RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10362
(388 letters)
>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 = 157 bits (399), Expect = 5e-47
Identities = 41/104 (39%), Positives = 63/104 (60%), Gaps = 6/104 (5%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
YF +YG V D +MK+ TGRSRGFGF++F P++V V++ H LDG+ IDPK PR
Sbjct: 23 YFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT-QHILDGKVIDPKRAIPR 81
Query: 280 TLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
Q K+F+GG+ +V + FF+++G +++ +M
Sbjct: 82 DEQDKTG-----KIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLM 120
Score = 88.4 bits (220), Expect = 4e-21
Identities = 25/60 (41%), Positives = 36/60 (60%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
+FS++G +ID +M + +TG+SRGFGFVT+ + V V QN R I+ K PR
Sbjct: 107 FFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166
Score = 50.6 bits (122), Expect = 7e-08
Identities = 15/32 (46%), Positives = 23/32 (71%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+GGL + TE +LR +F +YG V ++ IM
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIM 36
>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 = 156 bits (397), Expect = 2e-46
Identities = 42/107 (39%), Positives = 65/107 (60%), Gaps = 1/107 (0%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ +F ++G + DCVVM++ T RSRGFGFVT+A V + PH +DGR ++PK
Sbjct: 31 RSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV 90
Query: 278 PRT-LQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
R Q+P + + K+F+GG+ + E LR +F +YGK+ + IM
Sbjct: 91 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 137
Score = 86.2 bits (214), Expect = 5e-20
Identities = 19/69 (27%), Positives = 36/69 (52%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
YF +YG++ +M + +G+ RGF FVTF D ++V ++ HT++G + + +
Sbjct: 124 YFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 183
Query: 280 TLQKPKKNS 288
+S
Sbjct: 184 QEMASASSS 192
Score = 53.8 bits (130), Expect = 1e-08
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ PK+ K+F+GGL T+ LR+ F ++G + + V+M
Sbjct: 5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVM 46
>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 = 112 bits (283), Expect = 7e-31
Identities = 34/68 (50%), Positives = 44/68 (64%), Gaps = 1/68 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ YF ++GEV +C+VM++ T RSRGFGFVTF D V V+ H LD +TIDPK
Sbjct: 43 REYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAF 102
Query: 278 PRTLQKPK 285
PR +PK
Sbjct: 103 PRR-AQPK 109
Score = 58.0 bits (141), Expect = 5e-11
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 263 PHTLDGRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
H + P+ SS K+F+GGL T+ LR +F ++G+V E ++
Sbjct: 6 HHHHHSSGLVPR--------GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLV 57
Query: 323 M 323
M
Sbjct: 58 M 58
>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 = 112 bits (283), Expect = 7e-31
Identities = 44/71 (61%), Positives = 54/71 (76%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ YFS+YGEV+DCV+MK+ T +SRGFGFV F DPN VG V+ + PHTLDGR IDPKPC
Sbjct: 34 RSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCT 93
Query: 278 PRTLQKPKKNS 288
PR +Q +S
Sbjct: 94 PRGMQPSGPSS 104
Score = 49.5 bits (119), Expect = 5e-08
Identities = 15/42 (35%), Positives = 26/42 (61%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+GGL + T+ LR++F++YG+V++ VIM
Sbjct: 8 MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIM 49
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 110 bits (278), Expect = 2e-30
Identities = 30/57 (52%), Positives = 39/57 (68%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
+ YF ++GEV +C+VM++ T RSRGFGFVTF D V V+ H LD +TIDPK
Sbjct: 18 REYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK 74
Score = 51.3 bits (124), Expect = 6e-09
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+GGL T+ LR +F ++G+V E ++M
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVM 33
>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 = 112 bits (281), Expect = 2e-30
Identities = 27/114 (23%), Positives = 49/114 (42%), Gaps = 9/114 (7%)
Query: 194 NPSGPSAGKPPADYS-------AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGF 246
SG + ++ Y T ++YF +G++ + VV+ + +TG+SRG+GF
Sbjct: 4 GSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGF 63
Query: 247 VTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPS 300
VT AD ++ +DGR + KP+ + + + G S
Sbjct: 64 VTMADRAAAERACKDPNPIIDGRKANVNLAYLG--AKPRSLQTGFAIGVSGPSS 115
Score = 52.7 bits (127), Expect = 6e-09
Identities = 15/47 (31%), Positives = 29/47 (61%)
Query: 277 NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ +K+++F K+F+GGLP + T+ LR +F +G + E V++
Sbjct: 4 GSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVI 50
>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 = 110 bits (276), Expect = 8e-30
Identities = 27/71 (38%), Positives = 43/71 (60%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ Y+ ++G++ DCVVM++ + RSRGFGFVTF+ V + PH++DGR ++PK
Sbjct: 45 RNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV 104
Query: 278 PRTLQKPKKNS 288
R +S
Sbjct: 105 AREESGSGPSS 115
Score = 52.3 bits (126), Expect = 9e-09
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+K ++ F K+F+GGL TE LR ++ ++GK+ + V+M
Sbjct: 19 RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVM 60
>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 = 108 bits (273), Expect = 2e-29
Identities = 27/71 (38%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ YFS +GEV+ V K+ +TG S+GFGFV F + V+ H +DGR D K N
Sbjct: 33 KEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCDCKLPN 91
Query: 278 PRTLQKPKKNS 288
+ Q +S
Sbjct: 92 SKQSQDSGPSS 102
Score = 51.1 bits (123), Expect = 2e-08
Identities = 11/40 (27%), Positives = 21/40 (52%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ + + GLP TE DL+ +F+ +G+V+ V +
Sbjct: 9 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVK 48
>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 = 106 bits (268), Expect = 6e-29
Identities = 29/57 (50%), Positives = 39/57 (68%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
+ YF+++GEV+DC + + TGRSRGFGF+ F D +V V+ H LDGR IDPK
Sbjct: 29 KDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPK 85
Score = 52.2 bits (126), Expect = 4e-09
Identities = 12/40 (30%), Positives = 24/40 (60%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K K+F+GGL + ++ DL+ +F ++G+V++ I
Sbjct: 5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIK 44
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 104 bits (262), Expect = 3e-28
Identities = 20/56 (35%), Positives = 33/56 (58%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
YF ++G+V D ++M + T R RGFGFVTF + V V + H ++ + ++ K
Sbjct: 18 HYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECK 73
Score = 55.6 bits (135), Expect = 2e-10
Identities = 13/32 (40%), Positives = 23/32 (71%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+GGL N T D++ +F ++GKV + ++M
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLM 32
>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 = 104 bits (261), Expect = 7e-27
Identities = 25/111 (22%), Positives = 45/111 (40%), Gaps = 10/111 (9%)
Query: 219 RYFSRYGEVIDCVVMKNNETG--RSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPC 276
F +YG V + V+++ +S+G FVTF L + P
Sbjct: 22 ELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN----ALHNMKVLPGMH 77
Query: 277 NPRTLQKP----KKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+P ++ K+F+G + TE D+R F+ +G++ E I+
Sbjct: 78 HPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRIL 128
Score = 59.2 bits (144), Expect = 1e-10
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQ--NCPHTLDG 268
+ FS +G++ +C +++ G SRG FVTF I+ + T++G
Sbjct: 113 RVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEG 164
Score = 48.8 bits (117), Expect = 4e-07
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+G +P +E DLR F +YG V E+ ++
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVL 36
>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 = 103 bits (258), Expect = 2e-26
Identities = 22/103 (21%), Positives = 40/103 (38%), Gaps = 4/103 (3%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ S D V+ + TG +R FG+V F ++ ++ + G I +
Sbjct: 31 KVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK 89
Query: 278 PRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEV 320
R KK + + L N+TE +L+ F ++ V
Sbjct: 90 GR---DSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV 129
Score = 49.5 bits (119), Expect = 2e-07
Identities = 9/57 (15%), Positives = 20/57 (35%), Gaps = 9/57 (15%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPC 276
F E+ ++ G+S+G ++ F + ++ G ID +
Sbjct: 119 VFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNLE----EKQGAEIDGRSV 166
Score = 46.4 bits (111), Expect = 2e-06
Identities = 7/45 (15%), Positives = 22/45 (48%)
Query: 283 KPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
+ ++++ +F+G L N + +L+ + ++ ++ RT
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT 50
>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 = 99.9 bits (250), Expect = 2e-26
Identities = 16/55 (29%), Positives = 28/55 (50%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
YF +GEV + +N+T + RGF F+TF + V +++ H + + K
Sbjct: 19 YFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIK 73
Score = 56.4 bits (137), Expect = 1e-10
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+GGL + E +R +F +G+V + +
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELP 32
>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 = 102 bits (256), Expect = 3e-26
Identities = 27/104 (25%), Positives = 52/104 (50%), Gaps = 4/104 (3%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
F GE+ C ++++ TG+S G+GFV + DP + I TL+G + K
Sbjct: 22 LFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN----TLNGLRLQTKTIKVS 77
Query: 280 TLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ + +++ GLP +T+ +L F++YG+++ I+
Sbjct: 78 YARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRIL 121
Score = 63.0 bits (154), Expect = 4e-12
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
FS+YG +I ++ + TG SRG GF+ F I+ L+G+
Sbjct: 109 FSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK----GLNGQKPS 156
Score = 43.3 bits (103), Expect = 3e-05
Identities = 7/32 (21%), Positives = 17/32 (53%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ + LP N+T+ + R+ F G++ ++
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLV 35
>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 = 99 bits (250), Expect = 4e-26
Identities = 22/69 (31%), Positives = 37/69 (53%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
YF ++G V + V++ + E R RGFGF+TF D +V + H + G+ ++ K PR
Sbjct: 30 YFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEPR 89
Query: 280 TLQKPKKNS 288
+ +S
Sbjct: 90 DSKSSGPSS 98
Score = 56.8 bits (138), Expect = 1e-10
Identities = 17/40 (42%), Positives = 26/40 (65%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
S K+F+GG+P N ET+LR +F ++G V EVV++
Sbjct: 4 GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMI 43
Score = 27.5 bits (62), Expect = 2.1
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 19 QVEIKKAEPRDASNKGNDMG 38
+VE+K+AEPRD+ + G G
Sbjct: 80 KVEVKRAEPRDSKSSGPSSG 99
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 103 bits (258), Expect = 6e-26
Identities = 19/111 (17%), Positives = 49/111 (44%), Gaps = 7/111 (6%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTID------ 272
F+ +G + + ++ T + +GF FV + P + ++ L GR I
Sbjct: 48 AFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN 107
Query: 273 PKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
P Q ++ +F ++++ + ++++ D+++ F +GK+ +
Sbjct: 108 IGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLA 158
Score = 64.6 bits (158), Expect = 3e-12
Identities = 12/73 (16%), Positives = 29/73 (39%), Gaps = 6/73 (8%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI----- 271
+ F +G++ + ++ TG+ +G+GF+ + + + + L G+ +
Sbjct: 143 KSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
Query: 272 DPKPCNPRTLQKP 284
P T P
Sbjct: 203 VTPPMPLLTPATP 215
Score = 40.8 bits (96), Expect = 3e-04
Identities = 7/44 (15%), Positives = 19/44 (43%)
Query: 280 TLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
Q+ + +V++G + + E +R F +G + + +
Sbjct: 18 AAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMS 61
>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 = 99.2 bits (248), Expect = 4e-25
Identities = 25/106 (23%), Positives = 48/106 (45%), Gaps = 4/106 (3%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
F G + C +M++ +TG S G+ FV F + I+ L+G T+ K
Sbjct: 21 YALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK----VLNGITVRNKRLK 76
Query: 278 PRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ ++ +++ LP +T+ L T F +YG +++ I+
Sbjct: 77 VSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 122
Score = 62.6 bits (153), Expect = 5e-12
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
F +YG ++ ++++ TGR RG FV + I L+ +
Sbjct: 110 FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS----ALNNVIPE 157
Score = 44.5 bits (106), Expect = 9e-06
Identities = 9/36 (25%), Positives = 17/36 (47%)
Query: 288 SSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+S + + LP ++T+ +L F G + IM
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIM 36
>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 = 98.5 bits (246), Expect = 8e-25
Identities = 14/109 (12%), Positives = 37/109 (33%), Gaps = 10/109 (9%)
Query: 220 YFSRYGEVIDCV-----VMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
+F+ + + + + + F F+ F + + DG +
Sbjct: 24 FFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-----FDGIIFQGQ 78
Query: 275 PCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
R + K+F+GGLP+ + + ++ +G + ++
Sbjct: 79 SLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLV 127
Score = 68.8 bits (169), Expect = 4e-14
Identities = 11/56 (19%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTIDPK 274
+ +G + ++K++ TG S+G+ F + D N I L + + +
Sbjct: 114 LLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 169
Score = 46.1 bits (110), Expect = 3e-06
Identities = 8/43 (18%), Positives = 19/43 (44%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITR 334
++++G +P +TE + FFN ++ + + A
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN 48
>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 = 90.0 bits (224), Expect = 1e-22
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 6/62 (9%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
Q++F +YGEV+D + K R F FVTFAD + + G ++
Sbjct: 29 QQFFCQYGEVVDVFIPK-----PFRAFAFVTFADDKVAQSLCGE-DLIIKGISVHISNAE 82
Query: 278 PR 279
P+
Sbjct: 83 PK 84
Score = 59.5 bits (145), Expect = 1e-11
Identities = 14/43 (32%), Positives = 24/43 (55%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+ KVF+G ++T +L+ FF +YG+V++V I P
Sbjct: 5 HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF 47
>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 = 87.7 bits (218), Expect = 1e-21
Identities = 18/75 (24%), Positives = 37/75 (49%), Gaps = 2/75 (2%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
+F+RYG V + ++ + TG S+G+GFV+F + +V ++++ G+ + P +
Sbjct: 29 FFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVES-QINFHGKKLKLGPAIRK 86
Query: 280 TLQKPKKNSSFPKVF 294
P +F
Sbjct: 87 QNLSTYHVQPRPLIF 101
Score = 58.0 bits (141), Expect = 5e-11
Identities = 19/44 (43%), Positives = 28/44 (63%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
P+ VF+GG+ + ET++R+FF RYG V EV I++ RT
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT 46
>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 = 91.7 bits (228), Expect = 2e-21
Identities = 23/104 (22%), Positives = 38/104 (36%), Gaps = 16/104 (15%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
F RYGE + + R RGFGF+ + LDG + +P R
Sbjct: 42 LFERYGEPSEVFIN------RDRGFGFIRLESRTLAEIAK----AELDGTILKSRPLRIR 91
Query: 280 TLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ + L V+ L F+++G V + V++
Sbjct: 92 FATHG------AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVV 129
Score = 64.7 bits (158), Expect = 4e-12
Identities = 22/96 (22%), Positives = 38/96 (39%), Gaps = 1/96 (1%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
FS++G V VV+ + + GR+ G GFV FA ++ C T P+P
Sbjct: 116 AFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE 174
Query: 280 TLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYG 315
+++ P+ + E + F + G
Sbjct: 175 PMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPG 210
Score = 53.9 bits (130), Expect = 2e-08
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 268 GRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
G TID K K + ++F+G LP+++TE D + F RYG+ EV I
Sbjct: 3 GFTIDIKSFLKPG---EKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN 55
>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 = 86.5 bits (215), Expect = 2e-21
Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ +FS+YG+V+D + K R F FVTFAD + + G ++
Sbjct: 23 REFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAE 76
Query: 278 PRTLQKPKKNS 288
P+ +S
Sbjct: 77 PKHNSNSGPSS 87
Score = 59.2 bits (144), Expect = 2e-11
Identities = 17/40 (42%), Positives = 25/40 (62%)
Query: 287 NSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+S VF+G ++TE +LR FF++YG VM+V I P
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF 41
Score = 29.9 bits (68), Expect = 0.29
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 19 QVEIKKAEPRDASNKGNDMG 38
V I AEP+ SN G G
Sbjct: 69 SVHISNAEPKHNSNSGPSSG 88
>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 = 89.3 bits (222), Expect = 2e-20
Identities = 18/110 (16%), Positives = 37/110 (33%), Gaps = 14/110 (12%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTI-----DPK 274
+G + C ++ + TG+S+G+GF + ++ + L RT+ D
Sbjct: 116 VRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAG 175
Query: 275 PCNPRTLQKPKKNSSFPKVFLGGLPSNVTETD-LRTFFNRYGKVMEVVIM 323
P L + + + LP + D L + +
Sbjct: 176 QLTPALLH--SRC-----LCVDRLPPGFNDVDALCRALSAVHSPTFCQLA 218
Score = 68.9 bits (169), Expect = 2e-13
Identities = 13/103 (12%), Positives = 30/103 (29%), Gaps = 17/103 (16%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPRT 280
S Y + C V + +G FVT + I + +
Sbjct: 43 LSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAIN----AFHQSRLREREL---- 87
Query: 281 LQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ + + + LP ++T+ +G + ++
Sbjct: 88 --SVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLV 128
Score = 56.9 bits (138), Expect = 2e-09
Identities = 9/58 (15%), Positives = 17/58 (29%), Gaps = 5/58 (8%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
R S C + + G+ +GF + + Q DG ++
Sbjct: 203 CRALSAVHSPTFCQLACG-QDGQLKGFAVLEYETAEMAEEAQQQ----ADGLSLGGSH 255
Score = 43.8 bits (104), Expect = 4e-05
Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 6/59 (10%)
Query: 271 IDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
+DP+ R ++ + K+ + GLP +VT ++ + Y + +
Sbjct: 3 LDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE------LKYCFVDK 55
>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 = 85.8 bits (213), Expect = 4e-19
Identities = 17/107 (15%), Positives = 40/107 (37%), Gaps = 4/107 (3%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTIDPKPCNPR 279
V + + + SR F ++ + ++ ++G T+ K NP
Sbjct: 138 LQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPL 197
Query: 280 TLQKPKKNSSFP--KVFLGGLPSNVT-ETDLRTFFNRYGKVMEVVIM 323
K +++ ++ + L + + E LR F +G + ++ I
Sbjct: 198 EKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIP 244
Score = 76.2 bits (188), Expect = 7e-16
Identities = 16/109 (14%), Positives = 33/109 (30%), Gaps = 15/109 (13%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
YF G +I V ++ F + FA + I + I
Sbjct: 61 YFKHCGPIIHVDVAD--SLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSH---- 114
Query: 280 TLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKV-MEVVIMSPRT 327
+ +++ P + T+ ++R V + + + S R
Sbjct: 115 --------LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF 155
Score = 57.3 bits (139), Expect = 2e-09
Identities = 6/59 (10%), Positives = 20/59 (33%), Gaps = 6/59 (10%)
Query: 218 QRYFSRYGEVIDCVVMKN-NETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
+ F +G + + E + F+ F + ++ +Q ++ + +
Sbjct: 229 RESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-----MNRSLLGNRE 282
Score = 48.4 bits (116), Expect = 2e-06
Identities = 13/84 (15%), Positives = 26/84 (30%), Gaps = 11/84 (13%)
Query: 241 SRGFGFVTFADPNNVGVVIQNCPHTLD-GRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLP 299
S +G D LD G + + + +N V + LP
Sbjct: 1 SMEYGHHARPDSK----------RPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLP 50
Query: 300 SNVTETDLRTFFNRYGKVMEVVIM 323
+ + + +F G ++ V +
Sbjct: 51 KSYNQNKVYKYFKHCGPIIHVDVA 74
>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 = 83.2 bits (206), Expect = 6e-19
Identities = 15/124 (12%), Positives = 40/124 (32%), Gaps = 20/124 (16%)
Query: 220 YFSRYGEVIDCV-----VMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID-- 272
+F+ + + + + + F F+ F + + G+++
Sbjct: 24 FFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIR 83
Query: 273 -PKPCNPRTLQKPKKNSSFP------------KVFLGGLPSNVTETDLRTFFNRYGKVME 319
P P + P K+F+GGLP+ + + ++ +G +
Sbjct: 84 RPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKA 143
Query: 320 VVIM 323
++
Sbjct: 144 FNLV 147
Score = 64.7 bits (158), Expect = 2e-12
Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 4/69 (5%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
+ +G + ++K++ TG S+G+ F + D N I L+G + K +
Sbjct: 134 LLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA----GLNGMQLGDKKLLVQ 189
Query: 280 TLQKPKKNS 288
KN+
Sbjct: 190 RASVGAKNA 198
Score = 42.3 bits (100), Expect = 9e-05
Identities = 8/43 (18%), Positives = 19/43 (44%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITR 334
++++G +P +TE + FFN ++ + + A
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN 48
>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 = 78.4 bits (194), Expect = 3e-18
Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTIDPKPC 276
++ FS+YG++ + VV+K+ ET RSRGFGFVTF + ++ + ++DGR I
Sbjct: 30 EQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA 89
Query: 277 NPRTLQKPKKNS 288
+ + +S
Sbjct: 90 GKSSDNRSGPSS 101
Score = 46.1 bits (110), Expect = 8e-07
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
K+F+GGL + E L F++YG++ EVV++ R
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR 48
>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 = 80.0 bits (198), Expect = 1e-17
Identities = 21/105 (20%), Positives = 42/105 (40%), Gaps = 6/105 (5%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPC--NP 278
FS G ++ V ++ T RS G+ +V F P + + T++ I KP
Sbjct: 36 FSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD----TMNFDVIKGKPVRIMW 91
Query: 279 RTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ S +F+ L ++ L F+ +G ++ ++
Sbjct: 92 SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV 136
Score = 56.1 bits (136), Expect = 2e-09
Identities = 18/100 (18%), Positives = 39/100 (39%), Gaps = 14/100 (14%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP--CNP 278
FS +G ++ C V+ + S+G+GFV F I+ ++G ++ +
Sbjct: 124 FSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEK----MNGMLLNDRKVFVGR 177
Query: 279 RTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVM 318
+K ++ LG D+ + G+++
Sbjct: 178 FKSRKEREAE------LGARAKEFYPYDVPDYAGSSGRIV 211
Score = 32.3 bits (74), Expect = 0.16
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+++G L +VTE L F+ G ++ + +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVC 48
>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 = 78.3 bits (194), Expect = 2e-17
Identities = 21/108 (19%), Positives = 47/108 (43%), Gaps = 7/108 (6%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPC- 276
++YF G + + +M + + ++ + FV + ++ + +Q TL+G+ I+
Sbjct: 18 KQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQ----TLNGKQIENNIVK 72
Query: 277 -NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
N + + +F+G L NV + LR F + + +M
Sbjct: 73 INWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVM 120
Score = 59.8 bits (146), Expect = 4e-11
Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
F + + VM + +TG SRG+GFV+F ++ + ++ G+ ++ +P
Sbjct: 108 FKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD----SMQGQDLNGRP 158
Score = 34.4 bits (80), Expect = 0.026
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
+++G L +TE L+ +F G + + IM +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN 37
>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 = 76.2 bits (188), Expect = 2e-17
Identities = 16/75 (21%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTIDPKPC 276
+ F ++G + + +++K+ T +SRGF F+TF +P + ++ +L G+ I +
Sbjct: 25 KAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA 83
Query: 277 NPRTLQKPKKNSSFP 291
+ Q +
Sbjct: 84 KKPSFQSGGRRRPPA 98
Score = 49.2 bits (118), Expect = 9e-08
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
K+F+GGL E L+ F ++G + EV+++ RT +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSK 46
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 74.3 bits (183), Expect = 8e-17
Identities = 18/69 (26%), Positives = 26/69 (37%), Gaps = 5/69 (7%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
YF +G V V+ K + G F V D V+ H+L G + +P +
Sbjct: 28 YFLAFGPVASVVMDK--DKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQK 82
Query: 280 TLQKPKKNS 288
Q P S
Sbjct: 83 EFQSPASKS 91
Score = 52.7 bits (127), Expect = 3e-09
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
VF+ G P V L +F +G V VV+
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMD 41
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 73.8 bits (181), Expect = 5e-16
Identities = 24/121 (19%), Positives = 46/121 (38%), Gaps = 6/121 (4%)
Query: 169 QNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYS---AYGTYAQYQQRYFSRYG 225
Q+ P P+ P + A Y ++ T Q + G
Sbjct: 21 QSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIG 80
Query: 226 --EVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTIDPKPCNPRTLQ 282
+V++ +N G+S+G+ V A N+V +++ P L+G +D +P + L
Sbjct: 81 VYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140
Query: 283 K 283
+
Sbjct: 141 Q 141
Score = 35.3 bits (81), Expect = 0.011
Identities = 12/79 (15%), Positives = 23/79 (29%), Gaps = 15/79 (18%)
Query: 263 PHTLDGRTIDPKPCNPRTLQKPKKNSS-------------FPKVFLGGLPSNVTETDLRT 309
L ++++P P + N + V++G T+ L
Sbjct: 15 TENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQ 74
Query: 310 FFNRYG--KVMEVVIMSPR 326
G V+E+ R
Sbjct: 75 VIRSIGVYDVVELKFAENR 93
>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 = 72.4 bits (178), Expect = 5e-16
Identities = 13/76 (17%), Positives = 24/76 (31%), Gaps = 7/76 (9%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPH-------TLDGRTID 272
++G++ V+ + +T S+G F F + LDGR +
Sbjct: 35 VLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLK 94
Query: 273 PKPCNPRTLQKPKKNS 288
R +S
Sbjct: 95 VDLAVTRDEAASGPSS 110
Score = 44.6 bits (106), Expect = 3e-06
Identities = 8/41 (19%), Positives = 16/41 (39%)
Query: 283 KPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
P + VF+ L + E L ++G + V ++
Sbjct: 8 LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVV 48
>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 = 72.4 bits (178), Expect = 6e-16
Identities = 15/62 (24%), Positives = 28/62 (45%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ +FS G+V D ++ + + RS+G +V F + +V + I L G I +
Sbjct: 43 EDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ 102
Query: 278 PR 279
Sbjct: 103 AE 104
Score = 47.7 bits (114), Expect = 3e-07
Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 267 DGRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
G + P P++ + VF L + + DL FF+ GKV +V I+S R
Sbjct: 3 SGSSGKSPVREPVDNLSPEERDAR-TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 61
>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 = 69.5 bits (171), Expect = 4e-15
Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 9/85 (10%)
Query: 196 SGPSAGKPPADYS--------AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFV 247
SG S + D + + T + + FS+YG + D ++ + ++ RSRGF FV
Sbjct: 3 SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62
Query: 248 TFADPNNVGVVIQNCP-HTLDGRTI 271
F + ++ + LDGR I
Sbjct: 63 YFENVDDAKEAKERANGMELDGRRI 87
Score = 45.3 bits (108), Expect = 1e-06
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+ + GL TE DLR F++YG + +V I+ +
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ 51
>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 = 69.8 bits (171), Expect = 8e-15
Identities = 24/109 (22%), Positives = 41/109 (37%), Gaps = 12/109 (11%)
Query: 175 PAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYS-----------AYGTYAQYQQRYFSR 223
++G P G + G S + T + + FS+
Sbjct: 10 HSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSK 69
Query: 224 YGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
YG + D ++ + ++ RSRGF FV F + ++ + LDGR I
Sbjct: 70 YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 118
Score = 44.3 bits (105), Expect = 6e-06
Identities = 14/63 (22%), Positives = 22/63 (34%)
Query: 261 NCPHTLDGRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEV 320
H R + + + GL TE DLR F++YG + +V
Sbjct: 17 RGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADV 76
Query: 321 VIM 323
I+
Sbjct: 77 SIV 79
>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 = 70.3 bits (172), Expect = 9e-15
Identities = 25/95 (26%), Positives = 33/95 (34%), Gaps = 11/95 (11%)
Query: 188 AAPTGPNPSGPSAGKPPADYS----------AYGTYAQYQQRYFSRYGEVIDCVVMKNNE 237
A T G D Y T +R F +YG V D + ++
Sbjct: 48 ATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY 107
Query: 238 TGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
T SRGF FV F D + + LDGR +
Sbjct: 108 TKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 142
Score = 46.8 bits (111), Expect = 2e-06
Identities = 11/64 (17%), Positives = 17/64 (26%)
Query: 263 PHTLDGRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
D + + L + LR F +YG+V +V I
Sbjct: 43 WTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYI 102
Query: 323 MSPR 326
R
Sbjct: 103 PRDR 106
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 66.9 bits (163), Expect = 4e-14
Identities = 21/91 (23%), Positives = 31/91 (34%), Gaps = 22/91 (24%)
Query: 218 QRYF-----SRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
YF S G V+ R G +TF +P + V+ H L G +
Sbjct: 26 TLYFENRRRSGGGPVLSWQ--------RLGCGGVLTFREPADAERVLAQADHELHGAQLS 77
Query: 273 PKPCNPRTLQKPKKNSSFPKVFLGGLPSNVT 303
+P PR ++ L GLP +
Sbjct: 78 LRPAPPRAPA---------RLLLQGLPPGTS 99
Score = 28.0 bits (62), Expect = 1.7
Identities = 9/40 (22%), Positives = 15/40 (37%), Gaps = 5/40 (12%)
Query: 292 KVFLGGLPSNVTETDLRTFF-----NRYGKVMEVVIMSPR 326
V + GLP V + L +F + G V+ +
Sbjct: 10 AVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCG 49
>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 = 66.1 bits (162), Expect = 5e-14
Identities = 12/73 (16%), Positives = 24/73 (32%), Gaps = 4/73 (5%)
Query: 218 QRYFSRYG--EVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTIDPK 274
G ++++ +N G+S+GF V + ++ P L G+
Sbjct: 19 TEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVT 78
Query: 275 PCNPRTLQKPKKN 287
P N +
Sbjct: 79 PSNKLE-HHHHHH 90
Score = 36.4 bits (85), Expect = 0.001
Identities = 8/37 (21%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYG--KVMEVVIMSPR 326
+++G L T+ DL + G ++E+ R
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR 39
>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 = 66.0 bits (162), Expect = 5e-14
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
F + + VM + +TG SRG+GFV+F ++ + + L+GR +
Sbjct: 22 FKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL 73
Score = 43.6 bits (104), Expect = 4e-06
Identities = 9/32 (28%), Positives = 15/32 (46%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+F+G L NV + LR F + + +M
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVM 34
>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 = 66.1 bits (162), Expect = 7e-14
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 195 PSGPSAGKPPADYS------AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVT 248
SG S G P+ + + R FS+YG+V+ +MK+ +T +S+G F+
Sbjct: 5 SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFIL 64
Query: 249 FADPNNVGVVIQNC-PHTLDGRTI 271
F D ++ + L GR I
Sbjct: 65 FLDKDSAQNCTRAINNKQLFGRVI 88
Score = 45.7 bits (109), Expect = 1e-06
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
V++ LP ++T DL F++YGKV++V IM +
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK 52
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 67.1 bits (164), Expect = 9e-14
Identities = 26/113 (23%), Positives = 37/113 (32%), Gaps = 9/113 (7%)
Query: 168 PQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYS--------AYGTYAQYQQR 219
+ + G TG G P + Y T +R
Sbjct: 7 HHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRR 66
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
F +YG V D + ++ T SRGF FV F D + + LDGR +
Sbjct: 67 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 119
Score = 41.3 bits (97), Expect = 7e-05
Identities = 11/55 (20%), Positives = 19/55 (34%)
Query: 272 DPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+ + P + + L + LR F +YG+V +V I R
Sbjct: 29 QMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR 83
>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 = 64.9 bits (159), Expect = 1e-13
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTI 271
F +G++ D + + ET + RGF FV F + I N L GRTI
Sbjct: 28 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI 79
Score = 45.6 bits (109), Expect = 9e-07
Identities = 8/35 (22%), Positives = 16/35 (45%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+++GGL V + L F +G + ++ I
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY 43
>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 = 65.0 bits (159), Expect = 3e-13
Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 6/88 (6%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTIDPKPCNPR 279
FS +G ++ C V+ + S+G+GFV F I+ L+ R + R
Sbjct: 26 FSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 83
Query: 280 TLQKPKKNSSFPK---VFLGGLPSNVTE 304
++ + + + V++ T
Sbjct: 84 KEREAELGARAKEFTNVYIKNFGPGSTR 111
Score = 36.8 bits (86), Expect = 0.002
Identities = 5/36 (13%), Positives = 15/36 (41%)
Query: 288 SSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+F+ L ++ L F+ +G ++ ++
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVV 38
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 64.8 bits (158), Expect = 6e-13
Identities = 24/98 (24%), Positives = 32/98 (32%), Gaps = 7/98 (7%)
Query: 181 PAGGATGAAPTGPNPSGPSAGKPPADYS------AYGTYAQYQQRYFSRYGEVIDCVVMK 234
G SG S G A + F +G++ D +
Sbjct: 38 CVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 97
Query: 235 NNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTI 271
+ ET + RGF FV F + I N L GRTI
Sbjct: 98 DYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI 135
Score = 45.9 bits (109), Expect = 2e-06
Identities = 8/50 (16%), Positives = 17/50 (34%), Gaps = 1/50 (2%)
Query: 277 NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+ +++GGL V + L F +G + ++ I
Sbjct: 51 GGSGGSGGSATTKR-VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY 99
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 63.1 bits (154), Expect = 7e-13
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 218 QRYFSRYG--EVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-----PHTLDGRT 270
S Y V + ++K+ +T ++RGF FV + + ++Q P +DG+T
Sbjct: 27 MTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT 86
Query: 271 I 271
I
Sbjct: 87 I 87
Score = 39.6 bits (93), Expect = 1e-04
Identities = 4/42 (9%), Positives = 13/42 (30%), Gaps = 4/42 (9%)
Query: 286 KNSSFP--KVFLGGLPSNVTETDLRTFFNRYGK--VMEVVIM 323
+ + L + + + T + Y V + ++
Sbjct: 3 HHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLI 44
>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 = 63.0 bits (154), Expect = 9e-13
Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
+R F +YG V D + + T RGF FV F D + LDGR +
Sbjct: 31 RRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGREL 85
Score = 43.4 bits (103), Expect = 8e-06
Identities = 9/43 (20%), Positives = 15/43 (34%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+ + L + LR F +YG+V +V I
Sbjct: 7 GPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREP 49
>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 = 63.0 bits (154), Expect = 1e-12
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTI 271
F +G++ D + + ET + RGF FV F + I N L GRTI
Sbjct: 33 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI 84
Score = 43.7 bits (104), Expect = 6e-06
Identities = 8/35 (22%), Positives = 16/35 (45%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+++GGL V + L F +G + ++ I
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY 48
>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 = 62.2 bits (152), Expect = 2e-12
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 1/63 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTIDPKPC 276
++ FS YG + + ++ T + +GF FVTF P + GR + P
Sbjct: 26 EKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS 85
Query: 277 NPR 279
+
Sbjct: 86 TIK 88
Score = 44.1 bits (105), Expect = 4e-06
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+S ++F+ L +E DL F+ YG + E+
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYP 41
>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 = 61.8 bits (151), Expect = 2e-12
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI-----DPK 274
F+ +G + D V+K+ TG+S+G+GFV+F + + IQ L GR I K
Sbjct: 27 FAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
Query: 275 P 275
P
Sbjct: 87 P 87
Score = 41.8 bits (99), Expect = 2e-05
Identities = 9/39 (23%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRTIR 329
VF+G L +T + F +G++ + V+ T +
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGK 46
>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 = 63.2 bits (154), Expect = 2e-12
Identities = 23/117 (19%), Positives = 36/117 (30%), Gaps = 12/117 (10%)
Query: 167 MPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYS--------AYGTYAQYQQ 218
M Q + P+ P D +
Sbjct: 1 MSQIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLR 60
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
+ F RYG + ++ + ET +SRG+GFV F ++ I L+G I K
Sbjct: 61 QLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA----GLNGFNILNKR 113
Score = 39.7 bits (93), Expect = 3e-04
Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 3/77 (3%)
Query: 253 NNVGVVIQNCPHTLDGRTIDPKPCNPRTLQKPKKNSSFP---KVFLGGLPSNVTETDLRT 309
+ + +V Q P+ + + + + + N + + +P+ V E LR
Sbjct: 2 SQIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQ 61
Query: 310 FFNRYGKVMEVVIMSPR 326
F RYG + V I+ R
Sbjct: 62 LFERYGPIESVKIVCDR 78
>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 = 62.4 bits (152), Expect = 2e-12
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 6/80 (7%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTI----- 271
+ F+ +G + D V+K+ TG+S+G+GFV+F + + IQ L GR I
Sbjct: 33 KAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 92
Query: 272 DPKPCNPRTLQKPKKNSSFP 291
KP P++ + S P
Sbjct: 93 TRKPPAPKSTYESNTKQSGP 112
Score = 41.2 bits (97), Expect = 6e-05
Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRTIR 329
+ K S+ VF+G L +T D++ F +G++ + V+ T +
Sbjct: 7 GQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGK 55
>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 = 61.8 bits (151), Expect = 2e-12
Identities = 18/55 (32%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
+ F +G++ + V+MK+++TGRS+G+GF+TF+D ++ L GR +
Sbjct: 23 RGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPM 77
Score = 42.2 bits (100), Expect = 2e-05
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+++G L N+TE LR F +GK+ +V+M
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDS 41
>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 = 64.1 bits (156), Expect = 3e-12
Identities = 24/137 (17%), Positives = 45/137 (32%), Gaps = 36/137 (26%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTIDPKPCNPR 279
F YG+V ++ N + V AD N + + + H L G+ I +
Sbjct: 25 FGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ 79
Query: 280 TLQKPKKNSSFPK------------------------------VFLGGLPSNVTETDLRT 309
+Q P++ + L +P +V+E DL+
Sbjct: 80 NVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKV 139
Query: 310 FFNRYGKVMEVVIMSPR 326
F+ G V++ +
Sbjct: 140 LFSSNGGVVKGFKFFQK 156
Score = 32.9 bits (75), Expect = 0.092
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 293 VFLGGL-PSNVTETDLRTFFNRYGKVMEVVIM 323
+ + L P VT L F YG V V I+
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKIL 37
Score = 32.9 bits (75), Expect = 0.095
Identities = 5/56 (8%), Positives = 14/56 (25%), Gaps = 6/56 (10%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT--LDGRTI 271
+ FS G V+ + R + + + + + +
Sbjct: 138 KVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHL 189
>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 = 61.6 bits (150), Expect = 4e-12
Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 9/78 (11%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC--PHTLDG--RTIDPK 274
F +G++ + V+K+ TG +G F+T+ + + TL G R I K
Sbjct: 32 PLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVK 91
Query: 275 PCNPRTLQKPKKNSSFPK 292
P + + S P
Sbjct: 92 PADSE-----SRGGSGPS 104
Score = 47.7 bits (114), Expect = 3e-07
Identities = 12/32 (37%), Positives = 22/32 (68%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+G +P N+ E DL+ F +GK+ E+ ++
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVL 46
>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 = 61.1 bits (149), Expect = 4e-12
Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQN-CPHTLDGRTI-----DPK 274
S G VI+ +M + +TGRS+G+ F+ F D + ++N + L R +
Sbjct: 23 CSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNS 82
Query: 275 PCNPRTLQKPKKN 287
+ +L+ +
Sbjct: 83 DISGVSLEHHHHH 95
Score = 42.6 bits (101), Expect = 1e-05
Identities = 9/35 (25%), Positives = 17/35 (48%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
V+LG +P + TE + + G V+ + +M
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDP 38
>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 = 60.6 bits (148), Expect = 4e-12
Identities = 10/55 (18%), Positives = 22/55 (40%), Gaps = 4/55 (7%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
+ YG+++ + + T + +G+GFV F P+ + L +
Sbjct: 23 VKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT----ALKASGVQ 73
Score = 43.3 bits (103), Expect = 5e-06
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 287 NSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+S +++ GL T+ DL YGK++ +
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAI 38
>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 = 60.2 bits (147), Expect = 6e-12
Identities = 13/62 (20%), Positives = 25/62 (40%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ +F G V ++ + +G +GF ++ F+D +V + GR I P
Sbjct: 24 EAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKR 83
Query: 278 PR 279
Sbjct: 84 TN 85
Score = 42.1 bits (100), Expect = 1e-05
Identities = 8/35 (22%), Positives = 16/35 (45%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+++G + T +L F+ G V V I+ +
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDK 42
>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 = 59.5 bits (145), Expect = 1e-11
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
Q F +G + + K+ TG+S+GF F++F + I D +
Sbjct: 33 QELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLIL 87
Score = 41.1 bits (97), Expect = 4e-05
Identities = 7/40 (17%), Positives = 17/40 (42%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
++ + + L + ETDL+ F +G + + +
Sbjct: 9 NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLA 48
>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 = 59.7 bits (145), Expect = 2e-11
Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 3/72 (4%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ +FS G + ++ + +G +G+ ++ FA+ N+V + GRTI P
Sbjct: 54 EAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKR 113
Query: 278 PRTLQKPKKNSS 289
P +S+
Sbjct: 114 TN---MPGISST 122
Score = 42.8 bits (101), Expect = 2e-05
Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 273 PKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
P P + ++ K+ V++G + T DL F+ G + + I+
Sbjct: 20 EGPPQPLSAEEKKEIDKR-SVYVGNVDYGSTAQDLEAHFSSCGSINRITIL 69
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 59.7 bits (145), Expect = 2e-11
Identities = 27/118 (22%), Positives = 44/118 (37%), Gaps = 25/118 (21%)
Query: 176 AAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSAYGTYAQYQ------------------ 217
AAG P G A+ + + P A A +A +
Sbjct: 1 AAGLPQFGSASALSTS---PLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDL 57
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
F +G VI V + +T S+ FGFV+F +P++ V I+ ++G + K
Sbjct: 58 ASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK----AMNGFQVGTKR 111
Score = 33.9 bits (78), Expect = 0.023
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+F+ LP T+TDL + F +G V+ +
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVF 73
>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 = 59.6 bits (145), Expect = 2e-11
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 5/55 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
+G+VI ++++ +G SRG GF VI + +G+ I P
Sbjct: 46 LKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGH----FNGKFIKTPP 95
Score = 39.2 bits (92), Expect = 3e-04
Identities = 10/43 (23%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 282 QKPKKNSSFP-KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
Q K+ P +++ LP ++ E +L +G+V+ I+
Sbjct: 16 QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRIL 58
>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 = 58.3 bits (142), Expect = 3e-11
Identities = 12/43 (27%), Positives = 25/43 (58%)
Query: 209 AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD 251
Y ++ + FS++G+V + ++ + ET + +GFGFV +
Sbjct: 10 VYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE 52
Score = 42.2 bits (100), Expect = 1e-05
Identities = 9/35 (25%), Positives = 20/35 (57%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+++G L + T ++ F+++GKV V ++ R
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR 37
>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 = 59.3 bits (144), Expect = 3e-11
Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 6/81 (7%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI----- 271
F+ YGE+ + + + TG +G+ V + ++ L G+ I
Sbjct: 40 HDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 99
Query: 272 DPKPCNPRTLQKPKKNSSFPK 292
+ + ++ S P
Sbjct: 100 FVRGPPKGKRRGGRRRSRSPD 120
Score = 40.8 bits (96), Expect = 1e-04
Identities = 11/45 (24%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRT 327
P+++ +F+ G+ TE D+ F YG++ + + + RT
Sbjct: 16 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 60
>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 = 58.9 bits (143), Expect = 3e-11
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
F +G V+ V + +T S+ FGFV++ +P + IQ+ ++G I K
Sbjct: 46 FMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS----MNGFQIGMKR 96
Score = 35.0 bits (81), Expect = 0.008
Identities = 9/42 (21%), Positives = 16/42 (38%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+ +F+ LP + DL F +G V+ +
Sbjct: 17 GSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVF 58
>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 = 58.9 bits (143), Expect = 3e-11
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTIDPKPCNPR 279
F +G + +M ++ETGRS+G+GF+TF+D ++ L GR + R
Sbjct: 47 FEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTER 106
Query: 280 T 280
T
Sbjct: 107 T 107
Score = 43.8 bits (104), Expect = 6e-06
Identities = 11/50 (22%), Positives = 23/50 (46%)
Query: 277 NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
K ++ ++++G L N+TE LR F +G++ + +M
Sbjct: 13 AAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDS 62
>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 = 58.4 bits (142), Expect = 3e-11
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQN-CPHTLDGRTI 271
FS G V+ ++ + ETG+ +G+GF + D ++N GR +
Sbjct: 29 FSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRAL 80
Score = 42.2 bits (100), Expect = 2e-05
Identities = 13/43 (30%), Positives = 21/43 (48%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
P + S VF+G +P TE L+ F+ G V+ ++ R
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDR 44
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 58.8 bits (142), Expect = 4e-11
Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 9/71 (12%)
Query: 218 QRYFSRYGEVIDCVVMK--NNETGRSRGFGFVTFADPNNVGVVIQNCPH-------TLDG 268
F R+G ++ K + +G+ F+ F + ++V +I C +
Sbjct: 26 TASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCVSS 85
Query: 269 RTIDPKPCNPR 279
TI KP R
Sbjct: 86 PTIKDKPVQIR 96
Score = 53.4 bits (128), Expect = 3e-09
Identities = 11/43 (25%), Positives = 21/43 (48%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITR 334
KVF+GGLP ++ E ++ F R+G ++ + +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPK 52
>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 = 61.6 bits (149), Expect = 4e-11
Identities = 30/204 (14%), Positives = 62/204 (30%), Gaps = 45/204 (22%)
Query: 176 AAGGPPAGGATGAAPTGPNPSG---PSAGKPPA------DYSAYGTYAQYQQRYFSRYGE 226
+ ++G P G + P + + Q F YG+
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGD 61
Query: 227 VIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTIDPKPCNPRTLQKPK 285
V ++ N + V AD N + + + H L G+ I + +Q P+
Sbjct: 62 VQRVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPR 116
Query: 286 KNSSFPK------------------------------VFLGGLPSNVTETDLRTFFNRYG 315
+ + L +P +V+E DL+ F+ G
Sbjct: 117 EGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG 176
Query: 316 KVMEVVIMSPRTIRAGITRVPTQE 339
V++ + + + ++ + E
Sbjct: 177 GVVKGFKFFQKDRKMALIQMGSVE 200
Score = 28.4 bits (63), Expect = 3.1
Identities = 5/53 (9%), Positives = 12/53 (22%), Gaps = 6/53 (11%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT--LDGRTI 271
FS G V+ R + + + + + +
Sbjct: 172 FSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHL 220
>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 = 58.4 bits (142), Expect = 5e-11
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
FS +G + VM E GRS+GFGFV F+ P + ++GR + KP
Sbjct: 36 FSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATKAVT----EMNGRIVATKP 84
Score = 38.0 bits (89), Expect = 5e-04
Identities = 6/42 (14%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ + +++ L + + LR F+ +G + +M
Sbjct: 8 DRITRYQVV-NLYVKNLDDGIDDERLRKAFSPFGTITSAKVM 48
>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 = 59.8 bits (145), Expect = 6e-11
Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 1/70 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTIDPKPCNPR 279
F YGE+ + + + TG S+G+ V + + + G+TI C +
Sbjct: 93 FCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 152
Query: 280 TLQKPKKNSS 289
++ KK+
Sbjct: 153 GPKRVKKSEK 162
Score = 44.1 bits (104), Expect = 1e-05
Identities = 8/52 (15%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 277 NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRT 327
+ P+++ +F+ + E +++ F YG++ + + + RT
Sbjct: 59 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 110
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 57.8 bits (140), Expect = 7e-11
Identities = 9/57 (15%), Positives = 19/57 (33%), Gaps = 4/57 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+YGEV + ++ + T + G V F + L ++ +
Sbjct: 27 CRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA----KETVKNLHLTSVMGNIIH 79
Score = 45.1 bits (107), Expect = 2e-06
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRT 327
+V L NV ET L+ +YG+V EV +++ PRT
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRT 44
>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 = 57.7 bits (140), Expect = 1e-10
Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 4/67 (5%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTIDPKPCNPR 279
F YGE+ + + + TG S+G+ V + + + G+TI C +
Sbjct: 47 FCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 106
Query: 280 TLQKPKK 286
PK+
Sbjct: 107 ---GPKR 110
Score = 42.3 bits (100), Expect = 2e-05
Identities = 8/52 (15%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 277 NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRT 327
+ P+++ +F+ + E +++ F YG++ + + + RT
Sbjct: 13 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRT 64
>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 = 56.4 bits (137), Expect = 1e-10
Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 221 FSRYGEVIDCVVMKN-NETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
FS YG++ + S+G+ +V F +P+ +++ +DG+ I
Sbjct: 25 FSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEI 77
Score = 45.6 bits (109), Expect = 8e-07
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
KV +G L NVT+ + F+ YGK+ + + R
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERM 41
>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 = 56.9 bits (138), Expect = 1e-10
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTIDPKPC 276
++ F ++G+++D ++ N S+GFGFVTF + + + T ++GR I+
Sbjct: 33 RQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 90
Query: 277 NPRTLQKPK 285
R +
Sbjct: 91 TARVMTNSG 99
Score = 44.6 bits (106), Expect = 2e-06
Identities = 10/43 (23%), Positives = 23/43 (53%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+ S+ ++ + +P + DLR F ++GK+++V I+
Sbjct: 9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE 51
>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 = 56.5 bits (137), Expect = 2e-10
Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 1/62 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ S D V+ + TG +R FG+V F ++ ++ + G I +
Sbjct: 35 KVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK 93
Query: 278 PR 279
R
Sbjct: 94 GR 95
Score = 47.3 bits (113), Expect = 3e-07
Identities = 7/45 (15%), Positives = 22/45 (48%)
Query: 283 KPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
+ ++++ +F+G L N + +L+ + ++ ++ RT
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT 54
>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 = 56.7 bits (137), Expect = 2e-10
Identities = 14/71 (19%), Positives = 28/71 (39%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
++FS V + + + + GRS G FV FA ++ + R I+ +
Sbjct: 33 VQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 92
Query: 278 PRTLQKPKKNS 288
++ +S
Sbjct: 93 RAEVRTSGPSS 103
Score = 42.0 bits (99), Expect = 2e-05
Identities = 8/47 (17%), Positives = 19/47 (40%)
Query: 277 NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ + ++ V L GLP ++ ++ FF+ V + +
Sbjct: 2 SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTL 48
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 56.9 bits (138), Expect = 2e-10
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTIDPKPCNPR 279
F ++G+++D ++ N S+GFGFVTF + + + T ++GR I+ R
Sbjct: 50 FGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
Query: 280 TL 281
+
Sbjct: 108 VM 109
Score = 47.7 bits (114), Expect = 3e-07
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 278 PRTLQKPKKNSSFP-KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
PR +N S P ++ + +P + DLR F ++GK+++V I+
Sbjct: 16 PRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE 65
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 56.5 bits (137), Expect = 2e-10
Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
F+ YGE+ + + + TG +G+ V + ++ L G+ I
Sbjct: 44 FAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 95
Score = 41.1 bits (97), Expect = 5e-05
Identities = 11/45 (24%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRT 327
P+++ +F+ G+ TE D+ F YG++ + + + RT
Sbjct: 17 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 61
>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 = 55.7 bits (135), Expect = 3e-10
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 7/61 (11%)
Query: 218 QRYFSRYGEVIDCVVMKNNETG---RSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
+ FS+ G + C + K S GFGFV + P ++ L G T+D
Sbjct: 23 KGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK----QLQGHTVDGH 78
Query: 275 P 275
Sbjct: 79 K 79
Score = 40.3 bits (95), Expect = 8e-05
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 287 NSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+S +F+ L + TE L+ F++ G + I
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTIS 38
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 55.7 bits (135), Expect = 3e-10
Identities = 9/52 (17%), Positives = 20/52 (38%), Gaps = 2/52 (3%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
+G V D ++ N G+ +G +V + + + + T+ I
Sbjct: 38 CKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVMKMDGMTIKENII 88
Score = 46.9 bits (112), Expect = 5e-07
Identities = 10/51 (19%), Positives = 24/51 (47%)
Query: 277 NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
+ + + K+F+ GLP + T+ +L +G V ++ +++ R
Sbjct: 4 GSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA 54
>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 = 55.8 bits (135), Expect = 3e-10
Identities = 18/54 (33%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 221 FSRYGEVIDCVVMKNNE-TGRSRGFGFVTFADPNNVGVVIQNCPH--TLDGRTI 271
FS +GE+ + K TG RGFGFV F + H L GR +
Sbjct: 36 FSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL 89
Score = 43.8 bits (104), Expect = 6e-06
Identities = 7/42 (16%), Positives = 20/42 (47%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ K + K+ + +P + ++R F+ +G++ V +
Sbjct: 7 GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLP 48
>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 = 55.7 bits (135), Expect = 4e-10
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTI 271
F + G V++ + K+ TG+ +G+GFV F + I+ L G+ I
Sbjct: 36 FLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI 87
Score = 38.4 bits (90), Expect = 5e-04
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
V++GGL V+E L F + G V+ +
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMP 48
>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 = 55.3 bits (134), Expect = 4e-10
Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 5/56 (8%)
Query: 221 FSRYGEVIDC-VVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
FS +G ++ +M++ +TG S+G+ F+ FA + I+ ++G+ + +P
Sbjct: 26 FSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE----AMNGQYLCNRP 77
Score = 34.1 bits (79), Expect = 0.011
Identities = 9/38 (23%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVME--VVIMSPRT 327
+F+G L + E L F+ +G +++ ++ P T
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDT 44
>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 = 55.4 bits (134), Expect = 5e-10
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 5/55 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
F+ +G + V + +GRS G V F + ++ +G +D +P
Sbjct: 50 FAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMK----QYNGVPLDGRP 99
Score = 40.7 bits (96), Expect = 8e-05
Identities = 7/46 (15%), Positives = 19/46 (41%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
+ K+ + L V++ D++ F +G + + + R+
Sbjct: 21 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS 66
>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 = 55.4 bits (134), Expect = 6e-10
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 4/58 (6%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
F+R+ E + TGR RG F+TF + H ++G + K
Sbjct: 43 VSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIA----WQALHLVNGYKLYGKI 96
Score = 38.4 bits (90), Expect = 6e-04
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
++L L VTE DL + F R+ + I
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQ 58
>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 = 55.7 bits (134), Expect = 7e-10
Identities = 19/125 (15%), Positives = 40/125 (32%), Gaps = 8/125 (6%)
Query: 167 MPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSA--------YGTYAQYQQ 218
M + + G G+ A+ TG G + + +G +
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIV 60
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNP 278
++FS V + + + + G+ G FV FA + + R I+ +
Sbjct: 61 QFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQ 120
Query: 279 RTLQK 283
++
Sbjct: 121 EEVRS 125
Score = 42.6 bits (100), Expect = 2e-05
Identities = 9/42 (21%), Positives = 18/42 (42%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+++ V L GLP T+ ++ FF+ V + +
Sbjct: 34 SNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITL 75
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 53.7 bits (130), Expect = 1e-09
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 3/52 (5%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRTI 271
F+ G V+ + E G+S+G G V F P + L GR I
Sbjct: 29 FNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREI 78
Score = 36.4 bits (85), Expect = 0.002
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
++F+ LP + T L+ FN G V+ I
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIK 41
>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 = 54.8 bits (132), Expect = 2e-09
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
FS+ G++ ++ + + GF FV + + ++ T LD R I
Sbjct: 60 FSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRII 111
Score = 41.7 bits (98), Expect = 8e-05
Identities = 9/42 (21%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+K K S +++G L TE + F++ G + ++++
Sbjct: 33 EKLLKKSC--TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMG 72
>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 = 53.0 bits (128), Expect = 3e-09
Identities = 11/32 (34%), Positives = 20/32 (62%), Gaps = 3/32 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
FSR+G+++D +V + + + RG FV F +
Sbjct: 33 FSRFGQILDILVSR---SLKMRGQAFVIFKEV 61
Score = 36.1 bits (84), Expect = 0.002
Identities = 5/35 (14%), Positives = 21/35 (60%), Gaps = 4/35 (11%)
Query: 293 VFLGGLPSNVTETDLR----TFFNRYGKVMEVVIM 323
+++ L + + +L+ F+R+G+++++++
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS 45
>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 = 53.1 bits (128), Expect = 3e-09
Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 5/55 (9%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
Q F + + + N+ G+S+G+ F+ FA + + +C ++GR I
Sbjct: 33 QEVFEKATFI----KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAI 83
Score = 36.5 bits (85), Expect = 0.002
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKV 317
+ L L + TE L+ F + +
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFI 42
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 57.9 bits (139), Expect = 3e-09
Identities = 26/157 (16%), Positives = 30/157 (19%)
Query: 43 GPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQ 102
Q G P A M S Q Q Q
Sbjct: 12 AQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQ 71
Query: 103 TPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNN 162
+ + + P PQ G P QQ P G P + G N
Sbjct: 72 QIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQN 131
Query: 163 WNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPS 199
PP T P P
Sbjct: 132 MRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERM 168
Score = 57.5 bits (138), Expect = 4e-09
Identities = 22/159 (13%), Positives = 24/159 (15%), Gaps = 1/159 (0%)
Query: 67 AGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGP 126
G PQ G P G Q +
Sbjct: 11 QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLH 70
Query: 127 QAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGAT 186
Q Q +S PQ Q PA G P A
Sbjct: 71 QQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQ 130
Query: 187 GAAP-TGPNPSGPSAGKPPADYSAYGTYAQYQQRYFSRY 224
P P PP
Sbjct: 131 NMRPMNQLYPIDLLTELPPPITDLTLPPPPLVIPPERML 169
Score = 52.9 bits (126), Expect = 1e-07
Identities = 20/119 (16%), Positives = 24/119 (20%), Gaps = 8/119 (6%)
Query: 101 SQTPMNGYANPSAPQGYTNWGA-PPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGY 159
S Y G P PPQ ++ G Q G G Q +
Sbjct: 2 SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQF 61
Query: 160 GNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSAYGTYAQYQQ 218
P+A P GT Q QQ
Sbjct: 62 L-------TPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQ 113
Score = 52.1 bits (124), Expect = 2e-07
Identities = 17/123 (13%), Positives = 24/123 (19%), Gaps = 4/123 (3%)
Query: 99 PSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSG 158
P +Q A P P G PPQ P
Sbjct: 10 PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSY--GQMGMPPQGAVPSMGQQQFLTPAQE 67
Query: 159 YGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGP--NPSGPSAGKPPADYSAYGTYAQY 216
+ + P P P + + P AYG +
Sbjct: 68 QLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAA 127
Query: 217 QQR 219
+
Sbjct: 128 MGQ 130
Score = 51.0 bits (121), Expect = 5e-07
Identities = 17/136 (12%), Positives = 22/136 (16%), Gaps = 3/136 (2%)
Query: 43 GPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQ 102
+ P A TP A P G P P
Sbjct: 3 HHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFL 62
Query: 103 TPMNGYAN---PSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGY 159
TP + A + P P P Q A +
Sbjct: 63 TPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYG 122
Query: 160 GNNWNWNMPQNGPTTP 175
+
Sbjct: 123 QPSAAMGQNMRPMNQL 138
Score = 35.6 bits (81), Expect = 0.028
Identities = 15/87 (17%), Positives = 17/87 (19%), Gaps = 11/87 (12%)
Query: 139 PPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGP 198
P Q YG P P PAA G G G
Sbjct: 10 PQAQLQYGQNATPLQQPA-----------QFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQ 58
Query: 199 SAGKPPADYSAYGTYAQYQQRYFSRYG 225
PA + Q +
Sbjct: 59 QQFLTPAQEQLHQQIDQATTSMNDMHL 85
>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 = 55.5 bits (133), Expect = 3e-09
Identities = 20/140 (14%), Positives = 30/140 (21%), Gaps = 46/140 (32%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPC---- 276
F YG V MK+ G V AD V I + L+ + +
Sbjct: 26 FCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITH----LNNNFMFGQKMNVCV 76
Query: 277 ---------------------------------NPRTLQKPKKNSSFPKVFLGGLPSNVT 303
P K + + P VT
Sbjct: 77 SKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVT 136
Query: 304 ETDLRTFFNRYGKVMEVVIM 323
E + + G +
Sbjct: 137 EENFFEICDELGVKRPTSVK 156
Score = 41.6 bits (97), Expect = 1e-04
Identities = 4/55 (7%), Positives = 11/55 (20%), Gaps = 1/55 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
G V + G + + ++ + H +
Sbjct: 141 FEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNG 195
Score = 37.0 bits (85), Expect = 0.005
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 291 PKVFLGGL-PSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
P + + GL S + + F YG V +V M +
Sbjct: 5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP 42
>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 = 52.6 bits (127), Expect = 3e-09
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
F + G + + K+ G+ + FGFV F P +V I L+G + +P
Sbjct: 37 FLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESVSYAIAL----LNGIRLYGRP 86
Score = 41.5 bits (98), Expect = 3e-05
Identities = 13/46 (28%), Positives = 20/46 (43%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
P + + VF+G L + V E L F + G + +V I R
Sbjct: 8 MFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE 53
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 52.8 bits (127), Expect = 3e-09
Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 4/72 (5%)
Query: 201 GKPPADYSAYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQ 260
G P + + FS+ G+V++ + TG+++GF FV N+ +I+
Sbjct: 13 GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
Query: 261 NCPHTLDGRTID 272
+ G+ +D
Sbjct: 73 S----FHGKRLD 80
>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 = 53.5 bits (129), Expect = 4e-09
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 5/55 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
F+ +G + V + +GRS G V F + ++ G +D +P
Sbjct: 56 FAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ----YKGVPLDGRP 105
Score = 40.8 bits (96), Expect = 1e-04
Identities = 7/36 (19%), Positives = 18/36 (50%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
K+ + L V++ D++ F +G + + + R+
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS 72
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 52.8 bits (127), Expect = 4e-09
Identities = 13/57 (22%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
+ FS++G++ + + E G+++G+ F+ +A P + ++N DG +D +
Sbjct: 39 HKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKN----ADGYKLDKQ 89
Score = 35.5 bits (82), Expect = 0.005
Identities = 5/49 (10%), Positives = 17/49 (34%), Gaps = 7/49 (14%)
Query: 282 QKPKKNSSFP-KVFLGGLP------SNVTETDLRTFFNRYGKVMEVVIM 323
+P++ + + +P + + F+++GK+
Sbjct: 6 DRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP 54
>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 = 52.7 bits (127), Expect = 4e-09
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 12/64 (18%)
Query: 220 YFSRYGEVID--------CVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
YF + G + + + ETG+ +G V+F DP + I DG+
Sbjct: 33 YFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW----FDGKEF 88
Query: 272 DPKP 275
P
Sbjct: 89 SGNP 92
Score = 44.2 bits (105), Expect = 3e-06
Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 3/48 (6%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
N+ +F+ GL NVT + +F + G + I
Sbjct: 8 HSHSDNN---TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMIN 52
>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 = 52.3 bits (126), Expect = 4e-09
Identities = 9/63 (14%), Positives = 24/63 (38%), Gaps = 6/63 (9%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTIDPKPC 276
+ F E+ ++ G+S+G ++ F + ++ +DGR++
Sbjct: 34 KEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT 88
Query: 277 NPR 279
+
Sbjct: 89 GEK 91
Score = 42.6 bits (101), Expect = 1e-05
Identities = 9/45 (20%), Positives = 17/45 (37%), Gaps = 3/45 (6%)
Query: 279 RTLQKPKKNSSFP---KVFLGGLPSNVTETDLRTFFNRYGKVMEV 320
L+ P + + L N+TE +L+ F ++ V
Sbjct: 2 HMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV 46
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 52.4 bits (126), Expect = 5e-09
Identities = 8/69 (11%), Positives = 24/69 (34%), Gaps = 1/69 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ + G+V++ + M+ +G FV F + ++ + +
Sbjct: 29 KEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD 87
Query: 278 PRTLQKPKK 286
+K ++
Sbjct: 88 DYFAKKNEE 96
Score = 49.3 bits (118), Expect = 6e-08
Identities = 8/43 (18%), Positives = 20/43 (46%)
Query: 285 KKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
K + V++ G P++ T D++ + G+V+ + +
Sbjct: 6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH 48
>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 = 52.3 bits (126), Expect = 5e-09
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 224 YGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
+ + ++ + ETG S+GFGFV F + + +DG +
Sbjct: 36 FDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKV 84
Score = 34.5 bits (80), Expect = 0.009
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 3/45 (6%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
++ +F+ GL + TE L+ F + I++ R
Sbjct: 7 GPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDR 48
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 54.1 bits (130), Expect = 6e-09
Identities = 20/124 (16%), Positives = 32/124 (25%), Gaps = 24/124 (19%)
Query: 171 GPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSAYGTYAQYQQ------------ 218
G GG AP P + S G +
Sbjct: 40 GGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFG 99
Query: 219 -------RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
F+ +G + V + +GRS G V F + ++ G +
Sbjct: 100 VSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMK----QYKGVPL 154
Query: 272 DPKP 275
D +P
Sbjct: 155 DGRP 158
Score = 39.8 bits (93), Expect = 4e-04
Identities = 7/46 (15%), Positives = 20/46 (43%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
+ + K+ + L V++ D++ F +G + + + R+
Sbjct: 80 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS 125
>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 = 51.9 bits (125), Expect = 8e-09
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 5/53 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDP 273
F +G + +C V++ G S+G FV F+ I L G P
Sbjct: 36 FQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQAAIHA----LHGSQTMP 83
Score = 45.0 bits (107), Expect = 2e-06
Identities = 9/39 (23%), Positives = 18/39 (46%)
Query: 285 KKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ K+F+G L +E D+ F +G + E ++
Sbjct: 10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVL 48
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 52.0 bits (125), Expect = 9e-09
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 12/64 (18%)
Query: 220 YFSRYGEV--------IDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
YF + G + + + ETG+ +G V+F DP + I DG+
Sbjct: 27 YFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW----FDGKEF 82
Query: 272 DPKP 275
P
Sbjct: 83 SGNP 86
Score = 42.4 bits (100), Expect = 2e-05
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 3/48 (6%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
Q N+ +F+ GL NVT + +F + G + I
Sbjct: 2 QDNSDNN---TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMIN 46
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 51.1 bits (123), Expect = 1e-08
Identities = 12/55 (21%), Positives = 24/55 (43%)
Query: 269 RTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ P + + S ++F+ P +V E++L F +G + EV I+
Sbjct: 10 HSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL 64
Score = 45.4 bits (108), Expect = 2e-06
Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 12/58 (20%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
F +G + + ++ GF FV F + + I+ + G++ +P
Sbjct: 49 NEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEE----VHGKSFANQP 94
>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 = 51.5 bits (124), Expect = 1e-08
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 5/55 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
FS G V+ ++++ + G+SRG G VTF I +G+ + +P
Sbjct: 36 FSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQAIS----MFNGQLLFDRP 85
Score = 37.3 bits (87), Expect = 0.001
Identities = 9/32 (28%), Positives = 14/32 (43%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
VF+ L V L+ F+ G V+ I+
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADIL 48
>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 = 50.3 bits (121), Expect = 2e-08
Identities = 11/43 (25%), Positives = 26/43 (60%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
++ + +++GGL +TETDLR F ++G++ + ++ +
Sbjct: 6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ 48
Score = 38.8 bits (91), Expect = 2e-04
Identities = 10/56 (17%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPH--TLDGRTI 271
+ +F ++GE+ V++ + F+ FA V + + ++GR +
Sbjct: 30 RNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRL 79
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 50.5 bits (121), Expect = 2e-08
Identities = 13/57 (22%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
+ FS++G++ + + E G+++G+ F+ +A P + ++N DG +D +
Sbjct: 25 HKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVKN----ADGYKLDKQ 75
Score = 30.1 bits (68), Expect = 0.24
Identities = 4/37 (10%), Positives = 13/37 (35%), Gaps = 6/37 (16%)
Query: 293 VFLGGLPS------NVTETDLRTFFNRYGKVMEVVIM 323
+ + +P + + F+++GK+
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP 40
>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 = 51.3 bits (123), Expect = 2e-08
Identities = 10/72 (13%), Positives = 25/72 (34%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
++ + V + + G+ G V F + ++ + L+GR
Sbjct: 33 LQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVT 92
Query: 278 PRTLQKPKKNSS 289
+++ +KN
Sbjct: 93 LEDMREIEKNPP 104
Score = 42.8 bits (101), Expect = 1e-05
Identities = 7/42 (16%), Positives = 16/42 (38%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ NS+ + +P ++T+ D+ F V +
Sbjct: 7 GEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHV 48
>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 = 50.4 bits (121), Expect = 2e-08
Identities = 11/62 (17%), Positives = 20/62 (32%), Gaps = 1/62 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTIDPKPC 276
+F Y + V +K NE G G V F + + + + R +
Sbjct: 33 LDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG 92
Query: 277 NP 278
+
Sbjct: 93 SG 94
Score = 38.4 bits (90), Expect = 4e-04
Identities = 6/36 (16%), Positives = 14/36 (38%)
Query: 288 SSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ + +P V+ ++ FF Y + V +
Sbjct: 13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCL 48
>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 = 50.4 bits (121), Expect = 2e-08
Identities = 17/89 (19%), Positives = 30/89 (33%), Gaps = 12/89 (13%)
Query: 192 GPNPSGPSAGKPPAD--------YSAYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRG 243
SG S+GKP ++ + + +F Y + V +K NE G G
Sbjct: 2 SSGSSGSSSGKPGPTVIKVQNMPFTV--SIDEILD-FFYGYQVIPGSVCLKYNEKGMPTG 58
Query: 244 FGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
V F + + + + R +
Sbjct: 59 EAMVAFESRDEATAAVIDLNDRPIGSRKV 87
Score = 38.4 bits (90), Expect = 4e-04
Identities = 6/31 (19%), Positives = 14/31 (45%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ + +P V+ ++ FF Y + V +
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCL 48
>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 = 50.3 bits (121), Expect = 2e-08
Identities = 15/43 (34%), Positives = 25/43 (58%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
K + ++F+G LP ++TE ++R F +YGK EV I +
Sbjct: 9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK 51
Score = 44.9 bits (107), Expect = 2e-06
Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 10/55 (18%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
++ F +YG+ + + + +GFGF+ + LD +
Sbjct: 33 RKLFEKYGKAGEVFIH------KDKGFGFIRLETRTLAEIAKVE----LDNMPLR 77
>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 = 49.9 bits (120), Expect = 3e-08
Identities = 16/37 (43%), Positives = 25/37 (67%)
Query: 287 NSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+S K+F+G LP TE ++R+ F +YGKV+E I+
Sbjct: 5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII 41
Score = 45.7 bits (109), Expect = 9e-07
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 9/63 (14%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTIDPKPC 276
+ F +YG+V++C ++K +GFV D I+N H L G I+ +
Sbjct: 26 RSLFEQYGKVLECDIIK--------NYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS 77
Query: 277 NPR 279
+
Sbjct: 78 KNK 80
>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 = 52.8 bits (126), Expect = 4e-08
Identities = 25/133 (18%), Positives = 41/133 (30%), Gaps = 6/133 (4%)
Query: 166 NMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYS---AYGTYAQYQQRYFS 222
N PP G PN GK A Y + T +
Sbjct: 31 NGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVH 90
Query: 223 RYG--EVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTIDPKPCNPR 279
G ++++ +N G+S+GF V + ++ P L G+ P N +
Sbjct: 91 SLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ 150
Query: 280 TLQKPKKNSSFPK 292
L + + S
Sbjct: 151 FLSQFEMQSRKTT 163
Score = 32.4 bits (73), Expect = 0.19
Identities = 15/91 (16%), Positives = 22/91 (24%), Gaps = 2/91 (2%)
Query: 18 QQVEIKKAEPRDASNKGNDMGNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNM 77
Q + + S SG A P PG +
Sbjct: 140 QNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAV 199
Query: 78 MQGYQGWGSTPQTQGFPGQWAPSSQTPMNGY 108
G + P G P P+ QT + +
Sbjct: 200 PGGDRF--PGPAGPGGPPPPFPAGQTHHHHH 228
Score = 28.9 bits (64), Expect = 2.4
Identities = 10/77 (12%), Positives = 19/77 (24%)
Query: 74 PGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWG 133
+ + + G+ P + + +G P G + P G
Sbjct: 151 FLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAG 210
Query: 134 SSYGAPPQQTGYGSYGP 150
PP G +
Sbjct: 211 PGGPPPPFPAGQTHHHH 227
Score = 28.1 bits (62), Expect = 4.3
Identities = 9/57 (15%), Positives = 17/57 (29%), Gaps = 2/57 (3%)
Query: 272 DPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYG--KVMEVVIMSPR 326
D +++G L T+ DL + G ++E+ R
Sbjct: 50 DDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENR 106
>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 = 50.1 bits (120), Expect = 5e-08
Identities = 10/52 (19%), Positives = 20/52 (38%), Gaps = 4/52 (7%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
F +YG + V T +RG +V + D + + + + R +
Sbjct: 29 FGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYL 77
Score = 41.2 bits (97), Expect = 6e-05
Identities = 6/34 (17%), Positives = 18/34 (52%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+++ LP +T ++ F +YG + ++ + +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP 44
>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 = 49.1 bits (118), Expect = 5e-08
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+F+G + + T +LR+ F R G+V+E ++
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVV 42
Score = 45.7 bits (109), Expect = 9e-07
Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 12/55 (21%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
+ F R G VI+C V+K + FV + I L+G+ +
Sbjct: 27 RSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQ----LNGKEVK 69
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 50.2 bits (120), Expect = 6e-08
Identities = 20/121 (16%), Positives = 44/121 (36%), Gaps = 13/121 (10%)
Query: 184 GATGAAPTGPNPSGPSAGKPPADYSA--------YGTYAQYQQRYFSRYGEVIDCVVMKN 235
G++G++ P+ S + P + + ++ +F + V D + +
Sbjct: 1 GSSGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAY 60
Query: 236 NETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPRTLQKP-----KKNSSF 290
G++ G GFV F + + + + R I P + + + K+ S
Sbjct: 61 GPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSG 120
Query: 291 P 291
P
Sbjct: 121 P 121
Score = 42.9 bits (101), Expect = 2e-05
Identities = 9/51 (17%), Positives = 19/51 (37%)
Query: 273 PKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
P + + + + V+L GLP + FF + V + + +
Sbjct: 8 KSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYI 58
>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 = 49.2 bits (118), Expect = 6e-08
Identities = 14/47 (29%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 278 PRTLQKPKKNSSFPKVFLGGLPS-NVTETDLRTFFNRYGKVMEVVIM 323
+ + S ++F+G LP NV++ DL F+ YG +M++ I
Sbjct: 12 SGLVPRGSHMKS--RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK 56
Score = 46.2 bits (110), Expect = 7e-07
Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 12/55 (21%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
R FS YG ++ + FGF+ F +P +V ++
Sbjct: 41 FRIFSPYGHIMQINIKN--------AFGFIQFDNPQSV----RDAIEXESQEMNF 83
>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 = 53.3 bits (127), Expect = 6e-08
Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 4/80 (5%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+R F YG + ++ + +G+ RG+ F+ + ++ ++ DG+ ID +
Sbjct: 120 RREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH----ADGKKIDGRRVL 175
Query: 278 PRTLQKPKKNSSFPKVFLGG 297
+ P+ GG
Sbjct: 176 VDVERGRTVKGWRPRRLGGG 195
Score = 42.5 bits (99), Expect = 2e-04
Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 6/59 (10%)
Query: 265 TLDGRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ + DP +P K +F+ + + TE+ LR F YG + + ++
Sbjct: 83 ETELKMWDPHN-DPNAQGDAFKT-----LFVARVNYDTTESKLRREFEVYGPIKRIHMV 135
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 53.6 bits (128), Expect = 8e-08
Identities = 40/194 (20%), Positives = 66/194 (34%), Gaps = 25/194 (12%)
Query: 37 MGNNQWGPPQSGGPMAMGP-NMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPG 95
+ ++ +GG A G + G T G P PG + ++P
Sbjct: 1495 LVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSP 1554
Query: 96 QWAPSSQ--TPMNGYANPSAP------QGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYG- 146
++P+S +P + +P++P Y+ P +P +S P Y
Sbjct: 1555 AYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1614
Query: 147 ---SYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKP 203
SY PTS + ++ P PT+P+ +PT P+ S S
Sbjct: 1615 TSPSYSPTSPS--------YSPTSPSYSPTSPSYSPTSP----SYSPTSPSYSPTSPAYS 1662
Query: 204 PADYSAYGTYAQYQ 217
P S T Y
Sbjct: 1663 PTSPSYSPTSPSYS 1676
Score = 48.2 bits (114), Expect = 4e-06
Identities = 28/176 (15%), Positives = 47/176 (26%), Gaps = 9/176 (5%)
Query: 36 DMGNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPG 95
D + P+ G TP +G+ + +P
Sbjct: 1446 DEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDEL----MFSPLVDSGSN 1501
Query: 96 QWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGA--PPQQTGYGSYGPTSG 153
T G A + +G P + P +Y PTS
Sbjct: 1502 DAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSP 1561
Query: 154 APQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSA 209
+ S +++ P PT+P+ P + +P+ PS YS
Sbjct: 1562 SY-SPTSPSYSPTSPSYSPTSPS--YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1614
Score = 46.2 bits (109), Expect = 1e-05
Identities = 38/194 (19%), Positives = 64/194 (32%), Gaps = 21/194 (10%)
Query: 44 PPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQT 103
P S A P +P+ P +P P ++P ++P+S +
Sbjct: 1547 PTYSPTSPAYSPTSPSYSPTSP--SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1604
Query: 104 --PMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGN 161
P + +P++P Y+ P +P +S P Y P+ Y
Sbjct: 1605 YSPTSPSYSPTSP-SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSP 1663
Query: 162 NWNWNMPQNGPTTPA-AGGPPAGGATGAA--PTGPN---------PSGPSAGKPPADYSA 209
P PT+P+ + P+ T + PT PN P+ P YS
Sbjct: 1664 T----SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSP 1719
Query: 210 YGTYAQYQQRYFSR 223
++ + SR
Sbjct: 1720 KQDEQKHNENENSR 1733
Score = 43.9 bits (103), Expect = 8e-05
Identities = 34/179 (18%), Positives = 50/179 (27%), Gaps = 18/179 (10%)
Query: 53 MGPNMGMGTPS-------GPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPM 105
+G +GT + + P ++ Q G TP + G
Sbjct: 1430 LGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNE-SGLVNADLDVKD 1488
Query: 106 NGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNW 165
+P G + A G+ YG G PTS ++
Sbjct: 1489 ELMFSPLVDSGSNDAMAGG---FTAYGGADYGEATSPFGAYGEAPTSPGF-GVSSPGFSP 1544
Query: 166 NMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPAD--YSAYGTYAQYQQRYFS 222
P PT+PA P +PT P+ S S P YS +S
Sbjct: 1545 TSPTYSPTSPAYS--PTSP--SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1599
>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 = 48.8 bits (117), Expect = 8e-08
Identities = 11/74 (14%), Positives = 24/74 (32%), Gaps = 9/74 (12%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQ--NCPHTLDGRTIDPKP 275
++ F + + G+ FV + D N I+ + L G+ ++
Sbjct: 26 RQLFGDRKLPLAG------QVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDY 79
Query: 276 CNPRTLQKPKKNSS 289
+ + SS
Sbjct: 80 SVSKK-LRSSGPSS 92
Score = 48.4 bits (116), Expect = 1e-07
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 288 SSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
S K+++G L VT DLR F + ++
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS 44
>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 = 50.3 bits (120), Expect = 8e-08
Identities = 12/55 (21%), Positives = 21/55 (38%), Gaps = 2/55 (3%)
Query: 269 RTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
T + + KV++G L +N +T+L F YG + V +
Sbjct: 54 VTEGSHHHHHHMHRDSCPLDC--KVYVGNLGNNGNKTELERAFGYYGPLRSVWVA 106
Score = 49.9 bits (119), Expect = 1e-07
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 9/55 (16%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
+R F YG + V + GF FV F DP + + LDGRT+
Sbjct: 91 ERAFGYYGPLRSVWVAR-----NPPGFAFVEFEDPRDA----ADAVRELDGRTLC 136
>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 = 49.1 bits (117), Expect = 1e-07
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 217 QQRYFSRYGEVIDCVVMKNNETGRSR---GFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
+ YF ++G++ V+ + S+ +VT+ + IQ +DGRT+
Sbjct: 35 RPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL 93
Score = 37.5 bits (87), Expect = 0.001
Identities = 10/40 (25%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 293 VFLGGLPSNVTETDL---RTFFNRYGKVMEVVIMSPRTIR 329
VF+ GL + + ++ +F ++GK+ +VVI + +
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYA 57
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 48.8 bits (117), Expect = 1e-07
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 218 QRYFS-RYGEVIDCVVMKNNETGRSRGFGFVTFADPN 253
+F Y V+ + +TG S+G+GFV F D
Sbjct: 27 YEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDEL 62
Score = 31.5 bits (72), Expect = 0.12
Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 2/47 (4%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLR-TFFNRYGKVMEVVIMSPRT 327
+ +F+G L +V + L F Y ++ +T
Sbjct: 2 SSGSSGPEY-SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQT 47
>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 = 48.5 bits (116), Expect = 1e-07
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 221 FSRYGE-VIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
F+ GE V+ +++N TG G+ FV FAD + ++G+ +
Sbjct: 30 FATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH----KINGKPLP 78
Score = 33.1 bits (76), Expect = 0.029
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRAGITRVP 336
+++G L + E + F G+ +MS + IR +T +P
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGE----TVMSVKIIRNRLTGIP 51
>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 = 48.5 bits (116), Expect = 1e-07
Identities = 8/38 (21%), Positives = 21/38 (55%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
++++G LP ++ D+ F +YG + ++ + + R
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP 61
Score = 45.8 bits (109), Expect = 1e-06
Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 7/55 (12%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
+ F +YG + D + F FV F DP + ++ + DG D
Sbjct: 40 EDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDA----EDAVYGRDGYDYD 87
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 48.4 bits (116), Expect = 1e-07
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMS 324
KV++G L + + +L F+ YG + V I
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIAR 34
Score = 46.5 bits (111), Expect = 5e-07
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 9/55 (16%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
+R FS YG + + + GF FV F DP + ++ LDG+ I
Sbjct: 18 ERAFSYYGPLRTVWIAR-----NPPGFAFVEFEDPRDAEDAVRG----LDGKVIC 63
>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 = 47.6 bits (114), Expect = 2e-07
Identities = 8/35 (22%), Positives = 18/35 (51%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
++++GGL N + L F+R+G + + +
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD 53
Score = 39.5 bits (93), Expect = 1e-04
Identities = 6/58 (10%), Positives = 16/58 (27%), Gaps = 10/58 (17%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
R F R+G + + + F ++ + + + G +
Sbjct: 35 AREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACAK----MRGFPLGGPD 82
>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 = 47.6 bits (114), Expect = 2e-07
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
K+ +G + T +LR F YG V+E I+
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIV 43
Score = 44.5 bits (106), Expect = 3e-06
Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 12/55 (21%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
+ F YG VI+C ++ + + FV + I+ LD
Sbjct: 28 RAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRG----LDNTEFQ 70
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 48.0 bits (114), Expect = 3e-07
Identities = 8/32 (25%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
S G+++D VV + + G ++ FA
Sbjct: 54 ASSQGDILDIVVDL---SDDNSGKAYIVFATQ 82
Score = 37.2 bits (86), Expect = 0.002
Identities = 7/57 (12%), Positives = 18/57 (31%), Gaps = 4/57 (7%)
Query: 277 NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLR----TFFNRYGKVMEVVIMSPRTIR 329
+P P V + + V + L+ + G ++++V+
Sbjct: 16 SPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNS 72
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 46.0 bits (110), Expect = 7e-07
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 288 SSFP---KVFLGGLPS-NVTETDLRTFFNRYGKVMEVVIM 323
+ P ++F+G LP NV++ DL F+ YG +M++ I
Sbjct: 5 HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK 44
Score = 43.7 bits (104), Expect = 5e-06
Identities = 11/55 (20%), Positives = 19/55 (34%), Gaps = 12/55 (21%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
R FS YG ++ + FGF+ F +P +V ++
Sbjct: 29 FRIFSPYGHIMQINIK--------NAFGFIQFDNPQSV----RDAIECESQEMNF 71
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 46.1 bits (110), Expect = 9e-07
Identities = 11/56 (19%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 273 PKPCNPRTLQKPKKNSS--FPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
P NP+ + +++ ++G +P TE DL F +G +++ +
Sbjct: 8 PPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK 63
Score = 34.2 bits (79), Expect = 0.012
Identities = 9/55 (16%), Positives = 17/55 (30%), Gaps = 7/55 (12%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
F +G ++D +G F+ + V I + GR +
Sbjct: 45 IPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVALANFPFQGRNL 93
>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 = 46.0 bits (109), Expect = 9e-07
Identities = 10/69 (14%), Positives = 22/69 (31%), Gaps = 2/69 (2%)
Query: 220 YFSRYG--EVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+FS + + N G+ RG + +V ++ + R ++ N
Sbjct: 31 FFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVYEIN 90
Query: 278 PRTLQKPKK 286
+ K
Sbjct: 91 NEDVDALMK 99
Score = 34.8 bits (80), Expect = 0.007
Identities = 7/29 (24%), Positives = 11/29 (37%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVV 321
+ GLP + T D+ FF+
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGEN 42
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 45.7 bits (109), Expect = 1e-06
Identities = 14/93 (15%), Positives = 34/93 (36%), Gaps = 14/93 (15%)
Query: 185 ATGAAPTGPNPSGPSAGKPPADYSAY------GTYAQYQQRYFSRYGEVIDCVVMKNNET 238
+ + P+ P Y+AY T F + ++++ +T
Sbjct: 1 GSSGSSGKELPTEPP-------YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDT 52
Query: 239 GRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
+ +GF +V F + +++ + L R++
Sbjct: 53 DKFKGFCYVEFDEVDSLKEALTYDGALLGDRSL 85
Score = 34.6 bits (80), Expect = 0.010
Identities = 7/35 (20%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
++G LP N + D+ F + V ++ +
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDK 50
>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 = 45.8 bits (109), Expect = 1e-06
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 267 DGRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSN-VTETDLRTFFNRYGKVMEVVIM 323
G ++ + N PK +S +VF+G L + V ++D+ T F++YG+V +
Sbjct: 6 SGMSLKLQASNVTNKNDPKSINS--RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH 61
Score = 40.4 bits (95), Expect = 1e-04
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 12/55 (21%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
+ FS+YG V C V K G+ FV +++ + + +GR +
Sbjct: 46 ETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAAVLG----ENGRVLA 88
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 46.0 bits (109), Expect = 1e-06
Identities = 13/75 (17%), Positives = 25/75 (33%), Gaps = 3/75 (4%)
Query: 218 QRYFSRYGEV---IDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPK 274
+F ++ + + ++ GR G FV FA ++ L R I+
Sbjct: 41 VAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELF 100
Query: 275 PCNPRTLQKPKKNSS 289
+Q+ S
Sbjct: 101 RSTAAEVQQVLNRFS 115
Score = 37.9 bits (88), Expect = 0.001
Identities = 9/45 (20%), Positives = 17/45 (37%), Gaps = 1/45 (2%)
Query: 277 NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVV 321
+ Q K + V + GLP T ++ FF ++ +
Sbjct: 11 SNEVAQFLSKENQV-IVRMRGLPFTATAEEVVAFFGQHCPITGGK 54
>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 = 45.3 bits (108), Expect = 2e-06
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 288 SSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ +F+ L + VTE L F+++GK+ V +
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL 44
Score = 41.1 bits (97), Expect = 5e-05
Identities = 7/58 (12%), Positives = 26/58 (44%), Gaps = 12/58 (20%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
++ FS++G++ +K + F+ F + + ++ ++G+ ++ +
Sbjct: 29 EKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEE----MNGKDLEGEN 74
>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 = 45.5 bits (108), Expect = 2e-06
Identities = 11/61 (18%), Positives = 22/61 (36%), Gaps = 9/61 (14%)
Query: 220 YFSRYGEV--------IDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC-PHTLDGRT 270
+F + G V + + ETG+ +G V++ DP ++ G
Sbjct: 35 FFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSK 94
Query: 271 I 271
+
Sbjct: 95 L 95
Score = 40.1 bits (94), Expect = 2e-04
Identities = 13/48 (27%), Positives = 20/48 (41%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIR 329
P ++S +++ GL +VT DL FF + G V I
Sbjct: 7 GDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIH 54
>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 = 44.9 bits (106), Expect = 3e-06
Identities = 10/64 (15%), Positives = 24/64 (37%), Gaps = 2/64 (3%)
Query: 263 PHTLDGRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVI 322
H + P+ + + LP +VTE ++ + +GKV +++
Sbjct: 6 HHHHHSSGLVPR--GSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM 63
Query: 323 MSPR 326
+ +
Sbjct: 64 LKGK 67
>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 = 44.2 bits (105), Expect = 4e-06
Identities = 9/54 (16%), Positives = 22/54 (40%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
+ +F + + + R +GFG+ F D +++ + +L + I
Sbjct: 33 KEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRI 86
Score = 34.2 bits (79), Expect = 0.013
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
FLG LP +VTE ++ FF + P
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSN 52
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 44.1 bits (104), Expect = 4e-06
Identities = 8/34 (23%), Positives = 20/34 (58%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+ + LP +VTE ++ + +GKV ++++ +
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK 52
>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 = 43.8 bits (104), Expect = 4e-06
Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 10/75 (13%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
++ F+ V K R + FV F++ + ++ L+G+ +D P
Sbjct: 33 EKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKA----LNGKVLDGSPIE 82
Query: 278 PRTLQKPKKNSSFPK 292
+ K+SS P
Sbjct: 83 VTLAKPVDKDSSGPS 97
Score = 39.2 bits (92), Expect = 2e-04
Identities = 7/39 (17%), Positives = 14/39 (35%)
Query: 288 SSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
SS +++ L + +E + FN + R
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR 51
>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 = 43.8 bits (104), Expect = 5e-06
Identities = 10/54 (18%), Positives = 22/54 (40%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
+ +F + + + R +GFG+ F D +++ + +L R I
Sbjct: 37 KEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRI 90
Score = 35.3 bits (82), Expect = 0.005
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEV-VIMSPRT 327
FLG LP +VTE ++ FF + V + P
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSN 56
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 43.6 bits (103), Expect = 5e-06
Identities = 11/34 (32%), Positives = 16/34 (47%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
V + GL V E DL +G + VV+M +
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK 57
Score = 34.7 bits (80), Expect = 0.008
Identities = 8/54 (14%), Positives = 14/54 (25%), Gaps = 9/54 (16%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVI---QNCPHTLDGRTI 271
+G + VVM + V F D + + + G
Sbjct: 42 LQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPA 89
>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 = 43.5 bits (103), Expect = 9e-06
Identities = 10/40 (25%), Positives = 23/40 (57%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ + V+ GG+ S +T+ +R F+ +G++ME+ +
Sbjct: 19 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF 58
Score = 34.6 bits (80), Expect = 0.011
Identities = 12/59 (20%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPC 276
++ FS +G++++ V +G+ FV F+ + I +++G TI+
Sbjct: 43 RQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHAIV----SVNGTTIEGHVV 91
>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 = 42.9 bits (101), Expect = 1e-05
Identities = 6/35 (17%), Positives = 16/35 (45%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
++F+GG+P ++ + + + VI+
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYAS 44
Score = 42.9 bits (101), Expect = 2e-05
Identities = 13/83 (15%), Positives = 29/83 (34%), Gaps = 11/83 (13%)
Query: 218 QRYFSRYGEVIDCVVMKN--NETGRSRGFGFVTFADPNNVGVVIQ---NCPHTLDGRTI- 271
++ E + V++ + ++RGF FV + + + L G I
Sbjct: 26 LEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA 85
Query: 272 ----DPKP-CNPRTLQKPKKNSS 289
+P+ + ++ SS
Sbjct: 86 VDWAEPEIDVDEDVMETVSGPSS 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 = 42.6 bits (101), Expect = 1e-05
Identities = 11/56 (19%), Positives = 22/56 (39%), Gaps = 6/56 (10%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPC 276
FS+ G C ++ + + + FV F + + + ++GR I K
Sbjct: 36 FSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALA----AMNGRKILGKEV 85
Score = 37.2 bits (87), Expect = 0.001
Identities = 7/32 (21%), Positives = 16/32 (50%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+++G L +VTE + F++ G ++
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMI 48
>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 = 43.5 bits (102), Expect = 1e-05
Identities = 17/120 (14%), Positives = 34/120 (28%), Gaps = 11/120 (9%)
Query: 175 PAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSAYGTYAQYQ---------QRYFSRYG 225
++G P G + G S P + + Q + S
Sbjct: 10 HSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCT 69
Query: 226 --EVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPRTLQK 283
+ V GR G FV ++V + ++ ++ R I+ + +
Sbjct: 70 IHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMDW 129
Score = 31.9 bits (72), Expect = 0.15
Identities = 7/40 (17%), Positives = 13/40 (32%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVV 321
+ V L GLP + + D++ F +
Sbjct: 36 MLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAA 75
>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 = 42.4 bits (100), Expect = 2e-05
Identities = 12/62 (19%), Positives = 24/62 (38%)
Query: 228 IDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPRTLQKPKKN 287
+D V + + GR+ G G V F P + ++ + R ++ P R +
Sbjct: 42 VDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATERQWVAAGGH 101
Query: 288 SS 289
+
Sbjct: 102 IT 103
Score = 37.0 bits (86), Expect = 0.002
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ N V + G+P + E D+R FF+ +V V ++
Sbjct: 8 KPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLL 48
>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 = 41.7 bits (98), Expect = 2e-05
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+ + LP VTET++ +GKV ++++ +
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK 51
>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 = 42.2 bits (99), Expect = 3e-05
Identities = 13/76 (17%), Positives = 27/76 (35%), Gaps = 2/76 (2%)
Query: 218 QRYFSRYG--EVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
Q + S + + V GR G FV ++V + ++ ++ R I+
Sbjct: 35 QNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVFK 94
Query: 276 CNPRTLQKPKKNSSFP 291
+ + K+S
Sbjct: 95 SHRTEMDWVLKHSGPN 110
Score = 33.0 bits (75), Expect = 0.049
Identities = 8/45 (17%), Positives = 15/45 (33%)
Query: 277 NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVV 321
+ + V L GLP + + D++ F + V
Sbjct: 4 GSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVA 48
>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 = 41.7 bits (98), Expect = 3e-05
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
V + GL +V E DL ++G + V++M +
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFK 51
Score = 34.0 bits (78), Expect = 0.015
Identities = 7/72 (9%), Positives = 23/72 (31%), Gaps = 9/72 (12%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNC---PHTLDGRTIDPKPCN 277
++G + ++M + V F + ++ + P + G+
Sbjct: 36 LEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYST 89
Query: 278 PRTLQKPKKNSS 289
+ + +P +
Sbjct: 90 SKRITRPGNSGP 101
>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 = 44.1 bits (103), Expect = 4e-05
Identities = 23/179 (12%), Positives = 34/179 (18%), Gaps = 10/179 (5%)
Query: 96 QWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAP-PQQTGYGSYGPTSGA 154
+ + + G P G G P Q +
Sbjct: 102 VERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQP 161
Query: 155 PQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSAYGTYA 214
P G P A P P P P T
Sbjct: 162 PYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNE 221
Query: 215 QYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDP 273
F+++ + ++ FV F + G L G I
Sbjct: 222 LMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARDA----LQGFKITQ 271
Score = 43.7 bits (102), Expect = 5e-05
Identities = 14/55 (25%), Positives = 28/55 (50%), Gaps = 7/55 (12%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
FS++G+++D +V + + + RG FV F + ++ N ++ G KP
Sbjct: 34 FSQFGQILDILVSR---SLKMRGQAFVIFKEVSS----ATNALRSMQGFPFYDKP 81
Score = 29.5 bits (65), Expect = 1.9
Identities = 4/35 (11%), Positives = 21/35 (60%), Gaps = 4/35 (11%)
Query: 293 VFLGGLPSNVTETDLRT----FFNRYGKVMEVVIM 323
+++ L + + +L+ F+++G+++++++
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS 46
Score = 27.9 bits (61), Expect = 6.0
Identities = 14/55 (25%), Positives = 20/55 (36%)
Query: 273 PKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
P Q +N +FL LP E L FN++ EV ++ R
Sbjct: 190 LMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRH 244
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 41.3 bits (97), Expect = 4e-05
Identities = 10/52 (19%), Positives = 21/52 (40%), Gaps = 3/52 (5%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMS--PRTIRAGIT 333
PK+ K+ + +P ++ L + +YG V ++ T +T
Sbjct: 10 PKRQRIR-KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVT 60
Score = 35.9 bits (83), Expect = 0.003
Identities = 9/55 (16%), Positives = 17/55 (30%), Gaps = 4/55 (7%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCP-HTLDGRTI 271
+YG V C + T VT++ + + L+ T+
Sbjct: 33 DSLLVQYGVVESCEQVN---TDSETAVVNVTYSSKDQARQALDKLNGFQLENFTL 84
>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 = 41.0 bits (96), Expect = 7e-05
Identities = 7/46 (15%), Positives = 17/46 (36%)
Query: 283 KPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTI 328
S + LP+ +++ F+R+G + V++
Sbjct: 3 SGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGIT 48
Score = 31.7 bits (72), Expect = 0.12
Identities = 8/36 (22%), Positives = 13/36 (36%), Gaps = 6/36 (16%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPN 253
Q FSR+G + ++ V F +P
Sbjct: 28 QETFSRFGSLGRVLL------PEGGITAIVEFLEPL 57
>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 = 40.1 bits (94), Expect = 9e-05
Identities = 11/69 (15%), Positives = 21/69 (30%), Gaps = 2/69 (2%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPR 279
+FS V ++ GR G V FA + + + R ++ +
Sbjct: 35 FFSPLN--PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTA 92
Query: 280 TLQKPKKNS 288
+S
Sbjct: 93 GTSGSGPSS 101
Score = 33.9 bits (78), Expect = 0.016
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 286 KNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
++++ V + GLP TE D+ FF+ M V I
Sbjct: 11 QSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIE 47
>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 = 41.0 bits (96), Expect = 1e-04
Identities = 10/43 (23%), Positives = 16/43 (37%), Gaps = 11/43 (25%)
Query: 218 QRYFSRYGEV--------IDCVVMKNNETGRSRGFGFVTFADP 252
+ F RY + D +MK GR +G F+ +
Sbjct: 63 KYIFGRYVDFSSETQRIMFDIRLMK---EGRMKGQAFIGLPNE 102
Score = 34.4 bits (79), Expect = 0.019
Identities = 10/49 (20%), Positives = 18/49 (36%)
Query: 282 QKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTIRA 330
+ + ++++ L +V E DL+ F RY IR
Sbjct: 37 RSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRL 85
>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus} PDB: 3lvh_A
Length = 624
Score = 42.7 bits (100), Expect = 2e-04
Identities = 14/75 (18%), Positives = 26/75 (34%), Gaps = 4/75 (5%)
Query: 10 YYITCFLLQQVEIKKAEPRDASNKGNDMGNNQWGPPQSGGPMAM---GPNMGMGTPSGPM 66
Y+I ++ K + S + + + P G P M GP++ + +
Sbjct: 547 YFIQVMKEYLTKVDKLD-ASESLRKEEEQATETQPIVYGQPQLMLTAGPSVAVPPQAPFG 605
Query: 67 AGMTPMGPGNMMQGY 81
G T G G+
Sbjct: 606 YGYTAPAYGQPQPGF 620
Score = 40.4 bits (94), Expect = 9e-04
Identities = 9/63 (14%), Positives = 16/63 (25%), Gaps = 1/63 (1%)
Query: 16 LLQQVEIKKAEPRDASNKGNDMGNNQWGPPQS-GGPMAMGPNMGMGTPSGPMAGMTPMGP 74
L ++K E + + G Q + G G + P
Sbjct: 562 LDASESLRKEEEQATETQPIVYGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFG 621
Query: 75 GNM 77
+M
Sbjct: 622 YSM 624
Score = 31.9 bits (72), Expect = 0.39
Identities = 9/40 (22%), Positives = 11/40 (27%)
Query: 165 WNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPP 204
+ PQ T + P G T P P G
Sbjct: 583 YGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGY 622
Score = 31.9 bits (72), Expect = 0.44
Identities = 16/40 (40%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 124 PGPQAPPQWGSSYGAPPQQ-TGYGSYGPTSGAPQSGYGNN 162
PQ G S PPQ GYG P G PQ G+G +
Sbjct: 584 GQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGYS 623
Score = 30.3 bits (68), Expect = 1.1
Identities = 11/64 (17%), Positives = 15/64 (23%), Gaps = 18/64 (28%)
Query: 46 QSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPM 105
P+ G M T +A G G AP+ P
Sbjct: 576 TETQPIVYGQPQLMLTAGPSVAVPPQAPFGY------------------GYTAPAYGQPQ 617
Query: 106 NGYA 109
G+
Sbjct: 618 PGFG 621
>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 = 39.2 bits (92), Expect = 2e-04
Identities = 11/58 (18%), Positives = 21/58 (36%), Gaps = 10/58 (17%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
+ FS +G +ID + R FVT+ + + L+G ++
Sbjct: 31 RGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVAE----LNGTQVESVQ 78
Score = 35.7 bits (83), Expect = 0.003
Identities = 9/34 (26%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+++ G ++T T LR F+ +G ++++ + PR
Sbjct: 18 LYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR 49
>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 = 41.0 bits (95), Expect = 2e-04
Identities = 6/54 (11%), Positives = 18/54 (33%), Gaps = 1/54 (1%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
+ + G+V++ + + +G FV F + ++ +
Sbjct: 127 KEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDL 179
Score = 39.0 bits (90), Expect = 0.001
Identities = 10/72 (13%), Positives = 24/72 (33%)
Query: 256 GVVIQNCPHTLDGRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYG 315
+ P P + K + V++ G P++ T D++ + G
Sbjct: 75 KAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKG 134
Query: 316 KVMEVVIMSPRT 327
+V+ + +
Sbjct: 135 QVLNIQMRRTLH 146
>1deq_A Fibrinogen (alpha chain); coiled-coil, blood clotting; 3.50A {Bos
taurus} SCOP: i.9.1.1
Length = 390
Score = 41.8 bits (97), Expect = 3e-04
Identities = 28/171 (16%), Positives = 42/171 (24%), Gaps = 10/171 (5%)
Query: 44 PPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQT 103
P + M + G + G G P S
Sbjct: 228 APLEWKALLEMQQTKMVLETFGGDGHARGDSVSQGTGLAPGSPRKPGTSSIGNVNPGSYG 287
Query: 104 P-MNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNN 162
P +G NP P+ + PG P G+ P+ G++ P P S
Sbjct: 288 PGSSGTWNPGRPEPGSAGTWNPGRPEPGSAGTWNPGRPEPGSAGTWNPGRPEPGSA---- 343
Query: 163 WNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSAYGTY 213
P P G + + P G +GT+
Sbjct: 344 -----GTWNPGRPEPGSAGTWNTGSSGSSSFRPDSSGHGNIRPSSPDWGTF 389
Score = 39.1 bits (90), Expect = 0.002
Identities = 32/171 (18%), Positives = 41/171 (23%), Gaps = 1/171 (0%)
Query: 34 GNDMGNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGF 93
D N Q Q + P M+ +T P Q +
Sbjct: 178 LEDYKNQQKQLEQVIAINLLPSRDIQYLPILKMSTITGPVPREFKSQLQEAPLEWKALLE 237
Query: 94 PGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSG 153
Q +T AP P+ P P S G
Sbjct: 238 MQQTKMVLETFGGDGHARGDSVSQGTGLAPGSPRKPGTSSIGNVNPGSYGPGSSGTWNPG 297
Query: 154 APQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAA-PTGPNPSGPSAGKP 203
P+ G WN P+ G G P G+ G P P P P
Sbjct: 298 RPEPGSAGTWNPGRPEPGSAGTWNPGRPEPGSAGTWNPGRPEPGSAGTWNP 348
>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 = 39.1 bits (91), Expect = 3e-04
Identities = 8/35 (22%), Positives = 15/35 (42%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRT 327
V GGL + V+ L + G V +++ +
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP 64
Score = 29.5 bits (66), Expect = 0.68
Identities = 4/35 (11%), Positives = 10/35 (28%), Gaps = 6/35 (17%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADP 252
+ G V ++ N + + F +
Sbjct: 45 LPVLEKCGLVDALLMPPN------KPYSFARYRTT 73
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 41.6 bits (97), Expect = 4e-04
Identities = 36/171 (21%), Positives = 62/171 (36%), Gaps = 13/171 (7%)
Query: 44 PPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQ- 102
P S + P +P+ P + P ++P ++P+S
Sbjct: 1583 PSYSPTSPSYSPTSPSYSPTSP--SYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1640
Query: 103 -TPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYG----SYGPTSGAPQS 157
+P + +P++P Y+ P +P +S P Y SY PTS S
Sbjct: 1641 YSPTSPSYSPTSPS-YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS-PSYS 1698
Query: 158 GYGNNWNWNMPQNGPTTPA-AGGPPAGGATGAA--PTGPNPSGPSAGKPPA 205
+++ P PT+P+ + P+ T + PT P+ S S P
Sbjct: 1699 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1749
>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 = 39.0 bits (91), Expect = 4e-04
Identities = 9/47 (19%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 280 TLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPR 326
+ + + +++ G ++T T LR F+ +G ++++ + PR
Sbjct: 29 SFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR 73
Score = 39.0 bits (91), Expect = 4e-04
Identities = 20/105 (19%), Positives = 34/105 (32%), Gaps = 16/105 (15%)
Query: 175 PAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSAY----GTYAQYQQRYFSRYGEVIDC 230
++G P G G P + S P P + Y + FS +G +ID
Sbjct: 10 HSSGLVPRGSHMG--PFRRSDSFPERRAPRKGNTLYVYGEDMTPTLLRGAFSPFGNIIDL 67
Query: 231 VVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
+ R FVT+ + + L+G ++
Sbjct: 68 SMDPP------RNCAFVTYEKMESADQAVAE----LNGTQVESVQ 102
>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 = 37.9 bits (88), Expect = 0.001
Identities = 12/48 (25%), Positives = 18/48 (37%)
Query: 277 NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMS 324
PR P S +V + GLP + + DL+ G V +
Sbjct: 3 APRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR 50
Score = 30.6 bits (69), Expect = 0.26
Identities = 9/53 (16%), Positives = 15/53 (28%), Gaps = 11/53 (20%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTID 272
+ G+V V ++ G G V F ++ LD
Sbjct: 36 HMREAGDVCYADVYRD-------GTGVVEFVRKEDM----TYAVRKLDNTKFR 77
>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 = 38.3 bits (89), Expect = 0.001
Identities = 21/125 (16%), Positives = 33/125 (26%), Gaps = 13/125 (10%)
Query: 175 PAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSAYGTYAQ-----YQ------QRYFSR 223
++G P G + G S S G Y+ +FS
Sbjct: 10 HSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSP 69
Query: 224 YGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNPRTLQK 283
V V ++ GR G V FA + + R I+ +
Sbjct: 70 LNPV--RVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGASN 127
Query: 284 PKKNS 288
+S
Sbjct: 128 GAYSS 132
Score = 34.8 bits (80), Expect = 0.015
Identities = 10/45 (22%), Positives = 18/45 (40%)
Query: 273 PKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKV 317
+ ++++ V + GLP TE D+ FF+ V
Sbjct: 29 QMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV 73
>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 = 37.0 bits (86), Expect = 0.001
Identities = 7/37 (18%), Positives = 18/37 (48%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMSPRTI 328
++++G +P +TE + FFN ++ + +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPV 44
Score = 31.6 bits (72), Expect = 0.072
Identities = 6/59 (10%), Positives = 17/59 (28%), Gaps = 5/59 (8%)
Query: 218 QRYFSRYGEVIDCVVMKNNE-----TGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTI 271
+F+ + N + + F F+ F + + G+++
Sbjct: 24 MDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSL 82
>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 = 35.7 bits (83), Expect = 0.003
Identities = 10/59 (16%), Positives = 21/59 (35%), Gaps = 2/59 (3%)
Query: 220 YFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCNP 278
+ + + + N G G+ FV F++ V ++ + GR I+
Sbjct: 30 FLAPLK--PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREKS 86
Score = 35.4 bits (82), Expect = 0.004
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
++ V L G P NVTE ++ F K + + I+
Sbjct: 4 GSSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIV 42
>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 = 35.5 bits (82), Expect = 0.003
Identities = 5/30 (16%), Positives = 10/30 (33%), Gaps = 1/30 (3%)
Query: 292 KVFLGGLPSNVTETDLRTFFNRYG-KVMEV 320
+ + LP + ++ Y K V
Sbjct: 7 GILVKNLPQDSNCQEVHDLLKDYDLKYCYV 36
Score = 33.9 bits (78), Expect = 0.012
Identities = 9/52 (17%), Positives = 15/52 (28%), Gaps = 8/52 (15%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHT-LDGRTI 271
Y +K R++ FVT + IQ G+ +
Sbjct: 26 LKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDL 70
>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 = 35.9 bits (83), Expect = 0.004
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 284 PKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIMS 324
P + S +V + GLP + + DL+ G V +
Sbjct: 10 PSRRSEN-RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR 49
Score = 33.2 bits (76), Expect = 0.028
Identities = 15/86 (17%), Positives = 24/86 (27%), Gaps = 19/86 (22%)
Query: 195 PSGPSAGKPPADYS--------AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGF 246
SG S G P Q + + G+V V ++ G G
Sbjct: 2 SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 54
Query: 247 VTFADPNNVGVVIQNCPHTLDGRTID 272
V F ++ ++ LD
Sbjct: 55 VEFVRKEDMTYAVR----KLDNTKFR 76
>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 = 36.1 bits (83), Expect = 0.004
Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 2/57 (3%)
Query: 272 DPKPCNPRTLQKPKKNSSFPKV-FLGGLP-SNVTETDLRTFFNRYGKVMEVVIMSPR 326
K + QK + +V L LP S +++ + YGK+ ++M +
Sbjct: 6 SGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK 62
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 35.2 bits (81), Expect = 0.004
Identities = 11/56 (19%), Positives = 20/56 (35%), Gaps = 2/56 (3%)
Query: 272 DPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKV-MEVVIMSPR 326
P + + V++G LP + +DL+ G V + + PR
Sbjct: 2 SSGSSGPGSPPGEGAPLAA-DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPR 56
Score = 32.5 bits (74), Expect = 0.052
Identities = 12/94 (12%), Positives = 18/94 (19%), Gaps = 15/94 (15%)
Query: 188 AAPTGPNPSGPSAGKPPADYSAY------GTYAQYQQRYFSRYGEVIDCVVMKNNETGRS 241
+ P P P Y +R G V
Sbjct: 1 GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELG-----SVPLRLTWQGP 55
Query: 242 RGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKP 275
R F+ + D + L G +
Sbjct: 56 RRRAFLHYPDSAAAQQAVSC----LQGLRLGTDT 85
>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor,
chromophore, glycoprotein, lipoprotein, membrane,
palmitate phosphorylation; HET: BOG RET PLM TWT PC1;
2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A*
Length = 448
Score = 38.0 bits (88), Expect = 0.005
Identities = 26/87 (29%), Positives = 30/87 (34%), Gaps = 4/87 (4%)
Query: 62 PSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWG 121
PS A M M M + Q + P P Q PQGY G
Sbjct: 364 PSADAAQMKEMMAM-MQKMQQQQAAYPPQGYAPPPQGYPPQGY---PPQGYPPQGYPPQG 419
Query: 122 APPGPQAPPQWGSSYGAPPQQTGYGSY 148
PP PQ P G+ APPQ +Y
Sbjct: 420 YPPPPQGAPPQGAPPAAPPQGVDNQAY 446
Score = 34.5 bits (79), Expect = 0.055
Identities = 25/95 (26%), Positives = 26/95 (27%), Gaps = 11/95 (11%)
Query: 98 APSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQS 157
SS + A A P G APP Q P G P
Sbjct: 357 GESSDAAPSADAAQMKEMMAMMQKMQQQQAAYPPQGY---APPPQGYPPQGYPPQGYPPQ 413
Query: 158 GYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTG 192
GY P G P G PP G A P G
Sbjct: 414 GY--------PPQGYPPPPQGAPPQGAPPAAPPQG 440
Score = 33.7 bits (77), Expect = 0.092
Identities = 24/76 (31%), Positives = 25/76 (32%), Gaps = 3/76 (3%)
Query: 86 STPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGY 145
+ P GYA P PQGY G PP PPQ G PP G
Sbjct: 371 MKEMMAMMQKMQQQQAAYPPQGYAPP--PQGYPPQGYPPQG-YPPQGYPPQGYPPPPQGA 427
Query: 146 GSYGPTSGAPQSGYGN 161
G AP G N
Sbjct: 428 PPQGAPPAAPPQGVDN 443
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 3cw1_A
Length = 231
Score = 36.9 bits (85), Expect = 0.007
Identities = 29/153 (18%), Positives = 40/153 (26%), Gaps = 10/153 (6%)
Query: 31 SNKGNDMGNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQT 90
D G + + G +G G G P+G P G ++G G + Q
Sbjct: 84 GPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVG--GPSQQV 141
Query: 91 QGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGP 150
G+ ++ + AP Y P P P GP
Sbjct: 142 MTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGP 201
Query: 151 TSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAG 183
G P G P PP G
Sbjct: 202 PMGIPP--------GRGTPMGMPPPGMRPPPPG 226
Score = 31.2 bits (70), Expect = 0.50
Identities = 34/154 (22%), Positives = 40/154 (25%), Gaps = 11/154 (7%)
Query: 44 PPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQT 103
P +G G G AG M Q G + G P Q + Q
Sbjct: 87 PKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQG 146
Query: 104 PMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNW 163
A +A AP Q+ G PP G G+ P P G
Sbjct: 147 RGTVAAAAAAAT-------ASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRP-- 197
Query: 164 NWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSG 197
M P G P G P P G
Sbjct: 198 --PMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRG 229
Score = 29.6 bits (66), Expect = 1.3
Identities = 25/138 (18%), Positives = 29/138 (21%), Gaps = 3/138 (2%)
Query: 67 AGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGP 126
MT GP G PG + + G P AP G G G
Sbjct: 78 VSMTVEGPPPK-DTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGL--AGPVRGV 134
Query: 127 QAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGAT 186
P Q + + S A P G
Sbjct: 135 GGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPG 194
Query: 187 GAAPTGPNPSGPSAGKPP 204
P GP P P
Sbjct: 195 MRPPMGPPMGIPPGRGTP 212
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 36.6 bits (84), Expect = 0.011
Identities = 35/189 (18%), Positives = 53/189 (28%), Gaps = 36/189 (19%)
Query: 79 QGYQGWGSTPQ--TQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPG----PQAPPQW 132
+ TQ +P+ + M A PS PG P +
Sbjct: 5 HHHHVDDDDKMFSTQVNSSLTSPTGRGSM---AAPSLHPSLGPGIGSPGQLHSPISTLSS 61
Query: 133 GSSYGAPPQQTGYGSYGPTSGA----PQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATG- 187
+ PP GP S + P G+ P + + P G G
Sbjct: 62 PINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGV 121
Query: 188 -AAPTGPNPSGPSAGKPP----ADYSA---YGTYA------------QYQQRYFSRYGEV 227
P P+ + S K D S+ YG Y+ + Y R +
Sbjct: 122 LKVPAHPSGNMASFTKHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNK- 180
Query: 228 IDCVVMKNN 236
DC++ K
Sbjct: 181 -DCLIDKRQ 188
Score = 30.1 bits (67), Expect = 1.5
Identities = 19/114 (16%), Positives = 30/114 (26%), Gaps = 3/114 (2%)
Query: 45 PQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTP 104
P G M PS + +G + S+P P SS
Sbjct: 22 SSLTSPTGRGS---MAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMGPPFSVISSPMG 78
Query: 105 MNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSG 158
+ + P+ P + G+P SS P G + +
Sbjct: 79 PHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPSGNM 132
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 34.0 bits (78), Expect = 0.015
Identities = 18/102 (17%), Positives = 25/102 (24%), Gaps = 15/102 (14%)
Query: 190 PTGPNPSGPSAGKPPA-DYS------AYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSR 242
+G P G K PA Y G Q + + T
Sbjct: 11 SSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDFD 67
Query: 243 GFGFVTFADPNNVGVVIQNC-PHTLDGRTI----DPKPCNPR 279
G G + F + ++ G I D P R
Sbjct: 68 GTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPPPIR 109
Score = 32.5 bits (74), Expect = 0.060
Identities = 7/41 (17%), Positives = 13/41 (31%)
Query: 277 NPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKV 317
PR K + ++ + LP + DL+
Sbjct: 15 VPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLE 55
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 32.5 bits (74), Expect = 0.052
Identities = 6/43 (13%), Positives = 13/43 (30%), Gaps = 2/43 (4%)
Query: 282 QKPKKNSSFPKVFLGGLPSNV-TETDLRTFFNRYGKVMEVVIM 323
QK + + V + L +G + +I+
Sbjct: 8 QKGRVETR-RVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL 49
>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP,
translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A
Length = 504
Score = 34.5 bits (80), Expect = 0.053
Identities = 10/65 (15%), Positives = 15/65 (23%)
Query: 43 GPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQ 102
G M N+ + M M ++ G Q A +
Sbjct: 436 GIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMAGLQSMMRQFQQGAAGNM 495
Query: 103 TPMNG 107
M G
Sbjct: 496 KGMMG 500
Score = 33.8 bits (78), Expect = 0.098
Identities = 21/85 (24%), Positives = 29/85 (34%), Gaps = 9/85 (10%)
Query: 16 LLQQVE-----IKKAEPRDASNKGNDMGNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMT 70
LL Q +KK KG DM N + M M M GM
Sbjct: 420 LLTQYTKFAQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHH-MGGMA 478
Query: 71 PMGPGNMMQGYQGWGSTPQTQGFPG 95
+ +MM+ +Q G+ +G G
Sbjct: 479 GLQ--SMMRQFQQ-GAAGNMKGMMG 500
Score = 33.4 bits (77), Expect = 0.12
Identities = 13/71 (18%), Positives = 18/71 (25%), Gaps = 1/71 (1%)
Query: 37 MGNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQ 96
MG + G + G M + MA M + M G G S +
Sbjct: 434 MGGIK-GLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMAGLQSMMRQFQQGAA 492
Query: 97 WAPSSQTPMNG 107
N
Sbjct: 493 GNMKGMMGFNN 503
>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 = 32.4 bits (74), Expect = 0.057
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 8/48 (16%)
Query: 222 SRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGR 269
S++G++ ++ + G V+F DP C TLDGR
Sbjct: 48 SKFGQIRKLLLFDRHPDGV----ASVSFRDPEEA----DYCIQTLDGR 87
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 32.7 bits (74), Expect = 0.059
Identities = 18/107 (16%), Positives = 33/107 (30%), Gaps = 19/107 (17%)
Query: 177 AGGPPAGGATGAAPTGPNPSGPSA------GKPPADYSAYGTYAQYQQRYFSRYGEVIDC 230
+G + A G +G S Y + FS++G V+
Sbjct: 4 SGNLALAASAAAVDAGMAMAGQSPVLRIIVENLF-----YPVTLDVLHQIFSKFGTVLKI 58
Query: 231 VVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ N ++ + +ADP + + DG+ I C
Sbjct: 59 ITFTKN----NQFQALLQYADPVSAQHAKLSL----DGQNIYNACCT 97
Score = 29.6 bits (66), Expect = 0.79
Identities = 7/31 (22%), Positives = 16/31 (51%)
Query: 293 VFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ + L VT L F+++G V++++
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITF 61
>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 = 31.9 bits (73), Expect = 0.085
Identities = 11/49 (22%), Positives = 17/49 (34%), Gaps = 8/49 (16%)
Query: 221 FSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGR 269
+++G VI V KN+ G +V + L GR
Sbjct: 38 CNKHGGVIHIYVDKNSAQGN----VYVKCPSIAAA----IAAVNALHGR 78
>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 = 31.6 bits (72), Expect = 0.13
Identities = 8/53 (15%), Positives = 17/53 (32%), Gaps = 8/53 (15%)
Query: 222 SRYGEVIDCVVMKNNETGRSRGFG----FVTFADPNNVGVVIQNCPHTLDGRT 270
++G V ++ + + FV F+ + L+GR
Sbjct: 47 GKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASET----HKAIQALNGRW 95
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid
cyclase fold, DDXXXXD motif, NDXXSXXXE MOT
methylisoborneol biosynthesis; HET: GST; 1.80A
{Streptomyces coelicolor} PDB: 3v1x_A*
Length = 433
Score = 33.2 bits (75), Expect = 0.13
Identities = 20/120 (16%), Positives = 29/120 (24%), Gaps = 14/120 (11%)
Query: 85 GSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTG 144
GS+ S P + + + PP PP
Sbjct: 2 GSSH-----HHHHHSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPA- 55
Query: 145 YGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPP 204
P +G P + GPT P G + P P P++ P
Sbjct: 56 -----PAAGNPPDTVTGDSVLQRILRGPTGP---GTTSLAPAVRYGRQPGPEAPASAPPA 107
Score = 32.8 bits (74), Expect = 0.19
Identities = 14/105 (13%), Positives = 24/105 (22%), Gaps = 12/105 (11%)
Query: 127 QAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGAT 186
+ S G P+ + + + S + + + P P P AG
Sbjct: 3 SSHHHHHHSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPP 62
Query: 187 GA------------APTGPNPSGPSAGKPPADYSAYGTYAQYQQR 219
PTGP + + A
Sbjct: 63 DTVTGDSVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPA 107
>1dx0_A Prion protein; brain, repeat; NMR {Bos taurus} SCOP: d.6.1.1 PDB:
1dx1_A 1qlx_A 1qlz_A
Length = 219
Score = 32.5 bits (73), Expect = 0.17
Identities = 26/142 (18%), Positives = 34/142 (23%)
Query: 83 GWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQ 142
G P+ G + N PQG WG P G G +G P
Sbjct: 1 GSKKRPKPGGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGG 60
Query: 143 TGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGK 202
+G G P G G Q + AA G
Sbjct: 61 GWGQPHGGGWGQPHGGGGWGQGGTHGQWNKPSKPKTNMKHVAGAAAAGAVVGGLGGYMLG 120
Query: 203 PPADYSAYGTYAQYQQRYFSRY 224
+ Y+ RY+
Sbjct: 121 SAMSRPLIHFGSDYEDRYYREN 142
Score = 31.7 bits (71), Expect = 0.32
Identities = 19/116 (16%), Positives = 25/116 (21%)
Query: 43 GPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQ 102
P GG G G G G GWG Q
Sbjct: 5 RPKPGGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQ 64
Query: 103 TPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSG 158
G+ P G+ G P + ++ G+ G G
Sbjct: 65 PHGGGWGQPHGGGGWGQGGTHGQWNKPSKPKTNMKHVAGAAAAGAVVGGLGGYMLG 120
>3iz6_A 40S ribosomal protein SA (S2P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 305
Score = 32.0 bits (72), Expect = 0.24
Identities = 18/82 (21%), Positives = 27/82 (32%), Gaps = 6/82 (7%)
Query: 79 QGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGA 138
G + P + G+W + Q +W A P P A W ++ A
Sbjct: 229 YGAVAEYAAPAADTWGGEWGTDAAAQ----PAAIPAQAGADWTAAPAPAAGG-WDTA-AA 282
Query: 139 PPQQTGYGSYGPTSGAPQSGYG 160
P GS + AP +G
Sbjct: 283 PAPGWEQGSAPVPAAAPTPNWG 304
>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets,
alpha helices, AMY amyloidosis, blood coagulation,
disease mutation, glycoprot phosphoprotein; HET: NAG NDG
BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A*
2a45_G*
Length = 562
Score = 31.4 bits (70), Expect = 0.55
Identities = 28/134 (20%), Positives = 43/134 (32%), Gaps = 8/134 (5%)
Query: 72 MGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQ 131
M + G T+G + S+T + + + G P
Sbjct: 233 TDMPQMRMELERPGGNEITRGGSTSYGTGSETESPRNPSSAGSWNSGSSGPGSTGNRNP- 291
Query: 132 WGSSYGAPPQQTGYGSYGP----TSGAPQSGYGNNWNWNM--PQNGPTTPAAGGPPAGGA 185
GSS GS GP + + SG G+ N N P+ G T G G+
Sbjct: 292 -GSSGTGGTATWKPGSSGPGSTGSWNSGSSGTGSTGNQNPGSPRPGSTGTWNPGSSERGS 350
Query: 186 TGAAPTGPNPSGPS 199
G + + SG +
Sbjct: 351 AGHWTSESSVSGST 364
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 29.4 bits (65), Expect = 0.62
Identities = 15/60 (25%), Positives = 21/60 (35%), Gaps = 5/60 (8%)
Query: 202 KPPADYSAYGTYAQYQQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQN 261
D S G R +YGEV++ V+ G V FA + +QN
Sbjct: 19 CKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKK-----PGTAVVEFATVKAAELAVQN 73
Score = 28.6 bits (63), Expect = 1.3
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 301 NVTETDLRTFFNRYGKVMEVVIMSPRTIRA 330
++ L +YG+V+ +V+ S + A
Sbjct: 28 GYSKDVLLRLLQKYGEVLNLVLSSKKPGTA 57
>2b5u_A Colicin E3; high resolution colicin E3, ribosome inactivation,
ribosome inhibitor, hydrolase; HET: CIT; 2.30A
{Escherichia coli} SCOP: b.101.1.1 b.110.1.1 h.4.9.1
PDB: 1jch_A* 1ujw_B* 2ysu_B 1e44_B 2xfz_Y* 2xg1_Y*
Length = 551
Score = 31.1 bits (69), Expect = 0.71
Identities = 25/125 (20%), Positives = 38/125 (30%), Gaps = 2/125 (1%)
Query: 33 KGNDMGNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQG 92
+G++ G + +GGP +G G SG + P G G+ + G GS G
Sbjct: 7 RGHNTGAHSTSGNINGGPTGLGVGGGASDGSGWSSENNPWGGGSGSGIHWGGGSGHGNGG 66
Query: 93 FPGQ--WAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGP 150
G + ++ A P A G A + A GP
Sbjct: 67 GNGNSGGGSGTGGNLSAVAAPVAFGFPALSTPGAGGLAVSISAGALSAAIADIMAALKGP 126
Query: 151 TSGAP 155
Sbjct: 127 FKFGL 131
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 30.1 bits (67), Expect = 0.91
Identities = 7/45 (15%), Positives = 19/45 (42%), Gaps = 9/45 (20%)
Query: 293 VFLGGLPSNVT---------ETDLRTFFNRYGKVMEVVIMSPRTI 328
+++GG+ + E+ +R F+R G + + + +
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNC 181
Score = 28.6 bits (63), Expect = 2.8
Identities = 9/37 (24%), Positives = 16/37 (43%), Gaps = 6/37 (16%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNN 254
+ FSR G++ +++ + GFV F N
Sbjct: 161 RFVFSRLGDIDRIRYVES------KNCGFVKFKYQAN 191
>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 = 29.7 bits (66), Expect = 0.99
Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 8/59 (13%)
Query: 219 RYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPCN 277
+ FS++G V+ + N ++ + +ADP + + DG+ I C
Sbjct: 65 QIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL----DGQNIYNACCT 115
Score = 28.9 bits (64), Expect = 1.6
Identities = 8/56 (14%), Positives = 19/56 (33%)
Query: 268 GRTIDPKPCNPRTLQKPKKNSSFPKVFLGGLPSNVTETDLRTFFNRYGKVMEVVIM 323
+ S ++ + L VT L F+++G V++++
Sbjct: 24 NLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF 79
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 29.3 bits (65), Expect = 1.0
Identities = 12/78 (15%), Positives = 19/78 (24%), Gaps = 16/78 (20%)
Query: 218 QRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFADPNNVGVVIQNCPHTLDGRTIDPKPC- 276
+ G+V V+ K N V F +G I C
Sbjct: 43 YTVCNPVGKVQRIVIFKRN-----GIQAMVEFESVLCAQKAKAAL----NGADIYAGCCT 93
Query: 277 ------NPRTLQKPKKNS 288
P L + ++
Sbjct: 94 LKIEYARPTRLNVIRNDN 111
>4dpv_Z Protein (parvovirus coat protein); complex (virus/DNA), FULL
capsid, single-stranded DNA, icosahedral virus; HET:
DNA; 2.90A {Canine parvovirus} SCOP: b.121.5.2 PDB:
1c8h_A* 1c8d_A 1ijs_P* 1fpv_A 2cas_A 1p5w_A* 1p5y_A
1c8e_A 1c8f_A 1c8g_A
Length = 584
Score = 30.2 bits (67), Expect = 1.4
Identities = 20/133 (15%), Positives = 29/133 (21%), Gaps = 1/133 (0%)
Query: 62 PSGPMAGMTPMGPGNMMQGYQGWGSTPQTQG-FPGQWAPSSQTPMNGYANPSAPQGYTNW 120
+ + T M P + + TQG F A + +
Sbjct: 321 NTNYITEATIMRPAEVGYSAPYYSFEASTQGPFKTPIAAGRGGAQTDENQAADGNPRYAF 380
Query: 121 GAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGP 180
G G + + P Q+ N N PT P G
Sbjct: 381 GRQHGQKTTTTGETPERFTYIAHQDTGRYPEGDWIQNINFNLPVTNDNVLLPTDPIGGKT 440
Query: 181 PAGGATGAAPTGP 193
GP
Sbjct: 441 GINYTNIFNTYGP 453
>2zkq_b 40S ribosomal protein SA; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 295
Score = 28.9 bits (64), Expect = 2.5
Identities = 13/53 (24%), Positives = 18/53 (33%), Gaps = 9/53 (16%)
Query: 83 GWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPPQWGSS 135
W Q P Q P+ + SA +W A P QA +W +
Sbjct: 247 DWSEGVQVPSVPIQQFPTE--------DWSAQPSTEDWSAAPTAQA-TEWVGT 290
>2p7n_A Pathogenicity island 1 effector protein; CVR69, structural
genomics, PSI-2, protein structure initiative; 2.80A
{Chromobacterium violaceum}
Length = 407
Score = 29.3 bits (64), Expect = 2.6
Identities = 16/97 (16%), Positives = 24/97 (24%), Gaps = 4/97 (4%)
Query: 114 PQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAP----QSGYGNNWNWNMPQ 169
PQ A P AP A PQ + + Q+ +
Sbjct: 15 PQALETQAAAPQSDAPDASAGQTRAAPQGSAAPALAAARAKADELGQAAREVRASVERQT 74
Query: 170 NGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPAD 206
T AA A + G P + + +
Sbjct: 75 AYETRLAAQRSAAAFSGGEPPQARREAPGAELDEARN 111
>3lof_A Heat shock 70 kDa protein 1; structural genomics, HSPA1B, HSP70,
PSI-2, prote structure initiative; 2.40A {Homo sapiens}
PDB: 2lmg_A
Length = 113
Score = 27.6 bits (61), Expect = 3.1
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 176 AAGGPPAGGATGAAPTGPNPSGPS 199
AGGP GG P G + SGP+
Sbjct: 85 GAGGPGPGGFGAQGPKGGSGSGPT 108
>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane
fusion, viral P glycoprotein B, HSV-1, membrane; HET:
NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A*
3nwd_A*
Length = 703
Score = 28.8 bits (64), Expect = 3.3
Identities = 10/44 (22%), Positives = 13/44 (29%), Gaps = 2/44 (4%)
Query: 171 GPTTPAAGGPPAG--GATGAAPTGPNPSGPSAGKPPADYSAYGT 212
PT+P G A A G T P+ +A
Sbjct: 4 APTSPGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKKNKK 47
>1o9i_A Pseudocatalase; oxidoreductase, hexamer, dimanganese catalase,
metalloenzyme, preoxidase; HET: MES; 1.33A
{Lactobacillus plantarum} SCOP: a.25.1.3 PDB: 1jkv_A
1jku_A
Length = 266
Score = 28.5 bits (63), Expect = 3.8
Identities = 7/48 (14%), Positives = 9/48 (18%)
Query: 165 WNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPSAGKPPADYSAYGT 212
N + G G P G P D +
Sbjct: 217 MNFSDGDGSKAFEGQVAKDGEKFTYQENPEAMGGIPHIKPGDPRLHNH 264
>1cpn_A Circularly permuted; hydrolase(glucanase); 1.80A {Paenibacillus
macerans} SCOP: b.29.1.2 PDB: 1cpm_A
Length = 208
Score = 28.2 bits (63), Expect = 3.9
Identities = 16/84 (19%), Positives = 20/84 (23%), Gaps = 12/84 (14%)
Query: 89 QTQGFPGQWAPSSQTPMNGYANPSAPQGYTNWGAPPGPQAPP----QWGSSYGAPPQQTG 144
T P TP N G +W P W
Sbjct: 110 ATANIP-------STPGKIMMNLWNGTGVDDWLGSYNGANPLYAEYDWVKYTSNGSVFWE 162
Query: 145 YGSYG-PTSGAPQSGYGNNWNWNM 167
SY P++ GY N +N
Sbjct: 163 PKSYFNPSTWEKADGYSNGGVFNC 186
>3iyo_A Capsid protein; amino acid sequence, cryoelectron microscopy,
dimerization, image processing, computer-assist
molecular sequence DATA; 10.50A {Hepatitis e virus}
Length = 660
Score = 28.8 bits (63), Expect = 4.2
Identities = 25/153 (16%), Positives = 33/153 (21%), Gaps = 13/153 (8%)
Query: 51 MAMGPNMGMGTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQW-------APSSQT 103
+ M P G PSG G G G WG +Q F + AP
Sbjct: 14 LPMLPAPPPGQPSGRRRGRRSGGSGG-----GFWGDRVDSQPFAIPYIHPTNPFAPDVTA 68
Query: 104 PMNGYANPSAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNW 163
P Q P + P P ++
Sbjct: 69 AAGAGPRVRQPARPLGSAWRDQAQRPAVASRRRPTTAGAAPLTAVAPAHDTPPVPDVDSR 128
Query: 164 NWNM-PQNGPTTPAAGGPPAGGATGAAPTGPNP 195
+ Q +T A G P
Sbjct: 129 GAILRRQYNLSTSPLTSSVATGTNLVLYAAPLS 161
>2waa_A Acetyl esterase, xylan esterase, putative, AXE2C; carbohydrate
binding, plant cell WALL degradation, hydrolase,
cellulases; 1.80A {Cellvibrio japonicus}
Length = 347
Score = 28.3 bits (62), Expect = 4.4
Identities = 8/65 (12%), Positives = 12/65 (18%), Gaps = 1/65 (1%)
Query: 112 SAPQGYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNG 171
S G + W + G G +WN +
Sbjct: 141 SVTCGEAIDRVAGEDKNTRWWNARESYGMLTAKALDAQVQLVC-WGGRGLIRSWNGKTDD 199
Query: 172 PTTPA 176
P
Sbjct: 200 ANLPD 204
>3few_X Colicin S4; cell lysis, Y-RAY, cell killing, immune system; 2.45A
{Escherichia coli}
Length = 505
Score = 28.3 bits (62), Expect = 5.0
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 146 GSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTG 192
YGPT+G G G N N Q G + G GG +G+ G
Sbjct: 6 SVYGPTAGESMGGTGANLN----QQGGNNNSNSGVHWGGGSGSGNGG 48
>2zws_A Neutral ceramidase; prism fold and beta-sandwich fold, hydrolase,
lipid metaboli secreted; HET: PLM; 1.40A {Pseudomonas
aeruginosa} PDB: 2zxc_A*
Length = 646
Score = 28.3 bits (62), Expect = 5.1
Identities = 17/96 (17%), Positives = 22/96 (22%), Gaps = 8/96 (8%)
Query: 72 MGPGNMMQGYQGWGSTPQTQGFPGQ---WAPSSQTPMNGYANPSAPQGYTNWGAPPGPQA 128
G N Y Q + G + P +Q A A
Sbjct: 439 NGYANAYASYVTTREEYAAQEYEGGSTLYGPWTQAAYQQLFVDMAVALRERLPVETSAIA 498
Query: 129 PP----QWGSSYGAPPQQTGYG-SYGPTSGAPQSGY 159
P Q G G S+G P+ Y
Sbjct: 499 PDLSCCQMNFQTGVVADDPYIGKSFGDVLQQPRESY 534
>2p51_A SPCC18.06C protein; DEDD nuclease fold, hydrolase, gene regulation;
1.40A {Schizosaccharomyces pombe} PDB: 3g0z_A 3g10_A
Length = 333
Score = 27.8 bits (61), Expect = 6.9
Identities = 10/56 (17%), Positives = 14/56 (25%)
Query: 144 GYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPS 199
G + + PT AG P T +AP N +
Sbjct: 273 GSTGSVLWHNNSSTPQIQFRDLPGAHPSPTPSNAGIPTTLTNTSSAPNFANSTFRF 328
>1kb0_A Quinohemoprotein alcohol dehydrogenase; beta-propeller fold,
cytochrome C, oxidoreductase; HET: TRO HEC PQQ; 1.44A
{Comamonas testosteroni} SCOP: a.3.1.6 b.70.1.1
Length = 677
Score = 28.0 bits (62), Expect = 7.0
Identities = 24/91 (26%), Positives = 31/91 (34%)
Query: 116 GYTNWGAPPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTP 175
GY G P G A A P G ++ P S PQ+G N+P N
Sbjct: 363 GYDKHGKPIGIAAARDGSKPQDAVPGPYGAHNWHPMSFNPQTGLVYLPAQNVPVNLMDDK 422
Query: 176 AAGGPPAGGATGAAPTGPNPSGPSAGKPPAD 206
AG + TG N + +PP
Sbjct: 423 KWEFNQAGPGKPQSGTGWNTAKFFNAEPPKS 453
>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 = 26.8 bits (58), Expect = 7.4
Identities = 5/22 (22%), Positives = 11/22 (50%)
Query: 350 QQVLRRSSTTKVQAPFGATTLS 371
Q + + ++ K+ A A L+
Sbjct: 20 QALKKLQASLKLYADDSAPALA 41
>1xk7_A Crotonobetainyl-COA:carnitine COA-transferase; CAIB,
montreal-kingston bacterial structural genomics
initiative, BSGI, structural genomics; 1.60A
{Escherichia coli} SCOP: c.123.1.1 PDB: 1xk6_A 1xvt_A*
1xvu_A* 1xvv_A* 1xa3_A* 1xa4_A*
Length = 408
Score = 27.5 bits (62), Expect = 7.9
Identities = 18/94 (19%), Positives = 24/94 (25%), Gaps = 25/94 (26%)
Query: 143 TGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPPAGGATGAAPTGPNPSGPS-AG 201
+G+G YG Y + Q A G G P A
Sbjct: 127 SGFGQYGTEEYTNLPAYN-----TIAQ------AFSG-------YLIQNGD-VDQPMPAF 167
Query: 202 KPPAD-----YSAYGTYAQYQQRYFSRYGEVIDC 230
AD + A + + GE ID
Sbjct: 168 PYTADYFSGLTATTAALAALHKVRETGKGESIDI 201
>2oxa_A Extracellular serine protease; kexin, hydrolase; 1.65A {Aeromonas
sobria} PDB: 3hjr_A
Length = 600
Score = 27.6 bits (60), Expect = 8.7
Identities = 18/193 (9%), Positives = 40/193 (20%), Gaps = 24/193 (12%)
Query: 21 EIKKAEPRDASNKGNDMGNNQWGPPQSGGPMAMGPNMGMGTPSGPMAGMTPMGPGNMMQ- 79
+ A +++ N + N+ + S ++ T G
Sbjct: 157 DWLYALGDSNASRDNRVFNHSYRM--SVVDPRSANSLDQSQLDRLFEQQTLKAQGAAYIK 214
Query: 80 ------GYQGWGSTPQTQGFPGQWAPSSQTPMNGYAN------------PSAPQGYTNWG 121
G + G P + ++ + Y++ G
Sbjct: 215 AAGNGFNKIAAGGYVLNRTGNGPKLPFENSNLDPSNSNFWNLVVSALNADGVRSSYSSVG 274
Query: 122 APPGPQAPPQWGSSYGAPPQQTGYGSYGPTSGAPQSGYGNNWNWNMPQNGPTTPAAGGPP 181
+ A + T N + N +
Sbjct: 275 SNIFLSATGGEYGTDTPAMVTTDLPGCDMGYNRTDDPSTNRLHGNSQLDASCDYNGV--- 331
Query: 182 AGGATGAAPTGPN 194
G + A P+
Sbjct: 332 MNGTSSATPSTSG 344
>2pi6_A Chitinase-3-like protein 1; complex, signaling protein; HET: NAG
MAN; 1.65A {Ovis aries} SCOP: c.1.8.5 d.26.3.1 PDB:
2dpe_A* 1sr0_A* 1zl1_A* 1zbk_A* 2dsu_A* 2dsv_A* 2dsw_A*
2fdm_A* 2g41_A* 2g8z_A* 2dt1_A* 1zbv_A* 1zu8_A* 2aos_A*
2b31_A* 1zbw_A* 2dt0_A* 2dsz_A* 2dt2_A* 2dt3_A* ...
Length = 361
Score = 27.2 bits (61), Expect = 9.7
Identities = 5/31 (16%), Positives = 10/31 (32%)
Query: 159 YGNNWNWNMPQNGPTTPAAGGPPAGGATGAA 189
+G ++ + P +G G T
Sbjct: 239 FGRSFTLASSKTDVGAPVSGPGIPGRFTKEK 269
>1qho_A Alpha-amylase; glycoside hydrolase, starch degradation; HET: MAL
ABD; 1.70A {Geobacillus stearothermophilus} SCOP:
b.1.18.2 b.3.1.1 b.71.1.1 c.1.8.1 PDB: 1qhp_A*
Length = 686
Score = 27.5 bits (61), Expect = 9.8
Identities = 10/68 (14%), Positives = 22/68 (32%)
Query: 60 GTPSGPMAGMTPMGPGNMMQGYQGWGSTPQTQGFPGQWAPSSQTPMNGYANPSAPQGYTN 119
GT + + + P N+ G+ P+ + + + P+ P +
Sbjct: 579 GTQTSVVFTVKSAPPTNLGDKIYLTGNIPELGNWSTDTSGAVNNAQGPLLAPNYPDWFYV 638
Query: 120 WGAPPGPQ 127
+ P G
Sbjct: 639 FSVPAGKT 646
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
0.312 0.132 0.420
Gapped
Lambda K H
0.267 0.0437 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,131,360
Number of extensions: 380024
Number of successful extensions: 1617
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1219
Number of HSP's successfully gapped: 508
Length of query: 388
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 293
Effective length of database: 4,049,298
Effective search space: 1186444314
Effective search space used: 1186444314
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 58 (26.9 bits)