + AG + +++ + + FG
Sbjct: 70 VAARSPRELSS-VTAELGELGAGNVIGVRLDVSDPGSCADAARTVVDAFG 118
>2rhc_B Actinorhodin polyketide ketoreductase; oxidoreductase,
combinatorial biosynthesis, short chain
dehydrogenase/reductase; HET: NAP EMO; 2.10A
{Streptomyces coelicolor} SCOP: c.2.1.2 PDB: 2rh4_A*
1w4z_A* 3csd_B* 3qrw_A* 3ri3_B* 2rhr_B* 1x7g_A* 1x7h_A*
1xr3_A*
Length = 277
Score = 27.2 bits (61), Expect = 7.2
Identities = 8/50 (16%), Positives = 15/50 (30%), Gaps = 2/50 (4%)
Query: 189 LNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFG 238
+ EG T+K A ++ + AA + +G
Sbjct: 51 VCARGEEGLRT--TLKELREAGVEADGRTCDVRSVPEIEALVAAVVERYG 98
>1wuc_A Bouganin; alpha-beta protein; 1.80A {Bougainvillea spectabilis}
PDB: 3ctk_A
Length = 250
Score = 27.4 bits (60), Expect = 7.8
Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 4/72 (5%)
Query: 45 HLFSSVGEVESCKLIRDKTTAQSLGYGFVNYYRTE---DAERAIIELNGLKLQNKSIKVS 101
V V + KL T +L + +Y + +R +EL KL+ +
Sbjct: 87 VFLDKVPTVATSKLFPGVTNRVTLTFDG-SYQKLVNAAKVDRKDLELGVYKLEFSIEAIH 145
Query: 102 YARPSSEAIKRA 113
+ + I +
Sbjct: 146 GKTINGQEIAKF 157
>1x1t_A D(-)-3-hydroxybutyrate dehydrogenase; NAD, NADH, SDR, short chain
dehydrogenase, ketone BODY, beta hydroxybutyrate,
oxidoreductase; HET: NAD; 1.52A {Pseudomonas fragi}
SCOP: c.2.1.2 PDB: 1wmb_A* 2ztl_A* 2ztv_A* 2ztm_A*
2ztu_A* 2yz7_A 2zea_A* 3eew_A* 3vdq_A* 3vdr_A*
Length = 260
Score = 27.2 bits (61), Expect = 8.0
Identities = 11/50 (22%), Positives = 16/50 (32%)
Query: 189 LNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFG 238
LNG E + A + A+L+ A A+R G
Sbjct: 33 LNGFGDAAEIEKVRAGLAAQHGVKVLYDGADLSKGEAVRGLVDNAVRQMG 82
>3edm_A Short chain dehydrogenase; structural genomics, oxidoreductase,
PSI-2, P structure initiative; 2.30A {Agrobacterium
tumefaciens str}
Length = 259
Score = 27.1 bits (61), Expect = 8.3
Identities = 9/28 (32%), Positives = 12/28 (42%)
Query: 211 GRAKALAANLNAQAAAMRHFAAAMRHFG 238
A A+ A+L A +AA FG
Sbjct: 58 RSALAIKADLTNAAEVEAAISAAADKFG 85
>3afn_B Carbonyl reductase; alpha/beta/alpha, rossmann-fold,
oxidoreductase; HET: NAP; 1.63A {Sphingomonas SP} PDB:
3afm_A*
Length = 258
Score = 27.1 bits (61), Expect = 9.0
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 2/45 (4%)
Query: 194 PEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFG 238
P E T+ + G A AA+L A + + FG
Sbjct: 42 PANIDE--TIASMRADGGDAAFFAADLATSEACQQLVDEFVAKFG 84
>3sju_A Keto reductase; short-chain dehydrogenase, oxidoreductase; HET:
NDP; 2.40A {Streptomyces griseoruber}
Length = 279
Score = 26.8 bits (60), Expect = 9.6
Identities = 7/52 (13%), Positives = 14/52 (26%), Gaps = 2/52 (3%)
Query: 189 LNGTIPEGASEPITVKFANSPAGRAKALAANLNAQAAAMRHFAAAMRHFGNP 240
+ S V + + ++ + AAA+ FG
Sbjct: 53 GCARDAKNVSA--AVDGLRAAGHDVDGSSCDVTSTDEVHAAVAAAVERFGPI 102
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.318 0.132 0.388
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,348,063
Number of extensions: 318641
Number of successful extensions: 1929
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1430
Number of HSP's successfully gapped: 606
Length of query: 356
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 261
Effective length of database: 4,049,298
Effective search space: 1056866778
Effective search space used: 1056866778
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.1 bits)