RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3016
(305 letters)
>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 = 247 bits (634), Expect = 8e-83
Identities = 63/230 (27%), Positives = 105/230 (45%), Gaps = 42/230 (18%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
A++YVG L V+E +++E F +GP++++ + +D +T+ GY ++ F DA+
Sbjct: 13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAER 72
Query: 92 AIKIMNMIKLYGKPIRVNKASSHQKNLDVG-ANIFIGNLDPEVDEKLLYDTFSAFGVILQ 150
A+ MN + GKP+R+ + G NIFI NLD +D K LYDTFSAFG IL
Sbjct: 73 ALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILS 132
Query: 151 TPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYA 210
K++ D SKG+ F+++
Sbjct: 133 -CKVV----------------------------------------CDENGSKGYGFVHFE 151
Query: 211 SFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNP 260
+ EA++ +I+ M+G L +R + V + + G+ A+ P
Sbjct: 152 TQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVP 201
>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 = 240 bits (615), Expect = 1e-80
Identities = 50/205 (24%), Positives = 96/205 (46%), Gaps = 41/205 (20%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
+YVG LD ++E ++ + F GP+ N+ + D+ + Y F+E+ DA+ A++
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQT 60
Query: 96 MNMIKLYGKPIRVNKAS-SHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKI 154
+N ++ +++N A S Q + D N+F+G+L+ VD++ L + F F
Sbjct: 61 LNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSY------ 114
Query: 155 MNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEA 214
L +M D TG+S+G+ F+++ S +
Sbjct: 115 ---------------------------------LSGHVMWDMQTGSSRGYGFVSFTSQDD 141
Query: 215 SDASIDAMHGQYLCNRPISVSYAFK 239
+ ++D+M GQ L RP+ +++A K
Sbjct: 142 AQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 79.5 bits (197), Expect = 3e-18
Identities = 29/108 (26%), Positives = 51/108 (47%), Gaps = 11/108 (10%)
Query: 16 LQSLSQTKLEG-----------GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNV 64
LQ+L+ ++E S D ++VG L+ V + + F ++
Sbjct: 58 LQTLNGKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSG 117
Query: 65 HMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS 112
H+ D T + +GYGF+ F ++DA A+ M L G+P+R+N A+
Sbjct: 118 HVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA 165
Score = 68.3 bits (168), Expect = 3e-14
Identities = 22/120 (18%), Positives = 44/120 (36%), Gaps = 40/120 (33%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+++GNLD + E +L F G I ANI
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPI--------------------------------ANI 30
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
+IM D + +AF+ Y ++ ++ ++G+ + N + +++AF+
Sbjct: 31 -------KIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQS 82
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 219 bits (560), Expect = 1e-71
Identities = 46/231 (19%), Positives = 88/231 (38%), Gaps = 49/231 (21%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
+ + +YVG + ++ E + + F GP+ ++ M D VT H+G+ F+E+ E
Sbjct: 23 GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA 82
Query: 89 ADYAIKIMNMIKLYGKPIRVNKASSHQ----------KNLDVGANIFIGNLDPEVDEKLL 138
A A++ MN + L G+ I+V + S+ + I++ ++ ++ + +
Sbjct: 83 AQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 142
Query: 139 YDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT 198
F AFG I + RDP T
Sbjct: 143 KSVFEAFGKI---------------------------------------KSATLARDPTT 163
Query: 199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGS 249
G KG+ FI Y ++S ++ +M+ L + + V A +
Sbjct: 164 GKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPAT 214
Score = 97.4 bits (243), Expect = 2e-24
Identities = 28/151 (18%), Positives = 49/151 (32%), Gaps = 39/151 (25%)
Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
G+ + A+ Q L + + +++G++ E+ E + F+ FG I
Sbjct: 10 GQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIK------------- 56
Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
++ D T KGFAF+ Y EA+ +++ M
Sbjct: 57 --------------------------SIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 223 HGQYLCNRPISVSYAFKKDSKGDRHGSAAER 253
+ L R I V AE
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEE 121
Score = 92.0 bits (229), Expect = 2e-22
Identities = 31/108 (28%), Positives = 53/108 (49%), Gaps = 2/108 (1%)
Query: 4 GREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN 63
GR I+ G + Q+ Q ++ E IYV + +S+ + +F G + +
Sbjct: 97 GRNIKVGRPSNIGQA--QPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKS 154
Query: 64 VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
+ +D T H+GYGFIE+ + + A+ MN+ L G+ +RV KA
Sbjct: 155 ATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202
>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 = 215 bits (550), Expect = 8e-71
Identities = 45/205 (21%), Positives = 85/205 (41%), Gaps = 42/205 (20%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
+ V L +++ LF G + + + +D++T GYGF+ ++ +DA+ AI
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 95 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKI 154
+N ++L K I+V+ A ++ AN+++ L + +K L FS +G I+ +
Sbjct: 63 TLNGLRLQTKTIKVSYARPSSASIR-DANLYVSGLPKTMTQKELEQLFSQYGRIITS--- 118
Query: 155 MNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEA 214
I+ D TG S+G FI +
Sbjct: 119 ------------------------------------RILVDQVTGVSRGVGFIRFDKRIE 142
Query: 215 SDASIDAMHGQYL--CNRPISVSYA 237
++ +I ++GQ PI+V +A
Sbjct: 143 AEEAIKGLNGQKPSGATEPITVKFA 167
Score = 81.5 bits (202), Expect = 5e-19
Identities = 22/124 (17%), Positives = 42/124 (33%), Gaps = 39/124 (31%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
N+ + L + ++ F + G I
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESC------------------------------ 32
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
+++RD TG S G+ F+NY + ++ +I+ ++G L + I VSYA
Sbjct: 33 ---------KLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSS 83
Query: 242 SKGD 245
+
Sbjct: 84 ASIR 87
Score = 69.5 bits (171), Expect = 1e-14
Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 2/85 (2%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
+ DA +YV GL +++ + +LF Q G ++ + D+VT +G GFI F +
Sbjct: 83 SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIE 142
Query: 89 ADYAIKIMN--MIKLYGKPIRVNKA 111
A+ AIK +N +PI V A
Sbjct: 143 AEEAIKGLNGQKPSGATEPITVKFA 167
>1b7f_A Protein (SXL-lethal protein), RNA
(5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing
regulation, RNP domain, RNA complex; 2.60A {Drosophila
melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A*
1sxl_A 2sxl_A
Length = 168
Score = 214 bits (547), Expect = 3e-70
Identities = 46/207 (22%), Positives = 85/207 (41%), Gaps = 42/207 (20%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
+ + V L +++ ++ LF GP+ + +D T GY F++F E D+ A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 93 IKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTP 152
IK++N I + K ++V+ A +++ N+++ NL + + L F +G I+Q
Sbjct: 62 IKVLNGITVRNKRLKVSYARPGGESIK-DTNLYVTNLPRTITDDQLDTIFGKYGSIVQK- 119
Query: 153 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF 212
I+RD TG +G AF+ Y
Sbjct: 120 --------------------------------------NILRDKLTGRPRGVAFVRYNKR 141
Query: 213 EASDASIDAMHGQYL--CNRPISVSYA 237
E + +I A++ ++P+SV A
Sbjct: 142 EEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 85.7 bits (213), Expect = 1e-20
Identities = 27/127 (21%), Positives = 43/127 (33%), Gaps = 39/127 (30%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
N+ + L ++ ++ LY F A G I
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTC----------------------------- 33
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
IMRD TG S G+AF+++ S S +I ++G + N+ + VSYA
Sbjct: 34 ----------RIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG 83
Query: 241 DSKGDRH 247
Sbjct: 84 GESIKDT 90
>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 = 210 bits (537), Expect = 1e-67
Identities = 47/247 (19%), Positives = 83/247 (33%), Gaps = 55/247 (22%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G ++ ++VG L ++E LF + G V + +DR G+GFI
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRLESR 68
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFG 146
A+ A ++ L +P+R+ A+ GA + + NL P V +LL FS FG
Sbjct: 69 TLAEIAKAELDGTILKSRPLRIRFATH-------GAALTVKNLSPVVSNELLEQAFSQFG 121
Query: 147 VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAF 206
+ ++ D D G + G F
Sbjct: 122 PV---------------------------------------EKAVVVVD-DRGRATGKGF 141
Query: 207 INYASFEASDASIDAMH-GQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQAD 265
+ +A+ + +++ G +L + D G E+L+ +
Sbjct: 142 VEFAAKPPARKALERCGDGAFLLTTTPRPVIVEPMEQFDDEDG-LPEKLMQKTQQYHKER 200
Query: 266 RPHQLFA 272
FA
Sbjct: 201 EQPPRFA 207
Score = 74.7 bits (184), Expect = 9e-16
Identities = 24/138 (17%), Positives = 43/138 (31%), Gaps = 46/138 (33%)
Query: 103 GKPIRVNKASSH-QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLY 161
G I + +K +F+GNL ++ E+ F +G
Sbjct: 3 GFTIDIKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEP------------- 49
Query: 162 GKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
+ +FI RD +GF FI S ++ +
Sbjct: 50 -------------------SEVFI-------NRD------RGFGFIRLESRTLAEIAKAE 77
Query: 222 MHGQYLCNRPISVSYAFK 239
+ G L +RP+ + +A
Sbjct: 78 LDGTILKSRPLRIRFATH 95
>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 = 190 bits (486), Expect = 5e-61
Identities = 35/211 (16%), Positives = 75/211 (35%), Gaps = 46/211 (21%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMP-----KDRVTQTHQGYGFIEFMGE 86
+YVG + ++E M + F + + + + F+EF
Sbjct: 2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFG 146
++ A+ + I G+ +++ + +Q L +FIG L +++ + + ++FG
Sbjct: 62 DETTQAMA-FDGIIFQGQSLKIRRPHDYQ-PLPGAHKLFIGGLPNYLNDDQVKELLTSFG 119
Query: 147 VILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAF 206
+ +++D TG SKG+AF
Sbjct: 120 PL---------------------------------------KAFNLVKDSATGLSKGYAF 140
Query: 207 INYASFEASDASIDAMHGQYLCNRPISVSYA 237
Y +D +I ++G L ++ + V A
Sbjct: 141 CEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 91.9 bits (229), Expect = 8e-23
Identities = 24/81 (29%), Positives = 43/81 (53%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
G +++GGL + +++ + EL GP+ ++ KD T +GY F E++ D
Sbjct: 92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 151
Query: 92 AIKIMNMIKLYGKPIRVNKAS 112
AI +N ++L K + V +AS
Sbjct: 152 AIAGLNGMQLGDKKLLVQRAS 172
Score = 63.8 bits (156), Expect = 2e-12
Identities = 14/124 (11%), Positives = 34/124 (27%), Gaps = 35/124 (28%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+++GN+ + E+ + D F+A +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGG--------------------------------- 33
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
+ + K FAF+ + S + + ++ A G + + +
Sbjct: 34 -LTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPL 91
Query: 244 GDRH 247
H
Sbjct: 92 PGAH 95
>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 = 187 bits (477), Expect = 1e-59
Identities = 49/213 (23%), Positives = 83/213 (38%), Gaps = 48/213 (22%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQT--HQGYGFIEFMGEEDAD 90
++VG + SE + ELF Q G V +++ +DR +G F+ F + A
Sbjct: 2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 61
Query: 91 YAIKIMNMIKL---YGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGV 147
A ++ +K+ PI++ A S + N +FIG + + E + FS+FG
Sbjct: 62 EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQ 121
Query: 148 ILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFI 207
I + I+R PD G S+G AF+
Sbjct: 122 I---------------------------------------EECRILRGPD-GLSRGCAFV 141
Query: 208 NYASFEASDASIDAMHGQYL---CNRPISVSYA 237
+ + + +I AMH C+ P+ V +A
Sbjct: 142 TFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
Score = 75.3 bits (186), Expect = 1e-16
Identities = 18/126 (14%), Positives = 38/126 (30%), Gaps = 41/126 (32%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
+F+G + EK L + F +G + +
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEI------------------------------- 33
Query: 183 IFIGNLDPEIMRDPDTGN--SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
++RD SKG F+ + + +A+ + +A+H +
Sbjct: 34 --------NVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPA 85
Query: 241 DSKGDR 246
DS+ +
Sbjct: 86 DSEKNN 91
Score = 69.9 bits (172), Expect = 1e-14
Identities = 20/111 (18%), Positives = 42/111 (37%), Gaps = 8/111 (7%)
Query: 4 GREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN 63
++ G+ P + ++ E D +++G + K +E + +F G +
Sbjct: 69 NMKVLPGMHHPIQMKPADSEKNNAVE----DRKLFIGMISKKCTENDIRVMFSSFGQIEE 124
Query: 64 VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN---MIKLYGKPIRVNKA 111
+ + +G F+ F A AIK M+ ++ P+ V A
Sbjct: 125 CRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
>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 = 190 bits (486), Expect = 2e-59
Identities = 43/215 (20%), Positives = 82/215 (38%), Gaps = 48/215 (22%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPV-VNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
+ T+++ ++ + +L V +++ +P R T + + +I+ +EDA Y
Sbjct: 117 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-FNTSRRFAYIDVTSKEDARYC 175
Query: 93 IKIMNMIKLYGKPIRVN--KASSHQKNLDV----GANIFIGNLDPEV-DEKLLYDTFSAF 145
++ +N +K+ G + K D G I I NL E+ DE LL ++F F
Sbjct: 176 VEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGF 235
Query: 146 GVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFA 205
G I + + + A
Sbjct: 236 GSIEKINIPAGQ--------------------------------------KEHSFNNCCA 257
Query: 206 FINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
F+ + + ++++ ++ M+ L NR ISVS A KK
Sbjct: 258 FMVFENKDSAERAL-QMNRSLLGNREISVSLADKK 291
Score = 165 bits (421), Expect = 1e-49
Identities = 30/240 (12%), Positives = 73/240 (30%), Gaps = 50/240 (20%)
Query: 13 TPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVT 72
+P L+ K T+ V L ++ +++ F GP+++V +
Sbjct: 20 SPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--L 77
Query: 73 QTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPE 132
+ + + IEF + A AI + + + I V+ + +++ N P
Sbjct: 78 KKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSHLTE--------CTLWMTNFPPS 128
Query: 133 VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEI 192
++ + D V+ +
Sbjct: 129 YTQRNIRDLLQDINVVALS---------------------------------------IR 149
Query: 193 MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAE 252
+ S+ FA+I+ S E + ++ ++G + + + + + E
Sbjct: 150 LPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLE 209
Score = 73.5 bits (181), Expect = 3e-15
Identities = 20/137 (14%), Positives = 34/137 (24%), Gaps = 46/137 (33%)
Query: 103 GKPIRVNKASSHQKNLDV----GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMI 158
G P S + + NL ++ +Y F G I+
Sbjct: 19 GSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIH-------- 70
Query: 159 KLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDAS 218
+ V + FA I +A ++ + A+
Sbjct: 71 ------VDVAD---------------------------SLKKNFRFARIEFARYDGALAA 97
Query: 219 IDAMHGQYLCNRPISVS 235
I H + I VS
Sbjct: 98 ITKTHK-VVGQNEIIVS 113
Score = 71.9 bits (177), Expect = 1e-14
Identities = 22/110 (20%), Positives = 45/110 (40%), Gaps = 9/110 (8%)
Query: 4 GREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVS-ETLMWELFVQSGPVV 62
G + +S P + + + G I + L ++ E L+ E F G +
Sbjct: 186 GYTLVTKVSNPLEK---SKRTDSATLEG---REIMIRNLSTELLDENLLRESFEGFGSIE 239
Query: 63 NVHMPKDR-VTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
+++P + + F+ F ++ A+ A++ MN L + I V+ A
Sbjct: 240 KINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSLA 288
>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 = 181 bits (461), Expect = 3e-57
Identities = 35/210 (16%), Positives = 74/210 (35%), Gaps = 47/210 (22%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
+++G L+ S + + ++ + D T T++ +G+++F ED +
Sbjct: 11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEK 69
Query: 92 AIKIMNMIKLYGKPIRVNKASSH-QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQ 150
A++ + +K++G I++ K K + + NL + E L + F
Sbjct: 70 ALE-LTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL---- 124
Query: 151 TPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYA 210
EI G SKG A+I +
Sbjct: 125 ----------------------------------------EIRLVSQDGKSKGIAYIEFK 144
Query: 211 SFEASDASIDAMHGQYLCNRPISVSYAFKK 240
S ++ +++ G + R +S+ Y +K
Sbjct: 145 SEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174
Score = 78.8 bits (195), Expect = 6e-18
Identities = 21/127 (16%), Positives = 39/127 (30%), Gaps = 41/127 (32%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
N+FIGNL+P L S ++
Sbjct: 14 FNLFIGNLNPNKSVAELKVAISELFAKNDL-AVV-------------------------- 46
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
D TG ++ F ++++ S E + +++ + G + I + +D
Sbjct: 47 -------------DVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRD 92
Query: 242 SKGDRHG 248
SK R
Sbjct: 93 SKKVRAA 99
Score = 71.1 bits (175), Expect = 4e-15
Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 5/83 (6%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
+ T+ L ++E + E+F + + +G +IEF E D
Sbjct: 94 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEAD 148
Query: 89 ADYAIKIMNMIKLYGKPIRVNKA 111
A+ ++ ++ G+ + +
Sbjct: 149 AEKNLEEKQGAEIDGRSVSLYYT 171
>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 = 159 bits (404), Expect = 1e-48
Identities = 49/207 (23%), Positives = 82/207 (39%), Gaps = 43/207 (20%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
+++GGL+ +E + E F + G V ++ + KD T +G+GF+ F D +
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 94 KIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPK 153
K +++ GK I +A + G IF+G + P+V K + FS +G I
Sbjct: 63 KTQHILD--GKVIDPKRAIPRDEQDKTG-KIFVGGIGPDVRPKEFEEFFSQWGTI----- 114
Query: 154 IMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFE 213
+D ++M D DTG S+GF F+ Y S +
Sbjct: 115 ----------------------------------IDAQLMLDKDTGQSRGFGFVTYDSAD 140
Query: 214 ASDASIDAMHGQYLCNRPISVSYAFKK 240
A D +R I + A +
Sbjct: 141 AVDRVC-QNKFIDFKDRKIEIKRAEPR 166
Score = 77.6 bits (192), Expect = 1e-17
Identities = 18/79 (22%), Positives = 34/79 (43%), Gaps = 1/79 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I+VGG+ V E F Q G +++ + D+ T +G+GF+ + + D +
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-N 148
Query: 97 NMIKLYGKPIRVNKASSHQ 115
I + I + +A
Sbjct: 149 KFIDFKDRKIEIKRAEPRH 167
Score = 67.6 bits (166), Expect = 5e-14
Identities = 25/122 (20%), Positives = 42/122 (34%), Gaps = 41/122 (33%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
+FIG L+ + E L + F +G +
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVT-------------------------------- 31
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
D +IM+DP TG S+GF F+++ + D + H L + I A +D
Sbjct: 32 -------DLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH--ILDGKVIDPKRAIPRD 82
Query: 242 SK 243
+
Sbjct: 83 EQ 84
>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 = 159 bits (404), Expect = 2e-48
Identities = 38/242 (15%), Positives = 80/242 (33%), Gaps = 68/242 (28%)
Query: 31 GDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMP-----KDRVTQTHQGYGFIEFMG 85
G +YVG + ++E M + F + + + + F+EF
Sbjct: 1 GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASSHQKNL-------------------DVGANIFI 126
++ A+ + I G+ +++ + +Q D +FI
Sbjct: 61 VDETTQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 127 GNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIG 186
G L +++ + + ++FG +
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAF----------------------------------- 144
Query: 187 NLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDR 246
+++D TG SKG+AF Y +D +I ++G L ++ + V A S G +
Sbjct: 145 ----NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA----SVGAK 196
Query: 247 HG 248
+
Sbjct: 197 NA 198
Score = 97.0 bits (242), Expect = 2e-24
Identities = 26/92 (28%), Positives = 45/92 (48%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
D +++GGL + +++ + EL GP+ ++ KD T +GY F E++
Sbjct: 106 VSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 165
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
D AI +N ++L K + V +AS KN
Sbjct: 166 INVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 197
Score = 65.1 bits (159), Expect = 7e-13
Identities = 19/148 (12%), Positives = 46/148 (31%), Gaps = 36/148 (24%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+++GN+ + E+ + D F+A ++ + + G P+
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQM------RLGGLTQAPGNPVL----------------- 43
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
K FAF+ + S + + ++ A G + + +
Sbjct: 44 -----------AVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIRRPHDYQPL 91
Query: 244 GDRHGSAAERLLAAQNPLSQADRPHQLF 271
+ + + + D H+LF
Sbjct: 92 PGMSENPSVYVPGVVST-VVPDSAHKLF 118
>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 = 160 bits (408), Expect = 7e-48
Identities = 41/229 (17%), Positives = 69/229 (30%), Gaps = 47/229 (20%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
DA + V L +++ EL G + + T +GYGF E+M ++ A A
Sbjct: 95 DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAK 154
Query: 94 KIMNMIKLYGKPIRVNKASSHQKNLDV--GANIFIGNLDPEV-DEKLLYDTFSAFGVILQ 150
+ L + + V+ + Q + + + L P D L SA
Sbjct: 155 SDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTF 214
Query: 151 TPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYA 210
++ G KGFA + Y
Sbjct: 215 --------------CQL-------------------------ACGQ-DGQLKGFAVLEYE 234
Query: 211 SFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQN 259
+ E ++ + G L + VS+ S L+AAQ
Sbjct: 235 TAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG----RSMLAALIAAQA 279
Score = 150 bits (382), Expect = 4e-44
Identities = 33/221 (14%), Positives = 68/221 (30%), Gaps = 53/221 (23%)
Query: 21 QTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGF 80
+ +LE I + GL V+ + +L + + K + G F
Sbjct: 9 RKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYK------GTAF 61
Query: 81 IEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYD 140
+ + E A+ AI + +L + + V + A + + NL P + ++ +
Sbjct: 62 VTLLNGEQAEAAINAFHQSRLRERELSVQLQPTD-------ALLCVANLPPSLTQQQFEE 114
Query: 141 TFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN 200
FG + ++ TG
Sbjct: 115 LVRPFGSLE---------------------------------------RCFLVYSERTGQ 135
Query: 201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
SKG+ F Y +++ + + G+ L R + V +
Sbjct: 136 SKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQ 176
Score = 75.0 bits (185), Expect = 8e-16
Identities = 12/109 (11%), Positives = 32/109 (29%), Gaps = 12/109 (11%)
Query: 4 GREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSET-LMWELFVQSGPVV 62
R + + + + + V L ++ +
Sbjct: 164 PRTLYVHWTDAGQLTPALLH----------SRCLCVDRLPPGFNDVDALCRALSAVHSPT 213
Query: 63 NVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
+ + +G+ +E+ E A+ A + + + L G +RV+
Sbjct: 214 FCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFC 261
>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 = 145 bits (368), Expect = 3e-44
Identities = 70/85 (82%), Positives = 79/85 (92%)
Query: 34 DATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
DAT+YVGGLD+KVSE L+WELF+Q+GPVVN HMPKDRVT HQGYGF+EF+ EEDADYAI
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74
Query: 94 KIMNMIKLYGKPIRVNKASSHQKNL 118
KIM+MIKLYGKPIRVNKAS+H KNL
Sbjct: 75 KIMDMIKLYGKPIRVNKASAHNKNL 99
Score = 81.5 bits (202), Expect = 9e-20
Identities = 28/129 (21%), Positives = 48/129 (37%), Gaps = 41/129 (31%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
A +++G LD +V E LL++ F G + + +
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPV----------------VNTH------------- 46
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF--K 239
+ +D TG +G+ F+ + S E +D +I M L +PI V+ A
Sbjct: 47 ----------MPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHN 96
Query: 240 KDSKGDRHG 248
K+ G G
Sbjct: 97 KNLSGPSSG 105
>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 = 131 bits (332), Expect = 5e-39
Identities = 76/129 (58%), Positives = 85/129 (65%), Gaps = 38/129 (29%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
+ IFIGNLDPE+DEKLLYDTFSAFGVILQTPKIM
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIM-------------------------- 39
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
RDPDTGNSKG+AFIN+ASF+ASDA+I+AM+GQYLCNRPI+VSYAFKKD
Sbjct: 40 ------------RDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD 87
Query: 242 SKGDRHGSA 250
SKG S
Sbjct: 88 SKGSGPSSG 96
Score = 75.3 bits (186), Expect = 2e-17
Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 1/87 (1%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNV-HMPKDRVTQTHQGYGFIEFMGEEDAD 90
G + I++G LD ++ E L+++ F G ++ + +D T +GY FI F + +D
Sbjct: 3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62
Query: 91 YAIKIMNMIKLYGKPIRVNKASSHQKN 117
AI+ MN L +PI V+ A
Sbjct: 63 AAIEAMNGQYLCNRPITVSYAFKKDSK 89
>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 = 129 bits (326), Expect = 4e-38
Identities = 34/82 (41%), Positives = 55/82 (67%), Gaps = 1/82 (1%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
+ D T++VG L+ +V E +++ELF+Q+GP+ V + KDR + + +GF+ F E Y
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGK-PKSFGFVCFKHPESVSY 72
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
AI ++N I+LYG+PI V+ SS
Sbjct: 73 AIALLNGIRLYGRPINVSGPSS 94
Score = 72.7 bits (179), Expect = 2e-16
Identities = 26/127 (20%), Positives = 45/127 (35%), Gaps = 40/127 (31%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
+ + +F+GNL+ V E++LY+ F G + +V
Sbjct: 6 SGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPL----------------TKVT-- 47
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
I +D + G K F F+ + E+ +I ++G L R
Sbjct: 48 ---------------------ICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGR 85
Query: 231 PISVSYA 237
PI+VS
Sbjct: 86 PINVSGP 92
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 128 bits (323), Expect = 4e-37
Identities = 33/86 (38%), Positives = 51/86 (59%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G G S +YVGGL ++V + ++ F+ G + ++ +P D T+ H+G+ F+EF
Sbjct: 55 GSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 114
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKA 111
EDA AI MN +L+G+ IRVN A
Sbjct: 115 AEDAAAAIDNMNESELFGRTIRVNLA 140
Score = 82.9 bits (205), Expect = 7e-20
Identities = 30/163 (18%), Positives = 52/163 (31%), Gaps = 46/163 (28%)
Query: 82 EFMGEEDADYAIKIMNMIKLYGKPIR-------VNKASSHQKNLDVGANIFIGNLDPEVD 134
E + +E + + + + + +++G L EVD
Sbjct: 17 ENLSDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVD 76
Query: 135 EKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMR 194
+K+L+ F FG I + I
Sbjct: 77 DKVLHAAFIPFGDI----------------TDIQ-----------------------IPL 97
Query: 195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
D +T +GFAF+ + E + A+ID M+ L R I V+ A
Sbjct: 98 DYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>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 = 125 bits (317), Expect = 8e-37
Identities = 31/84 (36%), Positives = 49/84 (58%)
Query: 28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
G +YVGGL ++V + ++ F+ G + ++ +P D T+ H+G+ F+EF E
Sbjct: 1 GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60
Query: 88 DADYAIKIMNMIKLYGKPIRVNKA 111
DA AI MN +L+G+ IRVN A
Sbjct: 61 DAAAAIDNMNESELFGRTIRVNLA 84
Score = 76.8 bits (190), Expect = 3e-18
Identities = 29/116 (25%), Positives = 44/116 (37%), Gaps = 39/116 (33%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
+++G L EVD+K+L+ F FG I
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDIT-------------------------------- 35
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
D +I D +T +GFAF+ + E + A+ID M+ L R I V+ A
Sbjct: 36 -------DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84
>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 = 125 bits (316), Expect = 2e-36
Identities = 31/92 (33%), Positives = 46/92 (50%), Gaps = 2/92 (2%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G E T+YVG L V+E L+ +LF Q GP + M + + + Y F+EF
Sbjct: 7 GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYE 64
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
DA A+ MN K+ GK ++VN A++
Sbjct: 65 HRDAAAALAAMNGRKILGKEVKVNWATTPSSQ 96
Score = 67.3 bits (165), Expect = 2e-14
Identities = 21/140 (15%), Positives = 47/140 (33%), Gaps = 43/140 (30%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
+S ++ +++GNL +V E L+ FS G K
Sbjct: 5 SSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKS-------CK----------- 46
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
++ + + + F+ + + A++ AM+G+ + +
Sbjct: 47 ---------------------MITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGK 83
Query: 231 PISVSYAFKKDSK--GDRHG 248
+ V++A S+ G G
Sbjct: 84 EVKVNWATTPSSQKSGPSSG 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 = 117 bits (295), Expect = 2e-33
Identities = 31/86 (36%), Positives = 49/86 (56%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G +YVGGL ++V + ++ F+ G + ++ +P D T+ H+G+ F+EF
Sbjct: 4 GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFEL 63
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKA 111
EDA AI MN +L+G+ IRVN A
Sbjct: 64 AEDAAAAIDNMNESELFGRTIRVNLA 89
Score = 85.7 bits (213), Expect = 3e-21
Identities = 31/128 (24%), Positives = 46/128 (35%), Gaps = 39/128 (30%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
+++G L EVD+K+L+ F FG I
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDIT-------------------------------- 40
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
D +I D +T +GFAF+ + E + A+ID M+ L R I V+ A
Sbjct: 41 -------DIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMR 93
Query: 242 SKGDRHGS 249
K S
Sbjct: 94 IKESGPSS 101
>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 = 112 bits (283), Expect = 2e-31
Identities = 29/142 (20%), Positives = 56/142 (39%), Gaps = 43/142 (30%)
Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
+ +S + N+++ NLD +D++ L FS FG I
Sbjct: 3 SGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSA----------------- 45
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
++M + G SKGF F+ ++S E + ++ M+G+ +
Sbjct: 46 ----------------------KVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVA 81
Query: 229 NRPISVSYAFKKDSK--GDRHG 248
+P+ V+ A +K+ + G G
Sbjct: 82 TKPLYVALAQRKEERQSGPSSG 103
Score = 68.0 bits (167), Expect = 1e-14
Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 2/83 (2%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
+ +YV LDD + + + + F G + + + + +G+GF+ F E+
Sbjct: 10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEE 67
Query: 89 ADYAIKIMNMIKLYGKPIRVNKA 111
A A+ MN + KP+ V A
Sbjct: 68 ATKAVTEMNGRIVATKPLYVALA 90
>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 = 112 bits (282), Expect = 3e-31
Identities = 36/132 (27%), Positives = 54/132 (40%), Gaps = 42/132 (31%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
NIFI NLD +D K LYDTFSAFG IL +
Sbjct: 6 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC-------------------------- 39
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA-FKK 240
D SKG+ F+++ + EA++ +I+ M+G L +R + V +K
Sbjct: 40 ---------------DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRK 84
Query: 241 DSKGDRHGSAAE 252
+ + + A E
Sbjct: 85 EREAELGARAKE 96
Score = 86.1 bits (214), Expect = 3e-21
Identities = 24/110 (21%), Positives = 46/110 (41%), Gaps = 9/110 (8%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G I++ LD + +++ F G +++ + D +GYGF+ F +E A+ A
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERA 61
Query: 93 IKIMNMIKLYGKPIRVNKA-------SSHQKNLDVGANIFIGNLDPEVDE 135
I+ MN + L + + V + + N++I N P
Sbjct: 62 IEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTR 111
>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 = 112 bits (283), Expect = 2e-30
Identities = 44/230 (19%), Positives = 84/230 (36%), Gaps = 46/230 (20%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
+ + +++GGL + ++ + F Q G + + + +D T+ +G+GF+ + E+
Sbjct: 8 KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Query: 89 ADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGAN-----IFIGNLDPEVDEKLLYDTFS 143
D A+ K+ G+ + +A S + + GA+ IF+G + + +E L D F
Sbjct: 68 VDAAMN-ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE 126
Query: 144 AFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKG 203
+G I EIM D +G +G
Sbjct: 127 QYGKI---------------------------------------EVIEIMTDRGSGKKRG 147
Query: 204 FAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAER 253
FAF+ + ++ D + + V A K S R
Sbjct: 148 FAFVTFDDHDSVDKIV-IQKYHTVNGHNCEVRKALSKQEMASASSSQRGR 196
>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 = 100 bits (250), Expect = 1e-26
Identities = 28/141 (19%), Positives = 50/141 (35%), Gaps = 39/141 (27%)
Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
G + A+ QK GAN+FI +L E ++ L F FG ++
Sbjct: 7 GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSA----------- 55
Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
++ D T SK F F++Y + ++ A+I +M
Sbjct: 56 ----------------------------KVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 223 HGQYLCNRPISVSYAFKKDSK 243
+G + + + V K+
Sbjct: 88 NGFQIGMKRLKVQLKRSKNDS 108
Score = 74.3 bits (183), Expect = 6e-17
Identities = 21/96 (21%), Positives = 45/96 (46%), Gaps = 2/96 (2%)
Query: 18 SLSQTKLEGGGESGDGD--ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTH 75
L+Q + G +G A +++ L + + + ++F+ G VV+ + D+ T
Sbjct: 7 GLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLS 66
Query: 76 QGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
+ +GF+ + A AI+ MN ++ K ++V
Sbjct: 67 KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK 102
>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 = 96.8 bits (242), Expect = 9e-26
Identities = 27/120 (22%), Positives = 51/120 (42%), Gaps = 39/120 (32%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
N+F+G+L+ VD++ L + F F L
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYL-------------------------------- 29
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
+M D TG+S+G+ F+++ S + + ++D+M GQ L RP+ +++A K +
Sbjct: 30 -------SGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE 82
Score = 78.3 bits (194), Expect = 7e-19
Identities = 23/78 (29%), Positives = 41/78 (52%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
++VG L+ V + + F ++ H+ D T + +GYGF+ F ++DA A+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 95 IMNMIKLYGKPIRVNKAS 112
M L G+P+R+N A+
Sbjct: 62 SMQGQDLNGRPLRINWAA 79
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 95.0 bits (237), Expect = 7e-25
Identities = 25/130 (19%), Positives = 46/130 (35%), Gaps = 40/130 (30%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
++F+G+L P+VD+ +LY+ F + K++
Sbjct: 10 YSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVV-------------------------- 43
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY-LCNRPISVSYAFKK 240
D TG SKG+ F+ + ++ G L ++P+ +S A K
Sbjct: 44 ------------LDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPK 90
Query: 241 DSKGDRHGSA 250
S+ S
Sbjct: 91 ASRVKPVESG 100
Score = 68.1 bits (167), Expect = 9e-15
Identities = 23/89 (25%), Positives = 44/89 (49%), Gaps = 3/89 (3%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVV-NVHMPKDRVTQTHQGYGFIEFM 84
G S + +++VG L V + +++E FV+ P + D+ + +GYGF++F
Sbjct: 1 GSSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVS-KGYGFVKFT 59
Query: 85 GEEDADYAIKIMN-MIKLYGKPIRVNKAS 112
E + A+ + L KP+R++ A
Sbjct: 60 DELEQKRALTECQGAVGLGSKPVRLSVAI 88
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 95.1 bits (237), Expect = 7e-25
Identities = 22/131 (16%), Positives = 49/131 (37%), Gaps = 43/131 (32%)
Query: 119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
+ A++++G+L+P +DE + F+ G + + KI+
Sbjct: 7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKII----------------------- 43
Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN----RPISV 234
R+ TG G+ F+ +A ++ + ++G+ L + +
Sbjct: 44 ---------------RNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKL 88
Query: 235 SYA-FKKDSKG 244
+YA + S G
Sbjct: 89 NYATYSGPSSG 99
Score = 83.1 bits (206), Expect = 2e-20
Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSG-PVVNVHMPKDRVTQTHQGYGFIEFM 84
G S A++++G L+ + E + F G V++V + ++R+T GY F+EF
Sbjct: 1 GSSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFA 60
Query: 85 GEEDADYAIKIMNMIKLYG----KPIRVNKAS 112
A+ + +N L G K ++N A+
Sbjct: 61 DLATAEKCLHKINGKPLPGATPAKRFKLNYAT 92
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 94.0 bits (234), Expect = 3e-24
Identities = 25/149 (16%), Positives = 52/149 (34%), Gaps = 41/149 (27%)
Query: 91 YAIKIMNMIKLYGKPIRVNKASSHQKNLD--VGANIFIGNLDPEVDEKLLYDTFSAFGVI 148
+ ++ L + A++ K ++ G N+FI +L E + L TF FG +
Sbjct: 8 GSASALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNV 67
Query: 149 LQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFIN 208
+ ++ D T SK F F++
Sbjct: 68 ISA---------------------------------------KVFIDKQTSLSKCFGFVS 88
Query: 209 YASFEASDASIDAMHGQYLCNRPISVSYA 237
+ + +++ +I AM+G + + + V
Sbjct: 89 FDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117
Score = 70.9 bits (174), Expect = 1e-15
Identities = 20/86 (23%), Positives = 40/86 (46%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G G +++ L + ++T + F+ G V++ + D+ T + +GF+ F
Sbjct: 32 GKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDN 91
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKA 111
+ A AIK MN ++ K ++V
Sbjct: 92 PDSAQVAIKAMNGFQVGTKRLKVQLK 117
>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 = 95.9 bits (238), Expect = 9e-24
Identities = 29/205 (14%), Positives = 57/205 (27%), Gaps = 48/205 (23%)
Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
+ + ++IGNL ++ L + + GV
Sbjct: 50 DDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVN-------------- 95
Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
D+ L+ + + G SKGFA + S +S +D +
Sbjct: 96 ---------------DI--------LEIKFFENRANGQSKGFALVGVGSEASSKKLMDLL 132
Query: 223 HGQYLCNRPISVSYAFKKD-----------SKGDRHGSAAERLLAAQNPLSQADRPHQLF 271
+ L + V+ K+ ++ + + + + + +
Sbjct: 133 PKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGR 192
Query: 272 ADAPPPAPLPPPPPPINIMGLPPPP 296
P P P G PPPP
Sbjct: 193 GRFPGAVPGGDRFPGPAGPGGPPPP 217
Score = 64.7 bits (157), Expect = 2e-12
Identities = 11/85 (12%), Positives = 33/85 (38%), Gaps = 2/85 (2%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGP--VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
+Y+G L ++ + E G ++ + ++R +G+ + E +
Sbjct: 69 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 128
Query: 93 IKIMNMIKLYGKPIRVNKASSHQKN 117
+ ++ +L+G+ V + +
Sbjct: 129 MDLLPKRELHGQNPVVTPVNKQFLS 153
>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 = 91.9 bits (229), Expect = 1e-23
Identities = 25/92 (27%), Positives = 46/92 (50%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G DG T+ V L + S + +F + G V +V++P++ T+ +G+ F+ F
Sbjct: 5 SSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
DA A M+ +L G+ +RV A +++
Sbjct: 65 RRDAQDAEAAMDGAELDGRELRVQVARYGRRD 96
Score = 71.5 bits (176), Expect = 4e-16
Identities = 23/133 (17%), Positives = 36/133 (27%), Gaps = 39/133 (29%)
Query: 117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKN 176
++D + + NL L F +G +
Sbjct: 9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVG--------------------------- 41
Query: 177 LDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
D I R+P T +GFAF+ + + + AM G L R + V
Sbjct: 42 ------------DVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV 89
Query: 237 AFKKDSKGDRHGS 249
A S
Sbjct: 90 ARYGRRDLSGPSS 102
>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 = 92.0 bits (229), Expect = 2e-23
Identities = 29/145 (20%), Positives = 53/145 (36%), Gaps = 40/145 (27%)
Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
+ +S + +G+ +F+ NLD +V K L + FS GV+++
Sbjct: 3 SGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRA----------------- 45
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
+I+ D D G S+G + + + +I +GQ L
Sbjct: 46 ----------------------DILEDKD-GKSRGIGTVTFEQSIEAVQAISMFNGQLLF 82
Query: 229 NRPISVSYAFKKDSKGDRHGSAAER 253
+RP+ V + KGD +
Sbjct: 83 DRPMHVKMDERALPKGDFFPPERPQ 107
Score = 74.3 bits (183), Expect = 7e-17
Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 1/87 (1%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
G ++G +T++V LD KV + E+F +G VV + +D+ ++ +G G + F
Sbjct: 6 SGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKS-RGIGTVTFE 64
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKA 111
+A AI + N L+ +P+ V
Sbjct: 65 QSIEAVQAISMFNGQLLFDRPMHVKMD 91
>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 = 92.9 bits (231), Expect = 2e-23
Identities = 24/78 (30%), Positives = 45/78 (57%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
T+YVG L +E ++ELF +SG + + M D++ +T G+ F+E+ DA+ A++
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 95 IMNMIKLYGKPIRVNKAS 112
+N +L + IR + +
Sbjct: 100 YINGTRLDDRIIRTDWDA 117
Score = 69.8 bits (171), Expect = 8e-15
Identities = 23/126 (18%), Positives = 41/126 (32%), Gaps = 39/126 (30%)
Query: 112 SSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKAS 171
+K L +++GNL E+ +Y+ FS G I
Sbjct: 30 EEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI----------------------- 66
Query: 172 SHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRP 231
I +G D + GF F+ Y S ++ ++ ++G L +R
Sbjct: 67 ---------KKIIMG-------LDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI 110
Query: 232 ISVSYA 237
I +
Sbjct: 111 IRTDWD 116
>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 = 90.7 bits (226), Expect = 2e-23
Identities = 27/119 (22%), Positives = 48/119 (40%), Gaps = 39/119 (32%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
++F+G+L PE+ + F+ FG I RV
Sbjct: 7 FHVFVGDLSPEITTAAIAAAFAPFGRISD--------------ARV-------------- 38
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
++D TG SKG+ F+++ + ++ +I M GQ+L R I ++A +K
Sbjct: 39 -----------VKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
Score = 78.4 bits (194), Expect = 8e-19
Identities = 24/81 (29%), Positives = 40/81 (49%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
++VG L +++ + F G + + + KD T +GYGF+ F + DA+
Sbjct: 4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63
Query: 92 AIKIMNMIKLYGKPIRVNKAS 112
AI+ M L G+ IR N A+
Sbjct: 64 AIQQMGGQWLGGRQIRTNWAT 84
>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 = 93.0 bits (231), Expect = 5e-23
Identities = 39/241 (16%), Positives = 75/241 (31%), Gaps = 84/241 (34%)
Query: 33 GDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
G++ + V L+ ++V+ ++ LF G V V ++ + ++ A
Sbjct: 2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADGNQAQL 56
Query: 92 AIKIMNMIKLYGKPIRVNKA------------------------SSHQKNLDVGAN---- 123
A+ +N KL+GKPIR+ + H+ N
Sbjct: 57 AMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNI 116
Query: 124 ------IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNL 177
+ + N+ P V E+ L FS+ G +++ K
Sbjct: 117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ--------------------- 155
Query: 178 DVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL-CNRPISVSY 236
+ A I S E + ++ +H L N + VS+
Sbjct: 156 ----------------------KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF 193
Query: 237 A 237
+
Sbjct: 194 S 194
Score = 59.5 bits (144), Expect = 8e-11
Identities = 20/174 (11%), Positives = 51/174 (29%), Gaps = 48/174 (27%)
Query: 122 ANIFIGNLDPE-VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
+ + + NL+PE V + L+ F +G +
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQ------------------------------- 32
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
+I+ + K A + A + ++ ++G L +PI ++ +
Sbjct: 33 --------RVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS--- 76
Query: 241 DSKGDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPP 294
+ + + + + + PP +++ +PP
Sbjct: 77 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPP 130
>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 = 90.4 bits (225), Expect = 7e-23
Identities = 25/134 (18%), Positives = 44/134 (32%), Gaps = 40/134 (29%)
Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
+A ++ N++I NL +DE+ L + FG ++ T
Sbjct: 14 QAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVIST------------------ 55
Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
I+RD +G S+G F S E +A I +G+++
Sbjct: 56 ---------------------RILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKT 93
Query: 230 RPISVSYAFKKDSK 243
P + K
Sbjct: 94 PPGVSAPTEPLLCK 107
Score = 64.2 bits (157), Expect = 3e-13
Identities = 14/83 (16%), Positives = 28/83 (33%), Gaps = 1/83 (1%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
+ +Y+ L + E + + G V++ + +D + T +G GF E
Sbjct: 20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEK 78
Query: 89 ADYAIKIMNMIKLYGKPIRVNKA 111
+ I N + P
Sbjct: 79 CEAVIGHFNGKFIKTPPGVSAPT 101
>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 = 88.0 bits (219), Expect = 3e-22
Identities = 27/86 (31%), Positives = 40/86 (46%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G D +ATI V L + ET + ELF G + +++ KD+ T +G+ FI F
Sbjct: 7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 66
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKA 111
EDA AI ++ + V A
Sbjct: 67 REDAARAIAGVSGFGYDHLILNVEWA 92
Score = 78.0 bits (193), Expect = 2e-18
Identities = 28/138 (20%), Positives = 48/138 (34%), Gaps = 39/138 (28%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
+S + D A I + NL + E L + F FG +++
Sbjct: 5 SSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFG-------------------SISRI 45
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
+ +D TG SKGFAFI++ E + +I + G +
Sbjct: 46 Y--------------------LAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHL 85
Query: 231 PISVSYAFKKDSKGDRHG 248
++V +A + G G
Sbjct: 86 ILNVEWAKPSTNSGPSSG 103
>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 = 90.5 bits (224), Expect = 6e-22
Identities = 30/246 (12%), Positives = 60/246 (24%), Gaps = 81/246 (32%)
Query: 31 GDGDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDA 89
G + V GLD K++ ++ +F G V V K + G +E
Sbjct: 1 GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAV 55
Query: 90 DYAIKIMNMIKLYGKPIRVNKA------------------------------------SS 113
D AI +N ++G+ + V + ++
Sbjct: 56 DRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAA 115
Query: 114 HQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSH 173
+ + N EV E+ ++ GV T
Sbjct: 116 KNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPT---------------------- 153
Query: 174 QKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPIS 233
+ + + S + ++ ++ + N
Sbjct: 154 -----------------SVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGP 196
Query: 234 VSYAFK 239
Y K
Sbjct: 197 YPYTLK 202
Score = 60.1 bits (145), Expect = 6e-11
Identities = 12/106 (11%), Positives = 28/106 (26%)
Query: 4 GREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN 63
G S S + ++ +V+E +E+ + G
Sbjct: 93 GSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRP 152
Query: 64 VHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVN 109
+ G +E+ + DA + +N ++
Sbjct: 153 TSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYP 198
>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 = 86.1 bits (214), Expect = 1e-21
Identities = 26/88 (29%), Positives = 48/88 (54%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G + D + + V GL +E + E+F + GP+ +V + D+ ++ +G+ F+ F
Sbjct: 7 GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASS 113
+DA A + N ++L G+ IRV+ SS
Sbjct: 67 VDDAKEAKERANGMELDGRRIRVSGPSS 94
Score = 75.3 bits (186), Expect = 1e-17
Identities = 24/129 (18%), Positives = 44/129 (34%), Gaps = 39/129 (30%)
Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
+ +S ++ N D + + L E+ L + FS +G I
Sbjct: 3 SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIA------------------- 43
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
D I+ D + S+GFAF+ + + + + + + +G L
Sbjct: 44 --------------------DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD 83
Query: 229 NRPISVSYA 237
R I VS
Sbjct: 84 GRRIRVSGP 92
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 86.7 bits (215), Expect = 2e-21
Identities = 19/91 (20%), Positives = 35/91 (38%), Gaps = 3/91 (3%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
+ L+D V ET + ++ + G V V + T+ H G + F A +K
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67
Query: 96 MNMIKLYGKPIRVN---KASSHQKNLDVGAN 123
+++ + G I K K ++ N
Sbjct: 68 LHLTSVMGNIIHAQLDIKGQQRMKYYELIVN 98
Score = 84.4 bits (209), Expect = 9e-21
Identities = 19/138 (13%), Positives = 35/138 (25%), Gaps = 43/138 (31%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
+ L+ V E L D +G + +
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEV----------------------------- 36
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
EI+ P T G A + + S + ++ +H + I
Sbjct: 37 ----------EILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL---- 82
Query: 241 DSKGDRHGSAAERLLAAQ 258
D KG + E ++
Sbjct: 83 DIKGQQRMKYYELIVNGS 100
>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 = 89.3 bits (221), Expect = 3e-21
Identities = 41/246 (16%), Positives = 77/246 (31%), Gaps = 84/246 (34%)
Query: 28 GESGDGDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G +G G++ + V L+ ++V+ ++ LF G V V ++ + ++
Sbjct: 28 GLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRV-----KILFNKKENALVQMADG 82
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKASSH-------------------------------- 114
A A+ +N KL+GKPIR+ +
Sbjct: 83 NQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSK 142
Query: 115 --QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASS 172
Q A + + N+ P V E+ L FS+ G +++ K
Sbjct: 143 NFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ---------------- 186
Query: 173 HQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL-CNRP 231
+ A I S E + ++ +H L N
Sbjct: 187 ---------------------------KDRKMALIQMGSVEEAVQALIDLHNHDLGENHH 219
Query: 232 ISVSYA 237
+ VS++
Sbjct: 220 LRVSFS 225
Score = 53.8 bits (129), Expect = 8e-09
Identities = 23/175 (13%), Positives = 56/175 (32%), Gaps = 48/175 (27%)
Query: 121 GANIFIGNLDPE-VDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDV 179
+ + + NL+PE V + L+ F +G + + +++
Sbjct: 34 NSVLLVSNLNPERVTPQSLFILFGVYGDVQR--------------VKILF---------- 69
Query: 180 GANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
N K A + A + ++ ++G L +PI ++ +
Sbjct: 70 --------------------NKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH 109
Query: 240 KDSKGDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPP 294
++ + R G + L + + + PP +++ +PP
Sbjct: 110 QNVQLPREGQEDQGL---TKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPP 161
>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 = 85.4 bits (212), Expect = 3e-21
Identities = 24/94 (25%), Positives = 44/94 (46%), Gaps = 2/94 (2%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDR-VTQTHQGYGFIEFM 84
G + I V + + ++ + ELF G + V +PK T H+G+GF++F+
Sbjct: 7 GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66
Query: 85 GEEDADYAIKIM-NMIKLYGKPIRVNKASSHQKN 117
++DA A + + LYG+ + + A S
Sbjct: 67 TKQDAKKAFNALCHSTHLYGRRLVLEWADSEVTV 100
Score = 65.8 bits (161), Expect = 6e-14
Identities = 18/144 (12%), Positives = 48/144 (33%), Gaps = 41/144 (28%)
Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
+ +S + I + N+ + +++ + + FS FG +
Sbjct: 3 SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELK------------------- 43
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPD-TGNSKGFAFINYASFEASDASIDAM-HGQY 226
+ + TG +GF F+++ + + + + +A+ H +
Sbjct: 44 --------------------TVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTH 83
Query: 227 LCNRPISVSYAFKKDSKGDRHGSA 250
L R + + +A + + S
Sbjct: 84 LYGRRLVLEWADSEVTVQSGPSSG 107
>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 = 85.5 bits (212), Expect = 4e-21
Identities = 29/145 (20%), Positives = 57/145 (39%), Gaps = 39/145 (26%)
Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
+ +S +K+ ++F+G+L PE+ + + F+ FG I RV
Sbjct: 3 SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISD--------------ARV- 47
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
++D TG SKG+ F+++ + ++ +I M GQ+L
Sbjct: 48 ------------------------VKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG 83
Query: 229 NRPISVSYAFKKDSKGDRHGSAAER 253
R I ++A +K + +
Sbjct: 84 GRQIRTNWATRKPPAPKSTYESNTK 108
Score = 76.2 bits (188), Expect = 1e-17
Identities = 24/84 (28%), Positives = 41/84 (48%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
+ ++VG L +++ + F G + + + KD T +GYGF+ F + D
Sbjct: 10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 69
Query: 89 ADYAIKIMNMIKLYGKPIRVNKAS 112
A+ AI+ M L G+ IR N A+
Sbjct: 70 AENAIQQMGGQWLGGRQIRTNWAT 93
>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 = 85.4 bits (212), Expect = 4e-21
Identities = 22/96 (22%), Positives = 47/96 (48%)
Query: 16 LQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTH 75
+++ +LE G + ++V + ++ E + E F G + N+H+ DR T
Sbjct: 8 VRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS 67
Query: 76 QGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
+GY +E+ + A A + +N ++ G+ I+V+
Sbjct: 68 KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC 103
Score = 74.6 bits (184), Expect = 4e-17
Identities = 24/120 (20%), Positives = 45/120 (37%), Gaps = 39/120 (32%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
G +F+ ++ E E + + F +G I KN+
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEI--------------------------KNIH-- 57
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
+ D TG SKG+A + Y + + + A+ +A++G + + I V + F K
Sbjct: 58 -----------LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 106
>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 = 84.6 bits (210), Expect = 5e-21
Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 3/87 (3%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
G T++V GL + +E + E F V + DR T + +G+GF++F
Sbjct: 6 SGPNARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFN 62
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKA 111
EEDA A + M ++ G + ++ A
Sbjct: 63 SEEDAKAAKEAMEDGEIDGNKVTLDWA 89
Score = 70.0 bits (172), Expect = 2e-15
Identities = 25/142 (17%), Positives = 48/142 (33%), Gaps = 42/142 (29%)
Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
+ +S +F+ L + E+ L ++F +R
Sbjct: 3 SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESF-------------------DGSVRAR 43
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
I+ D +TG+SKGF F+++ S E + A+ +AM +
Sbjct: 44 -----------------------IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEID 80
Query: 229 NRPISVSYAFKKDSKGDRHGSA 250
+++ +A K G S
Sbjct: 81 GNKVTLDWAKPKGEGGSGPSSG 102
>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 = 85.5 bits (212), Expect = 6e-21
Identities = 25/144 (17%), Positives = 55/144 (38%), Gaps = 40/144 (27%)
Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
Q++++ G +F+ + E E+ ++D F+ +G I ++
Sbjct: 12 DEPGPQRSVE-GWILFVTGVHEEATEEDIHDKFAEYGEI----------------KNIH- 53
Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
+ D TG KG+ + Y +++ + A+++ ++GQ L
Sbjct: 54 ----------------------LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG 91
Query: 230 RPISVSYAFKKDSKGDRHGSAAER 253
+PISV + F + + R
Sbjct: 92 QPISVDWCFVRGPPKGKRRGGRRR 115
Score = 84.3 bits (209), Expect = 2e-20
Identities = 25/95 (26%), Positives = 49/95 (51%)
Query: 17 QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
S+ Q E G + ++V G+ ++ +E + + F + G + N+H+ DR T +
Sbjct: 5 DSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 64
Query: 77 GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
GY +E+ ++A A++ +N L G+PI V+
Sbjct: 65 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 99
>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 = 84.2 bits (209), Expect = 7e-21
Identities = 22/78 (28%), Positives = 40/78 (51%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
+Y+G + +E + +L GPV+N+ M D T +GY FIEF E + A++
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 95 IMNMIKLYGKPIRVNKAS 112
+N +L + ++ +S
Sbjct: 63 NLNGYQLGSRFLKCGYSS 80
Score = 77.7 bits (192), Expect = 2e-18
Identities = 24/125 (19%), Positives = 48/125 (38%), Gaps = 39/125 (31%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
+++G++ + E+ + D S G ++
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVI-------------------------------- 30
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
+ ++M DP TG SKG+AFI + E+S +++ ++G L +R + Y+ D
Sbjct: 31 -------NLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD 83
Query: 242 SKGDR 246
G
Sbjct: 84 ISGVS 88
>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 = 84.2 bits (209), Expect = 9e-21
Identities = 28/87 (32%), Positives = 47/87 (54%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
G + ++VGGL +E + ++F + G + V + KDR TQ +G+GF+ F
Sbjct: 3 SGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFE 62
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKA 111
+DA A+ MN + G+ IRV++A
Sbjct: 63 NIDDAKDAMMAMNGKSVDGRQIRVDQA 89
Score = 76.5 bits (189), Expect = 7e-18
Identities = 26/140 (18%), Positives = 48/140 (34%), Gaps = 40/140 (28%)
Query: 111 ASSHQK-NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
SS +F+G L + +E+ L FS +G I +
Sbjct: 1 GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEV------------------ 42
Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
+++D +T S+GF F+ + + + + ++ AM+G+ +
Sbjct: 43 ---------------------VVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDG 81
Query: 230 RPISVSYAFKKDSKGDRHGS 249
R I V A K S
Sbjct: 82 RQIRVDQAGKSSDNRSGPSS 101
>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 = 85.3 bits (211), Expect = 2e-20
Identities = 22/95 (23%), Positives = 46/95 (48%)
Query: 17 QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
++ +LE G + ++V + ++ E + E F G + N+H+ DR T +
Sbjct: 55 RNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSK 114
Query: 77 GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
GY +E+ + A A + +N ++ G+ I+V+
Sbjct: 115 GYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC 149
Score = 83.0 bits (205), Expect = 1e-19
Identities = 24/133 (18%), Positives = 47/133 (35%), Gaps = 39/133 (29%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
G +F+ ++ E E + + F +G I ++
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEI----------------KNIH------------ 103
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
+ D TG SKG+A + Y + + + A+ +A++G + + I V + F K
Sbjct: 104 -----------LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK 152
Query: 241 DSKGDRHGSAAER 253
K + R
Sbjct: 153 GPKRVKKSEKRRR 165
>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 = 82.3 bits (204), Expect = 3e-20
Identities = 25/92 (27%), Positives = 49/92 (53%), Gaps = 1/92 (1%)
Query: 20 SQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYG 79
S + GG + +T+YV L ++ ++ +F + G VV V + KD+ T+ +G
Sbjct: 3 SGSSGMSGGLAPSK-STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVA 61
Query: 80 FIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
FI F+ ++ A + +N +L+G+ I+ + A
Sbjct: 62 FILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93
Score = 70.7 bits (174), Expect = 8e-16
Identities = 26/117 (22%), Positives = 42/117 (35%), Gaps = 39/117 (33%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
+ +++ NL + LY FS +G +V K +
Sbjct: 16 KSTVYVSNLPFSLTNNDLYRIFSKYG-------------------KVVKVT--------- 47
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
IM+D DT SKG AFI + +++ A++ + L R I S A
Sbjct: 48 -----------IMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA 93
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 82.7 bits (205), Expect = 4e-20
Identities = 25/95 (26%), Positives = 49/95 (51%)
Query: 17 QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
S+ Q E G + ++V G+ ++ +E + + F + G + N+H+ DR T +
Sbjct: 6 DSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLK 65
Query: 77 GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
GY +E+ ++A A++ +N L G+PI V+
Sbjct: 66 GYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC 100
Score = 78.5 bits (194), Expect = 2e-18
Identities = 24/132 (18%), Positives = 53/132 (40%), Gaps = 40/132 (30%)
Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
Q++++ G +F+ + E E+ ++D F+ +G I ++
Sbjct: 12 GDEPGPQRSVE-GWILFVTGVHEEATEEDIHDKFAEYGEI----------------KNIH 54
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
+ D TG KG+ + Y +++ + A+++ ++GQ L
Sbjct: 55 -----------------------LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLM 91
Query: 229 NRPISVSYAFKK 240
+PISV + F +
Sbjct: 92 GQPISVDWCFVR 103
>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 = 82.3 bits (204), Expect = 5e-20
Identities = 21/86 (24%), Positives = 43/86 (50%), Gaps = 2/86 (2%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G ES ++V + + + + ++F Q G +++V + + + +G+GF+ F
Sbjct: 7 GNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFEN 64
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKA 111
DAD A + ++ + G+ I VN A
Sbjct: 65 SADADRAREKLHGTVVEGRKIEVNNA 90
Score = 66.5 bits (163), Expect = 3e-14
Identities = 24/139 (17%), Positives = 44/139 (31%), Gaps = 41/139 (29%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
+S + ++ + + N+ + L F FG IL
Sbjct: 5 SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKIL--------------------- 43
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
D EI+ + SKGF F+ + + +D + + +HG + R
Sbjct: 44 ------------------DVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGR 83
Query: 231 PISVSYAFKKDSKGDRHGS 249
I V+ A + S
Sbjct: 84 KIEVNNATARVMTNSGPSS 102
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 82.0 bits (203), Expect = 8e-20
Identities = 29/82 (35%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDA 89
D +++GGL+ + +E ++ +F + GP+ V + KDR T +G+ FI F DA
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61
Query: 90 DYAIKIMNMIKLYGKPIRVNKA 111
A K MN L+GK I+V +A
Sbjct: 62 KNAAKDMNGKSLHGKAIKVEQA 83
Score = 73.5 bits (181), Expect = 1e-16
Identities = 27/128 (21%), Positives = 44/128 (34%), Gaps = 40/128 (31%)
Query: 119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
D +FIG L+ E +EK+L F G I
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPIS----------------------------- 35
Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
+ +++D T S+GFAFI + + + + M+G+ L + I V A
Sbjct: 36 ----------EVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAK 84
Query: 239 KKDSKGDR 246
K +
Sbjct: 85 KPSFQSGG 92
>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 = 81.0 bits (201), Expect = 1e-19
Identities = 19/78 (24%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRV-TQTHQGYGFIEFMGEEDADYAI 93
+++G L V++ + E+F G + + MP +R+ +GY ++EF ++A+ A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 94 KIMNMIKLYGKPIRVNKA 111
K M+ ++ G+ I
Sbjct: 65 KHMDGGQIDGQEITATAV 82
Score = 64.5 bits (158), Expect = 1e-13
Identities = 17/116 (14%), Positives = 39/116 (33%), Gaps = 38/116 (32%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
+ IG L V + + + FS +G I K +D+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKI--------------------------KMIDM-- 36
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
+ SKG+A++ + + + ++ ++ M G + + I+ +
Sbjct: 37 ----------PVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV 82
>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 = 85.7 bits (211), Expect = 1e-19
Identities = 29/188 (15%), Positives = 53/188 (28%), Gaps = 47/188 (25%)
Query: 122 ANIFIGNLDPEVDE----KLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNL 177
I+I NL+ ++ + K LY FS FG IL
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILD--------------------------- 42
Query: 178 DVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
+ + +G AF+ + ++ ++ +M G ++P+ + YA
Sbjct: 43 ---------------ILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA 87
Query: 238 -FKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPP 296
D G+ ER + ++ P + PP
Sbjct: 88 KTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPM 147
Query: 297 PSGLRASA 304
R
Sbjct: 148 TQAPRIMH 155
Score = 68.4 bits (166), Expect = 2e-13
Identities = 19/83 (22%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 35 ATIYVGGLDDKVSE----TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDAD 90
TIY+ L++K+ + ++ +F Q G ++++ + + + +G F+ F A
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 66
Query: 91 YAIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 67 NALRSMQGFPFYDKPMRIQYAKT 89
Score = 46.0 bits (108), Expect = 5e-06
Identities = 17/103 (16%), Positives = 34/103 (33%), Gaps = 6/103 (5%)
Query: 8 QAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMP 67
G P Q + +++ L ++ +E ++ LF Q V +
Sbjct: 181 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV 240
Query: 68 KDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLY-GKPIRVN 109
R F+EF E A A + K+ ++++
Sbjct: 241 PGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS 278
Score = 46.0 bits (108), Expect = 5e-06
Identities = 24/184 (13%), Positives = 49/184 (26%), Gaps = 50/184 (27%)
Query: 57 QSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQK 116
P + HMP G + + P + +
Sbjct: 148 TQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPN 207
Query: 117 NLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKN 176
+ +F+ NL E +E +L F+ F + +++
Sbjct: 208 H-----ILFLTNLPEETNELMLSMLFNQFPGF-KEVRLVP-------------------- 241
Query: 177 LDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC-NRPISVS 235
AF+ + + + A+ DA+ G + N + +S
Sbjct: 242 -----------------------GRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS 278
Query: 236 YAFK 239
+A K
Sbjct: 279 FAKK 282
>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 = 83.0 bits (205), Expect = 1e-19
Identities = 26/110 (23%), Positives = 50/110 (45%)
Query: 2 SLGREIQAGISTPCLQSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPV 61
+ E +T + +G ++ V L + S + +F + G V
Sbjct: 38 GVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRV 97
Query: 62 VNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
+V++P+DR T+ +G+ F+ F + DA+ A+ M+ L G+ +RV A
Sbjct: 98 GDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147
Score = 77.2 bits (190), Expect = 2e-17
Identities = 31/188 (16%), Positives = 53/188 (28%), Gaps = 51/188 (27%)
Query: 72 TQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS------------HQKNLD 119
+T +G E + A+ K + A+ H +++
Sbjct: 9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVE 68
Query: 120 VGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDV 179
++ + NL L F +G +
Sbjct: 69 GMTSLKVDNLTYRTSPDTLRRVFEKYGRVG------------------------------ 98
Query: 180 GANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
D I RD T S+GFAF+ + ++ ++DAM G L R + V A
Sbjct: 99 ---------DVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARY 149
Query: 240 KDSKGDRH 247
H
Sbjct: 150 GRPPDSHH 157
>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 = 80.7 bits (200), Expect = 1e-19
Identities = 23/85 (27%), Positives = 39/85 (45%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G G ++V L SE + +LF GP+ +H P D +T+ +G+ F+ FM
Sbjct: 1 GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFP 60
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKA 111
E A A ++ G+ + V +
Sbjct: 61 EHAVKAYAEVDGQVFQGRMLHVLPS 85
Score = 67.2 bits (165), Expect = 2e-14
Identities = 24/127 (18%), Positives = 38/127 (29%), Gaps = 39/127 (30%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+F+ NL E+ L FSA+G + + H
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPL---------------------SELH---------- 39
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
D T KGFAF+ + E + + + GQ R + V + K
Sbjct: 40 --------YPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEA 91
Query: 244 GDRHGSA 250
S+
Sbjct: 92 SQSGPSS 98
>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 = 80.8 bits (200), Expect = 2e-19
Identities = 24/95 (25%), Positives = 45/95 (47%)
Query: 17 QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
++ + G +YVG L ++E ++ +F G + ++ + D T +
Sbjct: 9 SHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSK 68
Query: 77 GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
GYGFI F E A A++ +N +L G+P++V
Sbjct: 69 GYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV 103
Score = 69.3 bits (170), Expect = 4e-15
Identities = 26/132 (19%), Positives = 50/132 (37%), Gaps = 39/132 (29%)
Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
A++ QK +++G+L + E +L F FG R+
Sbjct: 15 MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFG-------------------RIES 55
Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
+M D +TG SKG+ FI ++ E + +++ ++G L
Sbjct: 56 IQ--------------------LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAG 95
Query: 230 RPISVSYAFKKD 241
RP+ V + ++
Sbjct: 96 RPMKVGHVTERT 107
>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 = 80.4 bits (199), Expect = 2e-19
Identities = 29/141 (20%), Positives = 50/141 (35%), Gaps = 43/141 (30%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
+S + +F+G L+ + E+ + F FGVI +
Sbjct: 5 SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDEC------------------- 45
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL--- 227
++R PD G+SKG AF+ ++S + A+I A+HG
Sbjct: 46 --------------------TVLRGPD-GSSKGCAFVKFSSHTEAQAAIHALHGSQTMPG 84
Query: 228 CNRPISVSYAFKKDSKGDRHG 248
+ + V +A G G
Sbjct: 85 ASSSLVVKFADTDKESGPSSG 105
Score = 64.2 bits (157), Expect = 2e-13
Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 4/95 (4%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G G D ++VG L+ + SE + LF G + + + + +G F++F
Sbjct: 7 GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSS 65
Query: 86 EEDADYAIKIMN---MIKLYGKPIRVNKASSHQKN 117
+A AI ++ + + V A + +++
Sbjct: 66 HTEAQAAIHALHGSQTMPGASSSLVVKFADTDKES 100
>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 = 80.0 bits (198), Expect = 3e-19
Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 6/88 (6%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
GG ++ + ++VG L ++E M +LF + G V + KD+ G+GFI
Sbjct: 7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLET 60
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASS 113
A+ A ++ + L GK +RV A
Sbjct: 61 RTLAEIAKVELDNMPLRGKQLRVRFACH 88
Score = 62.7 bits (153), Expect = 8e-13
Identities = 20/135 (14%), Positives = 43/135 (31%), Gaps = 45/135 (33%)
Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
+ +S +K + +F+GNL P++ E+ + F +G + + ++
Sbjct: 3 SGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGE--------------VFIH 48
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
K KGF FI + ++ + + L
Sbjct: 49 K-------------------------------DKGFGFIRLETRTLAEIAKVELDNMPLR 77
Query: 229 NRPISVSYAFKKDSK 243
+ + V +A S
Sbjct: 78 GKQLRVRFACHSASL 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 = 80.9 bits (200), Expect = 3e-19
Identities = 24/87 (27%), Positives = 47/87 (54%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
G + D + + V GL +E + E+F + GP+ +V + D+ ++ +G+ F+ F
Sbjct: 37 VGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFE 96
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKA 111
+DA A + N ++L G+ IRV+ +
Sbjct: 97 NVDDAKEAKERANGMELDGRRIRVDFS 123
Score = 72.8 bits (179), Expect = 3e-16
Identities = 22/122 (18%), Positives = 40/122 (32%), Gaps = 39/122 (31%)
Query: 119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
D + + L E+ L + FS +G I
Sbjct: 44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIA----------------------------- 74
Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
D I+ D + S+GFAF+ + + + + + + +G L R I V ++
Sbjct: 75 ----------DVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSI 124
Query: 239 KK 240
K
Sbjct: 125 TK 126
>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 = 79.5 bits (197), Expect = 4e-19
Identities = 27/80 (33%), Positives = 44/80 (55%)
Query: 32 DGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
G + +YVG L ++E ++ +F G + N+ + KD T +GYGFI F E A
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 92 AIKIMNMIKLYGKPIRVNKA 111
A++ +N +L G+P+RV
Sbjct: 63 ALEQLNGFELAGRPMRVGHV 82
Score = 74.9 bits (185), Expect = 2e-17
Identities = 26/128 (20%), Positives = 49/128 (38%), Gaps = 39/128 (30%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
+ +++G+L + E +L F FG I
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKID-------------------------------- 33
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
+ +M+D DTG SKG+ FI ++ E + +++ ++G L RP+ V + ++
Sbjct: 34 -------NIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERL 86
Query: 242 SKGDRHGS 249
G S
Sbjct: 87 DGGSGPSS 94
>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 = 78.8 bits (195), Expect = 8e-19
Identities = 24/77 (31%), Positives = 46/77 (59%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
+++VG + + +E + ++F + GPVV+ + DR T +GYGF E+ +E A A++
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 95 IMNMIKLYGKPIRVNKA 111
+N + G+ +RV+ A
Sbjct: 69 NLNGREFSGRALRVDNA 85
Score = 66.1 bits (162), Expect = 4e-14
Identities = 23/125 (18%), Positives = 44/125 (35%), Gaps = 39/125 (31%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
++F+GN+ E E+ L D FS G +
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSE----------------VGPVVSFR------------- 39
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
++ D +TG KG+ F Y E + +++ ++G+ R + V A +
Sbjct: 40 ----------LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK 89
Query: 242 SKGDR 246
+K +
Sbjct: 90 NKEEL 94
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 78.5 bits (194), Expect = 1e-18
Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T Y+G + +E + LF G +++ ++ G FI++ E A I
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDTHEQAAVCIVA 82
Query: 96 MNMIKLYGKPIRVN 109
+ G+ +R
Sbjct: 83 LANFPFQGRNLRTG 96
Score = 60.0 bits (146), Expect = 6e-12
Identities = 23/141 (16%), Positives = 34/141 (24%), Gaps = 48/141 (34%)
Query: 100 KLYGKPIRVNKASSHQKNLDVGAN---IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN 156
+ G P +VN + +IGN+ E L F FG IL
Sbjct: 3 QTIGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILD------ 56
Query: 157 MIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASD 216
+ KG FI Y + E +
Sbjct: 57 --------FKHYP-------------------------------EKGCCFIKYDTHEQAA 77
Query: 217 ASIDAMHGQYLCNRPISVSYA 237
I A+ R + +
Sbjct: 78 VCIVALANFPFQGRNLRTGWG 98
>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 98
Score = 78.1 bits (193), Expect = 1e-18
Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 3/82 (3%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ---GYGFIEFMGEEDA 89
G + +++ L+ +E + +F + G + + + K + G+GF+E+ E A
Sbjct: 4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQA 63
Query: 90 DYAIKIMNMIKLYGKPIRVNKA 111
A+K + + G + V +
Sbjct: 64 QKALKQLQGHTVDGHKLEVRIS 85
Score = 71.1 bits (175), Expect = 5e-16
Identities = 20/133 (15%), Positives = 35/133 (26%), Gaps = 42/133 (31%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
+ +FI NL+ E+ L FS G I
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIK------------------------------- 33
Query: 181 ANIFIGNLDPEIMRDPDTGN---SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
I + + S GF F+ Y E + ++ + G + + V +
Sbjct: 34 --------SCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS 85
Query: 238 FKKDSKGDRHGSA 250
+ S
Sbjct: 86 ERATKPASGPSSG 98
>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 78.5 bits (194), Expect = 2e-18
Identities = 19/84 (22%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T+++ L E + E+ Q G + V + T+ +G F +FM +E A +
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 96 MNM------IKLYGKPIRVNKASS 113
++ +KL G+ ++V+ A +
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDLAVT 100
Score = 70.5 bits (173), Expect = 1e-15
Identities = 27/143 (18%), Positives = 45/143 (31%), Gaps = 45/143 (31%)
Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
+S ++ G +FI NL + +E+ L + FG +
Sbjct: 4 GSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLK-------------------- 43
Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMH------ 223
++ PDT +SKG AF + + EA+ + A
Sbjct: 44 -------------------YVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGG 84
Query: 224 GQYLCNRPISVSYAFKKDSKGDR 246
G L R + V A +D
Sbjct: 85 GLKLDGRQLKVDLAVTRDEAASG 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 = 78.1 bits (193), Expect = 2e-18
Identities = 29/89 (32%), Positives = 37/89 (41%), Gaps = 11/89 (12%)
Query: 28 GESGDGDA-----TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIE 82
G SGD D +YV L SE ++ + F P + K R Y F+
Sbjct: 4 GSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR------DYAFVH 57
Query: 83 FMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
F EDA A+K +N L G PI V A
Sbjct: 58 FSNREDAVEAMKALNGKVLDGSPIEVTLA 86
Score = 62.3 bits (152), Expect = 1e-12
Identities = 23/142 (16%), Positives = 48/142 (33%), Gaps = 47/142 (33%)
Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
+ +S + + +++ NL E+++ F+ RV
Sbjct: 3 SGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPG--------------AVERVK 48
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
K + +AF+++++ E + ++ A++G+ L
Sbjct: 49 K-------------------------------IRDYAFVHFSNREDAVEAMKALNGKVLD 77
Query: 229 NRPISVSYA--FKKDSKGDRHG 248
PI V+ A KDS G G
Sbjct: 78 GSPIEVTLAKPVDKDSSGPSSG 99
>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 = 78.1 bits (193), Expect = 2e-18
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T++ L ++ + + F G V +V + DR ++ +G ++EF + AI
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG- 85
Query: 96 MNMIKLYGKPIRVNKA 111
+ +L G PI V +
Sbjct: 86 LTGQRLLGVPIIVQAS 101
Score = 64.3 bits (157), Expect = 3e-13
Identities = 23/127 (18%), Positives = 41/127 (32%), Gaps = 40/127 (31%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+F L + + L D FSA G + V
Sbjct: 28 VFCMQLAARIRPRDLEDFFSAVGKV----------------RDVR--------------- 56
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
I+ D ++ SKG A++ + ++ +I + GQ L PI V + + ++
Sbjct: 57 --------IISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKNR 107
Query: 244 GDRHGSA 250
S
Sbjct: 108 LSGPSSG 114
>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 115
Score = 78.1 bits (193), Expect = 2e-18
Identities = 21/85 (24%), Positives = 39/85 (45%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
G+ + +Y+ L +V+E + LF + + +T +G FI F +E
Sbjct: 20 NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 79
Query: 89 ADYAIKIMNMIKLYGKPIRVNKASS 113
A A+ ++N KLYGK + + +
Sbjct: 80 AWQALHLVNGYKLYGKILVIEFGKN 104
Score = 75.0 bits (185), Expect = 3e-17
Identities = 27/148 (18%), Positives = 46/148 (31%), Gaps = 41/148 (27%)
Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
G+ IR S + +++ NL P V E+ L F+ F
Sbjct: 7 GEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKK------------- 53
Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
P I TG +G AFI + + E + ++ +
Sbjct: 54 --------------------------GPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 223 HGQYLCNRPISVSYAFKKD--SKGDRHG 248
+G L + + + + K S G G
Sbjct: 88 NGYKLYGKILVIEFGKNKKQRSSGPSSG 115
>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 = 77.3 bits (191), Expect = 3e-18
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
T+YV G D ++ TL+ F G ++++ M R F+ + E AD A+
Sbjct: 16 NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVA 67
Query: 95 IMNMIKLYGKPIRVNKA 111
+N ++ ++VN A
Sbjct: 68 ELNGTQVESVQLKVNIA 84
Score = 66.2 bits (162), Expect = 4e-14
Identities = 20/141 (14%), Positives = 45/141 (31%), Gaps = 47/141 (33%)
Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
+ +S ++ G +++ D + LL FS FG I+ + ++
Sbjct: 3 SGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIID--------------LSMD 46
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
+ AF+ Y E++D ++ ++G +
Sbjct: 47 P-------------------------------PRNCAFVTYEKMESADQAVAELNGTQVE 75
Query: 229 NRPISVSYAFKKDSKGDRHGS 249
+ + V+ A K+ S
Sbjct: 76 SVQLKVNIARKQPMLDSGPSS 96
>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 = 76.9 bits (190), Expect = 3e-18
Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 7/86 (8%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G G +Y+G L V+ + +LF +P GY F+++ +
Sbjct: 1 GSSGSSGMNKLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQ 54
Query: 87 EDADYAIKIMN-MIKLYGKPIRVNKA 111
A AI+ ++ ++L+GK + V+ +
Sbjct: 55 NWAIRAIETLSGKVELHGKIMEVDYS 80
Score = 66.1 bits (162), Expect = 3e-14
Identities = 19/123 (15%), Positives = 34/123 (27%), Gaps = 46/123 (37%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
++IGNL P V L F + L
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPL---------------------------------- 36
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY-LCNRPISVSYAFKKDS 242
G+AF++Y + +I+ + G+ L + + V Y+ K
Sbjct: 37 -----------AGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL 85
Query: 243 KGD 245
+
Sbjct: 86 RSS 88
>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 = 77.4 bits (191), Expect = 3e-18
Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 6/75 (8%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
T+Y GG+ +++ LM + F G ++ + + ++ GY F+ F E A +AI
Sbjct: 26 CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIV 79
Query: 95 IMNMIKLYGKPIRVN 109
+N + G ++
Sbjct: 80 SVNGTTIEGHVVKCY 94
Score = 61.2 bits (149), Expect = 4e-12
Identities = 19/130 (14%), Positives = 48/130 (36%), Gaps = 47/130 (36%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGA 181
++ G + + ++L+ TFS FG I++ IR
Sbjct: 26 CTVYCGGIASGLTDQLMRQTFSPFGQIME--------------IR--------------- 56
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
+ + KG++F+ +++ E++ +I +++G + + + K+
Sbjct: 57 ----------VFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG--KE 98
Query: 242 SKGDRHGSAA 251
S G ++
Sbjct: 99 SPDMTSGPSS 108
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 76.6 bits (189), Expect = 4e-18
Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 6/93 (6%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSG--PVVNVHMPKDRVTQTHQGYGFIEFM 84
G TI + + + V N+ + KD+ TQ ++G+ F++
Sbjct: 2 GHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLS 61
Query: 85 GEEDADYAIKIMN----MIKLYGKPIRVNKASS 113
DA ++I+ +K+ GK I V+ A S
Sbjct: 62 SAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94
Score = 69.7 bits (171), Expect = 2e-15
Identities = 14/123 (11%), Positives = 34/123 (27%), Gaps = 41/123 (33%)
Query: 119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
I + N+ P + S + + +
Sbjct: 7 HHMDTIILRNIAPHTVVDSIMTALSPYASL---------------AVN------------ 39
Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQ----YLCNRPISV 234
+ +++D T ++GFAF+ +S + + + + + I V
Sbjct: 40 ----------NIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGV 89
Query: 235 SYA 237
+A
Sbjct: 90 DFA 92
>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 = 76.4 bits (189), Expect = 5e-18
Identities = 30/76 (39%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
IYVG L + + ELF Q G V NV + DR T+ +G+GF+E M EE AI
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAK 61
Query: 96 MNMIKLYGKPIRVNKA 111
++ G+ IRV +A
Sbjct: 62 LDNTDFMGRTIRVTEA 77
Score = 63.0 bits (154), Expect = 4e-13
Identities = 26/125 (20%), Positives = 39/125 (31%), Gaps = 40/125 (32%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
NI++GNL + + + FS FG +V
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFG-------------------KVFNVK----------- 32
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
++ D +T KGF F+ S+A I + R I V+ A K S
Sbjct: 33 ---------LIYDRETKKPKGFGFVEMQEESVSEA-IAKLDNTDFMGRTIRVTEANPKKS 82
Query: 243 KGDRH 247
H
Sbjct: 83 LEHHH 87
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 77.9 bits (192), Expect = 5e-18
Identities = 24/87 (27%), Positives = 45/87 (51%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
+G ++ V L + S + +F + G V +V++P+DR T+ +G+ F+ F
Sbjct: 38 GRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFH 97
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKA 111
+ DA+ A+ M+ L G+ +RV A
Sbjct: 98 DKRDAEDAMDAMDGAVLDGRELRVQMA 124
Score = 70.5 bits (173), Expect = 2e-15
Identities = 27/140 (19%), Positives = 43/140 (30%), Gaps = 40/140 (28%)
Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
+++ ++ + NL L F +G RV
Sbjct: 36 SYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYG-------------------RVGD 76
Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
I RD T S+GFAF+ + ++ ++DAM G L
Sbjct: 77 VY--------------------IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 116
Query: 230 RPISVSYAFKKDSKGDRHGS 249
R + V A + D H S
Sbjct: 117 RELRVQMA-RYGRPPDSHHS 135
>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 = 76.6 bits (189), Expect = 6e-18
Identities = 34/139 (24%), Positives = 48/139 (34%), Gaps = 43/139 (30%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
SS K+ D +FIG + +DEK L F FG I
Sbjct: 4 GSSGMKDHD-AIKLFIGQIPRNLDEKDLKPLFEEFGKIY--------------------- 41
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL--- 227
+ +++D TG KG AF+ Y E++ + A+H Q
Sbjct: 42 ------------------ELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPG 83
Query: 228 CNRPISVSYAFKKDSKGDR 246
NRPI V A + G
Sbjct: 84 MNRPIQVKPADSESRGGSG 102
Score = 75.8 bits (187), Expect = 1e-17
Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 3/95 (3%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G +++G + + E + LF + G + + + KDR T H+G F+ +
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64
Query: 86 EEDADYAIKIMN---MIKLYGKPIRVNKASSHQKN 117
E A A ++ + +PI+V A S +
Sbjct: 65 RESALKAQSALHEQKTLPGMNRPIQVKPADSESRG 99
>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 = 77.5 bits (191), Expect = 7e-18
Identities = 28/113 (24%), Positives = 48/113 (42%)
Query: 17 QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
Q D + V + V E + +LF + GP+ +V + DR T+ +
Sbjct: 25 QQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSR 84
Query: 77 GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNL 129
GYGF++F A AI +N + K ++V A+S + + + GN
Sbjct: 85 GYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNG 137
Score = 77.1 bits (190), Expect = 1e-17
Identities = 25/173 (14%), Positives = 55/173 (31%), Gaps = 41/173 (23%)
Query: 81 IEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYD 140
I + + D + +L + + + DV N+ + + VDE L
Sbjct: 4 IPLVSQYDPYGQTAQLQ--QLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQ 61
Query: 141 TFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGN 200
F +G + I+ D +T
Sbjct: 62 LFERYG-------------------PIESVK--------------------IVCDRETRQ 82
Query: 201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAER 253
S+G+ F+ + S ++ +I ++G + N+ + V+ A + G+ +
Sbjct: 83 SRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDG 135
>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 = 76.7 bits (189), Expect = 1e-17
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 8/76 (10%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T+YV G D ++ TL+ F G ++++ M R F+ + E AD A+
Sbjct: 41 TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAE 92
Query: 96 MNMIKLYGKPIRVNKA 111
+N ++ ++VN A
Sbjct: 93 LNGTQVESVQLKVNIA 108
Score = 66.3 bits (162), Expect = 7e-14
Identities = 21/149 (14%), Positives = 48/149 (32%), Gaps = 47/149 (31%)
Query: 102 YGKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLY 161
+ P R + + ++ G +++ D + LL FS FG I+
Sbjct: 20 HMGPFRRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIID----------- 66
Query: 162 GKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDA 221
+ ++ + AF+ Y E++D ++
Sbjct: 67 ---LSMDP-------------------------------PRNCAFVTYEKMESADQAVAE 92
Query: 222 MHGQYLCNRPISVSYAFKKDSKGDRHGSA 250
++G + + + V+ A K+ G +
Sbjct: 93 LNGTQVESVQLKVNIARKQPMLDAATGKS 121
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 75.4 bits (186), Expect = 1e-17
Identities = 15/83 (18%), Positives = 38/83 (45%), Gaps = 1/83 (1%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
+++ GL ++ + E+ G V ++ + +R +G ++E+ E A A+
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVM 76
Query: 95 IMNMIKLYGKPIRVNKASSHQKN 117
M+ + + I+V ++S +
Sbjct: 77 KMDGMTIKENIIKVAISNSGPSS 99
Score = 61.9 bits (151), Expect = 1e-12
Identities = 18/124 (14%), Positives = 35/124 (28%), Gaps = 40/124 (32%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
+FI L ++ L + A G +
Sbjct: 17 KHKLFISGLPFSCTKEELEEICKAHGTVK------------------------------- 45
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
D ++ + G KG A++ Y + + ++ M G + I V+ +
Sbjct: 46 --------DLRLVTN-RAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSG 96
Query: 241 DSKG 244
S G
Sbjct: 97 PSSG 100
>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 = 75.9 bits (187), Expect = 2e-17
Identities = 26/89 (29%), Positives = 41/89 (46%), Gaps = 1/89 (1%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
GGGE + A + V LD VS+ + ELF + G + + DR + G + F
Sbjct: 26 CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFE 84
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKASS 113
DA A+K + L G+P+ + +S
Sbjct: 85 RRADALKAMKQYKGVPLDGRPMDIQLVAS 113
Score = 67.0 bits (164), Expect = 3e-14
Identities = 18/134 (13%), Positives = 41/134 (30%), Gaps = 40/134 (29%)
Query: 107 RVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIR 166
+ + ++ GA + + NLD V + + + F+ FG + +
Sbjct: 21 LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKA--------------- 65
Query: 167 VNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY 226
+ D +G S G A +++ + ++ G
Sbjct: 66 ------------------------AVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVP 100
Query: 227 LCNRPISVSYAFKK 240
L RP+ + +
Sbjct: 101 LDGRPMDIQLVASQ 114
>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 = 74.5 bits (184), Expect = 2e-17
Identities = 18/81 (22%), Positives = 37/81 (45%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G + +Y+ GL ++ + +L G +V+ D+ T +GYGF++F A A
Sbjct: 4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63
Query: 93 IKIMNMIKLYGKPIRVNKASS 113
+ + + + + + SS
Sbjct: 64 VTALKASGVQAQMAKQSGPSS 84
Score = 72.6 bits (179), Expect = 1e-16
Identities = 16/115 (13%), Positives = 35/115 (30%), Gaps = 39/115 (33%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
+ ++I L P ++ L +G I+ S+
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIV---------------------STK------- 36
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVS 235
+ D T KG+ F+++ S A+ ++ A+ + + S
Sbjct: 37 -----------AILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQS 80
>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 = 74.2 bits (183), Expect = 3e-17
Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 8/87 (9%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G SG ++VG + + + F + GPV+ + K Y F+
Sbjct: 3 SGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERA 54
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKASS 113
EDA AI+ ++ + GK + V ++S
Sbjct: 55 EDAVEAIRGLDNTEFQGKRMHVQLSTS 81
Score = 47.2 bits (113), Expect = 2e-07
Identities = 13/129 (10%), Positives = 34/129 (26%), Gaps = 47/129 (36%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
+ +GN+ P + L F +G ++
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVI------------------------------- 38
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
+ +I++ +AF++ E + +I + + + V + +
Sbjct: 39 --------ECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSR 82
Query: 241 DSKGDRHGS 249
S
Sbjct: 83 LRTASGPSS 91
>2la6_A RNA-binding protein FUS; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative, RNA recognition; NMR {Homo sapiens}
Length = 99
Score = 74.6 bits (184), Expect = 3e-17
Identities = 28/117 (23%), Positives = 41/117 (35%), Gaps = 33/117 (28%)
Query: 122 ANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN-MIKLYGKPIRVNKASSHQKNLDVG 180
IF+ L V + + D F G+I K MI LY
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLY------------------- 54
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
D +TG KG A +++ ++ A+ID G+ PI VS+A
Sbjct: 55 -------------TDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
Score = 72.0 bits (177), Expect = 3e-16
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 8/86 (9%)
Query: 35 ATIYVGGLDDKVSETLMWELFVQSGPV--------VNVHMPKDRVTQTHQGYGFIEFMGE 86
TI+V GL + V+ + + F Q G + +++ DR T +G + F
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKAS 112
A AI + + G PI+V+ A+
Sbjct: 74 PSAKAAIDWFDGKEFSGNPIKVSFAT 99
>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 = 74.6 bits (184), Expect = 4e-17
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 1/88 (1%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
GGG + + V LD VS+ + ELF + G + + DR + G + F
Sbjct: 21 GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFER 79
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASS 113
+ DA A+K N + L G+P+ + +S
Sbjct: 80 KADALKAMKQYNGVPLDGRPMNIQLVTS 107
Score = 66.9 bits (164), Expect = 2e-14
Identities = 17/131 (12%), Positives = 40/131 (30%), Gaps = 40/131 (30%)
Query: 107 RVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIR 166
+ ++ G + + NLD V + + + F+ FG + +
Sbjct: 15 LFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKA--------------- 59
Query: 167 VNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY 226
+ D +G S G A +++ + ++ +G
Sbjct: 60 ------------------------AVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVP 94
Query: 227 LCNRPISVSYA 237
L RP+++
Sbjct: 95 LDGRPMNIQLV 105
>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 = 74.1 bits (183), Expect = 4e-17
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 2/81 (2%)
Query: 32 DGDA-TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDAD 90
+ DA +IYVG +D + + F G V V + D+ + +G+ +IEF +E
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 91 YAIKIMNMIKLYGKPIRVNKA 111
++ ++ G+ I+V
Sbjct: 63 TSLA-LDESLFRGRQIKVIPK 82
Score = 61.4 bits (150), Expect = 1e-12
Identities = 23/115 (20%), Positives = 38/115 (33%), Gaps = 40/115 (34%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
+I++GN+D + L F G + RV
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVN----------------RVT-------------- 37
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
I+ D +G+ KGFA+I ++ E+ S+ A+ R I V
Sbjct: 38 ---------ILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPK 82
>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 = 75.7 bits (186), Expect = 4e-17
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
+S D +YVG L + ++T + F GP+ +V + ++ G+ F+EF D
Sbjct: 68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRD 122
Query: 89 ADYAIKIMNMIKLYGKPIRVNKA 111
A A++ ++ L G +RV +
Sbjct: 123 AADAVRELDGRTLCGCRVRVELS 145
Score = 59.9 bits (145), Expect = 3e-11
Identities = 17/135 (12%), Positives = 40/135 (29%), Gaps = 44/135 (32%)
Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
+ + H+ + + +++GNL ++ L F +G +
Sbjct: 55 TEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLR------------- 101
Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
+ R+P GFAF+ + + ++ +
Sbjct: 102 --------------------------SVWVARNP-----PGFAFVEFEDPRDAADAVREL 130
Query: 223 HGQYLCNRPISVSYA 237
G+ LC + V +
Sbjct: 131 DGRTLCGCRVRVELS 145
>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 = 74.3 bits (183), Expect = 5e-17
Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 3/84 (3%)
Query: 28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
G +G+ D IYVG L + + ++F + G + ++ + R + F+EF
Sbjct: 16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPR 72
Query: 88 DADYAIKIMNMIKLYGKPIRVNKA 111
DA+ A+ + G +RV
Sbjct: 73 DAEDAVYGRDGYDYDGYRLRVEFP 96
Score = 49.6 bits (119), Expect = 4e-08
Identities = 18/127 (14%), Positives = 35/127 (27%), Gaps = 44/127 (34%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
I++GNL P++ K + D F +G I
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIR---------------------------------- 50
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA--FKKD 241
D ++ FAF+ + ++ ++ G + V + +
Sbjct: 51 -----DIDLKNRR---GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGT 102
Query: 242 SKGDRHG 248
G G
Sbjct: 103 GSGPSSG 109
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 74.7 bits (184), Expect = 5e-17
Identities = 29/131 (22%), Positives = 45/131 (34%), Gaps = 33/131 (25%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN-MIKLYGKPIRVNKASSHQKNLDVGA 181
IF+ L V + + D F G+I K MI LY
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLY-------------------- 48
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
D +TG KG A +++ ++ A+ID G+ PI VS+A ++
Sbjct: 49 ------------TDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRA 96
Query: 242 SKGDRHGSAAE 252
G+
Sbjct: 97 DFNRGGGNGRG 107
Score = 72.0 bits (177), Expect = 4e-16
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 8/84 (9%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPV--------VNVHMPKDRVTQTHQGYGFIEFMGEE 87
TI+V GL + V+ + + F Q G + +++ DR T +G + F
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68
Query: 88 DADYAIKIMNMIKLYGKPIRVNKA 111
A AI + + G PI+V+ A
Sbjct: 69 SAKAAIDWFDGKEFSGNPIKVSFA 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 = 74.3 bits (183), Expect = 5e-17
Identities = 19/85 (22%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
E+ ++V + + + + ++F Q G +++V + + + +G+GF+ F
Sbjct: 22 NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENS 79
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKA 111
DAD A + ++ + G+ I VN A
Sbjct: 80 ADADRAREKLHGTVVEGRKIEVNNA 104
Score = 67.0 bits (164), Expect = 2e-14
Identities = 23/136 (16%), Positives = 43/136 (31%), Gaps = 41/136 (30%)
Query: 105 PIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKP 164
+ + + +N + + N+ + L F FG IL
Sbjct: 13 GLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKIL--------------- 57
Query: 165 IRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHG 224
D EI+ + SKGF F+ + + +D + + +HG
Sbjct: 58 ------------------------DVEIIFNERG--SKGFGFVTFENSADADRAREKLHG 91
Query: 225 QYLCNRPISVSYAFKK 240
+ R I V+ A +
Sbjct: 92 TVVEGRKIEVNNATAR 107
>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 = 73.9 bits (182), Expect = 7e-17
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 8/76 (10%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
++V L + V+E ++ + F Q G + V KD Y FI F + A A++
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEE 64
Query: 96 MNMIKLYGKPIRVNKA 111
MN L G+ I + A
Sbjct: 65 MNGKDLEGENIEIVFA 80
Score = 63.1 bits (154), Expect = 6e-13
Identities = 24/139 (17%), Positives = 45/139 (32%), Gaps = 47/139 (33%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
SS + +F+ NL V E++L FS FG + + K +
Sbjct: 1 GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERV-KKL--------------- 44
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
K +AFI++ + + +++ M+G+ L
Sbjct: 45 -------------------------------KDYAFIHFDERDGAVKAMEEMNGKDLEGE 73
Query: 231 PISVSYAFKKDSKGDRHGS 249
I + +A D K +
Sbjct: 74 NIEIVFAKPPDQKRKERKA 92
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 73.9 bits (182), Expect = 9e-17
Identities = 13/76 (17%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
+Y+ L K++ M+++F + GP+ + + T+ G ++ + DA A+
Sbjct: 10 ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETR---GTAYVVYEDIFDAKNAVDH 66
Query: 96 MNMIKLYGKPIRVNKA 111
++ + + + V
Sbjct: 67 LSGFNVSNRYLVVLYY 82
Score = 67.0 bits (164), Expect = 3e-14
Identities = 25/141 (17%), Positives = 45/141 (31%), Gaps = 42/141 (29%)
Query: 119 DVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
+V ++I NL ++ + +YD F +G I Q IRV
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ--------------IRV----------- 40
Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
+T ++G A++ Y + ++D + G + NR + V Y
Sbjct: 41 -----------------GNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN 83
Query: 239 KKDSKGDRHGSAAERLLAAQN 259
+ E L
Sbjct: 84 ANRAFQKMDTKKKEEQLKLLK 104
>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 = 73.1 bits (180), Expect = 1e-16
Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 4/87 (4%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
G T+ + L +E + E+F ++ + +GY FIEF
Sbjct: 6 SGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYAFIEFA 61
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKA 111
EDA A+ N ++ G+ IR+
Sbjct: 62 SFEDAKEALNSCNKREIEGRAIRLELQ 88
Score = 63.5 bits (155), Expect = 4e-13
Identities = 20/123 (16%), Positives = 37/123 (30%), Gaps = 43/123 (34%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+ + NL E+ L + F I
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIK---------------------------------- 43
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
+ G SKG+AFI +ASFE + ++++ + + + R I + + S
Sbjct: 44 ---------VPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSP 94
Query: 244 GDR 246
Sbjct: 95 NSG 97
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 72.8 bits (179), Expect = 1e-16
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 1/80 (1%)
Query: 38 YVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN 97
+ V + + LF ++G VVN+ P D T +G+ F+E DA IK +
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75
Query: 98 MIKLYGKP-IRVNKASSHQK 116
+L K + + ++
Sbjct: 76 GKRLDLKHRLFLYTMKDVER 95
Score = 44.3 bits (105), Expect = 2e-06
Identities = 20/103 (19%), Positives = 30/103 (29%), Gaps = 39/103 (37%)
Query: 125 FIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIF 184
I + V +K L FS G ++
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVV----------------------------------- 40
Query: 185 IGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL 227
+ E D TG +KGF F+ S + I + HG+ L
Sbjct: 41 ----NMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL 79
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 72.6 bits (179), Expect = 1e-16
Identities = 23/121 (19%), Positives = 36/121 (29%), Gaps = 41/121 (33%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
IF+ NL + K+L D F+ G +L
Sbjct: 8 ACQIFVRNLPFDFTWKMLKDKFNECGHVLYA----------------------------- 38
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
+I + G SKG + + S E ++ + M+G L R I V
Sbjct: 39 ----------DIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNA 86
Query: 241 D 241
Sbjct: 87 S 87
Score = 66.4 bits (163), Expect = 2e-14
Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 2/85 (2%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G G I+V L + ++ + F + G V+ + + +G G ++F
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESP 58
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKA 111
E A+ A ++MN +KL G+ I V
Sbjct: 59 EVAERACRMMNGMKLSGREIDVRID 83
>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 = 72.7 bits (179), Expect = 2e-16
Identities = 16/90 (17%), Positives = 40/90 (44%), Gaps = 2/90 (2%)
Query: 28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
G +++G L+ S + + ++ + D T T++ +G+++F E
Sbjct: 11 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAE 69
Query: 88 DADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
D + A++ + +K++G I++ K
Sbjct: 70 DLEKALE-LTGLKVFGNEIKLEKPKGRDGT 98
Score = 68.8 bits (169), Expect = 5e-15
Identities = 19/121 (15%), Positives = 36/121 (29%), Gaps = 41/121 (33%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
N+FIGNL+P L S N
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFA-------------------KNDL------------ 47
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
+ D TG ++ F ++++ S E + +++ + G + I + +D
Sbjct: 48 ---------AVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPKGRDG 97
Query: 243 K 243
Sbjct: 98 T 98
>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 = 72.8 bits (179), Expect = 2e-16
Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 2/84 (2%)
Query: 29 ESGDGDA-TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
E + D ++YVG +D + + F G + + + D+ + +GY +IEF
Sbjct: 30 EKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERN 89
Query: 88 DADYAIKIMNMIKLYGKPIRVNKA 111
D A+ M+ G+ I+V
Sbjct: 90 SVDAAVA-MDETVFRGRTIKVLPK 112
Score = 59.3 bits (144), Expect = 2e-11
Identities = 24/115 (20%), Positives = 41/115 (35%), Gaps = 40/115 (34%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
++++GN+D + L FS+ G I R+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSI----------------NRIT-------------- 67
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
I+ D +G+ KG+A+I +A + DA++ AM R I V
Sbjct: 68 ---------ILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK 112
>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 = 72.4 bits (178), Expect = 2e-16
Identities = 26/131 (19%), Positives = 42/131 (32%), Gaps = 33/131 (25%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN-MIKLYGKPIRVNKASSHQKNLDV 179
+ I++ L+ V L D F GV+ + MI +Y
Sbjct: 15 NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIY------------------ 56
Query: 180 GANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
D +TG KG A ++Y + A+++ G+ + VS A K
Sbjct: 57 --------------LDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 102
Query: 240 KDSKGDRHGSA 250
K S
Sbjct: 103 KPPMNSGPSSG 113
Score = 69.7 bits (171), Expect = 3e-15
Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 8/95 (8%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPV--------VNVHMPKDRVTQTHQ 76
G + ++ IYV GL+D V+ + + F Q G V +H+ D+ T +
Sbjct: 6 SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPK 65
Query: 77 GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
G + + A A++ + G ++V+ A
Sbjct: 66 GDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLA 100
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 71.9 bits (177), Expect = 4e-16
Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
++V V E+ + E+F GP+ V + G+ F+EF E A AI+
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFGPMKEVKILN--------GFAFVEFEEAESAAKAIEE 84
Query: 96 MNMIKLYGKPIRVNKA 111
++ +P+ V +
Sbjct: 85 VHGKSFANQPLEVVYS 100
Score = 61.5 bits (150), Expect = 2e-12
Identities = 24/135 (17%), Positives = 44/135 (32%), Gaps = 51/135 (37%)
Query: 113 SHQKNLDVGA----NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
SH + G +F+ +V E L + F FG + + KI+
Sbjct: 19 SHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEV-KIL------------- 64
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
GFAF+ + E++ +I+ +HG+
Sbjct: 65 ---------------------------------NGFAFVEFEEAESAAKAIEEVHGKSFA 91
Query: 229 NRPISVSYAFKKDSK 243
N+P+ V Y+ +
Sbjct: 92 NQPLEVVYSKLPAKR 106
>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 = 71.1 bits (175), Expect = 5e-16
Identities = 22/125 (17%), Positives = 41/125 (32%), Gaps = 37/125 (29%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
++IGNL ++ L + + GV D+
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVN-----------------------------DI--- 30
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
L+ + + G SKGFA + S +S +D + + L + V+ + K +
Sbjct: 31 -----LEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEH 85
Query: 243 KGDRH 247
H
Sbjct: 86 HHHHH 90
Score = 69.5 bits (171), Expect = 2e-15
Identities = 11/83 (13%), Positives = 35/83 (42%), Gaps = 2/83 (2%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGP--VVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
+Y+G L ++ + E G ++ + ++R +G+ + E + +
Sbjct: 4 LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63
Query: 95 IMNMIKLYGKPIRVNKASSHQKN 117
++ +L+G+ V ++ + +
Sbjct: 64 LLPKRELHGQNPVVTPSNKLEHH 86
>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 = 71.4 bits (175), Expect = 6e-16
Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 7/86 (8%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
GG S + + V GL S + + ++G V + +D G G +EF+
Sbjct: 7 GGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVR 59
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKA 111
+ED YA++ ++ K
Sbjct: 60 KEDMTYAVRKLDNTKFRSHEGETAYI 85
Score = 39.8 bits (93), Expect = 1e-04
Identities = 12/130 (9%), Positives = 25/130 (19%), Gaps = 46/130 (35%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+ + L P + L D G +
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYA-------------------------------- 45
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
++ RD G + + E ++ + + +Y K
Sbjct: 46 -------DVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDG 91
Query: 244 GDRHGSAAER 253
R
Sbjct: 92 PRSPSYGRSR 101
>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 = 70.4 bits (173), Expect = 7e-16
Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 10/88 (11%)
Query: 26 GGGESGDGDA---TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIE 82
G S D T+YVGGL D ++ET + F Q G + + + + + FI+
Sbjct: 1 GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQ 54
Query: 83 FMGEEDADYAI-KIMNMIKLYGKPIRVN 109
F + A+ A K N + + G+ + V
Sbjct: 55 FATRQAAEVAAEKSFNKLIVNGRRLNVK 82
Score = 48.4 bits (116), Expect = 5e-08
Identities = 18/116 (15%), Positives = 35/116 (30%), Gaps = 46/116 (39%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
+++G L + E L + F FG I I V +
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRT--------------ITVVQ------------- 46
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFE-ASDASIDAMHGQYLCNRPISVSYA 237
+ AFI +A+ + A A+ + + + R ++V +
Sbjct: 47 ------------------RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG 84
>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 = 70.8 bits (174), Expect = 8e-16
Identities = 16/89 (17%), Positives = 40/89 (44%), Gaps = 9/89 (10%)
Query: 29 ESGDGDATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
+ +++G L VS+ ++ +F G ++ +++ +GFI+F +
Sbjct: 17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQ 68
Query: 88 DADYAIKIMNMIKLYGKPIRVNKASSHQK 116
AI+ + +GK + + +SS+ +
Sbjct: 69 SVRDAIEXESQEMNFGKKLILEVSSSNAR 97
Score = 43.5 bits (103), Expect = 5e-06
Identities = 11/72 (15%), Positives = 28/72 (38%), Gaps = 13/72 (18%)
Query: 179 VGANIFIGNLDPEIMRDPDT-------GN------SKGFAFINYASFEASDASIDAMHGQ 225
+ + +FIGNL + + D G+ F FI + + ++ +I+ +
Sbjct: 21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIEXESQE 80
Query: 226 YLCNRPISVSYA 237
+ + + +
Sbjct: 81 MNFGKKLILEVS 92
>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 = 70.3 bits (173), Expect = 8e-16
Identities = 24/91 (26%), Positives = 37/91 (40%), Gaps = 8/91 (8%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G S I+VG + + + LF + G V+ + K Y F+
Sbjct: 1 GSSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEK 52
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASSHQK 116
E DA AI +N ++ GK I V ++ QK
Sbjct: 53 EADAKAAIAQLNGKEVKGKRINVELSTKGQK 83
Score = 48.7 bits (117), Expect = 6e-08
Identities = 19/129 (14%), Positives = 40/129 (31%), Gaps = 48/129 (37%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
IF+GN+ + L F G ++
Sbjct: 9 TWKIFVGNVSAACTSQELRSLFERRGRVI------------------------------- 37
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
+ +++ K +AF++ + A+I ++G+ + + I+V + K
Sbjct: 38 --------ECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKG 81
Query: 241 DSK-GDRHG 248
K G G
Sbjct: 82 QKKSGPSSG 90
>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 = 69.9 bits (172), Expect = 1e-15
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 8/85 (9%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G G +++G L + +E + LF Q G V+ + K YGF+ +
Sbjct: 1 GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK--------NYGFVHIEDK 52
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKA 111
A+ AI+ ++ KL+G I V +
Sbjct: 53 TAAEDAIRNLHHYKLHGVNINVEAS 77
Score = 48.3 bits (116), Expect = 6e-08
Identities = 21/127 (16%), Positives = 37/127 (29%), Gaps = 47/127 (37%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
+FIGNL E E+ + F +G +L+ I+
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLEC-DII--------------------------- 41
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
K + F++ A++ +I +H L I+V + K
Sbjct: 42 -------------------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK 82
Query: 243 KGDRHGS 249
S
Sbjct: 83 ASSGPSS 89
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 72.6 bits (178), Expect = 1e-15
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 1/88 (1%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
GGGE + A + V LD VS+ + ELF + G + + DR + G + F
Sbjct: 80 GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFER 138
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASS 113
DA A+K + L G+P+ + +S
Sbjct: 139 RADALKAMKQYKGVPLDGRPMDIQLVAS 166
Score = 61.8 bits (150), Expect = 7e-12
Identities = 21/141 (14%), Positives = 43/141 (30%), Gaps = 40/141 (28%)
Query: 107 RVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIR 166
+ + ++ GA + + NLD V + + + F+ FG
Sbjct: 74 LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG-------------------T 114
Query: 167 VNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY 226
+ KA + D +G S G A +++ + ++ G
Sbjct: 115 LKKA--------------------AVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVP 153
Query: 227 LCNRPISVSYAFKKDSKGDRH 247
L RP+ + + H
Sbjct: 154 LDGRPMDIQLVASQIDLEHHH 174
>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 = 70.3 bits (173), Expect = 1e-15
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++VGG+D ++ ET + F + G V V + DR T +GYGF+ F + D +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKI--VE 68
Query: 97 NMIKLYGKPIRVNKA 111
+ I +GK +++ A
Sbjct: 69 SQINFHGKKLKLGPA 83
Score = 68.4 bits (168), Expect = 7e-15
Identities = 18/131 (13%), Positives = 42/131 (32%), Gaps = 42/131 (32%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
+F+G +D +DE + F+ +G +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVK--------------------------------- 37
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
+ +I+ D TG SKG+ F+++ + +++ + + + A +K +
Sbjct: 38 ------EVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQI--NFHGKKLKLGPAIRKQN 88
Query: 243 KGDRHGSAAER 253
H
Sbjct: 89 LSTYHVQPRPL 99
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 69.2 bits (170), Expect = 3e-15
Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 7/82 (8%)
Query: 36 TIYVGGLDDKVSE----TLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADY 91
TIY+ L++K+ + + +F + G ++++ + + + +G F+ F A
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATN 66
Query: 92 AIKIMNMIKLYGKPIRVNKASS 113
A++ M Y KP+R+ A +
Sbjct: 67 ALRSMQGFPFYDKPMRIQYAKT 88
Score = 62.2 bits (152), Expect = 8e-13
Identities = 25/125 (20%), Positives = 46/125 (36%), Gaps = 47/125 (37%)
Query: 123 NIFIGNLDPEVDE----KLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLD 178
I+I NL+ ++ + K L+ FS FG IL I V++
Sbjct: 10 TIYINNLNEKIKKDELKKSLHAIFSRFGQILD--------------ILVSR--------- 46
Query: 179 VGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
+ +G AF+ + ++ ++ +M G ++P+ + YA
Sbjct: 47 -------------------SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYA- 86
Query: 239 KKDSK 243
K DS
Sbjct: 87 KTDSD 91
>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 = 69.3 bits (170), Expect = 4e-15
Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 9/83 (10%)
Query: 36 TIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
+++G L+ V ++ + +F + G V + K GY F+++ E A A+
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK--------GYAFVQYSNERHARAAVL 80
Query: 95 IMNMIKLYGKPIRVNKASSHQKN 117
N L G+ + +N A + +
Sbjct: 81 GENGRVLAGQTLDINMAGEPKPD 103
Score = 53.2 bits (128), Expect = 3e-09
Identities = 20/97 (20%), Positives = 46/97 (47%), Gaps = 15/97 (15%)
Query: 165 IRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT-------GN------SKGFAFINYAS 211
++ + ++ + + +FIGNL+ +++ D G KG+AF+ Y++
Sbjct: 12 LQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSN 71
Query: 212 FEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHG 248
+ A++ +G+ L + + ++ A + K DR G
Sbjct: 72 ERHARAAVLGENGRVLAGQTLDINMA--GEPKPDRSG 106
>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 = 68.8 bits (169), Expect = 4e-15
Identities = 30/87 (34%), Positives = 42/87 (48%), Gaps = 1/87 (1%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G SG I+VGG+ ET + E F + G V V M D Q +G+GFI F E
Sbjct: 3 SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKASS 113
+ D A+ M+ + GK + V +A
Sbjct: 63 QSVDQAVN-MHFHDIMGKKVEVKRAEP 88
Score = 66.1 bits (162), Expect = 4e-14
Identities = 23/126 (18%), Positives = 41/126 (32%), Gaps = 40/126 (31%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
IF+G + E L + F FGV+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVT---------------------------------- 38
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
+ ++ D + +GF FI + ++ D ++ MH + + + V A +DSK
Sbjct: 39 -----EVVMIYDAEKQRPRGFGFITFEDEQSVDQAV-NMHFHDIMGKKVEVKRAEPRDSK 92
Query: 244 GDRHGS 249
S
Sbjct: 93 SSGPSS 98
>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 = 69.1 bits (169), Expect = 4e-15
Identities = 15/80 (18%), Positives = 37/80 (46%), Gaps = 6/80 (7%)
Query: 36 TIYVGGLDDKVSETLMW---ELFVQSGPVVNVHMPKDRVT---QTHQGYGFIEFMGEEDA 89
++V GL ++++ + E F + G + V + Q ++ ++ EDA
Sbjct: 17 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 76
Query: 90 DYAIKIMNMIKLYGKPIRVN 109
AI+ +N + + G+ ++ +
Sbjct: 77 LRAIQCVNNVVVDGRTLKAS 96
Score = 53.7 bits (129), Expect = 1e-09
Identities = 18/126 (14%), Positives = 34/126 (26%), Gaps = 44/126 (34%)
Query: 115 QKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQ 174
QKNL +F+ L + + + F +GK +V
Sbjct: 14 QKNL-----VFVVGLSQRLADPEVLKRPEYF-------------GKFGKIHKV------- 48
Query: 175 KNLDVGANIFIGNLDPEIMRDPDTGNSK---GFAFINYASFEASDASIDAMHGQYLCNRP 231
I S+ A++ Y E + +I ++ + R
Sbjct: 49 ----------------VINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT 92
Query: 232 ISVSYA 237
+ S
Sbjct: 93 LKASLG 98
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 68.0 bits (167), Expect = 7e-15
Identities = 16/83 (19%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 35 ATIYVGGLD-DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAI 93
+ +++G L VS+ ++ +F G ++ +++ +GFI+F + AI
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 62
Query: 94 KIMNMIKLYGKPIRVNKASSHQK 116
+ + +GK + + +SS+ +
Sbjct: 63 ECESQEMNFGKKLILEVSSSNAR 85
Score = 50.7 bits (122), Expect = 1e-08
Identities = 14/87 (16%), Positives = 31/87 (35%), Gaps = 13/87 (14%)
Query: 176 NLDVGANIFIGNLDPEIMRDPDT-------GN------SKGFAFINYASFEASDASIDAM 222
N+ + +FIGNL + + D G+ F FI + + ++ +I+
Sbjct: 6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECE 65
Query: 223 HGQYLCNRPISVSYAFKKDSKGDRHGS 249
+ + + + + HG
Sbjct: 66 SQEMNFGKKLILEVSSSNARPQFDHGD 92
Score = 37.6 bits (88), Expect = 6e-04
Identities = 18/80 (22%), Positives = 35/80 (43%), Gaps = 21/80 (26%)
Query: 117 NLDVGANIFIGNLDPE-VDEKLLYDTFSAFGVILQ-------------TP-------KIM 155
N+ + +FIGNL + V ++ L+ FS +G I+Q P +
Sbjct: 6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECE 65
Query: 156 NMIKLYGKPIRVNKASSHQK 175
+ +GK + + +SS+ +
Sbjct: 66 SQEMNFGKKLILEVSSSNAR 85
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 68.8 bits (168), Expect = 8e-15
Identities = 14/104 (13%), Positives = 39/104 (37%), Gaps = 7/104 (6%)
Query: 17 QSLSQTKLEGGGESGDGDATIYVGGLDDKVSE----TLMWELFVQSGPVVNVHMPKDRVT 72
Q + L + + + ++ +V + L++ L G ++++ + +
Sbjct: 12 QHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---S 68
Query: 73 QTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQK 116
+ G +I F +E A ++ G P+ + + + Q
Sbjct: 69 DDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQS 112
Score = 62.2 bits (151), Expect = 2e-12
Identities = 27/154 (17%), Positives = 53/154 (34%), Gaps = 46/154 (29%)
Query: 104 KPIRVNKASSHQKNLDVGANIFIGNLDPEVDE----KLLYDTFSAFGVILQTPKIMNMIK 159
+ + S + + + I N++PEV + LLY S+ G IL
Sbjct: 12 QHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD--------- 62
Query: 160 LYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASI 219
I V+ + ++ G A+I +A+ E++ A +
Sbjct: 63 -----IVVDL----------------------------SDDNSGKAYIVFATQESAQAFV 89
Query: 220 DAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAER 253
+A G P+ ++++ S+ GS
Sbjct: 90 EAFQGYPFQGNPLVITFSETPQSQVAEDGSLEHH 123
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 67.7 bits (166), Expect = 1e-14
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+YVG L + + F GP+ V + ++ G+ F+EF DA+ A++ +
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRGL 57
Query: 97 NMIKLYGKPIRVNKA 111
+ + G +RV +
Sbjct: 58 DGKVICGSRVRVELS 72
Score = 53.5 bits (129), Expect = 1e-09
Identities = 19/131 (14%), Positives = 38/131 (29%), Gaps = 45/131 (34%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
+++GNL + L FS +G +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLR--------------------------------- 28
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
I R+P GFAF+ + ++ ++ + G+ +C + V +
Sbjct: 29 ------TVWIARNP-----PGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS-TGMP 76
Query: 243 KGDRHGSAAER 253
+ R R
Sbjct: 77 RRSRFDRPPAR 87
>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 = 67.5 bits (165), Expect = 2e-14
Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 4/80 (5%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVV-NVHMPKD-RVTQTHQGYGFIEFMGEEDADYAI 93
+++GG+ + E + V +V + ++G+ F+E+ A A
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 94 KIMNM--IKLYGKPIRVNKA 111
+ + I+L+G I V+ A
Sbjct: 70 RKLMPGRIQLWGHQIAVDWA 89
Score = 54.8 bits (132), Expect = 7e-10
Identities = 15/125 (12%), Positives = 33/125 (26%), Gaps = 39/125 (31%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+FIG + + + + + + +
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAA------------------------ 46
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQ--YLCNRPISVSYAFKKD 241
D ++GFAF+ Y S A+ + + L I+V +A +
Sbjct: 47 -------------DKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEI 93
Query: 242 SKGDR 246
+
Sbjct: 94 DVDED 98
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 66.9 bits (164), Expect = 2e-14
Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 2/82 (2%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
T YVG L + + +F + +V + +D+ T +G+ ++EF + A+
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74
Query: 96 MNMIKLYGKPIRVNKASSHQKN 117
+ L + +RV+ A +++
Sbjct: 75 YDGALLGDRSLRVDIAEGRKQD 96
Score = 57.3 bits (139), Expect = 7e-11
Identities = 18/126 (14%), Positives = 37/126 (29%), Gaps = 41/126 (32%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
++GNL + + F + + +R
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLSI---------------RSVR----------------- 45
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
++RD DT KGF ++ + ++ ++ G L +R + V A +
Sbjct: 46 --------LVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRKQD 96
Query: 244 GDRHGS 249
S
Sbjct: 97 KSGPSS 102
>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain,
nucleolus, structural protein; NMR {Mesocricetus
auratus} SCOP: d.58.7.1
Length = 96
Score = 66.1 bits (162), Expect = 4e-14
Identities = 13/96 (13%), Positives = 32/96 (33%), Gaps = 5/96 (5%)
Query: 22 TKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFI 81
+ + T+ L ++E + E+F + + +G +I
Sbjct: 4 LEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYI 58
Query: 82 EFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
EF E DA+ ++ ++ G+ + +
Sbjct: 59 EFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94
Score = 62.7 bits (153), Expect = 6e-13
Identities = 20/134 (14%), Positives = 36/134 (26%), Gaps = 44/134 (32%)
Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
+ K + + NL + E L + F
Sbjct: 5 EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDAL----------------------- 41
Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
EI G SKG A+I + S ++ +++ G +
Sbjct: 42 ---------------------EIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG 80
Query: 230 RPISVSYAFKKDSK 243
R +S+ Y +K
Sbjct: 81 RSVSLYYTGEKGGT 94
>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 = 66.2 bits (162), Expect = 5e-14
Identities = 28/111 (25%), Positives = 43/111 (38%), Gaps = 6/111 (5%)
Query: 26 GGGESGDGDAT---IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIE 82
G D T I+VGGL ++ + + F G + + DR T +GYGF+
Sbjct: 6 SGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVT 65
Query: 83 FMGEEDADYAIKIMNMIKLYGKPIRVNKASS--HQKNLDVGANIFIGNLDP 131
A+ A K N + G+ VN A ++L G I +
Sbjct: 66 MADRAAAERACKDPN-PIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSS 115
Score = 58.8 bits (143), Expect = 3e-11
Identities = 20/118 (16%), Positives = 36/118 (30%), Gaps = 40/118 (33%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
IF+G L + L F FG I
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIE---------------------------------- 45
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
+ ++ D TG S+G+ F+ A A++ + + + R +V+ A+
Sbjct: 46 -----EAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PIIDGRKANVNLAYLGA 97
>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 = 64.8 bits (159), Expect = 6e-14
Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 1/75 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I+VGGL E + E F G V ++ +P D T +G+ FI F EE ++
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-K 60
Query: 97 NMIKLYGKPIRVNKA 111
+ + A
Sbjct: 61 KYHNVGLSKCEIKVA 75
Score = 57.5 bits (140), Expect = 3e-11
Identities = 18/114 (15%), Positives = 30/114 (26%), Gaps = 40/114 (35%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
IF+G L P+ E+ + + F FG +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVE---------------------------------- 27
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
E+ D T +GF FI + E + + + A
Sbjct: 28 -----SIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EKKYHNVGLSKCEIKVA 75
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 67.3 bits (164), Expect = 7e-14
Identities = 15/95 (15%), Positives = 35/95 (36%), Gaps = 2/95 (2%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGP--VVNVHMPKDRVTQTHQGYGFIE 82
+ A +YVG ++ + ++ G VV + ++R +GY +
Sbjct: 46 YTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVV 105
Query: 83 FMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKN 117
E ++++ L G+ + V A+ +
Sbjct: 106 VASENSVHKLLELLPGKVLNGEKVDVRPATRQNLS 140
Score = 66.9 bits (163), Expect = 8e-14
Identities = 18/145 (12%), Positives = 44/145 (30%), Gaps = 37/145 (25%)
Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
++ + A +++G+ ++ L + GV
Sbjct: 43 AILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVY-------------------- 82
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC 228
DV ++ + + G SKG+A + AS + ++ + G+ L
Sbjct: 83 ---------DV--------VELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLN 125
Query: 229 NRPISVSYAFKKDSKGDRHGSAAER 253
+ V A +++ +
Sbjct: 126 GEKVDVRPATRQNLSQFEAQARKRE 150
>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 = 65.0 bits (159), Expect = 1e-13
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 3/77 (3%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTH-QGYGFIEFMGEEDADYAIK 94
T ++G L V+E + E F + V +P++ +G+G+ EF + A+
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 95 IMNMIKLYGKPIRVNKA 111
+N L + IRV+ A
Sbjct: 80 -LNEESLGNRRIRVDVA 95
Score = 49.5 bits (119), Expect = 4e-08
Identities = 19/115 (16%), Positives = 40/115 (34%), Gaps = 42/115 (36%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
F+GNL +V E+ + + F + +R
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLNI---------------SAVR----------------- 49
Query: 184 FIGNLDPEIMRDP-DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
+ R+P + KGF + + ++ +++ +++ + L NR I V A
Sbjct: 50 --------LPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVDVA 95
>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 = 65.6 bits (160), Expect = 2e-13
Identities = 23/100 (23%), Positives = 38/100 (38%), Gaps = 5/100 (5%)
Query: 17 QSLSQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
+ + + E G+ + IYV L V E + +F + + + +
Sbjct: 28 EEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK 87
Query: 77 -----GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKA 111
G FI E+ A A+K N L+GKP+ V A
Sbjct: 88 EGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFA 127
Score = 64.8 bits (158), Expect = 3e-13
Identities = 27/168 (16%), Positives = 50/168 (29%), Gaps = 44/168 (26%)
Query: 89 ADYAIKIMNMIKLYGKPIRVNKASSHQ-------KNLDVGA---NIFIGNLDPEVDEKLL 138
M + + + + S + ++ + G I++ NL V EK L
Sbjct: 3 LGSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDL 62
Query: 139 YDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDT 198
F + + + D+ R
Sbjct: 63 KYIFGRYVDFSS--------------------ETQRIMFDI--------------RLMKE 88
Query: 199 GNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDR 246
G KG AFI + +A+ ++ +G L +P+ V +A K D
Sbjct: 89 GRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQDP 136
>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 = 64.4 bits (157), Expect = 2e-13
Identities = 14/79 (17%), Positives = 27/79 (34%), Gaps = 6/79 (7%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
I L + E F + G + V +P+ +EF+ +A A
Sbjct: 9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIVEFLEPLEARKA 62
Query: 93 IKIMNMIKLYGKPIRVNKA 111
+ + K + P+ + A
Sbjct: 63 FRHLAYSKFHHVPLYLEWA 81
Score = 36.7 bits (85), Expect = 0.001
Identities = 11/129 (8%), Positives = 28/129 (21%), Gaps = 45/129 (34%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
I NL + +TFS FG + +
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGR--------------------------------- 39
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
++ A + + + + + + P+ + +A
Sbjct: 40 --------VLLPE----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFG 87
Query: 244 GDRHGSAAE 252
++
Sbjct: 88 AAPQKKDSQ 96
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 63.8 bits (156), Expect = 2e-13
Identities = 19/89 (21%), Positives = 34/89 (38%), Gaps = 12/89 (13%)
Query: 31 GDGDA----TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G G A ++VGGL S + F + G + + K + +I++
Sbjct: 10 GYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESL 63
Query: 87 EDADYAIKIMN--MIKLYGKPIRVNKASS 113
+ A A M + + +RV+ A S
Sbjct: 64 DAAQAACAKMRGFPLGGPDRRLRVDFAKS 92
Score = 50.7 bits (122), Expect = 1e-08
Identities = 21/117 (17%), Positives = 33/117 (28%), Gaps = 47/117 (40%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
+++G L P L F FG I
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTI------------------------------- 47
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN--RPISVSYA 237
+ ++ FA+I Y S +A+ A+ M G L R + V +A
Sbjct: 48 --------DHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFA 90
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 64.0 bits (156), Expect = 3e-13
Identities = 21/90 (23%), Positives = 41/90 (45%), Gaps = 9/90 (10%)
Query: 34 DATIYVGGL----DDKVS--ETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
D+ I V + D++ + ++ ++F + G + N P++ +GY F+E+
Sbjct: 15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 72
Query: 88 DADYAIKIMNMIKLYGK-PIRVNKASSHQK 116
A A+K + KL + RVN + K
Sbjct: 73 HAVDAVKNADGYKLDKQHTFRVNLFTDFDK 102
Score = 43.2 bits (102), Expect = 7e-06
Identities = 18/115 (15%), Positives = 33/115 (28%), Gaps = 49/115 (42%)
Query: 120 VGANIFIGNLDPEVDE-------KLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASS 172
+ + I + N+ P+V +++ FS FG I
Sbjct: 14 IDSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKIT----------------------- 49
Query: 173 HQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL 227
+ G +KG+ F+ YAS + ++ G L
Sbjct: 50 ------------------NDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKL 86
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 64.0 bits (156), Expect = 3e-13
Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 2/73 (2%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
++Y+ G + + E G V+N+ M + + +G F+ F E A ++
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE- 70
Query: 96 MNMIKLYGKPIRV 108
K + +
Sbjct: 71 TPGQKYKETDLLI 83
Score = 42.0 bits (99), Expect = 2e-05
Identities = 12/104 (11%), Positives = 27/104 (25%), Gaps = 40/104 (38%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
+++I + + + G +L I+
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLN--------------IQ---------------- 42
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQY 226
MR KG F+ + S E++ ++ +Y
Sbjct: 43 ----------MRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKY 76
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 62.5 bits (153), Expect = 4e-13
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I+VGGL + + F Q G V + + D+ T H+G+GF+ F E+ + + +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-I 60
Query: 97 NMIKLYGKPIRVNKA 111
+ ++ K + KA
Sbjct: 61 HFHEINNKMVECKKA 75
Score = 60.9 bits (149), Expect = 1e-12
Identities = 18/114 (15%), Positives = 32/114 (28%), Gaps = 40/114 (35%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
IF+G L + + F FG +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVD---------------------------------- 27
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
D +M D T +GF F+ + S + + +H + N+ + A
Sbjct: 28 -----DAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHFHEINNKMVECKKA 75
>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 = 63.4 bits (155), Expect = 4e-13
Identities = 21/120 (17%), Positives = 37/120 (30%), Gaps = 41/120 (34%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+ + L + E+ L + FS FG +L
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVL---------------------------------- 43
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
++ +D TG+SKGF F+ + +E + H + R K S+
Sbjct: 44 -----MVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MIDGRWCDCKLPNSKQSQ 96
Score = 61.9 bits (151), Expect = 1e-12
Identities = 23/89 (25%), Positives = 37/89 (41%), Gaps = 2/89 (2%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
G + + + V GL K +E + E F G V+ V + KD T +G+GF+ F
Sbjct: 6 SGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFT 65
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKASS 113
E + +MI G+ +S
Sbjct: 66 EYETQVKVMSQRHMID--GRWCDCKLPNS 92
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 63.1 bits (154), Expect = 4e-13
Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 7/87 (8%)
Query: 28 GESGDGDA-TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G SG +++V G V + E F+ GPV +V M KD+ + +E
Sbjct: 1 GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDV 55
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKASS 113
+ + + L G +RV
Sbjct: 56 GAREAVLS-QSQHSLGGHRLRVRPREQ 81
Score = 43.5 bits (103), Expect = 5e-06
Identities = 19/128 (14%), Positives = 34/128 (26%), Gaps = 45/128 (35%)
Query: 123 NIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGAN 182
++F+ VD L + F AFG +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVA--------------------------------- 36
Query: 183 IFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDS 242
++ D D G FA + A +A + + L + V +K+
Sbjct: 37 --------SVVMDKDKG---VFAIVEMGDVGAREAVL-SQSQHSLGGHRLRVRPREQKEF 84
Query: 243 KGDRHGSA 250
+ S
Sbjct: 85 QSPASKSP 92
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 62.9 bits (153), Expect = 6e-13
Identities = 18/86 (20%), Positives = 30/86 (34%), Gaps = 5/86 (5%)
Query: 28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
GE A +YVG L + + + G V P Q + F+ +
Sbjct: 13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFLHYPDSA 67
Query: 88 DADYAIKIMNMIKLYGKPIRVNKASS 113
A A+ + ++L +RV A
Sbjct: 68 AAQQAVSCLQGLRLGTDTLRVALARQ 93
Score = 48.3 bits (115), Expect = 1e-07
Identities = 19/141 (13%), Positives = 40/141 (28%), Gaps = 44/141 (31%)
Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
G S + + A++++GNL + L G +
Sbjct: 1 GSSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-------------- 46
Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM 222
P+R+ + AF++Y A+ ++ +
Sbjct: 47 -PLRLT-----------------------------WQGPRRRAFLHYPDSAAAQQAVSCL 76
Query: 223 HGQYLCNRPISVSYAFKKDSK 243
G L + V+ A ++ K
Sbjct: 77 QGLRLGTDTLRVALARQQRDK 97
>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 = 61.7 bits (150), Expect = 1e-12
Identities = 14/79 (17%), Positives = 34/79 (43%), Gaps = 6/79 (7%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNV-HMPKDRV----TQTHQGYGFIEFMGEEDADY 91
+YVG + ++E M + F + + P + V + + F+EF ++
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 92 AIKIMNMIKLYGKPIRVNK 110
A+ + I G+ +++ +
Sbjct: 69 AMA-FDGIIFQGQSLKIRR 86
Score = 41.6 bits (98), Expect = 2e-05
Identities = 15/111 (13%), Positives = 37/111 (33%), Gaps = 35/111 (31%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+++GN+ + E+ + D F+A ++ + + G P+
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQM------RLGGLTQAPGNPVL----------------- 45
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
K FAF+ + S + + ++ A G + + +
Sbjct: 46 -----------AVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKI 84
>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 = 61.6 bits (150), Expect = 2e-12
Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 2/90 (2%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIEF 83
G G I V + VS + + F + V + + G + F
Sbjct: 6 SGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMVAF 64
Query: 84 MGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
++A A+ +N + + ++++ SS
Sbjct: 65 ESRDEATAAVIDLNDRPIGSRKVKLSGPSS 94
Score = 50.4 bits (121), Expect = 1e-08
Identities = 17/134 (12%), Positives = 38/134 (28%), Gaps = 43/134 (32%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
+S I + N+ V + D F + VI
Sbjct: 5 SSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIP--------------------- 43
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNR 230
++ + G G A + + S + + A++ ++ + + +R
Sbjct: 44 ------------------GSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSR 85
Query: 231 PISVSYAFKKDSKG 244
+ +S S G
Sbjct: 86 KVKLSGP----SSG 95
>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 = 60.7 bits (148), Expect = 2e-12
Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 7/81 (8%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++VG ++E + E F Q G V++V +PK + + F+ F ++ A
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGED 62
Query: 97 NMIKLYGKPIRVNKASSHQKN 117
+IK G + ++ A +
Sbjct: 63 LIIK--GISVHISNAEPKHNS 81
Score = 46.1 bits (110), Expect = 4e-07
Identities = 17/126 (13%), Positives = 36/126 (28%), Gaps = 46/126 (36%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+F+G ++ E L + FS +G ++
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVM---------------------------------- 33
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
D I + + FAF+ +A + + + + + +S A K +
Sbjct: 34 -----DVFIPKP-----FRAFAFVTFADDQIAQSLCGEDL--IIKGISVHISNAEPKHNS 81
Query: 244 GDRHGS 249
S
Sbjct: 82 NSGPSS 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 = 61.1 bits (149), Expect = 3e-12
Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 3/83 (3%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKD-RVTQTHQGYGFIEFMGEEDADYAIK 94
T ++G L V+E + E F + V +P++ + +G+G+ EF + A+
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 95 IMNMIKLYGKPIRVNKASSHQKN 117
+N L K IRV+ A Q
Sbjct: 76 -LNEESLGNKRIRVDVADQAQDK 97
Score = 51.1 bits (123), Expect = 1e-08
Identities = 20/128 (15%), Positives = 43/128 (33%), Gaps = 44/128 (34%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
F+GNL +V E+ + + F + +R
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLNI---------------SAVR----------------- 45
Query: 184 FIGNLDPEIMRDP-DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF--KK 240
+ R+P + KGF + + ++ +++ +++ + L N+ I V A +
Sbjct: 46 --------LPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDVADQAQD 96
Query: 241 DSKGDRHG 248
G G
Sbjct: 97 KDSGPSSG 104
>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 = 65.3 bits (158), Expect = 4e-12
Identities = 22/87 (25%), Positives = 40/87 (45%)
Query: 30 SGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDA 89
GD T++V ++ +E+ + F GP+ +HM + + +GY FIE+ E D
Sbjct: 98 QGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDM 157
Query: 90 DYAIKIMNMIKLYGKPIRVNKASSHQK 116
A K + K+ G+ + V+
Sbjct: 158 HSAYKHADGKKIDGRRVLVDVERGRTV 184
Score = 52.5 bits (125), Expect = 7e-08
Identities = 24/178 (13%), Positives = 46/178 (25%), Gaps = 39/178 (21%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+F+ ++ + E L F +G I +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRI-------------------------------- 132
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
++ +G +G+AFI Y ++ G+ + R + V + K
Sbjct: 133 -------HMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVK 185
Query: 244 GDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLR 301
G R L + + + H D P P P +
Sbjct: 186 GWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRE 243
>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 = 60.3 bits (147), Expect = 4e-12
Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 7/88 (7%)
Query: 24 LEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEF 83
+ G + ++VG + ++ + + F Q G VV+V +PK + + F+ F
Sbjct: 1 MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTF 55
Query: 84 MGEEDADYAIKIMNMIKLYGKPIRVNKA 111
++ A +IK G + ++ A
Sbjct: 56 ADDKVAQSLCGEDLIIK--GISVHISNA 81
Score = 46.8 bits (112), Expect = 3e-07
Identities = 15/120 (12%), Positives = 34/120 (28%), Gaps = 46/120 (38%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+F+G ++ + L F +G ++
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVV---------------------------------- 39
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
D I + + FAF+ +A + + + + + +S A K +K
Sbjct: 40 -----DVFIPKP-----FRAFAFVTFADDKVAQSLCGEDL--IIKGISVHISNAEPKHNK 87
>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 = 60.4 bits (147), Expect = 5e-12
Identities = 14/90 (15%), Positives = 30/90 (33%), Gaps = 2/90 (2%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIEF 83
G G I V + VS + + F + V + + G + F
Sbjct: 6 SGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMVAF 64
Query: 84 MGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
++A A+ +N + + +++ S
Sbjct: 65 ESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94
Score = 49.2 bits (118), Expect = 4e-08
Identities = 15/121 (12%), Positives = 35/121 (28%), Gaps = 40/121 (33%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
I + N+ V + D F + VI
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIP---------------------------------- 43
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
++ + G G A + + S + + A++ ++ + + +R + + S
Sbjct: 44 -----GSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG-SGPSS 97
Query: 244 G 244
G
Sbjct: 98 G 98
>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 = 60.6 bits (147), Expect = 5e-12
Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 7/85 (8%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
G S + + V GL S + + ++G V + +D G G +EF+ +
Sbjct: 9 GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRK 61
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKA 111
ED YA++ ++ K
Sbjct: 62 EDMTYAVRKLDNTKFRSHEGETAYI 86
Score = 39.4 bits (92), Expect = 2e-04
Identities = 9/85 (10%), Positives = 18/85 (21%), Gaps = 15/85 (17%)
Query: 183 IFIGNLDPEIMRDPD-------TG-------NSKGFAFINYASFEASDASIDAMHGQYLC 228
+ + L P D G G + + E ++ +
Sbjct: 19 VVVSGL-PPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKFR 77
Query: 229 NRPISVSYAFKKDSKGDRHGSAAER 253
+ +Y K R
Sbjct: 78 SHEGETAYIRVKVDGPRSPSYGRSR 102
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 59.7 bits (145), Expect = 5e-12
Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 11/84 (13%)
Query: 34 DATIYVGGL-------DDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGE 86
D+ I V + +K+ + ++F + G + N P++ +GY F+E+
Sbjct: 1 DSVIVVDNVPQVGPDRLEKLKNVIH-KIFSKFGKITNDFYPEE--DGKTKGYIFLEYASP 57
Query: 87 EDADYAIKIMNMIKLYGK-PIRVN 109
A A+K + KL + RVN
Sbjct: 58 AHAVDAVKNADGYKLDKQHTFRVN 81
Score = 41.2 bits (97), Expect = 2e-05
Identities = 18/111 (16%), Positives = 31/111 (27%), Gaps = 49/111 (44%)
Query: 124 IFIGNLDPEVDE-------KLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKN 176
I + N+ P+V +++ FS FG I
Sbjct: 4 IVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKIT--------------------------- 35
Query: 177 LDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYL 227
+ G +KG+ F+ YAS + ++ G L
Sbjct: 36 --------------NDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKL 72
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 59.4 bits (145), Expect = 7e-12
Identities = 23/115 (20%), Positives = 37/115 (32%), Gaps = 40/115 (34%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+FIG L + ++ L + F FG +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVK---------------------------------- 28
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAF 238
+ +MRDP T S+GF F+ + D + A L ++ I AF
Sbjct: 29 -----ECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTIDPKVAF 77
Score = 57.1 bits (139), Expect = 5e-11
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+++GGL + ++ + E F Q G V + +D +T+ +G+GF+ FM + D +
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-Q 61
Query: 97 NMIKLYGKPIRVNKA 111
+ +L K I A
Sbjct: 62 SRHELDSKTIDPKVA 76
>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 = 59.1 bits (144), Expect = 9e-12
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
++VGGL S+ + + F + G VV+ + D T +G+GFI F + +
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73
Query: 97 NMIKLYGKPIRVNKA 111
+L G+ I KA
Sbjct: 74 E-HRLDGRVIDPKKA 87
Score = 55.7 bits (135), Expect = 2e-10
Identities = 25/114 (21%), Positives = 38/114 (33%), Gaps = 40/114 (35%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+F+G L + +K L D F+ FG ++
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFGEVV---------------------------------- 39
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYA 237
D I DP+TG S+GF FI + + + +D L R I A
Sbjct: 40 -----DCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKE-HRLDGRVIDPKKA 87
>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 = 60.0 bits (146), Expect = 9e-12
Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 2/98 (2%)
Query: 17 QSLSQTKLEGGGESGDGDAT-IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTH 75
+ L G +++GGL + ++ + E F Q G V + +D +T+
Sbjct: 7 HHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRS 66
Query: 76 QGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
+G+GF+ FM + D + + +L K I A
Sbjct: 67 RGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVAFP 103
Score = 58.4 bits (142), Expect = 3e-11
Identities = 23/120 (19%), Positives = 40/120 (33%), Gaps = 40/120 (33%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+FIG L + ++ L + F FG +
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVK---------------------------------- 53
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
+ +MRDP T S+GF F+ + D + A L ++ I AF + ++
Sbjct: 54 -----ECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELDSKTIDPKVAFPRRAQ 107
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 58.6 bits (142), Expect = 2e-11
Identities = 11/84 (13%), Positives = 27/84 (32%), Gaps = 3/84 (3%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G + + + + ++ L VQ G V + + +
Sbjct: 7 GSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSS 63
Query: 86 EEDADYAIKIMNMIKLYGKPIRVN 109
++ A A+ +N +L ++V
Sbjct: 64 KDQARQALDKLNGFQLENFTLKVA 87
Score = 53.6 bits (129), Expect = 1e-09
Identities = 15/122 (12%), Positives = 37/122 (30%), Gaps = 42/122 (34%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
+ I N+ P + ++L +GV+ ++
Sbjct: 15 IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVN------------------------- 49
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
T + + Y+S + + ++D ++G L N + V+Y +
Sbjct: 50 -----------------TDSETAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDE 92
Query: 241 DS 242
+
Sbjct: 93 MA 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 = 58.3 bits (141), Expect = 3e-11
Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 9/83 (10%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
++V GL + V E + E + G + V M + +EF + A +
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFENIDSAKECVTF 70
Query: 96 MNMIKLY--GKPIRVNKASSHQK 116
+ +Y G+ N S+ ++
Sbjct: 71 AADVPVYIAGQQAFFNY-STSKR 92
Score = 38.2 bits (89), Expect = 4e-04
Identities = 14/137 (10%), Positives = 32/137 (23%), Gaps = 47/137 (34%)
Query: 111 ASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKA 170
+S + V + + L V E L + FG I + +
Sbjct: 5 SSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTI--------------CYVMMMP- 49
Query: 171 SSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAM--HGQYLC 228
K A + + + +++ + Y+
Sbjct: 50 ------------------------------FKRQALVEFENIDSAKECVTFAADVPVYIA 79
Query: 229 NRPISVSYAFKKDSKGD 245
+ +Y+ K
Sbjct: 80 GQQAFFNYSTSKRITRP 96
>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 = 58.1 bits (141), Expect = 4e-11
Identities = 25/126 (19%), Positives = 43/126 (34%), Gaps = 40/126 (31%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+FIG L E E+ L + + +G +
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLT---------------------------------- 55
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
D +MRDP + S+GF F+ ++S DA++ A + R + A ++
Sbjct: 56 -----DCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSIDGRVVEPKRAVAREES 109
Query: 244 GDRHGS 249
G S
Sbjct: 110 GSGPSS 115
Score = 56.9 bits (138), Expect = 1e-10
Identities = 15/77 (19%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+++GGL + +E + + Q G + + + +D ++ +G+GF+ F + D A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-A 88
Query: 97 NMIKLYGKPIRVNKASS 113
+ G+ + +A +
Sbjct: 89 RPHSIDGRVVEPKRAVA 105
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 57.8 bits (140), Expect = 5e-11
Identities = 21/83 (25%), Positives = 33/83 (39%), Gaps = 9/83 (10%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
+++ GL D V E + E + GP+ V + + +EF A A+
Sbjct: 23 VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK------RQALVEFEDVLGACNAVNY 76
Query: 96 MNM--IKLYGKPIRVNKASSHQK 116
I + G P VN S+ QK
Sbjct: 77 AADNQIYIAGHPAFVNY-STSQK 98
Score = 39.4 bits (92), Expect = 1e-04
Identities = 14/119 (11%), Positives = 29/119 (24%), Gaps = 47/119 (39%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+ I L V E L + FG I + ++
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISY----VVVMP------------------------ 55
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQ--YLCNRPISVSYAFKK 240
K A + + + +++ Y+ P V+Y+ +
Sbjct: 56 -----------------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ 97
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 57.9 bits (140), Expect = 6e-11
Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 3/88 (3%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
+ I + L + S + +L ++ T+ G G +EF
Sbjct: 20 HMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTF---SSVNTRDFDGTGALEFPS 76
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASS 113
EE A++ +N I+ G I V + +
Sbjct: 77 EEILVEALERLNNIEFRGSVITVERDDN 104
Score = 37.1 bits (86), Expect = 0.001
Identities = 9/69 (13%), Positives = 20/69 (28%), Gaps = 17/69 (24%)
Query: 183 IFIGNLDPE-----------------IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQ 225
I + NL +T + G + + S E +++ ++
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNI 90
Query: 226 YLCNRPISV 234
I+V
Sbjct: 91 EFRGSVITV 99
>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 = 57.4 bits (139), Expect = 6e-11
Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 3/88 (3%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIEFM 84
G D + + GL S+ + + F V N + +P D + G F++F
Sbjct: 7 GNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGR-STGEAFVQFA 65
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKAS 112
+E A+ A+K + ++ + I + K+S
Sbjct: 66 SQEIAEKALK-KHKERIGHRYIEIFKSS 92
Score = 36.6 bits (85), Expect = 0.001
Identities = 11/52 (21%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
+ G S G AF+ +AS E ++ ++ H + + +R I + + + + +
Sbjct: 47 TLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKSSRAEVR 97
>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 = 56.9 bits (138), Expect = 6e-11
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 3/88 (3%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
G SG T+ + G V+E + E PV + + ++ GY F++F
Sbjct: 2 SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAHGNKT-GYIFVDFSN 59
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKASS 113
EE+ A+K N + G+ I V + S
Sbjct: 60 EEEVKQALK-CNREYMGGRYIEVFREKS 86
Score = 41.5 bits (98), Expect = 2e-05
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 184 FIGNLDPE---IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
F+ L P I+R+ GN G+ F+++++ E ++ + +Y+ R I V
Sbjct: 30 FLAPLKPVAIRIVRNAH-GNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFREKSG 87
Query: 241 DSKG 244
S G
Sbjct: 88 PSSG 91
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 57.6 bits (139), Expect = 7e-11
Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 8/90 (8%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK- 94
I++ L V+E + L + G V N+ M K + FIE EE A+ +
Sbjct: 18 VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANTMVNY 71
Query: 95 -IMNMIKLYGKPIRVNKASSHQKNLDVGAN 123
L G+PI + ++ + D N
Sbjct: 72 YTSVTPVLRGQPIYIQFSNHKELKTDSSPN 101
Score = 38.7 bits (90), Expect = 3e-04
Identities = 22/143 (15%), Positives = 40/143 (27%), Gaps = 47/143 (32%)
Query: 106 IRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPI 165
+R + H + I I L +V E + FG + +
Sbjct: 1 MRGSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN--------------L 46
Query: 166 RVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDA--MH 223
+ K K AFI + EA++ ++
Sbjct: 47 LMLK-------------------------------GKNQAFIEMNTEEAANTMVNYYTSV 75
Query: 224 GQYLCNRPISVSYAFKKDSKGDR 246
L +PI + ++ K+ K D
Sbjct: 76 TPVLRGQPIYIQFSNHKELKTDS 98
>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 = 57.2 bits (139), Expect = 7e-11
Identities = 21/120 (17%), Positives = 35/120 (29%), Gaps = 40/120 (33%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+F+G LD ++ L FS +G ++
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVV---------------------------------- 44
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
D IM+D T S+GF F+ + + A L R I + +
Sbjct: 45 -----DCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-ASRPHTLDGRNIDPKPCTPRGMQ 98
Score = 56.9 bits (138), Expect = 1e-10
Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 2/90 (2%)
Query: 25 EGGGESGDGDAT-IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEF 83
G SG + ++VGGLD ++ + F Q G VV+ + KD+ T +G+GF++F
Sbjct: 6 SGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
Query: 84 MGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
+ L G+ I +
Sbjct: 66 KDPNCVGTVLA-SRPHTLDGRNIDPKPCTP 94
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 57.1 bits (138), Expect = 1e-10
Identities = 15/92 (16%), Positives = 35/92 (38%), Gaps = 3/92 (3%)
Query: 26 GGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIEFM 84
G G+ ++ + +++ + + N VH+ D G ++F
Sbjct: 7 GEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFK 65
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKASSHQK 116
E+DA + + ++ KL G+ V+ +
Sbjct: 66 NEDDARKSER-LHRKKLNGREAFVHVVTLEDM 96
Score = 39.7 bits (93), Expect = 1e-04
Identities = 14/134 (10%), Positives = 32/134 (23%), Gaps = 40/134 (29%)
Query: 110 KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNK 169
+S I N+ + + + V +
Sbjct: 4 GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENA-------------VH--- 47
Query: 170 ASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
++ D + G G A + + + + + S +H + L
Sbjct: 48 ----------------------VLVDNN-GQGLGQALVQFKNEDDARKSE-RLHRKKLNG 83
Query: 230 RPISVSYAFKKDSK 243
R V +D +
Sbjct: 84 REAFVHVVTLEDMR 97
>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 = 56.3 bits (136), Expect = 2e-10
Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
D + V G+ E + + F V VH+ KD V + + G G ++F+ +D
Sbjct: 11 PINPDDLYVSVHGMPFSAMENDVRDFF-HGLRVDAVHLLKDHVGR-NNGNGLVKFLSPQD 68
Query: 89 ADYAIKIMNMIKLYGKPIRVNKASSHQ 115
A+K N + + + + V+ A+ Q
Sbjct: 69 TFEALK-RNRMLMIQRYVEVSPATERQ 94
Score = 40.5 bits (95), Expect = 7e-05
Identities = 8/50 (16%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
+++D G + G + + S + + ++ + + R + VS A ++
Sbjct: 47 LLKDHV-GRNNGNGLVKFLSPQDTFEALK-RNRMLMIQRYVEVSPATERQ 94
>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 = 54.5 bits (131), Expect = 8e-10
Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 9/75 (12%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+ GGL + VS + + + G V + MP ++ Y F + E++ A +
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKRAYVTL 83
Query: 97 N---MIKLYGKPIRV 108
N ++ G+ I +
Sbjct: 84 NGKEVVDDLGQKITL 98
Score = 36.4 bits (84), Expect = 0.002
Identities = 15/130 (11%), Positives = 33/130 (25%), Gaps = 50/130 (38%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+ G L V L G++
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVD---------------------------------- 55
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLC-----NRPISVSYAF 238
++ P+ K ++F Y + E S + ++G+ + + +++
Sbjct: 56 -------ALLMPPN----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVE 104
Query: 239 KKDSKGDRHG 248
K G G
Sbjct: 105 KVQWSGPSSG 114
>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 = 54.8 bits (132), Expect = 8e-10
Identities = 16/91 (17%), Positives = 36/91 (39%), Gaps = 3/91 (3%)
Query: 23 KLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFI 81
K + +Y+ GL + + + F + V + +++ + G GF+
Sbjct: 14 KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT-GEGFV 72
Query: 82 EFMGEEDADYAIKIMNMIKLYGKPIRVNKAS 112
EF E D A+ + + + I+V+ +
Sbjct: 73 EFRNEADYKAALC-RHKQYMGNRFIQVHPIT 102
Score = 41.0 bits (96), Expect = 7e-05
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
I P+ G + G F+ + + A++ H QY+ NR I V KK
Sbjct: 58 IAYGPN-GKATGEGFVEFRNEADYKAAL-CRHKQYMGNRFIQVHPITKKG 105
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 54.1 bits (130), Expect = 9e-10
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 9/83 (10%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK- 94
+++ L +V+ET + L + G V N+ M K + F+E EE A +
Sbjct: 17 VLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAITMVNY 70
Query: 95 -IMNMIKLYGKPIRVNKASSHQK 116
L +PI + S+H++
Sbjct: 71 YSAVTPHLRNQPIYIQY-SNHKE 92
Score = 36.0 bits (83), Expect = 0.002
Identities = 24/144 (16%), Positives = 43/144 (29%), Gaps = 47/144 (32%)
Query: 109 NKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVN 168
+ +S + + + I L EV E + FG + I +
Sbjct: 3 SGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTN--------------ILML 48
Query: 169 KASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASID--AMHGQY 226
K K AF+ A+ EA+ ++ + +
Sbjct: 49 K-------------------------------GKNQAFLELATEEAAITMVNYYSAVTPH 77
Query: 227 LCNRPISVSYAFKKDSKGDRHGSA 250
L N+PI + Y+ K+ K S
Sbjct: 78 LRNQPIYIQYSNHKELKTSGPSSG 101
>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 = 53.6 bits (129), Expect = 1e-09
Identities = 13/81 (16%), Positives = 29/81 (35%), Gaps = 7/81 (8%)
Query: 33 GDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
G + I V L + + +L ++ +++ F+ + E A A
Sbjct: 4 GSSGILVKNLPQDSNCQEVHDLLKDYDLKY-CYVDRNK------RTAFVTLLNGEQAQNA 56
Query: 93 IKIMNMIKLYGKPIRVNKASS 113
I++ + GK + V +
Sbjct: 57 IQMFHQYSFRGKDLIVQLQPT 77
Score = 48.6 bits (116), Expect = 7e-08
Identities = 10/71 (14%), Positives = 21/71 (29%), Gaps = 13/71 (18%)
Query: 183 IFIGNLDPEI-------------MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCN 229
I + NL + ++ +K AF+ + E + +I H
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRG 67
Query: 230 RPISVSYAFKK 240
+ + V
Sbjct: 68 KDLIVQLQPTD 78
>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 = 54.2 bits (130), Expect = 1e-09
Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 8/90 (8%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK- 94
I++ L V+E + L + G V N+ M K + FIE EE A+ +
Sbjct: 33 VIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANTMVNY 86
Query: 95 -IMNMIKLYGKPIRVNKASSHQKNLDVGAN 123
L G+PI + ++ + D N
Sbjct: 87 YTSVTPVLRGQPIYIQFSNHKELKTDSSPN 116
Score = 39.1 bits (91), Expect = 2e-04
Identities = 22/146 (15%), Positives = 39/146 (26%), Gaps = 47/146 (32%)
Query: 103 GKPIRVNKASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYG 162
G R + + I I L +V E + FG +
Sbjct: 13 GLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTN------------ 60
Query: 163 KPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASID-- 220
+ + K K AFI + EA++ ++
Sbjct: 61 --LLMLK-------------------------------GKNQAFIEMNTEEAANTMVNYY 87
Query: 221 AMHGQYLCNRPISVSYAFKKDSKGDR 246
L +PI + ++ K+ K D
Sbjct: 88 TSVTPVLRGQPIYIQFSNHKELKTDS 113
>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 = 53.3 bits (128), Expect = 3e-09
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 3/85 (3%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN-VHMPKDRVTQTHQGYGFIEFMGEE 87
D + + GL ++ + + F V N + +P D + G F++F +E
Sbjct: 37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK-ITGEAFVQFASQE 95
Query: 88 DADYAIKIMNMIKLYGKPIRVNKAS 112
A+ A+ + ++ + I V K+S
Sbjct: 96 LAEKALG-KHKERIGHRYIEVFKSS 119
Score = 37.6 bits (87), Expect = 0.001
Identities = 18/124 (14%), Positives = 39/124 (31%), Gaps = 40/124 (32%)
Query: 112 SSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKAS 171
S+ + + + L ++ + FS ++ P +
Sbjct: 33 GSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIV---------------PNGI---- 73
Query: 172 SHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRP 231
+ DP+ G G AF+ +AS E ++ ++ H + + +R
Sbjct: 74 -------------------TLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRY 112
Query: 232 ISVS 235
I V
Sbjct: 113 IEVF 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 = 51.8 bits (124), Expect = 9e-09
Identities = 20/96 (20%), Positives = 32/96 (33%), Gaps = 5/96 (5%)
Query: 20 SQTKLEGGGESGDGDATIYVGGLDDKVSETLMWELFVQ---SGPVVNVHMPKDRVTQTHQ 76
S + G G + + GL S + V VH R +
Sbjct: 3 SGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGR-QS 61
Query: 77 GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKAS 112
G F+E E+D A+K + + + I V K+
Sbjct: 62 GEAFVELESEDDVKLALK-KDRESMGHRYIEVFKSH 96
Score = 34.1 bits (78), Expect = 0.014
Identities = 10/55 (18%), Positives = 19/55 (34%), Gaps = 2/55 (3%)
Query: 180 GANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
I G + + G G AF+ S + ++ + + +R I V
Sbjct: 40 DCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLAL-KKDRESMGHRYIEV 92
>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 = 51.4 bits (123), Expect = 1e-08
Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 5/87 (5%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQ---SGPVVNVHMPKDRVTQTHQGYGFIEFMG 85
E D I GL + + F +H +R +G IE
Sbjct: 6 EEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR-DGKRRGDALIEMES 64
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKAS 112
E+D A++ + + + + + V + +
Sbjct: 65 EQDVQKALE-KHRMYMGQRYVEVYEIN 90
Score = 34.4 bits (79), Expect = 0.009
Identities = 13/62 (20%), Positives = 22/62 (35%), Gaps = 2/62 (3%)
Query: 180 GANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFK 239
I G + + D G +G A I S + ++ H Y+ R + V
Sbjct: 34 DCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKAL-EKHRMYMGQRYVEVYEINN 91
Query: 240 KD 241
+D
Sbjct: 92 ED 93
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 53.6 bits (128), Expect = 1e-08
Identities = 20/104 (19%), Positives = 42/104 (40%), Gaps = 15/104 (14%)
Query: 26 GGGESGDGDATIYVGGLDDKVS---------ETLMWELFVQSGPVVNVHMPKDRVTQTHQ 76
G G + T+YVGG+D ++ E+ + +F + G + + + +
Sbjct: 126 GIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK------ 179
Query: 77 GYGFIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDV 120
GF++F + +A++A + M+ L + L V
Sbjct: 180 NCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLV 223
Score = 37.8 bits (87), Expect = 0.002
Identities = 16/130 (12%), Positives = 34/130 (26%), Gaps = 54/130 (41%)
Query: 123 NIFIGNLDPEVD---------EKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSH 173
+++G +D ++ E + FS G I + IR +
Sbjct: 136 TLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDR--------------IRYVE---- 177
Query: 174 QKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPIS 233
SK F+ + ++ + +AM Q L
Sbjct: 178 ---------------------------SKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDK 210
Query: 234 VSYAFKKDSK 243
++ +
Sbjct: 211 EWDDRREGTG 220
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 50.6 bits (121), Expect = 4e-08
Identities = 17/89 (19%), Positives = 32/89 (35%), Gaps = 3/89 (3%)
Query: 25 EGGGESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFM 84
+++ GL K +E ++ F PV VH+ G +EF
Sbjct: 37 SEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGP-DGRVTGEADVEFA 94
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKASS 113
E+A A+ + + + I + S+
Sbjct: 95 THEEAVAAMS-KDRANMQHRYIELFLNST 122
Score = 39.8 bits (93), Expect = 2e-04
Identities = 20/126 (15%), Positives = 38/126 (30%), Gaps = 42/126 (33%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANI 183
+ + L + E +Y+ FS P+RV
Sbjct: 49 VHMRGLPYKATENDIYNFFSPLN-----------------PVRV---------------- 75
Query: 184 FIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSK 243
I PD G G A + +A+ E + A++ + + +R I + +
Sbjct: 76 -------HIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLNSTTGAS 126
Query: 244 GDRHGS 249
+ S
Sbjct: 127 NGAYSS 132
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 49.3 bits (118), Expect = 5e-08
Identities = 17/94 (18%), Positives = 35/94 (37%), Gaps = 10/94 (10%)
Query: 27 GGESGDGDA-------TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYG 79
G G + +++ GL + +E ++ F P+ VH+ G
Sbjct: 1 GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEA 58
Query: 80 FIEFMGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
+EF EDA A+ + + + + + S+
Sbjct: 59 DVEFATHEDAVAAMA-KDKANMQHRYVELFLNST 91
Score = 40.1 bits (94), Expect = 8e-05
Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 5/69 (7%)
Query: 184 FIGNLDPE---IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
F L+P I PD G G A + +A+ E + A++ A + +R + +
Sbjct: 35 FFSPLNPMRVHIEIGPD-GRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFLNSTA 92
Query: 241 DSKGDRHGS 249
+ G S
Sbjct: 93 GTSGSGPSS 101
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 49.1 bits (117), Expect = 9e-08
Identities = 15/88 (17%), Positives = 32/88 (36%), Gaps = 6/88 (6%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVN----VHMPKDRVTQTHQGYGFIEFM 84
S + + + GL + + F Q P+ + + G F+ F
Sbjct: 18 LSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGR-PTGDAFVLFA 76
Query: 85 GEEDADYAIKIMNMIKLYGKPIRVNKAS 112
EE A A++ + L + I + +++
Sbjct: 77 CEEYAQNALR-KHKDLLGKRYIELFRST 103
Score = 35.6 bits (82), Expect = 0.004
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 2/43 (4%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISV 234
+ PD G G AF+ +A E + ++ H L R I +
Sbjct: 59 FVTYPD-GRPTGDAFVLFACEEYAQNAL-RKHKDLLGKRYIEL 99
>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 = 47.9 bits (114), Expect = 1e-07
Identities = 16/83 (19%), Positives = 31/83 (37%), Gaps = 9/83 (10%)
Query: 36 TIYVGGL-DDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
+++ K + +L G + N + FIE EDA A+
Sbjct: 17 VVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVD 70
Query: 95 --IMNMIKLYGKPIRVNKASSHQ 115
++GKP+RV+ + ++
Sbjct: 71 YYTTTPALVFGKPVRVHLSQKYK 93
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 49.8 bits (118), Expect = 2e-07
Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 2/73 (2%)
Query: 36 TIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKI 95
++Y+ G + + E G V+N+ M + + +G F+ F E A ++
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVET 169
Query: 96 MNMIKLYGKPIRV 108
K + +
Sbjct: 170 PGQ-KYKETDLLI 181
Score = 32.9 bits (74), Expect = 0.085
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 3/49 (6%)
Query: 193 MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
MR KG F+ + S E++ ++ +Y + + FK D
Sbjct: 141 MRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYK-ETDLLIL--FKDD 186
>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 = 46.9 bits (111), Expect = 4e-07
Identities = 15/84 (17%), Positives = 35/84 (41%), Gaps = 9/84 (10%)
Query: 36 TIYVGGL-DDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIK 94
I++ L S++ + +L G + N + + + FIE EDA +
Sbjct: 27 VIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK------SQAFIEMETREDAMAMVD 80
Query: 95 --IMNMIKLYGKPIRVNKASSHQK 116
+ + G+ ++V+ + ++K
Sbjct: 81 HCLKKALWFQGRCVKVDLSEKYKK 104
>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 = 5e-07
Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 12/92 (13%)
Query: 28 GESGDGDATIYVGGLDDKVSETLM----WELFVQSGPVVNV--HMPKDRVTQTHQGYGFI 81
G SG+G A + V +D ++S + E F + G V +V D +Q +
Sbjct: 4 GSSGNG-ADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTD-----YQLKAVV 57
Query: 82 EFMGEEDADYAIKIMNMIKLYGKPIRVNKASS 113
+ +DA A+ ++ K+ K I V+ A+
Sbjct: 58 QMENLQDAIGAVNSLHRYKIGSKKILVSLATG 89
Score = 33.4 bits (76), Expect = 0.018
Identities = 17/124 (13%), Positives = 38/124 (30%), Gaps = 38/124 (30%)
Query: 121 GANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVG 180
GA++ + N+D + K L + +GK V
Sbjct: 9 GADVQVSNIDYRLSRKELQQL------------LQEAFARHGKVKSV------------- 43
Query: 181 ANIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKK 240
E+ D + A + + + + +++++H + ++ I VS A
Sbjct: 44 ----------ELSPHTD---YQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGA 90
Query: 241 DSKG 244
Sbjct: 91 SGPS 94
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 45.0 bits (106), Expect = 2e-06
Identities = 20/93 (21%), Positives = 31/93 (33%), Gaps = 9/93 (9%)
Query: 28 GESGDGDAT-IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQ--GYGFIEFM 84
G SG + ++VGGL + E + F + GP+V K GY F+ F
Sbjct: 1 GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60
Query: 85 GEEDADYAIKIMNM------IKLYGKPIRVNKA 111
E I + + I+
Sbjct: 61 EESSVQALIDACLEEDGKLYLCVSSPTIKDKPV 93
Score = 37.3 bits (86), Expect = 9e-04
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMIKLYGKP 164
+F+G L P++DE + +F FG ++ K Y P
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPP 51
Score = 27.2 bits (60), Expect = 3.1
Identities = 13/63 (20%), Positives = 20/63 (31%), Gaps = 22/63 (34%)
Query: 183 IFIGNLDPEI----------------------MRDPDTGNSKGFAFINYASFEASDASID 220
+F+G L P+I KG+AF+ + + A ID
Sbjct: 11 VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70
Query: 221 AMH 223
A
Sbjct: 71 ACL 73
>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 = 45.0 bits (106), Expect = 3e-06
Identities = 16/80 (20%), Positives = 27/80 (33%), Gaps = 5/80 (6%)
Query: 36 TIYVGGLDDKVSETLMWELFVQ---SGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYA 92
+ + GL S + VH R + G F+E E+D A
Sbjct: 46 VVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGR-QSGEAFVELGSEDDVKMA 104
Query: 93 IKIMNMIKLYGKPIRVNKAS 112
+K + + + I V K+
Sbjct: 105 LK-KDRESMGHRYIEVFKSH 123
Score = 33.8 bits (77), Expect = 0.020
Identities = 8/50 (16%), Positives = 20/50 (40%), Gaps = 2/50 (4%)
Query: 192 IMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKD 241
+ + G G AF+ S + ++ + + +R I V + + +
Sbjct: 79 FIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEVFKSHRTE 126
>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 = 44.3 bits (104), Expect = 7e-06
Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 4/87 (4%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I V L V+ ++ ++F + G V+ + +Q +++ A +A +
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 104
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGAN 123
+ +Y + S +L+V N
Sbjct: 105 DGQNIYNACCTLRIDFSKLTSLNVKYN 131
Score = 34.7 bits (79), Expect = 0.014
Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 4/69 (5%)
Query: 87 EDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGAN----IFIGNLDPEVDEKLLYDTF 142
A A++ +N ++ + + A+ G + I + NL V +L+ F
Sbjct: 8 GSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIF 67
Query: 143 SAFGVILQT 151
S FG +L+
Sbjct: 68 SKFGTVLKI 76
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 43.1 bits (101), Expect = 1e-05
Identities = 13/87 (14%), Positives = 29/87 (33%), Gaps = 5/87 (5%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
+ + ++ +++ + G V + + K Q +EF A A +
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQ-----AMVEFESVLCAQKAKAAL 82
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGAN 123
N +Y + + L+V N
Sbjct: 83 NGADIYAGCCTLKIEYARPTRLNVIRN 109
Score = 27.3 bits (60), Expect = 2.9
Identities = 5/33 (15%), Positives = 11/33 (33%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMN 156
+ I N + +LY + G + +
Sbjct: 28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR 60
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 41.9 bits (98), Expect = 4e-05
Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 4/87 (4%)
Query: 37 IYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIM 96
I V L V+ ++ ++F + G V+ + +Q +++ A +A +
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSL 86
Query: 97 NMIKLYGKPIRVNKASSHQKNLDVGAN 123
+ +Y + S +L+V N
Sbjct: 87 DGQNIYNACCTLRIDFSKLTSLNVKYN 113
Score = 29.2 bits (65), Expect = 0.82
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 124 IFIGNLDPEVDEKLLYDTFSAFGVILQT 151
I + NL V +L+ FS FG +L+
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKI 58
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 39.3 bits (91), Expect = 1e-04
Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 6/88 (6%)
Query: 28 GESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEE 87
G G + + + L ++ + L +Q GP+V+ H +QG ++ E
Sbjct: 1 GAMAWGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPY------LNQGIALCKYTTRE 54
Query: 88 DADYAIKIMNMIKLYGKPIRVNKASSHQ 115
+A+ A +N L I S ++
Sbjct: 55 EANKAQMALNNCVLANTTIFAESPSENE 82
>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 = 42.3 bits (99), Expect = 2e-04
Identities = 48/323 (14%), Positives = 86/323 (26%), Gaps = 125/323 (38%)
Query: 41 GLDDKVSETLMWEL---FVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN 97
G D+V + E +++ ++H + +E+ +K
Sbjct: 78 GQFDQVLNLCLTEFENCYLEGN---DIHA-------------LAAKLLQENDTTLVKTKE 121
Query: 98 MIKLY-------GKPIRVNKASSHQKNLDVG-ANIFI-----GNLDPEVDE-KLLYDTFS 143
+IK Y +P S+ + + G A + GN D +E + LY T+
Sbjct: 122 LIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYH 181
Query: 144 AFGVILQTPKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKG 203
L + +L + K + L++ ++ N PD
Sbjct: 182 VLVGDLIKFSAETLSELIRTTLDAEKV--FTQGLNILE--WLENPSNT----PDK----- 228
Query: 204 FAFINYASFEASDASIDAMHGQYLCNRPIS---------VSYAFKKDSKGDRHGSAAERL 254
YL + PIS Y G G L
Sbjct: 229 ---------------------DYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYL 267
Query: 255 ----------LAAQNPLSQAD---------------------RPHQLFADAPPPAPLPP- 282
+ A +++ D R ++ + P LPP
Sbjct: 268 KGATGHSQGLVTAV-AIAETDSWESFFVSVRKAITVLFFIGVRCYEAY----PNTSLPPS 322
Query: 283 ------------PPPPINIMGLP 293
P P ++I L
Sbjct: 323 ILEDSLENNEGVPSPMLSISNLT 345
Score = 35.0 bits (80), Expect = 0.030
Identities = 43/239 (17%), Positives = 74/239 (30%), Gaps = 102/239 (42%)
Query: 76 QG---YGFIEFMGEE-------------DAD------YAIKIMNMIK-------LY---- 102
QG G MG + AD Y I++++ ++
Sbjct: 1624 QGSQEQG----MGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGE 1679
Query: 103 -GKPIRVN-KASSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSA-FGVILQT----PKIM 155
GK IR N A + +D + + E++E TF + G++ T P +
Sbjct: 1680 KGKRIRENYSAMIFETIVD--GKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALT 1737
Query: 156 NMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTGNSKGFAFINYASF--- 212
+ KA F E ++ SKG A+F
Sbjct: 1738 L----------MEKA------------AF------EDLK------SKGL-IPADATFAGH 1762
Query: 213 ---E----ASDASI----DAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNP 260
E AS A + + + + R +++ A +D G + + A NP
Sbjct: 1763 SLGEYAALASLADVMSIESLV--EVVFYRGMTMQVAVPRDELGRSNYG-----MIAINP 1814
>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 = 7e-04
Identities = 5/42 (11%), Positives = 18/42 (42%)
Query: 195 DPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
D + G ++ + E ++ ++ ++ ++ +PI
Sbjct: 61 DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAEL 102
Score = 35.6 bits (82), Expect = 0.003
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 44 DKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYG 103
D+ E + E+ + G V +++ D + G +++F EEDA+ A+ +N G
Sbjct: 37 DEFFEEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNG 95
Query: 104 KPIRV 108
+PI
Sbjct: 96 QPIHA 100
>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 = 35.5 bits (82), Expect = 0.003
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 59 GPVVNVHMPK--DRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV 108
G V ++ +P+ D V G F+EF D A++ + K + +
Sbjct: 40 GLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVT 91
Score = 32.8 bits (75), Expect = 0.033
Identities = 8/44 (18%), Positives = 15/44 (34%)
Query: 193 MRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
D G F+ + S ++ + G+ NR + Y
Sbjct: 50 PVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKY 93
>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 = 34.7 bits (80), Expect = 0.008
Identities = 8/37 (21%), Positives = 17/37 (45%)
Query: 200 NSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
+ G A +++ E +D I + G++ R I+
Sbjct: 62 HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQA 98
Score = 33.1 bits (76), Expect = 0.023
Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 4/50 (8%)
Query: 59 GPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV 108
G + + + G + F E+ADY I+ ++ G+ I
Sbjct: 51 GQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 96
>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 = 33.6 bits (77), Expect = 0.024
Identities = 6/50 (12%), Positives = 19/50 (38%)
Query: 187 NLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
+ E + + F+ ++ + +I A++G++ R +
Sbjct: 56 IIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105
Score = 32.4 bits (74), Expect = 0.048
Identities = 9/43 (20%), Positives = 18/43 (41%), Gaps = 4/43 (9%)
Query: 59 GPVVNVHMPKDRVTQTHQGYG----FIEFMGEEDADYAIKIMN 97
G V V + +++ + F+EF + AI+ +N
Sbjct: 50 GAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN 92
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 33.0 bits (75), Expect = 0.024
Identities = 20/113 (17%), Positives = 35/113 (30%), Gaps = 19/113 (16%)
Query: 27 GGESGDGDATIYVGGLDDKVSETLMWELFVQS-----GPVVNVHMPKDRVTQTHQGYGFI 81
G G + V GL V + L+ F GPV++ G +
Sbjct: 1 GSSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCG--------GVL 52
Query: 82 EFMGEEDADYAIKIMNMIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEVD 134
F DA+ + + +L+G + + A + + L P
Sbjct: 53 TFREPADAERVLAQADH-ELHGAQLSLRPAPPRAPA-----RLLLQGLPPGTS 99
>3avr_A Lysine-specific demethylase 6A; cupin superfamily,
TRI/dimethyllysine demethylase, oxidoredu structural
protein complex; HET: M3L OGA EDO; 1.80A {Homo sapiens}
PDB: 3avs_A*
Length = 531
Score = 34.1 bits (77), Expect = 0.054
Identities = 19/51 (37%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 249 SAAERLLAAQN-PLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPS 298
S+AE L A +N + L PPP P P PP+ L PP PS
Sbjct: 22 SSAEVLKACRNLGKNGLSNSSILLDKCPPPRPPSSPYPPLPKDKLNPPTPS 72
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 96
Score = 31.6 bits (71), Expect = 0.065
Identities = 9/39 (23%), Positives = 17/39 (43%)
Query: 70 RVTQTHQGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV 108
+V + F+ ++ A+ A K M ++G I V
Sbjct: 40 KVLSITGCSAILRFINQDSAERAQKRMENEDVFGNRIIV 78
Score = 26.6 bits (58), Expect = 4.8
Identities = 7/51 (13%), Positives = 22/51 (43%)
Query: 201 SKGFAFINYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAA 251
+ A + + + ++++ + M + + I VS+ K + G ++
Sbjct: 45 TGCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRELCETSGPSS 95
>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 = 31.9 bits (73), Expect = 0.067
Identities = 10/40 (25%), Positives = 25/40 (62%)
Query: 197 DTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
D +++G ++ S A+ A+++A+HG++ + I+ +Y
Sbjct: 50 DKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAY 89
Score = 31.9 bits (73), Expect = 0.067
Identities = 7/39 (17%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 59 GPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN 97
G V+++++ K+ + QG +++ A A+ ++
Sbjct: 42 GGVIHIYVDKN----SAQGNVYVKCPSIAAAIAAVNALH 76
>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 = 33.2 bits (75), Expect = 0.095
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 40 GGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEEDADYAIKIMN 97
GGL + VS + + + G V + MP ++ Y F + E++ A +N
Sbjct: 26 GGLGNGVSRNQLLPVLEKCGLVDALLMP------PNKPYSFARYRTTEESKRAYVTLN 77
Score = 27.0 bits (59), Expect = 7.8
Identities = 9/55 (16%), Positives = 22/55 (40%), Gaps = 3/55 (5%)
Query: 200 NSKGFAFINYASFEASDASIDAMHGQY---LCNRPISVSYAFKKDSKGDRHGSAA 251
+K ++F Y + E S + ++G+ + I++ F + + A
Sbjct: 54 PNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQA 108
>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA
binding protein; NMR {Saccharomyces cerevisiae}
Length = 117
Score = 31.2 bits (70), Expect = 0.13
Identities = 20/94 (21%), Positives = 36/94 (38%), Gaps = 6/94 (6%)
Query: 29 ESGDGDATIYVGGLDDKVSETLMWELFVQSGPVVNVHMPKDRVTQTHQGYGFIEFMGEED 88
S + + I + L DKVS +L+ + + + + K + G I F +
Sbjct: 16 NSKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNG-AIIIFRDSKF 74
Query: 89 ADYAIKIMNMIKLYGKPIRVN-----KASSHQKN 117
A + I+N + GK IR K + +
Sbjct: 75 AAKMLMILNGSQFQGKVIRSGTINDMKRYYNNQQ 108
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid
cyclase fold, DDXXXXD motif, NDXXSXXXE MOT
methylisoborneol biosynthesis; HET: GST; 1.80A
{Streptomyces coelicolor} PDB: 3v1x_A*
Length = 433
Score = 32.8 bits (74), Expect = 0.15
Identities = 14/58 (24%), Positives = 21/58 (36%)
Query: 248 GSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLRASAL 305
SAA LAA +P P AP P +++ P+G ++L
Sbjct: 29 TSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGDSVLQRILRGPTGPGTTSL 86
Score = 27.4 bits (60), Expect = 7.3
Identities = 11/48 (22%), Positives = 14/48 (29%)
Query: 256 AAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLRAS 303
+A + +D L P P PPPPP P
Sbjct: 25 SASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGDSVLQ 72
>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 = 32.5 bits (73), Expect = 0.21
Identities = 37/254 (14%), Positives = 70/254 (27%), Gaps = 70/254 (27%)
Query: 65 HMPKDRVTQTHQGYGFIEFMGEED--ADYAIK-IMNMIK----------LYGKPIRVNKA 111
HM + + Y I + E+ ++ K + +M K + V+
Sbjct: 6 HMDFE-TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGT 64
Query: 112 -------SSHQKNLDVGANIFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMNMI-----K 159
S Q+ F+ + ++ K L Q + M +
Sbjct: 65 LRLFWTLLSKQEE---MVQKFVEEVL-RINYKFLMSPIKT--EQRQPSMMTRMYIEQRDR 118
Query: 160 LYG-----KPIRVNKASSHQK------NLDVGANIFI-GNLDPEIMRDPDTGNSKGFAFI 207
LY V++ + K L N+ I G + G+ K
Sbjct: 119 LYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDG------V----LGSGK----- 163
Query: 208 NYASFEASDASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRP 267
++ A D + + C + + + + + S L Q L Q D
Sbjct: 164 ---TWVALDVCLSY---KVQCKMDFKIFWL----NLKNCN-SPETVLEMLQKLLYQIDPN 212
Query: 268 HQLFADAPPPAPLP 281
+D L
Sbjct: 213 WTSRSDHSSNIKLR 226
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB:
2peh_A
Length = 105
Score = 30.2 bits (68), Expect = 0.23
Identities = 10/55 (18%), Positives = 22/55 (40%), Gaps = 6/55 (10%)
Query: 182 NIFIGNLDPEIMRDPDTGNSKGFAFINYASFEASDASIDAMHGQYLCNRPISVSY 236
I EI PD + F+ + E++ ++ ++G+Y R + +
Sbjct: 42 KCVI----FEIPGAPD--DEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACF 90
Score = 29.4 bits (66), Expect = 0.41
Identities = 10/51 (19%), Positives = 18/51 (35%), Gaps = 1/51 (1%)
Query: 59 GPVVNVHMPKDRVTQTH-QGYGFIEFMGEEDADYAIKIMNMIKLYGKPIRV 108
G V + + F+EF E A A+ +N G+ ++
Sbjct: 38 GKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKA 88
>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET:
ATP; NMR {Saccharomyces cerevisiae}
Length = 608
Score = 31.5 bits (72), Expect = 0.33
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 160 LYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG 199
G P + A + + L G N F+ NL+ RDP++
Sbjct: 541 FEGIPSKNAHARAPESLLT-GCNRFLKNLNVTFRRDPNSF 579
>2kpy_A Major pollen allergen ART V 1; defensin-like, poly-proline; NMR
{Artemisia vulgaris}
Length = 108
Score = 29.0 bits (64), Expect = 0.74
Identities = 13/32 (40%), Positives = 13/32 (40%), Gaps = 5/32 (15%)
Query: 273 DAPPPAPLPPP-----PPPINIMGLPPPPPSG 299
PP PPP P P G PPPP G
Sbjct: 61 TPAPPGAAPPPAAGGSPSPPADGGSPPPPADG 92
Score = 26.7 bits (58), Expect = 4.4
Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 272 ADAPPPAPLPPPPPPINIMGLPPPPPSG 299
APPPA P PP + G PPPP+
Sbjct: 66 GAAPPPAAGGSPSPPAD--GGSPPPPAD 91
>2pzi_A Probable serine/threonine-protein kinase PKNG; ATP-recognition,
kinase-INH complex, rubredoxin fold, TPR domain,
transferase; HET: AXX; 2.40A {Mycobacterium
tuberculosis}
Length = 681
Score = 30.2 bits (68), Expect = 0.91
Identities = 9/69 (13%), Positives = 19/69 (27%), Gaps = 9/69 (13%)
Query: 245 DRHGSAAE---------RLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPP 295
R +A E R + AQ+ +F+ + + ++
Sbjct: 311 QRFTTAEEMSAQLTGVLREVVAQDTGVPRPGLSTIFSPSRSTFGVDLLVAHTDVYLDGQV 370
Query: 296 PPSGLRASA 304
L A+
Sbjct: 371 HAEKLTANE 379
>1jvr_A HTLV-II MA, MA, human T-cell leukemia virus type II matrix protein;
HTLV-II matrix protein, retroviral matrix protein; NMR
{Human t-lymphotropic virus 2} SCOP: a.61.1.2
Length = 137
Score = 28.7 bits (63), Expect = 1.3
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 258 QNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPP 295
+N +S + + P PPPPPP +PPP
Sbjct: 90 KNQVSPSAPAAPVPTPICPTTTPPPPPPPSPEAHVPPP 127
Score = 27.9 bits (61), Expect = 2.6
Identities = 12/27 (44%), Positives = 12/27 (44%)
Query: 272 ADAPPPAPLPPPPPPINIMGLPPPPPS 298
P AP P P PI PPPPP
Sbjct: 91 NQVSPSAPAAPVPTPICPTTTPPPPPP 117
Score = 27.9 bits (61), Expect = 2.7
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 274 APPPAPLPPPPPPINIMGLPPPPPS 298
+ P AP+P P P PPPP
Sbjct: 96 SAPAAPVPTPICPTTTPPPPPPPSP 120
Score = 26.4 bits (57), Expect = 8.6
Identities = 9/25 (36%), Positives = 10/25 (40%)
Query: 274 APPPAPLPPPPPPINIMGLPPPPPS 298
+P P P P PPPPP
Sbjct: 94 SPSAPAAPVPTPICPTTTPPPPPPP 118
>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION, membrane
protein; HET: ATP; 2.10A {Rattus norvegicus} SCOP:
c.30.1.5 d.142.1.3 PDB: 1px2_A*
Length = 422
Score = 29.4 bits (65), Expect = 1.4
Identities = 6/70 (8%), Positives = 15/70 (21%)
Query: 234 VSYAFKKDSKGDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLP 293
+Y ++ S + + + P + P +
Sbjct: 2 SNYLRRRLSDSNFMANLPNGYMTDLQRPQPPPPPPSAASPGATPGSAAASAERASTAAPV 61
Query: 294 PPPPSGLRAS 303
P + S
Sbjct: 62 ASPAAPSPGS 71
Score = 27.1 bits (59), Expect = 9.2
Identities = 13/44 (29%), Positives = 15/44 (34%)
Query: 261 LSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLRASA 304
LS ++ L P PPPP P P ASA
Sbjct: 9 LSDSNFMANLPNGYMTDLQRPQPPPPPPSAASPGATPGSAAASA 52
>2v8f_C MDIA1, profilin IIA; alternative splicing, protein-binding,
cytoplasm, acetylation, cytoskeleton, actin-binding;
1.1A {Mus musculus}
Length = 26
Score = 26.2 bits (57), Expect = 1.4
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 280 LPPPPPPINIMGLPPPPP 297
+PPPPP + +PPPPP
Sbjct: 1 IPPPPPLPGVASIPPPPP 18
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 3cw1_A
Length = 231
Score = 29.2 bits (65), Expect = 1.5
Identities = 15/46 (32%), Positives = 18/46 (39%)
Query: 258 QNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLRAS 303
Q P + P + APPP + PPP MG P P G
Sbjct: 167 QYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTP 212
Score = 28.8 bits (64), Expect = 1.7
Identities = 12/49 (24%), Positives = 16/49 (32%)
Query: 256 AAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLRASA 304
+Q ++ R A A A + P PPPP G A
Sbjct: 137 PSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPP 185
Score = 27.7 bits (61), Expect = 4.1
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 4/32 (12%)
Query: 274 APPPAPLPPPPPPINIMGLPPP----PPSGLR 301
P P+ PP MG+PPP PP G+R
Sbjct: 197 PPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMR 228
Score = 26.9 bits (59), Expect = 8.7
Identities = 9/25 (36%), Positives = 9/25 (36%)
Query: 275 PPPAPLPPPPPPINIMGLPPPPPSG 299
P PPP G PPP G
Sbjct: 166 TQYPPGRGGPPPPMGRGAPPPGMMG 190
>1jfi_B DR1 protein, transcription regulator NC2 beta chain; histone,
H2A/H2B, tata-DNA, transcription initiation, NC2,
negative cofactor, structural genomics, PSI; 2.62A {Homo
sapiens} SCOP: a.22.1.3
Length = 179
Score = 28.6 bits (63), Expect = 1.9
Identities = 18/117 (15%), Positives = 28/117 (23%), Gaps = 24/117 (20%)
Query: 206 FINYASFEASDAS-------------IDAMHG-----------QYLCNRPISVSYAFKKD 241
FI+ S EA++ I A+ + L K
Sbjct: 49 FIHLISSEANEICNKSEKKTISPEHVIQALESLGFGSYISEVKEVLQECKTVALKRRKAS 108
Query: 242 SKGDRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPS 298
S+ + G E LL Q L R Q + + +
Sbjct: 109 SRLENLGIPEEELLRQQQELFAKARQQQAELAQQEWLQMQQAAQQAQLAAASASASN 165
>2uv8_A Fatty acid synthase subunit alpha (FAS2); fatty acid biosynthesis,
malonyl/palmitoyl transferase, phosphopantetheine,
transferase; HET: GVL FMN; 3.10A {Saccharomyces
cerevisiae} PDB: 2vkz_A* 3hmj_A*
Length = 1887
Score = 29.2 bits (65), Expect = 1.9
Identities = 12/54 (22%), Positives = 19/54 (35%)
Query: 251 AERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLRASA 304
A+ + +P A + +AP P P P P P + A+A
Sbjct: 85 AKEIYYTPDPSELAAKEEPAKEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAA 138
>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor,
chromophore, glycoprotein, lipoprotein, membrane,
palmitate phosphorylation; HET: BOG RET PLM TWT PC1;
2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A*
Length = 448
Score = 29.1 bits (65), Expect = 2.1
Identities = 16/49 (32%), Positives = 17/49 (34%), Gaps = 1/49 (2%)
Query: 257 AQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPP-PPPSGLRASA 304
Q Q P PP PPPP G PP PP G+ A
Sbjct: 397 PQGYPPQGYPPQGYPPQGYPPQGYPPPPQGAPPQGAPPAAPPQGVDNQA 445
Score = 26.8 bits (59), Expect = 9.6
Identities = 14/47 (29%), Positives = 15/47 (31%), Gaps = 2/47 (4%)
Query: 260 PLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPP--PPSGLRASA 304
P A P PP PP P PP PP G +A
Sbjct: 390 PQGYAPPPQGYPPQGYPPQGYPPQGYPPQGYPPPPQGAPPQGAPPAA 436
>1mb1_A MBP1, MLU1-box binding protein; transcription regulation,
cell-cycle, transcription factor; 2.10A {Saccharomyces
cerevisiae} SCOP: d.34.1.1 PDB: 1l3g_A
Length = 130
Score = 28.0 bits (62), Expect = 2.1
Identities = 9/44 (20%), Positives = 14/44 (31%), Gaps = 2/44 (4%)
Query: 253 RLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPP 296
+ LA + + +P LF PPP P +
Sbjct: 84 KQLAEKFSVYDQLKP--LFDFTQTDGSASPPPAPKHHHASKVDH 125
>3swj_A CHUZ, putative uncharacterized protein; heme oxygenase, bacterial
iron aquisition, heme bindin; HET: HEM; 2.41A
{Campylobacter jejuni}
Length = 251
Score = 28.6 bits (63), Expect = 2.1
Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 6/63 (9%)
Query: 198 TGNSKGFAFINYASFEASD------ASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAA 251
T N+ G +YA F ++ S + H + P ++ F +D
Sbjct: 105 TLNANGEVVCSYAPFVSTQWGNYIYISEVSEHFNNIKVNPNNIEIMFLEDESKAASVILR 164
Query: 252 ERL 254
+RL
Sbjct: 165 KRL 167
>3gas_A Heme oxygenase; FMN-binding split barrel, oxidoreductase; HET: HEM;
1.80A {Helicobacter pylori}
Length = 259
Score = 28.5 bits (63), Expect = 2.2
Identities = 15/63 (23%), Positives = 22/63 (34%), Gaps = 6/63 (9%)
Query: 198 TGNSKGFAFINYASFEASD------ASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAA 251
T + G +YA + S A H L N P +V F +D +
Sbjct: 105 TLHPNGHVVCSYAPLMSDGKQYYIYVSEVAEHFAGLKNNPHNVEVMFLEDESKAKSAILR 164
Query: 252 ERL 254
+RL
Sbjct: 165 KRL 167
>2v7s_A Probable conserved lipoprotein LPPA; unknown function, putative
lipoprotein; 1.96A {Mycobacterium tuberculosis}
Length = 215
Score = 28.4 bits (62), Expect = 2.3
Identities = 13/72 (18%), Positives = 15/72 (20%), Gaps = 2/72 (2%)
Query: 217 ASIDAMHGQYLCNRPISVSYAFKKDSKGDRHGSAAERLLAAQNP--LSQADRPHQLFADA 274
A A L N Y + + R L L Q
Sbjct: 143 AKYGATTESSLFNESAKRDYDVQGNGYEFRLLQIKFATLNITGDCFLLQKVLDLPAGQLP 202
Query: 275 PPPAPLPPPPPP 286
P P P P
Sbjct: 203 PEPPIWPTTSTP 214
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 29.0 bits (64), Expect = 2.3
Identities = 12/43 (27%), Positives = 13/43 (30%)
Query: 256 AAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPS 298
AQ Q P Q A PP MG+PP
Sbjct: 11 QAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAV 53
Score = 27.9 bits (61), Expect = 5.9
Identities = 5/36 (13%), Positives = 11/36 (30%)
Query: 264 ADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSG 299
+ +++ A P +PP P+
Sbjct: 2 SHHKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAA 37
>2uv9_A Fatty acid synthase alpha subunits; fungal, dehydratase, enoyl
reductase, ketoacyl synthase, ketoacyl reductase; 3.1A
{Thermomyces lanuginosus} PDB: 2uvb_A*
Length = 1878
Score = 29.1 bits (65), Expect = 2.4
Identities = 12/54 (22%), Positives = 18/54 (33%)
Query: 251 AERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSGLRASA 304
A+ + P+ P A + AP P P P P P+ +A
Sbjct: 85 AKEIYYDVEPIEDEPEPTPAAASSADAAPAAAPAAPAAPAAAPAPAPASAGPAA 138
>3m1c_B GL, envelope glycoprotein L; glycoprotein H, GH/GL, envelope
protein, HER simplex virus, disulfide bond, HOST cell
MEMB HOST endosome; HET: NAG XYL; 3.00A {Human
herpesvirus 2}
Length = 204
Score = 28.5 bits (62), Expect = 2.6
Identities = 8/29 (27%), Positives = 11/29 (37%)
Query: 274 APPPAPLPPPPPPINIMGLPPPPPSGLRA 302
+ PL PP + + PP S R
Sbjct: 166 SSQSKPLATQPPVLALSNAPPRRVSPTRG 194
>3dbg_A Putative cytochrome P450; cytochrome P450 oxidoreductase, CYP170A1,
molecular mechanism, heme, iron, metal-binding,
monooxygenase; HET: HEM; 2.60A {Streptomyces coelicolor
A3} PDB: 3el3_A*
Length = 467
Score = 28.4 bits (64), Expect = 2.8
Identities = 6/29 (20%), Positives = 10/29 (34%)
Query: 272 ADAPPPAPLPPPPPPINIMGLPPPPPSGL 300
++ P P P + PP G+
Sbjct: 3 VESVNPETRAPAAPGAPELREPPVAGGGV 31
>4ask_A Lysine-specific demethylase 6B; oxidoreductase, KDM6B, GSK-J1,
inhibitor, lysine specific HI demethylase; HET: K0I;
1.86A {Homo sapiens} PDB: 2xue_A*
Length = 510
Score = 28.3 bits (62), Expect = 3.6
Identities = 9/47 (19%), Positives = 16/47 (34%)
Query: 252 ERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPS 298
+ + A++N + + A P + L PP PS
Sbjct: 2 DVVRASRNAKVKGKFRESYLSPAQSVKPKINTEEKLPREKLNPPTPS 48
>1f32_A Major pepsin inhibitor PI-3; proteinase inhibitor, hydrolase
inhibitor; 1.75A {Ascaris suum} SCOP: d.62.1.1 PDB:
1f34_B*
Length = 149
Score = 27.5 bits (60), Expect = 3.6
Identities = 10/36 (27%), Positives = 14/36 (38%)
Query: 251 AERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPP 286
E++ A + + A P L PPPPP
Sbjct: 108 REKIAAFEEQQENQPPSSGMPHGAVPAGGLSPPPPP 143
>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur
cluster, adenosine diphosphate, nucleotide-binding; HET:
ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*
Length = 607
Score = 28.0 bits (63), Expect = 4.1
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 157 MIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG 199
+I G+P R +A + G N F+ ++ RDPD+G
Sbjct: 542 LIVFEGEPGRHGRALPPMGMRE-GMNRFLASVGITFRRDPDSG 583
>1wwc_A Protein (NT-3 growth factor receptor TRKC); TRK receptor, receptor
tyrosine kinase, 3D-domain swapping, transferase; 1.90A
{Homo sapiens} SCOP: b.1.1.4
Length = 118
Score = 26.7 bits (59), Expect = 4.8
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 257 AQNPLSQADRPHQL-FADAPPPAPLPPPPPPINI 289
A+NPL A++ F P P P PPI +
Sbjct: 84 AKNPLGTANQTINGHFLKEPFPVDEVSPTPPITV 117
>3bbo_6 Ribosomal protein L36; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 104
Score = 26.2 bits (57), Expect = 5.4
Identities = 8/28 (28%), Positives = 9/28 (32%)
Query: 277 PAPLPPPPPPINIMGLPPPPPSGLRASA 304
P P PI L P G+ A
Sbjct: 48 ITPSPLFAEPIASQELVRLPGQGVSAGL 75
>1uk5_A BAG-family molecular chaperone regulator-3; triple helix bandle,
CAIR-1, BIS, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: a.7.7.1
Length = 111
Score = 26.6 bits (58), Expect = 5.5
Identities = 7/27 (25%), Positives = 8/27 (29%)
Query: 272 ADAPPPAPLPPPPPPINIMGLPPPPPS 298
+ AP P P PP P
Sbjct: 2 SSGSSGAPAEPAAPKSGEAETPPKHPG 28
>3a9l_A Poly-gamma-glutamate hydrolase; zinc ION binding, open alpha/beta
mixed core structure; 1.90A {Bacillus phage PHINIT1}
Length = 216
Score = 27.2 bits (60), Expect = 5.5
Identities = 7/27 (25%), Positives = 14/27 (51%)
Query: 28 GESGDGDATIYVGGLDDKVSETLMWEL 54
G D + VGGL+ ++ ++ +L
Sbjct: 104 GYKDDYNKNTLVGGLNTELRNLIVSKL 130
>3d5k_A OPRM, outer membrane protein OPRM; channel, beta-alpha-barrel,
antibiotic RES lipoprotein, palmitate, transmemb
transport; 2.40A {Pseudomonas aeruginosa} PDB: 1wp1_A
Length = 474
Score = 27.7 bits (62), Expect = 5.6
Identities = 7/27 (25%), Positives = 10/27 (37%), Gaps = 2/27 (7%)
Query: 274 APPPAPLPPPPPPINIMGLPPPPPSGL 300
+ PA LP + P+GL
Sbjct: 240 SGIPANLPQGLGLDQTL--LTEVPAGL 264
>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase;
1.70A {Bacillus subtilis} PDB: 3moj_B
Length = 76
Score = 25.6 bits (57), Expect = 6.0
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 86 EEDADYAIKIMNMIKLYGKPIRVNKA 111
+ +K+M + GK ++VNKA
Sbjct: 49 NGKGPHVLKVMKNTTVKGKQLKVNKA 74
>2qo3_A Eryaii erythromycin polyketide synthase modules 3; ketosynthase,
acyltransferase, phosphopantetheine, transfera; 2.59A
{Saccharopolyspora erythraea}
Length = 915
Score = 27.6 bits (62), Expect = 6.0
Identities = 15/78 (19%), Positives = 20/78 (25%), Gaps = 27/78 (34%)
Query: 249 SAAERLLAAQNPLSQADRP---------------HQLFADAPPPAPLPPPPPPINIMGLP 293
S LLA P + +R H + +AP
Sbjct: 391 SGGVALLAGNQPWRRGERTRRAAVSAFGISGTNAHVIVEEAPEREHRETTAHD-----GR 445
Query: 294 PPP-------PSGLRASA 304
P P + LRA A
Sbjct: 446 PVPLVVSARSTAALRAQA 463
>1q9j_A PAPA5, polyketide synthase associated protein 5; conjugating enzyme
PAPA5, structural genomics, PSI protein structure
initiative; 2.75A {Mycobacterium tuberculosis} SCOP:
c.43.1.2 c.43.1.2
Length = 422
Score = 27.4 bits (61), Expect = 6.5
Identities = 8/49 (16%), Positives = 13/49 (26%), Gaps = 6/49 (12%)
Query: 251 AERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPINIMGLPPPPPSG 299
A+R + Q ++A P P P P +
Sbjct: 169 AQRGIRKQGLSGAERFMSVMYAYEIPATETPAVLAH------PGLPQAV 211
>1yc9_A VCEC, multidrug resistance protein; outer membrane protein,
multidrug resistanc membrane protein; HET: BOG; 1.80A
{Vibrio cholerae}
Length = 442
Score = 27.3 bits (61), Expect = 7.5
Identities = 4/25 (16%), Positives = 5/25 (20%)
Query: 276 PPAPLPPPPPPINIMGLPPPPPSGL 300
P P + PS
Sbjct: 227 GPDRAASIEEPHITLTSRYGLPSEA 251
>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis,
hydrolyase/translation complex; HET: ADP; 1.90A
{Pyrococcus furiosus}
Length = 538
Score = 27.3 bits (61), Expect = 7.6
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 157 MIKLYGKPIRVNKASSHQKNLDVGANIFIGNLDPEIMRDPDTG 199
++ G+P + +A + G N F+ ++ RDPDTG
Sbjct: 472 LMVFEGEPGKYGRALP-PMGMREGMNRFLASIGITFRRDPDTG 513
>1ixc_A CBNR, LYSR-type regulatory protein; long alpha helix connecting DNA
binding and regulatory domai binding protein; 2.20A
{Cupriavidus necator} SCOP: a.4.5.37 c.94.1.1 PDB:
1iz1_A
Length = 294
Score = 27.1 bits (61), Expect = 7.7
Identities = 6/20 (30%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 246 RH-GSAAERLLAAQNPLSQA 264
+ +AA+RL +Q P+++
Sbjct: 16 GNMAAAAKRLHVSQPPITRQ 35
>3lzk_A Fumarylacetoacetate hydrolase family protein; structural genomics,
PSI-2, protein structure initiative; 1.90A
{Sinorhizobium meliloti}
Length = 359
Score = 27.2 bits (60), Expect = 7.9
Identities = 9/40 (22%), Positives = 13/40 (32%)
Query: 245 DRHGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPP 284
D A RL + +P F + +PLP
Sbjct: 61 DDWAHAGPRLERVAEGIETGAQPTMRFHEHDAASPLPRAF 100
>1jer_A Cucumber stellacyanin; electron transport, copper, glycoprotein,
hydroxylation; 1.60A {Cucumis sativus} SCOP: b.6.1.1
Length = 138
Score = 26.5 bits (58), Expect = 8.0
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 272 ADAPPPAPLPPPPPPINIMG---LPPPPPS 298
A+A P P PP ++M +PPP PS
Sbjct: 109 ANATVSMPPPSSSPPSSVMPPPVMPPPSPS 138
>2h98_A HTH-type transcriptional regulator CATM; BENM, LTTR; 1.80A
{Acinetobacter SP} PDB: 2h9q_A* 2f7b_A 2f7c_A* 3glb_A*
3m1e_A
Length = 313
Score = 26.8 bits (60), Expect = 8.4
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 246 RH-GSAAERLLAAQNPLSQA 264
+ AAE+L AQ PLS+
Sbjct: 16 QSISKAAEKLCIAQPPLSRQ 35
>3i96_A Ethanolamine utilization protein EUTS; structural protein; HET:
NHE; 1.65A {Escherichia coli} PDB: 3ia0_A
Length = 119
Score = 26.0 bits (57), Expect = 8.8
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 126 IGNLDPEVDEKLLYDTFSAFGVILQTP 152
I + E+ +K+ A G++ TP
Sbjct: 22 IAHPGEELAKKIGVPDAGAIGIMTLTP 48
>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex,
inter-protein beta sheet, protein-protein, metal
transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A
{Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A
Length = 229
Score = 26.6 bits (58), Expect = 8.8
Identities = 10/26 (38%), Positives = 12/26 (46%)
Query: 272 ADAPPPAPLPPPPPPINIMGLPPPPP 297
AD PP + PPP P+ P P
Sbjct: 43 ADLEPPQAVQPPPEPVVEPEPEPEPI 68
>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide
repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A
{Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3
b.26.1.2 PDB: 2fez_A*
Length = 388
Score = 27.0 bits (60), Expect = 9.2
Identities = 4/34 (11%), Positives = 6/34 (17%), Gaps = 4/34 (11%)
Query: 272 ADAPPPAPLPPPPPPINIMGLPPPPPSGLRASAL 305
DA A + A+
Sbjct: 260 LDAKKSAKTTAAGTV----TVLDQRTMASGQQAV 289
>3dmm_C T-cell surface glycoprotein CD8 alpha chain; T cell CO-receptor
CD8AB MHC complex, immune response, membrane, MHC I,
phosphoprotein, transmembrane; 2.60A {Mus musculus}
Length = 166
Score = 26.5 bits (58), Expect = 9.4
Identities = 6/33 (18%), Positives = 6/33 (18%)
Query: 272 ADAPPPAPLPPPPPPINIMGLPPPPPSGLRASA 304
L P P P P R
Sbjct: 128 NSTTTKPVLRTPSPVHPTGTSQPQRPEDCRPRG 160
>3fzv_A Probable transcriptional regulator; LYSR, structural genomics,
PSI-2, structure initiative; 2.71A {Pseudomonas
aeruginosa PA01}
Length = 306
Score = 26.8 bits (60), Expect = 9.5
Identities = 8/22 (36%), Positives = 11/22 (50%), Gaps = 3/22 (13%)
Query: 246 RHGS---AAERLLAAQNPLSQA 264
GS A+ +L AQ +S A
Sbjct: 17 ECGSVAEASRKLYIAQPSISTA 38
>3gjy_A Spermidine synthase; APC62791, structural genomics, PSI-2, protein
structure initiative; HET: MSE; 1.47A {Corynebacterium
glutamicum atcc 13032}
Length = 317
Score = 26.9 bits (59), Expect = 9.7
Identities = 5/42 (11%), Positives = 8/42 (19%), Gaps = 4/42 (9%)
Query: 247 HGSAAERLLAAQNPLSQADRPHQLFADAPPPAPLPPPPPPIN 288
S + + P P P P +
Sbjct: 275 DESWVRKFASGAQARHDGVST----LQMPSDTPQHPAETPEH 312
>2yew_A Capsid protein, coat protein; alphavirus, molecular dynamics; 5.00A
{Barmah forest virus}
Length = 253
Score = 26.5 bits (58), Expect = 9.7
Identities = 8/32 (25%), Positives = 9/32 (28%), Gaps = 1/32 (3%)
Query: 267 PHQLFADAPP-PAPLPPPPPPINIMGLPPPPP 297
P Q F PAP+ P P
Sbjct: 5 PTQTFYGRRWRPAPVQRYIPQPQPPAPPRRRR 36
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
0.316 0.136 0.403
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: 4,810,257
Number of extensions: 297017
Number of successful extensions: 3021
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2370
Number of HSP's successfully gapped: 644
Length of query: 305
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 212
Effective length of database: 4,105,140
Effective search space: 870289680
Effective search space used: 870289680
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: 57 (25.7 bits)