RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1534
(587 letters)
>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 = 108 bits (273), Expect = 1e-28
Identities = 48/81 (59%), Positives = 58/81 (71%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+ VFVANLDYKV KKL+EVF +AG V +I DKDGKSRG GTV F+ +EAVQ+ISM
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 220 LNNQNLFERRITVRMDRVADR 240
N Q LF+R + V+MD A
Sbjct: 76 FNGQLLFDRPMHVKMDERALP 96
Score = 67.3 bits (165), Expect = 5e-14
Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 504 SNRSMNQSSNIERDT-VVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGL 556
S+ S + V V NL + W++L++ F G + A+I K +G IG
Sbjct: 2 SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRG-IGT 60
Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
V F+ A +AI M + + + + V
Sbjct: 61 VTFEQSIEAVQAISMFNGQLLFDRPMHV 88
Score = 56.2 bits (136), Expect = 5e-10
Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 1/66 (1%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
S G V +IL D GK RG V F+ +A++ + R + +K E
Sbjct: 37 SMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD-ERAL 95
Query: 113 GRRNMG 118
+ +
Sbjct: 96 PKGDFF 101
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 94.6 bits (236), Expect = 8e-24
Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 1/81 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
++FV NL + K L++ F G V +I ++ +GKS+G G V+F+ P A ++ M
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRM 67
Query: 220 LNNQNLFERRITVRMDRVADR 240
+N L R I VR+DR A
Sbjct: 68 MNGMKLSGREIDVRIDRNASG 88
Score = 68.4 bits (168), Expect = 1e-14
Identities = 30/72 (41%), Positives = 45/72 (62%), Gaps = 6/72 (8%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVRFDSEWTAKRAIDMM 572
+ V+NLP TW+ L+DKF CG + +A+I K KG G+V+F+S A+RA MM
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKG-CGVVKFESPEVAERACRMM 68
Query: 573 DRTRIDGKIIDV 584
+ ++ G+ IDV
Sbjct: 69 NGMKLSGREIDV 80
Score = 53.0 bits (128), Expect = 4e-09
Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 4/75 (5%)
Query: 42 GDASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
L + G V Y +I + GK +G +V+F+SP++ +A M+ + GR+
Sbjct: 21 TWKMLKD--KFNECGHVLYADI-KMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGRE 77
Query: 102 LVIKEAVEDKGGRRN 116
+ ++ + G +
Sbjct: 78 IDVRID-RNASGPSS 91
>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 = 91.9 bits (229), Expect = 8e-23
Identities = 30/73 (41%), Positives = 42/73 (57%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
VFV NL+ +V E+ L E+F AG + V I D++GK + FG V F HP +I++
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76
Query: 220 LNNQNLFERRITV 232
LN L+ R I V
Sbjct: 77 LNGIRLYGRPINV 89
Score = 52.2 bits (126), Expect = 7e-09
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 43 DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
+ LY++ G +T V I D GKP+ V F+ P+ V A+ ++ GR +
Sbjct: 30 EEILYEL--FLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPI 87
Query: 103 VIKEA 107
+
Sbjct: 88 NVSGP 92
Score = 50.7 bits (122), Expect = 3e-08
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 7/73 (9%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDM 571
TV V NL + + L + F G + I K K G V F + AI +
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS-FGFVCFKHPESVSYAIAL 76
Query: 572 MDRTRIDGKIIDV 584
++ R+ G+ I+V
Sbjct: 77 LNGIRLYGRPINV 89
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 94.7 bits (236), Expect = 2e-22
Identities = 34/192 (17%), Positives = 80/192 (41%), Gaps = 36/192 (18%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
+ ++ Q + G + +++ D T K +G A VE++ P+ + A+ +M+ GR
Sbjct: 42 EDTIRQA--FAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRN 99
Query: 102 LVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINK 161
+ + + + L + F N+
Sbjct: 100 IKVGRPSNIGQAQPII-----------DQLAEEARAF---------------------NR 127
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
++VA++ + + ++ VF GK+++ +A D GK +G+G +E++ + ++S +
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 221 NNQNLFERRITV 232
N +L + + V
Sbjct: 188 NLFDLGGQYLRV 199
Score = 76.2 bits (188), Expect = 5e-16
Identities = 20/77 (25%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQ 215
++++V+V ++ Y++ E +R+ F G +++++++ D K +GF VE++ P A
Sbjct: 26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQL 85
Query: 216 SISMLNNQNLFERRITV 232
++ +N+ L R I V
Sbjct: 86 ALEQMNSVMLGGRNIKV 102
Score = 55.8 bits (135), Expect = 5e-09
Identities = 22/106 (20%), Positives = 41/106 (38%), Gaps = 15/106 (14%)
Query: 496 GNPRAGLDSNRSMNQSSNIERD-------TVVVKNLPPTITWQELRDKFRNCGDIKFAEI 548
G+ A + + M + S +R V V ++ + +R F G IK ++
Sbjct: 1 GSHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDM 60
Query: 549 -------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF 587
K KG V ++ A+ A++ M+ + G+ I V
Sbjct: 61 SWDSVTMKHKG-FAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP 105
Score = 48.5 bits (116), Expect = 1e-06
Identities = 15/98 (15%), Positives = 37/98 (37%), Gaps = 8/98 (8%)
Query: 494 GYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI----- 548
G + + + V ++ ++ +++ F G IK A +
Sbjct: 103 GRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPT 162
Query: 549 --KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
K KG G + ++ +++ A+ M+ + G+ + V
Sbjct: 163 TGKHKG-YGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
Score = 44.6 bits (106), Expect = 3e-05
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
G + + D TGK +G +E++ + AV+ M+ F+ G+ L + +AV
Sbjct: 147 EAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVT 204
>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 = 89.6 bits (223), Expect = 8e-22
Identities = 19/75 (25%), Positives = 41/75 (54%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
K+ V+NLD+ V + ++E+F G ++ + D+ G+S G V F+ +A++++
Sbjct: 30 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 89
Query: 220 LNNQNLFERRITVRM 234
N L R + +++
Sbjct: 90 YNGVPLDGRPMNIQL 104
Score = 58.1 bits (141), Expect = 9e-11
Identities = 15/93 (16%), Positives = 38/93 (40%), Gaps = 12/93 (12%)
Query: 500 AGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGD 553
+G + + +V NL ++ ++++ F G +K A + + G
Sbjct: 18 SGFGGGAGVETGGKL-----LVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG- 71
Query: 554 IGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
V F+ + A +A+ + +DG+ +++
Sbjct: 72 TADVHFERKADALKAMKQYNGVPLDGRPMNIQL 104
Score = 52.7 bits (127), Expect = 6e-09
Identities = 12/56 (21%), Positives = 24/56 (42%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
+ G + + D +G+ G+A V F+ KA+ + + GR + I+
Sbjct: 51 AEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT 106
>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 = 91.1 bits (227), Expect = 1e-21
Identities = 30/190 (15%), Positives = 68/190 (35%), Gaps = 48/190 (25%)
Query: 43 DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
A L +S + + +++ TG R V+F+S + + KA+ ++ + G ++
Sbjct: 27 VAELKVA--ISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEI 83
Query: 103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKV 162
+++ + +
Sbjct: 84 KLEKPKGRDSKKVRAA-----------------------------------------RTL 102
Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
NL + + E +L+EVF A ++ V +DGKS+G +EF +A +++
Sbjct: 103 LAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQG 158
Query: 223 QNLFERRITV 232
+ R +++
Sbjct: 159 AEIDGRSVSL 168
Score = 77.6 bits (192), Expect = 7e-17
Identities = 12/77 (15%), Positives = 32/77 (41%), Gaps = 1/77 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+F+ NL+ +L+ ++ + + G +R FG V+F+ + +++ +
Sbjct: 14 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALEL 73
Query: 220 LNNQNLFERRITVRMDR 236
+F I + +
Sbjct: 74 -TGLKVFGNEIKLEKPK 89
Score = 60.3 bits (147), Expect = 7e-11
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 3/72 (4%)
Query: 517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKG--KGDIGLVRFDSEWTAKRAIDMMDR 574
T++ KNL IT EL++ F + +I+ G KG I + F SE A++ ++
Sbjct: 100 RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKG-IAYIEFKSEADAEKNLEEKQG 158
Query: 575 TRIDGKIIDVTF 586
IDG+ + + +
Sbjct: 159 AEIDGRSVSLYY 170
Score = 54.1 bits (131), Expect = 1e-08
Identities = 12/73 (16%), Positives = 27/73 (36%), Gaps = 8/73 (10%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDM 571
+ + NL P + EL+ + + G V F+S ++A++
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK-FGYVDFESAEDLEKALE- 72
Query: 572 MDRTRIDGKIIDV 584
+ ++ G I +
Sbjct: 73 LTGLKVFGNEIKL 85
Score = 48.0 bits (115), Expect = 1e-06
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 5/60 (8%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
++ V GK +G A +EF+S K + + E GR + + E KG
Sbjct: 121 EDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE-KG 175
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 91.1 bits (226), Expect = 2e-21
Identities = 28/136 (20%), Positives = 53/136 (38%), Gaps = 2/136 (1%)
Query: 112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKV 171
G RRN R+ A G K+ V+NLD+ V
Sbjct: 41 GPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGV 100
Query: 172 DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT 231
+ ++E+F G ++ + D+ G+S G V F+ +A++++ L R +
Sbjct: 101 SDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMD 160
Query: 232 VRMDRVADRLDGPVRL 247
+++ VA ++D
Sbjct: 161 IQL--VASQIDLEHHH 174
Score = 59.5 bits (144), Expect = 1e-10
Identities = 19/133 (14%), Positives = 43/133 (32%), Gaps = 12/133 (9%)
Query: 460 SRNASNMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTV 519
+R GG + + +G + + +
Sbjct: 37 NRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKL----- 91
Query: 520 VVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMD 573
+V NL ++ ++++ F G +K A + + G V F+ A +A+
Sbjct: 92 LVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG-TADVHFERRADALKAMKQYK 150
Query: 574 RTRIDGKIIDVTF 586
+DG+ +D+
Sbjct: 151 GVPLDGRPMDIQL 163
Score = 53.7 bits (129), Expect = 1e-08
Identities = 12/65 (18%), Positives = 24/65 (36%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
+ G + + D +G+ G+A V F+ KA+ + GR + I+
Sbjct: 110 AEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQID 169
Query: 113 GRRNM 117
+
Sbjct: 170 LEHHH 174
>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 = 93.9 bits (234), Expect = 2e-21
Identities = 31/182 (17%), Positives = 59/182 (32%), Gaps = 51/182 (28%)
Query: 61 VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGG 120
E+ K +G+A V + + A+N H+ + R+L ++ D
Sbjct: 46 YELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD---------- 95
Query: 121 GGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVF 180
+ VANL + +++ E+
Sbjct: 96 ---------------------------------------ALLCVANLPPSLTQQQFEELV 116
Query: 181 RLAGKVENVEIALD-KDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV-RMDRVA 238
R G +E + + G+S+G+G E+ A ++ S L + L R + V D
Sbjct: 117 RPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ 176
Query: 239 DR 240
Sbjct: 177 LT 178
Score = 92.0 bits (229), Expect = 8e-21
Identities = 27/183 (14%), Positives = 53/183 (28%), Gaps = 42/183 (22%)
Query: 53 STVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
G + ++ + TG+ +G E+ D +A + + R L + D
Sbjct: 117 RPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT--DA 174
Query: 112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKV 171
G ALL + + V L
Sbjct: 175 GQLT------------PALLHSR--------------------------CLCVDRLPPGF 196
Query: 172 -DEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRI 230
D L ++A +DG+ +GF +E++ A ++ + +L +
Sbjct: 197 NDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHL 256
Query: 231 TVR 233
V
Sbjct: 257 RVS 259
Score = 67.3 bits (165), Expect = 1e-12
Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 6/82 (7%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
K+ + L V +++ ++ + E+ K +G V + +A +I+
Sbjct: 23 RKILIRGLPGDVTNQEVHDLL------SDYELKYCFVDKYKGTAFVTLLNGEQAEAAINA 76
Query: 220 LNNQNLFERRITVRMDRVADRL 241
+ L ER ++V++ L
Sbjct: 77 FHQSRLRERELSVQLQPTDALL 98
Score = 60.8 bits (148), Expect = 3e-10
Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
+ V NLPP++T Q+ + R G ++ + + KG G + + +A RA
Sbjct: 97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG-YGFAEYMKKDSAARAKS 155
Query: 571 MMDRTRIDGKIIDVTF 586
+ + + + V +
Sbjct: 156 DLLGKPLGPRTLYVHW 171
Score = 58.1 bits (141), Expect = 2e-09
Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 1/83 (1%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEW 563
+ R ++++ LP +T QE+ D + K KG V +
Sbjct: 10 KRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCFVDKYKG-TAFVTLLNGE 68
Query: 564 TAKRAIDMMDRTRIDGKIIDVTF 586
A+ AI+ ++R+ + + V
Sbjct: 69 QAEAAINAFHQSRLRERELSVQL 91
Score = 57.3 bits (139), Expect = 3e-09
Identities = 14/90 (15%), Positives = 31/90 (34%), Gaps = 8/90 (8%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTIT-WQELRDKFRNCGDIKFAEI------KGKGDIGL 556
++ + + + V LPP L F ++ + KG +
Sbjct: 172 TDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKG-FAV 230
Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
+ +++ A+ A D + G + V+F
Sbjct: 231 LEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing,
transcription, RNA binding protein, mRNA processing; NMR
{Homo sapiens} PDB: 2yh1_A
Length = 198
Score = 90.5 bits (225), Expect = 4e-21
Identities = 31/196 (15%), Positives = 70/196 (35%), Gaps = 29/196 (14%)
Query: 43 DASLYQI-SHLSTVGDVTYVE---ILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETK 98
+ ++ + +G +T +L + + A +EF+S D +A+ +
Sbjct: 18 EEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQ 76
Query: 99 GRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPL 158
G+ L I+ D M S
Sbjct: 77 GQSLKIRRP-HDYQPLPGMSENPS---------VYVPGVVSTVVPDSA------------ 114
Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSI 217
+K+F+ L +++ +++E+ G ++ + D G S+G+ E+ Q+I
Sbjct: 115 -HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173
Query: 218 SMLNNQNLFERRITVR 233
+ LN L ++++ V+
Sbjct: 174 AGLNGMQLGDKKLLVQ 189
Score = 62.0 bits (151), Expect = 3e-11
Identities = 11/80 (13%), Positives = 34/80 (42%), Gaps = 7/80 (8%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALD------KDGKSRGFGTVEFDHPVEA 213
+++V N+ + + E+ + + F ++ + A + + + F +EF E
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 214 VQSISMLNNQNLFERRITVR 233
Q+++ + + + +R
Sbjct: 65 TQAMAF-DGIIFQGQSLKIR 83
Score = 49.6 bits (119), Expect = 4e-07
Identities = 13/68 (19%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
D + ++ L++ G + ++ D TG +G A E+ ++ +A+ ++ + +K
Sbjct: 128 DDQVKEL--LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185
Query: 102 LVIKEAVE 109
L+++ A
Sbjct: 186 LLVQRASV 193
Score = 46.9 bits (112), Expect = 4e-06
Identities = 14/103 (13%), Positives = 34/103 (33%), Gaps = 14/103 (13%)
Query: 497 NPRAGLDSNRSMNQSSNIER------DTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-- 548
P G+ N S+ + + + LP + ++++ + G +K +
Sbjct: 89 QPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK 148
Query: 549 -----KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
KG + +AI ++ ++ K + V
Sbjct: 149 DSATGLSKG-YAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 190
Score = 38.9 bits (91), Expect = 0.002
Identities = 12/78 (15%), Positives = 24/78 (30%), Gaps = 12/78 (15%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI-----------GLVRFDSEWTAK 566
+ V N+P IT + + D F + + + F S
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 567 RAIDMMDRTRIDGKIIDV 584
+A+ D G+ + +
Sbjct: 66 QAMA-FDGIIFQGQSLKI 82
>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 = 88.8 bits (221), Expect = 7e-21
Identities = 36/195 (18%), Positives = 74/195 (37%), Gaps = 49/195 (25%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
+ ++G++ +++ D TG+ G V + P KA+N ++ + +
Sbjct: 16 QEEFRSL--FGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKT 73
Query: 102 LVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINK 161
+ + A + +S+ +
Sbjct: 74 IKVSYA------------------------RPSSASIRDA-------------------N 90
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
++V+ L + +K+L ++F G++ I +D+ G SRG G + FD +EA ++I L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 221 NNQNL--FERRITVR 233
N Q ITV+
Sbjct: 151 NGQKPSGATEPITVK 165
Score = 73.0 bits (180), Expect = 3e-15
Identities = 23/88 (26%), Positives = 43/88 (48%), Gaps = 1/88 (1%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
+ V L + +++ R +F G++E+ ++ DK G+S G+G V + P +A ++I+
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 220 LNNQNLFERRITVRMDRVADRLDGPVRL 247
LN L + I V R + L
Sbjct: 64 LNGLRLQTKTIKVSYARPSSASIRDANL 91
Score = 51.0 bits (123), Expect = 8e-08
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V LP +T +E R F + G+I+ ++ + G G V + A++AI+ ++
Sbjct: 7 VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLG-YGFVNYIDPKDAEKAINTLN 65
Query: 574 RTRIDGKIIDVTF 586
R+ K I V++
Sbjct: 66 GLRLQTKTIKVSY 78
Score = 49.5 bits (119), Expect = 3e-07
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 505 NRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLV 557
+ + S++I + V LP T+T +EL F G I + I +G +G +
Sbjct: 77 SYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG-VGFI 135
Query: 558 RFDSEWTAKRAIDMMDRTRIDG 579
RFD A+ AI ++ + G
Sbjct: 136 RFDKRIEAEEAIKGLNGQKPSG 157
Score = 34.9 bits (81), Expect = 0.031
Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 5/68 (7%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMH--RFETKG 99
L Q+ S G + IL D TG RG + F +A+ ++ +
Sbjct: 102 QKELEQL--FSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAT 159
Query: 100 RKLVIKEA 107
+ +K A
Sbjct: 160 EPITVKFA 167
>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 = 87.6 bits (218), Expect = 2e-20
Identities = 40/195 (20%), Positives = 69/195 (35%), Gaps = 49/195 (25%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
D LY + +G + I+ D TG G A V+F S ++A+ ++ + ++
Sbjct: 17 DRELYAL--FRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR 74
Query: 102 LVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINK 161
L + A GG
Sbjct: 75 LKVSYA--RPGGESIKDT-----------------------------------------N 91
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
++V NL + + +L +F G + I DK G+ RG V ++ EA ++IS L
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 221 NNQNL--FERRITVR 233
NN + ++VR
Sbjct: 152 NNVIPEGGSQPLSVR 166
Score = 76.1 bits (188), Expect = 2e-16
Identities = 18/85 (21%), Positives = 38/85 (44%), Gaps = 2/85 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
+ V L + +++L +FR G + I D G S G+ V+F +++ ++I +
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 220 LNNQNLFERRITV-RMDRVADRLDG 243
LN + +R+ V + +
Sbjct: 65 LNGITVRNKRLKVSYARPGGESIKD 89
Score = 52.6 bits (127), Expect = 3e-08
Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 8/82 (9%)
Query: 505 NRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLV 557
+ + +I+ + V NLP TIT +L F G I I + +G + V
Sbjct: 78 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRG-VAFV 136
Query: 558 RFDSEWTAKRAIDMMDRTRIDG 579
R++ A+ AI ++ +G
Sbjct: 137 RYNKREEAQEAISALNNVIPEG 158
Score = 52.2 bits (126), Expect = 4e-08
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 8/76 (10%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
++V LP +T +EL FR G I I G V F SE ++RAI
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYG-YAFVDFTSEMDSQRAIK 63
Query: 571 MMDRTRIDGKIIDVTF 586
+++ + K + V++
Sbjct: 64 VLNGITVRNKRLKVSY 79
Score = 36.8 bits (86), Expect = 0.007
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 5/68 (7%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKG-- 99
D L I G + IL D TG+PRG A V + + ++A++ ++ +G
Sbjct: 103 DDQLDTI--FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGS 160
Query: 100 RKLVIKEA 107
+ L ++ A
Sbjct: 161 QPLSVRLA 168
>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 = 86.3 bits (214), Expect = 2e-20
Identities = 21/88 (23%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
K+ V+NLD+ V + ++E+F G ++ + D+ G+S G V F+ +A++++
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95
Query: 220 LNNQNLFERRITVRMDRVADRLDGPVRL 247
L R + +++ VA ++D
Sbjct: 96 YKGVPLDGRPMDIQL--VASQIDLEHHH 121
Score = 56.2 bits (136), Expect = 7e-10
Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 7/72 (9%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMDR 574
V NL ++ ++++ F G +K A + + G V F+ A +A+
Sbjct: 40 VSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLG-TADVHFERRADALKAMKQYKG 98
Query: 575 TRIDGKIIDVTF 586
+DG+ +D+
Sbjct: 99 VPLDGRPMDIQL 110
Score = 54.3 bits (131), Expect = 3e-09
Identities = 12/63 (19%), Positives = 24/63 (38%), Gaps = 1/63 (1%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
+ G + + D +G+ G+A V F+ KA+ + GR + I+ +
Sbjct: 57 AEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV-ASQI 115
Query: 113 GRR 115
Sbjct: 116 DLE 118
>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 = 86.8 bits (216), Expect = 4e-20
Identities = 32/191 (16%), Positives = 63/191 (32%), Gaps = 44/191 (23%)
Query: 43 DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
+ L Q G + ++I+ D K A VE+ A+ ++ + + +
Sbjct: 14 EDILKQY--FQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIV 71
Query: 103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKV 162
I A + + + +
Sbjct: 72 KINWAFQSQQSSSDDTF-----------------------------------------NL 90
Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLN 221
FV +L+ VD++ LR F+ + + D G SRG+G V F +A ++ +
Sbjct: 91 FVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ 150
Query: 222 NQNLFERRITV 232
Q+L R + +
Sbjct: 151 GQDLNGRPLRI 161
Score = 74.9 bits (185), Expect = 6e-16
Identities = 18/71 (25%), Positives = 40/71 (56%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
++V NLD + E L++ F++ G + N++I +DK+ K+ + VE+ +A ++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 222 NQNLFERRITV 232
+ + + +
Sbjct: 63 GKQIENNIVKI 73
Score = 47.5 bits (114), Expect = 1e-06
Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 7/75 (9%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDM 571
+ V NL IT L+ F+ G I +I K V + A A+
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVN-YAFVEYHQSHDANIALQT 60
Query: 572 MDRTRIDGKIIDVTF 586
++ +I+ I+ + +
Sbjct: 61 LNGKQIENNIVKINW 75
Score = 47.5 bits (114), Expect = 1e-06
Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 8/73 (10%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V +L + + LR+ F++ + +G G V F S+ A+ A+D M
Sbjct: 92 VGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG-YGFVSFTSQDDAQNAMDSMQ 150
Query: 574 RTRIDGKIIDVTF 586
++G+ + + +
Sbjct: 151 GQDLNGRPLRINW 163
Score = 32.5 bits (75), Expect = 0.17
Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 3/66 (4%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
D +L ++ D TG RG V F S D + A++ M + GR
Sbjct: 101 DETLRNA--FKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP 158
Query: 102 LVIKEA 107
L I A
Sbjct: 159 LRINWA 164
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 84.8 bits (210), Expect = 4e-20
Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+V A L+ V E L+++ R G+VE VEI L K G V F A +++
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
Query: 219 MLNNQNLFERRITVRMDR 236
L+ ++ I ++D
Sbjct: 67 NLHLTSVMGNIIHAQLDI 84
Score = 62.8 bits (153), Expect = 2e-12
Identities = 19/76 (25%), Positives = 28/76 (36%), Gaps = 8/76 (10%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
V L + L+D R G+++ EI K G + V F S AK +
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLG-LARVLFTSTRGAKETVK 66
Query: 571 MMDRTRIDGKIIDVTF 586
+ T + G II
Sbjct: 67 NLHLTSVMGNIIHAQL 82
Score = 50.1 bits (120), Expect = 6e-08
Identities = 19/67 (28%), Positives = 28/67 (41%), Gaps = 3/67 (4%)
Query: 51 HLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
G+V VEIL T K G A V F S ++ V +H G + + ++
Sbjct: 26 MCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQ--LD 83
Query: 110 DKGGRRN 116
KG +R
Sbjct: 84 IKGQQRM 90
>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 = 89.3 bits (222), Expect = 6e-20
Identities = 34/184 (18%), Positives = 65/184 (35%), Gaps = 41/184 (22%)
Query: 53 STVGDVTY-VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
+ V + + + R A ++ S + R V K++ + +G LV K + +
Sbjct: 139 QDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS--NP 196
Query: 112 GGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKV 171
+ R SA L+ ++ + NL ++
Sbjct: 197 LEKS--------KRTDSATLEGR--------------------------EIMIRNLSTEL 222
Query: 172 -DEKKLREVFRLAGKVENVEIALDKD--GKSRGFGTVEFDHPVEAVQSISMLNNQNLFER 228
DE LRE F G +E + I + + + F++ A +++ M N L R
Sbjct: 223 LDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQM-NRSLLGNR 281
Query: 229 RITV 232
I+V
Sbjct: 282 EISV 285
Score = 87.7 bits (218), Expect = 3e-19
Identities = 21/182 (11%), Positives = 52/182 (28%), Gaps = 53/182 (29%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
G + +V++ D K A +EF D A+ K H+ ++++ E
Sbjct: 63 KHCGPIIHVDVA-DSLKKNFRFARIEFARYDGALAAITKTHKVV-GQNEIIVSHLTE--- 117
Query: 113 GRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVD 172
+++ N
Sbjct: 118 -----------------------------------------------CTLWMTNFPPSYT 130
Query: 173 EKKLREVFRLAGKVE-NVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRIT 231
++ +R++ + V ++ + + SR F ++ +A + LN + +
Sbjct: 131 QRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLV 190
Query: 232 VR 233
+
Sbjct: 191 TK 192
Score = 73.9 bits (182), Expect = 1e-14
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
V V NL ++ K+ + F+ G + +V++A K+ F +EF A+ +I+ +
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL-KKNFRFARIEFARYDGALAAITKTH 102
Query: 222 NQNLFERRITV 232
+ + I V
Sbjct: 103 KV-VGQNEIIV 112
Score = 61.5 bits (150), Expect = 1e-10
Identities = 11/77 (14%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKR 567
T+ + N PP+ T + +RD ++ + + + + S+ A+
Sbjct: 116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRR-FAYIDVTSKEDARY 174
Query: 568 AIDMMDRTRIDGKIIDV 584
++ ++ +I+G +
Sbjct: 175 CVEKLNGLKIEGYTLVT 191
Score = 57.7 bits (140), Expect = 3e-09
Identities = 23/99 (23%), Positives = 41/99 (41%), Gaps = 9/99 (9%)
Query: 496 GNPRAGLDSNRSMNQSSNIERD--TVVVKNLPPTITWQELRDKFRNCGDIK-----FAEI 548
G+P A +++ N++ R+ TV+VKNLP + ++ F++CG I +
Sbjct: 19 GSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK 78
Query: 549 KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF 587
K + F A AI + + I V+
Sbjct: 79 KNFR-FARIEFARYDGALAAITKTHK-VVGQNEIIVSHL 115
Score = 46.9 bits (112), Expect = 9e-06
Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 11/87 (12%)
Query: 509 NQSSNIERDTVVVKNLPPTIT-WQELRDKFRNCGDIKFAEI--------KGKGDIGLVRF 559
S+ +E ++++NL + LR+ F G I+ I + F
Sbjct: 203 TDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNC-CAFMVF 261
Query: 560 DSEWTAKRAIDMMDRTRIDGKIIDVTF 586
+++ +A+RA+ M+R+ + + I V+
Sbjct: 262 ENKDSAERALQ-MNRSLLGNREISVSL 287
>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 = 86.0 bits (214), Expect = 8e-20
Identities = 41/186 (22%), Positives = 69/186 (37%), Gaps = 48/186 (25%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
+ G VT ++I+ D TG+ RG + F+ P V + V H G+ + K A+
Sbjct: 22 EYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHIL--DGKVIDPKRAI 79
Query: 109 EDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLD 168
+ K+FV +
Sbjct: 80 PRDEQDKT-------------------------------------------GKIFVGGIG 96
Query: 169 YKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFE 227
V K+ E F G + + ++ LDKD G+SRGFG V +D +AV + + +
Sbjct: 97 PDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA-DAVDRVCQNKFIDFKD 155
Query: 228 RRITVR 233
R+I ++
Sbjct: 156 RKIEIK 161
Score = 62.9 bits (154), Expect = 8e-12
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHP--VEAVQS 216
K+F+ L++ E LRE F G V +++I D G+SRGFG + F+ P V+ V
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Score = 46.8 bits (112), Expect = 3e-06
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 51 HLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
S G + +++ D DTG+ RG V + S D V + + + K RK+ IK A
Sbjct: 107 FFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC-QNKFIDFKDRKIEIKRAE 164
Score = 43.7 bits (104), Expect = 3e-05
Identities = 16/90 (17%), Positives = 34/90 (37%), Gaps = 9/90 (10%)
Query: 502 LDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDI 554
+D R++ + + + V + P + +E + F G I A++ + +G
Sbjct: 73 IDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRG-F 131
Query: 555 GLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
G V +DS R + I++
Sbjct: 132 GFVTYDSADAVDRVCQ-NKFIDFKDRKIEI 160
Score = 40.2 bits (95), Expect = 5e-04
Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 10/74 (13%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
+ + L T LR+ F G + +I + +G G + F+ +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRG-FGFLSFEKPSSVDEV-- 61
Query: 571 MMDRTRIDGKIIDV 584
+ + +DGK+ID
Sbjct: 62 VKTQHILDGKVIDP 75
>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 = 85.4 bits (212), Expect = 2e-19
Identities = 32/187 (17%), Positives = 54/187 (28%), Gaps = 45/187 (24%)
Query: 53 STVGDVTYVEILNDDTGKP---RGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
G V + +L D + P +G V F + +A N +H + +
Sbjct: 25 EQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKP 84
Query: 110 DKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY 169
+ N K+F+ +
Sbjct: 85 ADSEKNNAVED---------------------------------------RKLFIGMISK 105
Query: 170 KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFE-- 227
K E +R +F G++E I DG SRG V F A +I ++ E
Sbjct: 106 KCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGC 165
Query: 228 -RRITVR 233
+ V+
Sbjct: 166 SSPMVVK 172
Score = 72.3 bits (178), Expect = 6e-15
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 3/83 (3%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDG---KSRGFGTVEFDHPVEAVQSI 217
K+FV + EK LRE+F G V + + D+ +S+G V F A+++
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 218 SMLNNQNLFERRITVRMDRVADR 240
+ L+N + + AD
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADS 87
Score = 47.2 bits (113), Expect = 2e-06
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 7/63 (11%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMDR 574
+ + T ++R F + G I+ I +G V F + A+ AI M +
Sbjct: 100 IGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRG-CAFVTFTTRAMAQTAIKAMHQ 158
Query: 575 TRI 577
+
Sbjct: 159 AQT 161
Score = 45.3 bits (108), Expect = 1e-05
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH---RFETKGRKLVIKEA 107
G + IL G RG A V F + + + A+ MH E +V+K A
Sbjct: 120 GQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
Score = 43.4 bits (103), Expect = 4e-05
Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 10/76 (13%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI---------KGKGDIGLVRFDSEWTAKRA 568
+ V +P T + ++LR+ F G + + + KG V F + A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKG-CCFVTFYTRKAALEA 63
Query: 569 IDMMDRTRIDGKIIDV 584
+ + ++ +
Sbjct: 64 QNALHNMKVLPGMHHP 79
>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 = 82.8 bits (205), Expect = 2e-19
Identities = 23/73 (31%), Positives = 41/73 (56%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
K+F+ L+ + +EK L+ VF G + V + D+ KSRGF + F++P +A +
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67
Query: 220 LNNQNLFERRITV 232
+N ++L + I V
Sbjct: 68 MNGKSLHGKAIKV 80
Score = 52.7 bits (127), Expect = 1e-08
Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 7/70 (10%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMDR 574
+ L + L+ F G I + K +G + F++ AK A M+
Sbjct: 12 IGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRG-FAFITFENPADAKNAAKDMNG 70
Query: 575 TRIDGKIIDV 584
+ GK I V
Sbjct: 71 KSLHGKAIKV 80
Score = 51.6 bits (124), Expect = 2e-08
Identities = 16/73 (21%), Positives = 32/73 (43%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
G ++ V ++ D T K RG A + F++P + A M+ G+ + +++A +
Sbjct: 32 GPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSG 91
Query: 116 NMGGGGGVDRDLS 128
R+ S
Sbjct: 92 GRRRPPASSRNRS 104
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 81.9 bits (203), Expect = 3e-19
Identities = 17/73 (23%), Positives = 43/73 (58%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+K+F++ L + +++L E+ + G V+++ + ++ GK +G VE+++ +A Q++
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMK 77
Query: 220 LNNQNLFERRITV 232
++ + E I V
Sbjct: 78 MDGMTIKENIIKV 90
Score = 55.4 bits (134), Expect = 6e-10
Identities = 23/93 (24%), Positives = 42/93 (45%), Gaps = 7/93 (7%)
Query: 500 AGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGD 553
S+ S+++E+ + + LP + T +EL + + G +K + K KG
Sbjct: 1 GSSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKG- 59
Query: 554 IGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
+ V +++E A +A+ MD I II V
Sbjct: 60 LAYVEYENESQASQAVMKMDGMTIKENIIKVAI 92
Score = 51.1 bits (123), Expect = 2e-08
Identities = 14/55 (25%), Positives = 26/55 (47%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
G V + ++ + GKP+G A VE+++ +AV KM K + + +
Sbjct: 39 KAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS 93
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 79.9 bits (198), Expect = 1e-18
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
++V L +VD+K L F G + +++I LD + K RGF VEF+ +A +I
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 219 MLNNQNLFERRITV 232
+N LF R I V
Sbjct: 68 NMNESELFGRTIRV 81
Score = 46.4 bits (111), Expect = 8e-07
Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 8/74 (10%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
+ V L + + L F GDI +I K +G V F+ A AID
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG-FAFVEFELAEDAAAAID 67
Query: 571 MMDRTRIDGKIIDV 584
M+ + + G+ I V
Sbjct: 68 NMNESELFGRTIRV 81
Score = 45.2 bits (108), Expect = 2e-06
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 56 GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
GD+T ++I D +T K RG A VEF+ + A++ M+ E GR + + A
Sbjct: 32 GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84
>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 = 79.8 bits (197), Expect = 2e-18
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 1/83 (1%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEW 563
S S S + VVV LPP+ +WQ+L+D R GD+ +A++ G G+V F +
Sbjct: 3 SGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKE 61
Query: 564 TAKRAIDMMDRTRIDGKIIDVTF 586
A+ +D T+ + +
Sbjct: 62 DMTYAVRKLDNTKFRSHEGETAY 84
Score = 63.3 bits (154), Expect = 1e-12
Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
N+V V+ L + L++ R AG V ++ G G VEF + ++
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADV------YRDGTGVVEFVRKEDMTYAVRK 69
Query: 220 LNNQNLFERRITVRMDRVADRLDGP 244
L+N RV ++DGP
Sbjct: 70 LDNTKFRSHEGETAYIRV--KVDGP 92
Score = 49.4 bits (118), Expect = 1e-07
Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 6/72 (8%)
Query: 51 HLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED 110
H+ GDV Y ++ D TG +VEF + + AV K+ + + +
Sbjct: 35 HMREAGDVCYADVYRDGTG------VVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 88
Query: 111 KGGRRNMGGGGG 122
G R+ G
Sbjct: 89 VDGPRSPSYGRS 100
>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 = 79.6 bits (197), Expect = 2e-18
Identities = 26/73 (35%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
V+V LD KV E L E+F AG V N + D+ G+ +G+G VEF +A +I +
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 220 LNNQNLFERRITV 232
++ L+ + I V
Sbjct: 77 MDMIKLYGKPIRV 89
Score = 50.7 bits (122), Expect = 4e-08
Identities = 16/79 (20%), Positives = 30/79 (37%), Gaps = 3/79 (3%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
+ L+++ G V + D TG+ +G VEF S + A+ M + G+
Sbjct: 29 EPLLWEL--FLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKP 86
Query: 102 LVIKEAVEDKGGRRNMGGG 120
+ + +A G
Sbjct: 87 IRVNKASAHNKNLSGPSSG 105
Score = 43.8 bits (104), Expect = 9e-06
Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 8/74 (10%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
TV V L ++ L + F G + + + +G G V F SE A AI
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQG-YGFVEFLSEEDADYAIK 75
Query: 571 MMDRTRIDGKIIDV 584
+MD ++ GK I V
Sbjct: 76 IMDMIKLYGKPIRV 89
>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 = 82.0 bits (203), Expect = 4e-18
Identities = 45/187 (24%), Positives = 71/187 (37%), Gaps = 43/187 (22%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVN-KMHRFETKGRKLVIKEA 107
SH G +T ++ D +T + RG V + + + V A+N + H+ + GR + K A
Sbjct: 32 SHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVD--GRVVEPKRA 89
Query: 108 VEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANL 167
V R + G + K+FV +
Sbjct: 90 V----SREDSQRPGAHLT---------------------------------VKKIFVGGI 112
Query: 168 DYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLF 226
+E LR+ F GK+E +EI D+ GK RGF V FD ++V I + +
Sbjct: 113 KEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIVIQKYHTVN 171
Query: 227 ERRITVR 233
VR
Sbjct: 172 GHNCEVR 178
Score = 60.4 bits (147), Expect = 1e-10
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEA 213
K+F+ L ++ ++ LR F G + + + D + +SRGFG V + E
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68
Score = 47.7 bits (114), Expect = 2e-06
Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 6/77 (7%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
+ G + +EI+ D +GK RG A V F D V K V G +++A+
Sbjct: 123 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKAL 181
Query: 109 EDKGGRRNMGGGGGVDR 125
++ M R
Sbjct: 182 S----KQEMASASSSQR 194
Score = 39.6 bits (93), Expect = 0.001
Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 9/71 (12%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V + LRD F G I+ EI K +G V FD + + +
Sbjct: 109 VGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRG-FAFVTFDDHDSVDKIVIQKY 167
Query: 574 RTRIDGKIIDV 584
T ++G +V
Sbjct: 168 HT-VNGHNCEV 177
Score = 38.4 bits (90), Expect = 0.003
Identities = 12/71 (16%), Positives = 28/71 (39%), Gaps = 9/71 (12%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
+ L T + LR F G + + + +G G V + + A++
Sbjct: 18 IGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG-FGFVTYATVEEVDAAMN-AR 75
Query: 574 RTRIDGKIIDV 584
++DG++++
Sbjct: 76 PHKVDGRVVEP 86
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 80.2 bits (198), Expect = 4e-18
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
++V L +VD+K L F G + +++I LD + K RGF VEF+ +A +I
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 219 MLNNQNLFERRITV 232
+N LF R I V
Sbjct: 124 NMNESELFGRTIRV 137
Score = 49.0 bits (117), Expect = 3e-07
Identities = 23/105 (21%), Positives = 39/105 (37%), Gaps = 9/105 (8%)
Query: 487 QASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFA 546
+ + + G + S+ +R + V L + + L F GDI
Sbjct: 35 AYTCVNCTERHVDGGSGGSGGSGGSATTKR-VLYVGGLAEEVDDKVLHAAFIPFGDITDI 93
Query: 547 EI-------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
+I K +G V F+ A AID M+ + + G+ I V
Sbjct: 94 QIPLDYETEKHRG-FAFVEFELAEDAAAAIDNMNESELFGRTIRV 137
Score = 44.4 bits (105), Expect = 1e-05
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 56 GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
GD+T ++I D +T K RG A VEF+ + A++ M+ E GR + + A
Sbjct: 88 GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 83.2 bits (206), Expect = 5e-18
Identities = 31/187 (16%), Positives = 52/187 (27%), Gaps = 56/187 (29%)
Query: 43 DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
+ ++ G+ + V I D RG + +S L A ++ K R L
Sbjct: 36 EEDFKRL--FERYGEPSEVFINRD-----RGFGFIRLESRTLAEIAKAELDGTILKSRPL 88
Query: 103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKV 162
I+ A +
Sbjct: 89 RIRFATHGA-------------------------------------------------AL 99
Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
V NL V + L + F G VE + +D G++ G G VEF A +++ +
Sbjct: 100 TVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGD 159
Query: 223 QNLFERR 229
Sbjct: 160 GAFLLTT 166
Score = 67.4 bits (165), Expect = 1e-12
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
++FV NL + E+ + +F G+ V I + RGFG + + A + +
Sbjct: 23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFI-----NRDRGFGFIRLESRTLAEIAKAE 77
Query: 220 LNNQNLFERRITVR 233
L+ L R + +R
Sbjct: 78 LDGTILKSRPLRIR 91
Score = 55.1 bits (133), Expect = 1e-08
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 515 ERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMD 573
+R + V NLP IT ++ + F G+ I + +G G +R +S A+ A +D
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRG-FGFIRLESRTLAEIAKAELD 79
Query: 574 RTRIDGKIIDVTF 586
T + + + + F
Sbjct: 80 GTILKSRPLRIRF 92
Score = 48.1 bits (115), Expect = 3e-06
Identities = 27/160 (16%), Positives = 47/160 (29%), Gaps = 20/160 (12%)
Query: 43 DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
+ L Q S G V ++ DD G+ G VEF + RKA+ +
Sbjct: 110 NELLEQA--FSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTT 167
Query: 103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINK- 161
VE + G L L + ++ P+F + ++
Sbjct: 168 PRPVIVEPMEQFDDEDG-------LPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRW 220
Query: 162 ----VFVANLDYKVD------EKKLREVFRLAGKVENVEI 191
+VD ++KL A + +
Sbjct: 221 KALDEMEKQQREQVDRNIREAKEKLEAEMEAARHEHQLML 260
Score = 45.1 bits (107), Expect = 3e-05
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMD 573
VKNL P ++ + L F G ++ A + + G G V F ++ A++A++
Sbjct: 101 VKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATG-KGFVEFAAKPPARKALERCG 158
>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 = 80.7 bits (200), Expect = 6e-18
Identities = 28/196 (14%), Positives = 69/196 (35%), Gaps = 49/196 (25%)
Query: 43 DASLYQI-SHLSTVGDVTYVE---ILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETK 98
+ ++ + +G +T +L + + A +EF+S D +A+ +
Sbjct: 18 EEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQ 76
Query: 99 GRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPL 158
G+ L I+ + +
Sbjct: 77 GQSLKIRRPHDYQPLPGA------------------------------------------ 94
Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSI 217
+K+F+ L +++ +++E+ G ++ + D G S+G+ E+ Q+I
Sbjct: 95 -HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Query: 218 SMLNNQNLFERRITVR 233
+ LN L ++++ V+
Sbjct: 154 AGLNGMQLGDKKLLVQ 169
Score = 61.9 bits (151), Expect = 2e-11
Identities = 14/93 (15%), Positives = 38/93 (40%), Gaps = 7/93 (7%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALD------KDGKSRGFGTVEFDHPVEAV 214
+++V N+ + + E+ + + F ++ + A + + + F +EF E
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 215 QSISMLNNQNLFERRITVRMDRVADRLDGPVRL 247
Q+++ + + + +R L G +L
Sbjct: 66 QAMAF-DGIIFQGQSLKIRRPHDYQPLPGAHKL 97
Score = 50.3 bits (121), Expect = 2e-07
Identities = 12/90 (13%), Positives = 30/90 (33%), Gaps = 8/90 (8%)
Query: 502 LDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDI 554
L R + + + LP + ++++ + G +K + KG
Sbjct: 80 LKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKG-Y 138
Query: 555 GLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
+ +AI ++ ++ K + V
Sbjct: 139 AFCEYVDINVTDQAIAGLNGMQLGDKKLLV 168
Score = 46.5 bits (111), Expect = 4e-06
Identities = 13/66 (19%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
D + ++ L++ G + ++ D TG +G A E+ ++ +A+ ++ + +K
Sbjct: 108 DDQVKEL--LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 165
Query: 102 LVIKEA 107
L+++ A
Sbjct: 166 LLVQRA 171
Score = 38.7 bits (91), Expect = 0.002
Identities = 12/78 (15%), Positives = 24/78 (30%), Gaps = 12/78 (15%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI-----------GLVRFDSEWTAK 566
+ V N+P IT + + D F + + + F S
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 567 RAIDMMDRTRIDGKIIDV 584
+A+ D G+ + +
Sbjct: 66 QAMA-FDGIIFQGQSLKI 82
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 77.2 bits (191), Expect = 1e-17
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+ V L E+ LREVF G + +V I D+ +SRGF V F++ +A ++
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
Query: 219 MLNNQNLFERRITV 232
N L RRI V
Sbjct: 76 RANGMELDGRRIRV 89
Score = 48.7 bits (117), Expect = 1e-07
Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 503 DSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIG 555
S S N+++ + V L T ++LR+ F G I I + +G
Sbjct: 2 SSGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRG-FA 60
Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
V F++ AK A + + +DG+ I V+
Sbjct: 61 FVYFENVDDAKEAKERANGMELDGRRIRVSG 91
Score = 46.8 bits (112), Expect = 6e-07
Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 56 GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
G + V I+ D + + RG A V F++ D ++A + + E GR++ +
Sbjct: 40 GPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP 92
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1;
RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 94
Score = 76.9 bits (190), Expect = 2e-17
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+ V+V+NL + + L +F GKV V I DKD KS+G + F A
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 219 MLNNQNLFERRITV 232
+NN+ LF R I
Sbjct: 77 AINNKQLFGRVIKA 90
Score = 50.3 bits (121), Expect = 4e-08
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
S G V V I+ D DT K +G A + F D + ++ + GR + A+
Sbjct: 38 SKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI 94
Score = 43.0 bits (102), Expect = 1e-05
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
TV V NLP ++T +L F G + I K KG + + F + +A+
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG-VAFILFLDKDSAQNCTR 76
Query: 571 MMDRTRIDGKIIDV 584
++ ++ G++I
Sbjct: 77 AINNKQLFGRVIKA 90
>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure
genomics, RRM domain, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 77.7 bits (192), Expect = 2e-17
Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 5/88 (5%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
++++NL +DE++L + + G+V + I D G SRG G + + I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 221 NNQNLFERRITV-----RMDRVADRLDG 243
N + + + + + G
Sbjct: 87 NGKFIKTPPGVSAPTEPLLCKFSGPSSG 114
Score = 55.3 bits (134), Expect = 1e-09
Identities = 14/70 (20%), Positives = 25/70 (35%), Gaps = 7/70 (10%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMDR 574
+ NLP ++ QEL + + G + I +G +G R +S + I +
Sbjct: 30 ISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG-VGFARMESTEKCEAVIGHFNG 88
Query: 575 TRIDGKIIDV 584
I
Sbjct: 89 KFIKTPPGVS 98
Score = 48.4 bits (116), Expect = 3e-07
Identities = 13/65 (20%), Positives = 20/65 (30%), Gaps = 2/65 (3%)
Query: 43 DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
+ L + L G V IL D +G RG +S + + + K
Sbjct: 39 EQELENM--LKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG 96
Query: 103 VIKEA 107
V
Sbjct: 97 VSAPT 101
>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 = 76.5 bits (189), Expect = 3e-17
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
++V L +VD+K L F G + +++I LD + K RGF VEF+ +A +I
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 219 MLNNQNLFERRITV 232
+N LF R I V
Sbjct: 73 NMNESELFGRTIRV 86
Score = 49.9 bits (120), Expect = 6e-08
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 56 GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
GD+T ++I D +T K RG A VEF+ + A++ M+ E GR + + A +
Sbjct: 37 GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR--I 94
Query: 115 RNMGGGGG 122
+ G G
Sbjct: 95 KESGPSSG 102
Score = 45.7 bits (109), Expect = 2e-06
Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 8/74 (10%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
+ V L + + L F GDI +I K +G V F+ A AID
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRG-FAFVEFELAEDAAAAID 72
Query: 571 MMDRTRIDGKIIDV 584
M+ + + G+ I V
Sbjct: 73 NMNESELFGRTIRV 86
>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 = 76.0 bits (188), Expect = 3e-17
Identities = 18/75 (24%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD--GKSRGFGTVEFDHPVEAVQSI 217
KV + L V + + E+F GK++ +++ +++ S+G+ VEF++P EA +++
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 218 SMLNNQNLFERRITV 232
++ + + IT
Sbjct: 65 KHMDGGQIDGQEITA 79
Score = 49.5 bits (119), Expect = 6e-08
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 9/77 (11%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI--------KGKGDIGLVRFDSEWTAKRAI 569
V + L +T + + F G IK ++ KG V F++ A++A+
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKG-YAYVEFENPDEAEKAL 64
Query: 570 DMMDRTRIDGKIIDVTF 586
MD +IDG+ I T
Sbjct: 65 KHMDGGQIDGQEITATA 81
Score = 47.5 bits (114), Expect = 3e-07
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 53 STVGDVTYVEILND--DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
ST G + +++ + +G A VEF++PD KA+ M + G+++
Sbjct: 26 STYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV 82
>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 = 75.6 bits (187), Expect = 3e-17
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 2/77 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
++V N+DY ++L F G V V I DK G +GF +EF E+V++
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 66
Query: 220 LNNQNLFERRITVRMDR 236
L+ R+I V R
Sbjct: 67 LDESLFRGRQIKVIPKR 83
Score = 54.1 bits (131), Expect = 1e-09
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
+H G V V IL D +G P+G A +EF + VR ++ + +GR++ +
Sbjct: 25 AHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR 83
Query: 109 EDKGG 113
++ G
Sbjct: 84 TNRPG 88
Score = 41.3 bits (98), Expect = 5e-05
Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 11/81 (13%)
Query: 514 IERD--TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWT 564
+E D ++ V N+ T +EL F CG + I KG + F + +
Sbjct: 2 MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG-FAYIEFSDKES 60
Query: 565 AKRAIDMMDRTRIDGKIIDVT 585
+ ++ +D + G+ I V
Sbjct: 61 VRTSLA-LDESLFRGRQIKVI 80
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 75.7 bits (187), Expect = 4e-17
Identities = 28/92 (30%), Positives = 48/92 (52%), Gaps = 3/92 (3%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+ ++V +L + + E LR +F GK++N+ + D D G+S+G+G + F A +++
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 219 MLNNQNLFERRITVRMDRVADRLDGPVRLPEG 250
LN L R + V V +RLDG G
Sbjct: 66 QLNGFELAGRPMRV--GHVTERLDGGSGPSSG 95
Score = 51.4 bits (124), Expect = 2e-08
Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 2/70 (2%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
G + + ++ D DTG+ +G + F + R+A+ +++ FE GR + + ++
Sbjct: 27 EPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV-TER 85
Query: 112 GGRRNMGGGG 121
+ G
Sbjct: 86 LDGGSGPSSG 95
Score = 41.0 bits (97), Expect = 8e-05
Identities = 18/71 (25%), Positives = 30/71 (42%), Gaps = 8/71 (11%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V +L IT LR F G I + + KG G + F A+RA++ ++
Sbjct: 10 VGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKG-YGFITFSDSECARRALEQLN 68
Query: 574 RTRIDGKIIDV 584
+ G+ + V
Sbjct: 69 GFELAGRPMRV 79
>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 = 79.4 bits (195), Expect = 4e-17
Identities = 25/189 (13%), Positives = 65/189 (34%), Gaps = 13/189 (6%)
Query: 45 SLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI 104
++ + G+V V+ + G+A+VE V +A+ ++ G+K+ +
Sbjct: 21 RVFNV--FCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNV 74
Query: 105 KEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFV 164
+ + G ++ +++F + + N +
Sbjct: 75 CVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRI------QHPSNVLHF 128
Query: 165 ANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQ 223
N +V E+ E+ G + + + G +E+D +A++++ LN+
Sbjct: 129 FNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHY 188
Query: 224 NLFERRITV 232
+
Sbjct: 189 QMKNPNGPY 197
Score = 56.3 bits (135), Expect = 3e-09
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 162 VFVANLDY-KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
+ V LD K++ ++ VF L G VE V+ K G VE ++I+ L
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK----PGAAMVEMADGYAVDRAITHL 62
Query: 221 NNQNLFERRITVRMDR 236
NN +F +++ V + +
Sbjct: 63 NNNFMFGQKMNVCVSK 78
Score = 52.8 bits (126), Expect = 4e-08
Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 6/75 (8%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIK------GKGDIGLVRFDSEWTAKRAIDM 571
+ N P +T + + G + +K + GL+ +DS+ A +
Sbjct: 125 VLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGF 184
Query: 572 MDRTRIDGKIIDVTF 586
++ ++ +
Sbjct: 185 LNHYQMKNPNGPYPY 199
Score = 52.4 bits (125), Expect = 7e-08
Identities = 12/71 (16%), Positives = 29/71 (40%), Gaps = 2/71 (2%)
Query: 518 TVVVKNLPP-TITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRT 575
++V L + + + F G+++ + K K +V + RAI ++
Sbjct: 6 VLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNN 65
Query: 576 RIDGKIIDVTF 586
+ G+ ++V
Sbjct: 66 FMFGQKMNVCV 76
>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 = 75.8 bits (187), Expect = 7e-17
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
VF L ++ + L + F GKV +V I D++ +S+G VEF ++V
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI-QSVPLAIG 85
Query: 220 LNNQNLFERRITV 232
L Q L I V
Sbjct: 86 LTGQRLLGVPIIV 98
Score = 55.0 bits (133), Expect = 1e-09
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 2/72 (2%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
S VG V V I++D ++ + +G A VEF V A+ + G ++++ +
Sbjct: 44 DFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQ 102
Query: 109 EDKGGRRNMGGG 120
+K G
Sbjct: 103 AEKNRLSGPSSG 114
Score = 44.6 bits (106), Expect = 5e-06
Identities = 24/91 (26%), Positives = 34/91 (37%), Gaps = 11/91 (12%)
Query: 504 SNRSMNQSSNIERD--TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDI 554
++ S ERD TV L I ++L D F G ++ I + KG I
Sbjct: 11 VREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG-I 69
Query: 555 GLVRFDSEWTAKRAIDMMDRTRIDGKIIDVT 585
V F + AI + R+ G I V
Sbjct: 70 AYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQ 99
>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 = 75.3 bits (186), Expect = 8e-17
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 1/73 (1%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
+ V NL Y+ LR VF G+V +V I + RGF V F +A + +
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 220 LNNQNLFERRITV 232
++ L R + V
Sbjct: 75 MDGAELDGRELRV 87
Score = 51.8 bits (125), Expect = 1e-08
Identities = 19/69 (27%), Positives = 25/69 (36%), Gaps = 1/69 (1%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
G V V I + T PRG A V F + A M E GR+L ++ A +
Sbjct: 35 EKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGR 94
Query: 112 GGRRNMGGG 120
G
Sbjct: 95 RDLSGPSSG 103
Score = 45.7 bits (109), Expect = 2e-06
Identities = 22/101 (21%), Positives = 33/101 (32%), Gaps = 19/101 (18%)
Query: 493 GGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI---- 548
G G+ +D + + V NL + LR F G + I
Sbjct: 1 GSSGSSGPDVDGMIT-----------LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREP 49
Query: 549 ---KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
+G VRF A+ A MD +DG+ + V
Sbjct: 50 HTKAPRG-FAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV 89
>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 = 78.5 bits (194), Expect = 9e-17
Identities = 44/191 (23%), Positives = 76/191 (39%), Gaps = 45/191 (23%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
+A LY+ S G + + + D T + G A V FQ P +A++ M+ KG+
Sbjct: 29 EAMLYEK--FSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKP 86
Query: 102 LVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINK 161
+ I + D R+ S GN
Sbjct: 87 VRIMWSQRDPSLRK--------------------SGVGN--------------------- 105
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
+F+ NLD +D K L + F G + + ++ D + S+G+G V F+ A ++I +N
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEKMN 164
Query: 222 NQNLFERRITV 232
L +R++ V
Sbjct: 165 GMLLNDRKVFV 175
Score = 63.8 bits (156), Expect = 8e-12
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISML 220
++V +L V E L E F AG + ++ + D +S G+ V F P +A +++ +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 221 NNQNLFERRITV 232
N + + + +
Sbjct: 78 NFDVIKGKPVRI 89
Score = 55.7 bits (135), Expect = 4e-09
Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 6/87 (6%)
Query: 506 RSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVRFD 560
+ + +KNL +I + L D F G+I ++ KG G V F+
Sbjct: 93 QRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG-YGFVHFE 151
Query: 561 SEWTAKRAIDMMDRTRIDGKIIDVTFF 587
++ A+RAI+ M+ ++ + + V F
Sbjct: 152 TQEAAERAIEKMNGMLLNDRKVFVGRF 178
Score = 43.8 bits (104), Expect = 4e-05
Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 9/86 (10%)
Query: 507 SMNQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVR 558
SMN S+ + V +L P +T L +KF G I + + G V
Sbjct: 5 SMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLG-YAYVN 63
Query: 559 FDSEWTAKRAIDMMDRTRIDGKIIDV 584
F A+RA+D M+ I GK + +
Sbjct: 64 FQQPADAERALDTMNFDVIKGKPVRI 89
Score = 31.1 bits (71), Expect = 0.73
Identities = 11/53 (20%), Positives = 21/53 (39%)
Query: 67 DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGG 119
D +G V F++ + +A+ KM+ RK+ + K +G
Sbjct: 138 DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGA 190
>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 = 75.0 bits (185), Expect = 1e-16
Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
N VFV +D ++DE ++R F G V+ V+I D+ G S+G+G V F + VQ I +
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYND-VDVQKI-V 67
Query: 220 LNNQNLFERRITVR 233
+ N +++ +
Sbjct: 68 ESQINFHGKKLKLG 81
Score = 54.9 bits (133), Expect = 1e-09
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
G V V+I+ D TG +G V F + V+K V F G+KL + A+
Sbjct: 34 GSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQINF--HGKKLKLGPAIR 85
Score = 45.7 bits (109), Expect = 2e-06
Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 9/70 (12%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMDR 574
V + + E+R F G +K +I KG G V F ++ ++ ++
Sbjct: 14 VGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKG-YGFVSFYNDVDVQKIVESQ-- 70
Query: 575 TRIDGKIIDV 584
GK + +
Sbjct: 71 INFHGKKLKL 80
>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 = 74.1 bits (183), Expect = 1e-16
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+FV +L+ VD++ LR F+ + + D G SRG+G V F +A ++
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 219 MLNNQNLFERRITV 232
+ Q+L R + +
Sbjct: 62 SMQGQDLNGRPLRI 75
Score = 45.2 bits (108), Expect = 2e-06
Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 8/71 (11%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V +L + + LR+ F++ + +G G V F S+ A+ A+D M
Sbjct: 6 VGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRG-YGFVSFTSQDDAQNAMDSMQ 64
Query: 574 RTRIDGKIIDV 584
++G+ + +
Sbjct: 65 GQDLNGRPLRI 75
Score = 41.7 bits (99), Expect = 3e-05
Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 3/66 (4%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
D +L ++ D TG RG V F S D + A++ M + GR
Sbjct: 15 DETLRNA--FKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRP 72
Query: 102 LVIKEA 107
L I A
Sbjct: 73 LRINWA 78
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 75.0 bits (185), Expect = 1e-16
Identities = 26/90 (28%), Positives = 49/90 (54%), Gaps = 1/90 (1%)
Query: 143 GLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGF 202
GL P+ N ++ V+N+ ++ + LR++F GK+ +VEI ++ G S+GF
Sbjct: 13 GLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGF 71
Query: 203 GTVEFDHPVEAVQSISMLNNQNLFERRITV 232
G V F++ +A ++ L+ + R+I V
Sbjct: 72 GFVTFENSADADRAREKLHGTVVEGRKIEV 101
Score = 51.2 bits (123), Expect = 3e-08
Identities = 27/106 (25%), Positives = 41/106 (38%), Gaps = 11/106 (10%)
Query: 484 GSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDI 543
GS PR + + +Q + V N+P +LR F G I
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMNTENKSQPKRL-----HVSNIPFRFRDPDLRQMFGQFGKI 56
Query: 544 KFAEI-----KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
EI KG G V F++ A RA + + T ++G+ I+V
Sbjct: 57 LDVEIIFNERGSKG-FGFVTFENSADADRAREKLHGTVVEGRKIEV 101
Score = 43.5 bits (103), Expect = 1e-05
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
G + VEI+ + +G V F++ +A K+H +GRK+ + A
Sbjct: 54 GKILDVEIIFN-ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104
>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A)
binding, structural genomics, protein structure
initiative, PSI-2; NMR {Xenopus laevis}
Length = 124
Score = 75.5 bits (186), Expect = 1e-16
Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 2/77 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
V+V N+DY + L F G + + I DK G +G+ +EF +V +
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER-NSVDAAVA 96
Query: 220 LNNQNLFERRITVRMDR 236
++ R I V R
Sbjct: 97 MDETVFRGRTIKVLPKR 113
Score = 52.8 bits (127), Expect = 1e-08
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
+H S+ G + + IL D +G P+G A +EF + V AV M +GR + +
Sbjct: 55 AHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR 113
Query: 109 EDKGGRRN 116
+ G +
Sbjct: 114 TNMPGISS 121
Score = 41.2 bits (97), Expect = 9e-05
Identities = 25/97 (25%), Positives = 36/97 (37%), Gaps = 9/97 (9%)
Query: 496 GNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI------- 548
G G S + I++ +V V N+ T Q+L F +CG I I
Sbjct: 16 GAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSG 75
Query: 549 KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVT 585
KG + F + A+ MD T G+ I V
Sbjct: 76 HPKG-YAYIEFAERNSVDAAVA-MDETVFRGRTIKVL 110
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 74.2 bits (183), Expect = 2e-16
Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 3/77 (3%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
K+FV L+ + E+ + +F+ G ++ + DG S+G V+F EA +I
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 220 LNNQNLFE---RRITVR 233
L+ + V+
Sbjct: 76 LHGSQTMPGASSSLVVK 92
Score = 45.0 bits (107), Expect = 4e-06
Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 3/66 (4%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH---RFETKGRKLVIKEAVEDKG 112
G + +L G +G A V+F S + A++ +H LV+K A DK
Sbjct: 40 GVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKE 99
Query: 113 GRRNMG 118
+ G
Sbjct: 100 SGPSSG 105
Score = 43.8 bits (104), Expect = 8e-06
Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 7/80 (8%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLV 557
S S ++S + V L + +++ F+ G I + KG V
Sbjct: 3 SGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKG-CAFV 61
Query: 558 RFDSEWTAKRAIDMMDRTRI 577
+F S A+ AI + ++
Sbjct: 62 KFSSHTEAQAAIHALHGSQT 81
>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 = 73.8 bits (182), Expect = 2e-16
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
++FV NL Y E+ L ++F G + + +D K +GF V F P AV++ +
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
Query: 219 MLNNQNLFERRITV 232
++ Q R + V
Sbjct: 69 EVDGQVFQGRMLHV 82
Score = 51.1 bits (123), Expect = 2e-08
Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 1/73 (1%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
S G ++ + D T KP+G A V F P+ KA ++ +GR L + +
Sbjct: 27 KLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST 86
Query: 109 EDKGGRRNMGGGG 121
K ++ G
Sbjct: 87 IKKEASQSGPSSG 99
Score = 44.1 bits (105), Expect = 5e-06
Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 8/73 (10%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V+NL T + ++L F G + K KG V F A +A +D
Sbjct: 13 VRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKG-FAFVTFMFPEHAVKAYAEVD 71
Query: 574 RTRIDGKIIDVTF 586
G+++ V
Sbjct: 72 GQVFQGRMLHVLP 84
>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 = 73.4 bits (181), Expect = 3e-16
Identities = 17/87 (19%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
V++ ++ Y E+++ ++ G V N+++ D G+S+G+ +EF + ++
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 220 LNNQNLFERRITVRMDRVADRLDGPVR 246
LN L R + ++ V
Sbjct: 64 LNGYQLGSRFLKC--GYSSNSDISGVS 88
Score = 48.8 bits (117), Expect = 1e-07
Identities = 15/66 (22%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
S VG V ++++ D TG+ +G A +EF+ + AV ++ ++ R L +
Sbjct: 24 SNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD 83
Query: 112 GGRRNM 117
++
Sbjct: 84 ISGVSL 89
Score = 38.4 bits (90), Expect = 6e-04
Identities = 10/74 (13%), Positives = 30/74 (40%), Gaps = 8/74 (10%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
V + ++P T +++ D N G + ++ + KG + F ++ A+
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKG-YAFIEFRDLESSASAVR 62
Query: 571 MMDRTRIDGKIIDV 584
++ ++ + +
Sbjct: 63 NLNGYQLGSRFLKC 76
>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 = 74.2 bits (183), Expect = 3e-16
Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+F+ NLD +D K L + F G + + ++ D+ S+G+G V F+ A ++I
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEK 64
Query: 220 LNNQNLFERRITV 232
+N L +R++ V
Sbjct: 65 MNGMLLNDRKVFV 77
Score = 53.8 bits (130), Expect = 4e-09
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVRFDSEWTAKRAIDMMD 573
+ +KNL +I + L D F G+I ++ KG G V F+++ A+RAI+ M+
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG-YGFVHFETQEAAERAIEKMN 66
Query: 574 RTRIDGKIIDVTFF 587
++ + + V F
Sbjct: 67 GMLLNDRKVFVGRF 80
Score = 37.2 bits (87), Expect = 0.002
Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 3/77 (3%)
Query: 43 DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
+ +LY S G++ +++ D +G V F++ + +A+ KM+ RK+
Sbjct: 19 NKALYD--TFSAFGNILSCKVVCD-ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKV 75
Query: 103 VIKEAVEDKGGRRNMGG 119
+ K +G
Sbjct: 76 FVGRFKSRKEREAELGA 92
>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 = 74.1 bits (182), Expect = 3e-16
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRI 577
VVV LPP+ +WQ+L+D R GD+ +A++ G G+V F + A+ +D T+
Sbjct: 18 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGT-GVVEFVRKEDMTYAVRKLDNTKF 76
Query: 578 DGKIIDVTF 586
+ +
Sbjct: 77 RSHEGETAY 85
Score = 61.8 bits (150), Expect = 5e-12
Identities = 22/91 (24%), Positives = 35/91 (38%), Gaps = 8/91 (8%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
N+V V+ L + L++ R AG V ++ G G VEF + ++
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADV------YRDGTGVVEFVRKEDMTYAVRK 70
Query: 220 LNNQNLFERRITVRMDRVADRLDGPVRLPEG 250
L+N RV ++DGP G
Sbjct: 71 LDNTKFRSHEGETAYIRV--KVDGPRSPSYG 99
Score = 51.4 bits (123), Expect = 3e-08
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 6/75 (8%)
Query: 51 HLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED 110
H+ GDV Y ++ D TG +VEF + + AV K+ + + +
Sbjct: 36 HMREAGDVCYADVYRDGTG------VVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK 89
Query: 111 KGGRRNMGGGGGVDR 125
G R+ G R
Sbjct: 90 VDGPRSPSYGRSRSR 104
>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1 PDB: 2rq4_A 2rqc_A
Length = 115
Score = 74.3 bits (183), Expect = 3e-16
Identities = 25/98 (25%), Positives = 51/98 (52%), Gaps = 3/98 (3%)
Query: 140 NTYGLSPQFLESLG--INCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD- 196
+ GL+ Q + + G P +F+ +L + ++ L ++F G V + ++ +DK
Sbjct: 4 GSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQT 63
Query: 197 GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM 234
S+ FG V +D+PV A +I +N + +R+ V++
Sbjct: 64 NLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL 101
Score = 48.9 bits (117), Expect = 2e-07
Identities = 21/102 (20%), Positives = 38/102 (37%), Gaps = 9/102 (8%)
Query: 493 GGYGNPRAGLDSNRSMNQSSNIERDT-VVVKNLPPTITWQELRDKFRNCGDIKFAEI--- 548
G G+ S + + + +LP Q+L F G++ A++
Sbjct: 1 GSSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFID 60
Query: 549 ----KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
K G V +D+ +A+ AI M+ +I K + V
Sbjct: 61 KQTNLSKC-FGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL 101
Score = 45.0 bits (107), Expect = 4e-06
Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 4/81 (4%)
Query: 42 GDASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
GD L Q G+V ++ D T + V + +P + A+ M+ F+ +
Sbjct: 38 GDQDLLQ--MFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMK 95
Query: 101 KLVIKEAVEDKGGRRNMGGGG 121
+L ++ K ++ G
Sbjct: 96 RLKVQLK-RSKNDSKSGPSSG 115
>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 = 73.4 bits (181), Expect = 3e-16
Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
K+FV L + +E+ L +VF G++ V + D++ +SRGFG V F++ +A ++
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Query: 219 MLNNQNLFERRITV 232
+N +++ R+I V
Sbjct: 73 AMNGKSVDGRQIRV 86
Score = 50.7 bits (122), Expect = 3e-08
Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 56 GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
G ++ V ++ D +T + RG V F++ D + A+ M+ GR++ + +A + R
Sbjct: 37 GQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNR 96
Query: 115 RNMGGG 120
G
Sbjct: 97 SGPSSG 102
Score = 43.4 bits (103), Expect = 1e-05
Identities = 19/71 (26%), Positives = 28/71 (39%), Gaps = 8/71 (11%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V L Q L F G I + + +G G V F++ AK A+ M+
Sbjct: 17 VGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRG-FGFVTFENIDDAKDAMMAMN 75
Query: 574 RTRIDGKIIDV 584
+DG+ I V
Sbjct: 76 GKSVDGRQIRV 86
>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 = 75.2 bits (185), Expect = 3e-16
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
++V NL + E+++ E+F +G ++ + + LDK + GF VE+ +A ++
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 219 MLNNQNLFERRITVRMDR 236
+N L +R I D
Sbjct: 100 YINGTRLDDRIIRTDWDA 117
Score = 48.3 bits (115), Expect = 6e-07
Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 3/81 (3%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
+ +Y+ S GD+ + + D G VE+ S A+ ++ R
Sbjct: 53 EEQIYE--LFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI 110
Query: 102 LVIKEAVEDKGGRRNMGGGGG 122
+ K GR+ G G
Sbjct: 111 IRTDWDAGFKEGRQYGRGRSG 131
Score = 47.1 bits (112), Expect = 2e-06
Identities = 24/112 (21%), Positives = 43/112 (38%), Gaps = 12/112 (10%)
Query: 484 GSGQASIQSGGYGNPRAGLDSNRSMNQSSNIER----DTVVVKNLPPTITWQELRDKFRN 539
G +++S Y D + + + T+ V NL T +++ + F
Sbjct: 3 GGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSK 62
Query: 540 CGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
GDIK + G V + S A+ A+ ++ TR+D +II
Sbjct: 63 SGDIKKIIMGLDKMKKTACG-FCFVEYYSRADAENAMRYINGTRLDDRIIRT 113
>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 = 73.4 bits (181), Expect = 3e-16
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+ V NL E L+E+FR G + + +A DK G+S+GF + F +A ++I+
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75
Query: 219 MLNNQNLFERRITV 232
++ + V
Sbjct: 76 GVSGFGYDHLILNV 89
Score = 50.7 bits (122), Expect = 3e-08
Identities = 21/88 (23%), Positives = 32/88 (36%), Gaps = 8/88 (9%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGL 556
S S + T+ V NL +L++ FR G I + + KG
Sbjct: 3 SGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKG-FAF 61
Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
+ F A RAI + D I++V
Sbjct: 62 ISFHRREDAARAIAGVSGFGYDHLILNV 89
Score = 44.5 bits (106), Expect = 5e-06
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 5/68 (7%)
Query: 56 GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
G ++ + + D TG+ +G A + F + +A+ + F L ++ A
Sbjct: 40 GSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKP----S 95
Query: 115 RNMGGGGG 122
N G G
Sbjct: 96 TNSGPSSG 103
>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 = 73.1 bits (180), Expect = 4e-16
Identities = 24/90 (26%), Positives = 46/90 (51%), Gaps = 5/90 (5%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGK----SRGFGTVEFDHPVEAVQ 215
+ +F+ NL++ E+ L+ VF G +++ I+ K+ S GFG VE+ P +A +
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 216 SISMLNNQNLFERRITVRM-DRVADRLDGP 244
++ L + ++ VR+ +R GP
Sbjct: 66 ALKQLQGHTVDGHKLEVRISERATKPASGP 95
Score = 53.0 bits (128), Expect = 5e-09
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 9/73 (12%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI---------GLVRFDSEWTAKRAIDM 571
+KNL + T + L+ F G IK I K + G V + A++A+
Sbjct: 10 IKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQ 69
Query: 572 MDRTRIDGKIIDV 584
+ +DG ++V
Sbjct: 70 LQGHTVDGHKLEV 82
Score = 42.6 bits (101), Expect = 2e-05
Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 5/73 (6%)
Query: 53 STVGDVTYVEILND-DTGKP---RGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
S VG + I + G VE++ P+ +KA+ ++ G KL ++ +
Sbjct: 27 SKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS- 85
Query: 109 EDKGGRRNMGGGG 121
E + G
Sbjct: 86 ERATKPASGPSSG 98
>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 = 73.1 bits (180), Expect = 5e-16
Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 3/92 (3%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
VFV N+ Y+ E++L+++F G V + + D++ GK +G+G E+ A+ ++
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 219 MLNNQNLFERRITVRMDRVADRLDGPVRLPEG 250
LN + R + V D A + G
Sbjct: 69 NLNGREFSGRALRV--DNAASEKNKEELKSLG 98
Score = 53.4 bits (129), Expect = 3e-09
Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
S VG V ++ D +TGKP+G E+Q + A+ ++ E GR L + A +K
Sbjct: 30 SEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK 89
Query: 112 GGRRNMGGGGG 122
G G
Sbjct: 90 NKEELKSLGTG 100
Score = 35.7 bits (83), Expect = 0.007
Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 8/74 (10%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
+V V N+P T ++L+D F G + + K KG G + + TA A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG-YGFCEYQDQETALSAMR 68
Query: 571 MMDRTRIDGKIIDV 584
++ G+ + V
Sbjct: 69 NLNGREFSGRALRV 82
>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 = 72.2 bits (178), Expect = 6e-16
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 159 INKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSI 217
+ ++V NL Y ++++E+F GKV NV++ D++ K +GFG VE ++I
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAI 59
Query: 218 SMLNNQNLFERRITVR 233
+ L+N + R I V
Sbjct: 60 AKLDNTDFMGRTIRVT 75
Score = 46.8 bits (112), Expect = 6e-07
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
S G V V+++ D +T KP+G VE Q V +A+ K+ + GR + + EA K
Sbjct: 23 SQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKK 81
Query: 112 GGRRN 116
+
Sbjct: 82 SLEHH 86
Score = 35.6 bits (83), Expect = 0.005
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 9/71 (12%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V NL + T +++++ F G + ++ K KG G V E + AI +D
Sbjct: 6 VGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKG-FGFVEMQEE-SVSEAIAKLD 63
Query: 574 RTRIDGKIIDV 584
T G+ I V
Sbjct: 64 NTDFMGRTIRV 74
>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 = 73.6 bits (181), Expect = 6e-16
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+ V L E+ LREVF G + +V I D+ +SRGF V F++ +A ++
Sbjct: 47 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106
Query: 219 MLNNQNLFERRITV 232
N L RRI V
Sbjct: 107 RANGMELDGRRIRV 120
Score = 49.0 bits (117), Expect = 3e-07
Identities = 27/120 (22%), Positives = 46/120 (38%), Gaps = 8/120 (6%)
Query: 474 SGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQEL 533
S + G + S + G + G S N+++ + V L T ++L
Sbjct: 4 SHHHHHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDL 63
Query: 534 RDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
R+ F G I I + +G V F++ AK A + + +DG+ I V F
Sbjct: 64 REVFSKYGPIADVSIVYDQQSRRSRG-FAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
Score = 44.7 bits (106), Expect = 7e-06
Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 56 GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
G + V I+ D + + RG A V F++ D ++A + + E GR++ + ++ +
Sbjct: 71 GPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKR 127
>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 = 73.2 bits (180), Expect = 6e-16
Identities = 21/105 (20%), Positives = 46/105 (43%), Gaps = 4/105 (3%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
+++ NL YK+ +++ ++F G + + + ++RG V ++ +A ++ L+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG--NTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 222 NQNLFERRITV--RMDRVADRLDGPVRLPEGLKSIGMGLGANGAP 264
N+ R + V A + + E LK + G N P
Sbjct: 69 GFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDP 113
Score = 54.3 bits (131), Expect = 3e-09
Identities = 16/73 (21%), Positives = 33/73 (45%), Gaps = 3/73 (4%)
Query: 517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD---IGLVRFDSEWTAKRAIDMMD 573
+ ++NLP IT +E+ D F G I+ + + V ++ + AK A+D +
Sbjct: 9 RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLS 68
Query: 574 RTRIDGKIIDVTF 586
+ + + V +
Sbjct: 69 GFNVSNRYLVVLY 81
Score = 46.2 bits (110), Expect = 1e-06
Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 2/64 (3%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
G + + + N T + RG+A V ++ + AV+ + F R LV+ ++
Sbjct: 30 GKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRA 87
Query: 113 GRRN 116
++
Sbjct: 88 FQKM 91
>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 72.7 bits (179), Expect = 7e-16
Identities = 22/73 (30%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
++ V+N+ ++ + LR++F GK+ +VEI ++ G S+GFG V F++ +A ++
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREK 74
Query: 220 LNNQNLFERRITV 232
L+ + R+I V
Sbjct: 75 LHGTVVEGRKIEV 87
Score = 50.0 bits (120), Expect = 6e-08
Identities = 26/86 (30%), Positives = 37/86 (43%), Gaps = 6/86 (6%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVR 558
S S N S + V N+P +LR F G I EI KG G V
Sbjct: 3 SGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG-FGFVT 61
Query: 559 FDSEWTAKRAIDMMDRTRIDGKIIDV 584
F++ A RA + + T ++G+ I+V
Sbjct: 62 FENSADADRAREKLHGTVVEGRKIEV 87
Score = 45.0 bits (107), Expect = 3e-06
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 2/69 (2%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
G + VEI+ + +G V F++ +A K+H +GRK+ + A +
Sbjct: 37 GQFGKILDVEIIFN-ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA-TARV 94
Query: 113 GRRNMGGGG 121
+ G
Sbjct: 95 MTNSGPSSG 103
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 72.7 bits (179), Expect = 7e-16
Identities = 20/74 (27%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+FV + + E+ + + F G+++N+ + LD+ G +G+ VE++ EA ++
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
Query: 219 MLNNQNLFERRITV 232
LN Q+L + I+V
Sbjct: 84 GLNGQDLMGQPISV 97
Score = 47.6 bits (114), Expect = 4e-07
Identities = 21/95 (22%), Positives = 41/95 (43%), Gaps = 9/95 (9%)
Query: 499 RAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGK 551
D + Q S +E + V + T +++ DKF G+IK + K
Sbjct: 7 SVEQDGDEPGPQRS-VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65
Query: 552 GDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
G LV +++ A+ A++ ++ + G+ I V +
Sbjct: 66 G-YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99
Score = 44.2 bits (105), Expect = 6e-06
Identities = 9/56 (16%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
+ G++ + + D TG +G +VE+++ + A+ ++ + G+ + +
Sbjct: 45 AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 100
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 73.6 bits (181), Expect = 7e-16
Identities = 26/100 (26%), Positives = 40/100 (40%), Gaps = 1/100 (1%)
Query: 134 NSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIAL 193
S G G + + + V NL Y+ LR VF G+V +V I
Sbjct: 22 ASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 81
Query: 194 DKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV 232
D+ +SRGF V F +A ++ ++ L R + V
Sbjct: 82 DRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121
Score = 48.6 bits (116), Expect = 4e-07
Identities = 22/102 (21%), Positives = 35/102 (34%), Gaps = 8/102 (7%)
Query: 492 SGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI--- 548
S G + ++ V NL + LR F G + I
Sbjct: 23 SMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD 82
Query: 549 ----KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
+ +G VRF + A+ A+D MD +DG+ + V
Sbjct: 83 RYTKESRG-FAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123
Score = 47.4 bits (113), Expect = 9e-07
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 1/62 (1%)
Query: 56 GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
G V V I D T + RG A V F A++ M GR+L ++ A +
Sbjct: 72 GRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD 131
Query: 115 RN 116
+
Sbjct: 132 SH 133
>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 = 72.3 bits (178), Expect = 1e-15
Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
+FV ++ + E +++E F G+++N+ + LD+ G S+G+ VE++ +A+ +
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 220 LNNQNLFERRITV 232
LN + + I V
Sbjct: 88 LNGAEIMGQTIQV 100
Score = 46.9 bits (112), Expect = 8e-07
Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
G++ + + D TG +G A+VE+++ A ++ E G+ + + K
Sbjct: 48 CDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC-FVK 106
Query: 112 GGRR 115
G +R
Sbjct: 107 GPKR 110
Score = 43.8 bits (104), Expect = 9e-06
Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 503 DSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIG 555
D ++E + V ++ E+++KF + G+IK + KG
Sbjct: 13 DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKG-YA 71
Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
LV +++ A A + ++ I G+ I V +
Sbjct: 72 LVEYETHKQALAAKEALNGAEIMGQTIQVDW 102
>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 = 71.9 bits (177), Expect = 1e-15
Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+FV L E+ L+E F I D++ G S+GFG V+F+ +A +
Sbjct: 16 KTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
Query: 219 MLNNQNLFERRITV 232
+ + + ++T+
Sbjct: 73 AMEDGEIDGNKVTL 86
Score = 44.9 bits (107), Expect = 4e-06
Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 2/67 (2%)
Query: 56 GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
I+ D +TG +G V+F S + + A M E G K+ + A + KG
Sbjct: 37 DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA-KPKGEG 95
Query: 115 RNMGGGG 121
+ G
Sbjct: 96 GSGPSSG 102
Score = 42.2 bits (100), Expect = 3e-05
Identities = 25/90 (27%), Positives = 37/90 (41%), Gaps = 11/90 (12%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGL 556
S S + + T+ VK L T + L++ F A I KG G
Sbjct: 3 SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKG-FGF 58
Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
V F+SE AK A + M+ IDG + + +
Sbjct: 59 VDFNSEEDAKAAKEAMEDGEIDGNKVTLDW 88
>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 = 71.4 bits (176), Expect = 1e-15
Identities = 16/74 (21%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
+++ L ++ L ++ + GK+ + + LDK K +G+G V+FD P A ++++
Sbjct: 7 GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66
Query: 220 LNNQNLFERRITVR 233
L + +
Sbjct: 67 LKASGVQAQMAKQS 80
Score = 46.4 bits (111), Expect = 7e-07
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 8/71 (11%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
++ L P T Q+L + G I + K KG G V FDS A++A+ +
Sbjct: 10 IRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKG-YGFVDFDSPSAAQKAVTALK 68
Query: 574 RTRIDGKIIDV 584
+ + ++
Sbjct: 69 ASGVQAQMAKQ 79
Score = 42.1 bits (100), Expect = 2e-05
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 56 GDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
G + + + D T K +G V+F SP +KAV + + +
Sbjct: 30 GKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA 77
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 72.4 bits (178), Expect = 1e-15
Identities = 26/117 (22%), Positives = 49/117 (41%), Gaps = 1/117 (0%)
Query: 121 GGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDYKVDEKKLREVF 180
G+ + SA + S + I P +F+ +L + + L F
Sbjct: 2 AGLPQFGSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTF 61
Query: 181 RLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDR 236
G V + ++ +DK S+ FG V FD+P A +I +N + +R+ V++ +
Sbjct: 62 LPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
Score = 48.1 bits (115), Expect = 3e-07
Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 8/73 (10%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
+ +LP T +L F G++ A++ K G V FD+ +A+ AI M+
Sbjct: 45 IYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKC-FGFVSFDNPDSAQVAIKAMN 103
Query: 574 RTRIDGKIIDVTF 586
++ K + V
Sbjct: 104 GFQVGTKRLKVQL 116
Score = 46.6 bits (111), Expect = 1e-06
Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 3/67 (4%)
Query: 42 GDASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
D L G+V ++ D T + V F +PD + A+ M+ F+ +
Sbjct: 53 TDTDLAS--TFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTK 110
Query: 101 KLVIKEA 107
+L ++
Sbjct: 111 RLKVQLK 117
>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 = 72.0 bits (177), Expect = 1e-15
Identities = 20/73 (27%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
+++V +L + + E LR +F G++E++++ +D + G+S+G+G + F A +++
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 220 LNNQNLFERRITV 232
LN L R + V
Sbjct: 88 LNGFELAGRPMKV 100
Score = 48.1 bits (115), Expect = 3e-07
Identities = 12/56 (21%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
G + ++++ D +TG+ +G + F + +KA+ +++ FE GR + +
Sbjct: 48 EPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV 103
Score = 42.7 bits (101), Expect = 2e-05
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V +L IT LR F G I+ ++ + KG G + F AK+A++ ++
Sbjct: 31 VGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKG-YGFITFSDSECAKKALEQLN 89
Query: 574 RTRIDGKIIDV 584
+ G+ + V
Sbjct: 90 GFELAGRPMKV 100
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT
arginine/serine-rich 2, S35, splicing factor SC35,; RRM
domain, cell WALL; NMR {Streptococcus SP}
Length = 158
Score = 73.0 bits (179), Expect = 2e-15
Identities = 28/134 (20%), Positives = 50/134 (37%), Gaps = 3/134 (2%)
Query: 100 RKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLI 159
+ EAV+ + + ++++K S + +
Sbjct: 13 KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGM-- 70
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+ V NL Y+ LR VF G+V +V I D+ +SRGF V F +A ++
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 219 MLNNQNLFERRITV 232
++ L R + V
Sbjct: 131 AMDGAVLDGRELRV 144
Score = 46.0 bits (109), Expect = 5e-06
Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 11/100 (11%)
Query: 497 NPRAGLDSNRSMNQSSNIERD---TVVVKNLPPTITWQELRDKFRNCGDIKFAEI----- 548
+ + S + +++ + ++ V NL + LR F G + I
Sbjct: 48 ATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRY 107
Query: 549 --KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
+ +G VRF + A+ A+D MD +DG+ + V
Sbjct: 108 TKESRG-FAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 146
Score = 45.2 bits (107), Expect = 7e-06
Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 1/60 (1%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
G V V I D T + RG A V F A++ M GR+L ++ A +
Sbjct: 92 EKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR 151
>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 = 71.1 bits (175), Expect = 2e-15
Identities = 21/74 (28%), Positives = 46/74 (62%), Gaps = 1/74 (1%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
++V NLD +D+++LR+ F G + + ++ ++ G+S+GFG V F P EA ++++ +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEM 75
Query: 221 NNQNLFERRITVRM 234
N + + + + V +
Sbjct: 76 NGRIVATKPLYVAL 89
Score = 51.1 bits (123), Expect = 3e-08
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 6/69 (8%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVRFDSEWTAKRAIDMMDRT 575
VKNL I + LR F G I A++ + KG G V F S A +A+ M+
Sbjct: 20 VKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKG-FGFVCFSSPEEATKAVTEMNGR 78
Query: 576 RIDGKIIDV 584
+ K + V
Sbjct: 79 IVATKPLYV 87
Score = 42.2 bits (100), Expect = 3e-05
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 67 DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGG 121
+ G+ +G V F SP+ KAV +M+ + L + A + K R++ G
Sbjct: 50 EGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA-QRKEERQSGPSSG 103
>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 = 73.8 bits (181), Expect = 3e-15
Identities = 33/187 (17%), Positives = 74/187 (39%), Gaps = 17/187 (9%)
Query: 43 DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
SL+ + GDV V+IL + + +A+V+ + + A++ ++ + G+ +
Sbjct: 18 PQSLFIL--FGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPI 71
Query: 103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKV 162
I + + ++ L ++ + + + ++ P +
Sbjct: 72 RITLS------KHQNVQLPREGQEDQGLTKDYGNSPLHRF--KKPGSKNFQNIFPPSATL 123
Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
++N+ V E+ L+ +F G V KD R ++ EAVQ++ L+N
Sbjct: 124 HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQMGSVEEAVQALIDLHN 180
Query: 223 QNLFERR 229
+L E
Sbjct: 181 HDLGENH 187
Score = 57.2 bits (138), Expect = 1e-09
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 162 VFVANLD-YKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
+ V+NL+ +V + L +F + G V+ V+I +K + V+ +A ++S L
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHL 61
Query: 221 NNQNLFERRITVRM 234
N L + I + +
Sbjct: 62 NGHKLHGKPIRITL 75
Score = 53.7 bits (129), Expect = 2e-08
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 518 TVVVKNLPP-TITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRT 575
++V NL P +T Q L F GD++ +I K + LV+ A+ A+ ++
Sbjct: 5 VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 64
Query: 576 RIDGKIIDVTF 586
++ GK I +T
Sbjct: 65 KLHGKPIRITL 75
Score = 51.8 bits (124), Expect = 8e-08
Identities = 19/123 (15%), Positives = 49/123 (39%), Gaps = 7/123 (5%)
Query: 467 YGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPP 526
+ E G + S + + G + +++ S T+ + N+PP
Sbjct: 75 LSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA----TLHLSNIPP 130
Query: 527 TITWQELRDKFRNCGDIK--FAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRI-DGKIID 583
+++ ++L+ F + G + F + + L++ S A +A+ + + + +
Sbjct: 131 SVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLR 190
Query: 584 VTF 586
V+F
Sbjct: 191 VSF 193
>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 = 72.6 bits (178), Expect = 4e-15
Identities = 25/140 (17%), Positives = 59/140 (42%), Gaps = 8/140 (5%)
Query: 94 RFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLG 153
+ G + +++ + K + G R+ + ++ + PQ
Sbjct: 14 EVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQ------ 67
Query: 154 INCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVE 212
+FV ++ + E +++E F G+++N+ + LD+ G S+G+ VE++ +
Sbjct: 68 -RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 126
Query: 213 AVQSISMLNNQNLFERRITV 232
A+ + LN + + I V
Sbjct: 127 ALAAKEALNGAEIMGQTIQV 146
Score = 48.3 bits (115), Expect = 9e-07
Identities = 22/111 (19%), Positives = 41/111 (36%), Gaps = 8/111 (7%)
Query: 483 GGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGD 542
G Y R D ++E + V ++ E+++KF + G+
Sbjct: 39 GSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGE 98
Query: 543 IKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
IK + KG LV +++ A A + ++ I G+ I V +
Sbjct: 99 IKNIHLNLDRRTGFSKG-YALVEYETHKQALAAKEALNGAEIMGQTIQVDW 148
Score = 44.8 bits (106), Expect = 1e-05
Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 2/70 (2%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
G++ + + D TG +G A+VE+++ A ++ E G+ + + K
Sbjct: 94 CDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC-FVK 152
Query: 112 GGRRNMGGGG 121
G +R
Sbjct: 153 GPKRVKKSEK 162
>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 = 71.7 bits (176), Expect = 4e-15
Identities = 26/81 (32%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 153 GINCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPV 211
++ + V + VDE +LR++F G +E+V+I D++ +SRG+G V+F
Sbjct: 36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGS 95
Query: 212 EAVQSISMLNNQNLFERRITV 232
A Q+I+ LN N+ +R+ V
Sbjct: 96 SAQQAIAGLNGFNILNKRLKV 116
Score = 47.8 bits (114), Expect = 6e-07
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 4/82 (4%)
Query: 42 GDASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
+ L Q+ G + V+I+ D +T + RG V+FQS ++A+ ++ F +
Sbjct: 55 DEVQLRQL--FERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNK 112
Query: 101 KLVIKEAVEDKGGRRNMGGGGG 122
+L + A R + G G
Sbjct: 113 RLKVALA-ASGHQRPGIAGAVG 133
Score = 46.3 bits (110), Expect = 2e-06
Identities = 25/117 (21%), Positives = 45/117 (38%), Gaps = 13/117 (11%)
Query: 477 NEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDK 536
++ D G + Q N + N+ +V +P T+ +LR
Sbjct: 8 SQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNL-----MVNYIPTTVDEVQLRQL 62
Query: 537 FRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
F G I+ +I + +G G V+F S +A++AI ++ I K + V
Sbjct: 63 FERYGPIESVKIVCDRETRQSRG-YGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL 118
>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 = 71.2 bits (175), Expect = 4e-15
Identities = 20/74 (27%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+FV + + E+ + + F G+++N+ + LD+ G +G+ VE++ EA ++
Sbjct: 23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82
Query: 219 MLNNQNLFERRITV 232
LN Q+L + I+V
Sbjct: 83 GLNGQDLMGQPISV 96
Score = 47.0 bits (112), Expect = 1e-06
Identities = 21/97 (21%), Positives = 41/97 (42%), Gaps = 9/97 (9%)
Query: 497 NPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------K 549
D + Q S +E + V + T +++ DKF G+IK +
Sbjct: 4 YDSVEQDGDEPGPQRS-VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 62
Query: 550 GKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
KG LV +++ A+ A++ ++ + G+ I V +
Sbjct: 63 LKG-YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
Score = 45.1 bits (107), Expect = 5e-06
Identities = 12/74 (16%), Positives = 31/74 (41%), Gaps = 1/74 (1%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
+ G++ + + D TG +G +VE+++ + A+ ++ + G+ + +
Sbjct: 44 AEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG 103
Query: 112 GGRRNMGGGGGVDR 125
+ GG R
Sbjct: 104 PPKGKRRGGRRRSR 117
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain,
poly(A) site recognition, RNA, nuclear, RNA BIND
protein; 2.70A {Homo sapiens} PDB: 3p6y_C
Length = 90
Score = 69.5 bits (171), Expect = 5e-15
Identities = 13/75 (17%), Positives = 32/75 (42%), Gaps = 3/75 (4%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAG--KVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSI 217
+++ NL + ++ L E G + ++ ++ G+S+GF V + + +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 218 SMLNNQNLFERRITV 232
+L + L + V
Sbjct: 63 DLLPKRELHGQNPVV 77
Score = 48.3 bits (116), Expect = 2e-07
Identities = 11/63 (17%), Positives = 27/63 (42%), Gaps = 2/63 (3%)
Query: 55 VGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGG 113
V D+ ++ + G+ +G A+V S +K ++ + + E G+ V+ +
Sbjct: 27 VNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPS-NKLEH 85
Query: 114 RRN 116
+
Sbjct: 86 HHH 88
Score = 44.1 bits (105), Expect = 4e-06
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 10/75 (13%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIK-------G--KGDIGLVRFDSEWTAKRAIDM 571
+ NL T ++L + + G EIK G KG LV SE ++K+ +D+
Sbjct: 6 IGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG-FALVGVGSEASSKKLMDL 64
Query: 572 MDRTRIDGKIIDVTF 586
+ + + G+ VT
Sbjct: 65 LPKRELHGQNPVVTP 79
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 69.6 bits (171), Expect = 6e-15
Identities = 19/73 (26%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+ ++NL Y E+ L+EVF A +++ +++GKS+G+ +EF +A ++++
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKAT---FIKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72
Query: 220 LNNQNLFERRITV 232
N + + R I +
Sbjct: 73 CNKREIEGRAIRL 85
Score = 50.0 bits (120), Expect = 6e-08
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI---KGKGDIGLVRFD 560
S S N + + E T+V+ NL + T + L++ F IK + K KG + F
Sbjct: 3 SGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKG-YAFIEFA 61
Query: 561 SEWTAKRAIDMMDRTRIDGKIIDVTF 586
S AK A++ ++ I+G+ I +
Sbjct: 62 SFEDAKEALNSCNKREIEGRAIRLEL 87
Score = 48.8 bits (117), Expect = 2e-07
Identities = 14/61 (22%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 61 VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGG 120
+++ + GK +G A +EF S + ++A+N ++ E +GR + ++ +G +
Sbjct: 42 IKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ-GPRGSPNSGPSS 100
Query: 121 G 121
G
Sbjct: 101 G 101
>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 = 70.0 bits (172), Expect = 6e-15
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
K+F+ + +DEK L+ +F GK+ + + D+ G +G + + A+++ S
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 220 LNNQNLFE---RRITVR 233
L+ Q R I V+
Sbjct: 75 LHEQKTLPGMNRPIQVK 91
Score = 44.2 bits (105), Expect = 6e-06
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 4/59 (6%)
Query: 53 STVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMH---RFETKGRKLVIKEA 107
G + + +L D TG +G A + + + KA + +H R + +K A
Sbjct: 35 EEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPA 93
Score = 38.1 bits (89), Expect = 0.001
Identities = 11/76 (14%), Positives = 25/76 (32%), Gaps = 11/76 (14%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
+ +P + ++L+ F G I + KG + + +A +A +
Sbjct: 18 IGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKG-CAFLTYCERESALKAQSALH 76
Query: 574 RTRI---DGKIIDVTF 586
+ + I V
Sbjct: 77 EQKTLPGMNRPIQVKP 92
>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 = 69.2 bits (170), Expect = 9e-15
Identities = 14/74 (18%), Positives = 33/74 (44%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
+ V N+ + V ++ + F + V + ++ G G V F+ EA ++
Sbjct: 16 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 219 MLNNQNLFERRITV 232
LN++ + R++ +
Sbjct: 76 DLNDRPIGSRKVKL 89
Score = 52.3 bits (126), Expect = 7e-09
Identities = 14/53 (26%), Positives = 23/53 (43%)
Query: 61 VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGG 113
V + ++ G P G A+V F+S D AV ++ RK+ + G
Sbjct: 46 VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPSSG 98
Score = 50.8 bits (122), Expect = 2e-08
Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 9/86 (10%)
Query: 509 NQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFD 560
SS T++ V+N+P T++ E+ D F I + G+ +V F+
Sbjct: 7 GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE-AMVAFE 65
Query: 561 SEWTAKRAIDMMDRTRIDGKIIDVTF 586
S A A+ ++ I + + +
Sbjct: 66 SRDEATAAVIDLNDRPIGSRKVKLVL 91
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 68.9 bits (169), Expect = 1e-14
Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 4/88 (4%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
KV+V NL + +L F G + V IA + GF VEF+ P +A ++ L
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGL 57
Query: 221 NNQNLFERRITVRMDRVADRLDGPVRLP 248
+ + + R+ V + R R P
Sbjct: 58 DGKVICGSRVRVELSTGMPRRSRFDRPP 85
Score = 51.5 bits (124), Expect = 2e-08
Identities = 16/67 (23%), Positives = 23/67 (34%), Gaps = 1/67 (1%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-IGLVRFDSEWTAKRAIDMMDRTRIDG 579
V NL EL F G ++ I V F+ A+ A+ +D I G
Sbjct: 5 VGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICG 64
Query: 580 KIIDVTF 586
+ V
Sbjct: 65 SRVRVEL 71
Score = 41.9 bits (99), Expect = 4e-05
Identities = 16/70 (22%), Positives = 25/70 (35%), Gaps = 7/70 (10%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
G + V I + P G A VEF+ P AV + G ++ ++ + G R
Sbjct: 25 GPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS---TGMPR 77
Query: 116 NMGGGGGVDR 125
R
Sbjct: 78 RSRFDRPPAR 87
>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 = 72.3 bits (177), Expect = 1e-14
Identities = 34/187 (18%), Positives = 73/187 (39%), Gaps = 17/187 (9%)
Query: 43 DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
SL+ + GDV V+IL + +A+V+ + + A++ ++ + G+ +
Sbjct: 49 PQSLFIL--FGVYGDVQRVKILF----NKKENALVQMADGNQAQLAMSHLNGHKLHGKPI 102
Query: 103 VIKEAVEDKGGRRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQFLESLGINCPLINKV 162
I + G ++ L ++ + + + ++ P +
Sbjct: 103 RITLSKHQNVQLPREG------QEDQGLTKDYGNSPLHRF--KKPGSKNFQNIFPPSATL 154
Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
++N+ V E+ L+ +F G V KD R ++ EAVQ++ L+N
Sbjct: 155 HLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQMGSVEEAVQALIDLHN 211
Query: 223 QNLFERR 229
+L E
Sbjct: 212 HDLGENH 218
Score = 60.0 bits (145), Expect = 2e-10
Identities = 24/106 (22%), Positives = 42/106 (39%), Gaps = 2/106 (1%)
Query: 484 GSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPP-TITWQELRDKFRNCGD 542
GS PR ++ + ++V NL P +T Q L F GD
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGD 61
Query: 543 IKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF 587
++ +I K + LV+ A+ A+ ++ ++ GK I +T
Sbjct: 62 VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS 107
Score = 54.2 bits (130), Expect = 2e-08
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 5/74 (6%)
Query: 162 VFVANLD-YKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
+ V+NL+ +V + L +F + G V+ V+I +K + V+ +A ++S L
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHL 92
Query: 221 NNQNLFERRITVRM 234
N L + I + +
Sbjct: 93 NGHKLHGKPIRITL 106
Score = 51.2 bits (122), Expect = 2e-07
Identities = 19/131 (14%), Positives = 51/131 (38%), Gaps = 7/131 (5%)
Query: 459 YSRNASNMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDT 518
+ + + E G + S + + G + +++ S T
Sbjct: 98 HGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSA----T 153
Query: 519 VVVKNLPPTITWQELRDKFRNCGDIK--FAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
+ + N+PP+++ ++L+ F + G + F + + L++ S A +A+ +
Sbjct: 154 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHD 213
Query: 577 I-DGKIIDVTF 586
+ + + V+F
Sbjct: 214 LGENHHLRVSF 224
>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 = 68.9 bits (169), Expect = 2e-14
Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 2/77 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+++V NL + K + +VF G + ++++ F VEF+ P +A ++
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK--NRRGGPPFAFVEFEDPRDAEDAVYG 80
Query: 220 LNNQNLFERRITVRMDR 236
+ + R+ V R
Sbjct: 81 RDGYDYDGYRLRVEFPR 97
Score = 59.3 bits (144), Expect = 4e-11
Identities = 27/107 (25%), Positives = 42/107 (39%), Gaps = 16/107 (14%)
Query: 484 GSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDI 543
GS +S SGG +++ + V NLPP I +++ D F G I
Sbjct: 1 GSSGSSGMSGGGVIRGPAGNNDC-----------RIYVGNLPPDIRTKDIEDVFYKYGAI 49
Query: 544 KFAEIK----GKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
+ ++K G V F+ A+ A+ D DG + V F
Sbjct: 50 RDIDLKNRRGGPP-FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF 95
Score = 43.8 bits (104), Expect = 8e-06
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 5/67 (7%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
G + +++ N A VEF+ P AV ++ G +L ++ + GR
Sbjct: 47 GAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP---RSGRG 101
Query: 116 NMGGGGG 122
G
Sbjct: 102 TGSGPSS 108
>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 = 68.5 bits (168), Expect = 2e-14
Identities = 14/74 (18%), Positives = 33/74 (44%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
+ V N+ + V ++ + F + V + ++ G G V F+ EA ++
Sbjct: 16 TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 219 MLNNQNLFERRITV 232
LN++ + R++ +
Sbjct: 76 DLNDRPIGSRKVKL 89
Score = 51.9 bits (125), Expect = 9e-09
Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 9/86 (10%)
Query: 509 NQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFD 560
SS TV+ V+N+P T++ E+ D F I + G+ +V F+
Sbjct: 7 GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGE-AMVAFE 65
Query: 561 SEWTAKRAIDMMDRTRIDGKIIDVTF 586
S A A+ ++ I + + ++
Sbjct: 66 SRDEATAAVIDLNDRPIGSRKVKLSG 91
Score = 50.8 bits (122), Expect = 2e-08
Identities = 13/44 (29%), Positives = 22/44 (50%)
Query: 61 VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI 104
V + ++ G P G A+V F+S D AV ++ RK+ +
Sbjct: 46 VCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL 89
>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 = 68.9 bits (169), Expect = 2e-14
Identities = 19/76 (25%), Positives = 46/76 (60%), Gaps = 3/76 (3%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD--GKSRGFGTVEFDHPVEAVQSI 217
+K+ V N+ ++ +++++RE+F G+++ V + G RGFG V+F +A ++
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Query: 218 -SMLNNQNLFERRITV 232
++ ++ +L+ RR+ +
Sbjct: 76 NALCHSTHLYGRRLVL 91
Score = 51.5 bits (124), Expect = 2e-08
Identities = 19/92 (20%), Positives = 40/92 (43%), Gaps = 10/92 (10%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI--------KGKGDIG 555
S S ++V+N+P +E+R+ F G++K + +G G
Sbjct: 3 SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRG-FG 61
Query: 556 LVRFDSEWTAKRAID-MMDRTRIDGKIIDVTF 586
V F ++ AK+A + + T + G+ + + +
Sbjct: 62 FVDFITKQDAKKAFNALCHSTHLYGRRLVLEW 93
Score = 46.5 bits (111), Expect = 1e-06
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 53 STVGDVTYVEILND--DTGKPRGSAIVEFQSPDLVRKAVNKM-HRFETKGRKLVIKEAVE 109
ST G++ V + TG RG V+F + +KA N + H GR+LV++ A
Sbjct: 37 STFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADS 96
Query: 110 DKGGRRNMGGGGG 122
+ G G
Sbjct: 97 EV--TVQSGPSSG 107
>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 = 68.9 bits (169), Expect = 2e-14
Identities = 15/74 (20%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+++ NL +V E+ L +F + + I G+ RG + F + A Q++
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 219 MLNNQNLFERRITV 232
++N L+ + + +
Sbjct: 86 LVNGYKLYGKILVI 99
Score = 46.9 bits (112), Expect = 1e-06
Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
+ L + + + I TG+ RG A + F + ++ +A++ ++ ++ G+
Sbjct: 39 ERDLVSL--FARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKI 96
Query: 102 LVIKEAVEDK 111
LVI+ K
Sbjct: 97 LVIEFGKNKK 106
Score = 44.6 bits (106), Expect = 5e-06
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
+KNL P +T ++L F + K I + +G + F ++ A +A+ +++
Sbjct: 30 LKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRG-QAFITFPNKEIAWQALHLVN 88
Query: 574 RTRIDGKIIDVTF 586
++ GKI+ + F
Sbjct: 89 GYKLYGKILVIEF 101
>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 = 67.6 bits (166), Expect = 2e-14
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
VFV +L ++ + F G++ + + D GKS+G+G V F + +A +I
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 220 LNNQNLFERRITVRM 234
+ Q L R+I
Sbjct: 68 MGGQWLGGRQIRTNW 82
Score = 42.9 bits (102), Expect = 1e-05
Identities = 22/71 (30%), Positives = 30/71 (42%), Gaps = 8/71 (11%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V +L P IT + F G I A + K KG G V F ++W A+ AI M
Sbjct: 11 VGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKG-YGFVSFFNKWDAENAIQQMG 69
Query: 574 RTRIDGKIIDV 584
+ G+ I
Sbjct: 70 GQWLGGRQIRT 80
Score = 41.4 bits (98), Expect = 5e-05
Identities = 14/69 (20%), Positives = 27/69 (39%), Gaps = 3/69 (4%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
A++ + G ++ ++ D TGK +G V F + A+ +M GR+
Sbjct: 20 TAAIAAA--FAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ 77
Query: 102 LVIKEAVED 110
+ A
Sbjct: 78 IRTNWATRK 86
>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 = 67.6 bits (166), Expect = 3e-14
Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
K+FV N+ ++LR +F G+V ++ + + V + +A +I+ L
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQL 63
Query: 221 NNQNLFERRITVRMDRVADRLDGP 244
N + + +RI V + + GP
Sbjct: 64 NGKEVKGKRINVELSTKGQKKSGP 87
Score = 52.2 bits (126), Expect = 7e-09
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGK 580
V N+ T QELR F G + ++ D V + E AK AI ++ + GK
Sbjct: 14 VGNVSAACTSQELRSLFERRGRVIECDV--VKDYAFVHMEKEADAKAAIAQLNGKEVKGK 71
Query: 581 IIDVTF 586
I+V
Sbjct: 72 RINVEL 77
Score = 38.0 bits (89), Expect = 8e-04
Identities = 11/67 (16%), Positives = 29/67 (43%), Gaps = 10/67 (14%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
G V +++ + A V + + A+ +++ E KG+++ ++ + G++
Sbjct: 34 GRVIECDVV-------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS---TKGQK 83
Query: 116 NMGGGGG 122
G G
Sbjct: 84 KSGPSSG 90
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 69.6 bits (170), Expect = 3e-14
Identities = 19/123 (15%), Positives = 46/123 (37%), Gaps = 6/123 (4%)
Query: 120 GGGVDRDLSALLQNNSSKFGNT---YGLSPQFLESLGINCPLINKVFVANLDYKVDEKKL 176
G + ++ + + +P L + V+V + + +++L
Sbjct: 13 LGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQL 72
Query: 177 REVFRLAGKVENVEIALDKD---GKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVR 233
+V R G + VE+ ++ G+S+G+ V + + +L + L ++ VR
Sbjct: 73 IQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR 132
Query: 234 MDR 236
Sbjct: 133 PAT 135
Score = 51.1 bits (122), Expect = 7e-08
Identities = 20/121 (16%), Positives = 39/121 (32%), Gaps = 10/121 (8%)
Query: 475 GGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELR 534
G + + ++ P + R V V + T Q+L
Sbjct: 14 GTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLI 73
Query: 535 DKFRNCGDIKFAEIK---------GKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVT 585
R+ G E+K KG V SE + + ++++ ++G+ +DV
Sbjct: 74 QVIRSIGVYDVVELKFAENRANGQSKG-YAEVVVASENSVHKLLELLPGKVLNGEKVDVR 132
Query: 586 F 586
Sbjct: 133 P 133
Score = 49.1 bits (117), Expect = 3e-07
Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 1/72 (1%)
Query: 55 VGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGG 113
V DV ++ + G+ +G A V S + V K + + G K+ ++ A
Sbjct: 81 VYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140
Query: 114 RRNMGGGGGVDR 125
+
Sbjct: 141 QFEAQARKRECV 152
>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 = 67.7 bits (166), Expect = 3e-14
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+ NL + + E +L+EVF A ++ V +DGKS+G +EF +A +++
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEE 72
Query: 220 LNNQNLFERRITV 232
+ R +++
Sbjct: 73 KQGAEIDGRSVSL 85
Score = 51.9 bits (125), Expect = 1e-08
Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 3/71 (4%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIK--FAEIKGKGDIGLVRFDSEWTAKRAIDMMDRT 575
T++ KNL IT EL++ F + +I+ + K KG I + F SE A++ ++
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKG-IAYIEFKSEADAEKNLEEKQGA 76
Query: 576 RIDGKIIDVTF 586
IDG+ + + +
Sbjct: 77 EIDGRSVSLYY 87
Score = 46.5 bits (111), Expect = 7e-07
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 60 YVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
+EI GK +G A +EF+S K + + E GR + + +KGG R
Sbjct: 40 ALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT-GEKGGTR 95
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 67.5 bits (165), Expect = 4e-14
Identities = 23/98 (23%), Positives = 41/98 (41%), Gaps = 6/98 (6%)
Query: 493 GGYGNPR---AGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCG-DIKFAEI 548
G + +GL S +R + +KNLP +WQ+L+D R + F+ +
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSV 61
Query: 549 KGKGD--IGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
+ G + F SE A++ ++ G +I V
Sbjct: 62 NTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99
Score = 66.8 bits (163), Expect = 9e-14
Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 2/77 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
++ + NL + L+++ R + G G +EF V+++
Sbjct: 29 YRITMKNLPEGCSWQDLKDLARENSLE--TTFSSVNTRDFDGTGALEFPSEEILVEALER 86
Query: 220 LNNQNLFERRITVRMDR 236
LNN ITV D
Sbjct: 87 LNNIEFRGSVITVERDD 103
Score = 49.1 bits (117), Expect = 1e-07
Identities = 11/63 (17%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
+ T+ + +T G+ +EF S +++ +A+ +++ E +G + ++
Sbjct: 51 ENSLETTFSSV---NTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDNPPP 107
Query: 113 GRR 115
RR
Sbjct: 108 IRR 110
>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 = 67.8 bits (166), Expect = 5e-14
Identities = 20/86 (23%), Positives = 40/86 (46%), Gaps = 9/86 (10%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN--------VEIALDKD-GKSRGFGTVEFDHP 210
+ ++V L+ V L + F+ G V+ + I LDK+ GK +G TV ++ P
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 211 VEAVQSISMLNNQNLFERRITVRMDR 236
A ++ + ++ ++ V + R
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVSLAR 101
Score = 56.6 bits (137), Expect = 3e-10
Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 14/82 (17%)
Query: 517 DTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI--------------GLVRFDSE 562
+ V+ L ++T +L D F+ CG +K + G+ I V ++
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 563 WTAKRAIDMMDRTRIDGKIIDV 584
TAK A++ D G + V
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKV 97
Score = 47.8 bits (114), Expect = 4e-07
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 2/60 (3%)
Query: 63 ILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGG 122
L+ +TGKP+G A V ++ P + AV + +G KL + A + N G G
Sbjct: 56 YLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP--PMNSGPSSG 113
>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 = 66.9 bits (164), Expect = 7e-14
Identities = 12/73 (16%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
+F+ NL+ +L+ ++ + + G +R FG V+F+ + +++ +
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALEL- 77
Query: 221 NNQNLFERRITVR 233
+F I +
Sbjct: 78 TGLKVFGNEIKLE 90
Score = 45.7 bits (109), Expect = 2e-06
Identities = 12/73 (16%), Positives = 27/73 (36%), Gaps = 8/73 (10%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDM 571
+ + NL P + EL+ + + G V F+S ++A++
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRK-FGYVDFESAEDLEKALE- 76
Query: 572 MDRTRIDGKIIDV 584
+ ++ G I +
Sbjct: 77 LTGLKVFGNEIKL 89
Score = 44.6 bits (106), Expect = 5e-06
Identities = 11/59 (18%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGR 114
+ +++ TG R V+F+S + + KA+ ++ + G ++ +++ G R
Sbjct: 42 FAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDGTR 99
>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 = 66.1 bits (162), Expect = 1e-13
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKV-ENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+F+ NLD ++DEK L + F G + + +I D D G S+G+ + F + +I
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 219 MLNNQNLFERRITV 232
+N Q L R ITV
Sbjct: 67 AMNGQYLCNRPITV 80
Score = 43.0 bits (102), Expect = 2e-05
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 521 VKNLPPTITWQELRDKFRNCGDI-KFAEI-------KGKGDIGLVRFDSEWTAKRAIDMM 572
+ NL P I + L D F G I + +I KG + F S + AI+ M
Sbjct: 10 IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKG-YAFINFASFDASDAAIEAM 68
Query: 573 DRTRIDGKIIDVTFF 587
+ + + I V++
Sbjct: 69 NGQYLCNRPITVSYA 83
Score = 35.3 bits (82), Expect = 0.007
Identities = 13/54 (24%), Positives = 20/54 (37%)
Query: 67 DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGG 120
DTG +G A + F S D A+ M+ R + + A + G
Sbjct: 43 DTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGSGPSSG 96
>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 = 66.2 bits (162), Expect = 1e-13
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
VFV +L ++ + ++ F G++ + + D GKS+G+G V F + +A +I
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 220 LNNQNLFERRITVRM 234
+ Q L R+I
Sbjct: 77 MGGQWLGGRQIRTNW 91
Score = 44.3 bits (105), Expect = 7e-06
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V +L P IT ++++ F G I A + K KG G V F ++W A+ AI M
Sbjct: 20 VGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKG-YGFVSFFNKWDAENAIQQMG 78
Query: 574 RTRIDGKIIDV 584
+ G+ I
Sbjct: 79 GQWLGGRQIRT 89
Score = 42.3 bits (100), Expect = 4e-05
Identities = 13/81 (16%), Positives = 27/81 (33%), Gaps = 3/81 (3%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
+ + G ++ ++ D TGK +G V F + A+ +M GR+
Sbjct: 29 TEDIKAA--FAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ 86
Query: 102 LVIKEAVEDKGGRRNMGGGGG 122
+ A ++
Sbjct: 87 IRTNWATRKPPAPKSTYESNT 107
>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 = 65.7 bits (161), Expect = 2e-13
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+++FV NL + E+++R++F GK V I K +GFG + + A +
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-----KDKGFGFIRLETRTLAEIAKVE 70
Query: 220 LNNQNLFERRITVRM 234
L+N L +++ VR
Sbjct: 71 LDNMPLRGKQLRVRF 85
Score = 59.6 bits (145), Expect = 2e-11
Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 2/85 (2%)
Query: 503 DSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDS 561
S S + + +R + V NLPP IT +E+R F G I K KG G +R ++
Sbjct: 2 SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-FGFIRLET 60
Query: 562 EWTAKRAIDMMDRTRIDGKIIDVTF 586
A+ A +D + GK + V F
Sbjct: 61 RTLAEIAKVELDNMPLRGKQLRVRF 85
Score = 36.9 bits (86), Expect = 0.002
Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 7/67 (10%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
G V I K +G + ++ L A ++ +G++L ++ A
Sbjct: 40 GKAGEVFIH-----KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA--CHSASL 92
Query: 116 NMGGGGG 122
G G
Sbjct: 93 TSGPSSG 99
>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 = 69.4 bits (169), Expect = 2e-13
Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 3/77 (3%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD---GKSRGFGTVEFDHPVEAVQS 216
+++ NL + ++ L E G + +EI ++ G+S+GF V + +
Sbjct: 69 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 128
Query: 217 ISMLNNQNLFERRITVR 233
+ +L + L + V
Sbjct: 129 MDLLPKRELHGQNPVVT 145
Score = 54.0 bits (129), Expect = 2e-08
Identities = 25/134 (18%), Positives = 49/134 (36%), Gaps = 12/134 (8%)
Query: 462 NASNMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVV 521
+ ++Y + S N ++ + G N + +R + +
Sbjct: 16 DQIDLYDDVISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTG--KRIALYI 73
Query: 522 KNLPPTITWQELRDKFRNCGDIKFAEIK---------GKGDIGLVRFDSEWTAKRAIDMM 572
NL T ++L + + G EIK KG LV SE ++K+ +D++
Sbjct: 74 GNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKG-FALVGVGSEASSKKLMDLL 132
Query: 573 DRTRIDGKIIDVTF 586
+ + G+ VT
Sbjct: 133 PKRELHGQNPVVTP 146
Score = 47.0 bits (111), Expect = 5e-06
Identities = 15/94 (15%), Positives = 34/94 (36%), Gaps = 1/94 (1%)
Query: 55 VGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGG 113
V D+ ++ + G+ +G A+V S +K ++ + + E G+ V+ +
Sbjct: 94 VNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLS 153
Query: 114 RRNMGGGGGVDRDLSALLQNNSSKFGNTYGLSPQ 147
+ M + G++ PQ
Sbjct: 154 QFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQ 187
>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 = 64.9 bits (159), Expect = 3e-13
Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 2/75 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
NK+FV + + E +LRE F+ G V V + D + + RGFG + F+ ++V
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE-QSVDQAV 69
Query: 219 MLNNQNLFERRITVR 233
++ ++ +++ V+
Sbjct: 70 NMHFHDIMGKKVEVK 84
Score = 46.8 bits (112), Expect = 7e-07
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
+ G VT V ++ D + +PRG + F+ V +AVN MH + G+K+ +K A
Sbjct: 29 EYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRAE 87
Query: 109 EDKGGRRNMGGGG 121
+ + + G
Sbjct: 88 P-RDSKSSGPSSG 99
Score = 39.5 bits (93), Expect = 3e-04
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 9/71 (12%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V +P ELR+ F+ G + + + +G G + F+ E + +A++ M
Sbjct: 15 VGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRG-FGFITFEDEQSVDQAVN-MH 72
Query: 574 RTRIDGKIIDV 584
I GK ++V
Sbjct: 73 FHDIMGKKVEV 83
>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 = 66.1 bits (161), Expect = 4e-13
Identities = 24/82 (29%), Positives = 41/82 (50%), Gaps = 4/82 (4%)
Query: 155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAV 214
+CPL KV+V NL ++ +L F G + +V +A + GF VEF+ P +A
Sbjct: 69 SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAA 124
Query: 215 QSISMLNNQNLFERRITVRMDR 236
++ L+ + L R+ V +
Sbjct: 125 DAVRELDGRTLCGCRVRVELSN 146
Score = 50.6 bits (121), Expect = 9e-08
Identities = 17/90 (18%), Positives = 28/90 (31%), Gaps = 1/90 (1%)
Query: 498 PRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-IGL 556
+ M++ S V V NL EL F G ++ +
Sbjct: 55 TEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAF 114
Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
V F+ A A+ +D + G + V
Sbjct: 115 VEFEDPRDAADAVRELDGRTLCGCRVRVEL 144
Score = 36.0 bits (83), Expect = 0.011
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 7/60 (11%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
G + V + + P G A VEF+ P AV ++ G ++ ++ + G +R
Sbjct: 98 GPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS---NGEKR 150
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 64.3 bits (157), Expect = 4e-13
Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 7/80 (8%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGK--VENVEIALDKD-GKSRGFGTVEFDHPVEAVQS 216
+ + + N+ + V N+ + DK ++RGF V+ ++A Q
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
Query: 217 ISMLNNQNLFE----RRITV 232
+ +L + + + I V
Sbjct: 70 LQILQSLHPPLKIDGKTIGV 89
Score = 49.2 bits (118), Expect = 8e-08
Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 14/92 (15%)
Query: 508 MNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIK---------GKGDIGLVR 558
M + DT++++N+ P + + I+ +G V+
Sbjct: 1 MGHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRG-FAFVQ 59
Query: 559 FDSEWTAKRAIDMMD----RTRIDGKIIDVTF 586
S A + + ++ +IDGK I V F
Sbjct: 60 LSSAMDASQLLQILQSLHPPLKIDGKTIGVDF 91
Score = 35.0 bits (81), Expect = 0.009
Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 5/56 (8%)
Query: 57 DVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMH----RFETKGRKLVIKEA 107
V + ++ D T + RG A V+ S + + + + G+ + + A
Sbjct: 37 AVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92
>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 = 64.2 bits (157), Expect = 5e-13
Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 9/82 (10%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKV--------ENVEIALDKD-GKSRGFGTVEFDHP 210
N +FV L V + + + F+ G + + + D++ GK +G TV FD P
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 211 VEAVQSISMLNNQNLFERRITV 232
A +I + + I V
Sbjct: 74 PSAKAAIDWFDGKEFSGNPIKV 95
Score = 53.8 bits (130), Expect = 2e-09
Identities = 26/97 (26%), Positives = 40/97 (41%), Gaps = 16/97 (16%)
Query: 505 NRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKG-------------- 550
+ S+ + +T+ V+ L +T + + D F+ G IK + G
Sbjct: 2 GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61
Query: 551 -KGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
KG+ V FD +AK AID D G I V+F
Sbjct: 62 LKGE-ATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97
Score = 41.9 bits (99), Expect = 4e-05
Identities = 12/45 (26%), Positives = 20/45 (44%)
Query: 63 ILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
+ +TGK +G A V F P + A++ E G + + A
Sbjct: 54 YTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>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 = 64.7 bits (158), Expect = 5e-13
Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 7/79 (8%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
VF+ NL + +E+ L EV + G ++ V + L D S+G +F A + ++
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 220 LNNQNLFE------RRITV 232
+ + R++ V
Sbjct: 77 ASLEAEGGGLKLDGRQLKV 95
Score = 49.3 bits (118), Expect = 1e-07
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 43 DASLYQISHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHR------F 95
+ +L + L GD+ YV ++ DT +G A +F + + +K +
Sbjct: 29 EEALGE--VLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL 86
Query: 96 ETKGRKLVIKEAVE 109
+ GR+L + AV
Sbjct: 87 KLDGRQLKVDLAVT 100
Score = 47.7 bits (114), Expect = 4e-07
Identities = 19/96 (19%), Positives = 36/96 (37%), Gaps = 14/96 (14%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGL 556
S S S E TV ++NL + L + + GD+K+ + KG
Sbjct: 3 SGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKG-CAF 61
Query: 557 VRFDSEWTAKRAIDMMDRTR------IDGKIIDVTF 586
+F ++ A++ + +DG+ + V
Sbjct: 62 AQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDL 97
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 64.7 bits (158), Expect = 5e-13
Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 9/84 (10%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN--------VEIALDKD-GKSRGFGTVEFDHP 210
N +FV L V + + + F+ G ++ + + D++ GK +G TV FD P
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 211 VEAVQSISMLNNQNLFERRITVRM 234
A +I + + I V
Sbjct: 68 PSAKAAIDWFDGKEFSGNPIKVSF 91
Score = 56.6 bits (137), Expect = 4e-10
Identities = 25/91 (27%), Positives = 38/91 (41%), Gaps = 14/91 (15%)
Query: 510 QSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI--------------G 555
+ N + +T+ V+ L +T + + D F+ G IK + G+ I
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
V FD +AK AID D G I V+F
Sbjct: 61 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 91
Score = 47.8 bits (114), Expect = 5e-07
Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 1/64 (1%)
Query: 63 ILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE-DKGGRRNMGGGG 121
+ +TGK +G A V F P + A++ E G + + A R G G
Sbjct: 48 YTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGGGNGRG 107
Query: 122 GVDR 125
G++
Sbjct: 108 GLEH 111
>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 = 63.8 bits (156), Expect = 5e-13
Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 7/75 (9%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
K+ V N+ ++LR F G V +I + + V + +AV++I
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRG 63
Query: 220 LNNQNLFERRITVRM 234
L+N +R+ V++
Sbjct: 64 LDNTEFQGKRMHVQL 78
Score = 46.8 bits (112), Expect = 5e-07
Identities = 23/64 (35%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGK 580
V N+ PT T QELR KF G + +I D V + A AI +D T GK
Sbjct: 15 VGNISPTCTNQELRAKFEEYGPVIECDI--VKDYAFVHMERAEDAVEAIRGLDNTEFQGK 72
Query: 581 IIDV 584
+ V
Sbjct: 73 RMHV 76
Score = 35.7 bits (83), Expect = 0.006
Identities = 10/67 (14%), Positives = 24/67 (35%), Gaps = 10/67 (14%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
G V +I + A V + + +A+ + E +G+++ ++ + R
Sbjct: 35 GPVIECDI-------VKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS---TSRLR 84
Query: 116 NMGGGGG 122
G
Sbjct: 85 TASGPSS 91
>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 = 64.2 bits (157), Expect = 5e-13
Identities = 18/84 (21%), Positives = 35/84 (41%)
Query: 503 DSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSE 562
S S ++ + + V+NL + + + + +F N +K D V F +
Sbjct: 2 SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNR 61
Query: 563 WTAKRAIDMMDRTRIDGKIIDVTF 586
A A+ ++ +DG I+VT
Sbjct: 62 EDAVEAMKALNGKVLDGSPIEVTL 85
Score = 61.9 bits (151), Expect = 3e-12
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 5/72 (6%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
++V NL E+ + + F + K R + V F + +AV+++ L
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKAL 71
Query: 221 NNQNLFERRITV 232
N + L I V
Sbjct: 72 NGKVLDGSPIEV 83
Score = 34.9 bits (81), Expect = 0.009
Identities = 10/63 (15%), Positives = 21/63 (33%), Gaps = 2/63 (3%)
Query: 60 YVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGG 119
+ K R A V F + + +A+ ++ G + + A + + G
Sbjct: 39 IKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA--KPVDKDSSGP 96
Query: 120 GGG 122
G
Sbjct: 97 SSG 99
>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 = 63.8 bits (156), Expect = 7e-13
Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 7/76 (9%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
K+F+ NL + E+++R +F GKV +I + +G V + A +I L
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNL 62
Query: 221 NNQNLFERRITVRMDR 236
++ L I V +
Sbjct: 63 HHYKLHGVNINVEASK 78
Score = 51.8 bits (125), Expect = 9e-09
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 2/64 (3%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGK 580
+ NLP T QE+R F G + +I K G V + + A+ AI + ++ G
Sbjct: 13 IGNLPREATEQEIRSLFEQYGKVLECDII-KN-YGFVHIEDKTAAEDAIRNLHHYKLHGV 70
Query: 581 IIDV 584
I+V
Sbjct: 71 NINV 74
Score = 39.1 bits (92), Expect = 3e-04
Identities = 8/65 (12%), Positives = 20/65 (30%), Gaps = 7/65 (10%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
G V +I+ + V + A+ +H ++ G + ++ +
Sbjct: 33 GKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASS 85
Query: 116 NMGGG 120
G
Sbjct: 86 GPSSG 90
>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 = 64.8 bits (158), Expect = 8e-13
Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 6/79 (7%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN------VEIALDKDGKSRGFGTVEFDHPVEA 213
+++V NL V EK L+ +F + +I L K+G+ +G + + A
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105
Query: 214 VQSISMLNNQNLFERRITV 232
+++ N LF + + V
Sbjct: 106 AKALKEANGYVLFGKPMVV 124
Score = 46.7 bits (111), Expect = 2e-06
Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 11/77 (14%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI-----------GLVRFDSEWTAKRAI 569
VKNL + ++L+ F D + DI + +E A +A+
Sbjct: 50 VKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKAL 109
Query: 570 DMMDRTRIDGKIIDVTF 586
+ + GK + V F
Sbjct: 110 KEANGYVLFGKPMVVQF 126
Score = 46.0 bits (109), Expect = 3e-06
Identities = 12/71 (16%), Positives = 28/71 (39%), Gaps = 7/71 (9%)
Query: 52 LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA---- 107
S+ +I G+ +G A + + KA+ + + + G+ +V++ A
Sbjct: 72 FSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSAR 131
Query: 108 ---VEDKGGRR 115
+G R+
Sbjct: 132 PKQDPKEGKRK 142
>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 = 63.2 bits (154), Expect = 9e-13
Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 3/76 (3%)
Query: 511 SSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAID 570
SS ++VKNLP QE+ D ++ +K+ + V + A+ AI
Sbjct: 2 SSG--SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58
Query: 571 MMDRTRIDGKIIDVTF 586
M + GK + V
Sbjct: 59 MFHQYSFRGKDLIVQL 74
Score = 58.6 bits (142), Expect = 4e-11
Identities = 11/86 (12%), Positives = 35/86 (40%), Gaps = 7/86 (8%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+ + V NL + +++ ++ + ++ + +++ V + +A +I M
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV-----DRNKRTAFVTLLNGEQAQNAIQM 59
Query: 220 LNNQNLFERRITVRMDRVADRL-DGP 244
+ + + + V++ L GP
Sbjct: 60 FHQYSFRGKDLIVQLQPTDALLCSGP 85
Score = 37.8 bits (88), Expect = 9e-04
Identities = 7/45 (15%), Positives = 21/45 (46%)
Query: 67 DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
+ + +A V + + + A+ H++ +G+ L+++ D
Sbjct: 35 YVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTDA 79
>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 = 63.6 bits (155), Expect = 1e-12
Identities = 18/95 (18%), Positives = 39/95 (41%), Gaps = 2/95 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
+ N+ + + + + + EN V + +D +G+ G V+F + +A +S
Sbjct: 16 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 75
Query: 219 MLNNQNLFERRITVRMDRVADRLDGPVRLPEGLKS 253
+ + + L R V + + D + P KS
Sbjct: 76 L-HRKKLNGREAFVHVVTLEDMREIEKNPPAQGKS 109
Score = 50.1 bits (120), Expect = 6e-08
Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 9/88 (10%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGL 556
S S N + + N+P +IT ++ + A +G G L
Sbjct: 3 SGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQ-AL 61
Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
V+F +E A+++ + R +++G+ V
Sbjct: 62 VQFKNEDDARKSER-LHRKKLNGREAFV 88
Score = 45.9 bits (109), Expect = 2e-06
Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 61 VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
V +L D+ G+ G A+V+F++ D RK+ ++HR + GR+ + +
Sbjct: 46 VHVLVDNNGQGLGQALVQFKNEDDARKSE-RLHRKKLNGREAFVHVVTLED 95
>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 = 63.3 bits (154), Expect = 1e-12
Identities = 14/76 (18%), Positives = 30/76 (39%), Gaps = 2/76 (2%)
Query: 511 SSNIERD--TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRA 568
S + R ++ KNLP E+++ F G + + G +V F A++A
Sbjct: 3 SGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKA 62
Query: 569 IDMMDRTRIDGKIIDV 584
+ ++ + +
Sbjct: 63 FRHLAYSKFHHVPLYL 78
Score = 51.0 bits (122), Expect = 3e-08
Identities = 13/71 (18%), Positives = 25/71 (35%), Gaps = 5/71 (7%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
+ NL +++E F G + V + + VEF P+EA ++ L
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLA 67
Query: 222 NQNLFERRITV 232
+ +
Sbjct: 68 YSKFHHVPLYL 78
Score = 34.0 bits (78), Expect = 0.025
Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 5/55 (9%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVED 110
G + V + + +AIVEF P RKA + + L ++ A
Sbjct: 35 GSLGRVLL-----PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG 84
>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 = 62.1 bits (152), Expect = 2e-12
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
K+FV L E+K+RE F G+VE++E+ +D K RGF + F E V+ I
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE-EPVKKIME 59
Query: 220 LNNQNLFERRITVR 233
N+ + ++
Sbjct: 60 KKYHNVGLSKCEIK 73
Score = 44.8 bits (107), Expect = 2e-06
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 4/59 (6%)
Query: 51 HLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAV-NKMHRFETKGRKLVIKEA 107
+ G+V +E+ D T K RG + F+ + V+K + K H K IK A
Sbjct: 19 YFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYH--NVGLSKCEIKVA 75
Score = 40.6 bits (96), Expect = 6e-05
Identities = 12/71 (16%), Positives = 28/71 (39%), Gaps = 9/71 (12%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V L P +++R+ F G+++ E+ K +G + F E K+ ++
Sbjct: 4 VGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRG-FCFITFKEEEPVKKIMEKKY 62
Query: 574 RTRIDGKIIDV 584
+ ++
Sbjct: 63 HN-VGLSKCEI 72
>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 = 62.3 bits (152), Expect = 2e-12
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 2/73 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+ V + + V EK + E K + I + G G+ V+F + E Q++
Sbjct: 11 HTVKLRGAPFNVTEKNVMEFLA-PLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKC 69
Query: 220 LNNQNLFERRITV 232
N + + R I V
Sbjct: 70 -NREYMGGRYIEV 81
Score = 46.1 bits (110), Expect = 1e-06
Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 7/81 (8%)
Query: 509 NQSSNIERDTVVVKNLPPTITWQELRDKFRNCG--DIKF---AEIKGKGDIGLVRFDSEW 563
+ SS TV ++ P +T + + + I+ A G V F +E
Sbjct: 3 SGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGY-IFVDFSNEE 61
Query: 564 TAKRAIDMMDRTRIDGKIIDV 584
K+A+ +R + G+ I+V
Sbjct: 62 EVKQALK-CNREYMGGRYIEV 81
Score = 37.3 bits (87), Expect = 0.001
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 57 DVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
+ I+ + G G V+F + + V++A+ K +R GR
Sbjct: 35 KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQAL-KCNREYMGGRY 78
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein
biosynthesis, RNA recognition motif, RNA binding domain,
RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 62.6 bits (153), Expect = 2e-12
Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 4/74 (5%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK--DGKSRGFGTVEFDHPVEAVQSIS 218
F+ NL Y V E+ ++E FR + V + + + +GFG EF+ ++++ S
Sbjct: 21 TAFLGNLPYDVTEESIKEFFR-GLNISAVRLPREPSNPERLKGFGYAEFED-LDSLLSAL 78
Query: 219 MLNNQNLFERRITV 232
LN ++L RRI V
Sbjct: 79 SLNEESLGNRRIRV 92
Score = 39.1 bits (92), Expect = 3e-04
Identities = 8/58 (13%), Positives = 27/58 (46%), Gaps = 3/58 (5%)
Query: 56 GDVTYVEILND--DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
+++ V + + + + +G EF+ D + A++ ++ R++ + A + +
Sbjct: 43 LNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNRRIRVDVADQAQ 99
Score = 34.9 bits (81), Expect = 0.012
Identities = 14/92 (15%), Positives = 31/92 (33%), Gaps = 12/92 (13%)
Query: 499 RAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD----- 553
R + ++ T + NLP +T + +++ FR + +
Sbjct: 2 RGSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLK 61
Query: 554 -IGLVRFDSEWTAKRAI-----DMMDRT-RID 578
G F+ + A+ + +R R+D
Sbjct: 62 GFGYAEFEDLDSLLSALSLNEESLGNRRIRVD 93
>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 = 63.7 bits (155), Expect = 2e-12
Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 2/80 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+ V + L YK E + F V I + DG+ G VEF EAV ++S
Sbjct: 47 HCVHMRGLPYKATENDIYNFFS-PLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSK 105
Query: 220 LNNQNLFERRITVRMDRVAD 239
+ N+ R I + ++
Sbjct: 106 -DRANMQHRYIELFLNSTTG 124
Score = 52.9 bits (127), Expect = 1e-08
Identities = 21/125 (16%), Positives = 42/125 (33%), Gaps = 19/125 (15%)
Query: 465 NMYGNSRYGSGGNEMDYGGGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNL 524
+ + +S G+ M + G + G S S + V ++ L
Sbjct: 7 HHHHSSGLVPRGSHM------------ASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGL 54
Query: 525 PPTITWQELRDKFRNCGDIKFAEIKG-----KGDIGLVRFDSEWTAKRAIDMMDRTRIDG 579
P T ++ + F ++ G G+ V F + A A+ DR +
Sbjct: 55 PYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGE-ADVEFATHEEAVAAMS-KDRANMQH 112
Query: 580 KIIDV 584
+ I++
Sbjct: 113 RYIEL 117
Score = 41.0 bits (96), Expect = 2e-04
Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 6/66 (9%)
Query: 61 VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI-----KEAVEDKGGRR 115
V I G+ G A VEF + + A+ R + R + + A +
Sbjct: 75 VHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGASNGAYSSQ 133
Query: 116 NMGGGG 121
M G G
Sbjct: 134 VMQGMG 139
>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 = 62.7 bits (153), Expect = 2e-12
Identities = 13/72 (18%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
++V NL V E + ++F G ++ ++ + + VEF +A +++ +
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAM 75
Query: 221 NNQNLFERRITV 232
N + + + + V
Sbjct: 76 NGRKILGKEVKV 87
Score = 45.7 bits (109), Expect = 2e-06
Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 6/72 (8%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVRFDSEWTAKRAIDMM 572
T+ V NL +T + F G K ++ V F A A+ M
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAM 75
Query: 573 DRTRIDGKIIDV 584
+ +I GK + V
Sbjct: 76 NGRKILGKEVKV 87
Score = 31.1 bits (71), Expect = 0.27
Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 5/80 (6%)
Query: 43 DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
+ + Q+ S +G +++ + T VEF A+ M+ + G+++
Sbjct: 29 EVLILQL--FSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAMNGRKILGKEV 85
Query: 103 VIKEAVEDKGGRRNMGGGGG 122
+ A + G G
Sbjct: 86 KVNWATTPS--SQKSGPSSG 103
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 62.3 bits (152), Expect = 3e-12
Identities = 19/74 (25%), Positives = 36/74 (48%), Gaps = 3/74 (4%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+V NL + + + +F+ + +V + DKD K +GF VEFD V++++
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFK-DLSIRSVRLVRDKDTDKFKGFCYVEFDE-VDSLKEAL 73
Query: 219 MLNNQNLFERRITV 232
+ L +R + V
Sbjct: 74 TYDGALLGDRSLRV 87
Score = 45.7 bits (109), Expect = 2e-06
Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 2/64 (3%)
Query: 58 VTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRN 116
+ V ++ D DT K +G VEF D +++A+ R L + A K +
Sbjct: 41 IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT-YDGALLGDRSLRVDIAEGRKQDKSG 99
Query: 117 MGGG 120
G
Sbjct: 100 PSSG 103
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 62.3 bits (152), Expect = 3e-12
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
++FV V E +L E+F G ++ V+I GF VEF+ A ++I
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEE 84
Query: 220 LNNQNLFERRITV 232
++ ++ + + V
Sbjct: 85 VHGKSFANQPLEV 97
Score = 56.9 bits (138), Expect = 3e-10
Identities = 22/103 (21%), Positives = 39/103 (37%), Gaps = 5/103 (4%)
Query: 484 GSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDI 543
GS PR +R + SN + V+ P + EL + F G +
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMHHRQEGELSNT---RLFVRPFPLDVQESELNEIFGPFGPM 58
Query: 544 KFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
K +I G V F+ +A +AI+ + + ++V +
Sbjct: 59 KEVKIL-NG-FAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY 99
Score = 36.5 bits (85), Expect = 0.004
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 7/52 (13%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
G + V+I G A VEF+ + KA+ ++H + L + +
Sbjct: 56 GPMKEVKI-------LNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS 100
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 60.9 bits (149), Expect = 4e-12
Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
K+FV L + ++ F GKV++ + DK + RGFG V F+ + V+ +
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE-DIVEKVCE 59
Query: 220 LNNQNLFERRITVR 233
++ + + + +
Sbjct: 60 IHFHEINNKMVECK 73
Score = 40.5 bits (96), Expect = 6e-05
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
+ G V ++ D T + RG V F+S D+V K ++H E + + K+A
Sbjct: 18 HYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHFHEINNKMVECKKA 75
Score = 37.8 bits (89), Expect = 5e-04
Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 9/71 (12%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V L T ++++ F G + A + + +G G V F+SE ++ ++
Sbjct: 4 VGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRG-FGFVTFESEDIVEKVCEIHF 62
Query: 574 RTRIDGKIIDV 584
I+ K+++
Sbjct: 63 HE-INNKMVEC 72
>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 = 61.5 bits (150), Expect = 4e-12
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 6/75 (8%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
NK+++ NL V LR++F ++ G+ V++ A+++I
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIET 63
Query: 220 LNNQ-NLFERRITVR 233
L+ + L + + V
Sbjct: 64 LSGKVELHGKIMEVD 78
Score = 48.4 bits (116), Expect = 2e-07
Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMD-RTR 576
+ + NL P +T +LR F + ++ K V + + A RAI+ + +
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVE 69
Query: 577 IDGKIIDV 584
+ GKI++V
Sbjct: 70 LHGKIMEV 77
Score = 39.9 bits (94), Expect = 2e-04
Identities = 12/64 (18%), Positives = 24/64 (37%), Gaps = 3/64 (4%)
Query: 60 YVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH-RFETKGRKLVIKEAVEDKGGRRNMG 118
L G A V++ + +A+ + + E G+ + + +V K R+ G
Sbjct: 32 RKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKK--LRSSG 89
Query: 119 GGGG 122
G
Sbjct: 90 PSSG 93
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 61.7 bits (150), Expect = 5e-12
Identities = 12/75 (16%), Positives = 25/75 (33%), Gaps = 1/75 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
V++ ++E G+V N+++ +G V FD A + +
Sbjct: 12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 71
Query: 220 LNNQNLFERRITVRM 234
Q E + +
Sbjct: 72 -PGQKYKETDLLILF 85
Score = 47.8 bits (114), Expect = 4e-07
Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 1/60 (1%)
Query: 50 SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
L G V +++ +GS V F S + +K V + + K L+I +
Sbjct: 30 EWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ETPGQKYKETDLLILFKDD 88
Score = 47.0 bits (112), Expect = 7e-07
Identities = 11/72 (15%), Positives = 29/72 (40%), Gaps = 6/72 (8%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-----IGLVRFDSEWTAKRAIDMM 572
+V +K P T ++++ + G + +++ V FDS +AK+ ++
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 72
Query: 573 DRTRIDGKIIDV 584
+ + +
Sbjct: 73 GQK-YKETDLLI 83
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 61.5 bits (150), Expect = 5e-12
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK--DGKSRGFGTVEFDHPVEAVQSIS 218
F+ NL Y V E+ ++E FR + V + + + +GFG EF+ ++++ S
Sbjct: 17 TAFLGNLPYDVTEESIKEFFR-GLNISAVRLPREPSNPERLKGFGYAEFED-LDSLLSAL 74
Query: 219 MLNNQNLFERRITVR 233
LN ++L +RI V
Sbjct: 75 SLNEESLGNKRIRVD 89
Score = 41.9 bits (99), Expect = 5e-05
Identities = 8/65 (12%), Positives = 27/65 (41%), Gaps = 3/65 (4%)
Query: 58 VTYVEILND--DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
++ V + + + + +G EF+ D + A++ ++ +++ + A + +
Sbjct: 41 ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVADQAQDKDS 99
Query: 116 NMGGG 120
G
Sbjct: 100 GPSSG 104
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 60.9 bits (148), Expect = 7e-12
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 2/81 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDK-DGKSRGFGTVEFDHPVEAVQSIS 218
+ + V +K L +F AGKV N+E +D+ GK++GF VE +A + I
Sbjct: 13 GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
Query: 219 MLNNQNLFERRITVRMDRVAD 239
+ + + + + + + D
Sbjct: 73 SFHGKR-LDLKHRLFLYTMKD 92
Score = 41.3 bits (97), Expect = 7e-05
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 52 LSTVGDVTYVEI-LNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
S G V +E +++ TGK +G VE S + +K + H +
Sbjct: 33 FSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK 82
Score = 38.9 bits (91), Expect = 5e-04
Identities = 16/68 (23%), Positives = 23/68 (33%), Gaps = 8/68 (11%)
Query: 520 VVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMM 572
V+ + + + L F G + E K KG V S AK+ I
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKG-FLFVECGSMNDAKKIIKSF 74
Query: 573 DRTRIDGK 580
R+D K
Sbjct: 75 HGKRLDLK 82
>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 = 60.7 bits (148), Expect = 7e-12
Identities = 14/90 (15%), Positives = 39/90 (43%), Gaps = 11/90 (12%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLA----GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQ 215
+ +++ NL+ K+ + +L++ G++ ++I + + K RG V F A
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQI--LDILVSRSLKMRGQAFVIFKEVSSATN 66
Query: 216 SISMLNNQNLFERRITV-----RMDRVADR 240
++ + +++ + + D +A
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 96
Score = 41.4 bits (98), Expect = 5e-05
Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 7/76 (9%)
Query: 518 TVVVKNLPPTITWQELRDK----FRNCGDIKFAEIKGKGDI---GLVRFDSEWTAKRAID 570
T+ + NL I EL+ F G I + + V F +A A+
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALR 69
Query: 571 MMDRTRIDGKIIDVTF 586
M K + + +
Sbjct: 70 SMQGFPFYDKPMRIQY 85
Score = 41.4 bits (98), Expect = 6e-05
Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 2/55 (3%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
S G + + + + K RG A V F+ A+ M F + + I+ A
Sbjct: 34 SRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 86
>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 = 61.8 bits (150), Expect = 8e-12
Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
V++ L ++ + K + + F+ VE+ + IA +GK+ G G VEF + + ++
Sbjct: 26 FCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC 85
Query: 219 MLNNQNLFERRITV 232
+ Q + R I V
Sbjct: 86 R-HKQYMGNRFIQV 98
Score = 45.2 bits (107), Expect = 4e-06
Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 9/86 (10%)
Query: 506 RSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVR 558
RS ++S + V +K LP + + D F+ ++ + K G+ G V
Sbjct: 15 RSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGE-GFVE 73
Query: 559 FDSEWTAKRAIDMMDRTRIDGKIIDV 584
F +E K A+ + + + I V
Sbjct: 74 FRNEADYKAALC-RHKQYMGNRFIQV 98
Score = 40.2 bits (94), Expect = 2e-04
Identities = 14/66 (21%), Positives = 23/66 (34%), Gaps = 6/66 (9%)
Query: 61 VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI-----KEAVEDKGGRR 115
+ I GK G VEF++ + A+ H+ R + + K +E R
Sbjct: 56 IYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKGMLEKIDMIR 114
Query: 116 NMGGGG 121
G
Sbjct: 115 KRLQSG 120
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 60.5 bits (147), Expect = 1e-11
Identities = 17/86 (19%), Positives = 40/86 (46%), Gaps = 8/86 (9%)
Query: 160 NKVFVANL------DYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEA 213
+ + V N+ + + + ++F GK+ N + DGK++G+ +E+ P A
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHA 74
Query: 214 VQSISMLNNQNLFERRITVRMDRVAD 239
V ++ + +++ T R++ D
Sbjct: 75 VDAVKNADGYK-LDKQHTFRVNLFTD 99
Score = 42.8 bits (101), Expect = 2e-05
Identities = 17/82 (20%), Positives = 27/82 (32%), Gaps = 13/82 (15%)
Query: 518 TVVVKNLPPTITWQE------LRDKFRNCGDIKFAEI-----KGKGDIGLVRFDSEWTAK 566
+VV N+P + + F G I K KG + + S A
Sbjct: 17 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKG-YIFLEYASPAHAV 75
Query: 567 RAIDMMDRTRIDGK-IIDVTFF 587
A+ D ++D + V F
Sbjct: 76 DAVKNADGYKLDKQHTFRVNLF 97
Score = 40.5 bits (95), Expect = 1e-04
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 52 LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
S G +T ++ GK +G +E+ SP AV ++ +
Sbjct: 42 FSKFGKITNDFY-PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 89
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 60.5 bits (147), Expect = 1e-11
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 2/71 (2%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
V V + + E +R+ F +V+ V + D G++ G G V+F P + +++ N
Sbjct: 19 VSVHGMPFSAMENDVRDFFH-GLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKR-N 76
Query: 222 NQNLFERRITV 232
+ +R + V
Sbjct: 77 RMLMIQRYVEV 87
Score = 46.3 bits (110), Expect = 1e-06
Identities = 17/90 (18%), Positives = 34/90 (37%), Gaps = 7/90 (7%)
Query: 501 GLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCG--DIKF---AEIKGKGDIG 555
G + N + V V +P + ++RD F + + G+ G
Sbjct: 1 GSSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGN-G 59
Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKIIDVT 585
LV+F S A+ +R + + ++V+
Sbjct: 60 LVKFLSPQDTFEALK-RNRMLMIQRYVEVS 88
Score = 44.0 bits (104), Expect = 8e-06
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 57 DVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK----G 112
V V +L D G+ G+ +V+F SP +A+ K +R R + + A E + G
Sbjct: 41 RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATERQWVAAG 99
Query: 113 GRRNMGGGGG 122
G G G
Sbjct: 100 GHITSGPSSG 109
>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 = 60.1 bits (146), Expect = 2e-11
Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 2/79 (2%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
V + L Y+ E + F V I + DG+ G VEF +AV +++ +
Sbjct: 18 VHMRGLPYRATENDIYNFFS-PLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAK-D 75
Query: 222 NQNLFERRITVRMDRVADR 240
N+ R + + ++ A
Sbjct: 76 KANMQHRYVELFLNSTAGT 94
Score = 42.4 bits (100), Expect = 3e-05
Identities = 13/86 (15%), Positives = 31/86 (36%), Gaps = 7/86 (8%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGD-----IKFAEIKGKGDIGLVR 558
S S + + V ++ LP T ++ + F + + G+ V
Sbjct: 3 SGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGE-ADVE 61
Query: 559 FDSEWTAKRAIDMMDRTRIDGKIIDV 584
F + A A+ D+ + + +++
Sbjct: 62 FATHEDAVAAMA-KDKANMQHRYVEL 86
Score = 38.1 bits (89), Expect = 8e-04
Identities = 13/62 (20%), Positives = 22/62 (35%), Gaps = 3/62 (4%)
Query: 61 VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGG 120
V I G+ G A VEF + + A+ + + R ++ + G G
Sbjct: 44 VHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANMQHRY--VELFLNSTAGTSGSGPS 100
Query: 121 GG 122
G
Sbjct: 101 SG 102
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 59.4 bits (144), Expect = 2e-11
Identities = 15/87 (17%), Positives = 38/87 (43%), Gaps = 3/87 (3%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI---KGKGDIGLVRFD 560
S S + + ++N+PP + W+ L G ++ E + + V +
Sbjct: 3 SGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYS 62
Query: 561 SEWTAKRAIDMMDRTRIDGKIIDVTFF 587
S+ A++A+D ++ +++ + V +
Sbjct: 63 SKDQARQALDKLNGFQLENFTLKVAYI 89
Score = 57.5 bits (139), Expect = 1e-10
Identities = 14/73 (19%), Positives = 26/73 (35%), Gaps = 2/73 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
K+ + N+ + + L + G VE+ E V + +A Q++
Sbjct: 16 RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV--NTDSETAVVNVTYSSKDQARQALDK 73
Query: 220 LNNQNLFERRITV 232
LN L + V
Sbjct: 74 LNGFQLENFTLKV 86
Score = 40.5 bits (95), Expect = 1e-04
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI 104
G V E +N D V + S D R+A++K++ F+ + L +
Sbjct: 37 VQYGVVESCEQVNTD--SETAVVNVTYSSKDQARQALDKLNGFQLENFTLKV 86
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kg0_A
Length = 126
Score = 59.9 bits (145), Expect = 3e-11
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 2/74 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
V + L + ++++ + F V N + + +D +GK G V+F A +++
Sbjct: 43 GFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG 102
Query: 219 MLNNQNLFERRITV 232
+ + + R I V
Sbjct: 103 K-HKERIGHRYIEV 115
Score = 39.5 bits (92), Expect = 5e-04
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 49 ISHLSTVGDVTY-VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
+ S + V + + D GK G A V+F S +L KA+ H+ R + + ++
Sbjct: 60 VQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL-GKHKERIGHRYIEVFKS 118
>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 = 65.6 bits (159), Expect = 3e-11
Identities = 57/378 (15%), Positives = 117/378 (30%), Gaps = 97/378 (25%)
Query: 16 HQDFPM------FQRIETGAPLEVPVVMDLIQGDASLYQISHL--STVGDVTYVEIL--- 64
H DF ++ I + V D + + + S + I+
Sbjct: 6 HMDFETGEHQYQYKDI-------LSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSK 58
Query: 65 NDDTGKPRGSAIVEFQSPDLVRKAVNKMH-----------RFETKGRKLVIKEAVEDKGG 113
+ +G R + + ++V+K V ++ + E + ++ + +E
Sbjct: 59 DAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQ--- 115
Query: 114 RRNMGGGG------GVDR-----DL-SALLQNNSSKFGNTYG--------LSPQFLESLG 153
R + V R L ALL+ +K G ++ S
Sbjct: 116 RDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYK 175
Query: 154 INCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEA 213
+ C + K+F NL + + E ++ + +D + SR + + +
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLE------MLQKLLYQIDPNWTSRSDHSSNIKLRIHS 229
Query: 214 VQS-ISMLNNQNLFER---------------------RI--TVRMDRVADRLDGPVRLPE 249
+Q+ + L +E +I T R +V D L
Sbjct: 230 IQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHI 289
Query: 250 GLKSIGMGLGANGAPLQDVANWLLQEKVQKLS--------LIIS--NRNTKEVLERWDF- 298
L M L + + + L + Q L +S + ++ L WD
Sbjct: 290 SLDHHSMTLTPDEV-KSLLLKY-LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNW 347
Query: 299 -KLQYDKSSDENDAASVN 315
+ DK + + +S+N
Sbjct: 348 KHVNCDKLTTIIE-SSLN 364
>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 = 59.2 bits (144), Expect = 3e-11
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+FV NL V E+ L + F GK+E V+ + + + FD AV+++
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKK-------LKDYAFIHFDERDGAVKAMEE 64
Query: 220 LNNQNLFERRITV 232
+N ++L I +
Sbjct: 65 MNGKDLEGENIEI 77
Score = 55.4 bits (134), Expect = 6e-10
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 509 NQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKR 567
+ SS + + V+ V+NL T+T + L F G ++ +K D + FD A +
Sbjct: 3 SGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLE--RVKKLKDYAFIHFDERDGAVK 60
Query: 568 AIDMMDRTRIDGKIIDVTF 586
A++ M+ ++G+ I++ F
Sbjct: 61 AMEEMNGKDLEGENIEIVF 79
Score = 33.4 bits (77), Expect = 0.033
Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 7/52 (13%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
G + V+ + A + F D KA+ +M+ + +G + I A
Sbjct: 36 GKLERVKK-------LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA 80
>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 = 58.5 bits (142), Expect = 5e-11
Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 2/76 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAG-KVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+++ +L+ +DE + F G V +V+I ++ G G+ VEF A + +
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70
Query: 219 MLNNQNLFERRITVRM 234
+N + L R
Sbjct: 71 KINGKPLPGATPAKRF 86
Score = 36.5 bits (85), Expect = 0.003
Identities = 13/86 (15%), Positives = 29/86 (33%), Gaps = 9/86 (10%)
Query: 509 NQSSNIERDTVVVKNLPPTITWQELRDKFRNCG-DIKFAEI-------KGKGDIGLVRFD 560
+ S+ ++ + +L P + + F G + +I G V F
Sbjct: 2 SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAG-YCFVEFA 60
Query: 561 SEWTAKRAIDMMDRTRIDGKIIDVTF 586
TA++ + ++ + G F
Sbjct: 61 DLATAEKCLHKINGKPLPGATPAKRF 86
Score = 30.0 bits (68), Expect = 0.59
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 43 DASLYQISHLSTVG-DVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMH 93
+ + + +T+G V V+I+ + TG P G VEF K ++K++
Sbjct: 23 ENFISRA--FATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKIN 73
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 58.1 bits (141), Expect = 6e-11
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 5/90 (5%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
VFV+ VD +L E F G V +V + DKD F VE A +++
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVM--DKD--KGVFAIVEMGDV-GAREAVLSQ 64
Query: 221 NNQNLFERRITVRMDRVADRLDGPVRLPEG 250
+ +L R+ VR + + P+G
Sbjct: 65 SQHSLGGHRLRVRPREQKEFQSPASKSPKG 94
Score = 50.0 bits (120), Expect = 5e-08
Identities = 12/68 (17%), Positives = 24/68 (35%), Gaps = 2/68 (2%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
+V V P + +L + F G + + K KG +V + + +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLS-QSQHS 68
Query: 577 IDGKIIDV 584
+ G + V
Sbjct: 69 LGGHRLRV 76
Score = 33.1 bits (76), Expect = 0.040
Identities = 14/71 (19%), Positives = 25/71 (35%), Gaps = 8/71 (11%)
Query: 51 HLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKM-HRFETKGRKLVIKEAVE 109
+ G V V +++ D G AIVE +++ H G +L ++ E
Sbjct: 28 YFLAFGPVASV-VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSL--GGHRLRVRPR-E 80
Query: 110 DKGGRRNMGGG 120
K +
Sbjct: 81 QKEFQSPASKS 91
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 58.1 bits (141), Expect = 8e-11
Identities = 12/71 (16%), Positives = 27/71 (38%), Gaps = 5/71 (7%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
++ N+ + E L +F+ G + + + +G +++D +A I L
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKH-----YPEKGCCFIKYDTHEQAAVCIVALA 84
Query: 222 NQNLFERRITV 232
N R +
Sbjct: 85 NFPFQGRNLRT 95
Score = 56.9 bits (138), Expect = 2e-10
Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 2/87 (2%)
Query: 497 NPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIG 555
P+ + + +S+ T + N+P T +L F+N G I + KG
Sbjct: 8 PPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKG-CC 66
Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKII 582
+++D+ A I + G+ +
Sbjct: 67 FIKYDTHEQAAVCIVALANFPFQGRNL 93
Score = 31.1 bits (71), Expect = 0.21
Identities = 7/54 (12%), Positives = 18/54 (33%), Gaps = 5/54 (9%)
Query: 49 ISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
I G + + +G +++ + + + + F +GR L
Sbjct: 45 IPLFQNFGFILDFKH-----YPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNL 93
>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 = 58.1 bits (141), Expect = 1e-10
Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 2/74 (2%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
K+FV L Y + LR+ F G +E + D+ GKSRG+G V A +
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR-AAAERAC 76
Query: 219 MLNNQNLFERRITV 232
N + R+ V
Sbjct: 77 KDPNPIIDGRKANV 90
Score = 43.1 bits (102), Expect = 2e-05
Identities = 17/82 (20%), Positives = 25/82 (30%), Gaps = 4/82 (4%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKM-HRFETKGRKLVIKEA 107
+ GD+ ++ D TGK RG V +A + GRK + A
Sbjct: 36 KYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIID--GRKANVNLA 93
Query: 108 VEDKGGRRNMGGGGGVDRDLSA 129
R G S+
Sbjct: 94 YLGAKPRSLQTGFAIGVSGPSS 115
Score = 38.0 bits (89), Expect = 0.001
Identities = 26/92 (28%), Positives = 36/92 (39%), Gaps = 10/92 (10%)
Query: 501 GLDSNRSMNQSSNIERDT-VVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKG 552
G + M+ S T + V LP T LR F GDI+ A + K +G
Sbjct: 1 GSSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60
Query: 553 DIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
G V A+RA + IDG+ +V
Sbjct: 61 -YGFVTMADRAAAERACKDPNPI-IDGRKANV 90
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 57.3 bits (138), Expect = 1e-10
Identities = 19/80 (23%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 161 KVFVANLDYKVDEKKLRE----VFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQS 216
V V+N+DY++ K+L++ F GKV++VE++ D + V+ ++ +A+ +
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGA 68
Query: 217 ISMLNNQNLFERRITVRMDR 236
++ L+ + ++I V +
Sbjct: 69 VNSLHRYKIGSKKILVSLAT 88
Score = 27.7 bits (61), Expect = 3.3
Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 52 LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
+ G V VE+ + + A+V+ ++ AVN +HR++ +K+++ A
Sbjct: 34 FARHGKVKSVELSPHTDYQLK--AVVQMENLQDAIGAVNSLHRYKIGSKKILVSLA 87
>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 = 61.0 bits (147), Expect = 2e-10
Identities = 13/77 (16%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 160 NKVFVANLDYKVDEKKLRE----VFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQ 215
+ +++ NL+ K+ + +L++ +F G++ ++I + + K RG V F A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLKMRGQAFVIFKEVSSATN 67
Query: 216 SISMLNNQNLFERRITV 232
++ + +++ + +
Sbjct: 68 ALRSMQGFPFYDKPMRI 84
Score = 53.0 bits (126), Expect = 8e-08
Identities = 27/157 (17%), Positives = 43/157 (27%), Gaps = 2/157 (1%)
Query: 432 SQGMQSQTSSLSSGNNVYSNQSAPSTDYSRNASNMYGNSRYGSGGNEMDYGGGSGQASIQ 491
+ + P T R +M G Y + G +
Sbjct: 123 KAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPP 182
Query: 492 SGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIK-FAEIKG 550
+ S N + + NLP L F K + G
Sbjct: 183 GAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPG 242
Query: 551 KGDIGLVRFDSEWTAKRAIDMMDRTRI-DGKIIDVTF 586
+ DI V FD+E A A D + +I + ++F
Sbjct: 243 RHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF 279
Score = 46.0 bits (108), Expect = 2e-05
Identities = 17/77 (22%), Positives = 27/77 (35%), Gaps = 9/77 (11%)
Query: 518 TVVVKNLPPTITWQELR----DKFRNCGDIKFAEI----KGKGDIGLVRFDSEWTAKRAI 569
T+ + NL I EL+ F G I + K +G V F +A A+
Sbjct: 11 TIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRG-QAFVIFKEVSSATNAL 69
Query: 570 DMMDRTRIDGKIIDVTF 586
M K + + +
Sbjct: 70 RSMQGFPFYDKPMRIQY 86
Score = 42.2 bits (98), Expect = 3e-04
Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 4/67 (5%)
Query: 163 FVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
F+ NL + +E L +F + V + + VEFD+ V+A + L
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAARDALQG 266
Query: 223 QNLFERR 229
+ +
Sbjct: 267 FKITQNN 273
Score = 40.2 bits (93), Expect = 0.001
Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 2/67 (2%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKG 112
S G + +IL + K RG A V F+ A+ M F + + I+ A D
Sbjct: 35 SQFGQIL--DILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSD 92
Query: 113 GRRNMGG 119
M G
Sbjct: 93 IIAKMKG 99
Score = 28.3 bits (62), Expect = 7.8
Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 1/39 (2%)
Query: 70 KPRGSAIVEFQSPDLVRKAVNKMHRFE-TKGRKLVIKEA 107
A VEF + A + + F+ T+ + I A
Sbjct: 242 GRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFA 280
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 56.2 bits (136), Expect = 2e-10
Identities = 15/77 (19%), Positives = 35/77 (45%), Gaps = 7/77 (9%)
Query: 160 NKVFVANL------DYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEA 213
+ + V N+ + + + ++F GK+ N + DGK++G+ +E+ P A
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHA 60
Query: 214 VQSISMLNNQNLFERRI 230
V ++ + L ++
Sbjct: 61 VDAVKNADGYKLDKQHT 77
Score = 41.2 bits (97), Expect = 5e-05
Identities = 15/74 (20%), Positives = 24/74 (32%), Gaps = 12/74 (16%)
Query: 518 TVVVKNLP------PTITWQELRDKFRNCGDIKFAEI-----KGKGDIGLVRFDSEWTAK 566
+VV N+P + F G I K KG + + S A
Sbjct: 3 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKG-YIFLEYASPAHAV 61
Query: 567 RAIDMMDRTRIDGK 580
A+ D ++D +
Sbjct: 62 DAVKNADGYKLDKQ 75
Score = 39.3 bits (92), Expect = 2e-04
Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 52 LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFE 96
S G +T ++ GK +G +E+ SP AV ++
Sbjct: 28 FSKFGKITNDFY-PEEDGKTKGYIFLEYASPAHAVDAVKNADGYK 71
>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 = 61.8 bits (149), Expect = 2e-10
Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSIS 218
+FVA ++Y E KLR F + G ++ + + K GK RG+ +E++H + +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 219 MLNNQNLFERRITVRMDR 236
+ + + RR+ V ++R
Sbjct: 163 HADGKKIDGRRVLVDVER 180
Score = 39.8 bits (92), Expect = 0.002
Identities = 18/76 (23%), Positives = 30/76 (39%), Gaps = 8/76 (10%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAID 570
T+ V + T +LR +F G IK + K +G + ++ E A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRG-YAFIEYEHERDMHSAYK 162
Query: 571 MMDRTRIDGKIIDVTF 586
D +IDG+ + V
Sbjct: 163 HADGKKIDGRRVLVDV 178
Score = 36.4 bits (83), Expect = 0.028
Identities = 11/61 (18%), Positives = 25/61 (40%), Gaps = 1/61 (1%)
Query: 51 HLSTVGDVTYVEILNDD-TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
G + + ++ +GKPRG A +E++ + A + GR++++
Sbjct: 122 EFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERG 181
Query: 110 D 110
Sbjct: 182 R 182
>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 = 56.6 bits (137), Expect = 3e-10
Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 8/82 (9%)
Query: 160 NKVFVANLDY-KVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
+++F+ NL V ++ L +F G + + I FG ++FD+P +I
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIE 75
Query: 219 MLNNQNLFERRITVRMDRVADR 240
+ + F +++ + + R
Sbjct: 76 XESQEMNFGKKLILEVSSSNAR 97
Score = 48.9 bits (117), Expect = 1e-07
Identities = 21/104 (20%), Positives = 37/104 (35%), Gaps = 15/104 (14%)
Query: 484 GSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLP-PTITWQELRDKFRNCGD 542
GS PR +R + + NLP ++ ++L F G
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMKSR------------LFIGNLPLKNVSKEDLFRIFSPYGH 49
Query: 543 IKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
I IK G ++FD+ + + AI+ + GK + +
Sbjct: 50 IMQINIK-NA-FGFIQFDNPQSVRDAIEXESQEMNFGKKLILEV 91
Score = 33.8 bits (78), Expect = 0.026
Identities = 11/60 (18%), Positives = 23/60 (38%), Gaps = 10/60 (16%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
G + + I ++F +P VR A+ + G+KL+++ + R
Sbjct: 48 GHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVS---SSNAR 97
>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 = 56.6 bits (137), Expect = 3e-10
Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 5/77 (6%)
Query: 157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQS 216
P V+ + + ++ +R+ F G++ + + +K G+ V F A +
Sbjct: 23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-----GYSFVRFSTHESAAHA 77
Query: 217 ISMLNNQNLFERRITVR 233
I +N + +
Sbjct: 78 IVSVNGTTIEGHVVKCY 94
Score = 55.8 bits (135), Expect = 5e-10
Identities = 24/96 (25%), Positives = 40/96 (41%), Gaps = 4/96 (4%)
Query: 492 SGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KG 550
SG GN + + S+ + TV + +T Q +R F G I +
Sbjct: 3 SGSSGNTKQL--RFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60
Query: 551 KGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
KG VRF + +A AI ++ T I+G ++ +
Sbjct: 61 KG-YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW 95
Score = 33.5 bits (77), Expect = 0.046
Identities = 11/78 (14%), Positives = 25/78 (32%), Gaps = 7/78 (8%)
Query: 43 DASLYQISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
D + Q S G + + + + +G + V F + + A+ ++ +G +
Sbjct: 39 DQLMRQ--TFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91
Query: 103 VIKEAVEDKGGRRNMGGG 120
E G
Sbjct: 92 KCYWGKESPDMTSGPSSG 109
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 56.1 bits (136), Expect = 3e-10
Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 8/87 (9%)
Query: 155 NCPLINKVFVANLDYK-VDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEA 213
N P +++F+ NL K V ++ L +F G + + I FG ++FD+P
Sbjct: 6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSV 58
Query: 214 VQSISMLNNQNLFERRITVRMDRVADR 240
+I + + F +++ + + R
Sbjct: 59 RDAIECESQEMNFGKKLILEVSSSNAR 85
Score = 43.7 bits (104), Expect = 7e-06
Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 521 VKNLPP-TITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDG 579
+ NLP ++ ++L F G I IK G ++FD+ + + AI+ + G
Sbjct: 15 IGNLPLKNVSKEDLFRIFSPYGHIMQINIK-NA-FGFIQFDNPQSVRDAIECESQEMNFG 72
Query: 580 KIIDVTF 586
K + +
Sbjct: 73 KKLILEV 79
Score = 41.0 bits (97), Expect = 6e-05
Identities = 12/66 (18%), Positives = 27/66 (40%), Gaps = 7/66 (10%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
G + + I ++F +P VR A+ + G+KL+++ + + +
Sbjct: 36 GHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNARPQF 88
Query: 116 NMGGGG 121
+ G G
Sbjct: 89 DHGDHG 94
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 56.5 bits (136), Expect = 4e-10
Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 10/88 (11%)
Query: 162 VFVANLDYKVDEKKLREVFR---LAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
V + L + + ++ + V V ++G+ G VE + + V+
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESE-DDVKLAL 78
Query: 219 MLNNQNLFERRITVR------MDRVADR 240
+ +++ R I V MD V
Sbjct: 79 KKDRESMGHRYIEVFKSHRTEMDWVLKH 106
Score = 38.0 bits (88), Expect = 0.001
Identities = 17/75 (22%), Positives = 27/75 (36%), Gaps = 8/75 (10%)
Query: 52 LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVI------- 104
+ V V + G+ G A VE +S D V+ A+ K R R + +
Sbjct: 41 CTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKK-DRESMGHRYIEVFKSHRTE 99
Query: 105 KEAVEDKGGRRNMGG 119
+ V G + G
Sbjct: 100 MDWVLKHSGPNSASG 114
>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 = 55.8 bits (135), Expect = 4e-10
Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 7/73 (9%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
N ++V D + LR F G + ++ + R V ++ A Q+++
Sbjct: 16 NTLYVYGED--MTPTLLRGAFSPFGNIIDLSM-----DPPRNCAFVTYEKMESADQAVAE 68
Query: 220 LNNQNLFERRITV 232
LN + ++ V
Sbjct: 69 LNGTQVESVQLKV 81
Score = 46.1 bits (110), Expect = 1e-06
Identities = 14/85 (16%), Positives = 33/85 (38%), Gaps = 5/85 (5%)
Query: 504 SNRSMNQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDS 561
S+ S + + + V +T LR F G+I + + V ++
Sbjct: 2 SSGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRN-CAFVTYEK 58
Query: 562 EWTAKRAIDMMDRTRIDGKIIDVTF 586
+A +A+ ++ T+++ + V
Sbjct: 59 MESADQAVAELNGTQVESVQLKVNI 83
Score = 33.4 bits (77), Expect = 0.034
Identities = 10/66 (15%), Positives = 27/66 (40%), Gaps = 6/66 (9%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
G++ + + PR A V ++ + +AV +++ + + +L + A +
Sbjct: 38 GNIIDLSM-----DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA-RKQPMLD 91
Query: 116 NMGGGG 121
+ G
Sbjct: 92 SGPSSG 97
>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 = 55.8 bits (135), Expect = 5e-10
Identities = 17/102 (16%), Positives = 42/102 (41%), Gaps = 8/102 (7%)
Query: 134 NSSKFGNTYGLSPQFLESLGINCPLINKVFVANLDY-KVDEKKLREVFRLAGKVENVEIA 192
+S G + L + + + ++VF+ NL+ V + + +F G+V +
Sbjct: 2 SSGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV- 60
Query: 193 LDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRM 234
+G+ V++ + A ++ N + L + + + M
Sbjct: 61 ------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM 96
Score = 45.8 bits (109), Expect = 2e-06
Identities = 18/96 (18%), Positives = 35/96 (36%), Gaps = 3/96 (3%)
Query: 492 SGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPP-TITWQELRDKFRNCGDIKFAEIKG 550
SG G SN + V + NL + ++ F G + +
Sbjct: 3 SGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH- 61
Query: 551 KGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
KG V++ +E A+ A+ + + G+ +D+
Sbjct: 62 KG-YAFVQYSNERHARAAVLGENGRVLAGQTLDINM 96
Score = 37.0 bits (86), Expect = 0.002
Identities = 16/65 (24%), Positives = 23/65 (35%), Gaps = 7/65 (10%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRR 115
G V + +G A V++ + R AV + G+ L I A E K R
Sbjct: 53 GRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRS 105
Query: 116 NMGGG 120
G
Sbjct: 106 GPSSG 110
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 56.4 bits (136), Expect = 6e-10
Identities = 16/89 (17%), Positives = 32/89 (35%), Gaps = 11/89 (12%)
Query: 162 VFVANLDYKVDEKKLREVF----RLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSI 217
V + L + +++ F + G E + DG+ G V F A ++
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 218 SMLNNQNLFERRITVR------MDRVADR 240
+ L +R I + + +V +R
Sbjct: 86 RK-HKDLLGKRYIELFRSTAAEVQQVLNR 113
Score = 37.2 bits (86), Expect = 0.003
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 55 VGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
G + + G+P G A V F + + A+ K H+ R
Sbjct: 51 TGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKR 95
>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 = 55.5 bits (134), Expect = 7e-10
Identities = 14/72 (19%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVEN-VEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
V + L + ++++ + F V N + + +D G+S G V+F A +++
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK- 76
Query: 221 NNQNLFERRITV 232
+ + + R I +
Sbjct: 77 HKERIGHRYIEI 88
Score = 46.7 bits (111), Expect = 1e-06
Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 8/88 (9%)
Query: 504 SNRSMNQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGD------IKFAEIKGKGDIGL 556
S+ S S + D V ++ LP + +E+ F +
Sbjct: 2 SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61
Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
V+F S+ A++A+ + RI + I++
Sbjct: 62 VQFASQEIAEKALK-KHKERIGHRYIEI 88
Score = 38.2 bits (89), Expect = 7e-04
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 61 VEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
+ + D G+ G A V+F S ++ KA+ K H+ R + I ++
Sbjct: 46 MTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIGHRYIEIFKS 91
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 56.5 bits (136), Expect = 7e-10
Identities = 16/93 (17%), Positives = 31/93 (33%), Gaps = 11/93 (11%)
Query: 161 KVFVANLDYKVDEKKLREVFR---LAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSI 217
V + L + + ++ + V ++G+ G VE + V+
Sbjct: 46 VVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSE-DDVKMA 104
Query: 218 SMLNNQNLFERRITVR------MDRVADRLDGP 244
+ +++ R I V MD V GP
Sbjct: 105 LKKDRESMGHRYIEVFKSHRTEMDWVLKH-SGP 136
Score = 41.5 bits (97), Expect = 1e-04
Identities = 20/112 (17%), Positives = 38/112 (33%), Gaps = 14/112 (12%)
Query: 485 SGQASIQSGGYGNPRAGLDS---NRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCG 541
+ G + G M E V ++ LP + + +++++ +C
Sbjct: 10 HSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCT 69
Query: 542 D---------IKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
I E + G+ V SE K A+ DR + + I+V
Sbjct: 70 IHDGAAGVHFIYTREGRQSGE-AFVELGSEDDVKMALK-KDRESMGHRYIEV 119
Score = 38.1 bits (88), Expect = 0.002
Identities = 13/50 (26%), Positives = 18/50 (36%), Gaps = 1/50 (2%)
Query: 52 LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
+ V + G+ G A VE S D V+ A+ K R R
Sbjct: 68 CTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKK-DRESMGHRY 116
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 55.2 bits (133), Expect = 9e-10
Identities = 16/89 (17%), Positives = 33/89 (37%), Gaps = 10/89 (11%)
Query: 162 VFVANLDYKVDEKKLREVF---RLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS 218
+ L + + + F R+ + L++DGK RG +E + + VQ
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESE-QDVQKAL 72
Query: 219 MLNNQNLFERRITV------RMDRVADRL 241
+ + +R + V +D + L
Sbjct: 73 EKHRMYMGQRYVEVYEINNEDVDALMKSL 101
Score = 37.1 bits (86), Expect = 0.002
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 52 LSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGR 100
+ L + GK RG A++E +S V+KA+ K HR R
Sbjct: 35 CRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEK-HRMYMGQR 82
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 54.8 bits (132), Expect = 9e-10
Identities = 18/82 (21%), Positives = 26/82 (31%), Gaps = 4/82 (4%)
Query: 155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAV 214
PL V+V NL L+ R G V R + + A
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTW----QGPRRRAFLHYPDSAAAQ 70
Query: 215 QSISMLNNQNLFERRITVRMDR 236
Q++S L L + V + R
Sbjct: 71 QAVSCLQGLRLGTDTLRVALAR 92
Score = 49.1 bits (117), Expect = 9e-08
Identities = 13/70 (18%), Positives = 25/70 (35%), Gaps = 1/70 (1%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRTR 576
V V NLP +L+ R G + +G + + A++A+ + R
Sbjct: 21 DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLR 80
Query: 577 IDGKIIDVTF 586
+ + V
Sbjct: 81 LGTDTLRVAL 90
Score = 34.0 bits (78), Expect = 0.023
Identities = 7/38 (18%), Positives = 14/38 (36%)
Query: 70 KPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
PR A + + ++AV+ + L + A
Sbjct: 54 GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA 91
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 54.9 bits (133), Expect = 1e-09
Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHP--VEAVQS 216
+ V L +K E+ L+E F G+V V++ D G S+GFG V F V S
Sbjct: 17 DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75
Score = 47.6 bits (114), Expect = 4e-07
Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 3/72 (4%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
+ ST G+V V++ D TG +G V F + K +++ H + GR K
Sbjct: 34 EYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMID--GRWCDCKLPN 91
Query: 109 EDKGGRRNMGGG 120
+ G
Sbjct: 92 SKQSQDSGPSSG 103
Score = 39.9 bits (94), Expect = 2e-04
Identities = 23/89 (25%), Positives = 39/89 (43%), Gaps = 11/89 (12%)
Query: 504 SNRSMNQSSNIERDT-VVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIG 555
S+ S +++ + ++V LP T Q+L++ F G++ ++ KG G
Sbjct: 2 SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG-FG 60
Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
VRF T + M R IDG+ D
Sbjct: 61 FVRFTEYETQVKV--MSQRHMIDGRWCDC 87
>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 = 55.1 bits (133), Expect = 1e-09
Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 7/73 (9%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
N ++V D + LR F G + ++ + R V ++ A Q+++
Sbjct: 40 NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAE 92
Query: 220 LNNQNLFERRITV 232
LN + ++ V
Sbjct: 93 LNGTQVESVQLKV 105
Score = 45.9 bits (109), Expect = 2e-06
Identities = 21/110 (19%), Positives = 38/110 (34%), Gaps = 10/110 (9%)
Query: 483 GGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERD-----TVVVKNLPPTITWQELRDKF 537
G S S G PR + S R T+ V +T LR F
Sbjct: 2 GSSHHHHHHSSGL-VPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAF 58
Query: 538 RNCGDIKFAEI-KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
G+I + + V ++ +A +A+ ++ T+++ + V
Sbjct: 59 SPFGNIIDLSMDPPRN-CAFVTYEKMESADQAVAELNGTQVESVQLKVNI 107
Score = 31.6 bits (72), Expect = 0.23
Identities = 8/47 (17%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
G++ + + PR A V ++ + +AV +++ + + +L
Sbjct: 62 GNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVESVQL 103
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 54.6 bits (132), Expect = 2e-09
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 162 VFVANLDYKVDEKKLREVFRLA-GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISML 220
+FV +L VD+ L E F ++ LD+ G S+G+G V+F +E ++++
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTEC 71
Query: 221 NNQ-NLFERRITVRM 234
L + + + +
Sbjct: 72 QGAVGLGSKPVRLSV 86
Score = 37.6 bits (88), Expect = 0.001
Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 9/72 (12%)
Query: 521 VKNLPPTITWQELRDKFRNC-GDIKFAEI------KGKGDIGLVRFDSEWTAKRAIDMMD 573
V +L P + L + F + ++ KG G V+F E KRA+
Sbjct: 14 VGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKG-YGFVKFTDELEQKRALTECQ 72
Query: 574 -RTRIDGKIIDV 584
+ K + +
Sbjct: 73 GAVGLGSKPVRL 84
Score = 31.1 bits (71), Expect = 0.22
Identities = 10/70 (14%), Positives = 24/70 (34%), Gaps = 3/70 (4%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH-RFETKGRKLVIKEAV--EDKG 112
+++ D TG +G V+F ++A+ + + + + A+ +
Sbjct: 35 PSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRV 94
Query: 113 GRRNMGGGGG 122
G G
Sbjct: 95 KPVESGPSSG 104
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 53.3 bits (129), Expect = 2e-09
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
K+F+ L ++ ++ LRE F G+V+ + D +SRGFG V F V +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ-AGVDKVLA 60
Query: 220 LNNQNLFERRITVR 233
+ L + I +
Sbjct: 61 QSRHELDSKTIDPK 74
Score = 36.3 bits (85), Expect = 0.002
Identities = 14/59 (23%), Positives = 22/59 (37%), Gaps = 2/59 (3%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
+ G+V ++ D T + RG V F V K + R E + + K A
Sbjct: 19 EYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA 76
Score = 32.1 bits (74), Expect = 0.063
Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 9/71 (12%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIGLVRFDSEWTAKRAIDMMD 573
+ L T + LR+ F G++K + + +G G V F + + +
Sbjct: 5 IGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG-FGFVTFMDQAGVDKVLAQSR 63
Query: 574 RTRIDGKIIDV 584
+D K ID
Sbjct: 64 HE-LDSKTIDP 73
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 54.5 bits (131), Expect = 2e-09
Identities = 11/77 (14%), Positives = 28/77 (36%), Gaps = 6/77 (7%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLA----GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQ 215
V + N++ +V ++KL+ + G + ++I +D + G + F A
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDI--LDIVVDLSDDNSGKAYIVFATQESAQA 87
Query: 216 SISMLNNQNLFERRITV 232
+ + +
Sbjct: 88 FVEAFQGYPFQGNPLVI 104
Score = 45.7 bits (108), Expect = 3e-06
Identities = 16/97 (16%), Positives = 36/97 (37%), Gaps = 8/97 (8%)
Query: 498 PRAGLDSNRSMNQSSNIE-RDTVVVKNLPPTITWQELR----DKFRNCG---DIKFAEIK 549
R +DS + + E V++ N+ P + ++L+ + G DI
Sbjct: 10 ERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSD 69
Query: 550 GKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
+ F ++ +A+ ++ G + +TF
Sbjct: 70 DNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF 106
Score = 39.1 bits (91), Expect = 6e-04
Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 53 STVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDK 111
S+ GD+ ++I+ D + G A + F + + + V + +G LVI + +
Sbjct: 55 SSQGDI--LDIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ 111
>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 = 53.4 bits (129), Expect = 2e-09
Identities = 16/70 (22%), Positives = 35/70 (50%), Gaps = 1/70 (1%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAI-DMMDRTR 576
T+ V L TIT +LR+ F G+I+ + + ++F + A+ A ++
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLI 73
Query: 577 IDGKIIDVTF 586
++G+ ++V +
Sbjct: 74 VNGRRLNVKW 83
Score = 48.4 bits (116), Expect = 1e-07
Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 6/78 (7%)
Query: 157 PLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQS 216
I ++V L + E LR F G++ + + + ++F A +
Sbjct: 10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ-----QCAFIQFATRQAAEVA 64
Query: 217 I-SMLNNQNLFERRITVR 233
N + RR+ V+
Sbjct: 65 AEKSFNKLIVNGRRLNVK 82
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 53.4 bits (129), Expect = 3e-09
Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 7/75 (9%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+++V L L F G + ++ K F ++++ A + +
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV-----KGDSFAYIQYESLDAAQAACAK 72
Query: 220 LNNQNLF--ERRITV 232
+ L +RR+ V
Sbjct: 73 MRGFPLGGPDRRLRV 87
Score = 47.2 bits (113), Expect = 5e-07
Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 8/88 (9%)
Query: 494 GYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEI-KGKG 552
G + ++ + + V L P + L +F G I+ + KG
Sbjct: 1 GSSGSSGKIGYGKANP--TT----RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS 54
Query: 553 DIGLVRFDSEWTAKRAIDMMDRTRIDGK 580
++++S A+ A M + G
Sbjct: 55 -FAYIQYESLDAAQAACAKMRGFPLGGP 81
Score = 31.8 bits (73), Expect = 0.14
Identities = 9/50 (18%), Positives = 20/50 (40%), Gaps = 5/50 (10%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIK 105
G + ++ + A ++++S D + A KM F G ++
Sbjct: 42 GSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR 86
>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 = 53.6 bits (129), Expect = 4e-09
Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 5/79 (6%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGK-VENVEIALDKD--GKSRGFGTVEFDHPVEAVQS 216
++F+ + +++ E + V +V + K+RGF VE++ A +
Sbjct: 9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68
Query: 217 ISMLNNQN--LFERRITVR 233
L L+ +I V
Sbjct: 69 RRKLMPGRIQLWGHQIAVD 87
Score = 48.3 bits (115), Expect = 3e-07
Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 10/86 (11%)
Query: 511 SSNIERDTVVVKNLPPTITWQELRDKFRNCGD-------IKFAEIKGKGD-IGLVRFDSE 562
S + + + +P +E+ ++ + A K K V ++S
Sbjct: 3 SGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESH 62
Query: 563 WTAKRAIDMM--DRTRIDGKIIDVTF 586
A A + R ++ G I V +
Sbjct: 63 RAAAMARRKLMPGRIQLWGHQIAVDW 88
Score = 37.5 bits (87), Expect = 0.002
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 5/62 (8%)
Query: 51 HLSTVGD-VTYVEILND--DTGKPRGSAIVEFQSPDLVRKAVNKMH--RFETKGRKLVIK 105
++ V + V V + D K RG A VE++S A K+ R + G ++ +
Sbjct: 28 EIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD 87
Query: 106 EA 107
A
Sbjct: 88 WA 89
>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 = 52.2 bits (126), Expect = 6e-09
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
K+FV L + +K L++ F G+V + I +D + G+SRGFG + F +V+ +
Sbjct: 13 KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA-ASVEKVLD 71
Query: 220 LNNQNLFERRITVR 233
L R I +
Sbjct: 72 QKEHRLDGRVIDPK 85
Score = 37.9 bits (89), Expect = 7e-04
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 2/59 (3%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEA 107
+ + G+V I D +TG+ RG + F+ V K +++ GR + K+A
Sbjct: 30 DYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEH-RLDGRVIDPKKA 87
Score = 36.4 bits (85), Expect = 0.003
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 8/84 (9%)
Query: 508 MNQSSNIERDT-VVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI------GLVRFD 560
+N S N E + V L + ++L+D F G++ IK + G + F
Sbjct: 2 INASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK 61
Query: 561 SEWTAKRAIDMMDRTRIDGKIIDV 584
+ ++ +D + +DG++ID
Sbjct: 62 DAASVEKVLDQKEHR-LDGRVIDP 84
>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 = 52.6 bits (126), Expect = 1e-08
Identities = 17/106 (16%), Positives = 36/106 (33%), Gaps = 6/106 (5%)
Query: 483 GGSGQASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGD 542
G S S G + + +RS S + ++ LP +T E+ G
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMGDSRSAGVPSR----VIHIRKLPIDVTEGEVISLGLPFGK 57
Query: 543 IKFAEIKGKGDIGLVRFDSEWTAKRAIDM--MDRTRIDGKIIDVTF 586
+ + + + ++E A ++ + G+ I + F
Sbjct: 58 VTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF 103
Score = 42.6 bits (100), Expect = 4e-05
Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 7/75 (9%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM-- 219
+ + L V E ++ + GKV N+ + K + +E + A ++
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLM-----LKGKNQAFIEMNTEEAANTMVNYYT 88
Query: 220 LNNQNLFERRITVRM 234
L + I ++
Sbjct: 89 SVTPVLRGQPIYIQF 103
Score = 27.2 bits (60), Expect = 6.9
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 7/58 (12%)
Query: 49 ISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVN--KMHRFETKGRKLVI 104
IS G VT + +L K + A +E + + VN +G+ + I
Sbjct: 49 ISLGLPFGKVTNLLML-----KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI 101
>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 = 52.2 bits (125), Expect = 1e-08
Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 7/80 (8%)
Query: 160 NKVFVANLDYKVDEK---KLREVFRLAGKVENVEIALDKDGK----SRGFGTVEFDHPVE 212
N VFV L ++ + K E F GK+ V I V + +
Sbjct: 16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75
Query: 213 AVQSISMLNNQNLFERRITV 232
A+++I +NN + R +
Sbjct: 76 ALRAIQCVNNVVVDGRTLKA 95
Score = 46.4 bits (110), Expect = 1e-06
Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 12/85 (14%)
Query: 514 IERDTVVVKNLPPTITWQEL---RDKFRNCGDIKFAEI---------KGKGDIGLVRFDS 561
++++ V V L + E+ + F G I I +G V +
Sbjct: 13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIR 72
Query: 562 EWTAKRAIDMMDRTRIDGKIIDVTF 586
A RAI ++ +DG+ + +
Sbjct: 73 SEDALRAIQCVNNVVVDGRTLKASL 97
Score = 35.6 bits (82), Expect = 0.009
Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 4/51 (7%)
Query: 56 GDVTYVEILNDDTGK----PRGSAIVEFQSPDLVRKAVNKMHRFETKGRKL 102
G + V I N + P SA V + + +A+ ++ GR L
Sbjct: 43 GKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL 93
>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 = 51.7 bits (124), Expect = 2e-08
Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 2/71 (2%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRT-- 575
V V+ L ++ +L + G I + + LV F++ +AK +
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPV 76
Query: 576 RIDGKIIDVTF 586
I G+ +
Sbjct: 77 YIAGQQAFFNY 87
Score = 40.6 bits (95), Expect = 1e-04
Identities = 13/74 (17%), Positives = 25/74 (33%), Gaps = 5/74 (6%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
V V L V E L E G + V + + VEF++ A + ++
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMM-----PFKRQALVEFENIDSAKECVTFAA 72
Query: 222 NQNLFERRITVRMD 235
+ ++ +
Sbjct: 73 DVPVYIAGQQAFFN 86
Score = 27.1 bits (60), Expect = 5.9
Identities = 11/58 (18%), Positives = 22/58 (37%), Gaps = 7/58 (12%)
Query: 49 ISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKM--HRFETKGRKLVI 104
+ L G + YV + + A+VEF++ D ++ V G++
Sbjct: 33 VEALEKFGTICYVMM-----MPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF 85
>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 = 51.9 bits (125), Expect = 2e-08
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 2/74 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
K+F+ L ++ E+ LR + GK+ + + D +SRGFG V F V +
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM-AEVDAAMA 87
Query: 220 LNNQNLFERRITVR 233
++ R + +
Sbjct: 88 ARPHSIDGRVVEPK 101
Score = 38.4 bits (90), Expect = 8e-04
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 8/75 (10%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVN-KMHRFETKGRKLVIKEA 107
++ G +T ++ D + + RG V F S V A+ + H + GR + K A
Sbjct: 46 NYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSID--GRVVEPKRA 103
Query: 108 VEDKGGRRNMGGGGG 122
V R G G
Sbjct: 104 VA----REESGSGPS 114
Score = 31.5 bits (72), Expect = 0.25
Identities = 15/102 (14%), Positives = 33/102 (32%), Gaps = 13/102 (12%)
Query: 494 GYGNPRAGLDSNRSMNQSSNIERDT----VVVKNLPPTITWQELRDKFRNCGDIKFAEI- 548
G + ++ + + L T + LR+ + G + +
Sbjct: 1 GSSGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVM 60
Query: 549 ------KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
+ +G G V F S A+ + IDG++++
Sbjct: 61 RDPASKRSRG-FGFVTFSSMAEVDAAMAARPHS-IDGRVVEP 100
>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 = 50.7 bits (122), Expect = 2e-08
Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 6/74 (8%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+ VFV + E +LRE F G V +V I R F V F + QS+
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP----KPFRAFAFVTFADD-QIAQSL-C 59
Query: 220 LNNQNLFERRITVR 233
+ + + +
Sbjct: 60 GEDLIIKGISVHIS 73
Score = 40.7 bits (96), Expect = 7e-05
Identities = 15/71 (21%), Positives = 19/71 (26%), Gaps = 6/71 (8%)
Query: 50 SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
S GDV V I R A V F + + + KG + I A
Sbjct: 24 EFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSLCGEDLII--KGISVHISNAEP 77
Query: 110 DKGGRRNMGGG 120
G
Sbjct: 78 KHNSNSGPSSG 88
Score = 38.4 bits (90), Expect = 5e-04
Identities = 14/66 (21%), Positives = 23/66 (34%), Gaps = 5/66 (7%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKG--KGDIGLVRFDSEWTAKRAIDMMDRTRID 578
V +T ELR+ F GD+ I + V F + A+ + I
Sbjct: 10 VGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRA-FAFVTFADDQIAQSL--CGEDLIIK 66
Query: 579 GKIIDV 584
G + +
Sbjct: 67 GISVHI 72
>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 = 50.7 bits (122), Expect = 4e-08
Identities = 25/73 (34%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
K+FV LD+ ++ LR F G+V + I DK +SRGFG V+F P V ++
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP-NCVGTVLA 76
Query: 220 LNNQNLFERRITV 232
L R I
Sbjct: 77 SRPHTLDGRNIDP 89
Score = 36.1 bits (84), Expect = 0.005
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 8/75 (10%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVN-KMHRFETKGRKLVIKEA 107
S+ S G+V I+ D T + RG V+F+ P+ V + + H + GR + K
Sbjct: 35 SYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLD--GRNIDPKPC 92
Query: 108 VEDKGGRRNMGGGGG 122
R G
Sbjct: 93 TP----RGMQPSGPS 103
Score = 33.4 bits (77), Expect = 0.044
Identities = 20/89 (22%), Positives = 33/89 (37%), Gaps = 10/89 (11%)
Query: 504 SNRSMNQSSNIERDT-VVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKGDIG 555
S S +S + + V L + T + LR F G++ I + +G G
Sbjct: 3 SGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRG-FG 61
Query: 556 LVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
V+F + T +DG+ ID
Sbjct: 62 FVKFKDPNCVGTVLASRPHT-LDGRNIDP 89
>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 = 50.1 bits (120), Expect = 4e-08
Identities = 10/79 (12%), Positives = 34/79 (43%), Gaps = 7/79 (8%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENV------EIALDKDGKSRGFGTVEFDHPVEAV 214
+++V N+ + + E+ + + F ++ + + + + + F +EF E
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 215 QSISMLNNQNLFERRITVR 233
Q+++ + + + +R
Sbjct: 68 QAMA-FDGIIFQGQSLKIR 85
Score = 37.0 bits (86), Expect = 0.002
Identities = 12/75 (16%), Positives = 23/75 (30%), Gaps = 12/75 (16%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDI-----------GLVRFDSEWTAKRAI 569
V N+P IT + + D F + + + F S +A+
Sbjct: 11 VGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM 70
Query: 570 DMMDRTRIDGKIIDV 584
D G+ + +
Sbjct: 71 -AFDGIIFQGQSLKI 84
>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 = 50.3 bits (121), Expect = 5e-08
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 2/73 (2%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD-GKSRGFGTVEFDHPVEAVQSISM 219
K+F+ L ++ ++ LRE F G+V+ + D +SRGFG V F V +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ-AGVDKVLA 85
Query: 220 LNNQNLFERRITV 232
+ L + I
Sbjct: 86 QSRHELDSKTIDP 98
Score = 36.1 bits (84), Expect = 0.005
Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 2/60 (3%)
Query: 50 SHLSTVGDVTYVEILND-DTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAV 108
+ G+V ++ D T + RG V F V K + R E + + K A
Sbjct: 44 EYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVAF 102
Score = 33.4 bits (77), Expect = 0.040
Identities = 18/92 (19%), Positives = 36/92 (39%), Gaps = 11/92 (11%)
Query: 502 LDSNRSMNQSSNIERDT--VVVKNLPPTITWQELRDKFRNCGDIKFAEI-------KGKG 552
S+ + + S++ + + L T + LR+ F G++K + + +G
Sbjct: 9 HHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG 68
Query: 553 DIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDV 584
G V F + + + R +D K ID
Sbjct: 69 -FGFVTFMDQAGVDKVLA-QSRHELDSKTIDP 98
>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 = 54.3 bits (130), Expect = 1e-07
Identities = 80/479 (16%), Positives = 141/479 (29%), Gaps = 152/479 (31%)
Query: 24 RIETGAPLEVPVVMDLIQ----GDASLY-----QISHLSTVGDV-TYVEILND--DTGKP 71
RI P + L + G+A L Q G+ Y E L D T
Sbjct: 130 RIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQ-------GNTDDYFEELRDLYQTYHV 182
Query: 72 RGSAIVEFQSPDLVR--KAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGGVDRDLSA 129
+++F + L + + T+G ++
Sbjct: 183 LVGDLIKFSAETLSELIRTTLDAEKVFTQGL-------------------------NILE 217
Query: 130 LLQNNSSKFGNTYGLSPQFLESLGINCPLIN-------KVFVANLDYKVDEKKLREVFR- 181
L+N S+ +L S+ I+CPLI V L + E LR +
Sbjct: 218 WLENPSNT------PDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGE--LRSYLKG 269
Query: 182 LAGKVENV----EIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMDRV 237
G + + IA +S F F +A+ LF I VR
Sbjct: 270 ATGHSQGLVTAVAIAETDSWES--F----FVSVRKAI--------TVLF--FIGVRCYEA 313
Query: 238 ADRLDGPVRLPEGLKSIGMG-----LGANGAPLQDVANWLLQ--------EKVQKLSLII 284
P + E G L + + V +++ + ++V+ +SL+
Sbjct: 314 YPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVE-ISLVN 372
Query: 285 SNRN-----TKEVLERWDFKLQYDKSSDENDAASVNTASKTDSTNAEKDKIGN--LPNMN 337
+N + L + L+ K+ D + + S+ K K N LP
Sbjct: 373 GAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRI-PFSE------RKLKFSNRFLP--- 422
Query: 338 TNPTPTASVSTP---AALAAAVTALTQ---AQQPPPPQPSLG------NLGLNLGLGGAA 385
V++P L A + + + G + L +
Sbjct: 423 --------VASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSD--LRVLS 472
Query: 386 NDLTSNLTSTLTSLA----AANQNTAY------P-----LNQLSSQS--GLGQSNILSG 427
++ + + L Q A P L L+ ++ G G I++G
Sbjct: 473 GSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAG 531
Score = 30.4 bits (68), Expect = 1.9
Identities = 23/122 (18%), Positives = 40/122 (32%), Gaps = 18/122 (14%)
Query: 250 GLKSIGMGLG--ANGAPLQDV---ANWLLQEKVQKLSLI-ISNRNTKEVLERWDFKLQYD 303
G + GMG+ QDV A+ ++ S++ I N + F +
Sbjct: 1625 GSQEQGMGMDLYKTSKAAQDVWNRADNHFKDTY-GFSILDIVINNPVNL--TIHFGGEKG 1681
Query: 304 KSSDENDAASVNTASKTDSTNAEKDKIGNLPNMNTNPTPTASVSTPAALAAAVTALTQAQ 363
K EN +A + EK + + + + + L + TQ
Sbjct: 1682 KRIRENYSAMIFETIVDGKLKTEK-----IFKEINEHSTSYTFRSEKGL----LSATQFT 1732
Query: 364 QP 365
QP
Sbjct: 1733 QP 1734
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 48.6 bits (116), Expect = 2e-07
Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 2/71 (2%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRT-- 575
V ++ L + +L + + G I + + K LV F+ A A++
Sbjct: 23 VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQI 82
Query: 576 RIDGKIIDVTF 586
I G V +
Sbjct: 83 YIAGHPAFVNY 93
Score = 44.0 bits (104), Expect = 8e-06
Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 5/74 (6%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
V + L V E L E + G + V + + VEF+ + A +++
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVM-----PKKRQALVEFEDVLGACNAVNYAA 78
Query: 222 NQNLFERRITVRMD 235
+ ++ ++
Sbjct: 79 DNQIYIAGHPAFVN 92
Score = 27.0 bits (60), Expect = 6.5
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 7/58 (12%)
Query: 49 ISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFET--KGRKLVI 104
+ L G ++YV ++ + A+VEF+ AVN + G +
Sbjct: 39 VEALQEFGPISYVVVM-----PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV 91
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 49.2 bits (117), Expect = 2e-07
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 4/84 (4%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKD---GKSRGFGTVEFDHPVEAVQS 216
KVFV L +DE ++ FR G + + +G+ + F +VQ+
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE-SSVQA 67
Query: 217 ISMLNNQNLFERRITVRMDRVADR 240
+ + + + V + D+
Sbjct: 68 LIDACLEEDGKLYLCVSSPTIKDK 91
Score = 33.4 bits (76), Expect = 0.042
Identities = 11/65 (16%), Positives = 22/65 (33%), Gaps = 3/65 (4%)
Query: 50 SHLSTVGDVTYVEILNDD---TGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKE 106
+ G + + P+G A + FQ V+ ++ + K V
Sbjct: 27 ASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCVSSP 86
Query: 107 AVEDK 111
++DK
Sbjct: 87 TIKDK 91
Score = 29.2 bits (65), Expect = 1.3
Identities = 14/68 (20%), Positives = 20/68 (29%), Gaps = 10/68 (14%)
Query: 521 VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD--------IGLVRFDSEWTAKRAIDMM 572
V LPP I E+ FR G + + F E + + +
Sbjct: 13 VGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL--ID 70
Query: 573 DRTRIDGK 580
DGK
Sbjct: 71 ACLEEDGK 78
>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions,
RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus
musculus}
Length = 89
Score = 48.0 bits (115), Expect = 2e-07
Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 6/74 (8%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISM 219
+KVFV + ++L++ F G+V +V I R F V F + QS+
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADD-KVAQSL-C 65
Query: 220 LNNQNLFERRITVR 233
+ + + +
Sbjct: 66 GEDLIIKGISVHIS 79
Score = 41.1 bits (97), Expect = 6e-05
Identities = 15/81 (18%), Positives = 27/81 (33%), Gaps = 7/81 (8%)
Query: 508 MNQSSNIERDT--VVVKNLPPTITWQELRDKFRNCGDIKFAEIKG--KGDIGLVRFDSEW 563
M S + V V +T +EL+ F G++ I + V F +
Sbjct: 1 MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRA-FAFVTFADDK 59
Query: 564 TAKRAIDMMDRTRIDGKIIDV 584
A+ + I G + +
Sbjct: 60 VAQSLC--GEDLIIKGISVHI 78
Score = 38.7 bits (91), Expect = 3e-04
Identities = 14/67 (20%), Positives = 20/67 (29%), Gaps = 7/67 (10%)
Query: 50 SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
G+V V I R A V F + + + KG + I A
Sbjct: 30 QFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQSLCGEDLII--KGISVHISNAE- 82
Query: 110 DKGGRRN 116
K + N
Sbjct: 83 PKHNKLN 89
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 47.5 bits (113), Expect = 5e-07
Identities = 12/85 (14%), Positives = 31/85 (36%), Gaps = 2/85 (2%)
Query: 504 SNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEW 563
S+ + S + + ++ LP +T E+ G + + + + ++E
Sbjct: 4 SHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEE 63
Query: 564 TAKRAID--MMDRTRIDGKIIDVTF 586
A ++ + G+ I + F
Sbjct: 64 AANTMVNYYTSVTPVLRGQPIYIQF 88
Score = 42.2 bits (99), Expect = 3e-05
Identities = 12/75 (16%), Positives = 27/75 (36%), Gaps = 7/75 (9%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS--M 219
+ + L V E ++ + GKV N+ + K + +E + A ++
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLM-----LKGKNQAFIEMNTEEAANTMVNYYT 73
Query: 220 LNNQNLFERRITVRM 234
L + I ++
Sbjct: 74 SVTPVLRGQPIYIQF 88
Score = 27.5 bits (61), Expect = 5.3
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 7/58 (12%)
Query: 49 ISHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVN--KMHRFETKGRKLVI 104
IS G VT + +L K + A +E + + VN +G+ + I
Sbjct: 34 ISLGLPFGKVTNLLML-----KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI 86
>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 = 49.1 bits (116), Expect = 7e-07
Identities = 13/60 (21%), Positives = 22/60 (36%), Gaps = 1/60 (1%)
Query: 50 SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVE 109
L G V +++ +GS V F S + +K V + K L+I +
Sbjct: 128 EWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD 186
Score = 48.7 bits (115), Expect = 8e-07
Identities = 13/80 (16%), Positives = 26/80 (32%), Gaps = 1/80 (1%)
Query: 155 NCPLINKVFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAV 214
N V++ ++E G+V N+++ +G V FD E+
Sbjct: 105 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSI-ESA 163
Query: 215 QSISMLNNQNLFERRITVRM 234
+ Q E + +
Sbjct: 164 KKFVETPGQKYKETDLLILF 183
Score = 37.5 bits (86), Expect = 0.005
Identities = 11/70 (15%), Positives = 30/70 (42%), Gaps = 5/70 (7%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGD-----IGLVRFDSEWTAKRAIDMM 572
+V +K P T ++++ + G + +++ V FDS +AK+ ++
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 170
Query: 573 DRTRIDGKII 582
+ + ++
Sbjct: 171 GQKYKETDLL 180
>4aez_B MAD2, mitotic spindle checkpoint component MAD2; cell cycle,
KEN-BOX, D-BOX, APC/C; 2.30A {Schizosaccharomyces pombe}
Length = 203
Score = 48.6 bits (115), Expect = 1e-06
Identities = 14/46 (30%), Positives = 29/46 (63%)
Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDEND 310
+ + W+ +K+QKL L+I+++ + E LERW F ++ ++D+
Sbjct: 68 VSQLHKWMFAKKIQKLILVITSKCSGEDLERWQFNVEMVDTADQFQ 113
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 46.6 bits (110), Expect = 2e-06
Identities = 23/104 (22%), Positives = 41/104 (39%), Gaps = 8/104 (7%)
Query: 489 SIQSGG--YGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFA 546
S+QSG A +D+ +M S + R ++V+NL +T L F G +
Sbjct: 1 SVQSGNLALAASAAAVDAGMAMAGQSPVLR--IIVENLFYPVTLDVLHQIFSKFGTVLKI 58
Query: 547 EI--KGKGDIGLVRFDSEWTAKRAIDMMDRTRI--DGKIIDVTF 586
K L+++ +A+ A +D I + + F
Sbjct: 59 ITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 102
Score = 44.2 bits (104), Expect = 1e-05
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
+ V NL Y V L ++F G V + ++ +++ PV A + L+
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLD 87
Query: 222 NQNLFERRITVRMD 235
QN++ T+R+D
Sbjct: 88 GQNIYNACCTLRID 101
>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 = 44.4 bits (105), Expect = 6e-06
Identities = 11/86 (12%), Positives = 29/86 (33%), Gaps = 3/86 (3%)
Query: 504 SNRSMNQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSE 562
S+ S + V+ ++ LP +T E+ G + + + + +E
Sbjct: 2 SSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATE 61
Query: 563 WTAKRAID--MMDRTRIDGKIIDVTF 586
A ++ + + I + +
Sbjct: 62 EAAITMVNYYSAVTPHLRNQPIYIQY 87
Score = 41.7 bits (98), Expect = 4e-05
Identities = 12/75 (16%), Positives = 29/75 (38%), Gaps = 7/75 (9%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSIS--M 219
+ + L +V E ++ + GKV N+ + K + +E A+ ++
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILM-----LKGKNQAFLELATEEAAITMVNYYS 72
Query: 220 LNNQNLFERRITVRM 234
+L + I ++
Sbjct: 73 AVTPHLRNQPIYIQY 87
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 45.5 bits (107), Expect = 8e-06
Identities = 29/114 (25%), Positives = 47/114 (41%), Gaps = 7/114 (6%)
Query: 126 DLSALLQ-NNSSKFGNTYGLSPQFLESLGINCPLINKVF---VANLDYKVDEKKLREVFR 181
A LQ NS + GN + G+ + V V NL Y V L ++F
Sbjct: 9 SAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFS 68
Query: 182 LAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITVRMD 235
G V I K+ + + +++ PV A + L+ QN++ T+R+D
Sbjct: 69 KFGTVLK-IITFTKNNQFQAL--LQYADPVSAQHAKLSLDGQNIYNACCTLRID 119
Score = 42.8 bits (100), Expect = 7e-05
Identities = 23/104 (22%), Positives = 41/104 (39%), Gaps = 8/104 (7%)
Query: 489 SIQSGG--YGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFA 546
S+QSG A +D+ +M S + R ++V+NL +T L F G +
Sbjct: 19 SVQSGNLALAASAAAVDAGMAMAGQSPVLR--IIVENLFYPVTLDVLHQIFSKFGTVLKI 76
Query: 547 EI--KGKGDIGLVRFDSEWTAKRAIDMMDRTRI--DGKIIDVTF 586
K L+++ +A+ A +D I + + F
Sbjct: 77 ITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF 120
>2vfx_A Mitotic spindle assembly checkpoint protein MAD2A; CDC2, nucleus,
mitosis, anaphase, cell cycle, CE division, spindle
checkpoint; HET: PE4 PE3; 1.95A {Homo sapiens} PDB:
2qyf_A 2v64_A 1s2h_A 1go4_A 3gmh_A 1klq_A 2v64_D 1duj_A
Length = 206
Score = 45.8 bits (108), Expect = 1e-05
Identities = 19/56 (33%), Positives = 34/56 (60%)
Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAASVNTASKT 320
++ + +WL + VQKL ++ISN + EVLERW F ++ DK++ ++ A +
Sbjct: 70 VEQLKDWLYKSSVQKLVVVISNIESGEVLERWQFDIESDKTAKDDSAPREKSQKAI 125
>3abd_A Mitotic spindle assembly checkpoint protein MAD2B; horma, DNA
replication, translesion DNA SYNT cell cycle, cell
division, mitosis, DNA damage; HET: DNA; 1.90A {Homo
sapiens} PDB: 3abe_C*
Length = 227
Score = 44.8 bits (105), Expect = 2e-05
Identities = 8/49 (16%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 265 LQDVANWLLQEKVQKLSLIISNRNTKEVLERWDFKLQYDKSSDENDAAS 313
L V L + V+K+ ++I ++ +E++ F++ + +
Sbjct: 84 LHCVKPLLEKNDVEKVVVVILDKEH-RPVEKFVFEITQPPLLSISSDSL 131
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 40.8 bits (95), Expect = 9e-05
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 516 RDTVVVKNLPPTITWQELRDKFR----NCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDM 571
+ V NLP + + ++ R NCG K I G ++RF ++ +A+RA
Sbjct: 9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGG-KVLSITG--CSAILRFINQDSAERAQKR 65
Query: 572 MDRTRIDGKIIDVTF 586
M+ + G I V+F
Sbjct: 66 MENEDVFGNRIIVSF 80
Score = 28.5 bits (63), Expect = 2.0
Identities = 10/50 (20%), Positives = 22/50 (44%)
Query: 73 GSAIVEFQSPDLVRKAVNKMHRFETKGRKLVIKEAVEDKGGRRNMGGGGG 122
SAI+ F + D +A +M + G ++++ +++ G G
Sbjct: 47 CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRELCETSGPSSG 96
>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 = 39.9 bits (93), Expect = 2e-04
Identities = 17/99 (17%), Positives = 34/99 (34%), Gaps = 4/99 (4%)
Query: 493 GGYGNPRAG--LDSNRSMNQSSNIERDTVV-VKNLPPTITWQELRDKFRNCGDIKFAEIK 549
G G+ A L + + S + VV L ++ +L CG + +
Sbjct: 1 GSSGSSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMP 60
Query: 550 GKGDIGLVRFDSEWTAKRAIDMMDRTRI-DGKIIDVTFF 587
R+ + +KRA ++ + D +T +
Sbjct: 61 PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY 99
Score = 38.4 bits (89), Expect = 8e-04
Identities = 11/68 (16%), Positives = 24/68 (35%), Gaps = 5/68 (7%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
V L V +L V G V+ + + +K + + E+ ++ LN
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-----PYSFARYRTTEESKRAYVTLN 84
Query: 222 NQNLFERR 229
+ + +
Sbjct: 85 GKEVVDDL 92
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 40.5 bits (94), Expect = 7e-04
Identities = 18/109 (16%), Positives = 31/109 (28%), Gaps = 16/109 (14%)
Query: 487 QASIQSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITW---------QELRDKF 537
+ Y G+ S R N+ T+ V + + +R F
Sbjct: 112 FGREKFADYREDMGGIGSFRKKNK-------TLYVGGIDGALNSKHLKPAQIESRIRFVF 164
Query: 538 RNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTF 586
GDI + G V+F + A+ A + M +
Sbjct: 165 SRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWD 213
Score = 37.5 bits (86), Expect = 0.008
Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 14/88 (15%)
Query: 162 VFVANLDYKVD---------EKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVE 212
++V +D ++ E ++R VF G ++ + +S+ G V+F +
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV-----ESKNCGFVKFKYQAN 191
Query: 213 AVQSISMLNNQNLFERRITVRMDRVADR 240
A + ++NQ L DR
Sbjct: 192 AEFAKEAMSNQTLLLPSDKEWDDRREGT 219
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 38.1 bits (88), Expect = 0.001
Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
+ + N Y + L V GKV+ I + K + VEF+ + A ++ + LN
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQ--RIVIFKRNGIQAM--VEFESVLCAQKAKAALN 83
Query: 222 NQNLFERRITVRMD 235
+++ T++++
Sbjct: 84 GADIYAGCCTLKIE 97
Score = 35.0 bits (80), Expect = 0.016
Identities = 16/91 (17%), Positives = 31/91 (34%), Gaps = 3/91 (3%)
Query: 491 QSGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDI-KFAEIK 549
SG G + + + + + ++N IT L G + + K
Sbjct: 2 SSGSSGKRITRPGNTDDPSGGNKVLL--LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK 59
Query: 550 GKGDIGLVRFDSEWTAKRAIDMMDRTRIDGK 580
G +V F+S A++A ++ I
Sbjct: 60 RNGIQAMVEFESVLCAQKAKAALNGADIYAG 90
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 34.8 bits (80), Expect = 0.011
Identities = 11/49 (22%), Positives = 22/49 (44%)
Query: 184 GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNNQNLFERRITV 232
G+VE + + + G V+F +A +++ LNN+ + I
Sbjct: 52 GEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHA 100
Score = 32.1 bits (73), Expect = 0.097
Identities = 9/41 (21%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH-RF 95
G+V + + ++ G+ V+F+ + KAV ++ R+
Sbjct: 52 GEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRW 92
>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator,
structural genomics, PSI-2, protei structure initiative;
NMR {Homo sapiens}
Length = 97
Score = 34.4 bits (79), Expect = 0.016
Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 508 MNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAE-IKGK 551
M + VV++ LPP +T ++L ++ R + E
Sbjct: 1 MGHHHHHHSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAAD 45
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 34.5 bits (79), Expect = 0.017
Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 4/70 (5%)
Query: 518 TVVVKNLPPTITWQELRDKFRNCGDIKFAEIKG---KGDIGLVRFDSEWTAKRAIDMMDR 574
V V+ LPP + + L F N + G G++ F A+R + D
Sbjct: 10 AVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERVLAQADH 69
Query: 575 TRIDGKIIDV 584
+ G + +
Sbjct: 70 E-LHGAQLSL 78
Score = 32.6 bits (74), Expect = 0.073
Identities = 13/79 (16%), Positives = 26/79 (32%), Gaps = 13/79 (16%)
Query: 160 NKVFVANLDYKVDEKKLREVFRLA-----GKVENVEIALDKDGKSRGFGTVEFDHPVEAV 214
V V L V ++ L F G V + + + G + F P
Sbjct: 9 VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ-------RLGCGGVLTFREP-ADA 60
Query: 215 QSISMLNNQNLFERRITVR 233
+ + + L ++++R
Sbjct: 61 ERVLAQADHELHGAQLSLR 79
Score = 29.5 bits (66), Expect = 0.83
Identities = 8/54 (14%), Positives = 18/54 (33%), Gaps = 3/54 (5%)
Query: 67 DTGKPRGSAIVEFQSPDLVRKAV-NKMHRFETKGRKLVIKEAVEDKGGRRNMGG 119
+ ++ F+ P + + H G +L ++ A R + G
Sbjct: 42 SWQRLGCGGVLTFREPADAERVLAQADHELH--GAQLSLRPAPPRAPARLLLQG 93
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 34.9 bits (79), Expect = 0.028
Identities = 8/32 (25%), Positives = 17/32 (53%), Gaps = 6/32 (18%)
Query: 433 QGMQSQTSSLSSGNNVYSNQSAPSTDYSRNAS 464
Q ++ +SL +Y++ SAP+ + A+
Sbjct: 20 QALKKLQASL----KLYADDSAPA--LAIKAT 45
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 35.2 bits (80), Expect = 0.078
Identities = 17/140 (12%), Positives = 29/140 (20%), Gaps = 7/140 (5%)
Query: 340 PTPTASVSTPAALAAAVTALTQAQQPPPPQPSLGNLGLNLGLGGAANDLTSNLTSTLTSL 399
P A Q P S G +G+ + LT L
Sbjct: 10 PQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQL 69
Query: 400 AAANQNTAYPLNQ-------LSSQSGLGQSNILSGMAAYSQGMQSQTSSLSSGNNVYSNQ 452
+N L + Q + M Q Q ++ + G +
Sbjct: 70 HQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMG 129
Query: 453 SAPSTDYSRNASNMYGNSRY 472
++
Sbjct: 130 QNMRPMNQLYPIDLLTELPP 149
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 32.7 bits (74), Expect = 0.086
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 2/61 (3%)
Query: 523 NLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKII 582
+L ++L F N G+IK+ + G++ F + AK A+ +
Sbjct: 26 DLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEK--AKEALGKAKDANNGNLQL 83
Query: 583 D 583
Sbjct: 84 R 84
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 32.4 bits (74), Expect = 0.095
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 2/59 (3%)
Query: 531 QELRDKFRNCGDIKFAEIKGKGDIGL--VRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF 587
++LR + G I+ + + G+ V F A I +D G+ I +
Sbjct: 41 EDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAW 99
Score = 29.7 bits (67), Expect = 1.00
Identities = 8/41 (19%), Positives = 16/41 (39%), Gaps = 4/41 (9%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMH-RF 95
G + + + P G A V F+ P+ + + R+
Sbjct: 51 GQIRKLLL---FDRHPDGVASVSFRDPEEADYCIQTLDGRW 88
Score = 28.9 bits (65), Expect = 1.8
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 3/39 (7%)
Query: 184 GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
G++ + + D G +V F P EA I L+
Sbjct: 51 GQIRKLLLF---DRHPDGVASVSFRDPEEADYCIQTLDG 86
>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken
structural genomics/proteomics initiative, RSGI, protein
transport; 2.70A {Mus musculus} SCOP: d.58.7.1
Length = 119
Score = 31.6 bits (71), Expect = 0.25
Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 7/77 (9%)
Query: 506 RSMNQSSNIERDTVVVKNLPPTITWQELRDKFRNCGDIKFAEIKGKGDIGLVRFDSEWTA 565
S+ +++ V V P L +F G+I + G+ +R+ S+ A
Sbjct: 14 DSLTSEDHLDDTWVTVFGFPQASASYILL-QFAQYGNILKHVMSNTGNWMHIRYQSKLQA 72
Query: 566 KRAIDMMDRTRIDGKII 582
++A+ DG+I
Sbjct: 73 RKALSK------DGRIF 83
>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 = 0.36
Identities = 14/98 (14%), Positives = 30/98 (30%), Gaps = 4/98 (4%)
Query: 492 SGGYGNPRAGLDSNRSMNQSSNIERDTVVVKNLP-PTITWQELRDKFRNCGDIKFAEIKG 550
S G + ++ +Q + R + + NLP + + G IK +
Sbjct: 2 SSGSSGKKPEGKPDQKFDQKQELGR-VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR 60
Query: 551 KGDIGLVRFDSEWTAKRAIDM--MDRTRIDGKIIDVTF 586
+ ++ A +D G+ + V
Sbjct: 61 MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDL 98
>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N
domain, MIF4G domain; 1.95A {Homo sapiens} SCOP:
d.58.7.4
Length = 91
Score = 30.1 bits (68), Expect = 0.41
Identities = 9/34 (26%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 519 VVVKNLPPTITWQELRDKFRNCGDIKFAE-IKGK 551
VV++ LPPT+T ++L++ + + + E
Sbjct: 4 VVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSND 37
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint
center for struc genomics, JCSG, protein structure
initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus
musculus} PDB: 2lq5_A
Length = 114
Score = 30.4 bits (69), Expect = 0.51
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 8/46 (17%)
Query: 56 GDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
G V ++ + D +G+ V+ S AVN +H GR
Sbjct: 42 GGVIHIYV---DKNSAQGNVYVKCPSIAAAIAAVNALH-----GRW 79
Score = 30.0 bits (68), Expect = 0.67
Identities = 9/60 (15%), Positives = 24/60 (40%), Gaps = 4/60 (6%)
Query: 531 QELRDKFRNCGDIKFAEI---KGKGDIGLVRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF 587
++ ++ G + + +G++ V+ S A A++ + GK+I +
Sbjct: 32 DDVIEECNKHGGVIHIYVDKNSAQGNV-YVKCPSIAAAIAAVNALHGRWFAGKMITAAYV 90
Score = 27.3 bits (61), Expect = 5.8
Identities = 6/39 (15%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 184 GKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLNN 222
G V ++ + ++G V+ A+ +++ L+
Sbjct: 42 GGVIHIYVD---KNSAQGNVYVKCPSIAAAIAAVNALHG 77
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 29.4 bits (66), Expect = 1.1
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 3/50 (6%)
Query: 176 LREVFRLAGKVENVEIALDKDGKS---RGFGTVEFDHPVEAVQSISMLNN 222
+R+ G V+++EI DG G VEF + +++ L
Sbjct: 32 VRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81
Score = 29.0 bits (65), Expect = 1.5
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 8/49 (16%)
Query: 56 GDVTYVEI---LNDDTGKPRGSAIVEFQSPDLVRKAVNKMHRFETKGRK 101
G V +EI ++ G VEF S +KA+ + GRK
Sbjct: 40 GLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT-----GRK 83
Score = 27.8 bits (62), Expect = 4.0
Identities = 11/65 (16%), Positives = 26/65 (40%), Gaps = 8/65 (12%)
Query: 531 QELRDKFRNCGDIKFAEIKGKGD--------IGLVRFDSEWTAKRAIDMMDRTRIDGKII 582
+++RD+ G +K EI D V F S + ++A+ + + +++
Sbjct: 30 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 89
Query: 583 DVTFF 587
+
Sbjct: 90 VTKYC 94
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 28.9 bits (64), Expect = 1.2
Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 5/69 (7%)
Query: 162 VFVANLDYKVDEKKLREVFRLAGKVENVEIALDKDGKSRGFGTVEFDHPVEAVQSISMLN 221
+ + NL ++D LR + G + + L ++G ++ EA ++ LN
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALN 64
Query: 222 NQNLFERRI 230
N L I
Sbjct: 65 NCVLANTTI 73
>2gr7_A Adhesin; trimeric autotransporter, adhesion, membrane protein,
protei secretion, microbial pathogenesis; HET: C8E;
2.30A {Haemophilus influenzae} SCOP: d.24.1.4
Length = 129
Score = 28.0 bits (62), Expect = 4.5
Identities = 21/116 (18%), Positives = 35/116 (30%), Gaps = 6/116 (5%)
Query: 382 GGAANDLTSNLTSTLTSLAAANQNTAYPLNQLSSQSGLGQSNILSG------MAAYSQGM 435
GG + S L ++A N A +N L + +G + Q
Sbjct: 13 GGGGLVPRGSNGSQLYAVAKGVTNLAGQVNNLEGKVNKVGKRADAGTASALAASQLPQAT 72
Query: 436 QSQTSSLSSGNNVYSNQSAPSTDYSRNASNMYGNSRYGSGGNEMDYGGGSGQASIQ 491
S ++ + Y Q+ + SR + N R N G + Q
Sbjct: 73 MPGKSMVAIAGSSYQGQNGLAIGVSRISDNGKVIIRLSGTTNSQGKTGVAAGVGYQ 128
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 27.0 bits (59), Expect = 7.0
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 4/43 (9%)
Query: 50 SHLSTVGDVTYVEILNDDTGKPRGSAIVEFQSPDLVRKAVNKM 92
L G+V + + + K G+A+VEF + AV
Sbjct: 36 RLLQKYGEVLNLVL----SSKKPGTAVVEFATVKAAELAVQNE 74
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 27.0 bits (60), Expect = 7.3
Identities = 5/31 (16%), Positives = 11/31 (35%)
Query: 557 VRFDSEWTAKRAIDMMDRTRIDGKIIDVTFF 587
V F +AI ++ G+ + +
Sbjct: 76 VEFSIASETHKAIQALNGRWFAGRKVVAEVY 106
>2opo_A Polcalcin CHE A 3; calcium-binding protein, dimer, domain-swapping,
EF-hand; 1.75A {Chenopodium album} SCOP: a.39.1.10 PDB:
1h4b_A
Length = 86
Score = 26.5 bits (59), Expect = 8.9
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 9/53 (16%)
Query: 161 KVFVANLDYKVDEKKLREVFRLAGKVENVEI-----ALDKDGKSRGFGTVEFD 208
K F N D K+ +L + + G V E+ +D DG G + FD
Sbjct: 18 KRFDTNGDGKISSSELGDALKTLGSVTPDEVRRMMAEIDTDGD----GFISFD 66
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
0.312 0.130 0.365
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,624,918
Number of extensions: 526907
Number of successful extensions: 1945
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1618
Number of HSP's successfully gapped: 587
Length of query: 587
Length of database: 6,701,793
Length adjustment: 99
Effective length of query: 488
Effective length of database: 3,937,614
Effective search space: 1921555632
Effective search space used: 1921555632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 60 (26.8 bits)