BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 015870
(399 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 245 bits (626), Expect = 3e-65, Method: Compositional matrix adjust.
Identities = 111/177 (62%), Positives = 144/177 (81%), Gaps = 1/177 (0%)
Query: 21 FGTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAAR 80
+ SLYVGDL +VT++ LY+ F+ G ++S+RVCRD+ TRRSLGY YVNF +A R
Sbjct: 8 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 67
Query: 81 ALEMLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILS 140
AL+ +NF + GKP+R+M+S RDPSLRKSG GNIFIKNLDK+ID+KAL+DTFSAFGNILS
Sbjct: 68 ALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 127
Query: 141 CKVATDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYVGHFLRKQERDTEI 197
CKV D NG SKGYGFV F+ +E+A++AIEK+NGMLLND++V+VG F ++ER+ E+
Sbjct: 128 CKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 183
Score = 106 bits (265), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 60/187 (32%), Positives = 104/187 (55%), Gaps = 6/187 (3%)
Query: 103 DPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDN 161
+PS ++++ +L + L++ FS G ILS +V D+ +S GY +V F
Sbjct: 2 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 61
Query: 162 EESAQKAIEKLNGMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQK 221
A++A++ +N ++ K V + +RD + KS N+++KNL +S + L
Sbjct: 62 PADAERALDTMNFDVIKGKPVRIMW----SQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 117
Query: 222 SFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALNGKKFDDKEWYVGKAQKK 281
+F +G I S V+ D +G SK +GFV+FE + A RA+E +NG +D++ +VG+ + +
Sbjct: 118 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 176
Query: 282 SERELEL 288
ERE EL
Sbjct: 177 KEREAEL 183
Score = 94.0 bits (232), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 66/190 (34%), Positives = 100/190 (52%), Gaps = 18/190 (9%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE 261
++YV +L TE L + F G I S V RD +S + +VNF+ DA RA++
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 70
Query: 262 ALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEK 321
+N K + S+R+ L+ K N++IKNLD SID++
Sbjct: 71 TMNFDVIKGKPVRI----MWSQRDPSLR------------KSGVGNIFIKNLDKSIDNKA 114
Query: 322 LKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMNGKMVVSKPLYVALA 381
L FS FG+I SCKV+ D +G S+G GFV F T E A RA+ +MNG ++ + ++V
Sbjct: 115 LYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 173
Query: 382 QRKEDRRARL 391
+ +++R A L
Sbjct: 174 KSRKEREAEL 183
Score = 55.1 bits (131), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 33/96 (34%), Positives = 50/96 (52%), Gaps = 5/96 (5%)
Query: 296 MKEAADKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISR---GSGFVA 352
M +A + A+LY+ +L + + L + FSP G I S +V RD I+R G +V
Sbjct: 1 MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRD--MITRRSLGYAYVN 58
Query: 353 FSTPEEASRALLEMNGKMVVSKPLYVALAQRKEDRR 388
F P +A RAL MN ++ KP+ + +QR R
Sbjct: 59 FQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLR 94
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 245 bits (625), Expect = 4e-65, Method: Compositional matrix adjust.
Identities = 111/177 (62%), Positives = 144/177 (81%), Gaps = 1/177 (0%)
Query: 21 FGTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAAR 80
+ SLYVGDL +VT++ LY+ F+ G ++S+RVCRD+ TRRSLGY YVNF +A R
Sbjct: 13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72
Query: 81 ALEMLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILS 140
AL+ +NF + GKP+R+M+S RDPSLRKSG GNIFIKNLDK+ID+KAL+DTFSAFGNILS
Sbjct: 73 ALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 132
Query: 141 CKVATDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYVGHFLRKQERDTEI 197
CKV D NG SKGYGFV F+ +E+A++AIEK+NGMLLND++V+VG F ++ER+ E+
Sbjct: 133 CKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAEL 188
Score = 106 bits (265), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 60/187 (32%), Positives = 104/187 (55%), Gaps = 6/187 (3%)
Query: 103 DPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDN 161
+PS ++++ +L + L++ FS G ILS +V D+ +S GY +V F
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 162 EESAQKAIEKLNGMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQK 221
A++A++ +N ++ K V + +RD + KS N+++KNL +S + L
Sbjct: 67 PADAERALDTMNFDVIKGKPVRI----MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYD 122
Query: 222 SFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALNGKKFDDKEWYVGKAQKK 281
+F +G I S V+ D +G SK +GFV+FE + A RA+E +NG +D++ +VG+ + +
Sbjct: 123 TFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 181
Query: 282 SERELEL 288
ERE EL
Sbjct: 182 KEREAEL 188
Score = 93.6 bits (231), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 66/190 (34%), Positives = 100/190 (52%), Gaps = 18/190 (9%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE 261
++YV +L TE L + F G I S V RD +S + +VNF+ DA RA++
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 75
Query: 262 ALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEK 321
+N K + S+R+ L+ K N++IKNLD SID++
Sbjct: 76 TMNFDVIKGKPVRI----MWSQRDPSLR------------KSGVGNIFIKNLDKSIDNKA 119
Query: 322 LKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMNGKMVVSKPLYVALA 381
L FS FG+I SCKV+ D +G S+G GFV F T E A RA+ +MNG ++ + ++V
Sbjct: 120 LYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF 178
Query: 382 QRKEDRRARL 391
+ +++R A L
Sbjct: 179 KSRKEREAEL 188
Score = 55.5 bits (132), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 33/97 (34%), Positives = 51/97 (52%), Gaps = 5/97 (5%)
Query: 295 NMKEAADKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISR---GSGFV 351
+M +A + A+LY+ +L + + L + FSP G I S +V RD I+R G +V
Sbjct: 5 SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRD--MITRRSLGYAYV 62
Query: 352 AFSTPEEASRALLEMNGKMVVSKPLYVALAQRKEDRR 388
F P +A RAL MN ++ KP+ + +QR R
Sbjct: 63 NFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLR 99
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 144 bits (363), Expect = 8e-35, Method: Compositional matrix adjust.
Identities = 69/108 (63%), Positives = 89/108 (82%), Gaps = 3/108 (2%)
Query: 110 GAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAI 169
G+GNIFIKNLDK+ID+KAL+DTFSAFGNILSCKV D NG SKGYGFV F+ +E+A++AI
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAI 62
Query: 170 EKLNGMLLNDKQVYVGHFLRKQERDTEIN--KSKFTNVYVKNLSESTT 215
EK+NGMLLND++V+VG F ++ER+ E+ +FTNVY+KN +T
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGST 110
Score = 76.6 bits (187), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 39/86 (45%), Positives = 58/86 (67%), Gaps = 1/86 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLE 365
N++IKNLD SID++ L FS FG+I SCKV+ D +G S+G GFV F T E A RA+ +
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEK 64
Query: 366 MNGKMVVSKPLYVALAQRKEDRRARL 391
MNG ++ + ++V + +++R A L
Sbjct: 65 MNGMLLNDRKVFVGRFKSRKEREAEL 90
Score = 68.9 bits (167), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 41/110 (37%), Positives = 65/110 (59%), Gaps = 11/110 (10%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEAL 263
N+++KNL +S + L +F +G I S V+ D +G SK +GFV+FE + A RA+E +
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 264 NGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNL 313
NG +D++ +VG+ + + ERE EL + A +F N+YIKN
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELGAR--------AKEF--TNVYIKNF 105
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 57/105 (54%), Gaps = 8/105 (7%)
Query: 21 FGTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAAR 80
G+ ++++ +L+ ++ + LYD F+ G ++S +V D + S GYG+V+F + A R
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAER 60
Query: 81 ALEMLNFTPLNGKPIRV-MYSHRDPSLRKSGA-----GNIFIKNL 119
A+E +N LN + + V + R + GA N++IKN
Sbjct: 61 AIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNF 105
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 144 bits (363), Expect = 8e-35, Method: Compositional matrix adjust.
Identities = 68/94 (72%), Positives = 83/94 (88%), Gaps = 1/94 (1%)
Query: 103 DPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNE 162
DPSLRKSG GNIFIKNLDK+ID+KAL+DTFSAFGNILSCKV D NG SKGYGFV F+ +
Sbjct: 3 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQ 61
Query: 163 ESAQKAIEKLNGMLLNDKQVYVGHFLRKQERDTE 196
E+A++AIEK+NGMLLND++V+VG F ++ER+ E
Sbjct: 62 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 95
Score = 75.5 bits (184), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 38/84 (45%), Positives = 57/84 (67%), Gaps = 1/84 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLE 365
N++IKNLD SID++ L FS FG+I SCKV+ D +G S+G GFV F T E A RA+ +
Sbjct: 12 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEK 70
Query: 366 MNGKMVVSKPLYVALAQRKEDRRA 389
MNG ++ + ++V + +++R A
Sbjct: 71 MNGMLLNDRKVFVGRFKSRKEREA 94
Score = 68.9 bits (167), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 36/94 (38%), Positives = 58/94 (61%), Gaps = 1/94 (1%)
Query: 194 DTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENS 253
D + KS N+++KNL +S + L +F +G I S V+ D +G SK +GFV+FE
Sbjct: 3 DPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQ 61
Query: 254 DDAARAVEALNGKKFDDKEWYVGKAQKKSERELE 287
+ A RA+E +NG +D++ +VG+ + + ERE E
Sbjct: 62 EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAE 95
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 45/76 (59%), Gaps = 2/76 (2%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G ++++ +L+ ++ + LYD F+ G ++S +V D + S GYG+V+F + A RA
Sbjct: 10 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERA 67
Query: 82 LEMLNFTPLNGKPIRV 97
+E +N LN + + V
Sbjct: 68 IEKMNGMLLNDRKVFV 83
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 122 bits (307), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 56/88 (63%), Positives = 75/88 (85%), Gaps = 1/88 (1%)
Query: 302 KFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASR 361
++Q NLY+KNLDD IDDE+L++ FSPFG+ITS KVM + G S+G GFV FS+PEEA++
Sbjct: 12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATK 70
Query: 362 ALLEMNGKMVVSKPLYVALAQRKEDRRA 389
A+ EMNG++V +KPLYVALAQRKE+R++
Sbjct: 71 AVTEMNGRIVATKPLYVALAQRKEERQS 98
Score = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 41/89 (46%), Positives = 59/89 (66%), Gaps = 1/89 (1%)
Query: 197 INKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDA 256
I + + N+YVKNL + +E L+K+F +GTITSA VM +G G+SK FGFV F + ++A
Sbjct: 10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEA 68
Query: 257 ARAVEALNGKKFDDKEWYVGKAQKKSERE 285
+AV +NG+ K YV AQ+K ER+
Sbjct: 69 TKAVTEMNGRIVATKPLYVALAQRKEERQ 97
Score = 76.3 bits (186), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 37/83 (44%), Positives = 53/83 (63%), Gaps = 1/83 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKL 172
N+++KNLD ID + L FS FG I S KV + G+SKG+GFV F + E A KA+ ++
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 173 NGMLLNDKQVYVGHFLRKQERDT 195
NG ++ K +YV RK+ER +
Sbjct: 76 NGRIVATKPLYVALAQRKEERQS 98
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 43/77 (55%), Gaps = 2/77 (2%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
LYV +L+ + D +L F+ G + S +V + RS G+G+V FS+ +EA +A+ +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 86 NFTPLNGKPIRVMYSHR 102
N + KP+ V + R
Sbjct: 76 NGRIVATKPLYVALAQR 92
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 103 bits (257), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 58/154 (37%), Positives = 86/154 (55%), Gaps = 3/154 (1%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G T+L V L N+T +L LF+ +G+V S ++ RD SLGYG+VN+ A++A RA
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 82 LEMLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSC 141
+ LN L K I+V Y+ PS N++I L + + K + D FS FG I++
Sbjct: 61 INTLNGLRLQSKTIKVSYAR--PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINS 118
Query: 142 KVATD-LNGQSKGYGFVQFDNEESAQKAIEKLNG 174
+V D G S+G F++FD A++AI NG
Sbjct: 119 RVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 85.5 bits (210), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 59/187 (31%), Positives = 91/187 (48%), Gaps = 22/187 (11%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE 261
TN+ V L ++ T+++L+ F G + SA ++RD G S +GFVN+ + DA RA+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 262 ALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEK 321
LNG + K V A+ SE + ANLYI L ++ +
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSE------------------VIKDANLYISGLPRTMTQKD 104
Query: 322 LKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEMNGKMVV--SKPLYV 378
++ +FS FG I + +V+ D +G+SRG F+ F EA A+ NG S+P+ V
Sbjct: 105 VEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITV 164
Query: 379 ALAQRKE 385
A E
Sbjct: 165 KFAANLE 171
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 47/160 (29%), Positives = 81/160 (50%), Gaps = 8/160 (5%)
Query: 110 GAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKA 168
G N+ + L + + L FS+ G + S K+ D + G S GYGFV + + A++A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 169 IEKLNGMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGT 228
I LNG+ L K + V + +E+ K N+Y+ L + T++D++ F +G
Sbjct: 61 INTLNGLRLQSKTIKVSY----ARPSSEVIKD--ANLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 229 ITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVEALNGKK 267
I ++ V+ D G S+ F+ F+ +A A+ + NG K
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHK 154
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 103 bits (257), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 58/154 (37%), Positives = 86/154 (55%), Gaps = 3/154 (1%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G T+L V L N+T +L LF+ +G+V S ++ RD SLGYG+VN+ A++A RA
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 82 LEMLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSC 141
+ LN L K I+V Y+ PS N++I L + + K + D FS FG I++
Sbjct: 61 INTLNGLRLQSKTIKVSYAR--PSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINS 118
Query: 142 KVATD-LNGQSKGYGFVQFDNEESAQKAIEKLNG 174
+V D G S+G F++FD A++AI NG
Sbjct: 119 RVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 85.9 bits (211), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 59/187 (31%), Positives = 91/187 (48%), Gaps = 22/187 (11%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE 261
TN+ V L ++ T+++L+ F G + SA ++RD G S +GFVN+ + DA RA+
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 262 ALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEK 321
LNG + K V A+ SE + ANLYI L ++ +
Sbjct: 63 TLNGLRLQSKTIKVSYARPSSE------------------VIKDANLYISGLPRTMTQKD 104
Query: 322 LKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEMNGKMVV--SKPLYV 378
++ +FS FG I + +V+ D +G+SRG F+ F EA A+ NG S+P+ V
Sbjct: 105 VEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITV 164
Query: 379 ALAQRKE 385
A E
Sbjct: 165 XFAANLE 171
Score = 77.4 bits (189), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 47/160 (29%), Positives = 81/160 (50%), Gaps = 8/160 (5%)
Query: 110 GAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKA 168
G N+ + L + + L FS+ G + S K+ D + G S GYGFV + + A++A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 169 IEKLNGMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGT 228
I LNG+ L K + V + +E+ K N+Y+ L + T++D++ F +G
Sbjct: 61 INTLNGLRLQSKTIKVSY----ARPSSEVIKD--ANLYISGLPRTMTQKDVEDMFSRFGR 114
Query: 229 ITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVEALNGKK 267
I ++ V+ D G S+ F+ F+ +A A+ + NG K
Sbjct: 115 IINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHK 154
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 100 bits (249), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 54/152 (35%), Positives = 88/152 (57%), Gaps = 3/152 (1%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
T+L V L N+T + LF +G++ S ++ RD T +SLGYG+VN+ + ++A +A+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 84 MLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKV 143
LN L K I+V Y+ PS N+++ L K + K L FS +G I++ ++
Sbjct: 63 TLNGLRLQTKTIKVSYAR--PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 144 ATD-LNGQSKGYGFVQFDNEESAQKAIEKLNG 174
D + G S+G GF++FD A++AI+ LNG
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Score = 88.6 bits (218), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 51/157 (32%), Positives = 87/157 (55%), Gaps = 8/157 (5%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEK 171
N+ + L + + + F + G I SCK+ D + GQS GYGFV + + + A+KAI
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 172 LNGMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYG-TIT 230
LNG+ L K + V + + I + N+YV L ++ T+++L++ F +YG IT
Sbjct: 64 LNGLRLQTKTIKVSY---ARPSSASIRDA---NLYVSGLPKTMTQKELEQLFSQYGRIIT 117
Query: 231 SAVVMRDGDGKSKCFGFVNFENSDDAARAVEALNGKK 267
S +++ G S+ GF+ F+ +A A++ LNG+K
Sbjct: 118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQK 154
Score = 88.2 bits (217), Expect = 7e-18, Method: Compositional matrix adjust.
Identities = 57/183 (31%), Positives = 94/183 (51%), Gaps = 22/183 (12%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE 261
TN+ V L ++ T+E+ + FG G I S ++RD G+S +GFVN+ + DA +A+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 262 ALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEK 321
LNG + K V A+ S + ANLY+ L ++ ++
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMTQKE 104
Query: 322 LKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLEMNGKMV--VSKPLYV 378
L+QLFS +G I + +++ D +G+SRG GF+ F EA A+ +NG+ ++P+ V
Sbjct: 105 LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 164
Query: 379 ALA 381
A
Sbjct: 165 KFA 167
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALL 364
NL + L ++ E+ + LF G I SCK++RD +G S G GFV + P++A +A+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 365 EMNGKMVVSKPLYVALAQ 382
+NG + +K + V+ A+
Sbjct: 63 TLNGLRLQTKTIKVSYAR 80
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 98.2 bits (243), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 54/152 (35%), Positives = 86/152 (56%), Gaps = 3/152 (1%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
T+L V L N+T + LF +G + S ++ RD T +SLGYG+VN+S+ +A +A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 84 MLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKV 143
LN L K I+V Y+ PS N+++ L K + K + FS +G I++ ++
Sbjct: 65 TLNGLKLQTKTIKVSYAR--PSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
Query: 144 ATD-LNGQSKGYGFVQFDNEESAQKAIEKLNG 174
D G S+G GF++FD A++AI+ LNG
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAIKGLNG 154
Score = 89.4 bits (220), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 56/183 (30%), Positives = 96/183 (52%), Gaps = 22/183 (12%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE 261
TN+ V L ++ T+++ + FG G I S ++RD G+S +GFVN+ + +DA +A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 262 ALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEK 321
LNG K K V A+ S + ANLY+ L ++ ++
Sbjct: 65 TLNGLKLQTKTIKVSYARPSSA------------------SIRDANLYVSGLPKTMSQKE 106
Query: 322 LKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEMNGK--MVVSKPLYV 378
++QLFS +G I + +++ D +G+SRG GF+ F EA A+ +NG+ + ++P+ V
Sbjct: 107 MEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITV 166
Query: 379 ALA 381
A
Sbjct: 167 KFA 169
Score = 86.3 bits (212), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 49/157 (31%), Positives = 85/157 (54%), Gaps = 8/157 (5%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEK 171
N+ + L + + F + G+I SCK+ D + GQS GYGFV + + A KAI
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 172 LNGMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYG-TIT 230
LNG+ L K + V + + I + N+YV L ++ +++++++ F +YG IT
Sbjct: 66 LNGLKLQTKTIKVSY---ARPSSASIRDA---NLYVSGLPKTMSQKEMEQLFSQYGRIIT 119
Query: 231 SAVVMRDGDGKSKCFGFVNFENSDDAARAVEALNGKK 267
S +++ G S+ GF+ F+ +A A++ LNG+K
Sbjct: 120 SRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQK 156
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALL 364
NL + L ++ ++ K LF G I SCK++RD +G S G GFV +S P +A +A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 365 EMNGKMVVSKPLYVALAQ 382
+NG + +K + V+ A+
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 90.9 bits (224), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 49/154 (31%), Positives = 85/154 (55%), Gaps = 3/154 (1%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
T+L V L + TD +LY LF +G + + R+ RD T S GY +V+F++ ++ RA++
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 84 MLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKV 143
+LN + K ++V Y+ P N+++ NL + I L F +G+I+ +
Sbjct: 75 VLNGITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 132
Query: 144 ATD-LNGQSKGYGFVQFDNEESAQKAIEKLNGML 176
D L G+ +G FV+++ E AQ+AI LN ++
Sbjct: 133 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166
Score = 85.5 bits (210), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 50/154 (32%), Positives = 82/154 (53%), Gaps = 8/154 (5%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEK 171
N+ + L + + L+ F A G I +C++ D G S GY FV F +E +Q+AI+
Sbjct: 16 NLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
Query: 172 LNGMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITS 231
LNG+ + +K++ V + E K TN+YV NL + T++ L FG+YG+I
Sbjct: 76 LNGITVRNKRLKVSYARPGGE------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ 129
Query: 232 AVVMRDG-DGKSKCFGFVNFENSDDAARAVEALN 264
++RD G+ + FV + ++A A+ ALN
Sbjct: 130 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 78.6 bits (192), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 56/184 (30%), Positives = 87/184 (47%), Gaps = 22/184 (11%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVE 261
TN+ V L + T+ +L F G I + + RD G S + FV+F + D+ RA++
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 262 ALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEK 321
LNG +K V A+ E + NLY+ NL +I D++
Sbjct: 75 VLNGITVRNKRLKVSYARPGGE------------------SIKDTNLYVTNLPRTITDDQ 116
Query: 322 LKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLEMNGKMVV--SKPLYV 378
L +F +GSI ++RD +G RG FV ++ EEA A+ +N + S+PL V
Sbjct: 117 LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 176
Query: 379 ALAQ 382
LA+
Sbjct: 177 RLAE 180
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 90.9 bits (224), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 49/154 (31%), Positives = 86/154 (55%), Gaps = 3/154 (1%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
T+L V L ++TD +LY LF +G + + R+ RD T S GY +V+F++ ++ RA++
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 84 MLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKV 143
+LN + K ++V Y+ P N+++ NL + I L F +G+I+ +
Sbjct: 64 VLNGITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNI 121
Query: 144 ATD-LNGQSKGYGFVQFDNEESAQKAIEKLNGML 176
D L G+ +G FV+++ E AQ+AI LN ++
Sbjct: 122 LRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
Score = 87.0 bits (214), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 50/154 (32%), Positives = 83/154 (53%), Gaps = 8/154 (5%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEK 171
N+ + L + + + L+ F A G I +C++ D G S GY FV F +E +Q+AI+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 172 LNGMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITS 231
LNG+ + +K++ V + E K TN+YV NL + T++ L FG+YG+I
Sbjct: 65 LNGITVRNKRLKVSYARPGGE------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQ 118
Query: 232 AVVMRDG-DGKSKCFGFVNFENSDDAARAVEALN 264
++RD G+ + FV + ++A A+ ALN
Sbjct: 119 KNILRDKLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 80.5 bits (197), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 57/183 (31%), Positives = 87/183 (47%), Gaps = 22/183 (12%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVE 261
TN+ V L + T+ +L F G I + +MRD G S + FV+F + D+ RA++
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 262 ALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEK 321
LNG +K V A+ E + NLY+ NL +I D++
Sbjct: 64 VLNGITVRNKRLKVSYARPGGE------------------SIKDTNLYVTNLPRTITDDQ 105
Query: 322 LKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLEMNGKMVV--SKPLYV 378
L +F +GSI ++RD +G RG FV ++ EEA A+ +N + S+PL V
Sbjct: 106 LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165
Query: 379 ALA 381
LA
Sbjct: 166 RLA 168
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALL 364
NL + L + D +L LF G I +C++MRD +G S G FV F++ ++ RA+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 365 EMNGKMVVSKPLYVALAQ 382
+NG V +K L V+ A+
Sbjct: 64 VLNGITVRNKRLKVSYAR 81
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 89.0 bits (219), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 55/180 (30%), Positives = 96/180 (53%), Gaps = 17/180 (9%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
+YV NL ++ TE+ L++ F G I + +M D + K+ + FV + S DA A++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 265 GKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEKLKQ 324
GK+ ++ +++ F+ + D F NL++ +L+ ++DDE L+
Sbjct: 63 GKQIENNI-------------VKINWAFQSQQSSSDDTF---NLFVGDLNVNVDDETLRN 106
Query: 325 LFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEMNGKMVVSKPLYVALAQR 383
F F S S VM D +G SRG GFV+F++ ++A A+ M G+ + +PL + A +
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 76.6 bits (187), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 42/160 (26%), Positives = 85/160 (53%), Gaps = 2/160 (1%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
LYVG+L+ +T+ L F G + ++++ D +++ Y +V + + +A AL+ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 86 NFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVAT 145
N + +++ ++ + N+F+ +L+ +D + L + F F + LS V
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 121
Query: 146 DL-NGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
D+ G S+GYGFV F +++ AQ A++ + G LN + + +
Sbjct: 122 DMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161
Score = 75.5 bits (184), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 46/168 (27%), Positives = 87/168 (51%), Gaps = 5/168 (2%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+++ NLDKAI L F G I + K+ D N ++ Y FV++ A A++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 174 GMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAV 233
G + + V + + Q+ ++ N++V +L+ + +E L+ +F ++ + S
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSD----DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118
Query: 234 VMRD-GDGKSKCFGFVNFENSDDAARAVEALNGKKFDDKEWYVGKAQK 280
VM D G S+ +GFV+F + DDA A++++ G+ + + + A K
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 59.3 bits (142), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 47/80 (58%)
Query: 23 TTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARAL 82
T +L+VGDL NV D L + F +S V D+ T S GYG+V+F++ +A A+
Sbjct: 87 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 146
Query: 83 EMLNFTPLNGKPIRVMYSHR 102
+ + LNG+P+R+ ++ +
Sbjct: 147 DSMQGQDLNGRPLRINWAAK 166
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 75.5 bits (184), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 44/172 (25%), Positives = 90/172 (52%), Gaps = 7/172 (4%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEKL 172
+++ ++ + + F+ FG I S ++ D + + KG+ FV+++ E+AQ A+E++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 173 NGMLLNDKQVYVGHFLRKQERDTEINK-----SKFTNVYVKNLSESTTEEDLQKSFGEYG 227
N ++L + + VG + I++ F +YV ++ + +++D++ F +G
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 150
Query: 228 TITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEALNGKKFDDKEWYVGKA 278
I SA + RD GK K +GF+ +E + + AV ++N + VGKA
Sbjct: 151 KIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 42/168 (25%), Positives = 78/168 (46%), Gaps = 9/168 (5%)
Query: 202 FTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAV 260
+ VYV ++ E+ ++++F +G I S + D K K F FV +E + A A+
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 261 EALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDE 320
E +N + VG+ + + + + E A F +Y+ ++ + D+
Sbjct: 88 EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQ-----LAEEARAFN--RIYVASVHQDLSDD 140
Query: 321 KLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLEMN 367
+K +F FG I S + RDP +G +G GF+ + + + A+ MN
Sbjct: 141 DIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
+YV + +++D + +F G++ S + RD +T + GYG++ + AQ + A+ +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 86 NFTPLNGKPIRV 97
N L G+ +RV
Sbjct: 188 NLFDLGGQYLRV 199
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 31/109 (28%), Positives = 54/109 (49%), Gaps = 12/109 (11%)
Query: 293 EQNMKEAADKFQGA-----NLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGI-SR 346
+Q + +A + QGA +Y+ ++ + ++ ++Q F+PFG I S + D + +
Sbjct: 11 QQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK 70
Query: 347 GSGFVAFSTPEEASRALLEMNGKMV------VSKPLYVALAQRKEDRRA 389
G FV + PE A AL +MN M+ V +P + AQ D+ A
Sbjct: 71 GFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLA 119
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 73.9 bits (180), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 89/172 (51%), Gaps = 7/172 (4%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEKL 172
+++ ++ + + F+ FG I S ++ D + + KG+ FV+++ E+AQ A+E++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 173 NGMLLNDKQVYVGHFLRKQERDTEINK-----SKFTNVYVKNLSESTTEEDLQKSFGEYG 227
N ++L + + VG + I++ F +YV ++ + +++D++ F +G
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 135
Query: 228 TITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEALNGKKFDDKEWYVGKA 278
I S + RD GK K +GF+ +E + + AV ++N + VGKA
Sbjct: 136 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 187
Score = 64.7 bits (156), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 43/165 (26%), Positives = 78/165 (47%), Gaps = 9/165 (5%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEAL 263
VYV ++ E+ ++++F +G I S + D K K F FV +E + A A+E +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 264 NGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEKLK 323
N + VG+ + + + + E A F +Y+ ++ + D+ +K
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQ-----LAEEARAFN--RIYVASVHQDLSDDDIK 128
Query: 324 QLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLEMN 367
+F FG I SC + RDP +G +G GF+ + + + A+ MN
Sbjct: 129 SVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
+YV + +++D + +F G++ S + RD +T + GYG++ + AQ + A+ +
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 172
Query: 86 NFTPLNGKPIRV 97
N L G+ +RV
Sbjct: 173 NLFDLGGQYLRV 184
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 45/89 (50%), Gaps = 7/89 (7%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGI-SRGSGFVAFSTPEEASRALLEM 366
+Y+ ++ + ++ ++Q F+PFG I S + D + +G FV + PE A AL +M
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 367 NGKMV------VSKPLYVALAQRKEDRRA 389
N M+ V +P + AQ D+ A
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLA 104
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 71.2 bits (173), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 38/87 (43%), Positives = 55/87 (63%), Gaps = 2/87 (2%)
Query: 109 SGAGNIFIKNLDKAIDHKALHDTFSAFGNIL-SCKVATDLN-GQSKGYGFVQFDNEESAQ 166
SG+ IFI NLD ID K L+DTFSAFG IL + K+ D + G SKGY F+ F + +++
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 167 KAIEKLNGMLLNDKQVYVGHFLRKQER 193
AIE +NG L ++ + V + +K +
Sbjct: 63 AAIEAMNGQYLCNRPITVSYAFKKDSK 89
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 54/84 (64%), Gaps = 2/84 (2%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSIT-SCKVMRDP-SGISRGSGFVAFSTPEEASRAL 363
+ ++I NLD ID++ L FS FG I + K+MRDP +G S+G F+ F++ + + A+
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 364 LEMNGKMVVSKPLYVALAQRKEDR 387
MNG+ + ++P+ V+ A +K+ +
Sbjct: 66 EAMNGQYLCNRPITVSYAFKKDSK 89
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVV-SVRVCRDLSTRRSLGYGYVNFSNAQEAAR 80
G++ +++G+L+ + + LYD F+ G ++ + ++ RD T S GY ++NF++ +
Sbjct: 4 GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63
Query: 81 ALEMLNFTPLNGKPIRVMYSHR 102
A+E +N L +PI V Y+ +
Sbjct: 64 AIEAMNGQYLCNRPITVSYAFK 85
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 46/84 (54%), Gaps = 2/84 (2%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTIT-SAVVMRDGD-GKSKCFGFVNFENSDDAARAV 260
+ +++ NL E+ L +F +G I + +MRD D G SK + F+NF + D + A+
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 261 EALNGKKFDDKEWYVGKAQKKSER 284
EA+NG+ ++ V A KK +
Sbjct: 66 EAMNGQYLCNRPITVSYAFKKDSK 89
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 40/146 (27%), Positives = 72/146 (49%), Gaps = 14/146 (9%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+VG+L ++T+ LF + G+ V + RD G+G++ + A A L
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 86 NFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVAT 145
+ T L +P+R+ ++ + + +KNL + ++ L FS FG + V
Sbjct: 79 DGTILKSRPLRIRFA--------THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVV 130
Query: 146 DLNGQSKGYGFVQFDNEESAQKAIEK 171
D G++ G GFV+F + A+KA+E+
Sbjct: 131 DDRGRATGKGFVEFAAKPPARKALER 156
Score = 61.6 bits (148), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 45/160 (28%), Positives = 66/160 (41%), Gaps = 29/160 (18%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEAL 263
++V NL TEED ++ F YG + + RD + FGF+ E+ A A L
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAEL 78
Query: 264 NGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEKLK 323
+G + + A GA L +KNL + +E L+
Sbjct: 79 DGTILKSRPLRIRFAT------------------------HGAALTVKNLSPVVSNELLE 114
Query: 324 QLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
Q FS FG + V+ D G + G GFV F+ A +AL
Sbjct: 115 QAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKAL 154
Score = 54.7 bits (130), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 36/149 (24%), Positives = 68/149 (45%), Gaps = 17/149 (11%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKL 172
+F+ NL I + F +G + D +G+GF++ ++ A+ A +L
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAEL 78
Query: 173 NGMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSA 232
+G +L + + + + + VKNLS + E L+++F ++G + A
Sbjct: 79 DGTILKSRPLRIRF------------ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKA 126
Query: 233 VVMRDGDGKSKCFGFVNFENSDDAARAVE 261
VV+ D G++ GFV F A +A+E
Sbjct: 127 VVVVDDRGRATGKGFVEFAAKPPARKALE 155
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 304 QGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
Q L++ NL I +E K+LF +G + + RD RG GF+ + A A
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAK 75
Query: 364 LEMNGKMVVSKPLYVALA 381
E++G ++ S+PL + A
Sbjct: 76 AELDGTILKSRPLRIRFA 93
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 69.3 bits (168), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 40/148 (27%), Positives = 75/148 (50%), Gaps = 14/148 (9%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
+ L+VG+L ++T+ ++ LF + G+ V + +D G+G++ A A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKV 76
Query: 84 MLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKV 143
L+ PL GK +RV ++ SL ++NL + + ++ L + FS FG + V
Sbjct: 77 ELDNMPLRGKQLRVRFACHSASLT--------VRNLPQYVSNELLEEAFSVFGQVERAVV 128
Query: 144 ATDLNGQSKGYGFVQFDNEESAQKAIEK 171
D G+ G G V+F + +A+KA+++
Sbjct: 129 IVDDRGRPSGKGIVEFSGKPAARKALDR 156
Score = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 43/161 (26%), Positives = 65/161 (40%), Gaps = 29/161 (18%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
+ ++V NL TEE+++K F +YG + +D K FGF+ E A A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVE 77
Query: 263 LNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEKL 322
L+ K+ V A A+L ++NL + +E L
Sbjct: 78 LDNMPLRGKQLRVRFA------------------------CHSASLTVRNLPQYVSNELL 113
Query: 323 KQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
++ FS FG + V+ D G G G V FS A +AL
Sbjct: 114 EEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKAL 154
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 36/148 (24%), Positives = 65/148 (43%), Gaps = 17/148 (11%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+F+ NL I + + F +G + D KG+GF++ + A+ A +L+
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELD 79
Query: 174 GMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAV 233
M L KQ+ V ++ V+NL + + E L+++F +G + AV
Sbjct: 80 NMPLRGKQLRVRFACHS------------ASLTVRNLPQYVSNELLEEAFSVFGQVERAV 127
Query: 234 VMRDGDGKSKCFGFVNFENSDDAARAVE 261
V+ D G+ G V F A +A++
Sbjct: 128 VIVDDRGRPSGKGIVEFSGKPAARKALD 155
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 68.9 bits (167), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 37/152 (24%), Positives = 79/152 (51%), Gaps = 11/152 (7%)
Query: 23 TTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNF---SNAQEAA 79
+ +++G L + T+ L + F + G V +++ +D +T RS G+G+++F S+ E
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 80 RALEMLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNIL 139
+ +L+ ++ P R + P + G IF+ + + K + FS +G I+
Sbjct: 63 KTQHILDGKVID--PKRAI-----PRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTII 115
Query: 140 SCKVATDLN-GQSKGYGFVQFDNEESAQKAIE 170
++ D + GQS+G+GFV +D+ ++ + +
Sbjct: 116 DAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ 147
Score = 65.1 bits (157), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 42/163 (25%), Positives = 83/163 (50%), Gaps = 28/163 (17%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENS---DDAARAV 260
+++ L+ TTE++L++ FG+YGT+T +M+D G+S+ FGF++FE D+ +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 261 EALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDE 320
L+GK D K +A + E++ + +++ + + +
Sbjct: 66 HILDGKVIDPK-----RAIPRDEQD------------------KTGKIFVGGIGPDVRPK 102
Query: 321 KLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRA 362
+ ++ FS +G+I ++M D +G SRG GFV + + + R
Sbjct: 103 EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV 145
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 38/153 (24%), Positives = 77/153 (50%), Gaps = 16/153 (10%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEK- 171
+FI L+ L + F +G + K+ D G+S+G+GF+ F+ S + ++
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 172 --LNGMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTI 229
L+G +++ K+ + + E+D K ++V + ++ ++ F ++GTI
Sbjct: 66 HILDGKVIDPKRA-----IPRDEQD------KTGKIFVGGIGPDVRPKEFEEFFSQWGTI 114
Query: 230 TSAVVMRDGD-GKSKCFGFVNFENSDDAARAVE 261
A +M D D G+S+ FGFV ++++D R +
Sbjct: 115 IDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ 147
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/94 (26%), Positives = 54/94 (57%), Gaps = 7/94 (7%)
Query: 304 QGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTP---EEA 359
+ ++I L+ ++ L++ F +G++T K+M+DP +G SRG GF++F P +E
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 360 SRALLEMNGKMVVSKPLYVALAQRKEDRRARLQV 393
+ ++GK++ K A+ + ++D+ ++ V
Sbjct: 62 VKTQHILDGKVIDPK---RAIPRDEQDKTGKIFV 92
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 68.9 bits (167), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 85/172 (49%), Gaps = 7/172 (4%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEKL 172
+++ ++ + + F+ FG I S + D + + KG+ FV+++ E+AQ A+E+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 173 NGMLLNDKQVYVGHFLRKQERDTEINK-----SKFTNVYVKNLSESTTEEDLQKSFGEYG 227
N + L + + VG + I++ F +YV ++ + +++D++ F +G
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG 134
Query: 228 TITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEALNGKKFDDKEWYVGKA 278
I S + RD GK K +GF+ +E + + AV + N + VGKA
Sbjct: 135 KIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRVGKA 186
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 42/165 (25%), Positives = 75/165 (45%), Gaps = 9/165 (5%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEAL 263
VYV ++ E+ ++++F +G I S D K K F FV +E + A A+E
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 264 NGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEKLK 323
N + VG+ + + + + E A F +Y+ ++ + D+ +K
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQ-----LAEEARAFN--RIYVASVHQDLSDDDIK 127
Query: 324 QLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLEMN 367
+F FG I SC + RDP +G +G GF+ + + + A+ N
Sbjct: 128 SVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
+YV + +++D + +F G++ S + RD +T + GYG++ + AQ + A+
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSX 171
Query: 86 NFTPLNGKPIRV 97
N L G+ +RV
Sbjct: 172 NLFDLGGQYLRV 183
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 68.6 bits (166), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 50/175 (28%), Positives = 84/175 (48%), Gaps = 13/175 (7%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L++G L TD L F Q G + V RD +T+RS G+G+V ++ +E A +
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 72
Query: 86 NFTP--LNGKPIRVMYSHRDPSLRKSGAG----NIFIKNLDKAIDHKALHDTFSAFGNIL 139
N P ++G+ + + ++ GA IF+ + + + L D F +G I
Sbjct: 73 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 132
Query: 140 SCKVATDL-NGQSKGYGFVQFDNEESAQK-AIEKLNGMLLNDKQVYVGHFLRKQE 192
++ TD +G+ +G+ FV FD+ +S K I+K + +N V L KQE
Sbjct: 133 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQE 185
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 40/164 (24%), Positives = 75/164 (45%), Gaps = 17/164 (10%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAVEAL 263
+++ LS TT+E L+ F ++GT+T VVMRD + K S+ FGFV + ++ A+ A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 74
Query: 264 NGKKFDDKEWYVGKAQKKSERELELKHQF-EQNMKEAADKFQGANLYIKNLDDSIDDEKL 322
+ K R +E K ++ + +++ + + ++ L
Sbjct: 75 -------------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 121
Query: 323 KQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLE 365
+ F +G I ++M D SG RG FV F + + +++
Sbjct: 122 RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 68.6 bits (166), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 50/175 (28%), Positives = 84/175 (48%), Gaps = 13/175 (7%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L++G L TD L F Q G + V RD +T+RS G+G+V ++ +E A +
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 71
Query: 86 NFTP--LNGKPIRVMYSHRDPSLRKSGAG----NIFIKNLDKAIDHKALHDTFSAFGNIL 139
N P ++G+ + + ++ GA IF+ + + + L D F +G I
Sbjct: 72 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 131
Query: 140 SCKVATDL-NGQSKGYGFVQFDNEESAQK-AIEKLNGMLLNDKQVYVGHFLRKQE 192
++ TD +G+ +G+ FV FD+ +S K I+K + +N V L KQE
Sbjct: 132 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQE 184
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 40/164 (24%), Positives = 75/164 (45%), Gaps = 17/164 (10%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAVEAL 263
+++ LS TT+E L+ F ++GT+T VVMRD + K S+ FGFV + ++ A+ A
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 73
Query: 264 NGKKFDDKEWYVGKAQKKSERELELKHQF-EQNMKEAADKFQGANLYIKNLDDSIDDEKL 322
+ K R +E K ++ + +++ + + ++ L
Sbjct: 74 -------------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 120
Query: 323 KQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLE 365
+ F +G I ++M D SG RG FV F + + +++
Sbjct: 121 RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 68.6 bits (166), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 50/175 (28%), Positives = 84/175 (48%), Gaps = 13/175 (7%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L++G L TD L F Q G + V RD +T+RS G+G+V ++ +E A +
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 73
Query: 86 NFTP--LNGKPIRVMYSHRDPSLRKSGAG----NIFIKNLDKAIDHKALHDTFSAFGNIL 139
N P ++G+ + + ++ GA IF+ + + + L D F +G I
Sbjct: 74 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 133
Query: 140 SCKVATDL-NGQSKGYGFVQFDNEESAQK-AIEKLNGMLLNDKQVYVGHFLRKQE 192
++ TD +G+ +G+ FV FD+ +S K I+K + +N V L KQE
Sbjct: 134 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQE 186
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 40/164 (24%), Positives = 75/164 (45%), Gaps = 17/164 (10%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAVEAL 263
+++ LS TT+E L+ F ++GT+T VVMRD + K S+ FGFV + ++ A+ A
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 75
Query: 264 NGKKFDDKEWYVGKAQKKSERELELKHQF-EQNMKEAADKFQGANLYIKNLDDSIDDEKL 322
+ K R +E K ++ + +++ + + ++ L
Sbjct: 76 -------------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 122
Query: 323 KQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLE 365
+ F +G I ++M D SG RG FV F + + +++
Sbjct: 123 RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 68.2 bits (165), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 42/151 (27%), Positives = 74/151 (49%), Gaps = 10/151 (6%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L++G L TD L F Q G + V RD +T+RS G+G+V ++ +E A +
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 70
Query: 86 NFTP--LNGKPIRVMYSHRDPSLRKSGAG----NIFIKNLDKAIDHKALHDTFSAFGNIL 139
N P ++G+ + + ++ GA IF+ + + + L D F +G I
Sbjct: 71 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 130
Query: 140 SCKVATDL-NGQSKGYGFVQFDNEESAQKAI 169
++ TD +G+ +G+ FV FD+ +S K +
Sbjct: 131 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 40/164 (24%), Positives = 75/164 (45%), Gaps = 17/164 (10%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAVEAL 263
+++ LS TT+E L+ F ++GT+T VVMRD + K S+ FGFV + ++ A+ A
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 72
Query: 264 NGKKFDDKEWYVGKAQKKSERELELKHQF-EQNMKEAADKFQGANLYIKNLDDSIDDEKL 322
+ K R +E K ++ + +++ + + ++ L
Sbjct: 73 -------------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 119
Query: 323 KQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLE 365
+ F +G I ++M D SG RG FV F + + +++
Sbjct: 120 RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 68.2 bits (165), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 50/175 (28%), Positives = 84/175 (48%), Gaps = 13/175 (7%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L++G L TD L F Q G + V RD +T+RS G+G+V ++ +E A +
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 65
Query: 86 NFTP--LNGKPIRVMYSHRDPSLRKSGAG----NIFIKNLDKAIDHKALHDTFSAFGNIL 139
N P ++G+ + + ++ GA IF+ + + + L D F +G I
Sbjct: 66 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 125
Query: 140 SCKVATDL-NGQSKGYGFVQFDNEESAQK-AIEKLNGMLLNDKQVYVGHFLRKQE 192
++ TD +G+ +G+ FV FD+ +S K I+K + +N V L KQE
Sbjct: 126 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH--TVNGHNCEVRKALSKQE 178
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 40/164 (24%), Positives = 75/164 (45%), Gaps = 17/164 (10%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAVEAL 263
+++ LS TT+E L+ F ++GT+T VVMRD + K S+ FGFV + ++ A+ A
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 67
Query: 264 NGKKFDDKEWYVGKAQKKSERELELKHQF-EQNMKEAADKFQGANLYIKNLDDSIDDEKL 322
+ K R +E K ++ + +++ + + ++ L
Sbjct: 68 -------------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 114
Query: 323 KQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLE 365
+ F +G I ++M D SG RG FV F + + +++
Sbjct: 115 RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 68.2 bits (165), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 42/151 (27%), Positives = 74/151 (49%), Gaps = 10/151 (6%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L++G L TD L F Q G + V RD +T+RS G+G+V ++ +E A +
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---M 72
Query: 86 NFTP--LNGKPIRVMYSHRDPSLRKSGAG----NIFIKNLDKAIDHKALHDTFSAFGNIL 139
N P ++G+ + + ++ GA IF+ + + + L D F +G I
Sbjct: 73 NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIE 132
Query: 140 SCKVATDL-NGQSKGYGFVQFDNEESAQKAI 169
++ TD +G+ +G+ FV FD+ +S K +
Sbjct: 133 VIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 40/164 (24%), Positives = 75/164 (45%), Gaps = 17/164 (10%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAVEAL 263
+++ LS TT+E L+ F ++GT+T VVMRD + K S+ FGFV + ++ A+ A
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 74
Query: 264 NGKKFDDKEWYVGKAQKKSERELELKHQF-EQNMKEAADKFQGANLYIKNLDDSIDDEKL 322
+ K R +E K ++ + +++ + + ++ L
Sbjct: 75 -------------RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHL 121
Query: 323 KQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLE 365
+ F +G I ++M D SG RG FV F + + +++
Sbjct: 122 RDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 67.0 bits (162), Expect = 2e-11, Method: Composition-based stats.
Identities = 32/76 (42%), Positives = 50/76 (65%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G++ LYVG L N+T+ L +F G++ ++ + +D T RS GYG++ FS+++ A RA
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 82 LEMLNFTPLNGKPIRV 97
LE LN L G+P+RV
Sbjct: 64 LEQLNGFELAGRPMRV 79
Score = 55.1 bits (131), Expect = 6e-08, Method: Composition-based stats.
Identities = 29/82 (35%), Positives = 49/82 (59%), Gaps = 1/82 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALL 364
+ LY+ +L +I ++ L+ +F PFG I + +M+D +G S+G GF+ FS E A RAL
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 365 EMNGKMVVSKPLYVALAQRKED 386
++NG + +P+ V + D
Sbjct: 66 QLNGFELAGRPMRVGHVTERLD 87
Score = 54.3 bits (129), Expect = 1e-07, Method: Composition-based stats.
Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 1/79 (1%)
Query: 109 SGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLN-GQSKGYGFVQFDNEESAQK 167
SG+ +++ +L I L F FG I + + D + G+SKGYGF+ F + E A++
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 168 AIEKLNGMLLNDKQVYVGH 186
A+E+LNG L + + VGH
Sbjct: 63 ALEQLNGFELAGRPMRVGH 81
Score = 52.8 bits (125), Expect = 4e-07, Method: Composition-based stats.
Identities = 29/80 (36%), Positives = 49/80 (61%), Gaps = 1/80 (1%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGD-GKSKCFGFVNFENSDDAARAVE 261
+ +YV +L + TE+ L+ F +G I + V+M+D D G+SK +GF+ F +S+ A RA+E
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 262 ALNGKKFDDKEWYVGKAQKK 281
LNG + + VG ++
Sbjct: 66 QLNGFELAGRPMRVGHVTER 85
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 66.2 bits (160), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 48/76 (63%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G LYVG L N+T+ L +F G++ S+++ D T RS GYG++ FS+++ A +A
Sbjct: 25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKA 84
Query: 82 LEMLNFTPLNGKPIRV 97
LE LN L G+P++V
Sbjct: 85 LEQLNGFELAGRPMKV 100
Score = 57.8 bits (138), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 33/85 (38%), Positives = 49/85 (57%), Gaps = 3/85 (3%)
Query: 105 SLRKSGAG--NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDN 161
+L+K AG +++ +L I L F FG I S ++ D G+SKGYGF+ F +
Sbjct: 18 NLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77
Query: 162 EESAQKAIEKLNGMLLNDKQVYVGH 186
E A+KA+E+LNG L + + VGH
Sbjct: 78 SECAKKALEQLNGFELAGRPMKVGH 102
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLEM 366
LY+ +L +I ++ L+ +F PFG I S ++M D +G S+G GF+ FS E A +AL ++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 367 NGKMVVSKPLYVALAQRKED 386
NG + +P+ V + D
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 48/80 (60%), Gaps = 1/80 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGD-GKSKCFGFVNFENSDDAARAVEAL 263
+YV +L + TE+ L+ F +G I S +M D + G+SK +GF+ F +S+ A +A+E L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 264 NGKKFDDKEWYVGKAQKKSE 283
NG + + VG ++++
Sbjct: 89 NGFELAGRPMKVGHVTERTD 108
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 47/183 (25%), Positives = 80/183 (43%), Gaps = 20/183 (10%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD---GDGKSKCFGFVNFENSDDAARAVE 261
++V + + +E+DL++ F +YG + V+RD +SK FV F A A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 262 ALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEK 321
AL+ K +++K + D+ L+I + +
Sbjct: 66 ALHNMK----------VLPGMHHPIQMKPADSEKNNAVEDR----KLFIGMISKKCTEND 111
Query: 322 LKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMNGKMVV---SKPLYV 378
++ +FS FG I C+++R P G+SRG FV F+T A A+ M+ + S P+ V
Sbjct: 112 IRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 171
Query: 379 ALA 381
A
Sbjct: 172 KFA 174
Score = 58.9 bits (141), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 45/156 (28%), Positives = 71/156 (45%), Gaps = 12/156 (7%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLS--TRRSLGYGYVNFSN---AQEAAR 80
++VG + ++ L +LF Q G V + V RD S +S G +V F A EA
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 81 ALEMLNFTPLNGKPIRVMYSHRDPSLRKSGA---GNIFIKNLDKAIDHKALHDTFSAFGN 137
AL + P PI++ + + K+ A +FI + K + FS+FG
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSE----KNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 121
Query: 138 ILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
I C++ +G S+G FV F AQ AI+ ++
Sbjct: 122 IEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 157
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 64.3 bits (155), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 47/183 (25%), Positives = 80/183 (43%), Gaps = 20/183 (10%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD---GDGKSKCFGFVNFENSDDAARAVE 261
++V + + +E+DL++ F +YG + V+RD +SK FV F A A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 262 ALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEK 321
AL+ K +++K + D+ L+I + +
Sbjct: 78 ALHNMK----------VLPGMHHPIQMKPADSEKNNAVEDR----KLFIGMISKKCTEND 123
Query: 322 LKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMNGKMVV---SKPLYV 378
++ +FS FG I C+++R P G+SRG FV F+T A A+ M+ + S P+ V
Sbjct: 124 IRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 183
Query: 379 ALA 381
A
Sbjct: 184 KFA 186
Score = 58.5 bits (140), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 45/156 (28%), Positives = 71/156 (45%), Gaps = 12/156 (7%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLS--TRRSLGYGYVNFSN---AQEAAR 80
++VG + ++ L +LF Q G V + V RD S +S G +V F A EA
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 81 ALEMLNFTPLNGKPIRVMYSHRDPSLRKSGA---GNIFIKNLDKAIDHKALHDTFSAFGN 137
AL + P PI++ + + K+ A +FI + K + FS+FG
Sbjct: 78 ALHNMKVLPGMHHPIQMKPADSE----KNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 133
Query: 138 ILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
I C++ +G S+G FV F AQ AI+ ++
Sbjct: 134 IEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMH 169
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 34/80 (42%), Positives = 52/80 (65%), Gaps = 1/80 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDG-KSKCFGFVNFENSDDAARAVEAL 263
++V LS T E+ L++ F +YG I+ VV++D + +S+ FGFV FEN DDA A+ A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 264 NGKKFDDKEWYVGKAQKKSE 283
NGK D ++ V +A K S+
Sbjct: 75 NGKSVDGRQIRVDQAGKSSD 94
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 43/72 (59%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+VG L + + L +F++ GQ+ V V +D T+RS G+G+V F N +A A+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 86 NFTPLNGKPIRV 97
N ++G+ IRV
Sbjct: 75 NGKSVDGRQIRV 86
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 28/83 (33%), Positives = 48/83 (57%), Gaps = 1/83 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEM 366
L++ L +++ L+Q+FS +G I+ V++D + SRG GFV F ++A A++ M
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 367 NGKMVVSKPLYVALAQRKEDRRA 389
NGK V + + V A + D R+
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNRS 97
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 112 GNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQ-SKGYGFVQFDNEESAQKAIE 170
G +F+ L + ++L FS +G I V D Q S+G+GFV F+N + A+ A+
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Query: 171 KLNGMLLNDKQVYV 184
+NG ++ +Q+ V
Sbjct: 73 AMNGKSVDGRQIRV 86
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 62.0 bits (149), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 33/79 (41%), Positives = 48/79 (60%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G T+L V L N+T +L LF+ +G+V S ++ RD SLGYG+VN+ A++A RA
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 82 LEMLNFTPLNGKPIRVMYS 100
+ LN L K I+V Y+
Sbjct: 63 INTLNGLRLQSKTIKVSYA 81
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE 261
TN+ V L ++ T+++L+ F G + SA ++RD G S +GFVN+ + DA RA+
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 262 ALNGKKFDDKEWYVGKAQ 279
LNG + K V A+
Sbjct: 65 TLNGLRLQSKTIKVSYAR 82
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 47/77 (61%), Gaps = 1/77 (1%)
Query: 307 NLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLE 365
NL + L ++ ++L+ LFS G + S K++RD +G S G GFV + T ++A RA+
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 366 MNGKMVVSKPLYVALAQ 382
+NG + SK + V+ A+
Sbjct: 66 LNGLRLQSKTIKVSYAR 82
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 110 GAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKA 168
G N+ + L + + L FS+ G + S K+ D + G S GYGFV + + A++A
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 169 IEKLNGMLLNDKQVYVGH 186
I LNG+ L K + V +
Sbjct: 63 INTLNGLRLQSKTIKVSY 80
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 62.0 bits (149), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 27/69 (39%), Positives = 42/69 (60%)
Query: 307 NLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEM 366
NLYI NL S+D+++L+ + PFG + S +++RD SG SRG GF + E+ +
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 367 NGKMVVSKP 375
NGK + + P
Sbjct: 87 NGKFIKTPP 95
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 36/65 (55%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKL 172
N++I NL ++D + L + FG ++S ++ D +G S+G GF + ++ E + I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 173 NGMLL 177
NG +
Sbjct: 87 NGKFI 91
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 186 HFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCF 245
++QE+D TN+Y+ NL S E++L+ +G + S ++RD G S+
Sbjct: 16 QMAKQQEQDP-------TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGV 68
Query: 246 GFVNFENSDDAARAVEALNGK 266
GF E+++ + NGK
Sbjct: 69 GFARMESTEKCEAVIGHFNGK 89
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 33/56 (58%), Gaps = 1/56 (1%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLS-TRRSLGYGYVNFSNAQEA 78
T+LY+ +L ++ + +L ++ GQV+S R+ RD S T R +G+ + + EA
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEA 81
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 33/80 (41%), Positives = 47/80 (58%)
Query: 21 FGTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAAR 80
F T+L V L N T +L LF+ +G+V S ++ RD SLGYG+VN+ A++A R
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 81 ALEMLNFTPLNGKPIRVMYS 100
A+ LN L K I+V Y+
Sbjct: 77 AINTLNGLRLQSKTIKVSYA 96
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 1/81 (1%)
Query: 303 FQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASR 361
FQG NL + L + ++L+ LFS G + S K++RD +G S G GFV + T ++A R
Sbjct: 17 FQGTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAER 76
Query: 362 ALLEMNGKMVVSKPLYVALAQ 382
A+ +NG + SK + V+ A+
Sbjct: 77 AINTLNGLRLQSKTIKVSYAR 97
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE 261
TN+ V L ++ T+++L+ F G + SA ++RD G S +GFVN+ + DA RA+
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 262 ALNGKKFDDKEWYVGKAQ 279
LNG + K V A+
Sbjct: 80 TLNGLRLQSKTIKVSYAR 97
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEK 171
N+ + L + L FS+ G + S K+ D + G S GYGFV + + A++AI
Sbjct: 21 NLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 80
Query: 172 LNGMLLNDKQVYVGH 186
LNG+ L K + V +
Sbjct: 81 LNGLRLQSKTIKVSY 95
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 28/74 (37%), Positives = 48/74 (64%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
++YVG L+ V++ L++LF Q G VV+ + +D T + GYG+V F + ++A A++
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 84 MLNFTPLNGKPIRV 97
+++ L GKPIRV
Sbjct: 76 IMDMIKLYGKPIRV 89
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEKL 172
+++ LD+ + L + F G +++ + D + GQ +GYGFV+F +EE A AI+ +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 173 NGMLLNDKQVYV 184
+ + L K + V
Sbjct: 78 DMIKLYGKPIRV 89
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 300 ADKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEE 358
+++ Q A +Y+ LD+ + + L +LF G + + + +D +G +G GFV F + E+
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69
Query: 359 ASRALLEMNGKMVVSKPLYV 378
A A+ M+ + KP+ V
Sbjct: 70 ADYAIKIMDMIKLYGKPIRV 89
Score = 35.0 bits (79), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE 261
VYV L E +E L + F + G + + + +D G+ + +GFV F + +DA A++
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 262 ALNGKKFDDKEWYVGKA 278
++ K K V KA
Sbjct: 76 IMDMIKLYGKPIRVNKA 92
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 44/164 (26%), Positives = 70/164 (42%), Gaps = 23/164 (14%)
Query: 206 YVKNLSESTTEEDLQKSFGEYGTITSAVVMRD---GDGKSKCFGFVNFENSDDAARAVEA 262
+V + + +E+DL++ F +YG + V+RD +SK FV F A A A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 263 LNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADK---FQGANLYIKNLDDSIDD 319
L+ K L H Q ++K + L+I + +
Sbjct: 67 LHNXKV-----------------LPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTE 109
Query: 320 EKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
++ FS FG I C+++R P G+SRG FV F+T A A+
Sbjct: 110 NDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAI 153
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 45/152 (29%), Positives = 66/152 (43%), Gaps = 12/152 (7%)
Query: 27 YVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLS--TRRSLGYGYVNFSN---AQEAARA 81
+VG + ++ L +LF Q G V + V RD S +S G +V F A EA A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 82 LEMLNFTPLNGKPIRVMYSHRDPSLRKSGA---GNIFIKNLDKAIDHKALHDTFSAFGNI 138
L P PI+ + + K+ A +FI + K + FS+FG I
Sbjct: 67 LHNXKVLPGXHHPIQXKPADSE----KNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQI 122
Query: 139 LSCKVATDLNGQSKGYGFVQFDNEESAQKAIE 170
C++ +G S+G FV F AQ AI+
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAXAQTAIK 154
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 59.3 bits (142), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 33/87 (37%), Positives = 50/87 (57%), Gaps = 1/87 (1%)
Query: 304 QGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRA 362
+GANL+I +L D+ L Q+F PFG++ S KV D + +S+ GFV++ P A A
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 363 LLEMNGKMVVSKPLYVALAQRKEDRRA 389
+ MNG + K L V L + K D ++
Sbjct: 84 IQSMNGFQIGMKRLKVQLKRSKNDSKS 110
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 50/89 (56%), Gaps = 3/89 (3%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQ-SKGYGFVQFDNEESAQKAIEK 171
N+FI +L + + L F FGN++S KV D SK +GFV +DN SAQ AI+
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 172 LNGMLLNDKQVYVGHFLRKQERDTEINKS 200
+NG + K++ V L++ + D++ S
Sbjct: 87 MNGFQIGMKRLKVQ--LKRSKNDSKSGPS 113
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAVE 261
N+++ +L + ++DL + F +G + SA V D SKCFGFV+++N A A++
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 262 ALNG 265
++NG
Sbjct: 86 SMNG 89
Score = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 35/72 (48%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L++ L D L +F G VVS +V D T S +G+V++ N A A++ +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 86 NFTPLNGKPIRV 97
N + K ++V
Sbjct: 88 NGFQIGMKRLKV 99
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 58.9 bits (141), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 46/78 (58%)
Query: 23 TTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARAL 82
T +L+VGDL NV D L + F +S V D+ T S GYG+V+F++ +A A+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 83 EMLNFTPLNGKPIRVMYS 100
+ + LNG+P+R+ ++
Sbjct: 61 DSMQGQDLNGRPLRINWA 78
Score = 58.2 bits (139), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 49/80 (61%), Gaps = 1/80 (1%)
Query: 307 NLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLE 365
NL++ +L+ ++DDE L+ F F S S VM D +G SRG GFV+F++ ++A A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 366 MNGKMVVSKPLYVALAQRKE 385
M G+ + +PL + A + E
Sbjct: 63 MQGQDLNGRPLRINWAAKLE 82
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEK 171
N+F+ +L+ +D + L + F F + LS V D+ G S+GYGFV F +++ AQ A++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 172 LNGMLLNDKQVYV 184
+ G LN + + +
Sbjct: 63 MQGQDLNGRPLRI 75
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVEA 262
N++V +L+ + +E L+ +F ++ + S VM D G S+ +GFV+F + DDA A+++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 263 LNGKKFDDKEWYVGKAQK 280
+ G+ + + + A K
Sbjct: 63 MQGQDLNGRPLRINWAAK 80
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 58.5 bits (140), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 30/78 (38%), Positives = 46/78 (58%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
T+L V L N+T + LF +G + S ++ RD T +SLGYG+VN+S+ +A +A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 84 MLNFTPLNGKPIRVMYSH 101
LN L K I+V Y+
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEK 171
N+ + L + + F + G+I SCK+ D + GQS GYGFV + + A KAI
Sbjct: 6 NLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65
Query: 172 LNGMLLNDKQVYVGH 186
LNG+ L K + V +
Sbjct: 66 LNGLKLQTKTIKVSY 80
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE 261
TN+ V L ++ T+++ + FG G I S ++RD G+S +GFVN+ + +DA +A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 262 ALNGKKFDDKEWYVGKAQKKS 282
LNG K K V A+ S
Sbjct: 65 TLNGLKLQTKTIKVSYARPSS 85
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALL 364
NL + L ++ ++ K LF G I SCK++RD +G S G GFV +S P +A +A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 365 EMNGKMVVSKPLYVALAQ 382
+NG + +K + V+ A+
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 46/78 (58%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
+++ L+ T E+ L+ FG++G I+ ++++D KS+ F F+ FEN DA A + +N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 265 GKKFDDKEWYVGKAQKKS 282
GK K V +A+K S
Sbjct: 70 GKSLHGKAIKVEQAKKPS 87
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 42/76 (55%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
L+I L+ +++ LK +F G I+ +++D + SRG F+ F P +A A +MN
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 368 GKMVVSKPLYVALAQR 383
GK + K + V A++
Sbjct: 70 GKSLHGKAIKVEQAKK 85
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%)
Query: 111 AGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIE 170
G +FI L++ + K L F G I + D +S+G+ F+ F+N A+ A +
Sbjct: 7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAK 66
Query: 171 KLNGMLLNDKQVYV 184
+NG L+ K + V
Sbjct: 67 DMNGKSLHGKAIKV 80
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 44/85 (51%), Gaps = 2/85 (2%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L++G L + L +F + G + V + +D T +S G+ ++ F N +A A + +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDM 68
Query: 86 NFTPLNGKPIRVMYSHRDPSLRKSG 110
N L+GK I+V + + PS + G
Sbjct: 69 NGKSLHGKAIKVEQA-KKPSFQSGG 92
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic
Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 56.6 bits (135), Expect = 2e-08, Method: Composition-based stats.
Identities = 28/84 (33%), Positives = 47/84 (55%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
++VGDL +T + F G++ RV +D++T +S GYG+V+F N +A A++ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 86 NFTPLNGKPIRVMYSHRDPSLRKS 109
L G+ IR ++ R P KS
Sbjct: 78 GGQWLGGRQIRTNWATRKPPAPKS 101
Score = 55.5 bits (132), Expect = 6e-08, Method: Composition-based stats.
Identities = 36/111 (32%), Positives = 60/111 (54%), Gaps = 8/111 (7%)
Query: 191 QERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVN 249
Q++DT S +V+V +LS T ED++ +F +G I+ A V++D GKSK +GFV+
Sbjct: 8 QKKDT----SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63
Query: 250 FENSDDAARAVEALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAA 300
F N DA A++ + G+ ++ A +K K +E N K++
Sbjct: 64 FFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAP---KSTYESNTKQSG 111
Score = 51.2 bits (121), Expect = 1e-06, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEK 171
++F+ +L I + + F+ FG I +V D+ G+SKGYGFV F N+ A+ AI++
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 172 LNGMLLNDKQVYVGHFLRK 190
+ G L +Q+ RK
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
Score = 48.5 bits (114), Expect = 7e-06, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 51/89 (57%), Gaps = 4/89 (4%)
Query: 297 KEAADKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFST 355
K+ ++ F ++++ +L I E +K F+PFG I+ +V++D +G S+G GFV+F
Sbjct: 10 KDTSNHF---HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 356 PEEASRALLEMNGKMVVSKPLYVALAQRK 384
+A A+ +M G+ + + + A RK
Sbjct: 67 KWDAENAIQQMGGQWLGGRQIRTNWATRK 95
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 56.2 bits (134), Expect = 3e-08, Method: Composition-based stats.
Identities = 27/77 (35%), Positives = 48/77 (62%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
T+L V L ++TD +LY LF +G + + R+ RD T S GY +V+F++ ++ RA++
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 84 MLNFTPLNGKPIRVMYS 100
+LN + K ++V Y+
Sbjct: 64 VLNGITVRNKRLKVSYA 80
Score = 50.1 bits (118), Expect = 2e-06, Method: Composition-based stats.
Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 307 NLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLE 365
NL + L + D +L LF G I +C++MRD +G S G FV F++ ++ RA+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 366 MNGKMVVSKPLYVALAQ 382
+NG V +K L V+ A+
Sbjct: 65 LNGITVRNKRLKVSYAR 81
Score = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEK 171
N+ + L + + + L+ F A G I +C++ D G S GY FV F +E +Q+AI+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 172 LNGMLLNDKQVYVGH 186
LNG+ + +K++ V +
Sbjct: 65 LNGITVRNKRLKVSY 79
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 41/82 (50%), Gaps = 1/82 (1%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVE 261
TN+ V L + T+ +L F G I + +MRD G S + FV+F + D+ RA++
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 262 ALNGKKFDDKEWYVGKAQKKSE 283
LNG +K V A+ E
Sbjct: 64 VLNGITVRNKRLKVSYARPGGE 85
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 31/73 (42%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEK 171
N+FI +L + L TF FGN++S KV D SK +GFV FDN +SAQ AI+
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
Query: 172 LNGMLLNDKQVYV 184
+NG + K++ V
Sbjct: 102 MNGFQVGTKRLKV 114
Score = 55.5 bits (132), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/81 (35%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 196 EINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSD 254
+I + N+++ +L + T+ DL +F +G + SA V D SKCFGFV+F+N D
Sbjct: 34 QIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPD 93
Query: 255 DAARAVEALNGKKFDDKEWYV 275
A A++A+NG + K V
Sbjct: 94 SAQVAIKAMNGFQVGTKRLKV 114
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 304 QGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRA 362
+G NL+I +L D L F PFG++ S KV D + +S+ GFV+F P+ A A
Sbjct: 39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 363 LLEMNGKMVVSKPLYVAL 380
+ MNG V +K L V L
Sbjct: 99 IKAMNGFQVGTKRLKVQL 116
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 31/61 (50%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L++ L TD+ L F G V+S +V D T S +G+V+F N A A++ +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 86 N 86
N
Sbjct: 103 N 103
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 31/82 (37%), Positives = 50/82 (60%), Gaps = 4/82 (4%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVM--RDPSGI--SRGSGFVAFSTPEEASR 361
+ L+IKNL+ S +E LK +FS G+I SC + ++ +G+ S G GFV + PE+A +
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 362 ALLEMNGKMVVSKPLYVALAQR 383
AL ++ G V L V +++R
Sbjct: 66 ALKQLQGHTVDGHKLEVRISER 87
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 32/92 (34%), Positives = 50/92 (54%), Gaps = 8/92 (8%)
Query: 109 SGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQ----SKGYGFVQFDNEES 164
SG+ +FIKNL+ + + L FS G I SC ++ N S G+GFV++ E
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 165 AQKAIEKLNGMLLNDKQVYVGHFLRKQERDTE 196
AQKA+++L G ++ ++ V R ER T+
Sbjct: 63 AQKALKQLQGHTVDGHKLEV----RISERATK 90
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD----GDGKSKCFGFVNFENSDDAAR 258
+ +++KNL+ STTEE L+ F + G I S + + G S FGFV ++ + A +
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 259 AVEALNGKKFDDKEWYV 275
A++ L G D + V
Sbjct: 66 ALKQLQGHTVDGHKLEV 82
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/84 (23%), Positives = 45/84 (53%), Gaps = 3/84 (3%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRD---LSTRRSLGYGYVNFSNAQEA 78
G++ L++ +L + T+ L +F+++G + S + + S+G+G+V + ++A
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 79 ARALEMLNFTPLNGKPIRVMYSHR 102
+AL+ L ++G + V S R
Sbjct: 64 QKALKQLQGHTVDGHKLEVRISER 87
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 55.5 bits (132), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/76 (38%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 109 SGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKA 168
SGA IF++NL K L D F+ G++L + + NG+SKG G V+F++ E A++A
Sbjct: 6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERA 64
Query: 169 IEKLNGMLLNDKQVYV 184
+NGM L+ +++ V
Sbjct: 65 CRMMNGMKLSGREIDV 80
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G ++V +L + T L D FN+ G V+ + + +S G G V F + + A RA
Sbjct: 7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERA 64
Query: 82 LEMLNFTPLNGKPIRV 97
M+N L+G+ I V
Sbjct: 65 CRMMNGMKLSGREIDV 80
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
++V+NL T + L+ F E G + A + + +GKSK G V FE+ + A RA +N
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMN 69
Query: 265 GKKFDDKE 272
G K +E
Sbjct: 70 GMKLSGRE 77
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLE 365
++++NL + LK F+ G + + + +G S+G G V F +PE A RA
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRM 67
Query: 366 MNGKMVVSKPLYVAL 380
MNG + + + V +
Sbjct: 68 MNGMKLSGREIDVRI 82
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 54.7 bits (130), Expect = 8e-08, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 44/79 (55%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
++VGDL +T + F G++ RV +D++T +S GYG+V+F N +A A+ +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 86 NFTPLNGKPIRVMYSHRDP 104
L G+ IR ++ R P
Sbjct: 78 GGQWLGGRQIRTNWATRKP 96
Score = 53.1 bits (126), Expect = 2e-07, Method: Composition-based stats.
Identities = 32/92 (34%), Positives = 52/92 (56%), Gaps = 5/92 (5%)
Query: 191 QERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVN 249
Q++DT S +V+V +LS T ED++ +F +G I+ A V++D GKSK +GFV+
Sbjct: 8 QKKDT----SNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVS 63
Query: 250 FENSDDAARAVEALNGKKFDDKEWYVGKAQKK 281
F N DA A+ + G+ ++ A +K
Sbjct: 64 FYNKLDAENAIVHMGGQWLGGRQIRTNWATRK 95
Score = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 27/89 (30%), Positives = 51/89 (57%), Gaps = 4/89 (4%)
Query: 297 KEAADKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFST 355
K+ ++ F ++++ +L I E +K F+PFG I+ +V++D +G S+G GFV+F
Sbjct: 10 KDTSNHF---HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYN 66
Query: 356 PEEASRALLEMNGKMVVSKPLYVALAQRK 384
+A A++ M G+ + + + A RK
Sbjct: 67 KLDAENAIVHMGGQWLGGRQIRTNWATRK 95
Score = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEK 171
++F+ +L I + + F+ FG I +V D+ G+SKGYGFV F N+ A+ AI
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 172 LNGMLLNDKQVYVGHFLRK 190
+ G L +Q+ RK
Sbjct: 77 MGGQWLGGRQIRTNWATRK 95
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 54.7 bits (130), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 109 SGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKA 168
SG+ IF++NL K L D F+ G++L + + NG+SKG G V+F++ E A++A
Sbjct: 3 SGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERA 61
Query: 169 IEKLNGMLLNDKQVYV 184
+NGM L+ +++ V
Sbjct: 62 CRMMNGMKLSGREIDV 77
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G++ ++V +L + T L D FN+ G V+ + + +S G G V F + + A RA
Sbjct: 4 GSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADI--KMENGKSKGCGVVKFESPEVAERA 61
Query: 82 LEMLNFTPLNGKPIRV 97
M+N L+G+ I V
Sbjct: 62 CRMMNGMKLSGREIDV 77
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
+ ++V+NL T + L+ F E G + A + + +GKSK G V FE+ + A RA
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRM 64
Query: 263 LNGKKFDDKE 272
+NG K +E
Sbjct: 65 MNGMKLSGRE 74
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLE 365
+ ++++NL + LK F+ G + + + +G S+G G V F +PE A RA
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRM 64
Query: 366 MNGKMVVSKPLYVAL 380
MNG + + + V +
Sbjct: 65 MNGMKLSGREIDVRI 79
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 47/79 (59%)
Query: 305 GANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALL 364
G+ +++ NLD + +KLK++FS G + ++ D G SRG G V F EA +A+
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAIS 74
Query: 365 EMNGKMVVSKPLYVALAQR 383
NG+++ +P++V + +R
Sbjct: 75 MFNGQLLFDRPMHVKMDER 93
Score = 52.8 bits (125), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 40/72 (55%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKL 172
+F+ NLD + K L + FS G ++ + D +G+S+G G V F+ A +AI
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 173 NGMLLNDKQVYV 184
NG LL D+ ++V
Sbjct: 77 NGQLLFDRPMHV 88
Score = 48.1 bits (113), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 43/84 (51%), Gaps = 4/84 (4%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
+ V+V NL + L++ F G + A ++ D DGKS+ G V FE S +A +A+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 263 LNGKKFDDKEWYVGKAQKKSEREL 286
NG+ D+ +V K ER L
Sbjct: 76 FNGQLLFDRPMHV----KMDERAL 95
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
++++V +L+ V +L ++F+ G VV + D +S G G V F + EA +A+
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQAIS 74
Query: 84 MLNFTPLNGKPIRVMYSHR 102
M N L +P+ V R
Sbjct: 75 MFNGQLLFDRPMHVKMDER 93
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 43/171 (25%), Positives = 80/171 (46%), Gaps = 21/171 (12%)
Query: 26 LYVGDLEANVTDSQLYDLFN-QM----------GQVVSVRVCRDLSTRRSLGYGYVNFSN 74
LYVG++ +T+ + D FN QM V++V++ +D + + ++ F +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRS 62
Query: 75 AQEAARALEMLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSA 134
E +A+ G+ +++ H L GA +FI L ++ + + ++
Sbjct: 63 VDETTQAMAFDGII-FQGQSLKIRRPHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTS 119
Query: 135 FGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
FG + + + D G SKGY F ++ + +AI LNGM L DK++ V
Sbjct: 120 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 170
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 42/181 (23%), Positives = 81/181 (44%), Gaps = 26/181 (14%)
Query: 205 VYVKNLSESTTEEDLQKSFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENSDDAAR 258
+YV N+ TEE + F G +T A V+ + K F F+ F + D+ +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 259 AVEALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSID 318
A+ A +G F + L+++ + A K L+I L + ++
Sbjct: 69 AM-AFDGIIFQGQS-------------LKIRRPHDYQPLPGAHK-----LFIGGLPNYLN 109
Query: 319 DEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEMNGKMVVSKPLY 377
D+++K+L + FG + + +++D +G+S+G F + +A+ +NG + K L
Sbjct: 110 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 169
Query: 378 V 378
V
Sbjct: 170 V 170
Score = 32.7 bits (73), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 35/76 (46%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G L++G L + D Q+ +L G + + + +D +T S GY + + + +A
Sbjct: 95 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 154
Query: 82 LEMLNFTPLNGKPIRV 97
+ LN L K + V
Sbjct: 155 IAGLNGMQLGDKKLLV 170
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 43/171 (25%), Positives = 80/171 (46%), Gaps = 21/171 (12%)
Query: 26 LYVGDLEANVTDSQLYDLFN-QM----------GQVVSVRVCRDLSTRRSLGYGYVNFSN 74
LYVG++ +T+ + D FN QM V++V++ +D + + ++ F +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRS 60
Query: 75 AQEAARALEMLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSA 134
E +A+ G+ +++ H L GA +FI L ++ + + ++
Sbjct: 61 VDETTQAMAFDGII-FQGQSLKIRRPHDYQPL--PGAHKLFIGGLPNYLNDDQVKELLTS 117
Query: 135 FGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
FG + + + D G SKGY F ++ + +AI LNGM L DK++ V
Sbjct: 118 FGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 168
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 42/181 (23%), Positives = 81/181 (44%), Gaps = 26/181 (14%)
Query: 205 VYVKNLSESTTEEDLQKSFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENSDDAAR 258
+YV N+ TEE + F G +T A V+ + K F F+ F + D+ +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 259 AVEALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSID 318
A+ A +G F + L+++ + A K L+I L + ++
Sbjct: 67 AM-AFDGIIFQGQS-------------LKIRRPHDYQPLPGAHK-----LFIGGLPNYLN 107
Query: 319 DEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEMNGKMVVSKPLY 377
D+++K+L + FG + + +++D +G+S+G F + +A+ +NG + K L
Sbjct: 108 DDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 167
Query: 378 V 378
V
Sbjct: 168 V 168
Score = 32.7 bits (73), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 35/76 (46%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G L++G L + D Q+ +L G + + + +D +T S GY + + + +A
Sbjct: 93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152
Query: 82 LEMLNFTPLNGKPIRV 97
+ LN L K + V
Sbjct: 153 IAGLNGMQLGDKKLLV 168
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 54.3 bits (129), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 44/73 (60%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
S++VG++ T+ QL D+F+++G VVS R+ D T + GYG+ + + + A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 85 LNFTPLNGKPIRV 97
LN +G+ +RV
Sbjct: 70 LNGREFSGRALRV 82
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 53/104 (50%), Gaps = 12/104 (11%)
Query: 103 DPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDN 161
D SLR ++F+ N+ + L D FS G ++S ++ D G+ KGYGF ++ +
Sbjct: 5 DRSLR-----SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59
Query: 162 EESAQKAIEKLNGMLLNDKQVYVGHFLRKQERDTEINKSKFTNV 205
+E+A A+ LNG + + G LR +E NK + ++
Sbjct: 60 QETALSAMRNLNG------REFSGRALRVDNAASEKNKEELKSL 97
Score = 47.4 bits (111), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 48/87 (55%), Gaps = 2/87 (2%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGD-GKSKCFGFVNFENSDDAARAVEA 262
+V+V N+ TEE L+ F E G + S ++ D + GK K +GF +++ + A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 263 LNGKKFDDKEWYVGKAQKKSERELELK 289
LNG++F + V A + +E ELK
Sbjct: 70 LNGREFSGRALRVDNAASEKNKE-ELK 95
Score = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 307 NLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLE 365
++++ N+ +E+LK +FS G + S +++ D +G +G GF + E A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 366 MNGKMVVSKPLYV 378
+NG+ + L V
Sbjct: 70 LNGREFSGRALRV 82
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 59/278 (21%), Positives = 118/278 (42%), Gaps = 37/278 (13%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+ +KNL K+ + ++ F G I+ VA L + + ++F + A AI K +
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR-FARIEFARYDGALAAITKTH 102
Query: 174 GMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAV 233
++ ++ V H TE ++ N S T+ +++ + + ++
Sbjct: 103 KVV-GQNEIIVSHL-------TE------CTLWXTNFPPSYTQRNIRDLLQDINVVALSI 148
Query: 234 VMRDGD-GKSKCFGFVNFENSDDAARAVEALNGKKFDDKEWYVGKAQKKSERELELKHQF 292
+ S+ F +++ + +DA VE LNG K + ++ +
Sbjct: 149 RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVT-----------KVSNPL 197
Query: 293 EQNMKEAADKFQGANLYIKNLDDSIDDEK-LKQLFSPFGSITSCKVMRDPSGISRGS--- 348
E++ + + +G + I+NL + DE L++ F FGSI + P+G S
Sbjct: 198 EKSKRTDSATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINI---PAGQKEHSFNN 254
Query: 349 --GFVAFSTPEEASRALLEMNGKMVVSKPLYVALAQRK 384
F F + A RA L+ N ++ ++ + V+LA +K
Sbjct: 255 CCAFXVFENKDSAERA-LQXNRSLLGNREISVSLADKK 291
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 49/79 (62%), Gaps = 3/79 (3%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALL 364
ANLY+ L ++ ++++QLFS +G I + +++ D +G+SRG GF+ F EA A+
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 365 EMNGK--MVVSKPLYVALA 381
+NG+ + ++P+ V A
Sbjct: 62 GLNGQKPLGAAEPITVKFA 80
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEK 171
N+++ L K + K + FS +G I++ ++ D G S+G GF++FD A++AI+
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 172 LNG 174
LNG
Sbjct: 63 LNG 65
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 42/65 (64%), Gaps = 1/65 (1%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYG-TITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
N+YV L ++ +++++++ F +YG ITS +++ G S+ GF+ F+ +A A++
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 263 LNGKK 267
LNG+K
Sbjct: 63 LNGQK 67
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 48/83 (57%), Gaps = 3/83 (3%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
+LYV L ++ ++ LF+Q G++++ R+ D +T S G G++ F EA A++
Sbjct: 3 NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKG 62
Query: 85 LNFT-PLN-GKPIRVMYSHRDPS 105
LN PL +PI V +++ +PS
Sbjct: 63 LNGQKPLGAAEPITVKFAN-NPS 84
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 53.1 bits (126), Expect = 3e-07, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
+++VG+LEA V + LY+LF Q G + V +C+D + +G+V F + + + A+ +
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPK-SFGFVCFKHPESVSYAIAL 76
Query: 85 LNFTPLNGKPIRV 97
LN L G+PI V
Sbjct: 77 LNGIRLYGRPINV 89
Score = 47.8 bits (112), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 44/83 (53%), Gaps = 4/83 (4%)
Query: 297 KEAADKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTP 356
+E AD+ +++ NL+ + +E L +LF G +T + +D G + GFV F P
Sbjct: 12 QEEADR----TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHP 67
Query: 357 EEASRALLEMNGKMVVSKPLYVA 379
E S A+ +NG + +P+ V+
Sbjct: 68 ESVSYAIALLNGIRLYGRPINVS 90
Score = 47.0 bits (110), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 35/61 (57%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
V+V NL EE L + F + G +T + +D +GK K FGFV F++ + + A+ LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 265 G 265
G
Sbjct: 79 G 79
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/71 (30%), Positives = 37/71 (52%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+F+ NL+ + + L++ F G + + D G+ K +GFV F + ES AI LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 174 GMLLNDKQVYV 184
G+ L + + V
Sbjct: 79 GIRLYGRPINV 89
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 34/93 (36%), Positives = 52/93 (55%), Gaps = 2/93 (2%)
Query: 189 RKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFV 248
R +TE NKS+ ++V N+ + DL++ FG++G I ++ + G SK FGFV
Sbjct: 17 RGSHMNTE-NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFV 74
Query: 249 NFENSDDAARAVEALNGKKFDDKEWYVGKAQKK 281
FENS DA RA E L+G + ++ V A +
Sbjct: 75 TFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V ++ D L +F Q G+++ V + + R S G+G+V F N+ +A RA E L
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAREKL 89
Query: 86 NFTPLNGKPIRV 97
+ T + G+ I V
Sbjct: 90 HGTVVEGRKIEV 101
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 108 KSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQK 167
KS + + N+ L F FG IL ++ + G SKG+GFV F+N A +
Sbjct: 26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADR 84
Query: 168 AIEKLNGMLLNDKQVYV 184
A EKL+G ++ +++ V
Sbjct: 85 AREKLHGTVVEGRKIEV 101
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 301 DKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEAS 360
+K Q L++ N+ D L+Q+F FG I +++ + G S+G GFV F +A
Sbjct: 25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADAD 83
Query: 361 RALLEMNGKMVVSKPLYV 378
RA +++G +V + + V
Sbjct: 84 RAREKLHGTVVEGRKIEV 101
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 52.8 bits (125), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 33/56 (58%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
L++ L DE ++++F PFG+I C V+R P G S+G FV F T EA A+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI 70
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
++V L + T+ED++K F +GTI V+R DG SK FV F+ +A A+ L+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
Query: 265 GKK 267
+
Sbjct: 75 SSR 77
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 28/60 (46%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+F+ L K + + F FG I C V +G SKG FV+F AQ AI L+
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTLH 74
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 52.4 bits (124), Expect = 4e-07, Method: Composition-based stats.
Identities = 27/66 (40%), Positives = 42/66 (63%), Gaps = 1/66 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGD-GKSKCFGFVNFENSDDAARAVEAL 263
+ V NLSE T E DLQ+ F +G+I+ + +D G+SK F F++F +DAARA+ +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 264 NGKKFD 269
+G +D
Sbjct: 78 SGFGYD 83
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 40/64 (62%), Gaps = 1/64 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALL 364
A + + NL + + L++LF PFGSI+ + +D +G S+G F++F E+A+RA+
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75
Query: 365 EMNG 368
++G
Sbjct: 76 GVSG 79
Score = 41.6 bits (96), Expect = 8e-04, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 104 PSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNE 162
P+ R I + NL + L + F FG+I +A D GQSKG+ F+ F
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 163 ESAQKAIEKLNG 174
E A +AI ++G
Sbjct: 68 EDAARAIAGVSG 79
Score = 36.6 bits (83), Expect = 0.024, Method: Composition-based stats.
Identities = 15/58 (25%), Positives = 35/58 (60%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARAL 82
++ V +L + ++ L +LF G + + + +D +T +S G+ +++F ++AARA+
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 52.4 bits (124), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIE-K 171
+F+ +D +D + F+ +G++ K+ TD G SKGYGFV F N+ QK +E +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 172 LNGMLLNDKQVYVGHFLRKQ 191
+N + K++ +G +RKQ
Sbjct: 71 IN---FHGKKLKLGPAIRKQ 87
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 33/52 (63%)
Query: 302 KFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAF 353
K +++ +D +D+ +++ F+ +GS+ K++ D +G+S+G GFV+F
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 4/79 (5%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA- 262
V+V + E +++ F YG++ ++ D G SK +GFV+F N D + VE+
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 263 LNGKKFDDKEWYVGKAQKK 281
+N F K+ +G A +K
Sbjct: 71 IN---FHGKKLKLGPAIRK 86
Score = 37.0 bits (84), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 48/85 (56%), Gaps = 10/85 (11%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE- 83
+++VG ++ + ++++ F + G V V++ D T S GYG+V+F N + + +E
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 84 MLNFTPLNGKPIRVMYSHRDPSLRK 108
+NF +GK +++ P++RK
Sbjct: 70 QINF---HGKKLKL-----GPAIRK 86
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 52.4 bits (124), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIE-K 171
+F+ +D +D + F+ +G++ K+ TD G SKGYGFV F N+ QK +E +
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 172 LNGMLLNDKQVYVGHFLRKQ 191
+N + K++ +G +RKQ
Sbjct: 72 IN---FHGKKLKLGPAIRKQ 88
Score = 42.0 bits (97), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 34/55 (61%)
Query: 299 AADKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAF 353
+ K +++ +D +D+ +++ F+ +GS+ K++ D +G+S+G GFV+F
Sbjct: 4 GSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 58
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 4/79 (5%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA- 262
V+V + E +++ F YG++ ++ D G SK +GFV+F N D + VE+
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 263 LNGKKFDDKEWYVGKAQKK 281
+N F K+ +G A +K
Sbjct: 72 IN---FHGKKLKLGPAIRK 87
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 48/85 (56%), Gaps = 10/85 (11%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE- 83
+++VG ++ + ++++ F + G V V++ D T S GYG+V+F N + + +E
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 70
Query: 84 MLNFTPLNGKPIRVMYSHRDPSLRK 108
+NF +GK +++ P++RK
Sbjct: 71 QINF---HGKKLKL-----GPAIRK 87
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 52.4 bits (124), Expect = 5e-07, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+F+ +D +D + F+ +G++ K+ TD G SKGYGFV F N+ QK +E +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--S 69
Query: 174 GMLLNDKQVYVGHFLRKQERDT 195
+ + K++ +G +RKQ T
Sbjct: 70 QINFHGKKLKLGPAIRKQNLST 91
Score = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 33/52 (63%)
Query: 302 KFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAF 353
K +++ +D +D+ +++ F+ +GS+ K++ D +G+S+G GFV+F
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSF 57
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 3/67 (4%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA-- 262
V+V + E +++ F YG++ ++ D G SK +GFV+F N D + VE+
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 71
Query: 263 -LNGKKF 268
+GKK
Sbjct: 72 NFHGKKL 78
Score = 35.8 bits (81), Expect = 0.044, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 48/85 (56%), Gaps = 10/85 (11%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE- 83
+++VG ++ + ++++ F + G V V++ D T S GYG+V+F N + + +E
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 84 MLNFTPLNGKPIRVMYSHRDPSLRK 108
+NF +GK +++ P++RK
Sbjct: 70 QINF---HGKKLKL-----GPAIRK 86
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 52.0 bits (123), Expect = 6e-07, Method: Composition-based stats.
Identities = 30/89 (33%), Positives = 49/89 (55%), Gaps = 3/89 (3%)
Query: 297 KEAADKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFST 355
+ + + NLY+ NL +I D++L +F +GSI ++RD +G RG FV ++
Sbjct: 5 RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 64
Query: 356 PEEASRALLEMNGKMVV--SKPLYVALAQ 382
EEA A+ +N + S+PL V LA+
Sbjct: 65 REEAQEAISALNNVIPEGGSQPLSVRLAE 93
Score = 48.5 bits (114), Expect = 6e-06, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 201 KFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARA 259
K TN+YV NL + T++ L FG+YG+I ++RD G+ + FV + ++A A
Sbjct: 12 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 71
Query: 260 VEALN 264
+ ALN
Sbjct: 72 ISALN 76
Score = 46.2 bits (108), Expect = 4e-05, Method: Composition-based stats.
Identities = 23/63 (36%), Positives = 35/63 (55%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
T+LYV +L +TD QL +F + G +V + RD T R G +V ++ +EA A+
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 84 MLN 86
LN
Sbjct: 74 ALN 76
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEK 171
N+++ NL + I L F +G+I+ + D L G+ +G FV+++ E AQ+AI
Sbjct: 15 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 74
Query: 172 LNGML 176
LN ++
Sbjct: 75 LNNVI 79
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 73/163 (44%), Gaps = 6/163 (3%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L V +L ++T Q +L G + + T +S GYG+ + AARA L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 86 NFTPLNGKPIRVMYS---HRDPSLRKSGAGNIFIKNLDKAI-DHKALHDTFSAFGNILSC 141
PL + + V ++ P+L S + + L D AL SA + C
Sbjct: 156 LGKPLGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTFC 213
Query: 142 KVATDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
++A +GQ KG+ ++++ E A++A ++ +G+ L + V
Sbjct: 214 QLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 256
Score = 51.2 bits (121), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 52/242 (21%), Positives = 104/242 (42%), Gaps = 20/242 (8%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
+ + L +VT+ +++DL + ++ C + G +V N ++A A+
Sbjct: 23 ILIRGLPGDVTNQEVHDLLSDY----ELKYC---FVDKYKGTAFVTLLNGEQAEAAINAF 75
Query: 86 NFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSC-KVA 144
+ + L + + V D L + NL ++ + + FG++ C V
Sbjct: 76 HQSRLRERELSVQLQPTDALL--------CVANLPPSLTQQQFEELVRPFGSLERCFLVY 127
Query: 145 TDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYVGHFLRKQERDTEINKSKFTN 204
++ GQSKGYGF ++ ++SA +A L G L + +YV H+ + + S+
Sbjct: 128 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV-HWTDAGQLTPALLHSRC-- 184
Query: 205 VYVKNLSESTTEED-LQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEAL 263
+ V L + D L ++ + T + DG+ K F + +E ++ A A +
Sbjct: 185 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 244
Query: 264 NG 265
+G
Sbjct: 245 DG 246
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 43/163 (26%), Positives = 72/163 (44%), Gaps = 19/163 (11%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
I I+ L + ++ +HD S + + C V + KG FV N E A+ AI +
Sbjct: 23 ILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAFH 76
Query: 174 GMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSA- 232
L ++++ V + Q D + V NL S T++ ++ +G++
Sbjct: 77 QSRLRERELSV----QLQPTDALLC--------VANLPPSLTQQQFEELVRPFGSLERCF 124
Query: 233 VVMRDGDGKSKCFGFVNFENSDDAARAVEALNGKKFDDKEWYV 275
+V + G+SK +GF + D AARA L GK + YV
Sbjct: 125 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 167
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 46/192 (23%), Positives = 77/192 (40%), Gaps = 31/192 (16%)
Query: 188 LRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGF 247
+RK+ TE + ++ L T +++ +Y V K K F
Sbjct: 6 IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAF 59
Query: 248 VNFENSDDAARAVEALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGAN 307
V N + A A+ A + + RE EL Q + A
Sbjct: 60 VTLLNGEQAEAAINAFHQSRL---------------RERELSVQLQPT---------DAL 95
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSC-KVMRDPSGISRGSGFVAFSTPEEASRALLEM 366
L + NL S+ ++ ++L PFGS+ C V + +G S+G GF + + A+RA ++
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 367 NGKMVVSKPLYV 378
GK + + LYV
Sbjct: 156 LGKPLGPRTLYV 167
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 73/163 (44%), Gaps = 6/163 (3%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L V +L ++T Q +L G + + T +S GYG+ + AARA L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 86 NFTPLNGKPIRVMYS---HRDPSLRKSGAGNIFIKNLDKAI-DHKALHDTFSAFGNILSC 141
PL + + V ++ P+L S + + L D AL SA + C
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTFC 215
Query: 142 KVATDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
++A +GQ KG+ ++++ E A++A ++ +G+ L + V
Sbjct: 216 QLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 52/242 (21%), Positives = 104/242 (42%), Gaps = 20/242 (8%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
+ + L +VT+ +++DL + ++ C + G +V N ++A A+
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDY----ELKYC---FVDKYKGTAFVTLLNGEQAEAAINAF 77
Query: 86 NFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSC-KVA 144
+ + L + + V D L + NL ++ + + FG++ C V
Sbjct: 78 HQSRLRERELSVQLQPTDALL--------CVANLPPSLTQQQFEELVRPFGSLERCFLVY 129
Query: 145 TDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYVGHFLRKQERDTEINKSKFTN 204
++ GQSKGYGF ++ ++SA +A L G L + +YV H+ + + S+
Sbjct: 130 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV-HWTDAGQLTPALLHSRC-- 186
Query: 205 VYVKNLSESTTEED-LQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEAL 263
+ V L + D L ++ + T + DG+ K F + +E ++ A A +
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 246
Query: 264 NG 265
+G
Sbjct: 247 DG 248
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 43/163 (26%), Positives = 72/163 (44%), Gaps = 19/163 (11%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
I I+ L + ++ +HD S + + C V + KG FV N E A+ AI +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAFH 78
Query: 174 GMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSA- 232
L ++++ V + Q D + V NL S T++ ++ +G++
Sbjct: 79 QSRLRERELSV----QLQPTDALLC--------VANLPPSLTQQQFEELVRPFGSLERCF 126
Query: 233 VVMRDGDGKSKCFGFVNFENSDDAARAVEALNGKKFDDKEWYV 275
+V + G+SK +GF + D AARA L GK + YV
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 46/192 (23%), Positives = 77/192 (40%), Gaps = 31/192 (16%)
Query: 188 LRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGF 247
+RK+ TE + ++ L T +++ +Y V K K F
Sbjct: 8 IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAF 61
Query: 248 VNFENSDDAARAVEALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGAN 307
V N + A A+ A + + RE EL Q + A
Sbjct: 62 VTLLNGEQAEAAINAFHQSRL---------------RERELSVQLQPT---------DAL 97
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSC-KVMRDPSGISRGSGFVAFSTPEEASRALLEM 366
L + NL S+ ++ ++L PFGS+ C V + +G S+G GF + + A+RA ++
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 367 NGKMVVSKPLYV 378
GK + + LYV
Sbjct: 158 LGKPLGPRTLYV 169
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 73/163 (44%), Gaps = 6/163 (3%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L V +L ++T Q +L G + + T +S GYG+ + AARA L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 86 NFTPLNGKPIRVMYS---HRDPSLRKSGAGNIFIKNLDKAI-DHKALHDTFSAFGNILSC 141
PL + + V ++ P+L S + + L D AL SA + C
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLTPALLHSRC--LCVDRLPPGFNDVDALCRALSAVHSPTFC 215
Query: 142 KVATDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
++A +GQ KG+ ++++ E A++A ++ +G+ L + V
Sbjct: 216 QLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV 258
Score = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 52/242 (21%), Positives = 104/242 (42%), Gaps = 20/242 (8%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
+ + L +VT+ +++DL + ++ C + G +V N ++A A+
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDY----ELKYC---FVDKYKGTAFVTLLNGEQAEAAINAF 77
Query: 86 NFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSC-KVA 144
+ + L + + V D L + NL ++ + + FG++ C V
Sbjct: 78 HQSRLRERELSVQLQPTDALL--------CVANLPPSLTQQQFEELVRPFGSLERCFLVY 129
Query: 145 TDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYVGHFLRKQERDTEINKSKFTN 204
++ GQSKGYGF ++ ++SA +A L G L + +YV H+ + + S+
Sbjct: 130 SERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV-HWTDAGQLTPALLHSRC-- 186
Query: 205 VYVKNLSESTTEED-LQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEAL 263
+ V L + D L ++ + T + DG+ K F + +E ++ A A +
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQA 246
Query: 264 NG 265
+G
Sbjct: 247 DG 248
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 43/163 (26%), Positives = 72/163 (44%), Gaps = 19/163 (11%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
I I+ L + ++ +HD S + + C V + KG FV N E A+ AI +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDY-ELKYCFV-----DKYKGTAFVTLLNGEQAEAAINAFH 78
Query: 174 GMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSA- 232
L ++++ V + Q D + V NL S T++ ++ +G++
Sbjct: 79 QSRLRERELSV----QLQPTDALLC--------VANLPPSLTQQQFEELVRPFGSLERCF 126
Query: 233 VVMRDGDGKSKCFGFVNFENSDDAARAVEALNGKKFDDKEWYV 275
+V + G+SK +GF + D AARA L GK + YV
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYV 169
Score = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 46/192 (23%), Positives = 77/192 (40%), Gaps = 31/192 (16%)
Query: 188 LRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGF 247
+RK+ TE + ++ L T +++ +Y V K K F
Sbjct: 8 IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFV------DKYKGTAF 61
Query: 248 VNFENSDDAARAVEALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGAN 307
V N + A A+ A + + RE EL Q + A
Sbjct: 62 VTLLNGEQAEAAINAFHQSRL---------------RERELSVQLQPT---------DAL 97
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSC-KVMRDPSGISRGSGFVAFSTPEEASRALLEM 366
L + NL S+ ++ ++L PFGS+ C V + +G S+G GF + + A+RA ++
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 367 NGKMVVSKPLYV 378
GK + + LYV
Sbjct: 158 LGKPLGPRTLYV 169
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 37/65 (56%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
L++ L+ +E + +LF PFG I C V+R P G S+G FV FS+ EA A+ ++
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 368 GKMVV 372
G +
Sbjct: 78 GSQTM 82
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 36/63 (57%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
++V L++ +EED+ + F +G I V+R DG SK FV F + +A A+ AL+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 265 GKK 267
G +
Sbjct: 78 GSQ 80
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 31/61 (50%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+F+ L+K + + F FG I C V +G SKG FV+F + AQ AI L+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 174 G 174
G
Sbjct: 78 G 78
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 48/82 (58%), Gaps = 1/82 (1%)
Query: 307 NLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLE 365
NL + + ++D+ +L+QLF +G I S K++ D + SRG GFV F + A +A+
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 366 MNGKMVVSKPLYVALAQRKEDR 387
+NG +++K L VALA R
Sbjct: 104 LNGFNILNKRLKVALAASGHQR 125
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNG-QSKGYGFVQFDNEESAQKAIEK 171
N+ + + +D L F +G I S K+ D QS+GYGFV+F + SAQ+AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 172 LNGMLLNDKQVYV 184
LNG + +K++ V
Sbjct: 104 LNGFNILNKRLKV 116
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 33/97 (34%), Positives = 53/97 (54%), Gaps = 6/97 (6%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
+L V + V + QL LF + G + SV++ D TR+S GYG+V F + A +A+
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 85 LN-FTPLNGKPIRVMYS---HRDPSLRKS-GAGNIFI 116
LN F LN K ++V + H+ P + + G GN ++
Sbjct: 104 LNGFNILN-KRLKVALAASGHQRPGIAGAVGDGNGYL 139
Score = 41.6 bits (96), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 3/94 (3%)
Query: 195 TEINKSK--FTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFE 251
T++N N+ V + + E L++ F YG I S ++ D + + S+ +GFV F+
Sbjct: 33 TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ 92
Query: 252 NSDDAARAVEALNGKKFDDKEWYVGKAQKKSERE 285
+ A +A+ LNG +K V A +R
Sbjct: 93 SGSSAQQAIAGLNGFNILNKRLKVALAASGHQRP 126
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 49.7 bits (117), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 48/82 (58%), Gaps = 1/82 (1%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
++YVG+L + T Q+ +LF+Q G+V +V++ D T++ G+G+V + + A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 85 LNFTPLNGKPIRVMYSHRDPSL 106
L+ T G+ IRV ++ SL
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSL 83
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 2/62 (3%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEK 171
NI++ NL + + + + FS FG + + K+ D + KG+GFV+ EES +AI K
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 172 LN 173
L+
Sbjct: 62 LD 63
Score = 35.8 bits (81), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 43/80 (53%), Gaps = 2/80 (2%)
Query: 307 NLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLE 365
N+Y+ NL S E++K+LFS FG + + K++ D + +G GFV E S A+ +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 366 MNGKMVVSKPLYVALAQRKE 385
++ + + + V A K+
Sbjct: 62 LDNTDFMGRTIRVTEANPKK 81
Score = 35.8 bits (81), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 42/83 (50%), Gaps = 2/83 (2%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDG-KSKCFGFVNFENSDDAARAVEA 262
N+YV NL S T E +++ F ++G + + ++ D + K K FGFV + + + A+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 263 LNGKKFDDKEWYVGKAQKKSERE 285
L+ F + V +A K E
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSLE 84
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 49.3 bits (116), Expect = 4e-06, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 46/79 (58%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
++VGDL +T + + F G++ RV +D++T +S GYG+V+F N +A A++ +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 86 NFTPLNGKPIRVMYSHRDP 104
L G+ IR ++ R P
Sbjct: 69 GGQWLGGRQIRTNWATRKP 87
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEK 171
++F+ +L I A+ F+ FG I +V D+ G+SKGYGFV F N+ A+ AI++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 172 LNGMLLNDKQVYVGHFLRK 190
+ G L +Q+ RK
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVEA 262
+V+V +LS T + +F +G I+ A V++D GKSK +GFV+F N DA A++
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 263 LNGKKFDDKEWYVGKAQKK 281
+ G+ ++ A +K
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 328 PFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEMNGKMVVSKPLYVALAQRK 384
PFG I+ +V++D +G S+G GFV+F +A A+ +M G+ + + + A RK
Sbjct: 29 PFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 47/172 (27%), Positives = 81/172 (47%), Gaps = 23/172 (13%)
Query: 25 SLYVGDLEANVTDSQL----YDLF--NQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEA 78
+L+VG+L N + +L D+F N + VV VR+ TR+ +GYV+F +A++
Sbjct: 9 NLFVGNLNFNKSAPELKTGISDVFAKNDLA-VVDVRIGM---TRK---FGYVDFESAEDL 61
Query: 79 ARALEMLNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNI 138
+ALE+ G I++ S ++ A + KNL + L + F I
Sbjct: 62 EKALELTGLKVF-GNEIKLEKPKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEI 120
Query: 139 -LSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQV---YVGH 186
L K +G+SKG +++F E A+K E+ G ++ + + Y G
Sbjct: 121 RLVSK-----DGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTGE 167
Score = 36.2 bits (82), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 39/168 (23%), Positives = 76/168 (45%), Gaps = 21/168 (12%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEAL 263
N++V NL+ + + +L+ + V+ G ++ FG+V+FE+++D +A+E
Sbjct: 9 NLFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIGMTRKFGYVDFESAEDLEKALELT 68
Query: 264 NGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEKLK 323
K F + E++L+ ++ K+ D L KNL + ++LK
Sbjct: 69 GLKVFGN--------------EIKLEKPKGKDSKKERD---ARTLLAKNLPYKVTQDELK 111
Query: 324 QLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMNGKMV 371
++F I V +D G S+G ++ F T +A + E G +
Sbjct: 112 EVFEDAAEIRL--VSKD--GKSKGIAYIEFKTEADAEKTFEEKQGTEI 155
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 49.3 bits (116), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 5/73 (6%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIE-- 170
+FI L K L D FS FG ++ C + D + G+S+G+GFV F ES K ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 171 --KLNGMLLNDKQ 181
KLNG +++ K+
Sbjct: 62 EHKLNGKVIDPKR 74
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
+++G L + T L D F++ G+VV + D T RS G+G+V F ++ + ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 86 NFTPLNGKPI 95
LNGK I
Sbjct: 62 EHK-LNGKVI 70
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRAL--- 363
++I L + LK FS FG + C + DP +G SRG GFV F E + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 364 -LEMNGKMVVSK 374
++NGK++ K
Sbjct: 62 EHKLNGKVIDPK 73
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE-- 261
+++ LS TT++DL+ F ++G + + D G+S+ FGFV F+ S+ + ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 262 --ALNGKKFDDK 271
LNGK D K
Sbjct: 62 EHKLNGKVIDPK 73
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 44/189 (23%), Positives = 83/189 (43%), Gaps = 37/189 (19%)
Query: 26 LYVGDLEANVTDSQLYDLFN-QM----------GQVVSVRVCRDLSTRRSLGYGYVNFSN 74
LYVG++ +T+ + D FN QM V++V++ +D + + ++ F +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN------FAFLEFRS 60
Query: 75 AQEAARALEMLNFTPLNGKPIRVMYSH---------RDPSLRKSG---------AGNIFI 116
E +A+ G+ +++ H +PS+ G A +FI
Sbjct: 61 VDETTQAMAFDGII-FQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 117 KNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEKLNGM 175
L ++ + + ++FG + + + D G SKGY F ++ + +AI LNGM
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 179
Query: 176 LLNDKQVYV 184
L DK++ V
Sbjct: 180 QLGDKKLLV 188
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 42/190 (22%), Positives = 87/190 (45%), Gaps = 24/190 (12%)
Query: 205 VYVKNLSESTTEEDLQKSFG---EYGTITSAV---VMRDGDGKSKCFGFVNFENSDDAAR 258
+YV N+ TEE + F G +T A V+ + K F F+ F + D+ +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 259 AV---------EALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLY 309
A+ ++L ++ D + G ++ S + + + ++A K L+
Sbjct: 67 AMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPS---VYVPGVVSTVVPDSAHK-----LF 118
Query: 310 IKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEMNG 368
I L + ++D+++K+L + FG + + +++D +G+S+G F + +A+ +NG
Sbjct: 119 IGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNG 178
Query: 369 KMVVSKPLYV 378
+ K L V
Sbjct: 179 MQLGDKKLLV 188
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/65 (43%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
++VK LSE TTEE L++SF G++ + +V G SK FGFV+F + +DA A EA+
Sbjct: 18 LFVKGLSEDTTEETLKESF--DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAME 75
Query: 265 GKKFD 269
+ D
Sbjct: 76 DGEID 80
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 104 PSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEE 163
P+ R + +F+K L + + L ++F G++ + V G SKG+GFV F++EE
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEE 65
Query: 164 SAQKAIEKLNGMLLNDKQVYV 184
A+ A E + ++ +V +
Sbjct: 66 DAKAAKEAMEDGEIDGNKVTL 86
Score = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
+L+V L + T+ L + F+ V R+ D T S G+G+V+F++ ++A A E
Sbjct: 17 TLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73
Query: 85 LNFTPLNGKPIRVMYS 100
+ ++G + + ++
Sbjct: 74 MEDGEIDGNKVTLDWA 89
Score = 32.7 bits (73), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEM 366
L++K L + +E LK+ F GS+ + V +G S+G GFV F++ E+A A M
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 48.9 bits (115), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 29/70 (41%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 207 VKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAVEALNG 265
V LS TTE DL++ F +YG I ++ D + S+ F FV FEN DDA A E NG
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 266 KKFDDKEWYV 275
+ D + V
Sbjct: 111 MELDGRRIRV 120
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 40/75 (53%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L V L T+ L ++F++ G + V + D +RRS G+ +V F N +A A E
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 86 NFTPLNGKPIRVMYS 100
N L+G+ IRV +S
Sbjct: 109 NGMELDGRRIRVDFS 123
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 126 KALHDTFSAFGNILSCKVATDLNGQ-SKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
+ L + FS +G I + D + S+G+ FV F+N + A++A E+ NGM L+ +++ V
Sbjct: 61 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
++V N+ + DL++ FG++G I ++ + G SK FGFV FENS DA RA E L+
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 265 GKKFDDKEWYVGKAQKK 281
G + ++ V A +
Sbjct: 77 GTVVEGRKIEVNNATAR 93
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V ++ D L +F Q G+++ V + + R S G+G+V F N+ +A RA E L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRAREKL 75
Query: 86 NFTPLNGKPIRV 97
+ T + G+ I V
Sbjct: 76 HGTVVEGRKIEV 87
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 128 LHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
L F FG IL ++ + G SKG+GFV F+N A +A EKL+G ++ +++ V
Sbjct: 32 LRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEV 87
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
L++ N+ D L+Q+F FG I +++ + G S+G GFV F +A RA +++
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLH 76
Query: 368 GKMVVSKPLYV 378
G +V + + V
Sbjct: 77 GTVVEGRKIEV 87
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 29/70 (41%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 207 VKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAVEALNG 265
V LS TTE DL++ F +YG I ++ D + S+ F FV FEN DDA A E NG
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 266 KKFDDKEWYV 275
+ D + V
Sbjct: 77 MELDGRRIRV 86
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 40/75 (53%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L V L T+ L ++F++ G + V + D +RRS G+ +V F N +A A E
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 86 NFTPLNGKPIRVMYS 100
N L+G+ IRV +S
Sbjct: 75 NGMELDGRRIRVDFS 89
Score = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 126 KALHDTFSAFGNILSCKVATDLNGQ-SKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
+ L + FS +G I + D + S+G+ FV F+N + A++A E+ NGM L+ +++ V
Sbjct: 27 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 86
Query: 185 GHFLRKQ 191
+ K+
Sbjct: 87 DFSITKR 93
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDG-KSKCFGFVNFENSDDAARAVE 261
+ VYV NL S T DL + F +YG + +M+D D KSK F+ F + D A
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 262 ALNGKKF 268
A+N K+
Sbjct: 77 AINNKQL 83
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 43/73 (58%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
+++YV +L ++T++ LY +F++ G+VV V + +D TR+S G ++ F + A
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 84 MLNFTPLNGKPIR 96
+N L G+ I+
Sbjct: 77 AINNKQLFGRVIK 89
Score = 35.0 bits (79), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALL 364
+ +Y+ NL S+ + L ++FS +G + +M+D + S+G F+ F + A
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 365 EMNGKMVVSKPLYVALA 381
+N K + + + ++A
Sbjct: 77 AINNKQLFGRVIKASIA 93
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNG-QSKGYGFVQFDNEESAQKAIEKL 172
+++ NL ++ + L+ FS +G ++ + D + +SKG F+ F +++SAQ +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 173 N 173
N
Sbjct: 79 N 79
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 48.5 bits (114), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 40/165 (24%), Positives = 81/165 (49%), Gaps = 9/165 (5%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
+L++G+L N + ++L +++ + V D+ T + +GYV+F +A++ +ALE+
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALEL 73
Query: 85 LNFTPLNGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVA 144
G I++ S + A + KNL I L + F + L ++
Sbjct: 74 TGLKVF-GNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFE---DALEIRLV 129
Query: 145 TDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQV---YVGH 186
+ +G+SKG +++F +E A+K +E+ G ++ + V Y G
Sbjct: 130 SQ-DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 37/168 (22%), Positives = 76/168 (45%), Gaps = 21/168 (12%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEAL 263
N+++ NL+ + + +L+ + E V+ G ++ FG+V+FE+++D +A+E L
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-L 73
Query: 264 NGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKEAADKFQGANLYIKNLDDSIDDEKLK 323
G K E + K + + +++ L KNL +I +++LK
Sbjct: 74 TGLKVFGNEIKLEKPKGRDSKKVRAAR----------------TLLAKNLSFNITEDELK 117
Query: 324 QLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMNGKMV 371
++F I + G S+G ++ F + +A + L E G +
Sbjct: 118 EVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 161
Score = 32.0 bits (71), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 25/102 (24%), Positives = 48/102 (47%), Gaps = 1/102 (0%)
Query: 295 NMKEAADKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFS 354
+M E ++ NL+I NL+ + +LK S + V+ +G +R G+V F
Sbjct: 3 HMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFE 62
Query: 355 TPEEASRALLEMNGKMVVSKPLYVALAQRKEDRRARLQVCLL 396
+ E+ +A LE+ G V + + + ++ ++ R LL
Sbjct: 63 SAEDLEKA-LELTGLKVFGNEIKLEKPKGRDSKKVRAARTLL 103
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 48.1 bits (113), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 37/64 (57%), Gaps = 4/64 (6%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
VYV NL + + +L+++FG YG + S V R+ G F FV FE+ DAA AV L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRELD 131
Query: 265 GKKF 268
G+
Sbjct: 132 GRTL 135
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
+Y+ NL ++ + +L++ F +G + S V R+P G + FV F P +A+ A+ E++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRELD 131
Query: 368 GKMVVSKPLYVALA 381
G+ + + V L+
Sbjct: 132 GRTLCGCRVRVELS 145
Score = 36.2 bits (82), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
+YVG+L N ++L F G + SV V R+ G+ +V F + ++AA A+ L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 130
Query: 86 NFTPLNGKPIRVMYSH 101
+ L G +RV S+
Sbjct: 131 DGRTLCGCRVRVELSN 146
Score = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+++ NL + L F +G + S VA + G+ FV+F++ A A+ +L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELD 131
Query: 174 GMLLNDKQVYV 184
G L +V V
Sbjct: 132 GRTLCGCRVRV 142
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 29/70 (41%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 207 VKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAVEALNG 265
V LS TTE DL++ F +YG I ++ D + S+ F FV FEN DDA A E NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 266 KKFDDKEWYV 275
+ D + V
Sbjct: 80 MELDGRRIRV 89
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 40/75 (53%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L V L T+ L ++F++ G + V + D +RRS G+ +V F N +A A E
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 86 NFTPLNGKPIRVMYS 100
N L+G+ IRV +S
Sbjct: 78 NGMELDGRRIRVDFS 92
Score = 41.6 bits (96), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 126 KALHDTFSAFGNILSCKVATDLNGQ-SKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
+ L + FS +G I + D + S+G+ FV F+N + A++A E+ NGM L+ +++ V
Sbjct: 30 RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 89
Query: 185 GHFLRKQ 191
+ K+
Sbjct: 90 DFSITKR 96
Score = 28.1 bits (61), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 305 GANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRAL 363
G +LY D L+++FS +G I ++ D S SRG FV F ++A A
Sbjct: 22 GLSLYTTERD-------LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 74
Query: 364 LEMNG 368
NG
Sbjct: 75 ERANG 79
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 37/64 (57%), Gaps = 4/64 (6%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
VYV NL + + +L+++FG YG + S V R+ G F FV FE+ DAA AV L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPG----FAFVEFEDPRDAADAVRDLD 131
Query: 265 GKKF 268
G+
Sbjct: 132 GRTL 135
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
+Y+ NL ++ + +L++ F +G + S V R+P G + FV F P +A+ A+ +++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFA----FVEFEDPRDAADAVRDLD 131
Query: 368 GKMVVSKPLYVALA 381
G+ + + V L+
Sbjct: 132 GRTLCGCRVRVELS 145
Score = 35.8 bits (81), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
+YVG+L N ++L F G + SV V R+ G+ +V F + ++AA A+ L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRDL 130
Query: 86 NFTPLNGKPIRVMYSH 101
+ L G +RV S+
Sbjct: 131 DGRTLCGCRVRVELSN 146
Score = 32.3 bits (72), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+++ NL + L F +G + S VA + G+ FV+F++ A A+ L+
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRDLD 131
Query: 174 GMLLNDKQVYV 184
G L +V V
Sbjct: 132 GRTLCGCRVRV 142
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 5/77 (6%)
Query: 111 AGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLN-GQSKGYGFVQFDNEESAQKAI 169
AG F+ L K L D F+ FG ++ C + D N G+S+G+GF+ F + S +K +
Sbjct: 11 AGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL 70
Query: 170 E----KLNGMLLNDKQV 182
+ +L+G +++ K+
Sbjct: 71 DQKEHRLDGRVIDPKKA 87
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 27 YVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
+VG L + + L D F + G+VV + D +T RS G+G++ F +A + L+
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLD 71
Score = 35.8 bits (81), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 322 LKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRAL 363
LK F+ FG + C + DP +G SRG GF+ F + L
Sbjct: 28 LKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL 70
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/70 (41%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 207 VKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAVEALNG 265
V LS TTE DL++ F +YG I ++ D + S+ F FV FEN DDA A E NG
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 266 KKFDDKEWYV 275
+ D + V
Sbjct: 80 MELDGRRIRV 89
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L V L T+ L ++F++ G + V + D +RRS G+ +V F N +A A E
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 86 NFTPLNGKPIRV 97
N L+G+ IRV
Sbjct: 78 NGMELDGRRIRV 89
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 125 HKALHDTFSAFGNILSCKVATDLNGQ-SKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVY 183
+ L + FS +G I + D + S+G+ FV F+N + A++A E+ NGM L+ +++
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Query: 184 V 184
V
Sbjct: 89 V 89
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/92 (27%), Positives = 51/92 (55%), Gaps = 7/92 (7%)
Query: 200 SKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARA 259
+K ++V+NL+ + TEE L+K+F ++G + ++D + F++F+ D A +A
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKA 61
Query: 260 VEALNGKKFDDKEWYVGKAQKKSERELELKHQ 291
+E +NGK + + + A+ ++ E K Q
Sbjct: 62 MEEMNGKDLEGENIEIVFAKPPDQKRKERKAQ 93
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 51/91 (56%), Gaps = 11/91 (12%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
L+++NL +++ +E L++ FS FG + K ++D F+ F + A +A+ EMN
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 66
Query: 368 GKMVVSKPLYVALA----QRKEDRRARLQVC 394
GK + + + + A Q++++R+A+ Q
Sbjct: 67 GKDLEGENIEIVFAKPPDQKRKERKAQRQAA 97
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+F++NL + + L FS FG + K D Y F+ FD + A KA+E++N
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEMN 66
Query: 174 GMLLNDKQVYV 184
G L + + +
Sbjct: 67 GKDLEGENIEI 77
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V +L VT+ L F+Q G++ V+ +D Y +++F A +A+E +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 86 NFTPLNGKPIRVMYSHRDPSLRK 108
N L G+ I ++++ RK
Sbjct: 66 NGKDLEGENIEIVFAKPPDQKRK 88
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 25 SLYVGDLEANVTDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAAR 80
++Y+ +L + +L Y +F+Q GQ++ + V R L R G +V F A
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 66
Query: 81 ALEMLNFTPLNGKPIRVMYSHRD 103
AL + P KP+R+ Y+ D
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTD 89
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 46/95 (48%), Gaps = 6/95 (6%)
Query: 307 NLYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRA 362
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ A
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 67
Query: 363 LLEMNGKMVVSKPLYVALAQRKEDRRARLQVCLLQ 397
L M G KP+ + A+ D A+++ ++
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVE 102
Score = 36.6 bits (83), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 6/93 (6%)
Query: 204 NVYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARA 259
+Y+ NL+E +++L+KS F ++G I +V R + + FV F+ A A
Sbjct: 10 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQA--FVIFKEVSSATNA 67
Query: 260 VEALNGKKFDDKEWYVGKAQKKSERELELKHQF 292
+ ++ G F DK + A+ S+ ++K F
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 46.6 bits (109), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G TSL V +L + L +F + G+V V + RD T+ S G+ +V F + ++A A
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 82 LEMLNFTPLNGKPIRV 97
++ ++ L+G+ +RV
Sbjct: 129 MDAMDGAVLDGRELRV 144
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 202 FTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAV 260
T++ V NL+ T+ + L++ F +YG + + RD K S+ F FV F + DA A+
Sbjct: 70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
Query: 261 EALNGKKFDDKEWYVGKAQ 279
+A++G D +E V A+
Sbjct: 130 DAMDGAVLDGRELRVQMAR 148
Score = 35.4 bits (80), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 110 GAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKA 168
G ++ + NL L F +G + + D +S+G+ FV+F ++ A+ A
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128
Query: 169 IEKLNGMLLNDKQVYV 184
++ ++G +L+ +++ V
Sbjct: 129 MDAMDGAVLDGRELRV 144
Score = 34.7 bits (78), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALL 364
+L + NL + L+++F +G + + RD + SRG FV F +A A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 365 EMNGKMVVSKPLYVALAQ 382
M+G ++ + L V +A+
Sbjct: 131 AMDGAVLDGRELRVQMAR 148
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 38/65 (58%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
L++ L+ ++ +++LF FG+I C ++R P G S+G FV +S+ EA A+ ++
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 368 GKMVV 372
G +
Sbjct: 78 GSQTM 82
Score = 45.4 bits (106), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 5/73 (6%)
Query: 102 RDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDN 161
+ PS RK +F+ L+K + F AFGNI C + +G SKG FV++ +
Sbjct: 11 QPPSHRK-----LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSS 65
Query: 162 EESAQKAIEKLNG 174
AQ AI L+G
Sbjct: 66 HAEAQAAINALHG 78
Score = 41.6 bits (96), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 37/63 (58%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
++V L++ +E+D+++ F +G I ++R DG SK FV + + +A A+ AL+
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINALH 77
Query: 265 GKK 267
G +
Sbjct: 78 GSQ 80
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 46.2 bits (108), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 7/73 (9%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
T ++V N+S + T ++L+ F EYG + +++D + FV+ E ++DA A+
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-------YAFVHMERAEDAVEAIRG 63
Query: 263 LNGKKFDDKEWYV 275
L+ +F K +V
Sbjct: 64 LDNTEFQGKRMHV 76
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 202 FTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSDDAARAV 260
T++ V NL+ T+ + L++ F +YG + + RD K S+ F FV F + DA A+
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 261 EALNGKKFDDKEWYVGKAQ 279
+A++G D +E V A+
Sbjct: 107 DAMDGAVLDGRELRVQMAR 125
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 43/76 (56%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G TSL V +L + L +F + G+V V + RD T+ S G+ +V F + ++A A
Sbjct: 46 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 105
Query: 82 LEMLNFTPLNGKPIRV 97
++ ++ L+G+ +RV
Sbjct: 106 MDAMDGAVLDGRELRV 121
Score = 36.6 bits (83), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 104 PSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNE 162
P G ++ + NL L F +G + + D +S+G+ FV+F ++
Sbjct: 40 PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 99
Query: 163 ESAQKAIEKLNGMLLNDKQVYV 184
A+ A++ ++G +L+ +++ V
Sbjct: 100 RDAEDAMDAMDGAVLDGRELRV 121
Score = 32.0 bits (71), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 307 NLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLE 365
+L + NL + L+++F +G + + RD + SRG FV F +A A+
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 366 MNGKMVVSKPLYVALAQ 382
M+G ++ + L V +A+
Sbjct: 109 MDGAVLDGRELRVQMAR 125
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 8/73 (10%)
Query: 194 DTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENS 253
D E+ +K ++V+NL+ + TEE L+KSF E+G + ++D + FV+FE+
Sbjct: 8 DPEVM-AKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDR 59
Query: 254 DDAARAVEALNGK 266
A +A++ +NGK
Sbjct: 60 GAAVKAMDEMNGK 72
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+F++NL + + L +FS FG + K D Y FV F++ +A KA++++N
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMN 70
Query: 174 G 174
G
Sbjct: 71 G 71
Score = 38.5 bits (88), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 45/82 (54%), Gaps = 7/82 (8%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
L+++NL ++ +E L++ FS FG + K ++D FV F A +A+ EMN
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD-------YAFVHFEDRGAAVKAMDEMN 70
Query: 368 GKMVVSKPLYVALAQRKEDRRA 389
GK + + + + LA+ + +R+
Sbjct: 71 GKEIEGEEIEIVLAKPPDKKRS 92
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V +L VT+ L F++ G++ V+ +D Y +V+F + A +A++ +
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEDRGAAVKAMDEM 69
Query: 86 N 86
N
Sbjct: 70 N 70
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 43/80 (53%), Gaps = 1/80 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEAL 263
++V+NLS +++EEDL+K F YG ++ D K K F FV F + A +A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 264 NGKKFDDKEWYVGKAQKKSE 283
+G+ F + +V + K E
Sbjct: 71 DGQVFQGRMLHVLPSTIKKE 90
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLEM 366
L+++NL + +E L++LFS +G ++ D + +G FV F PE A +A E+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 367 NGKMVVSKPLYVALAQRKED 386
+G++ + L+V + K++
Sbjct: 71 DGQVFQGRMLHVLPSTIKKE 90
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEKL 172
+F++NL + L FSA+G + D L + KG+ FV F E A KA ++
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 173 NGMLLNDKQVYV 184
+G + + ++V
Sbjct: 71 DGQVFQGRMLHV 82
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 35/75 (46%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V +L ++ L LF+ G + + D T++ G+ +V F + A +A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 86 NFTPLNGKPIRVMYS 100
+ G+ + V+ S
Sbjct: 71 DGQVFQGRMLHVLPS 85
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 45.8 bits (107), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 25 SLYVGDLEANVTDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAAR 80
++Y+ +L + +L Y +F+Q GQ++ + V R L R G +V F A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 81 ALEMLNFTPLNGKPIRVMYSHRD 103
AL + P KP+R+ Y+ D
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTD 90
Score = 41.2 bits (95), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 40/84 (47%), Gaps = 6/84 (7%)
Query: 307 NLYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRA 362
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 68
Query: 363 LLEMNGKMVVSKPLYVALAQRKED 386
L M G KP+ + A+ D
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSD 92
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 6/84 (7%)
Query: 204 NVYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARA 259
+Y+ NL+E +++L+KS F ++G I +V R + + FV F+ A A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQ--AFVIFKEVSSATNA 68
Query: 260 VEALNGKKFDDKEWYVGKAQKKSE 283
+ ++ G F DK + A+ S+
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSD 92
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 45/79 (56%), Gaps = 5/79 (6%)
Query: 198 NKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGK-SKCFGFVNFENSD-- 254
K +F +++ LS TTEE L+ + ++G +T VVMRD K S+ FGFV F +
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 255 DAARAV--EALNGKKFDDK 271
DAA A +++G+ + K
Sbjct: 83 DAAMAARPHSIDGRVVEPK 101
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 42/79 (53%), Gaps = 5/79 (6%)
Query: 301 DKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEA 359
+K Q L+I L +E L+ + +G +T C VMRDP S SRG GFV FS+ E
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
Query: 360 SRALL----EMNGKMVVSK 374
A+ ++G++V K
Sbjct: 83 DAAMAARPHSIDGRVVEPK 101
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 47/87 (54%), Gaps = 4/87 (4%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L++G L T+ L + + Q G++ V RD +++RS G+G+V FS+ E A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 86 NFTPLNGKPIRVMYSHRDPSLRKSGAG 112
+ ++G RV+ R + +SG+G
Sbjct: 90 PHS-IDG---RVVEPKRAVAREESGSG 112
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/90 (26%), Positives = 48/90 (53%)
Query: 23 TTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARAL 82
+ +LYVG+L T+ Q+Y+LF++ G + + + D + + G+ +V + + +A A+
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 83 EMLNFTPLNGKPIRVMYSHRDPSLRKSGAG 112
+N T L+ + IR + R+ G G
Sbjct: 99 RYINGTRLDDRIIRTDWDAGFKEGRQYGRG 128
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 32/96 (33%), Positives = 48/96 (50%), Gaps = 6/96 (6%)
Query: 186 HFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKC- 244
HF E ++ K T +YV NLS TTEE + + F + G I ++ D K+ C
Sbjct: 24 HFRGDNEEQEKLLKKSCT-LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 245 FGFVNFENSDDAARAVEALNGKKFDDK----EWYVG 276
F FV + + DA A+ +NG + DD+ +W G
Sbjct: 83 FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG 118
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEK 171
+++ NL + +++ FS G+I + D + + G+ FV++ + A+ A+
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 172 LNGMLLNDKQV 182
+NG L+D+ +
Sbjct: 101 INGTRLDDRII 111
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 25 SLYVGDLEANVTDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAAR 80
++Y+ +L + +L Y +F+Q GQ++ + V R L R G +V F A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMR---GQAFVIFKEVSSATN 67
Query: 81 ALEMLNFTPLNGKPIRVMYSHRD 103
AL + P KP+R+ Y+ D
Sbjct: 68 ALRSMQGFPFYDKPMRIQYAKTD 90
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 44/90 (48%), Gaps = 6/90 (6%)
Query: 307 NLYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRA 362
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 68
Query: 363 LLEMNGKMVVSKPLYVALAQRKEDRRARLQ 392
L M G KP+ + A+ D A+++
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 6/93 (6%)
Query: 204 NVYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARA 259
+Y+ NL+E +++L+KS F ++G I +V R + + FV F+ A A
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQA--FVIFKEVSSATNA 68
Query: 260 VEALNGKKFDDKEWYVGKAQKKSERELELKHQF 292
+ ++ G F DK + A+ S+ ++K F
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 101
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 45.1 bits (105), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 47/83 (56%), Gaps = 2/83 (2%)
Query: 307 NLYIKNLDDSIDDEKLKQLF-SPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLE 365
+L++ +L +DD L + F + S KV+ D +G+S+G GFV F+ E RAL E
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 366 MNGKM-VVSKPLYVALAQRKEDR 387
G + + SKP+ +++A K R
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASR 93
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 113 NIFIKNLDKAIDHKALHDTF-SAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEK 171
++F+ +L +D L++ F + + KV D G SKGYGFV+F +E ++A+ +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTE 70
Query: 172 LNGML-LNDKQVYVGHFLRKQER 193
G + L K V + + K R
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASR 93
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 29/75 (38%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQM-GQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARAL- 82
SL+VGDL +V D LY+ F ++ +V D T S GYG+V F++ E RAL
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRALT 69
Query: 83 EMLNFTPLNGKPIRV 97
E L KP+R+
Sbjct: 70 ECQGAVGLGSKPVRL 84
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 43/82 (52%)
Query: 305 GANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALL 364
GA L + NLD + D +++LF+ FG++ V D SG S G+ V F +A +A+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 365 EMNGKMVVSKPLYVALAQRKED 386
+ G + +P+ + L + D
Sbjct: 95 QYKGVPLDGRPMDIQLVASQID 116
Score = 41.6 bits (96), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L V +L+ V+D+ + +LF + G + V D S R SLG V+F +A +A++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFERRADALKAMKQY 96
Query: 86 NFTPLNGKPIRV 97
PL+G+P+ +
Sbjct: 97 KGVPLDGRPMDI 108
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
+ V NL ++ D+Q+ F E+GT+ A V D G+S V+FE DA +A++
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95
Query: 263 LNGKKFDDK 271
G D +
Sbjct: 96 YKGVPLDGR 104
Score = 35.8 bits (81), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 36/71 (50%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+ + NLD + + + F+ FG + V D +G+S G V F+ A KA+++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 174 GMLLNDKQVYV 184
G+ L+ + + +
Sbjct: 98 GVPLDGRPMDI 108
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 43/82 (52%)
Query: 305 GANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALL 364
GA L + NLD + D +++LF+ FG++ V D SG S G+ V F +A +A+
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
Query: 365 EMNGKMVVSKPLYVALAQRKED 386
+ G + +P+ + L + D
Sbjct: 95 QYKGVPLDGRPMDIQLVASQID 116
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L V +L+ V+D+ + +LF + G + V D S R SLG V+F +A +A++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFERRADALKAMKQY 96
Query: 86 NFTPLNGKPIRV 97
PL+G+P+ +
Sbjct: 97 KGVPLDGRPMDI 108
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 35/69 (50%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
+ V NL ++ D+Q+ F E+GT+ A V D G+S V+FE DA +A++
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95
Query: 263 LNGKKFDDK 271
G D +
Sbjct: 96 YKGVPLDGR 104
Score = 35.8 bits (81), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 36/71 (50%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+ + NLD + + + F+ FG + V D +G+S G V F+ A KA+++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 174 GMLLNDKQVYV 184
G+ L+ + + +
Sbjct: 98 GVPLDGRPMDI 108
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 44.7 bits (104), Expect = 9e-05, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 45/82 (54%), Gaps = 5/82 (6%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDA----ARA 259
+++ LS TT+E L++ FG++G + +VMRD +S+ FGFV F + A++
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 87
Query: 260 VEALNGKKFDDKEWYVGKAQKK 281
L+ K D K + +AQ K
Sbjct: 88 RHELDSKTIDPKVAFPRRAQPK 109
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 28/85 (32%), Positives = 39/85 (45%), Gaps = 5/85 (5%)
Query: 305 GANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRAL 363
G ++I L E L++ F FG + C VMRDP + SRG GFV F + L
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84
Query: 364 L----EMNGKMVVSKPLYVALAQRK 384
E++ K + K + AQ K
Sbjct: 85 AQSRHELDSKTIDPKVAFPRRAQPK 109
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNF 72
+++G L T L + F Q G+V V RD T+RS G+G+V F
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
Score = 35.4 bits (80), Expect = 0.063, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 109 SGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQK 167
S +FI L + L + F FG + C V D L +S+G+GFV F ++ K
Sbjct: 23 SSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 82
Query: 168 AIEK 171
+ +
Sbjct: 83 VLAQ 86
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 44.7 bits (104), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEM 366
LY+ L + +DD+ L F PFG IT ++ D + RG FV F E+A+ A+ M
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 367 NGKMVVSKPLYVALA 381
N + + + V LA
Sbjct: 126 NESELFGRTIRVNLA 140
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQ-SKGYGFVQFDNEESAQKAIEKL 172
+++ L + +D K LH F FG+I ++ D + +G+ FV+F+ E A AI+ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 173 N 173
N
Sbjct: 126 N 126
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDG-KSKCFGFVNFENSDDAARAVEAL 263
+YV L+E ++ L +F +G IT + D + K + F FV FE ++DAA A++ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 264 N 264
N
Sbjct: 126 N 126
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L V +L+ V+D+ + +LF + G + V D S R SLG V+F +A +A++
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADVHFERKADALKAMKQY 89
Query: 86 NFTPLNGKPIRV 97
N PL+G+P+ +
Sbjct: 90 NGVPLDGRPMNI 101
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
L + NLD + D +++LF+ FG++ V D SG S G+ V F +A +A+ + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 368 GKMVVSKPLYVAL 380
G + +P+ + L
Sbjct: 91 GVPLDGRPMNIQL 103
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 35/65 (53%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
+ V NL ++ D+Q+ F E+GT+ A V D G+S V+FE DA +A++ N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 265 GKKFD 269
G D
Sbjct: 91 GVPLD 95
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 38/71 (53%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+ + NLD + + + F+ FG + V D +G+S G V F+ + A KA+++ N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 174 GMLLNDKQVYV 184
G+ L+ + + +
Sbjct: 91 GVPLDGRPMNI 101
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 44/75 (58%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
+Y+G + + T+ Q+ DL + +G V+++++ D T RS GY ++ F + + +A A+ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 86 NFTPLNGKPIRVMYS 100
N L + ++ YS
Sbjct: 65 NGYQLGSRFLKCGYS 79
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEKL 172
+++ ++ + + D S G +++ K+ D G+SKGY F++F + ES+ A+ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 173 NGMLLNDKQVYVGH 186
NG L + + G+
Sbjct: 65 NGYQLGSRFLKCGY 78
Score = 33.5 bits (75), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGD-GKSKCFGFVNFENSDDAARAVEAL 263
VY+ ++ TEE + G + + +M D G+SK + F+ F + + +A AV L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 264 NGKKFDDK 271
NG + +
Sbjct: 65 NGYQLGSR 72
Score = 32.7 bits (73), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLEM 366
+Y+ ++ +E++ L S G + + K+M DP +G S+G F+ F E ++ A+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 367 NGKMVVSK 374
NG + S+
Sbjct: 65 NGYQLGSR 72
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 7/81 (8%)
Query: 291 QFEQNMKEAADKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGF 350
+FE + +++ K +Y + + D+ ++Q FSPFG I +V + +G F
Sbjct: 13 RFEDVVNQSSPK--NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSF 65
Query: 351 VAFSTPEEASRALLEMNGKMV 371
V FST E A+ A++ +NG +
Sbjct: 66 VRFSTHESAAHAIVSVNGTTI 86
Score = 42.4 bits (98), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
++Y G + + +TD + F+ GQ++ +RV + GY +V FS + AA A+
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS 80
Query: 85 LNFTPLNGKPIRVMYSHRDPSL 106
+N T + G ++ + P +
Sbjct: 81 VNGTTIEGHVVKCYWGKESPDM 102
Score = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
++ + + + + TFS FG I+ +V + KGY FV+F ESA AI +N
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVN 82
Query: 174 G 174
G
Sbjct: 83 G 83
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 44/75 (58%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
+Y+G + + T+ Q+ DL + +G V+++++ D T RS GY ++ F + + +A A+ L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 86 NFTPLNGKPIRVMYS 100
N L + ++ YS
Sbjct: 67 NGYQLGSRFLKCGYS 81
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEKL 172
+++ ++ + + D S G +++ K+ D G+SKGY F++F + ES+ A+ L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 173 NGMLLNDKQVYVGH 186
NG L + + G+
Sbjct: 67 NGYQLGSRFLKCGY 80
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGD-GKSKCFGFVNFENSDDAARAVEAL 263
VY+ ++ TEE + G + + +M D G+SK + F+ F + + +A AV L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 264 NGKKFDDK 271
NG + +
Sbjct: 67 NGYQLGSR 74
Score = 32.7 bits (73), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLEM 366
+Y+ ++ +E++ L S G + + K+M DP +G S+G F+ F E ++ A+ +
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 367 NGKMVVSK 374
NG + S+
Sbjct: 67 NGYQLGSR 74
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 44/75 (58%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
+Y+G + + T+ Q+ DL + +G V+++++ D T RS GY ++ F + + +A A+ L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 86 NFTPLNGKPIRVMYS 100
N L + ++ YS
Sbjct: 66 NGYQLGSRFLKCGYS 80
Score = 37.4 bits (85), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEKL 172
+++ ++ + + D S G +++ K+ D G+SKGY F++F + ES+ A+ L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 173 NGMLLNDKQVYVGH 186
NG L + + G+
Sbjct: 66 NGYQLGSRFLKCGY 79
Score = 33.1 bits (74), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGD-GKSKCFGFVNFENSDDAARAVEAL 263
VY+ ++ TEE + G + + +M D G+SK + F+ F + + +A AV L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 264 NGKKFDDK 271
NG + +
Sbjct: 66 NGYQLGSR 73
Score = 32.7 bits (73), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALLEM 366
+Y+ ++ +E++ L S G + + K+M DP +G S+G F+ F E ++ A+ +
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 367 NGKMVVSK 374
NG + S+
Sbjct: 66 NGYQLGSR 73
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEM 366
LY+ L + +DD+ L F PFG IT ++ D + RG FV F E+A+ A+ M
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 367 NGKMVVSKPLYVALAQ 382
N + + + V LA+
Sbjct: 70 NESELFGRTIRVNLAK 85
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQS-KGYGFVQFDNEESAQKAIEKL 172
+++ L + +D K LH F FG+I ++ D + +G+ FV+F+ E A AI+ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 173 N 173
N
Sbjct: 70 N 70
Score = 37.0 bits (84), Expect = 0.021, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDG-KSKCFGFVNFENSDDAARAVEAL 263
+YV L+E ++ L +F +G IT + D + K + F FV FE ++DAA A++ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 264 N 264
N
Sbjct: 70 N 70
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEM 366
LY+ L + +DD+ L F PFG IT ++ D + RG FV F E+A+ A+ M
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 367 NGKMVVSKPLYVALAQ 382
N + + + V LA+
Sbjct: 68 NESELFGRTIRVNLAK 83
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQS-KGYGFVQFDNEESAQKAIEKL 172
+++ L + +D K LH F FG+I ++ D + +G+ FV+F+ E A AI+ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 173 N 173
N
Sbjct: 68 N 68
Score = 37.0 bits (84), Expect = 0.022, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDG-KSKCFGFVNFENSDDAARAVEAL 263
+YV L+E ++ L +F +G IT + D + K + F FV FE ++DAA A++ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 264 N 264
N
Sbjct: 68 N 68
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEM 366
LY+ L + +DD+ L F PFG IT ++ D + RG FV F E+A+ A+ M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 367 NGKMVVSKPLYVALAQ 382
N + + + V LA+
Sbjct: 75 NESELFGRTIRVNLAK 90
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQS-KGYGFVQFDNEESAQKAIEKL 172
+++ L + +D K LH F FG+I ++ D + +G+ FV+F+ E A AI+ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 173 N 173
N
Sbjct: 75 N 75
Score = 36.6 bits (83), Expect = 0.022, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDG-KSKCFGFVNFENSDDAARAVEAL 263
+YV L+E ++ L +F +G IT + D + K + F FV FE ++DAA A++ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 264 N 264
N
Sbjct: 75 N 75
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
VYV NL + +L+++F YG + + + R+ G F FV FE+ DA AV L+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG----FAFVEFEDPRDAEDAVRGLD 58
Query: 265 GK 266
GK
Sbjct: 59 GK 60
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 43/84 (51%), Gaps = 5/84 (5%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
+Y+ NL +L++ FS +G + + + R+P G + FV F P +A A+ ++
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFA----FVEFEDPRDAEDAVRGLD 58
Query: 368 GKMVVSKPLYVALAQRKEDRRARL 391
GK++ + V L+ RR+R
Sbjct: 59 GKVICGSRVRVELSTGMP-RRSRF 81
Score = 31.6 bits (70), Expect = 0.72, Method: Composition-based stats.
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+++ NL L FS +G + + +A + G+ FV+F++ A+ A+ L+
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLD 58
Query: 174 GMLLNDKQVYV 184
G ++ +V V
Sbjct: 59 GKVICGSRVRV 69
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 43.9 bits (102), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 38/67 (56%), Gaps = 9/67 (13%)
Query: 205 VYVKNLSESTTEEDLQKSFGEY--GTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
+YV+NL ST+EE ++K F G + +RD + FV+F N +DA A++A
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-------YAFVHFSNREDAVEAMKA 70
Query: 263 LNGKKFD 269
LNGK D
Sbjct: 71 LNGKVLD 77
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 10/74 (13%)
Query: 26 LYVGDLEANVTDSQLYDLFNQM--GQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
LYV +L + ++ + FN + G V V+ RD Y +V+FSN ++A A++
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD--------YAFVHFSNREDAVEAMK 69
Query: 84 MLNFTPLNGKPIRV 97
LN L+G PI V
Sbjct: 70 ALNGKVLDGSPIEV 83
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 9/77 (11%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPF--GSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLE 365
LY++NL S +E +++ F+ G++ K +RD FV FS E+A A+
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-------YAFVHFSNREDAVEAMKA 70
Query: 366 MNGKMVVSKPLYVALAQ 382
+NGK++ P+ V LA+
Sbjct: 71 LNGKVLDGSPIEVTLAK 87
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 154 YGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
Y FV F N E A +A++ LNG +L+ + V
Sbjct: 53 YAFVHFSNREDAVEAMKALNGKVLDGSPIEV 83
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 35/64 (54%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G++ LY+ L+ TD L L G++VS + D +T + GYG+V+F + A +A
Sbjct: 4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
Query: 82 LEML 85
+ L
Sbjct: 64 VTAL 67
Score = 41.2 bits (95), Expect = 0.001, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 109 SGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQK 167
SG+ ++I+ L + L +G I+S K D + KGYGFV FD+ +AQK
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62
Query: 168 AIEKL 172
A+ L
Sbjct: 63 AVTAL 67
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRALL 364
+ LYI+ L D+ L +L P+G I S K + D + +G GFV F +P A +A+
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 365 EMNGKMVVSK 374
+ V ++
Sbjct: 66 ALKASGVQAQ 75
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE 261
+ +Y++ L TT++DL K YG I S + D K K +GFV+F++ A +AV
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 262 AL 263
AL
Sbjct: 66 AL 67
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 43.5 bits (101), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEM 366
LY+ L + +DD+ L F PFG IT ++ D + RG FV F E+A+ A+ M
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 367 NGKMVVSKPLYVALA 381
N + + + V LA
Sbjct: 65 NESELFGRTIRVNLA 79
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQS-KGYGFVQFDNEESAQKAIEKL 172
+++ L + +D K LH F FG+I ++ D + +G+ FV+F+ E A AI+ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 173 N 173
N
Sbjct: 65 N 65
Score = 37.0 bits (84), Expect = 0.020, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDG-KSKCFGFVNFENSDDAARAVEAL 263
+YV L+E ++ L +F +G IT + D + K + F FV FE ++DAA A++ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 264 N 264
N
Sbjct: 65 N 65
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 8/65 (12%)
Query: 114 IFIKNLDKAIDHKA-LHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKL 172
+FI NL+ A+ K+ + FS +G + C V KGY FVQ+ NE A+ A+
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGE 82
Query: 173 NGMLL 177
NG +L
Sbjct: 83 NGRVL 87
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
++VG + N +++L + F + G V V + D +R G+G++ F + Q +A+ M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM- 71
Query: 86 NFTPLNGKPIRV 97
+F + GK + V
Sbjct: 72 HFHDIMGKKVEV 83
Score = 32.0 bits (71), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQ-SKGYGFVQFDNEESAQKAI 169
IF+ + L + F FG + + D Q +G+GF+ F++E+S +A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 39/71 (54%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+FI L + + L + A G + ++ T+ G+ KG +V+++NE A +A+ K++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 174 GMLLNDKQVYV 184
GM + + + V
Sbjct: 80 GMTIKENIIKV 90
Score = 35.4 bits (80), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 35/61 (57%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
+++ L S T+E+L++ +GT+ ++ + GK K +V +EN A++AV ++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 265 G 265
G
Sbjct: 80 G 80
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 41/76 (53%)
Query: 305 GANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALL 364
GA L + NLD + D +++LF+ FG++ V D SG S G+ V F +A +A+
Sbjct: 88 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 147
Query: 365 EMNGKMVVSKPLYVAL 380
+ G + +P+ + L
Sbjct: 148 QYKGVPLDGRPMDIQL 163
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L V +L+ V+D+ + +LF + G + V D S R SLG V+F +A +A++
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFERRADALKAMKQY 149
Query: 86 NFTPLNGKPIRV 97
PL+G+P+ +
Sbjct: 150 KGVPLDGRPMDI 161
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 35/67 (52%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
+ V NL ++ D+Q+ F E+GT+ A V D G+S V+FE DA +A++
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 265 GKKFDDK 271
G D +
Sbjct: 151 GVPLDGR 157
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 36/71 (50%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+ + NLD + + + F+ FG + V D +G+S G V F+ A KA+++
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 174 GMLLNDKQVYV 184
G+ L+ + + +
Sbjct: 151 GVPLDGRPMDI 161
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 28/82 (34%), Positives = 44/82 (53%), Gaps = 5/82 (6%)
Query: 200 SKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGD-GKSKCFGFVNFENSDDAAR 258
+ FT ++V L TT+ L+K F +G I AVV+ D GKS+ +GFV + A R
Sbjct: 15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 74
Query: 259 AVE----ALNGKKFDDKEWYVG 276
A + ++G+K + Y+G
Sbjct: 75 ACKDPNPIIDGRKANVNLAYLG 96
Score = 38.5 bits (88), Expect = 0.006, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 29/58 (50%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
T ++VG L + TD+ L F G + V D T +S GYG+V ++ A RA
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
Score = 36.2 bits (82), Expect = 0.029, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLN-GQSKGYGFVQFDNEESAQKAIEKL 172
IF+ L +L F FG+I V TD G+S+GYGFV + +A++A +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 173 NGML 176
N ++
Sbjct: 80 NPII 83
Score = 32.3 bits (72), Expect = 0.49, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEM 366
+++ L D L++ F FG I V+ D +G SRG GFV + A RA +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 367 N 367
N
Sbjct: 80 N 80
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 44/89 (49%), Gaps = 6/89 (6%)
Query: 308 LYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ AL
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 65
Query: 364 LEMNGKMVVSKPLYVALAQRKEDRRARLQ 392
M G KP+ + A+ D A+++
Sbjct: 66 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 94
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 114 IFIKNLDKAIDH----KALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAI 169
I+I NL++ I K+LH FS FG IL V+ L + +G FV F SA A+
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 65
Query: 170 EKLNGMLLNDKQVYVGH 186
+ G DK + + +
Sbjct: 66 RSMQGFPFYDKPMRIQY 82
Score = 36.2 bits (82), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 205 VYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAV 260
+Y+ NL+E +++L+KS F +G I +V R + + FV F+ A A+
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATNAL 65
Query: 261 EALNGKKFDDKEWYVGKAQKKSE 283
++ G F DK + A+ S+
Sbjct: 66 RSMQGFPFYDKPMRIQYAKTDSD 88
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEA- 262
++V L STT+E L+ F +YG + V+M+D +S+ FGFV F++ + + +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 263 ---LNGKKFDDK 271
L+G+ D K
Sbjct: 79 PHTLDGRNIDPK 90
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 30/49 (61%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSN 74
L+VG L+ + T L F+Q G+VV + +D +T +S G+G+V F +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 112 GNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDN 161
G +F+ LD + + L FS +G ++ C + D QS+G+GFV+F +
Sbjct: 17 GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 44/90 (48%), Gaps = 6/90 (6%)
Query: 307 NLYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRA 362
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 67
Query: 363 LLEMNGKMVVSKPLYVALAQRKEDRRARLQ 392
L M G KP+ + A+ D A+++
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 113 NIFIKNLDKAIDH----KALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKA 168
I+I NL++ I K+LH FS FG IL V+ L + +G FV F SA A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 67
Query: 169 IEKLNGMLLNDKQVYVGH 186
+ + G DK + + +
Sbjct: 68 LRSMQGFPFYDKPMRIQY 85
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 204 NVYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARA 259
+Y+ NL+E +++L+KS F +G I +V R + + FV F+ A A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQA--FVIFKEVSSATNA 67
Query: 260 VEALNGKKFDDKEWYVGKAQKKSERELELKHQF 292
+ ++ G F DK + A+ S+ ++K F
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 100
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 1/75 (1%)
Query: 23 TTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARAL 82
+ +LYVG+L T+ Q+Y+LF++ G + + + D + + G+ +V + + +A A+
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD-KMKTACGFCFVEYYSRADAENAM 76
Query: 83 EMLNFTPLNGKPIRV 97
+N T L+ + IR
Sbjct: 77 RYINGTRLDDRIIRT 91
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 46/95 (48%), Gaps = 5/95 (5%)
Query: 186 HFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCF 245
HF E ++ K T +YV NLS TTEE + + F + G I ++ D + F
Sbjct: 3 HFRGDNEEQEKLLKKSCT-LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGF 61
Query: 246 GFVNFENSDDAARAVEALNGKKFDDK----EWYVG 276
FV + + DA A+ +NG + DD+ +W G
Sbjct: 62 CFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG 96
Score = 32.0 bits (71), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 106 LRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESA 165
L+KS +++ NL + +++ FS G+I + D + G+ FV++ + A
Sbjct: 15 LKKSCT--LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADA 72
Query: 166 QKAIEKLNGMLLNDKQV 182
+ A+ +NG L+D+ +
Sbjct: 73 ENAMRYINGTRLDDRII 89
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%)
Query: 304 QGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
+ LY+ NL +E++ +LFS G I + D + G FV + + +A A+
Sbjct: 17 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAM 76
Query: 364 LEMNG 368
+NG
Sbjct: 77 RYING 81
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 25 SLYVGDLEANVTDSQL----YDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAAR 80
++Y+ ++ + +L Y LF+Q G VV + + + R G +V F +
Sbjct: 8 TIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMR---GQAFVIFKELGSSTN 64
Query: 81 ALEMLNFTPLNGKPIRVMYSHRD 103
AL L P GKP+R+ Y+ D
Sbjct: 65 ALRQLQGFPFYGKPMRIQYAKTD 87
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/87 (32%), Positives = 42/87 (48%), Gaps = 12/87 (13%)
Query: 307 NLYIKNLDDSIDDEKLKQ----LFSPFGS---ITSCKVMRDPSGISRGSGFVAFSTPEEA 359
+YI N++D I E+LK+ LFS FG I + K M+ RG FV F +
Sbjct: 8 TIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMK-----MRGQAFVIFKELGSS 62
Query: 360 SRALLEMNGKMVVSKPLYVALAQRKED 386
+ AL ++ G KP+ + A+ D
Sbjct: 63 TNALRQLQGFPFYGKPMRIQYAKTDSD 89
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 6/84 (7%)
Query: 204 NVYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARA 259
+Y+ N+++ +E+L++S F ++G + V ++ + + FV F+ + A
Sbjct: 8 TIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQA--FVIFKELGSSTNA 65
Query: 260 VEALNGKKFDDKEWYVGKAQKKSE 283
+ L G F K + A+ S+
Sbjct: 66 LRQLQGFPFYGKPMRIQYAKTDSD 89
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
L+++ + + +L ++F PFG + K++ G FV F E A++A+ E++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAKAIEEVH 59
Query: 368 GKMVVSKPLYVALAQ 382
GK ++PL V ++
Sbjct: 60 GKSFANQPLEVVYSK 74
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
T L+V +V +S+L ++F G + V++ G+ +V F A+ AA+A+E
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIE 56
Query: 84 MLNFTPLNGKPIRVMYS 100
++ +P+ V+YS
Sbjct: 57 EVHGKSFANQPLEVVYS 73
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
T ++V+ E +L + FG +G + ++ F FV FE ++ AA+A+E
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEFEEAESAAKAIEE 57
Query: 263 LNGKKFDDKEWYV 275
++GK F ++ V
Sbjct: 58 VHGKSFANQPLEV 70
Score = 38.1 bits (87), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+F++ + L++ F FG + K+ LNG + FV+F+ ESA KAIE+++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKI---LNG----FAFVEFEEAESAAKAIEEVH 59
Query: 174 G 174
G
Sbjct: 60 G 60
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
+ V NL ++ D+Q+ F E+GT+ A V D G+S V+FE DA +A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 265 GKKFD 269
G D
Sbjct: 92 GVPLD 96
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L V +L+ V+D+ + +LF + G + V D S R SLG V+F +A +A +
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGR-SLGTADVHFERKADALKAXKQY 90
Query: 86 NFTPLNGKPIRV 97
N PL+G+P +
Sbjct: 91 NGVPLDGRPXNI 102
Score = 42.0 bits (97), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
L + NLD + D +++LF+ FG++ V D SG S G+ V F +A +A + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 368 GKMVVSKPLYVAL 380
G + +P + L
Sbjct: 92 GVPLDGRPXNIQL 104
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+ + NLD + + + F+ FG + V D +G+S G V F+ + A KA ++ N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 174 GMLLN 178
G+ L+
Sbjct: 92 GVPLD 96
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 44/90 (48%), Gaps = 6/90 (6%)
Query: 307 NLYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRA 362
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 67
Query: 363 LLEMNGKMVVSKPLYVALAQRKEDRRARLQ 392
L M G KP+ + A+ D A+++
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 113 NIFIKNLDKAIDH----KALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKA 168
I+I NL++ I K+LH FS FG IL V+ L + +G FV F SA A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 67
Query: 169 IEKLNGMLLNDKQVYVGH 186
+ + G DK + + +
Sbjct: 68 LRSMQGFPFYDKPMRIQY 85
Score = 36.2 bits (82), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 204 NVYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARA 259
+Y+ NL+E +++L+KS F +G I +V R + + FV F+ A A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATNA 67
Query: 260 VEALNGKKFDDKEWYVGKAQKKSE 283
+ ++ G F DK + A+ S+
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSD 91
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQ-VVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
SL++GDLE + ++ + F MG+ V+SV++ R+ T GY +V F++ A + L
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 84 MLNFTPLNG 92
+N PL G
Sbjct: 71 KINGKPLPG 79
Score = 36.6 bits (83), Expect = 0.024, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 111 AGNIFIKNLDKAIDHKALHDTFSAFG-NILSCKVATD-LNGQSKGYGFVQFDNEESAQKA 168
A ++++ +L+ +D + F+ G ++S K+ + L G GY FV+F + +A+K
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68
Query: 169 IEKLNG 174
+ K+NG
Sbjct: 69 LHKING 74
Score = 35.4 bits (80), Expect = 0.059, Method: Composition-based stats.
Identities = 20/67 (29%), Positives = 40/67 (59%), Gaps = 2/67 (2%)
Query: 305 GANLYIKNLDDSIDDEKLKQLFSPFG-SITSCKVMRDP-SGISRGSGFVAFSTPEEASRA 362
A+L++ +L+ +D+ + + F+ G ++ S K++R+ +GI G FV F+ A +
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68
Query: 363 LLEMNGK 369
L ++NGK
Sbjct: 69 LHKINGK 75
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 44/90 (48%), Gaps = 6/90 (6%)
Query: 307 NLYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRA 362
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 68
Query: 363 LLEMNGKMVVSKPLYVALAQRKEDRRARLQ 392
L M G KP+ + A+ D A+++
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 113 NIFIKNLDKAIDH----KALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKA 168
I+I NL++ I K+LH FS FG IL V+ L + +G FV F SA A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 68
Query: 169 IEKLNGMLLNDKQVYVGH 186
+ + G DK + + +
Sbjct: 69 LRSMQGFPFYDKPMRIQY 86
Score = 36.2 bits (82), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 204 NVYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARA 259
+Y+ NL+E +++L+KS F +G I +V R + + FV F+ A A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQA--FVIFKEVSSATNA 68
Query: 260 VEALNGKKFDDKEWYVGKAQKKSE 283
+ ++ G F DK + A+ S+
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSD 92
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 44/89 (49%), Gaps = 6/89 (6%)
Query: 308 LYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ AL
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 66
Query: 364 LEMNGKMVVSKPLYVALAQRKEDRRARLQ 392
M G KP+ + A+ D A+++
Sbjct: 67 RSMQGFPFYDKPMRIQYAKTDSDIIAKMK 95
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 114 IFIKNLDKAIDH----KALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAI 169
I+I NL++ I K+LH FS FG IL V+ L + +G FV F SA A+
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 66
Query: 170 EKLNGMLLNDKQVYVGH 186
+ G DK + + +
Sbjct: 67 RSMQGFPFYDKPMRIQY 83
Score = 36.2 bits (82), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 205 VYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAV 260
+Y+ NL+E +++L+KS F +G I +V R + + FV F+ A A+
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATNAL 66
Query: 261 EALNGKKFDDKEWYVGKAQKKSE 283
++ G F DK + A+ S+
Sbjct: 67 RSMQGFPFYDKPMRIQYAKTDSD 89
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 44/90 (48%), Gaps = 6/90 (6%)
Query: 307 NLYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRA 362
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 68
Query: 363 LLEMNGKMVVSKPLYVALAQRKEDRRARLQ 392
L M G KP+ + A+ D A+++
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 98
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 113 NIFIKNLDKAIDH----KALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKA 168
I+I NL++ I K+LH FS FG IL V+ L + +G FV F SA A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 68
Query: 169 IEKLNGMLLNDKQVYVGH 186
+ + G DK + + +
Sbjct: 69 LRSMQGFPFYDKPMRIQY 86
Score = 36.6 bits (83), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 204 NVYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARA 259
+Y+ NL+E +++L+KS F +G I +V R + + FV F+ A A
Sbjct: 11 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATNA 68
Query: 260 VEALNGKKFDDKEWYVGKAQKKSE 283
+ ++ G F DK + A+ S+
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSD 92
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 9/77 (11%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRR-----SLGYGYVNFSNAQEA 78
T +++G L NVT + ++F+ G++ + D+ R S GY YV F N EA
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMI----DMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 79 ARALEMLNFTPLNGKPI 95
+AL+ ++ ++G+ I
Sbjct: 61 EKALKHMDGGQIDGQEI 77
Score = 42.0 bits (97), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 201 KFTNVYVKNLSESTTEEDLQKSFGEYGTIT--SAVVMRDGDGKSKCFGFVNFENSDDAAR 258
K T V++ L+ + T++ + + F YG I V R SK + +V FEN D+A +
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 259 AVEALNGKKFDDKE 272
A++ ++G + D +E
Sbjct: 63 ALKHMDGGQIDGQE 76
Score = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSIT--SCKVMRDPSGISRGSGFVAFSTPEEASRALLE 365
++I L ++ + + ++FS +G I V R +S+G +V F P+EA +AL
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 366 MNGKMV 371
M+G +
Sbjct: 67 MDGGQI 72
Score = 35.8 bits (81), Expect = 0.039, Method: Composition-based stats.
Identities = 18/71 (25%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNI--LSCKVATDLNGQSKGYGFVQFDNEESAQKAIEK 171
+ I L + + + + FS +G I + V SKGY +V+F+N + A+KA++
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 172 LNGMLLNDKQV 182
++G ++ +++
Sbjct: 67 MDGGQIDGQEI 77
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/86 (24%), Positives = 42/86 (48%), Gaps = 7/86 (8%)
Query: 302 KFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASR 361
+ L+++ + + +L ++F PFG + K++ G FV F E A++
Sbjct: 28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFVEFEEAESAAK 80
Query: 362 ALLEMNGKMVVSKPLYVALAQRKEDR 387
A+ E++GK ++PL V ++ R
Sbjct: 81 AIEEVHGKSFANQPLEVVYSKLPAKR 106
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 21 FGTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAAR 80
T L+V +V +S+L ++F G + V++ G+ +V F A+ AA+
Sbjct: 29 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAK 80
Query: 81 ALEMLNFTPLNGKPIRVMYS 100
A+E ++ +P+ V+YS
Sbjct: 81 AIEEVHGKSFANQPLEVVYS 100
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 7/82 (8%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
T ++V+ E +L + FG +G + ++ F FV FE ++ AA+A+E
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-------FAFVEFEEAESAAKAIEE 84
Query: 263 LNGKKFDDKEWYVGKAQKKSER 284
++GK F ++ V ++ ++R
Sbjct: 85 VHGKSFANQPLEVVYSKLPAKR 106
Score = 35.8 bits (81), Expect = 0.042, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+F++ + L++ F FG + K+ LNG + FV+F+ ESA KAIE+++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKI---LNG----FAFVEFEEAESAAKAIEEVH 86
Query: 174 G 174
G
Sbjct: 87 G 87
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 30/89 (33%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 307 NLYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRA 362
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNA 67
Query: 363 LLEMNGKMVVSKPLYVALAQRKEDRRARL 391
L M G KP+ + A+ D A++
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSDIIAKM 96
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 113 NIFIKNLDKAIDH----KALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKA 168
I+I NL++ I K+LH FS FG IL V+ L + +G FV F SA A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNA 67
Query: 169 IEKLNGMLLNDKQVYVGH 186
+ + G DK + + +
Sbjct: 68 LRSMQGFPFYDKPMRIQY 85
Score = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 204 NVYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARA 259
+Y+ NL+E +++L+KS F +G I +V R + + FV F+ A A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATNA 67
Query: 260 VEALNGKKFDDKEWYVGKAQKKSE 283
+ ++ G F DK + A+ S+
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSD 91
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 308 LYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ AL
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 63
Query: 364 LEMNGKMVVSKPLYVALAQRKED 386
M G KP+ + A+ D
Sbjct: 64 RSMQGFPFYDKPMRIQYAKTDSD 86
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 114 IFIKNLDKAIDH----KALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAI 169
I+I NL++ I K+LH FS FG IL V+ L + +G FV F SA A+
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 63
Query: 170 EKLNGMLLNDKQVYVGH 186
+ G DK + + +
Sbjct: 64 RSMQGFPFYDKPMRIQY 80
Score = 36.2 bits (82), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 205 VYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAV 260
+Y+ NL+E +++L+KS F +G I +V R + + FV F+ A A+
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATNAL 63
Query: 261 EALNGKKFDDKEWYVGKAQKKSE 283
++ G F DK + A+ S+
Sbjct: 64 RSMQGFPFYDKPMRIQYAKTDSD 86
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 41.6 bits (96), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 308 LYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ AL
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNAL 64
Query: 364 LEMNGKMVVSKPLYVALAQRKED 386
M G KP+ + A+ D
Sbjct: 65 RSMQGFPFYDKPMRIQYAKTDSD 87
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 114 IFIKNLDKAIDH----KALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAI 169
I+I NL++ I K+LH FS FG IL V+ L + +G FV F SA A+
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KMRGQAFVIFKEVSSATNAL 64
Query: 170 EKLNGMLLNDKQVYVGH 186
+ G DK + + +
Sbjct: 65 RSMQGFPFYDKPMRIQY 81
Score = 36.2 bits (82), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 205 VYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAV 260
+Y+ NL+E +++L+KS F +G I +V R + + FV F+ A A+
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ--AFVIFKEVSSATNAL 64
Query: 261 EALNGKKFDDKEWYVGKAQKKSE 283
++ G F DK + A+ S+
Sbjct: 65 RSMQGFPFYDKPMRIQYAKTDSD 87
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 7/71 (9%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
IF+ N+ A + L F G ++ C V D Y FV + E A+ AI +LN
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64
Query: 174 GMLLNDKQVYV 184
G + K++ V
Sbjct: 65 GKEVKGKRINV 75
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 10/88 (11%)
Query: 23 TTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARAL 82
T ++VG++ A T +L LF + G+V+ V +D Y +V+ +A A+
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAI 60
Query: 83 EMLNFTPLNGKPIRVMYSHRDPSLRKSG 110
LN + GK I V S + +KSG
Sbjct: 61 AQLNGKEVKGKRINVELSTKGQ--KKSG 86
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
++V N+S + T ++L+ F G + V++D + FV+ E DA A+ LN
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKAAIAQLN 64
Query: 265 GKKFDDKEWYV---GKAQKKS 282
GK+ K V K QKKS
Sbjct: 65 GKEVKGKRINVELSTKGQKKS 85
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 202 FTNVYVKNLSESTTEEDLQKSFGEYGTITS-AVVMRDGDGKSKCFGFVNFENSDDAARAV 260
F ++V ++ TTE L++ F YG I +V GK + + F+ +E+ D A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 261 EALNGKKFD 269
+ +GKK D
Sbjct: 162 KHADGKKID 170
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 18/91 (19%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 95 IRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCK-VATDLNGQSKG 153
+++ H DP+ + +F+ ++ L F +G I V + +G+ +G
Sbjct: 86 LKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
Query: 154 YGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
Y F+++++E A + +G ++ ++V V
Sbjct: 146 YAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDA----ARA 259
+++ LS TT+E L++ FG++G + +VMRD +S+ FGFV F + A++
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62
Query: 260 VEALNGKKFDDK 271
L+ K D K
Sbjct: 63 RHELDSKTIDPK 74
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 20/47 (42%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAF 353
++I L E L++ F FG + C VMRDP + SRG GFV F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 38.5 bits (88), Expect = 0.007, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNF 72
+++G L T L + F Q G+V V RD T+RS G+G+V F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 34.3 bits (77), Expect = 0.11, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEK 171
+FI L + L + F FG + C V D L +S+G+GFV F ++ K + +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
>pdb|2XB2|D Chain D, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 90
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 37/72 (51%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V + T+ ++D F + G++ ++ + D T GY V + +EA A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 86 NFTPLNGKPIRV 97
N L G+PI V
Sbjct: 70 NGQDLMGQPISV 81
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVEAL 263
++V + E TEED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 264 NGK 266
NG+
Sbjct: 70 NGQ 72
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEKL 172
+F+ + + + +HD F+ +G I + + D G KGY V+++ + AQ A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 173 NGMLLNDKQVYV 184
NG L + + V
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 37/72 (51%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V + T+ ++D F + G++ ++ + D T GY V + +EA A+E L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 86 NFTPLNGKPIRV 97
N L G+PI V
Sbjct: 72 NGQDLMGQPISV 83
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVEAL 263
++V + E TEED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 264 NGK 266
NG+
Sbjct: 72 NGQ 74
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 104 PSLRKSGAGNI-FIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDN 161
P ++S G I F+ + + + +HD F+ +G I + + D G KGY V+++
Sbjct: 1 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYET 60
Query: 162 EESAQKAIEKLNGMLLNDKQVYV 184
+ AQ A+E LNG L + + V
Sbjct: 61 YKEAQAAMEGLNGQDLMGQPISV 83
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 6/83 (7%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
+ L+VG+L ++T+ ++ LF + G+ V + +D G+G++ A A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 69
Query: 84 MLNFTPLNGKPIRVMYSHRDPSL 106
L+ PL GK +RV ++ SL
Sbjct: 70 ELDNMPLRGKQLRVRFACHSASL 92
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
+ ++V NL TEE+++K F +YG + +D K FGF+ E A A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVE 70
Query: 263 LNGKKFDDKEWYV 275
L+ K+ V
Sbjct: 71 LDNMPLRGKQLRV 83
Score = 32.7 bits (73), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+F+ NL I + + F +G + D KG+GF++ + A+ A +L+
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELD 72
Query: 174 GMLLNDKQVYV 184
M L KQ+ V
Sbjct: 73 NMPLRGKQLRV 83
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 37/72 (51%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V + T+ ++D F + G++ ++ + D T GY V + +EA A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 86 NFTPLNGKPIRV 97
N L G+PI V
Sbjct: 70 NGQDLMGQPISV 81
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVEAL 263
++V + E TEED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 264 NGK 266
NG+
Sbjct: 70 NGQ 72
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEKL 172
+F+ + + + +HD F+ +G I + + D G KGY V+++ + AQ A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 173 NGMLLNDKQVYV 184
NG L + + V
Sbjct: 70 NGQDLMGQPISV 81
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
Length = 109
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 37/72 (51%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V + T+ ++D F + G++ ++ + D T GY V + +EA A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 86 NFTPLNGKPIRV 97
N L G+PI V
Sbjct: 70 NGQDLMGQPISV 81
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVEAL 263
++V + E TEED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 264 NGK 266
NG+
Sbjct: 70 NGQ 72
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEKL 172
+F+ + + + +HD F+ +G I + + D G KGY V+++ + AQ A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 173 NGMLLNDKQVYV 184
NG L + + V
Sbjct: 70 NGQDLMGQPISV 81
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 37/72 (51%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V + T+ ++D F + G++ ++ + D T GY V + +EA A+E L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 86 NFTPLNGKPIRV 97
N L G+PI V
Sbjct: 86 NGQDLMGQPISV 97
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVEAL 263
++V + E TEED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 264 NGK 266
NG+
Sbjct: 86 NGQ 88
Score = 39.3 bits (90), Expect = 0.004, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 2/84 (2%)
Query: 103 DPSLRKSGAGNI-FIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFD 160
+P ++S G I F+ + + + +HD F+ +G I + + D G KGY V+++
Sbjct: 14 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 73
Query: 161 NEESAQKAIEKLNGMLLNDKQVYV 184
+ AQ A+E LNG L + + V
Sbjct: 74 TYKEAQAAMEGLNGQDLMGQPISV 97
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 7/68 (10%)
Query: 200 SKFTNVYVKNLSESTTEEDLQKSFGEYG-TITSAVVMRDGDGKSKCFGFVNFENSDDAAR 258
S +Y+ NLS + T +DL++ FG+ + V+++ G + FV++ + + A R
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSG------YAFVDYPDQNWAIR 59
Query: 259 AVEALNGK 266
A+E L+GK
Sbjct: 60 AIETLSGK 67
Score = 33.1 bits (74), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 42/90 (46%), Gaps = 8/90 (8%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G LY+G+L VT L LF ++ +V GY +V++ + A RA
Sbjct: 7 GMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNWAIRA 60
Query: 82 LEMLNF-TPLNGKPIRVMYSHRDPSLRKSG 110
+E L+ L+GK + V YS LR SG
Sbjct: 61 IETLSGKVELHGKIMEVDYSVSK-KLRSSG 89
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 6/88 (6%)
Query: 109 SGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKA 168
SG ++I NL A+ L F L+ +V GY FV + ++ A +A
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRA 60
Query: 169 IEKLNGML-LNDKQVYVGHFLRKQERDT 195
IE L+G + L+ K + V + + K+ R +
Sbjct: 61 IETLSGKVELHGKIMEVDYSVSKKLRSS 88
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 40 LYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEMLNFTPLNGKPIRVMY 99
LY +F+Q GQ++ + + L R G +V F A+ AL + P KP+++ Y
Sbjct: 27 LYAIFSQFGQILDIVALKTLKMR---GQAFVIFKEIGSASNALRTMQGFPFYDKPMQIAY 83
Query: 100 SHRD 103
S D
Sbjct: 84 SKSD 87
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 6/90 (6%)
Query: 307 NLYIKNLDDSIDDE----KLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRA 362
+YI NL++ I E L +FS FG I ++ RG FV F AS A
Sbjct: 8 TIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLK--MRGQAFVIFKEIGSASNA 65
Query: 363 LLEMNGKMVVSKPLYVALAQRKEDRRARLQ 392
L M G KP+ +A ++ D A+++
Sbjct: 66 LRTMQGFPFYDKPMQIAYSKSDSDIVAKIK 95
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 50/99 (50%), Gaps = 6/99 (6%)
Query: 204 NVYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARA 259
+Y+ NL+E +E+L+KS F ++G I V ++ + + FV F+ A+ A
Sbjct: 8 TIYINNLNEKIKKEELKKSLYAIFSQFGQILDIVALKTLKMRGQA--FVIFKEIGSASNA 65
Query: 260 VEALNGKKFDDKEWYVGKAQKKSERELELKHQFEQNMKE 298
+ + G F DK + ++ S+ ++K F++ K+
Sbjct: 66 LRTMQGFPFYDKPMQIAYSKSDSDIVAKIKGTFKERPKK 104
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 29/86 (33%), Positives = 42/86 (48%), Gaps = 2/86 (2%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
+++ L A + L D F+ +G+V VR+ D ++RRS G YV F Q A+
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG- 85
Query: 85 LNFTPLNGKPIRVMYSHRDPSLRKSG 110
L L G PI V S + + R SG
Sbjct: 86 LTGQRLLGVPIIVQASQAEKN-RLSG 110
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 37/72 (51%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V + T+ ++D F + G++ ++ + D T GY V + +EA A+E L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 86 NFTPLNGKPIRV 97
N L G+PI V
Sbjct: 85 NGQDLMGQPISV 96
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVEAL 263
++V + E TEED+ F EYG I + + D G K + V +E +A A+E L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 264 NGK 266
NG+
Sbjct: 85 NGQ 87
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 2/84 (2%)
Query: 103 DPSLRKSGAGNI-FIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFD 160
+P ++S G I F+ + + + +HD F+ +G I + + D G KGY V+++
Sbjct: 13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYE 72
Query: 161 NEESAQKAIEKLNGMLLNDKQVYV 184
+ AQ A+E LNG L + + V
Sbjct: 73 TYKEAQAAMEGLNGQDLMGQPISV 96
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 39.7 bits (91), Expect = 0.003, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 207 VKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKS-KCFGFVNFENSDDAARAVEALNG 265
V NL+ T+ + L++ F +YG + + R+ K+ + F FV F + DA A A++G
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 266 KKFDDKEWYVGKAQ 279
+ D +E V A+
Sbjct: 78 AELDGRELRVQVAR 91
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 26/92 (28%), Positives = 45/92 (48%), Gaps = 3/92 (3%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G +L V +L + L +F + G+V V + R+ T+ G+ +V F + ++A A
Sbjct: 12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71
Query: 82 LEMLNFTPLNGKPIRVM---YSHRDPSLRKSG 110
++ L+G+ +RV Y RD S SG
Sbjct: 72 EAAMDGAELDGRELRVQVARYGRRDLSGPSSG 103
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 39.3 bits (90), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 114 IFIKNLDKAIDHKA-LHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKL 172
+FI NL+ + K+ + FS +G I+ C V KG+ FVQ+ NE +A+ A+
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGE 70
Query: 173 NGMLL 177
+G ++
Sbjct: 71 DGRMI 75
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 33/60 (55%)
Query: 23 TTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARAL 82
T+ L V L T+ L + F+ G+V+ V+V +DL T S G+G+V F+ + + +
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQKAIEK 171
++ + L + L + FS FG +L +V DL G SKG+GFV+F E+ K + +
Sbjct: 17 DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
Score = 35.0 bits (79), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 4/74 (5%)
Query: 201 KFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARA 259
K +++ V L TTE+DL++ F +G + V +D G SK FGFV F +
Sbjct: 14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET---Q 70
Query: 260 VEALNGKKFDDKEW 273
V+ ++ + D W
Sbjct: 71 VKVMSQRHMIDGRW 84
Score = 32.0 bits (71), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRAL 363
++L + L ++ LK+ FS FG + +V +D +G S+G GFV F+ E + +
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 194 DTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITS-AVVMRDGDGKSKCFGFVNFEN 252
D F ++V ++ TTE L++ F YG I +V GK + + F+ +E+
Sbjct: 94 DPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEH 153
Query: 253 SDDAARAVEALNGKKFD 269
D A + +GKK D
Sbjct: 154 ERDMHSAYKHADGKKID 170
Score = 36.2 bits (82), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 18/91 (19%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 95 IRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCK-VATDLNGQSKG 153
+++ H DP+ + +F+ ++ L F +G I V + +G+ +G
Sbjct: 86 LKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG 145
Query: 154 YGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
Y F+++++E A + +G ++ ++V V
Sbjct: 146 YAFIEYEHERDMHSAYKHADGKKIDGRRVLV 176
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVE 261
++V LS +TT ED++ F ++G + A++M D + + FGFV FE+ D + E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
Score = 35.0 bits (79), Expect = 0.065, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
++VG L N T + F Q G+V + D +T R G+G+V F + + E +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60
Query: 86 NFTPLNGKPI 95
+F +N K +
Sbjct: 61 HFHEINNKMV 70
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRD-PSGISRGSGFVAFSTPEEASRALLEM 366
L+I L + ++D+++K+L + FG + + +++D +G+S+G F + +A+ +
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 367 NGKMVVSKPLYV 378
NG + K L V
Sbjct: 64 NGMQLGDKKLLV 75
Score = 38.5 bits (88), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 111 AGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAI 169
A +FI L ++ + + ++FG + + + D G SKGY F ++ + +AI
Sbjct: 1 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60
Query: 170 EKLNGMLLNDKQVYV 184
LNGM L DK++ V
Sbjct: 61 AGLNGMQLGDKKLLV 75
Score = 32.0 bits (71), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 34/72 (47%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L++G L + D Q+ +L G + + + +D +T S GY + + + +A+ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 86 NFTPLNGKPIRV 97
N L K + V
Sbjct: 64 NGMQLGDKKLLV 75
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 15/75 (20%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD-GDGKSKCFGFVNFENSDDAARAVEAL 263
+++ L ++ +++ +G + + +++D G SK + F + + + +A+ L
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 264 NGKKFDDKEWYVGKA 278
NG + DK+ V +A
Sbjct: 64 NGMQLGDKKLLVQRA 78
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 38.1 bits (87), Expect = 0.010, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKV-MRDPSGISRGSGFVAFSTPEEASRALLEM 366
LY+KNL + + L LF+ F + R +G RG F+ F E A +AL +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 367 NGKMVVSKPLYVALAQRKEDRRA 389
NG + K L + + K+ R +
Sbjct: 88 NGYKLYGKILVIEFGKNKKQRSS 110
Score = 34.3 bits (77), Expect = 0.14, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 1/81 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITS-AVVMRDGDGKSKCFGFVNFENSDDAARAVEAL 263
+Y+KNLS TE DL F + + R G+ + F+ F N + A +A+ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 264 NGKKFDDKEWYVGKAQKKSER 284
NG K K + + K +R
Sbjct: 88 NGYKLYGKILVIEFGKNKKQR 108
Score = 33.5 bits (75), Expect = 0.21, Method: Composition-based stats.
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 1/85 (1%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
LY+ +L VT+ L LF + + + + T R G ++ F N + A +AL ++
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 86 NFTPLNGKPIRVMYSHRDPSLRKSG 110
N L GK I V+ ++ R SG
Sbjct: 88 NGYKLYGK-ILVIEFGKNKKQRSSG 111
Score = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 7/86 (8%)
Query: 114 IFIKNLDKAIDHKALHDTFSAF----GNILSCKVATDLNGQSKGYGFVQFDNEESAQKAI 169
+++KNL + + L F+ F G + ++ T G+ +G F+ F N+E A +A+
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMT---GRMRGQAFITFPNKEIAWQAL 84
Query: 170 EKLNGMLLNDKQVYVGHFLRKQERDT 195
+NG L K + + K++R +
Sbjct: 85 HLVNGYKLYGKILVIEFGKNKKQRSS 110
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 32/157 (20%), Positives = 68/157 (43%), Gaps = 16/157 (10%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+ +KNL K+ + ++ F G I+ VA L + + ++F + A AI K +
Sbjct: 7 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR-FARIEFARYDGALAAITKTH 65
Query: 174 GMLLNDKQVYVGHFLRKQERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAV 233
++ ++ V H TE +++ N S T+ +++ + + ++
Sbjct: 66 KVV-GQNEIIVSHL-------TE------CTLWMTNFPPSYTQRNIRDLLQDINVVALSI 111
Query: 234 VMRDGD-GKSKCFGFVNFENSDDAARAVEALNGKKFD 269
+ S+ F +++ + +DA VE LNG K +
Sbjct: 112 RLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIE 148
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 29/89 (32%), Positives = 41/89 (46%), Gaps = 6/89 (6%)
Query: 308 LYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ AL
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKXRGQAFVIFKEVSSATNAL 68
Query: 364 LEMNGKMVVSKPLYVALAQRKEDRRARLQ 392
G KP + A+ D A+ +
Sbjct: 69 RSXQGFPFYDKPXRIQYAKTDSDIIAKXK 97
Score = 37.0 bits (84), Expect = 0.018, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 114 IFIKNLDKAIDH----KALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAI 169
I+I NL++ I K+LH FS FG IL V+ L + +G FV F SA A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KXRGQAFVIFKEVSSATNAL 68
Query: 170 EKLNGMLLNDK 180
G DK
Sbjct: 69 RSXQGFPFYDK 79
Score = 33.1 bits (74), Expect = 0.29, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 205 VYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAV 260
+Y+ NL+E +++L+KS F +G I +V R + + FV F+ A A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEVSSATNAL 68
Query: 261 EALNGKKFDDKEWYVGKAQKKSE 283
+ G F DK + A+ S+
Sbjct: 69 RSXQGFPFYDKPXRIQYAKTDSD 91
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 37.7 bits (86), Expect = 0.010, Method: Composition-based stats.
Identities = 29/89 (32%), Positives = 41/89 (46%), Gaps = 6/89 (6%)
Query: 308 LYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ AL
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKXRGQAFVIFKEVSSATNAL 69
Query: 364 LEMNGKMVVSKPLYVALAQRKEDRRARLQ 392
G KP + A+ D A+ +
Sbjct: 70 RSXQGFPFYDKPXRIQYAKTDSDIIAKXK 98
Score = 37.0 bits (84), Expect = 0.018, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 114 IFIKNLDKAIDH----KALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAI 169
I+I NL++ I K+LH FS FG IL V+ L + +G FV F SA A+
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KXRGQAFVIFKEVSSATNAL 69
Query: 170 EKLNGMLLNDK 180
G DK
Sbjct: 70 RSXQGFPFYDK 80
Score = 33.1 bits (74), Expect = 0.29, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 205 VYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAV 260
+Y+ NL+E +++L+KS F +G I +V R + + FV F+ A A+
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEVSSATNAL 69
Query: 261 EALNGKKFDDKEWYVGKAQKKSE 283
+ G F DK + A+ S+
Sbjct: 70 RSXQGFPFYDKPXRIQYAKTDSD 92
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 28/83 (33%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 308 LYIKNLDDSIDDEKLKQ----LFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
+YI NL++ I ++LK+ +FS FG I V R S RG FV F A+ AL
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKXRGQAFVIFKEVSSATNAL 66
Query: 364 LEMNGKMVVSKPLYVALAQRKED 386
G KP + A+ D
Sbjct: 67 RSXQGFPFYDKPXRIQYAKTDSD 89
Score = 37.0 bits (84), Expect = 0.018, Method: Composition-based stats.
Identities = 26/71 (36%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 114 IFIKNLDKAIDH----KALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAI 169
I+I NL++ I K+LH FS FG IL V+ L + +G FV F SA A+
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL--KXRGQAFVIFKEVSSATNAL 66
Query: 170 EKLNGMLLNDK 180
G DK
Sbjct: 67 RSXQGFPFYDK 77
Score = 33.1 bits (74), Expect = 0.29, Method: Composition-based stats.
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 6/83 (7%)
Query: 205 VYVKNLSESTTEEDLQKS----FGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAV 260
+Y+ NL+E +++L+KS F +G I +V R + + FV F+ A A+
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQ--AFVIFKEVSSATNAL 66
Query: 261 EALNGKKFDDKEWYVGKAQKKSE 283
+ G F DK + A+ S+
Sbjct: 67 RSXQGFPFYDKPXRIQYAKTDSD 89
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 107 RKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQS--KGYGFVQFDNEES 164
+K I ++N+ + + + + FS FG + + ++ + G +G+GFV F ++
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 165 AQKAIEKL 172
A+KA L
Sbjct: 71 AKKAFNAL 78
Score = 34.7 bits (78), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGIS--RGSGFVAFSTPEEASRAL 363
+ + ++N+ + ++++LFS FG + + ++ + +G RG GFV F T ++A +A
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Score = 33.5 bits (75), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 23 TTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLS-TRRSLGYGYVNFSNAQEAARA 81
T+ + V ++ ++ +LF+ G++ +VR+ + ++ T G+G+V+F Q+A +A
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
Query: 82 LEML 85
L
Sbjct: 75 FNAL 78
Score = 33.1 bits (74), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 199 KSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMR--DGDGKSKCFGFVNFENSDDA 256
K + + V+N+ + ++++ F +G + + + + G G + FGFV+F DA
Sbjct: 12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71
Query: 257 ARAVEAL 263
+A AL
Sbjct: 72 KKAFNAL 78
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 8/58 (13%)
Query: 114 IFIKNLD-KAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIE 170
+FI NL K + + L FS +G+I+ + +GF+QFDN +S + AIE
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIE 75
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 203 TNVYVKNLS-ESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVE 261
+ +++ NL ++ ++EDL + F YG I + FGF+ F+N A+E
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 75
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 306 ANLYIKNLD-DSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
+ L+I NL ++ E L ++FSP+G I I GF+ F P+ A+
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQIN-------IKNAFGFIQFDNPQSVRDAI 74
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 37.4 bits (85), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 3/67 (4%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
+ + NLS S TEE LQ+ F E T V ++ +GKSK + F+ F + +DA A+ + N
Sbjct: 18 LVLSNLSYSATEETLQEVF-EKATFIK--VPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 265 GKKFDDK 271
++ + +
Sbjct: 75 KREIEGR 81
Score = 34.7 bits (78), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+ + NL + + L + F I KV + NG+SKGY F++F + E A++A+ N
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Score = 32.3 bits (72), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 3/73 (4%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
L + NL S +E L+++F T KV ++ +G S+G F+ F++ E+A AL N
Sbjct: 18 LVLSNLSYSATEETLQEVFE---KATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 368 GKMVVSKPLYVAL 380
+ + + + + L
Sbjct: 75 KREIEGRAIRLEL 87
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 37.0 bits (84), Expect = 0.018, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 45/83 (54%), Gaps = 3/83 (3%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
LY+ +L +T ++YD+F + G + +RV TR G YV + + +A A++ L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNAVDHL 67
Query: 86 NFTPLNGKPIRVMYSHRDPSLRK 108
+ ++ + + V+Y + + + +K
Sbjct: 68 SGFNVSNRYLVVLYYNANRAFQK 90
Score = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 2/71 (2%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
LYI+NL I E++ +F +G I +V P +RG+ +V + +A A+ ++
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNAVDHLS 68
Query: 368 GKMVVSKPLYV 378
G V ++ L V
Sbjct: 69 GFNVSNRYLVV 79
Score = 33.1 bits (74), Expect = 0.30, Method: Composition-based stats.
Identities = 20/99 (20%), Positives = 51/99 (51%), Gaps = 12/99 (12%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
++I+NL I + ++D F +G I +V +++G +V +++ A+ A++ L+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 174 GMLLNDKQVYVGHF----------LRKQERDTEINKSKF 202
G ++++ + V ++ +K+E ++ K K+
Sbjct: 69 GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKY 107
Score = 32.7 bits (73), Expect = 0.40, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDG-KSKCFGFVNFENSDDAARAVEAL 263
+Y++NL T E++ FG+YG I +R G+ +++ +V +E+ DA AV+ L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 264 NG 265
+G
Sbjct: 68 SG 69
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 109 SGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKA 168
SG +FI NL + + + F +G +L C + K YGFV +++ +A+ A
Sbjct: 6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDA 58
Query: 169 IEKLNGMLLNDKQVYV 184
I L+ L+ + V
Sbjct: 59 IRNLHHYKLHGVNINV 74
Score = 37.0 bits (84), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARA 81
G L++G+L T+ ++ LF Q G+V+ + ++ YG+V+ + A A
Sbjct: 7 GMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDA 58
Query: 82 LEMLNFTPLNGKPIRV 97
+ L+ L+G I V
Sbjct: 59 IRNLHHYKLHGVNINV 74
Score = 32.0 bits (71), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 7/84 (8%)
Query: 200 SKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARA 259
S +++ NL TE++++ F +YG + ++++ +GFV+ E+ A A
Sbjct: 6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN-------YGFVHIEDKTAAEDA 58
Query: 260 VEALNGKKFDDKEWYVGKAQKKSE 283
+ L+ K V ++ KS+
Sbjct: 59 IRNLHHYKLHGVNINVEASKNKSK 82
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 37.0 bits (84), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 8/58 (13%)
Query: 114 IFIKNLD-KAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIE 170
+FI NL K + + L FS +G+I+ + +GF+QFDN +S + AIE
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIE 75
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 203 TNVYVKNLS-ESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVE 261
+ +++ NL ++ ++EDL + F YG I + FGF+ F+N A+E
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 75
Query: 262 A 262
Sbjct: 76 C 76
Score = 28.9 bits (63), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 8/59 (13%)
Query: 306 ANLYIKNLD-DSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
+ L+I NL ++ E L ++FSP+G I I GF+ F P+ A+
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQIN-------IKNAFGFIQFDNPQSVRDAI 74
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 37.0 bits (84), Expect = 0.020, Method: Composition-based stats.
Identities = 28/86 (32%), Positives = 50/86 (58%), Gaps = 3/86 (3%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
+LYVG+L +VT+ + LF+Q+G S ++ + ++ Y +V F ++AA AL
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAA 74
Query: 85 LNFTPLNGKPIRVMYSHRDPSLRKSG 110
+N + GK ++V ++ PS +KSG
Sbjct: 75 MNGRKILGKEVKVNWA-TTPSSQKSG 99
Score = 34.7 bits (78), Expect = 0.095, Method: Composition-based stats.
Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 1/89 (1%)
Query: 301 DKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEAS 360
D Q LY+ NL + + + QLFS G SCK++ + + + FV F +A+
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAA 69
Query: 361 RALLEMNGKMVVSKPLYVALAQRKEDRRA 389
AL MNG+ ++ K + V A +++
Sbjct: 70 AALAAMNGRKILGKEVKVNWATTPSSQKS 98
Score = 28.9 bits (63), Expect = 5.8, Method: Composition-based stats.
Identities = 26/81 (32%), Positives = 39/81 (48%), Gaps = 1/81 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
+YV NLS TE + + F + G S ++ + + FV F DAA A+ A+N
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAMN 76
Query: 265 GKKFDDKEWYVGKAQKKSERE 285
G+K KE V A S ++
Sbjct: 77 GRKILGKEVKVNWATTPSSQK 97
Score = 28.1 bits (61), Expect = 8.6, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+++ NL + + + FS G SCK+ T+ + + Y FV+F A A+ +N
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-HTSNDPYCFVEFYEHRDAAAALAAMN 76
Query: 174 GMLLNDKQVYV 184
G + K+V V
Sbjct: 77 GRKILGKEVKV 87
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 37.0 bits (84), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 8/58 (13%)
Query: 114 IFIKNLD-KAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIE 170
+FI NL K + + L FS +G+I+ + +GF+QFDN +S + AIE
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIE 55
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 203 TNVYVKNLS-ESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVE 261
+ +++ NL ++ ++EDL + F YG I + FGF+ F+N A+E
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIE 55
Query: 262 A 262
Sbjct: 56 C 56
Score = 28.5 bits (62), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 8/57 (14%)
Query: 308 LYIKNLD-DSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRAL 363
L+I NL ++ E L ++FSP+G I I GF+ F P+ A+
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQI-------NIKNAFGFIQFDNPQSVRDAI 54
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 36.2 bits (82), Expect = 0.029, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 11/70 (15%)
Query: 101 HRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFD 160
H P + GN+ +KN+ K + L FS +G+I+ + +GF+QFD
Sbjct: 5 HNIPPKSRLFIGNLPLKNVSK----EDLFRIFSPYGHIMQINI-------KNAFGFIQFD 53
Query: 161 NEESAQKAIE 170
N +S + AIE
Sbjct: 54 NPQSVRDAIE 63
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 36.2 bits (82), Expect = 0.030, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEAL 263
++V ++ E E+++Q+ F +YG I + + D G SK + V +E A A EAL
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 264 NGKK 267
NG +
Sbjct: 89 NGAE 92
Score = 32.3 bits (72), Expect = 0.43, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 103 DPSLRKSGAGNI-FIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFD 160
+P ++S G I F+ ++ + + + F +G I + + D G SKGY V+++
Sbjct: 17 EPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYE 76
Query: 161 NEESAQKAIEKLNG 174
+ A A E LNG
Sbjct: 77 THKQALAAKEALNG 90
Score = 32.0 bits (71), Expect = 0.69, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 35/72 (48%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V + + ++ + F G++ ++ + D T S GY V + ++A A E L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 86 NFTPLNGKPIRV 97
N + G+ I+V
Sbjct: 89 NGAEIMGQTIQV 100
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 20/98 (20%), Positives = 48/98 (48%), Gaps = 9/98 (9%)
Query: 290 HQFEQNMKEAADKFQ--------GANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP 341
H +E+ E D+ + G L++ ++ + ++++++ F +G I + + D
Sbjct: 3 HSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR 62
Query: 342 -SGISRGSGFVAFSTPEEASRALLEMNGKMVVSKPLYV 378
+G S+G V + T ++A A +NG ++ + + V
Sbjct: 63 RTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 35.8 bits (81), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQ-SKGYGFVQFDNEESAQKAIEK 171
+FI+NL + +AL + FG++ +V + + SKG F QF +E+AQK +
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 172 LN------GMLLNDKQVYV 184
+ G+ L+ +Q+ V
Sbjct: 77 ASLEAEGGGLKLDGRQLKV 95
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 300 ADKFQGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEE 358
+D +G ++I+NL ++E L ++ FG + +V+ P + S+G F F T E
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69
Query: 359 ASRAL 363
A + L
Sbjct: 70 AQKCL 74
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.8 bits (81), Expect = 0.044, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 10/69 (14%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSK----CFGFVNFENSDDAARAV 260
+YV NL +D++ F +YG I RD D K++ F FV FE+ DA AV
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAI------RDIDLKNRRGGPPFAFVEFEDPRDAEDAV 78
Query: 261 EALNGKKFD 269
+G +D
Sbjct: 79 YGRDGYDYD 87
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 35.8 bits (81), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRA 362
L+I + ++D++ LK LF FG I V++D +G+ +G F+ + E A +A
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Score = 35.0 bits (79), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 106 LRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEES 164
++ A +FI + + +D K L F FG I V D G KG F+ + ES
Sbjct: 8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67
Query: 165 AQKAIEKLN 173
A KA L+
Sbjct: 68 ALKAQSALH 76
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEAL 263
+++ + + E+DL+ F E+G I V++D G K F+ + + A +A AL
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 264 NGKK 267
+ +K
Sbjct: 76 HEQK 79
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 35.8 bits (81), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEAL 263
++V ++ E E+++Q+ F +YG I + + D G SK + V +E A A EAL
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 264 NG 265
NG
Sbjct: 135 NG 136
Score = 34.3 bits (77), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 36/74 (48%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L+V + + ++ + F G++ ++ + D T S GY V + ++A A E L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 86 NFTPLNGKPIRVMY 99
N + G+ I+V +
Sbjct: 135 NGAEIMGQTIQVDW 148
Score = 33.9 bits (76), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 35/137 (25%), Positives = 59/137 (43%), Gaps = 19/137 (13%)
Query: 53 VRVCRDLSTRRSLGYGYVNFSNAQEAARALEMLNFTPLNGKPIRVMYSHRD---PSLRKS 109
VR+ R+ G+G + SN +EA + E RV D P ++S
Sbjct: 24 VRLKEKAKHRKGRGFG--SDSNTREAIHSYE------------RVRNEDDDELEPGPQRS 69
Query: 110 GAGNI-FIKNLDKAIDHKALHDTFSAFGNILSCKVATDL-NGQSKGYGFVQFDNEESAQK 167
G I F+ ++ + + + F +G I + + D G SKGY V+++ + A
Sbjct: 70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 129
Query: 168 AIEKLNGMLLNDKQVYV 184
A E LNG + + + V
Sbjct: 130 AKEALNGAEIMGQTIQV 146
Score = 32.3 bits (72), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 16/76 (21%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 304 QGANLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRA 362
+G L++ ++ + ++++++ F +G I + + D +G S+G V + T ++A A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 363 LLEMNGKMVVSKPLYV 378
+NG ++ + + V
Sbjct: 131 KEALNGAEIMGQTIQV 146
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 35.4 bits (80), Expect = 0.052, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 192 ERDTEINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNF 250
E EI+K +VYV N+ +T +DL+ F G+I ++ D G K + ++ F
Sbjct: 29 EEKKEIDKR---SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF 85
Query: 251 --ENSDDAARAVE 261
NS DAA A++
Sbjct: 86 AERNSVDAAVAMD 98
Score = 31.6 bits (70), Expect = 0.79, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFS--NAQEAARAL 82
S+YVG+++ T L F+ G + + + D + GY Y+ F+ N+ +AA A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
Query: 83 EMLNFTPLNGKPIRVM 98
+ T G+ I+V+
Sbjct: 98 DE---TVFRGRTIKVL 110
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 113 NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAI 169
++++ N+D + L FS+ G+I + D +G KGY +++F S A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 35.4 bits (80), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 8/86 (9%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVS--------VRVCRDLSTRRSLGYGYVNFSNAQ 76
+++V L NVT + D F Q+G + + + + D T + G V+F +
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68
Query: 77 EAARALEMLNFTPLNGKPIRVMYSHR 102
A A++ + +G PI+V ++ R
Sbjct: 69 SAKAAIDWFDGKEFSGNPIKVSFATR 94
Score = 33.9 bits (76), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 9/88 (10%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP---------SGISRGSGFVAFSTPEE 358
++++ L +++ E + F G I + K P +G +G V+F P
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 359 ASRALLEMNGKMVVSKPLYVALAQRKED 386
A A+ +GK P+ V+ A R+ D
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRRAD 97
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.0 bits (79), Expect = 0.067, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
LYI+NL I E++ +F +G I +V P +RG+ +V + +A A ++
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 72
Query: 368 GKMVVSKPLYV 378
G V ++ L V
Sbjct: 73 GFNVCNRYLVV 83
Score = 34.7 bits (78), Expect = 0.099, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
LY+ +L +T ++YD+F + G + +RV TR G YV + + +A A + L
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNACDHL 71
Query: 86 NFTPLNGKPIRVMY 99
+ + + + V+Y
Sbjct: 72 SGFNVCNRYLVVLY 85
Score = 32.0 bits (71), Expect = 0.64, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDG-KSKCFGFVNFENSDDAARAVEAL 263
+Y++NL T E++ FG+YG I +R G+ +++ +V +E+ DA A + L
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACDHL 71
Query: 264 NG 265
+G
Sbjct: 72 SG 73
Score = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 16/74 (21%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
++I+NL I + ++D F +G I +V +++G +V +++ A+ A + L+
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLS 72
Query: 174 GMLLNDKQVYVGHF 187
G + ++ + V ++
Sbjct: 73 GFNVCNRYLVVLYY 86
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 35.0 bits (79), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 128 LHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYVGHF 187
L FS FGNI+ + N FV ++ ESA +A+ +LNG + Q+ V +
Sbjct: 30 LRGAFSPFGNIIDLSMDPPRN-----CAFVTYEKMESADQAVAELNGTQVESVQLKV-NI 83
Query: 188 LRKQ 191
RKQ
Sbjct: 84 ARKQ 87
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 35.0 bits (79), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
S+YVG+++ T +L F+ G V V + D + G+ Y+ FS+ +E+ R
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSLA 65
Query: 85 LNFTPLNGKPIRVM 98
L+ + G+ I+V+
Sbjct: 66 LDESLFRGRQIKVI 79
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 111 AGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAI 169
A +I++ N+D + L F G++ + D +G KG+ +++F ++ES + ++
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
Query: 170 EKLNGMLLNDKQVYV 184
L+ L +Q+ V
Sbjct: 65 -ALDESLFRGRQIKV 78
Score = 29.3 bits (64), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEA 262
++YV N+ T E+L+ F G++ ++ D G K F ++ F + ++ R A
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 65
Query: 263 LNGKKFDDKEWYV 275
L+ F ++ V
Sbjct: 66 LDESLFRGRQIKV 78
Score = 28.1 bits (61), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 307 NLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP-SGISRGSGFVAFSTPEEASRAL 363
++Y+ N+D E+L+ F GS+ ++ D SG +G ++ FS E +L
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 35.0 bits (79), Expect = 0.079, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
LY+ +L +T ++YD+F + G + +RV TR G YV + + +A A + L
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNACDHL 77
Query: 86 NFTPLNGKPIRVMYSHRDPSLRK 108
+ + + + V+Y + + + +K
Sbjct: 78 SGFNVCNRYLVVLYYNANRAFQK 100
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 2/71 (2%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
LYI+NL I E++ +F +G I +V P +RG+ +V + +A A ++
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--TRGTAYVVYEDIFDAKNACDHLS 78
Query: 368 GKMVVSKPLYV 378
G V ++ L V
Sbjct: 79 GFNVCNRYLVV 89
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDG-KSKCFGFVNFENSDDAARAVEAL 263
+Y++NL T E++ FG+YG I +R G+ +++ +V +E+ DA A + L
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 264 NG 265
+G
Sbjct: 78 SG 79
Score = 30.0 bits (66), Expect = 2.1, Method: Composition-based stats.
Identities = 20/99 (20%), Positives = 49/99 (49%), Gaps = 12/99 (12%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
++I+NL I + ++D F +G I +V +++G +V +++ A+ A + L+
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 174 GMLLNDKQVYVGHF----------LRKQERDTEINKSKF 202
G + ++ + V ++ +K+E ++ K K+
Sbjct: 79 GFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKY 117
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 35.0 bits (79), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 7/92 (7%)
Query: 21 FGTTSLYVGDLEAN-VTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAA 79
G + L V +L VT L+ LF G V V++ + V ++ +A
Sbjct: 1 MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQ 55
Query: 80 RALEMLNFTPLNGKPIRVMYS-HRDPSLRKSG 110
A+ LN L+GKPIR+ S H++ L + G
Sbjct: 56 LAMSHLNGHKLHGKPIRITLSKHQNVQLPREG 87
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 34.7 bits (78), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 6/65 (9%)
Query: 128 LHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYVGHF 187
L FS FGNI+ + N FV ++ ESA +A+ +LNG + Q+ V +
Sbjct: 54 LRGAFSPFGNIIDLSMDPPRN-----CAFVTYEKMESADQAVAELNGTQVESVQLKV-NI 107
Query: 188 LRKQE 192
RKQ
Sbjct: 108 ARKQP 112
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 34.7 bits (78), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 29/103 (28%), Positives = 49/103 (47%), Gaps = 6/103 (5%)
Query: 91 NGKPIRVMYSHRDPSLRKSGAGNIFIKNLDKAIDHKALHDTFSAFG--NILSCKVATD-L 147
N K ++Y++ LR A +++ + + L + G +++ K A +
Sbjct: 38 NNKTPAILYTYS--GLRNRRAA-VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA 94
Query: 148 NGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYVGHFLRK 190
NGQSKGY V +E S K +E L G +LN ++V V R+
Sbjct: 95 NGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ 137
Score = 32.3 bits (72), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMG--QVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARAL 82
++YVG TD QL + +G VV ++ + + +S GY V ++ + L
Sbjct: 57 AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116
Query: 83 EMLNFTPLNGKPIRVMYSHR 102
E+L LNG+ + V + R
Sbjct: 117 ELLPGKVLNGEKVDVRPATR 136
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 34.7 bits (78), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 7/91 (7%)
Query: 22 GTTSLYVGDLEAN-VTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAAR 80
G + L V +L VT L+ LF G V V++ + V ++ +A
Sbjct: 33 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQL 87
Query: 81 ALEMLNFTPLNGKPIRVMYS-HRDPSLRKSG 110
A+ LN L+GKPIR+ S H++ L + G
Sbjct: 88 AMSHLNGHKLHGKPIRITLSKHQNVQLPREG 118
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 34/154 (22%), Positives = 61/154 (39%), Gaps = 36/154 (23%)
Query: 109 SGAGN--IFIKNLDKA-IDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESA 165
+GAGN + + NL+ + ++L F +G++ K+ + K VQ + A
Sbjct: 30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQA 85
Query: 166 QKAIEKLNGMLLNDKQVYVG-------HFLRKQERDTEINK---------------SKFT 203
Q A+ LNG L+ K + + R+ + D + K F
Sbjct: 86 QLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQ 145
Query: 204 NVY-------VKNLSESTTEEDLQKSFGEYGTIT 230
N++ + N+ S +EEDL+ F G +
Sbjct: 146 NIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVV 179
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
Length = 88
Score = 34.3 bits (77), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLS--TRRSLGYGYVNFSN---AQEAAR 80
++VG + ++ L +LF Q G V + V RD S +S G +V F A EA
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 81 ALEMLNFTPLNGKPIRV 97
AL + P PI++
Sbjct: 66 ALHNMKVLPGMHHPIQM 82
Score = 32.7 bits (73), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRD---GDGKSKCFGFVNFENSDDAARAVE 261
++V + + +E+DL++ F +YG + V+RD +SK FV F A A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 262 ALNGKK 267
AL+ K
Sbjct: 66 ALHNMK 71
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPS---GISRGSGFVAFSTPE---EASR 361
+++ + + ++ L++LF +G++ V+RD S S+G FV F T + EA
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 362 ALLEM 366
AL M
Sbjct: 66 ALHNM 70
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 140 SCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYVGHFLRKQERDTEIN 198
+ V D NGQ G VQF NE+ A+K+ E+L+ LN ++ +V + R+ E N
Sbjct: 45 AVHVLVDNNGQGLGQALVQFKNEDDARKS-ERLHRKKLNGREAFVHVVTLEDMREIEKN 102
Score = 33.5 bits (75), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 47/93 (50%), Gaps = 3/93 (3%)
Query: 196 EINKSKFTNVYVKNLSESTTEEDLQKSFGEYGTITSAV-VMRDGDGKSKCFGFVNFENSD 254
++N +K ++ N+ S T+ D+ + +AV V+ D +G+ V F+N D
Sbjct: 10 DVNSAKVC-AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 68
Query: 255 DAARAVEALNGKKFDDKEWYVGKAQKKSERELE 287
D AR E L+ KK + +E +V + RE+E
Sbjct: 69 D-ARKSERLHRKKLNGREAFVHVVTLEDMREIE 100
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 33.9 bits (76), Expect = 0.15, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAV-VMRD-GDGKSKCFGFVNFENSDDAARAVEA 262
V ++ L ++ TE+D++ +G V +MR+ G+S+ F FV F + DA R +EA
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA 63
Score = 33.5 bits (75), Expect = 0.19, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 3/62 (4%)
Query: 49 QVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEMLNFTPLN--GKPIRVMYSHRDPSL 106
Q VR+ R+ S+ +S G+ +V FS+ Q+A R +E N LN G+ + + YS P +
Sbjct: 28 QAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEA-NQHSLNILGQKVSMHYSDPKPKI 86
Query: 107 RK 108
+
Sbjct: 87 NE 88
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
Hypothetical Polyadenylate-Binding Protein (Pabpn1)
From Homo Sapiens At 1.95 A Resolution
Length = 89
Score = 33.9 bits (76), Expect = 0.17, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
S+YVG+++ T +L F+ G V V + D + G+ Y+ FS+ +E+ R
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSLA 66
Query: 85 LNFTPLNGKPIRVM 98
L+ + G+ I+V+
Sbjct: 67 LDESLFRGRQIKVI 80
Score = 32.3 bits (72), Expect = 0.50, Method: Composition-based stats.
Identities = 18/78 (23%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 108 KSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQ 166
++ A +I++ N+D + L F G++ + D +G KG+ +++F ++ES +
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 167 KAIEKLNGMLLNDKQVYV 184
++ L+ L +Q+ V
Sbjct: 63 TSL-ALDESLFRGRQIKV 79
Score = 28.9 bits (63), Expect = 5.5, Method: Composition-based stats.
Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEA 262
++YV N+ T E+L+ F G++ ++ D G K F ++ F + ++ R A
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 66
Query: 263 LNGKKFDDKE 272
L+ F ++
Sbjct: 67 LDESLFRGRQ 76
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 32.3 bits (72), Expect = 0.47, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
V V L S + +DL+ E G + A V RDG G V F +D AV L+
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT------GVVEFVRKEDMTYAVRKLD 71
Query: 265 GKKFDDKE 272
KF E
Sbjct: 72 NTKFRSHE 79
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 32.3 bits (72), Expect = 0.48, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
V V L S + +DL+ E G + A V RDG G V F +D AV L+
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT------GVVEFVRKEDMTYAVRKLD 72
Query: 265 GKKFDDKE 272
KF E
Sbjct: 73 NTKFRSHE 80
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 32.3 bits (72), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 9/86 (10%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITS---------AVVMRDGDGKSKCFGFVNFENSDD 255
+YV+ L++S T +DL F + G + + + GK K V++E+
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 256 AARAVEALNGKKFDDKEWYVGKAQKK 281
A AVE +GK F + V A+KK
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQV--------VSVRVCRDLSTRRSLGYGYVNFSNA 75
+++YV L +VT L D F Q G V + + D T + G V++ +
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 76 QEAARALEMLNFTPLNGKPIRVMYSHRDPSL 106
A A+E + G ++V + + P +
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVSLARKKPPM 106
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 9/86 (10%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDP---------SGISRGSGFVAFSTPEE 358
+Y++ L+DS+ + L F G + K P +G +G V++ P
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT 77
Query: 359 ASRALLEMNGKMVVSKPLYVALAQRK 384
A A+ +GK L V+LA++K
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKK 103
>pdb|3GB8|A Chain A, Crystal Structure Of Crm1SNURPORTIN-1 Complex
Length = 1071
Score = 32.0 bits (71), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 311 KNLDDSIDDEKLKQLFSPFGS-ITSCKVMRDPSGISRGSGFV----AFSTPEEASRALLE 365
KN+D D E +KQL S + + +CK + P I G ++ + E A ++
Sbjct: 674 KNVDILKDPETVKQLGSILKTNVRACKAVGHPFVIQLGRIYLDMLNVYKCLSENISAAIQ 733
Query: 366 MNGKMVVSKPL 376
NG+MV +PL
Sbjct: 734 ANGEMVTKQPL 744
>pdb|3GJX|A Chain A, Crystal Structure Of The Nuclear Export Complex Crm1-
Snurportin1-Rangtp
pdb|3GJX|D Chain D, Crystal Structure Of The Nuclear Export Complex Crm1-
Snurportin1-Rangtp
pdb|3NBY|A Chain A, Crystal Structure Of The Pki Nes-Crm1-Rangtp Nuclear
Export Complex
pdb|3NBY|D Chain D, Crystal Structure Of The Pki Nes-Crm1-Rangtp Nuclear
Export Complex
pdb|3NBZ|A Chain A, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear
Export Complex (Crystal I)
pdb|3NBZ|D Chain D, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear
Export Complex (Crystal I)
pdb|3NC0|A Chain A, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear
Export Complex (Crystal Ii)
pdb|3NC0|D Chain D, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear
Export Complex (Crystal Ii)
pdb|3NC1|A Chain A, Crystal Structure Of The Crm1-Rangtp Complex
Length = 1073
Score = 32.0 bits (71), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 311 KNLDDSIDDEKLKQLFSPFGS-ITSCKVMRDPSGISRGSGFV----AFSTPEEASRALLE 365
KN+D D E +KQL S + + +CK + P I G ++ + E A ++
Sbjct: 676 KNVDILKDPETVKQLGSILKTNVRACKAVGHPFVIQLGRIYLDMLNVYKCLSENISAAIQ 735
Query: 366 MNGKMVVSKPL 376
NG+MV +PL
Sbjct: 736 ANGEMVTKQPL 746
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 32.0 bits (71), Expect = 0.59, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
V V L S + +DL+ E G + A V RDG G V F +D AV L+
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT------GVVEFVRKEDMTYAVRKLD 71
Query: 265 GKKFDDKE 272
KF E
Sbjct: 72 NTKFRSHE 79
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 32.0 bits (71), Expect = 0.60, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 106 LRKSGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEES 164
++ A +F+ + + +D + L F FG I V D L G KG F+ + +S
Sbjct: 10 MKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDS 69
Query: 165 AQKAIEKLN 173
A KA L+
Sbjct: 70 ALKAQSALH 78
Score = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDG-DGKSKCFGFVNFENSDDAARAVEAL 263
++V + E+DL+ F E+G I V++D G K F+ + D A +A AL
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSAL 77
Query: 264 NGKK 267
+ +K
Sbjct: 78 HEQK 81
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 32.0 bits (71), Expect = 0.69, Method: Composition-based stats.
Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 3/83 (3%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEML 85
L + +L +T ++YD+F + G + +RV TR G YV + + +A A + L
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNACDHL 77
Query: 86 NFTPLNGKPIRVMYSHRDPSLRK 108
+ + + + V+Y + + + +K
Sbjct: 78 SGFNVCNRYLVVLYYNANRAFQK 100
Score = 28.9 bits (63), Expect = 4.9, Method: Composition-based stats.
Identities = 20/99 (20%), Positives = 48/99 (48%), Gaps = 12/99 (12%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLN 173
+ I+NL I + ++D F +G I +V +++G +V +++ A+ A + L+
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLS 78
Query: 174 GMLLNDKQVYVGHF----------LRKQERDTEINKSKF 202
G + ++ + V ++ +K+E ++ K K+
Sbjct: 79 GFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKY 117
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 31.6 bits (70), Expect = 0.81, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 34 NVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEMLNFTPLNGK 93
NVT+ + + + + V++R+ R+ ++ GY +V+FSN +E +AL+ N + G+
Sbjct: 21 NVTEKNVMEFLAPL-KPVAIRIVRNAHGNKT-GYIFVDFSNEEEVKQALK-CNREYMGGR 77
Query: 94 PIRVMYSHRDPS 105
I V PS
Sbjct: 78 YIEVFREKSGPS 89
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 31.6 bits (70), Expect = 0.81, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 33/65 (50%)
Query: 31 LEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEMLNFTPL 90
L NV ++ L D+ + G+V V + TR+ LG V F++ + A ++ L+ T +
Sbjct: 14 LNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSV 73
Query: 91 NGKPI 95
G I
Sbjct: 74 MGNII 78
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 31.6 bits (70), Expect = 0.84, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEK 171
IF+ L + + + F FG + S ++ D + +G+ F+ F EE +K +EK
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Score = 30.0 bits (66), Expect = 2.4, Method: Composition-based stats.
Identities = 12/58 (20%), Positives = 29/58 (50%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
++VG L + + ++ + F G+V S+ + D T + G+ ++ F + + +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 31.2 bits (69), Expect = 0.94, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEK 171
IF+ L + + + F FG + S ++ D + +G+ F+ F EE +K +EK
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
Score = 30.0 bits (66), Expect = 2.6, Method: Composition-based stats.
Identities = 12/58 (20%), Positives = 29/58 (50%)
Query: 26 LYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
++VG L + + ++ + F G+V S+ + D T + G+ ++ F + + +E
Sbjct: 4 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 31.2 bits (69), Expect = 0.99, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 11/75 (14%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
T +YV L ++ TE DL+ F ++G I + V++ + +C F+ F A A E
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ----RQQC-AFIQFATRQAAEVAAEK 67
Query: 263 ------LNGKKFDDK 271
+NG++ + K
Sbjct: 68 SFNKLIVNGRRLNVK 82
Score = 30.4 bits (67), Expect = 1.8, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 24 TSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALE 83
T+LYVG L +T++ L + F Q G++ ++ V + ++ F+ Q A A E
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQC------AFIQFATRQAAEVAAE 66
Query: 84 M-LNFTPLNGKPIRVMY 99
N +NG+ + V +
Sbjct: 67 KSFNKLIVNGRRLNVKW 83
Score = 28.5 bits (62), Expect = 6.1, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 308 LYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFVAFSTPEEASRALLEMN 367
LY+ L D+I + L+ F FG I + V++ + F+ F+T + A A +
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-----RQQCAFIQFATRQAAEVAAEKSF 69
Query: 368 GKMVVS 373
K++V+
Sbjct: 70 NKLIVN 75
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 100 SHRDPSLRKSGAG---NIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGF 156
SH D + +G I ++NL + LH FS FG +L T N Q +
Sbjct: 19 SHMDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-NNQFQ--AL 75
Query: 157 VQFDNEESAQKAIEKLNG 174
+Q+ + SAQ A L+G
Sbjct: 76 LQYADPVSAQHAKLSLDG 93
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 27 YVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARAL 82
YVG+L N + +F + + SVR+ RD T + G+ YV F AL
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 9/89 (10%)
Query: 103 DPSLRKS--GAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFD 160
DP K A + KNL I L + F + L ++ + +G+SKG +++F
Sbjct: 6 DPCTSKKVRAARTLLAKNLSFNITEDELKEVFE---DALEIRLVSQ-DGKSKGIAYIEFK 61
Query: 161 NEESAQKAIEKLNGMLLNDKQV---YVGH 186
+E A+K +E+ G ++ + V Y G
Sbjct: 62 SEADAEKNLEEKQGAEIDGRSVSLYYTGE 90
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 19/26 (73%)
Query: 146 DLNGQSKGYGFVQFDNEESAQKAIEK 171
D G+S G FVQF ++E A+KA++K
Sbjct: 51 DFQGRSTGEAFVQFASQEIAEKALKK 76
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 36/65 (55%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEAL 263
N+++ NL+ + + +L+ + E V+ G ++ FG+V+FE+++D +A+E
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELT 78
Query: 264 NGKKF 268
K F
Sbjct: 79 GLKVF 83
Score = 29.3 bits (64), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEM 84
+L++G+L N + ++L +++ + V D+ T + +GYV+F +A++ +ALE+
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALEL 77
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/90 (20%), Positives = 44/90 (48%), Gaps = 2/90 (2%)
Query: 294 QNMKEAADKFQGA--NLYIKNLDDSIDDEKLKQLFSPFGSITSCKVMRDPSGISRGSGFV 351
QN ++AD + A ++ ++ D +E ++ +G + V + G+ +V
Sbjct: 14 QNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYV 73
Query: 352 AFSTPEEASRALLEMNGKMVVSKPLYVALA 381
F E+A +A++++N + +P++ L+
Sbjct: 74 KFRREEDAEKAVIDLNNRWFNGQPIHAELS 103
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 42 DLFNQM----GQVVSVRVCRDLSTRRSLGYGYVNFSNAQEAARALEMLNFTPLNGKPIRV 97
++F +M G+V + VC +L +G YV F ++A +A+ LN NG+PI
Sbjct: 42 EVFTEMEEKYGEVEEMNVCDNLGDHL-VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100
Query: 98 MYS 100
S
Sbjct: 101 ELS 103
Score = 28.5 bits (62), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 24/49 (48%)
Query: 135 FGNILSCKVATDLNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVY 183
+G + V +L G +V+F EE A+KA+ LN N + ++
Sbjct: 51 YGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 126 KALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQVYV 184
KAL FS G +++ + D G++KG+ FV+ + A+K I+ +G L+ K
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLF 86
Query: 185 GHFLRKQER 193
+ ++ ER
Sbjct: 87 LYTMKDVER 95
>pdb|3EGN|A Chain A, C-Terminal Rna Recognition Motif Of The U11U12 65K PROTEIN
Length = 143
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 6/67 (8%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAV--VMRD----GDGKSKCFGFVNFENSDDAAR 258
+YVKNL++ E+DL+ FG Y +S +M D +G+ K F+ N AA+
Sbjct: 48 IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107
Query: 259 AVEALNG 265
A++ NG
Sbjct: 108 ALKEANG 114
Score = 29.3 bits (64), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 10/85 (11%)
Query: 306 ANLYIKNLDDSIDDEKLKQLFSPFGSITS--------CKVMRDPSGISRGSGFVAFSTPE 357
+Y+KNL + ++ LK +F + +S ++M++ G +G F+ +
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKE--GRMKGQAFIGLPNEK 103
Query: 358 EASRALLEMNGKMVVSKPLYVALAQ 382
A++AL E NG ++ KP+ V A+
Sbjct: 104 AAAKALKEANGYVLFGKPMVVQFAR 128
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 30.4 bits (67), Expect = 2.0, Method: Composition-based stats.
Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 25 SLYVGDLEANVTDSQLYDLFNQMGQVVS--------VRVCRDLSTRRSLGYGYVNFSNAQ 76
+++V L NVT + D F Q+G + + + + D T + G V+F +
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74
Query: 77 EAARALEMLNFTPLNGKPIRVMYS 100
A A++ + +G PI+V ++
Sbjct: 75 SAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 30.0 bits (66), Expect = 2.3, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 126 KALHDTFSAFGNILSCKVATD-LNGQSKGYGFVQFDNEESAQKAIEKLNGMLLNDKQ 181
KAL FS G +++ + D G++KG+ FV+ + A+K I+ +G L+ K
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH 83
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 8/64 (12%)
Query: 203 TNVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEA 262
+ V+V +E T E+LQ+ F +YG + + + + F FV F +DD + ++
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK----PFRAFAFVTF--ADD--KVAQS 63
Query: 263 LNGK 266
L G+
Sbjct: 64 LCGE 67
>pdb|1WI6|A Chain A, Solution Structure Of The Rna Binding Domain From Mouse
Hypothetical Protein Bab23670
Length = 88
Score = 29.3 bits (64), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 109 SGAGNIFIKNLDKAIDHKALHDTFSAFGNILSCKVATDLNGQSKGYGFVQFDNEESAQKA 168
SG+ I I+ L + ++ +HD S + + C V + KG FV N E A+ A
Sbjct: 3 SGSSGILIRGLPGDVTNQEVHDLLSDY-ELKYCFVD-----KYKGTAFVTLLNGEQAEAA 56
Query: 169 IEKLNGMLLNDKQVYV 184
I + L ++++ V
Sbjct: 57 INTFHQSRLRERELSV 72
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 28.9 bits (63), Expect = 5.3, Method: Composition-based stats.
Identities = 14/57 (24%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 22 GTTSLYVGDLEANVTDSQLYDLFNQMGQVVSVRVCRDLSTRRSLGYGYVNFSNAQEA 78
G++ ++VG ++T+ +L + F+Q G V+ V + + + +V F++ Q A
Sbjct: 4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIA 55
>pdb|1RKT|A Chain A, Crystal Structure Of Yfir, A Putative Transcriptional
Regulator From Bacillus Subtilis
pdb|1RKT|B Chain B, Crystal Structure Of Yfir, A Putative Transcriptional
Regulator From Bacillus Subtilis
Length = 205
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 332 ITSCKVMRDPSGISRGSGFVAFSTPEEASRALLE 365
+T+ K + + SG SRG ++ FS+ EE R ++E
Sbjct: 32 LTTXKDVVEESGFSRGGVYLYFSSTEEXFRRIIE 65
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 28.9 bits (63), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 205 VYVKNLSESTTEEDLQKS---FGEYGTITSAVVMRD----GDGKSKCFGFVNFENSDDAA 257
V+V LS+ + ++ K FG++G I V+ G +V + S+DA
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 258 RAVEALNGKKFDDK 271
RA++ +N D +
Sbjct: 78 RAIQCVNNVVVDGR 91
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 28.5 bits (62), Expect = 6.2, Method: Composition-based stats.
Identities = 14/73 (19%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 310 IKNLDDSIDDEKLKQLFSPFGSITSCKVMR-DPSGISRGSGFVAFSTPEEASRALLEMNG 368
++N+ ++ +++ F + I ++ + G+ G VAF + +EA+ A++++N
Sbjct: 20 VQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLND 79
Query: 369 KMVVSKPLYVALA 381
+ + S+ + + L
Sbjct: 80 RPIGSRKVKLVLG 92
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 28.5 bits (62), Expect = 7.0, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 219 LQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALNGKKFDDKEWY 274
+ K F ++G IT+ + DGK+K + F+ + + A AV+ +G K D + +
Sbjct: 24 IHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 78
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 28.5 bits (62), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 114 IFIKNLDKAIDHKALHDTFSAFGNIL-SCKVATDLNGQSKGYGFVQFDNEESAQKAI 169
+++K L ++K + D F + S +A NG++ G GFV+F NE + A+
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL 84
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 28.1 bits (61), Expect = 7.9, Method: Composition-based stats.
Identities = 18/81 (22%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 204 NVYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEAL 263
+VYV NL DL+++ E G++ + + ++ F+++ +S A +AV L
Sbjct: 21 DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRA----FLHYPDSAAAQQAVSCL 76
Query: 264 NGKKFDDKEWYVGKAQKKSER 284
G + V A+++ ++
Sbjct: 77 QGLRLGTDTLRVALARQQRDK 97
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 28.1 bits (61), Expect = 8.0, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 219 LQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALNGKKFDDKEWY 274
+ K F ++G IT+ + DGK+K + F+ + + A AV+ +G K D + +
Sbjct: 38 IHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 28.1 bits (61), Expect = 8.3, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 205 VYVKNLSESTTEEDLQKSFGEYGTITSAVVMRDGDGKSKCFGFVNFENSDDAARAVEALN 264
V V L S + +DL+ E G + A V +DG G V + +D A+ L+
Sbjct: 18 VLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG------MGMVEYLRKEDMEYALRKLD 71
Query: 265 GKKFDDKE 272
KF E
Sbjct: 72 DTKFRSHE 79
>pdb|2A3J|A Chain A, Structure Of Urndesign, A Complete Computational Redesign
Of Human U1a Protein
Length = 127
Score = 28.1 bits (61), Expect = 8.7, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 30/65 (46%), Gaps = 6/65 (9%)
Query: 114 IFIKNLDKAIDHKALHDTFSAF----GNILSCKVATDLNGQSKGYGFVQFDNEESAQKAI 169
+ I N++ + + L A G+IL + DL+ + G ++ F +ESAQ +
Sbjct: 32 VLITNINPEVPKEKLQALLYALASSQGDILD--IVVDLSDDNSGKAYIVFATQESAQAFV 89
Query: 170 EKLNG 174
E G
Sbjct: 90 EAFQG 94
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.317 0.133 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,854,694
Number of Sequences: 62578
Number of extensions: 449066
Number of successful extensions: 2325
Number of sequences better than 100.0: 229
Number of HSP's better than 100.0 without gapping: 173
Number of HSP's successfully gapped in prelim test: 56
Number of HSP's that attempted gapping in prelim test: 1365
Number of HSP's gapped (non-prelim): 708
length of query: 399
length of database: 14,973,337
effective HSP length: 101
effective length of query: 298
effective length of database: 8,652,959
effective search space: 2578581782
effective search space used: 2578581782
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)