RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1078
(199 letters)
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 142 bits (360), Expect = 2e-44
Identities = 27/105 (25%), Positives = 50/105 (47%)
Query: 12 KLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKIT 71
+ + + + +FV G+ + +E D+ F++YGEI N++L D+ T
Sbjct: 2 REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 61
Query: 72 GKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPP 116
G KG+ + YE + +++ LNG ++ + I VD PP
Sbjct: 62 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPP 106
>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 = 135 bits (342), Expect = 1e-41
Identities = 33/92 (35%), Positives = 54/92 (58%)
Query: 29 QYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRST 88
+ +FVG +PY+ +E + IFS+ G +V+ LV D+ TGK KG+ F Y+DQ +
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63
Query: 89 VLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNK 120
+ ++ NLNG + R +RVD+ K ++ K
Sbjct: 64 LSAMRNLNGREFSGRALRVDNAASEKNKEELK 95
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 135 bits (341), Expect = 1e-41
Identities = 27/88 (30%), Positives = 52/88 (59%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
S +++G +PYD +E ++ + S G ++NL ++ D TG+SKG+ FI + D S+ +V
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 93 DNLNGVKVLSRTIRVDHVNDYKPPKDNK 120
NLNG ++ SR ++ + ++ +
Sbjct: 62 RNLNGYQLGSRFLKCGYSSNSDISGVSL 89
>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 = 132 bits (335), Expect = 1e-40
Identities = 30/112 (26%), Positives = 57/112 (50%), Gaps = 5/112 (4%)
Query: 6 NVKNIKKLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNL 65
+ + ++ + EL G + S + +FV + + E ++ F YGEI N++L
Sbjct: 4 SYERVRNEDDDELEPGPQRSV-----EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHL 58
Query: 66 VRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPK 117
D+ TG SKG+ + YE + + + + LNG +++ +TI+VD P +
Sbjct: 59 NLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 110
>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 = 131 bits (331), Expect = 8e-40
Identities = 28/109 (25%), Positives = 52/109 (47%)
Query: 12 KLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKIT 71
+ + + + +FV G+ + +E D+ F++YGEI N++L D+ T
Sbjct: 1 REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 60
Query: 72 GKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNK 120
G KG+ + YE + +++ LNG ++ + I VD PPK +
Sbjct: 61 GYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKR 109
>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 = 128 bits (323), Expect = 6e-39
Identities = 29/91 (31%), Positives = 48/91 (52%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS + ++V LP+ L+ D+ IFS+YG++V + +++DK T KSKG
Sbjct: 2 SSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVA 61
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDH 109
FI + D+ S +N ++ R I+
Sbjct: 62 FILFLDKDSAQNCTRAINNKQLFGRVIKASI 92
>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 = 121 bits (306), Expect = 2e-35
Identities = 31/118 (26%), Positives = 59/118 (50%), Gaps = 5/118 (4%)
Query: 3 PLTNVKNIKKLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVN 62
+ + + ++ + EL G + S + +FV + + E ++ F YGEI N
Sbjct: 47 AIHSYERVRNEDDDELEPGPQRS-----VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKN 101
Query: 63 LNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNK 120
++L D+ TG SKG+ + YE + + + + LNG +++ +TI+VD P + K
Sbjct: 102 IHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKK 159
>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 = 104 bits (261), Expect = 1e-29
Identities = 28/88 (31%), Positives = 53/88 (60%), Gaps = 1/88 (1%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
S+ ++VG L ++++E + IF +G+I N+ L++D TG+SKG+ FI + D +
Sbjct: 4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 92 VDNLNGVKVLSRTIRVDHVNDYKPPKDN 119
++ LNG ++ R +RV HV + + +
Sbjct: 64 LEQLNGFELAGRPMRVGHVTE-RLDGGS 90
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 100 bits (251), Expect = 1e-27
Identities = 26/108 (24%), Positives = 50/108 (46%), Gaps = 2/108 (1%)
Query: 3 PLTNVKNIKKLSEQELS--SGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEI 60
P + +E+ + SG ++VGGL ++ + + F +G+I
Sbjct: 31 PESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDI 90
Query: 61 VNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVD 108
++ + D T K +GF F+ +E ++DN+N ++ RTIRV+
Sbjct: 91 TDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 138
>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 = 97.8 bits (244), Expect = 6e-27
Identities = 26/91 (28%), Positives = 41/91 (45%), Gaps = 8/91 (8%)
Query: 27 HDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEI--------VNLNLVRDKITGKSKGFC 78
H + D+ IFV GL +++ V F Q G I +NL D+ TGK KG
Sbjct: 7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 66
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDH 109
+ ++D S ++D +G + I+V
Sbjct: 67 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97
>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 = 98.8 bits (246), Expect = 1e-26
Identities = 25/101 (24%), Positives = 49/101 (48%), Gaps = 1/101 (0%)
Query: 22 SKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFIC 81
H + + V L Y S + +F +YG + ++ + RD+ T +S+GF F+
Sbjct: 59 HHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 118
Query: 82 YEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNKYT 122
+ D+R ++D ++G + R +RV Y P D+ ++
Sbjct: 119 FHDKRDAEDAMDAMDGAVLDGRELRVQMAR-YGRPPDSHHS 158
>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 = 94.3 bits (235), Expect = 1e-25
Identities = 28/95 (29%), Positives = 52/95 (54%), Gaps = 3/95 (3%)
Query: 21 GSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFI 80
GS S + D+ +F+G +P +L E D+ +F ++G+I L +++D+ TG KG F+
Sbjct: 1 GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60
Query: 81 CYEDQRSTVLSVDNLNGVKVL---SRTIRVDHVND 112
Y ++ S + + L+ K L +R I+V +
Sbjct: 61 TYCERESALKAQSALHEQKTLPGMNRPIQVKPADS 95
>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 = 94.2 bits (235), Expect = 2e-25
Identities = 21/89 (23%), Positives = 40/89 (44%)
Query: 21 GSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFI 80
GS S + V L Y S + +F +YG + ++ + R+ T +GF F+
Sbjct: 1 GSSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60
Query: 81 CYEDQRSTVLSVDNLNGVKVLSRTIRVDH 109
+ D+R + ++G ++ R +RV
Sbjct: 61 RFHDRRDAQDAEAAMDGAELDGRELRVQV 89
>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 = 92.7 bits (231), Expect = 5e-25
Identities = 27/93 (29%), Positives = 47/93 (50%), Gaps = 1/93 (1%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS + Q + +FVG L + E + +F Q G + + + +D+ GK K F
Sbjct: 2 SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFG 60
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVN 111
F+C++ S ++ LNG+++ R I V +
Sbjct: 61 FVCFKHPESVSYAIALLNGIRLYGRPINVSGPS 93
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 90.7 bits (226), Expect = 2e-24
Identities = 22/77 (28%), Positives = 42/77 (54%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
++VGGL ++ + + F +G+I ++ + D T K +GF F+ +E +
Sbjct: 6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65
Query: 92 VDNLNGVKVLSRTIRVD 108
+DN+N ++ RTIRV+
Sbjct: 66 IDNMNESELFGRTIRVN 82
>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 = 89.6 bits (223), Expect = 8e-24
Identities = 25/97 (25%), Positives = 56/97 (57%), Gaps = 1/97 (1%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS ++ +D+ ++VGGL +SE + +F Q G +VN ++ +D++TG+ +G+
Sbjct: 2 SSGSSGPISERNQDAT-VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYG 60
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKP 115
F+ + + ++ ++ +K+ + IRV+ + +
Sbjct: 61 FVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK 97
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 89.3 bits (222), Expect = 1e-23
Identities = 22/94 (23%), Positives = 46/94 (48%), Gaps = 1/94 (1%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
S S + + +F+ GLP+ ++ ++ I +G + +L LV ++ GK KG
Sbjct: 3 SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLA 61
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVND 112
++ YE++ +V ++G+ + I+V N
Sbjct: 62 YVEYENESQASQAVMKMDGMTIKENIIKVAISNS 95
>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 = 88.0 bits (219), Expect = 3e-23
Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 7/101 (6%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS ++VGGL ++ + + F +G+I ++ + D T K +GF
Sbjct: 2 SSGS----SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 57
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDN 119
F+ +E ++DN+N ++ RTIRV+ KP +
Sbjct: 58 FVEFELAEDAAAAIDNMNESELFGRTIRVNLA---KPMRIK 95
>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA
splicing factor, RNA recognition motif, RNA binding
protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A
Length = 172
Score = 90.4 bits (225), Expect = 3e-23
Identities = 25/76 (32%), Positives = 43/76 (56%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+GGLP L++ V + + +G + NLV+D TG SKG+ F Y D T ++ L
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 96 NGVKVLSRTIRVDHVN 111
NG+++ + + V +
Sbjct: 157 NGMQLGDKKLLVQRAS 172
Score = 66.5 bits (163), Expect = 3e-14
Identities = 15/86 (17%), Positives = 39/86 (45%), Gaps = 6/86 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNL-----VRDKITGKSKGFCFICYEDQRSTVL 90
++VG +P+ ++E ++ F+ + L V + K F F+ + T
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 91 SVDNLNGVKVLSRTIRVDHVNDYKPP 116
++ +G+ +++++ +DY+P
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPL 91
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 90.9 bits (226), Expect = 3e-23
Identities = 25/76 (32%), Positives = 43/76 (56%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+GGLP L++ V + + +G + NLV+D TG SKG+ F Y D T ++ L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 96 NGVKVLSRTIRVDHVN 111
NG+++ + + V +
Sbjct: 177 NGMQLGDKKLLVQRAS 192
Score = 68.9 bits (169), Expect = 6e-15
Identities = 15/86 (17%), Positives = 39/86 (45%), Gaps = 6/86 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNL-----VRDKITGKSKGFCFICYEDQRSTVL 90
++VG +P+ ++E ++ F+ + L V + K F F+ + T
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 91 SVDNLNGVKVLSRTIRVDHVNDYKPP 116
++ +G+ +++++ +DY+P
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPL 91
>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 = 87.0 bits (216), Expect = 1e-22
Identities = 25/98 (25%), Positives = 51/98 (52%)
Query: 15 EQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKS 74
+++ + ++VG L ++++E + IF +G I ++ L+ D TG+S
Sbjct: 8 HSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRS 67
Query: 75 KGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVND 112
KG+ FI + D +++ LNG ++ R ++V HV +
Sbjct: 68 KGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTE 105
>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 = 86.1 bits (214), Expect = 1e-22
Identities = 23/74 (31%), Positives = 44/74 (59%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V GL +E D+ +FS+YG I ++++V D+ + +S+GF F+ +E+ + +
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 96 NGVKVLSRTIRVDH 109
NG+++ R IRV
Sbjct: 78 NGMELDGRRIRVSG 91
>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 = 87.9 bits (218), Expect = 2e-22
Identities = 29/109 (26%), Positives = 51/109 (46%), Gaps = 7/109 (6%)
Query: 7 VKNIKKLSEQELSS-------GSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGE 59
+K ++ S ELS G K S ++VG L + +E + +FS+ G+
Sbjct: 6 LKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGD 65
Query: 60 IVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVD 108
I + + DK+ + GFCF+ Y + ++ +NG ++ R IR D
Sbjct: 66 IKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD 114
>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 = 86.7 bits (215), Expect = 2e-22
Identities = 27/97 (27%), Positives = 51/97 (52%), Gaps = 5/97 (5%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+++ LPY ++ ++ IF +YG I +R T +++G ++ YED +VD+L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 96 NGVKVLSRTIRVDHVNDYK--PPKDNKYTDEETKKLR 130
+G V +R + V + N + D K +E+ K L+
Sbjct: 68 SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLK 104
>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 = 85.5 bits (212), Expect = 7e-22
Identities = 25/80 (31%), Positives = 47/80 (58%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V GL +E D+ +FS+YG I ++++V D+ + +S+GF F+ +E+ + +
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 96 NGVKVLSRTIRVDHVNDYKP 115
NG+++ R IRVD +P
Sbjct: 109 NGMELDGRRIRVDFSITKRP 128
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 83.5 bits (207), Expect = 2e-21
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+VG LP++ +GD+ IF I ++ LVRDK T K KGFC++ +++ ++
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDE-VDSLKEALTY 75
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDN 119
+G + R++RVD K K
Sbjct: 76 DGALLGDRSLRVDIAEGRKQDKSG 99
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 84.4 bits (209), Expect = 2e-21
Identities = 23/84 (27%), Positives = 45/84 (53%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V L Y S + +F +YG + ++ + RD+ T +S+GF F+ + D+R ++D +
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDN 119
+G + R +RV +PP +
Sbjct: 110 DGAVLDGRELRVQMARYGRPPDSH 133
>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 = 84.0 bits (208), Expect = 3e-21
Identities = 23/108 (21%), Positives = 54/108 (50%)
Query: 2 NPLTNVKNIKKLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIV 61
+P +++L +Q+ T + + + V +P + E + +F +YG I
Sbjct: 11 DPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIE 70
Query: 62 NLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDH 109
++ +V D+ T +S+G+ F+ ++ S ++ LNG +L++ ++V
Sbjct: 71 SVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL 118
>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 = 82.3 bits (204), Expect = 5e-21
Identities = 34/91 (37%), Positives = 54/91 (59%), Gaps = 4/91 (4%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS D+ K +FVGGL +D +E + +FS+YG+I + +V+D+ T +S+GF
Sbjct: 2 SSGSSGMASDEGK----LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFG 57
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDH 109
F+ +E+ ++ +NG V R IRVD
Sbjct: 58 FVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ 88
>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 = 81.7 bits (202), Expect = 1e-20
Identities = 27/108 (25%), Positives = 48/108 (44%), Gaps = 9/108 (8%)
Query: 20 SGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEI--------VNLNLVRDKIT 71
S + D+ D++ I+V GL ++ D+ F Q G + +++ DK T
Sbjct: 2 SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61
Query: 72 GKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDN 119
GK KG + YED + +V+ +G ++V KPP ++
Sbjct: 62 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR-KKPPMNS 108
>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 = 80.7 bits (200), Expect = 2e-20
Identities = 27/86 (31%), Positives = 48/86 (55%), Gaps = 1/86 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I+VG L Y + V +FSQ+G++ N+ L+ D+ T K KGF F+ +++ + ++ L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKL 62
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNKY 121
+ + RTIRV N K + + +
Sbjct: 63 DNTDFMGRTIRVTEANPKKSLEHHHH 88
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 81.3 bits (201), Expect = 2e-20
Identities = 14/73 (19%), Positives = 29/73 (39%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ L ++ E + + +YGE+ + ++ T K G + + R +V NL
Sbjct: 9 VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68
Query: 96 NGVKVLSRTIRVD 108
+ V+ I
Sbjct: 69 HLTSVMGNIIHAQ 81
>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 = 80.7 bits (200), Expect = 2e-20
Identities = 24/77 (31%), Positives = 39/77 (50%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
D+A I V L D E D+ +F +G I + L +DK TG+SKGF FI + + +
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 92 VDNLNGVKVLSRTIRVD 108
+ ++G + V+
Sbjct: 74 IAGVSGFGYDHLILNVE 90
>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 = 80.1 bits (198), Expect = 5e-20
Identities = 22/74 (29%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+GGL + +E + +F ++G I + L++D+ T KS+GF FI +E+ + ++
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 96 NGVKVLSRTIRVDH 109
NG + + I+V+
Sbjct: 69 NGKSLHGKAIKVEQ 82
>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 = 79.5 bits (197), Expect = 5e-20
Identities = 16/84 (19%), Positives = 44/84 (52%), Gaps = 4/84 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKI-TGKSKGFCFICYEDQRSTVLSVDN 94
+ +G L ++++ ++ IFS YG+I +++ +++ SKG+ ++ +E+ ++ +
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 95 LNGVKVLSRTIRVDHVNDYKPPKD 118
++G ++ + I V P
Sbjct: 67 MDGGQIDGQEITATAV---LAPWP 87
>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 = 79.6 bits (197), Expect = 5e-20
Identities = 28/99 (28%), Positives = 41/99 (41%), Gaps = 5/99 (5%)
Query: 21 GSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFI 80
GS S S +FV L Y SE D+ +FS YG + L+ D +T K KGF F+
Sbjct: 1 GSSGS-----SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFV 55
Query: 81 CYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDN 119
+ V + ++G R + V K +
Sbjct: 56 TFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQS 94
>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 = 80.1 bits (198), Expect = 6e-20
Identities = 31/109 (28%), Positives = 53/109 (48%), Gaps = 2/109 (1%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS D + +FVG L +++ D+ F+ +G I + +V+D TGKSKG+
Sbjct: 2 SSGSSGQKKDTS-NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNKYTDEETK 127
F+ + ++ ++ + G + R IR + KPP + TK
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR-KPPAPKSTYESNTK 108
>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 = 79.1 bits (196), Expect = 6e-20
Identities = 16/87 (18%), Positives = 42/87 (48%), Gaps = 4/87 (4%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
+ +FVG L ++ + + F + ++ +++ D TG S+G+ F+ + Q ++
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 93 DNLNGVKVLSRTIRVDHVNDYKPPKDN 119
D++ G + R +R++ ++
Sbjct: 61 DSMQGQDLNGRPLRINWAA----KLEH 83
>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 = 79.1 bits (196), Expect = 7e-20
Identities = 18/76 (23%), Positives = 39/76 (51%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
S+ +++ GL ++ D++ + YG+IV+ + DK T K KG+ F+ ++ + +
Sbjct: 4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
Query: 92 VDNLNGVKVLSRTIRV 107
V L V ++ +
Sbjct: 64 VTALKASGVQAQMAKQ 79
>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 = 78.9 bits (195), Expect = 1e-19
Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 4/84 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ + L Y +E + +F + I V GKSKG+ FI + ++++
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDN 119
N ++ R IR++ P
Sbjct: 74 NKREIEGRAIRLELQGPRGSPNSG 97
>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 = 78.3 bits (194), Expect = 1e-19
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVL 90
D+ I+VG + Y + ++ F G + + ++ DK +G KGF +I + D+ +V
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVR 62
Query: 91 SVDNLNGVKVLSRTIRVD 108
+ L+ R I+V
Sbjct: 63 TSLALDESLFRGRQIKVI 80
>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 = 80.3 bits (199), Expect = 2e-19
Identities = 19/72 (26%), Positives = 40/72 (55%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V LP D+++ ++ +F G I ++RD TG S G+ F+ + + + ++ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 96 NGVKVLSRTIRV 107
NG+ V ++ ++V
Sbjct: 66 NGITVRNKRLKV 77
Score = 69.5 bits (171), Expect = 2e-15
Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++V LP +++ + IF +YG IV N++RDK+TG+ +G F+ Y + ++ L
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 96 NGVKVL--SRTIRV 107
N V S+ + V
Sbjct: 152 NNVIPEGGSQPLSV 165
>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 = 77.6 bits (192), Expect = 2e-19
Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG L +++ + F+ +G I + +V+D TGKSKG+ F+ + ++ ++ +
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 96 NGVKVLSRTIRVDHVNDYKP 115
G + R IR + KP
Sbjct: 69 GGQWLGGRQIRTNWATR-KP 87
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 78.2 bits (193), Expect = 3e-19
Identities = 25/98 (25%), Positives = 41/98 (41%), Gaps = 9/98 (9%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEI--------VNLNLVRDKITGKSKGFCFICY 82
D+ IFV GL +++ V F Q G I +NL D+ TGK KG + +
Sbjct: 5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64
Query: 83 EDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNK 120
+D S ++D +G + I+V + +
Sbjct: 65 DDPPSAKAAIDWFDGKEFSGNPIKVSFATR-RADFNRG 101
>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 = 79.5 bits (197), Expect = 3e-19
Identities = 26/72 (36%), Positives = 47/72 (65%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V LP ++++ + +F GEI + LVRDKITG+S G+ F+ Y D + +++ L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 96 NGVKVLSRTIRV 107
NG+++ ++TI+V
Sbjct: 65 NGLRLQTKTIKV 76
Score = 68.0 bits (167), Expect = 8e-15
Identities = 23/74 (31%), Positives = 43/74 (58%), Gaps = 2/74 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++V GLP +++ ++ +FSQYG I+ ++ D++TG S+G FI ++ + ++ L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 96 NGVKV--LSRTIRV 107
NG K + I V
Sbjct: 151 NGQKPSGATEPITV 164
>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 = 78.2 bits (193), Expect = 4e-19
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 1/104 (0%)
Query: 5 TNVKNIKKLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLN 64
T + + E ++ + D ++VG + Y + D+ FS G I +
Sbjct: 8 TTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRIT 67
Query: 65 LVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVD 108
++ DK +G KG+ +I + ++ S V + ++ RTI+V
Sbjct: 68 ILCDKFSGHPKGYAYIEFAERNS-VDAAVAMDETVFRGRTIKVL 110
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 77.8 bits (192), Expect = 4e-19
Identities = 18/72 (25%), Positives = 42/72 (58%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+ LP + ++ D+ F +G +++ + DK T SK F F+ +++ S +++ +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 96 NGVKVLSRTIRV 107
NG +V ++ ++V
Sbjct: 103 NGFQVGTKRLKV 114
>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 77.7 bits (192), Expect = 5e-19
Identities = 19/99 (19%), Positives = 43/99 (43%), Gaps = 1/99 (1%)
Query: 11 KKLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKI 70
S + + + +D+ +F L + D+ FS G++ ++ ++ D+
Sbjct: 3 SGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN 62
Query: 71 TGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDH 109
+ +SKG ++ + + +S V L G ++L I V
Sbjct: 63 SRRSKGIAYVEFCEIQS-VPLAIGLTGQRLLGVPIIVQA 100
>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 = 80.5 bits (198), Expect = 6e-19
Identities = 18/102 (17%), Positives = 42/102 (41%), Gaps = 3/102 (2%)
Query: 14 SEQELSSGSKTSWHDQYKD-SAWIFVGGLPYDLSEGDVICIFSQYG--EIVNLNLVRDKI 70
++ G+ + Y +++G L + ++ D+ G +I+ + ++
Sbjct: 48 VGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA 107
Query: 71 TGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVND 112
G+SKGF + + S+ +D L ++ + V VN
Sbjct: 108 NGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNK 149
>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 = 76.9 bits (190), Expect = 6e-19
Identities = 24/102 (23%), Positives = 49/102 (48%), Gaps = 6/102 (5%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS D + ++VG L D++E ++ +FSQ G + ++ + + +C
Sbjct: 2 SSGSSGMMEDDGQPRT-LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YC 58
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNK 120
F+ + + R ++ +NG K+L + ++V+ P K
Sbjct: 59 FVEFYEHRDAAAALAAMNGRKILGKEVKVNWA---TTPSSQK 97
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 79.7 bits (197), Expect = 9e-19
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 1/81 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I+V + DLS+ D+ +F +G+I + L RD TGK KG+ FI YE +S+ +V ++
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 96 NGVKVLSRTIRVDHVNDYKPP 116
N + + +RV P
Sbjct: 188 NLFDLGGQYLRVGKAVT-PPM 207
Score = 78.5 bits (194), Expect = 2e-18
Identities = 23/74 (31%), Positives = 43/74 (58%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VG + Y+L E + F+ +G I ++++ D +T K KGF F+ YE + L+++ +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 96 NGVKVLSRTIRVDH 109
N V + R I+V
Sbjct: 91 NSVMLGGRNIKVGR 104
>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 = 75.7 bits (187), Expect = 1e-18
Identities = 15/78 (19%), Positives = 35/78 (44%), Gaps = 2/78 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYG--EIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD 93
+++G L + ++ D+ G +I+ + ++ G+SKGF + + S+ +D
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 94 NLNGVKVLSRTIRVDHVN 111
L ++ + V N
Sbjct: 64 LLPKRELHGQNPVVTPSN 81
>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 = 76.2 bits (188), Expect = 2e-18
Identities = 23/97 (23%), Positives = 42/97 (43%), Gaps = 7/97 (7%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS D + +F+ L +D E + + Q+G++ + +V T SKG
Sbjct: 2 SSGSSGLPSDV-TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60
Query: 79 FICYEDQRSTVLSVDNLN------GVKVLSRTIRVDH 109
F + Q + + + G+K+ R ++VD
Sbjct: 61 FAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDL 97
>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 = 80.0 bits (198), Expect = 2e-18
Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 4/94 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V LP L++ + +G + LV + TG+SKG+ F Y + S + +L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKL 129
G + RT+ V + ++ L
Sbjct: 158 LGKPLGPRTLYV----HWTDAGQLTPALLHSRCL 187
Score = 66.5 bits (163), Expect = 1e-13
Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 2/74 (2%)
Query: 36 IFVGGLPYDLSEGDVIC-IFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDN 94
+ V LP ++ D +C S L + G+ KGF + YE +
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQ 245
Query: 95 LNGVKVLSRTIRVD 108
+G+ + +RV
Sbjct: 246 ADGLSLGGSHLRVS 259
Score = 60.4 bits (147), Expect = 2e-11
Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 7/72 (9%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I + GLP D++ +V + S Y ++ K KG F+ + +++
Sbjct: 25 ILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINAF 77
Query: 96 NGVKVLSRTIRV 107
+ ++ R + V
Sbjct: 78 HQSRLRERELSV 89
>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 = 75.7 bits (187), Expect = 2e-18
Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 6/84 (7%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKIT-GKSKGFCFICYEDQRSTVLSVDN 94
F+G LPYD++E + F I + L R+ + KGF + +ED ++LS +
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED-LDSLLSALS 79
Query: 95 LNGVKVLSRTIRVDHVNDYKPPKD 118
LN + +R IRVD + +D
Sbjct: 80 LNEESLGNRRIRVDVAD---QAQD 100
>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 = 75.8 bits (187), Expect = 2e-18
Identities = 15/82 (18%), Positives = 39/82 (47%), Gaps = 5/82 (6%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVL 90
+ + + L ++++E ++ +F EI LV GKSKG +I ++ +
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIR---LVSQ--DGKSKGIAYIEFKSEADAEK 68
Query: 91 SVDNLNGVKVLSRTIRVDHVND 112
+++ G ++ R++ + + +
Sbjct: 69 NLEEKQGAEIDGRSVSLYYTGE 90
>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 = 5e-18
Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 3/74 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKI-TGKSKGFCFICYEDQRSTVLSVDN 94
F+G LPYD++E + F I + L R+ + KGF + +ED ++LS +
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFED-LDSLLSALS 75
Query: 95 LNGVKVLSRTIRVD 108
LN + ++ IRVD
Sbjct: 76 LNEESLGNKRIRVD 89
>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 = 76.1 bits (188), Expect = 7e-18
Identities = 29/96 (30%), Positives = 51/96 (53%), Gaps = 5/96 (5%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITG--KSKGFCFICYEDQRSTVLSVD 93
+FVG +P SE D+ +F QYG + +N++RD+ +SKG CF+ + +++ + + +
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 94 NLNGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKL 129
L+ +KVL + KP K E +KL
Sbjct: 66 ALHNMKVLPGMHHPIQM---KPADSEKNNAVEDRKL 98
Score = 65.7 bits (161), Expect = 6e-14
Identities = 15/75 (20%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+G + +E D+ +FS +G+I ++R G S+G F+ + + ++ +
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 156
Query: 96 NGVKVL---SRTIRV 107
+ + + S + V
Sbjct: 157 HQAQTMEGCSSPMVV 171
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 75.7 bits (186), Expect = 8e-18
Identities = 18/113 (15%), Positives = 41/113 (36%), Gaps = 2/113 (1%)
Query: 1 MNPLTNVKNIKKLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYG-- 58
M P V+ + ++ A ++VG + ++ +I + G
Sbjct: 23 MEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVY 82
Query: 59 EIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVN 111
++V L ++ G+SKG+ + + S ++ L G + + V
Sbjct: 83 DVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPAT 135
>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 = 74.3 bits (183), Expect = 9e-18
Identities = 21/85 (24%), Positives = 46/85 (54%), Gaps = 4/85 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+ LP + + D++ +F +G +V+ + DK T SK F F+ Y++ S ++ ++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNK 120
NG ++ + ++V K K++
Sbjct: 88 NGFQIGMKRLKV----QLKRSKNDS 108
>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 = 76.5 bits (189), Expect = 1e-17
Identities = 18/73 (24%), Positives = 40/73 (54%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VG L D++E + FS G I+++ + RD IT +S G+ ++ ++ ++D +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 96 NGVKVLSRTIRVD 108
N + + +R+
Sbjct: 78 NFDVIKGKPVRIM 90
Score = 66.1 bits (162), Expect = 9e-14
Identities = 22/93 (23%), Positives = 43/93 (46%), Gaps = 5/93 (5%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IF+ L + + FS +G I++ +V D SKG+ F+ +E Q + +++ +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKK 128
NG+ + R + V +K K+ + K
Sbjct: 164 NGMLLNDRKVFVGR---FKSRKEREAELGARAK 193
>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 = 73.9 bits (182), Expect = 1e-17
Identities = 16/95 (16%), Positives = 48/95 (50%)
Query: 14 SEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGK 73
S +E+ S ++ + + +++ L ++E D++ +F+++ E + +TG+
Sbjct: 6 SGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGR 65
Query: 74 SKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVD 108
+G FI + ++ ++ +NG K+ + + ++
Sbjct: 66 MRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE 100
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 73.1 bits (180), Expect = 2e-17
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VG L +G++ FS YG + + + R+ GF F+ +ED R +V L
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 96 NGVKVLSRTIRVDH 109
+G + +RV+
Sbjct: 58 DGKVICGSRVRVEL 71
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 73.2 bits (180), Expect = 2e-17
Identities = 20/97 (20%), Positives = 44/97 (45%), Gaps = 12/97 (12%)
Query: 36 IFVGGLPY------DLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTV 89
I V G P + + + +FS+ G++VN+ D+ TGK+KGF F+
Sbjct: 9 IVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAK 68
Query: 90 LSVDNLNGVKVLSR-TIRVDHVNDYKPPKDNKYTDEE 125
+ + +G ++ + + + + D + +Y ++
Sbjct: 69 KIIKSFHGKRLDLKHRLFLYTMKDVE-----RYNSDD 100
>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 = 78.4 bits (192), Expect = 2e-17
Identities = 32/164 (19%), Positives = 63/164 (38%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FV + YD +E + F YG I +++V K +GK +G+ FI YE +R + +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKLRTIGCAPGTEFGSILPVKTEDIKQEK 155
+G K+ R + VD G A S + ++
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPG 224
Query: 156 DSKPTESKDKKRKHKEKKVKKEKKKKKKRKKSSSSSSSSSSDSD 199
S + + +E++ + ++ K++ ++ S S
Sbjct: 225 PSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRS 268
>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 = 71.6 bits (176), Expect = 8e-17
Identities = 19/92 (20%), Positives = 46/92 (50%), Gaps = 3/92 (3%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDK-ITGKSKGF 77
SSGS + + ++ I V +P+ ++ ++ +FS +GE+ + L + TG +GF
Sbjct: 2 SSGSSGQ-VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 78 CFICYEDQRSTVLSVDNL-NGVKVLSRTIRVD 108
F+ + ++ + + L + + R + ++
Sbjct: 61 GFVDFITKQDAKKAFNALCHSTHLYGRRLVLE 92
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 71.2 bits (175), Expect = 9e-17
Identities = 17/88 (19%), Positives = 33/88 (37%), Gaps = 6/88 (6%)
Query: 27 HDQYKDSAWIFVGGLPYDLSEGDVICIFSQYG--EIVNLNLVRDKITGKSKGFCFICYED 84
H + I + + ++ S Y + N+ L++DK T +++GF F+
Sbjct: 3 HHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSS 62
Query: 85 QRSTVLSVDNLNGVKVLS----RTIRVD 108
+ L + +TI VD
Sbjct: 63 AMDASQLLQILQSLHPPLKIDGKTIGVD 90
>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 = 72.9 bits (180), Expect = 1e-16
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IFVGG+ D+ + FSQ+G I++ L+ DK TG+S+GF F+ Y+ V V
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA-DAVDRVCQN 148
Query: 96 NGVKVLSRTIRVD 108
+ R I +
Sbjct: 149 KFIDFKDRKIEIK 161
Score = 62.2 bits (152), Expect = 1e-12
Identities = 21/57 (36%), Positives = 38/57 (66%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
K+S +F+GGL +D +E ++ F +YG + +L +++D TG+S+GF F+ +E S
Sbjct: 1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSS 57
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 71.2 bits (175), Expect = 1e-16
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++G +P+ +E D+I +F +G I++ + KG CFI Y+ + + L
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVAL 83
Query: 96 NGVKVLSRTIRVD 108
R +R
Sbjct: 84 ANFPFQGRNLRTG 96
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 69.8 bits (172), Expect = 2e-16
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IFVGGL + + DV F Q+G++ + L+ DK T + +GF F+ +E + V V +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDI-VEKVCEI 60
Query: 96 NGVKVLSRTIRVD 108
+ ++ ++ +
Sbjct: 61 HFHEINNKMVECK 73
>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 = 70.9 bits (174), Expect = 2e-16
Identities = 18/123 (14%), Positives = 49/123 (39%), Gaps = 12/123 (9%)
Query: 10 IKKLSEQELSSGSKTSW-HDQYKDSAW----------IFVGGLPYDLSEGDVICIFSQYG 58
+ ++ + W HD + + V L + +S+ D+ +F+++G
Sbjct: 1 MASMTGGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG 60
Query: 59 EIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKD 118
+ + D+ +G+S G + +E + + ++ GV + R + + V +
Sbjct: 61 TLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEH 119
Query: 119 NKY 121
+ +
Sbjct: 120 HHH 122
>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 = 71.8 bits (177), Expect = 3e-16
Identities = 16/73 (21%), Positives = 39/73 (53%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG L ++ + + F + ++ +++ D TG S+G+ F+ + Q ++D++
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 96 NGVKVLSRTIRVD 108
G + R +R++
Sbjct: 150 QGQDLNGRPLRIN 162
Score = 69.5 bits (171), Expect = 2e-15
Identities = 16/73 (21%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VG L ++E + F G I N+ ++ DK K+ + F+ Y +++ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 96 NGVKVLSRTIRVD 108
NG ++ + ++++
Sbjct: 62 NGKQIENNIVKIN 74
>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 = 70.0 bits (172), Expect = 3e-16
Identities = 16/76 (21%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V L + +S+ D+ +F+++G + + D+ +G+S G + +E + + ++
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 90
Query: 96 NGVKVLSRTIRVDHVN 111
NGV + R + + V
Sbjct: 91 NGVPLDGRPMNIQLVT 106
>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 = 69.9 bits (172), Expect = 3e-16
Identities = 20/73 (27%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IFVGG+P++ E ++ F ++G + + ++ D + +GF FI +ED++S V N+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQS-VDQAVNM 71
Query: 96 NGVKVLSRTIRVD 108
+ ++ + + V
Sbjct: 72 HFHDIMGKKVEVK 84
>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 = 70.0 bits (172), Expect = 3e-16
Identities = 23/102 (22%), Positives = 51/102 (50%), Gaps = 4/102 (3%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS + + + V +P+ + D+ +F Q+G+I+++ ++ ++ SKGF
Sbjct: 2 SSGS-SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFG 58
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNK 120
F+ +E+ + + L+G V R I V++ + ++
Sbjct: 59 FVTFENSADADRAREKLHGTVVEGRKIEVNNATA-RVMTNSG 99
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 70.0 bits (172), Expect = 4e-16
Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V +P+ + D+ +F Q+G+I+++ ++ ++ SKGF F+ +E+ + + L
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKL 89
Query: 96 NGVKVLSRTIRVDH 109
+G V R I V++
Sbjct: 90 HGTVVEGRKIEVNN 103
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 71.8 bits (176), Expect = 4e-16
Identities = 15/82 (18%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V L + +S+ D+ +F+++G + + D+ +G+S G + +E + + ++
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQY 149
Query: 96 NGVKVLSRTIRVDHVNDYKPPK 117
GV + R + + V +
Sbjct: 150 KGVPLDGRPMDIQLVASQIDLE 171
>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 = 69.6 bits (171), Expect = 4e-16
Identities = 19/89 (21%), Positives = 38/89 (42%), Gaps = 3/89 (3%)
Query: 20 SGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCF 79
S + + + + S +FV GL D +E + F +V D+ TG SKGF F
Sbjct: 2 SSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFGF 58
Query: 80 ICYEDQRSTVLSVDNLNGVKVLSRTIRVD 108
+ + + + + + ++ + +D
Sbjct: 59 VDFNSEEDAKAAKEAMEDGEIDGNKVTLD 87
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 69.3 bits (170), Expect = 5e-16
Identities = 17/85 (20%), Positives = 43/85 (50%), Gaps = 5/85 (5%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIV-NLNLVRDKITGKSKGFCFICYEDQRSTVLSVDN 94
+++G L + E + F+ GE V ++ ++R+++TG G+CF+ + D + +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 95 LNGVKV----LSRTIRVDHVNDYKP 115
+NG + ++ ++++ P
Sbjct: 72 INGKPLPGATPAKRFKLNYATYSGP 96
>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 = 69.3 bits (170), Expect = 6e-16
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I+VG LP D+ D+ +F +YG I +++L K F F+ +ED R +V
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVYGR 81
Query: 96 NGVKVLSRTIRVDH 109
+G +RV+
Sbjct: 82 DGYDYDGYRLRVEF 95
>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 = 69.9 bits (171), Expect = 1e-15
Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VG L + ++ ++ F YG + ++ + R+ GF F+ +ED R +V L
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 130
Query: 96 NGVKVLSRTIRVDH 109
+G + +RV+
Sbjct: 131 DGRTLCGCRVRVEL 144
>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 = 68.4 bits (168), Expect = 1e-15
Identities = 15/86 (17%), Positives = 35/86 (40%), Gaps = 10/86 (11%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+++G L ++ D+ +F + G+ F+ Y DQ + +++ L
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIETL 64
Query: 96 NG-VKVLSRTIRVDHVNDYKPPKDNK 120
+G V++ + + VD+ K
Sbjct: 65 SGKVELHGKIMEVDYS---VSKKLRS 87
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 68.4 bits (168), Expect = 1e-15
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IFV LP+D + + F++ G ++ ++ + GKSKG + +E + +
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 68
Query: 96 NGVKVLSRTIRVDHVNDYKPPK 117
NG+K+ R I V + P
Sbjct: 69 NGMKLSGREIDVRIDRNASGPS 90
>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 = 68.4 bits (168), Expect = 1e-15
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 2/73 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+G L + S ++ S+ +L V D TG ++ F ++ +E +++ L
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKALE-L 77
Query: 96 NGVKVLSRTIRVD 108
G+KV I+++
Sbjct: 78 TGLKVFGNEIKLE 90
>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 = 68.1 bits (167), Expect = 2e-15
Identities = 26/92 (28%), Positives = 42/92 (45%), Gaps = 5/92 (5%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS S + +FVG L SE DV+ +F +G I ++R G SKG
Sbjct: 2 SSGSSGS-ESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCA 59
Query: 79 FICYEDQRSTVLSVDNLNGVKVL---SRTIRV 107
F+ + ++ L+G + + S ++ V
Sbjct: 60 FVKFSSHTEAQAAIHALHGSQTMPGASSSLVV 91
>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 = 67.6 bits (166), Expect = 2e-15
Identities = 26/86 (30%), Positives = 46/86 (53%), Gaps = 5/86 (5%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVN-LNLVRDKITGKSKGFCFICYEDQRSTVLSVDN 94
IF+G L ++ E + FS +G I+ ++RD TG SKG+ FI + ++ +++
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 95 LNGVKVLSRTIRVDHVNDYKPPKDNK 120
+NG + +R I V + KD+K
Sbjct: 68 MNGQYLCNRPITVSYAF----KKDSK 89
>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 = 66.8 bits (164), Expect = 2e-15
Identities = 20/52 (38%), Positives = 30/52 (57%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
IFVGGL D E + F +GE+ ++ L D T K +GFCFI ++++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEP 53
>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 = 68.1 bits (167), Expect = 3e-15
Identities = 28/109 (25%), Positives = 49/109 (44%), Gaps = 11/109 (10%)
Query: 20 SGSKTSWHDQYKDSAW--IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGF 77
S + H KD+ + IFVGGLPY ++ + F +G+I ++ D+ TGKS+G+
Sbjct: 2 SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGY 61
Query: 78 CFICYEDQRS--TVLSVDN--LNGVKVLSRTIRVDHVNDYKPPKDNKYT 122
F+ D+ + N ++G R V+ P+ +
Sbjct: 62 GFVTMADRAAAERACKDPNPIIDG-----RKANVNLAYLGAKPRSLQTG 105
>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 = 66.9 bits (164), Expect = 4e-15
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG LP D++E ++ +F +YG+ + + +D KGF FI E + ++ L
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVEL 71
Query: 96 NGVKVLSRTIRVD 108
+ + + + +RV
Sbjct: 72 DNMPLRGKQLRVR 84
>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 = 67.3 bits (165), Expect = 4e-15
Identities = 15/88 (17%), Positives = 37/88 (42%), Gaps = 5/88 (5%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+++ LP + E ++ + +G++++ ++RD +G S+G F E + +
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNKYTD 123
NG + + P K++
Sbjct: 87 NGKFIKTPPGVS----APTEPLLCKFSG 110
>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 = 66.8 bits (164), Expect = 4e-15
Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+G LP + +E ++ +F QYG+++ +++ K + F+ ED+ + ++ NL
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNL 62
Query: 96 NGVKVLSRTIRVDH 109
+ K+ I V+
Sbjct: 63 HHYKLHGVNINVEA 76
>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 = 66.9 bits (164), Expect = 5e-15
Identities = 23/90 (25%), Positives = 43/90 (47%), Gaps = 3/90 (3%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS +Y+ ++V L + + + FS +G I + ++ + G+SKGF
Sbjct: 2 SSGSSGDRITRYQ-VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFG 58
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVD 108
F+C+ +V +NG V ++ + V
Sbjct: 59 FVCFSSPEEATKAVTEMNGRIVATKPLYVA 88
>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 = 69.2 bits (170), Expect = 5e-15
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IFVGG+ D E + F QYG+I + ++ D+ +GK +GF F+ ++D +V +
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIVIQ 165
Query: 96 NGVKVLSRTIRVD 108
V V
Sbjct: 166 KYHTVNGHNCEVR 178
Score = 68.1 bits (167), Expect = 1e-14
Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 2/94 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+GGL ++ ++ + F Q+G + + ++RD T +S+GF F+ Y V + N
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV-EEVDAAMNA 74
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKL 129
KV R + + KK+
Sbjct: 75 RPHKVDGRVVEPKRAVS-REDSQRPGAHLTVKKI 107
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 66.0 bits (162), Expect = 5e-15
Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+GGL + ++ + F Q+GE+ ++RD +T +S+GF F+ + DQ V V
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG-VDKVLAQ 61
Query: 96 NGVKVLSRTIRVDH 109
+ ++ S+TI
Sbjct: 62 SRHELDSKTIDPKV 75
>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 = 66.6 bits (163), Expect = 6e-15
Identities = 25/105 (23%), Positives = 51/105 (48%), Gaps = 9/105 (8%)
Query: 14 SEQELSSGSKTSWHDQYKDSAWIFVGGLPYDL-SEGDVICIFSQYGEIVNLNLVRDKITG 72
+L + + T+ +D ++ +F+G L L + DV IFS+YG + ++
Sbjct: 8 MSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV------- 60
Query: 73 KSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPK 117
KG+ F+ Y ++R +V NG + +T+ ++ + KP +
Sbjct: 61 -HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDR 104
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 66.1 bits (162), Expect = 7e-15
Identities = 20/97 (20%), Positives = 46/97 (47%), Gaps = 10/97 (10%)
Query: 24 TSWHDQYKDSAWIFVGGLPY-DLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICY 82
T H+ + +F+G LP ++S+ D+ IFS YG I+ +N+ F FI +
Sbjct: 2 TEMHN-IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQF 52
Query: 83 EDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDN 119
++ +S +++ + + + ++ + P+ +
Sbjct: 53 DNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQFD 89
>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 = 68.0 bits (167), Expect = 9e-15
Identities = 13/77 (16%), Positives = 35/77 (45%), Gaps = 5/77 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ L ++++E ++ +F EI GKSKG +I ++ + +++
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEEK 156
Query: 96 NGVKVLSRTIRVDHVND 112
G ++ R++ + + +
Sbjct: 157 QGAEIDGRSVSLYYTGE 173
Score = 63.8 bits (156), Expect = 4e-13
Identities = 19/94 (20%), Positives = 42/94 (44%), Gaps = 7/94 (7%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+G L + S ++ S+ +L +V + TG ++ F ++ +E +++ L
Sbjct: 16 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALE-L 73
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKL 129
G+KV I+++ KP + + L
Sbjct: 74 TGLKVFGNEIKLE-----KPKGRDSKKVRAARTL 102
>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 = 65.8 bits (161), Expect = 1e-14
Identities = 15/85 (17%), Positives = 37/85 (43%), Gaps = 9/85 (10%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++ GG+ L++ + FS +G+I+ + + + KG+ F+ + S ++ ++
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNK 120
NG + ++ K D
Sbjct: 82 NGTTIEGHVVKCYWG---KESPDMT 103
>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 = 65.8 bits (161), Expect = 1e-14
Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 2/89 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FV L Y + + +FS G +V +++ DK GKS+G + +E V ++
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNKYTDE 124
NG + R + V PK + + E
Sbjct: 77 NGQLLFDRPMHVKMDE-RALPKGDFFPPE 104
>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 = 69.2 bits (170), Expect = 2e-14
Identities = 13/94 (13%), Positives = 34/94 (36%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+++ P ++ ++ + + + S+ F +I + V+ L
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKL 129
NG+K+ T+ N + K E +++
Sbjct: 180 NGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREI 213
Score = 62.3 bits (152), Expect = 5e-12
Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 3/77 (3%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V LP ++ V F G I+++++ K+ F I + + ++
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKT 101
Query: 96 NGVKVLSRTIRVDHVND 112
+ V I V H+ +
Sbjct: 102 HK-VVGQNEIIVSHLTE 117
Score = 56.9 bits (138), Expect = 3e-10
Identities = 15/75 (20%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 36 IFVGGLPYDLSEGDVIC-IFSQYGEIVNLNLVRD-KITGKSKGFCFICYEDQRSTVLSVD 93
I + L +L + +++ F +G I +N+ K + F+ +E++ S ++
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL- 271
Query: 94 NLNGVKVLSRTIRVD 108
+N + +R I V
Sbjct: 272 QMNRSLLGNREISVS 286
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 65.2 bits (159), Expect = 2e-14
Identities = 14/86 (16%), Positives = 33/86 (38%), Gaps = 3/86 (3%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
+ + +P L + + QYG + + V + Y + +
Sbjct: 14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQA 70
Query: 92 VDNLNGVKVLSRTIRVDHVNDYKPPK 117
+D LNG ++ + T++V ++ D +
Sbjct: 71 LDKLNGFQLENFTLKVAYIPDEMAAQ 96
>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 = 65.7 bits (161), Expect = 2e-14
Identities = 23/96 (23%), Positives = 44/96 (45%), Gaps = 5/96 (5%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
IF+ L + + FS +G I++ +V D SKG+ F+ +E Q + +++ +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKLRT 131
NG+ + R + V +K K+ + K T
Sbjct: 66 NGMLLNDRKVF---VGRFKSRKEREAELGARAKEFT 98
>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 = 65.0 bits (159), Expect = 2e-14
Identities = 15/73 (20%), Positives = 32/73 (43%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I V +P+ +S +++ F Y I ++ G G + +E + +V +L
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77
Query: 96 NGVKVLSRTIRVD 108
N + SR +++
Sbjct: 78 NDRPIGSRKVKLV 90
>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 = 65.3 bits (160), Expect = 2e-14
Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 1/91 (1%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS + + +FVGGL + ++ + FSQYGE+V+ +++DK T +S+GF
Sbjct: 2 SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFG 61
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDH 109
F+ ++D V +V + R I
Sbjct: 62 FVKFKDPNC-VGTVLASRPHTLDGRNIDPKP 91
>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 = 64.6 bits (158), Expect = 2e-14
Identities = 15/72 (20%), Positives = 32/72 (44%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I V +P+ +S +++ F Y I ++ G G + +E + +V +L
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77
Query: 96 NGVKVLSRTIRV 107
N + SR +++
Sbjct: 78 NDRPIGSRKVKL 89
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 65.1 bits (159), Expect = 3e-14
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 9/86 (10%)
Query: 36 IFVGGLP------YDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTV 89
I V +P + + + IFS++G+I N + GK+KG+ F+ Y V
Sbjct: 18 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAV 75
Query: 90 LSVDNLNGVKVLSR-TIRVDHVNDYK 114
+V N +G K+ + T RV+ D+
Sbjct: 76 DAVKNADGYKLDKQHTFRVNLFTDFD 101
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 98
Score = 64.6 bits (158), Expect = 3e-14
Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 3/77 (3%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGK---SKGFCFICYEDQRSTVLSV 92
+F+ L + +E + +FS+ G I + + + K S GF F+ Y+ ++
Sbjct: 8 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 93 DNLNGVKVLSRTIRVDH 109
L G V + V
Sbjct: 68 KQLQGHTVDGHKLEVRI 84
>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 = 64.8 bits (158), Expect = 4e-14
Identities = 17/88 (19%), Positives = 39/88 (44%), Gaps = 4/88 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIV-NLNLVRD-KITGKSKGFCFICYEDQRSTVLSVD 93
+F+GG+P +++ ++ E V ++ + K++GF F+ YE R+ ++
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70
Query: 94 NLN--GVKVLSRTIRVDHVNDYKPPKDN 119
L +++ I VD ++
Sbjct: 71 KLMPGRIQLWGHQIAVDWAEPEIDVDED 98
>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 = 63.8 bits (156), Expect = 5e-14
Identities = 20/96 (20%), Positives = 41/96 (42%), Gaps = 12/96 (12%)
Query: 21 GSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFI 80
GS S + +K IFVG + + ++ +F + G ++ ++V K + F+
Sbjct: 1 GSSGSSGNTWK----IFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFV 48
Query: 81 CYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPP 116
E + ++ LNG +V + I V+ +
Sbjct: 49 HMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQKK 84
>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 = 64.2 bits (157), Expect = 5e-14
Identities = 23/91 (25%), Positives = 45/91 (49%), Gaps = 8/91 (8%)
Query: 20 SGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCF 79
S + + ++ + V GLP+ +E D+ FS +GE++ + + +D TG SKGF F
Sbjct: 2 SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61
Query: 80 ICYEDQRS--TVLSVDN-LNGVKVLSRTIRV 107
+ + + + V+S + ++G R
Sbjct: 62 VRFTEYETQVKVMSQRHMIDG-----RWCDC 87
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 63.8 bits (156), Expect = 8e-14
Identities = 22/74 (29%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+GGL + ++ + F Q+GE+ ++RD +T +S+GF F+ + DQ V V
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG-VDKVLAQ 86
Query: 96 NGVKVLSRTIRVDH 109
+ ++ S+TI
Sbjct: 87 SRHELDSKTIDPKV 100
>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 = 66.8 bits (162), Expect = 1e-13
Identities = 14/78 (17%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 36 IFVGGLPYDLSEGDV----ICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
I++ L + + ++ IFSQ+G+I++ + + K +G F+ +++ S +
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNA 68
Query: 92 VDNLNGVKVLSRTIRVDH 109
+ ++ G + +R+ +
Sbjct: 69 LRSMQGFPFYDKPMRIQY 86
Score = 51.4 bits (122), Expect = 3e-08
Identities = 13/72 (18%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 37 FVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLN 96
F+ LP + +E + +F+Q+ + LV + F+ ++++ + D L
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQ 265
Query: 97 GVKVL-SRTIRV 107
G K+ + +++
Sbjct: 266 GFKITQNNAMKI 277
>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 = 63.4 bits (155), Expect = 1e-13
Identities = 16/74 (21%), Positives = 38/74 (51%), Gaps = 3/74 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVGG+ + E ++ F++YG + + ++ D+ TG SKG+ F+ + + V++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 96 NGVKVLSRTIRVDH 109
+ +++
Sbjct: 71 INFH--GKKLKLGP 82
>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 = 63.0 bits (154), Expect = 1e-13
Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VGGL + S + F ++G I ++ V+ F +I YE + + +
Sbjct: 20 LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKM 73
Query: 96 NGVKV--LSRTIRVD 108
G + R +RVD
Sbjct: 74 RGFPLGGPDRRLRVD 88
>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 = 66.3 bits (162), Expect = 1e-13
Identities = 26/149 (17%), Positives = 57/149 (38%), Gaps = 7/149 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V L +S + FSQ+G + +V D G++ G F+ + + +++
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERC 157
Query: 96 NGVKVL-SRTIRVDHVNDYKPPKDNKYTDEETKKLRTIGCAPGTEFGSILPVKTEDIKQE 154
L + T R V D++ E +T E + + E
Sbjct: 158 GDGAFLLTTTPRPVIVE-PMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFA-QPGTFEFE 215
Query: 155 KDSKP---TESKDKKRKHKEKKVKKEKKK 180
S+ E + ++R+ ++ +++ K+K
Sbjct: 216 YASRWKALDEMEKQQREQVDRNIREAKEK 244
Score = 62.4 bits (152), Expect = 4e-12
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FVG LP D++E D +F +YGE + + RD +GF FI E + ++ L
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAEL 78
Query: 96 NGVKVLSRTIRV 107
+G + SR +R+
Sbjct: 79 DGTILKSRPLRI 90
>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 = 62.6 bits (153), Expect = 1e-13
Identities = 11/74 (14%), Positives = 30/74 (40%), Gaps = 8/74 (10%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ VG + + ++ F +YG ++ ++V+ + F+ E V ++ L
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGL 64
Query: 96 NGVKVLSRTIRVDH 109
+ + + + V
Sbjct: 65 DNTEFQGKRMHVQL 78
>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 = 63.2 bits (154), Expect = 2e-13
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVL 90
+ ++V G D++ + FS +G I++L++ + F+ YE S
Sbjct: 37 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQ 88
Query: 91 SVDNLNGVKVLSRTIRVD 108
+V LNG +V S ++V+
Sbjct: 89 AVAELNGTQVESVQLKVN 106
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 62.5 bits (152), Expect = 2e-13
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++VG LP D D+ + G V L L + F+ Y D + +V L
Sbjct: 22 VYVGNLPRDARVSDLKRALRELG-SVPLRLTWQG----PRRRAFLHYPDSAAAQQAVSCL 76
Query: 96 NGVKVLSRTIRVD 108
G+++ + T+RV
Sbjct: 77 QGLRLGTDTLRVA 89
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 62.7 bits (153), Expect = 2e-13
Identities = 15/74 (20%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+F+GGL ++ +E + + Q+G++ + ++RD + +S+GF F+ + V +
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE-VDAAMAA 88
Query: 96 NGVKVLSRTIRVDH 109
+ R +
Sbjct: 89 RPHSIDGRVVEPKR 102
>1x5p_A Negative elongation factor E; structure genomics, RRM domain,
PARP14, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 97
Score = 60.4 bits (147), Expect = 1e-12
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++V G D++ + FS +G I++L+ + F+ YE S +V L
Sbjct: 18 LYVYGE--DMTPTLLRGAFSPFGNIIDLS------MDPPRNCAFVTYEKMESADQAVAEL 69
Query: 96 NGVKVLSRTIRVDH 109
NG +V S ++V+
Sbjct: 70 NGTQVESVQLKVNI 83
>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 = 60.6 bits (147), Expect = 1e-12
Identities = 16/80 (20%), Positives = 35/80 (43%), Gaps = 6/80 (7%)
Query: 36 IFVGGLPYDLSEGDVIC---IFSQYGEIVNLNLVRDKITGKSK---GFCFICYEDQRSTV 89
+FV GL L++ +V+ F ++G+I + + S+ ++ Y +
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 90 LSVDNLNGVKVLSRTIRVDH 109
++ +N V V RT++
Sbjct: 78 RAIQCVNNVVVDGRTLKASL 97
>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 = 60.0 bits (146), Expect = 1e-12
Identities = 17/75 (22%), Positives = 38/75 (50%), Gaps = 9/75 (12%)
Query: 36 IFVGGLPY-DLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDN 94
+F+G LP ++S+ D+ IFS YG I+ +N+ F FI +++ +S +++
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEX 76
Query: 95 LNGVKVLSRTIRVDH 109
+ + + ++
Sbjct: 77 ESQEMNFGKKLILEV 91
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 60.4 bits (147), Expect = 1e-12
Identities = 17/85 (20%), Positives = 38/85 (44%), Gaps = 11/85 (12%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FV P D+ E ++ IF +G + + ++ GF F+ +E+ S +++ +
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEV 85
Query: 96 NGVKVLSRTIRVDHVNDYKPPKDNK 120
+G ++ + V + K P
Sbjct: 86 HGKSFANQPLEVVYS---KLPAKRY 107
>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 = 59.9 bits (146), Expect = 2e-12
Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 9/77 (11%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS--TVLSVD 93
+FVGGL +D S+ D+ F+++GE+V+ + D TG+S+GF FI ++D S VL
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73
Query: 94 N--LNGVKVLSRTIRVD 108
L+G R I
Sbjct: 74 EHRLDG-----RVIDPK 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 = 59.4 bits (144), Expect = 2e-12
Identities = 12/77 (15%), Positives = 34/77 (44%), Gaps = 6/77 (7%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNL-----VRDKITGKSKGFCFICYEDQRSTVL 90
++VG +P+ ++E ++ F+ + L V + K F F+ + T
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 91 SVDNLNGVKVLSRTIRV 107
++ +G+ +++++
Sbjct: 69 AM-AFDGIIFQGQSLKI 84
>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 = 59.5 bits (145), Expect = 3e-12
Identities = 13/77 (16%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 36 IFVGGLPYDLSEGD----VICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLS 91
I++ L + + + + IFS++G+I++ + + K +G F+ +++ S +
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILD---ILVSRSLKMRGQAFVIFKEVSSATNA 67
Query: 92 VDNLNGVKVLSRTIRVD 108
+ ++ G + +R+
Sbjct: 68 LRSMQGFPFYDKPMRIQ 84
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 58.2 bits (141), Expect = 5e-12
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 9/79 (11%)
Query: 36 IFVGGLP------YDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTV 89
I V +P + + + IFS++G+I N + GK+KG+ F+ Y V
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAV 61
Query: 90 LSVDNLNGVKV-LSRTIRV 107
+V N +G K+ T RV
Sbjct: 62 DAVKNADGYKLDKQHTFRV 80
>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 = 58.3 bits (141), Expect = 8e-12
Identities = 18/104 (17%), Positives = 38/104 (36%), Gaps = 9/104 (8%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS S H S + V GL + E D++ ++G I + ++ K
Sbjct: 2 SSGSSGSHHKV-SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQA 54
Query: 79 FICYEDQRS--TVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNK 120
+ +E+ S ++ V + + ++ + +
Sbjct: 55 LVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGN 98
>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 = 57.7 bits (140), Expect = 1e-11
Identities = 13/73 (17%), Positives = 27/73 (36%), Gaps = 6/73 (8%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
++V L SE + F+ + K + + F+ + ++ V ++ L
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKAL 71
Query: 96 NGVKVLSRTIRVD 108
NG + I V
Sbjct: 72 NGKVLDGSPIEVT 84
>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 = 57.7 bits (140), Expect = 2e-11
Identities = 16/73 (21%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FV L ++E + FSQ+G++ + K K + FI ++++ V +++ +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEEM 65
Query: 96 NGVKVLSRTIRVD 108
NG + I +
Sbjct: 66 NGKDLEGENIEIV 78
>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 = 56.9 bits (138), Expect = 2e-11
Identities = 18/73 (24%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVL-SVDN 94
++VGGL ++E D+ F Q+GEI + +V+ + FI + +++ + + +
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68
Query: 95 LNGVKVLSRTIRV 107
N + V R + V
Sbjct: 69 FNKLIVNGRRLNV 81
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 57.6 bits (139), Expect = 2e-11
Identities = 20/108 (18%), Positives = 40/108 (37%), Gaps = 8/108 (7%)
Query: 18 LSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGF 77
+ H S I + LP D++EG+VI + +G++ NL +++ K
Sbjct: 1 MRGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQ 54
Query: 78 CFICYEDQRSTVLSVDNL--NGVKVLSRTIRVDHVNDYKPPKDNKYTD 123
FI + + V+ + + I + N + D+
Sbjct: 55 AFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQ 102
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 57.7 bits (139), Expect = 2e-11
Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 8/83 (9%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDK--ITGKSKGFCFICYEDQRS--TVLS 91
+FVGGLP D+ E ++ F ++G +V + + KG+ F+ ++++ S ++
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
Query: 92 ----VDNLNGVKVLSRTIRVDHV 110
D + V S TI+ V
Sbjct: 71 ACLEEDGKLYLCVSSPTIKDKPV 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 = 56.6 bits (137), Expect = 3e-11
Identities = 10/72 (13%), Positives = 24/72 (33%), Gaps = 7/72 (9%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I V LP D + +V + Y ++ ++K F+ + ++
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60
Query: 96 NGVKVLSRTIRV 107
+ + + V
Sbjct: 61 HQYSFRGKDLIV 72
>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 = 56.8 bits (137), Expect = 3e-11
Identities = 18/103 (17%), Positives = 44/103 (42%), Gaps = 9/103 (8%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS D S + + LP +++E +VI + +G++ N+ +++ K
Sbjct: 2 SSGSSGDKMDG-APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQA 54
Query: 79 FICYEDQRSTVLSVD--NLNGVKVLSRTIRVDHVNDYKPPKDN 119
F+ + + + V+ + + ++ I + + N +
Sbjct: 55 FLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKELKTSG 97
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 56.3 bits (136), Expect = 5e-11
Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 8/78 (10%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
S + + GL + E D++ ++G I + ++ K + +ED +V
Sbjct: 21 SPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAV 74
Query: 93 D--NLNGVKVLSRTIRVD 108
+ N + + V+
Sbjct: 75 NYAADNQIYIAGHPAFVN 92
>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 = 58.2 bits (140), Expect = 6e-11
Identities = 7/83 (8%), Positives = 27/83 (32%)
Query: 28 DQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
S + P +++E + I + G ++ + + ++ +
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSD 177
Query: 88 TVLSVDNLNGVKVLSRTIRVDHV 110
+ ++ LN ++ + +
Sbjct: 178 ALETLGFLNHYQMKNPNGPYPYT 200
Score = 54.7 bits (131), Expect = 1e-09
Identities = 17/113 (15%), Positives = 39/113 (34%), Gaps = 7/113 (6%)
Query: 32 DSAWIFVGGLPYDLSEGDVIC-IFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVL 90
DS + V GL D + +F YG + + ++ K G + D +
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDR 57
Query: 91 SVDNLNGVKVLSRTIRVDHVN-DYKPPKDNKYTDEETKKLRTIGCAPGTEFGS 142
++ +LN + + + V P + ++ + + + F +
Sbjct: 58 AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFST 110
>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 = 54.8 bits (132), Expect = 2e-10
Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 3/90 (3%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS D ++ V G+P+ E DV F + ++L++D G++ G
Sbjct: 2 SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNG 59
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVD 108
+ + + T ++ N + ++ R + V
Sbjct: 60 LVKFLSPQDTFEALK-RNRMLMIQRYVEVS 88
>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 = 54.7 bits (132), Expect = 2e-10
Identities = 18/93 (19%), Positives = 33/93 (35%), Gaps = 2/93 (2%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS D + +P+ +++ DV+ N V G+ G
Sbjct: 2 SSGSSGE-GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVN 111
+ ++++ S L+ K+ R V V
Sbjct: 61 LVQFKNEDDARKSE-RLHRKKLNGREAFVHVVT 92
>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 = 56.5 bits (136), Expect = 3e-10
Identities = 17/91 (18%), Positives = 36/91 (39%), Gaps = 5/91 (5%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
++ + + SA + + +P +SE D+ +FS G +V K K +
Sbjct: 137 KKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKG----FKFFQKDRKMA 192
Query: 79 FICYEDQRSTVLSVDNLNGVKVL-SRTIRVD 108
I V ++ +L+ + + +RV
Sbjct: 193 LIQMGSVEEAVQALIDLHNHDLGENHHLRVS 223
Score = 55.8 bits (134), Expect = 7e-10
Identities = 18/93 (19%), Positives = 36/93 (38%), Gaps = 6/93 (6%)
Query: 36 IFVGGL-PYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDN 94
+ V L P ++ + +F YG++ R KI K + D L++ +
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQ-----RVKILFNKKENALVQMADGNQAQLAMSH 91
Query: 95 LNGVKVLSRTIRVDHVNDYKPPKDNKYTDEETK 127
LNG K+ + IR+ + +++
Sbjct: 92 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGL 124
>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 = 56.1 bits (135), Expect = 3e-10
Identities = 18/94 (19%), Positives = 36/94 (38%), Gaps = 6/94 (6%)
Query: 36 IFVGGL-PYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDN 94
+ V L P ++ + +F YG++ R KI K + D L++ +
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQ-----RVKILFNKKENALVQMADGNQAQLAMSH 60
Query: 95 LNGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKK 128
LNG K+ + IR+ + +++
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLT 94
Score = 55.3 bits (133), Expect = 6e-10
Identities = 17/91 (18%), Positives = 36/91 (39%), Gaps = 5/91 (5%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
++ + + SA + + +P +SE D+ +FS G +V K K +
Sbjct: 106 KKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMA 161
Query: 79 FICYEDQRSTVLSVDNLNGVKVL-SRTIRVD 108
I V ++ +L+ + + +RV
Sbjct: 162 LIQMGSVEEAVQALIDLHNHDLGENHHLRVS 192
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 53.7 bits (129), Expect = 5e-10
Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 3/82 (3%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I + LP S D+ + + T G + + + V +++ L
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETT---FSSVNTRDFDGTGALEFPSEEILVEALERL 87
Query: 96 NGVKVLSRTIRVDHVNDYKPPK 117
N ++ I V+ ++ P +
Sbjct: 88 NNIEFRGSVITVERDDNPPPIR 109
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 54.1 bits (130), Expect = 5e-10
Identities = 16/122 (13%), Positives = 41/122 (33%), Gaps = 10/122 (8%)
Query: 12 KLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGD----VICIFSQYGEIVNLNLVR 67
K Q + S S + S + + + ++ + + + S G+I++ +
Sbjct: 8 KFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD---IV 64
Query: 68 DKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNKYTDEETK 127
++ + G +I + Q S V+ G + + + P+ D +
Sbjct: 65 VDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFS---ETPQSQVAEDGSLE 121
Query: 128 KL 129
Sbjct: 122 HH 123
>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 = 53.8 bits (129), Expect = 6e-10
Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 8/75 (10%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD-- 93
I + LP D++EG+VI + +G++ NL +++ K FI + + V+
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 87
Query: 94 NLNGVKVLSRTIRVD 108
+ + I +
Sbjct: 88 TSVTPVLRGQPIYIQ 102
>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 = 53.3 bits (128), Expect = 6e-10
Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 7/76 (9%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V GLP S D+ + G++ ++ RD G + + + +V L
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKL 70
Query: 96 NGVKVLSRTIRVDHVN 111
+ K S ++
Sbjct: 71 DNTKFRSHEGETAYIR 86
>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 = 53.7 bits (129), Expect = 8e-10
Identities = 15/89 (16%), Positives = 35/89 (39%), Gaps = 1/89 (1%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
+ S + ++ + GLP+ ++ +++ FS + N + GK G
Sbjct: 28 QQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEA 87
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
F+ + Q ++ + ++ R I V
Sbjct: 88 FVQFASQELAEKALG-KHKERIGHRYIEV 115
>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 = 52.2 bits (126), Expect = 1e-09
Identities = 13/52 (25%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
+FVG D++E ++ FSQYG+++++ + + + F F+ + D +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQI 54
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 52.7 bits (127), Expect = 1e-09
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQ-YGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDN 94
+FVG L D+ +G + F + Y +V D+ TG SKG+ F+ + D+ ++
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70
Query: 95 LNGVKVL-SRTIRV 107
G L S+ +R+
Sbjct: 71 CQGAVGLGSKPVRL 84
>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 = 52.1 bits (125), Expect = 2e-09
Identities = 18/89 (20%), Positives = 39/89 (43%), Gaps = 2/89 (2%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS + + ++ + GLP+ S+ +++ FS + N + G+S G
Sbjct: 2 SSGSSGN-SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
F+ + Q ++ + ++ R I +
Sbjct: 61 FVQFASQEIAEKALK-KHKERIGHRYIEI 88
>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 = 52.2 bits (125), Expect = 2e-09
Identities = 19/94 (20%), Positives = 35/94 (37%), Gaps = 17/94 (18%)
Query: 19 SSGSKTSWHDQYKD-----------SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVR 67
SSGS + H + S + GGL +S ++ + + G + L
Sbjct: 2 SSGSSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDAL---- 57
Query: 68 DKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVL 101
+ +K + F Y + + LNG +V+
Sbjct: 58 --LMPPNKPYSFARYRTTEESKRAYVTLNGKEVV 89
>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 = 51.5 bits (124), Expect = 3e-09
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
+FVG D++ ++ F QYGE+V++ + + + F F+ + D +
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKV 60
>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 = 52.5 bits (126), Expect = 3e-09
Identities = 22/123 (17%), Positives = 52/123 (42%), Gaps = 8/123 (6%)
Query: 11 KKLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNL----- 65
++S +E+ + S ++ + + I+V L + E D+ IF +Y + +
Sbjct: 23 GRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFD 82
Query: 66 VRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNKYTDEE 125
+R G+ KG FI ++++ ++ NG + + + V + + + E
Sbjct: 83 IRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFA---RSARPKQDPKEG 139
Query: 126 TKK 128
+K
Sbjct: 140 KRK 142
>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 = 51.8 bits (124), Expect = 5e-09
Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 3/77 (3%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVL 90
+ + GLPY +E D+ FS V +++ G+ G + + V
Sbjct: 44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADVEFATHEEAVA 101
Query: 91 SVDNLNGVKVLSRTIRV 107
++ + + R I +
Sbjct: 102 AMS-KDRANMQHRYIEL 117
>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 = 50.6 bits (121), Expect = 1e-08
Identities = 18/119 (15%), Positives = 46/119 (38%), Gaps = 5/119 (4%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
S ++ ++ +++ GLP++ VI F + + + + GK+ G
Sbjct: 11 SGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEG 70
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKLRTIGCAPG 137
F+ + ++ ++ + + +R I+V + K + +K G + G
Sbjct: 71 FVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT----KKGMLEKIDMIRKRLQSGPSSG 124
>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 = 49.8 bits (119), Expect = 1e-08
Identities = 13/100 (13%), Positives = 33/100 (33%), Gaps = 10/100 (10%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
I LP ++ FS++G + + L + + + + + +L
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFRHL 66
Query: 96 NGVKVLSRTIRVD----HVNDYKPPKDNKYTDEETKKLRT 131
K + ++ V P K + ++ +K +
Sbjct: 67 AYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAES 106
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 49.7 bits (119), Expect = 2e-08
Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 2/82 (2%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+++ G P D + D+ G+++N+ + R KG F+ ++ S V+
Sbjct: 14 VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-T 71
Query: 96 NGVKVLSRTIRVDHVNDYKPPK 117
G K + + +DY K
Sbjct: 72 PGQKYKETDLLILFKDDYFAKK 93
>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 = 49.8 bits (119), Expect = 2e-08
Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 7/76 (9%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ V GLP S D+ + G++ ++ RD G + + + +V L
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKL 71
Query: 96 NGVKVLSRTIRVDHVN 111
+ K S ++
Sbjct: 72 DNTKFRSHEGETAYIR 87
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 49.2 bits (118), Expect = 2e-08
Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 6/72 (8%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+FV G P + + F +G + ++ + +DK F + D +V +
Sbjct: 11 VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGD-VGAREAVLSQ 64
Query: 96 NGVKVLSRTIRV 107
+ + +RV
Sbjct: 65 SQHSLGGHRLRV 76
>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 = 48.5 bits (116), Expect = 4e-08
Identities = 18/89 (20%), Positives = 35/89 (39%), Gaps = 4/89 (4%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFC 78
SSGS S Q + + GLPY +E D+ FS + +++ G+ G
Sbjct: 2 SSGSSGS-SFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEA 58
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
+ + V ++ + + R + +
Sbjct: 59 DVEFATHEDAVAAMA-KDKANMQHRYVEL 86
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 47.7 bits (114), Expect = 5e-08
Identities = 14/72 (19%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNL 95
+ + G P++++E +V+ + V + +VR+ G G+ F+ + ++ ++
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVDFSNEEEVKQALK-C 69
Query: 96 NGVKVLSRTIRV 107
N + R I V
Sbjct: 70 NREYMGGRYIEV 81
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 46.4 bits (110), Expect = 3e-07
Identities = 13/81 (16%), Positives = 31/81 (38%), Gaps = 6/81 (7%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLN----LVRDKITGKSKGFCFICYEDQR 86
++ + + GLP+ + +V+ F Q+ I V G+ G F+ + +
Sbjct: 21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEE 79
Query: 87 STVLSVDNLNGVKVLSRTIRV 107
++ + + R I +
Sbjct: 80 YAQNALR-KHKDLLGKRYIEL 99
>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 = 46.1 bits (109), Expect = 4e-07
Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 3/74 (4%)
Query: 36 IFVGGLPYDLSEGDVICIFSQYGEIVNLNLVR--DKITGKSKGFCFICYEDQRSTVLSVD 93
+ + GLP+ S DV S + V G+ G F+ E + L++
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79
Query: 94 NLNGVKVLSRTIRV 107
+ + R I V
Sbjct: 80 -KDRESMGHRYIEV 92
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 45.6 bits (108), Expect = 6e-07
Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 5/89 (5%)
Query: 21 GSKTSWHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVR--DKITGKSKGFC 78
GSK ++ D I GLP+ + DV+ FS N + GK +G
Sbjct: 1 GSKLE--EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDA 58
Query: 79 FICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
I E ++ +++ + + + R + V
Sbjct: 59 LIEMESEQDVQKALE-KHRMYMGQRYVEV 86
>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 = 44.2 bits (104), Expect = 3e-06
Identities = 14/79 (17%), Positives = 26/79 (32%), Gaps = 3/79 (3%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVR--DKITGKSKGFCFICYEDQRST 88
+ + + GLP+ S DV S V G+ G F+ +
Sbjct: 42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDV 101
Query: 89 VLSVDNLNGVKVLSRTIRV 107
+++ + + R I V
Sbjct: 102 KMALK-KDRESMGHRYIEV 119
>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 = 40.2 bits (94), Expect = 4e-05
Identities = 16/99 (16%), Positives = 29/99 (29%), Gaps = 10/99 (10%)
Query: 19 SSGSKTSWHDQYKDSAWIFVGGLPYDLS-EGDVICIFSQYGEIVNLNLVRDKITGKSKGF 77
SSGS + + + + ++ + +G I N ++
Sbjct: 2 SSGSSGQKGRV-ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLIL------NKINE 54
Query: 78 CFICYEDQRSTVLSVD--NLNGVKVLSRTIRVDHVNDYK 114
FI +VD V + +RV YK
Sbjct: 55 AFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYK 93
>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 = 40.3 bits (94), Expect = 5e-05
Identities = 21/82 (25%), Positives = 34/82 (41%), Gaps = 9/82 (10%)
Query: 36 IFVGGLPYD-LSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVD- 93
I + LP+ S+ V+ + YG+I N L+ + K FI E + + VD
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM------RMKSQAFIEMETREDAMAMVDH 81
Query: 94 -NLNGVKVLSRTIRVDHVNDYK 114
+ R ++VD YK
Sbjct: 82 CLKKALWFQGRCVKVDLSEKYK 103
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 38.9 bits (90), Expect = 1e-04
Identities = 12/80 (15%), Positives = 31/80 (38%), Gaps = 6/80 (7%)
Query: 33 SAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSV 92
S+W+ + L + + + Q+G +V+ + ++G Y + +
Sbjct: 7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQ 60
Query: 93 DNLNGVKVLSRTIRVDHVND 112
LN + + TI + ++
Sbjct: 61 MALNNCVLANTTIFAESPSE 80
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 40.6 bits (94), Expect = 1e-04
Identities = 17/93 (18%), Positives = 37/93 (39%), Gaps = 2/93 (2%)
Query: 26 WHDQYKDSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQ 85
+ + +++ G P D + D+ G+++N+ + R KG F+ ++
Sbjct: 102 EYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSI 160
Query: 86 RSTVLSVDNLNGVKVLSRTIRVDHVNDYKPPKD 118
S V+ G K + + +DY K+
Sbjct: 161 ESAKKFVETP-GQKYKETDLLILFKDDYFAKKN 192
>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 = 38.3 bits (89), Expect = 2e-04
Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 2/67 (2%)
Query: 43 YDLSEGDVICIFSQ-YGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVL 101
YD +V + YGE+ +N V D + G ++ + + +V +LN
Sbjct: 36 YDEFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFN 94
Query: 102 SRTIRVD 108
+ I +
Sbjct: 95 GQPIHAE 101
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 38.9 bits (90), Expect = 3e-04
Identities = 20/96 (20%), Positives = 41/96 (42%), Gaps = 10/96 (10%)
Query: 35 WIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDN 94
I V L Y ++ + IFS++G ++ + + + Y D S + +
Sbjct: 48 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLS 103
Query: 95 LNGVKVL--SRTIRVDHVNDYKPPKDN-KYTDEETK 127
L+G + T+R+D K N KY +++++
Sbjct: 104 LDGQNIYNACCTLRIDF---SKLTSLNVKYNNDKSR 136
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 39.4 bits (91), Expect = 3e-04
Identities = 15/86 (17%), Positives = 36/86 (41%), Gaps = 15/86 (17%)
Query: 36 IFVGGLPYDLS---------EGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQR 86
++VGG+ L+ E + +FS+ G+I + V +SK F+ ++ Q
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQA 190
Query: 87 STVLSVDNLNGVKVLSRTIRVDHVND 112
+ + + ++ +L + +
Sbjct: 191 NAEFAKEAMSNQTLLLPSDKEWDDRR 216
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 36.2 bits (83), Expect = 0.002
Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 35 WIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDN 94
I V L Y ++ + IFS++G ++ + + + Y D S + +
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLS 85
Query: 95 LNGVKVL--SRTIRVDH 109
L+G + T+R+D
Sbjct: 86 LDGQNIYNACCTLRIDF 102
>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 = 35.4 bits (81), Expect = 0.002
Identities = 16/89 (17%), Positives = 39/89 (43%), Gaps = 7/89 (7%)
Query: 32 DSAWIFVGGLPYDLSEGDV----ICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRS 87
+ A + V + Y LS ++ F+++G++ ++ L + + E+ +
Sbjct: 8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQD 64
Query: 88 TVLSVDNLNGVKVLSRTIRVDHVNDYKPP 116
+ +V++L+ K+ S+ I V P
Sbjct: 65 AIGAVNSLHRYKIGSKKILVSLATGASGP 93
>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 = 35.0 bits (80), Expect = 0.014
Identities = 15/85 (17%), Positives = 30/85 (35%), Gaps = 19/85 (22%)
Query: 38 VGGLPYDLSEGDVICIFSQYG---EIVNLNL-----VRDKITGKSKGFCFICYEDQRSTV 89
+ + V + + G EIVN N+ V G + D + V
Sbjct: 1818 AASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYV---AAGDLRAL------DTVTNV 1868
Query: 90 LSVDNLNGVKV--LSRTIRVDHVND 112
L+ L + + L +++ ++ V
Sbjct: 1869 LNFIKLQKIDIIELQKSLSLEEVEG 1893
Score = 31.6 bits (71), Expect = 0.16
Identities = 16/102 (15%), Positives = 32/102 (31%), Gaps = 28/102 (27%)
Query: 19 SSGSKTSWHDQYKDS-AWIFVGGLPYDLSEGDVICIFSQ--YGEI-VNLNLVRDKITGKS 74
+ S S+ + + +F G+ Y + +++ D +
Sbjct: 285 ETDSWESFFVSVRKAITVLFFIGVR------------CYEAYPNTSLPPSILEDSLEN-- 330
Query: 75 KGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRVDHVNDYKPP 116
E S +LS+ NL +V V+ N + P
Sbjct: 331 -N------EGVPSPMLSISNLTQEQVQDY---VNKTNSHLPA 362
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 32.0 bits (72), Expect = 0.042
Identities = 11/94 (11%), Positives = 33/94 (35%), Gaps = 7/94 (7%)
Query: 35 WIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDN 94
+ + Y ++ + + + G++ R I ++ + +E +
Sbjct: 27 LLSIQNPLYPITVDVLYTVCNPVGKV-----QRIVIFKRNGIQAMVEFESVLCAQKAKAA 81
Query: 95 LNGVKVLSRTIRVDHVNDYKPPKDN-KYTDEETK 127
LNG + + + + +P + N D ++
Sbjct: 82 LNGADIYAGCCTL-KIEYARPTRLNVIRNDNDSW 114
>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 95
Score = 30.8 bits (69), Expect = 0.073
Identities = 13/59 (22%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 49 DVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIRV 107
+++ YG IV + + + ++ + + D S LSV +++G+KV R +++
Sbjct: 40 ELMQTLGSYGTIVLVRINQGQM--------LVTFADSHS-ALSVLDVDGMKVKGRAVKI 89
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 32.1 bits (72), Expect = 0.097
Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 6/59 (10%)
Query: 39 GGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNG 97
GGL +S ++ + + G + L + +K + F Y + + LNG
Sbjct: 26 GGLGNGVSRNQLLPVLEKCGLVDAL------LMPPNKPYSFARYRTTEESKRAYVTLNG 78
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 31.3 bits (70), Expect = 0.13
Identities = 9/40 (22%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 153 QEKDS----KPTESKDKKRKHKEKKVKKEKKKKKKRKKSS 188
QE D+ E ++K +K E+ +++ ++ +K K ++
Sbjct: 99 QELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINN 138
Score = 28.6 bits (63), Expect = 1.2
Identities = 12/68 (17%), Positives = 27/68 (39%), Gaps = 17/68 (25%)
Query: 149 EDIK--QEKDSKPTESKDKKRKHKEKKVKKEKKK----------KKKRKKSSSSSSS--- 193
E I+ +E+ K + D K E++ +++ KK ++ K ++ +
Sbjct: 85 ESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRIADKA 144
Query: 194 --SSSDSD 199
D+D
Sbjct: 145 FYQQPDAD 152
>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 = 29.8 bits (67), Expect = 0.21
Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 2/66 (3%)
Query: 49 DVICIFSQYGEIVNLNLVR--DKITGKSKGFCFICYEDQRSTVLSVDNLNGVKVLSRTIR 106
DV S+YG + ++ + R D + G F+ + ++ L G K +R +
Sbjct: 31 DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVV 90
Query: 107 VDHVND 112
+ +
Sbjct: 91 TKYCDP 96
>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A
{Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A*
1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A*
1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A*
2ga2_A* 2oaz_A*
Length = 478
Score = 31.0 bits (70), Expect = 0.23
Identities = 15/85 (17%), Positives = 28/85 (32%), Gaps = 4/85 (4%)
Query: 114 KPPKDNKYTDEETKKLRTIG----CAPGTEFGSILPVKTEDIKQEKDSKPTESKDKKRKH 169
+ K + KK + P E G+ + +++ +D +
Sbjct: 30 TAEEAAKKKRRKKKKSKGPSAAGEQEPDKESGASVDEVARQLERSALEDKERDEDDEDGD 89
Query: 170 KEKKVKKEKKKKKKRKKSSSSSSSS 194
+ KKKKKK+KK +
Sbjct: 90 GDGDGATGKKKKKKKKKRGPKVQTD 114
Score = 26.0 bits (57), Expect = 8.6
Identities = 11/41 (26%), Positives = 20/41 (48%)
Query: 155 KDSKPTESKDKKRKHKEKKVKKEKKKKKKRKKSSSSSSSSS 195
D P + ++ E+ KK+++KKKK K S++
Sbjct: 16 GDLDPDDREEGAASTAEEAAKKKRRKKKKSKGPSAAGEQEP 56
Score = 26.0 bits (57), Expect = 8.7
Identities = 9/53 (16%), Positives = 17/53 (32%)
Query: 147 KTEDIKQEKDSKPTESKDKKRKHKEKKVKKEKKKKKKRKKSSSSSSSSSSDSD 199
+ + +E KK +KKKK + S++ +S
Sbjct: 9 ASGSHLNGDLDPDDREEGAASTAEEAAKKKRRKKKKSKGPSAAGEQEPDKESG 61
>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 = 30.6 bits (70), Expect = 0.34
Identities = 7/42 (16%), Positives = 13/42 (30%)
Query: 57 YGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNGV 98
+ KGF F+ + Q+S + + V
Sbjct: 13 QQLHSQTPRAEGVVKATEKGFGFLEVDAQKSYFIPPPQMKKV 54
>4ady_A RPN2, 26S proteasome regulatory subunit RPN2; protein binding, PC
repeat; 2.70A {Saccharomyces cerevisiae}
Length = 963
Score = 30.6 bits (68), Expect = 0.34
Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 1/79 (1%)
Query: 122 TDEETKKLRTIGCAPGTEFGSILPVKTEDIKQ-EKDSKPTESKDKKRKHKEKKVKKEKKK 180
+D+ K + A F + K+ EK + S + K + KK KKEK
Sbjct: 775 SDQAIPKFQMNCYAKEDAFSYPRMYEEASGKEVEKVATAVLSTTARAKARAKKTKKEKGP 834
Query: 181 KKKRKKSSSSSSSSSSDSD 199
++ KK +++
Sbjct: 835 NEEEKKKEHEEKEKERETN 853
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 29.2 bits (65), Expect = 0.40
Identities = 12/83 (14%), Positives = 28/83 (33%), Gaps = 17/83 (20%)
Query: 31 KDSAWIFVGGLPYDLSEGDVICIF-----SQYGEIVNLNLVRDKITGKSKGFCFICYEDQ 85
+ V GLP + + + F S G +++ + + + +
Sbjct: 6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ--------RLGCGGVLTFREP 57
Query: 86 RS--TVLSVDN--LNGVKVLSRT 104
VL+ + L+G ++ R
Sbjct: 58 ADAERVLAQADHELHGAQLSLRP 80
>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 = 28.8 bits (65), Expect = 0.42
Identities = 8/51 (15%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 47 EGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFICYEDQRSTVLSVDNLNG 97
+ DVI +++G ++++ + ++ G ++ + + +V+ L+G
Sbjct: 31 KDDVIEECNKHGGVIHIYVDKNSAQGN----VYVKCPSIAAAIAAVNALHG 77
>3izc_e 60S ribosomal protein RPL7 (L30P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_e
3o58_G 3o5h_G 3u5e_F 3u5i_F
Length = 244
Score = 29.8 bits (66), Expect = 0.51
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 154 EKDSKPTESKDKKRKHKEKKVKKEKKKKKKRKK 186
+ ES+ KK K ++K ++ ++ RK
Sbjct: 3 AEKILTPESQLKKSKAQQKTAEQVAAERAARKA 35
>2k9x_A Tburm1, uncharacterized protein; unknown function; NMR
{Trypanosoma brucei}
Length = 110
Score = 28.7 bits (64), Expect = 0.56
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFS 55
VGG+ Y L++GD + S
Sbjct: 74 SCDAEVVGGMDYVLNDGDTVEFIS 97
>4a17_V RPL7, 60S ribosomal protein L7; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_V 4a1c_V 4a1e_V
Length = 239
Score = 28.6 bits (63), Expect = 1.3
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 161 ESKDKKRKHKEKKVKKEKKKKKKRKK 186
E+ KK EK K + +++K
Sbjct: 7 ENVQKKLARDEKLRKAKAEQRKASSA 32
>2nqb_D Histone H2B; nucleosome, NCP, chromatin, structural protein/DNA
complex; 2.30A {Drosophila melanogaster} PDB: 2pyo_D*
Length = 123
Score = 27.7 bits (61), Expect = 1.4
Identities = 10/33 (30%), Positives = 14/33 (42%)
Query: 159 PTESKDKKRKHKEKKVKKEKKKKKKRKKSSSSS 191
P ++ K K K K K KK+K+ S
Sbjct: 2 PPKTSGKAAKKAGKAQKNITKTDKKKKRKRKES 34
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 28.5 bits (64), Expect = 1.5
Identities = 11/94 (11%), Positives = 32/94 (34%), Gaps = 8/94 (8%)
Query: 106 RVDHVNDYKPPKDNKYTDEETKKLRTIGCAPGTEFGSILPVKTEDIKQ--------EKDS 157
R+ +V + P R+ G + + ED + +
Sbjct: 320 RIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLLIA 379
Query: 158 KPTESKDKKRKHKEKKVKKEKKKKKKRKKSSSSS 191
+ ++ + KE + E+ +++ ++ + +S
Sbjct: 380 EEEIIEEAEANWKELVHEVEESRRRSERELTDTS 413
>2zkr_r 60S ribosomal protein L17; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 184
Score = 28.0 bits (62), Expect = 1.5
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 152 KQEKDSKPTESKDKKRKHKEKKVKKEKKKKKK 183
K++ KP E +K+K +KK+KK+K ++
Sbjct: 153 KEQIVPKPEEEVAQKKKISQKKLKKQKLMARE 184
>2crw_A ARF GAP 3, ADP-ribosylation factor GTPase-activating protein 3;
arfgap domain, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 149
Score = 27.6 bits (61), Expect = 2.0
Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 3/77 (3%)
Query: 118 DNKYTDEETKKLRTIGCAPGTEFGSILPVKTEDIKQEKDSKPTESKDKKRKHKEKKVKKE 177
D+ ++ + + ++ G A + F T D + +S+ + R+ + +
Sbjct: 75 DSNWSWFQLRCMQVGGNASASSFFHQHGCSTNDTNAKYNSR---AAQLYREKIKSLASQA 131
Query: 178 KKKKKKRKKSSSSSSSS 194
+K SS SS
Sbjct: 132 TRKHGTDLWLDSSGPSS 148
>2ew5_A Peptide deformylase; inhibitor, hydrolase; HET: Y12; 2.20A
{Helicobacter pylori} PDB: 2ew6_A* 2ew7_A
Length = 181
Score = 27.5 bits (62), Expect = 2.2
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 166 KRKHKEKKVKKEKKKKKKRKKSSS 189
KRK EK++K+ +KK+K + +
Sbjct: 155 KRKKFEKELKELQKKQKHKLEHHH 178
>3iz5_e 60S ribosomal protein L7 (L30P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_e
Length = 244
Score = 27.5 bits (60), Expect = 2.6
Identities = 7/34 (20%), Positives = 13/34 (38%)
Query: 153 QEKDSKPTESKDKKRKHKEKKVKKEKKKKKKRKK 186
+ E KR+ +E ++K+K K
Sbjct: 4 EAAKVAVPEKVILKRRREEVWAAEKKQKVAAEKI 37
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 27.3 bits (60), Expect = 2.6
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 43 YDLSEGDVICIFSQYGEIVNLNLV 66
SEGDV+C + G +++ LV
Sbjct: 36 ERFSEGDVVC--ALCGLVLSDKLV 57
>2ki8_A Tungsten formylmethanofuran dehydrogenase, subunit D (FWDD-2);
beta-barrel, structural genomics, PSI-2, protein
structure initiative; NMR {Archaeoglobus fulgidus}
Length = 146
Score = 26.9 bits (60), Expect = 3.2
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 43 YDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFI 80
L EGD + + +++GE+V V K KG FI
Sbjct: 65 LGLQEGDRVKVKTEFGEVV----VFAKKGDVPKGMIFI 98
>1y8q_B Anthracycline-, ubiquitin-like 2 activating enzyme E1B; SUMO,
heterodimer, UBL, ligase; HET: ATP; 2.25A {Homo sapiens}
PDB: 1y8r_B* 3kyc_B* 3kyd_B* 2px9_A
Length = 640
Score = 27.4 bits (60), Expect = 3.7
Identities = 15/111 (13%), Positives = 29/111 (26%), Gaps = 8/111 (7%)
Query: 97 GVKVLSRTIRVDHVNDYKPPKDNKYTDEETKKLRTIGCAPGTE--------FGSILPVKT 148
+ I ++ + KKL G G+ ++L
Sbjct: 474 AMVAPDVQIEDGKGTILISSEEGETEANNHKKLSEFGIRNGSRLQADDFLQDYTLLINIL 533
Query: 149 EDIKQEKDSKPTESKDKKRKHKEKKVKKEKKKKKKRKKSSSSSSSSSSDSD 199
KD + D K K+ + K + S+S++
Sbjct: 534 HSEDLGKDVEFEVVGDAPEKVGPKQAEDAAKSITNGSDDGAQPSTSTAQEQ 584
Score = 27.0 bits (59), Expect = 4.9
Identities = 9/68 (13%), Positives = 20/68 (29%)
Query: 114 KPPKDNKYTDEETKKLRTIGCAPGTEFGSILPVKTEDIKQEKDSKPTESKDKKRKHKEKK 173
T+ + + ++ E+ E + +KRK EK+
Sbjct: 559 AEDAAKSITNGSDDGAQPSTSTAQEQDDVLIVDSDEEDSSNNADVSEEERSRKRKLDEKE 618
Query: 174 VKKEKKKK 181
K+ +
Sbjct: 619 NLSAKRSR 626
>3ml1_A NAPA, periplasmic nitrate reductase; heterodimer, oxidoreductase;
HET: MGD HEC; 1.60A {Ralstonia eutropha} PDB: 3o5a_A*
1ogy_A* 2nya_A*
Length = 802
Score = 27.4 bits (61), Expect = 3.9
Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 3/55 (5%)
Query: 43 YDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGFCFI--CYEDQRSTVLSVDNL 95
L G + + S+ G + + R + +G F+ Q +++D
Sbjct: 730 LGLRRGVEVEVVSRRGRMRSRIETRGRDAPP-RGLVFVPWFDASQLINKVTLDAT 783
>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein,
signaling protein; 1.44A {Saccharomyces cerevisiae}
PDB: 2pko_A 2ax5_A
Length = 99
Score = 26.0 bits (57), Expect = 3.9
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFS 55
D+ W G Y L +GD+I S
Sbjct: 71 DTDWELEGEKDYILEDGDIISFTS 94
>2rf4_A DNA-directed RNA polymerase I subunit RPA4; transferase DNA/RNA,
DNA-binding, phosphorylation, POL I, POLI, rpoli,
nuclear protein; 3.10A {Saccharomyces cerevisiae}
Length = 214
Score = 27.0 bits (59), Expect = 4.4
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 164 DKKRKHKEKKVKKEKKKKKKRKKSSSSSSSSSS 196
KR ++ ++ + KK KK+ + + +S
Sbjct: 3 QVKRANENRETARFIKKHKKQVTNPIDEKNGTS 35
>1v9d_A Diaphanous protein homolog 1; helix bundle, protein binding; 2.60A
{Mus musculus} SCOP: a.207.1.1
Length = 340
Score = 26.6 bits (59), Expect = 5.7
Identities = 7/24 (29%), Positives = 16/24 (66%)
Query: 163 KDKKRKHKEKKVKKEKKKKKKRKK 186
++ + K + K+ KEK +K++ +K
Sbjct: 316 RETEEKMRRAKLAKEKAEKERLEK 339
>1jkw_A Cyclin H; cell cycle, cell division, nuclear protein; 2.60A {Homo
sapiens} SCOP: a.74.1.1 a.74.1.1 PDB: 1kxu_A
Length = 323
Score = 26.6 bits (58), Expect = 6.0
Identities = 9/39 (23%), Positives = 13/39 (33%)
Query: 157 SKPTESKDKKRKHKEKKVKKEKKKKKKRKKSSSSSSSSS 195
KKRK E KK K + ++ + S
Sbjct: 284 ELALNVITKKRKGYEDDDYVSKKSKHEEEEWTDDDLVES 322
>1wgk_A Riken cDNA 2900073H19 protein; THis domain, ubiqutin-like fold,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: d.15.3.3 PDB: 1xo3_A
Length = 114
Score = 25.7 bits (56), Expect = 6.3
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFS 55
D+ W +G L Y L + D I S
Sbjct: 80 DADWELLGELDYQLQDQDSILFIS 103
>2zkr_w 60S ribosomal protein L7; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 270
Score = 26.4 bits (57), Expect = 6.3
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 161 ESKDKKRKHKEKKVKKEKKKKKKRKK 186
E+ KKR++ + K +KK K
Sbjct: 38 ETLKKKRRNFAELKVKRLRKKFALKT 63
>1mj4_A Sulfite oxidase; cytochrome B5, heme, oxidoreductase; HET: HEM;
1.20A {Homo sapiens} SCOP: d.120.1.1
Length = 82
Score = 25.0 bits (55), Expect = 6.5
Identities = 8/40 (20%), Positives = 20/40 (50%), Gaps = 6/40 (15%)
Query: 8 KNIKKLSEQELSSGSKTSWHDQYKDSAWIFVGGLPYDLSE 47
++ +++E+SS H + W+ +G +D++E
Sbjct: 2 ESTHIYTKEEVSS------HTSPETGIWVTLGSEVFDVTE 35
>2q8k_A Proliferation-associated protein 2G4; EBP1, PA2G4, methionine
aminopeptidase, PITA-bread, transcri; 1.60A {Homo
sapiens} PDB: 2v6c_A
Length = 401
Score = 26.6 bits (59), Expect = 6.8
Identities = 9/49 (18%), Positives = 21/49 (42%)
Query: 142 SILPVKTEDIKQEKDSKPTESKDKKRKHKEKKVKKEKKKKKKRKKSSSS 190
S + V+ ++K S + KK+K K K + + +++ +
Sbjct: 352 SEMEVQDAELKALLQSSASRKTQKKKKKKASKTAENATSGETLEENEAG 400
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 26.1 bits (56), Expect = 7.2
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 11/28 (39%)
Query: 8 KNIKKLSEQELSSGSKTSWHDQYK-DSA 34
+ +KKL + L K Y DSA
Sbjct: 20 QALKKL-QASL----KL-----YADDSA 37
>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure
initiative, NE structural genomix research consortium,
nysgxrc; 2.35A {Pichia guilliermondii}
Length = 132
Score = 25.9 bits (56), Expect = 7.4
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 32 DSAWIFVGGLPYDLSEGDVICIFSQYGEIVNLNLVRDKITGKSKGF 77
I V G P ++ VI F ++G I+ V K + G
Sbjct: 6 GELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGL 50
>1tzy_B Histone H2B; histone-fold, tetramer-dimer-dimer, DNA binding
protein; 1.90A {Gallus gallus} SCOP: a.22.1.1 PDB:
1eqz_B 1hq3_B 2aro_B 2hio_B 3c9k_B 3azg_D 3a6n_D 3an2_D
3av1_D 3av2_D 3ayw_D 3aze_D 3azf_D 3afa_D 3azh_D 3azi_D
3azj_D 3azk_D 3azl_D 3azm_D ...
Length = 126
Score = 25.5 bits (55), Expect = 8.5
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 153 QEKDSKPTESKDKKRKHKEKKVKKEKKKKKKRKKS 187
+ S P K K+ + + K +KK+KK RK+S
Sbjct: 3 EPAKSAPAPKKGSKKAVTKTQKKGDKKRKKSRKES 37
Score = 25.5 bits (55), Expect = 9.1
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 162 SKDKKRKHKEKKVKKEKKKKKKRKKSSSSS 191
+ K+ K+ K +KK KKRKKS S
Sbjct: 8 APAPKKGSKKAVTKTQKKGDKKRKKSRKES 37
>2w3t_A Peptide deformylase; protein biosynthesis, iron, nickel, hydrolase,
metal-binding; 1.69A {Escherichia coli} PDB: 2w3u_A
Length = 188
Score = 25.9 bits (58), Expect = 8.6
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 166 KRKHKEKKVKKEKKKKKKRKKSSSSSSSSSS 196
K++ +KV+K + K + SSS +++
Sbjct: 150 KQQRIRQKVEKLDRLKARAPNSSSVDKLAAA 180
>4dh9_Y YAEJ; ribosome, YAEJ, ribosome stalling, ribosome rescue, rescue F
alternative rescue factor, ARFB, release factor, rescue
of ribosomes; 3.20A {Escherichia coli} PDB: 2jy9_A
Length = 140
Score = 25.5 bits (56), Expect = 9.9
Identities = 8/37 (21%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 152 KQEKDSKPTESKDKKRKHKEKKVKKEKKKKKKRKKSS 188
K + ++PT + ++R K K K + + +S
Sbjct: 103 KARRPTRPTRASKERRL-ASKAQKSSVKAMRGKVRSG 138
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
0.308 0.127 0.357
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: 2,717,921
Number of extensions: 151399
Number of successful extensions: 1388
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1150
Number of HSP's successfully gapped: 355
Length of query: 199
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 110
Effective length of database: 4,216,824
Effective search space: 463850640
Effective search space used: 463850640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 55 (24.9 bits)