RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2618
(390 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 = 286 bits (734), Expect = 1e-95
Identities = 58/303 (19%), Positives = 108/303 (35%), Gaps = 44/303 (14%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATA 62
+ + L VT + + L S +K C V + G AF+ ++ A A
Sbjct: 18 QFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKG---TAFVTLLNGEQAEAA 73
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEI 122
+ A ++ E+E+ V + + V +L P + Q +E PFG +
Sbjct: 74 INAFHQSRLRERELSVQLQPTDAL-----------LCVANLPPSLTQQQFEELVRPFGSL 122
Query: 123 SNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNE 182
C +V +T +SKGY F ++KK A A + + G+ LG R++ +W+
Sbjct: 123 ERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALL 182
Query: 183 RKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNE-ELVSKVFSPFGTIVDIRVF-- 239
R + N+ + + + S + ++
Sbjct: 183 HSR----------------------CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG 220
Query: 240 ---KEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKE-SENNSTLAQPSAPTTP 295
+ KG+A +++ T E A A + + G ++ + S LA A
Sbjct: 221 QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQAT 280
Query: 296 QPN 298
N
Sbjct: 281 ALN 283
Score = 148 bits (375), Expect = 4e-42
Identities = 34/222 (15%), Positives = 71/222 (31%), Gaps = 49/222 (22%)
Query: 73 EKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQ 132
+E++ ++ N I + L ++ Q + + + + + C + +
Sbjct: 5 PEEIRKRLE-----HTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDK--- 55
Query: 133 TLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKT 192
KG AFV+ + +AE AI A + L R +
Sbjct: 56 ---YKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL--------------------- 91
Query: 193 ITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAF 246
PT+ + L ++ ++ PFG++ + KGY F
Sbjct: 92 ----------QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGF 141
Query: 247 VKFTTKETATHAIESIHNTDINGHTVKCFWGKESENNSTLAQ 288
++ K++A A + + T+ W + L
Sbjct: 142 AEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLH 183
>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 = 234 bits (600), Expect = 4e-77
Identities = 58/168 (34%), Positives = 95/168 (56%), Gaps = 5/168 (2%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP--GNDPYAFLEFVHHTVAATALAAM 66
LYVGNLD ++TE++L F GP+ K++ + N YAF+E+ A AL +
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 67 NKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCR 126
N + +K+NWA + + + +++FVGDL+ ++ +TL+ AF F +
Sbjct: 62 NGKQIENNIVKINWAFQS---QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH 118
Query: 127 IVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTR 174
++ D QT S+GY FVSF + +A+NA+ +M GQ L R +R NW+ +
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 140 bits (356), Expect = 1e-40
Identities = 41/185 (22%), Positives = 86/185 (46%), Gaps = 30/185 (16%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L I LK+ F G I+N +I+ D + K+ YAFV + + +A A+ +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKD 217
NG+ + + ++ NW+ + + ++ ++ G +
Sbjct: 62 NGKQIENNIVKINWAFQSQ-----QSSSDDTF------------------NLFVGDLNVN 98
Query: 218 LNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGHT 271
+++E + F F + + V + +GY FV FT+++ A +A++S+ D+NG
Sbjct: 99 VDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP 158
Query: 272 VKCFW 276
++ W
Sbjct: 159 LRINW 163
Score = 69.9 bits (172), Expect = 2e-14
Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 3/83 (3%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVA 59
L+VG+L+V+V +E L F V+ + Y F+ F A
Sbjct: 83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 142
Query: 60 ATALAAMNKRVFLEKEMKVNWAS 82
A+ +M + + +++NWA+
Sbjct: 143 QNAMDSMQGQDLNGRPLRINWAA 165
Score = 66.0 bits (162), Expect = 3e-13
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK-----GYAFVKFTTKETATHAIESI 262
+Y G K + E+++ + F G I +I++ +K YAFV++ A A++++
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 263 HNTDINGHTVKCFW 276
+ I + VK W
Sbjct: 62 NGKQIENNIVKINW 75
>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 = 229 bits (586), Expect = 2e-74
Identities = 63/221 (28%), Positives = 91/221 (41%), Gaps = 21/221 (9%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGN---DPYAFLEFVHHTVA 59
+LYVG+L VTE +L FS GP+ +V R+ YA++ F A
Sbjct: 11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADA 70
Query: 60 ATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPF 119
AL MN V K +++ W+ P S +IF+ +L I+ + L + F+ F
Sbjct: 71 ERALDTMNFDVIKGKPVRIMWSQRD---PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAF 127
Query: 120 GEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAM 179
G I +C++V D SKGY FV F + AE AI MNG L R + +
Sbjct: 128 GNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKERE 185
Query: 180 TNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNE 220
R E Y P Y G G+ + +
Sbjct: 186 AELGAR---------AKEFYPYDVPD----YAGSSGRIVTD 213
Score = 185 bits (472), Expect = 3e-57
Identities = 57/235 (24%), Positives = 94/235 (40%), Gaps = 37/235 (15%)
Query: 88 PKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKK 147
P + ++VGDL P++ L E F+P G I + R+ RD T +S GYA+V+F +
Sbjct: 8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 67
Query: 148 AEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNC 207
A+AE A+ MN + + +R WS R P R++
Sbjct: 68 ADAERALDTMNFDVIKGKPVRIMWSQRDPSL------RKSGVG----------------- 104
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETATHAIESIH 263
++ K ++ + + FS FG I+ +V + KGY FV F T+E A AIE ++
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164
Query: 264 NTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQ 318
+N V + + + A +F +
Sbjct: 165 GMLLNDRKVFVGR----------FKSRKEREAELGARAKEFYPYDVPDYAGSSGR 209
>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 = 227 bits (580), Expect = 2e-72
Identities = 46/280 (16%), Positives = 104/280 (37%), Gaps = 39/280 (13%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG-NDPYAFLEFVHHTVAATAL 63
+ TT+ V NL S + + F GP+ V N +A +EF + A A+
Sbjct: 39 RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAI 98
Query: 64 AAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEIS 123
+K V + E+ V+ + +++ + P + +++ ++
Sbjct: 99 TKTHKVVG-QNEIIVSHLTEC------------TLWMTNFPPSYTQRNIRDLLQDINVVA 145
Query: 124 NCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNER 183
+ + S+ +A++ K +A + +NG + ++ T S
Sbjct: 146 LSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPL-------E 198
Query: 184 KRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-- 241
K + + + T+ E+ ++ T +E L+ + F FG+I I +
Sbjct: 199 KSKRTDSATLEGREIMIRNLSTELL----------DENLLRESFEGFGSIEKINIPAGQK 248
Query: 242 -----KGYAFVKFTTKETATHAIESIHNTDINGHTVKCFW 276
AF+ F K++A A++ ++ + + +
Sbjct: 249 EHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL 287
Score = 162 bits (412), Expect = 2e-47
Identities = 40/177 (22%), Positives = 70/177 (39%), Gaps = 10/177 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALA 64
TL++ N S T+ + L I V + + +A+++ A +
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177
Query: 65 AMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYH---IFVGDLSPEIET-QTLKEAFAPFG 120
+N + ++ P + K+ S I + +LS E+ L+E+F FG
Sbjct: 178 KLNGLKIEGYTLVTKVSN-PLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFG 236
Query: 121 EISNCRIVRD-PQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP 176
I I + + AF+ F K AE A+ MN LG+R I + + +KP
Sbjct: 237 SIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKKP 292
Score = 138 bits (351), Expect = 2e-38
Identities = 33/237 (13%), Positives = 71/237 (29%), Gaps = 46/237 (19%)
Query: 51 LEFVHHTVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQ 110
+E+ HH + +++ S N+ + V +L
Sbjct: 2 MEYGHHARPD-SKRPLDE----GSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQN 56
Query: 111 TLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTN 170
+ + F G I + + + K+ +A + F + A AIT + +G I +
Sbjct: 57 KVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVS 113
Query: 171 WSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF 230
T CT++ F + + +
Sbjct: 114 --------------------------------HLTECTLWMTNFPPSYTQRNIRDLLQDI 141
Query: 231 GTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKESE 281
+ + +A++ T+KE A + +E ++ I G+T+ E
Sbjct: 142 NVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLE 198
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 220 bits (563), Expect = 7e-71
Identities = 45/188 (23%), Positives = 86/188 (45%), Gaps = 9/188 (4%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEFVHHTVA 59
+ + +YVG++ + E+ + F+ GP+K + + +AF+E+ A
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83
Query: 60 ATALAAMNKRVFLEKEMKVNWASSPGN------QPKQDTSNHYHIFVGDLSPEIETQTLK 113
AL MN + + +KV S+ G Q ++ I+V + ++ +K
Sbjct: 84 QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIK 143
Query: 114 EAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWST 173
F FG+I + + RDP T K KGY F+ + K +++A+++MN LG + +R +
Sbjct: 144 SVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203
Query: 174 RKPPAMTN 181
P +
Sbjct: 204 TPPMPLLT 211
Score = 180 bits (458), Expect = 3e-55
Identities = 49/218 (22%), Positives = 94/218 (43%), Gaps = 22/218 (10%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
Q + + ++VG + E+ T+++AFAPFG I + + D T+K KG+A
Sbjct: 14 GRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFA 73
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYN 200
FV + A+ A+ MN LG R+I+ + A D++
Sbjct: 74 FVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQP-------------IIDQLAE 120
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKET 254
++ N +Y +DL+++ + VF FG I + ++ KGY F+++ ++
Sbjct: 121 EARAFN-RIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQS 179
Query: 255 ATHAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAP 292
+ A+ S++ D+ G ++ P+ P
Sbjct: 180 SQDAVSSMNLFDLGGQYLRVGKAVTPPMPLL--TPATP 215
Score = 73.5 bits (181), Expect = 2e-15
Identities = 17/97 (17%), Positives = 42/97 (43%), Gaps = 9/97 (9%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHH 56
+ +YV ++ ++++ + ++F G +K + R+P G Y F+E+
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKG---YGFIEYEKA 177
Query: 57 TVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
+ A+++MN + ++V A +P +
Sbjct: 178 QSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPAT 214
Score = 72.7 bits (179), Expect = 5e-15
Identities = 23/106 (21%), Positives = 43/106 (40%), Gaps = 7/106 (6%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKE 253
+ VY G +L E+ + + F+PFG I I + + KG+AFV++ E
Sbjct: 22 QGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPE 81
Query: 254 TATHAIESIHNTDINGHTVKCFW-GKESENNSTLAQPSAPTTPQPN 298
A A+E +++ + G +K + + Q +
Sbjct: 82 AAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNR 127
>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 = 208 bits (531), Expect = 1e-66
Identities = 49/172 (28%), Positives = 83/172 (48%), Gaps = 10/172 (5%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEFVHHTVAAT 61
+ T L V L +T+ L ALF IGP+ C+++R+ YAF++F +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGE 121
A+ +N K +KV++A +P ++ +++V +L I L F +G
Sbjct: 61 AIKVLNGITVRNKRLKVSYA-----RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGS 115
Query: 122 ISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWL--GSRSIRTNW 171
I I+RD T + +G AFV + K+ EA+ AI+A+N GS+ +
Sbjct: 116 IVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL 167
Score = 154 bits (391), Expect = 8e-46
Identities = 38/185 (20%), Positives = 83/185 (44%), Gaps = 31/185 (16%)
Query: 93 SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAEN 152
+++ ++ V L ++ + L F G I+ CRI+RD +T S GYAFV F + +++
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 153 AITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCG 212
AI +NG + ++ ++ +++ + +Y
Sbjct: 61 AIKVLNGITVRNKRLKVSYARPG-------GESIKDT------------------NLYVT 95
Query: 213 GFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTD 266
+ + ++ + +F +G+IV + ++ +G AFV++ +E A AI +++N
Sbjct: 96 NLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
Query: 267 INGHT 271
G +
Sbjct: 156 PEGGS 160
Score = 69.5 bits (171), Expect = 2e-14
Identities = 21/103 (20%), Positives = 42/103 (40%), Gaps = 18/103 (17%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETA 255
+S TN + +D+ + + +F G I R+ ++ GYAFV FT++ +
Sbjct: 1 ASNTN--LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDS 58
Query: 256 THAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPN 298
AI+ ++ + +K + A+P + N
Sbjct: 59 QRAIKVLNGITVRNKRLKVSY----------ARPGGESIKDTN 91
Score = 66.8 bits (164), Expect = 2e-13
Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 5/84 (5%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVA 59
+ + T LYV NL ++T++ L +F + G + ++R+ AF+ + A
Sbjct: 85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144
Query: 60 ATALAAMNKRVFL--EKEMKVNWA 81
A++A+N + + + V A
Sbjct: 145 QEAISALNNVIPEGGSQPLSVRLA 168
>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 = 201 bits (513), Expect = 6e-64
Identities = 44/177 (24%), Positives = 71/177 (40%), Gaps = 14/177 (7%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP-------GND-PYAFLEFVHH 56
LYVGN+ +TEE + F+ + G D +AFLEF
Sbjct: 2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 57 TVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAF 116
A+A + +F + +K+ Q + +F+G L + +KE
Sbjct: 62 DETTQAMA-FDGIIFQGQSLKIRRP-----HDYQPLPGAHKLFIGGLPNYLNDDQVKELL 115
Query: 117 APFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWST 173
FG + +V+D T SKGYAF +V + AI +NG LG + + ++
Sbjct: 116 TSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172
Score = 131 bits (333), Expect = 3e-37
Identities = 31/190 (16%), Positives = 63/190 (33%), Gaps = 37/190 (19%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNC-----RIVRDPQTLKSKGYAFVSFVKKAEAEN 152
++VG++ I + + + F + V Q + K +AF+ F E
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 153 AITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCG 212
A+ A +G +S++ P ++ G
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQP-----------------------LPGAHK--LFIG 100
Query: 213 GFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTD 266
G LN++ V ++ + FG + + K+ KGYAF ++ AI ++
Sbjct: 101 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ 160
Query: 267 INGHTVKCFW 276
+ +
Sbjct: 161 LGDKKLLVQR 170
Score = 78.0 bits (193), Expect = 2e-17
Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 3/83 (3%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVA 59
L++G L + ++ + L + GP+K ++++ YAF E+V V
Sbjct: 90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149
Query: 60 ATALAAMNKRVFLEKEMKVNWAS 82
A+A +N +K++ V AS
Sbjct: 150 DQAIAGLNGMQLGDKKLLVQRAS 172
Score = 52.2 bits (126), Expect = 2e-08
Identities = 13/89 (14%), Positives = 31/89 (34%), Gaps = 12/89 (13%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF-----------KEKGYAFVKFTTKETAT 256
+Y G + EE + F+ + + ++K +AF++F + + T
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 257 HAIESIHNTDINGHTVKCFWGKESENNST 285
A+ G ++K + +
Sbjct: 66 QAMA-FDGIIFQGQSLKIRRPHDYQPLPG 93
>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 = 197 bits (504), Expect = 9e-63
Identities = 47/169 (27%), Positives = 82/169 (48%), Gaps = 10/169 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALA 64
T L V L ++T+E +LF IG ++ CK++R+ Y F+ ++ A A+
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 65 AMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
+N K +KV++A +P + +++V L + + L++ F+ +G I
Sbjct: 63 TLNGLRLQTKTIKVSYA-----RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIIT 117
Query: 125 CRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWL--GSRSIRTNW 171
RI+ D T S+G F+ F K+ EAE AI +NGQ + I +
Sbjct: 118 SRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF 166
Score = 143 bits (362), Expect = 1e-41
Identities = 40/184 (21%), Positives = 81/184 (44%), Gaps = 31/184 (16%)
Query: 94 NHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
+ ++ V L + + + F GEI +C++VRD T +S GY FV+++ +AE A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 154 ITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGG 213
I +NG L +++I+ +++ +Y G
Sbjct: 61 INTLNGLRLQTKTIKVSYARP--------SSASIRDAN-----------------LYVSG 95
Query: 214 FGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDI 267
K + ++ + ++FS +G I+ R+ + +G F++F + A AI+ ++
Sbjct: 96 LPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKP 155
Query: 268 NGHT 271
+G T
Sbjct: 156 SGAT 159
Score = 66.4 bits (163), Expect = 2e-13
Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 8/88 (9%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETAT 256
S TN + +++ +E +F G I ++ ++K GY FV + + A
Sbjct: 1 SKTN--LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAE 58
Query: 257 HAIESIHNTDINGHTVKCFWGKESENNS 284
AI +++ + T+K + + S +
Sbjct: 59 KAINTLNGLRLQTKTIKVSYARPSSASI 86
Score = 60.3 bits (147), Expect = 3e-11
Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 5/84 (5%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVA 59
+ LYV L ++T++ L LFSQ G + +++ + F+ F A
Sbjct: 84 ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 143
Query: 60 ATALAAMNKRVF--LEKEMKVNWA 81
A+ +N + + + V +A
Sbjct: 144 EEAIKGLNGQKPSGATEPITVKFA 167
>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 = 187 bits (477), Expect = 3e-58
Identities = 45/195 (23%), Positives = 75/195 (38%), Gaps = 24/195 (12%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI-------REPGND-PYAFLEFVHH 56
+ LYVGN+ +TEE + F+ + G + D +AFLEF
Sbjct: 2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 57 TVAATALAAMNKRVFLEKEMKVNWAS---------------SPGNQPKQDTSNHYHIFVG 101
A+A + +F + +K+ PG + + +F+G
Sbjct: 62 DETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIG 120
Query: 102 DLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQW 161
L + +KE FG + +V+D T SKGYAF +V + AI +NG
Sbjct: 121 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ 180
Query: 162 LGSRSIRTNWSTRKP 176
LG + + ++
Sbjct: 181 LGDKKLLVQRASVGA 195
Score = 142 bits (361), Expect = 5e-41
Identities = 32/198 (16%), Positives = 68/198 (34%), Gaps = 17/198 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNC-----RIVRDPQTLKSKGYAFVSFVKKAEAEN 152
++VG++ I + + + F + V Q + K +AF+ F E
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 153 AITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCG 212
A+ A +G +S++ P ++ + ++ G
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVS-----TVVPDSAHKLFIG 120
Query: 213 GFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTD 266
G LN++ V ++ + FG + + K+ KGYAF ++ AI ++
Sbjct: 121 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ 180
Query: 267 INGHTVKCFWGKESENNS 284
+ + N+
Sbjct: 181 LGDKKLLVQRASVGAKNA 198
Score = 80.5 bits (199), Expect = 6e-18
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 3/88 (3%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVA 59
L++G L + ++ + L + GP+K ++++ YAF E+V V
Sbjct: 110 VPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 169
Query: 60 ATALAAMNKRVFLEKEMKVNWASSPGNQ 87
A+A +N +K++ V AS
Sbjct: 170 DQAIAGLNGMQLGDKKLLVQRASVGAKN 197
Score = 60.0 bits (146), Expect = 7e-11
Identities = 16/115 (13%), Positives = 40/115 (34%), Gaps = 14/115 (12%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF-----------KEKGYAFVKFTTKETA 255
+Y G + EE + F+ + + ++K +AF++F + +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 256 THAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNSTAPQFPY--IY 308
T A+ G ++K + + +++ + P ST ++
Sbjct: 65 TQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLF 118
>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 = 187 bits (478), Expect = 1e-57
Identities = 43/205 (20%), Positives = 80/205 (39%), Gaps = 18/205 (8%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATA 62
+Q L+VGNL +TEE LF + G + R+ G + F+ T+A A
Sbjct: 18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG---FGFIRLESRTLAEIA 74
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEI 122
A ++ + + +++ +A+ + V +LSP + + L++AF+ FG +
Sbjct: 75 KAELDGTILKSRPLRIRFATHGAA-----------LTVKNLSPVVSNELLEQAFSQFGPV 123
Query: 123 SNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN-GQWLGSRSIRTNWSTRKPPAMTN 181
+V D + ++ G FV F K A A+ G +L + + R +
Sbjct: 124 EKAVVVVDDRG-RATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQ--FD 180
Query: 182 ERKRQNSHTKTITFDEVYNQSSPTN 206
+ T + P
Sbjct: 181 DEDGLPEKLMQKTQQYHKEREQPPR 205
Score = 144 bits (365), Expect = 6e-41
Identities = 47/291 (16%), Positives = 88/291 (30%), Gaps = 78/291 (26%)
Query: 74 KEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQT 133
+ + P ++ + +FVG+L +I + K F +GE S I RD
Sbjct: 4 FTIDIKSFLKP---GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD--- 57
Query: 134 LKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTI 193
+G+ F+ + AE A ++G L SR +R ++T
Sbjct: 58 ---RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGA----------------- 97
Query: 194 TFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVK 248
+ ++ EL+ + FS FG + V + G FV+
Sbjct: 98 --------------ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVE 143
Query: 249 FTTKETATHAIESIHNTD-INGHTVKCFWGKESENNSTLAQPSAPTTPQPNSTAPQFPYI 307
F K A A+E + + T + + + P +
Sbjct: 144 FAAKPPARKALERCGDGAFLLTTTPRPVIVE-------PMEQFDDEDGLPEKLMQKTQQY 196
Query: 308 YNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGYVGMVGRQVPGWQG 358
+ ++ + P +F Q G + W+
Sbjct: 197 HKER----------------EQPPRFAQPGTFEFEYA---------SRWKA 222
>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 = 183 bits (468), Expect = 3e-57
Identities = 47/175 (26%), Positives = 76/175 (43%), Gaps = 10/175 (5%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP-GNDP----YAFLEFVHHTVA 59
S ++VG + + +E+ L LF Q G V V+R+ N P F+ F A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 60 ATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPF 119
A A++ L P + K + +F+G +S + ++ F+ F
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQMK-PADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSF 119
Query: 120 GEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQ---WLGSRSIRTNW 171
G+I CRI+R P S+G AFV+F +A A+ AI AM+ S + +
Sbjct: 120 GQIEECRILRGPDG-LSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKF 173
Score = 143 bits (362), Expect = 2e-41
Identities = 43/182 (23%), Positives = 72/182 (39%), Gaps = 28/182 (15%)
Query: 93 SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQT--LKSKGYAFVSFVKKAEA 150
S+ +FVG + + L+E F +G + ++RD +SKG FV+F + A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 151 ENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVY 210
A A++ + KP +E+ K ++
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQ--MKPA--DSEKNNAVEDRK-----------------LF 99
Query: 211 CGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESIHNT 265
G K E + +FS FG I + R+ + +G AFV FTT+ A AI+++H
Sbjct: 100 IGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159
Query: 266 DI 267
Sbjct: 160 QT 161
Score = 69.9 bits (172), Expect = 2e-14
Identities = 22/84 (26%), Positives = 41/84 (48%), Gaps = 5/84 (5%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAA 60
+ + L++G + TE + +FS G ++ C+++R P AF+ F +A
Sbjct: 91 NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQ 150
Query: 61 TALAAMNKRVFLE---KEMKVNWA 81
TA+ AM++ +E M V +A
Sbjct: 151 TAIKAMHQAQTMEGCSSPMVVKFA 174
Score = 66.1 bits (162), Expect = 5e-13
Identities = 18/91 (19%), Positives = 39/91 (42%), Gaps = 10/91 (10%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE--------KGYAFVKFTTKE 253
S ++ G + +E+ + ++F +G + +I V ++ KG FV F T++
Sbjct: 1 SDAIK--MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRK 58
Query: 254 TATHAIESIHNTDINGHTVKCFWGKESENNS 284
A A ++HN + K +++
Sbjct: 59 AALEAQNALHNMKVLPGMHHPIQMKPADSEK 89
>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 = 175 bits (445), Expect = 7e-54
Identities = 37/175 (21%), Positives = 69/175 (39%), Gaps = 11/175 (6%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI-REPGND-PYAFLEFVHHTVAA 60
+ + P L++GNL+ + + L S++ V+ G + + +++F
Sbjct: 9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 68
Query: 61 TALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFG 120
AL + E+K+ ++ + + +LS I LKE F
Sbjct: 69 KALE-LTGLKVFGNEIKLEKPKGRDSKKVRAART---LLAKNLSFNITEDELKEVFEDAL 124
Query: 121 EISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
EI Q KSKG A++ F +A+AE + G + RS+ ++ K
Sbjct: 125 EI-----RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
Score = 143 bits (364), Expect = 9e-42
Identities = 33/193 (17%), Positives = 78/193 (40%), Gaps = 26/193 (13%)
Query: 88 PKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKK 147
+++ +++F+G+L+P LK A + ++ +V D +T ++ + +V F
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESA 64
Query: 148 AEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNC 207
+ E A+ + G + I+ + +K + +
Sbjct: 65 EDLEKAL-ELTGLKVFGNEIKLEKPKGRD-----SKKVRAAR------------------ 100
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF-KEKGYAFVKFTTKETATHAIESIHNTD 266
T+ ++ E+ + +VF I + K KG A+++F ++ A +E +
Sbjct: 101 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 160
Query: 267 INGHTVKCFWGKE 279
I+G +V ++ E
Sbjct: 161 IDGRSVSLYYTGE 173
>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 = 164 bits (416), Expect = 3e-50
Identities = 71/126 (56%), Positives = 86/126 (68%), Gaps = 12/126 (9%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + K+DTSNH+H+FVGDLSPEI T+ +K AFAPFG IS+ R+V+D T KSKGY
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYN 200
FVSF K +AENAI M GQWLG R IRTNW+TRKPPA + S+TK
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPA---PKSTYESNTK--------- 108
Query: 201 QSSPTN 206
QS P++
Sbjct: 109 QSGPSS 114
Score = 78.2 bits (193), Expect = 6e-18
Identities = 23/100 (23%), Positives = 45/100 (45%), Gaps = 9/100 (9%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHH 56
D S ++VG+L +T E + A F+ G + +V+++ G Y F+ F +
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG---YGFVSFFNK 67
Query: 57 TVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHY 96
A A+ M + ++++ NWA+ PK ++
Sbjct: 68 WDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNT 107
Score = 68.5 bits (168), Expect = 1e-14
Identities = 27/105 (25%), Positives = 43/105 (40%), Gaps = 6/105 (5%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKET 254
+ + + V+ G ++ E + F+PFG I D RV K+ KGY FV F K
Sbjct: 10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 69
Query: 255 ATHAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
A +AI+ + + G ++ W S P+S
Sbjct: 70 AENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSS 114
>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 = 154 bits (392), Expect = 4e-47
Identities = 55/86 (63%), Positives = 64/86 (74%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEA 150
+H+H+FVGDLSPEI T + AFAPFG IS+ R+V+D T KSKGY FVSF K +A
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61
Query: 151 ENAITAMNGQWLGSRSIRTNWSTRKP 176
ENAI M GQWLG R IRTNW+TRKP
Sbjct: 62 ENAIQQMGGQWLGGRQIRTNWATRKP 87
Score = 71.4 bits (176), Expect = 5e-16
Identities = 18/86 (20%), Positives = 38/86 (44%), Gaps = 9/86 (10%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHH 56
++VG+L +T + A F+ G + +V+++ G Y F+ F +
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKG---YGFVSFFNK 58
Query: 57 TVAATALAAMNKRVFLEKEMKVNWAS 82
A A+ M + ++++ NWA+
Sbjct: 59 WDAENAIQQMGGQWLGGRQIRTNWAT 84
Score = 66.4 bits (163), Expect = 4e-14
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETAT 256
++ V+ G ++ ++ F+PFG I D RV K+ KGY FV F K A
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
Query: 257 HAIESIHNTDINGHTVKCFW 276
+AI+ + + G ++ W
Sbjct: 63 NAIQQMGGQWLGGRQIRTNW 82
>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 = 158 bits (401), Expect = 5e-47
Identities = 42/197 (21%), Positives = 84/197 (42%), Gaps = 19/197 (9%)
Query: 98 IFVGDLSPE-IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+ V +L+PE + Q+L F +G++ +I+ + K A V +A+ A++
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60
Query: 157 MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTIT----------FDEVYNQSSPTN 206
+NG L + IR S + + E + TK + + P +
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF--KEKGYAFVKFTTKETATHAIESIHN 264
T++ ++EE + +FS G +V F K++ A ++ + E A A+ +HN
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 180
Query: 265 TDI-NGHTVKCFWGKES 280
D+ H ++ + K +
Sbjct: 181 HDLGENHHLRVSFSKST 197
Score = 108 bits (271), Expect = 4e-28
Identities = 33/200 (16%), Positives = 66/200 (33%), Gaps = 38/200 (19%)
Query: 8 TTLYVGNLDV-SVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM 66
+ L V NL+ VT + L LF G V+ K++ A ++ A A++ +
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE--NALVQMADGNQAQLAMSHL 61
Query: 67 NKRVFLEKEMKVNWA----------SSPGNQPKQDTSNHYH------------------- 97
N K +++ + +D N
Sbjct: 62 NGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA 121
Query: 98 -IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+ + ++ P + + LK F+ G + K + A + EA A+
Sbjct: 122 TLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALID 177
Query: 157 MNGQWLG-SRSIRTNWSTRK 175
++ LG + +R ++S
Sbjct: 178 LHNHDLGENHHLRVSFSKST 197
Score = 69.5 bits (170), Expect = 5e-14
Identities = 19/143 (13%), Positives = 47/143 (32%), Gaps = 11/143 (7%)
Query: 206 NCTVYCGGFG-KDLNEELVSKVFSPFGTIVDIRV-FKEKGYAFVKFTTKETATHAIESIH 263
N + + + + + +F +G + +++ F +K A V+ A A+ ++
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62
Query: 264 NTDINGHTVKCFWGKESENNSTLAQPSAPTTPQP--NSTAPQFPYIYNQQMGYWYPQAA- 320
++G ++ K + NS +F ++ +P +A
Sbjct: 63 GHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSAT 122
Query: 321 ------AYTATAAQLPQQFYQYG 337
+ + L F G
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNG 145
>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 = 155 bits (393), Expect = 2e-45
Identities = 43/214 (20%), Positives = 86/214 (40%), Gaps = 19/214 (8%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPE-IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGY 139
P + + + V +L+PE + Q+L F +G++ +I+ K
Sbjct: 20 HMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILF-----NKKEN 74
Query: 140 AFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTIT----- 194
A V +A+ A++ +NG L + IR S + + E + TK
Sbjct: 75 ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLH 134
Query: 195 -----FDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF--KEKGYAFV 247
+ + P + T++ ++EE + +FS G +V F K++ A +
Sbjct: 135 RFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALI 194
Query: 248 KFTTKETATHAIESIHNTDI-NGHTVKCFWGKES 280
+ + E A A+ +HN D+ H ++ + K +
Sbjct: 195 QMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST 228
Score = 101 bits (252), Expect = 5e-25
Identities = 33/205 (16%), Positives = 70/205 (34%), Gaps = 38/205 (18%)
Query: 3 DESQPTTLYVGNLDV-SVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAAT 61
+ + L V NL+ VT + L LF G V+ K++ A ++ A
Sbjct: 30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE--NALVQMADGNQAQL 87
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQD-----------TSNHYH------------- 97
A++ +N K +++ + Q ++ ++ H
Sbjct: 88 AMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI 147
Query: 98 ------IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+ + ++ P + + LK F+ G + K + A + EA
Sbjct: 148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAV 203
Query: 152 NAITAMNGQWLG-SRSIRTNWSTRK 175
A+ ++ LG + +R ++S
Sbjct: 204 QALIDLHNHDLGENHHLRVSFSKST 228
Score = 66.6 bits (162), Expect = 6e-13
Identities = 15/148 (10%), Positives = 42/148 (28%), Gaps = 11/148 (7%)
Query: 201 QSSPTNCTVYCGGFG-KDLNEELVSKVFSPFGTIVDIRV-FKEKGYAFVKFTTKETATHA 258
+ N + + + + + +F +G + +++ F +K A V+ A A
Sbjct: 29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLA 88
Query: 259 IESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQ 318
+ ++ ++G ++ K + +P + +
Sbjct: 89 MSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIF 148
Query: 319 A---------AAYTATAAQLPQQFYQYG 337
+ + L F G
Sbjct: 149 PPSATLHLSNIPPSVSEEDLKVLFSSNG 176
>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 = 138 bits (349), Expect = 1e-40
Identities = 31/81 (38%), Positives = 51/81 (62%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
+++FVGDL+ ++ +TL+ AF F + ++ D QT S+GY FVSF + +A+NA+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 156 AMNGQWLGSRSIRTNWSTRKP 176
+M GQ L R +R NW+ +
Sbjct: 62 SMQGQDLNGRPLRINWAAKLE 82
Score = 68.7 bits (169), Expect = 6e-15
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 9/79 (11%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAATAL 63
L+VG+L+V+V +E L F V+ + G Y F+ F A A+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG---YGFVSFTSQDDAQNAM 60
Query: 64 AAMNKRVFLEKEMKVNWAS 82
+M + + +++NWA+
Sbjct: 61 DSMQGQDLNGRPLRINWAA 79
Score = 66.4 bits (163), Expect = 3e-14
Identities = 19/80 (23%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
++ G ++++E + F F + + V + +GY FV FT+++ A +A++S+
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 263 HNTDINGHTVKCFWGKESEN 282
D+NG ++ W + E+
Sbjct: 64 QGQDLNGRPLRINWAAKLEH 83
>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 = 136 bits (345), Expect = 4e-40
Identities = 37/99 (37%), Positives = 57/99 (57%), Gaps = 6/99 (6%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNC-RIVRDPQTLKSKGYAFVSFVKKAEA 150
+S IF+G+L PEI+ + L + F+ FG I +I+RDP T SKGYAF++F +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 151 ENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSH 189
+ AI AMNGQ+L +R I +++ +K + S
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYAFKKD-----SKGSGPSS 95
Score = 65.7 bits (161), Expect = 9e-14
Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 4/93 (4%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGC-KVIREPGNDP---YAFLEFVHHTVAA 60
S + +++GNLD + E+LL FS G + K++R+P YAF+ F +
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 61 TALAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
A+ AMN + + + V++A ++ +S
Sbjct: 63 AAIEAMNGQYLCNRPITVSYAFKKDSKGSGPSS 95
Score = 59.5 bits (145), Expect = 2e-11
Identities = 18/90 (20%), Positives = 45/90 (50%), Gaps = 7/90 (7%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVD-IRVFKE------KGYAFVKFTTKETA 255
S + ++ G +++E+L+ FS FG I+ ++ ++ KGYAF+ F + + +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 256 THAIESIHNTDINGHTVKCFWGKESENNST 285
AIE+++ + + + + ++ +
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYAFKKDSKGS 91
>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 = 132 bits (334), Expect = 3e-38
Identities = 29/98 (29%), Positives = 49/98 (50%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + P + ++ I V +LS + L+E F PFG IS + +D T +SKG+A
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPA 178
F+SF ++ +A AI ++G + W+ +
Sbjct: 61 FISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS 98
Score = 69.2 bits (170), Expect = 5e-15
Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 14/97 (14%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHH 56
T+ V NL E L LF G + + ++ G +AF+ F
Sbjct: 11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKG---FAFISFHRR 67
Query: 57 TVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
AA A+A ++ + + V WA +P ++
Sbjct: 68 EDAARAIAGVSGFGYDHLILNVEWA-----KPSTNSG 99
Score = 65.7 bits (161), Expect = 1e-13
Identities = 25/91 (27%), Positives = 42/91 (46%), Gaps = 6/91 (6%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKE 253
N+ + N T+ +D E + ++F PFG+I I + K+ KG+AF+ F +E
Sbjct: 9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
Query: 254 TATHAIESIHNTDINGHTVKCFWGKESENNS 284
A AI + + + W K S N+
Sbjct: 69 DAARAIAGVSGFGYDHLILNVEWAKPSTNSG 99
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 128 bits (323), Expect = 3e-36
Identities = 33/98 (33%), Positives = 51/98 (52%)
Query: 75 EMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTL 134
E V+ S + ++VG L+ E++ + L AF PFG+I++ +I D +T
Sbjct: 43 ERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETE 102
Query: 135 KSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWS 172
K +G+AFV F +A AI MN L R+IR N +
Sbjct: 103 KHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
Score = 70.2 bits (172), Expect = 7e-15
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHH 56
+ LYVG L V +++L A F G + ++ + G +AF+EF
Sbjct: 59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG---FAFVEFELA 115
Query: 57 TVAATALAAMNKRVFLEKEMKVNWA 81
AA A+ MN+ + ++VN A
Sbjct: 116 EDAAAAIDNMNESELFGRTIRVNLA 140
Score = 68.7 bits (168), Expect = 2e-14
Identities = 23/80 (28%), Positives = 48/80 (60%), Gaps = 6/80 (7%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKET 254
S+ T +Y GG ++++++++ F PFG I DI++ + +G+AFV+F E
Sbjct: 58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 117
Query: 255 ATHAIESIHNTDINGHTVKC 274
A AI++++ +++ G T++
Sbjct: 118 AAAAIDNMNESELFGRTIRV 137
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 126 bits (318), Expect = 6e-36
Identities = 30/93 (32%), Positives = 47/93 (50%), Gaps = 3/93 (3%)
Query: 89 KQDTSNHYHIFVGDLSPEIETQTLKEAF-APFGEISNCRIVRDPQTLKSKGYAFVSFVKK 147
+ Y +FVGDL+P+++ L E F + ++V D QT SKGY FV F +
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDE 61
Query: 148 AEAENAITAMNGQ-WLGSRSIRTNWSTRKPPAM 179
E + A+T G LGS+ +R + + K +
Sbjct: 62 LEQKRALTECQGAVGLGSKPVRLSVAIPKASRV 94
Score = 70.0 bits (172), Expect = 4e-15
Identities = 22/95 (23%), Positives = 40/95 (42%), Gaps = 4/95 (4%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGP-VKGCKVIREPGNDP--YAFLEFVHHTVA 59
+L+VG+L V + +L F ++ P +G KV+ + Y F++F
Sbjct: 5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQ 64
Query: 60 ATALAAMNKRVFLE-KEMKVNWASSPGNQPKQDTS 93
AL V L K ++++ A ++ K S
Sbjct: 65 KRALTECQGAVGLGSKPVRLSVAIPKASRVKPVES 99
Score = 57.7 bits (140), Expect = 7e-11
Identities = 20/101 (19%), Positives = 40/101 (39%), Gaps = 9/101 (8%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFS-PFGTIVDIRVFKE-----KGYAFVKFTTKE 253
+ SS +++ G D+++ ++ + F + + +V + KGY FVKFT +
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDEL 62
Query: 254 TATHAIESIHN-TDINGHTVKCFWG--KESENNSTLAQPSA 291
A+ + V+ K S + PS+
Sbjct: 63 EQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPVESGPSS 103
>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 = 125 bits (317), Expect = 7e-36
Identities = 30/108 (27%), Positives = 57/108 (52%), Gaps = 7/108 (6%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
SS + + +++V +L I+ + L++AF+PFG I++ +++ + +SKG+ F
Sbjct: 2 SSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGF 59
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSH 189
V F EA A+T MNG+ + ++ + + RK ER+ S
Sbjct: 60 VCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKE-----ERQSGPSS 102
Score = 76.9 bits (190), Expect = 1e-17
Identities = 28/94 (29%), Positives = 40/94 (42%), Gaps = 6/94 (6%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-YAFLEFVHHTVAAT 61
Q LYV NLD + +E L FS G + KV+ E G + F+ F A
Sbjct: 11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATK 70
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNH 95
A+ MN R+ K + V A Q K++ +
Sbjct: 71 AVTEMNGRIVATKPLYVALA-----QRKEERQSG 99
Score = 62.2 bits (152), Expect = 2e-12
Identities = 26/97 (26%), Positives = 41/97 (42%), Gaps = 14/97 (14%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETATHAIESI 262
+Y +++E + K FSPFGTI +V E KG+ FV F++ E AT A+ +
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 263 HNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
+ + + LAQ P+S
Sbjct: 76 NGRIVATKPLYV----------ALAQRKEERQSGPSS 102
>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 = 125 bits (316), Expect = 1e-35
Identities = 57/106 (53%), Positives = 79/106 (74%), Gaps = 2/106 (1%)
Query: 186 QNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYA 245
+ +TK + F++V NQSSP NCTVYCGG L ++L+ + FSPFG I++IRVF EKGY+
Sbjct: 5 SSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYS 64
Query: 246 FVKFTTKETATHAIESIHNTDINGHTVKCFWGKESENNSTLAQPSA 291
FV+F+T E+A HAI S++ T I GH VKC+WGKES + + + PS+
Sbjct: 65 FVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMT--SGPSS 108
Score = 97.8 bits (244), Expect = 3e-25
Identities = 24/105 (22%), Positives = 48/105 (45%), Gaps = 12/105 (11%)
Query: 79 NWASSPGNQPK------QDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQ 132
+ +S Q + Q + + ++ G ++ + Q +++ F+PFG+I R+ +
Sbjct: 3 SGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-- 60
Query: 133 TLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
KGY+FV F A +AI ++NG + ++ W P
Sbjct: 61 ----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD 101
Score = 87.4 bits (217), Expect = 2e-21
Identities = 22/89 (24%), Positives = 39/89 (43%), Gaps = 3/89 (3%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALA 64
+ T+Y G + +T++L+ FS G + +V E G Y+F+ F H AA A+
Sbjct: 23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG---YSFVRFSTHESAAHAIV 79
Query: 65 AMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
++N +K W + +S
Sbjct: 80 SVNGTTIEGHVVKCYWGKESPDMTSGPSS 108
>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 = 125 bits (317), Expect = 6e-35
Identities = 34/166 (20%), Positives = 67/166 (40%), Gaps = 11/166 (6%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATA 62
+ +++G L+ TE+ L F + G V K++++P + FL F +
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEI 122
+ + K + A Q K IFVG + P++ + +E F+ +G I
Sbjct: 62 VKTQHI--LDGKVIDPKRAIPRDEQDKTGK-----IFVGGIGPDVRPKEFEEFFSQWGTI 114
Query: 123 SNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIR 168
+ +++ D T +S+G+ FV++ + R I
Sbjct: 115 IDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIE 159
Score = 118 bits (297), Expect = 5e-32
Identities = 33/183 (18%), Positives = 75/183 (40%), Gaps = 34/183 (18%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G L+ + L+E F +G +++ +I++DP T +S+G+ F+SF K + + +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKD 217
+ L + I + + ++ GG G D
Sbjct: 66 H--ILDGKVIDPKRAIPR-------------------------DEQDKTGKIFVGGIGPD 98
Query: 218 LNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDINGHT 271
+ + + FS +GTI+D ++ + +G+ FV + + + ++ D
Sbjct: 99 VRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQN-KFIDFKDRK 157
Query: 272 VKC 274
++
Sbjct: 158 IEI 160
Score = 52.1 bits (126), Expect = 3e-08
Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIE 260
C ++ GG D E+ + + F +GT+ D+++ K+ G+ F+ F + ++
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 261 SIHNTDINGHTVKC 274
+ H ++G +
Sbjct: 64 TQH--ILDGKVIDP 75
Score = 49.1 bits (118), Expect = 3e-07
Identities = 11/91 (12%), Positives = 34/91 (37%), Gaps = 9/91 (9%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVA 59
++ + ++VG + V + FSQ G + +++ + + F+ +
Sbjct: 83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142
Query: 60 ATALAAMNKRVFLEKEMKVNWASSPGNQPKQ 90
F ++++++ A +P+
Sbjct: 143 DRVC-QNKFIDFKDRKIEIKRA-----EPRH 167
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 122 bits (309), Expect = 1e-34
Identities = 26/86 (30%), Positives = 39/86 (45%)
Query: 194 TFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKE 253
D + + P T Y G E + +F FG I+D + + EKG F+K+ T E
Sbjct: 15 AVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHE 74
Query: 254 TATHAIESIHNTDINGHTVKCFWGKE 279
A I ++ N G ++ WGKE
Sbjct: 75 QAAVCIVALANFPFQGRNLRTGWGKE 100
Score = 88.5 bits (220), Expect = 6e-22
Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 6/90 (6%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
+ + + ++G++ L F FG I + + + KG F
Sbjct: 14 QAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCF 67
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNW 171
+ + +A I A+ R++RT W
Sbjct: 68 IKYDTHEQAAVCIVALANFPFQGRNLRTGW 97
Score = 80.8 bits (200), Expect = 4e-19
Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
TT Y+GN+ TE L LF G + K E G F+++ H AA + A+
Sbjct: 28 TTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKG---CCFIKYDTHEQAAVCIVALA 84
Query: 68 KRVFLEKEMKVNWASS 83
F + ++ W
Sbjct: 85 NFPFQGRNLRTGWGKE 100
>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 = 127 bits (319), Expect = 3e-34
Identities = 50/289 (17%), Positives = 93/289 (32%), Gaps = 19/289 (6%)
Query: 1 MCDESQP--TTLYVGNLDVSVTEE----LLCALFSQIGPVKGCKVIREPGNDPYAFLEFV 54
M T+Y+ NL+ + ++ L A+FSQ G + V R AF+ F
Sbjct: 1 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK 60
Query: 55 HHTVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQ---DTSNHYHIFVGDLSPEIETQT 111
+ A AL +M F +K M++ +A + + + ET
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA 120
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNW 171
K+A G V+ P + + G
Sbjct: 121 TKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMI--------PP 172
Query: 172 STRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFG 231
P + +P N ++ ++ NE ++S +F+ F
Sbjct: 173 PGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFP 232
Query: 232 TIVDIRVF-KEKGYAFVKFTTKETATHAIESIHNTDI-NGHTVKCFWGK 278
++R+ AFV+F + A A +++ I + +K + K
Sbjct: 233 GFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK 281
Score = 78.0 bits (191), Expect = 2e-16
Identities = 31/198 (15%), Positives = 61/198 (30%), Gaps = 8/198 (4%)
Query: 201 QSSPTNCTVYCGGFGKDLNEE----LVSKVFSPFGTIVDIRVFKE---KGYAFVKFTTKE 253
+ N T+Y + + ++ + +FS FG I+DI V + +G AFV F
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVS 63
Query: 254 TATHAIESIHNTDINGHTVKCFWGK-ESENNSTLAQPSAPTTPQPNSTAPQFPYIYNQQM 312
+AT+A+ S+ ++ + K +S+ + + + P+ +
Sbjct: 64 SATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKK 123
Query: 313 GYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGYVGMVGRQVPGWQGIPGAQPTAQQMAVA 372
A Q ++ +P IP Q+
Sbjct: 124 AVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPG 183
Query: 373 QAQPSMMAAYAMQQFPTQ 390
P + M
Sbjct: 184 AMPPQQLMPGQMPPAQPL 201
>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 = 120 bits (304), Expect = 5e-34
Identities = 54/92 (58%), Positives = 63/92 (68%), Gaps = 1/92 (1%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP-GNDPYAFLEFVHHTVAAT 61
D+ QP TLYVGNL VTE L+ LFSQIGP K CK+I E NDPY F+EF H AA
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 70
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
ALAAMN R L KE+KVNWA++P +Q +S
Sbjct: 71 ALAAMNGRKILGKEVKVNWATTPSSQKSGPSS 102
Score = 113 bits (285), Expect = 3e-31
Identities = 23/94 (24%), Positives = 49/94 (52%), Gaps = 2/94 (2%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
SS + +D ++VG+LS ++ + + F+ G +C+++ + + + Y F
Sbjct: 2 SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCF 59
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
V F + +A A+ AMNG+ + + ++ NW+T
Sbjct: 60 VEFYEHRDAAAALAAMNGRKILGKEVKVNWATTP 93
Score = 71.5 bits (176), Expect = 8e-16
Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 4/90 (4%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETA 255
+ T+Y G +D+ E L+ ++FS G ++ E Y FV+F A
Sbjct: 9 MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDA 68
Query: 256 THAIESIHNTDINGHTVKCFWGKESENNST 285
A+ +++ I G VK W + +
Sbjct: 69 AAALAAMNGRKILGKEVKVNWATTPSSQKS 98
>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 (307), Expect = 3e-33
Identities = 40/183 (21%), Positives = 78/183 (42%), Gaps = 27/183 (14%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G LS E ++L+ F +G +++C ++RDP T +S+G+ FV++ E + A+
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NA 74
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKD 217
+ R + + + ++R + K I + GG +D
Sbjct: 75 RPHKVDGRVVEPKRAVSRED---SQRPGAHLTVKKI----------------FVGGIKED 115
Query: 218 LNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDINGHT 271
E + F +G I I + K++G+AFV F ++ + +NGH
Sbjct: 116 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHN 174
Query: 272 VKC 274
+
Sbjct: 175 CEV 177
Score = 121 bits (306), Expect = 4e-33
Identities = 38/188 (20%), Positives = 75/188 (39%), Gaps = 6/188 (3%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVA 59
+ Q L++G L T+E L + F Q G + C V+R+P + F+ +
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 60 ATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYH-IFVGDLSPEIETQTLKEAFAP 118
A+ A +V + ++ A S + + IFVG + + E L++ F
Sbjct: 69 DAAMNARPHKV-DGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQ 127
Query: 119 FGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPA 178
+G+I I+ D + K +G+AFV+F + + + + + K
Sbjct: 128 YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEM 186
Query: 179 MTNERKRQ 186
+ ++
Sbjct: 187 ASASSSQR 194
Score = 48.8 bits (117), Expect = 5e-07
Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 7/80 (8%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKET 254
+ ++ GG + +E + F +GT+ D V ++ G+ FV + T E
Sbjct: 8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Query: 255 ATHAIESIHNTDINGHTVKC 274
A+ + ++G V+
Sbjct: 68 VDAAMNA-RPHKVDGRVVEP 86
>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 = 120 bits (301), Expect = 2e-32
Identities = 21/195 (10%), Positives = 57/195 (29%), Gaps = 24/195 (12%)
Query: 98 IFVGDLSPE-IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+ V L + + F +G + + ++ G A V + AIT
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITH 61
Query: 157 MNGQWLGSRSIRTNWS--------TRKPPAMTNERKRQNSHTKTITF----DEVYNQSSP 204
+N ++ + + S + + S ++ F N+
Sbjct: 62 LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQH 121
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHA 258
+ ++ ++ EE ++ G V + +++ +K A
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181
Query: 259 IESIHNTDINGHTVK 273
+ +++ +
Sbjct: 182 LGFLNHYQMKNPNGP 196
Score = 115 bits (288), Expect = 2e-30
Identities = 24/203 (11%), Positives = 56/203 (27%), Gaps = 35/203 (17%)
Query: 5 SQPTTLYVGNLDVS-VTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATAL 63
+ L V LD S + + + +F G V+ K ++ A +E A+
Sbjct: 2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS--KPGAAMVEMADGYAVDRAI 59
Query: 64 AAMNKRVFLEKEMKVNWASSPGNQPKQDT------------------------------- 92
+N ++M V + P P Q
Sbjct: 60 THLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRI 119
Query: 93 -SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+ + E+ + E G + + + + K++A
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179
Query: 152 NAITAMNGQWLGSRSIRTNWSTR 174
+ +N + + + ++ +
Sbjct: 180 ETLGFLNHYQMKNPNGPYPYTLK 202
Score = 60.1 bits (145), Expect = 7e-11
Identities = 20/146 (13%), Positives = 42/146 (28%), Gaps = 13/146 (8%)
Query: 206 NCTVYCGGFGKD-LNEELVSKVFSPFGTIVDIRVFKEK-GYAFVKFTTKETATHAIESIH 263
+ + G + +N + V VF +G + ++ K K G A V+ AI ++
Sbjct: 4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLN 63
Query: 264 NTDINGHTVKCFWGK---------ESENNSTLAQPSAPTTPQPNSTAPQFPYIYNQQMGY 314
N + G + K + + + + + P+ Q
Sbjct: 64 NNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPS 123
Query: 315 WYPQAA--AYTATAAQLPQQFYQYGQ 338
T + + G
Sbjct: 124 NVLHFFNAPLEVTEENFFEICDELGV 149
Score = 53.2 bits (127), Expect = 2e-08
Identities = 14/79 (17%), Positives = 24/79 (30%), Gaps = 3/79 (3%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEFVHHTVAA 60
+ L+ N + VTEE + ++G + V G LE+ + A
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179
Query: 61 TALAAMNKRVFLEKEMKVN 79
L +N
Sbjct: 180 ETLGFLNHYQMKNPNGPYP 198
>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 = 115 bits (290), Expect = 8e-32
Identities = 29/99 (29%), Positives = 54/99 (54%), Gaps = 2/99 (2%)
Query: 91 DTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEA 150
+ + +F+G L+ E + LK F G IS +++D +T KS+G+AF++F A+A
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADA 61
Query: 151 ENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSH 189
+NA MNG+ L ++I+ + + + R+R +
Sbjct: 62 KNAAKDMNGKSLHGKAIKVEQAKKPSFQ-SGGRRRPPAS 99
Score = 75.8 bits (187), Expect = 4e-17
Identities = 25/90 (27%), Positives = 43/90 (47%), Gaps = 2/90 (2%)
Query: 1 MCDESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTV 58
M + P L++G L+ E++L A+F + GP+ +I++ + +AF+ F +
Sbjct: 1 MVEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPAD 60
Query: 59 AATALAAMNKRVFLEKEMKVNWASSPGNQP 88
A A MN + K +KV A P Q
Sbjct: 61 AKNAAKDMNGKSLHGKAIKVEQAKKPSFQS 90
Score = 67.4 bits (165), Expect = 4e-14
Identities = 19/112 (16%), Positives = 48/112 (42%), Gaps = 7/112 (6%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETAT 256
+ ++ GG ++ NE+++ VF G I ++ + K+ +G+AF+ F A
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAK 62
Query: 257 HAIESIHNTDINGHTVKCFW--GKESENNSTLAQPSAPTTPQPNSTAPQFPY 306
+A + ++ ++G +K ++ P++ P+ + +
Sbjct: 63 NAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEHHHH 114
>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 = 114 bits (288), Expect = 2e-31
Identities = 35/128 (27%), Positives = 51/128 (39%), Gaps = 19/128 (14%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+IF+ +L I+ + L + F+ FG I +C++V D SKGY FV F + AE AI
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEK 64
Query: 157 MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGK 216
MNG L R + + ER+ + + VY FG
Sbjct: 65 MNGMLLNDRKVFVGRFKSRK-----EREAEL------------GARAKEFTNVYIKNFGP 107
Query: 217 DLNEELVS 224
S
Sbjct: 108 GSTRAAAS 115
Score = 80.0 bits (198), Expect = 1e-18
Identities = 20/112 (17%), Positives = 43/112 (38%), Gaps = 14/112 (12%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-YAFLEFVHHTVAATAL 63
+++ NLD S+ + L FS G + CKV+ + Y F+ F A A+
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 62
Query: 64 AAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYH--------IFVGDLSPEI 107
MN + ++++ V + +++ +++ + P
Sbjct: 63 EKMNGMLLNDRKVFVGRF-----KSRKEREAELGARAKEFTNVYIKNFGPGS 109
Score = 65.7 bits (161), Expect = 1e-13
Identities = 25/111 (22%), Positives = 43/111 (38%), Gaps = 16/111 (14%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETATH 257
N ++ K ++ + + FS FG I+ +V + KGY FV F T+E A
Sbjct: 3 LGSGN--IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAER 60
Query: 258 AIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNSTAPQFPYIY 308
AIE ++ +N V + + + A +F +Y
Sbjct: 61 AIEKMNGMLLNDRKVFV----------GRFKSRKEREAELGARAKEFTNVY 101
Score = 29.1 bits (66), Expect = 0.78
Identities = 4/20 (20%), Positives = 7/20 (35%)
Query: 3 DESQPTTLYVGNLDVSVTEE 22
+ T +Y+ N T
Sbjct: 93 RAKEFTNVYIKNFGPGSTRA 112
>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 = 113 bits (284), Expect = 3e-31
Identities = 30/80 (37%), Positives = 47/80 (58%)
Query: 93 SNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAEN 152
+ ++VG L+ E++ + L AF PFG+I++ +I D +T K +G+AFV F +A
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 153 AITAMNGQWLGSRSIRTNWS 172
AI MN L R+IR N +
Sbjct: 65 AIDNMNESELFGRTIRVNLA 84
Score = 70.3 bits (173), Expect = 1e-15
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 9/84 (10%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHT 57
+ LYVG L V +++L A F G + ++ + G +AF+EF
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG---FAFVEFELAE 60
Query: 58 VAATALAAMNKRVFLEKEMKVNWA 81
AA A+ MN+ + ++VN A
Sbjct: 61 DAAAAIDNMNESELFGRTIRVNLA 84
Score = 69.1 bits (170), Expect = 5e-15
Identities = 22/78 (28%), Positives = 47/78 (60%), Gaps = 6/78 (7%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETAT 256
+ T +Y GG ++++++++ F PFG I DI++ + +G+AFV+F E A
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
Query: 257 HAIESIHNTDINGHTVKC 274
AI++++ +++ G T++
Sbjct: 64 AAIDNMNESELFGRTIRV 81
>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 = 113 bits (285), Expect = 4e-31
Identities = 32/99 (32%), Positives = 50/99 (50%), Gaps = 2/99 (2%)
Query: 88 PKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKK 147
+ ++VG L+ E++ + L AF PFG+I++ +I D +T K +G+AFV F
Sbjct: 5 SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 64
Query: 148 AEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQ 186
+A AI MN L R+IR N + KP +
Sbjct: 65 EDAAAAIDNMNESELFGRTIRVNLA--KPMRIKESGPSS 101
Score = 72.6 bits (179), Expect = 3e-16
Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 3/93 (3%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHTVAA 60
+ LYVG L V +++L A F G + ++ E +AF+EF AA
Sbjct: 9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68
Query: 61 TALAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
A+ MN+ + ++VN A + +S
Sbjct: 69 AAIDNMNESELFGRTIRVNLAKPMRIKESGPSS 101
Score = 66.9 bits (164), Expect = 5e-14
Identities = 23/90 (25%), Positives = 48/90 (53%), Gaps = 6/90 (6%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKET 254
+ T +Y GG ++++++++ F PFG I DI++ + +G+AFV+F E
Sbjct: 7 GMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 66
Query: 255 ATHAIESIHNTDINGHTVKCFWGKESENNS 284
A AI++++ +++ G T++ K
Sbjct: 67 AAAAIDNMNESELFGRTIRVNLAKPMRIKE 96
>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 = 113 bits (286), Expect = 4e-31
Identities = 29/108 (26%), Positives = 49/108 (45%), Gaps = 5/108 (4%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
S +++ ++F+ L E Q L + F PFG + + ++ D QT SK + F
Sbjct: 12 SIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGF 71
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSH 189
VS+ A+ AI +MNG +G + ++ K N+ K S
Sbjct: 72 VSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK-----NDSKSGPSS 114
Score = 67.7 bits (166), Expect = 3e-14
Identities = 18/96 (18%), Positives = 38/96 (39%), Gaps = 8/96 (8%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVA 59
+ + L++ +L ++ L +F G V KV + + + F+ + + A
Sbjct: 21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 80
Query: 60 ATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNH 95
A+ +MN K +KV + K D+ +
Sbjct: 81 QAAIQSMNGFQIGMKRLKVQLK-----RSKNDSKSG 111
Score = 61.2 bits (149), Expect = 7e-12
Identities = 20/106 (18%), Positives = 43/106 (40%), Gaps = 16/106 (15%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKE 253
+ P ++ ++ ++ + ++F PFG +V +VF + K + FV +
Sbjct: 19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78
Query: 254 TATHAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
+A AI+S++ I +K L + + P+S
Sbjct: 79 SAQAAIQSMNGFQIGMKRLKV----------QLKRSKNDSKSGPSS 114
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 112 bits (281), Expect = 2e-30
Identities = 29/110 (26%), Positives = 51/110 (46%), Gaps = 2/110 (1%)
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGE 121
+ +A++ + A++ G Q + ++F+ L E L F PFG
Sbjct: 9 SASALSTSPLASVALSAAAAAAAGKQI--EGPEGCNLFIYHLPQEFTDTDLASTFLPFGN 66
Query: 122 ISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNW 171
+ + ++ D QT SK + FVSF A+ AI AMNG +G++ ++
Sbjct: 67 VISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL 116
Score = 65.9 bits (161), Expect = 1e-13
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 3/82 (3%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVA 59
+ + L++ +L T+ L + F G V KV + + F+ F + A
Sbjct: 36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
Query: 60 ATALAAMNKRVFLEKEMKVNWA 81
A+ AMN K +KV
Sbjct: 96 QVAIKAMNGFQVGTKRLKVQLK 117
Score = 57.8 bits (140), Expect = 9e-11
Identities = 16/80 (20%), Positives = 36/80 (45%), Gaps = 6/80 (7%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKET 254
P C ++ ++ + ++ F PFG ++ +VF + K + FV F ++
Sbjct: 35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94
Query: 255 ATHAIESIHNTDINGHTVKC 274
A AI++++ + +K
Sbjct: 95 AQVAIKAMNGFQVGTKRLKV 114
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 111 bits (280), Expect = 2e-30
Identities = 28/97 (28%), Positives = 44/97 (45%), Gaps = 3/97 (3%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
PG Q + +FV + E + + + FA +GEI N + D +T KGY
Sbjct: 12 GDEPGPQRSVEGWI---LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 68
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
V + EA+ A+ +NGQ L + I +W + P
Sbjct: 69 LVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105
Score = 65.7 bits (161), Expect = 1e-13
Identities = 23/101 (22%), Positives = 44/101 (43%), Gaps = 6/101 (5%)
Query: 185 RQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE--- 241
R++ + DE Q S ++ G ++ EE + F+ +G I +I + +
Sbjct: 2 REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 61
Query: 242 ---KGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKE 279
KGY V++ T + A A+E ++ D+ G + W
Sbjct: 62 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFV 102
Score = 64.2 bits (157), Expect = 4e-13
Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAAT 61
L+V + TEE + F++ G +K + + G Y +E+ + A
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG---YTLVEYETYKEAQA 80
Query: 62 ALAAMNKRVFLEKEMKVNWA 81
A+ +N + + + + V+W
Sbjct: 81 AMEGLNGQDLMGQPISVDWC 100
>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 = 111 bits (279), Expect = 3e-30
Identities = 26/103 (25%), Positives = 48/103 (46%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + P + + ++VG L ++ L E F G + N + +D T + +GY
Sbjct: 1 GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNER 183
FV F+ + +A+ AI M+ L + IR N ++ ++
Sbjct: 61 FVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPS 103
Score = 86.2 bits (214), Expect = 4e-21
Identities = 31/92 (33%), Positives = 44/92 (47%), Gaps = 3/92 (3%)
Query: 1 MCDESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGND-PYAFLEFVHHT 57
+ + +Q T+YVG LD V+E LL LF Q GPV + R G Y F+EF+
Sbjct: 9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEE 68
Query: 58 VAATALAAMNKRVFLEKEMKVNWASSPGNQPK 89
A A+ M+ K ++VN AS+
Sbjct: 69 DADYAIKIMDMIKLYGKPIRVNKASAHNKNLS 100
Score = 67.3 bits (165), Expect = 3e-14
Identities = 22/89 (24%), Positives = 43/89 (48%), Gaps = 6/89 (6%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKET 254
+ TVY GG + ++E L+ ++F G +V+ + K+ +GY FV+F ++E
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69
Query: 255 ATHAIESIHNTDINGHTVKCFWGKESENN 283
A +AI+ + + G ++ N
Sbjct: 70 ADYAIKIMDMIKLYGKPIRVNKASAHNKN 98
>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 = 110 bits (278), Expect = 4e-30
Identities = 27/99 (27%), Positives = 49/99 (49%), Gaps = 7/99 (7%)
Query: 85 GNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGE-ISNCRIVRDPQTLKSKGYAFVS 143
G+ + +++GDL P ++ + AFA GE + + +I+R+ T GY FV
Sbjct: 1 GSSGSSGMAAS--LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVE 58
Query: 144 FVKKAEAENAITAMNGQWLG----SRSIRTNWSTRKPPA 178
F A AE + +NG+ L ++ + N++T P+
Sbjct: 59 FADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPS 97
Score = 80.1 bits (198), Expect = 8e-19
Identities = 22/92 (23%), Positives = 38/92 (41%), Gaps = 8/92 (8%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIG-PVKGCKVIREP---GNDPYAFLEFVHHTV 58
+L++G+L+ + E + F+ +G V K+IR Y F+EF
Sbjct: 5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT 64
Query: 59 AATALAAMNKRVF----LEKEMKVNWASSPGN 86
A L +N + K K+N+A+ G
Sbjct: 65 AEKCLHKINGKPLPGATPAKRFKLNYATYSGP 96
Score = 57.7 bits (140), Expect = 6e-11
Identities = 21/96 (21%), Positives = 42/96 (43%), Gaps = 11/96 (11%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFG-TIVDIRVFKE------KGYAFVKFTTK 252
+ SS +++ G ++E +S+ F+ G T++ +++ + GY FV+F
Sbjct: 3 SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62
Query: 253 ETATHAIESIHNTDINGHT----VKCFWGKESENNS 284
TA + I+ + G T K + S +S
Sbjct: 63 ATAEKCLHKINGKPLPGATPAKRFKLNYATYSGPSS 98
>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 = 110 bits (276), Expect = 3e-29
Identities = 34/139 (24%), Positives = 57/139 (41%), Gaps = 8/139 (5%)
Query: 47 PYAFLEFVHHTVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYH--------I 98
E V A ++ E + A+ + +H+H +
Sbjct: 14 GETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSL 73
Query: 99 FVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
V +L+ TL+ F +G + + I RD T +S+G+AFV F K +AE+A+ AM+
Sbjct: 74 KVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMD 133
Query: 159 GQWLGSRSIRTNWSTRKPP 177
G L R +R + P
Sbjct: 134 GAVLDGRELRVQMARYGRP 152
Score = 70.3 bits (172), Expect = 9e-15
Identities = 22/163 (13%), Positives = 56/163 (34%), Gaps = 20/163 (12%)
Query: 126 RIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKR 185
+++ + +TLK G V A AE + +T+
Sbjct: 4 KLILNGKTLK--GETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHH 61
Query: 186 QNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE---- 241
+ + ++ + + + +VF +G + D+ + ++
Sbjct: 62 HH------------HMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTK 109
Query: 242 --KGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKESEN 282
+G+AFV+F K A A++++ ++G ++ +
Sbjct: 110 ESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP 152
Score = 63.3 bits (154), Expect = 3e-12
Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 11/86 (12%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPY-------AFLEFVH 55
D T+L V NL + + L +F + G V + R D Y AF+ F
Sbjct: 66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR----DRYTKESRGFAFVRFHD 121
Query: 56 HTVAATALAAMNKRVFLEKEMKVNWA 81
A A+ AM+ V +E++V A
Sbjct: 122 KRDAEDAMDAMDGAVLDGRELRVQMA 147
>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 = 108 bits (272), Expect = 4e-29
Identities = 29/107 (27%), Positives = 46/107 (42%), Gaps = 3/107 (2%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
PG Q + +FV + E + + + FA +GEI N + D +T KGY
Sbjct: 11 GDEPGPQRSVEGWI---LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 67
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQN 187
V + EA+ A+ +NGQ L + I +W + P R +
Sbjct: 68 LVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRR 114
Score = 66.2 bits (162), Expect = 1e-13
Identities = 16/96 (16%), Positives = 35/96 (36%), Gaps = 14/96 (14%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAAT 61
L+V + TEE + F++ G +K + + G Y +E+ + A
Sbjct: 23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG---YTLVEYETYKEAQA 79
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYH 97
A+ +N + + + + V+W +
Sbjct: 80 AMEGLNGQDLMGQPISVDWC-----FVRGPPKGKRR 110
Score = 63.9 bits (156), Expect = 7e-13
Identities = 20/90 (22%), Positives = 38/90 (42%), Gaps = 6/90 (6%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKET 254
Q S ++ G ++ EE + F+ +G I +I + + KGY V++ T +
Sbjct: 17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 76
Query: 255 ATHAIESIHNTDINGHTVKCFWGKESENNS 284
A A+E ++ D+ G + W
Sbjct: 77 AQAAMEGLNGQDLMGQPISVDWCFVRGPPK 106
>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 = 106 bits (267), Expect = 1e-28
Identities = 20/97 (20%), Positives = 43/97 (44%), Gaps = 6/97 (6%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + ++ + +FVG+L P+I + +++ F +G+ I +D KG+
Sbjct: 1 GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFG 54
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
F+ + AE A ++ L + +R ++
Sbjct: 55 FIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSAS 91
Score = 90.8 bits (226), Expect = 8e-23
Identities = 17/86 (19%), Positives = 41/86 (47%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAI 259
++ ++ G D+ EE + K+F +G ++ + K+KG+ F++ T+ A A
Sbjct: 9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAK 68
Query: 260 ESIHNTDINGHTVKCFWGKESENNST 285
+ N + G ++ + S + ++
Sbjct: 69 VELDNMPLRGKQLRVRFACHSASLTS 94
Score = 84.2 bits (209), Expect = 2e-20
Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 3/91 (3%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATA 62
+Q + L+VGNL +TEE + LF + G + ++ G + F+ T+A A
Sbjct: 11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG---FGFIRLETRTLAEIA 67
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
++ K+++V +A + +S
Sbjct: 68 KVELDNMPLRGKQLRVRFACHSASLTSGPSS 98
>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 = 107 bits (268), Expect = 1e-28
Identities = 27/100 (27%), Positives = 51/100 (51%)
Query: 77 KVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKS 136
+ A++ N ++ ++ ++VG L I L+ F PFG I + +++ D +T +S
Sbjct: 8 HSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRS 67
Query: 137 KGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP 176
KGY F++F A+ A+ +NG L R ++ T +
Sbjct: 68 KGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT 107
Score = 66.2 bits (162), Expect = 8e-14
Identities = 24/94 (25%), Positives = 40/94 (42%), Gaps = 8/94 (8%)
Query: 1 MCDESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHT 57
+ P LYVG+L ++TE++L +F G ++ +++ E G Y F+ F
Sbjct: 20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSE 79
Query: 58 VAATALAAMNKRVFLEKEMKVNWASSPGNQPKQD 91
A AL +N + MKV + D
Sbjct: 80 CAKKALEQLNGFELAGRPMKVGHV-----TERTD 108
Score = 58.5 bits (142), Expect = 5e-11
Identities = 22/89 (24%), Positives = 42/89 (47%), Gaps = 6/89 (6%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKE 253
+ S +Y G ++ E+++ +F PFG I I++ + KGY F+ F+ E
Sbjct: 20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSE 79
Query: 254 TATHAIESIHNTDINGHTVKCFWGKESEN 282
A A+E ++ ++ G +K E +
Sbjct: 80 CAKKALEQLNGFELAGRPMKVGHVTERTD 108
>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 = 106 bits (267), Expect = 1e-28
Identities = 16/90 (17%), Positives = 40/90 (44%), Gaps = 2/90 (2%)
Query: 88 PKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKK 147
+++ +++F+G+L+P LK A + ++ +V D +T ++ + +V F
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESA 68
Query: 148 AEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
+ E A+ + G + I+ +
Sbjct: 69 EDLEKAL-ELTGLKVFGNEIKLEKPKGRDG 97
Score = 63.8 bits (156), Expect = 4e-13
Identities = 16/93 (17%), Positives = 32/93 (34%), Gaps = 6/93 (6%)
Query: 196 DEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF-----KEKGYAFVKFT 250
D V S T ++ G + + + S D+ V + + +V F
Sbjct: 7 DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFE 66
Query: 251 TKETATHAIESIHNTDINGHTVKCFWGKESENN 283
+ E A+E + + G+ +K K +
Sbjct: 67 SAEDLEKALE-LTGLKVFGNEIKLEKPKGRDGT 98
Score = 60.0 bits (146), Expect = 1e-11
Identities = 14/92 (15%), Positives = 33/92 (35%), Gaps = 8/92 (8%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAA 60
+ + P L++GNL+ + + L S++ V+ + +++F
Sbjct: 13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 72
Query: 61 TALAAMNKRVFLEKEMKVNWASSPGNQPKQDT 92
AL + E+K+ + + T
Sbjct: 73 KAL-ELTGLKVFGNEIKLEKP-----KGRDGT 98
>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 = 107 bits (268), Expect = 2e-28
Identities = 32/99 (32%), Positives = 50/99 (50%), Gaps = 2/99 (2%)
Query: 79 NWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG 138
+ GN+ D + + V LS + L+E F+ +G I++ IV D Q+ +S+G
Sbjct: 32 RGSRHVGNRANPDPNCC--LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG 89
Query: 139 YAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
+AFV F +A+ A NG L R IR ++S K P
Sbjct: 90 FAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRP 128
Score = 64.0 bits (156), Expect = 7e-13
Identities = 21/122 (17%), Positives = 43/122 (35%), Gaps = 15/122 (12%)
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKD 217
+ R + R ++ + + NC + G
Sbjct: 7 HHHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRA---------NPDPNCCLGVFGLSLY 57
Query: 218 LNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGHT 271
E + +VFS +G I D+ + + +G+AFV F + A A E + +++G
Sbjct: 58 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 117
Query: 272 VK 273
++
Sbjct: 118 IR 119
Score = 62.1 bits (151), Expect = 4e-12
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAAT 61
L V L + TE L +FS+ GP+ ++ + G +AF+ F + A
Sbjct: 47 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG---FAFVYFENVDDAKE 103
Query: 62 ALAAMNKRVFLEKEMKVNWA 81
A N + ++V+++
Sbjct: 104 AKERANGMELDGRRIRVDFS 123
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 107 bits (269), Expect = 2e-28
Identities = 31/108 (28%), Positives = 49/108 (45%), Gaps = 5/108 (4%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
S +P D + V +L+ TL+ F +G + + I RD T +S+G+A
Sbjct: 33 GSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFA 92
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNS 188
FV F K +AE+A+ AM+G L R +R + P +S
Sbjct: 93 FVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP-----PDSHHS 135
Score = 65.9 bits (161), Expect = 2e-13
Identities = 25/101 (24%), Positives = 41/101 (40%), Gaps = 16/101 (15%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPY-------AFLEFVH 55
D T+L V NL + + L +F + G V + R D Y AF+ F
Sbjct: 43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR----DRYTKESRGFAFVRFHD 98
Query: 56 HTVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHY 96
A A+ AM+ V +E++V A + + +H+
Sbjct: 99 KRDAEDAMDAMDGAVLDGRELRVQMA-----RYGRPPDSHH 134
Score = 57.4 bits (139), Expect = 2e-10
Identities = 16/106 (15%), Positives = 41/106 (38%), Gaps = 17/106 (16%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKE 253
++ + + + +VF +G + D+ + ++ +G+AFV+F K
Sbjct: 41 PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKR 100
Query: 254 TATHAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
A A++++ ++G ++ A+ P +S
Sbjct: 101 DAEDAMDAMDGAVLDGRELRVQM----------ARYGRP-PDSHHS 135
>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 = 105 bits (265), Expect = 2e-28
Identities = 23/92 (25%), Positives = 49/92 (53%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G + + + + + + G + N +++ DPQT +SKGYAF+ F + +A+ +
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSH 189
NG LGSR ++ +S+ + + + H
Sbjct: 65 NGYQLGSRFLKCGYSSNSDISGVSLEHHHHHH 96
Score = 72.3 bits (178), Expect = 4e-16
Identities = 25/96 (26%), Positives = 46/96 (47%), Gaps = 9/96 (9%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAAT 61
+Y+G++ TEE + L S +GPV K++ +P G YAF+EF +A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKG---YAFIEFRDLESSAS 59
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYH 97
A+ +N + +K ++S+ +H+H
Sbjct: 60 AVRNLNGYQLGSRFLKCGYSSNSDISGVSLEHHHHH 95
Score = 67.6 bits (166), Expect = 2e-14
Identities = 19/85 (22%), Positives = 41/85 (48%), Gaps = 6/85 (7%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIE 260
VY G D EE + + S G ++++++ + KGYAF++F E++ A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 261 SIHNTDINGHTVKCFWGKESENNST 285
+++ + +KC + S+ +
Sbjct: 63 NLNGYQLGSRFLKCGYSSNSDISGV 87
>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 = 107 bits (270), Expect = 2e-28
Identities = 31/110 (28%), Positives = 52/110 (47%), Gaps = 6/110 (5%)
Query: 79 NWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG 138
+ PG Q + +FV + E + ++E F +GEI N + D +T SKG
Sbjct: 59 DDELEPGPQRSVEGWI---LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG 115
Query: 139 YAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP---AMTNERKR 185
YA V + +A A A+NG + ++I+ +W K P + +R+R
Sbjct: 116 YALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKRRR 165
Score = 73.7 bits (181), Expect = 8e-16
Identities = 25/142 (17%), Positives = 53/142 (37%), Gaps = 21/142 (14%)
Query: 164 SRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELV 223
R ++ +TR+ + ++ E Q S ++ ++ E+ +
Sbjct: 35 GRGFGSDSNTREAIHSYERVRNEDDDEL-----EPGPQRSVEGWILFVTSIHEEAQEDEI 89
Query: 224 SKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWG 277
+ F +G I +I + KGYA V++ T + A A E+++ +I G T++ W
Sbjct: 90 QEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW- 148
Query: 278 KESENNSTLAQPSAPTTPQPNS 299
P + +
Sbjct: 149 ---------CFVKGPKRVKKSE 161
Score = 71.0 bits (174), Expect = 6e-15
Identities = 18/93 (19%), Positives = 37/93 (39%), Gaps = 9/93 (9%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAAT 61
L+V ++ E+ + F G +K + + G YA +E+ H A
Sbjct: 73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG---YALVEYETHKQALA 129
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
A A+N + + ++V+W G + + +
Sbjct: 130 AKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEK 162
>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 = 106 bits (266), Expect = 3e-28
Identities = 21/91 (23%), Positives = 39/91 (42%), Gaps = 2/91 (2%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAI 259
++ T+Y G D+ L+ FSPFG I+D+ + + AFV + E+A A+
Sbjct: 33 RRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAV 90
Query: 260 ESIHNTDINGHTVKCFWGKESENNSTLAQPS 290
++ T + +K ++ S
Sbjct: 91 AELNGTQVESVQLKVNIARKQPMLDAATGKS 121
Score = 82.5 bits (204), Expect = 2e-19
Identities = 20/96 (20%), Positives = 43/96 (44%), Gaps = 9/96 (9%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
S + + + ++V ++ L+ AF+PFG I + + + AF
Sbjct: 27 SDSFPERRAPRKGN-TLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAF 77
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
V++ K A+ A+ +NG + S ++ N + ++P
Sbjct: 78 VTYEKMESADQAVAELNGTQVESVQLKVNIARKQPM 113
Score = 73.2 bits (180), Expect = 4e-16
Identities = 24/90 (26%), Positives = 35/90 (38%), Gaps = 8/90 (8%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALA 64
+ TLYV D+ T LL FS G + + AF+ + A A+A
Sbjct: 37 RKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPPRN---CAFVTYEKMESADQAVA 91
Query: 65 AMNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
+N ++KVN A QP D +
Sbjct: 92 ELNGTQVESVQLKVNIARK---QPMLDAAT 118
>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 = 105 bits (264), Expect = 3e-28
Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 4/92 (4%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAI 259
++ T+Y G D+ L+ FSPFG I+D+ + + AFV + E+A A+
Sbjct: 9 RRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAV 66
Query: 260 ESIHNTDINGHTVKCFWGKESENNSTLAQPSA 291
++ T + +K ++ + PS+
Sbjct: 67 AELNGTQVESVQLKVNIARKQPMLD--SGPSS 96
Score = 90.0 bits (224), Expect = 2e-22
Identities = 21/96 (21%), Positives = 44/96 (45%), Gaps = 8/96 (8%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + ++ ++V ++ L+ AF+PFG I + + + A
Sbjct: 1 GSSGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCA 52
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP 176
FV++ K A+ A+ +NG + S ++ N + ++P
Sbjct: 53 FVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP 88
Score = 70.4 bits (173), Expect = 2e-15
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 5/79 (6%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATA 62
+ TLYV D+ T LL FS G + + AF+ + A A
Sbjct: 11 APRKGNTLYVYGEDM--TPTLLRGAFSPFGNIIDLSMDPPRN---CAFVTYEKMESADQA 65
Query: 63 LAAMNKRVFLEKEMKVNWA 81
+A +N ++KVN A
Sbjct: 66 VAELNGTQVESVQLKVNIA 84
>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 = 105 bits (264), Expect = 3e-28
Identities = 30/94 (31%), Positives = 48/94 (51%), Gaps = 2/94 (2%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+ S GN+ D + + V LS + L+E F+ +G I++ IV D Q+ +S+G+A
Sbjct: 3 SGSSGNRANPDPNCC--LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTR 174
FV F +A+ A NG L R IR + +
Sbjct: 61 FVYFENVDDAKEAKERANGMELDGRRIRVSGPSS 94
Score = 65.3 bits (160), Expect = 1e-13
Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 9/82 (10%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAAT 61
L V L + TE L +FS+ GP+ ++ + G +AF+ F + A
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG---FAFVYFENVDDAKE 72
Query: 62 ALAAMNKRVFLEKEMKVNWASS 83
A N + ++V+ SS
Sbjct: 73 AKERANGMELDGRRIRVSGPSS 94
Score = 61.8 bits (151), Expect = 2e-12
Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 6/80 (7%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKE 253
+ NC + G E + +VFS +G I D+ + + +G+AFV F +
Sbjct: 9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 254 TATHAIESIHNTDINGHTVK 273
A A E + +++G ++
Sbjct: 69 DAKEAKERANGMELDGRRIR 88
>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 = 105 bits (263), Expect = 4e-28
Identities = 31/97 (31%), Positives = 56/97 (57%), Gaps = 3/97 (3%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + D +FVG LS + Q+L++ F+ +G+IS +V+D +T +S+G+
Sbjct: 1 GSSGSSGMASDEGK---LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFG 57
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
FV+F +A++A+ AMNG+ + R IR + + +
Sbjct: 58 FVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD 94
Score = 70.3 bits (173), Expect = 2e-15
Identities = 21/91 (23%), Positives = 40/91 (43%), Gaps = 9/91 (9%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHT 57
S L+VG L E+ L +FS+ G + V+++ G + F+ F +
Sbjct: 9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRG---FGFVTFENID 65
Query: 58 VAATALAAMNKRVFLEKEMKVNWASSPGNQP 88
A A+ AMN + ++++V+ A +
Sbjct: 66 DAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR 96
Score = 63.4 bits (155), Expect = 6e-13
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 16/104 (15%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETA 255
+ ++ GG D NE+ + +VFS +G I ++ V K+ +G+ FV F + A
Sbjct: 8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 256 THAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
A+ +++ ++G ++ A S+ P+S
Sbjct: 68 KDAMMAMNGKSVDGRQIRVDQ----------AGKSSDNRSGPSS 101
>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 = 103 bits (260), Expect = 8e-28
Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAI 259
+ T T+Y GG G + E + F FG I I V + + AF++F T++ A A
Sbjct: 6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAA 65
Query: 260 ESIHN-TDINGHTVKCFWGK 278
E N +NG + WG+
Sbjct: 66 EKSFNKLIVNGRRLNVKWGR 85
Score = 81.9 bits (203), Expect = 1e-19
Identities = 23/90 (25%), Positives = 36/90 (40%), Gaps = 9/90 (10%)
Query: 83 SPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFV 142
S G+ +D + ++VG L I L+ F FGEI +V+ + AF+
Sbjct: 2 SSGSSG-EDKTIT-TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFI 53
Query: 143 SFVKKAEAENAITAM-NGQWLGSRSIRTNW 171
F + AE A N + R + W
Sbjct: 54 QFATRQAAEVAAEKSFNKLIVNGRRLNVKW 83
Score = 74.6 bits (184), Expect = 5e-17
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 4/75 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM- 66
TTLYVG L ++TE L F Q G ++ V++ AF++F A A
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ---CAFIQFATRQAAEVAAEKSF 69
Query: 67 NKRVFLEKEMKVNWA 81
NK + + + V W
Sbjct: 70 NKLIVNGRRLNVKWG 84
>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 = 104 bits (262), Expect = 1e-27
Identities = 24/106 (22%), Positives = 43/106 (40%), Gaps = 4/106 (3%)
Query: 73 EKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQ 132
+E++ S P + +++ +LSP + + L FA F E I
Sbjct: 7 GEEIRKIPMFSS-YNPGEPNKV---LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM 62
Query: 133 TLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPA 178
T + +G AF++F K A A+ +NG L + + + K
Sbjct: 63 TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQR 108
Score = 73.1 bits (180), Expect = 3e-16
Identities = 22/92 (23%), Positives = 37/92 (40%), Gaps = 9/92 (9%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAAT 61
LY+ NL VTE L +LF++ KG + G AF+ F + +A
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRG---QAFITFPNKEIAWQ 82
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
AL +N K + + + + + +S
Sbjct: 83 ALHLVNGYKLYGKILVIEFGKNKKQRSSGPSS 114
Score = 64.6 bits (158), Expect = 3e-13
Identities = 22/99 (22%), Positives = 39/99 (39%), Gaps = 9/99 (9%)
Query: 199 YNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTK 252
YN P N +Y + E + +F+ F + +G AF+ F K
Sbjct: 19 YNPGEP-NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNK 77
Query: 253 ETATHAIESIHNTDINGHTVKCFWGKESENNSTLAQPSA 291
E A A+ ++ + G + +GK + S + PS+
Sbjct: 78 EIAWQALHLVNGYKLYGKILVIEFGKNKKQRS--SGPSS 114
>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 = 105 bits (264), Expect = 1e-27
Identities = 33/124 (26%), Positives = 52/124 (41%), Gaps = 9/124 (7%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+LS + + E F+ G+I + D + G+ FV + +A+AENA+ +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKD 217
NG L R IRT+W R R + DE GG+GK
Sbjct: 102 NGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVR----DEYRQDYDAGR-----GGYGKL 152
Query: 218 LNEE 221
+
Sbjct: 153 AQNQ 156
Score = 69.1 bits (169), Expect = 3e-14
Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALA 64
TLYVGNL TEE + LFS+ G +K + + + F+E+ A A+
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 65 AMNKRVFLEKEMKVNWAS 82
+N ++ ++ +W +
Sbjct: 100 YINGTRLDDRIIRTDWDA 117
Score = 67.9 bits (166), Expect = 6e-14
Identities = 24/126 (19%), Positives = 55/126 (43%), Gaps = 17/126 (13%)
Query: 157 MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGK 216
M+G L +++R++ + ++ + +E + +CT+Y G
Sbjct: 1 MSGGLL--KALRSDSY--VELSQYRDQHFRGD-------NEEQEKLLKKSCTLYVGNLSF 49
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGH 270
EE + ++FS G I I + + G+ FV++ ++ A +A+ I+ T ++
Sbjct: 50 YTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDR 109
Query: 271 TVKCFW 276
++ W
Sbjct: 110 IIRTDW 115
>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 = 102 bits (256), Expect = 5e-27
Identities = 27/81 (33%), Positives = 41/81 (50%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG L I L+ F PFG+I N +++D T +SKGY F++F A A+ +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 158 NGQWLGSRSIRTNWSTRKPPA 178
NG L R +R T +
Sbjct: 68 NGFELAGRPMRVGHVTERLDG 88
Score = 64.1 bits (157), Expect = 3e-13
Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 8/93 (8%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHTVAAT 61
S + LYVG+L ++TE++L +F G + ++ + G Y F+ F A
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
AL +N + M+V + D +
Sbjct: 63 ALEQLNGFELAGRPMRVGHV-----TERLDGGS 90
Score = 62.6 bits (153), Expect = 1e-12
Identities = 22/89 (24%), Positives = 44/89 (49%), Gaps = 6/89 (6%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETAT 256
S + +Y G ++ E+++ +F PFG I +I + K+ KGY F+ F+ E A
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 257 HAIESIHNTDINGHTVKCFWGKESENNST 285
A+E ++ ++ G ++ E + +
Sbjct: 62 RALEQLNGFELAGRPMRVGHVTERLDGGS 90
>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 = 102 bits (255), Expect = 9e-27
Identities = 29/97 (29%), Positives = 43/97 (44%), Gaps = 1/97 (1%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + Q +FV +L ++ + LKE F+ G + I+ D KS+G
Sbjct: 1 GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDG-KSRGIG 59
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
V+F + EA AI+ NGQ L R + R P
Sbjct: 60 TVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALP 96
Score = 68.5 bits (168), Expect = 1e-14
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 2/76 (2%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATALAA 65
+T++V NLD V + L +FS G V ++ + + F A A++
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 66 MNKRVFLEKEMKVNWA 81
N ++ ++ M V
Sbjct: 76 FNGQLLFDRPMHVKMD 91
Score = 63.1 bits (154), Expect = 1e-12
Identities = 18/104 (17%), Positives = 35/104 (33%), Gaps = 5/104 (4%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETA 255
Q+ TV+ + + + +VFS G +V + ++ +G V F A
Sbjct: 10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEA 69
Query: 256 THAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
AI + + + + + P P P+S
Sbjct: 70 VQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSS 113
>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 = 101 bits (254), Expect = 1e-26
Identities = 29/97 (29%), Positives = 46/97 (47%), Gaps = 3/97 (3%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
PG Q + +FV + E + ++E F +GEI N + D +T SKGYA
Sbjct: 15 ELEPGPQRSVEGWI---LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYA 71
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
V + +A A A+NG + ++I+ +W K P
Sbjct: 72 LVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP 108
Score = 65.4 bits (160), Expect = 1e-13
Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 9/79 (11%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAATA 62
L+V ++ E+ + F G +K + + G YA +E+ H A A
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG---YALVEYETHKQALAA 84
Query: 63 LAAMNKRVFLEKEMKVNWA 81
A+N + + ++V+W
Sbjct: 85 KEALNGAEIMGQTIQVDWC 103
Score = 65.0 bits (159), Expect = 2e-13
Identities = 21/102 (20%), Positives = 46/102 (45%), Gaps = 9/102 (8%)
Query: 178 AMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIR 237
A+ + + +N + Q S ++ ++ E+ + + F +G I +I
Sbjct: 1 AIHSYERVRNEDDDELEPG---PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIH 57
Query: 238 VFKE------KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
+ + KGYA V++ T + A A E+++ +I G T++
Sbjct: 58 LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ 99
>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 = 101 bits (254), Expect = 1e-26
Identities = 24/97 (24%), Positives = 45/97 (46%), Gaps = 2/97 (2%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + + S + V ++ L++ F FG+I + I+ + + SKG+
Sbjct: 1 GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFG 58
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
FV+F A+A+ A ++G + R I N +T +
Sbjct: 59 FVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM 95
Score = 73.9 bits (182), Expect = 1e-16
Identities = 19/93 (20%), Positives = 40/93 (43%), Gaps = 6/93 (6%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG-NDPYAFLEFVHHTVAAT 61
+S P L+V N+ + L +F Q G + ++I + + F+ F + A
Sbjct: 11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 70
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
A ++ V ++++VN A + T++
Sbjct: 71 AREKLHGTVVEGRKIEVNNA-----TARVMTNS 98
Score = 64.2 bits (157), Expect = 4e-13
Identities = 22/104 (21%), Positives = 39/104 (37%), Gaps = 14/104 (13%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETA 255
++S T ++ + + ++F FG I+D+ + KG+ FV F A
Sbjct: 9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 68
Query: 256 THAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
A E +H T + G ++ A T P+S
Sbjct: 69 DRAREKLHGTVVEGRKIEV----------NNATARVMTNSGPSS 102
>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 = 101 bits (253), Expect = 2e-26
Identities = 22/80 (27%), Positives = 40/80 (50%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L+ +L+ F +G + + I R+P T +G+AFV F + +A++A AM
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75
Query: 158 NGQWLGSRSIRTNWSTRKPP 177
+G L R +R +
Sbjct: 76 DGAELDGRELRVQVARYGRR 95
Score = 64.9 bits (159), Expect = 2e-13
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHH 56
D TL V NL + + L +F + G V + REP G +AF+ F
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRG---FAFVRFHDR 65
Query: 57 TVAATALAAMNKRVFLEKEMKVNWA 81
A A AAM+ +E++V A
Sbjct: 66 RDAQDAEAAMDGAELDGRELRVQVA 90
Score = 62.6 bits (153), Expect = 1e-12
Identities = 17/100 (17%), Positives = 41/100 (41%), Gaps = 16/100 (16%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAI 259
T+ + + + +VF +G + D+ + +E +G+AFV+F + A A
Sbjct: 13 MITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAE 72
Query: 260 ESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
++ +++G ++ +A+ P+S
Sbjct: 73 AAMDGAELDGRELRV----------QVARYGRRDLSGPSS 102
>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 = 99.2 bits (248), Expect = 7e-26
Identities = 27/94 (28%), Positives = 43/94 (45%), Gaps = 3/94 (3%)
Query: 85 GNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
G+ + +FV +LS + L++ F+ +G +S D T K KG+AFV+F
Sbjct: 1 GSSGSSGSGR---LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57
Query: 145 VKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPA 178
+ A A ++GQ R + ST K A
Sbjct: 58 MFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA 91
Score = 64.2 bits (157), Expect = 3e-13
Identities = 24/98 (24%), Positives = 41/98 (41%), Gaps = 9/98 (9%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHH 56
S L+V NL + +EE L LFS GP+ + G +AF+ F+
Sbjct: 4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKG---FAFVTFMFP 60
Query: 57 TVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
A A A ++ +VF + + V ++ + S+
Sbjct: 61 EHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98
Score = 55.7 bits (135), Expect = 3e-10
Identities = 18/91 (19%), Positives = 34/91 (37%), Gaps = 6/91 (6%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKE 253
+ S + ++ +EE + K+FS +G + ++ + KG+AFV F E
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61
Query: 254 TATHAIESIHNTDINGHTVKCFWGKESENNS 284
A A + G + + S
Sbjct: 62 HAVKAYAEVDGQVFQGRMLHVLPSTIKKEAS 92
>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 = 98.5 bits (246), Expect = 1e-25
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQT---LKSKGYAFVSFVKKAEAENAI 154
+F+ +L+ +TLK F+ G I +C I + L S G+ FV + K +A+ A+
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 155 TAMNGQWLGSRSIRTNWSTRKP 176
+ G + + S R
Sbjct: 68 KQLQGHTVDGHKLEVRISERAT 89
Score = 74.6 bits (184), Expect = 7e-17
Identities = 20/97 (20%), Positives = 41/97 (42%), Gaps = 11/97 (11%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP----YAFLEFVHHT 57
S + L++ NL+ S TEE L +FS++G +K C + + + F+E+
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 58 VAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
A AL + +++V + + ++
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRIS-----ERATKPAS 93
Score = 64.2 bits (157), Expect = 3e-13
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 9/80 (11%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE---------KGYAFVKFTTKE 253
S + ++ EE + VFS G I + K+ G+ FV++ E
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 254 TATHAIESIHNTDINGHTVK 273
A A++ + ++GH ++
Sbjct: 62 QAQKALKQLQGHTVDGHKLE 81
>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 = 98.2 bits (245), Expect = 3e-25
Identities = 27/103 (26%), Positives = 47/103 (45%), Gaps = 6/103 (5%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
SS + D + +F+ +LS + E + L E FG++ R+V P T SKG AF
Sbjct: 2 SSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 61
Query: 142 VSFVKKAEAENAITAMN------GQWLGSRSIRTNWSTRKPPA 178
F+ + A+ + A + G L R ++ + + + A
Sbjct: 62 AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEA 104
Score = 67.4 bits (165), Expect = 3e-14
Identities = 23/100 (23%), Positives = 41/100 (41%), Gaps = 9/100 (9%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG-NDP--YAFLEFVHHTVA 59
D ++ T+++ NL EE L + Q G +K +V+ P AF +F+ A
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 60 ATALAAMNKRVFLE------KEMKVNWASSPGNQPKQDTS 93
LAA + +++KV+ A + +S
Sbjct: 71 QKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPSS 110
Score = 53.5 bits (129), Expect = 3e-09
Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 7/74 (9%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAI 259
TV+ D EE + +V FG + +RV KG AF +F T+E A +
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCL 74
Query: 260 ESIHN-TDINGHTV 272
+ + G +
Sbjct: 75 AAASLEAEGGGLKL 88
>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 = 97.3 bits (243), Expect = 3e-25
Identities = 24/92 (26%), Positives = 44/92 (47%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+S + ++V +L + L F+ +G++ I++D T KSKG A
Sbjct: 2 SSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVA 61
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWS 172
F+ F+ K A+N A+N + L R I+ + +
Sbjct: 62 FILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93
Score = 68.0 bits (167), Expect = 1e-14
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETAT 256
+P+ TVY L + ++FS +G +V + + K+ KG AF+ F K++A
Sbjct: 13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 257 HAIESIHNTDINGHTVKC 274
+ +I+N + G +K
Sbjct: 73 NCTRAINNKQLFGRVIKA 90
Score = 62.6 bits (153), Expect = 9e-13
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP--YAFLEFVHHTVAATAL 63
+T+YV NL S+T L +FS+ G V ++ ++ AF+ F+ A
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRK-SKGVAFILFLDKDSAQNCT 75
Query: 64 AAMNKRVFLEKEMKVNWA 81
A+N + + +K + A
Sbjct: 76 RAINNKQLFGRVIKASIA 93
>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 = 96.9 bits (242), Expect = 4e-25
Identities = 29/97 (29%), Positives = 44/97 (45%), Gaps = 3/97 (3%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + P + +FV LS + +TLKE+F RIV D +T SKG+
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFG 57
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
FV F + +A+ A AM + + +W+ K
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGE 94
Score = 57.3 bits (139), Expect = 1e-10
Identities = 22/91 (24%), Positives = 37/91 (40%), Gaps = 13/91 (14%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP--YAFLEFVHHTVAATAL 63
TL+V L TEE L F +++ RE G+ + F++F A A
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGS-SKGFGFVDFNSEEDAKAAK 71
Query: 64 AAMNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
AM ++ ++WA +PK + +
Sbjct: 72 EAMEDGEIDGNKVTLDWA-----KPKGEGGS 97
Score = 56.5 bits (137), Expect = 2e-10
Identities = 24/91 (26%), Positives = 41/91 (45%), Gaps = 9/91 (9%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKE 253
N S + T++ G +D EE + + F V R+ + KG+ FV F ++E
Sbjct: 9 NARSQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEE 65
Query: 254 TATHAIESIHNTDINGHTVKCFWGKESENNS 284
A A E++ + +I+G+ V W K
Sbjct: 66 DAKAAKEAMEDGEIDGNKVTLDWAKPKGEGG 96
>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 = 98.3 bits (245), Expect = 5e-25
Identities = 24/111 (21%), Positives = 49/111 (44%), Gaps = 2/111 (1%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
P Q + ++ V + ++ L++ F +G I + +IV D +T +S+GY
Sbjct: 28 QHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYG 87
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP--PAMTNERKRQNSH 189
FV F + A+ AI +NG + ++ ++ + P + N +
Sbjct: 88 FVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNGY 138
Score = 63.6 bits (155), Expect = 2e-12
Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 3/94 (3%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHTVA 59
+ L V + +V E L LF + GP++ K++ RE Y F++F + A
Sbjct: 38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97
Query: 60 ATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
A+A +N L K +KV A+S +P +
Sbjct: 98 QQAIAGLNGFNILNKRLKVALAASGHQRPGIAGA 131
Score = 57.1 bits (138), Expect = 3e-10
Identities = 18/105 (17%), Positives = 41/105 (39%), Gaps = 10/105 (9%)
Query: 175 KPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIV 234
+ + +++Q H N + ++E + ++F +G I
Sbjct: 15 QTAQLQQLQQQQQQHIPPTQM----NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIE 70
Query: 235 DIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
+++ + +GY FVKF + +A AI ++ +I +K
Sbjct: 71 SVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK 115
>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 = 96.5 bits (241), Expect = 6e-25
Identities = 27/89 (30%), Positives = 43/89 (48%), Gaps = 8/89 (8%)
Query: 89 KQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKA 148
+ N + IFVG++S +Q L+ F G + C +V K YAFV K+A
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEA 54
Query: 149 EAENAITAMNGQWLGSRSIRTNWSTRKPP 177
+A+ AI +NG+ + + I ST+
Sbjct: 55 DAKAAIAQLNGKEVKGKRINVELSTKGQK 83
Score = 69.2 bits (170), Expect = 4e-15
Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 5/82 (6%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM 66
++VGN+ + T + L +LF + G V C V+++ YAF+ A A+A +
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-----YAFVHMEKEADAKAAIAQL 63
Query: 67 NKRVFLEKEMKVNWASSPGNQP 88
N + K + V ++ +
Sbjct: 64 NGKEVKGKRINVELSTKGQKKS 85
Score = 68.8 bits (169), Expect = 7e-15
Identities = 16/85 (18%), Positives = 33/85 (38%), Gaps = 2/85 (2%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAI 259
+ SS ++ G + + +F G +++ V K YAFV + A AI
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--DYAFVHMEKEADAKAAI 60
Query: 260 ESIHNTDINGHTVKCFWGKESENNS 284
++ ++ G + + + S
Sbjct: 61 AQLNGKEVKGKRINVELSTKGQKKS 85
>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 = 96.6 bits (241), Expect = 7e-25
Identities = 25/98 (25%), Positives = 49/98 (50%), Gaps = 4/98 (4%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDP-QTLKSKGY 139
+ S G PK+ T++ I V ++ + + ++E F+ FGE+ R+ + T +G+
Sbjct: 3 SGSSGQVPKKQTTSK--ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 140 AFVSFVKKAEAENAITAM-NGQWLGSRSIRTNWSTRKP 176
FV F+ K +A+ A A+ + L R + W+ +
Sbjct: 61 GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV 98
Score = 67.3 bits (165), Expect = 4e-14
Identities = 14/97 (14%), Positives = 36/97 (37%), Gaps = 10/97 (10%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP----YAFLEFVHHTV 58
+ + + V N+ + + LFS G +K ++ ++ + F++F+
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 59 AATALAAM-NKRVFLEKEMKVNWASSPGNQPKQDTSN 94
A A A+ + + + + WA + +
Sbjct: 71 AKKAFNALCHSTHLYGRRLVLEWA-----DSEVTVQS 102
Score = 64.2 bits (157), Expect = 4e-13
Identities = 19/93 (20%), Positives = 37/93 (39%), Gaps = 8/93 (8%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-------KGYAFVKFTTKE 253
T + N+ + ++FS FG + +R+ K+ +G+ FV F TK+
Sbjct: 10 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 69
Query: 254 TATHAIESIHN-TDINGHTVKCFWGKESENNST 285
A A ++ + T + G + W +
Sbjct: 70 DAKKAFNALCHSTHLYGRRLVLEWADSEVTVQS 102
>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 = 94.9 bits (237), Expect = 2e-24
Identities = 20/71 (28%), Positives = 37/71 (52%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++ L P Q L + P+G+I + + + D T K KGY FV F + A+ A+TA+
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 158 NGQWLGSRSIR 168
+ ++ +
Sbjct: 68 KASGVQAQMAK 78
Score = 64.9 bits (159), Expect = 1e-13
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 8/79 (10%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETA 255
S + +Y G ++ + K+ P+G IV + + KGY FV F + A
Sbjct: 3 SGSSG--LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 256 THAIESIHNTDINGHTVKC 274
A+ ++ + + K
Sbjct: 61 QKAVTALKASGVQAQMAKQ 79
Score = 59.8 bits (146), Expect = 7e-12
Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 11/86 (12%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-------YAFLEFVHHT 57
S + LY+ L T++ L L G + K I D Y F++F +
Sbjct: 3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAIL----DKTTNKCKGYGFVDFDSPS 58
Query: 58 VAATALAAMNKRVFLEKEMKVNWASS 83
A A+ A+ + K + SS
Sbjct: 59 AAQKAVTALKASGVQAQMAKQSGPSS 84
>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 = 95.0 bits (237), Expect = 3e-24
Identities = 30/110 (27%), Positives = 47/110 (42%), Gaps = 11/110 (10%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
SS + + +FVG L+ + + + F PFG I C ++R P SKG AF
Sbjct: 2 SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDG-SSKGCAF 60
Query: 142 VSFVKKAEAENAITAMNGQWL---GSRSIRTNWSTRKPPAMTNERKRQNS 188
V F EA+ AI A++G S S+ ++ ++ S
Sbjct: 61 VKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTD-------KESGPS 103
Score = 70.4 bits (173), Expect = 3e-15
Identities = 24/94 (25%), Positives = 41/94 (43%), Gaps = 6/94 (6%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAA 60
+ L+VG L+ +EE + LF G + C V+R P AF++F HT A
Sbjct: 11 RGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQ 70
Query: 61 TALAAMNKRVFLE---KEMKVNWASSPG-NQPKQ 90
A+ A++ + + V +A + + P
Sbjct: 71 AAIHALHGSQTMPGASSSLVVKFADTDKESGPSS 104
Score = 66.9 bits (164), Expect = 4e-14
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETA 255
+ ++ G K +EE V ++F PFG I + V + KG AFVKF++ A
Sbjct: 10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEA 69
Query: 256 THAIESIHNTDI 267
AI ++H +
Sbjct: 70 QAAIHALHGSQT 81
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 95.2 bits (237), Expect = 3e-24
Identities = 15/71 (21%), Positives = 28/71 (39%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ L+ + LK+ +GE+ I+ P+T K G A V F A+ + +
Sbjct: 9 VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68
Query: 158 NGQWLGSRSIR 168
+ + I
Sbjct: 69 HLTSVMGNIIH 79
Score = 72.4 bits (178), Expect = 6e-16
Identities = 13/102 (12%), Positives = 35/102 (34%), Gaps = 6/102 (5%)
Query: 204 PTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATH 257
V ++ E + + +G + ++ + G A V FT+ A
Sbjct: 4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE 63
Query: 258 AIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
++++H T + G+ + + + + + P +
Sbjct: 64 TVKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQT 105
Score = 62.8 bits (153), Expect = 1e-12
Identities = 10/78 (12%), Positives = 25/78 (32%), Gaps = 3/78 (3%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATAL 63
+ L+ +V E L + + G V+ +++ P A + F A +
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65
Query: 64 AAMNKRVFLEKEMKVNWA 81
++ + +
Sbjct: 66 KNLHLTSVMGNIIHAQLD 83
>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 = 92.3 bits (230), Expect = 2e-23
Identities = 26/93 (27%), Positives = 42/93 (45%), Gaps = 2/93 (2%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+ S G P Q+ ++ +FVG+L + + L E F G ++ I +D + K K +
Sbjct: 3 SGSSGMFPAQEEADR-TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFG 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWST 173
FV F AI +NG L R I + +
Sbjct: 61 FVCFKHPESVSYAIALLNGIRLYGRPINVSGPS 93
Score = 88.5 bits (220), Expect = 6e-22
Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAA 60
E T++VGNL+ V EE+L LF Q GP+ + ++ P + F+ F H +
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVS 71
Query: 61 TALAAMNKRVFLEKEMKVNWASS 83
A+A +N + + V+ SS
Sbjct: 72 YAIALLNGIRLYGRPINVSGPSS 94
Score = 63.4 bits (155), Expect = 6e-13
Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKET 254
+ TV+ G + EE++ ++F G + + + K+ K + FV F E+
Sbjct: 10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPES 69
Query: 255 ATHAIESIHNTDINGHTVK 273
++AI ++ + G +
Sbjct: 70 VSYAIALLNGIRLYGRPIN 88
>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 = 92.7 bits (231), Expect = 2e-23
Identities = 26/102 (25%), Positives = 50/102 (49%), Gaps = 9/102 (8%)
Query: 85 GNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
G+ + +FV +L+ + + L++AF+ FG++ + ++D YAF+ F
Sbjct: 1 GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHF 52
Query: 145 VKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQ 186
++ A A+ MNG+ L +I ++ + P ERK Q
Sbjct: 53 DERDGAVKAMEEMNGKDLEGENIEIVFA-KPPDQKRKERKAQ 93
Score = 90.0 bits (224), Expect = 2e-22
Identities = 25/95 (26%), Positives = 46/95 (48%), Gaps = 5/95 (5%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATA 62
++ L+V NL +VTEE+L FSQ G ++ K +++ YAF+ F A A
Sbjct: 7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD-----YAFIHFDERDGAVKA 61
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYH 97
+ MN + + +++ +A P + K+ +
Sbjct: 62 MEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQA 96
Score = 74.6 bits (184), Expect = 8e-17
Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 2/92 (2%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTDI 267
++ + EE++ K FS FG + ++ K YAF+ F ++ A A+E ++ D+
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--DYAFIHFDERDGAVKAMEEMNGKDL 70
Query: 268 NGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
G ++ + K + + P+S
Sbjct: 71 EGENIEIVFAKPPDQKRKERKAQRQAASGPSS 102
>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 = 92.8 bits (231), Expect = 2e-23
Identities = 23/97 (23%), Positives = 47/97 (48%), Gaps = 4/97 (4%)
Query: 83 SPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFV 142
S G+ +D +F+G + ++ + LK F FG+I +++D T KG AF+
Sbjct: 2 SSGSSGMKDHDA-IKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60
Query: 143 SFVKKAEAENAITAMNGQ---WLGSRSIRTNWSTRKP 176
++ ++ A A +A++ Q +R I+ + +
Sbjct: 61 TYCERESALKAQSALHEQKTLPGMNRPIQVKPADSES 97
Score = 67.0 bits (164), Expect = 5e-14
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 6/73 (8%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKET 254
++ G ++L+E+ + +F FG I ++ V K+ KG AF+ + +E+
Sbjct: 8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES 67
Query: 255 ATHAIESIHNTDI 267
A A ++H
Sbjct: 68 ALKAQSALHEQKT 80
Score = 59.3 bits (144), Expect = 2e-11
Identities = 20/95 (21%), Positives = 42/95 (44%), Gaps = 9/95 (9%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAA 60
+ L++G + ++ E+ L LF + G + V+++ AFL + A
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69
Query: 61 TALAAMNKRVFLE---KEMKVNWA---SSPGNQPK 89
A +A++++ L + ++V A S G+ P
Sbjct: 70 KAQSALHEQKTLPGMNRPIQVKPADSESRGGSGPS 104
>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 = 92.3 bits (230), Expect = 4e-23
Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 4/89 (4%)
Query: 87 QPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
Q +QD +N +++ +L ++ Q L+ PFG++ + RI+RD + S+G F
Sbjct: 20 QQEQDPTN---LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMES 75
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWSTRK 175
+ E I NG+++ + + +
Sbjct: 76 TEKCEAVIGHFNGKFIKTPPGVSAPTEPL 104
Score = 67.7 bits (166), Expect = 3e-14
Identities = 16/90 (17%), Positives = 28/90 (31%), Gaps = 7/90 (7%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAA 60
E PT LY+ NL +S+ E+ L + G V +++R+ F
Sbjct: 21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCE 80
Query: 61 TALAAMNKRVFLEKEMKVNWASSPGNQPKQ 90
+ N + +P
Sbjct: 81 AVIGHFNGKFIKTPPGVSAPT-----EPLL 105
Score = 63.8 bits (156), Expect = 7e-13
Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 5/74 (6%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETA 255
Q +Y ++E+ + + PFG ++ R+ ++ +G F + + E
Sbjct: 20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKC 79
Query: 256 THAIESIHNTDING 269
I + I
Sbjct: 80 EAVIGHFNGKFIKT 93
>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 = 92.5 bits (230), Expect = 4e-23
Identities = 22/125 (17%), Positives = 52/125 (41%), Gaps = 3/125 (2%)
Query: 60 ATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPF 119
A + + + + P + ++ + ++VG++ Q L+ F+
Sbjct: 3 APCMQTTHSK--MTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60
Query: 120 GEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAM 179
G I+ I+ D + KGYA++ F ++ + A+ AM+ R+I+ P +
Sbjct: 61 GSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTNMPGI 119
Query: 180 TNERK 184
++ +
Sbjct: 120 SSTDR 124
Score = 61.3 bits (149), Expect = 7e-12
Identities = 27/96 (28%), Positives = 47/96 (48%), Gaps = 8/96 (8%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP--YAFLEFVHHTV 58
E ++YVGN+D T + L A FS G + ++ + G+ P YA++EF
Sbjct: 32 KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGH-PKGYAYIEFAERNS 90
Query: 59 AATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
A+ AM++ VF + +KV + N P +++
Sbjct: 91 VDAAV-AMDETVFRGRTIKVLPKRT--NMPGISSTD 123
Score = 47.4 bits (113), Expect = 5e-07
Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 7/80 (8%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKE 253
+ +VY G + + FS G+I I + KGYA+++F +
Sbjct: 30 EKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERN 89
Query: 254 TATHAIESIHNTDINGHTVK 273
+ A+ + T G T+K
Sbjct: 90 SVDAAVA-MDETVFRGRTIK 108
>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 = 91.1 bits (227), Expect = 5e-23
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 1/81 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRD-PQTLKSKGYAFVSFVKKAEAENAITA 156
+ +G L+ + + E F+ +G+I + + SKGYA+V F EAE A+
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 157 MNGQWLGSRSIRTNWSTRKPP 177
M+G + + I P
Sbjct: 67 MDGGQIDGQEITATAVLAPWP 87
Score = 67.2 bits (165), Expect = 2e-14
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP--YAFLEFVHHTVAATA 62
PT +++G L +VT++ + +FS G +K + R + YA++EF + A A
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKA 63
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQ 87
L M+ +E+ +P +
Sbjct: 64 LKHMDGGQIDGQEITATAVLAPWPR 88
Score = 64.9 bits (159), Expect = 1e-13
Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 7/78 (8%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-------KGYAFVKFTTKETA 255
S V+ G +++ ++ + ++FS +G I I + E KGYA+V+F + A
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 256 THAIESIHNTDINGHTVK 273
A++ + I+G +
Sbjct: 61 EKALKHMDGGQIDGQEIT 78
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 91.2 bits (227), Expect = 5e-23
Identities = 16/94 (17%), Positives = 43/94 (45%), Gaps = 9/94 (9%)
Query: 85 GNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFG--EISNCRIVRDPQTLKSKGYAFV 142
G+ I + +++P ++ A +P+ ++N R+++D QT +++G+AFV
Sbjct: 2 GHHHHHHMDT---IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFV 58
Query: 143 SFVKKAEAENAITAMNGQ----WLGSRSIRTNWS 172
+A + + + ++I +++
Sbjct: 59 QLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92
Score = 59.6 bits (145), Expect = 1e-11
Identities = 13/90 (14%), Positives = 30/90 (33%), Gaps = 10/90 (11%)
Query: 4 ESQPT-TLYVGNLDVSVTEELLCALFSQIG--PVKGCKVIREP-GNDP--YAFLEFVHHT 57
T+ + N+ + + S V ++I++ +AF++
Sbjct: 5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64
Query: 58 VAATALAAMNKRVFLE----KEMKVNWASS 83
A+ L + K + V++A S
Sbjct: 65 DASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
Score = 58.5 bits (142), Expect = 3e-11
Identities = 15/93 (16%), Positives = 39/93 (41%), Gaps = 12/93 (12%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGT--IVDIRVFKE------KGYAFVKFTT 251
+ T+ + + SP+ + + +IR+ K+ +G+AFV+ ++
Sbjct: 3 HHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSS 62
Query: 252 KETATHAIESIHNTD----INGHTVKCFWGKES 280
A+ ++ + + I+G T+ + K +
Sbjct: 63 AMDASQLLQILQSLHPPLKIDGKTIGVDFAKSA 95
>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 = 92.1 bits (229), Expect = 5e-23
Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 6/92 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ V +L + ++E FA FG + + D + +S G A V F ++A+A A+
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQY 96
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSH 189
G L R + + + + + H
Sbjct: 97 KGVPLDGRPMDIQLVASQI-----DLEHHHHH 123
Score = 75.1 bits (185), Expect = 7e-17
Identities = 19/95 (20%), Positives = 33/95 (34%), Gaps = 7/95 (7%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATA 62
L V NLD V++ + LF++ G +K V + A + F A A
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKA 92
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYH 97
+ + M + + D +H+H
Sbjct: 93 MKQYKGVPLDGRPMDIQLV-----ASQIDLEHHHH 122
Score = 57.0 bits (138), Expect = 2e-10
Identities = 14/103 (13%), Positives = 32/103 (31%), Gaps = 15/103 (14%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETA 255
+ T + +++ + ++F+ FGT+ V + G A V F + A
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 89
Query: 256 THAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPN 298
A++ ++G + L +
Sbjct: 90 LKAMKQYKGVPLDGRPMDI----------QLVASQIDLEHHHH 122
>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 = 90.8 bits (226), Expect = 8e-23
Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 7/95 (7%)
Query: 83 SPGNQPKQDTSNHY-HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
S G+ +DT + ++V +L + +++ F + R+ K + YAF
Sbjct: 2 SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAF 55
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP 176
V F + +A A+ A+NG+ L I +
Sbjct: 56 VHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD 90
Score = 85.0 bits (211), Expect = 1e-20
Identities = 25/89 (28%), Positives = 40/89 (44%), Gaps = 3/89 (3%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALA 64
S LYV NL +S +EE++ F+ I P +V + YAF+ F + A A+
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD---YAFVHFSNREDAVEAMK 69
Query: 65 AMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
A+N +V ++V A +S
Sbjct: 70 ALNGKVLDGSPIEVTLAKPVDKDSSGPSS 98
Score = 83.5 bits (207), Expect = 4e-20
Identities = 19/94 (20%), Positives = 41/94 (43%)
Query: 196 DEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETA 255
+ + +Y +EE++ K F+ RV K + YAFV F+ +E A
Sbjct: 5 SSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDA 64
Query: 256 THAIESIHNTDINGHTVKCFWGKESENNSTLAQP 289
A+++++ ++G ++ K + +S+
Sbjct: 65 VEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSS 98
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 89.9 bits (224), Expect = 1e-22
Identities = 27/97 (27%), Positives = 34/97 (35%), Gaps = 9/97 (9%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + Q IFV +L + + LK+ F G + I + KSKG
Sbjct: 1 GSSGSSGACQ-------IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCG 51
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
V F AE A MNG L R I
Sbjct: 52 VVKFESPEVAERACRMMNGMKLSGREIDVRIDRNASG 88
Score = 65.3 bits (160), Expect = 1e-13
Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 4/76 (5%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETATH 257
S C ++ D +++ F+ G ++ + E KG VKF + E A
Sbjct: 4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAER 63
Query: 258 AIESIHNTDINGHTVK 273
A ++ ++G +
Sbjct: 64 ACRMMNGMKLSGREID 79
Score = 63.4 bits (155), Expect = 5e-13
Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 1/78 (1%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-YAFLEFVHHTVAATAL 63
S ++V NL T ++L F++ G V + E G ++F VA A
Sbjct: 6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERAC 65
Query: 64 AAMNKRVFLEKEMKVNWA 81
MN +E+ V
Sbjct: 66 RMMNGMKLSGREIDVRID 83
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 90.4 bits (225), Expect = 1e-22
Identities = 21/96 (21%), Positives = 42/96 (43%), Gaps = 1/96 (1%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+ S G + + +F+ L + L+E G + + R+V + + K KG A
Sbjct: 3 SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLA 61
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP 176
+V + +++A A+ M+G + I+ S P
Sbjct: 62 YVEYENESQASQAVMKMDGMTIKENIIKVAISNSGP 97
Score = 68.5 bits (168), Expect = 1e-14
Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAAT 61
+ L++ L S T+E L + G VK +++ P A++E+ + + A+
Sbjct: 14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQ 73
Query: 62 ALAAMNKRVFLEKEMKVNWASSP 84
A+ M+ E +KV ++S
Sbjct: 74 AVMKMDGMTIKENIIKVAISNSG 96
Score = 61.5 bits (150), Expect = 3e-12
Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 5/79 (6%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKET 254
+S ++ G +E + ++ GT+ D+R+ KG A+V++ +
Sbjct: 11 YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQ 70
Query: 255 ATHAIESIHNTDINGHTVK 273
A+ A+ + I + +K
Sbjct: 71 ASQAVMKMDGMTIKENIIK 89
>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 = 89.5 bits (223), Expect = 2e-22
Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 1/82 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I+VG++ + L+ F G ++ I+ D + KG+A++ F K ++ A+
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 67
Query: 158 NGQWLGSRSIRTNWSTRKPPAM 179
+ R I+ P +
Sbjct: 68 DESLFRGRQIKVIPKRTNRPGI 89
Score = 63.3 bits (155), Expect = 6e-13
Identities = 26/88 (29%), Positives = 46/88 (52%), Gaps = 8/88 (9%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP--YAFLEFVHHTVA 59
E+ ++YVGN+D T E L A F G V ++ + G+ P +A++EF
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGH-PKGFAYIEFSDKESV 61
Query: 60 ATALAAMNKRVFLEKEMKVNWASS--PG 85
T+L A+++ +F +++KV + PG
Sbjct: 62 RTSL-ALDESLFRGRQIKVIPKRTNRPG 88
Score = 49.4 bits (119), Expect = 5e-08
Identities = 13/72 (18%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIES 261
++Y G E + F G++ + + + KG+A+++F+ KE+ ++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA- 66
Query: 262 IHNTDINGHTVK 273
+ + G +K
Sbjct: 67 LDESLFRGRQIK 78
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 90.1 bits (224), Expect = 2e-22
Identities = 23/95 (24%), Positives = 43/95 (45%), Gaps = 5/95 (5%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
S + K + V ++ L++ F FG+I + I+ + + SKG+ F
Sbjct: 19 SHMNTENKSQPKR---LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGF 73
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP 176
V+F A+A+ A ++G + R I N +T +
Sbjct: 74 VTFENSADADRAREKLHGTVVEGRKIEVNNATARV 108
Score = 67.3 bits (165), Expect = 3e-14
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND-PYAFLEFVHHTVAATA 62
+SQP L+V N+ + L +F Q G + ++I + F+ F + A A
Sbjct: 26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRA 85
Query: 63 LAAMNKRVFLEKEMKVNWA 81
++ V ++++VN A
Sbjct: 86 REKLHGTVVEGRKIEVNNA 104
Score = 62.7 bits (153), Expect = 1e-12
Identities = 17/95 (17%), Positives = 35/95 (36%), Gaps = 4/95 (4%)
Query: 183 RKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE- 241
+S + ++ ++ + + ++F FG I+D+ +
Sbjct: 6 HHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE 65
Query: 242 ---KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
KG+ FV F A A E +H T + G ++
Sbjct: 66 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIE 100
>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 = 89.3 bits (222), Expect = 4e-22
Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 4/101 (3%)
Query: 73 EKEMKVNWASSPGNQPKQDTSNHYH---IFVGDLSPEIETQTLKEAFAPFGEISNCRIVR 129
K++ W + + + V +L + ++E FA FG + +
Sbjct: 4 PKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHY 63
Query: 130 DPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTN 170
D + +S G A V F +KA+A A+ NG L R +
Sbjct: 64 DR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 103
Score = 75.0 bits (185), Expect = 6e-17
Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 2/81 (2%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATA 62
L V NLD V++ + LF++ G +K V + A + F A A
Sbjct: 27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKA 86
Query: 63 LAAMNKRVFLEKEMKVNWASS 83
+ N + M + +S
Sbjct: 87 MKQYNGVPLDGRPMNIQLVTS 107
Score = 58.1 bits (141), Expect = 6e-11
Identities = 17/95 (17%), Positives = 35/95 (36%), Gaps = 10/95 (10%)
Query: 182 ERKRQNSHTKTITFDEVYN--QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF 239
+ + H FD + T + +++ + ++F+ FGT+ V
Sbjct: 6 QLPDKWQHDL---FDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVH 62
Query: 240 KE-----KGYAFVKFTTKETATHAIESIHNTDING 269
+ G A V F K A A++ + ++G
Sbjct: 63 YDRSGRSLGTADVHFERKADALKAMKQYNGVPLDG 97
>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 = 88.5 bits (220), Expect = 8e-22
Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 1/91 (1%)
Query: 87 QPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
P D S +FVG++ E + LK+ F+ G + + R+V D +T K KGY F +
Sbjct: 1 DPAVDRSLRS-VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQD 59
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
+ A +A+ +NG+ R++R + + +
Sbjct: 60 QETALSAMRNLNGREFSGRALRVDNAASEKN 90
Score = 65.0 bits (159), Expect = 2e-13
Identities = 28/85 (32%), Positives = 48/85 (56%), Gaps = 5/85 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP--YAFLEFVHHTVAATAL 63
+++VGN+ TEE L +FS++GPV +++ RE G P Y F E+ A +A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGK-PKGYGFCEYQDQETALSAM 67
Query: 64 AAMNKRVFLEKEMKVNWASSPGNQP 88
+N R F + ++V+ A+S N+
Sbjct: 68 RNLNGREFSGRALRVDNAASEKNKE 92
Score = 59.6 bits (145), Expect = 1e-11
Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 6/72 (8%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAIES 261
+V+ G + EE + +FS G +V R+ K KGY F ++ +ETA A+ +
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 262 IHNTDINGHTVK 273
++ + +G ++
Sbjct: 70 LNGREFSGRALR 81
>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 = 88.6 bits (220), Expect = 8e-22
Identities = 24/105 (22%), Positives = 44/105 (41%), Gaps = 8/105 (7%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN--------CRIVRDPQ 132
SS + + S++ I+V L+ + L + F G + I D +
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 133 TLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
T K KG A VS+ A+ A+ +G+ ++ + + +KPP
Sbjct: 61 TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105
Score = 60.9 bits (148), Expect = 7e-12
Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 13/91 (14%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVK--------GCKVI--REPGNDP--YAF 50
++S + +YV L+ SVT + L F Q G VK + +E G P A
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGK-PKGDAT 69
Query: 51 LEFVHHTVAATALAAMNKRVFLEKEMKVNWA 81
+ + A A+ + + F ++KV+ A
Sbjct: 70 VSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 100
Score = 55.5 bits (134), Expect = 6e-10
Identities = 17/92 (18%), Positives = 29/92 (31%), Gaps = 14/92 (15%)
Query: 196 DEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTI--------VDIRVFKE------ 241
N +Y G + + ++ F G + I ++ +
Sbjct: 5 SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKP 64
Query: 242 KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
KG A V + TA A+E D G +K
Sbjct: 65 KGDATVSYEDPPTAKAAVEWFDGKDFQGSKLK 96
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 90.3 bits (224), Expect = 1e-21
Identities = 22/119 (18%), Positives = 42/119 (35%), Gaps = 9/119 (7%)
Query: 74 KEMKVNWASSPGNQPKQDTSNHYH---IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRD 130
K + W + + V +L + ++E FA FG + + D
Sbjct: 64 KPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD 123
Query: 131 PQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSH 189
+ +S G A V F ++A+A A+ G L R + + + + + H
Sbjct: 124 R-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI-----DLEHHHHH 176
Score = 73.3 bits (180), Expect = 1e-15
Identities = 19/95 (20%), Positives = 33/95 (34%), Gaps = 7/95 (7%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATA 62
L V NLD V++ + LF++ G +K V + A + F A A
Sbjct: 86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKA 145
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYH 97
+ + M + + D +H+H
Sbjct: 146 MKQYKGVPLDGRPMDIQLV-----ASQIDLEHHHH 175
Score = 57.6 bits (139), Expect = 4e-10
Identities = 19/107 (17%), Positives = 38/107 (35%), Gaps = 7/107 (6%)
Query: 174 RKPPAMTNERKRQNSHTKTITFDEVYN--QSSPTNCTVYCGGFGKDLNEELVSKVFSPFG 231
R PA + K + FD + T + +++ + ++F+ FG
Sbjct: 54 RNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG 113
Query: 232 TIVDIRVFKE-----KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
T+ V + G A V F + A A++ ++G +
Sbjct: 114 TLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMD 160
>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 = 88.1 bits (219), Expect = 1e-21
Identities = 23/97 (23%), Positives = 42/97 (43%), Gaps = 1/97 (1%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
P + + + +F L+ I + L++ F+ G++ + RI+ D + +SKG A
Sbjct: 11 VREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIA 70
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
+V F + AI + GQ L I S +
Sbjct: 71 YVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKN 106
Score = 61.2 bits (149), Expect = 5e-12
Identities = 18/97 (18%), Positives = 37/97 (38%), Gaps = 10/97 (10%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHH 56
+E T++ L + L FS +G V+ ++I + G A++EF
Sbjct: 21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG---IAYVEFCEI 77
Query: 57 TVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
A+ + + L + V + + N+ +S
Sbjct: 78 QSVPLAI-GLTGQRLLGVPIIVQASQAEKNRLSGPSS 113
Score = 54.6 bits (132), Expect = 1e-09
Identities = 19/100 (19%), Positives = 35/100 (35%), Gaps = 17/100 (17%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAI 259
TV+C + + FS G + D+R+ + KG A+V+F ++ AI
Sbjct: 25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 84
Query: 260 ESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
+ + G + +Q P+S
Sbjct: 85 G-LTGQRLLGVPIIV----------QASQAEKNRLSGPSS 113
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 87.4 bits (217), Expect = 2e-21
Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 5/86 (5%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
++VG+L L+ AF+ +G + I R+P G+AFV F +AE+A+ +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 57
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNER 183
+G+ + +R ST P +R
Sbjct: 58 DGKVICGSRVRVELSTGMPRRSRFDR 83
Score = 68.1 bits (167), Expect = 2e-14
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
+YVGNL + L FS GP++ + R P +AF+EF A A+ ++ +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP--GFAFVEFEDPRDAEDAVRGLDGK 60
Query: 70 VFLEKEMKVNWASSPGNQPKQD 91
V ++V ++ + + D
Sbjct: 61 VICGSRVRVELSTGMPRRSRFD 82
Score = 58.8 bits (143), Expect = 3e-11
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 1/88 (1%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-KGYAFVKFTTKETATHAIESIHNTDI 267
VY G G + + + FS +G + + + + G+AFV+F A A+ + I
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 268 NGHTVKCFWGKESENNSTLAQPSAPTTP 295
G V+ S +P A
Sbjct: 63 CGSRVRVELSTGMPRRSRFDRPPARRKL 90
>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 = 88.0 bits (218), Expect = 4e-21
Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 5/88 (5%)
Query: 89 KQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKA 148
+ ++VG+L L+ AF +G + + + R+P G+AFV F
Sbjct: 67 RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPR 121
Query: 149 EAENAITAMNGQWLGSRSIRTNWSTRKP 176
+A +A+ ++G+ L +R S +
Sbjct: 122 DAADAVRELDGRTLCGCRVRVELSNGEK 149
Score = 82.2 bits (203), Expect = 4e-19
Identities = 28/140 (20%), Positives = 50/140 (35%), Gaps = 10/140 (7%)
Query: 135 KSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTIT 194
KG V A AE Q+ + W+ + +
Sbjct: 11 TLKGETTTEAVDAATAEKVF----KQYANDNGVDGEWTYDDA-----TKTFTVTEGSHHH 61
Query: 195 FDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-KGYAFVKFTTKE 253
++ S P +C VY G G + N+ + + F +G + + V + G+AFV+F
Sbjct: 62 HHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPR 121
Query: 254 TATHAIESIHNTDINGHTVK 273
A A+ + + G V+
Sbjct: 122 DAADAVRELDGRTLCGCRVR 141
Score = 66.8 bits (163), Expect = 2e-13
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 2/78 (2%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM 66
+YVGNL + + L F GP++ V R P +AF+EF AA A+ +
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP--GFAFVEFEDPRDAADAVREL 130
Query: 67 NKRVFLEKEMKVNWASSP 84
+ R ++V ++
Sbjct: 131 DGRTLCGCRVRVELSNGE 148
>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 = 86.1 bits (214), Expect = 4e-21
Identities = 23/90 (25%), Positives = 43/90 (47%), Gaps = 3/90 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
I+VG+L ++ +KE F+ FG++ N +++ D +T K KG+ FV ++ AI +
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEM-QEESVSEAIAKL 62
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQN 187
+ R+IR + P +
Sbjct: 63 DNTDFMGRTIRVTEA--NPKKSLEHHHHHH 90
Score = 60.6 bits (148), Expect = 4e-12
Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 4/89 (4%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVI--REPGNDP-YAFLEFVHHTVAATALAA 65
+YVGNL S T E + LFSQ G V K+I RE + F+E + + A+A
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61
Query: 66 MNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
++ F+ + ++V A+ + +
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSLEHHHHHH 90
Score = 49.5 bits (119), Expect = 4e-08
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIES 261
+Y G E V ++FS FG + ++++ + KG+ FV+ E+ + AI
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAK 61
Query: 262 IHNTDINGHTVK 273
+ NTD G T++
Sbjct: 62 LDNTDFMGRTIR 73
>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 = 86.9 bits (215), Expect = 4e-21
Identities = 15/95 (15%), Positives = 36/95 (37%), Gaps = 4/95 (4%)
Query: 187 NSHTKTITFDEVYNQSSPTNCTVYC-GGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYA 245
+ + + + S T V GG G ++ + V G + + + K Y+
Sbjct: 7 GAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYS 66
Query: 246 FVKFTTKETATHAIESIHNTDI---NGHTVKCFWG 277
F ++ T E + A +++ ++ G + +
Sbjct: 67 FARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLN 101
Score = 64.2 bits (156), Expect = 5e-13
Identities = 13/93 (13%), Positives = 27/93 (29%), Gaps = 14/93 (15%)
Query: 67 NKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCR 126
+ L + + S + + G L + L G +
Sbjct: 7 GAKHTLLRHEGIETVSYA--------TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL 58
Query: 127 IVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
+ + K Y+F + E++ A +NG
Sbjct: 59 MPPN------KPYSFARYRTTEESKRAYVTLNG 85
Score = 50.7 bits (121), Expect = 3e-08
Identities = 17/72 (23%), Positives = 29/72 (40%), Gaps = 6/72 (8%)
Query: 5 SQPT-TLYVGN--LDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAAT 61
S T +L V N L V+ L + + G V + P N PY+F + +
Sbjct: 22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM---PPNKPYSFARYRTTEESKR 78
Query: 62 ALAAMNKRVFLE 73
A +N + ++
Sbjct: 79 AYVTLNGKEVVD 90
>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 = 87.0 bits (216), Expect = 4e-21
Identities = 33/113 (29%), Positives = 48/113 (42%), Gaps = 8/113 (7%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + ++DT+ IFVG L +L++ F FG+I ++ D QT KS+GY
Sbjct: 4 GSSGMHGSQKDTT-FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYG 62
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTI 193
FV+ +A AE A N + R N A + R I
Sbjct: 63 FVTMADRAAAERACKDPNPI-IDGRKANVN------LAYLGAKPRSLQTGFAI 108
Score = 59.6 bits (145), Expect = 2e-11
Identities = 24/108 (22%), Positives = 40/108 (37%), Gaps = 12/108 (11%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHT 57
++ T ++VG L T+ L F G ++ VI + G Y F+
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG---YGFVTMADRA 70
Query: 58 VAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSP 105
A A N + ++ VN A G +P+ + + I V S
Sbjct: 71 AAERACKDPNP-IIDGRKANVNLA-YLGAKPRSLQTG-FAIGVSGPSS 115
Score = 47.7 bits (114), Expect = 4e-07
Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 7/81 (8%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKE 253
+Q T ++ GG + + K F FG I + V ++ GY FV +
Sbjct: 11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRA 70
Query: 254 TATHAIESIHNTDINGHTVKC 274
A A + N I+G
Sbjct: 71 AAERACKD-PNPIIDGRKANV 90
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 87.7 bits (217), Expect = 5e-21
Identities = 17/109 (15%), Positives = 37/109 (33%), Gaps = 2/109 (1%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFG--EISNCRIVRDPQTLKSKG 138
+ + ++VG S Q L + G ++ + + +SKG
Sbjct: 41 TPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKG 100
Query: 139 YAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQN 187
YA V + + + G+ L + +TR+ + + R+
Sbjct: 101 YAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKR 149
Score = 68.0 bits (166), Expect = 5e-14
Identities = 27/155 (17%), Positives = 52/155 (33%), Gaps = 10/155 (6%)
Query: 151 ENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVY 210
+ +G LG+ ++ PP + N+ T I Y+ VY
Sbjct: 2 HHHHHHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAIL--YTYSGLRNRRAAVY 59
Query: 211 CGGFGKDLNEELVSKVFSPFGT--IVDIRVFKE------KGYAFVKFTTKETATHAIESI 262
G F ++ + +V G +V+++ + KGYA V ++ + +E +
Sbjct: 60 VGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELL 119
Query: 263 HNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQP 297
+NG V + AQ +
Sbjct: 120 PGKVLNGEKVDVRPATRQNLSQFEAQARKRECVRV 154
Score = 59.2 bits (143), Expect = 8e-11
Identities = 16/97 (16%), Positives = 32/97 (32%), Gaps = 5/97 (5%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGP--VKGCKVIREPGNDP---YAFLEFVHHT 57
++ +YVG+ T++ L + IG V K N YA +
Sbjct: 51 LRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASEN 110
Query: 58 VAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
L + +V +++ V A+ + +
Sbjct: 111 SVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQAR 147
>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 = 85.4 bits (212), Expect = 8e-21
Identities = 24/96 (25%), Positives = 39/96 (40%), Gaps = 8/96 (8%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
++ + + +LS I LKE F EI R+V KSKG A+
Sbjct: 6 DPCTSKKVRAART---LLAKNLSFNITEDELKEVFEDALEI---RLVSQ--DGKSKGIAY 57
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
+ F +A+AE + G + RS+ ++ K
Sbjct: 58 IEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG 93
Score = 61.1 bits (149), Expect = 3e-12
Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 6/87 (6%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAAT 61
TL NL ++TE+ L +F + +++ + G A++EF A
Sbjct: 13 VRAARTLLAKNLSFNITEDELKEVFEDALEI---RLVSQDGK-SKGIAYIEFKSEADAEK 68
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQP 88
L + + + + G
Sbjct: 69 NLEEKQGAEIDGRSVSLYYTGEKGGTR 95
Score = 60.4 bits (147), Expect = 6e-12
Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 1/86 (1%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIR-VFKEKGYAFVKFTTKETATHA 258
++ T+ ++ E+ + +VF I + K KG A+++F ++ A
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKN 69
Query: 259 IESIHNTDINGHTVKCFWGKESENNS 284
+E +I+G +V ++ E
Sbjct: 70 LEEKQGAEIDGRSVSLYYTGEKGGTR 95
>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 = 85.4 bits (212), Expect = 8e-21
Identities = 20/84 (23%), Positives = 33/84 (39%), Gaps = 8/84 (9%)
Query: 97 HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
++VG L P L F FG I V+ +A++ + A+ A
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72
Query: 157 MNGQWLG--SRSIRTNWSTRKPPA 178
M G LG R +R +++ P +
Sbjct: 73 MRGFPLGGPDRRLRVDFAKSGPSS 96
Score = 81.9 bits (203), Expect = 2e-19
Identities = 16/76 (21%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 199 YNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHA 258
Y +++PT ++ GG G + + +++ F FG+I I K +A++++ + + A A
Sbjct: 11 YGKANPTTR-LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAA 69
Query: 259 IESIHNTDINGHTVKC 274
+ + G +
Sbjct: 70 CAKMRGFPLGGPDRRL 85
Score = 69.6 bits (171), Expect = 4e-15
Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 5 SQPTT-LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATAL 63
+ PTT L+VG L + + L F + G ++ ++ +A++++ A A
Sbjct: 14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS---FAYIQYESLDAAQAAC 70
Query: 64 AAMNKRVF--LEKEMKVNWASSP 84
A M ++ ++V++A S
Sbjct: 71 AKMRGFPLGGPDRRLRVDFAKSG 93
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 85.1 bits (211), Expect = 2e-20
Identities = 26/97 (26%), Positives = 44/97 (45%), Gaps = 8/97 (8%)
Query: 89 KQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN--------CRIVRDPQTLKSKGYA 140
+QD S++ IFV L + +++ + F G I + D +T K KG A
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
VSF A+ AI +G+ I+ +++TR+
Sbjct: 61 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRAD 97
Score = 62.0 bits (151), Expect = 3e-12
Identities = 24/99 (24%), Positives = 40/99 (40%), Gaps = 11/99 (11%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG----NDP-------YAFL 51
D S T++V L +VT E + F QIG +K K +P D A +
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62
Query: 52 EFVHHTVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQ 90
F A A+ + + F +KV++A+ + +
Sbjct: 63 SFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRG 101
Score = 61.3 bits (149), Expect = 6e-12
Identities = 21/98 (21%), Positives = 40/98 (40%), Gaps = 14/98 (14%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTI--------VDIRVFKE------KGYAF 246
Q + N T++ G G+++ E V+ F G I I ++ + KG A
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61
Query: 247 VKFTTKETATHAIESIHNTDINGHTVKCFWGKESENNS 284
V F +A AI+ + +G+ +K + + +
Sbjct: 62 VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFN 99
>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 = 83.9 bits (208), Expect = 3e-20
Identities = 25/97 (25%), Positives = 41/97 (42%), Gaps = 4/97 (4%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + + + + +LS +TL+E F I V Q KSKGYA
Sbjct: 1 GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYA 56
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
F+ F +A+ A+ + N + + R+IR +
Sbjct: 57 FIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGS 93
Score = 62.7 bits (153), Expect = 1e-12
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 3/85 (3%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGN-DPYAFLEFVHHTVAATAL 63
+ TL + NL S TEE L +F + +K + + G YAF+EF A AL
Sbjct: 13 GESKTLVLSNLSYSATEETLQEVFEKATFIKVPQ--NQNGKSKGYAFIEFASFEDAKEAL 70
Query: 64 AAMNKRVFLEKEMKVNWASSPGNQP 88
+ NKR + +++ G+
Sbjct: 71 NSCNKREIEGRAIRLELQGPRGSPN 95
Score = 61.5 bits (150), Expect = 3e-12
Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 2/76 (2%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIV--DIRVFKEKGYAFVKFTTKETATH 257
+ S + T+ EE + +VF I + K KGYAF++F + E A
Sbjct: 9 STWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKE 68
Query: 258 AIESIHNTDINGHTVK 273
A+ S + +I G ++
Sbjct: 69 ALNSCNKREIEGRAIR 84
>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 = 83.4 bits (207), Expect = 3e-20
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 8/79 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G+L E Q ++ F +G++ C I+ K Y FV K AE+AI +
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNL 62
Query: 158 NGQWLGSRSIRTNWSTRKP 176
+ L +I S K
Sbjct: 63 HHYKLHGVNINVEASKNKS 81
Score = 70.3 bits (173), Expect = 2e-15
Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 5/86 (5%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATAL 63
S L++GNL TE+ + +LF Q G V C +I+ Y F+ T A A+
Sbjct: 5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN-----YGFVHIEDKTAAEDAI 59
Query: 64 AAMNKRVFLEKEMKVNWASSPGNQPK 89
++ + V + +
Sbjct: 60 RNLHHYKLHGVNINVEASKNKSKASS 85
Score = 65.7 bits (161), Expect = 7e-14
Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 2/84 (2%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
S ++ G ++ E+ + +F +G +++ + K Y FV K A AI +
Sbjct: 4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--NYGFVHIEDKTAAEDAIRN 61
Query: 262 IHNTDINGHTVKCFWGKESENNST 285
+H+ ++G + K S+
Sbjct: 62 LHHYKLHGVNINVEASKNKSKASS 85
>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 = 83.5 bits (207), Expect = 5e-20
Identities = 22/96 (22%), Positives = 40/96 (41%), Gaps = 3/96 (3%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
S G +N I+VG+L P+I T+ +++ F +G I + + +AF
Sbjct: 9 SGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAF 65
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
V F +AE+A+ +G +R +
Sbjct: 66 VEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRG 101
Score = 75.4 bits (186), Expect = 4e-17
Identities = 18/91 (19%), Positives = 37/91 (40%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATA 62
+ +YVGNL + + + +F + G ++ + G P+AF+EF A A
Sbjct: 18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDA 77
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
+ + + ++V + S +S
Sbjct: 78 VYGRDGYDYDGYRLRVEFPRSGRGTGSGPSS 108
Score = 68.1 bits (167), Expect = 2e-14
Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 3/86 (3%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE---KGYAFVKFTTKETATHA 258
+ +C +Y G D+ + + VF +G I DI + +AFV+F A A
Sbjct: 18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDA 77
Query: 259 IESIHNTDINGHTVKCFWGKESENNS 284
+ D +G+ ++ + +
Sbjct: 78 VYGRDGYDYDGYRLRVEFPRSGRGTG 103
>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 = 86.7 bits (214), Expect = 6e-20
Identities = 17/110 (15%), Positives = 43/110 (39%), Gaps = 2/110 (1%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFG--EISNCRIVRDPQTLKSKG 138
+ N T +++G+L+ + L EA G +I + + +SKG
Sbjct: 54 KGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG 113
Query: 139 YAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNS 188
+A V +A ++ + + + L ++ ++ + + R+ +
Sbjct: 114 FALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTT 163
Score = 71.3 bits (174), Expect = 2e-14
Identities = 24/190 (12%), Positives = 54/190 (28%), Gaps = 13/190 (6%)
Query: 174 RKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGT- 232
+ T + K + VY + +Y G +E +++ G
Sbjct: 37 DRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRI-ALYIGNLTWWTTDEDLTEAVHSLGVN 95
Query: 233 -IVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKESENNST 285
I++I+ F+ KG+A V ++ ++ ++ + +++G + +
Sbjct: 96 DILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQF 155
Query: 286 LAQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGY 345
Q T S + + + P + P G
Sbjct: 156 EMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGR----GRFPGAVPGGDRFPGPAGP 211
Query: 346 VGMVGRQVPG 355
G G
Sbjct: 212 GGPPPPFPAG 221
Score = 61.7 bits (149), Expect = 4e-11
Identities = 16/97 (16%), Positives = 29/97 (29%), Gaps = 5/97 (5%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGP--VKGCKVIREPGNDP---YAFLEFVHHT 57
+ LY+GNL T+E L +G + K N +A +
Sbjct: 64 YTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEA 123
Query: 58 VAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
+ + + KR + V + + S
Sbjct: 124 SSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSR 160
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 83.1 bits (206), Expect = 7e-20
Identities = 22/113 (19%), Positives = 45/113 (39%), Gaps = 13/113 (11%)
Query: 73 EKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQ 132
+ S + ++ ++ +FV +++ L E F PFG + +I+
Sbjct: 9 HHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL---- 64
Query: 133 TLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKR 185
G+AFV F + A AI ++G+ ++ + +S +R R
Sbjct: 65 ----NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPA-----KRYR 108
Score = 78.9 bits (195), Expect = 2e-18
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 5/87 (5%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATA 62
E T L+V + V E L +F GP+K K++ +AF+EF AA A
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG-----FAFVEFEEAESAAKA 81
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQPK 89
+ ++ + F + ++V ++ P + +
Sbjct: 82 IEEVHGKSFANQPLEVVYSKLPAKRYR 108
Score = 69.2 bits (170), Expect = 6e-15
Identities = 22/103 (21%), Positives = 46/103 (44%), Gaps = 8/103 (7%)
Query: 180 TNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF 239
++ + SH + +N ++ F D+ E ++++F PFG + ++++
Sbjct: 11 SSGLVPRGSHMHHR------QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL 64
Query: 240 KEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKESEN 282
G+AFV+F E+A AIE +H ++ + K
Sbjct: 65 N--GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105
>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 = 82.3 bits (204), Expect = 8e-20
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 7/81 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++G+LSP + L++ F + Q L GYAFV + + A AI +
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIETL 64
Query: 158 NGQW-LGSRSIRTNWSTRKPP 177
+G+ L + + ++S K
Sbjct: 65 SGKVELHGKIMEVDYSVSKKL 85
Score = 79.2 bits (196), Expect = 1e-18
Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 4/90 (4%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALA 64
S LY+GNL +VT + L LF +V+ + G YAF+++ A A+
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSG---YAFVDYPDQNWAIRAIE 62
Query: 65 AMNKRVFLE-KEMKVNWASSPGNQPKQDTS 93
++ +V L K M+V+++ S + +S
Sbjct: 63 TLSGKVELHGKIMEVDYSVSKKLRSSGPSS 92
Score = 69.6 bits (171), Expect = 3e-15
Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 1/85 (1%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
S +Y G + + + ++F + +V + GYAFV + + A AIE+
Sbjct: 4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63
Query: 262 IH-NTDINGHTVKCFWGKESENNST 285
+ +++G ++ + + S+
Sbjct: 64 LSGKVELHGKIMEVDYSVSKKLRSS 88
>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 = 82.4 bits (204), Expect = 2e-19
Identities = 16/89 (17%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++ +L +I + + + F +G I R+ P +++G A+V + +A+NA+ +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNAVDHL 67
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQ 186
+G + +R + + + K++
Sbjct: 68 SGFNVSNRYLVVLYYNANRAFQKMDTKKK 96
Score = 68.9 bits (169), Expect = 1e-14
Identities = 18/85 (21%), Positives = 37/85 (43%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
LY+ NL +T E + +F + GP++ +V P A++ + A A+ ++
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 68 KRVFLEKEMKVNWASSPGNQPKQDT 92
+ + V + ++ K DT
Sbjct: 69 GFNVSNRYLVVLYYNANRAFQKMDT 93
Score = 63.2 bits (154), Expect = 1e-12
Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 3/71 (4%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE---KGYAFVKFTTKETATHA 258
N +Y + E + +F +G I IRV +G A+V + A +A
Sbjct: 4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 63
Query: 259 IESIHNTDING 269
++ + +++
Sbjct: 64 VDHLSGFNVSN 74
>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 = 81.1 bits (201), Expect = 2e-19
Identities = 15/84 (17%), Positives = 35/84 (41%), Gaps = 2/84 (2%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFG--EISNCRIVRDPQTLKSKGYAFVSFVKKAEAENA 153
+++G+L+ + L EA G +I + + +SKG+A V +A ++
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61
Query: 154 ITAMNGQWLGSRSIRTNWSTRKPP 177
+ + + L ++ S +
Sbjct: 62 MDLLPKRELHGQNPVVTPSNKLEH 85
Score = 55.7 bits (135), Expect = 3e-10
Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 5/84 (5%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGP--VKGCKVI--REPGNDP-YAFLEFVHHTVAATALA 64
LY+GNL T+E L +G + K R G +A + + +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 65 AMNKRVFLEKEMKVNWASSPGNQP 88
+ KR + V ++ +
Sbjct: 64 LLPKRELHGQNPVVTPSNKLEHHH 87
Score = 53.4 bits (129), Expect = 2e-09
Identities = 12/74 (16%), Positives = 32/74 (43%), Gaps = 8/74 (10%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGT--IVDIRVFKE------KGYAFVKFTTKETATHAIE 260
+Y G +E +++ G I++I+ F+ KG+A V ++ ++ ++
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 261 SIHNTDINGHTVKC 274
+ +++G
Sbjct: 64 LLPKRELHGQNPVV 77
>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 = 80.7 bits (200), Expect = 3e-19
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 8/79 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ VG++SP Q L+ F +G + C IV+ YAFV + +A AI +
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGL 64
Query: 158 NGQWLGSRSIRTNWSTRKP 176
+ + + ST +
Sbjct: 65 DNTEFQGKRMHVQLSTSRL 83
Score = 69.6 bits (171), Expect = 3e-15
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 5/87 (5%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM 66
T L+VGN+ + T + L A F + GPV C +++ YAF+ A A+ +
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK-----DYAFVHMERAEDAVEAIRGL 64
Query: 67 NKRVFLEKEMKVNWASSPGNQPKQDTS 93
+ F K M V ++S +S
Sbjct: 65 DNTEFQGKRMHVQLSTSRLRTASGPSS 91
Score = 67.6 bits (166), Expect = 2e-14
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 2/72 (2%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
S + ++ G + + F +G +++ + K YAFV E A AI
Sbjct: 6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--DYAFVHMERAEDAVEAIRG 63
Query: 262 IHNTDINGHTVK 273
+ NT+ G +
Sbjct: 64 LDNTEFQGKRMH 75
>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 = 80.4 bits (199), Expect = 4e-19
Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 8/96 (8%)
Query: 86 NQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEIS--------NCRIVRDPQTLKSK 137
+ S++ IFV L + +++ + F G I + D +T K K
Sbjct: 4 HHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLK 63
Query: 138 GYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWST 173
G A VSF A+ AI +G+ I+ +++T
Sbjct: 64 GEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 99
Score = 60.4 bits (147), Expect = 7e-12
Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 13/92 (14%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVK--------GCKVI--REPGNDP--YAF 50
S T++V L +VT E + F QIG +K + RE G A
Sbjct: 9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK-LKGEAT 67
Query: 51 LEFVHHTVAATALAAMNKRVFLEKEMKVNWAS 82
+ F A A+ + + F +KV++A+
Sbjct: 68 VSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 99
Score = 59.6 bits (145), Expect = 2e-11
Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 14/88 (15%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVD--------IRVFKE------KGYA 245
+ S N T++ G G+++ E V+ F G I I ++ + KG A
Sbjct: 7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 66
Query: 246 FVKFTTKETATHAIESIHNTDINGHTVK 273
V F +A AI+ + +G+ +K
Sbjct: 67 TVSFDDPPSAKAAIDWFDGKEFSGNPIK 94
>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 = 81.1 bits (200), Expect = 5e-19
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 6/84 (7%)
Query: 98 IFVGDLSPEI---ETQTLKEAFAPFGEISNCRIVRDPQTLKSK---GYAFVSFVKKAEAE 151
+FV LS + E E F FG+I I S+ A+V++++ +A
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 152 NAITAMNGQWLGSRSIRTNWSTRK 175
AI +N + R+++ + T K
Sbjct: 78 RAIQCVNNVVVDGRTLKASLGTTK 101
Score = 66.0 bits (161), Expect = 9e-14
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 12/83 (14%)
Query: 207 CTVYCGGFGKDLNEELVSK---VFSPFGTIVDIRVFKEK---------GYAFVKFTTKET 254
V+ G + L + V K F FG I + + A+V + E
Sbjct: 16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75
Query: 255 ATHAIESIHNTDINGHTVKCFWG 277
A AI+ ++N ++G T+K G
Sbjct: 76 ALRAIQCVNNVVVDGRTLKASLG 98
Score = 51.8 bits (124), Expect = 1e-08
Identities = 11/85 (12%), Positives = 28/85 (32%), Gaps = 9/85 (10%)
Query: 6 QPTTLYVGNLDVSVTEELLCA---LFSQIGPVKGCKVIREPGNDP------YAFLEFVHH 56
Q ++V L + + + F + G + + A++ ++
Sbjct: 14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73
Query: 57 TVAATALAAMNKRVFLEKEMKVNWA 81
A A+ +N V + +K +
Sbjct: 74 EDALRAIQCVNNVVVDGRTLKASLG 98
>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 = 80.3 bits (199), Expect = 5e-19
Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 2/97 (2%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + K+ + V L + Q LKE F+ FGE+ ++ +D +T SKG+
Sbjct: 1 GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
FV F + ++ + + R K
Sbjct: 61 FVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQS 95
Score = 49.5 bits (119), Expect = 5e-08
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 8/81 (9%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKE 253
++ + G E+ + + FS FG ++ ++V K+ G+ FV+FT E
Sbjct: 9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
Query: 254 TATHAIESIHNTDINGHTVKC 274
T + H I+G C
Sbjct: 69 TQVKVMSQRHM--IDGRWCDC 87
Score = 43.4 bits (103), Expect = 8e-06
Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 9/72 (12%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHH 56
+ + L V L TE+ L FS G V +V ++ G + F+ F +
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG---FGFVRFTEY 67
Query: 57 TVAATALAAMNK 68
++ +
Sbjct: 68 ETQVKVMSQRHM 79
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 80.4 bits (199), Expect = 6e-19
Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 5/97 (5%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS P + Y +VG+L + F I + R+VRD T K KG+
Sbjct: 4 GSSGKELPTEP---PYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFC 59
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
+V F + + A+ +G LG RS+R + + +
Sbjct: 60 YVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQ 95
Score = 52.7 bits (127), Expect = 5e-09
Identities = 18/90 (20%), Positives = 40/90 (44%), Gaps = 5/90 (5%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATAL 63
P T YVGNL + + + A+F + ++ +++R+ D + ++EF AL
Sbjct: 15 PYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
Query: 64 AAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
+ + ++ ++V+ A +S
Sbjct: 74 -TYDGALLGDRSLRVDIAEGRKQDKSGPSS 102
Score = 46.9 bits (112), Expect = 5e-07
Identities = 11/72 (15%), Positives = 29/72 (40%), Gaps = 8/72 (11%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIES 261
T Y G + + + +F I +R+ ++ KG+ +V+F ++ A+
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74
Query: 262 IHNTDINGHTVK 273
+ +++
Sbjct: 75 YDGALLGDRSLR 86
>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 = 80.4 bits (199), Expect = 6e-19
Identities = 20/99 (20%), Positives = 43/99 (43%), Gaps = 8/99 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG + ++ ++ FA +G + +I+ D +T SKGY FVSF + + +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV--E 68
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFD 196
+ + ++ + RK + + + F+
Sbjct: 69 SQINFHGKKLKLGPAIRK-----QNLSTYHVQPRPLIFN 102
Score = 63.4 bits (155), Expect = 7e-13
Identities = 23/94 (24%), Positives = 44/94 (46%), Gaps = 9/94 (9%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAAT 61
+ P T++VG +DV + E + + F++ G VK K+I + Y F+ F +
Sbjct: 6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNH 95
+ ++ F K++K+ A KQ+ S +
Sbjct: 66 IV--ESQINFHGKKLKLGPA-----IRKQNLSTY 92
Score = 58.8 bits (143), Expect = 3e-11
Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAI 259
TV+ GG ++E + F+ +G++ ++++ + KGY FV F +
Sbjct: 8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 67
Query: 260 ESIHNTDINGHTVK 273
ES + +G +K
Sbjct: 68 ESQI--NFHGKKLK 79
>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 = 81.0 bits (200), Expect = 1e-18
Identities = 22/132 (16%), Positives = 45/132 (34%), Gaps = 13/132 (9%)
Query: 59 AATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYH-------IFVGDLSPEIETQT 111
+ M +E++ S Y I+V +L+ ++ +
Sbjct: 3 LGSDSDEMPSECISRRELEKGRIS-REEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKD 61
Query: 112 LKEAFAPFGEISNCRI-----VRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRS 166
LK F + + S+ +R + + KG AF+ + A A+ NG L +
Sbjct: 62 LKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP 121
Query: 167 IRTNWSTRKPPA 178
+ ++ P
Sbjct: 122 MVVQFARSARPK 133
Score = 64.1 bits (156), Expect = 1e-12
Identities = 20/92 (21%), Positives = 34/92 (36%), Gaps = 13/92 (14%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPV--KGCKVIREPGNDP------YAFLEFVHHTVA 59
+YV NL V E+ L +F + + +++ + AF+ + A
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
Query: 60 ATALAAMNKRVFLEKEMKVNWASSPGNQPKQD 91
A AL N V K M V +A + +
Sbjct: 106 AKALKEANGYVLFGKPMVVQFA-----RSARP 132
Score = 58.3 bits (141), Expect = 1e-10
Identities = 20/95 (21%), Positives = 38/95 (40%), Gaps = 12/95 (12%)
Query: 199 YNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTI--------VDIRVFKE---KGYAFV 247
Y P NC +Y K + E+ + +F + DIR+ KE KG AF+
Sbjct: 39 YEPGEP-NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFI 97
Query: 248 KFTTKETATHAIESIHNTDINGHTVKCFWGKESEN 282
++ A A++ + + G + + + +
Sbjct: 98 GLPNEKAAAKALKEANGYVLFGKPMVVQFARSARP 132
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 78.7 bits (195), Expect = 1e-18
Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFVG LS + +K F FG++ + ++ D T + +G+ FV+F + E +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60
Query: 158 NGQWLGSRSIRTN 170
+ + ++ +
Sbjct: 61 HFHEINNKMVECK 73
Score = 50.2 bits (121), Expect = 2e-08
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
++ GG + E V F FG + D + +K G+ FV F +++ E I
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60
Query: 263 HNTDINGHTVKC 274
H +IN V+C
Sbjct: 61 HFHEINNKMVEC 72
Score = 37.4 bits (88), Expect = 5e-04
Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 10/78 (12%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAATAL 63
++VG L V+ T E + F Q G V ++ + G + F+ F +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRG---FGFVTFESEDIVEKVC 58
Query: 64 AAMNKRVFLEKEMKVNWA 81
++ K ++ A
Sbjct: 59 -EIHFHEINNKMVECKKA 75
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 78.3 bits (194), Expect = 2e-18
Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G LS + + L+E F FGE+ C ++RDP T +S+G+ FV+F+ +A + + A
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 61
Query: 158 NGQWLGSRSIRTN 170
+ L S++I
Sbjct: 62 SRHELDSKTIDPK 74
Score = 46.7 bits (112), Expect = 2e-07
Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 7/74 (9%)
Query: 207 CTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIE 260
C ++ GG +E + + F FG + + V ++ G+ FV F + +
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 261 SIHNTDINGHTVKC 274
+++ T+
Sbjct: 61 Q-SRHELDSKTIDP 73
Score = 38.2 bits (90), Expect = 3e-04
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 9/67 (13%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAATAL 63
+++G L T+E L F Q G VK C V+R+P G + F+ F+ L
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG---FGFVTFMDQAGVDKVL 59
Query: 64 AAMNKRV 70
A +
Sbjct: 60 AQSRHEL 66
>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 = 78.4 bits (194), Expect = 2e-18
Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 1/86 (1%)
Query: 85 GNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
G ++ + +FVG LS + + LK+ F FGE+ +C I DP T +S+G+ F+ F
Sbjct: 1 GINASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60
Query: 145 VKKAEAENAITAMNGQWLGSRSIRTN 170
A E + L R I
Sbjct: 61 KDAASVEKVLDQKE-HRLDGRVIDPK 85
Score = 45.6 bits (109), Expect = 9e-07
Identities = 12/72 (16%), Positives = 31/72 (43%), Gaps = 7/72 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
++ GG D +++ + F+ FG +VD + + G+ F+ F + ++
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73
Query: 263 HNTDINGHTVKC 274
+ ++G +
Sbjct: 74 EHR-LDGRVIDP 84
Score = 43.3 bits (103), Expect = 6e-06
Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 9/74 (12%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHH 56
+E ++VG L +++ L F++ G V C + +P G + F+ F
Sbjct: 7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRG---FGFILFKDA 63
Query: 57 TVAATALAAMNKRV 70
L R+
Sbjct: 64 ASVEKVLDQKEHRL 77
>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 = 85.3 bits (210), Expect = 2e-18
Identities = 31/208 (14%), Positives = 69/208 (33%), Gaps = 7/208 (3%)
Query: 11 YVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG-NDPYAFLEFVHHTVAATALAAMNKR 69
Y+ L+ E+ + I P + +P P E + + +R
Sbjct: 21 YLPPLEKLPHEKHHNQPYCGIAPYI--REFEDPRDAPPPTRAETREERMERKRREKIERR 78
Query: 70 VFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVR 129
+ W P N P +FV ++ + L+ F +G I +V
Sbjct: 79 QQEVETELKMW--DPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136
Query: 130 DPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSH 189
++ K +GYAF+ + + + +A +G+ + R + + + + R R+
Sbjct: 137 SKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE--RGRTVKGWRPRRLGG 194
Query: 190 TKTITFDEVYNQSSPTNCTVYCGGFGKD 217
T + + + + +
Sbjct: 195 GLGGTRRGGADVNIRHSGRDDTSRYDER 222
Score = 61.0 bits (147), Expect = 2e-10
Identities = 27/186 (14%), Positives = 56/186 (30%), Gaps = 12/186 (6%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGND---PYAFLEFVHHTVAATALAA 65
TL+V ++ TE L F GP+K ++ + YAF+E+ H +A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 66 MNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNC 125
+ + + + V+ + G + + + S
Sbjct: 164 ADGKKIDGRRVLVDVE----RGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRY 219
Query: 126 RIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKR 185
P L + + E E + R + R+ ++ +R
Sbjct: 220 DERPGPSPLPHRDRD-----RDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEER 274
Query: 186 QNSHTK 191
+ S +
Sbjct: 275 RRSRER 280
Score = 60.6 bits (146), Expect = 3e-10
Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 6/77 (7%)
Query: 206 NCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETATHAI 259
T++ D E + + F +G I I + K +GYAF+++ + A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 260 ESIHNTDINGHTVKCFW 276
+ I+G V
Sbjct: 162 KHADGKKIDGRRVLVDV 178
>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 = 78.4 bits (194), Expect = 3e-18
Identities = 15/73 (20%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFVG + L+E F FG ++ ++ D + + +G+ F++F + + A+ M
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NM 71
Query: 158 NGQWLGSRSIRTN 170
+ + + +
Sbjct: 72 HFHDIMGKKVEVK 84
Score = 49.5 bits (119), Expect = 5e-08
Identities = 20/97 (20%), Positives = 41/97 (42%), Gaps = 17/97 (17%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
++ GG + E + + F FG + ++ + + G+ F+ F +++ A+ +
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-M 71
Query: 263 HNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
H DI G V+ K A+P + P+S
Sbjct: 72 HFHDIMGKKVEV---KR-------AEPRDSKSSGPSS 98
Score = 45.6 bits (109), Expect = 1e-06
Identities = 18/91 (19%), Positives = 36/91 (39%), Gaps = 15/91 (16%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHTVAATAL 63
++VG + + E L F + G V +I + G + F+ F A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRG---FGFITFEDEQSVDQAV 69
Query: 64 AAMNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
M+ + K+++V A +P+ S+
Sbjct: 70 -NMHFHDIMGKKVEVKRA-----EPRDSKSS 94
>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 = 78.0 bits (193), Expect = 3e-18
Identities = 24/98 (24%), Positives = 49/98 (50%), Gaps = 13/98 (13%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKSK 137
+ P +P I++ +L+ +I+ LK++ F+ FG+I + + ++LK +
Sbjct: 1 AVPETRPNH------TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMR 51
Query: 138 GYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
G AFV F + + A NA+ +M G + +R ++
Sbjct: 52 GQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTD 89
Score = 74.2 bits (183), Expect = 9e-17
Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 5/92 (5%)
Query: 4 ESQPT-TLYVGNLDVSVTEE----LLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTV 58
E++P T+Y+ NL+ + ++ L A+FS+ G + V R AF+ F +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 59 AATALAAMNKRVFLEKEMKVNWASSPGNQPKQ 90
A AL +M F +K M++ +A + + +
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 95
Score = 66.9 bits (164), Expect = 3e-14
Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 7/88 (7%)
Query: 202 SSPTNCTVYCGGFGKDLNEE----LVSKVFSPFGTIVDIRVFKE---KGYAFVKFTTKET 254
+ N T+Y + + ++ + +FS FG I+DI V + +G AFV F +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS 63
Query: 255 ATHAIESIHNTDINGHTVKCFWGKESEN 282
AT+A+ S+ ++ + K +
Sbjct: 64 ATNALRSMQGFPFYDKPMRIQYAKTDSD 91
>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 = 77.7 bits (192), Expect = 7e-18
Identities = 23/90 (25%), Positives = 38/90 (42%), Gaps = 1/90 (1%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+S +FVG L +TL+ F+ +GE+ +C I++D T +S+G+
Sbjct: 2 SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTN 170
FV F + A L R+I
Sbjct: 62 FVKFKDPNCVGTVL-ASRPHTLDGRNIDPK 90
Score = 44.9 bits (107), Expect = 2e-06
Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 7/81 (8%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKE 253
N + ++ GG +E + FS +G +VD + K+K G+ FVKF
Sbjct: 10 NSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPN 69
Query: 254 TATHAIESIHNTDINGHTVKC 274
+ S ++G +
Sbjct: 70 CVGTVLAS-RPHTLDGRNIDP 89
Score = 40.7 bits (96), Expect = 7e-05
Identities = 25/97 (25%), Positives = 41/97 (42%), Gaps = 10/97 (10%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHH 56
+ L+VG LD S T+E L + FSQ G V C ++++ G + F++F
Sbjct: 12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRG---FGFVKFKDP 68
Query: 57 TVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
T LA+ + + + G QP +S
Sbjct: 69 NCVGTVLASRPH-TLDGRNIDPKPCTPRGMQPSGPSS 104
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 77.1 bits (190), Expect = 8e-18
Identities = 16/97 (16%), Positives = 38/97 (39%), Gaps = 6/97 (6%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
SS +Q + + ++ P ++ + L +G + +C V
Sbjct: 5 SSGSVPKRQRIRK---LQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVN 58
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPA 178
V++ K +A A+ +NG L + +++ + + A
Sbjct: 59 VTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMAA 95
Score = 68.2 bits (167), Expect = 1e-14
Identities = 15/81 (18%), Positives = 29/81 (35%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATAL 63
+ L + N+ + E+L +L Q G V+ C+ + + + A AL
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQAL 71
Query: 64 AAMNKRVFLEKEMKVNWASSP 84
+N +KV +
Sbjct: 72 DKLNGFQLENFTLKVAYIPDE 92
Score = 57.5 bits (139), Expect = 8e-11
Identities = 10/83 (12%), Positives = 28/83 (33%), Gaps = 3/83 (3%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFK---EKGYAFVKFTTKETATHA 258
+ L E++ + +G + E V +++K+ A A
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQA 70
Query: 259 IESIHNTDINGHTVKCFWGKESE 281
++ ++ + T+K + +
Sbjct: 71 LDKLNGFQLENFTLKVAYIPDEM 93
>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 = 77.3 bits (191), Expect = 1e-17
Identities = 24/95 (25%), Positives = 51/95 (53%), Gaps = 1/95 (1%)
Query: 76 MKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLK 135
M+ + P + K++ +F+G LS E ++L+ + +G++++C ++RDP + +
Sbjct: 8 MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKR 67
Query: 136 SKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTN 170
S+G+ FV+F AE + A+ A + R +
Sbjct: 68 SRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPK 101
Score = 43.8 bits (104), Expect = 7e-06
Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 7/72 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
++ GG + EE + + +G + D V ++ G+ FV F++ A+ +
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA- 88
Query: 263 HNTDINGHTVKC 274
I+G V+
Sbjct: 89 RPHSIDGRVVEP 100
Score = 40.0 bits (94), Expect = 2e-04
Identities = 20/74 (27%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHH 56
++ Q L++G L TEE L + Q G + C V+R+P G + F+ F
Sbjct: 23 EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG---FGFVTFSSM 79
Query: 57 TVAATALAAMNKRV 70
A+AA +
Sbjct: 80 AEVDAAMAARPHSI 93
>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 = 76.9 bits (190), Expect = 1e-17
Identities = 25/73 (34%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+F+G LS + + L+E F FGE+ C ++RDP T +S+G+ FV+F+ +A + + A
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQ 86
Query: 158 NGQWLGSRSIRTN 170
+ L S++I
Sbjct: 87 SRHELDSKTIDPK 99
Score = 44.2 bits (105), Expect = 5e-06
Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 7/80 (8%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKET 254
+ C ++ GG +E + + F FG + + V ++ G+ FV F +
Sbjct: 20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 79
Query: 255 ATHAIESIHNTDINGHTVKC 274
+ +++ T+
Sbjct: 80 VDKVLAQ-SRHELDSKTIDP 98
Score = 41.9 bits (99), Expect = 3e-05
Identities = 25/92 (27%), Positives = 37/92 (40%), Gaps = 10/92 (10%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP------GNDPYAFLEFVHHT 57
S +++G L T+E L F Q G VK C V+R+P G + F+ F+
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG---FGFVTFMDQA 78
Query: 58 VAATALAAMNKRVFLEKEMKVNWASSPGNQPK 89
L A ++ K + A QPK
Sbjct: 79 GVDKVL-AQSRHELDSKTIDPKVAFPRRAQPK 109
>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 = 76.1 bits (188), Expect = 2e-17
Identities = 24/98 (24%), Positives = 48/98 (48%), Gaps = 3/98 (3%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQ-TLKSKGY 139
SS + + S Y F+G+L ++ +++KE F IS R+ R+P + KG+
Sbjct: 1 GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF 59
Query: 140 AFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPP 177
+ F +A+ ++N + LG++ IR + + +
Sbjct: 60 GYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQD 96
Score = 54.6 bits (132), Expect = 1e-09
Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 6/91 (6%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP----YAFLEFVHHTVAATA 62
P T ++GNL VTEE + F + + ++ REP N + + EF +A
Sbjct: 15 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
L ++N+ K ++V+ A ++ +S
Sbjct: 74 L-SLNEESLGNKRIRVDVADQAQDKDSGPSS 103
Score = 50.7 bits (122), Expect = 2e-08
Identities = 13/84 (15%), Positives = 35/84 (41%), Gaps = 9/84 (10%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-------KGYAFVKFTTKETATHAIE 260
T + G D+ EE + + F I +R+ +E KG+ + +F ++ A+
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 261 SIHNTDINGHTVKCFWGKESENNS 284
++ + ++ ++++
Sbjct: 76 -LNEESLGNKRIRVDVADQAQDKD 98
>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 = 74.8 bits (185), Expect = 2e-17
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
IFVG LSP+ + ++E F FGE+ + + D +T K +G+ F++F ++ + +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60
Query: 158 NGQWLGSRSIRTN 170
+G
Sbjct: 61 KYHNVGLSKCEIK 73
Score = 49.4 bits (119), Expect = 3e-08
Identities = 14/72 (19%), Positives = 29/72 (40%), Gaps = 7/72 (9%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK------GYAFVKFTTKETATHAIESI 262
++ GG D EE + + F FG + I + + G+ F+ F +E +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 263 HNTDINGHTVKC 274
++ + +
Sbjct: 62 YHN-VGLSKCEI 72
Score = 35.6 bits (83), Expect = 0.003
Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 3/59 (5%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPG-NDP--YAFLEFVHHTVAATALAA 65
++VG L EE + F G V+ ++ + N + F+ F +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 76.5 bits (188), Expect = 3e-17
Identities = 22/100 (22%), Positives = 42/100 (42%), Gaps = 5/100 (5%)
Query: 3 DESQPT-TLYVGNLDVSVTEE----LLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHT 57
++P+ + + N++ V +E LL AL S G + V N A++ F
Sbjct: 24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQE 83
Query: 58 VAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYH 97
A + A F + + ++ +P +Q +D S +H
Sbjct: 84 SAQAFVEAFQGYPFQGNPLVITFSETPQSQVAEDGSLEHH 123
Score = 71.1 bits (174), Expect = 3e-15
Identities = 14/99 (14%), Positives = 37/99 (37%), Gaps = 8/99 (8%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEA----FAPFGEISNCRIVRDPQTLKS 136
+ G+ P + + + +++PE+ + L+ + G+I + + +
Sbjct: 16 SPDLGSTPPHTEPSQ-VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSD---DN 71
Query: 137 KGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
G A++ F + A+ + A G + +S
Sbjct: 72 SGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP 110
Score = 66.5 bits (162), Expect = 1e-13
Identities = 21/112 (18%), Positives = 43/112 (38%), Gaps = 8/112 (7%)
Query: 178 AMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEE----LVSKVFSPFGTI 233
T K + H + + P + V ++ +E L+ + S G I
Sbjct: 2 KETAAAKFERQHMDSPDLGSTPPHTEP-SQVVLITNINPEVPKEKLQALLYALASSQGDI 60
Query: 234 VDIRVFKE---KGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKESEN 282
+DI V G A++ F T+E+A +E+ G+ + + + ++
Sbjct: 61 LDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS 112
>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 = 75.0 bits (185), Expect = 5e-17
Identities = 23/98 (23%), Positives = 46/98 (46%), Gaps = 5/98 (5%)
Query: 81 ASSPGNQPKQDTSNH--YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTL-KSK 137
S + + Y F+G+L ++ +++KE F IS R+ R+P + K
Sbjct: 3 GSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLK 61
Query: 138 GYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
G+ + F +A+ ++N + LG+R IR + + +
Sbjct: 62 GFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQA 98
Score = 53.8 bits (130), Expect = 1e-09
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 7 PTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP----YAFLEFVHHTVAATA 62
P T ++GNL VTEE + F + + ++ REP N + + EF +A
Sbjct: 19 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 77
Query: 63 LAAMNKRVFLEKEMKVNWASSPGN 86
L ++N+ + ++V+ A +
Sbjct: 78 L-SLNEESLGNRRIRVDVADQAQD 100
Score = 50.3 bits (121), Expect = 2e-08
Identities = 13/82 (15%), Positives = 35/82 (42%), Gaps = 9/82 (10%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-------KGYAFVKFTTKETATHAIE 260
T + G D+ EE + + F I +R+ +E KG+ + +F ++ A+
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 261 SIHNTDINGHTVKCFWGKESEN 282
++ + ++ ++++
Sbjct: 80 -LNEESLGNRRIRVDVADQAQD 100
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 74.4 bits (183), Expect = 7e-17
Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 1/73 (1%)
Query: 99 FVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
+ + + L F+ G++ N D T K+KG+ FV +A+ I + +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 159 GQWL-GSRSIRTN 170
G+ L +
Sbjct: 76 GKRLDLKHRLFLY 88
Score = 53.6 bits (129), Expect = 2e-09
Identities = 13/65 (20%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKE------KGYAFVKFTTKETATHAIESIHNTDING 269
+ ++ ++ +FS G +V++ + KG+ FV+ + A I+S H ++
Sbjct: 22 VPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDL 81
Query: 270 -HTVK 273
H +
Sbjct: 82 KHRLF 86
Score = 50.1 bits (120), Expect = 3e-08
Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 3/60 (5%)
Query: 11 YVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP---YAFLEFVHHTVAATALAAMN 67
+ + V V ++ L +LFS+ G V + + + F+E A + + +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
>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 = 74.7 bits (184), Expect = 7e-17
Identities = 19/81 (23%), Positives = 41/81 (50%), Gaps = 9/81 (11%)
Query: 98 IFVGDLSPEIETQT-LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+G+L+ + ++ ++ F+ +G ++ C + KGYAFV + + A A+
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLG 81
Query: 157 MNGQWLGSRSIRTNWSTRKPP 177
NG+ L +++ N + P
Sbjct: 82 ENGRVLAGQTLDINMAGEPKP 102
Score = 69.3 bits (170), Expect = 6e-15
Identities = 23/100 (23%), Positives = 43/100 (43%), Gaps = 5/100 (5%)
Query: 187 NSHTKTITFDEVYNQSSP--TNCTVYCGGFGKDL-NEELVSKVFSPFGTIVDIRVFKEKG 243
+ + + V N++ P N V+ G L + V +FS +G + V K G
Sbjct: 6 SGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--G 63
Query: 244 YAFVKFTTKETATHAIESIHNTDINGHTVKCFWGKESENN 283
YAFV+++ + A A+ + + G T+ E + +
Sbjct: 64 YAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPD 103
Score = 68.2 bits (167), Expect = 2e-14
Identities = 24/91 (26%), Positives = 45/91 (49%), Gaps = 6/91 (6%)
Query: 4 ESQPTTLYVGNLDVS-VTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATA 62
+S + +++GNL+ + V + + +FS+ G V GC V + YAF+++ + A A
Sbjct: 24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK-----GYAFVQYSNERHARAA 78
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
+ N RV + + +N A P +S
Sbjct: 79 VLGENGRVLAGQTLDINMAGEPKPDRSGPSS 109
>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 = 74.4 bits (183), Expect = 9e-17
Identities = 18/93 (19%), Positives = 33/93 (35%), Gaps = 8/93 (8%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGP-VKGCKVIREP----GNDPYAFLEFVHHTVAATA 62
L++G + E + +++ V V N +AF+E+ H AA A
Sbjct: 9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68
Query: 63 LAAMNKRVFL--EKEMKVNWASSPGNQPKQDTS 93
+ ++ V+WA P +D
Sbjct: 69 RRKLMPGRIQLWGHQIAVDWA-EPEIDVDEDVM 100
Score = 71.4 bits (175), Expect = 1e-15
Identities = 17/94 (18%), Positives = 37/94 (39%), Gaps = 6/94 (6%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGE-ISNCRIVRDPQ-TLKSKGYAFVSFVKKAEAENAIT 155
+F+G + + + + E A E + + + +K++G+AFV + A A
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70
Query: 156 AMNGQ--WLGSRSIRTNWSTRKPPAMTNERKRQN 187
+ L I +W+ +P +E +
Sbjct: 71 KLMPGRIQLWGHQIAVDWA--EPEIDVDEDVMET 102
Score = 66.7 bits (163), Expect = 5e-14
Identities = 21/104 (20%), Positives = 40/104 (38%), Gaps = 12/104 (11%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIV-DIRVFKE-------KGYAFVKFTTKE 253
S NC ++ GG K E + + + V D+ V+ +G+AFV++ +
Sbjct: 4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63
Query: 254 TATHAIESIHNTD--INGHTVKCFW--GKESENNSTLAQPSAPT 293
A A + + GH + W + + + S P+
Sbjct: 64 AAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGPS 107
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 77.9 bits (191), Expect = 1e-16
Identities = 25/88 (28%), Positives = 35/88 (39%), Gaps = 9/88 (10%)
Query: 201 QSSPTNCTVYCGGFGKDLN---------EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTT 251
N T+Y GG LN E + VFS G I IR + K FVKF
Sbjct: 129 SFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKY 188
Query: 252 KETATHAIESIHNTDINGHTVKCFWGKE 279
+ A A E++ N + + K + +
Sbjct: 189 QANAEFAKEAMSNQTLLLPSDKEWDDRR 216
Score = 68.3 bits (166), Expect = 2e-13
Identities = 25/142 (17%), Positives = 46/142 (32%), Gaps = 28/142 (19%)
Query: 66 MNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIET---------QTLKEAF 116
+E ++ G N ++VG + + + ++ F
Sbjct: 106 TEVLDCFGREKFADYREDMGGIGSFRKKNK-TLYVGGIDGALNSKHLKPAQIESRIRFVF 164
Query: 117 APFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLG------------S 164
+ G+I R ++SK FV F +A AE A AM+ Q L
Sbjct: 165 SRLGDIDRIRY------VESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREG 218
Query: 165 RSIRTNWSTRKPPAMTNERKRQ 186
+ W+ P +R ++
Sbjct: 219 TGLLVKWANEDPDPAAQKRLQE 240
Score = 57.1 bits (137), Expect = 2e-09
Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 12/94 (12%)
Query: 2 CDESQPTTLYVGNLDVSVT---------EELLCALFSQIGPVKGCKVIREPGNDPYAFLE 52
+ TLYVG +D ++ E + +FS++G + + + F++
Sbjct: 129 SFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKN---CGFVK 185
Query: 53 FVHHTVAATALAAMNKRVFLEKEMKVNWASSPGN 86
F + A A AM+ + L K G
Sbjct: 186 FKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGT 219
>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 = 71.7 bits (176), Expect = 1e-15
Identities = 16/111 (14%), Positives = 34/111 (30%), Gaps = 5/111 (4%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNC-RIVRDPQTLKSKGY 139
SS + S + ++ I + + N ++ D + G
Sbjct: 1 GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNG-QGLGQ 59
Query: 140 AFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP--PAMTNERKRQNS 188
A V F + +A + ++ + L R + T + N + S
Sbjct: 60 ALVQFKNEDDARKSE-RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKS 109
Score = 55.9 bits (135), Expect = 4e-10
Identities = 14/106 (13%), Positives = 30/106 (28%), Gaps = 7/106 (6%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVD-IRVF-----KEKGYAFVKFTTKE 253
+ + + + V + + + V + G A V+F ++
Sbjct: 9 GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 68
Query: 254 TATHAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
A + +H +NG + P A P+S
Sbjct: 69 DARKSER-LHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSS 113
Score = 48.2 bits (115), Expect = 2e-07
Identities = 10/93 (10%), Positives = 33/93 (35%), Gaps = 8/93 (8%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-----YAFLEFVHHTV 58
S ++ N+ S+T+ + I + + ++ A ++F +
Sbjct: 12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDEN--AVHVLVDNNGQGLGQALVQFKNEDD 69
Query: 59 AATALAAMNKRVFLEKEMKVNWASSPGNQPKQD 91
A + ++++ +E V+ + + +
Sbjct: 70 ARKSE-RLHRKKLNGREAFVHVVTLEDMREIEK 101
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 70.7 bits (174), Expect = 1e-15
Identities = 14/89 (15%), Positives = 31/89 (34%), Gaps = 9/89 (10%)
Query: 98 IFVGDLSPE-IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+G+L + + + L F+P+G I I + F+ F +AI
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIEC 64
Query: 157 MNGQWLGSRSIRTNWSTRKPPAMTNERKR 185
+ + + + S+ +
Sbjct: 65 ESQEMNFGKKLILEVSSSNARPQFDHGDH 93
Score = 61.8 bits (151), Expect = 2e-12
Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 201 QSSPTNCTVYCGGF-GKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAI 259
+ P ++ G K++++E + ++FSP+G I+ I + + + F++F ++ AI
Sbjct: 5 HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAI 62
Query: 260 ESIHNTDINGHTVK 273
E G +
Sbjct: 63 ECESQEMNFGKKLI 76
Score = 60.7 bits (148), Expect = 6e-12
Identities = 18/89 (20%), Positives = 43/89 (48%), Gaps = 7/89 (7%)
Query: 8 TTLYVGNLDV-SVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAM 66
+ L++GNL + +V++E L +FS G + + + F++F + A+
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-----AFGFIQFDNPQSVRDAIECE 65
Query: 67 NKRVFLEKEMKVNWASSPGNQPKQDTSNH 95
++ + K++ + + S +P+ D +H
Sbjct: 66 SQEMNFGKKLILEVS-SSNARPQFDHGDH 93
>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 = 70.4 bits (173), Expect = 2e-15
Identities = 17/93 (18%), Positives = 37/93 (39%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + I V ++ + + + F + I ++ + G A
Sbjct: 1 GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWST 173
V+F + EA A+ +N + +GSR ++ + +
Sbjct: 61 MVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS 93
Score = 58.9 bits (143), Expect = 3e-11
Identities = 13/88 (14%), Positives = 28/88 (31%), Gaps = 6/88 (6%)
Query: 194 TFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFV 247
+ + P + ++ + + F + I G A V
Sbjct: 3 SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 248 KFTTKETATHAIESIHNTDINGHTVKCF 275
F +++ AT A+ +++ I VK
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLS 90
Score = 53.5 bits (129), Expect = 2e-09
Identities = 17/84 (20%), Positives = 35/84 (41%), Gaps = 3/84 (3%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIR-EPGNDP--YAFLEFVHHTVA 59
+ PT + V N+ +V+ + + F + G ++ P A + F A
Sbjct: 11 GKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 70
Query: 60 ATALAAMNKRVFLEKEMKVNWASS 83
A+ +N R +++K++ SS
Sbjct: 71 TAAVIDLNDRPIGSRKVKLSGPSS 94
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 70.6 bits (173), Expect = 2e-15
Identities = 21/94 (22%), Positives = 42/94 (44%), Gaps = 5/94 (5%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
S PG+ P + ++VG+L + LK A G + R+ + AF
Sbjct: 6 SGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-PLRLTWQ----GPRRRAF 60
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
+ + A A+ A++ + G LG+ ++R + ++
Sbjct: 61 LHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94
Score = 64.1 bits (156), Expect = 3e-13
Identities = 11/84 (13%), Positives = 31/84 (36%), Gaps = 1/84 (1%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTI-VDIRVFKEKGYAFVKFTTKETATHA 258
+ +P VY G +D + + G++ + + + AF+ + A A
Sbjct: 13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQA 72
Query: 259 IESIHNTDINGHTVKCFWGKESEN 282
+ + + T++ ++ +
Sbjct: 73 VSCLQGLRLGTDTLRVALARQQRD 96
Score = 55.6 bits (134), Expect = 3e-10
Identities = 16/84 (19%), Positives = 27/84 (32%), Gaps = 2/84 (2%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATA 62
+YVGNL L ++G V + G AFL + A A
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALRELGSV--PLRLTWQGPRRRAFLHYPDSAAAQQA 72
Query: 63 LAAMNKRVFLEKEMKVNWASSPGN 86
++ + ++V A +
Sbjct: 73 VSCLQGLRLGTDTLRVALARQQRD 96
>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 = 70.2 bits (172), Expect = 3e-15
Identities = 23/110 (20%), Positives = 39/110 (35%), Gaps = 12/110 (10%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
S G P + + + V L P Q LK+ G++ + RD G
Sbjct: 4 GSSGGPPSRRSE--NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 54
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWST---RKPPAMTNERKRQNS 188
V FV+K + A+ ++ S T + P + + R R +
Sbjct: 55 VEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSG 104
Score = 61.4 bits (149), Expect = 4e-12
Identities = 17/101 (16%), Positives = 34/101 (33%), Gaps = 1/101 (0%)
Query: 199 YNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHA 258
S + V G + + + G + V++ G V+F KE T+A
Sbjct: 8 GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-DGTGVVEFVRKEDMTYA 66
Query: 259 IESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
+ + NT H + + + + + P+S
Sbjct: 67 VRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSS 107
Score = 54.4 bits (131), Expect = 1e-09
Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 4/76 (5%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAA 65
+ V L S + + L + G V V R D +EFV A+
Sbjct: 14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----DGTGVVEFVRKEDMTYAVRK 69
Query: 66 MNKRVFLEKEMKVNWA 81
++ F E + +
Sbjct: 70 LDNTKFRSHEGETAYI 85
>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 = 68.9 bits (169), Expect = 7e-15
Identities = 17/95 (17%), Positives = 36/95 (37%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
SS + I V ++ + + + F + I ++ + G A
Sbjct: 2 SSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP 176
V+F + EA A+ +N + +GSR ++ +
Sbjct: 62 VAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS 96
Score = 57.7 bits (140), Expect = 7e-11
Identities = 14/94 (14%), Positives = 31/94 (32%), Gaps = 6/94 (6%)
Query: 194 TFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVD-IRVFKE-----KGYAFV 247
+ + P + ++ + + F + I + + G A V
Sbjct: 3 SGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 248 KFTTKETATHAIESIHNTDINGHTVKCFWGKESE 281
F +++ AT A+ +++ I VK G
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS 96
Score = 56.2 bits (136), Expect = 2e-10
Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 3/85 (3%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI-REPGNDP--YAFLEFVHHTVA 59
+ PT + V N+ +V+ + + F + G + P A + F A
Sbjct: 11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 70
Query: 60 ATALAAMNKRVFLEKEMKVNWASSP 84
A+ +N R +++K+ S P
Sbjct: 71 TAAVIDLNDRPIGSRKVKLVLGSGP 95
>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 = 67.9 bits (166), Expect = 2e-14
Identities = 12/95 (12%), Positives = 35/95 (36%), Gaps = 3/95 (3%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+S +P + ++ V + +++ F + +++D ++ G
Sbjct: 2 SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVG-RNNGNG 59
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
V F+ + A+ N + R + + +T +
Sbjct: 60 LVKFLSPQDTFEALK-RNRMLMIQRYVEVSPATER 93
Score = 48.2 bits (115), Expect = 2e-07
Identities = 17/103 (16%), Positives = 32/103 (31%), Gaps = 11/103 (10%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETAT 256
+P + V G E V F + + + K+ G VKF + +
Sbjct: 12 INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTF 70
Query: 257 HAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
A++ + + V+ E + T P+S
Sbjct: 71 EALKR-NRMLMIQRYVEVSPATERQ----WVAAGGHITSGPSS 108
Score = 41.3 bits (97), Expect = 5e-05
Identities = 11/82 (13%), Positives = 31/82 (37%), Gaps = 4/82 (4%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAA 60
+ V + S E + F + V ++++ ++F+
Sbjct: 12 INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTF 70
Query: 61 TALAAMNKRVFLEKEMKVNWAS 82
AL N+ + +++ ++V+ A+
Sbjct: 71 EAL-KRNRMLMIQRYVEVSPAT 91
>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 = 67.0 bits (164), Expect = 3e-14
Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 9/80 (11%)
Query: 98 IFVGDLSPE-IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITA 156
+F+G+L + + + L F+P+G I I + F+ F +AI
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEX 76
Query: 157 MNGQWLGSRSIRTNWSTRKP 176
+ + + + S+
Sbjct: 77 ESQEMNFGKKLILEVSSSNA 96
Score = 62.3 bits (152), Expect = 2e-12
Identities = 16/73 (21%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 202 SSPTNCTVYCGGF-GKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE 260
S ++ G K++++E + ++FSP+G I+ I + + + F++F ++ AIE
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--KNAFGFIQFDNPQSVRDAIE 75
Query: 261 SIHNTDINGHTVK 273
G +
Sbjct: 76 XESQEMNFGKKLI 88
Score = 61.6 bits (150), Expect = 3e-12
Identities = 16/83 (19%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 3 DESQPTTLYVGNLDV-SVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAAT 61
+ L++GNL + +V++E L +FS G + + + F++F +
Sbjct: 18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN-----AFGFIQFDNPQSVRD 72
Query: 62 ALAAMNKRVFLEKEMKVNWASSP 84
A+ ++ + K++ + +SS
Sbjct: 73 AIEXESQEMNFGKKLILEVSSSN 95
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 67.1 bits (164), Expect = 3e-14
Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATHAIESI 262
+VY GF D + + + G +++I++ + KG FV F + E+A +E+
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET- 71
Query: 263 HNTDINGHTVKCFWGKE 279
+ + +
Sbjct: 72 PGQKYKETDLLILFKDD 88
Score = 65.5 bits (160), Expect = 1e-13
Identities = 16/90 (17%), Positives = 33/90 (36%), Gaps = 3/90 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+++ + +KE G++ N ++ R KG FV F A+ +
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHK-AFKGSIFVVFDSIESAKKFVETP 72
Query: 158 NGQWLGSRSIRTNWSTRKPPAMTNERKRQN 187
++ + + A NE ++QN
Sbjct: 73 GQKYKETDLLIL--FKDDYFAKKNEERKQN 100
Score = 58.2 bits (141), Expect = 5e-11
Identities = 9/82 (10%), Positives = 27/82 (32%), Gaps = 3/82 (3%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAA 60
++ + ++Y+ T + + G V ++ R F+ F A
Sbjct: 7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 66
Query: 61 TALAAMNKRVFLEKEMKVNWAS 82
+ + + E ++ + +
Sbjct: 67 KFV-ETPGQKYKETDLLILFKD 87
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 66.7 bits (163), Expect = 4e-14
Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 2/83 (2%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE 260
+P + V+ G + E + + FG I + V +K A V+F A +A+
Sbjct: 16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVN 75
Query: 261 SIHNTD--INGHTVKCFWGKESE 281
+ I GH + +
Sbjct: 76 YAADNQIYIAGHPAFVNYSTSQK 98
Score = 63.2 bits (154), Expect = 7e-13
Identities = 18/80 (22%), Positives = 28/80 (35%), Gaps = 8/80 (10%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ + L + L EA FG IS ++ K A V F A NA+
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYA 77
Query: 158 NGQ--WLGSRSIRTNWSTRK 175
++ N+ST +
Sbjct: 78 ADNQIYIAGHPAFVNYSTSQ 97
Score = 51.7 bits (124), Expect = 1e-08
Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 5/77 (6%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
+++ L V E L + GP+ V+ + A +EF A A+
Sbjct: 23 VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKR---QALVEFEDVLGACNAVNYAAD 79
Query: 69 RVFLE--KEMKVNWASS 83
VN+++S
Sbjct: 80 NQIYIAGHPAFVNYSTS 96
>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 = 66.8 bits (163), Expect = 7e-14
Identities = 21/102 (20%), Positives = 37/102 (36%), Gaps = 12/102 (11%)
Query: 96 YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT 155
+ V L P Q LK+ G++ + RD G V FV+K + A+
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVR 69
Query: 156 AMNGQWLGSRSIRTNW-----STRKPPAMTNERKRQNSHTKT 192
++ S T + + P+ R R S +++
Sbjct: 70 KLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRS 111
Score = 56.8 bits (137), Expect = 2e-10
Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 1/80 (1%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
S + V G + + + G + V++ G V+F KE T+A+
Sbjct: 12 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR-DGTGVVEFVRKEDMTYAVRK 70
Query: 262 IHNTDINGHTVKCFWGKESE 281
+ NT H + + +
Sbjct: 71 LDNTKFRSHEGETAYIRVKV 90
Score = 50.6 bits (121), Expect = 3e-08
Identities = 15/73 (20%), Positives = 25/73 (34%), Gaps = 4/73 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
+ V L S + + L + G V V R D +EFV A+ ++
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR----DGTGVVEFVRKEDMTYAVRKLDN 73
Query: 69 RVFLEKEMKVNWA 81
F E + +
Sbjct: 74 TKFRSHEGETAYI 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 = 66.0 bits (161), Expect = 9e-14
Identities = 16/95 (16%), Positives = 33/95 (34%), Gaps = 3/95 (3%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAI 259
+ + V+ G + + E + + FGTI + + K A V+F ++A +
Sbjct: 9 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECV 68
Query: 260 E--SIHNTDINGHTVKCFWGKESE-NNSTLAQPSA 291
+ I G + + PS+
Sbjct: 69 TFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSS 103
Score = 65.2 bits (159), Expect = 2e-13
Identities = 21/97 (21%), Positives = 32/97 (32%), Gaps = 8/97 (8%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
SS + S + V L + L EA FG I ++ K A
Sbjct: 1 GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQA 54
Query: 141 FVSFVKKAEAENAITAM--NGQWLGSRSIRTNWSTRK 175
V F A+ +T ++ + N+ST K
Sbjct: 55 LVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK 91
Score = 52.1 bits (125), Expect = 6e-09
Identities = 13/88 (14%), Positives = 31/88 (35%), Gaps = 7/88 (7%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNK 68
++V L SV E L + G + ++ A +EF + A +
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR---QALVEFENIDSAKECVTFAAD 73
Query: 69 RVFLE--KEMKVNWASSPGNQPKQDTSN 94
++ N+++S + + ++
Sbjct: 74 VPVYIAGQQAFFNYSTS--KRITRPGNS 99
>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 = 9e-14
Identities = 15/87 (17%), Positives = 27/87 (31%), Gaps = 7/87 (8%)
Query: 85 GNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
G+ S I +L ++E F+ FG + + + A V F
Sbjct: 1 GSSGSSGRSKTV-ILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEF 53
Query: 145 VKKAEAENAITAMNGQWLGSRSIRTNW 171
++ EA A + + W
Sbjct: 54 LEPLEARKAFRHLAYSKFHHVPLYLEW 80
Score = 59.4 bits (144), Expect = 2e-11
Identities = 14/74 (18%), Positives = 24/74 (32%), Gaps = 3/74 (4%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
T + NL + FS+ G + + A +EF+ A A +
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGI---TAIVEFLEPLEARKAFRHLA 67
Query: 68 KRVFLEKEMKVNWA 81
F + + WA
Sbjct: 68 YSKFHHVPLYLEWA 81
Score = 56.0 bits (135), Expect = 4e-10
Identities = 15/102 (14%), Positives = 30/102 (29%), Gaps = 1/102 (0%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAI 259
S + + + + FS FG++ + + + A V+F A A
Sbjct: 4 GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAF 63
Query: 260 ESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNSTA 301
+ + + + W + Q QP A
Sbjct: 64 RHLAYSKFHHVPLYLEWAPIGVFGAA-PQKKDSQHEQPAEKA 104
>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 = 65.4 bits (159), Expect = 1e-13
Identities = 15/90 (16%), Positives = 36/90 (40%), Gaps = 4/90 (4%)
Query: 3 DESQPTTLYVGNLDVSVTE----ELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTV 58
+ V N+D ++ +LL F++ G VK ++ A ++ +
Sbjct: 5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQD 64
Query: 59 AATALAAMNKRVFLEKEMKVNWASSPGNQP 88
A A+ ++++ K++ V+ A+
Sbjct: 65 AIGAVNSLHRYKIGSKKILVSLATGASGPS 94
Score = 42.7 bits (100), Expect = 1e-05
Identities = 17/90 (18%), Positives = 37/90 (41%), Gaps = 7/90 (7%)
Query: 91 DTSNHYHIFVGDLSPEIET----QTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVK 146
+ N + V ++ + Q L+EAFA G++ + + + A V
Sbjct: 5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMEN 61
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWSTRKP 176
+A A+ +++ +GS+ I + +T
Sbjct: 62 LQDAIGAVNSLHRYKIGSKKILVSLATGAS 91
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 64.9 bits (158), Expect = 2e-13
Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 2/82 (2%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
S + ++ D+ E V + PFG + ++ + K K AF++ T+E A +
Sbjct: 12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNY 71
Query: 262 IHNTD--INGHTVKCFWGKESE 281
+ + G + + E
Sbjct: 72 YTSVTPVLRGQPIYIQFSNHKE 93
Score = 62.6 bits (152), Expect = 2e-12
Identities = 18/114 (15%), Positives = 36/114 (31%), Gaps = 16/114 (14%)
Query: 83 SPGNQPKQDTSNH--YHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+ S I + L ++ + PFG+++N +++ K A
Sbjct: 2 RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQA 55
Query: 141 FVSFVKKAEAENAITA--MNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKT 192
F+ + A + L + I +S K E K +S +
Sbjct: 56 FIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK------ELKTDSSPNQA 103
Score = 52.9 bits (127), Expect = 4e-09
Identities = 13/88 (14%), Positives = 32/88 (36%), Gaps = 5/88 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAA--M 66
+++ L + VTE + +L G V +++ AF+E A T +
Sbjct: 18 VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN---QAFIEMNTEEAANTMVNYYTS 74
Query: 67 NKRVFLEKEMKVNWASSPGNQPKQDTSN 94
V + + + +++ + +
Sbjct: 75 VTPVLRGQPIYIQFSNHKELKTDSSPNQ 102
>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 = 64.5 bits (157), Expect = 5e-13
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 5/104 (4%)
Query: 88 PKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNC-RIVRDPQTLKSKGYAFVSFVK 146
+ + +++ L E E + + + F + + I P K+ G FV F
Sbjct: 18 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNG-KATGEGFVEFRN 76
Query: 147 KAEAENAITAMNGQWLGSRSIRTNWSTRK--PPAMTNERKRQNS 188
+A+ + A+ + Q++G+R I+ + T+K + RKR S
Sbjct: 77 EADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQS 119
Score = 45.6 bits (108), Expect = 2e-06
Identities = 15/106 (14%), Positives = 27/106 (25%), Gaps = 7/106 (6%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKE 253
VY G + + V F + D K G FV+F +
Sbjct: 19 RSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEA 78
Query: 254 TATHAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
A+ H + ++ + + P+S
Sbjct: 79 DYKAALCR-HKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGPSS 123
Score = 44.8 bits (106), Expect = 4e-06
Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 4/82 (4%)
Query: 4 ESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGC-KVIREPGNDP--YAFLEFVHHTVAA 60
+Y+ L + + F ++ V+ + P F+EF +
Sbjct: 22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK 81
Query: 61 TALAAMNKRVFLEKEMKVNWAS 82
AL +K+ + ++V+ +
Sbjct: 82 AAL-CRHKQYMGNRFIQVHPIT 102
>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 = 63.2 bits (154), Expect = 7e-13
Identities = 13/84 (15%), Positives = 30/84 (35%), Gaps = 7/84 (8%)
Query: 92 TSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAE 151
+S I V +L + Q + + + ++ ++K AFV+ + +A+
Sbjct: 2 SSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQ 54
Query: 152 NAITAMNGQWLGSRSIRTNWSTRK 175
NAI + + +
Sbjct: 55 NAIQMFHQYSFRGKDLIVQLQPTD 78
Score = 60.5 bits (147), Expect = 5e-12
Identities = 16/79 (20%), Positives = 30/79 (37%), Gaps = 4/79 (5%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALA 64
S + + V NL + + L +K C V R AF+ ++ A A+
Sbjct: 3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKR---TAFVTLLNGEQAQNAIQ 58
Query: 65 AMNKRVFLEKEMKVNWASS 83
++ F K++ V +
Sbjct: 59 MFHQYSFRGKDLIVQLQPT 77
Score = 59.7 bits (145), Expect = 8e-12
Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 1/72 (1%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESI 262
S + + +D N + V + + + V + K AFV E A +AI+
Sbjct: 2 SSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60
Query: 263 HNTDINGHTVKC 274
H G +
Sbjct: 61 HQYSFRGKDLIV 72
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 63.6 bits (155), Expect = 7e-13
Identities = 21/92 (22%), Positives = 41/92 (44%), Gaps = 11/92 (11%)
Query: 87 QPKQDTSNHYHIFVGDLSPEIET-------QTLKEAFAPFGEISNCRIVRDPQTLKSKGY 139
+P++ I V ++ P++ + + F+ FG+I+N + K+KGY
Sbjct: 7 RPQEADGIDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGY 63
Query: 140 AFVSFVKKAEAENAITAMNGQWL-GSRSIRTN 170
F+ + A A +A+ +G L + R N
Sbjct: 64 IFLEYASPAHAVDAVKNADGYKLDKQHTFRVN 95
Score = 56.7 bits (137), Expect = 2e-10
Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 11/79 (13%)
Query: 206 NCTVYCGGF------GKDLNEELVSKVFSPFGTIVDIRVFKE----KGYAFVKFTTKETA 255
+ + + + ++ K+FS FG I + +E KGY F+++ + A
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 74
Query: 256 THAIESIHNTDING-HTVK 273
A+++ ++ HT +
Sbjct: 75 VDAVKNADGYKLDKQHTFR 93
Score = 48.6 bits (116), Expect = 1e-07
Identities = 15/88 (17%), Positives = 33/88 (37%), Gaps = 8/88 (9%)
Query: 3 DESQPTTLYVGNL------DVSVTEELLCALFSQIGPVKGCKVIREPGNDP-YAFLEFVH 55
+ + + V N+ + + ++ +FS+ G + E G Y FLE+
Sbjct: 11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYAS 70
Query: 56 HTVAATALAAMNKRVFLEKE-MKVNWAS 82
A A+ + ++ +VN +
Sbjct: 71 PAHAVDAVKNADGYKLDKQHTFRVNLFT 98
>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 = 63.2 bits (154), Expect = 9e-13
Identities = 24/95 (25%), Positives = 41/95 (43%), Gaps = 3/95 (3%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+ S GN P DT+N + + L + + + F+ + N + +S G A
Sbjct: 3 SGSSGNSP--DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
FV F + AE A+ + + +G R I S+R
Sbjct: 61 FVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRA 94
Score = 46.3 bits (110), Expect = 7e-07
Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 7/86 (8%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKETA 255
+ + V G ++E + + FS + + + G AFV+F ++E A
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70
Query: 256 THAIESIHNTDINGHTVKCFWGKESE 281
A++ H I ++ F +E
Sbjct: 71 EKALK-KHKERIGHRYIEIFKSSRAE 95
Score = 42.4 bits (100), Expect = 2e-05
Identities = 14/83 (16%), Positives = 32/83 (38%), Gaps = 4/83 (4%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI-REPGNDP--YAFLEFVHHTVA 59
D + + + L ++E + FS + V + + AF++F +A
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70
Query: 60 ATALAAMNKRVFLEKEMKVNWAS 82
AL +K + +++ +S
Sbjct: 71 EKAL-KKHKERIGHRYIEIFKSS 92
>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 = 63.4 bits (154), Expect = 1e-12
Identities = 17/123 (13%), Positives = 37/123 (30%), Gaps = 20/123 (16%)
Query: 79 NWASSPGNQPKQDTSNHYH--------IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRD 130
+ S G P+ I + L ++ + PFG+++N +++
Sbjct: 7 HHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG 66
Query: 131 PQTLKSKGYAFVSFVKKAEAENAIT--AMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNS 188
K AF+ + A + L + I +S K + +
Sbjct: 67 ------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHK----ELKTDSSPN 116
Query: 189 HTK 191
+
Sbjct: 117 QAR 119
Score = 63.0 bits (153), Expect = 2e-12
Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 2/83 (2%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIE 260
+ + ++ D+ E V + PFG + ++ + K K AF++ T+E A +
Sbjct: 26 SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVN 85
Query: 261 SIHNTD--INGHTVKCFWGKESE 281
+ + G + + E
Sbjct: 86 YYTSVTPVLRGQPIYIQFSNHKE 108
Score = 52.2 bits (125), Expect = 8e-09
Identities = 13/88 (14%), Positives = 32/88 (36%), Gaps = 5/88 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATAL--AAM 66
+++ L + VTE + +L G V +++ AF+E A T +
Sbjct: 33 VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN---QAFIEMNTEEAANTMVNYYTS 89
Query: 67 NKRVFLEKEMKVNWASSPGNQPKQDTSN 94
V + + + +++ + +
Sbjct: 90 VTPVLRGQPIYIQFSNHKELKTDSSPNQ 117
>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 = 63.7 bits (155), Expect = 1e-12
Identities = 15/107 (14%), Positives = 34/107 (31%), Gaps = 3/107 (2%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
S ++ ++ + + + L + + F+P I P + G A
Sbjct: 33 GSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDG-RVTGEAD 90
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNS 188
V F EA A+ + + + R I ++ + +
Sbjct: 91 VEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGASNGAYSSQVMQ 136
Score = 46.4 bits (110), Expect = 1e-06
Identities = 18/81 (22%), Positives = 28/81 (34%), Gaps = 7/81 (8%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKET 254
S T V+ G E + FSP V + + G A V+F T E
Sbjct: 40 TVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEE 98
Query: 255 ATHAIESIHNTDINGHTVKCF 275
A A+ ++ ++ F
Sbjct: 99 AVAAMSK-DRANMQHRYIELF 118
Score = 44.8 bits (106), Expect = 5e-06
Identities = 16/87 (18%), Positives = 34/87 (39%), Gaps = 4/87 (4%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAA 60
+ +++ L TE + FS + PV+ + P A +EF H A
Sbjct: 42 QSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR-VHIEIGPDGRVTGEADVEFATHEEAV 100
Query: 61 TALAAMNKRVFLEKEMKVNWASSPGNQ 87
A+ + ++ + +++ S+ G
Sbjct: 101 AAM-SKDRANMQHRYIELFLNSTTGAS 126
>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 = 62.2 bits (152), Expect = 1e-12
Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 7/73 (9%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG + ++ L+E F+ +G++ + I + + +AFV+F A++
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLC--G 60
Query: 158 NGQWLGSRSIRTN 170
+ S+ +
Sbjct: 61 EDLIIKGISVHIS 73
Score = 51.8 bits (125), Expect = 5e-09
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 3/67 (4%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-KGYAFVKFTTKETATHAIESIHNTDI 267
V+ G D+ E+ + + FS +G ++D+ + K + +AFV F + A I
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDL--II 65
Query: 268 NGHTVKC 274
G +V
Sbjct: 66 KGISVHI 72
Score = 41.8 bits (99), Expect = 2e-05
Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 11/86 (12%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP-GNDPYAFLEFVHHTVAATALAAMNK 68
++VG +TE+ L FSQ G V + + +AF+ F +A +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRA---FAFVTFADDQIAQSLCG--ED 62
Query: 69 RVFLEKEMKVNWASSPGNQPKQDTSN 94
+ + ++ A +PK ++++
Sbjct: 63 LIIKGISVHISNA-----EPKHNSNS 83
>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 = 62.4 bits (152), Expect = 1e-12
Identities = 15/95 (15%), Positives = 31/95 (32%), Gaps = 3/95 (3%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAF 141
SS + ++ + + + L + F+P I P + G A
Sbjct: 2 SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDG-RVTGEAD 59
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKP 176
V F +A A+ A + + R + ++
Sbjct: 60 VEFATHEDAVAAM-AKDKANMQHRYVELFLNSTAG 93
Score = 44.3 bits (105), Expect = 3e-06
Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 4/93 (4%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAA 60
+ +++ L TE + FS + P+ + P A +EF H A
Sbjct: 11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAV 69
Query: 61 TALAAMNKRVFLEKEMKVNWASSPGNQPKQDTS 93
A+ A +K + +++ S+ G +S
Sbjct: 70 AAM-AKDKANMQHRYVELFLNSTAGTSGSGPSS 101
Score = 43.9 bits (104), Expect = 5e-06
Identities = 18/78 (23%), Positives = 28/78 (35%), Gaps = 7/78 (8%)
Query: 203 SPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETATH 257
S T V+ G E + FSP + + + G A V+F T E A
Sbjct: 12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVA 70
Query: 258 AIESIHNTDINGHTVKCF 275
A+ ++ V+ F
Sbjct: 71 AMAK-DKANMQHRYVELF 87
>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 = 61.9 bits (151), Expect = 2e-12
Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 4/94 (4%)
Query: 85 GNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
G+ T+ H + + + + + E AP RIVR+ GY FV F
Sbjct: 1 GSSGSSGTTCHT-VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHG-NKTGYIFVDF 57
Query: 145 VKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPA 178
+ E + A+ N +++G R I P +
Sbjct: 58 SNEEEVKQALK-CNREYMGGRYIEVFREKSGPSS 90
Score = 46.9 bits (112), Expect = 4e-07
Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 4/82 (4%)
Query: 5 SQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATA 62
+ T+ + +VTE+ + + + PV +++R + Y F++F + A
Sbjct: 8 TTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGNKTGYIFVDFSNEEEVKQA 66
Query: 63 LAAMNKRVFLEKEMKVNWASSP 84
L N+ + ++V S
Sbjct: 67 L-KCNREYMGGRYIEVFREKSG 87
Score = 45.8 bits (109), Expect = 8e-07
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 7/87 (8%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-----KGYAFVKFTTKETAT 256
S T TV G ++ E+ V + +P V IR+ + GY FV F+ +E
Sbjct: 6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVK 64
Query: 257 HAIESIHNTDINGHTVKCFWGKESENN 283
A++ + + G ++ F K ++
Sbjct: 65 QALKC-NREYMGGRYIEVFREKSGPSS 90
>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 = 61.4 bits (149), Expect = 3e-12
Identities = 21/112 (18%), Positives = 40/112 (35%), Gaps = 16/112 (14%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+ S G++ S + + L E+ + PFG+++N + LK K A
Sbjct: 3 SGSSGDKMDGAPSRV--LHIRKLPGEVTETEVIALGLPFGKVTNILM------LKGKNQA 54
Query: 141 FVSFVKKAEAENAIT--AMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHT 190
F+ + A + + L ++ I +S K E K +
Sbjct: 55 FLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHK------ELKTSGPSS 100
Score = 60.2 bits (146), Expect = 9e-12
Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 2/76 (2%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHNTD- 266
++ ++ E V + PFG + +I + K K AF++ T+E A +
Sbjct: 17 VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTP 76
Query: 267 -INGHTVKCFWGKESE 281
+ + + E
Sbjct: 77 HLRNQPIYIQYSNHKE 92
Score = 50.2 bits (120), Expect = 3e-08
Identities = 16/87 (18%), Positives = 32/87 (36%), Gaps = 5/87 (5%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALA--AM 66
L++ L VTE + AL G V +++ AFLE A T + +
Sbjct: 17 VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN---QAFLELATEEAAITMVNYYSA 73
Query: 67 NKRVFLEKEMKVNWASSPGNQPKQDTS 93
+ + + +++ + +S
Sbjct: 74 VTPHLRNQPIYIQYSNHKELKTSGPSS 100
>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 = 61.1 bits (149), Expect = 3e-12
Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 7/73 (9%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FVG + ++ + L++ F +GE+ + I + + +AFV+F A++
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLC--G 66
Query: 158 NGQWLGSRSIRTN 170
+ S+ +
Sbjct: 67 EDLIIKGISVHIS 79
Score = 54.2 bits (131), Expect = 9e-10
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 209 VYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE-KGYAFVKFTTKETATHAIESIHNTDI 267
V+ G +D+ E + + F +G +VD+ + K + +AFV F + A I
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGEDL--II 71
Query: 268 NGHTVKC 274
G +V
Sbjct: 72 KGISVHI 78
Score = 43.0 bits (102), Expect = 7e-06
Identities = 18/93 (19%), Positives = 33/93 (35%), Gaps = 11/93 (11%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREP-GNDPYAFLEFVHHTVAAT 61
+ ++VG +T E L F Q G V + + +AF+ F VA +
Sbjct: 7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRA---FAFVTFADDKVAQS 63
Query: 62 ALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSN 94
+ + ++ A +PK + N
Sbjct: 64 LCG--EDLIIKGISVHISNA-----EPKHNKLN 89
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 61.4 bits (149), Expect = 5e-12
Identities = 15/98 (15%), Positives = 25/98 (25%), Gaps = 3/98 (3%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
G+ + + Y I + +L Q LK+ T G
Sbjct: 14 LVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDFDGTG 70
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPA 178
+ F + A+ +N I PP
Sbjct: 71 ALEFPSEEILVEALERLNNIEFRGSVITVERDDNPPPI 108
Score = 56.0 bits (135), Expect = 3e-10
Identities = 7/79 (8%), Positives = 25/79 (31%), Gaps = 3/79 (3%)
Query: 199 YNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIV---DIRVFKEKGYAFVKFTTKETA 255
++ + + + + + + + G ++F ++E
Sbjct: 21 MSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEIL 80
Query: 256 THAIESIHNTDINGHTVKC 274
A+E ++N + G +
Sbjct: 81 VEALERLNNIEFRGSVITV 99
Score = 44.0 bits (104), Expect = 5e-06
Identities = 14/75 (18%), Positives = 24/75 (32%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
+ + NL + + L L + + D LEF + AL +N
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90
Query: 70 VFLEKEMKVNWASSP 84
F + V +P
Sbjct: 91 EFRGSVITVERDDNP 105
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 60.4 bits (147), Expect = 7e-12
Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 7/90 (7%)
Query: 208 TVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKG-YAFVKFTTKETATHAIESIHNTD 266
+V+ GF + ++ +S+ F FG + + + K+KG +A V+ A+ S
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAR-EAVLSQSQHS 68
Query: 267 INGHTVKCFWGKESENNSTLAQPSAPTTPQ 296
+ GH ++ + E Q A +P+
Sbjct: 69 LGGHRLRV---RPREQKE--FQSPASKSPK 93
Score = 57.3 bits (139), Expect = 9e-11
Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 6/71 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+FV +++ L E F FG +++ + +D +A V E + +
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDVGAREAVL-SQ 64
Query: 158 NGQWLGSRSIR 168
+ LG +R
Sbjct: 65 SQHSLGGHRLR 75
Score = 51.9 bits (125), Expect = 6e-09
Identities = 15/86 (17%), Positives = 28/86 (32%), Gaps = 7/86 (8%)
Query: 9 TLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN- 67
+++V V L F GPV + ++ G +A +E L+
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV--FAIVEMGDVGAREAVLSQSQH 67
Query: 68 ----KRVFLEKEMKVNWASSPGNQPK 89
R+ + + + S PK
Sbjct: 68 SLGGHRLRVRPREQKEFQSPASKSPK 93
>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 = 61.0 bits (148), Expect = 9e-12
Identities = 20/95 (21%), Positives = 39/95 (41%), Gaps = 3/95 (3%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNC-RIVRDPQTLKSKGYA 140
D++N + + L + + + F+ + N + DP+ K G A
Sbjct: 29 QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEG-KITGEA 87
Query: 141 FVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
FV F + AE A+ + + +G R I S+++
Sbjct: 88 FVQFASQELAEKAL-GKHKERIGHRYIEVFKSSQE 121
Score = 44.9 bits (106), Expect = 4e-06
Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 7/88 (7%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVF------KEKGYAFVKFTTKE 253
+ S + V G +E + + FS + + K G AFV+F ++E
Sbjct: 36 SADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQE 95
Query: 254 TATHAIESIHNTDINGHTVKCFWGKESE 281
A A+ H I ++ F + E
Sbjct: 96 LAEKALGK-HKERIGHRYIEVFKSSQEE 122
Score = 43.3 bits (102), Expect = 1e-05
Identities = 17/83 (20%), Positives = 33/83 (39%), Gaps = 4/83 (4%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVI-REPGNDP--YAFLEFVHHTVA 59
D + + + L T+E + FS + V + +P AF++F +A
Sbjct: 38 DSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELA 97
Query: 60 ATALAAMNKRVFLEKEMKVNWAS 82
AL +K + ++V +S
Sbjct: 98 EKAL-GKHKERIGHRYIEVFKSS 119
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 58.9 bits (143), Expect = 2e-11
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 11/81 (13%)
Query: 98 IFVGDLSPEIET-------QTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEA 150
I V ++ P++ + + F+ FG+I+N + K+KGY F+ + A A
Sbjct: 4 IVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHA 60
Query: 151 ENAITAMNGQWLGSR-SIRTN 170
+A+ +G L + + R N
Sbjct: 61 VDAVKNADGYKLDKQHTFRVN 81
Score = 53.9 bits (130), Expect = 9e-10
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 11/79 (13%)
Query: 206 NCTVYCGGF---GKDLNEELVS---KVFSPFGTIVDIRVFKE----KGYAFVKFTTKETA 255
+ + G D E+L + K+FS FG I + +E KGY F+++ + A
Sbjct: 1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHA 60
Query: 256 THAIESIHNTDING-HTVK 273
A+++ ++ HT +
Sbjct: 61 VDAVKNADGYKLDKQHTFR 79
Score = 43.5 bits (103), Expect = 4e-06
Identities = 15/80 (18%), Positives = 31/80 (38%), Gaps = 8/80 (10%)
Query: 8 TTLYVGNL------DVSVTEELLCALFSQIGPVKGCKVIREPGNDP-YAFLEFVHHTVAA 60
+ + V N+ + + ++ +FS+ G + E G Y FLE+ A
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 61
Query: 61 TALAAMNKRVFLEKE-MKVN 79
A+ + ++ +VN
Sbjct: 62 DAVKNADGYKLDKQHTFRVN 81
>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 = 58.6 bits (142), Expect = 2e-11
Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 6/78 (7%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRI-----VRDPQTLKSKGYAFVSFVKKAEAEN 152
++VG++ I + + + F + V Q + K +AF+ F E
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 153 AITAMNGQWLGSRSIRTN 170
A+ A +G +S++
Sbjct: 69 AM-AFDGIIFQGQSLKIR 85
Score = 57.8 bits (140), Expect = 4e-11
Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 15/81 (18%)
Query: 10 LYVGNLDVSVTEELLCALFSQI-----------GPVKGCKVIREPGNDPYAFLEFVHHTV 58
LYVGN+ +TEE + F+ PV ++ ++ +AFLEF
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN---FAFLEFRSVDE 65
Query: 59 AATALAAMNKRVFLEKEMKVN 79
A+ A + +F + +K+
Sbjct: 66 TTQAM-AFDGIIFQGQSLKIR 85
Score = 47.0 bits (112), Expect = 3e-07
Identities = 14/76 (18%), Positives = 33/76 (43%), Gaps = 12/76 (15%)
Query: 209 VYCGGFGKDLNEELVSKVFS-----------PFGTIVDIRVFKEKGYAFVKFTTKETATH 257
+Y G + EE + F+ P ++ +++ ++K +AF++F + + T
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 258 AIESIHNTDINGHTVK 273
A+ G ++K
Sbjct: 69 AMA-FDGIIFQGQSLK 83
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 57.6 bits (139), Expect = 1e-10
Identities = 21/99 (21%), Positives = 32/99 (32%), Gaps = 6/99 (6%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNC----RIVRDPQTLKS 136
+S N + + L + + F I+ V P +
Sbjct: 9 GTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDG-RP 67
Query: 137 KGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
G AFV F + A+NA+ + LG R I ST
Sbjct: 68 TGDAFVLFACEEYAQNAL-RKHKDLLGKRYIELFRSTAA 105
Score = 47.2 bits (112), Expect = 6e-07
Identities = 22/103 (21%), Positives = 32/103 (31%), Gaps = 10/103 (9%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVD----IRVFKE-----KGYAFVKFTTK 252
S V G E V F I I G AFV F +
Sbjct: 19 SKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACE 78
Query: 253 ETATHAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTP 295
E A +A+ H + ++ F +E L + S+ + P
Sbjct: 79 EYAQNALR-KHKDLLGKRYIELFRSTAAEVQQVLNRFSSASGP 120
Score = 41.4 bits (97), Expect = 5e-05
Identities = 21/92 (22%), Positives = 32/92 (34%), Gaps = 13/92 (14%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCK----VIREPGNDP--YAFLEFVHH 56
+ + + L + T E + A F Q P+ G K + P P AF+ F
Sbjct: 19 SKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACE 78
Query: 57 TVAATALA----AMNKR---VFLEKEMKVNWA 81
A AL + KR +F +V
Sbjct: 79 EYAQNALRKHKDLLGKRYIELFRSTAAEVQQV 110
>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 = 55.7 bits (134), Expect = 5e-10
Identities = 14/97 (14%), Positives = 33/97 (34%), Gaps = 5/97 (5%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPF---GEISNCRIVRDPQTLKSKG 138
S G + Y + + L + ++ + ++ + + + G
Sbjct: 4 GSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREG-RQSG 62
Query: 139 YAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
AFV + + + A+ + + +G R I S R
Sbjct: 63 EAFVELESEDDVKLAL-KKDRESMGHRYIEVFKSHRT 98
Score = 48.4 bits (115), Expect = 2e-07
Identities = 15/106 (14%), Positives = 31/106 (29%), Gaps = 9/106 (8%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPF---GTIVDIRVFKE-----KGYAFVKFTTKE 253
V G + E V S + + G AFV+ +++
Sbjct: 13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESED 72
Query: 254 TATHAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
A++ + ++ F +E + L + P+S
Sbjct: 73 DVKLALKK-DRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSS 117
Score = 40.7 bits (95), Expect = 8e-05
Identities = 13/91 (14%), Positives = 25/91 (27%), Gaps = 12/91 (13%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-----YAFLEFVHHT 57
+ + + + L S + E + S G + AF+E
Sbjct: 13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESED 72
Query: 58 VAATALAAMNK-------RVFLEKEMKVNWA 81
AL + VF +++W
Sbjct: 73 DVKLALKKDRESMGHRYIEVFKSHRTEMDWV 103
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 55.0 bits (132), Expect = 9e-10
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 2/61 (3%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRD--PQTLKSKGYAFVSFVKKAEAENAIT 155
+FVG L P+I+ + +F FG + + KGYAF+ F +++ + I
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
Query: 156 A 156
A
Sbjct: 71 A 71
Score = 43.0 bits (101), Expect = 1e-05
Identities = 21/89 (23%), Positives = 38/89 (42%), Gaps = 14/89 (15%)
Query: 200 NQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKE--------KGYAFVKFTT 251
+ S + V+ GG D++E+ ++ F FG +V K KGYAF+ F
Sbjct: 2 SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61
Query: 252 KETATHAIESIHNTD------INGHTVKC 274
+ + I++ D ++ T+K
Sbjct: 62 ESSVQALIDACLEEDGKLYLCVSSPTIKD 90
Score = 39.2 bits (91), Expect = 3e-04
Identities = 14/61 (22%), Positives = 24/61 (39%), Gaps = 5/61 (8%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-----YAFLEFVHHTVAATALA 64
++VG L + E+ + A F + GP+ + YAFL F + +
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
Query: 65 A 65
A
Sbjct: 71 A 71
>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 = 55.9 bits (134), Expect = 1e-09
Identities = 23/123 (18%), Positives = 45/123 (36%), Gaps = 6/123 (4%)
Query: 55 HHTVAATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKE 114
HH A AL A+N + + A+ S I V +L + L +
Sbjct: 6 HHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQ 65
Query: 115 AFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWL--GSRSIRTNWS 172
F+ FG + + A + + A++A +++GQ + ++R ++S
Sbjct: 66 IFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS 121
Query: 173 TRK 175
Sbjct: 122 KLT 124
Score = 48.9 bits (116), Expect = 3e-07
Identities = 20/113 (17%), Positives = 41/113 (36%), Gaps = 3/113 (2%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
+ V NL VT ++L +FS+ G V + N A L++ A A +++ +
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKI-ITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 107
Query: 70 VFLEKE--MKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFG 120
++++++ K + DL +L + A
Sbjct: 108 NIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTMAAAF 160
Score = 44.7 bits (105), Expect = 8e-06
Identities = 31/168 (18%), Positives = 56/168 (33%), Gaps = 32/168 (19%)
Query: 150 AENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTV 209
A+ A+ A+N G+ ++ + + S I V N P V
Sbjct: 10 AQAALQAVNSVQSGNLALAASAAAVDA----GMAMAGQSPVLRII---VENLFYPVTLDV 62
Query: 210 YCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEK--GYAFVKFTTKETATHAIESIHNTDI 267
++FS FGT++ I F + A +++ +A HA S+ +I
Sbjct: 63 LH-------------QIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNI 109
Query: 268 --NGHTVKCFWGKESE-----NNST---LAQPSAPTTPQPNSTAPQFP 305
T++ + K + NN +P P+ S
Sbjct: 110 YNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTMA 157
>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 = 55.2 bits (132), Expect = 3e-09
Identities = 11/85 (12%), Positives = 28/85 (32%), Gaps = 1/85 (1%)
Query: 79 NWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKG 138
+ ++ + +++ + +KE G++ N ++ R KG
Sbjct: 93 SKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHK-AFKG 151
Query: 139 YAFVSFVKKAEAENAITAMNGQWLG 163
FV F A+ + ++
Sbjct: 152 SIFVVFDSIESAKKFVETPGQKYKE 176
Score = 51.4 bits (122), Expect = 6e-08
Identities = 23/134 (17%), Positives = 50/134 (37%), Gaps = 8/134 (5%)
Query: 132 QTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTK 191
Q +G+ + + K N + + + + ++ K + S +K
Sbjct: 38 QIKLDEGWVPLEIMIK---FNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSK 94
Query: 192 TITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRV-----FKEKGYAF 246
+ ++ N +VY GF D + + + G +++I++ KG F
Sbjct: 95 PLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIF 154
Query: 247 VKFTTKETATHAIE 260
V F + E+A +E
Sbjct: 155 VVFDSIESAKKFVE 168
Score = 39.8 bits (92), Expect = 6e-04
Identities = 9/79 (11%), Positives = 25/79 (31%), Gaps = 3/79 (3%)
Query: 6 QPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP--YAFLEFVHHTVAATAL 63
+ ++Y+ T + + G V ++ R F+ F A +
Sbjct: 108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV 167
Query: 64 AAMNKRVFLEKEMKVNWAS 82
+ + E ++ + +
Sbjct: 168 ETPGQ-KYKETDLLILFKD 185
>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 = 52.9 bits (127), Expect = 4e-09
Identities = 11/107 (10%), Positives = 37/107 (34%), Gaps = 5/107 (4%)
Query: 85 GNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPF---GEISNCRIVRDPQTLKSKGYAF 141
G++ +++ + + I L + + F+ + + + K +G A
Sbjct: 1 GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDG-KRRGDAL 59
Query: 142 VSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNS 188
+ + + + A+ + ++G R + + + + S
Sbjct: 60 IEMESEQDVQKAL-EKHRMYMGQRYVEVYEINNEDVDALMKSLQVKS 105
Score = 46.0 bits (109), Expect = 9e-07
Identities = 13/103 (12%), Positives = 31/103 (30%), Gaps = 9/103 (8%)
Query: 201 QSSPTNCTVYCGGFGKDLNEELVSKVFSPF---GTIVDIRVFKE-----KGYAFVKFTTK 252
+ + G E V FS I +G A ++ ++
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65
Query: 253 ETATHAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTP 295
+ A+E H + V+ + + ++ + ++P
Sbjct: 66 QDVQKALE-KHRMYMGQRYVEVYEINNEDVDALMKSLQVKSSP 107
Score = 40.6 bits (95), Expect = 8e-05
Identities = 17/91 (18%), Positives = 24/91 (26%), Gaps = 12/91 (13%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-----YAFLEFVHHT 57
+ + L S T E + FS G I N A +E
Sbjct: 7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQ 66
Query: 58 VAATALAA----MNKR---VFLEKEMKVNWA 81
AL M +R V+ V+
Sbjct: 67 DVQKALEKHRMYMGQRYVEVYEINNEDVDAL 97
>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 = 53.1 bits (127), Expect = 6e-09
Identities = 11/97 (11%), Positives = 30/97 (30%), Gaps = 5/97 (5%)
Query: 82 SSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPF---GEISNCRIVRDPQTLKSKG 138
+ + + + L + ++ + + + + + G
Sbjct: 31 GRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREG-RQSG 89
Query: 139 YAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWSTRK 175
AFV + + + A+ + + +G R I S R
Sbjct: 90 EAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRT 125
Score = 43.5 bits (102), Expect = 1e-05
Identities = 16/134 (11%), Positives = 33/134 (24%), Gaps = 21/134 (15%)
Query: 163 GSRSIRTNWSTRKPPAMT-NERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEE 221
S + R + V + P +C+ E
Sbjct: 11 SSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCS-----------VE 59
Query: 222 LVSKVFSPF---GTIVDIRVFKE-----KGYAFVKFTTKETATHAIESIHNTDINGHTVK 273
V S + G AFV+ +++ A++ + ++
Sbjct: 60 DVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKK-DRESMGHRYIE 118
Query: 274 CFWGKESENNSTLA 287
F +E + L
Sbjct: 119 VFKSHRTEMDWVLK 132
Score = 38.8 bits (90), Expect = 6e-04
Identities = 15/91 (16%), Positives = 27/91 (29%), Gaps = 12/91 (13%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDP-----YAFLEFVHHT 57
+ + + + L S + E + S G + AF+E
Sbjct: 40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSED 99
Query: 58 VAATALA----AMNKR---VFLEKEMKVNWA 81
AL +M R VF +++W
Sbjct: 100 DVKMALKKDRESMGHRYIEVFKSHRTEMDWV 130
>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 = 51.0 bits (122), Expect = 1e-08
Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 3/78 (3%)
Query: 200 NQSSPTNCTVYCGGFGKDLN-EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHA 258
T V+ F + N + ++ PFG I + + + AF++ T E A A
Sbjct: 9 KGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAA 68
Query: 259 IESIHNTD--INGHTVKC 274
++ T + G V+
Sbjct: 69 VDYYTTTPALVFGKPVRV 86
Score = 45.2 bits (107), Expect = 2e-06
Identities = 21/98 (21%), Positives = 36/98 (36%), Gaps = 11/98 (11%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQT-LKEAFAPFGEISNCRIVRDPQTLKSKGY 139
+ S G + + +T HI D + L + PFG ISN I L
Sbjct: 3 SGSSGQKGRVETRRVVHI--MDFQRGKNLRYQLLQLVEPFGVISNHLI------LNKINE 54
Query: 140 AFVSFVKKAEAENAIT--AMNGQWLGSRSIRTNWSTRK 175
AF+ +A+ A+ + + +R + S +
Sbjct: 55 AFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY 92
Score = 31.4 bits (71), Expect = 0.14
Identities = 10/78 (12%), Positives = 24/78 (30%), Gaps = 6/78 (7%)
Query: 9 TLYVGNL-DVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATAL--AA 65
+++ + L L G + ++ AF+E A A+
Sbjct: 17 VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN---KINEAFIEMATTEDAQAAVDYYT 73
Query: 66 MNKRVFLEKEMKVNWASS 83
+ K ++V+ +
Sbjct: 74 TTPALVFGKPVRVHLSQK 91
>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 = 51.1 bits (122), Expect = 2e-08
Identities = 15/90 (16%), Positives = 35/90 (38%), Gaps = 3/90 (3%)
Query: 199 YNQSSPTNCTVYCGGFGKD-LNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATH 257
++Q ++ ++ V K+ P+G I + + + K AF++ T+E A
Sbjct: 18 FDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMA 77
Query: 258 AIESIHNTD--INGHTVKCFWGKESENNST 285
++ G VK ++ + +
Sbjct: 78 MVDHCLKKALWFQGRCVKVDLSEKYKKLVS 107
Score = 41.1 bits (96), Expect = 6e-05
Identities = 13/81 (16%), Positives = 31/81 (38%), Gaps = 9/81 (11%)
Query: 98 IFVGDLSPEIET-QTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAIT- 155
I + +L + + + P+G+I N + ++ K AF+ + +A +
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL------MRMKSQAFIEMETREDAMAMVDH 81
Query: 156 -AMNGQWLGSRSIRTNWSTRK 175
W R ++ + S +
Sbjct: 82 CLKKALWFQGRCVKVDLSEKY 102
Score = 34.1 bits (78), Expect = 0.016
Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 6/78 (7%)
Query: 9 TLYVGNLDVS-VTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALA--A 65
+++ NL S ++ + L G +K ++R AF+E A +
Sbjct: 27 VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKS---QAFIEMETREDAMAMVDHCL 83
Query: 66 MNKRVFLEKEMKVNWASS 83
F + +KV+ +
Sbjct: 84 KKALWFQGRCVKVDLSEK 101
>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 = 52.7 bits (126), Expect = 1e-07
Identities = 73/455 (16%), Positives = 121/455 (26%), Gaps = 198/455 (43%)
Query: 5 SQPTTLYVGNLDVS--VTEELLCAL------FSQIGPVKGCKVIREP------GNDPYA- 49
++P TL G+L+ V F++I P EP ++P
Sbjct: 6 TRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILP--------EPTEGFAADDEPTTP 57
Query: 50 ------FLEFVHHTVAATALAAMN----------KRVFLEKEMKVNWASSPGNQPKQDTS 93
FL +V V + + + + +LE GN D
Sbjct: 58 AELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLE-----------GN----DI- 101
Query: 94 NHYHIFVGDLSPEIETQTLKEAFAPFGEISN----CRIVRDPQTLKSKGYAFVSFVKKAE 149
H L E +T +K I N + + P KS + +
Sbjct: 102 ---HALAAKLLQENDTTLVKTKEL----IKNYITARIMAKRPFDKKSNS----ALFRAVG 150
Query: 150 AENA--ITAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHTKTITFDE---VYNQSSP 204
NA + GQ G N+ F+E +Y
Sbjct: 151 EGNAQLVAIFGGQ--G-----------------------NTDD---YFEELRDLYQTYHV 182
Query: 205 TNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIESIHN 264
L +L+ ++ + EK + T +
Sbjct: 183 -------------LVGDLIKFSAETLSELIRTTLDAEKVF-----------TQGL----- 213
Query: 265 TDINGHTVKCFWGKESENNSTLAQPSAPTTPQPN--STAP-QFPYIYNQQMGYWYPQAAA 321
+I W L PS TP + + P P I Q+ A
Sbjct: 214 -NILE------W---------LENPS--NTPDKDYLLSIPISCPLIGVIQL-------AH 248
Query: 322 YTATAAQL---PQQFYQY--GQLGYPQG----------------------------YVGM 348
Y TA L P + Y G G+ QG ++G+
Sbjct: 249 YVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGV 308
Query: 349 VGRQVPGWQGIPGAQPTAQQMAVA--QAQPSMMAA 381
+ +P P+ + ++ + PS M +
Sbjct: 309 RCYEAYPNTSLP---PSILEDSLENNEGVPSPMLS 340
Score = 47.0 bits (111), Expect = 9e-06
Identities = 72/428 (16%), Positives = 124/428 (28%), Gaps = 124/428 (28%)
Query: 4 ESQPTTLYV-----GNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTV 58
L GN D E L L+ + G ++F T+
Sbjct: 150 GEGNAQLVAIFGGQGNTDDYFEE--LRDLYQTYHVLVG------------DLIKFSAETL 195
Query: 59 AATALAAMNKRVFLEKEMKV-NWASSPGNQPKQDTSNHY--HIFVGDLS-PEIE-TQTLK 113
+ ++ + + + W +P N P +D Y I + S P I Q
Sbjct: 196 SELIRTTLDAEKVFTQGLNILEWLENPSNTPDKD----YLLSIPI---SCPLIGVIQ--- 245
Query: 114 EAFAPFGEISNCRIV-RDPQTLKS--KGY----------AFVSFVKKAEA--ENAITAMN 158
A + + +++ P L+S KG ++ E+ + A+
Sbjct: 246 --LAHY--VVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAIT 301
Query: 159 GQ-WLGSRSIRTNWSTRKPPAMTNERKRQNSHTKT-------ITFDEV------YNQSSP 204
++G R +T PP++ + N + +T ++V N P
Sbjct: 302 VLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLP 361
Query: 205 TNCTVY-----------CGGFGKDL---NEELVSKVFSPFGTIVDI-RV-FKEKGYAFVK 248
V G + L N L K +P G D R+ F E+ F
Sbjct: 362 AGKQVEISLVNGAKNLVVSGPPQSLYGLNLTL-RKAKAPSGL--DQSRIPFSERKLKFSN 418
Query: 249 --------FTTK--ETATHAIESIHNTDINGHTVKCFWGKE-------SENNSTLAQPSA 291
F + A+ I D+ + V F K+ + + S L S
Sbjct: 419 RFLPVASPFHSHLLVPASDLINK----DLVKNNVS-FNAKDIQIPVYDTFDGSDLRVLSG 473
Query: 292 PTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGYVGMVGR 351
+ I + W + AT +G G G + R
Sbjct: 474 SISE---RIVDC---IIRLPV-KW-ETTTQFKAT------HILDFGP-GGASGLGVLTHR 518
Query: 352 QVPGWQGI 359
G G+
Sbjct: 519 NKDG-TGV 525
Score = 38.5 bits (89), Expect = 0.004
Identities = 40/218 (18%), Positives = 63/218 (28%), Gaps = 73/218 (33%)
Query: 195 FDEVYNQS-------SPTNCTVYCGGF-GKDLNEELVSKVFSPF--GTIVDIRVFKEKGY 244
F + Y S +P N T++ GG GK + E + +F G + ++FKE
Sbjct: 1653 FKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKE--- 1709
Query: 245 AFVKFTTKETATHAIESIHNTDINGHTVKCFWGKESENNST-LAQPSAPTTPQPNSTAPQ 303
S F ++ ++T QP+ A
Sbjct: 1710 ----------INEHSTSY-----------TFRSEKGLLSATQFTQPALTLM----EKA-A 1743
Query: 304 FPYIYNQQMGYWYPQAAA--------YTATAA------------------QLPQQFYQYG 337
F + + G P A Y A A+ Q
Sbjct: 1744 FEDL--KSKGL-IPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRD 1800
Query: 338 QLGYPQGYVGMVGRQVPGWQGIPGAQPTAQQMAVAQAQ 375
+LG + GM+ PG +Q A Q V +
Sbjct: 1801 ELG--RSNYGMIAI-NPGRVAASFSQ-EALQYVVERVG 1834
>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 = 47.2 bits (112), Expect = 4e-07
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 119 FGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRTNWS 172
+GE+ + D G +V F ++ +AE A+ +N +W + I S
Sbjct: 51 YGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS 103
Score = 39.1 bits (91), Expect = 3e-04
Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 5/63 (7%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFK-----EKGYAFVKFTTKETATHAIESIHNTDINGHT 271
+ EE+ +++ +G + ++ V G +VKF +E A A+ ++N NG
Sbjct: 38 EFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQP 97
Query: 272 VKC 274
+
Sbjct: 98 IHA 100
Score = 32.5 bits (74), Expect = 0.044
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 4/66 (6%)
Query: 21 EELLCALFSQIGPVKGCKVIREPGNDPY--AFLEFVHHTVAATALAAMNKRVFLEKEMKV 78
EE+ + + G V+ V G+ +++F A A+ +N R F + +
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100
Query: 79 NWASSP 84
SP
Sbjct: 101 EL--SP 104
>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 = 45.8 bits (108), Expect = 1e-06
Identities = 19/102 (18%), Positives = 37/102 (36%), Gaps = 4/102 (3%)
Query: 202 SSPTNCTVYC----GGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATH 257
SS ++ + C F + +F + + FK + F+ +A
Sbjct: 2 SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLSAAD 61
Query: 258 AIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNS 299
A +H T+ G +K ++ + S+ P P P+S
Sbjct: 62 ARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSGPSS 103
Score = 33.8 bits (77), Expect = 0.021
Identities = 23/106 (21%), Positives = 36/106 (33%), Gaps = 13/106 (12%)
Query: 5 SQPTTLYVGNLDVSV-----TEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVA 59
S + L + V T +LF + + + + F + A
Sbjct: 3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK---SFKRVRINFSNPLSA 59
Query: 60 ATALAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSP 105
A A ++K FL KEMK+ +A Q S+H D S
Sbjct: 60 ADARLRLHKTEFLGKEMKLYFA-----QTLHIGSSHLAPPNPDKSG 100
>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 = 47.9 bits (113), Expect = 3e-06
Identities = 21/166 (12%), Positives = 45/166 (27%), Gaps = 16/166 (9%)
Query: 196 DEVYNQSSPTNCTVYC-GGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKET 254
+ + S T V GG G ++ + V G + + + K Y+F ++ T E
Sbjct: 9 EGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEE 68
Query: 255 ATHAIESIHNTDINGHTVKCFWGKESENNSTLAQPSAPTTPQPNSTAPQFPYIYNQQMGY 314
+ A +++ ++ + TL P G
Sbjct: 69 SKRAYVTLNGKEVV---------DDLGQKITLYLNFVEKVQWKELRPQALP------PGL 113
Query: 315 WYPQAAAYTATAAQLPQQFYQYGQLGYPQGYVGMVGRQVPGWQGIP 360
+ + L + + R+V +
Sbjct: 114 MVVEEIISSEEEKMLLESVDWTEDTDNQNSQKSLKHRRVKHFGYEF 159
Score = 39.4 bits (91), Expect = 0.001
Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 6/66 (9%)
Query: 5 SQPT-TLYVGN--LDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAAT 61
S T +L V N L V+ L + + G V ++ P PY+F + +
Sbjct: 15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDA--LLMPPNK-PYSFARYRTTEESKR 71
Query: 62 ALAAMN 67
A +N
Sbjct: 72 AYVTLN 77
Score = 39.0 bits (90), Expect = 0.002
Identities = 15/91 (16%), Positives = 29/91 (31%), Gaps = 18/91 (19%)
Query: 72 LEKEMKVNWASSPGNQPKQDTSNHYHIFV--GDLSPEIETQTLKEAFAPFGEISNCRIVR 129
L + + S + V G L + L G + ++
Sbjct: 5 LLRHEGIETVSYATQ----------SLVVANGGLGNGVSRNQLLPVLEKCGLV--DALLM 52
Query: 130 DPQTLKSKGYAFVSFVKKAEAENAITAMNGQ 160
P +K Y+F + E++ A +NG+
Sbjct: 53 PP----NKPYSFARYRTTEESKRAYVTLNGK 79
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 45.0 bits (106), Expect = 3e-06
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
+ V NL VT ++L +FS+ G V + N A L++ A A +++ +
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKI-ITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 89
Query: 70 VFLEKE--MKVNWA 81
++++++
Sbjct: 90 NIYNACCTLRIDFS 103
Score = 45.0 bits (106), Expect = 4e-06
Identities = 16/97 (16%), Positives = 35/97 (36%), Gaps = 6/97 (6%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
A+ S I V +L + L + F+ FG + + A
Sbjct: 14 AAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----A 69
Query: 141 FVSFVKKAEAENAITAMNGQ--WLGSRSIRTNWSTRK 175
+ + A++A +++GQ + ++R ++S
Sbjct: 70 LLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLT 106
Score = 41.6 bits (97), Expect = 5e-05
Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 217 DLNEELVSKVFSPFGTIVDIRVFKEK--GYAFVKFTTKETATHAIESIHNTDI--NGHTV 272
+ +++ ++FS FGT++ I F + A +++ +A HA S+ +I T+
Sbjct: 39 PVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL 98
Query: 273 KCFWGKESENN 283
+ + K + N
Sbjct: 99 RIDFSKLTSLN 109
>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 = 44.4 bits (105), Expect = 3e-06
Identities = 11/60 (18%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKS--KGYAFVSFVKKAEAENAITAMNGQWLGSRSIRT 169
+++ + +G + + I R ++ G FV F + + A+ + G+ +R + T
Sbjct: 32 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 91
Score = 37.1 bits (86), Expect = 0.001
Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 10/72 (13%)
Query: 214 FGKDLNEELVSKVFSPFGTIVDIRVFKEK--------GYAFVKFTTKETATHAIESIHNT 265
+++ E+ V S +G + I + + G FV+FT+ A++ +
Sbjct: 24 EYEEIVED-VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR 82
Query: 266 DINGHTVKC-FW 276
V +
Sbjct: 83 KFANRVVVTKYC 94
Score = 32.5 bits (74), Expect = 0.063
Identities = 11/49 (22%), Positives = 17/49 (34%), Gaps = 5/49 (10%)
Query: 28 FSQIGPVKGCKVIREPGNDPY-----AFLEFVHHTVAATALAAMNKRVF 71
S+ G VK ++ R F+EF A+ + R F
Sbjct: 36 CSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF 84
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 43.1 bits (101), Expect = 7e-06
Identities = 15/87 (17%), Positives = 34/87 (39%)
Query: 202 SSPTNCTVYCGGFGKDLNEELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETATHAIES 261
+ + + ++ + + G +V + +G A K+TT+E A A +
Sbjct: 3 MAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMA 62
Query: 262 IHNTDINGHTVKCFWGKESENNSTLAQ 288
++N + T+ E+E S +
Sbjct: 63 LNNCVLANTTIFAESPSENEVQSIMQH 89
Score = 38.1 bits (88), Expect = 4e-04
Identities = 14/70 (20%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 98 IFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAM 157
+ + +L+ +I+ TL+ G + + ++G A + + EA A A+
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMAL 63
Query: 158 NGQWLGSRSI 167
N L + +I
Sbjct: 64 NNCVLANTTI 73
Score = 27.3 bits (60), Expect = 2.8
Identities = 14/60 (23%), Positives = 21/60 (35%), Gaps = 3/60 (5%)
Query: 8 TTLYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMN 67
+ L + NL + L L Q GP+ G A ++ A A A+N
Sbjct: 8 SWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGI---ALCKYTTREEANKAQMALN 64
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 43.9 bits (103), Expect = 7e-06
Identities = 18/97 (18%), Positives = 35/97 (36%), Gaps = 8/97 (8%)
Query: 82 SSPGNQPKQDTSNHY-HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+ PGN N + + + I L P G++ I + ++ A
Sbjct: 11 TRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-----RNGIQA 65
Query: 141 FVSFVKKAEAENAITAMNGQ--WLGSRSIRTNWSTRK 175
V F A+ A A+NG + G +++ ++
Sbjct: 66 MVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPT 102
Score = 42.0 bits (98), Expect = 4e-05
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 218 LNEELVSKVFSPFGTIVDIRVFKEKG-YAFVKFTTKETATHAIESIHNTDING 269
+ +++ V +P G + I +FK G A V+F + A A +++ DI
Sbjct: 37 ITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQKAKAALNGADIYA 89
Score = 38.5 bits (89), Expect = 5e-04
Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 10 LYVGNLDVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
L + N +T ++L + + +G V+ +++ N A +EF A A AA+N
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQ--RIVIFKRNGIQAMVEFESVLCAQKAKAALNGA 85
Query: 70 VFLEKE--MKVNWA 81
+K+ +A
Sbjct: 86 DIYAGCCTLKIEYA 99
>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 = 46.4 bits (109), Expect = 1e-05
Identities = 54/478 (11%), Positives = 118/478 (24%), Gaps = 174/478 (36%)
Query: 11 YVGNLDVSVTEELLCALFSQIGPVKGCK-VIREPGNDPYAFLEFVHHTVAATALAAMNKR 69
+V N D +++ ++ S+ + +I F L + +
Sbjct: 29 FVDNFDCKDVQDMPKSILSK----EEIDHIIMSKDAVSGTLRLF-------WTLLSKQEE 77
Query: 70 V---FLEKEMKVN--WASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISN 124
+ F+E+ +++N + SP ++ S +++ + FA +
Sbjct: 78 MVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDR---LYNDNQVFAKY----- 129
Query: 125 CRIVRDP---------QTLKSKGYAFV---------SFVKKAEAENAI-TAMNGQ--WL- 162
+ R L+ + + M+ + WL
Sbjct: 130 -NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN 188
Query: 163 -GSRS---------------IRTNWSTR-----KPPAMTNE-----------RKRQNS-- 188
+ + I NW++R + + +N
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL 248
Query: 189 ------HTKTI-TFD------------EVYNQSSPTNCTVYC-----GGFGKDLNEELVS 224
+ K F+ +V + S T D + L+
Sbjct: 249 VLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL 308
Query: 225 KVF--------------SPF--GTIVD-IRVFKEKGYAFVKFTTKETATHAIE-SIH--- 263
K +P I + IR + K + T IE S++
Sbjct: 309 KYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLAT-WDNWKHVNCDKLTTIIESSLNVLE 367
Query: 264 ----------------NTDINGHTVKCFWGKESENN-----STLAQPSAPTTPQPNSTAP 302
+ I + W +++ + L + S ST
Sbjct: 368 PAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTI- 426
Query: 303 QFPYIYNQQMGY----------------WYPQAAAYTATAAQLPQQ---FYQYGQLGY 341
I + + Y + + P FY + +G+
Sbjct: 427 ---SIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH--IGH 479
Score = 38.3 bits (88), Expect = 0.004
Identities = 22/104 (21%), Positives = 32/104 (30%), Gaps = 18/104 (17%)
Query: 43 PGNDPYAFLEFVHHTVAA--TALAAMNKRVFLE---KEMKVNWASSPGNQPK------QD 91
P D Y + HH + + VFL+ E K+ S+ N Q
Sbjct: 467 PYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQ 526
Query: 92 TSNHY--HIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQT 133
Y +I D E + + F P E N + T
Sbjct: 527 LKF-YKPYICDNDPKYERLVNAILD-FLPKIE-ENL--ICSKYT 565
Score = 37.5 bits (86), Expect = 0.008
Identities = 33/247 (13%), Positives = 74/247 (29%), Gaps = 66/247 (26%)
Query: 16 DVSVTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKRVFLEKE 75
+ LL ++ + +D + +H K +EK
Sbjct: 384 SAHIPTILLSLIWFDV-----------IKSDVMVVVNKLH------------KYSLVEK- 419
Query: 76 MKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIET-----QTLKEAFAPFGEISNCRIVRD 130
QPK+ T + I++ +L ++E +++ + + I D
Sbjct: 420 -----------QPKESTISIPSIYL-ELKVKLENEYALHRSIVDHY----NIPKTFDSDD 463
Query: 131 PQTLKSKGYAFVSFV----KKAEAENAITAM-----NGQWLGSRSIRTNWSTRKPPAMTN 181
Y F S + K E +T + ++L + + + ++ N
Sbjct: 464 LIPPYLDQY-FYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILN 522
Query: 182 ERKRQNSHTKTITFDEVYNQSSPTNCTVYC--GGFGKDLNEELVSKVFSPFGTIVDIRVF 239
++ + I + P + F + E L+ S + ++ I +
Sbjct: 523 TLQQLKFYKPYIC------DNDPKYERLVNAILDFLPKIEENLIC---SKYTDLLRIALM 573
Query: 240 KEKGYAF 246
E F
Sbjct: 574 AEDEAIF 580
>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 = 42.0 bits (99), Expect = 3e-05
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 4/58 (6%)
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIRT 169
L+ + FG+I + G A VSF EA+ I ++G+W G R I
Sbjct: 43 LRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 96
Score = 40.1 bits (94), Expect = 2e-04
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 214 FGKDLNEELVSKVFSPFGTIVDIRVFK--EKGYAFVKFTTKETATHAIESIHNTDINGHT 271
++ E+L + S FG I + +F G A V F E A + I+++ G
Sbjct: 35 VLNEIREDLRVE-CSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQ 93
Query: 272 VKC-FW 276
+ W
Sbjct: 94 ITAQAW 99
Score = 30.1 bits (68), Expect = 0.38
Identities = 9/53 (16%), Positives = 18/53 (33%), Gaps = 6/53 (11%)
Query: 19 VTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKRVF 71
+ E S+ G ++ + D A + F A + ++ R F
Sbjct: 43 LRVE-----CSKFGQIRKLLLFDRHP-DGVASVSFRDPEEADYCIQTLDGRWF 89
>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 = 41.3 bits (97), Expect = 7e-05
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 101 GDLSPEIETQTLKEAFAPFGEISNCRIVRDPQ----TLKSKGYAFVSFVKKAEAENAITA 156
D+ ++E + E FG ++ I ++ Q + FV F +E AI A
Sbjct: 32 KDIDDDLE-GEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQA 90
Query: 157 MNGQWLGSRSIRT 169
+NG+W R +
Sbjct: 91 LNGRWFAGRKVVA 103
Score = 36.3 bits (84), Expect = 0.004
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 14/75 (18%)
Query: 216 KDLNEELVSKVF---SPFGTIVDIRVFKEK----------GYAFVKFTTKETATHAIESI 262
KD++++L +V FG + + +++EK FV+F+ AI+++
Sbjct: 32 KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 91
Query: 263 HNTDINGHTVKC-FW 276
+ G V +
Sbjct: 92 NGRWFAGRKVVAEVY 106
Score = 32.4 bits (74), Expect = 0.068
Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 12/60 (20%)
Query: 19 VTEELLCALFSQIGPVKGCKVIREPGNDPY-------AFLEFVHHTVAATALAAMNKRVF 71
VTEE C + G V + +E + F+EF + A+ A+N R F
Sbjct: 42 VTEE--C---GKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWF 96
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 44.0 bits (103), Expect = 7e-05
Identities = 20/109 (18%), Positives = 26/109 (23%)
Query: 282 NNSTLAQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGY 341
N + L QP+ PQ + A P Q Q Q
Sbjct: 19 NATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATT 78
Query: 342 PQGYVGMVGRQVPGWQGIPGAQPTAQQMAVAQAQPSMMAAYAMQQFPTQ 390
+ + + Q Q Q Q MAA A Q
Sbjct: 79 SMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAA 127
Score = 42.9 bits (100), Expect = 1e-04
Identities = 19/96 (19%), Positives = 25/96 (26%), Gaps = 1/96 (1%)
Query: 295 PQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGYVGMVGRQVP 354
PQ Q Q + PQ A A + G + + Q
Sbjct: 10 PQAQLQYGQNATPLQQPAQFMPPQDPAA-AGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQ 68
Query: 355 GWQGIPGAQPTAQQMAVAQAQPSMMAAYAMQQFPTQ 390
Q I A + M + AY Q P Q
Sbjct: 69 LHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQ 104
Score = 41.0 bits (95), Expect = 6e-04
Identities = 13/104 (12%), Positives = 21/104 (20%)
Query: 287 AQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGYV 346
Q P Q + Q N + P Q+P Q Q
Sbjct: 59 QQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAA 118
Query: 347 GMVGRQVPGWQGIPGAQPTAQQMAVAQAQPSMMAAYAMQQFPTQ 390
G+ + + P + + P
Sbjct: 119 PAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLV 162
Score = 39.8 bits (92), Expect = 0.002
Identities = 15/104 (14%), Positives = 26/104 (25%), Gaps = 2/104 (1%)
Query: 287 AQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGYV 346
Q + P+ Q P +QQ+ L Y Q P
Sbjct: 49 PQGAVPSMGQQQFLTPAQEQ-LHQQIDQATTSMNDMHLHNVPLVDP-NAYMQPQVPVQMG 106
Query: 347 GMVGRQVPGWQGIPGAQPTAQQMAVAQAQPSMMAAYAMQQFPTQ 390
+ +Q QP+A + + + + P
Sbjct: 107 TPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPP 150
Score = 37.9 bits (87), Expect = 0.006
Identities = 14/104 (13%), Positives = 20/104 (19%), Gaps = 1/104 (0%)
Query: 287 AQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGYV 346
P P+ QF +Q+ QA
Sbjct: 44 QMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNA-YMQPQVP 102
Query: 347 GMVGRQVPGWQGIPGAQPTAQQMAVAQAQPSMMAAYAMQQFPTQ 390
+G + Q A Q A M T+
Sbjct: 103 VQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTE 146
Score = 35.6 bits (81), Expect = 0.030
Identities = 11/104 (10%), Positives = 14/104 (13%)
Query: 287 AQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGYV 346
TP Q A PQ Q G Q
Sbjct: 56 MGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQP 115
Query: 347 GMVGRQVPGWQGIPGAQPTAQQMAVAQAQPSMMAAYAMQQFPTQ 390
+ Q+ + P
Sbjct: 116 MAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPP 159
Score = 34.4 bits (78), Expect = 0.067
Identities = 13/64 (20%), Positives = 16/64 (25%), Gaps = 1/64 (1%)
Query: 328 QLPQQFYQYGQLGYPQGYVGMVGR-QVPGWQGIPGAQPTAQQMAVAQAQPSMMAAYAMQQ 386
PQ QYGQ P Q P G+ Q + Q+
Sbjct: 8 VYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQE 67
Query: 387 FPTQ 390
Q
Sbjct: 68 QLHQ 71
Score = 34.0 bits (77), Expect = 0.10
Identities = 13/83 (15%), Positives = 19/83 (22%)
Query: 308 YNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGYVGMVGRQVPGWQGIPGAQPTAQ 367
Y Q + A A +P Q + Y Q + G Q Q
Sbjct: 9 YPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQ 68
Query: 368 QMAVAQAQPSMMAAYAMQQFPTQ 390
+ M + P
Sbjct: 69 LHQQIDQATTSMNDMHLHNVPLV 91
Score = 33.6 bits (76), Expect = 0.14
Identities = 14/107 (13%), Positives = 21/107 (19%), Gaps = 4/107 (3%)
Query: 286 LAQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLP----QQFYQYGQLGY 341
L Q + ++ + P A Q+ QQ Y
Sbjct: 62 LTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAY 121
Query: 342 PQGYVGMVGRQVPGWQGIPGAQPTAQQMAVAQAQPSMMAAYAMQQFP 388
Q M P Q P T + +
Sbjct: 122 GQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERM 168
Score = 29.4 bits (65), Expect = 2.3
Identities = 9/64 (14%), Positives = 17/64 (26%)
Query: 327 AQLPQQFYQYGQLGYPQGYVGMVGRQVPGWQGIPGAQPTAQQMAVAQAQPSMMAAYAMQQ 386
+ ++ Y QL Y Q + P A + Q ++ + Q
Sbjct: 2 SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQF 61
Query: 387 FPTQ 390
Sbjct: 62 LTPA 65
>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 = 11/61 (18%), Positives = 27/61 (44%), Gaps = 3/61 (4%)
Query: 216 KDLNEELVSKVFSPFGTIVDIRVFKEK--GYAFVKFTTKETATHAIESIHNTDINGHTVK 273
++ ++++ + + G ++ I V K G +VK + A A+ ++H G +
Sbjct: 28 TEIKDDVIEE-CNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMIT 86
Query: 274 C 274
Sbjct: 87 A 87
Score = 40.8 bits (96), Expect = 7e-05
Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 10/75 (13%)
Query: 112 LKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNGQWLGSRSIR--- 168
+ E G + + + ++ G +V A A A+ A++G+W + I
Sbjct: 34 VIEECNKHGGVIHIYVDKNSAQ----GNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAY 89
Query: 169 ---TNWSTRKPPAMT 180
+ P +MT
Sbjct: 90 VPLPTYHNLFPDSMT 104
Score = 30.8 bits (70), Expect = 0.24
Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 6/53 (11%)
Query: 19 VTEELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTVAATALAAMNKRVF 71
V EE ++ G V V + +++ A A+ A++ R F
Sbjct: 34 VIEE-----CNKHGGVIHIYVDKNSA-QGNVYVKCPSIAAAIAAVNALHGRWF 80
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 39.8 bits (93), Expect = 2e-04
Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 2/70 (2%)
Query: 101 GDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLK-SKGYAFVSFVKKAEAENAITAMNG 159
G++ ++E KE +G++ C I P F+ F + A A+ +NG
Sbjct: 20 GEVDEDLE-VETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNG 78
Query: 160 QWLGSRSIRT 169
++ G R ++
Sbjct: 79 RYFGGRVVKA 88
Score = 36.3 bits (84), Expect = 0.002
Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 11/75 (14%)
Query: 216 KDLNEELVSKVF---SPFGTIVDIRVFK-------EKGYAFVKFTTKETATHAIESIHNT 265
+++E+L + +G + +F+ E F++F E+A A+ ++
Sbjct: 20 GEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGR 79
Query: 266 DINGHTVKC-FWGKE 279
G VK F+ +
Sbjct: 80 YFGGRVVKACFYNLD 94
Score = 29.0 bits (65), Expect = 0.80
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 4/54 (7%)
Query: 29 SQIGPVKGCKVIREPGNDPY----AFLEFVHHTVAATALAAMNKRVFLEKEMKV 78
+ G V C + PG FLEF A A+ +N R F + +K
Sbjct: 35 EKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKA 88
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 37.8 bits (87), Expect = 7e-04
Identities = 11/67 (16%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 219 NEELVSKVFSPFGTIVDIRV-FKEKGYAFVKFTTKETATHAIESIHNTDINGHTVKCFWG 277
+++++ ++ +G ++++ + K+ G A V+F T + A A+++ N + G
Sbjct: 30 SKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWLEG 89
Query: 278 KESENNS 284
+ + +
Sbjct: 90 QPQDASG 96
>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 = 36.7 bits (85), Expect = 0.007
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 100 VGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA----FVSFVKKAEAENAIT 155
D+ ++E + +E FG ++ I ++ Q + FV F +E AI
Sbjct: 135 PKDIDDDLEGEVTEEC-GKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQ 193
Query: 156 AMNGQWLGSRSIR 168
A+NG+W R +
Sbjct: 194 ALNGRWFAGRKVV 206
Score = 28.3 bits (63), Expect = 4.1
Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 13/72 (18%)
Query: 216 KDLNEELVSKVF---SPFGTIVDIRVFKEKGYA----------FVKFTTKETATHAIESI 262
KD++++L +V FG + + +++EK FV+F+ AI+++
Sbjct: 136 KDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQAL 195
Query: 263 HNTDINGHTVKC 274
+ G V
Sbjct: 196 NGRWFAGRKVVA 207
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 34.5 bits (79), Expect = 0.009
Identities = 12/74 (16%), Positives = 26/74 (35%), Gaps = 17/74 (22%)
Query: 98 IFVGDLSPEIETQTLKEAFAPF-----GEISNCRIVRDPQTLKSKGYAFVSFVKKAEAEN 152
+ V L P + + L F G + + + + ++F + A+AE
Sbjct: 11 VEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ--------RLGCGGVLTFREPADAER 62
Query: 153 AIT----AMNGQWL 162
+ ++G L
Sbjct: 63 VLAQADHELHGAQL 76
Score = 30.3 bits (68), Expect = 0.36
Identities = 15/64 (23%), Positives = 19/64 (29%), Gaps = 4/64 (6%)
Query: 3 DESQPTTLYVGNLDVSVTEELLCALFSQIGPVKG--CKVIREPGNDPYAFLEFVHHTVAA 60
S + V L +V +ELL F G + G L F A
Sbjct: 4 GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGC--GGVLTFREPADAE 61
Query: 61 TALA 64
LA
Sbjct: 62 RVLA 65
>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule,
ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}
Length = 350
Score = 31.4 bits (72), Expect = 0.50
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 7/62 (11%)
Query: 173 TRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-G 231
PP + +T TFD VY+Q+S N ++ + + L+ V F
Sbjct: 38 IVDPPEQEKSATQAKKVPRTFTFDAVYDQTS-CNYGIF-----QASFKPLIDAVLEGFNS 91
Query: 232 TI 233
TI
Sbjct: 92 TI 93
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 30.0 bits (67), Expect = 0.58
Identities = 18/75 (24%), Positives = 28/75 (37%), Gaps = 8/75 (10%)
Query: 99 FVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
F GDL + + L F+ GEI VR + + F K +A+ A+
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKE------GIILF--KEKAKEALGKAK 74
Query: 159 GQWLGSRSIRTNWST 173
G+ +R T
Sbjct: 75 DANNGNLQLRNKEVT 89
Score = 29.2 bits (65), Expect = 1.0
Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 7/78 (8%)
Query: 204 PTNCTVY-CGGFGKDLNEELVSKVFSPFGTI--VDIRVFKEKGYAFVKFTTKETATHAIE 260
C + G E + +FS G I +D ++G + F KE A A+
Sbjct: 16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGI--ILF--KEKAKEALG 71
Query: 261 SIHNTDINGHTVKCFWGK 278
+ + ++
Sbjct: 72 KAKDANNGNLQLRNKEVT 89
>2heh_A KIF2C protein; kinesin, motor domain, ADP, structural genomics,
structural genomics consortium, SGC, structural protein;
HET: ADP; 2.15A {Homo sapiens} PDB: 3edl_D*
Length = 387
Score = 29.9 bits (68), Expect = 1.3
Identities = 9/44 (20%), Positives = 18/44 (40%), Gaps = 7/44 (15%)
Query: 191 KTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-GTI 233
+ FD +++++ +N VY + LV +F T
Sbjct: 101 QAFCFDFAFDETA-SNEVVY-----RFTARPLVQTIFEGGKATC 138
>1v8k_A Kinesin-like protein KIF2C; microtubule destabilizer, structural P;
HET: ANP; 2.25A {Mus musculus} SCOP: c.37.1.9 PDB:
1v8j_A* 2gry_A*
Length = 410
Score = 29.9 bits (68), Expect = 1.4
Identities = 9/44 (20%), Positives = 18/44 (40%), Gaps = 7/44 (15%)
Query: 191 KTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-GTI 233
+ FD +++++ +N VY + LV +F T
Sbjct: 121 QAFCFDFAFDETA-SNEVVY-----RFTARPLVQTIFEGGKATC 158
>3ghj_A Putative integron gene cassette protein; integron cassette
protein, mobIle metagenome, structural genomics, PSI-2;
1.47A {Uncultured bacterium}
Length = 141
Score = 28.4 bits (64), Expect = 2.0
Identities = 9/53 (16%), Positives = 14/53 (26%), Gaps = 13/53 (24%)
Query: 8 TTLYVGNLDVSVT--EELLCALFSQIGPVKGCKVIREPGNDPYAFLEFVHHTV 58
+ V NL+ S E+L G + + FL
Sbjct: 32 VAVKVKNLEKSSQFYTEIL-----------GFEAGLLDSARRWNFLWVSGRAG 73
>3b6u_A Kinesin-like protein KIF3B; structural genomics consortium, motor
domain, ADP, SGC, ATP-binding, coiled coil, microtubule,
motor protein; HET: ADP; 1.80A {Homo sapiens} PDB:
3b6v_A*
Length = 372
Score = 29.5 bits (67), Expect = 2.2
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 180 TNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-GTI 233
N + + KT TFD VY+ ++ +Y + LV V F GTI
Sbjct: 57 KNPKGTAHEMPKTFTFDAVYDWNAKQF-ELY-----DETFRPLVDSVLQGFNGTI 105
>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone
methyltransferase, RRM fold, telomere, nuclear protein;
3.0A {Saccharomyces cerevisiae}
Length = 136
Score = 28.2 bits (62), Expect = 2.3
Identities = 9/38 (23%), Positives = 17/38 (44%)
Query: 107 IETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSF 144
I+ ++K F +GEIS+ DP + + +
Sbjct: 18 IQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKY 55
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 27.7 bits (61), Expect = 2.4
Identities = 11/96 (11%), Positives = 30/96 (31%), Gaps = 9/96 (9%)
Query: 95 HYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYAFVSFVKKAEAENAI 154
H ++V +L + +++ + +++ + A + F+ + AE A
Sbjct: 9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLS-----ITGCSAILRFINQDSAERAQ 63
Query: 155 TAMNGQWLGSRSIRTNWSTRKPPAMTNERKRQNSHT 190
M + + I P + +
Sbjct: 64 KRMENEDVFGNRI----IVSFTPKNRELCETSGPSS 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 = 27.4 bits (60), Expect = 2.9
Identities = 19/78 (24%), Positives = 29/78 (37%), Gaps = 13/78 (16%)
Query: 81 ASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEISNCRIVRDPQTLKSKGYA 140
+ P QPK+D H+ E +T L + F+ FG I I A
Sbjct: 6 SGGPDLQPKRD-----HVLHVTFPKEWKTSDLYQLFSAFGNIQISWI--------DDTSA 52
Query: 141 FVSFVKKAEAENAITAMN 158
FVS + + + A+
Sbjct: 53 FVSLSQPEQVQIAVNTSK 70
>3dev_A SH1221; alpha-beta protein., structural genomics, PSI-2, protein
STR initiative, northeast structural genomics
consortium, NESG; 3.10A {Staphylococcus haemolyticus}
Length = 320
Score = 28.7 bits (65), Expect = 2.9
Identities = 11/64 (17%), Positives = 26/64 (40%), Gaps = 12/64 (18%)
Query: 25 CALFSQIGP---VKGCKVIR---EPGNDPYAFLEFVHHTVAATA------LAAMNKRVFL 72
A +I + G +I+ P D Y + FV+ ++T+ ++ N +
Sbjct: 84 TANAPRIDDQRYLNGQSLIKIDHHPATDQYGDVNFVNTEASSTSEIIFDFISHFNDLSII 143
Query: 73 EKEM 76
++ +
Sbjct: 144 DEHV 147
>3lre_A Kinesin-like protein KIF18A; motor protein, nucleotide binding,
microtubule binding, ATP- cell projection, cytoskeleton,
glycoprotein, microtubule; HET: ADP; 2.20A {Homo
sapiens}
Length = 355
Score = 28.8 bits (65), Expect = 3.0
Identities = 7/62 (11%), Positives = 22/62 (35%), Gaps = 7/62 (11%)
Query: 173 TRKPPAMTNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-G 231
++ + FD V++++S T V+ + + ++ + +
Sbjct: 54 FHGKKTTNQNVIKKQNKDLKFVFDAVFDETS-TQSEVF-----EHTTKPILRSFLNGYNC 107
Query: 232 TI 233
T+
Sbjct: 108 TV 109
>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease,
hydrolase, magnesium, metal nonsense-mediated mRNA
decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}
Length = 507
Score = 28.8 bits (63), Expect = 3.2
Identities = 18/96 (18%), Positives = 34/96 (35%), Gaps = 11/96 (11%)
Query: 63 LAAMNKRVFLEKEMKVNWASSPGNQPKQDTSNHYHIFVGDLSPEIETQTLKEAFAPFGEI 122
+ ++FL + M + + + G + H+ E +T L + F+ FG I
Sbjct: 410 IEPFFNKLFLMRVMDIPYLNLEGPDLQ---PKRDHVLHVTFPKEWKTSDLYQLFSAFGNI 466
Query: 123 SNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMN 158
I AFVS + + + A+
Sbjct: 467 QISWI--------DDTSAFVSLSQPEQVQIAVNTSK 494
>1dx0_A Prion protein; brain, repeat; NMR {Bos taurus} SCOP: d.6.1.1 PDB:
1dx1_A 1qlx_A 1qlz_A
Length = 219
Score = 28.3 bits (62), Expect = 3.6
Identities = 11/103 (10%), Positives = 16/103 (15%), Gaps = 6/103 (5%)
Query: 276 WGKESENNSTLAQPSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAA--QLPQQF 333
W P P + G+ P +
Sbjct: 12 WNTGGSRYPGQGSPGGNRYPPQ----GGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHG 67
Query: 334 YQYGQLGYPQGYVGMVGRQVPGWQGIPGAQPTAQQMAVAQAQP 376
+GQ G+ P A A
Sbjct: 68 GGWGQPHGGGGWGQGGTHGQWNKPSKPKTNMKHVAGAAAAGAV 110
>1t5c_A CENP-E protein, centromeric protein E; kinesin motor-domain-ADP
complex, stranded beta-sheet core with solvent exposed
alpha-helices; HET: ADP PIN; 2.50A {Homo sapiens}
Length = 349
Score = 28.7 bits (65), Expect = 3.8
Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 7/49 (14%)
Query: 186 QNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-GTI 233
Q +K+ FD V++ + T VY +++ ++ + GTI
Sbjct: 39 QVDGSKSFNFDRVFHGNETTK-NVY-----EEIAAPIIDSAIQGYNGTI 81
>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase,
phosphoprotein, transfe two-component regulatory system;
3.80A {Thermotoga maritima}
Length = 349
Score = 28.4 bits (64), Expect = 4.5
Identities = 17/56 (30%), Positives = 18/56 (32%), Gaps = 26/56 (46%)
Query: 220 EELVSKVFSPFGTIVDIRVFKEKGYAFVKFTTKETAT--------HAIESIHNTDI 267
EEL K+FSPF FTTK T IE H I
Sbjct: 290 EELKEKIFSPF------------------FTTKTQGTGLGLSICRKIIEDEHGGKI 327
>4a14_A Kinesin, kinesin-like protein KIF7; motor protein, motor domain;
HET: ADP; 1.60A {Homo sapiens} PDB: 2xt3_A*
Length = 344
Score = 27.9 bits (63), Expect = 5.2
Identities = 8/54 (14%), Positives = 16/54 (29%), Gaps = 7/54 (12%)
Query: 181 NERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-GTI 233
+ + F V + + VY + + L+ F F T+
Sbjct: 40 GLGRVTLGRDRHFGFHVVLAEDA-GQEAVY-----QACVQPLLEAFFEGFNATV 87
>1xsq_A Ureidoglycolate hydrolase; northeast structural genomics
consortium, NESG, structural genomics, protein structure
initiative, PSI, ET81, X-RAY; 1.60A {Escherichia coli}
SCOP: b.82.1.14 PDB: 1xsr_A 1yqc_A
Length = 168
Score = 27.5 bits (60), Expect = 5.2
Identities = 11/77 (14%), Positives = 33/77 (42%), Gaps = 9/77 (11%)
Query: 106 EIETQTL-KEAFAPFGEI-----SNCRIVRDPQTLKSKGYAFVSFVKKAEAENAITAMNG 159
+++ L +EAF+ +G++ + + + + Y ++ V+ E + + ++N
Sbjct: 2 KLQVLPLSQEAFSAYGDVIETQQRDFFHINNGLVER---YHDLALVEILEQDCTLISINR 58
Query: 160 QWLGSRSIRTNWSTRKP 176
+ + + R P
Sbjct: 59 AQPANLPLTIHELERHP 75
>3bfn_A Kinesin-like protein KIF22; limited proteolysis, structural
genomics consortium domain, ADP, SGC, ATP-binding,
DNA-binding, microtubule, MO protein; HET: ADP; 2.30A
{Homo sapiens}
Length = 388
Score = 28.0 bits (63), Expect = 5.5
Identities = 8/50 (16%), Positives = 17/50 (34%), Gaps = 7/50 (14%)
Query: 185 RQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-GTI 233
R + T FD Y + S T +Y + ++ + ++
Sbjct: 59 RNHQETLKYQFDAFYGERS-TQQDIY-----AGSVQPILRHLLEGQNASV 102
>1bg2_A Kinesin; motor protein, ATPase, microtubule associated; HET: ADP;
1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 2p4n_K* 1mkj_A*
2kin_A* 3kin_A*
Length = 325
Score = 27.9 bits (63), Expect = 6.0
Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 7/54 (12%)
Query: 181 NERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-GTI 233
+K FD V+ S+ + VY D +++V V + GTI
Sbjct: 34 QGEDTVVIASKPYAFDRVFQSST-SQEQVY-----NDCAKKIVKDVLEGYNGTI 81
>2wbe_C Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mitosis,
GTP-binding, motor protein, cell division, cell cycle,
microtubule, ATP-binding; HET: GTP ANP GDP TA1; 9.40A
{Drosophila melanogaster}
Length = 373
Score = 28.0 bits (63), Expect = 6.4
Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 7/52 (13%)
Query: 183 RKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-GTI 233
+ TK TFD + S C VY + L+ +V + + T+
Sbjct: 59 HTLDSKLTKKFTFDRSFGPES-KQCDVY-----SVVVSPLIEEVLNGYNCTV 104
>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A
{Drosophila melanogaster} PDB: 2y5w_A*
Length = 365
Score = 27.6 bits (62), Expect = 8.1
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 7/45 (15%)
Query: 190 TKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-GTI 233
K FD+V+ ++ + VY + + +V+ V + + GTI
Sbjct: 50 GKVYLFDKVFKPNA-SQEKVY-----NEAAKSIVTDVLAGYNGTI 88
>3gzs_A Uncharacterized SUSD superfamily protein; structural genomics,
joint center for structural genomics, J protein
structure initiative, PSI-2; 2.09A {Bacteroides
fragilis}
Length = 515
Score = 27.6 bits (60), Expect = 8.5
Identities = 12/70 (17%), Positives = 19/70 (27%), Gaps = 3/70 (4%)
Query: 289 PSAPTTPQPNSTAPQFPYIYNQQMGYWYPQAAAYTATAAQLPQQFYQYGQLGYPQGYVGM 348
P PT + P TA+ + P YQ G + G
Sbjct: 9 PLLPTKEDEKMDGVIYGAYLPNLEKSVIP---IGTASESTEPVNRYQIGVNLAGDAWAGY 65
Query: 349 VGRQVPGWQG 358
+ + + G
Sbjct: 66 MSPRDNKFNG 75
>1x88_A Kinesin-like protein KIF11; switch II, motor domain, NECK linker,
cell cycle; HET: ADP NAT; 1.80A {Homo sapiens} SCOP:
c.37.1.9 PDB: 3hqd_A* 3ken_A* 2pg2_A* 1yrs_A* 2fme_A*
2g1q_A* 2gm1_A* 1ii6_A* 2uyi_A* 2uym_A* 2wog_A* 2x2r_A*
2x7c_A* 2x7d_A* 2x7e_A* 2xae_A* 3k3b_A* 3k5e_A* 3l9h_A*
1q0b_A* ...
Length = 359
Score = 27.5 bits (62), Expect = 8.6
Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 7/55 (12%)
Query: 180 TNERKRQNSHTKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-GTI 233
S KT TFD V+ S+ VY + + ++ +V + TI
Sbjct: 44 RTGGLADKSSRKTYTFDMVFGASTKQI-DVY-----RSVVCPILDEVIMGYNCTI 92
>3r9q_A Enoyl-COA hydratase/isomerase; ssgcid, lyase,isomerase; 2.10A
{Mycobacterium abscessus} PDB: 3qka_A
Length = 262
Score = 27.2 bits (61), Expect = 8.8
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 347 GMVGRQVPGWQGIPGAQPTAQQMAVAQAQPSMMAA 381
G+V R V Q A+ A ++A A Q + A
Sbjct: 181 GLVNRVVARGQAREAAETLAAEIA-AFPQQCVRAD 214
>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A
{Neurospora crassa} SCOP: c.37.1.9
Length = 355
Score = 27.2 bits (61), Expect = 9.0
Identities = 8/45 (17%), Positives = 18/45 (40%), Gaps = 7/45 (15%)
Query: 190 TKTITFDEVYNQSSPTNCTVYCGGFGKDLNEELVSKVFSPF-GTI 233
+ TFD V++ S ++ + V + + + GT+
Sbjct: 46 QGSFTFDRVFDMSC-KQSDIF-----DFSIKPTVDDILNGYNGTV 84
>3gbj_A KIF13B protein; kinesin, motor domain, ADP, structural genomics,
structural genomics consortium, SGC, ATP-binding,
microtubule, motor protein; HET: ADP; 2.10A {Homo
sapiens}
Length = 354
Score = 27.1 bits (61), Expect = 9.7
Identities = 9/66 (13%), Positives = 16/66 (24%), Gaps = 13/66 (19%)
Query: 176 PPAMTNERKRQNSHTKTITFDEVY----NQSSPTNCT---VYCGGFGKDLNEELVSKVFS 228
P + K +D + V+ K L E ++ F
Sbjct: 36 PVNTNLSKGDARGQPKVFAYDHCFWSMDESVKEKYAGQDIVF-----KCLGENILQNAFD 90
Query: 229 PF-GTI 233
+ I
Sbjct: 91 GYNACI 96
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
0.316 0.130 0.395
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: 5,874,334
Number of extensions: 339730
Number of successful extensions: 1862
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1328
Number of HSP's successfully gapped: 612
Length of query: 390
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 295
Effective length of database: 4,049,298
Effective search space: 1194542910
Effective search space used: 1194542910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.1 bits)