RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11527
(206 letters)
>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 = 69.9 bits (171), Expect = 3e-15
Identities = 27/138 (19%), Positives = 55/138 (39%), Gaps = 12/138 (8%)
Query: 48 VHPALHPQVPSLNIPHPTAALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCST 107
+ + H V LT + + + F N P +T
Sbjct: 73 ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPG----------SKNFQNIFPPSAT 122
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSY 167
L ++N+ VSE+++K +F S G + + +A I+ V A+QA+ +L+
Sbjct: 123 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 182
Query: 168 LASSDRGAIRIEYAKTKM 185
L + +R+ ++K+ +
Sbjct: 183 LGEN--HHLRVSFSKSTI 198
Score = 53.0 bits (127), Expect = 5e-09
Identities = 31/97 (31%), Positives = 46/97 (47%), Gaps = 7/97 (7%)
Query: 106 STLFVANLGQF-VSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAFIEYTDVNFAIQAMSNL 163
S L V+NL V+ Q + +FG + RV+ + NK + A ++ D N A AMS+L
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN--ALVQMADGNQAQLAMSHL 61
Query: 164 NGSYLASSDRGAIRIEYAKTKMAEFTTEHRTRHQGTK 200
NG L IRI +K + + E + TK
Sbjct: 62 NGHKLHGK---PIRITLSKHQNVQLPREGQEDQGLTK 95
>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 = 66.5 bits (163), Expect = 6e-15
Identities = 23/94 (24%), Positives = 39/94 (41%), Gaps = 3/94 (3%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEY 150
S G +P + L+V LG S + F F + G A+I+Y
Sbjct: 3 SGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH--VKGDSFAYIQY 60
Query: 151 TDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
++ A A + + G L DR +R+++AK+
Sbjct: 61 ESLDAAQAACAKMRGFPLGGPDR-RLRVDFAKSG 93
>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 = 67.0 bits (164), Expect = 7e-15
Identities = 21/98 (21%), Positives = 47/98 (47%), Gaps = 4/98 (4%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQAMSN 162
L++ NL ++ +E+ DIFG + ++R+ N + A++ Y D+ A A+ +
Sbjct: 7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDH 66
Query: 163 LNGSYLASSDRGAIRIEYAKTKMAEFTTEHRTRHQGTK 200
L+G ++ +R + + Y A + + + + K
Sbjct: 67 LSGFNVS--NR-YLVVLYYNANRAFQKMDTKKKEEQLK 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 = 67.7 bits (165), Expect = 3e-14
Identities = 27/138 (19%), Positives = 55/138 (39%), Gaps = 12/138 (8%)
Query: 48 VHPALHPQVPSLNIPHPTAALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCST 107
+ + H V LT + + + F N P +T
Sbjct: 104 ITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPG----------SKNFQNIFPPSAT 153
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSY 167
L ++N+ VSE+++K +F S G + + +A I+ V A+QA+ +L+
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 213
Query: 168 LASSDRGAIRIEYAKTKM 185
L + +R+ ++K+ +
Sbjct: 214 LGEN--HHLRVSFSKSTI 229
Score = 59.6 bits (144), Expect = 3e-11
Identities = 36/132 (27%), Positives = 56/132 (42%), Gaps = 10/132 (7%)
Query: 74 ANGMPHFLPSPALPSPVGSSPPSQGMNGM--SPCSTLFVANLGQF-VSEQEIKDIFGSFP 130
+ H + P GS + G+ + S L V+NL V+ Q + +FG +
Sbjct: 2 GSSHHHH-HHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYG 60
Query: 131 GFSRVR-MHNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTKMAEFT 189
RV+ + NK + A ++ D N A AMS+LNG L IRI +K + +
Sbjct: 61 DVQRVKILFNKKEN--ALVQMADGNQAQLAMSHLNGHKLHGK---PIRITLSKHQNVQLP 115
Query: 190 TEHRTRHQGTKY 201
E + TK
Sbjct: 116 REGQEDQGLTKD 127
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 99
Score = 64.6 bits (158), Expect = 4e-14
Identities = 28/95 (29%), Positives = 42/95 (44%), Gaps = 7/95 (7%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAFIE 149
GSS S + MS L+V NL SE+ I+ F + + R + AF+
Sbjct: 1 GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD---YAFVH 57
Query: 150 YTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+++ A++AM LNG L S I + AK
Sbjct: 58 FSNREDAVEAMKALNGKVLDGS---PIEVTLAKPV 89
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 63.6 bits (155), Expect = 9e-14
Identities = 18/97 (18%), Positives = 38/97 (39%), Gaps = 4/97 (4%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAFIE 149
GSS S + L + N+ + + + + + ++ + V +
Sbjct: 1 GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVT 60
Query: 150 YTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTKMA 186
Y+ + A QA+ LNG L + +++ Y +MA
Sbjct: 61 YSSKDQARQALDKLNGFQLENF---TLKVAYIPDEMA 94
>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 = 65.3 bits (158), Expect = 4e-13
Identities = 41/182 (22%), Positives = 69/182 (37%), Gaps = 6/182 (3%)
Query: 1 MEKSNAKVLDIGAPFFHAGGPELWHHPLAYATAADLPGTASLHQHTLVHPALHPQVPSLN 60
++ K P P+ A +PG + Q + + Q P +
Sbjct: 106 RKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMP 165
Query: 61 IPHPTAALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQ 120
P + P +P L PP+Q ++ P LF+ NL + +E
Sbjct: 166 -PPGMIPPPGLAPGQIPPGAMPPQQLMPG--QMPPAQPLSENPPNHILFLTNLPEETNEL 222
Query: 121 EIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEY 180
+ +F FPGF VR+ G +AF+E+ + A A L G + + A++I +
Sbjct: 223 MLSMLFNQFPGFKEVRLV-PGRHDIAFVEFDNEVQAGAARDALQGFKI--TQNNAMKISF 279
Query: 181 AK 182
AK
Sbjct: 280 AK 281
Score = 60.7 bits (146), Expect = 2e-11
Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 8/86 (9%)
Query: 104 PCSTLFVANLGQFVSEQEIK----DIFGSFPGFSRVRMHNKGGS-PVAFIEYTDVNFAIQ 158
P T+++ NL + + + E+K IF F + + AF+ + +V+ A
Sbjct: 8 PNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 159 AMSNLNGSYLASSDRGAIRIEYAKTK 184
A+ ++ G +RI+YAKT
Sbjct: 68 ALRSMQGFPFYDK---PMRIQYAKTD 90
>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 = 61.5 bits (150), Expect = 5e-13
Identities = 31/103 (30%), Positives = 48/103 (46%), Gaps = 8/103 (7%)
Query: 96 SQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNF 155
S G +GM+ LFV NL V+E+ ++ F F RV+ K AFI + + +
Sbjct: 2 SSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-KD---YAFIHFDERDG 57
Query: 156 AIQAMSNLNGSYLASSDRGAIRIEYAKTKMAEFTTEHRTRHQG 198
A++AM +NG L I I +AK + E + + Q
Sbjct: 58 AVKAMEEMNGKDLEGE---NIEIVFAKPP-DQKRKERKAQRQA 96
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 61.4 bits (149), Expect = 6e-13
Identities = 25/97 (25%), Positives = 41/97 (42%), Gaps = 4/97 (4%)
Query: 88 SPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAF 147
S S P S G + ++V NL + ++K G +R+ +G AF
Sbjct: 2 SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALREL-GSVPLRLTWQGPRRRAF 60
Query: 148 IEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+ Y D A QA+S L G L + +R+ A+ +
Sbjct: 61 LHYPDSAAAQQAVSCLQGLRLGTD---TLRVALARQQ 94
>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 = 61.5 bits (150), Expect = 7e-13
Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 5/96 (5%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM--HNKGGSPVAFI 148
GSS S M TL+V NL + V+E I +F +M + P F+
Sbjct: 1 GSSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFV 60
Query: 149 EYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
E+ + A A++ +NG + + +++ +A T
Sbjct: 61 EFYEHRDAAAALAAMNGRKIL--GK-EVKVNWATTP 93
>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 = 60.8 bits (148), Expect = 1e-12
Identities = 24/97 (24%), Positives = 38/97 (39%), Gaps = 7/97 (7%)
Query: 92 SSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR--MHNKGGSP--VAF 147
P N P L++ NL V+E+++ +F F G AF
Sbjct: 12 KIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAF 71
Query: 148 IEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
I + + A QA+ +NG L + + IE+ K K
Sbjct: 72 ITFPNKEIAWQALHLVNGYKLY--GK-ILVIEFGKNK 105
>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 = 59.8 bits (145), Expect = 3e-12
Identities = 17/94 (18%), Positives = 37/94 (39%), Gaps = 3/94 (3%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEY 150
GSS S + +S + V L + V E ++ + F V M A +E+
Sbjct: 1 GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQ--ALVEF 58
Query: 151 TDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+++ A + ++ + + + Y+ +K
Sbjct: 59 ENIDSAKECVTFAADVPVYIAGQ-QAFFNYSTSK 91
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 59.5 bits (144), Expect = 6e-12
Identities = 13/108 (12%), Positives = 33/108 (30%), Gaps = 10/108 (9%)
Query: 84 PALPSPVGSSPPSQGMNG--MSPCSTLFVANLGQFVSEQEIK----DIFGSFPGFSRVRM 137
A P G P + + N+ V +++++ + S + +
Sbjct: 6 AAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV 65
Query: 138 HNKGGS-PVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+ A+I + A + G + + I +++T
Sbjct: 66 DLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGN---PLVITFSETP 110
>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 = 58.1 bits (141), Expect = 1e-11
Identities = 26/95 (27%), Positives = 44/95 (46%), Gaps = 5/95 (5%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP-VAFIE 149
GSS S TL ++NL +E+ ++++F F +V + G S AFIE
Sbjct: 1 GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKA-TFIKVPQNQNGKSKGYAFIE 59
Query: 150 YTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+ A +A+++ N + R AIR+E +
Sbjct: 60 FASFEDAKEALNSCNKREIE--GR-AIRLELQGPR 91
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 57.3 bits (139), Expect = 2e-11
Identities = 19/104 (18%), Positives = 38/104 (36%), Gaps = 8/104 (7%)
Query: 83 SPALPSPVGSSPPSQGMNGMSP-CSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMH-NK 140
+ LP V + P +T ++ N+ F +E ++ +F +F + + K
Sbjct: 4 TIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK 63
Query: 141 GGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
G FI+Y A + L + +R + K +
Sbjct: 64 G---CCFIKYDTHEQAAVCIVALANFPFQGRN---LRTGWGKER 101
>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 = 58.4 bits (141), Expect = 2e-11
Identities = 20/100 (20%), Positives = 38/100 (38%), Gaps = 6/100 (6%)
Query: 86 LPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPV 145
+ + ++V NLG ++ E++ FG + V + P
Sbjct: 54 VTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWV--ARNPPG 111
Query: 146 -AFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
AF+E+ D A A+ L+G L +R+E + +
Sbjct: 112 FAFVEFEDPRDAADAVRELDGRTL---CGCRVRVELSNGE 148
>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 = 59.0 bits (142), Expect = 2e-11
Identities = 28/125 (22%), Positives = 50/125 (40%), Gaps = 3/125 (2%)
Query: 60 NIPHPTAALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSE 119
+ H +A A+ N + + AL + + M G SP + V NL V+
Sbjct: 3 HHHHHGSAQAALQAVNSVQ--SGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTL 60
Query: 120 QEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIE 179
+ IF F ++ K A ++Y D A A +L+G + + +RI+
Sbjct: 61 DVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIY-NACCTLRID 119
Query: 180 YAKTK 184
++K
Sbjct: 120 FSKLT 124
>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 = 58.3 bits (141), Expect = 2e-11
Identities = 23/102 (22%), Positives = 45/102 (44%), Gaps = 12/102 (11%)
Query: 92 SSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFS--------RVRMHNKGGS 143
+ + P ++V NL + V E+++K IFG + FS +R+ +G
Sbjct: 32 TLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRM 91
Query: 144 P-VAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
AFI + A +A+ NG L + + +++A++
Sbjct: 92 KGQAFIGLPNEKAAAKALKEANGYVLF--GK-PMVVQFARSA 130
>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 = 56.9 bits (138), Expect = 3e-11
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 8/86 (9%)
Query: 104 PCSTLFVANLGQFVSEQEIK----DIFGSFPGFSRVRMHNKGGSP-VAFIEYTDVNFAIQ 158
P T+++ NL + + + E+K IF F + + AF+ + +V+ A
Sbjct: 7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 159 AMSNLNGSYLASSDRGAIRIEYAKTK 184
A+ ++ G D+ +RI+YAKT
Sbjct: 67 ALRSMQGFPFY--DK-PMRIQYAKTD 89
>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 = 56.5 bits (137), Expect = 3e-11
Identities = 23/90 (25%), Positives = 45/90 (50%), Gaps = 10/90 (11%)
Query: 98 GMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPG--FSRVRMHNKGGSPVAFIEYTDVNF 155
G +G S + L++ NL V+ +++ +FG + + G AF++Y D N+
Sbjct: 1 GSSGSSGMNKLYIGNLSPAVTADDLRQLFGDR-KLPLAGQVLLKSG---YAFVDYPDQNW 56
Query: 156 AIQAMSNLNGSY-LASSDRGAIRIEYAKTK 184
AI+A+ L+G L + ++Y+ +K
Sbjct: 57 AIRAIETLSGKVELHGK---IMEVDYSVSK 83
>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 = 56.6 bits (137), Expect = 4e-11
Identities = 23/96 (23%), Positives = 45/96 (46%), Gaps = 5/96 (5%)
Query: 88 SPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPV-A 146
S + +G G + C ++V NL + ++I+D+F + + + N+ G P A
Sbjct: 6 SGMSGGGVIRGPAGNNDC-RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFA 64
Query: 147 FIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAK 182
F+E+ D A A+ +G D +R+E+ +
Sbjct: 65 FVEFEDPRDAEDAVYGRDGYDY---DGYRLRVEFPR 97
>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition
motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 99
Score = 56.1 bits (136), Expect = 5e-11
Identities = 26/95 (27%), Positives = 40/95 (42%), Gaps = 7/95 (7%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMH-NKGGSPVAFIE 149
GSS S G + S LFV NL ++E+E++ +F + V +H +KG FI
Sbjct: 1 GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG---FGFIR 57
Query: 150 YTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
A A L+ L +R+ +A
Sbjct: 58 LETRTLAEIAKVELDNMPLRGK---QLRVRFACHS 89
>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 = 58.1 bits (141), Expect = 6e-11
Identities = 24/110 (21%), Positives = 43/110 (39%), Gaps = 13/110 (11%)
Query: 82 PSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---- 137
+P P LF+ L ++++ ++K++ SF +
Sbjct: 91 LPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS 150
Query: 138 ---HNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+KG AF EY D+N QA++ LNG L D+ + ++ A
Sbjct: 151 ATGLSKG---YAFCEYVDINVTDQAIAGLNGMQLG--DK-KLLVQRASVG 194
Score = 39.2 bits (92), Expect = 3e-04
Identities = 18/96 (18%), Positives = 35/96 (36%), Gaps = 20/96 (20%)
Query: 101 GMSPCSTLFVANLGQFVSEQEIKDIFGSF------------PGFSRVRMHNKGGSPVAFI 148
G L+V N+ ++E+ + D F + P + +K AF+
Sbjct: 1 GAMAR-RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKN---FAFL 56
Query: 149 EYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
E+ V+ QAM+ +G +++I
Sbjct: 57 EFRSVDETTQAMA-FDGIIF---QGQSLKIRRPHDY 88
>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 = 56.1 bits (136), Expect = 7e-11
Identities = 25/98 (25%), Positives = 42/98 (42%), Gaps = 5/98 (5%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGF---SRVRMHNKGGSP-VA 146
GSS S + LFV L + SE+++ +F F G V G S A
Sbjct: 1 GSSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPF-GVIDECTVLRGPDGSSKGCA 59
Query: 147 FIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
F++++ A A+ L+GS ++ +++A T
Sbjct: 60 FVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTD 97
>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 = 56.4 bits (136), Expect = 2e-10
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 7/87 (8%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM--HNKGGSP--VAFIEYTDVNFAI 157
+ TL+V NL + +E++I ++F ++ M + F+EY A
Sbjct: 36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
Query: 158 QAMSNLNGSYLASSDRGAIRIEYAKTK 184
AM +NG+ L DR IR ++
Sbjct: 96 NAMRYINGTRLD--DR-IIRTDWDAGF 119
>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 = 57.0 bits (137), Expect = 2e-10
Identities = 16/103 (15%), Positives = 37/103 (35%), Gaps = 5/103 (4%)
Query: 75 NGMPHFLPSPALPSPVGSSPPSQGMNGMSPCS-TLFVANLGQFVSEQEIKDIFGSF--PG 131
+G + + S+P N + S L N V+E+ +I
Sbjct: 92 DGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKR 151
Query: 132 FSRVRMHNKGG--SPVAFIEYTDVNFAIQAMSNLNGSYLASSD 172
+ V++ + S +E+ + A++ + LN + + +
Sbjct: 152 PTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPN 194
Score = 51.6 bits (123), Expect = 1e-08
Identities = 16/106 (15%), Positives = 39/106 (36%), Gaps = 7/106 (6%)
Query: 103 SPCSTLFVANLG-QFVSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAFIEYTDVNFAIQAM 160
+ L V L ++ + ++F + +V+ M +K G+ A +E D +A+
Sbjct: 2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGA--AMVEMADGYAVDRAI 59
Query: 161 SNLNGSYLASSDRGAIRIEYAKTKMAEFTTEHRTRHQGTKYGYTIH 206
++LN +++ + + +K + Y
Sbjct: 60 THLNNNFMFGQ---KMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSE 102
>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 = 54.8 bits (132), Expect = 3e-10
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 7/84 (8%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSF-PGFSRVRMH----NKGGS-PVAFIEYTDVNFAIQAM 160
LF+ + + +EI + G V ++ +K + AF+EY A A
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 161 SNLNGSYLASSDRGAIRIEYAKTK 184
L + I +++A+ +
Sbjct: 70 RKLMPGRIQLWGH-QIAVDWAEPE 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 = 54.0 bits (130), Expect = 3e-10
Identities = 17/85 (20%), Positives = 31/85 (36%), Gaps = 8/85 (9%)
Query: 101 GMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAM 160
G S S + V NL Q + QE+ D+ + + + AF+ + A A+
Sbjct: 1 GSSGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRT--AFVTLLNGEQAQNAI 57
Query: 161 SNLNGSYLASSDRG-AIRIEYAKTK 184
+ RG + ++ T
Sbjct: 58 QMFHQYSF----RGKDLIVQLQPTD 78
>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 = 54.4 bits (131), Expect = 3e-10
Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 5/80 (6%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
+ + NL EI++ F F RV + G + A +E+ + A +A +L
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGIT--AIVEFLEPLEARKAFRHLAY 68
Query: 166 SYLASSDRGAIRIEYAKTKM 185
S + +E+A +
Sbjct: 69 SKFHHV---PLYLEWAPIGV 85
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 55.0 bits (132), Expect = 3e-10
Identities = 24/102 (23%), Positives = 42/102 (41%), Gaps = 1/102 (0%)
Query: 83 SPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGG 142
+ AL + + M G SP + V NL V+ + IF F ++ K
Sbjct: 6 NLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN 65
Query: 143 SPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
A ++Y D A A +L+G + + +RI+++K
Sbjct: 66 QFQALLQYADPVSAQHAKLSLDGQNIY-NACCTLRIDFSKLT 106
>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 = 54.2 bits (131), Expect = 4e-10
Identities = 25/101 (24%), Positives = 45/101 (44%), Gaps = 13/101 (12%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMH-------NKGGS 143
GSS S +T+ V NL + E +++++F F SR+ + +KG
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKG-- 58
Query: 144 PVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
AFI + A +A++ ++G D + +E+AK
Sbjct: 59 -FAFISFHRREDAARAIAGVSGFGY---DHLILNVEWAKPS 95
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 54.2 bits (131), Expect = 4e-10
Identities = 25/96 (26%), Positives = 43/96 (44%), Gaps = 8/96 (8%)
Query: 89 PVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFI 148
P GS + +S + LFV V E E+ +IFG F V++ G AF+
Sbjct: 16 PRGSHMHHRQEGELSN-TRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-NG---FAFV 70
Query: 149 EYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
E+ + A +A+ ++G A+ + + Y+K
Sbjct: 71 EFEEAESAAKAIEEVHGKSFANQ---PLEVVYSKLP 103
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 54.0 bits (130), Expect = 4e-10
Identities = 16/93 (17%), Positives = 34/93 (36%), Gaps = 12/93 (12%)
Query: 92 SSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYT 151
+P S + + L V E ++ + F S V + K A +E+
Sbjct: 17 KTPASP---------VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQ--ALVEFE 65
Query: 152 DVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
DV A A++ + + + + Y+ ++
Sbjct: 66 DVLGACNAVNYAADNQIYIAGH-PAFVNYSTSQ 97
>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 = 55.2 bits (133), Expect = 4e-10
Identities = 19/88 (21%), Positives = 37/88 (42%), Gaps = 13/88 (14%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFA 156
LFV ++ + E EI++ F + + + +KG A +EY A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG---YALVEYETHKQA 127
Query: 157 IQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+ A LNG+ + + I++++ K
Sbjct: 128 LAAKEALNGAEIM--GQ-TIQVDWCFVK 152
>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 = 53.4 bits (129), Expect = 7e-10
Identities = 14/88 (15%), Positives = 32/88 (36%), Gaps = 13/88 (14%)
Query: 103 SPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM------HNKGGSPVAFIEYTDVNFA 156
+ LF+ NL S E+K + + + N+ ++++
Sbjct: 15 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK---FGYVDFESAEDL 71
Query: 157 IQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+A+ L G + + I++E K +
Sbjct: 72 EKALE-LTGLKVFGN---EIKLEKPKGR 95
>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 = 54.9 bits (133), Expect = 8e-10
Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 8/85 (9%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP--VAFIEYTDVNFAIQA 159
+ TL NL ++E E+K++F +R+ ++ G +A+IE+ A +
Sbjct: 96 VRAARTLLAKNLSFNITEDELKEVFEDA-L--EIRLVSQDGKSKGIAYIEFKSEADAEKN 152
Query: 160 MSNLNGSYLASSDRGAIRIEYAKTK 184
+ G+ + ++ + Y K
Sbjct: 153 LEEKQGAEIDGR---SVSLYYTGEK 174
Score = 42.2 bits (100), Expect = 2e-05
Identities = 16/95 (16%), Positives = 35/95 (36%), Gaps = 7/95 (7%)
Query: 103 SPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM--HNKGGS-PVAFIEYTDVNFAIQA 159
+ LF+ NL S E+K + + + G + ++++ +A
Sbjct: 11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKA 70
Query: 160 MSNLNGSYLASSDRGAIRIEYAKTKMAEFTTEHRT 194
+ L G + I++E K + ++ RT
Sbjct: 71 L-ELTGLKV--FGN-EIKLEKPKGRDSKKVRAART 101
>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 = 52.6 bits (127), Expect = 8e-10
Identities = 25/94 (26%), Positives = 38/94 (40%), Gaps = 14/94 (14%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEY 150
GSS S + LF+ NL + +EQEI+ +F + + K F+
Sbjct: 1 GSSGSSGMVK-------LFIGNLPREATEQEIRSLFEQYGKVLECDII-KN---YGFVHI 49
Query: 151 TDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
D A A+ NL+ L I +E +K K
Sbjct: 50 EDKTAAEDAIRNLHHYKL---HGVNINVEASKNK 80
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 54.9 bits (132), Expect = 9e-10
Identities = 24/119 (20%), Positives = 44/119 (36%), Gaps = 9/119 (7%)
Query: 82 PSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMH-NK 140
P P G G+ + L V+NL VS+ +I+++F F + + ++
Sbjct: 65 PLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR 124
Query: 141 GGSP--VAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTKMAEFTTEHRTRHQ 197
G A + + A++AM G L + I+ ++ EH H
Sbjct: 125 SGRSLGTADVHFERRADALKAMKQYKGVPLDGR---PMDIQLVASQ---IDLEHHHHHH 177
>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 = 52.6 bits (127), Expect = 9e-10
Identities = 14/89 (15%), Positives = 34/89 (38%), Gaps = 8/89 (8%)
Query: 96 SQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNF 155
S G +G + L V N+ + QE++ F + + AF+
Sbjct: 2 SSGSSGKAST-KLHVGNISPTCTNQELRAKFEEYGPVIECDIVK----DYAFVHMERAED 56
Query: 156 AIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
A++A+ L+ + + ++ + ++
Sbjct: 57 AVEAIRGLDNTEF---QGKRMHVQLSTSR 82
>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 = 55.8 bits (135), Expect = 1e-09
Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 13/97 (13%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFAIQ 158
+ L VANL +++Q+ +++ F R + +KG F EY + A +
Sbjct: 96 ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG---YGFAEYMKKDSAAR 152
Query: 159 AMSNLNGSYLASSDRGAIRIEYAKTKMAEFTTEHRTR 195
A S+L G L + + + H
Sbjct: 153 AKSDLLGKPLGPR---TLYVHWTDAGQLTPALLHSRC 186
Score = 51.1 bits (123), Expect = 4e-08
Identities = 15/99 (15%), Positives = 31/99 (31%), Gaps = 7/99 (7%)
Query: 90 VGSSPPSQGMNGMSPCSTLFVANLGQFVSEQE-IKDIFGSFPGFSRVR-MHNKGGSP--V 145
V + Q + L V L ++ + + + + + + G
Sbjct: 169 VHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGF 228
Query: 146 AFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
A +EY A +A +G L S +R+ +
Sbjct: 229 AVLEYETAEMAEEAQQQADGLSLGGS---HLRVSFCAPG 264
Score = 49.6 bits (119), Expect = 1e-07
Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 6/79 (7%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
+ + L V+ QE+ D+ + KG AF+ + A A++ +
Sbjct: 23 RKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKG---TAFVTLLNGEQAEAAINAFHQ 79
Query: 166 SYLASSDRGAIRIEYAKTK 184
S L +R + ++ T
Sbjct: 80 SRL--RER-ELSVQLQPTD 95
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 52.3 bits (126), Expect = 1e-09
Identities = 18/84 (21%), Positives = 37/84 (44%), Gaps = 10/84 (11%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP--VAFIEYTDVNFAIQAMS 161
TL NL ++E E+K++F +R+ ++ G +A+IE+ A + +
Sbjct: 15 AARTLLAKNLSFNITEDELKEVFED---ALEIRLVSQDGKSKGIAYIEFKSEADAEKNLE 71
Query: 162 NLNGSYLASSDRG-AIRIEYAKTK 184
G+ + G ++ + Y K
Sbjct: 72 EKQGAEID----GRSVSLYYTGEK 91
>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 = 54.2 bits (131), Expect = 1e-09
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 13/93 (13%)
Query: 96 SQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMH-------NKGGSPVAFI 148
+ LF+ L ++++ ++K++ SF + +KG AF
Sbjct: 85 PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG---YAFC 141
Query: 149 EYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYA 181
EY D+N QA++ LNG L D+ + ++ A
Sbjct: 142 EYVDINVTDQAIAGLNGMQLG--DK-KLLVQRA 171
Score = 36.1 bits (84), Expect = 0.003
Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 14/73 (19%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPV-----------AFIEYTDVNF 155
L+V N+ ++E+ + D F + + G+PV AF+E+ V+
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQ--APGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 156 AIQAMSNLNGSYL 168
QAM+ +G
Sbjct: 64 TTQAMA-FDGIIF 75
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA
processing, mRNA splicing, transport, nucleus,
RNA-binding, spliceosome, transport; NMR {Mus musculus}
Length = 124
Score = 53.1 bits (128), Expect = 1e-09
Identities = 26/130 (20%), Positives = 46/130 (35%), Gaps = 9/130 (6%)
Query: 71 MHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFP 130
M G P G G+ + L V+NL VS+ +I+++F F
Sbjct: 1 MASMTGGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG 60
Query: 131 GFSRVR-MHNKGGSP--VAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTKMAE 187
+ +++ G A + + A++AM G L R + I+ ++
Sbjct: 61 TLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDG--R-PMDIQLVASQ--- 114
Query: 188 FTTEHRTRHQ 197
EH H
Sbjct: 115 IDLEHHHHHH 124
>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 = 52.7 bits (127), Expect = 1e-09
Identities = 31/121 (25%), Positives = 47/121 (38%), Gaps = 15/121 (12%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------KGGS 143
GSS S S +FV +L ++ ++IK F F S R+ KG
Sbjct: 1 GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG-- 58
Query: 144 PVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYA--KTKMAEFTTEHRTRHQGTKY 201
F+ + + A A+ + G +L R IR +A K + T E T+ G
Sbjct: 59 -YGFVSFFNKWDAENAIQQMGGQWLGG--R-QIRTNWATRKPPAPKSTYESNTKQSGPSS 114
Query: 202 G 202
G
Sbjct: 115 G 115
>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 = 52.3 bits (126), Expect = 2e-09
Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 5/96 (5%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGS-PVAFI 148
GSS S S L V+N+ + +++ +FG F V + N+ GS F+
Sbjct: 1 GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFV 60
Query: 149 EYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+ + A +A L+G+ + R I + A +
Sbjct: 61 TFENSADADRAREKLHGTVVE--GR-KIEVNNATAR 93
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 52.2 bits (126), Expect = 2e-09
Identities = 16/85 (18%), Positives = 36/85 (42%), Gaps = 8/85 (9%)
Query: 99 MNGMSPCSTLFVANL-GQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAI 157
M+ + P S LF+ NL + VS++++ IF + ++ + N FI++ +
Sbjct: 4 MHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN----AFGFIQFDNPQSVR 59
Query: 158 QAMSNLNGSYLASSDRGAIRIEYAK 182
A+ + + +E +
Sbjct: 60 DAIECESQEMNFGK---KLILEVSS 81
>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 = 53.8 bits (130), Expect = 2e-09
Identities = 26/124 (20%), Positives = 48/124 (38%), Gaps = 10/124 (8%)
Query: 63 HPTAALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEI 122
AAL A + + M LP P + P N LF+ + + +E +I
Sbjct: 56 TRKAALEAQNALHNM-KVLPGMHHPIQM--KPADSEKNNAVEDRKLFIGMISKKCTENDI 112
Query: 123 KDIFGSFPG---FSRVRMHNKGGSP--VAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIR 177
+ +F SF G R+ + G AF+ +T A A+ ++ + +
Sbjct: 113 RVMFSSF-GQIEECRI-LRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV 170
Query: 178 IEYA 181
+++A
Sbjct: 171 VKFA 174
Score = 45.3 bits (108), Expect = 2e-06
Identities = 13/93 (13%), Positives = 38/93 (40%), Gaps = 6/93 (6%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSF-PGFS-RVRMHNKGGSP----VAFIEYTDVNFAIQAM 160
+FV + + SE++++++F + + V P F+ + A++A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 161 SNLNGSYLASSDRGAIRIEYAKTKMAEFTTEHR 193
+ L+ + I+++ A ++ + +
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRK 97
>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 = 52.1 bits (125), Expect = 2e-09
Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 3/94 (3%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEY 150
GSS S +P L + L V+E E+ + F + + M AF+E
Sbjct: 1 GSSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQ--AFLEL 58
Query: 151 TDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
AI ++ + ++ I I+Y+ K
Sbjct: 59 ATEEAAITMVNYYSAVTPHLRNQ-PIYIQYSNHK 91
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 54.2 bits (131), Expect = 2e-09
Identities = 27/131 (20%), Positives = 46/131 (35%), Gaps = 15/131 (11%)
Query: 64 PTAALTAMHHANGMPHFL------PSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFV 117
P AA A+ N + L Q + ++VA++ Q +
Sbjct: 80 PEAAQLALEQMNSV--MLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDL 137
Query: 118 SEQEIKDIFGSFPGFSRVRM---HNKGGSP-VAFIEYTDVNFAIQAMSNLNGSYLASSDR 173
S+ +IK +F +F + G FIEY + A+S++N L
Sbjct: 138 SDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQ-- 195
Query: 174 GAIRIEYAKTK 184
+R+ A T
Sbjct: 196 -YLRVGKAVTP 205
Score = 46.2 bits (110), Expect = 1e-06
Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 4/84 (4%)
Query: 89 PVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGS-P 144
+G +Q ++ S ++V ++ + E I+ F F + M
Sbjct: 12 QMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKG 71
Query: 145 VAFIEYTDVNFAIQAMSNLNGSYL 168
AF+EY A A+ +N L
Sbjct: 72 FAFVEYEVPEAAQLALEQMNSVML 95
>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 = 51.9 bits (125), Expect = 2e-09
Identities = 23/102 (22%), Positives = 45/102 (44%), Gaps = 14/102 (13%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------KGGSPVAFIEYTDVNFA 156
P +++ ++ +E++I D+ + ++M KG AFIE+ D+ +
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKG---YAFIEFRDLESS 57
Query: 157 IQAMSNLNGSYLASSDRGAIRIEYAKTK-MAEFTTEHRTRHQ 197
A+ NLNG L R ++ Y+ ++ + EH H
Sbjct: 58 ASAVRNLNGYQLG--SR-FLKCGYSSNSDISGVSLEHHHHHH 96
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 51.5 bits (124), Expect = 3e-09
Identities = 20/97 (20%), Positives = 48/97 (49%), Gaps = 7/97 (7%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSP--VAF 147
GSS + + LF++ L +++E+++I + +R + N+ G P +A+
Sbjct: 4 GSSGVFRYSTSLEK-HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAY 62
Query: 148 IEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+EY + + A QA+ ++G + + I++ + +
Sbjct: 63 VEYENESQASQAVMKMDGMTIK--EN-IIKVAISNSG 96
>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 = 51.5 bits (124), Expect = 4e-09
Identities = 21/101 (20%), Positives = 41/101 (40%), Gaps = 17/101 (16%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------KGGS 143
P + + G LFV ++ + E EI++ F + + ++ KG
Sbjct: 16 LEPGPQRSVEGW----ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG-- 69
Query: 144 PVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
A +EY A+ A LNG+ + + I++++ K
Sbjct: 70 -YALVEYETHKQALAAKEALNGAEIM--GQ-TIQVDWCFVK 106
>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 = 53.1 bits (128), Expect = 5e-09
Identities = 19/97 (19%), Positives = 40/97 (41%), Gaps = 10/97 (10%)
Query: 89 PVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM----HNKGGSP 144
P+GS PS P ++L+V +L V+E + + F +R+ +
Sbjct: 2 PLGSMNPSAPSY---PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLG 58
Query: 145 VAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYA 181
A++ + A +A+ +N + +RI ++
Sbjct: 59 YAYVNFQQPADAERALDTMNFDVIKGK---PVRIMWS 92
Score = 53.1 bits (128), Expect = 5e-09
Identities = 15/80 (18%), Positives = 35/80 (43%), Gaps = 5/80 (6%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSP-VAFIEYTDVNFAIQAMSNLN 164
+F+ NL + + + + D F +F + + ++ GS F+ + A +A+ +N
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 164
Query: 165 GSYLASSDRGAIRIEYAKTK 184
G L + + K++
Sbjct: 165 GMLLNDR---KVFVGRFKSR 181
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition
motif, RRM, RNA binding domain, RBD, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 51.2 bits (123), Expect = 5e-09
Identities = 30/117 (25%), Positives = 51/117 (43%), Gaps = 8/117 (6%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSP--VAF 147
GSS S + ST+FVANL V +++K++F R + +K G +
Sbjct: 1 GSSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGT 60
Query: 148 IEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTKM--AEFTTEHRTRHQGTKYG 202
+ + A+QA+S NG L DR + ++ + + +F R + G G
Sbjct: 61 VTFEQSIEAVQAISMFNGQLLF--DR-PMHVKMDERALPKGDFFPPERPQQSGPSSG 114
>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 = 50.7 bits (122), Expect = 6e-09
Identities = 23/101 (22%), Positives = 42/101 (41%), Gaps = 15/101 (14%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------KGGS 143
GSS S P L V L + +E++++++F + + V + +G
Sbjct: 1 GSSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG-- 58
Query: 144 PVAFIEYTDVNFAIQAMSNLNGSYLASSDRG-AIRIEYAKT 183
AF+ + +V+ A +A NG L G IR+ +
Sbjct: 59 -FAFVYFENVDDAKEAKERANGMELD----GRRIRVSGPSS 94
>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 = 50.7 bits (122), Expect = 7e-09
Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 6/96 (6%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP--VAFI 148
GSS S P TLFV L + +E+ +K+ F +R+ + GS F+
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVR-ARIVTDRETGSSKGFGFV 59
Query: 149 EYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
++ A A + + D + +++AK K
Sbjct: 60 DFNSEEDAKAAKEAMEDGEI---DGNKVTLDWAKPK 92
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 50.2 bits (120), Expect = 9e-09
Identities = 15/94 (15%), Positives = 29/94 (30%), Gaps = 5/94 (5%)
Query: 93 SPPSQGMN--GMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEY 150
+ P + + L V+E E+ + F + + M AFIE
Sbjct: 2 RGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQ--AFIEM 59
Query: 151 TDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
A ++ + I I+++ K
Sbjct: 60 NTEEAANTMVNYYTSVTPVLRGQ-PIYIQFSNHK 92
>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 = 50.5 bits (121), Expect = 1e-08
Identities = 22/116 (18%), Positives = 45/116 (38%), Gaps = 9/116 (7%)
Query: 70 AMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSF 129
+ HH + +P + P S +TL+V ++ ++ F F
Sbjct: 4 SHHHHHHSSGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPF 61
Query: 130 PGFSRVRMH-NKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+ M + AF+ Y + A QA++ LNG+ + S +++ A+ +
Sbjct: 62 GNIIDLSMDPPRN---CAFVTYEKMESADQAVAELNGTQVESV---QLKVNIARKQ 111
>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 = 50.5 bits (121), Expect = 1e-08
Identities = 23/111 (20%), Positives = 39/111 (35%), Gaps = 23/111 (20%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSF--------PGFSRVRM----- 137
GSS S + S S ++V L V+ ++ D F G + +
Sbjct: 1 GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60
Query: 138 --HNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRG-AIRIEYAKTKM 185
KG A + Y D A A+ +G +G +++ A+ K
Sbjct: 61 TGKPKG---DATVSYEDPPTAKAAVEWFDGKDF----QGSKLKVSLARKKP 104
>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 90
Score = 49.5 bits (119), Expect = 1e-08
Identities = 20/94 (21%), Positives = 33/94 (35%), Gaps = 13/94 (13%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEY 150
GSS S +FV N+ + QE++ +F + K AF+
Sbjct: 1 GSSGSSGNT------WKIFVGNVSAACTSQELRSLFERRGRVIECDVV-KD---YAFVHM 50
Query: 151 TDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
A A++ LNG + I +E +
Sbjct: 51 EKEADAKAAIAQLNGKEV---KGKRINVELSTKG 81
>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 = 51.0 bits (123), Expect = 1e-08
Identities = 20/94 (21%), Positives = 39/94 (41%), Gaps = 9/94 (9%)
Query: 92 SSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFS--RVRMHNKGGSP--VAF 147
+ P + + + L+V NL + +++ ++ IFG + + G P VAF
Sbjct: 80 ARPGGESIKD----TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAF 135
Query: 148 IEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYA 181
+ Y A +A+S LN + + + A
Sbjct: 136 VRYNKREEAQEAISALNNVIPEGGSQ-PLSVRLA 168
Score = 41.0 bits (97), Expect = 5e-05
Identities = 18/86 (20%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 103 SPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGS-PVAFIEYTDVNFAIQ 158
+ + L V L Q ++++E+ +F + + R+ + G S AF+++T + +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 159 AMSNLNGSYLASSDRGAIRIEYAKTK 184
A+ LNG + +++ YA+
Sbjct: 61 AIKVLNGITV---RNKRLKVSYARPG 83
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 49.6 bits (119), Expect = 1e-08
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 6/78 (7%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPV-AFIEYTDVNFAIQAMSNLNGS 166
++V NLG + E++ F + V + P AF+E+ D A A+ L+G
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWI--ARNPPGFAFVEFEDPRDAEDAVRGLDGK 60
Query: 167 YLASSDRGAIRIEYAKTK 184
+ +R+E +
Sbjct: 61 VI---CGSRVRVELSTGM 75
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 49.6 bits (119), Expect = 2e-08
Identities = 21/107 (19%), Positives = 40/107 (37%), Gaps = 17/107 (15%)
Query: 85 ALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN----- 139
++ P + + G LFV + + +E++I D F + + ++
Sbjct: 7 SVEQDGDEPGPQRSVEG----WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTG 62
Query: 140 --KGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
KG +EY A AM LNG L + I +++ +
Sbjct: 63 YLKG---YTLVEYETYKEAQAAMEGLNGQDLM--GQ-PISVDWCFVR 103
>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 = 49.9 bits (119), Expect = 2e-08
Identities = 19/107 (17%), Positives = 33/107 (30%), Gaps = 5/107 (4%)
Query: 78 PHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM 137
H S L S + P + + L V+E E+ + F + + M
Sbjct: 6 HHHHHSSGLVP--RGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM 63
Query: 138 HNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
AFIE A ++ + I I+++ K
Sbjct: 64 LKGKNQ--AFIEMNTEEAANTMVNYYTSVTPVLRGQ-PIYIQFSNHK 107
>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 = 49.6 bits (119), Expect = 2e-08
Identities = 16/104 (15%), Positives = 40/104 (38%), Gaps = 15/104 (14%)
Query: 91 GSSPPSQGMNGMSP----------CSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNK 140
GSS S + T++ + +++Q ++ F F +R+ +
Sbjct: 1 GSSGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60
Query: 141 GGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
G +F+ ++ A A+ ++NG+ + ++ + K
Sbjct: 61 KG--YSFVRFSTHESAAHAIVSVNGTTIEGH---VVKCYWGKES 99
>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 = 51.0 bits (123), Expect = 2e-08
Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 103 SPCSTLFVANLGQFVSEQEIKDIFGSFPGFS--RVRMHNKGGSP--VAFIEYTDVNFAIQ 158
LFV +L V ++ +++ F FP + V + GS F+ +T + A
Sbjct: 85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Query: 159 AMSNLNGSYLASSDRGAIRIEYA 181
AM ++ G L + R +RI +A
Sbjct: 145 AMDSMQGQDL--NGR-PLRINWA 164
Score = 44.8 bits (107), Expect = 2e-06
Identities = 19/89 (21%), Positives = 39/89 (43%), Gaps = 6/89 (6%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGSPVAFIEYTDVNFAIQAMSNL 163
L+V NL + ++E +K F + +++ N AF+EY + A A+ L
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTL 61
Query: 164 NGSYLASSDRGAIRIEYAKTKMAEFTTEH 192
NG + ++ ++I +A + +
Sbjct: 62 NGKQIENN---IVKINWAFQSQQSSSDDT 87
>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 = 49.2 bits (118), Expect = 3e-08
Identities = 22/101 (21%), Positives = 47/101 (46%), Gaps = 11/101 (10%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGSPV-- 145
GSS S + S + V N+ +++EI+++F +F VR+ G+
Sbjct: 1 GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 146 AFIEYTDVNFAIQAMSNL-NGSYLASSDRG-AIRIEYAKTK 184
F+++ A +A + L + ++L G + +E+A ++
Sbjct: 61 GFVDFITKQDAKKAFNALCHSTHLY----GRRLVLEWADSE 97
>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 = 48.8 bits (117), Expect = 3e-08
Identities = 26/100 (26%), Positives = 42/100 (42%), Gaps = 16/100 (16%)
Query: 91 GSSPPSQGMNGMSPCS-TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------KGG 142
GSS S G++P T++V+NL ++ ++ IF + +V + KG
Sbjct: 1 GSSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG- 59
Query: 143 SPVAFIEYTDVNFAIQAMSNLNGSYLASSDRG-AIRIEYA 181
VAFI + D + A +N L G I+ A
Sbjct: 60 --VAFILFLDKDSAQNCTRAINNKQLF----GRVIKASIA 93
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 48.9 bits (117), Expect = 3e-08
Identities = 15/89 (16%), Positives = 31/89 (34%), Gaps = 13/89 (14%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSF--PGFSRVRM-------HNKGGSPVAFIEYTDVN 154
T+ + N+ I + + +R+ N+G AF++ +
Sbjct: 8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRG---FAFVQLSSAM 64
Query: 155 FAIQAMSNLNGSYLASSDRG-AIRIEYAK 182
A Q + L + G I +++AK
Sbjct: 65 DASQLLQILQSLHPPLKIDGKTIGVDFAK 93
>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 = 48.3 bits (116), Expect = 3e-08
Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 13/90 (14%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVN 154
+ +FV +L ++ I F F S R+ +KG F+ + +
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKG---YGFVSFFNKW 59
Query: 155 FAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
A A+ + G +L R IR +A K
Sbjct: 60 DAENAIQQMGGQWLGG--R-QIRTNWATRK 86
>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 = 49.8 bits (119), Expect = 3e-08
Identities = 22/107 (20%), Positives = 41/107 (38%), Gaps = 10/107 (9%)
Query: 83 SPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HN 139
+ GS M+ + ++L V NL S ++ +F + V +
Sbjct: 49 TKTFTVTEGSHHHHHHMD-VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY 107
Query: 140 KGGSP-VAFIEYTDVNFAIQAMSNLNGSYLASSDRG-AIRIEYAKTK 184
S AF+ + D A AM ++G+ L G +R++ A+
Sbjct: 108 TKESRGFAFVRFHDKRDAEDAMDAMDGAVLD----GRELRVQMARYG 150
>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 = 48.9 bits (117), Expect = 3e-08
Identities = 21/99 (21%), Positives = 42/99 (42%), Gaps = 11/99 (11%)
Query: 93 SPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPV 145
S S GM LF+ + + + E+++K +F F + + +KG
Sbjct: 2 SSGSSGMKDHDAIK-LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKG---C 57
Query: 146 AFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
AF+ Y + A++A S L+ I+++ A ++
Sbjct: 58 AFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSE 96
>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 = 49.3 bits (118), Expect = 4e-08
Identities = 22/110 (20%), Positives = 42/110 (38%), Gaps = 7/110 (6%)
Query: 79 HFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR-- 136
H S P L V L + +E++++++F + + V
Sbjct: 20 HMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIV 79
Query: 137 MHNKGGSP--VAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+ AF+ + +V+ A +A NG L R IR++++ TK
Sbjct: 80 YDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD--GR-RIRVDFSITK 126
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 48.6 bits (116), Expect = 4e-08
Identities = 10/84 (11%), Positives = 28/84 (33%), Gaps = 3/84 (3%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGSPVAFIEYTDVNFAIQAMSNL 163
++++ + +IK+ ++M +K F+ + + A + +
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 72
Query: 164 NGSYLASSDRGAIRIEYAKTKMAE 187
Y + + +Y K E
Sbjct: 73 GQKYKETDLLILFKDDYFAKKNEE 96
>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 = 48.4 bits (116), Expect = 4e-08
Identities = 17/91 (18%), Positives = 32/91 (35%), Gaps = 10/91 (10%)
Query: 101 GMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFS--RVRMHNKGGSPV-----AFIEYTDV 153
G S S LF+ NL +E+ +K +F + + F+EY
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 154 NFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
A +A+ L G + + + ++
Sbjct: 61 EQAQKALKQLQGHTVDGH---KLEVRISERA 88
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 48.5 bits (116), Expect = 4e-08
Identities = 16/85 (18%), Positives = 32/85 (37%), Gaps = 7/85 (8%)
Query: 101 GMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR--MHNKGGSP--VAFIEYTDVNFA 156
G P + A L V E +KD+ + V +H + +A + +T A
Sbjct: 2 GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61
Query: 157 IQAMSNLNGSYLASSDRGAIRIEYA 181
+ + NL+ + + + I +
Sbjct: 62 KETVKNLHLTSVMGN---IIHAQLD 83
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 48.1 bits (115), Expect = 5e-08
Identities = 20/98 (20%), Positives = 40/98 (40%), Gaps = 12/98 (12%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSF---PGFSRVRMHNKGGSPV-- 145
GSS S ++L++ +L ++ E I F + ++ + G P
Sbjct: 1 GSSGSS------GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGY 54
Query: 146 AFIEYTDVNFAIQAMSNLNGSYLASSDRG-AIRIEYAK 182
F+E+ D+ A + + +NG L + ++ YA
Sbjct: 55 CFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYAT 92
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA
splicing, mRNA transport, nonsense-mediated mRNA decay,
nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*
Length = 126
Score = 48.9 bits (117), Expect = 5e-08
Identities = 19/88 (21%), Positives = 34/88 (38%), Gaps = 13/88 (14%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------KGGSPVAFIEYTDVNFA 156
LFV + + +E++I D F + + ++ KG +EY A
Sbjct: 21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG---YTLVEYETYKEA 77
Query: 157 IQAMSNLNGSYLASSDRGAIRIEYAKTK 184
AM LNG L + I +++ +
Sbjct: 78 QAAMEGLNGQDLM--GQ-PISVDWCFVR 102
>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 = 48.0 bits (115), Expect = 5e-08
Identities = 26/108 (24%), Positives = 45/108 (41%), Gaps = 20/108 (18%)
Query: 82 PSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---H 138
S + S + SPP T F+ NL V+E+ IK+ F S VR+
Sbjct: 2 SSGSSGSRLPKSPPY----------TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREP 50
Query: 139 NKGGSP--VAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+ + E+ D++ + A+ +LN L ++ IR++ A
Sbjct: 51 SNPERLKGFGYAEFEDLDSLLSAL-SLNEESLG--NK-RIRVDVADQA 94
>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 = 48.5 bits (116), Expect = 6e-08
Identities = 21/105 (20%), Positives = 43/105 (40%), Gaps = 15/105 (14%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGS 143
GSS S + ++ T+F+ NL E+ + ++ F VR+ H+KG
Sbjct: 1 GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKG-- 58
Query: 144 PVAFIEYTDVNFAIQAMSNLNGSYLAS----SDRGAIRIEYAKTK 184
AF ++ A + ++ + R ++++ A T+
Sbjct: 59 -CAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR-QLKVDLAVTR 101
>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 = 48.1 bits (115), Expect = 6e-08
Identities = 21/108 (19%), Positives = 37/108 (34%), Gaps = 26/108 (24%)
Query: 90 VGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSF--------PGFSRVRM---- 137
+G S +T+FV LG+ V+ + + D F G + +
Sbjct: 1 MGHHHHHHSH---SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR 57
Query: 138 ---HNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRG-AIRIEYA 181
KG A + + D A A+ +G G I++ +A
Sbjct: 58 ETGKLKG---EATVSFDDPPSAKAAIDWFDGKEF----SGNPIKVSFA 98
>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 = 50.4 bits (121), Expect = 7e-08
Identities = 14/102 (13%), Positives = 37/102 (36%), Gaps = 14/102 (13%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSF-PGFSRVRM------HNKGGSPVAFIEYTDVNFAIQ 158
TL++ N +++ I+D+ +R+ ++ A+I+ T A
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRR---FAYIDVTSKEDARY 174
Query: 159 AMSNLNGSYLASSDRGAIRIEYAKTKMAEFTTEHRTRHQGTK 200
+ LNG + + + + + + + +G +
Sbjct: 175 CVEKLNGLKI---EGYTLVTKVSN-PLEKSKRTDSATLEGRE 212
Score = 44.2 bits (105), Expect = 8e-06
Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 2/62 (3%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSF-PGFS-RVRMHNKGGSPVAFIEYTDVNFAIQAMSNL 163
+T+ V NL + ++ ++ F P V K A IE+ + A+ A++
Sbjct: 42 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKT 101
Query: 164 NG 165
+
Sbjct: 102 HK 103
>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 = 48.1 bits (115), Expect = 7e-08
Identities = 22/103 (21%), Positives = 42/103 (40%), Gaps = 8/103 (7%)
Query: 83 SPALPSPVGSSPPSQGMNGMSPCSTLFVANLG-QFVSEQEIKDIFGSFPGFSRVRMHNKG 141
S + + +S + + S S +F+ NL V + +++ IF + + +H
Sbjct: 5 SSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK-- 62
Query: 142 GSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
AF++Y++ A A+ NG LA + I A
Sbjct: 63 --GYAFVQYSNERHARAAVLGENGRVLAGQ---TLDINMAGEP 100
>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 = 47.7 bits (114), Expect = 7e-08
Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 4/82 (4%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSF-PGFSRVRMH-NKGGSP--VA 146
GSS S +G + + V N+ VS EI D F + V + N+ G P A
Sbjct: 1 GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 147 FIEYTDVNFAIQAMSNLNGSYL 168
+ + + A A+ +LN +
Sbjct: 61 MVAFESRDEATAAVIDLNDRPI 82
>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 = 49.1 bits (118), Expect = 8e-08
Identities = 26/123 (21%), Positives = 53/123 (43%), Gaps = 12/123 (9%)
Query: 63 HPTAALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEI 122
P A A++ NG+ S + P S + + L+V+ L + ++++E+
Sbjct: 53 DPKDAEKAINTLNGLR-LQTKTIKVSY--ARPSSASIRD----ANLYVSGLPKTMTQKEL 105
Query: 123 KDIFGSFPGF--SRVRMHNKGGSP--VAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRI 178
+ +F + SR+ + G V FI + A +A+ LNG + + I +
Sbjct: 106 EQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATE-PITV 164
Query: 179 EYA 181
++A
Sbjct: 165 KFA 167
Score = 39.9 bits (94), Expect = 1e-04
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 7/81 (8%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGS-PVAFIEYTDVNFAIQAMS 161
+ L V L Q ++++E + +FGS ++ G S F+ Y D A +A++
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 162 NLNGSYLASSDRGAIRIEYAK 182
LNG L I++ YA+
Sbjct: 63 TLNGLRL---QTKTIKVSYAR 80
>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 = 47.7 bits (114), Expect = 8e-08
Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 9/95 (9%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMH-NKGGSPVAFIE 149
GSS S +TL+V ++ ++ F F + M + AF+
Sbjct: 1 GSSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRN---CAFVT 55
Query: 150 YTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
Y + A QA++ LNG+ + S +++ A+ +
Sbjct: 56 YEKMESADQAVAELNGTQVESV---QLKVNIARKQ 87
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 48.1 bits (115), Expect = 8e-08
Identities = 15/112 (13%), Positives = 38/112 (33%), Gaps = 10/112 (8%)
Query: 66 AALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDI 125
AA + P ++ ++ + LF+ +L Q ++ ++
Sbjct: 1 AAGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLAST 60
Query: 126 FGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLAS 170
F F ++ +K F+ + + + A A+ +NG + +
Sbjct: 61 FLPFGNVISAKVFIDKQTSLSKC---FGFVSFDNPDSAQVAIKAMNGFQVGT 109
>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 = 47.1 bits (113), Expect = 8e-08
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 15/85 (17%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKG-GSPVAFIEYTDVNFAIQA 159
LFV +L V ++ +++ F FP + + ++G G F+ +T + A A
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYG----FVSFTSQDDAQNA 59
Query: 160 MSNLNGSYLASSDRGAIRIEYAKTK 184
M ++ G L + +RI +A
Sbjct: 60 MDSMQGQDL---NGRPLRINWAAKL 81
>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 = 47.7 bits (114), Expect = 8e-08
Identities = 17/100 (17%), Positives = 37/100 (37%), Gaps = 9/100 (9%)
Query: 87 PSPVGSSPPSQGM-NGMSPCSTLFVANL-GQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP 144
S S + G S LF+ NL + VS++++ IF + ++ + N
Sbjct: 3 SSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN----A 58
Query: 145 VAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
FI++ + A+ + + +E + +
Sbjct: 59 FGFIQFDNPQSVRDAIEXESQEMNFGK---KLILEVSSSN 95
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 47.9 bits (114), Expect = 9e-08
Identities = 18/94 (19%), Positives = 31/94 (32%), Gaps = 11/94 (11%)
Query: 78 PHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIF---GSFPGFSR 134
H S +P S + + NL + S Q++KD+ FS
Sbjct: 7 HHHHSSGLVPRGSHMSKLPAKRY------RITMKNLPEGCSWQDLKDLARENSLETTFSS 60
Query: 135 VRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSYL 168
V + G +E+ ++A+ LN
Sbjct: 61 VNTRDFDG--TGALEFPSEEILVEALERLNNIEF 92
>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 = 48.0 bits (114), Expect = 9e-08
Identities = 17/86 (19%), Positives = 31/86 (36%), Gaps = 8/86 (9%)
Query: 103 SPCSTLFVAN--LGQFVSEQEIKDIFGSFPGFSRVRM-HNKGGSPVAFIEYTDVNFAIQA 159
+L VAN LG VS ++ + + M NK +F Y + +A
Sbjct: 23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP---YSFARYRTTEESKRA 79
Query: 160 MSNLNGSYLASSD--RGAIRIEYAKT 183
LNG + + + + + +
Sbjct: 80 YVTLNGKEVVDDLGQKITLYLNFVEK 105
>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 = 47.7 bits (114), Expect = 1e-07
Identities = 22/106 (20%), Positives = 45/106 (42%), Gaps = 15/106 (14%)
Query: 87 PSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN------- 139
S + ++ + G + L+V +L ++E ++ IF F +++
Sbjct: 8 HSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRS 67
Query: 140 KGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRG-AIRIEYAKTK 184
KG FI ++D A +A+ LNG LA G +++ + +
Sbjct: 68 KG---YGFITFSDSECAKKALEQLNGFELA----GRPMKVGHVTER 106
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 47.2 bits (113), Expect = 1e-07
Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 9/81 (11%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP--VAFI 148
GSS S +FV NL + + +KD F + + G +
Sbjct: 1 GSSGSSGACQ-------IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVV 53
Query: 149 EYTDVNFAIQAMSNLNGSYLA 169
++ A +A +NG L+
Sbjct: 54 KFESPEVAERACRMMNGMKLS 74
>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 = 47.2 bits (113), Expect = 1e-07
Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 101 GMSPCSTLFVANLGQFVSEQEIKDIFGSFPGF---SRVRMHNKGGSP--VAFIEYTDVNF 155
G S S +F+ NL + E+ + D F +F ++ G+ AFI + +
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 156 AIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+ A+ +NG YL +R I + YA K
Sbjct: 61 SDAAIEAMNGQYL--CNR-PITVSYAFKK 86
>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 = 47.2 bits (113), Expect = 1e-07
Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 9/92 (9%)
Query: 98 GMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR--MHNKGGSP--VAFIEYTDV 153
G +G S LFV NL SE++++ +F ++ S + + + P AF+ +
Sbjct: 1 GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60
Query: 154 NFAIQAMSNLNGSYLASSDRG-AIRIEYAKTK 184
A++A + ++G G + + + K
Sbjct: 61 EHAVKAYAEVDGQVFQ----GRMLHVLPSTIK 88
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 47.3 bits (113), Expect = 1e-07
Identities = 21/100 (21%), Positives = 42/100 (42%), Gaps = 12/100 (12%)
Query: 88 SPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGS-PV 145
S + + SQ L V+N+ + +++ +FG F V + N+ GS
Sbjct: 19 SHMNTENKSQPKR-------LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGF 71
Query: 146 AFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTKM 185
F+ + + A +A L+G+ + R I + A ++
Sbjct: 72 GFVTFENSADADRAREKLHGTVVEG--R-KIEVNNATARV 108
>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 = 46.5 bits (111), Expect = 1e-07
Identities = 14/79 (17%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAFIEYTDVNFAIQAMSN-L 163
+TL+V LG ++E ++++ F F + + + AFI++ A A
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ---CAFIQFATRQAAEVAAEKSF 69
Query: 164 NGSYLASSDRGAIRIEYAK 182
N + + +++ +
Sbjct: 70 NKLIVNGR---RLNVKWGR 85
>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 = 47.4 bits (113), Expect = 2e-07
Identities = 22/119 (18%), Positives = 48/119 (40%), Gaps = 16/119 (13%)
Query: 83 SPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM----- 137
+ + P S +++V N+ + Q+++ F S +R+ +
Sbjct: 14 TAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKF 73
Query: 138 --HNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRG-AIRIEYAKTKMAEFTTEHR 193
H KG A+IE+ + N ++ A ++ + RG I++ +T M ++ R
Sbjct: 74 SGHPKG---YAYIEFAERN-SVDAAVAMDETVF----RGRTIKVLPKRTNMPGISSTDR 124
>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 = 46.5 bits (111), Expect = 2e-07
Identities = 24/98 (24%), Positives = 40/98 (40%), Gaps = 7/98 (7%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSF-PGFSRVRMH-NKGGSP--VA 146
GSS S +G + + V N+ VS EI D F + V + N+ G P A
Sbjct: 1 GSSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 147 FIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+ + + A A+ +LN + S R +++
Sbjct: 61 MVAFESRDEATAAVIDLNDRPIGS--R-KVKLVLGSGP 95
>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 = 46.1 bits (110), Expect = 2e-07
Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 4/82 (4%)
Query: 91 GSSPPSQGMNGM-SPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSP--VA 146
GSS S T+FV NL V E+ + ++F ++V ++ G P
Sbjct: 1 GSSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60
Query: 147 FIEYTDVNFAIQAMSNLNGSYL 168
F+ + A++ LNG L
Sbjct: 61 FVCFKHPESVSYAIALLNGIRL 82
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 46.5 bits (111), Expect = 2e-07
Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 9/86 (10%)
Query: 103 SPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM--HNKGGSP--VAFIEYTDVNFAIQ 158
P T +V NL + +I IF VR+ ++E+ +V+ +
Sbjct: 13 EPPYTAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71
Query: 159 AMSNLNGSYLASSDRGAIRIEYAKTK 184
A+ +G+ L DR ++R++ A+ +
Sbjct: 72 AL-TYDGALL--GDR-SLRVDIAEGR 93
>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 = 46.0 bits (110), Expect = 2e-07
Identities = 22/90 (24%), Positives = 38/90 (42%), Gaps = 14/90 (15%)
Query: 101 GMSPCS-TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------KGGSPVAFIEYTD 152
M+ L+V L + V ++ + F F + +++ +G AF+E+
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG---FAFVEFEL 58
Query: 153 VNFAIQAMSNLNGSYLASSDRGAIRIEYAK 182
A A+ N+N S L R IR+ AK
Sbjct: 59 AEDAAAAIDNMNESELFG--R-TIRVNLAK 85
>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 = 46.5 bits (111), Expect = 3e-07
Identities = 22/110 (20%), Positives = 47/110 (42%), Gaps = 20/110 (18%)
Query: 87 PSPVGSSPPSQGMNGMSP----CSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM----- 137
G SP + ++ +SP T+F L + ++++D F + VR+
Sbjct: 3 SGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN 62
Query: 138 --HNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRG-AIRIEYAKTK 184
+KG +A++E+ ++ A+ L G L G I ++ ++ +
Sbjct: 63 SRRSKG---IAYVEFCEIQSVPLAIG-LTGQRL----LGVPIIVQASQAE 104
>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 = 46.1 bits (110), Expect = 3e-07
Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 18/101 (17%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------KGGS 143
GSS P + TL V NL S ++ +F + V + +G
Sbjct: 4 GSSGPD-----VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRG-- 56
Query: 144 PVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
AF+ + D A A + ++G+ L D +R++ A+
Sbjct: 57 -FAFVRFHDRRDAQDAEAAMDGAEL---DGRELRVQVARYG 93
>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 = 46.1 bits (110), Expect = 3e-07
Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 10/87 (11%)
Query: 103 SPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGSP--VAFIEYTDVNFAI 157
SP T F+ NL V+E+ IK+ F S VR+ + + E+ D++ +
Sbjct: 17 SPPYTAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLL 75
Query: 158 QAMSNLNGSYLASSDRGAIRIEYAKTK 184
A+ +LN L +R IR++ A
Sbjct: 76 SAL-SLNEESLG--NR-RIRVDVADQA 98
>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 = 47.0 bits (112), Expect = 3e-07
Identities = 18/134 (13%), Positives = 46/134 (34%), Gaps = 21/134 (15%)
Query: 58 SLNIPHPTAALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFV 117
+ + + P+ + P N L V + V
Sbjct: 3 QIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDV-LRN-------LMVNYIPTTV 54
Query: 118 SEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLAS 170
E +++ +F + V++ ++G F+++ + A QA++ LNG + +
Sbjct: 55 DEVQLRQLFERYGPIESVKIVCDRETRQSRG---YGFVKFQSGSSAQQAIAGLNGFNILN 111
Query: 171 SDRGAIRIEYAKTK 184
+ +++ A +
Sbjct: 112 --K-RLKVALAASG 122
>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 = 46.1 bits (110), Expect = 3e-07
Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 12/95 (12%)
Query: 95 PSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN------KGGSPVAFI 148
G G+ L V+NL VS+ +I+++F F + +H G A +
Sbjct: 19 GFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG---TADV 75
Query: 149 EYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKT 183
+ A++AM NG L R + I+ +
Sbjct: 76 HFERKADALKAMKQYNGVPLDG--R-PMNIQLVTS 107
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 46.7 bits (111), Expect = 4e-07
Identities = 22/101 (21%), Positives = 38/101 (37%), Gaps = 13/101 (12%)
Query: 88 SPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------K 140
GS + L+V L + V ++ + F F + +++ +
Sbjct: 46 VDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 105
Query: 141 GGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYA 181
G AF+E+ A A+ N+N S L R IR+ A
Sbjct: 106 G---FAFVEFELAEDAAAAIDNMNESELFG--R-TIRVNLA 140
>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 = 45.6 bits (109), Expect = 4e-07
Identities = 24/92 (26%), Positives = 40/92 (43%), Gaps = 15/92 (16%)
Query: 101 GMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------KGGSPVAFIEYTDV 153
G S S L+V +L ++E ++ IF F + + KG FI ++D
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKG---YGFITFSDS 57
Query: 154 NFAIQAMSNLNGSYLASSDRG-AIRIEYAKTK 184
A +A+ LNG LA G +R+ + +
Sbjct: 58 ECARRALEQLNGFELA----GRPMRVGHVTER 85
>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 = 45.7 bits (109), Expect = 5e-07
Identities = 21/96 (21%), Positives = 42/96 (43%), Gaps = 5/96 (5%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSP-VAFI 148
GSS S L+V NL + ++ ++ F F + + M G S F+
Sbjct: 1 GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFV 60
Query: 149 EYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
++ A +A++ +NG +A+ + + + A+ K
Sbjct: 61 CFSSPEEATKAVTEMNGRIVAT--K-PLYVALAQRK 93
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 45.6 bits (108), Expect = 6e-07
Identities = 19/89 (21%), Positives = 39/89 (43%), Gaps = 13/89 (14%)
Query: 106 STLFVANLGQFVSEQEI---KDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNF 155
+ +FV L Q +++ E+ + FG F +V + ++G S A++ Y
Sbjct: 16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75
Query: 156 AIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
A++A+ +N + R ++ TK
Sbjct: 76 ALRAIQCVNNVVVD--GR-TLKASLGTTK 101
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 45.5 bits (108), Expect = 7e-07
Identities = 23/118 (19%), Positives = 42/118 (35%), Gaps = 25/118 (21%)
Query: 103 SPCSTLFVANLGQFVSEQEIKDIFGSF--------PGFSRVRM-------HNKGGSPVAF 147
S +T+FV LG+ V+ + + D F G + + KG A
Sbjct: 5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKG---EAT 61
Query: 148 IEYTDVNFAIQAMSNLNGSYLASSDRG-AIRIEYAKTKMAEFTTEHRTRHQGT-KYGY 203
+ + D A A+ +G G I++ +A + A+F G + +
Sbjct: 62 VSFDDPPSAKAAIDWFDGKEF----SGNPIKVSFATRR-ADFNRGGGNGRGGLEHHHH 114
>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 = 45.0 bits (107), Expect = 9e-07
Identities = 24/109 (22%), Positives = 41/109 (37%), Gaps = 6/109 (5%)
Query: 99 MNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSP--VAFIEYTDVNF 155
M LF+ L + +E+ +K +FG S V + ++ AFI + +
Sbjct: 1 MVEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPAD 60
Query: 156 AIQAMSNLNGSYLASSDRGAIRIEYAKTKMAEFTTEHRTRHQGTKYGYT 204
A A ++NG L AI++E AK + R +
Sbjct: 61 AKNAAKDMNGKSL---HGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPS 106
>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 = 44.8 bits (106), Expect = 1e-06
Identities = 18/94 (19%), Positives = 32/94 (34%), Gaps = 6/94 (6%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEY 150
GSS S G + + V+ L S Q++KD ++ G +E+
Sbjct: 1 GSSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEF 57
Query: 151 TDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
A+ L+ + S + Y + K
Sbjct: 58 VRKEDMTYAVRKLDNTKFRSHE---GETAYIRVK 88
>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 = 44.6 bits (106), Expect = 1e-06
Identities = 22/102 (21%), Positives = 40/102 (39%), Gaps = 15/102 (14%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGS 143
GSS S ++ + +T++V L + VSE + ++F M ++G
Sbjct: 1 GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQG-- 58
Query: 144 PVAFIEYTDVNFAIQAMSNLNGSYLASSDRG-AIRIEYAKTK 184
F+E+ A A+ ++ L G IR+ A
Sbjct: 59 -YGFVEFLSEEDADYAIKIMDMIKLY----GKPIRVNKASAH 95
>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 = 44.2 bits (105), Expect = 2e-06
Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 12/79 (15%)
Query: 96 SQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPG---FSRVRMHNKGGSP-VAFIEYT 151
N L+++NL + EQE++++ F G +R+ + G S V F
Sbjct: 23 QDPTN-------LYISNLPLSMDEQELENMLKPF-GQVISTRILRDSSGTSRGVGFARME 74
Query: 152 DVNFAIQAMSNLNGSYLAS 170
+ + NG ++ +
Sbjct: 75 STEKCEAVIGHFNGKFIKT 93
>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 = 44.3 bits (105), Expect = 2e-06
Identities = 13/82 (15%), Positives = 32/82 (39%), Gaps = 5/82 (6%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPG-FSRVRMH-NKGGSP--VA 146
GSS S + S + N+ +++ ++ P + V + + G A
Sbjct: 1 GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60
Query: 147 FIEYTDVNFAIQAMSNLNGSYL 168
+++ + + A ++ L+ L
Sbjct: 61 LVQFKNEDDARKSER-LHRKKL 81
>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 = 45.8 bits (109), Expect = 2e-06
Identities = 14/85 (16%), Positives = 27/85 (31%), Gaps = 5/85 (5%)
Query: 103 SPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSP--VAFIEYTDVNFAIQA 159
+ + L V NL VS + ++ F F + + + G F+E+ A +A
Sbjct: 94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKA 153
Query: 160 MSNLNGSYLASSDRGAIRIEYAKTK 184
+ R +
Sbjct: 154 LERCGDGAFL--LTTTPRPVIVEPM 176
Score = 43.1 bits (102), Expect = 2e-05
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 7/76 (9%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSPVAFIEYTDVNFAIQAMSNLNG 165
LFV NL ++E++ K +F + S V ++G FI A A + L+G
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG---FGFIRLESRTLAEIAKAELDG 80
Query: 166 SYLASSDRGAIRIEYA 181
+ L +RI +A
Sbjct: 81 TIL---KSRPLRIRFA 93
>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 = 43.7 bits (104), Expect = 2e-06
Identities = 24/97 (24%), Positives = 42/97 (43%), Gaps = 14/97 (14%)
Query: 96 SQGMNGMSPCS-TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAF 147
S G +GM+ L+V L + V ++ + F F + +++ ++G AF
Sbjct: 2 SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG---FAF 58
Query: 148 IEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+E+ A A+ N+N S L IR+ AK
Sbjct: 59 VEFELAEDAAAAIDNMNESEL---FGRTIRVNLAKPM 92
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 44.3 bits (105), Expect = 2e-06
Identities = 22/118 (18%), Positives = 42/118 (35%), Gaps = 15/118 (12%)
Query: 75 NGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSR 134
G + GS + + ++L V NL S ++ +F +
Sbjct: 17 RGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGD 76
Query: 135 VRMHN-------KGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRG-AIRIEYAKTK 184
V + +G AF+ + D A AM ++G+ L G +R++ A+
Sbjct: 77 VYIPRDRYTKESRG---FAFVRFHDKRDAEDAMDAMDGAVLD----GRELRVQMARYG 127
>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 = 43.4 bits (103), Expect = 3e-06
Identities = 24/94 (25%), Positives = 41/94 (43%), Gaps = 8/94 (8%)
Query: 96 SQGMNGMS-PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGSP-VAFIEY 150
S G +GM+ LFV L +EQ ++ +F + S V + S F+ +
Sbjct: 2 SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61
Query: 151 TDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+++ A AM +NG + D IR++ A
Sbjct: 62 ENIDDAKDAMMAMNGKSV---DGRQIRVDQAGKS 92
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 43.9 bits (103), Expect = 3e-06
Identities = 17/94 (18%), Positives = 37/94 (39%), Gaps = 4/94 (4%)
Query: 93 SPPSQGMNGMSPCSTLF--VANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEY 150
+ P + L + N ++ + + R+ + + G A +E+
Sbjct: 11 TRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGI-QAMVEF 69
Query: 151 TDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
V A +A + LNG+ + + ++IEYA+
Sbjct: 70 ESVLCAQKAKAALNGADIY-AGCCTLKIEYARPT 102
>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 = 42.9 bits (102), Expect = 3e-06
Identities = 16/91 (17%), Positives = 38/91 (41%), Gaps = 15/91 (16%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM--------HNKGGSPVAFIEYTDV 153
M P + + L + V++ I +IF ++ + M +KG A++E+ +
Sbjct: 2 MKPT-KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKG---YAYVEFENP 57
Query: 154 NFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+ A +A+ +++G + + I
Sbjct: 58 DEAEKALKHMDGGQID--GQ-EITATAVLAP 85
>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 = 42.6 bits (101), Expect = 5e-06
Identities = 27/86 (31%), Positives = 41/86 (47%), Gaps = 13/86 (15%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------KGGSPVAFIEYTDVNFAIQ 158
++FV N+ +E+++KDIF R+ KG F EY D A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG---YGFCEYQDQETALS 65
Query: 159 AMSNLNGSYLASSDRGAIRIEYAKTK 184
AM NLNG S R A+R++ A ++
Sbjct: 66 AMRNLNGREF--SGR-ALRVDNAASE 88
>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 = 43.0 bits (102), Expect = 6e-06
Identities = 18/86 (20%), Positives = 39/86 (45%), Gaps = 5/86 (5%)
Query: 101 GMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSP-VAFIEYTDVNFAIQ 158
G +F+ NL + + + + D F +F + + ++ GS F+ + A +
Sbjct: 1 GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAER 60
Query: 159 AMSNLNGSYLASSDRGAIRIEYAKTK 184
A+ +NG L +DR + + K++
Sbjct: 61 AIEKMNGMLL--NDR-KVFVGRFKSR 83
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 42.3 bits (100), Expect = 8e-06
Identities = 22/98 (22%), Positives = 42/98 (42%), Gaps = 12/98 (12%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGS-FPGFSRVR-MHNKGGSP--VA 146
GSS S P +LFV +L V + + + F +P + + ++ G
Sbjct: 1 GSSGSS------GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYG 54
Query: 147 FIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
F+++TD +A++ G+ S + +R+ A K
Sbjct: 55 FVKFTDELEQKRALTECQGAVGLGS-K-PVRLSVAIPK 90
>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 = 41.7 bits (99), Expect = 1e-05
Identities = 19/86 (22%), Positives = 39/86 (45%), Gaps = 16/86 (18%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFAIQA 159
+++V N+ + +E++ F +RV + H KG A+IE++D +
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG---FAYIEFSDKESVRTS 64
Query: 160 MSNLNGSYLASSDRG-AIRIEYAKTK 184
++ L+ S RG I++ +T
Sbjct: 65 LA-LDESLF----RGRQIKVIPKRTN 85
>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 = 44.1 bits (103), Expect = 1e-05
Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 4/69 (5%)
Query: 104 PCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM----HNKGGSPVAFIEYTDVNFAIQA 159
TLFVA + +E +++ F + R+ M + AFIEY A
Sbjct: 101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
Query: 160 MSNLNGSYL 168
+ +G +
Sbjct: 161 YKHADGKKI 169
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 41.5 bits (97), Expect = 1e-05
Identities = 14/83 (16%), Positives = 36/83 (43%), Gaps = 8/83 (9%)
Query: 107 TLFVANLGQFVSEQEIK-DIFGSFPGFSRVR----MHNKGGSPVAFIEYTDVNFAIQAMS 161
+ V+N+ +S +E++ + +F +V+ + A ++ ++ AI A++
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVN 70
Query: 162 NLNGSYLASSDRGAIRIEYAKTK 184
+L+ + S I + A
Sbjct: 71 SLHRYKIGSK---KILVSLATGA 90
>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 = 41.8 bits (98), Expect = 2e-05
Identities = 19/105 (18%), Positives = 36/105 (34%), Gaps = 9/105 (8%)
Query: 71 MHHANGMP----HFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIF 126
HH++G+ H S S+ + + + L +E +I + F
Sbjct: 8 HHHSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFF 67
Query: 127 GSFPGFSRVRM-HNKGGSP--VAFIEYTDVNFAIQAMSNLNGSYL 168
RV + G A +E+ A+ AMS + + +
Sbjct: 68 SPL-NPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMS-KDRANM 110
>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 = 40.8 bits (96), Expect = 3e-05
Identities = 18/110 (16%), Positives = 42/110 (38%), Gaps = 17/110 (15%)
Query: 82 PSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---- 137
S + +G G + LF+ +L Q +Q++ +F F ++
Sbjct: 6 SGLTQQSIGAAGSQKEGPEG----ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK 61
Query: 138 ---HNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
+K F+ Y + A A+ ++NG + ++++ ++K
Sbjct: 62 QTNLSKC---FGFVSYDNPVSAQAAIQSMNGFQIGMK---RLKVQLKRSK 105
>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 = 40.1 bits (94), Expect = 4e-05
Identities = 20/101 (19%), Positives = 37/101 (36%), Gaps = 10/101 (9%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSF-PGFSRVRMH-NKGGSPV--A 146
GSS S + + + L S++EI F + + + + G A
Sbjct: 1 GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60
Query: 147 FIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTKMAE 187
F+++ A +A+ + + G IE K+ AE
Sbjct: 61 FVQFASQEIAEKALK-KHKERI-----GHRYIEIFKSSRAE 95
>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 = 40.1 bits (94), Expect = 6e-05
Identities = 12/115 (10%), Positives = 31/115 (26%), Gaps = 10/115 (8%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMH-NKGGSP--VAF 147
S + + + V + E +++D F V + + G
Sbjct: 2 SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGL 60
Query: 148 IEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTKMAEFTTEHRTRHQGTKYG 202
+++ +A+ N + +E + ++ G G
Sbjct: 61 VKFLSPQDTFEALK-RNRMLM-----IQRYVEVSPATERQWVAAGGHITSGPSSG 109
>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 = 39.3 bits (92), Expect = 8e-05
Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 5/81 (6%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMH-NKGGSP--VAF 147
GSS S + + + L +E +I + F RV + G A
Sbjct: 1 GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEAD 59
Query: 148 IEYTDVNFAIQAMSNLNGSYL 168
+E+ A+ AM+ + + +
Sbjct: 60 VEFATHEDAVAAMA-KDKANM 79
>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 = 40.6 bits (94), Expect = 1e-04
Identities = 7/69 (10%), Positives = 22/69 (31%), Gaps = 3/69 (4%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGSPVAFIEYTDVNFAIQ 158
++++ + +IK+ ++M +K F+ + + A +
Sbjct: 106 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKK 165
Query: 159 AMSNLNGSY 167
+ Y
Sbjct: 166 FVETPGQKY 174
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 40.2 bits (93), Expect = 2e-04
Identities = 21/132 (15%), Positives = 36/132 (27%), Gaps = 20/132 (15%)
Query: 50 PALHPQVPSLNIPHPTAALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLF 109
LH +P A T + G F +GS TL+
Sbjct: 88 EYLH-HIPDEEDIGKLALRTEVLDCFGREKFADYREDMGGIGSF--------RKKNKTLY 138
Query: 110 VANLGQFVS---------EQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAM 160
V + ++ E I+ +F R+R F+++ A A
Sbjct: 139 VGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKN--CGFVKFKYQANAEFAK 196
Query: 161 SNLNGSYLASSD 172
++ L
Sbjct: 197 EAMSNQTLLLPS 208
>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 = 37.1 bits (87), Expect = 3e-04
Identities = 13/73 (17%), Positives = 29/73 (39%), Gaps = 10/73 (13%)
Query: 101 GMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDV 153
G S S L++ L ++Q++ + + + KG F+++
Sbjct: 1 GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKG---YGFVDFDSP 57
Query: 154 NFAIQAMSNLNGS 166
+ A +A++ L S
Sbjct: 58 SAAQKAVTALKAS 70
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 37.4 bits (87), Expect = 3e-04
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 14/72 (19%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPV-----------AFIEYTDVNFA 156
L+V N+ ++E+ + D F + + G+PV AF+E+ V+
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQ--MRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 157 IQAMSNLNGSYL 168
QAM +G
Sbjct: 67 TQAM-AFDGIIF 77
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 37.8 bits (88), Expect = 3e-04
Identities = 17/71 (23%), Positives = 27/71 (38%), Gaps = 8/71 (11%)
Query: 106 STLFVANLGQFVSEQE------IKDIFGSFPGFSRVRMHNKGGSP--VAFIEYTDVNFAI 157
S + V N+ Q ++ I IF F + + G F+EY A+
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 75
Query: 158 QAMSNLNGSYL 168
A+ N +G L
Sbjct: 76 DAVKNADGYKL 86
>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 = 37.2 bits (87), Expect = 4e-04
Identities = 12/98 (12%), Positives = 28/98 (28%), Gaps = 20/98 (20%)
Query: 108 LFVANLGQFVSEQEIKDIFGSF--PGFSRVRMHN-------KGGSPVAFIEYTDVNFAIQ 158
L++ NL + +++++ + S ++ KG A + + +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG---FALVGVGSEASSKK 60
Query: 159 AMSNLNGSYLASSDRGAIRIEYAKTKMAEFTTEHRTRH 196
M L L + + H H
Sbjct: 61 LMDLLPKREL---HGQNPVVTPSNKL-----EHHHHHH 90
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 37.9 bits (88), Expect = 4e-04
Identities = 15/93 (16%), Positives = 30/93 (32%), Gaps = 9/93 (9%)
Query: 95 PSQGMNGMSPCST---LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYT 151
+G G + + V+ L S Q++KD ++ G +E+
Sbjct: 3 APRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG---TGVVEFV 59
Query: 152 DVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK 184
A+ L+ + S + Y + K
Sbjct: 60 RKEDMTYAVRKLDNTKFRSHE---GETAYIRVK 89
>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 = 39.0 bits (90), Expect = 5e-04
Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 4/66 (6%)
Query: 103 SPCSTLFVANLGQF--VSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAM 160
+L VAN G VS ++ + + M P +F Y + +A
Sbjct: 16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP--NKPYSFARYRTTEESKRAY 73
Query: 161 SNLNGS 166
LNG
Sbjct: 74 VTLNGK 79
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 36.9 bits (86), Expect = 6e-04
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 7/73 (9%)
Query: 98 GMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM-HNKGGSPVAFIEYTDVNFA 156
G +G S ++FV+ + V ++ + F +F + V M +KG A +E DV
Sbjct: 1 GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV--FAIVEMGDVGAR 58
Query: 157 IQAMSN----LNG 165
+S L G
Sbjct: 59 EAVLSQSQHSLGG 71
>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 = 38.5 bits (89), Expect = 6e-04
Identities = 17/142 (11%), Positives = 40/142 (28%), Gaps = 10/142 (7%)
Query: 64 PTAALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIK 123
P+A LP + P+ L++ NL + +++++
Sbjct: 27 PSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLT 86
Query: 124 DIFGSFPGFS----RVRMHNKGGSP--VAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIR 177
+ S + + G A + + + M L L
Sbjct: 87 EAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQ---NPV 143
Query: 178 IEYAKTK-MAEFTTEHRTRHQG 198
+ + +++F + R Q
Sbjct: 144 VTPVNKQFLSQFEMQSRKTTQS 165
>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 = 37.1 bits (86), Expect = 8e-04
Identities = 20/122 (16%), Positives = 38/122 (31%), Gaps = 15/122 (12%)
Query: 82 PSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSF-PGFSRVRMH-N 139
SP+ S P + +++ L + + D F + +
Sbjct: 8 KSPSGQKRSRSRSPHE------AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG 61
Query: 140 KGGSP--VAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYA-KTKMAEFTTEHRTRH 196
G F+E+ + A+ + Y+ +R I++ K M E R R
Sbjct: 62 PNGKATGEGFVEFRNEADYKAALC-RHKQYMG--NR-FIQVHPITKKGMLEKIDMIRKRL 117
Query: 197 QG 198
Q
Sbjct: 118 QS 119
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 37.2 bits (86), Expect = 0.001
Identities = 16/118 (13%), Positives = 41/118 (34%), Gaps = 12/118 (10%)
Query: 87 PSPVGSSPPSQGMNGMSPC--STLFVANLGQFVSEQEIKDIFGSFPGF----SRVRMHNK 140
P P +P + ++V + + ++Q++ + S + + +
Sbjct: 35 PKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA 94
Query: 141 GGSP--VAFIEYTDVNFAIQAMSNLNGSYLASSDRGAIRIEYAKTK-MAEFTTEHRTR 195
G A + N + + L G L + + + A + +++F + R R
Sbjct: 95 NGQSKGYAEVVVASENSVHKLLELLPGKVL---NGEKVDVRPATRQNLSQFEAQARKR 149
>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 = 36.8 bits (85), Expect = 0.001
Identities = 13/101 (12%), Positives = 34/101 (33%), Gaps = 5/101 (4%)
Query: 72 HHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPG 131
HH++G+ A + + + + L +++EI F
Sbjct: 9 HHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEI 68
Query: 132 -FSRVRMH-NKGGSP--VAFIEYTDVNFAIQAMSNLNGSYL 168
+ + + + G AF+++ A +A+ + +
Sbjct: 69 VPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERI 108
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 35.4 bits (82), Expect = 0.001
Identities = 17/71 (23%), Positives = 27/71 (38%), Gaps = 8/71 (11%)
Query: 106 STLFVANLGQFVSEQE------IKDIFGSFPGFSRVRMHNKGGSP--VAFIEYTDVNFAI 157
S + V N+ Q ++ I IF F + + G F+EY A+
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 61
Query: 158 QAMSNLNGSYL 168
A+ N +G L
Sbjct: 62 DAVKNADGYKL 72
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 34.8 bits (81), Expect = 0.002
Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 14/85 (16%)
Query: 107 TLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHN-------KGGSPVAFIEYTDVNFAIQA 159
++V NL + +++K++F F V++ KG F+E + +A
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKG---FGFVEMQE-ESVSEA 58
Query: 160 MSNLNGSYLASSDRGAIRIEYAKTK 184
++ L+ + IR+ A K
Sbjct: 59 IAKLDNTDF---MGRTIRVTEANPK 80
>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 = 34.9 bits (81), Expect = 0.004
Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 6/66 (9%)
Query: 106 STLFVANLGQFVSEQEIKDIFGSFPGFSRVR-MHNKGGSP-----VAFIEYTDVNFAIQA 159
+T+FV + + E EI+ F + V+ + ++ G V+F DV +++
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 160 MSNLNG 165
N +G
Sbjct: 70 QINFHG 75
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 33.6 bits (77), Expect = 0.008
Identities = 10/67 (14%), Positives = 23/67 (34%), Gaps = 10/67 (14%)
Query: 109 FVANLGQFVSEQEIKDIFGSFPGFSRVRM-------HNKGGSPVAFIEYTDVNFAIQAMS 161
+ + V ++ + +F + KG F+E +N A + +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKG---FLFVECGSMNDAKKIIK 72
Query: 162 NLNGSYL 168
+ +G L
Sbjct: 73 SFHGKRL 79
>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 = 33.8 bits (78), Expect = 0.020
Identities = 25/149 (16%), Positives = 46/149 (30%), Gaps = 32/149 (21%)
Query: 63 HPTAALTAMHHANGMPHFL------PSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQF 116
AM N PH + P A+ P + +FV + +
Sbjct: 64 TVEEVDAAM---NARPHKVDGRVVEPKRAVSREDSQRPGAH-----LTVKKIFVGGIKED 115
Query: 117 VSEQEIKDIFGSFPGFSRVRM---HNKGGS-PVAFIEYTDVNFAIQAMSN----LNGSYL 168
E ++D F + + + G AF+ + D + + + +NG
Sbjct: 116 TEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGH-- 173
Query: 169 ASSDRGAIRIEYA--KTKMAEFTTEHRTR 195
+ A K +MA ++ R R
Sbjct: 174 ------NCEVRKALSKQEMASASSSQRGR 196
>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 = 33.3 bits (77), Expect = 0.026
Identities = 14/91 (15%), Positives = 29/91 (31%), Gaps = 16/91 (17%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRM---HNKGGS-PVAFIEYTDVNFAI 157
+FV +G V +E ++ F + ++ + G S F+ Y +
Sbjct: 84 QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVD 143
Query: 158 QAMSN----LNGSYLASSDRGAIRIEYAKTK 184
+ N I I+ A+ +
Sbjct: 144 RVCQNKFIDFKDR--------KIEIKRAEPR 166
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 34.1 bits (77), Expect = 0.027
Identities = 22/164 (13%), Positives = 38/164 (23%), Gaps = 63/164 (38%)
Query: 63 HPTAALTAMHHANG--MPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLG------ 114
H + + F + FV N
Sbjct: 6 HMDFETGEHQYQYKDILSVFEDA-------------------------FVDNFDCKDVQD 40
Query: 115 ---QFVSEQEIKDIFGSFPGFSRVR-----MHNKGGSPVA-FIEYTDVNFAIQAMSNLNG 165
+S++EI I S S + +K V F+E +N
Sbjct: 41 MPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVL---------RINY 91
Query: 166 SYLASS------DRGAIRIEYAKTK------MAEFTTEHRTRHQ 197
+L S + Y + + F + +R Q
Sbjct: 92 KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ 135
>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 = 32.5 bits (74), Expect = 0.028
Identities = 12/93 (12%), Positives = 29/93 (31%), Gaps = 12/93 (12%)
Query: 102 MSPCSTLFVANLGQFVSEQEIKDIFGSF---PGFSRVRM-HNKGGSP--VAFIEYTDVNF 155
+ + L + +++ + F G + + N+ G A IE
Sbjct: 8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQD 67
Query: 156 AIQAMSNLNGSYLASSDRGAIRIEYAKTKMAEF 188
+A+ + Y+ G +E + +
Sbjct: 68 VQKALE-KHRMYM-----GQRYVEVYEINNEDV 94
>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 = 30.1 bits (68), Expect = 0.21
Identities = 7/51 (13%), Positives = 21/51 (41%)
Query: 119 EQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSYLA 169
++++ F ++ + ++ VA + + D A + L+G +
Sbjct: 40 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFG 90
>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 = 29.6 bits (67), Expect = 0.26
Identities = 6/49 (12%), Positives = 20/49 (40%)
Query: 119 EQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQAMSNLNGSY 167
+ ++ + G + + +++ + AI A++ L+G +
Sbjct: 31 KDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRW 79
>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 = 30.8 bits (69), Expect = 0.32
Identities = 24/183 (13%), Positives = 40/183 (21%), Gaps = 56/183 (30%)
Query: 13 APFFHAGGPEL--W-HHP--------LAYATAADLPG---------TASLHQHTLVHPAL 52
A G + W +P L + P + L
Sbjct: 205 AEKVFTQGLNILEWLENPSNTPDKDYLLSIPIS-CPLIGVIQLAHYVVTAKLLGFTPGEL 263
Query: 53 HPQVPSLNIPH----PTAALTAMHHANGMPHFL---------------------PSPALP 87
+ H TA A + F P+ +LP
Sbjct: 264 RSYLKGA-TGHSQGLVTAVAIAE--TDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLP 320
Query: 88 SPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVR--MHNKGGSPV 145
+ SP L ++NL Q + + P +V + N
Sbjct: 321 PSILEDSLENNEGVPSP--MLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVN---GAK 375
Query: 146 AFI 148
+
Sbjct: 376 NLV 378
Score = 30.4 bits (68), Expect = 0.53
Identities = 11/54 (20%), Positives = 16/54 (29%), Gaps = 16/54 (29%)
Query: 9 LDIGAPFFHAGGPELWHHPLAYATAADLPGTASLHQHTLVHPALHPQVPSLNIP 62
L + +PF H L L + L LV + + IP
Sbjct: 421 LPVASPF---------HSHL-------LVPASDLINKDLVKNNVSFNAKDIQIP 458
Score = 28.9 bits (64), Expect = 1.5
Identities = 24/141 (17%), Positives = 41/141 (29%), Gaps = 44/141 (31%)
Query: 21 PELWHHPLAYATAADLPGTASLHQHTL----------------VHPALHPQVPSLNIPHP 64
EL L Y ++ P L +H AL L +
Sbjct: 58 AELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIH-AL---AAKLLQEND 113
Query: 65 T----------AALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLG 114
T +TA A + AL VG G + +F G
Sbjct: 114 TTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGE--------GNAQLVAIFG---G 162
Query: 115 QFVSE---QEIKDIFGSFPGF 132
Q ++ +E++D++ ++
Sbjct: 163 QGNTDDYFEELRDLYQTYHVL 183
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 28.1 bits (62), Expect = 0.74
Identities = 18/97 (18%), Positives = 32/97 (32%), Gaps = 13/97 (13%)
Query: 100 NGMSPCSTLFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQA 159
S L + NL + ++ + + G +A +YT A +A
Sbjct: 2 AMAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQG--IALCKYTTREEANKA 59
Query: 160 MSNLNGSYLASSDRGAIRIEYAKTKMAEFTTEHRTRH 196
LN LA++ T AE +E+ +
Sbjct: 60 QMALNNCVLANT-----------TIFAESPSENEVQS 85
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 28.0 bits (62), Expect = 0.92
Identities = 11/61 (18%), Positives = 18/61 (29%), Gaps = 6/61 (9%)
Query: 108 LFVANLGQFVSEQEIKDIFGSFPGFSRVRMHNKGGSP------VAFIEYTDVNFAIQAMS 161
+FV L + E EI F F H AF+ + + + +
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
Query: 162 N 162
Sbjct: 71 A 71
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.4 bits (62), Expect = 1.0
Identities = 6/41 (14%), Positives = 16/41 (39%), Gaps = 15/41 (36%)
Query: 119 EQEIKDIFGSFPGFSRVRMHNKGGSPVAFIEYTDVNFAIQA 159
+Q +K + + ++++ +P AI+A
Sbjct: 19 KQALKKLQ------ASLKLYADDSAPA---------LAIKA 44
>3li6_A Calcium-binding protein; calcium signaling protein, assemble free
energy, dynamic behaviour, cytoskeleton, metal binding;
2.50A {Entamoeba histolytica}
Length = 66
Score = 26.8 bits (60), Expect = 1.4
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 109 FVANLGQFVSEQEIKDIFGSF 129
FV+ +EQ ++ IF S
Sbjct: 25 FVSKKRAIKNEQLLQLIFKSI 45
>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 = 26.8 bits (60), Expect = 2.1
Identities = 13/39 (33%), Positives = 19/39 (48%)
Query: 91 GSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFGSF 129
GSS S + S L V L +EQ++K+ F +F
Sbjct: 1 GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTF 39
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 27.1 bits (60), Expect = 3.3
Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 8/59 (13%)
Query: 119 EQEIKDIFGSFPGFSRVRMHNKGGSPVA--------FIEYTDVNFAIQAMSNLNGSYLA 169
E E+ + G F +RV ++ + F+E++ + +A+ LNG + A
Sbjct: 143 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA 201
>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 = 27.0 bits (59), Expect = 5.2
Identities = 10/76 (13%), Positives = 18/76 (23%), Gaps = 2/76 (2%)
Query: 25 HHPLAYATAADLPGTASLHQHTLVHPA--LHPQVPSLNIPHPTAALTAMHHANGMPHFLP 82
HH + + L P + +P P A P +
Sbjct: 7 HHHHSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVT 66
Query: 83 SPALPSPVGSSPPSQG 98
++ + P G
Sbjct: 67 GDSVLQRILRGPTGPG 82
>3eps_A Isocitrate dehydrogenase kinase/phosphatase; ATP-binding,
glyoxylate bypass, nucleotide-binding, protein
phosphatase; HET: AMP ATP; 2.80A {Escherichia coli O157}
PDB: 3lcb_A* 3lc6_A*
Length = 578
Score = 26.8 bits (59), Expect = 7.0
Identities = 10/49 (20%), Positives = 17/49 (34%), Gaps = 9/49 (18%)
Query: 122 IKDIFGSFPGFSR---------VRMHNKGGSPVAFIEYTDVNFAIQAMS 161
IKD F S V+ H++ G E+ + + +S
Sbjct: 338 IKDKFAPQKEMSAAHVRACYQLVKEHDRVGRMADTQEFENFVLEKRHIS 386
>3nxu_A Cytochrome P450 3A4; alpha beta protein, cytochrome P450 fold,
hemoprotein, monoo cytochrome P450 reductase,
endoplasmic reticulum; HET: HEM RIT; 2.00A {Homo
sapiens} PDB: 1w0e_A* 1w0g_A* 2j0d_A* 2v0m_A* 1w0f_A*
1tqn_A* 3ua1_A* 3tjs_A*
Length = 485
Score = 26.4 bits (59), Expect = 7.4
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 7/38 (18%)
Query: 99 MNGMSP----CSTLFVANLGQFVSEQ---EIKDIFGSF 129
+ M P + V NL + +KD+FG++
Sbjct: 120 LKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAY 157
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 26.3 bits (57), Expect = 8.7
Identities = 9/55 (16%), Positives = 16/55 (29%)
Query: 50 PALHPQVPSLNIPHPTAALTAMHHANGMPHFLPSPALPSPVGSSPPSQGMNGMSP 104
Q P AA + GMP P++ +P + ++
Sbjct: 20 ATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQID 74
>2q01_A Uronate isomerase; structural genomics, protein structure
initiative NEW YORK SGX research center for structural
genomics, nysgx; 2.34A {Caulobacter crescentus}
Length = 497
Score = 26.2 bits (57), Expect = 9.1
Identities = 21/107 (19%), Positives = 30/107 (28%), Gaps = 16/107 (14%)
Query: 30 YATAADLPGTASLHQHTLVHPALHPQVPSLNIPHPTAA---------LTAMHHANGMPHF 80
YA DLP S H H P + N P A L M ++ G+
Sbjct: 29 YALVKDLP-IISPHGH------TDPSWFATNAPFQDATDLLLAPDHYLFRMLYSQGVSLD 81
Query: 81 LPSPALPSPVGSSPPSQGMNGMSPCSTLFVANLGQFVSEQEIKDIFG 127
+ V + P + + LF +FG
Sbjct: 82 ALKVRSKAGVPDTDPREAWRVFASHFYLFRGTPSWVWLNHVFSQVFG 128
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.318 0.132 0.408
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: 3,235,147
Number of extensions: 187971
Number of successful extensions: 816
Number of sequences better than 10.0: 1
Number of HSP's gapped: 670
Number of HSP's successfully gapped: 195
Length of query: 206
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 117
Effective length of database: 4,216,824
Effective search space: 493368408
Effective search space used: 493368408
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (24.9 bits)