RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1185
(131 letters)
>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 = 105 bits (264), Expect = 7e-31
Identities = 35/118 (29%), Positives = 61/118 (51%), Gaps = 25/118 (21%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L++ + + E++ E + G+ VI+Y+S
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVT-------------------------EGVLDVIVYASA 45
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKV 124
D KNRGF F+EY+SH++A++A+++L GR+++WG I VDWA+P+ + D + M V
Sbjct: 46 ADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV 103
>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 = 90.0 bits (224), Expect = 7e-25
Identities = 31/51 (60%), Positives = 43/51 (84%)
Query: 1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
M+KVKVL+VRNL TEE L++AF Q+G++ERVK++KDYAF+HF++R A
Sbjct: 8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGA 58
>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 = 85.0 bits (211), Expect = 5e-23
Identities = 28/54 (51%), Positives = 39/54 (72%), Gaps = 2/54 (3%)
Query: 1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYG--RVERVKRIKDYAFVHFEDRQEAI 52
MS VK+LYVRNL +EE +++ F VERVK+I+DYAFVHF +R++A+
Sbjct: 12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAV 65
>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 = 88.9 bits (221), Expect = 1e-22
Identities = 23/168 (13%), Positives = 49/168 (29%), Gaps = 55/168 (32%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA--------- 51
+ V+NL + + K+ + F+ G + V +A + F A
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK 103
Query: 52 ------ITV------------------------------TGLSQVIIYSSPDDNKKNRGF 75
I V + + S +R F
Sbjct: 104 VVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPS--LRFNTSRRF 161
Query: 76 CFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSK 123
+++ S + A ++L LK+ G ++ ++P E+ +
Sbjct: 162 AYIDVTSKEDARYCVEKL--NGLKIEGYTLVTKVSNPLEKSKRTDSAT 207
Score = 60.0 bits (146), Expect = 5e-12
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 1 MSKVKVLYVRNLTQYCTEEK-LKEAFEQYGRVERVK---------RIKDYAFVHFEDRQE 50
+ + + +RNL+ +E L+E+FE +G +E++ AF+ FE++
Sbjct: 207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDS 266
Query: 51 A 51
A
Sbjct: 267 A 267
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 80.4 bits (199), Expect = 1e-19
Identities = 28/172 (16%), Positives = 52/172 (30%), Gaps = 52/172 (30%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVE-RVKRIKDYAFVHFEDRQEA--------- 51
+ + +R L T +++ + Y V + K AFV + ++A
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQ 79
Query: 52 ------------------ITVTGLSQ--------------------VIIYSSPDDNKKNR 73
+ V L ++YS + +++
Sbjct: 80 SRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYS--ERTGQSK 137
Query: 74 GFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKVL 125
G+ F EY SA+ AK L + + V W D + S+ L
Sbjct: 138 GYGFAEYMKKDSAARAKSDL--LGKPLGPRTLYVHWTDAGQLTPALLHSRCL 187
Score = 63.5 bits (155), Expect = 3e-13
Identities = 9/59 (15%), Positives = 20/59 (33%), Gaps = 8/59 (13%)
Query: 1 MSKVKVLYVRNLTQYCTE-EKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEA 51
+ + L V L + + L A + ++K +A + +E + A
Sbjct: 181 LLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMA 239
>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 = 75.3 bits (186), Expect = 3e-19
Identities = 20/45 (44%), Positives = 30/45 (66%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
L+V N++ CT ++L+ FE+YG V +KDYAFVH E ++A
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDA 57
>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 = 74.2 bits (183), Expect = 8e-19
Identities = 19/45 (42%), Positives = 29/45 (64%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
++V N++ CT ++L+ FE+ GRV +KDYAFVH E +A
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADA 56
>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 = 72.2 bits (178), Expect = 4e-18
Identities = 21/50 (42%), Positives = 32/50 (64%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
S + L++ NL + TE++++ FEQYG+V IK+Y FVH ED+ A
Sbjct: 6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAA 55
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 71.2 bits (175), Expect = 2e-17
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
L+VR E +L E F +G ++ VK + +AFV FE+ + A
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESA 78
>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 = 70.0 bits (172), Expect = 5e-17
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA 51
L+V NL TEE++++ FE+YG+ V KD + F+ E R A
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLA 64
>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 = 69.6 bits (171), Expect = 9e-17
Identities = 20/116 (17%), Positives = 44/116 (37%), Gaps = 27/116 (23%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
+ VRN+ + +++E F +G ++ V+ K
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKK--------------------------M 51
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMS 122
+RGF F+++ + + A A L ++G ++++WAD + + S
Sbjct: 52 TGTGAHRGFGFVDFITKQDAKKAFNALCHST-HLYGRRLVLEWADSEVTVQSGPSS 106
>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 = 65.7 bits (161), Expect = 2e-15
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVE--RVKRIKDYAFVHFEDRQEA 51
M+K LY+ NL+ T + L++ F +V YAFV + D+ A
Sbjct: 8 MNK---LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWA 57
>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 = 65.0 bits (159), Expect = 4e-15
Identities = 10/50 (20%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEAI 52
L+V L + L F+++G + + +K +A++ +E A
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQ 67
>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 = 65.2 bits (159), Expect = 4e-15
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAIT 53
V++VR L + E L EA E++G + V K A V FE+ A
Sbjct: 16 PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKE 66
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 64.7 bits (158), Expect = 5e-15
Identities = 24/110 (21%), Positives = 38/110 (34%), Gaps = 31/110 (28%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGR--VERVKRIKDYAFVHFEDRQEAITVTGLSQVII 62
+ +RN+ + + + A Y V ++ IKD T +
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKD-------------KQTQQN---- 52
Query: 63 YSSPDDNKKNRGFCFLEYDSHKSASLAKKRL--ATGRLKVWGCDIIVDWA 110
RGF F++ S AS + L LK+ G I VD+A
Sbjct: 53 ----------RGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92
>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 = 63.8 bits (156), Expect = 1e-14
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
+ + LYV NL++ TE + + F Q G + K I + Y FV F + ++A
Sbjct: 13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDA 68
>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 = 63.5 bits (155), Expect = 2e-14
Identities = 20/111 (18%), Positives = 41/111 (36%), Gaps = 31/111 (27%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L+V L + +EE + F+ +G ++ ++
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLR---------------------------- 49
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD--IIVDWADPQEE 115
+ ++G F+++ SH A A L G + G ++V +AD +E
Sbjct: 50 GPDGSSKGCAFVKFSSHTEAQAAIHAL-HGSQTMPGASSSLVVKFADTDKE 99
>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 = 64.1 bits (157), Expect = 3e-14
Identities = 26/114 (22%), Positives = 39/114 (34%), Gaps = 29/114 (25%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L V L Q T+E+ + F G +E K ++D +TG S
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK-------------ITGQS-------- 43
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTET 120
G+ F+ Y K A A L L++ I V +A P +
Sbjct: 44 ------LGYGFVNYIDPKDAEKAINTL--NGLRLQTKTIKVSYARPSSASIRDA 89
Score = 51.4 bits (124), Expect = 2e-09
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
LYV L + T+++L++ F QYGR+ + + D F+ F+ R EA
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEA 143
>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 = 64.1 bits (156), Expect = 4e-14
Identities = 29/109 (26%), Positives = 41/109 (37%), Gaps = 29/109 (26%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LYV NL+ Y TEE++ E F + G ++++ D
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLD--------------------------- 74
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
K GFCF+EY S A A + + RL I DW +E
Sbjct: 75 KMKKTACGFCFVEYYSRADAENAMRYINGTRLD--DRIIRTDWDAGFKE 121
>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 = 64.1 bits (157), Expect = 4e-14
Identities = 25/114 (21%), Positives = 40/114 (35%), Gaps = 29/114 (25%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L V L Q T+ +L F G + + ++DY TG S
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDY-------------KTGYS-------- 44
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTET 120
G+ F+++ S + A K L + V + V +A P E +T
Sbjct: 45 ------YGYAFVDFTSEMDSQRAIKVL--NGITVRNKRLKVSYARPGGESIKDT 90
Score = 53.0 bits (128), Expect = 7e-10
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
LYV NL + T+++L F +YG + + ++D AFV + R+EA
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144
>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 = 65.1 bits (158), Expect = 5e-14
Identities = 30/117 (25%), Positives = 43/117 (36%), Gaps = 27/117 (23%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LY+ NLT + T+E L EA G + + IK F FE+R G S
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVND-ILEIK---F--FENR-----ANGQS-------- 111
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSK 123
+GF + S S+ L L G + +V + Q E S+
Sbjct: 112 ------KGFALVGVGSEASSKKLMDLLPKRELH--GQNPVVTPVNKQFLSQFEMQSR 160
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 61.9 bits (151), Expect = 6e-14
Identities = 10/47 (21%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA 51
Y+ N+ + TE L F+ +G + K + F+ ++ ++A
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQA 76
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 62.8 bits (153), Expect = 6e-14
Identities = 28/116 (24%), Positives = 40/116 (34%), Gaps = 37/116 (31%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L V NLT + + L+ FE+YGRV V +D T S
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY-------------TKES-------- 88
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEEPDT 118
RGF F+ + + A A + GR ++ V A PD+
Sbjct: 89 ------RGFAFVRFHDKRDAEDAMDAMDGAVLDGR------ELRVQMARYGRPPDS 132
>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 = 62.0 bits (151), Expect = 8e-14
Identities = 9/47 (19%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA 51
+Y + T++ +++ F +G++ ++ + Y+FV F + A
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESA 74
>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 = 61.9 bits (151), Expect = 8e-14
Identities = 26/116 (22%), Positives = 39/116 (33%), Gaps = 30/116 (25%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L V NLT + + L+ FE+YGRV V ++ T
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREP-------------HTKAP-------- 54
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMS 122
RGF F+ + + A A+ + L G ++ V A D S
Sbjct: 55 ------RGFAFVRFHDRRDAQDAEAAMDGAELD--GRELRVQVARYG-RRDLSGPS 101
>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 = 64.7 bits (158), Expect = 9e-14
Identities = 35/159 (22%), Positives = 55/159 (34%), Gaps = 48/159 (30%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA------------- 51
L+V NL TEE K FE+YG V +D + F+ E R A
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 84
Query: 52 --------------ITVTGLSQVI--------------IYSS---PDDNKKNRGFCFLEY 80
+TV LS V+ + + DD + G F+E+
Sbjct: 85 SRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEF 144
Query: 81 DSHKSASLAKKRLATGRLKVWGCD--IIVDWADPQEEPD 117
+ A A +R G + +IV+ + ++ D
Sbjct: 145 AAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDED 183
>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 = 61.1 bits (149), Expect = 1e-13
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
+ V NL++ E L+E F +G + R+ KD +AF+ F R++A
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 70
>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 = 60.8 bits (148), Expect = 2e-13
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
S K L+V N+ + L++ F Q+G++ V+ I + + FV FE+ +A
Sbjct: 13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 68
>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 = 59.8 bits (146), Expect = 3e-13
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
LY+R L T++ L + + YG++ K I D Y FV F+ A
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 60.3 bits (146), Expect = 3e-13
Identities = 14/119 (11%), Positives = 41/119 (34%), Gaps = 33/119 (27%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
+V+++R L TE ++ +G+V + +K
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------------------------- 51
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSK 123
+ F+E ++ ++A+ + + G I + +++ +E + ++
Sbjct: 52 --------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQ 102
>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 = 61.4 bits (149), Expect = 4e-13
Identities = 28/113 (24%), Positives = 40/113 (35%), Gaps = 29/113 (25%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L V NLT + + L+ FE+YGRV V +D T S
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY-------------TKES-------- 111
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTE 119
RGF F+ + + A A + L G ++ V A PD+
Sbjct: 112 ------RGFAFVRFHDKRDAEDAMDAMDGAVLD--GRELRVQMARYGRPPDSH 156
>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 = 59.6 bits (145), Expect = 4e-13
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA 51
LYV L TE L+ F Q+G + + ++ AF+ F RQ A
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAA 61
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 59.8 bits (145), Expect = 4e-13
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITV 54
+VL++R L TE ++ +G+V + + K+ AF+ + AIT+
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITM 67
>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 = 59.6 bits (145), Expect = 6e-13
Identities = 24/112 (21%), Positives = 43/112 (38%), Gaps = 30/112 (26%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L++ + + E+ LK FE++G++ + +KD TG+
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF-------------TGMH-------- 54
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD--IIVDWADPQEEP 116
+G FL Y +SA A+ L + + G + I V AD +
Sbjct: 55 ------KGCAFLTYCERESALKAQSAL-HEQKTLPGMNRPIQVKPADSESRG 99
>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 = 59.2 bits (144), Expect = 6e-13
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
++V NL EE L E F Q G + +V KD + FV F+ +
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESV 70
>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 = 60.1 bits (146), Expect = 6e-13
Identities = 27/113 (23%), Positives = 41/113 (36%), Gaps = 37/113 (32%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
L V L+ Y TE L+E F +YG + V + D + S
Sbjct: 47 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ-------------QSRRS------ 87
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLA----TGRLKVWGCDIIVDWADPQ 113
RGF F+ +++ A AK+R GR I VD++ +
Sbjct: 88 --------RGFAFVYFENVDDAKEAKERANGMELDGR------RIRVDFSITK 126
>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 = 59.2 bits (144), Expect = 7e-13
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK----RIKDYAFVHFEDRQEA 51
K L + NL+ TEE L+E FE+ ++ + + K YAF+ F ++A
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDA 66
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 59.1 bits (144), Expect = 7e-13
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L V L+ Y TE L+E F +YG + V + D +AFV+FE+ +A
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition
motif, RRM, RNA binding domain, RBD, RNP, structural
genomics; NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 59.2 bits (144), Expect = 8e-13
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L+VRNL+ +EE L++ F YG + + D +AFV F + A
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63
>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 = 59.3 bits (144), Expect = 8e-13
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 7 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
+++ NL T + ++ F +YGRV K YAFV + + + A
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHA 75
>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-13
Identities = 14/119 (11%), Positives = 41/119 (34%), Gaps = 33/119 (27%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
+V+++R L TE ++ +G+V + +K
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------------------------- 66
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSK 123
+ F+E ++ ++A+ + + G I + +++ +E + ++
Sbjct: 67 --------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDSSPNQ 117
>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 = 58.8 bits (143), Expect = 1e-12
Identities = 27/109 (24%), Positives = 39/109 (35%), Gaps = 29/109 (26%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
+YV L + +E L E F Q G V KD VTG
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR-------------VTGQH-------- 56
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
+G+ F+E+ S + A A K + +L G I V+ A +
Sbjct: 57 ------QGYGFVEFLSEEDADYAIKIMDMIKLY--GKPIRVNKASAHNK 97
>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 = 58.9 bits (143), Expect = 1e-12
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQEA 51
+YV NL + +++ F +YG + + +AFV FED ++A
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDA 74
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 58.6 bits (142), Expect = 1e-12
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITV 54
V+++R L E L EA +++G + V K A V FED A
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNA 73
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 58.4 bits (142), Expect = 1e-12
Identities = 13/52 (25%), Positives = 29/52 (55%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
L++ L CT+E+L+E + +G V+ ++ + + A+V +E+ +A
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQA 71
>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 = 58.4 bits (142), Expect = 1e-12
Identities = 24/111 (21%), Positives = 39/111 (35%), Gaps = 29/111 (26%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LYV L + ++ L AF +G + ++ DY T
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDY-------------ETEKH-------- 53
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
RGF F+E++ + A+ A + L G I V+ A P +
Sbjct: 54 ------RGFAFVEFELAEDAAAAIDNMNESELF--GRTIRVNLAKPMRIKE 96
>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 = 58.0 bits (141), Expect = 2e-12
Identities = 19/119 (15%), Positives = 43/119 (36%), Gaps = 37/119 (31%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
+V+Y+ ++ TEE++ + G V +K + D Q TG
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMF--------DPQ-----TG-------- 41
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEEPDTE 119
+++G+ F+E+ +S++ A + L R + ++ +
Sbjct: 42 ------RSKGYAFIEFRDLESSASAVRNLNGYQLGSR------FLKCGYSSNSDISGVS 88
>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 = 57.9 bits (141), Expect = 2e-12
Identities = 18/109 (16%), Positives = 41/109 (37%), Gaps = 28/109 (25%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
+++ LT+ T++ + E F YG+++ + +R LS
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPV--------ERMH----PHLS-------- 46
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
+G+ ++E+++ A A K + G++ G +I
Sbjct: 47 ------KGYAYVEFENPDEAEKALKHMDGGQID--GQEITATAVLAPWP 87
>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 = 58.5 bits (142), Expect = 2e-12
Identities = 24/115 (20%), Positives = 44/115 (38%), Gaps = 31/115 (26%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
K +++RNL+ EE L E +Q+G ++ V+ + T S
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD-------------TEHS------ 56
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLA----KKRLATGRLKVWGCDIIVDWADPQEE 115
+G F ++ + ++A G LK+ G + VD A ++E
Sbjct: 57 --------KGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103
>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 = 58.4 bits (142), Expect = 2e-12
Identities = 26/113 (23%), Positives = 42/113 (37%), Gaps = 37/113 (32%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L+V L+ E+ L++ F +YG++ V +K DR+ T S
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVK--------DRE-----TQRS-------- 53
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEE 115
RGF F+ +++ A A + GR I VD A +
Sbjct: 54 ------RGFGFVTFENIDDAKDAMMAMNGKSVDGR------QIRVDQAGKSSD 94
>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 = 58.1 bits (141), Expect = 2e-12
Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 7 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
L++ NL + ++E L F YG + ++ + F+ F++ Q
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSV 70
>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 = 59.5 bits (145), Expect = 3e-12
Identities = 27/120 (22%), Positives = 51/120 (42%), Gaps = 30/120 (25%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
+VLYV NL + TE+ LK+ F+ G + +K I+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIK-------------------------IMI- 34
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSKV 124
D N KN + F+EY A++A + L G+ ++ + ++WA ++ ++ +
Sbjct: 35 --DKNNKNVNYAFVEYHQSHDANIALQTL-NGK-QIENNIVKINWAFQSQQSSSDDTFNL 90
Score = 46.0 bits (110), Expect = 2e-07
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L+V +L +E L+ AF+ + + D Y FV F + +A
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 142
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 57.5 bits (139), Expect = 3e-12
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----YAFVHFEDRQEA 51
+++ L +RN+ + E L QYG VE +++ V + + +A
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQA 67
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 57.3 bits (139), Expect = 3e-12
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEA 51
+YV NL + +L+ AF YG + V ++ +AFV FED ++A
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDA 50
>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 = 57.3 bits (139), Expect = 4e-12
Identities = 27/117 (23%), Positives = 47/117 (40%), Gaps = 37/117 (31%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
+ ++V N+ TEE+LK+ F + G V + + DR+ TG
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVY--------DRE-----TG-------- 47
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEEPD 117
K +G+ F EY ++A A + L +GR + VD A ++ +
Sbjct: 48 ------KPKGYGFCEYQDQETALSAMRNLNGREFSGR------ALRVDNAASEKNKE 92
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 56.9 bits (138), Expect = 4e-12
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 3/64 (4%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITVTGLS 58
S ++ ++V + +L E F +G V V KD +A V D V S
Sbjct: 6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQS 65
Query: 59 QVII 62
Q +
Sbjct: 66 QHSL 69
>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 = 56.8 bits (138), Expect = 5e-12
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 9/60 (15%)
Query: 1 MSKVKV-LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
M+ K LYV L + ++ L AF +G + ++ D +AFV FE ++A
Sbjct: 3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 56.6 bits (137), Expect = 5e-12
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYG-RVERVKRIKDYAFVHFEDRQEA 51
+ V+NL Q +++ + + Y + V R K AFV + ++A
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQA 53
>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 = 56.9 bits (138), Expect = 6e-12
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
L V NL ++ ++E F ++G +++ D A VHFE + +A
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADA 83
>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 = 58.3 bits (141), Expect = 7e-12
Identities = 24/115 (20%), Positives = 46/115 (40%), Gaps = 29/115 (25%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
+L+V ++ + E++++E F YG ++ + D TG
Sbjct: 73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR-------------TG-------- 111
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTE 119
++G+ +EY++HK A AK+ L + G I VDW + +
Sbjct: 112 ------FSKGYALVEYETHKQALAAKEALNGAEIM--GQTIQVDWCFVKGPKRVK 158
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 56.4 bits (137), Expect = 8e-12
Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 7 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEA 51
L++ NL + ++E L F YG + ++ + F+ F++ Q
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSV 58
>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 = 56.1 bits (136), Expect = 1e-11
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
+YV NL T L F +YG+V +V +KD AF+ F D+ A
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
>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 = 56.5 bits (137), Expect = 1e-11
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 8/55 (14%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
KVLY++NL+ TE L F ++ + AF+ F +++ A
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIA 80
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 57.6 bits (139), Expect = 1e-11
Identities = 19/121 (15%), Positives = 38/121 (31%), Gaps = 35/121 (28%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
+YV + + + T+++L + G + + + F E+R G S
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYD----VVELKFA--ENRA-----NGQS-------- 98
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLAT----GRLKVWGCDIIVDWADPQEEPDTETMS 122
+G+ + S S + L G + V A Q E +
Sbjct: 99 ------KGYAEVVVASENSVHKLLELLPGKVLNGE------KVDVRPATRQNLSQFEAQA 146
Query: 123 K 123
+
Sbjct: 147 R 147
>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 = 57.0 bits (138), Expect = 1e-11
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
L V NL ++ ++E F ++G +++ D A VHFE R +A
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 89
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 56.3 bits (136), Expect = 1e-11
Identities = 16/89 (17%), Positives = 26/89 (29%), Gaps = 27/89 (30%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
K + L E LK+ +YG VE V+ +
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLH------------------------- 41
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRL 93
+K+ G + + S + A K L
Sbjct: 42 --PRTRKHLGLARVLFTSTRGAKETVKNL 68
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 57.1 bits (138), Expect = 1e-11
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
LYV L + ++ L AF +G + ++ D +AFV FE ++A
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 118
>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 = 57.6 bits (140), Expect = 1e-11
Identities = 18/107 (16%), Positives = 41/107 (38%), Gaps = 31/107 (28%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L++ +++ CTE ++ F +G++E + ++
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRILR---------------------------- 129
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCD--IIVDWAD 111
+ +RG F+ + + A A K + + GC ++V +AD
Sbjct: 130 GPDGLSRGCAFVTFTTRAMAQTAIKAM-HQAQTMEGCSSPMVVKFAD 175
Score = 56.1 bits (136), Expect = 6e-11
Identities = 23/120 (19%), Positives = 44/120 (36%), Gaps = 34/120 (28%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
++V + + +E+ L+E FEQYG V + ++D Q
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDR-------------SQNPPQ------- 45
Query: 67 DDNKKNRGFCFLEYDSHKSASLA-----KKRLATGRLKVWGCDIIVDWADPQEEPDTETM 121
++G CF+ + + K+A A ++ G I + AD ++ E
Sbjct: 46 -----SKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHP----IQMKPADSEKNNAVEDR 96
>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 = 57.6 bits (140), Expect = 1e-11
Identities = 17/123 (13%), Positives = 40/123 (32%), Gaps = 31/123 (25%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVI 61
+ L++ NL + +LK A + + +
Sbjct: 11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-------------------------V 45
Query: 62 IYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETM 121
+ NR F +++++S + A + TG KV+G +I ++ ++
Sbjct: 46 VD---VRTGTNRKFGYVDFESAEDLEKALE--LTGL-KVFGNEIKLEKPKGRDSKKVRAA 99
Query: 122 SKV 124
+
Sbjct: 100 RTL 102
Score = 54.9 bits (133), Expect = 1e-10
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK---RIKDYAFVHFEDRQEA 51
L +NL+ TE++LKE FE + V + K A++ F+ +A
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADA 149
>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 = 56.0 bits (135), Expect = 1e-11
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEA 51
V+ +NL +++E F ++G + RV A V F + EA
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEA 59
>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 = 57.2 bits (139), Expect = 2e-11
Identities = 17/118 (14%), Positives = 37/118 (31%), Gaps = 25/118 (21%)
Query: 1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQV 60
+ + LYV N+ TEE + + F R+ + +
Sbjct: 1 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPG--------------------N 40
Query: 61 IIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDT 118
+ + +++ F FLE+ S + A +A + G + + +
Sbjct: 41 PVLA--VQINQDKNFAFLEFRSVDETTQA---MAFDGIIFQGQSLKIRRPHDYQPLPG 93
Score = 53.4 bits (129), Expect = 5e-10
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L++ L Y ++++KE +G ++ +KD YAF + D
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 149
>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 = 55.8 bits (135), Expect = 2e-11
Identities = 26/112 (23%), Positives = 49/112 (43%), Gaps = 29/112 (25%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
+L+V ++ + E++++E F YG ++ + D R+ TG
Sbjct: 27 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD--------RR-----TG-------- 65
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP 116
++G+ +EY++HK A AK+ L G ++ G I VDW +
Sbjct: 66 ------FSKGYALVEYETHKQALAAKEAL-NGA-EIMGQTIQVDWCFVKGPK 109
>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 = 56.7 bits (137), Expect = 2e-11
Identities = 24/109 (22%), Positives = 38/109 (34%), Gaps = 29/109 (26%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L V + E +L++ FE+YG +E VK + D T S
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE-------------TRQS-------- 83
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
RG+ F+++ S SA A L + + V A +
Sbjct: 84 ------RGYGFVKFQSGSSAQQAIAGLNGFNIL--NKRLKVALAASGHQ 124
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 55.8 bits (135), Expect = 2e-11
Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
L+V N+ + L++ F Q+G++ V+ I + + FV FE+ +A
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 82
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 55.3 bits (134), Expect = 2e-11
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 6/51 (11%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
++VRNL T + LK+ F + G V + V FE + A
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVA 61
>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 = 55.8 bits (135), Expect = 2e-11
Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
++V NL +KLKE F G V R ++D V FE EA
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEA 69
>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 = 55.3 bits (134), Expect = 2e-11
Identities = 26/109 (23%), Positives = 41/109 (37%), Gaps = 27/109 (24%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LY+ NLT + T+E L EA G + + IK FE+R
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVND-ILEIK-----FFENR------------------ 39
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
N +++GF + S S+ L L G + +V ++ E
Sbjct: 40 -ANGQSKGFALVGVGSEASSKKLMDLLPKRELH--GQNPVVTPSNKLEH 85
>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 = 56.4 bits (136), Expect = 2e-11
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEA 51
+YV NL + +L+ AF YG + V ++ +AFV FED ++A
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDA 123
>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 = 55.8 bits (135), Expect = 3e-11
Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 29/110 (26%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L+V + + TEE + + F +YG ++ + DR+ TG
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL--------DRR-----TGYL-------- 63
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP 116
+G+ +EY+++K A A + L G+ + G I VDW + P
Sbjct: 64 ------KGYTLVEYETYKEAQAAMEGL-NGQ-DLMGQPISVDWCFVRGPP 105
>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 = 55.3 bits (134), Expect = 3e-11
Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
LY+ NL E++L+ + +G+V + ++D F E ++
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKC 79
>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 = 54.9 bits (133), Expect = 3e-11
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 7/57 (12%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
++V + E +++ F +YG V+ VK I D Y FV F + +
Sbjct: 7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
>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 = 54.9 bits (133), Expect = 3e-11
Identities = 23/113 (20%), Positives = 42/113 (37%), Gaps = 37/113 (32%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LYV +L TE+ L+ FE +G+++ + +K D TG S
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMK--------DSD-----TGRS-------- 46
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEE 115
+G+ F+ + + A A ++L GR + V + +
Sbjct: 47 ------KGYGFITFSDSECARRALEQLNGFELAGR------PMRVGHVTERLD 87
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 56.9 bits (138), Expect = 4e-11
Identities = 20/109 (18%), Positives = 44/109 (40%), Gaps = 29/109 (26%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
+YV ++ E+ +++AF +G ++ + D +VT
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWD-------------SVTMKH-------- 69
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
+GF F+EY+ ++A LA +++ + + G +I V +
Sbjct: 70 ------KGFAFVEYEVPEAAQLALEQM--NSVMLGGRNIKVGRPSNIGQ 110
Score = 53.1 bits (128), Expect = 9e-10
Identities = 12/53 (22%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
+YV ++ Q +++ +K FE +G+++ +D Y F+ +E Q +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSS 180
>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 = 55.0 bits (133), Expect = 4e-11
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
L++ L + E+ LK F ++G + V IKD +AF+ FE+ +A
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADA 61
>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 = 54.6 bits (132), Expect = 5e-11
Identities = 24/113 (21%), Positives = 43/113 (38%), Gaps = 37/113 (32%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LYV +L TE+ L+ FE +GR+E ++ + D + TG S
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMM--------DSE-----TGRS-------- 67
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRL----ATGRLKVWGCDIIVDWADPQEE 115
+G+ F+ + + A A ++L GR + V + +
Sbjct: 68 ------KGYGFITFSDSECAKKALEQLNGFELAGR------PMKVGHVTERTD 108
>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 = 54.2 bits (131), Expect = 5e-11
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK---RIKDYAFVHFEDRQEA 51
+ L +NL+ TE++LKE FE + V + K A++ F+ +A
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADA 66
>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 = 54.6 bits (132), Expect = 5e-11
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 11/61 (18%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----------YAFVHFEDRQE 50
S L+++NL TEE LK F + G ++ K + FV ++ ++
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 51 A 51
A
Sbjct: 63 A 63
>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 = 56.1 bits (136), Expect = 5e-11
Identities = 27/122 (22%), Positives = 48/122 (39%), Gaps = 30/122 (24%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVI 61
VK ++V + + E L++ FEQYG++E ++ + D
Sbjct: 102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR--------------------- 140
Query: 62 IYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETM 121
+ K RGF F+ +D H S K + V G + V A ++E + +
Sbjct: 141 ------GSGKKRGFAFVTFDDHDS---VDKIVIQKYHTVNGHNCEVRKALSKQEMASASS 191
Query: 122 SK 123
S+
Sbjct: 192 SQ 193
Score = 45.7 bits (109), Expect = 4e-07
Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
L++ L+ T+E L+ FEQ+G + ++D + FV + +E
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 54.6 bits (132), Expect = 6e-11
Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 29/110 (26%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
L+V + + TEE + + F +YG ++ + D R+ TG
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD--------RR-----TG---------- 62
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEP 116
+G+ +EY+++K A A + L G+ + G I VDW + P
Sbjct: 63 ----YLKGYTLVEYETYKEAQAAMEGL-NGQ-DLMGQPISVDWCFVRGPP 106
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 56.0 bits (135), Expect = 7e-11
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
L V NL ++ ++E F ++G +++ D A VHFE R +A
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADA 142
>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 = 54.0 bits (130), Expect = 1e-10
Identities = 22/111 (19%), Positives = 40/111 (36%), Gaps = 21/111 (18%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
+YV+ L T + L + F+Q G V+ KR + D++ TG
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE-----TG---------- 62
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
K +G + Y+ +A A + + G + V A + +
Sbjct: 63 ----KPKGDATVSYEDPPTAKAAVEWFDGKDFQ--GSKLKVSLARKKPPMN 107
>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 = 52.9 bits (128), Expect = 1e-10
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
+ +YV N+ T E+L+ F G V RV + D +A++ F D++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61
>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 = 55.4 bits (134), Expect = 2e-10
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
LYV +L TE L E F G + ++ +D YA+V+F+ +A
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADA 70
Score = 50.0 bits (120), Expect = 1e-08
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
++++NL + + L + F +G + K + D Y FVHFE ++ A
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAA 156
>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 = 53.5 bits (129), Expect = 2e-10
Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 5/52 (9%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQEA 51
++LY+RNL T E++ + F +YG + +++ + A+V +ED +A
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDA 60
>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 = 2e-10
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----KDYAFVHFEDRQEAIT 53
L++ N+ +EE LK F G V + + + A + +EA+
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQ 204
Score = 54.6 bits (131), Expect = 3e-10
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 2 SKVKVLYVRNLTQY-CTEEKLKEAFEQYGRVERVKRI---KDYAFVHFEDRQEAIT-VTG 56
+ VL V NL T + L F YG V+RVK + K+ A V D +A ++
Sbjct: 32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH 91
Query: 57 LSQVIIYSSP 66
L+ ++ P
Sbjct: 92 LNGHKLHGKP 101
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 53.6 bits (129), Expect = 2e-10
Identities = 22/111 (19%), Positives = 41/111 (36%), Gaps = 21/111 (18%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
++V+ L + T E + + F+Q G ++ K+ + DR+ TG
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE-----TG---------- 54
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
K +G + +D SA A G I V +A + + +
Sbjct: 55 ----KLKGEATVSFDDPPSAKAAIDWFDGKEFS--GNPIKVSFATRRADFN 99
>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 = 55.0 bits (133), Expect = 2e-10
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L++ L Y ++++KE +G ++ +KD YAF + D
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 169
Score = 54.7 bits (132), Expect = 2e-10
Identities = 17/117 (14%), Positives = 37/117 (31%), Gaps = 25/117 (21%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LYV N+ TEE + + F R+ + + + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN--------------------PVLA-- 44
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPDTETMSK 123
+++ F FLE+ S + A +A + G + + + + +
Sbjct: 45 VQINQDKNFAFLEFRSVDETTQA---MAFDGIIFQGQSLKIRRPHDYQPLPGMSENP 98
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation
initiation, RNA-binding, EIF4G-binding translation;
1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 53.0 bits (128), Expect = 2e-10
Identities = 14/51 (27%), Positives = 26/51 (50%), Gaps = 6/51 (11%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
++++NL + + L + F +G + K + D Y FVHFE ++ A
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAA 58
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA
recognition motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 53.1 bits (128), Expect = 3e-10
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L++ +L Q T+ L F +G V K D + FV F++ A
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSA 95
>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 = 54.5 bits (131), Expect = 3e-10
Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 5 KVLYVRNLTQY-CTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEA 51
VL V NL T + L F YG V+RVK + + A V D +A
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQA 54
Score = 51.8 bits (124), Expect = 3e-09
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----KDYAFVHFEDRQEAIT 53
L++ N+ +EE LK F G V + + + A + +EA+
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQ 173
>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 = 52.7 bits (127), Expect = 3e-10
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L++ +L Q ++ L + F +G V K D + FV +++ A
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 80
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain,
structural genomics, NPPSFA; NMR {Mus musculus} PDB:
2rne_A 2dh7_A
Length = 115
Score = 52.7 bits (127), Expect = 3e-10
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
++V +L+ T E +K AF +GR+ + +KD Y FV F ++ +A
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70
>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 = 52.2 bits (126), Expect = 4e-10
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 51
LYV+NL +E+L++AF +G + K + + + FV F +EA
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEA 68
>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 = 51.8 bits (125), Expect = 4e-10
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
++V +L+ T + AF +GR+ + +KD Y FV F ++ +A
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 61
>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 = 52.4 bits (126), Expect = 5e-10
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA 51
LYV T L+ AF +G + + AFV +E + A
Sbjct: 42 LYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESA 86
>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 = 54.5 bits (130), Expect = 6e-10
Identities = 15/70 (21%), Positives = 32/70 (45%), Gaps = 10/70 (14%)
Query: 7 LYVRNLTQYCTEEKLKEA----FEQYGRVERVKRIKD-----YAFVHFEDRQEAIT-VTG 56
+Y+ NL + +++LK++ F Q+G++ + + AFV F++ A +
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 57 LSQVIIYSSP 66
+ Y P
Sbjct: 72 MQGFPFYDKP 81
Score = 46.8 bits (110), Expect = 2e-07
Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 8 YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEA 51
++ NL + E L F Q+ + V+ + AFV F++ +A
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQA 257
>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 = 52.9 bits (128), Expect = 6e-10
Identities = 18/112 (16%), Positives = 36/112 (32%), Gaps = 30/112 (26%)
Query: 1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQV 60
K ++V + ++ +E F Q+G + + + D
Sbjct: 84 QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK-------------------- 123
Query: 61 IIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADP 112
D ++RGF F+ YDS + + + I + A+P
Sbjct: 124 -------DTGQSRGFGFVTYDSADA---VDRVCQNKFIDFKDRKIEIKRAEP 165
>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 = 51.1 bits (123), Expect = 7e-10
Identities = 22/58 (37%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITVTGLSQVI 61
++V T TE++L+E F QYG V V K +AFV F D Q A ++ G +I
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLII 65
>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 = 51.0 bits (123), Expect = 9e-10
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 10/59 (16%)
Query: 4 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDR--QEAI 52
++ +YV NL T E++KE F Q+G+V VK I D + FV ++ EAI
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAI 59
>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 = 51.6 bits (124), Expect = 1e-09
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 8/62 (12%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITVTG 56
+ ++ L L++ F G+V V+ I D A+V F + Q G
Sbjct: 26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 85
Query: 57 LS 58
L+
Sbjct: 86 LT 87
>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 = 51.1 bits (123), Expect = 1e-09
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEA 51
LYV T L+ AF +G + + AFV +E + A
Sbjct: 18 LYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESA 62
>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 = 51.1 bits (123), Expect = 1e-09
Identities = 32/113 (28%), Positives = 51/113 (45%), Gaps = 32/113 (28%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
K L+V+ L++ TEE LKE+F+ R V DR+ TG S
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDGSVRARIVT-----------DRE-----TGSS------ 53
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
+GF F++++S + A AK+ + G + G + +DWA P+ E
Sbjct: 54 --------KGFGFVDFNSEEDAKAAKEAMEDGEID--GNKVTLDWAKPKGEGG 96
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 51.6 bits (123), Expect = 1e-09
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAI 52
+KV +L ++N T + L G+V+R+ K A V FE A
Sbjct: 22 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLCAQ 76
>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 = 51.6 bits (124), Expect = 1e-09
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
+YV N+ T + L+ F G + R+ + D YA++ F +R
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSV 91
>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 = 51.1 bits (122), Expect = 1e-09
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 5 KVLYVRN--LTQYCTEEKLKEAFEQYGRVERVKRI--KDYAFVHFEDRQEAIT 53
+ L V N L + +L E+ G V+ + K Y+F + +E+
Sbjct: 26 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKR 78
>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 = 51.1 bits (122), Expect = 1e-09
Identities = 13/53 (24%), Positives = 30/53 (56%), Gaps = 3/53 (5%)
Query: 5 KVLYVRNL-TQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITV 54
+V+++ NL ++ + + E YG+++ R+K AF+ E R++A+ +
Sbjct: 26 RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAM 78
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 50.2 bits (121), Expect = 2e-09
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L+V +L +E L+ AF+ + + D Y FV F + +A
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDA 56
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 49.8 bits (119), Expect = 3e-09
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRV---ERVKRIKDYAFVHFEDRQEA 51
+YV NL + LK A + G V + + AF+H+ D A
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAA 69
>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 = 52.0 bits (124), Expect = 3e-09
Identities = 15/51 (29%), Positives = 20/51 (39%), Gaps = 4/51 (7%)
Query: 5 KVLYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEA 51
VL V L +++ F YG VE+VK +K A V D
Sbjct: 5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAV 55
Score = 48.9 bits (116), Expect = 3e-08
Identities = 9/55 (16%), Positives = 18/55 (32%), Gaps = 8/55 (14%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKDYAFVHFEDRQEAI 52
VL+ N TEE E ++ G + ++ + +A+
Sbjct: 125 VLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179
>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 = 50.0 bits (120), Expect = 3e-09
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
++V L + T+ L++ FE +G +E I D Y FV DR A
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 50.3 bits (120), Expect = 3e-09
Identities = 9/56 (16%), Positives = 21/56 (37%), Gaps = 9/56 (16%)
Query: 5 KVLYVRNLTQYCTEEKLKEA----FEQYGRVERVK-----RIKDYAFVHFEDRQEA 51
+V+ + N+ +EKL+ G + + A++ F ++ A
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESA 85
>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 = 49.6 bits (119), Expect = 4e-09
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 9/54 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYG-RVERVKRIKD--------YAFVHFEDRQEA 51
L++ +L Y E + AF G V VK I++ Y FV F D A
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATA 65
>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 = 49.5 bits (119), Expect = 4e-09
Identities = 22/114 (19%), Positives = 44/114 (38%), Gaps = 30/114 (26%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVI 61
SK ++V + C E +L+E F+++G V V I D
Sbjct: 8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDA--------------------- 46
Query: 62 IYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
+ ++ RGF F+ ++ +S + + + G + V A+P++
Sbjct: 47 ------EKQRPRGFGFITFEDEQS---VDQAVNMHFHDIMGKKVEVKRAEPRDS 91
>2la6_A RNA-binding protein FUS; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative, RNA recognition; NMR {Homo
sapiens}
Length = 99
Score = 48.1 bits (115), Expect = 1e-08
Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 19/87 (21%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
++V+ L + T E + + F+Q G ++ K+ + DR
Sbjct: 16 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR------------------ 57
Query: 67 DDNKKNRGFCFLEYDSHKSASLAKKRL 93
+ K +G + +D SA A
Sbjct: 58 -ETGKLKGEATVSFDDPPSAKAAIDWF 83
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif,
RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2adb_A
Length = 164
Score = 49.3 bits (117), Expect = 1e-08
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV----KRIKDYAFVHFEDRQEAI 52
S V + V NL T + L + F ++G V ++ K + A + + D A
Sbjct: 44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQ 98
>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 = 48.0 bits (115), Expect = 1e-08
Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI---------KDYAFVHFEDRQEA 51
+++ NL E+ L + F +G + + +I K YAF++F +
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
>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 = 48.3 bits (115), Expect = 2e-08
Identities = 9/46 (19%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-YAFVHFEDRQEA 51
+ V L + + LK+ + G V +D V F +++
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDM 63
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 47.1 bits (113), Expect = 2e-08
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
++V L+ T E +K FEQ+G+V+ + D + FV FE
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIV 54
>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 = 46.7 bits (112), Expect = 3e-08
Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 27/80 (33%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
++V L+ EEK++E F +G VE ++ D
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMD--------------------------N 35
Query: 67 DDNKKNRGFCFLEYDSHKSA 86
NK+ RGFCF+ + +
Sbjct: 36 KTNKR-RGFCFITFKEEEPV 54
>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 = 46.9 bits (112), Expect = 4e-08
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 8/54 (14%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
V+ V+N+ + +++ + F Y + +K A V FE R EA
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 70
>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 = 46.9 bits (112), Expect = 4e-08
Identities = 9/52 (17%), Positives = 20/52 (38%), Gaps = 7/52 (13%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYAFVHFEDRQEA 51
L++ NL + +LK A + + + + +V FE ++
Sbjct: 20 LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDL 71
>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 = 46.4 bits (111), Expect = 5e-08
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITVTGLSQVI 61
++V T+ T E+L++ F QYG V V K +AFV F D + A ++ G +I
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGEDLII 71
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 47.3 bits (112), Expect = 5e-08
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 4/56 (7%)
Query: 2 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV----KRIKDYAFVHFEDRQEAIT 53
S V + V NL T + L + F ++G V ++ K + A + + D A
Sbjct: 26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQH 81
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding
domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 98
Score = 46.5 bits (111), Expect = 5e-08
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 8/54 (14%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
++ V+N+ + +++ + F Y + +K A V FE R EA
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEA 70
>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 = 46.5 bits (111), Expect = 6e-08
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
L V L TE+ LKE F +G V V+ KD + FV F + + + V
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
>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 = 48.7 bits (115), Expect = 6e-08
Identities = 24/113 (21%), Positives = 40/113 (35%), Gaps = 29/113 (25%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
K L+V + TE KL+ FE YG ++R+ +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYS------------------------- 137
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
+ K RG+ F+EY+ + A K K+ G ++VD +
Sbjct: 138 --KRSGKPRGYAFIEYEHERDMHSAYKHA--DGKKIDGRRVLVDVERGRTVKG 186
>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 = 46.7 bits (111), Expect = 9e-08
Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 13/60 (21%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-------------RIKDYAFVHFEDRQEA 51
+YV+NL ++ E+ LK F +Y R+K AF+ + + A
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 45.7 bits (109), Expect = 1e-07
Identities = 22/113 (19%), Positives = 40/113 (35%), Gaps = 30/113 (26%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
++ NL TEE +KE F + V+ ++
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPRE------------------------- 49
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEEPD 117
P + ++ +GF + E++ S A L+ + I VD AD ++ D
Sbjct: 50 -PSNPERLKGFGYAEFEDLDSLLSA---LSLNEESLGNKRIRVDVADQAQDKD 98
>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 = 44.9 bits (107), Expect = 2e-07
Identities = 14/93 (15%), Positives = 33/93 (35%), Gaps = 34/93 (36%)
Query: 5 KVLYVRNLTQYCTEEKLKEA----FEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQV 60
+Y+ NL + +++LK++ F ++G++ + +
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL-------------------- 48
Query: 61 IIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRL 93
K RG F+ + SA+ A + +
Sbjct: 49 ----------KMRGQAFVIFKEVSSATNALRSM 71
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 44.0 bits (105), Expect = 3e-07
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 8/56 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
+++ L+ T+E L+E F Q+G V+ ++D + FV F D+ V
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58
>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 = 44.5 bits (106), Expect = 3e-07
Identities = 21/111 (18%), Positives = 39/111 (35%), Gaps = 30/111 (27%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYS 64
++ NL TEE +KE F + V+ ++
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPRE------------------------- 53
Query: 65 SPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWGCDIIVDWADPQEE 115
P + ++ +GF + E++ S A L+ + I VD AD ++
Sbjct: 54 -PSNPERLKGFGYAEFEDLDSLLSA---LSLNEESLGNRRIRVDVADQAQD 100
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 44.3 bits (105), Expect = 3e-07
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 7/56 (12%)
Query: 3 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV-------KRIKDYAFVHFEDRQEA 51
K + +Y++ T + +KE E G+V + K K FV F+ + A
Sbjct: 10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 65
>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 = 44.5 bits (105), Expect = 4e-07
Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 14/60 (23%)
Query: 6 VLYVRNLTQYCTEE---KLKEAFEQYGRVERVKRIKD-----------YAFVHFEDRQEA 51
+++V L+Q + K E F ++G++ +V A+V + ++A
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 44.7 bits (106), Expect = 4e-07
Identities = 8/55 (14%), Positives = 18/55 (32%), Gaps = 8/55 (14%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
++ N+ T+ + + E E + A V F++ +A
Sbjct: 16 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 44.2 bits (105), Expect = 5e-07
Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 9/55 (16%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
YV NL + + F+ + V+ ++D + +V F++
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSL 69
>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 = 43.8 bits (104), Expect = 6e-07
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
L+V L T+E L+ F QYG V +KD + FV F+D TV
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74
>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 = 44.0 bits (104), Expect = 6e-07
Identities = 9/46 (19%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-YAFVHFEDRQEA 51
+ V L + + LK+ + G V +D V F +++
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDM 64
>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 = 43.7 bits (103), Expect = 7e-07
Identities = 7/53 (13%), Positives = 20/53 (37%), Gaps = 3/53 (5%)
Query: 5 KVLYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEAITV 54
+V+++ + +L + E +G + + AF+ ++A
Sbjct: 16 RVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAA 68
>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 = 43.2 bits (102), Expect = 8e-07
Identities = 15/83 (18%), Positives = 28/83 (33%), Gaps = 22/83 (26%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSP 66
LYV N+ TEE + + F R+ + + + +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------------------ 50
Query: 67 DDNKKNRGFCFLEYDSHKSASLA 89
+++ F FLE+ S + A
Sbjct: 51 ----QDKNFAFLEFRSVDETTQA 69
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 43.6 bits (103), Expect = 9e-07
Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 8/55 (14%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
+ +R L C++E++ + F V + AFV F ++ A
Sbjct: 16 GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 45.2 bits (106), Expect = 1e-06
Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 11/63 (17%)
Query: 1 MSKVKVLYVRNLTQYCT---------EEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQ 49
K K LYV + E +++ F + G ++R++ K+ FV F+ +
Sbjct: 131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQA 190
Query: 50 EAI 52
A
Sbjct: 191 NAE 193
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 43.0 bits (102), Expect = 1e-06
Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAF-EQYGRVERVKRIKD-------YAFVHFEDRQEA 51
L+V +LT + L E F + Y K + D Y FV F D E
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQ 64
>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 = 43.4 bits (103), Expect = 1e-06
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
L++ L+ TEE L+ +EQ+G++ ++D + FV F E
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82
>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 = 43.0 bits (102), Expect = 1e-06
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 8/56 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
+++ L+ T+E L+E F Q+G V+ ++D + FV F D+ V
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 83
>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 = 42.6 bits (101), Expect = 1e-06
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 8/56 (14%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITV 54
++V L+ +++ LK+ F ++G V D + F+ F+D V
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKV 69
>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 = 42.9 bits (101), Expect = 2e-06
Identities = 9/54 (16%), Positives = 19/54 (35%), Gaps = 8/54 (14%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYAFVHFEDRQEA 51
+Y++ L + + + F++ VE I FV F + +
Sbjct: 27 CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADY 80
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kg0_A
Length = 126
Score = 42.9 bits (101), Expect = 2e-06
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEA 51
+ +R L CT+E++ + F V + AFV F ++ A
Sbjct: 44 FVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELA 97
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 42.0 bits (99), Expect = 3e-06
Identities = 13/88 (14%), Positives = 24/88 (27%), Gaps = 27/88 (30%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSS 65
+ + ++ L F + G+V ++ D
Sbjct: 14 APVIPSAKVPVLKKALTSLFSKAGKVVNMEFPID-------------------------- 47
Query: 66 PDDNKKNRGFCFLEYDSHKSASLAKKRL 93
+ K +GF F+E S A K
Sbjct: 48 -EATGKTKGFLFVECGSMNDAKKIIKSF 74
>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 = 43.3 bits (101), Expect = 4e-06
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 7/54 (12%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERV-------KRIKDYAFVHFEDRQEA 51
+ +Y++ T + +KE E G+V + K K FV F+ + A
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 163
>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 = 41.6 bits (98), Expect = 5e-06
Identities = 11/54 (20%), Positives = 17/54 (31%), Gaps = 8/54 (14%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
+++R L TE + F RV A V F ++A
Sbjct: 16 HCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDA 68
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA
binding protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 41.8 bits (98), Expect = 7e-06
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 6/53 (11%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYG--RVERVK----RIKDYAFVHFEDRQEA 51
+++R L TE + F RV R+ A V F +EA
Sbjct: 47 HCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEA 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 = 1e-05
Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 8/54 (14%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
+ V + E +++ F RV+ V +KD V F Q+
Sbjct: 17 LYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDT 69
>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 = 39.2 bits (92), Expect = 3e-05
Identities = 9/54 (16%), Positives = 20/54 (37%), Gaps = 8/54 (14%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 51
+ +R TE+ + E ++ +++ Y FV F + +E
Sbjct: 11 HTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEV 63
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 39.9 bits (93), Expect = 3e-05
Identities = 12/87 (13%), Positives = 27/87 (31%), Gaps = 24/87 (27%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSS 65
++ +R L T E++ F Q+ + K + F
Sbjct: 25 IVRMRGLPFTATAEEVVAFFGQHCPITGGKEG-----ILFVT------------------ 61
Query: 66 PDDNKKNRGFCFLEYDSHKSASLAKKR 92
+ + G F+ + + A A ++
Sbjct: 62 -YPDGRPTGDAFVLFACEEYAQNALRK 87
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 38.8 bits (90), Expect = 6e-05
Identities = 13/55 (23%), Positives = 20/55 (36%), Gaps = 5/55 (9%)
Query: 5 KVLYVRNLTQYCTEEKLKEAFEQY-----GRVERVKRIKDYAFVHFEDRQEAITV 54
+ VR L +E L FE G V +R+ + F + +A V
Sbjct: 9 VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERV 63
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Mus musculus}
Length = 118
Score = 37.6 bits (87), Expect = 2e-04
Identities = 10/56 (17%), Positives = 18/56 (32%), Gaps = 10/56 (17%)
Query: 6 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----------KDYAFVHFEDRQEA 51
V+ +R L C+ E ++ + V + AFV E +
Sbjct: 19 VVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDV 74
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 36.6 bits (85), Expect = 2e-04
Identities = 13/77 (16%), Positives = 25/77 (32%), Gaps = 29/77 (37%)
Query: 17 TEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGFC 76
+ + + F ++G++ P+++ K +G+
Sbjct: 20 LKNVIHKIFSKFGKITNDFY-----------------------------PEEDGKTKGYI 50
Query: 77 FLEYDSHKSASLAKKRL 93
FLEY S A A K
Sbjct: 51 FLEYASPAHAVDAVKNA 67
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 36.9 bits (85), Expect = 2e-04
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 9/57 (15%)
Query: 7 LYVRNLTQYCTEEKLKE----AFEQYGRVERV-----KRIKDYAFVHFEDRQEAITV 54
+ V N+ + ++L++ AF ++G+V+ V + A V E+ Q+AI
Sbjct: 12 VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGA 68
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 37.0 bits (86), Expect = 2e-04
Identities = 16/95 (16%), Positives = 30/95 (31%), Gaps = 35/95 (36%)
Query: 5 KVLYVRNL------TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLS 58
V+ V N+ + + + F ++G++
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFY---------------------- 53
Query: 59 QVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRL 93
P+++ K +G+ FLEY S A A K
Sbjct: 54 -------PEEDGKTKGYIFLEYASPAHAVDAVKNA 81
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 36.0 bits (83), Expect = 6e-04
Identities = 10/61 (16%), Positives = 18/61 (29%), Gaps = 10/61 (16%)
Query: 1 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----------KDYAFVHFEDRQE 50
+ V ++ + L CT E + F I + A + E Q+
Sbjct: 8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQD 67
Query: 51 A 51
Sbjct: 68 V 68
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 35.7 bits (82), Expect = 8e-04
Identities = 10/58 (17%), Positives = 23/58 (39%), Gaps = 10/58 (17%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERV----------KRIKDYAFVHFEDRQEAITV 54
++V L E+++ +F ++G + K YAF+ F++ +
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 35.2 bits (81), Expect = 0.001
Identities = 6/50 (12%), Positives = 17/50 (34%), Gaps = 5/50 (10%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----YAFVHFEDRQEA 51
+ ++NL + C+ + LK+ + + + F +
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEIL 80
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 34.4 bits (78), Expect = 0.006
Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 4/54 (7%)
Query: 5 KVLYVRNLTQYC--TEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEAITV 54
+ L V N + +L E+ G V+ + K Y+F + +E+
Sbjct: 19 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRA 72
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR
{Drosophila melanogaster}
Length = 89
Score = 33.1 bits (75), Expect = 0.006
Identities = 11/48 (22%), Positives = 19/48 (39%), Gaps = 2/48 (4%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAI 52
L ++NLT L+ Q+G + + A + R+EA
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEAN 57
>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 = 32.3 bits (73), Expect = 0.018
Identities = 10/77 (12%), Positives = 19/77 (24%), Gaps = 25/77 (32%)
Query: 16 CTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVIIYSSPDDNKKNRGF 75
C+ E ++ + + IY + G
Sbjct: 56 CSVEDVQNFLSDCTIHDGAAGVH----------------------FIY---TREGRQSGE 90
Query: 76 CFLEYDSHKSASLAKKR 92
F+E S +A K+
Sbjct: 91 AFVELGSEDDVKMALKK 107
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 33.1 bits (75), Expect = 0.019
Identities = 27/151 (17%), Positives = 48/151 (31%), Gaps = 36/151 (23%)
Query: 7 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI---------------KD-YAFVHFEDRQE 50
L + NLTQ ++ + + + I + Y + +
Sbjct: 339 LSISNLTQEQVQDYV-NKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAK 397
Query: 51 AITVTGLSQVIIYSSPDDNKKNR-GFCFLE----YDSH---KSASLAKKRLATGRLKVWG 102
A +GL Q I P +K + FL + SH ++ L K L +
Sbjct: 398 A--PSGLDQSRI---PFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNA 452
Query: 103 CD--IIV----DWADPQEEPDTETMSKVLML 127
D I V D +D + + + V +
Sbjct: 453 KDIQIPVYDTFDGSDLRVLSGSISERIVDCI 483
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 29.4 bits (65), Expect = 0.16
Identities = 8/43 (18%), Positives = 16/43 (37%), Gaps = 3/43 (6%)
Query: 17 TEEKLKEAFEQYGRVERV---KRIKDYAFVHFEDRQEAITVTG 56
+++ L ++YG V + + A V F + A
Sbjct: 30 SKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQ 72
>2lie_A CCL2 lectin; sugar binding protein; NMR {Coprinopsis cinerea} PDB:
2liq_A*
Length = 153
Score = 29.1 bits (64), Expect = 0.32
Identities = 11/52 (21%), Positives = 19/52 (36%)
Query: 51 AITVTGLSQVIIYSSPDDNKKNRGFCFLEYDSHKSASLAKKRLATGRLKVWG 102
A+T G + + SP D + + YDS+ + + WG
Sbjct: 39 ALTYPGRQRTPVTVSPLDGSSEQAWILRSYDSNSNTWTISPVGSPNSQIGWG 90
>3ram_A HMRA protein; two-domain, catalytic (alpha-beta-alpha) motif,
tetramerisat (alpha,beta,BETA,alpha), endoprotease,
hydrolase; 2.70A {Staphylococcus aureus}
Length = 394
Score = 28.0 bits (63), Expect = 0.99
Identities = 9/47 (19%), Positives = 17/47 (36%), Gaps = 11/47 (23%)
Query: 86 ASLAKKRLA---TGRLKVWGCDIIVDWADPQEEPDTETMSKVLMLDQ 129
++ K++ G++ V GC P EE +K +
Sbjct: 105 GAIGLKQVIDQIGGKVVVLGC--------PAEEGGENGSAKASYVKA 143
>2w2k_A D-mandelate dehydrogenase; 2-hydroxyacid dehydrogenase,
oxidoreductase; 1.85A {Rhodotorula graminis} PDB:
2w2l_A* 2w2l_D* 2w2k_B
Length = 348
Score = 27.6 bits (62), Expect = 1.2
Identities = 5/28 (17%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 1 MSKVKVLYVRNLTQYCTE--EKLKEAFE 26
M + +VL + + ++ + ++ FE
Sbjct: 1 MPRPRVLLLGDPARHLDDLWSDFQQKFE 28
>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 91
Score = 26.5 bits (58), Expect = 1.3
Identities = 10/44 (22%), Positives = 23/44 (52%)
Query: 19 EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITVTGLSQVII 62
++L + F +G V ++ ++D +V F + A+ V L+ +
Sbjct: 30 DELLQQFASFGEVILIRFVEDKMWVTFLEGSSALNVLSLNGKEL 73
>2qq8_A TBC1 domain family member 14; structural genomics consortium,
RAB-GAP, SGC, GTPase activation, hydrolase activator;
2.00A {Homo sapiens}
Length = 334
Score = 26.7 bits (59), Expect = 2.3
Identities = 5/32 (15%), Positives = 12/32 (37%)
Query: 78 LEYDSHKSASLAKKRLATGRLKVWGCDIIVDW 109
+ + H S+ + W +I+ +W
Sbjct: 1 MHHHHHHSSGRENLYFQGNAVLTWNNEILPNW 32
>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 = 25.4 bits (56), Expect = 3.5
Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 18 EEKLKEAFEQYGRVERV----KRIKDYAFVHFEDRQEA 51
E L+ ++G++ ++ + A V F D +EA
Sbjct: 40 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEA 77
>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 = 24.6 bits (54), Expect = 8.6
Identities = 7/38 (18%), Positives = 15/38 (39%), Gaps = 4/38 (10%)
Query: 18 EEKLKEAFEQYGRVERVKRIKDYA----FVHFEDRQEA 51
++ + E ++G V + K+ A +V A
Sbjct: 31 KDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAA 68
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
0.319 0.134 0.391
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,058,867
Number of extensions: 115345
Number of successful extensions: 825
Number of sequences better than 10.0: 1
Number of HSP's gapped: 594
Number of HSP's successfully gapped: 261
Length of query: 131
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 48
Effective length of database: 4,384,350
Effective search space: 210448800
Effective search space used: 210448800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (23.7 bits)