RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1188
(230 letters)
>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 = 128 bits (323), Expect = 2e-38
Identities = 45/103 (43%), Positives = 69/103 (66%), Gaps = 3/103 (2%)
Query: 88 DTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMN 147
+ M+KVKVL+VRNL TEE L++AF Q+G++ERVK++KDYAF+HF++R A+ AM
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAME 63
Query: 148 ELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQG 190
E+NG+ + G +E+ AKPP K+K+ + + + G
Sbjct: 64 EMNGKDLEGENIEIVFAKPPDQKRKE---RKAQRQAASGPSSG 103
>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 = 127 bits (320), Expect = 4e-38
Identities = 43/92 (46%), Positives = 59/92 (64%), Gaps = 2/92 (2%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYG--RVERVKRIKDYAFVHFEDR 139
D +TMS VK+LYVRNL +EE +++ F VERVK+I+DYAFVHF +R
Sbjct: 2 SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNR 61
Query: 140 QEAITAMNELNGQTVAGSTLEVSLAKPPSDKK 171
++A+ AM LNG+ + GS +EV+LAKP
Sbjct: 62 EDAVEAMKALNGKVLDGSPIEVTLAKPVDKDS 93
>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 = 113 bits (285), Expect = 1e-30
Identities = 22/121 (18%), Positives = 42/121 (34%), Gaps = 10/121 (8%)
Query: 73 GCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTE-EKLKEAFEQYGRVERVK----- 126
+ V W D + T + + L V L + + L A +
Sbjct: 164 PRTLYVHWTDAGQL--TPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ 221
Query: 127 --RIKDYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRM 184
++K +A + +E + A A + +G ++ GS L VS P + L +
Sbjct: 222 DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATA 281
Query: 185 M 185
+
Sbjct: 282 L 282
Score = 79.3 bits (196), Expect = 6e-18
Identities = 20/91 (21%), Positives = 36/91 (39%), Gaps = 11/91 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L V NL T+++ +E +G +ER + Y F + + A A ++L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 150 NGQTVAGSTLEVSLAKPPSDKKKKEEILRNR 180
G+ + TL V + +L +R
Sbjct: 158 LGKPLGPRTLYVHWTDA---GQLTPALLHSR 185
Score = 73.1 bits (180), Expect = 1e-15
Identities = 18/119 (15%), Positives = 39/119 (32%), Gaps = 14/119 (11%)
Query: 68 HLLSRGCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVE-RVK 126
H+L +I + + + + +R L T +++ + Y V
Sbjct: 1 HMLD-PEEIRKRLEHTERQF-----RNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVD 54
Query: 127 RIKDYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPS-------DKKKKEEILR 178
+ K AFV + ++A A+N + + L V L + ++
Sbjct: 55 KYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFE 113
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 108 bits (271), Expect = 2e-30
Identities = 26/92 (28%), Positives = 46/92 (50%), Gaps = 1/92 (1%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQ 140
+S + L+VR E +L E F +G ++ VK + +AFV FE+ +
Sbjct: 18 GSHMHHRQEGELSNTR-LFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAE 76
Query: 141 EAITAMNELNGQTVAGSTLEVSLAKPPSDKKK 172
A A+ E++G++ A LEV +K P+ + +
Sbjct: 77 SAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108
>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 = 98.0 bits (245), Expect = 7e-27
Identities = 28/73 (38%), Positives = 43/73 (58%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAGS 157
++V N++ CT ++L+ FE+ GRV +KDYAFVH E +A A+ +LNG+ V G
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEVKGK 71
Query: 158 TLEVSLAKPPSDK 170
+ V L+ K
Sbjct: 72 RINVELSTKGQKK 84
>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 = 97.7 bits (244), Expect = 1e-26
Identities = 25/75 (33%), Positives = 40/75 (53%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAGS 157
L+V N++ CT ++L+ FE+YG V +KDYAFVH E ++A+ A+ L+ G
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQGK 72
Query: 158 TLEVSLAKPPSDKKK 172
+ V L+
Sbjct: 73 RMHVQLSTSRLRTAS 87
>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 = 97.7 bits (244), Expect = 1e-26
Identities = 26/93 (27%), Positives = 41/93 (44%), Gaps = 2/93 (2%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFED 138
+T ++ L+V NL TEE++++ FE+YG+ V KD + F+ E
Sbjct: 1 GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLET 60
Query: 139 RQEAITAMNELNGQTVAGSTLEVSLAKPPSDKK 171
R A A EL+ + G L V A +
Sbjct: 61 RTLAEIAKVELDNMPLRGKQLRVRFACHSASLT 93
>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 = 95.7 bits (239), Expect = 5e-26
Identities = 27/80 (33%), Positives = 43/80 (53%)
Query: 93 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQ 152
S + L++ NL + TE++++ FEQYG+V IK+Y FVH ED+ A A+ L+
Sbjct: 6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHY 65
Query: 153 TVAGSTLEVSLAKPPSDKKK 172
+ G + V +K S
Sbjct: 66 KLHGVNINVEASKNKSKASS 85
>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 = 98.9 bits (247), Expect = 4e-25
Identities = 26/108 (24%), Positives = 51/108 (47%), Gaps = 15/108 (13%)
Query: 73 GCDIIVDWADPQEEPDTETMSK--VKVLYVRNLTQYCTEEK-LKEAFEQYGRVERVK--- 126
G ++ ++P E+ + + + +RNL+ +E L+E+FE +G +E++
Sbjct: 186 GYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPA 245
Query: 127 ------RIKDYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLA--KP 166
AF+ FE++ A A+ ++N + + VSLA KP
Sbjct: 246 GQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKKP 292
Score = 75.0 bits (185), Expect = 2e-16
Identities = 15/86 (17%), Positives = 36/86 (41%), Gaps = 8/86 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L++ N T+ +++ + V R+ +A++ +++A + +L
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179
Query: 150 NGQTVAGSTLEVSLAKPPSDKKKKEE 175
NG + G TL ++ P K+ +
Sbjct: 180 NGLKIEGYTLVTKVSNPLEKSKRTDS 205
Score = 64.2 bits (157), Expect = 2e-12
Identities = 18/126 (14%), Positives = 41/126 (32%), Gaps = 13/126 (10%)
Query: 66 GKHLLSRGCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV 125
K L G + ++ + V+NL + + K+ + F+ G + V
Sbjct: 12 SKRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHV 71
Query: 126 KRIKD------YAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPS------DKKKK 173
+A + F A+ A+ + + V + + VS +
Sbjct: 72 DVADSLKKNFRFARIEFARYDGALAAITKTHK-VVGQNEIIVSHLTECTLWMTNFPPSYT 130
Query: 174 EEILRN 179
+ +R+
Sbjct: 131 QRNIRD 136
>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 = 89.6 bits (223), Expect = 1e-23
Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 6/88 (6%)
Query: 87 PDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVE--RVKRIKDYAFVHFEDRQEAIT 144
+ M+K LY+ NL+ T + L++ F +V YAFV + D+ AI
Sbjct: 3 SGSSGMNK---LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIR 59
Query: 145 AMNELNGQT-VAGSTLEVSLAKPPSDKK 171
A+ L+G+ + G +EV + +
Sbjct: 60 AIETLSGKVELHGKIMEVDYSVSKKLRS 87
>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 = 88.8 bits (221), Expect = 3e-23
Identities = 27/92 (29%), Positives = 46/92 (50%), Gaps = 6/92 (6%)
Query: 87 PDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQ 140
E + + LYV NL++ TE + + F Q G + K I + Y FV F + +
Sbjct: 7 GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHR 66
Query: 141 EAITAMNELNGQTVAGSTLEVSLAKPPSDKKK 172
+A A+ +NG+ + G ++V+ A PS +K
Sbjct: 67 DAAAALAAMNGRKILGKEVKVNWATTPSSQKS 98
>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 = 87.8 bits (218), Expect = 1e-22
Identities = 18/92 (19%), Positives = 41/92 (44%), Gaps = 2/92 (2%)
Query: 83 PQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQ 140
E+ ++ K +Y + T++ +++ F +G++ ++ + Y+FV F +
Sbjct: 13 RFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHE 72
Query: 141 EAITAMNELNGQTVAGSTLEVSLAKPPSDKKK 172
A A+ +NG T+ G ++ K D
Sbjct: 73 SAAHAIVSVNGTTIEGHVVKCYWGKESPDMTS 104
>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 = 87.3 bits (217), Expect = 8e-22
Identities = 20/97 (20%), Positives = 40/97 (41%), Gaps = 6/97 (6%)
Query: 73 GCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK---RIK 129
G +I ++ ++ L +NL+ TE++LKE FE + V + K
Sbjct: 80 GNEIKLEKPKGRDSKKVRAART---LLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSK 136
Query: 130 DYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKP 166
A++ F+ +A + E G + G ++ +
Sbjct: 137 GIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 173
Score = 70.3 bits (173), Expect = 2e-15
Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 9/98 (9%)
Query: 84 QEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHF 136
+E+ + L++ NL + +LK A + + + + +V F
Sbjct: 3 HMVEGSES-TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 61
Query: 137 EDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKE 174
E ++ A+ EL G V G+ +++ K KK +
Sbjct: 62 ESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRA 98
>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 = 85.0 bits (211), Expect = 9e-22
Identities = 25/92 (27%), Positives = 45/92 (48%), Gaps = 6/92 (6%)
Query: 88 DTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQE 141
++E+ S K L+V N+ + L++ F Q+G++ V+ I + + FV FE+ +
Sbjct: 8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD 67
Query: 142 AITAMNELNGQTVAGSTLEVSLAKPPSDKKKK 173
A A +L+G V G +EV+ A
Sbjct: 68 ADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99
>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 = 83.8 bits (208), Expect = 3e-21
Identities = 22/104 (21%), Positives = 47/104 (45%), Gaps = 16/104 (15%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEA----FEQYGRVERVK-----RIKDY 131
A P+ P+ +Y+ NL + +++LK++ F ++G++ + +++
Sbjct: 1 AVPETRPN-------HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ 53
Query: 132 AFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEE 175
AFV F++ A A+ + G + + AK SD K +
Sbjct: 54 AFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMK 97
>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 = 84.3 bits (209), Expect = 3e-21
Identities = 30/110 (27%), Positives = 50/110 (45%), Gaps = 14/110 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
L++ L + E+ LK F ++G + V IKD +AF+ FE+ +A A ++N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 151 GQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRGGPGPSGAH 200
G+++ G ++V AK PS + RR + R G H
Sbjct: 70 GKSLHGKAIKVEQAKKPSFQ-------SGGRRRPPASSRNRSPSGSLEHH 112
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 84.2 bits (208), Expect = 5e-21
Identities = 18/114 (15%), Positives = 41/114 (35%), Gaps = 11/114 (9%)
Query: 78 VDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEA----FEQYGRVERVK-----RI 128
+D D P S+V + + N+ +EKL+ G + +
Sbjct: 14 MDSPDLGSTPPHTEPSQV--VLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDN 71
Query: 129 KDYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRER 182
A++ F ++ A + G G+ L ++ ++ P + ++ L +
Sbjct: 72 SGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAEDGSLEHHHH 125
>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 = 84.9 bits (211), Expect = 6e-21
Identities = 26/83 (31%), Positives = 38/83 (45%), Gaps = 8/83 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L V L Q T+ +L F G + + ++D YAFV F ++ A+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 150 NGQTVAGSTLEVSLAKPPSDKKK 172
NG TV L+VS A+P + K
Sbjct: 66 NGITVRNKRLKVSYARPGGESIK 88
Score = 81.1 bits (201), Expect = 2e-19
Identities = 30/97 (30%), Positives = 46/97 (47%), Gaps = 15/97 (15%)
Query: 78 VDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------- 130
V +A P E +T LYV NL + T+++L F +YG + + ++D
Sbjct: 77 VSYARPGGESIKDTN-----LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPR 131
Query: 131 -YAFVHFEDRQEAITAMNELNGQTVAGST--LEVSLA 164
AFV + R+EA A++ LN G + L V LA
Sbjct: 132 GVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 82.9 bits (205), Expect = 7e-21
Identities = 19/90 (21%), Positives = 38/90 (42%), Gaps = 5/90 (5%)
Query: 87 PDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----YAFVHFEDRQE 141
+++ L +RN+ + E L QYG VE +++ V + + +
Sbjct: 7 GSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQ 66
Query: 142 AITAMNELNGQTVAGSTLEVSLAKPPSDKK 171
A A+++LNG + TL+V+ +
Sbjct: 67 ARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 82.7 bits (205), Expect = 8e-21
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 4/76 (5%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEAITAMNELNGQT 153
L+V L + L F+++G + + +K +A++ +E A A ++ G
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFP 77
Query: 154 VAGST--LEVSLAKPP 167
+ G L V AK
Sbjct: 78 LGGPDRRLRVDFAKSG 93
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 82.4 bits (204), Expect = 1e-20
Identities = 15/86 (17%), Positives = 30/86 (34%), Gaps = 2/86 (2%)
Query: 83 PQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQ 140
+ +V Y+ N+ + TE L F+ +G + K + F+ ++ +
Sbjct: 15 AVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHE 74
Query: 141 EAITAMNELNGQTVAGSTLEVSLAKP 166
+A + L G L K
Sbjct: 75 QAAVCIVALANFPFQGRNLRTGWGKE 100
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 81.9 bits (203), Expect = 2e-20
Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 8/82 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
+ V NL++ E L+E F +G + R+ KD +AF+ F R++A A+ +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 150 NGQTVAGSTLEVSLAKPPSDKK 171
+G L V AKP ++
Sbjct: 78 SGFGYDHLILNVEWAKPSTNSG 99
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 82.0 bits (203), Expect = 2e-20
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 98 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAG 156
+++ NL T + ++ F +YGRV K YAFV + + + A A+ NG+ +AG
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLAG 89
Query: 157 STLEVSLAKPPSDKKK 172
TL++++A P +
Sbjct: 90 QTLDINMAGEPKPDRS 105
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex,
AU-rich element, transcription/RNA complex; 1.80A {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H
1d8z_A 1d9a_A 3hi9_A
Length = 167
Score = 83.4 bits (207), Expect = 2e-20
Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 8/83 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L V L Q T+E+ + F G +E K ++D Y FV++ D ++A A+N L
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 150 NGQTVAGSTLEVSLAKPPSDKKK 172
NG + T++VS A+P S +
Sbjct: 65 NGLRLQTKTIKVSYARPSSASIR 87
Score = 75.3 bits (186), Expect = 2e-17
Identities = 30/99 (30%), Positives = 47/99 (47%), Gaps = 15/99 (15%)
Query: 76 IIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD----- 130
I V +A P + LYV L + T+++L++ F QYGR+ + + D
Sbjct: 74 IKVSYARPSSASIRDAN-----LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGV 128
Query: 131 ---YAFVHFEDRQEAITAMNELNGQTVAGST--LEVSLA 164
F+ F+ R EA A+ LNGQ +G+T + V A
Sbjct: 129 SRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 81.6 bits (202), Expect = 2e-20
Identities = 17/80 (21%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
L++ L CT+E+L+E + +G V+ ++ + + A+V +E+ +A A+ +++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 151 GQTVAGSTLEVSLAKPPSDK 170
G T+ + ++V+++
Sbjct: 80 GMTIKENIIKVAISNSGPSS 99
>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 = 81.1 bits (201), Expect = 3e-20
Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L+VRNL+ +EE L++ F YG + + D +AFV F + A+ A E+
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 150 NGQTVAGSTLEVSLAKPPSDKKK 172
+GQ G L V + + +
Sbjct: 71 DGQVFQGRMLHVLPSTIKKEASQ 93
>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 = 80.8 bits (200), Expect = 5e-20
Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 8/84 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L++ +L Q ++ L + F +G V K D + FV +++ A A+ +
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 150 NGQTVAGSTLEVSLAKPPSDKKKK 173
NG + L+V L + +D K
Sbjct: 88 NGFQIGMKRLKVQLKRSKNDSKSG 111
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription,
splicing, RNA processing, nonsense mediated D NMD, HDAC,
histone deacetylation; 1.90A {Homo sapiens}
Length = 88
Score = 79.5 bits (197), Expect = 8e-20
Identities = 20/89 (22%), Positives = 42/89 (47%), Gaps = 10/89 (11%)
Query: 91 TMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---------YAFVHFEDRQE 141
+M K +++ LT+ T++ + E F YG+++ + + YA+V FE+ E
Sbjct: 1 SMKPTK-VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDE 59
Query: 142 AITAMNELNGQTVAGSTLEVSLAKPPSDK 170
A A+ ++G + G + + P +
Sbjct: 60 AEKALKHMDGGQIDGQEITATAVLAPWPR 88
>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 = 80.5 bits (199), Expect = 9e-20
Identities = 23/100 (23%), Positives = 50/100 (50%), Gaps = 5/100 (5%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQEAITAMNELN 150
++LY+RNL T E++ + F +YG + +++ + A+V +ED +A A++ L+
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 151 GQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQG 190
G V+ L V +K + + + ++++ G
Sbjct: 69 GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYG 108
>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 = 80.5 bits (199), Expect = 1e-19
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 7/81 (8%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
L V NL ++ ++E F ++G +++ D A VHFE R +A+ AM +
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 97
Query: 151 GQTVAGSTLEVSLAKPPSDKK 171
G + G +++ L D +
Sbjct: 98 GVPLDGRPMDIQLVASQIDLE 118
>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 = 80.0 bits (198), Expect = 1e-19
Identities = 29/89 (32%), Positives = 44/89 (49%), Gaps = 11/89 (12%)
Query: 87 PDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 138
PD + M L V NLT + + L+ FE+YGRV V ++ +AFV F D
Sbjct: 8 PDVDGMIT---LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64
Query: 139 RQEAITAMNELNGQTVAGSTLEVSLAKPP 167
R++A A ++G + G L V +A+
Sbjct: 65 RRDAQDAEAAMDGAELDGRELRVQVARYG 93
>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 = 79.3 bits (196), Expect = 1e-19
Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 4/93 (4%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFED 138
+ K LYV T L+ AF +G + + AFV +E
Sbjct: 1 GSSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEK 58
Query: 139 RQEAITAMNELNGQTVAGSTLEVSLAKPPSDKK 171
+ A A+ ELNG V L+V++A+
Sbjct: 59 MESADQAVAELNGTQVESVQLKVNIARKQPMLD 91
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 79.7 bits (197), Expect = 1e-19
Identities = 26/89 (29%), Positives = 45/89 (50%), Gaps = 6/89 (6%)
Query: 84 QEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFE 137
+TE S+ K L+V N+ + L++ F Q+G++ V+ I + + FV FE
Sbjct: 18 GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFE 77
Query: 138 DRQEAITAMNELNGQTVAGSTLEVSLAKP 166
+ +A A +L+G V G +EV+ A
Sbjct: 78 NSADADRAREKLHGTVVEGRKIEVNNATA 106
>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 = 80.0 bits (198), Expect = 1e-19
Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 6/84 (7%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEAITAMNELNG 151
++++NL + + L + F +G + K + D Y FVHFE ++ A A+ ++NG
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
Query: 152 QTVAGSTLEVSLAKPPSDKKKKEE 175
+ + V K +++ +
Sbjct: 68 MLLNDRKVFVGRFKSRKEREAELG 91
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 79.2 bits (196), Expect = 1e-19
Identities = 23/87 (26%), Positives = 42/87 (48%), Gaps = 4/87 (4%)
Query: 88 DTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK----RIKDYAFVHFEDRQEAI 143
++ + K L + NL+ TEE L+E FE+ ++ + + K YAF+ F ++A
Sbjct: 8 NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAK 67
Query: 144 TAMNELNGQTVAGSTLEVSLAKPPSDK 170
A+N N + + G + + L P
Sbjct: 68 EALNSCNKREIEGRAIRLELQGPRGSP 94
>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 = 79.3 bits (196), Expect = 2e-19
Identities = 26/102 (25%), Positives = 38/102 (37%), Gaps = 12/102 (11%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
++V NL +KLKE F G V R ++D V FE EA+ A++ N
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFN 77
Query: 151 GQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRG 192
GQ + + V + + K R Q G
Sbjct: 78 GQLLFDRPMHVKMDERALPKGD-----FFPPERPQQSGPSSG 114
>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 = 78.8 bits (195), Expect = 2e-19
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 7/74 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
++V NL EE L E F Q G + +V KD + FV F+ + A+ LN
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 151 GQTVAGSTLEVSLA 164
G + G + VS
Sbjct: 79 GIRLYGRPINVSGP 92
>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 = 78.3 bits (194), Expect = 3e-19
Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 8/76 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
LY+R L T++ L + + YG++ K I D Y FV F+ A A+ L
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67
Query: 150 NGQTVAGSTLEVSLAK 165
V + S
Sbjct: 68 KASGVQAQMAKQSGPS 83
>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 = 81.5 bits (201), Expect = 3e-19
Identities = 29/116 (25%), Positives = 46/116 (39%), Gaps = 4/116 (3%)
Query: 96 KVLYVRNLTQY-CTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITAMNELNG 151
VL V NL T + L F YG V+RVK + + A V D +A AM+ LNG
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNG 63
Query: 152 QTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRGGPGPSGAHAPLLTGP 207
+ G + ++L+K + + +E + P + + P
Sbjct: 64 HKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPP 119
Score = 73.0 bits (179), Expect = 4e-16
Identities = 19/90 (21%), Positives = 35/90 (38%), Gaps = 5/90 (5%)
Query: 83 PQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----KDYAFVHFED 138
P + L++ N+ +EE LK F G V + + + A +
Sbjct: 108 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGS 167
Query: 139 RQEAITAMNELNGQTVA-GSTLEVSLAKPP 167
+EA+ A+ +L+ + L VS +K
Sbjct: 168 VEEAVQALIDLHNHDLGENHHLRVSFSKST 197
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 115
Score = 78.5 bits (194), Expect = 4e-19
Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 8/84 (9%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMN 147
KVLY++NL+ TE L F ++ + AF+ F +++ A A++
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 148 ELNGQTVAGSTLEVSLAKPPSDKK 171
+NG + G L + K +
Sbjct: 86 LVNGYKLYGKILVIEFGKNKKQRS 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 = 79.4 bits (196), Expect = 4e-19
Identities = 27/106 (25%), Positives = 45/106 (42%), Gaps = 11/106 (10%)
Query: 83 PQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFV 134
Q P+ + + L V + E +L++ FE+YG +E VK + D Y FV
Sbjct: 33 TQMNPEPDVLRN---LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFV 89
Query: 135 HFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNR 180
F+ A A+ LNG + L+V+LA + + +
Sbjct: 90 KFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDG 135
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 78.0 bits (193), Expect = 4e-19
Identities = 27/91 (29%), Positives = 45/91 (49%), Gaps = 9/91 (9%)
Query: 89 TETMSKVKV-LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDR 139
+ M+ K LYV L + ++ L AF +G + ++ D +AFV FE
Sbjct: 5 SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 64
Query: 140 QEAITAMNELNGQTVAGSTLEVSLAKPPSDK 170
++A A++ +N + G T+ V+LAKP K
Sbjct: 65 EDAAAAIDNMNESELFGRTIRVNLAKPMRIK 95
>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 = 78.1 bits (193), Expect = 5e-19
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
L V NL ++ ++E F ++G +++ D A VHFE + +A+ AM + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 91
Query: 151 GQTVAGSTLEVSLA 164
G + G + + L
Sbjct: 92 GVPLDGRPMNIQLV 105
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 78.2 bits (193), Expect = 5e-19
Identities = 21/92 (22%), Positives = 35/92 (38%), Gaps = 8/92 (8%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMN 147
K + L E LK+ +YG VE V+ + A V F + A +
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
Query: 148 ELNGQTVAGSTLEVSLAKPPSDKKKKEEILRN 179
L+ +V G+ + L + K E++ N
Sbjct: 67 NLHLTSVMGNIIHAQLDIKGQQRMKYYELIVN 98
>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 = 77.7 bits (192), Expect = 6e-19
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 11/90 (12%)
Query: 93 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----------YAFVHFEDRQE 141
S L+++NL TEE LK F + G ++ K + FV ++ ++
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 142 AITAMNELNGQTVAGSTLEVSLAKPPSDKK 171
A A+ +L G TV G LEV +++ +
Sbjct: 63 AQKALKQLQGHTVDGHKLEVRISERATKPA 92
>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 = 82.2 bits (202), Expect = 6e-19
Identities = 26/127 (20%), Positives = 51/127 (40%), Gaps = 9/127 (7%)
Query: 98 LYVRNLTQYCTEEKLKEA----FEQYGRVERVKRIKD-----YAFVHFEDRQEAITAMNE 148
+Y+ NL + +++LK++ F Q+G++ + + AFV F++ A A+
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 149 LNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRGGPGPSGAHAPLLTGPP 208
+ G + + AK SD K + R + + + P+ A G
Sbjct: 72 MQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGAT 131
Query: 209 MPRGSVP 215
G+V
Sbjct: 132 PVVGAVQ 138
Score = 61.4 bits (148), Expect = 2e-11
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 99 YVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITAMNELNGQTVA 155
++ NL + E L F Q+ + V+ + AFV F++ +A A + L G +
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKIT 270
Query: 156 GS-TLEVSLAK 165
+ +++S AK
Sbjct: 271 QNNAMKISFAK 281
>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 = 77.6 bits (192), Expect = 6e-19
Identities = 27/93 (29%), Positives = 40/93 (43%), Gaps = 13/93 (13%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YA 132
+ + PD L V L+ Y TE L+E F +YG + V + D +A
Sbjct: 6 SGNRANPDPN-----CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFA 60
Query: 133 FVHFEDRQEAITAMNELNGQTVAGSTLEVSLAK 165
FV+FE+ +A A NG + G + VS
Sbjct: 61 FVYFENVDDAKEAKERANGMELDGRRIRVSGPS 93
>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 = 79.6 bits (197), Expect = 8e-19
Identities = 20/100 (20%), Positives = 36/100 (36%), Gaps = 13/100 (13%)
Query: 73 GCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-- 130
G + + + L++ L Y ++++KE +G ++ +KD
Sbjct: 77 GQSLKIRRPHDYQPLP-----GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA 131
Query: 131 ------YAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLA 164
YAF + D A+ LNG + L V A
Sbjct: 132 TGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 64.9 bits (159), Expect = 2e-13
Identities = 18/98 (18%), Positives = 34/98 (34%), Gaps = 14/98 (14%)
Query: 92 MSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------------YAFVHFED 138
+ + LYV N+ TEE + + F R+ + + +AF+ F
Sbjct: 1 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 139 RQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEI 176
E AM +G G +L++ ++
Sbjct: 61 VDETTQAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHKL 97
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 77.8 bits (192), Expect = 9e-19
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L++ +L Q T+ L F +G V K D + FV F++ A A+ +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 150 NGQTVAGSTLEVSLAK 165
NG V L+V L K
Sbjct: 103 NGFQVGTKRLKVQLKK 118
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 77.3 bits (191), Expect = 1e-18
Identities = 27/89 (30%), Positives = 46/89 (51%), Gaps = 6/89 (6%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITAMNELNGQTV 154
+YV NL + +L+ AF YG + V ++ +AFV FED ++A A+ L+G+ +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVI 62
Query: 155 AGSTLEVSLAKPPSDKKKKEEILRNRERR 183
GS + V L+ + + + R RR
Sbjct: 63 CGSRVRVELSTGMPRRSRFD---RPPARR 88
>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 = 76.9 bits (190), Expect = 1e-18
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 8/75 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
+YV NL T L F +YG+V +V +KD AF+ F D+ A +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 150 NGQTVAGSTLEVSLA 164
N + + G ++ S+A
Sbjct: 79 NNKQLFGRVIKASIA 93
>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 = 77.9 bits (192), Expect = 1e-18
Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 4/85 (4%)
Query: 84 QEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQE 141
P+ K LYV T L+ AF +G + + AFV +E +
Sbjct: 28 DSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMES 85
Query: 142 AITAMNELNGQTVAGSTLEVSLAKP 166
A A+ ELNG V L+V++A+
Sbjct: 86 ADQAVAELNGTQVESVQLKVNIARK 110
>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 = 77.3 bits (191), Expect = 1e-18
Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 7/76 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
LY+ NL E++L+ + +G+V + ++D F E ++ + N
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFN 87
Query: 151 GQTVAGSTLEVSLAKP 166
G+ + + +P
Sbjct: 88 GKFIKTPPGVSAPTEP 103
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 77.9 bits (192), Expect = 1e-18
Identities = 27/77 (35%), Positives = 41/77 (53%), Gaps = 8/77 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------AFVHFEDRQEAITAMNEL 149
L V NLT + + L+ FE+YGRV V +D AFV F D+++A AM+ +
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 150 NGQTVAGSTLEVSLAKP 166
+G + G L V +A+
Sbjct: 110 DGAVLDGRELRVQMARY 126
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 76.8 bits (189), Expect = 2e-18
Identities = 26/96 (27%), Positives = 38/96 (39%), Gaps = 7/96 (7%)
Query: 78 VDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRV---ERVKRIKDYAFV 134
P E +YV NL + LK A + G V + + AF+
Sbjct: 6 SGPGSPPGEGAPLAAD----VYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFL 61
Query: 135 HFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDK 170
H+ D A A++ L G + TL V+LA+ DK
Sbjct: 62 HYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQRDK 97
>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 = 76.0 bits (188), Expect = 2e-18
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 9/84 (10%)
Query: 91 TMSKVKV-LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQE 141
+M+ K LYV L + ++ L AF +G + ++ D +AFV FE ++
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 61
Query: 142 AITAMNELNGQTVAGSTLEVSLAK 165
A A++ +N + G T+ V+LAK
Sbjct: 62 AAAAIDNMNESELFGRTIRVNLAK 85
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 76.1 bits (188), Expect = 2e-18
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 6/86 (6%)
Query: 89 TETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEA 142
+ S ++VRNL T + LK+ F + G V + V FE + A
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVA 61
Query: 143 ITAMNELNGQTVAGSTLEVSLAKPPS 168
A +NG ++G ++V + + S
Sbjct: 62 ERACRMMNGMKLSGREIDVRIDRNAS 87
>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 = 76.1 bits (188), Expect = 2e-18
Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 8/82 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L+V L+ E+ L++ F +YG++ V +KD + FV FE+ +A AM +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 150 NGQTVAGSTLEVSLAKPPSDKK 171
NG++V G + V A SD +
Sbjct: 75 NGKSVDGRQIRVDQAGKSSDNR 96
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 76.6 bits (189), Expect = 2e-18
Identities = 20/89 (22%), Positives = 35/89 (39%), Gaps = 8/89 (8%)
Query: 87 PDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVHFEDRQE 141
P ++ YV NL + +++ F +YG + + +AFV FED ++
Sbjct: 17 PAGNNDCRI---YVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRD 73
Query: 142 AITAMNELNGQTVAGSTLEVSLAKPPSDK 170
A A+ +G G L V +
Sbjct: 74 AEDAVYGRDGYDYDGYRLRVEFPRSGRGT 102
>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 = 76.6 bits (189), Expect = 2e-18
Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 11/95 (11%)
Query: 83 PQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFV 134
+ + + LYV +L TE+ L+ FE +GR+E ++ + D Y F+
Sbjct: 17 NNLQKGSAGPMR---LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFI 73
Query: 135 HFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSD 169
F D + A A+ +LNG +AG ++V +D
Sbjct: 74 TFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108
>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 = 76.2 bits (188), Expect = 2e-18
Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 10/85 (11%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
L+V L + +EE + F+ +G ++ ++ AFV F EA A++ L+
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALH 77
Query: 151 GQTV---AGSTLEVSLAKPPSDKKK 172
G A S+L V A +
Sbjct: 78 GSQTMPGASSSLVVKFADTDKESGP 102
>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 = 76.2 bits (188), Expect = 3e-18
Identities = 18/91 (19%), Positives = 40/91 (43%), Gaps = 3/91 (3%)
Query: 84 QEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK---RIKDYAFVHFEDRQ 140
++ ++ + + L +NL+ TE++LKE FE + V + K A++ F+
Sbjct: 5 EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEA 64
Query: 141 EAITAMNELNGQTVAGSTLEVSLAKPPSDKK 171
+A + E G + G ++ + +
Sbjct: 65 DAEKNLEEKQGAEIDGRSVSLYYTGEKGGTR 95
>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 = 76.1 bits (188), Expect = 3e-18
Identities = 26/80 (32%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEAITAMNELNG 151
LYV+NL +E+L++AF +G + K + + + FV F +EA A+ E+NG
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 152 QTVAGSTLEVSLAKPPSDKK 171
+ VA L V+LA+ +++
Sbjct: 78 RIVATKPLYVALAQRKEERQ 97
>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 = 75.9 bits (187), Expect = 3e-18
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 1/72 (1%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYG-RVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAG 156
+ V+NL Q +++ + + Y + V R K AFV + ++A A+ + + G
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRG 67
Query: 157 STLEVSLAKPPS 168
L V L +
Sbjct: 68 KDLIVQLQPTDA 79
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 78.9 bits (195), Expect = 3e-18
Identities = 24/109 (22%), Positives = 45/109 (41%), Gaps = 14/109 (12%)
Query: 73 GCDIIVDWA------DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK 126
G +I V P + E +YV ++ Q +++ +K FE +G+++
Sbjct: 97 GRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSAT 156
Query: 127 RIKD--------YAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPP 167
+D Y F+ +E Q + A++ +N + G L V A P
Sbjct: 157 LARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205
Score = 73.5 bits (181), Expect = 3e-16
Identities = 19/110 (17%), Positives = 42/110 (38%), Gaps = 9/110 (8%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAF 133
+ +V YV ++ E+ +++AF +G ++ + D +AF
Sbjct: 16 GSAAQRQGALAIMSRV-YVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAF 74
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERR 183
V +E + A A+ ++N + G ++V + + L R
Sbjct: 75 VEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124
>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 = 77.2 bits (190), Expect = 4e-18
Identities = 36/150 (24%), Positives = 61/150 (40%), Gaps = 14/150 (9%)
Query: 21 KFTMAESSREAEEKPSSERTPDYTKLLEYGLDKRIAGKLDDIFKTGKHLLSRGCDIIVDW 80
K E++ EA + ++E+ +Y D + G+ T +
Sbjct: 10 KTLKGETTTEAVDAATAEK-----VFKQYANDNGVDGEWTYDDATKT---FTVTEGSHHH 61
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFE 137
KV YV NL + +L+ AF YG + V ++ +AFV FE
Sbjct: 62 HHHMHRDSCPLDCKV---YVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFE 118
Query: 138 DRQEAITAMNELNGQTVAGSTLEVSLAKPP 167
D ++A A+ EL+G+T+ G + V L+
Sbjct: 119 DPRDAADAVRELDGRTLCGCRVRVELSNGE 148
>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 = 75.4 bits (186), Expect = 4e-18
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 8/88 (9%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMN 147
+V+Y+ ++ TEE++ + G V +K + D YAF+ F D + + +A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 148 ELNGQTVAGSTLEVSLAKPPSDKKKKEE 175
LNG + L+ + E
Sbjct: 63 NLNGYQLGSRFLKCGYSSNSDISGVSLE 90
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 76.7 bits (189), Expect = 4e-18
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 8/95 (8%)
Query: 78 VDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------- 130
VD + + +VLYV L + ++ L AF +G + ++ D
Sbjct: 46 VDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHR 105
Query: 131 -YAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLA 164
+AFV FE ++A A++ +N + G T+ V+LA
Sbjct: 106 GFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 75.4 bits (186), Expect = 4e-18
Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 98 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAG 156
L++ NL + ++E L F YG + ++ + F+ F++ Q A+ + + G
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEXESQEMNFG 84
Query: 157 STLEVSLAKPPS 168
L + ++ +
Sbjct: 85 KKLILEVSSSNA 96
>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 = 78.1 bits (193), Expect = 4e-18
Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L++ L Y ++++KE +G ++ +KD YAF + D A+ L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176
Query: 150 NGQTVAGSTLEVSLAKPPS 168
NG + L V A +
Sbjct: 177 NGMQLGDKKLLVQRASVGA 195
Score = 65.1 bits (159), Expect = 3e-13
Identities = 20/102 (19%), Positives = 35/102 (34%), Gaps = 14/102 (13%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVK-------------RIKDYAFVHFEDRQEAIT 144
LYV N+ TEE + + F R+ + + K++AF+ F E
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 145 AMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQ 186
AM +G G +L++ E ++
Sbjct: 67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVS 107
>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 = 75.8 bits (187), Expect = 4e-18
Identities = 27/102 (26%), Positives = 49/102 (48%), Gaps = 14/102 (13%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAF 133
DP + + ++V N+ TEE+LK+ F + G V + + D Y F
Sbjct: 1 DPAVDRSL------RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGF 54
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEE 175
++D++ A++AM LNG+ +G L V A +K++ +
Sbjct: 55 CEYQDQETALSAMRNLNGREFSGRALRVDNAASEKNKEELKS 96
>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 = 75.8 bits (187), Expect = 4e-18
Identities = 24/98 (24%), Positives = 47/98 (47%), Gaps = 8/98 (8%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAF 133
D + EP + + +L+V ++ + E++++E F YG ++ + D YA
Sbjct: 13 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 72
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKK 171
V +E ++A+ A LNG + G T++V K+
Sbjct: 73 VEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR 110
>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 = 75.0 bits (185), Expect = 5e-18
Identities = 24/86 (27%), Positives = 34/86 (39%), Gaps = 9/86 (10%)
Query: 83 PQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQ 140
E+ T LYV L TE L+ F Q+G + + ++ AF+ F RQ
Sbjct: 6 SGEDKTITT------LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQ 59
Query: 141 EAITAMNE-LNGQTVAGSTLEVSLAK 165
A A + N V G L V +
Sbjct: 60 AAEVAAEKSFNKLIVNGRRLNVKWGR 85
>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 = 79.0 bits (194), Expect = 5e-18
Identities = 30/143 (20%), Positives = 50/143 (34%), Gaps = 14/143 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYG--RVERVKRIKD--------YAFVHFEDRQEAITAMN 147
LY+ NLT + T+E L EA G + +K ++ +A V + M+
Sbjct: 71 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130
Query: 148 ELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRGGPGPSGAHAPLLTGP 207
L + + G V+ + + ++R+ M G G GP G + P
Sbjct: 131 LLPKRELHGQNPVVTPVNKQFLSQFEM---QSRKTTQSGQMSGEGKAGPPGGSSR-AAFP 186
Query: 208 PMPRGSVPLQAALSSTRMGRGDY 230
RG A+ G
Sbjct: 187 QGGRGRGRFPGAVPGGDRFPGPA 209
>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 = 75.3 bits (186), Expect = 5e-18
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
LYV +L TE+ L+ FE +G+++ + +KD Y F+ F D + A A+ +L
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 150 NGQTVAGSTLEVSLAKP 166
NG +AG + V
Sbjct: 68 NGFELAGRPMRVGHVTE 84
>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 = 75.4 bits (186), Expect = 6e-18
Identities = 21/85 (24%), Positives = 33/85 (38%), Gaps = 8/85 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
+YV L + +E L E F Q G V KD Y FV F ++A A+ +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 150 NGQTVAGSTLEVSLAKPPSDKKKKE 174
+ + G + V+ A +
Sbjct: 78 DMIKLYGKPIRVNKASAHNKNLSGP 102
>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 = 76.8 bits (189), Expect = 6e-18
Identities = 27/107 (25%), Positives = 51/107 (47%), Gaps = 8/107 (7%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAF 133
D + EP + + +L+V ++ + E++++E F YG ++ + D YA
Sbjct: 59 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 118
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNR 180
V +E ++A+ A LNG + G T++V K+ K+ R R
Sbjct: 119 VEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVKKSEKRRR 165
>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 = 77.3 bits (191), Expect = 7e-18
Identities = 24/92 (26%), Positives = 38/92 (41%), Gaps = 10/92 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD----------YAFVHFEDRQEAITAMN 147
++V + + +E+ L+E FEQYG V + ++D FV F R+ A+ A N
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 148 ELNGQTVAGSTLEVSLAKPPSDKKKKEEILRN 179
L+ V KP +K R
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKNNAVEDRK 97
Score = 75.7 bits (187), Expect = 2e-17
Identities = 21/109 (19%), Positives = 41/109 (37%), Gaps = 13/109 (11%)
Query: 66 GKHLLSRGCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV 125
+L P + + K L++ +++ CTE ++ F +G++E
Sbjct: 69 NMKVLPG--MHHPIQMKPADSEKNNAVEDRK-LFIGMISKKCTENDIRVMFSSFGQIEEC 125
Query: 126 KRIKD-------YAFVHFEDRQEAITAMNELNGQTV---AGSTLEVSLA 164
+ ++ AFV F R A TA+ ++ S + V A
Sbjct: 126 RILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 74.9 bits (185), Expect = 7e-18
Identities = 14/76 (18%), Positives = 34/76 (44%), Gaps = 1/76 (1%)
Query: 98 LYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAG 156
L++ NL + ++E L F YG + ++ + F+ F++ Q A+ + + G
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFG 72
Query: 157 STLEVSLAKPPSDKKK 172
L + ++ + +
Sbjct: 73 KKLILEVSSSNARPQF 88
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 74.8 bits (184), Expect = 8e-18
Identities = 20/84 (23%), Positives = 32/84 (38%), Gaps = 4/84 (4%)
Query: 86 EPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAI 143
+S V++VR L + E L EA E++G + V K A V FE+ A
Sbjct: 6 SGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAK 65
Query: 144 TAMNEL--NGQTVAGSTLEVSLAK 165
+ +AG + +
Sbjct: 66 ECVTFAADVPVYIAGQQAFFNYST 89
>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 = 76.0 bits (187), Expect = 1e-17
Identities = 27/94 (28%), Positives = 43/94 (45%), Gaps = 8/94 (8%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKDY--------A 132
+ + L V NLT + + L+ FE+YGRV V +D A
Sbjct: 56 EGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFA 115
Query: 133 FVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKP 166
FV F D+++A AM+ ++G + G L V +A+
Sbjct: 116 FVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARY 149
>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 = 75.1 bits (185), Expect = 1e-17
Identities = 27/93 (29%), Positives = 40/93 (43%), Gaps = 8/93 (8%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L+V + + TEE + + F +YG ++ + D Y V +E +EA AM L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 150 NGQTVAGSTLEVSLAKPPSDKKKKEEILRNRER 182
NGQ + G + V K K R R R
Sbjct: 85 NGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSR 117
>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 = 74.8 bits (184), Expect = 2e-17
Identities = 24/79 (30%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMN 147
L V L+ Y TE L+E F +YG + V + D +AFV+FE+ +A A
Sbjct: 47 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106
Query: 148 ELNGQTVAGSTLEVSLAKP 166
NG + G + V +
Sbjct: 107 RANGMELDGRRIRVDFSIT 125
>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 = 75.2 bits (185), Expect = 2e-17
Identities = 24/96 (25%), Positives = 40/96 (41%), Gaps = 13/96 (13%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-------------RIKDYAFVHFEDRQEA 142
+YV+NL ++ E+ LK F +Y R+K AF+ + + A
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
Query: 143 ITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILR 178
A+ E NG + G + V A+ K+ +E R
Sbjct: 106 AKALKEANGYVLFGKPMVVQFARSARPKQDPKEGKR 141
>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 = 76.7 bits (188), Expect = 2e-17
Identities = 25/111 (22%), Positives = 40/111 (36%), Gaps = 4/111 (3%)
Query: 96 KVLYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITAMNELNG 151
VL V L +++ F YG VE+VK +K A V D A+ LN
Sbjct: 5 PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNN 64
Query: 152 QTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRGGPGPSGAHAP 202
+ G + V ++K P+ + L + + R + A
Sbjct: 65 NFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAA 115
Score = 65.9 bits (160), Expect = 2e-13
Identities = 12/93 (12%), Positives = 27/93 (29%), Gaps = 8/93 (8%)
Query: 79 DWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--------RIKD 130
++ P++ VL+ N TEE E ++ G
Sbjct: 107 RFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSS 166
Query: 131 YAFVHFEDRQEAITAMNELNGQTVAGSTLEVSL 163
+ ++ + +A+ + LN +
Sbjct: 167 SGLLEWDSKSDALETLGFLNHYQMKNPNGPYPY 199
>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 = 76.6 bits (188), Expect = 3e-17
Identities = 30/129 (23%), Positives = 49/129 (37%), Gaps = 4/129 (3%)
Query: 83 PQEEPDTETMSKVKVLYVRNLTQY-CTEEKLKEAFEQYGRVERVKRI---KDYAFVHFED 138
+ + VL V NL T + L F YG V+RVK + K+ A V D
Sbjct: 22 GRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMAD 81
Query: 139 RQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRGGPGPSG 198
+A AM+ LNG + G + ++L+K + + +E + P
Sbjct: 82 GNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGS 141
Query: 199 AHAPLLTGP 207
+ + P
Sbjct: 142 KNFQNIFPP 150
Score = 72.7 bits (178), Expect = 7e-16
Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----KDYAFVHFEDRQEAITAMNELNG 151
L++ N+ +EE LK F G V + + + A + +EA+ A+ +L+
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 211
Query: 152 QTVA-GSTLEVSLAKPP 167
+ L VS +K
Sbjct: 212 HDLGENHHLRVSFSKST 228
>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 = 72.5 bits (179), Expect = 3e-17
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 8/77 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L+V +L +E L+ AF+ + + D Y FV F + +A AM+ +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 150 NGQTVAGSTLEVSLAKP 166
GQ + G L ++ A
Sbjct: 64 QGQDLNGRPLRINWAAK 80
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 73.4 bits (181), Expect = 4e-17
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L+V + + TEE + + F +YG ++ + D Y V +E +EA AM L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 150 NGQTVAGSTLEVSLAKP 166
NGQ + G + V
Sbjct: 86 NGQDLMGQPISVDWCFV 102
>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 = 73.5 bits (181), Expect = 4e-17
Identities = 23/102 (22%), Positives = 42/102 (41%), Gaps = 13/102 (12%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---------Y 131
+ P +T SK + VRN+ + +++E F +G ++ V+ K +
Sbjct: 4 GSSGQVPKKQTTSK---ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60
Query: 132 AFVHFEDRQEAITAMNEL-NGQTVAGSTLEVSLAKPPSDKKK 172
FV F +Q+A A N L + + G L + A +
Sbjct: 61 GFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQS 102
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} PDB: 2dgq_A
Length = 106
Score = 73.1 bits (180), Expect = 4e-17
Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 11/85 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L++ + + E+ LK FE++G++ + +KD AF+ + +R+ A+ A + L
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75
Query: 150 NGQTV---AGSTLEVSLAKPPSDKK 171
+ Q ++V A S
Sbjct: 76 HEQKTLPGMNRPIQVKPADSESRGG 100
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 74.9 bits (184), Expect = 5e-17
Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 7/81 (8%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
L V NL ++ ++E F ++G +++ D A VHFE R +A+ AM +
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYK 150
Query: 151 GQTVAGSTLEVSLAKPPSDKK 171
G + G +++ L D +
Sbjct: 151 GVPLDGRPMDIQLVASQIDLE 171
>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 = 73.1 bits (180), Expect = 5e-17
Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 14/94 (14%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMN 147
K +++RNL+ EE L E +Q+G ++ V+ + AF F ++ A +
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 148 ELN------GQTVAGSTLEVSLAKPPSDKKKKEE 175
+ G + G L+V LA +
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 72.4 bits (178), Expect = 7e-17
Identities = 18/85 (21%), Positives = 31/85 (36%), Gaps = 14/85 (16%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGR--VERVKRIKD--------YAFVHFEDRQEAITA 145
+ +RN+ + + + A Y V ++ IKD +AFV +A
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
Query: 146 MNELNGQ----TVAGSTLEVSLAKP 166
+ L + G T+ V AK
Sbjct: 70 LQILQSLHPPLKIDGKTIGVDFAKS 94
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 75.4 bits (186), Expect = 7e-17
Identities = 30/129 (23%), Positives = 54/129 (41%), Gaps = 20/129 (15%)
Query: 78 VDWA--DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD----- 130
+ W+ DP S V ++++NL + + L + F +G + K + D
Sbjct: 89 IMWSQRDPSLR-----KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK 143
Query: 131 -YAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRM----M 185
Y FVHFE ++ A A+ ++NG + + V K +K++E L R + +
Sbjct: 144 GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS---RKEREAELGARAKEFYPYDV 200
Query: 186 QMMQGRGGP 194
G G
Sbjct: 201 PDYAGSSGR 209
Score = 71.5 bits (176), Expect = 2e-15
Identities = 23/100 (23%), Positives = 43/100 (43%), Gaps = 10/100 (10%)
Query: 84 QEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVH 135
P + + LYV +L TE L E F G + ++ +D YA+V+
Sbjct: 5 SMNPSAPS-YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVN 63
Query: 136 FEDRQEAITAMNELNGQTVAGSTLEVSLA-KPPSDKKKKE 174
F+ +A A++ +N + G + + + + PS +K
Sbjct: 64 FQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGV 103
>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 = 72.3 bits (178), Expect = 7e-17
Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 8/94 (8%)
Query: 83 PQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFV 134
+ ++ V+N+ + +++ + F Y + +K A V
Sbjct: 3 SGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 135 HFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPS 168
FE R EA A+ +LN + + +++ L PS
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS 96
>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 = 74.1 bits (183), Expect = 7e-17
Identities = 24/84 (28%), Positives = 42/84 (50%), Gaps = 7/84 (8%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNE 148
+VLYV NL + TE+ LK+ F+ G + +K + D YAFV + +A A+
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 149 LNGQTVAGSTLEVSLAKPPSDKKK 172
LNG+ + + ++++ A
Sbjct: 61 LNGKQIENNIVKINWAFQSQQSSS 84
Score = 71.0 bits (175), Expect = 1e-15
Identities = 22/95 (23%), Positives = 42/95 (44%), Gaps = 11/95 (11%)
Query: 78 VDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------- 130
++WA ++ ++ L+V +L +E L+ AF+ + + D
Sbjct: 73 INWAFQSQQSSSDDTFN---LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSR 129
Query: 131 -YAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLA 164
Y FV F + +A AM+ + GQ + G L ++ A
Sbjct: 130 GYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164
>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 = 71.9 bits (177), Expect = 9e-17
Identities = 20/99 (20%), Positives = 39/99 (39%), Gaps = 11/99 (11%)
Query: 80 WADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-------RIKDYA 132
DP E ++ T L++ NL + +LK A + + + +
Sbjct: 5 LEDPVEGSESTTPFN---LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFG 61
Query: 133 FVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKK 171
+V FE ++ A+ EL G V G+ +++ K +
Sbjct: 62 YVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDGTR 99
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 71.4 bits (176), Expect = 1e-16
Identities = 25/89 (28%), Positives = 42/89 (47%), Gaps = 9/89 (10%)
Query: 95 VKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAM 146
++ +YV NL T E++KE F Q+G+V VK I D + FV ++ + A+
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAI 59
Query: 147 NELNGQTVAGSTLEVSLAKPPSDKKKKEE 175
+L+ G T+ V+ A P +
Sbjct: 60 AKLDNTDFMGRTIRVTEANPKKSLEHHHH 88
>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 = 72.0 bits (177), Expect = 1e-16
Identities = 24/126 (19%), Positives = 49/126 (38%), Gaps = 23/126 (18%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YA 132
+ Q++ + ++V +L+ T E +K AF +GR+ + +KD Y
Sbjct: 5 SSGQKKDTSNHFH----VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60
Query: 133 FVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRG 192
FV F ++ +A A+ ++ GQ + G + + A + + +
Sbjct: 61 FVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATR-----------KPPAPKSTYESNTKQ 109
Query: 193 GPGPSG 198
SG
Sbjct: 110 SGPSSG 115
>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 = 72.9 bits (179), Expect = 1e-16
Identities = 24/97 (24%), Positives = 44/97 (45%), Gaps = 9/97 (9%)
Query: 84 QEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVH 135
EE + + + K LYV NL+ Y TEE++ E F + G ++++ D + FV
Sbjct: 29 NEEQE-KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVE 87
Query: 136 FEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKK 172
+ R +A AM +NG + + + ++
Sbjct: 88 YYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQ 124
>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 = 74.7 bits (184), Expect = 2e-16
Identities = 26/95 (27%), Positives = 37/95 (38%), Gaps = 5/95 (5%)
Query: 76 IIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--YAF 133
I + E + L+V NL TEE K FE+YG V +D + F
Sbjct: 6 IDIKSFLKPGEKTYTQRCR---LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGF 62
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPS 168
+ E R A A EL+G + L + A +
Sbjct: 63 IRLESRTLAEIAKAELDGTILKSRPLRIRFATHGA 97
Score = 74.0 bits (182), Expect = 4e-16
Identities = 23/113 (20%), Positives = 41/113 (36%), Gaps = 11/113 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNELN 150
L V+NL+ + E L++AF Q+G VE+ + D FV F + A A+
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCG 158
Query: 151 GQTV----AGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRGGPGPSGA 199
+ V + D+ E L + ++ + + G
Sbjct: 159 DGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGT 211
>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 = 70.3 bits (173), Expect = 3e-16
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
++V +L+ T + AF +GR+ + +KD Y FV F ++ +A A+ ++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 150 NGQTVAGSTLEVSLAKP 166
GQ + G + + A
Sbjct: 69 GGQWLGGRQIRTNWATR 85
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 70.9 bits (174), Expect = 3e-16
Identities = 24/91 (26%), Positives = 39/91 (42%), Gaps = 10/91 (10%)
Query: 79 DWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHF 136
++ DP + P + V+++R L E L EA +++G + V K A V F
Sbjct: 11 NYDDPHKTPAS------PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEF 64
Query: 137 EDRQEAITAMNELNGQ--TVAGSTLEVSLAK 165
ED A A+N +AG V+ +
Sbjct: 65 EDVLGACNAVNYAADNQIYIAGHPAFVNYST 95
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 70.7 bits (173), Expect = 3e-16
Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 4/83 (4%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITAMNEL--NG 151
+V+++R L TE ++ +G+V + + K+ AF+ + A T +N
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 76
Query: 152 QTVAGSTLEVSLAKPPSDKKKKE 174
+ G + + + K
Sbjct: 77 PVLRGQPIYIQFSNHKELKTDSS 99
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 71.3 bits (174), Expect = 4e-16
Identities = 25/98 (25%), Positives = 38/98 (38%), Gaps = 5/98 (5%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFE 137
P D +KV +L ++N T + L G+V+R+ K A V FE
Sbjct: 11 TRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFE 70
Query: 138 DRQEAITAMNELNGQTVAG--STLEVSLAKPPSDKKKK 173
A A LNG + TL++ A+P +
Sbjct: 71 SVLCAQKAKAALNGADIYAGCCTLKIEYARPTRLNVIR 108
>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 = 69.8 bits (171), Expect = 8e-16
Identities = 20/95 (21%), Positives = 32/95 (33%), Gaps = 8/95 (8%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITAMNELNGQT 153
V+ +NL +++E F ++G + RV A V F + EA A L
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSK 70
Query: 154 VAGSTLEVSLA------KPPSDKKKKEEILRNRER 182
L + A P K + E +
Sbjct: 71 FHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAE 105
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 69.5 bits (170), Expect = 8e-16
Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 4/83 (4%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITAMN--ELNG 151
+VL++R L TE ++ +G+V + + K+ AF+ + AIT +N
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVT 75
Query: 152 QTVAGSTLEVSLAKPPSDKKKKE 174
+ + + + K
Sbjct: 76 PHLRNQPIYIQYSNHKELKTSGP 98
>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 = 69.9 bits (171), Expect = 8e-16
Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 4/83 (4%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITAMN--ELNG 151
+V+++R L TE ++ +G+V + + K+ AF+ + A T +N
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 91
Query: 152 QTVAGSTLEVSLAKPPSDKKKKE 174
+ G + + + K
Sbjct: 92 PVLRGQPIYIQFSNHKELKTDSS 114
>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 = 69.1 bits (170), Expect = 8e-16
Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 10/83 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYG--RVERVKRIKD--------YAFVHFEDRQEAITAMN 147
LY+ NLT + T+E L EA G + +K ++ +A V + M+
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 148 ELNGQTVAGSTLEVSLAKPPSDK 170
L + + G V+ +
Sbjct: 64 LLPKRELHGQNPVVTPSNKLEHH 86
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 69.0 bits (169), Expect = 2e-15
Identities = 25/119 (21%), Positives = 46/119 (38%), Gaps = 29/119 (24%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVE--------RVKRIKD--------YAFVHFEDRQE 141
++V+ L + T E + + F+Q G ++ + D A V F+D
Sbjct: 10 IFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS 69
Query: 142 AITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRGGPGPSGAH 200
A A++ +G+ +G+ ++VS A +D + GRGG H
Sbjct: 70 AKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGG-------------NGRGGLEHHHHH 115
>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 = 67.9 bits (167), Expect = 2e-15
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 9/79 (11%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMN 147
+ +YV N+ T E+L+ F G V RV + D +A++ F D++ T++
Sbjct: 7 RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 65
Query: 148 ELNGQTVAGSTLEVSLAKP 166
L+ G ++V +
Sbjct: 66 ALDESLFRGRQIKVIPKRT 84
>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 = 68.0 bits (167), Expect = 3e-15
Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 9/82 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI---------KDYAFVHFEDRQEAITAMNE 148
+++ NL E+ L + F +G + + +I K YAF++F + A+
Sbjct: 8 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 149 LNGQTVAGSTLEVSLAKPPSDK 170
+NGQ + + VS A K
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSK 89
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 68.8 bits (168), Expect = 6e-15
Identities = 16/96 (16%), Positives = 37/96 (38%), Gaps = 10/96 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYG--RVERVKRIKD--------YAFVHFEDRQEAITAMN 147
+YV + + + T+++L + G V +K ++ YA V +
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 148 ELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERR 183
L G+ + G ++V A + + + + + R
Sbjct: 118 LLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECVR 153
>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 = 67.3 bits (165), Expect = 7e-15
Identities = 24/95 (25%), Positives = 42/95 (44%), Gaps = 6/95 (6%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-----RIKDYAFVH 135
+ P+ + K L+V+ L++ TEE LKE+F+ R V K + FV
Sbjct: 2 SSGSSGPNARSQPS-KTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVD 60
Query: 136 FEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDK 170
F ++A A + + G+ + + AKP +
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEG 95
>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 = 66.1 bits (162), Expect = 1e-14
Identities = 18/92 (19%), Positives = 33/92 (35%), Gaps = 9/92 (9%)
Query: 90 ETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEA 142
E ++V + E +++ F +YG V+ VK I D Y FV F + +
Sbjct: 4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDV 63
Query: 143 ITAMNELNGQTVAGSTLEVSLAKPPSDKKKKE 174
+ + G L++ A +
Sbjct: 64 QKIVE--SQINFHGKKLKLGPAIRKQNLSTYH 93
>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 = 66.2 bits (162), Expect = 2e-14
Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 8/92 (8%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YA 132
+ V+ V+N+ + +++ + F Y + +K A
Sbjct: 1 GSSGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEA 60
Query: 133 FVHFEDRQEAITAMNELNGQTVAGSTLEVSLA 164
V FE R EA A+ +LN + + +++S
Sbjct: 61 MVAFESRDEATAAVIDLNDRPIGSRKVKLSGP 92
>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 = 66.7 bits (163), Expect = 2e-14
Identities = 19/94 (20%), Positives = 39/94 (41%), Gaps = 13/94 (13%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YA 132
+E+ + + S +YV N+ T + L+ F G + R+ + D YA
Sbjct: 26 LSAEEKKEIDKRS----VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYA 81
Query: 133 FVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKP 166
++ F +R A+ ++ G T++V +
Sbjct: 82 YIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT 114
>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 66.2 bits (162), Expect = 2e-14
Identities = 21/93 (22%), Positives = 35/93 (37%), Gaps = 10/93 (10%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAF 133
+P + E V + L L++ F G+V V+ I D A+
Sbjct: 13 EPVDNLSPEERDARTV-FCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAY 71
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLAKP 166
V F + Q A+ L GQ + G + V ++
Sbjct: 72 VEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA 103
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 65.0 bits (159), Expect = 4e-14
Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 4/84 (4%)
Query: 93 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITAMNEL 149
S ++ ++V + +L E F +G V V KD +A V D +
Sbjct: 6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVL-SQ 64
Query: 150 NGQTVAGSTLEVSLAKPPSDKKKK 173
+ ++ G L V + +
Sbjct: 65 SQHSLGGHRLRVRPREQKEFQSPA 88
>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 = 65.0 bits (159), Expect = 4e-14
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 9/75 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYG-RVERVKRIKD--------YAFVHFEDRQEAITAMNE 148
L++ +L Y E + AF G V VK I++ Y FV F D A +++
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 149 LNGQTVAGSTLEVSL 163
+NG+ + G+T
Sbjct: 72 INGKPLPGATPAKRF 86
>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 = 64.9 bits (158), Expect = 6e-14
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 14/82 (17%)
Query: 97 VLYVRNLTQYCTEE---KLKEAFEQYGRVERVKRIKD-----------YAFVHFEDRQEA 142
+++V L+Q + K E F ++G++ +V A+V + ++A
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76
Query: 143 ITAMNELNGQTVAGSTLEVSLA 164
+ A+ +N V G TL+ SL
Sbjct: 77 LRAIQCVNNVVVDGRTLKASLG 98
>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 = 64.7 bits (158), Expect = 7e-14
Identities = 27/104 (25%), Positives = 41/104 (39%), Gaps = 16/104 (15%)
Query: 85 EEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK----------------RI 128
D + S +YV+ L T + L + F+Q G V+ K +
Sbjct: 5 SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKP 64
Query: 129 KDYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKK 172
K A V +ED A A+ +G+ GS L+VSLA+
Sbjct: 65 KGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS 108
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 64.4 bits (157), Expect = 9e-14
Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 12/88 (13%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGR-VERVKRIKD---------YAFVHFEDRQEAITAMN 147
L++ + + E++ E + V V +AFV +E + A A
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70
Query: 148 ELNGQTVA--GSTLEVSLAKPPSDKKKK 173
+L + G + V A+P D +
Sbjct: 71 KLMPGRIQLWGHQIAVDWAEPEIDVDED 98
Score = 40.9 bits (96), Expect = 4e-05
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 73 GCDIIVDWADPQEEPDTETMSKVK 96
G I VDWA+P+ + D + M V
Sbjct: 81 GHQIAVDWAEPEIDVDEDVMETVS 104
>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 = 63.7 bits (155), Expect = 2e-13
Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 1/87 (1%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-YAFVHFEDRQEAITAMNELNGQTVAG 156
+ V L + + LK+ + G V +D V F +++ A+ +L+
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRS 77
Query: 157 STLEVSLAKPPSDKKKKEEILRNRERR 183
E + + D + R+R
Sbjct: 78 HEGETAYIRVKVDGPRSPSYGRSRSSG 104
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 63.4 bits (154), Expect = 2e-13
Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 12/93 (12%)
Query: 66 GKHLLSRGCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV 125
KH L R I + ++ V+ L + +L E+ G V+ +
Sbjct: 8 AKHTLLRHEGI-----ETVSYA-----TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDAL 57
Query: 126 KRI--KDYAFVHFEDRQEAITAMNELNGQTVAG 156
K Y+F + +E+ A LNG+ V
Sbjct: 58 LMPPNKPYSFARYRTTEESKRAYVTLNGKEVVD 90
>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 = 64.7 bits (157), Expect = 3e-13
Identities = 31/138 (22%), Positives = 50/138 (36%), Gaps = 13/138 (9%)
Query: 78 VDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV----KRIKDYAF 133
VD S V + V NL T + L + F ++G V ++ K + A
Sbjct: 34 VDAGMAMAGQ-----SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQAL 88
Query: 134 VHFEDRQEAITAMNELNGQTV--AGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGR 191
+ + D A A L+GQ + A TL + +K S K ++R+ + G
Sbjct: 89 LQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNND-KSRDYTRPDLPSGD 147
Query: 192 GGPGPSGAHAPLLTGPPM 209
P A G +
Sbjct: 148 SQPSLDQTMAAAF-GLSV 164
>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 = 62.6 bits (153), Expect = 3e-13
Identities = 21/96 (21%), Positives = 39/96 (40%), Gaps = 19/96 (19%)
Query: 83 PQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---------YAF 133
P+ P T ++ NL TEE +KE F + V+ ++ + +
Sbjct: 15 PKSPPYT--------AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGY 65
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSD 169
FED ++A+ LN +++ + V +A D
Sbjct: 66 AEFEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQD 100
>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 = 64.5 bits (158), Expect = 3e-13
Identities = 16/97 (16%), Positives = 35/97 (36%), Gaps = 14/97 (14%)
Query: 78 VDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD------- 130
A P++E D K ++V + ++ +E F Q+G + + + D
Sbjct: 75 PKRAIPRDEQD-----KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSR 129
Query: 131 -YAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKP 166
+ FV ++ + +E+ A+P
Sbjct: 130 GFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRAEP 165
Score = 58.3 bits (142), Expect = 6e-11
Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 12/86 (13%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
+++ L TE+ L+E F +YG V +K +KD + F+ FE +
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-- 63
Query: 150 NGQTVAGSTLEVSLAKP--PSDKKKK 173
+ G ++ A P DK K
Sbjct: 64 TQHILDGKVIDPKRAIPRDEQDKTGK 89
>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 = 62.7 bits (153), Expect = 4e-13
Identities = 22/97 (22%), Positives = 41/97 (42%), Gaps = 19/97 (19%)
Query: 83 PQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---------YAF 133
P+ P T ++ NL TEE +KE F + V+ ++ + +
Sbjct: 11 PKSPPYT--------AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGY 61
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDK 170
FED ++A++ LN +++ + V +A DK
Sbjct: 62 AEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQDK 97
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 61.9 bits (151), Expect = 5e-13
Identities = 26/87 (29%), Positives = 37/87 (42%), Gaps = 9/87 (10%)
Query: 98 LYVRNLTQYCTEEKLKEAF-EQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNEL 149
L+V +LT + L E F + Y K + D Y FV F D E A+ E
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 150 NGQTVAGS-TLEVSLAKPPSDKKKKEE 175
G GS + +S+A P + + K E
Sbjct: 72 QGAVGLGSKPVRLSVAIPKASRVKPVE 98
>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 = 61.9 bits (151), Expect = 6e-13
Identities = 19/100 (19%), Positives = 38/100 (38%), Gaps = 19/100 (19%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRV--------ERVKRIKD-- 130
+ + +V+ L + T E + + F+Q G + + D
Sbjct: 2 GHHHHHHSHSDNNTI---FVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE 58
Query: 131 ------YAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLA 164
A V F+D A A++ +G+ +G+ ++VS A
Sbjct: 59 TGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 61.9 bits (151), Expect = 7e-13
Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 18/97 (18%)
Query: 83 PQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFV 134
P E P T YV NL + + F+ + V+ ++D + +V
Sbjct: 11 PTEPPYT--------AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYV 61
Query: 135 HFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKK 171
F++ A+ +G + +L V +A+ K
Sbjct: 62 EFDEVDSLKEALT-YDGALLGDRSLRVDIAEGRKQDK 97
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 61.5 bits (150), Expect = 1e-12
Identities = 30/116 (25%), Positives = 45/116 (38%), Gaps = 24/116 (20%)
Query: 90 ETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQE 141
T +K ++V L + T+ L++ FE +G +E I D Y FV DR
Sbjct: 15 TTFTK---IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA 71
Query: 142 AITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRGGPGPS 197
A A + N + G V+LA + + R +Q G GPS
Sbjct: 72 AERACKDPN-PIIDGRKANVNLAYLGA------------KPRSLQTGFAIGVSGPS 114
>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 = 63.5 bits (155), Expect = 1e-12
Identities = 30/131 (22%), Positives = 50/131 (38%), Gaps = 13/131 (9%)
Query: 60 DDIFKTGKHLL-SRGCDIIVDWADPQEEPDTETMS-KVKVLYVRNLTQYCTEEKLKEAFE 117
D H + R + A +E+ VK ++V + + E L++ FE
Sbjct: 69 DAAMNARPHKVDGRVVE--PKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 126
Query: 118 QYGRVERVKRIKD--------YAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSD 169
QYG++E ++ + D +AFV F+D + + TV G EV A +
Sbjct: 127 QYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKALSKQE 185
Query: 170 KKKKEEILRNR 180
R R
Sbjct: 186 MASASSSQRGR 196
Score = 56.9 bits (138), Expect = 3e-10
Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 9/91 (9%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
L++ L+ T+E L+ FEQ+G + ++D + FV + +E AMN
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA- 74
Query: 150 NGQTVAGSTLEVSLAKPPSDKKKKEEILRNR 180
V G +E A D ++ L +
Sbjct: 75 RPHKVDGRVVEPKRAVSREDSQRPGAHLTVK 105
>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 = 59.9 bits (146), Expect = 3e-12
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 9/82 (10%)
Query: 93 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAIT 144
SK ++V + C E +L+E F+++G V V I D + F+ FED Q
Sbjct: 8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQ 67
Query: 145 AMNELNGQTVAGSTLEVSLAKP 166
A+ ++ + G +EV A+P
Sbjct: 68 AV-NMHFHDIMGKKVEVKRAEP 88
>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 = 59.6 bits (145), Expect = 5e-12
Identities = 20/100 (20%), Positives = 42/100 (42%), Gaps = 12/100 (12%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YA 132
P+ + K +++ L+ T+E L+E F Q+G V+ ++D +
Sbjct: 14 LVPRGSHMGSSGCK---MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG 70
Query: 133 FVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKK 172
FV F D+ + + + + T++ +A P + K
Sbjct: 71 FVTFMDQAGVDKVLAQ-SRHELDSKTIDPKVAFPRRAQPK 109
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 59.4 bits (144), Expect = 5e-12
Identities = 21/88 (23%), Positives = 35/88 (39%), Gaps = 8/88 (9%)
Query: 94 KVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV-------KRIKDYAFVHFEDRQEAITAM 146
K + +Y++ T + +KE E G+V + K K FV F+ + A +
Sbjct: 10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV 69
Query: 147 NELNGQTVAGSTLEVSLAKPPSDKKKKE 174
E GQ + L + KK +E
Sbjct: 70 -ETPGQKYKETDLLILFKDDYFAKKNEE 96
>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 = 58.8 bits (143), Expect = 7e-12
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 5/78 (6%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITAMNELNGQTV 154
++V T TE++L+E F QYG V V K +AFV F D Q A + E +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE--DLII 65
Query: 155 AGSTLEVSLAKPPSDKKK 172
G ++ +S A+P +
Sbjct: 66 KGISVHISNAEPKHNSNS 83
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 59.7 bits (144), Expect = 1e-11
Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 6/88 (6%)
Query: 93 SKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV----KRIKDYAFVHFEDRQEAITAMNE 148
S V + V NL T + L + F ++G V ++ K + A + + D A A
Sbjct: 26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLS 85
Query: 149 LNGQTV--AGSTLEVSLAKPPSDKKKKE 174
L+GQ + A TL + +K S K
Sbjct: 86 LDGQNIYNACCTLRIDFSKLTSLNVKYN 113
>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 = 58.7 bits (142), Expect = 1e-11
Identities = 16/87 (18%), Positives = 32/87 (36%), Gaps = 1/87 (1%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-YAFVHFEDRQEAITAMNELNGQTVAG 156
+ V L + + LK+ + G V +D V F +++ A+ +L+
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFRS 78
Query: 157 STLEVSLAKPPSDKKKKEEILRNRERR 183
E + + D + R+R R
Sbjct: 79 HEGETAYIRVKVDGPRSPSYGRSRSRS 105
>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 = 57.1 bits (138), Expect = 5e-11
Identities = 18/108 (16%), Positives = 35/108 (32%), Gaps = 19/108 (17%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMN 147
++ N+ T+ + + E E + A V F++ +A +
Sbjct: 16 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE- 74
Query: 148 ELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRGGPG 195
L+ + + G V + EI +N QG+ GP
Sbjct: 75 RLHRKKLNGREAFVH----VVTLEDMREIEKNPPA------QGKSGPS 112
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 55.6 bits (135), Expect = 7e-11
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
++V L+ T E +K FEQ+G+V+ + D + FV FE E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60
Query: 150 NGQTVAGSTLEVSLA 164
+ + +E A
Sbjct: 61 HFHEINNKMVECKKA 75
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 59.0 bits (142), Expect = 8e-11
Identities = 19/110 (17%), Positives = 41/110 (37%), Gaps = 12/110 (10%)
Query: 72 RGCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCT---------EEKLKEAFEQYGRV 122
G + D+ + + K K LYV + E +++ F + G +
Sbjct: 112 FGREKFADYREDMGGIGSF-RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDI 170
Query: 123 ERVK--RIKDYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDK 170
+R++ K+ FV F+ + A A ++ QT+ + + +
Sbjct: 171 DRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTG 220
>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 = 55.7 bits (135), Expect = 8e-11
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD---YAFVHFEDRQEAITAMNELNGQTV 154
++V T+ T E+L++ F QYG V V K +AFV F D + A + E +
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGE--DLII 71
Query: 155 AGSTLEVSLAKPPSDKK 171
G ++ +S A+P +K
Sbjct: 72 KGISVHISNAEPKHNKL 88
>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 = 55.7 bits (134), Expect = 2e-10
Identities = 16/75 (21%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 96 KVLYVRNL-TQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITAMN--ELN 150
+V+++ NL ++ + + E YG+++ R+K AF+ E R++A+ ++
Sbjct: 26 RVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKK 85
Query: 151 GQTVAGSTLEVSLAK 165
G ++V L++
Sbjct: 86 ALWFQGRCVKVDLSE 100
>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding
protein, hnRNP, telomere, DNA-binding protein, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wtb_A 1x0f_A
Length = 75
Score = 54.4 bits (132), Expect = 2e-10
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 9/75 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
++V L+ EEK++E F +G VE ++ D + F+ F++ + M E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EK 60
Query: 150 NGQTVAGSTLEVSLA 164
V S E+ +A
Sbjct: 61 KYHNVGLSKCEIKVA 75
>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 = 55.6 bits (134), Expect = 2e-10
Identities = 19/124 (15%), Positives = 40/124 (32%), Gaps = 19/124 (15%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI--------KDYA 132
+ + +Y++ L + + + F++ VE I
Sbjct: 11 SGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEG 70
Query: 133 FVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRG 192
FV F + + A+ + Q + ++V P KK E + +R+ +
Sbjct: 71 FVEFRNEADYKAAL-CRHKQYMGNRFIQVH----PITKKGMLEKIDMIRKRL------QS 119
Query: 193 GPGP 196
GP
Sbjct: 120 GPSS 123
>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 = 57.2 bits (137), Expect = 2e-10
Identities = 21/101 (20%), Positives = 38/101 (37%), Gaps = 8/101 (7%)
Query: 80 WADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERV-------KRIKDYA 132
P+ + + K + +Y++ T + +KE E G+V + K K
Sbjct: 94 KPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSI 153
Query: 133 FVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKK 173
FV F+ + A + E GQ + L + KK +
Sbjct: 154 FVVFDSIESAKKFV-ETPGQKYKETDLLILFKDDYFAKKNE 193
>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 = 55.0 bits (132), Expect = 2e-10
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 9/82 (10%)
Query: 98 LYVRNLTQYCTEEKLKE----AFEQYGRVERV-----KRIKDYAFVHFEDRQEAITAMNE 148
+ V N+ + ++L++ AF ++G+V+ V + A V E+ Q+AI A+N
Sbjct: 12 VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVNS 71
Query: 149 LNGQTVAGSTLEVSLAKPPSDK 170
L+ + + VSLA S
Sbjct: 72 LHRYKIGSKKILVSLATGASGP 93
>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 = 54.9 bits (133), Expect = 3e-10
Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 10/85 (11%)
Query: 90 ETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQE 141
+ K L V L TE+ LKE F +G V V+ KD + FV F + +
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69
Query: 142 AITAMNELNGQTVAGSTLEVSLAKP 166
+ M++ + + G + L
Sbjct: 70 QVKVMSQRH--MIDGRWCDCKLPNS 92
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 53.6 bits (130), Expect = 3e-10
Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 9/75 (12%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNEL 149
+++ L+ T+E L+E F Q+G V+ ++D + FV F D+ + +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ- 61
Query: 150 NGQTVAGSTLEVSLA 164
+ + T++ +A
Sbjct: 62 SRHELDSKTIDPKVA 76
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 54.6 bits (132), Expect = 3e-10
Identities = 22/95 (23%), Positives = 35/95 (36%), Gaps = 12/95 (12%)
Query: 87 PDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFED 138
+ + K L+V L T+E L+ F QYG V +KD + FV F+D
Sbjct: 11 SGADEIGK---LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
Query: 139 RQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKK 173
T + T+ G ++ P +
Sbjct: 68 PNCVGTVLAS-RPHTLDGRNIDPKPCTPRGMQPSG 101
>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 = 54.4 bits (131), Expect = 3e-10
Identities = 13/90 (14%), Positives = 34/90 (37%), Gaps = 9/90 (10%)
Query: 85 EEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHF 136
++ + + +R L C++E++ + F V + AFV F
Sbjct: 5 SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64
Query: 137 EDRQEAITAMNELNGQTVAGSTLEVSLAKP 166
++ A A+ + + + + +E+ +
Sbjct: 65 ASQEIAEKAL-KKHKERIGHRYIEIFKSSR 93
>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 = 54.0 bits (130), Expect = 4e-10
Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 14/77 (18%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-------------KDYAFVHFEDRQEAIT 144
LYV N+ TEE + + F R+ + + K++AF+ F E
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 145 AMNELNGQTVAGSTLEV 161
AM +G G +L++
Sbjct: 69 AM-AFDGIIFQGQSLKI 84
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 54.2 bits (131), Expect = 6e-10
Identities = 23/94 (24%), Positives = 37/94 (39%), Gaps = 10/94 (10%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YA 132
P E E K L++ L+ TEE L+ +EQ+G++ ++D +
Sbjct: 14 TVPLERKKREKEQFRK-LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFG 72
Query: 133 FVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKP 166
FV F E AM ++ G +E A
Sbjct: 73 FVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA 105
>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 = 52.6 bits (126), Expect = 3e-09
Identities = 15/93 (16%), Positives = 33/93 (35%), Gaps = 9/93 (9%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAF 133
++ + + +R L CT+E++ + F V + AF
Sbjct: 29 QMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAF 88
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLAKP 166
V F ++ A A+ + + + +EV +
Sbjct: 89 VQFASQELAEKAL-GKHKERIGHRYIEVFKSSQ 120
>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 = 54.9 bits (131), Expect = 4e-09
Identities = 27/140 (19%), Positives = 52/140 (37%), Gaps = 9/140 (6%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAF 133
DP +P+ + + K L+V + TE KL+ FE YG ++R+ + YAF
Sbjct: 90 DPHNDPNAQGDAF-KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAF 148
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRGG 193
+ +E ++ +A +G+ + G + V + + + K + L +
Sbjct: 149 IEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNI 208
Query: 194 PGPSGAHAPLLTGPPMPRGS 213
P P
Sbjct: 209 RHSGRDDTSRYDERPGPSPL 228
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 51.0 bits (122), Expect = 8e-09
Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 5/80 (6%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-----YAFVHFEDRQEAITAMNELNGQ 152
+ ++NL + C+ + LK+ + + + F + + A+ LN
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90
Query: 153 TVAGSTLEVSLAKPPSDKKK 172
GS + V P ++
Sbjct: 91 EFRGSVITVERDDNPPPIRR 110
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 50.9 bits (122), Expect = 9e-09
Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 9/78 (11%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNE 148
+ V + E +++ F RV+ V +KD V F Q+ A+ +
Sbjct: 17 LYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-K 74
Query: 149 LNGQTVAGSTLEVSLAKP 166
N + +EVS A
Sbjct: 75 RNRMLMIQRYVEVSPATE 92
>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 = 50.2 bits (120), Expect = 1e-08
Identities = 12/81 (14%), Positives = 31/81 (38%), Gaps = 5/81 (6%)
Query: 91 TMSKVKVLYVRNL-TQYCTEEKLKEAFEQYGRVERVKRIKD--YAFVHFEDRQEAITAMN 147
+ +V+++ + +L + E +G + + AF+ ++A A++
Sbjct: 11 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTEDAQAAVD 70
Query: 148 --ELNGQTVAGSTLEVSLAKP 166
V G + V L++
Sbjct: 71 YYTTTPALVFGKPVRVHLSQK 91
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 49.7 bits (119), Expect = 2e-08
Identities = 11/78 (14%), Positives = 26/78 (33%), Gaps = 9/78 (11%)
Query: 97 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAFVHFEDRQEAITAMNE 148
+ + ++ L F + G+V ++ D + FV +A +
Sbjct: 14 APVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73
Query: 149 LNGQTVAGS-TLEVSLAK 165
+G+ + L + K
Sbjct: 74 FHGKRLDLKHRLFLYTMK 91
>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 = 49.5 bits (119), Expect = 2e-08
Identities = 14/91 (15%), Positives = 35/91 (38%), Gaps = 14/91 (15%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD--------YAF 133
+ + + K ++V L+ +++ LK+ F ++G V D + F
Sbjct: 3 NASKNEEDAG----K-MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGF 57
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLA 164
+ F+D +++ + G ++ A
Sbjct: 58 ILFKDAASVEKVLDQKE-HRLDGRVIDPKKA 87
>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 = 49.6 bits (119), Expect = 2e-08
Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 9/79 (11%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNE 148
+ +R TE+ + E ++ +++ Y FV F + +E A+ +
Sbjct: 11 HTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQAL-K 68
Query: 149 LNGQTVAGSTLEVSLAKPP 167
N + + G +EV K
Sbjct: 69 CNREYMGGRYIEVFREKSG 87
>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 = 50.6 bits (121), Expect = 2e-08
Identities = 23/117 (19%), Positives = 38/117 (32%), Gaps = 16/117 (13%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYG--RVERVK----RIKDYAFVH 135
+ T + +++R L TE + F RV R+ A V
Sbjct: 33 GSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVE 92
Query: 136 FEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQGRG 192
F +EA+ AM + + +E+ L + Q+MQG G
Sbjct: 93 FATHEEAVAAM-SKDRANMQHRYIELFLNSTTG---------ASNGAYSSQVMQGMG 139
>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 = 49.3 bits (118), Expect = 3e-08
Identities = 15/79 (18%), Positives = 26/79 (32%), Gaps = 9/79 (11%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRIKD-------YAFVHFEDRQEAITAMNE 148
+++R L TE + F RV A V F ++A+ AM
Sbjct: 16 HCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAM-A 73
Query: 149 LNGQTVAGSTLEVSLAKPP 167
+ + +E+ L
Sbjct: 74 KDKANMQHRYVELFLNSTA 92
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 48.2 bits (115), Expect = 6e-08
Identities = 15/98 (15%), Positives = 35/98 (35%), Gaps = 13/98 (13%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNL------TQYCTEEKLKEAFEQYGRVERVKRIKD---- 130
D ++ E V+ V N+ + + + F ++G++ ++
Sbjct: 1 GDVLKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT 60
Query: 131 --YAFVHFEDRQEAITAMNELNGQTVAGS-TLEVSLAK 165
Y F+ + A+ A+ +G + T V+L
Sbjct: 61 KGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFT 98
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 48.3 bits (115), Expect = 8e-08
Identities = 19/123 (15%), Positives = 36/123 (29%), Gaps = 19/123 (15%)
Query: 81 ADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVK-----------RIK 129
E + ++ +R L T E++ F Q+ + K R
Sbjct: 9 GTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPT 68
Query: 130 DYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERRMMQMMQ 189
AFV F + A A+ + + +E+ + E+ + R
Sbjct: 69 GDAFVLFACEEYAQNAL-RKHKDLLGKRYIELFRSTA-------AEVQQVLNRFSSASGP 120
Query: 190 GRG 192
G
Sbjct: 121 SSG 123
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 46.2 bits (109), Expect = 3e-07
Identities = 16/70 (22%), Positives = 27/70 (38%), Gaps = 2/70 (2%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERVK--RIKDYAFVHFEDRQEAITAMNELNGQTVA 155
L ++NLT L+ Q+G + + A + R+EA A LN +A
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQMALNNCVLA 69
Query: 156 GSTLEVSLAK 165
+T+
Sbjct: 70 NTTIFAESPS 79
>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 = 46.0 bits (109), Expect = 5e-07
Identities = 16/110 (14%), Positives = 37/110 (33%), Gaps = 20/110 (18%)
Query: 84 QEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----------KDYAF 133
+EE D ++ + L CT E + F I + A
Sbjct: 5 EEEVDDVF-----LIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDAL 59
Query: 134 VHFEDRQEAITAMNELNGQTVAGSTLEVSLAKPPSDKKKKEEILRNRERR 183
+ E Q+ A+ E + + +EV + + + ++++ + +
Sbjct: 60 IEMESEQDVQKAL-EKHRMYMGQRYVEVY----EINNEDVDALMKSLQVK 104
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 43.1 bits (102), Expect = 3e-06
Identities = 7/50 (14%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 108 TEEKLKEAFEQYGRVERVKRIKD------YAFVHFEDRQEAITAMNELNG 151
+ + + F ++G++ ++ Y F+ + A+ A+ +G
Sbjct: 20 LKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADG 69
>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 = 44.1 bits (104), Expect = 3e-06
Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 11/80 (13%)
Query: 97 VLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----------KDYAFVHFEDRQEAITAM 146
V+ +R L C+ E ++ + V + AFV E + A+
Sbjct: 19 VVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL 78
Query: 147 NELNGQTVAGSTLEVSLAKP 166
+ + +++ +EV +
Sbjct: 79 -KKDRESMGHRYIEVFKSHR 97
>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 = 42.4 bits (100), Expect = 1e-05
Identities = 13/71 (18%), Positives = 28/71 (39%), Gaps = 4/71 (5%)
Query: 109 EEKLKEAFEQYGRVERV----KRIKDYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLA 164
E L+ ++G++ ++ + A V F D +EA + L+G+ G +
Sbjct: 40 REDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 99
Query: 165 KPPSDKKKKEE 175
+D +
Sbjct: 100 DGTTDYQSGPS 110
>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 = 43.2 bits (101), Expect = 3e-05
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 4/61 (6%)
Query: 96 KVLYVRNLTQYC--TEEKLKEAFEQYGRVERV--KRIKDYAFVHFEDRQEAITAMNELNG 151
+ L V N + +L E+ G V+ + K Y+F + +E+ A LNG
Sbjct: 19 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNG 78
Query: 152 Q 152
+
Sbjct: 79 K 79
>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 91
Score = 39.2 bits (91), Expect = 9e-05
Identities = 14/57 (24%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 110 EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKP 166
++L + F +G V ++ ++D +V F + A+ ++ LNG+ + T+ ++L P
Sbjct: 30 DELLQQFASFGEVILIRFVEDKMWVTFLEGSSALNVLS-LNGKELLNRTITIALKSP 85
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 39.6 bits (92), Expect = 1e-04
Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 6/81 (7%)
Query: 96 KVLYVRNLTQYCTEEKLKEAFEQY-----GRVERVKRIKDYAFVHFEDRQEAITAMNELN 150
+ VR L +E L FE G V +R+ + F + +A + + +
Sbjct: 9 VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERVLAQAD 68
Query: 151 GQTVAGSTLEVSLAKPPSDKK 171
+ G+ L + A P + +
Sbjct: 69 -HELHGAQLSLRPAPPRAPAR 88
>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 = 40.0 bits (93), Expect = 1e-04
Identities = 11/95 (11%), Positives = 28/95 (29%), Gaps = 11/95 (11%)
Query: 82 DPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAFEQYGRVERVKRI----------KDY 131
+ V+ +R L C+ E ++ + +
Sbjct: 31 GRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGE 90
Query: 132 AFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKP 166
AFV + A+ + + +++ +EV +
Sbjct: 91 AFVELGSEDDVKMAL-KKDRESMGHRYIEVFKSHR 124
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 38.7 bits (90), Expect = 2e-04
Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 7/62 (11%)
Query: 109 EEKLKEAFEQYGRVERVKRIKDY-------AFVHFEDRQEAITAMNELNGQTVAGSTLEV 161
EE E E+YG VE + + +V F ++A A+ +LN + G +
Sbjct: 41 EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100
Query: 162 SL 163
L
Sbjct: 101 EL 102
>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 95
Score = 37.7 bits (87), Expect = 3e-04
Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 110 EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAGSTLEVSLAKP 166
+L + YG + V+ + V F D A++ ++ ++G V G +++S
Sbjct: 39 TELMQTLGSYGTIVLVRINQGQMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPSS 94
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 38.4 bits (89), Expect = 3e-04
Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 10/61 (16%)
Query: 98 LYVRNLTQYCTEEKLKEAFEQYGRVERV----------KRIKDYAFVHFEDRQEAITAMN 147
++V L E+++ +F ++G + K YAF+ F++ ++
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
Query: 148 E 148
Sbjct: 71 A 71
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 39.8 bits (92), Expect = 5e-04
Identities = 32/218 (14%), Positives = 70/218 (32%), Gaps = 55/218 (25%)
Query: 1 MAIQASIKNQKP---------IVIF---VNVRKFTMA----ESSREAEE-------KPSS 37
I++S+ +P + +F ++ ++ + + K S
Sbjct: 357 TIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL 416
Query: 38 -ERTPDYTKLLEYGLDKRIAGKLDDIFKTGKHLLSRGCDIIVDWADPQEEPDTETMSKVK 96
E+ P + + + + KL++ + H IVD + + D++ +
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLEN--EYALH------RSIVDHYNIPKTFDSDDLIPPY 468
Query: 97 V-LYVRNLTQYCTEEKLKEAFEQYGRVERVKRI-KDYAFVHFEDRQEAITAMNELNGQTV 154
+ Y + + LK E R+ + + D+ F+ Q+ N
Sbjct: 469 LDQYFYSHIGH----HLKNI-EHPERMTLFRMVFLDFRFL----EQKIRHDSTAWNASGS 519
Query: 155 AGSTLEVSLAKPPSDKKK-KEEILRN---RERRMMQMM 188
+TL K K I N ER + ++
Sbjct: 520 ILNTL--------QQLKFYKPYICDNDPKYERLVNAIL 549
>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 = 36.9 bits (86), Expect = 8e-04
Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 109 EEKLKEAFEQYGRVERVKRIKDYA----FVHFEDRQEAITAMNELNGQTVAGSTLEVSL 163
++ + E ++G V + K+ A +V AI A+N L+G+ AG + +
Sbjct: 31 KDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAY 89
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 36.3 bits (84), Expect = 0.001
Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 10/65 (15%)
Query: 109 EEKLKEAFEQYGRVERVK--RIKD--------YAFVHFEDRQEAITAMNELNGQTVAGST 158
E +++ +YG V+ ++ R D FV F + AM L G+ A
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRV 88
Query: 159 LEVSL 163
+
Sbjct: 89 VVTKY 93
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 36.3 bits (84), Expect = 0.002
Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 12/67 (17%)
Query: 109 EEKLKEAFEQYGRVERVKRIKDYA------------FVHFEDRQEAITAMNELNGQTVAG 156
E ++ E ++G V RV ++ FV F E A+ LNG+ AG
Sbjct: 39 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG 98
Query: 157 STLEVSL 163
+ +
Sbjct: 99 RKVVAEV 105
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 35.4 bits (81), Expect = 0.002
Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 7/78 (8%)
Query: 97 VLYVRNLTQYCTEEKLKEAFEQY-----GRVERVKRIKDYAFVHFEDRQEAITAMNELNG 151
+LYV NL + + + G+V + A + F ++ A A +
Sbjct: 11 LLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT--GCSAILRFINQDSAERAQKRMEN 68
Query: 152 QTVAGSTLEVSLAKPPSD 169
+ V G+ + VS +
Sbjct: 69 EDVFGNRIIVSFTPKNRE 86
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 34.4 bits (78), Expect = 0.006
Identities = 17/97 (17%), Positives = 33/97 (34%), Gaps = 10/97 (10%)
Query: 85 EEPDTETMSKVKVLYVRNLTQYC----TEEKLKEAFEQYGRVERV---KRIKDYAFVHFE 137
+ K+K+ + +++ L ++YG V + + A V F
Sbjct: 3 SGSSGQGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFA 62
Query: 138 DRQEAITAMNELNGQTVAGSTLEVS-LAKPPSDKKKK 173
+ A A+ G + L++S L P D
Sbjct: 63 TVKAAELAVQNEVGL--VDNPLKISWLEGQPQDASGP 97
>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 = 33.9 bits (77), Expect = 0.043
Identities = 26/142 (18%), Positives = 55/142 (38%), Gaps = 27/142 (19%)
Query: 55 IAGKLDDIFKTGKHLLS-RGCDIIVDWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLK 113
+A + ++ ++ RG + + A P++E + + R + ++E L+
Sbjct: 1773 LADVMS--IESLVEVVFYRG--MTMQVAVPRDELGRSNYGMIAINPGR-VAASFSQEALQ 1827
Query: 114 EAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAGSTLE-----VSLAKPPS 168
VERV + + V E I N N Q VA L ++
Sbjct: 1828 YV------VERVGKRTGW-LV------E-IVNYNVENQQYVAAGDLRALDTVTNVLN--F 1871
Query: 169 DKKKKEEILRNRERRMMQMMQG 190
K +K +I+ ++ ++ ++G
Sbjct: 1872 IKLQKIDIIELQKSLSLEEVEG 1893
Score = 31.9 bits (72), Expect = 0.21
Identities = 34/241 (14%), Positives = 63/241 (26%), Gaps = 93/241 (38%)
Query: 33 EKPSSERTPDY-------------TKLLEYGLDKRIAG----KLDDIFKTGKHLLSRGCD 75
E PS+ DY +L Y + ++ G +L K
Sbjct: 220 ENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKG---ATGHSQG 276
Query: 76 IIV--------DWADPQEEPDTETMSKVKVLYVRNLTQYCTEEKLKEAF-------EQYG 120
++ W + ++ + + F E Y
Sbjct: 277 LVTAVAIAETDSWES----------------FFVSVRKA-----ITVLFFIGVRCYEAYP 315
Query: 121 RVERVKRIKDYAFVHFE------------DRQEAITAMNELNGQTVAGSTLEVSL----- 163
I + + + E +++ +N+ N AG +E+SL
Sbjct: 316 NTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAK 375
Query: 164 ----AKPPSDKKKKEEILRNRERRMMQMMQGRGGPG------------PSGA--HAPLLT 205
+ PP LR + + + Q R P P + H+ LL
Sbjct: 376 NLVVSGPPQSLYGLNLTLR-KAKAPSGLDQSR-IPFSERKLKFSNRFLPVASPFHSHLLV 433
Query: 206 G 206
Sbjct: 434 P 434
Score = 30.4 bits (68), Expect = 0.52
Identities = 24/127 (18%), Positives = 37/127 (29%), Gaps = 49/127 (38%)
Query: 2 AIQASIKN-QKPIVI---------FV-NVRKFTMAESSREAEEKPSSERTPDY------- 43
++ S+ N K +V+ +RK A S + P SER +
Sbjct: 365 QVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAK-APSGLDQSRIPFSERKLKFSNRFLPV 423
Query: 44 -----TKLLEYGLDK--------RIAGKLDD----IFKT--GKHL-------LSRGCDII 77
+ LL D ++ D ++ T G L R D I
Sbjct: 424 ASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCI 483
Query: 78 ----VDW 80
V W
Sbjct: 484 IRLPVKW 490
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 31.0 bits (70), Expect = 0.086
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 9/64 (14%)
Query: 109 EEKLKEAFEQYGRVERVK--RIKDY-------AFVHFEDRQEAITAMNELNGQTVAGSTL 159
E + KE E+YG+V + I F+ FE + AI A+ +LNG+ G +
Sbjct: 27 EVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV 86
Query: 160 EVSL 163
+
Sbjct: 87 KACF 90
>2y8n_A 4-hydroxyphenylacetate decarboxylase large subuni; lyase, radical
chemistry, metalloenzyme, iron-sulfur center; 1.75A
{Clostridium scatologenes} PDB: 2yaj_A*
Length = 897
Score = 29.3 bits (65), Expect = 1.4
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 40 TPDYTKLLEYGLDKRIAGKLDDI 62
+Y L+YG D I + I
Sbjct: 225 VINYYMPLQYGFDGIIKLCDEKI 247
>2p0v_A Hypothetical protein BT3781; alpha-beta protein, structural
genomics, PSI-2, protein structure initiative; 2.10A
{Bacteroides thetaiotaomicron vpi-5482} SCOP: a.102.1.8
Length = 489
Score = 28.8 bits (64), Expect = 1.4
Identities = 29/129 (22%), Positives = 46/129 (35%), Gaps = 32/129 (24%)
Query: 96 KVLYVRNLTQYCTE--EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQT 153
V L + CT +++++A ++Y K K YAF E++G
Sbjct: 294 TVNRKPALAKECTALADEVEKALKKYAVCNHPKYGKIYAF--------------EVDG-- 337
Query: 154 VAGSTLEVSLAKPPS--------DKKKKEEILRNRERRMMQ-----MMQGRGGPGPSGAH 200
G+ L + A PS D K + I +N + + +G G G G H
Sbjct: 338 -FGNQLLMDDANVPSLIALPYLGDVKVTDPIYQNTRKFVWSEDNPYFFKGSAGEGIGGPH 396
Query: 201 APLLTGPPM 209
PM
Sbjct: 397 IGYDMIWPM 405
>3qt9_A Putative uncharacterized protein CPE0426; alpha-alpha six fold,
glycoside hydrolase, mannosidase, HYDR; HET: YDR; 2.05A
{Clostridium perfringens} PDB: 3qt3_A* 2nvp_A
Length = 427
Score = 28.8 bits (64), Expect = 1.8
Identities = 21/123 (17%), Positives = 43/123 (34%), Gaps = 32/123 (26%)
Query: 102 NLTQYCTE--EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAGSTL 159
L + E++ A E++G+V + + YA+ E +G G+
Sbjct: 254 ELKEKADSLREEIDNAIEKHGKVYKEGFGEVYAY--------------ETDG---MGNYN 296
Query: 160 EVSLAKPPS--------DKKKKEEILRNRERRMMQ-----MMQGRGGPGPSGAHAPLLTG 206
+ A PS K ++E+ +N + ++ +G+ G H P
Sbjct: 297 FMDDANVPSLLSIPYLEYKGIEDEVYQNTRKFILSKNNRFFFEGKAAKGIGSPHTPDQYI 356
Query: 207 PPM 209
+
Sbjct: 357 WHI 359
>2f3o_A PFLD, PFL2, pyruvate formate-lyase 2; glycerol dehydratase, glycyl
R hyperthermophilic, unknown function; HET: PGE; 2.90A
{Archaeoglobus fulgidus}
Length = 776
Score = 28.4 bits (63), Expect = 2.7
Identities = 5/23 (21%), Positives = 7/23 (30%)
Query: 40 TPDYTKLLEYGLDKRIAGKLDDI 62
+Y LL G + I
Sbjct: 157 AVNYPYLLRRGFRWFLEESERRI 179
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 3cw1_A
Length = 231
Score = 27.7 bits (61), Expect = 2.9
Identities = 10/45 (22%), Positives = 13/45 (28%)
Query: 184 MMQMMQGRGGPGPSGAHAPLLTGPPMPRGSVPLQAALSSTRMGRG 228
Q+M +G + A A P MGRG
Sbjct: 138 SQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRG 182
>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP,
translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A
Length = 504
Score = 27.6 bits (62), Expect = 3.8
Identities = 6/39 (15%), Positives = 16/39 (41%)
Query: 182 RRMMQMMQGRGGPGPSGAHAPLLTGPPMPRGSVPLQAAL 220
+M++ M G G G + ++ M + + + +
Sbjct: 428 AQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMM 466
>3p2c_A Putative glycosyl hydrolase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-biology; HET: MSE PGE; 1.60A {Bacteroides ovatus}
PDB: 3on6_A*
Length = 463
Score = 27.6 bits (61), Expect = 4.1
Identities = 26/123 (21%), Positives = 44/123 (35%), Gaps = 32/123 (26%)
Query: 102 NLTQYCTE--EKLKEAFEQYGRVERVKRIKDYAFVHFEDRQEAITAMNELNGQTVAGSTL 159
L++ C + ++++ A ++Y K K YAF E++G G+
Sbjct: 282 ALSKECKDLAQEVETALKKYAVYNHPKYGKIYAF--------------EVDG---FGNHH 324
Query: 160 EVSLAKPPS--------DKKKKEEILRNRERRMMQ-----MMQGRGGPGPSGAHAPLLTG 206
+ A PS D + I +N R + +G+ G G G H
Sbjct: 325 LMDDANVPSLLAMPYLGDVNVNDPIYQNTRRFVWSEDNPYFFKGKAGEGIGGPHIGYDMV 384
Query: 207 PPM 209
PM
Sbjct: 385 WPM 387
>3ba1_A HPPR, hydroxyphenylpyruvate reductase; two domain protein,
substrate binding domain, cofactor bindi domain,
oxidoreductase; 1.47A {Solenostemon scutellarioides}
PDB: 3baz_A*
Length = 333
Score = 27.2 bits (61), Expect = 5.1
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 87 PDTETMSKVKVLYVRNLTQYCTEEKLKEAFE 117
P M + VL + ++ Y E++L + F+
Sbjct: 16 PRGSHMEAIGVLMMCPMSTY-LEQELDKRFK 45
>1r9d_A Glycerol dehydratase; radical SAM, lyase; 1.80A {Clostridium
butyricum} SCOP: c.7.1.1 PDB: 1r8w_A 1r9e_A
Length = 787
Score = 27.2 bits (60), Expect = 6.3
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 40 TPDYTKLLEYGLDKRIAGKLDDI 62
+ DY K+L G + I + +
Sbjct: 166 SVDYGKVLRVGFNGIINEAKEQL 188
>2w2k_A D-mandelate dehydrogenase; 2-hydroxyacid dehydrogenase,
oxidoreductase; 1.85A {Rhodotorula graminis} PDB:
2w2l_A* 2w2l_D* 2w2k_B
Length = 348
Score = 26.5 bits (59), Expect = 7.6
Identities = 5/28 (17%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 92 MSKVKVLYVRNLTQYCTE--EKLKEAFE 117
M + +VL + + ++ + ++ FE
Sbjct: 1 MPRPRVLLLGDPARHLDDLWSDFQQKFE 28
>3ic4_A Glutaredoxin (GRX-1); structural genomics, PSI, MCSG, protein
structure initiative, midwest center for structural
genomic oxidoreductase; 1.70A {Archaeoglobus fulgidus}
Length = 92
Score = 24.9 bits (55), Expect = 8.8
Identities = 12/69 (17%), Positives = 26/69 (37%), Gaps = 16/69 (23%)
Query: 90 ETMSKVKVLYVRNLTQYCTEEK--LKE---AFEQYGRVERVKRIKDYAFVHFEDRQEAIT 144
+ M++V + Y + +C LK FE + E+R++ I
Sbjct: 9 QGMAEVLM-YGLSTCPHCKRTLEFLKREGVDFEVI----------WIDKLEGEERKKVIE 57
Query: 145 AMNELNGQT 153
++ ++G
Sbjct: 58 KVHSISGSY 66
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 26.3 bits (58), Expect = 8.9
Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 12/67 (17%)
Query: 109 EEKLKEAFEQYGRVERVKRIKDYA------------FVHFEDRQEAITAMNELNGQTVAG 156
E ++ E ++G V RV ++ FV F E A+ LNG+ AG
Sbjct: 143 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG 202
Query: 157 STLEVSL 163
+ +
Sbjct: 203 RKVVAEV 209
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.315 0.132 0.374
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,561,056
Number of extensions: 219398
Number of successful extensions: 979
Number of sequences better than 10.0: 1
Number of HSP's gapped: 734
Number of HSP's successfully gapped: 236
Length of query: 230
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 140
Effective length of database: 4,188,903
Effective search space: 586446420
Effective search space used: 586446420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (25.3 bits)