RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2871
(178 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 = 230 bits (588), Expect = 4e-78
Identities = 97/168 (57%), Positives = 127/168 (75%), Gaps = 1/168 (0%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EPE LRK+FIGGL + TTDESL++ FEQWG + D VVM+DP TKRSRGFGF+TY+ + V
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQF 130
D AM+ RPH +DGRVVE KRAV R++ +P A+ TVKK+FVGG+K D EE LR+YF Q+
Sbjct: 69 DAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY 128
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRVE 178
G IE + ++T++ +G KRGFAF+ F+D+D VDKIV+ K + E
Sbjct: 129 GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCE 176
Score = 117 bits (294), Expect = 1e-33
Identities = 27/103 (26%), Positives = 57/103 (55%)
Query: 3 PRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGF 62
R D + +++K+F+GG+ T + L+ +FEQ+G+I + +M D + + RGF F
Sbjct: 91 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 150
Query: 63 ITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANA 105
+T+ + VD + + H ++G E ++A+ + E+ ++
Sbjct: 151 VTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQ 193
Score = 77.3 bits (191), Expect = 3e-18
Identities = 22/80 (27%), Positives = 43/80 (53%), Gaps = 1/80 (1%)
Query: 100 KPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
P+ ++K+F+GGL + ++ LR +F Q+GT+ ++ + T RGF F+ +
Sbjct: 6 SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65
Query: 159 DVVDKIVLSKITLLLDRRVE 178
+ VD + ++ + R VE
Sbjct: 66 EEVDAAMNARPHKVDGRVVE 85
>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 = 213 bits (544), Expect = 9e-72
Identities = 65/166 (39%), Positives = 108/166 (65%), Gaps = 8/166 (4%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
+ K+FIGGL++ TT+++L+ +F ++G + D+ +MKDP T RSRGFGF+++ + VD+
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 74 AMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGT 132
+ + H +DG+V++ KRA+PRDE K K+FVGG+ D + E+FSQ+GT
Sbjct: 61 VVKTQ-HILDGKVIDPKRAIPRDEQDKT------GKIFVGGIGPDVRPKEFEEFFSQWGT 113
Query: 133 IESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRVE 178
I ++ +K+TG RGF F+ ++ D VD++ +K DR++E
Sbjct: 114 IIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIE 159
Score = 108 bits (272), Expect = 1e-30
Identities = 34/84 (40%), Positives = 47/84 (55%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E + K+F+GG+ + + FF QWG I+D +M D T +SRGFGF+TY A V
Sbjct: 83 EQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAV 142
Query: 72 DDAMSNRPHNIDGRVVETKRAVPR 95
D N+ + R +E KRA PR
Sbjct: 143 DRVCQNKFIDFKDRKIEIKRAEPR 166
>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 = 159 bits (404), Expect = 2e-50
Identities = 32/155 (20%), Positives = 71/155 (45%), Gaps = 12/155 (7%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVV-----VMKDPITKRSRGFGFITYSEAKMV 71
R++++G + + T+E++ FF + + + + + F F+ +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQF 130
AM+ G+ ++ +R + K+F+GGL +D ++E + F
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGA------HKLFIGGLPNYLNDDQVKELLTSF 118
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
G +++ N+V + TG +G+AF E+ D +V D+ +
Sbjct: 119 GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Score = 85.7 bits (213), Expect = 8e-22
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
K+FIGGL D+ ++ +G + ++KD T S+G+ F Y + +
Sbjct: 90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149
Query: 72 DDAMSN-RPHNIDGRVVETKRA 92
D A++ + + + +RA
Sbjct: 150 DQAIAGLNGMQLGDKKLLVQRA 171
>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 = 154 bits (391), Expect = 2e-49
Identities = 36/104 (34%), Positives = 55/104 (52%), Gaps = 3/104 (2%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + K+F+GGL Y TTD SL+ +FE +G+I + VV+ D T +SRG+GF+T ++
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAA 72
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL 115
+ A + IDGR A KP + T + V G
Sbjct: 73 ERACKDPNPIIDGRKANVNLAYLG---AKPRSLQTGFAIGVSGP 113
Score = 77.3 bits (191), Expect = 4e-19
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 101 PEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+ + T K+FVGGL + LR+YF FG IE ++T+++TG RG+ F+ D
Sbjct: 11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRA 70
Query: 160 VVDKIVLSKITLLLDRRVE 178
++ ++ R+
Sbjct: 71 AAERACKDPNPIIDGRKAN 89
>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 = 150 bits (380), Expect = 1e-47
Identities = 56/102 (54%), Positives = 74/102 (72%), Gaps = 2/102 (1%)
Query: 3 PRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGF 62
P + E E RK+FIGGL + TT+ESL+ ++EQWG++ D VVM+DP +KRSRGFGF
Sbjct: 16 PLERKKR--EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 73
Query: 63 ITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEAN 104
+T+S VD AM+ RPH+IDGRVVE KRAV R+E G ++
Sbjct: 74 VTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGSGPSS 115
Score = 88.9 bits (221), Expect = 1e-23
Identities = 25/97 (25%), Positives = 46/97 (47%), Gaps = 3/97 (3%)
Query: 83 DGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTN 141
+ +T VP + K +K+F+GGL + E+ LR Y+ Q+G + ++ +
Sbjct: 5 SSGMEKTLETVPLER--KKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRD 62
Query: 142 KETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRVE 178
+ RGF F+ F+ VD + ++ + R VE
Sbjct: 63 PASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVE 99
>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 = 149 bits (379), Expect = 1e-47
Identities = 37/92 (40%), Positives = 60/92 (65%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + K+F+GGLD+ TT E+L+++F Q+GE+VD V+MKD T +SRGFGF+ + + V
Sbjct: 12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCV 71
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEA 103
+++RPH +DGR ++ K PR +
Sbjct: 72 GTVLASRPHTLDGRNIDPKPCTPRGMQPSGPS 103
Score = 74.6 bits (184), Expect = 3e-18
Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 96 DEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIE 154
+ K+FVGGL ++ LR YFSQ+G + ++ +K T RGF F++
Sbjct: 5 SSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVK 64
Query: 155 FNDYDVVDKIVLSKITLLLDRRVE 178
F D + V ++ S+ L R ++
Sbjct: 65 FKDPNCVGTVLASRPHTLDGRNID 88
>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 = 147 bits (372), Expect = 1e-46
Identities = 40/102 (39%), Positives = 61/102 (59%), Gaps = 6/102 (5%)
Query: 5 YDDSKCTEP------ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSR 58
+ S P S K+FIGGL ++TT E L+ +F Q+GE+ + +VM+DP+TKRSR
Sbjct: 8 HHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSR 67
Query: 59 GFGFITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGK 100
GFGF+T+ + VD ++ H +D + ++ K A PR K
Sbjct: 68 GFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQPK 109
Score = 80.8 bits (200), Expect = 1e-20
Identities = 30/104 (28%), Positives = 48/104 (46%), Gaps = 10/104 (9%)
Query: 76 SNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIE 134
S+ H+ VPR ++ KMF+GGL ++ LREYF QFG ++
Sbjct: 3 SSHHHHHHS-----SGLVPRG----SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVK 53
Query: 135 SVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRVE 178
++ + T RGF F+ F D VDK++ L + ++
Sbjct: 54 ECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTID 97
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 99
Score = 137 bits (347), Expect = 9e-43
Identities = 33/97 (34%), Positives = 58/97 (59%)
Query: 8 SKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
S + K+F+GG+ + + L+ +F+++G + +VV++ D +R RGFGFIT+ +
Sbjct: 2 SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED 61
Query: 68 AKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEAN 104
+ VD A++ H+I G+ VE KRA PRD ++
Sbjct: 62 EQSVDQAVNMHFHDIMGKKVEVKRAEPRDSKSSGPSS 98
Score = 91.1 bits (227), Expect = 1e-24
Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 101 PEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+ + K+FVGG+ E +LREYF +FG + V M+ + E RGF FI F D
Sbjct: 4 GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQ 63
Query: 160 VVDKIVLSKITLLLDRRVE 178
VD+ V ++ ++VE
Sbjct: 64 SVDQAVNMHFHDIMGKKVE 82
>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 = 136 bits (344), Expect = 2e-42
Identities = 33/81 (40%), Positives = 53/81 (65%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E K+F+GGL + T+ + L+ +F ++GE+VD + DP T RSRGFGFI + +A V
Sbjct: 7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASV 66
Query: 72 DDAMSNRPHNIDGRVVETKRA 92
+ + + H +DGRV++ K+A
Sbjct: 67 EKVLDQKEHRLDGRVIDPKKA 87
Score = 75.3 bits (186), Expect = 1e-18
Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 1/82 (1%)
Query: 98 IGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
I + KMFVGGL D + DL++YF++FG + + + TG RGF FI F
Sbjct: 2 INASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK 61
Query: 157 DYDVVDKIVLSKITLLLDRRVE 178
D V+K++ K L R ++
Sbjct: 62 DAASVEKVLDQKEHRLDGRVID 83
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 134 bits (340), Expect = 5e-42
Identities = 34/75 (45%), Positives = 54/75 (72%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+FIGGL ++TT E L+ +F Q+GE+ + +VM+DP+TKRSRGFGF+T+ + VD ++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 78 RPHNIDGRVVETKRA 92
H +D + ++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76
Score = 72.5 bits (179), Expect = 9e-18
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
KMF+GGL ++ LREYF QFG ++ ++ + T RGF F+ F D VDK++
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 168 KITLLLDRRVE 178
L + ++
Sbjct: 62 SRHELDSKTID 72
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 138 bits (351), Expect = 6e-42
Identities = 33/161 (20%), Positives = 70/161 (43%), Gaps = 7/161 (4%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ +V++G + Y +++++ F +G I + + D +T + +GF F+ Y +
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAA 83
Query: 72 DDAMSNR-PHNIDGRVVETKRAVPRDEIGK-----PEANATVKKMFVGGL-KDQEEDDLR 124
A+ + GR ++ R + E +++V + +D +DD++
Sbjct: 84 QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIK 143
Query: 125 EYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
F FG I+S + + TG +G+ FIE+ V
Sbjct: 144 SVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
Score = 86.2 bits (214), Expect = 1e-21
Identities = 23/99 (23%), Positives = 50/99 (50%), Gaps = 1/99 (1%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
D E + ++++ + +D+ +++ FE +G+I + +DP T + +G+GFI Y
Sbjct: 116 DQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE 175
Query: 67 EAKMVDDAMSN-RPHNIDGRVVETKRAVPRDEIGKPEAN 104
+A+ DA+S+ ++ G+ + +AV A
Sbjct: 176 KAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPAT 214
>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 = 134 bits (340), Expect = 9e-42
Identities = 27/86 (31%), Positives = 46/86 (53%), Gaps = 1/86 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + + GL ++TT++ L+ +F +GE++ V V KD T S+GFGF+ ++E +
Sbjct: 11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 70
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDE 97
MS H IDGR + K +
Sbjct: 71 VKVMSQ-RHMIDGRWCDCKLPNSKQS 95
Score = 85.0 bits (211), Expect = 3e-22
Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 99 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G A + V GL + E DL+EYFS FG + V + + +TG +GF F+ F +
Sbjct: 7 GVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE 66
Query: 158 YDVVDKIVLSKITLLLDRRVE 178
Y+ K V+S+ ++ R +
Sbjct: 67 YETQVK-VMSQRHMIDGRWCD 86
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 133 bits (337), Expect = 5e-40
Identities = 34/167 (20%), Positives = 74/167 (44%), Gaps = 20/167 (11%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVV-----VMKDPITKRSRGFGFITYSEAKMV 71
R++++G + + T+E++ FF + + + + + F F+ +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVK--------------KMFVGGLKD 117
AM+ G+ ++ +R + N +V K+F+GGL +
Sbjct: 65 TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 118 Q-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+D ++E + FG +++ N+V + TG +G+AF E+ D +V D+
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Score = 81.6 bits (202), Expect = 6e-20
Identities = 21/88 (23%), Positives = 41/88 (46%), Gaps = 1/88 (1%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
P+S K+FIGGL D+ ++ +G + ++KD T S+G+ F Y + +
Sbjct: 109 VVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV 168
Query: 71 VDDAMSN-RPHNIDGRVVETKRAVPRDE 97
D A++ + + + +RA +
Sbjct: 169 TDQAIAGLNGMQLGDKKLLVQRASVGAK 196
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 125 bits (316), Expect = 2e-38
Identities = 30/75 (40%), Positives = 48/75 (64%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL TT E ++ +FEQ+G++ D ++M D T R RGFGF+T+ +V+
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 78 RPHNIDGRVVETKRA 92
H I+ ++VE K+A
Sbjct: 61 HFHEINNKMVECKKA 75
Score = 83.3 bits (207), Expect = 5e-22
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
K+FVGGL +D++ YF QFG ++ ++ +K T RGF F+ F D+V+K+
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 168 KITLLLDRRVE 178
+ ++ VE
Sbjct: 61 HFHEINNKMVE 71
>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 = 123 bits (311), Expect = 2e-36
Identities = 40/155 (25%), Positives = 73/155 (47%), Gaps = 11/155 (7%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK--RSRGFGFITYSEAKMVDDA 74
K+F+G + +++ L+ FEQ+G + ++ V++D +S+G F+T+ K +A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 75 MSNRPHNIDGRVVETKRAVP-RDEIGKPEANATVK--KMFVGGL-KDQEEDDLREYFSQF 130
+ + V P + + E N V+ K+F+G + K E+D+R FS F
Sbjct: 64 Q----NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSF 119
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
G IE ++ G RG AF+ F + +
Sbjct: 120 GQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAI 153
Score = 71.1 bits (175), Expect = 3e-16
Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
++ + DS+ RK+FIG + + T+ ++ F +G+I + +++ P SRG
Sbjct: 80 IQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGC 138
Query: 61 GFITYSEAKMVDDAMSN 77
F+T++ M A+
Sbjct: 139 AFVTFTTRAMAQTAIKA 155
>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 = 122 bits (308), Expect = 5e-36
Identities = 38/154 (24%), Positives = 72/154 (46%), Gaps = 10/154 (6%)
Query: 15 SLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA 74
S + + L T E ++ F GEI +++D IT +S G+GF+ Y + K + A
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 75 MS--NRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFG 131
++ N + + ++ A P + ++V GL K + +L + FSQ+G
Sbjct: 61 INTLNG-LRLQTKTIKVSYARPSSA------SIRDANLYVSGLPKTMTQKELEQLFSQYG 113
Query: 132 TIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
I + ++ ++ TG RG FI F+ ++ +
Sbjct: 114 RIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
Score = 72.2 bits (178), Expect = 1e-16
Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA-- 74
+++ GL T + L+ F Q+G I+ ++ D +T SRG GFI + + ++A
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 75 -MSNRPHNIDGRVVETKRA 92
++ + + + K A
Sbjct: 149 GLNGQKPSGATEPITVKFA 167
>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 = 119 bits (301), Expect = 6e-35
Identities = 34/156 (21%), Positives = 65/156 (41%), Gaps = 11/156 (7%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+E + +FIG L+ + L+ + D+ V+ D T +R FG++ + A+
Sbjct: 8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAED 66
Query: 71 VDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQ 129
++ A+ + G ++ ++ RD A + L + ED+L+E F
Sbjct: 67 LEKALELTGLKVFGNEIKLEKPKGRDSKKVRAAR----TLLAKNLSFNITEDELKEVFED 122
Query: 130 FGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
I V + G +G A+IEF +K +
Sbjct: 123 ALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNL 153
Score = 63.0 bits (154), Expect = 4e-13
Identities = 17/87 (19%), Positives = 32/87 (36%), Gaps = 10/87 (11%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EA 68
+ + R + L + T++ L+ FE EI +S+G +I + +A
Sbjct: 95 KVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADA 149
Query: 69 KMVDDAMSNRPHNIDGRVVETKRAVPR 95
+ + IDGR V +
Sbjct: 150 EKNLEEKQG--AEIDGRSVSLYYTGEK 174
>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 = 118 bits (298), Expect = 1e-34
Identities = 36/152 (23%), Positives = 65/152 (42%), Gaps = 10/152 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+ + L TD L A F G I +M+D T S G+ F+ ++ A+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 77 --NRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTI 133
N + + ++ A P E + N ++V L + +D L F ++G+I
Sbjct: 64 VLNG-ITVRNKRLKVSYARPGGE-SIKDTN-----LYVTNLPRTITDDQLDTIFGKYGSI 116
Query: 134 ESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
N++ +K TG RG AF+ +N + + +
Sbjct: 117 VQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Score = 68.0 bits (167), Expect = 4e-15
Identities = 18/66 (27%), Positives = 34/66 (51%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E +++ L TD+ L F ++G IV +++D +T R RG F+ Y++ +
Sbjct: 85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144
Query: 72 DDAMSN 77
+A+S
Sbjct: 145 QEAISA 150
>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 = 115 bits (290), Expect = 2e-34
Identities = 26/75 (34%), Positives = 41/75 (54%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
K+F+GGL T +E ++ +F +GE+ + + D T + RGF FIT+ E + V M
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 78 RPHNIDGRVVETKRA 92
+ HN+ E K A
Sbjct: 61 KYHNVGLSKCEIKVA 75
Score = 87.2 bits (217), Expect = 2e-23
Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
K+FVGGL D E+ +REYF FG +ES+ + + +T +RGF FI F + + V KI+
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 168 KITLLLDRRVE 178
K + + E
Sbjct: 61 KYHNVGLSKCE 71
>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 = 115 bits (289), Expect = 4e-34
Identities = 27/87 (31%), Positives = 37/87 (42%), Gaps = 6/87 (6%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
KVF+G T E LQ FF Q+GE+VDV + K R F F+T+++ K+
Sbjct: 6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKV 60
Query: 71 VDDAMSNRPHNIDGRVVETKRAVPRDE 97
I G V A P+
Sbjct: 61 AQSLCG-EDLIIKGISVHISNAEPKHN 86
Score = 66.9 bits (164), Expect = 2e-15
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 7/81 (8%)
Query: 99 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G + K+FVG D ++L+++F Q+G + V + R FAF+ F D
Sbjct: 3 GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFAD 57
Query: 158 YDVVDKIVLSKITLLLDRRVE 178
V + + ++ V
Sbjct: 58 DKVAQS-LCGEDLIIKGISVH 77
>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 = 119 bits (301), Expect = 1e-33
Identities = 23/156 (14%), Positives = 49/156 (31%), Gaps = 11/156 (7%)
Query: 9 KCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS-- 66
+ + + L T + + +G + ++ T +S+G+GF Y
Sbjct: 88 SVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKK 147
Query: 67 -EAKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQ--EEDDL 123
A + +P + R + A + + V L + D L
Sbjct: 148 DSAARAKSDLLGKP--LGPRTLYVHWTDAGQL---TPALLHSRCLCVDRLPPGFNDVDAL 202
Query: 124 REYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
S + + + G +GFA +E+ +
Sbjct: 203 CRALSAVHSPTFCQLACG-QDGQLKGFAVLEYETAE 237
Score = 92.0 bits (229), Expect = 3e-23
Identities = 25/149 (16%), Positives = 54/149 (36%), Gaps = 19/149 (12%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + RK+ I GL T++ + + +K + +G F+T +
Sbjct: 18 QFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQA 70
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQF 130
+ A++ + + + +A + V L + E F
Sbjct: 71 EAAIN----AFHQSRLREREL----SVQLQPTDALL---CVANLPPSLTQQQFEELVRPF 119
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFNDYD 159
G++E +V ++ TG +G+ F E+ D
Sbjct: 120 GSLERCFLVYSERTGQSKGYGFAEYMKKD 148
Score = 62.3 bits (152), Expect = 2e-12
Identities = 10/85 (11%), Positives = 21/85 (24%), Gaps = 7/85 (8%)
Query: 17 RKVFIGGLDYRTTD-ESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVD 72
R + + L D ++L + + +GF + Y A+
Sbjct: 185 RCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQ 243
Query: 73 DAMSNRPHNIDGRVVETKRAVPRDE 97
+ G + P
Sbjct: 244 QQADGLS--LGGSHLRVSFCAPGPP 266
>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 = 112 bits (282), Expect = 4e-33
Identities = 21/92 (22%), Positives = 39/92 (42%), Gaps = 6/92 (6%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
VF+G T++ L+ FF Q+G+++DV + K R F F+T+++ ++
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQ 56
Query: 73 DAMSNRPHNIDGRVVETKRAVPRDEIGKPEAN 104
I G V A P+ ++
Sbjct: 57 SLCG-EDLIIKGISVHISNAEPKHNSNSGPSS 87
Score = 69.9 bits (172), Expect = 2e-16
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 7/77 (9%)
Query: 103 ANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVV 161
++ +FVG D ED+LRE+FSQ+G + V + R FAF+ F D +
Sbjct: 1 GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIA 55
Query: 162 DKIVLSKITLLLDRRVE 178
+ + + V
Sbjct: 56 QSLCGEDLI-IKGISVH 71
>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 = 112 bits (283), Expect = 3e-31
Identities = 38/155 (24%), Positives = 65/155 (41%), Gaps = 19/155 (12%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
++F+G L T+E + FE++GE +V + +D RGFGFI +
Sbjct: 18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLA 71
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQF 130
+ A +DG +++++ R A + V L + L + FSQF
Sbjct: 72 EIAK----AELDGTILKSRPLRIR------FATHG-AALTVKNLSPVVSNELLEQAFSQF 120
Query: 131 GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
G +E +V + + G G F+EF K +
Sbjct: 121 GPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKAL 154
Score = 72.0 bits (177), Expect = 7e-16
Identities = 27/154 (17%), Positives = 54/154 (35%), Gaps = 17/154 (11%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDA--- 74
+ + L ++E L+ F Q+G + VV+ D R+ G GF+ ++ A
Sbjct: 98 ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALER 156
Query: 75 MSNRPH--NIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQEEDDLREYFSQFGT 132
+ R V + D + + +K+ + +E + F+Q GT
Sbjct: 157 CGDGAFLLTTTPRPVIVEPMEQFD-----DEDGLPEKLMQKTQQYHKEREQPPRFAQPGT 211
Query: 133 IESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVL 166
E + +E + VD+ +
Sbjct: 212 FEFEYA------SRWKALDEMEKQQREQVDRNIR 239
>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 = 113 bits (285), Expect = 3e-31
Identities = 29/150 (19%), Positives = 65/150 (43%), Gaps = 9/150 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDD 73
+++ T +++ + + + + SR F +I + +A+ +
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177
Query: 74 AMSNRPHNIDGRVVETKRAVPRDEIGKPE-ANATVKKMFVGGLKDQ--EEDDLREYFSQF 130
++ I+G + TK + P ++ + + A +++ + L + +E+ LRE F F
Sbjct: 178 KLNGLK--IEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGF 235
Query: 131 GTIESVNMVTN-KETGAKRGFAFIEFNDYD 159
G+IE +N+ KE AF+ F + D
Sbjct: 236 GSIEKINIPAGQKEHSFNNCCAFMVFENKD 265
Score = 95.4 bits (238), Expect = 2e-24
Identities = 17/140 (12%), Positives = 42/140 (30%), Gaps = 16/140 (11%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
V + L + +F+ G I+ V V K++ F I ++ A++
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKT 101
Query: 79 PHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVN 137
+ + T+ ++ + ++R+ +
Sbjct: 102 HKVVGQNEIIVSHLT----------ECTL---WMTNFPPSYTQRNIRDLLQDINVVALSI 148
Query: 138 MVTNKETGAKRGFAFIEFND 157
+ + R FA+I+
Sbjct: 149 RLPSLRFNTSRRFAYIDVTS 168
Score = 63.9 bits (156), Expect = 7e-13
Identities = 14/81 (17%), Positives = 28/81 (34%), Gaps = 2/81 (2%)
Query: 17 RKVFIGGLDYRTTDE-SLQAFFEQWGEIVDVVVMKD-PITKRSRGFGFITYSEAKMVDDA 74
R++ I L DE L+ FE +G I + + + F+ + + A
Sbjct: 211 REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 270
Query: 75 MSNRPHNIDGRVVETKRAVPR 95
+ + R + A +
Sbjct: 271 LQMNRSLLGNREISVSLADKK 291
Score = 59.6 bits (145), Expect = 3e-11
Identities = 23/108 (21%), Positives = 36/108 (33%), Gaps = 13/108 (12%)
Query: 57 SRGFGFITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL- 115
S +G ++K D S T + + + + TV V L
Sbjct: 1 SMEYGHHARPDSKRPLDEGSP------AAAGLTSKK-ANEALTRNRELTTV---LVKNLP 50
Query: 116 KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
K ++ + +YF G I V++ FA IEF YD
Sbjct: 51 KSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALA 96
>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 = 102 bits (257), Expect = 2e-28
Identities = 34/152 (22%), Positives = 72/152 (47%), Gaps = 13/152 (8%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDD 73
R +++G LD T++ L+ +F+ G I ++ +M D ++ + F+ Y +A +
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 74 AMSNRPHNIDGRVVETKRAVPRDEIGK-PEANATVKKMFVGGL-KDQEEDDLREYFSQFG 131
++ + I+ +V+ A + N +FVG L + +++ LR F F
Sbjct: 60 TLNGKQ--IENNIVKINWAFQSQQSSSDDTFN-----LFVGDLNVNVDDETLRNAFKDFP 112
Query: 132 TIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+ S +++ + +TG+ RG+ F+ F D
Sbjct: 113 SYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Score = 64.9 bits (159), Expect = 7e-14
Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 2/77 (2%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
++ +F+G L+ DE+L+ F+ + + VM D T SRG+
Sbjct: 74 NWAFQSQQSSSDDTF--NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGY 131
Query: 61 GFITYSEAKMVDDAMSN 77
GF++++ +AM +
Sbjct: 132 GFVSFTSQDDAQNAMDS 148
>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 = 98.5 bits (246), Expect = 2e-27
Identities = 32/87 (36%), Positives = 51/87 (58%), Gaps = 1/87 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
K+F+GGL + T ++SL+ F ++G+I +VVV+KD T+RSRGFGF+T+
Sbjct: 8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 72 DDAMSN-RPHNIDGRVVETKRAVPRDE 97
DAM ++DGR + +A +
Sbjct: 68 KDAMMAMNGKSVDGRQIRVDQAGKSSD 94
Score = 69.2 bits (170), Expect = 3e-16
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 99 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G + K+FVGGL D E L + FS++G I V +V ++ET RGF F+ F +
Sbjct: 4 GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFEN 63
Query: 158 YDVVDK 163
D
Sbjct: 64 IDDAKD 69
>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 = 96.9 bits (242), Expect = 5e-27
Identities = 20/88 (22%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
VF+GG+D R + +++FF ++G + +V ++ D T S+G+GF+++ V + +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVES 69
Query: 78 RPHNIDGRVVETKRAVPRDEIGKPEANA 105
N G+ ++ A+ + +
Sbjct: 70 -QINFHGKKLKLGPAIRKQNLSTYHVQP 96
Score = 84.2 bits (209), Expect = 7e-22
Identities = 23/72 (31%), Positives = 45/72 (62%), Gaps = 2/72 (2%)
Query: 101 PEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
PE +FVGG+ + +E ++R +F+++G+++ V ++T++ TG +G+ F+ F +
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDV 61
Query: 160 VVDKIVLSKITL 171
V KIV S+I
Sbjct: 62 DVQKIVESQINF 73
>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 = 96.3 bits (240), Expect = 2e-26
Identities = 23/100 (23%), Positives = 45/100 (45%), Gaps = 7/100 (7%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
++ + VFI L + + +E+L +Q+G++ V V+ P T+ S+G F + +
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69
Query: 71 VDDAMSNRPHN-------IDGRVVETKRAVPRDEIGKPEA 103
++ +DGR ++ AV RDE +
Sbjct: 70 AQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109
Score = 71.6 bits (176), Expect = 6e-17
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 99 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G P K +F+ L D EE+ L E QFG ++ V +V + +T +G AF +F
Sbjct: 7 GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMT 66
Query: 158 YDVVDK 163
+ K
Sbjct: 67 QEAAQK 72
>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 = 97.4 bits (243), Expect = 8e-26
Identities = 36/157 (22%), Positives = 68/157 (43%), Gaps = 12/157 (7%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SE 67
+ +++G L T+ L F G I+ + V +D IT+RS G+ ++ + ++
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 69
Query: 68 AKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREY 126
A+ D M+ I G+ V + RD + + F+ L K + L +
Sbjct: 70 AERALDTMNFDV--IKGKPVRIMWS-QRDPSLRKSGVGNI---FIKNLDKSIDNKALYDT 123
Query: 127 FSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
FS FG I S +V + +G+ F+ F + ++
Sbjct: 124 FSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAER 158
Score = 66.1 bits (162), Expect = 5e-14
Identities = 28/120 (23%), Positives = 49/120 (40%), Gaps = 16/120 (13%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+FI LD +++L F +G I+ V+ D S+G+GF+ + + + A+
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK- 162
Query: 79 PHN---IDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIES 135
N ++ R V R R E + E A K+ + + D Y G I +
Sbjct: 163 -MNGMLLNDRKVFVGRFKSRKE-REAELGARAKEFYPYDVPD--------YAGSSGRIVT 212
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 93.5 bits (233), Expect = 2e-25
Identities = 27/87 (31%), Positives = 49/87 (56%), Gaps = 2/87 (2%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E + K+FIGGL+ T ++ L+A F + G I +V+++KD T +SRGF FIT+
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61
Query: 72 DDAMSN-RPHNIDGRVVETKRAVPRDE 97
+A + ++ G+ ++ ++A
Sbjct: 62 KNAAKDMNGKSLHGKAIKVEQAKKPSF 88
Score = 59.3 bits (144), Expect = 4e-12
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 2/56 (3%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
K+F+GGL + E L+ F + G I V ++ ++ T RGFAFI F +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKN 63
>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 = 92.8 bits (231), Expect = 3e-25
Identities = 20/84 (23%), Positives = 37/84 (44%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
E R VF L R L+ FF G++ DV ++ D ++RS+G ++ + E + V
Sbjct: 21 EERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSV 80
Query: 72 DDAMSNRPHNIDGRVVETKRAVPR 95
A+ + G + + +
Sbjct: 81 PLAIGLTGQRLLGVPIIVQASQAE 104
Score = 73.1 bits (180), Expect = 2e-17
Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 3/84 (3%)
Query: 83 DGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTN 141
G ++ P D + E +A + +F L DL ++FS G + V ++++
Sbjct: 3 SGSSGKSPVREPVDNLSPEERDA--RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISD 60
Query: 142 KETGAKRGFAFIEFNDYDVVDKIV 165
+ + +G A++EF + V +
Sbjct: 61 RNSRRSKGIAYVEFCEIQSVPLAI 84
>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 = 84.7 bits (210), Expect = 4e-22
Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 4/96 (4%)
Query: 8 SKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
S + K+FIG + ++ L+ FE++G+I ++ V+KD T +G F+TY E
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
Query: 68 AKMVDDAMSN----RPHNIDGRVVETKRAVPRDEIG 99
+ A S + R ++ K A G
Sbjct: 65 RESALKAQSALHEQKTLPGMNRPIQVKPADSESRGG 100
Score = 70.0 bits (172), Expect = 2e-16
Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 99 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+ K+F+G + ++ +E DL+ F +FG I + ++ ++ TG +G AF+ + +
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
Query: 158 YDVVDK 163
+ K
Sbjct: 65 RESALK 70
>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 = 84.6 bits (210), Expect = 4e-22
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 77 N-RPHNIDGRVVETKRAVPRDE 97
N + GR + A P
Sbjct: 73 NMNESELFGRTIRVNLAKPMRI 94
Score = 69.2 bits (170), Expect = 4e-16
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 99 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G T + ++VGGL ++ ++ L F FG I + + + ET RGFAF+EF
Sbjct: 4 GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63
>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 = 85.5 bits (212), Expect = 4e-22
Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 3/87 (3%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
P+ + + GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ +
Sbjct: 41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 100
Query: 71 VDDAMS--NRPHNIDGRVVETKRAVPR 95
+A N +DGR + ++ +
Sbjct: 101 AKEAKERANG-MELDGRRIRVDFSITK 126
Score = 67.1 bits (164), Expect = 5e-15
Identities = 25/95 (26%), Positives = 39/95 (41%), Gaps = 11/95 (11%)
Query: 76 SNRPHNIDGRVVETKRAVPRD----------EIGKPEANATVKKMFVGGL-KDQEEDDLR 124
+ H+ G V +G + V GL E DLR
Sbjct: 5 HHHHHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLR 64
Query: 125 EYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
E FS++G I V++V ++++ RGFAF+ F + D
Sbjct: 65 EVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 99
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 85.6 bits (212), Expect = 5e-22
Identities = 20/66 (30%), Positives = 35/66 (53%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+
Sbjct: 59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 118
Query: 72 DDAMSN 77
A+ N
Sbjct: 119 AAAIDN 124
Score = 69.4 bits (170), Expect = 8e-16
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 5/88 (5%)
Query: 75 MSNRPHNIDGRVVETKRAVPRDEIGKPEANATV----KKMFVGGLKDQ-EEDDLREYFSQ 129
+SN P ++ V G + + ++VGGL ++ ++ L F
Sbjct: 27 LSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIP 86
Query: 130 FGTIESVNMVTNKETGAKRGFAFIEFND 157
FG I + + + ET RGFAF+EF
Sbjct: 87 FGDITDIQIPLDYETEKHRGFAFVEFEL 114
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 83.5 bits (207), Expect = 9e-22
Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 5/84 (5%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
LR VF+ G L +F +G + VV+ KD F + + +
Sbjct: 5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDVGARE 59
Query: 73 DAMSNRPHNIDGRVVETKRAVPRD 96
+S H++ G + + ++
Sbjct: 60 AVLSQSQHSLGGHRLRVRPREQKE 83
Score = 73.5 bits (181), Expect = 6e-18
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 6/77 (7%)
Query: 103 ANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVV 161
++ ++ +FV G + L EYF FG + SV V +K+ G FA +E D
Sbjct: 4 GSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKG---VFAIVEMGDVGAR 58
Query: 162 DKIVLSKITLLLDRRVE 178
+ ++ L R+
Sbjct: 59 EAVLSQSQHSLGGHRLR 75
>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 = 83.4 bits (207), Expect = 1e-21
Identities = 24/87 (27%), Positives = 46/87 (52%), Gaps = 1/87 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + + + + L YRT+ +SL+ FE++G + DV + ++P TK RGF F+ + + +
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68
Query: 72 DDAMSNRP-HNIDGRVVETKRAVPRDE 97
DA + +DGR + + A
Sbjct: 69 QDAEAAMDGAELDGRELRVQVARYGRR 95
Score = 66.9 bits (164), Expect = 3e-15
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+ V L D LR F ++G + V + T A RGFAF+ F+D
Sbjct: 14 ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 82.8 bits (205), Expect = 2e-21
Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 7/83 (8%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSRGFGFITYS---EAKMV 71
+ + + T +S+ + + ++ ++KD T+++RGF F+ S +A +
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
Query: 72 DDAMSNR--PHNIDGRVVETKRA 92
+ + P IDG+ + A
Sbjct: 70 LQILQSLHPPLKIDGKTIGVDFA 92
Score = 59.6 bits (145), Expect = 1e-12
Identities = 9/55 (16%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGT--IESVNMVTNKETGAKRGFAFIEFNDYD 159
+ + + D + S + + + ++ ++ +K+T RGFAF++ +
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64
>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 = 82.2 bits (204), Expect = 3e-21
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 3/78 (3%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
P+ + + GL TT+ L+ F ++G I DV ++ D ++RSRGF F+ +
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 72 DDAMS--NRPHNIDGRVV 87
+A N +DGR +
Sbjct: 71 KEAKERANG-MELDGRRI 87
Score = 66.1 bits (162), Expect = 5e-15
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 99 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G + V GL E DLRE FS++G I V++V ++++ RGFAF+ F +
Sbjct: 7 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 158 YD 159
D
Sbjct: 67 VD 68
>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 = 81.9 bits (203), Expect = 3e-21
Identities = 17/66 (25%), Positives = 32/66 (48%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
S V++ L + T+ L F ++G++V V +MKD T++S+G FI + +
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 72 DDAMSN 77
+
Sbjct: 72 QNCTRA 77
Score = 67.6 bits (166), Expect = 1e-15
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
++V L +DL FS++G + V ++ +K+T +G AFI F D D
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain,
structural genomics, NPPSFA; NMR {Mus musculus} PDB:
2rne_A 2dh7_A
Length = 115
Score = 82.0 bits (203), Expect = 5e-21
Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 1/94 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
VF+G L T E ++A F +G I D V+KD T +S+G+GF+++ ++A+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 78 -RPHNIDGRVVETKRAVPRDEIGKPEANATVKKM 110
+ GR + T A + K + K+
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQS 110
Score = 58.5 bits (142), Expect = 7e-12
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 99 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G+ + + +FVG L + +D++ F+ FG I +V + TG +G+ F+ F +
Sbjct: 7 GQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66
Query: 158 YD 159
Sbjct: 67 KW 68
>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 = 81.0 bits (201), Expect = 5e-21
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++GGL D+ L A F +G+I D+ + D T++ RGF F+ + A+ A+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 77 N 77
N
Sbjct: 68 N 68
Score = 66.8 bits (164), Expect = 2e-15
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 108 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+ ++VGGL ++ ++ L F FG I + + + ET RGFAF+EF
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 58
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 83.0 bits (205), Expect = 7e-21
Identities = 16/98 (16%), Positives = 38/98 (38%), Gaps = 3/98 (3%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSR 58
P + V++G + TTD+ L G ++V++ ++ +S+
Sbjct: 40 KTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSK 99
Query: 59 GFGFITYSEAKMVDDAMSNRP-HNIDGRVVETKRAVPR 95
G+ + + V + P ++G V+ + A +
Sbjct: 100 GYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ 137
Score = 59.5 bits (144), Expect = 6e-12
Identities = 13/95 (13%), Positives = 26/95 (27%), Gaps = 3/95 (3%)
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQF 130
+M P + P ++VG + L +
Sbjct: 20 FQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSI 79
Query: 131 GTIE--SVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
G + + N+ G +G+A + + V K
Sbjct: 80 GVYDVVELKFAENRANGQSKGYAEVVVASENSVHK 114
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 82.1 bits (203), Expect = 9e-21
Identities = 28/92 (30%), Positives = 49/92 (53%), Gaps = 6/92 (6%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ E + + + L YRT+ ++L+ FE++G + DV + +D TK SRGF F+ + + +
Sbjct: 43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102
Query: 72 DDAMS--NRPHNIDGR---VVETKRAVPRDEI 98
+DAM + +DGR V + P D
Sbjct: 103 EDAMDAMDG-AVLDGRELRVQMARYGRPPDSH 133
Score = 68.2 bits (167), Expect = 2e-15
Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 1/74 (1%)
Query: 85 RVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKE 143
+ P + + V L + D LR F ++G + V + ++
Sbjct: 25 TGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY 84
Query: 144 TGAKRGFAFIEFND 157
T RGFAF+ F+D
Sbjct: 85 TKESRGFAFVRFHD 98
>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 = 80.6 bits (200), Expect = 9e-21
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+G L+ DE+L+ F+ + + VM D T SRG+GF++++ +AM +
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 78 -RPHNIDGRVVETKRAVPRD 96
+ +++GR + A +
Sbjct: 63 MQGQDLNGRPLRINWAAKLE 82
Score = 56.7 bits (138), Expect = 1e-11
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+FVG L + +++ LR F F + S +++ + +TG+ RG+ F+ F
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 52
>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 = 79.9 bits (198), Expect = 2e-20
Identities = 25/81 (30%), Positives = 47/81 (58%), Gaps = 1/81 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+++G L + T++ L+ FE +G+I ++V+MKD T RS+G+GFIT+S+++ A+
Sbjct: 7 GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
Query: 78 -RPHNIDGRVVETKRAVPRDE 97
+ GR + R +
Sbjct: 67 LNGFELAGRPMRVGHVTERLD 87
Score = 68.3 bits (168), Expect = 6e-16
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 103 ANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
++ ++VG L + ED LR F FG I+++ ++ + +TG +G+ FI F+D +
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSE 58
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 80.0 bits (198), Expect = 3e-20
Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 1/88 (1%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+E V++GGLD + ++ L F Q G +V+ + KD +T + +G+GF+ + +
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 69
Query: 71 VDDAMSN-RPHNIDGRVVETKRAVPRDE 97
D A+ + G+ + +A ++
Sbjct: 70 ADYAIKIMDMIKLYGKPIRVNKASAHNK 97
Score = 65.7 bits (161), Expect = 9e-15
Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 108 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++VGGL ++ E L E F Q G + + +M ++ TG +G+ F+EF
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66
>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 = 79.6 bits (197), Expect = 3e-20
Identities = 21/87 (24%), Positives = 42/87 (48%), Gaps = 1/87 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V++G + Y T+E + G ++++ +M DP T RS+G+ FI + + + A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 77 N-RPHNIDGRVVETKRAVPRDEIGKPE 102
N + + R ++ + D G
Sbjct: 63 NLNGYQLGSRFLKCGYSSNSDISGVSL 89
Score = 69.2 bits (170), Expect = 3e-16
Identities = 16/53 (30%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+ +++G + DQ E+ + + S G + ++ M+ + +TG +G+AFIEF D +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLE 55
>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 = 78.9 bits (195), Expect = 7e-20
Identities = 22/87 (25%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ +++ + + +R D L+ F Q+G+I+DV ++ + + S+GFGF+T+ +
Sbjct: 11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADA 68
Query: 72 DDAMSNRP-HNIDGRVVETKRAVPRDE 97
D A ++GR +E A R
Sbjct: 69 DRAREKLHGTVVEGRKIEVNNATARVM 95
Score = 61.1 bits (149), Expect = 4e-13
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 99 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G E+ +T K++ V + + DLR+ F QFG I V ++ N+ +GF F+ F +
Sbjct: 7 GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFEN 64
Query: 158 YDVVDK 163
D+
Sbjct: 65 SADADR 70
>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 = 78.9 bits (195), Expect = 7e-20
Identities = 23/86 (26%), Positives = 45/86 (52%), Gaps = 1/86 (1%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
++++G L + T++ L+ FE +G I + +M D T RS+G+GFIT+S+++
Sbjct: 23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAK 82
Query: 73 DAMSN-RPHNIDGRVVETKRAVPRDE 97
A+ + GR ++ R +
Sbjct: 83 KALEQLNGFELAGRPMKVGHVTERTD 108
Score = 64.6 bits (158), Expect = 3e-14
Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 101 PEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+ +A +++VG L + ED LR F FG IES+ ++ + ETG +G+ FI F+D
Sbjct: 20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSD 77
>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 = 80.3 bits (198), Expect = 8e-20
Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 1/85 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ E + + + L YRT+ ++L+ FE++G + DV + +D TK SRGF F+ + + +
Sbjct: 66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125
Query: 72 DDAMSN-RPHNIDGRVVETKRAVPR 95
+DAM +DGR + + A
Sbjct: 126 EDAMDAMDGAVLDGRELRVQMARYG 150
Score = 68.7 bits (168), Expect = 3e-15
Identities = 22/114 (19%), Positives = 37/114 (32%), Gaps = 14/114 (12%)
Query: 58 RGFGFITYSEAKMVDDA-------MSNRPHNIDGRVVETKRAVP------RDEIGKPEAN 104
G + + VD A + +DG
Sbjct: 8 NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67
Query: 105 ATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+ + V L + D LR F ++G + V + ++ T RGFAF+ F+D
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHD 121
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 78.5 bits (194), Expect = 1e-19
Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 3/96 (3%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
+ PR +++ + + +R D L+ F Q+G+I+DV ++ + + S+GF
Sbjct: 14 LVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGF 71
Query: 61 GFITYSEAKMVDDAMSN-RPHNIDGRVVETKRAVPR 95
GF+T+ + D A ++GR +E A R
Sbjct: 72 GFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR 107
Score = 63.9 bits (156), Expect = 5e-14
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 93 VPRDEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFA 151
VPR E + K++ V + + + DLR+ F QFG I V ++ N+ +GF
Sbjct: 15 VPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFG 72
Query: 152 FIEFNDYDVVDK 163
F+ F + D+
Sbjct: 73 FVTFENSADADR 84
>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 = 81.7 bits (201), Expect = 1e-19
Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 3/82 (3%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++IG L + TTDE L G +I+++ ++ +S+GF + M
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129
Query: 76 SNRP-HNIDGRVVETKRAVPRD 96
P + G+ +
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQF 151
Score = 59.3 bits (143), Expect = 2e-11
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIE--SVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+++G L ++DL E G + + N+ G +GFA + K
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 127
>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 = 77.6 bits (192), Expect = 1e-19
Identities = 19/79 (24%), Positives = 38/79 (48%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R +++G +DY T E L+A F G + V ++ D + +GF +I +S+ + V +++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 77 NRPHNIDGRVVETKRAVPR 95
GR ++
Sbjct: 67 LDESLFRGRQIKVIPKRTN 85
Score = 70.2 bits (173), Expect = 1e-16
Identities = 16/59 (27%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+ ++VG + ++L +F G++ V ++ +K +G +GFA+IEF+D + V +
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
>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 = 77.2 bits (191), Expect = 2e-19
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
VF+G L T ++ A F +G I D V+KD T +S+G+GF+++ ++A+
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 78 -RPHNIDGRVVETKRAVPR 95
+ GR + T A +
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86
Score = 54.9 bits (133), Expect = 9e-11
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+FVG L + + F+ FG I +V + TG +G+ F+ F +
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 57
>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 = 77.2 bits (191), Expect = 2e-19
Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 7/86 (8%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAK 69
++I GL TTD+ L + +G+IV + D T + +G+GF+ + A+
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 70 MVDDAMSNRPHNIDGRVVETKRAVPR 95
A+ + ++ K++ P
Sbjct: 62 KAVTALKAS--GVQAQMA--KQSGPS 83
Score = 62.9 bits (154), Expect = 5e-14
Identities = 12/53 (22%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 108 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+++ GL+ + DL + +G I S + +K T +G+ F++F+
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPS 58
>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 = 77.6 bits (192), Expect = 2e-19
Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 1/81 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++F+ L Y +++E L+ F +G + ++ D +TK+ +GF F+T+ + A +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 78 -RPHNIDGRVVETKRAVPRDE 97
GR++ + + E
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKE 90
Score = 66.5 bits (163), Expect = 4e-15
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++FV L E+DL + FS +G + ++ + T +GFAF+ F
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMF 59
>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 = 77.3 bits (191), Expect = 2e-19
Identities = 18/92 (19%), Positives = 41/92 (44%), Gaps = 1/92 (1%)
Query: 6 DDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY 65
D + +E + +FIG L+ + L+ + D+ V+ T +R FG++ +
Sbjct: 7 DPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDF 65
Query: 66 SEAKMVDDAMSNRPHNIDGRVVETKRAVPRDE 97
A+ ++ A+ + G ++ ++ RD
Sbjct: 66 ESAEDLEKALELTGLKVFGNEIKLEKPKGRDG 97
Score = 56.9 bits (138), Expect = 2e-11
Identities = 13/65 (20%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 100 KPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
+ + T +F+G L ++ +L+ S+ + V + TG R F +++F
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESA 68
Query: 159 DVVDK 163
+ ++K
Sbjct: 69 EDLEK 73
>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 = 78.2 bits (193), Expect = 3e-19
Identities = 24/101 (23%), Positives = 46/101 (45%), Gaps = 5/101 (4%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
EP+ LR + + + + L+ FE++G I V ++ D T++SRG+GF+ +
Sbjct: 38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97
Query: 72 DDAMS--NRPHNIDGRVVETKRAVPRDEIGKPEANATVKKM 110
A++ N NI + ++ A + +P V
Sbjct: 98 QQAIAGLNG-FNILNKRLKVALAASGHQ--RPGIAGAVGDG 135
Score = 63.6 bits (155), Expect = 1e-13
Identities = 19/86 (22%), Positives = 41/86 (47%), Gaps = 6/86 (6%)
Query: 78 RPHNIDGRVVETKRAVPRDEIGKPEANA-----TVKKMFVGGLK-DQEEDDLREYFSQFG 131
++ G+ + ++ + + P ++ + V + +E LR+ F ++G
Sbjct: 8 SQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYG 67
Query: 132 TIESVNMVTNKETGAKRGFAFIEFND 157
IESV +V ++ET RG+ F++F
Sbjct: 68 PIESVKIVCDRETRQSRGYGFVKFQS 93
>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 = 76.5 bits (189), Expect = 5e-19
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 8/86 (9%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITK---RSRGFGFITYS---EAKMV 71
+FI L++ TT+E+L+ F + G I + K S GFGF+ Y +A+
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDE 97
+ H +DG +E + + +
Sbjct: 67 LKQLQG--HTVDGHKLEVRISERATK 90
Score = 56.5 bits (137), Expect = 3e-11
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 103 ANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAK---RGFAFIEFND 157
++ +F+ L E+ L+ FS+ G I+S + K GF F+E+
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKK 59
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 76.7 bits (189), Expect = 6e-19
Identities = 14/97 (14%), Positives = 37/97 (38%), Gaps = 5/97 (5%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAK 69
L++V L+ + L+ ++GE+ +V ++ P T++ G + ++ AK
Sbjct: 3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK 62
Query: 70 MVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANAT 106
+ + G ++ + + + K
Sbjct: 63 ETVKNLHLTS--VMGNIIHAQLDIKGQQRMKYYELIV 97
Score = 62.4 bits (152), Expect = 2e-13
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 108 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K++ L D E L++ ++G +E V ++ + T G A + F
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTR 59
>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 = 76.5 bits (189), Expect = 6e-19
Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 3/88 (3%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + + L T + LQ F +G I + + KD T +S+GF FI++ +
Sbjct: 11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 70
Query: 72 DDAMS--NRPHNIDGRVVETKRAVPRDE 97
A++ + D ++ + A P
Sbjct: 71 ARAIAGVSG-FGYDHLILNVEWAKPSTN 97
Score = 66.1 bits (162), Expect = 5e-15
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+ V L +D E DL+E F FG+I + + +K TG +GFAFI F+ +
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 68
>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 = 76.5 bits (189), Expect = 6e-19
Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 1/86 (1%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
SLR VF+G + Y T+E L+ F + G +V ++ D T + +G+GF Y + +
Sbjct: 5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETAL 64
Query: 73 DAMSN-RPHNIDGRVVETKRAVPRDE 97
AM N GR + A
Sbjct: 65 SAMRNLNGREFSGRALRVDNAASEKN 90
Score = 69.2 bits (170), Expect = 3e-16
Identities = 18/66 (27%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 101 PEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
P + +++ +FVG + + E+ L++ FS+ G + S +V ++ETG +G+ F E+ D +
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Query: 160 VVDKIV 165
+
Sbjct: 62 TALSAM 67
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 76.2 bits (187), Expect = 1e-18
Identities = 18/94 (19%), Positives = 34/94 (36%), Gaps = 9/94 (9%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKD--PITKRSRGFGFITYSEA 68
+ RKVF+GGL ++ + A F ++G +V K +G+ F+ + E
Sbjct: 3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE 62
Query: 69 KMVDDAMSNRPH-------NIDGRVVETKRAVPR 95
V + + ++ K R
Sbjct: 63 SSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIR 96
Score = 59.2 bits (143), Expect = 3e-12
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMV--TNKETGAKRGFAFIEFNDYDVVDKI 164
+K+FVGGL D +ED++ F +FG + +K +G+AF+ F + V +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 165 V 165
+
Sbjct: 69 I 69
>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 = 76.3 bits (188), Expect = 1e-18
Identities = 21/94 (22%), Positives = 44/94 (46%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
P+ ++ + R V++G +DY +T + L+A F G I + ++ D + +G+
Sbjct: 22 PPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYA 81
Query: 62 FITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPR 95
+I ++E VD A++ GR ++
Sbjct: 82 YIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTN 115
Score = 70.9 bits (174), Expect = 1e-16
Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 88 ETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGA 146
P+ + + + ++VG + DL +FS G+I + ++ +K +G
Sbjct: 17 AYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGH 76
Query: 147 KRGFAFIEFNDYDVVDKIV 165
+G+A+IEF + + VD V
Sbjct: 77 PKGYAYIEFAERNSVDAAV 95
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 75.4 bits (186), Expect = 2e-18
Identities = 15/99 (15%), Positives = 35/99 (35%), Gaps = 2/99 (2%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
+ + K+FI GL + T E L+ + G + D+ ++ + + +G
Sbjct: 3 SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLA 61
Query: 62 FITYSEAKMVDDAMSNRP-HNIDGRVVETKRAVPRDEIG 99
++ Y A+ I +++ + G
Sbjct: 62 YVEYENESQASQAVMKMDGMTIKENIIKVAISNSGPSSG 100
Score = 62.7 bits (153), Expect = 9e-14
Identities = 15/65 (23%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 94 PRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAF 152
+ + + K+F+ GL +++L E GT++ + +VTN+ G +G A+
Sbjct: 4 GSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAY 62
Query: 153 IEFND 157
+E+ +
Sbjct: 63 VEYEN 67
>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 = 74.9 bits (185), Expect = 2e-18
Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 3/83 (3%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++IG L + TTDE L G +I+++ ++ +S+GF + M
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 76 SNRP-HNIDGRVVETKRAVPRDE 97
P + G+ + +
Sbjct: 63 DLLPKRELHGQNPVVTPSNKLEH 85
Score = 56.8 bits (138), Expect = 1e-11
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIE--SVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+++G L ++DL E G + + N+ G +GFA + K
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60
>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 = 74.2 bits (183), Expect = 3e-18
Identities = 15/87 (17%), Positives = 33/87 (37%), Gaps = 8/87 (9%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
+ K++IG L T + L+ F + V+ G+ F+ Y +
Sbjct: 5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNWAI 58
Query: 73 DAMS--NRPHNIDGRVVETKRAVPRDE 97
A+ + + G+++E +V +
Sbjct: 59 RAIETLSGKVELHGKIMEVDYSVSKKL 85
Score = 52.6 bits (127), Expect = 6e-10
Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 7/64 (10%)
Query: 101 PEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
++ + K+++G L DDLR+ F + + K G+AF+++ D +
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAG------QVLLKSGYAFVDYPDQN 55
Query: 160 VVDK 163
+
Sbjct: 56 WAIR 59
>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 = 73.8 bits (182), Expect = 4e-18
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ E+ R VF+G L+ R +E L F Q G + V + KD + + FGF+ + + V
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESV 70
Query: 72 DDAMSN 77
A++
Sbjct: 71 SYAIAL 76
Score = 58.8 bits (143), Expect = 3e-12
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 108 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+ +FVG L+ + E+ L E F Q G + V + ++E G + F F+ F + V
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSY 72
>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 = 73.4 bits (181), Expect = 7e-18
Identities = 23/83 (27%), Positives = 45/83 (54%), Gaps = 2/83 (2%)
Query: 16 LRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+R +++G L Y T E ++ F Q+G++ +V ++ D TK+ +GFGF+ E + +A+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAI 59
Query: 76 SN-RPHNIDGRVVETKRAVPRDE 97
+ + GR + A P+
Sbjct: 60 AKLDNTDFMGRTIRVTEANPKKS 82
Score = 66.4 bits (163), Expect = 3e-15
Identities = 16/52 (30%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 107 VKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++ ++VG L + ++E FSQFG + +V ++ ++ET +GF F+E +
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE 52
>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 = 73.4 bits (181), Expect = 8e-18
Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 6/92 (6%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDV-VVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+FIG LD ++ L F +G I+ +M+DP T S+G+ FI ++ D A+
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 77 NRPHN---IDGRVVETKRAVPRDEIGKPEANA 105
N + R + A +D G ++
Sbjct: 67 AM--NGQYLCNRPITVSYAFKKDSKGSGPSSG 96
Score = 51.0 bits (123), Expect = 2e-09
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 103 ANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESV-NMVTNKETGAKRGFAFIEFNDYD 159
++ +F+G L + +E L + FS FG I ++ + +TG +G+AFI F +D
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFD 59
>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 = 73.4 bits (181), Expect = 9e-18
Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 4/88 (4%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+ + +F+ GL TT+E+L+ F V ++ D T S+GFGF+ ++ +
Sbjct: 10 ARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEED 66
Query: 71 VDDAMSN-RPHNIDGRVVETKRAVPRDE 97
A IDG V A P+ E
Sbjct: 67 AKAAKEAMEDGEIDGNKVTLDWAKPKGE 94
Score = 54.6 bits (132), Expect = 2e-10
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 95 RDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFI 153
G + K +FV GL D E+ L+E F +VT++ETG+ +GF F+
Sbjct: 3 SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFV 59
Query: 154 EFNDYD 159
+FN +
Sbjct: 60 DFNSEE 65
>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 = 72.6 bits (179), Expect = 1e-17
Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 2/82 (2%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPI-TKRSRGFGFITYSEAKMVDDAMS 76
KV IG L T + + F +G+I + + + + S+G+ ++ + + A+
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 77 NRP-HNIDGRVVETKRAVPRDE 97
+ IDG+ + +
Sbjct: 66 HMDGGQIDGQEITATAVLAPWP 87
Score = 61.8 bits (151), Expect = 2e-13
Identities = 14/51 (27%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNK-ETGAKRGFAFIEFND 157
K+ +G L ++ +D + E FS +G I+ ++M + +G+A++EF +
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFEN 56
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 72.7 bits (179), Expect = 2e-17
Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 1/79 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84
Query: 78 -RPHNIDGRVVETKRAVPR 95
++ G+ + R
Sbjct: 85 LNGQDLMGQPISVDWCFVR 103
Score = 67.7 bits (166), Expect = 2e-15
Identities = 14/70 (20%), Positives = 37/70 (52%), Gaps = 1/70 (1%)
Query: 91 RAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRG 149
+ P+ + +FV G+ + E+D+ + F+++G I+++++ ++ TG +G
Sbjct: 7 SVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 66
Query: 150 FAFIEFNDYD 159
+ +E+ Y
Sbjct: 67 YTLVEYETYK 76
>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 = 72.7 bits (179), Expect = 2e-17
Identities = 19/101 (18%), Positives = 44/101 (43%), Gaps = 5/101 (4%)
Query: 7 DSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDP-ITKRSRGFGFITY 65
+ + ++ K+ + + ++ ++ F +GE+ V + K T RGFGF+ +
Sbjct: 6 SGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDF 65
Query: 66 S---EAKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEA 103
+AK +A+ + H + GR + + A + +
Sbjct: 66 ITKQDAKKAFNALCHSTH-LYGRRLVLEWADSEVTVQSGPS 105
Score = 63.9 bits (156), Expect = 5e-14
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 99 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKE-TGAKRGFAFIEFN 156
G+ T K+ V + + ++RE FS FG +++V + TGA RGF F++F
Sbjct: 7 GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66
Query: 157 DYD 159
Sbjct: 67 TKQ 69
>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 = 74.1 bits (182), Expect = 2e-17
Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+++G L + TT+E + F + G+I +++ D + K + GF F+ Y ++AM
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 77 NRP-HNIDGRVVETKRAVPRDE 97
+D R++ T E
Sbjct: 100 YINGTRLDDRIIRTDWDAGFKE 121
Score = 61.4 bits (149), Expect = 1e-12
Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 1/70 (1%)
Query: 91 RAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRG 149
+ D + + ++VG L E+ + E FS+ G I+ + M +K G
Sbjct: 23 QHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 150 FAFIEFNDYD 159
F F+E+
Sbjct: 83 FCFVEYYSRA 92
>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 = 72.8 bits (179), Expect = 3e-17
Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 1/79 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+ G+ T+E + F ++GEI ++ + D T +G+ + Y K AM
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83
Query: 78 -RPHNIDGRVVETKRAVPR 95
++ G+ + R
Sbjct: 84 LNGQDLMGQPISVDWCFVR 102
Score = 65.1 bits (159), Expect = 3e-14
Identities = 13/52 (25%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 109 KMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+FV G+ + E+D+ + F+++G I+++++ ++ TG +G+ +E+ Y
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 75
>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 = 72.0 bits (177), Expect = 4e-17
Identities = 19/83 (22%), Positives = 36/83 (43%), Gaps = 5/83 (6%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDA 74
+FI L D+ L F +G +V V D T S+ FGF++Y A+ +
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 75 MSNRPHNIDGRVVETKRAVPRDE 97
M+ I + ++ + +++
Sbjct: 87 MNGFQ--IGMKRLKVQLKRSKND 107
Score = 58.9 bits (143), Expect = 4e-12
Identities = 12/52 (23%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+F+ L + + DL + F FG + S + +K+T + F F+ +++
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78
>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 = 71.9 bits (177), Expect = 4e-17
Identities = 25/116 (21%), Positives = 45/116 (38%), Gaps = 11/116 (9%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
P +FI LD +++L F +G I+ V+ D S+G+GF+ + + +
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAE 59
Query: 73 DAMSNRPHN---IDGRVVETKRAVPRDEIGKPEANATVKKM---FVGGLKDQEEDD 122
A+ N ++ R V R R E + E A K+ ++
Sbjct: 60 RAIEK--MNGMLLNDRKVFVGRFKSRKE-REAELGARAKEFTNVYIKNFGPGSTRA 112
Score = 49.6 bits (119), Expect = 1e-08
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 107 VKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+F+ L K + L + FS FG I S +V + +G+ F+ F + ++
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAER 60
>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 = 70.7 bits (174), Expect = 1e-16
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDA 74
+++ LD DE L+ F +G I VM + RS+GFGF+ +S EA
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
Query: 75 MSNRPHNIDGRVVETKRAVPRDE 97
M+ R + + + A ++E
Sbjct: 75 MNGRI--VATKPLYVALAQRKEE 95
Score = 51.8 bits (125), Expect = 2e-09
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 109 KMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
++V L D +++ LR+ FS FGTI S ++ E G +GF F+ F+ + K
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMM--EGGRSKGFGFVCFSSPEEATK 70
>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 = 70.6 bits (173), Expect = 1e-16
Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 6/102 (5%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIV-DVVVMKDP-ITKRSRGFGFITYS---EAKMV 71
++FIGG+ E + + E V DV+V ++RGF F+ Y A M
Sbjct: 9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVG 113
+ + G + A P ++ + TV G
Sbjct: 69 RRKLMPGRIQLWGHQIAVDWAEPEIDV-DEDVMETVSGPSSG 109
Score = 49.0 bits (117), Expect = 2e-08
Identities = 12/54 (22%), Positives = 30/54 (55%), Gaps = 3/54 (5%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGT-IESVNMVTN-KETGAKRGFAFIEFNDYD 159
++F+GG+ K ++ +++ E ++ + V + + + RGFAF+E+ +
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63
>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 = 70.4 bits (173), Expect = 1e-16
Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 5/88 (5%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
RK+F+G L+ + ++E + F+ +G I + V++ P S+G F+ +S A+
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIH 74
Query: 77 --NRPHNIDG--RVVETKRAVPRDEIGK 100
+ + G + K A E G
Sbjct: 75 ALHGSQTMPGASSSLVVKFADTDKESGP 102
Score = 59.6 bits (145), Expect = 2e-12
Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
K+FVG L K Q E+D+ F FG I+ ++ G+ +G AF++F+
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSS 65
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 70.5 bits (173), Expect = 2e-16
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+FI L TD L + F +G ++ V D T S+ FGF+++ A+
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK- 100
Query: 78 RPHNIDGRVVETKR 91
++G V TKR
Sbjct: 101 ---AMNGFQVGTKR 111
Score = 58.9 bits (143), Expect = 5e-12
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 109 KMFVGGLKDQE--EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+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 = 70.0 bits (172), Expect = 2e-16
Identities = 19/88 (21%), Positives = 40/88 (45%), Gaps = 5/88 (5%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
T + + + L Y T+E+LQ FE+ + + +S+G+ FI ++ +
Sbjct: 10 TWSGESKTLVLSNLSYSATEETLQEVFEKATF----IKVPQNQNGKSKGYAFIEFASFED 65
Query: 71 VDDAMSNRP-HNIDGRVVETKRAVPRDE 97
+A+++ I+GR + + PR
Sbjct: 66 AKEALNSCNKREIEGRAIRLELQGPRGS 93
Score = 55.7 bits (135), Expect = 4e-11
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 99 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G + K + + L E+ L+E F + I+ V + G +G+AFIEF
Sbjct: 7 GNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFAS 62
Query: 158 YD 159
++
Sbjct: 63 FE 64
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 70.0 bits (171), Expect = 2e-16
Identities = 20/112 (17%), Positives = 37/112 (33%), Gaps = 23/112 (20%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQW-----GEIVDVVVMKDPITKRSRGFGFITY 65
+ V + GL DE L +FE G ++ +R G +T+
Sbjct: 3 SGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLTF 54
Query: 66 SEAKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKD 117
E + ++ H + G + + A PR ++ + GL
Sbjct: 55 REPADAERVLAQADHELHGAQLSLRPAPPRAP----------ARLLLQGLPP 96
Score = 40.3 bits (94), Expect = 3e-05
Identities = 15/84 (17%), Positives = 27/84 (32%), Gaps = 16/84 (19%)
Query: 99 GKPEANATVKKMFVGGL-KDQEEDDLREYF-----SQFGTIESVNMVTNKETGAKRGFAF 152
G ++ V + V GL ++ L YF S G + S
Sbjct: 1 GSSGSSGGVA-VEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQR--------LGCGGV 51
Query: 153 IEFNDYDVVDKIVLSKITLLLDRR 176
+ F + ++ VL++ L
Sbjct: 52 LTFREPADAER-VLAQADHELHGA 74
>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 = 70.0 bits (172), Expect = 3e-16
Identities = 24/92 (26%), Positives = 42/92 (45%), Gaps = 9/92 (9%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDD 73
VF+ LDY+ + L+ F G +V +++D +SRG G +T+ EA
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAIS 74
Query: 74 AMSNRPHNIDGR---VVETKRAVPRDEIGKPE 102
+ + + R V +RA+P+ + PE
Sbjct: 75 MFNGQL--LFDRPMHVKMDERALPKGDFFPPE 104
Score = 50.8 bits (122), Expect = 5e-09
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 2/60 (3%)
Query: 99 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G +A +FV L + L+E FS G + +++ +K+ G RG + F
Sbjct: 7 GALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQ 65
>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 = 69.2 bits (170), Expect = 4e-16
Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 1/79 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+ + ++ +Q F +GEI ++ + D T S+G+ + Y K A
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 78 -RPHNIDGRVVETKRAVPR 95
I G+ ++ +
Sbjct: 88 LNGAEIMGQTIQVDWCFVK 106
Score = 67.3 bits (165), Expect = 2e-15
Identities = 13/53 (24%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+FV + + +ED+++E F +G I+++++ ++ TG +G+A +E+ +
Sbjct: 27 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 79
>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 = 68.9 bits (169), Expect = 9e-16
Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 6/88 (6%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAK 69
E+ K+ + LD+ +D +Q F ++G + V D + RS G + + +A
Sbjct: 32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADAL 90
Query: 70 MVDDAMSNRPHNIDGRVVETKRAVPRDE 97
P +DGR ++ + + +
Sbjct: 91 KAMKQYKGVP--LDGRPMDIQLVASQID 116
Score = 50.4 bits (121), Expect = 7e-09
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 96 DEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIE 154
G E T K+ V L + D++E F++FGT++ + + +G G A +
Sbjct: 24 SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVH 82
Query: 155 FND 157
F
Sbjct: 83 FER 85
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 70.5 bits (172), Expect = 1e-15
Identities = 20/175 (11%), Positives = 47/175 (26%), Gaps = 39/175 (22%)
Query: 19 VFIGGLDY-RTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM-- 75
+ + GLD + + + F +G + V MK G + ++ VD A+
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITH 61
Query: 76 ---------------SNRPHNIDGRVVETKRAVPRDEIGKPEANATVKK----------- 109
S +P + G+ + + N
Sbjct: 62 LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQH 121
Query: 110 ----MFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+ + E++ E + G ++ + +E++
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKS 176
Score = 45.5 bits (107), Expect = 2e-06
Identities = 6/78 (7%), Positives = 20/78 (25%), Gaps = 5/78 (6%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDAM 75
+ T+E+ ++ G V G + + +A +
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185
Query: 76 SNRPHNIDGRVVETKRAV 93
++ + + +
Sbjct: 186 NH--YQMKNPNGPYPYTL 201
>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 = 67.7 bits (166), Expect = 1e-15
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 7/81 (8%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
++F+G L T+E ++ FE++G+ +V + KD +GFGFI + + A
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 78 RP-HNIDGRVVETKRAVPRDE 97
+ G+ + + A
Sbjct: 71 LDNMPLRGKQLRVRFACHSAS 91
Score = 55.0 bits (133), Expect = 8e-11
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 7/62 (11%)
Query: 99 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G + ++FVG L D E+++R+ F ++G V + +K GF FI
Sbjct: 7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLET 60
Query: 158 YD 159
Sbjct: 61 RT 62
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 66.8 bits (164), Expect = 2e-15
Identities = 13/82 (15%), Positives = 35/82 (42%), Gaps = 5/82 (6%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
++F+ L + T + L+ F + G ++ + + +S+G G + + ++ +
Sbjct: 5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE 62
Query: 73 DAMS--NRPHNIDGRVVETKRA 92
A N + GR ++ +
Sbjct: 63 RACRMMNG-MKLSGREIDVRID 83
Score = 48.3 bits (116), Expect = 3e-08
Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 107 VKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++FV L D L++ F++ G + ++ E G +G ++F
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVKFES 57
>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 = 67.3 bits (165), Expect = 3e-15
Identities = 14/59 (23%), Positives = 28/59 (47%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+ +++ L R T+ L + F ++ E + +T R RG FIT+ ++ A+
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84
Score = 58.8 bits (143), Expect = 4e-12
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K +++ L E DL F++F + + TG RG AFI F + +
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKE 78
>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 = 66.9 bits (164), Expect = 3e-15
Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 8/87 (9%)
Query: 4 RYDDSKC--TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
+D E+ K+ + LD+ +D +Q F ++G + V D + RS G
Sbjct: 15 LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTA 73
Query: 62 FITYS---EAKMVDDAMSNRPHNIDGR 85
+ + +A + P +DGR
Sbjct: 74 DVHFERKADALKAMKQYNGVP--LDGR 98
Score = 53.8 bits (130), Expect = 3e-10
Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 5/82 (6%)
Query: 77 NRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIES 135
+RP + + E K+ V L + D++E F++FGT++
Sbjct: 2 SRPKQLPDKWQHDLFDSGFGGGAGVETGG---KLLVSNLDFGVSDADIQELFAEFGTLKK 58
Query: 136 VNMVTNKETGAKRGFAFIEFND 157
+ + +G G A + F
Sbjct: 59 AAVHYD-RSGRSLGTADVHFER 79
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 66.1 bits (162), Expect = 4e-15
Identities = 14/90 (15%), Positives = 37/90 (41%), Gaps = 9/90 (10%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
+ K+F+G + T + L++ FE+ G +++ V+K + F+ +
Sbjct: 6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAK 57
Query: 73 DAMSNRP-HNIDGRVVETKRAVPRDEIGKP 101
A++ + G+ + + + + P
Sbjct: 58 AAIAQLNGKEVKGKRINVELSTKGQKKSGP 87
Score = 49.9 bits (120), Expect = 7e-09
Identities = 10/53 (18%), Positives = 20/53 (37%), Gaps = 9/53 (16%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K+FVG + +LR F + G + ++ + +AF+
Sbjct: 10 WKIFVGNVSAACTSQELRSLFERRGRVIECDV--------VKDYAFVHMEKEA 54
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 66.6 bits (163), Expect = 4e-15
Identities = 20/90 (22%), Positives = 36/90 (40%), Gaps = 11/90 (12%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
D + P + +IG + + T+ L F+ +G I+D + +G
Sbjct: 12 NPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGC 65
Query: 61 GFITYS---EAKMVDDAMSNRPHNIDGRVV 87
FI Y +A + A++N P GR +
Sbjct: 66 CFIKYDTHEQAAVCIVALANFP--FQGRNL 93
Score = 55.4 bits (134), Expect = 7e-11
Identities = 14/58 (24%), Positives = 20/58 (34%), Gaps = 10/58 (17%)
Query: 101 PEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
P T ++G + E DL F FG I K G FI+++
Sbjct: 24 PPRVTTA---YIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDT 72
>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 = 66.2 bits (162), Expect = 5e-15
Identities = 19/89 (21%), Positives = 41/89 (46%), Gaps = 11/89 (12%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
+ R++D V+ GG+ TD+ ++ F +G+I+++ V + +G+
Sbjct: 11 QLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYS 64
Query: 62 FITYS---EAKMVDDAMSNRPHNIDGRVV 87
F+ +S A +++ I+G VV
Sbjct: 65 FVRFSTHESAAHAIVSVNGTT--IEGHVV 91
Score = 53.5 bits (129), Expect = 4e-10
Identities = 14/65 (21%), Positives = 29/65 (44%), Gaps = 7/65 (10%)
Query: 94 PRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAF 152
R E +++ ++ GG+ + +R+ FS FG I + + K G++F
Sbjct: 12 LRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSF 65
Query: 153 IEFND 157
+ F+
Sbjct: 66 VRFST 70
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 66.3 bits (162), Expect = 8e-15
Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 9/97 (9%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEI--------VDVVVMKDPITKRSRGFGFITYSEA 68
+F+ GL T ES+ +F+Q G I + + D T + +G +++ +
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 69 KMVDDAMSN-RPHNIDGRVVETKRAVPRDEIGKPEAN 104
A+ G ++ A R + + N
Sbjct: 68 PSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGN 104
Score = 57.0 bits (138), Expect = 2e-11
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 9/65 (13%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIES--------VNMVTNKETGAKRGFAFIEFNDY 158
+FV GL ++ + + +YF Q G I++ +N+ T++ETG +G A + F+D
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 159 DVVDK 163
Sbjct: 68 PSAKA 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 = 65.9 bits (161), Expect = 9e-15
Identities = 27/107 (25%), Positives = 45/107 (42%), Gaps = 9/107 (8%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
PE R ++I L Y+ T E + F ++G I + V P +RG ++ Y +
Sbjct: 5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAK 61
Query: 73 DAMSNRPH-NIDGR--VVE---TKRAVPRDEIGKPEANATVKKMFVG 113
+A+ + N+ R VV RA + + K E + K G
Sbjct: 62 NAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYG 108
Score = 50.1 bits (120), Expect = 8e-09
Identities = 13/60 (21%), Positives = 27/60 (45%), Gaps = 7/60 (11%)
Query: 101 PEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
PE N + ++ L +++ + F ++G I + + ET RG A++ + D
Sbjct: 5 PEVNRIL---YIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIF 58
>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 = 65.0 bits (159), Expect = 1e-14
Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 6/87 (6%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + R + L + T++ L+ FE E + +S+G +I +
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIEFKSEADA 66
Query: 72 DDAMSNRP-HNIDGRVVETKRAVPRDE 97
+ + + IDGR V +
Sbjct: 67 EKNLEEKQGAEIDGRSVSLYYTGEKGG 93
Score = 54.6 bits (132), Expect = 1e-10
Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 100 KPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
+ + + L + ED+L+E F I V+ + G +G A+IEF
Sbjct: 9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSE 63
Query: 159 DVVDK 163
+K
Sbjct: 64 ADAEK 68
>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 = 66.8 bits (163), Expect = 1e-14
Identities = 15/81 (18%), Positives = 32/81 (39%), Gaps = 1/81 (1%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+F+ + ++ +Q F +GEI ++ + D T S+G+ + Y K A
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133
Query: 78 -RPHNIDGRVVETKRAVPRDE 97
I G+ ++ +
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGP 154
Score = 63.7 bits (155), Expect = 2e-13
Identities = 14/71 (19%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 90 KRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKR 148
+ + P+ + +FV + ++ +ED+++E F +G I+++++ ++ TG +
Sbjct: 55 RNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 114
Query: 149 GFAFIEFNDYD 159
G+A +E+ +
Sbjct: 115 GYALVEYETHK 125
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 65.0 bits (159), Expect = 2e-14
Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 1/81 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
++G L + T + A F+ I V +++D T + +GF ++ + E + +A++
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKD-LSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74
Query: 77 NRPHNIDGRVVETKRAVPRDE 97
+ R + A R +
Sbjct: 75 YDGALLGDRSLRVDIAEGRKQ 95
Score = 57.3 bits (139), Expect = 1e-11
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+VG L + + D+ F I SV +V +K+T +GF ++EF++ D + + +
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
>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 = 64.7 bits (158), Expect = 2e-14
Identities = 10/62 (16%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVV-VMKDPITKRSRGFGFITYSEAKMVDDAM 75
+++G L+ + + F GE V V ++++ +T G+ F+ +++ + +
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 76 SN 77
Sbjct: 70 HK 71
Score = 59.6 bits (145), Expect = 1e-12
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 99 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFG-TIESVNMVTNKETGAKRGFAFIEFN 156
G ++ +++G L+ +E+ + F+ G T+ SV ++ N+ TG G+ F+EF
Sbjct: 1 GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60
Query: 157 DYDVVDK 163
D +K
Sbjct: 61 DLATAEK 67
>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
PDB: 2dk2_A
Length = 103
Score = 64.2 bits (157), Expect = 3e-14
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 13/84 (15%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+ +F+ L T+E L+ F Q+G++ V +KD + FI + E AM
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAME 63
Query: 77 NRPHN---IDGRVVETKRAVPRDE 97
N ++G +E A P D+
Sbjct: 64 E--MNGKDLEGENIEIVFAKPPDQ 85
Score = 53.1 bits (128), Expect = 6e-10
Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 9/56 (16%)
Query: 105 ATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
A VK +FV L + E+ L + FSQFG +E V + + +AFI F++ D
Sbjct: 9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERD 56
>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 = 66.8 bits (163), Expect = 3e-14
Identities = 23/173 (13%), Positives = 47/173 (27%), Gaps = 41/173 (23%)
Query: 19 VFIGGLD-YRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+ + L+ R T +SL F +G++ V ++ + + + ++ AMS+
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60
Query: 78 ------------------------------RPHNIDGRVVETKRAVPRDEIGKPEANATV 107
+ D R
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+ + + E+DL+ FS G + K R A I+ +
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVE 169
Score = 40.3 bits (94), Expect = 9e-05
Identities = 11/57 (19%), Positives = 22/57 (38%), Gaps = 10/57 (17%)
Query: 103 ANATVKKMFVGGLKDQE--EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
N+ + V L + L F +G ++ V ++ N K+ A ++ D
Sbjct: 2 GNSVL---LVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMAD 50
Score = 40.3 bits (94), Expect = 1e-04
Identities = 10/64 (15%), Positives = 19/64 (29%), Gaps = 7/64 (10%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDAM 75
+ + + ++E L+ F G +V + R I EA +
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDL 178
Query: 76 SNRP 79
N
Sbjct: 179 HNHD 182
>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 = 64.2 bits (157), Expect = 3e-14
Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 7/86 (8%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
S++ +++ L T++E ++ F V K+ R + F+ +S +
Sbjct: 12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAV 65
Query: 73 DAMSN-RPHNIDGRVVETKRAVPRDE 97
+AM +DG +E A P D+
Sbjct: 66 EAMKALNGKVLDGSPIEVTLAKPVDK 91
Score = 51.9 bits (125), Expect = 2e-09
Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 7/60 (11%)
Query: 99 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G + ++VK ++V L E+ + + F+ R +AF+ F++
Sbjct: 7 GDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVE------RVKKIRDYAFVHFSN 60
>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 = 64.6 bits (158), Expect = 3e-14
Identities = 13/83 (15%), Positives = 32/83 (38%), Gaps = 6/83 (7%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDA 74
++I L ++ L+ + +G+++ +++D + SRG GF + + V
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGH 85
Query: 75 MSNRPHNIDGRVVETKRAVPRDE 97
+ + I + P
Sbjct: 86 FNGKF--IKTPPGVSAPTEPLLC 106
Score = 52.3 bits (126), Expect = 1e-09
Identities = 10/58 (17%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+++ L +E +L FG + S ++ + +G RG F + + ++
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVI 83
>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 = 63.4 bits (155), Expect = 5e-14
Identities = 17/86 (19%), Positives = 43/86 (50%), Gaps = 9/86 (10%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
+ K+FIG L T++ +++ FEQ+G++++ ++K +GF+ + +
Sbjct: 5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDKTAAE 56
Query: 73 DAMSNRP-HNIDGRVVETKRAVPRDE 97
DA+ N + + G + + + + +
Sbjct: 57 DAIRNLHHYKLHGVNINVEASKNKSK 82
Score = 50.3 bits (121), Expect = 4e-09
Identities = 11/64 (17%), Positives = 29/64 (45%), Gaps = 9/64 (14%)
Query: 103 ANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVV 161
++ + K+F+G L ++ E ++R F Q+G + ++ + + F+ D
Sbjct: 4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDKTAA 55
Query: 162 DKIV 165
+ +
Sbjct: 56 EDAI 59
>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 = 63.8 bits (156), Expect = 5e-14
Identities = 19/82 (23%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPI-TKRSRGFGFITYSEAKMVDDAM 75
F+G L Y T+ES++ FF I V + ++P +R +GFG+ + + + A+
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74
Query: 76 SNRPHNIDGRVVETKRAVPRDE 97
S ++ + + A +
Sbjct: 75 SLNEESLGNKRIRVDVADQAQD 96
Score = 52.6 bits (127), Expect = 8e-10
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 3/72 (4%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAK-RGFAFIEFNDYDVVDKIV 165
F+G L D E+ ++E+F I +V + + +GF + EF D D + +
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74
Query: 166 LSKITLLLDRRV 177
L ++R+
Sbjct: 75 SLNEESLGNKRI 86
>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 = 66.6 bits (162), Expect = 5e-14
Identities = 26/173 (15%), Positives = 53/173 (30%), Gaps = 41/173 (23%)
Query: 19 VFIGGLD-YRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
+ + L+ R T +SL F +G++ V ++ + + + ++ AMS+
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 91
Query: 78 --------RPHNI---DGRVVETKRAVPRDE-------------------IGKPEANATV 107
+P I + V+ R D+
Sbjct: 92 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 151
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+ + + E+DL+ FS G + K R A I+ +
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVE 200
Score = 42.7 bits (100), Expect = 2e-05
Identities = 10/64 (15%), Positives = 20/64 (31%), Gaps = 7/64 (10%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAKMVDDAM 75
+ + + ++E L+ F G +V ++ R I EA +
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQALIDL 209
Query: 76 SNRP 79
N
Sbjct: 210 HNHD 213
>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 = 63.4 bits (155), Expect = 5e-14
Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPIT-KRSRGFGFITYSEAKMVDDAM 75
F+G L Y T+ES++ FF I V + ++P +R +GFG+ + + + A+
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78
Query: 76 SNRPHNIDGRVVETKRAVPRDE 97
S ++ R + A +
Sbjct: 79 SLNEESLGNRRIRVDVADQAQD 100
Score = 51.5 bits (124), Expect = 2e-09
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 108 KKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAK-RGFAFIEFNDYDVVDKIV 165
F+G L D E+ ++E+F I +V + + +GF + EF D D + +
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 78
>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 = 62.6 bits (153), Expect = 8e-14
Identities = 13/86 (15%), Positives = 38/86 (44%), Gaps = 9/86 (10%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
++ K+ +G + T++ L+A FE++G +++ ++ + + F+ A+
Sbjct: 7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAV 58
Query: 73 DAMSNR-PHNIDGRVVETKRAVPRDE 97
+A+ G+ + + + R
Sbjct: 59 EAIRGLDNTEFQGKRMHVQLSTSRLR 84
Score = 50.7 bits (122), Expect = 4e-09
Identities = 9/53 (16%), Positives = 21/53 (39%), Gaps = 9/53 (16%)
Query: 108 KKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K+ VG + +LR F ++G + ++ + +AF+ +
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDI--------VKDYAFVHMERAE 55
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 63.2 bits (154), Expect = 9e-14
Identities = 14/85 (16%), Positives = 35/85 (41%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + V + GL + + E + FF + + + + RS G F+ ++ ++
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRD 96
+ A+ I R +E ++ +
Sbjct: 71 EKALKKHKERIGHRYIEIFKSSRAE 95
Score = 43.6 bits (103), Expect = 2e-06
Identities = 12/69 (17%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKI 169
+ GL ++++ ++FS + + + G G AF++F ++ +K +
Sbjct: 19 RLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHK 78
Query: 170 TLLLDRRVE 178
+ R +E
Sbjct: 79 ERIGHRYIE 87
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 62.7 bits (153), Expect = 1e-13
Identities = 21/101 (20%), Positives = 40/101 (39%), Gaps = 9/101 (8%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
KV++G L L+ F +G + V + ++P GF F+ + + + +DA+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56
Query: 78 RP-HNIDGR---VVETKRAVPRDEIGKPEANATVKKMFVGG 114
I G V + R +P A + ++ G
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNG 97
Score = 48.8 bits (117), Expect = 2e-08
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 6/58 (10%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
K++VG L + +L FS +G + +V + N GFAF+EF D + V
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAV 54
>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 = 63.1 bits (154), Expect = 1e-13
Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
++++G L + ++ F ++G I D+ + F F+ + + + +DA+
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAEDAVY 79
Query: 77 NRP-HNIDGR 85
R ++ DG
Sbjct: 80 GRDGYDYDGY 89
Score = 50.4 bits (121), Expect = 6e-09
Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 4/70 (5%)
Query: 91 RAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRG 149
+ + + A +++VG L D D+ + F ++G I +++ K
Sbjct: 6 SGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPP 62
Query: 150 FAFIEFNDYD 159
FAF+EF D
Sbjct: 63 FAFVEFEDPR 72
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 64.5 bits (157), Expect = 1e-13
Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 6/89 (6%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EA 68
E+ K+ + LD+ +D +Q F ++G + V D + RS G + + +A
Sbjct: 84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADA 142
Query: 69 KMVDDAMSNRPHNIDGRVVETKRAVPRDE 97
P +DGR ++ + + +
Sbjct: 143 LKAMKQYKGVP--LDGRPMDIQLVASQID 169
Score = 52.5 bits (126), Expect = 4e-09
Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 88 ETKRAVPRDEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGA 146
+ + + G E T K+ V L + D++E F++FGT++ + + +G
Sbjct: 69 KWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGR 127
Query: 147 KRGFAFIEFND 157
G A + F
Sbjct: 128 SLGTADVHFER 138
>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 = 62.8 bits (153), Expect = 1e-13
Identities = 16/101 (15%), Positives = 35/101 (34%), Gaps = 9/101 (8%)
Query: 6 DDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEI--------VDVVVMKDPITKRS 57
E +++ GL+ T + L FF+Q G + + + D T +
Sbjct: 5 SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKP 64
Query: 58 RGFGFITYSEAKMVDDAMSN-RPHNIDGRVVETKRAVPRDE 97
+G ++Y + A+ + G ++ A +
Sbjct: 65 KGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 105
Score = 58.2 bits (141), Expect = 7e-12
Identities = 18/79 (22%), Positives = 34/79 (43%), Gaps = 9/79 (11%)
Query: 94 PRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIES--------VNMVTNKET 144
G P+ ++ ++V GL DDL ++F Q G ++ +++ +KET
Sbjct: 2 SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61
Query: 145 GAKRGFAFIEFNDYDVVDK 163
G +G A + + D
Sbjct: 62 GKPKGDATVSYEDPPTAKA 80
>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 = 62.6 bits (152), Expect = 2e-13
Identities = 14/89 (15%), Positives = 35/89 (39%)
Query: 8 SKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSE 67
S + + V + GL + T E + FF + + + + + G F+ ++
Sbjct: 34 SNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFAS 93
Query: 68 AKMVDDAMSNRPHNIDGRVVETKRAVPRD 96
++ + A+ I R +E ++ +
Sbjct: 94 QELAEKALGKHKERIGHRYIEVFKSSQEE 122
Score = 46.8 bits (111), Expect = 2e-07
Identities = 14/105 (13%), Positives = 36/105 (34%), Gaps = 1/105 (0%)
Query: 75 MSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTI 133
S+ + +A + + GL ++++ ++FS +
Sbjct: 10 HSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIV 69
Query: 134 ESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRVE 178
+ + G G AF++F ++ +K + + R +E
Sbjct: 70 PNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIE 114
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 61.7 bits (150), Expect = 3e-13
Identities = 10/81 (12%), Positives = 28/81 (34%), Gaps = 1/81 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
R V+I G T + ++ + E G+++++ + + K +G F+ + + +
Sbjct: 12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE 70
Query: 77 NRPHNIDGRVVETKRAVPRDE 97
+
Sbjct: 71 TPGQKYKETDLLILFKDDYFA 91
Score = 54.0 bits (130), Expect = 2e-10
Identities = 13/65 (20%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 102 EANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDV 160
+ + + +++ G D DD++E+ G + ++ M A +G F+ F+ +
Sbjct: 6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIES 64
Query: 161 VDKIV 165
K V
Sbjct: 65 AKKFV 69
>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 = 61.1 bits (149), Expect = 3e-13
Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 10/74 (13%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDD 73
+++GGL T+ L+ F Q+GEI + V++ + FI + A++ +
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAE 66
Query: 74 AMSNRPHNIDGRVV 87
N+ ++GR +
Sbjct: 67 KSFNK-LIVNGRRL 79
Score = 57.7 bits (140), Expect = 6e-12
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 7/60 (11%)
Query: 99 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G + T+ ++VGGL E DLR +F QFG I ++ +V + AFI+F
Sbjct: 4 GSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFAT 57
>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 = 61.6 bits (150), Expect = 3e-13
Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 8/74 (10%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVD--------VVVMKDPITKRSRGFGFI 63
+F+ GL T ES+ +F+Q G I + + D T + +G +
Sbjct: 9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 68
Query: 64 TYSEAKMVDDAMSN 77
++ + A+
Sbjct: 69 SFDDPPSAKAAIDW 82
Score = 58.9 bits (143), Expect = 3e-12
Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 12/79 (15%)
Query: 94 PRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIES--------VNMVTNKET 144
N T+ FV GL ++ + + +YF Q G I++ +N+ T++ET
Sbjct: 3 HHHHHHSHSDNNTI---FVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRET 59
Query: 145 GAKRGFAFIEFNDYDVVDK 163
G +G A + F+D
Sbjct: 60 GKLKGEATVSFDDPPSAKA 78
>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 = 62.6 bits (152), Expect = 4e-13
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 8/82 (9%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
KV++G L L+ F +G + V V ++P GF F+ + + + DA+
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVR 128
Query: 77 NRP-HNIDGR--VVETKRAVPR 95
+ G VE R
Sbjct: 129 ELDGRTLCGCRVRVELSNGEKR 150
Score = 49.5 bits (118), Expect = 3e-08
Identities = 23/117 (19%), Positives = 41/117 (35%), Gaps = 17/117 (14%)
Query: 55 KRSRGFGFITYSEAKMVDDAMS--NRPHNIDGR---------VVETKRAVPRDEIGKPEA 103
K +G +A + + +DG T+ + ++
Sbjct: 10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDS 69
Query: 104 NATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K++VG L + + +L F +G + SV + N GFAF+EF D
Sbjct: 70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPR 121
>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 = 60.0 bits (146), Expect = 1e-12
Identities = 10/66 (15%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ R +++G L T+ + F Q G ++ + + + F+ + E +
Sbjct: 11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDA 68
Query: 72 DDAMSN 77
A++
Sbjct: 69 AAALAA 74
Score = 57.6 bits (140), Expect = 1e-11
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 99 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G E + + ++VG L E + + FSQ G +S M+T + + F+EF +
Sbjct: 7 GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYE 64
>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 = 60.5 bits (147), Expect = 1e-12
Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 13/79 (16%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EA 68
P +++ G D T L+ F +G I+D+ + R F+TY A
Sbjct: 35 APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESA 86
Query: 69 KMVDDAMSNRPHNIDGRVV 87
++ ++ +
Sbjct: 87 DQAVAELNGT--QVESVQL 103
Score = 58.2 bits (141), Expect = 1e-11
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 10/68 (14%)
Query: 90 KRAVPRDEIGKPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRG 149
+R+ E P T+ +V G D LR FS FG I ++M +
Sbjct: 25 RRSDSFPERRAPRKGNTL---YVYGE-DMTPTLLRGAFSPFGNIIDLSMDPPR------N 74
Query: 150 FAFIEFND 157
AF+ +
Sbjct: 75 CAFVTYEK 82
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 60.0 bits (146), Expect = 1e-12
Identities = 15/99 (15%), Positives = 34/99 (34%), Gaps = 11/99 (11%)
Query: 2 KPRYDDSKCTEPESL--RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRG 59
PR + L ++F+ + L F +G + +V ++ G
Sbjct: 15 VPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------G 66
Query: 60 FGFITYSEAKMVDDAMSNRP-HNIDGRVVETKRAVPRDE 97
F F+ + EA+ A+ + + +E + +
Sbjct: 67 FAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105
Score = 49.6 bits (119), Expect = 1e-08
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 9/59 (15%)
Query: 102 EANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
E + ++FV +E +L E F FG ++ V + GFAF+EF + +
Sbjct: 26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAE 76
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 59.6 bits (145), Expect = 2e-12
Identities = 20/91 (21%), Positives = 38/91 (41%), Gaps = 4/91 (4%)
Query: 19 VFIGGLDYRTTDESLQAFF-EQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS- 76
+F+G L D L FF + + V+ D T S+G+GF+ +++ A++
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70
Query: 77 -NRPHNIDGRVVETKRAVPRDEIGKPEANAT 106
+ + V A+P+ KP +
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASRVKPVESGP 101
Score = 40.7 bits (96), Expect = 2e-05
Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 3/49 (6%)
Query: 111 FVGGLKDQ-EEDDLREYFSQ-FGTIESVNMVTNKETGAKRGFAFIEFND 157
FVG L ++ L E+F + + + +V ++ TG +G+ F++F D
Sbjct: 13 FVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTD 60
>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 = 58.5 bits (142), Expect = 4e-12
Identities = 10/83 (12%), Positives = 24/83 (28%), Gaps = 1/83 (1%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
+ + + + + + + FF + I V +K G + +
Sbjct: 12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71
Query: 73 DAMSNRP-HNIDGRVVETKRAVP 94
A+ + I R V+
Sbjct: 72 AAVIDLNDRPIGSRKVKLVLGSG 94
Score = 43.4 bits (103), Expect = 2e-06
Identities = 10/54 (18%), Positives = 18/54 (33%), Gaps = 1/54 (1%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
V + D++ ++F + I + E G G A + F D
Sbjct: 19 KVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
>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 = 58.5 bits (142), Expect = 5e-12
Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 12/80 (15%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
P +++ G D T L+ F +G I+D+ + R F+TY + +
Sbjct: 11 APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESA 62
Query: 72 DDAMSNRPHNIDGRVVETKR 91
D A++ ++G VE+ +
Sbjct: 63 DQAVA----ELNGTQVESVQ 78
Score = 54.6 bits (132), Expect = 1e-10
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 10/58 (17%)
Query: 100 KPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
P T+ +V G D LR FS FG I ++M + AF+ +
Sbjct: 11 APRKGNTL---YVYGE-DMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEK 58
>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 = 58.7 bits (142), Expect = 6e-12
Identities = 12/86 (13%), Positives = 34/86 (39%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+ E+ V++ GL + ++ + FF++ + D + + ++ G GF+ +
Sbjct: 20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEAD 79
Query: 71 VDDAMSNRPHNIDGRVVETKRAVPRD 96
A+ + R ++ +
Sbjct: 80 YKAALCRHKQYMGNRFIQVHPITKKG 105
Score = 45.2 bits (107), Expect = 8e-07
Identities = 13/92 (14%), Positives = 32/92 (34%), Gaps = 3/92 (3%)
Query: 88 ETKRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGA 146
++ R P +++ GL + E + ++F + +E + G
Sbjct: 8 KSPSGQKRSRSRSPHEAGFC--VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK 65
Query: 147 KRGFAFIEFNDYDVVDKIVLSKITLLLDRRVE 178
G F+EF + + + +R ++
Sbjct: 66 ATGEGFVEFRNEADYKAALCRHKQYMGNRFIQ 97
>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 = 58.3 bits (141), Expect = 7e-12
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 11/80 (13%)
Query: 19 VFIGGLDYRTTDESL---QAFFEQWGEIVDVVVMKDPIT---KRSRGFGFITYS---EAK 69
VF+ GL R D + +F ++G+I VV+ + ++TY +A
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 70 MVDDAMSNRPHNIDGRVVET 89
++N +DGR ++
Sbjct: 78 RAIQCVNNVV--VDGRTLKA 95
Score = 43.3 bits (102), Expect = 3e-06
Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 7/56 (12%)
Query: 111 FVGGL--KDQEEDDLR--EYFSQFGTIESVNMVTNKETGAKR---GFAFIEFNDYD 159
FV GL + + + L+ EYF +FG I V + + + A++ + +
Sbjct: 19 FVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74
>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 = 57.7 bits (140), Expect = 8e-12
Identities = 10/77 (12%), Positives = 24/77 (31%), Gaps = 1/77 (1%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
+ + + + + + + FF + I V +K G + +
Sbjct: 12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71
Query: 73 DAMSNRP-HNIDGRVVE 88
A+ + I R V+
Sbjct: 72 AAVIDLNDRPIGSRKVK 88
Score = 45.0 bits (107), Expect = 5e-07
Identities = 10/54 (18%), Positives = 18/54 (33%), Gaps = 1/54 (1%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
V + D++ ++F + I + E G G A + F D
Sbjct: 19 KVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
>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 = 57.8 bits (140), Expect = 1e-11
Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 2/78 (2%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
V + G+ + + ++ FF + V ++KD R+ G G + + + +A+
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEALKRN 76
Query: 79 PHNIDGRVVETKRAVPRD 96
+ R VE A R
Sbjct: 77 RMLMIQRYVEVSPATERQ 94
Score = 41.7 bits (98), Expect = 1e-05
Identities = 14/69 (20%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKI 169
V G+ E+D+R++F +++V+++ + G G ++F + +
Sbjct: 20 SVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNR 77
Query: 170 TLLLDRRVE 178
L++ R VE
Sbjct: 78 MLMIQRYVE 86
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 56.3 bits (136), Expect = 3e-11
Identities = 18/89 (20%), Positives = 28/89 (31%), Gaps = 11/89 (12%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
YDD T V I GL + L +++G I VVVM +
Sbjct: 9 MENYDDPHKTPAS--PVVHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQA 60
Query: 62 FITY---SEAKMVDDAMSNRPHNIDGRVV 87
+ + A + ++ I G
Sbjct: 61 LVEFEDVLGACNAVNYAADNQIYIAGHPA 89
Score = 48.2 bits (115), Expect = 3e-08
Identities = 22/92 (23%), Positives = 31/92 (33%), Gaps = 19/92 (20%)
Query: 75 MSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTI 133
M + H+ D+ K A+ V + GL E DL E +FG I
Sbjct: 1 MGHHHHH---------HMENYDDPHKTPASPVV---HIRGLIDGVVEADLVEALQEFGPI 48
Query: 134 ESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
V ++ K A +EF D V
Sbjct: 49 SYVVVMPKK------RQALVEFEDVLGACNAV 74
>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 = 56.7 bits (137), Expect = 3e-11
Identities = 10/89 (11%), Positives = 25/89 (28%), Gaps = 1/89 (1%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
I + + T + F E + V + + G + + +
Sbjct: 16 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 75
Query: 77 NRPHNIDGRVVETKRAVPRDEIGKPEANA 105
++GR +++ + E N
Sbjct: 76 LHRKKLNGREAFVHVV-TLEDMREIEKNP 103
Score = 45.1 bits (107), Expect = 7e-07
Identities = 11/66 (16%), Positives = 24/66 (36%), Gaps = 1/66 (1%)
Query: 99 GKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G+ + N+ + + + D+ ++ E+ V G G A ++F +
Sbjct: 7 GEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKN 66
Query: 158 YDVVDK 163
D K
Sbjct: 67 EDDARK 72
>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 = 54.6 bits (132), Expect = 1e-10
Identities = 14/82 (17%), Positives = 35/82 (42%), Gaps = 2/82 (2%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+ + V + G + T++++ F + V + ++++ G+ F+ +S +
Sbjct: 5 SSGTTCHTVKLRGAPFNVTEKNVMEFLAP-LKPVAIRIVRNA-HGNKTGYIFVDFSNEEE 62
Query: 71 VDDAMSNRPHNIDGRVVETKRA 92
V A+ + GR +E R
Sbjct: 63 VKQALKCNREYMGGRYIEVFRE 84
Score = 39.6 bits (93), Expect = 4e-05
Identities = 13/69 (18%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKI 169
+ G + E ++ E+ + ++ +V N G K G+ F++F++ + V + +
Sbjct: 14 KLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAH-GNKTGYIFVDFSNEEEVKQALKCNR 71
Query: 170 TLLLDRRVE 178
+ R +E
Sbjct: 72 EYMGGRYIE 80
>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 = 54.5 bits (132), Expect = 1e-10
Identities = 14/65 (21%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 17 RKVFIGGLDYRTTDESLQ----AFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
++I L+ + + L+ A F ++G+I+D++V + + RG F+ + E
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSSAT 65
Query: 73 DAMSN 77
+A+ +
Sbjct: 66 NALRS 70
Score = 43.8 bits (104), Expect = 1e-06
Identities = 13/52 (25%), Positives = 28/52 (53%), Gaps = 8/52 (15%)
Query: 111 FVGGLKDQ-EEDDLRE----YFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
++ L ++ ++D+L++ FS+FG I + + + RG AF+ F +
Sbjct: 12 YINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVIFKE 60
>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 = 54.6 bits (132), Expect = 1e-10
Identities = 12/61 (19%), Positives = 25/61 (40%), Gaps = 6/61 (9%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
++++GGL T+ +L F+++G I + + F +I Y A +
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDH------VKGDSFAYIQYESLDAAQAACA 71
Query: 77 N 77
Sbjct: 72 K 72
Score = 53.4 bits (129), Expect = 4e-10
Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 99 GKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
GK + +VGGL L F +FG+I +++ V FA+I++
Sbjct: 12 GKANPTTRL---WVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYES 62
Query: 158 YD 159
D
Sbjct: 63 LD 64
>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 = 57.9 bits (139), Expect = 2e-10
Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 3/95 (3%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
P D + + + +F+ ++Y TT+ L+ FE +G I + ++ + + RG+
Sbjct: 90 DPHNDPNAQGDAF--KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYA 147
Query: 62 FITYSEAKMVDDAMSNRPH-NIDGRVVETKRAVPR 95
FI Y + + A + IDGR V R
Sbjct: 148 FIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGR 182
Score = 52.9 bits (126), Expect = 7e-09
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
K +FV + D E LR F +G I+ ++MV +K +G RG+AFIE+
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHER 155
>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 = 53.2 bits (128), Expect = 4e-10
Identities = 18/77 (23%), Positives = 31/77 (40%), Gaps = 2/77 (2%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + V + GL YR T+ + FF + V + P R G + ++ +
Sbjct: 11 QSTTGHCVHMRGLPYRATENDIYNFFSP-LNPMRVHIEIGP-DGRVTGEADVEFATHEDA 68
Query: 72 DDAMSNRPHNIDGRVVE 88
AM+ N+ R VE
Sbjct: 69 VAAMAKDKANMQHRYVE 85
Score = 39.3 bits (92), Expect = 7e-05
Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 3/81 (3%)
Query: 99 GKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
G + T + + GL E+D+ +FS V++ + G G A +EF
Sbjct: 7 GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFAT 64
Query: 158 YDVVDKIVLSKITLLLDRRVE 178
++ + + R VE
Sbjct: 65 HEDAVAAMAKDKANMQHRYVE 85
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 52.8 bits (127), Expect = 4e-10
Identities = 13/80 (16%), Positives = 35/80 (43%), Gaps = 5/80 (6%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVM-KDPI----TKRSRGFGFITYSEAKMV 71
R++++G + + T+E++ FF + + +P+ + + F F+ +
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 72 DDAMSNRPHNIDGRVVETKR 91
AM+ G+ ++ +R
Sbjct: 67 TQAMAFDGIIFQGQSLKIRR 86
Score = 41.6 bits (98), Expect = 7e-06
Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 6/62 (9%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFG-----TIESVNMVTNKETGAKRGFAFIEFNDYDVV 161
++++VG + E+ + ++F+ T N V + + FAF+EF D
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 162 DK 163
+
Sbjct: 67 TQ 68
>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 = 54.1 bits (130), Expect = 4e-10
Identities = 19/95 (20%), Positives = 33/95 (34%), Gaps = 2/95 (2%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
+ D + + V + GL Y+ T+ + FF V V + P R G
Sbjct: 32 RGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEA 89
Query: 62 FITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRD 96
+ ++ + AMS N+ R +E
Sbjct: 90 DVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTG 124
Score = 42.5 bits (100), Expect = 8e-06
Identities = 13/77 (16%), Positives = 27/77 (35%), Gaps = 3/77 (3%)
Query: 88 ETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGA 146
+ + + T + + GL E+D+ +FS V++ + G
Sbjct: 27 GQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GR 84
Query: 147 KRGFAFIEFNDYDVVDK 163
G A +EF ++
Sbjct: 85 VTGEADVEFATHEEAVA 101
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A
Length = 282
Score = 56.0 bits (134), Expect = 5e-10
Identities = 19/89 (21%), Positives = 39/89 (43%), Gaps = 12/89 (13%)
Query: 17 RKVFIGGLDYRTTDE----SLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS---EAK 69
++I L+ + + SL A F Q+G+I+D++V + + + RG F+ + A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 66
Query: 70 MVDDAMSNRPHNIDGRVVETKRAVPRDEI 98
+M P + + + A +I
Sbjct: 67 NALRSMQGFP--FYDKPMRIQYAKTDSDI 93
Score = 45.3 bits (106), Expect = 3e-06
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 11/61 (18%)
Query: 102 EANATVKKMFVGGL-KDQEEDDLRE----YFSQFGTIESVNMVTNKETGAKRGFAFIEFN 156
N T+ ++ L + ++D+L++ FSQFG I + + + RG AF+ F
Sbjct: 7 RPNHTI---YINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFVIFK 60
Query: 157 D 157
+
Sbjct: 61 E 61
Score = 42.2 bits (98), Expect = 3e-05
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+ E L F+QF + V +V + AF+EF++
Sbjct: 218 ETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEV 255
Score = 37.9 bits (87), Expect = 7e-04
Identities = 12/80 (15%), Positives = 24/80 (30%), Gaps = 8/80 (10%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
+E +F+ L T + L F Q+ +V ++
Sbjct: 192 PGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG-----RHDI 246
Query: 61 GFITYS---EAKMVDDAMSN 77
F+ + +A DA+
Sbjct: 247 AFVEFDNEVQAGAARDALQG 266
>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 = 52.4 bits (126), Expect = 1e-09
Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 10/81 (12%)
Query: 17 RKVFIGGLDY-RTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
+VFIG L+ ++ F ++G + V K G+ F+ YS + A+
Sbjct: 28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAAV 79
Query: 76 SNRP-HNIDGRVVETKRAVPR 95
+ G+ ++ A
Sbjct: 80 LGENGRVLAGQTLDINMAGEP 100
Score = 48.5 bits (116), Expect = 4e-08
Identities = 11/59 (18%), Positives = 28/59 (47%), Gaps = 10/59 (16%)
Query: 109 KMFVGGLKDQE--EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++F+G L + D+ FS++G + ++ +G+AF+++++ V
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAV 79
>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 = 52.2 bits (125), Expect = 1e-09
Identities = 12/89 (13%), Positives = 34/89 (38%), Gaps = 10/89 (11%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
DS+ S R + I L T+ + + +G++ +++++ + +
Sbjct: 18 GSHMGDSRSAGVPS-RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQA 70
Query: 62 FITY---SEAKMVDDAMSNRPHNIDGRVV 87
FI A + + ++ + G+ +
Sbjct: 71 FIEMNTEEAANTMVNYYTSVTPVLRGQPI 99
Score = 45.7 bits (108), Expect = 4e-07
Identities = 16/91 (17%), Positives = 33/91 (36%), Gaps = 10/91 (10%)
Query: 76 SNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIE 134
S+ H+ + + + D + + + L D E ++ FG +
Sbjct: 3 SSHHHHHHSSGLVPRGSHMGDSRSAGVPSRVI---HIRKLPIDVTEGEVISLGLPFGKVT 59
Query: 135 SVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
++ M+ K AFIE N + + +V
Sbjct: 60 NLLMLKGK------NQAFIEMNTEEAANTMV 84
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 51.7 bits (124), Expect = 1e-09
Identities = 11/76 (14%), Positives = 24/76 (31%), Gaps = 4/76 (5%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMV 71
+ + +RK+ I + E L + Q+G + + +TYS
Sbjct: 11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT---DSETAVVNVTYSSKDQA 67
Query: 72 DDAMSNRP-HNIDGRV 86
A+ ++
Sbjct: 68 RQALDKLNGFQLENFT 83
Score = 43.6 bits (103), Expect = 2e-06
Identities = 8/53 (15%), Positives = 19/53 (35%), Gaps = 4/53 (7%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
+K+ + + + + L Q+G +ES V + ++ D
Sbjct: 16 RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKD 65
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 51.4 bits (124), Expect = 2e-09
Identities = 20/102 (19%), Positives = 39/102 (38%), Gaps = 15/102 (14%)
Query: 11 TEPESLR---KVFIGGLDYRTTDES-LQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYS 66
TE ++ ++FIG L + + L F +G I+ + + FGFI +
Sbjct: 2 TEMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFD 53
Query: 67 EAKMVDDAMSNRP-HNIDGR--VVETKRAVPRDEIGKPEANA 105
+ V DA+ G+ ++E + R + +
Sbjct: 54 NPQSVRDAIECESQEMNFGKKLILEVSSSNARPQFDHGDHGT 95
Score = 48.7 bits (117), Expect = 2e-08
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 10/53 (18%)
Query: 109 KMFVGGL--KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
++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 = 50.8 bits (122), Expect = 4e-09
Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 12/83 (14%)
Query: 17 RKVFIGGLDYRTTDES-LQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAM 75
++FIG L + + L F +G I+ + + FGFI + + V DA+
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAI 74
Query: 76 SNRP-HNIDGR--VVETKRAVPR 95
G+ ++E + R
Sbjct: 75 EXESQEMNFGKKLILEVSSSNAR 97
Score = 48.9 bits (117), Expect = 2e-08
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 10/67 (14%)
Query: 101 PEANATVKKMFVGGL--KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
P + ++F+G L K+ ++DL FS +G I +N+ K F FI+F++
Sbjct: 16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNP 67
Query: 159 DVVDKIV 165
V +
Sbjct: 68 QSVRDAI 74
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 50.1 bits (120), Expect = 7e-09
Identities = 10/58 (17%), Positives = 24/58 (41%)
Query: 20 FIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSN 77
I ++L + F + G++V++ D T +++GF F+ + +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73
Score = 49.3 bits (118), Expect = 1e-08
Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 111 FVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+ K + L FS+ G + ++ ++ TG +GF F+E + KI+
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKII 71
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 50.7 bits (121), Expect = 7e-09
Identities = 18/87 (20%), Positives = 35/87 (40%), Gaps = 3/87 (3%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEI---VDVVVMKDPITKRSRGFGFITYSEAK 69
E+ V + GL + T E + AFF Q I + ++ R G F+ ++ +
Sbjct: 20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEE 79
Query: 70 MVDDAMSNRPHNIDGRVVETKRAVPRD 96
+A+ + R +E R+ +
Sbjct: 80 YAQNALRKHKDLLGKRYIELFRSTAAE 106
Score = 41.4 bits (97), Expect = 2e-05
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 5/63 (7%)
Query: 120 EDDLREYFSQFGTI----ESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDR 175
+++ +F Q I E + VT + G G AF+ F + + LL R
Sbjct: 37 AEEVVAFFGQHCPITGGKEGILFVTYPD-GRPTGDAFVLFACEEYAQNALRKHKDLLGKR 95
Query: 176 RVE 178
+E
Sbjct: 96 YIE 98
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 50.7 bits (121), Expect = 7e-09
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 7/79 (8%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDE----SLQAFFEQWGEIVDVVVMKDPITKR 56
M S E + V I ++ E L A G+I+D+VV +
Sbjct: 14 MDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDD 70
Query: 57 SRGFGFITYSEAKMVDDAM 75
+ G +I ++ + +
Sbjct: 71 NSGKAYIVFATQESAQAFV 89
Score = 43.4 bits (102), Expect = 4e-06
Identities = 11/76 (14%), Positives = 24/76 (31%), Gaps = 8/76 (10%)
Query: 87 VETKRAVPRDEIGKPEANATVKKMFVGGLKDQ-EEDDLRE----YFSQFGTIESVNMVTN 141
E + D P + + + + + ++ L+ S G I + +
Sbjct: 9 FERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV--- 65
Query: 142 KETGAKRGFAFIEFND 157
+ G A+I F
Sbjct: 66 DLSDDNSGKAYIVFAT 81
>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 = 49.5 bits (118), Expect = 1e-08
Identities = 17/102 (16%), Positives = 32/102 (31%), Gaps = 8/102 (7%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWG--EIVDVVVMKDPITKRSRGFGFITYSEA 68
E + + + GL + T E + FF + + + RG I
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE 65
Query: 69 KMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKM 110
+ V A+ + R VE + +A +K +
Sbjct: 66 QDVQKALEKHRMYMGQRYVEVYEINNE------DVDALMKSL 101
Score = 38.7 bits (90), Expect = 1e-04
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 2/61 (3%)
Query: 120 EDDLREYFSQFGTIESVNMV--TNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRV 177
+D+ +FS N + G +RG A IE V K + + R V
Sbjct: 25 MEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYV 84
Query: 178 E 178
E
Sbjct: 85 E 85
>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 = 49.2 bits (117), Expect = 2e-08
Identities = 12/80 (15%), Positives = 28/80 (35%), Gaps = 10/80 (12%)
Query: 3 PRYDDSKCTE-PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
R++ + V GGL + L E+ G + +++ + + +
Sbjct: 13 LRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYS 66
Query: 62 FITYS---EAKMVDDAMSNR 78
F Y E+K ++ +
Sbjct: 67 FARYRTTEESKRAYVTLNGK 86
Score = 43.4 bits (102), Expect = 3e-06
Identities = 9/48 (18%), Positives = 18/48 (37%), Gaps = 7/48 (14%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
GGL + L + G ++++ M NK ++F +
Sbjct: 31 ANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRT 72
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 51.3 bits (122), Expect = 2e-08
Identities = 20/97 (20%), Positives = 33/97 (34%), Gaps = 17/97 (17%)
Query: 72 DDAMSNRPHNIDGRVVETKRAVPRDE-IGKPEANATVKKMFVGGLKD----------QEE 120
D + K A R++ G K ++VGG+ Q E
Sbjct: 98 DIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIE 157
Query: 121 DDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+R FS+ G I+ + V +K F++F
Sbjct: 158 SRIRFVFSRLGDIDRIRYVESK------NCGFVKFKY 188
Score = 43.2 bits (101), Expect = 1e-05
Identities = 14/75 (18%), Positives = 34/75 (45%), Gaps = 18/75 (24%)
Query: 17 RKVFIGGLDY---------RTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY-- 65
+ +++GG+D + ++ F + G+I + ++ S+ GF+ +
Sbjct: 135 KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKY 188
Query: 66 -SEAKMVDDAMSNRP 79
+ A+ +AMSN+
Sbjct: 189 QANAEFAKEAMSNQT 203
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 49.1 bits (117), Expect = 2e-08
Identities = 10/74 (13%), Positives = 30/74 (40%), Gaps = 9/74 (12%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDD 73
R + I L T+ + + +G++ +++++K + FI A + +
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVN 70
Query: 74 AMSNRPHNIDGRVV 87
++ + G+ +
Sbjct: 71 YYTSVTPVLRGQPI 84
Score = 43.3 bits (102), Expect = 2e-06
Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 7/59 (11%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+ + + L D E ++ FG + ++ M+ K AFIE N + + +V
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANTMV 69
>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 = 48.6 bits (116), Expect = 3e-08
Identities = 14/88 (15%), Positives = 26/88 (29%), Gaps = 11/88 (12%)
Query: 3 PRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGF 62
V + GL + L E++G I V++M +
Sbjct: 4 GSSGSHHKVSVS--PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQAL 55
Query: 63 ITY---SEAKMVDDAMSNRPHNIDGRVV 87
+ + AK ++ P I G+
Sbjct: 56 VEFENIDSAKECVTFAADVPVYIAGQQA 83
Score = 44.8 bits (106), Expect = 8e-07
Identities = 21/67 (31%), Positives = 28/67 (41%), Gaps = 10/67 (14%)
Query: 100 KPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDY 158
K + V V GL + E DL E +FGTI V M+ K A +EF +
Sbjct: 11 KVSVSPVV---HVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFENI 61
Query: 159 DVVDKIV 165
D + V
Sbjct: 62 DSAKECV 68
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 47.9 bits (114), Expect = 5e-08
Identities = 11/86 (12%), Positives = 25/86 (29%), Gaps = 6/86 (6%)
Query: 11 TEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
V++G L L+ + G + + + R F+ Y ++
Sbjct: 14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLT-----WQGPRRRAFLHYPDSAA 68
Query: 71 VDDAMSNRP-HNIDGRVVETKRAVPR 95
A+S + + A +
Sbjct: 69 AQQAVSCLQGLRLGTDTLRVALARQQ 94
Score = 39.0 bits (91), Expect = 8e-05
Identities = 13/73 (17%), Positives = 25/73 (34%), Gaps = 6/73 (8%)
Query: 94 PRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAF 152
E ++VG L +D DL+ + G++ + + R AF
Sbjct: 6 SGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-PLRLTWQG----PRRRAF 60
Query: 153 IEFNDYDVVDKIV 165
+ + D + V
Sbjct: 61 LHYPDSAAAQQAV 73
>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 = 47.2 bits (112), Expect = 1e-07
Identities = 15/88 (17%), Positives = 29/88 (32%), Gaps = 4/88 (4%)
Query: 12 EPESLRKVFIGGLDYRTTDESLQAFFEQ---WGEIVDVVVMKDPITKRSRGFGFITYSEA 68
E V + GL + + E +Q F + V + R G F+
Sbjct: 13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESE 71
Query: 69 KMVDDAMSNRPHNIDGRVVETKRAVPRD 96
V A+ ++ R +E ++ +
Sbjct: 72 DDVKLALKKDRESMGHRYIEVFKSHRTE 99
Score = 40.3 bits (94), Expect = 4e-05
Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 4/62 (6%)
Query: 120 EDDLREYFSQF---GTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRR 176
+D++ + S + V+ + +E G + G AF+E D V + + R
Sbjct: 31 IEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRY 89
Query: 177 VE 178
+E
Sbjct: 90 IE 91
>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 = 46.7 bits (111), Expect = 1e-07
Identities = 10/74 (13%), Positives = 29/74 (39%), Gaps = 9/74 (12%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY---SEAKMVDD 73
R + I L T+ + A +G++ +++++K + F+ A + +
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVN 69
Query: 74 AMSNRPHNIDGRVV 87
S ++ + +
Sbjct: 70 YYSAVTPHLRNQPI 83
Score = 41.0 bits (96), Expect = 1e-05
Identities = 10/56 (17%), Positives = 21/56 (37%), Gaps = 7/56 (12%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+ L + E ++ FG + ++ M+ K AF+E + +V
Sbjct: 19 HIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAITMV 68
>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 = 46.7 bits (111), Expect = 1e-07
Identities = 12/82 (14%), Positives = 29/82 (35%), Gaps = 10/82 (12%)
Query: 18 KVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS- 76
+V + GL + + L+ + G++ V +D G G + + + + A+
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 69
Query: 77 -NRPHNIDGRVVETKRAVPRDE 97
+ ET + +
Sbjct: 70 LDN-TKFRSHEGETAYIRVKVD 90
Score = 37.9 bits (88), Expect = 2e-04
Identities = 11/71 (15%), Positives = 26/71 (36%), Gaps = 8/71 (11%)
Query: 94 PRDEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNKETGAKRGFAF 152
G P + + ++ V GL DL+++ + G + ++ + G
Sbjct: 2 SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGV 54
Query: 153 IEFNDYDVVDK 163
+EF + +
Sbjct: 55 VEFVRKEDMTY 65
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein;
2.50A {Homo sapiens}
Length = 143
Score = 47.1 bits (112), Expect = 2e-07
Identities = 17/87 (19%), Positives = 30/87 (34%), Gaps = 11/87 (12%)
Query: 82 IDGRVVETKRAVPRDEIGKP-----EANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIES 135
I R +E R + E +++V L +E DL+ F ++ S
Sbjct: 15 ISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSS 74
Query: 136 VNM-----VTNKETGAKRGFAFIEFND 157
+ + G +G AFI +
Sbjct: 75 ETQRIMFDIRLMKEGRMKGQAFIGLPN 101
Score = 45.2 bits (107), Expect = 9e-07
Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 11/67 (16%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEI--------VDVVVMKDPITKRSRGFGFITYSEA 68
++++ L ++ L+ F ++ + D+ +MK R +G FI
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK---EGRMKGQAFIGLPNE 102
Query: 69 KMVDDAM 75
K A+
Sbjct: 103 KAAAKAL 109
>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 = 45.8 bits (108), Expect = 6e-07
Identities = 16/98 (16%), Positives = 29/98 (29%), Gaps = 4/98 (4%)
Query: 2 KPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQ---WGEIVDVVVMKDPITKRSR 58
R E V + GL + + E +Q F V + R
Sbjct: 30 MGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR-EGRQS 88
Query: 59 GFGFITYSEAKMVDDAMSNRPHNIDGRVVETKRAVPRD 96
G F+ V A+ ++ R +E ++ +
Sbjct: 89 GEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTE 126
Score = 40.0 bits (93), Expect = 6e-05
Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 2/61 (3%)
Query: 120 EDDLREYFSQFGTIESVNMV--TNKETGAKRGFAFIEFNDYDVVDKIVLSKITLLLDRRV 177
+D++ + S + V G + G AF+E D V + + R +
Sbjct: 58 VEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYI 117
Query: 178 E 178
E
Sbjct: 118 E 118
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 44.3 bits (105), Expect = 8e-07
Identities = 7/70 (10%), Positives = 24/70 (34%), Gaps = 8/70 (11%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+ + L + + + + + +K R++ F+T + +A+
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58
Query: 77 NR-PHNIDGR 85
++ G+
Sbjct: 59 MFHQYSFRGK 68
Score = 38.2 bits (89), Expect = 1e-04
Identities = 5/57 (8%), Positives = 16/57 (28%), Gaps = 8/57 (14%)
Query: 108 KKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
+ V L +D ++ + + + + AF+ + +
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQN 55
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 44.3 bits (105), Expect = 9e-07
Identities = 11/76 (14%), Positives = 31/76 (40%), Gaps = 9/76 (11%)
Query: 17 RKVFIGGLDYRTTD------ESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+ + + D + F ++G+I + ++ +++G+ F+ Y+
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAH 73
Query: 71 VDDAMSNR-PHNIDGR 85
DA+ N + +D +
Sbjct: 74 AVDAVKNADGYKLDKQ 89
Score = 42.8 bits (101), Expect = 4e-06
Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 9/62 (14%)
Query: 111 FVGGL-------KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
V + ++ ++ + + FS+FG I + +E G +G+ F+E+
Sbjct: 19 VVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY--PEEDGKTKGYIFLEYASPAHAVD 76
Query: 164 IV 165
V
Sbjct: 77 AV 78
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 44.8 bits (106), Expect = 9e-07
Identities = 12/90 (13%), Positives = 30/90 (33%), Gaps = 6/90 (6%)
Query: 13 PESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
P ++ + L + + L+ + T+ G G + + +++
Sbjct: 25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTGALEFPSEEILV 81
Query: 73 DAMS--NRPHNIDGRVVETKRAVPRDEIGK 100
+A+ N G V+ +R I +
Sbjct: 82 EALERLNN-IEFRGSVITVERDDNPPPIRR 110
Score = 33.6 bits (77), Expect = 0.009
Identities = 7/56 (12%), Positives = 21/56 (37%), Gaps = 4/56 (7%)
Query: 109 KMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
++ + L + DL++ + ++ T G +EF +++ +
Sbjct: 30 RITMKNLPEGCSWQDLKDLARENSL---ETTFSSVNTRDFDGTGALEFPSEEILVE 82
>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 = 45.6 bits (107), Expect = 1e-06
Identities = 10/90 (11%), Positives = 29/90 (32%), Gaps = 1/90 (1%)
Query: 1 MKPRYDDSKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGF 60
+ R V+I G T + ++ + E G+++++ + + K +G
Sbjct: 94 KPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGS 152
Query: 61 GFITYSEAKMVDDAMSNRPHNIDGRVVETK 90
F+ + + + +
Sbjct: 153 IFVVFDSIESAKKFVETPGQKYKETDLLIL 182
Score = 43.3 bits (101), Expect = 8e-06
Identities = 16/100 (16%), Positives = 36/100 (36%), Gaps = 2/100 (2%)
Query: 67 EAKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKKMFVGGL-KDQEEDDLRE 125
EA A ++ + + + + + + +++ G D DD++E
Sbjct: 69 EALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKE 128
Query: 126 YFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+ G + ++ M K G F+ F+ + K V
Sbjct: 129 WLEDKGQVLNIQMRRTLHKAFK-GSIFVVFDSIESAKKFV 167
>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 = 43.7 bits (103), Expect = 2e-06
Identities = 12/87 (13%), Positives = 30/87 (34%), Gaps = 10/87 (11%)
Query: 17 RKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMS 76
+V + GL + + L+ + G++ V +D G G + + + + A+
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVR 69
Query: 77 --NRPHNIDGRVVETKRAVPRDEIGKP 101
+ ET + + +
Sbjct: 70 KLDN-TKFRSHEGETAYIRVKVDGPRS 95
Score = 35.6 bits (82), Expect = 0.002
Identities = 13/71 (18%), Positives = 27/71 (38%), Gaps = 9/71 (12%)
Query: 94 PRDEIGKPEANATVKKMFVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAF 152
PR G P + ++ V GL DL+++ + G + ++ + G
Sbjct: 4 PRGRYGPPSRR-SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGV 55
Query: 153 IEFNDYDVVDK 163
+EF + +
Sbjct: 56 VEFVRKEDMTY 66
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 41.2 bits (97), Expect = 8e-06
Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 9/62 (14%)
Query: 111 FVGGL-------KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDK 163
V + ++ ++ + + FS+FG I + +E G +G+ F+E+
Sbjct: 5 VVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVD 62
Query: 164 IV 165
V
Sbjct: 63 AV 64
Score = 40.5 bits (95), Expect = 2e-05
Identities = 9/65 (13%), Positives = 26/65 (40%), Gaps = 8/65 (12%)
Query: 19 VFIGGL------DYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVD 72
+ + + + F ++G+I + ++ +++G+ F+ Y+
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAV 61
Query: 73 DAMSN 77
DA+ N
Sbjct: 62 DAVKN 66
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 41.3 bits (97), Expect = 2e-05
Identities = 13/105 (12%), Positives = 29/105 (27%), Gaps = 12/105 (11%)
Query: 8 SKCTEPESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITY-- 65
S + S + L T +Q F ++G + V++ + +
Sbjct: 2 SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLE 55
Query: 66 -SEAKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEANATVKK 109
EA+ ++ + + A P G +
Sbjct: 56 PLEARKAFRHLAYSK--FHHVPLYLEWA-PIGVFGAAPQKKDSQH 97
Score = 41.0 bits (96), Expect = 2e-05
Identities = 10/48 (20%), Positives = 19/48 (39%), Gaps = 7/48 (14%)
Query: 111 FVGGL-KDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
L +++E FS+FG++ V + A +EF +
Sbjct: 14 LAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLE 55
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 112
Score = 38.0 bits (88), Expect = 2e-04
Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 10/80 (12%)
Query: 12 EPESLRKVFIGGLDY-RTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKM 70
+ E R + + L + +D ++ E +G+I + ++M+ + FI +
Sbjct: 21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETRED 74
Query: 71 VDDAMS---NRPHNIDGRVV 87
+ + GR V
Sbjct: 75 AMAMVDHCLKKALWFQGRCV 94
Score = 36.1 bits (83), Expect = 0.001
Identities = 8/46 (17%), Positives = 18/46 (39%), Gaps = 6/46 (13%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+ + + +G I++ ++ K AFIE + +V
Sbjct: 40 DSAVLKLAEPYGKIKNYILMRMK------SQAFIEMETREDAMAMV 79
>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 = 39.5 bits (91), Expect = 4e-04
Identities = 20/143 (13%), Positives = 42/143 (29%), Gaps = 47/143 (32%)
Query: 14 ESLRKVFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDD 73
F+ D + + ++ + EI +++ KD ++ R F + + +MV
Sbjct: 23 SVFEDAFVDNFDCKDVQDMPKSILSK-EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQK 81
Query: 74 AMS--------------------------------NRPHNIDGRVVETKRAVPRDEIG-- 99
+ +R +N D +V K V R +
Sbjct: 82 FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN-DNQVF-AKYNVSRLQPYLK 139
Query: 100 --------KPEANATVKKMFVGG 114
+P N + + G
Sbjct: 140 LRQALLELRPAKNVLIDGV--LG 160
Score = 32.5 bits (73), Expect = 0.072
Identities = 13/121 (10%), Positives = 31/121 (25%), Gaps = 44/121 (36%)
Query: 28 TTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAK--------MVDDAMSNRP 79
T DE ++ +D P E ++ +++ +
Sbjct: 299 TPDEVKS-LLLKY---LDCRPQDLP-------------REVLTTNPRRLSIIAESIRDGL 341
Query: 80 HNIDG-RVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQEEDDLREYFSQFGTI--ESV 136
D + V + + + L E + R+ F + + S
Sbjct: 342 ATWDNWKHVNCDK---------------LTTIIESSLNVLEPAEYRKMFDRLS-VFPPSA 385
Query: 137 N 137
+
Sbjct: 386 H 386
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 35.5 bits (81), Expect = 0.001
Identities = 9/46 (19%), Positives = 19/46 (41%), Gaps = 5/46 (10%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+D L ++G + ++ + + K G A +EF + V
Sbjct: 31 KDVLLRLLQKYGEVLNLVLSSK-----KPGTAVVEFATVKAAELAV 71
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 36.2 bits (83), Expect = 0.002
Identities = 10/60 (16%), Positives = 25/60 (41%), Gaps = 4/60 (6%)
Query: 19 VFIGGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNR 78
+ + L Y T + L F ++G ++ ++ TK ++ + Y++ A +
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPVSAQHAKLSL 104
Score = 34.7 bits (79), Expect = 0.006
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYD 159
D L + FS+FGT+ + T + A +++ D
Sbjct: 60 LDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPV 95
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 37.0 bits (85), Expect = 0.002
Identities = 35/231 (15%), Positives = 62/231 (26%), Gaps = 107/231 (46%)
Query: 4 RYD----DSKCTEPESLRKVFIGGLDYRTT-------DESL------Q--------AFFE 38
Y ++ K+F ++ +T L Q A FE
Sbjct: 1687 NYSAMIFETIVDGKLKTEKIF-KEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFE 1745
Query: 39 QWGEIVDVVVMKDPITKRSRGF----------------------GFITYSEA-KMVDDAM 75
+S+G ++ ++V
Sbjct: 1746 DL---------------KSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVV---- 1786
Query: 76 SNRPHNIDGRVVETKRAVPRDEIGKPE---ANATVKKMFVGGLKDQEEDDLREYFSQFGT 132
R G ++ AVPRDE+G+ ++ ++ L+
Sbjct: 1787 FYR-----GMTMQV--AVPRDELGRSNYGMIAINPGRVAASF----SQEALQYV------ 1829
Query: 133 IESVNMVTNKETGAKRGFAFIE---FND----YDVV--DKIVLSKITLLLD 174
+E V K TG +E +N Y V D L +T +L+
Sbjct: 1830 VERV----GKRTG-----WLVEIVNYNVENQQY-VAAGDLRALDTVTNVLN 1870
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 35.4 bits (81), Expect = 0.003
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 5/75 (6%)
Query: 84 GRVVETKRAVPRDEIGKPEANATVKKMFVGGLKDQ-EEDDLREYFSQFGTIESVNMVTNK 142
G + A D + V ++ V L D L + FS+FGT+ + T
Sbjct: 5 GNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN 64
Query: 143 ETGAKRGFAFIEFND 157
+ A +++ D
Sbjct: 65 ----NQFQALLQYAD 75
>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 = 34.8 bits (79), Expect = 0.009
Identities = 10/54 (18%), Positives = 21/54 (38%), Gaps = 5/54 (9%)
Query: 111 FVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKI 164
+ + E+ +Y SQFG I + + +A +EF + + +
Sbjct: 57 LIHCPEKISENKFLKYLSQFGPINNHFFYESFGL-----YAVVEFCQKESIGSL 105
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 30.0 bits (67), Expect = 0.20
Identities = 10/69 (14%), Positives = 18/69 (26%), Gaps = 6/69 (8%)
Query: 90 KRAVPRDEIGKPEANATVKKMFVGGLK-DQEEDDLREYFSQFGTIESVNMVTNKETGAKR 148
KR P V + + D L + G ++ + +
Sbjct: 8 KRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NG 62
Query: 149 GFAFIEFND 157
A +EF
Sbjct: 63 IQAMVEFES 71
>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 = 29.7 bits (67), Expect = 0.23
Identities = 12/65 (18%), Positives = 25/65 (38%), Gaps = 5/65 (7%)
Query: 108 KKMF-VGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKR----GFAFIEFNDYDVVD 162
+ M + D E ++ E +FG + V + K+ + F+EF+
Sbjct: 26 RNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETH 85
Query: 163 KIVLS 167
K + +
Sbjct: 86 KAIQA 90
>2hzl_A Trap-T family sorbitol/mannitol transporter, periplasmic binding
protein, SMOM; trap transporter, periplasmic subunit,
ligand binding; 1.40A {Rhodobacter sphaeroides 2} PDB:
2hzk_A
Length = 365
Score = 29.7 bits (67), Expect = 0.47
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 26 YRTTDESLQAFFEQWGEIVDVVVMKDPITKR 56
+ E LQA FE E+ + +P K+
Sbjct: 299 RPFSPEILQACFEAANEVYAEMEASNPAFKK 329
>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 = 28.3 bits (63), Expect = 0.63
Identities = 10/49 (20%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 117 DQEEDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+ E+ E ++G +E +N V + G +++F + +K V
Sbjct: 38 EFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAV 85
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 28.6 bits (63), Expect = 1.1
Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 12/81 (14%)
Query: 4 RYDDSKCTEPESLRKVFI--GGLDYRTTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFG 61
R++ + + + + + GGL + L E+ G VD ++M ++ +
Sbjct: 7 RHEGIETVS-YATQSLVVANGGLGNGVSRNQLLPVLEKCGL-VDALLMPP-----NKPYS 59
Query: 62 FITYS---EAKMVDDAMSNRP 79
F Y E+K ++ +
Sbjct: 60 FARYRTTEESKRAYVTLNGKE 80
>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 = 27.0 bits (60), Expect = 1.9
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFNDYDVVDKIV 165
+DLR S+FG I + + G A + F D + D +
Sbjct: 40 REDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCI 81
>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 = 2.0
Identities = 6/38 (15%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 120 EDDLREYFSQFGTIESVNMVTNKETGAKRGFAFIEFND 157
+DD+ E ++ G + + + N +G +++
Sbjct: 31 KDDVIEECNKHGGVIHIYVDKNSA----QGNVYVKCPS 64
>1w2l_A Cytochrome oxidase subunit II; cytochrome C domain, oxidoreductase;
HET: HEM; 1.3A {Rhodothermus marinus}
Length = 99
Score = 26.0 bits (57), Expect = 3.9
Identities = 11/64 (17%), Positives = 17/64 (26%), Gaps = 5/64 (7%)
Query: 68 AKMVDDAMSNRPHNIDGRVVETKRAVPRDEIGKPEA---NATVKKM--FVGGLKDQEEDD 122
+ DG R+ I +P A M L ++E
Sbjct: 31 GPSFKGLYGSTRTFEDGTTAVADENYLRESILQPGAKVVQGYPNVMPASYASLSEREVAA 90
Query: 123 LREY 126
L E+
Sbjct: 91 LIEF 94
>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 = 26.9 bits (60), Expect = 4.1
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 131 GT--IESVNMVTNKETGAKRGFAFIEFNDYD 159
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 = 26.9 bits (60), Expect = 4.3
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 131 GT--IESVNMVTNKETGAKRGFAFIEFNDYD 159
GT IE+ + N G R FAF E+ D
Sbjct: 206 GTFCIEAAMIGMNIAPGFNRDFAFEEWPWVD 236
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 25.6 bits (56), Expect = 5.3
Identities = 8/52 (15%), Positives = 18/52 (34%), Gaps = 1/52 (1%)
Query: 115 LKDQEEDDLREYFSQFGTIESVNMVTNKETGAK-RGFAFIEFNDYDVVDKIV 165
+ + E + +E ++G + + F+EF + K V
Sbjct: 22 VDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAV 73
>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 = 5.4
Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 7/71 (9%)
Query: 91 RAVPRDEIGKPEANATVKKMFVGGLKDQEEDDLREYFSQFGTIESVNMVTNKETGAKRGF 150
R R + + +A + V + +++ + DL E+ + N + N+
Sbjct: 91 REEQRKRLQELDAASKVMEQ---EWREKAKKDLEEWNQRQSEQVEKNKINNRIADK---- 143
Query: 151 AFIEFNDYDVV 161
AF + D D++
Sbjct: 144 AFYQQPDADII 154
>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 = 26.5 bits (59), Expect = 5.5
Identities = 8/31 (25%), Positives = 12/31 (38%), Gaps = 2/31 (6%)
Query: 131 GT--IESVNMVTNKETGAKRGFAFIEFNDYD 159
GT IE+ + N G R F ++
Sbjct: 213 GTIPIEAALIGQNIAPGFNREFVSETWDWMP 243
>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 = 25.1 bits (55), Expect = 7.0
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 2/50 (4%)
Query: 120 EDDLREYFSQFGTIESVN--MVTNKETGAKRGFAFIEFNDYDVVDKIVLS 167
+D+R+ S++G ++S+ + G F+EF K +
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQG 78
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 26.4 bits (58), Expect = 7.6
Identities = 16/157 (10%), Positives = 37/157 (23%), Gaps = 45/157 (28%)
Query: 28 TTDESLQAFFEQWGEIVDVVVMKDPITKRSRGFGFITYSEAKMVDDAMSNRPHNIDGRVV 87
+ E+ + F Q G+ VD+ + + + A + + G++
Sbjct: 937 ASKETAEQFKHQHGDKVDIFEIPETGEYSVKL-----LKGATLYIPKALRFDRLVAGQIP 991
Query: 88 E----TKRAVPRDEIGKPEANATVKKM--FV-------------GGLKDQEEDDLREYFS 128
+ D I ++ G+ D E + S
Sbjct: 992 TGWNAKTYGISDDII---------SQVDPITLFVLVSVVEAFIASGITDPYEMYKYVHVS 1042
Query: 129 QFG-----------TIESVNMVTNKETGAKRGFAFIE 154
+ G + + + E
Sbjct: 1043 EVGNCSGSGMGGVSALRG-MFKDRFKDEPVQNDILQE 1078
>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 = 7.9
Identities = 9/54 (16%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 102 EANATVKKMFVGGLKDQEEDDL-REYFSQFGTIESVNMVTNKETGAKRGFAFIE 154
+ +V+ + L + DL + S GT+ + + ++ +R F ++
Sbjct: 296 NGHPSVRWVRYPYLPSHPQYDLAKRQMSGGGTVVTFALDCPEDVAKQRAFEVLD 349
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
0.318 0.137 0.389
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,819,308
Number of extensions: 168823
Number of successful extensions: 1016
Number of sequences better than 10.0: 1
Number of HSP's gapped: 723
Number of HSP's successfully gapped: 375
Length of query: 178
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 91
Effective length of database: 4,272,666
Effective search space: 388812606
Effective search space used: 388812606
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 (21.7 bits)
S2: 54 (24.5 bits)