RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16184
(363 letters)
>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 = 104 bits (261), Expect = 6e-28
Identities = 27/101 (26%), Positives = 46/101 (45%), Gaps = 4/101 (3%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+S + KTL ++ ++Y +E L+ FE IK V GK +GYAFIE
Sbjct: 4 GSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIE 59
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRR 190
+ D A + ++I+GR + ++++ R P
Sbjct: 60 FASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100
>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 = 101 bits (251), Expect = 7e-24
Identities = 189/340 (55%), Positives = 223/340 (65%), Gaps = 1/340 (0%)
Query: 1 MTQFLPPNLLALFAPRDPVPYLPPVEKLPHEKK-THGYSGIAAFLNEFEDPKDTPPPTRV 59
MTQFLPPNLLALFAPRDP+PYLPP+EKLPHEK Y GIA ++ EFEDP+D PPPTR
Sbjct: 1 MTQFLPPNLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRA 60
Query: 60 ETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLR 119
ETREER+ER+RRE+ E+ ++E E+ +WDP++ PNA D FKTLF+ARVNYDT+ESKLR
Sbjct: 61 ETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLR 120
Query: 120 REFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 179
REFEVYGPIK+I MV++K +GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER
Sbjct: 121 REFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
Query: 180 SRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARS 239
RTVKGW PRRLGGGLGGTRRGG DVN++HSGR+D R ER R R
Sbjct: 181 GRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERE 240
Query: 240 GSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDR 299
+ R R + R RSRSRD+ RR D + + R +R R
Sbjct: 241 RRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSRSRERAR 300
Query: 300 DRDRKRRRERENSEDRNERKRDRKERRKERERNNEEREEK 339
++ R D E + +
Sbjct: 301 RERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGP 340
Score = 32.9 bits (74), Expect = 0.15
Identities = 26/190 (13%), Positives = 48/190 (25%)
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKH 209
+ D + + R D ER R + + R +
Sbjct: 210 HSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSR 269
Query: 210 SGREDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRD 269
E +R+R+ R R+ +E R + D
Sbjct: 270 DKEERRRSRERSKDKDRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDD 329
Query: 270 RRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKER 329
D E+ R ++R R +RR + + E KR + + R
Sbjct: 330 GPPGELGPDGPDGPEEKGRDRDRERRRSHRSERERRRDRDRDRDRDREHKRGERGSERGR 389
Query: 330 ERNNEEREEK 339
+ +
Sbjct: 390 DEARGGGGGQ 399
Score = 30.2 bits (67), Expect = 1.0
Identities = 35/255 (13%), Positives = 62/255 (24%)
Query: 108 RVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKK 167
V+ + + G ++ + +
Sbjct: 175 LVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRD 234
Query: 168 IDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRLERE 227
D R + R R + R R + S +++R+R R
Sbjct: 235 RDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDKDRDRKRRSSR 294
Query: 228 RELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEV 287
R R S + + E D E
Sbjct: 295 SRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPEEKGRDRDRER 354
Query: 288 EFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERERNNEEREEKVFIKQEPV 347
+ +R RDRDR R R+RE+ +R R E R + E ++
Sbjct: 355 RRSHRSERERRRDRDRDRDRDREHKRGERGSERGRDEARGGGGGQDNGLEGLGNDSRDMY 414
Query: 348 DDYQEYDNYEDEASS 362
+ + D Y +
Sbjct: 415 MESEGGDGYLAPENG 429
>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 = 93.1 bits (232), Expect = 1e-23
Identities = 29/101 (28%), Positives = 52/101 (51%), Gaps = 3/101 (2%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+S PNA P KTLF+ ++ DT+E L+ F + +V ++ TG +G+ F++
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVD 60
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRR 190
+ E D +A + + +IDG +V +D + + G P
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101
>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 = 86.9 bits (216), Expect = 2e-21
Identities = 31/96 (32%), Positives = 43/96 (44%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
+D TL + + Y TS LRR FE YG + + + T PRG+AF+ +
Sbjct: 6 SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDR 65
Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPR 189
RD A DG ++DGR + V V R P
Sbjct: 66 RDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPS 101
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 84.2 bits (209), Expect = 2e-20
Identities = 30/92 (32%), Positives = 51/92 (55%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
+S A DP L + ++ T+E LR F YGPI + +V+++ + + RG+AF+
Sbjct: 3 SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62
Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
+E+ D A + A+G ++DGRR+ V S
Sbjct: 63 YFENVDDAKEAKERANGMELDGRRIRVSGPSS 94
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 82.0 bits (203), Expect = 1e-19
Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 6/88 (6%)
Query: 99 DPFKTLFIARVNYDTSESKLRREFEVYG--PIKKIVMVHNKVTGKPRGYAFIEYEHERDM 156
T+ + + T + Y + I ++ +K T + RG+AF++ D
Sbjct: 7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDA 66
Query: 157 HSAYKHADGK----KIDGRRVLVDVERS 180
+ KIDG+ + VD +S
Sbjct: 67 SQLLQILQSLHPPLKIDGKTIGVDFAKS 94
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 80.1 bits (198), Expect = 6e-19
Identities = 17/96 (17%), Positives = 38/96 (39%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
P K + AR+N + E+ L+ YG ++++ ++ + T K G A + + R
Sbjct: 5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKET 64
Query: 160 YKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGL 195
K+ + G + ++ + + G
Sbjct: 65 VKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGS 100
>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 = 76.9 bits (190), Expect = 7e-18
Identities = 21/88 (23%), Positives = 41/88 (46%), Gaps = 5/88 (5%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
+ + +TL ++++ +E +L+ FE I+ + GK +G A+IE++ E
Sbjct: 9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSE 63
Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSR 181
D + G +IDGR V + +
Sbjct: 64 ADAEKNLEEKQGAEIDGRSVSLYYTGEK 91
>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 = 77.5 bits (191), Expect = 1e-17
Identities = 29/94 (30%), Positives = 52/94 (55%)
Query: 88 WDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
+ A DP L + ++ T+E LR F YGPI + +V+++ + + RG+AF
Sbjct: 33 GSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 92
Query: 148 IEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
+ +E+ D A + A+G ++DGRR+ VD ++
Sbjct: 93 VYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 74.2 bits (183), Expect = 7e-17
Identities = 20/86 (23%), Positives = 43/86 (50%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
P + +++ + YD +E ++ GP+ + M+ + TG+ +GYAFIE+ SA
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 160 YKHADGKKIDGRRVLVDVERSRTVKG 185
++ +G ++ R + + + G
Sbjct: 61 VRNLNGYQLGSRFLKCGYSSNSDISG 86
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 75.2 bits (185), Expect = 1e-16
Identities = 19/89 (21%), Positives = 40/89 (44%)
Query: 88 WDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
+ + + L++ + + + L F +G I I + + T K RG+AF
Sbjct: 50 SGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAF 109
Query: 148 IEYEHERDMHSAYKHADGKKIDGRRVLVD 176
+E+E D +A + + ++ GR + V+
Sbjct: 110 VEFELAEDAAAAIDNMNESELFGRTIRVN 138
>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 = 73.4 bits (181), Expect = 2e-16
Identities = 30/106 (28%), Positives = 53/106 (50%), Gaps = 5/106 (4%)
Query: 91 NSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
+S + LF+ +++DT+E L + F YG I ++V+V ++ T + RG+ F+ +
Sbjct: 2 SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61
Query: 151 EHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLG 196
E+ D A +GK +DGR++ VD + R G G
Sbjct: 62 ENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSS-----DNRSGPSSG 102
>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 = 72.6 bits (179), Expect = 3e-16
Identities = 17/87 (19%), Positives = 40/87 (45%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+ T++++ + + + + L R F YG + K+ ++ +K T K +G AFI
Sbjct: 5 SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFIL 64
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVD 176
+ + + + + K++ GR +
Sbjct: 65 FLDKDSAQNCTRAINNKQLFGRVIKAS 91
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 72.7 bits (179), Expect = 3e-16
Identities = 26/96 (27%), Positives = 45/96 (46%), Gaps = 1/96 (1%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
F +T LFI+ + + ++ +L + +G +K + +V N+ GKP+G A++E
Sbjct: 6 SGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVE 64
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKG 185
YE+E A DG I + V + S G
Sbjct: 65 YENESQASQAVMKMDGMTIKENIIKVAISNSGPSSG 100
>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 = 72.3 bits (178), Expect = 4e-16
Identities = 26/94 (27%), Positives = 44/94 (46%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
+S PN D T+ + ++ DT E+ L+ F +G I +I + +K TG+ +G+AFI
Sbjct: 3 SGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFI 62
Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
+ D A G D + V+ + T
Sbjct: 63 SFHRREDAARAIAGVSGFGYDHLILNVEWAKPST 96
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 71.7 bits (176), Expect = 7e-16
Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 5/74 (6%)
Query: 111 YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 170
+ L F G + + ++ TGK +G+ F+E D K GK++D
Sbjct: 22 VPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDL 81
Query: 171 RRVLV-----DVER 179
+ L DVER
Sbjct: 82 KHRLFLYTMKDVER 95
>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 = 72.0 bits (177), Expect = 7e-16
Identities = 30/108 (27%), Positives = 54/108 (50%), Gaps = 1/108 (0%)
Query: 96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
D LFI +N +T+E L+ F +GPI +++++ ++ T K RG+AFI +E+ D
Sbjct: 2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPAD 60
Query: 156 MHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGP 203
+A K +GK + G+ + V+ + + + RR G
Sbjct: 61 AKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGS 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 = 70.3 bits (173), Expect = 1e-15
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 1/83 (1%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKV-TGKPRGYAFIEYEHERDMHS 158
+ I R+ + ++ + F YG IK I M ++ +GYA++E+E+ +
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 159 AYKHADGKKIDGRRVLVDVERSR 181
A KH DG +IDG+ + +
Sbjct: 63 ALKHMDGGQIDGQEITATAVLAP 85
>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 = 71.7 bits (176), Expect = 2e-15
Identities = 29/112 (25%), Positives = 49/112 (43%), Gaps = 5/112 (4%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
P + N D + L + + E +LR+ FE YGPI+ + +V ++ T + RGY F++
Sbjct: 31 PPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVK 90
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRG 201
++ A +G I +R+ V + S R G G G
Sbjct: 91 FQSGSSAQQAIAGLNGFNILNKRLKVALAASGH-----QRPGIAGAVGDGNG 137
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif,
C-terminal helix, N-terminal helix, RNA binding protein;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 70.4 bits (173), Expect = 2e-15
Identities = 29/102 (28%), Positives = 52/102 (50%), Gaps = 3/102 (2%)
Query: 96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
A +++F+ + Y+ +E +L+ F GP+ +V+++ TGKP+GY F EY+ +
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 156 MHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGG 197
SA ++ +G++ GR + VD S K G G
Sbjct: 63 ALSAMRNLNGREFSGRALRVDNAASEKNK---EELKSLGTGA 101
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 70.4 bits (173), Expect = 2e-15
Identities = 24/93 (25%), Positives = 45/93 (48%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
D + LF+ V+ + +E + +F YG IK I + ++ TG +GY +
Sbjct: 11 DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 70
Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
EYE ++ +A + +G+ + G+ + VD R
Sbjct: 71 EYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR 103
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 73.5 bits (181), Expect = 2e-15
Identities = 25/112 (22%), Positives = 46/112 (41%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
+ + +++ + Y+ E +R+ F +GPIK I M + VT K +G+AF+
Sbjct: 16 GSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75
Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRR 200
EYE A + + + GR + V + + +L R
Sbjct: 76 EYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNR 127
Score = 63.1 bits (154), Expect = 8e-12
Identities = 23/83 (27%), Positives = 39/83 (46%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
F +++A V+ D S+ ++ FE +G IK + + TGK +GY FIEYE
Sbjct: 118 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKA 177
Query: 154 RDMHSAYKHADGKKIDGRRVLVD 176
+ A + + G+ + V
Sbjct: 178 QSSQDAVSSMNLFDLGGQYLRVG 200
>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 = 70.0 bits (172), Expect = 2e-15
Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 1/87 (1%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+ A + +T+F+ + E L F GP+ K+ + ++ GKP+ + F+
Sbjct: 5 SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVC 63
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVD 176
++H + A +G ++ GR + V
Sbjct: 64 FKHPESVSYAIALLNGIRLYGRPINVS 90
>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 = 69.9 bits (172), Expect = 3e-15
Identities = 22/103 (21%), Positives = 45/103 (43%), Gaps = 3/103 (2%)
Query: 92 SFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
S + + L++ + + + L F +G I I + + T K RG+AF+E+E
Sbjct: 3 SGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 62
Query: 152 HERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGG 194
D +A + + ++ GR + V++ + +K G
Sbjct: 63 LAEDAAAAIDNMNESELFGRTIRVNLAKPMRIK---ESGPSSG 102
>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 = 71.8 bits (176), Expect = 3e-15
Identities = 29/142 (20%), Positives = 57/142 (40%), Gaps = 5/142 (3%)
Query: 45 NEFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDP---- 100
EFE +D + + + R ++ + P
Sbjct: 11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSV 70
Query: 101 -FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
LF+ ++ + E +++ +F YG IK I + ++ TG +GYA +EYE + +A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 130
Query: 160 YKHADGKKIDGRRVLVDVERSR 181
+ +G +I G+ + VD +
Sbjct: 131 KEALNGAEIMGQTIQVDWCFVK 152
>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 = 70.1 bits (172), Expect = 3e-15
Identities = 24/102 (23%), Positives = 46/102 (45%), Gaps = 6/102 (5%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
+ + KT+FI +++D+ E L + +G +K + +V + T +G AF ++ +
Sbjct: 8 LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 67
Query: 154 RDMHSAYKHAD------GKKIDGRRVLVDVERSRTVKGWLPR 189
A G K+DGR++ VD+ +R P
Sbjct: 68 EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109
>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and
splicing factor,...; protein-RNA complex RRM alpha-beta
sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR
{Streptococcus SP} PDB: 2i38_A
Length = 150
Score = 71.4 bits (175), Expect = 3e-15
Identities = 25/136 (18%), Positives = 56/136 (41%), Gaps = 6/136 (4%)
Query: 46 EFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLF 105
E D + + ++ + + + + ++ K ++
Sbjct: 19 EAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCK-VY 77
Query: 106 IARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADG 165
+ + + ++++L R F YGP++ + + N P G+AF+E+E RD A + DG
Sbjct: 78 VGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDG 132
Query: 166 KKIDGRRVLVDVERSR 181
+ + G RV V++
Sbjct: 133 RTLCGCRVRVELSNGE 148
>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 = 69.6 bits (171), Expect = 4e-15
Identities = 23/80 (28%), Positives = 40/80 (50%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
LF+ ++Y +SE L + F YGP+ ++ + +T KP+G+AF+ + AY
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
Query: 162 HADGKKIDGRRVLVDVERSR 181
DG+ GR + V +
Sbjct: 69 EVDGQVFQGRMLHVLPSTIK 88
>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 = 69.6 bits (171), Expect = 5e-15
Identities = 25/90 (27%), Positives = 44/90 (48%)
Query: 92 SFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
S P + + T+++ ++ SE L F GP+ M ++VTG+ +GY F+E+
Sbjct: 6 SGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFL 65
Query: 152 HERDMHSAYKHADGKKIDGRRVLVDVERSR 181
E D A K D K+ G+ + V+ +
Sbjct: 66 SEEDADYAIKIMDMIKLYGKPIRVNKASAH 95
>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 = 68.7 bits (169), Expect = 5e-15
Identities = 19/75 (25%), Positives = 38/75 (50%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+ L++ + + + L F +G I I + + T K RG+AF+E+E D +A
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 162 HADGKKIDGRRVLVD 176
+ + ++ GR + V+
Sbjct: 68 NMNESELFGRTIRVN 82
>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 = 70.6 bits (173), Expect = 7e-15
Identities = 30/136 (22%), Positives = 59/136 (43%), Gaps = 11/136 (8%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
+ TL++ +++ T+E ++ F G IKKI+M +K+ G+ F+EY
Sbjct: 32 QEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSR 91
Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGRE 213
D +A ++ +G ++D R + D + R+ G G G + + R+
Sbjct: 92 ADAENAMRYINGTRLDDRIIRTDWDAGFKE----GRQYGRGRSGGQV-------RDEYRQ 140
Query: 214 DNERERERYRLERERE 229
D + R Y + +
Sbjct: 141 DYDAGRGGYGKLAQNQ 156
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 68.9 bits (169), Expect = 7e-15
Identities = 30/103 (29%), Positives = 47/103 (45%), Gaps = 11/103 (10%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
+++ + + +L R F YGP++ + + N P G+AF+E+E RD A +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 164 DGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVN 206
DGK I G RV V++ PRR RR +V
Sbjct: 58 DGKVICGSRVRVELSTGM------PRRSRFDRPPARRKLLEVL 94
>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 = 68.9 bits (169), Expect = 7e-15
Identities = 23/82 (28%), Positives = 44/82 (53%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
LF+ ++ + E +++ +F YG IK I + ++ TG +GYA +EYE + +A
Sbjct: 25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
Query: 160 YKHADGKKIDGRRVLVDVERSR 181
+ +G +I G+ + VD +
Sbjct: 85 KEALNGAEIMGQTIQVDWCFVK 106
>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 = 68.4 bits (168), Expect = 7e-15
Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 6/86 (6%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
P L++ + +TS + L REF+ +G I+ I V K +A+I+YE +A
Sbjct: 16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAA 69
Query: 160 YKHADGKKIDGRRVLVDVERSRTVKG 185
G + G + V+ +++
Sbjct: 70 CAKMRGFPLGGPDRRLRVDFAKSGPS 95
>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 = 67.2 bits (165), Expect = 2e-14
Identities = 23/87 (26%), Positives = 42/87 (48%)
Query: 99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
L++ ++++ +E LR FE +G I IV++ + TG+ +GY FI +
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 159 AYKHADGKKIDGRRVLVDVERSRTVKG 185
A + +G ++ GR + V R G
Sbjct: 63 ALEQLNGFELAGRPMRVGHVTERLDGG 89
>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 = 69.7 bits (171), Expect = 3e-14
Identities = 24/107 (22%), Positives = 46/107 (42%)
Query: 70 RRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIK 129
RR Q + + +++ P D LFI + ++ +++ +GP+K
Sbjct: 83 RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLK 142
Query: 130 KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 176
+V + TG +GYAF EY A +G ++ +++LV
Sbjct: 143 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 189
Score = 53.5 bits (129), Expect = 1e-08
Identities = 11/83 (13%), Positives = 29/83 (34%), Gaps = 6/83 (7%)
Query: 99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVM-----VHNKVTGKPRGYAFIEYEHE 153
+ L++ + + +E + F + + V + + +AF+E+
Sbjct: 2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 154 RDMHSAYKHADGKKIDGRRVLVD 176
+ A DG G+ + +
Sbjct: 62 DETTQAMA-FDGIIFQGQSLKIR 83
>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 = 66.6 bits (163), Expect = 5e-14
Identities = 25/101 (24%), Positives = 49/101 (48%), Gaps = 1/101 (0%)
Query: 82 EQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGK 141
+A N+ + P + L++ ++++ +E LR FE +G I+ I ++ + TG+
Sbjct: 8 HSHMAAAMANNLQKGSAGPMR-LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGR 66
Query: 142 PRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
+GY FI + A + +G ++ GR + V RT
Sbjct: 67 SKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT 107
>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 = 66.5 bits (163), Expect = 6e-14
Identities = 28/98 (28%), Positives = 47/98 (47%), Gaps = 1/98 (1%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
+F+ + Y T+++ LR+ FE +G I++ V++ ++ TGK RGY F+ A K
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK-D 78
Query: 164 DGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRG 201
IDGR+ V++ L G+ G G
Sbjct: 79 PNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSSG 116
>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 = 66.2 bits (162), Expect = 1e-13
Identities = 18/83 (21%), Positives = 41/83 (49%)
Query: 99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
+P K L++ ++ +E L F + K + +TG+ RG AFI + ++
Sbjct: 23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 159 AYKHADGKKIDGRRVLVDVERSR 181
A +G K+ G+ ++++ +++
Sbjct: 83 ALHLVNGYKLYGKILVIEFGKNK 105
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 65.9 bits (161), Expect = 1e-13
Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 7/74 (9%)
Query: 111 YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 170
+ ++ + + F +G I + GK +GY F+EY A K+ADG K+D
Sbjct: 31 LEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK 88
Query: 171 RRVLV-----DVER 179
+ D ++
Sbjct: 89 QHTFRVNLFTDFDK 102
>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 = 67.2 bits (165), Expect = 1e-13
Identities = 20/75 (26%), Positives = 35/75 (46%)
Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
L + + D ++ +L F GPI ++ + TG GYAF+++ E D A
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 62
Query: 161 KHADGKKIDGRRVLV 175
K +G + +R+ V
Sbjct: 63 KVLNGITVRNKRLKV 77
Score = 51.4 bits (124), Expect = 4e-08
Identities = 17/68 (25%), Positives = 33/68 (48%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
L++ + ++ +L F YG I + ++ +K+TG+PRG AF+ Y + A
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 164 DGKKIDGR 171
+ +G
Sbjct: 152 NNVIPEGG 159
>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 = 69.6 bits (171), Expect = 1e-13
Identities = 16/77 (20%), Positives = 34/77 (44%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
L +A + ++ + +G +++ +V+++ TG+ +GY F EY + A
Sbjct: 94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Query: 160 YKHADGKKIDGRRVLVD 176
GK + R + V
Sbjct: 154 KSDLLGKPLGPRTLYVH 170
Score = 55.0 bits (133), Expect = 1e-08
Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 2/92 (2%)
Query: 94 PNATMDPFKTLFIARVNYDTSES-KLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEH 152
+ + L + R+ ++ L R + + G+ +G+A +EYE
Sbjct: 177 LTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYET 235
Query: 153 ERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
A + ADG + G + V
Sbjct: 236 AEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG 267
Score = 48.8 bits (117), Expect = 8e-07
Identities = 10/81 (12%), Positives = 27/81 (33%), Gaps = 7/81 (8%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+ + I + D + ++ Y + K +G AF+ + +A
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAIN 75
Query: 162 HADGKKIDGRRVLVDVERSRT 182
++ R + V ++ +
Sbjct: 76 AFHQSRLRERELSVQLQPTDA 96
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 64.3 bits (157), Expect = 2e-13
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 111 YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 170
+ ++ + + F +G I + GK +GY F+EY A K+ADG K+D
Sbjct: 17 LEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK 74
Query: 171 RRVL 174
+
Sbjct: 75 QHTF 78
>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 = 64.1 bits (157), Expect = 2e-13
Identities = 15/77 (19%), Positives = 30/77 (38%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
L+I + T++ L + + YG I + +K T K +GY F++++ A
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 164 DGKKIDGRRVLVDVERS 180
+ + S
Sbjct: 68 KASGVQAQMAKQSGPSS 84
>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 = 66.0 bits (161), Expect = 2e-13
Identities = 31/133 (23%), Positives = 54/133 (40%), Gaps = 1/133 (0%)
Query: 49 DPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIAR 108
+ D +V + E A K + + ++ +L +
Sbjct: 19 EAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEG-SHHHHHHMDVEGMTSLKVDN 77
Query: 109 VNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKI 168
+ Y TS LRR FE YG + + + ++ T + RG+AF+ + +RD A DG +
Sbjct: 78 LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 137
Query: 169 DGRRVLVDVERSR 181
DGR + V + R
Sbjct: 138 DGRELRVQMARYG 150
>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 = 64.6 bits (158), Expect = 3e-13
Identities = 18/90 (20%), Positives = 39/90 (43%), Gaps = 8/90 (8%)
Query: 95 NATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHER 154
++ M K LF+ + +E L + F +G ++++ K + YAFI ++
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERD 56
Query: 155 DMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
A + +GK ++G + + + K
Sbjct: 57 GAVKAMEEMNGKDLEGENIEIVFAKPPDQK 86
>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 = 64.7 bits (158), Expect = 3e-13
Identities = 22/114 (19%), Positives = 50/114 (43%), Gaps = 6/114 (5%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+ T + F +F+ ++ + + ++ F +G I +V + TGK +GY F+
Sbjct: 5 SSGQKKDTSNHFH-VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGP 203
+ ++ D +A + G+ + GR++ + + P T++ GP
Sbjct: 64 FFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP-----PAPKSTYESNTKQSGP 112
>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 = 66.1 bits (162), Expect = 3e-13
Identities = 17/73 (23%), Positives = 35/73 (47%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
L + + + ++ + R F G I+ +V +K+TG+ GY F+ Y +D A
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 163 ADGKKIDGRRVLV 175
+G ++ + + V
Sbjct: 64 LNGLRLQTKTIKV 76
Score = 50.6 bits (122), Expect = 8e-08
Identities = 18/68 (26%), Positives = 35/68 (51%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
L+++ + ++ +L + F YG I ++ ++VTG RG FI ++ + A K
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 164 DGKKIDGR 171
+G+K G
Sbjct: 151 NGQKPSGA 158
>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 = 63.8 bits (156), Expect = 4e-13
Identities = 19/94 (20%), Positives = 42/94 (44%), Gaps = 3/94 (3%)
Query: 88 WDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
+ + + PF LFI +N + S ++L+ + +V + TG R + +
Sbjct: 5 LEDPVEGSESTTPF-NLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGY 62
Query: 148 IEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
+++E D+ A + G K+ G + ++ + R
Sbjct: 63 VDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGR 95
>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 = 67.1 bits (163), Expect = 4e-13
Identities = 17/139 (12%), Positives = 44/139 (31%), Gaps = 2/139 (1%)
Query: 67 ERRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYG 126
R+ + + + ++ + L+I + + T++ L G
Sbjct: 34 APEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLG 93
Query: 127 P--IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
I +I N+ G+ +G+A + E +++ G+ +V + +
Sbjct: 94 VNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLS 153
Query: 185 GWLPRRLGGGLGGTRRGGP 203
+ + G G
Sbjct: 154 QFEMQSRKTTQSGQMSGEG 172
>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 = 64.3 bits (157), Expect = 5e-13
Identities = 29/116 (25%), Positives = 51/116 (43%), Gaps = 5/116 (4%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
D + LF+ V+ + +E + +F YG IK I + ++ TG +GY +
Sbjct: 10 DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLV 69
Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPD 204
EYE ++ +A + +G+ + G+ + VD R P + G R PD
Sbjct: 70 EYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG-----PPKGKRRGGRRRSRSPD 120
>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 = 63.5 bits (155), Expect = 5e-13
Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 8/83 (9%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIK--------KIVMVHNKVTGKPRGYAFIEYEHE 153
T+F+ + + + + F+ G IK I + ++ TGK +G A + ++
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 154 RDMHSAYKHADGKKIDGRRVLVD 176
+A DGK+ G + V
Sbjct: 74 PSAKAAIDWFDGKEFSGNPIKVS 96
>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 = 62.5 bits (153), Expect = 9e-13
Identities = 17/80 (21%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+++++ V+Y + +L F G + ++ ++ +K +G P+G+A+IE+ + + ++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 162 HADGKKIDGRRVLVDVERSR 181
D GR++ V +R+
Sbjct: 67 L-DESLFRGRQIKVIPKRTN 85
>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 = 63.1 bits (154), Expect = 9e-13
Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 3/89 (3%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
LFI ++ + E L+ FE +G I ++ ++ ++ TG +G AF+ Y A
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 164 DGKKI---DGRRVLVDVERSRTVKGWLPR 189
+K R + V S + G P
Sbjct: 76 HEQKTLPGMNRPIQVKPADSESRGGSGPS 104
>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 = 62.1 bits (152), Expect = 1e-12
Identities = 17/78 (21%), Positives = 36/78 (46%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
LF+ +N + + LR F+ + ++ + TG RGY F+ + + D +A
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 164 DGKKIDGRRVLVDVERSR 181
G+ ++GR + ++
Sbjct: 64 QGQDLNGRPLRINWAAKL 81
>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 = 62.2 bits (152), Expect = 1e-12
Identities = 16/84 (19%), Positives = 41/84 (48%)
Query: 98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMH 157
+ +F+ ++ + + + + F +G I +V + TGK +GY F+ + ++ D
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
Query: 158 SAYKHADGKKIDGRRVLVDVERSR 181
+A + G+ + GR++ + +
Sbjct: 63 NAIQQMGGQWLGGRQIRTNWATRK 86
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 63.2 bits (154), Expect = 1e-12
Identities = 27/88 (30%), Positives = 45/88 (51%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
P ++ +L + + Y TS LRR FE YG + + + ++ T + RG+AF+ + +
Sbjct: 40 PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 99
Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSR 181
RD A DG +DGR + V + R
Sbjct: 100 RDAEDAMDAMDGAVLDGRELRVQMARYG 127
>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 = 62.3 bits (152), Expect = 2e-12
Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 6/80 (7%)
Query: 97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDM 156
TM K L++ + TSE + +EF P + K R YAF+ + + D
Sbjct: 11 TMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHFSNREDA 64
Query: 157 HSAYKHADGKKIDGRRVLVD 176
A K +GK +DG + V
Sbjct: 65 VEAMKALNGKVLDGSPIEVT 84
>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 = 63.8 bits (156), Expect = 2e-12
Identities = 19/85 (22%), Positives = 37/85 (43%)
Query: 92 SFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
+ LFI + ++ +++ +GP+K +V + TG +GYAF EY
Sbjct: 85 PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 144
Query: 152 HERDMHSAYKHADGKKIDGRRVLVD 176
A +G ++ +++LV
Sbjct: 145 DINVTDQAIAGLNGMQLGDKKLLVQ 169
Score = 56.5 bits (137), Expect = 8e-10
Identities = 11/79 (13%), Positives = 29/79 (36%), Gaps = 6/79 (7%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVM-----VHNKVTGKPRGYAFIEYEHERDM 156
+ L++ + + +E + F + + V + + +AF+E+ +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 157 HSAYKHADGKKIDGRRVLV 175
A DG G+ + +
Sbjct: 65 TQAMA-FDGIIFQGQSLKI 82
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 61.0 bits (149), Expect = 3e-12
Identities = 13/70 (18%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
+FI +++ T++ LR F +G +K+ +++ + +T + RG+ F+ + + +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61
Query: 164 DGKKIDGRRV 173
++D + +
Sbjct: 62 SRHELDSKTI 71
>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 = 63.4 bits (155), Expect = 3e-12
Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 2/88 (2%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
+ LFI +N + S ++L+ + +V + TG R + ++++E
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESA 64
Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSR 181
D+ A + G K+ G + ++ + R
Sbjct: 65 EDLEKALE-LTGLKVFGNEIKLEKPKGR 91
Score = 61.9 bits (151), Expect = 1e-11
Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 5/94 (5%)
Query: 83 QEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKP 142
EI L P + + +TL ++++ +E +L+ FE +I +V GK
Sbjct: 81 NEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL---EIRLVSQ--DGKS 135
Query: 143 RGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD 176
+G A+IE++ E D + G +IDGR V +
Sbjct: 136 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 169
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 63.0 bits (153), Expect = 3e-12
Identities = 15/92 (16%), Positives = 40/92 (43%), Gaps = 2/92 (2%)
Query: 95 NATMDPFKTLFIARVNYDTSESKLRREFEVYGP--IKKIVMVHNKVTGKPRGYAFIEYEH 152
+ + +++ ++ T++ +L + G + ++ N+ G+ +GYA +
Sbjct: 49 SGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVAS 108
Query: 153 ERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
E +H + GK ++G +V V + +
Sbjct: 109 ENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140
>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 = 60.6 bits (148), Expect = 3e-12
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
+F+ ++ DT E K+R F +G ++ I + + T K RG+ FI ++ E + +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60
Query: 164 DGKKIDGRRV 173
+ +
Sbjct: 61 KYHNVGLSKC 70
>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 = 65.4 bits (160), Expect = 3e-12
Identities = 12/79 (15%), Positives = 31/79 (39%)
Query: 101 FKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
TL++ ++ +R + + + + + R +A+I+ + D
Sbjct: 117 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 176
Query: 161 KHADGKKIDGRRVLVDVER 179
+ +G KI+G ++ V
Sbjct: 177 EKLNGLKIEGYTLVTKVSN 195
Score = 56.1 bits (136), Expect = 3e-09
Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 3/81 (3%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
T+ + + +++K+ + F+ GPI + + + K +A IE+ +A
Sbjct: 43 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITK 100
Query: 163 ADGKKIDGRRVLVDVERSRTV 183
K + ++V T+
Sbjct: 101 -THKVVGQNEIIVSHLTECTL 120
Score = 53.1 bits (128), Expect = 4e-08
Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 3/83 (3%)
Query: 96 ATMDPFKTLFIARVNYD-TSESKLRREFEVYGPIKKI-VMVHNKVTGKPRGYAFIEYEHE 153
+ + + I ++ + E+ LR FE +G I+KI + K AF+ +E++
Sbjct: 205 SATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENK 264
Query: 154 RDMHSAYKHADGKKIDGRRVLVD 176
A + + + R + V
Sbjct: 265 DSAERALQ-MNRSLLGNREISVS 286
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 60.2 bits (147), Expect = 4e-12
Identities = 14/73 (19%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
+F+ ++ +T+ ++ FE +G + +++ +K T + RG+ F+ +E E + +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60
Query: 164 DGKKIDGRRVLVD 176
+I+ + V
Sbjct: 61 HFHEINNKMVECK 73
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 61.6 bits (150), Expect = 4e-12
Identities = 24/109 (22%), Positives = 41/109 (37%), Gaps = 11/109 (10%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIK--------KIVMVHNKVTGKPRGYAFIEYEHE 153
T+F+ + + + + F+ G IK I + ++ TGK +G A + ++
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGG 202
+A DGK+ G + V R R G G GG
Sbjct: 68 PSAKAAIDWFDGKEFSGNPIKVSFATRRADF---NRGGGNGRGGLEHHH 113
>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 = 62.5 bits (153), Expect = 5e-12
Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 2/94 (2%)
Query: 89 DPN-SFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
DP + P D +F+ + D + F +G I ++ +K TG+ RG+ F
Sbjct: 74 DPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGF 133
Query: 148 IEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
+ Y+ + ++ R++ + R
Sbjct: 134 VTYDSADAVDRVCQN-KFIDFKDRKIEIKRAEPR 166
Score = 61.8 bits (151), Expect = 8e-12
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+FI +N+DT+E LR F YG + + ++ + TG+ RG+ F+ +E + K
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 162 HADGKKIDGRRVLVDVERSR 181
+DG+ + R
Sbjct: 64 --TQHILDGKVIDPKRAIPR 81
>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 = 60.4 bits (147), Expect = 7e-12
Identities = 16/95 (16%), Positives = 41/95 (43%), Gaps = 2/95 (2%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNK-VTGKPRGYAF 147
+S + + + + ++ ++R F +G +K + + TG RG+ F
Sbjct: 3 SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62
Query: 148 IEYEHERDMHSAYKH-ADGKKIDGRRVLVDVERSR 181
+++ ++D A+ + GRR++++ S
Sbjct: 63 VDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSE 97
>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 = 60.3 bits (147), Expect = 8e-12
Identities = 22/88 (25%), Positives = 46/88 (52%), Gaps = 2/88 (2%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
++ K +F+ + ++ E++LR F+ +G + ++VM+++ +PRG+ FI +E E
Sbjct: 4 GSSGSKSNK-IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62
Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSR 181
+ + A I G++V V R
Sbjct: 63 QSVDQAVN-MHFHDIMGKKVEVKRAEPR 89
>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 59.9 bits (146), Expect = 8e-12
Identities = 18/96 (18%), Positives = 39/96 (40%), Gaps = 14/96 (14%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
LFI + + +E ++R FE YG + + ++ + Y F+ E + A +
Sbjct: 9 VKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIR 60
Query: 162 HADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGG 197
+ K+ G + V+ +++ + G G
Sbjct: 61 NLHHYKLHGVNINVEASKNK------SKASSGPSSG 90
>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 = 60.0 bits (146), Expect = 9e-12
Identities = 20/94 (21%), Positives = 36/94 (38%), Gaps = 6/94 (6%)
Query: 91 NSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
+S T LF+ + D +E ++R+ FE YG ++ + K +G+ FI
Sbjct: 5 SSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRL 58
Query: 151 EHERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
E A D + G+++ V
Sbjct: 59 ETRTLAEIAKVELDNMPLRGKQLRVRFACHSASL 92
>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 = 62.7 bits (153), Expect = 1e-11
Identities = 21/80 (26%), Positives = 40/80 (50%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
P+A P +L++ ++ D +E+ L +F GPI I + + +T + GYA++ ++
Sbjct: 8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 67
Query: 154 RDMHSAYKHADGKKIDGRRV 173
D A + I G+ V
Sbjct: 68 ADAERALDTMNFDVIKGKPV 87
Score = 45.3 bits (108), Expect = 7e-06
Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 6/94 (6%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYE 151
P+ +FI ++ L F +G I K+V +GY F+ +E
Sbjct: 96 PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV----CDENGSKGYGFVHFE 151
Query: 152 HERDMHSAYKHADGKKIDGRRVLVDVERSRTVKG 185
+ A + +G ++ R+V V +SR +
Sbjct: 152 TQEAAERAIEKMNGMLLNDRKVFVGRFKSRKERE 185
>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 = 59.1 bits (144), Expect = 2e-11
Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 2/80 (2%)
Query: 104 LFIARVNYDTSESKLRREFEVYGP--IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
L+I + + T++ L G I +I N+ G+ +G+A + E
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 162 HADGKKIDGRRVLVDVERSR 181
+++ G+ +V
Sbjct: 64 LLPKRELHGQNPVVTPSNKL 83
>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 = 59.2 bits (144), Expect = 2e-11
Identities = 19/93 (20%), Positives = 45/93 (48%), Gaps = 2/93 (2%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
+S + + K L ++ + + + LR+ F +G I + ++ N+ +G+ F+
Sbjct: 3 SGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFV 60
Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
+E+ D A + G ++GR++ V+ +R
Sbjct: 61 TFENSADADRAREKLHGTVVEGRKIEVNNATAR 93
>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 = 58.8 bits (143), Expect = 2e-11
Identities = 24/96 (25%), Positives = 40/96 (41%), Gaps = 14/96 (14%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
L + ++ + +LR +FE YGP+ + +V + YAF+ E D A +
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIR 62
Query: 162 HADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGG 197
D + G+R+ V + SR R G G
Sbjct: 63 GLDNTEFQGKRMHVQLSTSR------LRTASGPSSG 92
>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 = 59.6 bits (145), Expect = 2e-11
Identities = 12/80 (15%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+T+F ++ L F G ++ + ++ ++ + + +G A++E+ + + A
Sbjct: 26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 85
Query: 162 HADGKKIDGRRVLVDVERSR 181
G+++ G ++V ++
Sbjct: 86 -LTGQRLLGVPIIVQASQAE 104
>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 = 59.3 bits (144), Expect = 2e-11
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
+ + L+I + Y + ++ F YGPI++I + T + RG A++ YE D +
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKN 62
Query: 159 AYKHADGKKIDGRRVLVD 176
A H G + R ++V
Sbjct: 63 AVDHLSGFNVSNRYLVVL 80
>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 = 58.3 bits (142), Expect = 2e-11
Identities = 16/70 (22%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
+F+ +++DTS+ L+ F +G + + + TG+ RG+ FI ++ +
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-Q 72
Query: 164 DGKKIDGRRV 173
++DGR +
Sbjct: 73 KEHRLDGRVI 82
>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 = 59.0 bits (143), Expect = 3e-11
Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 4/78 (5%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHN--KVTGKPRGYAFIEYEHERDMHSAY 160
LFI + ++ E V+V+ K RG+AF+EYE R A
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 161 K--HADGKKIDGRRVLVD 176
+ ++ G ++ VD
Sbjct: 70 RKLMPGRIQLWGHQIAVD 87
>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 = 59.3 bits (144), Expect = 3e-11
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+++++ V+Y ++ L F G I +I ++ +K +G P+GYA+IE+ + +A
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Query: 162 HADGKKIDGRRVLVDVERSR 181
D GR + V +R+
Sbjct: 97 -MDETVFRGRTIKVLPKRTN 115
>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 = 58.8 bits (143), Expect = 3e-11
Identities = 23/86 (26%), Positives = 35/86 (40%), Gaps = 3/86 (3%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKP---RGYAFIEYEHERDM 156
LFI +N+ T+E L+ F G IK + K G+ F+EY+
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 157 HSAYKHADGKKIDGRRVLVDVERSRT 182
A K G +DG ++ V + T
Sbjct: 64 QKALKQLQGHTVDGHKLEVRISERAT 89
>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 = 61.2 bits (149), Expect = 3e-11
Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
+ + LFI ++++T++ LR FE +G + V++ + T + RG+ F+ Y ++ +
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70
Query: 159 AYKHADGKKIDGRRVLVDVERSR 181
A A K+DGR V SR
Sbjct: 71 AMN-ARPHKVDGRVVEPKRAVSR 92
Score = 60.4 bits (147), Expect = 5e-11
Identities = 25/112 (22%), Positives = 49/112 (43%), Gaps = 9/112 (8%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+S K +F+ + DT E LR FE YG I+ I ++ ++ +GK RG+AF+
Sbjct: 93 EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVT 152
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRG 201
++ + ++G +V ++ L ++ ++RG
Sbjct: 153 FDDHDSVDKIVIQ-KYHTVNGHN--CEVRKA------LSKQEMASASSSQRG 195
>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 = 58.7 bits (142), Expect = 3e-11
Identities = 15/98 (15%), Positives = 34/98 (34%), Gaps = 8/98 (8%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
+S + + + + + E+ L E +G I ++M+ K A +
Sbjct: 3 SGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALV 56
Query: 149 EYEHERDMHSAYKHADGKK--IDGRRVLVDVERSRTVK 184
E+E+ A I G++ + S+ +
Sbjct: 57 EFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRIT 94
>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 = 58.5 bits (142), Expect = 3e-11
Identities = 16/83 (19%), Positives = 34/83 (40%), Gaps = 1/83 (1%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYG-PIKKIVMVHNKVTGKPRGYAFIEYEH 152
+ + +L++ + E+ + R F G + + ++ N++TG P GY F+E+
Sbjct: 2 SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61
Query: 153 ERDMHSAYKHADGKKIDGRRVLV 175
+GK + G
Sbjct: 62 LATAEKCLHKINGKPLPGATPAK 84
>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 = 58.4 bits (142), Expect = 3e-11
Identities = 22/95 (23%), Positives = 42/95 (44%), Gaps = 14/95 (14%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+F+ V+ + +LR FE G + + +V + YAF+ E E D +A
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIA 61
Query: 162 HADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLG 196
+GK++ G+R+ V++ ++ G G
Sbjct: 62 QLNGKEVKGKRINVELSTKG------QKKSGPSSG 90
>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 = 58.4 bits (142), Expect = 3e-11
Identities = 18/90 (20%), Positives = 45/90 (50%), Gaps = 4/90 (4%)
Query: 92 SFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYE 151
S P + P T+F+ ++ E+++R F YG +K++ ++ ++ TG +GY F+ +
Sbjct: 1 SLPEGKIMP-NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY 58
Query: 152 HERDMHSAYKHADGKKIDGRRVLVDVERSR 181
++ D+ + G+++ + +
Sbjct: 59 NDVDVQKIVE--SQINFHGKKLKLGPAIRK 86
>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 = 58.4 bits (142), Expect = 3e-11
Identities = 16/93 (17%), Positives = 34/93 (36%), Gaps = 2/93 (2%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
+S + L + + + T+E L+ F +G + + + + TG +G+ F+
Sbjct: 3 SGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFV 62
Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
+ IDGR + S+
Sbjct: 63 RFTEYETQVKVMS--QRHMIDGRWCDCKLPNSK 93
>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 = 60.2 bits (147), Expect = 4e-11
Identities = 22/75 (29%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+ L++ ++ +E L++ F+V GPI I ++ +K K YAF+EY D + A +
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 162 HADGKKIDGRRVLVD 176
+GK+I+ V ++
Sbjct: 60 TLNGKQIENNIVKIN 74
Score = 49.8 bits (120), Expect = 1e-07
Identities = 18/84 (21%), Positives = 39/84 (46%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
++ D LF+ +N + + LR F+ + ++ + TG RGY F+ + +
Sbjct: 80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ 139
Query: 154 RDMHSAYKHADGKKIDGRRVLVDV 177
D +A G+ ++GR + ++
Sbjct: 140 DDAQNAMDSMQGQDLNGRPLRINW 163
>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 = 58.5 bits (142), Expect = 4e-11
Identities = 24/88 (27%), Positives = 36/88 (40%), Gaps = 3/88 (3%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
+++ + D + F YG I+ I + K +AF+E+E RD A
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVYG 80
Query: 163 ADGKKIDGRRVLVDVERSRTVKGWLPRR 190
DG DG R+ V+ RS G P
Sbjct: 81 RDGYDYDGYRLRVEFPRSGRGTGSGPSS 108
>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 = 58.0 bits (141), Expect = 5e-11
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 2/87 (2%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+S +TL++ ++ D +E + + F GP K M+ + Y F+E
Sbjct: 4 GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVE 61
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVD 176
+ RD +A +G+KI G+ V V+
Sbjct: 62 FYEHRDAAAALAAMNGRKILGKEVKVN 88
>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 = 59.9 bits (146), Expect = 5e-11
Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 8/91 (8%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKP--RGYAFIEYEHERDMHSAY 160
+F+ +V SE LR FE YG + +I ++ ++ P +G F+ + + A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 161 KHADGKKIDGRRVLV------DVERSRTVKG 185
K+ D E++ V+
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVED 95
Score = 47.6 bits (114), Expect = 9e-07
Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
LFI ++ +E+ +R F +G I++ ++ G RG AF+ + +A K
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 164 DGKKI 168
+
Sbjct: 157 HQAQT 161
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 58.5 bits (142), Expect = 5e-11
Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 4/78 (5%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
LFI + + +++ L F +G + K+ + +K T + + F+ +++ A K
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFI--DKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 162 HADGKKIDGRRVLVDVER 179
+G ++ +R+ V +++
Sbjct: 101 AMNGFQVGTKRLKVQLKK 118
>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 = 57.6 bits (140), Expect = 6e-11
Identities = 19/85 (22%), Positives = 42/85 (49%), Gaps = 1/85 (1%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
+ N+ D LF+ +++ T++ LR F YG + V++ +K T + RG+ F+
Sbjct: 4 GSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63
Query: 149 EYEHERDMHSAYKHADGKKIDGRRV 173
+++ + + + +DGR +
Sbjct: 64 KFKDPNCVGTVLA-SRPHTLDGRNI 87
>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 = 58.2 bits (141), Expect = 6e-11
Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 8/87 (9%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIK--------KIVMVHNKVTGKPRGYAFIEYEHER 154
+++ +N + L F+ G +K I + +K TGKP+G A + YE
Sbjct: 17 AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76
Query: 155 DMHSAYKHADGKKIDGRRVLVDVERSR 181
+A + DGK G ++ V + R +
Sbjct: 77 TAKAAVEWFDGKDFQGSKLKVSLARKK 103
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 57.7 bits (140), Expect = 8e-11
Identities = 15/78 (19%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
+FI +++ T++ LR F +G +K+ +++ + +T + RG+ F+ + + +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 86
Query: 164 DGKKIDGRRVLVDVERSR 181
++D + + V R
Sbjct: 87 SRHELDSKTIDPKVAFPR 104
>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 = 57.8 bits (140), Expect = 9e-11
Identities = 19/112 (16%), Positives = 39/112 (34%), Gaps = 1/112 (0%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+S I + + ++ + + E + V V G+ G A ++
Sbjct: 4 GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQ 63
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRG 201
+++E D + + KK++GR V V ++ G G G
Sbjct: 64 FKNEDDARKSER-LHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSSG 114
>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 = 57.5 bits (139), Expect = 1e-10
Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 9/92 (9%)
Query: 91 NSFPNATMDPFK-TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+SFP TL++ D + + LR F +G I + M PR AF+
Sbjct: 28 DSFPERRAPRKGNTLYVY--GEDMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVT 79
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
YE A +G +++ ++ V++ R +
Sbjct: 80 YEKMESADQAVAELNGTQVESVQLKVNIARKQ 111
>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 = 56.4 bits (137), Expect = 1e-10
Identities = 15/80 (18%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+ +++ + Y + +++ F +G + + +++++ T KP+G+ F+E + E + A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAIA 60
Query: 162 HADGKKIDGRRVLVDVERSR 181
D GR + V +
Sbjct: 61 KLDNTDFMGRTIRVTEANPK 80
>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 = 56.9 bits (138), Expect = 1e-10
Identities = 20/82 (24%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
A ++ L ++ +++ S++ ++ F +G +KK VH +G+ G A + +E + D
Sbjct: 24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKK-AAVHYDRSGRSLGTADVHFERKAD 82
Query: 156 MHSAYKHADGKKIDGRRVLVDV 177
A K +G +DGR + + +
Sbjct: 83 ALKAMKQYNGVPLDGRPMNIQL 104
>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 = 56.4 bits (137), Expect = 2e-10
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 5/86 (5%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPI---KKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
+FI ++ + E L F +G I KI+ + TG +GYAFI + +A
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMR--DPDTGNSKGYAFINFASFDASDAA 64
Query: 160 YKHADGKKIDGRRVLVDVERSRTVKG 185
+ +G+ + R + V + KG
Sbjct: 65 IEAMNGQYLCNRPITVSYAFKKDSKG 90
>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 = 55.7 bits (135), Expect = 2e-10
Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
TL++ + +E+ LR F +G I+ I +V + AFI++ + A +
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFATRQAAEVAAE 66
Query: 162 H-ADGKKIDGRRV 173
+ ++GRR+
Sbjct: 67 KSFNKLIVNGRRL 79
>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 = 56.1 bits (136), Expect = 2e-10
Identities = 18/98 (18%), Positives = 41/98 (41%), Gaps = 13/98 (13%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRRE----FEVYGPIKKIVMVHNKVTGKPRG 144
P + PN T++I +N + +L++ F +G I I++ + K RG
Sbjct: 2 VPETRPN------HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRG 52
Query: 145 YAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
AF+ ++ +A + G + + + ++ +
Sbjct: 53 QAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 90
>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 = 56.1 bits (136), Expect = 2e-10
Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 7/85 (8%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
L+I ++ + LR+ F + GYAF++Y + A +
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIE 62
Query: 162 HADGK-KIDGRRVLVDVERSRTVKG 185
GK ++ G+ + VD S+ ++
Sbjct: 63 TLSGKVELHGKIMEVDYSVSKKLRS 87
>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 = 56.6 bits (137), Expect = 2e-10
Identities = 18/80 (22%), Positives = 41/80 (51%), Gaps = 4/80 (5%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
LFI + + + L + F +G + K+ + +K T + + F+ Y++ +A +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFI--DKQTNLSKCFGFVSYDNPVSAQAAIQ 85
Query: 162 HADGKKIDGRRVLVDVERSR 181
+G +I +R+ V ++RS+
Sbjct: 86 SMNGFQIGMKRLKVQLKRSK 105
>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 = 56.5 bits (137), Expect = 2e-10
Identities = 23/92 (25%), Positives = 45/92 (48%), Gaps = 1/92 (1%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
P + F+ LFI ++++T+E LR +E +G + V++ + + + RG+ F+
Sbjct: 16 PLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 75
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
+ ++ +A A IDGR V +R
Sbjct: 76 FSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAR 106
>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 = 55.8 bits (135), Expect = 2e-10
Identities = 15/86 (17%), Positives = 33/86 (38%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+S ++ + + + + S ++ F Y I V + G P G A +
Sbjct: 4 GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLV 175
+E + +A + + I R+V +
Sbjct: 64 FESRDEATAAVIDLNDRPIGSRKVKL 89
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 55.8 bits (135), Expect = 3e-10
Identities = 14/79 (17%), Positives = 26/79 (32%), Gaps = 6/79 (7%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
T +I + + +E+ L F+ +G I +G FI+Y+
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKH------YPEKGCCFIKYDTHEQAAVCIVA 82
Query: 163 ADGKKIDGRRVLVDVERSR 181
GR + + R
Sbjct: 83 LANFPFQGRNLRTGWGKER 101
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 54.9 bits (133), Expect = 4e-10
Identities = 16/84 (19%), Positives = 39/84 (46%), Gaps = 8/84 (9%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKV---TGKPRGYAFIEYEHERDMHS 158
+F+ + +D + L+ +F G + ++ + GK +G +++E
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHV-----LYADIKMENGKSKGCGVVKFESPEVAER 63
Query: 159 AYKHADGKKIDGRRVLVDVERSRT 182
A + +G K+ GR + V ++R+ +
Sbjct: 64 ACRMMNGMKLSGREIDVRIDRNAS 87
>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 = 55.5 bits (134), Expect = 5e-10
Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 14/95 (14%)
Query: 103 TLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+FI +N +S + F YG + + +GYAF++Y +ER +A
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80
Query: 162 HADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLG 196
+G+ + G+ + +++ P R G G
Sbjct: 81 GENGRVLAGQTLDINMAGEPK-----PDRSGPSSG 110
>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 = 55.0 bits (133), Expect = 6e-10
Identities = 15/87 (17%), Positives = 33/87 (37%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+S ++ + + + + S ++ F Y I V + G P G A +
Sbjct: 4 GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVD 176
+E + +A + + I R+V +
Sbjct: 64 FESRDEATAAVIDLNDRPIGSRKVKLV 90
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 54.5 bits (132), Expect = 6e-10
Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 9/85 (10%)
Query: 98 MDPFKTLFIARVNY-DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDM 156
+ P LFI + + S+ L R F YG I +I + + FI++++ + +
Sbjct: 7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSV 58
Query: 157 HSAYKHADGKKIDGRRVLVDVERSR 181
A + + G++++++V S
Sbjct: 59 RDAIECESQEMNFGKKLILEVSSSN 83
>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 = 54.6 bits (132), Expect = 7e-10
Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 9/94 (9%)
Query: 92 SFPNATMDPFK-TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
S TL++ D + + LR F +G I + M PR AF+ Y
Sbjct: 5 SSGERRAPRKGNTLYVY--GEDMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTY 56
Query: 151 EHERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
E A +G +++ ++ V++ R + +
Sbjct: 57 EKMESADQAVAELNGTQVESVQLKVNIARKQPML 90
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 55.0 bits (133), Expect = 7e-10
Identities = 19/109 (17%), Positives = 36/109 (33%), Gaps = 8/109 (7%)
Query: 73 RAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIV 132
+ + + LF+ D ES+L F +GP+K++
Sbjct: 3 SSHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK 62
Query: 133 MVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSR 181
+ G+AF+E+E A + GK + + V +
Sbjct: 63 I--------LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP 103
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 54.6 bits (132), Expect = 9e-10
Identities = 18/83 (21%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
K L ++ + + + LR+ F +G I + ++ N+ +G+ F+ +E+ D
Sbjct: 27 SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADR 84
Query: 159 AYKHADGKKIDGRRVLVDVERSR 181
A + G ++GR++ V+ +R
Sbjct: 85 AREKLHGTVVEGRKIEVNNATAR 107
>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 = 54.7 bits (132), Expect = 1e-09
Identities = 19/87 (21%), Positives = 41/87 (47%), Gaps = 1/87 (1%)
Query: 96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
++ L ++ +++ S++ ++ F +G +KK V +G+ G A + +E D
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKK-AAVDYDRSGRSLGTADVHFERRAD 88
Query: 156 MHSAYKHADGKKIDGRRVLVDVERSRT 182
A K G +DGR + + + S+
Sbjct: 89 ALKAMKQYKGVPLDGRPMDIQLVASQI 115
>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 = 56.9 bits (137), Expect = 1e-09
Identities = 16/98 (16%), Positives = 39/98 (39%), Gaps = 6/98 (6%)
Query: 88 WDPNSFPNATMDPFKTLFIARVNYDT-SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYA 146
+ P L ++ +N + + L F VYG ++++ K+ + A
Sbjct: 21 MGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENA 75
Query: 147 FIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
++ A H +G K+ G+ + + + + + V+
Sbjct: 76 LVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQ 113
Score = 49.2 bits (117), Expect = 5e-07
Identities = 15/86 (17%), Positives = 24/86 (27%), Gaps = 4/86 (4%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
+ P TL ++ + SE L+ F G + K K R A I
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK----FFQKDRKMALI 194
Query: 149 EYEHERDMHSAYKHADGKKIDGRRVL 174
+ + A + L
Sbjct: 195 QMGSVEEAVQALIDLHNHDLGENHHL 220
>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 = 53.8 bits (130), Expect = 2e-09
Identities = 18/91 (19%), Positives = 35/91 (38%), Gaps = 1/91 (1%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
P T F+ + YD +E ++ F + + +G+ + E+E + SA
Sbjct: 14 PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73
Query: 160 YKHADGKKIDGRRVLVDVERSRTVKGWLPRR 190
+ + + +R+ VDV K P
Sbjct: 74 LS-LNEESLGNKRIRVDVADQAQDKDSGPSS 103
>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 = 53.7 bits (129), Expect = 2e-09
Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 103 TLFIARVNYDTSESKLRREFEV---YGPIKKIVMVHNKVTGK---PRGYAFIEYEHERDM 156
+F+ ++ ++ ++ + E +G I K+V+ ++ P A++ Y D
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76
Query: 157 HSAYKHADGKKIDGRRVLVD 176
A + + +DGR +
Sbjct: 77 LRAIQCVNNVVVDGRTLKAS 96
>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 = 52.7 bits (127), Expect = 3e-09
Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 9/79 (11%)
Query: 104 LFIARVNYDT-SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
LFI + S+ L R F YG I +I + + FI++++ + + A +
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEX 76
Query: 163 ADGKKIDGRRVLVDVERSR 181
+ G++++++V S
Sbjct: 77 ESQEMNFGKKLILEVSSSN 95
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 53.4 bits (128), Expect = 3e-09
Identities = 18/113 (15%), Positives = 39/113 (34%), Gaps = 7/113 (6%)
Query: 74 AEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRRE----FEVYGPIK 129
E A K E++ +P + + I +N + + KL+ G I
Sbjct: 2 KETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDIL 61
Query: 130 KIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
IV+ ++ G A+I + + + + G G +++ +
Sbjct: 62 DIVV---DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ 111
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 52.5 bits (126), Expect = 4e-09
Identities = 18/96 (18%), Positives = 30/96 (31%), Gaps = 5/96 (5%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
P S P +++ + D S L+R G + PR AF+
Sbjct: 7 GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-----LRLTWQGPRRRAFL 61
Query: 149 EYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
Y A G ++ + V + R + K
Sbjct: 62 HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRDK 97
>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 = 53.1 bits (128), Expect = 4e-09
Identities = 22/111 (19%), Positives = 41/111 (36%), Gaps = 1/111 (0%)
Query: 91 NSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
+S T+F+A ++Y KL+ F + G + + + GK RG + +
Sbjct: 5 SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVR-ADILEDKDGKSRGIGTVTF 63
Query: 151 EHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRG 201
E + A +G+ + R + V ++ KG G G
Sbjct: 64 EQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSSG 114
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 52.7 bits (127), Expect = 4e-09
Identities = 20/98 (20%), Positives = 43/98 (43%), Gaps = 8/98 (8%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
P T ++ + ++T + + F+ I+ + +V +K T K +G+ ++E++ + A
Sbjct: 14 PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA 72
Query: 160 YKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGG 197
DG + R + VD+ R + G G
Sbjct: 73 LT-YDGALLGDRSLRVDIAEGR------KQDKSGPSSG 103
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 52.3 bits (126), Expect = 4e-09
Identities = 14/92 (15%), Positives = 33/92 (35%), Gaps = 6/92 (6%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+++F++ ++L F +GP+ +VM +K +A +E +
Sbjct: 9 RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDVGAREAVLS 63
Query: 162 HADGKKIDGRRVLVDVERSRTVKGWLPRRLGG 193
+ G R+ V + + + G
Sbjct: 64 Q-SQHSLGGHRLRVRPREQKEFQSPASKSPKG 94
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation,
RNA-binding, EIF4G-binding translation; 1.90A {Homo
sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 52.6 bits (127), Expect = 5e-09
Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 6/82 (7%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
+FI ++ L F +G I K+V +GY F+ +E + A
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD----ENGSKGYGFVHFETQEAAERA 61
Query: 160 YKHADGKKIDGRRVLVDVERSR 181
+ +G ++ R+V V +SR
Sbjct: 62 IEKMNGMLLNDRKVFVGRFKSR 83
>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 = 55.7 bits (133), Expect = 6e-09
Identities = 16/93 (17%), Positives = 38/93 (40%), Gaps = 7/93 (7%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRRE----FEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
P T++I +N + +L++ F +G I I++ + K RG AF+
Sbjct: 2 AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVI 58
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
++ +A + G + + + ++ +
Sbjct: 59 FKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS 91
Score = 45.6 bits (107), Expect = 1e-05
Identities = 24/159 (15%), Positives = 47/159 (29%), Gaps = 5/159 (3%)
Query: 16 RDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAE 75
+ V + + PP +
Sbjct: 122 KKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIP 181
Query: 76 QVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVH 135
A +Q + P + P + P LF+ + +T+E L F + K++ +V
Sbjct: 182 PGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP 241
Query: 136 NKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL 174
+ AF+E+++E +A G KI +
Sbjct: 242 GR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAM 275
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 51.7 bits (124), Expect = 9e-09
Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 8/79 (10%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
+ I + E+ L + +GPI +V++ + A +E+E +A
Sbjct: 20 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNA 73
Query: 160 YKHADGK--KIDGRRVLVD 176
+A I G V+
Sbjct: 74 VNYAADNQIYIAGHPAFVN 92
>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 = 51.5 bits (124), Expect = 1e-08
Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 3/82 (3%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKI-VMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
L+I+ + E +L + +G + ++ + +G RG F E + H
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDS--SGTSRGVGFARMESTEKCEAVIGH 85
Query: 163 ADGKKIDGRRVLVDVERSRTVK 184
+GK I + K
Sbjct: 86 FNGKFIKTPPGVSAPTEPLLCK 107
>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 = 50.7 bits (122), Expect = 2e-08
Identities = 17/82 (20%), Positives = 33/82 (40%), Gaps = 1/82 (1%)
Query: 100 PFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSA 159
P T F+ + YD +E ++ F + + +G+ + E+E + SA
Sbjct: 18 PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 77
Query: 160 YKHADGKKIDGRRVLVDVERSR 181
+ + + RR+ VDV
Sbjct: 78 LS-LNEESLGNRRIRVDVADQA 98
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 52.5 bits (126), Expect = 2e-08
Identities = 21/115 (18%), Positives = 51/115 (44%), Gaps = 1/115 (0%)
Query: 68 RRRRERAEQVAYKLEQEIALWDPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGP 127
R + + + L+D ++ L ++ +++ S++ ++ F +G
Sbjct: 55 NRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGT 114
Query: 128 IKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
+KK + +++ +G+ G A + +E D A K G +DGR + + + S+
Sbjct: 115 LKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 168
>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 = 50.4 bits (121), Expect = 3e-08
Identities = 16/93 (17%), Positives = 33/93 (35%), Gaps = 6/93 (6%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
N + T++ + ++ +R+ F +G I +I + K GY+F+
Sbjct: 14 FEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVR 67
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
+ A +G I+G V +
Sbjct: 68 FSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP 100
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 50.1 bits (120), Expect = 3e-08
Identities = 10/75 (13%), Positives = 22/75 (29%), Gaps = 3/75 (4%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+ L I + L YG ++ V+ + Y + A
Sbjct: 16 RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQALD 72
Query: 162 HADGKKIDGRRVLVD 176
+G +++ + V
Sbjct: 73 KLNGFQLENFTLKVA 87
>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 = 49.9 bits (120), Expect = 4e-08
Identities = 15/91 (16%), Positives = 40/91 (43%), Gaps = 6/91 (6%)
Query: 96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHE 153
T L++ ++ + +LR+ F +G I K++M G+ +G+ F+ +
Sbjct: 10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME----GGRSKGFGFVCFSSP 65
Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSRTVK 184
+ A +G+ + + + V + + + +
Sbjct: 66 EEATKAVTEMNGRIVATKPLYVALAQRKEER 96
>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 = 51.8 bits (124), Expect = 4e-08
Identities = 16/84 (19%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 102 KTLFIARVNYDT-SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
L ++ +N + + L F VYG ++++ ++ NK + A ++ A
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAM 58
Query: 161 KHADGKKIDGRRVLVDVERSRTVK 184
H +G K+ G+ + + + + + V+
Sbjct: 59 SHLNGHKLHGKPIRITLSKHQNVQ 82
Score = 48.7 bits (116), Expect = 5e-07
Identities = 16/86 (18%), Positives = 25/86 (29%), Gaps = 4/86 (4%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
+ P TL ++ + SE L+ F G + K K K R A I
Sbjct: 108 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMALI 163
Query: 149 EYEHERDMHSAYKHADGKKIDGRRVL 174
+ + A + L
Sbjct: 164 QMGSVEEAVQALIDLHNHDLGENHHL 189
>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 = 49.8 bits (119), Expect = 4e-08
Identities = 14/96 (14%), Positives = 36/96 (37%), Gaps = 8/96 (8%)
Query: 91 NSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEY 150
+S P + L I ++ + +E+++ +G + I+M+ K AF+E
Sbjct: 5 SSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLEL 58
Query: 151 EHERDMHSAYKHADGKK--IDGRRVLVDVERSRTVK 184
E + + + + + + + +K
Sbjct: 59 ATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELK 94
>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 = 52.0 bits (124), Expect = 5e-08
Identities = 20/119 (16%), Positives = 44/119 (36%), Gaps = 6/119 (5%)
Query: 102 KTLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAY 160
L + ++ + ++ F +YG ++K+ + +K G A +E + A
Sbjct: 5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAI 59
Query: 161 KHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERER 219
H + + G+++ V V + + L G + N + S E + R
Sbjct: 60 THLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNR 118
Score = 50.5 bits (120), Expect = 1e-07
Identities = 7/87 (8%), Positives = 21/87 (24%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+ N P L + +E + G + + + +E
Sbjct: 112 EQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLE 171
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVD 176
++ + D + ++
Sbjct: 172 WDSKSDALETLGFLNHYQMKNPNGPYP 198
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 49.1 bits (117), Expect = 7e-08
Identities = 15/90 (16%), Positives = 37/90 (41%), Gaps = 8/90 (8%)
Query: 97 TMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDM 156
+ P + + I ++ D +E ++ +G + ++M+ K AFIE E
Sbjct: 12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAA 65
Query: 157 HSA--YKHADGKKIDGRRVLVDVERSRTVK 184
++ Y + + G+ + + + +K
Sbjct: 66 NTMVNYYTSVTPVLRGQPIYIQFSNHKELK 95
>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 = 49.0 bits (117), Expect = 8e-08
Identities = 8/75 (10%), Positives = 29/75 (38%), Gaps = 6/75 (8%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+ + T ++++ F +G + ++++ + A +E+ + A++
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFR 64
Query: 162 HADGKKIDGRRVLVD 176
H K + ++
Sbjct: 65 HLAYSKFHHVPLYLE 79
>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 = 48.4 bits (116), Expect = 9e-08
Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 7/73 (9%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
+F+ R D +E +LR F YG + + + R +AF+ + ++ S
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTFADDQIAQSLCG-- 60
Query: 164 DGKKIDGRRVLVD 176
+ I G V +
Sbjct: 61 EDLIIKGISVHIS 73
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 48.8 bits (116), Expect = 1e-07
Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 8/80 (10%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIK--KIVMVHNKVTGKPRGYAFIEYEHERDMH-- 157
+ +F+ + D E ++ F +GP+ +K P+GYAF+ ++ E +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 158 -SAYKHADGK---KIDGRRV 173
A DGK + +
Sbjct: 69 IDACLEEDGKLYLCVSSPTI 88
>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 = 48.4 bits (116), Expect = 1e-07
Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
LF+ +N SE + R F+ +G I + ++ G +G AF+++ + +A
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 164 DGKKI 168
G +
Sbjct: 77 HGSQT 81
>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 = 50.5 bits (121), Expect = 2e-07
Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 6/82 (7%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
T LF+ + D +E +R FE YG ++ + + RG+ FI E
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN------RDRGFGFIRLESR 68
Query: 154 RDMHSAYKHADGKKIDGRRVLV 175
A DG + R + +
Sbjct: 69 TLAEIAKAELDGTILKSRPLRI 90
Score = 44.7 bits (106), Expect = 2e-05
Identities = 27/161 (16%), Positives = 51/161 (31%), Gaps = 30/161 (18%)
Query: 99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKI-VMVHNKVTGKPRGYAFIEYEHERDMH 157
L + ++ S L + F +GP++K V+V + G+ G F+E+ +
Sbjct: 94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD--RGRATGKGFVEFAAKPPAR 151
Query: 158 SAYKHADGKKI----DGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGP---------D 204
A + R V+V+ + LP +L +
Sbjct: 152 KALERCGDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGT 211
Query: 205 VNLKHSGRE--------------DNERERERYRLERERELA 231
+++ R D + +LE E E A
Sbjct: 212 FEFEYASRWKALDEMEKQQREQVDRNIREAKEKLEAEMEAA 252
>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 = 47.6 bits (113), Expect = 3e-07
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 8/71 (11%)
Query: 100 PFKTLFIARVN--YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMH 157
++L +A S ++L E G + ++M NK Y+F Y +
Sbjct: 24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESK 77
Query: 158 SAYKHADGKKI 168
AY +GK++
Sbjct: 78 RAYVTLNGKEV 88
>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 = 47.6 bits (113), Expect = 3e-07
Identities = 15/91 (16%), Positives = 37/91 (40%), Gaps = 8/91 (8%)
Query: 96 ATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERD 155
+ P + + I ++ D +E ++ +G + ++M+ K AFIE E
Sbjct: 26 SAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEA 79
Query: 156 MHSA--YKHADGKKIDGRRVLVDVERSRTVK 184
++ Y + + G+ + + + +K
Sbjct: 80 ANTMVNYYTSVTPVLRGQPIYIQFSNHKELK 110
>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 = 47.1 bits (112), Expect = 7e-07
Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 5/88 (5%)
Query: 99 DPFKTLFIARVNYDTSESKLRREFEVYGPI-----KKIVMVHNKVTGKPRGYAFIEYEHE 153
+P +++ + E L+ F Y + + + G+ +G AFI +E
Sbjct: 43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNE 102
Query: 154 RDMHSAYKHADGKKIDGRRVLVDVERSR 181
+ A K A+G + G+ ++V RS
Sbjct: 103 KAAAKALKEANGYVLFGKPMVVQFARSA 130
>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 = 45.9 bits (109), Expect = 8e-07
Identities = 11/86 (12%), Positives = 32/86 (37%), Gaps = 1/86 (1%)
Query: 99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
+ + + + S+ ++ + F + + + G+ G AF+++ +
Sbjct: 13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEK 72
Query: 159 AYKHADGKKIDGRRVLVDVERSRTVK 184
A K ++I R + + V+
Sbjct: 73 ALKK-HKERIGHRYIEIFKSSRAEVR 97
>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 = 47.9 bits (113), Expect = 9e-07
Identities = 16/146 (10%), Positives = 41/146 (28%), Gaps = 2/146 (1%)
Query: 30 HEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQEIALWD 89
K G+ + + + T + + + E +E
Sbjct: 38 QIKLDEGWVPLEIMIKFNRLNRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLP 97
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+ ++++I D + ++ E G + I M +G F+
Sbjct: 98 EVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVV 156
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLV 175
++ + G+K +L+
Sbjct: 157 FDSIESAKKFVE-TPGQKYKETDLLI 181
>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 = 45.3 bits (108), Expect = 9e-07
Identities = 14/78 (17%), Positives = 31/78 (39%), Gaps = 7/78 (8%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
+F+ R D + +L++ F YG + + + R +AF+ + ++ S
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVF-----IPKPFRAFAFVTFADDKVAQSLCG-- 66
Query: 164 DGKKIDGRRVLVDVERSR 181
+ I G V + +
Sbjct: 67 EDLIIKGISVHISNAEPK 84
>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 = 44.6 bits (106), Expect = 2e-06
Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 3/87 (3%)
Query: 99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
T+ + ++ +E + P I +V N G GY F+++ +E ++
Sbjct: 8 TTCHTVKLRGAPFNVTEKNVMEFLAPLKP-VAIRIVRNA-HGNKTGYIFVDFSNEEEVKQ 65
Query: 159 AYKHADGKKIDGRRVLVDVERSRTVKG 185
A K + + + GR + V E+S G
Sbjct: 66 ALK-CNREYMGGRYIEVFREKSGPSSG 91
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 45.8 bits (108), Expect = 2e-06
Identities = 13/79 (16%), Positives = 29/79 (36%), Gaps = 4/79 (5%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
+ + + Y + L + F +G + KI+ + A ++Y A
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 86
Query: 164 DGKKIDGRRVLVDVERSRT 182
DG+ I + ++ S+
Sbjct: 87 DGQNIYNACCTLRIDFSKL 105
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 44.7 bits (106), Expect = 2e-06
Identities = 11/74 (14%), Positives = 27/74 (36%), Gaps = 2/74 (2%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
++++I D + ++ E G + I M +G F+ ++ +
Sbjct: 12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE 70
Query: 162 HADGKKIDGRRVLV 175
G+K +L+
Sbjct: 71 -TPGQKYKETDLLI 83
>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 = 44.3 bits (105), Expect = 3e-06
Identities = 7/84 (8%), Positives = 29/84 (34%), Gaps = 7/84 (8%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+ + + D++ ++ + Y + + + AF+ + +A +
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58
Query: 162 HADGKKIDGRRVLVDVERSRTVKG 185
G+ ++V ++ + +
Sbjct: 59 MFHQYSFRGKDLIVQLQPTDALLC 82
>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 = 45.9 bits (108), Expect = 3e-06
Identities = 13/79 (16%), Positives = 29/79 (36%), Gaps = 4/79 (5%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
+ + + Y + L + F +G + KI+ + A ++Y A
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 104
Query: 164 DGKKIDGRRVLVDVERSRT 182
DG+ I + ++ S+
Sbjct: 105 DGQNIYNACCTLRIDFSKL 123
>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 = 44.8 bits (106), Expect = 4e-06
Identities = 11/83 (13%), Positives = 32/83 (38%), Gaps = 1/83 (1%)
Query: 94 PNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHE 153
+ + +++ + ++ + F+ ++ + + GK G F+E+ +E
Sbjct: 18 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77
Query: 154 RDMHSAYKHADGKKIDGRRVLVD 176
D +A + + R + V
Sbjct: 78 ADYKAALCR-HKQYMGNRFIQVH 99
>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 = 44.0 bits (104), Expect = 5e-06
Identities = 15/108 (13%), Positives = 34/108 (31%), Gaps = 3/108 (2%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+ P + + + + E+ +R F + + ++ + G+ G ++
Sbjct: 5 SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDH-VGRNNGNGLVK 62
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGG 197
+ +D A K + + R V V R G G
Sbjct: 63 FLSPQDTFEALKR-NRMLMIQRYVEVSPATERQWVAAGGHITSGPSSG 109
>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 = 43.8 bits (103), Expect = 8e-06
Identities = 17/115 (14%), Positives = 38/115 (33%), Gaps = 5/115 (4%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRR---EFEVYGPIKKIVMVHNKVTGKPRGYA 146
+ + + + S ++ + ++ + + ++ + G+ G A
Sbjct: 6 SGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEA 64
Query: 147 FIEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRG 201
F+E E E D+ A K D + + R + V + L G G
Sbjct: 65 FVELESEDDVKLALKK-DRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSSG 118
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 43.9 bits (103), Expect = 8e-06
Identities = 16/95 (16%), Positives = 30/95 (31%), Gaps = 7/95 (7%)
Query: 90 PNSFPNATMDPFKTLFIARVN--YDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
+ K L ++ N Y + L G +++IV+ A
Sbjct: 12 RPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN-----GIQAM 66
Query: 148 IEYEHERDMHSAYKHADGKKIDGRRVLVDVERSRT 182
+E+E A +G I + +E +R
Sbjct: 67 VEFESVLCAQKAKAALNGADIYAGCCTLKIEYARP 101
>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 = 42.9 bits (101), Expect = 2e-05
Identities = 11/86 (12%), Positives = 31/86 (36%), Gaps = 1/86 (1%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+A + + + + ++ ++ + F + + + GK G AF++
Sbjct: 31 GRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQ 90
Query: 150 YEHERDMHSAYKHADGKKIDGRRVLV 175
+ + A ++I R + V
Sbjct: 91 FASQELAEKALGK-HKERIGHRYIEV 115
>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 = 46.0 bits (108), Expect = 2e-05
Identities = 37/285 (12%), Positives = 73/285 (25%), Gaps = 104/285 (36%)
Query: 4 FLPPNLLALFAPRDPVPYLP-PVEKLPHEKKTHG---YSGIAAFLNEFEDPKDTPPPTRV 59
P + +L YL + LP E T S IA + +
Sbjct: 298 LTPDEVKSLLLK-----YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLA---------- 342
Query: 60 ETREERLERRRRERAEQVAYKLEQEIALWDPNS----------FPNATMDPFKTLFIARV 109
+ + +++ +E + + +P FP + P L +
Sbjct: 343 -----TWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF 397
Query: 110 NYDTSE-----SKLRRE------------------FEVYGPIKKIVMVHNKVTGKPRGYA 146
+ S+ +KL + E+ ++ +H + Y
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDH---YN 454
Query: 147 FIEYEHERDM-----------HSAYKHADGKKIDG-----RRVLVDVERSRTVKGWLPRR 190
+ D+ H + H + R V +D +L ++
Sbjct: 455 IPKTFDSDDLIPPYLDQYFYSHIGH-HLKNIEHPERMTLFRMVFLDF-------RFLEQK 506
Query: 191 LGGGLGGTRRGGPDVNLKHSGRE-------------DNERERERY 222
+ R N S DN+ + ER
Sbjct: 507 I-------RHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERL 544
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 42.6 bits (100), Expect = 2e-05
Identities = 11/90 (12%), Positives = 32/90 (35%), Gaps = 4/90 (4%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIK---KIVMVHNKVTGKPRGY 145
+ + + + + + + ++ F + PI + ++ G+P G
Sbjct: 11 SNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGD 70
Query: 146 AFIEYEHERDMHSAYKHADGKKIDGRRVLV 175
AF+ + E +A + + R + +
Sbjct: 71 AFVLFACEEYAQNALRK-HKDLLGKRYIEL 99
>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 = 41.5 bits (97), Expect = 3e-05
Identities = 14/87 (16%), Positives = 37/87 (42%), Gaps = 7/87 (8%)
Query: 103 TLFIARVNYDTSESKLRRE----FEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
+ ++ ++Y S +L++ F +G +K + + + + A ++ E+ +D
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQDAIG 67
Query: 159 AYKHADGKKIDGRRVLVDVERSRTVKG 185
A KI +++LV + +
Sbjct: 68 AVNSLHRYKIGSKKILVSLATGASGPS 94
>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 = 41.6 bits (98), Expect = 3e-05
Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 3/91 (3%)
Query: 99 DPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHS 158
+ + + Y +E+ + F P++ V + G+ G A +E+ D +
Sbjct: 13 TTGHCVHMRGLPYRATENDIYNFFSPLNPMR--VHIEIGPDGRVTGEADVEFATHEDAVA 70
Query: 159 AYKHADGKKIDGRRVLVDVERSRTVKGWLPR 189
A D + R V + + + G P
Sbjct: 71 AMA-KDKANMQHRYVELFLNSTAGTSGSGPS 100
>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 = 41.9 bits (98), Expect = 4e-05
Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 3/88 (3%)
Query: 90 PNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVH--NKVTGKPRGYAF 147
+ + + + + S ++ VH G+ G AF
Sbjct: 33 GSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAF 92
Query: 148 IEYEHERDMHSAYKHADGKKIDGRRVLV 175
+E E D+ A K D + + R + V
Sbjct: 93 VELGSEDDVKMALKK-DRESMGHRYIEV 119
>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA
dependent ATPase, RNA helicase; HET: ANP; 1.91A
{Saccharomyces cerevisiae S288C}
Length = 579
Score = 44.4 bits (105), Expect = 4e-05
Identities = 14/92 (15%), Positives = 31/92 (33%)
Query: 187 LPRRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARSGSNDRER 246
+ RR LG +R + + + Y + + E++ + + +
Sbjct: 487 VSRRFLDKLGLSRSPIGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRGNKNYNNRSQNRD 546
Query: 247 ERERRRSRSRERKRRTSRSRSRDRRRRRSRER 278
+ RS +R SRS ++ R+
Sbjct: 547 YDDEPFRRSNNNRRSFSRSNDKNNYSSRNSNI 578
Score = 42.1 bits (99), Expect = 2e-04
Identities = 17/106 (16%), Positives = 32/106 (30%), Gaps = 2/106 (1%)
Query: 165 GKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDNERERERYRL 224
G ++ ++ + V R K L R G R + + + ++ +R
Sbjct: 475 GVLLNDPQLKIPVSRRFLDKLGLSRSPIGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRG 534
Query: 225 ERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDR 270
+ R RRS SR + SR+ +
Sbjct: 535 NKNYN--NRSQNRDYDDEPFRRSNNNRRSFSRSNDKNNYSSRNSNI 578
Score = 41.7 bits (98), Expect = 3e-04
Identities = 13/82 (15%), Positives = 24/82 (29%)
Query: 199 RRGGPDVNLKHSGREDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRER 258
P R+ + R+ + + + ++ +N + R
Sbjct: 497 LSRSPIGKAMFEIRDYSSRDGNNKSYDYDDDSEISFRGNKNYNNRSQNRDYDDEPFRRSN 556
Query: 259 KRRTSRSRSRDRRRRRSRERIR 280
R S SRS D+ SR
Sbjct: 557 NNRRSFSRSNDKNNYSSRNSNI 578
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 42.2 bits (98), Expect = 4e-05
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 6/32 (18%)
Query: 72 ERAEQVAYKLEQEIALWDPNSFP----NATMD 99
E+ Q KL+ + L+ +S P ATM+
Sbjct: 18 EK--QALKKLQASLKLYADDSAPALAIKATME 47
Score = 28.4 bits (62), Expect = 2.2
Identities = 6/13 (46%), Positives = 7/13 (53%), Gaps = 1/13 (7%)
Query: 10 LALFAPRDPVPYL 22
L L+A D P L
Sbjct: 29 LKLYAD-DSAPAL 40
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 40.0 bits (94), Expect = 1e-04
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 103 TLFIARVNYDTSESKLRREF-EVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYK 161
+LF+ + D + L F +VY + +V ++ TG +GY F+++ E + A
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALT 69
Query: 162 HADGKKIDGRR 172
G G +
Sbjct: 70 ECQGAVGLGSK 80
>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 = 39.1 bits (91), Expect = 2e-04
Identities = 17/80 (21%), Positives = 27/80 (33%), Gaps = 3/80 (3%)
Query: 98 MDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVH--NKVTGKPRGYAFIEYEHERD 155
+D + + + + + F +H GK RG A IE E E+D
Sbjct: 8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQD 67
Query: 156 MHSAYKHADGKKIDGRRVLV 175
+ A + R V V
Sbjct: 68 VQKA-LEKHRMYMGQRYVEV 86
>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 = 38.8 bits (90), Expect = 3e-04
Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 9/92 (9%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAF 147
P+ + + + + ++ + + S+S + + E YG IK +++ K AF
Sbjct: 13 KPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK------SQAF 66
Query: 148 IEYEHERDMHSAYKHADGK--KIDGRRVLVDV 177
IE E D + H K GR V VD+
Sbjct: 67 IEMETREDAMAMVDHCLKKALWFQGRCVKVDL 98
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin
subfragment 2, heavy meromyosin, essential light chain,
motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP:
i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 41.4 bits (97), Expect = 4e-04
Identities = 15/118 (12%), Positives = 50/118 (42%), Gaps = 1/118 (0%)
Query: 236 RARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRS 295
R + ++ E +R++ R++K + + E+ + + E +
Sbjct: 852 VTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEA 911
Query: 296 DRDRDRDRKRRRERENSEDRNERKRDRKERR-KERERNNEEREEKVFIKQEPVDDYQE 352
+ R R +++E E E + + +E R ++ + ++ ++++ +E +++ +
Sbjct: 912 EEMRVRLAAKKQELEEILHEMEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEA 969
Score = 32.9 bits (75), Expect = 0.20
Identities = 16/131 (12%), Positives = 51/131 (38%), Gaps = 1/131 (0%)
Query: 216 ERERERYRLERERELAGGPPRA-RSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRR 274
E E++ +L E+ L +A + E R R ++ +E + +R
Sbjct: 882 ELEQKHTQLCEEKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEE 941
Query: 275 SRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERERNNE 334
++++ + + + + + +++ + E + K+ + ++NN+
Sbjct: 942 RSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVTADGKIKKMEDDILIMEDQNNK 1001
Query: 335 EREEKVFIKQE 345
+E+ +++
Sbjct: 1002 LTKERKLLEER 1012
Score = 32.1 bits (73), Expect = 0.31
Identities = 13/109 (11%), Positives = 35/109 (32%), Gaps = 1/109 (0%)
Query: 245 ERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRD-DDIEEVEFRPKDRSDRDRDRDR 303
+R + + + E R + ++ E K+ +
Sbjct: 833 NVXHWPWMXLFFXIXPLLKVTRQEEEMQAKDEELQRTKERQQKAEAELKELEQKHTQLCE 892
Query: 304 KRRRERENSEDRNERKRDRKERRKERERNNEEREEKVFIKQEPVDDYQE 352
++ +E + E + +E R +E EE + + +++ +E
Sbjct: 893 EKNLLQEKLQAETELYAEAEEMRVRLAAKKQELEEILHEMEARIEEEEE 941
>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 = 37.9 bits (88), Expect = 6e-04
Identities = 10/65 (15%), Positives = 27/65 (41%), Gaps = 1/65 (1%)
Query: 112 DTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR 171
+ E E YG ++++ V + + G ++++ E D A + + +G+
Sbjct: 38 EFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96
Query: 172 RVLVD 176
+ +
Sbjct: 97 PIHAE 101
>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 = 38.7 bits (90), Expect = 7e-04
Identities = 13/85 (15%), Positives = 30/85 (35%), Gaps = 3/85 (3%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFI 148
+S + + + Y +E+ + F P++ V + G+ G A +
Sbjct: 34 SGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVR--VHIEIGPDGRVTGEADV 91
Query: 149 EYEHERDMHSAYKHADGKKIDGRRV 173
E+ + +A D + R +
Sbjct: 92 EFATHEEAVAAMSK-DRANMQHRYI 115
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 38.6 bits (89), Expect = 0.002
Identities = 15/101 (14%), Positives = 37/101 (36%), Gaps = 15/101 (14%)
Query: 89 DPNSFPNATMDPFKTLFIARVNYDTS---------ESKLRREFEVYGPIKKIVMVHNKVT 139
+ + KTL++ ++ + ES++R F G I +I V +K
Sbjct: 122 EDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK-- 179
Query: 140 GKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERS 180
F++++++ + A + + + +R
Sbjct: 180 ----NCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRR 216
>2j1d_G DAAM1, disheveled-associated activator of morphogenesis; actin
assembly, protein binding; 2.55A {Homo sapiens} PDB:
2z6e_A
Length = 483
Score = 37.6 bits (87), Expect = 0.006
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 2/78 (2%)
Query: 244 RERERERRRSRSR-ERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRD 302
+++E E RR+R + K + R R + + S E DD+ R + D+D +
Sbjct: 400 KKKEEEERRARMEAQLKEQRERERKMRKAKENSEESGEFDDLVS-ALRSGEVFDKDLSKL 458
Query: 303 RKRRRERENSEDRNERKR 320
++ R+ N + R+R
Sbjct: 459 KRNRKRITNQMTDSSRER 476
Score = 32.6 bits (74), Expect = 0.18
Identities = 16/80 (20%), Positives = 26/80 (32%), Gaps = 11/80 (13%)
Query: 212 REDNERERERYRLERERELAGGPPRARSGSNDRERE-----------RERRRSRSRERKR 260
R+ E E R R+E + + R + + E R K
Sbjct: 399 RKKKEEEERRARMEAQLKEQRERERKMRKAKENSEESGEFDDLVSALRSGEVFDKDLSKL 458
Query: 261 RTSRSRSRDRRRRRSRERIR 280
+ +R R ++ SRER
Sbjct: 459 KRNRKRITNQMTDSSRERPI 478
Score = 32.6 bits (74), Expect = 0.22
Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 3/79 (3%)
Query: 244 RERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDR 303
++ E ERR + K + R R + + S E DD+ + D+D +
Sbjct: 401 KKEEEERRARMEAQLKEQRERERKMRKAKENSEESGEFDDLVS---ALRSGEVFDKDLSK 457
Query: 304 KRRRERENSEDRNERKRDR 322
+R + + + R+R
Sbjct: 458 LKRNRKRITNQMTDSSRER 476
>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 = 35.2 bits (81), Expect = 0.006
Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 9/88 (10%)
Query: 91 NSFPNATMDPFKTLFIARVNYD-TSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIE 149
+S ++ + + I +L + E +G I ++++ AFIE
Sbjct: 5 SSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIE 58
Query: 150 YEHERDMHSAYKHADGK--KIDGRRVLV 175
D +A + + G+ V V
Sbjct: 59 MATTEDAQAAVDYYTTTPALVFGKPVRV 86
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 36.3 bits (83), Expect = 0.006
Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 6/83 (7%)
Query: 267 SRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSE-DRNERKRDRKER 325
++ R + E IR + E + K + D + RE ++ D E + + E+
Sbjct: 75 AQADRLTQEPESIR----KWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQ 130
Query: 326 RKERERNNEEREEKVFIKQEPVD 348
++ + NN ++ F +Q D
Sbjct: 131 VEKNKINNRIADKA-FYQQPDAD 152
Score = 30.1 bits (67), Expect = 0.86
Identities = 13/89 (14%), Positives = 31/89 (34%), Gaps = 17/89 (19%)
Query: 212 REDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRR 271
++ E R+ +R E+ + L D + + R + +K ++ + +
Sbjct: 81 TQEPESIRK-WREEQRKRLQ---------ELDAASKVMEQEWREKAKKDLEEWNQRQSEQ 130
Query: 272 RRRSRERIRDDDIEEVEFRPKDRSDRDRD 300
+++ R I + F D D
Sbjct: 131 VEKNKINNR---IADKAF----YQQPDAD 152
Score = 29.0 bits (64), Expect = 1.7
Identities = 9/66 (13%), Positives = 26/66 (39%), Gaps = 11/66 (16%)
Query: 294 RSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERERNNEEREEKVFIKQEPVDDYQEY 353
++DR R+ RE R + + D + E+E + +++ ++++
Sbjct: 76 QADRLTQEPESIRKWREEQRKRLQ-ELDAASKVMEQEWREKAKKD--------LEEW--N 124
Query: 354 DNYEDE 359
++
Sbjct: 125 QRQSEQ 130
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 35.2 bits (81), Expect = 0.007
Identities = 10/78 (12%), Positives = 25/78 (32%), Gaps = 3/78 (3%)
Query: 104 LFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHA 163
+ + + S L+ V+ T G +E+ E + A +
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVN---TRDFDGTGALEFPSEEILVEALERL 87
Query: 164 DGKKIDGRRVLVDVERSR 181
+ + G + V+ + +
Sbjct: 88 NNIEFRGSVITVERDDNP 105
>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 = 34.3 bits (79), Expect = 0.007
Identities = 11/79 (13%), Positives = 29/79 (36%), Gaps = 6/79 (7%)
Query: 102 KTLFIARVNYDTSESKLRREFEVYGPIKKIVM-----VHNKVTGKPRGYAFIEYEHERDM 156
+ L++ + + +E + F + + V + + +AF+E+ +
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 157 HSAYKHADGKKIDGRRVLV 175
A DG G+ + +
Sbjct: 67 TQAMA-FDGIIFQGQSLKI 84
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 34.0 bits (77), Expect = 0.014
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 5/53 (9%)
Query: 114 SESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGK 166
S+ L R + YG + +V+ K G A +E+ + A ++ G
Sbjct: 30 SKDVLLRLLQKYGEVLNLVLSSKK-----PGTAVVEFATVKAAELAVQNEVGL 77
>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex,
cytoplasm, ribonucleoprotein, structural protein; 3.50A
{Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A
Length = 861
Score = 36.3 bits (83), Expect = 0.015
Identities = 20/130 (15%), Positives = 41/130 (31%), Gaps = 12/130 (9%)
Query: 212 REDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRR 271
+ + +R + R ER+ + E E+ R+ E S +
Sbjct: 674 KHEAQRLEQEARGRLERQKI---------LDQSEAEKARKELLELEAMSMAVESTGNAKA 724
Query: 272 RRRSR---ERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKE 328
SR RI + + + + +R ++ E R + E K
Sbjct: 725 EAESRAEAARIEGEGSVLQAKLKAQALAIETEAELERVKKVREMELIYARAQLELEVSKA 784
Query: 329 RERNNEEREE 338
++ N E ++
Sbjct: 785 QQLANVEAKK 794
Score = 35.2 bits (80), Expect = 0.032
Identities = 15/129 (11%), Positives = 38/129 (29%), Gaps = 1/129 (0%)
Query: 212 REDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRR 271
+ +E E+ R L ++ + + E E R E ++ +++
Sbjct: 694 LDQSEAEKARKELLELEAMSMAVESTGNAKAEAESRAEAAR-IEGEGSVLQAKLKAQALA 752
Query: 272 RRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERER 331
E R + E+E ++ E + + + ++
Sbjct: 753 IETEAELERVKKVREMELIYARAQLELEVSKAQQLANVEAKKFKEMTEALGPGTIRDLAV 812
Query: 332 NNEEREEKV 340
E + K+
Sbjct: 813 AGPEMQVKL 821
Score = 30.9 bits (69), Expect = 0.75
Identities = 17/133 (12%), Positives = 42/133 (31%), Gaps = 4/133 (3%)
Query: 213 EDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRR 272
+ R+ + ++ E+ A + + E+E R R++ +S +
Sbjct: 647 DQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKILD----QSEAEKA 702
Query: 273 RRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERERN 332
R+ + + R + E + + + + E E ER
Sbjct: 703 RKELLELEAMSMAVESTGNAKAEAESRAEAARIEGEGSVLQAKLKAQALAIETEAELERV 762
Query: 333 NEEREEKVFIKQE 345
+ RE ++ +
Sbjct: 763 KKVREMELIYARA 775
Score = 30.5 bits (68), Expect = 0.95
Identities = 14/139 (10%), Positives = 38/139 (27%), Gaps = 1/139 (0%)
Query: 201 GGPDVNLKHSGREDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKR 260
G + R++ + + D+ +RS +
Sbjct: 605 GFEMSEDTGPDGTLLPKARDQAVFPQNGLVVSSVDVQSVEPVDQRTRDALQRSVQLAIEI 664
Query: 261 RTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKR 320
T+ + + + E+ +E + + +++ R ++ + + +
Sbjct: 665 TTNSQEAAAKHEAQRLEQEARGRLERQKILDQSEAEKAR-KELLELEAMSMAVESTGNAK 723
Query: 321 DRKERRKERERNNEEREEK 339
E R E R E
Sbjct: 724 AEAESRAEAARIEGEGSVL 742
>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM,
protein engineering, structural protein; HET: ADP; 2.80A
{Dictyostelium discoideum} SCOP: k.1.1.1
Length = 1010
Score = 33.9 bits (78), Expect = 0.084
Identities = 13/128 (10%), Positives = 39/128 (30%), Gaps = 3/128 (2%)
Query: 212 REDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRR 271
++ ++ R+ ++ E GSN+ +++ + + +S + +
Sbjct: 882 KKIAVLLQKYNRILKKLENWATTKSVYLGSNETGDSITAVQAKLKNLEAFDGECQSLEGQ 941
Query: 272 RRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERER 331
I + E + +D ++ + E ++ ER +
Sbjct: 942 SNSDLLSILA---QLTELNYNGVPELTERKDTFFAQQWTGVKSSAETYKNTLLAELERLQ 998
Query: 332 NNEEREEK 339
E+
Sbjct: 999 KIEDLHHH 1006
>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 = 31.7 bits (72), Expect = 0.085
Identities = 11/79 (13%), Positives = 24/79 (30%), Gaps = 7/79 (8%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
+ ++ + S L+ G + + + G +E+ + DM A +
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 69
Query: 163 ADGKKIDGRRVLVDVERSR 181
D K R +
Sbjct: 70 LDNTKFRSHEGETAYIRVK 88
>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 = 30.4 bits (69), Expect = 0.24
Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 4/58 (6%)
Query: 118 LRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 175
LR E +G I+K+++ P G A + + + + DG+ GR++
Sbjct: 43 LRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 96
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 32.4 bits (74), Expect = 0.25
Identities = 13/101 (12%), Positives = 30/101 (29%), Gaps = 4/101 (3%)
Query: 244 RERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEF--RPKDRSDRDRDR 301
R + + RE K + R R R + R + + + +
Sbjct: 851 GYLVRNKYQMMLREHKSIIIQKHVRGWLARVHYHRTLKAIVYLQCCYRRMMAKRELKKLK 910
Query: 302 DRKRRRE--RENSEDRNERKRDRKERRKERERNNEEREEKV 340
R E ++ + + + E+ + + EK+
Sbjct: 911 IEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKM 951
Score = 30.1 bits (68), Expect = 1.3
Identities = 12/123 (9%), Positives = 43/123 (34%)
Query: 218 ERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRE 277
+RE +L+ E + G ++ + +R+ + + + +
Sbjct: 903 KRELKKLKIEARSVERYKKLHIGLENKIMQLQRKIDEQNKEYKSLLEKMNNLEITYSTET 962
Query: 278 RIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERERNNEERE 337
D+E + ++ + + + ++ ++ + ++K + ++ E E
Sbjct: 963 EKLRSDVERLRMSEEEAKNATNRVLSLQEEIAKLRKELHQTQTEKKTIEEWADKYKHETE 1022
Query: 338 EKV 340
+ V
Sbjct: 1023 QLV 1025
>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 = 30.1 bits (68), Expect = 0.30
Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 118 LRREFEVYGPIKKIVMVHNK--VTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV 175
+R E YG +K I + V G F+E+ D A + G+K R V+
Sbjct: 32 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 91
>4dh9_Y YAEJ; ribosome, YAEJ, ribosome stalling, ribosome rescue, rescue F
alternative rescue factor, ARFB, release factor, rescue
of ribosomes; 3.20A {Escherichia coli} PDB: 2jy9_A
Length = 140
Score = 30.5 bits (69), Expect = 0.42
Identities = 18/85 (21%), Positives = 29/85 (34%), Gaps = 2/85 (2%)
Query: 246 RERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKR 305
S + RS++ R + R+ I+E+ K R R K
Sbjct: 58 AASHHLISSDGVIVIKAQEYRSQELNREAALARLVAM-IKELTTEKKARRPTRPTRASKE 116
Query: 306 RRERENSEDRNERKRDRKERRKERE 330
RR + ++ K R + R RE
Sbjct: 117 RR-LASKAQKSSVKAMRGKVRSGRE 140
>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 = 31.6 bits (71), Expect = 0.53
Identities = 21/106 (19%), Positives = 33/106 (31%), Gaps = 39/106 (36%)
Query: 50 PKDTPPPTRVETREERLERR-------RRERAEQVAYKLEQEIALWDPNSFPNATMDPFK 102
P + PP+ +E E E EQV + + N+ + K
Sbjct: 315 PNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKT----------NSHLPAGK 364
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRG-YAF 147
+ I+ VN G K +V V+G P+ Y
Sbjct: 365 QVEISLVN---------------GA-KNLV-----VSGPPQSLYGL 389
Score = 30.0 bits (67), Expect = 1.8
Identities = 18/81 (22%), Positives = 28/81 (34%), Gaps = 27/81 (33%)
Query: 233 GPPRARSGSNDRERER------ERRRSRSRERKRRTSRSRSRDRRR-------------R 273
GPP++ G N R+ ++ R ERK + S R
Sbjct: 381 GPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFS-------NRFLPVASPFHSHLLV 433
Query: 274 RSRERIRDDDIE-EVEFRPKD 293
+ + I D ++ V F KD
Sbjct: 434 PASDLINKDLVKNNVSFNAKD 454
>3obv_E Protein diaphanous homolog 1; autoinhibition, actin, nucleation,
cytoskeleton, structural; HET: SUC; 2.75A {Mus musculus}
PDB: 3o4x_E 2bap_D
Length = 457
Score = 30.6 bits (69), Expect = 0.78
Identities = 8/66 (12%), Positives = 26/66 (39%)
Query: 244 RERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDR 303
E+ R + ++ + K R + + R++ + E ++ + + + R R
Sbjct: 390 EEKMRRAKLAKEKAEKERLEKQQKREQLIDMNAEGDETGVMDSLLEALQSGAAFRRKRGP 449
Query: 304 KRRRER 309
++ +
Sbjct: 450 RQVNRK 455
Score = 28.3 bits (63), Expect = 4.6
Identities = 11/76 (14%), Positives = 26/76 (34%), Gaps = 9/76 (11%)
Query: 212 REDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRER---------KRRT 262
++N++ RE R +LA ++RE+ + + ++
Sbjct: 380 VKENQKRRETEEKMRRAKLAKEKAEKERLEKQQKREQLIDMNAEGDETGVMDSLLEALQS 439
Query: 263 SRSRSRDRRRRRSRER 278
+ R R R+ +
Sbjct: 440 GAAFRRKRGPRQVNRK 455
>4a0g_A Adenosylmethionine-8-amino-7-oxononanoate aminotransferase;
BIO3-BIO1, biotin synthesis; HET: PLP; 2.50A
{Arabidopsis thaliana} PDB: 4a0h_A* 4a0r_A* 4a0f_A*
Length = 831
Score = 30.7 bits (69), Expect = 1.0
Identities = 11/63 (17%), Positives = 19/63 (30%)
Query: 9 LLALFAPRDPVPYLPPVEKLPHEKKTHGYSGIAAFLNEFEDPKDTPPPTRVETREERLER 68
L + + PV LPPV K P + + ++ R+E +
Sbjct: 278 LTSYLRNKVPVLVLPPVPKDPSDDLIEWFVESDGVFKALKETMVLANLERLERLNGMAKL 337
Query: 69 RRR 71
Sbjct: 338 AGE 340
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 28.6 bits (64), Expect = 1.1
Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 1/67 (1%)
Query: 111 YDTSESKLRREFEVYGPIKKIVMVHNKVTGKP-RGYAFIEYEHERDMHSAYKHADGKKID 169
+ E + + E E YG + K V+ F+E+E A +G+
Sbjct: 23 DEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFG 82
Query: 170 GRRVLVD 176
GR V
Sbjct: 83 GRVVKAC 89
>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 = 28.5 bits (64), Expect = 1.2
Identities = 8/56 (14%), Positives = 20/56 (35%), Gaps = 4/56 (7%)
Query: 118 LRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV 173
+ E +G + I + N +G +++ +A G+ G+ +
Sbjct: 34 VIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMI 85
>3uwp_A Histone-lysine N-methyltransferase, H3 lysine-79; epigenetics,
tubercidin, structu genomics, structural genomics
consortium, SGC; HET: 5ID; 2.05A {Homo sapiens} PDB:
4eqz_A* 3sx0_A* 4er0_A* 4er7_A* 1nw3_A* 4er6_A* 4er5_A*
3qow_A* 3qox_A* 4er3_A* 3sr4_A*
Length = 438
Score = 30.2 bits (67), Expect = 1.3
Identities = 11/86 (12%), Positives = 27/86 (31%)
Query: 244 RERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDR 303
+ + R + R+R+ S+S + E + + +
Sbjct: 346 SLKNPKLREEQEAARRRQQRESKSNAATPTKGPEGKVAGPADAPMDSGAEEEKAGAATVK 405
Query: 304 KRRRERENSEDRNERKRDRKERRKER 329
K + + N++ R R++ R
Sbjct: 406 KPSPSKARKKKLNKKGRKMAGRKRGR 431
>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A
{Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A*
Length = 995
Score = 30.0 bits (68), Expect = 1.4
Identities = 13/124 (10%), Positives = 32/124 (25%), Gaps = 23/124 (18%)
Query: 245 ERERERRRSRS-------------RERKRRTSRSRSRDR--------RRRRSRERIRDDD 283
E ER +++S +++ D + ++
Sbjct: 751 EEERASEQTKSDYLKRANELVQWINDKQASLESRDFGDSIESVQSFMNAHKEYKKTEKPP 810
Query: 284 IEE--VEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERERNNEEREEKVF 341
+ E S + + R KR + ++ E+ + E
Sbjct: 811 KGQEVSELEAIYNSLQTKLRLIKREPFVAPAGLTPNEIDSTWSALEKAEQEHAEALRIEL 870
Query: 342 IKQE 345
+Q+
Sbjct: 871 KRQK 874
>1lxi_A Bone morphogenetic protein 7; cystine-knot growth factor,
hormone-growth factor complex; HET: NAG; 2.00A {Homo
sapiens} SCOP: g.17.1.2 PDB: 1lx5_A* 1bmp_A* 1m4u_L*
2qcw_A 2r53_A
Length = 139
Score = 28.8 bits (64), Expect = 1.6
Identities = 4/34 (11%), Positives = 14/34 (41%)
Query: 245 ERERERRRSRSRERKRRTSRSRSRDRRRRRSRER 278
++R + RS++ + + + + R+
Sbjct: 4 SKQRSQNRSKTPKNQEALRMANVAENSSSDQRQA 37
Score = 28.1 bits (62), Expect = 2.9
Identities = 4/41 (9%), Positives = 15/41 (36%)
Query: 241 SNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRD 281
+ ++R + R ++ + R + +R + +
Sbjct: 2 TGSKQRSQNRSKTPKNQEALRMANVAENSSSDQRQACKKHE 42
>1f5n_A Interferon-induced guanylate-binding protein 1; GBP, GTP
hydrolysis, GDP, GMP, dynamin related, large GTPase
family. GMPPNP, GPPNHP.; HET: GNP; 1.70A {Homo sapiens}
SCOP: a.114.1.1 c.37.1.8 PDB: 1dg3_A* 2b8w_A* 2b92_A*
2bc9_A* 2d4h_A*
Length = 592
Score = 29.5 bits (65), Expect = 1.7
Identities = 20/138 (14%), Positives = 48/138 (34%), Gaps = 1/138 (0%)
Query: 208 KHSGREDNERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRS 267
K + E R ++ E L S ++ + + + +E + ++ S
Sbjct: 439 KLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAES 498
Query: 268 RDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRK 327
+ E R ++ + +E + + + + K +R ER K + +
Sbjct: 499 AQASAKMLHEMQRKNE-QMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQ 557
Query: 328 ERERNNEEREEKVFIKQE 345
E+ ++E +K E
Sbjct: 558 EQLLKEGFQKESRIMKNE 575
>2r52_A BMP-6, bone morphogenetic protein 6; TGF-beta ligand,
chondrogenesis, cleavage on PAIR of basic residues,
cytokine, developmental protein; 2.50A {Homo sapiens}
Length = 143
Score = 28.8 bits (64), Expect = 1.7
Identities = 7/38 (18%), Positives = 16/38 (42%)
Query: 241 SNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRER 278
++ R R++ R+RS + + S + D +
Sbjct: 4 TSASSRRRQQSRNRSTQSQDVARVSSASDYNSSELKTA 41
Score = 28.1 bits (62), Expect = 2.9
Identities = 8/34 (23%), Positives = 15/34 (44%)
Query: 253 SRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEE 286
+ + R+R+ SR+RS + D + E
Sbjct: 4 TSASSRRRQQSRNRSTQSQDVARVSSASDYNSSE 37
Score = 27.7 bits (61), Expect = 4.0
Identities = 7/38 (18%), Positives = 15/38 (39%)
Query: 249 ERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEE 286
S R ++ R ++S+D R S +++
Sbjct: 3 PTSASSRRRQQSRNRSTQSQDVARVSSASDYNSSELKT 40
Score = 26.5 bits (58), Expect = 8.5
Identities = 5/35 (14%), Positives = 13/35 (37%)
Query: 247 ERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRD 281
R ++ + R+++S+ R S +
Sbjct: 3 PTSASSRRRQQSRNRSTQSQDVARVSSASDYNSSE 37
>4f3l_B BMAL1B; BHLH, PAS, circadian rhythm proteins,
transcription-activato; 2.27A {Mus musculus}
Length = 387
Score = 29.6 bits (66), Expect = 1.9
Identities = 9/31 (29%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 284 IEEVEFRPKDRSDRDRDRD-RKRRRERENSE 313
+E E + + ++ R+ KRRR++ NS
Sbjct: 1 MEYAEHQGRIKNAREAHSQIEKRRRDKMNSF 31
>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 = 28.2 bits (63), Expect = 1.9
Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 112 DTSESKLRREFEVYGPIKKIVMVHNKVTGKPR----GYAFIEYEHERDMHSAYKHADGKK 167
D E ++ E +G + ++++ K + F+E+ + H A + +G+
Sbjct: 36 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW 95
Query: 168 IDGRRVLV 175
GR+V+
Sbjct: 96 FAGRKVVA 103
>2x7l_M HIV REV; nuclear export, immune system, post-transcriptional
regulation; 3.17A {Human immunodeficiency virus type 3}
Length = 115
Score = 27.6 bits (62), Expect = 3.0
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 54 PPPTRVETREERLERRRRERAEQ 76
PPP TR+ R RRRR R Q
Sbjct: 26 PPPNPEGTRQARRNRRRRWRERQ 48
>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 = 27.5 bits (61), Expect = 3.2
Identities = 11/79 (13%), Positives = 24/79 (30%), Gaps = 7/79 (8%)
Query: 103 TLFIARVNYDTSESKLRREFEVYGPIKKIVMVHNKVTGKPRGYAFIEYEHERDMHSAYKH 162
+ ++ + S L+ G + + + G +E+ + DM A +
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 70
Query: 163 ADGKKIDGRRVLVDVERSR 181
D K R +
Sbjct: 71 LDNTKFRSHEGETAYIRVK 89
>1a0r_P Phosducin, MEKA, PP33; transducin, beta-gamma, signal transduction,
regulation, phosphorylation, G proteins, thioredoxin,
vision; HET: FAR; 2.80A {Bos taurus} SCOP: c.47.1.6 PDB:
1b9y_C 1b9x_C
Length = 245
Score = 28.5 bits (63), Expect = 3.4
Identities = 13/78 (16%), Positives = 25/78 (32%)
Query: 245 ERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRK 304
+ E E S + +K + S R + + + E+ + D + RK
Sbjct: 33 KLESEDSDSVAHSKKEILRQMSSPQSRDDKDSKERFSRKMSVQEYELIHKDKEDENCLRK 92
Query: 305 RRRERENSEDRNERKRDR 322
RR+ + R
Sbjct: 93 YRRQCMQDMHQKLSFGPR 110
>1nov_A Nodamura virus coat proteins; insect virus, icosahedral VIRU; 3.50A
{Nodamura virus} SCOP: b.121.4.4
Length = 355
Score = 28.3 bits (62), Expect = 3.7
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 241 SNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRER 278
S R R R + R++ R S R R RR R++
Sbjct: 3 SKAARRRRAAPRQQQRQQSNRASNQPRRRRARRTRRQQ 40
>3bbo_Q Ribosomal protein L18; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 161
Score = 27.4 bits (61), Expect = 4.5
Identities = 6/34 (17%), Positives = 12/34 (35%)
Query: 247 ERERRRSRSRERKRRTSRSRSRDRRRRRSRERIR 280
+ S + +R R R R R+++
Sbjct: 27 AKPLLPSFPIIEAKAKTRREDRTARHVRIRKKVE 60
>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 = 28.0 bits (63), Expect = 4.7
Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 9/77 (11%)
Query: 245 ERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRD-- 302
+ +RE +R+++ E + + ++ I++ +E P +D +
Sbjct: 16 KNKREEKRAQNSELRIKRAQEYDSSFPNWEFARMIKEFR-VTMECSPLTVTDPIEEHRIC 74
Query: 303 ---RKR---RRERENSE 313
RKR ++E E
Sbjct: 75 VCVRKRPLNKQELAKKE 91
>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS,
circadian rhythm proteins, transcription-activato; 2.27A
{Mus musculus}
Length = 361
Score = 28.0 bits (62), Expect = 4.9
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 288 EFRPKDRSDRDRDRDRKRRRERENSE 313
E R++ K+RR++ N
Sbjct: 5 EDDKDKAKRVSRNKSEKKRRDQFNVL 30
>4ffb_C Protein STU2; tubulin fold, heat repeats, cytoskeleton,
microtubule, tubul domain, hydrolase; HET: GTP; 2.88A
{Saccharomyces cerevisiae}
Length = 278
Score = 27.8 bits (61), Expect = 4.9
Identities = 7/38 (18%), Positives = 15/38 (39%)
Query: 46 EFEDPKDTPPPTRVETREERLERRRRERAEQVAYKLEQ 83
F D P +++ E+ E ++ E+ A+
Sbjct: 240 LFAKVGDEPSSSKMLFEWEKRELEKKRSQEEEAHHHHH 277
>3oqs_A Importin subunit alpha-2; importin alpha, karyopherin alpha,
nuclear localisation SIGN recognition, chloride
intracellular channel 4, CLIC4 NLS; 2.00A {Mus musculus}
PDB: 3rz9_A 3rzx_A 1q1s_C 1q1t_C 3tpo_A 3knd_A 1ejy_I
1iq1_C 1ejl_I 1pjn_B 1pjm_B 3q5u_A 3fey_C 3fex_C 1ial_A
1y2a_C 3btr_C 3l3q_A* 3ve6_A 2c1m_A ...
Length = 510
Score = 28.1 bits (62), Expect = 4.9
Identities = 4/52 (7%), Positives = 13/52 (25%)
Query: 297 RDRDRDRKRRRERENSEDRNERKRDRKERRKERERNNEEREEKVFIKQEPVD 348
R + +R + ++++ + Q V+
Sbjct: 5 HHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGSNQGTVN 56
Score = 27.7 bits (61), Expect = 6.5
Identities = 6/45 (13%), Positives = 14/45 (31%), Gaps = 3/45 (6%)
Query: 242 NDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEE 286
+ R + + + +R+ S + DDD +
Sbjct: 3 HHHHHSSGLVP---RGSGMKETAAAKFERQHMDSPDLGTDDDDKA 44
>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA
recognition motif, ATP-BIND helicase,
nucleotide-binding; 2.80A {Thermus thermophilus}
Length = 300
Score = 27.8 bits (62), Expect = 5.0
Identities = 14/100 (14%), Positives = 28/100 (28%), Gaps = 8/100 (8%)
Query: 230 LAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEF 289
L GG P RS E R ++ + R + + + ++ + +
Sbjct: 208 LLGGAPAERS---LLTGEEGWRTYKATGPRLSLPRLVALLKGQGLEVGKVAEAEGGFYVD 264
Query: 290 RPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKER 329
+ + R E + + RR R
Sbjct: 265 LRPEARPEVAGLRLEPARRVEGLL-----EIPSRTRRPAR 299
>1wa5_B Importin alpha subunit; nuclear transport/complex, nuclear
transport, exportin, RAN GTPase, protein transport; HET:
GTP; 2.0A {Saccharomyces cerevisiae} SCOP: a.118.1.1
PDB: 1un0_A 2c1t_A 1bk5_A 1ee5_A 1bk6_A 1ee4_A
Length = 530
Score = 28.1 bits (62), Expect = 5.3
Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 18/83 (21%)
Query: 258 RKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNE 317
+S S+ RR + F+ K R D + +RRR+ + E R
Sbjct: 3 NGTDSSTSKFVPEYRRTN-------------FKNKGRFSAD---ELRRRRDTQQVELRKA 46
Query: 318 RKRDR--KERRKERERNNEEREE 338
++ + K R + + +E
Sbjct: 47 KRDEALAKRRNFIPPTDGADSDE 69
>3l9w_A Glutathione-regulated potassium-efflux system Pro linker, ancillary
protein KEFF; potassium channel regulation, domains,
antiport; HET: FMN AMP GSH; 1.75A {Escherichia coli}
PDB: 3eyw_A* 3l9x_A*
Length = 413
Score = 27.8 bits (62), Expect = 6.0
Identities = 6/92 (6%), Positives = 20/92 (21%), Gaps = 2/92 (2%)
Query: 257 ERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSD--RDRDRDRKRRRERENSED 314
E + R R + + + +D + + DR+ +
Sbjct: 144 EARERADVFRRFNIQMVEEMAMVENDTKARAAVYKRTSAMLSEIITEDREHLSLIQRHGW 203
Query: 315 RNERKRDRKERRKERERNNEEREEKVFIKQEP 346
+ + + + +
Sbjct: 204 QGTEEGKHTGNMADEPETKPSSTSGGLVPRGS 235
>2trc_P Phosducin, MEKA, PP33; transducin, beta-gamma, signal transduction,
regulation, phosphorylation, G proteins, thioredoxin,
vision; 2.40A {Rattus norvegicus} SCOP: c.47.1.6
Length = 217
Score = 27.3 bits (60), Expect = 6.2
Identities = 13/81 (16%), Positives = 23/81 (28%)
Query: 242 NDRERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDR 301
+ E E S +K + S R + + + E+ + D
Sbjct: 17 RKFKLESEDGDSIPPSKKEILRQMSSPQSRDDKDSKERMSRKMSIQEYELIHQDKEDEGC 76
Query: 302 DRKRRRERENSEDRNERKRDR 322
RK RR+ + R
Sbjct: 77 LRKYRRQCMQDMHQKLSFGPR 97
>3s6p_A Capsid protein; coat protein, beta barrel, IG-like domain, IC
virus; 2.50A {Helicoverpa armigera stunt virus}
Length = 575
Score = 28.1 bits (61), Expect = 6.4
Identities = 10/39 (25%), Positives = 17/39 (43%)
Query: 245 ERERERRRSRSRERKRRTSRSRSRDRRRRRSRERIRDDD 283
+R RR +R+ T R +RRR+ ++ D
Sbjct: 9 QRPHNRRGTRNVRVSANTVTVNGRRNQRRRTGRQVSPPD 47
>1rqg_A Methionyl-tRNA synthetase; translation, dimerization, ligase; 2.90A
{Pyrococcus abyssi} SCOP: a.27.1.1 c.26.1.1 g.41.1.1
Length = 722
Score = 27.8 bits (62), Expect = 7.2
Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 2/78 (2%)
Query: 277 ERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKERRKERERNNEER 336
+++ DD I F + + + R + ED +++ E +
Sbjct: 546 KKVTDDQII--YFILNYMAKGNPEGARILLDKYYKREDVIRVAKEKFGDEAEVVLRRVYK 603
Query: 337 EEKVFIKQEPVDDYQEYD 354
+ K+ K+E + Y ++D
Sbjct: 604 DIKLKEKKEGKEMYVKFD 621
>2zjr_Z 50S ribosomal protein L32; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: g.41.8.5 PDB: 1j5a_M* 1jzy_M* 1jzz_M*
1k01_M* 1nkw_Z 1ond_Z* 1sm1_Z* 1yl3_5 2b66_5 2b9n_5
2b9p_5 2zjp_Y* 2zjq_Z 1jzx_M 3cf5_Y* 3dll_Y* 3pio_Z*
3pip_Z* 1nwy_Z* 1nwx_Z* ...
Length = 60
Score = 25.2 bits (56), Expect = 7.5
Identities = 8/17 (47%), Positives = 12/17 (70%), Gaps = 3/17 (17%)
Query: 259 KRRTSRSRSRDRRRRRS 275
K++TS+S+ R RRS
Sbjct: 8 KKKTSKSK---RDMRRS 21
>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate
hydrolases fold, S genomics, joint center for structural
genomics, JCSG; HET: MSE; 1.70A {Chloroflexus
aurantiacus}
Length = 193
Score = 27.2 bits (60), Expect = 7.8
Identities = 8/78 (10%), Positives = 18/78 (23%)
Query: 265 SRSRDRRRRRSRERIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDRNERKRDRKE 324
D R ++ I ++ +R R + R + D +
Sbjct: 87 RVDLDTERMQNLHTIAPFTPIQIRCVASGDVLVERILSRIAQGARHPGHCDDRSPADLEL 146
Query: 325 RRKERERNNEEREEKVFI 342
R + +
Sbjct: 147 VRSRGDIPPLPLGGPLLT 164
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR
family, hydrolase; 2.35A {Escherichia coli} SCOP:
b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A
Length = 644
Score = 27.5 bits (62), Expect = 8.4
Identities = 7/64 (10%), Positives = 17/64 (26%), Gaps = 15/64 (23%)
Query: 125 YGPIKKIVMVHNKVTGKPRGYAFIEYE-------HERDMHSAYKHADGKKIDGRRVLVDV 177
+ V +G+ F+E + M + G R++ +
Sbjct: 13 QQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKV--------MHGDRIIAVI 64
Query: 178 ERSR 181
+
Sbjct: 65 HSEK 68
>3hdx_A SUSD homolog, SUSD superfamily protein; NP_809182.1, structural
genomics, joint center for structural genomics, JCSG;
HET: MSE; 1.50A {Bacteroides thetaiotaomicron vpi-5482}
Length = 478
Score = 27.5 bits (61), Expect = 8.6
Identities = 12/35 (34%), Positives = 15/35 (42%)
Query: 198 TRRGGPDVNLKHSGREDNERERERYRLERERELAG 232
T RG +V+ K + E ER REL G
Sbjct: 392 TNRGLREVSFKKDFGNNRESLIAEIFEERRRELMG 426
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2
PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D*
2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D*
3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Length = 1524
Score = 27.4 bits (61), Expect = 9.3
Identities = 13/105 (12%), Positives = 33/105 (31%), Gaps = 1/105 (0%)
Query: 256 RERKRRTSRSRSRDRRRRRSRERIRDDDIE-EVEFRPKDRSDRDRDRDRKRRRERENSED 314
+ K ++R+ + E R+ + + D + + +E +
Sbjct: 135 LDPKGAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPG 194
Query: 315 RNERKRDRKERRKERERNNEEREEKVFIKQEPVDDYQEYDNYEDE 359
R R R E +++ + P+ + E + Y+
Sbjct: 195 VVSRLDGVALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPG 239
>2pk2_A Cyclin-T1, protein TAT; TAR, twinning, transcription regulation P-
TEFB, cell cycle; 2.67A {Homo sapiens} SCOP: a.74.1.1
a.74.1.1 PDB: 2w2h_C
Length = 358
Score = 27.1 bits (59), Expect = 9.3
Identities = 8/105 (7%), Positives = 26/105 (24%), Gaps = 5/105 (4%)
Query: 216 ERERERYRLERERELAGGPPRARSGSNDRERERERRRSRSRERKRRTSRSRSRDRRRRRS 275
E+ R + + ++ + + + +
Sbjct: 246 EKTPNRLKRIWNWRACEAAKKTKADDRGTDEKTSEQGGTGGGSGGGSGGGSGGGTSGGVP 305
Query: 276 RE-----RIRDDDIEEVEFRPKDRSDRDRDRDRKRRRERENSEDR 315
+ R + ++ F D RK+ ++R + +
Sbjct: 306 GQNTGGQEARPNYHCQLCFLRSLGIDYLDASLRKKNKQRLKAIQQ 350
>3v2d_5 50S ribosomal protein L32; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2hgq_4 2hgj_4 2hgu_4 2j03_5 2jl6_5 2jl8_5 2v47_5 2v49_5
2wdi_5 2wdj_5 2wdl_5 2wdn_5 2wh2_5 2wh4_5 2wrj_5 2wrl_5
2wro_5 2wrr_5 2x9s_5 2x9u_5 ...
Length = 60
Score = 24.9 bits (55), Expect = 9.6
Identities = 8/22 (36%), Positives = 13/22 (59%), Gaps = 3/22 (13%)
Query: 259 KRRTSRSRSRDRRRRRSRERIR 280
K++TS++R R RRS +
Sbjct: 8 KKKTSKAR---RDARRSHHALT 26
>2iwq_A Multiple PDZ domain protein; SGC, MPDZ, MUPP1, MUPP- 1, membrane,
HOST- interaction, structural genomics consortium,
synaptosome, T junction; 1.80A {Homo sapiens}
Length = 123
Score = 26.3 bits (58), Expect = 9.8
Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 2/61 (3%)
Query: 156 MHSAYKHADGKKIDGRRVLVDVERSRTVKGWLPRRLGGGLGGTRRGGPDVNLKHSGREDN 215
MH + H+ G + + + R V+ L R LG + GG + + S E
Sbjct: 1 MHHHHHHSSGVDLGTENLYFQSMQPRRVE--LWREPSKSLGISIVGGRGMGSRLSNGEVM 58
Query: 216 E 216
Sbjct: 59 R 59
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
0.315 0.135 0.389
Gapped
Lambda K H
0.267 0.0509 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,919,104
Number of extensions: 391440
Number of successful extensions: 2594
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2089
Number of HSP's successfully gapped: 497
Length of query: 363
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 268
Effective length of database: 4,049,298
Effective search space: 1085211864
Effective search space used: 1085211864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 58 (26.6 bits)