RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8956
(333 letters)
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 189 bits (483), Expect = 1e-58
Identities = 41/278 (14%), Positives = 92/278 (33%), Gaps = 40/278 (14%)
Query: 33 KENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
++ + L V NQ + + + + D+ +G A + +A+ A
Sbjct: 21 NRRKILIRGLPGDVTNQEVHDLLSDYE------LKYCFVDKYKGTAFVTLLNGEQAEAAI 74
Query: 93 VEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFI 152
+ + + + + Q + V NL ++ +++ +
Sbjct: 75 NAFHQSRLRERELSVQL-----------------QPTDALLCVANLPPSLTQQQFEELVR 117
Query: 153 KFGNIIEVKIVRDE-NGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIVPG 211
FG++ +V E G+SKG+GF ++ +A +A ++ G+ + + +V +
Sbjct: 118 PFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD---- 173
Query: 212 KKVFPKVKPPLLQPARKNKIFVANLPSNINNSE-FEELFARFGTITSSSLVSD-----KH 265
+ V LP N+ + + + T L K
Sbjct: 174 ------AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKG 227
Query: 266 IGFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
+E+ + A A +G L+V+ P
Sbjct: 228 FAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP 265
Score = 150 bits (381), Expect = 1e-43
Identities = 30/181 (16%), Positives = 68/181 (37%), Gaps = 10/181 (5%)
Query: 29 NKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESRGFAIIVFNTPAE 87
+ L V NL PS+ Q + FG+L + ++ +S+G+ +
Sbjct: 90 QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 149
Query: 88 AKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETV-DEEE 146
A +A+ ++ G +G + + + + + V L D +
Sbjct: 150 AARAKSDLLGKPLGPRTLYV--------HWTDAGQLTPALLHSRCLCVDRLPPGFNDVDA 201
Query: 147 LKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
L + ++ ++G+ KGF +++ + + AE+A + +G + + VS
Sbjct: 202 LCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
Query: 207 E 207
Sbjct: 262 A 262
Score = 129 bits (326), Expect = 1e-35
Identities = 42/218 (19%), Positives = 76/218 (34%), Gaps = 36/218 (16%)
Query: 111 ELKPGQRSKPVGPEEKQYKKDK-VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK 169
L P + K + E+Q++ + + ++ L V +E+ + + + K
Sbjct: 2 MLDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DK 55
Query: 170 SKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKN 229
KG F+ + + AE AI + ++ V L
Sbjct: 56 YKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP-------------------TDA 96
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVST 283
+ VANLP ++ +FEEL FG++ LV + GF E++ A A S
Sbjct: 97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 284 MNGHVFKSKPLKVTLSGTKPGVSITNPTKAPKKPAYID 321
+ G + L V + P + +D
Sbjct: 157 LLGKPLGPRTLYVHWTDAGQ----LTPALLHSRCLCVD 190
Score = 81.6 bits (202), Expect = 5e-18
Identities = 21/108 (19%), Positives = 44/108 (40%), Gaps = 1/108 (0%)
Query: 22 ARSNKENNKVYKENELHVNNLEPSV-DNQALINEFKKFGTLRDVRVARNKNDESRGFAII 80
+ + + L V+ L P D AL + ++A ++ + +GFA++
Sbjct: 172 TDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVL 231
Query: 81 VFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQY 128
+ T A++A+ + +G +G + ++F P RS Q
Sbjct: 232 EYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQA 279
>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA
binding domain, RNA recognition motif, SP factor, snRNP,
spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP:
d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A
Length = 292
Score = 183 bits (467), Expect = 3e-56
Identities = 51/311 (16%), Positives = 111/311 (35%), Gaps = 43/311 (13%)
Query: 2 KSKGKILEASWDEGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTL 61
+G A +++ R N+E V V NL S + + FK G +
Sbjct: 16 LDEGSPAAAGLTSKKANEALTR-NRELTTVL------VKNLPKSYNQNKVYKYFKHCGPI 68
Query: 62 RDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPV 121
V VA + ++ FA I F A A + + + ++ ++
Sbjct: 69 IHVDVADSLK-KNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL------------ 115
Query: 122 GPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNI-IEVKIVRDENGKSKGFGFIQFFS 180
+ +++ N + + ++ + + +++ S+ F +I S
Sbjct: 116 -------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTS 168
Query: 181 YKAAEKAIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNI 240
+ A + ++NG I+ + ++ K K +I + NL + +
Sbjct: 169 KEDARYCVEKLNGLKIEGYTLVTKVS------NPLEKSKRTDSATLEGREIMIRNLSTEL 222
Query: 241 NN-SEFEELFARFGTITSSSLVSDKH-------IGFIEFIMPKHATHAVSTMNGHVFKSK 292
+ + E F FG+I ++ + + F+ F A A+ MN + ++
Sbjct: 223 LDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNR 281
Query: 293 PLKVTLSGTKP 303
+ V+L+ KP
Sbjct: 282 EISVSLADKKP 292
Score = 129 bits (327), Expect = 1e-35
Identities = 37/253 (14%), Positives = 78/253 (30%), Gaps = 44/253 (17%)
Query: 74 SRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKV 133
S + + ++K+ E + G K + + V
Sbjct: 1 SMEYG---HHARPDSKRPLDEGSPAAAGLTS-------------KKANEALTRNRELTTV 44
Query: 134 FVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNG 193
VKNL ++ ++ ++ +F G II V + K+ F I+F Y A AI + +
Sbjct: 45 LVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL-KKNFRFARIEFARYDGALAAITKTHK 103
Query: 194 RMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFG 253
+V ++ + + +++ N P + +L
Sbjct: 104 --------------VVGQNEII-------VSHLTECTLWMTNFPPSYTQRNIRDLLQDIN 142
Query: 254 TITSSSLVSDKHI------GFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKPGVSI 307
+ S + +I+ + A + V +NG + L +S
Sbjct: 143 VVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKR 202
Query: 308 TNPTKAPKKPAYI 320
T+ + I
Sbjct: 203 TDSATLEGREIMI 215
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 154 bits (392), Expect = 4e-46
Identities = 49/206 (23%), Positives = 94/206 (45%), Gaps = 9/206 (4%)
Query: 113 KPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDEN-GKSK 171
+ R + +V+V ++ + E+ ++ F FG I + + D K K
Sbjct: 11 QQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK 70
Query: 172 GFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKI 231
GF F+++ +AA+ A+ +MN M+ + V + P + + N+I
Sbjct: 71 GFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP--SNIGQAQPIIDQLAEEARAFNRI 128
Query: 232 FVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVSTMN 285
+VA++ ++++ + + +F FG I S++L D K GFIE+ + + AVS+MN
Sbjct: 129 YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Query: 286 GHVFKSKPLKVTLSGTKPGVSITNPT 311
+ L+V + T P +T T
Sbjct: 189 LFDLGGQYLRVGKAVTPPMPLLTPAT 214
Score = 153 bits (388), Expect = 2e-45
Identities = 35/171 (20%), Positives = 80/171 (46%), Gaps = 2/171 (1%)
Query: 39 VNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEMNG 97
V ++ + + F FG ++ + ++ + + +GFA + + P A+ A +MN
Sbjct: 33 VGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNS 92
Query: 98 HLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNI 157
++G + + + + E+ ++++V ++ + + ++++KS F FG I
Sbjct: 93 VMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKI 152
Query: 158 IEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
+ RD GK KG+GFI++ ++++ A+ MN + V A
Sbjct: 153 KSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203
Score = 70.8 bits (174), Expect = 1e-14
Identities = 18/124 (14%), Positives = 49/124 (39%), Gaps = 2/124 (1%)
Query: 1 MKSKGKILEASWDEGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGT 60
+ G+ ++ I + ++ + N ++V ++ + + + + F+ FG
Sbjct: 93 VMLGGRNIKVGRPSNIGQAQ-PIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGK 151
Query: 61 LRDVRVARNKND-ESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSK 119
++ +AR+ + +G+ I + ++ A MN +G + + + P
Sbjct: 152 IKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLT 211
Query: 120 PVGP 123
P P
Sbjct: 212 PATP 215
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP,
RBD, poly(U) binding, tandem, acetylation, cytopla
nucleus; 2.70A {Saccharomyces cerevisiae}
Length = 166
Score = 152 bits (386), Expect = 1e-45
Identities = 40/172 (23%), Positives = 81/172 (47%), Gaps = 10/172 (5%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L+V NL+ ++ L F+ G + ++++ +KN+++ +A + ++ +A A +N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGN 156
G I + V I + S +FV +L VD+E L++ F F +
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSDDTF---------NLFVGDLNVNVDDETLRNAFKDFPS 113
Query: 157 IIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
+ ++ D + G S+G+GF+ F S A+ A+ M G+ + ++ A
Sbjct: 114 YLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165
Score = 126 bits (319), Expect = 7e-36
Identities = 39/173 (22%), Positives = 78/173 (45%), Gaps = 17/173 (9%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
++V NL + + E+ LK +F G I +KI+ D+N K+ + F+++ A A+ +N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 193 GRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARF 252
G+ I++N ++ A + +FV +L N+++ F F
Sbjct: 63 GKQIENNIVKINWAF-----------QSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDF 111
Query: 253 GTITSSSLVSD------KHIGFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLS 299
+ S ++ D + GF+ F A +A+ +M G +PL++ +
Sbjct: 112 PSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>1b7f_A Protein (SXL-lethal protein), RNA
(5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing
regulation, RNP domain, RNA complex; 2.60A {Drosophila
melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A*
1sxl_A 2sxl_A
Length = 168
Score = 146 bits (372), Expect = 1e-43
Identities = 44/174 (25%), Positives = 85/174 (48%), Gaps = 15/174 (8%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
L VN L + ++ L F+ G + R+ R+ S G+A + F + ++++A +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFG 155
NG + +K LK P + K ++V NL T+ +++L + F K+G
Sbjct: 66 NGITVRNKR-------LKVSYAR----PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYG 114
Query: 156 NIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNST--FVSLA 206
+I++ I+RD G+ +G F+++ + A++AI +N + + S V LA
Sbjct: 115 SIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 138 bits (350), Expect = 2e-40
Identities = 44/176 (25%), Positives = 84/176 (47%), Gaps = 22/176 (12%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
+ V L + + + EL + F G I +I+RD + G S G+ F+ F S +++AI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 191 MNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFA 250
+NG +++ VS A P + + ++V NLP I + + + +F
Sbjct: 65 LNGITVRNKRLKVSYAR-------------PGGESIKDTNLYVTNLPRTITDDQLDTIFG 111
Query: 251 RFGTITSSSLVSDKH------IGFIEFIMPKHATHAVSTMNGHVFK--SKPLKVTL 298
++G+I +++ DK + F+ + + A A+S +N + + S+PL V L
Sbjct: 112 KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL 167
Score = 69.5 bits (171), Expect = 1e-14
Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 6/91 (6%)
Query: 22 ARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVAR-NKNDESRGFAII 80
AR E+ K L+V NL ++ + L F K+G++ + R RG A +
Sbjct: 80 ARPGGESIKDTN---LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 136
Query: 81 VFNTPAEAKKARVEMNGHLI--GSKPVIITF 109
+N EA++A +N + GS+P+ +
Sbjct: 137 RYNKREEAQEAISALNNVIPEGGSQPLSVRL 167
Score = 64.1 bits (157), Expect = 1e-12
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 6/77 (7%)
Query: 226 ARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIMPKHATH 279
A + V LP ++ + E LF G I + ++ D F++F +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 280 AVSTMNGHVFKSKPLKV 296
A+ +NG ++K LKV
Sbjct: 61 AIKVLNGITVRNKRLKV 77
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA
binding protein-RNA complex; 1.85A {Homo sapiens} PDB:
3nna_A 3nnc_A 2dhs_A 3nnh_A
Length = 175
Score = 145 bits (368), Expect = 6e-43
Identities = 35/175 (20%), Positives = 74/175 (42%), Gaps = 13/175 (7%)
Query: 39 VNNLEPSVDNQALINEFKKFGTLRDVRVARNKN---DESRGFAIIVFNTPAEAKKARVEM 95
V + + + L F+++G + ++ V R+++ +S+G + F T A +A+ +
Sbjct: 8 VGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNAL 67
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFG 155
+ + P Q + + K+F+ + + E +++ F FG
Sbjct: 68 HNMKVLPG-------MHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFG 120
Query: 156 NIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNST---FVSLAE 207
I E +I+R +G S+G F+ F + A+ AI M+ + V A+
Sbjct: 121 QIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175
Score = 135 bits (341), Expect = 5e-39
Identities = 38/181 (20%), Positives = 74/181 (40%), Gaps = 26/181 (14%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENG---KSKGFGFIQFFSYKAAEKAI 188
K+FV + T E++L+ F ++G + E+ ++RD + +SKG F+ F++ KAA +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 189 IEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARK---NKIFVANLPSNINNSEF 245
++ + PG ++KP + K+F+ + ++
Sbjct: 65 NALHNMKVL------------PGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDI 112
Query: 246 EELFARFGTITSSSLVSDKH-----IGFIEFIMPKHATHAVSTMNGHVFK---SKPLKVT 297
+F+ FG I ++ F+ F A A+ M+ S P+ V
Sbjct: 113 RVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK 172
Query: 298 L 298
Sbjct: 173 F 173
Score = 74.2 bits (183), Expect = 3e-16
Identities = 21/91 (23%), Positives = 40/91 (43%), Gaps = 3/91 (3%)
Query: 24 SNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFN 83
++ E N ++ +L + + + F FG + + R+ R + SRG A + F
Sbjct: 85 ADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFT 144
Query: 84 TPAEAKKARVEMNGHLI---GSKPVIITFVE 111
T A A+ A M+ S P+++ F +
Sbjct: 145 TRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 143 bits (364), Expect = 6e-42
Identities = 66/222 (29%), Positives = 103/222 (46%), Gaps = 28/222 (12%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
L+V +L P V L +F G + +RV R+ S G+A + F PA+A++A M
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFG 155
N +I KPV I + + P R VG +F+KNL +++D + L F FG
Sbjct: 78 NFDVIKGKPVRIMWSQRDPSLRKSGVG---------NIFIKNLDKSIDNKALYDTFSAFG 128
Query: 156 NIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIVPGKKVF 215
NI+ K+V DENG SKG+GF+ F + +AAE+AI +MNG ++ FV
Sbjct: 129 NILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF--------K 179
Query: 216 PKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITS 257
+ R+ ++ + + G I +
Sbjct: 180 SR-------KEREAEL--GARAKEFYPYDVPDYAGSSGRIVT 212
Score = 130 bits (329), Expect = 1e-36
Identities = 48/192 (25%), Positives = 84/192 (43%), Gaps = 19/192 (9%)
Query: 120 PVG---PEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGF 175
P+G P Y ++V +L V E L F G I+ +++ RD +S G+ +
Sbjct: 2 PLGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 61
Query: 176 IQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVAN 235
+ F AE+A+ MN +I+ + ++ + P L+ + IF+ N
Sbjct: 62 VNFQQPADAERALDTMNFDVIKGKPVRIMWSQ-----------RDPSLRKSGVGNIFIKN 110
Query: 236 LPSNINNSEFEELFARFGTITSSSLVSD----KHIGFIEFIMPKHATHAVSTMNGHVFKS 291
L +I+N + F+ FG I S +V D K GF+ F + A A+ MNG +
Sbjct: 111 LDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLND 170
Query: 292 KPLKVTLSGTKP 303
+ + V ++
Sbjct: 171 RKVFVGRFKSRK 182
Score = 72.7 bits (179), Expect = 3e-15
Identities = 26/110 (23%), Positives = 55/110 (50%), Gaps = 2/110 (1%)
Query: 22 ARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIV 81
++ + K + + NL+ S+DN+AL + F FG + +V ++N S+G+ +
Sbjct: 92 SQRDPSLRKS-GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVH 149
Query: 82 FNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKD 131
F T A++A +MNG L+ + V + + + + ++ ++ Y D
Sbjct: 150 FETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYD 199
Score = 57.3 bits (139), Expect = 5e-10
Identities = 22/91 (24%), Positives = 36/91 (39%), Gaps = 6/91 (6%)
Query: 220 PPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIM 273
P ++V +L ++ + E F+ G I S + D ++ F
Sbjct: 7 NPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Query: 274 PKHATHAVSTMNGHVFKSKPLKVTLSGTKPG 304
P A A+ TMN V K KP+++ S P
Sbjct: 67 PADAERALDTMNFDVIKGKPVRIMWSQRDPS 97
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 140 bits (356), Expect = 3e-41
Identities = 43/189 (22%), Positives = 73/189 (38%), Gaps = 21/189 (11%)
Query: 19 DEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFA 78
EG+ S N L + NL P+ L + D+ V + +R F
Sbjct: 5 VEGSESTTPFN-------LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFG 57
Query: 79 IIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNL 138
+ F + + +KA +E+ G + + + + + ++ + + KNL
Sbjct: 58 YVDFESAEDLEKA-LELTGLKVFGNEIKLEKPKGRDSKKVRA---------ARTLLAKNL 107
Query: 139 VETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQH 198
+ E+ELK F I V ++GKSKG +I+F S AEK + E G I
Sbjct: 108 SFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG 163
Query: 199 NSTFVSLAE 207
S +
Sbjct: 164 RSVSLYYTG 172
Score = 131 bits (331), Expect = 2e-37
Identities = 37/175 (21%), Positives = 63/175 (36%), Gaps = 19/175 (10%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+F+ NL ELK + ++ +V G ++ FG++ F S + EKA +E+
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA-LEL 73
Query: 192 NGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFAR 251
G + N + + + + NL NI E +E+F
Sbjct: 74 TGLKVFGNEIKLEKPK-----------GRDSKKVRAARTLLAKNLSFNITEDELKEVFED 122
Query: 252 FGTITSSSLVSD----KHIGFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTK 302
I VS K I +IEF A + G + + + +G K
Sbjct: 123 ALEIRL---VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
Score = 61.9 bits (151), Expect = 8e-12
Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 10/94 (10%)
Query: 20 EGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAI 79
++ + + NL ++ L F+ +R V ++ +S+G A
Sbjct: 91 RDSKKVRAARTLL------AKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAY 140
Query: 80 IVFNTPAEAKKARVEMNGHLIGSKPVIITFVELK 113
I F + A+A+K E G I + V + + K
Sbjct: 141 IEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
Score = 54.9 bits (133), Expect = 2e-09
Identities = 11/97 (11%), Positives = 31/97 (31%), Gaps = 6/97 (6%)
Query: 221 PLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPK 275
+ +F+ NL N + +E + + ++V + G+++F +
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 65
Query: 276 HATHAVSTMNGHVFKSKPLKVTLSGTKPGVSITNPTK 312
A+ + G +K+ + +
Sbjct: 66 DLEKALE-LTGLKVFGNEIKLEKPKGRDSKKVRAART 101
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex,
AU-rich element, transcription/RNA complex; 1.80A {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H
1d8z_A 1d9a_A 3hi9_A
Length = 167
Score = 139 bits (353), Expect = 7e-41
Identities = 43/163 (26%), Positives = 78/163 (47%), Gaps = 13/163 (7%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
L VN L ++ + + F G + ++ R+K +S G+ + + P +A+KA +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFG 155
NG + +K +K P + ++V L +T+ ++EL+ F ++G
Sbjct: 65 NGLRLQTKT-------IKVSYAR----PSSASIRDANLYVSGLPKTMTQKELEQLFSQYG 113
Query: 156 NIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQ 197
II +I+ D G S+G GFI+F AE+AI +NG+
Sbjct: 114 RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPS 156
Score = 132 bits (335), Expect = 4e-38
Identities = 50/176 (28%), Positives = 81/176 (46%), Gaps = 22/176 (12%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
+ V L + + +EE +S F G I K+VRD G+S G+GF+ + K AEKAI
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 191 MNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFA 250
+NG +Q K + P R ++V+ LP + E E+LF+
Sbjct: 64 LNGLRLQ-------------TKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFS 110
Query: 251 RFGTITSSSLVSDKH------IGFIEFIMPKHATHAVSTMNGHVF--KSKPLKVTL 298
++G I +S ++ D+ +GFI F A A+ +NG ++P+ V
Sbjct: 111 QYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF 166
Score = 68.4 bits (168), Expect = 4e-14
Identities = 21/91 (23%), Positives = 43/91 (47%), Gaps = 6/91 (6%)
Query: 22 ARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESRGFAII 80
AR + + + L+V+ L ++ + L F ++G + R+ ++ SRG I
Sbjct: 79 ARPSSASIRDAN---LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFI 135
Query: 81 VFNTPAEAKKARVEMNGHLI--GSKPVIITF 109
F+ EA++A +NG ++P+ + F
Sbjct: 136 RFDKRIEAEEAIKGLNGQKPSGATEPITVKF 166
Score = 61.4 bits (150), Expect = 9e-12
Identities = 29/75 (38%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIMPKHATHAV 281
K + V LP N+ EF LF G I S LV DK GF+ +I PK A A+
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 282 STMNGHVFKSKPLKV 296
+T+NG ++K +KV
Sbjct: 62 NTLNGLRLQTKTIKV 76
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 137 bits (348), Expect = 5e-39
Identities = 40/178 (22%), Positives = 71/178 (39%), Gaps = 22/178 (12%)
Query: 19 DEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFA 78
D + + L V NL + + F+++G +V + R RGF
Sbjct: 7 DIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-----DRGFG 61
Query: 79 IIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNL 138
I + A+ A+ E++G ++ S+P+ I + VKNL
Sbjct: 62 FIRLESRTLAEIAKAELDGTILKSRPLRI-----------------RFATHGAALTVKNL 104
Query: 139 VETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMI 196
V E L+ F +FG + + +V D+ G++ G GF++F + A KA+
Sbjct: 105 SPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAF 162
Score = 126 bits (318), Expect = 1e-34
Identities = 49/194 (25%), Positives = 78/194 (40%), Gaps = 34/194 (17%)
Query: 113 KPGQRSKPVGPEEKQYKKD-KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSK 171
+ P EK Y + ++FV NL + EE+ K F ++G EV I RD +
Sbjct: 4 FTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----R 58
Query: 172 GFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKI 231
GFGFI+ S AE A E++G +++ + A +
Sbjct: 59 GFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFAT-------------------HGAAL 99
Query: 232 FVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHATHAVSTMNG 286
V NL ++N E+ F++FG + + +V D GF+EF A A+
Sbjct: 100 TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGD 159
Query: 287 HVF----KSKPLKV 296
F +P+ V
Sbjct: 160 GAFLLTTTPRPVIV 173
Score = 71.6 bits (176), Expect = 1e-14
Identities = 26/88 (29%), Positives = 47/88 (53%), Gaps = 2/88 (2%)
Query: 211 GKKVFPK--VKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGF 268
G + K +KP ++ ++FV NLP++I +F+ LF R+G + + D+ GF
Sbjct: 3 GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGF 62
Query: 269 IEFIMPKHATHAVSTMNGHVFKSKPLKV 296
I A A + ++G + KS+PL++
Sbjct: 63 IRLESRTLAEIAKAELDGTILKSRPLRI 90
Score = 70.1 bits (172), Expect = 4e-14
Identities = 25/110 (22%), Positives = 37/110 (33%), Gaps = 2/110 (1%)
Query: 29 NKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEA 88
L V NL P V N+ L F +FG + V + + G + F A
Sbjct: 91 RFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPA 150
Query: 89 KKARVEMNGH-LIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKN 137
+KA + + VE Q G EK +K + + K
Sbjct: 151 RKALERCGDGAFLLTTTPRPVIVEPME-QFDDEDGLPEKLMQKTQQYHKE 199
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 133 bits (337), Expect = 5e-38
Identities = 35/188 (18%), Positives = 75/188 (39%), Gaps = 17/188 (9%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARN------KNDESRGFAIIVFNTPAEAKK 90
L+V N+ + +A+++ F L + A + ++ + FA + F + E +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 91 ARVEMNGHLIGSKPVIITF---------VELKPGQRSKPVGPEEKQYKKDKVFVKNLVET 141
A + +G + + + I + P V K+F+ L
Sbjct: 67 A-MAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125
Query: 142 VDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNS 200
++++++K FG + +V+D G SKG+ F ++ ++AI +NG +
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185
Query: 201 TFVSLAEI 208
V A +
Sbjct: 186 LLVQRASV 193
Score = 130 bits (328), Expect = 8e-37
Identities = 37/191 (19%), Positives = 76/191 (39%), Gaps = 20/191 (10%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVK------IVRDENGKSKGFGFIQFFSYKAAE 185
+++V N+ + EE + F + + ++ + + K F F++F S
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 186 KAIIEMNGRMIQHNSTFVSLAE-------IVPGKKVFPKVKPPLLQPARKNKIFVANLPS 238
+A+ +G + Q S + + V+ + P +K+F+ LP+
Sbjct: 66 QAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 239 NINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVSTMNGHVFKSK 292
+N+ + +EL FG + + +LV D K F E++ A++ +NG K
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 184
Query: 293 PLKVTLSGTKP 303
L V +
Sbjct: 185 KLLVQRASVGA 195
Score = 70.1 bits (172), Expect = 2e-14
Identities = 13/96 (13%), Positives = 34/96 (35%), Gaps = 1/96 (1%)
Query: 22 ARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVAR-NKNDESRGFAII 80
++L + L +++ + FG L+ + + + S+G+A
Sbjct: 102 VPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFC 161
Query: 81 VFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQ 116
+ +A +NG +G K +++ +
Sbjct: 162 EYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 197
Score = 55.4 bits (134), Expect = 2e-09
Identities = 21/118 (17%), Positives = 42/118 (35%), Gaps = 14/118 (11%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVS-----------DKHIGFIEFIM 273
AR+ ++V N+P I + F + + DK+ F+EF
Sbjct: 3 MARR--LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 274 PKHATHAVSTMNGHVFKSKPLKVTLSGTKPGVSITNPTKAPKKPAYIDEVKNVIGIKV 331
T A++ +G +F+ + LK+ + + + P + V K+
Sbjct: 61 VDETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKL 117
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA
splicing factor, RNA recognition motif, RNA binding
protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A
Length = 172
Score = 130 bits (328), Expect = 4e-37
Identities = 33/167 (19%), Positives = 73/167 (43%), Gaps = 19/167 (11%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARN------KNDESRGFAIIVFNTPAEAKK 90
L+V N+ + +A+++ F L + A + ++ + FA + F + E +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 91 ARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSH 150
A + +G + + + I +R P +K +F+ L ++++++K
Sbjct: 67 A-MAFDGIIFQGQSLKI--------RRPHDYQPLPGAHK---LFIGGLPNYLNDDQVKEL 114
Query: 151 FIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMNGRMI 196
FG + +V+D G SKG+ F ++ ++AI +NG +
Sbjct: 115 LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 161
Score = 123 bits (312), Expect = 1e-34
Identities = 34/177 (19%), Positives = 71/177 (40%), Gaps = 26/177 (14%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVK------IVRDENGKSKGFGFIQFFSYKAAE 185
+++V N+ + EE + F + + ++ + + K F F++F S
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 186 KAIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEF 245
+A+ +G + Q G+ + + +K+F+ LP+ +N+ +
Sbjct: 66 QAM-AFDGIIFQ-------------GQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQV 111
Query: 246 EELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVSTMNGHVFKSKPLKV 296
+EL FG + + +LV D F E++ A++ +NG K L V
Sbjct: 112 KELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 168
Score = 65.7 bits (161), Expect = 4e-13
Identities = 13/74 (17%), Positives = 31/74 (41%), Gaps = 1/74 (1%)
Query: 33 KENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKA 91
++L + L +++ + FG L+ + ++ S+G+A + +A
Sbjct: 93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152
Query: 92 RVEMNGHLIGSKPV 105
+NG +G K +
Sbjct: 153 IAGLNGMQLGDKKL 166
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 122 bits (309), Expect = 4e-34
Identities = 45/187 (24%), Positives = 84/187 (44%), Gaps = 18/187 (9%)
Query: 16 ISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DES 74
+S E + ++ K++ + L +++L + F+++GTL D V R+ N S
Sbjct: 1 MSKSESPKEPEQLRKLF------IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRS 54
Query: 75 RGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVF 134
RGF + + T E A + H + + V E K + K+F
Sbjct: 55 RGFGFVTYATVEEVDAA-MNARPHKVDGRVV-----EPKRAVSREDSQRPGAHLTVKKIF 108
Query: 135 VKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAII---- 189
V + E +E L+ +F ++G I ++I+ D +GK +GF F+ F + + +K +I
Sbjct: 109 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 168
Query: 190 EMNGRMI 196
+NG
Sbjct: 169 TVNGHNC 175
Score = 109 bits (274), Expect = 7e-29
Identities = 40/199 (20%), Positives = 76/199 (38%), Gaps = 29/199 (14%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDEN-GKSKGFGFI 176
SK P+E + + K+F+ L +E L+SHF ++G + + ++RD N +S+GFGF+
Sbjct: 2 SKSESPKEPEQLR-KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKV------KPPLLQPARKNK 230
+ + + + A+ + G+ V PK K
Sbjct: 61 TYATVEEVDAAM-NARPHKVD-------------GRVVEPKRAVSREDSQRPGAHLTVKK 106
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVSTM 284
IFV + + + F ++G I +++D+ F+ F V
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-Q 165
Query: 285 NGHVFKSKPLKVTLSGTKP 303
H +V + +K
Sbjct: 166 KYHTVNGHNCEVRKALSKQ 184
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding,
RNA processing, mRNA processing, nonsense-mediated mRNA
decay, cleavage; NMR {Saccharomyces cerevisiae} PDB:
2km8_C
Length = 167
Score = 121 bits (306), Expect = 6e-34
Identities = 40/164 (24%), Positives = 74/164 (45%), Gaps = 19/164 (11%)
Query: 39 VNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEMNG 97
+ L L F K+GT+ D+++ ++ SRGF + F P+ +
Sbjct: 8 IGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ-- 65
Query: 98 HLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNI 157
H++ K + K P ++Q K K+FV + V +E + F ++G I
Sbjct: 66 HILDGKVI-----------DPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTI 114
Query: 158 IEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAI----IEMNGRMI 196
I+ +++ D + G+S+GFGF+ + S A ++ I+ R I
Sbjct: 115 IDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKI 158
Score = 116 bits (292), Expect = 8e-32
Identities = 43/172 (25%), Positives = 80/172 (46%), Gaps = 23/172 (13%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDEN-GKSKGFGFIQFFSYKAAEKAIIE 190
K+F+ L E+ L+ +F K+G + ++KI++D G+S+GFGF+ F + ++ +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 191 MNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFA 250
+ I+ GK + PK P + + KIFV + ++ EFEE F+
Sbjct: 65 QH---------------ILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFS 109
Query: 251 RFGTITSSSLVSDKH------IGFIEFIMPKHATHAVSTMNGHVFKSKPLKV 296
++GTI + L+ DK GF+ + FK + +++
Sbjct: 110 QWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEI 160
Score = 55.6 bits (135), Expect = 1e-09
Identities = 16/85 (18%), Positives = 36/85 (42%), Gaps = 5/85 (5%)
Query: 22 ARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESRGFAII 80
A E +K K + V + P V + F ++GT+ D ++ +K+ +SRGF +
Sbjct: 78 AIPRDEQDKTGK---IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFV 134
Query: 81 VFNTPAEAKKARVEMNGHLIGSKPV 105
+++ + + + +
Sbjct: 135 TYDSADAVDRV-CQNKFIDFKDRKI 158
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A
Length = 282
Score = 115 bits (289), Expect = 2e-30
Identities = 52/274 (18%), Positives = 94/274 (34%), Gaps = 16/274 (5%)
Query: 37 LHVNNLEPSVD----NQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + ++L F +FG + D+ V+R+ RG A ++F + A A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 69
Query: 93 VEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFI 152
M G KP+ I + + +K G ++ +K K ++ + K
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRK---REKRKPKSQETPATKKAVQ 126
Query: 153 KFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVS-----LAE 207
G V V+ + + MI
Sbjct: 127 GGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMP 186
Query: 208 IVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-I 266
PL + + +F+ NLP N LF +F LV +H I
Sbjct: 187 PQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDI 246
Query: 267 GFIEFIMPKHATHAVSTMNGH-VFKSKPLKVTLS 299
F+EF A A + G + ++ +K++ +
Sbjct: 247 AFVEFDNEVQAGAARDALQGFKITQNNAMKISFA 280
Score = 59.5 bits (143), Expect = 2e-10
Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 7/82 (8%)
Query: 229 NKIFVANLPSNINNSE----FEELFARFGTITSSSLVSD---KHIGFIEFIMPKHATHAV 281
+ I++ NL I E +F++FG I + + F+ F AT+A+
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 69
Query: 282 STMNGHVFKSKPLKVTLSGTKP 303
+M G F KP+++ + T
Sbjct: 70 RSMQGFPFYDKPMRIQYAKTDS 91
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 108 bits (271), Expect = 3e-28
Identities = 41/190 (21%), Positives = 77/190 (40%), Gaps = 32/190 (16%)
Query: 37 LHVNNLEP-SVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEM 95
L V+NL P V Q+L F +G ++ V++ NK + A++ +A+ A +
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHL 92
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDK----------------------- 132
NGH + KP+ IT + + Q + ++ K
Sbjct: 93 NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 152
Query: 133 -VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+ + N+ +V EE+LK F G +++ K + IQ S + A +A+I++
Sbjct: 153 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDL 209
Query: 192 NGRMIQHNST 201
+ + N
Sbjct: 210 HNHDLGENHH 219
Score = 98.9 bits (246), Expect = 1e-24
Identities = 38/218 (17%), Positives = 78/218 (35%), Gaps = 42/218 (19%)
Query: 114 PGQRSKPVGPEEKQYKKDKVFVKNL-VETVDEEELKSHFIKFGNIIEVKIVRDENGKSKG 172
+ P + V NL E V + L F +G++ VKI+ K
Sbjct: 18 GSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF----NKKE 73
Query: 173 FGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEI------------------------ 208
+Q A+ A+ +NG + ++L++
Sbjct: 74 NALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPL 133
Query: 209 ----VPGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLV--S 262
PG K F + PP + ++N+P +++ + + LF+ G +
Sbjct: 134 HRFKKPGSKNFQNIFPP------SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK 187
Query: 263 DKHIGFIEFIMPKHATHAVSTMNGH-VFKSKPLKVTLS 299
D+ + I+ + A A+ ++ H + ++ L+V+ S
Sbjct: 188 DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 225
Score = 58.1 bits (140), Expect = 4e-10
Identities = 24/97 (24%), Positives = 43/97 (44%), Gaps = 2/97 (2%)
Query: 209 VPGKKVFPKVKPPLLQPARKNKIFVANL-PSNINNSEFEELFARFGTITSSSLVSD-KHI 266
VP ++ P L A + + V+NL P + LF +G + ++ + K
Sbjct: 15 VPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN 74
Query: 267 GFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
++ A A+S +NGH KP+++TLS +
Sbjct: 75 ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN 111
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA,
spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1
d.58.7.1
Length = 198
Score = 105 bits (263), Expect = 2e-27
Identities = 41/190 (21%), Positives = 77/190 (40%), Gaps = 32/190 (16%)
Query: 37 LHVNNLEP-SVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEM 95
L V+NL P V Q+L F +G ++ V++ NK + A++ +A+ A +
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHL 61
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKK------------------------D 131
NGH + KP+ IT + + Q + ++ K
Sbjct: 62 NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 121
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+ + N+ +V EE+LK F G +++ K + IQ S + A +A+I++
Sbjct: 122 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDL 178
Query: 192 NGRMIQHNST 201
+ + N
Sbjct: 179 HNHDLGENHH 188
Score = 98.4 bits (245), Expect = 9e-25
Identities = 35/193 (18%), Positives = 74/193 (38%), Gaps = 30/193 (15%)
Query: 133 VFVKNLV-ETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+ V NL E V + L F +G++ VKI+ + K +Q A+ A+ +
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSHL 61
Query: 192 NGRMIQHNSTFVSLA------------EIVPGKKVF----------PKVKPPLLQPARKN 229
NG + ++L+ E K + P K
Sbjct: 62 NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 121
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLV--SDKHIGFIEFIMPKHATHAVSTMNGH 287
+ ++N+P +++ + + LF+ G + D+ + I+ + A A+ ++ H
Sbjct: 122 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNH 181
Query: 288 -VFKSKPLKVTLS 299
+ ++ L+V+ S
Sbjct: 182 DLGENHHLRVSFS 194
Score = 55.3 bits (133), Expect = 2e-09
Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 2/88 (2%)
Query: 231 IFVANL-PSNINNSEFEELFARFGTITSSSLVSD-KHIGFIEFIMPKHATHAVSTMNGHV 288
+ V+NL P + LF +G + ++ + K ++ A A+S +NGH
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 65
Query: 289 FKSKPLKVTLSGTKPGVSITNPTKAPKK 316
KP+++TLS + +
Sbjct: 66 LHGKPIRITLSKHQNVQLPREGQEDQGL 93
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 102 bits (256), Expect = 2e-26
Identities = 23/188 (12%), Positives = 57/188 (30%), Gaps = 32/188 (17%)
Query: 37 LHVNNLEPS-VDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEM 95
L V L+ S ++ + N F +G + V+ ++K G A++ +A +
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRAITHL 62
Query: 96 NGHLIGSKPVIITF-----VELKPGQRSKPVGPEEKQYKKDK------------------ 132
N + + + + + + + K + + +
Sbjct: 63 NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHP 122
Query: 133 ---VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDEN-GKSKGFGFIQFFSYKAAEKAI 188
+ N V EE + G + + G +++ S A + +
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182
Query: 189 IEMNGRMI 196
+N +
Sbjct: 183 GFLNHYQM 190
Score = 95.2 bits (236), Expect = 2e-23
Identities = 25/195 (12%), Positives = 57/195 (29%), Gaps = 35/195 (17%)
Query: 133 VFVKNLV-ETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+ V L ++ + + + F +GN+ +VK ++ G ++ A ++AI +
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHL 62
Query: 192 NGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARK----------------------- 228
N + V +++ +
Sbjct: 63 NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHP 122
Query: 229 -NKIFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAV 281
N + N P + F E+ G +S+ G +E+ A +
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182
Query: 282 STMNGHVFKSKPLKV 296
+N + K+
Sbjct: 183 GFLNHYQMKNPNGPY 197
Score = 56.3 bits (135), Expect = 1e-09
Identities = 12/92 (13%), Positives = 29/92 (31%), Gaps = 1/92 (1%)
Query: 20 EGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESRGFA 78
+N + N LH N V + + G R V E
Sbjct: 109 STPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSG 168
Query: 79 IIVFNTPAEAKKARVEMNGHLIGSKPVIITFV 110
++ +++ ++A + +N + + + +
Sbjct: 169 LLEWDSKSDALETLGFLNHYQMKNPNGPYPYT 200
Score = 53.6 bits (128), Expect = 1e-08
Identities = 14/97 (14%), Positives = 33/97 (34%), Gaps = 2/97 (2%)
Query: 231 IFVANL-PSNINNSEFEELFARFGTITSSSLVSDK-HIGFIEFIMPKHATHAVSTMNGHV 288
+ V L S +N +F +G + + K +E A++ +N +
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNF 66
Query: 289 FKSKPLKVTLSGTKPGVSITNPTKAPKKPAYIDEVKN 325
+ + V +S + + +Y D ++
Sbjct: 67 MFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSES 103
>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure
genomics, RRM domain, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 97.7 bits (244), Expect = 1e-25
Identities = 24/83 (28%), Positives = 45/83 (54%)
Query: 125 EKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAA 184
+++ +++ NL ++DE+EL++ FG +I +I+RD +G S+G GF + S +
Sbjct: 20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKC 79
Query: 185 EKAIIEMNGRMIQHNSTFVSLAE 207
E I NG+ I+ + E
Sbjct: 80 EAVIGHFNGKFIKTPPGVSAPTE 102
Score = 73.1 bits (180), Expect = 2e-16
Identities = 21/86 (24%), Positives = 36/86 (41%)
Query: 20 EGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAI 79
G ++ + L+++NL S+D Q L N K FG + R+ R+ + SRG
Sbjct: 11 SGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGF 70
Query: 80 IVFNTPAEAKKARVEMNGHLIGSKPV 105
+ + + NG I + P
Sbjct: 71 ARMESTEKCEAVIGHFNGKFIKTPPG 96
Score = 71.5 bits (176), Expect = 8e-16
Identities = 17/93 (18%), Positives = 36/93 (38%), Gaps = 5/93 (5%)
Query: 212 KKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----I 266
K + + Q ++++NLP +++ E E + FG + S+ ++ D +
Sbjct: 9 KASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGV 68
Query: 267 GFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLS 299
GF + + NG K+ P +
Sbjct: 69 GFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT 101
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition
motif, RRM, RNA binding domain, RBD, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 97.4 bits (243), Expect = 2e-25
Identities = 28/90 (31%), Positives = 43/90 (47%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
VFV NL V ++LK F G ++ I+ D++GKS+G G + F A +AI
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 192 NGRMIQHNSTFVSLAEIVPGKKVFPKVKPP 221
NG+++ V + E K F + P
Sbjct: 77 NGQLLFDRPMHVKMDERALPKGDFFPPERP 106
Score = 79.3 bits (196), Expect = 1e-18
Identities = 21/104 (20%), Positives = 40/104 (38%), Gaps = 6/104 (5%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRG 76
++ + + V+ V NL+ V + L F G + + +K+ +SRG
Sbjct: 4 GSSGALQAGRLGSTVF------VANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRG 57
Query: 77 FAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
+ F EA +A NG L+ +P+ + E +
Sbjct: 58 IGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFF 101
Score = 69.6 bits (171), Expect = 3e-15
Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSD-----KHIGFIEFIMPKHATHAVST 283
+ +FVANL + + +E+F+ G + + ++ D + IG + F A A+S
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 284 MNGHVFKSKPLKVTLSGTKP 303
NG + +P+ V +
Sbjct: 76 FNGQLLFDRPMHVKMDERAL 95
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 94.7 bits (236), Expect = 2e-24
Identities = 28/93 (30%), Positives = 46/93 (49%), Gaps = 3/93 (3%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQ 177
S G E + + K+FV L + EE++ F FG I E ++R +G SKG F++
Sbjct: 3 SGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVK 62
Query: 178 FFSYKAAEKAIIEMNGRMIQHNST---FVSLAE 207
F S+ A+ AI ++G ++ V A+
Sbjct: 63 FSSHTEAQAAIHALHGSQTMPGASSSLVVKFAD 95
Score = 65.0 bits (159), Expect = 2e-13
Identities = 19/89 (21%), Positives = 42/89 (47%), Gaps = 3/89 (3%)
Query: 24 SNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFN 83
S+ ++ ++ +L V L + ++ F+ FG + + V R + S+G A + F+
Sbjct: 5 SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFS 64
Query: 84 TPAEAKKARVEMNGHLI---GSKPVIITF 109
+ EA+ A ++G S +++ F
Sbjct: 65 SHTEAQAAIHALHGSQTMPGASSSLVVKF 93
Score = 61.5 bits (150), Expect = 3e-12
Identities = 19/87 (21%), Positives = 32/87 (36%), Gaps = 8/87 (9%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHAT 278
+ R K+FV L + + LF FG I +++ F++F A
Sbjct: 11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQ 70
Query: 279 HAVSTMNGHVF---KSKPLKVTLSGTK 302
A+ ++G S L V + T
Sbjct: 71 AAIHALHGSQTMPGASSSLVVKFADTD 97
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 94.2 bits (235), Expect = 2e-24
Identities = 35/91 (38%), Positives = 55/91 (60%), Gaps = 1/91 (1%)
Query: 117 RSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFI 176
S G +Y+ ++VKNL + +D+E L+ F FG I K++ + G+SKGFGF+
Sbjct: 2 SSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFV 60
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
F S + A KA+ EMNGR++ +V+LA+
Sbjct: 61 CFSSPEEATKAVTEMNGRIVATKPLYVALAQ 91
Score = 74.2 bits (183), Expect = 7e-17
Identities = 31/97 (31%), Positives = 53/97 (54%), Gaps = 1/97 (1%)
Query: 24 SNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFN 83
S+ + Y+ L+V NL+ +D++ L F FGT+ +V S+GF + F+
Sbjct: 5 SSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGG-RSKGFGFVCFS 63
Query: 84 TPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
+P EA KA EMNG ++ +KP+ + + K ++S P
Sbjct: 64 SPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSGP 100
Score = 69.2 bits (170), Expect = 5e-15
Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 4/78 (5%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSD----KHIGFIEFIMPKHATHAVSTMN 285
++V NL I++ + F+ FGTITS+ ++ + K GF+ F P+ AT AV+ MN
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 286 GHVFKSKPLKVTLSGTKP 303
G + +KPL V L+ K
Sbjct: 77 GRIVATKPLYVALAQRKE 94
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation,
RNA-binding, EIF4G-binding translation; 1.90A {Homo
sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 94.6 bits (236), Expect = 2e-24
Identities = 35/114 (30%), Positives = 57/114 (50%), Gaps = 6/114 (5%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+F+KNL +++D + L F FGNI+ K+V DENG SKG+GF+ F + +AAE+AI +M
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-SKGYGFVHFETQEAAERAIEKM 65
Query: 192 NGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEF 245
NG ++ FV K + + +++ N +
Sbjct: 66 NGMLLNDRKVFVGRF-----KSRKEREAELGARAKEFTNVYIKNFGPGSTRAAA 114
Score = 83.1 bits (206), Expect = 4e-20
Identities = 28/110 (25%), Positives = 53/110 (48%), Gaps = 4/110 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
+ + NL+ S+DN+AL + F FG + +V ++N S+G+ + F T A++A +MN
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMN 66
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEE 146
G L+ + V FV ++ + + + V++KN
Sbjct: 67 GMLLNDRKV---FVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTRAA 113
Score = 63.8 bits (156), Expect = 6e-13
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH----IGFIEFIMPKHATHA 280
P IF+ NL +I+N + F+ FG I S +V D++ GF+ F + A A
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERA 61
Query: 281 VSTMNGHVFKSKPLKV 296
+ MNG + + + V
Sbjct: 62 IEKMNGMLLNDRKVFV 77
>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1 PDB: 2rq4_A 2rqc_A
Length = 115
Score = 94.3 bits (235), Expect = 3e-24
Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 1/93 (1%)
Query: 116 QRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFG 174
Q G +++ + +F+ +L + +++L F+ FGN++ K+ D + SK FG
Sbjct: 11 QSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFG 70
Query: 175 FIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
F+ + + +A+ AI MNG I V L
Sbjct: 71 FVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR 103
Score = 71.6 bits (176), Expect = 9e-16
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIMPKHATHAVS 282
+F+ +LP + + ++F FG + S+ + DK GF+ + P A A+
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 283 TMNGHVFKSKPLKVTL 298
+MNG K LKV L
Sbjct: 86 SMNGFQIGMKRLKVQL 101
Score = 67.7 bits (166), Expect = 2e-14
Identities = 23/102 (22%), Positives = 42/102 (41%), Gaps = 1/102 (0%)
Query: 20 EGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESRGFA 78
+ + + + L + +L +Q L+ F FG + +V +K S+ F
Sbjct: 11 QSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFG 70
Query: 79 IIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
+ ++ P A+ A MNG IG K + + K +S P
Sbjct: 71 FVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSGP 112
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 93.5 bits (233), Expect = 6e-24
Identities = 25/65 (38%), Positives = 39/65 (60%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+F+ L +E+ LK+ F K G I EV +++D KS+GF FI F + A+ A +M
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 192 NGRMI 196
NG+ +
Sbjct: 69 NGKSL 73
Score = 69.7 bits (171), Expect = 4e-15
Identities = 25/91 (27%), Positives = 42/91 (46%)
Query: 33 KENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+L + L + + L F K G + +V + +++ +SRGFA I F PA+AK A
Sbjct: 6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65
Query: 93 VEMNGHLIGSKPVIITFVELKPGQRSKPVGP 123
+MNG + K + + + Q P
Sbjct: 66 KDMNGKSLHGKAIKVEQAKKPSFQSGGRRRP 96
Score = 64.7 bits (158), Expect = 3e-13
Identities = 21/82 (25%), Positives = 32/82 (39%), Gaps = 5/82 (6%)
Query: 227 RKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHATHAV 281
K+F+ L N + +F + G I+ L+ D+ FI F P A +A
Sbjct: 6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65
Query: 282 STMNGHVFKSKPLKVTLSGTKP 303
MNG K +KV +
Sbjct: 66 KDMNGKSLHGKAIKVEQAKKPS 87
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.54A {Homo sapiens}
Length = 95
Score = 92.7 bits (231), Expect = 8e-24
Identities = 28/92 (30%), Positives = 40/92 (43%)
Query: 115 GQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFG 174
G ++ VFV NL V EE L F++ G + +V I +D GK K FG
Sbjct: 1 GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60
Query: 175 FIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
F+ F ++ AI +NG + VS
Sbjct: 61 FVCFKHPESVSYAIALLNGIRLYGRPINVSGP 92
Score = 65.0 bits (159), Expect = 1e-13
Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD-----KHIGFIEFIMPKHAT 278
Q +FV NL + + ELF + G +T ++ D K GF+ F P+ +
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVS 71
Query: 279 HAVSTMNGHVFKSKPLKV 296
+A++ +NG +P+ V
Sbjct: 72 YAIALLNGIRLYGRPINV 89
Score = 63.8 bits (156), Expect = 3e-13
Identities = 21/91 (23%), Positives = 37/91 (40%), Gaps = 4/91 (4%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDES 74
G S G +E + + V NLE V + L F + G L V + +++ +
Sbjct: 1 GSSGSSGMFPAQEEA----DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKP 56
Query: 75 RGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
+ F + F P A +NG + +P+
Sbjct: 57 KSFGFVCFKHPESVSYAIALLNGIRLYGRPI 87
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 92.4 bits (230), Expect = 2e-23
Identities = 26/95 (27%), Positives = 46/95 (48%), Gaps = 1/95 (1%)
Query: 114 PGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKG 172
+ G + + + +F+ +L + + +L S F+ FGN+I K+ D + SK
Sbjct: 24 SAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKC 83
Query: 173 FGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
FGF+ F + +A+ AI MNG + V L +
Sbjct: 84 FGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
Score = 72.8 bits (179), Expect = 4e-16
Identities = 23/93 (24%), Positives = 37/93 (39%), Gaps = 6/93 (6%)
Query: 212 KKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI----- 266
++ +F+ +LP +++ F FG + S+ + DK
Sbjct: 24 SAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKC 83
Query: 267 -GFIEFIMPKHATHAVSTMNGHVFKSKPLKVTL 298
GF+ F P A A+ MNG +K LKV L
Sbjct: 84 FGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL 116
Score = 67.8 bits (166), Expect = 2e-14
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESRGFAIIVFNTPAEAKKARVEM 95
L + +L + L + F FG + +V +K S+ F + F+ P A+ A M
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 96 NGHLIGSKPV 105
NG +G+K +
Sbjct: 103 NGFQVGTKRL 112
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 89.6 bits (223), Expect = 1e-22
Identities = 19/76 (25%), Positives = 35/76 (46%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+ V NL V + +++ F +FG + + + D +G+S G + F A KA+ +
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 90
Query: 192 NGRMIQHNSTFVSLAE 207
NG + + L
Sbjct: 91 NGVPLDGRPMNIQLVT 106
Score = 80.0 bits (198), Expect = 5e-19
Identities = 30/109 (27%), Positives = 48/109 (44%), Gaps = 4/109 (3%)
Query: 3 SKGKILEASWDEGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLR 62
S+ K L W + D V +L V+NL+ V + + F +FGTL+
Sbjct: 2 SRPKQLPDKWQHDLFDS----GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLK 57
Query: 63 DVRVARNKNDESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVE 111
V +++ S G A + F A+A KA + NG + +P+ I V
Sbjct: 58 KAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106
Score = 71.5 bits (176), Expect = 7e-16
Identities = 20/92 (21%), Positives = 39/92 (42%), Gaps = 5/92 (5%)
Query: 215 FPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFI 269
F K+ V+NL +++++ +ELFA FGT+ +++ D+ +
Sbjct: 16 FDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADV 75
Query: 270 EFIMPKHATHAVSTMNGHVFKSKPLKVTLSGT 301
F A A+ NG +P+ + L +
Sbjct: 76 HFERKADALKAMKQYNGVPLDGRPMNIQLVTS 107
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 87.6 bits (218), Expect = 5e-22
Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
++FV+NL + LK F + G+++ I + NGKSKG G ++F S + AE+A M
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMM 68
Query: 192 NGRMIQHNSTFVSLAE 207
NG + V +
Sbjct: 69 NGMKLSGREIDVRIDR 84
Score = 66.1 bits (162), Expect = 4e-14
Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 1/84 (1%)
Query: 35 NELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVE 94
++ V NL + L ++F + G + + +S+G ++ F +P A++A
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENG-KSKGCGVVKFESPEVAERACRM 67
Query: 95 MNGHLIGSKPVIITFVELKPGQRS 118
MNG + + + + G S
Sbjct: 68 MNGMKLSGREIDVRIDRNASGPSS 91
Score = 59.9 bits (146), Expect = 6e-12
Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 4/84 (4%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD----KHIGFIEFIMPKHATHA 280
+ +IFV NLP + ++ F G + + + + K G ++F P+ A A
Sbjct: 5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERA 64
Query: 281 VSTMNGHVFKSKPLKVTLSGTKPG 304
MNG + + V + G
Sbjct: 65 CRMMNGMKLSGREIDVRIDRNASG 88
>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A
{Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A
Length = 102
Score = 86.9 bits (216), Expect = 1e-21
Identities = 27/77 (35%), Positives = 45/77 (58%), Gaps = 4/77 (5%)
Query: 123 PEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYK 182
PE K VFV + +DE E++S F ++G++ EVKI+ D G SKG+GF+ F++
Sbjct: 3 PEGKIMPN-TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDV 61
Query: 183 AAEKAI---IEMNGRMI 196
+K + I +G+ +
Sbjct: 62 DVQKIVESQINFHGKKL 78
Score = 55.7 bits (135), Expect = 3e-10
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 7/73 (9%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSD-----KHIGFIEFIMPKHATHAVST 283
N +FV + ++ +E FAR+G++ +++D K GF+ F V
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV-- 67
Query: 284 MNGHVFKSKPLKV 296
+ F K LK+
Sbjct: 68 ESQINFHGKKLKL 80
Score = 54.5 bits (132), Expect = 8e-10
Identities = 15/100 (15%), Positives = 41/100 (41%), Gaps = 8/100 (8%)
Query: 29 NKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEA 88
N V+ V ++ +D + + F ++G++++V++ ++ S+G+ + F +
Sbjct: 10 NTVF------VGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
Query: 89 KKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQY 128
+K + K + + K + V P +
Sbjct: 64 QKIV--ESQINFHGKKLKLGPAIRKQNLSTYHVQPRPLIF 101
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 86.6 bits (215), Expect = 2e-21
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIK-FGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV +L VD+ L F+K + + K+V D+ G SKG+GF++F ++A+ E
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 192 NGRM 195
G +
Sbjct: 72 QGAV 75
Score = 69.2 bits (170), Expect = 4e-15
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 2/84 (2%)
Query: 37 LHVNNLEPSVDNQALINEF-KKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEM 95
L V +L P VD+ L F K + + R +V ++ S+G+ + F E K+A E
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 96 NGH-LIGSKPVIITFVELKPGQRS 118
G +GSKPV ++ K +
Sbjct: 72 QGAVGLGSKPVRLSVAIPKASRVK 95
Score = 49.6 bits (119), Expect = 4e-08
Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 7/80 (8%)
Query: 231 IFVANLPSNINNSEFEELF-ARFGTITSSSLVSD-----KHIGFIEFIMPKHATHAVSTM 284
+FV +L ++++ E F + + +V D K GF++F A++
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 285 NGHVF-KSKPLKVTLSGTKP 303
G V SKP++++++ K
Sbjct: 72 QGAVGLGSKPVRLSVAIPKA 91
>1x4e_A RNA binding motif, single-stranded interacting protein 2;
structural genomics, RRM domain, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 85
Score = 85.3 bits (212), Expect = 4e-21
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
++++ L +++L +G I+ K + D K KG+GF+ F S AA+KA+
Sbjct: 7 GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66
Query: 191 MNGRMIQ 197
+ +Q
Sbjct: 67 LKASGVQ 73
Score = 68.3 bits (168), Expect = 5e-15
Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 6/78 (7%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHAT 278
+ + +++ L + + +L +G I S+ + DK GF++F P A
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 279 HAVSTMNGHVFKSKPLKV 296
AV+ + +++ K
Sbjct: 62 KAVTALKASGVQAQMAKQ 79
Score = 55.2 bits (134), Expect = 3e-10
Identities = 13/70 (18%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
L++ L+P +Q L+ + +G + + +K ++ +G+ + F++P+ A+KA +
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 96 NGHLIGSKPV 105
+ ++
Sbjct: 68 KASGVQAQMA 77
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 84.9 bits (211), Expect = 5e-21
Identities = 21/66 (31%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
+FV +L VD+E L++ F F + + ++ D + G S+G+GF+ F S A+ A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 191 MNGRMI 196
M G+ +
Sbjct: 63 MQGQDL 68
Score = 63.3 bits (155), Expect = 4e-13
Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 6/81 (7%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVS 282
+FV +L N+++ F F + S ++ D GF+ F A +A+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 283 TMNGHVFKSKPLKVTLSGTKP 303
+M G +PL++ +
Sbjct: 62 SMQGQDLNGRPLRINWAAKLE 82
Score = 62.5 bits (153), Expect = 5e-13
Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
L V +L +VD++ L N FK F + V + SRG+ + F + +A+ A M
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 96 NGHLIGSKPVIITFVELKP 114
G + +P+ I +
Sbjct: 64 QGQDLNGRPLRINWAAKLE 82
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 96
Score = 84.6 bits (210), Expect = 7e-21
Identities = 31/77 (40%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEV-KIVRD-ENGKSKGFGFIQFFSYKAAEKAII 189
+F+ NL +DE+ L F FG I++ KI+RD + G SKG+ FI F S+ A++ AI
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 190 EMNGRMIQHNSTFVSLA 206
MNG+ + + VS A
Sbjct: 67 AMNGQYLCNRPITVSYA 83
Score = 64.1 bits (157), Expect = 2e-13
Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 2/84 (2%)
Query: 39 VNNLEPSVDNQALINEFKKFGT-LRDVRVARN-KNDESRGFAIIVFNTPAEAKKARVEMN 96
+ NL+P +D + L + F FG L+ ++ R+ S+G+A I F + + A MN
Sbjct: 10 IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN 69
Query: 97 GHLIGSKPVIITFVELKPGQRSKP 120
G + ++P+ +++ K + S P
Sbjct: 70 GQYLCNRPITVSYAFKKDSKGSGP 93
Score = 53.7 bits (130), Expect = 1e-09
Identities = 21/82 (25%), Positives = 35/82 (42%), Gaps = 7/82 (8%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSS-LVSD------KHIGFIEFIMPKHATHAVS 282
IF+ NL I+ + F+ FG I + ++ D K FI F + A+
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 283 TMNGHVFKSKPLKVTLSGTKPG 304
MNG ++P+ V+ + K
Sbjct: 67 AMNGQYLCNRPITVSYAFKKDS 88
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA
processing, mRNA splicing, transport, nucleus,
RNA-binding, spliceosome, transport; NMR {Mus musculus}
Length = 124
Score = 85.5 bits (212), Expect = 7e-21
Identities = 18/76 (23%), Positives = 34/76 (44%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+ V NL V + +++ F +FG + + + D +G+S G + F A KA+ +
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 192 NGRMIQHNSTFVSLAE 207
G + + L
Sbjct: 97 KGVPLDGRPMDIQLVA 112
Score = 79.7 bits (197), Expect = 1e-18
Identities = 25/102 (24%), Positives = 42/102 (41%)
Query: 19 DEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFA 78
D V +L V+NL+ V + + F +FGTL+ V +++ S G A
Sbjct: 20 DLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTA 79
Query: 79 IIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
+ F A+A KA + G + +P+ I V +
Sbjct: 80 DVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHH 121
Score = 72.4 bits (178), Expect = 5e-16
Identities = 19/94 (20%), Positives = 39/94 (41%), Gaps = 5/94 (5%)
Query: 215 FPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFI 269
F K+ V+NL +++++ +ELFA FGT+ +++ D+ +
Sbjct: 22 FDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADV 81
Query: 270 EFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
F A A+ G +P+ + L ++
Sbjct: 82 HFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 115
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition
motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 99
Score = 84.6 bits (210), Expect = 1e-20
Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 5/90 (5%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQ 177
S G E+ ++ ++FV NL + EEE++ F K+G EV I +D KGFGFI+
Sbjct: 3 SGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIR 57
Query: 178 FFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
+ AE A +E++ ++ V A
Sbjct: 58 LETRTLAEIAKVELDNMPLRGKQLRVRFAC 87
Score = 73.4 bits (181), Expect = 1e-16
Identities = 20/79 (25%), Positives = 35/79 (44%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTM 284
+++++FV NLP +I E +LF ++G + DK GFI A A +
Sbjct: 12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVEL 71
Query: 285 NGHVFKSKPLKVTLSGTKP 303
+ + K L+V +
Sbjct: 72 DNMPLRGKQLRVRFACHSA 90
Score = 62.3 bits (152), Expect = 1e-12
Identities = 22/100 (22%), Positives = 42/100 (42%), Gaps = 5/100 (5%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAII 80
+ S+ + + L V NL P + + + F+K+G +V + + +GF I
Sbjct: 2 SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK-----DKGFGFI 56
Query: 81 VFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
T A+ A+VE++ + K + + F S P
Sbjct: 57 RLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGP 96
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 98
Score = 84.2 bits (209), Expect = 1e-20
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 4/80 (5%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGK----SKGFGFIQFFSYKAAEKA 187
+F+KNL + EE LK F K G I I + +N S GFGF+++ + A+KA
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66
Query: 188 IIEMNGRMIQHNSTFVSLAE 207
+ ++ G + + V ++E
Sbjct: 67 LKQLQGHTVDGHKLEVRISE 86
Score = 67.3 bits (165), Expect = 2e-14
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 9/84 (10%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI---------GFIEFIMPKHATH 279
+ +F+ NL + + +F++ G I S ++ K+ GF+E+ P+ A
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 280 AVSTMNGHVFKSKPLKVTLSGTKP 303
A+ + GH L+V +S
Sbjct: 66 ALKQLQGHTVDGHKLEVRISERAT 89
Score = 66.1 bits (162), Expect = 5e-14
Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 4/88 (4%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN----DESRGFAIIVFNTPAEAKKAR 92
L + NL S + L F K G ++ +++ KN S GF + + P +A+KA
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 93 VEMNGHLIGSKPVIITFVELKPGQRSKP 120
++ GH + + + E S P
Sbjct: 68 KQLQGHTVDGHKLEVRISERATKPASGP 95
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 84.0 bits (208), Expect = 2e-20
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 130 KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAI 188
+V L + V E LK K+G + EV+I+ K G + F S + A++ +
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65
Query: 189 IEMNGRMIQ 197
++ +
Sbjct: 66 KNLHLTSVM 74
Score = 67.4 bits (165), Expect = 2e-14
Identities = 10/102 (9%), Positives = 29/102 (28%), Gaps = 8/102 (7%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHAT 278
++ A L N+ + +++ ++G + ++ + + F + A
Sbjct: 3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK 62
Query: 279 HAVSTMNGHVFKSKPLKVTLS--GTKPGVSITNPTKAPKKPA 318
V ++ + L G + P
Sbjct: 63 ETVKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQ 104
Score = 67.0 bits (164), Expect = 3e-14
Identities = 12/76 (15%), Positives = 30/76 (39%), Gaps = 1/76 (1%)
Query: 35 NELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARV 93
E+ L +V L + +K+G + +V + + + G A ++F + AK+
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
Query: 94 EMNGHLIGSKPVIITF 109
++ + +
Sbjct: 67 NLHLTSVMGNIIHAQL 82
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 84.0 bits (208), Expect = 2e-20
Identities = 20/93 (21%), Positives = 42/93 (45%), Gaps = 7/93 (7%)
Query: 114 PGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGF 173
P +RS K + ++V + L+ F FGNII++ + +
Sbjct: 23 PFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP-----RNC 75
Query: 174 GFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
F+ + ++A++A+ E+NG ++ V++A
Sbjct: 76 AFVTYEKMESADQAVAELNGTQVESVQLKVNIA 108
Score = 63.2 bits (154), Expect = 1e-12
Identities = 23/110 (20%), Positives = 46/110 (41%), Gaps = 3/110 (2%)
Query: 197 QHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTIT 256
H+S V + + P P + N ++V ++ + F+ FG I
Sbjct: 9 HHSSGLVPRGSHMGPFRRSDS-FPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNII 65
Query: 257 SSSLVSDKHIGFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKPGVS 306
S+ ++ F+ + + A AV+ +NG +S LKV ++ +P +
Sbjct: 66 DLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQPMLD 115
Score = 54.8 bits (132), Expect = 1e-09
Identities = 17/96 (17%), Positives = 36/96 (37%), Gaps = 13/96 (13%)
Query: 23 RSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVF 82
R+ ++ N +Y V + + L F FG + D+ + + A + +
Sbjct: 34 RAPRKGNTLY------VYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-----NCAFVTY 80
Query: 83 NTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRS 118
A +A E+NG + S + + +P +
Sbjct: 81 EKMESADQAVAELNGTQVESVQLKVNIARKQPMLDA 116
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 83.4 bits (207), Expect = 3e-20
Identities = 29/90 (32%), Positives = 42/90 (46%), Gaps = 1/90 (1%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFI 176
S GP + + V NL E E +L+ F FG+I + + +D G+SKGF FI
Sbjct: 3 SGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 62
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
F + A +AI ++G H V A
Sbjct: 63 SFHRREDAARAIAGVSGFGYDHLILNVEWA 92
Score = 62.6 bits (153), Expect = 9e-13
Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 6/89 (6%)
Query: 221 PLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMP 274
P + I V NL + ++ +ELF FG+I+ L DK FI F
Sbjct: 8 PNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRR 67
Query: 275 KHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
+ A A++ ++G + L V +
Sbjct: 68 EDAARAIAGVSGFGYDHLILNVEWAKPST 96
Score = 60.3 bits (147), Expect = 7e-12
Identities = 27/107 (25%), Positives = 45/107 (42%), Gaps = 8/107 (7%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DE 73
G S G ++N + V NL L F+ FG++ + +A++K +
Sbjct: 1 GSSGSSGPNRRADDN-----ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQ 55
Query: 74 SRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
S+GFA I F+ +A +A ++G I+ KP S P
Sbjct: 56 SKGFAFISFHRREDAARAIAGVSGFGYDHL--ILNVEWAKPSTNSGP 100
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 83.0 bits (206), Expect = 3e-20
Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 122 GPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFS 180
G K ++V L E VD++ L + FI FG+I +++I D E K +GF F++F
Sbjct: 4 GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63
Query: 181 YKAAEKAIIEMNGRMI 196
+ A AI MN +
Sbjct: 64 AEDAAAAIDNMNESEL 79
Score = 59.9 bits (146), Expect = 9e-12
Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 6/75 (8%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAV 281
K ++V L +++ F FG IT + D F+EF + + A A+
Sbjct: 12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71
Query: 282 STMNGHVFKSKPLKV 296
MN + ++V
Sbjct: 72 DNMNESELFGRTIRV 86
Score = 51.8 bits (125), Expect = 6e-09
Identities = 26/88 (29%), Positives = 40/88 (45%), Gaps = 4/88 (4%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
L+V L VD++ L F FG + D+++ + ++ RGFA + F +A A M
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 96 NGHLIGSKPVIITFVELKPGQRSKPVGP 123
N + + I KP R K GP
Sbjct: 75 NESELFGRT--IRVNLAKP-MRIKESGP 99
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 84.9 bits (210), Expect = 6e-20
Identities = 20/90 (22%), Positives = 36/90 (40%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQ 177
G E K+ V NL V + +++ F +FG + + + D +G+S G +
Sbjct: 76 DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVH 135
Query: 178 FFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
F A KA+ + G + + L
Sbjct: 136 FERRADALKAMKQYKGVPLDGRPMDIQLVA 165
Score = 82.2 bits (203), Expect = 5e-19
Identities = 25/107 (23%), Positives = 43/107 (40%)
Query: 13 DEGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND 72
+ D V +L V+NL+ V + + F +FGTL+ V +++
Sbjct: 67 PDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSG 126
Query: 73 ESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSK 119
S G A + F A+A KA + G + +P+ I V +
Sbjct: 127 RSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHH 173
Score = 76.8 bits (189), Expect = 5e-17
Identities = 19/99 (19%), Positives = 40/99 (40%), Gaps = 5/99 (5%)
Query: 210 PGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH---- 265
+F K+ V+NL +++++ +ELFA FGT+ +++ D+
Sbjct: 70 WQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL 129
Query: 266 -IGFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
+ F A A+ G +P+ + L ++
Sbjct: 130 GTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 168
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 82.3 bits (204), Expect = 6e-20
Identities = 22/93 (23%), Positives = 48/93 (51%)
Query: 115 GQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFG 174
S V +K K+F+ L + +EEL+ G + ++++V + GK KG
Sbjct: 2 SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLA 61
Query: 175 FIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
++++ + A +A+++M+G I+ N V+++
Sbjct: 62 YVEYENESQASQAVMKMDGMTIKENIIKVAISN 94
Score = 66.9 bits (164), Expect = 2e-14
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 5/84 (5%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD-----KHIGFIEFIMPKHATH 279
K+K+F++ LP + E EE+ GT+ LV++ K + ++E+ A+
Sbjct: 14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQ 73
Query: 280 AVSTMNGHVFKSKPLKVTLSGTKP 303
AV M+G K +KV +S + P
Sbjct: 74 AVMKMDGMTIKENIIKVAISNSGP 97
Score = 64.2 bits (157), Expect = 2e-13
Identities = 20/85 (23%), Positives = 41/85 (48%), Gaps = 2/85 (2%)
Query: 34 ENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARV 93
+++L ++ L S + L K GT++D+R+ N+ + +G A + + ++A +A +
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVM 76
Query: 94 EMNGHLIGSKPVIITFVELKPGQRS 118
+M+G I I G S
Sbjct: 77 KMDGMTIKENI--IKVAISNSGPSS 99
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 82.3 bits (204), Expect = 7e-20
Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 131 DKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAII 189
++FV+NL T EE+L+ F +G + E+ D K KGF F+ F + A KA
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
Query: 190 EMNGRMIQ 197
E++G++ Q
Sbjct: 69 EVDGQVFQ 76
Score = 64.9 bits (159), Expect = 1e-13
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVS 282
++FV NL + + E+LF+ +G ++ D F+ F+ P+HA A +
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
Query: 283 TMNGHVFKSKPLKVTLSGTKP 303
++G VF+ + L V S K
Sbjct: 69 EVDGQVFQGRMLHVLPSTIKK 89
Score = 56.8 bits (138), Expect = 1e-10
Identities = 20/104 (19%), Positives = 43/104 (41%), Gaps = 9/104 (8%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAI 79
G+ + + +++ V NL + + L F +G L ++ + + +GFA
Sbjct: 1 GSSGSSGSGRLF------VRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAF 54
Query: 80 IVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGP 123
+ F P A KA E++G + + + + + + GP
Sbjct: 55 VTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS--TIKKEASQSGP 96
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 82.0 bits (203), Expect = 7e-20
Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 7/89 (7%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQ 177
S G K + ++V + L+ F FGNII++ + + F+
Sbjct: 3 SGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM-----DPPRNCAFVT 55
Query: 178 FFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
+ ++A++A+ E+NG ++ V++A
Sbjct: 56 YEKMESADQAVAELNGTQVESVQLKVNIA 84
Score = 63.1 bits (154), Expect = 6e-13
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVST 283
P + N ++V ++ + F+ FG I S+ ++ F+ + + A AV+
Sbjct: 11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAE 68
Query: 284 MNGHVFKSKPLKVTLSGTKP 303
+NG +S LKV ++ +P
Sbjct: 69 LNGTQVESVQLKVNIARKQP 88
Score = 60.4 bits (147), Expect = 6e-12
Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 7/99 (7%)
Query: 22 ARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIV 81
+ S+ E K N L+V + + L F FG + D+ + + A +
Sbjct: 3 SGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-----NCAFVT 55
Query: 82 FNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
+ A +A E+NG + S + + +P S P
Sbjct: 56 YEKMESADQAVAELNGTQVESVQLKVNIARKQPMLDSGP 94
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA
binding domain, RBD, RNA splicing, apoptosis,
phosphoprotein, RNA-binding; 1.95A {Homo sapiens}
Length = 87
Score = 81.4 bits (202), Expect = 1e-19
Identities = 27/76 (35%), Positives = 42/76 (55%), Gaps = 4/76 (5%)
Query: 122 GPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFS 180
GP + VFV +L + + + F FG I + ++V+D GKSKG+GF+ FF+
Sbjct: 1 GPLGSHFH---VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 57
Query: 181 YKAAEKAIIEMNGRMI 196
AE AI +M G+ +
Sbjct: 58 KWDAENAIQQMGGQWL 73
Score = 66.0 bits (162), Expect = 3e-14
Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
+ V +L P + A+ F FG + D RV ++ +S+G+ + F +A+ A +M
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 96 NGHLIGSKPVIITFVELKP 114
G +G + + + KP
Sbjct: 69 GGQWLGGRQIRTNWATRKP 87
Score = 63.7 bits (156), Expect = 3e-13
Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 6/80 (7%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVST 283
+FV +L I + FA FG I+ + +V D GF+ F A +A+
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 284 MNGHVFKSKPLKVTLSGTKP 303
M G + ++ + KP
Sbjct: 68 MGGQWLGGRQIRTNWATRKP 87
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain,
structural genomics, NPPSFA; NMR {Mus musculus} PDB:
2rne_A 2dh7_A
Length = 115
Score = 82.0 bits (203), Expect = 1e-19
Identities = 29/80 (36%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFI 176
S G ++ VFV +L + E++K+ F FG I + ++V+D GKSKG+GF+
Sbjct: 3 SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62
Query: 177 QFFSYKAAEKAIIEMNGRMI 196
FF+ AE AI +M G+ +
Sbjct: 63 SFFNKWDAENAIQQMGGQWL 82
Score = 65.1 bits (159), Expect = 2e-13
Identities = 22/108 (20%), Positives = 44/108 (40%), Gaps = 1/108 (0%)
Query: 22 ARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAII 80
+ S+ + + V +L P + + + F FG + D RV ++ +S+G+ +
Sbjct: 3 SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFV 62
Query: 81 VFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQY 128
F +A+ A +M G +G + + + KP KQ
Sbjct: 63 SFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQS 110
Score = 63.9 bits (156), Expect = 4e-13
Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 6/92 (6%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVST 283
+FV +L I + + FA FG I+ + +V D GF+ F A +A+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 284 MNGHVFKSKPLKVTLSGTKPGVSITNPTKAPK 315
M G + ++ + KP + K
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPKSTYESNTK 108
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 85.2 bits (210), Expect = 1e-19
Identities = 21/112 (18%), Positives = 46/112 (41%), Gaps = 3/112 (2%)
Query: 113 KPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFG--NIIEVKIVRD-ENGK 169
G+ + P K+ +++ NL +E+L G +I+E+K + NG+
Sbjct: 51 DVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQ 110
Query: 170 SKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPP 221
SKGF + S +++K + + R + + V+ + + +
Sbjct: 111 SKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKT 162
Score = 68.6 bits (167), Expect = 9e-14
Identities = 21/114 (18%), Positives = 46/114 (40%), Gaps = 3/114 (2%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGT--LRDVRVARNK-NDE 73
+GA N K L++ NL ++ L G + +++ N+ N +
Sbjct: 51 DVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQ 110
Query: 74 SRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQ 127
S+GFA++ + A +KK + + + ++T V + + + + Q
Sbjct: 111 SKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQ 164
Score = 58.2 bits (140), Expect = 4e-10
Identities = 7/102 (6%), Positives = 25/102 (24%), Gaps = 8/102 (7%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGT--ITSSSLVSDKH------IGFIEFIMPK 275
++ +++ NL + + E G I ++ +
Sbjct: 64 YTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEA 123
Query: 276 HATHAVSTMNGHVFKSKPLKVTLSGTKPGVSITNPTKAPKKP 317
+ + + + VT + ++ +
Sbjct: 124 SSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQS 165
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 82.5 bits (204), Expect = 1e-19
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFI 176
G K ++V L E VD++ L + FI FG+I +++I D E K +GF F+
Sbjct: 51 GGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFV 110
Query: 177 QFFSYKAAEKAIIEMNGRMI 196
+F + A AI MN +
Sbjct: 111 EFELAEDAAAAIDNMNESEL 130
Score = 62.9 bits (153), Expect = 2e-12
Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 6/75 (8%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIMPKHATHAV 281
K ++V L +++ F FG IT + D F+EF + + A A+
Sbjct: 63 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122
Query: 282 STMNGHVFKSKPLKV 296
MN + ++V
Sbjct: 123 DNMNESELFGRTIRV 137
Score = 56.3 bits (136), Expect = 4e-10
Identities = 22/98 (22%), Positives = 39/98 (39%), Gaps = 1/98 (1%)
Query: 9 EASWDEGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVAR 68
+ E D S + L+V L VD++ L F FG + D+++
Sbjct: 38 CVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 97
Query: 69 NKN-DESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
+ ++ RGFA + F +A A MN + + +
Sbjct: 98 DYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI 135
>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 81.5 bits (202), Expect = 1e-19
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
+ V NL + L+ F K+G + +V I R+ +GF F++F + A+ A
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 191 MNGRMIQHNSTFVSLAE 207
M+G + V +A
Sbjct: 75 MDGAELDGRELRVQVAR 91
Score = 61.1 bits (149), Expect = 3e-12
Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 6/79 (7%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHA 277
+ V NL + +F ++G + + + H F+ F + A
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68
Query: 278 THAVSTMNGHVFKSKPLKV 296
A + M+G + L+V
Sbjct: 69 QDAEAAMDGAELDGRELRV 87
Score = 59.2 bits (144), Expect = 2e-11
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 1/85 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
L V+NL +L F+K+G + DV + R + RGFA + F+ +A+ A M
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 96 NGHLIGSKPVIITFVELKPGQRSKP 120
+G + + + + S P
Sbjct: 76 DGAELDGRELRVQVARYGRRDLSGP 100
>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 81.6 bits (202), Expect = 1e-19
Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 1/86 (1%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFI 176
S G + VF++NL +EE L +FG++ V++V + SKG F
Sbjct: 3 SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 62
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTF 202
QF + +AA+K + +
Sbjct: 63 QFMTQEAAQKCLAAASLEAEGGGLKL 88
Score = 50.4 bits (121), Expect = 3e-08
Identities = 23/106 (21%), Positives = 44/106 (41%), Gaps = 7/106 (6%)
Query: 22 ARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAII 80
+ S+ + V + + + NL + +AL ++FG L+ VRV + + + S+G A
Sbjct: 3 SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFA 62
Query: 81 VFNTPAEAKKA------RVEMNGHLIGSKPVIITFVELKPGQRSKP 120
F T A+K E G + + + + + S P
Sbjct: 63 QFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGP 108
Score = 49.7 bits (119), Expect = 5e-08
Identities = 16/86 (18%), Positives = 32/86 (37%), Gaps = 12/86 (13%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVST 283
+F+ NL + E+ +FG + +V F +F+ + A ++
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 284 MN------GHVFKSKPLKVTLSGTKP 303
+ G + LKV L+ T+
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDLAVTRD 102
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 80.3 bits (199), Expect = 2e-19
Identities = 25/65 (38%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 130 KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAI 188
K ++V L E VD++ L + FI FG+I +++I D E K +GF F++F + A AI
Sbjct: 7 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
Query: 189 IEMNG 193
MN
Sbjct: 67 DNMNE 71
Score = 60.2 bits (147), Expect = 4e-12
Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 6/75 (8%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIMPKHATHAV 281
K ++V L +++ F FG IT + D F+EF + + A A+
Sbjct: 7 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66
Query: 282 STMNGHVFKSKPLKV 296
MN + ++V
Sbjct: 67 DNMNESELFGRTIRV 81
Score = 52.1 bits (126), Expect = 3e-09
Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 8/86 (9%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAI 79
G+ + +Y V L VD++ L F FG + D+++ + ++ RGFA
Sbjct: 1 GSMAT-TKRVLY------VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAF 53
Query: 80 IVFNTPAEAKKARVEMNGHLIGSKPV 105
+ F +A A MN + + +
Sbjct: 54 VEFELAEDAAAAIDNMNESELFGRTI 79
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi}
SCOP: d.58.7.1
Length = 139
Score = 82.1 bits (203), Expect = 2e-19
Identities = 32/95 (33%), Positives = 50/95 (52%), Gaps = 1/95 (1%)
Query: 114 PGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKG 172
Q P + + V + TVDE +L+ F ++G I VKIV D E +S+G
Sbjct: 26 QQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRG 85
Query: 173 FGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
+GF++F S +A++AI +NG I + V+LA
Sbjct: 86 YGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA 120
Score = 66.7 bits (163), Expect = 7e-14
Identities = 24/97 (24%), Positives = 43/97 (44%), Gaps = 9/97 (9%)
Query: 216 PKVKPPLLQPAR---KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------I 266
+ PP + V +P+ ++ + +LF R+G I S +V D+
Sbjct: 27 QQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGY 86
Query: 267 GFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
GF++F A A++ +NG +K LKV L+ +
Sbjct: 87 GFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGH 123
Score = 52.8 bits (127), Expect = 7e-09
Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
L VN + +VD L F+++G + V++ ++ +SRG+ + F + + A++A +
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 96 NGHLIGSKP 104
NG I +K
Sbjct: 105 NGFNILNKR 113
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 80.8 bits (200), Expect = 3e-19
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFI 176
S GP ++ + V+V L E V E L F++ G ++ + +D G+ +G+GF+
Sbjct: 3 SGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFV 62
Query: 177 QFFSYKAAEKAIIEMNGRMI 196
+F S + A+ AI M+ +
Sbjct: 63 EFLSEEDADYAIKIMDMIKL 82
Score = 61.9 bits (151), Expect = 2e-12
Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 6/83 (7%)
Query: 220 PPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIM 273
P+ + + ++V L ++ ELF + G + ++ + D+ GF+EF+
Sbjct: 7 GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66
Query: 274 PKHATHAVSTMNGHVFKSKPLKV 296
+ A +A+ M+ KP++V
Sbjct: 67 EEDADYAIKIMDMIKLYGKPIRV 89
Score = 52.6 bits (127), Expect = 4e-09
Identities = 15/90 (16%), Positives = 37/90 (41%), Gaps = 1/90 (1%)
Query: 32 YKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKK 90
++ ++V L+ V L F + G + + + +++ + +G+ + F + +A
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 91 ARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
A M+ + KP+ + S P
Sbjct: 73 AIKIMDMIKLYGKPIRVNKASAHNKNLSGP 102
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 80.8 bits (200), Expect = 3e-19
Identities = 28/103 (27%), Positives = 48/103 (46%), Gaps = 8/103 (7%)
Query: 111 ELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKS 170
L P + S +E + ++FV+ V E EL F FG + EVKI+
Sbjct: 13 GLVP-RGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL------- 64
Query: 171 KGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIVPGKK 213
GF F++F ++A KAI E++G+ + V +++ +
Sbjct: 65 NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107
Score = 66.9 bits (164), Expect = 3e-14
Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 2/80 (2%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVST 283
++FV P ++ SE E+F FG + ++ F+EF + A A+
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--NGFAFVEFEEAESAAKAIEE 84
Query: 284 MNGHVFKSKPLKVTLSGTKP 303
++G F ++PL+V S
Sbjct: 85 VHGKSFANQPLEVVYSKLPA 104
Score = 61.2 bits (149), Expect = 3e-12
Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 7/97 (7%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAII 80
G+ + L V V L F FG +++V++ GFA +
Sbjct: 18 GSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN-------GFAFV 70
Query: 81 VFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQR 117
F A KA E++G ++P+ + + +L +
Sbjct: 71 EFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 80.3 bits (199), Expect = 3e-19
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
+ V L E +L+ F K+G I +V IV D ++ +S+GF F+ F + A++A
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 191 MNGRMI 196
NG +
Sbjct: 77 ANGMEL 82
Score = 59.5 bits (145), Expect = 1e-11
Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 6/82 (7%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHA 277
P + V L + E+F+++G I S+V D+ F+ F A
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 278 THAVSTMNGHVFKSKPLKVTLS 299
A NG + ++V+
Sbjct: 71 KEAKERANGMELDGRRIRVSGP 92
Score = 58.8 bits (143), Expect = 2e-11
Identities = 26/84 (30%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DE 73
G S G R+N + N L V L + L F K+G + DV + ++
Sbjct: 1 GSSGSSGNRANPDPNCC-----LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR 55
Query: 74 SRGFAIIVFNTPAEAKKARVEMNG 97
SRGFA + F +AK+A+ NG
Sbjct: 56 SRGFAFVYFENVDDAKEAKERANG 79
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 81.3 bits (201), Expect = 3e-19
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
+ V NL + L+ F K+G + +V I RD +S+GF F++F + AE A+
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 191 MNGRMIQHNSTFVSLAE 207
M+G ++ V +A
Sbjct: 109 MDGAVLDGRELRVQMAR 125
Score = 60.9 bits (148), Expect = 8e-12
Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 6/79 (7%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHA 277
+ V NL + +F ++G + + D++ F+ F + A
Sbjct: 43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102
Query: 278 THAVSTMNGHVFKSKPLKV 296
A+ M+G V + L+V
Sbjct: 103 EDAMDAMDGAVLDGRELRV 121
Score = 58.6 bits (142), Expect = 6e-11
Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
L V+NL L F+K+G + DV + R++ ESRGFA + F+ +A+ A M
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 96 NGHLIG 101
+G ++
Sbjct: 110 DGAVLD 115
>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing
factor, RNA protein complex, SMN, binding protein-RNA
complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A
Length = 129
Score = 81.3 bits (201), Expect = 4e-19
Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 113 KPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSK 171
+ G+ S+ VG + V L E +L+ F K+G I +V IV D ++ +S+
Sbjct: 29 QMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSR 88
Query: 172 GFGFIQFFSYKAAEKAIIEMNGRMI 196
GF F+ F + A++A NG +
Sbjct: 89 GFAFVYFENVDDAKEAKERANGMEL 113
Score = 62.8 bits (153), Expect = 2e-12
Identities = 25/93 (26%), Positives = 37/93 (39%), Gaps = 1/93 (1%)
Query: 10 ASWDEGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARN 69
AS G G+R L V L + L F K+G + DV + +
Sbjct: 22 ASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYD 81
Query: 70 KN-DESRGFAIIVFNTPAEAKKARVEMNGHLIG 101
+ SRGFA + F +AK+A+ NG +
Sbjct: 82 QQSRRSRGFAFVYFENVDDAKEAKERANGMELD 114
Score = 60.9 bits (148), Expect = 7e-12
Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 6/86 (6%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIMPKHA 277
P + V L + E+F+++G I S+V D+ F+ F A
Sbjct: 42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 101
Query: 278 THAVSTMNGHVFKSKPLKVTLSGTKP 303
A NG + ++V S TK
Sbjct: 102 KEAKERANGMELDGRRIRVDFSITKR 127
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 80.0 bits (198), Expect = 4e-19
Identities = 26/90 (28%), Positives = 50/90 (55%), Gaps = 1/90 (1%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQ 177
S G E + ++ V N+ + +L+ F +FG I++V+I+ +E G SKGFGF+
Sbjct: 3 SGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVT 61
Query: 178 FFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
F + A++A +++G +++ V+ A
Sbjct: 62 FENSADADRAREKLHGTVVEGRKIEVNNAT 91
Score = 64.2 bits (157), Expect = 3e-13
Identities = 25/101 (24%), Positives = 47/101 (46%), Gaps = 3/101 (2%)
Query: 20 EGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAI 79
G+ N E+ LHV+N+ + L F +FG + DV + N+ S+GF
Sbjct: 3 SGSSGNSESK--STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-RGSKGFGF 59
Query: 80 IVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
+ F A+A +AR +++G ++ + + + + S P
Sbjct: 60 VTFENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGP 100
Score = 60.4 bits (147), Expect = 6e-12
Identities = 15/79 (18%), Positives = 37/79 (46%), Gaps = 4/79 (5%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH----IGFIEFIMPKHATHAVSTM 284
++ V+N+P + + ++F +FG I ++ ++ GF+ F A A +
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 285 NGHVFKSKPLKVTLSGTKP 303
+G V + + ++V + +
Sbjct: 76 HGTVVEGRKIEVNNATARV 94
>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 101
Score = 79.6 bits (197), Expect = 6e-19
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+F+ NL ELK + ++ +V G ++ FG++ F S + EKA +E+
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA-LEL 77
Query: 192 NGRMIQ 197
G +
Sbjct: 78 TGLKVF 83
Score = 64.2 bits (157), Expect = 3e-13
Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 1/69 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L + NL P+ L + D+ V + +R F + F + + +KA +E+
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA-LELT 78
Query: 97 GHLIGSKPV 105
G + +
Sbjct: 79 GLKVFGNEI 87
Score = 48.8 bits (117), Expect = 7e-08
Identities = 12/76 (15%), Positives = 27/76 (35%), Gaps = 8/76 (10%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIMPKHATHAVST 283
+F+ NL N + +E + + + V D G+++F + A+
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAK-NDLAVVDVRTGTNRKFGYVDFESAEDLEKALE- 76
Query: 284 MNGHVFKSKPLKVTLS 299
+ G +K+
Sbjct: 77 LTGLKVFGNEIKLEKP 92
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 79.6 bits (197), Expect = 6e-19
Identities = 26/66 (39%), Positives = 42/66 (63%), Gaps = 1/66 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
K+FV L +E+ L+ F K+G I EV +V+D E +S+GFGF+ F + A+ A++
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 191 MNGRMI 196
MNG+ +
Sbjct: 74 MNGKSV 79
Score = 63.4 bits (155), Expect = 5e-13
Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 6/85 (7%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHAT 278
+ + K+FV L + N E++F+++G I+ +V D+ GF+ F A
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 279 HAVSTMNGHVFKSKPLKVTLSGTKP 303
A+ MNG + ++V +G
Sbjct: 69 DAMMAMNGKSVDGRQIRVDQAGKSS 93
Score = 61.1 bits (149), Expect = 4e-12
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 1/88 (1%)
Query: 34 ENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKAR 92
E +L V L + Q+L F K+G + +V V +++ SRGF + F +AK A
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 93 VEMNGHLIGSKPVIITFVELKPGQRSKP 120
+ MNG + + + + RS P
Sbjct: 72 MAMNGKSVDGRQIRVDQAGKSSDNRSGP 99
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 79.7 bits (197), Expect = 8e-19
Identities = 25/101 (24%), Positives = 50/101 (49%), Gaps = 7/101 (6%)
Query: 113 KPGQRSKPVGPEEKQYKKD------KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDE 166
S + P + ++ V N+ + +L+ F +FG I++V+I+ +E
Sbjct: 6 HHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE 65
Query: 167 NGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
G SKGFGF+ F + A++A +++G +++ V+ A
Sbjct: 66 RG-SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 105
Score = 62.3 bits (152), Expect = 1e-12
Identities = 15/79 (18%), Positives = 37/79 (46%), Gaps = 4/79 (5%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH----IGFIEFIMPKHATHAVSTM 284
++ V+N+P + + ++F +FG I ++ ++ GF+ F A A +
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 89
Query: 285 NGHVFKSKPLKVTLSGTKP 303
+G V + + ++V + +
Sbjct: 90 HGTVVEGRKIEVNNATARV 108
Score = 60.8 bits (148), Expect = 5e-12
Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 1/83 (1%)
Query: 23 RSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVF 82
S+ + LHV+N+ + L F +FG + DV + N+ S+GF + F
Sbjct: 18 GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE-RGSKGFGFVTF 76
Query: 83 NTPAEAKKARVEMNGHLIGSKPV 105
A+A +AR +++G ++ + +
Sbjct: 77 ENSADADRAREKLHGTVVEGRKI 99
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT
arginine/serine-rich 2, S35, splicing factor SC35,; RRM
domain, cell WALL; NMR {Streptococcus SP}
Length = 158
Score = 81.0 bits (200), Expect = 8e-19
Identities = 29/136 (21%), Positives = 53/136 (38%), Gaps = 3/136 (2%)
Query: 75 RGFAIIVFNTPAEAKKA-RVEMNGHLIGSKPVIITFVELKP-GQRSKPVGPEEKQYKKDK 132
+G A A+K + N + + + + + S
Sbjct: 13 KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTS 72
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
+ V NL + L+ F K+G + +V I RD +S+GF F++F + AE A+ M
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 192 NGRMIQHNSTFVSLAE 207
+G ++ V +A
Sbjct: 133 DGAVLDGRELRVQMAR 148
Score = 60.6 bits (147), Expect = 2e-11
Identities = 19/135 (14%), Positives = 42/135 (31%), Gaps = 9/135 (6%)
Query: 175 FIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVA 234
+ + + K NG + + V + + V
Sbjct: 20 AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGS--HHHHHHM-DVEGMTSLKVD 76
Query: 235 NLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVSTMNGHV 288
NL + +F ++G + + D++ F+ F + A A+ M+G V
Sbjct: 77 NLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAV 136
Query: 289 FKSKPLKVTLSGTKP 303
+ L+V ++
Sbjct: 137 LDGRELRVQMARYGR 151
Score = 59.1 bits (143), Expect = 6e-11
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 1/83 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
L V+NL L F+K+G + DV + R++ ESRGFA + F+ +A+ A M
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 96 NGHLIGSKPVIITFVELKPGQRS 118
+G ++ + + + S
Sbjct: 133 DGAVLDGRELRVQMARYGRPPDS 155
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar
mRNA localization, translation; 1.90A {Drosophila
melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A
Length = 165
Score = 81.0 bits (200), Expect = 1e-18
Identities = 23/118 (19%), Positives = 52/118 (44%), Gaps = 1/118 (0%)
Query: 81 VFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVE 140
+ +AK + G ++ I ++ ++ + ++ + +FV ++ E
Sbjct: 23 IVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHE 82
Query: 141 TVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQ 197
E+E++ F +G I + + D G SKG+ +++ ++K A A +NG I
Sbjct: 83 EAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIM 140
Score = 57.9 bits (140), Expect = 2e-10
Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 6/94 (6%)
Query: 216 PKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FI 269
+++P + +FV ++ E +E F +G I + L D+ G +
Sbjct: 60 DELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 119
Query: 270 EFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
E+ K A A +NG + ++V K
Sbjct: 120 EYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 153
Score = 57.5 bits (139), Expect = 2e-10
Identities = 17/115 (14%), Positives = 50/115 (43%), Gaps = 1/115 (0%)
Query: 13 DEGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN- 71
E + +++ + + L V ++ + +F +G ++++ + ++
Sbjct: 51 YERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 110
Query: 72 DESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEK 126
S+G+A++ + T +A A+ +NG I + + + + +K +R K +
Sbjct: 111 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKRRR 165
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 78.8 bits (195), Expect = 1e-18
Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 5/86 (5%)
Query: 115 GQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGF 173
G Q + V L E++LK +F FG ++ V++ +D + G SKGF
Sbjct: 1 GSSGSSGVKRAVQKTS-DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGF 59
Query: 174 GFIQFFSYKAAEKAIIEM---NGRMI 196
GF++F Y+ K + + +GR
Sbjct: 60 GFVRFTEYETQVKVMSQRHMIDGRWC 85
Score = 44.9 bits (107), Expect = 2e-06
Identities = 22/103 (21%), Positives = 33/103 (32%), Gaps = 6/103 (5%)
Query: 19 DEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGF 77
+ + K L V L Q L F FG + V+V ++ S+GF
Sbjct: 3 SGSSGVKRAVQKTSD---LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGF 59
Query: 78 AIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
+ F K + H+I + K Q S P
Sbjct: 60 GFVRFTEYETQVKVMSQR--HMIDGRWCDCKLPNSKQSQDSGP 100
Score = 39.1 bits (92), Expect = 2e-04
Identities = 12/68 (17%), Positives = 24/68 (35%), Gaps = 6/68 (8%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHA 277
+ + + V LP + +E F+ FG + + D GF+ F +
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70
Query: 278 THAVSTMN 285
+S +
Sbjct: 71 VKVMSQRH 78
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1;
RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 94
Score = 78.4 bits (194), Expect = 2e-18
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
V+V NL ++ +L F K+G +++V I++D + KSKG FI F +A+
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 191 MNGRMIQHNSTFVSLA 206
+N + + S+A
Sbjct: 78 INNKQLFGRVIKASIA 93
Score = 62.6 bits (153), Expect = 8e-13
Identities = 16/79 (20%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHA 277
K+ ++V+NLP ++ N++ +F+++G + +++ DK + FI F+ A
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 278 THAVSTMNGHVFKSKPLKV 296
+ +N + +K
Sbjct: 72 QNCTRAINNKQLFGRVIKA 90
Score = 52.6 bits (127), Expect = 3e-09
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 34 ENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKAR 92
++ ++V+NL S+ N L F K+G + V + ++K+ +S+G A I+F A+
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Query: 93 VEMNG 97
+N
Sbjct: 76 RAINN 80
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 78.5 bits (194), Expect = 2e-18
Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
++ N+ E +L F FG I++ K + KG FI++ +++ A I+ +
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCIVALA 84
Query: 193 GRMIQ 197
Q
Sbjct: 85 NFPFQ 89
Score = 64.6 bits (158), Expect = 2e-13
Identities = 15/72 (20%), Positives = 29/72 (40%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTM 284
P R ++ N+P ++ LF FG I +K FI++ + A + +
Sbjct: 24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVAL 83
Query: 285 NGHVFKSKPLKV 296
F+ + L+
Sbjct: 84 ANFPFQGRNLRT 95
Score = 56.5 bits (137), Expect = 1e-10
Identities = 15/88 (17%), Positives = 27/88 (30%), Gaps = 11/88 (12%)
Query: 18 DDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGF 77
D + Y + N+ LI F+ FG + D + K G
Sbjct: 17 DHIIRSAPPRVTTAY------IGNIPHFATEADLIPLFQNFGFILDFKHYPEK-----GC 65
Query: 78 AIIVFNTPAEAKKARVEMNGHLIGSKPV 105
I ++T +A V + + +
Sbjct: 66 CFIKYDTHEQAAVCIVALANFPFQGRNL 93
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription,
splicing, RNA processing, nonsense mediated D NMD, HDAC,
histone deacetylation; 1.90A {Homo sapiens}
Length = 88
Score = 78.0 bits (193), Expect = 2e-18
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 2/78 (2%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD--ENGKSKGFGFIQFFSYKAAEKAII 189
KV + L V ++ + F +G I + + + SKG+ +++F + AEKA+
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 190 EMNGRMIQHNSTFVSLAE 207
M+G I +
Sbjct: 66 HMDGGQIDGQEITATAVL 83
Score = 59.9 bits (146), Expect = 6e-12
Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 7/78 (8%)
Query: 227 RKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD-------KHIGFIEFIMPKHATH 279
+ K+ + L N+ E+F+ +G I + + K ++EF P A
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 280 AVSTMNGHVFKSKPLKVT 297
A+ M+G + + T
Sbjct: 63 ALKHMDGGQIDGQEITAT 80
Score = 58.3 bits (142), Expect = 2e-11
Identities = 20/84 (23%), Positives = 39/84 (46%), Gaps = 2/84 (2%)
Query: 33 KENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND--ESRGFAIIVFNTPAEAKK 90
K ++H+ L +V ++ F +G ++ + + + S+G+A + F P EA+K
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 91 ARVEMNGHLIGSKPVIITFVELKP 114
A M+G I + + T V
Sbjct: 63 ALKHMDGGQIDGQEITATAVLAPW 86
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} PDB: 2dgq_A
Length = 106
Score = 78.5 bits (194), Expect = 2e-18
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 120 PVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQF 178
K + K+F+ + +DE++LK F +FG I E+ +++D G KG F+ +
Sbjct: 3 SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62
Query: 179 FSYKAAEKAIIEMNGRMI 196
++A KA ++ +
Sbjct: 63 CERESALKAQSALHEQKT 80
Score = 53.9 bits (130), Expect = 1e-09
Identities = 16/89 (17%), Positives = 40/89 (44%), Gaps = 9/89 (10%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHA 277
+ K+F+ +P N++ + + LF FG I +++ D+ F+ + + A
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESA 68
Query: 278 THAVSTMNGHV---FKSKPLKVTLSGTKP 303
A S ++ ++P++V + ++
Sbjct: 69 LKAQSALHEQKTLPGMNRPIQVKPADSES 97
Score = 52.3 bits (126), Expect = 6e-09
Identities = 15/92 (16%), Positives = 41/92 (44%), Gaps = 4/92 (4%)
Query: 33 KENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESRGFAIIVFNTPAEAKKA 91
+L + + ++D + L F++FG + ++ V +++ +G A + + A KA
Sbjct: 12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Query: 92 RVEMNGHLI---GSKPVIITFVELKPGQRSKP 120
+ ++ ++P+ + + + S P
Sbjct: 72 QSALHEQKTLPGMNRPIQVKPADSESRGGSGP 103
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related
protein, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 78.5 bits (194), Expect = 2e-18
Identities = 16/74 (21%), Positives = 39/74 (52%), Gaps = 5/74 (6%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
V+ + + ++ ++ F FG I+E+++ + KG+ F++F ++++A AI+ +N
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVN 82
Query: 193 GRMIQHNSTFVSLA 206
G I+ +
Sbjct: 83 GTTIEGHVVKCYWG 96
Score = 65.8 bits (161), Expect = 7e-14
Identities = 15/79 (18%), Positives = 32/79 (40%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTM 284
+ ++ + S + + + F+ FG I + +K F+ F + A HA+ ++
Sbjct: 22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSV 81
Query: 285 NGHVFKSKPLKVTLSGTKP 303
NG + +K P
Sbjct: 82 NGTTIEGHVVKCYWGKESP 100
Score = 64.3 bits (157), Expect = 3e-13
Identities = 25/104 (24%), Positives = 43/104 (41%), Gaps = 11/104 (10%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRG 76
+D +S+ +N VY + + +Q + F FG + ++RV K G
Sbjct: 14 FEDVVNQSSPKNCTVY------CGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-----G 62
Query: 77 FAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
++ + F+T A A V +NG I V + + P S P
Sbjct: 63 YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGP 106
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A
Length = 103
Score = 78.1 bits (193), Expect = 2e-18
Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV+NL TV EE L+ F +FG + VK ++D + FI F A KA+ EM
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-------YAFIHFDERDGAVKAMEEM 65
Query: 192 NGRMIQHNSTFVSLA 206
NG+ ++ + + A
Sbjct: 66 NGKDLEGENIEIVFA 80
Score = 65.4 bits (160), Expect = 9e-14
Identities = 18/79 (22%), Positives = 34/79 (43%), Gaps = 2/79 (2%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTM 284
A+ +FV NL + + E+ F++FG + + K FI F A A+ M
Sbjct: 8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--KDYAFIHFDERDGAVKAMEEM 65
Query: 285 NGHVFKSKPLKVTLSGTKP 303
NG + + +++ +
Sbjct: 66 NGKDLEGENIEIVFAKPPD 84
Score = 57.7 bits (140), Expect = 6e-11
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 7/77 (9%)
Query: 33 KENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
K L V NL +V + L F +FG L V+ + +A I F+ A KA
Sbjct: 10 KVKVLFVRNLANTVTEEILEKAFSQFGKLERVKK-------LKDYAFIHFDERDGAVKAM 62
Query: 93 VEMNGHLIGSKPVIITF 109
EMNG + + + I F
Sbjct: 63 EEMNGKDLEGENIEIVF 79
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 77.3 bits (191), Expect = 4e-18
Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 122 GPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSY 181
G + + + NL + EE L+ F K +K+ +++NGKSKG+ FI+F S+
Sbjct: 7 GNSTWSGESKTLVLSNLSYSATEETLQEVFEKAT---FIKVPQNQNGKSKGYAFIEFASF 63
Query: 182 KAAEKAIIEMNGRMI 196
+ A++A+ N R I
Sbjct: 64 EDAKEALNSCNKREI 78
Score = 60.4 bits (147), Expect = 6e-12
Identities = 25/101 (24%), Positives = 48/101 (47%), Gaps = 4/101 (3%)
Query: 21 GARSNKENNKVYKENE-LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAI 79
G+ + N+ E++ L ++NL S + L F+K ++V +N+N +S+G+A
Sbjct: 1 GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATF---IKVPQNQNGKSKGYAF 57
Query: 80 IVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
I F + +AK+A N I + + + + S P
Sbjct: 58 IEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGP 98
Score = 49.2 bits (118), Expect = 5e-08
Identities = 15/86 (17%), Positives = 32/86 (37%), Gaps = 10/86 (11%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHA 277
+ ++NL + +E+F + I V FIEF + A
Sbjct: 11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASFEDA 66
Query: 278 THAVSTMNGHVFKSKPLKVTLSGTKP 303
A+++ N + + +++ L G +
Sbjct: 67 KEALNSCNKREIEGRAIRLELQGPRG 92
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 77.2 bits (191), Expect = 5e-18
Identities = 21/63 (33%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
++V +L + E+ L+ F FG I + +++D + G+SKG+GFI F + A +A+ +
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 191 MNG 193
+NG
Sbjct: 67 LNG 69
Score = 57.9 bits (141), Expect = 4e-11
Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 6/81 (7%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVS 282
+ ++V +L NI +F FG I + L+ D GFI F + A A+
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 283 TMNGHVFKSKPLKVTLSGTKP 303
+NG +P++V +
Sbjct: 66 QLNGFELAGRPMRVGHVTERL 86
Score = 52.6 bits (127), Expect = 3e-09
Identities = 19/85 (22%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
L+V +L ++ L F+ FG + ++ + ++ + S+G+ I F+ A++A ++
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 96 NGHLIGSKPVIITFVELKPGQRSKP 120
NG + +P+ + V + S P
Sbjct: 68 NGFELAGRPMRVGHVTERLDGGSGP 92
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 115
Score = 77.7 bits (192), Expect = 5e-18
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
+++KNL V E +L S F +F I G+ +G FI F + + A +A+
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 191 MNGRMIQ 197
+NG +
Sbjct: 87 VNGYKLY 93
Score = 65.0 bits (159), Expect = 2e-13
Identities = 25/94 (26%), Positives = 41/94 (43%), Gaps = 7/94 (7%)
Query: 28 NNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVA-RNKNDESRGFAIIVFNTPA 86
N +Y + NL P V + L++ F +F + + R RG A I F
Sbjct: 25 NKVLY------LKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKE 78
Query: 87 EAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
A +A +NG+ + K ++I F + K + S P
Sbjct: 79 IAWQALHLVNGYKLYGKILVIEFGKNKKQRSSGP 112
Score = 63.5 bits (155), Expect = 7e-13
Identities = 17/80 (21%), Positives = 29/80 (36%), Gaps = 6/80 (7%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVS 282
+++ NL + + LFARF + + FI F + A A+
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 283 TMNGHVFKSKPLKVTLSGTK 302
+NG+ K L + K
Sbjct: 86 LVNGYKLYGKILVIEFGKNK 105
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 99
Score = 76.9 bits (190), Expect = 7e-18
Identities = 19/89 (21%), Positives = 42/89 (47%), Gaps = 5/89 (5%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQ 177
S G E+ ++V+NL+ + EE ++ F ++ K + + F+
Sbjct: 3 SGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVH 57
Query: 178 FFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
F + + A +A+ +NG+++ + V+LA
Sbjct: 58 FSNREDAVEAMKALNGKVLDGSPIEVTLA 86
Score = 65.0 bits (159), Expect = 1e-13
Identities = 16/75 (21%), Positives = 31/75 (41%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTM 284
+ ++V NL + + E+ F + + F+ F + A A+ +
Sbjct: 12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKAL 71
Query: 285 NGHVFKSKPLKVTLS 299
NG V P++VTL+
Sbjct: 72 NGKVLDGSPIEVTLA 86
Score = 64.2 bits (157), Expect = 2e-13
Identities = 24/106 (22%), Positives = 41/106 (38%), Gaps = 10/106 (9%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDES 74
G S G + K+ L+V NL S + + EF RV +
Sbjct: 1 GSSGSSGDEDTMSSVKI-----LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK-----I 50
Query: 75 RGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
R +A + F+ +A +A +NG ++ P+ +T + S P
Sbjct: 51 RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGP 96
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 76.6 bits (189), Expect = 9e-18
Identities = 23/87 (26%), Positives = 46/87 (52%), Gaps = 3/87 (3%)
Query: 113 KPGQRSKPVGPEEKQYKKD--KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGK 169
+ + ++ +++V +L + E+ L+ F FG I ++++ D E G+
Sbjct: 7 HHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGR 66
Query: 170 SKGFGFIQFFSYKAAEKAIIEMNGRMI 196
SKG+GFI F + A+KA+ ++NG +
Sbjct: 67 SKGYGFITFSDSECAKKALEQLNGFEL 93
Score = 58.9 bits (143), Expect = 2e-11
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSD------KHIGFIEFIMPKHATHAVST 283
+++V +L NI +F FG I S L+ D K GFI F + A A+
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 284 MNGHVFKSKPLKV 296
+NG +P+KV
Sbjct: 88 LNGFELAGRPMKV 100
Score = 47.7 bits (114), Expect = 2e-07
Identities = 19/79 (24%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVEM 95
L+V +L ++ L F+ FG + +++ + S+G+ I F+ AKKA ++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 96 NGHLIGSKPVIITFVELKP 114
NG + +P+ + V +
Sbjct: 89 NGFELAGRPMKVGHVTERT 107
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 76.5 bits (189), Expect = 1e-17
Identities = 21/83 (25%), Positives = 42/83 (50%), Gaps = 2/83 (2%)
Query: 115 GQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGF 173
Q GP+ + + +FV + E EE++ F ++G I + + D G KG+
Sbjct: 9 EQDGDEPGPQ-RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 67
Query: 174 GFIQFFSYKAAEKAIIEMNGRMI 196
+++ +YK A+ A+ +NG+ +
Sbjct: 68 TLVEYETYKEAQAAMEGLNGQDL 90
Score = 56.5 bits (137), Expect = 2e-10
Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 6/86 (6%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHA 277
+ +FV + + + FA +G I + L D+ G +E+ K A
Sbjct: 19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEA 78
Query: 278 THAVSTMNGHVFKSKPLKVTLSGTKP 303
A+ +NG +P+ V +
Sbjct: 79 QAAMEGLNGQDLMGQPISVDWCFVRG 104
Score = 50.7 bits (122), Expect = 2e-08
Identities = 14/99 (14%), Positives = 47/99 (47%), Gaps = 7/99 (7%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESR 75
D+ G + + E ++ V + + + ++F ++G ++++ + ++ +
Sbjct: 12 GDEPGPQRSVEGWILF------VTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65
Query: 76 GFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKP 114
G+ ++ + T EA+ A +NG + +P+ + + ++
Sbjct: 66 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG 104
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 76.2 bits (188), Expect = 2e-17
Identities = 34/112 (30%), Positives = 50/112 (44%), Gaps = 20/112 (17%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
K+FV L + L+ +F FG+I E ++ D + GKS+G+GF+ AAE+A +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 191 MN----GRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPS 238
N GR V+LA + KP LQ I V+ S
Sbjct: 79 PNPIIDGRKAN-----VNLA--------YLGAKPRSLQTGF--AIGVSGPSS 115
Score = 49.6 bits (119), Expect = 6e-08
Identities = 18/90 (20%), Positives = 38/90 (42%), Gaps = 8/90 (8%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESR 75
S G++ + K++ V L + +L F+ FG + + V ++ +SR
Sbjct: 6 SGMHGSQKDTTFTKIF------VGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSR 59
Query: 76 GFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
G+ + A A++A + N +I +
Sbjct: 60 GYGFVTMADRAAAERACKDPN-PIIDGRKA 88
Score = 49.2 bits (118), Expect = 8e-08
Identities = 19/96 (19%), Positives = 33/96 (34%), Gaps = 7/96 (7%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHA 277
+ KIFV LP + ++ + F FG I + +++D+ GF+ A
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 278 THAVSTMNGHVFKSKPLKVTLSGTKPGVSITNPTKA 313
A N + + V L+ A
Sbjct: 73 ERACKDPN-PIIDGRKANVNLAYLGAKPRSLQTGFA 107
>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP
domain, MIF4G domain, RNA maturation, RNA export,
nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP:
d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B
3fey_B 1h6k_X
Length = 156
Score = 77.5 bits (191), Expect = 2e-17
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
Query: 110 VELKPGQRSKPVGPEEKQYKK----DKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD 165
VEL + G E+Q K ++V NL EE++ F K G+I ++ + D
Sbjct: 15 VELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD 74
Query: 166 -ENGKSKGFGFIQFFSYKAAEKAIIEMNGRMI 196
+ GF F++++S AE A+ +NG +
Sbjct: 75 KMKKTACGFCFVEYYSRADAENAMRYINGTRL 106
Score = 63.7 bits (155), Expect = 2e-12
Identities = 23/120 (19%), Positives = 51/120 (42%), Gaps = 11/120 (9%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESR 75
++E + K++ +Y V NL + + F K G ++ + + +K +
Sbjct: 28 DNEEQEKLLKKSCTLY------VGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTAC 81
Query: 76 GFAIIVFNTPAEAKKARVEMNGHLIGSKPVII----TFVELKPGQRSKPVGPEEKQYKKD 131
GF + + + A+A+ A +NG + + + F E + R + G +Y++D
Sbjct: 82 GFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQD 141
Score = 57.1 bits (138), Expect = 3e-10
Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 6/81 (7%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVS 282
++V NL + ELF++ G I + DK F+E+ A +A+
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 283 TMNGHVFKSKPLKVTLSGTKP 303
+NG + ++
Sbjct: 100 YINGTRLDDRIIRTDWDAGFK 120
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 75.4 bits (186), Expect = 2e-17
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD--ENGKSKGFGF 175
S G K+ K+ V+N+ ++ E++ F FG + V++ + G +GFGF
Sbjct: 3 SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62
Query: 176 IQFFSYKAAEKAI------IEMNGRMI 196
+ F + + A+KA + GR +
Sbjct: 63 VDFITKQDAKKAFNALCHSTHLYGRRL 89
Score = 57.3 bits (139), Expect = 8e-11
Identities = 21/100 (21%), Positives = 46/100 (46%), Gaps = 3/100 (3%)
Query: 24 SNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND--ESRGFAIIV 81
S+ + K +++ V N+ + + + F FG L+ VR+ + RGF +
Sbjct: 5 SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64
Query: 82 FNTPAEAKKARVEM-NGHLIGSKPVIITFVELKPGQRSKP 120
F T +AKKA + + + + +++ + + + +S P
Sbjct: 65 FITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSGP 104
Score = 56.2 bits (136), Expect = 2e-10
Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI-------GFIEFIMPKH 276
+ +KI V N+P N E ELF+ FG + + L GF++FI +
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 277 ATHAVSTM-NGHVFKSKPLKVTLSGTKPGVS 306
A A + + + + L + + ++ V
Sbjct: 71 AKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 101
>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 102
Score = 75.4 bits (186), Expect = 2e-17
Identities = 32/91 (35%), Positives = 41/91 (45%), Gaps = 4/91 (4%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFI 176
S GP + +FVK L E EE LK F + +IV D E G SKGFGF+
Sbjct: 3 SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFV 59
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
F S + A+ A M I N + A+
Sbjct: 60 DFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90
Score = 47.6 bits (114), Expect = 2e-07
Identities = 22/102 (21%), Positives = 39/102 (38%), Gaps = 5/102 (4%)
Query: 21 GARSNKENNKVYKENE-LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFA 78
G+ + N + ++ L V L + L F R+ ++ S+GF
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFG 57
Query: 79 IIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
+ FN+ +AK A+ M I V + + + K S P
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGP 99
Score = 46.5 bits (111), Expect = 5e-07
Identities = 15/91 (16%), Positives = 29/91 (31%), Gaps = 9/91 (9%)
Query: 219 KPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFI 272
P + +FV L + +E F + +V+D+ GF++F
Sbjct: 6 SGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFN 62
Query: 273 MPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
+ A A M + + + K
Sbjct: 63 SEEDAKAAKEAMEDGEIDGNKVTLDWAKPKG 93
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA
splicing, mRNA transport, nonsense-mediated mRNA decay,
nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*
Length = 126
Score = 75.9 bits (187), Expect = 3e-17
Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 115 GQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGF 173
Q GP+ + +FV + E EE++ F ++G I + + D G KG+
Sbjct: 8 EQDGDEPGPQRSV-EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 66
Query: 174 GFIQFFSYKAAEKAIIEMNGRMI 196
+++ +YK A+ A+ +NG+ +
Sbjct: 67 TLVEYETYKEAQAAMEGLNGQDL 89
Score = 55.5 bits (134), Expect = 6e-10
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 6/74 (8%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATHAVS 282
+FV + + + FA +G I + L D+ G +E+ K A A+
Sbjct: 23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82
Query: 283 TMNGHVFKSKPLKV 296
+NG +P+ V
Sbjct: 83 GLNGQDLMGQPISV 96
Score = 52.4 bits (126), Expect = 7e-09
Identities = 16/112 (14%), Positives = 51/112 (45%), Gaps = 7/112 (6%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESR 75
D+ G + + E ++ V + + + ++F ++G ++++ + ++ +
Sbjct: 11 GDEPGPQRSVEGWILF------VTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64
Query: 76 GFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQ 127
G+ ++ + T EA+ A +NG + +P+ + + ++ + K G +
Sbjct: 65 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRS 116
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 113
Score = 75.1 bits (185), Expect = 3e-17
Identities = 23/99 (23%), Positives = 42/99 (42%), Gaps = 9/99 (9%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIE--------VKIVRD-ENG 168
S G ++ ++V+ L ++V ++L F + G + + I D E G
Sbjct: 3 SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 62
Query: 169 KSKGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
K KG + + A+ A+ +G+ Q + VSLA
Sbjct: 63 KPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 101
Score = 56.3 bits (136), Expect = 2e-10
Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 14/94 (14%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSS--------LVSDKHIG------FI 269
+ + + I+V L ++ + + F + G + + + DK G +
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70
Query: 270 EFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
+ P A AV +G F+ LKV+L+ KP
Sbjct: 71 SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 104
Score = 47.8 bits (114), Expect = 2e-07
Identities = 25/116 (21%), Positives = 44/116 (37%), Gaps = 16/116 (13%)
Query: 15 GISDDEG-ARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLR--------DVR 65
G S G + +N+ +Y V L SV L + FK+ G ++ +
Sbjct: 1 GSSGSSGDPDEDSDNSAIY------VQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIH 54
Query: 66 VARNKND-ESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
+ +K + +G A + + P AK A +G + ++ KP S P
Sbjct: 55 IYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGP 110
>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 75.4 bits (186), Expect = 3e-17
Identities = 20/96 (20%), Positives = 40/96 (41%), Gaps = 2/96 (2%)
Query: 113 KPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDEN-GKSK 171
K R ++ VF L + +L+ F G + +V+I+ D N +SK
Sbjct: 8 KSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 67
Query: 172 GFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
G +++F ++ A I + G+ + V ++
Sbjct: 68 GIAYVEFCEIQSVPLA-IGLTGQRLLGVPIIVQASQ 102
Score = 58.9 bits (143), Expect = 3e-11
Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 8/97 (8%)
Query: 210 PGKKVFPKVKPPLLQPAR-KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH--- 265
GK + L R +F L + I + E+ F+ G + ++SD++
Sbjct: 6 SGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRR 65
Query: 266 ---IGFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLS 299
I ++EF + A+ + G P+ V S
Sbjct: 66 SKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQAS 101
Score = 54.2 bits (131), Expect = 1e-09
Identities = 21/103 (20%), Positives = 42/103 (40%), Gaps = 8/103 (7%)
Query: 19 DEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESRGF 77
D + ++ V+ L + + L + F G +RDVR+ ++N S+G
Sbjct: 16 DNLSPEERDARTVF------CMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGI 69
Query: 78 AIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
A + F A + + G + P+I+ + + + S P
Sbjct: 70 AYVEFCEIQSVPLA-IGLTGQRLLGVPIIVQASQAEKNRLSGP 111
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 74.6 bits (184), Expect = 4e-17
Identities = 17/66 (25%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
V++ ++ EE++ G +I +K++ D + G+SKG+ FI+F +++ A+
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 191 MNGRMI 196
+NG +
Sbjct: 64 LNGYQL 69
Score = 57.6 bits (140), Expect = 5e-11
Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 8/85 (9%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHAT 278
P+R +++ ++P + + +L + G + + ++ D G FIEF + +
Sbjct: 1 PSRV--VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSA 58
Query: 279 HAVSTMNGHVFKSKPLKVTLSGTKP 303
AV +NG+ S+ LK S
Sbjct: 59 SAVRNLNGYQLGSRFLKCGYSSNSD 83
Score = 49.2 bits (118), Expect = 6e-08
Identities = 11/79 (13%), Positives = 35/79 (44%), Gaps = 1/79 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
+++ ++ + +++ G + ++++ + S+G+A I F + A +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 96 NGHLIGSKPVIITFVELKP 114
NG+ +GS+ + +
Sbjct: 65 NGYQLGSRFLKCGYSSNSD 83
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 99
Score = 74.5 bits (184), Expect = 4e-17
Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 5/79 (6%)
Query: 123 PEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSY 181
K +K+FV + E EL+ +F KFG + EV ++ D E + +GFGFI F
Sbjct: 3 SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62
Query: 182 KAAEKAII----EMNGRMI 196
++ ++A+ ++ G+ +
Sbjct: 63 QSVDQAVNMHFHDIMGKKV 81
Score = 51.0 bits (123), Expect = 1e-08
Identities = 23/83 (27%), Positives = 33/83 (39%), Gaps = 5/83 (6%)
Query: 24 SNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVF 82
S +K K + V + + L FKKFG + +V + + RGF I F
Sbjct: 3 SGSSGSKSNK---IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITF 59
Query: 83 NTPAEAKKARVEMNGHLIGSKPV 105
+A V M+ H I K V
Sbjct: 60 EDEQSVDQA-VNMHFHDIMGKKV 81
Score = 50.7 bits (122), Expect = 2e-08
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 7/78 (8%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIMPKHAT 278
++ NKIFV +P N +E E F +FG +T ++ D GFI F +
Sbjct: 7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVD 66
Query: 279 HAVSTMNGHVFKSKPLKV 296
AV+ M+ H K ++V
Sbjct: 67 QAVN-MHFHDIMGKKVEV 83
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 74.6 bits (184), Expect = 4e-17
Identities = 26/85 (30%), Positives = 36/85 (42%), Gaps = 4/85 (4%)
Query: 123 PEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYK 182
+K + KNL + E+ELK F I V ++GKSKG +I+F S
Sbjct: 9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEA 64
Query: 183 AAEKAIIEMNGRMIQHNSTFVSLAE 207
AEK + E G I S +
Sbjct: 65 DAEKNLEEKQGAEIDGRSVSLYYTG 89
Score = 56.9 bits (138), Expect = 9e-11
Identities = 22/104 (21%), Positives = 41/104 (39%), Gaps = 10/104 (9%)
Query: 14 EGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE 73
+ D ++ + + NL ++ L F+ +R V ++ +
Sbjct: 2 HMLEDPCTSKKVRAARTLL------AKNLSFNITEDELKEVFEDALEIRLVS----QDGK 51
Query: 74 SRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQR 117
S+G A I F + A+A+K E G I + V + + K G R
Sbjct: 52 SKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95
Score = 51.9 bits (125), Expect = 6e-09
Identities = 21/92 (22%), Positives = 31/92 (33%), Gaps = 10/92 (10%)
Query: 219 KPPLLQPAR-KNKIFVANLPSNINNSEFEELFARFGTI-----TSSSLVSDKHIGFIEFI 272
P + R + NL NI E +E+F I S K I +IEF
Sbjct: 6 DPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKS----KGIAYIEFK 61
Query: 273 MPKHATHAVSTMNGHVFKSKPLKVTLSGTKPG 304
A + G + + + +G K G
Sbjct: 62 SEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG 93
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain,
RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 74.6 bits (184), Expect = 4e-17
Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 1/79 (1%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQ 177
S G E + ++V NL V E + F + G K++ + + F++
Sbjct: 3 SGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVE 61
Query: 178 FFSYKAAEKAIIEMNGRMI 196
F+ ++ A A+ MNGR I
Sbjct: 62 FYEHRDAAAALAAMNGRKI 80
Score = 59.2 bits (144), Expect = 2e-11
Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 4/81 (4%)
Query: 220 PPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI----GFIEFIMPK 275
+ + ++V NL ++ +LF++ G S ++++ F+EF +
Sbjct: 7 GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66
Query: 276 HATHAVSTMNGHVFKSKPLKV 296
A A++ MNG K +KV
Sbjct: 67 DAAAALAAMNGRKILGKEVKV 87
Score = 54.2 bits (131), Expect = 1e-09
Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 1/84 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L+V NL V ++ F + G + ++ + + + F +A A MN
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT-SNDPYCFVEFYEHRDAAAALAAMN 76
Query: 97 GHLIGSKPVIITFVELKPGQRSKP 120
G I K V + + Q+S P
Sbjct: 77 GRKILGKEVKVNWATTPSSQKSGP 100
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG, protein
structure initiative; HET: PGE; 1.95A {Homo sapiens}
PDB: 3b4d_A 3b4m_A
Length = 89
Score = 73.7 bits (182), Expect = 6e-17
Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
++V N+ EEL++HF G++ V I+ D +G KGF +I+F K + + +
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD-KESVRTSLA 66
Query: 191 MNGRMIQ 197
++ + +
Sbjct: 67 LDESLFR 73
Score = 58.3 bits (142), Expect = 3e-11
Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 8/85 (9%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATHAV 281
I+V N+ E E F G++ +++ DK G +IEF + ++
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 282 STMNGHVFKSKPLKVTLSGT-KPGV 305
+ ++ +F+ + +KV T +PG+
Sbjct: 66 A-LDESLFRGRQIKVIPKRTNRPGI 89
Score = 49.4 bits (119), Expect = 3e-08
Identities = 13/73 (17%), Positives = 32/73 (43%), Gaps = 2/73 (2%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESRGFAIIVFNTPAEAKKARVEM 95
++V N++ + L F G++ V + +K +GFA I F+ + + + +
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS-LAL 67
Query: 96 NGHLIGSKPVIIT 108
+ L + + +
Sbjct: 68 DESLFRGRQIKVI 80
>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A)
binding, structural genomics, protein structure
initiative, PSI-2; NMR {Xenopus laevis}
Length = 124
Score = 74.8 bits (184), Expect = 8e-17
Identities = 21/86 (24%), Positives = 42/86 (48%), Gaps = 2/86 (2%)
Query: 113 KPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSK 171
G E+K+ K V+V N+ ++L++HF G+I + I+ D +G K
Sbjct: 19 TEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPK 78
Query: 172 GFGFIQFFSYKAAEKAIIEMNGRMIQ 197
G+ +I+F + + A + M+ + +
Sbjct: 79 GYAYIEFAE-RNSVDAAVAMDETVFR 103
Score = 59.7 bits (145), Expect = 2e-11
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 8/89 (8%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATHAV 281
K ++V N+ + E F+ G+I +++ DK G +IEF +++ A
Sbjct: 36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF-AERNSVDAA 94
Query: 282 STMNGHVFKSKPLKVTLSGTK-PGVSITN 309
M+ VF+ + +KV T PG+S T+
Sbjct: 95 VAMDETVFRGRTIKVLPKRTNMPGISSTD 123
Score = 49.7 bits (119), Expect = 6e-08
Identities = 16/97 (16%), Positives = 36/97 (37%), Gaps = 2/97 (2%)
Query: 13 DEGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND 72
++ + E K + ++V N++ Q L F G++ + + +K
Sbjct: 15 AGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFS 74
Query: 73 -ESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIIT 108
+G+A I F A V M+ + + + +
Sbjct: 75 GHPKGYAYIEFAERNSVDAA-VAMDETVFRGRTIKVL 110
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 73.5 bits (181), Expect = 9e-17
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 2/77 (2%)
Query: 122 GPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFG-NIIEVKIVRD-ENGKSKGFGFIQFF 179
G +++ +L +DE + F G ++ VKI+R+ G G+ F++F
Sbjct: 1 GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60
Query: 180 SYKAAEKAIIEMNGRMI 196
AEK + ++NG+ +
Sbjct: 61 DLATAEKCLHKINGKPL 77
Score = 56.2 bits (136), Expect = 2e-10
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 2/75 (2%)
Query: 37 LHVNNLEPSVDNQALINEFKKFG-TLRDVRVARNK-NDESRGFAIIVFNTPAEAKKARVE 94
L + +LEP +D + F G T+ V++ RN+ G+ + F A A+K +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 95 MNGHLIGSKPVIITF 109
+NG + F
Sbjct: 72 INGKPLPGATPAKRF 86
Score = 45.4 bits (108), Expect = 1e-06
Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 11/80 (13%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFG-TITSSSLVSDKHIG------FIEFIMPKHATHA 280
+++ +L ++ + FA G T+ S ++ ++ G F+EF A
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKC 68
Query: 281 VSTMNGHVFK----SKPLKV 296
+ +NG +K K+
Sbjct: 69 LHKINGKPLPGATPAKRFKL 88
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 72.7 bits (179), Expect = 1e-16
Identities = 23/81 (28%), Positives = 41/81 (50%), Gaps = 8/81 (9%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQ 177
S E+K ++V L +T+ E +L++HF +FG I + +V+ + FIQ
Sbjct: 2 SSGSSGEDKTITT--LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQ 54
Query: 178 FFSYKAAEKAIIEM-NGRMIQ 197
F + +AAE A + N ++
Sbjct: 55 FATRQAAEVAAEKSFNKLIVN 75
Score = 58.1 bits (141), Expect = 3e-11
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHA-VSTMNGHV 288
++V L I ++ F +FG I + ++V + FI+F + A A + N +
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLI 73
Query: 289 FKSKPLKV 296
+ L V
Sbjct: 74 VNGRRLNV 81
Score = 51.9 bits (125), Expect = 4e-09
Identities = 18/87 (20%), Positives = 35/87 (40%), Gaps = 12/87 (13%)
Query: 24 SNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFN 83
+K +Y V L ++ L N F +FG +R + V + + A I F
Sbjct: 8 EDKTITTLY------VGGLGDTITETDLRNHFYQFGEIRTITVVQRQ-----QCAFIQFA 56
Query: 84 TPAEAKKARVEM-NGHLIGSKPVIITF 109
T A+ A + N ++ + + + +
Sbjct: 57 TRQAAEVAAEKSFNKLIVNGRRLNVKW 83
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 73.0 bits (180), Expect = 2e-16
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+++V L L F +FG+I + V+ F +IQ+ S AA+ A +M
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKM 73
Query: 192 NGRMI 196
G +
Sbjct: 74 RGFPL 78
Score = 62.6 bits (153), Expect = 9e-13
Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 2/78 (2%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGHV 288
+++V L N + + F RFG+I + V +I++ A A + M G
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFP 77
Query: 289 F--KSKPLKVTLSGTKPG 304
+ L+V + + P
Sbjct: 78 LGGPDRRLRVDFAKSGPS 95
Score = 60.3 bits (147), Expect = 6e-12
Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 5/87 (5%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAII 80
G+ K L V L P+ AL EF +FG++R + + FA I
Sbjct: 4 GSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYI 58
Query: 81 VFNTPAEAKKARVEMNGHLIGSKPVII 107
+ + A+ A +M G +G +
Sbjct: 59 QYESLDAAQAACAKMRGFPLGGPDRRL 85
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein
complex, EXON junct complex, signaling protein; 1.85A
{Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B*
2j0s_D* 2xb2_D*
Length = 110
Score = 73.1 bits (180), Expect = 2e-16
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
+FV ++ E E+E++ F +G I + + D G SKG+ +++ ++K A A
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 191 MNG 193
+NG
Sbjct: 88 LNG 90
Score = 55.0 bits (133), Expect = 7e-10
Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 6/94 (6%)
Query: 216 PKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FI 269
+++P + +FV ++ E +E F +G I + L D+ G +
Sbjct: 14 DELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALV 73
Query: 270 EFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
E+ K A A +NG + ++V K
Sbjct: 74 EYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 107
Score = 47.7 bits (114), Expect = 2e-07
Identities = 16/106 (15%), Positives = 49/106 (46%), Gaps = 7/106 (6%)
Query: 13 DEGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN- 71
++ + G + + E ++ V ++ + +F +G ++++ + ++
Sbjct: 11 EDDDELEPGPQRSVEGWILF------VTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 64
Query: 72 DESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQR 117
S+G+A++ + T +A A+ +NG I + + + + +K +R
Sbjct: 65 GFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 110
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 74.6 bits (183), Expect = 2e-16
Identities = 16/81 (19%), Positives = 37/81 (45%), Gaps = 3/81 (3%)
Query: 129 KKDKVFVKNLVETVDEEELKSHFIKFG--NIIEVKIVRD-ENGKSKGFGFIQFFSYKAAE 185
++ V+V + +++L G +++E+K + NG+SKG+ + S +
Sbjct: 54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVH 113
Query: 186 KAIIEMNGRMIQHNSTFVSLA 206
K + + G+++ V A
Sbjct: 114 KLLELLPGKVLNGEKVDVRPA 134
Score = 57.6 bits (139), Expect = 2e-10
Identities = 18/101 (17%), Positives = 41/101 (40%), Gaps = 9/101 (8%)
Query: 33 KENELHVNNLEPSVDNQALINEFKKFGTLR--DVRVARNK-NDESRGFAIIVFNTPAEAK 89
+ ++V + +Q LI + G +++ A N+ N +S+G+A +V +
Sbjct: 54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVH 113
Query: 90 KARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKK 130
K + G ++ + V + + + E Q +K
Sbjct: 114 KLLELLPGKVLNGEKVDVRPA------TRQNLSQFEAQARK 148
Score = 53.8 bits (129), Expect = 4e-09
Identities = 6/89 (6%), Positives = 24/89 (26%), Gaps = 8/89 (8%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGT--ITSSSLVSDKH------IGFIEFIMPK 275
R+ ++V + + + ++ G + ++ +
Sbjct: 51 LRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASEN 110
Query: 276 HATHAVSTMNGHVFKSKPLKVTLSGTKPG 304
+ + G V + + V + +
Sbjct: 111 SVHKLLELLPGKVLNGEKVDVRPATRQNL 139
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 72.0 bits (177), Expect = 4e-16
Identities = 9/67 (13%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 131 DKVFVKNLVETVDEEELKSHFIKFGN--IIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKA 187
D + ++N+ + + + + + + +++++D + +++GF F+Q S A +
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
Query: 188 IIEMNGR 194
+ +
Sbjct: 70 LQILQSL 76
Score = 55.0 bits (133), Expect = 4e-10
Identities = 14/96 (14%), Positives = 39/96 (40%), Gaps = 13/96 (13%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTL--RDVRVARNKN-DESRGF 77
G + + + + N+ P +++ + +L ++R+ ++K ++RGF
Sbjct: 2 GHHHHHHMDTII------LRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGF 55
Query: 78 AIIVFNTPAEAKKARVEMNG----HLIGSKPVIITF 109
A + ++ +A + + I K + + F
Sbjct: 56 AFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDF 91
Score = 45.8 bits (109), Expect = 8e-07
Identities = 7/66 (10%), Positives = 23/66 (34%), Gaps = 8/66 (12%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSS--LVSDKH------IGFIEFIMPKHATHA 280
+ I + N+ + + + ++ ++ L+ DK F++ A+
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
Query: 281 VSTMNG 286
+ +
Sbjct: 70 LQILQS 75
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 71.0 bits (175), Expect = 4e-16
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAII- 189
K+FV L E++K +F +FG + + ++ D + +GFGF+ F S EK
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 190 ---EMNGRMI 196
E+N +M+
Sbjct: 61 HFHEINNKMV 70
Score = 45.9 bits (110), Expect = 4e-07
Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 39 VNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEMNG 97
V L + + + + F++FG + D + +K + RGF + F + +K E++
Sbjct: 4 VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV-CEIHF 62
Query: 98 HLIGSKPV 105
H I +K V
Sbjct: 63 HEINNKMV 70
Score = 41.7 bits (99), Expect = 1e-05
Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 7/73 (9%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVST 283
KIFV L N + + F +FG + + L+ DK GF+ F
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59
Query: 284 MNGHVFKSKPLKV 296
++ H +K ++
Sbjct: 60 IHFHEINNKMVEC 72
>2la6_A RNA-binding protein FUS; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative, RNA recognition; NMR {Homo sapiens}
Length = 99
Score = 71.2 bits (175), Expect = 6e-16
Identities = 24/93 (25%), Positives = 37/93 (39%), Gaps = 9/93 (9%)
Query: 123 PEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIE--------VKIVRD-ENGKSKGF 173
+ +FV+ L E V E + +F + G I + + D E GK KG
Sbjct: 6 HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65
Query: 174 GFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
+ F +A+ AI +G+ N VS A
Sbjct: 66 ATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
Score = 56.9 bits (138), Expect = 1e-10
Identities = 19/92 (20%), Positives = 29/92 (31%), Gaps = 14/92 (15%)
Query: 219 KPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------------ 266
+ N IFV L N+ + F + G I ++ I
Sbjct: 4 HHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLK 63
Query: 267 --GFIEFIMPKHATHAVSTMNGHVFKSKPLKV 296
+ F P A A+ +G F P+KV
Sbjct: 64 GEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV 95
Score = 49.2 bits (118), Expect = 5e-08
Identities = 18/99 (18%), Positives = 41/99 (41%), Gaps = 15/99 (15%)
Query: 16 ISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRD--------VRVA 67
+ S+ +NN ++ V L +V +++ + FK+ G ++ + +
Sbjct: 1 MGHHHHHHSHSDNNTIF------VQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLY 54
Query: 68 RNKND-ESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
++ + +G A + F+ P AK A +G P+
Sbjct: 55 TDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPI 93
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 70.2 bits (173), Expect = 9e-16
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAII- 189
K+F+ L +E L+ +F +FG + E ++RD +S+GFGF+ F +K +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 190 ---EMNGRMI 196
E++ + I
Sbjct: 62 SRHELDSKTI 71
Score = 49.0 bits (118), Expect = 3e-08
Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 2/68 (2%)
Query: 39 VNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEMNG 97
+ L + L F +FG +++ V R+ SRGF + F A K + +
Sbjct: 5 IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQSR 63
Query: 98 HLIGSKPV 105
H + SK +
Sbjct: 64 HELDSKTI 71
Score = 38.6 bits (91), Expect = 1e-04
Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 7/69 (10%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVST 283
K+F+ L E F +FG + ++ D GF+ F+ ++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA- 60
Query: 284 MNGHVFKSK 292
+ H SK
Sbjct: 61 QSRHELDSK 69
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain,
poly(A) site recognition, RNA, nuclear, RNA BIND
protein; 2.70A {Homo sapiens} PDB: 3p6y_C
Length = 90
Score = 70.3 bits (173), Expect = 1e-15
Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFG--NIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAI 188
+++ NL +E+L G +I+E+K + NG+SKGF + S +++K +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 189 IEMNGRMIQHNSTFVSLAE 207
+ R + + V+ +
Sbjct: 63 DLLPKRELHGQNPVVTPSN 81
Score = 51.4 bits (124), Expect = 8e-09
Identities = 15/86 (17%), Positives = 35/86 (40%), Gaps = 3/86 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGT--LRDVRVARNK-NDESRGFAIIVFNTPAEAKKARV 93
L++ NL ++ L G + +++ N+ N +S+GFA++ + A +KK
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 94 EMNGHLIGSKPVIITFVELKPGQRSK 119
+ + + ++T
Sbjct: 64 LLPKRELHGQNPVVTPSNKLEHHHHH 89
Score = 49.5 bits (119), Expect = 3e-08
Identities = 7/78 (8%), Positives = 20/78 (25%), Gaps = 8/78 (10%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGT--ITSSSLVSDKH------IGFIEFIMPKHATH 279
+ +++ NL + + E G I ++ + +
Sbjct: 1 RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60
Query: 280 AVSTMNGHVFKSKPLKVT 297
+ + + VT
Sbjct: 61 LMDLLPKRELHGQNPVVT 78
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif,
C-terminal helix, N-terminal helix, RNA binding protein;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 70.4 bits (173), Expect = 1e-15
Identities = 24/64 (37%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
VFV N+ EE+LK F + G ++ ++V D E GK KG+GF ++ + A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 191 MNGR 194
+NGR
Sbjct: 70 LNGR 73
Score = 55.3 bits (134), Expect = 4e-10
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATHAVS 282
+FV N+P + +++F+ G + S LV D+ G F E+ + A A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 283 TMNGHVFKSKPLKV 296
+NG F + L+V
Sbjct: 69 NLNGREFSGRALRV 82
Score = 43.4 bits (103), Expect = 6e-06
Identities = 11/63 (17%), Positives = 25/63 (39%), Gaps = 1/63 (1%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
+ V N+ + L + F + G + R+ ++ + +G+ + A A +
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 96 NGH 98
NG
Sbjct: 71 NGR 73
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 70.9 bits (174), Expect = 2e-15
Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 9/93 (9%)
Query: 124 EEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNI--------IEVKIVRD-ENGKSKGFG 174
E+ + +FV+ L E V E + +F + G I + + D E GK KG
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 175 FIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
+ F +A+ AI +G+ N VS A
Sbjct: 61 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 93
Score = 56.3 bits (136), Expect = 2e-10
Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 14/94 (14%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSS--------LVSDKHIG------FI 269
+ N IFV L N+ + F + G I ++ L +D+ G +
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62
Query: 270 EFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
F P A A+ +G F P+KV+ + +
Sbjct: 63 SFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRA 96
Score = 47.0 bits (112), Expect = 5e-07
Identities = 19/99 (19%), Positives = 43/99 (43%), Gaps = 15/99 (15%)
Query: 25 NKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLR--------DVRVARNKND-ESR 75
N +NN ++ V L +V +++ + FK+ G ++ + + ++ + +
Sbjct: 4 NSDNNTIF------VQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLK 57
Query: 76 GFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKP 114
G A + F+ P AK A +G P+ ++F +
Sbjct: 58 GEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRA 96
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 70.0 bits (172), Expect = 2e-15
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
KV+V NL + EL+ F +G + V I R+ GF F++F + AE A+ +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 192 NGRMI 196
+G++I
Sbjct: 58 DGKVI 62
Score = 63.1 bits (154), Expect = 6e-13
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 1/76 (1%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-IGFIEFIMPKHATHAVSTMNGHV 288
K++V NL + E E F+ +G + + + + F+EF P+ A AV ++G V
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 289 FKSKPLKVTLSGTKPG 304
++V LS P
Sbjct: 62 ICGSRVRVELSTGMPR 77
Score = 60.0 bits (146), Expect = 7e-12
Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 4/87 (4%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
++V NL L F +G LR V +ARN GFA + F P +A+ A ++
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLD 58
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVGP 123
G +I V + P + P
Sbjct: 59 GKVICGSRVRVELSTGMPRRSRFDRPP 85
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 70.5 bits (173), Expect = 2e-15
Identities = 12/67 (17%), Positives = 34/67 (50%), Gaps = 2/67 (2%)
Query: 131 DKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIE 190
++++NL + EE+ F K+G I ++++ +++G ++ + A+ A+
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDH 66
Query: 191 MNGRMIQ 197
++G +
Sbjct: 67 LSGFNVS 73
Score = 61.2 bits (149), Expect = 4e-12
Identities = 22/96 (22%), Positives = 47/96 (48%), Gaps = 2/96 (2%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L++ NL + + + + F K+G +R +RV E+RG A +V+ +AK A ++
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--ETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDK 132
G + ++ +++ + + +E+Q K K
Sbjct: 69 GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLK 104
Score = 58.5 bits (142), Expect = 4e-11
Identities = 20/111 (18%), Positives = 39/111 (35%), Gaps = 6/111 (5%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH---IGFIEFIMPKHATHAV 281
P +++ NLP I E ++F ++G I + + ++ + A +AV
Sbjct: 5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAV 64
Query: 282 STMNGHVFKSKPLKVTLSGTKPGVSITNPTKAPKKPAYIDEVKNVIGIKVQ 332
++G ++ L V KK + +K GI
Sbjct: 65 DHLSGFNVSNRYLVVLYYNANRAFQ---KMDTKKKEEQLKLLKEKYGINTD 112
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 69.1 bits (170), Expect = 2e-15
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAII- 189
K+FV L EE+++ +F FG + +++ D + K +GF FI F + +K +
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 190 ---EMNGRMI 196
+
Sbjct: 61 KYHNVGLSKC 70
Score = 44.8 bits (107), Expect = 1e-06
Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 2/68 (2%)
Query: 39 VNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEMNG 97
V L P + + F FG + + + + ++ RGF I F KK +E
Sbjct: 4 VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-MEKKY 62
Query: 98 HLIGSKPV 105
H +G
Sbjct: 63 HNVGLSKC 70
Score = 41.3 bits (98), Expect = 2e-05
Identities = 16/73 (21%), Positives = 23/73 (31%), Gaps = 7/73 (9%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVST 283
KIFV L + + E F FG + S L D FI F + +
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME- 59
Query: 284 MNGHVFKSKPLKV 296
H ++
Sbjct: 60 KKYHNVGLSKCEI 72
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 70.0 bits (172), Expect = 3e-15
Identities = 21/92 (22%), Positives = 48/92 (52%), Gaps = 7/92 (7%)
Query: 110 VELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDEN-G 168
+ + E++Q++K +F+ L EE L++++ ++G + + ++RD
Sbjct: 9 EKTLETVPLERKKREKEQFRK--LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASK 66
Query: 169 KSKGFGFIQFFSYKAAEKAII----EMNGRMI 196
+S+GFGF+ F S + A+ ++GR++
Sbjct: 67 RSRGFGFVTFSSMAEVDAAMAARPHSIDGRVV 98
Score = 50.0 bits (120), Expect = 4e-08
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 14 EGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-D 72
E + + R ++ K++ + L ++L N ++++G L D V R+
Sbjct: 13 ETVPLERKKREKEQFRKLF------IGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASK 66
Query: 73 ESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
SRGF + F++ AE A + H I + V
Sbjct: 67 RSRGFGFVTFSSMAEVDAA-MAARPHSIDGRVV 98
Score = 40.0 bits (94), Expect = 1e-04
Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 8/91 (8%)
Query: 212 KKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------ 265
+ P + + + K+F+ L + ++G +T ++ D
Sbjct: 12 LETVPLERKKR-EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG 70
Query: 266 IGFIEFIMPKHATHAVSTMNGHVFKSKPLKV 296
GF+ F A++ H + ++
Sbjct: 71 FGFVTFSSMAEVDAAMA-ARPHSIDGRVVEP 100
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 71.1 bits (174), Expect = 3e-15
Identities = 26/129 (20%), Positives = 50/129 (38%), Gaps = 9/129 (6%)
Query: 73 ESRGFAIIVFNTPAEAKKARVEM-NGHLIGSKPVIITFVE-LKPGQRSKPVGPEEKQYKK 130
+G A A+K + N + + + + + S +
Sbjct: 11 TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSC 70
Query: 131 D---KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKA 187
KV+V NL ++ EL+ F +G + V + R+ GF F++F + A A
Sbjct: 71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADA 126
Query: 188 IIEMNGRMI 196
+ E++GR +
Sbjct: 127 VRELDGRTL 135
Score = 69.1 bits (169), Expect = 2e-14
Identities = 32/142 (22%), Positives = 57/142 (40%), Gaps = 5/142 (3%)
Query: 167 NGKS-KGFGFIQFFSYKAAEKAIIEM-NGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQ 224
NGK+ KG + AEK + N + T+ + + + +
Sbjct: 8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHR 67
Query: 225 PARKN--KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-IGFIEFIMPKHATHAV 281
+ K++V NL +N N +E E F +G + S + + F+EF P+ A AV
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAV 127
Query: 282 STMNGHVFKSKPLKVTLSGTKP 303
++G ++V LS +
Sbjct: 128 RELDGRTLCGCRVRVELSNGEK 149
Score = 59.5 bits (144), Expect = 4e-11
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
++V NL + + L F +G LR V VARN GFA + F P +A A E++
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELD 131
Query: 97 GHLIGSKPVIITF 109
G + V +
Sbjct: 132 GRTLCGCRVRVEL 144
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 70.0 bits (172), Expect = 3e-15
Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+++V NL + ++++ F K+G I ++ + G F F++F + AE A+
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG--PPFAFVEFEDPRDAEDAVYGR 81
Query: 192 NGRMI 196
+G
Sbjct: 82 DGYDY 86
Score = 65.0 bits (159), Expect = 2e-13
Identities = 22/107 (20%), Positives = 41/107 (38%), Gaps = 11/107 (10%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRG 76
+ + ++Y V NL P + + + + F K+G +RD+ + +
Sbjct: 11 GGVIRGPAGNNDCRIY------VGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG--GPP 62
Query: 77 FAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGP 123
FA + F P +A+ A +G+ + VE R GP
Sbjct: 63 FAFVEFEDPRDAEDAVYGRDGYDYDGYRLR---VEFPRSGRGTGSGP 106
Score = 60.8 bits (148), Expect = 6e-12
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH---IGFIEFIMPKHATHAVSTMN 285
+I+V NLP +I + E++F ++G I L + + F+EF P+ A AV +
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRD 82
Query: 286 GHVFKSKPLKVTLS 299
G+ + L+V
Sbjct: 83 GYDYDGYRLRVEFP 96
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 69.1 bits (170), Expect = 3e-15
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 5/84 (5%)
Query: 121 VGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFF 179
+ + + K+FV L +++LK +F KFG +++ I D G+S+GFGFI F
Sbjct: 2 INASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK 61
Query: 180 SYKAAEKAIIEM----NGRMIQHN 199
+ EK + + +GR+I
Sbjct: 62 DAASVEKVLDQKEHRLDGRVIDPK 85
Score = 48.3 bits (116), Expect = 7e-08
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 5/86 (5%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAI 79
G ++K K + V L + L + F KFG + D + + N SRGF
Sbjct: 1 GINASKNEEDAGK---MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGF 57
Query: 80 IVFNTPAEAKKARVEMNGHLIGSKPV 105
I+F A +K ++ H + + +
Sbjct: 58 ILFKDAASVEKV-LDQKEHRLDGRVI 82
Score = 40.6 bits (96), Expect = 4e-05
Identities = 13/79 (16%), Positives = 27/79 (34%), Gaps = 7/79 (8%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIMPKHA 277
K+FV L + + + ++ F +FG + ++ D + GFI F
Sbjct: 7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASV 66
Query: 278 THAVSTMNGHVFKSKPLKV 296
+ H + +
Sbjct: 67 EKVLDQKE-HRLDGRVIDP 84
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 69.6 bits (171), Expect = 3e-15
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 7/87 (8%)
Query: 117 RSKPVGPEEKQYKKD--KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGF 173
S + P K+F+ L +E L+ +F +FG + E ++RD +S+GF
Sbjct: 10 HSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGF 69
Query: 174 GFIQFFSYKAAEKAII----EMNGRMI 196
GF+ F +K + E++ + I
Sbjct: 70 GFVTFMDQAGVDKVLAQSRHELDSKTI 96
Score = 50.0 bits (120), Expect = 3e-08
Identities = 19/94 (20%), Positives = 34/94 (36%), Gaps = 8/94 (8%)
Query: 13 DEGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN- 71
G+ K++ + L + L F +FG +++ V R+
Sbjct: 10 HSSGLVPRGSHMGSSGCKMF------IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLT 63
Query: 72 DESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
SRGF + F A K + + H + SK +
Sbjct: 64 KRSRGFGFVTFMDQAGVDKV-LAQSRHELDSKTI 96
Score = 38.8 bits (91), Expect = 3e-04
Identities = 15/88 (17%), Positives = 29/88 (32%), Gaps = 10/88 (11%)
Query: 211 GKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH----- 265
+ P+ + K+F+ L E F +FG + ++ D
Sbjct: 11 SSGLVPRGSH---MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSR 67
Query: 266 -IGFIEFIMPKHATHAVSTMNGHVFKSK 292
GF+ F+ ++ + H SK
Sbjct: 68 GFGFVTFMDQAGVDKVLA-QSRHELDSK 94
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein;
2.50A {Homo sapiens}
Length = 143
Score = 70.2 bits (172), Expect = 4e-15
Identities = 31/123 (25%), Positives = 52/123 (42%), Gaps = 20/123 (16%)
Query: 88 AKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKD-------KVFVKNLVE 140
EM I + EL+ G+ S+ ++ +++VKNL +
Sbjct: 3 LGSDSDEMPSECISRR-------ELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAK 55
Query: 141 TVDEEELKSHFIKFGNI------IEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGR 194
V E++LK F ++ + I I + G+ KG FI + KAA KA+ E NG
Sbjct: 56 HVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGY 115
Query: 195 MIQ 197
++
Sbjct: 116 VLF 118
Score = 64.5 bits (157), Expect = 5e-13
Identities = 23/131 (17%), Positives = 41/131 (31%), Gaps = 13/131 (9%)
Query: 183 AAEKAIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINN 242
EM I + + +P +I+V NL ++
Sbjct: 2 PLGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEP--NCRIYVKNLAKHVQE 59
Query: 243 SEFEELFARFGTITSSSLVSDKHI-----------GFIEFIMPKHATHAVSTMNGHVFKS 291
+ + +F R+ +S + I FI K A A+ NG+V
Sbjct: 60 KDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG 119
Query: 292 KPLKVTLSGTK 302
KP+ V + +
Sbjct: 120 KPMVVQFARSA 130
Score = 59.8 bits (145), Expect = 3e-11
Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 6/79 (7%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRD------VRVARNKNDESRGFAIIVFNTPAEAKK 90
++V NL V + L F ++ + K +G A I A K
Sbjct: 48 IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107
Query: 91 ARVEMNGHLIGSKPVIITF 109
A E NG+++ KP+++ F
Sbjct: 108 ALKEANGYVLFGKPMVVQF 126
>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 93
Score = 68.8 bits (169), Expect = 5e-15
Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+++ NL V ++L+ F + ++ G+ F+ + A +AI +
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETL 64
Query: 192 NGRM 195
+G++
Sbjct: 65 SGKV 68
Score = 63.0 bits (154), Expect = 6e-13
Identities = 15/76 (19%), Positives = 33/76 (43%), Gaps = 1/76 (1%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTM 284
+ NK+++ NL + + +LF + ++ F+++ A A+ T+
Sbjct: 5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETL 64
Query: 285 NGHV-FKSKPLKVTLS 299
+G V K ++V S
Sbjct: 65 SGKVELHGKIMEVDYS 80
Score = 49.2 bits (118), Expect = 4e-08
Identities = 20/104 (19%), Positives = 39/104 (37%), Gaps = 15/104 (14%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAII 80
G+ + NK+Y + NL P+V L F +V G+A +
Sbjct: 1 GSSGSSGMNKLY------IGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFV 49
Query: 81 VFNTPAEAKKARVEMNGHL-IGSKPVIITFVELKPGQRSKPVGP 123
+ A +A ++G + + K + V+ ++ + GP
Sbjct: 50 DYPDQNWAIRAIETLSGKVELHGKIME---VDYSVSKKLRSSGP 90
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 68.8 bits (169), Expect = 5e-15
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 6/78 (7%)
Query: 133 VFVKNLVETVDEEELKSH----FIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI 188
+++ NL E + ++ELK F +FG I+++ + R K +G F+ F +A A+
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS--LKMRGQAFVIFKEVSSATNAL 68
Query: 189 IEMNGRMIQHNSTFVSLA 206
M G + A
Sbjct: 69 RSMQGFPFYDKPMRIQYA 86
Score = 63.8 bits (156), Expect = 3e-13
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 6/77 (7%)
Query: 37 LHVNNLEPSVDNQALINE----FKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+++NNL + L F +FG + D+ V+R+ RG A ++F + A A
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK--MRGQAFVIFKEVSSATNAL 68
Query: 93 VEMNGHLIGSKPVIITF 109
M G KP+ I +
Sbjct: 69 RSMQGFPFYDKPMRIQY 85
Score = 56.9 bits (138), Expect = 1e-10
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 7/82 (8%)
Query: 228 KNKIFVANLPSNINNSEFEE----LFARFGTITSSSLVSDKHI---GFIEFIMPKHATHA 280
+ I++ NL I E ++ +F+RFG I + + F+ F AT+A
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 281 VSTMNGHVFKSKPLKVTLSGTK 302
+ +M G F KP+++ + T
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTD 89
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 68.6 bits (168), Expect = 6e-15
Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 3/75 (4%)
Query: 227 RKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG---FIEFIMPKHATHAVST 283
R K+ + N+P ++ + L ++G + S V+ + + A A+
Sbjct: 14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDK 73
Query: 284 MNGHVFKSKPLKVTL 298
+NG ++ LKV
Sbjct: 74 LNGFQLENFTLKVAY 88
Score = 64.8 bits (158), Expect = 1e-13
Identities = 15/91 (16%), Positives = 42/91 (46%), Gaps = 4/91 (4%)
Query: 117 RSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFI 176
S P+ ++ +K + ++N+ + E L S +++G + + V ++ +
Sbjct: 4 GSSGSVPKRQRIRK--LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS--ETAVVNV 59
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
+ S A +A+ ++NG +++ + V+
Sbjct: 60 TYSSKDQARQALDKLNGFQLENFTLKVAYIP 90
Score = 57.1 bits (138), Expect = 9e-11
Identities = 12/90 (13%), Positives = 39/90 (43%), Gaps = 2/90 (2%)
Query: 22 ARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIV 81
+ S+ K + +L + N+ P + + L + ++G + D +
Sbjct: 3 SGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT--DSETAVVNVT 60
Query: 82 FNTPAEAKKARVEMNGHLIGSKPVIITFVE 111
+++ +A++A ++NG + + + + ++
Sbjct: 61 YSSKDQARQALDKLNGFQLENFTLKVAYIP 90
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 68.4 bits (168), Expect = 8e-15
Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 5/70 (7%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAII- 189
K+FV L + +E L+S+F ++G +++ I++D +S+GFGF++F +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 190 ---EMNGRMI 196
++GR I
Sbjct: 78 RPHTLDGRNI 87
Score = 53.0 bits (128), Expect = 3e-09
Identities = 19/90 (21%), Positives = 39/90 (43%), Gaps = 5/90 (5%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESR 75
S +N +++ K L V L+ S + L + F ++G + D + ++K ++SR
Sbjct: 2 SSGSSGMNNSGADEIGK---LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSR 58
Query: 76 GFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
GF + F P + H + + +
Sbjct: 59 GFGFVKFKDPNCVGTV-LASRPHTLDGRNI 87
Score = 38.4 bits (90), Expect = 3e-04
Identities = 13/78 (16%), Positives = 27/78 (34%), Gaps = 7/78 (8%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI------GFIEFIMPKHAT 278
K+FV L + F+++G + ++ DK GF++F P
Sbjct: 13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVG 72
Query: 279 HAVSTMNGHVFKSKPLKV 296
++ H + +
Sbjct: 73 TVLA-SRPHTLDGRNIDP 89
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 68.4 bits (168), Expect = 9e-15
Identities = 23/97 (23%), Positives = 40/97 (41%), Gaps = 8/97 (8%)
Query: 113 KPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD--ENGKS 170
G + P+ Y F+ NL V EE +K F I V++ R+ +
Sbjct: 2 SSGSSGSRL-PKSPPYT---AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERL 56
Query: 171 KGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
KGFG+ +F + A + +N + + V +A+
Sbjct: 57 KGFGYAEFEDLDSLLSA-LSLNEESLGNKRIRVDVAD 92
Score = 45.7 bits (109), Expect = 1e-06
Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 4/86 (4%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE--SRGFAIIVFNTPAEAKKARVE 94
+ NL V +++ F+ + VR+ R ++ +GF F A +
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-LS 75
Query: 95 MNGHLIGSKPVIITFVELKPGQRSKP 120
+N +G+K + + + + S P
Sbjct: 76 LNEESLGNKRIRVDVADQAQDKDSGP 101
Score = 45.3 bits (108), Expect = 1e-06
Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 9/81 (11%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-------IGFIEFIMPKHATHAVS 282
F+ NLP ++ +E F I++ L + G+ EF A+
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL- 74
Query: 283 TMNGHVFKSKPLKVTLSGTKP 303
++N +K ++V ++
Sbjct: 75 SLNEESLGNKRIRVDVADQAQ 95
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; 2.00A {Homo sapiens} PDB:
2ek6_A
Length = 95
Score = 67.7 bits (166), Expect = 1e-14
Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 1/90 (1%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIE-VKIVRDENGKSKGFGFI 176
S G + + V+N+ TV +E+ F + I V + +E G G +
Sbjct: 3 SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
F S A A+I++N R I +S
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLSGP 92
Score = 56.5 bits (137), Expect = 1e-10
Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 6/92 (6%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRD-VRVARNKNDE 73
G S G+ S K V + V N+ +V +++ F + + V + N+
Sbjct: 1 GSSGSSGSSSGKPGPTV-----IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGM 55
Query: 74 SRGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
G A++ F + EA A +++N IGS+ V
Sbjct: 56 PTGEAMVAFESRDEATAAVIDLNDRPIGSRKV 87
Score = 46.9 bits (112), Expect = 3e-07
Identities = 17/86 (19%), Positives = 29/86 (33%), Gaps = 6/86 (6%)
Query: 220 PPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIM 273
I V N+P ++ E + F + I S + G + F
Sbjct: 7 GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66
Query: 274 PKHATHAVSTMNGHVFKSKPLKVTLS 299
AT AV +N S+ +K++
Sbjct: 67 RDEATAAVIDLNDRPIGSRKVKLSGP 92
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding
domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 98
Score = 67.7 bits (166), Expect = 1e-14
Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 1/90 (1%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIE-VKIVRDENGKSKGFGFI 176
S G + + V+N+ TV +E+ F + I V + +E G G +
Sbjct: 3 SGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
F S A A+I++N R I + L
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLVLG 92
Score = 58.8 bits (143), Expect = 2e-11
Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 6/92 (6%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRD-VRVARNKNDE 73
G S GA S K + + V N+ +V +++ F + + V + N+
Sbjct: 1 GSSGSSGASSGKPGPTI-----IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGM 55
Query: 74 SRGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
G A++ F + EA A +++N IGS+ V
Sbjct: 56 PTGEAMVAFESRDEATAAVIDLNDRPIGSRKV 87
Score = 47.3 bits (113), Expect = 2e-07
Identities = 18/86 (20%), Positives = 29/86 (33%), Gaps = 6/86 (6%)
Query: 220 PPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIM 273
I V N+P ++ E + F + I S + G + F
Sbjct: 7 GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66
Query: 274 PKHATHAVSTMNGHVFKSKPLKVTLS 299
AT AV +N S+ +K+ L
Sbjct: 67 RDEATAAVIDLNDRPIGSRKVKLVLG 92
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 66.8 bits (164), Expect = 2e-14
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+FV N+ +EL+S F + G +IE +V K + F+ A+ AI ++
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQL 63
Query: 192 NGRMIQ 197
NG+ ++
Sbjct: 64 NGKEVK 69
Score = 62.2 bits (152), Expect = 9e-13
Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 2/81 (2%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVST 283
KIFV N+ + + E LF R G + +V D F+ A A++
Sbjct: 5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--YAFVHMEKEADAKAAIAQ 62
Query: 284 MNGHVFKSKPLKVTLSGTKPG 304
+NG K K + V LS
Sbjct: 63 LNGKEVKGKRINVELSTKGQK 83
Score = 51.4 bits (124), Expect = 6e-09
Identities = 16/86 (18%), Positives = 35/86 (40%), Gaps = 7/86 (8%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
+ V N+ + +Q L + F++ G + + V + +A + A+AK A ++N
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLN 64
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVG 122
G + K + + + G
Sbjct: 65 GKEVKGKRINVELSTKGQKKSGPSSG 90
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 66.8 bits (164), Expect = 2e-14
Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIE 190
++V NLV + E++K F +FG + VK++ D E K KGFGF++ ++ +AI +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAK 61
Query: 191 MNG 193
++
Sbjct: 62 LDN 64
Score = 53.3 bits (129), Expect = 1e-09
Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 7/73 (9%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVST 283
I+V NL + + + +ELF++FG + + L+ D+ GF+E + + A++
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAK 61
Query: 284 MNGHVFKSKPLKV 296
++ F + ++V
Sbjct: 62 LDNTDFMGRTIRV 74
Score = 38.7 bits (91), Expect = 2e-04
Identities = 11/63 (17%), Positives = 30/63 (47%), Gaps = 2/63 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
++V NL S ++ + F +FG + +V++ ++ + +GF + +A ++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62
Query: 96 NGH 98
+
Sbjct: 63 DNT 65
>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 92
Score = 66.9 bits (164), Expect = 3e-14
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 7/66 (10%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+ V N+ T +EL++ F ++G +IE IV+ + F+ + A +AI +
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGL 64
Query: 192 NGRMIQ 197
+ Q
Sbjct: 65 DNTEFQ 70
Score = 63.8 bits (156), Expect = 3e-13
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 2/75 (2%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGHV 288
K+ V N+ N E F +G + +V D F+ + A A+ ++
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--YAFVHMERAEDAVEAIRGLDNTE 68
Query: 289 FKSKPLKVTLSGTKP 303
F+ K + V LS ++
Sbjct: 69 FQGKRMHVQLSTSRL 83
Score = 55.3 bits (134), Expect = 3e-10
Identities = 17/100 (17%), Positives = 39/100 (39%), Gaps = 13/100 (13%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAII 80
S K + K++ V N+ P+ NQ L +F+++G + + + + +A +
Sbjct: 3 SGSSGKASTKLH------VGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFV 49
Query: 81 VFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
+A +A ++ K + + + S P
Sbjct: 50 HMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTASGP 89
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 66.5 bits (163), Expect = 3e-14
Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 7/65 (10%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
K+F+ NL E+E++S F ++G ++E I+ K +GF+ AAE AI +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNL 62
Query: 192 NGRMI 196
+ +
Sbjct: 63 HHYKL 67
Score = 60.3 bits (147), Expect = 4e-12
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 2/74 (2%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGHVF 289
K+F+ NLP E LF ++G + ++ K+ GF+ A A+ ++ +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--KNYGFVHIEDKTAAEDAIRNLHHYKL 67
Query: 290 KSKPLKVTLSGTKP 303
+ V S K
Sbjct: 68 HGVNINVEASKNKS 81
Score = 53.4 bits (129), Expect = 1e-09
Identities = 13/103 (12%), Positives = 36/103 (34%), Gaps = 16/103 (15%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAII 80
G+ + K++ + NL Q + + F+++G + + + + + +
Sbjct: 1 GSSGSSGMVKLF------IGNLPREATEQEIRSLFEQYGKVLECDIIK-------NYGFV 47
Query: 81 VFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGP 123
A+ A ++ + + + VE + GP
Sbjct: 48 HIEDKTAAEDAIRNLHHYKLHGVNIN---VEASKNKSKASSGP 87
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 66.7 bits (163), Expect = 3e-14
Identities = 13/68 (19%), Positives = 30/68 (44%)
Query: 125 EKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAA 184
+ K V++K +++K G ++ +++ R + KG F+ F S ++A
Sbjct: 6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 65
Query: 185 EKAIIEMN 192
+K +
Sbjct: 66 KKFVETPG 73
Score = 55.5 bits (134), Expect = 4e-10
Identities = 18/97 (18%), Positives = 40/97 (41%), Gaps = 5/97 (5%)
Query: 33 KENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
K +++ + + G + ++++ R + +G +VF++ AKK
Sbjct: 10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF- 68
Query: 93 VEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYK 129
VE G ++I F + ++++ E KQ K
Sbjct: 69 VETPGQKYKETDLLILFKDDYFAKKNE----ERKQNK 101
Score = 45.9 bits (109), Expect = 9e-07
Identities = 11/76 (14%), Positives = 26/76 (34%), Gaps = 6/76 (7%)
Query: 226 ARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHATHA 280
+ +++ P++ + +E G + + + H F+ F + A
Sbjct: 9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF 68
Query: 281 VSTMNGHVFKSKPLKV 296
V G +K L +
Sbjct: 69 VE-TPGQKYKETDLLI 83
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 67.0 bits (164), Expect = 4e-14
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 8/66 (12%)
Query: 132 KVFVKNL-VETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIE 190
+VF+ NL V + ++++ F K+G + + KG+ F+Q+ + + A A++
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLG 81
Query: 191 MNGRMI 196
NGR++
Sbjct: 82 ENGRVL 87
Score = 58.2 bits (141), Expect = 4e-11
Identities = 19/78 (24%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 228 KNKIFVANLPSN-INNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNG 286
+++F+ NL + + S+ E +F+++G + S+ K F+++ +HA AV NG
Sbjct: 27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--KGYAFVQYSNERHARAAVLGENG 84
Query: 287 HVFKSKPLKVTLSGTKPG 304
V + L + ++G
Sbjct: 85 RVLAGQTLDINMAGEPKP 102
Score = 50.5 bits (121), Expect = 2e-08
Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 14/97 (14%)
Query: 25 NKENNKVYKENELHVNNLEPS-VDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFN 83
N++V+ + NL + V + F K+G + V +G+A + ++
Sbjct: 24 KSINSRVF------IGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYS 70
Query: 84 TPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
A+ A + NG ++ + + I RS P
Sbjct: 71 NERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSGP 107
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 66.1 bits (162), Expect = 5e-14
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 132 KVFVKNL-VETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIE 190
++F+ NL ++ V +E+L F +G+I+++ I FGFIQF + ++ AI
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDNPQSVRDAIEC 64
Query: 191 MNGRMI 196
+ M
Sbjct: 65 ESQEMN 70
Score = 56.8 bits (138), Expect = 9e-11
Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 228 KNKIFVANLPS-NINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNG 286
K+++F+ NLP N++ + +F+ +G I ++ GFI+F P+ A+ +
Sbjct: 10 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIECESQ 67
Query: 287 HVFKSKPLKVTLSGTKP 303
+ K L + +S +
Sbjct: 68 EMNFGKKLILEVSSSNA 84
Score = 45.3 bits (108), Expect = 1e-06
Identities = 15/97 (15%), Positives = 34/97 (35%), Gaps = 18/97 (18%)
Query: 26 KENNKVYKENELHVNNLEP-SVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNT 84
++++ + NL +V + L F +G + + + F I F+
Sbjct: 8 PPKSRLF------IGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQFDN 54
Query: 85 PAEAKKARVEMNGHLIGSKPVIITFVEL-KPGQRSKP 120
P + A + + K +I +E+ R +
Sbjct: 55 PQSVRDAIECESQEMNFGKKLI---LEVSSSNARPQF 88
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein
biosynthesis, RNA recognition motif, RNA binding domain,
RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 66.1 bits (162), Expect = 5e-14
Identities = 22/97 (22%), Positives = 39/97 (40%), Gaps = 7/97 (7%)
Query: 113 KPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD--ENGKS 170
+ P+ Y F+ NL V EE +K F I V++ R+ +
Sbjct: 5 HHHHHHRSRLPKSPPYT---AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERL 60
Query: 171 KGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
KGFG+ +F + A + +N + + V +A+
Sbjct: 61 KGFGYAEFEDLDSLLSA-LSLNEESLGNRRIRVDVAD 96
Score = 43.0 bits (102), Expect = 8e-06
Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 4/71 (5%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE--SRGFAIIVFNTPAEAKKARVE 94
+ NL V +++ F+ + VR+ R ++ +GF F A +
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA-LS 79
Query: 95 MNGHLIGSKPV 105
+N +G++ +
Sbjct: 80 LNEESLGNRRI 90
Score = 42.2 bits (100), Expect = 2e-05
Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 9/77 (11%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-------IGFIEFIMPKHATHAVS 282
F+ NLP ++ +E F I++ L + G+ EF A+S
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 283 TMNGHVFKSKPLKVTLS 299
+N ++ ++V ++
Sbjct: 80 -LNEESLGNRRIRVDVA 95
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 66.3 bits (162), Expect = 6e-14
Identities = 15/91 (16%), Positives = 34/91 (37%), Gaps = 2/91 (2%)
Query: 117 RSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIE-VKIVRDENGKSKGFGF 175
S G + K + N+ ++ + ++ V ++ D NG+ G
Sbjct: 2 SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61
Query: 176 IQFFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
+QF + A K+ ++ + + FV +
Sbjct: 62 VQFKNEDDARKS-ERLHRKKLNGREAFVHVV 91
Score = 55.5 bits (134), Expect = 5e-10
Identities = 16/105 (15%), Positives = 43/105 (40%), Gaps = 2/105 (1%)
Query: 24 SNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRD-VRVARNKNDESRGFAIIVF 82
S+ E + + H+ N+ S+ ++ + + V V + N + G A++ F
Sbjct: 5 SSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQF 64
Query: 83 NTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQ 127
+A+K+ ++ + + + V L+ + + P + +
Sbjct: 65 KNEDDARKS-ERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGK 108
Score = 40.5 bits (95), Expect = 7e-05
Identities = 8/78 (10%), Positives = 25/78 (32%), Gaps = 7/78 (8%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSS-SLVSDKH-----IGFIEFIMPKHATHAV 281
K + N+P +I + + ++ ++ D + ++F A +
Sbjct: 15 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE 74
Query: 282 STMNGHVFKSKPLKVTLS 299
++ + V +
Sbjct: 75 R-LHRKKLNGREAFVHVV 91
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 66.4 bits (162), Expect = 6e-14
Identities = 20/98 (20%), Positives = 34/98 (34%), Gaps = 5/98 (5%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+ KNL E++ F +FG++ V + + ++F A KA +
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLL-----PEGGITAIVEFLEPLEARKAFRHLA 67
Query: 193 GRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNK 230
H ++ A I K QPA K +
Sbjct: 68 YSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAE 105
Score = 65.2 bits (159), Expect = 1e-13
Identities = 20/69 (28%), Positives = 30/69 (43%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGH 287
K I NLP+ +E +E F+RFG++ L +EF+ P A A +
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS 69
Query: 288 VFKSKPLKV 296
F PL +
Sbjct: 70 KFHHVPLYL 78
Score = 52.5 bits (126), Expect = 4e-09
Identities = 18/96 (18%), Positives = 34/96 (35%), Gaps = 5/96 (5%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
+ NL + F +FG+L V + E AI+ F P EA+KA +
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLA 67
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDK 132
P+ + + + + + + +K
Sbjct: 68 YSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEK 103
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 65.0 bits (159), Expect = 1e-13
Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 132 KVFVKNL-VETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIE 190
++F+ NL ++ V +E+L F +G+I+++ I FGFIQF + ++ AI
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEX 76
Query: 191 MNGRMI 196
+ M
Sbjct: 77 ESQEMN 82
Score = 58.5 bits (142), Expect = 3e-11
Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 228 KNKIFVANLPS-NINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNG 286
K+++F+ NLP N++ + +F+ +G I ++ GFI+F P+ A+ +
Sbjct: 22 KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--NAFGFIQFDNPQSVRDAIEXESQ 79
Query: 287 HVFKSKPLKVTLSGTKP 303
+ K L + +S +
Sbjct: 80 EMNFGKKLILEVSSSNA 96
Score = 44.6 bits (106), Expect = 2e-06
Identities = 14/88 (15%), Positives = 32/88 (36%), Gaps = 14/88 (15%)
Query: 23 RSNKENNKVYKENELHVNNL-EPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIV 81
R + ++++ + NL +V + L F +G + + + F I
Sbjct: 17 RGSHMKSRLF------IGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-------AFGFIQ 63
Query: 82 FNTPAEAKKARVEMNGHLIGSKPVIITF 109
F+ P + A + + K +I+
Sbjct: 64 FDNPQSVRDAIEXESQEMNFGKKLILEV 91
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions,
RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus
musculus}
Length = 89
Score = 64.6 bits (158), Expect = 1e-13
Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 7/78 (8%)
Query: 122 GPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSY 181
G + KVFV E + EEL+ F ++G +++V I + + F F+ F
Sbjct: 3 GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADD 58
Query: 182 KAAEKAIIEM---NGRMI 196
K A+ E G +
Sbjct: 59 KVAQSLCGEDLIIKGISV 76
Score = 43.4 bits (103), Expect = 5e-06
Identities = 11/74 (14%), Positives = 26/74 (35%), Gaps = 3/74 (4%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD-KHIGFIEFIMPKHATHAVS 282
+K+FV ++ E ++ F ++G + + + F+ F K A
Sbjct: 7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLC- 65
Query: 283 TMNGHVFKSKPLKV 296
+ K + +
Sbjct: 66 -GEDLIIKGISVHI 78
Score = 40.7 bits (96), Expect = 4e-05
Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 9/82 (10%)
Query: 24 SNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFN 83
S+ ++ K + V + + L F ++G + DV + + R FA + F
Sbjct: 4 SHHHHHHGSK---VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK----PFRAFAFVTFA 56
Query: 84 TPAEAKKARVEMNGHLIGSKPV 105
A+ + +I V
Sbjct: 57 DDKVAQ--SLCGEDLIIKGISV 76
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 64.2 bits (157), Expect = 2e-13
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 7/68 (10%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
VFV + E+EL+ F ++G++++V I + + F F+ F + A+ E
Sbjct: 7 GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGED 62
Query: 192 ---NGRMI 196
G +
Sbjct: 63 LIIKGISV 70
Score = 42.6 bits (101), Expect = 8e-06
Identities = 10/69 (14%), Positives = 25/69 (36%), Gaps = 3/69 (4%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSD-KHIGFIEFIMPKHATHAVSTMNGH 287
+ +FV ++ E E F+++G + + + F+ F + A
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLC--GEDL 63
Query: 288 VFKSKPLKV 296
+ K + +
Sbjct: 64 IIKGISVHI 72
Score = 41.8 bits (99), Expect = 2e-05
Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 6/88 (6%)
Query: 33 KENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+ + V + L F ++G + DV + + R FA + F A+
Sbjct: 4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQS-- 57
Query: 93 VEMNGHLIGSKPVIITFVELKPGQRSKP 120
+ +I V I+ E K S P
Sbjct: 58 LCGEDLIIKGISVHISNAEPKHNSNSGP 85
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 65.2 bits (159), Expect = 3e-13
Identities = 15/86 (17%), Positives = 34/86 (39%), Gaps = 2/86 (2%)
Query: 113 KPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKG 172
+ G+ S + V ++ L E ++ + F + V I +G+ G
Sbjct: 29 QMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTG 87
Query: 173 FGFIQFFSYKAAEKAIIEMNGRMIQH 198
++F +++ A A + + +QH
Sbjct: 88 EADVEFATHEEAVAA-MSKDRANMQH 112
Score = 51.8 bits (124), Expect = 2e-08
Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 2/96 (2%)
Query: 10 ASWDEGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARN 69
AS G G+ ++ + + +H+ L + N F +R V +
Sbjct: 22 ASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VHIEIG 80
Query: 70 KNDESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
+ G A + F T EA A + + + + +
Sbjct: 81 PDGRVTGEADVEFATHEEAVAA-MSKDRANMQHRYI 115
Score = 36.7 bits (85), Expect = 0.003
Identities = 13/118 (11%), Positives = 37/118 (31%), Gaps = 8/118 (6%)
Query: 191 MNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINNSEFEELFA 250
+ ++ S S+ + + + Q + + + LP ++ F+
Sbjct: 10 HSSGLVPRGSHMASMTGGQQMGRGSGDSEFTV-QSTTGHCVHMRGLPYKATENDIYNFFS 68
Query: 251 RFGTITSSSLVSDKH-----IGFIEFIMPKHATHAVSTMNGHVFKSKPLKVTLSGTKP 303
+ +EF + A A+S + + + +++ L+ T
Sbjct: 69 PLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMS-KDRANMQHRYIELFLNSTTG 124
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 64.2 bits (157), Expect = 3e-13
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 3/78 (3%)
Query: 131 DKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAII 189
+V NL + ++ + F I V++VRD + K KGF +++F + ++A +
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA-L 73
Query: 190 EMNGRMIQHNSTFVSLAE 207
+G ++ S V +AE
Sbjct: 74 TYDGALLGDRSLRVDIAE 91
Score = 44.2 bits (105), Expect = 4e-06
Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 3/85 (3%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKN-DESRGFAIIVFNTPAEAKKARVEM 95
+V NL + + FK +R VR+ R+K+ D+ +GF + F+ K+A +
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA-LTY 75
Query: 96 NGHLIGSKPVIITFVELKPGQRSKP 120
+G L+G + + + E + +S P
Sbjct: 76 DGALLGDRSLRVDIAEGRKQDKSGP 100
Score = 43.8 bits (104), Expect = 4e-06
Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 8/81 (9%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH------IGFIEFIMPKHATHAVS 282
+V NLP N + + +F I S LV DK ++EF A+
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL- 73
Query: 283 TMNGHVFKSKPLKVTLSGTKP 303
T +G + + L+V ++ +
Sbjct: 74 TYDGALLGDRSLRVDIAEGRK 94
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 64.0 bits (156), Expect = 3e-13
Identities = 18/93 (19%), Positives = 37/93 (39%), Gaps = 2/93 (2%)
Query: 115 GQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFG 174
G P V V + + E +++ F + V +++D G++ G G
Sbjct: 1 GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNG 59
Query: 175 FIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
++F S + +A ++ N ++ VS A
Sbjct: 60 LVKFLSPQDTFEA-LKRNRMLMIQRYVEVSPAT 91
Score = 47.1 bits (112), Expect = 4e-07
Identities = 11/69 (15%), Positives = 30/69 (43%), Gaps = 2/69 (2%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
+ V+ + S + + F + V + ++ + G ++ F +P + +A ++ N
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTFEA-LKRN 76
Query: 97 GHLIGSKPV 105
L+ + V
Sbjct: 77 RMLMIQRYV 85
Score = 37.4 bits (87), Expect = 0.001
Identities = 13/85 (15%), Positives = 33/85 (38%), Gaps = 7/85 (8%)
Query: 220 PPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMP 274
PL + V +P + ++ + F + + L+ D G ++F+ P
Sbjct: 8 KPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSP 66
Query: 275 KHATHAVSTMNGHVFKSKPLKVTLS 299
+ A+ N + + ++V+ +
Sbjct: 67 QDTFEALK-RNRMLMIQRYVEVSPA 90
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 63.0 bits (153), Expect = 8e-13
Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 7/85 (8%)
Query: 129 KKDKVFVKNLVETVDEEEL---KSHFIKFGNIIEVKIVRDENGK----SKGFGFIQFFSY 181
+K+ VFV L + + + E+ +F KFG I +V I + ++ +
Sbjct: 14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73
Query: 182 KAAEKAIIEMNGRMIQHNSTFVSLA 206
+ A +AI +N ++ + SL
Sbjct: 74 EDALRAIQCVNNVVVDGRTLKASLG 98
Score = 54.5 bits (131), Expect = 1e-09
Identities = 21/87 (24%), Positives = 35/87 (40%), Gaps = 12/87 (13%)
Query: 228 KNKIFVANLPSNINNSEF---EELFARFGTITSSSLVSDKHI---------GFIEFIMPK 275
KN +FV L + + E E F +FG I + + ++ +I +
Sbjct: 15 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74
Query: 276 HATHAVSTMNGHVFKSKPLKVTLSGTK 302
A A+ +N V + LK +L TK
Sbjct: 75 DALRAIQCVNNVVVDGRTLKASLGTTK 101
Score = 54.1 bits (130), Expect = 1e-09
Identities = 14/91 (15%), Positives = 38/91 (41%), Gaps = 7/91 (7%)
Query: 22 ARSNKENNKVYKENELHVNNLEPSVDNQALINE---FKKFGTLRDVRVARNKNDE----S 74
+ S+ + +V ++N + V L + + ++ F KFG + V + + +
Sbjct: 3 SGSSGASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGP 62
Query: 75 RGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
A + + +A +A +N ++ + +
Sbjct: 63 SASAYVTYIRSEDALRAIQCVNNVVVDGRTL 93
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 61.7 bits (150), Expect = 1e-12
Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 1/75 (1%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGH 287
+ I V NLP + N E +L + + + +K F+ + + A +A+ + +
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQY 63
Query: 288 VFKSKPLKVTLSGTK 302
F+ K L V L T
Sbjct: 64 SFRGKDLIVQLQPTD 78
Score = 54.7 bits (132), Expect = 4e-10
Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 6/76 (7%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+ VKNL + + +E+ + +K ++K F+ + + A+ AI
Sbjct: 7 GILVKNLPQDSNCQEVHDLLKDYD----LKYC--YVDRNKRTAFVTLLNGEQAQNAIQMF 60
Query: 192 NGRMIQHNSTFVSLAE 207
+ + V L
Sbjct: 61 HQYSFRGKDLIVQLQP 76
Score = 47.0 bits (112), Expect = 2e-07
Identities = 20/89 (22%), Positives = 35/89 (39%), Gaps = 9/89 (10%)
Query: 35 NELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVE 94
+ + V NL + Q + + K + L+ V RNK A + +A+ A
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNK-----RTAFVTLLNGEQAQNAIQM 59
Query: 95 MNGHLIGSKPVIITFVELKPGQRSKPVGP 123
+ + K +I V+L+P GP
Sbjct: 60 FHQYSFRGKDLI---VQLQPTDALLCSGP 85
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 108
Score = 61.4 bits (149), Expect = 3e-12
Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 8/83 (9%)
Query: 115 GQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFG 174
S P + +++V V L + ++LK H + G++ + RD G G
Sbjct: 2 SSGSSGGPPSRRS--ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTG 53
Query: 175 FIQFFSYKAAEKAIIEMNGRMIQ 197
++F + A+ +++ +
Sbjct: 54 VVEFVRKEDMTYAVRKLDNTKFR 76
Score = 54.8 bits (132), Expect = 8e-10
Identities = 14/69 (20%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGH 287
+N++ V+ LP + + + ++ G + + + D G +EF+ + T+AV ++
Sbjct: 15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNT 73
Query: 288 VFKSKPLKV 296
F+S +
Sbjct: 74 KFRSHEGET 82
Score = 51.3 bits (123), Expect = 1e-08
Identities = 18/100 (18%), Positives = 36/100 (36%), Gaps = 6/100 (6%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAII 80
+ S+ EN + V+ L PS Q L + ++ G + V R+ G ++
Sbjct: 2 SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVV 55
Query: 81 VFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
F + A +++ S ++ +K P
Sbjct: 56 EFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSP 95
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 60.5 bits (147), Expect = 5e-12
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 134 FVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+ + V ++ L S F K G ++ ++ D GK+KGF F++ S A+K I +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 193 GRMIQHNSTF 202
G+ +
Sbjct: 76 GKRLDLKHRL 85
Score = 50.1 bits (120), Expect = 3e-08
Identities = 13/80 (16%), Positives = 34/80 (42%), Gaps = 1/80 (1%)
Query: 28 NNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND-ESRGFAIIVFNTPA 86
+ + + + + V +AL + F K G + ++ ++ +++GF + +
Sbjct: 6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMN 65
Query: 87 EAKKARVEMNGHLIGSKPVI 106
+AKK +G + K +
Sbjct: 66 DAKKIIKSFHGKRLDLKHRL 85
Score = 41.6 bits (98), Expect = 2e-05
Identities = 14/82 (17%), Positives = 26/82 (31%), Gaps = 15/82 (18%)
Query: 229 NKIFVANLPSNINNSEFE-------ELFARFGTITSSSLVSD------KHIGFIEFIMPK 275
I V P I +++ LF++ G + + D K F+E
Sbjct: 7 QYIVVNGAPV-IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMN 65
Query: 276 HATHAVSTMNGHVF-KSKPLKV 296
A + + +G L +
Sbjct: 66 DAKKIIKSFHGKRLDLKHRLFL 87
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kg0_A
Length = 126
Score = 61.4 bits (149), Expect = 5e-12
Identities = 22/94 (23%), Positives = 35/94 (37%), Gaps = 2/94 (2%)
Query: 114 PGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIE-VKIVRDENGKSKG 172
GQ+ V ++ L +EE+ F + + + D GK G
Sbjct: 26 GGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITG 85
Query: 173 FGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
F+QF S + AEKA + + I H V +
Sbjct: 86 EAFVQFASQELAEKA-LGKHKERIGHRYIEVFKS 118
Score = 48.0 bits (114), Expect = 3e-07
Identities = 10/70 (14%), Positives = 26/70 (37%), Gaps = 2/70 (2%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGT-LRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEM 95
+ + L + ++ F + + + + G A + F + A+KA +
Sbjct: 45 VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKA-LGK 103
Query: 96 NGHLIGSKPV 105
+ IG + +
Sbjct: 104 HKERIGHRYI 113
Score = 39.5 bits (92), Expect = 2e-04
Identities = 12/87 (13%), Positives = 27/87 (31%), Gaps = 7/87 (8%)
Query: 219 KPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFI 272
A + + LP E + F+ + + + G F++F
Sbjct: 33 GSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFA 92
Query: 273 MPKHATHAVSTMNGHVFKSKPLKVTLS 299
+ A A+ + + ++V S
Sbjct: 93 SQELAEKALG-KHKERIGHRYIEVFKS 118
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 60.6 bits (147), Expect = 6e-12
Identities = 13/68 (19%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 130 KDKVFVKNLVETVDEEELKSHFIKFG-NIIEVKIVRD--ENGKSKGFGFIQFFSYKAAEK 186
++F+ + + EE+ K +++V + + K++GF F+++ S++AA
Sbjct: 8 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 67
Query: 187 AIIEMNGR 194
A ++
Sbjct: 68 ARRKLMPG 75
Score = 48.3 bits (115), Expect = 1e-07
Identities = 16/98 (16%), Positives = 37/98 (37%), Gaps = 9/98 (9%)
Query: 35 NELHVNNLEPSVDNQALINEFKKFGT-LRDVRVARNKND--ESRGFAIIVFNTPAEAKKA 91
L + + + ++ E K + DV V + D ++RGFA + + + A A
Sbjct: 9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68
Query: 92 RVEMNGH--LIGSKPVIITF----VELKPGQRSKPVGP 123
R ++ + + + + +++ GP
Sbjct: 69 RRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGP 106
Score = 46.7 bits (111), Expect = 6e-07
Identities = 13/97 (13%), Positives = 30/97 (30%), Gaps = 15/97 (15%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGT-ITSSSLVSD-------KHIGFIEFIMPKHATH 279
++F+ +P E E A+ + + + + F+E+ + A
Sbjct: 8 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 67
Query: 280 AVSTMNGHVFKSKPLKVTLSGTKPGVSITNPTKAPKK 316
A + ++ L G + V P +
Sbjct: 68 ARRKLMPG-------RIQLWGHQIAVDWAEPEIDVDE 97
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 60.2 bits (146), Expect = 6e-12
Identities = 19/94 (20%), Positives = 34/94 (36%), Gaps = 4/94 (4%)
Query: 114 PGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGF 173
G P E V+V NL +LK + G +R +
Sbjct: 3 SGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELG----SVPLRLTWQGPRRR 58
Query: 174 GFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLAE 207
F+ + AA++A+ + G + ++ V+LA
Sbjct: 59 AFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 92
Score = 56.8 bits (137), Expect = 1e-10
Identities = 17/85 (20%), Positives = 32/85 (37%), Gaps = 1/85 (1%)
Query: 216 PKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSS-SLVSDKHIGFIEFIMP 274
PP ++V NLP + S+ + G++ + + F+ +
Sbjct: 7 GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDS 66
Query: 275 KHATHAVSTMNGHVFKSKPLKVTLS 299
A AVS + G + L+V L+
Sbjct: 67 AAAQQAVSCLQGLRLGTDTLRVALA 91
Score = 49.4 bits (118), Expect = 4e-08
Identities = 20/98 (20%), Positives = 32/98 (32%), Gaps = 13/98 (13%)
Query: 22 ARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIV 81
VY V NL L ++ G++ R R A +
Sbjct: 13 GEGAPLAADVY------VGNLPRDARVSDLKRALRELGSV----PLRLTWQGPRRRAFLH 62
Query: 82 FNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSK 119
+ A A++A + G +G+ + V L QR K
Sbjct: 63 YPDSAAAQQAVSCLQGLRLGTDTLR---VALARQQRDK 97
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 61.0 bits (148), Expect = 6e-12
Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 5/95 (5%)
Query: 113 KPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIE-VKIVRDENGKSK 171
+RS+ P E + V++K L + + + F K + + + I NGK+
Sbjct: 11 SGQKRSRSRSPHEAGFC---VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT 67
Query: 172 GFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSLA 206
G GF++F + + A + + + + + V
Sbjct: 68 GEGFVEFRNEADYKAA-LCRHKQYMGNRFIQVHPI 101
Score = 51.4 bits (123), Expect = 2e-08
Identities = 16/90 (17%), Positives = 40/90 (44%), Gaps = 2/90 (2%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRD-VRVARNKNDESR 75
G + ++ + +++ L +N+ +I+ FKK + D + +A N ++
Sbjct: 8 KSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT 67
Query: 76 GFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
G + F A+ K A + + +G++ +
Sbjct: 68 GEGFVEFRNEADYKAA-LCRHKQYMGNRFI 96
Score = 38.7 bits (90), Expect = 4e-04
Identities = 12/90 (13%), Positives = 27/90 (30%), Gaps = 7/90 (7%)
Query: 216 PKVKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSS-SLVSDKH-----IGFI 269
K +++ LP N + F + + S + + GF+
Sbjct: 13 QKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFV 72
Query: 270 EFIMPKHATHAVSTMNGHVFKSKPLKVTLS 299
EF A+ + ++ ++V
Sbjct: 73 EFRNEADYKAALC-RHKQYMGNRFIQVHPI 101
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 60.0 bits (146), Expect = 6e-12
Identities = 14/83 (16%), Positives = 33/83 (39%), Gaps = 2/83 (2%)
Query: 130 KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAII 189
V ++ V E+ + + ++IVR+ +G G+ F+ F + + ++A +
Sbjct: 10 CHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQA-L 67
Query: 190 EMNGRMIQHNSTFVSLAEIVPGK 212
+ N + V + P
Sbjct: 68 KCNREYMGGRYIEVFREKSGPSS 90
Score = 45.8 bits (109), Expect = 7e-07
Identities = 11/69 (15%), Positives = 29/69 (42%), Gaps = 2/69 (2%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
+ + +V + ++ +R+ RN + G+ + F+ E K+A ++ N
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQA-LKCN 70
Query: 97 GHLIGSKPV 105
+G + +
Sbjct: 71 REYMGGRYI 79
Score = 38.8 bits (91), Expect = 2e-04
Identities = 12/85 (14%), Positives = 27/85 (31%), Gaps = 7/85 (8%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHAT 278
+ + + P N+ E A + +V + H F++F +
Sbjct: 6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVK 64
Query: 279 HAVSTMNGHVFKSKPLKVTLSGTKP 303
A+ N + ++V + P
Sbjct: 65 QALK-CNREYMGGRYIEVFREKSGP 88
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 60.0 bits (146), Expect = 7e-12
Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 8/69 (11%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI--- 188
VFV VD +L +F+ FG + V + +D F ++ A E +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD----KGVFAIVEMGDVGAREAVLSQS 65
Query: 189 -IEMNGRMI 196
+ G +
Sbjct: 66 QHSLGGHRL 74
Score = 49.2 bits (118), Expect = 4e-08
Identities = 17/68 (25%), Positives = 30/68 (44%), Gaps = 2/68 (2%)
Query: 230 KIFVANLPSNINNSEFEELFARFGTITSSSLVSDK-HIGFIEFIMPKHATHAVSTMNGHV 288
+FV+ P +++++ E F FG + S + DK +E A AV + + H
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEM-GDVGAREAVLSQSQHS 68
Query: 289 FKSKPLKV 296
L+V
Sbjct: 69 LGGHRLRV 76
Score = 48.1 bits (115), Expect = 1e-07
Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 5/88 (5%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
+ V+ VD+ L F FG + V + ++K FAI+ + + +
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKG----VFAIVEMGDVGAREAV-LSQS 65
Query: 97 GHLIGSKPVIITFVELKPGQRSKPVGPE 124
H +G + + E K Q P+
Sbjct: 66 QHSLGGHRLRVRPREQKEFQSPASKSPK 93
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 59.9 bits (145), Expect = 1e-11
Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 2/86 (2%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVS--TMNGHV 288
I + LP ++ E L FG +T+ ++ K+ FIE + A V+ T V
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPV 78
Query: 289 FKSKPLKVTLSGTKPGVSITNPTKAP 314
+ +P+ + S K + ++P +A
Sbjct: 79 LRGQPIYIQFSNHKELKTDSSPNQAR 104
Score = 53.3 bits (128), Expect = 2e-09
Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI--IE 190
+ ++ L V E E+ S + FG + + +++ K FI+ + +AA +
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73
Query: 191 MNGRMIQHNSTFVSLA 206
+++ ++ +
Sbjct: 74 SVTPVLRGQPIYIQFS 89
Score = 44.5 bits (105), Expect = 3e-06
Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 12/89 (13%)
Query: 23 RSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVF 82
+ ++V +H+ L V +I+ FG + ++ + + KN A I
Sbjct: 10 HGSGVPSRV-----IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN-----QAFIEM 59
Query: 83 NTPAEAKKA--RVEMNGHLIGSKPVIITF 109
NT A ++ +P+ I F
Sbjct: 60 NTEEAANTMVNYYTSVTPVLRGQPIYIQF 88
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 59.3 bits (144), Expect = 1e-11
Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
V ++ L E ++ + F N + V I +G+ G ++F +++ A A + +
Sbjct: 18 VHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEADVEFATHEDAVAA-MAKD 75
Query: 193 GRMIQH 198
+QH
Sbjct: 76 KANMQH 81
Score = 50.1 bits (120), Expect = 3e-08
Identities = 18/106 (16%), Positives = 32/106 (30%), Gaps = 7/106 (6%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDES 74
G S G+ +H+ L + N F +R V + +
Sbjct: 1 GSSGSSGSSFQSTTGHC-----VHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPDGRV 54
Query: 75 RGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
G A + F T +A A + + + + V + S P
Sbjct: 55 TGEADVEFATHEDAVAA-MAKDKANMQHRYVELFLNSTAGTSGSGP 99
Score = 35.1 bits (81), Expect = 0.005
Identities = 10/86 (11%), Positives = 28/86 (32%), Gaps = 7/86 (8%)
Query: 223 LQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHA 277
Q + + + LP ++ F+ + +EF + A
Sbjct: 10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDA 68
Query: 278 THAVSTMNGHVFKSKPLKVTLSGTKP 303
A++ + + + +++ L+ T
Sbjct: 69 VAAMA-KDKANMQHRYVELFLNSTAG 93
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 59.9 bits (145), Expect = 1e-11
Identities = 16/80 (20%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 132 KVFVKNLVETVDEEELKSH----FIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKA 187
V + N+ V +E+L++ G+I+++ + D + + G +I F + ++A+
Sbjct: 31 VVLITNINPEVPKEKLQALLYALASSQGDILDIVV--DLSDDNSGKAYIVFATQESAQAF 88
Query: 188 IIEMNGRMIQHNSTFVSLAE 207
+ G Q N ++ +E
Sbjct: 89 VEAFQGYPFQGNPLVITFSE 108
Score = 57.2 bits (138), Expect = 2e-10
Identities = 22/97 (22%), Positives = 37/97 (38%), Gaps = 6/97 (6%)
Query: 37 LHVNNLEPSVDN----QALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKAR 92
+ + N+ P V L G + D+ V + ++ G A IVF T A+
Sbjct: 32 VLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSD--DNSGKAYIVFATQESAQAFV 89
Query: 93 VEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYK 129
G+ P++ITF E Q ++ E +
Sbjct: 90 EAFQGYPFQGNPLVITFSETPQSQVAEDGSLEHHHHH 126
Score = 51.4 bits (123), Expect = 1e-08
Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 7/81 (8%)
Query: 229 NKIFVANLPSNINNSE----FEELFARFGTITSSSLVSD---KHIGFIEFIMPKHATHAV 281
+ + N+ + + L + G I + +I F + A V
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFV 89
Query: 282 STMNGHVFKSKPLKVTLSGTK 302
G+ F+ PL +T S T
Sbjct: 90 EAFQGYPFQGNPLVITFSETP 110
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 59.4 bits (144), Expect = 2e-11
Identities = 13/66 (19%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEM 191
+V V L + ++LK H + G++ + RD G G ++F + A+ ++
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKL 71
Query: 192 NGRMIQ 197
+ +
Sbjct: 72 DNTKFR 77
Score = 53.3 bits (128), Expect = 3e-09
Identities = 14/70 (20%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 228 KNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGH 287
+N++ V+ LP + + + ++ G + + + D G +EF+ + T+AV ++
Sbjct: 16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-GTGVVEFVRKEDMTYAVRKLDNT 74
Query: 288 VFKSKPLKVT 297
F+S +
Sbjct: 75 KFRSHEGETA 84
Score = 51.0 bits (122), Expect = 2e-08
Identities = 19/110 (17%), Positives = 37/110 (33%), Gaps = 12/110 (10%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRG 76
G S + N+V V+ L PS Q L + ++ G + V R+ G
Sbjct: 5 RGRYGPPSRRSENRVV------VSGLPPSGSWQDLKDHMREAGDVCYADVYRD------G 52
Query: 77 FAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEK 126
++ F + A +++ S ++ +K P +
Sbjct: 53 TGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSR 102
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 59.2 bits (143), Expect = 3e-11
Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 2/85 (2%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVS--TMNGHV 288
I + LP ++ E L FG +T+ ++ K+ FIE + A V+ T V
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPV 93
Query: 289 FKSKPLKVTLSGTKPGVSITNPTKA 313
+ +P+ + S K + ++P +A
Sbjct: 94 LRGQPIYIQFSNHKELKTDSSPNQA 118
Score = 52.6 bits (126), Expect = 5e-09
Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI--IE 190
+ ++ L V E E+ S + FG + + +++ K FI+ + +AA +
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 88
Query: 191 MNGRMIQHNSTFVSLA 206
+++ ++ +
Sbjct: 89 SVTPVLRGQPIYIQFS 104
Score = 45.7 bits (108), Expect = 2e-06
Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 12/95 (12%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRG 76
S +RS ++V +H+ L V +I+ FG + ++ + + KN
Sbjct: 19 SHMGDSRSAGVPSRV-----IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN----- 68
Query: 77 FAIIVFNTPAEAKKA--RVEMNGHLIGSKPVIITF 109
A I NT A ++ +P+ I F
Sbjct: 69 QAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF 103
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 58.7 bits (142), Expect = 3e-11
Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 2/83 (2%)
Query: 115 GQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFG 174
G + + K+ ++ +KNL E ++LK + +E G G
Sbjct: 13 GLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENS--LETTFSSVNTRDFDGTG 70
Query: 175 FIQFFSYKAAEKAIIEMNGRMIQ 197
++F S + +A+ +N +
Sbjct: 71 ALEFPSEEILVEALERLNNIEFR 93
Score = 51.8 bits (124), Expect = 9e-09
Identities = 11/95 (11%), Positives = 27/95 (28%), Gaps = 2/95 (2%)
Query: 13 DEGISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKND 72
S R + + K + + NL Q L + ++ + +
Sbjct: 7 HHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSL--ETTFSSVNTR 64
Query: 73 ESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVII 107
+ G + F + +A +N + +
Sbjct: 65 DFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99
Score = 51.4 bits (123), Expect = 1e-08
Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 3/75 (4%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD---KHIGFIEFIMPKHATHAV 281
PA++ +I + NLP + + ++L T+ S V+ G +EF + A+
Sbjct: 25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEAL 84
Query: 282 STMNGHVFKSKPLKV 296
+N F+ + V
Sbjct: 85 ERLNNIEFRGSVITV 99
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 62.6 bits (151), Expect = 4e-11
Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 1/76 (1%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRD-ENGKSKGFGFIQFFSYKAAEKAIIEM 191
+FV + E +L+ F +G I + +V +GK +G+ FI++ + A
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 192 NGRMIQHNSTFVSLAE 207
+G+ I V +
Sbjct: 165 DGKKIDGRRVLVDVER 180
Score = 56.0 bits (134), Expect = 6e-09
Identities = 19/141 (13%), Positives = 48/141 (34%), Gaps = 1/141 (0%)
Query: 34 ENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNK-NDESRGFAIIVFNTPAEAKKAR 92
L V + L EF+ +G ++ + + +K + + RG+A I + + A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 93 VEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFI 152
+G I + V++ + + +P + + ++ +
Sbjct: 162 KHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDE 221
Query: 153 KFGNIIEVKIVRDENGKSKGF 173
+ G RD + + +
Sbjct: 222 RPGPSPLPHRDRDRDRERERR 242
Score = 49.5 bits (117), Expect = 7e-07
Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 6/80 (7%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHATHAVS 282
+FVA + + S+ F +G I +V K G FIE+ + A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 283 TMNGHVFKSKPLKVTLSGTK 302
+G + + V + +
Sbjct: 163 HADGKKIDGRRVLVDVERGR 182
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM
domain, riken structural genomics/proteomics initiative,
RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 57.4 bits (139), Expect = 6e-11
Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 2/82 (2%)
Query: 118 SKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIE-VKIVRDENGKSKGFGFI 176
S G V ++ L +EE+ F + + + D G+S G F+
Sbjct: 3 SGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFV 62
Query: 177 QFFSYKAAEKAIIEMNGRMIQH 198
QF S + AEKA ++ + I H
Sbjct: 63 QFASQEIAEKA-LKKHKERIGH 83
Score = 51.3 bits (123), Expect = 1e-08
Identities = 18/107 (16%), Positives = 39/107 (36%), Gaps = 7/107 (6%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRD-VRVARNKNDE 73
G S G + N+ + + L + ++ F + + + + +
Sbjct: 1 GSSGSSGNSPDTANDGF-----VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR 55
Query: 74 SRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
S G A + F + A+KA ++ + IG + + I + S P
Sbjct: 56 STGEAFVQFASQEIAEKA-LKKHKERIGHRYIEIFKSSRAEVRTSGP 101
Score = 40.1 bits (94), Expect = 9e-05
Identities = 11/82 (13%), Positives = 28/82 (34%), Gaps = 7/82 (8%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIG------FIEFIMPKHA 277
A + + LP + E + F+ + + + G F++F + A
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70
Query: 278 THAVSTMNGHVFKSKPLKVTLS 299
A+ + + +++ S
Sbjct: 71 EKALK-KHKERIGHRYIEIFKS 91
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 57.4 bits (139), Expect = 7e-11
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 7/86 (8%)
Query: 123 PEEKQYKKDKVFVKNL------VETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFI 176
P+E + V N+ + + F KFG I +E+GK+KG+ F+
Sbjct: 8 PQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITND-FYPEEDGKTKGYIFL 66
Query: 177 QFFSYKAAEKAIIEMNGRMIQHNSTF 202
++ S A A+ +G + TF
Sbjct: 67 EYASPAHAVDAVKNADGYKLDKQHTF 92
Score = 42.8 bits (101), Expect = 1e-05
Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 34 ENELHVNNLEPSVDN-------QALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPA 86
++ + V+N+ P V + F KFG + + + +++G+ + + +PA
Sbjct: 15 DSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPA 72
Query: 87 EAKKARVEMNGHLIGSKPVI 106
A A +G+ + +
Sbjct: 73 HAVDAVKNADGYKLDKQHTF 92
Score = 42.0 bits (99), Expect = 2e-05
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 13/82 (15%)
Query: 229 NKIFVANLPSNINNSEFEEL-------FARFGTITSSSLVSD----KHIGFIEFIMPKHA 277
+ I V N+P + E+L F++FG IT+ + K F+E+ P HA
Sbjct: 16 SVIVVDNVPQ-VGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 74
Query: 278 THAVSTMNGHVF-KSKPLKVTL 298
AV +G+ K +V L
Sbjct: 75 VDAVKNADGYKLDKQHTFRVNL 96
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 57.6 bits (139), Expect = 8e-11
Identities = 11/64 (17%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
V L V +L K G + + + + K + F ++ + + +++A + +N
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLN 84
Query: 193 GRMI 196
G+ +
Sbjct: 85 GKEV 88
Score = 49.2 bits (117), Expect = 8e-08
Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 10/79 (12%)
Query: 41 NLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMNGHLI 100
L V L+ +K G + + + NK ++ + T E+K+A V +NG +
Sbjct: 34 GLGNGVSRNQLLPVLEKCGLVDALLMPPNK-----PYSFARYRTTEESKRAYVTLNGKEV 88
Query: 101 G-----SKPVIITFVELKP 114
+ + FVE
Sbjct: 89 VDDLGQKITLYLNFVEKVQ 107
Score = 49.2 bits (117), Expect = 9e-08
Identities = 8/64 (12%), Positives = 25/64 (39%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVST 283
+ + L + ++ ++ + + G + + + +K F + + + A T
Sbjct: 23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVT 82
Query: 284 MNGH 287
+NG
Sbjct: 83 LNGK 86
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 56.7 bits (137), Expect = 1e-10
Identities = 14/74 (18%), Positives = 26/74 (35%), Gaps = 2/74 (2%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVS--TMNGHV 288
+ V L ++ ++ E +FGTI ++ K +EF A V+
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVY 77
Query: 289 FKSKPLKVTLSGTK 302
+ S +K
Sbjct: 78 IAGQQAFFNYSTSK 91
Score = 54.4 bits (131), Expect = 1e-09
Identities = 25/111 (22%), Positives = 37/111 (33%), Gaps = 12/111 (10%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDES 74
G S G+ + V +HV L SV L+ +KFGT+ V + K
Sbjct: 1 GSSGSSGSHHKVSVSPV-----VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR--- 52
Query: 75 RGFAIIVFNTPAEAKKA--RVEMNGHLIGSKPVIITFVELKPGQRSKPVGP 123
A++ F AK+ I + + K R GP
Sbjct: 53 --QALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGP 101
Score = 53.6 bits (129), Expect = 2e-09
Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 5/65 (7%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
V V+ L E+V E +L KFG I V ++ K ++F + +A++ +
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAA 72
Query: 193 GRMIQ 197
+
Sbjct: 73 DVPVY 77
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 55.6 bits (134), Expect = 3e-10
Identities = 14/71 (19%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVS--TMNGHV 288
+ + LP + +E L FG +T+ ++ K+ F+E + A V+ +
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPH 77
Query: 289 FKSKPLKVTLS 299
+++P+ + S
Sbjct: 78 LRNQPIYIQYS 88
Score = 49.8 bits (119), Expect = 4e-08
Identities = 10/56 (17%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI 188
+ ++ L V E E+ + + FG + + +++ K F++ + +AA +
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMV 68
Score = 47.9 bits (114), Expect = 2e-07
Identities = 21/108 (19%), Positives = 39/108 (36%), Gaps = 12/108 (11%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDES 74
G S G + + ++V LH+ L V +I FG + ++ + + KN
Sbjct: 1 GSSGSSGDKMDGAPSRV-----LHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN--- 52
Query: 75 RGFAIIVFNTPAEAKKA--RVEMNGHLIGSKPVIITFVELKPGQRSKP 120
A + T A + ++P+ I + K + S P
Sbjct: 53 --QAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKTSGP 98
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 55.4 bits (133), Expect = 4e-10
Identities = 20/99 (20%), Positives = 42/99 (42%), Gaps = 13/99 (13%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDEN---GKSKGFGFIQFFSYKAAEKAI 188
KVFV L +DE+E+ + F +FG ++ + E+ KG+ F+ F + +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL- 68
Query: 189 IEMNGRMIQHNSTFVSLAEIVPGKKVFPK---VKPPLLQ 224
++ + + ++ V + K ++P L
Sbjct: 69 --IDACLEEDGKLYLC----VSSPTIKDKPVQIRPWNLS 101
Score = 43.0 bits (101), Expect = 1e-05
Identities = 14/66 (21%), Positives = 21/66 (31%), Gaps = 8/66 (12%)
Query: 225 PARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSD--------KHIGFIEFIMPKH 276
+ K+FV LP +I+ E F RFG + K F+ F
Sbjct: 5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESS 64
Query: 277 ATHAVS 282
+
Sbjct: 65 VQALID 70
Score = 38.8 bits (90), Expect = 4e-04
Identities = 17/103 (16%), Positives = 39/103 (37%), Gaps = 15/103 (14%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDE---SRGF 77
G+ + + KV+ V L P +D + F++FG L + ++ +G+
Sbjct: 1 GSSGSSGSRKVF------VGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGY 54
Query: 78 AIIVFNTPAEAKKA------RVEMNGHLIGSKPVIITFVELKP 114
A ++F + + + S + V+++P
Sbjct: 55 AFLLFQEESSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIRP 97
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 54.8 bits (132), Expect = 6e-10
Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 5/65 (7%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
V ++ L++ V E +L +FG I V ++ K ++F A A+
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAA 78
Query: 193 GRMIQ 197
I
Sbjct: 79 DNQIY 83
Score = 53.6 bits (129), Expect = 1e-09
Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 2/74 (2%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVS--TMNGHV 288
+ + L + ++ E FG I+ ++ K +EF A +AV+ N
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIY 83
Query: 289 FKSKPLKVTLSGTK 302
P V S ++
Sbjct: 84 IAGHPAFVNYSTSQ 97
Score = 49.8 bits (119), Expect = 3e-08
Identities = 17/94 (18%), Positives = 30/94 (31%), Gaps = 12/94 (12%)
Query: 18 DDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGF 77
++ + V +H+ L V L+ ++FG + V V K
Sbjct: 10 ENYDDPHKTPASPV-----VHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK-----RQ 59
Query: 78 AIIVFNTPAEAKKA--RVEMNGHLIGSKPVIITF 109
A++ F A A N I P + +
Sbjct: 60 ALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNY 93
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 57.5 bits (138), Expect = 8e-10
Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 5/78 (6%)
Query: 130 KDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAII 189
+ K+L E ++ F + G+I ++ V +SK GF++F AE A
Sbjct: 143 DGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-----ESKNCGFVKFKYQANAEFAKE 197
Query: 190 EMNGRMIQHNSTFVSLAE 207
M+ + + S
Sbjct: 198 AMSNQTLLLPSDKEWDDR 215
Score = 44.8 bits (105), Expect = 2e-05
Identities = 15/81 (18%), Positives = 29/81 (35%), Gaps = 9/81 (11%)
Query: 231 IFVANLPSNINNSEFE---------ELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAV 281
++V + +N+ + +F+R G I V K+ GF++F +A A
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAK 196
Query: 282 STMNGHVFKSKPLKVTLSGTK 302
M+ K +
Sbjct: 197 EAMSNQTLLLPSDKEWDDRRE 217
Score = 42.9 bits (100), Expect = 5e-05
Identities = 12/80 (15%), Positives = 28/80 (35%), Gaps = 5/80 (6%)
Query: 34 ENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARV 93
+ L+ +L+P+ + F + G + +R +K + F A A+ A+
Sbjct: 143 DGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK-----NCGFVKFKYQANAEFAKE 197
Query: 94 EMNGHLIGSKPVIITFVELK 113
M+ + +
Sbjct: 198 AMSNQTLLLPSDKEWDDRRE 217
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 54.9 bits (132), Expect = 1e-09
Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 5/88 (5%)
Query: 115 GQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIE----VKIVRDENGKS 170
G S V + + V ++ L T EE+ + F + I + V +G+
Sbjct: 8 GGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRP 67
Query: 171 KGFGFIQFFSYKAAEKAIIEMNGRMIQH 198
G F+ F + A+ A + + ++
Sbjct: 68 TGDAFVLFACEEYAQNA-LRKHKDLLGK 94
Score = 44.1 bits (104), Expect = 5e-06
Identities = 14/95 (14%), Positives = 36/95 (37%), Gaps = 10/95 (10%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRD----VRVARNK 70
G S++ +KEN + + + L + + ++ F + + +
Sbjct: 9 GTSNEVAQFLSKENQVI-----VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP 63
Query: 71 NDESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
+ G A ++F A+ A + + L+G + +
Sbjct: 64 DGRPTGDAFVLFACEEYAQNA-LRKHKDLLGKRYI 97
Score = 34.9 bits (80), Expect = 0.008
Identities = 12/78 (15%), Positives = 27/78 (34%), Gaps = 10/78 (12%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSS----LVSDKH-----IGFIEFIMPKHATHAV 281
+ + LP E F + IT V+ F+ F ++A +A+
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 282 STMNGHVFKSKPLKVTLS 299
+ + + +++ S
Sbjct: 86 R-KHKDLLGKRYIELFRS 102
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 52.8 bits (127), Expect = 2e-09
Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 7/76 (9%)
Query: 133 VFVKNL------VETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEK 186
+ V N+ + + F KFG I + +GK+KG+ F+++ S A
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVD 62
Query: 187 AIIEMNGRMIQHNSTF 202
A+ +G + TF
Sbjct: 63 AVKNADGYKLDKQHTF 78
Score = 43.1 bits (102), Expect = 5e-06
Identities = 14/77 (18%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 34 ENELHVNNLEPSVDN-------QALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPA 86
++ + V+N+ P V + F KFG + + ++ +++G+ + + +PA
Sbjct: 1 DSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE-EDGKTKGYIFLEYASPA 58
Query: 87 EAKKARVEMNGHLIGSK 103
A A +G+ + +
Sbjct: 59 HAVDAVKNADGYKLDKQ 75
Score = 41.6 bits (98), Expect = 1e-05
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 13/80 (16%)
Query: 229 NKIFVANLPSNINNSEFEEL-------FARFGTITSSSLVSD----KHIGFIEFIMPKHA 277
+ I V N+P + E+L F++FG IT+ + K F+E+ P HA
Sbjct: 2 SVIVVDNVPQ-VGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 60
Query: 278 THAVSTMNGHVF-KSKPLKV 296
AV +G+ K +V
Sbjct: 61 VDAVKNADGYKLDKQHTFRV 80
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 52.4 bits (126), Expect = 3e-09
Identities = 13/72 (18%), Positives = 31/72 (43%), Gaps = 7/72 (9%)
Query: 132 KVFVKNLVETVDEEELKSHFIKFGNIIEVK------IVRDENGKSKGFGFIQFFSYKAAE 185
+++V N+ + EE + F + + ++ + + K F F++F S
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 186 KAIIEMNGRMIQ 197
+A + +G + Q
Sbjct: 68 QA-MAFDGIIFQ 78
Score = 52.0 bits (125), Expect = 4e-09
Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 13/84 (15%)
Query: 225 PARKNK-IFVANLPSNINNSEFEELFARFGT-----------ITSSSLVSDKHIGFIEFI 272
P + ++V N+P I + F + + + DK+ F+EF
Sbjct: 2 PLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR 61
Query: 273 MPKHATHAVSTMNGHVFKSKPLKV 296
T A++ +G +F+ + LK+
Sbjct: 62 SVDETTQAMA-FDGIIFQGQSLKI 84
Score = 40.5 bits (95), Expect = 5e-05
Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 7/78 (8%)
Query: 36 ELHVNNLEPSVDNQALINEFKKFGTLRDVRVARN------KNDESRGFAIIVFNTPAEAK 89
L+V N+ + +A+++ F L + A + ++ + FA + F + E
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 90 KARVEMNGHLIGSKPVII 107
+A + +G + + + I
Sbjct: 68 QA-MAFDGIIFQGQSLKI 84
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 52.2 bits (125), Expect = 5e-09
Identities = 12/58 (20%), Positives = 25/58 (43%)
Query: 53 NEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFV 110
+K+G + ++ V N D G + F +A+KA +++N +P+
Sbjct: 46 EMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103
Score = 51.0 bits (122), Expect = 1e-08
Identities = 14/51 (27%), Positives = 26/51 (50%)
Query: 144 EEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGR 194
EE K+G + E+ + + G +++F + AEKA+I++N R
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNR 91
Score = 33.3 bits (76), Expect = 0.026
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 5/61 (8%)
Query: 244 EFEELFARFGTITS---SSLVSDKHIG--FIEFIMPKHATHAVSTMNGHVFKSKPLKVTL 298
F E+ ++G + + D +G +++F + A AV +N F +P+ L
Sbjct: 43 VFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102
Query: 299 S 299
S
Sbjct: 103 S 103
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 54.1 bits (129), Expect = 6e-09
Identities = 15/104 (14%), Positives = 36/104 (34%)
Query: 89 KKARVEMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELK 148
+A + L+ + + K V++K +++K
Sbjct: 68 VEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIK 127
Query: 149 SHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
G ++ +++ R + KG F+ F S ++A+K +
Sbjct: 128 EWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPG 171
Score = 45.2 bits (106), Expect = 7e-06
Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 1/82 (1%)
Query: 28 NNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAE 87
K +++ + + G + ++++ R + +G +VF++
Sbjct: 103 YKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIES 162
Query: 88 AKKARVEMNGHLIGSKPVIITF 109
AKK VE G ++I F
Sbjct: 163 AKKF-VETPGQKYKETDLLILF 183
Score = 34.4 bits (78), Expect = 0.029
Identities = 12/76 (15%), Positives = 26/76 (34%), Gaps = 6/76 (7%)
Query: 229 NKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKH-----IGFIEFIMPKHATHAVST 283
+++ P++ + +E G + + + H F+ F + A V T
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 169
Query: 284 MNGHVFKSKPLKVTLS 299
G +K L +
Sbjct: 170 P-GQKYKETDLLILFK 184
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 51.5 bits (123), Expect = 1e-08
Identities = 14/88 (15%), Positives = 31/88 (35%), Gaps = 9/88 (10%)
Query: 114 PGQRSKPVGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKF---GNIIEVKIVRDENGKS 170
G P G E V ++ L + E++++ + V + G+
Sbjct: 6 SGMMLGPEGGEGY-----VVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQ 60
Query: 171 KGFGFIQFFSYKAAEKAIIEMNGRMIQH 198
G F++ S + A ++ + + H
Sbjct: 61 SGEAFVELESEDDVKLA-LKKDRESMGH 87
Score = 44.1 bits (104), Expect = 5e-06
Identities = 14/94 (14%), Positives = 30/94 (31%), Gaps = 7/94 (7%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKF---GTLRDVRVARNKN 71
G S G E + Y + + L S + + N + V +
Sbjct: 1 GSSGSSGMMLGPEGGEGYV---VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE 57
Query: 72 DESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
G A + + + K A ++ + +G + +
Sbjct: 58 GRQSGEAFVELESEDDVKLA-LKKDRESMGHRYI 90
Score = 32.6 bits (74), Expect = 0.050
Identities = 7/84 (8%), Positives = 24/84 (28%), Gaps = 9/84 (10%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARF---GTITSSSLVSDKH-----IGFIEFIMPK 275
+ + + LP + + + + + + + + F+E
Sbjct: 13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESED 72
Query: 276 HATHAVSTMNGHVFKSKPLKVTLS 299
A+ + + ++V S
Sbjct: 73 DVKLALK-KDRESMGHRYIEVFKS 95
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 52.4 bits (125), Expect = 1e-07
Identities = 49/286 (17%), Positives = 90/286 (31%), Gaps = 89/286 (31%)
Query: 95 MNGHLIGSKPVIITFVELKPGQRSKPVGPEE-----KQYKKDKVFVKNLVE-----TVDE 144
M+ + ++P+ ++ L + V P Q ++ F K L E D+
Sbjct: 1 MDAY--STRPLTLSHGSL---EHVLLV-PTASFFIASQLQEQ--FNKILPEPTEGFAADD 52
Query: 145 E-----ELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQHN 199
E EL F+ + + + E K F + E + G I H
Sbjct: 53 EPTTPAELVGKFLGY---VSSLV---EPSKVGQFDQVLNLCLTEFENCY--LEGNDI-H- 102
Query: 200 STFV-SL--------------------AEIVPGKKVFPKVKPPLLQPARKN--KIFVANL 236
L A I+ + K L + + ++
Sbjct: 103 -ALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVA--- 158
Query: 237 PSNI-----NNSE-FEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNGHVFK 290
I N + FEEL + T LV D I+F + +T++
Sbjct: 159 ---IFGGQGNTDDYFEELRDLYQ--TYHVLVGD----LIKFSAETLSELIRTTLDAEKVF 209
Query: 291 SKPLKVTLSGTKPGVS-ITNPTKAPKKPAYIDEVK---NVIGIKVQ 332
++ L + + + NP+ P K Y+ + +IG+ +Q
Sbjct: 210 TQGLNI--------LEWLENPSNTPDKD-YLLSIPISCPLIGV-IQ 245
Score = 42.7 bits (100), Expect = 2e-04
Identities = 36/209 (17%), Positives = 59/209 (28%), Gaps = 84/209 (40%)
Query: 6 KILEASWDEGISDDEGARS-----------------NKENNKVYKENELHVNNLEPSVDN 48
ILE S + EG S NK N+ + ++ +
Sbjct: 322 SILEDSLENN----EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI--------- 368
Query: 49 QALINEFKKF---G----------TLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEM 95
+L+N K G TLR + A + D+SR P +K +
Sbjct: 369 -SLVNGAKNLVVSGPPQSLYGLNLTLRKAK-APSGLDQSR--------IPFSERKLKFSN 418
Query: 96 NG-------H---LIGSKPVIIT-----FVELKPGQRSKPV-----GPEEKQYKKDKVFV 135
H L+ + +I V PV G + +
Sbjct: 419 RFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGS--IS 476
Query: 136 KNLV-----ETVD-EEELK---SHFIKFG 155
+ +V V E + +H + FG
Sbjct: 477 ERIVDCIIRLPVKWETTTQFKATHILDFG 505
Score = 40.0 bits (93), Expect = 0.001
Identities = 31/179 (17%), Positives = 56/179 (31%), Gaps = 64/179 (35%)
Query: 158 IEVKIVRD--ENGKS--------KGFGFIQFFSYKAAEKAIIEMNGRMIQHNSTFVSL-- 205
+ I+ D EN + + + + + + N + +SL
Sbjct: 319 LPPSILEDSLENNEGVPSPMLSISNL------TQEQVQDYVNKTNSHLPAGKQVEISLVN 372
Query: 206 ---AEIVPGKKVFPKVKPP-----LLQPARKNKIFVANLPSNINNS--EFEE----LFAR 251
+V G PP L RK K PS ++ S F E R
Sbjct: 373 GAKNLVVSG--------PPQSLYGLNLTLRKAKA-----PSGLDQSRIPFSERKLKFSNR 419
Query: 252 FGTITS---SSLVSDKHIGFIEFIMPKHATHAVST--MNGHV-FKSKPLKVTLSGTKPG 304
F + S S L+ A+ ++ + +V F +K +++ + T G
Sbjct: 420 FLPVASPFHSHLLVP-------------ASDLINKDLVKNNVSFNAKDIQIPVYDTFDG 465
Score = 38.1 bits (88), Expect = 0.005
Identities = 75/419 (17%), Positives = 128/419 (30%), Gaps = 146/419 (34%)
Query: 6 KILEASWDEGISDDEGARSNKENNKVYKENEL------HVNNL-EPSVDNQ------ALI 52
KIL + +DDE + EL +V++L EPS Q +
Sbjct: 39 KILPEPTEGFAADDE-PTTPA---------ELVGKFLGYVSSLVEPSKVGQFDQVLNLCL 88
Query: 53 NEF-KKFGTLR--DV--RVAR----NKNDESRGFAIIVFNTPAEAKKARVEMNGH---LI 100
EF + L D+ A+ N + +I A R L
Sbjct: 89 TEFENCY--LEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALF 146
Query: 101 -----GSKPVIITFVELKPGQRSKPVGP-----EEKQ--YKKDKVFVKNLVETVDE--EE 146
G+ ++ F GQ G EE + Y+ V V +L++ E E
Sbjct: 147 RAVGEGNAQLVAIF----GGQ-----GNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSE 197
Query: 147 LKSHFIK----FGNIIEVK--IVRDENGKSKGF-----------GFIQFFSYKAAEKAI- 188
L + F + + + N K + G IQ Y K +
Sbjct: 198 LIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLG 257
Query: 189 ---IEMNGRM---------------IQHNSTFVSLAEIVP------------GKKVFPK- 217
E+ + I ++ S V + +P
Sbjct: 258 FTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNT 317
Query: 218 -VKPPLLQPARKNKIFVANLPS---NINNSEFEELFARFGTITSSSLVSDKHIGFIEFIM 273
+ P +L+ + +N +PS +I+N E++ T+S L + K +
Sbjct: 318 SLPPSILEDSLENNE---GVPSPMLSISNLTQEQVQDYVNK-TNSHLPAGKQV------- 366
Query: 274 PKHATHAVSTMNGH---VFKSKP-----LKVTLSGTK--PGVSITNPTKAP---KKPAY 319
+S +NG V P L +TL K G + ++ P +K +
Sbjct: 367 ------EISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSG---LDQSRIPFSERKLKF 416
Score = 28.9 bits (64), Expect = 2.8
Identities = 24/121 (19%), Positives = 37/121 (30%), Gaps = 45/121 (37%)
Query: 59 GTLRDVRVARNKNDESRG--FAI----IVFNTPAEAKKARVEMNGHLIGSKPVIITFVEL 112
G V V R++ S AI + + EA + VE G G VE+
Sbjct: 1790 GMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGW------LVEI 1843
Query: 113 ----KPGQRSKPVGPEEKQY-------------------KKDKVFVKNLVETVDEEELKS 149
Q QY K K+ + L +++ EE++
Sbjct: 1844 VNYNVENQ----------QYVAAGDLRALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEG 1893
Query: 150 H 150
H
Sbjct: 1894 H 1894
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 47.9 bits (114), Expect = 2e-07
Identities = 12/78 (15%), Positives = 29/78 (37%), Gaps = 4/78 (5%)
Query: 133 VFVKNLVETVDEEELKSHFIKF---GNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAII 189
+ + L + E++ + F + + + +GK +G I+ S + +KA +
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKA-L 72
Query: 190 EMNGRMIQHNSTFVSLAE 207
E + + V
Sbjct: 73 EKHRMYMGQRYVEVYEIN 90
Score = 40.2 bits (94), Expect = 9e-05
Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 7/88 (7%)
Query: 21 GARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKF---GTLRDVRVARNKNDESRGF 77
G++ +E + V+ + L S + ++N F + N++ + RG
Sbjct: 1 GSKLEEEVDDVFL---IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGD 57
Query: 78 AIIVFNTPAEAKKARVEMNGHLIGSKPV 105
A+I + + +KA +E + +G + V
Sbjct: 58 ALIEMESEQDVQKA-LEKHRMYMGQRYV 84
Score = 26.7 bits (59), Expect = 4.9
Identities = 8/77 (10%), Positives = 20/77 (25%), Gaps = 9/77 (11%)
Query: 231 IFVANLPSNINNSEFEELFARF---GTITSSSLVSDKH-----IGFIEFIMPKHATHAVS 282
I LP + + F+ + ++ IE + A+
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE 73
Query: 283 TMNGHVFKSKPLKVTLS 299
+ + ++V
Sbjct: 74 -KHRMYMGQRYVEVYEI 89
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 48.5 bits (115), Expect = 2e-07
Identities = 14/103 (13%), Positives = 33/103 (32%), Gaps = 6/103 (5%)
Query: 101 GSKPVIITFVELKPGQRSKPVGPEEKQYKKDK--VFVKNLVETVDEEELKSHFIKF---G 155
G P + GQ+ + V ++ L + E++++
Sbjct: 13 GLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHD 72
Query: 156 NIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMIQH 198
V + G+ G F++ S + A ++ + + H
Sbjct: 73 GAAGVHFIYTREGRQSGEAFVELGSEDDVKMA-LKKDRESMGH 114
Score = 41.1 bits (96), Expect = 8e-05
Identities = 11/91 (12%), Positives = 27/91 (29%), Gaps = 4/91 (4%)
Query: 18 DDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKF---GTLRDVRVARNKNDES 74
G S + + + + L S + + N V +
Sbjct: 28 QQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQ 87
Query: 75 RGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
G A + + + K A ++ + +G + +
Sbjct: 88 SGEAFVELGSEDDVKMA-LKKDRESMGHRYI 117
Score = 33.1 bits (75), Expect = 0.051
Identities = 10/125 (8%), Positives = 34/125 (27%), Gaps = 12/125 (9%)
Query: 183 AAEKAIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSNINN 242
+ + ++ S S+ G+++ + + + LP + +
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMASMT---GGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSV 58
Query: 243 SEFEELFARF---GTITSSSLVSDKH-----IGFIEFIMPKHATHAVSTMNGHVFKSKPL 294
+ + + + + F+E A+ + + +
Sbjct: 59 EDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI 117
Query: 295 KVTLS 299
+V S
Sbjct: 118 EVFKS 122
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 46.7 bits (111), Expect = 4e-07
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 11/77 (14%)
Query: 121 VGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKS---KGFGFIQ 177
V PEE D + +VE V +E K+G + ++I R +G G F++
Sbjct: 14 VLPEEL---LDDEEYEEIVEDVRDE-----CSKYGLVKSIEIPRPVDGVEVPGCGKIFVE 65
Query: 178 FFSYKAAEKAIIEMNGR 194
F S +KA+ + GR
Sbjct: 66 FTSVFDCQKAMQGLTGR 82
Score = 41.7 bits (98), Expect = 3e-05
Identities = 10/65 (15%), Positives = 27/65 (41%), Gaps = 3/65 (4%)
Query: 49 QALINEFKKFGTLRDVRVAR---NKNDESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPV 105
+ + +E K+G ++ + + R G + F + + +KA + G ++ V
Sbjct: 30 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 89
Query: 106 IITFV 110
+ +
Sbjct: 90 VTKYC 94
Score = 27.4 bits (61), Expect = 2.4
Identities = 10/63 (15%), Positives = 22/63 (34%), Gaps = 8/63 (12%)
Query: 244 EFEELFARFGTITS------SSLVSDKHIG--FIEFIMPKHATHAVSTMNGHVFKSKPLK 295
+ + +++G + S V G F+EF A+ + G F ++ +
Sbjct: 31 DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVV 90
Query: 296 VTL 298
Sbjct: 91 TKY 93
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 48.2 bits (114), Expect = 5e-07
Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+ V+NL V + L F KFG ++++ N +Q+ +A+ A + ++
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSLD 105
Query: 193 GRMIQHNS 200
G+ I +
Sbjct: 106 GQNIYNAC 113
Score = 44.3 bits (104), Expect = 9e-06
Identities = 14/75 (18%), Positives = 32/75 (42%), Gaps = 2/75 (2%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI--GFIEFIMPKHATHAVSTMNGHV 288
I V NL + ++F++FGT+ + + +++ P A HA +++G
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 108
Query: 289 FKSKPLKVTLSGTKP 303
+ + + +K
Sbjct: 109 IYNACCTLRIDFSKL 123
Score = 42.4 bits (99), Expect = 4e-05
Identities = 19/75 (25%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
+ V NL V L F KFGT+ + N + A++ + P A+ A++ ++
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN---QFQALLQYADPVSAQHAKLSLD 105
Query: 97 GHLI--GSKPVIITF 109
G I + I F
Sbjct: 106 GQNIYNACCTLRIDF 120
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 45.8 bits (108), Expect = 9e-07
Identities = 16/87 (18%), Positives = 40/87 (45%), Gaps = 6/87 (6%)
Query: 36 ELHVNNLEPSVD----NQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKA 91
++ V+N++ + Q L F + G ++ V ++ + + + A++ +A A
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT--DYQLKAVVQMENLQDAIGA 68
Query: 92 RVEMNGHLIGSKPVIITFVELKPGQRS 118
++ + IGSK ++++ G S
Sbjct: 69 VNSLHRYKIGSKKILVSLATGASGPSS 95
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 45.8 bits (108), Expect = 2e-06
Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 3/68 (4%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+ V+NL V + L F KFG ++++ N +Q+ +A+ A + ++
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSLD 87
Query: 193 GRMIQHNS 200
G+ I +
Sbjct: 88 GQNIYNAC 95
Score = 43.5 bits (102), Expect = 1e-05
Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 4/83 (4%)
Query: 224 QPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI--GFIEFIMPKHATHAV 281
+ +I V NL + ++F++FGT+ + + +++ P A HA
Sbjct: 24 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAK 83
Query: 282 STMNGHVF--KSKPLKVTLSGTK 302
+++G L++ S
Sbjct: 84 LSLDGQNIYNACCTLRIDFSKLT 106
Score = 41.9 bits (98), Expect = 4e-05
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 5/79 (6%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
+ V NL V L F KFGT+ + N + A++ + P A+ A++ ++
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN---QFQALLQYADPVSAQHAKLSLD 87
Query: 97 GHLI--GSKPVIITFVELK 113
G I + I F +L
Sbjct: 88 GQNIYNACCTLRIDFSKLT 106
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 47.2 bits (111), Expect = 6e-06
Identities = 42/376 (11%), Positives = 95/376 (25%), Gaps = 122/376 (32%)
Query: 8 LEASWDEGISDDEGARSNKENNKVYKENELHVNNLEPS------VDNQALINEFKKFG-- 59
++ +W + + + L E V N N F
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFN-LSCK 267
Query: 60 ---TLRDVRVARNKN------------------DESRG-FA----IIVFNTPAEAKKARV 93
T R +V + DE + + P E
Sbjct: 268 ILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLT--- 324
Query: 94 EMNGHLIGSKPVIIT-FVELKPGQRSKPVGPEE-KQYKKDKV--FVKNLVETVDEEELKS 149
+ P ++ E R + K DK+ +++ + ++ E +
Sbjct: 325 ---TN-----PRRLSIIAESI---RDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRK 373
Query: 150 HFIKFG------NI--------------IEVKIVRDE-------NGKSKGFGF----IQF 178
F + +I +V +V ++ + K I
Sbjct: 374 MFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIY- 432
Query: 179 FSYKAAEKAIIEMNGRMIQH--------NSTFVS--------------LAEIVPGKKV-- 214
K + ++ ++ H + + L I +++
Sbjct: 433 LELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTL 492
Query: 215 FPKVKPPLLQPAR--KNKIFVANLPSNINNSEFEEL-----FARFGTITSSSLVSDKHIG 267
F + R + KI + N + S L + + I + ++ +
Sbjct: 493 FRM----VFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPY--ICDNDPKYERLVN 546
Query: 268 FIEFIMPKHATHAVST 283
I +PK + + +
Sbjct: 547 AILDFLPKIEENLICS 562
Score = 29.4 bits (65), Expect = 2.0
Identities = 12/112 (10%), Positives = 32/112 (28%), Gaps = 30/112 (26%)
Query: 223 LQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVS 282
L A I + + + E + L ++ L P+
Sbjct: 281 LSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL-------------PREVL---- 323
Query: 283 TMNGHVFKSKPLKVTLSGT--KPGVSITNPTKAPKKPAYIDEVKNVIGIKVQ 332
+ P ++++ + G++ + K D++ +I +
Sbjct: 324 -------TTNPRRLSIIAESIRDGLATWDNWKHVN----CDKLTTIIESSLN 364
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 43.4 bits (102), Expect = 7e-06
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 3/75 (4%)
Query: 231 IFVANLP-SNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVS--TMNGH 287
I ++NLP S ++S +L +G I + L+ K FIE + A V
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKAL 87
Query: 288 VFKSKPLKVTLSGTK 302
F+ + +KV LS
Sbjct: 88 WFQGRCVKVDLSEKY 102
Score = 43.4 bits (102), Expect = 8e-06
Identities = 14/102 (13%), Positives = 33/102 (32%), Gaps = 13/102 (12%)
Query: 113 KPGQRSKPVGPEEKQYKKDK-----VFVKNL-VETVDEEELKSHFIKFGNIIEVKIVRDE 166
KP G ++++ + + + + NL + + +G I ++
Sbjct: 3 SGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM--- 59
Query: 167 NGKSKGFGFIQFFSYKAAEKAI--IEMNGRMIQHNSTFVSLA 206
+ K FI+ + + A + Q V L+
Sbjct: 60 --RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLS 99
Score = 38.8 bits (90), Expect = 4e-04
Identities = 19/109 (17%), Positives = 37/109 (33%), Gaps = 12/109 (11%)
Query: 17 SDDEGARSNKENNKVYKENELHVNNL-EPSVDNQALINEFKKFGTLRDVRVARNKNDESR 75
EG K + K +H++NL + A++ + +G +++ + R K+
Sbjct: 8 KKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKS---- 63
Query: 76 GFAIIVFNTPAEAKKA--RVEMNGHLIGSKPVIITF----VELKPGQRS 118
A I T +A + V + +L G S
Sbjct: 64 -QAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVSGPSS 111
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 45.9 bits (108), Expect = 9e-06
Identities = 23/111 (20%), Positives = 46/111 (41%), Gaps = 12/111 (10%)
Query: 118 SKPVGPEEKQYKKDKVFVKN--LVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGF 175
+ G E Y + V N L V +L K G V + K + F
Sbjct: 6 LRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCG---LVDALLMPPNKP--YSF 60
Query: 176 IQFFSYKAAEKAIIEMNGRMI-----QHNSTFVSLAEIVPGKKVFPKVKPP 221
++ + + +++A + +NG+ + Q + +++ E V K++ P+ PP
Sbjct: 61 ARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQALPP 111
Score = 29.4 bits (65), Expect = 1.7
Identities = 11/61 (18%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 229 NKIFVAN--LPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVSTMNG 286
+ VAN L + ++ ++ + + G + + + +K F + + + A T+NG
Sbjct: 19 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNG 78
Query: 287 H 287
Sbjct: 79 K 79
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 42.4 bits (100), Expect = 2e-05
Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 17/92 (18%)
Query: 115 GQRSKPVGPEEKQYKKDKVFV-KNLVETVD-----------EEELKSHFIKFGNIIEVKI 162
G GP + ++V + KN+ +D E+L+ KFG I ++ +
Sbjct: 1 GSSGSSGGPSRM--RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL 58
Query: 163 VRDENGKSKGFGFIQFFSYKAAEKAIIEMNGR 194
G + F + A+ I ++GR
Sbjct: 59 FDRH---PDGVASVSFRDPEEADYCIQTLDGR 87
Score = 38.9 bits (91), Expect = 3e-04
Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 3/56 (5%)
Query: 54 EFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITF 109
E KFG +R + + G A + F P EA ++G G + +
Sbjct: 46 ECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 98
Score = 29.7 bits (67), Expect = 0.41
Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 2/57 (3%)
Query: 244 EFEELFARFGTITSSSLVSDKHIG--FIEFIMPKHATHAVSTMNGHVFKSKPLKVTL 298
+ ++FG I L G + F P+ A + + T++G F + +
Sbjct: 42 DLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 98
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 42.4 bits (100), Expect = 2e-05
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 11/74 (14%)
Query: 132 KVFV-KNLV---ETVDE--EELKSHFIKFGNIIEVKIVRDENGKSK-----GFGFIQFFS 180
V V +N+V + D+ E+ KFG + V I +++ G+ + F++F
Sbjct: 21 TVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSI 80
Query: 181 YKAAEKAIIEMNGR 194
KAI +NGR
Sbjct: 81 ASETHKAIQALNGR 94
Score = 37.8 bits (88), Expect = 9e-04
Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 5/62 (8%)
Query: 54 EFKKFGTLRDVRVARNKNDESR-----GFAIIVFNTPAEAKKARVEMNGHLIGSKPVIIT 108
E KFG + V + + K E + F+ +E KA +NG + V+
Sbjct: 45 ECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAE 104
Query: 109 FV 110
Sbjct: 105 VY 106
Score = 26.6 bits (59), Expect = 6.6
Identities = 7/31 (22%), Positives = 14/31 (45%)
Query: 268 FIEFIMPKHATHAVSTMNGHVFKSKPLKVTL 298
F+EF + A+ +NG F + + +
Sbjct: 75 FVEFSIASETHKAIQALNGRWFAGRKVVAEV 105
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 41.2 bits (96), Expect = 3e-05
Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 5/73 (6%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L + NL +D L + G L N+ G A+ + T EA KA++ +N
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQ-----GIALCKYTTREEANKAQMALN 64
Query: 97 GHLIGSKPVIITF 109
++ + +
Sbjct: 65 NCVLANTTIFAES 77
Score = 37.7 bits (87), Expect = 4e-04
Identities = 12/74 (16%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+ +KNL +D L++ ++ G ++ ++G ++ + + A KA + +N
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALN 64
Query: 193 GRMIQHNSTFVSLA 206
++ + + F
Sbjct: 65 NCVLANTTIFAESP 78
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 42.0 bits (98), Expect = 3e-05
Identities = 12/68 (17%), Positives = 28/68 (41%), Gaps = 4/68 (5%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
+ ++N + + + L + G + + I + ++ ++F S A+KA +N
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK----RNGIQAMVEFESVLCAQKAKAALN 83
Query: 193 GRMIQHNS 200
G I
Sbjct: 84 GADIYAGC 91
Score = 40.4 bits (94), Expect = 1e-04
Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 6/75 (8%)
Query: 37 LHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMN 96
L + N + L G ++ + + + A++ F + A+KA+ +N
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN----GIQAMVEFESVLCAQKAKAALN 83
Query: 97 GHLI--GSKPVIITF 109
G I G + I +
Sbjct: 84 GADIYAGCCTLKIEY 98
Score = 39.7 bits (92), Expect = 2e-04
Identities = 12/75 (16%), Positives = 22/75 (29%), Gaps = 3/75 (4%)
Query: 231 IFVANLPSNINNSEFEELFARFGTITSSSLVSDKHI-GFIEFIMPKHATHAVSTMNGHVF 289
+ + N I + G + + I +EF A A + +NG
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADI 87
Query: 290 --KSKPLKVTLSGTK 302
LK+ +
Sbjct: 88 YAGCCTLKIEYARPT 102
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint
center for struc genomics, JCSG, protein structure
initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus
musculus} PDB: 2lq5_A
Length = 114
Score = 40.8 bits (96), Expect = 7e-05
Identities = 14/74 (18%), Positives = 32/74 (43%), Gaps = 11/74 (14%)
Query: 121 VGPEEKQYKKDKVFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFS 180
P+ + ++ + + + V EE K G +I + + ++ G +++ S
Sbjct: 16 FNPQTE---EEVGWDTEIKDDVIEE-----CNKHGGVIHIYVDKNSAQ---GNVYVKCPS 64
Query: 181 YKAAEKAIIEMNGR 194
AA A+ ++GR
Sbjct: 65 IAAAIAAVNALHGR 78
Score = 40.4 bits (95), Expect = 9e-05
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 3/62 (4%)
Query: 49 QALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIIT 108
+I E K G + + V +N G + + A A A ++G K +
Sbjct: 32 DDVIEECNKHGGVIHIYVDKNSAQ---GNVYVKCPSIAAAIAAVNALHGRWFAGKMITAA 88
Query: 109 FV 110
+V
Sbjct: 89 YV 90
Score = 26.2 bits (58), Expect = 9.2
Identities = 10/57 (17%), Positives = 21/57 (36%), Gaps = 3/57 (5%)
Query: 245 FEELFARFGTITSSSLVSDKHIG--FIEFIMPKHATHAVSTMNGHVFKSKPLKVTLS 299
EE + G + + + G +++ A AV+ ++G F K +
Sbjct: 35 IEE-CNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYV 90
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 39.4 bits (92), Expect = 2e-04
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 7/69 (10%)
Query: 133 VFVKNLVETVD-----EEELKSHFIKFGNIIEVKIVRDENGKSKGFG--FIQFFSYKAAE 185
V ++N+V + E E K K+G + + I F++F ++A
Sbjct: 11 VLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAI 70
Query: 186 KAIIEMNGR 194
KA++++NGR
Sbjct: 71 KAVVDLNGR 79
Score = 39.0 bits (91), Expect = 2e-04
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 2/59 (3%)
Query: 54 EFKKFGTLRDVRVAR--NKNDESRGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFV 110
E +K+G + + D+ + F A KA V++NG G + V F
Sbjct: 33 ECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFY 91
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 38.3 bits (89), Expect = 3e-04
Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 3/75 (4%)
Query: 231 IFVANLPSNINN-SEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVS--TMNGH 287
+ + + N + +L FG I++ +++ + FIE + A AV T
Sbjct: 18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVDYYTTTPA 77
Query: 288 VFKSKPLKVTLSGTK 302
+ KP++V LS
Sbjct: 78 LVFGKPVRVHLSQKY 92
Score = 34.1 bits (78), Expect = 0.011
Identities = 21/111 (18%), Positives = 40/111 (36%), Gaps = 17/111 (15%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINE-FKKFGTLRDVRVARNKNDE 73
G S G + E +V +H+ + + + + + + + FG + + + N
Sbjct: 1 GSSGSSGQKGRVETRRV-----VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN-- 53
Query: 74 SRGFAIIVFNTPAEAKKA--RVEMNGHLIGSKPVIITF----VELKPGQRS 118
A I T +A+ A L+ KPV + +K G S
Sbjct: 54 ---EAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKSGPSS 101
Score = 33.3 bits (76), Expect = 0.026
Identities = 12/77 (15%), Positives = 24/77 (31%), Gaps = 8/77 (10%)
Query: 133 VFVKNLV-ETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAI--I 189
V + + +L FG I I+ FI+ + + A+ A+
Sbjct: 18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL-----NKINEAFIEMATTEDAQAAVDYY 72
Query: 190 EMNGRMIQHNSTFVSLA 206
++ V L+
Sbjct: 73 TTTPALVFGKPVRVHLS 89
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 38.4 bits (89), Expect = 4e-04
Identities = 18/113 (15%), Positives = 36/113 (31%), Gaps = 30/113 (26%)
Query: 132 KVFVKNLVETVDEEELKSHFIKF-----GNIIEVKIVRDENGKSKGFGFIQFFSYKAAEK 186
V V+ L V +E L +F G ++ + + G + F AE+
Sbjct: 10 AVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ-------RLGCGGVLTFREPADAER 62
Query: 187 AIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLLQPARKNKIFVANLPSN 239
+ + H + G ++ + PP ++ + LP
Sbjct: 63 VLAQ-----ADH---------ELHGAQLSLRPAPPR----APARLLLQGLPPG 97
Score = 27.6 bits (61), Expect = 2.3
Identities = 15/105 (14%), Positives = 34/105 (32%), Gaps = 18/105 (17%)
Query: 34 ENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARV 93
+ V L P+V ++ L F+ V ++ F PA+A++ +
Sbjct: 8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVL--SWQRLGCGGVLTFREPADAERV-L 64
Query: 94 EMNGHLIGSKPVIITFVELKPGQRSKPVGPEEKQYKKDKVFVKNL 138
H + + + +P P ++ ++ L
Sbjct: 65 AQADHELHGAQLSL-----------RPAPPRA----PARLLLQGL 94
Score = 26.8 bits (59), Expect = 4.7
Identities = 17/94 (18%), Positives = 28/94 (29%), Gaps = 19/94 (20%)
Query: 229 NKIFVANLPSNINNSEFEELFARF-----GTITSSSLVSDKHIGFIEFIMPKHATHAVST 283
+ V LP + + F G + S + G + F P A ++
Sbjct: 9 VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCG--GVLTFREPADAERVLAQ 66
Query: 284 MNGHVFKSKPL-----------KVTLSGTKPGVS 306
+ H L ++ L G PG S
Sbjct: 67 AD-HELHGAQLSLRPAPPRAPARLLLQGLPPGTS 99
>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 36.9 bits (85), Expect = 0.001
Identities = 20/96 (20%), Positives = 36/96 (37%), Gaps = 11/96 (11%)
Query: 229 NKIFVANLPSNI-----NNSEFEELFARFGTITS-SSLVSDKHIGFIEFIMPKHATHAVS 282
+ + ++ ++FE LF + T+ S K + I F P A A
Sbjct: 6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRV-RINFSNPLSAADARL 64
Query: 283 TMNGHVFKSKPLKV----TLSGTKPGVSITNPTKAP 314
++ F K +K+ TL ++ NP K+
Sbjct: 65 RLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSG 100
Score = 30.4 bits (68), Expect = 0.21
Identities = 13/81 (16%), Positives = 26/81 (32%), Gaps = 2/81 (2%)
Query: 35 NELHVNNLEPSV-DNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARV 93
+ L V +F+ D + + +S I F+ P A AR+
Sbjct: 6 SGLIACVANDDVFSESETRAKFESLFRTYD-KDTTFQYFKSFKRVRINFSNPLSAADARL 64
Query: 94 EMNGHLIGSKPVIITFVELKP 114
++ K + + F +
Sbjct: 65 RLHKTEFLGKEMKLYFAQTLH 85
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 35.5 bits (81), Expect = 0.003
Identities = 23/106 (21%), Positives = 42/106 (39%), Gaps = 9/106 (8%)
Query: 15 GISDDEGARSNKENNKVYKENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDES 74
G S G + K K + E L+ +K+G + ++ ++ K
Sbjct: 1 GSSGSSGQGTPKLKLKWKCKKEDESKG---GYSKDVLLRLLQKYGEVLNLVLSSKK---- 53
Query: 75 RGFAIIVFNTPAEAKKARVEMNGHLIGSKPVIITFVELKPGQRSKP 120
G A++ F T A+ A G + P+ I+++E +P S P
Sbjct: 54 PGTAVVEFATVKAAELAVQNEVGLV--DNPLKISWLEGQPQDASGP 97
Score = 35.5 bits (81), Expect = 0.004
Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 140 ETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRM 195
++ L K+G ++ + + + K G ++F + KAAE A+ G +
Sbjct: 27 GGYSKDVLLRLLQKYGEVLNLVL----SSKKPGTAVVEFATVKAAELAVQNEVGLV 78
>3ojy_A Complement component C8 alpha chain; macpf, lipocalin, immune
system; HET: TPO BMA; 2.51A {Homo sapiens}
Length = 554
Score = 34.6 bits (78), Expect = 0.050
Identities = 13/102 (12%), Positives = 26/102 (25%), Gaps = 14/102 (13%)
Query: 168 GKSKGFGFIQFFSYKAA----EKAIIEMNGRMIQHNSTFVSLAEIVPGKKVFPKVKPPLL 223
G + + + + + F + V + +L
Sbjct: 221 TIGIGPAGSPLLVGVGVSHSQDTSFLNELNKYNEKKFIFTRIFTKVQTAHFKMRKDDIML 280
Query: 224 QPARKNKIF---VANLPSNINNSEFEELFARFGT--ITSSSL 260
+ LP N + + +GT ITS S+
Sbjct: 281 DEG-----MLQSLMELPDQYNYGMYAKFINDYGTHYITSGSM 317
>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken
structural genomics/proteomics initiative, RSGI, protein
transport; 2.70A {Mus musculus} SCOP: d.58.7.1
Length = 119
Score = 32.0 bits (72), Expect = 0.079
Identities = 11/63 (17%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 44 PSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVEMNGHLIGSK 103
P ++ +F ++G + ++ N + I + + +A+KA + +G + G
Sbjct: 33 PQASASYILLQFAQYGNILKHVMSNTGN-----WMHIRYQSKLQARKA-LSKDGRIFGES 86
Query: 104 PVI 106
+I
Sbjct: 87 IMI 89
Score = 29.3 bits (65), Expect = 0.80
Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 6/48 (12%)
Query: 149 SHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMNGRMI 196
F ++GNI++ + N + I++ S A KA+ + +GR+
Sbjct: 42 LQFAQYGNILKHVMSNTGN-----WMHIRYQSKLQARKALSK-DGRIF 83
>3t5o_A Complement component C6; macpf, MAC, membrane attack complex,
innate IMMU system, blood, membrane, cytolysin, immune
SYST; HET: NAG FUL FUC BGC MAN; 2.87A {Homo sapiens}
PDB: 4a5w_B* 4e0s_B*
Length = 913
Score = 33.3 bits (75), Expect = 0.13
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 233 VANLPSNINNSEFEELFARFGT--ITSSSL 260
+ +LP N++ + +F FGT TS SL
Sbjct: 321 LNHLPLEYNSALYSRIFDDFGTHYFTSGSL 350
>3ojy_B Complement component C8 beta chain; macpf, lipocalin, immune
system; HET: TPO BMA; 2.51A {Homo sapiens}
Length = 537
Score = 32.5 bits (73), Expect = 0.19
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 233 VANLPSNINNSEFEELFARFGT--ITSSSL 260
V LP + E+ +LF FGT IT + L
Sbjct: 267 VKRLPLEYSYGEYRDLFRDFGTHYITEAVL 296
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 31.0 bits (70), Expect = 0.38
Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 5/58 (8%)
Query: 53 NEFKKFGTLRDVRVARNKNDESRGFAIIV-----FNTPAEAKKARVEMNGHLIGSKPV 105
E KFG + V + + K E IIV F+ +E KA +NG + V
Sbjct: 148 EECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKV 205
Score = 29.0 bits (65), Expect = 1.7
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 10/72 (13%)
Query: 133 VFVKNLV--ETVD---EEELKSHFIKFGNIIEVKIVRDENGKSKGFG-----FIQFFSYK 182
+ ++N+V + +D E E+ KFG + V I +++ G+ + F++F
Sbjct: 127 MVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIAS 186
Query: 183 AAEKAIIEMNGR 194
KAI +NGR
Sbjct: 187 ETHKAIQALNGR 198
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 29.7 bits (66), Expect = 0.44
Identities = 15/76 (19%), Positives = 32/76 (42%), Gaps = 4/76 (5%)
Query: 34 ENELHVNNLEPSVDNQALINEFKKFGTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARV 93
L+V NL + D +++ N ++ +V + AI+ F A++A+
Sbjct: 9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLS----ITGCSAILRFINQDSAERAQK 64
Query: 94 EMNGHLIGSKPVIITF 109
M + +I++F
Sbjct: 65 RMENEDVFGNRIIVSF 80
Score = 27.4 bits (60), Expect = 2.2
Identities = 15/89 (16%), Positives = 32/89 (35%), Gaps = 7/89 (7%)
Query: 133 VFVKNLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGFGFIQFFSYKAAEKAIIEMN 192
++V NL D + + + + + K++ ++F + +AE+A M
Sbjct: 12 LYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSITGCS----AILRFINQDSAERAQKRME 67
Query: 193 GRMIQHNSTFVSLAEIVPGKKVFPKVKPP 221
+ N VS P + + P
Sbjct: 68 NEDVFGNRIIVSFT---PKNRELCETSGP 93
Score = 26.2 bits (57), Expect = 6.3
Identities = 14/77 (18%), Positives = 25/77 (32%), Gaps = 15/77 (19%)
Query: 231 IFVANLPSNINNSE--------FEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHAVS 282
++V NLP+N + + + +IT S + FI A A
Sbjct: 12 LYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSITGCS-------AILRFINQDSAERAQK 64
Query: 283 TMNGHVFKSKPLKVTLS 299
M + V+ +
Sbjct: 65 RMENEDVFGNRIIVSFT 81
>1o9g_A RRNA methyltransferase; antibiotic resistance, Se-MAD; 1.5A
{Streptomyces viridochromogenes} SCOP: c.66.1.29 PDB:
1o9h_A
Length = 250
Score = 30.3 bits (67), Expect = 0.85
Identities = 20/93 (21%), Positives = 32/93 (34%), Gaps = 1/93 (1%)
Query: 218 VKPPLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHA 277
V P L+ A KN ++ E E RFG + E + +
Sbjct: 85 VDPAPLELAAKNLALLSPAGLTARELERREQSERFGKPSYLEAAQAAR-RLRERLTAEGG 143
Query: 278 THAVSTMNGHVFKSKPLKVTLSGTKPGVSITNP 310
+ VF + L L+G+ P V +T+
Sbjct: 144 ALPCAIRTADVFDPRALSAVLAGSAPDVVLTDL 176
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.0 bits (61), Expect = 2.5
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 16/43 (37%)
Query: 53 NEFKKF-GTLRDVRVARNKNDESRGFAIIVFNTPAEAKKARVE 94
KK +L+ A D+S PA A KA +E
Sbjct: 20 QALKKLQASLK--LYA----DDS---------APALAIKATME 47
>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA
binding protein; NMR {Saccharomyces cerevisiae}
Length = 117
Score = 27.7 bits (61), Expect = 2.6
Identities = 15/68 (22%), Positives = 24/68 (35%), Gaps = 5/68 (7%)
Query: 235 NLPSNINNSEFEELFARFGTITSSS-----LVSDKHIGFIEFIMPKHATHAVSTMNGHVF 289
L ++ S + I LVSD + I F K A + +NG F
Sbjct: 28 PLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQF 87
Query: 290 KSKPLKVT 297
+ K ++
Sbjct: 88 QGKVIRSG 95
>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, PARN, structural genomics; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*
Length = 100
Score = 27.0 bits (59), Expect = 3.5
Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 3/68 (4%)
Query: 221 PLLQPARKNKIFVANLPSNINNSEFEELFARFGTITSSSLVSDKHIGFIEFIMPKHATHA 280
P LQP R + + P S+ +LF+ FG I S + D F+ P+ A
Sbjct: 9 PDLQPKRDH-VLHVTFPKEWKTSDLYQLFSAFGNIQISWI--DDTSAFVSLSQPEQVQIA 65
Query: 281 VSTMNGHV 288
V+T
Sbjct: 66 VNTSKYAE 73
>1req_A Methylmalonyl-COA mutase; isomerase, intramolecular transferase;
HET: B12 DCA; 2.00A {Propionibacterium freudenreichii
subspshermanii} SCOP: c.1.19.1 c.23.6.1 PDB: 2req_A*
3req_A* 4req_A* 6req_A* 7req_A* 5req_A* 1e1c_A*
Length = 727
Score = 28.5 bits (64), Expect = 4.0
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 76 GFAIIV---FNTPAEAKKARVEMNGHLIG 101
GF + V F TP E + VE + H++G
Sbjct: 624 GFDVDVGPLFQTPEETARQAVEADVHVVG 652
>3iu1_A Glycylpeptide N-tetradecanoyltransferase 1; N-myristoyltransferase,
NMT1, acyltransferase, phosphoprotein, structural
genomics; HET: MYA; 1.42A {Homo sapiens} PDB: 3iu2_A*
3iwe_A* 3jtk_A*
Length = 383
Score = 28.0 bits (62), Expect = 5.4
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 137 NLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGF 173
+L + +EE++ F NII+ +V + NG+ F
Sbjct: 248 HLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDF 284
>2lfv_A Protein DAMX; cell division, peptidoglycan binding domain, murein
binding bacterial cell division protein, RNP fold, RNP
domain, cell; NMR {Escherichia coli}
Length = 106
Score = 26.4 bits (58), Expect = 5.4
Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 2/71 (2%)
Query: 45 SVDNQALINEFKKFGTLRDVRVARNKNDESRGFAII--VFNTPAEAKKARVEMNGHLIGS 102
S N +N + K L++ V + + ++ V+ + EAKKA + +
Sbjct: 32 SSSNYDNLNGWAKKENLKNYVVYETTRNGQPWYVLVSGVYASKEEAKKAVSTLPADVQAK 91
Query: 103 KPVIITFVELK 113
P +++
Sbjct: 92 NPWAKPLRQVQ 102
>1rxt_A Myristoyl-, glycylpeptide N-tetradecanoyltransferase 1; alpha-beta
structure, unique N-myristoyltransferase fold; 3.00A
{Homo sapiens} SCOP: d.108.1.2 d.108.1.2
Length = 496
Score = 27.4 bits (60), Expect = 7.9
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 137 NLVETVDEEELKSHFIKFGNIIEVKIVRDENGKSKGF 173
+L + +EE++ F NII+ +V + NG+ F
Sbjct: 361 HLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDF 397
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.314 0.133 0.372
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,017,057
Number of extensions: 308191
Number of successful extensions: 1586
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1042
Number of HSP's successfully gapped: 585
Length of query: 333
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 239
Effective length of database: 4,077,219
Effective search space: 974455341
Effective search space used: 974455341
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 57 (25.7 bits)