RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy40
(168 letters)
>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 = 95.1 bits (237), Expect = 2e-25
Identities = 44/129 (34%), Positives = 69/129 (53%), Gaps = 15/129 (11%)
Query: 30 VRLAVEAGVLEVVTTRP-TINNKAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATVKK 88
V A V + RP ++ + +E + + +P A+ TVKK
Sbjct: 60 VTYATVEEVDAAMNARPHKVDGRVVE-------PKRAVSRE------DSQRPGAHLTVKK 106
Query: 89 MFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFA 147
+FVGG+K D EE LR+YF Q+G IE + ++T++ +G KRGFAF+ F+D+D VDKI
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166
Query: 148 FIEFNDYDV 156
+ N ++
Sbjct: 167 YHTVNGHNC 175
Score = 75.8 bits (187), Expect = 7e-18
Identities = 19/65 (29%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 79 KPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
P+ ++K+F+GGL + ++ LR +F Q+GT+ ++ + T RGF F+ +
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65
Query: 138 DVVDK 142
+ VD
Sbjct: 66 EEVDA 70
>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 = 88.8 bits (221), Expect = 5e-24
Identities = 26/74 (35%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 80 PEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+ + K+FVGG+ E +LREYF +FG + V M+ + E RGF FI F D
Sbjct: 4 GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQ 63
Query: 139 VVDKIRGFAFIEFN 152
VD+ F +
Sbjct: 64 SVDQAVNMHFHDIM 77
>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 = 88.0 bits (219), Expect = 7e-23
Identities = 27/74 (36%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 81 EANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDV 139
+ K+FVGG+ D + E+FSQ+GTI ++ +K+TG RGF F+ ++ D
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141
Query: 140 VDKIRGFAFIEFND 153
VD++ FI+F D
Sbjct: 142 VDRVCQNKFIDFKD 155
Score = 73.7 bits (182), Expect = 2e-17
Identities = 25/57 (43%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
KMF+GGL D ED+LREYF ++GT+ + ++ + TG RGF F+ F VD+
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 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 = 85.0 bits (211), Expect = 2e-22
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 78 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G A + V GL + E DL+EYFS FG + V + + +TG +GF F+ F +
Sbjct: 7 GVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE 66
Query: 137 YDVVDKI 143
Y+ K+
Sbjct: 67 YETQVKV 73
>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 = 83.7 bits (208), Expect = 3e-22
Identities = 26/57 (45%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 88 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
K+FVGGL D E+ +REYF FG +ES+ + + +T +RGF FI F + + V KI
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57
>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 = 82.3 bits (204), Expect = 3e-21
Identities = 20/65 (30%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 80 PEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
PE +FVGG+ + +E ++R +F+++G+++ V ++T++ TG +G+ F+ F +
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61
Query: 139 VVDKI 143
V KI
Sbjct: 62 DVQKI 66
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 80.6 bits (200), Expect = 5e-21
Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 88 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
K+FVGGL +D++ YF QFG ++ ++ +K T RGF F+ F D+V+K+
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57
>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 = 77.3 bits (191), Expect = 3e-19
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 80 PEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+ + T K+FVGGL + LR+YF FG IE ++T+++TG RG+ F+ D
Sbjct: 11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRA 70
Query: 139 VVDK 142
++
Sbjct: 71 AAER 74
>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 = 77.1 bits (190), Expect = 4e-19
Identities = 23/107 (21%), Positives = 45/107 (42%), Gaps = 9/107 (8%)
Query: 51 KAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQF 109
M+ S+ GPP E + + ++VG + DL +FS
Sbjct: 4 PCMQTTHSKMTAGAYTEGPPQPLSAE---EKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60
Query: 110 GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDV 156
G+I + ++ +K +G +G+A+IEF + + VD + ++
Sbjct: 61 GSINRITILCDKFSGHPKGYAYIEFAERNSVDAA-----VAMDETVF 102
>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 = 75.8 bits (187), Expect = 1e-18
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 79 KPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
++ KMF+GGL ++ LREYF QFG ++ ++ + T RGF F+ F D
Sbjct: 18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
Query: 138 DVVDKI 143
VDK+
Sbjct: 78 AGVDKV 83
>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 = 75.8 bits (187), Expect = 1e-18
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 79 KPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
K +K+F+GGL + E+ LR Y+ Q+G + ++ + + RGF F+ F+
Sbjct: 20 KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 79
Query: 138 DVVDKI 143
VD
Sbjct: 80 AEVDAA 85
>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 = 74.1 bits (183), Expect = 2e-18
Identities = 26/67 (38%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 77 IGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 135
I + KMFVGGL D + DL++YF++FG + + + TG RGF FI F
Sbjct: 2 INASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK 61
Query: 136 DYDVVDK 142
D V+K
Sbjct: 62 DAASVEK 68
>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 = 76.5 bits (189), Expect = 2e-18
Identities = 35/143 (24%), Positives = 63/143 (44%), Gaps = 14/143 (9%)
Query: 32 LAVEAGVLEVVTTRPTINNK--AMEEAQSEEEVD--MEIPGPPHMDK-LEIGKP---EAN 83
+ V +K A E +S +E M G + L+I +P +
Sbjct: 32 GGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPL 91
Query: 84 ATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
K+F+GGL +D ++E + FG +++ N+V + TG +G+AF E+ D +V D+
Sbjct: 92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151
Query: 143 IRGFAFIEFNDYDVVDK-IVCKY 164
A N + DK ++ +
Sbjct: 152 ----AIAGLNGMQLGDKKLLVQR 170
Score = 55.3 bits (134), Expect = 2e-10
Identities = 12/81 (14%), Positives = 32/81 (39%), Gaps = 11/81 (13%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNM-----VTNKETGAKRGFAFIEFNDYDVV 140
++++VG + E+ + ++F+ + + V + + FAF+EF D
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 141 DKIRGFAFIEFNDYDVVDKIV 161
+ + F+ + +
Sbjct: 65 TQA-----MAFDGIIFQGQSL 80
>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 = 72.7 bits (179), Expect = 2e-17
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 79 KPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+ K+FVGGL ++ LR YFSQ+G + ++ +K T RGF F++F D
Sbjct: 9 NNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68
Query: 138 DVVDKI 143
+ V +
Sbjct: 69 NCVGTV 74
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 72.4 bits (178), Expect = 2e-17
Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 6/72 (8%)
Query: 82 ANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVV 140
++ ++ +FV G + L EYF FG + SV V +K+ G FA +E D
Sbjct: 4 GSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKG---VFAIVEMGDVGAR 58
Query: 141 DKIRGFAFIEFN 152
+ + +
Sbjct: 59 EAVLSQSQHSLG 70
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 71.8 bits (177), Expect = 2e-17
Identities = 24/57 (42%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 88 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
KMF+GGL ++ LREYF QFG ++ ++ + T RGF F+ F D VDK+
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58
>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 = 2e-17
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 78 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G P K +F+ L D EE+ L E QFG ++ V +V + +T +G AF +F
Sbjct: 7 GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMT 66
Query: 137 YDVVDK 142
+ K
Sbjct: 67 QEAAQK 72
>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 = 71.5 bits (176), Expect = 4e-17
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 5/78 (6%)
Query: 80 PEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
P + +++ +FVG + + E+ L++ FS+ G + S +V ++ETG +G+ F E+ D +
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 139 VVDKIRGFAFIEFNDYDV 156
A N +
Sbjct: 62 TALS----AMRNLNGREF 75
>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 = 71.0 bits (175), Expect = 4e-17
Identities = 16/70 (22%), Positives = 36/70 (51%), Gaps = 6/70 (8%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
+ ++VG + ++L +F G++ V ++ +K +G +GFA+IEF+D + V
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS-- 64
Query: 146 FAFIEFNDYD 155
+ ++
Sbjct: 65 ---LALDESL 71
>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 = 70.7 bits (174), Expect = 6e-17
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 5/71 (7%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
+ +++G + DQ E+ + + S G + ++ M+ + +TG +G+AFIEF D +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS--- 59
Query: 146 FAFIEFNDYDV 156
A N Y +
Sbjct: 60 -AVRNLNGYQL 69
>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 = 70.3 bits (173), Expect = 1e-16
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 78 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G + K+FVGGL D E L + FS++G I V +V ++ET RGF F+ F +
Sbjct: 4 GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN 63
Query: 137 YDVVDK 142
D
Sbjct: 64 IDDAKD 69
>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 = 70.0 bits (172), Expect = 2e-16
Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 78 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
+ K+F+G + ++ +E DL+ F +FG I + ++ ++ TG +G AF+ + +
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
Query: 137 YDVVDK 142
+ K
Sbjct: 65 RESALK 70
>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 = 69.2 bits (170), Expect = 2e-16
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 82 ANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVV 140
++ +FVG D ED+LRE+FSQ+G + V + R FAF+ F D +
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIA 55
Query: 141 DKI 143
+
Sbjct: 56 QSL 58
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 69.2 bits (170), Expect = 2e-16
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 78 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G T + ++VGGL ++ ++ L F FG I + + + ET RGFAF+EF
Sbjct: 4 GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63
>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 = 69.2 bits (170), Expect = 3e-16
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
+ V L D LR F ++G + V + T A RGFAF+ F+D
Sbjct: 14 ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64
>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 = 71.6 bits (176), Expect = 3e-16
Identities = 25/109 (22%), Positives = 52/109 (47%), Gaps = 6/109 (5%)
Query: 58 SEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVN 116
+ + + P + + + K+F+GGL + +D ++E + FG +++ N
Sbjct: 86 HDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFN 145
Query: 117 MVTNKETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDVVDK-IVCKY 164
+V + TG +G+AF E+ D +V D+ A N + DK ++ +
Sbjct: 146 LVKDSATGLSKGYAFCEYVDINVTDQ----AIAGLNGMQLGDKKLLVQR 190
Score = 51.6 bits (124), Expect = 9e-09
Identities = 11/62 (17%), Positives = 27/62 (43%), Gaps = 6/62 (9%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNM-----VTNKETGAKRGFAFIEFNDYDVV 140
++++VG + E+ + ++F+ + + V + + FAF+EF D
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 141 DK 142
+
Sbjct: 65 TQ 66
>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 = 68.7 bits (169), Expect = 3e-16
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 82 ANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
++ ++VG L + ED LR F FG I+++ ++ + +TG +G+ FI F+D +
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSE 58
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 69.8 bits (171), Expect = 3e-16
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 78 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
P + + V L + D LR F ++G + V + ++ T RGFAF+ F+D
Sbjct: 39 RPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 98
>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 = 68.4 bits (168), Expect = 5e-16
Identities = 18/61 (29%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 86 VKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIR 144
++ ++VG L + ++E FSQFG + +V ++ ++ET +GF F+E + V + I
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIA 60
Query: 145 G 145
Sbjct: 61 K 61
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein
complex, EXON junct complex, signaling protein; 1.85A
{Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B*
2j0s_D* 2xb2_D*
Length = 110
Score = 68.9 bits (169), Expect = 5e-16
Identities = 17/88 (19%), Positives = 42/88 (47%), Gaps = 10/88 (11%)
Query: 52 AMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFG 110
A+ + D + P P+ + +FV + + +ED+++E F +G
Sbjct: 1 AIHSYERVRNEDDDELEP---------GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYG 51
Query: 111 TIESVNMVTNKETGAKRGFAFIEFNDYD 138
I+++++ ++ TG +G+A +E+ +
Sbjct: 52 EIKNIHLNLDRRTGFSKGYALVEYETHK 79
>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 = 68.5 bits (168), Expect = 6e-16
Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
+ +F L DL ++FS G + V +++++ + +G A++EF + V
Sbjct: 26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA 83
>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 = 69.9 bits (171), Expect = 6e-16
Identities = 24/120 (20%), Positives = 44/120 (36%), Gaps = 12/120 (10%)
Query: 29 EVRLAVEAGVLEVVTTRPTINNKAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATVK- 87
+ +L + L+ TT ++ E+ + D + G D +
Sbjct: 2 QYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHH 61
Query: 88 ----------KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
+ V L + D LR F ++G + V + ++ T RGFAF+ F+D
Sbjct: 62 HHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 121
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 68.1 bits (167), Expect = 7e-16
Identities = 13/52 (25%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 88 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+FV G+ + E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 76
>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 = 67.6 bits (166), Expect = 8e-16
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
++V L +DL FS++G + V ++ +K+T +G AFI F D D
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
>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 = 68.6 bits (168), Expect = 1e-15
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 78 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G + V GL E DLRE FS++G I V++V ++++ RGFAF+ F +
Sbjct: 38 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 97
Query: 137 YD 138
D
Sbjct: 98 VD 99
>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 = 67.6 bits (166), Expect = 1e-15
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+ V L +D E DL+E F FG+I + + +K TG +GFAFI F+ +
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
>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 = 67.6 bits (166), Expect = 1e-15
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 78 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G + V GL E DLRE FS++G I V++V ++++ RGFAF+ F +
Sbjct: 7 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 137 YD 138
D
Sbjct: 67 VD 68
>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 = 67.6 bits (166), Expect = 1e-15
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
++FV L E+DL + FS +G + ++ + T +GFAF+ F
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMF 59
>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 = 67.2 bits (165), Expect = 1e-15
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 87 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
+ ++VGGL ++ ++ L F FG I + + + ET RGFAF+EF
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 58
>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 = 67.8 bits (166), Expect = 2e-15
Identities = 13/52 (25%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 88 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+FV G+ + E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 75
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 67.9 bits (166), Expect = 2e-15
Identities = 27/128 (21%), Positives = 45/128 (35%), Gaps = 15/128 (11%)
Query: 10 STVYSGSGGWWFESKCPSHEVRLAVEAGVLEVVTTRPTINNKAMEEAQSEEEVDMEIPGP 69
S + G W SKC + + + E+++ P
Sbjct: 1 SMMQCGKCDRWVHSKCEN------LSDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSG 54
Query: 70 PHMDKLEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRG 128
A + ++VGGL ++ ++ L F FG I + + + ET RG
Sbjct: 55 GS-------GGSATTK-RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG 106
Query: 129 FAFIEFND 136
FAF+EF
Sbjct: 107 FAFVEFEL 114
>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 = 71.4 bits (174), Expect = 2e-15
Identities = 29/120 (24%), Positives = 54/120 (45%), Gaps = 8/120 (6%)
Query: 51 KAMEEAQSEEEVDMEIPGP-PHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQ 108
+ + + ++EV+ E+ PH D G K +FV + D E LR F
Sbjct: 71 RREKIERRQQEVETELKMWDPHNDPNAQGDAF-----KTLFVARVNYDTTESKLRREFEV 125
Query: 109 FGTIESVNMVTNKETGAKRGFAFIEFND-YDVVDKIRGFAFIEFNDYDVVDKIVCKYNIE 167
+G I+ ++MV +K +G RG+AFIE+ D+ + + + V+ + ++
Sbjct: 126 YGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVK 185
>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 = 66.5 bits (163), Expect = 3e-15
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 6/67 (8%)
Query: 78 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G + K+FVG D ++L+++F Q+G + V + R FAF+ F D
Sbjct: 3 GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFAD 57
Query: 137 YDVVDKI 143
V +
Sbjct: 58 DKVAQSL 64
>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 = 66.5 bits (163), Expect = 3e-15
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 87 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK-IR 144
++VGGL ++ E L E F Q G + + +M ++ TG +G+ F+EF + D I+
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 145 GFAFIEFN 152
I+
Sbjct: 76 IMDMIKLY 83
>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 = 67.9 bits (166), Expect = 4e-15
Identities = 16/95 (16%), Positives = 44/95 (46%), Gaps = 1/95 (1%)
Query: 45 RPTINNKAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLR 103
+ ++ + E + D P+ + +FV + ++ +ED+++
Sbjct: 31 KHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ 90
Query: 104 EYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
E F +G I+++++ ++ TG +G+A +E+ +
Sbjct: 91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 125
>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 = 67.1 bits (164), Expect = 6e-15
Identities = 18/92 (19%), Positives = 38/92 (41%), Gaps = 1/92 (1%)
Query: 48 INNKAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGLK-DQEEDDLREYF 106
++ ++ +S+ V++ H + + ++VG L E+ + E F
Sbjct: 1 MSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELF 60
Query: 107 SQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
S+ G I+ + M +K GF F+E+
Sbjct: 61 SKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA 92
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 68.1 bits (167), Expect = 8e-15
Identities = 21/84 (25%), Positives = 43/84 (51%), Gaps = 5/84 (5%)
Query: 79 KPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+ A A + +++VG + + ED +R+ F+ FG I+S++M + T +GFAF+E+
Sbjct: 21 RQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVP 80
Query: 138 DVVDKIRGFAFIEFNDYDVVDKIV 161
+ A + N + + +
Sbjct: 81 EAAQL----ALEQMNSVMLGGRNI 100
Score = 63.5 bits (155), Expect = 4e-13
Identities = 22/101 (21%), Positives = 42/101 (41%), Gaps = 6/101 (5%)
Query: 62 VDMEIPGPPHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTN 120
V ++ EA A +++V + +D +DD++ F FG I+S + +
Sbjct: 102 VGRPSNIGQAQPIIDQLAEEARAF-NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARD 160
Query: 121 KETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDVVDKIV 161
TG +G+ FIE+ A N +D+ + +
Sbjct: 161 PTTGKHKGYGFIEYEKAQSSQD----AVSSMNLFDLGGQYL 197
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 65.0 bits (159), Expect = 1e-14
Identities = 16/79 (20%), Positives = 38/79 (48%), Gaps = 6/79 (7%)
Query: 79 KPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+ + K+F+ GL +++L E GT++ + +VTN+ G +G A++E+ +
Sbjct: 10 RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENE 68
Query: 138 DVVDKIRGFAFIEFNDYDV 156
+ A ++ + +
Sbjct: 69 SQASQ----AVMKMDGMTI 83
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 65.0 bits (159), Expect = 1e-14
Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 80 PEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
+ +A +++VG L + ED LR F FG IES+ ++ + ETG +G+ FI F+D
Sbjct: 20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77
>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 = 64.6 bits (158), Expect = 2e-14
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 78 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKE-TGAKRGFAFIEFN 135
G+ T K+ V + + ++RE FS FG +++V + TGA RGF F++F
Sbjct: 7 GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66
Query: 136 DYD 138
Sbjct: 67 TKQ 69
>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 = 63.7 bits (156), Expect = 2e-14
Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 5/71 (7%)
Query: 87 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
+++ GL+ + DL + +G I S + +K T +G+ F++F+ K
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK--- 62
Query: 146 FAFIEFNDYDV 156
A V
Sbjct: 63 -AVTALKASGV 72
>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 = 62.9 bits (154), Expect = 6e-14
Identities = 14/51 (27%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNK-ETGAKRGFAFIEFND 136
K+ +G L ++ +D + E FS +G I+ ++M + +G+A++EF +
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFEN 56
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 63.2 bits (154), Expect = 8e-14
Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 5/76 (6%)
Query: 87 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
K++ L D E L++ ++G +E V ++ + T G A + F +
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE--- 63
Query: 146 FAFIEFNDYDVVDKIV 161
+ V+ I+
Sbjct: 64 -TVKNLHLTSVMGNII 78
>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 = 64.2 bits (157), Expect = 1e-13
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAK--RGFAFIEFNDYDVVDK 142
KMFVG + + E DLRE F Q+G + +N++ ++ +G F+ F +
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62
Score = 59.5 bits (145), Expect = 7e-12
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
+K+F+G + K E+D+R FS FG IE ++ G RG AF+ F +
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQT 151
>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 = 64.1 bits (157), Expect = 1e-13
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGF 146
+ V L ++ +++ R F G IES +V +K TG G+ F+ + D +K
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK---- 59
Query: 147 AFIEFNDYDVVDKIV 161
A N + K +
Sbjct: 60 AINTLNGLRLQTKTI 74
Score = 56.8 bits (138), Expect = 6e-11
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
++V GL K + +L + FSQ+G I + ++ ++ TG RG FI F+ ++
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 146
>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 = 62.3 bits (152), Expect = 2e-13
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 78 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G E+ +T K++ V + + DLR+ F QFG I V ++ N+ +GF F+ F +
Sbjct: 7 GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFEN 64
Query: 137 YDVVDK 142
D+
Sbjct: 65 SADADR 70
>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 = 62.3 bits (152), Expect = 2e-13
Identities = 26/109 (23%), Positives = 42/109 (38%), Gaps = 11/109 (10%)
Query: 58 SEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVN 116
S EI P G+P K +++ L E DL F++F +
Sbjct: 2 SSGSSGEEIRKIPMFSSYNPGEPN-----KVLYLKNLSPRVTERDLVSLFARFQEKKGPP 56
Query: 117 MVTNKETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDVVDK-IVCKY 164
+ TG RG AFI F + ++ + A N Y + K +V ++
Sbjct: 57 IQFRMMTGRMRGQAFITFPNKEIAWQ----ALHLVNGYKLYGKILVIEF 101
>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 = 62.8 bits (153), Expect = 2e-13
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 80 PEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
++ + V + +E LR+ F ++G IESV +V ++ET RG+ F++F
Sbjct: 36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 61.2 bits (149), Expect = 3e-13
Identities = 9/55 (16%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGT--IESVNMVTNKETGAKRGFAFIEFNDYD 138
+ + + D + S + + + ++ ++ +K+T RGFAF++ +
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 61.6 bits (150), Expect = 3e-13
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 70 PHMDKLEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRG 128
+ + E + K++ V + + + DLR+ F QFG I V ++ N+ +G
Sbjct: 13 GLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KG 70
Query: 129 FAFIEFNDYDVVDK 142
F F+ F + D+
Sbjct: 71 FGFVTFENSADADR 84
>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 = 60.8 bits (148), Expect = 5e-13
Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 16/87 (18%)
Query: 79 KPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIES--------VNMVTNKETGAKRGF 129
N T+ FV GL ++ + + +YF Q G I++ +N+ T++ETG +G
Sbjct: 9 SHSDNNTI---FVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65
Query: 130 AFIEFNDYDVVDKIRGFAFIEFNDYDV 156
A + F+D A F+ +
Sbjct: 66 ATVSFDDPPSAKA----AIDWFDGKEF 88
>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 = 63.6 bits (154), Expect = 5e-13
Identities = 16/120 (13%), Positives = 34/120 (28%), Gaps = 7/120 (5%)
Query: 40 EVVTTRPTINNKAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGLKDQ-E 98
+ V + N A E+ + + + +++G L
Sbjct: 22 DDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTT 81
Query: 99 EDDLREYFSQFGTIE--SVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDV 156
++DL E G + + N+ G +GFA + K ++
Sbjct: 82 DEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK----LMDLLPKREL 137
>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 = 62.2 bits (152), Expect = 6e-13
Identities = 17/75 (22%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGF 146
+ V L +D + +L F G I + ++ + +TG G+AF++F +
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR---- 60
Query: 147 AFIEFNDYDVVDKIV 161
A N V +K +
Sbjct: 61 AIKVLNGITVRNKRL 75
Score = 56.4 bits (137), Expect = 9e-11
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
++V L + +D L F ++G+I N++ +K TG RG AF+ +N + +
Sbjct: 91 NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 146
>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 = 60.8 bits (148), Expect = 7e-13
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 88 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
K+F+GGL + E L+ F + G I V ++ ++ T RGFAFI F +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKN 63
>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 = 60.5 bits (147), Expect = 8e-13
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 13/87 (14%)
Query: 78 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIES--------VNMVTNKETGAKRG 128
G P+ ++ ++V GL DDL ++F Q G ++ +++ +KETG +G
Sbjct: 7 GDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKG 66
Query: 129 FAFIEFNDYDVVDKIRGFAFIEFNDYD 155
A + + D A F+ D
Sbjct: 67 DATVSYEDPPTAKA----AVEWFDGKD 89
>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 = 59.6 bits (145), Expect = 1e-12
Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
K+FVG L K Q E+D+ F FG I+ ++ G+ +G AF++F+
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSS 65
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 59.6 bits (145), Expect = 1e-12
Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
+VG L + + D+ F I SV +V +K+T +GF ++EF++ D + +
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA-- 72
Query: 146 FAFIEFNDYDV 156
+ ++ +
Sbjct: 73 ---LTYDGALL 80
>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 = 59.3 bits (144), Expect = 2e-12
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 78 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFG-TIESVNMVTNKETGAKRGFAFIEFN 135
G ++ +++G L+ +E+ + F+ G T+ SV ++ N+ TG G+ F+EF
Sbjct: 1 GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60
Query: 136 DYDVVDK 142
D +K
Sbjct: 61 DLATAEK 67
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 59.7 bits (145), Expect = 2e-12
Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 13/79 (16%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIES--------VNMVTNKETGAKRGFAFIEFNDY 137
+FV GL ++ + + +YF Q G I++ +N+ T++ETG +G A + F+D
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 138 DVVDKIRGFAFIEFNDYDV 156
A F+ +
Sbjct: 68 PSAKA----AIDWFDGKEF 82
>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 = 58.8 bits (143), Expect = 2e-12
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 87 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
+ +FVG L+ + E+ L E F Q G + V + ++E G + F F+ F + V
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSY--- 72
Query: 146 FAFIEFNDYDVVDK 159
A N + +
Sbjct: 73 -AIALLNGIRLYGR 85
>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 = 59.3 bits (144), Expect = 2e-12
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 78 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G+ + + +FVG L + +D++ F+ FG I +V + TG +G+ F+ F +
Sbjct: 7 GQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 137 YD 138
Sbjct: 67 KW 68
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 59.2 bits (143), Expect = 2e-12
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMV--TNKETGAKRGFAFIEFNDYDVVDKI 143
+K+FVGGL D +ED++ F +FG + +K +G+AF+ F + V +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
>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 = 4e-12
Identities = 12/52 (23%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 88 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+F+ L + + DL + F FG + S + +K+T + F F+ +++
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78
>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 = 58.0 bits (141), Expect = 5e-12
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 88 KMFVGGLK-DQEEDDLREYFSQFGTIE--SVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
+++G L ++DL E G + + N+ G +GFA + K
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60
>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 = 57.5 bits (140), Expect = 5e-12
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 88 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
+FVG L + +++ LR F F + S +++ + +TG+ RG+ F+ F
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 52
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 59.2 bits (143), Expect = 6e-12
Identities = 10/59 (16%), Positives = 21/59 (35%), Gaps = 3/59 (5%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIE--SVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
++VG + L + G + + N+ G +G+A + + V K
Sbjct: 56 AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHK 114
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 58.1 bits (141), Expect = 7e-12
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 88 KMFVGGLKDQE--EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+F+ L QE + DL F FG + S + +K+T + F F+ F++ D
Sbjct: 42 NLFIYHL-PQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPD 93
>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 = 57.7 bits (140), Expect = 7e-12
Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 9/80 (11%)
Query: 78 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G + K + + L E+ L+E F + I+ V + G +G+AFIEF
Sbjct: 7 GNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFAS 62
Query: 137 YDVVDKIRGFAFIEFNDYDV 156
++ + A N ++
Sbjct: 63 FEDAKE----ALNSCNKREI 78
>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 = 57.6 bits (140), Expect = 7e-12
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 78 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G E + + ++VG L E + + FSQ G +S M+T + + F+EF +
Sbjct: 7 GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYE 64
>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 = 57.7 bits (140), Expect = 8e-12
Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 7/79 (8%)
Query: 79 KPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+ + T +F+G L ++ +L+ S+ + V + TG R F +++F
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESA 68
Query: 138 DVVDKIRGFAFIEFNDYDV 156
+ ++K +E V
Sbjct: 69 EDLEKA-----LELTGLKV 82
>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 = 56.9 bits (138), Expect = 9e-12
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 7/60 (11%)
Query: 78 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G + T+ ++VGGL E DLR +F QFG I ++ +V + AFI+F
Sbjct: 4 GSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFAT 57
>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 = 58.8 bits (143), Expect = 1e-11
Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 7/76 (9%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
+F+G L ++ +L+ S+ + +V TG R F +++F + ++K
Sbjct: 14 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESAEDLEK--- 69
Query: 146 FAFIEFNDYDVVDKIV 161
+E V +
Sbjct: 70 --ALELTGLKVFGNEI 83
Score = 52.2 bits (126), Expect = 3e-09
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 6/65 (9%)
Query: 79 KPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+ + + L + ED+L+E F I V + G +G A+IEF
Sbjct: 92 DSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSE 146
Query: 138 DVVDK 142
+K
Sbjct: 147 ADAEK 151
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 57.3 bits (139), Expect = 1e-11
Identities = 16/70 (22%), Positives = 24/70 (34%), Gaps = 10/70 (14%)
Query: 68 GPPHMDKLEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAK 126
P +D + P T ++G + E DL F FG I K
Sbjct: 12 NPQAVDHIIRSAPPRVTTA---YIGNIPHFATEADLIPLFQNFGFILDFKHYPEK----- 63
Query: 127 RGFAFIEFND 136
G FI+++
Sbjct: 64 -GCCFIKYDT 72
>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 = 60.0 bits (146), Expect = 2e-11
Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 8/84 (9%)
Query: 81 EANATVKKMFVGGLKDQ--EEDDLREYFSQFGTIESVNMVTN-KETGAKRGFAFIEFNDY 137
A +++ + L + +E+ LRE F FG+IE +N+ KE AF+ F +
Sbjct: 205 SATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENK 264
Query: 138 DVVDKIRGFAFIEFNDYDVVDKIV 161
D ++ A ++ N + ++ +
Sbjct: 265 DSAER----A-LQMNRSLLGNREI 283
Score = 55.4 bits (134), Expect = 6e-10
Identities = 17/61 (27%), Positives = 23/61 (37%), Gaps = 6/61 (9%)
Query: 83 NATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVD 141
TV V L K ++ + +YF G I V++ FA IEF YD
Sbjct: 41 LTTV---LVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGAL 95
Query: 142 K 142
Sbjct: 96 A 96
Score = 48.8 bits (117), Expect = 1e-07
Identities = 7/81 (8%), Positives = 22/81 (27%), Gaps = 8/81 (9%)
Query: 80 PEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
T+ ++ + ++R+ + + + R FA+I+ +
Sbjct: 114 HLTECTL---WMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKE 170
Query: 139 VVDKIRGFAFIEFNDYDVVDK 159
+ N +
Sbjct: 171 DARY----CVEKLNGLKIEGY 187
>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 = 56.5 bits (137), Expect = 2e-11
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 82 ANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAK---RGFAFIEFND 136
++ +F+ L E+ L+ FS+ G I+S + K GF F+E+
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKK 59
>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 = 56.5 bits (137), Expect = 2e-11
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 10/66 (15%)
Query: 74 KLEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFI 132
K+ GK + +VGGL L F +FG+I +++ V FA+I
Sbjct: 8 KIGYGKANPTTRL---WVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYI 58
Query: 133 EFNDYD 138
++ D
Sbjct: 59 QYESLD 64
>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 = 56.1 bits (136), Expect = 2e-11
Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 11/80 (13%)
Query: 78 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G + ++FVG L D E+++R+ F ++G V + +K GF FI
Sbjct: 7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLET 60
Query: 137 YDVVDKIRGFAFIEFNDYDV 156
+ + A +E ++ +
Sbjct: 61 RTLAEI----AKVELDNMPL 76
>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 = 56.1 bits (136), Expect = 3e-11
Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 10/79 (12%)
Query: 79 KPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+ + + L + ED+L+E F I V+ + G +G A+IEF
Sbjct: 9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSE 63
Query: 138 DVVDKIRGFAFIEFNDYDV 156
+K E ++
Sbjct: 64 ADAEK----NLEEKQGAEI 78
>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 = 55.6 bits (135), Expect = 3e-11
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 88 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
+FVG L + + F+ FG I +V + TG +G+ F+ F +
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 57
>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 = 58.5 bits (142), Expect = 4e-11
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 87 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
+ V L + L + FSQFG +E +V + + G G F+EF K
Sbjct: 97 AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARK 152
Score = 53.9 bits (130), Expect = 2e-09
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 11/73 (15%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGF 146
++FVG L D E+D + F ++G V + + RGF FI + +
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEI---- 73
Query: 147 AFIEFNDYDVVDK 159
A E + + +
Sbjct: 74 AKAELDGTILKSR 86
>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 = 55.7 bits (135), Expect = 4e-11
Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 78 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G + K +FV GL D E+ L+E F +VT++ETG+ +GF F++FN
Sbjct: 7 GPNARSQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNS 63
Query: 137 YD 138
+
Sbjct: 64 EE 65
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 55.9 bits (135), Expect = 4e-11
Identities = 13/77 (16%), Positives = 33/77 (42%), Gaps = 2/77 (2%)
Query: 81 EANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDV 139
+ + + +++ G D DD++E+ G + ++ M A +G F+ F+ +
Sbjct: 6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIES 64
Query: 140 VDKIRGFAFIEFNDYDV 156
K ++ + D+
Sbjct: 65 AKKFVETPGQKYKETDL 81
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 57.2 bits (138), Expect = 5e-11
Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 6/80 (7%)
Query: 78 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G E T K+ V L + D++E F++FGT++ + + +G G A + F
Sbjct: 80 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFER 138
Query: 137 YDVVDKIRGFAFIEFNDYDV 156
K A ++ +
Sbjct: 139 RADALK----AMKQYKGVPL 154
>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 = 58.1 bits (141), Expect = 7e-11
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+ V L + E FG++E +V ++ TG +G+ F E+ D
Sbjct: 97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKD 148
Score = 57.3 bits (139), Expect = 1e-10
Identities = 12/85 (14%), Positives = 29/85 (34%), Gaps = 7/85 (8%)
Query: 79 KPEANATVKKMFVGGLKDQ--EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
A + + V L + D L S + + + G +GFA +E+
Sbjct: 177 LTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEYET 235
Query: 137 YDVVDKIRGFAFIEFNDYDVVDKIV 161
++ ++ A + + + +
Sbjct: 236 AEMAEE----AQQQADGLSLGGSHL 256
Score = 42.7 bits (101), Expect = 2e-05
Identities = 12/98 (12%), Positives = 34/98 (34%), Gaps = 13/98 (13%)
Query: 65 EIPGPPHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKET 123
+ +LE + + +K+ + GL D ++ + S + +
Sbjct: 2 MLDPEEIRKRLEHTERQF-RNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFV 53
Query: 124 GAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDVVDKIV 161
+G AF+ + + + A F+ + ++ +
Sbjct: 54 DKYKGTAFVTLLNGEQAEA----AINAFHQSRLREREL 87
>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 = 55.0 bits (133), Expect = 8e-11
Identities = 19/96 (19%), Positives = 37/96 (38%), Gaps = 8/96 (8%)
Query: 64 MEIPGPPHMDKLEIGKPEANATVK--KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTN 120
++P D + G K+ V L + D++E F++FGT++ + +
Sbjct: 5 KQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD 64
Query: 121 KETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDV 156
+G G A + F K A ++N +
Sbjct: 65 -RSGRSLGTADVHFERKADALK----AMKQYNGVPL 95
>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 = 55.5 bits (134), Expect = 8e-11
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 10/58 (17%)
Query: 79 KPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
P T+ +V G D LR FS FG I ++M + AF+ +
Sbjct: 35 APRKGNTL---YVYGE-DMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEK 82
>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 = 55.4 bits (134), Expect = 8e-11
Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 6/83 (7%)
Query: 78 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G +A +FV L + L+E FS G + +++ +K+ G RG + F
Sbjct: 7 GALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQ 65
Query: 137 YDVVDKIRGFAFIEFNDYDVVDK 159
+ A FN + D+
Sbjct: 66 SIEAVQ----AISMFNGQLLFDR 84
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 55.0 bits (133), Expect = 9e-11
Identities = 22/108 (20%), Positives = 40/108 (37%), Gaps = 18/108 (16%)
Query: 56 AQSEEEVDME-IPGPPHMDKLEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIE 113
+ +P HM + G+ ++FV +E +L E F FG ++
Sbjct: 4 SHHHHHHSSGLVPRGSHMHHRQEGELSNT----RLFVRPFPLDVQESELNEIFGPFGPMK 59
Query: 114 SVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDVVDKIV 161
V + GFAF+EF + + K A E + ++ +
Sbjct: 60 EVKI--------LNGFAFVEFEEAESAAK----AIEEVHGKSFANQPL 95
>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 = 54.6 bits (132), Expect = 1e-10
Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 7/71 (9%)
Query: 67 PGPPHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGA 125
G + E +++ ++ GG+ + +R+ FS FG I + + K
Sbjct: 6 SGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK---- 61
Query: 126 KRGFAFIEFND 136
G++F+ F+
Sbjct: 62 --GYSFVRFST 70
>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 = 54.2 bits (131), Expect = 2e-10
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 8/72 (11%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAK-RGFAFIEFNDYDVVDKIR 144
F+G L D E+ ++E+F I +V + + +GF + EF D D +
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA- 73
Query: 145 GFAFIEFNDYDV 156
+ N+ +
Sbjct: 74 ----LSLNEESL 81
>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 = 54.2 bits (131), Expect = 2e-10
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 8/72 (11%)
Query: 87 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAK-RGFAFIEFNDYDVVDKIR 144
F+G L D E+ ++E+F I +V + + +GF + EF D D +
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA- 77
Query: 145 GFAFIEFNDYDV 156
+ N+ +
Sbjct: 78 ----LSLNEESL 85
>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 = 53.8 bits (130), Expect = 2e-10
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 10/58 (17%)
Query: 79 KPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
P T+ +V G D LR FS FG I ++M + AF+ +
Sbjct: 11 APRKGNTL---YVYGE-DMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEK 58
>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 = 56.1 bits (136), Expect = 2e-10
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 90 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
+VG L D E L E FS G I S+ + + T G+A++ F
Sbjct: 19 YVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66
Score = 46.5 bits (111), Expect = 6e-07
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 90 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
F+ L K + L + FS FG I S +V + +G+ F+ F + ++
Sbjct: 107 FIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAER 158
>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 = 53.9 bits (130), Expect = 4e-10
Identities = 18/93 (19%), Positives = 34/93 (36%), Gaps = 8/93 (8%)
Query: 67 PGPPHMDKLEIGKPEANATVK--KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKET 123
P D + G K+ V L + D++E F++FGT++ + + +
Sbjct: 14 PDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RS 72
Query: 124 GAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDV 156
G G A + F K A ++ +
Sbjct: 73 GRSLGTADVHFERRADALK----AMKQYKGVPL 101
>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 = 53.4 bits (129), Expect = 4e-10
Identities = 12/73 (16%), Positives = 25/73 (34%), Gaps = 6/73 (8%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGF 146
+++ L +E +L FG + S ++ + +G RG F + +
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEA---- 81
Query: 147 AFIEFNDYDVVDK 159
FN +
Sbjct: 82 VIGHFNGKFIKTP 94
>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 = 53.1 bits (128), Expect = 4e-10
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 9/56 (16%)
Query: 84 ATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
A VK +FV L + E+ L + FSQFG +E V + + +AFI F++ D
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERD 56
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 53.1 bits (128), Expect = 5e-10
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY-DVVDKIRG 145
K++VG L + +L FS +G + +V + N GFAF+EF D D D +RG
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56
Query: 146 F 146
Sbjct: 57 L 57
>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 = 52.3 bits (126), Expect = 6e-10
Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 7/64 (10%)
Query: 80 PEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
++ + K+++G L DDLR+ F + + K G+AF+++ D +
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAG------QVLLKSGYAFVDYPDQN 55
Query: 139 VVDK 142
+
Sbjct: 56 WAIR 59
>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 = 52.7 bits (127), Expect = 7e-10
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+++VG L D D+ + F ++G I +++ K FAF+EF D
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPR 72
>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 = 52.8 bits (127), Expect = 8e-10
Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 11/81 (13%)
Query: 80 PEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
PE N + ++ L +++ + F ++G I + + ET RG A++ + D
Sbjct: 5 PEVNRIL---YIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIF 58
Query: 139 VVDKIRGFAFIEFNDYDVVDK 159
A + ++V ++
Sbjct: 59 DAKN----AVDHLSGFNVSNR 75
>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 = 52.2 bits (126), Expect = 1e-09
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 88 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
++V L D +++ LR+ FS FGTI S ++ E G +GF F+ F+ + K
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATK 70
>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 = 51.9 bits (125), Expect = 1e-09
Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 11/80 (13%)
Query: 78 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G + ++VK ++V L E+ + + F+ R +AF+ F++
Sbjct: 7 GDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVE------RVKKIRDYAFVHFSN 60
Query: 137 YDVVDKIRGFAFIEFNDYDV 156
+ + A N +
Sbjct: 61 REDAVE----AMKALNGKVL 76
>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 = 51.9 bits (125), Expect = 1e-09
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 87 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY-DVVDKIR 144
K+ VG + +LR F ++G + ++ + +AF+ D V+ IR
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDI--------VKDYAFVHMERAEDAVEAIR 62
Query: 145 G 145
G
Sbjct: 63 G 63
>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 = 52.9 bits (128), Expect = 1e-09
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 90 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
FVG L + +++ LR F F + S +++ + +TG+ RG+ F+ F D
Sbjct: 91 FVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Score = 51.0 bits (123), Expect = 8e-09
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
+ ++VG L K ED L++YF G I ++ ++ +K +AF+E++ +
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANI--- 56
Query: 146 FAFIEFNDYDVVDKIV 161
A N + + IV
Sbjct: 57 -ALQTLNGKQIENNIV 71
>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 = 51.4 bits (124), Expect = 1e-09
Identities = 14/66 (21%), Positives = 30/66 (45%), Gaps = 10/66 (15%)
Query: 82 ANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY-DV 139
++ + K+F+G L ++ E ++R F Q+G + ++ + + F+ D
Sbjct: 4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDKTAA 55
Query: 140 VDKIRG 145
D IR
Sbjct: 56 EDAIRN 61
>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 = 51.0 bits (123), Expect = 2e-09
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 82 ANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESV-NMVTNKETGAKRGFAFIEFNDYD 138
++ +F+G L + +E L + FS FG I ++ + +TG +G+AFI F +D
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFD 59
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 51.0 bits (123), Expect = 2e-09
Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 7/77 (9%)
Query: 86 VKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIR 144
++FV L D L++ F++ G + ++ E G +G ++F +V ++
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFESPEVAER-- 63
Query: 145 GFAFIEFNDYDVVDKIV 161
A N + + +
Sbjct: 64 --ACRMMNGMKLSGREI 78
>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 = 50.7 bits (122), Expect = 2e-09
Identities = 10/53 (18%), Positives = 20/53 (37%), Gaps = 9/53 (16%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
K+FVG + +LR F + G + ++ + +AF+
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDV--------VKDYAFVHMEKEA 54
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 50.7 bits (122), Expect = 3e-09
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 10/53 (18%)
Query: 88 KMFVGGL--KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
++F+G L K+ ++DL FS +G I +N+ K F FI+F++
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQ 56
>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 = 50.4 bits (121), Expect = 4e-09
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 10/74 (13%)
Query: 67 PGPPHMDKLEIGKPEANATVKKMFVGGL--KDQEEDDLREYFSQFGTIESVNMVTNKETG 124
H P + ++F+G L K+ ++DL FS +G I +N+
Sbjct: 3 SSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI------- 55
Query: 125 AKRGFAFIEFNDYD 138
K F FI+F++
Sbjct: 56 -KNAFGFIQFDNPQ 68
>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 = 51.4 bits (123), Expect = 4e-09
Identities = 23/121 (19%), Positives = 42/121 (34%), Gaps = 17/121 (14%)
Query: 47 TINNKAM--EEAQSEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGLKDQ-EEDDLR 103
+ ++ + E + E+ E G+P +++V L +E DL+
Sbjct: 9 EMPSECISRRELEKGRISREEMETLSVFRSYEPGEPN-----CRIYVKNLAKHVQEKDLK 63
Query: 104 EYFSQFGTIESVNM-----VTNKETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDVVD 158
F ++ S + + G +G AFI + K A E N Y +
Sbjct: 64 YIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK----ALKEANGYVLFG 119
Query: 159 K 159
K
Sbjct: 120 K 120
>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 = 51.0 bits (122), Expect = 7e-09
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 7/60 (11%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY-DVVDKIRG 145
K++VG L + + +L F +G + SV + N GFAF+EF D D D +R
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 129
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 49.3 bits (118), Expect = 1e-08
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 90 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+ K + L FS+ G + ++ ++ TG +GF F+E +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMN 65
>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 = 49.4 bits (118), Expect = 1e-08
Identities = 12/54 (22%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGT-IESVNMVTN-KETGAKRGFAFIEFNDYD 138
++F+GG+ K ++ +++ E ++ + V + + + RGFAF+E+ +
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63
>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 = 49.3 bits (118), Expect = 1e-08
Identities = 11/61 (18%), Positives = 29/61 (47%), Gaps = 11/61 (18%)
Query: 88 KMFVGGLKDQE--EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY-DVVDKIR 144
++F+G L + D+ FS++G + ++ +G+AF+++++ +
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80
Query: 145 G 145
G
Sbjct: 81 G 81
>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 = 49.6 bits (119), Expect = 1e-08
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 86 VKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
+F+ L K + L + FS FG I S +V + +G+ F+ F + ++
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAER 60
>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 = 47.2 bits (113), Expect = 5e-08
Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 12/75 (16%)
Query: 90 FVGGLKDQ-EEDDLRE----YFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIR 144
++ L ++ ++D+L++ FS+FG I + + + RG AF+ F +
Sbjct: 12 YINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKEVSSATN-- 66
Query: 145 GFAFIEFNDYDVVDK 159
A + DK
Sbjct: 67 --ALRSMQGFPFYDK 79
>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 = 49.3 bits (117), Expect = 6e-08
Identities = 6/72 (8%), Positives = 20/72 (27%), Gaps = 5/72 (6%)
Query: 89 MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFA 147
+ + E++ E + G ++ + +E++ +
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE----T 181
Query: 148 FIEFNDYDVVDK 159
N Y + +
Sbjct: 182 LGFLNHYQMKNP 193
Score = 39.3 bits (91), Expect = 2e-04
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 7/55 (12%)
Query: 90 FVGGLKDQE--EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
V GL + D + F +G +E V + + K G A +E D VD+
Sbjct: 8 MVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDR 57
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 49.4 bits (117), Expect = 7e-08
Identities = 16/69 (23%), Positives = 26/69 (37%), Gaps = 16/69 (23%)
Query: 78 GKPEANATVKKMFVGGLKD----------QEEDDLREYFSQFGTIESVNMVTNKETGAKR 127
G K ++VGG+ Q E +R FS+ G I+ + V +K
Sbjct: 126 GIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------ 179
Query: 128 GFAFIEFND 136
F++F
Sbjct: 180 NCGFVKFKY 188
>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 = 46.9 bits (112), Expect = 8e-08
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 5/68 (7%)
Query: 90 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFAF 148
V + D++ ++F + I + E G G A + F D A
Sbjct: 19 KVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA----AV 74
Query: 149 IEFNDYDV 156
I+ ND +
Sbjct: 75 IDLNDRPI 82
>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 = 45.9 bits (109), Expect = 3e-07
Identities = 11/66 (16%), Positives = 24/66 (36%), Gaps = 1/66 (1%)
Query: 78 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G+ + N+ + + + D+ ++ E+ V G G A ++F +
Sbjct: 7 GEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKN 66
Query: 137 YDVVDK 142
D K
Sbjct: 67 EDDARK 72
>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 = 47.9 bits (113), Expect = 3e-07
Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 15/84 (17%)
Query: 81 EANATVKKMFVGGL-KDQEEDDLRE----YFSQFGTIESVNMVTNKETGAKRGFAFIEFN 135
N T+ ++ L + ++D+L++ FSQFG I + + + RG AF+ F
Sbjct: 7 RPNHTI---YINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFK 60
Query: 136 DYDVVDKIRGFAFIEFNDYDVVDK 159
+ A + DK
Sbjct: 61 EVSSATN----ALRSMQGFPFYDK 80
Score = 42.9 bits (100), Expect = 2e-05
Identities = 15/93 (16%), Positives = 25/93 (26%), Gaps = 5/93 (5%)
Query: 46 PTINNKAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGLKDQEEDDLREY 105
I + Q P E ++ E L
Sbjct: 168 GMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSML 227
Query: 106 FSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
F+QF + V +V + AF+EF++
Sbjct: 228 FNQFPGFKEVRLVPG-----RHDIAFVEFDNEV 255
>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 = 45.0 bits (107), Expect = 4e-07
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 5/68 (7%)
Query: 90 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFAF 148
V + D++ ++F + I + E G G A + F D A
Sbjct: 19 KVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA----AV 74
Query: 149 IEFNDYDV 156
I+ ND +
Sbjct: 75 IDLNDRPI 82
>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 = 45.6 bits (108), Expect = 4e-07
Identities = 12/77 (15%), Positives = 25/77 (32%), Gaps = 3/77 (3%)
Query: 67 PGPPHMDKLEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGA 125
P + P +++ GL + E + ++F + +E + G
Sbjct: 8 KSPSGQKRSRSRSPHEAGFC--VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK 65
Query: 126 KRGFAFIEFNDYDVVDK 142
G F+EF +
Sbjct: 66 ATGEGFVEFRNEADYKA 82
>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 = 45.2 bits (107), Expect = 4e-07
Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 11/79 (13%)
Query: 90 FVGGL--KDQEEDDLR--EYFSQFGTIESVNMVTNKETGAKR---GFAFIEFNDYDVVDK 142
FV GL + + + L+ EYF +FG I V + + + A++ + + +
Sbjct: 19 FVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALR 78
Query: 143 IRGFAFIEFNDYDVVDKIV 161
A N+ V + +
Sbjct: 79 ----AIQCVNNVVVDGRTL 93
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 44.7 bits (106), Expect = 6e-07
Identities = 18/61 (29%), Positives = 24/61 (39%), Gaps = 10/61 (16%)
Query: 79 KPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
K A+ V + GL E DL E +FG I V ++ K A +EF D
Sbjct: 17 KTPASPVV---HIRGLIDGVVEADLVEALQEFGPISYVVVMPKK------RQALVEFEDV 67
Query: 138 D 138
Sbjct: 68 L 68
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 44.4 bits (105), Expect = 7e-07
Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 8/75 (10%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
+K+ + + + + L Q+G +ES V + ++ D +
Sbjct: 16 RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQ--- 69
Query: 146 FAFIEFNDYDVVDKI 160
A + N + + +
Sbjct: 70 -ALDKLNGFQLENFT 83
>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 = 44.9 bits (106), Expect = 9e-07
Identities = 11/77 (14%), Positives = 28/77 (36%), Gaps = 1/77 (1%)
Query: 67 PGPPHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGA 125
+A + + GL ++++ ++FS + + + G
Sbjct: 23 SMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK 82
Query: 126 KRGFAFIEFNDYDVVDK 142
G AF++F ++ +K
Sbjct: 83 ITGEAFVQFASQELAEK 99
>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 = 43.6 bits (103), Expect = 1e-06
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFG-----TIESVNMVTNKETGAKRGFAFIEFNDYDVV 140
++++VG + E+ + ++F+ T N V + + FAF+EF D
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 141 DKIRGFAFIEFN 152
+ F I F
Sbjct: 67 TQAMAFDGIIFQ 78
>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 = 44.1 bits (104), Expect = 1e-06
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+ + + L D E ++ FG + ++ M+ K AFIE N +
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEE 78
>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 = 43.6 bits (103), Expect = 1e-06
Identities = 20/61 (32%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 79 KPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
K + V V GL + E DL E +FGTI V M+ K A +EF +
Sbjct: 11 KVSVSPVV---HVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFENI 61
Query: 138 D 138
D
Sbjct: 62 D 62
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 44.1 bits (104), Expect = 2e-06
Identities = 15/99 (15%), Positives = 30/99 (30%), Gaps = 13/99 (13%)
Query: 67 PGPPHMDKLEIGK-PEANATVKKMFVGGLKDQ-EEDDLRE----YFSQFGTIESVNMVTN 120
HMD ++G P + + + + + ++ L+ S G I + +
Sbjct: 9 FERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV--- 65
Query: 121 KETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDVVDK 159
+ G A+I F + F Y
Sbjct: 66 DLSDDNSGKAYIVFATQESAQA----FVEAFQGYPFQGN 100
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 43.3 bits (102), Expect = 2e-06
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+ + + L D E ++ FG + ++ M+ K AFIE N +
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEE 63
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 43.2 bits (102), Expect = 2e-06
Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 9/56 (16%)
Query: 90 FVGGL-------KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
V + ++ ++ + + FS+FG I + +E G +G+ F+E+
Sbjct: 19 VVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPA 72
>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 = 43.2 bits (102), Expect = 2e-06
Identities = 10/54 (18%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 90 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
+ GL ++++ ++FS + + + G G AF++F ++ +K
Sbjct: 19 RLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEK 72
>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 = 42.6 bits (100), Expect = 5e-06
Identities = 10/73 (13%), Positives = 24/73 (32%), Gaps = 11/73 (15%)
Query: 90 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD----VVDKIR 144
GGL + L + G ++++ M NK ++F + + +
Sbjct: 31 ANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTLN 84
Query: 145 GFAFIEFNDYDVV 157
G ++ +
Sbjct: 85 GKEVVDDLGQKIT 97
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 43.7 bits (102), Expect = 6e-06
Identities = 16/114 (14%), Positives = 41/114 (35%), Gaps = 2/114 (1%)
Query: 45 RPTINNKAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLR 103
++ E + E+ P + + + + +++ G D DD++
Sbjct: 68 VEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIK 127
Query: 104 EYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDVV 157
E+ G + ++ M K G F+ F+ + K ++ + D++
Sbjct: 128 EWLEDKGQVLNIQMRRTLHKAFK-GSIFVVFDSIESAKKFVETPGQKYKETDLL 180
>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 = 42.1 bits (99), Expect = 7e-06
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 8/66 (12%)
Query: 90 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK-IRGFA 147
L +++E FS+FG++ V + A +EF + K R A
Sbjct: 14 LAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFRHLA 67
Query: 148 FIEFND 153
+ +F+
Sbjct: 68 YSKFHH 73
>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 = 43.4 bits (102), Expect = 7e-06
Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 9/81 (11%)
Query: 79 KPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 137
+ + + E+DL+ FS G + K R A I+
Sbjct: 144 FQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSV 199
Query: 138 DVVDKIRGFAFIEFNDYDVVD 158
+ + A I+ +++D+ +
Sbjct: 200 EEAVQ----ALIDLHNHDLGE 216
Score = 39.6 bits (92), Expect = 2e-04
Identities = 10/50 (20%), Positives = 20/50 (40%), Gaps = 7/50 (14%)
Query: 89 MFVGGL--KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
+ V L + L F +G ++ V ++ N K+ A ++ D
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMAD 81
>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 = 43.3 bits (102), Expect = 7e-06
Identities = 15/117 (12%), Positives = 32/117 (27%), Gaps = 10/117 (8%)
Query: 44 TRPTINNKAMEEAQSEEEVDMEIPGPPHMDKLEI-GKPEANATVKKMFVGGL-KDQEEDD 101
+ + D K + + + E+D
Sbjct: 77 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEED 136
Query: 102 LREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDVVD 158
L+ FS G + K R A I+ + + A I+ +++D+ +
Sbjct: 137 LKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQ----ALIDLHNHDLGE 185
Score = 39.5 bits (92), Expect = 1e-04
Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 10/57 (17%)
Query: 82 ANATVKKMFVGGLKDQE--EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
N+ + V L + L F +G ++ V ++ N K+ A ++ D
Sbjct: 2 GNSVL---LVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMAD 50
>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 = 42.1 bits (99), Expect = 9e-06
Identities = 14/88 (15%), Positives = 28/88 (31%), Gaps = 3/88 (3%)
Query: 56 AQSEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIES 114
+ M + + T + + GL E+D+ +FS
Sbjct: 16 PRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVR 74
Query: 115 VNMVTNKETGAKRGFAFIEFNDYDVVDK 142
V++ + G G A +EF ++
Sbjct: 75 VHIEIGPD-GRVTGEADVEFATHEEAVA 101
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 40.8 bits (96), Expect = 1e-05
Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 9/56 (16%)
Query: 90 FVGGL-------KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
V + ++ ++ + + FS+FG I + +E G +G+ F+E+
Sbjct: 5 VVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPA 58
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 41.1 bits (97), Expect = 1e-05
Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 90 FVGGLKDQ-EEDDLREYFSQ-FGTIESVNMVTNKETGAKRGFAFIEFND 136
FVG L ++ L E+F + + + +V ++ TG +G+ F++F D
Sbjct: 13 FVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTD 60
>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 = 41.3 bits (97), Expect = 1e-05
Identities = 10/54 (18%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 90 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
V G+ E+D+R++F +++V+++ + G G ++F +
Sbjct: 20 SVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHV-GRNNGNGLVKFLSPQDTFE 71
>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 = 40.2 bits (94), Expect = 2e-05
Identities = 9/50 (18%), Positives = 19/50 (38%), Gaps = 7/50 (14%)
Query: 90 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+ L + E ++ FG + ++ M+ K AF+E +
Sbjct: 19 HIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEE 62
>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 = 40.6 bits (95), Expect = 3e-05
Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 9/81 (11%)
Query: 78 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G P + + ++ V GL DL+++ + G + ++ + G +EF
Sbjct: 7 GGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVR 59
Query: 137 YDVVDK-IRGFAFIEFNDYDV 156
+ + +R +F ++
Sbjct: 60 KEDMTYAVRKLDNTKFRSHEG 80
>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 = 39.2 bits (92), Expect = 4e-05
Identities = 11/54 (20%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 90 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
+ G + E ++ E+ + ++ +V N G K G+ F++F++ + V +
Sbjct: 14 KLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAH-GNKTGYIFVDFSNEEEVKQ 65
>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 = 38.9 bits (91), Expect = 7e-05
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 3/66 (4%)
Query: 78 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G + T + + GL E+D+ +FS V++ + G G A +EF
Sbjct: 7 GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFAT 64
Query: 137 YDVVDK 142
++
Sbjct: 65 HEDAVA 70
>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 = 39.0 bits (91), Expect = 9e-05
Identities = 12/79 (15%), Positives = 31/79 (39%), Gaps = 9/79 (11%)
Query: 80 PEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
P + + ++ V GL DL+++ + G + ++ + G +EF +
Sbjct: 10 PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKE 62
Query: 139 VVDK-IRGFAFIEFNDYDV 156
+ +R +F ++
Sbjct: 63 DMTYAVRKLDNTKFRSHEG 81
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 39.1 bits (91), Expect = 9e-05
Identities = 11/48 (22%), Positives = 19/48 (39%), Gaps = 5/48 (10%)
Query: 99 EDDLREYFSQFGTI----ESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
+++ +F Q I E + VT + G G AF+ F +
Sbjct: 37 AEEVVAFFGQHCPITGGKEGILFVTYPD-GRPTGDAFVLFACEEYAQN 83
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 38.7 bits (90), Expect = 1e-04
Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 6/76 (7%)
Query: 68 GPPHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAK 126
G E ++VG L +D DL+ + G++ + +
Sbjct: 1 GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-PLRLTWQG----P 55
Query: 127 RGFAFIEFNDYDVVDK 142
R AF+ + D +
Sbjct: 56 RRRAFLHYPDSAAAQQ 71
>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 = 38.8 bits (90), Expect = 1e-04
Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 3/77 (3%)
Query: 65 EIPGPPHMDKLEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMV--TNK 121
+ G M + + + + GL +D++ + S + V
Sbjct: 23 SMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYT 82
Query: 122 ETGAKRGFAFIEFNDYD 138
G + G AF+E D
Sbjct: 83 REGRQSGEAFVELGSED 99
>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 = 38.5 bits (89), Expect = 3e-04
Identities = 21/132 (15%), Positives = 47/132 (35%), Gaps = 23/132 (17%)
Query: 37 GVLEVVTTRPTINNKAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGLKD 96
L+ V + + N A+ + + + M + G + ++ + T
Sbjct: 12 AALQAVNSVQS-GNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVT----------- 59
Query: 97 QEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDV 156
D L + FS+FGT+ + T + A +++ D A + + ++
Sbjct: 60 --LDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQH----AKLSLDGQNI 109
Query: 157 VDKIVCKYNIEF 168
+ C I+F
Sbjct: 110 YNAC-CTLRIDF 120
>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 = 37.2 bits (86), Expect = 4e-04
Identities = 10/43 (23%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 99 EDDLREYFSQF---GTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+D++ + S + V+ + +E G + G AF+E D
Sbjct: 31 IEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESED 72
>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 = 36.8 bits (85), Expect = 6e-04
Identities = 10/42 (23%), Positives = 15/42 (35%), Gaps = 2/42 (4%)
Query: 99 EDDLREYFSQFGTIESVNMV--TNKETGAKRGFAFIEFNDYD 138
+D+ +FS N + G +RG A IE
Sbjct: 25 MEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQ 66
>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA
binding domain, poly(A polymerase, mitochondria,
transferase; 3.10A {Homo sapiens}
Length = 464
Score = 36.4 bits (83), Expect = 0.003
Identities = 10/61 (16%), Positives = 22/61 (36%), Gaps = 5/61 (8%)
Query: 90 FVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFAFI 149
+ + E+ +Y SQFG I + + +A +EF + + ++
Sbjct: 57 LIHCPEKISENKFLKYLSQFGPINNHFFYESFGL-----YAVVEFCQKESIGSLQNGTHT 111
Query: 150 E 150
Sbjct: 112 P 112
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 34.5 bits (79), Expect = 0.003
Identities = 10/87 (11%), Positives = 26/87 (29%), Gaps = 22/87 (25%)
Query: 78 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
G ++ V + V GL ++ L YF + G +
Sbjct: 1 GSSGSSGGVA-VEVRGLPPAVPDELLTLYFENRR---------------RSGGGPVL--- 41
Query: 137 YDVVDKIRGFAFIEFNDYDVVDKIVCK 163
++ + F + ++++ +
Sbjct: 42 --SWQRLGCGGVLTFREPADAERVLAQ 66
>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 = 34.9 bits (80), Expect = 0.003
Identities = 7/38 (18%), Positives = 15/38 (39%), Gaps = 6/38 (15%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
+ + + +G I++ ++ K AFIE
Sbjct: 40 DSAVLKLAEPYGKIKNYILMRMK------SQAFIEMET 71
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 36.6 bits (84), Expect = 0.003
Identities = 25/147 (17%), Positives = 47/147 (31%), Gaps = 47/147 (31%)
Query: 2 TKLSGIVVSTVYSGSGGW---------------WFESKC----PSHEVRLAVEAGVLEVV 42
G+V + + + W + +C P+ + ++ LE
Sbjct: 272 GHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENN 331
Query: 43 TTRPT----INNKAMEEAQSE-EEVDMEIPGPPHMDKLEI------------GKPEA--- 82
P+ I+N E+ Q + + +P +EI G P++
Sbjct: 332 EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQ---VEISLVNGAKNLVVSGPPQSLYG 388
Query: 83 -NATVKKMFVGGLKDQEEDDLREYFSQ 108
N T++K DQ R FS+
Sbjct: 389 LNLTLRKAKAPSGLDQS----RIPFSE 411
Score = 30.4 bits (68), Expect = 0.27
Identities = 19/96 (19%), Positives = 31/96 (32%), Gaps = 31/96 (32%)
Query: 32 LAVEAGVL------EVVTTRPTINNKAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANAT 85
LA A V+ EVV R M+ A +E+ G M + G
Sbjct: 1770 LASLADVMSIESLVEVVFYR----GMTMQVAVPRDELGRSNYG---MIAINPG------- 1815
Query: 86 VKKMFVGGLKDQEEDDLREYFSQFGT-----IESVN 116
++ ++ L+ + G +E VN
Sbjct: 1816 --RVAASF----SQEALQYVVERVGKRTGWLVEIVN 1845
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 35.0 bits (80), Expect = 0.004
Identities = 15/88 (17%), Positives = 32/88 (36%), Gaps = 17/88 (19%)
Query: 49 NNKAMEEAQSEEEVDMEIPGPPHMDKLEIGKPEANATVKKMFVGGLKDQEEDDLREYFSQ 108
N A+ + + + M + G + ++ + T D L + FS+
Sbjct: 5 GNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVT-------------LDVLHQIFSK 51
Query: 109 FGTIESVNMVTNKETGAKRGFAFIEFND 136
FGT+ + T + A +++ D
Sbjct: 52 FGTVLKIITFTKN----NQFQALLQYAD 75
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 34.4 bits (78), Expect = 0.004
Identities = 8/45 (17%), Positives = 18/45 (40%), Gaps = 5/45 (11%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 143
+D L ++G + ++ + + K G A +EF +
Sbjct: 31 KDVLLRLLQKYGEVLNLVLSSK-----KPGTAVVEFATVKAAELA 70
>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 = 33.5 bits (77), Expect = 0.006
Identities = 7/80 (8%), Positives = 23/80 (28%), Gaps = 25/80 (31%)
Query: 87 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRG 145
+ V L +D ++ + + ++ VD+ +
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-LKYCY-----------------------VDRNKR 41
Query: 146 FAFIEFNDYDVVDKIVCKYN 165
AF+ + + + ++
Sbjct: 42 TAFVTLLNGEQAQNAIQMFH 61
>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 = 33.2 bits (76), Expect = 0.013
Identities = 15/76 (19%), Positives = 28/76 (36%), Gaps = 5/76 (6%)
Query: 72 MDKLEIGKPEANATVKKMF-VGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKR--- 127
M KL + ++ M + D E ++ E +FG + V + K+ +
Sbjct: 11 MQKLLRKQESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEI 70
Query: 128 -GFAFIEFNDYDVVDK 142
F+EF+ K
Sbjct: 71 IVKIFVEFSIASETHK 86
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 34.1 bits (77), Expect = 0.017
Identities = 17/149 (11%), Positives = 43/149 (28%), Gaps = 49/149 (32%)
Query: 7 IVVSTVYSGSGGWW----FESKCPSHEVRLAV---EAGVLEVV----TTRPTIN--NKAM 53
+V+ V + F C ++ + V + + TT +++ + +
Sbjct: 248 LVLLNVQN----AKAWNAFNLSC-----KILLTTRFKQVTDFLSAATTTHISLDHHSMTL 298
Query: 54 EEAQSEE----EVDMEIPG-PPHMDKLE------IGK--PEANAT-----------VKKM 89
+ + +D P + I + + AT + +
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI 358
Query: 90 FVGGLKDQEEDDLREYFSQFGTI--ESVN 116
L E + R+ F + + S +
Sbjct: 359 IESSLNVLEPAEYRKMFDRLS-VFPPSAH 386
Score = 27.9 bits (61), Expect = 2.1
Identities = 19/164 (11%), Positives = 42/164 (25%), Gaps = 46/164 (28%)
Query: 19 WWFESKCPSHEVRLAVEAGVLEVVTTRPTINNKAMEEAQSEEEVDMEIPGPP-------- 70
ES + L ++ + ++ ++ + D + PP
Sbjct: 420 QPKESTISIPSIYLELKVKLEN----EYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYS 475
Query: 71 ----HMDKLEIGKPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIESVNMVTNK--ETG 124
H+ +E + R F F +E K
Sbjct: 476 HIGHHLKNIE------------------HPERMTLFRMVFLDFRFLE------QKIRHDS 511
Query: 125 AKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDVVDKIVCKYNIEF 168
+ N + + +I ND +++V ++F
Sbjct: 512 TAWNASGSILNTLQQLKFYKP--YICDND-PKYERLVNAI-LDF 551
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 30.6 bits (69), Expect = 0.092
Identities = 8/79 (10%), Positives = 26/79 (32%), Gaps = 21/79 (26%)
Query: 88 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGF 146
++ + L + DL++ + + + V ++ G
Sbjct: 30 RITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDF--------------------DGT 69
Query: 147 AFIEFNDYDVVDKIVCKYN 165
+EF +++ + + + N
Sbjct: 70 GALEFPSEEILVEALERLN 88
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 30.4 bits (68), Expect = 0.13
Identities = 13/70 (18%), Positives = 21/70 (30%), Gaps = 10/70 (14%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIRGFAFIEFNDYDVVD 158
D L + G ++ + + A +EF K A N D+
Sbjct: 39 VDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQK----AKAALNGADIYA 89
Query: 159 KIVCKYNIEF 168
C IE+
Sbjct: 90 GC-CTLKIEY 98
>3p16_A DNA polymerase III subunit beta; DNA polymerase III sliding clamp,
transferase; HET: DNA; 2.89A {Mycobacterium
tuberculosis} PDB: 3rb9_A*
Length = 408
Score = 29.6 bits (67), Expect = 0.43
Identities = 9/49 (18%), Positives = 19/49 (38%), Gaps = 11/49 (22%)
Query: 30 VRLAVEAGVLEVVTTRPTINNKAMEEAQSEEEVDMEIPGPPHMDKLEIG 78
VR+ G + + + ++EE++ ++ G P L I
Sbjct: 303 VRMEFADGSVRLSAGAD-------DVGRAEEDLVVDYAGEP----LTIA 340
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 27.9 bits (62), Expect = 0.76
Identities = 8/43 (18%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 96 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 138
+ E+ E ++G +E +N+ N G +++F +
Sbjct: 38 EFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREE 79
>2l4d_A SCO1/SENC family protein/cytochrome C; electron transfer, electron
transport; HET: HEC; NMR {Pseudomonas putida}
Length = 110
Score = 26.9 bits (59), Expect = 1.7
Identities = 17/95 (17%), Positives = 27/95 (28%), Gaps = 14/95 (14%)
Query: 21 FESKCPS-HEVRLAVEAGVLEVVTTRPTINNKAMEEAQSEEEVDMEIPGPPHMDKLEIGK 79
F ++C S H V P + + + + + P M L
Sbjct: 10 FRTRCSSCH----TVGNTEPGQPGIGPDLLG--VTRQRDANWLVRWLKVPDQM--LAEKD 61
Query: 80 PEANATVKK-----MFVGGLKDQEEDDLREYFSQF 109
P A ++ M L D E L Y +
Sbjct: 62 PLAMLLFEQYNRLAMPNMRLGDAEVSALISYLEEE 96
>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 = 26.9 bits (60), Expect = 1.8
Identities = 6/38 (15%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 136
+DD+ E ++ G + + + N +G +++
Sbjct: 31 KDDVIEECNKHGGVIHIYVDKNSA----QGNVYVKCPS 64
>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 = 26.6 bits (59), Expect = 2.6
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 4/44 (9%)
Query: 99 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 142
+DLR S+FG I + + G A + F D + D
Sbjct: 40 REDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADY 79
>3ldu_A Putative methylase; structural genomics, PSI-2, protein structure
initiative, midwest center for structural genomics,
MCSG; HET: MSE GTP; 1.70A {Clostridium difficile}
Length = 385
Score = 27.3 bits (61), Expect = 2.7
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 110 GT--IESVNMVTNKETGAKRGFAFIEFNDYD 138
GT IE+ + N G R F ++ D
Sbjct: 207 GTILIEAAMIGINMAPGLNREFISEKWRTLD 237
>3ldg_A Putative uncharacterized protein SMU.472; YPSC, methyltransferase,
transferase; HET: SAH; 1.96A {Streptococcus mutans}
Length = 384
Score = 27.3 bits (61), Expect = 2.7
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 110 GT--IESVNMVTNKETGAKRGFAFIEFNDYD 138
GT IE+ + N G R FAF E+ D
Sbjct: 206 GTFCIEAAMIGMNIAPGFNRDFAFEEWPWVD 236
>3k0b_A Predicted N6-adenine-specific DNA methylase; methylase,PF01170,
putative RNA methylase, PSI,MCSG, structu genomics;
1.50A {Listeria monocytogenes str}
Length = 393
Score = 26.9 bits (60), Expect = 3.5
Identities = 8/31 (25%), Positives = 12/31 (38%), Gaps = 2/31 (6%)
Query: 110 GT--IESVNMVTNKETGAKRGFAFIEFNDYD 138
GT IE+ + N G R F ++
Sbjct: 213 GTIPIEAALIGQNIAPGFNREFVSETWDWMP 243
>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM:
PF02562, ST genomics, PSI-2, protein structure
initiative; 2.35A {Corynebacterium glutamicum atcc
13032}
Length = 208
Score = 26.4 bits (59), Expect = 4.3
Identities = 8/32 (25%), Positives = 11/32 (34%), Gaps = 5/32 (15%)
Query: 138 DVVDKIRGFAFIEFNDYDV-----VDKIVCKY 164
++ + F E DV V IV Y
Sbjct: 176 HILRGVDDVHFSELTSSDVVRHQLVGHIVDAY 207
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 26.3 bits (57), Expect = 5.1
Identities = 11/67 (16%), Positives = 28/67 (41%), Gaps = 7/67 (10%)
Query: 74 KLEIGKPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIE 133
+ + + +A + V + +++ + DL E+ + N + N+ AF +
Sbjct: 95 RKRLQELDAASKVMEQ---EWREKAKKDLEEWNQRQSEQVEKNKINNRIADK----AFYQ 147
Query: 134 FNDYDVV 140
D D++
Sbjct: 148 QPDADII 154
>3ndn_A O-succinylhomoserine sulfhydrylase; seattle structural genomics
center for infectious disease, S mycobacterium, PLP,
schiff base; HET: LLP; 1.85A {Mycobacterium
tuberculosis}
Length = 414
Score = 26.0 bits (58), Expect = 7.4
Identities = 9/54 (16%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 81 EANATVKKMFVGGLKDQEEDDL-REYFSQFGTIESVNMVTNKETGAKRGFAFIE 133
+ +V+ + L + DL + S GT+ + + ++ +R F ++
Sbjct: 296 NGHPSVRWVRYPYLPSHPQYDLAKRQMSGGGTVVTFALDCPEDVAKQRAFEVLD 349
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 24.8 bits (54), Expect = 8.2
Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 99 EDDLREYFSQFGTIESVN--MVTNKETGAKRGFAFIEFNDYDVVDK 142
+D+R+ S++G ++S+ + G F+EF K
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQK 74
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 24.8 bits (54), Expect = 8.2
Identities = 7/50 (14%), Positives = 17/50 (34%), Gaps = 1/50 (2%)
Query: 94 LKDQEEDDLREYFSQFGTIESVNMVTNKETGAK-RGFAFIEFNDYDVVDK 142
+ + E + +E ++G + + F+EF + K
Sbjct: 22 VDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIK 71
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.316 0.135 0.395
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,713,919
Number of extensions: 162495
Number of successful extensions: 918
Number of sequences better than 10.0: 1
Number of HSP's gapped: 751
Number of HSP's successfully gapped: 227
Length of query: 168
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 81
Effective length of database: 4,272,666
Effective search space: 346085946
Effective search space used: 346085946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (24.5 bits)