RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13181
(137 letters)
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 114 bits (287), Expect = 3e-34
Identities = 51/98 (52%), Positives = 71/98 (72%), Gaps = 1/98 (1%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 73
G + K LPTEPPYTA+VGNLP QGD++ F + + SVRLV+DK+TD+FKGFCYVEF
Sbjct: 4 GSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEF 63
Query: 74 VDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGG 111
+V++L++AL DG + +R+DIA+G++ D G
Sbjct: 64 DEVDSLKEALTYDGA-LLGDRSLRVDIAEGRKQDKSGP 100
>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 = 108 bits (272), Expect = 5e-32
Identities = 35/99 (35%), Positives = 59/99 (59%), Gaps = 2/99 (2%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDK-ETDRFKGFCYVE 72
G + LP PPYTAF+GNLP +T+ ++ FF + +VRL ++ +R KGF Y E
Sbjct: 4 GSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAE 63
Query: 73 FVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGG 111
F D+++L AL + ++ ++R+D+AD ++ + G
Sbjct: 64 FEDLDSLLSALSLNEE-SLGNKRIRVDVADQAQDKDSGP 101
>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 = 105 bits (265), Expect = 6e-31
Identities = 33/96 (34%), Positives = 58/96 (60%), Gaps = 2/96 (2%)
Query: 12 RYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKET-DRFKGFCY 70
+ ++ LP PPYTAF+GNLP +T+ ++ FF + +VRL ++ +R KGF Y
Sbjct: 6 HHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGY 65
Query: 71 VEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRN 106
EF D+++L AL + ++ ++R+D+AD ++
Sbjct: 66 AEFEDLDSLLSALSLNEE-SLGNRRIRVDVADQAQD 100
>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 = 83.1 bits (206), Expect = 4e-22
Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 2/90 (2%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLR 80
+ P+ F+GNL + +++ E + V D T + F YV+F E+L
Sbjct: 13 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 72
Query: 81 QALLKDGRITVDGLQVRLDIADGKRNDNKG 110
+AL G V G +++L+ R+ +G
Sbjct: 73 KALELTGL-KVFGNEIKLEKPK-GRDGTRG 100
>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 = 77.7 bits (192), Expect = 7e-20
Identities = 27/106 (25%), Positives = 50/106 (47%), Gaps = 2/106 (1%)
Query: 2 ADYSYGGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDK 60
+ S G P R + + T F L I D+E FF K+ VR++ D+
Sbjct: 2 SSGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDR 61
Query: 61 ETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRN 106
+ R KG YVEF +++++ A+ G+ + G+ + + + ++N
Sbjct: 62 NSRRSKGIAYVEFCEIQSVPLAIGLTGQ-RLLGVPIIVQASQAEKN 106
>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 = 72.1 bits (177), Expect = 1e-17
Identities = 26/109 (23%), Positives = 44/109 (40%), Gaps = 3/109 (2%)
Query: 13 YGRNQKTLPTEP-PYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYV 71
G + K LP P V +P + DV FF ++ +V L+KD R G V
Sbjct: 3 SGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVG-RNNGNGLV 61
Query: 72 EFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGG 120
+F+ ++ +AL ++ + V + A ++ GG G
Sbjct: 62 KFLSPQDTFEALKRNRM-LMIQRYVEVSPATERQWVAAGGHITSGPSSG 109
>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 = 71.0 bits (174), Expect = 5e-17
Identities = 25/125 (20%), Positives = 48/125 (38%), Gaps = 4/125 (3%)
Query: 2 ADYSYGGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLV--SVRLVKD 59
+ S G P R++ P E + ++ LP V FF + +V S+ +
Sbjct: 2 SSGSSGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG 61
Query: 60 KETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRG 119
+ G +VEF + + + AL + + + +++ K K K+ +
Sbjct: 62 P-NGKATGEGFVEFRNEADYKAALCRHKQ-YMGNRFIQVHPITKKGMLEKIDMIRKRLQS 119
Query: 120 GGSGG 124
G S G
Sbjct: 120 GPSSG 124
>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 = 67.0 bits (164), Expect = 9e-16
Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 1/75 (1%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 73
G + + + + + LP T+ D+ FF + V + + R G VEF
Sbjct: 4 GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDG-RVTGEADVEF 62
Query: 74 VDVENLRQALLKDGR 88
E+ A+ KD
Sbjct: 63 ATHEDAVAAMAKDKA 77
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 66.2 bits (162), Expect = 1e-15
Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 23 EPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
+T + P +T+ +V F K V++R+V++ G+ +V+F + E ++QA
Sbjct: 8 TTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHG-NKTGYIFVDFSNEEEVKQA 66
Query: 83 LLKDG 87
L +
Sbjct: 67 LKCNR 71
>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 = 67.0 bits (164), Expect = 1e-15
Identities = 30/112 (26%), Positives = 52/112 (46%), Gaps = 1/112 (0%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVE 72
G + + T + FVG+L IT D++ F ++ R+VKD T + KG+ +V
Sbjct: 4 GSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63
Query: 73 FVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGG 124
F + + A+ + G + G Q+R + A K K + + + G S G
Sbjct: 64 FFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115
>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 = 66.1 bits (162), Expect = 2e-15
Identities = 14/95 (14%), Positives = 41/95 (43%), Gaps = 1/95 (1%)
Query: 24 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
P ++G++P T+ + +++++++ D +T R KG+ ++EF D+E+ A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 83 LLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQN 117
+ + ++ + ++ +
Sbjct: 61 VRNLNGYQLGSRFLKCGYSSNSDISGVSLEHHHHH 95
>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 = 65.6 bits (161), Expect = 2e-15
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 2/84 (2%)
Query: 23 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 81
+ +VGN+ G T ++E F + V ++ DK + KGF Y+EF D E++R
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63
Query: 82 ALLKDGRITVDGLQVRLDIADGKR 105
+L D G Q+++ R
Sbjct: 64 SLALDES-LFRGRQIKVIPKRTNR 86
>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 = 66.4 bits (162), Expect = 3e-15
Identities = 25/118 (21%), Positives = 41/118 (34%), Gaps = 8/118 (6%)
Query: 9 YPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGF 68
G ++ T+ + + + LP T+ D+ FF V V + + R G
Sbjct: 30 MGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPD-GRVTGE 88
Query: 69 CYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMG 126
VEF E A+ KD + + L + + G +N GMG
Sbjct: 89 ADVEFATHEEAVAAMSKDRA-NMQHRYIELFLN------STTGASNGAYSSQVMQGMG 139
>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 = 65.5 bits (160), Expect = 5e-15
Identities = 20/113 (17%), Positives = 45/113 (39%), Gaps = 4/113 (3%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLV--SVRLVKDKETDRFKGFCYV 71
G + + A + N+P IT+ DV +F + +V ++ D + G V
Sbjct: 4 GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNG-QGLGQALV 62
Query: 72 EFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGG 124
+F + ++ R++ + ++G + + + + Q + G S G
Sbjct: 63 QFKNEDDARKSERLHRK-KLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSSG 114
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 64.7 bits (158), Expect = 7e-15
Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 7/88 (7%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPE---QKLVSVRLVKDKETDRFKGFCYVEFVDVE 77
T + N+ + + ++RL+KDK+T + +GF +V+
Sbjct: 5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64
Query: 78 NLRQAL----LKDGRITVDGLQVRLDIA 101
+ Q L + +DG + +D A
Sbjct: 65 DASQLLQILQSLHPPLKIDGKTIGVDFA 92
>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 = 66.5 bits (163), Expect = 1e-14
Identities = 17/102 (16%), Positives = 45/102 (44%), Gaps = 2/102 (1%)
Query: 16 NQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFV 74
+Q+ FVG + + + +F + K+ + ++ D+ + + +GF +V F
Sbjct: 95 SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFD 154
Query: 75 DVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQ 116
D +++ + +++ TV+G + A K+ + +
Sbjct: 155 DHDSVDKIVIQKY-HTVNGHNCEVRKALSKQEMASASSSQRG 195
Score = 54.2 bits (131), Expect = 3e-10
Identities = 23/92 (25%), Positives = 38/92 (41%), Gaps = 4/92 (4%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
F+G L T + F EQ L +++D T R +GF +V + VE + A+
Sbjct: 17 FIGGLSFETTDESLRSHF-EQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75
Query: 87 GRITVDGLQVRLDIADGKRNDNKGGFNNKQNR 118
VDG V A + + + G + +
Sbjct: 76 PH-KVDGRVVEPKRAVSREDSQRPGAHLTVKK 106
>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 = 64.4 bits (157), Expect = 1e-14
Identities = 22/97 (22%), Positives = 45/97 (46%), Gaps = 1/97 (1%)
Query: 10 PERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGF 68
+P V L T+ D+ F + + V +V D+++ R +GF
Sbjct: 31 GRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 90
Query: 69 CYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKR 105
+V F +V++ ++A + + +DG ++R+D + KR
Sbjct: 91 AFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 127
>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 = 63.4 bits (155), Expect = 2e-14
Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 1/90 (1%)
Query: 23 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 81
+ T V NL + + R F + ++ V + ++ T +GF +V F D + +
Sbjct: 11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQD 70
Query: 82 ALLKDGRITVDGLQVRLDIADGKRNDNKGG 111
A +DG ++R+ +A R D G
Sbjct: 71 AEAAMDGAELDGRELRVQVARYGRRDLSGP 100
>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 = 64.0 bits (156), Expect = 2e-14
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 26 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 84
+ +VGN+ G T D+E F + + ++ DK + KG+ Y+EF + ++ A+
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Query: 85 KDG 87
D
Sbjct: 97 MDE 99
>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 = 63.0 bits (154), Expect = 3e-14
Identities = 29/99 (29%), Positives = 44/99 (44%), Gaps = 4/99 (4%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 73
G + ++P T FV L T+ ++ F V R+V D+ET KGF +V+F
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDG--SVRARIVTDRETGSSKGFGFVDF 61
Query: 74 VDVENLRQALLK-DGRITVDGLQVRLDIADGKRNDNKGG 111
E+ + A + +DG +V LD A K G
Sbjct: 62 NSEEDAKAAKEAMEDG-EIDGNKVTLDWAKPKGEGGSGP 99
>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 = 64.5 bits (157), Expect = 3e-14
Identities = 22/88 (25%), Positives = 41/88 (46%), Gaps = 3/88 (3%)
Query: 23 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 81
E + V NL + + R F + ++ V + +D+ T +GF +V F D +
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127
Query: 82 ALLK-DGRITVDGLQVRLDIADGKRNDN 108
A+ DG +DG ++R+ +A R +
Sbjct: 128 AMDAMDGA-VLDGRELRVQMARYGRPPD 154
>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 = 63.4 bits (154), Expect = 4e-14
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 3/80 (3%)
Query: 11 ERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLV--SVRLVKDKETDRFKGF 68
++ GR + + + LP G T+ ++ +FF ++V + L D E + G
Sbjct: 28 QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEG-KITGE 86
Query: 69 CYVEFVDVENLRQALLKDGR 88
+V+F E +AL K
Sbjct: 87 AFVQFASQELAEKALGKHKE 106
>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 = 63.7 bits (155), Expect = 5e-14
Identities = 28/124 (22%), Positives = 48/124 (38%), Gaps = 8/124 (6%)
Query: 15 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEF 73
++ + T +VGNL T+ + F + + + + DK GFC+VE+
Sbjct: 29 NEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEY 88
Query: 74 VDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQH 133
+ A+ +D +R D G + +Q G SGG ++Y Q
Sbjct: 89 YSRADAENAMRYINGTRLDDRIIRTDWDAGFK-------EGRQYGRGRSGGQVRDEYRQD 141
Query: 134 QDKG 137
D G
Sbjct: 142 YDAG 145
>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 = 61.8 bits (151), Expect = 7e-14
Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 3/94 (3%)
Query: 22 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLR 80
+ +VG+L IT+ + F K+ ++ L+KD +T R KG+ ++ F D E R
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 81 QALLK-DGRITVDGLQVRLDIADGKRNDNKGGFN 113
+AL + +G + G +R+ + + G +
Sbjct: 62 RALEQLNGF-ELAGRPMRVGHVTERLDGGSGPSS 94
>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 = 63.7 bits (156), Expect = 7e-14
Identities = 15/83 (18%), Positives = 37/83 (44%), Gaps = 2/83 (2%)
Query: 23 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 81
+ FVG + + + E FF + ++ +L+ DK+T + +GF +V + + + +
Sbjct: 85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144
Query: 82 ALLKDGRITVDGLQVRLDIADGK 104
I ++ + A+ +
Sbjct: 145 VCQNKF-IDFKDRKIEIKRAEPR 166
Score = 48.7 bits (117), Expect = 3e-08
Identities = 17/85 (20%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
F+G L T+ ++ +F + + ++++KD T R +GF ++ F ++ + +
Sbjct: 7 FIGGLNWDTTEDNLREYF-GKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT- 64
Query: 87 GRITVDGLQVRLDIADGKRNDNKGG 111
+ +DG + A + +K G
Sbjct: 65 -QHILDGKVIDPKRAIPRDEQDKTG 88
>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 = 61.9 bits (151), Expect = 7e-14
Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 1/90 (1%)
Query: 23 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 81
+ FVGN+P T+ ++ F E +VS RLV D+ET + KG+ + E+ D E
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 82 ALLKDGRITVDGLQVRLDIADGKRNDNKGG 111
A+ G +R+D A ++N +
Sbjct: 66 AMRNLNGREFSGRALRVDNAASEKNKEELK 95
>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 = 62.0 bits (151), Expect = 8e-14
Identities = 21/96 (21%), Positives = 41/96 (42%), Gaps = 7/96 (7%)
Query: 22 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLR 80
T F+ NL + + + L VR+V +T+ KG + +F+ E +
Sbjct: 12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ 71
Query: 81 QAL------LKDGRITVDGLQVRLDIADGKRNDNKG 110
+ L + G + +DG Q+++D+A + G
Sbjct: 72 KCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 107
>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 = 61.9 bits (151), Expect = 9e-14
Identities = 23/102 (22%), Positives = 44/102 (43%), Gaps = 5/102 (4%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKE-TDRFKGFCYV 71
G + + + V N+P Q ++ F +L +VRL K T +GF +V
Sbjct: 4 GSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 63
Query: 72 EFVDVENLRQAL--LKDGRITVDGLQVRLDIADGKRNDNKGG 111
+F+ ++ ++A L + G ++ L+ AD + G
Sbjct: 64 DFITKQDAKKAFNALCHST-HLYGRRLVLEWADSEVTVQSGP 104
>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 = 63.4 bits (155), Expect = 9e-14
Identities = 23/99 (23%), Positives = 40/99 (40%), Gaps = 1/99 (1%)
Query: 4 YSYGGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKET 62
+ G + R P + F+G LPN + V+ L + LVKD T
Sbjct: 73 IIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSAT 132
Query: 63 DRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIA 101
KG+ + E+VD+ QA+ + + ++ + A
Sbjct: 133 GLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 51.1 bits (123), Expect = 5e-09
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 29 FVGNLPNGITQGDVERFFPEQ------KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
+VGN+P GIT+ + FF Q V + ++ K F ++EF V+ QA
Sbjct: 8 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 67
Query: 83 LLKDGRITVDGLQVR 97
+ DG I G ++
Sbjct: 68 MAFDG-IIFQGQSLK 81
>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 = 60.3 bits (147), Expect = 3e-13
Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 3/81 (3%)
Query: 23 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 81
T +V NLP +T D+ R F + K+V V ++KDK+T + KG ++ F+D ++ +
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 82 ALLK-DGRITVDGLQVRLDIA 101
+ + + G ++ IA
Sbjct: 74 CTRAINNK-QLFGRVIKASIA 93
>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 = 59.9 bits (146), Expect = 4e-13
Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 86
FV NL ++ D+E+ F L + D T + KGF +V F+ E+ +A + D
Sbjct: 12 FVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVD 71
Query: 87 GRITVDGLQVRLDIADGKRNDNKGG 111
G++ G + + + K+ ++ G
Sbjct: 72 GQV-FQGRMLHVLPSTIKKEASQSG 95
>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 = 59.5 bits (145), Expect = 5e-13
Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 1/82 (1%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
+P V L T+ D+ F + + V +V D+++ R +GF +V F +V++
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 80 RQALLKDGRITVDGLQVRLDIA 101
++A + + +DG ++R+
Sbjct: 71 KEAKERANGMELDGRRIRVSGP 92
>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 = 62.0 bits (151), Expect = 5e-13
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 16 NQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFV 74
T+ + + F+G LPN + V+ L + LVKD T KG+ + E+V
Sbjct: 105 VVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 164
Query: 75 DVENLRQAL 83
D+ QA+
Sbjct: 165 DINVTDQAI 173
Score = 58.9 bits (143), Expect = 8e-12
Identities = 24/109 (22%), Positives = 42/109 (38%), Gaps = 7/109 (6%)
Query: 29 FVGNLPNGITQGDVERFFPEQ------KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
+VGN+P GIT+ + FF Q V + ++ K F ++EF V+ QA
Sbjct: 8 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 67
Query: 83 LLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYN 131
+ DG I G +++ + N G + + +
Sbjct: 68 MAFDG-IIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAH 115
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 60.5 bits (147), Expect = 6e-13
Identities = 22/99 (22%), Positives = 41/99 (41%), Gaps = 3/99 (3%)
Query: 10 PERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGF 68
+ E + V NL + + R F + ++ V + +D+ T +GF
Sbjct: 32 RGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGF 91
Query: 69 CYVEFVDVENLRQALLK-DGRITVDGLQVRLDIADGKRN 106
+V F D + A+ DG +DG ++R+ +A R
Sbjct: 92 AFVRFHDKRDAEDAMDAMDGA-VLDGRELRVQMARYGRP 129
>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 = 59.6 bits (145), Expect = 7e-13
Identities = 27/99 (27%), Positives = 51/99 (51%), Gaps = 1/99 (1%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVE 72
G + + FVG L + +E+ F + ++ V +VKD+ET R +GF +V
Sbjct: 1 GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60
Query: 73 FVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGG 111
F ++++ + A++ +VDG Q+R+D A ++ G
Sbjct: 61 FENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGP 99
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 59.7 bits (145), Expect = 8e-13
Identities = 25/103 (24%), Positives = 42/103 (40%), Gaps = 11/103 (10%)
Query: 27 TAFVGNLPNGITQGDVERFF---------PEQKLVSVRLVKDKETDRFKGFCYVEFVDVE 77
T FV L +T V +F + + L D+ET + KG V F D
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68
Query: 78 NLRQAL-LKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRG 119
+ + A+ DG+ G +++ A + + N+GG N +
Sbjct: 69 SAKAAIDWFDGK-EFSGNPIKVSFATRRADFNRGGGNGRGGLE 110
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 58.1 bits (141), Expect = 2e-12
Identities = 20/88 (22%), Positives = 42/88 (47%), Gaps = 4/88 (4%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
+ + F+ LP T+ ++E + +RLV ++ + KG YVE+ +
Sbjct: 13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQA 71
Query: 80 RQALLK-DGRITVDGLQVRLDIADGKRN 106
QA++K DG T+ +++ I++ +
Sbjct: 72 SQAVMKMDGM-TIKENIIKVAISNSGPS 98
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 59.5 bits (144), Expect = 2e-12
Identities = 12/98 (12%), Positives = 37/98 (37%), Gaps = 4/98 (4%)
Query: 24 PPYTAFVGNLPNGITQGDVERFFPE---QKLVSVRLVKDKETDRFKGFCYVEFVDVENLR 80
+VG+ T + + +V ++ +++ + KG+ V ++
Sbjct: 54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVH 113
Query: 81 QALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNR 118
+ L ++G +V + A ++N ++ ++
Sbjct: 114 KLLELLPGKVLNGEKVDVRPA-TRQNLSQFEAQARKRE 150
>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 = 59.5 bits (145), Expect = 3e-12
Identities = 22/98 (22%), Positives = 42/98 (42%), Gaps = 3/98 (3%)
Query: 18 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDV 76
+ + P+ F+GNL + +++ E + +V D T + F YV+F
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESA 64
Query: 77 ENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNN 114
E+L +AL G V G +++L+ G+ +
Sbjct: 65 EDLEKALELTGL-KVFGNEIKLEKPKGRDSKKVRAART 101
Score = 54.1 bits (131), Expect = 3e-10
Identities = 17/90 (18%), Positives = 34/90 (37%), Gaps = 4/90 (4%)
Query: 15 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFV 74
+ + + T NL IT+ +++ F + + + + + KG Y+EF
Sbjct: 89 KGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDA----LEIRLVSQDGKSKGIAYIEFK 144
Query: 75 DVENLRQALLKDGRITVDGLQVRLDIADGK 104
+ + L + +DG V L K
Sbjct: 145 SEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
>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 = 58.5 bits (142), Expect = 3e-12
Identities = 20/114 (17%), Positives = 42/114 (36%), Gaps = 2/114 (1%)
Query: 11 ERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFC 69
E+ G + + FV + T+ D+ F E ++ ++ L D+ T KG+
Sbjct: 8 EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 67
Query: 70 YVEFVDVENLRQALLKDGRITVDGLQVRLDIA-DGKRNDNKGGFNNKQNRGGGS 122
VE+ + + A+ + G + +D K +++R
Sbjct: 68 LVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRSPDR 121
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 57.3 bits (139), Expect = 4e-12
Identities = 19/98 (19%), Positives = 44/98 (44%), Gaps = 3/98 (3%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEF 73
G + + + T + NL T+ ++ F + + V + + KG+ ++EF
Sbjct: 4 GSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEF 60
Query: 74 VDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGG 111
E+ ++AL + ++G +RL++ + + N G
Sbjct: 61 ASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGP 98
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 56.5 bits (137), Expect = 8e-12
Identities = 19/93 (20%), Positives = 34/93 (36%), Gaps = 6/93 (6%)
Query: 17 QKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDV 76
+ T NL IT+ +++ F + ++ + + + KG Y+EF
Sbjct: 8 CTSKKVRAARTLLAKNLSFNITEDELKEVFED----ALEIRLVSQDGKSKGIAYIEFKSE 63
Query: 77 ENLRQALL-KDGRITVDGLQVRLDIADGKRNDN 108
+ + L K G +DG V L K
Sbjct: 64 ADAEKNLEEKQGA-EIDGRSVSLYYTGEKGGTR 95
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 57.7 bits (139), Expect = 8e-12
Identities = 18/86 (20%), Positives = 29/86 (33%), Gaps = 5/86 (5%)
Query: 7 GGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFF----PEQKLVSVRLVKDKET 62
GG G + + LP + DV+ F V + +E
Sbjct: 26 GGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREG 85
Query: 63 DRFKGFCYVEFVDVENLRQALLKDGR 88
R G +VE ++++ AL KD
Sbjct: 86 -RQSGEAFVELGSEDDVKMALKKDRE 110
>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 = 56.9 bits (138), Expect = 8e-12
Identities = 13/79 (16%), Positives = 33/79 (41%), Gaps = 1/79 (1%)
Query: 24 PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
+ FV ++ + +++ F + ++ ++ L D+ T KG+ VE+ + A
Sbjct: 25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAA 84
Query: 83 LLKDGRITVDGLQVRLDIA 101
+ G +++D
Sbjct: 85 KEALNGAEIMGQTIQVDWC 103
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 57.5 bits (139), Expect = 9e-12
Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 8/87 (9%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVE 72
G +VG L + + F + +++ D ET++ +GF +VE
Sbjct: 52 GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 111
Query: 73 FVDVENLRQALLK------DGR-ITVD 92
F E+ A+ GR I V+
Sbjct: 112 FELAEDAAAAIDNMNESELFGRTIRVN 138
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 56.5 bits (137), Expect = 1e-11
Identities = 19/93 (20%), Positives = 39/93 (41%), Gaps = 3/93 (3%)
Query: 11 ERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFC 69
E+ G + + FV + T+ D+ F E ++ ++ L D+ T KG+
Sbjct: 9 EQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYT 68
Query: 70 YVEFVDVENLRQALLK-DGRITVDGLQVRLDIA 101
VE+ + + A+ +G + G + +D
Sbjct: 69 LVEYETYKEAQAAMEGLNG-QDLMGQPISVDWC 100
>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 = 56.5 bits (137), Expect = 1e-11
Identities = 19/91 (20%), Positives = 37/91 (40%), Gaps = 1/91 (1%)
Query: 22 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLR 80
+VG L + + F + +++ D ET++ +GF +VEF E+
Sbjct: 9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68
Query: 81 QALLKDGRITVDGLQVRLDIADGKRNDNKGG 111
A+ + G +R+++A R G
Sbjct: 69 AAIDNMNESELFGRTIRVNLAKPMRIKESGP 99
>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper),
RRM2 domain, solution structure, structural genomics,
PSI-2; NMR {Homo sapiens}
Length = 108
Score = 56.2 bits (136), Expect = 2e-11
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 8/85 (9%)
Query: 16 NQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFV 74
N + P +VG+L IT+ + F ++ S++L+ D ET R KG+ ++ F
Sbjct: 17 NNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Query: 75 DVENLRQALLK------DGR-ITVD 92
D E ++AL + GR + V
Sbjct: 77 DSECAKKALEQLNGFELAGRPMKVG 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 = 55.8 bits (135), Expect = 2e-11
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 11/83 (13%)
Query: 29 FVGNLPNGITQGDVERFF---------PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
FV L +T V +F + + L D+ET + KG V F D +
Sbjct: 17 FVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSA 76
Query: 80 RQAL-LKDGRITVDGLQVRLDIA 101
+ A+ DG+ G +++ A
Sbjct: 77 KAAIDWFDGK-EFSGNPIKVSFA 98
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 55.7 bits (134), Expect = 3e-11
Identities = 22/115 (19%), Positives = 35/115 (30%), Gaps = 9/115 (7%)
Query: 15 RNQKTLPTEPPYTAFVGNLPNGITQGDVERFF-----PEQKLVSVRLVKDKETDRFKGFC 69
+ L E + LP T +V FF + V + R G
Sbjct: 13 EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDG-RPTGDA 71
Query: 70 YVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGG 124
+V F E + AL K + + L + + + N + G S G
Sbjct: 72 FVLFACEEYAQNALRKHKD-LLGKRYIELFRS--TAAEVQQVLNRFSSASGPSSG 123
>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 = 54.9 bits (133), Expect = 3e-11
Identities = 11/74 (14%), Positives = 27/74 (36%), Gaps = 10/74 (13%)
Query: 29 FVGNLPNGITQGDVERFFPE---QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
++GNL T D+ ++ ++ +++ + KGF V + ++ +
Sbjct: 5 YIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDL 64
Query: 86 ------DGR-ITVD 92
G+ V
Sbjct: 65 LPKRELHGQNPVVT 78
>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 = 54.4 bits (132), Expect = 4e-11
Identities = 16/83 (19%), Positives = 39/83 (46%), Gaps = 3/83 (3%)
Query: 26 YTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 84
+ FVG+L + + F + +S ++ D +T +G+ +V F ++ + A+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 85 K-DGRITVDGLQVRLDIADGKRN 106
G+ ++G +R++ A +
Sbjct: 62 SMQGQ-DLNGRPLRINWAAKLEH 83
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 56.9 bits (138), Expect = 5e-11
Identities = 17/97 (17%), Positives = 38/97 (39%), Gaps = 3/97 (3%)
Query: 12 RYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFC 69
R Q+ +VG++ + + + + F + S+ + D T + KGF
Sbjct: 15 RGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAF-APFGPIKSIDMSWDSVTMKHKGFA 73
Query: 70 YVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRN 106
+VE+ E + AL + + + G +++
Sbjct: 74 FVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQ 110
Score = 56.6 bits (137), Expect = 6e-11
Identities = 15/87 (17%), Positives = 36/87 (41%), Gaps = 1/87 (1%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
+V ++ ++ D++ F K+ S L +D T + KG+ ++E+ ++
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180
Query: 80 RQALLKDGRITVDGLQVRLDIADGKRN 106
+ A+ + G +R+ A
Sbjct: 181 QDAVSSMNLFDLGGQYLRVGKAVTPPM 207
>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 = 56.0 bits (135), Expect = 5e-11
Identities = 14/89 (15%), Positives = 35/89 (39%), Gaps = 1/89 (1%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 87
FV ++ + +++ F + ++ ++ L D+ T KG+ VE+ + A
Sbjct: 76 FVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALN 135
Query: 88 RITVDGLQVRLDIADGKRNDNKGGFNNKQ 116
+ G +++D K ++
Sbjct: 136 GAEIMGQTIQVDWCFVKGPKRVKKSEKRR 164
>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 = 57.0 bits (137), Expect = 6e-11
Identities = 16/125 (12%), Positives = 39/125 (31%), Gaps = 3/125 (2%)
Query: 7 GGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPE---QKLVSVRLVKDKETD 63
+ N T ++GNL T D+ ++ ++ +++
Sbjct: 50 DDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANG 109
Query: 64 RFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSG 123
+ KGF V + ++ + + + G + + + + K + G
Sbjct: 110 QSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMS 169
Query: 124 GMGGN 128
G G
Sbjct: 170 GEGKA 174
>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 = 54.6 bits (132), Expect = 6e-11
Identities = 20/89 (22%), Positives = 42/89 (47%), Gaps = 1/89 (1%)
Query: 23 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 81
T +VG L +++ + F + +V+ + KD+ T + +G+ +VEF+ E+
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 82 ALLKDGRITVDGLQVRLDIADGKRNDNKG 110
A+ I + G +R++ A + G
Sbjct: 73 AIKIMDMIKLYGKPIRVNKASAHNKNLSG 101
>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 = 53.7 bits (130), Expect = 7e-11
Identities = 14/62 (22%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 23 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 81
+VG L + + F + +++ D ET++ +GF +VEF E+
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64
Query: 82 AL 83
A+
Sbjct: 65 AI 66
>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 = 7e-11
Identities = 23/100 (23%), Positives = 39/100 (39%), Gaps = 3/100 (3%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVE 72
G + + T V NL + D++ F + + L KDK T + KGF ++
Sbjct: 4 GSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFIS 63
Query: 73 FVDVENLRQALLK-DGRITVDGLQVRLDIADGKRNDNKGG 111
F E+ +A+ G D L + ++ A N
Sbjct: 64 FHRREDAARAIAGVSGF-GYDHLILNVEWAKPSTNSGPSS 102
>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 = 53.7 bits (130), Expect = 8e-11
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 1/85 (1%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
P + FVG+L IT + F ++ R+VKD T + KG+ +V F + +
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61
Query: 80 RQALLKDGRITVDGLQVRLDIADGK 104
A+ + G + G Q+R + A K
Sbjct: 62 ENAIQQMGGQWLGGRQIRTNWATRK 86
>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 = 52.9 bits (128), Expect = 1e-10
Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 4/88 (4%)
Query: 22 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDK-ETDRFKGFCYVEFVDVENL 79
+ P +G L +T+ + F K+ + + ++ KG+ YVEF + +
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 80 RQALLK-DGRITVDGLQVRLDIADGKRN 106
+AL DG +DG ++
Sbjct: 61 EKALKHMDGG-QIDGQEITATAVLAPWP 87
>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 = 53.5 bits (129), Expect = 2e-10
Identities = 15/67 (22%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPE--QKLVSVRLVKDKETDRFKGFCYVEFVDVEN 78
+ + ++G+L + + + R F + ++SV++++++ T G+C+VEF D+
Sbjct: 5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT 64
Query: 79 LRQALLK 85
+ L K
Sbjct: 65 AEKCLHK 71
>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 = 53.0 bits (128), Expect = 2e-10
Identities = 17/84 (20%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 29 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-DG 87
++GNL +T D+ + F ++KL + G+ +V++ D +A+ G
Sbjct: 12 YIGNLSPAVTADDLRQLFGDRKLP-----LAGQVLLKSGYAFVDYPDQNWAIRAIETLSG 66
Query: 88 RITVDGLQVRLDIADGKRNDNKGG 111
++ + G + +D + K+ + G
Sbjct: 67 KVELHGKIMEVDYSVSKKLRSSGP 90
>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 = 54.5 bits (132), Expect = 2e-10
Identities = 16/86 (18%), Positives = 41/86 (47%), Gaps = 3/86 (3%)
Query: 18 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDV 76
+ ++ + FVG+L + + F + +S ++ D +T +G+ +V F
Sbjct: 80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ 139
Query: 77 ENLRQALLK-DGRITVDGLQVRLDIA 101
++ + A+ G+ ++G +R++ A
Sbjct: 140 DDAQNAMDSMQGQD-LNGRPLRINWA 164
Score = 49.8 bits (120), Expect = 1e-08
Identities = 16/89 (17%), Positives = 41/89 (46%), Gaps = 2/89 (2%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
+VGNL IT+ ++++F + +++++ DK ++ + +VE+ + AL
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQT 60
Query: 86 DGRITVDGLQVRLDIADGKRNDNKGGFNN 114
++ V+++ A + + N
Sbjct: 61 LNGKQIENNIVKINWAFQSQQSSSDDTFN 89
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 52.9 bits (127), Expect = 2e-10
Identities = 18/100 (18%), Positives = 36/100 (36%), Gaps = 4/100 (4%)
Query: 7 GGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFK 66
G + +VGNLP D++R E V +RL +
Sbjct: 1 GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLT----WQGPR 56
Query: 67 GFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRN 106
++ + D +QA+ + + +R+ +A +R+
Sbjct: 57 RRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRD 96
>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 = 53.3 bits (128), Expect = 2e-10
Identities = 17/83 (20%), Positives = 38/83 (45%), Gaps = 5/83 (6%)
Query: 29 FVGNLPNGITQGDVERFFPE--QKLVSVRLVKD-KETDRFKGFCYVEFVDVENLRQAL-- 83
F+G +P + ++ + + ++ V + + + +GF +VE+ A
Sbjct: 12 FIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRK 71
Query: 84 LKDGRITVDGLQVRLDIADGKRN 106
L GRI + G Q+ +D A+ + +
Sbjct: 72 LMPGRIQLWGHQIAVDWAEPEID 94
>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 = 52.6 bits (127), Expect = 2e-10
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 6/89 (6%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLR--QALLK 85
+VGNL T V+ F + K+ +V+L+ D+ET + KGF +VE + L
Sbjct: 5 YVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKL-- 62
Query: 86 DGRITVDGLQVRLDIADGKRNDNKGGFNN 114
D G +R+ A+ K++ ++
Sbjct: 63 DNT-DFMGRTIRVTEANPKKSLEHHHHHH 90
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 53.4 bits (128), Expect = 3e-10
Identities = 20/108 (18%), Positives = 39/108 (36%), Gaps = 6/108 (5%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPEQKLV----SVRLVKDKETDRFKGFCYVEFVDV 76
Y + LP + DV+ F + + V + +E R G +VE
Sbjct: 13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREG-RQSGEAFVELESE 71
Query: 77 ENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGG 124
++++ AL KD ++ + + + D + + G S G
Sbjct: 72 DDVKLALKKDRE-SMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSSG 118
>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 = 52.7 bits (127), Expect = 3e-10
Identities = 21/114 (18%), Positives = 47/114 (41%), Gaps = 3/114 (2%)
Query: 22 TEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLR 80
+ P F+G L + ++ F + + V L+KD+ T + +GF ++ F + + +
Sbjct: 4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAK 62
Query: 81 QALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQ 134
A ++ G ++++ A K + GG G +++ H
Sbjct: 63 NAAKDMNGKSLHGKAIKVEQA-KKPSFQSGGRRRPPASSRNRSPSGSLEHHHHH 115
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 52.8 bits (127), Expect = 4e-10
Identities = 20/91 (21%), Positives = 37/91 (40%), Gaps = 4/91 (4%)
Query: 20 LPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVEN 78
LP E ++ NLP IT ++ F + + +R+ ET +G YV + D+ +
Sbjct: 3 LPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET---RGTAYVVYEDIFD 59
Query: 79 LRQALLKDGRITVDGLQVRLDIADGKRNDNK 109
+ A+ V + + + R K
Sbjct: 60 AKNAVDHLSGFNVSNRYLVVLYYNANRAFQK 90
>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 = 51.7 bits (124), Expect = 7e-10
Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 3/77 (3%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLV--SVRLVKDKETDRFKGFCYV 71
G + + T + LP G ++ ++ +FF ++V + L D + R G +V
Sbjct: 4 GSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQG-RSTGEAFV 62
Query: 72 EFVDVENLRQALLKDGR 88
+F E +AL K
Sbjct: 63 QFASQEIAEKALKKHKE 79
>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 = 51.6 bits (124), Expect = 8e-10
Identities = 28/108 (25%), Positives = 41/108 (37%), Gaps = 4/108 (3%)
Query: 5 SYGGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDR 64
S G G + +VGNLP I D+E F K ++R + K
Sbjct: 2 SSGSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVF--YKYGAIRDIDLKNRRG 59
Query: 65 FKGFCYVEFVDVENLRQALLK-DGRITVDGLQVRLDIADGKRNDNKGG 111
F +VEF D + A+ DG DG ++R++ R G
Sbjct: 60 GPPFAFVEFEDPRDAEDAVYGRDGY-DYDGYRLRVEFPRSGRGTGSGP 106
>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 = 51.1 bits (123), Expect = 1e-09
Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 3/81 (3%)
Query: 23 EPPYTAFVGNLPNGITQGDVERFFPEQKLV--SVRLVKDKETDRFKGFCYVEFVDVENLR 80
P V N+P ++ ++ FF +++ SV L + E G V F +
Sbjct: 13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEAT 71
Query: 81 QALLKDGRITVDGLQVRLDIA 101
A++ + +V+L +
Sbjct: 72 AAVIDLNDRPIGSRKVKLVLG 92
>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 = 51.3 bits (123), Expect = 1e-09
Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 9/64 (14%)
Query: 29 FVGNLPNGITQGDVERFF---------PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
+V L + +T D+ FF + + DKET + KG V + D
Sbjct: 19 YVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTA 78
Query: 80 RQAL 83
+ A+
Sbjct: 79 KAAV 82
>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 = 50.4 bits (121), Expect = 2e-09
Identities = 16/82 (19%), Positives = 31/82 (37%), Gaps = 3/82 (3%)
Query: 22 TEPPYTAFVGNLPNGITQGDVERFFPEQKLV--SVRLVKDKETDRFKGFCYVEFVDVENL 79
P V N+P ++ ++ FF +++ SV L + E G V F +
Sbjct: 12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYN-EKGMPTGEAMVAFESRDEA 70
Query: 80 RQALLKDGRITVDGLQVRLDIA 101
A++ + +V+L
Sbjct: 71 TAAVIDLNDRPIGSRKVKLSGP 92
>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 = 51.0 bits (122), Expect = 2e-09
Identities = 13/79 (16%), Positives = 32/79 (40%), Gaps = 6/79 (7%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLV----SVRLVKDKETDRFKGFC 69
G + + + LP T DV FF + ++ + + +++ + +G
Sbjct: 1 GSKLEEEVDDV-FLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDG-KRRGDA 58
Query: 70 YVEFVDVENLRQALLKDGR 88
+E +++++AL K
Sbjct: 59 LIEMESEQDVQKALEKHRM 77
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 53.1 bits (128), Expect = 2e-09
Identities = 18/96 (18%), Positives = 32/96 (33%), Gaps = 1/96 (1%)
Query: 11 ERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFC 69
R V NLP +TQ E P L LV + T + KG+
Sbjct: 81 RLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYG 140
Query: 70 YVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKR 105
+ E++ ++ +A + + + D +
Sbjct: 141 FAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ 176
Score = 44.2 bits (105), Expect = 3e-06
Identities = 18/115 (15%), Positives = 30/115 (26%), Gaps = 10/115 (8%)
Query: 1 MADYSYGGYPERYGRNQKTLPTEPPYTA---FVGNLPNGITQGDV--ERFFPEQKLVSVR 55
+ G T + V LP G D +
Sbjct: 157 LLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQ 216
Query: 56 LVKDKETDRFKGFCYVEFVDVENLRQALLK-DGRITVDGLQVRLDIADGKRNDNK 109
L + + KGF +E+ E +A + DG + G +R+
Sbjct: 217 LACG-QDGQLKGFAVLEYETAEMAEEAQQQADGLS-LGGSHLRVSFC--APGPPG 267
Score = 43.4 bits (103), Expect = 4e-06
Identities = 11/78 (14%), Positives = 27/78 (34%), Gaps = 6/78 (7%)
Query: 29 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 88
+ LP +T +V + +L + K KG +V ++ E A+ +
Sbjct: 26 LIRGLPGDVTNQEVHDLLSDYELKYCFVDKY------KGTAFVTLLNGEQAEAAINAFHQ 79
Query: 89 ITVDGLQVRLDIADGKRN 106
+ ++ + +
Sbjct: 80 SRLRERELSVQLQPTDAL 97
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 50.9 bits (122), Expect = 2e-09
Identities = 10/87 (11%), Positives = 27/87 (31%), Gaps = 1/87 (1%)
Query: 24 PPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
P L + + + ++ ++ V ++ T + G V F ++
Sbjct: 5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKET 64
Query: 83 LLKDGRITVDGLQVRLDIADGKRNDNK 109
+ +V G + + + K
Sbjct: 65 VKNLHLTSVMGNIIHAQLDIKGQQRMK 91
>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 = 53.1 bits (128), Expect = 2e-09
Identities = 16/114 (14%), Positives = 40/114 (35%), Gaps = 10/114 (8%)
Query: 7 GGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPE--QKLVSVRLVKDKETDR 64
G + T ++ N P TQ ++ + +S+RL + +
Sbjct: 106 GQNEIIVSHLTEC-------TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNT 157
Query: 65 FKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNR 118
+ F Y++ E+ R + K + ++G + +++ + + R
Sbjct: 158 SRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGR 211
Score = 46.9 bits (112), Expect = 3e-07
Identities = 19/97 (19%), Positives = 33/97 (34%), Gaps = 11/97 (11%)
Query: 8 GYPERYGRNQKTLPTEPP-----YTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDK 60
G P G K T V NLP Q V ++F + ++ V +
Sbjct: 19 GSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYF-KHCGPIIHVDVADS- 76
Query: 61 ETDRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVR 97
+ F +EF + A+ K ++ V ++
Sbjct: 77 -LKKNFRFARIEFARYDGALAAITKTHKV-VGQNEII 111
Score = 45.4 bits (108), Expect = 9e-07
Identities = 12/79 (15%), Positives = 32/79 (40%), Gaps = 4/79 (5%)
Query: 29 FVGNLPNGITQGDV--ERFFPEQKLVSVRLVKD-KETDRFKGFCYVEFVDVENLRQALLK 85
+ NL + ++ E F + + + KE ++ F + ++ +AL
Sbjct: 214 MIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM 273
Query: 86 DGRITVDGLQVRLDIADGK 104
+ + + ++ + +AD K
Sbjct: 274 NRSL-LGNREISVSLADKK 291
>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 = 50.4 bits (121), Expect = 3e-09
Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 3/101 (2%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVE 72
G + + P V N+P D+ + F + K++ V ++ ++ KGF +V
Sbjct: 4 GSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVT 61
Query: 73 FVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFN 113
F + + +A K V+G ++ ++ A + N G +
Sbjct: 62 FENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPSS 102
>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 = 50.4 bits (121), Expect = 3e-09
Identities = 18/82 (21%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK- 85
F+G +P + + D++ F E+ K+ + ++KD+ T KG ++ + + E+ +A
Sbjct: 17 FIGQIPRNLDEKDLKPLF-EEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 86 DGRITVDG--LQVRLDIADGKR 105
+ T+ G +++ AD +
Sbjct: 76 HEQKTLPGMNRPIQVKPADSES 97
>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 = 49.7 bits (119), Expect = 3e-09
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 29 FVGNLPNGITQGDVERFFPEQ------KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
+VGN+P GIT+ + FF Q V + ++ K F ++EF V+ QA
Sbjct: 10 YVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQA 69
Query: 83 LLKDGRITVDGLQVR 97
+ DG I G ++
Sbjct: 70 MAFDG-IIFQGQSLK 83
>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 = 51.4 bits (124), Expect = 3e-09
Identities = 17/84 (20%), Positives = 37/84 (44%), Gaps = 1/84 (1%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 87
V LP +T ++ F + + R+++D +T G+ +V+F + ++A+
Sbjct: 7 IVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLN 66
Query: 88 RITVDGLQVRLDIADGKRNDNKGG 111
ITV ++++ A K
Sbjct: 67 GITVRNKRLKVSYARPGGESIKDT 90
Score = 48.3 bits (116), Expect = 4e-08
Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 1/84 (1%)
Query: 1 MADYSYGGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKD 59
+ + + + + +V NLP IT ++ F + +V +++D
Sbjct: 65 LNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRD 124
Query: 60 KETDRFKGFCYVEFVDVENLRQAL 83
K T R +G +V + E ++A+
Sbjct: 125 KLTGRPRGVAFVRYNKREEAQEAI 148
>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 = 51.4 bits (124), Expect = 3e-09
Identities = 17/85 (20%), Positives = 38/85 (44%), Gaps = 3/85 (3%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
V LP +TQ + F ++ S +LV+DK T + G+ +V ++D ++ +A+
Sbjct: 6 IVNYLPQNMTQEEFRSLF-GSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 87 GRITVDGLQVRLDIADGKRNDNKGG 111
+ + +++ A +
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIRDA 89
Score = 43.3 bits (103), Expect = 3e-06
Identities = 13/56 (23%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
+V LP +TQ ++E+ F + ++++ R++ D+ T +G ++ F +A+
Sbjct: 92 YVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 49.7 bits (119), Expect = 3e-09
Identities = 10/62 (16%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
+ ++ P T D++ + ++ +++++++ + FKG +V F +E+ ++ +
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVET 71
Query: 86 DG 87
G
Sbjct: 72 PG 73
>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 = 51.5 bits (124), Expect = 5e-09
Identities = 26/97 (26%), Positives = 47/97 (48%), Gaps = 1/97 (1%)
Query: 19 TLPTEPPYTAFVGNLPNGITQGDV-ERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVE 77
+ P+ P + +VG+L +T+ + E+F P ++S+R+ +D T R G+ YV F
Sbjct: 9 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 68
Query: 78 NLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNN 114
+ +AL + G VR+ + + K G N
Sbjct: 69 DAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 105
Score = 38.4 bits (90), Expect = 2e-04
Identities = 17/91 (18%), Positives = 36/91 (39%), Gaps = 4/91 (4%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDG 87
F+ NL I + F ++S ++V D + KG+ +V F E +A+ K
Sbjct: 107 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMN 164
Query: 88 RITVDGLQVRLDIADGKRNDNKGGFNNKQNR 118
+ ++ +V + R + + +
Sbjct: 165 GMLLNDRKVFVGRFK-SRKEREAELGARAKE 194
>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 = 48.7 bits (117), Expect = 8e-09
Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
++ L G T D+ + K+VS + + DK T++ KG+ +V+F ++A+
Sbjct: 9 YIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 99
Score = 48.7 bits (117), Expect = 1e-08
Identities = 19/87 (21%), Positives = 45/87 (51%), Gaps = 4/87 (4%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
FVG +P+ + ++ +F ++ + V ++ D E R +GF ++ F D +++ QA+
Sbjct: 14 FVGGIPHNCGETELREYF-KKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 87 GRITVDGLQVRLDIADGKRNDNKGGFN 113
+ G +V + A+ + + + G +
Sbjct: 73 F-HDIMGKKVEVKRAEPRDSKSSGPSS 98
>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 = 48.8 bits (117), Expect = 1e-08
Identities = 21/92 (22%), Positives = 39/92 (42%), Gaps = 3/92 (3%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
P EP ++ NL +T+ D+ F Q+ + T R +G ++ F + E
Sbjct: 21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIA 80
Query: 80 RQALLK-DGRITVDGLQVRLDIADGKRNDNKG 110
QAL +G + G + ++ K+ + G
Sbjct: 81 WQALHLVNGYK-LYGKILVIEFGKNKKQRSSG 111
>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 = 49.4 bits (118), Expect = 1e-08
Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
V +P + + + + F + SV++V D+ET + +G+ +V+F + +QA+
Sbjct: 46 MVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
>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 = 48.0 bits (115), Expect = 2e-08
Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 7/88 (7%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKET---DRFKGFCYVEFVDVENLRQALL 84
F+ NL T+ ++ F + + S + K K GF +VE+ E ++AL
Sbjct: 9 FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 68
Query: 85 K-DGRITVDGLQVRLDIADGKRNDNKGG 111
+ G VDG ++ + I++ + G
Sbjct: 69 QLQGHT-VDGHKLEVRISE-RATKPASG 94
>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 = 48.5 bits (116), Expect = 2e-08
Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 4/88 (4%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
E V NL G++ D++ F E L + D + R G V F +
Sbjct: 31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADA 89
Query: 80 RQALLK-DGRITVDGLQVRLDIADGKRN 106
+A+ + G +DG + + + + +
Sbjct: 90 LKAMKQYKGVP-LDGRPMDIQLVASQID 116
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 48.1 bits (115), Expect = 2e-08
Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 4/98 (4%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
FVG LP T + ++F E + ++ D++T + +G+ +V D +A KD
Sbjct: 21 FVGGLPYHTTDASLRKYF-EGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA-CKD 78
Query: 87 GRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGG 124
+DG + +++A G S G
Sbjct: 79 PNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSSG 116
>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 = 47.6 bits (114), Expect = 3e-08
Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 2/80 (2%)
Query: 23 EPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 81
E T FVGNL + + + F + L V + KD+E + K F +V F E++
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPESVSY 72
Query: 82 ALLKDGRITVDGLQVRLDIA 101
A+ I + G + +
Sbjct: 73 AIALLNGIRLYGRPINVSGP 92
>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 = 48.3 bits (115), Expect = 3e-08
Identities = 26/98 (26%), Positives = 48/98 (48%), Gaps = 8/98 (8%)
Query: 10 PERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGF 68
+ + +VGNL N + ++ER F L SV + ++ GF
Sbjct: 58 SHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGF 112
Query: 69 CYVEFVDVENLRQALLK-DGRITVDGLQVRLDIADGKR 105
+VEF D + A+ + DGR T+ G +VR+++++G++
Sbjct: 113 AFVEFEDPRDAADAVRELDGR-TLCGCRVRVELSNGEK 149
>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 = 46.9 bits (112), Expect = 5e-08
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 9/85 (10%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 86
FVGNLP IT+ ++ + F + K V + KD KGF ++ A ++ D
Sbjct: 19 FVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELD 72
Query: 87 GRITVDGLQVRLDIADGKRNDNKGG 111
+ G Q+R+ A + G
Sbjct: 73 NM-PLRGKQLRVRFACHSASLTSGP 96
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 46.5 bits (111), Expect = 6e-08
Identities = 24/85 (28%), Positives = 44/85 (51%), Gaps = 8/85 (9%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 86
+VGNL G +G++ER F L +V + ++ GF +VEF D + A+ D
Sbjct: 4 YVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGLD 58
Query: 87 GRITVDGLQVRLDIADGKRNDNKGG 111
G+ + G +VR++++ G ++
Sbjct: 59 GK-VICGSRVRVELSTGMPRRSRFD 82
>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 = 48.0 bits (115), Expect = 6e-08
Identities = 19/92 (20%), Positives = 40/92 (43%), Gaps = 8/92 (8%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKET--DRFKGFCYVEFVDVENLRQALL 84
FVG +P ++ D+ F EQ + + +++D+ + KG C+V F + +A
Sbjct: 7 FVGQVPRTWSEKDLRELF-EQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 85 K-DGRITVDG--LQVRLDIADGKRNDNKGGFN 113
+ G +++ AD ++N+
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRK 97
Score = 37.6 bits (88), Expect = 3e-04
Identities = 15/81 (18%), Positives = 32/81 (39%), Gaps = 11/81 (13%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK- 85
F+G + T+ D+ F ++ R+++ +G +V F + A+
Sbjct: 99 FIGMISKKCTENDIRVMF-SSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 86 DGRITVDG----LQVRLDIAD 102
T++G + V+ AD
Sbjct: 157 HQAQTMEGCSSPMVVKF--AD 175
>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 = 48.3 bits (114), Expect = 6e-08
Identities = 10/80 (12%), Positives = 33/80 (41%), Gaps = 2/80 (2%)
Query: 9 YPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKG 67
+ + ++ P T D++ + ++ +++++++ + FKG
Sbjct: 93 SKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHK-AFKG 151
Query: 68 FCYVEFVDVENLRQALLKDG 87
+V F +E+ ++ + G
Sbjct: 152 SIFVVFDSIESAKKFVETPG 171
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 49.1 bits (116), Expect = 6e-08
Identities = 19/129 (14%), Positives = 43/129 (33%), Gaps = 2/129 (1%)
Query: 11 ERYGRNQKTLPTEPPY-TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGF 68
+ + + + T FV + T+ + R F + + +V K + + +G+
Sbjct: 87 KMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGY 146
Query: 69 CYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGN 128
++E+ ++ A +DG +V +D+ G+ GG G
Sbjct: 147 AFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADV 206
Query: 129 KYNQHQDKG 137
Sbjct: 207 NIRHSGRDD 215
>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 = 46.1 bits (110), Expect = 9e-08
Identities = 14/93 (15%), Positives = 32/93 (34%), Gaps = 11/93 (11%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
+ VGN+ T ++ F E ++ +V K + +V E+
Sbjct: 6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDA 57
Query: 80 RQALLK-DGRITVDGLQVRLDIADGKRNDNKGG 111
+A+ D G ++ + ++ + G
Sbjct: 58 VEAIRGLDNT-EFQGKRMHVQLSTSRLRTASGP 89
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 47.5 bits (113), Expect = 1e-07
Identities = 18/95 (18%), Positives = 34/95 (35%), Gaps = 4/95 (4%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVE 72
E V NL G++ D++ F E L + D + R G V
Sbjct: 77 SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVH 135
Query: 73 FVDVENLRQALLK-DGRITVDGLQVRLDIADGKRN 106
F + +A+ + G +DG + + + + +
Sbjct: 136 FERRADALKAMKQYKGVP-LDGRPMDIQLVASQID 169
>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 = 46.2 bits (110), Expect = 1e-07
Identities = 19/105 (18%), Positives = 43/105 (40%), Gaps = 9/105 (8%)
Query: 10 PERYGRNQKTLPTEPPY--TAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFK 66
+ R + + P T + G + +G+T + + F P +++ +R+ + K
Sbjct: 8 NTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------K 61
Query: 67 GFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGG 111
G+ +V F E+ A++ T++G V+ + G
Sbjct: 62 GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSGP 106
>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 = 1e-07
Identities = 18/90 (20%), Positives = 33/90 (36%), Gaps = 4/90 (4%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVE 72
E V NL G++ D++ F E L + D + R G V
Sbjct: 18 SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVH 76
Query: 73 FVDVENLRQALLK-DGRITVDGLQVRLDIA 101
F + +A+ + +G +DG + + +
Sbjct: 77 FERKADALKAMKQYNGVP-LDGRPMNIQLV 105
>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 = 45.7 bits (109), Expect = 1e-07
Identities = 20/98 (20%), Positives = 43/98 (43%), Gaps = 3/98 (3%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVE 72
G + P T +VGNL +T+ + + F + S +++ + ++ +C+VE
Sbjct: 4 GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSND--PYCFVE 61
Query: 73 FVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKG 110
F + + AL + G +V+++ A + G
Sbjct: 62 FYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSG 99
>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 = 45.8 bits (109), Expect = 2e-07
Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 12/86 (13%)
Query: 29 FVGNLP-NGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK- 85
F+GNL + + DVE F + ++ + K G+ +V++ + + R A+L
Sbjct: 31 FIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAAVLGE 82
Query: 86 DGRITVDGLQVRLDIADGKRNDNKGG 111
+GR + G + +++A + D G
Sbjct: 83 NGR-VLAGQTLDINMAGEPKPDRSGP 107
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 44.8 bits (107), Expect = 2e-07
Identities = 16/75 (21%), Positives = 37/75 (49%), Gaps = 4/75 (5%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
FVG L + + +F ++ S+ L D +T++ +GFC++ F + E +++ ++
Sbjct: 3 FVGGLSPDTPEEKIREYF-GGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-MEK 60
Query: 87 GRITVDGLQVRLDIA 101
V + + +A
Sbjct: 61 KYHNVGLSKCEIKVA 75
>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 = 44.9 bits (107), Expect = 2e-07
Identities = 15/85 (17%), Positives = 34/85 (40%), Gaps = 11/85 (12%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 86
F+GNLP T+ ++ F + K++ ++ K + +V D A+
Sbjct: 12 FIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLH 63
Query: 87 GRITVDGLQVRLDIADGKRNDNKGG 111
+ G+ + ++ + K + G
Sbjct: 64 HY-KLHGVNINVEASKNKSKASSGP 87
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 45.0 bits (107), Expect = 3e-07
Identities = 29/110 (26%), Positives = 49/110 (44%), Gaps = 10/110 (9%)
Query: 18 KTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVD 75
+ + P Y+ FVG+L + G + FF + ++V D+ T KG+ +V+F D
Sbjct: 2 SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTD 60
Query: 76 VENLRQALLK-DGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGG 124
++AL + G + + VRL +A K + K G S G
Sbjct: 61 ELEQKRALTECQGAVGLGSKPVRLSVAIPKAS------RVKPVESGPSSG 104
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 44.8 bits (106), Expect = 3e-07
Identities = 17/81 (20%), Positives = 28/81 (34%), Gaps = 2/81 (2%)
Query: 5 SYGGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDR 64
+ + + Y + NLP G + D++ E L + T
Sbjct: 8 HHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTF--SSVNTRD 65
Query: 65 FKGFCYVEFVDVENLRQALLK 85
F G +EF E L +AL +
Sbjct: 66 FDGTGALEFPSEEILVEALER 86
>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 = 44.1 bits (105), Expect = 4e-07
Identities = 13/93 (13%), Positives = 39/93 (41%), Gaps = 11/93 (11%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
+ + FVGN+ T ++ F + +++ +V K + +V +
Sbjct: 5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADA 56
Query: 80 RQALLK-DGRITVDGLQVRLDIADGKRNDNKGG 111
+ A+ + +G+ V G ++ ++++ + +
Sbjct: 57 KAAIAQLNGK-EVKGKRINVELSTKGQKKSGPS 88
>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 = 44.2 bits (105), Expect = 5e-07
Identities = 19/86 (22%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK- 85
+V NL ++ +E+ F K +V VK + + + +V F + E+ +A+
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHFSNREDAVEAMKAL 71
Query: 86 DGRITVDGLQVRLDIADGKRNDNKGG 111
+G++ +DG + + +A D+ G
Sbjct: 72 NGKV-LDGSPIEVTLAKPVDKDSSGP 96
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 44.2 bits (105), Expect = 5e-07
Identities = 22/95 (23%), Positives = 40/95 (42%), Gaps = 10/95 (10%)
Query: 12 RYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCY 70
G + T P V N+P D+ + F + K++ V ++ ++ KGF +
Sbjct: 16 PRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGF 73
Query: 71 VEFVDVENLRQALLK------DGR-ITVDGLQVRL 98
V F + + +A K +GR I V+ R+
Sbjct: 74 VTFENSADADRAREKLHGTVVEGRKIEVNNATARV 108
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 43.2 bits (103), Expect = 7e-07
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 4/75 (5%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
FVG L T DV+ +F EQ K+ L+ DK T+R +GF +V F + + +
Sbjct: 3 FVGGLSVNTTVEDVKHYF-EQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 87 GRITVDGLQVRLDIA 101
++ V A
Sbjct: 62 FH-EINNKMVECKKA 75
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 43.8 bits (104), Expect = 8e-07
Identities = 14/75 (18%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALL 84
TA++GN+P+ T+ D+ F + ++ + + KG C++++ E ++
Sbjct: 29 TAYIGNIPHFATEADLIPLF-QNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIV 81
Query: 85 KDGRITVDGLQVRLD 99
G +R
Sbjct: 82 ALANFPFQGRNLRTG 96
>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 = 43.4 bits (103), Expect = 9e-07
Identities = 21/85 (24%), Positives = 41/85 (48%), Gaps = 5/85 (5%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
V LP T+ D++ +F +++ V++ KD +T KGF +V F + E + +
Sbjct: 19 IVLGLPWKTTEQDLKEYF-STFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM--S 75
Query: 87 GRITVDGLQVRLDIADGKRNDNKGG 111
R +DG + + K++ + G
Sbjct: 76 QRHMIDGRWCDCKLPNSKQSQDSGP 100
>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 = 43.0 bits (102), Expect = 1e-06
Identities = 17/96 (17%), Positives = 41/96 (42%), Gaps = 5/96 (5%)
Query: 22 TEPPYTAFVGNLPNGITQGDVERFFPE--QKLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
+ F+GNL I + + F L + ++++D +T KG+ ++ F +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 80 RQALLK-DGRITVDGLQVRLDIADGKRNDNKGGFNN 114
A+ +G+ + + + A K++ G ++
Sbjct: 62 DAAIEAMNGQY-LCNRPITVSYA-FKKDSKGSGPSS 95
>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 = 43.0 bits (102), Expect = 1e-06
Identities = 24/99 (24%), Positives = 45/99 (45%), Gaps = 13/99 (13%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK- 85
FV NL N +T+ +E+ F Q KL V+ +KD + ++ F + + +A+ +
Sbjct: 15 FVRNLANTVTEEILEKAF-SQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEEM 65
Query: 86 DGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGG 124
+G+ ++G + + A K +Q G S G
Sbjct: 66 NGKD-LEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103
>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 = 42.8 bits (101), Expect = 1e-06
Identities = 13/76 (17%), Positives = 26/76 (34%), Gaps = 6/76 (7%)
Query: 29 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGR 88
V NLP +V + +K DR K +V ++ E + A+ +
Sbjct: 9 LVKNLPQDSNCQEVHDLLKDYD------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQ 62
Query: 89 ITVDGLQVRLDIADGK 104
+ G + + +
Sbjct: 63 YSFRGKDLIVQLQPTD 78
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 42.5 bits (101), Expect = 1e-06
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
F+G L TQ + +F Q ++ +++D T R +GF +V F+D + + L
Sbjct: 4 FIGGLSWQTTQEGLREYF-GQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 61
Query: 87 GRITVDGLQVRLDIA 101
R +D + +A
Sbjct: 62 SRHELDSKTIDPKVA 76
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA
recognition motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 43.1 bits (102), Expect = 1e-06
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
F+ +LP T D+ F ++S ++ DK+T K F +V F + ++ + A+
Sbjct: 44 FIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI 99
>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 = 43.0 bits (101), Expect = 2e-06
Identities = 18/113 (15%), Positives = 35/113 (30%), Gaps = 9/113 (7%)
Query: 5 SYGGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETD 63
S G P P + LP +T+G+V P K+ ++ ++K
Sbjct: 11 SSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG---- 66
Query: 64 RFKGFCYVEFVDVENLRQAL--LKDGRITVDGLQVRLDIADGKRNDNKGGFNN 114
K ++E E + + G + + ++ K N
Sbjct: 67 --KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQ 117
>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 = 41.9 bits (99), Expect = 3e-06
Identities = 14/81 (17%), Positives = 37/81 (45%), Gaps = 9/81 (11%)
Query: 21 PTEPPYTA-FVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVEN 78
+ T +VG L + IT+ D+ F + ++ ++ +V+ + +++F +
Sbjct: 7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQA 60
Query: 79 LRQALLK-DGRITVDGLQVRL 98
A K ++ V+G ++ +
Sbjct: 61 AEVAAEKSFNKLIVNGRRLNV 81
>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 = 42.5 bits (100), Expect = 3e-06
Identities = 19/114 (16%), Positives = 33/114 (28%), Gaps = 8/114 (7%)
Query: 12 RYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCY 70
G + V LP + D++ E + + +D G
Sbjct: 2 SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 54
Query: 71 VEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGG 124
VEFV E++ A+ K + K + + + G S G
Sbjct: 55 VEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSSG 108
>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 = 41.9 bits (99), Expect = 3e-06
Identities = 14/80 (17%), Positives = 37/80 (46%), Gaps = 12/80 (15%)
Query: 29 FVGNLP-NGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL-LK 85
F+GNLP +++ D+ R F ++ + + F +++F + +++R A+ +
Sbjct: 26 FIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIEXE 77
Query: 86 DGRITVDGLQVRLDIADGKR 105
G ++ L+++
Sbjct: 78 SQE-MNFGKKLILEVSSSNA 96
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 42.2 bits (99), Expect = 3e-06
Identities = 16/109 (14%), Positives = 35/109 (32%), Gaps = 11/109 (10%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVE 72
+ P + LP +T+G+V P K+ ++ ++K K ++E
Sbjct: 5 HHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIE 58
Query: 73 FVDVENLRQAL--LKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRG 119
E + + G + + + + K + Q R
Sbjct: 59 MNTEEAANTMVNYYTSVTPVLRGQPIYIQFS--NHKELKTDSSPNQARA 105
>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 = 42.3 bits (100), Expect = 3e-06
Identities = 14/56 (25%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
F+ +LP D+ + F +VS ++ DK+T+ K F +V + + + + A+
Sbjct: 29 FIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 84
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 41.8 bits (99), Expect = 4e-06
Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 29 FVGNLP-NGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK- 85
F+GNLP +++ D+ R F P ++ + + F +++F + +++R A+
Sbjct: 14 FIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIECE 65
Query: 86 DGRITVDGLQVRLDIADGKRNDNKG 110
G ++ L+++
Sbjct: 66 SQE-MNFGKKLILEVSSSNARPQFD 89
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 41.9 bits (99), Expect = 5e-06
Identities = 20/85 (23%), Positives = 37/85 (43%), Gaps = 4/85 (4%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
F+G L T+ + ++ EQ KL +++D + R +GF +V F + + A+
Sbjct: 31 FIGGLSFETTEESLRNYY-EQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 87 GRITVDGLQVRLDIADGKRNDNKGG 111
++DG V A + G
Sbjct: 90 PH-SIDGRVVEPKRAVAREESGSGP 113
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 41.5 bits (98), Expect = 5e-06
Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 9/85 (10%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
FV P G+ + +F + SV + KDK F VE DV L +
Sbjct: 12 FVSGFPRGVDSAQLSEYF-LAFGPVASVVMDKDK-----GVFAIVEMGDVGAREAVLSQS 65
Query: 87 GRITVDGLQVRLDIADGKRNDNKGG 111
++ G ++R+ + K +
Sbjct: 66 Q-HSLGGHRLRVRPREQKEFQSPAS 89
>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 = 41.4 bits (98), Expect = 5e-06
Identities = 18/90 (20%), Positives = 43/90 (47%), Gaps = 6/90 (6%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
FVG + + + ++ FF + + V+++ D+ T KG+ +V F + ++++ +
Sbjct: 13 FVGGIDVRMDETEIRSFF-ARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 87 GRITVDGLQVRLDIADGKRNDNKGGFNNKQ 116
I G +++L A K+N + +
Sbjct: 71 --INFHGKKLKLGPAIRKQNLSTYHVQPRP 98
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 41.5 bits (98), Expect = 5e-06
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 4/85 (4%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
FVG L TQ + +F Q ++V ++KDK T++ +GF +V+F D + L
Sbjct: 20 FVGGLDWSTTQETLRSYF-SQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV-LAS 77
Query: 87 GRITVDGLQVRLDIADGKRNDNKGG 111
T+DG + + G
Sbjct: 78 RPHTLDGRNIDPKPCTPRGMQPSGP 102
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 41.0 bits (97), Expect = 5e-06
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
FVG L ++ D++ +F + ++V + D T R +GF ++ F D ++ + L
Sbjct: 15 FVGGLSWDTSKKDLKDYF-TKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKV-LDQ 72
Query: 87 GRITVDGLQVRLDIA 101
+DG + A
Sbjct: 73 KEHRLDGRVIDPKKA 87
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 41.5 bits (98), Expect = 6e-06
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 4/83 (4%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
F+G L TQ + +F Q ++ +++D T R +GF +V F+D + + L
Sbjct: 29 FIGGLSWQTTQEGLREYF-GQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 86
Query: 87 GRITVDGLQVRLDIADGKRNDNK 109
R +D + +A +R K
Sbjct: 87 SRHELDSKTIDPKVAFPRRAQPK 109
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 41.3 bits (97), Expect = 6e-06
Identities = 17/103 (16%), Positives = 37/103 (35%), Gaps = 11/103 (10%)
Query: 8 GYPERYGRNQKTLPTEPPYTA--FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDR 64
G+ + P + P + + L +G+ + D+ + V ++
Sbjct: 2 GHHHHHHMENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK----- 56
Query: 65 FKGFCYVEFVDVENLRQAL--LKDGRITVDGLQVRLDIADGKR 105
K VEF DV A+ D +I + G ++ + ++
Sbjct: 57 -KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQK 98
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 41.1 bits (97), Expect = 9e-06
Identities = 17/103 (16%), Positives = 36/103 (34%), Gaps = 12/103 (11%)
Query: 7 GGYPERYGRNQKTLPTEPPYTA-FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDR 64
G R E T FV P + + ++ F + V+++
Sbjct: 12 SGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL------- 64
Query: 65 FKGFCYVEFVDVENLRQALLK-DGRITVDGLQVRLDIADGKRN 106
GF +VEF + E+ +A+ + G+ + + + +
Sbjct: 65 -NGFAFVEFEEAESAAKAIEEVHGK-SFANQPLEVVYSKLPAK 105
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 40.6 bits (95), Expect = 1e-05
Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 9/91 (9%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVE 72
G + + P + LP +T+ +V P K+ ++ ++K K ++E
Sbjct: 4 GSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLE 57
Query: 73 FVDVENLRQAL--LKDGRITVDGLQVRLDIA 101
E + + + + +
Sbjct: 58 LATEEAAITMVNYYSAVTPHLRNQPIYIQYS 88
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 42.0 bits (98), Expect = 1e-05
Identities = 6/63 (9%), Positives = 14/63 (22%), Gaps = 1/63 (1%)
Query: 24 PPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
P N P +T+ + + +E+ + +
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181
Query: 83 LLK 85
L
Sbjct: 182 LGF 184
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 40.3 bits (95), Expect = 1e-05
Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 10/87 (11%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
FVG +T+ ++ FF Q ++ V + K F+ F +V F D + + +D
Sbjct: 9 FVGRCTGDMTEDELREFF-SQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGED 62
Query: 87 GRITVDGLQVRLDIADGKRNDNKGGFN 113
I G+ V + A+ K N N G +
Sbjct: 63 LII--KGISVHISNAEPKHNSNSGPSS 87
>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 = 40.3 bits (95), Expect = 1e-05
Identities = 21/88 (23%), Positives = 35/88 (39%), Gaps = 7/88 (7%)
Query: 29 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 86
FVG L ++ DV R F P + +++ KG +V+F + A+
Sbjct: 19 FVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 87 GRITVDG----LQVRLDIADGKRNDNKG 110
G T+ G L V+ D + + G
Sbjct: 78 GSQTMPGASSSLVVKFADTDKESGPSSG 105
>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 = 41.4 bits (97), Expect = 2e-05
Identities = 15/100 (15%), Positives = 34/100 (34%), Gaps = 9/100 (9%)
Query: 7 GGYPERYGRNQKTLPTE---PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKET 62
R+ + P T + N+P +++ D++ F +V K+
Sbjct: 99 NSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD- 157
Query: 63 DRFKGFCYVEFVDVENLRQALLK-DGRITVDGLQVRLDIA 101
+ ++ VE QAL+ + +R+ +
Sbjct: 158 ---RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 194
>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 = 39.0 bits (91), Expect = 5e-05
Identities = 17/109 (15%), Positives = 37/109 (33%), Gaps = 11/109 (10%)
Query: 14 GRNQKTLPTEPPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVE 72
G + V L + + D+ + V ++ K VE
Sbjct: 4 GSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVE 57
Query: 73 FVDVENLRQAL--LKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRG 119
F ++++ ++ + D + + G Q + + KR G N+ + G
Sbjct: 58 FENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPG--NSGPSSG 104
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 38.6 bits (90), Expect = 6e-05
Identities = 11/70 (15%), Positives = 30/70 (42%), Gaps = 7/70 (10%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-- 85
+ + + + + F + K+V++ D+ T + KGF +VE + + ++ +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 86 ----DGRITV 91
D + +
Sbjct: 76 GKRLDLKHRL 85
>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 = 39.3 bits (92), Expect = 1e-04
Identities = 21/112 (18%), Positives = 41/112 (36%), Gaps = 4/112 (3%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL--LK 85
V NL ++ +E+ F + + +V D + R G +VEF R+AL
Sbjct: 100 TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCG 158
Query: 86 DGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMGGNKYNQHQDKG 137
DG + + + ++ D++ G K + + + G
Sbjct: 159 DGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPG 210
Score = 38.5 bits (90), Expect = 2e-04
Identities = 19/80 (23%), Positives = 32/80 (40%), Gaps = 9/80 (11%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
FVGNLP IT+ D +R F E+ + V + +D+ GF ++ A +
Sbjct: 26 FVGNLPTDITEEDFKRLF-ERYGEPSEVFINRDR------GFGFIRLESRTLAEIAKAEL 78
Query: 87 GRITVDGLQVRLDIADGKRN 106
+ +R+ A
Sbjct: 79 DGTILKSRPLRIRFATHGAA 98
>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 = 37.6 bits (88), Expect = 1e-04
Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 11/73 (15%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK- 85
+VG L + + R F ++ + ++ VK F Y+++ ++ + A K
Sbjct: 21 WVGGLGPNTSLAALAREF-DRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKM 73
Query: 86 DGRITVDGLQVRL 98
G + G RL
Sbjct: 74 RGFP-LGGPDRRL 85
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 38.3 bits (89), Expect = 1e-04
Identities = 10/86 (11%), Positives = 27/86 (31%), Gaps = 2/86 (2%)
Query: 21 PTEPPYTAFVGNLPNGITQGDVERFFPE--QKLVSVRLVKDKETDRFKGFCYVEFVDVEN 78
TEP + N+ + + ++ + + +D G Y+ F E+
Sbjct: 25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQES 84
Query: 79 LRQALLKDGRITVDGLQVRLDIADGK 104
+ + G + + ++
Sbjct: 85 AQAFVEAFQGYPFQGNPLVITFSETP 110
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions,
RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus
musculus}
Length = 89
Score = 37.2 bits (87), Expect = 2e-04
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 10/81 (12%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKD 86
FVG +T ++++FF Q ++V V + K F+ F +V F D + + +D
Sbjct: 15 FVGRCTEDMTAEELQQFF-CQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCGED 68
Query: 87 GRITVDGLQVRLDIADGKRND 107
I G+ V + A+ K N
Sbjct: 69 LII--KGISVHISNAEPKHNK 87
>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 = 38.8 bits (90), Expect = 2e-04
Identities = 18/102 (17%), Positives = 37/102 (36%), Gaps = 10/102 (9%)
Query: 6 YGGYP-ERYGRNQKTLPTE---PPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDK 60
YG P R+ + P T + N+P +++ D++ F +V K
Sbjct: 128 YGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK 187
Query: 61 ETDRFKGFCYVEFVDVENLRQALLK-DGRITVDGLQVRLDIA 101
+ + ++ VE QAL+ + +R+ +
Sbjct: 188 D----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS 225
Score = 31.9 bits (72), Expect = 0.038
Identities = 20/134 (14%), Positives = 41/134 (30%), Gaps = 9/134 (6%)
Query: 5 SYGGYPERYGRNQKTLPTEPPYTAFVGNL-PNGITQGDVERFFPEQ-KLVSVRLVKDKET 62
G + R L V NL P +T + F + V+++ +K
Sbjct: 16 PRGSHMGRIAIP--GLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-- 71
Query: 63 DRFKGFCYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQNRGGGS 122
K V+ D + A+ + G +R+ ++ + Q
Sbjct: 72 ---KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDY 128
Query: 123 GGMGGNKYNQHQDK 136
G +++ + K
Sbjct: 129 GNSPLHRFKKPGSK 142
>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 = 37.8 bits (88), Expect = 2e-04
Identities = 16/109 (14%), Positives = 41/109 (37%), Gaps = 20/109 (18%)
Query: 9 YPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKG 67
+PER + T +V +T + F ++ + + +
Sbjct: 30 FPERRAPRKGN-------TLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR------N 74
Query: 68 FCYVEFVDVENLRQALLK-DGRITVDGLQVRLDIADGKRNDNKGGFNNK 115
+V + +E+ QA+ + +G V+ +Q++++I ++ K
Sbjct: 75 CAFVTYEKMESADQAVAELNGT-QVESVQLKVNI--ARKQPMLDAATGK 120
>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 = 37.5 bits (87), Expect = 2e-04
Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 7/80 (8%)
Query: 29 FVGNLPNGITQGDVER----FFPEQKLVSVRLVKDKETDRFK---GFCYVEFVDVENLRQ 81
FV L + +V + F K+ V + + YV ++ E+ +
Sbjct: 19 FVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALR 78
Query: 82 ALLKDGRITVDGLQVRLDIA 101
A+ + VDG ++ +
Sbjct: 79 AIQCVNNVVVDGRTLKASLG 98
>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 = 37.1 bits (86), Expect = 3e-04
Identities = 20/122 (16%), Positives = 39/122 (31%), Gaps = 15/122 (12%)
Query: 8 GYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFK 66
G R + +E V LP + D++ E + + +D
Sbjct: 1 GGAPRGRYGPPSRRSE--NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------- 51
Query: 67 GFCYVEFVDVENLRQALLK-DGRI----TVDGLQVRLDIADGKRNDNKGGFNNKQNRGGG 121
G VEFV E++ A+ K D + +R+ + + + ++R
Sbjct: 52 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRS 111
Query: 122 SG 123
Sbjct: 112 RS 113
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 36.7 bits (85), Expect = 3e-04
Identities = 11/57 (19%), Positives = 20/57 (35%), Gaps = 2/57 (3%)
Query: 29 FVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
+ N+P + ++ + V + TD V + + RQAL K
Sbjct: 19 QIRNIPPHLQWEVLDSLL--VQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDK 73
>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 = 37.1 bits (86), Expect = 4e-04
Identities = 13/73 (17%), Positives = 29/73 (39%), Gaps = 6/73 (8%)
Query: 17 QKTLPTEPPYTAFVGNLPNGITQGDVERFFPE------QKLVSVRLVKDKETDRFKGFCY 70
+ P EP +V NL + + D++ F + + ++ + R KG +
Sbjct: 37 RSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAF 96
Query: 71 VEFVDVENLRQAL 83
+ + + +AL
Sbjct: 97 IGLPNEKAAAKAL 109
>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 = 36.5 bits (85), Expect = 5e-04
Identities = 10/56 (17%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 29 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQAL 83
++ NLP + + ++E P +++S R+++D + +G + E +
Sbjct: 29 YISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVI 83
>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 = 36.3 bits (84), Expect = 5e-04
Identities = 15/76 (19%), Positives = 24/76 (31%), Gaps = 7/76 (9%)
Query: 27 TAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK 85
NLP G +++ F L V L VEF++ R+A
Sbjct: 12 VILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFRH 65
Query: 86 DGRITVDGLQVRLDIA 101
+ + L+ A
Sbjct: 66 LAYSKFHHVPLYLEWA 81
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 36.0 bits (84), Expect = 5e-04
Identities = 19/95 (20%), Positives = 33/95 (34%), Gaps = 13/95 (13%)
Query: 19 TLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVE 77
+ + FV NLP T ++ F E ++ + + + KG V+F E
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPE 59
Query: 78 NLRQALLK------DGRITVDGLQVRLDIADGKRN 106
+A GR + VR+D +
Sbjct: 60 VAERACRMMNGMKLSGRE----IDVRIDRNASGPS 90
>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 = 36.1 bits (84), Expect = 5e-04
Identities = 21/102 (20%), Positives = 41/102 (40%), Gaps = 10/102 (9%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 86
FV NL + ++ F +V +++DK+ + +G V F QA+ +
Sbjct: 19 FVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAISMFN 77
Query: 87 GRITVDG--LQVRLDIADGKRNDNKGGFNNKQNRGGGSGGMG 126
G++ + + V++D +R KG F + G
Sbjct: 78 GQL-LFDRPMHVKMD----ERALPKGDFFPPERPQQSGPSSG 114
>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 = 35.3 bits (82), Expect = 0.001
Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 6/88 (6%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 86
+V NL +GI + + F + S +++ + R KGF +V F E +A+ + +
Sbjct: 19 YVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 87 GRITVDGLQVRLDIADGKRNDNKGGFNN 114
GRI V + + +A ++ + + G ++
Sbjct: 77 GRI-VATKPLYVALAQ-RKEERQSGPSS 102
>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 = 35.0 bits (81), Expect = 0.001
Identities = 19/109 (17%), Positives = 43/109 (39%), Gaps = 18/109 (16%)
Query: 5 SYGGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETD 63
S G ER + T +V +T + F P ++ + + +
Sbjct: 2 SSGSSGERRAPRKGN-------TLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR--- 49
Query: 64 RFKGFCYVEFVDVENLRQALLK-DGRITVDGLQVRLDIADGKRNDNKGG 111
+V + +E+ QA+ + +G V+ +Q++++IA + + G
Sbjct: 50 ---NCAFVTYEKMESADQAVAELNGTQ-VESVQLKVNIARKQPMLDSGP 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 = 36.4 bits (83), Expect = 0.001
Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 22 TEPPYTAFVGNLPNGITQGDVERFFPE--QKLVSVRLVKDKETDRFKGFCYVEFVDVENL 79
T P +T ++ NL I + ++++ + + + + + +G +V F +V +
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 80 RQAL 83
AL
Sbjct: 66 TNAL 69
Score = 35.6 bits (81), Expect = 0.003
Identities = 16/76 (21%), Positives = 25/76 (32%), Gaps = 6/76 (7%)
Query: 9 YPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKG 67
P + Q P + F+ NLP + + F + VRLV +
Sbjct: 191 MPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HD 245
Query: 68 FCYVEFVDVENLRQAL 83
+VEF + A
Sbjct: 246 IAFVEFDNEVQAGAAR 261
>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 = 34.5 bits (80), Expect = 0.002
Identities = 13/67 (19%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 22 TEPPYTAFVGNLPNGITQGDVER-----FFPEQKLVSVRLVKDKETDRFKGFCYVEFVDV 76
T P +T ++ NL I + ++++ F +++ + + + + +G +V F +V
Sbjct: 5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEV 61
Query: 77 ENLRQAL 83
+ AL
Sbjct: 62 SSATNAL 68
>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 = 35.6 bits (81), Expect = 0.003
Identities = 20/95 (21%), Positives = 32/95 (33%), Gaps = 29/95 (30%)
Query: 3 DYSYGGYPERYGRNQKTLPTEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKET 62
+Y + P + + Q ++ T Y L N D + F VS
Sbjct: 90 NYKFLMSPIKTEQRQPSMMTRM-YIEQRDRLYN-----DNQVFAKYN--VS--------- 132
Query: 63 DRFKGFCYVEFVDVENLRQALLKD---GRITVDGL 94
R + LRQALL+ + +DG+
Sbjct: 133 -RLQ--------PYLKLRQALLELRPAKNVLIDGV 158
>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 = 34.1 bits (78), Expect = 0.004
Identities = 11/74 (14%), Positives = 31/74 (41%), Gaps = 8/74 (10%)
Query: 29 FVGNLPNGITQGDVERFF-PEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLK-D 86
G L NG+++ + + ++ + +K + + + E ++A + +
Sbjct: 31 ANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTLN 84
Query: 87 GRITVDGLQVRLDI 100
G+ VD L ++ +
Sbjct: 85 GKEVVDDLGQKITL 98
>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 = 33.4 bits (77), Expect = 0.007
Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 11/94 (11%)
Query: 29 FVGNLPNGITQGDVERFFPEQ-KLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA----- 82
F+ NL I + F ++S ++V D + KG+ +V F E +A
Sbjct: 9 FIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMN 66
Query: 83 --LLKDGRITVDGLQVRLDIADGKRNDNKGGFNN 114
LL D ++ V + R + + + F N
Sbjct: 67 GMLLNDRKVFVGRFKSRKE-REAELGARAKEFTN 99
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 33.4 bits (76), Expect = 0.007
Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 9/85 (10%)
Query: 29 FVGNLPNGITQGDVERFFPEQ--KLVSVRLVKDKETDRF--KGFCYVEFVDVENLRQALL 84
FVG LP I + ++ F + LV K + F KG+ ++ F + ++ QAL+
Sbjct: 12 FVGGLPPDIDEDEITASF-RRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSV-QALI 69
Query: 85 KDGRITVDGLQVRLDIADGKRNDNK 109
L + + +K
Sbjct: 70 DACLEEDGKLYLCV---SSPTIKDK 91
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 33.2 bits (76), Expect = 0.008
Identities = 9/61 (14%), Positives = 22/61 (36%), Gaps = 7/61 (11%)
Query: 29 FVGNLP------NGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
V N+P + + + F + +E + KG+ ++E+ + A
Sbjct: 19 VVDNVPQVGPDRLEKLKNVIHKIF-SKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDA 77
Query: 83 L 83
+
Sbjct: 78 V 78
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 30.5 bits (68), Expect = 0.097
Identities = 16/89 (17%), Positives = 37/89 (41%), Gaps = 3/89 (3%)
Query: 30 VGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQALLKDGRI 89
V NL +T + + F + V ++++ + ++F+ +++ D + + A L
Sbjct: 51 VENLFYPVTLDVLHQIFSKFGTV-LKIITFTKNNQFQAL--LQYADPVSAQHAKLSLDGQ 107
Query: 90 TVDGLQVRLDIADGKRNDNKGGFNNKQNR 118
+ L I K +NN ++R
Sbjct: 108 NIYNACCTLRIDFSKLTSLNVKYNNDKSR 136
>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 = 31.2 bits (70), Expect = 0.10
Identities = 15/82 (18%), Positives = 25/82 (30%), Gaps = 32/82 (39%)
Query: 26 YTAFVGNLPNGITQGDVERFFPE-QKLVSVRLVKDKETDRFKGFCYVEFVD--VENLRQA 82
F G QG+ + +F E + L Y V ++ +
Sbjct: 157 VAIFGG-------QGNTDDYFEELRDLYQT---------------YHVLVGDLIKFSAET 194
Query: 83 LLKDGRITVD-------GLQVR 97
L + R T+D GL +
Sbjct: 195 LSELIRTTLDAEKVFTQGLNIL 216
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 29.3 bits (66), Expect = 0.12
Identities = 9/61 (14%), Positives = 22/61 (36%), Gaps = 7/61 (11%)
Query: 29 FVGNLP------NGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQA 82
V N+P + + + F + +E + KG+ ++E+ + A
Sbjct: 5 VVDNVPQVGPDRLEKLKNVIHKIF-SKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDA 63
Query: 83 L 83
+
Sbjct: 64 V 64
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 28.8 bits (64), Expect = 0.32
Identities = 8/64 (12%), Positives = 19/64 (29%), Gaps = 2/64 (3%)
Query: 22 TEPPYTAFVGNLPNGITQGDVERFFPEQKLVSVRLVKDKETDRFKGFCYVEFVDVENLRQ 81
+ V LP + + +F ++ V R + F + + +
Sbjct: 5 SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLS--WQRLGCGGVLTFREPADAER 62
Query: 82 ALLK 85
L +
Sbjct: 63 VLAQ 66
>2xqy_A GH, envelope glycoprotein H; immune system-viral protein complex,
envelope protein; HET: NAG; 2.05A {Suid herpesvirus}
Length = 572
Score = 28.7 bits (63), Expect = 0.76
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 6/54 (11%)
Query: 83 LLKDGRITVDGLQVRLDIADGKRNDNKGGFNNKQ-NRGGGS-GGMGGNKYNQHQ 134
L +G TV + + + + +D+K G+++ Q +GGGS GG GG ++ Q
Sbjct: 520 LFPNG--TV--VDLLSFTSTFEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQ 569
>2h0u_A NADPH-flavin oxidoreductase; structur genomics, PSI-2, protein
structure initiative, midwest CENT structural genomics,
MCSG; HET: FMN; 1.90A {Helicobacter pylori}
Length = 217
Score = 26.9 bits (59), Expect = 2.3
Identities = 10/41 (24%), Positives = 15/41 (36%)
Query: 69 CYVEFVDVENLRQALLKDGRITVDGLQVRLDIADGKRNDNK 109
C +E D E + L + G + V + G RN
Sbjct: 161 CPIEGYDQEKVEAYLEEKGYLNTAEFGVSVMACFGYRNQEI 201
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding,
lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB:
2ist_A 1qyu_A 1prz_A
Length = 325
Score = 26.3 bits (59), Expect = 3.4
Identities = 4/17 (23%), Positives = 8/17 (47%)
Query: 81 QALLKDGRITVDGLQVR 97
+ + D R+ V+G
Sbjct: 36 KEWILDQRVLVNGKVCD 52
>3iwa_A FAD-dependent pyridine nucleotide-disulphide oxidoreductase;
structural genomics, PSI-2, protein structur initiative;
2.30A {Desulfovibrio vulgaris}
Length = 472
Score = 26.3 bits (59), Expect = 3.8
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 37 ITQGDVERFFPEQKLVSVRLVKDKETDRFKG 67
+ Q D F+PE+ +++++LV D+ T R G
Sbjct: 371 VEQFDRAHFYPEKTIMTLQLVVDRPTRRVLG 401
>3kd9_A Coenzyme A disulfide reductase; PSI-II, NYSGXRC, oxidoreductase,
structural genomics structure initiative; 2.75A
{Pyrococcus horikoshii}
Length = 449
Score = 26.3 bits (59), Expect = 4.1
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 37 ITQGDVERFFPEQKLVSVRLVKDKETDRFKG 67
I ++P + + ++ V D ET+R G
Sbjct: 357 IKASTRPHYYPGGREIWLKGVVDNETNRLLG 387
>3oc4_A Oxidoreductase, pyridine nucleotide-disulfide FAM; structural
genomics, PSI-2, protein structure initiative; HET: FAD;
2.60A {Enterococcus faecalis}
Length = 452
Score = 25.9 bits (58), Expect = 5.1
Identities = 7/31 (22%), Positives = 10/31 (32%)
Query: 37 ITQGDVERFFPEQKLVSVRLVKDKETDRFKG 67
I + +L+ DK T R G
Sbjct: 354 IIVRQPAPPLQHGTEILGKLIYDKVTQRVLG 384
>3n44_F E1 envelope glycoprotein; viral protein, immature heterodimer,
alphavirus, receptor BI membrane fusion; HET: NAG; 2.35A
{Chikungunya virus} PDB: 3n41_F* 3n42_F* 3n43_F* 2xfc_A
Length = 473
Score = 25.8 bits (56), Expect = 5.4
Identities = 13/31 (41%), Positives = 21/31 (67%), Gaps = 2/31 (6%)
Query: 106 NDNKGGFNNKQ-NRGGGS-GGMGGNKYNQHQ 134
+D+K G+++ Q +GGGS GG GG ++ Q
Sbjct: 440 DDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQ 470
>3cgb_A Pyridine nucleotide-disulfide oxidoreductase, CLA; coenzyme A,
flavin adenine dinucleotide, selenomethionine, F
flavoprotein; HET: COA FAD; 1.90A {Bacillus anthracis
str} PDB: 3cgc_A* 3cgd_A* 3cge_A*
Length = 480
Score = 25.9 bits (58), Expect = 5.4
Identities = 5/31 (16%), Positives = 16/31 (51%)
Query: 37 ITQGDVERFFPEQKLVSVRLVKDKETDRFKG 67
+ ++ ++P K + ++L+ +T + G
Sbjct: 395 VDSTNMAGYYPNAKPLYLKLLYRSDTKQLLG 425
>1yqz_A Coenzyme A disulfide reductase; oxidoreductase; HET: COA FAD; 1.54A
{Staphylococcus aureus}
Length = 438
Score = 25.9 bits (58), Expect = 5.6
Identities = 6/31 (19%), Positives = 13/31 (41%)
Query: 37 ITQGDVERFFPEQKLVSVRLVKDKETDRFKG 67
+TQG ++P + +R+ D +
Sbjct: 353 VTQGAHANYYPGNSPLHLRVYYDTSNRQILR 383
>1nhp_A NADH peroxidase; oxidoreductase (H2O2(A)); HET: FAD; 2.00A
{Enterococcus faecalis} SCOP: c.3.1.5 c.3.1.5 d.87.1.1
PDB: 1npx_A* 1joa_A* 2npx_A* 1nhq_A* 1nhs_A* 1nhr_A*
1f8w_A*
Length = 447
Score = 25.5 bits (57), Expect = 6.0
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 37 ITQGDVERFFPEQKLVSVRLVKDKETDRFKG 67
+ + + F P+++ +LV D ET + G
Sbjct: 358 VVEDYLMDFNPDKQKAWFKLVYDPETTQILG 388
>3ics_A Coenzyme A-disulfide reductase; pyridine nucleotide-disulfide
oxidoreductase class I, rhodan coenzyme A, flavin
adenine dinucleotide; HET: FAD COA ADP; 1.94A {Bacillus
anthracis} PDB: 3icr_A* 3ict_A*
Length = 588
Score = 25.6 bits (57), Expect = 6.6
Identities = 5/31 (16%), Positives = 15/31 (48%)
Query: 37 ITQGDVERFFPEQKLVSVRLVKDKETDRFKG 67
+ ++P V ++L+ +K++ + G
Sbjct: 396 VQANSHAGYYPNATPVLIKLIFNKDSGKIYG 426
>3ntd_A FAD-dependent pyridine nucleotide-disulphide oxidoreductase; COA,
persulfide reductase, rhodanese; HET: COA FAD; 1.99A
{Shewanella loihica} PDB: 3nta_A* 3nt6_A*
Length = 565
Score = 25.6 bits (57), Expect = 6.7
Identities = 6/31 (19%), Positives = 13/31 (41%)
Query: 37 ITQGDVERFFPEQKLVSVRLVKDKETDRFKG 67
+ ++P ++VS +L+ D G
Sbjct: 380 VHTASHASYYPGAEVVSFKLLFDPVKGTIFG 410
>2cdu_A NADPH oxidase; flavoenzyme, oxidoreductase; HET: FAD ADP; 1.8A
{Lactobacillus sanfranciscensis}
Length = 452
Score = 25.5 bits (57), Expect = 6.7
Identities = 8/31 (25%), Positives = 10/31 (32%)
Query: 37 ITQGDVERFFPEQKLVSVRLVKDKETDRFKG 67
I F V + LV D +T G
Sbjct: 359 IADNYRPEFMLSTDEVLMSLVYDPKTRVILG 389
>1fot_A TPK1 delta, CAMP-dependent protein kinase type 1; open
conformation, transferase; HET: TPO; 2.80A
{Saccharomyces cerevisiae} SCOP: d.144.1.7
Length = 318
Score = 25.2 bits (56), Expect = 7.8
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 7/48 (14%)
Query: 23 EPPYTAFVGNLPNGITQGDVERF--FPEQKLVSVRLVKDKETDRFKGF 68
E PY + GD +F +PE+ + +D D F+ F
Sbjct: 276 ETPYEPPIQQGQ-----GDTSQFDKYPEEDINYGVQGEDPYADLFRDF 318
>2bol_A TSP36, small heat shock protein; A-crystallin, molecular chaperone;
2.5A {Taenia saginata}
Length = 314
Score = 25.2 bits (54), Expect = 8.9
Identities = 8/69 (11%), Positives = 23/69 (33%), Gaps = 18/69 (26%)
Query: 41 DVERFFPEQKLVSVRLVKD-------KETDRFKGFCYVEF---------VDVENLRQALL 84
+V+ F E+ ++++ K+ K VD +++ +
Sbjct: 119 NVKNFKAEE--ITIKADKNKLVVRAQKSVACGDAAMSESVGRSIPLPPSVDRNHIQATIT 176
Query: 85 KDGRITVDG 93
D + ++
Sbjct: 177 TDDVLVIEA 185
>3q9p_A Heat shock protein beta-1; alpha-crystallin domain, chaperone,
charcot-marie-tooth DISE neuronopathy, IG-like fold,
stress response; 2.00A {Homo sapiens} PDB: 3q9q_A
Length = 85
Score = 24.2 bits (53), Expect = 9.6
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 17/68 (25%)
Query: 41 DVERFFPEQ-------KLVSVRLVKDKETDRFKGFCYVEF---------VDVENLRQALL 84
DV F P++ +V + D G+ F VD + +L
Sbjct: 14 DVNHFAPDELTVKTKDGVVEITGKHAARQDE-HGYISRCFTRKYTLPPGVDPTQVSSSLS 72
Query: 85 KDGRITVD 92
+G +TV+
Sbjct: 73 PEGTLTVE 80
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.316 0.140 0.418
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,208,990
Number of extensions: 128946
Number of successful extensions: 598
Number of sequences better than 10.0: 1
Number of HSP's gapped: 434
Number of HSP's successfully gapped: 212
Length of query: 137
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 53
Effective length of database: 4,356,429
Effective search space: 230890737
Effective search space used: 230890737
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: 42 (22.0 bits)
S2: 52 (23.7 bits)