RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2136
(166 letters)
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 147 bits (372), Expect = 2e-45
Identities = 87/121 (71%), Positives = 103/121 (85%), Gaps = 7/121 (5%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
RVYVGSI +EL EDTIRQAF PFGPIKSI+MSWD +T KHKGFAFVEY++PEAAQL+LEQ
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDI 165
MN VMLGGRNIK VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DI
Sbjct: 90 MNSVMLGGRNIK-------VGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 142
Query: 166 K 166
K
Sbjct: 143 K 143
Score = 100 bits (252), Expect = 3e-27
Identities = 30/79 (37%), Positives = 50/79 (63%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+ + R+YV S+ +L +D I+ F FG IKS ++ DP T KHKG+ F+EY+ +++
Sbjct: 121 EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180
Query: 100 QLSLEQMNGVMLGGRNIKV 118
Q ++ MN LGG+ ++V
Sbjct: 181 QDAVSSMNLFDLGGQYLRV 199
>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 = 125 bits (315), Expect = 5e-36
Identities = 22/125 (17%), Positives = 45/125 (36%), Gaps = 15/125 (12%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
+ + V ++ L + + PFG ++ + + T + KG+ F EY ++A
Sbjct: 92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAA 151
Query: 101 LSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDL 160
+ + G LG R + VH+ ++ Q + V + P
Sbjct: 152 RAKSDLLGKPLGPRTLYVHW--------TDAGQLT-------PALLHSRCLCVDRLPPGF 196
Query: 161 TEEDI 165
+ D
Sbjct: 197 NDVDA 201
Score = 89.7 bits (223), Expect = 2e-22
Identities = 17/121 (14%), Positives = 38/121 (31%), Gaps = 31/121 (25%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++ + + ++ + + +K K+KG AFV E A+ ++
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDYE-LKYC------FVDKYKGTAFVTLLNGEQAEAAINA 76
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDI 165
+ L R + V + VA++ P LT++
Sbjct: 77 FHQSRLRERELSVQL------------------------QPTDALLCVANLPPSLTQQQF 112
Query: 166 K 166
+
Sbjct: 113 E 113
Score = 83.9 bits (208), Expect = 2e-20
Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 5/93 (5%)
Query: 32 VGPITPDVNSNSPLR---VYVGSISFELKE-DTIRQAFLPFGPIKSINMSWDPITQKHKG 87
V + + L + V + + D + +A ++ + KG
Sbjct: 169 VHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKG 227
Query: 88 FAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
FA +EY+ E A+ + +Q +G+ LGG +++V F
Sbjct: 228 FAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
Score = 28.8 bits (65), Expect = 0.78
Identities = 3/32 (9%), Positives = 15/32 (46%)
Query: 135 QSVIDEITEEAKLYNRIYVASIHPDLTEEDIK 166
+ ++ + + +I + + D+T +++
Sbjct: 9 RKRLEHTERQFRNRRKILIRGLPGDVTNQEVH 40
>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 = 118 bits (299), Expect = 8e-36
Identities = 25/91 (27%), Positives = 46/91 (50%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
VY+GSI ++ E+ I GP+ ++ M +DP T + KG+AF+E+ E++ ++
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQS 136
+NG LG R +K + ++
Sbjct: 64 LNGYQLGSRFLKCGYSSNSDISGVSLEHHHH 94
Score = 27.6 bits (62), Expect = 0.72
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 150 RIYVASIHPDLTEEDIK 166
+Y+ SI D TEE I
Sbjct: 4 VVYLGSIPYDQTEEQIL 20
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 117 bits (296), Expect = 9e-35
Identities = 31/86 (36%), Positives = 51/86 (59%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G ++ + +YVG ++ E+ + + AF+PFG I I + D T+KH+GFAFVE
Sbjct: 52 GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 111
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKV 118
+++ E A +++ MN L GR I+V
Sbjct: 112 FELAEDAAAAIDNMNESELFGRTIRV 137
Score = 25.9 bits (57), Expect = 5.6
Identities = 8/72 (11%), Positives = 19/72 (26%), Gaps = 20/72 (27%)
Query: 95 IPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVA 154
+PE+ + HV G + A +YV
Sbjct: 30 LPESVAYTCVNCTER------------HVDGGSGGSGGSGG--------SATTKRVLYVG 69
Query: 155 SIHPDLTEEDIK 166
+ ++ ++ +
Sbjct: 70 GLAEEVDDKVLH 81
>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 = 115 bits (290), Expect = 1e-34
Identities = 30/78 (38%), Positives = 49/78 (62%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
+ + +YVG ++ E+ + + AF+PFG I I + D T+KH+GFAFVE+++ E A
Sbjct: 4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63
Query: 101 LSLEQMNGVMLGGRNIKV 118
+++ MN L GR I+V
Sbjct: 64 AAIDNMNESELFGRTIRV 81
>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 = 115 bits (289), Expect = 5e-33
Identities = 24/128 (18%), Positives = 54/128 (42%), Gaps = 8/128 (6%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMS-----WDPITQKHKGFAFVEYDIPEAAQ 100
R+YVG+I F + E+ + F + + + + K FAF+E+ +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 101 LSLEQMNGVMLGGRNIKVHFPHVQVGRP--SNMPQAQSVIDEITEEAKLYNRIYVASIHP 158
++ +G++ G+++K+ PH P S P T +++++ +
Sbjct: 66 QAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 159 DLTEEDIK 166
L ++ +K
Sbjct: 125 YLNDDQVK 132
Score = 110 bits (277), Expect = 3e-31
Identities = 24/89 (26%), Positives = 45/89 (50%)
Query: 30 KQVGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFA 89
V + V +S ++++G + L +D +++ FGP+K+ N+ D T KG+A
Sbjct: 100 VYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 159
Query: 90 FVEYDIPEAAQLSLEQMNGVMLGGRNIKV 118
F EY ++ +NG+ LG + + V
Sbjct: 160 FCEYVDINVTDQAIAGLNGMQLGDKKLLV 188
Score = 25.4 bits (56), Expect = 7.9
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 149 NRIYVASIHPDLTEEDIK 166
R+YV +I +TEE +
Sbjct: 5 RRLYVGNIPFGITEEAMM 22
>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 = 111 bits (281), Expect = 6e-33
Identities = 31/86 (36%), Positives = 50/86 (58%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G + + +YVG ++ E+ + + AF+PFG I I + D T+KH+GFAFVE
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKV 118
+++ E A +++ MN L GR I+V
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRV 86
>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 = 110 bits (278), Expect = 2e-32
Identities = 35/79 (44%), Positives = 50/79 (63%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
S P+R+YVGS+ F + ED +R F PFG I+SI + D T + KG+ F+ + E A
Sbjct: 22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECA 81
Query: 100 QLSLEQMNGVMLGGRNIKV 118
+ +LEQ+NG L GR +KV
Sbjct: 82 KKALEQLNGFELAGRPMKV 100
Score = 28.4 bits (64), Expect = 0.47
Identities = 8/37 (21%), Positives = 22/37 (59%)
Query: 130 NMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIK 166
+ A ++ + + + + R+YV S+H ++TE+ ++
Sbjct: 8 HSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLR 44
>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 = 114 bits (287), Expect = 2e-32
Identities = 28/135 (20%), Positives = 59/135 (43%), Gaps = 16/135 (11%)
Query: 32 VGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFV 91
+G + P S +YVG + ++ E + + F P GPI SI + D IT++ G+A+V
Sbjct: 3 LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62
Query: 92 EYDIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRI 151
+ P A+ +L+ MN ++ G+ ++ + P + I
Sbjct: 63 NFQQPADAERALDTMNFDVIKGKPVR-------IMWSQRDPSLRKSGV---------GNI 106
Query: 152 YVASIHPDLTEEDIK 166
++ ++ + + +
Sbjct: 107 FIKNLDKSIDNKALY 121
Score = 81.2 bits (201), Expect = 8e-20
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++ ++ + + F FG I S + D KG+ FV ++ EAA+ ++E+
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEK 162
Query: 106 MNGVMLGGRNIKV 118
MNG++L R + V
Sbjct: 163 MNGMLLNDRKVFV 175
>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 = 108 bits (272), Expect = 6e-31
Identities = 29/97 (29%), Positives = 51/97 (52%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
S ++V SI E +ED I++ F +G IK+I+++ D T KG+A VEY+
Sbjct: 65 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQ 133
+ A + E +NG + G+ I+V + V+ + +
Sbjct: 125 KQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSE 161
Score = 28.6 bits (64), Expect = 0.62
Identities = 6/18 (33%), Positives = 12/18 (66%)
Query: 149 NRIYVASIHPDLTEEDIK 166
++V SIH + E++I+
Sbjct: 73 WILFVTSIHEEAQEDEIQ 90
>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 = 105 bits (263), Expect = 2e-29
Identities = 21/129 (16%), Positives = 52/129 (40%), Gaps = 24/129 (18%)
Query: 43 SPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSW-----DPITQKHKGFAFVEYDIPE 97
S R+YVG+I F + E+ + F + + + + K FAF+E+ +
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 98 AAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIH 157
++ +G++ G+++K + RP + +++++ +
Sbjct: 63 ETTQAMA-FDGIIFQGQSLK-------IRRPHDYQPLPG-----------AHKLFIGGLP 103
Query: 158 PDLTEEDIK 166
L ++ +K
Sbjct: 104 NYLNDDQVK 112
Score = 103 bits (260), Expect = 5e-29
Identities = 21/82 (25%), Positives = 40/82 (48%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
++++G + L +D +++ FGP+K+ N+ D T KG+AF EY
Sbjct: 87 DYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 146
Query: 97 EAAQLSLEQMNGVMLGGRNIKV 118
++ +NG+ LG + + V
Sbjct: 147 NVTDQAIAGLNGMQLGDKKLLV 168
>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 = 102 bits (256), Expect = 3e-29
Identities = 27/86 (31%), Positives = 47/86 (54%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G P N VYVG + ++ E + + FL GP+ + +M D +T +H+G+ FVE
Sbjct: 4 GSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE 63
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKV 118
+ E A +++ M+ + L G+ I+V
Sbjct: 64 FLSEEDADYAIKIMDMIKLYGKPIRV 89
>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 = 101 bits (253), Expect = 7e-29
Identities = 24/79 (30%), Positives = 47/79 (59%), Gaps = 1/79 (1%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPI-TQKHKGFAFVEYDIPEAA 99
S P +V++G ++ + +D I + F +G IK I+M + + KG+A+VE++ P+ A
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 100 QLSLEQMNGVMLGGRNIKV 118
+ +L+ M+G + G+ I
Sbjct: 61 EKALKHMDGGQIDGQEITA 79
Score = 25.6 bits (57), Expect = 4.4
Identities = 2/18 (11%), Positives = 11/18 (61%)
Query: 149 NRIYVASIHPDLTEEDIK 166
++++ + ++T++ I
Sbjct: 5 TKVHIGRLTRNVTKDHIM 22
>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 = 99 bits (250), Expect = 2e-28
Identities = 31/78 (39%), Positives = 47/78 (60%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
S+ +YVGS+ F + ED +R F PFG I +I + D T + KG+ F+ + E A+
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 101 LSLEQMNGVMLGGRNIKV 118
+LEQ+NG L GR ++V
Sbjct: 62 RALEQLNGFELAGRPMRV 79
Score = 25.2 bits (56), Expect = 5.7
Identities = 6/18 (33%), Positives = 14/18 (77%)
Query: 149 NRIYVASIHPDLTEEDIK 166
+ +YV S+H ++TE+ ++
Sbjct: 6 SGLYVGSLHFNITEDMLR 23
>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 = 99.7 bits (249), Expect = 5e-28
Identities = 25/91 (27%), Positives = 42/91 (46%), Gaps = 11/91 (12%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
VY G I+ L + +RQ F PFG I I + KG++FV + E+A ++
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRV------FPEKGYSFVRFSTHESAAHAIVS 80
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQS 136
+NG + G +K ++ G+ S +
Sbjct: 81 VNGTTIEGHVVKCYW-----GKESPDMTSGP 106
Score = 31.9 bits (73), Expect = 0.027
Identities = 6/39 (15%), Positives = 15/39 (38%)
Query: 128 PSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIK 166
S + D + + + +Y I LT++ ++
Sbjct: 5 SSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMR 43
>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 = 98.4 bits (246), Expect = 1e-27
Identities = 24/81 (29%), Positives = 46/81 (56%)
Query: 38 DVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPE 97
S+ R++V ++S+ E+ + + F +GP+ ++ D +T+K KGFAFV + PE
Sbjct: 2 SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61
Query: 98 AAQLSLEQMNGVMLGGRNIKV 118
A + +++G + GR + V
Sbjct: 62 HAVKAYAEVDGQVFQGRMLHV 82
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 98.5 bits (246), Expect = 1e-27
Identities = 26/81 (32%), Positives = 42/81 (51%)
Query: 38 DVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPE 97
S ++V + E E+ I F +G IK+I+++ D T KG+ VEY+ +
Sbjct: 17 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 76
Query: 98 AAQLSLEQMNGVMLGGRNIKV 118
AQ ++E +NG L G+ I V
Sbjct: 77 EAQAAMEGLNGQDLMGQPISV 97
Score = 26.8 bits (60), Expect = 1.9
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 149 NRIYVASIHPDLTEEDIK 166
++V +H + TEEDI
Sbjct: 24 WILFVTGVHEEATEEDIH 41
>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 = 98.5 bits (246), Expect = 1e-27
Identities = 28/81 (34%), Positives = 46/81 (56%)
Query: 38 DVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPE 97
S ++V SI E +ED I++ F +G IK+I+++ D T KG+A VEY+ +
Sbjct: 20 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 79
Query: 98 AAQLSLEQMNGVMLGGRNIKV 118
A + E +NG + G+ I+V
Sbjct: 80 QALAAKEALNGAEIMGQTIQV 100
Score = 27.3 bits (61), Expect = 1.4
Identities = 6/17 (35%), Positives = 12/17 (70%)
Query: 150 RIYVASIHPDLTEEDIK 166
++V SIH + E++I+
Sbjct: 28 ILFVTSIHEEAQEDEIQ 44
>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 = 98.6 bits (246), Expect = 1e-27
Identities = 29/86 (33%), Positives = 46/86 (53%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G ++++ V+VG +S E+ + I+ AF PFG I + D T K KG+ FV
Sbjct: 4 GSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKV 118
+ A+ +++QM G LGGR I+
Sbjct: 64 FFNKWDAENAIQQMGGQWLGGRQIRT 89
>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 = 97.3 bits (243), Expect = 2e-27
Identities = 25/88 (28%), Positives = 47/88 (53%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G N + + V +S E +R+ F +GPI +++ +D +++ +GFAFV
Sbjct: 4 GSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 63
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
++ + A+ + E+ NG+ L GR I+V
Sbjct: 64 FENVDDAKEAKERANGMELDGRRIRVSG 91
>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 = 96.9 bits (242), Expect = 4e-27
Identities = 21/92 (22%), Positives = 44/92 (47%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+ + + + V ++++ D++R+ F +G + + + +P T+ +GFAFV + A
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68
Query: 100 QLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNM 131
Q + M+G L GR ++V S
Sbjct: 69 QDAEAAMDGAELDGRELRVQVARYGRRDLSGP 100
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA
splicing, mRNA transport, nonsense-mediated mRNA decay,
nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*
Length = 126
Score = 97.8 bits (244), Expect = 4e-27
Identities = 28/92 (30%), Positives = 47/92 (51%)
Query: 29 LKQVGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGF 88
++Q G S ++V + E E+ I F +G IK+I+++ D T KG+
Sbjct: 7 VEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 66
Query: 89 AFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
VEY+ + AQ ++E +NG L G+ I V +
Sbjct: 67 TLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
Score = 26.2 bits (58), Expect = 3.6
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 149 NRIYVASIHPDLTEEDIK 166
++V +H + TEEDI
Sbjct: 23 WILFVTGVHEEATEEDIH 40
>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 = 98.3 bits (245), Expect = 5e-27
Identities = 30/105 (28%), Positives = 46/105 (43%), Gaps = 5/105 (4%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
+ +YVG++SF E+ I + F G IK I M D + + GF FVEY
Sbjct: 32 QEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSR 91
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHF-----PHVQVGRPSNMPQAQS 136
A+ ++ +NG L R I+ + Q GR + Q +
Sbjct: 92 ADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRD 136
>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 = 96.1 bits (240), Expect = 5e-27
Identities = 29/78 (37%), Positives = 40/78 (51%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
S V+VG +S E+ I AF PFG I + D T K KG+ FV + A+
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
Query: 101 LSLEQMNGVMLGGRNIKV 118
+++QM G LGGR I+
Sbjct: 63 NAIQQMGGQWLGGRQIRT 80
>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 = 95.4 bits (238), Expect = 2e-26
Identities = 22/86 (25%), Positives = 43/86 (50%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G P+ ++ + V ++S + +E +++ F PFG I I ++ D T + KGFAF+
Sbjct: 4 GSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFIS 63
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKV 118
+ E A ++ ++G + V
Sbjct: 64 FHRREDAARAIAGVSGFGYDHLILNV 89
>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 = 95.4 bits (238), Expect = 2e-26
Identities = 25/86 (29%), Positives = 47/86 (54%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G ++ +++VG +SF+ E ++ Q F +G I + + D TQ+ +GF FV
Sbjct: 1 GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKV 118
++ + A+ ++ MNG + GR I+V
Sbjct: 61 FENIDDAKDAMMAMNGKSVDGRQIRV 86
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1;
RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 94
Score = 94.2 bits (235), Expect = 4e-26
Identities = 22/73 (30%), Positives = 37/73 (50%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
VYV ++ F L + + + F +G + + + D T+K KG AF+ + ++AQ
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 106 MNGVMLGGRNIKV 118
+N L GR IK
Sbjct: 78 INNKQLFGRVIKA 90
Score = 25.3 bits (56), Expect = 5.4
Identities = 5/18 (27%), Positives = 11/18 (61%)
Query: 149 NRIYVASIHPDLTEEDIK 166
+ +YV+++ LT D+
Sbjct: 17 STVYVSNLPFSLTNNDLY 34
>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 = 94.3 bits (235), Expect = 4e-26
Identities = 22/90 (24%), Positives = 39/90 (43%), Gaps = 13/90 (14%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YV ++ +R AF PFG I ++M + AFV Y+ E+A ++ ++
Sbjct: 18 LYVYG--EDMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAEL 69
Query: 107 NGVMLGGRNIKVHFPHVQVGRPSNMPQAQS 136
NG + +K V + R M +
Sbjct: 70 NGTQVESVQLK-----VNIARKQPMLDSGP 94
>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 = 95.7 bits (238), Expect = 7e-26
Identities = 20/87 (22%), Positives = 45/87 (51%)
Query: 34 PITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEY 93
++ + V ++++ DT+R+ F +G + + + D T++ +GFAFV +
Sbjct: 60 HHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF 119
Query: 94 DIPEAAQLSLEQMNGVMLGGRNIKVHF 120
A+ +++ M+G +L GR ++V
Sbjct: 120 HDKRDAEDAMDAMDGAVLDGRELRVQM 146
>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 = 93.1 bits (232), Expect = 9e-26
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+ V+VG++ ++E+ + + FL GP+ + + D K K F FV + PE+
Sbjct: 12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPESV 70
Query: 100 QLSLEQMNGVMLGGRNIKV 118
++ +NG+ L GR I V
Sbjct: 71 SYAIALLNGIRLYGRPINV 89
>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 = 94.0 bits (234), Expect = 1e-25
Identities = 23/91 (25%), Positives = 40/91 (43%), Gaps = 13/91 (14%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+YV ++ +R AF PFG I ++M + AFV Y+ E+A ++ +
Sbjct: 41 TLYVYGE--DMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAE 92
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQS 136
+NG + +KV+ R M A +
Sbjct: 93 LNGTQVESVQLKVNI-----ARKQPMLDAAT 118
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 93.1 bits (232), Expect = 1e-25
Identities = 24/92 (26%), Positives = 35/92 (38%), Gaps = 10/92 (10%)
Query: 31 QVGPITPD--VNSNSPL--RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHK 86
QV P D + S P Y+G+I E + F FG I K
Sbjct: 10 QVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKH------YPEK 63
Query: 87 GFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKV 118
G F++YD E A + + + GRN++
Sbjct: 64 GCCFIKYDTHEQAAVCIVALANFPFQGRNLRT 95
Score = 30.0 bits (68), Expect = 0.11
Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 128 PSNMPQAQSVIDEITEEAKLYNR-IYVASIHPDLTEEDIK 166
P PQA +D I A Y+ +I TE D+
Sbjct: 9 PQVNPQA---VDHIIRSAPPRVTTAYIGNIPHFATEADLI 45
>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 = 94.0 bits (234), Expect = 1e-25
Identities = 27/91 (29%), Positives = 49/91 (53%), Gaps = 5/91 (5%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
N + + V +S E +R+ F +GPI +++ +D +++ +GFAFV ++
Sbjct: 39 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 98
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHF-----PH 122
+ A+ + E+ NG+ L GR I+V F PH
Sbjct: 99 DDAKEAKERANGMELDGRRIRVDFSITKRPH 129
>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 = 93.1 bits (232), Expect = 2e-25
Identities = 18/75 (24%), Positives = 36/75 (48%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+Y+ ++S + E + F F K + + +T + +G AF+ + E A +L
Sbjct: 27 VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
Query: 106 MNGVMLGGRNIKVHF 120
+NG L G+ + + F
Sbjct: 87 VNGYKLYGKILVIEF 101
Score = 25.7 bits (57), Expect = 4.5
Identities = 5/18 (27%), Positives = 11/18 (61%)
Query: 149 NRIYVASIHPDLTEEDIK 166
+Y+ ++ P +TE D+
Sbjct: 26 KVLYLKNLSPRVTERDLV 43
>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 = 92.2 bits (230), Expect = 2e-25
Identities = 20/81 (24%), Positives = 36/81 (44%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
S+ +Y+ + + + + P+G I S D T K KG+ FV++D P AAQ
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 101 LSLEQMNGVMLGGRNIKVHFP 121
++ + + + K P
Sbjct: 62 KAVTALKASGVQAQMAKQSGP 82
>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 = 92.7 bits (231), Expect = 2e-25
Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 2/86 (2%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G + P +YVG++S ++ E I Q F GP KS M + + + + FVE
Sbjct: 4 GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVE 61
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKV 118
+ A +L MNG + G+ +KV
Sbjct: 62 FYEHRDAAAALAAMNGRKILGKEVKV 87
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 93.2 bits (232), Expect = 2e-25
Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 39 VNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEA 98
V ++ P ++++G ++ E E ++ F GPI + + D T K +GFAF+ ++ P
Sbjct: 2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPAD 60
Query: 99 AQLSLEQMNGVMLGGRNIKV 118
A+ + + MNG L G+ IKV
Sbjct: 61 AKNAAKDMNGKSLHGKAIKV 80
Score = 25.4 bits (56), Expect = 6.9
Identities = 4/23 (17%), Positives = 13/23 (56%)
Query: 144 EAKLYNRIYVASIHPDLTEEDIK 166
EA ++++ ++ + E+ +K
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLK 25
>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 = 91.4 bits (228), Expect = 3e-25
Identities = 21/73 (28%), Positives = 41/73 (56%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++VG ++ + ++T+R AF F S ++ WD T +G+ FV + + AQ +++
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 106 MNGVMLGGRNIKV 118
M G L GR +++
Sbjct: 63 MQGQDLNGRPLRI 75
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 91.7 bits (228), Expect = 7e-25
Identities = 13/78 (16%), Positives = 33/78 (42%)
Query: 44 PLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSL 103
V ++ ++E ++ +G ++ + + P T+KH G A V + A+ ++
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65
Query: 104 EQMNGVMLGGRNIKVHFP 121
+ ++ + G I
Sbjct: 66 KNLHLTSVMGNIIHAQLD 83
>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 = 92.6 bits (230), Expect = 7e-25
Identities = 22/77 (28%), Positives = 45/77 (58%), Gaps = 5/77 (6%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+VYVG++ + + +AF +GP++S+ ++ +P GFAFVE++ P A ++ +
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVRE 129
Query: 106 MNGVMLGGRNIKVHFPH 122
++G L G ++V +
Sbjct: 130 LDGRTLCGCRVRVELSN 146
Score = 28.3 bits (63), Expect = 0.76
Identities = 10/85 (11%), Positives = 25/85 (29%), Gaps = 4/85 (4%)
Query: 83 QKHKGFAFVEYDIPEAAQLSLEQM-NGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEI 141
+ KG E A+ +Q N + G +
Sbjct: 10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHH---MH 66
Query: 142 TEEAKLYNRIYVASIHPDLTEEDIK 166
+ L ++YV ++ + + +++
Sbjct: 67 RDSCPLDCKVYVGNLGNNGNKTELE 91
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 91.7 bits (228), Expect = 1e-24
Identities = 21/88 (23%), Positives = 45/88 (51%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
P + + V ++++ DT+R+ F +G + + + D T++ +GFAFV
Sbjct: 36 SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 95
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
+ A+ +++ M+G +L GR ++V
Sbjct: 96 FHDKRDAEDAMDAMDGAVLDGRELRVQM 123
>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 = 90.8 bits (226), Expect = 1e-24
Identities = 26/97 (26%), Positives = 51/97 (52%), Gaps = 2/97 (2%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G + ++P R++V +I F ++ +RQ F FG I + + ++ + KGF FV
Sbjct: 4 GSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVT 61
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPS 129
++ A + E+++G ++ GR I+V+ +V S
Sbjct: 62 FENSADADRAREKLHGTVVEGRKIEVNNATARVMTNS 98
>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 = 90.0 bits (224), Expect = 2e-24
Identities = 17/75 (22%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
R++VG++ ++ E+ +R+ F +G + + K KGF F+ + A+++ +
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVE 70
Query: 106 MNGVMLGGRNIKVHF 120
++ + L G+ ++V F
Sbjct: 71 LDNMPLRGKQLRVRF 85
Score = 28.8 bits (65), Expect = 0.31
Identities = 7/19 (36%), Positives = 16/19 (84%)
Query: 148 YNRIYVASIHPDLTEEDIK 166
+R++V ++ PD+TEE+++
Sbjct: 15 RSRLFVGNLPPDITEEEMR 33
>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 = 89.6 bits (223), Expect = 2e-24
Identities = 17/85 (20%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 36 TPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDI 95
+ + ++SF + ED +++ F I+ ++ K KG A++E+
Sbjct: 8 CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKS 62
Query: 96 PEAAQLSLEQMNGVMLGGRNIKVHF 120
A+ +LE+ G + GR++ +++
Sbjct: 63 EADAEKNLEEKQGAEIDGRSVSLYY 87
>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 = 91.9 bits (229), Expect = 3e-24
Identities = 19/130 (14%), Positives = 56/130 (43%), Gaps = 18/130 (13%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
S +P +++G+++ ++ A + + D T ++ F +V+++
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESA 64
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASI 156
E + +LE + G+ + G IK+ P+ + +++ + + ++
Sbjct: 65 EDLEKALE-LTGLKVFGNEIKL-----------EKPKGRD-----SKKVRAARTLLAKNL 107
Query: 157 HPDLTEEDIK 166
++TE+++K
Sbjct: 108 SFNITEDELK 117
Score = 86.1 bits (214), Expect = 5e-22
Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 5/84 (5%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
+ + ++SF + ED +++ F I+ K KG A++E+
Sbjct: 92 DSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSE 146
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHF 120
A+ +LE+ G + GR++ +++
Sbjct: 147 ADAEKNLEEKQGAEIDGRSVSLYY 170
>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 = 90.1 bits (224), Expect = 3e-24
Identities = 28/105 (26%), Positives = 48/105 (45%), Gaps = 5/105 (4%)
Query: 31 QVGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAF 90
+G +++ + E + + Q F+PFG + S + D T K F F
Sbjct: 12 SIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGF 71
Query: 91 VEYDIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQ 135
V YD P +AQ +++ MNG +G + +K VQ+ R N ++
Sbjct: 72 VSYDNPVSAQAAIQSMNGFQIGMKRLK-----VQLKRSKNDSKSG 111
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 88.9 bits (221), Expect = 6e-24
Identities = 17/79 (21%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
S ++++ + F ++ + + G +K + + + K KG A+VEY+ A
Sbjct: 13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQA 71
Query: 100 QLSLEQMNGVMLGGRNIKV 118
++ +M+G+ + IKV
Sbjct: 72 SQAVMKMDGMTIKENIIKV 90
Score = 26.1 bits (58), Expect = 2.8
Identities = 2/18 (11%), Positives = 13/18 (72%)
Query: 149 NRIYVASIHPDLTEEDIK 166
++++++ + T+E+++
Sbjct: 18 HKLFISGLPFSCTKEELE 35
>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 = 89.8 bits (223), Expect = 7e-24
Identities = 22/89 (24%), Positives = 46/89 (51%)
Query: 30 KQVGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFA 89
+ + P + + + V I + E +RQ F +GPI+S+ + D T++ +G+
Sbjct: 28 QHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYG 87
Query: 90 FVEYDIPEAAQLSLEQMNGVMLGGRNIKV 118
FV++ +AQ ++ +NG + + +KV
Sbjct: 88 FVKFQSGSSAQQAIAGLNGFNILNKRLKV 116
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 88.6 bits (220), Expect = 1e-23
Identities = 23/80 (28%), Positives = 42/80 (52%)
Query: 39 VNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEA 98
+ +++ + E + + FLPFG + S + D T K F FV +D P++
Sbjct: 35 IEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94
Query: 99 AQLSLEQMNGVMLGGRNIKV 118
AQ++++ MNG +G + +KV
Sbjct: 95 AQVAIKAMNGFQVGTKRLKV 114
>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 = 88.6 bits (220), Expect = 1e-23
Identities = 25/94 (26%), Positives = 44/94 (46%), Gaps = 6/94 (6%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G + V++ ++SF+ +E+ + + FG +K + + P T+ KG AF +
Sbjct: 4 GSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQ 63
Query: 93 YDIPEAAQLSLEQMN------GVMLGGRNIKVHF 120
+ EAAQ L + G+ L GR +KV
Sbjct: 64 FMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDL 97
>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 = 88.6 bits (220), Expect = 1e-23
Identities = 19/103 (18%), Positives = 42/103 (40%), Gaps = 2/103 (1%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
+ ++ V ++ F + + I++ F FG +K + +D + + G A V
Sbjct: 24 SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVH 82
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQ 135
++ A +++Q GV L GR + + Q+ +
Sbjct: 83 FERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHH-HHHH 124
Score = 27.0 bits (60), Expect = 2.2
Identities = 3/18 (16%), Positives = 12/18 (66%)
Query: 149 NRIYVASIHPDLTEEDIK 166
++ V+++ +++ DI+
Sbjct: 36 AKLLVSNLDFGVSDADIQ 53
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 89.2 bits (221), Expect = 2e-23
Identities = 21/106 (19%), Positives = 35/106 (33%), Gaps = 2/106 (1%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGP--IKSINMSWDPITQKHKGFAF 90
T N VYVGS S+ + + Q G + + + + + KG+A
Sbjct: 44 ILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAE 103
Query: 91 VEYDIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQS 136
V + LE + G +L G + V Q +
Sbjct: 104 VVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQARKR 149
Score = 26.0 bits (57), Expect = 5.0
Identities = 12/68 (17%), Positives = 23/68 (33%), Gaps = 5/68 (7%)
Query: 104 EQMNGVMLGGRNIKVHF-----PHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHP 158
+GV LG N+ P Q P + +++ + +YV S
Sbjct: 6 HHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSW 65
Query: 159 DLTEEDIK 166
T++ +
Sbjct: 66 WTTDQQLI 73
>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 = 87.3 bits (217), Expect = 2e-23
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 3/81 (3%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKH---KGFAFVEYDIPE 97
S+ +++ +++F E+T++ F G IKS +S GF FVEY PE
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 98 AAQLSLEQMNGVMLGGRNIKV 118
AQ +L+Q+ G + G ++V
Sbjct: 62 QAQKALKQLQGHTVDGHKLEV 82
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 87.4 bits (217), Expect = 3e-23
Identities = 24/79 (30%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
N + P R++V +I F ++ +RQ F FG I + + ++ + KGF FV ++ A
Sbjct: 25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADA 82
Query: 100 QLSLEQMNGVMLGGRNIKV 118
+ E+++G ++ GR I+V
Sbjct: 83 DRAREKLHGTVVEGRKIEV 101
>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 = 86.9 bits (216), Expect = 3e-23
Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKS-INMSWDPITQKHKGFAFVEYDIPEAA 99
S+ +++G++ E+ E + F FG I + DP T KG+AF+ + +A+
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 100 QLSLEQMNGVMLGGRNIKV 118
++E MNG L R I V
Sbjct: 62 DAAIEAMNGQYLCNRPITV 80
>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 = 87.0 bits (216), Expect = 4e-23
Identities = 25/97 (25%), Positives = 46/97 (47%), Gaps = 3/97 (3%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G + N+ R+YVG++ +++ I F +G I+ I++ + FAFVE
Sbjct: 11 GGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVE 67
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPS 129
++ P A+ ++ +G G ++V FP G S
Sbjct: 68 FEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGS 104
Score = 26.1 bits (58), Expect = 3.6
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 149 NRIYVASIHPDLTEEDIK 166
RIYV ++ PD+ +DI+
Sbjct: 23 CRIYVGNLPPDIRTKDIE 40
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 86.7 bits (215), Expect = 4e-23
Identities = 15/69 (21%), Positives = 28/69 (40%)
Query: 48 YVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMN 107
+ S + + + F G + ++ D T K KGF FVE A+ ++ +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 108 GVMLGGRNI 116
G L ++
Sbjct: 76 GKRLDLKHR 84
>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 = 86.5 bits (215), Expect = 5e-23
Identities = 25/73 (34%), Positives = 40/73 (54%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
V+VG+I +E E+ ++ F GP+ S + +D T K KG+ F EY E A ++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 106 MNGVMLGGRNIKV 118
+NG GR ++V
Sbjct: 70 LNGREFSGRALRV 82
>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 = 88.4 bits (220), Expect = 6e-23
Identities = 23/120 (19%), Positives = 52/120 (43%), Gaps = 18/120 (15%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+ V + ++ + + F GPI + + D T G+AFV++ +Q +++ +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 107 NGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIK 166
NG+ + + +KV + RP E ++ L YV ++ +T++ +
Sbjct: 66 NGITVRNKRLKVSYA-----RPGG---------ESIKDTNL----YVTNLPRTITDDQLD 107
Score = 77.2 bits (191), Expect = 1e-18
Identities = 22/83 (26%), Positives = 40/83 (48%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
P S +YV ++ + +D + F +G I N+ D +T + +G AFV Y+
Sbjct: 82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR 141
Query: 97 EAAQLSLEQMNGVMLGGRNIKVH 119
E AQ ++ +N V+ G + +
Sbjct: 142 EEAQEAISALNNVIPEGGSQPLS 164
>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 = 86.2 bits (214), Expect = 7e-23
Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 4/84 (4%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
S + + ++S+ E+T+++ F IK K KG+AF+E+
Sbjct: 8 NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYAFIEFASF 63
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHF 120
E A+ +L N + GR I++
Sbjct: 64 EDAKEALNSCNKREIEGRAIRLEL 87
>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 = 86.2 bits (214), Expect = 7e-23
Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 1/81 (1%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+ ++ V ++ F + + I++ F FG +K + +D + + G A V ++ A
Sbjct: 25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADA 83
Query: 100 QLSLEQMNGVMLGGRNIKVHF 120
+++Q NGV L GR + +
Sbjct: 84 LKAMKQYNGVPLDGRPMNIQL 104
Score = 26.5 bits (59), Expect = 2.2
Identities = 3/18 (16%), Positives = 12/18 (66%)
Query: 149 NRIYVASIHPDLTEEDIK 166
++ V+++ +++ DI+
Sbjct: 30 GKLLVSNLDFGVSDADIQ 47
>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 = 89.4 bits (221), Expect = 9e-23
Identities = 19/104 (18%), Positives = 41/104 (39%), Gaps = 2/104 (1%)
Query: 30 KQVGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGP--IKSINMSWDPITQKHKG 87
K P + + +Y+G++++ ++ + +A G I I + + KG
Sbjct: 54 KGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG 113
Query: 88 FAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNM 131
FA V +++ ++ + L G+N V + Q M
Sbjct: 114 FALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEM 157
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 88.0 bits (218), Expect = 1e-22
Identities = 19/101 (18%), Positives = 42/101 (41%), Gaps = 1/101 (0%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
+ ++ V ++ F + + I++ F FG +K + +D + + G A V
Sbjct: 77 SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVH 135
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQ 133
++ A +++Q GV L GR + + Q+ +
Sbjct: 136 FERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEHHHHH 176
Score = 28.3 bits (63), Expect = 0.99
Identities = 8/55 (14%), Positives = 20/55 (36%)
Query: 112 GGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIK 166
GGRN + + E + ++ V+++ +++ DI+
Sbjct: 52 GGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQ 106
>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 = 90.4 bits (225), Expect = 1e-22
Identities = 21/128 (16%), Positives = 50/128 (39%), Gaps = 13/128 (10%)
Query: 39 VNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIK-SINMSWDPITQKHKGFAFVEYDIPE 97
V+ + +++ + + IR + SI + + FA+++ E
Sbjct: 112 VSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKE 170
Query: 98 AAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIH 157
A+ +E++NG+ + G + SN + D T E + I + ++
Sbjct: 171 DARYCVEKLNGLKIEGYTLVTKV--------SNPLEKSKRTDSATLEGR---EIMIRNLS 219
Query: 158 PDLTEEDI 165
+L +E++
Sbjct: 220 TELLDENL 227
Score = 81.6 bits (202), Expect = 2e-19
Identities = 17/120 (14%), Positives = 46/120 (38%), Gaps = 28/120 (23%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
V V ++ ++ + + F GPI ++++ +K+ FA +E+ + A ++ +
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKT 101
Query: 107 NGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIK 166
+ ++G I V + +++ + P T+ +I+
Sbjct: 102 HK-VVGQNEII-------VSHLTE------------------CTLWMTNFPPSYTQRNIR 135
Score = 78.5 bits (194), Expect = 3e-18
Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 3/76 (3%)
Query: 47 VYVGSISFEL-KEDTIRQAFLPFGPIKSIN-MSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
+ + ++S EL E+ +R++F FG I+ IN + + AF+ ++ ++A+ +L+
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ 272
Query: 105 QMNGVMLGGRNIKVHF 120
MN +LG R I V
Sbjct: 273 -MNRSLLGNREISVSL 287
>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 = 85.4 bits (212), Expect = 1e-22
Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 3/84 (3%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
P+ S ++V +S + E+T++++F + D T KGF FV+++
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSE 64
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHF 120
E A+ + E M + G + + +
Sbjct: 65 EDAKAAKEAMEDGEIDGNKVTLDW 88
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation,
RNA-binding, EIF4G-binding translation; 1.90A {Homo
sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 85.4 bits (212), Expect = 2e-22
Identities = 26/117 (22%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+++ ++ + + F FG I S + D KG+ FV ++ EAA+ ++E+M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65
Query: 107 NGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEE 163
NG++L R + V + R + + AK + +Y+ + P T
Sbjct: 66 NGMLLNDRKVFVGRFKSRKEREAELG----------ARAKEFTNVYIKNFGPGSTRA 112
>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 = 84.6 bits (210), Expect = 2e-22
Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 7/80 (8%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
S+ ++Y+G++S + D +RQ F G+AFV+Y A
Sbjct: 4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWA 57
Query: 100 QLSLEQMNG-VMLGGRNIKV 118
++E ++G V L G+ ++V
Sbjct: 58 IRAIETLSGKVELHGKIMEV 77
Score = 29.1 bits (66), Expect = 0.21
Identities = 5/18 (27%), Positives = 14/18 (77%)
Query: 149 NRIYVASIHPDLTEEDIK 166
N++Y+ ++ P +T +D++
Sbjct: 9 NKLYIGNLSPAVTADDLR 26
>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 = 86.9 bits (216), Expect = 2e-22
Identities = 28/120 (23%), Positives = 56/120 (46%), Gaps = 18/120 (15%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+ V + + ++ R F G I+S + D IT + G+ FV Y P+ A+ ++ +
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 107 NGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIK 166
NG+ L + IKV + RPS+ + N +YV+ + +T+++++
Sbjct: 65 NGLRLQTKTIKVSYA-----RPSS------------ASIRDAN-LYVSGLPKTMTQKELE 106
Score = 72.6 bits (179), Expect = 6e-17
Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 2/86 (2%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
P S +YV + + + + Q F +G I + + D +T +G F+ +D
Sbjct: 81 PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKR 140
Query: 97 EAAQLSLEQMNGVMLGGRN--IKVHF 120
A+ +++ +NG G I V F
Sbjct: 141 IEAEEAIKGLNGQKPSGATEPITVKF 166
>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 = 85.0 bits (211), Expect = 2e-22
Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+YV ++ + ++ +R+AF PFG I S + + + KGF FV + PE A ++ +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74
Query: 106 MNGVMLGGRNIKV 118
MNG ++ + + V
Sbjct: 75 MNGRIVATKPLYV 87
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 85.1 bits (211), Expect = 2e-22
Identities = 19/83 (22%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDP-ITQKHKGFAFVEYDIPEA 98
+ ++ V +I F+ + IR+ F FG +K++ + T H+GF FV++ +
Sbjct: 11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD 70
Query: 99 AQLSLEQM-NGVMLGGRNIKVHF 120
A+ + + + L GR + + +
Sbjct: 71 AKKAFNALCHSTHLYGRRLVLEW 93
>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 = 84.2 bits (209), Expect = 3e-22
Identities = 15/87 (17%), Positives = 36/87 (41%), Gaps = 2/87 (2%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGP--IKSINMSWDPITQKHKGFAFVEYDIPEAAQLS 102
+ +Y+G++++ ++ + +A G I I + + KGFA V +++
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61
Query: 103 LEQMNGVMLGGRNIKVHFPHVQVGRPS 129
++ + L G+N V +
Sbjct: 62 MDLLPKRELHGQNPVVTPSNKLEHHHH 88
>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 = 84.2 bits (209), Expect = 4e-22
Identities = 15/83 (18%), Positives = 38/83 (45%), Gaps = 2/83 (2%)
Query: 36 TPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDI 95
S +P +++G+++ ++ A + + D T ++ F +V+++
Sbjct: 9 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFES 67
Query: 96 PEAAQLSLEQMNGVMLGGRNIKV 118
E + +LE + G+ + G IK+
Sbjct: 68 AEDLEKALE-LTGLKVFGNEIKL 89
>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 = 84.3 bits (209), Expect = 5e-22
Identities = 23/123 (18%), Positives = 54/123 (43%), Gaps = 13/123 (10%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
P+VN +Y+ ++ +++ + + F +GPI+ I + T + +G A+V Y+
Sbjct: 5 PEVNRI----LYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDI 57
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASI 156
A+ +++ ++G + R + V + + + + E+ KL Y +
Sbjct: 58 FDAKNAVDHLSGFNVSNRYLVVLYYNANRAFQKMDTKKK------EEQLKLLKEKYGINT 111
Query: 157 HPD 159
P
Sbjct: 112 DPP 114
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 83.4 bits (207), Expect = 6e-22
Identities = 22/94 (23%), Positives = 46/94 (48%), Gaps = 7/94 (7%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
S+ +++V ++ F+ ++ F G + ++ + K KG V+++ PE A+
Sbjct: 5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE 62
Query: 101 LSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQA 134
+ MNG+ L GR I V++ R ++ P +
Sbjct: 63 RACRMMNGMKLSGREID-----VRIDRNASGPSS 91
>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 = 83.5 bits (207), Expect = 8e-22
Identities = 21/75 (28%), Positives = 43/75 (57%), Gaps = 8/75 (10%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++V +++ + E+ + +AF FG ++ + +K K +AF+ +D + A ++E+
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERDGAVKAMEE 64
Query: 106 MNGVMLGGRNIKVHF 120
MNG L G NI++ F
Sbjct: 65 MNGKDLEGENIEIVF 79
Score = 25.7 bits (57), Expect = 4.4
Identities = 4/19 (21%), Positives = 11/19 (57%)
Query: 148 YNRIYVASIHPDLTEEDIK 166
++V ++ +TEE ++
Sbjct: 11 VKVLFVRNLANTVTEEILE 29
>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 = 85.4 bits (212), Expect = 1e-21
Identities = 27/127 (21%), Positives = 51/127 (40%), Gaps = 16/127 (12%)
Query: 42 NSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPIT--QKHKGFAFVEYDIPEAA 99
+ ++++VG + E +R+ F +G + IN+ D + KG FV + +AA
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 100 QLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPD 159
+ ++ + + P M A S + E+ KL ++ I
Sbjct: 61 LEAQNALHNMKVLPGMHH----------PIQMKPADSEKNNAVEDRKL----FIGMISKK 106
Query: 160 LTEEDIK 166
TE DI+
Sbjct: 107 CTENDIR 113
Score = 77.3 bits (191), Expect = 1e-18
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G IS + E+ IR F FG I+ + P +G AFV + AQ +++
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKA 155
Query: 106 MNGVML---GGRNIKVHF 120
M+ + V F
Sbjct: 156 MHQAQTMEGCSSPMVVKF 173
>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 = 84.5 bits (210), Expect = 2e-21
Identities = 22/82 (26%), Positives = 44/82 (53%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
+S+ ++VG ++ + ++T+R AF F S ++ WD T +G+ FV +
Sbjct: 80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ 139
Query: 97 EAAQLSLEQMNGVMLGGRNIKV 118
+ AQ +++ M G L GR +++
Sbjct: 140 DDAQNAMDSMQGQDLNGRPLRI 161
Score = 80.3 bits (199), Expect = 6e-20
Identities = 25/120 (20%), Positives = 55/120 (45%), Gaps = 17/120 (14%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG++ + ED ++Q F GPI +I + D K+ +AFVEY A ++L+ +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 107 NGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIK 166
NG + +K+++ + + ++V ++ ++ +E ++
Sbjct: 62 NGKQIENNIVKINWAF----QSQQSSSDDT------------FNLFVGDLNVNVDDETLR 105
>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 = 82.4 bits (204), Expect = 2e-21
Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFG-PIKSINMSWDPITQKHKGFAFVEYDIPEA 98
+S +++G + + E+ I +AF G + S+ + + +T G+ FVE+
Sbjct: 5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT 64
Query: 99 AQLSLEQMNGVMLGGRNIKVHF 120
A+ L ++NG L G F
Sbjct: 65 AEKCLHKINGKPLPGATPAKRF 86
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 82.3 bits (204), Expect = 2e-21
Identities = 21/87 (24%), Positives = 47/87 (54%), Gaps = 5/87 (5%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
++VYVG++ + + +AF +GP++++ ++ +P GFAFVE++ P A+ ++
Sbjct: 1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVR 55
Query: 105 QMNGVMLGGRNIKVHFPHVQVGRPSNM 131
++G ++ G ++V R
Sbjct: 56 GLDGKVICGSRVRVELSTGMPRRSRFD 82
Score = 25.3 bits (56), Expect = 5.0
Identities = 2/17 (11%), Positives = 10/17 (58%)
Query: 150 RIYVASIHPDLTEEDIK 166
++YV ++ + +++
Sbjct: 2 KVYVGNLGTGAGKGELE 18
>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 = 81.9 bits (203), Expect = 3e-21
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 6/74 (8%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YV ++ E+ I + F P +K + +AFV + E A +++ +
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYAFVHFSNREDAVEAMKAL 71
Query: 107 NGVMLGGRNIKVHF 120
NG +L G I+V
Sbjct: 72 NGKVLDGSPIEVTL 85
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 82.3 bits (204), Expect = 3e-21
Identities = 20/75 (26%), Positives = 42/75 (56%), Gaps = 8/75 (10%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
R++V +++E + + F PFGP+K + + GFAFVE++ E+A ++E+
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEE 84
Query: 106 MNGVMLGGRNIKVHF 120
++G + ++V +
Sbjct: 85 VHGKSFANQPLEVVY 99
Score = 28.8 bits (65), Expect = 0.36
Identities = 7/40 (17%), Positives = 14/40 (35%)
Query: 127 RPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIK 166
S + S + E R++V D+ E ++
Sbjct: 10 HSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELN 49
>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 = 82.5 bits (204), Expect = 3e-21
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
VYVG++ + + F G I I + D + KG+A++E+ + ++
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA- 96
Query: 106 MNGVMLGGRNIKV 118
M+ + GR IKV
Sbjct: 97 MDETVFRGRTIKV 109
>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 = 81.0 bits (201), Expect = 4e-21
Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
+ ++ S +YVG++ + + + F G + + + D + KGFA++E+
Sbjct: 2 MEADARS---IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK 58
Query: 97 EAAQLSLEQMNGVMLGGRNIKV 118
E+ + SL ++ + GR IKV
Sbjct: 59 ESVRTSLA-LDESLFRGRQIKV 79
>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 = 81.1 bits (201), Expect = 5e-21
Identities = 19/89 (21%), Positives = 39/89 (43%), Gaps = 8/89 (8%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
S+ +++++G++ E E IR F +G + ++ K + FV + AA+
Sbjct: 5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDKTAAE 56
Query: 101 LSLEQMNGVMLGGRNIKVHFPHVQVGRPS 129
++ ++ L G NI V + S
Sbjct: 57 DAIRNLHHYKLHGVNINVEASKNKSKASS 85
>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 81.6 bits (202), Expect = 5e-21
Identities = 15/72 (20%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
V+ ++ ++ + F G ++ + + D +++ KG A+VE+ ++ L++ +
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-L 86
Query: 107 NGVMLGGRNIKV 118
G L G I V
Sbjct: 87 TGQRLLGVPIIV 98
>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 = 81.1 bits (201), Expect = 5e-21
Identities = 17/90 (18%), Positives = 38/90 (42%), Gaps = 8/90 (8%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+ + +++VG+IS +R F +GP+ ++ K +AFV + E A
Sbjct: 6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDI--------VKDYAFVHMERAEDA 57
Query: 100 QLSLEQMNGVMLGGRNIKVHFPHVQVGRPS 129
++ ++ G+ + V ++ S
Sbjct: 58 VEAIRGLDNTEFQGKRMHVQLSTSRLRTAS 87
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 81.7 bits (202), Expect = 6e-21
Identities = 22/89 (24%), Positives = 42/89 (47%), Gaps = 8/89 (8%)
Query: 38 DVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKS--------INMSWDPITQKHKGFA 89
+ +++ ++V + + +++ F G IK+ IN+ D T K KG A
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 90 FVEYDIPEAAQLSLEQMNGVMLGGRNIKV 118
V +D P +A+ +++ +G G IKV
Sbjct: 61 TVSFDDPPSAKAAIDWFDGKEFSGNPIKV 89
Score = 25.1 bits (55), Expect = 7.3
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 149 NRIYVASIHPDLTEEDIK 166
N I+V + ++T E +
Sbjct: 8 NTIFVQGLGENVTIESVA 25
>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 = 80.3 bits (199), Expect = 1e-20
Identities = 18/90 (20%), Positives = 38/90 (42%), Gaps = 8/90 (8%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+S + +++VG++S +R F G + ++ K +AFV + A
Sbjct: 5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDV--------VKDYAFVHMEKEADA 56
Query: 100 QLSLEQMNGVMLGGRNIKVHFPHVQVGRPS 129
+ ++ Q+NG + G+ I V +
Sbjct: 57 KAAIAQLNGKEVKGKRINVELSTKGQKKSG 86
>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 = 80.4 bits (199), Expect = 2e-20
Identities = 15/91 (16%), Positives = 37/91 (40%), Gaps = 1/91 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
V+V ++ +++ +++ F G + ++ D K +G V ++ A ++
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISM 75
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQS 136
NG +L R + V + + P +
Sbjct: 76 FNGQLLFDRPMHVKMDERALPKGDFFPPERP 106
>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 = 79.1 bits (196), Expect = 3e-20
Identities = 20/73 (27%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+YVG++ + + +++ F FG + ++ + +D T+K KGF FVE E+ ++ +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 106 MNGVMLGGRNIKV 118
++ GR I+V
Sbjct: 62 LDNTDFMGRTIRV 74
>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 = 79.3 bits (196), Expect = 3e-20
Identities = 24/101 (23%), Positives = 45/101 (44%), Gaps = 6/101 (5%)
Query: 36 TPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDI 95
+ + + +++++G I L E ++ F FG I + + D T HKG AF+ Y
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
Query: 96 PEAAQLSLEQMNG---VMLGGRNIKVHF--PHVQVG-RPSN 130
E+A + ++ + R I+V + G PS+
Sbjct: 65 RESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSGPSS 105
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 78.8 bits (195), Expect = 5e-20
Identities = 24/82 (29%), Positives = 44/82 (53%), Gaps = 2/82 (2%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
++ + P YVG++ F + I F I+S+ + D T K KGF +VE+D
Sbjct: 8 KELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEV 66
Query: 97 EAAQLSLEQMNGVMLGGRNIKV 118
++ + +L +G +LG R+++V
Sbjct: 67 DSLKEALT-YDGALLGDRSLRV 87
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 78.5 bits (194), Expect = 6e-20
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 47 VYVGSISFELKEDTIRQAFLPFG--PIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
+ + +I+ D+I A P+ + +I + D TQ+++GFAFV+ A L+
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 105 QMNGV----MLGGRNIKVHF 120
+ + + G+ I V F
Sbjct: 72 ILQSLHPPLKIDGKTIGVDF 91
>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 = 84.5 bits (208), Expect = 6e-20
Identities = 23/128 (17%), Positives = 53/128 (41%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
P+ ++ ++V ++++ E +R+ F +GPIK I+M + + K +G+AF+EY+
Sbjct: 95 PNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE 154
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASI 156
+ + +G + GR + V + + + + N +
Sbjct: 155 RDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRD 214
Query: 157 HPDLTEED 164
+E
Sbjct: 215 DTSRYDER 222
Score = 30.2 bits (67), Expect = 0.30
Identities = 5/19 (26%), Positives = 12/19 (63%)
Query: 148 YNRIYVASIHPDLTEEDIK 166
+ ++VA ++ D TE ++
Sbjct: 102 FKTLFVARVNYDTTESKLR 120
>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 = 78.1 bits (193), Expect = 1e-19
Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 8/95 (8%)
Query: 32 VGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKS--------INMSWDPITQ 83
+G + + ++V + + +++ F G IK+ IN+ D T
Sbjct: 1 MGHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETG 60
Query: 84 KHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKV 118
K KG A V +D P +A+ +++ +G G IKV
Sbjct: 61 KLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKV 95
Score = 25.0 bits (55), Expect = 6.7
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 149 NRIYVASIHPDLTEEDIK 166
N I+V + ++T E +
Sbjct: 14 NTIFVQGLGENVTIESVA 31
>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 = 77.7 bits (192), Expect = 1e-19
Identities = 19/88 (21%), Positives = 43/88 (48%), Gaps = 9/88 (10%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQA----FLPFGPIKSINMSWDPITQKHKGFAFVE 92
P+ N +Y+ +++ ++K+D ++++ F FG I I + + K +G AFV
Sbjct: 3 PETRPNH--TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV---SRSLKMRGQAFVI 57
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
+ +A +L M G + +++ +
Sbjct: 58 FKEVSSATNALRSMQGFPFYDKPMRIQY 85
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 77.1 bits (190), Expect = 1e-19
Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSIN-MSWDPI----TQKHKGFAFVEYDIPEAAQ 100
R+YVG+I F + E+ + F + + +P+ + K FAF+E+ +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 101 LSLEQMNGVMLGGRNIKVHFP 121
++ +G++ G+++K+ P
Sbjct: 68 QAM-AFDGIIFQGQSLKIRRP 87
Score = 29.3 bits (66), Expect = 0.18
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 150 RIYVASIHPDLTEEDIK 166
R+YV +I +TEE +
Sbjct: 8 RLYVGNIPFGITEEAMM 24
>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 = 76.9 bits (190), Expect = 2e-19
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 8/84 (9%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
R++VG + + + F FG I++I+ K FA+++Y+ +AAQ + +
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDH------VKGDSFAYIQYESLDAAQAACAK 72
Query: 106 MNGVMLGG--RNIKVHFPHVQVGR 127
M G LGG R ++V F
Sbjct: 73 MRGFPLGGPDRRLRVDFAKSGPSS 96
>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 = 77.1 bits (190), Expect = 4e-19
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKS--------INMSWDPITQKHKGFAFVEYDIPE 97
+YV ++ + D + F G +K I++ D T K KG A V Y+ P
Sbjct: 17 AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76
Query: 98 AAQLSLEQMNGVMLGGRNIKV 118
A+ ++E +G G +KV
Sbjct: 77 TAKAAVEWFDGKDFQGSKLKV 97
Score = 25.4 bits (56), Expect = 6.1
Identities = 5/18 (27%), Positives = 11/18 (61%)
Query: 149 NRIYVASIHPDLTEEDIK 166
+ IYV ++ +T +D+
Sbjct: 16 SAIYVQGLNDSVTLDDLA 33
>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 = 76.2 bits (188), Expect = 4e-19
Identities = 19/75 (25%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+YVG + + E +R F FG I++I + + AF+++ +AA+++ E+
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68
Query: 107 -NGVMLGGRNIKVHF 120
N +++ GR + V +
Sbjct: 69 FNKLIVNGRRLNVKW 83
Score = 25.7 bits (57), Expect = 3.2
Identities = 5/16 (31%), Positives = 10/16 (62%)
Query: 151 IYVASIHPDLTEEDIK 166
+YV + +TE D++
Sbjct: 15 LYVGGLGDTITETDLR 30
>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 = 76.6 bits (189), Expect = 5e-19
Identities = 20/85 (23%), Positives = 41/85 (48%), Gaps = 9/85 (10%)
Query: 46 RVYVGSISFEL-KEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
RV++G+++ L K+ + F +G + ++ HKG+AFV+Y A+ ++
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80
Query: 105 QMNGVMLGGRNIKVHFPHVQVGRPS 129
NG +L G+ + ++ S
Sbjct: 81 GENGRVLAGQTLDINMAGEPKPDRS 105
>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 = 77.6 bits (192), Expect = 6e-19
Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 1/83 (1%)
Query: 36 TPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDI 95
P + +++VG I +++ + F +G I + D T + +GF FV YD
Sbjct: 79 IPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDS 138
Query: 96 PEAAQLSLEQMNGVMLGGRNIKV 118
+A + + R I++
Sbjct: 139 ADAVDRVCQN-KFIDFKDRKIEI 160
Score = 73.7 bits (182), Expect = 2e-17
Identities = 22/121 (18%), Positives = 54/121 (44%), Gaps = 20/121 (16%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G ++++ ED +R+ F +G + + + DP T + +GF F+ ++ P + ++
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDI 165
+ +L G+ I + R +I+V I PD+ ++
Sbjct: 65 QH--ILDGKVIDPKRA---IPRDEQDKT---------------GKIFVGGIGPDVRPKEF 104
Query: 166 K 166
+
Sbjct: 105 E 105
>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 = 74.6 bits (184), Expect = 3e-18
Identities = 17/83 (20%), Positives = 45/83 (54%), Gaps = 3/83 (3%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPI-TQKHKGFAFVEYDI 95
+ + P ++G++ +++ E++I++ F I ++ + +P ++ KGF + E++
Sbjct: 8 SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED 66
Query: 96 PEAAQLSLEQMNGVMLGGRNIKV 118
++ +L +N LG + I+V
Sbjct: 67 LDSLLSALS-LNEESLGNKRIRV 88
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 74.6 bits (184), Expect = 3e-18
Identities = 20/91 (21%), Positives = 39/91 (42%), Gaps = 4/91 (4%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G + +++VG ++ + E+ + + F PFG I + P KG AFV+
Sbjct: 4 GSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVK 62
Query: 93 YDIPEAAQLSLEQMNGVML---GGRNIKVHF 120
+ AQ ++ ++G ++ V F
Sbjct: 63 FSSHTEAQAAIHALHGSQTMPGASSSLVVKF 93
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 74.0 bits (182), Expect = 3e-18
Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 3/81 (3%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
++ + +I L+ + + + +G ++S T V Y + A+
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV---NTDSETAVVNVTYSSKDQAR 68
Query: 101 LSLEQMNGVMLGGRNIKVHFP 121
+L+++NG L +KV +
Sbjct: 69 QALDKLNGFQLENFTLKVAYI 89
Score = 25.9 bits (57), Expect = 3.6
Identities = 4/18 (22%), Positives = 9/18 (50%)
Query: 149 NRIYVASIHPDLTEEDIK 166
++ + +I P L E +
Sbjct: 16 RKLQIRNIPPHLQWEVLD 33
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 73.8 bits (182), Expect = 3e-18
Identities = 17/99 (17%), Positives = 44/99 (44%), Gaps = 9/99 (9%)
Query: 35 ITPDVNSNSPLRVYVGSISFE-LKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEY 93
+T N R+++G++ + + ++ + + F P+G I IN+ F F+++
Sbjct: 1 MTEMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQF 52
Query: 94 DIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMP 132
D P++ + ++E + M G+ + + +
Sbjct: 53 DNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQFDHG 91
>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 = 74.2 bits (183), Expect = 4e-18
Identities = 13/79 (16%), Positives = 27/79 (34%), Gaps = 1/79 (1%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
P +Y+ ++ + E + PFG + S + D + +G F + E
Sbjct: 21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKC 79
Query: 100 QLSLEQMNGVMLGGRNIKV 118
+ + NG +
Sbjct: 80 EAVIGHFNGKFIKTPPGVS 98
>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 = 73.4 bits (181), Expect = 5e-18
Identities = 18/79 (22%), Positives = 43/79 (54%), Gaps = 3/79 (3%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQ-KHKGFAFVEYDIPEAA 99
+ P ++G++ +++ E++I++ F I ++ + +P + KGF + E++ ++
Sbjct: 16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSL 74
Query: 100 QLSLEQMNGVMLGGRNIKV 118
+L +N LG R I+V
Sbjct: 75 LSALS-LNEESLGNRRIRV 92
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 73.1 bits (180), Expect = 8e-18
Identities = 16/83 (19%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 41 SNSPLRVYVGSISFE-LKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
S+ R+++G++ + + ++ + + F P+G I IN+ F F+++D P++
Sbjct: 19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSV 70
Query: 100 QLSLEQMNGVMLGGRNIKVHFPH 122
+ ++E + M G+ + +
Sbjct: 71 RDAIEXESQEMNFGKKLILEVSS 93
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 76.7 bits (189), Expect = 8e-18
Identities = 18/130 (13%), Positives = 52/130 (40%), Gaps = 30/130 (23%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
+ R++VG++ ++ E+ ++ F +G + + + +GF F+ +
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESR 68
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASI 156
A+++ +++G +L R +++ F A + V ++
Sbjct: 69 TLAEIAKAELDGTILKSRPLRIRF-------------ATHG-----------AALTVKNL 104
Query: 157 HPDLTEEDIK 166
P ++ E ++
Sbjct: 105 SPVVSNELLE 114
Score = 71.6 bits (176), Expect = 7e-16
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 2/74 (2%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+ V ++S + + + QAF FGP++ + D + G FVE+ A+ +LE+
Sbjct: 98 ALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALER 156
Query: 106 MNGVM-LGGRNIKV 118
L +
Sbjct: 157 CGDGAFLLTTTPRP 170
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 72.2 bits (177), Expect = 2e-17
Identities = 22/95 (23%), Positives = 42/95 (44%), Gaps = 6/95 (6%)
Query: 31 QVGPITPDVNSNSPLR-VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFA 89
GP +P VYVG++ + + +++A G + + ++W Q + A
Sbjct: 5 SSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-PLRLTW----QGPRRRA 59
Query: 90 FVEYDIPEAAQLSLEQMNGVMLGGRNIKVHFPHVQ 124
F+ Y AAQ ++ + G+ LG ++V Q
Sbjct: 60 FLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94
>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 = 73.3 bits (180), Expect = 2e-17
Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSW-----DPITQKHKGFAFVEYDIPEAAQ 100
R+YV +++ ++E ++ F + S + KG AF+ +AA
Sbjct: 47 RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106
Query: 101 LSLEQMNGVMLGGRNIKVHF 120
+L++ NG +L G+ + V F
Sbjct: 107 KALKEANGYVLFGKPMVVQF 126
Score = 27.1 bits (60), Expect = 1.8
Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 7/69 (10%)
Query: 98 AAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIH 157
++M + R + + GR S + E + RIYV ++
Sbjct: 2 PLGSDSDEMPSECISRREL-------EKGRISREEMETLSVFRSYEPGEPNCRIYVKNLA 54
Query: 158 PDLTEEDIK 166
+ E+D+K
Sbjct: 55 KHVQEKDLK 63
>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 = 71.9 bits (177), Expect = 2e-17
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 3/75 (4%)
Query: 44 PLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSL 103
P V+VG I + E IR F +G +K + + D T KG+ FV + Q +
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIV 67
Query: 104 EQMNGVMLGGRNIKV 118
E + + G+ +K+
Sbjct: 68 E--SQINFHGKKLKL 80
Score = 26.0 bits (58), Expect = 2.8
Identities = 7/25 (28%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 143 EEAKL-YNRIYVASIHPDLTEEDIK 166
E K+ N ++V I + E +I+
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIR 27
>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 = 73.9 bits (182), Expect = 3e-17
Identities = 22/101 (21%), Positives = 45/101 (44%), Gaps = 3/101 (2%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
+ +++VG I + +E +R F +G I+ I + D + K +GFAFV +D
Sbjct: 97 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 156
Query: 97 EAAQLSLEQMNGVMLGGRNIKVHF--PHVQVGRPSNMPQAQ 135
++ + Q + G N +V ++ S+ + +
Sbjct: 157 DSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMASASSSQRGR 196
Score = 73.1 bits (180), Expect = 8e-17
Identities = 25/127 (19%), Positives = 51/127 (40%), Gaps = 13/127 (10%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
++++G +SFE ++++R F +G + + DP T++ +GF FV Y E
Sbjct: 9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Query: 100 QLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPD 159
++ + GR ++ V R + + +I+V I D
Sbjct: 69 DAAMNA-RPHKVDGRVVEPKRA---VSREDSQRPGAHLTV---------KKIFVGGIKED 115
Query: 160 LTEEDIK 166
E ++
Sbjct: 116 TEEHHLR 122
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 71.9 bits (176), Expect = 4e-17
Identities = 17/94 (18%), Positives = 38/94 (40%), Gaps = 9/94 (9%)
Query: 31 QVGPITPDVNSNSPLRVYVGSISFELKEDTIRQA----FLPFGPIKSINMSWDPITQKHK 86
+G P + V + +I+ E+ ++ ++ G I I + ++ +
Sbjct: 18 DLGSTPPHTEPSQ--VVLITNINPEVPKEKLQALLYALASSQGDILDIVV---DLSDDNS 72
Query: 87 GFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
G A++ + E+AQ +E G G + + F
Sbjct: 73 GKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF 106
>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 = 70.4 bits (173), Expect = 7e-17
Identities = 17/89 (19%), Positives = 37/89 (41%), Gaps = 4/89 (4%)
Query: 33 GPITPDVNSNSP--LRVYVGSISFELKEDTIRQAFLPFGPIK-SINMSWDPITQKHKGFA 89
+ +S P + V ++ F + D I F + I S+ + ++ G A
Sbjct: 2 SSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEA 60
Query: 90 FVEYDIPEAAQLSLEQMNGVMLGGRNIKV 118
V ++ + A ++ +N +G R +K+
Sbjct: 61 MVAFESRDEATAAVIDLNDRPIGSRKVKL 89
>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 = 71.0 bits (174), Expect = 8e-17
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 4/79 (5%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGP-IKSINMSWDP-ITQKHKGFAFVEYDIPEAAQLSL 103
R+++G I K + I + + + + K++GFAFVEY+ AA ++
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 104 EQMN--GVMLGGRNIKVHF 120
++ + L G I V +
Sbjct: 70 RKLMPGRIQLWGHQIAVDW 88
Score = 26.7 bits (59), Expect = 1.8
Identities = 4/18 (22%), Positives = 8/18 (44%)
Query: 149 NRIYVASIHPDLTEEDIK 166
R+++ I E+I
Sbjct: 9 CRLFIGGIPKMKKREEIL 26
>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 = 70.4 bits (173), Expect = 1e-16
Identities = 16/85 (18%), Positives = 34/85 (40%), Gaps = 2/85 (2%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIK-SINMSWDPITQKHKGFAFVEYDI 95
P + V ++ F + D I F + I S+ + ++ G A V ++
Sbjct: 8 ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMVAFES 66
Query: 96 PEAAQLSLEQMNGVMLGGRNIKVHF 120
+ A ++ +N +G R +K+
Sbjct: 67 RDEATAAVIDLNDRPIGSRKVKLVL 91
>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 = 69.9 bits (171), Expect = 2e-16
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 6/80 (7%)
Query: 47 VYVGSISFELKEDTI---RQAFLPFGPIKSINMSWDPIT---QKHKGFAFVEYDIPEAAQ 100
V+V +S L + + + F FG I + ++ Q A+V Y E A
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 101 LSLEQMNGVMLGGRNIKVHF 120
+++ +N V++ GR +K
Sbjct: 78 RAIQCVNNVVVDGRTLKASL 97
>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 99
Score = 69.1 bits (170), Expect = 2e-16
Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++VG I E +R+ F FG + + M +D Q+ +GF F+ ++ ++ ++
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN- 70
Query: 106 MNGVMLGGRNIKV 118
M+ + G+ ++V
Sbjct: 71 MHFHDIMGKKVEV 83
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 67.5 bits (165), Expect = 1e-15
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 2/72 (2%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
VY+ + D I++ G + +I M + KG FV +D E+A+ +E
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-T 71
Query: 107 NGVMLGGRNIKV 118
G ++ +
Sbjct: 72 PGQKYKETDLLI 83
>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 = 67.1 bits (164), Expect = 2e-15
Identities = 19/99 (19%), Positives = 40/99 (40%), Gaps = 10/99 (10%)
Query: 36 TPDVNSNSPLRV-YVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYD 94
+ + S V +V + + E + +A FG I + M K A VE++
Sbjct: 6 SGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFE 59
Query: 95 IPEAAQ--LSLEQMNGVMLGGRNIKVHFP-HVQVGRPSN 130
++A+ ++ V + G+ ++ ++ RP N
Sbjct: 60 NIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGN 98
>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 = 66.0 bits (162), Expect = 2e-15
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++VG +S + E+ IR+ F FG ++SI + D T K +GF F+ + E + +E+
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 106 MNGVMLGGRNIKV 118
+G ++
Sbjct: 61 -KYHNVGLSKCEI 72
>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 = 66.9 bits (164), Expect = 3e-15
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++VG + + + ++R+ F FG I+ + D T K +G+ FV AA+ + +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 106 MNGVMLGGRNIKV 118
N + + GR V
Sbjct: 79 PNPI-IDGRKANV 90
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 66.0 bits (161), Expect = 5e-15
Identities = 22/93 (23%), Positives = 44/93 (47%), Gaps = 9/93 (9%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ--LSLE 104
+++ + ++ E + LPFG + ++ M K K AF+E + EAA ++
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLM------LKGKNQAFIEMNTEEAANTMVNYY 72
Query: 105 QMNGVMLGGRNIKVHF-PHVQVGRPSNMPQAQS 136
+L G+ I + F H ++ S+ QA++
Sbjct: 73 TSVTPVLRGQPIYIQFSNHKELKTDSSPNQARA 105
>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 = 66.1 bits (161), Expect = 7e-15
Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 9/92 (9%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE-- 104
+++ + ++ E + LPFG + ++ M K K AF+E + EAA +
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLM------LKGKNQAFIEMNTEEAANTMVNYY 87
Query: 105 QMNGVMLGGRNIKVHF-PHVQVGRPSNMPQAQ 135
+L G+ I + F H ++ S+ QA+
Sbjct: 88 TSVTPVLRGQPIYIQFSNHKELKTDSSPNQAR 119
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 65.4 bits (160), Expect = 8e-15
Identities = 14/81 (17%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFL-PFGPIKSINMSWDPITQKHKGFAFVEYDIPEA 98
+S ++VG ++ ++ + + + F+ + + + D T KG+ FV++
Sbjct: 5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELE 63
Query: 99 AQLSLEQMNGVM-LGGRNIKV 118
+ +L + G + LG + +++
Sbjct: 64 QKRALTECQGAVGLGSKPVRL 84
>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 = 67.6 bits (165), Expect = 8e-15
Identities = 25/138 (18%), Positives = 56/138 (40%), Gaps = 23/138 (16%)
Query: 47 VYVGSISFE-LKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+ V +++ E + ++ F +G ++ + + ++ K A V+ AQL++
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60
Query: 106 MNGVMLGGRNIKVHF-PHVQVGRPSNMPQAQSV----------------IDEITEEAKLY 148
+NG L G+ I++ H V P + Q +
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120
Query: 149 NRIYVASIHPDLTEEDIK 166
+++++I P ++EED+K
Sbjct: 121 ATLHLSNIPPSVSEEDLK 138
Score = 63.4 bits (154), Expect = 3e-13
Identities = 19/104 (18%), Positives = 43/104 (41%), Gaps = 5/104 (4%)
Query: 18 TYPFLSTPLYDLKQVGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMS 77
T + ++PL+ K+ G +++ +I + E+ ++ F G + +
Sbjct: 94 TKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGV----VK 149
Query: 78 WDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLG-GRNIKVHF 120
QK + A ++ E A +L ++ LG +++V F
Sbjct: 150 GFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF 193
>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 = 67.8 bits (165), Expect = 8e-15
Identities = 10/106 (9%), Positives = 30/106 (28%)
Query: 15 TKCTYPFLSTPLYDLKQVGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSI 74
+ F + + + ++ + E+ E+ + G +
Sbjct: 94 SCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPT 153
Query: 75 NMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
++ + +E+D A +L +N + N +
Sbjct: 154 SVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 199
Score = 62.4 bits (151), Expect = 1e-12
Identities = 21/140 (15%), Positives = 42/140 (30%), Gaps = 25/140 (17%)
Query: 47 VYVGSISFE-LKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+ V + + D + F +G ++ + + G A VE A ++
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVK-----FMKSKPGAAMVEMADGYAVDRAITH 61
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQS------------VIDEITEEAKLYNRI-- 151
+N + G+ + V P + T E NRI
Sbjct: 62 LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQH 121
Query: 152 -----YVASIHPDLTEEDIK 166
+ + ++TEE+
Sbjct: 122 PSNVLHFFNAPLEVTEENFF 141
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 64.4 bits (158), Expect = 8e-15
Identities = 14/73 (19%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++VG +S + ++ F FG + + +D T +H+GF FV ++ + + E
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE- 59
Query: 106 MNGVMLGGRNIKV 118
++ + + ++
Sbjct: 60 IHFHEINNKMVEC 72
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 64.0 bits (156), Expect = 2e-14
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 2/68 (2%)
Query: 49 VGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNG 108
VG E ++ I + F FG I + + K KG+ F+EY P A +++ +G
Sbjct: 12 VGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADG 69
Query: 109 VMLGGRNI 116
L ++
Sbjct: 70 YKLDKQHT 77
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 64.4 bits (157), Expect = 2e-14
Identities = 18/86 (20%), Positives = 34/86 (39%), Gaps = 8/86 (9%)
Query: 37 PDVNSNSPLRVYVGSI------SFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAF 90
P + V ++ E ++ I + F FG I + + K KG+ F
Sbjct: 8 PQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIF 65
Query: 91 VEYDIPEAAQLSLEQMNGVMLGGRNI 116
+EY P A +++ +G L ++
Sbjct: 66 LEYASPAHAVDAVKNADGYKLDKQHT 91
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 66.9 bits (163), Expect = 2e-14
Identities = 24/138 (17%), Positives = 56/138 (40%), Gaps = 23/138 (16%)
Query: 47 VYVGSISFE-LKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+ V +++ E + ++ F +G ++ + + + K A V+ AQL++
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILF-----NKKENALVQMADGNQAQLAMSH 91
Query: 106 MNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKL-----------------Y 148
+NG L G+ I++ Q + Q + + + L
Sbjct: 92 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 151
Query: 149 NRIYVASIHPDLTEEDIK 166
+++++I P ++EED+K
Sbjct: 152 ATLHLSNIPPSVSEEDLK 169
Score = 61.6 bits (149), Expect = 3e-12
Identities = 19/107 (17%), Positives = 42/107 (39%), Gaps = 5/107 (4%)
Query: 15 TKCTYPFLSTPLYDLKQVGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSI 74
T + ++PL+ K+ G +++ +I + E+ ++ F G +
Sbjct: 122 QGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKG 181
Query: 75 NMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLG-GRNIKVHF 120
QK + A ++ E A +L ++ LG +++V F
Sbjct: 182 ----FKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF 224
>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 = 64.1 bits (156), Expect = 3e-14
Identities = 13/101 (12%), Positives = 31/101 (30%), Gaps = 7/101 (6%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+ ++ I++ F FG + + + + A VE+ P A+ + +
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFRHL 66
Query: 107 NGVMLGGRNIKVHF-PHVQVGRPSNMPQAQSVIDEITEEAK 146
+ + + P G +Q E+
Sbjct: 67 AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESG 107
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 63.6 bits (155), Expect = 4e-14
Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 9/86 (10%)
Query: 38 DVNSNSPLRV-YVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
D + V ++ + + E + +A FGPI + + K A VE++
Sbjct: 14 DPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVV------MPKKRQALVEFEDV 67
Query: 97 EAAQLSLEQM--NGVMLGGRNIKVHF 120
A ++ N + + G V++
Sbjct: 68 LGACNAVNYAADNQIYIAGHPAFVNY 93
>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 = 63.2 bits (154), Expect = 5e-14
Identities = 12/80 (15%), Positives = 29/80 (36%), Gaps = 7/80 (8%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
S+ + V ++ + + + +K ++K AFV E AQ
Sbjct: 2 SSGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCY------VDRNKRTAFVTLLNGEQAQ 54
Query: 101 LSLEQMNGVMLGGRNIKVHF 120
+++ + G+++ V
Sbjct: 55 NAIQMFHQYSFRGKDLIVQL 74
>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 = 63.4 bits (155), Expect = 5e-14
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 2/72 (2%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQM 106
+ V + ++ E +++ F FG + + + D T KGF FV + E + Q
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 107 NGVMLGGRNIKV 118
+ M+ GR
Sbjct: 78 H--MIDGRWCDC 87
>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 = 66.4 bits (161), Expect = 6e-14
Identities = 19/89 (21%), Positives = 43/89 (48%), Gaps = 9/89 (10%)
Query: 36 TPDVNSNSPLRVYVGSISFELKEDTIRQA----FLPFGPIKSINMSWDPITQKHKGFAFV 91
P+ N +Y+ +++ ++K+D ++++ F FG I I + + K +G AFV
Sbjct: 3 VPETRPNH--TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILV---SRSLKMRGQAFV 57
Query: 92 EYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
+ +A +L M G + +++ +
Sbjct: 58 IFKEVSSATNALRSMQGFPFYDKPMRIQY 86
Score = 54.1 bits (129), Expect = 2e-09
Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 48 YVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMN 107
++ ++ E E + F F K + + AFVE+D A + + +
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRL-----VPGRHDIAFVEFDNEVQAGAARDALQ 265
Query: 108 GVMLGGRN-IKVHF 120
G + N +K+ F
Sbjct: 266 GFKITQNNAMKISF 279
>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 = 63.4 bits (154), Expect = 6e-14
Identities = 14/101 (13%), Positives = 37/101 (36%), Gaps = 13/101 (12%)
Query: 40 NSNSPLR---VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
+ + V G + + + + G + ++ M +K ++F Y
Sbjct: 20 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM------PPNKPYSFARYRTT 73
Query: 97 EAAQLSLEQMNGVML---GGRNIKVHFPHVQVGRPSNMPQA 134
E ++ + +NG + G+ I ++ V+ + P +
Sbjct: 74 EESKRAYVTLNGKEVVDDLGQKITLYLNFVE-KVQWSGPSS 113
>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 = 62.4 bits (152), Expect = 1e-13
Identities = 15/88 (17%), Positives = 37/88 (42%), Gaps = 3/88 (3%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIK-SINMSWDPITQKHKGFAFV 91
G +++ + ++ +I F + + + Q + ++++ D + G A V
Sbjct: 4 GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALV 62
Query: 92 EYDIPEAAQLSLEQMNGVMLGGRNIKVH 119
++ + A+ S ++ L GR VH
Sbjct: 63 QFKNEDDARKSER-LHRKKLNGREAFVH 89
>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 = 62.6 bits (152), Expect = 3e-13
Identities = 18/86 (20%), Positives = 37/86 (43%), Gaps = 3/86 (3%)
Query: 33 GPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVE 92
G V S + V++ + ++ E+ I F P P+ +++ P + G A VE
Sbjct: 35 GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGP-DGRVTGEADVE 92
Query: 93 YDIPEAAQLSLEQMNGVMLGGRNIKV 118
+ E A ++ + + R I++
Sbjct: 93 FATHEEAVAAMS-KDRANMQHRYIEL 117
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kg0_A
Length = 126
Score = 62.2 bits (151), Expect = 3e-13
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 3/91 (3%)
Query: 30 KQVGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPI-KSINMSWDPITQKHKGF 88
+Q+G + +S + V + + F ++ I Q F + I + DP K G
Sbjct: 28 QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDP-EGKITGE 86
Query: 89 AFVEYDIPEAAQLSLEQMNGVMLGGRNIKVH 119
AFV++ E A+ +L + +G R I+V
Sbjct: 87 AFVQFASQELAEKALG-KHKERIGHRYIEVF 116
>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 = 61.0 bits (149), Expect = 3e-13
Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 1/84 (1%)
Query: 35 ITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYD 94
I N +++VG +S++ + ++ F FG + + DP T + +GF F+ +
Sbjct: 2 INASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK 61
Query: 95 IPEAAQLSLEQMNGVMLGGRNIKV 118
+ + L+Q L GR I
Sbjct: 62 DAASVEKVLDQKEHR-LDGRVIDP 84
>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 = 61.4 bits (149), Expect = 6e-13
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 3/80 (3%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIK-SINMSWDPITQKHKGFAFVEYDIPEAA 99
+ VY+ + FE + + F ++ SI +++ P K G FVE+
Sbjct: 22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP-NGKATGEGFVEFRNEADY 80
Query: 100 QLSLEQMNGVMLGGRNIKVH 119
+ +L + +G R I+VH
Sbjct: 81 KAALC-RHKQYMGNRFIQVH 99
>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 = 60.6 bits (147), Expect = 6e-13
Identities = 12/91 (13%), Positives = 29/91 (31%), Gaps = 7/91 (7%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+ S RV V + ++ G + ++ G VE+ E
Sbjct: 11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGVVEFVRKEDM 63
Query: 100 QLSLEQMNGVMLGGRNIKVHFPHVQVGRPSN 130
++ +++ + + V+V P +
Sbjct: 64 TYAVRKLDNTKFRSHEGETAYIRVKVDGPRS 94
>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 = 60.1 bits (146), Expect = 1e-12
Identities = 18/92 (19%), Positives = 39/92 (42%), Gaps = 4/92 (4%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
S + V++ + + E+ I F P P+ +++ P + G A VE+ E A
Sbjct: 12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAV 69
Query: 101 LSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMP 132
++ + + R +++ F + G + P
Sbjct: 70 AAMA-KDKANMQHRYVEL-FLNSTAGTSGSGP 99
>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 = 59.6 bits (145), Expect = 1e-12
Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+ + V + F + E + + P P +I + + G+ FV++ E
Sbjct: 6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPLKP-VAIRIVRNA-HGNKTGYIFVDFSNEEEV 63
Query: 100 QLSLEQMNGVMLGGRNIKVH 119
+ +L+ N +GGR I+V
Sbjct: 64 KQALK-CNREYMGGRYIEVF 82
>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 = 59.8 bits (145), Expect = 1e-12
Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 8/76 (10%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ--LSLE 104
+++ + E+ E + LPFG + +I M K K AF+E EAA ++
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILM------LKGKNQAFLELATEEAAITMVNYY 71
Query: 105 QMNGVMLGGRNIKVHF 120
L + I + +
Sbjct: 72 SAVTPHLRNQPIYIQY 87
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 62.5 bits (151), Expect = 1e-12
Identities = 33/176 (18%), Positives = 47/176 (26%), Gaps = 42/176 (23%)
Query: 1 TCCIVVTTTCCIVVTKCTY------------PFLSTPLYDLKQVGPITPDVNSNSPLR-- 46
C+ C + KC Y L T + D +
Sbjct: 71 FFCLFFAKGMCCLGPKCEYLHHIPDEEDIGKLALRTEVLDCFGREKFADYREDMGGIGSF 130
Query: 47 ------VYVGSISFELK---------EDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFV 91
+YVG I L E IR F G I I + K FV
Sbjct: 131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFV 184
Query: 92 EYDIPEAAQLSLEQMNGVMLGGRNIKVHFPH-------VQVGRPSNMPQAQSVIDE 140
++ A+ + E M+ L + K V+ P AQ + E
Sbjct: 185 KFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANEDPDPAAQKRLQE 240
>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 = 60.1 bits (146), Expect = 1e-12
Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
P + L V V + F E+ +R F + ++++ D ++ G V++ P
Sbjct: 9 PLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDH-VGRNNGNGLVKFLSP 66
Query: 97 EAAQLSLEQMNGVMLGGRNIKV 118
+ +L+ N +++ R ++V
Sbjct: 67 QDTFEALK-RNRMLMIQRYVEV 87
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 59.4 bits (144), Expect = 2e-12
Identities = 12/91 (13%), Positives = 29/91 (31%), Gaps = 7/91 (7%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+ S RV V + ++ G + ++ G VE+ E
Sbjct: 12 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGVVEFVRKEDM 64
Query: 100 QLSLEQMNGVMLGGRNIKVHFPHVQVGRPSN 130
++ +++ + + V+V P +
Sbjct: 65 TYAVRKLDNTKFRSHEGETAYIRVKVDGPRS 95
>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 = 58.6 bits (142), Expect = 4e-12
Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPIK-SINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
V + + F ++ I Q F + + + D + G AFV++ E A+ +L+
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDF-QGRSTGEAFVQFASQEIAEKALK- 75
Query: 106 MNGVMLGGRNIKVH 119
+ +G R I++
Sbjct: 76 KHKERIGHRYIEIF 89
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 57.5 bits (140), Expect = 4e-12
Identities = 17/73 (23%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G +S++ ++ +R+ F FG +K + DP+T++ +GF FV + L
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA- 60
Query: 106 MNGVMLGGRNIKV 118
+ L + I
Sbjct: 61 QSRHELDSKTIDP 73
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 57.7 bits (140), Expect = 7e-12
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 6/73 (8%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
V+V + + + FL FGP+ S+ M + FA VE A + L Q
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVM-----DKDKGVFAIVEMGDVGAREAVLSQ 64
Query: 106 MNGVMLGGRNIKV 118
+ LGG ++V
Sbjct: 65 -SQHSLGGHRLRV 76
>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 = 57.6 bits (140), Expect = 8e-12
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 1/73 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+++VG + + ++T+R F +G + + D T + +GF FV++ P L
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA- 76
Query: 106 MNGVMLGGRNIKV 118
L GRNI
Sbjct: 77 SRPHTLDGRNIDP 89
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 58.0 bits (140), Expect = 1e-11
Identities = 22/103 (21%), Positives = 39/103 (37%), Gaps = 14/103 (13%)
Query: 47 VYVGSISFELKEDTIRQAFLPFGPI----KSINMSWDPITQKHKGFAFVEYDIPEAAQLS 102
V + + F + + F PI + I P + G AFV + E AQ +
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNA 84
Query: 103 LEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEA 145
L + +LG R I++ S + Q V++ + +
Sbjct: 85 LR-KHKDLLGKRYIELF--------RSTAAEVQQVLNRFSSAS 118
>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 = 57.3 bits (139), Expect = 1e-11
Identities = 15/73 (20%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
++++G +SFE E+++R + +G + + DP +++ +GF FV + ++
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA- 87
Query: 106 MNGVMLGGRNIKV 118
+ GR ++
Sbjct: 88 ARPHSIDGRVVEP 100
>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 = 56.5 bits (137), Expect = 1e-11
Identities = 17/78 (21%), Positives = 37/78 (47%), Gaps = 7/78 (8%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
S+ V+VG + ++ ED +R+ F +G + + I + + FAFV + + AQ
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVF-----IPKPFRAFAFVTFADDQIAQ 56
Query: 101 LSLEQMNGVMLGGRNIKV 118
+ ++ G ++ +
Sbjct: 57 SLCGEDL--IIKGISVHI 72
>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 = 56.5 bits (137), Expect = 3e-11
Identities = 18/79 (22%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+S ++++G +S++ ++ +R+ F FG +K + DP+T++ +GF FV +
Sbjct: 21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 80
Query: 100 QLSLEQMNGVMLGGRNIKV 118
L + L + I
Sbjct: 81 DKVLA-QSRHELDSKTIDP 98
>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 = 56.2 bits (135), Expect = 6e-11
Identities = 13/101 (12%), Positives = 34/101 (33%), Gaps = 13/101 (12%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPF---GPIKSINMSWDPITQKHKGFAFVEYDIPE 97
V + + + + ++ ++ + + G AFVE +
Sbjct: 41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR-EGRQSGEAFVELGSED 99
Query: 98 AAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVI 138
+++L+ + +G R I+V S+ + V+
Sbjct: 100 DVKMALK-KDRESMGHRYIEVF--------KSHRTEMDWVL 131
>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 = 54.9 bits (132), Expect = 1e-10
Identities = 14/97 (14%), Positives = 36/97 (37%), Gaps = 13/97 (13%)
Query: 47 VYVGSISFELKEDTIRQAFLPF---GPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSL 103
V + + + + ++ + ++ + + G AFVE + + +L+L
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLAL 78
Query: 104 EQMNGVMLGGRNIKVHFPHVQVGRPSNMPQAQSVIDE 140
+ + +G R I+V S+ + V+
Sbjct: 79 K-KDRESMGHRYIEVF--------KSHRTEMDWVLKH 106
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 54.1 bits (130), Expect = 2e-10
Identities = 11/78 (14%), Positives = 26/78 (33%), Gaps = 3/78 (3%)
Query: 41 SNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ 100
R+ + ++ ++ + + T+ G +E+ E
Sbjct: 25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTGALEFPSEEILV 81
Query: 101 LSLEQMNGVMLGGRNIKV 118
+LE++N + G I V
Sbjct: 82 EALERLNNIEFRGSVITV 99
>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 = 53.7 bits (129), Expect = 3e-10
Identities = 12/83 (14%), Positives = 31/83 (37%), Gaps = 5/83 (6%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPF---GPIKSINMSWDPITQKHKGFAFVEYDIP 96
+ + + + + + F I+ + K +G A +E +
Sbjct: 7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR-DGKRRGDALIEMESE 65
Query: 97 EAAQLSLEQMNGVMLGGRNIKVH 119
+ Q +LE + + +G R ++V+
Sbjct: 66 QDVQKALE-KHRMYMGQRYVEVY 87
>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 = 53.2 bits (127), Expect = 1e-09
Identities = 18/84 (21%), Positives = 37/84 (44%), Gaps = 8/84 (9%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGF-AFVEYDIPEA 98
+ LR+ V ++ + + D + Q F FG + I K+ F A ++Y P +
Sbjct: 42 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIIT-----FTKNNQFQALLQYADPVS 96
Query: 99 AQLSLEQMNGVML--GGRNIKVHF 120
AQ + ++G + +++ F
Sbjct: 97 AQHAKLSLDGQNIYNACCTLRIDF 120
>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 = 51.1 bits (123), Expect = 2e-09
Identities = 14/73 (19%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQ 105
+V+VG + ++ + ++Q F +G + + I + + FAFV + + AQ +
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVF-----IPKPFRAFAFVTFADDKVAQSLCGE 67
Query: 106 MNGVMLGGRNIKV 118
++ G ++ +
Sbjct: 68 DL--IIKGISVHI 78
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 52.0 bits (124), Expect = 2e-09
Identities = 17/83 (20%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAA 99
+ LR+ V ++ + + D + Q F FG + I T+ ++ A ++Y P +A
Sbjct: 24 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIIT----FTKNNQFQALLQYADPVSA 79
Query: 100 QLSLEQMNGVML--GGRNIKVHF 120
Q + ++G + +++ F
Sbjct: 80 QHAKLSLDGQNIYNACCTLRIDF 102
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 49.7 bits (118), Expect = 1e-08
Identities = 19/94 (20%), Positives = 40/94 (42%), Gaps = 13/94 (13%)
Query: 35 ITPDVNSNSP------LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGF 88
IT N++ P L + + + + + D + P G ++ I I +++
Sbjct: 10 ITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRI-----VIFKRNGIQ 64
Query: 89 AFVEYDIPEAAQLSLEQMNG--VMLGGRNIKVHF 120
A VE++ AQ + +NG + G +K+ +
Sbjct: 65 AMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY 98
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 49.1 bits (117), Expect = 2e-08
Identities = 16/95 (16%), Positives = 37/95 (38%), Gaps = 1/95 (1%)
Query: 26 LYDLKQVGPITPDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKH 85
+Y Q + D ++ V + E E+ + +G ++ +N+ D +
Sbjct: 9 IYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNV-CDNLGDHL 67
Query: 86 KGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVHF 120
G +V++ E A+ ++ +N G+ I
Sbjct: 68 VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102
>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 = 50.6 bits (120), Expect = 2e-08
Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 2/82 (2%)
Query: 37 PDVNSNSPLRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIP 96
N VY+ + D I++ G + +I M + KG FV +D
Sbjct: 102 EYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSI 160
Query: 97 EAAQLSLEQMNGVMLGGRNIKV 118
E+A+ +E ++ +
Sbjct: 161 ESAKKFVETPGQKY-KETDLLI 181
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 112
Score = 48.8 bits (116), Expect = 2e-08
Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 9/79 (11%)
Query: 47 VYVGSISFE-LKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ--LSL 103
+++ ++ + + + P+G IK+ + + K AF+E + E A +
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM------RMKSQAFIEMETREDAMAMVDH 81
Query: 104 EQMNGVMLGGRNIKVHFPH 122
+ GR +KV
Sbjct: 82 CLKKALWFQGRCVKVDLSE 100
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 48.1 bits (114), Expect = 3e-08
Identities = 20/94 (21%), Positives = 40/94 (42%), Gaps = 7/94 (7%)
Query: 40 NSNSPLRVYVGSISFELKEDTIRQ----AFLPFGPIKSINMSWDPITQKHKGFAFVEYDI 95
+S + V V +I + L ++Q AF G +KS+ +S ++ A V+ +
Sbjct: 5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPH---TDYQLKAVVQMEN 61
Query: 96 PEAAQLSLEQMNGVMLGGRNIKVHFPHVQVGRPS 129
+ A ++ ++ +G + I V G S
Sbjct: 62 LQDAIGAVNSLHRYKIGSKKILVSLATGASGPSS 95
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 45.6 bits (108), Expect = 3e-07
Identities = 15/79 (18%), Positives = 27/79 (34%), Gaps = 9/79 (11%)
Query: 47 VYVGSISFEL-KEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQ--LSL 103
V++ + Q PFG I + + AF+E E AQ +
Sbjct: 18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLI------LNKINEAFIEMATTEDAQAAVDY 71
Query: 104 EQMNGVMLGGRNIKVHFPH 122
++ G+ ++VH
Sbjct: 72 YTTTPALVFGKPVRVHLSQ 90
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 45.0 bits (106), Expect = 6e-07
Identities = 25/102 (24%), Positives = 45/102 (44%), Gaps = 9/102 (8%)
Query: 46 RVYVGSISFELKEDTIRQAFLPFGPIK--SINMSWDPITQKHKGFAFVEYDIPEAAQLSL 103
+V+VG + ++ ED I +F FGP+ + + KG+AF+ + + Q +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69
Query: 104 EQMNGVMLGGRNIKVHFP-----HVQVGRPSNMPQAQSVIDE 140
+ G + V P VQ+ RP N+ + V+D
Sbjct: 70 DACL-EEDGKLYLCVSSPTIKDKPVQI-RPWNLSDSDFVMDS 109
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 44.7 bits (106), Expect = 7e-07
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 55 ELKEDTIRQAFLPFGPIKSINMSWDPITQKH-KGFAFVEYDIPEAAQLSLEQMNGVMLGG 113
E++ED +R FG I+ + + +H G A V + PE A ++ ++G GG
Sbjct: 38 EIRED-LRVECSKFGQIRKLL-----LFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG 91
Query: 114 RNIKVHF 120
R I
Sbjct: 92 RQITAQA 98
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 44.0 bits (104), Expect = 9e-07
Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 3/68 (4%)
Query: 55 ELKEDTIRQAFLPFGPIKSIN--MSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLG 112
E+ ED +R +G +KSI D + G FVE+ Q +++ + G
Sbjct: 27 EIVED-VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFA 85
Query: 113 GRNIKVHF 120
R + +
Sbjct: 86 NRVVVTKY 93
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 44.8 bits (105), Expect = 3e-06
Identities = 22/118 (18%), Positives = 45/118 (38%), Gaps = 17/118 (14%)
Query: 45 LRVYVGSISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLE 104
L V G + + + + G + ++ + +K ++F Y E ++ +
Sbjct: 21 LVVANGGLGNGVSRNQLLPVLEKCGLVDAL------LMPPNKPYSFARYRTTEESKRAYV 74
Query: 105 QMNGVM---LGGRNIKVHFPHVQV-----GRPSNMPQAQSVIDEI---TEEAKLYNRI 151
+NG G+ I ++ V+ RP +P V++EI EE L +
Sbjct: 75 TLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQALPPGLMVVEEIISSEEEKMLLESV 132
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 42.4 bits (99), Expect = 4e-06
Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 6/71 (8%)
Query: 51 SISFELKEDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVM 110
+++ ++ T+R + GP+ S + ++G A +Y E A + +N +
Sbjct: 14 NLTAQIDGPTLRTLCMQHGPLVSFHPY------LNQGIALCKYTTREEANKAQMALNNCV 67
Query: 111 LGGRNIKVHFP 121
L I P
Sbjct: 68 LANTTIFAESP 78
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 40.5 bits (95), Expect = 2e-05
Identities = 11/70 (15%), Positives = 26/70 (37%), Gaps = 5/70 (7%)
Query: 55 ELKEDTIRQAFLPFGPIKSI----NMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVM 110
+L+ + + + FG + + + + FVE+ I +++ +NG
Sbjct: 37 DLEGE-VTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW 95
Query: 111 LGGRNIKVHF 120
GR +
Sbjct: 96 FAGRKVVAEV 105
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint
center for struc genomics, JCSG, protein structure
initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus
musculus} PDB: 2lq5_A
Length = 114
Score = 38.9 bits (91), Expect = 9e-05
Identities = 12/67 (17%), Positives = 27/67 (40%), Gaps = 7/67 (10%)
Query: 55 ELKEDTIRQAFLPFGPIKSINMSWDPITQKHK-GFAFVEYDIPEAAQLSLEQMNGVMLGG 113
E+K+D + + G + I + + G +V+ AA ++ ++G G
Sbjct: 29 EIKDD-VIEECNKHGGVIHIY-----VDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAG 82
Query: 114 RNIKVHF 120
+ I +
Sbjct: 83 KMITAAY 89
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 36.3 bits (84), Expect = 8e-04
Identities = 14/67 (20%), Positives = 30/67 (44%), Gaps = 2/67 (2%)
Query: 55 ELKEDTIRQAFLPFGPIKSINMSWDPITQKH-KGFAFVEYDIPEAAQLSLEQMNGVMLGG 113
+L+ + ++ +G + + P F+E++ E+A ++ +NG GG
Sbjct: 25 DLEVE-TKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGG 83
Query: 114 RNIKVHF 120
R +K F
Sbjct: 84 RVVKACF 90
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 35.1 bits (80), Expect = 0.002
Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 58 EDTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNG 108
+D + + +G + ++ +S K G A VE+ +AA+L+++ G
Sbjct: 31 KDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG 76
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 31.5 bits (71), Expect = 0.043
Identities = 13/77 (16%), Positives = 26/77 (33%), Gaps = 14/77 (18%)
Query: 47 VYVGSISFELKEDTIRQAFLPF-----GPIKSINMSWDPITQKHKGFAFVEYDIPEAAQL 101
V V + + ++ + F GP+ S Q+ + + P A+
Sbjct: 11 VEVRGLPPAVPDELLTLYFENRRRSGGGPVLSW--------QRLGCGGVLTFREPADAER 62
Query: 102 SLEQMNGVMLGGRNIKV 118
L Q + L G + +
Sbjct: 63 VLAQADHE-LHGAQLSL 78
>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 = 32.3 bits (73), Expect = 0.063
Identities = 22/165 (13%), Positives = 53/165 (32%), Gaps = 54/165 (32%)
Query: 17 CTYPFLSTPLYDLKQVG--PITPDVNSNSP--LRVYVGSISFELKEDTIRQAFLPFGPIK 72
+ P S PL + Q+ +T + +P LR Y+ + + + +
Sbjct: 232 LSIPI-SCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQ-GLVTAVAI------ 283
Query: 73 SINMSWDPITQKHKGFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKVH--FPHVQV----- 125
+ SW+ +F + + ++ + +G R + +P+ +
Sbjct: 284 AETDSWE---------SFFV-----SVRKAITVL--FFIGVR---CYEAYPNTSLPPSIL 324
Query: 126 --------GRPSNM--------PQAQSVIDEITEEAKLYNRIYVA 154
G PS M Q Q +++ ++ ++
Sbjct: 325 EDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEIS 369
Score = 29.6 bits (66), Expect = 0.50
Identities = 18/74 (24%), Positives = 29/74 (39%), Gaps = 23/74 (31%)
Query: 39 VNSNSPLRVYVGSISFELKE-DTIRQAFLPFGPIKSINMSWDPITQKHKGFAFVEYDIPE 97
VN N + YV + +L+ DT+ L F ++ I++ I
Sbjct: 1844 VNYNVENQQYV--AAGDLRALDTVTNV-LNFIKLQKIDI------------------IEL 1882
Query: 98 AAQLSLEQMNGVML 111
LSLE++ G L
Sbjct: 1883 QKSLSLEEVEG-HL 1895
>3jz0_A Lincosamide nucleotidyltransferase; alpha-beta structure,
transferase-antibiotic CO; HET: APC CLY; 2.00A
{Enterococcus faecium} PDB: 3jyy_A*
Length = 287
Score = 30.6 bits (68), Expect = 0.20
Identities = 9/41 (21%), Positives = 17/41 (41%)
Query: 111 LGGRNIKVHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRI 151
+G + H V R S+M + + +I + + RI
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMLKQKELIANVKNLTESDERI 41
>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 = 30.2 bits (67), Expect = 0.37
Identities = 34/248 (13%), Positives = 59/248 (23%), Gaps = 111/248 (44%)
Query: 2 CCIVVTT-------------TCCIVVTKCTYPF------------LSTPLYDLKQVGPIT 36
C I++TT T I + + L DL P
Sbjct: 266 CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDL----P-- 319
Query: 37 PDVNSNSPLRV------------------YVG--------SISFE-LKEDTIRQAFLPFG 69
+V + +P R+ +V S L+ R+ F
Sbjct: 320 REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS 379
Query: 70 --------PIKSINMSW-DPITQ----------------KH-KGFAFVEYDIPEAAQLSL 103
P +++ W D I K K I L L
Sbjct: 380 VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI----YLEL 435
Query: 104 E-------QMNGVMLGGRNIKVHFPHVQVGRPSN-----------MPQAQSVIDEITEEA 145
+ ++ ++ NI F + P + E E
Sbjct: 436 KVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNI-----EHPERM 490
Query: 146 KLYNRIYV 153
L+ +++
Sbjct: 491 TLFRMVFL 498
>4f06_A Extracellular ligand-binding receptor; PSI-biology, MCSG, midwest
center for structural genomics, transporter; HET: MSE
PHB; 1.30A {Rhodopseudomonas palustris} PDB: 4evs_A*
Length = 371
Score = 27.7 bits (62), Expect = 2.1
Identities = 2/32 (6%), Positives = 9/32 (28%), Gaps = 1/32 (3%)
Query: 87 GFAFVEYDIPEAAQLSLEQMNGVMLGGRNIKV 118
+A + + + + G ++
Sbjct: 17 PYALFGKNYKMGIDAWVAEHGN-KVAGHTVEF 47
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR
family, hydrolase; 2.35A {Escherichia coli} SCOP:
b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A
Length = 644
Score = 27.1 bits (61), Expect = 3.0
Identities = 12/31 (38%), Positives = 13/31 (41%), Gaps = 12/31 (38%)
Query: 86 KGFAFVEYD------IPEAAQLSLEQMNGVM 110
KGF F+E D IP QM VM
Sbjct: 31 KGFGFLEVDAQKSYFIPP------PQMKKVM 55
>3bux_B E3 ubiquitin-protein ligase CBL; TKB, signal transduction,
proto-oncogene, complex, ATP-binding, glycoprotein,
kinase, membrane, nucleotide-binding; HET: PTR; 1.35A
{Homo sapiens} SCOP: a.39.1.7 a.48.1.1 d.93.1.1 PDB:
1yvh_A* 3bun_B* 3buo_B* 3bum_B* 3buw_B* 3ob1_B* 3ob2_B*
3plf_B* 2cbl_A* 1b47_A 3pfv_A*
Length = 329
Score = 27.0 bits (59), Expect = 3.2
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 68 FGPIKSINMSWDPITQKHKGF-AFVEYD 94
F P S+ +W+ + H G+ AF+ YD
Sbjct: 226 FQPWSSLLRNWNSLAVTHPGYMAFLTYD 253
>3op0_A Signal transduction protein CBL-C; structural genomics, structural
genomics consortium, SGC, SI transduction protein,
SH3-binding protein; HET: PTR; 2.52A {Homo sapiens}
Length = 323
Score = 27.1 bits (59), Expect = 3.3
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 68 FGPIKSINMSWDPITQKHKGF-AFVEYD 94
F P ++ +W + H G+ AF+ YD
Sbjct: 211 FQPWPTLLKNWQLLAVNHPGYMAFLTYD 238
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 26.7 bits (59), Expect = 3.5
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 90 FVEYDIPEAAQLSLEQMNGVMLGGRNIK 117
FVE+ I +++ +NG GR +
Sbjct: 179 FVEFSIASETHKAIQALNGRWFAGRKVV 206
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 26.8 bits (59), Expect = 4.6
Identities = 17/83 (20%), Positives = 39/83 (46%), Gaps = 10/83 (12%)
Query: 90 FVEYDIP----EAAQLSLEQMNGVMLGG----RNIKVHFPHVQVGRPSNMPQAQSVIDEI 141
FV+ + + + L+L+Q R +++F + + RP+ M +A +
Sbjct: 41 FVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEINFGQIYLSRPT-MTEADGSTTTM 99
Query: 142 T-EEAKLYNRIYVASIHPDLTEE 163
+EA+L N Y + ++ D+ ++
Sbjct: 100 FPQEARLRNLTYSSPLYVDMRKK 122
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Length = 1224
Score = 26.4 bits (58), Expect = 6.0
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 90 FVEYDIP----EAAQLSLEQMNGVMLGG----RNIKVHFPHVQVGRPSNMPQAQSVIDEI 141
FV+Y + E + L LEQ+ R ++ F + V +P + ++ V +
Sbjct: 54 FVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPM-VNESDGVTHAL 112
Query: 142 T-EEAKLYNRIYVASIHPDLT 161
+EA+L N Y + + D+
Sbjct: 113 YPQEARLRNLTYSSGLFVDVK 133
>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase;
1.70A {Bacillus subtilis} PDB: 3moj_B
Length = 76
Score = 24.8 bits (55), Expect = 6.0
Identities = 8/35 (22%), Positives = 14/35 (40%), Gaps = 3/35 (8%)
Query: 85 HKGFAFVEYDIPEA-AQLSLEQMNGVMLGGRNIKV 118
++VE I L+ M + G+ +KV
Sbjct: 39 MDNASYVE--ILNGKGPHVLKVMKNTTVKGKQLKV 71
>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, PARN, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*
Length = 100
Score = 25.1 bits (54), Expect = 7.5
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 43 SPLRVYVGSISF--ELKEDTIRQAFLPFGPIKSINMSW 78
P R +V ++F E K + Q F FG I+ +SW
Sbjct: 12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ---ISW 46
>2y1q_A CLPC N-domain, negative regulator of genetic competence CLPC/MEC;
transcription, proteolysis; 1.50A {Bacillus subtilis}
PDB: 2y1r_A* 2k77_A
Length = 150
Score = 25.3 bits (56), Expect = 9.0
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 132 PQAQSVIDEITEEAKLYNRIYVASIH 157
P+A+ VI+ +EA+ YV + H
Sbjct: 82 PRAKKVIELSMDEARKLGHSYVGTEH 107
>2y1n_A E3 ubiquitin-protein ligase; ligase-transferase complex, ubiquitin
ring E3 ligase; HET: PTR; 2.00A {Homo sapiens} PDB:
2y1m_A* 4a4c_A* 4a4b_A* 1fbv_A* 3vgo_A 4a49_A* 2k4d_A
2ldr_A*
Length = 389
Score = 25.5 bits (55), Expect = 9.1
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 68 FGPIKSINMSWDPITQKHKGF-AFVEYD 94
F P S+ +W+ + H G+ AF+ YD
Sbjct: 202 FQPWSSLLRNWNSLAVTHPGYMAFLTYD 229
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
0.320 0.137 0.415
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: 2,577,665
Number of extensions: 144791
Number of successful extensions: 778
Number of sequences better than 10.0: 1
Number of HSP's gapped: 606
Number of HSP's successfully gapped: 258
Length of query: 166
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 79
Effective length of database: 4,272,666
Effective search space: 337540614
Effective search space used: 337540614
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.1 bits)