RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10308
(225 letters)
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 135 bits (342), Expect = 1e-41
Identities = 58/87 (66%), Positives = 70/87 (80%)
Query: 52 GGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGN 111
W +W+LLKNLT QIDG TL+TLC+QHGPL +FH YLN +AL KY+TREEA KAQ
Sbjct: 3 MAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMA 62
Query: 112 LNNCILGNTTIFAEAPSDAEVQSLLAH 138
LNNC+L NTTIFAE+PS+ EVQS++ H
Sbjct: 63 LNNCVLANTTIFAESPSENEVQSIMQH 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 = 48.3 bits (115), Expect = 7e-08
Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 1/83 (1%)
Query: 48 SQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIK 107
S G S T +L KNL + ++ + G L L A+ ++ EA K
Sbjct: 2 SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARK 61
Query: 108 AQGNLNNCILGNTTIFAE-APSD 129
A +L + ++ E AP
Sbjct: 62 AFRHLAYSKFHHVPLYLEWAPIG 84
>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 = 42.0 bits (98), Expect = 4e-05
Identities = 16/128 (12%), Positives = 35/128 (27%), Gaps = 14/128 (10%)
Query: 1 MSSNDLWGPPKPRGPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQGGWSGTWVL 60
+S P + G G S S +
Sbjct: 76 VSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNV--------LH 127
Query: 61 LKNLTPQIDGSTLKTLCVQHGPLQNFHLYL------NHSLALAKYSTREEAIKAQGNLNN 114
N ++ +C + G + + + S L ++ ++ +A++ G LN+
Sbjct: 128 FFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNH 187
Query: 115 CILGNTTI 122
+ N
Sbjct: 188 YQMKNPNG 195
Score = 35.4 bits (81), Expect = 0.007
Identities = 7/66 (10%), Positives = 25/66 (37%), Gaps = 2/66 (3%)
Query: 59 VLLKNLTPQ-IDGSTLKTLCVQHGPLQNFHLYLNH-SLALAKYSTREEAIKAQGNLNNCI 116
+++ L ++ + + +G ++ + A+ + + +A +LNN
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNF 66
Query: 117 LGNTTI 122
+ +
Sbjct: 67 MFGQKM 72
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 39.1 bits (91), Expect = 1e-04
Identities = 13/58 (22%), Positives = 23/58 (39%)
Query: 57 TWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNN 114
V L + + L + + G + + N + A+Y T EE+ +A LN
Sbjct: 28 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNG 85
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 39.8 bits (93), Expect = 2e-04
Identities = 24/137 (17%), Positives = 46/137 (33%), Gaps = 6/137 (4%)
Query: 8 GPPKPRGPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQGGWSGTWVLLKNLTPQ 67
G P+ P G P + P+ G +G +G +L+ NL
Sbjct: 40 GGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFG 99
Query: 68 IDGSTLKTLCVQHGPLQNFHLYLNHS-----LALAKYSTREEAIKAQGNLNNCILGNTTI 122
+ + ++ L + G L+ + + S A + R +A+KA L +
Sbjct: 100 VSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPM 159
Query: 123 -FAEAPSDAEVQSLLAH 138
S +++ H
Sbjct: 160 DIQLVASQIDLEHHHHH 176
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 37.8 bits (88), Expect = 3e-04
Identities = 19/96 (19%), Positives = 41/96 (42%), Gaps = 6/96 (6%)
Query: 42 GNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS---LALAK 98
G++ + + ++N+ P + L +L VQ+G +++ S +
Sbjct: 1 GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVT 60
Query: 99 YSTREEAIKAQGNLNNCILGNTTI---FAEAPSDAE 131
YS++++A +A LN L N T+ + A+
Sbjct: 61 YSSKDQARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA,
spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1
d.58.7.1
Length = 198
Score = 39.1 bits (91), Expect = 4e-04
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 61 LKNLTPQIDGSTLKTLCVQHGPLQNFHLYL--NHSLALAKYSTREEAIKAQGNLNNCILG 118
L N+ P + LK L +G + + + +AL + + EEA++A +L+N LG
Sbjct: 125 LSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLG 184
Query: 119 NT 120
Sbjct: 185 EN 186
Score = 34.9 bits (80), Expect = 0.010
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 2/67 (2%)
Query: 59 VLLKNLTPQ-IDGSTLKTLCVQHGPLQNFHLYLNH-SLALAKYSTREEAIKAQGNLNNCI 116
+L+ NL P+ + +L L +G +Q + N AL + + +A A +LN
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHK 65
Query: 117 LGNTTIF 123
L I
Sbjct: 66 LHGKPIR 72
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A
Length = 282
Score = 39.5 bits (91), Expect = 5e-04
Identities = 17/113 (15%), Positives = 28/113 (24%), Gaps = 3/113 (2%)
Query: 9 PPKPRGPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQGGWSGTWVLLKNLTPQI 68
P P G G M G ++ NL +
Sbjct: 162 PYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFL--TNLPEET 219
Query: 69 DGSTLKTLCVQHGPLQNFHLYLN-HSLALAKYSTREEAIKAQGNLNNCILGNT 120
+ L L Q + L H +A ++ +A A+ L +
Sbjct: 220 NELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQN 272
Score = 35.6 bits (81), Expect = 0.008
Identities = 22/157 (14%), Positives = 41/157 (26%), Gaps = 10/157 (6%)
Query: 62 KNLTPQIDGSTLKT----LCVQHGPLQNFHLYLNHSL---ALAKYSTREEAIKAQGNLNN 114
NL +I LK + Q G + + + + + A + A A ++
Sbjct: 15 NNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQG 74
Query: 115 CILGNTTI---FAEAPSDAEVQSLLAHLSATANNNNNNNGGTGGWARGSSALSNKDTWSS 171
+ + +A+ SD + + A + T
Sbjct: 75 FPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVV 134
Query: 172 GGGGGNTSQLWGTPSNPSSGGSLWGAPPLDSVDRATP 208
G G + P + G PP P
Sbjct: 135 GAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIP 171
>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 = 38.3 bits (89), Expect = 5e-04
Identities = 22/118 (18%), Positives = 42/118 (35%), Gaps = 11/118 (9%)
Query: 11 KPRGPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQGGWSGTWVLLKNLTPQIDG 70
+G G + + VR PQ G + + ++ +
Sbjct: 32 HRKGRGFGSDSNTREAIHSYERVRNEDDDELE-----PGPQRSVEGWILFVTSIHEEAQE 86
Query: 71 STLKTLCVQHGPLQNFHLYLNHS------LALAKYSTREEAIKAQGNLNNCILGNTTI 122
++ +G ++N HL L+ AL +Y T ++A+ A+ LN + TI
Sbjct: 87 DEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI 144
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 37.4 bits (87), Expect = 6e-04
Identities = 22/100 (22%), Positives = 39/100 (39%), Gaps = 16/100 (16%)
Query: 39 GGGGNTWGTSQPQGGWSGTWVLLKNL-TP---QIDGSTLKTL-------CVQHGPLQNFH 87
G G++ G S+ + V++KN+ P + D L + C + G ++
Sbjct: 1 GSSGSSGGPSRMR--HERV-VIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLL 57
Query: 88 LYLNHSLALA--KYSTREEAIKAQGNLNNCILGNTTIFAE 125
L+ H +A + EEA L+ G I A+
Sbjct: 58 LFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 97
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 36.6 bits (85), Expect = 0.001
Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 6/79 (7%)
Query: 59 VLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS------LALAKYSTREEAIKAQGNL 112
V L + + LK +C ++G ++ + L+ LA +++ A + NL
Sbjct: 9 VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68
Query: 113 NNCILGNTTIFAEAPSDAE 131
+ + I A+ +
Sbjct: 69 HLTSVMGNIIHAQLDIKGQ 87
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 36.5 bits (85), Expect = 0.001
Identities = 13/60 (21%), Positives = 19/60 (31%)
Query: 63 NLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCILGNTTI 122
N+ + L L G + +F Y KY T E+A L N +
Sbjct: 34 NIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNL 93
>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 = 38.1 bits (89), Expect = 0.001
Identities = 14/72 (19%), Positives = 25/72 (34%), Gaps = 1/72 (1%)
Query: 62 KNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCILGNTT 121
NL I K L ++G + + + +R A A+ L+ IL +
Sbjct: 28 GNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILKSRP 87
Query: 122 IF-AEAPSDAEV 132
+ A A +
Sbjct: 88 LRIRFATHGAAL 99
>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 = 35.7 bits (83), Expect = 0.002
Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 9/87 (10%)
Query: 39 GGGGNT----WGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSL 94
G G++ +G + P T + + L P + L + G ++ S
Sbjct: 1 GSSGSSGKIGYGKANP-----TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSF 55
Query: 95 ALAKYSTREEAIKAQGNLNNCILGNTT 121
A +Y + + A A + LG
Sbjct: 56 AYIQYESLDAAQAACAKMRGFPLGGPD 82
>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 = 37.7 bits (88), Expect = 0.002
Identities = 12/78 (15%), Positives = 31/78 (39%), Gaps = 5/78 (6%)
Query: 59 VLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSL----ALAKYSTREEAIKAQGNLNN 114
VL+KNL + + + GP+ + + + A +++ + A+ A +
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK 103
Query: 115 CILGNTTIFAEAPSDAEV 132
++G I ++ +
Sbjct: 104 -VVGQNEIIVSHLTECTL 120
Score = 31.1 bits (71), Expect = 0.20
Identities = 10/70 (14%), Positives = 20/70 (28%), Gaps = 6/70 (8%)
Query: 62 KNLTPQIDGSTLKTLCVQHGP-LQNFHLYLNHS-----LALAKYSTREEAIKAQGNLNNC 115
N P ++ L + L A +++E+A LN
Sbjct: 123 TNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL 182
Query: 116 ILGNTTIFAE 125
+ T+ +
Sbjct: 183 KIEGYTLVTK 192
Score = 29.2 bits (66), Expect = 0.90
Identities = 13/72 (18%), Positives = 32/72 (44%), Gaps = 9/72 (12%)
Query: 59 VLLKNLTPQI-DGSTLKTLCVQHGPLQNFHLYLNHSL-------ALAKYSTREEAIKAQG 110
++++NL+ ++ D + L+ G ++ ++ A + ++ A +A
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL- 271
Query: 111 NLNNCILGNTTI 122
+N +LGN I
Sbjct: 272 QMNRSLLGNREI 283
>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 = 35.9 bits (83), Expect = 0.002
Identities = 14/96 (14%), Positives = 33/96 (34%), Gaps = 2/96 (2%)
Query: 27 PSNGWMVRPNGGGGGGNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNF 86
S+G + R + G + + + G + + + + L+ G + +
Sbjct: 10 HSSGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDL 67
Query: 87 HLYLNHSLALAKYSTREEAIKAQGNLNNCILGNTTI 122
+ + A Y E A +A LN + + +
Sbjct: 68 SMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQL 103
>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 = 36.4 bits (85), Expect = 0.002
Identities = 14/86 (16%), Positives = 32/86 (37%), Gaps = 9/86 (10%)
Query: 55 SGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHL----YLNHSL--ALAKYSTREEAIKA 108
S T +++ L + L L GP+ + +S A +++ ++ +A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 109 QGNLNNCILGNTTI---FAEAPSDAE 131
LN + N + +A ++
Sbjct: 62 IKVLNGITVRNKRLKVSYARPGGESI 87
>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 = 35.3 bits (82), Expect = 0.002
Identities = 12/83 (14%), Positives = 29/83 (34%), Gaps = 10/83 (12%)
Query: 61 LKNLTPQIDGSTLK----TLCVQHGPLQNFHLYLNHSL---ALAKYSTREEAIKAQGNLN 113
+ NL +I LK + + G + + + + + A + A A ++
Sbjct: 13 INNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQ 72
Query: 114 NCILGNTTI---FAEAPSDAEVQ 133
+ + +A+ SD +
Sbjct: 73 GFPFYDKPMRIQYAKTDSDIIAK 95
>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 = 36.5 bits (84), Expect = 0.003
Identities = 24/113 (21%), Positives = 40/113 (35%), Gaps = 9/113 (7%)
Query: 10 PKPRGPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQGGWSGTWVL-LKNLTPQI 68
+ P G G + G N P + L L N+ P +
Sbjct: 110 QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP------SATLHLSNIPPSV 163
Query: 69 DGSTLKTLCVQHGPLQNFHLYL--NHSLALAKYSTREEAIKAQGNLNNCILGN 119
LK L +G + + + +AL + + EEA++A +L+N LG
Sbjct: 164 SEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGE 216
Score = 35.7 bits (82), Expect = 0.007
Identities = 23/106 (21%), Positives = 37/106 (34%), Gaps = 5/106 (4%)
Query: 20 MGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQGGWSGTWVLLKNLTPQ-IDGSTLKTLCV 78
MG + + P G G G +L+ NL P+ + +L L
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSV---LLVSNLNPERVTPQSLFILFG 57
Query: 79 QHGPLQNFHLYLNH-SLALAKYSTREEAIKAQGNLNNCILGNTTIF 123
+G +Q + N AL + + +A A +LN L I
Sbjct: 58 VYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIR 103
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint
center for struc genomics, JCSG, protein structure
initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus
musculus} PDB: 2lq5_A
Length = 114
Score = 35.0 bits (81), Expect = 0.004
Identities = 15/79 (18%), Positives = 26/79 (32%), Gaps = 12/79 (15%)
Query: 59 VLLKNL-TPQ--IDGSTLKTL-------CVQHGPLQNFHLYLNHSLALA--KYSTREEAI 106
L N+ PQ + + C +HG + + ++ N + K + AI
Sbjct: 10 FQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAI 69
Query: 107 KAQGNLNNCILGNTTIFAE 125
A L+ I A
Sbjct: 70 AAVNALHGRWFAGKMITAA 88
>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 = 34.3 bits (79), Expect = 0.005
Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 3/84 (3%)
Query: 53 GWSGTW-VLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGN 111
G SG+ +L+KNL + + L + L+ ++ N A E+A A
Sbjct: 1 GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQM 59
Query: 112 LNNCILGNTTIFAE-APSDAEVQS 134
+ + + P+DA + S
Sbjct: 60 FHQYSFRGKDLIVQLQPTDALLCS 83
>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 = 36.1 bits (84), Expect = 0.005
Identities = 18/94 (19%), Positives = 29/94 (30%), Gaps = 11/94 (11%)
Query: 62 KNLTPQI-DGSTLKTLCVQHGPLQNFHLYLNHSL-----ALAKYSTREEAIKAQGNLNNC 115
L P D L L A+ +Y T E A +AQ +
Sbjct: 190 DRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGL 249
Query: 116 ILGNTTI---FAEAPSD--AEVQSLLAHLSATAN 144
LG + + F + + +L+A + N
Sbjct: 250 SLGGSHLRVSFCAPGPPGRSMLAALIAAQATALN 283
Score = 34.6 bits (80), Expect = 0.017
Identities = 11/77 (14%), Positives = 27/77 (35%), Gaps = 6/77 (7%)
Query: 59 VLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSL--ALAKYSTREEAIKAQGNLNNCI 116
+L++ L + + L + + +++ A E+A A +
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYELK---YCFVDKYKGTAFVTLLNGEQAEAAINAFHQSR 81
Query: 117 LGNTTIFAE-APSDAEV 132
L + + P+DA +
Sbjct: 82 LRERELSVQLQPTDALL 98
Score = 33.4 bits (77), Expect = 0.045
Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 9/79 (11%)
Query: 62 KNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAK------YSTREEAIKAQGNLNNC 115
NL P + + L G L+ L + +K Y ++ A +A+ +L
Sbjct: 101 ANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGK 160
Query: 116 ILGNTTI---FAEAPSDAE 131
LG T+ + +A
Sbjct: 161 PLGPRTLYVHWTDAGQLTP 179
>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 = 34.4 bits (79), Expect = 0.006
Identities = 8/67 (11%), Positives = 20/67 (29%), Gaps = 2/67 (2%)
Query: 59 VLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKA--QGNLNNCI 116
V ++ L + + L + G + + AL ++ + A +
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVY 77
Query: 117 LGNTTIF 123
+ F
Sbjct: 78 IAGQQAF 84
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 34.2 bits (79), Expect = 0.008
Identities = 12/84 (14%), Positives = 29/84 (34%), Gaps = 17/84 (20%)
Query: 55 SGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAK------YSTREEAIKA 108
S T + ++ + S L + GP++ + + + E A KA
Sbjct: 30 SNTRLFVRPFPLDVQESELNEIFGPFGPMK--------EVKILNGFAFVEFEEAESAAKA 81
Query: 109 QGNLNNCILGNTTI---FAEAPSD 129
++ N + +++ P+
Sbjct: 82 IEEVHGKSFANQPLEVVYSKLPAK 105
>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 = 34.9 bits (81), Expect = 0.009
Identities = 15/67 (22%), Positives = 23/67 (34%), Gaps = 6/67 (8%)
Query: 62 KNLTPQIDGSTLKTLCVQHGPLQNFHL----YLNHSL--ALAKYSTREEAIKAQGNLNNC 115
L + ++L G +++ L SL Y ++A KA LN
Sbjct: 8 NYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGL 67
Query: 116 ILGNTTI 122
L TI
Sbjct: 68 RLQTKTI 74
>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 = 33.4 bits (77), Expect = 0.010
Identities = 12/61 (19%), Positives = 25/61 (40%), Gaps = 1/61 (1%)
Query: 63 NLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKA-QGNLNNCILGNTT 121
L I + L+ Q G ++ + A +++TR+ A A + + N I+
Sbjct: 19 GLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLIVNGRR 78
Query: 122 I 122
+
Sbjct: 79 L 79
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 33.7 bits (77), Expect = 0.010
Identities = 19/86 (22%), Positives = 28/86 (32%), Gaps = 1/86 (1%)
Query: 38 GGGGGNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNH-SLAL 96
G G + G+ +G V + NL S LK + G + + A
Sbjct: 1 GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAF 60
Query: 97 AKYSTREEAIKAQGNLNNCILGNTTI 122
Y A +A L LG T+
Sbjct: 61 LHYPDSAAAQQAVSCLQGLRLGTDTL 86
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 33.7 bits (77), Expect = 0.010
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 5/58 (8%)
Query: 73 LKTLCVQHGPLQNFHLYLNHS-----LALAKYSTREEAIKAQGNLNNCILGNTTIFAE 125
+ ++G ++ ++ N K+ E+A KA +LNN I AE
Sbjct: 44 FTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101
>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 = 33.4 bits (77), Expect = 0.016
Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 6/79 (7%)
Query: 50 PQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS------LALAKYSTRE 103
PQ G + + ++ + ++ +G ++N HL L+ AL +Y T +
Sbjct: 20 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 79
Query: 104 EAIKAQGNLNNCILGNTTI 122
+A+ A+ LN + TI
Sbjct: 80 QALAAKEALNGAEIMGQTI 98
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 32.8 bits (75), Expect = 0.019
Identities = 11/67 (16%), Positives = 21/67 (31%), Gaps = 2/67 (2%)
Query: 59 VLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKA--QGNLNNCI 116
V ++ L + + L + GP+ + AL ++ A A N
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIY 83
Query: 117 LGNTTIF 123
+ F
Sbjct: 84 IAGHPAF 90
>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 = 32.6 bits (75), Expect = 0.021
Identities = 11/81 (13%), Positives = 29/81 (35%), Gaps = 2/81 (2%)
Query: 42 GNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYST 101
G++ + + + G + + + + L+ G + + + + A Y
Sbjct: 1 GSSGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEK 58
Query: 102 REEAIKAQGNLNNCILGNTTI 122
E A +A LN + + +
Sbjct: 59 MESADQAVAELNGTQVESVQL 79
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 31.9 bits (73), Expect = 0.044
Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 5/88 (5%)
Query: 40 GGGNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS-----L 94
G + G + + + L L+ +C HG +++ L N + L
Sbjct: 1 GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGL 60
Query: 95 ALAKYSTREEAIKAQGNLNNCILGNTTI 122
A +Y +A +A ++ + I
Sbjct: 61 AYVEYENESQASQAVMKMDGMTIKENII 88
>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 = 31.9 bits (73), Expect = 0.051
Identities = 7/60 (11%), Positives = 21/60 (35%)
Query: 63 NLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCILGNTTI 122
+ + ++ G + ++ + ++ST E A A ++N + +
Sbjct: 32 GIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91
>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 = 32.7 bits (75), Expect = 0.056
Identities = 16/67 (23%), Positives = 27/67 (40%), Gaps = 6/67 (8%)
Query: 62 KNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAK------YSTREEAIKAQGNLNNC 115
L ++ +K L GPL+ F+L + + L+K Y +A LN
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 179
Query: 116 ILGNTTI 122
LG+ +
Sbjct: 180 QLGDKKL 186
>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 = 32.2 bits (74), Expect = 0.063
Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 10/87 (11%)
Query: 62 KNLTPQIDGSTLKTLCVQHGPLQNFHL------YLNHSLALA--KYSTREEAIKAQGNLN 113
+ L+ L Q+G + ++ S + TR+ A++AQ L+
Sbjct: 9 GQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALH 68
Query: 114 N-CILGNTTIFAEA-PSDAEVQSLLAH 138
N +L + P+D+E + +
Sbjct: 69 NMKVLPGMHHPIQMKPADSEKNNAVED 95
>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 = 32.9 bits (74), Expect = 0.075
Identities = 25/107 (23%), Positives = 36/107 (33%), Gaps = 27/107 (25%)
Query: 33 VRPN------GGGGGGNTWGTSQ------PQGGWSGT--WVLLKNL-TPQIDGSTLKTLC 77
+RP G G G TW Q W+ LKN +P+ L+ L
Sbjct: 147 LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLL 206
Query: 78 VQHGPLQNFHLYLNHSLALAKYSTREEAIK-------AQGNLNNCIL 117
Q P N+ +HS + R +I+ NC+L
Sbjct: 207 YQIDP--NWTSRSDHS---SNIKLRIHSIQAELRRLLKSKPYENCLL 248
>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 = 30.7 bits (70), Expect = 0.11
Identities = 13/61 (21%), Positives = 23/61 (37%)
Query: 62 KNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCILGNTT 121
+NL ++ P + A +S RE+A++A LN +L +
Sbjct: 21 RNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSP 80
Query: 122 I 122
I
Sbjct: 81 I 81
>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 = 30.7 bits (70), Expect = 0.11
Identities = 13/78 (16%), Positives = 24/78 (30%), Gaps = 5/78 (6%)
Query: 42 GNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS-----LAL 96
G++ + G + + L Q + L G + + A
Sbjct: 1 GSSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAF 60
Query: 97 AKYSTREEAIKAQGNLNN 114
K+S+ EA A L+
Sbjct: 61 VKFSSHTEAQAAIHALHG 78
>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 = 30.8 bits (70), Expect = 0.12
Identities = 11/70 (15%), Positives = 27/70 (38%), Gaps = 3/70 (4%)
Query: 59 VLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSL---ALAKYSTREEAIKAQGNLNNC 115
+ ++NL +I + + ++GP++ + A Y +A A +L+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGF 70
Query: 116 ILGNTTIFAE 125
+ N +
Sbjct: 71 NVSNRYLVVL 80
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 30.6 bits (69), Expect = 0.13
Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 12/79 (15%)
Query: 59 VLLKNL-TPQ-IDGST---LKTLCVQHGPLQNFHLYLNHSL-------ALAKYSTREEAI 106
VLL+N+ +D K C ++G + ++ ++ E AI
Sbjct: 11 VLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAI 70
Query: 107 KAQGNLNNCILGNTTIFAE 125
KA +LN G + A
Sbjct: 71 KAVVDLNGRYFGGRVVKAC 89
>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 = 30.3 bits (69), Expect = 0.14
Identities = 16/93 (17%), Positives = 35/93 (37%), Gaps = 3/93 (3%)
Query: 42 GNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYST 101
G++ + + + + + NL P I ++ L ++G ++ + + T
Sbjct: 1 GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLET 60
Query: 102 REEAIKAQGNLNNCILGNTTI---FAEAPSDAE 131
R A A+ L+N L + FA +
Sbjct: 61 RTLAEIAKVELDNMPLRGKQLRVRFACHSASLT 93
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 30.8 bits (69), Expect = 0.15
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 47 TSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSL-ALAKYSTREEA 105
T P GG + ++N I L T+C G +Q ++ + + A+ ++ + A
Sbjct: 16 TDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCA 75
Query: 106 IKAQGNLNNC 115
KA+ LN
Sbjct: 76 QKAKAALNGA 85
>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 = 30.4 bits (69), Expect = 0.17
Identities = 18/99 (18%), Positives = 37/99 (37%), Gaps = 6/99 (6%)
Query: 46 GTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS-----LALAKYS 100
G +G +G +L+ NL + + ++ L + G L+ + + S A +
Sbjct: 25 GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFE 84
Query: 101 TREEAIKAQGNLNNCILGNTTIF-AEAPSDAEVQSLLAH 138
R +A+KA L + S +++ H
Sbjct: 85 RRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHH 123
>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 = 30.4 bits (69), Expect = 0.17
Identities = 18/83 (21%), Positives = 30/83 (36%), Gaps = 6/83 (7%)
Query: 46 GTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS------LALAKY 99
PQ G + + + + + ++G ++N HL L+ L +Y
Sbjct: 12 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 71
Query: 100 STREEAIKAQGNLNNCILGNTTI 122
T +EA A LN L I
Sbjct: 72 ETYKEAQAAMEGLNGQDLMGQPI 94
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 31.1 bits (71), Expect = 0.19
Identities = 23/142 (16%), Positives = 46/142 (32%), Gaps = 22/142 (15%)
Query: 14 GPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTL 73
G M GG + G + G + V + ++ ++ T+
Sbjct: 1 GSHMASMTGG-QQMGRGSAAQRQGALAIMSR--------------VYVGSIYYELGEDTI 45
Query: 74 KTLCVQHGPLQNFHLYLNHSLALAK------YSTREEAIKAQGNLNNCILGNTTIF-AEA 126
+ GP+++ + + K Y E A A +N+ +LG I
Sbjct: 46 RQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP 105
Query: 127 PSDAEVQSLLAHLSATANNNNN 148
+ + Q ++ L+ A N
Sbjct: 106 SNIGQAQPIIDQLAEEARAFNR 127
Score = 27.3 bits (61), Expect = 3.6
Identities = 9/68 (13%), Positives = 25/68 (36%), Gaps = 6/68 (8%)
Query: 62 KNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAK------YSTREEAIKAQGNLNNC 115
++ + +K++ G +++ L + + K Y + + A ++N
Sbjct: 131 ASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLF 190
Query: 116 ILGNTTIF 123
LG +
Sbjct: 191 DLGGQYLR 198
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 30.1 bits (68), Expect = 0.23
Identities = 11/59 (18%), Positives = 17/59 (28%), Gaps = 10/59 (16%)
Query: 77 CVQHGPLQNFHLYLNHSLALA----------KYSTREEAIKAQGNLNNCILGNTTIFAE 125
C + G + +Y ++S E KA LN + AE
Sbjct: 46 CGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAE 104
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 29.5 bits (67), Expect = 0.27
Identities = 18/83 (21%), Positives = 30/83 (36%), Gaps = 6/83 (7%)
Query: 46 GTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS------LALAKY 99
PQ G + + + + + ++G ++N HL L+ L +Y
Sbjct: 13 DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 72
Query: 100 STREEAIKAQGNLNNCILGNTTI 122
T +EA A LN L I
Sbjct: 73 ETYKEAQAAMEGLNGQDLMGQPI 95
>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 = 30.3 bits (69), Expect = 0.28
Identities = 16/67 (23%), Positives = 27/67 (40%), Gaps = 6/67 (8%)
Query: 62 KNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAK------YSTREEAIKAQGNLNNC 115
L ++ +K L GPL+ F+L + + L+K Y +A LN
Sbjct: 100 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGM 159
Query: 116 ILGNTTI 122
LG+ +
Sbjct: 160 QLGDKKL 166
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 29.8 bits (67), Expect = 0.29
Identities = 16/95 (16%), Positives = 30/95 (31%), Gaps = 3/95 (3%)
Query: 34 RPNGGGGGGNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNF---HLYL 90
+ G G+ + + +KNL LK L ++ F +
Sbjct: 6 HHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRD 65
Query: 91 NHSLALAKYSTREEAIKAQGNLNNCILGNTTIFAE 125
++ + E ++A LNN + I E
Sbjct: 66 FDGTGALEFPSEEILVEALERLNNIEFRGSVITVE 100
>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 = 29.6 bits (67), Expect = 0.30
Identities = 14/83 (16%), Positives = 30/83 (36%), Gaps = 5/83 (6%)
Query: 46 GTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS-----LALAKYS 100
+ Q G G+ V + NL ++ LK + G + + + + +
Sbjct: 5 SSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFE 64
Query: 101 TREEAIKAQGNLNNCILGNTTIF 123
EA++A N +L + +
Sbjct: 65 QSIEAVQAISMFNGQLLFDRPMH 87
>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 = 29.1 bits (66), Expect = 0.32
Identities = 17/87 (19%), Positives = 26/87 (29%), Gaps = 5/87 (5%)
Query: 41 GGNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS-----LA 95
G + P + V + NL ++ L L +Q GPL + +
Sbjct: 1 GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60
Query: 96 LAKYSTREEAIKAQGNLNNCILGNTTI 122
+ E A LN L I
Sbjct: 61 FVCFKHPESVSYAIALLNGIRLYGRPI 87
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 30.5 bits (68), Expect = 0.35
Identities = 10/61 (16%), Positives = 24/61 (39%)
Query: 62 KNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYSTREEAIKAQGNLNNCILGNTT 121
K+L P S ++ + + G + + + K+ + A A+ ++N L +
Sbjct: 149 KHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPS 208
Query: 122 I 122
Sbjct: 209 D 209
>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 = 0.37
Identities = 12/88 (13%), Positives = 29/88 (32%), Gaps = 13/88 (14%)
Query: 56 GTWVLLKNLTPQIDGST-------LKTLCVQHGPLQNFHLYLN----HSLALAKYSTREE 104
+ +++ N+ PQ+ + + + G + N +Y++
Sbjct: 15 DSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAH 73
Query: 105 AIKAQGNLNNCIL-GNTTIFAEAPSDAE 131
A+ A N + L T +D +
Sbjct: 74 AVDAVKNADGYKLDKQHTFRVNLFTDFD 101
>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 = 30.1 bits (67), Expect = 0.41
Identities = 12/64 (18%), Positives = 27/64 (42%), Gaps = 2/64 (3%)
Query: 58 WVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYL--NHSLALAKYSTREEAIKAQGNLNNC 115
++++NL + L + + G + + N AL +Y+ A A+ +L+
Sbjct: 48 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 107
Query: 116 ILGN 119
+ N
Sbjct: 108 NIYN 111
>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 = 28.8 bits (65), Expect = 0.41
Identities = 14/87 (16%), Positives = 34/87 (39%), Gaps = 6/87 (6%)
Query: 42 GNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQN-FHLYLNHS-----LA 95
G++ + G T + ++N+ + + + + L N A
Sbjct: 1 GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 96 LAKYSTREEAIKAQGNLNNCILGNTTI 122
+ + +R+EA A +LN+ +G+ +
Sbjct: 61 MVAFESRDEATAAVIDLNDRPIGSRKV 87
>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 = 28.8 bits (65), Expect = 0.45
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 9/79 (11%)
Query: 48 SQPQGGWSGTWVL-LKNLTPQIDGSTLKTLCVQHGPLQNFHL---YLNHSLALAKYSTRE 103
S G + VL ++NL + L+ Q G L+ Y A + R+
Sbjct: 2 SSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY-----AFIHFDERD 56
Query: 104 EAIKAQGNLNNCILGNTTI 122
A+KA +N L I
Sbjct: 57 GAVKAMEEMNGKDLEGENI 75
>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 = 28.8 bits (65), Expect = 0.60
Identities = 13/74 (17%), Positives = 26/74 (35%), Gaps = 7/74 (9%)
Query: 63 NLTPQIDGSTLKTLCVQHGPLQNFHLYL----NHSLALAKYSTREEAIKAQGNLNNCILG 118
NL+ + + L Q GP ++ + N ++ +A A +N +
Sbjct: 22 NLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKIL 81
Query: 119 NTTI---FAEAPSD 129
+ +A PS
Sbjct: 82 GKEVKVNWATTPSS 95
>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 = 28.4 bits (64), Expect = 0.65
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 6/58 (10%)
Query: 63 NLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS------LALAKYSTREEAIKAQGNLNN 114
+ +D LK L + G + + + A Y RE A+KAQ L+
Sbjct: 20 QIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHE 77
>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 = 29.6 bits (67), Expect = 0.73
Identities = 11/66 (16%), Positives = 24/66 (36%), Gaps = 6/66 (9%)
Query: 63 NLTPQIDGSTLKTLCVQHGPLQNFHL----YLNHSL--ALAKYSTREEAIKAQGNLNNCI 116
+L P + + L GP+ + + SL A + +A +A +N +
Sbjct: 22 DLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDV 81
Query: 117 LGNTTI 122
+ +
Sbjct: 82 IKGKPV 87
Score = 26.5 bits (59), Expect = 6.5
Identities = 21/118 (17%), Positives = 42/118 (35%), Gaps = 8/118 (6%)
Query: 45 WGTSQPQGGWSGTW-VLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSL----ALAKY 99
W P SG + +KNL ID L G + + + + + +
Sbjct: 91 WSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHF 150
Query: 100 STREEAIKAQGNLNNCILGNTTIF---AEAPSDAEVQSLLAHLSATANNNNNNNGGTG 154
T+E A +A +N +L + +F ++ + E + + + G +G
Sbjct: 151 ETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAGSSG 208
>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 = 29.0 bits (66), Expect = 0.76
Identities = 16/70 (22%), Positives = 27/70 (38%), Gaps = 7/70 (10%)
Query: 58 WVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLN---HSL--ALAKYSTREEAIKAQGNL 112
+V NL I LK GP+ N + ++ ++ A +Y +A A L
Sbjct: 4 YV--GNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 113 NNCILGNTTI 122
N + N +
Sbjct: 62 NGKQIENNIV 71
>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 = 28.0 bits (63), Expect = 0.94
Identities = 14/80 (17%), Positives = 33/80 (41%), Gaps = 7/80 (8%)
Query: 42 GNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSL------- 94
G++ + Q + + +L++N+ Q + ++ L G L+ L +
Sbjct: 1 GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 95 ALAKYSTREEAIKAQGNLNN 114
+ T+++A KA L +
Sbjct: 61 GFVDFITKQDAKKAFNALCH 80
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 28.1 bits (63), Expect = 1.0
Identities = 15/115 (13%), Positives = 37/115 (32%), Gaps = 12/115 (10%)
Query: 14 GPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTL 73
P G P + G + G G + + +L + + L
Sbjct: 4 LPQFGSASALSTSPLASVALSAAAAAAAG------KQIEGPEGCNLFIYHLPQEFTDTDL 57
Query: 74 KTLCVQHGPLQNFHLYLNHSLALAK------YSTREEAIKAQGNLNNCILGNTTI 122
+ + G + + ++++ +L+K + + A A +N +G +
Sbjct: 58 ASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRL 112
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 27.8 bits (62), Expect = 1.2
Identities = 10/68 (14%), Positives = 22/68 (32%), Gaps = 7/68 (10%)
Query: 71 STLKTLCVQHGPLQNFHLYLNHS------LALAKYSTREEAIKAQGNLNNCIL-GNTTIF 123
L +L + G + N ++ + + + +A K + + L +F
Sbjct: 27 KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLF 86
Query: 124 AEAPSDAE 131
D E
Sbjct: 87 LYTMKDVE 94
>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 = 27.2 bits (61), Expect = 1.9
Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 5/82 (6%)
Query: 46 GTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS-----LALAKYS 100
G G +G +L+ NL + + ++ L + G L+ ++ + S A +
Sbjct: 19 GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFE 78
Query: 101 TREEAIKAQGNLNNCILGNTTI 122
+ +A+KA N L +
Sbjct: 79 RKADALKAMKQYNGVPLDGRPM 100
>3bc8_A O-phosphoseryl-tRNA(SEC) selenium transferase; disorder-order
transition, phosphate-loop, pyridoxal phospha
selenocysteine synthase (SECS, sepsecs); HET: LLP; 1.65A
{Mus musculus} SCOP: c.67.1.9 PDB: 3bca_A* 3bcb_A*
Length = 450
Score = 28.5 bits (63), Expect = 2.0
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 1/75 (1%)
Query: 103 EEAIKAQGNLNNCILGNTTIFAEAPSDAEVQSLLAHLSATANNNNNNNGGTGGW-ARGSS 161
EA +A +L +L + ++ ++ L L+ +NN N G G R +S
Sbjct: 4 CEARRAHEHLIRLLLEQGKCPEDGWDESTLELFLHELAVMDSNNFLGNCGVGEREGRVAS 63
Query: 162 ALSNKDTWSSGGGGG 176
AL + + G G
Sbjct: 64 ALVARRHYRFIHGIG 78
>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 = 27.1 bits (60), Expect = 2.3
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 99 YSTREEAIKAQGNLNNCILGNTTIFAE 125
Y E+A++A +NN ++ T+ A
Sbjct: 70 YIRSEDALRAIQCVNNVVVDGRTLKAS 96
>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 = 26.9 bits (60), Expect = 2.4
Identities = 16/84 (19%), Positives = 34/84 (40%), Gaps = 7/84 (8%)
Query: 46 GTSQPQGGWSGTWVL-LKNLTPQIDGSTLKTLCVQHGPLQN-FHLYLNHS-----LALAK 98
G+S G G V+ ++N+ + + + + L N A+
Sbjct: 4 GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVA 63
Query: 99 YSTREEAIKAQGNLNNCILGNTTI 122
+ +R+EA A +LN+ +G+ +
Sbjct: 64 FESRDEATAAVIDLNDRPIGSRKV 87
>3rao_A Putative luciferase-like monooxygenase; unknown, structural
genomics, PSI-biology, midwest center FO structural
genomics, MCSG, enzyme; 2.30A {Bacillus cereus}
Length = 371
Score = 28.1 bits (63), Expect = 2.4
Identities = 9/60 (15%), Positives = 17/60 (28%)
Query: 126 APSDAEVQSLLAHLSATANNNNNNNGGTGGWARGSSALSNKDTWSSGGGGGNTSQLWGTP 185
++ E ++ ++ G ++ K S G L GTP
Sbjct: 263 RHTEEEALEEWRRITDVKDDALGYAGYQDFVSKSQLEQQVKLNDYSVSNRGLRPNLIGTP 322
>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 = 26.8 bits (60), Expect = 2.4
Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 6/66 (9%)
Query: 63 NLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS------LALAKYSTREEAIKAQGNLNNCI 116
++ + LC GP+ N + + A ++ E + A NLN
Sbjct: 9 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 68
Query: 117 LGNTTI 122
LG+ +
Sbjct: 69 LGSRFL 74
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid
cyclase fold, DDXXXXD motif, NDXXSXXXE MOT
methylisoborneol biosynthesis; HET: GST; 1.80A
{Streptomyces coelicolor} PDB: 3v1x_A*
Length = 433
Score = 28.2 bits (62), Expect = 2.6
Identities = 10/41 (24%), Positives = 12/41 (29%)
Query: 10 PKPRGPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQP 50
P P PPP G P + G GT+
Sbjct: 46 PDPAPPPPPAPAAGNPPDTVTGDSVLQRILRGPTGPGTTSL 86
>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 = 26.4 bits (59), Expect = 2.9
Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 10/92 (10%)
Query: 37 GGGGGGNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS--- 93
G G G P S + V + NL + + L + ++G + + +
Sbjct: 1 GSSGSSGMSGGLAP----SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRK 56
Query: 94 ---LALAKYSTREEAIKAQGNLNNCILGNTTI 122
+A + ++ A +NN L I
Sbjct: 57 SKGVAFILFLDKDSAQNCTRAINNKQLFGRVI 88
>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 = 26.3 bits (59), Expect = 3.3
Identities = 14/75 (18%), Positives = 23/75 (30%), Gaps = 6/75 (8%)
Query: 62 KNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAK------YSTREEAIKAQGNLNNC 115
+ L P L LC +G + + L+ + K + + A KA L
Sbjct: 11 RGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKAS 70
Query: 116 ILGNTTIFAEAPSDA 130
+ PS
Sbjct: 71 GVQAQMAKQSGPSSG 85
>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 = 26.4 bits (59), Expect = 3.3
Identities = 10/68 (14%), Positives = 24/68 (35%), Gaps = 5/68 (7%)
Query: 61 LKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS-----LALAKYSTREEAIKAQGNLNNC 115
+ NL +D L+ + G + + + + S + A+ + E+ G+ N
Sbjct: 30 ISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGK 89
Query: 116 ILGNTTIF 123
+
Sbjct: 90 FIKTPPGV 97
>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 = 26.5 bits (59), Expect = 3.7
Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 6/66 (9%)
Query: 63 NLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAK------YSTREEAIKAQGNLNNCI 116
L ++ L L +Q GP+ N H+ + + + + E+A A ++
Sbjct: 22 GLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIK 81
Query: 117 LGNTTI 122
L I
Sbjct: 82 LYGKPI 87
>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 = 26.3 bits (58), Expect = 4.0
Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 1/82 (1%)
Query: 41 GGNTWGTSQPQGGWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAKYS 100
GG G P S V++ L P LK + G + +Y + + + ++
Sbjct: 1 GGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT-GVVEFV 59
Query: 101 TREEAIKAQGNLNNCILGNTTI 122
+E+ A L+N +
Sbjct: 60 RKEDMTYAVRKLDNTKFRSHEG 81
>2b81_A Luciferase-like monooxygenase; TIM barrel, structural genomics,
PSI, protein structure INIT midwest center for
structural genomics, MCSG; HET: MES; 2.50A {Bacillus
cereus}
Length = 323
Score = 27.1 bits (60), Expect = 4.8
Identities = 9/38 (23%), Positives = 12/38 (31%), Gaps = 7/38 (18%)
Query: 5 DLWGPPKPRGPPPGMMGGGGKPP-------SNGWMVRP 35
PKP P + G + +GWM P
Sbjct: 184 GANLVPKPSKRVPTFITGFSQQNMEWFAEHGDGWMYYP 221
>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 = 25.7 bits (57), Expect = 6.2
Identities = 15/94 (15%), Positives = 34/94 (36%), Gaps = 7/94 (7%)
Query: 36 NGGGGGGNTWGTSQPQG-GWSGTWVLLKNLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSL 94
G + G + Q G G + + +L + L + + G + + ++++
Sbjct: 4 GSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 63
Query: 95 ALAK------YSTREEAIKAQGNLNNCILGNTTI 122
L+K Y A A ++N +G +
Sbjct: 64 NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRL 97
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 3cw1_A
Length = 231
Score = 26.5 bits (58), Expect = 7.1
Identities = 10/45 (22%), Positives = 10/45 (22%)
Query: 8 GPPKPRGPPPGMMGGGGKPPSNGWMVRPNGGGGGGNTWGTSQPQG 52
P G GG PP G P G G
Sbjct: 158 TASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPP 202
>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 = 25.3 bits (56), Expect = 7.7
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 6/62 (9%)
Query: 63 NLTPQIDGSTLKTLCVQHGPLQNFHLYLNHS------LALAKYSTREEAIKAQGNLNNCI 116
NL+ L+ L +GPL H ++ A + E A+KA ++ +
Sbjct: 15 NLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQV 74
Query: 117 LG 118
Sbjct: 75 FQ 76
>1rhc_A F420-dependent alcohol dehydrogenase; (alpha, beta)8 barrel,
oxidoreductase; HET: F42; 1.80A {Methanoculleus
thermophilus} SCOP: c.1.16.3
Length = 330
Score = 26.2 bits (58), Expect = 8.5
Identities = 5/15 (33%), Positives = 5/15 (33%)
Query: 10 PKPRGPPPGMMGGGG 24
KP P G G
Sbjct: 162 TKPDDEVPLYFSGMG 176
>3ghg_A Fibrinogen alpha chain; triple-stranded coiled coil, beta sheets,
alpha helices, AMY amyloidosis, blood coagulation,
disease mutation, glycoprot phosphoprotein; HET: NAG NDG
BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 3h32_A*
2a45_G*
Length = 562
Score = 26.4 bits (57), Expect = 8.6
Identities = 13/72 (18%), Positives = 22/72 (30%)
Query: 142 TANNNNNNNGGTGGWARGSSALSNKDTWSSGGGGGNTSQLWGTPSNPSSGGSLWGAPPLD 201
T N ++ G G W SS + W S G + P++
Sbjct: 340 TWNPGSSERGSAGHWTSESSVSGSTGQWHSESGSFRPDSPGSGNARPNNPDWGTFEEVSG 399
Query: 202 SVDRATPSSLNS 213
+V T ++
Sbjct: 400 NVSPGTRREYHT 411
>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 = 25.9 bits (57), Expect = 9.5
Identities = 13/66 (19%), Positives = 24/66 (36%), Gaps = 6/66 (9%)
Query: 63 NLTPQIDGSTLKTLCVQHGPLQNFHLYLNHSLALAK------YSTREEAIKAQGNLNNCI 116
NL+ + L + G ++ + L+ A Y +R +A A +N
Sbjct: 46 NLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTR 105
Query: 117 LGNTTI 122
L + I
Sbjct: 106 LDDRII 111
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
0.309 0.131 0.422
Gapped
Lambda K H
0.267 0.0454 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,524,338
Number of extensions: 204961
Number of successful extensions: 839
Number of sequences better than 10.0: 1
Number of HSP's gapped: 730
Number of HSP's successfully gapped: 178
Length of query: 225
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 135
Effective length of database: 4,188,903
Effective search space: 565501905
Effective search space used: 565501905
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 55 (25.6 bits)