RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2204
(231 letters)
>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 = 197 bits (504), Expect = 2e-64
Identities = 128/197 (64%), Positives = 141/197 (71%), Gaps = 42/197 (21%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
ARRLYVGNIPFG+TE+ MM+FFN QM L GL QA GNPVLA QIN DKNFAFLEFRS+D
Sbjct: 3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 105 ETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKIFIGG 164
ETTQAMAFDGI F+GQSLKIRRPHDYQP PG+++N +V VP GV+STVVPDS HK+FIGG
Sbjct: 63 ETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVP-GVVSTVVPDSAHKLFIGG 121
Query: 165 LPNYLNEDQ-----------------------------------------AIAGLNGMQL 183
LPNYLN+DQ AIAGLNGMQL
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 181
Query: 184 GDKKLIVQRASVGAKNA 200
GDKKL+VQRASVGAKNA
Sbjct: 182 GDKKLLVQRASVGAKNA 198
Score = 57.3 bits (139), Expect = 2e-10
Identities = 24/117 (20%), Positives = 48/117 (41%), Gaps = 18/117 (15%)
Query: 17 PANVIIPETTVAAAAAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGL 76
P + + VV + + A +L++G +P + +D++ E
Sbjct: 85 PHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELL--------- 135
Query: 77 AQAAGNPVLACQINLD------KNFAFLEFRSIDETTQAM-AFDGINFKGQSLKIRR 126
+ G P+ A + D K +AF E+ I+ T QA+ +G+ + L ++R
Sbjct: 136 -TSFG-PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 190
Score = 27.3 bits (61), Expect = 3.7
Identities = 8/53 (15%), Positives = 17/53 (32%), Gaps = 1/53 (1%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRASVGAKNASGQQAPVQIQVPGLTQVGQAGPAT 224
QA+A +G+ + L ++R + P ++ V
Sbjct: 65 TQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHK 116
>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 = 162 bits (412), Expect = 7e-51
Identities = 107/191 (56%), Positives = 115/191 (60%), Gaps = 62/191 (32%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
ARRLYVGNIPFG+TE+ MM+FFN QM L GL QA GNPVLA QIN DKNFAFLEFRS+D
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 105 ETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKIFIGG 164
ETTQAMAFDGI F+GQSLKIRRPHDYQP HK+FIGG
Sbjct: 63 ETTQAMAFDGIIFQGQSLKIRRPHDYQP---------------------LPGAHKLFIGG 101
Query: 165 LPNYLNEDQ-----------------------------------------AIAGLNGMQL 183
LPNYLN+DQ AIAGLNGMQL
Sbjct: 102 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 161
Query: 184 GDKKLIVQRAS 194
GDKKL+VQRAS
Sbjct: 162 GDKKLLVQRAS 172
Score = 53.0 bits (128), Expect = 4e-09
Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 18/91 (19%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FA 96
A +L++G +P + +D++ E G + A + D +A
Sbjct: 91 LPGAHKLFIGGLPNYLNDDQVKELLTSF----------GP-LKAFNLVKDSATGLSKGYA 139
Query: 97 FLEFRSIDETTQAMA-FDGINFKGQSLKIRR 126
F E+ I+ T QA+A +G+ + L ++R
Sbjct: 140 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170
>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 = 131 bits (331), Expect = 7e-40
Identities = 68/84 (80%), Positives = 73/84 (86%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSI 103
ARRLYVGNIPFG+TE+ MM+FFN QM L GL QA GNPVLA QIN DKNFAFLEFRS+
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 63
Query: 104 DETTQAMAFDGINFKGQSLKIRRP 127
DETTQAMAFDGI F+GQSLKIRRP
Sbjct: 64 DETTQAMAFDGIIFQGQSLKIRRP 87
>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 = 71.9 bits (177), Expect = 3e-15
Identities = 31/181 (17%), Positives = 61/181 (33%), Gaps = 35/181 (19%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRS 102
R R++ + +P VT E+ + + + C ++ K AF+ +
Sbjct: 19 FRNRRKILIRGLPGDVTNQEVHDLLSD----------YE--LKYCFVDKYKGTAFVTLLN 66
Query: 103 IDETTQAM-AFDGINFKGQSLKIRRPHDYQPT--------PGVTDN--AAVAVPAGVIST 151
++ A+ AF + + L ++ P +T + P G +
Sbjct: 67 GEQAEAAINAFHQSRLRERELSVQLQ--PTDALLCVANLPPSLTQQQFEELVRPFGSLER 124
Query: 152 --VVPDSP---HKIFIGGLPNYLNED---QAIAGLNGMQLGDKKLIVQRASVGAKNASGQ 203
+V K + G Y+ +D +A + L G LG + L V G +
Sbjct: 125 CFLVYSERTGQSKGY--GFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALL 182
Query: 204 Q 204
Sbjct: 183 H 183
Score = 58.1 bits (141), Expect = 2e-10
Identities = 31/207 (14%), Positives = 58/207 (28%), Gaps = 49/207 (23%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAF 97
L V N+P +T+ + E + G + C + K + F
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELV----------RPFG-SLERCFLVYSERTGQSKGYGF 141
Query: 98 LEFRSIDETTQAM-AFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAV------------ 144
E+ D +A G ++L + Q TP + + + V
Sbjct: 142 AEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDA 201
Query: 145 ------PAGVIST--VVPDSPHKI----FIGGLPNYLNEDQ---AIAGLNGMQLGDKKLI 189
+ + ++ + Y + A +G+ LG L
Sbjct: 202 LCRALSAVHSPTFCQLACGQDGQLKGFAVL----EYETAEMAEEAQQQADGLSLGGSHLR 257
Query: 190 VQRASVGAKNASGQQAPVQIQVPGLTQ 216
V + G S A + Q L +
Sbjct: 258 VSFCAPGPPGRSMLAALIAAQATALNR 284
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 64.0 bits (156), Expect = 1e-13
Identities = 19/92 (20%), Positives = 33/92 (35%), Gaps = 16/92 (17%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFL 98
+ R +Y+ P T D++ E+ + VL Q+ + F+
Sbjct: 9 VKNRSVYIKGFPTDATLDDIKEWLEDK-----------GQVLNIQMRRTLHKAFKGSIFV 57
Query: 99 EFRSIDETTQAMAFDGINFKGQSLKIRRPHDY 130
F SI+ + + G +K L I DY
Sbjct: 58 VFDSIESAKKFVETPGQKYKETDLLILFKDDY 89
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG, protein
structure initiative; HET: PGE; 1.95A {Homo sapiens}
PDB: 3b4d_A 3b4m_A
Length = 89
Score = 62.9 bits (154), Expect = 2e-13
Identities = 24/91 (26%), Positives = 41/91 (45%), Gaps = 17/91 (18%)
Query: 42 ITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNF 95
+ AR +YVGN+ +G T +E+ F+ G+ V I D K F
Sbjct: 2 MEADARSIYVGNVDYGATAEELEAHFHG----------CGS-VNRVTILCDKFSGHPKGF 50
Query: 96 AFLEFRSIDETTQAMAFDGINFKGQSLKIRR 126
A++EF + ++A D F+G+ +K+
Sbjct: 51 AYIEFSDKESVRTSLALDESLFRGRQIKVIP 81
>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 = 64.9 bits (159), Expect = 2e-13
Identities = 16/192 (8%), Positives = 47/192 (24%), Gaps = 71/192 (36%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-----KNFAF 97
+ L++GN+ + E+ ++ + + F +
Sbjct: 10 STTPFNLFIGNLNPNKSVAELKVAISE----------LF-AKNDLAVVDVRTGTNRKFGY 58
Query: 98 LEFRSIDETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSP 157
++F S ++ +A+ G+ G +K+ +P +
Sbjct: 59 VDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKK-------------------VRAA 99
Query: 158 HKIFIGGLPNYLNEDQ------------------------------------AIAGLNGM 181
+ L + ED+ + G
Sbjct: 100 RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGA 159
Query: 182 QLGDKKLIVQRA 193
++ + + +
Sbjct: 160 EIDGRSVSLYYT 171
>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 = 65.5 bits (160), Expect = 4e-13
Identities = 25/130 (19%), Positives = 40/130 (30%), Gaps = 39/130 (30%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
Q RL+VGN+P +TE++ F + G IN D+ F F+ S
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFER----------YG-EPSEVFINRDRGFGFIRLESRT 69
Query: 105 ETTQAM-AFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKIFIG 163
A DG K + L+IR + +
Sbjct: 70 LAEIAKAELDGTILKSRPLRIRF---------------------------ATHGAALTVK 102
Query: 164 GLPNYLNEDQ 173
L ++ +
Sbjct: 103 NLSPVVSNEL 112
Score = 38.5 bits (90), Expect = 0.001
Identities = 13/73 (17%), Positives = 25/73 (34%), Gaps = 16/73 (21%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFL 98
L V N+ V+ + + + F+Q G V + +D F+
Sbjct: 94 THGAALTVKNLSPVVSNELLEQAFSQF----------GP-VEKAVVVVDDRGRATGKGFV 142
Query: 99 EFRSIDETTQAMA 111
EF + +A+
Sbjct: 143 EFAAKPPARKALE 155
>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 = 61.9 bits (151), Expect = 7e-13
Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 12/83 (14%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
Q RL+VGN+P +TE+EM + F + G I+ DK F F+ +
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEK----------YG-KAGEVFIHKDKGFGFIRLETRT 62
Query: 105 ETTQAM-AFDGINFKGQSLKIRR 126
A D + +G+ L++R
Sbjct: 63 LAEIAKVELDNMPLRGKQLRVRF 85
Score = 28.8 bits (65), Expect = 0.55
Identities = 16/84 (19%), Positives = 25/84 (29%), Gaps = 35/84 (41%)
Query: 154 PDSPHKIFIGGLPNYLNEDQ-----------------------------------AIAGL 178
++F+G LP + E++ A L
Sbjct: 12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVEL 71
Query: 179 NGMQLGDKKLIVQRASVGAKNASG 202
+ M L K+L V+ A A SG
Sbjct: 72 DNMPLRGKQLRVRFACHSASLTSG 95
>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 = 61.1 bits (149), Expect = 1e-12
Identities = 19/89 (21%), Positives = 41/89 (46%), Gaps = 13/89 (14%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFL 98
GS+ + +LY+GN+ VT D++ + F P+ A Q+ L +AF+
Sbjct: 1 GSSGSSGMNKLYIGNLSPAVTADDLRQLFGD----------RKLPL-AGQVLLKSGYAFV 49
Query: 99 EFRSIDETTQAM-AFDG-INFKGQSLKIR 125
++ + +A+ G + G+ +++
Sbjct: 50 DYPDQNWAIRAIETLSGKVELHGKIMEVD 78
>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 = 62.0 bits (151), Expect = 1e-12
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 17/87 (19%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLE 99
R +YVGN+ +G T ++ F+ G + I DK +A++E
Sbjct: 36 KRSVYVGNVDYGSTAQDLEAHFSS----------CG-SINRITILCDKFSGHPKGYAYIE 84
Query: 100 FRSIDETTQAMAFDGINFKGQSLKIRR 126
F + A+A D F+G+++K+
Sbjct: 85 FAERNSVDAAVAMDETVFRGRTIKVLP 111
>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 = 61.2 bits (149), Expect = 2e-12
Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 17/89 (19%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAF 97
R AR ++ + + ++ +FF+ G V +I D+N A+
Sbjct: 23 RDARTVFCMQLAARIRPRDLEDFFSA----------VG-KVRDVRIISDRNSRRSKGIAY 71
Query: 98 LEFRSIDETTQAMAFDGINFKGQSLKIRR 126
+EF I A+ G G + ++
Sbjct: 72 VEFCEIQSVPLAIGLTGQRLLGVPIIVQA 100
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 61.0 bits (148), Expect = 2e-12
Identities = 18/99 (18%), Positives = 36/99 (36%), Gaps = 15/99 (15%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD--KNFA 96
S + + R+ + N+P G + ++ + + +N
Sbjct: 21 MSKLPAKRYRITMKNLPEGCSWQDLKDLARE----------NSLETTFSSVNTRDFDGTG 70
Query: 97 FLEFRSIDETTQAMA-FDGINFKGQSLKIRRPHDYQPTP 134
LEF S + +A+ + I F+G + + R D P P
Sbjct: 71 ALEFPSEEILVEALERLNNIEFRGSVITVER--DDNPPP 107
>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 = 60.0 bits (146), Expect = 4e-12
Identities = 22/98 (22%), Positives = 46/98 (46%), Gaps = 18/98 (18%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAF 97
R R ++VGNIP+ TE+++ + F++ G PV++ ++ D+ + F
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSE----------VG-PVVSFRLVYDRETGKPKGYGF 54
Query: 98 LEFRSIDETTQAM-AFDGINFKGQSLKIRRPHDYQPTP 134
E++ + AM +G F G++L++ +
Sbjct: 55 CEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKE 92
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 59.6 bits (145), Expect = 5e-12
Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 18/88 (20%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FA 96
T YVGN+PF + ++ F + + ++ DK+ F
Sbjct: 12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS------------IRSVRLVRDKDTDKFKGFC 59
Query: 97 FLEFRSIDETTQAMAFDGINFKGQSLKI 124
++EF +D +A+ +DG +SL++
Sbjct: 60 YVEFDEVDSLKEALTYDGALLGDRSLRV 87
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar
mRNA localization, translation; 1.90A {Drosophila
melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A
Length = 165
Score = 61.0 bits (148), Expect = 5e-12
Identities = 21/97 (21%), Positives = 38/97 (39%), Gaps = 23/97 (23%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
L+V +I EDE+ E F G + +NLD K +A +E+
Sbjct: 74 ILFVTSIHEEAQEDEIQEKFCD----------YG-EIKNIHLNLDRRTGFSKGYALVEYE 122
Query: 102 SIDETTQAM-AFDGINFKGQSLKI-----RRPHDYQP 132
+ + A A +G GQ++++ + P +
Sbjct: 123 THKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKK 159
>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 = 59.2 bits (144), Expect = 5e-12
Identities = 20/97 (20%), Positives = 44/97 (45%), Gaps = 18/97 (18%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLE 99
+R +Y+G+IP+ TE+++++ + G PV+ ++ D +AF+E
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSN----------VG-PVINLKMMFDPQTGRSKGYAFIE 50
Query: 100 FRSIDETTQAM-AFDGINFKGQSLKIRRPHDYQPTPG 135
FR ++ + A+ +G + LK + +
Sbjct: 51 FRDLESSASAVRNLNGYQLGSRFLKCGYSSNSDISGV 87
Score = 26.0 bits (58), Expect = 5.1
Identities = 13/87 (14%), Positives = 23/87 (26%), Gaps = 41/87 (47%)
Query: 159 KIFIGGLPNYLNEDQ-----------------------------------------AIAG 177
+++G +P E+Q A+
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 178 LNGMQLGDKKLIVQRASVGAKNASGQQ 204
LNG QLG + L +S + +
Sbjct: 64 LNGYQLGSRFLKCGYSSNSDISGVSLE 90
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 58.9 bits (143), Expect = 6e-12
Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 12/89 (13%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-FAF 97
GS+ + R ++V P GV ++ E+F G PV + ++ DK FA
Sbjct: 1 GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLA----------FG-PVASVVMDKDKGVFAI 49
Query: 98 LEFRSIDETTQAMAFDGINFKGQSLKIRR 126
+E + ++ + G L++R
Sbjct: 50 VEMGDVGAREAVLSQSQHSLGGHRLRVRP 78
>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 = 59.2 bits (144), Expect = 8e-12
Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 18/93 (19%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------ 92
G + + L+V +I EDE+ E F G + +NLD
Sbjct: 19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCD----------YG-EIKNIHLNLDRRTGFS 67
Query: 93 KNFAFLEFRSIDETTQAM-AFDGINFKGQSLKI 124
K +A +E+ + + A A +G GQ++++
Sbjct: 68 KGYALVEYETHKQALAAKEALNGAEIMGQTIQV 100
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA
splicing, mRNA transport, nonsense-mediated mRNA decay,
nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*
Length = 126
Score = 59.3 bits (144), Expect = 9e-12
Identities = 19/95 (20%), Positives = 36/95 (37%), Gaps = 18/95 (18%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
L+V + TE+++ + F + G + +NLD K + +E+
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAE----------YGE-IKNIHLNLDRRTGYLKGYTLVEYE 72
Query: 102 SIDETTQAM-AFDGINFKGQSLKIRRPHDYQPTPG 135
+ E AM +G + GQ + + P G
Sbjct: 73 TYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKG 107
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 58.4 bits (142), Expect = 1e-11
Identities = 17/101 (16%), Positives = 44/101 (43%), Gaps = 17/101 (16%)
Query: 30 AAAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQI 89
++ + V + + + +L++ +PF T++E+ E G V ++
Sbjct: 1 GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKA----------HG-TVKDLRL 49
Query: 90 NLDKN-----FAFLEFRSIDETTQAM-AFDGINFKGQSLKI 124
++ A++E+ + + +QA+ DG+ K +K+
Sbjct: 50 VTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKV 90
Score = 28.4 bits (64), Expect = 0.77
Identities = 14/95 (14%), Positives = 28/95 (29%), Gaps = 40/95 (42%)
Query: 145 PAGVISTVVPDSPHKIFIGGLPNYLNEDQ------------------------------- 173
+GV HK+FI GLP +++
Sbjct: 5 SSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVE 64
Query: 174 ---------AIAGLNGMQLGDKKLIVQRASVGAKN 199
A+ ++GM + + + V ++ G +
Sbjct: 65 YENESQASQAVMKMDGMTIKENIIKVAISNSGPSS 99
>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; 1.54A {Homo sapiens}
Length = 95
Score = 58.0 bits (141), Expect = 1e-11
Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 17/100 (17%)
Query: 31 AAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQIN 90
++ + R ++VGN+ V E+ + E F Q AG P+ I
Sbjct: 1 GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQ----------AG-PLTKVTIC 49
Query: 91 LDKN-----FAFLEFRSIDETTQAM-AFDGINFKGQSLKI 124
D+ F F+ F+ + + A+ +GI G+ + +
Sbjct: 50 KDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINV 89
Score = 28.0 bits (63), Expect = 1.0
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRASVG 196
AIA LNG++L + + V S G
Sbjct: 71 SYAIALLNGIRLYGRPINVSGPSSG 95
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 58.4 bits (142), Expect = 2e-11
Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 23/92 (25%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
L+V + TE+++ + F + G + +NLD K + +E+
Sbjct: 25 ILFVTGVHEEATEEDIHDKFAE----------YG-EIKNIHLNLDRRTGYLKGYTLVEYE 73
Query: 102 SIDETTQAM-AFDGINFKGQSLKI-----RRP 127
+ E AM +G + GQ + + R P
Sbjct: 74 TYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 105
>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 = 58.0 bits (141), Expect = 2e-11
Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 19/85 (22%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-------FAFLE 99
++GN+P+ VTE+ + EFF G + A ++ + + F + E
Sbjct: 20 YTAFLGNLPYDVTEESIKEFF------------RGLNISAVRLPREPSNPERLKGFGYAE 67
Query: 100 FRSIDETTQAMAFDGINFKGQSLKI 124
F +D A++ + + + +++
Sbjct: 68 FEDLDSLLSALSLNEESLGNRRIRV 92
>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 = 57.4 bits (139), Expect = 2e-11
Identities = 16/95 (16%), Positives = 35/95 (36%), Gaps = 14/95 (14%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRS 102
+ + + V N+P E+ + C ++ +K AF+ +
Sbjct: 2 SSGSSGILVKNLPQDSNCQEVHDLLKD----------YDLKY--CYVDRNKRTAFVTLLN 49
Query: 103 IDETTQAM-AFDGINFKGQSLKIRR-PHDYQPTPG 135
++ A+ F +F+G+ L ++ P D G
Sbjct: 50 GEQAQNAIQMFHQYSFRGKDLIVQLQPTDALLCSG 84
Score = 31.6 bits (72), Expect = 0.048
Identities = 15/61 (24%), Positives = 20/61 (32%), Gaps = 7/61 (11%)
Query: 145 PAGVISTVVPDSPHKIFIGGLPNYLNEDQ---AIAGLNGMQLGDKKLIVQRASVGAKNAS 201
+ V + F+ LN +Q AI + K LIVQ A S
Sbjct: 28 DYDLKYCYVDRNKRTAFV----TLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDALLCS 83
Query: 202 G 202
G
Sbjct: 84 G 84
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 60.0 bits (146), Expect = 2e-11
Identities = 33/202 (16%), Positives = 68/202 (33%), Gaps = 69/202 (34%)
Query: 40 STITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------K 93
R+YVG+I + + ED + + F G P+ + ++ D K
Sbjct: 22 QGALAIMSRVYVGSIYYELGEDTIRQAFAP----------FG-PIKSIDMSWDSVTMKHK 70
Query: 94 NFAFLEFRSIDETTQAM-AFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTV 152
FAF+E+ + A+ + + G+++K+ RP + + D A
Sbjct: 71 GFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEE--------- 121
Query: 153 VPDSPHKIFIGGLPNYLNED---------------------------------------- 172
+ ++I++ + L++D
Sbjct: 122 -ARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180
Query: 173 -QAIAGLNGMQLGDKKLIVQRA 193
A++ +N LG + L V +A
Sbjct: 181 QDAVSSMNLFDLGGQYLRVGKA 202
Score = 46.5 bits (111), Expect = 1e-06
Identities = 19/106 (17%), Positives = 40/106 (37%), Gaps = 24/106 (22%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFA 96
R R+YV ++ +++D++ F G + + + D K +
Sbjct: 122 ARAFNRIYVASVHQDLSDDDIKSVFEAF----------GK-IKSATLARDPTTGKHKGYG 170
Query: 97 FLEFRSIDETTQAM-AFDGINFKGQSLKI------RRPHDYQPTPG 135
F+E+ + A+ + + + GQ L++ P TPG
Sbjct: 171 FIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPG 216
Score = 30.0 bits (68), Expect = 0.49
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRAS 194
A+ +N + LG + + V R S
Sbjct: 84 QLALEQMNSVMLGGRNIKVGRPS 106
>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 = 57.2 bits (139), Expect = 2e-11
Identities = 21/98 (21%), Positives = 35/98 (35%), Gaps = 14/98 (14%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFL 98
GS+ + +L++GN+P TE E+ F Q G VL C I KN+ F+
Sbjct: 1 GSSGSSGMVKLFIGNLPREATEQEIRSLFEQ----------YG-KVLECDII--KNYGFV 47
Query: 99 EFRSIDETTQAM-AFDGINFKGQSLKIRRPHDYQPTPG 135
A+ G ++ + +
Sbjct: 48 HIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASS 85
Score = 29.1 bits (66), Expect = 0.38
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRASVGAKNASG 202
+ AI L+ +L + V+ + +K +SG
Sbjct: 56 EDAIRNLHHYKLHGVNINVEASKNKSKASSG 86
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 56.9 bits (138), Expect = 5e-11
Identities = 18/93 (19%), Positives = 39/93 (41%), Gaps = 17/93 (18%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---- 94
G +L V N+ FGV++ ++ E F + G + ++ D++
Sbjct: 22 GGAGVETGGKLLVSNLDFGVSDADIQELFAE----------FG-TLKKAAVHYDRSGRSL 70
Query: 95 -FAFLEFRSIDETTQAM-AFDGINFKGQSLKIR 125
A + F + +AM ++G+ G+ + I+
Sbjct: 71 GTADVHFERKADALKAMKQYNGVPLDGRPMNIQ 103
>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 = 56.9 bits (138), Expect = 5e-11
Identities = 16/90 (17%), Positives = 37/90 (41%), Gaps = 19/90 (21%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-------F 95
++GN+P+ VTE+ + EFF G + A ++ + + F
Sbjct: 12 KSPPYTAFLGNLPYDVTEESIKEFF------------RGLNISAVRLPREPSNPERLKGF 59
Query: 96 AFLEFRSIDETTQAMAFDGINFKGQSLKIR 125
+ EF +D A++ + + + +++
Sbjct: 60 GYAEFEDLDSLLSALSLNEESLGNKRIRVD 89
>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 = 58.3 bits (142), Expect = 6e-11
Identities = 33/195 (16%), Positives = 60/195 (30%), Gaps = 77/195 (39%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFR 101
R LYVGN+ +TED + ++F G P+ +I +DKN +AF+E+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQV----------GG-PIANIKIMIDKNNKNVNYAFVEYH 49
Query: 102 SIDETTQAM-AFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKI 160
+ A+ +G + +KI Q + D +
Sbjct: 50 QSHDANIALQTLNGKQIENNIVKINWAFQSQQSS-------------------SDDTFNL 90
Query: 161 FIGGLPNYLNE-----------------------------------------DQAIAGLN 179
F+G L +++ A+ +
Sbjct: 91 FVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ 150
Query: 180 GMQLGDKKLIVQRAS 194
G L + L + A+
Sbjct: 151 GQDLNGRPLRINWAA 165
>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 = 57.0 bits (138), Expect = 6e-11
Identities = 17/93 (18%), Positives = 37/93 (39%), Gaps = 15/93 (16%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
+Y G I G+T+ M + F G ++ ++ +K ++F+ F + +
Sbjct: 26 CTVYCGGIASGLTDQLMRQTF----------SPFG-QIMEIRVFPEKGYSFVRFSTHESA 74
Query: 107 TQAM-AFDGINFKGQSLKI---RRPHDYQPTPG 135
A+ + +G +G +K + D P
Sbjct: 75 AHAIVSVNGTTIEGHVVKCYWGKESPDMTSGPS 107
>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 = 56.5 bits (137), Expect = 6e-11
Identities = 23/103 (22%), Positives = 44/103 (42%), Gaps = 21/103 (20%)
Query: 29 AAAAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQ 88
++ ++ P+ Q +YVG + V+E + E F Q AG PV+
Sbjct: 1 GSSGSSGPISERN---QDATVYVGGLDEKVSEPLLWELFLQ----------AG-PVVNTH 46
Query: 89 INLDKN------FAFLEFRSIDETTQAM-AFDGINFKGQSLKI 124
+ D+ + F+EF S ++ A+ D I G+ +++
Sbjct: 47 MPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV 89
>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 = 56.1 bits (136), Expect = 7e-11
Identities = 18/94 (19%), Positives = 36/94 (38%), Gaps = 14/94 (14%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRS 102
+ +++VGN+ T E+ F + G V+ C + K++AF+
Sbjct: 6 SGNTWKIFVGNVSAACTSQELRSLFER----------RG-RVIECDVV--KDYAFVHMEK 52
Query: 103 IDETTQAM-AFDGINFKGQSLKIRRPHDYQPTPG 135
+ A+ +G KG+ + + Q G
Sbjct: 53 EADAKAAIAQLNGKEVKGKRINVELSTKGQKKSG 86
Score = 28.7 bits (65), Expect = 0.42
Identities = 13/77 (16%), Positives = 24/77 (31%), Gaps = 33/77 (42%)
Query: 150 STVVPDSPHKIFIGGLPNYLNEDQ---------------------------------AIA 176
S+ + KIF+G + + AIA
Sbjct: 2 SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIA 61
Query: 177 GLNGMQLGDKKLIVQRA 193
LNG ++ K++ V+ +
Sbjct: 62 QLNGKEVKGKRINVELS 78
>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 = 57.0 bits (138), Expect = 7e-11
Identities = 18/92 (19%), Positives = 37/92 (40%), Gaps = 17/92 (18%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---- 94
G +L V N+ FGV++ ++ E F + G + ++ D++
Sbjct: 28 GGEGVETGAKLLVSNLDFGVSDADIQELFAE----------FG-TLKKAAVDYDRSGRSL 76
Query: 95 -FAFLEFRSIDETTQAM-AFDGINFKGQSLKI 124
A + F + +AM + G+ G+ + I
Sbjct: 77 GTADVHFERRADALKAMKQYKGVPLDGRPMDI 108
>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 = 56.1 bits (136), Expect = 7e-11
Identities = 20/87 (22%), Positives = 39/87 (44%), Gaps = 14/87 (16%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRS 102
+ + +L+VGNI T E+ F + G PV+ C I K++AF+
Sbjct: 7 GKASTKLHVGNISPTCTNQELRAKFEE----------YG-PVIECDIV--KDYAFVHMER 53
Query: 103 IDETTQAM-AFDGINFKGQSLKIRRPH 128
++ +A+ D F+G+ + ++
Sbjct: 54 AEDAVEAIRGLDNTEFQGKRMHVQLST 80
Score = 29.5 bits (67), Expect = 0.28
Identities = 12/82 (14%), Positives = 24/82 (29%), Gaps = 33/82 (40%)
Query: 154 PDSPHKIFIGGLPNYLNEDQ---------------------------------AIAGLNG 180
+ K+ +G + + AI GL+
Sbjct: 7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDN 66
Query: 181 MQLGDKKLIVQRASVGAKNASG 202
+ K++ VQ ++ + ASG
Sbjct: 67 TEFQGKRMHVQLSTSRLRTASG 88
>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 = 56.2 bits (136), Expect = 9e-11
Identities = 20/96 (20%), Positives = 38/96 (39%), Gaps = 15/96 (15%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---FAFLEF 100
R+YVGN+P + ++ + F + G + + + FAF+EF
Sbjct: 20 NNDCRIYVGNLPPDIRTKDIEDVFYK----------YG-AIRDIDLKNRRGGPPFAFVEF 68
Query: 101 RSIDETTQAM-AFDGINFKGQSLKIRRPHDYQPTPG 135
+ A+ DG ++ G L++ P + T
Sbjct: 69 EDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGS 104
Score = 28.1 bits (63), Expect = 1.1
Identities = 8/31 (25%), Positives = 13/31 (41%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRASVGAKNASG 202
+ A+ G +G +L V+ G SG
Sbjct: 75 EDAVYGRDGYDYDGYRLRVEFPRSGRGTGSG 105
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 55.8 bits (135), Expect = 1e-10
Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 12/79 (15%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
Y+GNIP TE +++ F Q G +L + +K F+++ + ++
Sbjct: 28 TTAYIGNIPHFATEADLIPLF----------QNFG-FILDFKHYPEKGCCFIKYDTHEQA 76
Query: 107 TQAM-AFDGINFKGQSLKI 124
+ A F+G++L+
Sbjct: 77 AVCIVALANFPFQGRNLRT 95
>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 = 56.2 bits (136), Expect = 1e-10
Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 15/82 (18%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD---KNFAFLEFRSI 103
R LY+ N+P+ +T +EM + F + G P+ ++ + A++ + I
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGK----------YG-PIRQIRVGNTPETRGTAYVVYEDI 57
Query: 104 DETTQAM-AFDGINFKGQSLKI 124
+ A+ G N + L +
Sbjct: 58 FDAKNAVDHLSGFNVSNRYLVV 79
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 57.6 bits (139), Expect = 1e-10
Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 17/93 (18%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---- 94
G +L V N+ FGV++ ++ E F + G + ++ D++
Sbjct: 81 GGEGVETGAKLLVSNLDFGVSDADIQELFAE----------FG-TLKKAAVDYDRSGRSL 129
Query: 95 -FAFLEFRSIDETTQAMA-FDGINFKGQSLKIR 125
A + F + +AM + G+ G+ + I+
Sbjct: 130 GTADVHFERRADALKAMKQYKGVPLDGRPMDIQ 162
>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 = 55.7 bits (135), Expect = 1e-10
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 16/87 (18%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD----KNFAFL 98
Q R LYVGN+ VTE +++ F+Q G P +C++ + + F+
Sbjct: 12 DGQPRTLYVGNLSRDVTEVLILQLFSQ----------IG-PCKSCKMITEHTSNDPYCFV 60
Query: 99 EFRSIDETTQAM-AFDGINFKGQSLKI 124
EF + A+ A +G G+ +K+
Sbjct: 61 EFYEHRDAAAALAAMNGRKILGKEVKV 87
>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 = 57.2 bits (139), Expect = 1e-10
Identities = 27/195 (13%), Positives = 62/195 (31%), Gaps = 82/195 (42%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDK------NFAFLEFRS 102
L V +P +T++E F G + +C++ DK + F+ +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGS----------IG-EIESCKLVRDKITGQSLGYGFVNYID 53
Query: 103 IDETTQAM-AFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKIF 161
+ +A+ +G+ + +++K+ +P+ +A ++
Sbjct: 54 PKDAEKAINTLNGLRLQTKTIKVSYA---RPSSASIRDA------------------NLY 92
Query: 162 IGGLPNYLNE-----------------------------------------DQAIAGLNG 180
+ GLP + + ++AI GLNG
Sbjct: 93 VSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNG 152
Query: 181 MQL--GDKKLIVQRA 193
+ + + V+ A
Sbjct: 153 QKPSGATEPITVKFA 167
Score = 38.3 bits (90), Expect = 6e-04
Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 18/86 (20%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEF 100
LYV +P +T+ E+ + F+Q G ++ +I +D+ F+ F
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQY----------GR-IITSRILVDQVTGVSRGVGFIRF 137
Query: 101 RSIDETTQAM-AFDGINFKGQSLKIR 125
E +A+ +G G + I
Sbjct: 138 DKRIEAEEAIKGLNGQKPSGATEPIT 163
>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 = 55.4 bits (134), Expect = 2e-10
Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 12/81 (14%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
+ LYV N+ +E+ + + FN P ++ +++AF+ F + +
Sbjct: 14 SVKILYVRNLMLSTSEEMIEKEFNN-----------IKPGAVERVKKIRDYAFVHFSNRE 62
Query: 105 ETTQAM-AFDGINFKGQSLKI 124
+ +AM A +G G +++
Sbjct: 63 DAVEAMKALNGKVLDGSPIEV 83
Score = 26.1 bits (58), Expect = 3.9
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRASVGAKNASG 202
+A+ LNG L + V A K++SG
Sbjct: 65 VEAMKALNGKVLDGSPIEVTLAKPVDKDSSG 95
>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 = 57.3 bits (139), Expect = 2e-10
Identities = 27/137 (19%), Positives = 49/137 (35%), Gaps = 36/137 (26%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
Q R+L++G + F T++ + F Q G + C + D N F F+
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQ----------WGT-LTDCVVMRDPNTKRSRGFGFV 60
Query: 99 EFRSIDETTQAMAFDGINFKGQSLKIRR--PHDYQPTPGVTDNAAVAVPAGVISTVVPDS 156
+ +++E AM G+ ++ +R + PG +
Sbjct: 61 TYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPG-----------------AHLT 103
Query: 157 PHKIFIGGLPNYLNEDQ 173
KIF+GG+ E
Sbjct: 104 VKKIFVGGIKEDTEEHH 120
Score = 51.9 bits (125), Expect = 1e-08
Identities = 16/88 (18%), Positives = 33/88 (37%), Gaps = 17/88 (19%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
++++VG I E + ++F Q G + +I D+ FAF+
Sbjct: 103 TVKKIFVGGIKEDTEEHHLRDYFEQY----------GK-IEVIEIMTDRGSGKKRGFAFV 151
Query: 99 EFRSIDETTQAMAFDGINFKGQSLKIRR 126
F D + + G + ++R+
Sbjct: 152 TFDDHDSVDKIVIQKYHTVNGHNCEVRK 179
Score = 26.5 bits (59), Expect = 6.9
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 154 PDSPHKIFIGGLPNYLNEDQ 173
P+ K+FIGGL ++
Sbjct: 10 PEQLRKLFIGGLSFETTDES 29
>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 = 54.5 bits (132), Expect = 3e-10
Identities = 21/93 (22%), Positives = 41/93 (44%), Gaps = 18/93 (19%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---- 94
GS+ + + RL+V N+ + +E+++ + F+ G P+ +D
Sbjct: 1 GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSA----------YG-PLSELHYPIDSLTKKP 49
Query: 95 --FAFLEFRSIDETTQAM-AFDGINFKGQSLKI 124
FAF+ F + +A DG F+G+ L +
Sbjct: 50 KGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHV 82
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 56.9 bits (138), Expect = 3e-10
Identities = 36/195 (18%), Positives = 64/195 (32%), Gaps = 76/195 (38%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDK------NFAFL 98
LYVG++ VTE + E F+ AG P+L+ ++ D +A++
Sbjct: 14 PMASLYVGDLHPDVTEAMLYEKFSP----------AG-PILSIRVCRDMITRRSLGYAYV 62
Query: 99 EFRSIDETTQAM-AFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSP 157
F+ + +A+ + KG+ ++I Q P + +
Sbjct: 63 NFQQPADAERALDTMNFDVIKGKPVRIMWS---QRDPSLRKSGV---------------- 103
Query: 158 HKIFIGGLPNYLNE---------------------------------------DQAIAGL 178
IFI L ++ ++AI +
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 163
Query: 179 NGMQLGDKKLIVQRA 193
NGM L D+K+ V R
Sbjct: 164 NGMLLNDRKVFVGRF 178
>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 = 55.6 bits (134), Expect = 5e-10
Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 18/88 (20%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAF 97
+++ LYVGN+ F TE+++ E F++ +G + + LDK F F
Sbjct: 37 KKSCTLYVGNLSFYTTEEQIYELFSK----------SG-DIKKIIMGLDKMKKTACGFCF 85
Query: 98 LEFRSIDETTQAM-AFDGINFKGQSLKI 124
+E+ S + AM +G + ++
Sbjct: 86 VEYYSRADAENAMRYINGTRLDDRIIRT 113
>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 = 56.9 bits (138), Expect = 5e-10
Identities = 27/181 (14%), Positives = 61/181 (33%), Gaps = 36/181 (19%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN----FAFLEFRSID 104
+ V N+P ++++ ++F G P++ + FA +EF D
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKH----------CG-PIIHVDVADSLKKNFRFARIEFARYD 92
Query: 105 ETTQAMAFDGINFKGQSLKIRRPHDYQPT-------PGVTDNA--AVAVPAGVI--STVV 153
A+ +I H + T P T + V+ S +
Sbjct: 93 GALAAITKTHKVVGQN--EIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRL 150
Query: 154 PDSP---HKIFIGGLPNYLNED---QAIAGLNGMQLGDKKLIVQRASVGAKNASGQQAPV 207
P + F + +++ + LNG+++ L+ + ++ K+ A +
Sbjct: 151 PSLRFNTSRRF--AYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATL 208
Query: 208 Q 208
+
Sbjct: 209 E 209
Score = 50.4 bits (121), Expect = 1e-07
Identities = 19/137 (13%), Positives = 44/137 (32%), Gaps = 34/137 (24%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFR 101
L++ N P T+ + + L+ ++ + FA+++
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQD----------INVVALSIRLPSLRFNTSRRFAYIDVT 167
Query: 102 SIDETTQAM-AFDGINFKGQSL--KIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPH 158
S ++ + +G+ +G +L K+ P + A G
Sbjct: 168 SKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKS------KRTDSATLEGR---------- 211
Query: 159 KIFIGGLPNYLNEDQAI 175
+I I L L ++ +
Sbjct: 212 EIMIRNLSTELLDENLL 228
Score = 46.1 bits (110), Expect = 3e-06
Identities = 14/114 (12%), Positives = 35/114 (30%), Gaps = 23/114 (20%)
Query: 26 TVAAAAAAAVPVVGSTITRQARRLYVGNIPFGVT-EDEMMEFFNQQMHLSGLAQAAGNPV 84
+ + T + R + + N+ + E+ + E F G+ +
Sbjct: 190 VTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEG----------FGS-I 238
Query: 85 LACQINLD-------KNFAFLEFRSIDETTQAMAFDGINFKGQSLKI----RRP 127
I AF+ F + D +A+ + + + + ++P
Sbjct: 239 EKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKKP 292
>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 = 54.0 bits (130), Expect = 6e-10
Identities = 19/98 (19%), Positives = 34/98 (34%), Gaps = 20/98 (20%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------ 92
GS+ + RL++G IP +E++E + VL +
Sbjct: 1 GSSGSSGNCRLFIGGIPKMKKREEILEEIAK----------VTEGVLDVIVYASAADKMK 50
Query: 93 -KNFAFLEFRSIDETTQA---MAFDGINFKGQSLKIRR 126
+ FAF+E+ S A + I G + +
Sbjct: 51 NRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW 88
Score = 26.3 bits (58), Expect = 4.3
Identities = 5/16 (31%), Positives = 10/16 (62%)
Query: 158 HKIFIGGLPNYLNEDQ 173
++FIGG+P ++
Sbjct: 9 CRLFIGGIPKMKKREE 24
>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 = 54.4 bits (131), Expect = 8e-10
Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 1/82 (1%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSI 103
R+YV N+ V E ++ F + + S Q + + K AF+ +
Sbjct: 43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNE 102
Query: 104 DETTQAM-AFDGINFKGQSLKI 124
+A+ +G G+ + +
Sbjct: 103 KAAAKALKEANGYVLFGKPMVV 124
Score = 27.9 bits (62), Expect = 1.5
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 173 QAIAGLNGMQLGDKKLIVQRA 193
+A+ NG L K ++VQ A
Sbjct: 107 KALKEANGYVLFGKPMVVQFA 127
>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 = 53.6 bits (129), Expect = 9e-10
Identities = 25/105 (23%), Positives = 40/105 (38%), Gaps = 17/105 (16%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSG-LAQAAGNPVLACQINLD------KNFA 96
+YV + VT D++ +FF Q G + I LD K A
Sbjct: 13 SDNSAIYVQGLNDSVTLDDLADFFKQ----CGVVKMNKRTGQPMIHIYLDKETGKPKGDA 68
Query: 97 FLEFRSIDETTQAM-AFDGINFKGQSLKI-----RRPHDYQPTPG 135
+ + A+ FDG +F+G LK+ + P + P+ G
Sbjct: 69 TVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSSG 113
Score = 25.8 bits (57), Expect = 6.2
Identities = 8/32 (25%), Positives = 10/32 (31%)
Query: 171 EDQAIAGLNGMQLGDKKLIVQRASVGAKNASG 202
A+ +G KL V A SG
Sbjct: 78 AKAAVEWFDGKDFQGSKLKVSLARKKPPMNSG 109
>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 = 53.4 bits (129), Expect = 1e-09
Identities = 19/101 (18%), Positives = 36/101 (35%), Gaps = 23/101 (22%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEF 100
+ LY+ N+ VTE +++ F + I + AF+ F
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARF-----------QEKKGPPIQFRMMTGRMRGQAFITF 74
Query: 101 RSIDETTQAM-AFDGINFKGQSLKI-----RRPHDYQPTPG 135
+ + QA+ +G G+ L I ++ P+ G
Sbjct: 75 PNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSSGPSSG 115
Score = 28.4 bits (64), Expect = 0.81
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
QA+ +NG +L K L+++
Sbjct: 81 WQALHLVNGYKLYGKILVIEFG 102
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 53.1 bits (128), Expect = 1e-09
Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 14/83 (16%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
RL+V P V E E+ E F G P+ +I FAF+EF +
Sbjct: 30 SNTRLFVRPFPLDVQESELNEIFGP----------FG-PMKEVKIL--NGFAFVEFEEAE 76
Query: 105 ETTQAM-AFDGINFKGQSLKIRR 126
+A+ G +F Q L++
Sbjct: 77 SAAKAIEEVHGKSFANQPLEVVY 99
Score = 29.2 bits (66), Expect = 0.43
Identities = 5/22 (22%), Positives = 11/22 (50%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
+AI ++G ++ L V +
Sbjct: 79 AKAIEEVHGKSFANQPLEVVYS 100
>2la6_A RNA-binding protein FUS; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative, RNA recognition; NMR {Homo sapiens}
Length = 99
Score = 52.7 bits (127), Expect = 1e-09
Identities = 17/89 (19%), Positives = 30/89 (33%), Gaps = 12/89 (13%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSG-LAQAAGNPVLACQINLD------KNFA 96
++V + VT + + ++F Q G + + D K A
Sbjct: 11 SDNNTIFVQGLGENVTIESVADYFKQ----IGIIKTNKKTGQPMINLYTDRETGKLKGEA 66
Query: 97 FLEFRSIDETTQAM-AFDGINFKGQSLKI 124
+ F A+ FDG F G +K+
Sbjct: 67 TVSFDDPPSAKAAIDWFDGKEFSGNPIKV 95
Score = 25.3 bits (56), Expect = 8.4
Identities = 5/24 (20%), Positives = 9/24 (37%)
Query: 171 EDQAIAGLNGMQLGDKKLIVQRAS 194
AI +G + + V A+
Sbjct: 76 AKAAIDWFDGKEFSGNPIKVSFAT 99
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 52.6 bits (127), Expect = 1e-09
Identities = 21/92 (22%), Positives = 42/92 (45%), Gaps = 16/92 (17%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD----KN 94
GS+ + A +++V N+PF T + + FN+ G+ VL I ++ K
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNE----------CGH-VLYADIKMENGKSKG 49
Query: 95 FAFLEFRSIDETTQAM-AFDGINFKGQSLKIR 125
++F S + +A +G+ G+ + +R
Sbjct: 50 CGVVKFESPEVAERACRMMNGMKLSGREIDVR 81
Score = 32.9 bits (76), Expect = 0.016
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRASVGAKNASG 202
++A +NGM+L +++ V+ + +SG
Sbjct: 62 ERACRMMNGMKLSGREIDVRIDRNASGPSSG 92
>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 = 52.6 bits (127), Expect = 1e-09
Identities = 15/99 (15%), Positives = 36/99 (36%), Gaps = 18/99 (18%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FA 96
+ L++GN+ + E+ ++ + +D F
Sbjct: 14 STTPFNLFIGNLNPNKSVAELKVAISEL-----------FAKNDLAV-VDVRTGTNRKFG 61
Query: 97 FLEFRSIDETTQAMAFDGINFKGQSLKIRRPHDYQPTPG 135
+++F S ++ +A+ G+ G +K+ +P T G
Sbjct: 62 YVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDGTRG 100
Score = 25.7 bits (57), Expect = 6.4
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 154 PDSPHKIFIGGLPNYLNEDQ 173
+P +FIG L + +
Sbjct: 14 STTPFNLFIGNLNPNKSVAE 33
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition
motif, RRM, RNA binding domain, RBD, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 53.1 bits (128), Expect = 2e-09
Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 17/88 (19%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFL 98
R ++V N+ + V ++ E F+ AG V+ I DK+ +
Sbjct: 13 RLGSTVFVANLDYKVGWKKLKEVFSM----------AGV-VVRADILEDKDGKSRGIGTV 61
Query: 99 EFRSIDETTQAM-AFDGINFKGQSLKIR 125
F E QA+ F+G + + ++
Sbjct: 62 TFEQSIEAVQAISMFNGQLLFDRPMHVK 89
Score = 27.7 bits (62), Expect = 1.4
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
QAI+ NG L D+ + V+
Sbjct: 70 VQAISMFNGQLLFDRPMHVKMD 91
>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 = 52.8 bits (127), Expect = 2e-09
Identities = 13/88 (14%), Positives = 33/88 (37%), Gaps = 15/88 (17%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFL 98
++ NIPF +T+ ++++F + A + +D N A +
Sbjct: 13 SAKVCAHITNIPFSITKMDVLQFL----------EGIPVDENAVHVLVDNNGQGLGQALV 62
Query: 99 EFRSIDETTQAMAFDGINFKGQSLKIRR 126
+F++ D+ ++ G+ +
Sbjct: 63 QFKNEDDARKSERLHRKKLNGREAFVHV 90
>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 = 54.5 bits (130), Expect = 2e-09
Identities = 20/89 (22%), Positives = 32/89 (35%), Gaps = 16/89 (17%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-----KNFAFLEFR 101
R +Y+ P T D++ E+ + VL Q+ K F+ F
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDK-----------GQVLNIQMRRTLHKAFKGSIFVVFD 158
Query: 102 SIDETTQAMAFDGINFKGQSLKIRRPHDY 130
SI+ + + G +K L I DY
Sbjct: 159 SIESAKKFVETPGQKYKETDLLILFKDDY 187
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 52.5 bits (126), Expect = 2e-09
Identities = 15/87 (17%), Positives = 28/87 (32%), Gaps = 11/87 (12%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRS 102
A +YVGN+P ++ + G+ L + AFL +
Sbjct: 16 APLAADVYVGNLPRDARVSDLKRALRE----------LGSVPLRLTWQGPRRRAFLHYPD 65
Query: 103 IDETTQAM-AFDGINFKGQSLKIRRPH 128
QA+ G+ +L++
Sbjct: 66 SAAAQQAVSCLQGLRLGTDTLRVALAR 92
Score = 28.6 bits (64), Expect = 0.61
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
QA++ L G++LG L V A
Sbjct: 70 QQAVSCLQGLRLGTDTLRVALA 91
>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 = 52.5 bits (126), Expect = 2e-09
Identities = 18/96 (18%), Positives = 34/96 (35%), Gaps = 16/96 (16%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSI 103
R R+ V +P + ++ + + AG+ V + D +EF
Sbjct: 13 RSENRVVVSGLPPSGSWQDLKDHMRE----------AGD-VCYADVYRD-GTGVVEFVRK 60
Query: 104 DETTQAMA-FDGINFKGQSLK---IRRPHDYQPTPG 135
++ T A+ D F+ + IR D +P
Sbjct: 61 EDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPS 96
>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 = 52.2 bits (126), Expect = 2e-09
Identities = 19/85 (22%), Positives = 33/85 (38%), Gaps = 18/85 (21%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEF 100
+YV N+PF +T +++ F++ G V+ I DK+ AF+ F
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSK----------YG-KVVKVTIMKDKDTRKSKGVAFILF 65
Query: 101 RSIDETTQAM-AFDGINFKGQSLKI 124
D A + G+ +K
Sbjct: 66 LDKDSAQNCTRAINNKQLFGRVIKA 90
>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 = 52.2 bits (126), Expect = 2e-09
Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 18/86 (20%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLE 99
+ LYVG++ F +TED + F G + + D K + F+
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEP----------FGK-IDNIVLMKDSDTGRSKGYGFIT 53
Query: 100 FRSIDETTQAM-AFDGINFKGQSLKI 124
F + +A+ +G G+ +++
Sbjct: 54 FSDSECARRALEQLNGFELAGRPMRV 79
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 52.1 bits (125), Expect = 3e-09
Identities = 18/92 (19%), Positives = 34/92 (36%), Gaps = 13/92 (14%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN--FAFLEF 100
++ R+L + NIP + + + Q G Q+N D + +
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQ----------YGVVESCEQVNTDSETAVVNVTY 61
Query: 101 RSIDETTQAM-AFDGINFKGQSLKIRRPHDYQ 131
S D+ QA+ +G + +LK+ D
Sbjct: 62 SSKDQARQALDKLNGFQLENFTLKVAYIPDEM 93
Score = 27.8 bits (62), Expect = 1.0
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 172 DQAIAGLNGMQLGDKKLIVQ 191
QA+ LNG QL + L V
Sbjct: 68 RQALDKLNGFQLENFTLKVA 87
>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 = 52.6 bits (126), Expect = 3e-09
Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 14/82 (17%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
R +++ +P VTE E++ G V + KN AF+E + +
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLP----------FG-KVTNLLMLKGKNQAFIEMNTEEAA 80
Query: 107 TQAMAF---DGINFKGQSLKIR 125
+ + +GQ + I+
Sbjct: 81 NTMVNYYTSVTPVLRGQPIYIQ 102
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 52.9 bits (127), Expect = 3e-09
Identities = 21/119 (17%), Positives = 39/119 (32%), Gaps = 21/119 (17%)
Query: 16 IPANVIIPETT---VAAAAAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMH 72
+P +V + R LYVG + V + + F
Sbjct: 30 LPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIP--- 86
Query: 73 LSGLAQAAGNPVLACQINLD------KNFAFLEFRSIDETTQAM-AFDGINFKGQSLKI 124
G + QI LD + FAF+EF ++ A+ + G+++++
Sbjct: 87 -------FG-DITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 137
>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 = 51.4 bits (124), Expect = 3e-09
Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 18/87 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
LY+ + G T+ ++++ G +++ + LDK + F++F
Sbjct: 7 GLYIRGLQPGTTDQDLVKLCQPY----------GK-IVSTKAILDKTTNKCKGYGFVDFD 55
Query: 102 SIDETTQAM-AFDGINFKGQSLKIRRP 127
S +A+ A + Q K P
Sbjct: 56 SPSAAQKAVTALKASGVQAQMAKQSGP 82
Score = 27.1 bits (61), Expect = 1.7
Identities = 7/84 (8%), Positives = 14/84 (16%), Gaps = 41/84 (48%)
Query: 154 PDSPHKIFIGGLPNYLNED----------------------------------------- 172
++I GL +
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 173 QAIAGLNGMQLGDKKLIVQRASVG 196
+A+ L + + S G
Sbjct: 62 KAVTALKASGVQAQMAKQSGPSSG 85
>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 = 52.3 bits (126), Expect = 3e-09
Identities = 15/95 (15%), Positives = 35/95 (36%), Gaps = 24/95 (25%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FA 96
+ + +++ N+ F E+ + E Q G + ++ L + A
Sbjct: 12 VTEGKTVFIRNLSFDSEEEALGEVLQQ----------FG-DLKYVRVVLHPDTEHSKGCA 60
Query: 97 FLEFRSIDETTQAMA-------FDGINFKGQSLKI 124
F +F + + + +A G+ G+ LK+
Sbjct: 61 FAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKV 95
>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 = 53.3 bits (129), Expect = 3e-09
Identities = 33/195 (16%), Positives = 61/195 (31%), Gaps = 82/195 (42%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFRS 102
L V +P +T+ E+ F G P+ C+I D +AF++F S
Sbjct: 6 LIVNYLPQDMTDRELYALFRA----------IG-PINTCRIMRDYKTGYSYGYAFVDFTS 54
Query: 103 IDETTQAM-AFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKIF 161
++ +A+ +GI + + LK+ +P + ++
Sbjct: 55 EMDSQRAIKVLNGITVRNKRLKVSYA---RPGGESIKDT------------------NLY 93
Query: 162 IGGLPNYLNEDQ-----------------------------------------AIAGLNG 180
+ LP + +DQ AI+ LN
Sbjct: 94 VTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN 153
Query: 181 MQL--GDKKLIVQRA 193
+ G + L V+ A
Sbjct: 154 VIPEGGSQPLSVRLA 168
Score = 40.2 bits (95), Expect = 1e-04
Identities = 18/90 (20%), Positives = 39/90 (43%), Gaps = 18/90 (20%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFA 96
+ + LYV N+P +T+D++ F + G+ ++ I D + A
Sbjct: 86 SIKDTNLYVTNLPRTITDDQLDTIFGKY----------GS-IVQKNILRDKLTGRPRGVA 134
Query: 97 FLEFRSIDETTQAM-AFDGINFKGQSLKIR 125
F+ + +E +A+ A + + +G S +
Sbjct: 135 FVRYNKREEAQEAISALNNVIPEGGSQPLS 164
Score = 27.2 bits (61), Expect = 3.6
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 167 NYLNE---DQAIAGLNGMQLGDKKLIVQRAS 194
++ +E +AI LNG+ + +K+L V A
Sbjct: 51 DFTSEMDSQRAIKVLNGITVRNKRLKVSYAR 81
>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 = 52.4 bits (126), Expect = 3e-09
Identities = 21/94 (22%), Positives = 40/94 (42%), Gaps = 23/94 (24%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEF 100
L V + TE ++ E F++ G P+ I D + FAF+ F
Sbjct: 47 CCLGVFGLSLYTTERDLREVFSKY----G-------PIADVSIVYDQQSRRSRGFAFVYF 95
Query: 101 RSIDETTQAM-AFDGINFKGQSLKI-----RRPH 128
++D+ +A +G+ G+ +++ +RPH
Sbjct: 96 ENVDDAKEAKERANGMELDGRRIRVDFSITKRPH 129
>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 = 51.5 bits (124), Expect = 4e-09
Identities = 25/113 (22%), Positives = 50/113 (44%), Gaps = 17/113 (15%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFL 98
GS+ + + L+V N+ VTE+ + + F+Q G + + K++AF+
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQ----------FG-KLERVKKL--KDYAFI 50
Query: 99 EFRSIDETTQAM-AFDGINFKGQSLKI---RRPHDYQPTPGVTDNAAVAVPAG 147
F D +AM +G + +G++++I + P + AA +G
Sbjct: 51 HFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103
Score = 26.1 bits (58), Expect = 5.3
Identities = 5/22 (22%), Positives = 11/22 (50%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
+A+ +NG L + + + A
Sbjct: 59 VKAMEEMNGKDLEGENIEIVFA 80
>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 = 52.9 bits (128), Expect = 4e-09
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 17/86 (19%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEF 100
+++VG I V E EFF+Q G ++ Q+ LDK+ F F+ +
Sbjct: 88 GKIFVGGIGPDVRPKEFEEFFSQW----------GT-IIDAQLMLDKDTGQSRGFGFVTY 136
Query: 101 RSIDETTQAMAFDGINFKGQSLKIRR 126
S D + I+FK + ++I+R
Sbjct: 137 DSADAVDRVCQNKFIDFKDRKIEIKR 162
Score = 52.5 bits (127), Expect = 6e-09
Identities = 23/136 (16%), Positives = 45/136 (33%), Gaps = 39/136 (28%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAF 97
+++ ++++G + + TED + E+F + G V +I D F F
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGK----------YG-TVTDLKIMKDPATGRSRGFGF 49
Query: 98 LEFRSIDETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSP 157
L F + + G+ + +R I D
Sbjct: 50 LSFEKPSSVDEVVK-TQHILDGKVIDPKRA---------------------IPRDEQDKT 87
Query: 158 HKIFIGGLPNYLNEDQ 173
KIF+GG+ + +
Sbjct: 88 GKIFVGGIGPDVRPKE 103
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 51.5 bits (124), Expect = 5e-09
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 16/85 (18%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD----KNFAFLEF 100
Q +RL+V NIPF + ++ + F Q G +L +I + K F F+ F
Sbjct: 28 QPKRLHVSNIPFRFRDPDLRQMFGQ----------FG-KILDVEIIFNERGSKGFGFVTF 76
Query: 101 RSIDETTQAM-AFDGINFKGQSLKI 124
+ + +A G +G+ +++
Sbjct: 77 ENSADADRAREKLHGTVVEGRKIEV 101
Score = 28.1 bits (63), Expect = 0.97
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
D+A L+G + +K+ V A
Sbjct: 83 DRAREKLHGTVVEGRKIEVNNA 104
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 51.1 bits (123), Expect = 5e-09
Identities = 19/90 (21%), Positives = 33/90 (36%), Gaps = 13/90 (14%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-KNFAFLEFRSIDET 106
++YVGN+ G + E+ F+ G P+ I + FAF+EF +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSY----------YG-PLRTVWIARNPPGFAFVEFEDPRDA 50
Query: 107 TQAM-AFDGINFKGQSLKIRRPHDYQPTPG 135
A+ DG G +++
Sbjct: 51 EDAVRGLDGKVICGSRVRVELSTGMPRRSR 80
>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 = 51.1 bits (123), Expect = 5e-09
Identities = 21/101 (20%), Positives = 42/101 (41%), Gaps = 21/101 (20%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN----FAFLEF 100
+RL+V NIPF + ++ + F Q G +L +I ++ F F+ F
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQ----------FGK-ILDVEIIFNERGSKGFGFVTF 62
Query: 101 RSIDETTQAM-AFDGINFKGQSLKI-----RRPHDYQPTPG 135
+ + +A G +G+ +++ R + P+ G
Sbjct: 63 ENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPSSG 103
Score = 26.9 bits (60), Expect = 2.9
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
D+A L+G + +K+ V A
Sbjct: 69 DRAREKLHGTVVEGRKIEVNNA 90
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 51.6 bits (124), Expect = 6e-09
Identities = 17/89 (19%), Positives = 30/89 (33%), Gaps = 12/89 (13%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSG-LAQAAGNPVLACQINLD------KNFA 96
++V + VT + + ++F Q G + + D K A
Sbjct: 5 SDNNTIFVQGLGENVTIESVADYFKQ----IGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 97 FLEFRSIDETTQAM-AFDGINFKGQSLKI 124
+ F A+ FDG F G +K+
Sbjct: 61 TVSFDDPPSAKAAIDWFDGKEFSGNPIKV 89
>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 = 51.4 bits (123), Expect = 6e-09
Identities = 18/106 (16%), Positives = 30/106 (28%), Gaps = 13/106 (12%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSI 103
R + N+P G E+ E F++ G + + A +EF
Sbjct: 8 RSKTVILAKNLPAGTLAAEIQETFSR----------FG-SLGRVLLPEGGITAIVEFLEP 56
Query: 104 DETTQAM-AFDGINFKGQSLKIRR-PHDYQPTPGVTDNAAVAVPAG 147
E +A F L + P ++ PA
Sbjct: 57 LEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAE 102
>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 = 50.7 bits (122), Expect = 7e-09
Identities = 14/94 (14%), Positives = 32/94 (34%), Gaps = 18/94 (19%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
LY+GN+ + T++++ E N +L + ++ FA +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAV---------HSLGVNDILEIKFFENRANGQSKGFALVGVG 53
Query: 102 SIDETTQAM-AFDGINFKGQSLKIR--RPHDYQP 132
S + + M GQ+ + ++
Sbjct: 54 SEASSKKLMDLLPKRELHGQNPVVTPSNKLEHHH 87
>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 = 50.7 bits (122), Expect = 7e-09
Identities = 20/93 (21%), Positives = 35/93 (37%), Gaps = 18/93 (19%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---- 94
S + R LYVG + V + + F G + QI LD
Sbjct: 5 SSGMATTKRVLYVGGLAEEVDDKVLHAAFIP----------FG-DITDIQIPLDYETEKH 53
Query: 95 --FAFLEFRSIDETTQAM-AFDGINFKGQSLKI 124
FAF+EF ++ A+ + G+++++
Sbjct: 54 RGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 86
>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 = 50.7 bits (122), Expect = 8e-09
Identities = 21/100 (21%), Positives = 34/100 (34%), Gaps = 23/100 (23%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
L V N+ + + D + F + G V I + + FAF+ F
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEK----------YG-RVGDVYIPREPHTKAPRGFAFVRFH 63
Query: 102 SIDETTQAM-AFDGINFKGQSLKI-----RRPHDYQPTPG 135
+ A A DG G+ L++ R P+ G
Sbjct: 64 DRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPSSG 103
Score = 26.4 bits (59), Expect = 3.8
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 171 EDQAIAGLNGMQLGDKKLIVQRASVGAKNASG 202
A A ++G +L ++L VQ A G ++ SG
Sbjct: 68 AQDAEAAMDGAELDGRELRVQVARYGRRDLSG 99
>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 = 50.8 bits (122), Expect = 9e-09
Identities = 23/100 (23%), Positives = 42/100 (42%), Gaps = 18/100 (18%)
Query: 32 AAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINL 91
AAA+ + RLYVG++ F +TED + F G + + Q+ +
Sbjct: 12 AAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEP----------FG-RIESIQLMM 60
Query: 92 D------KNFAFLEFRSIDETTQAM-AFDGINFKGQSLKI 124
D K + F+ F + +A+ +G G+ +K+
Sbjct: 61 DSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100
>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 = 50.8 bits (122), Expect = 9e-09
Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 20/90 (22%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-------FA 96
+ ++ V NIPF + E+ E F+ G + ++ F
Sbjct: 13 QTTSKILVRNIPFQANQREIRELFST----------FG-ELKTVRLPKKMTGTGAHRGFG 61
Query: 97 FLEFRSIDETTQAMA--FDGINFKGQSLKI 124
F++F + + +A + G+ L +
Sbjct: 62 FVDFITKQDAKKAFNALCHSTHLYGRRLVL 91
>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 = 50.3 bits (121), Expect = 9e-09
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 11/82 (13%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSI 103
R AR L N+ F +TEDE+ E F A L Q K A++EF+S
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFED----------ALEIRLVSQDGKSKGIAYIEFKSE 63
Query: 104 DETTQAM-AFDGINFKGQSLKI 124
+ + + G G+S+ +
Sbjct: 64 ADAEKNLEEKQGAEIDGRSVSL 85
>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 = 50.2 bits (121), Expect = 9e-09
Identities = 19/88 (21%), Positives = 34/88 (38%), Gaps = 18/88 (20%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAF 97
R LYVG + V + + F G + QI LD + FAF
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIP----------FG-DITDIQIPLDYETEKHRGFAF 53
Query: 98 LEFRSIDETTQAM-AFDGINFKGQSLKI 124
+EF ++ A+ + G+++++
Sbjct: 54 VEFELAEDAAAAIDNMNESELFGRTIRV 81
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 50.0 bits (120), Expect = 1e-08
Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 13/84 (15%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSI 103
+ LYVG + +TE ++ F Q G + + + AF++F +
Sbjct: 10 KTITTLYVGGLGDTITETDLRNHFYQ----FG-------EIRTITVVQRQQCAFIQFATR 58
Query: 104 DETTQAM--AFDGINFKGQSLKIR 125
A +F+ + G+ L ++
Sbjct: 59 QAAEVAAEKSFNKLIVNGRRLNVK 82
>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 = 50.6 bits (121), Expect = 1e-08
Identities = 19/101 (18%), Positives = 35/101 (34%), Gaps = 16/101 (15%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFL 98
G R R+ V +P + ++ + + AG+ V + D +
Sbjct: 9 GPPSRRSENRVVVSGLPPSGSWQDLKDHMRE----------AGD-VCYADVYRD-GTGVV 56
Query: 99 EFRSIDETTQAMA-FDGINFKGQSLK---IRRPHDYQPTPG 135
EF ++ T A+ D F+ + IR D +P
Sbjct: 57 EFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPS 97
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 50.1 bits (120), Expect = 1e-08
Identities = 12/81 (14%), Positives = 28/81 (34%), Gaps = 14/81 (17%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
+++ + GV E +++E + P+ + K A +EF +
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQE-----------FGPISYVVVMPKKRQALVEFEDVLGA 70
Query: 107 TQAMAF---DGINFKGQSLKI 124
A+ + + I G +
Sbjct: 71 CNAVNYAADNQIYIAGHPAFV 91
>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 = 51.4 bits (123), Expect = 1e-08
Identities = 23/94 (24%), Positives = 34/94 (36%), Gaps = 23/94 (24%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
L V N+ + + D + F + G V I D+ FAF+ F
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEK----------YG-RVGDVYIPRDRYTKESRGFAFVRFH 120
Query: 102 SIDETTQAM-AFDGINFKGQSLKI-----RRPHD 129
+ AM A DG G+ L++ RP D
Sbjct: 121 DKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD 154
>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 = 49.9 bits (120), Expect = 2e-08
Identities = 22/104 (21%), Positives = 41/104 (39%), Gaps = 25/104 (24%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFRS 102
++VG I + E E+ FF + G+ V +I D+ + F+ F +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFAR----------YGS-VKEVKIITDRTGVSKGYGFVSFYN 59
Query: 103 IDETTQAMAFDGINFKGQSLKI--------RRPHDYQPTPGVTD 138
+ + + INF G+ LK+ + QP P + +
Sbjct: 60 DVDVQKIVE-SQINFHGKKLKLGPAIRKQNLSTYHVQPRPLIFN 102
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 49.8 bits (119), Expect = 2e-08
Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 14/82 (17%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
R L++ +P VTE E++ G V + KN AFLE + +
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLP----------FG-KVTNILMLKGKNQAFLELATEEAA 64
Query: 107 TQAMAF---DGINFKGQSLKIR 125
+ + + + Q + I+
Sbjct: 65 ITMVNYYSAVTPHLRNQPIYIQ 86
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 49.9 bits (119), Expect = 2e-08
Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 14/82 (17%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
R +++ +P VTE E++ G V + KN AF+E + +
Sbjct: 17 RVIHIRKLPIDVTEGEVISLG----------LPFG-KVTNLLMLKGKNQAFIEMNTEEAA 65
Query: 107 TQAMAF---DGINFKGQSLKIR 125
+ + +GQ + I+
Sbjct: 66 NTMVNYYTSVTPVLRGQPIYIQ 87
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 49.5 bits (119), Expect = 2e-08
Identities = 20/96 (20%), Positives = 37/96 (38%), Gaps = 21/96 (21%)
Query: 48 RLYVGNIPF-GVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
RL++GN+P V+++++ F+ H+ QIN+ F F++F +
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIM-------------QINIKNAFGFIQFDNPQSV 58
Query: 107 TQAM-AFDGINFKGQSLKI------RRPHDYQPTPG 135
A+ G+ L + RP G
Sbjct: 59 RDAIECESQEMNFGKKLILEVSSSNARPQFDHGDHG 94
Score = 28.3 bits (64), Expect = 0.68
Identities = 8/35 (22%), Positives = 13/35 (37%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRASVGAKNASGQQAP 206
AI + KKLI++ +S A+
Sbjct: 59 RDAIECESQEMNFGKKLILEVSSSNARPQFDHGDH 93
>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 = 49.5 bits (119), Expect = 2e-08
Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 12/80 (15%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
RL+VG + + + F++ G + +FA++++ S+D
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDR----------FG-SIRTIDHVKGDSFAYIQYESLDAA 66
Query: 107 TQAM-AFDGINFKGQSLKIR 125
A G G ++R
Sbjct: 67 QAACAKMRGFPLGGPDRRLR 86
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 50.5 bits (121), Expect = 2e-08
Identities = 23/96 (23%), Positives = 34/96 (35%), Gaps = 23/96 (23%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLE 99
L V N+ + + D + F + G V I D+ FAF+
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKY----G-------RVGDVYIPRDRYTKESRGFAFVR 95
Query: 100 FRSIDETTQAM-AFDGINFKGQSLKI-----RRPHD 129
F + AM A DG G+ L++ RP D
Sbjct: 96 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD 131
>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 = 49.5 bits (119), Expect = 2e-08
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 17/85 (20%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEF 100
R +YVGN+ + T +++ E F+Q G V ++ D+ F F+E
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQ----------FG-KVFNVKLIYDRETKKPKGFGFVEM 50
Query: 101 RSIDETTQAMAFDGINFKGQSLKIR 125
+ + D +F G+++++
Sbjct: 51 QEESVSEAIAKLDNTDFMGRTIRVT 75
>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 = 49.2 bits (118), Expect = 3e-08
Identities = 20/108 (18%), Positives = 50/108 (46%), Gaps = 25/108 (23%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---- 94
ST + +++ L + N+ + TE+ + E F + A ++ ++N
Sbjct: 8 NSTWSGESKTLVLSNLSYSATEETLQEVFEK----------ATF----IKVPQNQNGKSK 53
Query: 95 -FAFLEFRSIDETTQAM-AFDGINFKGQSLKI-----RRPHDYQPTPG 135
+AF+EF S ++ +A+ + + +G+++++ R + P+ G
Sbjct: 54 GYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSSG 101
>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 = 49.4 bits (118), Expect = 3e-08
Identities = 19/100 (19%), Positives = 36/100 (36%), Gaps = 22/100 (22%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
++V + V E +++E + G + + K A +EF +ID
Sbjct: 16 PVVHVRGLCESVVEADLVEALEK----------FG-TICYVMMMPFKRQALVEFENIDSA 64
Query: 107 TQAMAF---DGINFKGQSL--------KIRRPHDYQPTPG 135
+ + F + GQ +I RP + P+ G
Sbjct: 65 KECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104
>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 = 49.1 bits (118), Expect = 3e-08
Identities = 17/98 (17%), Positives = 33/98 (33%), Gaps = 21/98 (21%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
+ V N+ E ++ E F G + + DK FAF+ F
Sbjct: 17 TIRVTNLSEDTRETDLQELFRP----------FG-SISRIYLAKDKTTGQSKGFAFISFH 65
Query: 102 SIDETTQAM-AFDGINFKGQSLKI---RRPHDYQPTPG 135
++ +A+ G + L + + + P+ G
Sbjct: 66 RREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103
Score = 25.6 bits (57), Expect = 7.4
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 171 EDQAIAGLNGMQLGDKKLIVQRA 193
+AIAG++G L V+ A
Sbjct: 70 AARAIAGVSGFGYDHLILNVEWA 92
>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 = 48.9 bits (117), Expect = 3e-08
Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 15/84 (17%)
Query: 47 RRLYVGNIPF-GVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
RL++GN+P V+++++ F+ H+ QIN+ F F++F +
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIM-------------QINIKNAFGFIQFDNPQS 69
Query: 106 TTQAMA-FDGINFKGQSLKIRRPH 128
A+ G+ L +
Sbjct: 70 VRDAIEXESQEMNFGKKLILEVSS 93
Score = 27.7 bits (62), Expect = 1.2
Identities = 18/86 (20%), Positives = 27/86 (31%), Gaps = 37/86 (43%)
Query: 150 STVVPDSPH---KIFIGGLP----------------------------------NYLNED 172
S +VP H ++FIG LP N +
Sbjct: 12 SGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVR 71
Query: 173 QAIAGLNGMQLGDKKLIVQRASVGAK 198
AI + KKLI++ +S A+
Sbjct: 72 DAIEXESQEMNFGKKLILEVSSSNAR 97
>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 = 50.7 bits (122), Expect = 4e-08
Identities = 24/139 (17%), Positives = 43/139 (30%), Gaps = 41/139 (29%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN--------FAF 97
A +++VG +P +E ++ E F Q G V + D++ F
Sbjct: 3 AIKMFVGQVPRTWSEKDLRELFEQ----------YG-AVYEINVLRDRSQNPPQSKGCCF 51
Query: 98 LEFRSIDETTQAM-AFDGINFKGQSLK--IRRPHDYQPTPGVTDNAAVAVPAGVISTVVP 154
+ F + +A A + +P D + V D
Sbjct: 52 VTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVED---------------- 95
Query: 155 DSPHKIFIGGLPNYLNEDQ 173
K+FIG + E+
Sbjct: 96 ---RKLFIGMISKKCTEND 111
Score = 41.4 bits (98), Expect = 6e-05
Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 16/72 (22%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLE 99
+ R+L++G I TE+++ F+ G + C+I + AF+
Sbjct: 94 EDRKLFIGMISKKCTENDIRVMFSSF----------GQ-IEECRILRGPDGLSRGCAFVT 142
Query: 100 FRSIDETTQAMA 111
F + A+
Sbjct: 143 FTTRAMAQTAIK 154
Score = 26.0 bits (58), Expect = 9.2
Identities = 3/22 (13%), Positives = 8/22 (36%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
+A L+ M++ +
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQM 82
>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 = 48.8 bits (117), Expect = 4e-08
Identities = 17/84 (20%), Positives = 33/84 (39%), Gaps = 16/84 (19%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFRSI 103
+ V N+PF V+ DE+++FF + + ++ A + F S
Sbjct: 18 IKVQNMPFTVSIDEILDFFYG----------YQVIPGSVCLKYNEKGMPTGEAMVAFESR 67
Query: 104 DETTQAMA-FDGINFKGQSLKIRR 126
DE T A+ + + +K+
Sbjct: 68 DEATAAVIDLNDRPIGSRKVKLVL 91
>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 = 49.9 bits (119), Expect = 4e-08
Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 13/85 (15%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-KNFAFLEFRSIDE 105
++YVGN+ + E+ F G P+ + + + FAF+EF +
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGY----------YG-PLRSVWVARNPPGFAFVEFEDPRD 122
Query: 106 TTQAM-AFDGINFKGQSLKIRRPHD 129
A+ DG G +++ +
Sbjct: 123 AADAVRELDGRTLCGCRVRVELSNG 147
>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 = 48.9 bits (117), Expect = 4e-08
Identities = 20/96 (20%), Positives = 41/96 (42%), Gaps = 20/96 (20%)
Query: 47 RRLYVGNIPF-GVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
R+++GN+ V + ++ F++ G V C ++ K +AF+++ +
Sbjct: 28 SRVFIGNLNTALVKKSDVETIFSK----------YG-RVAGCSVH--KGYAFVQYSNERH 74
Query: 106 TTQAM-AFDGINFKGQSLKI-----RRPHDYQPTPG 135
A+ +G GQ+L I +P P+ G
Sbjct: 75 ARAAVLGENGRVLAGQTLDINMAGEPKPDRSGPSSG 110
Score = 29.7 bits (67), Expect = 0.31
Identities = 9/31 (29%), Positives = 13/31 (41%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRASVGAKNASG 202
A+ G NG L + L + A + SG
Sbjct: 76 RAAVLGENGRVLAGQTLDINMAGEPKPDRSG 106
>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 = 49.5 bits (118), Expect = 5e-08
Identities = 14/93 (15%), Positives = 36/93 (38%), Gaps = 15/93 (16%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---- 94
S + + + +PFG T++E+++FF+ + +D
Sbjct: 35 NSADSANDGFVRLRGLPFGCTKEEIVQFFSG----------LEIVPNGITLPVDPEGKIT 84
Query: 95 -FAFLEFRSIDETTQAMAFDGINFKGQSLKIRR 126
AF++F S + +A+ + +++ +
Sbjct: 85 GEAFVQFASQELAEKALGKHKERIGHRYIEVFK 117
>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 = 48.5 bits (116), Expect = 5e-08
Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 16/86 (18%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFRS 102
+ V N+PF V+ DE+++FF + + ++ A + F S
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYG----------YQVIPGSVCLKYNEKGMPTGEAMVAFES 66
Query: 103 IDETTQAMA-FDGINFKGQSLKIRRP 127
DE T A+ + + +K+ P
Sbjct: 67 RDEATAAVIDLNDRPIGSRKVKLSGP 92
>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 = 47.9 bits (115), Expect = 6e-08
Identities = 18/85 (21%), Positives = 38/85 (44%), Gaps = 19/85 (22%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-------FAFLEF 100
++++G + VT+D +ME F+ G + + +++ +A++EF
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFST----------YG-KIKMIDMPVERMHPHLSKGYAYVEF 54
Query: 101 RSIDETTQAM-AFDGINFKGQSLKI 124
+ DE +A+ DG GQ +
Sbjct: 55 ENPDEAEKALKHMDGGQIDGQEITA 79
Score = 25.6 bits (57), Expect = 5.8
Identities = 3/23 (13%), Positives = 12/23 (52%)
Query: 171 EDQAIAGLNGMQLGDKKLIVQRA 193
++A+ ++G Q+ +++
Sbjct: 60 AEKALKHMDGGQIDGQEITATAV 82
>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 = 48.4 bits (116), Expect = 6e-08
Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 18/85 (21%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEF 100
L V + TE ++ E F++ G P+ I D+ FAF+ F
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSK----------YG-PIADVSIVYDQQSRRSRGFAFVYF 64
Query: 101 RSIDETTQAM-AFDGINFKGQSLKI 124
++D+ +A +G+ G+ +++
Sbjct: 65 ENVDDAKEAKERANGMELDGRRIRV 89
Score = 26.4 bits (59), Expect = 2.8
Identities = 14/84 (16%), Positives = 20/84 (23%), Gaps = 41/84 (48%)
Query: 154 PDSPHKIFIGGLPNYLNEDQ---------------------------------------- 173
PD + + GL Y E
Sbjct: 12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAK 71
Query: 174 -AIAGLNGMQLGDKKLIVQRASVG 196
A NGM+L +++ V S G
Sbjct: 72 EAKERANGMELDGRRIRVSGPSSG 95
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 49.5 bits (118), Expect = 6e-08
Identities = 14/135 (10%), Positives = 41/135 (30%), Gaps = 18/135 (13%)
Query: 10 TGAAGQIPANVIIPETTVAAAAAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFNQ 69
+ + P V + A+ S + + +YVG+ + T+ ++++
Sbjct: 19 YFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVI-- 76
Query: 70 QMHLSGLAQAAGNPVLACQINLDKN------FAFLEFRSIDETTQAM-AFDGINFKGQSL 122
V+ + ++ +A + S + + + G G+ +
Sbjct: 77 -------RSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV 129
Query: 123 KIR--RPHDYQPTPG 135
+R +
Sbjct: 130 DVRPATRQNLSQFEA 144
Score = 26.4 bits (58), Expect = 5.1
Identities = 12/94 (12%), Positives = 31/94 (32%), Gaps = 6/94 (6%)
Query: 104 DETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKIFIG 163
+ + N QS++ P +P+P + + + + +++G
Sbjct: 5 HHHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTP---AILYTYSGLRNRRAAVYVG 61
Query: 164 GLPNYLNED---QAIAGLNGMQLGDKKLIVQRAS 194
+ + Q I + + + K RA+
Sbjct: 62 SFSWWTTDQQLIQVIRSIGVYDVVELKFAENRAN 95
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 48.7 bits (116), Expect = 7e-08
Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 12/93 (12%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNP--VLACQINLDKNFAFLEF 100
T ++ + + NI V ++++ L LA + G+ ++ + + A++ F
Sbjct: 26 TEPSQVVLITNINPEVPKEKLQA------LLYALASSQGDILDIVVDLSDDNSGKAYIVF 79
Query: 101 RSIDETTQAM-AFDGINFKGQSLKI---RRPHD 129
+ + + AF G F+G L I P
Sbjct: 80 ATQESAQAFVEAFQGYPFQGNPLVITFSETPQS 112
>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 = 48.2 bits (115), Expect = 8e-08
Identities = 14/83 (16%), Positives = 32/83 (38%), Gaps = 17/83 (20%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFRSI 103
+ V +PF E+++ +FF G V A + D ++F S
Sbjct: 19 VSVHGMPFSAMENDVRDFF------------HGLRVDAVHLLKDHVGRNNGNGLVKFLSP 66
Query: 104 DETTQAMAFDGINFKGQSLKIRR 126
+T +A+ + + + +++
Sbjct: 67 QDTFEALKRNRMLMIQRYVEVSP 89
>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 = 47.8 bits (114), Expect = 1e-07
Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 7/85 (8%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-FAFLEFR 101
T + + +PFG +++E+++FF SGL L AF++F
Sbjct: 12 TANDGFVRLRGLPFGCSKEEIVQFF------SGLEIVPNGMTLPVDFQGRSTGEAFVQFA 65
Query: 102 SIDETTQAMAFDGINFKGQSLKIRR 126
S + +A+ + ++I +
Sbjct: 66 SQEIAEKALKKHKERIGHRYIEIFK 90
>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 = 47.2 bits (113), Expect = 2e-07
Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 17/88 (19%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
++ +++VG IP E E+ E+F + G V + D F F+
Sbjct: 9 KSNKIFVGGIPHNCGETELREYFKKF----------GV-VTEVVMIYDAEKQRPRGFGFI 57
Query: 99 EFRSIDETTQAMAFDGINFKGQSLKIRR 126
F QA+ + G+ ++++R
Sbjct: 58 TFEDEQSVDQAVNMHFHDIMGKKVEVKR 85
Score = 26.0 bits (58), Expect = 5.2
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 154 PDSPHKIFIGGLPNYLNEDQ 173
+KIF+GG+P+ E +
Sbjct: 7 GSKSNKIFVGGIPHNCGETE 26
>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 = 47.2 bits (113), Expect = 2e-07
Identities = 21/109 (19%), Positives = 43/109 (39%), Gaps = 23/109 (21%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---- 94
S + +L+VG + F E + + F++ G + + D+
Sbjct: 5 SSGMASDEGKLFVGGLSFDTNEQSLEQVFSK----------YG-QISEVVVVKDRETQRS 53
Query: 95 --FAFLEFRSIDETTQAM-AFDGINFKGQSLKI-----RRPHDYQPTPG 135
F F+ F +ID+ AM A +G + G+ +++ + P+ G
Sbjct: 54 RGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSSG 102
>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 = 46.8 bits (112), Expect = 2e-07
Identities = 16/90 (17%), Positives = 37/90 (41%), Gaps = 14/90 (15%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD---KNFAFLEFRSI 103
+Y+ N+ + +DE+ + L + G +L ++ + AF+ F+ +
Sbjct: 9 HTIYINNLNEKIKKDELKK------SLHAIFSRFG-QILDILVSRSLKMRGQAFVIFKEV 61
Query: 104 DETTQAM-AFDGINFKGQSLKI---RRPHD 129
T A+ + G F + ++I + D
Sbjct: 62 SSATNALRSMQGFPFYDKPMRIQYAKTDSD 91
Score = 27.2 bits (61), Expect = 2.0
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 173 QAIAGLNGMQLGDKKLIVQRA 193
A+ + G DK + +Q A
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>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 = 46.5 bits (111), Expect = 2e-07
Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 17/83 (20%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFRSI 103
+ + PF VTE +MEF A +A +I + + + F++F +
Sbjct: 13 VKLRGAPFNVTEKNVMEFL------------APLKPVAIRIVRNAHGNKTGYIFVDFSNE 60
Query: 104 DETTQAMAFDGINFKGQSLKIRR 126
+E QA+ + G+ +++ R
Sbjct: 61 EEVKQALKCNREYMGGRYIEVFR 83
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 49.8 bits (118), Expect = 2e-07
Identities = 15/91 (16%), Positives = 30/91 (32%), Gaps = 18/91 (19%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEF 100
+ L+V + + TE ++ F G P+ + K +AF+E+
Sbjct: 103 KTLFVARVNYDTTESKLRREFEV----YG-------PIKRIHMVYSKRSGKPRGYAFIEY 151
Query: 101 RSIDETTQAMA-FDGINFKGQSLKIRRPHDY 130
+ A DG G+ + +
Sbjct: 152 EHERDMHSAYKHADGKKIDGRRVLVDVERGR 182
>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 = 46.5 bits (111), Expect = 3e-07
Identities = 17/105 (16%), Positives = 38/105 (36%), Gaps = 26/105 (24%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FA 96
++ ++ L+V + TE+ + E F+ + +I D+ F
Sbjct: 12 SQPSKTLFVKGLSEDTTEETLKESFDG--------------SVRARIVTDRETGSSKGFG 57
Query: 97 FLEFRSIDETTQAM-AFDGINFKGQSLKI-----RRPHDYQPTPG 135
F++F S ++ A A + G + + + P+ G
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSSG 102
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 47.1 bits (112), Expect = 3e-07
Identities = 13/89 (14%), Positives = 28/89 (31%), Gaps = 15/89 (16%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAF 97
+Y+ +PF +++FF L + I N F
Sbjct: 22 HEAGFCVYLKGLPFEAENKHVIDFF------KKL----DIVEDSIYIAYGPNGKATGEGF 71
Query: 98 LEFRSIDETTQAMAFDGINFKGQSLKIRR 126
+EFR+ + A+ + +++
Sbjct: 72 VEFRNEADYKAALCRHKQYMGNRFIQVHP 100
>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 = 45.9 bits (109), Expect = 4e-07
Identities = 14/89 (15%), Positives = 36/89 (40%), Gaps = 17/89 (19%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAF 97
+ +++ +P+ TE+++ FF + + I + + A
Sbjct: 12 STTGHCVHMRGLPYRATENDIYNFF------------SPLNPMRVHIEIGPDGRVTGEAD 59
Query: 98 LEFRSIDETTQAMAFDGINFKGQSLKIRR 126
+EF + ++ AMA D N + + +++
Sbjct: 60 VEFATHEDAVAAMAKDKANMQHRYVELFL 88
>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 = 46.8 bits (111), Expect = 5e-07
Identities = 14/89 (15%), Positives = 36/89 (40%), Gaps = 17/89 (19%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAF 97
+ +++ +P+ TE+++ FF + + I + + A
Sbjct: 43 STTGHCVHMRGLPYKATENDIYNFF------------SPLNPVRVHIEIGPDGRVTGEAD 90
Query: 98 LEFRSIDETTQAMAFDGINFKGQSLKIRR 126
+EF + +E AM+ D N + + +++
Sbjct: 91 VEFATHEEAVAAMSKDRANMQHRYIELFL 119
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 46.0 bits (109), Expect = 6e-07
Identities = 14/104 (13%), Positives = 33/104 (31%), Gaps = 12/104 (11%)
Query: 28 AAAAAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLAC 87
++ + V + + +PF T +E++ FF Q ++G
Sbjct: 5 SSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITG-------GKEGI 57
Query: 88 QINLDKN-----FAFLEFRSIDETTQAMAFDGINFKGQSLKIRR 126
+ AF+ F + A+ + +++ R
Sbjct: 58 LFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFR 101
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi}
SCOP: d.58.7.1
Length = 139
Score = 46.7 bits (111), Expect = 6e-07
Identities = 23/129 (17%), Positives = 42/129 (32%), Gaps = 21/129 (16%)
Query: 17 PANVIIPETTVAAAAAAAVPVVGSTITRQA-RRLYVGNIPFGVTEDEMMEFFNQQMHLSG 75
P + +P R L V IP V E ++ + F +
Sbjct: 12 PYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFER------ 65
Query: 76 LAQAAGNPVLACQINLDKN------FAFLEFRSIDETTQAM-AFDGINFKGQSLKIR--R 126
G + + +I D+ + F++F+S QA+ +G N + LK+
Sbjct: 66 ----YGP-IESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA 120
Query: 127 PHDYQPTPG 135
+P
Sbjct: 121 SGHQRPGIA 129
Score = 28.9 bits (65), Expect = 0.67
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
QAIAGLNG + +K+L V A
Sbjct: 98 QQAIAGLNGFNILNKRLKVALA 119
>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 = 45.3 bits (108), Expect = 7e-07
Identities = 18/91 (19%), Positives = 37/91 (40%), Gaps = 21/91 (23%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---------FAFL 98
L++ N+ F TE+ + F++ + +C I+ KN F F+
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKV-----------GAIKSCTISKKKNKAGVLLSMGFGFV 55
Query: 99 EFRSIDETTQAM-AFDGINFKGQSLKIRRPH 128
E++ ++ +A+ G G L++R
Sbjct: 56 EYKKPEQAQKALKQLQGHTVDGHKLEVRISE 86
Score = 29.5 bits (67), Expect = 0.24
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRASVGAKNASG 202
+A+ L G + KL V+ + K ASG
Sbjct: 64 QKALKQLQGHTVDGHKLEVRISERATKPASG 94
>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 = 47.2 bits (112), Expect = 8e-07
Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 13/81 (16%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLAC-QINLDKNFAFLEFRSIDE 105
L++ NIP V+E+++ F+ G V D+ A ++ S++E
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSN----------GGVVKGFKFFQKDRKMALIQMGSVEE 170
Query: 106 TTQAM-AFDGINFK-GQSLKI 124
QA+ + L++
Sbjct: 171 AVQALIDLHNHDLGENHHLRV 191
Score = 26.4 bits (58), Expect = 6.3
Identities = 6/22 (27%), Positives = 12/22 (54%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
A++ LNG +L K + + +
Sbjct: 55 QLAMSHLNGHKLHGKPIRITLS 76
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 45.1 bits (107), Expect = 1e-06
Identities = 10/90 (11%), Positives = 23/90 (25%), Gaps = 18/90 (20%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEF 100
+ + + V E + + + G V +I L A + F
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRK----------YG-EVEEVEILLHPRTRKHLGLARVLF 55
Query: 101 RSIDETTQAM-AFDGINFKGQSLKIRRPHD 129
S + + + G + +
Sbjct: 56 TSTRGAKETVKNLHLTSVMGNIIHAQLDIK 85
>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 = 46.6 bits (110), Expect = 1e-06
Identities = 23/124 (18%), Positives = 41/124 (33%), Gaps = 16/124 (12%)
Query: 9 NTGAAGQIPANVIIPETTVAAAAAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFN 68
N A +P T A P V T T + LY+GN+ + T++++ E
Sbjct: 31 NGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAV- 89
Query: 69 QQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFRSIDETTQAM-AFDGINFKGQS 121
N +L + ++ FA + S + + M GQ+
Sbjct: 90 --------HSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQN 141
Query: 122 LKIR 125
+
Sbjct: 142 PVVT 145
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 44.2 bits (105), Expect = 2e-06
Identities = 17/93 (18%), Positives = 30/93 (32%), Gaps = 17/93 (18%)
Query: 38 VGSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN--- 94
+G + + NI D +M + A V ++ DK
Sbjct: 1 MGHHHHHHMDTIILRNIAPHTVVDSIMTALSPY---------ASLAVNNIRLIKDKQTQQ 51
Query: 95 ---FAFLEFRSIDETTQAMAFDGINFKGQSLKI 124
FAF++ S + +Q + + LKI
Sbjct: 52 NRGFAFVQLSSAMDASQLL--QILQSLHPPLKI 82
>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 = 43.8 bits (104), Expect = 2e-06
Identities = 18/97 (18%), Positives = 36/97 (37%), Gaps = 17/97 (17%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRS 102
R+ LYV +T + F+ GN ++ ++ +N AF+ +
Sbjct: 12 PRKGNTLYVYG--EDMTPTLLRGAFSPF----------GN-IIDLSMDPPRNCAFVTYEK 58
Query: 103 IDETTQAM-AFDGINFKGQSLKI---RRPHDYQPTPG 135
++ QA+ +G + LK+ R+ P
Sbjct: 59 MESADQAVAELNGTQVESVQLKVNIARKQPMLDSGPS 95
>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 = 43.3 bits (103), Expect = 3e-06
Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 22/92 (23%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
L+VG++ V ++ + F + L+ + D + F+ F
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDF----------PS-YLSGHVMWDMQTGSSRGYGFVSFT 51
Query: 102 SIDETTQAM-AFDGINFKGQSLKI----RRPH 128
S D+ AM + G + G+ L+I + H
Sbjct: 52 SQDDAQNAMDSMQGQDLNGRPLRINWAAKLEH 83
>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 = 43.3 bits (102), Expect = 4e-06
Identities = 10/83 (12%), Positives = 30/83 (36%), Gaps = 13/83 (15%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFRSI 103
+ +P+ T ++++ FF+ N L+++ A +E S
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIR--------NGENGIHFLLNRDGKRRGDALIEMESE 65
Query: 104 DETTQAMAFDGINFKGQSLKIRR 126
+ +A+ + + +++
Sbjct: 66 QDVQKALEKHRMYMGQRYVEVYE 88
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 43.4 bits (102), Expect = 5e-06
Identities = 10/83 (12%), Positives = 30/83 (36%), Gaps = 13/83 (15%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFRSI 103
+ + +P+ + +++ F + + V + AF+E S
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCT--------IHDGVAGVHFIYTREGRQSGEAFVELESE 71
Query: 104 DETTQAMAFDGINFKGQSLKIRR 126
D+ A+ D + + +++ +
Sbjct: 72 DDVKLALKKDRESMGHRYIEVFK 94
>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 = 45.6 bits (107), Expect = 6e-06
Identities = 26/206 (12%), Positives = 59/206 (28%), Gaps = 61/206 (29%)
Query: 25 TTVAAAAAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFNQ--QMHLSGLAQAA-- 80
TT + +T + + + +T DE+ + L +
Sbjct: 271 TTRFKQVTDFLSAATTT------HISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLT 324
Query: 81 GNPVLACQI-NLDKNFA----FLEFRSIDETTQAMAFDGINFKGQSLKIRRPHDYQPT-- 133
NP I ++ + + D+ T + SL + P +Y+
Sbjct: 325 TNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIE--------SSLNVLEPAEYRKMFD 376
Query: 134 -----PGVTDNAAVAVPAGVISTVVPDSPHKIFIGGLPNYLNEDQAIAGLNGMQLGDKKL 188
P + +P ++S + D ++ + +N + K
Sbjct: 377 RLSVFP---PS--AHIPTILLSLIWFDVIK-----------SDVMVV--VNKLH---KYS 415
Query: 189 IVQRASVGAKNASGQQAPVQIQVPGL 214
+V++ Q I +P +
Sbjct: 416 LVEK----------QPKESTISIPSI 431
Score = 34.8 bits (79), Expect = 0.021
Identities = 28/167 (16%), Positives = 56/167 (33%), Gaps = 33/167 (19%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQM-HLSGLAQAAGNPVLACQINLDKNFAFLEFRSI 103
+ + + D F++ HL + L + LD F FLE +
Sbjct: 454 NIPKTFDSDDLIPPYLD--QYFYSHIGHHLKN-IEHPERMTLFRMVFLD--FRFLEQKIR 508
Query: 104 DETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKIFIG 163
++T A I Q LK +P+ + DN D ++ +
Sbjct: 509 HDSTAWNASGSILNTLQQLKFYKPY-------ICDN---------------DPKYERLVN 546
Query: 164 GLPNYLNEDQAIAGLNGMQLGDKKLIVQRASVGAKNASGQQAPVQIQ 210
+ ++L + N + +++ A + A ++A Q+Q
Sbjct: 547 AILDFLPK----IEEN-LICSKYTDLLRIALMAEDEAIFEEAHKQVQ 588
>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 = 42.7 bits (101), Expect = 7e-06
Identities = 15/85 (17%), Positives = 34/85 (40%), Gaps = 17/85 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFRS 102
+L++G + E + F + G P+ + D+ FAF+ F +
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGK----------HG-PISEVLLIKDRTSKSRGFAFITFEN 57
Query: 103 IDETTQAM-AFDGINFKGQSLKIRR 126
+ A +G + G+++K+ +
Sbjct: 58 PADAKNAAKDMNGKSLHGKAIKVEQ 82
Score = 29.2 bits (66), Expect = 0.49
Identities = 19/92 (20%), Positives = 28/92 (30%), Gaps = 40/92 (43%)
Query: 155 DSPHKIFIGGLPNYLNEDQ----------------------------------------A 174
D P K+FIGGL NE A
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNA 64
Query: 175 IAGLNGMQLGDKKLIVQRASVGAKNASGQQAP 206
+NG L K + V++A + + G++ P
Sbjct: 65 AKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRP 96
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 43.1 bits (101), Expect = 9e-06
Identities = 10/89 (11%), Positives = 30/89 (33%), Gaps = 13/89 (14%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAF 97
+ + + +P+ + +++ F S + + AF
Sbjct: 41 GGEGFVVKLRGLPWSCSVEDVQNFL------SDCTIH--DGAAGVHFIYTREGRQSGEAF 92
Query: 98 LEFRSIDETTQAMAFDGINFKGQSLKIRR 126
+E S D+ A+ D + + +++ +
Sbjct: 93 VELGSEDDVKMALKKDRESMGHRYIEVFK 121
>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 = 42.8 bits (101), Expect = 9e-06
Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 14/82 (17%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSI 103
R+ LYV +T + F+ GN ++ ++ +N AF+ + +
Sbjct: 37 RKGNTLYVYGE--DMTPTLLRGAFSPF----------GN-IIDLSMDPPRNCAFVTYEKM 83
Query: 104 DETTQAM-AFDGINFKGQSLKI 124
+ QA+ +G + LK+
Sbjct: 84 ESADQAVAELNGTQVESVQLKV 105
>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 = 42.3 bits (100), Expect = 9e-06
Identities = 16/90 (17%), Positives = 31/90 (34%), Gaps = 19/90 (21%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAF 97
A +L++G IP + E ++ F + G + + D+ AF
Sbjct: 11 HDAIKLFIGQIPRNLDEKDLKPLFEE----------FGK-IYELTVLKDRFTGMHKGCAF 59
Query: 98 LEFRSIDETTQAM-AFDGIN-FKGQSLKIR 125
L + + +A A G + I+
Sbjct: 60 LTYCERESALKAQSALHEQKTLPGMNRPIQ 89
Score = 26.1 bits (58), Expect = 4.7
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 154 PDSPHKIFIGGLPNYLNEDQ 173
K+FIG +P L+E
Sbjct: 10 DHDAIKLFIGQIPRNLDEKD 29
>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 = 42.3 bits (100), Expect = 1e-05
Identities = 20/104 (19%), Positives = 40/104 (38%), Gaps = 23/104 (22%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFL 98
+ R+L+VG + +E++++ F G + C + + AF+
Sbjct: 13 GRDRKLFVGMLNKQQSEEDVLRLFQP----------FGV-IDECTVLRGPDGSSKGCAFV 61
Query: 99 EFRSIDETTQAM-AFDG---INFKGQSLKIR---RPHDYQPTPG 135
+F S E A+ A G + SL ++ + P+ G
Sbjct: 62 KFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESGPSSG 105
>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 = 42.2 bits (100), Expect = 1e-05
Identities = 15/87 (17%), Positives = 28/87 (32%), Gaps = 17/87 (19%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFL 98
+ LY+ N+P + E E+ G V++ +I D + F
Sbjct: 23 QDPTNLYISNLPLSMDEQELENMLKP----------FGQ-VISTRILRDSSGTSRGVGFA 71
Query: 99 EFRSIDETTQAM-AFDGINFKGQSLKI 124
S ++ + F+G K
Sbjct: 72 RMESTEKCEAVIGHFNGKFIKTPPGVS 98
Score = 28.4 bits (64), Expect = 0.79
Identities = 3/22 (13%), Positives = 6/22 (27%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
+ I NG + +
Sbjct: 80 EAVIGHFNGKFIKTPPGVSAPT 101
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 43.8 bits (103), Expect = 1e-05
Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 11/66 (16%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLAC-QINLDKNFAFLEFRSIDE 105
L++ NIP V+E+++ F+ G V D+ A ++ S++E
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSN----------GGVVKGFKFFQKDRKMALIQMGSVEE 201
Query: 106 TTQAMA 111
QA+
Sbjct: 202 AVQALI 207
>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 = 41.5 bits (98), Expect = 2e-05
Identities = 14/88 (15%), Positives = 33/88 (37%), Gaps = 17/88 (19%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
A L++G++ + E+ + F G V++ +I ++ + F+
Sbjct: 8 MAASLWMGDLEPYMDENFISRAFAT----------MGETVMSVKIIRNRLTGIPAGYCFV 57
Query: 99 EFRSIDETTQAM-AFDGINFKGQSLKIR 125
EF + + + +G G + R
Sbjct: 58 EFADLATAEKCLHKINGKPLPGATPAKR 85
>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 = 41.8 bits (98), Expect = 2e-05
Identities = 12/89 (13%), Positives = 35/89 (39%), Gaps = 15/89 (16%)
Query: 47 RRLYVGNIPF-GVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
R +++ N+P G ++ +++ + + K+ AF+E + ++
Sbjct: 26 RVIHLSNLPHSGYSDSAVLKLAEP-----------YGKIKNYILMRMKSQAFIEMETRED 74
Query: 106 TTQAMAF---DGINFKGQSLKIRRPHDYQ 131
+ + F+G+ +K+ Y+
Sbjct: 75 AMAMVDHCLKKALWFQGRCVKVDLSEKYK 103
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 41.5 bits (97), Expect = 2e-05
Identities = 22/117 (18%), Positives = 44/117 (37%), Gaps = 29/117 (24%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------ 92
GS+ + +R+++VG +P + EDE+ F + G P++ +
Sbjct: 1 GSSGSSGSRKVFVGGLPPDIDEDEITASFRR----------FG-PLVVDWPHKAESKSYF 49
Query: 93 --KNFAFLEFRS-------IDETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNA 140
K +AFL F+ ID + + ++K + Q P ++
Sbjct: 50 PPKGYAFLLFQEESSVQALIDACLEEDGKLYLCVSSPTIKDKPV---QIRPWNLSDS 103
Score = 28.4 bits (63), Expect = 0.97
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 154 PDSPHKIFIGGLPNYLNEDQ 173
K+F+GGLP ++ED+
Sbjct: 5 SSGSRKVFVGGLPPDIDEDE 24
>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 = 40.7 bits (96), Expect = 3e-05
Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 13/85 (15%)
Query: 43 TRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-KNFAFLEFR 101
+ + ++VG +TEDE+ EFF+Q G+ V+ I + FAF+ F
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQ----------YGD-VMDVFIPKPFRAFAFVTFA 50
Query: 102 SIDETTQAMAFDGINFKGQSLKIRR 126
D+ Q++ + + KG S+ I
Sbjct: 51 D-DQIAQSLCGEDLIIKGISVHISN 74
Score = 26.8 bits (60), Expect = 2.2
Identities = 4/20 (20%), Positives = 8/20 (40%)
Query: 154 PDSPHKIFIGGLPNYLNEDQ 173
+F+G + ED+
Sbjct: 2 SSGSSGVFVGRCTGDMTEDE 21
>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 = 40.7 bits (96), Expect = 3e-05
Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 13/84 (15%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-KNFAFLEFRS 102
+++VG +T +E+ +FF Q G V+ I + FAF+ F
Sbjct: 9 HHGSKVFVGRCTEDMTAEELQQFFCQ----------YGE-VVDVFIPKPFRAFAFVTFAD 57
Query: 103 IDETTQAMAFDGINFKGQSLKIRR 126
D+ Q++ + + KG S+ I
Sbjct: 58 -DKVAQSLCGEDLIIKGISVHISN 80
Score = 27.6 bits (62), Expect = 1.3
Identities = 3/20 (15%), Positives = 8/20 (40%)
Query: 154 PDSPHKIFIGGLPNYLNEDQ 173
K+F+G + ++
Sbjct: 8 HHHGSKVFVGRCTEDMTAEE 27
>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 = 40.7 bits (96), Expect = 4e-05
Identities = 20/98 (20%), Positives = 41/98 (41%), Gaps = 23/98 (23%)
Query: 39 GSTITRQAR-------RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINL 91
GS+ + R LYV N+ G+ ++ + + F G + + ++ +
Sbjct: 1 GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAF----------SPFGT-ITSAKVMM 49
Query: 92 D----KNFAFLEFRSIDETTQAM-AFDGINFKGQSLKI 124
+ K F F+ F S +E T+A+ +G + L +
Sbjct: 50 EGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV 87
Score = 28.3 bits (64), Expect = 0.79
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
+A+ +NG + K L V A
Sbjct: 69 TKAVTEMNGRIVATKPLYVALA 90
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 40.8 bits (96), Expect = 5e-05
Identities = 22/125 (17%), Positives = 47/125 (37%), Gaps = 22/125 (17%)
Query: 12 AAGQIPANVIIPETTVAAAAAAAVPVVGSTITRQAR----RLYVGNIPFGVTEDEMMEFF 67
A + T+ A+ A + + + L++ ++P T+ ++ F
Sbjct: 2 AGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTF 61
Query: 68 NQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFRSIDETTQAM-AFDGINFKGQ 120
GN V++ ++ +DK F F+ F + D A+ A +G +
Sbjct: 62 ----------LPFGN-VISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTK 110
Query: 121 SLKIR 125
LK++
Sbjct: 111 RLKVQ 115
Score = 29.6 bits (67), Expect = 0.38
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
AI +NG Q+G K+L VQ
Sbjct: 96 QVAIKAMNGFQVGTKRLKVQLK 117
>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 = 39.5 bits (93), Expect = 6e-05
Identities = 14/91 (15%), Positives = 32/91 (35%), Gaps = 22/91 (24%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
++VG++ +T + F G + ++ D K + F+ F
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAP----------FG-RISDARVVKDMATGKSKGYGFVSFF 56
Query: 102 SIDETTQAM-AFDGINFKGQSLKI----RRP 127
+ + A+ G G+ ++ R+P
Sbjct: 57 NKWDAENAIQQMGGQWLGGRQIRTNWATRKP 87
>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1 PDB: 2rq4_A 2rqc_A
Length = 115
Score = 40.4 bits (95), Expect = 6e-05
Identities = 14/82 (17%), Positives = 35/82 (42%), Gaps = 18/82 (21%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFRS 102
L++ ++P + ++++ F GN V++ ++ +DK F F+ + +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMP----------FGN-VVSAKVFIDKQTNLSKCFGFVSYDN 76
Query: 103 IDETTQAM-AFDGINFKGQSLK 123
A+ + +G + LK
Sbjct: 77 PVSAQAAIQSMNGFQIGMKRLK 98
Score = 30.4 bits (69), Expect = 0.18
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
AI +NG Q+G K+L VQ
Sbjct: 81 QAAIQSMNGFQIGMKRLKVQLK 102
>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 = 40.3 bits (95), Expect = 7e-05
Identities = 14/83 (16%), Positives = 37/83 (44%), Gaps = 16/83 (19%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN----FAFLEFRSID 104
+++ N+ + + + F A GN +L+C++ D+N + F+ F + +
Sbjct: 8 IFIKNLDKSIDNKALYDTF----------SAFGN-ILSCKVVCDENGSKGYGFVHFETQE 56
Query: 105 ETTQAM-AFDGINFKGQSLKIRR 126
+A+ +G+ + + + R
Sbjct: 57 AAERAIEKMNGMLLNDRKVFVGR 79
Score = 33.4 bits (77), Expect = 0.014
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRA 193
++AI +NGM L D+K+ V R
Sbjct: 59 ERAIEKMNGMLLNDRKVFVGRF 80
Score = 26.8 bits (60), Expect = 2.8
Identities = 4/14 (28%), Positives = 6/14 (42%)
Query: 49 LYVGNIPFGVTEDE 62
+Y+ N G T
Sbjct: 100 VYIKNFGPGSTRAA 113
>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 = 40.8 bits (95), Expect = 1e-04
Identities = 12/93 (12%), Positives = 27/93 (29%), Gaps = 18/93 (19%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------ 92
+ I + L+ N P VTE+ E ++ + +
Sbjct: 116 KNRIQHPSNVLHFFNAPLEVTEENFFEICDEL-----------GVKRPTSVKVFSGKSER 164
Query: 93 KNFAFLEFRSIDETTQAMA-FDGINFKGQSLKI 124
+ LE+ S + + + + K +
Sbjct: 165 SSSGLLEWDSKSDALETLGFLNHYQMKNPNGPY 197
>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 = 41.0 bits (95), Expect = 1e-04
Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 11/82 (13%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---FAFLEFRSI 103
+Y+ N+ + +DE+ + L + G +L ++ AF+ F+ +
Sbjct: 10 HTIYINNLNEKIKKDELKK------SLYAIFSQFGQ-ILDILVSRSLKMRGQAFVIFKEV 62
Query: 104 DETTQAM-AFDGINFKGQSLKI 124
T A+ + G F + ++I
Sbjct: 63 SSATNALRSMQGFPFYDKPMRI 84
Score = 32.9 bits (74), Expect = 0.074
Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 12/82 (14%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
L++ N+P E + FNQ + + AF+EF +
Sbjct: 206 PNHILFLTNLPEETNELMLSMLFNQF----------PGFKEVRLVPGRHDIAFVEFDNEV 255
Query: 105 ETTQAM-AFDGINF-KGQSLKI 124
+ A A G + ++KI
Sbjct: 256 QAGAARDALQGFKITQNNAMKI 277
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 39.1 bits (91), Expect = 2e-04
Identities = 12/66 (18%), Positives = 29/66 (43%), Gaps = 13/66 (19%)
Query: 47 RRLYVGN--IPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
+ L V N + GV+ ++++ + V A + +K ++F +R+ +
Sbjct: 26 QSLVVANGGLGNGVSRNQLLPVLEK-----------CGLVDALLMPPNKPYSFARYRTTE 74
Query: 105 ETTQAM 110
E+ +A
Sbjct: 75 ESKRAY 80
>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 = 38.7 bits (91), Expect = 2e-04
Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 17/74 (22%)
Query: 44 RQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAF 97
++ L V +P+ TE ++ E+F+ G VL Q+ D F F
Sbjct: 13 QKTSDLIVLGLPWKTTEQDLKEYFSTF----------GE-VLMVQVKKDLKTGHSKGFGF 61
Query: 98 LEFRSIDETTQAMA 111
+ F + + M+
Sbjct: 62 VRFTEYETQVKVMS 75
>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 = 38.9 bits (91), Expect = 2e-04
Identities = 15/100 (15%), Positives = 35/100 (35%), Gaps = 18/100 (18%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
++VG++ +T +++ F G + ++ D K + F+ F
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAP----------FGR-ISDARVVKDMATGKSKGYGFVSFF 65
Query: 102 SIDETTQAM-AFDGINFKGQSLKIRRPHDYQPTPGVTDNA 140
+ + A+ G G+ ++ P P T +
Sbjct: 66 NKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYES 105
>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 = 37.9 bits (89), Expect = 2e-04
Identities = 14/85 (16%), Positives = 32/85 (37%), Gaps = 17/85 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
+++VG + E+++ E+F G V + ++ +D F F+ F+
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGG----FG-------EVESIELPMDNKTNKRRGFCFITFK 49
Query: 102 SIDETTQAMAFDGINFKGQSLKIRR 126
+ + M N +I+
Sbjct: 50 EEEPVKKIMEKKYHNVGLSKCEIKV 74
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 39.2 bits (91), Expect = 2e-04
Identities = 24/109 (22%), Positives = 40/109 (36%), Gaps = 16/109 (14%)
Query: 22 IPETTVAAAAAAAVPVVGSTITRQAR--RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQA 79
+ +A AA+AA G + Q+ R+ V N+ + VT D + + F++
Sbjct: 2 VQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKF--------- 52
Query: 80 AGNPVLACQINLDKN--FAFLEFRSIDETTQAM-AFDGINFKGQSLKIR 125
VL N A L++ A + DG N +R
Sbjct: 53 --GTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR 99
>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 = 37.5 bits (88), Expect = 3e-04
Identities = 13/73 (17%), Positives = 31/73 (42%), Gaps = 17/73 (23%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
A +++VG + + ++ ++ ++F + G V+ C I +D N F F+
Sbjct: 10 DAGKMFVGGLSWDTSKKDLKDYFTKF----------GE-VVDCTIKMDPNTGRSRGFGFI 58
Query: 99 EFRSIDETTQAMA 111
F+ + +
Sbjct: 59 LFKDAASVEKVLD 71
>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 = 38.0 bits (89), Expect = 4e-04
Identities = 13/96 (13%), Positives = 33/96 (34%), Gaps = 22/96 (22%)
Query: 30 AAAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQI 89
++ + + GS +++VG +P+ T+ + ++F G+ + +
Sbjct: 1 GSSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEG----------FGD-IEEAVV 49
Query: 90 NLDKN------FAFLEFRSIDETTQAMA-----FDG 114
D+ + F+ +A DG
Sbjct: 50 ITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDG 85
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 38.5 bits (89), Expect = 5e-04
Identities = 25/127 (19%), Positives = 48/127 (37%), Gaps = 14/127 (11%)
Query: 3 VNNEVLNTGAAGQIPANVIIPETTVAAAAAAAVPVVGSTITRQAR--RLYVGNIPFGVTE 60
+++ + A + A + +A AA+AA G + Q+ R+ V N+ + VT
Sbjct: 1 MHHHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTL 60
Query: 61 DEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNF-AFLEFRSIDETTQAM-AFDGINFK 118
D + + F++ G + + F A L++ A + DG N
Sbjct: 61 DVLHQIFSKF----------GTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIY 110
Query: 119 GQSLKIR 125
+R
Sbjct: 111 NACCTLR 117
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 37.2 bits (86), Expect = 6e-04
Identities = 25/128 (19%), Positives = 43/128 (33%), Gaps = 33/128 (25%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFL 98
GS+ + + V +P V ++ + +F + SG G PVL+ Q L
Sbjct: 1 GSSGSSGGVAVEVRGLPPAVPDELLTLYF-ENRRRSG-----GGPVLSWQR--LGCGGVL 52
Query: 99 EFRSIDETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPH 158
FR + + +A G L +R P +P
Sbjct: 53 TFREPADAERVLAQADHELHGAQLSLRP-------------------------APPRAPA 87
Query: 159 KIFIGGLP 166
++ + GLP
Sbjct: 88 RLLLQGLP 95
>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 = 36.5 bits (85), Expect = 0.001
Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 17/79 (21%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN---- 94
GS + ++++G + + T++ + E+F Q G V C + D
Sbjct: 18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQF----------GE-VKECLVMRDPLTKRS 66
Query: 95 --FAFLEFRSIDETTQAMA 111
F F+ F + +A
Sbjct: 67 RGFGFVTFMDQAGVDKVLA 85
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 35.5 bits (83), Expect = 0.001
Identities = 14/85 (16%), Positives = 30/85 (35%), Gaps = 17/85 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
+++VG + T +++ +F Q G V + DK F F+ F
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQ----------FGK-VDDAMLMFDKTTNRHRGFGFVTFE 49
Query: 102 SIDETTQAMAFDGINFKGQSLKIRR 126
S D + + ++ ++
Sbjct: 50 SEDIVEKVCEIHFHEINNKMVECKK 74
>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 = 37.7 bits (87), Expect = 0.003
Identities = 33/219 (15%), Positives = 54/219 (24%), Gaps = 88/219 (40%)
Query: 61 DEMMEFFNQQMHLSGLAQAAGNPV--------------------LACQINLDKNFAFLE- 99
+ F S L NPV + + +D +
Sbjct: 1647 NRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKI 1706
Query: 100 FRSIDETTQAMAFDGINFKGQSLKIRRPHDYQP--------------TPGVTDN------ 139
F+ I+E + F+ + + QP + G+
Sbjct: 1707 FKEINEHST-----SYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAG 1761
Query: 140 ------AAVAVPAGVIS----------------TVVPDSPHKIFIGGLPNY----LNEDQ 173
AA+A A V+S VP G NY +N +
Sbjct: 1762 HSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDEL-----GRSNYGMIAINPGR 1816
Query: 174 AIAGLNGMQLGDKKLIVQRASVGAK--------NASGQQ 204
A + L + +V+R N QQ
Sbjct: 1817 VAASFSQEAL---QYVVERVGKRTGWLVEIVNYNVENQQ 1852
Score = 34.3 bits (78), Expect = 0.035
Identities = 36/217 (16%), Positives = 64/217 (29%), Gaps = 61/217 (28%)
Query: 23 PETTVAAAAAAAVPVVGSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGN 82
P+ + + P++G Q V G T E+ +L G +
Sbjct: 226 PDKDYLLSIPISCPLIGVI---QLAHYVVTAKLLGFTPGELRS------YLKGATGHSQG 276
Query: 83 PVLACQINLDKNFAFLEFRSIDETTQAMAFDGINFKGQ------SLKIRRPHDY------ 130
V A I ++ F + F I + SL D
Sbjct: 277 LVTAVAIAETDSWE--SFFVSVRKAITVLF-FIGVRCYEAYPNTSLPPSILEDSLENNEG 333
Query: 131 QPTP--GVTD-------------NAAVAVPAGVISTVVPDSPHKIFIGGLPNYLNEDQAI 175
P+P +++ N+ + + + + + + G P Q++
Sbjct: 334 VPSPMLSISNLTQEQVQDYVNKTNSHLP-AGKQVEISLVNGAKNLVVSGPP------QSL 386
Query: 176 AGLNGMQLGDKKLIVQRASVGAKNASGQQAPVQIQVP 212
GLN + L R AK SG Q ++P
Sbjct: 387 YGLN-LTL--------R---KAKAPSGLD---QSRIP 408
Score = 33.9 bits (77), Expect = 0.046
Identities = 43/263 (16%), Positives = 72/263 (27%), Gaps = 98/263 (37%)
Query: 30 AAAAAVPVVGSTITRQARRL---Y-----VGNIPFGVTEDEMMEFFNQQMHLSGLAQAA- 80
A AA + T + + L Y + PF + S L +A
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITARIMAKRPF------------DKKSNSALFRAVG 150
Query: 81 -GN-PVLAC---QINLDKNFAFLEFRSIDETTQAMAFDGINFKGQSLK--IRRPHDYQP- 132
GN ++A Q N D F E R + +T + D I F ++L IR D +
Sbjct: 151 EGNAQLVAIFGGQGNTDDYFE--ELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKV 208
Query: 133 ----------------TPGV--TDNAAVAVPAGVISTVVPDSPHKIFIGGLPNY------ 168
TP + ++ P I + L +Y
Sbjct: 209 FTQGLNILEWLENPSNTPDKDYLLSIPISCPL-------------IGVIQLAHYVVTAKL 255
Query: 169 --LNEDQAIAGLNGMQLGDKKLIVQRASVGA---------KNAS------------GQQA 205
+ + L G + L+ A A + +A
Sbjct: 256 LGFTPGELRSYLKGATGHSQGLVT--AVAIAETDSWESFFVSVRKAITVLFFIGVRCYEA 313
Query: 206 -PVQIQVPGLTQ----VGQAGPA 223
P P + + + P+
Sbjct: 314 YPNTSLPPSILEDSLENNEGVPS 336
>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 = 35.3 bits (82), Expect = 0.003
Identities = 20/99 (20%), Positives = 41/99 (41%), Gaps = 19/99 (19%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
+ +L+VG + + T++ + +F+Q G V+ C I DK F F+
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQY----------GE-VVDCVIMKDKTTNQSRGFGFV 63
Query: 99 EFRSIDETTQAMAFDGINFKGQSLKIRR--PHDYQPTPG 135
+F+ + +A G+++ + P QP+
Sbjct: 64 KFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPSGP 102
Score = 25.3 bits (56), Expect = 9.2
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 154 PDSPHKIFIGGLP 166
D K+F+GGL
Sbjct: 13 ADEIGKLFVGGLD 25
>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 = 35.3 bits (82), Expect = 0.003
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 17/73 (23%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
Q R+L++G + F TE+ + ++ Q G + C + D F F+
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQW----------GK-LTDCVVMRDPASKRSRGFGFV 74
Query: 99 EFRSIDETTQAMA 111
F S+ E AMA
Sbjct: 75 TFSSMAEVDAAMA 87
>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 = 35.2 bits (81), Expect = 0.004
Identities = 12/92 (13%), Positives = 34/92 (36%), Gaps = 24/92 (26%)
Query: 45 QARRLYVGNIPFGVTEDEMM---EFFNQQMHLSGLAQAAGNPVLACQINLDKN------- 94
Q ++V + + + E++ E+F + + IN +
Sbjct: 14 QKNLVFVVGLSQRLADPEVLKRPEYFGKF-----------GKIHKVVINNSTSYAGSQGP 62
Query: 95 --FAFLEFRSIDETTQAM-AFDGINFKGQSLK 123
A++ + ++ +A+ + + G++LK
Sbjct: 63 SASAYVTYIRSEDALRAIQCVNNVVVDGRTLK 94
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 33.6 bits (78), Expect = 0.006
Identities = 13/70 (18%), Positives = 27/70 (38%), Gaps = 17/70 (24%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
++++G + + T++ + E+F Q G V C + D F F+ F
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQF----------GE-VKECLVMRDPLTKRSRGFGFVTFM 50
Query: 102 SIDETTQAMA 111
+ +A
Sbjct: 51 DQAGVDKVLA 60
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 34.3 bits (78), Expect = 0.008
Identities = 13/79 (16%), Positives = 25/79 (31%), Gaps = 11/79 (13%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
L + N + +T D + N G + A +EF S+
Sbjct: 27 LLSIQNPLYPITVDVLYTVCNPV----------GKVQRIVIFKRNGIQAMVEFESVLCAQ 76
Query: 108 QAM-AFDGINFKGQSLKIR 125
+A A +G + ++
Sbjct: 77 KAKAALNGADIYAGCCTLK 95
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 33.4 bits (77), Expect = 0.013
Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 15/69 (21%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN-----FAFLEFRS 102
L+VG++ V + + EFF ++ LD+ + F++F
Sbjct: 11 SLFVGDLTPDVDDGMLYEFF----------VKVYPSCRGGKVVLDQTGVSKGYGFVKFTD 60
Query: 103 IDETTQAMA 111
E +A+
Sbjct: 61 ELEQKRALT 69
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 32.8 bits (75), Expect = 0.019
Identities = 14/90 (15%), Positives = 34/90 (37%), Gaps = 19/90 (21%)
Query: 50 YVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFRSI 103
+ + V + + F++ AG V+ + +D+ F F+E S+
Sbjct: 16 VIPSAKVPVLKKALTSLFSK----------AG-KVVNMEFPIDEATGKTKGFLFVECGSM 64
Query: 104 DETTQAM-AFDGINFKGQ-SLKIRRPHDYQ 131
++ + + +F G + L + D +
Sbjct: 65 NDAKKIIKSFHGKRLDLKHRLFLYTMKDVE 94
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 33.2 bits (75), Expect = 0.047
Identities = 13/84 (15%), Positives = 24/84 (28%), Gaps = 3/84 (3%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
+ LYVG I + + + ++ + + KN F++F+
Sbjct: 135 KTLYVGGIDGALNSKHLKPAQIESRIRFVFSRL--GDIDRIRYVESKNCGFVKFKYQANA 192
Query: 107 TQAM-AFDGINFKGQSLKIRRPHD 129
A A S K
Sbjct: 193 EFAKEAMSNQTLLLPSDKEWDDRR 216
>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 = 33.2 bits (75), Expect = 0.063
Identities = 20/115 (17%), Positives = 48/115 (41%), Gaps = 21/115 (18%)
Query: 47 RRLYVGN--IPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
+ L V N + GV+ ++++ + V A + +K ++F +R+ +
Sbjct: 19 QSLVVANGGLGNGVSRNQLLPVLEK-----------CGLVDALLMPPNKPYSFARYRTTE 67
Query: 105 ETTQAM-AFDG---INFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPD 155
E+ +A +G ++ GQ + + ++ + A+P G+ VV +
Sbjct: 68 ESKRAYVTLNGKEVVDDLGQKITLY--LNFVEKVQWKELRPQALPPGL--MVVEE 118
>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 = 30.6 bits (70), Expect = 0.095
Identities = 10/33 (30%), Positives = 14/33 (42%)
Query: 172 DQAIAGLNGMQLGDKKLIVQRASVGAKNASGQQ 204
D AI +NG L ++ + V A SG
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYAFKKDSKGSGPS 94
Score = 30.6 bits (70), Expect = 0.10
Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 16/70 (22%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
+++GN+ + E + + F A G + +I D K +AF+ F
Sbjct: 7 GIFIGNLDPEIDEKLLYDTF----------SAFGVILQTPKIMRDPDTGNSKGYAFINFA 56
Query: 102 SIDETTQAMA 111
S D + A+
Sbjct: 57 SFDASDAAIE 66
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 29.3 bits (66), Expect = 0.43
Identities = 17/91 (18%), Positives = 32/91 (35%), Gaps = 11/91 (12%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD----KNFAFLEFRS 102
+ V N+P V D + + N + + G + + K + FLE+ S
Sbjct: 16 SVIVVDNVPQ-VGPDRLEKLKNV---IHKIFSKFG-KITNDFYPEEDGKTKGYIFLEYAS 70
Query: 103 IDETTQAM-AFDGINFKGQ-SLKIRRPHDYQ 131
A+ DG Q + ++ D+
Sbjct: 71 PAHAVDAVKNADGYKLDKQHTFRVNLFTDFD 101
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 27.9 bits (62), Expect = 1.1
Identities = 10/89 (11%), Positives = 30/89 (33%), Gaps = 15/89 (16%)
Query: 47 RRLYVGNIPFGV-TEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
R +++ + G ++++ + I N AF+E + ++
Sbjct: 16 RVVHIMDFQRGKNLRYQLLQLVEP-----------FGVISNHLILNKINEAFIEMATTED 64
Query: 106 TTQAMAF---DGINFKGQSLKIRRPHDYQ 131
A+ + G+ +++ Y+
Sbjct: 65 AQAAVDYYTTTPALVFGKPVRVHLSQKYK 93
>3kdw_A Putative sugar binding protein; structural genomics, joint C
structural genomics, JCSG, protein structure initiative;
HET: MSE; 1.70A {Bacteroides vulgatus atcc 8482} PDB:
3g6i_A*
Length = 221
Score = 28.2 bits (62), Expect = 1.9
Identities = 13/54 (24%), Positives = 18/54 (33%), Gaps = 1/54 (1%)
Query: 131 QPTPGVTDNAAVAVPAGVISTVVPDSPHKIFIGGLPNYLNEDQAIAGLNGMQLG 184
+ G AV + + H F L YL+ Q A +GM G
Sbjct: 85 ETLTGDAKQEAVKAAEAEKDAALYRT-HFAFPADLSLYLDAKQIDAVKDGMTYG 137
>3ee4_A Probable ribonucleoside-diphosphate reductase; manganese, iron,
DIIRON, carboxylate, oxidase, ligand, C monooxygenase;
HET: MYR; 1.90A {Mycobacterium tuberculosis}
Length = 323
Score = 28.2 bits (63), Expect = 2.1
Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 8/74 (10%)
Query: 42 ITRQARRLYVGNIPFGVTEDEMMEF----FNQQMHLSGLAQAAGNPVLACQINLDKNFAF 97
+ + LY PF +++D+ +++ ++ ++ A G PV +I++D + A
Sbjct: 250 LIEEGFALYGDQPPFDLSKDDFLQYSTDKGMRR--FGTISNARGRPVA--EIDVDYSPAQ 305
Query: 98 LEFRSIDETTQAMA 111
LE DE + +A
Sbjct: 306 LEDTFADEDRRTLA 319
>2e5f_A Hypothetical protein PH0510; structural genomics, sugar binding
protein, NPPSFA, national on protein structural and
functional analyses; 1.35A {Pyrococcus horikoshii} PDB:
2dec_A* 2df8_A 2cb0_A*
Length = 325
Score = 26.7 bits (60), Expect = 7.0
Identities = 6/30 (20%), Positives = 10/30 (33%), Gaps = 7/30 (23%)
Query: 24 ET--TVAA-----AAAAAVPVVGSTITRQA 46
ET + A + S++TR
Sbjct: 91 ETTEILLALEKINVKKLGITTRESSLTRMC 120
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.316 0.133 0.381
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: 3,553,103
Number of extensions: 223613
Number of successful extensions: 1247
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1080
Number of HSP's successfully gapped: 282
Length of query: 231
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 141
Effective length of database: 4,188,903
Effective search space: 590635323
Effective search space used: 590635323
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.3 bits)