RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3721
(207 letters)
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 125 bits (317), Expect = 2e-36
Identities = 23/176 (13%), Positives = 70/176 (39%), Gaps = 27/176 (15%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKE 88
++++G++ + IR F +G + D+ K + FV E E + A+++
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 89 LNGQIVNEKPLKIEAATSRK----------GPNTPTTKVFVGNLSDNTRAPEVRELFVPY 138
+N ++ + +K+ ++ +++V ++ + +++ +F +
Sbjct: 90 MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 149
Query: 139 GTVVECDIV--------RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSR 185
G + + + YGF+ + + +N + G+ ++V + +
Sbjct: 150 GKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205
Score = 82.4 bits (204), Expect = 8e-20
Identities = 21/114 (18%), Positives = 54/114 (47%), Gaps = 9/114 (7%)
Query: 91 GQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--- 147
+ + + +A R+G ++V+VG++ +R+ F P+G + D+
Sbjct: 5 ASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDS 64
Query: 148 -----RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPGVDEV 195
+ + FV + P ++++N +M+ G+ +KV ++ + +P +D++
Sbjct: 65 VTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQL 118
Score = 77.4 bits (191), Expect = 7e-18
Identities = 23/112 (20%), Positives = 47/112 (41%), Gaps = 8/112 (7%)
Query: 10 VKVSRYSNNQINISCRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV- 68
+KV R SN + + +I++ +V+ S + I+ +FE +GK+ +
Sbjct: 100 IKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLAR 159
Query: 69 -------KNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTP 113
K YGF+ E + + A+ +N + + L++ A + P
Sbjct: 160 DPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLT 211
>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 = 123 bits (312), Expect = 3e-36
Identities = 41/168 (24%), Positives = 69/168 (41%), Gaps = 24/168 (14%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN----------YGFVHMENDEEGRTAI 86
K+F+G V S + +R LFE+YG V E +V+++ FV + A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 87 KELNGQIVNEK---PLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVE 143
L+ V P++++ A S K K+F+G +S ++R +F +G + E
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 124
Query: 144 CDIVRN-------YGFVHIDSPD-INKCIKELNGMMV---DGKPMKVQ 180
C I+R FV + IK ++ PM V+
Sbjct: 125 CRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK 172
Score = 64.9 bits (159), Expect = 1e-13
Identities = 18/86 (20%), Positives = 32/86 (37%), Gaps = 15/86 (17%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN----------YGFVHIDSP-DINKC 163
K+FVG + ++RELF YG V E +++R+ FV + +
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
Query: 164 IKELNGMMVDGKPMKVQISTSRVRQR 189
L+ M V +++
Sbjct: 64 QNALHNMKVLPGMHHP----IQMKPA 85
Score = 64.9 bits (159), Expect = 1e-13
Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 10/77 (12%)
Query: 35 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIK 87
K+FIG ++ + IR +F +G++ EC +++ FV +TAIK
Sbjct: 95 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIK 154
Query: 88 ELNGQIVNE---KPLKI 101
++ E P+ +
Sbjct: 155 AMHQAQTMEGCSSPMVV 171
>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 = 123 bits (312), Expect = 4e-36
Identities = 37/162 (22%), Positives = 70/162 (43%), Gaps = 20/162 (12%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKE 88
+ + + + + LF G + C ++ Y FV ++ + + AIK
Sbjct: 5 NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
Query: 89 LNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR 148
LNG V K LK+ A G + T ++V NL ++ +F YG++V+ +I+R
Sbjct: 65 LNGITVRNKRLKVSYA-RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR 123
Query: 149 N--------YGFVHIDSP-DINKCIKELNGMMVDG--KPMKV 179
+ FV + + + I LN ++ +G +P+ V
Sbjct: 124 DKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165
Score = 69.9 bits (172), Expect = 2e-15
Identities = 24/87 (27%), Positives = 34/87 (39%), Gaps = 9/87 (10%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIK 165
T + V L + E+ LF G + C I+R+ Y FV S D + IK
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 166 ELNGMMVDGKPMKVQISTSRVRQRPGV 192
LNG+ V K +KV +
Sbjct: 64 VLNGITVRNKRLKVSYARPGGESIKDT 90
Score = 66.4 bits (163), Expect = 3e-14
Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 10/87 (11%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMEND 79
PG S+ +++ N+ + + + +F KYG +V+ +++ + FV
Sbjct: 82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKR 141
Query: 80 EEGRTAIKELNGQIVN--EKPLKIEAA 104
EE + AI LN I +PL + A
Sbjct: 142 EEAQEAISALNNVIPEGGSQPLSVRLA 168
>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 = 122 bits (309), Expect = 1e-35
Identities = 39/170 (22%), Positives = 69/170 (40%), Gaps = 13/170 (7%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMENDE 80
G S F +FIGN+NP SV ++ + + VV + +G+V E+ E
Sbjct: 6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 65
Query: 81 EGRTAIKELNGQIVNEKPLKIEAATSRKG-PNTPTTKVFVGNLSDNTRAPEVRELFVPYG 139
+ A+ EL G V +K+E R + NLS N E++E+F
Sbjct: 66 DLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL 124
Query: 140 TVVECD---IVRNYGFVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSR 185
+ + ++ S D K ++E G +DG+ + + + +
Sbjct: 125 EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
Score = 69.2 bits (170), Expect = 3e-15
Identities = 21/91 (23%), Positives = 40/91 (43%), Gaps = 9/91 (9%)
Query: 108 KGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSP-D 159
+T +F+GNL+ N E++ + +V R +G+V +S D
Sbjct: 7 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED 66
Query: 160 INKCIKELNGMMVDGKPMKVQISTSRVRQRP 190
+ K + EL G+ V G +K++ R ++
Sbjct: 67 LEKAL-ELTGLKVFGNEIKLEKPKGRDSKKV 96
>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 = 119 bits (302), Expect = 1e-34
Identities = 38/162 (23%), Positives = 68/162 (41%), Gaps = 20/162 (12%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
+ + + + E R LF G++ C +V++ YGFV+ + ++ AI
Sbjct: 4 NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63
Query: 89 LNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR 148
LNG + K +K+ A + ++V L E+ +LF YG ++ I+
Sbjct: 64 LNGLRLQTKTIKVSYARPSS-ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILV 122
Query: 149 N--------YGFVHIDSP-DINKCIKELNGMMVDG--KPMKV 179
+ GF+ D + + IK LNG G +P+ V
Sbjct: 123 DQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 164
Score = 68.4 bits (168), Expect = 7e-15
Identities = 26/83 (31%), Positives = 35/83 (42%), Gaps = 9/83 (10%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIK 165
T + V L N E R LF G + C +VR+ YGFV+ P D K I
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 166 ELNGMMVDGKPMKVQISTSRVRQ 188
LNG+ + K +KV +
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSAS 85
Score = 66.8 bits (164), Expect = 2e-14
Identities = 18/87 (20%), Positives = 41/87 (47%), Gaps = 10/87 (11%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMEND 79
P +S+ +++ + + + + LF +YG+++ ++ + GF+ +
Sbjct: 81 PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKR 140
Query: 80 EEGRTAIKELNGQIVN--EKPLKIEAA 104
E AIK LNGQ + +P+ ++ A
Sbjct: 141 IEAEEAIKGLNGQKPSGATEPITVKFA 167
>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 = 122 bits (307), Expect = 3e-34
Identities = 31/163 (19%), Positives = 59/163 (36%), Gaps = 19/163 (11%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKELNGQIV 94
KI I + + + + L Y + C V K FV + N E+ AI + +
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRL 82
Query: 95 NEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN----- 149
E+ L ++ + + V NL + + EL P+G++ C +V +
Sbjct: 83 RERELSVQLQPTD-------ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQ 135
Query: 150 ---YGFVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQ 188
YGF + +L G + + + V + +
Sbjct: 136 SKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLT 178
Score = 120 bits (304), Expect = 8e-34
Identities = 19/168 (11%), Positives = 56/168 (33%), Gaps = 19/168 (11%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
+ + N+ P + + L +G + C +V + YGF + A +
Sbjct: 97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 89 LNGQIVNEKPLKIEAATSRK--GPNTPTTKVFVGNLSDNTRAPE-VRELFVPYGTVVECD 145
L G+ + + L + + + + + V L + + + C
Sbjct: 157 LLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQ 216
Query: 146 IVRN-------YGFVHIDSPDI-NKCIKELNGMMVDGKPMKVQISTSR 185
+ + + ++ ++ + ++ +G+ + G ++V
Sbjct: 217 LACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 264
Score = 72.3 bits (178), Expect = 1e-15
Identities = 12/94 (12%), Positives = 34/94 (36%), Gaps = 5/94 (5%)
Query: 94 VNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--YG 151
++ + ++ + + K+ + L + EV +L Y + C + +
Sbjct: 3 LDPEEIRKRLEHTERQF-RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTA 60
Query: 152 FVHIDSP-DINKCIKELNGMMVDGKPMKVQISTS 184
FV + + I + + + + VQ+ +
Sbjct: 61 FVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT 94
>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 = 118 bits (297), Expect = 5e-34
Identities = 35/169 (20%), Positives = 70/169 (41%), Gaps = 24/169 (14%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------------KNYGFVHMENDEEGR 83
++++GN+ G + E + F ++ KN+ F+ + +E
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 84 TAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVE 143
A+ +G I + LKI P K+F+G L + +V+EL +G +
Sbjct: 66 QAMA-FDGIIFQGQSLKIRRP-HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKA 123
Query: 144 CDIVRN--------YGFVHIDSPDI-NKCIKELNGMMVDGKPMKVQIST 183
++V++ Y F ++ ++ I LNGM + K + VQ ++
Sbjct: 124 FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172
Score = 68.4 bits (168), Expect = 8e-15
Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 8/80 (10%)
Query: 34 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTA 85
G K+FIG + + + ++ L +G + ++VK+ Y F + A
Sbjct: 93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 152
Query: 86 IKELNGQIVNEKPLKIEAAT 105
I LNG + +K L ++ A+
Sbjct: 153 IAGLNGMQLGDKKLLVQRAS 172
Score = 55.7 bits (135), Expect = 3e-10
Identities = 10/90 (11%), Positives = 30/90 (33%), Gaps = 15/90 (16%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------------RNYGFVHIDSP-DIN 161
+++VGN+ + + F + +N+ F+ S +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 162 KCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+ + +G++ G+ +K++
Sbjct: 66 QAMA-FDGIIFQGQSLKIRRPHDYQPLPGA 94
>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 = 116 bits (294), Expect = 1e-33
Identities = 32/163 (19%), Positives = 75/163 (46%), Gaps = 17/163 (10%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIKELN 90
+++GN++ + ++++ F+ G + ++ + Y FV + A++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 91 GQIVNEKPLKIE-AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 149
G+ + +KI A S++ + T +FVG+L+ N +R F + + + ++ +
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD 122
Query: 150 --------YGFVHIDSP-DINKCIKELNGMMVDGKPMKVQIST 183
YGFV S D + + G ++G+P+++ +
Sbjct: 123 MQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165
Score = 70.2 bits (173), Expect = 1e-15
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 34 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTA 85
TF +F+G++N E +R F+ + + V+ + YGFV + ++ + A
Sbjct: 86 DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145
Query: 86 IKELNGQIVNEKPLKIEAAT 105
+ + GQ +N +PL+I A
Sbjct: 146 MDSMQGQDLNGRPLRINWAA 165
Score = 61.8 bits (151), Expect = 2e-12
Identities = 16/85 (18%), Positives = 32/85 (37%), Gaps = 8/85 (9%)
Query: 117 VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSP-DINKCIKELN 168
++VGNL +++ F G + I+ + Y FV D N ++ LN
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 169 GMMVDGKPMKVQISTSRVRQRPGVD 193
G ++ +K+ + +
Sbjct: 63 GKQIENNIVKINWAFQSQQSSSDDT 87
>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 = 118 bits (297), Expect = 5e-33
Identities = 37/168 (22%), Positives = 66/168 (39%), Gaps = 20/168 (11%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKELNGQIV 94
++F+GN+ + E + LFE+YG+ E + + +GF+ +E+ A EL+G I+
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL 83
Query: 95 NEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------- 147
+PL+I A T + V NLS + + F +G V + +V
Sbjct: 84 KSRPLRIRFA-------THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRA 136
Query: 148 RNYGFVHIDSPD-INKCIKELNGMMVDGKPMKVQISTSRVRQRPGVDE 194
GFV + K ++ + V D+
Sbjct: 137 TGKGFVEFAAKPPARKALERCGDGAF---LLTTTPRPVIVEPMEQFDD 181
Score = 72.8 bits (179), Expect = 7e-16
Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 4/87 (4%)
Query: 97 KPLKIEAATSRKGPN-TPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR--NYGFV 153
+ I++ T ++FVGNL + + + LF YG E I R +GF+
Sbjct: 4 FTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFI 63
Query: 154 HIDSP-DINKCIKELNGMMVDGKPMKV 179
++S EL+G ++ +P+++
Sbjct: 64 RLESRTLAEIAKAELDGTILKSRPLRI 90
Score = 60.5 bits (147), Expect = 2e-11
Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 11/84 (13%)
Query: 35 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMENDEEGRTAIK 87
+ + N++P S EL+ F ++G V + VV GFV R A++
Sbjct: 96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALE 155
Query: 88 ELNGQIV----NEKPLKIEAATSR 107
+P+ +E
Sbjct: 156 RCGDGAFLLTTTPRPVIVEPMEQF 179
>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 = 113 bits (286), Expect = 5e-32
Identities = 34/193 (17%), Positives = 72/193 (37%), Gaps = 42/193 (21%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------------KNYGFVHMENDEEGR 83
++++GN+ G + E + F ++ KN+ F+ + +E
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 84 TAIKELNGQIVNEKPLKIEAATSRKGPNTPT-------------------TKVFVGNLSD 124
A+ +G I + LKI + + K+F+G L +
Sbjct: 66 QAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 125 NTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDI-NKCIKELNGMMVDGK 175
+V+EL +G + ++V++ Y F ++ ++ I LNGM + K
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 184
Query: 176 PMKVQISTSRVRQ 188
+ VQ ++ +
Sbjct: 185 KLLVQRASVGAKN 197
Score = 66.2 bits (162), Expect = 7e-14
Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 8/82 (9%)
Query: 34 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTA 85
K+FIG + + + ++ L +G + ++VK+ Y F + A
Sbjct: 113 SAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQA 172
Query: 86 IKELNGQIVNEKPLKIEAATSR 107
I LNG + +K L ++ A+
Sbjct: 173 IAGLNGMQLGDKKLLVQRASVG 194
Score = 57.0 bits (138), Expect = 2e-10
Identities = 10/93 (10%), Positives = 31/93 (33%), Gaps = 15/93 (16%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------------RNYGFVHIDSP-DIN 161
+++VGN+ + + F + +N+ F+ S +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 162 KCIKELNGMMVDGKPMKVQISTSRVRQRPGVDE 194
+ + +G++ G+ +K++ +
Sbjct: 66 QAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSEN 97
>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 = 115 bits (290), Expect = 1e-31
Identities = 22/172 (12%), Positives = 62/172 (36%), Gaps = 24/172 (13%)
Query: 34 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN------YGFVHMENDEEGRTAIK 87
+ + N+ + + F+ G ++ DV + + + + AI
Sbjct: 40 ELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAIT 99
Query: 88 ELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV 147
+ + +V + + + T +++ N + +R+L V +
Sbjct: 100 KTHK-VVGQNEIIVSHLTE--------CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRL 150
Query: 148 --------RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRP 190
R + ++ + S D C+++LNG+ ++G + ++S + +
Sbjct: 151 PSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKR 202
Score = 110 bits (276), Expect = 1e-29
Identities = 24/174 (13%), Positives = 66/174 (37%), Gaps = 26/174 (14%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKE 88
+++ N P + IR L + V + + + ++ + + E+ R +++
Sbjct: 119 TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 178
Query: 89 LNGQIVNEKPLKIEAATSR------KGPNTPTTKVFVGNLSDN-TRAPEVRELFVPYGTV 141
LNG + L + + ++ + NLS +RE F +G++
Sbjct: 179 LNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSI 238
Query: 142 VECDIVRN---------YGFVHIDSPD-INKCIKELNGMMVDGKPMKVQISTSR 185
+ +I F+ ++ D + + ++N ++ + + V ++ +
Sbjct: 239 EKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKK 291
Score = 60.0 bits (146), Expect = 4e-11
Identities = 18/116 (15%), Positives = 36/116 (31%), Gaps = 14/116 (12%)
Query: 71 YGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPE 130
YG + + + E + K A +R T V V NL + +
Sbjct: 4 YGHH---ARPDSKRPLDEGSPAAAGLTSKKANEALTRNRELT---TVLVKNLPKSYNQNK 57
Query: 131 VRELFVPYGTVVECDIVRN------YGFVHIDSP-DINKCIKELNGMMVDGKPMKV 179
V + F G ++ D+ + + + I + + +V + V
Sbjct: 58 VYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK-VVGQNEIIV 112
>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 = 110 bits (278), Expect = 1e-30
Identities = 33/174 (18%), Positives = 79/174 (45%), Gaps = 16/174 (9%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMEND 79
P S +++G+++P + ++ F G ++ V ++ Y +V+ +
Sbjct: 8 PSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQP 67
Query: 80 EEGRTAIKELNGQIVNEKPLKIEAATSRKGPN-TPTTKVFVGNLSDNTRAPEVRELFVPY 138
+ A+ +N ++ KP++I + + +F+ NL + + + F +
Sbjct: 68 ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAF 127
Query: 139 GTVVECDIV------RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSR 185
G ++ C +V + YGFVH ++ + I+++NGM+++ + + V SR
Sbjct: 128 GNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 181
Score = 80.0 bits (198), Expect = 7e-19
Identities = 32/133 (24%), Positives = 56/133 (42%), Gaps = 12/133 (9%)
Query: 17 NNQINIS-CRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------K 69
+ I + P G IFI N++ + + F +G ++ C VV K
Sbjct: 84 GKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK 143
Query: 70 NYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAP 129
YGFVH E E AI+++NG ++N++ + + SRK + +G +
Sbjct: 144 GYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK-----EREAELGARAKEFYPY 198
Query: 130 EVRELFVPYGTVV 142
+V + G +V
Sbjct: 199 DVPDYAGSSGRIV 211
Score = 62.3 bits (152), Expect = 2e-12
Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 9/90 (10%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-D 159
P+ P ++VG+L + + E F P G ++ + R+ Y +V+ P D
Sbjct: 10 APSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD 69
Query: 160 INKCIKELNGMMVDGKPMKVQISTSRVRQR 189
+ + +N ++ GKP+++ S R
Sbjct: 70 AERALDTMNFDVIKGKPVRIMWSQRDPSLR 99
>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 = 109 bits (275), Expect = 1e-30
Identities = 40/165 (24%), Positives = 76/165 (46%), Gaps = 19/165 (11%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
K+FIG +N T+ + +R F KYG V + ++K+ +GF+ E +K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK- 63
Query: 89 LNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV- 147
I++ K + + A R + T K+FVG + + R E E F +GT+++ ++
Sbjct: 64 -TQHILDGKVIDPKRAIPRDEQD-KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLML 121
Query: 148 -------RNYGFVHIDSPDINKCIKELNGMMVDGKPMKVQISTSR 185
R +GFV DS D + + + + ++++ + R
Sbjct: 122 DKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166
Score = 59.5 bits (145), Expect = 1e-11
Identities = 16/91 (17%), Positives = 38/91 (41%), Gaps = 9/91 (9%)
Query: 25 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHM 76
R +P T KIF+G + P + F ++G +++ ++ + +GFV
Sbjct: 77 RAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
Query: 77 ENDEEGRTAIKELNGQIVNEKPLKIEAATSR 107
++ + + ++ ++I+ A R
Sbjct: 137 DSADAVDRVC-QNKFIDFKDRKIEIKRAEPR 166
Score = 57.5 bits (140), Expect = 8e-11
Identities = 22/86 (25%), Positives = 45/86 (52%), Gaps = 11/86 (12%)
Query: 114 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCI 164
+ K+F+G L+ +T +RE F YGTV + I+++ +GF+ + P +++ +
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 165 KELNGMMVDGKPMKVQISTSRVRQRP 190
K + ++DGK + + + R Q
Sbjct: 63 KTQH--ILDGKVIDPKRAIPRDEQDK 86
>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 = 105 bits (264), Expect = 6e-30
Identities = 36/87 (41%), Positives = 50/87 (57%), Gaps = 1/87 (1%)
Query: 106 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCI 164
S +TK+ VGN+S E+R F YG V+ECDIV++Y FVH++ D + I
Sbjct: 2 SSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAI 61
Query: 165 KELNGMMVDGKPMKVQISTSRVRQRPG 191
+ L+ GK M VQ+STSR+R G
Sbjct: 62 RGLDNTEFQGKRMHVQLSTSRLRTASG 88
Score = 93.8 bits (234), Expect = 2e-25
Identities = 31/82 (37%), Positives = 50/82 (60%)
Query: 29 GFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKE 88
G S + K+ +GN++P + + +R FE+YG V+ECD+VK+Y FVHME E+ AI+
Sbjct: 4 GSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRG 63
Query: 89 LNGQIVNEKPLKIEAATSRKGP 110
L+ K + ++ +TSR
Sbjct: 64 LDNTEFQGKRMHVQLSTSRLRT 85
>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 = 106 bits (267), Expect = 3e-29
Identities = 43/176 (24%), Positives = 78/176 (44%), Gaps = 22/176 (12%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
K+FIG ++ T+ E +R FE++G + +C V+++ +GFV EE A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 89 LNGQIVNEKPLKIEAATSRKGPNTP-----TTKVFVGNLSDNTRAPEVRELFVPYGTVVE 143
V+ + ++ + A SR+ P K+FVG + ++T +R+ F YG +
Sbjct: 75 -RPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 133
Query: 144 CDIV--------RNYGFVHIDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+I+ R + FV D D I V+G +V+ + S+
Sbjct: 134 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASA 189
Score = 58.8 bits (143), Expect = 3e-11
Identities = 17/97 (17%), Positives = 41/97 (42%), Gaps = 9/97 (9%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMEND 79
+ + KIF+G + T +R FE+YGK+ +++ + + FV ++
Sbjct: 97 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 156
Query: 80 EEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTK 116
+ + + VN ++ A S++ + ++
Sbjct: 157 DSVDKIVIQ-KYHTVNGHNCEVRKALSKQEMASASSS 192
Score = 53.5 bits (129), Expect = 3e-09
Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 10/87 (11%)
Query: 114 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-INKCI 164
K+F+G LS T +R F +GT+ +C ++R+ +GFV + + ++ +
Sbjct: 13 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72
Query: 165 KELNGMMVDGKPMKVQISTSRVRQRPG 191
VDG+ ++ + + SR +
Sbjct: 73 NA-RPHKVDGRVVEPKRAVSREDSQRP 98
>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 = 101 bits (253), Expect = 4e-28
Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 2/104 (1%)
Query: 90 NGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVR 148
+G L+ T++ P + ++VF+GNL+ + +V +F YG V C + +
Sbjct: 3 SGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK 62
Query: 149 NYGFVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
Y FV + + NG ++ G+ + + ++ R G
Sbjct: 63 GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEPKPDRSG 106
Score = 82.4 bits (204), Expect = 7e-21
Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 37 KIFIGNVNP-GTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQIVN 95
++FIGN+N + +F KYG+V C V K Y FV N+ R A+ NG+++
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLA 88
Query: 96 EKPLKIEAATSRKGPNT 112
+ L I A K +
Sbjct: 89 GQTLDINMAGEPKPDRS 105
>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 = 99 bits (250), Expect = 7e-28
Identities = 37/84 (44%), Positives = 58/84 (69%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELN 90
SS T+KIF+GNV+ + + +R LFE+ G+V+ECDVVK+Y FVHME + + + AI +LN
Sbjct: 5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLN 64
Query: 91 GQIVNEKPLKIEAATSRKGPNTPT 114
G+ V K + +E +T + + P+
Sbjct: 65 GKEVKGKRINVELSTKGQKKSGPS 88
Score = 95.7 bits (239), Expect = 3e-26
Identities = 34/85 (40%), Positives = 52/85 (61%), Gaps = 2/85 (2%)
Query: 108 KGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKE 166
G + T K+FVGN+S + E+R LF G V+ECD+V++Y FVH++ D I +
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQ 62
Query: 167 LNGMMVDGKPMKVQISTSRVRQRPG 191
LNG V GK + V++ST +++ G
Sbjct: 63 LNGKEVKGKRINVELSTKG-QKKSG 86
>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 = 97.3 bits (242), Expect = 2e-25
Identities = 32/198 (16%), Positives = 72/198 (36%), Gaps = 44/198 (22%)
Query: 33 VGTFKIFIGNVNP-GTSVELIRPLFEKYGKVVECDVVKN---YGFVHMENDEEGRTAIKE 88
+G + + N+NP + + + LF YG V ++ N V M + + + A+
Sbjct: 1 MGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSH 60
Query: 89 LNGQIVNEKPLKIEAATSRKGP----------------------------------NTPT 114
LNG ++ KP++I + + P+
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----RNYGFVHIDSPDI-NKCIKELNG 169
+ + N+ + +++ LF G VV+ R + + S + + + +L+
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHN 180
Query: 170 -MMVDGKPMKVQISTSRV 186
+ + ++V S S +
Sbjct: 181 HDLGENHHLRVSFSKSTI 198
Score = 55.3 bits (133), Expect = 6e-10
Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 5/82 (6%)
Query: 114 TTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKELN 168
+ + V NL+ + + LF YG V I+ N V + + LN
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLN 62
Query: 169 GMMVDGKPMKVQISTSRVRQRP 190
G + GKP+++ +S + Q P
Sbjct: 63 GHKLHGKPIRITLSKHQNVQLP 84
>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 = 93.4 bits (233), Expect = 2e-25
Identities = 29/83 (34%), Positives = 46/83 (55%), Gaps = 1/83 (1%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELN 168
++ K+F+GNL E+R LF YG V+ECDI++NYGFVHI+ I+ L+
Sbjct: 4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLH 63
Query: 169 GMMVDGKPMKVQISTSRVRQRPG 191
+ G + V+ S ++ + G
Sbjct: 64 HYKLHGVNINVEASKNKSKASSG 86
Score = 92.3 bits (230), Expect = 7e-25
Identities = 34/86 (39%), Positives = 56/86 (65%), Gaps = 1/86 (1%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELN 90
S G K+FIGN+ + + IR LFE+YGKV+ECD++KNYGFVH+E+ AI+ L+
Sbjct: 4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLH 63
Query: 91 GQIVNEKPLKIEAATSR-KGPNTPTT 115
++ + +EA+ ++ K + P++
Sbjct: 64 HYKLHGVNINVEASKNKSKASSGPSS 89
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 90.0 bits (224), Expect = 6e-24
Identities = 22/81 (27%), Positives = 45/81 (55%), Gaps = 2/81 (2%)
Query: 113 PTTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINKCIKELNGM 170
P +++F+GNL N ++ +F PYG +++ +I +GF+ D+P + I+ +
Sbjct: 9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQE 68
Query: 171 MVDGKPMKVQISTSRVRQRPG 191
M GK + +++S+S R +
Sbjct: 69 MNFGKKLILEVSSSNARPQFD 89
Score = 81.9 bits (203), Expect = 8e-21
Identities = 20/75 (26%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 37 KIFIGNVNP-GTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQIVN 95
++FIGN+ S E + +F YG +++ ++ +GF+ +N + R AI+ + ++
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNF 71
Query: 96 EKPLKIEAATSRKGP 110
K L +E ++S P
Sbjct: 72 GKKLILEVSSSNARP 86
>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 = 90.0 bits (224), Expect = 1e-23
Identities = 29/108 (26%), Positives = 50/108 (46%), Gaps = 13/108 (12%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFVHMENDEEGRTA 85
+G+ IFI N++ + + F +G ++ C VV K YGFVH E E A
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERA 61
Query: 86 IKELNGQIVNEKPLKIEAATSRK-------GPNTPTTKVFVGNLSDNT 126
I+++NG ++N++ + + SRK T V++ N +
Sbjct: 62 IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGS 109
Score = 69.6 bits (171), Expect = 7e-16
Identities = 20/85 (23%), Positives = 45/85 (52%), Gaps = 8/85 (9%)
Query: 114 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFVHIDSPDI-NKCIKE 166
+ +F+ NL + + + F +G ++ C +V + YGFVH ++ + + I++
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 64
Query: 167 LNGMMVDGKPMKVQISTSRVRQRPG 191
+NGM+++ + + V SR ++R
Sbjct: 65 MNGMLLNDRKVFVGRFKSR-KEREA 88
>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 = 91.6 bits (227), Expect = 4e-23
Identities = 34/205 (16%), Positives = 76/205 (37%), Gaps = 44/205 (21%)
Query: 26 NMPGFSSVGTFKIFIGNVNPGT-SVELIRPLFEKYGKVVECDVVKN---YGFVHMENDEE 81
+PG + G + + N+NP + + + LF YG V ++ N V M + +
Sbjct: 25 AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQ 84
Query: 82 GRTAIKELNGQIVNEKPLKIE----------------------------------AATSR 107
+ A+ LNG ++ KP++I + +
Sbjct: 85 AQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF 144
Query: 108 KGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----RNYGFVHIDSPDI-NK 162
+ P+ + + N+ + +++ LF G VV+ R + + S + +
Sbjct: 145 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQ 204
Query: 163 CIKELNG-MMVDGKPMKVQISTSRV 186
+ +L+ + + ++V S S +
Sbjct: 205 ALIDLHNHDLGENHHLRVSFSKSTI 229
Score = 53.1 bits (127), Expect = 7e-09
Identities = 20/86 (23%), Positives = 34/86 (39%), Gaps = 5/86 (5%)
Query: 110 PNTPTTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCI 164
+ + V NL+ + + LF YG V I+ N V + +
Sbjct: 30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAM 89
Query: 165 KELNGMMVDGKPMKVQISTSRVRQRP 190
LNG + GKP+++ +S + Q P
Sbjct: 90 SHLNGHKLHGKPIRITLSKHQNVQLP 115
>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 = 86.2 bits (214), Expect = 2e-22
Identities = 21/87 (24%), Positives = 46/87 (52%), Gaps = 2/87 (2%)
Query: 103 AATSRKGPNTPTTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DI 160
++ + +++F+GNL N ++ +F PYG +++ +I +GF+ D+P +
Sbjct: 11 SSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSV 70
Query: 161 NKCIKELNGMMVDGKPMKVQISTSRVR 187
I+ + M GK + +++S+S R
Sbjct: 71 RDAIEXESQEMNFGKKLILEVSSSNAR 97
Score = 80.4 bits (199), Expect = 3e-20
Identities = 22/89 (24%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 21 NISCRNMPGFSSVGTFKIFIGNVNPGT-SVELIRPLFEKYGKVVECDVVKNYGFVHMEND 79
+ S +P S + + ++FIGN+ S E + +F YG +++ ++ +GF+ +N
Sbjct: 9 HHSSGLVPRGSHMKS-RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNP 67
Query: 80 EEGRTAIKELNGQIVNEKPLKIEAATSRK 108
+ R AI+ + ++ K L +E ++S
Sbjct: 68 QSVRDAIEXESQEMNFGKKLILEVSSSNA 96
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 82.0 bits (203), Expect = 9e-21
Identities = 20/96 (20%), Positives = 42/96 (43%), Gaps = 1/96 (1%)
Query: 95 NEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVH 154
+ + R+ T++FV + + E+ E+F P+G + E I+ + FV
Sbjct: 12 SGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVE 71
Query: 155 IDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQR 189
+ K I+E++G +P++V S ++
Sbjct: 72 FEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAKRY 107
Score = 77.0 bits (190), Expect = 9e-19
Identities = 14/72 (19%), Positives = 32/72 (44%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQIVNE 96
++F+ + +F +G + E ++ + FV E E AI+E++G+
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFAN 92
Query: 97 KPLKIEAATSRK 108
+PL++ +
Sbjct: 93 QPLEVVYSKLPA 104
>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 = 80.8 bits (200), Expect = 3e-20
Identities = 17/88 (19%), Positives = 41/88 (46%), Gaps = 1/88 (1%)
Query: 104 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSP-DINK 162
+S +FV NL++ + + F +G + +++Y F+H D K
Sbjct: 1 GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVK 60
Query: 163 CIKELNGMMVDGKPMKVQISTSRVRQRP 190
++E+NG ++G+ +++ + ++R
Sbjct: 61 AMEEMNGKDLEGENIEIVFAKPPDQKRK 88
Score = 80.0 bits (198), Expect = 4e-20
Identities = 16/71 (22%), Positives = 38/71 (53%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQIVNE 96
+F+ N+ + E++ F ++GK+ +K+Y F+H + + A++E+NG+ +
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEG 72
Query: 97 KPLKIEAATSR 107
+ ++I A
Sbjct: 73 ENIEIVFAKPP 83
>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 = 80.4 bits (199), Expect = 4e-20
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKELNGQIV 94
++F+GN+ P + E +R LFEKYGK E + K +GF+ +E A EL+ +
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPL 76
Query: 95 NEKPLKIEAATSRKGPNT 112
K L++ A +
Sbjct: 77 RGKQLRVRFACHSASLTS 94
Score = 80.0 bits (198), Expect = 4e-20
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 5/94 (5%)
Query: 103 AATSRKGPNTPT--TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP 158
++ S G T T +++FVGNL + E+R+LF YG E I + +GF+ +++
Sbjct: 2 SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETR 61
Query: 159 -DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
EL+ M + GK ++V+ + G
Sbjct: 62 TLAEIAKVELDNMPLRGKQLRVRFACHSASLTSG 95
>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 = 79.8 bits (197), Expect = 5e-20
Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 5/86 (5%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYG-KVVECDVVKNYGFVHMENDEEGRTAIKELN 90
S G+ I + N+ ++ + + L + Y K D K FV + N E+ + AI+ +
Sbjct: 2 SSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFH 61
Query: 91 GQIVNEKPLKIEAATSRK----GPNT 112
K L ++ + GP++
Sbjct: 62 QYSFRGKDLIVQLQPTDALLCSGPSS 87
Score = 74.8 bits (184), Expect = 3e-18
Identities = 16/80 (20%), Positives = 31/80 (38%), Gaps = 2/80 (2%)
Query: 114 TTKVFVGNLSDNTRAPEVRELFVPYG-TVVECDIVRNYGFVHIDSPDI-NKCIKELNGMM 171
++ + V NL ++ EV +L Y D + FV + + + I+ +
Sbjct: 5 SSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYS 64
Query: 172 VDGKPMKVQISTSRVRQRPG 191
GK + VQ+ + G
Sbjct: 65 FRGKDLIVQLQPTDALLCSG 84
>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 = 79.2 bits (196), Expect = 8e-20
Identities = 21/81 (25%), Positives = 43/81 (53%), Gaps = 3/81 (3%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKE 88
S G K++IGN++P + + +R LF + V+ Y FV + AI+
Sbjct: 4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63
Query: 89 LNGQI-VNEKPLKIEAATSRK 108
L+G++ ++ K ++++ + S+K
Sbjct: 64 LSGKVELHGKIMEVDYSVSKK 84
Score = 73.1 bits (180), Expect = 2e-17
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 112 TPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP-DINKCIKELN 168
+ K+++GNLS A ++R+LF + ++ Y FV + I+ L+
Sbjct: 6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETLS 65
Query: 169 GMM-VDGKPMKVQISTSRVRQRPG 191
G + + GK M+V S S+ + G
Sbjct: 66 GKVELHGKIMEVDYSVSKKLRSSG 89
>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 = 78.8 bits (195), Expect = 1e-19
Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 12/93 (12%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-----------YGFVHIDSP- 158
++ ++ +F+ NL+ +T ++ +F G + C I + +GFV P
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 159 DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
K +K+L G VDG ++V+IS + G
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRISERATKPASG 94
Score = 76.1 bits (188), Expect = 1e-18
Identities = 24/96 (25%), Positives = 45/96 (46%), Gaps = 11/96 (11%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-----------YGFVHMENDE 80
S G+ +FI N+N T+ E ++ +F K G + C + K +GFV + E
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 81 EGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTK 116
+ + A+K+L G V+ L++ + P + +
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRISERATKPASGPSS 97
>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 = 79.9 bits (197), Expect = 2e-19
Identities = 27/126 (21%), Positives = 48/126 (38%), Gaps = 4/126 (3%)
Query: 66 DVVKNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDN 125
K + +N +G + + + KV+VGNL +N
Sbjct: 25 TAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNN 84
Query: 126 TRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKELNGMMVDGKPMKVQI 181
E+ F YG + + RN + FV + P D ++EL+G + G ++V++
Sbjct: 85 GNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL 144
Query: 182 STSRVR 187
S R
Sbjct: 145 SNGEKR 150
Score = 69.5 bits (170), Expect = 2e-15
Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 3/87 (3%)
Query: 25 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---YGFVHMENDEE 81
+M S K+++GN+ + + F YG + V +N + FV E+ +
Sbjct: 63 HHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRD 122
Query: 82 GRTAIKELNGQIVNEKPLKIEAATSRK 108
A++EL+G+ + +++E + K
Sbjct: 123 AADAVRELDGRTLCGCRVRVELSNGEK 149
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 78.5 bits (194), Expect = 3e-19
Identities = 23/93 (24%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 100 KIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGF 152
++ K+ V NL +++ELF +GT+ + +
Sbjct: 15 LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTAD 74
Query: 153 VHIDSP-DINKCIKELNGMMVDGKPMKVQISTS 184
VH + D K +K+ NG+ +DG+PM +Q+ TS
Sbjct: 75 VHFERKADALKAMKQYNGVPLDGRPMNIQLVTS 107
Score = 73.9 bits (182), Expect = 1e-17
Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMENDEEGRTAIKEL 89
K+ + N++ G S I+ LF ++G + + V VH E + A+K+
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 90
Query: 90 NGQIVNEKPLKIEAATS 106
NG ++ +P+ I+ TS
Sbjct: 91 NGVPLDGRPMNIQLVTS 107
>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 = 77.7 bits (192), Expect = 4e-19
Identities = 21/97 (21%), Positives = 53/97 (54%), Gaps = 7/97 (7%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------RNYGFVHI 155
++ + ++ V N+ R P++R++F +G +++ +I+ + +GFV
Sbjct: 3 SGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTF 62
Query: 156 DSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
++ D ++ ++L+G +V+G+ ++V +T+RV G
Sbjct: 63 ENSADADRAREKLHGTVVEGRKIEVNNATARVMTNSG 99
Score = 74.2 bits (183), Expect = 9e-18
Identities = 19/81 (23%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN------YGFVHMENDEEGRTAIKELN 90
++ + N+ +R +F ++GK+++ +++ N +GFV EN + A ++L+
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLH 76
Query: 91 GQIVNEKPLKIEAATSRKGPN 111
G +V + +++ AT+R N
Sbjct: 77 GTVVEGRKIEVNNATARVMTN 97
>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 = 78.2 bits (193), Expect = 5e-19
Identities = 21/97 (21%), Positives = 41/97 (42%), Gaps = 8/97 (8%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVH 154
++ K+ V NL +++ELF +GT+ + + VH
Sbjct: 23 DSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVH 82
Query: 155 IDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRP 190
+ D K +K+ G+ +DG+PM +Q+ S++
Sbjct: 83 FERRADALKAMKQYKGVPLDGRPMDIQLVASQIDLEH 119
Score = 72.4 bits (178), Expect = 7e-17
Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 7/78 (8%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMENDEEGRTAIKEL 89
K+ + N++ G S I+ LF ++G + + V VH E + A+K+
Sbjct: 37 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQY 96
Query: 90 NGQIVNEKPLKIEAATSR 107
G ++ +P+ I+ S+
Sbjct: 97 KGVPLDGRPMDIQLVASQ 114
>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 = 76.4 bits (189), Expect = 9e-19
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 8/81 (9%)
Query: 35 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAI 86
TF +F+G++N E +R F+ + + V+ + YGFV + ++ + A+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 87 KELNGQIVNEKPLKIEAATSR 107
+ GQ +N +PL+I A
Sbjct: 61 DSMQGQDLNGRPLRINWAAKL 81
Score = 69.4 bits (171), Expect = 4e-16
Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 9/81 (11%)
Query: 114 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCI 164
T +FVG+L+ N +R F + + + ++ R YGFV S D +
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 165 KELNGMMVDGKPMKVQISTSR 185
+ G ++G+P+++ +
Sbjct: 61 DSMQGQDLNGRPLRINWAAKL 81
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 96
Score = 76.1 bits (188), Expect = 1e-18
Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 9/90 (10%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV---------KNYGFVHMENDEEG 82
S G+ IFIGN++P +L+ F +G +++ + K Y F++ + +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 83 RTAIKELNGQIVNEKPLKIEAATSRKGPNT 112
AI+ +NGQ + +P+ + A + +
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYAFKKDSKGS 91
Score = 68.0 bits (167), Expect = 2e-15
Identities = 15/91 (16%), Positives = 40/91 (43%), Gaps = 10/91 (10%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV---------RNYGFVHIDSP-DI 160
++ ++ +F+GNL + + F +G +++ + + Y F++ S
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 161 NKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+ I+ +NG + +P+ V + + + G
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYAFKKDSKGSG 92
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 76.2 bits (188), Expect = 2e-18
Identities = 21/98 (21%), Positives = 52/98 (53%), Gaps = 7/98 (7%)
Query: 96 EKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------RN 149
L + + ++ V N+ R P++R++F +G +++ +I+ +
Sbjct: 11 SSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKG 70
Query: 150 YGFVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSRV 186
+GFV ++ D ++ ++L+G +V+G+ ++V +T+RV
Sbjct: 71 FGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV 108
Score = 72.4 bits (178), Expect = 6e-17
Identities = 19/89 (21%), Positives = 46/89 (51%), Gaps = 6/89 (6%)
Query: 25 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFVHMEN 78
+M + ++ + N+ +R +F ++GK+++ +++ K +GFV EN
Sbjct: 19 SHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFEN 78
Query: 79 DEEGRTAIKELNGQIVNEKPLKIEAATSR 107
+ A ++L+G +V + +++ AT+R
Sbjct: 79 SADADRAREKLHGTVVEGRKIEVNNATAR 107
>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 = 75.8 bits (187), Expect = 2e-18
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 3/83 (3%)
Query: 112 TPTTKVFVGNLSDNTRAPEVRELFVPYG--TVVECDIVRNYGFVHIDSP-DINKCIKELN 168
+ ++V NL +T + + F V +R+Y FVH + D + +K LN
Sbjct: 13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALN 72
Query: 169 GMMVDGKPMKVQISTSRVRQRPG 191
G ++DG P++V ++ + G
Sbjct: 73 GKVLDGSPIEVTLAKPVDKDSSG 95
Score = 70.8 bits (174), Expect = 1e-16
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYG--KVVECDVVKNYGFVHMENDEEGRTAIKELNGQIV 94
+++ N+ TS E+I F V +++Y FVH N E+ A+K LNG+++
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVL 76
Query: 95 NEKPLKIEAATSRK 108
+ P+++ A
Sbjct: 77 DGSPIEVTLAKPVD 90
>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 = 75.5 bits (186), Expect = 4e-18
Identities = 23/94 (24%), Positives = 45/94 (47%), Gaps = 8/94 (8%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEG 82
+ F +F+G+++P + E I+ F +G++ + VV K YGFV N +
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDA 70
Query: 83 RTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTK 116
AI+++ GQ + + ++ AT + T +
Sbjct: 71 ENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYE 104
Score = 72.0 bits (177), Expect = 9e-17
Identities = 20/97 (20%), Positives = 43/97 (44%), Gaps = 9/97 (9%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 154
++ +K + VFVG+LS +++ F P+G + + +V + YGFV
Sbjct: 4 GSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63
Query: 155 IDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRP 190
+ D I+++ G + G+ ++ +T +
Sbjct: 64 FFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPK 100
>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 = 75.0 bits (185), Expect = 4e-18
Identities = 17/86 (19%), Positives = 38/86 (44%), Gaps = 3/86 (3%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP-DINKCIK 165
G PTT+++VG L NT + F +G++ D V ++ ++ +S
Sbjct: 12 GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACA 71
Query: 166 ELNGMMVDGKPMKVQISTSRVRQRPG 191
++ G + G ++++ ++ G
Sbjct: 72 KMRGFPLGGPDRRLRVDFAKSGPSSG 97
Score = 68.4 bits (168), Expect = 1e-15
Identities = 14/77 (18%), Positives = 40/77 (51%), Gaps = 4/77 (5%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKELNGQIV 94
++++G + P TS+ + F+++G + D V ++ ++ E+ + + A ++ G +
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPL 78
Query: 95 N--EKPLKIEAATSRKG 109
++ L+++ A S
Sbjct: 79 GGPDRRLRVDFAKSGPS 95
>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 = 75.0 bits (185), Expect = 5e-18
Identities = 17/98 (17%), Positives = 37/98 (37%), Gaps = 9/98 (9%)
Query: 25 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHM 76
+ P + I + N++ T ++ LF +G + + K+ + F+
Sbjct: 5 SSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Query: 77 ENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPT 114
E+ AI ++G + L +E A + P+
Sbjct: 65 HRREDAARAIAGVSGFGYDHLILNVEWAKPST-NSGPS 101
Score = 70.7 bits (174), Expect = 2e-16
Identities = 21/100 (21%), Positives = 43/100 (43%), Gaps = 12/100 (12%)
Query: 103 AATSRKGPNT---PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YG 151
++ GPN + V NLS++TR +++ELF P+G++ + ++ +
Sbjct: 1 GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60
Query: 152 FVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRP 190
F+ D + I ++G D + V+ + P
Sbjct: 61 FISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGP 100
>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 = 74.2 bits (183), Expect = 7e-18
Identities = 23/91 (25%), Positives = 43/91 (47%), Gaps = 9/91 (9%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 154
++ + P + V LS T ++RE+F YG + + IV R + FV+
Sbjct: 4 GSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 63
Query: 155 IDSP-DINKCIKELNGMMVDGKPMKVQISTS 184
++ D + + NGM +DG+ ++V +S
Sbjct: 64 FENVDDAKEAKERANGMELDGRRIRVSGPSS 94
Score = 68.8 bits (169), Expect = 1e-15
Identities = 15/84 (17%), Positives = 40/84 (47%), Gaps = 8/84 (9%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEG 82
+ + + ++ T+ +R +F KYG + + +V + + FV+ EN ++
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 83 RTAIKELNGQIVNEKPLKIEAATS 106
+ A + NG ++ + +++ +S
Sbjct: 71 KEAKERANGMELDGRRIRVSGPSS 94
>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition
motif, RRM, RNA binding domain, RBD, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 74.3 bits (183), Expect = 1e-17
Identities = 20/96 (20%), Positives = 39/96 (40%), Gaps = 8/96 (8%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVH 154
++ + VFV NL +++E+F G VV DI+ + G V
Sbjct: 3 SGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVT 62
Query: 155 IDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQR 189
+ + + I NG ++ +PM V++ + +
Sbjct: 63 FEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKG 98
Score = 71.2 bits (175), Expect = 2e-16
Identities = 18/91 (19%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 25 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHME 77
+G+ +F+ N++ + ++ +F G VV D++ + G V E
Sbjct: 6 SGALQAGRLGS-TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFE 64
Query: 78 NDEEGRTAIKELNGQIVNEKPLKIEAATSRK 108
E AI NGQ++ ++P+ ++
Sbjct: 65 QSIEAVQAISMFNGQLLFDRPMHVKMDERAL 95
>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 = 74.2 bits (183), Expect = 1e-17
Identities = 20/106 (18%), Positives = 42/106 (39%), Gaps = 10/106 (9%)
Query: 95 NEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------- 147
E+ KI +S P P +++ NLS ++ LF + I
Sbjct: 7 GEEIRKIPMFSSYN-PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGR 65
Query: 148 -RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
R F+ + +I + + +NG + GK + ++ ++ ++ G
Sbjct: 66 MRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQRSSG 111
Score = 70.0 bits (172), Expect = 4e-16
Identities = 20/102 (19%), Positives = 40/102 (39%), Gaps = 13/102 (12%)
Query: 25 RNMPGFSSVG----TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYG 72
R +P FSS +++ N++P + + LF ++ + + +
Sbjct: 11 RKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQA 70
Query: 73 FVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPT 114
F+ N E A+ +NG + K L IE ++K +
Sbjct: 71 FITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKK-QRSSG 111
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 76.0 bits (187), Expect = 1e-17
Identities = 21/95 (22%), Positives = 42/95 (44%), Gaps = 8/95 (8%)
Query: 100 KIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGF 152
++ K+ V NL +++ELF +GT+ + + +
Sbjct: 74 LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTAD 133
Query: 153 VHIDSP-DINKCIKELNGMMVDGKPMKVQISTSRV 186
VH + D K +K+ G+ +DG+PM +Q+ S++
Sbjct: 134 VHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 168
Score = 68.3 bits (167), Expect = 8e-15
Identities = 19/93 (20%), Positives = 38/93 (40%), Gaps = 7/93 (7%)
Query: 25 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHME 77
G K+ + N++ G S I+ LF ++G + + V + VH E
Sbjct: 78 GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFE 137
Query: 78 NDEEGRTAIKELNGQIVNEKPLKIEAATSRKGP 110
+ A+K+ G ++ +P+ I+ S+
Sbjct: 138 RRADALKAMKQYKGVPLDGRPMDIQLVASQIDL 170
>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 = 73.9 bits (182), Expect = 1e-17
Identities = 21/93 (22%), Positives = 40/93 (43%), Gaps = 7/93 (7%)
Query: 106 SRKGPNTPT-TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-----RNYGFVHIDSP- 158
+GP +++VGNL + R ++ ++F YG + + D+ + FV + P
Sbjct: 13 VIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPR 72
Query: 159 DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
D + +G DG ++V+ S G
Sbjct: 73 DAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSG 105
Score = 67.7 bits (166), Expect = 3e-15
Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-----KNYGFVHMENDEEGRTAIKELNG 91
+I++GN+ P + I +F KYG + + D+ + FV E+ + A+ +G
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 92 QIVNEKPLKIEAATSRKGPN 111
+ L++E S +G
Sbjct: 84 YDYDGYRLRVEFPRSGRGTG 103
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 74.0 bits (182), Expect = 2e-17
Identities = 23/108 (21%), Positives = 43/108 (39%), Gaps = 13/108 (12%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-D 159
G P +V L+DN R ++++ YG V E +I+ + V S
Sbjct: 2 GQ-IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRG 60
Query: 160 INKCIKELNGMMVDGKPMKVQISTSRVRQRPGVDEVVIGQ---KSVPV 204
+ +K L+ V G + Q+ ++ + +V G ++VP
Sbjct: 61 AKETVKNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYTPQTVPT 108
Score = 63.6 bits (155), Expect = 1e-13
Identities = 10/80 (12%), Positives = 28/80 (35%), Gaps = 8/80 (10%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
++ +N ++ + KYG+V E +++ + V + + +K
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67
Query: 89 LNGQIVNEKPLKIEAATSRK 108
L+ V + + +
Sbjct: 68 LHLTSVMGNIIHAQLDIKGQ 87
>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 = 73.4 bits (181), Expect = 2e-17
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFVHMENDEEGRTAIKEL 89
+++ N++ G E +R F +G + V+ K +GFV + EE A+ E+
Sbjct: 16 VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 90 NGQIVNEKPLKIEAATSR 107
NG+IV KPL + A +
Sbjct: 76 NGRIVATKPLYVALAQRK 93
Score = 71.9 bits (177), Expect = 6e-17
Identities = 23/96 (23%), Positives = 45/96 (46%), Gaps = 7/96 (7%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFVHID 156
++ + ++V NL D +R+ F P+GT+ ++ +GFV
Sbjct: 4 GSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFS 63
Query: 157 SP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
SP + K + E+NG +V KP+ V ++ + ++ G
Sbjct: 64 SPEEATKAVTEMNGRIVATKPLYVALAQRKEERQSG 99
>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 = 73.5 bits (181), Expect = 2e-17
Identities = 22/83 (26%), Positives = 47/83 (56%), Gaps = 7/83 (8%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIKE 88
K+FIG +N T+ ++++ +F K+G + E ++K+ + F+ EN + + A K+
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKD 67
Query: 89 LNGQIVNEKPLKIEAATSRKGPN 111
+NG+ ++ K +K+E A +
Sbjct: 68 MNGKSLHGKAIKVEQAKKPSFQS 90
Score = 71.6 bits (176), Expect = 1e-16
Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 113 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSP-DINKCI 164
K+F+G L+ T ++ +F +G + E ++ R + F+ ++P D
Sbjct: 6 HPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAA 65
Query: 165 KELNGMMVDGKPMKVQISTSRVRQRPG 191
K++NG + GK +KV+ + Q G
Sbjct: 66 KDMNGKSLHGKAIKVEQAKKPSFQSGG 92
>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 = 72.2 bits (178), Expect = 3e-17
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIK 87
F +F+G+++P + I F +G++ + VV K YGFV N + AI+
Sbjct: 7 FHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
Query: 88 ELNGQIVNEKPLKIEAATSR 107
++ GQ + + ++ AT +
Sbjct: 67 QMGGQWLGGRQIRTNWATRK 86
Score = 71.0 bits (175), Expect = 8e-17
Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 9/86 (10%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-D 159
GP VFVG+LS + F P+G + + +V + YGFV + D
Sbjct: 1 GPLGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60
Query: 160 INKCIKELNGMMVDGKPMKVQISTSR 185
I+++ G + G+ ++ +T +
Sbjct: 61 AENAIQQMGGQWLGGRQIRTNWATRK 86
>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 = 72.6 bits (179), Expect = 3e-17
Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 8/86 (9%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEG 82
S G+ ++F+ N++ +S E + LF YG + E + + FV E
Sbjct: 4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63
Query: 83 RTAIKELNGQIVNEKPLKIEAATSRK 108
A E++GQ+ + L + +T +K
Sbjct: 64 VKAYAEVDGQVFQGRMLHVLPSTIKK 89
Score = 65.7 bits (161), Expect = 2e-14
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 9/85 (10%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DI 160
++ + ++FV NLS + ++ +LF YG + E + + FV P
Sbjct: 4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63
Query: 161 NKCIKELNGMMVDGKPMKVQISTSR 185
K E++G + G+ + V ST +
Sbjct: 64 VKAYAEVDGQVFQGRMLHVLPSTIK 88
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 72.2 bits (178), Expect = 4e-17
Identities = 20/90 (22%), Positives = 38/90 (42%), Gaps = 7/90 (7%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------YGFVHIDSP-DIN 161
++ ++FV NL + +++ F G V+ DI G V +SP
Sbjct: 3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAE 62
Query: 162 KCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+ + +NGM + G+ + V+I + G
Sbjct: 63 RACRMMNGMKLSGREIDVRIDRNASGPSSG 92
Score = 71.8 bits (177), Expect = 6e-17
Identities = 19/88 (21%), Positives = 41/88 (46%), Gaps = 6/88 (6%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFVHMENDEEGRT 84
S G +IF+ N+ + ++++ F + G V+ D+ K G V E+ E
Sbjct: 4 GSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAER 63
Query: 85 AIKELNGQIVNEKPLKIEAATSRKGPNT 112
A + +NG ++ + + + + GP++
Sbjct: 64 ACRMMNGMKLSGREIDVRIDRNASGPSS 91
>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 = 72.6 bits (179), Expect = 4e-17
Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 10/97 (10%)
Query: 105 TSRKGPNT-PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHI 155
+ GP+ + V NL+ T +R +F YG V + I R + FV
Sbjct: 3 SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62
Query: 156 DSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
D ++G +DG+ ++VQ++ R G
Sbjct: 63 HDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSG 99
Score = 72.3 bits (178), Expect = 5e-17
Identities = 19/89 (21%), Positives = 42/89 (47%), Gaps = 9/89 (10%)
Query: 34 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTA 85
G + + N+ TS + +R +FEKYG+V + + + + FV + + + A
Sbjct: 12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71
Query: 86 IKELNGQIVNEKPLKI-EAATSRKGPNTP 113
++G ++ + L++ A R+ + P
Sbjct: 72 EAAMDGAELDGRELRVQVARYGRRDLSGP 100
>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 = 74.7 bits (183), Expect = 5e-17
Identities = 20/191 (10%), Positives = 47/191 (24%), Gaps = 49/191 (25%)
Query: 38 IFIGNVNP-GTSVELIRPLFEKYGKVVECDVVKN---YGFVHMENDEEGRTAIKELNGQI 93
+ + ++ + + + +F YG V + +K+ V M + AI LN
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNF 66
Query: 94 VNEKPLKIE------------------------------------AATSRKGPNTPTTKV 117
+ + + + ++ P+ +
Sbjct: 67 MFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVL 126
Query: 118 FVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDI-NKCIKELN 168
N E+ G + + G + DS + + LN
Sbjct: 127 HFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLN 186
Query: 169 GMMVDGKPMKV 179
+
Sbjct: 187 HYQMKNPNGPY 197
Score = 52.8 bits (126), Expect = 7e-09
Identities = 7/79 (8%), Positives = 20/79 (25%), Gaps = 8/79 (10%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGR 83
+ + N + E + ++ G V + G + ++ +
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179
Query: 84 TAIKELNGQIVNEKPLKIE 102
+ LN +
Sbjct: 180 ETLGFLNHYQMKNPNGPYP 198
Score = 51.6 bits (123), Expect = 2e-08
Identities = 17/94 (18%), Positives = 32/94 (34%), Gaps = 5/94 (5%)
Query: 113 PTTKVFVGNLS-DNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKEL 167
+ + V L V +F YG V + +++ V + +++ I L
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 62
Query: 168 NGMMVDGKPMKVQISTSRVRQRPGVDEVVIGQKS 201
N + G+ M V +S + G S
Sbjct: 63 NNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCS 96
>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 = 71.9 bits (177), Expect = 5e-17
Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 8/90 (8%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHI 155
++ VFVGNL R + ELF+ G + + I +++GFV
Sbjct: 5 SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCF 64
Query: 156 DSP-DINKCIKELNGMMVDGKPMKVQISTS 184
P ++ I LNG+ + G+P+ V +S
Sbjct: 65 KHPESVSYAIALLNGIRLYGRPINVSGPSS 94
Score = 70.0 bits (172), Expect = 3e-16
Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMENDEEGRTAIKEL 89
+F+GN+ E++ LF + G + + + K++GFV ++ E AI L
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALL 77
Query: 90 NGQIVNEKPLKIEAATS 106
NG + +P+ + +S
Sbjct: 78 NGIRLYGRPINVSGPSS 94
>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 = 7e-17
Identities = 21/100 (21%), Positives = 52/100 (52%), Gaps = 8/100 (8%)
Query: 17 NNQINISCRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------- 68
++ + + N S G ++++G+++ + +++R +FE +G++ ++
Sbjct: 8 HSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRS 67
Query: 69 KNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 108
K YGF+ + E + A+++LNG + +P+K+ T R
Sbjct: 68 KGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT 107
Score = 65.0 bits (159), Expect = 3e-14
Identities = 23/91 (25%), Positives = 44/91 (48%), Gaps = 9/91 (9%)
Query: 104 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHI 155
A + + + +++VG+L N +R +F P+G + ++ + YGF+
Sbjct: 16 ANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITF 75
Query: 156 DSPDI-NKCIKELNGMMVDGKPMKVQISTSR 185
+ K +++LNG + G+PMKV T R
Sbjct: 76 SDSECAKKALEQLNGFELAGRPMKVGHVTER 106
>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 = 72.0 bits (177), Expect = 7e-17
Identities = 22/105 (20%), Positives = 41/105 (39%), Gaps = 5/105 (4%)
Query: 90 NGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-- 147
+G N K L+ E ++ P V+ G ++ +R+ F P+G ++E +
Sbjct: 3 SGSSGNTKQLRFEDVVNQSSPKN--CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE 60
Query: 148 RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+ Y FV + I +NG ++G +K G
Sbjct: 61 KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTSG 105
Score = 71.6 bits (176), Expect = 1e-16
Identities = 23/102 (22%), Positives = 40/102 (39%), Gaps = 2/102 (1%)
Query: 13 SRYSNNQINISCRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KN 70
S S N + ++ SS ++ G + G + +L+R F +G+++E V K
Sbjct: 3 SGSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG 62
Query: 71 YGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNT 112
Y FV E AI +NG + +K +
Sbjct: 63 YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDMTS 104
>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 = 71.9 bits (177), Expect = 8e-17
Identities = 26/98 (26%), Positives = 45/98 (45%), Gaps = 9/98 (9%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 154
++ G + K+FVG LS +T + ++F YG + E +V R +GFV
Sbjct: 1 GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60
Query: 155 IDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
++ D + +NG VDG+ ++V + R G
Sbjct: 61 FENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSG 98
Score = 70.3 bits (173), Expect = 2e-16
Identities = 22/79 (27%), Positives = 46/79 (58%), Gaps = 8/79 (10%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
K+F+G ++ T+ + + +F KYG++ E VVK+ +GFV EN ++ + A+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 89 LNGQIVNEKPLKIEAATSR 107
+NG+ V+ + ++++ A
Sbjct: 74 MNGKSVDGRQIRVDQAGKS 92
>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 = 72.5 bits (178), Expect = 9e-17
Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 12/93 (12%)
Query: 107 RKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP 158
+ P + V LS T ++RE+F YG + + IV R + FV+ ++
Sbjct: 39 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 98
Query: 159 -DINKCIKELNGMMVDGKPMKVQISTSRVRQRP 190
D + + NGM +DG+ ++V S ++ RP
Sbjct: 99 DDAKEAKERANGMELDGRRIRVDFSITK---RP 128
Score = 69.4 bits (170), Expect = 1e-15
Identities = 14/92 (15%), Positives = 43/92 (46%), Gaps = 8/92 (8%)
Query: 25 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHM 76
+ + + ++ T+ +R +F KYG + + +V + + FV+
Sbjct: 36 HVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 95
Query: 77 ENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 108
EN ++ + A + NG ++ + ++++ + +++
Sbjct: 96 ENVDDAKEAKERANGMELDGRRIRVDFSITKR 127
>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 = 71.6 bits (176), Expect = 1e-16
Identities = 22/99 (22%), Positives = 43/99 (43%), Gaps = 9/99 (9%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV 153
A + +F+ +L ++ ++F+P+G VV + + +GFV
Sbjct: 13 IGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFV 72
Query: 154 HIDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
D+P I+ +NG + K +KVQ+ S+ + G
Sbjct: 73 SYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKNDSKSG 111
Score = 68.9 bits (169), Expect = 1e-15
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 8/79 (10%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKE 88
+FI ++ + + +F +G VV V K +GFV +N + AI+
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 89 LNGQIVNEKPLKIEAATSR 107
+NG + K LK++ S+
Sbjct: 87 MNGFQIGMKRLKVQLKRSK 105
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 71.6 bits (176), Expect = 1e-16
Identities = 22/101 (21%), Positives = 40/101 (39%), Gaps = 9/101 (8%)
Query: 90 NGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN 149
+ AA ++ +F+ +L ++ F+P+G V+ + +
Sbjct: 16 SPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFID 75
Query: 150 --------YGFVHIDSP-DINKCIKELNGMMVDGKPMKVQI 181
+GFV D+P IK +NG V K +KVQ+
Sbjct: 76 KQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL 116
Score = 66.6 bits (163), Expect = 1e-14
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 8/77 (10%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIK 87
+FI ++ + + F +G V+ V K +GFV +N + + AIK
Sbjct: 41 CNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 88 ELNGQIVNEKPLKIEAA 104
+NG V K LK++
Sbjct: 101 AMNGFQVGTKRLKVQLK 117
>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 = 72.0 bits (177), Expect = 1e-16
Identities = 22/88 (25%), Positives = 40/88 (45%), Gaps = 8/88 (9%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGR 83
SV + +F+ V+ + E I F +YG++ + K Y V E +E +
Sbjct: 19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78
Query: 84 TAIKELNGQIVNEKPLKIEAATSRKGPN 111
A++ LNGQ + +P+ ++ R P
Sbjct: 79 AAMEGLNGQDLMGQPISVDWCFVRGPPK 106
Score = 60.1 bits (146), Expect = 4e-12
Identities = 14/100 (14%), Positives = 35/100 (35%), Gaps = 9/100 (9%)
Query: 95 NEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------- 147
+ ++ + + +FV + + ++ + F YG + +
Sbjct: 3 DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 62
Query: 148 -RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKVQISTSR 185
+ Y V ++ ++ LNG + G+P+ V R
Sbjct: 63 LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR 102
>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 = 70.7 bits (174), Expect = 2e-16
Identities = 22/96 (22%), Positives = 39/96 (40%), Gaps = 7/96 (7%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------RNYGFVHID 156
++ + ++VGNLS + + +LF G C ++ Y FV
Sbjct: 4 GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFY 63
Query: 157 SP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
D + +NG + GK +KV +T+ Q+ G
Sbjct: 64 EHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSG 99
Score = 65.3 bits (160), Expect = 2e-14
Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------KNYGFVHMENDEEGRTAIKELN 90
+++GN++ + LI LF + G C ++ Y FV + A+ +N
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMN 76
Query: 91 GQIVNEKPLKIEAATSRK 108
G+ + K +K+ AT+
Sbjct: 77 GRKILGKEVKVNWATTPS 94
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 70.4 bits (173), Expect = 3e-16
Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 7/85 (8%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGR 83
+S+ K+FI + + E + + + +G V + +V N +V EN+ +
Sbjct: 13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQAS 72
Query: 84 TAIKELNGQIVNEKPLKIEAATSRK 108
A+ +++G + E +K+ + S
Sbjct: 73 QAVMKMDGMTIKENIIKVAISNSGP 97
Score = 69.2 bits (170), Expect = 6e-16
Identities = 19/93 (20%), Positives = 40/93 (43%), Gaps = 8/93 (8%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHI 155
+ R + K+F+ L + E+ E+ +GTV + +V N +V
Sbjct: 6 SGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEY 65
Query: 156 DSP-DINKCIKELNGMMVDGKPMKVQISTSRVR 187
++ ++ + +++GM + +KV IS S
Sbjct: 66 ENESQASQAVMKMDGMTIKENIIKVAISNSGPS 98
>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 = 70.7 bits (174), Expect = 3e-16
Identities = 18/91 (19%), Positives = 33/91 (36%), Gaps = 8/91 (8%)
Query: 100 KIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGF 152
A K T +++ NL + E+ + P+G V+ I+R+ GF
Sbjct: 11 SGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGF 70
Query: 153 VHIDSPDI-NKCIKELNGMMVDGKPMKVQIS 182
++S + I NG + P +
Sbjct: 71 ARMESTEKCEAVIGHFNGKFIKTPPGVSAPT 101
Score = 66.9 bits (164), Expect = 7e-15
Identities = 13/75 (17%), Positives = 31/75 (41%), Gaps = 7/75 (9%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIKEL 89
++I N+ + + + + +G+V+ ++++ GF ME+ E+ I
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 86
Query: 90 NGQIVNEKPLKIEAA 104
NG+ + P
Sbjct: 87 NGKFIKTPPGVSAPT 101
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 70.4 bits (173), Expect = 3e-16
Identities = 14/84 (16%), Positives = 31/84 (36%), Gaps = 2/84 (2%)
Query: 26 NMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGR 83
++ + +IGN+ + + PLF+ +G +++ K F+ + E+
Sbjct: 18 HIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQAA 77
Query: 84 TAIKELNGQIVNEKPLKIEAATSR 107
I L + L+ R
Sbjct: 78 VCIVALANFPFQGRNLRTGWGKER 101
Score = 66.9 bits (164), Expect = 5e-15
Identities = 15/95 (15%), Positives = 34/95 (35%), Gaps = 5/95 (5%)
Query: 88 ELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV 147
+ G P ++ P T ++GN+ ++ LF +G +++
Sbjct: 3 QTIGLPPQVNPQAVDHIIRSAPPRV--TTAYIGNIPHFATEADLIPLFQNFGFILDFKHY 60
Query: 148 --RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKV 179
+ F+ D+ + CI L G+ ++
Sbjct: 61 PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRT 95
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 70.4 bits (173), Expect = 3e-16
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 8/87 (9%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGR 83
SV + +F+ V+ + E I F +YG++ + K Y V E +E +
Sbjct: 20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79
Query: 84 TAIKELNGQIVNEKPLKIEAATSRKGP 110
A++ LNGQ + +P+ ++ R P
Sbjct: 80 AAMEGLNGQDLMGQPISVDWCFVRGPP 106
Score = 59.2 bits (144), Expect = 5e-12
Identities = 14/100 (14%), Positives = 35/100 (35%), Gaps = 9/100 (9%)
Query: 95 NEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV------- 147
+ ++ + + +FV + + ++ + F YG + +
Sbjct: 4 DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 63
Query: 148 -RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKVQISTSR 185
+ Y V ++ ++ LNG + G+P+ V R
Sbjct: 64 LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR 103
>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 = 69.9 bits (172), Expect = 4e-16
Identities = 18/98 (18%), Positives = 39/98 (39%), Gaps = 9/98 (9%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 154
++ G T ++VG L++ + F+P+G + + I R + FV
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 155 IDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+ D I +N + G+ ++V ++ + G
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESG 98
Score = 69.2 bits (170), Expect = 6e-16
Identities = 11/83 (13%), Positives = 32/83 (38%), Gaps = 8/83 (9%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
+++G + +++ F +G + + + + + FV E E+ AI
Sbjct: 14 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 89 LNGQIVNEKPLKIEAATSRKGPN 111
+N + + +++ A +
Sbjct: 74 MNESELFGRTIRVNLAKPMRIKE 96
>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 = 69.5 bits (171), Expect = 4e-16
Identities = 23/93 (24%), Positives = 52/93 (55%), Gaps = 9/93 (9%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGR 83
S G+ +++G+++ + +++R +FE +GK+ ++ K YGF+ + E R
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 84 TAIKELNGQIVNEKPLKIEAATSRK-GPNTPTT 115
A+++LNG + +P+++ T R G + P++
Sbjct: 62 RALEQLNGFELAGRPMRVGHVTERLDGGSGPSS 94
Score = 64.1 bits (157), Expect = 5e-14
Identities = 21/90 (23%), Positives = 45/90 (50%), Gaps = 9/90 (10%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDI-N 161
++ ++ ++VG+L N +R +F P+G + ++ + YGF+ +
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 162 KCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+ +++LNG + G+PM+V T R+ G
Sbjct: 62 RALEQLNGFELAGRPMRVGHVTERLDGGSG 91
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 69.6 bits (171), Expect = 5e-16
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSP-DINKCIKELNGMM 171
KV+VGNL E+ F YG + I RN + FV + P D ++ L+G +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 172 VDGKPMKVQISTSRVRQRPG 191
+ G ++V++ST R+
Sbjct: 62 ICGSRVRVELSTGMPRRSRF 81
Score = 67.3 bits (165), Expect = 4e-15
Identities = 16/74 (21%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---YGFVHMENDEEGRTAIKELNGQI 93
K+++GN+ G + F YG + + +N + FV E+ + A++ L+G++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 94 VNEKPLKIEAATSR 107
+ +++E +T
Sbjct: 62 ICGSRVRVELSTGM 75
>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 = 71.4 bits (175), Expect = 5e-16
Identities = 15/88 (17%), Positives = 36/88 (40%), Gaps = 8/88 (9%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGR 83
SV + +F+ +++ + I+ F YG++ + K Y V E ++
Sbjct: 69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128
Query: 84 TAIKELNGQIVNEKPLKIEAATSRKGPN 111
A + LNG + + ++++ +
Sbjct: 129 AAKEALNGAEIMGQTIQVDWCFVKGPKR 156
Score = 60.6 bits (147), Expect = 5e-12
Identities = 22/145 (15%), Positives = 48/145 (33%), Gaps = 30/145 (20%)
Query: 76 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNT---------------------PT 114
E DE+G I L + + K + ++ +
Sbjct: 13 FEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEG 72
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIK 165
+FV ++ + + E++E F YG + + + Y V ++ +
Sbjct: 73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132
Query: 166 ELNGMMVDGKPMKVQISTSRVRQRP 190
LNG + G+ ++V + +R
Sbjct: 133 ALNGAEIMGQTIQVDWCFVKGPKRV 157
>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 = 69.7 bits (171), Expect = 6e-16
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 11/83 (13%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
K+FIG + + ++PLFE++GK+ E V+K+ F+ E A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 89 LNGQIVNE---KPLKIEAATSRK 108
L+ Q +P++++ A S
Sbjct: 75 LHEQKTLPGMNRPIQVKPADSES 97
Score = 61.6 bits (150), Expect = 7e-13
Identities = 17/101 (16%), Positives = 39/101 (38%), Gaps = 12/101 (11%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVH 154
++ S + K+F+G + N +++ LF +G + E ++++ F+
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 155 IDSP-DINKCIKELNGMMV---DGKPMKVQISTSRVRQRPG 191
K L+ +P++V+ + S R G
Sbjct: 62 YCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSG 102
>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 = 68.7 bits (169), Expect = 6e-16
Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGR 83
S G+ ++I + PGT+ + + L + YGK+V + K YGFV ++ +
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 84 TAIKELNGQIVNEKPLKIEAATS 106
A+ L V + K +S
Sbjct: 62 KAVTALKASGVQAQMAKQSGPSS 84
Score = 66.0 bits (162), Expect = 6e-15
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 9/78 (11%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DIN 161
++ ++ +++ L T ++ +L PYG +V + + YGFV DSP
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQ 61
Query: 162 KCIKELNGMMVDGKPMKV 179
K + L V + K
Sbjct: 62 KAVTALKASGVQAQMAKQ 79
>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 = 71.0 bits (174), Expect = 7e-16
Identities = 20/119 (16%), Positives = 50/119 (42%), Gaps = 8/119 (6%)
Query: 1 MSRFDQQQLVKVSRYSNNQINISCRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYG 60
+ D + + + S + G + + N+ TS + +R +FEKYG
Sbjct: 36 DNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYG 95
Query: 61 KVVECDVVKNY--------GFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPN 111
+V + + ++ FV + + A+ ++G +++ + L+++ A + P+
Sbjct: 96 RVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD 154
Score = 69.5 bits (170), Expect = 2e-15
Identities = 27/137 (19%), Positives = 47/137 (34%), Gaps = 19/137 (13%)
Query: 73 FVHMENDEEGRTAIKELNG---QIVNEKPLKIEAATSRKGPNT------PTTKVFVGNLS 123
V E+ NG + + K T + T + V NL+
Sbjct: 20 AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLT 79
Query: 124 DNTRAPEVRELFVPYGTVVECDIVRNY--------GFVHIDSP-DINKCIKELNGMMVDG 174
T +R +F YG V + I R+ FV D + ++G ++DG
Sbjct: 80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 139
Query: 175 KPMKVQISTSRVRQRPG 191
+ ++VQ++ R
Sbjct: 140 RELRVQMARYG-RPPDS 155
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 70.2 bits (172), Expect = 8e-16
Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 9/86 (10%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 154
+ G T ++VG L++ + F+P+G + + I R + FV
Sbjct: 52 GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 111
Query: 155 IDSP-DINKCIKELNGMMVDGKPMKV 179
+ D I +N + G+ ++V
Sbjct: 112 FELAEDAAAAIDNMNESELFGRTIRV 137
Score = 66.3 bits (162), Expect = 2e-14
Identities = 13/85 (15%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMEND 79
G S+ +++G + +++ F +G + + + + + FV E
Sbjct: 56 SGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 115
Query: 80 EEGRTAIKELNGQIVNEKPLKIEAA 104
E+ AI +N + + +++ A
Sbjct: 116 EDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 68.3 bits (168), Expect = 9e-16
Identities = 19/86 (22%), Positives = 37/86 (43%), Gaps = 9/86 (10%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---------YGFVHMENDEEG 82
S+ K+ IG + + + I +F YGK+ D+ Y +V EN +E
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60
Query: 83 RTAIKELNGQIVNEKPLKIEAATSRK 108
A+K ++G ++ + + A +
Sbjct: 61 EKALKHMDGGQIDGQEITATAVLAPW 86
Score = 68.0 bits (167), Expect = 1e-15
Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 10/83 (12%)
Query: 113 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV---------RNYGFVHIDSP-DINK 162
TKV +G L+ N + E+F YG + D+ + Y +V ++P + K
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62
Query: 163 CIKELNGMMVDGKPMKVQISTSR 185
+K ++G +DG+ + +
Sbjct: 63 ALKHMDGGQIDGQEITATAVLAP 85
>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 = 69.8 bits (171), Expect = 1e-15
Identities = 26/123 (21%), Positives = 43/123 (34%), Gaps = 10/123 (8%)
Query: 7 QQLVKVSRYSNNQINISCRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECD 66
Q ++ + Q + + + +R LFE+YG +
Sbjct: 14 GQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVK 73
Query: 67 VV--------KNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVF 118
+V + YGFV ++ + AI LNG + K LK+ A S P
Sbjct: 74 IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASG--HQRPGIAGA 131
Query: 119 VGN 121
VG+
Sbjct: 132 VGD 134
Score = 68.2 bits (167), Expect = 4e-15
Identities = 30/131 (22%), Positives = 45/131 (34%), Gaps = 15/131 (11%)
Query: 70 NYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAP 129
V + +++L Q P + V +
Sbjct: 3 QIPLVSQYDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDVL-----RNLMVNYIPTTVDEV 57
Query: 130 EVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIKELNGMMVDGKPMKVQ 180
++R+LF YG + IV R YGFV S + I LNG + K +KV
Sbjct: 58 QLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA 117
Query: 181 ISTSRVRQRPG 191
++ S QRPG
Sbjct: 118 LAASG-HQRPG 127
>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 = 68.9 bits (169), Expect = 1e-15
Identities = 15/85 (17%), Positives = 36/85 (42%), Gaps = 8/85 (9%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGR 83
SV + +F+ +++ + I+ F YG++ + K Y V E ++
Sbjct: 23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 82
Query: 84 TAIKELNGQIVNEKPLKIEAATSRK 108
A + LNG + + ++++ +
Sbjct: 83 AAKEALNGAEIMGQTIQVDWCFVKG 107
Score = 56.9 bits (138), Expect = 3e-11
Identities = 17/101 (16%), Positives = 37/101 (36%), Gaps = 11/101 (10%)
Query: 96 EKPLKIEAATSRKGPNT--PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---- 149
E+ + GP +FV ++ + + E++E F YG + + +
Sbjct: 6 ERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTG 65
Query: 150 ----YGFVHIDSPDI-NKCIKELNGMMVDGKPMKVQISTSR 185
Y V ++ + LNG + G+ ++V +
Sbjct: 66 FSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 106
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 69.0 bits (169), Expect = 2e-15
Identities = 18/92 (19%), Positives = 42/92 (45%), Gaps = 8/92 (8%)
Query: 25 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKNY--------GFVHM 76
P G + + N+ TS + +R +FEKYG+V + + ++ FV
Sbjct: 37 YGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRF 96
Query: 77 ENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 108
+ + A+ ++G +++ + L+++ A +
Sbjct: 97 HDKRDAEDAMDAMDGAVLDGRELRVQMARYGR 128
Score = 68.6 bits (168), Expect = 3e-15
Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 10/99 (10%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY--------GFV 153
+ T + V NL+ T +R +F YG V + I R+ FV
Sbjct: 35 MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94
Query: 154 HIDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
D + ++G ++DG+ ++VQ++ R
Sbjct: 95 RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG-RPPDS 132
>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 = 68.1 bits (167), Expect = 2e-15
Identities = 26/89 (29%), Positives = 40/89 (44%), Gaps = 8/89 (8%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------KNYGFVHMENDE 80
G S F +FIGN+NP SV ++ + + VV + +G+V E+ E
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 69
Query: 81 EGRTAIKELNGQIVNEKPLKIEAATSRKG 109
+ A+ EL G V +K+E R G
Sbjct: 70 DLEKAL-ELTGLKVFGNEIKLEKPKGRDG 97
Score = 64.6 bits (158), Expect = 4e-14
Identities = 20/91 (21%), Positives = 37/91 (40%), Gaps = 7/91 (7%)
Query: 106 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSP 158
+T +F+GNL+ N E++ + +V R +G+V +S
Sbjct: 9 VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 68
Query: 159 DINKCIKELNGMMVDGKPMKVQISTSRVRQR 189
+ + EL G+ V G +K++ R R
Sbjct: 69 EDLEKALELTGLKVFGNEIKLEKPKGRDGTR 99
>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 = 67.7 bits (166), Expect = 3e-15
Identities = 24/98 (24%), Positives = 43/98 (43%), Gaps = 9/98 (9%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVH 154
++ V+VG L + P + ELF+ G VV + + YGFV
Sbjct: 4 GSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE 63
Query: 155 IDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
S D + IK ++ + + GKP++V +++ + G
Sbjct: 64 FLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSG 101
Score = 65.4 bits (160), Expect = 2e-14
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 8/80 (10%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
+++G ++ S L+ LF + G VV + K+ YGFV ++E+ AIK
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 89 LNGQIVNEKPLKIEAATSRK 108
++ + KP+++ A++
Sbjct: 77 MDMIKLYGKPIRVNKASAHN 96
>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 = 68.3 bits (167), Expect = 4e-15
Identities = 25/125 (20%), Positives = 49/125 (39%), Gaps = 24/125 (19%)
Query: 85 AIKELNGQIVNEKPL-------KIEAATSRK---GPNTPTTKVFVGNLSDNTRAPEVREL 134
E+ + ++ + L + S P P +++V NL+ + + +++ +
Sbjct: 6 DSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYI 65
Query: 135 FVPYGTVVEC------DIV-------RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKVQ 180
F Y DI + F+ + + K +KE NG ++ GKPM VQ
Sbjct: 66 FGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQ 125
Query: 181 ISTSR 185
+ S
Sbjct: 126 FARSA 130
Score = 59.8 bits (145), Expect = 7e-12
Identities = 22/122 (18%), Positives = 50/122 (40%), Gaps = 22/122 (18%)
Query: 4 FDQQQLVKVSRYSNNQINISCRNMPGFSSVG----TFKIFIGNVNPGTSVELIRPLFEKY 59
+++L + R S ++ + F S +I++ N+ + ++ +F +Y
Sbjct: 15 ISRREL-EKGRISREEM----ETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRY 69
Query: 60 GKVVEC------DVV-------KNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAATS 106
D+ K F+ + N++ A+KE NG ++ KP+ ++ A S
Sbjct: 70 VDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARS 129
Query: 107 RK 108
+
Sbjct: 130 AR 131
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 66.7 bits (163), Expect = 5e-15
Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 5/77 (6%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-----YGFVHMENDEEGRTAIKELNG 91
K+ I N+ P E++ L +YG V C+ V V + ++ R A+ +LNG
Sbjct: 17 KLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNG 76
Query: 92 QIVNEKPLKIEAATSRK 108
+ LK+
Sbjct: 77 FQLENFTLKVAYIPDEM 93
Score = 66.3 bits (162), Expect = 8e-15
Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 10/87 (11%)
Query: 104 ATSRKGPNTP----TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-----YGFVH 154
+S + P K+ + N+ + + + L V YG V C+ V V
Sbjct: 1 GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVT 60
Query: 155 IDSP-DINKCIKELNGMMVDGKPMKVQ 180
S + + +LNG ++ +KV
Sbjct: 61 YSSKDQARQALDKLNGFQLENFTLKVA 87
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 67.3 bits (165), Expect = 6e-15
Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 11/97 (11%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
KIF+G + T+ +R FE +G + E V+ + YGFV M + A K+
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 89 LNGQIVNEKPLKIEAATSRKGP--NTPTTKVFVGNLS 123
N I++ + + A P + V S
Sbjct: 79 PN-PIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPS 114
Score = 58.8 bits (143), Expect = 9e-12
Identities = 22/89 (24%), Positives = 41/89 (46%), Gaps = 10/89 (11%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-IN 161
+T TK+FVG L +T +R+ F +G + E ++ + YGFV +
Sbjct: 14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73
Query: 162 KCIKELNGMMVDGKPMKVQISTSRVRQRP 190
+ K+ N ++DG+ V ++ + R
Sbjct: 74 RACKDPNP-IIDGRKANVNLAYLGAKPRS 101
>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 = 66.4 bits (163), Expect = 6e-15
Identities = 11/76 (14%), Positives = 31/76 (40%), Gaps = 8/76 (10%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
+++G + +++ F +G + + + + + FV E E+ AI
Sbjct: 9 VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 89 LNGQIVNEKPLKIEAA 104
+N + + +++ A
Sbjct: 69 MNESELFGRTIRVNLA 84
Score = 66.0 bits (162), Expect = 6e-15
Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 9/74 (12%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINKCIK 165
++VG L++ + F+P+G + + I R + FV + D I
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 166 ELNGMMVDGKPMKV 179
+N + G+ ++V
Sbjct: 68 NMNESELFGRTIRV 81
>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 = 66.5 bits (163), Expect = 7e-15
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 10/82 (12%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIKEL 89
K+F+G +N S E + LF+ +G + EC V++ FV + E + AI L
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 90 NGQIVNE---KPLKIEAATSRK 108
+G L ++ A + K
Sbjct: 77 HGSQTMPGASSSLVVKFADTDK 98
Score = 64.6 bits (158), Expect = 4e-14
Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 11/99 (11%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHI 155
++ + K+FVG L+ +V LF P+G + EC ++R FV
Sbjct: 4 GSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKF 63
Query: 156 DSPDI-NKCIKELNGMMV---DGKPMKVQISTSRVRQRP 190
S I L+G + V+ + + P
Sbjct: 64 SSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKESGP 102
>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 = 66.5 bits (163), Expect = 7e-15
Identities = 15/86 (17%), Positives = 37/86 (43%), Gaps = 8/86 (9%)
Query: 27 MPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMEN 78
M G + +++ N+ + + +F KYGKVV+ ++K+ F+ +
Sbjct: 8 MSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLD 67
Query: 79 DEEGRTAIKELNGQIVNEKPLKIEAA 104
+ + + +N + + + +K A
Sbjct: 68 KDSAQNCTRAINNKQLFGRVIKASIA 93
Score = 64.6 bits (158), Expect = 4e-14
Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 9/88 (10%)
Query: 104 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHI 155
+ G + V+V NL + ++ +F YG VV+ I+ + F+
Sbjct: 6 SGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF 65
Query: 156 DSP-DINKCIKELNGMMVDGKPMKVQIS 182
C + +N + G+ +K I+
Sbjct: 66 LDKDSAQNCTRAINNKQLFGRVIKASIA 93
>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 = 66.5 bits (163), Expect = 7e-15
Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 8/85 (9%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKE 88
+++G++ + E I L G V+ ++ K Y F+ + E +A++
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 89 LNGQIVNEKPLKIEAATSRKGPNTP 113
LNG + + LK +++
Sbjct: 64 LNGYQLGSRFLKCGYSSNSDISGVS 88
Score = 61.1 bits (149), Expect = 7e-13
Identities = 13/82 (15%), Positives = 35/82 (42%), Gaps = 9/82 (10%)
Query: 113 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPDI-NKC 163
P+ V++G++ + ++ +L G V+ ++ + Y F+ +
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 164 IKELNGMMVDGKPMKVQISTSR 185
++ LNG + + +K S++
Sbjct: 61 VRNLNGYQLGSRFLKCGYSSNS 82
>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 = 66.1 bits (162), Expect = 1e-14
Identities = 13/95 (13%), Positives = 36/95 (37%), Gaps = 5/95 (5%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----RNYGFVHIDS 157
++ + + + + NLS + ++E+F + + Y F+ S
Sbjct: 3 SGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFAS 62
Query: 158 P-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
D + + N ++G+ +++++ R G
Sbjct: 63 FEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSG 97
Score = 65.4 bits (160), Expect = 2e-14
Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 4/79 (5%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV----KNYGFVHMENDEEGRTAIKELNGQ 92
+ + N++ + E ++ +FEK + K Y F+ + E+ + A+ N +
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKR 76
Query: 93 IVNEKPLKIEAATSRKGPN 111
+ + +++E R PN
Sbjct: 77 EIEGRAIRLELQGPRGSPN 95
>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 = 65.8 bits (161), Expect = 2e-14
Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 10/92 (10%)
Query: 35 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---------YGFVHMENDEEGRTA 85
T KI + N+ + IR LF +G++ + K +GFV ++ + A
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
Query: 86 IKEL-NGQIVNEKPLKIEAATSRKGPNTPTTK 116
L + + + L +E A S + +
Sbjct: 75 FNALCHSTHLYGRRLVLEWADSEVTVQSGPSS 106
Score = 63.1 bits (154), Expect = 1e-13
Identities = 20/100 (20%), Positives = 41/100 (41%), Gaps = 11/100 (11%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---------YGFV 153
++ + T+K+ V N+ E+RELF +G + + + +GFV
Sbjct: 4 GSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFV 63
Query: 154 HIDSP-DINKCIKEL-NGMMVDGKPMKVQISTSRVRQRPG 191
+ D K L + + G+ + ++ + S V + G
Sbjct: 64 DFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQSG 103
>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 = 65.5 bits (160), Expect = 2e-14
Identities = 14/89 (15%), Positives = 32/89 (35%), Gaps = 6/89 (6%)
Query: 108 KGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-----YGFVHIDSP-DIN 161
+ P +++ NL A E+ ++F YG + + + +V + D
Sbjct: 2 RLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAK 61
Query: 162 KCIKELNGMMVDGKPMKVQISTSRVRQRP 190
+ L+G V + + V + +
Sbjct: 62 NAVDHLSGFNVSNRYLVVLYYNANRAFQK 90
Score = 64.3 bits (157), Expect = 6e-14
Identities = 15/77 (19%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-----YGFVHMENDEEGRTAIKELNGQ 92
++I N+ + E + +F KYG + + V +V E+ + + A+ L+G
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGF 70
Query: 93 IVNEKPLKIEAATSRKG 109
V+ + L + + +
Sbjct: 71 NVSNRYLVVLYYNANRA 87
>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 = 64.6 bits (158), Expect = 4e-14
Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 35 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAI 86
+F+GN+ + E ++ +F + G VV +V K YGF ++ E +A+
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 87 KELNGQIVNEKPLKIEAATSRKGPN 111
+ LNG+ + + L+++ A S K
Sbjct: 68 RNLNGREFSGRALRVDNAASEKNKE 92
Score = 56.5 bits (137), Expect = 4e-11
Identities = 20/87 (22%), Positives = 35/87 (40%), Gaps = 9/87 (10%)
Query: 113 PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHI-DSPDINKC 163
VFVGN+ +++++F G VV +V + YGF D
Sbjct: 7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66
Query: 164 IKELNGMMVDGKPMKVQISTSRVRQRP 190
++ LNG G+ ++V + S +
Sbjct: 67 MRNLNGREFSGRALRVDNAASEKNKEE 93
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 65.3 bits (159), Expect = 4e-14
Identities = 12/109 (11%), Positives = 35/109 (32%), Gaps = 10/109 (9%)
Query: 87 KELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRE----LFVPYGTVV 142
KE + + S P+ V + N++ +++ L G ++
Sbjct: 2 KETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDIL 61
Query: 143 ECDIVRN-----YGFVHIDSPDI-NKCIKELNGMMVDGKPMKVQISTSR 185
+ + + ++ + + ++ G G P+ + S +
Sbjct: 62 DIVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETP 110
Score = 58.4 bits (141), Expect = 2e-11
Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 9/81 (11%)
Query: 37 KIFIGNVNPGTSVE----LIRPLFEKYGKVVECDVVKN-----YGFVHMENDEEGRTAIK 87
+ I N+NP E L+ L G +++ V + ++ E + ++
Sbjct: 31 VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQESAQAFVE 90
Query: 88 ELNGQIVNEKPLKIEAATSRK 108
G PL I + + +
Sbjct: 91 AFQGYPFQGNPLVITFSETPQ 111
>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 = 65.6 bits (160), Expect = 7e-14
Identities = 15/80 (18%), Positives = 38/80 (47%), Gaps = 8/80 (10%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
+++GN++ T+ E I LF K G + + + + + FV + + A++
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 89 LNGQIVNEKPLKIEAATSRK 108
+NG ++++ ++ + K
Sbjct: 101 INGTRLDDRIIRTDWDAGFK 120
Score = 64.8 bits (158), Expect = 1e-13
Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 9/94 (9%)
Query: 106 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDS 157
++ + ++VGNLS T ++ ELF G + + + + + FV S
Sbjct: 31 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYS 90
Query: 158 P-DINKCIKELNGMMVDGKPMKVQISTSRVRQRP 190
D ++ +NG +D + ++ R
Sbjct: 91 RADAENAMRYINGTRLDDRIIRTDWDAGFKEGRQ 124
>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 = 63.3 bits (155), Expect = 9e-14
Identities = 17/83 (20%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDINKCIKEL 167
++VGNL + + +V+ELF +G V ++ + +GFV + +++ I +L
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKL 62
Query: 168 NGMMVDGKPMKVQISTSRVRQRP 190
+ G+ ++V + +
Sbjct: 63 DNTDFMGRTIRVTEANPKKSLEH 85
Score = 60.6 bits (148), Expect = 1e-12
Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKE 88
I++GN+ + E ++ LF ++GKV ++ K +GFV M+ +E AI +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 89 LNGQIVNEKPLKIEAATSRKGPN 111
L+ + +++ A +K
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSLE 84
>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 = 63.4 bits (155), Expect = 1e-13
Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 9/79 (11%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIKEL 89
+F+G ++ IR F +YG V E ++ + YGFV ND + + ++
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-- 68
Query: 90 NGQIVNEKPLKIEAATSRK 108
+ + K LK+ A ++
Sbjct: 69 SQINFHGKKLKLGPAIRKQ 87
Score = 60.3 bits (147), Expect = 2e-12
Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 10/80 (12%)
Query: 114 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-------RNYGFVHIDSPD-INKCIK 165
VFVG + E+R F YG+V E I+ + YGFV + + K ++
Sbjct: 9 PNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68
Query: 166 ELNGMMVDGKPMKVQISTSR 185
+ + GK +K+ + +
Sbjct: 69 --SQINFHGKKLKLGPAIRK 86
>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 = 2e-13
Identities = 18/81 (22%), Positives = 27/81 (33%), Gaps = 2/81 (2%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDV--VKNYGFVHMENDEEGRTAIKELNGQIVN 95
I N+ GT I+ F ++G + + V E R A + L +
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKFH 72
Query: 96 EKPLKIEAATSRKGPNTPTTK 116
PL +E A P K
Sbjct: 73 HVPLYLEWAPIGVFGAAPQKK 93
Score = 59.4 bits (144), Expect = 4e-12
Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 3/69 (4%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDI--VRNYGFVHIDSP-DINKCIKELNGMM 171
T + NL T A E++E F +G++ + V P + K + L
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSK 70
Query: 172 VDGKPMKVQ 180
P+ ++
Sbjct: 71 FHHVPLYLE 79
>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 = 63.2 bits (154), Expect = 2e-13
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 4/79 (5%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKELNGQIVN 95
+++ + + L+R F +G +++ + +N FV E E A+ ELNG V
Sbjct: 42 LYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVE 99
Query: 96 EKPLKIEAATSRKGPNTPT 114
LK+ A + + T
Sbjct: 100 SVQLKVNIARKQPMLDAAT 118
Score = 60.9 bits (148), Expect = 1e-12
Identities = 20/98 (20%), Positives = 42/98 (42%), Gaps = 6/98 (6%)
Query: 100 KIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDS 157
+ ++ R+ P T ++V + +R F P+G +++ + RN FV +
Sbjct: 26 RSDSFPERRAPRKGNT-LYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEK 82
Query: 158 P-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPGVDE 194
++ + ELNG V+ +KV I+ + +
Sbjct: 83 MESADQAVAELNGTQVESVQLKVNIARKQPMLDAATGK 120
>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 = 62.7 bits (153), Expect = 2e-13
Identities = 21/92 (22%), Positives = 41/92 (44%), Gaps = 6/92 (6%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP-D 159
++ R+ P T ++V + +R F P+G +++ + RN FV +
Sbjct: 5 SSGERRAPRKGNT-LYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMES 61
Query: 160 INKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
++ + ELNG V+ +KV I+ + G
Sbjct: 62 ADQAVAELNGTQVESVQLKVNIARKQPMLDSG 93
Score = 60.0 bits (146), Expect = 2e-12
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 4/76 (5%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKELNGQIVN 95
+++ + + L+R F +G +++ + +N FV E E A+ ELNG V
Sbjct: 18 LYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVE 75
Query: 96 EKPLKIEAATSRKGPN 111
LK+ A + +
Sbjct: 76 SVQLKVNIARKQPMLD 91
>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural
genomics, joint center for struc genomics, JCSG, protein
structure initiative; HET: PGE; 1.95A {Homo sapiens}
PDB: 3b4d_A 3b4m_A
Length = 89
Score = 62.1 bits (152), Expect = 2e-13
Identities = 15/82 (18%), Positives = 35/82 (42%), Gaps = 9/82 (10%)
Query: 35 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAI 86
I++GNV+ G + E + F G V ++ K + ++ + E RT++
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 87 KELNGQIVNEKPLKIEAATSRK 108
L+ + + +K+ + +
Sbjct: 66 -ALDESLFRGRQIKVIPKRTNR 86
Score = 60.2 bits (147), Expect = 1e-12
Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 11/92 (11%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPDI 160
G ++VGN+ A E+ F G+V I+ + + ++ +
Sbjct: 1 GMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES 60
Query: 161 NKCIKELNGMMVDGKPMKVQISTSRVRQRPGV 192
+ L+ + G+ +KV + RPG+
Sbjct: 61 VRTSLALDESLFRGRQIKVIPKRTN---RPGI 89
>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 = 61.9 bits (151), Expect = 3e-13
Identities = 15/84 (17%), Positives = 31/84 (36%), Gaps = 4/84 (4%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV---RNYGFVHIDSP-DINKCIK 165
+ NLS N E++E+F + + ++ S D K ++
Sbjct: 12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLE 71
Query: 166 ELNGMMVDGKPMKVQISTSRVRQR 189
E G +DG+ + + + + R
Sbjct: 72 EKQGAEIDGRSVSLYYTGEKGGTR 95
Score = 59.2 bits (144), Expect = 4e-12
Identities = 7/78 (8%), Positives = 31/78 (39%), Gaps = 3/78 (3%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV---KNYGFVHMENDEEGRTAIKELNGQI 93
+ N++ + + ++ +FE ++ K ++ +++ + ++E G
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAE 77
Query: 94 VNEKPLKIEAATSRKGPN 111
++ + + + + G
Sbjct: 78 IDGRSVSLYYTGEKGGTR 95
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 62.2 bits (151), Expect = 4e-13
Identities = 14/89 (15%), Positives = 31/89 (34%), Gaps = 5/89 (5%)
Query: 107 RKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIK- 165
G P+ + + L + EV L +P+G V +++ I+
Sbjct: 9 HHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTM 68
Query: 166 ----ELNGMMVDGKPMKVQISTSRVRQRP 190
++ G+P+ +Q S + +
Sbjct: 69 VNYYTSVTPVLRGQPIYIQFSNHKELKTD 97
Score = 52.9 bits (127), Expect = 1e-09
Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 4/75 (5%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKEL--NGQI 93
I I + + + L +GKV ++ KN F+ M +E T + +
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPV 78
Query: 94 VNEKPLKIEAATSRK 108
+ +P+ I+ + ++
Sbjct: 79 LRGQPIYIQFSNHKE 93
>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 = 62.2 bits (151), Expect = 5e-13
Identities = 13/90 (14%), Positives = 31/90 (34%), Gaps = 5/90 (5%)
Query: 106 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIK 165
+ P+ + + L + EV L +P+G V +++ I+
Sbjct: 23 DSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANT 82
Query: 166 -----ELNGMMVDGKPMKVQISTSRVRQRP 190
++ G+P+ +Q S + +
Sbjct: 83 MVNYYTSVTPVLRGQPIYIQFSNHKELKTD 112
Score = 52.6 bits (126), Expect = 2e-09
Identities = 14/75 (18%), Positives = 31/75 (41%), Gaps = 4/75 (5%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIK--ELNGQI 93
I I + + + L +GKV ++ KN F+ M +E T + +
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPV 93
Query: 94 VNEKPLKIEAATSRK 108
+ +P+ I+ + ++
Sbjct: 94 LRGQPIYIQFSNHKE 108
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 61.5 bits (150), Expect = 5e-13
Identities = 16/87 (18%), Positives = 39/87 (44%), Gaps = 11/87 (12%)
Query: 110 PNT-PTTKVFVGNLSDNTRAPEVRE----LFVPYGTVVECDIVRN-----YGFVHIDSPD 159
P T P +++ NL++ + E+++ +F +G +++ + R+ FV
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVS 62
Query: 160 I-NKCIKELNGMMVDGKPMKVQISTSR 185
++ + G KPM++Q + +
Sbjct: 63 SATNALRSMQGFPFYDKPMRIQYAKTD 89
Score = 59.5 bits (145), Expect = 3e-12
Identities = 15/79 (18%), Positives = 38/79 (48%), Gaps = 9/79 (11%)
Query: 38 IFIGNVNPGTSVELIR----PLFEKYGKVVECDVVKN-----YGFVHMENDEEGRTAIKE 88
I+I N+N + ++ +F ++G++++ V ++ FV + A++
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 89 LNGQIVNEKPLKIEAATSR 107
+ G +KP++I+ A +
Sbjct: 71 MQGFPFYDKPMRIQYAKTD 89
>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 = 64.4 bits (156), Expect = 6e-13
Identities = 11/99 (11%), Positives = 33/99 (33%), Gaps = 10/99 (10%)
Query: 26 NMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYG--KVVECDVVKN--------YGFVH 75
N+ + ++IGN+ T+ E + G ++E +N + V
Sbjct: 59 NVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVG 118
Query: 76 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPT 114
+ ++ + + L + ++ + + +
Sbjct: 119 VGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEM 157
Score = 62.8 bits (152), Expect = 2e-12
Identities = 18/123 (14%), Positives = 35/123 (28%), Gaps = 11/123 (8%)
Query: 78 NDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVP 137
D + V + K A +++GNL+ T ++ E
Sbjct: 32 GDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHS 91
Query: 138 YGT--VVECDIVRN--------YGFVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSRV 186
G ++E N + V + S K + L + G+ V +
Sbjct: 92 LGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQF 151
Query: 187 RQR 189
+
Sbjct: 152 LSQ 154
>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 = 64.5 bits (156), Expect = 8e-13
Identities = 21/169 (12%), Positives = 53/169 (31%), Gaps = 16/169 (9%)
Query: 38 IFIGNVNPGTSVE----LIRPLFEKYGKVVECDVVKN-----YGFVHMENDEEGRTAIKE 88
I+I N+N + + +F ++G++++ V ++ FV + A++
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 89 LNGQIVNEKPLKIEAATSRK-------GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTV 141
+ G +KP++I+ A + G + + P ++ G
Sbjct: 72 MQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGAT 131
Query: 142 VECDIVRNYGFVHIDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQRP 190
V+ + + + G P + +
Sbjct: 132 PVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQI 180
Score = 61.4 bits (148), Expect = 1e-11
Identities = 14/85 (16%), Positives = 37/85 (43%), Gaps = 10/85 (11%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRE----LFVPYGTVVECDIVRN-----YGFVHIDSPDI- 160
P +++ NL++ + E+++ +F +G +++ + R+ FV
Sbjct: 6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 161 NKCIKELNGMMVDGKPMKVQISTSR 185
++ + G KPM++Q + +
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYAKTD 90
Score = 54.1 bits (129), Expect = 4e-09
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 4/68 (5%)
Query: 39 FIGNVNPGTSVELIRPLFEKYGKVVECDVV---KNYGFVHMENDEEGRTAIKELNG-QIV 94
F+ N+ T+ ++ LF ++ E +V + FV +N+ + A L G +I
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKIT 270
Query: 95 NEKPLKIE 102
+KI
Sbjct: 271 QNNAMKIS 278
Score = 50.3 bits (119), Expect = 7e-08
Identities = 17/76 (22%), Positives = 26/76 (34%), Gaps = 5/76 (6%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSPDI-NKCIK 165
N P +F+ NL + T + LF + E +V FV D+
Sbjct: 203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARD 262
Query: 166 ELNGM-MVDGKPMKVQ 180
L G + MK+
Sbjct: 263 ALQGFKITQNNAMKIS 278
>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 = 61.2 bits (149), Expect = 1e-12
Identities = 14/87 (16%), Positives = 34/87 (39%), Gaps = 14/87 (16%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIK 87
+FI N++ + E + + +++G + VV + F E + +
Sbjct: 16 KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75
Query: 88 ELN------GQIVNEKPLKIEAATSRK 108
+ G ++ + LK++ A +R
Sbjct: 76 AASLEAEGGGLKLDGRQLKVDLAVTRD 102
Score = 60.4 bits (147), Expect = 2e-12
Identities = 19/95 (20%), Positives = 38/95 (40%), Gaps = 15/95 (15%)
Query: 112 TPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSP-DINK 162
T VF+ NLS ++ + E+ +G + +V + F + K
Sbjct: 13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 163 CIKELN------GMMVDGKPMKVQISTSRVRQRPG 191
C+ + G+ +DG+ +KV ++ +R G
Sbjct: 73 CLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAASG 107
>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 = 61.3 bits (149), Expect = 1e-12
Identities = 10/80 (12%), Positives = 31/80 (38%), Gaps = 9/80 (11%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKE 88
+++GNV+ G++ + + F G + ++ K Y ++ A+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-A 96
Query: 89 LNGQIVNEKPLKIEAATSRK 108
++ + + +K+ +
Sbjct: 97 MDETVFRGRTIKVLPKRTNM 116
Score = 57.0 bits (138), Expect = 5e-11
Identities = 12/93 (12%), Positives = 35/93 (37%), Gaps = 8/93 (8%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFV 153
+ ++ + V+VGN+ + A ++ F G++ I+ + Y ++
Sbjct: 24 QPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYI 83
Query: 154 HIDSPDINKCIKELNGMMVDGKPMKVQISTSRV 186
+ ++ + G+ +KV + +
Sbjct: 84 EFAERNSVDAAVAMDETVFRGRTIKVLPKRTNM 116
>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 = 60.0 bits (146), Expect = 2e-12
Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 3/68 (4%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKE-LNGQI 93
+++G + + +R F ++G++ VV + F+ + A ++ N I
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKLI 73
Query: 94 VNEKPLKI 101
VN + L +
Sbjct: 74 VNGRRLNV 81
Score = 58.8 bits (143), Expect = 4e-12
Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 5/77 (6%)
Query: 109 GPNTPT-TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP-DINKCI 164
T T ++VG L D ++R F +G + +V + F+ +
Sbjct: 6 SGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAA 65
Query: 165 KE-LNGMMVDGKPMKVQ 180
++ N ++V+G+ + V+
Sbjct: 66 EKSFNKLIVNGRRLNVK 82
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 59.6 bits (145), Expect = 2e-12
Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 3/79 (3%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVHIDSPDINKCIKELNGMMV 172
VFV + ++ E F+ +G V + ++ + V + + + + +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGAREAVLSQSQHSL 69
Query: 173 DGKPMKVQISTSRVRQRPG 191
G ++V+ + Q P
Sbjct: 70 GGHRLRVRPREQKEFQSPA 88
Score = 58.1 bits (141), Expect = 9e-12
Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 4/85 (4%)
Query: 32 SVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---YGFVHMENDEEGRTAIKE 88
S G +F+ G + F +G V + K+ + V M D R A+
Sbjct: 5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMG-DVGAREAVLS 63
Query: 89 LNGQIVNEKPLKIEAATSRKGPNTP 113
+ + L++ ++ +
Sbjct: 64 QSQHSLGGHRLRVRPREQKEFQSPA 88
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 59.6 bits (145), Expect = 3e-12
Identities = 15/84 (17%), Positives = 32/84 (38%), Gaps = 14/84 (16%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGK--VVECDVVKN--------YGFVHMENDEEGRTAI 86
I + N+ P T V+ I Y V ++K+ + FV + + + +
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70
Query: 87 KELNGQ----IVNEKPLKIEAATS 106
+ L ++ K + ++ A S
Sbjct: 71 QILQSLHPPLKIDGKTIGVDFAKS 94
Score = 58.5 bits (142), Expect = 7e-12
Identities = 15/90 (16%), Positives = 37/90 (41%), Gaps = 15/90 (16%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGT--VVECDIVRN--------YGFVHIDSP- 158
+ + + N++ +T + PY + V ++++ + FV + S
Sbjct: 5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64
Query: 159 DINKCIKELNGM----MVDGKPMKVQISTS 184
D ++ ++ L + +DGK + V + S
Sbjct: 65 DASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
>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 = 60.0 bits (146), Expect = 3e-12
Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 9/80 (11%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEEGRTAIKE 88
+F + + F GKV + ++ K +V + AI
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-G 85
Query: 89 LNGQIVNEKPLKIEAATSRK 108
L GQ + P+ ++A+ + K
Sbjct: 86 LTGQRLLGVPIIVQASQAEK 105
Score = 60.0 bits (146), Expect = 3e-12
Identities = 18/98 (18%), Positives = 31/98 (31%), Gaps = 8/98 (8%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFV 153
E + VF L+ R ++ + F G V + I+ + +V
Sbjct: 13 EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYV 72
Query: 154 HIDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
L G + G P+ VQ S + + G
Sbjct: 73 EFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSG 110
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 59.2 bits (144), Expect = 4e-12
Identities = 20/95 (21%), Positives = 41/95 (43%), Gaps = 10/95 (10%)
Query: 108 KGPNTPTTKVFVGNLSDNTRAPEVRELFV-PYGTVVECDIVRN-------YGFVHIDSP- 158
G + P +FVG+L+ + + E FV Y + +V + YGFV
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDEL 62
Query: 159 DINKCIKELNG-MMVDGKPMKVQISTSRVRQRPGV 192
+ + + E G + + KP+++ ++ + + V
Sbjct: 63 EQKRALTECQGAVGLGSKPVRLSVAIPKASRVKPV 97
Score = 56.5 bits (137), Expect = 5e-11
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 9/82 (10%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEK-YGKVVECDVV-------KNYGFVHMENDEEGRTAIK 87
+ +F+G++ P ++ F K Y VV K YGFV ++ E + A+
Sbjct: 10 YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALT 69
Query: 88 ELNGQI-VNEKPLKIEAATSRK 108
E G + + KP+++ A +
Sbjct: 70 ECQGAVGLGSKPVRLSVAIPKA 91
>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM
domain, riken structural genomics/proteomics initiative
RSGI, RNA binding protein; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 88
Score = 58.8 bits (143), Expect = 4e-12
Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 5/80 (6%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVK---NYGFVHMENDEEGRTAIKELNGQI 93
+F+G + + +R F +YG V++ + K + FV +D+ ++ E I
Sbjct: 7 GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE--DLI 64
Query: 94 VNEKPLKIEAATSRKGPNTP 113
+ + I A + N+
Sbjct: 65 IKGISVHISNAEPKHNSNSG 84
Score = 57.2 bits (139), Expect = 1e-11
Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 6/85 (7%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV---RNYGFVHIDSPDI-NKCIKE 166
++ ++ VFVG + + E+RE F YG V++ I R + FV I E
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGE 61
Query: 167 LNGMMVDGKPMKVQISTSRVRQRPG 191
+++ G + + + + G
Sbjct: 62 --DLIIKGISVHISNAEPKHNSNSG 84
>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 = 59.2 bits (144), Expect = 4e-12
Identities = 22/101 (21%), Positives = 40/101 (39%), Gaps = 15/101 (14%)
Query: 103 AATSRKGPNT---PTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYG 151
++ GPN P+ +FV LS++T ++E F V IV + +G
Sbjct: 1 GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFG 57
Query: 152 FVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
FV +S D + + +DG + + + + G
Sbjct: 58 FVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSG 98
Score = 58.8 bits (143), Expect = 7e-12
Identities = 17/97 (17%), Positives = 43/97 (44%), Gaps = 12/97 (12%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMEND 79
P S + +F+ ++ T+ E ++ F V +V K +GFV ++
Sbjct: 8 PNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSE 64
Query: 80 EEGRTAIKELNGQIVNEKPLKIEAATSR-KGPNTPTT 115
E+ + A + + ++ + ++ A + +G + P++
Sbjct: 65 EDAKAAKEAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 59.0 bits (143), Expect = 4e-12
Identities = 13/80 (16%), Positives = 27/80 (33%), Gaps = 5/80 (6%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIK----- 165
+ V + L D ++ E +G + ++ ++ D+
Sbjct: 18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYA 77
Query: 166 ELNGMMVDGKPMKVQISTSR 185
N + + G P V STS+
Sbjct: 78 ADNQIYIAGHPAFVNYSTSQ 97
Score = 51.3 bits (123), Expect = 4e-09
Identities = 12/75 (16%), Positives = 26/75 (34%), Gaps = 4/75 (5%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKELNGQ--I 93
+ I + G + +++G + V+ K V E+ A+
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADNQIY 83
Query: 94 VNEKPLKIEAATSRK 108
+ P + +TS+K
Sbjct: 84 IAGHPAFVNYSTSQK 98
>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 = 59.4 bits (144), Expect = 5e-12
Identities = 11/74 (14%), Positives = 28/74 (37%), Gaps = 1/74 (1%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-YGFVHMENDEEGRTAIKELNGQIV 94
++ + + P S + ++ + G V DV ++ G V E+ A+++L+
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF 75
Query: 95 NEKPLKIEAATSRK 108
+ +
Sbjct: 76 RSHEGETAYIRVKV 89
Score = 54.0 bits (130), Expect = 5e-10
Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 4/90 (4%)
Query: 106 SRKGPNTPTT--KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-YGFVHIDSP-DIN 161
S GP + + +V V L + ++++ G V D+ R+ G V D+
Sbjct: 5 SSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMT 64
Query: 162 KCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+++L+ + +V
Sbjct: 65 YAVRKLDNTKFRSHEGETAYIRVKVDGPRS 94
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 59.0 bits (143), Expect = 5e-12
Identities = 15/93 (16%), Positives = 36/93 (38%), Gaps = 5/93 (5%)
Query: 104 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP-DI 160
++ + + V V L ++ ++ E +GT+ ++ + V ++
Sbjct: 5 SSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSA 64
Query: 161 NKCIKEL--NGMMVDGKPMKVQISTSRVRQRPG 191
+C+ + + G+ STS+ RPG
Sbjct: 65 KECVTFAADVPVYIAGQQAFFNYSTSKRITRPG 97
Score = 51.7 bits (124), Expect = 2e-09
Identities = 9/75 (12%), Positives = 25/75 (33%), Gaps = 4/75 (5%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKEL--NGQI 93
+ + + + EK+G + ++ K V EN + + +
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADVPVY 77
Query: 94 VNEKPLKIEAATSRK 108
+ + +TS++
Sbjct: 78 IAGQQAFFNYSTSKR 92
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 60.3 bits (146), Expect = 6e-12
Identities = 20/98 (20%), Positives = 41/98 (41%), Gaps = 11/98 (11%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGT--VVECDIVRN--------YGF 152
+ G V+VG+ S T ++ ++ G VVE N Y
Sbjct: 44 ILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAE 103
Query: 153 VHIDSP-DINKCIKELNGMMVDGKPMKVQISTSRVRQR 189
V + S ++K ++ L G +++G+ + V+ +T + +
Sbjct: 104 VVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQ 141
Score = 59.9 bits (145), Expect = 8e-12
Identities = 14/90 (15%), Positives = 36/90 (40%), Gaps = 10/90 (11%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYG--KVVECDVVKN--------YGFVHMENDE 80
+++G+ + T+ + + + G VVE +N Y V + ++
Sbjct: 51 LRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASEN 110
Query: 81 EGRTAIKELNGQIVNEKPLKIEAATSRKGP 110
++ L G+++N + + + AT +
Sbjct: 111 SVHKLLELLPGKVLNGEKVDVRPATRQNLS 140
>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 = 58.4 bits (142), Expect = 6e-12
Identities = 10/82 (12%), Positives = 30/82 (36%), Gaps = 10/82 (12%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYG--KVVECDVVKN--------YGFVHMENDEEGRTA 85
++IGN+ T+ E + G ++E +N + V + ++ +
Sbjct: 2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 61
Query: 86 IKELNGQIVNEKPLKIEAATSR 107
+ L + ++ + + +
Sbjct: 62 MDLLPKRELHGQNPVVTPSNKL 83
Score = 55.3 bits (134), Expect = 1e-10
Identities = 15/86 (17%), Positives = 28/86 (32%), Gaps = 12/86 (13%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGT--VVECDIVRN--------YGFVHIDSP-DINKCI 164
+++GNL+ T ++ E G ++E N + V + S K +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 165 KELNGMMVDGKPMKVQISTSRVRQRP 190
L + G+ V S
Sbjct: 63 DLLPKRELHGQNPVVTPSNKL-EHHH 87
>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 = 58.4 bits (142), Expect = 9e-12
Identities = 16/98 (16%), Positives = 35/98 (35%), Gaps = 10/98 (10%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---------YGFV 153
++ + P +P F+GNL + ++E F + + R +G+
Sbjct: 4 GSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYA 62
Query: 154 HIDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+ D LN + K ++V ++ + G
Sbjct: 63 EFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSG 100
Score = 51.1 bits (123), Expect = 4e-09
Identities = 13/82 (15%), Positives = 34/82 (41%), Gaps = 11/82 (13%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---------YGFVHMENDEEGRTAI 86
+ F+GN+ + E I+ F + + + +G+ E+ + +A+
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74
Query: 87 KELNGQIVNEKPLKIEAATSRK 108
LN + + K ++++ A +
Sbjct: 75 S-LNEESLGNKRIRVDVADQAQ 95
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 58.3 bits (141), Expect = 9e-12
Identities = 17/95 (17%), Positives = 36/95 (37%), Gaps = 13/95 (13%)
Query: 103 AATSRKGPNTP-------TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----RNYG 151
++ GP +P V+VGNL + R +++ G V + R
Sbjct: 1 GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELG-SVPLRLTWQGPRRRA 59
Query: 152 FVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSR 185
F+H + + L G+ + ++V ++ +
Sbjct: 60 FLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ 94
Score = 57.1 bits (138), Expect = 2e-11
Identities = 14/84 (16%), Positives = 33/84 (39%), Gaps = 3/84 (3%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKV---VECDVVKNYGFVHMENDEEGRT 84
PG + +++GN+ V ++ + G V + + F+H + +
Sbjct: 12 PGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQ 71
Query: 85 AIKELNGQIVNEKPLKIEAATSRK 108
A+ L G + L++ A ++
Sbjct: 72 AVSCLQGLRLGTDTLRVALARQQR 95
>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 = 58.0 bits (141), Expect = 1e-11
Identities = 17/87 (19%), Positives = 41/87 (47%), Gaps = 9/87 (10%)
Query: 35 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAI 86
+ KIF+G + +R F+K+G V E ++ + +GF+ E+++ A+
Sbjct: 10 SNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
Query: 87 KELNGQIVNEKPLKIEAATSRKGPNTP 113
++ + K ++++ A R ++
Sbjct: 70 -NMHFHDIMGKKVEVKRAEPRDSKSSG 95
Score = 57.2 bits (139), Expect = 2e-11
Identities = 21/94 (22%), Positives = 40/94 (42%), Gaps = 8/94 (8%)
Query: 106 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDS 157
S + + K+FVG + N E+RE F +G V E ++ R +GF+ +
Sbjct: 2 SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED 61
Query: 158 PDINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
++ + GK ++V+ + R + G
Sbjct: 62 EQSVDQAVNMHFHDIMGKKVEVKRAEPRDSKSSG 95
>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 = 57.1 bits (138), Expect = 2e-11
Identities = 14/89 (15%), Positives = 30/89 (33%), Gaps = 5/89 (5%)
Query: 108 KGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIK-- 165
K P+ + + L EV L +P+G V +++ ++ I
Sbjct: 9 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMV 68
Query: 166 ---ELNGMMVDGKPMKVQISTSRVRQRPG 191
+ +P+ +Q S + + G
Sbjct: 69 NYYSAVTPHLRNQPIYIQYSNHKELKTSG 97
Score = 50.2 bits (120), Expect = 1e-08
Identities = 12/82 (14%), Positives = 32/82 (39%), Gaps = 4/82 (4%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIK--ELNGQI 93
+ I + + + L +GKV ++ KN F+ + +E T +
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEAAITMVNYYSAVTPH 77
Query: 94 VNEKPLKIEAATSRKGPNTPTT 115
+ +P+ I+ + ++ + +
Sbjct: 78 LRNQPIYIQYSNHKELKTSGPS 99
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 56.9 bits (138), Expect = 3e-11
Identities = 20/97 (20%), Positives = 42/97 (43%), Gaps = 9/97 (9%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVH 154
++ ++ P P +VGNL NT ++ +F + +VR+ + +V
Sbjct: 4 GSSGKELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVE 62
Query: 155 IDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
D D K +G ++ + ++V I+ R + + G
Sbjct: 63 FDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKSG 99
Score = 50.3 bits (121), Expect = 9e-09
Identities = 14/90 (15%), Positives = 37/90 (41%), Gaps = 10/90 (11%)
Query: 30 FSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV--------KNYGFVHMENDEE 81
+ + ++GN+ T I +F+ + +V K + +V + +
Sbjct: 10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDS 68
Query: 82 GRTAIKELNGQIVNEKPLKIEAATSRKGPN 111
+ A+ +G ++ ++ L+++ A RK
Sbjct: 69 LKEAL-TYDGALLGDRSLRVDIAEGRKQDK 97
>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 = 57.1 bits (138), Expect = 4e-11
Identities = 11/79 (13%), Positives = 28/79 (35%), Gaps = 1/79 (1%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-YGFVHMENDEEGRTAIKELNGQIV 94
++ + + P S + ++ + G V DV ++ G V E+ A+++L+
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF 76
Query: 95 NEKPLKIEAATSRKGPNTP 113
+ +
Sbjct: 77 RSHEGETAYIRVKVDGPRS 95
Score = 53.7 bits (129), Expect = 6e-10
Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 4/90 (4%)
Query: 106 SRKGPNTPTT--KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-YGFVHIDSP-DIN 161
R GP + + +V V L + ++++ G V D+ R+ G V D+
Sbjct: 6 GRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMT 65
Query: 162 KCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+++L+ + +V
Sbjct: 66 YAVRKLDNTKFRSHEGETAYIRVKVDGPRS 95
>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 = 55.8 bits (135), Expect = 9e-11
Identities = 14/85 (16%), Positives = 30/85 (35%), Gaps = 16/85 (18%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV----------------KNYGFVHMENDE 80
IF+ + ++E + F++ G + K V ++
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74
Query: 81 EGRTAIKELNGQIVNEKPLKIEAAT 105
+ AI +G+ + P+K+ AT
Sbjct: 75 SAKAAIDWFDGKEFSGNPIKVSFAT 99
Score = 52.3 bits (126), Expect = 2e-09
Identities = 17/90 (18%), Positives = 27/90 (30%), Gaps = 17/90 (18%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----------------RNYGFVH 154
++ +FV L +N V + F G + + V
Sbjct: 10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 69
Query: 155 -IDSPDINKCIKELNGMMVDGKPMKVQIST 183
D P I +G G P+KV +T
Sbjct: 70 FDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 99
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 55.9 bits (135), Expect = 1e-10
Identities = 20/98 (20%), Positives = 29/98 (29%), Gaps = 17/98 (17%)
Query: 111 NTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----------------RNYGFVH 154
N+ +FV L +N V + F G + + V
Sbjct: 4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63
Query: 155 -IDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
D P I +G G P+KV +T R G
Sbjct: 64 FDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRG 101
Score = 55.5 bits (134), Expect = 2e-10
Identities = 15/88 (17%), Positives = 31/88 (35%), Gaps = 16/88 (18%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV----------------KNYGFVHMENDE 80
IF+ + ++E + F++ G + K V ++
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68
Query: 81 EGRTAIKELNGQIVNEKPLKIEAATSRK 108
+ AI +G+ + P+K+ AT R
Sbjct: 69 SAKAAIDWFDGKEFSGNPIKVSFATRRA 96
>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 = 55.9 bits (135), Expect = 1e-10
Identities = 14/96 (14%), Positives = 34/96 (35%), Gaps = 17/96 (17%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV----------------KNYGFVHMENDE 80
I++ +N +++ + F++ G V K V E+
Sbjct: 17 AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76
Query: 81 EGRTAIKELNGQIVNEKPLKIEAATSR-KGPNTPTT 115
+ A++ +G+ LK+ A + + P++
Sbjct: 77 TAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSS 112
Score = 49.7 bits (119), Expect = 2e-08
Identities = 13/94 (13%), Positives = 30/94 (31%), Gaps = 17/94 (18%)
Query: 115 TKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----------------RNYGFVHIDSP 158
+ ++V L+D+ ++ + F G V + V + P
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 159 D-INKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
++ +G G +KV ++ + G
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSG 109
>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 = 54.6 bits (132), Expect = 2e-10
Identities = 14/85 (16%), Positives = 30/85 (35%), Gaps = 10/85 (11%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---------YGFVHIDSPDI 160
P +P F+GNL + ++E F + + R +G+ + D
Sbjct: 15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDS 73
Query: 161 NKCIKELNGMMVDGKPMKVQISTSR 185
LN + + ++V ++
Sbjct: 74 LLSALSLNEESLGNRRIRVDVADQA 98
Score = 50.7 bits (122), Expect = 5e-09
Identities = 12/93 (12%), Positives = 35/93 (37%), Gaps = 11/93 (11%)
Query: 25 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN---------YGFVH 75
+ + F+GN+ + E I+ F + + + +G+
Sbjct: 9 HHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAE 67
Query: 76 MENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 108
E+ + +A+ LN + + + ++++ A +
Sbjct: 68 FEDLDSLLSAL-SLNEESLGNRRIRVDVADQAQ 99
>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 = 53.8 bits (130), Expect = 3e-10
Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVK---NYGFVHMENDEEGRTAIKELNGQI 93
K+F+G + E ++ F +YG+VV+ + K + FV +D+ ++ E I
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGE--DLI 70
Query: 94 VNEKPLKIEAATSRK 108
+ + I A +
Sbjct: 71 IKGISVHISNAEPKH 85
Score = 52.2 bits (126), Expect = 1e-09
Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 114 TTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV---RNYGFVHIDSPDI-NKCIKELNG 169
+KVFVG +++ A E+++ F YG VV+ I R + FV + E
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGEDL- 69
Query: 170 MMVDGKPMKVQISTSR 185
++ G + + + +
Sbjct: 70 -IIKGISVHISNAEPK 84
>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 = 53.8 bits (130), Expect = 4e-10
Identities = 19/98 (19%), Positives = 41/98 (41%), Gaps = 11/98 (11%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVH 154
++ K T+ + V L T +++E F +G V+ + ++ +GFV
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVR 63
Query: 155 IDSPD-INKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+ K + + + M+DG+ ++ S+ Q G
Sbjct: 64 FTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQDSG 99
Score = 53.4 bits (129), Expect = 7e-10
Identities = 13/88 (14%), Positives = 34/88 (38%), Gaps = 16/88 (18%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIK- 87
+ + + T+ + ++ F +G+V+ V K+ +GFV E +
Sbjct: 17 DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
Query: 88 --ELNGQIVNEKPLKIEAATSRKGPNTP 113
++G+ + K S++ ++
Sbjct: 77 RHMIDGRWCDCKL-----PNSKQSQDSG 99
>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 = 53.5 bits (129), Expect = 6e-10
Identities = 18/91 (19%), Positives = 34/91 (37%), Gaps = 13/91 (14%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYG-KVVECDVVKN--------YGFVHMENDEE 81
SS +++G++ P I F G V+ +++N Y FV +
Sbjct: 5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT 64
Query: 82 GRTAIKELNGQIVN----EKPLKIEAATSRK 108
+ ++NG+ + K K+ AT
Sbjct: 65 AEKCLHKINGKPLPGATPAKRFKLNYATYSG 95
Score = 51.9 bits (125), Expect = 2e-09
Identities = 18/83 (21%), Positives = 31/83 (37%), Gaps = 10/83 (12%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYG-TVVECDIVRN--------YGFVHIDSP- 158
G + +++G+L + F G TV+ I+RN Y FV
Sbjct: 4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLA 63
Query: 159 DINKCIKELNGMMVDGKPMKVQI 181
KC+ ++NG + G +
Sbjct: 64 TAEKCLHKINGKPLPGATPAKRF 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 = 7e-10
Identities = 16/93 (17%), Positives = 31/93 (33%), Gaps = 12/93 (12%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV----------KNYGFVHMENDE 80
S G ++FIG + E I K + V +V + + FV E+
Sbjct: 4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63
Query: 81 EGRTAIKELNGQ--IVNEKPLKIEAATSRKGPN 111
A ++L + + ++ A +
Sbjct: 64 AAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVD 96
Score = 43.2 bits (102), Expect = 4e-06
Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 13/83 (15%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----------RNYGFVHIDSPD 159
++ ++F+G + + E+ E V IV R + FV +S
Sbjct: 4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 63
Query: 160 I-NKCIKELN--GMMVDGKPMKV 179
++L + + G + V
Sbjct: 64 AAAMARRKLMPGRIQLWGHQIAV 86
>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 = 52.4 bits (126), Expect = 1e-09
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 13/84 (15%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELF-----------VPYGTVVECDIV--RNYGFVHI 155
GP +++VGN+ + + F P V+ I +N+ F+
Sbjct: 1 GPLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 60
Query: 156 DSPDINKCIKELNGMMVDGKPMKV 179
S D +G++ G+ +K+
Sbjct: 61 RSVDETTQAMAFDGIIFQGQSLKI 84
Score = 48.6 bits (116), Expect = 3e-08
Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 14/78 (17%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-------------KNYGFVHMENDEEGR 83
++++GN+ G + E + F ++ KN+ F+ + +E
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 84 TAIKELNGQIVNEKPLKI 101
A+ +G I + LKI
Sbjct: 68 QAM-AFDGIIFQGQSLKI 84
>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 = 56.4 bits (135), Expect = 1e-09
Identities = 23/123 (18%), Positives = 44/123 (35%), Gaps = 9/123 (7%)
Query: 77 ENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFV 136
E E R E Q V + + +FV ++ +T ++R F
Sbjct: 65 ERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFE 124
Query: 137 PYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELNGMMVDGKPMKVQISTSRVR 187
YG + +V + Y F+ + D++ K +G +DG+ + V + R
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV 184
Query: 188 QRP 190
+
Sbjct: 185 KGW 187
Score = 54.1 bits (129), Expect = 6e-09
Identities = 17/82 (20%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKEL 89
+F+ VN T+ +R FE YG + +V + Y F+ E++ + +A K
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 90 NGQIVNEKPLKIEAATSRKGPN 111
+G+ ++ + + ++ R
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKG 186
>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 = 52.6 bits (126), Expect = 1e-09
Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 15/84 (17%)
Query: 117 VFVGNLSDNTRAPEV---RELFVPYGTVVECDIVRN-----------YGFVHIDSPDI-N 161
VFV LS PEV E F +G + + I + +V +
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 162 KCIKELNGMMVDGKPMKVQISTSR 185
+ I+ +N ++VDG+ +K + T++
Sbjct: 78 RAIQCVNNVVVDGRTLKASLGTTK 101
Score = 52.6 bits (126), Expect = 2e-09
Identities = 17/93 (18%), Positives = 37/93 (39%), Gaps = 18/93 (19%)
Query: 38 IFIGNVNPGTSVELI---RPLFEKYGKVVECDVVKN-----------YGFVHMENDEEGR 83
+F+ ++ + + F K+GK+ + + + +V E+
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 84 TAIKELNGQIVNEKPLKIEAAT----SRKGPNT 112
AI+ +N +V+ + LK T S GP++
Sbjct: 78 RAIQCVNNVVVDGRTLKASLGTTKYCSYSGPSS 110
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 50.9 bits (123), Expect = 3e-09
Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 12/73 (16%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIK- 87
KIF+G ++ T+VE ++ FE++GKV + ++ + +GFV E+++ +
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 88 ---ELNGQIVNEK 97
E+N ++V K
Sbjct: 61 HFHEINNKMVECK 73
Score = 49.8 bits (120), Expect = 7e-09
Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 13/73 (17%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD-INKCIK- 165
K+FVG LS NT +V+ F +G V + ++ R +GFV +S D + K +
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 166 ---ELNGMMVDGK 175
E+N MV+ K
Sbjct: 61 HFHEINNKMVECK 73
>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 = 51.0 bits (123), Expect = 3e-09
Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 12/73 (16%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIK- 87
KIF+G ++P T E IR F +G+V ++ + + F+ + +E + ++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 88 ---ELNGQIVNEK 97
+ K
Sbjct: 61 KYHNVGLSKCEIK 73
Score = 48.7 bits (117), Expect = 2e-08
Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 13/73 (17%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--------RNYGFVHIDSPD-INKCIK- 165
K+FVG LS +T ++RE F +G V ++ R + F+ + + K ++
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 166 ---ELNGMMVDGK 175
+ + K
Sbjct: 61 KYHNVGLSKCEIK 73
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 51.4 bits (123), Expect = 4e-09
Identities = 12/88 (13%), Positives = 29/88 (32%), Gaps = 5/88 (5%)
Query: 25 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-----KNYGFVHMEND 79
+ ++I + N+ G S + ++ L + V G + ++
Sbjct: 18 GSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSE 77
Query: 80 EEGRTAIKELNGQIVNEKPLKIEAATSR 107
E A++ LN + +E +
Sbjct: 78 EILVEALERLNNIEFRGSVITVERDDNP 105
Score = 46.7 bits (111), Expect = 2e-07
Identities = 11/90 (12%), Positives = 28/90 (31%), Gaps = 6/90 (6%)
Query: 106 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV-----RNYGFVHIDSP-D 159
++ + NL + ++++L V G + S
Sbjct: 20 HMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEI 79
Query: 160 INKCIKELNGMMVDGKPMKVQISTSRVRQR 189
+ + ++ LN + G + V+ + R
Sbjct: 80 LVEALERLNNIEFRGSVITVERDDNPPPIR 109
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 51.1 bits (122), Expect = 6e-09
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 2/59 (3%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKELNGQIV 94
+ G + G S + P+ EK G V + K Y F EE + A LNG+ V
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEV 88
Score = 39.1 bits (91), Expect = 1e-04
Identities = 15/83 (18%), Positives = 30/83 (36%), Gaps = 4/83 (4%)
Query: 112 TPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHIDSP-DINKCIKELN 168
T + V G L + ++ + G V + + Y F + + + LN
Sbjct: 25 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLN 84
Query: 169 G-MMVDGKPMKVQISTSRVRQRP 190
G +VD K+ + + V +
Sbjct: 85 GKEVVDDLGQKITLYLNFVEKVQ 107
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 49.8 bits (120), Expect = 7e-09
Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 12/73 (16%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIK- 87
K+FIG ++ T+ E +R F ++G+V EC V+++ +GFV + +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 88 ---ELNGQIVNEK 97
EL+ + ++ K
Sbjct: 62 SRHELDSKTIDPK 74
Score = 45.6 bits (109), Expect = 3e-07
Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 13/73 (17%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSPD-INKCIK- 165
K+F+G LS T +RE F +G V EC ++R+ +GFV ++K +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 166 ---ELNGMMVDGK 175
EL+ +D K
Sbjct: 62 SRHELDSKTIDPK 74
>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 = 50.4 bits (121), Expect = 8e-09
Identities = 16/87 (18%), Positives = 32/87 (36%), Gaps = 8/87 (9%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMEND 79
G I + N+ S++ I F Y + +K V E+
Sbjct: 8 SSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67
Query: 80 EEGRTAIKELNGQIVNEKPLKIEAATS 106
+E A+ +LN + + + +K+ +S
Sbjct: 68 DEATAAVIDLNDRPIGSRKVKLSGPSS 94
Score = 49.6 bits (119), Expect = 1e-08
Identities = 16/92 (17%), Positives = 32/92 (34%), Gaps = 10/92 (10%)
Query: 103 AATSRKGPNTP-TTKVFVGNLSDNTRAPEVRELFVPYGTVVEC-DIVRN-------YGFV 153
+ +S P T + V N+ E+ + F Y + + N V
Sbjct: 3 SGSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMV 62
Query: 154 HIDSPDI-NKCIKELNGMMVDGKPMKVQISTS 184
+S D + +LN + + +K+ +S
Sbjct: 63 AFESRDEATAAVIDLNDRPIGSRKVKLSGPSS 94
>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 = 1e-08
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 17/85 (20%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIK- 87
K+FIG ++ T+ E +R F ++G+V EC V+++ +GFV + +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 88 ---ELNGQIVNEKPLKIEAATSRKG 109
EL+ + ++ K A R+
Sbjct: 87 SRHELDSKTIDPKV-----AFPRRA 106
Score = 47.3 bits (113), Expect = 1e-07
Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 8/87 (9%)
Query: 107 RKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP 158
+ K+F+G LS T +RE F +G V EC ++R+ +GFV
Sbjct: 18 GSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
Query: 159 DINKCIKELNGMMVDGKPMKVQISTSR 185
+ + +D K + +++ R
Sbjct: 78 AGVDKVLAQSRHELDSKTIDPKVAFPR 104
>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 = 50.4 bits (121), Expect = 1e-08
Identities = 22/105 (20%), Positives = 45/105 (42%), Gaps = 10/105 (9%)
Query: 96 EKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN------ 149
EK L+ +K K+F+G LS T +R + +G + +C ++R+
Sbjct: 9 EKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRS 68
Query: 150 --YGFVHIDSPD-INKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+GFV S ++ + +DG+ ++ + + +R G
Sbjct: 69 RGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVAREESGSG 112
Score = 49.6 bits (119), Expect = 2e-08
Identities = 19/85 (22%), Positives = 44/85 (51%), Gaps = 9/85 (10%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKE 88
K+FIG ++ T+ E +R +E++GK+ +C V+++ +GFV + E A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 89 LNGQIVNEKPLKIEAATSRKGPNTP 113
++ + ++ + A +R+ +
Sbjct: 89 -RPHSIDGRVVEPKRAVAREESGSG 112
>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 = 49.6 bits (119), Expect = 1e-08
Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 8/87 (9%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMEND 79
G I + N+ S++ I F Y + +K V E+
Sbjct: 8 ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67
Query: 80 EEGRTAIKELNGQIVNEKPLKIEAATS 106
+E A+ +LN + + + +K+ +
Sbjct: 68 DEATAAVIDLNDRPIGSRKVKLVLGSG 94
Score = 49.2 bits (118), Expect = 2e-08
Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 9/80 (11%)
Query: 114 TTKVFVGNLSDNTRAPEVRELFVPYGTVVEC-DIVRN-------YGFVHIDSPDI-NKCI 164
T + V N+ E+ + F Y + + N V +S D +
Sbjct: 15 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74
Query: 165 KELNGMMVDGKPMKVQISTS 184
+LN + + +K+ + +
Sbjct: 75 IDLNDRPIGSRKVKLVLGSG 94
>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 = 48.7 bits (117), Expect = 2e-08
Identities = 18/85 (21%), Positives = 36/85 (42%), Gaps = 10/85 (11%)
Query: 104 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHI 155
+ K+FVG LS +T ++++ F +G VV+C I + +GF+
Sbjct: 1 GINASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILF 60
Query: 156 DSPD-INKCIKELNGMMVDGKPMKV 179
+ K + + +DG+ +
Sbjct: 61 KDAASVEKVLDQKEH-RLDGRVIDP 84
Score = 48.7 bits (117), Expect = 2e-08
Identities = 16/73 (21%), Positives = 38/73 (52%), Gaps = 12/73 (16%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIK- 87
K+F+G ++ TS + ++ F K+G+VV+C + + +GF+ ++ +
Sbjct: 13 KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 88 ---ELNGQIVNEK 97
L+G++++ K
Sbjct: 73 KEHRLDGRVIDPK 85
>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 = 48.8 bits (117), Expect = 3e-08
Identities = 25/98 (25%), Positives = 42/98 (42%), Gaps = 9/98 (9%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFV 153
+ + G + K+FVG L +T +R F YG VV+C I+++ +GFV
Sbjct: 5 SSGMNNSGADEIG-KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63
Query: 154 HIDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
P+ + +DG+ + + T R Q G
Sbjct: 64 KFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPSG 101
Score = 48.8 bits (117), Expect = 3e-08
Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 17/83 (20%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIK- 87
K+F+G ++ T+ E +R F +YG+VV+C ++K+ +GFV ++ T +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 88 ---ELNGQIVNEKPLKIEAATSR 107
L+G+ ++ KP T R
Sbjct: 78 RPHTLDGRNIDPKP-----CTPR 95
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 49.0 bits (116), Expect = 2e-07
Identities = 18/112 (16%), Positives = 34/112 (30%), Gaps = 17/112 (15%)
Query: 1 MSRFDQQQLVKVSRYSNNQINISCRNMPGFSSVGTFKIFIGNVNPGTSV---------EL 51
D K + Y + G +++G ++ +
Sbjct: 106 TEVLDCFGREKFADYREDM------GGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESR 159
Query: 52 IRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIKELNGQIVNEKPLKI 101
IR +F + G + V KN GFV + A + ++ Q + K
Sbjct: 160 IRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKE 211
Score = 37.5 bits (86), Expect = 0.002
Identities = 15/132 (11%), Positives = 37/132 (28%), Gaps = 16/132 (12%)
Query: 64 ECDVVKNYGFVH-MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGP---NTPTTKVFV 119
C + ++H + ++E+ + + G ++V
Sbjct: 80 MCCLGPKCEYLHHIPDEEDIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYV 139
Query: 120 GNLSDNTRAP---------EVRELFVPYGTVVECDIV--RNYGFVH-IDSPDINKCIKEL 167
G + + +R +F G + V +N GFV + + +
Sbjct: 140 GGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQANAEFAKEAM 199
Query: 168 NGMMVDGKPMKV 179
+ + K
Sbjct: 200 SNQTLLLPSDKE 211
>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 = 46.1 bits (109), Expect = 2e-07
Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 9/85 (10%)
Query: 37 KIFIGNVNPGTSV----ELIRPLFEKYGKVVECDVVKN-----YGFVHMENDEEGRTAIK 87
+ + N++ S +L++ F ++GKV ++ + V MEN ++ A+
Sbjct: 11 DVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIGAVN 70
Query: 88 ELNGQIVNEKPLKIEAATSRKGPNT 112
L+ + K + + AT GP++
Sbjct: 71 SLHRYKIGSKKILVSLATGASGPSS 95
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 46.3 bits (110), Expect = 3e-07
Identities = 12/81 (14%), Positives = 25/81 (30%), Gaps = 7/81 (8%)
Query: 116 KVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSPDINKCIKELN 168
V++ + +++E G V+ + R FV DS + K E
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 72
Query: 169 GMMVDGKPMKVQISTSRVRQR 189
G + + ++
Sbjct: 73 GQKYKETDLLILFKDDYFAKK 93
Score = 44.3 bits (105), Expect = 1e-06
Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 8/72 (11%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIKEL 89
++I +++ I+ E G+V+ + + FV ++ E + + E
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFV-ET 71
Query: 90 NGQIVNEKPLKI 101
GQ E L I
Sbjct: 72 PGQKYKETDLLI 83
>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 = 45.6 bits (108), Expect = 7e-07
Identities = 11/88 (12%), Positives = 26/88 (29%), Gaps = 8/88 (9%)
Query: 106 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC-DIVRN-------YGFVHIDS 157
S + V + L E+ + F V + + FV S
Sbjct: 34 SNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFAS 93
Query: 158 PDINKCIKELNGMMVDGKPMKVQISTSR 185
++ + + + + ++V S+
Sbjct: 94 QELAEKALGKHKERIGHRYIEVFKSSQE 121
Score = 36.0 bits (83), Expect = 0.002
Identities = 9/81 (11%), Positives = 25/81 (30%), Gaps = 9/81 (11%)
Query: 35 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAI 86
+ + + G + E I F V + FV + E A+
Sbjct: 42 DGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL 101
Query: 87 KELNGQIVNEKPLKIEAATSR 107
+ + + + +++ ++
Sbjct: 102 -GKHKERIGHRYIEVFKSSQE 121
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 44.7 bits (106), Expect = 1e-06
Identities = 13/73 (17%), Positives = 27/73 (36%), Gaps = 12/73 (16%)
Query: 37 KIFIGNV------NPGTSVELIRPLFEKYGKVVECDVVKN------YGFVHMENDEEGRT 84
I + NV +I +F K+GK+ + Y F+ +
Sbjct: 17 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVD 76
Query: 85 AIKELNGQIVNEK 97
A+K +G ++++
Sbjct: 77 AVKNADGYKLDKQ 89
Score = 38.9 bits (91), Expect = 1e-04
Identities = 11/74 (14%), Positives = 24/74 (32%), Gaps = 13/74 (17%)
Query: 115 TKVFVGNLSDNTRA------PEVRELFVPYGTVVECDIVRN------YGFVHIDSPDI-N 161
+ + V N+ + ++F +G + Y F+ SP
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 75
Query: 162 KCIKELNGMMVDGK 175
+K +G +D +
Sbjct: 76 DAVKNADGYKLDKQ 89
>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 = 44.8 bits (106), Expect = 2e-06
Identities = 13/89 (14%), Positives = 27/89 (30%), Gaps = 8/89 (8%)
Query: 105 TSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC-DIVRN-------YGFVHID 156
+ + P+ V++ L V + F V + I GFV
Sbjct: 16 SRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFR 75
Query: 157 SPDINKCIKELNGMMVDGKPMKVQISTSR 185
+ K + + + ++V T +
Sbjct: 76 NEADYKAALCRHKQYMGNRFIQVHPITKK 104
Score = 36.4 bits (84), Expect = 0.001
Identities = 12/92 (13%), Positives = 33/92 (35%), Gaps = 9/92 (9%)
Query: 25 RNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVEC-DVVKN-------YGFVHM 76
R+ F +++ + + + F+K V + + GFV
Sbjct: 15 RSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEF 74
Query: 77 ENDEEGRTAIKELNGQIVNEKPLKIEAATSRK 108
N+ + + A+ + Q + + +++ T +
Sbjct: 75 RNEADYKAAL-CRHKQYMGNRFIQVHPITKKG 105
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 44.0 bits (104), Expect = 2e-06
Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 8/62 (12%)
Query: 39 FIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEGRTAIKELN 90
I + + + LF K GKVV + + + FV + + + IK +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 91 GQ 92
G+
Sbjct: 76 GK 77
Score = 39.7 bits (93), Expect = 7e-05
Identities = 15/67 (22%), Positives = 23/67 (34%), Gaps = 9/67 (13%)
Query: 118 FVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGFVHIDSP-DINKCIKELN 168
+ + + LF G VV + + + FV S D K IK +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 169 GMMVDGK 175
G +D K
Sbjct: 76 GKRLDLK 82
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 44.0 bits (104), Expect = 3e-06
Identities = 9/97 (9%), Positives = 29/97 (29%), Gaps = 8/97 (8%)
Query: 103 AATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVEC-DIVRN-------YGFVH 154
++ N+ + N+ + +V + ++ + V
Sbjct: 4 GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQ 63
Query: 155 IDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+ D + + L+ ++G+ V + T +
Sbjct: 64 FKNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIE 100
Score = 38.6 bits (90), Expect = 2e-04
Identities = 13/90 (14%), Positives = 28/90 (31%), Gaps = 11/90 (12%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV---------KNYGFVHMEN 78
G + I N+ + + E V E V V +N
Sbjct: 8 EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIP-VDENAVHVLVDNNGQGLGQALVQFKN 66
Query: 79 DEEGRTAIKELNGQIVNEKPLKIEAATSRK 108
+++ R + + L+ + +N + + T
Sbjct: 67 EDDARKSER-LHRKKLNGREAFVHVVTLED 95
>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 = 43.8 bits (103), Expect = 3e-06
Identities = 13/83 (15%), Positives = 25/83 (30%), Gaps = 6/83 (7%)
Query: 108 KGPNTPTTKVFVGNL-SDNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPDINKCIK- 165
+ + NL V +L PYG + ++R I+ +
Sbjct: 19 DQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAM 78
Query: 166 ----ELNGMMVDGKPMKVQISTS 184
+ G+ +KV +S
Sbjct: 79 VDHCLKKALWFQGRCVKVDLSEK 101
Score = 41.1 bits (96), Expect = 3e-05
Identities = 18/84 (21%), Positives = 36/84 (42%), Gaps = 9/84 (10%)
Query: 38 IFIGNV-NPGTSVELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTAIK--ELNGQ 92
I + N+ + G S + L E YGK+ ++ K+ F+ ME E+ +
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETREDAMAMVDHCLKKAL 87
Query: 93 IVNEKPLKIEAATSRK----GPNT 112
+ +K++ + K GP++
Sbjct: 88 WFQGRCVKVDLSEKYKKLVSGPSS 111
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 43.4 bits (102), Expect = 4e-06
Identities = 18/109 (16%), Positives = 34/109 (31%), Gaps = 19/109 (17%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKY-----GKVVECDVVKNYGFVHMENDEEGRTA 85
S G + + + P EL+ FE G V+ + G + +
Sbjct: 4 GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERV 63
Query: 86 IK----ELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGNLSDNTRAPE 130
+ EL+G ++ +P P ++ + L T P
Sbjct: 64 LAQADHELHGAQLSLRP----------APPRAPARLLLQGLPPGTSGPS 102
Score = 31.1 bits (70), Expect = 0.073
Identities = 13/73 (17%), Positives = 22/73 (30%), Gaps = 10/73 (13%)
Query: 114 TTKVFVGNLSDNTRAPEVRELF-----VPYGTVVECDIVRNYGFVHIDSP-DINKCIK-- 165
V V L + F G V+ + G + P D + +
Sbjct: 8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPADAERVLAQA 67
Query: 166 --ELNGMMVDGKP 176
EL+G + +P
Sbjct: 68 DHELHGAQLSLRP 80
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 41.9 bits (98), Expect = 1e-05
Identities = 20/99 (20%), Positives = 35/99 (35%), Gaps = 21/99 (21%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----------RNYGFVHIDSP 158
++ + KVFVG L + E+ F +G +V + Y F+
Sbjct: 3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEE 62
Query: 159 D-----INKCIKELNGM--MVDGKPMKVQISTSRVRQRP 190
I+ C++E + V +K V+ RP
Sbjct: 63 SSVQALIDACLEEDGKLYLCVSSPTIKD----KPVQIRP 97
Score = 38.8 bits (90), Expect = 2e-04
Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 10/54 (18%)
Query: 37 KIFIGNVNPGTSVELIRPLFEKYGKVVECDVV----------KNYGFVHMENDE 80
K+F+G + P + I F ++G +V K Y F+ + +
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63
>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 = 41.7 bits (98), Expect = 1e-05
Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 8/83 (9%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSPDINK 162
N V V + + +VR+ F V ++++ G V SP
Sbjct: 12 INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGRNNGNGLVKFLSPQDTF 70
Query: 163 CIKELNGMMVDGKPMKVQISTSR 185
+ N M++ + ++V +T R
Sbjct: 71 EALKRNRMLMIQRYVEVSPATER 93
Score = 33.2 bits (76), Expect = 0.015
Identities = 11/82 (13%), Positives = 32/82 (39%), Gaps = 9/82 (10%)
Query: 34 GTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAI 86
+ + + +R F +V ++K+ G V + ++ A+
Sbjct: 15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL 73
Query: 87 KELNGQIVNEKPLKIEAATSRK 108
+ N ++ ++ +++ AT R+
Sbjct: 74 -KRNRMLMIQRYVEVSPATERQ 94
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 40.8 bits (96), Expect = 2e-05
Identities = 13/66 (19%), Positives = 23/66 (34%), Gaps = 12/66 (18%)
Query: 38 IFIGNV------NPGTSVELIRPLFEKYGKVVECDVVKN------YGFVHMENDEEGRTA 85
I + NV +I +F K+GK+ + Y F+ + A
Sbjct: 4 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDA 63
Query: 86 IKELNG 91
+K +G
Sbjct: 64 VKNADG 69
Score = 33.9 bits (78), Expect = 0.004
Identities = 11/74 (14%), Positives = 24/74 (32%), Gaps = 13/74 (17%)
Query: 115 TKVFVGNLSDNTRA------PEVRELFVPYGTVVECDIVRN------YGFVHIDSP-DIN 161
+ + V N+ + ++F +G + Y F+ SP
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAV 61
Query: 162 KCIKELNGMMVDGK 175
+K +G +D +
Sbjct: 62 DAVKNADGYKLDKQ 75
>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 = 41.3 bits (97), Expect = 2e-05
Identities = 15/99 (15%), Positives = 32/99 (32%), Gaps = 12/99 (12%)
Query: 105 TSRKGPNTPTTK----VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN--------YGF 152
+S N+P T V + L E+ + F V + F
Sbjct: 2 SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61
Query: 153 VHIDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
V S +I + + + + + +++ S+ + G
Sbjct: 62 VQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTSG 100
Score = 33.2 bits (76), Expect = 0.014
Identities = 11/85 (12%), Positives = 27/85 (31%), Gaps = 9/85 (10%)
Query: 31 SSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN--------YGFVHMENDEEG 82
+ + + + G S E I F V + FV + E
Sbjct: 11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70
Query: 83 RTAIKELNGQIVNEKPLKIEAATSR 107
A+ + + + + + ++I ++
Sbjct: 71 EKAL-KKHKERIGHRYIEIFKSSRA 94
>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 = 40.7 bits (96), Expect = 2e-05
Identities = 20/86 (23%), Positives = 28/86 (32%), Gaps = 8/86 (9%)
Query: 106 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSP 158
S T V + N V E P V IVRN Y FV +
Sbjct: 2 SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNE 60
Query: 159 DINKCIKELNGMMVDGKPMKVQISTS 184
+ K + N + G+ ++V S
Sbjct: 61 EEVKQALKCNREYMGGRYIEVFREKS 86
Score = 35.4 bits (82), Expect = 0.002
Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 11/92 (11%)
Query: 28 PGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDE 80
G S + + + + + K V +V+N Y FV N+E
Sbjct: 3 SGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEE 61
Query: 81 EGRTAIKELNGQIVNEKPLKIEAATSRKGPNT 112
E + A+K N + + + IE + GP++
Sbjct: 62 EVKQALK-CNREYMGGRY--IEVFREKSGPSS 90
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 41.4 bits (97), Expect = 3e-05
Identities = 8/95 (8%), Positives = 25/95 (26%), Gaps = 8/95 (8%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVH 154
+ +T V + L ++ F P V I V
Sbjct: 34 SGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVE 92
Query: 155 IDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQR 189
+ + + + + +++ ++++
Sbjct: 93 FATHEEAVAAMSKDRANMQHRYIELFLNSTTGASN 127
Score = 32.9 bits (75), Expect = 0.024
Identities = 8/85 (9%), Positives = 22/85 (25%), Gaps = 9/85 (10%)
Query: 36 FKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEGRTAIKE 88
+ + + + I F V + V EE A+
Sbjct: 47 HCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-S 104
Query: 89 LNGQIVNEKPLKIEAATSRKGPNTP 113
+ + + +++ ++ N
Sbjct: 105 KDRANMQHRYIELFLNSTTGASNGA 129
>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 = 40.1 bits (94), Expect = 4e-05
Identities = 8/91 (8%), Positives = 25/91 (27%), Gaps = 8/91 (8%)
Query: 108 KGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN-------YGFVHIDSPDI 160
+T V + L ++ F P + I V + +
Sbjct: 9 SFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHED 67
Query: 161 NKCIKELNGMMVDGKPMKVQISTSRVRQRPG 191
+ + + +++ ++++ G
Sbjct: 68 AVAAMAKDKANMQHRYVELFLNSTAGTSGSG 98
Score = 32.8 bits (75), Expect = 0.020
Identities = 12/94 (12%), Positives = 28/94 (29%), Gaps = 13/94 (13%)
Query: 30 FSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVVKN-------YGFVHMENDEEG 82
F S + + + + I F + + V E+
Sbjct: 10 FQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEADVEFATHEDA 68
Query: 83 RTAIKELNGQIVNEKPLKI----EAATSRKGPNT 112
A+ + + + +++ A TS GP++
Sbjct: 69 VAAM-AKDKANMQHRYVELFLNSTAGTSGSGPSS 101
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 39.5 bits (92), Expect = 9e-05
Identities = 18/96 (18%), Positives = 39/96 (40%), Gaps = 7/96 (7%)
Query: 103 AATSRKGPNTPTTKV-FVGNL-SDNTRAPEVRELFVPYGTVVECDIV--RNYGFVHI-DS 157
+ +S + T +V + + ++ +L P+G + I+ N F+ + +
Sbjct: 3 SGSSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATT 62
Query: 158 PDINKCIK--ELNGMMVDGKPMKVQISTSRVRQRPG 191
D + +V GKP++V +S R + G
Sbjct: 63 EDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKSG 98
>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 = 40.6 bits (94), Expect = 1e-04
Identities = 13/95 (13%), Positives = 31/95 (32%), Gaps = 8/95 (8%)
Query: 15 YSNNQINISCRNMPGFSSVGTFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV------ 68
+ + + V ++I +++ I+ E G+V+ +
Sbjct: 89 RRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKA 148
Query: 69 -KNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIE 102
K FV ++ E + ++ + E L I
Sbjct: 149 FKGSIFVVFDSIESAKKFVETPGQK-YKETDLLIL 182
Score = 30.6 bits (68), Expect = 0.26
Identities = 8/81 (9%), Positives = 23/81 (28%), Gaps = 9/81 (11%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNY-----GFVHI---DSPDIN 161
+ V++ + +++E G V+ + R G + +
Sbjct: 105 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 164
Query: 162 KCIKELNGMMVDGKPMKVQIS 182
K ++ G + +
Sbjct: 165 KFVETP-GQKYKETDLLILFK 184
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 40.2 bits (93), Expect = 3e-04
Identities = 36/242 (14%), Positives = 66/242 (27%), Gaps = 70/242 (28%)
Query: 4 FDQQQLVKVSRYSNNQI----------NISCRNMPGF-SSVGTFKIFIGNVNPGTSVELI 52
F+ + +Y I N C+++ S+ + + + +V
Sbjct: 9 FETGEH----QYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGT 64
Query: 53 RPLF--------EKYGKVVECDVVKNYGFVHMENDEEGRTAIKELNGQIVNEKPLKIEAA 104
LF E K VE + NY F+ + IK Q + IE
Sbjct: 65 LRLFWTLLSKQEEMVQKFVEEVLRINYKFLM--------SPIKTEQRQPSMMTRMYIEQR 116
Query: 105 TSRKGPNTPTTKVFVGNLSDNTRAPEVREL------------FVPYG------TVVECDI 146
N K V +R +L + G T V D+
Sbjct: 117 DRLYNDNQVFAKYNV------SRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDV 170
Query: 147 VRNYGFV-------------HIDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQRPGVD 193
+Y + +SP+ ++ L ++ P S + +
Sbjct: 171 CLSYKVQCKMDFKIFWLNLKNCNSPE--TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIH 228
Query: 194 EV 195
+
Sbjct: 229 SI 230
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 37.9 bits (88), Expect = 4e-04
Identities = 12/95 (12%), Positives = 28/95 (29%), Gaps = 11/95 (11%)
Query: 106 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECD----IVRN-------YGFVH 154
++ V + L A EV F + + V FV
Sbjct: 15 AQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVL 74
Query: 155 IDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQR 189
+ + + ++ + +++ ST+ Q+
Sbjct: 75 FACEEYAQNALRKHKDLLGKRYIELFRSTAAEVQQ 109
Score = 27.9 bits (62), Expect = 1.2
Identities = 7/84 (8%), Positives = 28/84 (33%), Gaps = 12/84 (14%)
Query: 35 TFKIFIGNVNPGTSVELIRPLFEKYGKVVECDVV-----------KNYGFVHMENDEEGR 83
+ + + + E + F ++ + FV +E +
Sbjct: 23 QVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQ 82
Query: 84 TAIKELNGQIVNEKPLKIEAATSR 107
A+ + ++ ++ +++ +T+
Sbjct: 83 NAL-RKHKDLLGKRYIELFRSTAA 105
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 39.4 bits (91), Expect = 4e-04
Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 4/73 (5%)
Query: 30 FSSVGTFKIFIGNVNPGTSV--ELIRPLFEKYGKVVECDVV--KNYGFVHMENDEEGRTA 85
S T + + N G V + P+ EK G V + K Y F EE + A
Sbjct: 13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRA 72
Query: 86 IKELNGQIVNEKP 98
LNG+ V +
Sbjct: 73 YVTLNGKEVVDDL 85
>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 = 37.5 bits (87), Expect = 4e-04
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 7/60 (11%)
Query: 50 ELIRPLFEKYGKVVECDVVKNYG-------FVHMENDEEGRTAIKELNGQIVNEKPLKIE 102
E+ + EKYG+V E +V N G +V +E+ A+ +LN + N +P+ E
Sbjct: 42 EVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101
Score = 33.7 bits (77), Expect = 0.010
Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 8/67 (11%)
Query: 124 DNTRAPEVRELFVPYGTVVECDIVRN-----YGFVHI---DSPDINKCIKELNGMMVDGK 175
D E+ YG V E ++ N G V++ D K + +LN +G+
Sbjct: 37 DEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ 96
Query: 176 PMKVQIS 182
P+ ++S
Sbjct: 97 PIHAELS 103
>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 = 38.2 bits (88), Expect = 6e-04
Identities = 14/102 (13%), Positives = 37/102 (36%), Gaps = 8/102 (7%)
Query: 8 QLVKVSRYSNNQINISCRNMPGFSSVG----TFKIFIGNVNPGTSVELIRPLFEKYGKVV 63
Q V + N + S + ++ +I + N+ +++++ +F K+G V+
Sbjct: 15 QAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVL 74
Query: 64 ECDVVK----NYGFVHMENDEEGRTAIKELNGQIVNEKPLKI 101
+ + + + A L+GQ + +
Sbjct: 75 KIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL 116
Score = 35.8 bits (82), Expect = 0.004
Identities = 19/123 (15%), Positives = 41/123 (33%), Gaps = 9/123 (7%)
Query: 75 HMENDEEGRTAIKELNGQIVNEKPLKIEAAT----SRKGPNTPTTKVFVGNLSDNTRAPE 130
H + + A++ +N L AA +P ++ V NL
Sbjct: 3 HHHHHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDV 62
Query: 131 VRELFVPYGTVVECDIV----RNYGFVHIDSPDI-NKCIKELNGMMVDGKPMKVQISTSR 185
+ ++F +GTV++ + + P L+G + ++I S+
Sbjct: 63 LHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK 122
Query: 186 VRQ 188
+
Sbjct: 123 LTS 125
>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 = 37.7 bits (87), Expect = 6e-04
Identities = 10/98 (10%), Positives = 23/98 (23%), Gaps = 10/98 (10%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPY---GTVVECDIVRN-------YG 151
+ V + L + +V+ +
Sbjct: 32 RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91
Query: 152 FVHIDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQR 189
FV + S D K + + + + ++V S
Sbjct: 92 FVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMDW 129
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 36.9 bits (85), Expect = 0.001
Identities = 12/73 (16%), Positives = 31/73 (42%), Gaps = 6/73 (8%)
Query: 38 IFIGNVNPGTSVELIRPLFEKYGKVVECDVVK----NYGFVHMENDEEGRTAIKELNGQI 93
I + N+ +++++ +F K+G V++ + + + A L+GQ
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQN 90
Query: 94 VNEKP--LKIEAA 104
+ L+I+ +
Sbjct: 91 IYNACCTLRIDFS 103
Score = 28.8 bits (64), Expect = 0.73
Identities = 13/88 (14%), Positives = 30/88 (34%), Gaps = 5/88 (5%)
Query: 106 SRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIV----RNYGFVHIDSPDI- 160
+P ++ V NL + ++F +GTV++ + + P
Sbjct: 20 MAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSA 79
Query: 161 NKCIKELNGMMVDGKPMKVQISTSRVRQ 188
L+G + ++I S++
Sbjct: 80 QHAKLSLDGQNIYNACCTLRIDFSKLTS 107
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 35.1 bits (80), Expect = 0.003
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 5/62 (8%)
Query: 44 NPGTSVELIRPLFEKYGKV---VECDVVKNYGFVHMENDEEGRTAIKELNGQIVNEKPLK 100
G S +++ L +KYG+V V V + A++ G + N PLK
Sbjct: 26 KGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKAAELAVQNEVGLVDN--PLK 83
Query: 101 IE 102
I
Sbjct: 84 IS 85
>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 = 37.0 bits (85), Expect = 0.004
Identities = 24/136 (17%), Positives = 48/136 (35%), Gaps = 37/136 (27%)
Query: 65 CDVVKNYG-FVH--MENDEEGRTAIKELNGQIVNEKPLKIEAATSRKGPNTPTTKVFVGN 121
+VV G + + DE GR+ N ++ P ++ A+ S++ + V
Sbjct: 1783 VEVVFYRGMTMQVAVPRDELGRS-----NYGMIAINPGRVAASFSQE-----ALQYVVER 1832
Query: 122 LSDNTRAPEVRELFVPYGTVVECDIVRNY---GFVHIDSPDIN------KCIKELNGMMV 172
+ T G +VE IV NY ++ + D+ + + +
Sbjct: 1833 VGKRT------------GWLVE--IV-NYNVENQQYVAAGDLRALDTVTNVLNFIKLQKI 1877
Query: 173 DGKPMKVQISTSRVRQ 188
D ++ +S V
Sbjct: 1878 DIIELQKSLSLEEVEG 1893
Score = 30.8 bits (69), Expect = 0.32
Identities = 25/142 (17%), Positives = 50/142 (35%), Gaps = 44/142 (30%)
Query: 45 PGTSVELI-RPLFEKY-GKVVECDVVKNYG---------F---------VH-----MEND 79
P T EL+ + F Y +VE V + F +H + +
Sbjct: 54 PTTPAELVGK--FLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQE 111
Query: 80 EEGR-TAIKEL-----NGQIVNEKPLKIEAATSR--KGPNTPTTKVFV-----GNLSDNT 126
+ KEL +I+ ++P + + S + ++ GN +
Sbjct: 112 NDTTLVKTKELIKNYITARIMAKRPFD-KKSNSALFRAVGEGNAQLVAIFGGQGN--TDD 168
Query: 127 RAPEVRELFVPYGTVVECDIVR 148
E+R+L+ Y +V D+++
Sbjct: 169 YFEELRDLYQTYHVLVG-DLIK 189
>3ec8_A Putative uncharacterized protein FLJ10324; beta barrel, helix,
structural genomics, structural genomics consortium,
SGC, cell adhesion; 2.60A {Homo sapiens}
Length = 166
Score = 35.1 bits (80), Expect = 0.007
Identities = 19/87 (21%), Positives = 28/87 (32%), Gaps = 25/87 (28%)
Query: 34 GTFKIFIGNVNPG------------TSVELIRPLFEKYGKVVE-------CDVVKNYGFV 74
G K+F +V G ++ EL++ E+Y CDVV G
Sbjct: 36 GVLKVFGDSVCTGTHYKSVLATGTSSARELVKEALERYALDPRQAGQYVLCDVVGQAGDA 95
Query: 75 HMENDEEGRTAIKELNGQIVNEKPLKI 101
+ +EKPL I
Sbjct: 96 GQRWQARCFRVFGD------SEKPLLI 116
>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 = 34.5 bits (79), Expect = 0.007
Identities = 11/98 (11%), Positives = 24/98 (24%), Gaps = 10/98 (10%)
Query: 102 EAATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR----------NYG 151
+ V + L + +V+ V
Sbjct: 5 SSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEA 64
Query: 152 FVHIDSPDINKCIKELNGMMVDGKPMKVQISTSRVRQR 189
FV ++S D K + + + + ++V S
Sbjct: 65 FVELESEDDVKLALKKDRESMGHRYIEVFKSHRTEMDW 102
>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 = 33.3 bits (76), Expect = 0.014
Identities = 7/92 (7%), Positives = 25/92 (27%), Gaps = 11/92 (11%)
Query: 104 ATSRKGPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN----------YGFV 153
+ + + + L + +V F + + +
Sbjct: 2 SKLEEEVDDVFL-IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALI 60
Query: 154 HIDSPDINKCIKELNGMMVDGKPMKVQISTSR 185
++S + E + M + + ++V +
Sbjct: 61 EMESEQDVQKALEKHRMYMGQRYVEVYEINNE 92
>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 = 32.0 bits (73), Expect = 0.041
Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 50 ELIRPLFEKYGKVVECDVVKNYG----FVHMENDEEGRTAIKELNG 91
E +R K+G++ + + + V + EE I+ L+G
Sbjct: 41 EDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDG 86
Score = 29.3 bits (66), Expect = 0.35
Identities = 10/56 (17%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 130 EVRELFVPYGTVVECDIVRNY--GFVHI---DSPDINKCIKELNGMMVDGKPMKVQ 180
++R +G + + + + G + D + + CI+ L+G G+ + Q
Sbjct: 42 DLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 97
>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 = 30.8 bits (70), Expect = 0.10
Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 4/44 (9%)
Query: 52 IRPLFEKYGKVVECDVVKNYG----FVHMENDEEGRTAIKELNG 91
+ K+G V+ V KN +V + A+ L+G
Sbjct: 34 VIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHG 77
Score = 29.2 bits (66), Expect = 0.37
Identities = 11/55 (20%), Positives = 20/55 (36%), Gaps = 5/55 (9%)
Query: 130 EVRELFVPYGTVVECDIVRNYG----FVHIDSPDI-NKCIKELNGMMVDGKPMKV 179
+V E +G V+ + +N +V S + L+G GK +
Sbjct: 33 DVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITA 87
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 30.0 bits (67), Expect = 0.14
Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 3/78 (3%)
Query: 109 GPNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVRNYGFVHI---DSPDINKCIK 165
++ + + NL+ P +R L + +G +V N G + NK
Sbjct: 2 AMAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREEANKAQM 61
Query: 166 ELNGMMVDGKPMKVQIST 183
LN ++ + + +
Sbjct: 62 ALNNCVLANTTIFAESPS 79
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 30.3 bits (68), Expect = 0.17
Identities = 13/72 (18%), Positives = 27/72 (37%), Gaps = 5/72 (6%)
Query: 39 FIGNVNPGTSVELIRPLFEKYGKVVECDVVK--NYGFVHMENDEE---GRTAIKELNGQI 93
F G+++ T E + LF +G++ D V+ G + + + G+
Sbjct: 23 FSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNLQ 82
Query: 94 VNEKPLKIEAAT 105
+ K + E
Sbjct: 83 LRNKEVTWEVLE 94
>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 = 29.8 bits (67), Expect = 0.22
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 10/53 (18%)
Query: 49 VELIRPLFEKYGKVVECDVVKNY----------GFVHMENDEEGRTAIKELNG 91
VE +R KYG V ++ + FV + + + A++ L G
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81
Score = 28.6 bits (64), Expect = 0.53
Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 11/61 (18%)
Query: 130 EVRELFVPYGTVVECDIVRNY----------GFVHIDSPDI-NKCIKELNGMMVDGKPMK 178
+VR+ YG V +I R FV S K ++ L G + +
Sbjct: 31 DVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVV 90
Query: 179 V 179
Sbjct: 91 T 91
>1wxa_A Afadin, AF-6 protein; RAS-binding domain, ubiquitin-like fold,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.15.1.5
Length = 116
Score = 29.5 bits (66), Expect = 0.32
Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 17/83 (20%)
Query: 34 GTFKIFIGNVNPG------------TSVELIRPLFEKYGKVVECDVVKNYGFVHMENDEE 81
GT +I+ ++ P T+ + EKYG +E + K+Y +
Sbjct: 10 GTLRIYADSLKPNIPYKTILLSTTDTADFAVAESLEKYG--LEKENPKDYCIARVMLPPG 67
Query: 82 GRTAIKELNGQIV---NEKPLKI 101
+ + + +I+ +E PL+I
Sbjct: 68 AQHSDERGAKEIILDDDECPLQI 90
>1dhk_B Bean lectin-like inhibitor, porcine pancreatic alpha-amylase; CO
(hydrolase-inhibitor), complex (hydrolase-inhibitor)
comple; HET: NAG; 1.85A {Phaseolus vulgaris} SCOP:
b.29.1.1 PDB: 1viw_B*
Length = 223
Score = 29.7 bits (66), Expect = 0.48
Identities = 16/100 (16%), Positives = 35/100 (35%), Gaps = 10/100 (10%)
Query: 91 GQIVNEKPLKIEAATSRKGPNTPTTKVF-VGNLSDNTRAPEVRELFVPYGTV-------V 142
+ P++I +T+ + T + A + + VP V
Sbjct: 41 SRAFYSAPIQIRDSTTGNVASFDTNFTMNIRTHRQANSAVGLDFVLVPVQPESKGDTVTV 100
Query: 143 ECDIVRNYGFVHIDSPDINKCIKELNGMMVDGKPMKVQIS 182
E D + + +++ DI + DG+ +V+I+
Sbjct: 101 EFDTFLSRISIDVNNNDIK--SVPWDVHDYDGQNAEVRIT 138
>2kvo_A Photosystem II reaction center PSB28 protein; membrane,
photosynthesis, thylakoid, structural genom 2, protein
structure initiative; NMR {Synechocystis SP}
Length = 120
Score = 29.1 bits (65), Expect = 0.49
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 79 DEEGRTAIKELNGQIVNEKPLKIEA 103
D+EG +E+ G+ +N +P IEA
Sbjct: 56 DDEGEIITREVKGKFINGRPTAIEA 80
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.1 bits (64), Expect = 0.62
Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 8/28 (28%)
Query: 83 RTAIKELNGQIVNEKPLKIEAATSRKGP 110
+ A+K+L + LK+ A S P
Sbjct: 19 KQALKKL------QASLKLYADDS--AP 38
>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase;
1.70A {Bacillus subtilis} PDB: 3moj_B
Length = 76
Score = 27.9 bits (63), Expect = 0.63
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 145 DIVRNYGFVHIDSPDINKCIKELNGMMVDGKPMKVQIS 182
I+ N +V I + +K + V GK +KV +
Sbjct: 37 TIMDNASYVEILNGKGPHVLKVMKNTTVKGKQLKVNKA 74
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 28.5 bits (63), Expect = 0.73
Identities = 15/92 (16%), Positives = 28/92 (30%), Gaps = 6/92 (6%)
Query: 100 KIEAATSRKGPNTPTTK--VFVGNLSDNTRAPEVRELFVPYGTVVECDIVRN---YGFVH 154
+I + P+ + + N + + P G V I + V
Sbjct: 9 RITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVE 68
Query: 155 IDSP-DINKCIKELNGMMVDGKPMKVQISTSR 185
+S K LNG + ++I +R
Sbjct: 69 FESVLCAQKAKAALNGADIYAGCCTLKIEYAR 100
>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA
binding protein; NMR {Saccharomyces cerevisiae}
Length = 117
Score = 27.7 bits (61), Expect = 1.2
Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 8/67 (11%)
Query: 121 NLSDNTRAPEVRELFVPYGTVVECDI-----VRNYGFVHI---DSPDINKCIKELNGMMV 172
LSD + + + E DI V ++ I DS K + LNG
Sbjct: 28 PLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKFAAKMLMILNGSQF 87
Query: 173 DGKPMKV 179
GK ++
Sbjct: 88 QGKVIRS 94
>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 = 27.8 bits (62), Expect = 1.4
Identities = 11/47 (23%), Positives = 15/47 (31%), Gaps = 12/47 (25%)
Query: 57 EKYGKVVECDVVKNYG------------FVHMENDEEGRTAIKELNG 91
K+G V + + FV E AI+ LNG
Sbjct: 47 GKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG 93
Score = 27.0 bits (60), Expect = 2.4
Identities = 14/63 (22%), Positives = 21/63 (33%), Gaps = 13/63 (20%)
Query: 130 EVRELFVPYGTVVECDIVRNYGFVHIDSPDI-------------NKCIKELNGMMVDGKP 176
EV E +G V I + D+ I +K I+ LNG G+
Sbjct: 41 EVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRK 100
Query: 177 MKV 179
+
Sbjct: 101 VVA 103
>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 91
Score = 26.5 bits (58), Expect = 2.8
Identities = 13/84 (15%), Positives = 30/84 (35%), Gaps = 6/84 (7%)
Query: 106 SRKGPNTPTTKVFVGNLS------DNTRAPEVRELFVPYGTVVECDIVRNYGFVHIDSPD 159
G + T V + + D+ E+ + F +G V+ V + +V
Sbjct: 1 GSSGSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDKMWVTFLEGS 60
Query: 160 INKCIKELNGMMVDGKPMKVQIST 183
+ LNG + + + + + +
Sbjct: 61 SALNVLSLNGKELLNRTITIALKS 84
>3ngj_A Deoxyribose-phosphate aldolase; lyase, structural genomics,
structural genomics center for infectious disease,
ssgcid; 1.70A {Entamoeba histolytica}
Length = 239
Score = 27.2 bits (61), Expect = 4.0
Identities = 10/43 (23%), Positives = 17/43 (39%), Gaps = 3/43 (6%)
Query: 64 ECDVVKNYGFVHMENDEEGRTAIKELNGQIVNEKPLK--IEAA 104
E D+V N G V + ++ +K + + K IE
Sbjct: 111 EVDMVINIGMVKAKKYDDVEKDVKAVV-DASGKALTKVIIECC 152
>3r12_A Deoxyribose-phosphate aldolase; TIM beta/alpha-barrel, structural
genomics, joint center for structural genomics, JCSG;
HET: MSE CIT; 1.75A {Thermotoga maritima} PDB: 1o0y_A*
3r13_A*
Length = 260
Score = 26.5 bits (59), Expect = 6.0
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 64 ECDVVKNYGFVHMENDEEGRTAIKELNGQIVNEKPLK--IEAA 104
E D+V N G + + E I+ + + V K +K IE
Sbjct: 127 EIDMVINVGMLKAKEWEYVYEDIRSVV-ESVKGKVVKVIIETC 168
>1ub3_A Aldolase protein; schiff base, deoxyribose phosphate,
carbinolamine, structural genomics, riken structural
genomics/proteomics initiative; HET: HPD; 1.40A {Thermus
thermophilus} SCOP: c.1.10.1 PDB: 1j2w_A*
Length = 220
Score = 26.4 bits (59), Expect = 6.4
Identities = 8/43 (18%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 64 ECDVVKNYGFVHMENDEEGRTAIKELNGQIVNEKPLK--IEAA 104
E D+V + G + + ++ + + V + LK +E
Sbjct: 87 EVDMVLHLGRAKAGDLDYLEAEVRAVR-EAVPQAVLKVILETG 128
>3oa3_A Aldolase; structural genomics, seattle structural genomics center
for infectious disease, ssgcid, pathogenic fungus; 1.60A
{Coccidioides immitis}
Length = 288
Score = 26.1 bits (58), Expect = 8.4
Identities = 9/43 (20%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 64 ECDVVKNYGFVHMENDEEGRTAIKELNGQIVNEKPLK--IEAA 104
E D+V NY ++ + + I+ + + LK +E +
Sbjct: 142 ELDMVMNYPWLSEKRYTDVFQDIRAVR-LAAKDAILKVILETS 183
>3ndo_A Deoxyribose-phosphate aldolase; ssgcid, NIH, niaid, SBRI, UW,
emerald biostructures, ALS collaborative
crystallography; HET: GOL; 1.25A {Mycobacterium
smegmatis} PDB: 3ng3_A
Length = 231
Score = 26.0 bits (58), Expect = 8.8
Identities = 10/43 (23%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 64 ECDVVKNYGFVHMENDEEGRTAIKELNGQIVNEKPLK--IEAA 104
E D+V + G + + I + + V LK +E+A
Sbjct: 96 EIDMVIDVGAALAGDLDAVSADITAVR-KAVRAATLKVIVESA 137
>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I
ABC type importer, methionine uptake transporter,
membrane protein; HET: ADP; 2.90A {Escherichia coli}
PDB: 3tuj_C 3tuz_C* 3dhw_C
Length = 366
Score = 26.1 bits (58), Expect = 8.9
Identities = 9/60 (15%), Positives = 23/60 (38%), Gaps = 1/60 (1%)
Query: 110 PNTPTTKVFVGNLSDNTRAPEVRELFVPYGTVVECDIVR-NYGFVHIDSPDINKCIKELN 168
P TP + F+ + + +E ++R + +D+P +++ + N
Sbjct: 255 PKTPLAQKFIQSTLHLDIPEDYQERLQAEPFTDCVPMLRLEFTGQSVDAPLLSETARRFN 314
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
0.317 0.136 0.392
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,190,564
Number of extensions: 192208
Number of successful extensions: 1273
Number of sequences better than 10.0: 1
Number of HSP's gapped: 894
Number of HSP's successfully gapped: 405
Length of query: 207
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 118
Effective length of database: 4,216,824
Effective search space: 497585232
Effective search space used: 497585232
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (24.9 bits)