RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5142
(410 letters)
>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 = 123 bits (310), Expect = 9e-34
Identities = 91/231 (39%), Positives = 132/231 (57%), Gaps = 38/231 (16%)
Query: 11 GNSGAEAEVSKLENQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKM 70
G++G +++ LE +I QIEYYF D NL RDKFL+ +IK D+GWV L M+KF RL ++
Sbjct: 1 GSNGDNEKMAALEAKICHQIEYYFGDFNLPRDKFLKEQIKLDEGWVPLEIMIKFNRLNRL 60
Query: 71 TTEAKVIVDALKKSTSKLIEVNEDGTKIRRNPEKELPTFDIDFVKDLIAQSLYVKYIPVD 130
TT+ VIV+AL KS ++L+E++ED TKIRR+P K LP ++ D+ +S+Y+K P D
Sbjct: 61 TTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTD 120
Query: 131 ATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKENAEKFLNENK 190
ATLDDIK++ + ++ NI MR K FKGSIFV FD+ E+A+KF+
Sbjct: 121 ATLDDIKEWLEDKG----QVLNIQMRRTLHK-----AFKGSIFVVFDSIESAKKFVETP- 170
Query: 191 DKNLKFNENCEHKNAEKFLNENKDKNLKFNENCEHSLLIKWQQEYHEEKKQ 241
K+ E LLI ++ +Y +K +
Sbjct: 171 -------------------------GQKYKET---DLLILFKDDYFAKKNE 193
>1s29_A LA protein; winged helix-turn-helix, autoantigen, RNA-binding, RNA
binding protein; 1.60A {Trypanosoma brucei} SCOP:
a.4.5.46
Length = 92
Score = 100 bits (250), Expect = 3e-26
Identities = 33/89 (37%), Positives = 61/89 (68%), Gaps = 5/89 (5%)
Query: 20 SKLENQIIEQIEYYFSDINLARDKFLQGEIKKD-DGWVELTTMLKFARLAKMTTEAKVIV 78
S+ + ++ +Q+E+YFSD+N+ RD FL+G++ ++ +G+V L T+L F R+ +TT+ K +V
Sbjct: 8 SENKQKLQKQVEFYFSDVNVQRDIFLKGKMAENAEGFVSLETLLTFKRVNSVTTDVKEVV 67
Query: 79 DALKKSTSKLIEVNEDGTKIRRNPEKELP 107
+A++ S + ++EDG +RR LP
Sbjct: 68 EAIRPSE--KLVLSEDGLMVRRR--DPLP 92
>2cqk_A C-MPL binding protein; LA domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: a.4.5.46
Length = 101
Score = 97.6 bits (243), Expect = 4e-25
Identities = 23/98 (23%), Positives = 54/98 (55%), Gaps = 3/98 (3%)
Query: 10 NGNSGAEAEVSKLENQIIEQIEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAK 69
+ S L+ + +Q+E+ FS NL++D +L ++ D ++ + T+ + K
Sbjct: 2 SSGSSGAVSTEDLKECLKKQLEFCFSRENLSKDLYLISQMDS-DQFIPIWTVANMEEIKK 60
Query: 70 MTTEAKVIVDALKKSTSKLIEVNEDGTKIRRNPEKELP 107
+TT+ +I++ L+ S +++V+E G K+R + ++ +
Sbjct: 61 LTTDPDLILEVLRSSP--MVQVDEKGEKVRPSHKRCIS 96
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 61.5 bits (149), Expect = 5e-12
Identities = 29/124 (23%), Positives = 55/124 (44%), Gaps = 6/124 (4%)
Query: 259 EGNTEGSKQVVLELPTGALLKIS-DIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPT 317
G+ LE G LLK S D+ + RED+ + EI +I+F G
Sbjct: 2 RGSHHHHHHGSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHG----EIKWIDFVRGAKE 57
Query: 318 AFVRYKKENN-AEAVLKALGSKEIVIKDVKVSIEVVTGEEEQTVLDRMKIDIFKRRQKLM 376
+ +K++ A K + + +++ +V+ EV+ GE E+ L ++ D + K
Sbjct: 58 GIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVLEGEVEKEALKKIIEDQQESLNKWK 117
Query: 377 NEKK 380
++ +
Sbjct: 118 SKGR 121
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 58.2 bits (141), Expect = 6e-11
Identities = 39/137 (28%), Positives = 61/137 (44%), Gaps = 38/137 (27%)
Query: 113 FVKDLIAQSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSI 172
D+ +S+Y+K P DATLDDIK++ + ++ NI MR K FKGSI
Sbjct: 5 LKNDVKNRSVYIKGFPTDATLDDIKEWLEDKG----QVLNIQMRRTLHK-----AFKGSI 55
Query: 173 FVTFDNKENAEKFLNENKDKNLKFNENCEHKNAEKFLNENKDKNLKFNENCEHSLLIKWQ 232
FV FD+ E+A+KF+ K+ E LLI ++
Sbjct: 56 FVVFDSIESAKKFVETP---GQKYK--------------------------ETDLLILFK 86
Query: 233 QEYHEEKKQEVRSKRDK 249
+Y +K +E + + +
Sbjct: 87 DDYFAKKNEERKQNKVE 103
>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 = 54.9 bits (131), Expect = 3e-08
Identities = 51/425 (12%), Positives = 124/425 (29%), Gaps = 114/425 (26%)
Query: 15 AEAEVSKL--ENQIIEQIEYYFSDINLAR-----DKFLQGEIKKDDGWVELTTMLKFARL 67
++ E+ + + F L++ KF++ ++ + ++ + +
Sbjct: 47 SKEEIDHIIMSKDAVSGTLRLF-WTLLSKQEEMVQKFVEEVLRINYKFL-------MSPI 98
Query: 68 AKMTTEAKVIVDALKKSTSKLIEVNEDGTKI---RRNPEKELPTFDIDFVKDLIAQSLYV 124
+ ++ + +L N+ K R P +L + + +
Sbjct: 99 KTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKL--------RQALLELRPA 150
Query: 125 KYIPVDATLDDIKDFFK----KNTSEDVKITNIIMRNYQDKLANQKKFKGSIF-VTFDNK 179
K + +D + K + K+ Q K IF + N
Sbjct: 151 KNV----LIDGVLGSGKTWVALDVCLSYKV--------------QCKMDFKIFWLNLKNC 192
Query: 180 ENAEKFLNENKDKNL------KFNENCEH-KNAEKFLNENKD--KNLKFNENCEHSLLIK 230
+ E L + L + +H N + ++ + + L ++ E+ LL+
Sbjct: 193 NSPETVL--EMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL 250
Query: 231 ---WQQEYHEEKKQEVRSK-----RDKS-----------KKSTEGDGEGNTEG-SKQVVL 270
+ + K R K S + T K ++L
Sbjct: 251 LNVQNAK--AWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL 308
Query: 271 --------ELP----TGALLKISDIKEPVSREDIR-EVLEKVQTDDQEIVFIEFNVGEPT 317
+LP T ++S I E + + + V D + IE
Sbjct: 309 KYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI-IE------- 360
Query: 318 AFVRYKKENNAEAVLKALGSKEIVIKDVKVSIEV-------VTGEEEQTVLDRM-KIDIF 369
+ + + + L + + + V + V++++ K +
Sbjct: 361 SSLNVLEPAEYRKMFDRLS---VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV 417
Query: 370 KRRQK 374
+++ K
Sbjct: 418 EKQPK 422
Score = 53.3 bits (127), Expect = 9e-08
Identities = 44/324 (13%), Positives = 94/324 (29%), Gaps = 95/324 (29%)
Query: 106 LPTFDIDFVKDLIAQSLYVKYIPVDATLDDIKDFFKKNTSED-VKITNIIMRNYQDKLAN 164
L F+ FV + K + D K K + + + + +
Sbjct: 22 LSVFEDAFVDN-----FDCKDVQ-----DMPKSILSKEEIDHIIMSKDAVSGTLR----- 66
Query: 165 QKKFKGSIFVTFDNKEN--AEKFLNENKDKNLKFNENCEHKNAEKFLNENKDKNLK---- 218
+F T +K+ +KF+ E N KF E + ++
Sbjct: 67 -------LFWTLLSKQEEMVQKFVEEVLRINYKF-------LMSPIKTEQRQPSMMTRMY 112
Query: 219 -------FNENCEHSLLIKWQQEYH---EEKKQEVRSK----RDKSKKSTEGDGEGNTEG 264
+N+N + K Y+ + ++R R +G G
Sbjct: 113 IEQRDRLYNDN---QVFAK----YNVSRLQPYLKLRQALLELRPAKNVLIDGVL-----G 160
Query: 265 S-KQV-VLE----------LPTGAL-LKISDIKEPVSREDIREVLEKV----------QT 301
S K L+ + L + + P E + E+L+K+ ++
Sbjct: 161 SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP---ETVLEMLQKLLYQIDPNWTSRS 217
Query: 302 DDQEIVFIEFNVGEP--TAFVRYKKENNAEAVLKALGSKEIVIK-DVKVSIEVVTGEEEQ 358
D + + + + ++ K N VL + + + ++ I + T +
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTT--RFK 275
Query: 359 TVLDRMKIDIFKRRQKLMNEKKSG 382
V D + ++
Sbjct: 276 QVTDF--LSAATTTHISLDHHSMT 297
Score = 46.8 bits (110), Expect = 1e-05
Identities = 38/267 (14%), Positives = 76/267 (28%), Gaps = 81/267 (30%)
Query: 28 EQIEYYFSDINLARDKFLQGEIKK------DDGWVELTTMLKFARLAK--MTTEAKVIVD 79
I+ I + L+ + + + F K +TT K + D
Sbjct: 221 SNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ-NAKAWNAFNLSCKILLTTRFKQVTD 279
Query: 80 ALKKSTSKLIEVNEDGTKIRRNPEKELPTFDIDFVKDLIAQSLYVKY--IPVDATL---- 133
L +T+ I + + T D VK L+ + L + +P +
Sbjct: 280 FLSAATTTHISL-----------DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR 328
Query: 134 ----------DDIK--DFFKKNTSEDVKITNIIMR--NYQDKLANQKKFKG-SIFVTFDN 178
D + D +K + K+T II N + +K F S+F
Sbjct: 329 RLSIIAESIRDGLATWDNWKHVNCD--KLTTIIESSLNVLEPAEYRKMFDRLSVF----- 381
Query: 179 KENAEKFLNENKDKNLKFN------ENCEHKNAEKFLNENKDKNLKFNENCEHSLLIKWQ 232
++ + + +N+ SL+ K
Sbjct: 382 ----------PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY----------SLVEKQP 421
Query: 233 QEY-------HEEKKQEVRSKRDKSKK 252
+E + E K ++ ++ +
Sbjct: 422 KESTISIPSIYLELKVKLENEYALHRS 448
Score = 36.8 bits (84), Expect = 0.014
Identities = 27/157 (17%), Positives = 51/157 (32%), Gaps = 35/157 (22%)
Query: 18 EVSKLENQIIEQIEYYFSDINLARDKFLQGEIK-KDDGWV--ELTTMLKFARLAKMTTE- 73
L I++ Y N+ + I D + + LK + T
Sbjct: 441 NEYALHRSIVDH---Y----NIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLF 493
Query: 74 AKVIVDALKKSTSKLIEVNEDGTKIRRN-PEKELPTFDIDFVKDLIAQSLYVKYI----P 128
V +D + +E KIR + ++ ++ L Y YI P
Sbjct: 494 RMVFLDF------RFLEQ-----KIRHDSTAWNASGSILNTLQQLK---FYKPYICDNDP 539
Query: 129 V-DATLDDIKDFFKKNTSEDV---KITNIIMRNYQDK 161
+ ++ I DF K E++ K T+++ +
Sbjct: 540 KYERLVNAILDFLPK-IEENLICSKYTDLLRIALMAE 575
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 54.7 bits (131), Expect = 4e-08
Identities = 50/311 (16%), Positives = 90/311 (28%), Gaps = 100/311 (32%)
Query: 119 AQS------LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGS- 171
+Q LY + + FK I +I++ N + + F G
Sbjct: 1626 SQEQGMGMDLYKTSKAAQDVWNRADNHFKDTYGFS--ILDIVINNPVNLTIH---FGGEK 1680
Query: 172 -----------IFVTF-DNKENAEKFLNENKDKNLKFNENC-EHKNAEKFLNEN------ 212
IF T D K EK K+ N + +
Sbjct: 1681 GKRIRENYSAMIFETIVDGKLKTEKIF---KEINEHSTSYTFRSEKGLLSATQFTQPALT 1737
Query: 213 ----------KDKNLKFNENCE---HSLLIKWQQEYH-----------EEKKQEVRSKRD 248
K K L + HSL EY E + V R
Sbjct: 1738 LMEKAAFEDLKSKGL-IPADATFAGHSL-----GEYAALASLADVMSIESLVEVVF-YRG 1790
Query: 249 KS-KKSTEGDGEGNTEGSKQVVLELPTGALLKISDIKEPVSREDIREVLEKVQTDDQEIV 307
+ + + D G + + + S+E ++ V+E+V +V
Sbjct: 1791 MTMQVAVPRDELGRSNYG---------MIAINPGRVAASFSQEALQYVVERVGKRTGWLV 1841
Query: 308 FIE-FNV--------GEPTAFVRYKKENNAEAVLKALGSKEIVIKDVKVSIEVVTGEEEQ 358
I +NV G+ A + + VL + ++I I +++ S+
Sbjct: 1842 EIVNYNVENQQYVAAGDLRA-L-----DTVTNVLNFIKLQKIDIIELQKSLS-------- 1887
Query: 359 TVLDRMKIDIF 369
L+ ++ +F
Sbjct: 1888 --LEEVEGHLF 1896
Score = 42.3 bits (99), Expect = 3e-04
Identities = 46/282 (16%), Positives = 82/282 (29%), Gaps = 95/282 (33%)
Query: 32 YYFSDINLAR------DKFLQ---G----EIKKDDGWVELTTMLKF---------ARLAK 69
Y S A+ D + G +I ++ V LT + F +
Sbjct: 1636 YKTSKA--AQDVWNRADNHFKDTYGFSILDIVINNP-VNLT--IHFGGEKGKRIRENYSA 1690
Query: 70 MTTEAKVIVDALKKSTSKLIEVNEDGTKIR-RNPEKEL-------P---TFDIDFVKDLI 118
M E IVD K+ E+NE T R+ + L P + +DL
Sbjct: 1691 MIFET--IVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLK 1748
Query: 119 AQ------------SL--YV------KYIPVDATLDDIKDFFK--KNTSEDVKITNIIMR 156
++ SL Y + +++ ++ + F V +
Sbjct: 1749 SKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVV---FYRGMTMQVAVPRDELGRS 1805
Query: 157 NYQDKLANQKKFKGSIFVTFDNKENAEKFLNENKDKNLKF----NENCE--------HKN 204
NY N G + +F +E + + + N N E
Sbjct: 1806 NYGMIAIN----PGRVAASFS-QEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLR 1860
Query: 205 A----EKFLNENKDKNLKFNENCEHSLLIKWQQEYHEEKKQE 242
A LN K + + +I+ Q+ E+ +
Sbjct: 1861 ALDTVTNVLNFIKLQKID---------IIELQKSLSLEEVEG 1893
Score = 37.7 bits (87), Expect = 0.007
Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 15/92 (16%)
Query: 262 TEGSKQVVLELPTGALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVR 321
+ GS + VL +PT + S ++E ++ + E E DD+ E VG+ +V
Sbjct: 12 SHGSLEHVLLVPTASFFIASQLQEQFNK-ILPEPTEGFAADDEPTTPAEL-VGKFLGYVS 69
Query: 322 YKKENNA----EAVLKA---------LGSKEI 340
E + + VL L +I
Sbjct: 70 SLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI 101
Score = 36.2 bits (83), Expect = 0.022
Identities = 31/196 (15%), Positives = 56/196 (28%), Gaps = 74/196 (37%)
Query: 17 AEVSKLENQIIEQIEYYF---SDINLARDKFLQGE----------IKKDDGWVELTTMLK 63
A L+++ + + F S L GE + + VE+
Sbjct: 1742 AAFEDLKSKGLIPADATFAGHS---------L-GEYAALASLADVMSIESL-VEVV---- 1786
Query: 64 FARLAKMTTEAKVIVDALKKSTSKLIEVNEDGTKIRRNPEKELPTFDIDFVKDLIAQSLY 123
F R A V D L +S +I +N P + +F + ++ ++ +
Sbjct: 1787 FYR-GMTMQVA-VPRDELGRSNYGMIAIN---------PGRVAASFSQEALQYVVER--- 1832
Query: 124 VKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFV---TFDNKE 180
K T V+I N Y N + +V +
Sbjct: 1833 ----------------VGKRTGWLVEIVN-----Y-----N---VENQQYVAAGDLRALD 1863
Query: 181 NAEKFLNENKDKNLKF 196
LN K + +
Sbjct: 1864 TVTNVLNFIKLQKIDI 1879
>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 = 45.1 bits (107), Expect = 2e-06
Identities = 14/71 (19%), Positives = 29/71 (40%), Gaps = 10/71 (14%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
++++ +P AT +DI +FF + + + D + G V F E+
Sbjct: 18 VHMRGLPYRATENDIYNFFS-----PLNPMRVHIEIGPD-----GRVTGEADVEFATHED 67
Query: 182 AEKFLNENKDK 192
A + ++K
Sbjct: 68 AVAAMAKDKAN 78
>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 = 46.0 bits (109), Expect = 2e-06
Identities = 17/118 (14%), Positives = 39/118 (33%), Gaps = 15/118 (12%)
Query: 80 ALKK----STSKLIEVNEDGTKIRRNPEKELPTFDIDFVKDLIAQ-SLYVKYIPVDATLD 134
+S L+ + + + D +F ++++ +P AT +
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATEN 61
Query: 135 DIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKENAEKFLNENKDK 192
DI +FF + + + D + G V F E A +++++
Sbjct: 62 DIYNFFS-----PLNPVRVHIEIGPD-----GRVTGEADVEFATHEEAVAAMSKDRAN 109
>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 = 43.4 bits (103), Expect = 7e-06
Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 8/74 (10%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ V+ +P ++D+I DFF I + Y + + G V F++++
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQ----VIPGSVCLKYNE----KGMPTGEAMVAFESRDE 69
Query: 182 AEKFLNENKDKNLK 195
A + + D+ +
Sbjct: 70 ATAAVIDLNDRPIG 83
Score = 33.8 bits (78), Expect = 0.019
Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 2/81 (2%)
Query: 262 TEGSKQVVLELPTGALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPT--AF 319
+ GS P ++K+ ++ VS ++I + Q + G PT A
Sbjct: 2 SSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61
Query: 320 VRYKKENNAEAVLKALGSKEI 340
V ++ + A A + L + I
Sbjct: 62 VAFESRDEATAAVIDLNDRPI 82
>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 = 43.1 bits (102), Expect = 9e-06
Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 10/72 (13%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
++ ++ P + T ++ +F ++ I+RN G IFV F N+E
Sbjct: 12 TVKLRGAPFNVTEKNVMEFLAPLKPVAIR----IVRNA------HGNKTGYIFVDFSNEE 61
Query: 181 NAEKFLNENKDK 192
++ L N++
Sbjct: 62 EVKQALKCNREY 73
>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 = 43.7 bits (103), Expect = 9e-06
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ ++ +P T ++I FF ++ I + + K G FV F ++E
Sbjct: 45 VRLRGLPFGCTKEEIVQFFSGL---EIVPNGITLPVDPE-----GKITGEAFVQFASQEL 96
Query: 182 AEKFLNENKDK 192
AEK L ++K++
Sbjct: 97 AEKALGKHKER 107
Score = 33.7 bits (77), Expect = 0.031
Identities = 18/102 (17%), Positives = 39/102 (38%), Gaps = 5/102 (4%)
Query: 260 GNTEGSKQVVLELPTGALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPT-- 317
G G + +++ + ++E+I + ++ I G+ T
Sbjct: 27 GQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGE 86
Query: 318 AFVRYKKENNAEAVLKALGSKEIVIKDVKVSIEVVTGEEEQT 359
AFV++ + E KALG + I + + + EE ++
Sbjct: 87 AFVQFA---SQELAEKALGKHKERIGHRYIEVFKSSQEEVRS 125
>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 = 43.6 bits (103), Expect = 9e-06
Identities = 12/71 (16%), Positives = 29/71 (40%), Gaps = 10/71 (14%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ V +P A +D++DFF +++ + + + G+ V F + ++
Sbjct: 19 VSVHGMPFSAMENDVRDFFH-----GLRVDAVHLLKDHV-----GRNNGNGLVKFLSPQD 68
Query: 182 AEKFLNENKDK 192
+ L N+
Sbjct: 69 TFEALKRNRML 79
>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 = 43.1 bits (102), Expect = 1e-05
Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 8/73 (10%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ V+ +P ++D+I DFF I + Y + + G V F++++
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQ----VIPGSVCLKYNE----KGMPTGEAMVAFESRDE 69
Query: 182 AEKFLNENKDKNL 194
A + + D+ +
Sbjct: 70 ATAAVIDLNDRPI 82
Score = 33.0 bits (76), Expect = 0.030
Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 2/70 (2%)
Query: 273 PTGALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPT--AFVRYKKENNAEA 330
P ++K+ ++ VS ++I + Q + G PT A V ++ + A A
Sbjct: 13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
Query: 331 VLKALGSKEI 340
+ L + I
Sbjct: 73 AVIDLNDRPI 82
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 43.2 bits (102), Expect = 1e-05
Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 8/72 (11%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
++ IP T D+ F + ++ + ++ + N + G V F N++
Sbjct: 17 CAHITNIPFSITKMDVLQFLEGIPVDENAVH--VLVD------NNGQGLGQALVQFKNED 68
Query: 181 NAEKFLNENKDK 192
+A K ++ K
Sbjct: 69 DARKSERLHRKK 80
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 43.3 bits (102), Expect = 1e-05
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 5/71 (7%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ ++ +P AT +++ FF ++ I+ Y D + G FV F +E
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD-----GRPTGDAFVLFACEEY 80
Query: 182 AEKFLNENKDK 192
A+ L ++KD
Sbjct: 81 AQNALRKHKDL 91
>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 = 41.6 bits (98), Expect = 3e-05
Identities = 15/74 (20%), Positives = 26/74 (35%), Gaps = 15/74 (20%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ VK +P D+ ++ D K Y K + K + FVT N E
Sbjct: 8 ILVKNLPQDSNCQEVHDLLKD---------------YDLKYCYVDRNKRTAFVTLLNGEQ 52
Query: 182 AEKFLNENKDKNLK 195
A+ + + +
Sbjct: 53 AQNAIQMFHQYSFR 66
Score = 27.4 bits (61), Expect = 2.8
Identities = 6/54 (11%), Positives = 21/54 (38%), Gaps = 5/54 (9%)
Query: 287 VSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKEI 340
+ +++ ++L+ ++ + + + TAFV A+ ++
Sbjct: 17 SNCQEVHDLLKDY-----DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSF 65
>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 = 40.9 bits (96), Expect = 6e-05
Identities = 15/71 (21%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ ++ +P + ++I FF + + ++ Q + G FV F ++E
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGM--TLPVDF------QGRSTGEAFVQFASQEI 69
Query: 182 AEKFLNENKDK 192
AEK L ++K++
Sbjct: 70 AEKALKKHKER 80
>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative,
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kfy_A
Length = 136
Score = 40.4 bits (94), Expect = 2e-04
Identities = 9/71 (12%), Positives = 31/71 (43%), Gaps = 6/71 (8%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ ++ +P +++D+++F T D + + + G FV ++++
Sbjct: 47 VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYT------REGRQSGEAFVELGSEDD 100
Query: 182 AEKFLNENKDK 192
+ L ++++
Sbjct: 101 VKMALKKDRES 111
>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 = 40.2 bits (94), Expect = 2e-04
Identities = 19/71 (26%), Positives = 29/71 (40%), Gaps = 8/71 (11%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+Y+K +P +A + DFFKK + I I K G FV F N+ +
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIY--IAYGPNG------KATGEGFVEFRNEAD 79
Query: 182 AEKFLNENKDK 192
+ L +K
Sbjct: 80 YKAALCRHKQY 90
>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 = 39.9 bits (93), Expect = 2e-04
Identities = 9/71 (12%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ ++ +P +++D+++F T D + + + G FV +++++
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYT------REGRQSGEAFVELESEDD 73
Query: 182 AEKFLNENKDK 192
+ L ++++
Sbjct: 74 VKLALKKDRES 84
>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 = 39.7 bits (93), Expect = 2e-04
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK--NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
++YV+ + TLDD+ DFFK+ + + ++ Y DK K KG V++++
Sbjct: 17 AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDK--ETGKPKGDATVSYED 74
Query: 179 KENAEK 184
A+
Sbjct: 75 PPTAKA 80
>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 = 38.8 bits (91), Expect = 3e-04
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK--NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
+++V+ + + T++ + D+FK+ + K ++ Y D+ K KG V+FD+
Sbjct: 15 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR--ETGKLKGEATVSFDD 72
Query: 179 KENAEK 184
+A+
Sbjct: 73 PPSAKA 78
>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 = 38.8 bits (91), Expect = 4e-04
Identities = 14/70 (20%), Positives = 33/70 (47%), Gaps = 10/70 (14%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNK 179
+ ++ +P D T + IK+FF + I+ + + R + ++ KG + F++
Sbjct: 17 TAFLGNLPYDVTEESIKEFF-----RGLNISAVRLPREPSN----PERLKGFGYAEFEDL 67
Query: 180 ENAEKFLNEN 189
++ L+ N
Sbjct: 68 DSLLSALSLN 77
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 38.9 bits (91), Expect = 4e-04
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK--NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
+++V+ + + T++ + D+FK+ + K ++ Y D+ K KG V+FD+
Sbjct: 9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETG--KLKGEATVSFDD 66
Query: 179 KENAEK 184
+A+
Sbjct: 67 PPSAKA 72
>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 = 39.5 bits (93), Expect = 6e-04
Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNKE 180
++V +P + D+++ F + + I ++R D+ N + KG FVTF ++
Sbjct: 6 MFVGQVPRTWSEKDLRELF----EQYGAVYEINVLR---DRSQNPPQSKGCCFVTFYTRK 58
Query: 181 NAEK 184
A +
Sbjct: 59 AALE 62
Score = 36.8 bits (86), Expect = 0.004
Identities = 15/68 (22%), Positives = 26/68 (38%), Gaps = 11/68 (16%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L++ I T +DI+ F E+ +I +R +G FVTF +
Sbjct: 98 LFIGMISKKCTENDIRVMFSSFGQIEECRI----LRG------PDGLSRGCAFVTFTTRA 147
Query: 181 NAEKFLNE 188
A+ +
Sbjct: 148 MAQTAIKA 155
Score = 27.6 bits (62), Expect = 5.5
Identities = 7/49 (14%), Positives = 16/49 (32%)
Query: 318 AFVRYKKENNAEAVLKALGSKEIVIKDVKVSIEVVTGEEEQTVLDRMKI 366
FV + A AL + +++ E+ ++ K+
Sbjct: 50 CFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKL 98
>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 = 38.0 bits (89), Expect = 7e-04
Identities = 14/70 (20%), Positives = 33/70 (47%), Gaps = 10/70 (14%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNK 179
+ ++ +P D T + IK+FF + I+ + + R + ++ KG + F++
Sbjct: 21 TAFLGNLPYDVTEESIKEFF-----RGLNISAVRLPREPSN----PERLKGFGYAEFEDL 71
Query: 180 ENAEKFLNEN 189
++ L+ N
Sbjct: 72 DSLLSALSLN 81
>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 = 36.8 bits (85), Expect = 0.002
Identities = 10/71 (14%), Positives = 31/71 (43%), Gaps = 6/71 (8%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ + +P T++D+ +FF + + + N K +G + +++++
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNR------DGKRRGDALIEMESEQD 67
Query: 182 AEKFLNENKDK 192
+K L +++
Sbjct: 68 VQKALEKHRMY 78
>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 = 36.5 bits (85), Expect = 0.002
Identities = 11/64 (17%), Positives = 23/64 (35%), Gaps = 11/64 (17%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L+V + + +D+ F+ ++ ++R KG FV F +
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECT----VLRG------PDGSSKGCAFVKFSSHT 67
Query: 181 NAEK 184
A+
Sbjct: 68 EAQA 71
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 36.3 bits (84), Expect = 0.002
Identities = 8/63 (12%), Positives = 21/63 (33%), Gaps = 11/63 (17%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
L ++ IP + + + + + + N + VT+ +K+
Sbjct: 18 LQIRNIPPHLQWEVLDSLL----VQYGVVESC-------EQVNTDSETAVVNVTYSSKDQ 66
Query: 182 AEK 184
A +
Sbjct: 67 ARQ 69
>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 = 35.9 bits (83), Expect = 0.003
Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 7/83 (8%)
Query: 119 AQSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
A+ LYV IP T + + DFF ++ K F F+ F +
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNF---AFLEFRS 62
Query: 179 KENAEKFLNEN----KDKNLKFN 197
+ + + + + ++LK
Sbjct: 63 VDETTQAMAFDGIIFQGQSLKIR 85
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 36.1 bits (84), Expect = 0.003
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 11/70 (15%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNK 179
+ YV +P + DI F +D+ I ++ ++R DK + KFKG +V FD
Sbjct: 17 TAYVGNLPFNTVQGDIDAIF-----KDLSIRSVRLVR---DK--DTDKFKGFCYVEFDEV 66
Query: 180 ENAEKFLNEN 189
++ ++ L +
Sbjct: 67 DSLKEALTYD 76
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 35.4 bits (82), Expect = 0.006
Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 11/63 (17%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+YV +P D DI+D F K I +I L N++ FV F++ +
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYG----AIRDI-------DLKNRRGGPPFAFVEFEDPRD 73
Query: 182 AEK 184
AE
Sbjct: 74 AED 76
>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 = 36.4 bits (85), Expect = 0.007
Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNKE 180
++V I D + ++FF S+ I + +M DK + + +G FVT+D+ +
Sbjct: 90 IFVGGIGPDVRPKEFEEFF----SQWGTIIDAQLML---DK--DTGQSRGFGFVTYDSAD 140
Query: 181 NAEKFLNENKDKNLKFNENCEHKNAEK 207
++ + K + E K AE
Sbjct: 141 AVDRVCQNKF-IDFK-DRKIEIKRAEP 165
>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 = 36.8 bits (84), Expect = 0.009
Identities = 14/70 (20%), Positives = 27/70 (38%), Gaps = 9/70 (12%)
Query: 120 QSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDN 178
++Y+ + D++K S+ +I +I + R+ K +G FV F
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRS--------LKMRGQAFVIFKE 61
Query: 179 KENAEKFLNE 188
+A L
Sbjct: 62 VSSATNALRS 71
>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 = 36.1 bits (84), Expect = 0.009
Identities = 24/86 (27%), Positives = 39/86 (45%), Gaps = 12/86 (13%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNKE 180
++V I D ++D+F + KI I IM D+ K +G FVTFD+ +
Sbjct: 107 IFVGGIKEDTEEHHLRDYF----EQYGKIEVIEIMT---DR--GSGKKRGFAFVTFDDHD 157
Query: 181 NAEKFLNENKDKNLKFNENCEHKNAE 206
+ +K + K + NCE + A
Sbjct: 158 SVDKIV-IQKYHTVN-GHNCEVRKAL 181
Score = 26.9 bits (60), Expect = 9.6
Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 10/69 (14%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L++ + + T + ++ F++ T D ++MR+ N K+ +G FVT+ E
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDC----VVMRD-----PNTKRSRGFGFVTYATVE 66
Query: 181 NAEKFLNEN 189
+ +N
Sbjct: 67 EVDAAMNAR 75
>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 = 34.4 bits (79), Expect = 0.011
Identities = 12/63 (19%), Positives = 22/63 (34%), Gaps = 15/63 (23%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ V +P + D+KD ++ DV ++ G+ V F KE+
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAG--DVCYADVYR-------------DGTGVVEFVRKED 62
Query: 182 AEK 184
Sbjct: 63 MTY 65
>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 = 34.4 bits (79), Expect = 0.015
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 6/63 (9%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
L++ IP ++I + K T + + I+ + DK K +G FV +++
Sbjct: 11 LFIGGIPKMKKREEILEEIAKVT--EGVLDVIVYASAADK----MKNRGFAFVEYESHRA 64
Query: 182 AEK 184
A
Sbjct: 65 AAM 67
Score = 30.9 bits (70), Expect = 0.19
Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 4/75 (5%)
Query: 287 VSREDIREVLEKVQTDDQEIVFI----EFNVGEPTAFVRYKKENNAEAVLKALGSKEIVI 342
RE+I E + KV +++ + AFV Y+ A + L I +
Sbjct: 20 KKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQL 79
Query: 343 KDVKVSIEVVTGEEE 357
+++++ E +
Sbjct: 80 WGHQIAVDWAEPEID 94
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 33.8 bits (78), Expect = 0.016
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 6/68 (8%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
++ ++ I +D I S V +I DK Q +G FV +
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIK----DKQTQQ--NRGFAFVQLSSAM 64
Query: 181 NAEKFLNE 188
+A + L
Sbjct: 65 DASQLLQI 72
>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 = 36.1 bits (84), Expect = 0.016
Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 15/68 (22%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+ ++ +P D T ++ D D ++ + Y KG+ FVT N E
Sbjct: 24 KILIRGLPGDVTNQEVHDLL-----SDYELKYCFVDKY----------KGTAFVTLLNGE 68
Query: 181 NAEKFLNE 188
AE +N
Sbjct: 69 QAEAAINA 76
Score = 34.6 bits (80), Expect = 0.040
Identities = 9/68 (13%), Positives = 25/68 (36%), Gaps = 10/68 (14%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNKE 180
L V +P T ++ + + ++ + + + KG F + K+
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFG----SLERCFLVYSERT-----GQSKGYGFAEYMKKD 148
Query: 181 NAEKFLNE 188
+A + ++
Sbjct: 149 SAARAKSD 156
Score = 29.6 bits (67), Expect = 1.7
Identities = 11/67 (16%), Positives = 21/67 (31%), Gaps = 12/67 (17%)
Query: 120 QSLYVKYIPVDAT-LDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFD 177
+ L V +P +D + S T + + KG + ++
Sbjct: 185 RCLCVDRLPPGFNDVDALCRAL----SAVHSPTFCQLACG------QDGQLKGFAVLEYE 234
Query: 178 NKENAEK 184
E AE+
Sbjct: 235 TAEMAEE 241
Score = 27.3 bits (61), Expect = 8.3
Identities = 16/113 (14%), Positives = 41/113 (36%), Gaps = 23/113 (20%)
Query: 236 HEEKKQEVRSKRDKSKKSTEGDGEGNTEGSKQVVLELPTGALLKISDIKEPVSREDIREV 295
H +E+R + + +++ + + I + V+ +++ ++
Sbjct: 1 HMLDPEEIRKRLEHTERQFRNRRK------------------ILIRGLPGDVTNQEVHDL 42
Query: 296 LEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKEIVIKDVKVS 348
L E+ + + + TAFV AEA + A + +++ V
Sbjct: 43 LSDY-----ELKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQ 90
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 35.5 bits (81), Expect = 0.021
Identities = 9/64 (14%), Positives = 24/64 (37%), Gaps = 6/64 (9%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+LY+ + T +D+ + D+ ++ + KG V ++
Sbjct: 70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFE----NRANG--QSKGFALVGVGSEA 123
Query: 181 NAEK 184
+++K
Sbjct: 124 SSKK 127
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 33.6 bits (77), Expect = 0.021
Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 11/67 (16%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ +K +P + D+KD ++N+ E +++ R F G+ + F ++E
Sbjct: 31 ITMKNLPEGCSWQDLKDLARENSLE-TTFSSVNTR----------DFDGTGALEFPSEEI 79
Query: 182 AEKFLNE 188
+ L
Sbjct: 80 LVEALER 86
>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 = 33.5 bits (77), Expect = 0.026
Identities = 12/65 (18%), Positives = 31/65 (47%), Gaps = 11/65 (16%)
Query: 120 QSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
+ LY++ +P T +++ D F + I I ++ N + +G+ +V +++
Sbjct: 9 RILYIRNLPYKITAEEMYDIF----GKYGPIRQI-------RVGNTPETRGTAYVVYEDI 57
Query: 180 ENAEK 184
+A+
Sbjct: 58 FDAKN 62
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 33.3 bits (76), Expect = 0.026
Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 14/76 (18%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
++++ +P+D T ++ K+TN++M K K F+ + +E
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFG----KVTNLLM----------LKGKNQAFIEMNTEEA 64
Query: 182 AEKFLNENKDKNLKFN 197
A +N
Sbjct: 65 ANTMVNYYTSVTPVLR 80
Score = 28.3 bits (63), Expect = 1.9
Identities = 10/71 (14%), Positives = 26/71 (36%), Gaps = 4/71 (5%)
Query: 280 ISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKE 339
I + V+ ++ + ++ + G+ AF+ E A ++ S
Sbjct: 21 IRKLPIDVTEGEVISLGLPFG----KVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVT 76
Query: 340 IVIKDVKVSIE 350
V++ + I+
Sbjct: 77 PVLRGQPIYIQ 87
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 33.5 bits (77), Expect = 0.027
Identities = 11/69 (15%), Positives = 26/69 (37%), Gaps = 10/69 (14%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
+ + + +KD +K E+V+I + + + + K G V F +
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYGEVEEVEI----LLHPRTR-----KHLGLARVLFTST 58
Query: 180 ENAEKFLNE 188
A++ +
Sbjct: 59 RGAKETVKN 67
>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 = 35.0 bits (80), Expect = 0.029
Identities = 11/67 (16%), Positives = 24/67 (35%), Gaps = 12/67 (17%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
L++ IP + +D+K F S + + +D+ + + E
Sbjct: 154 LHLSNIPPSVSEEDLKVLF----SSNGGVVKGFKFFQKDR--------KMALIQMGSVEE 201
Query: 182 AEKFLNE 188
A + L +
Sbjct: 202 AVQALID 208
Score = 33.8 bits (77), Expect = 0.064
Identities = 35/232 (15%), Positives = 66/232 (28%), Gaps = 50/232 (21%)
Query: 122 LYVKYI-PVDATLDDIKDFFKKNTS-EDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
L V + P T + F + VKI K + V +
Sbjct: 37 LLVSNLNPERVTPQSLFILFGVYGDVQRVKI--------------LFNKKENALVQMADG 82
Query: 180 ENAEKFLNENKDKNLKFNENCEHKNAEKFLNENK--DKNLKFNENCEHSLLIKWQQEYHE 237
A+ A LN +K K ++ + ++ + + + +
Sbjct: 83 NQAQ--------------------LAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQ 122
Query: 238 EKKQEVRSKRDKSKKSTEGDGEGNTEGSKQVVLELPTGALLKISDIKEPVSREDIREVLE 297
++ + K N P A L +S+I VS ED++ +
Sbjct: 123 GLTKDYGNSPLHRFKKPGSKNFQNIF---------PPSATLHLSNIPPSVSEEDLKVLFS 173
Query: 298 KVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKEIVI-KDVKVS 348
F F A ++ A L L + ++ ++VS
Sbjct: 174 --SNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS 223
>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 = 33.4 bits (77), Expect = 0.030
Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 16/97 (16%)
Query: 94 DGTKIRRNPEKELPTFDIDFVKDLIAQSLYVKYIPVDATLDDIKDFFKKN-TSEDVKITN 152
G R P L + D A++++ + D++DFF DV+
Sbjct: 6 SGKSPVREPVDNLSPEERD------ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVR--- 56
Query: 153 IIMRNYQDKLANQKKFKGSIFVTFDNKENAEKFLNEN 189
II D+ N ++ KG +V F ++ +
Sbjct: 57 IIS----DR--NSRRSKGIAYVEFCEIQSVPLAIGLT 87
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 33.0 bits (76), Expect = 0.030
Identities = 13/65 (20%), Positives = 31/65 (47%), Gaps = 11/65 (16%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
L++ +P T +++++ K T +D+++ + R K KG +V ++N+
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRL--VTNRA--------GKPKGLAYVEYENE 68
Query: 180 ENAEK 184
A +
Sbjct: 69 SQASQ 73
>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 = 33.0 bits (76), Expect = 0.031
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 16/64 (25%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L+V +P D T ++++ F+K + +V I K KG F+ + +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFI---------------HKDKGFGFIRLETRT 62
Query: 181 NAEK 184
AE
Sbjct: 63 LAEI 66
>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 = 33.3 bits (76), Expect = 0.032
Identities = 12/63 (19%), Positives = 22/63 (34%), Gaps = 15/63 (23%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
+ V +P + D+KD ++ DV ++ G+ V F KE+
Sbjct: 19 VVVSGLPPSGSWQDLKDHMREAG--DVCYADVYR-------------DGTGVVEFVRKED 63
Query: 182 AEK 184
Sbjct: 64 MTY 66
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 32.9 bits (75), Expect = 0.034
Identities = 11/64 (17%), Positives = 27/64 (42%), Gaps = 13/64 (20%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+YV +P DA + D+K ++ S +++T + + F+ + +
Sbjct: 21 DVYVGNLPRDARVSDLKRALRELGSVPLRLTW-------------QGPRRRAFLHYPDSA 67
Query: 181 NAEK 184
A++
Sbjct: 68 AAQQ 71
Score = 26.3 bits (58), Expect = 6.9
Identities = 9/63 (14%), Positives = 23/63 (36%), Gaps = 3/63 (4%)
Query: 273 PTGALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVL 332
P A + + ++ D++ L ++ + + + AF+ Y A+ +
Sbjct: 17 PLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTW---QGPRRRAFLHYPDSAAAQQAV 73
Query: 333 KAL 335
L
Sbjct: 74 SCL 76
>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 = 32.9 bits (75), Expect = 0.040
Identities = 14/76 (18%), Positives = 26/76 (34%), Gaps = 14/76 (18%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
L+++ +P + T ++ K+TNI+M K K F+ +E
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFG----KVTNILML----------KGKNQAFLELATEEA 63
Query: 182 AEKFLNENKDKNLKFN 197
A +N
Sbjct: 64 AITMVNYYSAVTPHLR 79
>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 = 32.6 bits (75), Expect = 0.040
Identities = 13/76 (17%), Positives = 26/76 (34%), Gaps = 7/76 (9%)
Query: 120 QSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
++Y+ + D++K S +I +I ++ K +G FV F
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDI-------LVSRSLKMRGQAFVIFKEV 61
Query: 180 ENAEKFLNENKDKNLK 195
+A L +
Sbjct: 62 SSATNALRSMQGFPFY 77
>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 = 33.4 bits (76), Expect = 0.042
Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 14/76 (18%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
++++ +P+D T ++ K+TN++M K K F+ + +E
Sbjct: 34 IHIRKLPIDVTEGEVISLGLPFG----KVTNLLML----------KGKNQAFIEMNTEEA 79
Query: 182 AEKFLNENKDKNLKFN 197
A +N
Sbjct: 80 ANTMVNYYTSVTPVLR 95
>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 = 32.7 bits (75), Expect = 0.044
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 10/71 (14%)
Query: 115 KDLIAQSLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIF 173
KD A L++ IP + D+K F++ ++ + ++ D+ K G F
Sbjct: 9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTV----LK---DRFTGMHK--GCAF 59
Query: 174 VTFDNKENAEK 184
+T+ +E+A K
Sbjct: 60 LTYCERESALK 70
>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 = 32.7 bits (75), Expect = 0.051
Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 9/64 (14%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+ V+ IP A +I++ F + V++ K+ +G FV F K+
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPK--------KMTGTGAHRGFGFVDFITKQ 69
Query: 181 NAEK 184
+A+K
Sbjct: 70 DAKK 73
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 32.7 bits (75), Expect = 0.056
Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 18/64 (28%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L+V+ P+D ++ + F ++VKI G FV F+ E
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----------------NGFAFVEFEEAE 76
Query: 181 NAEK 184
+A K
Sbjct: 77 SAAK 80
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 32.4 bits (74), Expect = 0.060
Identities = 8/76 (10%), Positives = 25/76 (32%), Gaps = 14/76 (18%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
++++ + D+ + ++ I+ +++ K V F++
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFG----PISYVVVM----------PKKRQALVEFEDVLG 69
Query: 182 AEKFLNENKDKNLKFN 197
A +N D +
Sbjct: 70 ACNAVNYAADNQIYIA 85
>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 = 33.9 bits (78), Expect = 0.061
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 119 AQSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQ-KKFKGSIFVTFD 177
A+ LYV IP T + + DFF + +++ + LA Q + K F+ F
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFF----NAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR 59
Query: 178 NKENAEK 184
+ + +
Sbjct: 60 SVDETTQ 66
Score = 26.9 bits (60), Expect = 9.2
Identities = 7/64 (10%), Positives = 21/64 (32%), Gaps = 10/64 (15%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L++ +P D +K+ + + +++ KG F + +
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNL----VKDSATG-----LSKGYAFCEYVDIN 167
Query: 181 NAEK 184
++
Sbjct: 168 VTDQ 171
>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 = 32.5 bits (74), Expect = 0.062
Identities = 12/76 (15%), Positives = 28/76 (36%), Gaps = 14/76 (18%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
++V+ + D+ + +K I ++M FK V F+N ++
Sbjct: 18 VHVRGLCESVVEADLVEALEKFG----TICYVMMM----------PFKRQALVEFENIDS 63
Query: 182 AEKFLNENKDKNLKFN 197
A++ + D +
Sbjct: 64 AKECVTFAADVPVYIA 79
Score = 31.3 bits (71), Expect = 0.13
Identities = 14/89 (15%), Positives = 33/89 (37%), Gaps = 4/89 (4%)
Query: 262 TEGSKQVVLELPTGALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVR 321
+ GS ++ ++ + + E V D+ E LEK I ++ + A V
Sbjct: 2 SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFG----TICYVMMMPFKRQALVE 57
Query: 322 YKKENNAEAVLKALGSKEIVIKDVKVSIE 350
++ ++A+ + + I +
Sbjct: 58 FENIDSAKECVTFAADVPVYIAGQQAFFN 86
>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 = 31.7 bits (73), Expect = 0.081
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 8/66 (12%)
Query: 119 AQSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
A+S+YV + AT ++++ F V I+ DK KG ++ F +
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHG--CGSVNRVTILC----DK--FSGHPKGFAYIEFSD 57
Query: 179 KENAEK 184
KE+
Sbjct: 58 KESVRT 63
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 32.6 bits (74), Expect = 0.085
Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 7/75 (9%)
Query: 120 QSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
Q + + I + + ++ S I +I++ G ++ F +
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL-------SDDNSGKAYIVFATQ 82
Query: 180 ENAEKFLNENKDKNL 194
E+A+ F+ +
Sbjct: 83 ESAQAFVEAFQGYPF 97
>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 = 31.9 bits (73), Expect = 0.090
Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 14/64 (21%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
LYV+ + + + + I+ F + + + KK + FV F N+E
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNN--IKPGAVERV------------KKIRDYAFVHFSNRE 62
Query: 181 NAEK 184
+A +
Sbjct: 63 DAVE 66
>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 = 31.8 bits (73), Expect = 0.094
Identities = 9/65 (13%), Positives = 26/65 (40%), Gaps = 11/65 (16%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
+L++ + + ++ ++K + D+ + D + +V F++
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVV--------DVRTG--TNRKFGYVDFESA 68
Query: 180 ENAEK 184
E+ EK
Sbjct: 69 EDLEK 73
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 32.0 bits (73), Expect = 0.097
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 10/68 (14%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L++ ++P + T D+ F K+ DK + K FV+FDN +
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKV----FI---DKQTSLSK--CFGFVSFDNPD 93
Query: 181 NAEKFLNE 188
+A+ +
Sbjct: 94 SAQVAIKA 101
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 31.5 bits (72), Expect = 0.11
Identities = 15/65 (23%), Positives = 21/65 (32%), Gaps = 16/65 (24%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
+ Y+ IP AT D+ F+ D K KG F+ +D
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILDFKHY---------------PEKGCCFIKYDTH 73
Query: 180 ENAEK 184
E A
Sbjct: 74 EQAAV 78
Score = 27.7 bits (62), Expect = 2.6
Identities = 7/62 (11%), Positives = 22/62 (35%), Gaps = 4/62 (6%)
Query: 287 VSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKEIVIKDVK 346
+ D+ + + I+ + + F++Y A + AL + ++++
Sbjct: 39 ATEADLIPLFQNFG----FILDFKHYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLR 94
Query: 347 VS 348
Sbjct: 95 TG 96
>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 = 31.8 bits (72), Expect = 0.12
Identities = 12/70 (17%), Positives = 28/70 (40%), Gaps = 8/70 (11%)
Query: 122 LYVKYIPVDATLDDI---KDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
++V + ++ ++F K KI +++ N A + S +VT+
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFG----KIHKVVI-NNSTSYAGSQGPSASAYVTYIR 72
Query: 179 KENAEKFLNE 188
E+A + +
Sbjct: 73 SEDALRAIQC 82
>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 = 31.4 bits (72), Expect = 0.12
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 11/71 (15%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
++V I V +I+ FF + + ++VKI + D+ KG FV+F N
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKI----IT---DR---TGVSKGYGFVSFYNDV 61
Query: 181 NAEKFLNENKD 191
+ +K + +
Sbjct: 62 DVQKIVESQIN 72
>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 = 33.0 bits (76), Expect = 0.13
Identities = 11/72 (15%), Positives = 25/72 (34%), Gaps = 8/72 (11%)
Query: 113 FVKDLIAQSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSI 172
V L +L++ P T +I+D + V ++ + +
Sbjct: 111 IVSHLTECTLWMTNFPPSYTQRNIRDLLQDIN--VVALSIRLPSL------RFNTSRRFA 162
Query: 173 FVTFDNKENAEK 184
++ +KE+A
Sbjct: 163 YIDVTSKEDARY 174
Score = 31.9 bits (73), Expect = 0.31
Identities = 11/92 (11%), Positives = 34/92 (36%), Gaps = 2/92 (2%)
Query: 260 GNTEGSKQVVLELPTGALLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPT-- 317
G ++++ T L +++ ++ +IR++L+ + I
Sbjct: 102 HKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRF 161
Query: 318 AFVRYKKENNAEAVLKALGSKEIVIKDVKVSI 349
A++ + +A ++ L +I + +
Sbjct: 162 AYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV 193
Score = 30.3 bits (69), Expect = 1.1
Identities = 9/64 (14%), Positives = 21/64 (32%), Gaps = 10/64 (15%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
++ VK +P + + +F I ++ + + KK + F +
Sbjct: 43 TVLVKNLPKSYNQNKVYKYF----KHCGPIIHVDV------ADSLKKNFRFARIEFARYD 92
Query: 181 NAEK 184
A
Sbjct: 93 GALA 96
Score = 29.6 bits (67), Expect = 2.0
Identities = 10/65 (15%), Positives = 27/65 (41%), Gaps = 10/65 (15%)
Query: 122 LYVKYIPVDATLDD-IKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNK 179
+ ++ + + ++ +++ F I I I ++ F+ F+NK
Sbjct: 213 IMIRNLSTELLDENLLRESF----EGFGSIEKINIPAGQKE----HSFNNCCAFMVFENK 264
Query: 180 ENAEK 184
++AE+
Sbjct: 265 DSAER 269
>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 = 31.0 bits (71), Expect = 0.13
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 15/69 (21%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
++V D T D++++FF + DV I K F+ FVTF + +
Sbjct: 8 VFVGRCTGDMTEDELREFFSQYGDVMDVFIP--------------KPFRAFAFVTFADDQ 53
Query: 181 NAEKFLNEN 189
A+ E+
Sbjct: 54 IAQSLCGED 62
>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 = 32.6 bits (75), Expect = 0.13
Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 13/67 (19%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
L K + + T D++K+ F + ++I ++ ++ K KG ++ F ++ +
Sbjct: 102 LLAKNLSFNITEDELKEVF----EDALEIR-LVSQD--------GKSKGIAYIEFKSEAD 148
Query: 182 AEKFLNE 188
AEK L E
Sbjct: 149 AEKNLEE 155
Score = 32.6 bits (75), Expect = 0.13
Identities = 8/69 (11%), Positives = 25/69 (36%), Gaps = 9/69 (13%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+L++ + + ++ ++K + ++ + +V F++ E
Sbjct: 15 NLFIGNLNPNKSVAELKVAISE--LFAKNDLAVVDV-------RTGTNRKFGYVDFESAE 65
Query: 181 NAEKFLNEN 189
+ EK L
Sbjct: 66 DLEKALELT 74
>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 = 31.5 bits (72), Expect = 0.14
Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 16/64 (25%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L+V+ + T + ++ F S+ K+ + KK K F+ FD ++
Sbjct: 13 VLFVRNLANTVTEEILEKAF----SQFGKLERV------------KKLKDYAFIHFDERD 56
Query: 181 NAEK 184
A K
Sbjct: 57 GAVK 60
>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 = 32.2 bits (74), Expect = 0.14
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 10/65 (15%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNK 179
+L V Y+P D T ++ F I IMR D G FV F ++
Sbjct: 5 NLIVNYLPQDMTDRELYALF----RAIGPINTCRIMR---DYKTGYS--YGYAFVDFTSE 55
Query: 180 ENAEK 184
++++
Sbjct: 56 MDSQR 60
Score = 29.5 bits (67), Expect = 1.1
Identities = 18/64 (28%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
LYV +P T D + F K + I +R DKL + + G FV ++ +E
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNI----LR---DKLTGRPR--GVAFVRYNKRE 142
Query: 181 NAEK 184
A++
Sbjct: 143 EAQE 146
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 31.1 bits (71), Expect = 0.16
Identities = 10/64 (15%), Positives = 22/64 (34%), Gaps = 13/64 (20%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+YV + A +++ F + + + + G FV F++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYG----PLRTVWIA---------RNPPGFAFVEFEDPR 48
Query: 181 NAEK 184
+AE
Sbjct: 49 DAED 52
>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 = 31.5 bits (72), Expect = 0.16
Identities = 16/70 (22%), Positives = 27/70 (38%), Gaps = 10/70 (14%)
Query: 120 QSLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
+ LY+K + T D+ F + + I + +G F+TF N
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPI---------QFRMMTGRMRGQAFITFPN 76
Query: 179 KENAEKFLNE 188
KE A + L+
Sbjct: 77 KEIAWQALHL 86
>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 = 32.4 bits (73), Expect = 0.17
Identities = 9/69 (13%), Positives = 28/69 (40%), Gaps = 8/69 (11%)
Query: 120 QSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
L+ P++ T ++ + + + T++ + + + + S + +D+K
Sbjct: 124 NVLHFFNAPLEVTEENFFEICDELGV--KRPTSVKVFS------GKSERSSSGLLEWDSK 175
Query: 180 ENAEKFLNE 188
+A + L
Sbjct: 176 SDALETLGF 184
>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 = 30.7 bits (70), Expect = 0.18
Identities = 11/64 (17%), Positives = 24/64 (37%), Gaps = 18/64 (28%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L+V I T +++ F++ + I+++Y FV + E
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECD----IVKDYA-------------FVHMERAE 55
Query: 181 NAEK 184
+A +
Sbjct: 56 DAVE 59
>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 = 31.1 bits (70), Expect = 0.18
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 287 VSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKEIV 341
VSR + VLEK + + +P +F RY+ ++ L KE+V
Sbjct: 39 VSRNQLLPVLEKCG----LVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVV 89
>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 = 30.3 bits (69), Expect = 0.19
Identities = 10/65 (15%), Positives = 23/65 (35%), Gaps = 16/65 (24%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
+LYV + T D+++ F + + + + + F+ F +
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVV---------------QRQQCAFIQFATR 58
Query: 180 ENAEK 184
+ AE
Sbjct: 59 QAAEV 63
Score = 27.6 bits (62), Expect = 2.1
Identities = 12/70 (17%), Positives = 27/70 (38%), Gaps = 5/70 (7%)
Query: 280 ISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAE-AVLKALGSK 338
+ + + ++ D+R + EI I + AF+++ AE A K+
Sbjct: 17 VGGLGDTITETDLRNHFYQFG----EIRTITVVQRQQCAFIQFATRQAAEVAAEKSFNKL 72
Query: 339 EIVIKDVKVS 348
+ + + V
Sbjct: 73 IVNGRRLNVK 82
>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 = 31.6 bits (72), Expect = 0.19
Identities = 21/104 (20%), Positives = 34/104 (32%), Gaps = 17/104 (16%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSE--DVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
+L V YIP ++ F ++ I+ D+ Q +G FV F +
Sbjct: 44 NLMVNYIPTTVDEVQLRQLF----ERYGPIESVKIVC----DRETRQS--RGYGFVKFQS 93
Query: 179 KENAEK---FLN--ENKDKNLKFNENCEHKNAEKFLNENKDKNL 217
+A++ LN +K LK D N
Sbjct: 94 GSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAVGDGNG 137
>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 = 31.2 bits (71), Expect = 0.20
Identities = 10/66 (15%), Positives = 27/66 (40%), Gaps = 12/66 (18%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSE--DVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
+++++ + D+ + + + + D+K +++ KG F F
Sbjct: 17 TVFIRNLSFDSEEEALGEVL----QQFGDLKYVRVVL----HPDTE--HSKGCAFAQFMT 66
Query: 179 KENAEK 184
+E A+K
Sbjct: 67 QEAAQK 72
>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 = 31.8 bits (73), Expect = 0.21
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 10/65 (15%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNK 179
+L V Y+P + T ++ + F +I + ++R DK+ Q G FV + +
Sbjct: 4 NLIVNYLPQNMTQEEFRSLF----GSIGEIESCKLVR---DKITGQS--LGYGFVNYIDP 54
Query: 180 ENAEK 184
++AEK
Sbjct: 55 KDAEK 59
Score = 29.8 bits (68), Expect = 0.83
Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 10/64 (15%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
LYV +P T +++ F + +I + D++ + G F+ FD +
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRI----LV---DQVTGVSR--GVGFIRFDKRI 141
Query: 181 NAEK 184
AE+
Sbjct: 142 EAEE 145
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 30.4 bits (69), Expect = 0.22
Identities = 9/70 (12%), Positives = 24/70 (34%), Gaps = 13/70 (18%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
S++V P + ++F + +++M + A V +
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAF----GPVASVVMDKDKGVFA---------IVEMGDVG 56
Query: 181 NAEKFLNENK 190
E L++++
Sbjct: 57 AREAVLSQSQ 66
>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 = 30.2 bits (69), Expect = 0.24
Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 10/64 (15%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
LY++ + T D+ + K I+ DK N+ K G FV FD+
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKA---IL----DKTTNKCK--GYGFVDFDSPS 58
Query: 181 NAEK 184
A+K
Sbjct: 59 AAQK 62
>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 = 30.8 bits (70), Expect = 0.27
Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 10/64 (15%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L++ ++P + D+ F K+ DK N K FV++DN
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKV----FI---DKQTNLSK--CFGFVSYDNPV 78
Query: 181 NAEK 184
+A+
Sbjct: 79 SAQA 82
>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 = 30.3 bits (68), Expect = 0.27
Identities = 15/79 (18%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 274 TGALLKISDIKEPVSREDIREVLEKV---QTDDQEIVFIEFNVGEPTAFVRYKKENNAEA 330
GA +++S+I +SR++++++L++ + + + A V+ + +A
Sbjct: 8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQDAIG 67
Query: 331 VLKALGSKEIVIKDVKVSI 349
+ +L +I K + VS+
Sbjct: 68 AVNSLHRYKIGSKKILVSL 86
>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 = 29.9 bits (68), Expect = 0.33
Identities = 14/69 (20%), Positives = 24/69 (34%), Gaps = 7/69 (10%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
L++K + T + +K F K + I + G FV +
Sbjct: 7 GLFIKNLNFSTTEETLKGVFSKVGAIKSCTI----SKKKNKA--GVLLSMGFGFVEYKKP 60
Query: 180 ENAEKFLNE 188
E A+K L +
Sbjct: 61 EQAQKALKQ 69
>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 = 30.9 bits (70), Expect = 0.35
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+LYV + T + I + F S+ I IIM + K K G FV + ++
Sbjct: 41 TLYVGNLSFYTTEEQIYELF----SKSGDIKKIIMGLDKMK----KTACGFCFVEYYSRA 92
Query: 181 NAEK 184
+AE
Sbjct: 93 DAEN 96
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 31.5 bits (72), Expect = 0.35
Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 10/64 (15%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNKE 180
+YV + D + DDIK F KI + + R+ K KG F+ ++ +
Sbjct: 128 IYVASVHQDLSDDDIKSVF----EAFGKIKSATLARDPTTG-----KHKGYGFIEYEKAQ 178
Query: 181 NAEK 184
+++
Sbjct: 179 SSQD 182
Score = 28.8 bits (65), Expect = 2.5
Identities = 23/131 (17%), Positives = 45/131 (34%), Gaps = 19/131 (14%)
Query: 95 GTKIRRNPEKELPTFDIDFVKDLIAQSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNII 154
G ++ R + + +YV I + D I+ F +K ++
Sbjct: 10 GQQMGRGSAAQRQGALAIMSR------VYVGSIYYELGEDTIRQAF--APFGPIKSIDMS 61
Query: 155 MRNYQDKLANQKKFKGSIFVTFDNKENAEKFLNEN-----KDKNLKFNENCEHKNAEKFL 209
D K KG FV ++ E A+ L + +N+K A+ +
Sbjct: 62 W----DS--VTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPII 115
Query: 210 NENKDKNLKFN 220
++ ++ FN
Sbjct: 116 DQLAEEARAFN 126
>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 = 29.9 bits (68), Expect = 0.37
Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 15/69 (21%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
++V D T ++++ FF + DV I K F+ FVTF + +
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIP--------------KPFRAFAFVTFADDK 59
Query: 181 NAEKFLNEN 189
A+ E+
Sbjct: 60 VAQSLCGED 68
>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 = 31.6 bits (72), Expect = 0.43
Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 16/65 (24%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNK 179
L+V +P D T +D K F + + + I R+ +G F+ +++
Sbjct: 24 RLFVGNLPTDITEEDFKRLF----ERYGEPSEVFINRD-----------RGFGFIRLESR 68
Query: 180 ENAEK 184
AE
Sbjct: 69 TLAEI 73
Score = 28.1 bits (63), Expect = 5.3
Identities = 13/68 (19%), Positives = 25/68 (36%), Gaps = 11/68 (16%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L VK + + + ++ F + E + + + ++ + G FV F K
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVV----VVD------DRGRATGKGFVEFAAKP 148
Query: 181 NAEKFLNE 188
A K L
Sbjct: 149 PARKALER 156
>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif,
U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein;
2.50A {Homo sapiens}
Length = 143
Score = 30.6 bits (69), Expect = 0.51
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 5/70 (7%)
Query: 120 QSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQK-KFKGSIFVTFDN 178
+YVK + D+K F V ++ R D ++ + KG F+ N
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIF----GRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPN 101
Query: 179 KENAEKFLNE 188
++ A K L E
Sbjct: 102 EKAAAKALKE 111
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 31.8 bits (72), Expect = 0.52
Identities = 32/184 (17%), Positives = 50/184 (27%), Gaps = 68/184 (36%)
Query: 255 EGDGEGNTEGSKQVVLELP--TGALLKISD---------------IKEPVSREDIREVLE 297
E GE + EG +E+ G + + KEPV +D++ E
Sbjct: 841 EAFGEFSLEG----CVEMAWIMG-FISYHNGNLKGRPYTGWVDSKTKEPVDDKDVKAKYE 895
Query: 298 KVQTDDQEIV------FIE---FNVGEP---------------TAFVRYKKENNAEAVLK 333
I+ IE FN P F K+ AE
Sbjct: 896 ------TSILEHSGIRLIEPELFNGYNPEKKEMIQEVIVEEDLEPFEASKET--AEQFKH 947
Query: 334 ALGSKEIVIKDVKVSIEV-VTGEEEQTVLDRMKIDIFKRR-----------QKLMNEKKS 381
G K + I ++ + E V + T+ K F R +
Sbjct: 948 QHGDK-VDIFEIPETGEYSVKLLKGATLYIP-KALRFDRLVAGQIPTGWNAKTYGISDDI 1005
Query: 382 GRKF 385
+
Sbjct: 1006 ISQV 1009
>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 = 29.5 bits (67), Expect = 0.54
Identities = 10/65 (15%), Positives = 20/65 (30%), Gaps = 16/65 (24%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
LY+ + T DD++ F ++ G FV + ++
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV---------------LLKSGYAFVDYPDQ 54
Query: 180 ENAEK 184
A +
Sbjct: 55 NWAIR 59
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 30.9 bits (69), Expect = 0.56
Identities = 11/52 (21%), Positives = 25/52 (48%)
Query: 305 EIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKEIVIKDVKVSIEVVTGEE 356
+I I + + FV++K + NAE +A+ ++ +++ K + G
Sbjct: 169 DIDRIRYVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTG 220
>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 = 29.0 bits (66), Expect = 0.58
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 12/80 (15%)
Query: 127 IPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKENAEKF 185
+ D + I+++F E + + D N+++ G F+TF +E +K
Sbjct: 7 LSPDTPEEKIREYFGGFGEVESI----ELPM---DNKTNKRR--GFCFITFKEEEPVKKI 57
Query: 186 LNENKDKNLKFNENCEHKNA 205
+ E K N+ CE K A
Sbjct: 58 M-EKKYHNVG-LSKCEIKVA 75
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 30.6 bits (69), Expect = 0.60
Identities = 11/64 (17%), Positives = 24/64 (37%), Gaps = 11/64 (17%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNKE 180
L V + + DI++ F +E + + + + G+ V F+ +
Sbjct: 91 LLVSNLDFGVSDADIQELF----AEFGTLKKAAVDYDRSG------RSLGTADVHFERRA 140
Query: 181 NAEK 184
+A K
Sbjct: 141 DALK 144
>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 = 29.1 bits (66), Expect = 0.62
Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 18/64 (28%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L++ +P +AT +I+ F++ + I++NY FV ++K
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECD----IIKNYG-------------FVHIEDKT 53
Query: 181 NAEK 184
AE
Sbjct: 54 AAED 57
>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 = 29.1 bits (66), Expect = 0.70
Identities = 13/64 (20%), Positives = 27/64 (42%), Gaps = 8/64 (12%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
++ V + D D+++ F+ + + DK Q K G F++F +E
Sbjct: 17 TIRVTNLSEDTRETDLQELFRP--FGSISRIYLAK----DKTTGQSK--GFAFISFHRRE 68
Query: 181 NAEK 184
+A +
Sbjct: 69 DAAR 72
>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 = 29.9 bits (67), Expect = 0.73
Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 9/65 (13%)
Query: 30 IEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAKMTTEAKVIVDALKKSTSKLI 89
E+ S ++ + K D WV T +LK A AK +++ + K T + +
Sbjct: 16 YEFIHSTGSIMKRK--------KDDWVNATHILKAANFAK-AKRTRILEKEVLKETHEKV 66
Query: 90 EVNED 94
+
Sbjct: 67 QGGFG 71
>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 = 30.2 bits (68), Expect = 0.75
Identities = 11/69 (15%), Positives = 25/69 (36%), Gaps = 12/69 (17%)
Query: 120 QSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
+L++ IP + +D+K F S + + +D+ + +
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLF----SSNGGVVKGFKFFQKDR--------KMALIQMGSV 168
Query: 180 ENAEKFLNE 188
E A + L +
Sbjct: 169 EEAVQALID 177
Score = 29.9 bits (67), Expect = 1.2
Identities = 34/230 (14%), Positives = 65/230 (28%), Gaps = 46/230 (20%)
Query: 122 LYVK-YIPVDATLDDIKDFFKKNTS-EDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
L V P T + F + VKI K + V +
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKI--------------LFNKKENALVQMADG 51
Query: 180 ENAEKFLNENKDKNLKFNENCEHKNAEKFLNENKDKNLKFNENCEHSLLIKWQQEYHEEK 239
A+ + H N K K ++ + ++ + + + +
Sbjct: 52 NQAQLAM--------------SHLNGHKL----HGKPIRITLSKHQNVQLPREGQEDQGL 93
Query: 240 KQEVRSKRDKSKKSTEGDGEGNTEGSKQVVLELPTGALLKISDIKEPVSREDIREVLEKV 299
++ + K N P A L +S+I VS ED++ +
Sbjct: 94 TKDYGNSPLHRFKKPGSKNFQNI---------FPPSATLHLSNIPPSVSEEDLKVLFSSN 144
Query: 300 QTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKEIVI-KDVKVS 348
+ F F A ++ A L L + ++ ++VS
Sbjct: 145 GGVVKGFKF--FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS 192
>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 = 29.7 bits (67), Expect = 0.77
Identities = 14/88 (15%), Positives = 34/88 (38%), Gaps = 12/88 (13%)
Query: 115 KDLIAQSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFV 174
K++ +S+YV + +T D++ F + I+ DK KG ++
Sbjct: 32 KEIDKRSVYVGNVDYGSTAQDLEAHFSS--CGSINRITILC----DK--FSGHPKGYAYI 83
Query: 175 TFDNKENAEKFLNEN----KDKNLKFNE 198
F + + + + + + + +K
Sbjct: 84 EFAERNSVDAAVAMDETVFRGRTIKVLP 111
>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 = 28.7 bits (65), Expect = 0.78
Identities = 7/64 (10%), Positives = 24/64 (37%), Gaps = 18/64 (28%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
++V + T +++ F++ + ++++Y FV + +
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECD----VVKDYA-------------FVHMEKEA 54
Query: 181 NAEK 184
+A+
Sbjct: 55 DAKA 58
>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 = 28.7 bits (65), Expect = 0.84
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 12/66 (18%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSE--DVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
++YV +P T +D+ F S+ V I+ DK + +K KG F+ F +
Sbjct: 18 TVYVSNLPFSLTNNDLYRIF----SKYGKVVKVTIMK----DK--DTRKSKGVAFILFLD 67
Query: 179 KENAEK 184
K++A+
Sbjct: 68 KDSAQN 73
>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 = 29.4 bits (66), Expect = 0.85
Identities = 8/75 (10%), Positives = 20/75 (26%), Gaps = 14/75 (18%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+ K +P +I++ F + + +++ + + V F
Sbjct: 12 VILAKNLPAGTLAAEIQETFSRFG----SLGRVLL----------PEGGITAIVEFLEPL 57
Query: 181 NAEKFLNENKDKNLK 195
A K
Sbjct: 58 EARKAFRHLAYSKFH 72
>2xws_A Sirohydrochlorin cobaltochelatase; lyase, beta-alpha-beta,
cobalamin biosynthesis, metal-bindin parallel beta
sheet; 1.60A {Archaeoglobus fulgidus} PDB: 2dj5_A*
2xwq_A
Length = 133
Score = 29.7 bits (67), Expect = 0.86
Identities = 7/63 (11%), Positives = 20/63 (31%), Gaps = 15/63 (23%)
Query: 284 KEPVSREDIREVLEKVQ----TDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKE 339
+ RE + ++++ D+ +I F P + ++ +
Sbjct: 14 QLNHYREVMELHRKRIEESGAFDEVKIAFAARK-RRPMP----------DEAIREMNCDI 62
Query: 340 IVI 342
I +
Sbjct: 63 IYV 65
>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 = 29.2 bits (66), Expect = 0.88
Identities = 11/65 (16%), Positives = 22/65 (33%), Gaps = 16/65 (24%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
++Y I T ++ F ++++ + +K G FV F
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-------FPEK--------GYSFVRFSTH 71
Query: 180 ENAEK 184
E+A
Sbjct: 72 ESAAH 76
>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 = 29.2 bits (66), Expect = 0.92
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 9/63 (14%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKEN 181
++V + +K+ F + V +I+ DK K +G VTF+
Sbjct: 18 VFVANLDYKVGWKKLKEVFSM--AGVVVRADILE----DK---DGKSRGIGTVTFEQSIE 68
Query: 182 AEK 184
A +
Sbjct: 69 AVQ 71
>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 = 28.7 bits (65), Expect = 1.00
Identities = 13/69 (18%), Positives = 39/69 (56%), Gaps = 10/69 (14%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
++V IP + +++++FKK +V +++ D +++ +G F+TF++++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEV----VMIY---DA--EKQRPRGFGFITFEDEQ 63
Query: 181 NAEKFLNEN 189
+ ++ +N +
Sbjct: 64 SVDQAVNMH 72
>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 = 28.7 bits (65), Expect = 1.1
Identities = 8/46 (17%), Positives = 22/46 (47%)
Query: 305 EIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKEIVIKDVKVSIE 350
I I+ G+ A+++Y+ + A+A + + D ++ ++
Sbjct: 43 SIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD 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 = 28.4 bits (64), Expect = 1.1
Identities = 20/86 (23%), Positives = 27/86 (31%), Gaps = 16/86 (18%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
SL++ + + I F E V II ++L G FV F +
Sbjct: 11 SLWMGDLEPYMDENFISRAFAT-MGETVMSVKIIR----NRLTGIPA--GYCFVEFADLA 63
Query: 181 NAEKFL---------NENKDKNLKFN 197
AEK L K K N
Sbjct: 64 TAEKCLHKINGKPLPGATPAKRFKLN 89
>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 = 28.3 bits (64), Expect = 1.3
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L+V+ + ++ +D++ F + + + D KK KG FVTF E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSA--YGPLSELHYPI----DS--LTKKPKGFAFVTFMFPE 61
Query: 181 NAEK 184
+A K
Sbjct: 62 HAVK 65
>3bsu_A Ribonuclease H1, RNAse H1; RNAse H, RNA/DNA hybrid; HET: DNA 5IU;
2.10A {Homo sapiens}
Length = 53
Score = 27.3 bits (61), Expect = 1.3
Identities = 6/36 (16%), Positives = 16/36 (44%)
Query: 154 IMRNYQDKLANQKKFKGSIFVTFDNKENAEKFLNEN 189
+ + + A +F + F F ++ A F+ ++
Sbjct: 16 VFLTWNECRAQVDRFPAARFKKFATEDEAWAFVRKS 51
>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 = 28.4 bits (64), Expect = 1.4
Identities = 14/66 (21%), Positives = 31/66 (46%), Gaps = 12/66 (18%)
Query: 119 AQSLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
+++L + + AT + +++ F+K T +K+ K KG F+ F +
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKAT--FIKVPQ----------NQNGKSKGYAFIEFAS 62
Query: 179 KENAEK 184
E+A++
Sbjct: 63 FEDAKE 68
>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 = 29.1 bits (66), Expect = 1.5
Identities = 13/68 (19%), Positives = 23/68 (33%), Gaps = 7/68 (10%)
Query: 119 AQSLYVKYIPVDATLDDIKDFFKK--NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTF 176
A+ LYV IP T + + DFF + + + K F+ F
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLA-----VQINQDKNFAFLEF 58
Query: 177 DNKENAEK 184
+ + +
Sbjct: 59 RSVDETTQ 66
Score = 28.0 bits (63), Expect = 3.6
Identities = 8/64 (12%), Positives = 21/64 (32%), Gaps = 10/64 (15%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L++ +P D +K+ + + ++ D K G F + +
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNL----VK---DSATGLSK--GYAFCEYVDIN 147
Query: 181 NAEK 184
++
Sbjct: 148 VTDQ 151
>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 = 28.4 bits (64), Expect = 1.5
Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 11/64 (17%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L++ + + +K F K +V + ++ D+ K +G F+TF+N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLL----IK---DR---TSKSRGFAFITFENPA 59
Query: 181 NAEK 184
+A+
Sbjct: 60 DAKN 63
>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 = 28.9 bits (65), Expect = 1.5
Identities = 13/65 (20%), Positives = 26/65 (40%), Gaps = 13/65 (20%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSE--DVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
L V + + DI++ F +E +K + D+ + G+ V F+ +
Sbjct: 38 LLVSNLDFGVSDADIQELF----AEFGTLKKAAVDY----DR---SGRSLGTADVHFERR 86
Query: 180 ENAEK 184
+A K
Sbjct: 87 ADALK 91
>3oe2_A Peptidyl-prolyl CIS-trans isomerase; FKBP, ppiase, FK506; HET: TAR
SRT; 1.60A {Pseudomonas syringae PV}
Length = 219
Score = 29.7 bits (67), Expect = 1.5
Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 4/78 (5%)
Query: 118 IAQSLYVKYIPVD--ATLDDIKDFFKKNTSE-DVKITNIIMRNYQDKLANQKKFKGSIFV 174
+ + L+ + +D A +D +K ++ + + I+R + +A Q + G+
Sbjct: 33 LGERLHQEVPDLDLKALVDGLKQAYQGKPLALKQERIDQILREHDAAIA-QAETAGTDAP 91
Query: 175 TFDNKENAEKFLNENKDK 192
T + F+ K K
Sbjct: 92 TEAALKAERTFMAGEKAK 109
>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 = 27.9 bits (63), Expect = 1.6
Identities = 14/65 (21%), Positives = 31/65 (47%), Gaps = 11/65 (16%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSE--DVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
+++ + + T D I + F S +K+ ++ + +++ KG +V F+N
Sbjct: 7 VHIGRLTRNVTKDHIMEIF----STYGKIKMIDMPV----ERMHPHLS-KGYAYVEFENP 57
Query: 180 ENAEK 184
+ AEK
Sbjct: 58 DEAEK 62
>1tjn_A Sirohydrochlorin cobaltochelatase; AF0721, APC5049, midwest
consortium for structural genomics, structure
initiative, A. fulgidus; 2.01A {Archaeoglobus fulgidus}
SCOP: c.92.1.3
Length = 156
Score = 29.1 bits (65), Expect = 1.7
Identities = 6/63 (9%), Positives = 20/63 (31%), Gaps = 15/63 (23%)
Query: 284 KEPVSREDIREVLEKVQT----DDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKE 339
+ RE + ++++ D+ +I F + + ++ +
Sbjct: 35 QLNHYREVMELHRKRIEESGAFDEVKIAFAARK-----------RRPMPDEAIREMNCDI 83
Query: 340 IVI 342
I +
Sbjct: 84 IYV 86
>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 = 28.0 bits (63), Expect = 1.9
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 13/68 (19%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+L K + + T D++K+ F+ I + + K KG ++ F ++
Sbjct: 18 TLLAKNLSFNITEDELKEVFED-------ALEIRLVS------QDGKSKGIAYIEFKSEA 64
Query: 181 NAEKFLNE 188
+AEK L E
Sbjct: 65 DAEKNLEE 72
>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 = 28.4 bits (64), Expect = 1.9
Identities = 9/68 (13%), Positives = 26/68 (38%), Gaps = 11/68 (16%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNKE 180
LY+ +P+ ++++ ++ + I+R+ + +G F ++ E
Sbjct: 28 LYISNLPLSMDEQELENML----KPFGQVISTRILRD------SSGTSRGVGFARMESTE 77
Query: 181 NAEKFLNE 188
E +
Sbjct: 78 KCEAVIGH 85
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 28.6 bits (64), Expect = 1.9
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 10/65 (15%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
SL V + + D ++ F+K DV I R+ K+ +G FV F +K
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVY----IPRDRYT-----KESRGFAFVRFHDK 99
Query: 180 ENAEK 184
+AE
Sbjct: 100 RDAED 104
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 28.4 bits (63), Expect = 1.9
Identities = 10/80 (12%), Positives = 30/80 (37%), Gaps = 6/80 (7%)
Query: 127 IPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKENAEKFL 186
+P D D+I F++ ++ ++ + + KG F+ F + + + +
Sbjct: 16 LPPDIDEDEITASFRRFG------PLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69
Query: 187 NENKDKNLKFNENCEHKNAE 206
+ +++ K +
Sbjct: 70 DACLEEDGKLYLCVSSPTIK 89
>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 = 28.0 bits (63), Expect = 2.0
Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 10/65 (15%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
+L V + + D ++ F+K DV I R K +G FV F ++
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVY----IPREPHT-----KAPRGFAFVRFHDR 65
Query: 180 ENAEK 184
+A+
Sbjct: 66 RDAQD 70
>2v95_A Corticosteroid-binding globulin; transport protein, CBG, RCL,
serpin, secreted, transport, glycoprotein,
lipid-binding, glucocorticoids; HET: HCY; 1.93A {Rattus
norvegicus}
Length = 371
Score = 29.5 bits (67), Expect = 2.1
Identities = 3/33 (9%), Positives = 14/33 (42%), Gaps = 3/33 (9%)
Query: 65 ARLAKMTTEAKVIVDALKKSTSKLIEVNEDGTK 97
+ + T + + + + K+ ++++E
Sbjct: 296 SDFSGNTKDVPLTLTMVHKAM---LQLDEGNVL 325
>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 = 28.0 bits (63), Expect = 2.2
Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 13/65 (20%)
Query: 122 LYVKYIPVDATLDDIKDFFKKNTSE--DVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
L V + + DI++ F +E +K + D+ + G+ V F+ K
Sbjct: 32 LLVSNLDFGVSDADIQELF----AEFGTLKKAAVHY----DR---SGRSLGTADVHFERK 80
Query: 180 ENAEK 184
+A K
Sbjct: 81 ADALK 85
>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 = 28.7 bits (64), Expect = 2.3
Identities = 8/64 (12%), Positives = 22/64 (34%), Gaps = 13/64 (20%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+YV + + +++ F + ++ + + G FV F++
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYG----PLRSVWVA---------RNPPGFAFVEFEDPR 121
Query: 181 NAEK 184
+A
Sbjct: 122 DAAD 125
>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 = 27.6 bits (62), Expect = 2.4
Identities = 12/65 (18%), Positives = 26/65 (40%), Gaps = 11/65 (16%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNI-IMRNYQDKLANQKKFKGSIFVTFDNK 179
+++V + + + + F + +T + I + D+ K F G FV F +
Sbjct: 18 TVFVGNLEARVREEILYELF----LQAGPLTKVTICK---DREGKPKSF-G--FVCFKHP 67
Query: 180 ENAEK 184
E+
Sbjct: 68 ESVSY 72
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 27.2 bits (61), Expect = 3.4
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 12/70 (17%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKN--TSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
SL+V + D + +FF K + K+ + + KG FV F +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKV----VLD------QTGVSKGYGFVKFTD 60
Query: 179 KENAEKFLNE 188
+ ++ L E
Sbjct: 61 ELEQKRALTE 70
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 28.0 bits (62), Expect = 3.5
Identities = 9/64 (14%), Positives = 19/64 (29%), Gaps = 6/64 (9%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
++YV T + + DV ++ + KG V ++
Sbjct: 57 AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAE----NRANG--QSKGYAEVVVASEN 110
Query: 181 NAEK 184
+ K
Sbjct: 111 SVHK 114
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 27.4 bits (61), Expect = 3.9
Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 8/65 (12%)
Query: 122 LYVKYIPV--DATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
+ V +P L+ +K+ K S+ KITN K KG IF+ + +
Sbjct: 18 IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE------EDGKTKGYIFLEYASP 71
Query: 180 ENAEK 184
+A
Sbjct: 72 AHAVD 76
>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 = 27.2 bits (61), Expect = 3.9
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 11/64 (17%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+L+VK + D T + +K+ F + I+ D+ K G FV F+++E
Sbjct: 17 TLFVKGLSEDTTEETLKESF-----DGSVRARIVT----DRETGSSK--GFGFVDFNSEE 65
Query: 181 NAEK 184
+A+
Sbjct: 66 DAKA 69
>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 = 27.2 bits (61), Expect = 3.9
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 12/64 (18%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L+V IP D++ F + DV+I I N++ KG FVTF+N
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEI---IF--------NERGSKGFGFVTFENSA 66
Query: 181 NAEK 184
+A++
Sbjct: 67 DADR 70
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 27.3 bits (61), Expect = 4.2
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 12/64 (18%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
L+V IP D++ F + DV+I I N++ KG FVTF+N
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEI---IF--------NERGSKGFGFVTFENSA 80
Query: 181 NAEK 184
+A++
Sbjct: 81 DADR 84
>3v1h_A 1-phosphatidylinositol phosphodiesterase; PI-cation, TIM barrel,
phospholipase, lyase; HET: INS; 1.90A {Staphylococcus
aureus subsp} PDB: 3v18_A 3v16_A*
Length = 306
Score = 28.5 bits (63), Expect = 4.2
Identities = 8/40 (20%), Positives = 15/40 (37%), Gaps = 5/40 (12%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQD 160
+ + + LDD K + +E I+M +D
Sbjct: 79 GMVYLHHELGKFLDDAKYYLSAYPNE-----TIVMSMKKD 113
>1bm8_A Transcription factor MBP1; cell cycle, cyclins, DNA synthesis,
helix-turn-helix DNA- binding domain; 1.71A
{Saccharomyces cerevisiae} SCOP: d.34.1.1
Length = 99
Score = 26.7 bits (59), Expect = 4.6
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 8/40 (20%)
Query: 30 IEYYFSDINLARDKFLQGEIKKDDGWVELTTMLKFARLAK 69
E+ S ++ + K D WV T +LK A AK
Sbjct: 13 YEFIHSTGSIMKRK--------KDDWVNATHILKAANFAK 44
>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 = 26.8 bits (59), Expect = 5.3
Identities = 12/107 (11%), Positives = 38/107 (35%), Gaps = 5/107 (4%)
Query: 252 KSTEGDGEGNTEGSKQVVLELPTGALLKISDI-KEPVSREDIREVLEKVQTDDQEIVFIE 310
S + + ++ + G ++ +S++ S + ++ E I
Sbjct: 2 SSGSSGKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGK----IKNYI 57
Query: 311 FNVGEPTAFVRYKKENNAEAVLKALGSKEIVIKDVKVSIEVVTGEEE 357
+ AF+ + +A A++ K + + V +++ ++
Sbjct: 58 LMRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKK 104
>1bw0_A TAT, protein (tyrosine aminotransferase); tyrosine catabolism,
pyridoxal-5'-phosphate, PLP; HET: LLP; 2.50A
{Trypanosoma cruzi} SCOP: c.67.1.1
Length = 416
Score = 28.4 bits (64), Expect = 5.4
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 3/45 (6%)
Query: 291 DIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKAL 335
IR V + + I+ +VG+PT K + A +K L
Sbjct: 18 PIRTVSDNAKPSPSPKPIIKLSVGDPTLD---KNLLTSAAQIKKL 59
>3dyd_A Tyrosine aminotransferase; PLP, SGC, structural genomics,
structural genomics consortium, disease mutation,
phenylalani catabolism; HET: PLP; 2.30A {Homo sapiens}
PDB: 3pdx_A*
Length = 427
Score = 28.4 bits (64), Expect = 5.4
Identities = 10/47 (21%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 291 DIREVLEKV-QTDDQEIVFIEFNVGEPTAFVRYKKENNA-EAVLKAL 335
IR +++ + + I ++G+PT F + +A+ AL
Sbjct: 38 PIRAIVDNMKVKPNPNKTMISLSIGDPTVFGNLPTDPEVTQAMKDAL 84
>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 = 27.0 bits (60), Expect = 5.6
Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 12/66 (18%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSE--DVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
L+V + +AT +DI D F +E ++K ++ + D+ KG V ++
Sbjct: 24 ILFVTGVHEEATEEDIHDKF----AEYGEIKNIHLNL----DR--RTGYLKGYTLVEYET 73
Query: 179 KENAEK 184
+ A+
Sbjct: 74 YKEAQA 79
>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 = 26.4 bits (59), Expect = 5.9
Identities = 9/64 (14%), Positives = 24/64 (37%), Gaps = 6/64 (9%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+LY+ + T +D+ + D+ ++ + KG V ++
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFE----NR--ANGQSKGFALVGVGSEA 56
Query: 181 NAEK 184
+++K
Sbjct: 57 SSKK 60
>1by1_A Protein (PIX); RHO-GTPase exchange factor, transport protein; NMR
{Homo sapiens} SCOP: a.87.1.1
Length = 209
Score = 27.6 bits (62), Expect = 6.3
Identities = 9/48 (18%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 162 LANQKKFKGSIFVTF-DNKENAEKFLNENKDKNLKFNENCEHKNAEKF 208
L + K ++++T+ N +A L E+ ++ +F E +
Sbjct: 93 LNLMPQMK-TLYLTYCANHPSAVNVLTEHSEELGEFMETKGASSPGIL 139
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 26.9 bits (59), Expect = 6.9
Identities = 13/74 (17%), Positives = 33/74 (44%), Gaps = 2/74 (2%)
Query: 277 LLKISDIKEPVSREDIREVLEKVQTDDQEIVFIEFNVGEPTAFVRYKKENNAEAVLKALG 336
+ + ++ PV+ + + ++ K T + I F + N + A ++Y +A+ +L
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ--ALLQYADPVSAQHAKLSLD 87
Query: 337 SKEIVIKDVKVSIE 350
+ I + I+
Sbjct: 88 GQNIYNACCTLRID 101
>1ryp_D 20S proteasome; multicatalytic proteinase, protein degradation,
antigen processing, hydrolase, protease; 1.90A
{Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_C*
1g65_C 2f16_C* 2fak_C* 2fny_C* 2gpl_C* 3d29_C* 3dy3_C*
3dy4_C* 3e47_C* 3gpj_C* 3gpt_C* 3gpw_C* 3hye_C* 3mg0_C*
3mg4_C* 3oeu_C* 3oev_C* 3okj_C* 3shj_C* ...
Length = 241
Score = 27.6 bits (62), Expect = 7.0
Identities = 6/23 (26%), Positives = 13/23 (56%)
Query: 76 VIVDALKKSTSKLIEVNEDGTKI 98
V++ ++ST KL + +K+
Sbjct: 40 VVLGCERRSTLKLQDTRITPSKV 62
>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 = 26.5 bits (59), Expect = 7.5
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 12/66 (18%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSE--DVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
LYV + + T D ++ F ++ ++M D + KG F+TF +
Sbjct: 28 RLYVGSLHFNITEDMLRGIF----EPFGRIESIQLMM----DSETG--RSKGYGFITFSD 77
Query: 179 KENAEK 184
E A+K
Sbjct: 78 SECAKK 83
>2hpu_A NOSL protein; alpha beta topology, metal transport; NMR
{Achromobacter cycloclastes} SCOP: d.357.1.1 PDB: 2hq3_A
Length = 175
Score = 27.0 bits (59), Expect = 8.1
Identities = 5/26 (19%), Positives = 11/26 (42%)
Query: 173 FVTFDNKENAEKFLNENKDKNLKFNE 198
V F +++ A F+ + L +
Sbjct: 114 AVPFSSRDEAAAFVLAEGGQVLALAD 139
>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 = 26.0 bits (58), Expect = 8.2
Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 12/68 (17%)
Query: 119 AQSLYVKYIPVDATLDDIKDFFKKNTSE--DVKITNIIMRNYQDKLANQKKFKGSIFVTF 176
++ +Y+ IP D T + I D S V ++ D + KG F+ F
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLC----SNVGPVINLKMMF----DPQTG--RSKGYAFIEF 51
Query: 177 DNKENAEK 184
+ E++
Sbjct: 52 RDLESSAS 59
>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 = 26.0 bits (58), Expect = 8.5
Identities = 17/68 (25%), Positives = 25/68 (36%), Gaps = 12/68 (17%)
Query: 122 LYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
LYVK + + ++ F T K+ M + KG FV F + E
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKV----MME-------GGRSKGFGFVCFSSPE 66
Query: 181 NAEKFLNE 188
A K + E
Sbjct: 67 EATKAVTE 74
>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing
factor, RNA protein complex, SMN, binding protein-RNA
complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A
Length = 129
Score = 26.6 bits (59), Expect = 9.2
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 10/65 (15%)
Query: 121 SLYVKYIPVDATLDDIKDFFKK-NTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNK 179
L V + + T D+++ F K DV I + + Q + + +G FV F+N
Sbjct: 48 CLGVFGLSLYTTERDLREVFSKYGPIADVSI----VYDQQSR-----RSRGFAFVYFENV 98
Query: 180 ENAEK 184
++A++
Sbjct: 99 DDAKE 103
>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 = 26.1 bits (58), Expect = 9.3
Identities = 14/64 (21%), Positives = 21/64 (32%), Gaps = 10/64 (15%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSEDVKITNIIMRNYQDKLANQKKFKGSIFVTFDNKE 180
+LYV + D T I F S+ + M + +N FV F
Sbjct: 17 TLYVGNLSRDVTEVLILQLF----SQIGPCKSCKM--ITEHTSN----DPYCFVEFYEHR 66
Query: 181 NAEK 184
+A
Sbjct: 67 DAAA 70
>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 = 26.1 bits (58), Expect = 9.3
Identities = 10/44 (22%), Positives = 21/44 (47%)
Query: 305 EIVFIEFNVGEPTAFVRYKKENNAEAVLKALGSKEIVIKDVKVS 348
I+ + + AFV Y+K +A+ + L ++ +KV+
Sbjct: 39 NIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN 82
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 26.1 bits (58), Expect = 9.7
Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 12/66 (18%)
Query: 121 SLYVKYIPVDATLDDIKDFFKKNTSE--DVKITNIIMRNYQDKLANQKKFKGSIFVTFDN 178
L+V + +AT +DI D F +E ++K ++ + D+ KG V ++
Sbjct: 25 ILFVTGVHEEATEEDIHDKF----AEYGEIKNIHLNL----DRRTG--YLKGYTLVEYET 74
Query: 179 KENAEK 184
+ A+
Sbjct: 75 YKEAQA 80
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
0.310 0.130 0.349
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,904,424
Number of extensions: 366532
Number of successful extensions: 1630
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1492
Number of HSP's successfully gapped: 290
Length of query: 410
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 314
Effective length of database: 4,021,377
Effective search space: 1262712378
Effective search space used: 1262712378
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 58 (26.1 bits)