RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy222
(225 letters)
>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 = 90.2 bits (224), Expect = 3e-23
Identities = 28/106 (26%), Positives = 40/106 (37%), Gaps = 5/106 (4%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
D R L + + E L Q F YG + SV++V D T S+ YGF+++ +
Sbjct: 37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSS 96
Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNS 190
AI LN N + V R G G+ N
Sbjct: 97 AQQAIAGLNGFNILNKRLKVALAASG-----HQRPGIAGAVGDGNG 137
>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 = 86.5 bits (215), Expect = 2e-22
Identities = 19/78 (24%), Positives = 40/78 (51%)
Query: 89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
P+R +++G + + E + + G VI+++++ D TG SK Y F+E+ ++ +A
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 149 IRALNRQNFQGSEIIVDF 166
+R LN + +
Sbjct: 61 VRNLNGYQLGSRFLKCGY 78
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 87.1 bits (216), Expect = 2e-22
Identities = 16/78 (20%), Positives = 31/78 (39%)
Query: 89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
P + + RLN N RE L+ +YG+V V ++ T + + +
Sbjct: 5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKET 64
Query: 149 IRALNRQNFQGSEIIVDF 166
++ L+ + G+ I
Sbjct: 65 VKNLHLTSVMGNIIHAQL 82
>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 = 84.9 bits (211), Expect = 6e-22
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
S+ + L+I L + + DL + YGK++S + + D T K YGF+++D A
Sbjct: 2 SSGSSG-LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
Query: 146 LAAIRALNRQNFQGSEI 162
A+ AL Q
Sbjct: 61 QKAVTALKASGVQAQMA 77
>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 = 85.0 bits (211), Expect = 8e-22
Identities = 32/103 (31%), Positives = 49/103 (47%), Gaps = 5/103 (4%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
+ R++F+G + + E L+ F+E G V+S R+V D TG K YGF EY ++
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62
Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGN 187
L+A+R LN + F G + VD K + G
Sbjct: 63 ALSAMRNLNGREFSGRALRVDNAASE-----KNKEELKSLGTG 100
>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 = 83.8 bits (208), Expect = 2e-21
Identities = 25/95 (26%), Positives = 52/95 (54%), Gaps = 3/95 (3%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
+ + P++TLF+ L++++ E L+++F + R+V D TG SK +GF++++ E+
Sbjct: 10 ARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEED 66
Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRR 179
AA A+ G+++ +D+ + G P
Sbjct: 67 AKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101
>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 = 83.8 bits (208), Expect = 2e-21
Identities = 20/82 (24%), Positives = 36/82 (43%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
++ DP L + L+ + E DL + F++YG + V +V D + S+ + F+ ++
Sbjct: 10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69
Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
A N G I V
Sbjct: 70 AKEAKERANGMELDGRRIRVSG 91
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 83.5 bits (207), Expect = 3e-21
Identities = 14/88 (15%), Positives = 33/88 (37%), Gaps = 6/88 (6%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGK--VISVRVVRDFVTGHSKRYGFLEYDCE 142
T+ + + ++ + A + Y V ++R+++D T ++ + F++
Sbjct: 4 HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSA 63
Query: 143 KACLAAIRALN----RQNFQGSEIIVDF 166
++ L G I VDF
Sbjct: 64 MDASQLLQILQSLHPPLKIDGKTIGVDF 91
>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 = 83.5 bits (207), Expect = 4e-21
Identities = 29/114 (25%), Positives = 53/114 (46%), Gaps = 5/114 (4%)
Query: 66 IPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRD 125
I + +P + LF+ +++ ++E ++++ F +YG++ ++ + D
Sbjct: 2 IHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD 61
Query: 126 FVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRR 179
TG SK Y +EY+ K LAA ALN G I VD+ + P+R
Sbjct: 62 RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK-----GPKR 110
>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 = 83.4 bits (207), Expect = 4e-21
Identities = 19/91 (20%), Positives = 34/91 (37%)
Query: 88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
D TL + L + L + F +YG+V V + R+ T + + F+ + +
Sbjct: 11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQD 70
Query: 148 AIRALNRQNFQGSEIIVDFECGRVLPGWKPR 178
A A++ G E+ V P
Sbjct: 71 AEAAMDGAELDGRELRVQVARYGRRDLSGPS 101
>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 = 84.0 bits (208), Expect = 5e-21
Identities = 24/113 (21%), Positives = 43/113 (38%)
Query: 54 PIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAE 113
G+ S + + ++ DP L + L+ + E DL + F++
Sbjct: 10 HSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSK 69
Query: 114 YGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
YG + V +V D + S+ + F+ ++ A N G I VDF
Sbjct: 70 YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 84.1 bits (208), Expect = 6e-21
Identities = 20/97 (20%), Positives = 39/97 (40%)
Query: 70 RAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTG 129
+ S R L++G L + + L AF +G + +++ D+ T
Sbjct: 43 ERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETE 102
Query: 130 HSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
+ + F+E++ + AAI +N G I V+
Sbjct: 103 KHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
>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 = 82.3 bits (204), Expect = 8e-21
Identities = 20/79 (25%), Positives = 37/79 (46%)
Query: 88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
T+++ L + DL + F++YGKV+ V +++D T SK F+ + + +
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73
Query: 148 AIRALNRQNFQGSEIIVDF 166
RA+N + G I
Sbjct: 74 CTRAINNKQLFGRVIKASI 92
>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 = 81.1 bits (201), Expect = 3e-20
Identities = 18/82 (21%), Positives = 41/82 (50%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
D T+ + L++++RE DL++ F +G + + + +D TG SK + F+ + +
Sbjct: 10 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED 69
Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
AI ++ + + V++
Sbjct: 70 AARAIAGVSGFGYDHLILNVEW 91
>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 = 81.2 bits (201), Expect = 3e-20
Identities = 20/95 (21%), Positives = 43/95 (45%), Gaps = 4/95 (4%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
+ + ++TL + L+ ++ E L++ F + + V G SK Y F+E+ +
Sbjct: 10 TWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASFED 65
Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRR 179
A+ + N++ +G I ++ + R P P
Sbjct: 66 AKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100
>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 = 82.6 bits (204), Expect = 3e-20
Identities = 20/90 (22%), Positives = 39/90 (43%)
Query: 77 RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
S + H + +L + L + L + F +YG+V V + RD T S+ + F
Sbjct: 57 GSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAF 116
Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
+ + ++ A+ A++ G E+ V
Sbjct: 117 VRFHDKRDAEDAMDAMDGAVLDGRELRVQM 146
>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 = 80.8 bits (200), Expect = 4e-20
Identities = 22/82 (26%), Positives = 38/82 (46%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
+ L++G L+ N E L F +G++ S++++ D TG SK YGF+ + +
Sbjct: 21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC 80
Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
A+ LN G + V
Sbjct: 81 AKKALEQLNGFELAGRPMKVGH 102
>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 = 80.3 bits (199), Expect = 5e-20
Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 6/100 (6%)
Query: 87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACL 146
+ + L++G L+ N E L F +GK+ ++ +++D TG SK YGF+ + +
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 147 AAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGG 186
A+ LN G + V V + G G
Sbjct: 62 RALEQLNGFELAGRPMRVGH----VTE--RLDGGSGPSSG 95
>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 = 80.0 bits (198), Expect = 7e-20
Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 5/102 (4%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
S + + LF+ L+ S E DLE+ F+ YG + + D +T K + F+ + +
Sbjct: 3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62
Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGG 186
+ A ++ Q FQG + V + K G G
Sbjct: 63 AVKAYAEVDGQVFQGRMLHVLPSTIK-----KEASQSGPSSG 99
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 79.5 bits (197), Expect = 8e-20
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
R +++G L ++ +++ F+++GKV +V+++ D T K +GF+E E AI
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAIA 60
Query: 151 ALNRQNFQGSEIIVD 165
L+ +F G I V
Sbjct: 61 KLDNTDFMGRTIRVT 75
>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 = 81.9 bits (203), Expect = 9e-20
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 2/84 (2%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
+ L++ L + + L+ F +YG ++ ++RD +TG + F+ Y+ +
Sbjct: 84 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE 143
Query: 145 CLAAIRALNRQNFQGS--EIIVDF 166
AI ALN +G + V
Sbjct: 144 AQEAISALNNVIPEGGSQPLSVRL 167
Score = 80.3 bits (199), Expect = 3e-19
Identities = 19/76 (25%), Positives = 37/76 (48%)
Query: 91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
L + L ++ + +L F G + + R++RD+ TG+S Y F+++ E AI+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 151 ALNRQNFQGSEIIVDF 166
LN + + V +
Sbjct: 64 VLNGITVRNKRLKVSY 79
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 80.0 bits (198), Expect = 9e-20
Identities = 27/93 (29%), Positives = 47/93 (50%)
Query: 74 RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
+ +P + LF+ +++ + E D+ FAEYG++ ++ + D TG+ K
Sbjct: 7 SVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 66
Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
Y +EY+ K AA+ LN Q+ G I VD+
Sbjct: 67 YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
>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 = 79.1 bits (196), Expect = 1e-19
Identities = 20/81 (24%), Positives = 38/81 (46%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
S R L++G L + + L AF +G + +++ D+ T + + F+E++ +
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 145 CLAAIRALNRQNFQGSEIIVD 165
AAI +N G I V+
Sbjct: 62 AAAAIDNMNESELFGRTIRVN 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 = 78.7 bits (195), Expect = 2e-19
Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 2/82 (2%)
Query: 86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRD-FVTGHSKRYGFLEYDCEKA 144
S PT+ + IGRL +N + + + F+ YGK+ + + + SK Y ++E++
Sbjct: 1 SMKPTK-VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDE 59
Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
A++ ++ G EI
Sbjct: 60 AEKALKHMDGGQIDGQEITATA 81
>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 = 80.6 bits (199), Expect = 2e-19
Identities = 30/128 (23%), Positives = 57/128 (44%), Gaps = 5/128 (3%)
Query: 61 DGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISV 120
+ + I + +P + LF+ +++ ++E ++++ F +YG++ ++
Sbjct: 43 NTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNI 102
Query: 121 RVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRL 180
+ D TG SK Y +EY+ K LAA ALN G I VD+ + P+R+
Sbjct: 103 HLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK-----GPKRV 157
Query: 181 GGGWGGNR 188
R
Sbjct: 158 KKSEKRRR 165
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 82.0 bits (203), Expect = 2e-19
Identities = 22/90 (24%), Positives = 39/90 (43%)
Query: 77 RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
R + + +++G + E + QAFA +G + S+ + D VT K + F
Sbjct: 15 RGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAF 74
Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
+EY+ +A A+ +N G I V
Sbjct: 75 VEYEVPEAAQLALEQMNSVMLGGRNIKVGR 104
Score = 74.7 bits (184), Expect = 1e-16
Identities = 20/99 (20%), Positives = 42/99 (42%), Gaps = 1/99 (1%)
Query: 69 DRAILRALRSTYKPHT-SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV 127
R +++ ++++ + D++ F +GK+ S + RD
Sbjct: 103 GRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPT 162
Query: 128 TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
TG K YGF+EY+ ++ A+ ++N + G + V
Sbjct: 163 TGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGK 201
>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 = 78.9 bits (195), Expect = 2e-19
Identities = 28/88 (31%), Positives = 41/88 (46%), Gaps = 4/88 (4%)
Query: 83 HTSSTDPTRT-LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
+ D LFIG++ +N E DL+ F E+GK+ + V++D TG K FL Y
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
Query: 142 EKACLAAIRALNRQN---FQGSEIIVDF 166
++ L A AL+ Q I V
Sbjct: 65 RESALKAQSALHEQKTLPGMNRPIQVKP 92
>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA
splicing, mRNA transport, nonsense-mediated mRNA decay,
nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*
Length = 126
Score = 79.3 bits (196), Expect = 3e-19
Identities = 33/122 (27%), Positives = 55/122 (45%), Gaps = 2/122 (1%)
Query: 74 RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
+ +P + LF+ +++ + E D+ FAEYG++ ++ + D TG+ K
Sbjct: 6 SVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 65
Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQL 193
Y +EY+ K AA+ LN Q+ G I VD+ V K +R GG +
Sbjct: 66 YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW--CFVRGPPKGKRRGGRRRSRSPDRRR 123
Query: 194 RF 195
R
Sbjct: 124 RL 125
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 78.5 bits (194), Expect = 3e-19
Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 1/83 (1%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
S++ LFI L + + +LE+ +G V +R+V + G K ++EY+ E
Sbjct: 11 YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENES 69
Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
A+ ++ + + I V
Sbjct: 70 QASQAVMKMDGMTIKENIIKVAI 92
>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 = 78.0 bits (193), Expect = 3e-19
Identities = 26/102 (25%), Positives = 40/102 (39%), Gaps = 14/102 (13%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
SS + L +G ++ +L F EYG VI +V+D+ F+ + +
Sbjct: 5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY--------AFVHMERAED 56
Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGG 186
+ AIR L+ FQG + V R R G G
Sbjct: 57 AVEAIRGLDNTEFQGKRMHVQLSTSR------LRTASGPSSG 92
>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 = 78.4 bits (194), Expect = 3e-19
Identities = 26/83 (31%), Positives = 46/83 (55%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
+ LF+G L+ ++ E LEQ F++YG++ V VV+D T S+ +GF+ ++
Sbjct: 6 SGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENID 65
Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
A+ A+N ++ G +I VD
Sbjct: 66 DAKDAMMAMNGKSVDGRQIRVDQ 88
>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 = 78.9 bits (195), Expect = 3e-19
Identities = 19/105 (18%), Positives = 43/105 (40%), Gaps = 4/105 (3%)
Query: 62 GTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVR 121
G+ + + S+Y P +P + L++ L+ E DL FA + +
Sbjct: 1 GSSGSSGEEIRKIPMFSSYNPG----EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPP 56
Query: 122 VVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
+ +TG + F+ + ++ A+ +N G ++++F
Sbjct: 57 IQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF 101
>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 = 78.5 bits (194), Expect = 3e-19
Identities = 26/105 (24%), Positives = 47/105 (44%), Gaps = 6/105 (5%)
Query: 82 PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
S + T+++G L++ E L + F + G V++ + +D VTG + YGF+E+
Sbjct: 7 GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66
Query: 142 EKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGG 186
E+ AI+ ++ G I V+ + L G G
Sbjct: 67 EEDADYAIKIMDMIKLYGKPIRVNKASAH------NKNLSGPSSG 105
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex,
AU-rich element, transcription/RNA complex; 1.80A {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H
1d8z_A 1d9a_A 3hi9_A
Length = 167
Score = 79.9 bits (198), Expect = 4e-19
Identities = 30/88 (34%), Positives = 49/88 (55%), Gaps = 3/88 (3%)
Query: 81 KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
+P ++S L++ L K + +LEQ F++YG++I+ R++ D VTG S+ GF+ +D
Sbjct: 80 RPSSASIRDAN-LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFD 138
Query: 141 CEKACLAAIRALNRQNFQGSE--IIVDF 166
AI+ LN Q G+ I V F
Sbjct: 139 KRIEAEEAIKGLNGQKPSGATEPITVKF 166
Score = 77.6 bits (192), Expect = 3e-18
Identities = 24/75 (32%), Positives = 35/75 (46%)
Query: 92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
L + L +N + + F G++ S ++VRD +TG S YGF+ Y K AI
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 152 LNRQNFQGSEIIVDF 166
LN Q I V +
Sbjct: 64 LNGLRLQTKTIKVSY 78
>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 = 78.0 bits (193), Expect = 4e-19
Identities = 19/83 (22%), Positives = 38/83 (45%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
+ R L++G L + + L AF +G + +++ D+ T + + F+E++ +
Sbjct: 6 SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65
Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
AAI +N G I V+
Sbjct: 66 DAAAAIDNMNESELFGRTIRVNL 88
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 78.6 bits (194), Expect = 4e-19
Identities = 31/111 (27%), Positives = 43/111 (38%)
Query: 56 QAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYG 115
Q GS T P L A + LFI L + + DL F +G
Sbjct: 6 QFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFG 65
Query: 116 KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
VIS +V D T SK +GF+ +D + AI+A+N + V
Sbjct: 66 NVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL 116
>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 = 79.5 bits (196), Expect = 4e-19
Identities = 23/121 (19%), Positives = 49/121 (40%), Gaps = 4/121 (3%)
Query: 74 RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
+ R + + TL++G L+ + E + + F++ G + + + D + +
Sbjct: 23 QHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACG 82
Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQL 193
+ F+EY A+R +N I D++ G + R+ G G G + +
Sbjct: 83 FCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK----EGRQYGRGRSGGQVRDEY 138
Query: 194 R 194
R
Sbjct: 139 R 139
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 78.6 bits (194), Expect = 7e-19
Identities = 19/90 (21%), Positives = 38/90 (42%)
Query: 77 RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
+Y + +L + L + L + F +YG+V V + RD T S+ + F
Sbjct: 34 SMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAF 93
Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
+ + ++ A+ A++ G E+ V
Sbjct: 94 VRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123
>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 = 76.9 bits (190), Expect = 9e-19
Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 14/102 (13%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
+ S+ T +F+G ++ +L F G+VI VV+D+ F+ + E
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDY--------AFVHMEKEA 54
Query: 144 ACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWG 185
AAI LN + +G I V+ ++ G G
Sbjct: 55 DAKAAIAQLNGKEVKGKRINVELSTKG------QKKSGPSSG 90
>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 = 77.4 bits (191), Expect = 1e-18
Identities = 27/92 (29%), Positives = 40/92 (43%), Gaps = 1/92 (1%)
Query: 74 RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
+R + RT+F +L R DLE F+ GKV VR++ D + SK
Sbjct: 9 SPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 68
Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEIIVD 165
++E+ ++ AI L Q G IIV
Sbjct: 69 IAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQ 99
>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 = 81.2 bits (201), Expect = 1e-18
Identities = 17/75 (22%), Positives = 29/75 (38%)
Query: 92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
L + L + + E+ +G + +V TG SK YGF EY + + A
Sbjct: 97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 152 LNRQNFQGSEIIVDF 166
L + + V +
Sbjct: 157 LLGKPLGPRTLYVHW 171
Score = 75.8 bits (187), Expect = 1e-16
Identities = 19/95 (20%), Positives = 35/95 (36%), Gaps = 2/95 (2%)
Query: 73 LRALRSTYKPHTSSTDPTRTLFIGRLNKNSREAD-LEQAFAEYGKVISVRVVRDFVTGHS 131
L + T + +R L + RL + D L +A + ++ G
Sbjct: 167 LYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQL 225
Query: 132 KRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
K + LEY+ + A + + + GS + V F
Sbjct: 226 KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
Score = 59.6 bits (145), Expect = 7e-11
Identities = 14/91 (15%), Positives = 29/91 (31%), Gaps = 7/91 (7%)
Query: 76 LRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYG 135
+R + R + I L + ++ ++Y + V K
Sbjct: 8 IRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTA 60
Query: 136 FLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
F+ + AAI A ++ + E+ V
Sbjct: 61 FVTLLNGEQAEAAINAFHQSRLRERELSVQL 91
>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 = 76.4 bits (189), Expect = 1e-18
Identities = 19/77 (24%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
R++++G ++ + +LE F G V V ++ D +GH K + ++E+ +++ +
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 149 IRALNRQNFQGSEIIVD 165
+ AL+ F+G +I V
Sbjct: 65 L-ALDESLFRGRQIKVI 80
>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 = 77.4 bits (191), Expect = 1e-18
Identities = 26/109 (23%), Positives = 45/109 (41%), Gaps = 1/109 (0%)
Query: 86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
D LFIG LN+ + E L+ F ++G + V +++D T S+ + F+ ++
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADA 61
Query: 146 LAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLR 194
A + +N ++ G I V+ RR SG L
Sbjct: 62 KNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLE 110
>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 = 75.6 bits (187), Expect = 2e-18
Identities = 21/74 (28%), Positives = 39/74 (52%)
Query: 93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
LF+G LN N + L AF ++ +S V+ D TG S+ YGF+ + + A+ ++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 153 NRQNFQGSEIIVDF 166
Q+ G + +++
Sbjct: 64 QGQDLNGRPLRINW 77
>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 = 76.2 bits (188), Expect = 3e-18
Identities = 25/72 (34%), Positives = 37/72 (51%)
Query: 93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
LFI L + + DL Q F +G V+S +V D T SK +GF+ YD + AAI+++
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 153 NRQNFQGSEIIV 164
N + V
Sbjct: 88 NGFQIGMKRLKV 99
>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 = 75.5 bits (186), Expect = 6e-18
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 6/88 (6%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
S +T+FI L+ +S E L + ++G + VRVV T HSK F ++ ++A
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 69
Query: 145 CLAAIRALNRQN------FQGSEIIVDF 166
+ A + + G ++ VD
Sbjct: 70 AQKCLAAASLEAEGGGLKLDGRQLKVDL 97
>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 = 75.4 bits (186), Expect = 6e-18
Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 2/80 (2%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
DPT L+I L + E +LE +G+VIS R++RD +G S+ GF + +
Sbjct: 21 QEQDPTN-LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEK 78
Query: 145 CLAAIRALNRQNFQGSEIIV 164
C A I N + + +
Sbjct: 79 CEAVIGHFNGKFIKTPPGVS 98
>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 = 76.9 bits (190), Expect = 6e-18
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 2/76 (2%)
Query: 91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTG--HSKRYGFLEYDCEKACLAA 148
+F+G++ + E DL + F +YG V + V+RD SK F+ + KA L A
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 149 IRALNRQNFQGSEIIV 164
AL+
Sbjct: 64 QNALHNMKVLPGMHHP 79
Score = 75.0 bits (185), Expect = 3e-17
Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 4/89 (4%)
Query: 81 KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
++ R LFIG ++K E D+ F+ +G++ R++R G S+ F+ +
Sbjct: 86 DSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFT 144
Query: 141 CEKACLAAIRALNRQNF---QGSEIIVDF 166
AI+A+++ S ++V F
Sbjct: 145 TRAMAQTAIKAMHQAQTMEGCSSPMVVKF 173
>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 = 74.5 bits (184), Expect = 7e-18
Identities = 24/102 (23%), Positives = 43/102 (42%), Gaps = 14/102 (13%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
S + LFIG L + + E ++ F +YGKV+ +++++ GF+ + + A
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNY--------GFVHIEDKTA 54
Query: 145 CLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGG 186
AIR L+ G I V+ + + G G
Sbjct: 55 AEDAIRNLHHYKLHGVNINVEASKNK------SKASSGPSSG 90
>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 = 74.5 bits (184), Expect = 7e-18
Identities = 24/79 (30%), Positives = 39/79 (49%)
Query: 87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACL 146
+F+G L+ A + AFA +G++ RVV+D TG SK YGF+ + +
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAE 62
Query: 147 AAIRALNRQNFQGSEIIVD 165
AI+ + Q G +I +
Sbjct: 63 NAIQQMGGQWLGGRQIRTN 81
>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 = 74.5 bits (184), Expect = 7e-18
Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 2/76 (2%)
Query: 93 LFIGRLNKNSREADLEQAFAEYG--KVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
L+IG L + + DL +A G ++ ++ + G SK + + E + +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 151 ALNRQNFQGSEIIVDF 166
L ++ G +V
Sbjct: 64 LLPKRELHGQNPVVTP 79
>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 = 74.7 bits (184), Expect = 8e-18
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYG-KVISVRVVRDFVTGHSKRYGFLEYDCE 142
+ S+ +L++G L E + +AFA G V+SV+++R+ +TG Y F+E+
Sbjct: 3 SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62
Query: 143 KACLAAIRALNRQNFQGSEIIVDF 166
+ +N + G+ F
Sbjct: 63 ATAEKCLHKINGKPLPGATPAKRF 86
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 74.5 bits (184), Expect = 8e-18
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 2/81 (2%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
+S + +F+ L + L+ F E G V+ + + G SK G ++++ +
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPE 59
Query: 144 ACLAAIRALNRQNFQGSEIIV 164
A R +N G EI V
Sbjct: 60 VAERACRMMNGMKLSGREIDV 80
>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 = 74.6 bits (184), Expect = 8e-18
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 1/85 (1%)
Query: 82 PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
+ + RT+F+G L RE L + F + G + V + +D G K +GF+ +
Sbjct: 8 MFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKH 66
Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
++ AI LN G I V
Sbjct: 67 PESVSYAIALLNGIRLYGRPINVSG 91
>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 = 76.4 bits (189), Expect = 9e-18
Identities = 25/87 (28%), Positives = 46/87 (52%)
Query: 80 YKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
++ SS+D T LF+G LN N + L AF ++ +S V+ D TG S+ YGF+ +
Sbjct: 77 FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSF 136
Query: 140 DCEKACLAAIRALNRQNFQGSEIIVDF 166
+ A+ ++ Q+ G + +++
Sbjct: 137 TSQDDAQNAMDSMQGQDLNGRPLRINW 163
Score = 69.9 bits (172), Expect = 3e-15
Identities = 18/76 (23%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
R L++G L+K E L+Q F G + +++++ D + Y F+EY A++
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQ 59
Query: 151 ALNRQNFQGSEIIVDF 166
LN + + + + +++
Sbjct: 60 TLNGKQIENNIVKINW 75
>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 = 75.1 bits (185), Expect = 1e-17
Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 1/84 (1%)
Query: 82 PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
R++++G ++ S DLE F+ G + + ++ D +GH K Y ++E+
Sbjct: 28 AEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE 87
Query: 142 EKACLAAIRALNRQNFQGSEIIVD 165
+ AA+ A++ F+G I V
Sbjct: 88 RNSVDAAV-AMDETVFRGRTIKVL 110
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 74.2 bits (183), Expect = 1e-17
Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
S R LF+G LNK E D+ + F +G + V+R G SK F+++
Sbjct: 10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTE 68
Query: 145 CLAAIRALN-RQNFQGSE--IIVDF 166
AAI AL+ Q G+ ++V F
Sbjct: 69 AQAAIHALHGSQTMPGASSSLVVKF 93
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 73.4 bits (181), Expect = 2e-17
Identities = 25/104 (24%), Positives = 47/104 (45%), Gaps = 13/104 (12%)
Query: 85 SSTDPTRTLFIGRLN-KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
+ P LFIG L KN + DL + F+ YG ++ + + F GF+++D +
Sbjct: 5 HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAF--------GFIQFDNPQ 56
Query: 144 ACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGN 187
+ AI +++ G ++I++ +P+ G G N
Sbjct: 57 SVRDAIECESQEMNFGKKLILEVSSSNA----RPQFDHGDHGTN 96
>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 = 73.4 bits (181), Expect = 2e-17
Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 8/80 (10%)
Query: 89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
PT L++G L N+ A L + F +G + ++ V+ + +++Y+ A AA
Sbjct: 16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAA 69
Query: 149 IRALNRQNFQGSE--IIVDF 166
+ G + + VDF
Sbjct: 70 CAKMRGFPLGGPDRRLRVDF 89
>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 = 73.9 bits (182), Expect = 2e-17
Identities = 25/81 (30%), Positives = 42/81 (51%)
Query: 86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
T +F+G L+ D++ AFA +G++ RVV+D TG SK YGF+ + +
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70
Query: 146 LAAIRALNRQNFQGSEIIVDF 166
AI+ + Q G +I ++
Sbjct: 71 ENAIQQMGGQWLGGRQIRTNW 91
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 75.0 bits (184), Expect = 3e-17
Identities = 13/88 (14%), Positives = 32/88 (36%), Gaps = 2/88 (2%)
Query: 81 KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYG--KVISVRVVRDFVTGHSKRYGFLE 138
++ + +++G + + + L Q G V+ ++ + G SK Y +
Sbjct: 46 YTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVV 105
Query: 139 YDCEKACLAAIRALNRQNFQGSEIIVDF 166
E + + L + G ++ V
Sbjct: 106 VASENSVHKLLELLPGKVLNGEKVDVRP 133
>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 = 74.9 bits (185), Expect = 4e-17
Identities = 22/82 (26%), Positives = 41/82 (50%), Gaps = 2/82 (2%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
S + LFIG LN N A+L+ A +E + VV TG ++++G+++++ +
Sbjct: 8 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAED 66
Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
A+ L G+EI ++
Sbjct: 67 LEKAL-ELTGLKVFGNEIKLEK 87
Score = 61.9 bits (151), Expect = 3e-12
Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 5/79 (6%)
Query: 88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
RTL L+ N E +L++ F + ++ V G SK ++E+ E
Sbjct: 97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEK 151
Query: 148 AIRALNRQNFQGSEIIVDF 166
+ G + + +
Sbjct: 152 NLEEKQGAEIDGRSVSLYY 170
>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 = 73.1 bits (180), Expect = 4e-17
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
+FI L+K+ L F+ +G ++S +VV D SK YGF+ ++ ++A AI +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65
Query: 153 NRQNFQGSEIIVDF 166
N ++ V
Sbjct: 66 NGMLLNDRKVFVGR 79
>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 = 75.4 bits (186), Expect = 5e-17
Identities = 20/83 (24%), Positives = 43/83 (51%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
++ + P +L++G L+ + EA L + F+ G ++S+RV RD +T S Y ++ +
Sbjct: 9 SAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 68
Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
A+ +N +G + + +
Sbjct: 69 DAERALDTMNFDVIKGKPVRIMW 91
Score = 70.4 bits (173), Expect = 4e-15
Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 3/94 (3%)
Query: 73 LRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSK 132
+R + S P + +FI L+K+ L F+ +G ++S +VV D SK
Sbjct: 87 VRIMWSQRDPSLRKSGVGN-IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSK 143
Query: 133 RYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
YGF+ ++ ++A AI +N ++ V
Sbjct: 144 GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
>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 = 72.7 bits (179), Expect = 5e-17
Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 2/83 (2%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
+ S + L + + R+ DL Q F ++GK++ V ++ + SK +GF+ ++
Sbjct: 9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSA 66
Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
A L+ +G +I V+
Sbjct: 67 DADRAREKLHGTVVEGRKIEVNN 89
>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 = 72.8 bits (179), Expect = 5e-17
Identities = 29/106 (27%), Positives = 46/106 (43%), Gaps = 17/106 (16%)
Query: 84 TSSTDP---TRTLFIGRLNKNS-READLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
T+ DP +FIG LN +++D+E F++YG+V V K Y F++Y
Sbjct: 18 TNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQY 69
Query: 140 DCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWG 185
E+ AA+ N + G + ++ KP R G G
Sbjct: 70 SNERHARAAVLGENGRVLAGQTLDINMAGEP-----KPDRSGPSSG 110
>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 = 72.7 bits (179), Expect = 5e-17
Identities = 14/91 (15%), Positives = 43/91 (47%), Gaps = 2/91 (2%)
Query: 78 STYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDF-VTGHSKRYGF 136
S T + + + + + ++ + F+ +G++ +VR+ + TG + +GF
Sbjct: 3 SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62
Query: 137 LEYDCEKACLAAIRAL-NRQNFQGSEIIVDF 166
+++ ++ A AL + + G +++++
Sbjct: 63 VDFITKQDAKKAFNALCHSTHLYGRRLVLEW 93
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 72.3 bits (178), Expect = 5e-17
Identities = 23/98 (23%), Positives = 45/98 (45%), Gaps = 11/98 (11%)
Query: 93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
+++G L + + +LE+AF+ YG + +V + R+ + F+E++ + A+R L
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 153 NRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNS 190
+ + GS + V+ G PRR R
Sbjct: 58 DGKVICGSRVRVELSTGM------PRRSRFDRPPARRK 89
>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 = 77.6 bits (190), Expect = 6e-17
Identities = 40/152 (26%), Positives = 68/152 (44%), Gaps = 3/152 (1%)
Query: 71 AILRALRSTYKPHT---SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV 127
+ + PH + D +TLF+ R+N ++ E+ L + F YG + + +V
Sbjct: 80 QEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKR 139
Query: 128 TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGN 187
+G + Y F+EY+ E+ +A + + + G ++VD E GR + GW+PRRLGGG GG
Sbjct: 140 SGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGT 199
Query: 188 RNSGQLRFGGRNKPWVKPVQLMNERELGEWRK 219
R G + +
Sbjct: 200 RRGGADVNIRHSGRDDTSRYDERPGPSPLPHR 231
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 72.7 bits (179), Expect = 6e-17
Identities = 24/105 (22%), Positives = 48/105 (45%), Gaps = 3/105 (2%)
Query: 68 HDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV 127
H + R ++ + + P R L + + R+ DL Q F ++GK++ V ++ +
Sbjct: 8 HHHSSGLVPRGSHMNTENKSQPKR-LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN-- 64
Query: 128 TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVL 172
SK +GF+ ++ A L+ +G +I V+ RV+
Sbjct: 65 ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM 109
>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 = 74.2 bits (183), Expect = 8e-17
Identities = 21/80 (26%), Positives = 33/80 (41%)
Query: 86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
LFIG L + +++ +G + + +V+D TG SK Y F EY
Sbjct: 90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149
Query: 146 LAAIRALNRQNFQGSEIIVD 165
AI LN +++V
Sbjct: 150 DQAIAGLNGMQLGDKKLLVQ 169
Score = 65.3 bits (160), Expect = 1e-13
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 6/79 (7%)
Query: 91 RTLFIGRLNKNSREADLEQAFAEYGKVISV-----RVVRDFVTGHSKRYGFLEYDCEKAC 145
R L++G + E + F ++ + V K + FLE+
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 146 LAAIRALNRQNFQGSEIIV 164
A+ A + FQG + +
Sbjct: 65 TQAM-AFDGIIFQGQSLKI 82
>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain,
RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 71.9 bits (177), Expect = 9e-17
Identities = 21/89 (23%), Positives = 43/89 (48%), Gaps = 2/89 (2%)
Query: 78 STYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFL 137
S RTL++G L+++ E + Q F++ G S +++ + + Y F+
Sbjct: 3 SGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFV 60
Query: 138 EYDCEKACLAAIRALNRQNFQGSEIIVDF 166
E+ + AA+ A+N + G E+ V++
Sbjct: 61 EFYEHRDAAAALAAMNGRKILGKEVKVNW 89
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 74.7 bits (184), Expect = 9e-17
Identities = 23/100 (23%), Positives = 38/100 (38%)
Query: 67 PHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDF 126
+ ++ T D LFIG L + +++ +G + + +V+D
Sbjct: 91 LPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS 150
Query: 127 VTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
TG SK Y F EY AI LN +++V
Sbjct: 151 ATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 190
Score = 69.7 bits (171), Expect = 6e-15
Identities = 15/84 (17%), Positives = 28/84 (33%), Gaps = 6/84 (7%)
Query: 88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISV-----RVVRDFVTGHSKRYGFLEYDCE 142
R L++G + E + F ++ + V K + FLE+
Sbjct: 2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 143 KACLAAIRALNRQNFQGSEIIVDF 166
A+ A + FQG + +
Sbjct: 62 DETTQAM-AFDGIIFQGQSLKIRR 84
>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 = 71.9 bits (177), Expect = 9e-17
Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 3/81 (3%)
Query: 89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTG---HSKRYGFLEYDCEKAC 145
+ LFI LN ++ E L+ F++ G + S + + S +GF+EY +
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 146 LAAIRALNRQNFQGSEIIVDF 166
A++ L G ++ V
Sbjct: 64 QKALKQLQGHTVDGHKLEVRI 84
>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 = 75.1 bits (184), Expect = 1e-16
Identities = 18/119 (15%), Positives = 40/119 (33%), Gaps = 2/119 (1%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYG--KVISVRVVRDFVTGHSKRYGFLEYDCE 142
+ T L+IG L + + DL +A G ++ ++ + G SK + + E
Sbjct: 63 TYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSE 122
Query: 143 KACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKP 201
+ + L ++ G +V + L ++ + G +
Sbjct: 123 ASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSS 181
>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 = 71.1 bits (175), Expect = 2e-16
Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 5/83 (6%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
+ RTL L+ N E +L++ F + ++ V G SK ++E+ E
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEA 64
Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
+ G + + +
Sbjct: 65 DAEKNLEEKQGAEIDGRSVSLYY 87
>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 = 72.6 bits (178), Expect = 2e-16
Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 5/90 (5%)
Query: 81 KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
H S +++G L N + +LE+AF YG + SV V R+ + F+E++
Sbjct: 64 HMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFE 118
Query: 141 CEKACLAAIRALNRQNFQGSEIIVDFECGR 170
+ A+R L+ + G + V+ G
Sbjct: 119 DPRDAADAVRELDGRTLCGCRVRVELSNGE 148
>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 = 71.2 bits (175), Expect = 2e-16
Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 3/79 (3%)
Query: 88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
+ R L+I L ++ F +YG + +RV T ++ ++ Y+
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKN 62
Query: 148 AIRALNRQNFQGSEIIVDF 166
A+ L+ N ++V +
Sbjct: 63 AVDHLSGFNVSNRYLVVLY 81
>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 = 70.7 bits (174), Expect = 3e-16
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 1/81 (1%)
Query: 87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISV-RVVRDFVTGHSKRYGFLEYDCEKAC 145
+ + +FIG L+ E L F+ +G ++ +++RD TG+SK Y F+ + A
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 146 LAAIRALNRQNFQGSEIIVDF 166
AAI A+N Q I V +
Sbjct: 62 DAAIEAMNGQYLCNRPITVSY 82
>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 = 70.7 bits (174), Expect = 3e-16
Identities = 16/86 (18%), Positives = 36/86 (41%), Gaps = 2/86 (2%)
Query: 81 KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
+ L++ L+ + L +AF+ +G + S +V+ + G SK +GF+ +
Sbjct: 6 SGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFS 63
Query: 141 CEKACLAAIRALNRQNFQGSEIIVDF 166
+ A+ +N + + V
Sbjct: 64 SPEEATKAVTEMNGRIVATKPLYVAL 89
>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 = 70.4 bits (173), Expect = 4e-16
Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 8/83 (9%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
+S + LF+ L E LE+AF+++GK+ V+ ++D+ F+ +D
Sbjct: 5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY--------AFIHFDERD 56
Query: 144 ACLAAIRALNRQNFQGSEIIVDF 166
+ A+ +N ++ +G I + F
Sbjct: 57 GAVKAMEEMNGKDLEGENIEIVF 79
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 70.0 bits (172), Expect = 6e-16
Identities = 16/112 (14%), Positives = 40/112 (35%), Gaps = 8/112 (7%)
Query: 74 RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
+ + + +++G L + R D+E F +YG + + +
Sbjct: 6 SGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPP 62
Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWG 185
+ F+E++ + A+ + ++ G + V+F + G G
Sbjct: 63 FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSG-----RGTGSGPSSG 109
>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 = 69.8 bits (171), Expect = 8e-16
Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 4/87 (4%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVI-SVRVVRD-FVTGHSKRYGFLEYDC 141
+S + LFIG + K + ++ + A+ + + V V ++ + F+EY+
Sbjct: 2 SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61
Query: 142 EKACLAAIRALNRQNFQ--GSEIIVDF 166
+A A R L Q G +I VD+
Sbjct: 62 HRAAAMARRKLMPGRIQLWGHQIAVDW 88
>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 = 68.0 bits (167), Expect = 2e-15
Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 7/83 (8%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
S + L+IG L+ DL Q F + ++ + Y F++Y +
Sbjct: 3 SGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNW 56
Query: 145 CLAAIRALN-RQNFQGSEIIVDF 166
+ AI L+ + G + VD+
Sbjct: 57 AIRAIETLSGKVELHGKIMEVDY 79
>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 = 68.5 bits (168), Expect = 2e-15
Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 6/85 (7%)
Query: 82 PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
+ + L++ L ++ E +E+ F RV + + Y F+ +
Sbjct: 7 GDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSN 60
Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
+ + A++ALN + GS I V
Sbjct: 61 REDAVEAMKALNGKVLDGSPIEVTL 85
>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 = 68.1 bits (167), Expect = 3e-15
Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 6/81 (7%)
Query: 86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
+ LF+G L + E ++ + F +YGK V + +D K +GF+ +
Sbjct: 11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLA 64
Query: 146 LAAIRALNRQNFQGSEIIVDF 166
A L+ +G ++ V F
Sbjct: 65 EIAKVELDNMPLRGKQLRVRF 85
>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 = 67.7 bits (166), Expect = 3e-15
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 2/81 (2%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
S + LFIG LN N A+L+ A +E + VV TG ++++G+++++ +
Sbjct: 12 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAED 70
Query: 145 CLAAIRALNRQNFQGSEIIVD 165
A+ L G+EI ++
Sbjct: 71 LEKAL-ELTGLKVFGNEIKLE 90
>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 = 67.3 bits (165), Expect = 6e-15
Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 8/94 (8%)
Query: 81 KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVIS--------VRVVRDFVTGHSK 132
H S T+F+ L +N + F + G + + + + D TG K
Sbjct: 4 HHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLK 63
Query: 133 RYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
+ +D + AAI + + F G+ I V F
Sbjct: 64 GEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97
>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 = 67.7 bits (166), Expect = 6e-15
Identities = 30/110 (27%), Positives = 44/110 (40%), Gaps = 6/110 (5%)
Query: 75 ALRSTYKPHTSSTDPTRT-LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
+ H S D T T +F+G L ++ +A L + F +G + V+ D TG S+
Sbjct: 1 GSSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60
Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGG 183
YGF+ A A + N G + G KPR L G
Sbjct: 61 YGFVTMADRAAAERACKDPN-PIIDGRKA----NVNLAYLGAKPRSLQTG 105
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 66.9 bits (164), Expect = 8e-15
Identities = 17/99 (17%), Positives = 40/99 (40%), Gaps = 8/99 (8%)
Query: 68 HDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV 127
H + L S LF+ + +E++L + F +G + V+++ F
Sbjct: 9 HHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGF- 67
Query: 128 TGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
F+E++ ++ AI ++ ++F + V +
Sbjct: 68 -------AFVEFEEAESAAKAIEEVHGKSFANQPLEVVY 99
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 66.9 bits (164), Expect = 9e-15
Identities = 27/108 (25%), Positives = 46/108 (42%), Gaps = 7/108 (6%)
Query: 78 STYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFL 137
S T+P T ++G L N+ + D++ F + + SVR+VRD T K + ++
Sbjct: 3 SGSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYV 61
Query: 138 EYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWG 185
E+D + A+ + + VD GR K + G G
Sbjct: 62 EFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGR-----KQDKSGPSSG 103
>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 = 65.8 bits (161), Expect = 2e-14
Identities = 17/91 (18%), Positives = 40/91 (43%), Gaps = 9/91 (9%)
Query: 77 RSTYKPHTSSTDPTRTLFIGRLNKNS-READLEQAFAEYGKVISVRVVRDFVTGHSKRYG 135
+ + LFIG L + + DL + F+ YG ++ + + +G
Sbjct: 9 HHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFG 60
Query: 136 FLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
F+++D ++ AI +++ G ++I++
Sbjct: 61 FIQFDNPQSVRDAIEXESQEMNFGKKLILEV 91
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 65.4 bits (160), Expect = 2e-14
Identities = 21/90 (23%), Positives = 34/90 (37%), Gaps = 7/90 (7%)
Query: 78 STYKPHTSSTDPT-RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
S P T +IG + + EADL F +G ++ + + K F
Sbjct: 14 QAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCF 67
Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
++YD + I AL FQG + +
Sbjct: 68 IKYDTHEQAAVCIVALANFPFQGRNLRTGW 97
>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 = 63.8 bits (156), Expect = 6e-14
Identities = 21/87 (24%), Positives = 43/87 (49%), Gaps = 8/87 (9%)
Query: 82 PHTSSTDPT-RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
+S D T TL++G L E DL F ++G++ ++ VV+ ++ F+++
Sbjct: 3 SGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFA 56
Query: 141 C-EKACLAAIRALNRQNFQGSEIIVDF 166
+ A +AA ++ N+ G + V +
Sbjct: 57 TRQAAEVAAEKSFNKLIVNGRRLNVKW 83
>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 = 68.1 bits (167), Expect = 6e-14
Identities = 8/76 (10%), Positives = 27/76 (35%)
Query: 91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
TL++ + + ++ + V + S+R+ +++ ++ +
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177
Query: 151 ALNRQNFQGSEIIVDF 166
LN +G ++
Sbjct: 178 KLNGLKIEGYTLVTKV 193
Score = 67.3 bits (165), Expect = 1e-13
Identities = 20/96 (20%), Positives = 37/96 (38%), Gaps = 8/96 (8%)
Query: 74 RALRSTYKPHTSSTDPTR-----TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVT 128
+ ++ TR T+ + L K+ + + + F G +I V V
Sbjct: 20 SPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--L 77
Query: 129 GHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIV 164
+ R+ +E+ LAAI ++ +EIIV
Sbjct: 78 KKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIV 112
Score = 64.2 bits (157), Expect = 1e-12
Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 3/88 (3%)
Query: 81 KPHTSSTDPTRTLFIGRLNKN-SREADLEQAFAEYGKVISVRVVRDF-VTGHSKRYGFLE 138
K S+T R + I L+ E L ++F +G + + + + F+
Sbjct: 201 KRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMV 260
Query: 139 YDCEKACLAAIRALNRQNFQGSEIIVDF 166
++ + + A+ +NR EI V
Sbjct: 261 FENKDSAERAL-QMNRSLLGNREISVSL 287
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 64.9 bits (158), Expect = 9e-14
Identities = 13/90 (14%), Positives = 37/90 (41%), Gaps = 7/90 (7%)
Query: 81 KPHTSSTDPTRTLFIGRLNKNSREADLEQA----FAEYGKVISVRVVRDFVTGHSKRYGF 136
T+P++ + I +N + L+ + G ++ + V + + +
Sbjct: 20 GSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAY 76
Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
+ + +++ A + A FQG+ +++ F
Sbjct: 77 IVFATQESAQAFVEAFQGYPFQGNPLVITF 106
>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 = 67.4 bits (165), Expect = 9e-14
Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 1/73 (1%)
Query: 88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
L + L+ LEQAF+++G V VV D G + GF+E+ +
Sbjct: 94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARK 152
Query: 148 AIRALNRQNFQGS 160
A+ F +
Sbjct: 153 ALERCGDGAFLLT 165
Score = 63.2 bits (154), Expect = 3e-12
Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 6/86 (6%)
Query: 81 KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
KP + LF+G L + E D ++ F YG+ V + RD + +GF+ +
Sbjct: 13 KPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLE 66
Query: 141 CEKACLAAIRALNRQNFQGSEIIVDF 166
A L+ + + + F
Sbjct: 67 SRTLAEIAKAELDGTILKSRPLRIRF 92
>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 = 63.8 bits (156), Expect = 1e-13
Identities = 16/82 (19%), Positives = 35/82 (42%), Gaps = 1/82 (1%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
+ + L + L+ +AD+++ FAE+G + V D +G S + ++ +
Sbjct: 24 AGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKAD 82
Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
L A++ N G + +
Sbjct: 83 ALKAMKQYNGVPLDGRPMNIQL 104
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 64.3 bits (157), Expect = 1e-13
Identities = 25/111 (22%), Positives = 40/111 (36%), Gaps = 11/111 (9%)
Query: 89 PTRTLFIGRLNKNSREADLEQAFAEYGKV--------ISVRVVRDFVTGHSKRYGFLEYD 140
T+F+ L +N + F + G + + + D TG K + +D
Sbjct: 6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65
Query: 141 CEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSG 191
+ AAI + + F G+ I V F R R G G GG +
Sbjct: 66 DPPSAKAAIDWFDGKEFSGNPIKVSFATRR---ADFNRGGGNGRGGLEHHH 113
>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 = 63.9 bits (156), Expect = 1e-13
Identities = 15/89 (16%), Positives = 40/89 (44%), Gaps = 7/89 (7%)
Query: 79 TYKPHTSSTDPTR-TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFL 137
++ + + P T++ G + + + Q F+ +G+++ +RV + K Y F+
Sbjct: 13 RFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFV 66
Query: 138 EYDCEKACLAAIRALNRQNFQGSEIIVDF 166
+ ++ AI ++N +G + +
Sbjct: 67 RFSTHESAAHAIVSVNGTTIEGHVVKCYW 95
>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 = 2e-13
Identities = 15/85 (17%), Positives = 42/85 (49%), Gaps = 7/85 (8%)
Query: 86 STDPTRTLFIGRLNKNSREADLEQA----FAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
T P T++I LN+ ++ +L+++ F+++G+++ + V R + + F+ +
Sbjct: 5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKE 61
Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
+ A+R++ F + + +
Sbjct: 62 VSSATNALRSMQGFPFYDKPMRIQY 86
Score = 43.7 bits (102), Expect = 2e-05
Identities = 21/110 (19%), Positives = 33/110 (30%), Gaps = 5/110 (4%)
Query: 54 PIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAE 113
P + L + S P LF+ L + + E L F +
Sbjct: 171 PPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQ 230
Query: 114 YGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
+ VR+V F+E+D E AA AL + +
Sbjct: 231 FPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARDALQGFKITQNNAM 275
>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 = 63.5 bits (155), Expect = 2e-13
Identities = 21/107 (19%), Positives = 40/107 (37%), Gaps = 6/107 (5%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
+ T+F+ L+ L++ F+ G V+ ++ D G S+ G + ++
Sbjct: 9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSI 67
Query: 144 ACLAAIRALNRQNFQGSEIIVDF-----ECGRVLPGWKPRRLGGGWG 185
+ AI N Q + V G P +P++ G G
Sbjct: 68 EAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSSG 114
>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 = 62.6 bits (153), Expect = 3e-13
Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
T+F+G ++ E ++ FA YG V V+++ D TG SK YGF+ + + +
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV 67
Query: 150 RALNRQNFQGSEIIV 164
++ NF G ++ +
Sbjct: 68 E--SQINFHGKKLKL 80
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 62.4 bits (152), Expect = 3e-13
Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 5/79 (6%)
Query: 94 FIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALN 153
I + L F++ GKV+++ D TG +K + F+E I++ +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 154 RQNFQGSEIIV-----DFE 167
+ + D E
Sbjct: 76 GKRLDLKHRLFLYTMKDVE 94
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 62.2 bits (151), Expect = 4e-13
Identities = 18/94 (19%), Positives = 34/94 (36%), Gaps = 5/94 (5%)
Query: 77 RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
P +++G L +++R +DL++A E G + +R+ +R F
Sbjct: 6 SGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELG-SVPLRLTWQ----GPRRRAF 60
Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDFECGR 170
L Y A A+ L + V +
Sbjct: 61 LHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94
>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 = 62.4 bits (152), Expect = 5e-13
Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 8/83 (9%)
Query: 91 RTLFIGRLNKNSREADLEQAFAEYGKVIS--------VRVVRDFVTGHSKRYGFLEYDCE 142
+++ LN + DL F + G V + + D TG K + Y+
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 143 KACLAAIRALNRQNFQGSEIIVD 165
AA+ + ++FQGS++ V
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVS 98
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 61.3 bits (149), Expect = 8e-13
Identities = 18/84 (21%), Positives = 30/84 (35%), Gaps = 8/84 (9%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
T + + I L EADL +A E+G + V V+ KR +E++
Sbjct: 16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLG 69
Query: 145 CLAAIRALNRQNFQ--GSEIIVDF 166
A+ G V++
Sbjct: 70 ACNAVNYAADNQIYIAGHPAFVNY 93
>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 = 61.1 bits (149), Expect = 9e-13
Identities = 15/85 (17%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 86 STDPTRTLFIGRLNKNSREADLEQA----FAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
T P T++I LN+ ++ +L+++ F+ +G+++ + V R + + F+ +
Sbjct: 4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKE 60
Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
+ A+R++ F + + +
Sbjct: 61 VSSATNALRSMQGFPFYDKPMRIQY 85
>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA
processing, mRNA splicing, transport, nucleus,
RNA-binding, spliceosome, transport; NMR {Mus musculus}
Length = 124
Score = 62.0 bits (151), Expect = 1e-12
Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 1/82 (1%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
+ L + L+ +AD+++ FAE+G + V D +G S + ++
Sbjct: 30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRAD 88
Query: 145 CLAAIRALNRQNFQGSEIIVDF 166
L A++ G + +
Sbjct: 89 ALKAMKQYKGVPLDGRPMDIQL 110
>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 = 61.1 bits (149), Expect = 1e-12
Identities = 21/96 (21%), Positives = 43/96 (44%), Gaps = 4/96 (4%)
Query: 73 LRALRSTYKPHTS-STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVT-GH 130
+R + + P T F+G L + E +++ F + +VR+ R+
Sbjct: 1 MRGSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPER 59
Query: 131 SKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
K +G+ E++ + L+A+ +LN ++ I VD
Sbjct: 60 LKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDV 94
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein;
2.50A {Homo sapiens}
Length = 143
Score = 62.2 bits (151), Expect = 1e-12
Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 5/87 (5%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVIS--VRVVRDFV---TGHSKRYGFLEY 139
+P +++ L K+ +E DL+ F Y S R++ D G K F+
Sbjct: 40 EPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGL 99
Query: 140 DCEKACLAAIRALNRQNFQGSEIIVDF 166
EKA A++ N G ++V F
Sbjct: 100 PNEKAAAKALKEANGYVLFGKPMVVQF 126
>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 = 62.5 bits (153), Expect = 1e-12
Identities = 18/62 (29%), Positives = 37/62 (59%)
Query: 90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
+ +FIG LN ++ E +L + F +YG V +++++D TG S+ +GFL ++ + +
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 150 RA 151
+
Sbjct: 63 KT 64
Score = 62.5 bits (153), Expect = 1e-12
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
D T +F+G + + R + E+ F+++G +I +++ D TG S+ +GF+ YD A
Sbjct: 85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR 144
Query: 148 AIRALNRQNFQGSEIIVDF 166
+F+ +I +
Sbjct: 145 VC-QNKFIDFKDRKIEIKR 162
>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 = 60.7 bits (148), Expect = 1e-12
Identities = 17/83 (20%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Query: 85 SSTDPTRT--LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCE 142
S + +++ +F+G + N E +L + F ++G V V ++ D + +GF+ ++ E
Sbjct: 3 SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62
Query: 143 KACLAAIRALNRQNFQGSEIIVD 165
++ A+ ++ + G ++ V
Sbjct: 63 QSVDQAV-NMHFHDIMGKKVEVK 84
>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 = 61.9 bits (151), Expect = 3e-12
Identities = 20/64 (31%), Positives = 33/64 (51%)
Query: 88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
+ R LFIG L+ + + L F ++G + V+RD T S+ +GF+ Y + A
Sbjct: 11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70
Query: 148 AIRA 151
A+ A
Sbjct: 71 AMNA 74
Score = 61.9 bits (151), Expect = 3e-12
Identities = 20/107 (18%), Positives = 42/107 (39%), Gaps = 6/107 (5%)
Query: 60 IDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVIS 119
+DG + RA+ R H + +F+G + +++ E L F +YGK+
Sbjct: 79 VDGR-VVEPKRAVSREDSQRPGAH----LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 133
Query: 120 VRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
+ ++ D +G + + F+ +D + + G V
Sbjct: 134 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRK 179
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 59.7 bits (145), Expect = 3e-12
Identities = 10/74 (13%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
R+++I ++ D+++ + G+V+++++ R K F+ +D ++ +
Sbjct: 12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFV- 69
Query: 151 ALNRQNFQGSEIIV 164
Q ++ +++++
Sbjct: 70 ETPGQKYKETDLLI 83
>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 = 60.0 bits (146), Expect = 3e-12
Identities = 22/106 (20%), Positives = 43/106 (40%), Gaps = 8/106 (7%)
Query: 81 KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV-TGHSKRYGFLEY 139
P T F+G L + E +++ F + +VR+ R+ K +G+ E+
Sbjct: 6 SGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEF 64
Query: 140 DCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWG 185
+ + L+A+ +LN ++ I VD + + G G
Sbjct: 65 EDLDSLLSAL-SLNEESLGNKRIRVDVADQA-----QDKDSGPSSG 104
>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 = 58.7 bits (143), Expect = 5e-12
Identities = 14/62 (22%), Positives = 32/62 (51%)
Query: 90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
+F+G L+ ++ + DL+ F ++G+V+ + D TG S+ +GF+ + + +
Sbjct: 11 AGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVL 70
Query: 150 RA 151
Sbjct: 71 DQ 72
>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 = 59.5 bits (144), Expect = 8e-12
Identities = 20/101 (19%), Positives = 40/101 (39%), Gaps = 8/101 (7%)
Query: 68 HDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFV 127
H + L S S+ P+R + I +L + E ++ +GKV ++ +++
Sbjct: 9 HHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-- 66
Query: 128 TGHSKRYGFLEYDCEKACLAAIR--ALNRQNFQGSEIIVDF 166
K F+E + E+A + +G I + F
Sbjct: 67 ----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF 103
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 59.1 bits (143), Expect = 8e-12
Identities = 18/86 (20%), Positives = 36/86 (41%), Gaps = 8/86 (9%)
Query: 83 HTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCE 142
H S P+R + I +L + E ++ +GKV ++ +++ K F+E + E
Sbjct: 9 HHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTE 62
Query: 143 KACLAAIRAL--NRQNFQGSEIIVDF 166
+A + +G I + F
Sbjct: 63 EAANTMVNYYTSVTPVLRGQPIYIQF 88
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 59.0 bits (143), Expect = 8e-12
Identities = 12/83 (14%), Positives = 31/83 (37%), Gaps = 8/83 (9%)
Query: 86 STDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKAC 145
+ + + L ++ EADL +A ++G + V ++ KR +E++ +
Sbjct: 11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSA 64
Query: 146 LAAIRALNRQNFQ--GSEIIVDF 166
+ G + ++
Sbjct: 65 KECVTFAADVPVYIAGQQAFFNY 87
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 58.6 bits (142), Expect = 8e-12
Identities = 14/85 (16%), Positives = 25/85 (29%), Gaps = 3/85 (3%)
Query: 82 PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
R L I + + + L+ +YG V S V + Y
Sbjct: 7 GSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSS 63
Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
+ A+ LN + + V +
Sbjct: 64 KDQARQALDKLNGFQLENFTLKVAY 88
>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A
Length = 205
Score = 60.9 bits (147), Expect = 1e-11
Identities = 13/78 (16%), Positives = 21/78 (26%)
Query: 89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
P+ L E + + E G V G LE+D + L
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181
Query: 149 IRALNRQNFQGSEIIVDF 166
+ LN + +
Sbjct: 182 LGFLNHYQMKNPNGPYPY 199
Score = 57.8 bits (139), Expect = 1e-10
Identities = 19/114 (16%), Positives = 35/114 (30%), Gaps = 6/114 (5%)
Query: 89 PTRTLFIGRLN-KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
+ L + L+ + F YG V V+ ++ +E A
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDR 57
Query: 148 AIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFGGRNKP 201
AI LN G ++ V + + L G ++ + R + P
Sbjct: 58 AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTP 111
>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 = 58.2 bits (141), Expect = 1e-11
Identities = 12/77 (15%), Positives = 32/77 (41%), Gaps = 7/77 (9%)
Query: 90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
+ + + L ++S ++ +Y ++ +KR F+ + AI
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAI 57
Query: 150 RALNRQNFQGSEIIVDF 166
+ ++ +F+G ++IV
Sbjct: 58 QMFHQYSFRGKDLIVQL 74
>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 = 58.2 bits (141), Expect = 2e-11
Identities = 16/90 (17%), Positives = 36/90 (40%), Gaps = 8/90 (8%)
Query: 77 RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
RS P + TL++ ++ L AF+ +G +I + + + F
Sbjct: 26 RSDSFPERRAPRKGNTLYVY--GEDMTPTLLRGAFSPFGNIIDLSMDPP------RNCAF 77
Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
+ Y+ ++ A+ LN + ++ V+
Sbjct: 78 VTYEKMESADQAVAELNGTQVESVQLKVNI 107
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 56.3 bits (137), Expect = 4e-11
Identities = 15/59 (25%), Positives = 31/59 (52%)
Query: 93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
+FIG L+ + + L + F ++G+V V+RD +T S+ +GF+ + + +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 58.7 bits (142), Expect = 4e-11
Identities = 17/100 (17%), Positives = 35/100 (35%), Gaps = 1/100 (1%)
Query: 67 PHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDF 126
P L + + L + L+ +AD+++ FAE+G + V D
Sbjct: 65 PLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD- 123
Query: 127 VTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
+G S + ++ L A++ G + +
Sbjct: 124 RSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 163
>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 = 56.1 bits (136), Expect = 7e-11
Identities = 19/66 (28%), Positives = 36/66 (54%)
Query: 88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
T L + L + E DL++ F+ +G+V+ V+V +D TGHSK +GF+ + + +
Sbjct: 13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 72
Query: 148 AIRALN 153
+ +
Sbjct: 73 VMSQRH 78
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 55.2 bits (134), Expect = 8e-11
Identities = 14/59 (23%), Positives = 29/59 (49%)
Query: 93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
+F+G L+ N+ D++ F ++GKV ++ D T + +GF+ ++ E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 56.1 bits (136), Expect = 8e-11
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 82 PHTSSTDPT-RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
P S + +FIG L+ + + L + F ++G+V V+RD +T S+ +GF+ +
Sbjct: 16 PRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 75
Query: 141 CEKACLAAIRA 151
+ +
Sbjct: 76 DQAGVDKVLAQ 86
>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 = 54.8 bits (133), Expect = 1e-10
Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 1/73 (1%)
Query: 93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
+F+G L+ ++ E + + F +G+V S+ + D T + + F+ + E+ +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK- 60
Query: 153 NRQNFQGSEIIVD 165
N S+ +
Sbjct: 61 KYHNVGLSKCEIK 73
>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 = 55.2 bits (133), Expect = 2e-10
Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 8/82 (9%)
Query: 87 TDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACL 146
P+R L I +L E ++ +GKV ++ +++ K FLE E+A +
Sbjct: 12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAI 65
Query: 147 AAIR--ALNRQNFQGSEIIVDF 166
+ + + + I + +
Sbjct: 66 TMVNYYSAVTPHLRNQPIYIQY 87
>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 = 54.9 bits (133), Expect = 3e-10
Identities = 16/67 (23%), Positives = 35/67 (52%)
Query: 85 SSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
S D LF+G L+ ++ + L F++YG+V+ +++D T S+ +GF+++
Sbjct: 11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNC 70
Query: 145 CLAAIRA 151
+ +
Sbjct: 71 VGTVLAS 77
>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 = 54.2 bits (131), Expect = 3e-10
Identities = 14/89 (15%), Positives = 34/89 (38%), Gaps = 8/89 (8%)
Query: 78 STYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFL 137
S + TL++ ++ L AF+ +G +I + + + F+
Sbjct: 3 SGSSGERRAPRKGNTLYVY--GEDMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFV 54
Query: 138 EYDCEKACLAAIRALNRQNFQGSEIIVDF 166
Y+ ++ A+ LN + ++ V+
Sbjct: 55 TYEKMESADQAVAELNGTQVESVQLKVNI 83
>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 = 54.6 bits (132), Expect = 4e-10
Identities = 19/64 (29%), Positives = 33/64 (51%)
Query: 88 DPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLA 147
+ R LFIG L+ + E L + ++GK+ V+RD + S+ +GF+ + A
Sbjct: 25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDA 84
Query: 148 AIRA 151
A+ A
Sbjct: 85 AMAA 88
>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 = 56.4 bits (136), Expect = 4e-10
Identities = 15/78 (19%), Positives = 25/78 (32%), Gaps = 6/78 (7%)
Query: 90 TRTLFIGRLN-KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
L + LN + L F YG V V+++ + K ++ A
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLA 57
Query: 149 IRALNRQNFQGSEIIVDF 166
+ LN G I +
Sbjct: 58 MSHLNGHKLHGKPIRITL 75
Score = 54.9 bits (132), Expect = 1e-09
Identities = 15/94 (15%), Positives = 35/94 (37%), Gaps = 5/94 (5%)
Query: 74 RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
R + K + P+ TL + + + E DL+ F+ G V+ ++
Sbjct: 104 RFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRK 159
Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEII-VDF 166
++ + + A+ L+ + + + V F
Sbjct: 160 MALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF 193
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 53.8 bits (130), Expect = 5e-10
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 2/79 (2%)
Query: 83 HTSSTDPTRTLFIGRLNKNSREADLEQAFAE-YGKVISVRVVRDFVTGHSKRYGFLEYDC 141
+ S+ P +LF+G L + + L + F + Y +VV D TG SK YGF+++
Sbjct: 2 SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTD 60
Query: 142 EKACLAAIRALNRQNFQGS 160
E A+ GS
Sbjct: 61 ELEQKRALTECQGAVGLGS 79
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 53.1 bits (128), Expect = 8e-10
Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 6/81 (7%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEK 143
+S + R++F+ + A L + F +G V SV + +D + +E
Sbjct: 2 SSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDVG 56
Query: 144 ACLAAIRALNRQNFQGSEIIV 164
A A + + ++ + G + V
Sbjct: 57 AREAVL-SQSQHSLGGHRLRV 76
>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 = 55.4 bits (133), Expect = 1e-09
Identities = 15/86 (17%), Positives = 26/86 (30%), Gaps = 6/86 (6%)
Query: 82 PHTSSTDPTRTLFIGRLN-KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
+ L + LN + L F YG V V+++ + K ++
Sbjct: 26 IPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMA 80
Query: 141 CEKACLAAIRALNRQNFQGSEIIVDF 166
A+ LN G I +
Sbjct: 81 DGNQAQLAMSHLNGHKLHGKPIRITL 106
Score = 53.1 bits (127), Expect = 7e-09
Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 5/79 (6%)
Query: 89 PTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAA 148
P+ TL + + + E DL+ F+ G V+ ++ ++ + + A
Sbjct: 150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQA 205
Query: 149 IRALNRQNFQGSEII-VDF 166
+ L+ + + + V F
Sbjct: 206 LIDLHNHDLGENHHLRVSF 224
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 52.0 bits (125), Expect = 3e-09
Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 7/69 (10%)
Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
+ + + F+++GK+ + + G +K Y FLEY + A++ +
Sbjct: 35 KNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92
Query: 164 V-----DFE 167
DF+
Sbjct: 93 RVNLFTDFD 101
>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 = 51.0 bits (122), Expect = 7e-09
Identities = 10/76 (13%), Positives = 26/76 (34%), Gaps = 6/76 (7%)
Query: 91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIR 150
+ L + A++++ F+ +G + V + +E+ A R
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFR 64
Query: 151 ALNRQNFQGSEIIVDF 166
L F + +++
Sbjct: 65 HLAYSKFHHVPLYLEW 80
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 49.4 bits (118), Expect = 2e-08
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 6/79 (7%)
Query: 91 RTLFIGRLNKNSREADLEQAFAEYGKVISVRV-----VRDFVTGHSKRYGFLEYDCEKAC 145
R L++G + E + F ++ + V K + FLE+
Sbjct: 7 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 146 LAAIRALNRQNFQGSEIIV 164
A+ A + FQG + +
Sbjct: 67 TQAM-AFDGIIFQGQSLKI 84
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 50.0 bits (119), Expect = 2e-08
Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 2/70 (2%)
Query: 84 TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDF--VTGHSKRYGFLEYDC 141
+S + +R +F+G L + E ++ +F +G ++ + K Y FL +
Sbjct: 2 SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61
Query: 142 EKACLAAIRA 151
E + A I A
Sbjct: 62 ESSVQALIDA 71
>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 = 49.5 bits (118), Expect = 3e-08
Identities = 16/81 (19%), Positives = 29/81 (35%), Gaps = 13/81 (16%)
Query: 85 SSTDPTRTLFI--GRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCE 142
+ + T++L + G L L + G V ++ + + K Y F Y
Sbjct: 20 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTT 73
Query: 143 KACLAAIRALNRQNFQGSEII 163
+ A LN G E++
Sbjct: 74 EESKRAYVTLN-----GKEVV 89
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 51.3 bits (122), Expect = 3e-08
Identities = 19/119 (15%), Positives = 38/119 (31%), Gaps = 15/119 (12%)
Query: 53 DPIQAGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKN---------SR 103
+ I ++ R R S +TL++G ++
Sbjct: 97 EDIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQI 156
Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI 162
E+ + F+ G + +R V SK GF+++ + A A++ Q
Sbjct: 157 ESRIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD 209
>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 = 48.6 bits (116), Expect = 5e-08
Identities = 21/99 (21%), Positives = 34/99 (34%), Gaps = 11/99 (11%)
Query: 92 TLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRA 151
+ + L + DL+ E G V V RD G +E+ ++ A+R
Sbjct: 17 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 69
Query: 152 LNRQNFQGSEIIVDF----ECGRVLPGWKPRRLGGGWGG 186
L+ F+ E + G P + R G G
Sbjct: 70 LDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSSG 108
>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 = 49.0 bits (117), Expect = 5e-08
Identities = 27/123 (21%), Positives = 46/123 (37%), Gaps = 12/123 (9%)
Query: 77 RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
R Y P + ++ + + L + DL+ E G V V RD G
Sbjct: 5 RGRYGPPSRRSE--NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGV 55
Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVDFECGRVLPGWKPRRLGGGWGGNRNSGQLRFG 196
+E+ ++ A+R L+ F+ E + RV PR G +R+ + R
Sbjct: 56 VEFVRKEDMTYAVRKLDNTKFRSHEGETAY--IRVKVD-GPRSPSYGRSRSRSRSRSRSR 112
Query: 197 GRN 199
R+
Sbjct: 113 SRS 115
>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 = 48.0 bits (115), Expect = 5e-08
Identities = 13/85 (15%), Positives = 34/85 (40%), Gaps = 7/85 (8%)
Query: 81 KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYD 140
+ +F+GR ++ +L+Q F +YG+V+ V + + + + F+ +
Sbjct: 2 RGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFA 56
Query: 141 CEKACLAAIRALNRQNFQGSEIIVD 165
+K + +G + +
Sbjct: 57 DDKVAQSLCG--EDLIIKGISVHIS 79
>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 = 48.1 bits (115), Expect = 6e-08
Identities = 10/86 (11%), Positives = 27/86 (31%), Gaps = 2/86 (2%)
Query: 82 PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVI-SVRVVRDFVTGHSKRYGFLEYD 140
+S + + + ++ F Y + SV + + G + ++
Sbjct: 7 GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMVAFE 65
Query: 141 CEKACLAAIRALNRQNFQGSEIIVDF 166
AA+ LN + ++ +
Sbjct: 66 SRDEATAAVIDLNDRPIGSRKVKLVL 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 = 47.7 bits (114), Expect = 8e-08
Identities = 8/85 (9%), Positives = 25/85 (29%)
Query: 82 PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
+S + + + ++ F Y + ++ G + ++
Sbjct: 7 GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66
Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
AA+ LN + ++ +
Sbjct: 67 RDEATAAVIDLNDRPIGSRKVKLSG 91
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 47.4 bits (113), Expect = 9e-08
Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 2/60 (3%)
Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
+ + + F+++GK+ + + G +K Y FLEY + A++ +
Sbjct: 21 KNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 78
>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif,
RRM, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 111
Score = 47.9 bits (114), Expect = 1e-07
Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 6/81 (7%)
Query: 92 TLFIGRLNKNSREADL---EQAFAEYGKVISVRVVRDFVTGHSKR---YGFLEYDCEKAC 145
+F+ L++ + ++ + F ++GK+ V + S+ ++ Y +
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76
Query: 146 LAAIRALNRQNFQGSEIIVDF 166
L AI+ +N G +
Sbjct: 77 LRAIQCVNNVVVDGRTLKASL 97
>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 = 46.8 bits (112), Expect = 2e-07
Identities = 12/76 (15%), Positives = 33/76 (43%), Gaps = 7/76 (9%)
Query: 90 TRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAI 149
+ +F+GR + E +L + F++YG V+ V + + + + F+ + ++ +
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLC 59
Query: 150 RALNRQNFQGSEIIVD 165
+G + +
Sbjct: 60 G--EDLIIKGISVHIS 73
>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 = 46.3 bits (110), Expect = 4e-07
Identities = 15/89 (16%), Positives = 27/89 (30%), Gaps = 3/89 (3%)
Query: 77 RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVI-SVRVVRDFVTGHSKRYG 135
S I + + + D+ Q +V V+ D G
Sbjct: 2 SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQA 60
Query: 136 FLEYDCEKACLAAIRALNRQNFQGSEIIV 164
+++ E + R L+R+ G E V
Sbjct: 61 LVQFKNEDDARKSER-LHRKKLNGREAFV 88
>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 = 46.7 bits (110), Expect = 1e-06
Identities = 11/87 (12%), Positives = 39/87 (44%), Gaps = 2/87 (2%)
Query: 80 YKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEY 139
+ R+++I ++ D+++ + G+V+++++ R K F+ +
Sbjct: 99 VTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVF 157
Query: 140 DCEKACLAAIRALNRQNFQGSEIIVDF 166
D ++ + Q ++ +++++ F
Sbjct: 158 DSIESAKKFVETPG-QKYKETDLLILF 183
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 44.4 bits (105), Expect = 2e-06
Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 3/72 (4%)
Query: 93 LFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRAL 152
+ + L + DL+ E T G LE+ E+ + A+ L
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLET---TFSSVNTRDFDGTGALEFPSEEILVEALERL 87
Query: 153 NRQNFQGSEIIV 164
N F+GS I V
Sbjct: 88 NNIEFRGSVITV 99
>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 = 44.2 bits (104), Expect = 3e-06
Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 9/84 (10%)
Query: 86 STDPTRTLFIGRL-NKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
+ R + + L + ++ + + YGK+ + ++R K F+E + +
Sbjct: 21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETRED 74
Query: 145 CLAAIR--ALNRQNFQGSEIIVDF 166
+A + FQG + VD
Sbjct: 75 AMAMVDHCLKKALWFQGRCVKVDL 98
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 42.2 bits (99), Expect = 9e-06
Identities = 13/63 (20%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
E + +YG+V + V + + H ++++ E+ A+ LN + F G I
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
Query: 164 VDF 166
+
Sbjct: 100 AEL 102
>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 = 41.9 bits (99), Expect = 1e-05
Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 3/83 (3%)
Query: 82 PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
SS T+ + N E ++ + A K +++R+VR+ G+ Y F+++
Sbjct: 2 SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNA-HGNKTGYIFVDFSN 59
Query: 142 EKACLAAIRALNRQNFQGSEIIV 164
E+ A++ NR+ G I V
Sbjct: 60 EEEVKQALK-CNREYMGGRYIEV 81
>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 = 41.4 bits (97), Expect = 3e-05
Identities = 15/90 (16%), Positives = 30/90 (33%), Gaps = 3/90 (3%)
Query: 77 RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVI-SVRVVRDFVTGHSKRYG 135
S + +++ L + + F + V S+ + G + G
Sbjct: 12 GQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP-NGKATGEG 70
Query: 136 FLEYDCEKACLAAIRALNRQNFQGSEIIVD 165
F+E+ E AA+ ++Q I V
Sbjct: 71 FVEFRNEADYKAAL-CRHKQYMGNRFIQVH 99
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 40.5 bits (95), Expect = 4e-05
Identities = 16/89 (17%), Positives = 37/89 (41%), Gaps = 4/89 (4%)
Query: 77 RSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGF 136
S+ KP + D + + + ++ E D+ F +V +V +++D G + G
Sbjct: 4 GSSGKPLPINPDD-LYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGL 60
Query: 137 LEYDCEKACLAAIRALNRQNFQGSEIIVD 165
+++ + A++ NR + V
Sbjct: 61 VKFLSPQDTFEALK-RNRMLMIQRYVEVS 88
>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 = 39.0 bits (91), Expect = 2e-04
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 2/63 (3%)
Query: 106 DLEQAFAEYGKVISVRVVR--DFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
D+ ++YG V S+ + R D V F+E+ C A++ L + F ++
Sbjct: 31 DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVV 90
Query: 164 VDF 166
+
Sbjct: 91 TKY 93
>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 = 37.9 bits (88), Expect = 3e-04
Identities = 9/69 (13%), Positives = 20/69 (28%), Gaps = 7/69 (10%)
Query: 86 STDPTRTLFIGRL-NKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKA 144
+ R + I + L Q +G + + ++ F+E +
Sbjct: 11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILN------KINEAFIEMATTED 64
Query: 145 CLAAIRALN 153
AA+
Sbjct: 65 AQAAVDYYT 73
>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 = 36.6 bits (85), Expect = 8e-04
Identities = 12/81 (14%), Positives = 29/81 (35%), Gaps = 3/81 (3%)
Query: 82 PHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
+ + + + L + E D+ F+ + V + G +E+
Sbjct: 7 GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGP-DGRVTGEADVEFAT 64
Query: 142 EKACLAAIRALNRQNFQGSEI 162
+ +AA+ A ++ N Q +
Sbjct: 65 HEDAVAAM-AKDKANMQHRYV 84
>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 = 37.1 bits (86), Expect = 0.001
Identities = 15/89 (16%), Positives = 30/89 (33%), Gaps = 3/89 (3%)
Query: 74 RALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKR 133
S T + + + L + E D+ F+ + V + G
Sbjct: 30 MGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTG 87
Query: 134 YGFLEYDCEKACLAAIRALNRQNFQGSEI 162
+E+ + +AA+ + +R N Q I
Sbjct: 88 EADVEFATHEEAVAAM-SKDRANMQHRYI 115
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 38.3 bits (88), Expect = 0.001
Identities = 23/151 (15%), Positives = 47/151 (31%), Gaps = 39/151 (25%)
Query: 3 DEQKSAKNSPSSHHSEVRDSKSSSQTVEPRDAKSSSGQTVKYWYPYCITYDPIQAGSIDG 62
+ + +N + H + D + +T + D +Y+Y + I + +
Sbjct: 434 ELKVKLENEYA-LHRSIVDHYNIPKTFDSDDL--IPPYLDQYFYSH-IGHHLKNIEHPER 489
Query: 63 TDTIPH---D-RAILRALRST-------------------YKPHTSSTDPTRTL------ 93
D R + + +R YKP+ DP
Sbjct: 490 MTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAIL 549
Query: 94 -FIGRLNKN---SREADLEQA--FAEYGKVI 118
F+ ++ +N S+ DL + AE +
Sbjct: 550 DFLPKIEENLICSKYTDLLRIALMAEDEAIF 580
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 35.5 bits (82), Expect = 0.003
Identities = 18/110 (16%), Positives = 41/110 (37%), Gaps = 14/110 (12%)
Query: 57 AGSIDGTDTIPHDRAILRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGK 116
+GS G + H+R ++ +++ + P DP I DL +++G+
Sbjct: 3 SGSSGGPSRMRHERVVI--IKNMFHPMDFEDDPLVLNEI--------REDLRVECSKFGQ 52
Query: 117 VISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEIIVDF 166
+ + + H + + + I+ L+ + F G +I
Sbjct: 53 IRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 98
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 34.7 bits (80), Expect = 0.005
Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 4/67 (5%)
Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYG----FLEYDCEKACLAAIRALNRQNFQG 159
E ++ + ++G V V + ++ F+E+ AI+ALN + F G
Sbjct: 39 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG 98
Query: 160 SEIIVDF 166
+++ +
Sbjct: 99 RKVVAEV 105
>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 = 33.1 bits (75), Expect = 0.024
Identities = 11/87 (12%), Positives = 25/87 (28%), Gaps = 5/87 (5%)
Query: 81 KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEY---GKVISVRVVRDFVTGHSKRYGFL 137
+ + L + D++ ++ V + G F+
Sbjct: 35 MMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTR-EGRQSGEAFV 93
Query: 138 EYDCEKACLAAIRALNRQNFQGSEIIV 164
E E A++ +R++ I V
Sbjct: 94 ELGSEDDVKMALK-KDRESMGHRYIEV 119
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 32.5 bits (74), Expect = 0.028
Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 1/64 (1%)
Query: 104 EADLEQAFAEYGKVISVRVVRDFVTG-HSKRYGFLEYDCEKACLAAIRALNRQNFQGSEI 162
E + ++ +YGKV + FLE++ ++ + A+ LN + F G +
Sbjct: 27 EVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV 86
Query: 163 IVDF 166
F
Sbjct: 87 KACF 90
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint
center for struc genomics, JCSG, protein structure
initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus
musculus} PDB: 2lq5_A
Length = 114
Score = 32.3 bits (74), Expect = 0.036
Identities = 14/63 (22%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 104 EADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDCEKACLAAIRALNRQNFQGSEII 163
+ D+ + ++G VI + V ++ G+ +++ A +AA+ AL+ + F G I
Sbjct: 31 KDDVIEECNKHGGVIHIYVDKNSAQGN----VYVKCPSIAAAIAAVNALHGRWFAGKMIT 86
Query: 164 VDF 166
+
Sbjct: 87 AAY 89
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 31.9 bits (72), Expect = 0.067
Identities = 15/87 (17%), Positives = 29/87 (33%), Gaps = 8/87 (9%)
Query: 84 TSSTDPTRTLF--IGRLNKNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
+ + L + L L Q F+++G V+ + L+Y
Sbjct: 20 MAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYAD 75
Query: 142 EKACLAAIRALNRQNF--QGSEIIVDF 166
+ A +L+ QN + +DF
Sbjct: 76 PVSAQHAKLSLDGQNIYNACCTLRIDF 102
>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 28.8 bits (64), Expect = 0.58
Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 11/85 (12%)
Query: 87 TDPTRTLFIGRLN-----KNSREADLEQAFAEYGKVISVRVVRDFVTGHSKRYGFLEYDC 141
+ + L N ++ A E F Y K + + + F + + +
Sbjct: 2 SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSN 55
Query: 142 EKACLAAIRALNRQNFQGSEIIVDF 166
+ A L++ F G E+ + F
Sbjct: 56 PLSAADARLRLHKTEFLGKEMKLYF 80
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.0 bits (61), Expect = 1.9
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 10/36 (27%)
Query: 73 LRALRSTYKPHTSSTDPTRTLFIGRLNKNSREADLE 108
L+ L+++ K + + P L I +A +E
Sbjct: 22 LKKLQASLKLYADDSAP--ALAI--------KATME 47
>1a12_A RCC1, regulator of chromosome condensation 1; guanine nucleotide
exchange factor, GEF, RAN, RAS-like nuclear GTP binding
protein; 1.70A {Homo sapiens} SCOP: b.69.5.1 PDB: 1i2m_B
Length = 413
Score = 27.3 bits (61), Expect = 4.7
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 183 GWGGNRNS-GQLRFGGRNKPWVKPVQLM 209
WG R++ G + K + PVQ+
Sbjct: 134 LWGSFRDNNGVIGLLEPMKKSMVPVQVQ 161
>3df6_A ORF99; archaeal virus, extremophiles, protein fold,
lipothrixviridae, viral protein, unknown function; 2.05A
{Acidianus filamentous virus 1} PDB: 3djw_A
Length = 99
Score = 25.8 bits (56), Expect = 5.5
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 7/54 (12%)
Query: 81 KPHTSSTDPTRTLFIGRLNKNSREADLEQAFAEYGK-------VISVRVVRDFV 127
KP +S++ +FI + ++ E +++ F EY + V+S++ V D+V
Sbjct: 44 KPDSSNSAENNGIFIDEYSYDASENAMKKLFVEYVRQPEFKYTVLSIKGVNDWV 97
>3n7l_A Neurotoxin; HCR/D-SA, ganglioside binding loop; 2.00A {Clostridium
botulinum} PDB: 3azw_A 3azv_A 3n7m_A 3n7k_A 3r4s_A*
3r4u_A
Length = 424
Score = 26.9 bits (58), Expect = 6.3
Identities = 16/121 (13%), Positives = 38/121 (31%), Gaps = 13/121 (10%)
Query: 19 VRDSKSSSQTVEPRDAKSSSGQTVKYWYPYCITYD------------PIQAGSIDGTDTI 66
++ +++S Q + S + W+ IT + I + I
Sbjct: 116 LKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKELTGI 175
Query: 67 PHDRAILRALRSTYKPH-TSSTDPTRTLFIGRLNKNSREADLEQAFAEYGKVISVRVVRD 125
+ I + +S ++I ++E D + + + VV+D
Sbjct: 176 NFSKTITFQMNKIPNTGLITSDSDNINMWIRDFYIFAKELDDKDINILFNSLQYTNVVKD 235
Query: 126 F 126
+
Sbjct: 236 Y 236
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
0.315 0.133 0.407
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,528,134
Number of extensions: 208143
Number of successful extensions: 700
Number of sequences better than 10.0: 1
Number of HSP's gapped: 592
Number of HSP's successfully gapped: 198
Length of query: 225
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 135
Effective length of database: 4,188,903
Effective search space: 565501905
Effective search space used: 565501905
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (24.9 bits)