RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3698
(534 letters)
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 66.9 bits (163), Expect = 9e-14
Identities = 26/103 (25%), Positives = 43/103 (41%), Gaps = 15/103 (14%)
Query: 19 SDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKVEWPQGTPESPTA-PKAISL------ 71
S S K+F+GG+P D E + F +FGP+ V+WP PK +
Sbjct: 3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE 62
Query: 72 ----DVISELVLILGQWATEGNL----CGRVEVVPWAISDSNY 106
+I + G+ + V++ PW +SDS++
Sbjct: 63 SSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIRPWNLSDSDF 105
Score = 50.7 bits (121), Expect = 4e-08
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 486 SDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRAEMSS 530
S S K+F+GG+P D E + F +FGP+ ++AE S
Sbjct: 3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKS 47
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 55.8 bits (135), Expect = 5e-09
Identities = 34/183 (18%), Positives = 66/183 (36%), Gaps = 43/183 (23%)
Query: 20 DEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV---KVEW------PQG-------TPESP 63
+ +++++G + ++ E + F+ FGP+ + W +G PE+
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA- 82
Query: 64 TAPKAI-SLDVISELVLILGQWATEGNLCGRVEVVPWAISDSNYSPQGHSTK--LEPGKT 120
A A+ ++ L GR V + P
Sbjct: 83 -AQLALEQMN---------SVM-----LGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNR 127
Query: 121 IFVGALHGRLTAQALYNVMNDLFGDVVYAGI----DTDKHKYPIGSGRITFGSTRAYSDA 176
I+V ++H L+ + +V FG + A + T KHK G G I + ++ DA
Sbjct: 128 IYVASVHQDLSDDDIKSVFEA-FGKIKSATLARDPTTGKHK---GYGFIEYEKAQSSQDA 183
Query: 177 IRA 179
+ +
Sbjct: 184 VSS 186
Score = 41.9 bits (99), Expect = 2e-04
Identities = 8/37 (21%), Positives = 22/37 (59%)
Query: 487 DEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+ +++++G + ++ E + F+ FGP+K++ M
Sbjct: 24 ALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM 60
Score = 38.8 bits (91), Expect = 0.002
Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 481 LRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
+ + N+I++ V D + + +VF FG +K A +
Sbjct: 115 IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLA 158
Score = 36.1 bits (84), Expect = 0.017
Identities = 8/38 (21%), Positives = 17/38 (44%)
Query: 14 LRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
+ + N+I++ V D + + +VF FG +
Sbjct: 115 IDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKI 152
Score = 28.4 bits (64), Expect = 4.5
Identities = 13/72 (18%), Positives = 24/72 (33%), Gaps = 8/72 (11%)
Query: 112 STKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGI----DTDKHKYPIGSGRITF 167
L ++VG+++ L + FG + + T KHK G + +
Sbjct: 22 QGALAIMSRVYVGSIYYELGEDTIRQAFAP-FGPIKSIDMSWDSVTMKHK---GFAFVEY 77
Query: 168 GSTRAYSDAIRA 179
A A+
Sbjct: 78 EVPEAAQLALEQ 89
>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain,
RNA-protein complex, nucleolus, structural protein/RNA
complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1
d.58.7.1 PDB: 1rkj_A 2krr_A
Length = 175
Score = 54.5 bits (132), Expect = 6e-09
Identities = 26/182 (14%), Positives = 46/182 (25%), Gaps = 47/182 (25%)
Query: 15 RTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK-----------------VEWPQ 57
+ S+ +FIG + + L S+ V++
Sbjct: 4 MVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFE- 62
Query: 58 GTPESPTAPKAISLDVISELVLILGQWATEGNLCGRVEVVPWAISDSNYSPQGHSTKLEP 117
+ E KA+ L G + G + + K+
Sbjct: 63 -SAED--LEKALELT---------GLK-----VFGNEIKLEKPKGRDS-------KKVRA 98
Query: 118 GKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTRAYSDAI 177
+T+ L +T L V D ++ K K G I F S +
Sbjct: 99 ARTLLAKNLSFNITEDELKEVFED-ALEIRLVS-QDGKSK---GIAYIEFKSEADAEKNL 153
Query: 178 RA 179
Sbjct: 154 EE 155
Score = 39.9 bits (94), Expect = 6e-04
Identities = 7/45 (15%), Positives = 16/45 (35%), Gaps = 1/45 (2%)
Query: 482 RTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV-VMNR 525
+ S+ +FIG + + L S+ + V++
Sbjct: 4 MVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV 48
Score = 35.7 bits (83), Expect = 0.016
Identities = 5/31 (16%), Positives = 12/31 (38%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
+ + + ++ E L VF ++ V
Sbjct: 99 ARTLLAKNLSFNITEDELKEVFEDALEIRLV 129
Score = 30.7 bits (70), Expect = 0.76
Identities = 9/71 (12%), Positives = 22/71 (30%), Gaps = 1/71 (1%)
Query: 107 SPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRIT 166
S ++ +F+G L+ + L +++ + + G +
Sbjct: 2 SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISE-LFAKNDLAVVDVRTGTNRKFGYVD 60
Query: 167 FGSTRAYSDAI 177
F S A+
Sbjct: 61 FESAEDLEKAL 71
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 50.0 bits (120), Expect = 4e-08
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+F+ G P L F FGPV +VVM++
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDK 42
Score = 44.2 bits (105), Expect = 5e-06
Identities = 9/27 (33%), Positives = 11/27 (40%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+ G P L F FGPV
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVA 36
>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 = 52.7 bits (127), Expect = 4e-08
Identities = 35/186 (18%), Positives = 58/186 (31%), Gaps = 40/186 (21%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGP-----VKVEWPQG-----------TPESPTAPKAI 69
K+FIGG+ ++T + L + F Q+G V + T E A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE--VDAAM 72
Query: 70 SLDVISELVLILGQWATEGNLCGR-VEVVPWAISDSNYSPQGHSTKLEPGKTIFVGALHG 128
+ + GR VE + + P H K IFVG +
Sbjct: 73 NAR--------------PHKVDGRVVEPKRAVSREDSQRPGAH----LTVKKIFVGGIKE 114
Query: 129 RLTAQALYNVMNDLFGDVVYAGIDTDKH-KYPIGSGRITFGSTRAYSDAIRAAFIEVKSG 187
L + +G + I TD+ G +TF + + + V
Sbjct: 115 DTEEHHLRDYFEQ-YGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGH 173
Query: 188 RI-CKK 192
+K
Sbjct: 174 NCEVRK 179
Score = 47.3 bits (113), Expect = 3e-06
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
KIF+GG+ DT E+ L F Q+G ++ + +
Sbjct: 104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEI 136
Score = 45.0 bits (107), Expect = 1e-05
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
KIF+GG+ DT E+ L F Q+G +
Sbjct: 104 VKKIFVGGIKEDTEEHHLRDYFEQYGKI 131
Score = 44.6 bits (106), Expect = 2e-05
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
K+FIGG+ ++T + L + F Q+G + VVM
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVM 46
>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 = 49.5 bits (119), Expect = 5e-08
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVMNR 525
S+ +F+G D E L FSQ+G V +
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP 40
Score = 45.3 bits (108), Expect = 2e-06
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
S+ +F+G D E L FSQ+G V
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDV 32
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 49.0 bits (118), Expect = 6e-08
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
KIF+GG+ +T + F QFG V A++M
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLM 32
Score = 45.2 bits (108), Expect = 1e-06
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
KIF+GG+ +T + F QFG V
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKV 26
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions,
RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus
musculus}
Length = 89
Score = 48.4 bits (116), Expect = 1e-07
Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 1/46 (2%)
Query: 481 LRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVMNR 525
+R +K+F+G D L F Q+G V +
Sbjct: 1 MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP 46
Score = 44.5 bits (106), Expect = 3e-06
Identities = 10/38 (26%), Positives = 15/38 (39%)
Query: 14 LRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
+R +K+F+G D L F Q+G V
Sbjct: 1 MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEV 38
>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 = 47.9 bits (115), Expect = 1e-07
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPV-KAVVM 523
KIF+GG+ DTPE + F FG V +
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELP 32
Score = 44.8 bits (107), Expect = 1e-06
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
KIF+GG+ DTPE + F FG V
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEV 26
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 48.2 bits (115), Expect = 2e-07
Identities = 9/44 (20%), Positives = 17/44 (38%)
Query: 482 RTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
R +++ + ++I G P D + G V + M R
Sbjct: 2 RWILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR 45
Score = 41.6 bits (98), Expect = 5e-05
Identities = 7/38 (18%), Positives = 14/38 (36%)
Query: 15 RTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
R +++ + ++I G P D + G V
Sbjct: 2 RWILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVL 39
Score = 30.5 bits (69), Expect = 0.37
Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 2/82 (2%)
Query: 119 KTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTRAYSDAIR 178
+++++ T + + D G V+ + HK GS + F S + +
Sbjct: 12 RSVYIKGFPTDATLDDIKEWLED-KGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 70
Query: 179 AAFIEVKSGRICKKLQIDPYLE 200
+ K + + D Y
Sbjct: 71 TPGQKYKETDLLILFKDD-YFA 91
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 46.7 bits (112), Expect = 4e-07
Identities = 16/32 (50%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
K+FIGG+ W T + L F QFG VK +VM
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVM 33
Score = 42.5 bits (101), Expect = 1e-05
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+FIGG+ W T + L F QFG V
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEV 27
>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 = 46.8 bits (112), Expect = 5e-07
Identities = 9/34 (26%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
N +F+GG+ E + + F+++G VK ++
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKII 42
Score = 44.5 bits (106), Expect = 4e-06
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
N +F+GG+ E + + F+++G VK
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVK 37
>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 = 48.9 bits (117), Expect = 7e-07
Identities = 28/185 (15%), Positives = 57/185 (30%), Gaps = 42/185 (22%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-VEWPQGTP-----------------ESP-T 64
+ ++++G +P+ E ++ F+ + + G P S
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 65 APKAISLDVISELVLILGQ-----WATEGNLCGRVEVVPWAISDSNYSPQGHSTKL-EPG 118
+A++ D I GQ + + + + S Y P ST + +
Sbjct: 64 TTQAMAFDGII----FQGQSLKIRRPHD-----YQPLPGMSENPSVYVPGVVSTVVPDSA 114
Query: 119 KTIFVGALHGRLTAQALYNVMNDLFGDVVYAGI----DTDKHKYPIGSGRITFGSTRAYS 174
+F+G L L + ++ FG + + T K G +
Sbjct: 115 HKLFIGGLPNYLNDDQVKELLTS-FGPLKAFNLVKDSATGLSK---GYAFCEYVDINVTD 170
Query: 175 DAIRA 179
AI
Sbjct: 171 QAIAG 175
Score = 41.2 bits (97), Expect = 3e-04
Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 2/63 (3%)
Query: 461 HHRSSANSQIPQKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKA 520
H + + T D ++K+FIGG+P + + + + FGP+KA
Sbjct: 86 HDYQPLPGMSENPSVYVPGVVSTVVPDS--AHKLFIGGLPNYLNDDQVKELLTSFGPLKA 143
Query: 521 VVM 523
+
Sbjct: 144 FNL 146
Score = 36.9 bits (86), Expect = 0.007
Identities = 4/37 (10%), Positives = 16/37 (43%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRAE 527
+ ++++G +P+ E ++ F+ + +
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN 40
>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 = 46.9 bits (112), Expect = 7e-07
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 12/67 (17%)
Query: 458 AARHHRSSANSQIPQKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGP 517
++ HH ++ +P+ + + + K+FIGG+ W T + L F QFG
Sbjct: 3 SSHHHHHHSSGLVPRGS-----HMGSSGC------KMFIGGLSWQTTQEGLREYFGQFGE 51
Query: 518 VK-AVVM 523
VK +VM
Sbjct: 52 VKECLVM 58
Score = 40.7 bits (96), Expect = 1e-04
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+FIGG+ W T + L F QFG V
Sbjct: 25 GCKMFIGGLSWQTTQEGLREYFGQFGEV 52
>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 = 48.3 bits (116), Expect = 8e-07
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+ KIF+GG+ D FSQ+G + +
Sbjct: 87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQL 119
Score = 47.5 bits (114), Expect = 1e-06
Identities = 40/190 (21%), Positives = 68/190 (35%), Gaps = 51/190 (26%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGP-----VKVEWPQG-----------TPESPTAPK 67
S K+FIGG+ WDT E L F ++G + + G P S +
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSS--VDE 60
Query: 68 AISLDVISELVLILGQWATEGNLCGRVEVVPWAISDSNYSPQGHSTKLEPGKTIFVGALH 127
+ T+ L G+V AI + + IFVG +
Sbjct: 61 VV---------------KTQHILDGKVIDPKRAIPRD---------EQDKTGKIFVGGIG 96
Query: 128 GRLTAQALYNVMNDLFGDVVYAGI----DTDKHKYPIGSGRITFGSTRAYSDAIRAAFIE 183
+ + + +G ++ A + DT + + G G +T+ S A + FI+
Sbjct: 97 PDVRPKEFEEFFSQ-WGTIIDAQLMLDKDTGQSR---GFGFVTYDSADAVDRVCQNKFID 152
Query: 184 VKSGRI-CKK 192
K +I K+
Sbjct: 153 FKDRKIEIKR 162
Score = 45.6 bits (109), Expect = 6e-06
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
S K+FIGG+ WDT E L F ++G V +M
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIM 36
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 46.1 bits (110), Expect = 1e-06
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
++ + + G+PW T E L FS FG V V
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVK 48
Score = 42.6 bits (101), Expect = 2e-05
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
++ + + G+PW T E L FS FG V
Sbjct: 15 TSDLIVLGLPWKTTEQDLKEYFSTFGEV 42
>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 = 45.6 bits (109), Expect = 1e-06
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
SNKIF+GG+P + E L F +FG V V++
Sbjct: 10 SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMI 43
Score = 42.6 bits (101), Expect = 2e-05
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
SNKIF+GG+P + E L F +FG V
Sbjct: 10 SNKIFVGGIPHNCGETELREYFKKFGVV 37
>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 = 48.5 bits (116), Expect = 2e-06
Identities = 27/168 (16%), Positives = 47/168 (27%), Gaps = 47/168 (27%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGPVK------------VEWPQGTPESPTAPKAI-SL 71
++F+G +P D E +F ++G + + A A L
Sbjct: 23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRL--ESRTL--AEIAKAEL 78
Query: 72 DVISELVLILGQWATEGNLCGRVEVVPWAISDSNYSPQGHSTKLEPGKTIFVGALHGRLT 131
D L R + +A G + V L ++
Sbjct: 79 DGTI--------------LKSRPLRIRFA---------------THGAALTVKNLSPVVS 109
Query: 132 AQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTRAYSDAIRA 179
+ L + FG V A + D G G + F + A+
Sbjct: 110 NELLEQAFSQ-FGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER 156
Score = 45.8 bits (109), Expect = 1e-05
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
++F+G +P D E +F ++G V +NR
Sbjct: 23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR 56
Score = 41.2 bits (97), Expect = 5e-04
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 480 PLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV-KAVVM 523
PLR +F+ + + + LL FSQFGPV KAVV+
Sbjct: 87 PLRIRFATH--GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVV 129
Score = 37.7 bits (88), Expect = 0.006
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 13 PLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
PLR +F+ + + + LL FSQFGPV
Sbjct: 87 PLRIRFATH--GAALTVKNLSPVVSNELLEQAFSQFGPV 123
>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 = 44.9 bits (107), Expect = 2e-06
Identities = 12/32 (37%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
K+F+GG+ WDT + L F++FG V +
Sbjct: 13 KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIK 44
Score = 41.0 bits (97), Expect = 5e-05
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+F+GG+ WDT + L F++FG V
Sbjct: 13 KMFVGGLSWDTSKKDLKDYFTKFGEV 38
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 45.3 bits (108), Expect = 2e-06
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 11/60 (18%)
Query: 484 QFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNRA---------EMSSDD 532
++S + +K+FI G+P+ + L + G VK + V NRA E ++
Sbjct: 10 RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENES 69
Score = 41.1 bits (97), Expect = 6e-05
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 17 QFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
++S + +K+FI G+P+ + L + G VK
Sbjct: 10 RYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVK 45
Score = 36.5 bits (85), Expect = 0.002
Identities = 17/78 (21%), Positives = 30/78 (38%), Gaps = 2/78 (2%)
Query: 102 SDSNYSPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIG 161
S + +ST LE K +F+ L T + L + G V + T++ P G
Sbjct: 2 SSGSSGVFRYSTSLEKHK-LFISGLPFSCTKEELEEICKA-HGTVKDLRLVTNRAGKPKG 59
Query: 162 SGRITFGSTRAYSDAIRA 179
+ + + S A+
Sbjct: 60 LAYVEYENESQASQAVMK 77
>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 = 45.4 bits (108), Expect = 3e-06
Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
KIF+GG+P+ T + L F FG ++ AVV+
Sbjct: 17 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVI 50
Score = 41.1 bits (97), Expect = 8e-05
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
KIF+GG+P+ T + L F FG +
Sbjct: 17 FTKIFVGGLPYHTTDASLRKYFEGFGDI 44
>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 = 46.5 bits (111), Expect = 3e-06
Identities = 20/179 (11%), Positives = 49/179 (27%), Gaps = 54/179 (30%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV--------------KVEWPQG-------TPES 62
+ ++++G +P+ E ++ F+ + ++ + + +
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 63 PTAPKAISLDVISELVLILGQWATEGNLCGRVEVVPWAISDSNYSPQGHSTKLEPGKTIF 122
+A++ D I G+ + L +F
Sbjct: 64 --TTQAMAFDGII--------------FQGQSLKIRRPHDYQP---------LPGAHKLF 98
Query: 123 VGALHGRLTAQALYNVMNDLFGDVVYAGI----DTDKHKYPIGSGRITFGSTRAYSDAI 177
+G L L + ++ FG + + T K G + AI
Sbjct: 99 IGGLPNYLNDDQVKELLTS-FGPLKAFNLVKDSATGLSK---GYAFCEYVDINVTDQAI 153
Score = 43.4 bits (103), Expect = 4e-05
Identities = 10/34 (29%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
++K+FIGG+P + + + + FGP+K ++
Sbjct: 94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLV 127
Score = 39.9 bits (94), Expect = 6e-04
Identities = 4/37 (10%), Positives = 16/37 (43%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRAE 527
+ ++++G +P+ E ++ F+ + +
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN 40
>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 = 45.3 bits (108), Expect = 3e-06
Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
K+FIGG+ ++T E L + Q+G + VVM
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVM 60
Score = 41.1 bits (97), Expect = 1e-04
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+FIGG+ ++T E L + Q+G +
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKL 54
>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 = 44.9 bits (107), Expect = 4e-06
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
K+F+GG+ W T + L + FSQ+G V V+M
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIM 49
Score = 40.7 bits (96), Expect = 1e-04
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+F+GG+ W T + L + FSQ+G V
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEV 43
>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 = 43.8 bits (104), Expect = 8e-06
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 12/54 (22%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK--AVVMNRA----------EMSSDD 532
K+F+GG+ +DT E L VFS++G + VV +R + D
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENID 65
Score = 41.8 bits (99), Expect = 4e-05
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+F+GG+ +DT E L VFS++G +
Sbjct: 12 EGKLFVGGLSFDTNEQSLEQVFSKYGQIS 40
>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex,
mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB:
2x1b_A 2x1a_A 2km8_B
Length = 96
Score = 43.4 bits (103), Expect = 9e-06
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
S +++G +P+D E +L + S GPV + M
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKM 34
Score = 42.2 bits (100), Expect = 2e-05
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S +++G +P+D E +L + S GPV
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVI 30
>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 = 43.4 bits (103), Expect = 1e-05
Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 12/54 (22%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNR----------AEMSSDD 532
+F+G +P++ E L +FS+ GPV + V +R E +
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61
Score = 41.1 bits (97), Expect = 6e-05
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+G +P++ E L +FS+ GPV
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVV 36
Score = 30.3 bits (69), Expect = 0.39
Identities = 12/70 (17%), Positives = 27/70 (38%), Gaps = 12/70 (17%)
Query: 116 EPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGR------ITFGS 169
+++FVG + T + L ++ ++ G VV + D+ +G+ +
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSE-VGPVVSFRLVYDRE-----TGKPKGYGFCEYQD 59
Query: 170 TRAYSDAIRA 179
A+R
Sbjct: 60 QETALSAMRN 69
>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 = 43.5 bits (103), Expect = 1e-05
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 486 SDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKA--VVMNR 525
SD +FI + +D+ E L V QFG +K VV++
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHP 51
Score = 41.9 bits (99), Expect = 4e-05
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 19 SDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
SD +FI + +D+ E L V QFG +K
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLK 43
Score = 41.9 bits (99), Expect = 4e-05
Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 2/75 (2%)
Query: 107 SPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKH-KYPIGSGRI 165
G + + GKT+F+ L +AL V+ FGD+ Y + ++ G
Sbjct: 4 GSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQ-FGDLKYVRVVLHPDTEHSKGCAFA 62
Query: 166 TFGSTRAYSDAIRAA 180
F + A + AA
Sbjct: 63 QFMTQEAAQKCLAAA 77
>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 = 43.4 bits (103), Expect = 1e-05
Identities = 11/68 (16%), Positives = 23/68 (33%), Gaps = 14/68 (20%)
Query: 458 AARHHRSSANSQIPQKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGP 517
R+ PQ++ EG +F+ + + E + F +G
Sbjct: 7 RVRNEDDDELEPGPQRSVEG--------------WILFVTSIHEEAQEDEIQEKFCDYGE 52
Query: 518 VKAVVMNR 525
+K + +N
Sbjct: 53 IKNIHLNL 60
Score = 40.4 bits (95), Expect = 2e-04
Identities = 5/29 (17%), Positives = 12/29 (41%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+ + + E + F +G +K
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIK 54
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 43.1 bits (102), Expect = 2e-05
Identities = 10/84 (11%), Positives = 29/84 (34%), Gaps = 17/84 (20%)
Query: 459 ARHHRSSANSQIPQKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 518
+ HH ++ +P+ + ++ ++ + +P+ + L +F QFG +
Sbjct: 4 SHHHHHHSSGLVPRGS-------HMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKI 56
Query: 519 KA--VVMNRA--------EMSSDD 532
++ N +
Sbjct: 57 LDVEIIFNERGSKGFGFVTFENSA 80
Score = 38.8 bits (91), Expect = 4e-04
Identities = 6/28 (21%), Positives = 14/28 (50%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
++ + +P+ + L +F QFG +
Sbjct: 29 PKRLHVSNIPFRFRDPDLRQMFGQFGKI 56
>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 = 42.1 bits (100), Expect = 2e-05
Identities = 6/33 (18%), Positives = 16/33 (48%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+++GG+ + + +L F FG + + +
Sbjct: 7 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 39
Score = 40.6 bits (96), Expect = 7e-05
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+++GG+ + + +L F FG +
Sbjct: 7 KRVLYVGGLAEEVDDKVLHAAFIPFGDIT 35
Score = 37.5 bits (88), Expect = 0.001
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 8/68 (11%)
Query: 116 EPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGI----DTDKHKYPIGSGRITFGSTR 171
+ ++VG L + + L+ FGD+ I +T+KH+ G + F
Sbjct: 5 TTKRVLYVGGLAEEVDDKVLHAAFIP-FGDITDIQIPLDYETEKHR---GFAFVEFELAE 60
Query: 172 AYSDAIRA 179
+ AI
Sbjct: 61 DAAAAIDN 68
>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 = 45.7 bits (109), Expect = 2e-05
Identities = 22/183 (12%), Positives = 48/183 (26%), Gaps = 39/183 (21%)
Query: 13 PLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV---KVEWPQGTPES------- 62
L Q + + +P + + FG + + + + T +S
Sbjct: 86 ELSVQLQPT--DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAE 143
Query: 63 ----PTAPKAI-SLDVISELVLILGQWATEGNLCGRVEVVPWAISDSNYSPQGHSTKLEP 117
+A +A L G+ L R V W + L
Sbjct: 144 YMKKDSAARAKSDLL---------GKP-----LGPRTLYVHWT------DAGQLTPALLH 183
Query: 118 GKTIFVGALHGRLT-AQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTRAYSDA 176
+ + V L AL ++ + + + G + + + +A
Sbjct: 184 SRCLCVDRLPPGFNDVDALCRALSA-VHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEA 242
Query: 177 IRA 179
+
Sbjct: 243 QQQ 245
Score = 36.9 bits (86), Expect = 0.012
Identities = 5/45 (11%), Positives = 14/45 (31%), Gaps = 3/45 (6%)
Query: 480 PLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
L Q + + +P + + FG ++ ++
Sbjct: 86 ELSVQLQPT--DALLCVANLPPSLTQQQFEELVRPFGSLERCFLV 128
Score = 33.4 bits (77), Expect = 0.15
Identities = 7/34 (20%), Positives = 11/34 (32%)
Query: 20 DEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
KI I G+P D + + S +
Sbjct: 18 QFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYC 51
Score = 33.0 bits (76), Expect = 0.19
Identities = 8/38 (21%), Positives = 12/38 (31%)
Query: 487 DEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMN 524
KI I G+P D + + S + V
Sbjct: 18 QFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDK 55
Score = 31.9 bits (73), Expect = 0.43
Identities = 6/56 (10%), Positives = 14/56 (25%), Gaps = 8/56 (14%)
Query: 480 PLRTQFSD-------EILSNKIFIGGVPWD-TPEYLLLTVFSQFGPVKAVVMNRAE 527
L ++D + S + + +P L S + +
Sbjct: 166 TLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ 221
>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 = 43.1 bits (102), Expect = 2e-05
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVMN 524
K+FIGG+ +T E +L VF + GP+ +++
Sbjct: 7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIK 41
Score = 40.4 bits (95), Expect = 2e-04
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
K+FIGG+ +T E +L VF + GP+
Sbjct: 7 PGKLFIGGLNRETNEKMLKAVFGKHGPI 34
Score = 30.0 bits (68), Expect = 0.61
Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 1/64 (1%)
Query: 116 EPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTRAYSD 175
+ +F+G L+ + L V G + + D+ G ITF + +
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGK-HGPISEVLLIKDRTSKSRGFAFITFENPADAKN 63
Query: 176 AIRA 179
A +
Sbjct: 64 AAKD 67
>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 = 42.1 bits (100), Expect = 2e-05
Identities = 8/39 (20%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNRAE 527
K+ IG + + + ++ +FS +G +K + + R
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMH 42
Score = 37.9 bits (89), Expect = 6e-04
Identities = 7/29 (24%), Positives = 16/29 (55%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+ IG + + + ++ +FS +G +K
Sbjct: 4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIK 32
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 42.2 bits (100), Expect = 3e-05
Identities = 8/35 (22%), Positives = 18/35 (51%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+F+ GV + E + F+++G +K + +N
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL 57
Score = 39.9 bits (94), Expect = 2e-04
Identities = 7/29 (24%), Positives = 15/29 (51%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+ GV + E + F+++G +K
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIK 51
>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 = 41.9 bits (99), Expect = 3e-05
Identities = 10/37 (27%), Positives = 16/37 (43%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKVEWPQGTP 60
+N IF+ G+ + + F Q G +K G P
Sbjct: 13 NNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQP 49
Score = 39.2 bits (92), Expect = 3e-04
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 519
+N IF+ G+ + + F Q G +K
Sbjct: 13 NNTIFVQGLGENVTIESVADYFKQIGIIK 41
>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 = 41.8 bits (99), Expect = 3e-05
Identities = 7/37 (18%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNR 525
+ +++ +P+ L +FS++G V V + ++
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDK 52
Score = 39.9 bits (94), Expect = 1e-04
Identities = 6/29 (20%), Positives = 15/29 (51%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ +++ +P+ L +FS++G V
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYGKVV 44
>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 = 41.4 bits (98), Expect = 4e-05
Identities = 6/33 (18%), Positives = 16/33 (48%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+++GG+ + + +L F FG + + +
Sbjct: 12 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 44
Score = 39.9 bits (94), Expect = 2e-04
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+++GG+ + + +L F FG +
Sbjct: 12 KRVLYVGGLAEEVDDKVLHAAFIPFGDIT 40
Score = 35.7 bits (83), Expect = 0.005
Identities = 17/76 (22%), Positives = 29/76 (38%), Gaps = 8/76 (10%)
Query: 108 PQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGI----DTDKHKYPIGSG 163
G S + ++VG L + + L+ FGD+ I +T+KH+ G
Sbjct: 2 SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIP-FGDITDIQIPLDYETEKHR---GFA 57
Query: 164 RITFGSTRAYSDAIRA 179
+ F + AI
Sbjct: 58 FVEFELAEDAAAAIDN 73
>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 = 41.4 bits (98), Expect = 4e-05
Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 12/52 (23%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKA--VVMNR----------AEMSSDD 532
I++G + + + +FSQFG V ++ +R EM +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES 54
Score = 37.5 bits (88), Expect = 9e-04
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
I++G + + + +FSQFG V
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVF 29
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA
binding protein-RNA complex; 1.85A {Homo sapiens} PDB:
3nna_A 3nnc_A 2dhs_A 3nnh_A
Length = 175
Score = 43.0 bits (102), Expect = 5e-05
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
K+F+G VP E L +F Q+G V + + R
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLR 37
Score = 42.6 bits (101), Expect = 8e-05
Identities = 33/172 (19%), Positives = 58/172 (33%), Gaps = 39/172 (22%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK-----------VEWPQG-------TPESPTAPK 67
K+F+G VP E L +F Q+G V +G T ++ A +
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA--ALE 62
Query: 68 AISLDVISELVLILGQWATEGNLCGRVEVVPWAISDSNYSPQGHSTKLEPGKTIFVGALH 127
A + + + + L G + +DS + KL F+G +
Sbjct: 63 AQ--NALHNMKV----------LPGMHHPIQMKPADSEKNNAVEDRKL------FIGMIS 104
Query: 128 GRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTRAYSDAIRA 179
+ T + + + FG + I G +TF + AI+A
Sbjct: 105 KKCTENDIRVMFSS-FGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 155
Score = 34.9 bits (81), Expect = 0.027
Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 472 QKTWEGVL-PLRTQFSDE-----ILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
K G+ P++ + +D + K+FIG + E + +FS FG ++ ++
Sbjct: 70 MKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRIL 128
Score = 34.5 bits (80), Expect = 0.043
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 6/53 (11%)
Query: 5 QKTWEGVL-PLRTQFSDE-----ILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
K G+ P++ + +D + K+FIG + E + +FS FG +
Sbjct: 70 MKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122
>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 = 40.9 bits (97), Expect = 5e-05
Identities = 7/34 (20%), Positives = 13/34 (38%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
+ +F+G + + + L F F VM
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVM 34
Score = 39.0 bits (92), Expect = 2e-04
Identities = 5/29 (17%), Positives = 11/29 (37%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ +F+G + + + L F F
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYL 29
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 42.5 bits (100), Expect = 5e-05
Identities = 6/33 (18%), Positives = 16/33 (48%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+++GG+ + + +L F FG + + +
Sbjct: 63 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQI 95
Score = 40.5 bits (95), Expect = 2e-04
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+++GG+ + + +L F FG +
Sbjct: 63 KRVLYVGGLAEEVDDKVLHAAFIPFGDIT 91
>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 = 41.1 bits (97), Expect = 5e-05
Identities = 7/35 (20%), Positives = 19/35 (54%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+ ++++GG+ +T L F +FG ++ + +
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVK 51
Score = 40.3 bits (95), Expect = 1e-04
Identities = 8/36 (22%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV-KVEWPQG 58
+ ++++GG+ +T L F +FG + ++ +G
Sbjct: 17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG 52
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 41.3 bits (97), Expect = 6e-05
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
S + I G+ E L+ +FGP+ VV+
Sbjct: 21 SPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP 55
Score = 36.7 bits (85), Expect = 0.003
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S + I G+ E L+ +FGP+
Sbjct: 21 SPVVHIRGLIDGVVEADLVEALQEFGPIS 49
>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 = 42.5 bits (100), Expect = 6e-05
Identities = 6/35 (17%), Positives = 15/35 (42%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+F+ + + E + F +G +K + +N
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL 106
Score = 39.8 bits (93), Expect = 7e-04
Identities = 5/29 (17%), Positives = 12/29 (41%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+ + + E + F +G +K
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEIK 100
>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 = 41.0 bits (97), Expect = 6e-05
Identities = 8/54 (14%), Positives = 22/54 (40%), Gaps = 12/54 (22%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKA--VVMNRA----------EMSSDD 532
S+ +++G + ++ E +L +F FG + ++ + S +
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSE 58
Score = 39.1 bits (92), Expect = 3e-04
Identities = 7/29 (24%), Positives = 17/29 (58%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S+ +++G + ++ E +L +F FG +
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKID 33
>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 = 41.4 bits (97), Expect = 7e-05
Identities = 14/68 (20%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 458 AARHHRSSANSQIPQKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGP 517
++ HH ++ +P+ + + S + S I I +P D E ++++ FG
Sbjct: 3 SSHHHHHHSSGLVPRGS-----HMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGK 57
Query: 518 VKAVVMNR 525
V ++M +
Sbjct: 58 VTNLLMLK 65
Score = 34.1 bits (78), Expect = 0.030
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S I I +P D E ++++ FG V
Sbjct: 31 SRVIHIRKLPIDVTEGEVISLGLPFGKVT 59
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 41.3 bits (97), Expect = 7e-05
Identities = 9/47 (19%), Positives = 19/47 (40%), Gaps = 6/47 (12%)
Query: 487 DEILSNKIFIGGVPWDTPEYL------LLTVFSQFGPVKAVVMNRAE 527
+ + + I + VP P+ L + +FS+FG + +
Sbjct: 11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEED 57
Score = 37.8 bits (88), Expect = 0.001
Identities = 10/50 (20%), Positives = 23/50 (46%), Gaps = 7/50 (14%)
Query: 20 DEILSNKIFIGGVPWDTPEYL------LLTVFSQFGPVK-VEWPQGTPES 62
+ + + I + VP P+ L + +FS+FG + +P+ ++
Sbjct: 11 ADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT 60
>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 = 41.6 bits (98), Expect = 7e-05
Identities = 8/35 (22%), Positives = 18/35 (51%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+F+ GV + E + F+++G +K + +N
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL 56
Score = 38.9 bits (91), Expect = 6e-04
Identities = 7/29 (24%), Positives = 15/29 (51%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+ GV + E + F+++G +K
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIK 50
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 41.1 bits (97), Expect = 7e-05
Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 459 ARHHRSSANSQIPQKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 518
+ HH ++ +P+ + + + E+ + ++F+ P D E L +F FGP+
Sbjct: 4 SHHHHHHSSGLVPRGS-----HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPM 58
Query: 519 KAV-VMN 524
K V ++N
Sbjct: 59 KEVKILN 65
Score = 35.0 bits (81), Expect = 0.012
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 13 PLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ + E+ + ++F+ P D E L +F FGP+K
Sbjct: 20 HMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMK 59
>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 = 40.8 bits (96), Expect = 8e-05
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK--AVVMNRA 526
+ K+FIG +P + E L +F +FG + V+ +R
Sbjct: 13 AIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF 50
Score = 40.8 bits (96), Expect = 1e-04
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
+ K+FIG +P + E L +F +FG +
Sbjct: 13 AIKLFIGQIPRNLDEKDLKPLFEEFGKI 40
>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP
domain, MIF4G domain, RNA maturation, RNA export,
nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP:
d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B
3fey_B 1h6k_X
Length = 156
Score = 42.1 bits (99), Expect = 9e-05
Identities = 9/33 (27%), Positives = 20/33 (60%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
S +++G + + T E + +FS+ G +K ++M
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIM 71
Score = 38.2 bits (89), Expect = 0.002
Identities = 8/29 (27%), Positives = 17/29 (58%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S +++G + + T E + +FS+ G +K
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIK 67
>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 = 40.7 bits (96), Expect = 1e-04
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+++GG+ E LL +F Q GPV M
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHM 47
Score = 38.8 bits (91), Expect = 5e-04
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+++GG+ E LL +F Q GPV
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVV 43
Score = 32.2 bits (74), Expect = 0.093
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 8/74 (10%)
Query: 110 GHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGI----DTDKHKYPIGSGRI 165
G ++ T++VG L +++ L+ + G VV + T +H+ G G +
Sbjct: 7 GPISERNQDATVYVGGLDEKVSEPLLWELFLQ-AGPVVNTHMPKDRVTGQHQ---GYGFV 62
Query: 166 TFGSTRAYSDAIRA 179
F S AI+
Sbjct: 63 EFLSEEDADYAIKI 76
>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 = 40.3 bits (95), Expect = 1e-04
Identities = 10/37 (27%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK--AVVMNR 525
+ + + G+ T E L VFS++GP+ ++V ++
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ 51
Score = 39.1 bits (92), Expect = 3e-04
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ + + G+ T E L VFS++GP+
Sbjct: 15 NCCLGVFGLSLYTTERDLREVFSKYGPIA 43
>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 = 40.7 bits (96), Expect = 1e-04
Identities = 7/52 (13%), Positives = 18/52 (34%), Gaps = 10/52 (19%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKA--VVMNRA--------EMSSDD 532
++ + +P+ + L +F QFG + ++ N +
Sbjct: 15 PKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSA 66
Score = 38.4 bits (90), Expect = 6e-04
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
++ + +P+ + L +F QFG +
Sbjct: 15 PKRLHVSNIPFRFRDPDLRQMFGQFGKIL 43
>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 = 40.4 bits (95), Expect = 1e-04
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
++KI + +P+ + + +FS FG +K V
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTV 45
Score = 38.4 bits (90), Expect = 6e-04
Identities = 8/29 (27%), Positives = 17/29 (58%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
++KI + +P+ + + +FS FG +K
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELK 43
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 40.5 bits (95), Expect = 1e-04
Identities = 11/41 (26%), Positives = 17/41 (41%)
Query: 20 DEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKVEWPQGTP 60
D +N IF+ G+ + + F Q G +K G P
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQP 43
Score = 38.1 bits (89), Expect = 0.001
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 487 DEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 519
D +N IF+ G+ + + F Q G +K
Sbjct: 3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIK 35
>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 = 40.0 bits (94), Expect = 1e-04
Identities = 7/30 (23%), Positives = 13/30 (43%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
S + + + + E L VF + +KV
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFIKV 44
Score = 38.4 bits (90), Expect = 5e-04
Identities = 6/29 (20%), Positives = 12/29 (41%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 519
S + + + + E L VF + +K
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFIK 43
Score = 34.2 bits (79), Expect = 0.016
Identities = 16/74 (21%), Positives = 24/74 (32%), Gaps = 4/74 (5%)
Query: 107 SPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRIT 166
G+ST KT+ + L T + L V + K K G I
Sbjct: 4 GSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEK-ATFIKVPQNQNGKSK---GYAFIE 59
Query: 167 FGSTRAYSDAIRAA 180
F S +A+ +
Sbjct: 60 FASFEDAKEALNSC 73
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 40.2 bits (94), Expect = 1e-04
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
S I I +P D E ++++ FG V ++M +
Sbjct: 16 SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLK 50
Score = 35.2 bits (81), Expect = 0.009
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S I I +P D E ++++ FG V
Sbjct: 16 SRVIHIRKLPIDVTEGEVISLGLPFGKVT 44
Score = 27.5 bits (61), Expect = 4.0
Identities = 9/51 (17%), Positives = 18/51 (35%), Gaps = 1/51 (1%)
Query: 107 SPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHK 157
H P + I + L +T + ++ FG V + K++
Sbjct: 5 HHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLP-FGKVTNLLMLKGKNQ 54
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 39.6 bits (93), Expect = 2e-04
Identities = 5/31 (16%), Positives = 12/31 (38%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKVE 54
+ I + + T ++T S + + V
Sbjct: 9 MDTIILRNIAPHTVVDSIMTALSPYASLAVN 39
Score = 38.1 bits (89), Expect = 6e-04
Identities = 5/35 (14%), Positives = 13/35 (37%), Gaps = 2/35 (5%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFG--PVKAVVM 523
+ I + + T ++T S + V + +
Sbjct: 9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRL 43
Score = 28.8 bits (65), Expect = 1.3
Identities = 10/73 (13%), Positives = 22/73 (30%), Gaps = 5/73 (6%)
Query: 110 GHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFG--DVVYAGIDTDKH-KYPIGSGRIT 166
GH TI + + ++ ++ + V + DK + G +
Sbjct: 2 GHHHH-HHMDTIILRNIAPHTVVDSIMTALSP-YASLAVNNIRLIKDKQTQQNRGFAFVQ 59
Query: 167 FGSTRAYSDAIRA 179
S S ++
Sbjct: 60 LSSAMDASQLLQI 72
>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 = 39.5 bits (93), Expect = 2e-04
Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 4/46 (8%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRA----EMSSDD 532
S K+ +G + L F ++GPV + + M +
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAE 55
Score = 37.2 bits (87), Expect = 0.001
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S K+ +G + L F ++GPV
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVI 38
>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 = 43.5 bits (102), Expect = 2e-04
Identities = 59/317 (18%), Positives = 99/317 (31%), Gaps = 130/317 (41%)
Query: 53 VEW---PQGTPESP---TAPKAISLDVISELVLILGQWATEGNLCGRVEVVPWAISDSNY 106
+EW P TP+ + P IS +I V+ L + L G +
Sbjct: 216 LEWLENPSNTPDKDYLLSIP--ISCPLIG--VIQLAHYVVTAKLLG-------------F 258
Query: 107 SPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRIT 166
+P + L+ G T L +TA A+ A D+ + +
Sbjct: 259 TPGELRSYLK-GATGHSQGL---VTAVAI-------------AETDSWE----------S 291
Query: 167 FGSTRAYSDAIRAAF-IEVKSGRICKKLQIDP--YLEDNVCSECQTHSGPYFCREGICYR 223
F + AI F I V+ + P L ++ + ++ EG+
Sbjct: 292 F--FVSVRKAITVLFFIGVRC------YEAYPNTSLPPSILEDSLENN------EGV--- 334
Query: 224 YFCRSCWLKV----------HIGEYSQHDP------I-VRNVRKS-----PPSS------ 255
S L + ++ + + H P I + N K+ PP S
Sbjct: 335 ---PSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNL 391
Query: 256 -------PSG------PHSGGLTLNTLNGFSSREDITTSS--ATSSPWFDSPLLTPMTPQ 300
PSG P FS R+ ++ +SP F S LL P +
Sbjct: 392 TLRKAKAPSGLDQSRIP------------FSERKLKFSNRFLPVASP-FHSHLLVPASDL 438
Query: 301 IVRSPFESNSYAIHGSS 317
I + N+ + +
Sbjct: 439 INKD-LVKNNVSFNAKD 454
Score = 38.1 bits (88), Expect = 0.008
Identities = 89/538 (16%), Positives = 139/538 (25%), Gaps = 227/538 (42%)
Query: 110 GH-STKLEPGKTIFVGALHGRLTAQALYNVMND-----LFG-DV--VYAGIDTDKHKYPI 160
G+ S+ +EP K VG Q L + + L G D+ + A + + +
Sbjct: 66 GYVSSLVEPSK---VGQ-----FDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLV 117
Query: 161 GSGRITFGSTRAYSDAIRAA------------FIEVKSGRICKKL------Q--IDPYLE 200
+ + + Y A A F V G +L Q D Y E
Sbjct: 118 KTKELI----KNYITARIMAKRPFDKKSNSALFRAVGEGNA--QLVAIFGGQGNTDDYFE 171
Query: 201 DNVCSECQT--HSGPYFCREGI----------------CYRYFCRSC----WLKVHIGEY 238
E + + + I + F + WL
Sbjct: 172 -----ELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWL------- 219
Query: 239 SQHDPIVRNVRKSPP-----SSP-SGP--------------HSGGLT----LNTLNGFSS 274
N +P S P S P G T + L G +
Sbjct: 220 -------ENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATG 272
Query: 275 R-EDITTSS--ATSSPWFDSPLLTPMTPQIVRSPFESNSY-AIHGSSHSPPFGSHSME-- 328
+ + T+ A + W +S F + AI G E
Sbjct: 273 HSQGLVTAVAIAETDSW-ES--------------FFVSVRKAITVLFFI---GVRCYEAY 314
Query: 329 --SCSPPYLTDEGDYSPYYQTGGSTDYFSYNNAPSH-LNLNG-------SMTDSSNLDNI 378
+ PP + ++ PS L+++ + +N
Sbjct: 315 PNTSLPPSILED------SLENN-------EGVPSPMLSISNLTQEQVQDYVNKTNSHLP 361
Query: 379 EDLLASLSLNNTGQSNVRANGTAGS------------VPS-------PHTS--------- 410
+SL N ++ V + G S PS P +
Sbjct: 362 AGKQVEISLVNGAKNLVVS-GPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF 420
Query: 411 -PLNSPRSSGARHSPPSNGGYYGGGGGGQYLHNGDGGGQGGLQSTLDIAARHHRSSANS- 468
P+ SP HS L + D+ + +A
Sbjct: 421 LPVASP-----FHSH--------------LL----VPASDLINK--DLVKNNVSFNAKDI 455
Query: 469 QIPQK-TWEGVLPLRTQFSDEILSN---KIFIGGVPWDTPEYLLLTVFSQ-----FGP 517
QIP T++G LR S I I V W+T T F FGP
Sbjct: 456 QIPVYDTFDGS-DLRV-LSGSISERIVDCIIRLPVKWET-----TTQFKATHILDFGP 506
Score = 37.3 bits (86), Expect = 0.016
Identities = 35/206 (16%), Positives = 69/206 (33%), Gaps = 80/206 (38%)
Query: 20 DEILSNKIFIGGVPWDTPEYLL-LTVFSQFGPVKVEWPQGTPESPTAPKAISLDVISELV 78
+E ++ F + LL T F+Q P A++L +
Sbjct: 1711 NEHSTSYTFRS------EKGLLSATQFTQ--P-----------------ALTL--ME--K 1741
Query: 79 LILGQWATEGNLCGRVEVVPWAISDSNYSPQGHSTKLEPGKTIFVG---ALHGRLTAQAL 135
++G ++P +D+ ++ GHS +G A L + A
Sbjct: 1742 AAFEDLKSKG-------LIP---ADATFA--GHS----------LGEYAA----LASLA- 1774
Query: 136 YNVMNDLFGD---VVYA-GIDTDKHKYPIGS-GRITFGSTRAYSDAIRAAFIEVKSGRIC 190
+VM+ VV+ G+ T + P GR +G + A+F + +
Sbjct: 1775 -DVMS--IESLVEVVFYRGM-TMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVV 1830
Query: 191 KKL--QIDPYLE---DN------VCS 205
+++ + +E N V +
Sbjct: 1831 ERVGKRTGWLVEIVNYNVENQQYVAA 1856
Score = 32.3 bits (73), Expect = 0.45
Identities = 29/191 (15%), Positives = 53/191 (27%), Gaps = 57/191 (29%)
Query: 376 DNIEDLLASLSLNNTG---------QSNVRANGTAG-SVPSPHTSPLNSPRSSGARHSPP 425
++I L A L N ++ + A A S L R
Sbjct: 99 NDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSAL-------FRAVGE 151
Query: 426 SNGGYYGGGGGGQYLHNGDGGGQGGLQSTLD-IAARHHRSSAN-SQIPQKTWEGVLPLRT 483
N + GGQG + + + + + + E + L
Sbjct: 152 GNAQLVA-----IF------GGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIR 200
Query: 484 QFSDEILSNKIFIGGVP---W-----DTP--EYLL----------LTVFSQFGPVKAVVM 523
D + K+F G+ W +TP +YLL + + + V
Sbjct: 201 TTLD---AEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHY----VVTA 253
Query: 524 NRAEMSSDDVR 534
+ ++R
Sbjct: 254 KLLGFTPGELR 264
Score = 29.2 bits (65), Expect = 4.1
Identities = 20/110 (18%), Positives = 38/110 (34%), Gaps = 37/110 (33%)
Query: 421 RHSPPSNGGYYGGGGGGQYLHNGDGGGQGGLQSTLDIAARHHRSSANSQIPQKTWEGVLP 480
++P + ++GG G + R + ++ I + +G L
Sbjct: 1666 INNPVNLTIHFGGEKG-----------------------KRIRENYSAMIFETIVDGKLK 1702
Query: 481 LRTQFS--DEILSNKIFIGGVPWDTPEYLL-LTVFSQFGPVKA-VVMNRA 526
F +E ++ F + LL T F+Q P A +M +A
Sbjct: 1703 TEKIFKEINEHSTSYTFRS------EKGLLSATQFTQ--P--ALTLMEKA 1742
>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 = 39.8 bits (93), Expect = 2e-04
Identities = 8/35 (22%), Positives = 15/35 (42%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
S + + G+ E L+ +FG + V+M
Sbjct: 15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP 49
Score = 34.8 bits (80), Expect = 0.014
Identities = 6/29 (20%), Positives = 12/29 (41%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S + + G+ E L+ +FG +
Sbjct: 15 SPVVHVRGLCESVVEADLVEALEKFGTIC 43
Score = 27.8 bits (62), Expect = 3.5
Identities = 9/48 (18%), Positives = 15/48 (31%), Gaps = 1/48 (2%)
Query: 109 QGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKH 156
G K+ + V L + L + FG + Y + K
Sbjct: 6 SGSHHKVSVSPVVHVRGLCESVVEADLVEALEK-FGTICYVMMMPFKR 52
>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 = 39.8 bits (93), Expect = 2e-04
Identities = 6/31 (19%), Positives = 15/31 (48%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKVE 54
+ ++FIGG+P +L ++ ++
Sbjct: 8 NCRLFIGGIPKMKKREEILEEIAKVTEGVLD 38
Score = 39.8 bits (93), Expect = 2e-04
Identities = 8/36 (22%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGP-VKAVVMNR 525
+ ++FIGG+P +L ++ V V++
Sbjct: 8 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYA 43
>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 = 39.1 bits (92), Expect = 2e-04
Identities = 10/46 (21%), Positives = 18/46 (39%), Gaps = 4/46 (8%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRA----EMSSDD 532
+ KIF+G V L ++F + G V + + M +
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEA 54
Score = 36.8 bits (86), Expect = 0.002
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ KIF+G V L ++F + G V
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVI 37
>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 = 40.5 bits (95), Expect = 3e-04
Identities = 14/87 (16%), Positives = 37/87 (42%), Gaps = 13/87 (14%)
Query: 458 AARHHRSSANSQIPQKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGP 517
+ +++ Q+ Q+ + + P + ++L N + + +P E L +F ++GP
Sbjct: 10 YDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRN-LMVNYIPTTVDEVQLRQLFERYGP 68
Query: 518 VKA--VVMNRA----------EMSSDD 532
+++ +V +R + S
Sbjct: 69 IESVKIVCDRETRQSRGYGFVKFQSGS 95
Score = 36.6 bits (85), Expect = 0.005
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ + +P E L +F ++GP++
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIE 70
>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 = 39.0 bits (92), Expect = 3e-04
Identities = 11/57 (19%), Positives = 19/57 (33%), Gaps = 12/57 (21%)
Query: 488 EILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNRA----------EMSSDD 532
E + I++G V + L F G V V + ++ E S +
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 59
Score = 35.6 bits (83), Expect = 0.005
Identities = 8/32 (25%), Positives = 12/32 (37%)
Query: 21 EILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
E + I++G V + L F G V
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVN 34
Score = 32.1 bits (74), Expect = 0.074
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 2/63 (3%)
Query: 116 EPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKH-KYPIGSGRITFGSTRAYS 174
++I+VG + TA+ L + G V I DK +P G I F +
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHG-CGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 175 DAI 177
++
Sbjct: 63 TSL 65
>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 = 39.2 bits (92), Expect = 3e-04
Identities = 8/35 (22%), Positives = 20/35 (57%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+++F+G +P D E + +F ++G V +++
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK 49
Score = 34.9 bits (81), Expect = 0.008
Identities = 7/28 (25%), Positives = 16/28 (57%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
+++F+G +P D E + +F ++G
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKA 42
>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 = 39.6 bits (93), Expect = 3e-04
Identities = 8/54 (14%), Positives = 24/54 (44%), Gaps = 12/54 (22%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKA--VVMNRA----------EMSSDD 532
++++G + ++ E +L +F FG +++ ++M+ S +
Sbjct: 26 PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSE 79
Score = 37.3 bits (87), Expect = 0.002
Identities = 6/29 (20%), Positives = 17/29 (58%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
++++G + ++ E +L +F FG ++
Sbjct: 26 PMRLYVGSLHFNITEDMLRGIFEPFGRIE 54
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 39.1 bits (92), Expect = 3e-04
Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 2/68 (2%)
Query: 112 STKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTR 171
S+ IFV L T + L + N+ G V+YA I + K G G + F S
Sbjct: 2 SSGSSGACQIFVRNLPFDFTWKMLKDKFNE-CGHVLYADIKMENGK-SKGCGVVKFESPE 59
Query: 172 AYSDAIRA 179
A R
Sbjct: 60 VAERACRM 67
Score = 34.5 bits (80), Expect = 0.011
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 16/61 (26%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV---KVEWPQG-----------TPESPTAPKAI 69
+ +IF+ +P+D +L F++ G V ++ G +PE A +A
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEV--AERAC 65
Query: 70 S 70
Sbjct: 66 R 66
Score = 34.1 bits (79), Expect = 0.015
Identities = 8/28 (28%), Positives = 16/28 (57%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 518
+ +IF+ +P+D +L F++ G V
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHV 35
>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 = 39.1 bits (92), Expect = 3e-04
Identities = 8/33 (24%), Positives = 18/33 (54%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
S ++F+ + + + E L +FS +GP+ +
Sbjct: 8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHY 40
Score = 37.6 bits (88), Expect = 0.001
Identities = 8/29 (27%), Positives = 17/29 (58%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S ++F+ + + + E L +FS +GP+
Sbjct: 8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLS 36
>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 = 39.3 bits (92), Expect = 4e-04
Identities = 11/65 (16%), Positives = 24/65 (36%), Gaps = 12/65 (18%)
Query: 480 PLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNRA----------E 527
PL + EI +++G V + + L FS G + + + ++ E
Sbjct: 25 PLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIE 84
Query: 528 MSSDD 532
+ +
Sbjct: 85 FAERN 89
Score = 36.6 bits (85), Expect = 0.003
Identities = 10/40 (25%), Positives = 17/40 (42%)
Query: 13 PLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
PL + EI +++G V + + L FS G +
Sbjct: 25 PLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSIN 64
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 38.9 bits (91), Expect = 4e-04
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 9/88 (10%)
Query: 117 PGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGI----DTDKHKYPIGSGRITFGSTRA 172
P K + L+ + L ++ +G+V I T KH G R+ F STR
Sbjct: 5 PLKEVTFARLNDNVRETFLKDMCRK-YGEVEEVEILLHPRTRKHL---GLARVLFTSTRG 60
Query: 173 YSDAIRAAFIEVKSGRICKKLQIDPYLE 200
+ ++ + G I Q+D +
Sbjct: 61 AKETVKNLHLTSVMGNII-HAQLDIKGQ 87
Score = 36.2 bits (84), Expect = 0.004
Identities = 5/35 (14%), Positives = 14/35 (40%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
++ + + E L + ++G V+ V +
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILL 40
Score = 34.3 bits (79), Expect = 0.022
Identities = 4/29 (13%), Positives = 12/29 (41%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
++ + + E L + ++G V+
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVE 34
>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 = 40.2 bits (95), Expect = 4e-04
Identities = 4/35 (11%), Positives = 15/35 (42%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+ + +P + + ++F G +++ + R
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVR 36
Score = 38.7 bits (91), Expect = 0.001
Identities = 3/29 (10%), Positives = 12/29 (41%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ + +P + + ++F G ++
Sbjct: 2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIE 30
Score = 34.1 bits (79), Expect = 0.050
Identities = 11/57 (19%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 13 PLRTQFSD----EILSNKIFIGGVPWDTPEYLLLTVFSQFGPV---KVEWPQGTPES 62
++ ++ I +++ G+P + L +FSQ+G + ++ Q T S
Sbjct: 73 TIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVS 129
Score = 33.7 bits (78), Expect = 0.075
Identities = 8/43 (18%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 480 PLRTQFSD----EILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 518
++ ++ I +++ G+P + L +FSQ+G +
Sbjct: 73 TIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRI 115
>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 = 38.4 bits (90), Expect = 5e-04
Identities = 9/33 (27%), Positives = 16/33 (48%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+F+G + E +L +F Q GP+ V +
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTI 48
Score = 36.5 bits (85), Expect = 0.002
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+G + E +L +F Q GP+
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLT 44
Score = 36.5 bits (85), Expect = 0.003
Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 1/76 (1%)
Query: 104 SNYSPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSG 163
S+ S + E +T+FVG L R+ + LY + G + I D+ P G
Sbjct: 2 SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQ-AGPLTKVTICKDREGKPKSFG 60
Query: 164 RITFGSTRAYSDAIRA 179
+ F + S AI
Sbjct: 61 FVCFKHPESVSYAIAL 76
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 40.2 bits (94), Expect = 5e-04
Identities = 14/114 (12%), Positives = 30/114 (26%), Gaps = 23/114 (20%)
Query: 414 SPRSSGARHSPPSNGGYYGGGGGGQYLHNGDGGGQGGLQSTLDIAARHHRSSANSQIPQK 473
+ R P N GG + A +
Sbjct: 32 NQRRVNRGGGPRRNRPAIARGGRNRP------------------APYSRPKPLPDKWQHD 73
Query: 474 TWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK--AVVMNR 525
++ K+ + + + + + +F++FG +K AV +R
Sbjct: 74 LFDSGCGGGEGVET---GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR 124
Score = 34.8 bits (80), Expect = 0.031
Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 4/73 (5%)
Query: 107 SPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRIT 166
S G +E G + V L ++ + + + FG + A +D D+ +G+ +
Sbjct: 77 SGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAE-FGTLKKAAVDYDRSGRSLGTADVH 135
Query: 167 FGSTRAYSDAIRA 179
F +DA++A
Sbjct: 136 FERR---ADALKA 145
Score = 33.7 bits (77), Expect = 0.075
Identities = 5/29 (17%), Positives = 15/29 (51%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+ + + + + + +F++FG +K
Sbjct: 88 GAKLLVSNLDFGVSDADIQELFAEFGTLK 116
>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 = 38.4 bits (90), Expect = 5e-04
Identities = 7/33 (21%), Positives = 14/33 (42%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+ + + + T L VF ++G V V +
Sbjct: 13 MITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYI 45
Score = 37.2 bits (87), Expect = 0.001
Identities = 6/29 (20%), Positives = 12/29 (41%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ + + + T L VF ++G V
Sbjct: 13 MITLKVDNLTYRTSPDSLRRVFEKYGRVG 41
>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 = 38.8 bits (91), Expect = 5e-04
Identities = 24/126 (19%), Positives = 36/126 (28%), Gaps = 32/126 (25%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV---KVEWPQG-----------TPESPTAPKAI 69
S IFI + L FS FG + KV + T E+ A +AI
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA--AERAI 62
Query: 70 S-LDVISELVLILGQWATEGNLCGRVEVVPWAISDSNYSPQGHSTKLEPGKTIFVGALHG 128
++ G L R V S + + E +++
Sbjct: 63 EKMN---------GML-----LNDRKVFVGRFKSRKEREAELGARAKE-FTNVYIKNFGP 107
Query: 129 RLTAQA 134
T A
Sbjct: 108 GSTRAA 113
Score = 36.1 bits (84), Expect = 0.005
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKA--VVMNR 525
S IFI + L FS FG + + VV +
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE 41
>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 = 38.9 bits (91), Expect = 6e-04
Identities = 10/37 (27%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKA--VVMNR 525
+ + + G+ T E L VFS++GP+ +V ++
Sbjct: 46 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQ 82
Score = 37.8 bits (88), Expect = 0.001
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ + + G+ T E L VFS++GP+
Sbjct: 46 NCCLGVFGLSLYTTERDLREVFSKYGPIA 74
>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 = 37.9 bits (89), Expect = 6e-04
Identities = 6/34 (17%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPV-KAVVM 523
S+ ++I G+ T + L+ + +G + +
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAI 38
Score = 37.5 bits (88), Expect = 7e-04
Identities = 6/28 (21%), Positives = 15/28 (53%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
S+ ++I G+ T + L+ + +G +
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKI 32
>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 = 37.9 bits (89), Expect = 6e-04
Identities = 7/34 (20%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPV-KAVVM 523
+F+G + + + F+ FG + A V+
Sbjct: 6 HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVV 39
Score = 36.4 bits (85), Expect = 0.002
Identities = 5/29 (17%), Positives = 12/29 (41%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+G + + + F+ FG +
Sbjct: 6 HFHVFVGDLSPEITTAAIAAAFAPFGRIS 34
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 39.5 bits (92), Expect = 7e-04
Identities = 15/107 (14%), Positives = 29/107 (27%), Gaps = 15/107 (14%)
Query: 441 HNGDGGGQGGLQSTLDIAARHHRSSANSQIPQKTWEGVLPLRTQFSDEI-LSNKIFIGGV 499
H+ G L + + K + +S +++G
Sbjct: 4 HHHHSSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSF 63
Query: 500 PWDTPEYLLLTVFSQFGPVK----AVVMNRA----------EMSSDD 532
W T + L+ V G NRA ++S++
Sbjct: 64 SWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASEN 110
Score = 37.2 bits (86), Expect = 0.004
Identities = 7/30 (23%), Positives = 12/30 (40%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
+++G W T + L+ V G V
Sbjct: 55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDV 84
>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 = 38.0 bits (89), Expect = 8e-04
Identities = 5/31 (16%), Positives = 12/31 (38%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
+ + + ++ E L VF ++ V
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFEDALEIRLV 46
Score = 37.2 bits (87), Expect = 0.001
Identities = 4/30 (13%), Positives = 12/30 (40%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
+ + + ++ E L VF +++
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFEDALEIRL 45
Score = 32.6 bits (75), Expect = 0.059
Identities = 14/68 (20%), Positives = 21/68 (30%), Gaps = 5/68 (7%)
Query: 112 STKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTR 171
S K+ +T+ L +T L V D ++ K K G I F S
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFED-ALEIRLVS-QDGKSK---GIAYIEFKSEA 64
Query: 172 AYSDAIRA 179
+
Sbjct: 65 DAEKNLEE 72
>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 = 38.2 bits (89), Expect = 8e-04
Identities = 10/41 (24%), Positives = 18/41 (43%)
Query: 20 DEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKVEWPQGTP 60
++ ++ I++ G+ L F Q G VK+ G P
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQP 51
Score = 35.8 bits (83), Expect = 0.007
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 487 DEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 519
++ ++ I++ G+ L F Q G VK
Sbjct: 11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVK 43
>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 = 38.0 bits (89), Expect = 8e-04
Identities = 8/37 (21%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV--VMNR 525
+ I + + DT E L +F FG + + ++
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDK 51
Score = 36.4 bits (85), Expect = 0.003
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ I + + DT E L +F FG +
Sbjct: 15 NATIRVTNLSEDTRETDLQELFRPFGSIS 43
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 41.2 bits (96), Expect = 9e-04
Identities = 36/196 (18%), Positives = 66/196 (33%), Gaps = 14/196 (7%)
Query: 241 HDPIVRNVRKSPPSSPSGPHSGGLT-LNTLNGFSSREDITTSSATSSPWFDSPLLTPMTP 299
+ +V+ + + + GG+T + +G + + SP DS M
Sbjct: 1447 EESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAM-- 1504
Query: 300 QIVRSPFESNSYAIHGSSHSPPFGSHSMESCSPPYLTDEGDYSPY--YQTGGSTDY--FS 355
+ + + PFG++ SP + +SP + S Y S
Sbjct: 1505 ----AGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTS 1560
Query: 356 YNNAPSHLNLN-GSMTDSSNLDNIEDLLASLSLNNTGQSNVRANGTAGSVPSPHTSPLNS 414
+ +P+ + + S + S + S S + S + + S TSP S
Sbjct: 1561 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1620
Query: 415 PRSSGARHSPPSNGGY 430
P S +SP S
Sbjct: 1621 PTSP--SYSPTSPSYS 1634
Score = 38.2 bits (88), Expect = 0.008
Identities = 39/178 (21%), Positives = 59/178 (33%), Gaps = 7/178 (3%)
Query: 253 PSSPSGPHSGGLTLNTLNGFSSREDITTSSATSSPWFDSPLLTPMTPQIVRSPFESNSYA 312
P SG + T G + + T+ SP +P SP S +Y+
Sbjct: 1494 PLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGF--SPT-SPTYS 1550
Query: 313 IHGSSHSPPFGSHSMESCSPPYLTDEGDYSPYYQTGGSTDYFSYNNAPSHLNLNGSMTDS 372
++SP S+S S P Y YSP + T +PS+ S + S
Sbjct: 1551 PTSPAYSPTSPSYSPTS--PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP--TSPSYS 1606
Query: 373 SNLDNIEDLLASLSLNNTGQSNVRANGTAGSVPSPHTSPLNSPRSSGARHSPPSNGGY 430
+ S S + S + + S TSP SP S + P+
Sbjct: 1607 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPT 1664
Score = 30.4 bits (68), Expect = 2.0
Identities = 25/123 (20%), Positives = 43/123 (34%), Gaps = 11/123 (8%)
Query: 251 SPPSSPSGPHSGGLTLNTLNGFSSREDITTSSATSSPWFD--SPLLTPMTPQIVRSPFES 308
SP SP+ P + + S + S + +SP + SP +P +P +
Sbjct: 1574 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1633
Query: 309 NSYAIHGSSHSPPFG---------SHSMESCSPPYLTDEGDYSPYYQTGGSTDYFSYNNA 359
+ + S SP + S + SP Y YSP + T +
Sbjct: 1634 SPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1693
Query: 360 PSH 362
P++
Sbjct: 1694 PNY 1696
Score = 29.3 bits (65), Expect = 4.1
Identities = 24/126 (19%), Positives = 36/126 (28%), Gaps = 16/126 (12%)
Query: 321 PFGSHSMESCSPPYLTDEGDYSPYYQTGGSTDYFSYNNAPSHLNLNGSMTDSSNLDNIED 380
P+ + S + + DE +SP +G + G T D E
Sbjct: 1472 PYSNESGLVNADLDVKDELMFSPLVDSGSNDAM------------AGGFTAYGGADYGEA 1519
Query: 381 LLASLSLNNTGQSNVRANGTAGSVP-SPH---TSPLNSPRSSGARHSPPSNGGYYGGGGG 436
+ S + G P SP TSP SP S + PS
Sbjct: 1520 TSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSP 1579
Query: 437 GQYLHN 442
++
Sbjct: 1580 TSPSYS 1585
>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 = 37.3 bits (87), Expect = 9e-04
Identities = 8/33 (24%), Positives = 17/33 (51%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+++GG+ E L F QFG ++ + + +
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ 46
Score = 33.4 bits (77), Expect = 0.022
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+++GG+ E L F QFG ++
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIR 40
>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 = 37.6 bits (88), Expect = 9e-04
Identities = 10/54 (18%), Positives = 16/54 (29%), Gaps = 14/54 (25%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVK----AVVMNRA----------EMSSDD 532
++IG + W T + L G NRA + S+
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEA 56
Score = 35.6 bits (83), Expect = 0.004
Identities = 6/29 (20%), Positives = 11/29 (37%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVKVE 54
++IG + W T + L G +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDIL 31
>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 = 37.5 bits (87), Expect = 0.001
Identities = 8/35 (22%), Positives = 17/35 (48%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
S + I +P + E ++ + FG V ++M +
Sbjct: 15 SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLK 49
Score = 32.5 bits (74), Expect = 0.067
Identities = 7/29 (24%), Positives = 13/29 (44%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S + I +P + E ++ + FG V
Sbjct: 15 SRVLHIRKLPGEVTETEVIALGLPFGKVT 43
>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 = 40.0 bits (94), Expect = 0.001
Identities = 16/165 (9%), Positives = 43/165 (26%), Gaps = 42/165 (25%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVKVEWPQGTPESPTAPKAISLDVISELVLILGQWAT 86
+ + +P + + F GP+ +DV
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPII-----------------HVDVADS---------L 77
Query: 87 EGNLC-GRV-----EVVPWAISDSNYSPQGHSTKLEPGK--TIFVGALHGRLTAQALYNV 138
+ N R+ + AI+ ++ + + T+++ T + + ++
Sbjct: 78 KKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDL 137
Query: 139 MNDLFGDVVYAGI----DTDKHKYPIGSGRITFGSTRAYSDAIRA 179
+ D V + + + I S +
Sbjct: 138 LQD-INVVALSIRLPSLRFNTSR---RFAYIDVTSKEDARYCVEK 178
Score = 39.6 bits (93), Expect = 0.002
Identities = 5/37 (13%), Positives = 14/37 (37%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRAEMSS 530
+ + +P + + F GP+ V + + +
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN 80
Score = 36.5 bits (85), Expect = 0.017
Identities = 18/112 (16%), Positives = 34/112 (30%), Gaps = 12/112 (10%)
Query: 95 EVVPWAISDSNYSPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGI--D 152
E P A ++ T+ T+ V L +Y G +++ +
Sbjct: 18 EGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKH-CGPIIHVDVADS 76
Query: 153 TDKHKYPIGSGRITFGSTRAYSDAIRAAFIEVKSGRIC-KKLQIDPYLEDNV 203
K+ RI F Y A+ A I + ++ + E +
Sbjct: 77 LKKNF---RFARIEFAR---YDGALAA--ITKTHKVVGQNEIIVSHLTECTL 120
Score = 34.2 bits (79), Expect = 0.084
Identities = 20/174 (11%), Positives = 45/174 (25%), Gaps = 39/174 (22%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK--VEWP-------QG-------TPESPTAPK 67
+++ P + + + V + P + + E A
Sbjct: 117 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKED--ARY 174
Query: 68 AI-SLDVISELVLILGQWATEGNLCGRVEVVPWAISDSNYSPQGHSTKLEPGKTIFVGAL 126
+ L+ G + G V + + + + G+ I + L
Sbjct: 175 CVEKLN---------GLK-----IEGYTLVTKVS--NPLEKSKRTDSATLEGREIMIRNL 218
Query: 127 HGRLT-AQALYNVMNDLFGDVVYAGI--DTDKHKYPIGSGRITFGSTRAYSDAI 177
L L FG + I +H + + F + + A+
Sbjct: 219 STELLDENLLRESFEG-FGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 271
Score = 33.8 bits (78), Expect = 0.11
Identities = 2/34 (5%), Positives = 11/34 (32%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
+++ P + + + V ++ +
Sbjct: 117 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRL 150
Score = 30.7 bits (70), Expect = 1.00
Identities = 8/32 (25%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 493 KIFIGGVPWD-TPEYLLLTVFSQFGPVKAVVM 523
+I I + + E LL F FG ++ + +
Sbjct: 212 EIMIRNLSTELLDENLLRESFEGFGSIEKINI 243
>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 = 37.6 bits (88), Expect = 0.001
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 483 TQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
D+ +++G + D E L+L +FSQ GP K+ M
Sbjct: 7 GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKM 47
Score = 35.3 bits (82), Expect = 0.007
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 16 TQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
D+ +++G + D E L+L +FSQ GP K
Sbjct: 7 GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCK 43
>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 = 40.6 bits (94), Expect = 0.001
Identities = 63/458 (13%), Positives = 117/458 (25%), Gaps = 132/458 (28%)
Query: 114 KLEPGKTIFVGALHGR-------LTAQAL--YNVMNDLFGDV------------------ 146
+L P K + + G + Y V + +
Sbjct: 146 ELRPAKNVLI---DGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEML 202
Query: 147 --VYAGIDTDKHKYPIGSGRITFGSTRAYSDAIRAAFIEVKSGRICKKLQIDPYLEDNVC 204
+ ID + S I + +R ++ K C L + L NV
Sbjct: 203 QKLLYQIDPNWTSRSDHSSNIKL-RIHSIQAELRR-LLKSKPYENC--LLV---L-LNVQ 254
Query: 205 SECQTHSGPYFCREGICYRYFCRSCWLKVHI--GEYSQHDPIVRNVRKSPPSSPSGPHSG 262
+ + F SC K+ + D + HS
Sbjct: 255 N-----------AKAW--NAFNLSC--KILLTTRFKQVTDFLSAATTTHISLDH---HSM 296
Query: 263 GLTL-NTLNGFSSREDITTSS----ATSSPWFDSPLLTPMTPQIVRSPFESNSYAIHGSS 317
LT + D ++ +P + + +R + H
Sbjct: 297 TLTPDEVKSLLLKYLDCRPQDLPREVLTT----NPRRLSIIAESIRDGLATWDNWKH--V 350
Query: 318 HSPPFGSHSMESCSPPYLT--DEGDYSPYYQTGGSTDY--FSYN-NAPSH-LNLNGSMTD 371
+ + +ES L + +Y + F + + P+ L+L
Sbjct: 351 NCDKL-TTIIESS----LNVLEPAEYRKMFD-----RLSVFPPSAHIPTILLSLIWFDVI 400
Query: 372 SSNLDNIEDLLASLSL----NNTGQSNV-----RANGTAGSVPSPHTSPLNS---PRSSG 419
S++ + + L SL ++ + + H S ++ P++
Sbjct: 401 KSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFD 460
Query: 420 ARH-SPPSNGGYYGGGGGGQYLHNGDGGGQGGLQSTLDIAARHHRSSANSQIPQKTWEGV 478
+ PP Y+ Y H G HH + E +
Sbjct: 461 SDDLIPPYLDQYF-------YSHIG-----------------HHLKNIEHP------ERM 490
Query: 479 LPLRTQFSD-EILSNKIFIGGVPWDTPEYLLLTVFSQF 515
R F D L KI W+ +L Q
Sbjct: 491 TLFRMVFLDFRFLEQKIRHDSTAWNASGS-ILNTLQQL 527
>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 = 37.7 bits (88), Expect = 0.001
Identities = 9/42 (21%), Positives = 15/42 (35%)
Query: 480 PLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
P+ +E + +F + L FS G V+ V
Sbjct: 14 PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDV 55
Score = 36.1 bits (84), Expect = 0.005
Identities = 8/40 (20%), Positives = 14/40 (35%)
Query: 13 PLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
P+ +E + +F + L FS G V+
Sbjct: 14 PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVR 53
Score = 32.3 bits (74), Expect = 0.10
Identities = 16/82 (19%), Positives = 29/82 (35%), Gaps = 12/82 (14%)
Query: 102 SDSNYSPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIG 161
S S + +T+F L R+ + L + + G V I +D++
Sbjct: 9 SPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSA-VGKVRDVRIISDRN----- 62
Query: 162 SGR------ITFGSTRAYSDAI 177
S R + F ++ AI
Sbjct: 63 SRRSKGIAYVEFCEIQSVPLAI 84
>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 = 38.3 bits (89), Expect = 0.001
Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 14/83 (16%)
Query: 457 IAARHHRSSANSQIPQKTWEGVLPLRTQFSDEI--------------LSNKIFIGGVPWD 502
A + + AN W +T E L K+++G + +
Sbjct: 25 TAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNN 84
Query: 503 TPEYLLLTVFSQFGPVKAVVMNR 525
+ L F +GP+++V + R
Sbjct: 85 GNKTELERAFGYYGPLRSVWVAR 107
Score = 34.9 bits (80), Expect = 0.026
Identities = 7/30 (23%), Positives = 16/30 (53%)
Query: 23 LSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
L K+++G + + + L F +GP++
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLR 101
>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 = 38.7 bits (90), Expect = 0.001
Identities = 7/31 (22%), Positives = 13/31 (41%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
+ + + + T L VF ++G V V
Sbjct: 70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV 100
Score = 37.5 bits (87), Expect = 0.003
Identities = 6/29 (20%), Positives = 12/29 (41%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ + + + T L VF ++G V
Sbjct: 70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVG 98
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 38.2 bits (89), Expect = 0.001
Identities = 7/31 (22%), Positives = 13/31 (41%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
+ + + + T L VF ++G V V
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDV 77
Score = 37.0 bits (86), Expect = 0.003
Identities = 6/29 (20%), Positives = 12/29 (41%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ + + + T L VF ++G V
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVG 75
>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 = 36.8 bits (86), Expect = 0.002
Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRA----EMSSDD 532
K+FIG +P + E + ++F Q+G V + + +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKT 53
Score = 34.5 bits (80), Expect = 0.012
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+FIG +P + E + ++F Q+G V
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVL 36
>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 = 36.9 bits (86), Expect = 0.002
Identities = 6/34 (17%), Positives = 12/34 (35%), Gaps = 1/34 (2%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVMNR 525
+FIG + + L S+ V++
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV 52
Score = 33.8 bits (78), Expect = 0.026
Identities = 5/28 (17%), Positives = 9/28 (32%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
+FIG + + L S+
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKND 46
>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 = 37.9 bits (89), Expect = 0.002
Identities = 28/176 (15%), Positives = 55/176 (31%), Gaps = 53/176 (30%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK-----------------VEWPQGTPESPTAPKAI 69
+++G + E +L F GP+ VE+ A A+
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEY--HQSHD--ANIAL 58
Query: 70 SLDVISELVLILGQWATEGNLCGRVEVVPWAISDSNYSPQGHSTKLEPGKTIFVGALHGR 129
L E N+ ++ N++ Q + + +FVG L+
Sbjct: 59 Q---------TLNGKQIENNIV-KI----------NWAFQSQQSSSDDTFNLFVGDLNVN 98
Query: 130 LTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGR------ITFGSTRAYSDAIRA 179
+ + L N D F + + D +G ++F S +A+ +
Sbjct: 99 VDDETLRNAFKD-FPSYLSGHVMWDMQ-----TGSSRGYGFVSFTSQDDAQNAMDS 148
Score = 34.4 bits (80), Expect = 0.040
Identities = 6/32 (18%), Positives = 14/32 (43%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+++G + E +L F GP+ + +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMI 34
Score = 32.9 bits (76), Expect = 0.12
Identities = 12/74 (16%), Positives = 28/74 (37%), Gaps = 3/74 (4%)
Query: 119 KTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGSTRAYSDAIR 178
+ ++VG L +T L G + I DK+ + + + + + A++
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQV-GGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ 59
Query: 179 A-AFIEVKSGRICK 191
+++ I K
Sbjct: 60 TLNGKQIE-NNIVK 72
Score = 32.9 bits (76), Expect = 0.13
Identities = 7/34 (20%), Positives = 13/34 (38%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
+ +F+G + + + L F F VM
Sbjct: 87 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVM 120
Score = 32.5 bits (75), Expect = 0.15
Identities = 5/29 (17%), Positives = 11/29 (37%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ +F+G + + + L F F
Sbjct: 87 TFNLFVGDLNVNVDDETLRNAFKDFPSYL 115
>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 = 36.8 bits (86), Expect = 0.002
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
S+ +FI + + T E L VFS+ G +K +
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTIS 38
Score = 34.5 bits (80), Expect = 0.011
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S+ +FI + + T E L VFS+ G +K
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIK 33
>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 = 37.9 bits (89), Expect = 0.002
Identities = 7/33 (21%), Positives = 14/33 (42%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+ + +P D + L +F GP+ + R
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMR 37
Score = 36.4 bits (85), Expect = 0.009
Identities = 6/27 (22%), Positives = 12/27 (44%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ + +P D + L +F GP+
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPIN 31
Score = 31.8 bits (73), Expect = 0.27
Identities = 7/47 (14%), Positives = 19/47 (40%), Gaps = 3/47 (6%)
Query: 19 SDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV---KVEWPQGTPES 62
+ I +++ +P + L T+F ++G + + + T
Sbjct: 84 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP 130
Score = 31.8 bits (73), Expect = 0.28
Identities = 6/39 (15%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 486 SDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
+ I +++ +P + L T+F ++G + ++
Sbjct: 84 GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 122
>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 = 38.4 bits (90), Expect = 0.002
Identities = 33/170 (19%), Positives = 60/170 (35%), Gaps = 42/170 (24%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPV---KVEWPQGTPES-----------PTAPKAISLD 72
+++G + D E +L FS GP+ +V T S A +A+
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD-- 75
Query: 73 VISELVLIL-GQWATEGNLCGRVEVVPWAISDSNYSPQGHSTKLEPGKTIFVGALHGRLT 131
+ + G+ + W+ D + G IF+ L +
Sbjct: 76 -------TMNFDV-----IKGKPVRIMWSQRDPSLRKSGVGN-------IFIKNLDKSID 116
Query: 132 AQALYNVMNDLFGDVVYAGI--DTDKHKYPIGSGRITFGSTRAYSDAIRA 179
+ALY+ + FG+++ + D + K G G + F + A AI
Sbjct: 117 NKALYDTFSA-FGNILSCKVVCDENGSK---GYGFVHFETQEAAERAIEK 162
Score = 34.6 bits (80), Expect = 0.044
Identities = 9/32 (28%), Positives = 18/32 (56%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+++G + D E +L FS GP+ ++ + R
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCR 49
Score = 33.8 bits (78), Expect = 0.076
Identities = 11/49 (22%), Positives = 15/49 (30%), Gaps = 3/49 (6%)
Query: 15 RTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV---KVEWPQGTP 60
R + IFI + L FS FG + KV +
Sbjct: 94 RDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS 142
Score = 32.6 bits (75), Expect = 0.22
Identities = 9/38 (23%), Positives = 12/38 (31%)
Query: 482 RTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 519
R + IFI + L FS FG +
Sbjct: 94 RDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNIL 131
>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 = 36.9 bits (86), Expect = 0.002
Identities = 7/32 (21%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
+F+G + + + F+ FG + A V+
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVV 48
Score = 35.8 bits (83), Expect = 0.006
Identities = 5/27 (18%), Positives = 12/27 (44%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+G + + + F+ FG +
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRIS 43
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 36.1 bits (84), Expect = 0.003
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
K+++G + + L FS +GP++ V + R
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIAR 34
Score = 33.4 bits (77), Expect = 0.035
Identities = 7/27 (25%), Positives = 15/27 (55%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+++G + + L FS +GP++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLR 28
>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 = 36.1 bits (84), Expect = 0.004
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+F+ + E +L FSQFG ++ V +
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK 45
Score = 33.8 bits (78), Expect = 0.027
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+ + E +L FSQFG ++
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLE 39
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 35.4 bits (82), Expect = 0.004
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 6/45 (13%)
Query: 492 NKIFIGGVPWDTPEYL------LLTVFSQFGPVKAVVMNRAEMSS 530
+ I + VP P+ L + +FS+FG + + +
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT 46
Score = 33.1 bits (76), Expect = 0.032
Identities = 10/45 (22%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 25 NKIFIGGVPWDTPEYL------LLTVFSQFGPVK-VEWPQGTPES 62
+ I + VP P+ L + +FS+FG + +P+ ++
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT 46
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 35.7 bits (83), Expect = 0.005
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+IG +P E L+ +F FG +
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYP 61
Score = 33.1 bits (76), Expect = 0.043
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 27 IFIGGVPWDTPEYLLLTVFSQFGPVK 52
+IG +P E L+ +F FG +
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFIL 55
>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 = 35.6 bits (83), Expect = 0.005
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK--AVVMN 524
S+ IFIG + + E LL FS FG + +M
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMR 40
Score = 34.9 bits (81), Expect = 0.009
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
S+ IFIG + + E LL FS FG +
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVI 32
>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 = 35.7 bits (83), Expect = 0.005
Identities = 7/34 (20%), Positives = 12/34 (35%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
NK++IG + L +F A +
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL 42
Score = 34.9 bits (81), Expect = 0.008
Identities = 6/27 (22%), Positives = 10/27 (37%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGPV 51
NK++IG + L +F
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLP 35
>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 = 35.7 bits (83), Expect = 0.006
Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 11/52 (21%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRA----------EMSSDD 532
S +F+ G+ DT E L F + +V +R + +S++
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFDGSVRAR-IVTDRETGSSKGFGFVDFNSEE 65
Score = 34.2 bits (79), Expect = 0.019
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
S +F+ G+ DT E L F ++
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFDGSVRARI 44
Score = 34.2 bits (79), Expect = 0.021
Identities = 20/79 (25%), Positives = 29/79 (36%), Gaps = 15/79 (18%)
Query: 107 SPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGR-- 164
G + + +P KT+FV L T + L + F V A I TD+ +G
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEETLK----ESFDGSVRARIVTDRE-----TGSSK 54
Query: 165 ----ITFGSTRAYSDAIRA 179
+ F S A A
Sbjct: 55 GFGFVDFNSEEDAKAAKEA 73
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 35.1 bits (81), Expect = 0.007
Identities = 7/33 (21%), Positives = 15/33 (45%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
K+ I +P +L ++ Q+G V++
Sbjct: 15 IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ 47
Score = 34.3 bits (79), Expect = 0.015
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+ I +P +L ++ Q+G V+
Sbjct: 15 IRKLQIRNIPPHLQWEVLDSLLVQYGVVE 43
>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 = 35.4 bits (82), Expect = 0.008
Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 5/62 (8%)
Query: 464 SSANSQIPQKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
S ++ Q +E V+ + ++ GG+ + L+ FS FG + + +
Sbjct: 3 SGSSGNTKQLRFEDVVN-----QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV 57
Query: 524 NR 525
Sbjct: 58 FP 59
Score = 31.9 bits (73), Expect = 0.13
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
+ ++ GG+ + L+ FS FG +
Sbjct: 25 NCTVYCGGIASGLTDQLMRQTFSPFGQI 52
>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 = 35.0 bits (81), Expect = 0.009
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 1/39 (2%)
Query: 486 SDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV-VM 523
S K+F+G + E +L +F FG + V+
Sbjct: 10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVL 48
Score = 35.0 bits (81), Expect = 0.011
Identities = 9/34 (26%), Positives = 15/34 (44%)
Query: 19 SDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
S K+F+G + E +L +F FG +
Sbjct: 10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVID 43
>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 = 35.4 bits (82), Expect = 0.010
Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 5/82 (6%)
Query: 98 PWAISDSNYSPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHK 157
W + G E G + V L ++ + + + FG + A +D D+
Sbjct: 16 KWQHDLFDSGCGGGEGV-ETGAKLLVSNLDFGVSDADIQELFAE-FGTLKKAAVDYDRSG 73
Query: 158 YPIGSGRITFGSTRAYSDAIRA 179
+G+ + F +DA++A
Sbjct: 74 RSLGTADVHFERR---ADALKA 92
Score = 34.7 bits (80), Expect = 0.016
Identities = 9/41 (21%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK--AVVMNRAEMS 529
K+ + + + + + +F++FG +K AV +R+ S
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS 75
Score = 33.1 bits (76), Expect = 0.066
Identities = 5/29 (17%), Positives = 15/29 (51%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+ + + + + + +F++FG +K
Sbjct: 35 GAKLLVSNLDFGVSDADIQELFAEFGTLK 63
>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 = 35.0 bits (81), Expect = 0.012
Identities = 7/33 (21%), Positives = 18/33 (54%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+I++G +P D + VF ++G ++ + +
Sbjct: 22 DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL 54
Score = 33.1 bits (76), Expect = 0.057
Identities = 7/29 (24%), Positives = 16/29 (55%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+I++G +P D + VF ++G ++
Sbjct: 22 DCRIYVGNLPPDIRTKDIEDVFYKYGAIR 50
>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 = 34.7 bits (80), Expect = 0.014
Identities = 5/33 (15%), Positives = 18/33 (54%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+ ++I +P+ + +F ++GP++ + +
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV 40
Score = 33.1 bits (76), Expect = 0.052
Identities = 5/29 (17%), Positives = 16/29 (55%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ ++I +P+ + +F ++GP++
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIR 36
>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 = 36.7 bits (84), Expect = 0.016
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+F+ V +DT E L F +GP+K + M
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136
Score = 34.1 bits (77), Expect = 0.11
Identities = 21/144 (14%), Positives = 38/144 (26%), Gaps = 14/144 (9%)
Query: 116 EPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKH-KYPIGSGRITFGSTRAYS 174
+ KT+FV ++ T L +G + + K P G I + R
Sbjct: 100 DAFKTLFVARVNYDTTESKLRREFEV-YGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMH 158
Query: 175 DAIRAAFIEVKSGRICKKLQIDPYLEDNVCSECQTHSGPYFCREGICYRYFCRSCWLKVH 234
A + A +ID + + + + +
Sbjct: 159 SAYKHA----------DGKKIDGR--RVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADV 206
Query: 235 IGEYSQHDPIVRNVRKSPPSSPSG 258
+S D R + PS
Sbjct: 207 NIRHSGRDDTSRYDERPGPSPLPH 230
Score = 34.1 bits (77), Expect = 0.12
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+F+ V +DT E L F +GP+K
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIK 130
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 37.0 bits (85), Expect = 0.017
Identities = 46/186 (24%), Positives = 69/186 (37%), Gaps = 31/186 (16%)
Query: 253 PSSPSGPHSGGLTLNT--LNGFSSREDITTSS-ATSSPWF--DSPLLTPMTPQIVRSPFE 307
PSSP S ++ + S T+ S + +SP + SP + +P SP
Sbjct: 1560 PSSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSY--SPT- 1616
Query: 308 SNSYAIHGSSHSPPFGSHSMES-----CSPPYLTDEGDYSPYYQTGGSTDYFSYNNAPSH 362
S SY+ S+SP S+S S SP Y YSP + T S + +P+
Sbjct: 1617 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT---SPSYSPTS 1673
Query: 363 LNLNGSMTDSSNLDNIEDLLASLSLNNTGQSNVRANGTAGSVPSPHTSPLNSPRSSGARH 422
+ + + S S + S + + S TSP SP S +
Sbjct: 1674 PSYSPTS-------------PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS--Y 1718
Query: 423 SPPSNG 428
SP S
Sbjct: 1719 SPTSPS 1724
Score = 31.2 bits (70), Expect = 1.00
Identities = 48/185 (25%), Positives = 61/185 (32%), Gaps = 41/185 (22%)
Query: 251 SPPSSPSGPHSGGLTLNTLNGFSSREDITTS--SATSSPWFDSPLLTPMTPQIVRSPFES 308
S G S G T + S +T+ S +S + SP P +P SP S
Sbjct: 1526 GAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSY--SP-TS 1582
Query: 309 NSYAIHGSSHSPPFGSHSMESCSPPYLTDEGDYSPYYQTGGSTDYFSYNNAPSHLNLNGS 368
SY+ S+SP S+S SP Y YSP + T +PS+ S
Sbjct: 1583 PSYSPTSPSYSPTSPSYS--PTSPSYSATSPSYSPTSPSYSPT-------SPSY-----S 1628
Query: 369 MTDSSNLDNIEDLLASLSLNNTGQSNVRANGTAGSVPSPHTSPLNSPRSSGARHSPPSNG 428
T S S + T S S SP SP SP S S
Sbjct: 1629 PT-------------SPSYSPTSPSY--------SPTSPSYSP-TSPSYSPTSPSYSPTS 1666
Query: 429 GYYGG 433
Y
Sbjct: 1667 PSYSP 1671
Score = 30.0 bits (67), Expect = 2.5
Identities = 33/188 (17%), Positives = 58/188 (30%), Gaps = 18/188 (9%)
Query: 253 PSSPSGPHSGGLTLNTLNGFSSREDITTSSATSSPWFDSPLLTPMTPQIVRSPFESNSYA 312
+ P G S + +A SP + + +
Sbjct: 1473 MGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAFSPLVQGG---SEGREGFGDYGLLGAAS 1529
Query: 313 IHGSSHSPPFGSHSMESCSPPYLTDEGDYSPYYQTGGSTDYFS-----YNNA-------- 359
+ SP + S + SP Y YSP ++ + Y+
Sbjct: 1530 PYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYSPTS 1589
Query: 360 PSHLNLNGSMTDSSNLDNIEDLLASLSLNNTGQSNVRANGTAGSVPSPHTSPLNSPRSSG 419
PS+ + S + +S + S + + ++ + T+ S SP TSP SP S
Sbjct: 1590 PSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPS-YSP-TSPSYSPTSPS 1647
Query: 420 ARHSPPSN 427
+ PS
Sbjct: 1648 YSPTSPSY 1655
>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 = 34.2 bits (79), Expect = 0.018
Identities = 7/34 (20%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
K+ + + + + + +F++FG +K A V
Sbjct: 29 GGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVH 62
Score = 33.0 bits (76), Expect = 0.051
Identities = 5/29 (17%), Positives = 15/29 (51%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
K+ + + + + + +F++FG +K
Sbjct: 29 GGKLLVSNLDFGVSDADIQELFAEFGTLK 57
Score = 32.3 bits (74), Expect = 0.10
Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 5/82 (6%)
Query: 98 PWAISDSNYSPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHK 157
W + G + E G + V L ++ + + + FG + A + D+
Sbjct: 10 KWQHDLFDSGFGGGAGV-ETGGKLLVSNLDFGVSDADIQELFAE-FGTLKKAAVHYDRSG 67
Query: 158 YPIGSGRITFGSTRAYSDAIRA 179
+G+ + F +DA++A
Sbjct: 68 RSLGTADVHFERK---ADALKA 86
>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 = 35.8 bits (82), Expect = 0.018
Identities = 6/31 (19%), Positives = 11/31 (35%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKVE 54
++IG + W T + L G +
Sbjct: 68 RIALYIGNLTWWTTDEDLTEAVHSLGVNDIL 98
Score = 34.3 bits (78), Expect = 0.058
Identities = 6/31 (19%), Positives = 11/31 (35%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
++IG + W T + L G +
Sbjct: 68 RIALYIGNLTWWTTDEDLTEAVHSLGVNDIL 98
>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 99
Score = 33.8 bits (78), Expect = 0.021
Identities = 6/31 (19%), Positives = 13/31 (41%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKVE 54
+++ + T E ++ F+ P VE
Sbjct: 15 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVE 45
Score = 32.2 bits (74), Expect = 0.089
Identities = 4/31 (12%), Positives = 11/31 (35%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
+++ + T E ++ F+ P
Sbjct: 15 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVE 45
>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 = 33.8 bits (78), Expect = 0.031
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 490 LSNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
L + +F+ + + L VFS G V A ++
Sbjct: 14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADIL 48
Score = 33.8 bits (78), Expect = 0.034
Identities = 21/70 (30%), Positives = 28/70 (40%), Gaps = 1/70 (1%)
Query: 110 GHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGS 169
G G T+FV L ++ + L V + G VV A I DK G G +TF
Sbjct: 7 GALQAGRLGSTVFVANLDYKVGWKKLKEVFSM-AGVVVRADILEDKDGKSRGIGTVTFEQ 65
Query: 170 TRAYSDAIRA 179
+ AI
Sbjct: 66 SIEAVQAISM 75
Score = 32.3 bits (74), Expect = 0.11
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 23 LSNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
L + +F+ + + L VFS G V
Sbjct: 14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVV 43
>2jp9_A Wilms tumor 1; DNA binding, nucleic acid recognition, X-RAY; HET:
DNA; NMR {Homo sapiens} PDB: 2jpa_A* 2prt_A*
Length = 119
Score = 33.6 bits (78), Expect = 0.035
Identities = 16/54 (29%), Positives = 20/54 (37%), Gaps = 20/54 (37%)
Query: 197 PYLEDNVCSECQ--------------THSG--PYFCREGICYRYFCRSCWLKVH 234
P+ C CQ TH+G P+ CR C + F RS L H
Sbjct: 66 PF----QCKTCQRKFSRSDHLKTHTRTHTGEKPFSCRWPSCQKKFARSDELVRH 115
Score = 31.0 bits (71), Expect = 0.36
Identities = 13/28 (46%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVH 234
H+G PY C C R F RS LK H
Sbjct: 30 KHTGEKPYQCDFKDCERRFSRSDQLKRH 57
Score = 29.8 bits (68), Expect = 0.74
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 8/35 (22%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVHI----GE 237
H+G P+ C+ C R F RS LK H GE
Sbjct: 60 RHTGVKPFQCKT--CQRKFSRSDHLKTHTRTHTGE 92
Score = 29.0 bits (66), Expect = 1.6
Identities = 5/22 (22%), Positives = 11/22 (50%)
Query: 213 PYFCREGICYRYFCRSCWLKVH 234
P+ C C + + + L++H
Sbjct: 6 PFMCAYPGCNKRYFKLSHLQMH 27
>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 = 33.2 bits (76), Expect = 0.041
Identities = 8/33 (24%), Positives = 14/33 (42%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
I +P T + FS+FG + V++
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL 42
Score = 29.4 bits (66), Expect = 0.92
Identities = 7/29 (24%), Positives = 11/29 (37%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
I +P T + FS+FG +
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLG 38
>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 = 32.8 bits (75), Expect = 0.044
Identities = 4/31 (12%), Positives = 11/31 (35%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKVE 54
S+ I + +P D+ + + +
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYDLKYCY 35
Score = 31.6 bits (72), Expect = 0.095
Identities = 6/35 (17%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
S+ I + +P D+ + + + +K ++R
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDR 38
>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 = 33.0 bits (76), Expect = 0.050
Identities = 8/34 (23%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
+++ + + L FS FG + A VM
Sbjct: 15 VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVM 48
Score = 32.6 bits (75), Expect = 0.077
Identities = 16/92 (17%), Positives = 30/92 (32%), Gaps = 31/92 (33%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV---KVEWPQG-----------TPESPTAPKAI 69
+++ + + L FS FG + KV G +PE A KA+
Sbjct: 15 VVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEE--ATKAV 72
Query: 70 S-LDVISELVLILGQWATEGNLCGRVEVVPWA 100
+ ++ G+ + + V A
Sbjct: 73 TEMN---------GRI-----VATKPLYVALA 90
>1f2i_G Fusion of N-terminal 17-MER peptide extension to ZIF12; zinc
finger, dimer, protein-DNA complex, cooperativity,
transcription/DNA complex; 2.35A {Mus musculus} SCOP:
g.37.1.1 g.37.1.1
Length = 73
Score = 31.9 bits (73), Expect = 0.065
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 208 QTHSG--PYFCREGICYRYFCRSCWLKVHI 235
+ H+G P+ CR C R F RS L HI
Sbjct: 42 RIHTGQKPFQCRI--CMRNFSRSDHLTTHI 69
Score = 30.0 bits (68), Expect = 0.31
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 195 IDPYLEDNVCSECQTHSGPYFCREGICYRYFCRSCWLKVHI 235
++P+ +N+ + PY C C R F RS L HI
Sbjct: 1 MEPHPMNNLLNYVVPKMRPYACPVESCDRRFSRSDELTRHI 41
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 32.4 bits (74), Expect = 0.067
Identities = 8/40 (20%), Positives = 14/40 (35%), Gaps = 6/40 (15%)
Query: 490 LSNKIFIGGVP------WDTPEYLLLTVFSQFGPVKAVVM 523
I + G P + L ++FS+ G V +
Sbjct: 5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEF 44
Score = 30.1 bits (68), Expect = 0.56
Identities = 8/36 (22%), Positives = 13/36 (36%), Gaps = 6/36 (16%)
Query: 23 LSNKIFIGGVP------WDTPEYLLLTVFSQFGPVK 52
I + G P + L ++FS+ G V
Sbjct: 5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVV 40
>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 = 32.9 bits (75), Expect = 0.069
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 492 NKIFIGGVPWDTPEYLLL---TVFSQFGPVKAVVMNR 525
N +F+ G+ + +L F +FG + VV+N
Sbjct: 16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINN 52
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 33.0 bits (75), Expect = 0.072
Identities = 12/76 (15%), Positives = 26/76 (34%), Gaps = 5/76 (6%)
Query: 107 SPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLF---GDVVYAGIDTDKHKYPIGSG 163
EP + + + ++ + + L ++ L GD++ I D G
Sbjct: 18 DLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDIL--DIVVDLSDDNSGKA 75
Query: 164 RITFGSTRAYSDAIRA 179
I F + + + A
Sbjct: 76 YIVFATQESAQAFVEA 91
Score = 32.2 bits (73), Expect = 0.15
Identities = 8/39 (20%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 491 SNKIFIGGVPWDTPE----YLLLTVFSQFGPVKAVVMNR 525
S + I + + P+ LL + S G + +V++
Sbjct: 29 SQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL 67
Score = 29.1 bits (65), Expect = 1.8
Identities = 7/33 (21%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 24 SNKIFIGGVPWDTPE----YLLLTVFSQFGPVK 52
S + I + + P+ LL + S G +
Sbjct: 29 SQVVLITNINPEVPKEKLQALLYALASSQGDIL 61
>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 = 32.7 bits (75), Expect = 0.073
Identities = 8/37 (21%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 491 SNKIFIGGVPWD-TPEYLLLTVFSQFGPVKAVVMNRA 526
++++FIG + + + T+FS++G V +++
Sbjct: 27 NSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG 63
Score = 29.7 bits (67), Expect = 0.90
Identities = 8/30 (26%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 24 SNKIFIGGVPWD-TPEYLLLTVFSQFGPVK 52
++++FIG + + + T+FS++G V
Sbjct: 27 NSRVFIGNLNTALVKKSDVETIFSKYGRVA 56
>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 = 32.7 bits (75), Expect = 0.073
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVK-AVVM 523
+FI +P + + LL +F FG V A V
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVF 58
Score = 31.9 bits (73), Expect = 0.13
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGPV 51
+FI +P + + LL +F FG V
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNV 52
>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 = 32.6 bits (75), Expect = 0.074
Identities = 7/30 (23%), Positives = 11/30 (36%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
F+G +P+D E + F V
Sbjct: 15 PYTAFLGNLPYDVTEESIKEFFRGLNISAV 44
Score = 30.3 bits (69), Expect = 0.42
Identities = 6/33 (18%), Positives = 11/33 (33%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
F+G +P+D E + F +
Sbjct: 15 PYTAFLGNLPYDVTEESIKEFFRGLNISAVRLP 47
>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 = 32.6 bits (75), Expect = 0.088
Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 18/82 (21%)
Query: 104 SNYSPQGHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSG 163
S+Y+P EP K +++ L R+T + L ++ F + I +G
Sbjct: 17 SSYNPG------EPNKVLYLKNLSPRVTERDLVSLFA-RFQEKKGPPIQFRMM-----TG 64
Query: 164 R------ITFGSTRAYSDAIRA 179
R ITF + A+
Sbjct: 65 RMRGQAFITFPNKEIAWQALHL 86
Score = 32.3 bits (74), Expect = 0.12
Identities = 5/38 (13%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPV-KAVVMNRAE 527
+ +++ + E L+++F++F + R
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM 62
Score = 30.3 bits (69), Expect = 0.42
Identities = 5/29 (17%), Positives = 15/29 (51%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+ +++ + E L+++F++F K
Sbjct: 25 NKVLYLKNLSPRVTERDLVSLFARFQEKK 53
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 32.1 bits (73), Expect = 0.089
Identities = 10/50 (20%), Positives = 20/50 (40%), Gaps = 4/50 (8%)
Query: 13 PLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFG--PVKVEW--PQG 58
P L+ +++G +P D L + G P+++ W P+
Sbjct: 8 PGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRR 57
Score = 31.7 bits (72), Expect = 0.11
Identities = 8/46 (17%), Positives = 16/46 (34%)
Query: 480 PLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
P L+ +++G +P D L + G V + +
Sbjct: 8 PGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQ 53
>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 = 32.4 bits (74), Expect = 0.10
Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 5/70 (7%)
Query: 459 ARHHRSSANSQIPQKTWEGVLPLRTQFSDE---ILSNKIFIGGVPWDTPEYLLLTVFSQF 515
+ HH ++ +P+ + G F + N +++ G D LL FS F
Sbjct: 4 SHHHHHHSSGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPF 61
Query: 516 GPVKAVVMNR 525
G + + M+
Sbjct: 62 GNIIDLSMDP 71
Score = 28.9 bits (65), Expect = 1.4
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 14/55 (25%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGP---VKVEWPQG-------TPESPTAPKAI 69
N +++ G D LL FS FG + ++ P+ ES A +A+
Sbjct: 40 NTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMES--ADQAV 90
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 32.3 bits (74), Expect = 0.11
Identities = 11/66 (16%), Positives = 21/66 (31%), Gaps = 8/66 (12%)
Query: 466 ANSQIPQKTWEGVLPLRTQFSDEILSN-------KIFIGGVPWDTPEYLLLTVFSQFGPV 518
++ + + L + +FI +P + + L + F FG V
Sbjct: 8 GSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNV 67
Query: 519 K-AVVM 523
A V
Sbjct: 68 ISAKVF 73
Score = 31.2 bits (71), Expect = 0.23
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 26 KIFIGGVPWDTPEYLLLTVFSQFGPV 51
+FI +P + + L + F FG V
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNV 67
>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 = 32.2 bits (74), Expect = 0.11
Identities = 10/50 (20%), Positives = 15/50 (30%), Gaps = 7/50 (14%)
Query: 9 EGVLPLRTQFS-------DEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
G L+ E ++I +P E L + FG V
Sbjct: 3 SGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQV 52
Score = 32.2 bits (74), Expect = 0.11
Identities = 10/50 (20%), Positives = 15/50 (30%), Gaps = 7/50 (14%)
Query: 476 EGVLPLRTQFS-------DEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 518
G L+ E ++I +P E L + FG V
Sbjct: 3 SGSSGLKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQV 52
>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 = 33.7 bits (76), Expect = 0.11
Identities = 21/153 (13%), Positives = 45/153 (29%)
Query: 373 SNLDNIEDLLASLSLNNTGQSNVRANGTAGSVPSPHTSPLNSPRSSGARHSPPSNGGYYG 432
++ D I + + + + + + GA P
Sbjct: 89 TDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMT 148
Query: 433 GGGGGQYLHNGDGGGQGGLQSTLDIAARHHRSSANSQIPQKTWEGVLPLRTQFSDEILSN 492
+ G + + PQ+ G +P S+ ++
Sbjct: 149 QAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNH 208
Query: 493 KIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
+F+ +P +T E +L +F+QF K V +
Sbjct: 209 ILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP 241
Score = 30.2 bits (67), Expect = 1.4
Identities = 9/39 (23%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 491 SNKIFIGGVPWDTPE----YLLLTVFSQFGPVKAVVMNR 525
++ I+I + + L +FSQFG + ++++R
Sbjct: 9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR 47
>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 = 32.1 bits (73), Expect = 0.12
Identities = 8/47 (17%), Positives = 15/47 (31%), Gaps = 5/47 (10%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR-----AEMSSDD 532
N++ + G+P L + G V + R E +
Sbjct: 15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKE 61
Score = 30.9 bits (70), Expect = 0.31
Identities = 6/28 (21%), Positives = 11/28 (39%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
N++ + G+P L + G V
Sbjct: 15 ENRVVVSGLPPSGSWQDLKDHMREAGDV 42
>2dlk_A Novel protein; ZF-C2H2 domain, zinc finger protein 692, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
g.37.1.1 g.37.1.1
Length = 79
Score = 31.0 bits (71), Expect = 0.14
Identities = 8/28 (28%), Positives = 10/28 (35%), Gaps = 2/28 (7%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVH 234
H + C E C + F LK H
Sbjct: 32 QHIHQKSFSCPEPACGKSFNFKKHLKEH 59
Score = 27.1 bits (61), Expect = 4.0
Identities = 8/27 (29%), Positives = 9/27 (33%), Gaps = 2/27 (7%)
Query: 210 HSG--PYFCREGICYRYFCRSCWLKVH 234
SG C C R F +L H
Sbjct: 2 SSGSSGMPCDFPGCGRIFSNRQYLNHH 28
>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 = 31.4 bits (72), Expect = 0.15
Identities = 7/30 (23%), Positives = 11/30 (36%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
F+G +P+D E + F V
Sbjct: 19 PYTAFLGNLPYDVTEESIKEFFRGLNISAV 48
Score = 29.9 bits (68), Expect = 0.61
Identities = 9/35 (25%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
F+G +P+D E + F + AV + R
Sbjct: 19 PYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPR 52
>2gli_A Protein (five-finger GLI); protein/DNA complex, transcription/DNA
complex; HET: DNA; 2.60A {Homo sapiens} SCOP: g.37.1.1
g.37.1.1 g.37.1.1 g.37.1.1 g.37.1.1
Length = 155
Score = 32.2 bits (74), Expect = 0.17
Identities = 8/28 (28%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVH 234
+H+G PY C C + F + H
Sbjct: 91 SHTGEKPYMCEHEGCSKAFSNASDRAKH 118
Score = 30.6 bits (70), Expect = 0.54
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVHI 235
THS PY C+ C + + L+ H+
Sbjct: 122 THSNEKPYVCKLPGCTKRYTDPSSLRKHV 150
Score = 30.6 bits (70), Expect = 0.58
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 6/35 (17%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVHI----GE 237
H+G P+ C C + + R LK H+ GE
Sbjct: 61 RHTGEKPHKCTFEGCRKSYSRLENLKTHLRSHTGE 95
Score = 27.2 bits (61), Expect = 9.1
Identities = 6/29 (20%), Positives = 7/29 (24%), Gaps = 2/29 (6%)
Query: 213 PYFCREGICYRYFCRSCWLKVHIGEYSQH 241
C + F L HI H
Sbjct: 3 DCRWDG--CSQEFDSQEQLVHHINSEHIH 29
>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 = 31.1 bits (71), Expect = 0.18
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 492 NKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
N +++ G D LL FS FG + + M+
Sbjct: 16 NTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP 47
Score = 29.2 bits (66), Expect = 0.97
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 14/56 (25%)
Query: 25 NKIFIGGVPWDTPEYLLLTVFSQFGP---VKVEWPQG-------TPESPTAPKAIS 70
N +++ G D LL FS FG + ++ P+ ES A +A++
Sbjct: 16 NTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMES--ADQAVA 67
>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 = 31.1 bits (71), Expect = 0.18
Identities = 8/37 (21%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 490 LSNKIFIGGVPWDTP-EYLLLTVFSQFGPVKAVVMNR 525
+ +++FIG +P + L +FS +G + + +
Sbjct: 21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 57
Score = 28.0 bits (63), Expect = 2.0
Identities = 8/31 (25%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 23 LSNKIFIGGVPWDTP-EYLLLTVFSQFGPVK 52
+ +++FIG +P + L +FS +G +
Sbjct: 21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIM 51
>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 = 31.8 bits (72), Expect = 0.22
Identities = 12/67 (17%), Positives = 24/67 (35%), Gaps = 4/67 (5%)
Query: 460 RHHRSS----ANSQIPQKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQF 515
HH SS S + T + + +D + + G+P+ + ++ FS
Sbjct: 7 HHHHSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGL 66
Query: 516 GPVKAVV 522
V +
Sbjct: 67 EIVPNGI 73
Score = 27.5 bits (61), Expect = 5.1
Identities = 5/30 (16%), Positives = 12/30 (40%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
+ + G+P+ + ++ FS V
Sbjct: 42 DGFVRLRGLPFGCTKEEIVQFFSGLEIVPN 71
>2drp_A Protein (tramtrack DNA-binding domain); protein-DNA complex, double
helix, transcription/DNA complex; HET: DNA; 2.80A
{Drosophila melanogaster} SCOP: g.37.1.1 g.37.1.1
Length = 66
Score = 30.2 bits (69), Expect = 0.23
Identities = 7/29 (24%), Positives = 9/29 (31%), Gaps = 4/29 (13%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVHI 235
T G Y C+ C R + H
Sbjct: 4 TKEGEHTYRCKV--CSRVYTHISNFCRHY 30
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 31.3 bits (71), Expect = 0.23
Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 8/79 (10%)
Query: 103 DSNYSPQGHSTKLEPGK--TIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPI 160
S P+G P K I + L + Q L ++ + + ++ ++T
Sbjct: 11 SSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFD--- 67
Query: 161 GSGRITFGSTRAYSDAIRA 179
G+G + F S + A
Sbjct: 68 GTGALEFPS---EEILVEA 83
>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 = 30.8 bits (70), Expect = 0.30
Identities = 7/43 (16%), Positives = 16/43 (37%), Gaps = 4/43 (9%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGP----VKVEWPQGTPES 62
+ +++G + E + F+ G VK+ + T
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIP 51
Score = 29.6 bits (67), Expect = 0.64
Identities = 7/36 (19%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFG-PVKAVVMNR 525
+ +++G + E + F+ G V +V + R
Sbjct: 9 AASLWMGDLEPYMDENFISRAFATMGETVMSVKIIR 44
Score = 28.4 bits (64), Expect = 1.9
Identities = 9/71 (12%), Positives = 21/71 (29%), Gaps = 1/71 (1%)
Query: 110 GHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKH-KYPIGSGRITFG 168
G S ++++G L + + + V+ I ++ P G + F
Sbjct: 1 GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60
Query: 169 STRAYSDAIRA 179
+
Sbjct: 61 DLATAEKCLHK 71
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 30.7 bits (70), Expect = 0.33
Identities = 5/30 (16%), Positives = 13/30 (43%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
++G +P++T + + +F V
Sbjct: 15 PYTAYVGNLPFNTVQGDIDAIFKDLSIRSV 44
Score = 30.3 bits (69), Expect = 0.44
Identities = 7/53 (13%), Positives = 18/53 (33%), Gaps = 11/53 (20%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKA-VVMNR----------AEMSSDD 532
++G +P++T + + +F +V ++ E D
Sbjct: 15 PYTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVD 67
>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 = 30.7 bits (69), Expect = 0.40
Identities = 6/33 (18%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 494 IFIGGVPWD-TPEYLLLTVFSQFGPVKAVVMNR 525
I + +P + +L + +G +K ++ R
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR 60
>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 = 31.0 bits (70), Expect = 0.42
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
+ + + G+P+ E + FS PV+V
Sbjct: 46 GHCVHMRGLPYKATENDIYNFFSPLNPVRV 75
Score = 29.0 bits (65), Expect = 1.9
Identities = 7/37 (18%), Positives = 16/37 (43%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRAE 527
+ + + G+P+ E + FS PV+ + +
Sbjct: 46 GHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPD 82
>2ebt_A Krueppel-like factor 5; C2H2-type zinc-finger, metal BIND,
transcription factor, kruppel-like factor, GC-box
promoter elements, structural genomics; NMR {Homo
sapiens}
Length = 100
Score = 30.3 bits (69), Expect = 0.43
Identities = 12/28 (42%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVH 234
TH+G PY C C F RS L H
Sbjct: 39 THTGEKPYKCTWEGCDWRFARSDELTRH 66
Score = 29.5 bits (67), Expect = 0.69
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 4/29 (13%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVHI 235
H+G P+ C C R F RS L +H+
Sbjct: 69 KHTGAKPFQCGV--CNRSFSRSDHLALHM 95
>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 = 30.6 bits (69), Expect = 0.44
Identities = 7/35 (20%), Positives = 13/35 (37%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNR 525
N++ + G+P L + G V + R
Sbjct: 16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR 50
Score = 29.8 bits (67), Expect = 0.76
Identities = 6/28 (21%), Positives = 11/28 (39%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
N++ + G+P L + G V
Sbjct: 16 ENRVVVSGLPPSGSWQDLKDHMREAGDV 43
>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 = 29.9 bits (68), Expect = 0.47
Identities = 12/68 (17%), Positives = 30/68 (44%), Gaps = 7/68 (10%)
Query: 116 EPGKTIFVGALHGRLTAQALYNVMNDLF---GDVVYAGIDTD-KHKYPIGSGRITFGSTR 171
P TI++ L+ ++ L ++ +F G ++ + K + G + F
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMR---GQAFVIFKEVS 62
Query: 172 AYSDAIRA 179
+ ++A+R+
Sbjct: 63 SATNALRS 70
Score = 29.1 bits (66), Expect = 0.99
Identities = 8/39 (20%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 491 SNKIFIGGVPWDTPE----YLLLTVFSQFGPVKAVVMNR 525
++ I+I + + L +FS+FG + ++++R
Sbjct: 8 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 46
>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 = 29.8 bits (67), Expect = 0.64
Identities = 6/31 (19%), Positives = 11/31 (35%), Gaps = 1/31 (3%)
Query: 494 IFIGGVPWD-TPEYLLLTVFSQFGPVKAVVM 523
+ I Y LL + FG + ++
Sbjct: 18 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLI 48
>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 = 31.0 bits (70), Expect = 0.64
Identities = 9/34 (26%), Positives = 13/34 (38%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFG-PVKAVVM 523
S + + +P E L +FS G VK
Sbjct: 120 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF 153
Score = 31.0 bits (70), Expect = 0.72
Identities = 8/28 (28%), Positives = 12/28 (42%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
S + + +P E L +FS G V
Sbjct: 120 SATLHLSNIPPSVSEEDLKVLFSSNGGV 147
Score = 27.6 bits (61), Expect = 9.8
Identities = 6/34 (17%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 491 SNKIFIGGV-PWDTPEYLLLTVFSQFGPVKAVVM 523
++ + + + P L +F +G V+ V +
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI 36
>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 = 31.0 bits (69), Expect = 0.66
Identities = 10/64 (15%), Positives = 26/64 (40%)
Query: 462 HRSSANSQIPQKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
S ++I + + + + ++ +++ + ++I G P D + G V +
Sbjct: 80 EISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNI 139
Query: 522 VMNR 525
M R
Sbjct: 140 QMRR 143
>1tf6_A Protein (transcription factor IIIA); complex (transcription
regulation/DNA), RNA polymerase III, transcription
initiation, zinc finger protein; HET: DNA; 3.10A
{Xenopus laevis} SCOP: g.37.1.1 g.37.1.1 g.37.1.1
g.37.1.1 g.37.1.1 g.37.1.1 PDB: 1tf3_A
Length = 190
Score = 31.0 bits (71), Expect = 0.67
Identities = 8/28 (28%), Positives = 11/28 (39%), Gaps = 2/28 (7%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVH 234
TH+G + C C F +K H
Sbjct: 66 THTGEKNFTCDSDGCDLRFTTKANMKKH 93
Score = 30.3 bits (69), Expect = 0.98
Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVH 234
H+G P+ C+E C + F L H
Sbjct: 36 KHTGEKPFPCKEEGCEKGFTSLHHLTRH 63
Score = 29.5 bits (67), Expect = 1.7
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVH 234
+H+ PY C C + F LK H
Sbjct: 128 SHTQQLPYECPHEGCDKRFSLPSRLKRH 155
>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 = 29.6 bits (67), Expect = 0.68
Identities = 5/32 (15%), Positives = 11/32 (34%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVV 522
I + +P+ +L F + + V
Sbjct: 15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSV 46
Score = 28.0 bits (63), Expect = 2.1
Identities = 4/29 (13%), Positives = 10/29 (34%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
I + +P+ +L F + +
Sbjct: 15 PTVIKVQNMPFTVSIDEILDFFYGYQVIP 43
>2w0c_L Protein 2; virus, member of PRD1-adeno viral lineage,
membrane-containing bacteriophage, virus virion,
membrane; 7.00A {Pseudoalteromonas phage PM2}
Length = 335
Score = 31.2 bits (70), Expect = 0.77
Identities = 30/115 (26%), Positives = 47/115 (40%), Gaps = 15/115 (13%)
Query: 272 FSSREDITTSSATSSPWFDSPLLTPMTPQIVRSPFESNSYAIHGSSHSPPFGSHSMESCS 331
++ E T A + P+FD + P++ PF + H S G ++ S
Sbjct: 180 YAQNEGRTALEANNVPFFD----IDVPPELDGVPFSLKARVRHKSKGVDGLGDYTSISVK 235
Query: 332 PPYLTDEGDYSPYYQTGGSTDYFSYNNAPSHLNLNGSMTDSSNLDNIEDLLASLS 386
P + EGD + T Y SY + SH +G D DN D++ +LS
Sbjct: 236 PAFYITEGDET----TDTLIKYTSYGSTGSH---SGYDFD----DNTLDVMVTLS 279
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 29.1 bits (66), Expect = 0.89
Identities = 10/45 (22%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 483 TQFSDEILSNKIFIGGVPWDTP-EYLLLTVFSQFGPVKAVVMNRA 526
T+ + +++FIG +P + L +FS +G + + + A
Sbjct: 2 TEMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA 46
>2j1n_A Outer membrane protein C; transport protein, beta-barrel, ION
transport, osmoporin; HET: D12; 2.0A {Escherichia coli}
PDB: 2j4u_P 2zle_D 3nb3_D 4a8d_M 2ixx_A* 2xe1_A* 2xe2_A*
2ixw_A* 2xe5_A* 2xe3_A* 2xg6_A 1osm_A*
Length = 346
Score = 30.9 bits (69), Expect = 0.89
Identities = 17/119 (14%), Positives = 27/119 (22%), Gaps = 5/119 (4%)
Query: 341 YSPYYQTGGSTDYFSY--NNAPSHLNLNGSMTDSS---NLDNIEDLLASLSLNNTGQSNV 395
Y Y TD + N + + L+ L+ Q
Sbjct: 94 YGVVYDVTSWTDVLPEFGGDTYGSDNFMQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKN 153
Query: 396 RANGTAGSVPSPHTSPLNSPRSSGARHSPPSNGGYYGGGGGGQYLHNGDGGGQGGLQST 454
G + ++ R +G Y G G GG + Q
Sbjct: 154 GNPSGEGFTSGVTNNGRDALRQNGDGVGGSITYDYEGFGIGGAISSSKRTDAQNTAAYI 212
>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 = 29.5 bits (66), Expect = 0.91
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
+ GG+ LL V + G V A++M
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLM 59
>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 = 30.2 bits (68), Expect = 0.91
Identities = 5/47 (10%), Positives = 16/47 (34%)
Query: 5 QKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
+ L + + + +I++ + E L +F ++
Sbjct: 26 SREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDF 72
Score = 30.2 bits (68), Expect = 0.91
Identities = 5/47 (10%), Positives = 16/47 (34%)
Query: 472 QKTWEGVLPLRTQFSDEILSNKIFIGGVPWDTPEYLLLTVFSQFGPV 518
+ L + + + +I++ + E L +F ++
Sbjct: 26 SREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDF 72
>3gx1_A LIN1832 protein; APC63308.2, structural genomics, protein structure
initiative, midwest center for structural genomics,
MCSG; 2.30A {Listeria innocua CLIP11262}
Length = 130
Score = 29.6 bits (67), Expect = 0.93
Identities = 8/33 (24%), Positives = 14/33 (42%), Gaps = 3/33 (9%)
Query: 123 VGAL---HGRLTAQALYNVMNDLFGDVVYAGID 152
V + HGR TA ++ + +L +D
Sbjct: 5 VEVIVMMHGRSTATSMVETVQELLSIESGIALD 37
>2vhf_A Ubiquitin carboxyl-terminal hydrolase CYLD; cytokine signalling,
linkage specificity, deubiquitinating enzyme, Lys63-
linked, anti-oncogene; 2.8A {Homo sapiens}
Length = 374
Score = 30.9 bits (69), Expect = 0.94
Identities = 21/80 (26%), Positives = 30/80 (37%), Gaps = 16/80 (20%)
Query: 191 KKLQIDPYLEDN--VCSECQTHSGPYFCREGICY----------RYFCRSCWLKVHIG-E 237
+L I LED C C Y CRE CY + FC++C +VH+ +
Sbjct: 191 LELNITDLLEDTPRQCRICG-GLAMYECRE--CYDDPDISAGKIKQFCKTCNTQVHLHPK 247
Query: 238 YSQHDPIVRNVRKSPPSSPS 257
H ++ K P
Sbjct: 248 RLNHKYNPVSLPKDLPDWDW 267
>1p7a_A BF3, BKLF, kruppel-like factor 3; classical zinc finger,
transcription factor, DNA binding protein; NMR {Mus
musculus} SCOP: g.37.1.1 PDB: 1u85_A 1u86_A
Length = 37
Score = 27.7 bits (62), Expect = 0.94
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 208 QTHSG--PYFCREGICYRYFCRSCWLKVHI 235
+ +G P+ C C R F RS L +H
Sbjct: 4 RGSTGIKPFQCP--DCDRSFSRSDHLALHR 31
>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 = 29.2 bits (66), Expect = 0.99
Identities = 5/32 (15%), Positives = 11/32 (34%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVV 522
I + +P+ +L F + + V
Sbjct: 15 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSV 46
Score = 28.0 bits (63), Expect = 2.6
Identities = 4/29 (13%), Positives = 10/29 (34%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
I + +P+ +L F + +
Sbjct: 15 PTIIKVQNMPFTVSIDEILDFFYGYQVIP 43
>2hih_A Lipase 46 kDa form; A1 phospholipase, phospholipid binding,
hydrolase; 2.86A {Staphylococcus hyicus}
Length = 431
Score = 30.8 bits (68), Expect = 1.0
Identities = 29/177 (16%), Positives = 54/177 (30%), Gaps = 7/177 (3%)
Query: 257 SGPHSGGLTLNTLNGFSSREDITTSSATSSPWFDSPLLTPMTPQIVRSPFESNSYAIHGS 316
+ PH+G + + + +I S A S + R ES +
Sbjct: 209 ATPHNGTHASDDIGNTPTIRNILYSFAQMSSHLGTIDFGMDHWGFKRKDGESLTDYNKRI 268
Query: 317 SHSPPFGSHSMESCSPPYLTDEG--DYSPYYQTGGSTDYFSYNNAPSHLNLNGSMTDSSN 374
+ S + S E LT EG + + + Y +Y +H G
Sbjct: 269 AESKIWDS---EDTGLYDLTREGAEKINQKTELNPNIYYKTYTGVATHETQLGKHIADLG 325
Query: 375 LDNIEDLLASLSLNNTGQSNVRANGTAGSVPSPHTSPLNSPRSSGARHSPPSNGGYY 431
++ + L + + +G + S H P + S +S G +
Sbjct: 326 MEFTKILTGNYIGSVDDILWRPNDGLVSEISSQH--PSDEKNISVDENSELHKGTWQ 380
>2lbm_A Transcriptional regulator ATRX; metal binding protein-structural
protein compl; HET: M3L; NMR {Homo sapiens} PDB: 2ld1_A
Length = 142
Score = 29.8 bits (66), Expect = 1.2
Identities = 7/41 (17%), Positives = 11/41 (26%), Gaps = 1/41 (2%)
Query: 190 CKKLQIDPYLEDNVCSECQTHSGPYFCREG-ICYRYFCRSC 229
+ P L+ +C C + CR C
Sbjct: 29 KDSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWC 69
>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 = 29.3 bits (66), Expect = 1.2
Identities = 4/32 (12%), Positives = 9/32 (28%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVV 522
I +P+ + +L + V
Sbjct: 15 KVCAHITNIPFSITKMDVLQFLEGIPVDENAV 46
Score = 27.8 bits (62), Expect = 3.2
Identities = 3/29 (10%), Positives = 8/29 (27%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
I +P+ + +L +
Sbjct: 15 KVCAHITNIPFSITKMDVLQFLEGIPVDE 43
>2vve_A Spike protein P1; viral stem-receptor binding domain, viral
protein; 1.77A {Pseudoalteromonas phage PM2} PDB: 2vvd_A
Length = 254
Score = 30.5 bits (68), Expect = 1.2
Identities = 30/115 (26%), Positives = 47/115 (40%), Gaps = 15/115 (13%)
Query: 272 FSSREDITTSSATSSPWFDSPLLTPMTPQIVRSPFESNSYAIHGSSHSPPFGSHSMESCS 331
++ E T A + P+FD + P++ PF + H S G ++ S
Sbjct: 99 YAQNEGRTALEANNVPFFD----IDVPPELDGVPFSLKARVRHKSKGVDGLGDYTSISVK 154
Query: 332 PPYLTDEGDYSPYYQTGGSTDYFSYNNAPSHLNLNGSMTDSSNLDNIEDLLASLS 386
P + EGD + T Y SY + SH +G D DN D++ +LS
Sbjct: 155 PAFYITEGDET----TDTLIKYTSYGSTGSH---SGYDFD----DNTLDVMVTLS 198
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 29.2 bits (65), Expect = 1.2
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 5/45 (11%)
Query: 486 SDEILSNKIFIGGVPWDTPEYLLLTVF-----SQFGPVKAVVMNR 525
S + + G+P P+ LL F S GPV +
Sbjct: 3 SGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG 47
Score = 28.0 bits (62), Expect = 2.5
Identities = 7/31 (22%), Positives = 11/31 (35%)
Query: 19 SDEILSNKIFIGGVPWDTPEYLLLTVFSQFG 49
S + + G+P P+ LL F
Sbjct: 3 SGSSGGVAVEVRGLPPAVPDELLTLYFENRR 33
>2vrw_B P95VAV, VAV1, proto-oncogene VAV; lipoprotein, GTP-binding,
metal-binding, phosphoprotein, exchange factor, RAC,
GTPase, membrane domain; 1.85A {Mus musculus} PDB:
3bji_A 1f5x_A
Length = 406
Score = 30.6 bits (69), Expect = 1.3
Identities = 11/63 (17%), Positives = 16/63 (25%), Gaps = 8/63 (12%)
Query: 175 DAIRAAFIEVKSGRICKK---LQIDPYLEDNVCSECQTHSGPYFCREGICYRYFCRSCWL 231
+ A + Q+ + E C CQ F + Y C C
Sbjct: 328 EQFEMAISNIYPENATANGHDFQMFSFEETTSCKACQMLLRGTFYQ-----GYRCYRCRA 382
Query: 232 KVH 234
H
Sbjct: 383 PAH 385
>3gdw_A Sigma-54 interaction domain protein; structural genomics, PSI-2,
protein structure initiative, M center for structural
genomics, MCSG; HET: MSE; 2.00A {Enterococcus faecalis}
Length = 139
Score = 29.7 bits (67), Expect = 1.3
Identities = 8/33 (24%), Positives = 14/33 (42%), Gaps = 3/33 (9%)
Query: 123 VGAL---HGRLTAQALYNVMNDLFGDVVYAGID 152
VG HG TA ++ +L G + ++
Sbjct: 5 VGVFVLMHGDSTASSMLKTAQELLGTSIGTAMN 37
>2rpc_A Zinc finger protein ZIC 3; ZF-C2H2, zinc finger protein of the
cerebellum 3, disease mutation, DNA-binding,
metal-binding, nucleus, polymorphism; NMR {Homo sapiens}
Length = 155
Score = 29.6 bits (67), Expect = 1.3
Identities = 12/47 (25%), Positives = 16/47 (34%), Gaps = 16/47 (34%)
Query: 204 CSECQ--------------THSG--PYFCREGICYRYFCRSCWLKVH 234
C H+G P+ C C + F RS LK+H
Sbjct: 65 CPREGKSFKAKYKLVNHIRVHTGEKPFPCPFPGCGKIFARSENLKIH 111
Score = 27.6 bits (62), Expect = 6.3
Identities = 11/28 (39%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVH 234
TH+G P+ C C R F S K H
Sbjct: 114 THTGEKPFKCEFEGCDRRFANSSDRKKH 141
>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 = 30.0 bits (67), Expect = 1.4
Identities = 8/33 (24%), Positives = 12/33 (36%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVM 523
S + + +P E L +FS G V
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFK 183
Score = 29.6 bits (66), Expect = 2.4
Identities = 8/28 (28%), Positives = 12/28 (42%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
S + + +P E L +FS G V
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGV 178
Score = 28.0 bits (62), Expect = 7.2
Identities = 10/67 (14%), Positives = 27/67 (40%), Gaps = 3/67 (4%)
Query: 458 AARHHRSSANSQIPQKTWEGVLPLRTQFSDEILSNKIFIGGV-PWDTPEYLLLTVFSQFG 516
++ HH ++ +P+ + G + ++ + + + P L +F +G
Sbjct: 3 SSHHHHHHSSGLVPRGSHMGRI--AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYG 60
Query: 517 PVKAVVM 523
V+ V +
Sbjct: 61 DVQRVKI 67
>3h0g_I DNA-directed RNA polymerases I, II, and III subunit rpabc5;
transcription, multi-protein complex, DNA- binding,
magnesium; 3.65A {Schizosaccharomyces pombe}
Length = 113
Score = 28.9 bits (64), Expect = 1.5
Identities = 8/26 (30%), Positives = 10/26 (38%)
Query: 204 CSECQTHSGPYFCREGICYRYFCRSC 229
C EC P + R CR+C
Sbjct: 7 CIECNNMLYPREDKVDRVLRLACRNC 32
>3ql9_A Transcriptional regulator ATRX; zinc finger, transcription, lysine
trimethylation, protein, histone-binding protein,
transcription-structural complex; HET: M3L; 0.93A {Homo
sapiens} PDB: 3qla_A* 3qlc_A 3qln_A 2jm1_A
Length = 129
Score = 29.4 bits (65), Expect = 1.5
Identities = 7/40 (17%), Positives = 11/40 (27%), Gaps = 1/40 (2%)
Query: 191 KKLQIDPYLEDNVCSECQTHSGPYFCREG-ICYRYFCRSC 229
+ P L+ +C C + CR C
Sbjct: 24 DSIYRHPSLQVLICKNCFKYYMSDDISRDSDGMDEQCRWC 63
>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 = 28.4 bits (64), Expect = 1.6
Identities = 5/30 (16%), Positives = 14/30 (46%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
+ + + G P++ E ++ + PV +
Sbjct: 10 CHTVKLRGAPFNVTEKNVMEFLAPLKPVAI 39
>2b5u_A Colicin E3; high resolution colicin E3, ribosome inactivation,
ribosome inhibitor, hydrolase; HET: CIT; 2.30A
{Escherichia coli} SCOP: b.101.1.1 b.110.1.1 h.4.9.1
PDB: 1jch_A* 1ujw_B* 2ysu_B 1e44_B 2xfz_Y* 2xg1_Y*
Length = 551
Score = 30.4 bits (67), Expect = 1.6
Identities = 15/66 (22%), Positives = 22/66 (33%), Gaps = 3/66 (4%)
Query: 388 NNTGQSNVRANGTAGSVPSPHTSPLNSPRSSGARHSPPSNGGYYGGGGGGQYLHNGDGGG 447
+NTG + N G + + ++P G G GG +G G G
Sbjct: 9 HNTGAHSTSGNINGGPTGLGVGGGASDGSGWSSENNPWGGGSGSGIHWGG---GSGHGNG 65
Query: 448 QGGLQS 453
G S
Sbjct: 66 GGNGNS 71
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 28.8 bits (65), Expect = 1.6
Identities = 14/70 (20%), Positives = 23/70 (32%)
Query: 110 GHSTKLEPGKTIFVGALHGRLTAQALYNVMNDLFGDVVYAGIDTDKHKYPIGSGRITFGS 169
G S P ++FVG L + LY ++ + D+ G G + F
Sbjct: 1 GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTD 60
Query: 170 TRAYSDAIRA 179
A+
Sbjct: 61 ELEQKRALTE 70
Score = 28.4 bits (64), Expect = 1.9
Identities = 7/32 (21%), Positives = 14/32 (43%), Gaps = 2/32 (6%)
Query: 494 IFIGGVPWDTPEYLLLTVFSQFGPV--KAVVM 523
+F+G + D + +L F + P V+
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVV 43
>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 = 28.6 bits (64), Expect = 1.8
Identities = 5/32 (15%), Positives = 13/32 (40%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVV 522
+ + G+P+ + ++ FS V +
Sbjct: 15 DGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGM 46
Score = 27.4 bits (61), Expect = 4.9
Identities = 5/30 (16%), Positives = 12/30 (40%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
+ + G+P+ + ++ FS V
Sbjct: 15 DGFVRLRGLPFGCSKEEIVQFFSGLEIVPN 44
>2j7j_A Transcription factor IIIA; zinc finger module, alternative
initiation, nuclear protein, phosphorylation,
hydrophobic core, zinc, RNA-binding; 1.65A {Xenopus
laevis} SCOP: g.37.1.1 g.37.1.1 g.37.1.1 PDB: 1un6_B
2hgh_A
Length = 85
Score = 28.0 bits (63), Expect = 1.8
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVH 234
+H+ PY C C + F LK H
Sbjct: 25 SHTQQLPYECPHEGCDKRFSLPSRLKRH 52
>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 = 29.0 bits (65), Expect = 1.8
Identities = 4/32 (12%), Positives = 15/32 (46%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVV 522
+++ G+P++ ++ F + V+ +
Sbjct: 25 GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSI 56
Score = 27.5 bits (61), Expect = 6.2
Identities = 4/29 (13%), Positives = 14/29 (48%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
+++ G+P++ ++ F + V+
Sbjct: 25 GFCVYLKGLPFEAENKHVIDFFKKLDIVE 53
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 29.8 bits (66), Expect = 1.9
Identities = 16/99 (16%), Positives = 28/99 (28%), Gaps = 24/99 (24%)
Query: 438 QYLH----NGDGGGQGGLQSTLDIAARHHRSSANSQIPQKTWEGVLPLRTQFSDEILSNK 493
+YLH D G LD R + + S +
Sbjct: 88 EYLHHIPDEEDIGKLALRTEVLDCFGREKFADYRE-----------DMGGIGSFRKKNKT 136
Query: 494 IFIGGVP---------WDTPEYLLLTVFSQFGPVKAVVM 523
+++GG+ E + VFS+ G + +
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRY 175
>2xcm_E RAR1, cytosolic heat shock protein 90; chaperone-protein binding
complex, stress response; HET: ADP; 2.20A {Arabidopsis
thaliana}
Length = 74
Score = 27.6 bits (61), Expect = 2.0
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 6/45 (13%)
Query: 179 AAFIEVKSGRICK----KLQIDPYLEDNVCSECQTHSGPYFCREG 219
AA I++ ++CK DN + C H GP +
Sbjct: 1 AAVIDINQPQVCKNKGCGQTFKE--RDNHETACSHHPGPAVFHDR 43
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 30.1 bits (67), Expect = 2.0
Identities = 25/140 (17%), Positives = 33/140 (23%), Gaps = 16/140 (11%)
Query: 234 HIGEYSQHDPIVRNVRKSPPSSPSGPHSGGLTLNTLNGFSSREDITTSSATSSPWFDSPL 293
H D + S +SP+G S + + P SP
Sbjct: 5 HHHHVDDDDKMFSTQVNSSLTSPTGRGS--------------MAAPSLHPSLGPGIGSPG 50
Query: 294 LTPMTPQIVRSPFESNSYAIHGSSHSPPFGSHSMESCSPPYLTDEGDYSPYYQTGGSTDY 353
+ SP N S S P G HSM + P L
Sbjct: 51 QLHSPISTLSSP--INGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSS 108
Query: 354 FSYNNAPSHLNLNGSMTDSS 373
P LN +
Sbjct: 109 SEDIKPPLGLNGVLKVPAHP 128
Score = 28.9 bits (64), Expect = 4.9
Identities = 25/125 (20%), Positives = 33/125 (26%), Gaps = 19/125 (15%)
Query: 304 SPFESNSYAIHGSSHSPPFGSHSMESCSPPYLTDEGDYSPYYQTGGSTDYFSYNNAPSHL 363
S SS + P G SM + S G SP + + S +
Sbjct: 13 DKMFSTQV---NSSLTSPTGRGSMAAPSLHPSLGPGIGSP------GQLHSPISTLSSPI 63
Query: 364 NLNGSMTDSSNLDNIEDLLASLSLNNTGQSNVRANGTAGSVPSPHTSPLNSPRSSGARHS 423
N G + S + S S SP S +P SS
Sbjct: 64 NGMGPPF----------SVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIK 113
Query: 424 PPSNG 428
PP
Sbjct: 114 PPLGL 118
Score = 27.8 bits (61), Expect = 9.5
Identities = 16/81 (19%), Positives = 28/81 (34%)
Query: 251 SPPSSPSGPHSGGLTLNTLNGFSSREDITTSSATSSPWFDSPLLTPMTPQIVRSPFESNS 310
SP + P S + + S T +T SP SP+ + + ++ P N
Sbjct: 61 SPINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNG 120
Query: 311 YAIHGSSHSPPFGSHSMESCS 331
+ S S + C+
Sbjct: 121 VLKVPAHPSGNMASFTKHICA 141
>2dkt_A Ring finger and CHY zinc finger domain- containing protein 1;
RCHY1, structural genomics, NPPSFA; NMR {Mus musculus}
SCOP: g.89.1.1 g.93.1.1 PDB: 2k2c_A
Length = 143
Score = 28.9 bits (64), Expect = 2.0
Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 10/58 (17%)
Query: 190 CKKLQIDPYLEDNVCSECQTHSGPYFCREGICYR-----YFCRSCWL-KVHIGEYSQH 241
C+KLQ C +C T G Y+C + Y C SC + ++ E H
Sbjct: 64 CEKLQ----HAQQTCEDCSTLFGEYYCSICHLFDKDKRQYHCESCGICRIGPKEDFFH 117
>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 = 27.8 bits (62), Expect = 2.1
Identities = 4/37 (10%), Positives = 16/37 (43%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAVVMNRAE 527
+ ++++G +P+ E ++ F+ + +
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGN 42
Score = 27.4 bits (61), Expect = 3.4
Identities = 4/28 (14%), Positives = 15/28 (53%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPV 51
+ ++++G +P+ E ++ F+ +
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRL 33
>2d8v_A Zinc finger FYVE domain-containing protein 19; zfyve19, ZF- B_BOX,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
g.43.1.1
Length = 67
Score = 27.3 bits (60), Expect = 2.2
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 225 FCRSCWLKVHIG-EYSQHDPIVRNVRKSPPSSPSGPHSG 262
+C C+ + H + +H + P SGP SG
Sbjct: 30 YCARCFREGHDNFDLKEH-QTSPYHPRRPCQEHSGPSSG 67
>2ent_A Krueppel-like factor 15; zinc binding, transcription factor,
adipogenesis, CLCNKA, chloride channel Ka, rhodopsin,
IRBP; NMR {Homo sapiens} SCOP: k.12.1.1
Length = 48
Score = 26.9 bits (60), Expect = 2.3
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVH 234
+ +G P+ C C F RS L H
Sbjct: 6 SGTGEKPFACTWPGCGWRFSRSDELSRH 33
>4fbd_A Putative uncharacterized protein; conserved hypothetical,
structural genomics, niaid, national institute of
allergy and infectious diseases; 2.35A {Toxoplasma
gondii}
Length = 243
Score = 29.7 bits (66), Expect = 2.3
Identities = 12/71 (16%), Positives = 21/71 (29%), Gaps = 3/71 (4%)
Query: 50 PVKVEWPQGTPESPTAPKAISLDVI--SELVLIL-GQWATEGNLCGRVEVVPWAISDSNY 106
PV W + A LD+I S + + + W+I
Sbjct: 129 PVLTRWFPMSYAKDALMPAAFLDLILYSREQIAKETAAESNTAVVIDPNAPAWSIIAVKA 188
Query: 107 SPQGHSTKLEP 117
+ +S + P
Sbjct: 189 QNEKYSLPMAP 199
>1ubd_C Protein (YY1 zinc finger domain); transcription initiation,
initiator element, zinc finger protein, DNA- protein
recognition; HET: DNA; 2.50A {Homo sapiens} SCOP:
g.37.1.1 g.37.1.1 g.37.1.1 g.37.1.1 PDB: 1znm_A*
Length = 124
Score = 28.6 bits (65), Expect = 2.4
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVHI 235
H+G PY C C + F +S LK HI
Sbjct: 86 IHTGDRPYVCPFDGCNKKFAQSTNLKSHI 114
Score = 28.3 bits (64), Expect = 2.9
Identities = 12/54 (22%), Positives = 18/54 (33%), Gaps = 20/54 (37%)
Query: 197 PYLEDNVCSEC--------------QTHSG--PYFCREGICYRYFCRSCWLKVH 234
+ VC+EC H+G P+ C C + F L+ H
Sbjct: 34 VH----VCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTH 83
>3sjr_A Uncharacterized protein; PSI-biology, MCSG, midwest center for
structural genomics, U function, structural genomics;
2.94A {Chromobacterium violaceum}
Length = 175
Score = 29.0 bits (64), Expect = 2.6
Identities = 15/85 (17%), Positives = 32/85 (37%), Gaps = 2/85 (2%)
Query: 69 ISLDVISELVLILGQWATEG-NLCGRVEVVPWAISDSNYSPQGHSTKLEPGKTIFVGALH 127
ISL ++ +L A + + +++ P + +S + HS L G I +
Sbjct: 50 ISLSQGAQAAALLFSAAMDQISRLAELDIEPVRLPESELTGDSHSQHLLLGMEILMELYR 109
Query: 128 GRLTAQALYNVMNDLFGDVVYAGID 152
+ + F + AG++
Sbjct: 110 QQHPDWTAPAIRQA-FAPLARAGLE 133
>2xag_A Lysine-specific histone demethylase 1; amine oxidase, chromatin
regulator, histone inhibitor binding, methylation,
nucleosome core, oxidoreductase; HET: FAD TCF; 3.10A
{Homo sapiens} PDB: 2xaf_A* 2xah_A* 2xaj_A* 2xaq_A*
2xas_A* 2com_A
Length = 852
Score = 29.6 bits (65), Expect = 3.1
Identities = 18/168 (10%), Positives = 38/168 (22%), Gaps = 21/168 (12%)
Query: 251 SPPSSPSGPHSGGLTLNTLNGFSSREDITTSSATSSPWFDSPLLTPMTPQIVRSPFESNS 310
+ + +GP + G + N + ++ + + TP+ P S
Sbjct: 17 AATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVG-----PGAVGERTPRKKEPPRASPP 71
Query: 311 YAIHGSSHSPPFGSHSMESCSPPYLTDEGDYSPYYQTGGSTDYFSYNNAPSHLNLNGSMT 370
+ S + + P +
Sbjct: 72 GGLAEPPGSAGPQAGPTVVPGSA----------------TPMETGIAETPEGRRTSRRKR 115
Query: 371 DSSNLDNIEDLLASLSLNNTGQSNVRANGTAGSVPSPHTSPLNSPRSS 418
+++ LA+LS + R P P P
Sbjct: 116 AKVEYREMDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAPPEEE 163
>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 = 28.9 bits (64), Expect = 3.1
Identities = 5/31 (16%), Positives = 10/31 (32%)
Query: 491 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKAV 521
SN + P + E + + G +
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPT 153
Score = 28.5 bits (63), Expect = 4.7
Identities = 5/29 (17%), Positives = 10/29 (34%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVK 52
SN + P + E + + G +
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKR 151
>2wbs_A Krueppel-like factor 4; transcription-DNA complex, DNA-binding,
transcription, metal-binding, DNA, protein, nucleus,
activator; 1.70A {Mus musculus} PDB: 2wbu_A
Length = 89
Score = 27.5 bits (62), Expect = 3.1
Identities = 12/28 (42%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 209 THSG--PYFCREGICYRYFCRSCWLKVH 234
TH+G PY C C F RS L H
Sbjct: 29 THTGEKPYHCDWDGCGWKFARSDELTRH 56
>2i50_A Ubiquitin carboxyl-terminal hydrolase 16; alpha/beta zinc-finger,
ring-finger, ZNF-UBP, metalloprotein, ubiquitin-binding
protein, USP; NMR {Homo sapiens}
Length = 126
Score = 28.1 bits (62), Expect = 3.4
Identities = 8/42 (19%), Positives = 15/42 (35%), Gaps = 2/42 (4%)
Query: 185 KSGRICKKLQIDPYLEDNVCSECQTHSGPYFCREGICYRYFC 226
IC+ + D ++D E + + C + C C
Sbjct: 26 VEWNICQDCKTDNKVKDKAEEETEEKPSVWLCLK--CGHQGC 65
>2pv0_B DNA (cytosine-5)-methyltransferase 3-like; DNMT3L, unmethylated
H3K4, de novo DNA methylation, transferase regulator;
HET: DNA; 3.30A {Homo sapiens} PDB: 2pvc_B*
Length = 386
Score = 29.2 bits (64), Expect = 3.5
Identities = 10/47 (21%), Positives = 15/47 (31%), Gaps = 1/47 (2%)
Query: 191 KKLQIDPYLEDNVCSECQTHSGPYFCREGICYRYFCRSCWLKVHIGE 237
D + CS C + C C R +C C + +G
Sbjct: 83 ALFLYDDDGYQSYCSICCSGETLLICGNPDCTRCYCFEC-VDSLVGP 128
>3mcr_A NADH dehydrogenase, subunit C; structural genomics, joint center
for structural genomics, J protein structure initiative,
PSI-2; 2.65A {Thermobifida fusca}
Length = 213
Score = 29.0 bits (65), Expect = 3.5
Identities = 20/109 (18%), Positives = 34/109 (31%), Gaps = 15/109 (13%)
Query: 398 NGTAGSVPSPHTSPLNSPRSSGARHSPPSNGGYYGGGGGGQYLHNGDGGGQGGLQSTLDI 457
NG G P L + +SP + G +G G D G G L+ +
Sbjct: 5 NGQQGKPNLPEKDNLPRELGTQRINSPIARMGMFGAKTTG------DTSGYGRLRVYRHV 58
Query: 458 AARHHRSSANSQIPQKTW---------EGVLPLRTQFSDEILSNKIFIG 497
A R ++ P+ + + + T + I + G
Sbjct: 59 PAAAQRPYSDPSDPRTAYFDEVADALERSLKEIGTPYDTAISRVVVDRG 107
>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 = 27.7 bits (62), Expect = 3.5
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 24 SNKIFIGGVPWDTPEYLLLTVFSQFGPVKV 53
+ + + G+P+ E + FS P++V
Sbjct: 15 GHCVHMRGLPYRATENDIYNFFSPLNPMRV 44
>1iue_A Ferredoxin; electron transport, iron-sulfur; 1.70A {Plasmodium
falciparum} SCOP: d.15.4.1
Length = 98
Score = 27.6 bits (62), Expect = 3.6
Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 5/30 (16%)
Query: 213 PYFCREGICYRYFCRSCWLKVHIGEYSQHD 242
PY CR G C +C K+ GE D
Sbjct: 36 PYSCRGGS-----CSTCAAKLVEGEVDNDD 60
>3a2s_X Outer membrane protein II; beta barrel, porin, neisseria mening
cell membrane, cell outer membrane, ION transport,
membrane transmembrane; HET: SUC LDA; 2.20A {Neisseria
meningitidis} PDB: 3a2r_X* 3a2t_X* 3a2u_X*
Length = 355
Score = 29.0 bits (65), Expect = 3.8
Identities = 2/37 (5%), Positives = 13/37 (35%)
Query: 341 YSPYYQTGGSTDYFSYNNAPSHLNLNGSMTDSSNLDN 377
+ +G + + + + + G++ + +
Sbjct: 110 NTVLKDSGDNVNAWESGSNTEDVLGLGTIGRVESREI 146
>1jq4_A Methane monooxygenase component C; [2Fe-2S] ferredoxin,
oxidoreductase; NMR {Methylococcus capsulatus str} SCOP:
d.15.4.2
Length = 98
Score = 27.2 bits (61), Expect = 4.0
Identities = 8/30 (26%), Positives = 10/30 (33%), Gaps = 5/30 (16%)
Query: 213 PYFCREGICYRYFCRSCWLKVHIGEYSQHD 242
CREG C +C G+Y
Sbjct: 39 MSSCREGG-----CATCKALCSEGDYDLKG 63
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 28.5 bits (63), Expect = 4.8
Identities = 9/40 (22%), Positives = 14/40 (35%), Gaps = 13/40 (32%)
Query: 203 VCSECQTHSGPYFCREGICYRY-----FCRSCWLKVHIGE 237
C EC+ + I R+ C C L V + +
Sbjct: 23 TCPECKVYPP------KIVERFSEGDVVCALCGL-V-LSD 54
>3a1b_A DNA (cytosine-5)-methyltransferase 3A, histone H3; zinc-finger,
histone binding, chromosomal protein, DNA damag repair,
DNA-binding, methylation; HET: DNA; 2.29A {Homo sapiens}
PDB: 3a1a_A*
Length = 159
Score = 28.2 bits (62), Expect = 4.8
Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 3/42 (7%)
Query: 196 DPYLEDNVCSECQTHSGPYFCREGICYRYFCRSCWLKVHIGE 237
D Y + C+ C C C R FC C + + +G
Sbjct: 76 DGY--QSYCTICCGGREVLMCGNNNCCRCFCVEC-VDLLVGP 114
>3p1u_A SUSD homolog; structural genomics, joint center for structural
genomics, J protein structure initiative, PSI-biology;
2.05A {Parabacteroides distasonis atcc 8503}
Length = 529
Score = 28.7 bits (63), Expect = 6.0
Identities = 21/164 (12%), Positives = 44/164 (26%), Gaps = 8/164 (4%)
Query: 311 YAIHGSSHSPPFGSHSME---SCSPPYLTDEGDYSPYYQTGGSTDYFSYNNAPSHLNLNG 367
A+ + S ++D+ D + + YN + +G
Sbjct: 193 LAVRLTEVDQEKCIAEANAAISSPAGLISDKADNAYMPPKADGSWGQDYNYTMFQITWSG 252
Query: 368 SMTDSSNLDNIEDLLASLSLNNTGQSNVRANGTAGSVPSPHTSPLNSPRSSGARHSPPSN 427
+ S +++ + ++ N T+G S PR+ N
Sbjct: 253 PICMSKSVEKLVT-----NIGGVAWPQGVVNQTSGVAVSSVHPEKVDPRAPKIFQPGIEN 307
Query: 428 GGYYGGGGGGQYLHNGDGGGQGGLQSTLDIAARHHRSSANSQIP 471
G + G G + G Q + L + +
Sbjct: 308 GDWKGLVYGPKAEEANTGIYQSKQCAELGFIIKDGYPYKSRPYD 351
>2wbt_A B-129; zinc finger; 2.70A {Sulfolobus virus 1}
Length = 129
Score = 27.6 bits (60), Expect = 6.0
Identities = 8/27 (29%), Positives = 10/27 (37%), Gaps = 2/27 (7%)
Query: 209 THSGPYFCREGICYRYFCRSCWLKVHI 235
+ C +C F S LK HI
Sbjct: 70 KAISQFVCP--LCLMPFSSSVSLKQHI 94
>1wx6_A Cytoplasmic protein NCK2; SH3 domain, structural genomics, signal
transduction, riken structural genomics/proteomics
initiative, RSGI; NMR {Homo sapiens}
Length = 91
Score = 26.7 bits (59), Expect = 6.6
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 397 ANGTAGSVPSPHTSPLNSPRSSGARHSPPSNG 428
A G G VP + L+ + HS PS+G
Sbjct: 60 ARGQVGLVPKNYVVVLSDGPALHPAHSGPSSG 91
>3c5k_A HD6, histone deacetylase 6; HDAC6, zinc finger, actin-binding,
chromatin regulator, cytoplasm, hydrolase,
metal-binding, nucleus, phosphoprotein; 1.55A {Homo
sapiens} PDB: 3gv4_A 3phd_A
Length = 109
Score = 26.9 bits (59), Expect = 6.8
Identities = 7/35 (20%), Positives = 12/35 (34%), Gaps = 2/35 (5%)
Query: 192 KLQIDPYLEDNVCSECQTHSGPYFCREGICYRYFC 226
+ C +C T + C CY+ +C
Sbjct: 15 PIPAAGLDVTQPCGDCGTIQENWVCL--SCYQVYC 47
>2bjr_A MFP2B; motility, nematode, MSP; 1.8A {Ascaris suum} SCOP: b.169.1.1
b.169.1.1
Length = 368
Score = 28.3 bits (62), Expect = 7.6
Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 7/78 (8%)
Query: 288 WFDSPLLTPMTPQIVRSPFESNSYAIHGSSHSPPFGSHSMES-----CSPPYLTDEGDYS 342
W P+ +P V++ + N Y + P + + CS PY ++ + +
Sbjct: 11 WAFGPIGSPFPDNPVKALGQQNMYVALWYKNGRPMHGRAWNNGGVIECSFPY--NKSELT 68
Query: 343 PYYQTGGSTDYFSYNNAP 360
GG Y
Sbjct: 69 GVKDLGGQIQVLQYKGNH 86
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
0.314 0.133 0.413
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,296,966
Number of extensions: 506073
Number of successful extensions: 1343
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1309
Number of HSP's successfully gapped: 484
Length of query: 534
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 436
Effective length of database: 3,965,535
Effective search space: 1728973260
Effective search space used: 1728973260
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: 60 (27.4 bits)