RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6597
(305 letters)
>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 = 40.8 bits (95), Expect = 5e-04
Identities = 33/162 (20%), Positives = 53/162 (32%), Gaps = 55/162 (33%)
Query: 64 YWAQPEEFSSLKVTKSTLEFVRLDGEIENRSKLLPVLARLDGRTIKLSGFADGLRVRATE 123
Y+ EE L T L + I+ ++ L L R K+ F GL +
Sbjct: 169 YF---EELRDLYQTYHVL----VGDLIKFSAETLSELIRTTLDAEKV--FTQGLNI---- 215
Query: 124 AKPDFPTRHDWDSYFRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRV 183
+W P PD YL ++P+ P L V
Sbjct: 216 --------LEWLE-----------NPSNTPDKDYLLSIPISC------P-------LIGV 243
Query: 184 FQ--NYGDIREV-DIPINDPYRAQMKPYISGMTLFSHAQSLI 222
Q +Y ++ P +++ Y+ G T H+Q L+
Sbjct: 244 IQLAHYVVTAKLLGF---TP--GELRSYLKGAT--GHSQGLV 278
Score = 37.7 bits (87), Expect = 0.005
Identities = 24/116 (20%), Positives = 39/116 (33%), Gaps = 35/116 (30%)
Query: 21 KILSAAYQLFLKPVARLNISVQIPELKI------TGKSLSNY--EVIEKIK--------Y 64
+L A L K + + N+S +++I G L + E+I
Sbjct: 430 HLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVK 489
Query: 65 WAQPEEFSSLKVTKSTLEFVRLDGEIENRSKLLPVLAR-LDGRTIKLSGFADGLRV 119
W +F + + L+F G S L + R DG G+RV
Sbjct: 490 WETTTQFKATHI----LDFGP--GGA---SGLGVLTHRNKDGT---------GVRV 527
Score = 36.2 bits (83), Expect = 0.016
Identities = 34/219 (15%), Positives = 59/219 (26%), Gaps = 75/219 (34%)
Query: 44 PELKITGKSLSNYEVIEKIKYWAQ--PEEFS-SLKVTKSTLEFVRLDGEIENRSKLLPV- 99
P L I+ L+ +V + + P + + V + G P
Sbjct: 337 PMLSISN--LTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLV-VSG--------PPQS 385
Query: 100 LARLDG--RTIKLSGFADGLRVRATEAKPDFPTR--------H----------------- 132
L L+ R K D R+ +E K F R H
Sbjct: 386 LYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVK 445
Query: 133 ---DWDS-------Y-FRDAKNMNEMKPGERPDTIY-LSNLPVKWFSTKARPNQPS---- 176
+++ Y D ++ + + + LPVKW + +
Sbjct: 446 NNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKW--ETTTQFKATHILD 503
Query: 177 ---------EAMLRRVFQNYGDIREV-----DIPINDPY 201
+ R G +R + DI +D Y
Sbjct: 504 FGPGGASGLGVLTHRNKDGTG-VRVIVAGTLDINPDDDY 541
Score = 35.4 bits (81), Expect = 0.023
Identities = 45/277 (16%), Positives = 81/277 (29%), Gaps = 105/277 (37%)
Query: 2 TSQEISKDVFSYCTDT---------SDAKILSAAYQL--FLK-PVAR------LNISVQI 43
T + D+ + +T K+ + + +L+ P L+I +
Sbjct: 179 TYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISC 238
Query: 44 PELKITGKSLSNYEVIEKIKYWAQPEEFSSLKVTKSTLEFVRLDGEIENRSKLLPVLARL 103
P + + L++Y V K+ + P E + L
Sbjct: 239 PLIGVI--QLAHYVVTAKLLGF-TPGEL----------------------------RSYL 267
Query: 104 DGRTIKLSGFADGLRVRATEAKPDFPTRHDWDSYFRDAKNMNEMKPGERPDTIYLSNLPV 163
G +G + GL A+ D W+S+F + ++ L
Sbjct: 268 KG----ATGHSQGLVTAVAIAETD-----SWESFFVSVRKA-------------ITVL-- 303
Query: 164 KWF-----STKARPNQPSEAMLRRVFQNYGDIREVDIPINDPYRAQMKPYISGMTLFSHA 218
F +A PN + ++ + E +P P M IS +T
Sbjct: 304 --FFIGVRCYEAYPNTSLPP---SILEDSLENNE-GVP--SP----MLS-ISNLTQ-EQV 349
Query: 219 QSLIFKTQLGKLPGTDHV--------TMFIQVDIISG 247
Q + KT LP V ++SG
Sbjct: 350 QDYVNKTN-SHLPAGKQVEISLVNGAKNL----VVSG 381
Score = 33.5 bits (76), Expect = 0.11
Identities = 33/190 (17%), Positives = 59/190 (31%), Gaps = 52/190 (27%)
Query: 131 RHDW---DSYFRDAKNMNEMKPGERPDTIYLSNLPVK--WFSTKARPNQPSEAMLRRVFQ 185
+ W D++F+D G I ++N PV + + E +F+
Sbjct: 1643 QDVWNRADNHFKDTY-------GFSILDIVINN-PVNLTIHFGGEKGKRIRENYSAMIFE 1694
Query: 186 NYGDIREVDIPINDPYRAQMKPYISGMTLFSHAQSLIFKTQLGKLPGTDHVTMFIQVDII 245
D + I Y F + L+ TQ F Q +
Sbjct: 1695 TIVDGKLKTEKIFKEINEHSTSYT-----FRSEKGLLSATQ------------FTQPALT 1737
Query: 246 SGMDYTTIIMLKASRKTSGGASKSMCVTYVVMCMA----MEISALHAL--HLTLDHAMPL 299
M+ LK+ G + A E +AL +L ++++ + +
Sbjct: 1738 L-MEKAAFEDLKSK-----GLIPADAT------FAGHSLGEYAALASLADVMSIESLVEV 1785
Query: 300 ---R-KTVQV 305
R T+QV
Sbjct: 1786 VFYRGMTMQV 1795
>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 = 37.1 bits (87), Expect = 7e-04
Identities = 8/47 (17%), Positives = 21/47 (44%), Gaps = 10/47 (21%)
Query: 152 RPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
+P +++ L + ++ + +F YG I+ +D+P+
Sbjct: 3 KPTKVHIGRLT---RNV-------TKDHIMEIFSTYGKIKMIDMPVE 39
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 36.8 bits (86), Expect = 9e-04
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 12/53 (22%)
Query: 143 NMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
M+ + P R +++ NLP S+ L R+F YG I +++I
Sbjct: 3 EMHNIPPKSR---LFIGNLP---------LKNVSKEDLFRIFSPYGHIMQINI 43
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 36.9 bits (86), Expect = 0.001
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
T Y+ N+P +EA L +FQN+G I +
Sbjct: 29 TAYIGNIP---HFA-------TEADLIPLFQNFGFILDFKHY 60
>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 = 36.8 bits (86), Expect = 0.001
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 14/58 (24%)
Query: 147 MKPGERPD---TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDPY 201
G D T+ + NL + T S LRRVF+ YG + +V IP +P+
Sbjct: 4 GSSGPDVDGMITLKVDNLT---YRT-------SPDSLRRVFEKYGRVGDVYIPR-EPH 50
>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 = 37.5 bits (87), Expect = 0.001
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 11/65 (16%)
Query: 134 WDSYFRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREV 193
D +FR N + K ++ T+Y+ NL F T +E + +F GDI+++
Sbjct: 21 RDQHFR-GDNEEQEKLLKKSCTLYVGNLS---FYT-------TEEQIYELFSKSGDIKKI 69
Query: 194 DIPIN 198
+ ++
Sbjct: 70 IMGLD 74
>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 = 36.4 bits (85), Expect = 0.002
Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 10/51 (19%)
Query: 148 KPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
+++ NL +++ SE L ++F YG + E+ PI+
Sbjct: 3 SGSSGSGRLFVRNLS---YTS-------SEEDLEKLFSAYGPLSELHYPID 43
>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 = 36.1 bits (84), Expect = 0.002
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
T+Y+ L +E LR F +G+IR + +
Sbjct: 14 TLYVGGLGDTI----------TETDLRNHFYQFGEIRTITVV 45
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 38.2 bits (88), Expect = 0.002
Identities = 17/83 (20%), Positives = 30/83 (36%), Gaps = 3/83 (3%)
Query: 114 ADGLRVRATEAKPDFPTRHDWDSYFRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPN 173
D ++ D R + Y D + + + T+Y+ + S +P
Sbjct: 97 EDIGKLALRTEVLDCFGREKFADYREDMGGIGSFRKKNK--TLYVGGIDGALNSKHLKPA 154
Query: 174 QPSEAMLRRVFQNYGDIREVDIP 196
Q E+ +R VF GDI +
Sbjct: 155 Q-IESRIRFVFSRLGDIDRIRYV 176
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 35.8 bits (83), Expect = 0.003
Identities = 7/62 (11%), Positives = 19/62 (30%), Gaps = 9/62 (14%)
Query: 135 DSYFRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVD 194
+ + N+ P +++ NL ++ + +F YG +
Sbjct: 9 SLKLQASNVTNKNDPKSINSRVFIGNLN---------TALVKKSDVETIFSKYGRVAGCS 59
Query: 195 IP 196
+
Sbjct: 60 VH 61
>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 = 35.8 bits (83), Expect = 0.003
Identities = 13/48 (27%), Positives = 18/48 (37%), Gaps = 10/48 (20%)
Query: 149 PGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
G IY+ NLP + VF YG IR++D+
Sbjct: 18 AGNNDCRIYVGNLP---PDI-------RTKDIEDVFYKYGAIRDIDLK 55
>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 = 35.3 bits (82), Expect = 0.003
Identities = 11/42 (26%), Positives = 19/42 (45%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
+++ NLP +E +R++F+ YG EV I
Sbjct: 17 RLFVGNLP---PDI-------TEEEMRKLFEKYGKAGEVFIH 48
>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related
protein, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 35.4 bits (82), Expect = 0.004
Identities = 7/42 (16%), Positives = 17/42 (40%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
T+Y + ++ ++R+ F +G I E+ +
Sbjct: 27 TVYCGGIA---SGL-------TDQLMRQTFSPFGQIMEIRVF 58
>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 = 34.9 bits (81), Expect = 0.004
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 10/47 (21%)
Query: 149 PGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
G+ +++ N+ + + LR F+ YG + E DI
Sbjct: 6 SGKASTKLHVGNIS---PTC-------TNQELRAKFEEYGPVIECDI 42
>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 = 35.9 bits (83), Expect = 0.004
Identities = 13/70 (18%), Positives = 24/70 (34%), Gaps = 10/70 (14%)
Query: 129 PTRHDWDSYFRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYG 188
+ R ++++ + + + L T +E LR VF YG
Sbjct: 22 ASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLS---LYT-------TERDLREVFSKYG 71
Query: 189 DIREVDIPIN 198
I +V I +
Sbjct: 72 PIADVSIVYD 81
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 34.7 bits (80), Expect = 0.008
Identities = 10/61 (16%), Positives = 25/61 (40%), Gaps = 12/61 (19%)
Query: 138 FRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPI 197
FR + + E + + +T+Y+ + + +LR F +G+I ++ +
Sbjct: 24 FRRSDSFPERRAPRKGNTLYVYGEDM------------TPTLLRGAFSPFGNIIDLSMDP 71
Query: 198 N 198
Sbjct: 72 P 72
>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 = 34.2 bits (79), Expect = 0.010
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 10/53 (18%)
Query: 141 AKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREV 193
++ K T+ NL F+ +E L+ VF++ +IR V
Sbjct: 4 LEDPCTSKKVRAARTLLAKNLS---FNI-------TEDELKEVFEDALEIRLV 46
>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 = 33.7 bits (78), Expect = 0.011
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 12/54 (22%)
Query: 145 NEMKPGERPD--TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
+ M G P T+Y+SNLP FS + L R+F YG + +V I
Sbjct: 6 SGMSGGLAPSKSTVYVSNLP---FSL-------TNNDLYRIFSKYGKVVKVTIM 49
>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 = 33.7 bits (78), Expect = 0.014
Identities = 11/58 (18%), Positives = 22/58 (37%), Gaps = 12/58 (20%)
Query: 143 NMNEMKPGERPD--TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
+ + D TI ++NL T E L+ +F+ +G I + + +
Sbjct: 3 SGSSGPNRRADDNATIRVTNLS---EDT-------RETDLQELFRPFGSISRIYLAKD 50
>2kn4_A Immunoglobulin G-binding protein G, splicing FACT
arginine/serine-rich 2, S35, splicing factor SC35,; RRM
domain, cell WALL; NMR {Streptococcus SP}
Length = 158
Score = 34.8 bits (80), Expect = 0.014
Identities = 23/110 (20%), Positives = 35/110 (31%), Gaps = 18/110 (16%)
Query: 95 KLLPVLARLDGR-TIKLSGFADGLRVRATEAKPDFPTRHDWDSYFRDAKNMNEMKPGERP 153
KL+ L G T + A +V A + + E
Sbjct: 4 KLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHH 63
Query: 154 D-------TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
++ + NL + T S LRRVF+ YG + +V IP
Sbjct: 64 HMDVEGMTSLKVDNLT---YRT-------SPDTLRRVFEKYGRVGDVYIP 103
>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 = 33.4 bits (77), Expect = 0.015
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 176 SEAMLRRVFQNYGDIREVDIPINDPY 201
S A L R F +G IR +D D +
Sbjct: 30 SLAALAREFDRFGSIRTIDHVKGDSF 55
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 33.9 bits (78), Expect = 0.017
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 14/66 (21%)
Query: 139 RDAKNMNEMKPGERPD---TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
+M+ +P + ++ + NL + T S LRRVF+ YG + +V I
Sbjct: 30 MGRGSMSYGRPPPDVEGMTSLKVDNLT---YRT-------SPDTLRRVFEKYGRVGDVYI 79
Query: 196 PINDPY 201
P D Y
Sbjct: 80 PR-DRY 84
>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 = 0.021
Identities = 8/47 (17%), Positives = 19/47 (40%), Gaps = 10/47 (21%)
Query: 153 PDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIND 199
+ + L + E L+ + + YG++ EV+I ++
Sbjct: 6 LKEVTFARLN---DNV-------RETFLKDMCRKYGEVEEVEILLHP 42
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 32.9 bits (76), Expect = 0.021
Identities = 10/44 (22%), Positives = 20/44 (45%), Gaps = 10/44 (22%)
Query: 153 PDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
+Y+ +L F+ +E MLR +F+ +G I + +
Sbjct: 5 SSGLYVGSLH---FNI-------TEDMLRGIFEPFGKIDNIVLM 38
>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 = 33.0 bits (76), Expect = 0.021
Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 11/58 (18%)
Query: 145 NEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDPYR 202
+ P +++SN+P F + LR++F +G I +V+I I +
Sbjct: 7 GNSESKSTPKRLHVSNIP---FRF-------RDPDLRQMFGQFGKILDVEI-IFNERG 53
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 33.0 bits (76), Expect = 0.027
Identities = 13/45 (28%), Positives = 17/45 (37%), Gaps = 10/45 (22%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDP 200
+Y+ NL + L R F YG +R V I N P
Sbjct: 3 VYVGNLG---TGA-------GKGELERAFSYYGPLRTVWIARNPP 37
>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 = 33.0 bits (76), Expect = 0.028
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 145 NEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
N K P +Y+ +L F+ +E MLR +F+ +G I + +
Sbjct: 18 NLQKGSAGPMRLYVGSLH---FNI-------TEDMLRGIFEPFGRIESIQLM 59
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 32.7 bits (75), Expect = 0.029
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 9/48 (18%)
Query: 148 KPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
+ +++ NLP S+ L R+F YG I +++I
Sbjct: 17 RGSHMKSRLFIGNLP---------LKNVSKEDLFRIFSPYGHIMQINI 55
>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 = 32.6 bits (75), Expect = 0.030
Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 10/40 (25%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
+++ NLP +E +R +F+ YG + E DI
Sbjct: 11 LFIGNLP---REA-------TEQEIRSLFEQYGKVLECDI 40
>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 = 32.6 bits (75), Expect = 0.033
Identities = 11/73 (15%), Positives = 24/73 (32%), Gaps = 15/73 (20%)
Query: 123 EAKPDFPTRHDWDSYFRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRR 182
+ +HD E + +SNL F S+A ++
Sbjct: 4 PKQLPDKWQHD-----LFDSGFGGGAGVETGGKLLVSNLD---FGV-------SDADIQE 48
Query: 183 VFQNYGDIREVDI 195
+F +G +++ +
Sbjct: 49 LFAEFGTLKKAAV 61
>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 = 0.035
Identities = 10/96 (10%), Positives = 29/96 (30%), Gaps = 20/96 (20%)
Query: 103 LDGRTIKLSGFADG--LRVRATEAKPDFPTRHDWDSYFRDAKNMNEMKPGERPDTIYLSN 160
DG G L++R P + S + + +++
Sbjct: 70 FDGIIF------QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDS--AHKLFIGG 121
Query: 161 LPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
LP ++ ++ + ++G ++ ++
Sbjct: 122 LPNYL----------NDDQVKELLTSFGPLKAFNLV 147
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 32.6 bits (75), Expect = 0.036
Identities = 11/66 (16%), Positives = 25/66 (37%), Gaps = 11/66 (16%)
Query: 131 RHDWDSYFRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDI 190
R D+DS +D + E ++++ + +E + F YG+I
Sbjct: 2 REDYDSVEQDGDEPGPQRSVE-GWILFVTGVH---EEA-------TEEDIHDKFAEYGEI 50
Query: 191 REVDIP 196
+ + +
Sbjct: 51 KNIHLN 56
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 32.2 bits (74), Expect = 0.039
Identities = 12/49 (24%), Positives = 17/49 (34%), Gaps = 10/49 (20%)
Query: 149 PGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPI 197
+ + + L T +E LR VF YG I +V I
Sbjct: 11 NPDPNCCLGVFGLS---LYT-------TERDLREVFSKYGPIADVSIVY 49
>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 = 32.2 bits (74), Expect = 0.047
Identities = 11/56 (19%), Positives = 20/56 (35%), Gaps = 12/56 (21%)
Query: 139 RDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVD 194
+ + + T+ LSNL +S +E L+ VF+ I+
Sbjct: 3 SGSSGNSTWSGESK--TLVLSNLS---YSA-------TEETLQEVFEKATFIKVPQ 46
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 32.3 bits (74), Expect = 0.050
Identities = 9/61 (14%), Positives = 19/61 (31%), Gaps = 12/61 (19%)
Query: 136 SYFRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
+ E + +++ P E+ L +F +G ++EV I
Sbjct: 16 PRGSHMHHRQEGELSNT--RLFVRPFP---LDV-------QESELNEIFGPFGPMKEVKI 63
Query: 196 P 196
Sbjct: 64 L 64
>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 = 31.8 bits (73), Expect = 0.051
Identities = 8/41 (19%), Positives = 17/41 (41%), Gaps = 10/41 (24%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
I++ N+ + + LR +F+ G + E D+
Sbjct: 11 KIFVGNVS---AAC-------TSQELRSLFERRGRVIECDV 41
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 33.3 bits (76), Expect = 0.053
Identities = 20/110 (18%), Positives = 36/110 (32%), Gaps = 12/110 (10%)
Query: 86 LDGEIENRSKLLPVLARLDGRTIKLSGFADGLRVRATEAKPDFPTRHDWDSYFRDAKNMN 145
LD +I ++ + R G A G R R P W
Sbjct: 23 LD-DIIKLNRNQRRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQH-DLFDSGCG 80
Query: 146 EMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
+ E + +SNL F S+A ++ +F +G +++ +
Sbjct: 81 GGEGVETGAKLLVSNLD---FGV-------SDADIQELFAEFGTLKKAAV 120
>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 = 32.3 bits (74), Expect = 0.054
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 10/43 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPI 197
T+++ NL F + E L V Q +GD++ V + +
Sbjct: 17 TVFIRNLS---FDS-------EEEALGEVLQQFGDLKYVRVVL 49
>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 = 32.3 bits (74), Expect = 0.054
Identities = 11/66 (16%), Positives = 25/66 (37%), Gaps = 11/66 (16%)
Query: 131 RHDWDSYFRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDI 190
R D+DS +D + E ++++ + +E + F YG+I
Sbjct: 1 REDYDSVEQDGDEPGPQRSVE-GWILFVTGVH---EEA-------TEEDIHDKFAEYGEI 49
Query: 191 REVDIP 196
+ + +
Sbjct: 50 KNIHLN 55
>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 = 32.4 bits (74), Expect = 0.056
Identities = 7/44 (15%), Positives = 17/44 (38%), Gaps = 10/44 (22%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
++Y+ N+ + + + L F + G I + I +
Sbjct: 38 SVYVGNVD---YGS-------TAQDLEAHFSSCGSINRITILCD 71
>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 = 32.3 bits (74), Expect = 0.056
Identities = 9/48 (18%), Positives = 21/48 (43%), Gaps = 10/48 (20%)
Query: 148 KPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
+ E + +SNL F S+A ++ +F +G +++ +
Sbjct: 30 EGVETGAKLLVSNLD---FGV-------SDADIQELFAEFGTLKKAAV 67
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 32.3 bits (74), Expect = 0.056
Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 11/72 (15%)
Query: 131 RHDWDSYFRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDI 190
H S + + +P +++SN+P F + LR++F +G I
Sbjct: 7 HHHHSSGLVPRGSHMNTENKSQPKRLHVSNIP---FRF-------RDPDLRQMFGQFGKI 56
Query: 191 REVDIPINDPYR 202
+V+I I +
Sbjct: 57 LDVEI-IFNERG 67
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 32.1 bits (72), Expect = 0.060
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 161 LPVKWFSTKARPNQP--SEAMLRRVFQNYGDIREVDIPINDPYRA 203
L +KW K ++ S+ +L R+ Q YG++ + + P A
Sbjct: 13 LKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTA 57
>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 = 32.2 bits (73), Expect = 0.063
Identities = 9/30 (30%), Positives = 13/30 (43%)
Query: 172 PNQPSEAMLRRVFQNYGDIREVDIPINDPY 201
N S L V + G + + +P N PY
Sbjct: 36 GNGVSRNQLLPVLEKCGLVDALLMPPNKPY 65
>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 = 33.4 bits (77), Expect = 0.068
Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 9/54 (16%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDPYRAQMKPY 208
I + NL E +LR F+ +G I +++IP +
Sbjct: 212 EIMIRNLS---------TELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCC 256
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 31.8 bits (73), Expect = 0.071
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 10/46 (21%)
Query: 151 ERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
+++ L F T +E L +VF YG I EV +
Sbjct: 10 SDEGKLFVGGLS---FDT-------NEQSLEQVFSKYGQISEVVVV 45
>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar
mRNA localization, translation; 1.90A {Drosophila
melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A
Length = 165
Score = 32.9 bits (75), Expect = 0.071
Identities = 14/88 (15%), Positives = 35/88 (39%), Gaps = 15/88 (17%)
Query: 115 DGLRVRATEAKPDFPTRHDWDSYFR-DAKNMNEMKPGERP----DTIYLSNLPVKWFSTK 169
+ D TR SY R ++ +E++PG + ++++++
Sbjct: 29 KAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIH---EEA- 84
Query: 170 ARPNQPSEAMLRRVFQNYGDIREVDIPI 197
E ++ F +YG+I+ + + +
Sbjct: 85 ------QEDEIQEKFCDYGEIKNIHLNL 106
>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 = 31.9 bits (73), Expect = 0.073
Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 10/50 (20%)
Query: 147 MKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
M + P +++ L T +E ML+ VF +G I EV +
Sbjct: 1 MVEADHPGKLFIGGLN---RET-------NEKMLKAVFGKHGPISEVLLI 40
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 31.0 bits (71), Expect = 0.084
Identities = 9/42 (21%), Positives = 16/42 (38%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
+Y+ L + +L F +GDI ++ IP
Sbjct: 9 VLYVGGLA---EEV-------DDKVLHAAFIPFGDITDIQIP 40
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 32.1 bits (73), Expect = 0.087
Identities = 10/60 (16%), Positives = 18/60 (30%), Gaps = 12/60 (20%)
Query: 139 RDAKNMNEMKPGERPD--TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
+ G +Y+ L + +L F +GDI ++ IP
Sbjct: 47 DGGSGGSGGSGGSATTKRVLYVGGLA---EEV-------DDKVLHAAFIPFGDITDIQIP 96
>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 = 30.9 bits (71), Expect = 0.090
Identities = 8/42 (19%), Positives = 14/42 (33%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
+IY+ N+ + + L F G + V I
Sbjct: 8 SIYVGNVD---YGA-------TAEELEAHFHGCGSVNRVTIL 39
>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 = 30.7 bits (70), Expect = 0.12
Identities = 11/51 (21%), Positives = 17/51 (33%), Gaps = 11/51 (21%)
Query: 150 GERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIRE-VDIPIND 199
P I + N+P F+ S + F Y I V + N+
Sbjct: 12 KPGPTVIKVQNMP---FTV-------SIDEILDFFYGYQVIPGSVCLKYNE 52
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 30.4 bits (69), Expect = 0.13
Identities = 8/45 (17%), Positives = 17/45 (37%), Gaps = 4/45 (8%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIND 199
I + N+P + + ++ ++F +G I P D
Sbjct: 3 VIVVDNVPQVGPDRLEK----LKNVIHKIFSKFGKITNDFYPEED 43
>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 = 30.7 bits (70), Expect = 0.15
Identities = 7/44 (15%), Positives = 17/44 (38%), Gaps = 12/44 (27%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
T+Y+ + + +LR F +G+I ++ +
Sbjct: 17 TLYVYGEDM------------TPTLLRGAFSPFGNIIDLSMDPP 48
>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 = 30.7 bits (70), Expect = 0.16
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 11/46 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDP 200
+++ NL FST +E L+ VF G I+ I
Sbjct: 7 GLFIKNLN---FST-------TEETLKGVFSKVGAIKSCTI-SKKK 41
>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 = 31.4 bits (71), Expect = 0.16
Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 13/57 (22%)
Query: 146 EMKPGERPD--TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDP 200
M P +Y+ NL N ++ L R F YG +R V + +P
Sbjct: 64 HMHRDSCPLDCKVYVGNLG----------NNGNKTELERAFGYYGPLRSVWVA-RNP 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 = 30.3 bits (69), Expect = 0.18
Identities = 11/51 (21%), Positives = 17/51 (33%), Gaps = 11/51 (21%)
Query: 150 GERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIRE-VDIPIND 199
P I + N+P F+ S + F Y I V + N+
Sbjct: 12 KPGPTIIKVQNMP---FTV-------SIDEILDFFYGYQVIPGSVCLKYNE 52
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 30.5 bits (69), Expect = 0.20
Identities = 8/45 (17%), Positives = 17/45 (37%), Gaps = 4/45 (8%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIND 199
I + N+P + + ++ ++F +G I P D
Sbjct: 17 VIVVDNVPQVGPDRLEK----LKNVIHKIFSKFGKITNDFYPEED 57
>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 = 30.1 bits (68), Expect = 0.24
Identities = 7/44 (15%), Positives = 13/44 (29%), Gaps = 10/44 (22%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
+++ L EA L + +G I V +
Sbjct: 17 VVHVRGLCESV----------VEADLVEALEKFGTICYVMMMPF 50
>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein
complex, EXON junct complex, signaling protein; 1.85A
{Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B*
2j0s_D* 2xb2_D*
Length = 110
Score = 30.3 bits (69), Expect = 0.24
Identities = 8/61 (13%), Positives = 27/61 (44%), Gaps = 14/61 (22%)
Query: 140 DAKNMNEMKPGERP----DTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
++ +E++PG + ++++++ E ++ F +YG+I+ + +
Sbjct: 9 RNEDDDELEPGPQRSVEGWILFVTSIH---EEA-------QEDEIQEKFCDYGEIKNIHL 58
Query: 196 P 196
Sbjct: 59 N 59
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 30.1 bits (68), Expect = 0.24
Identities = 8/45 (17%), Positives = 18/45 (40%), Gaps = 4/45 (8%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIND 199
I ++ PV + + L +F G + ++ PI++
Sbjct: 8 YIVVNGAPV----IPSAKVPVLKKALTSLFSKAGKVVNMEFPIDE 48
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 30.6 bits (69), Expect = 0.25
Identities = 10/69 (14%), Positives = 27/69 (39%), Gaps = 12/69 (17%)
Query: 142 KNMNEMKPGERPD------TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
++M+ G P + ++N+ + K + L + + GDI ++ +
Sbjct: 12 QHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQAL------LYALASSQGDILDIVV 65
Query: 196 PINDPYRAQ 204
++D +
Sbjct: 66 DLSDDNSGK 74
>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 = 30.3 bits (69), Expect = 0.26
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 11/51 (21%)
Query: 149 PGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIND 199
P P T +L NLP + +E ++ F+ I V +P
Sbjct: 11 PKSPPYTAFLGNLP---YDV-------TEESIKEFFRGLN-ISAVRLPREP 50
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 30.0 bits (68), Expect = 0.26
Identities = 8/50 (16%), Positives = 13/50 (26%), Gaps = 10/50 (20%)
Query: 148 KPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPI 197
DTI L N+ T + Y + +I +
Sbjct: 4 HHHHHMDTIILRNIA---PHT-------VVDSIMTALSPYASLAVNNIRL 43
>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 = 31.0 bits (71), Expect = 0.28
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 10/47 (21%)
Query: 148 KPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVD 194
K T+ NL F+ +E L+ VF++ +IR V
Sbjct: 94 KKVRAARTLLAKNLS---FNI-------TEDELKEVFEDALEIRLVS 130
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA,
spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1
d.58.7.1
Length = 198
Score = 31.0 bits (70), Expect = 0.28
Identities = 19/103 (18%), Positives = 37/103 (35%), Gaps = 14/103 (13%)
Query: 102 RLDGRTIKLSGFADGLRVRATEAKPDFPTRHDWDSYF--RDAKNMNEMKPGERPD--TIY 157
+L G+ I+++ E + D D+ + R K ++ P T++
Sbjct: 65 KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLH 124
Query: 158 LSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDP 200
LSN+P SE L+ +F + G + +
Sbjct: 125 LSNIP----------PSVSEEDLKVLFSSNGGVVKGFKFFQKD 157
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 29.9 bits (68), Expect = 0.29
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 11/48 (22%)
Query: 149 PGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
P E P T Y+ NLP F+T + + +F++ IR V +
Sbjct: 11 PTEPPYTAYVGNLP---FNT-------VQGDIDAIFKDLS-IRSVRLV 47
>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 = 29.9 bits (68), Expect = 0.30
Identities = 6/42 (14%), Positives = 16/42 (38%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
+YL ++P + +E + + N G + + +
Sbjct: 4 VVYLGSIP---YDQ-------TEEQILDLCSNVGPVINLKMM 35
>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 = 29.9 bits (68), Expect = 0.34
Identities = 7/42 (16%), Positives = 16/42 (38%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
+++ NL + +E +L + F +G + V
Sbjct: 13 VLFVRNLA---NTV-------TEEILEKAFSQFGKLERVKKL 44
>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 = 29.5 bits (67), Expect = 0.38
Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 11/51 (21%)
Query: 149 PGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIND 199
P P T +L NLP + +E ++ F+ I V +P
Sbjct: 15 PKSPPYTAFLGNLP---YDV-------TEESIKEFFRGLN-ISAVRLPREP 54
>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 = 31.4 bits (70), Expect = 0.39
Identities = 22/153 (14%), Positives = 46/153 (30%), Gaps = 59/153 (38%)
Query: 147 MKPGERPDTIYLSNLPVKWFSTK--ARPNQPSEAMLRRVFQNYGDIREVDIPINDPY--- 201
++ R + Y K+ + QPS M+ R++ D D + Y
Sbjct: 83 VEEVLRIN--Y------KFLMSPIKTEQRQPS--MMTRMYIEQRDRLYNDNQVFAKYNVS 132
Query: 202 RAQMKPYISGMTLFSHAQSLIFKTQLGKLPGTDHVTMFIQVDIISGMDYTTIIMLKASRK 261
R Q + + L +L +V +I G+
Sbjct: 133 RLQPYLKL--------------RQALLELRPAKNV-------LIDGV------------- 158
Query: 262 TSGGASKSMCVTYVVMCMAMEISALHALHLTLD 294
G+ K+ +A+++ + + +D
Sbjct: 159 --LGSGKT--------WVALDVCLSYKVQCKMD 181
>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 = 29.6 bits (67), Expect = 0.41
Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 10/49 (20%)
Query: 147 MKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
++ G T++++NL + L+ VF G + DI
Sbjct: 9 LQAGRLGSTVFVANLD---YKV-------GWKKLKEVFSMAGVVVRADI 47
>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 = 29.5 bits (67), Expect = 0.42
Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 12/52 (23%)
Query: 147 MKPGERPD--TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
M P + T+++ NL E +L +F G + +V I
Sbjct: 8 MFPAQEEADRTVFVGNLE---ARV-------REEILYELFLQAGPLTKVTIC 49
>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 = 29.6 bits (67), Expect = 0.43
Identities = 11/50 (22%), Positives = 16/50 (32%), Gaps = 10/50 (20%)
Query: 148 KPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPI 197
PGE +YL NL E L +F + + + I
Sbjct: 20 NPGEPNKVLYLKNLS---PRVT-------ERDLVSLFARFQEKKGPPIQF 59
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} PDB: 2dgq_A
Length = 106
Score = 29.2 bits (66), Expect = 0.48
Identities = 8/30 (26%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 172 PNQPSEAMLRRVFQNYGDIREVDIPINDPY 201
P E L+ +F+ +G I E+ + + D +
Sbjct: 22 PRNLDEKDLKPLFEEFGKIYELTV-LKDRF 50
>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49)
(SAP 49) (SF3B50)...; structure genomics,RRM
domain,splicing factor 3B; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 105
Score = 29.2 bits (66), Expect = 0.57
Identities = 9/42 (21%), Positives = 15/42 (35%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
T+Y+ L SE +L +F G + +P
Sbjct: 17 TVYVGGLD---EKV-------SEPLLWELFLQAGPVVNTHMP 48
>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 = 28.6 bits (65), Expect = 0.65
Identities = 8/42 (19%), Positives = 15/42 (35%), Gaps = 10/42 (23%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPI 197
+Y+ L T ++ L ++ Q YG I +
Sbjct: 8 LYIRGLQ---PGT-------TDQDLVKLCQPYGKIVSTKAIL 39
>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 = 28.8 bits (65), Expect = 0.72
Identities = 7/42 (16%), Positives = 16/42 (38%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
T+Y+ NL +E ++ ++F G + +
Sbjct: 17 TLYVGNLS---RDV-------TEVLILQLFSQIGPCKSCKMI 48
>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 = 30.1 bits (67), Expect = 0.74
Identities = 6/69 (8%), Positives = 20/69 (28%), Gaps = 10/69 (14%)
Query: 131 RHDWDSYFRDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDI 190
++ F + + + + ++ N P++ +E + G
Sbjct: 101 SESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEV----------TEENFFEICDELGVK 150
Query: 191 REVDIPIND 199
R + +
Sbjct: 151 RPTSVKVFS 159
>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 = 28.8 bits (65), Expect = 0.74
Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 16/58 (27%)
Query: 140 DAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPI 197
D M+ +K +Y+ NL ST SE M+ + F N +
Sbjct: 8 DEDTMSSVK------ILYVRNLM---LST-------SEEMIEKEFNNIKPGAVERVKK 49
>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 = 28.8 bits (65), Expect = 0.74
Identities = 6/41 (14%), Positives = 14/41 (34%), Gaps = 10/41 (24%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
+Y+ NL + + LR++F + +
Sbjct: 10 KLYIGNLS---PAV-------TADDLRQLFGDRKLPLAGQV 40
>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 = 28.8 bits (65), Expect = 0.90
Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 10/41 (24%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
+++ L + SE + R+FQ +G I E +
Sbjct: 18 LFVGMLNKQQ----------SEEDVLRLFQPFGVIDECTVL 48
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 28.1 bits (63), Expect = 1.1
Identities = 7/42 (16%), Positives = 14/42 (33%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
++++S P A L F +G + V +
Sbjct: 10 SVFVSGFP---RGV-------DSAQLSEYFLAFGPVASVVMD 41
>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif,
C-terminal helix, N-terminal helix, RNA binding protein;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 28.4 bits (64), Expect = 1.1
Identities = 6/42 (14%), Positives = 17/42 (40%), Gaps = 10/42 (23%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
++++ N+P + +E L+ +F G + +
Sbjct: 10 SVFVGNIP---YEA-------TEEQLKDIFSEVGPVVSFRLV 41
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 28.5 bits (64), Expect = 1.1
Identities = 6/41 (14%), Positives = 14/41 (34%), Gaps = 10/41 (24%)
Query: 152 RPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIRE 192
+TI++ L + + + F+ G I+
Sbjct: 6 DNNTIFVQGLG---ENV-------TIESVADYFKQIGIIKT 36
>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 = 28.0 bits (63), Expect = 1.4
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 13/57 (22%)
Query: 143 NMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIND 199
++ E K P+T+++ + E +R F YG ++EV I I D
Sbjct: 1 SLPEGKIM--PNTVFVGGID---VRM-------DETEIRSFFARYGSVKEVKI-ITD 44
>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 = 28.2 bits (63), Expect = 1.7
Identities = 6/55 (10%), Positives = 19/55 (34%), Gaps = 11/55 (20%)
Query: 146 EMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIRE-VDIPIND 199
E +++N+P FS ++ + + + V + +++
Sbjct: 8 EGDVNSAKVCAHITNIP---FSI-------TKMDVLQFLEGIPVDENAVHVLVDN 52
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 28.3 bits (63), Expect = 1.7
Identities = 8/57 (14%), Positives = 19/57 (33%), Gaps = 10/57 (17%)
Query: 141 AKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPI 197
A R +Y+ + + T ++ L +V ++ G V++
Sbjct: 43 AILYTYSGLRNRRAAVYVGSFS---WWT-------TDQQLIQVIRSIGVYDVVELKF 89
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 28.3 bits (63), Expect = 1.8
Identities = 9/53 (16%), Positives = 15/53 (28%), Gaps = 11/53 (20%)
Query: 148 KPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIRE-VDIPIND 199
P E +YL LP F + F+ + + + I
Sbjct: 20 SPHEAGFCVYLKGLP---FEA-------ENKHVIDFFKKLDIVEDSIYIAYGP 62
>3ne5_B Cation efflux system protein CUSB; transmembrane helix, metal
transport; 2.90A {Escherichia coli} PDB: 3ooc_A 3opo_A
3ow7_A 3h9i_A 3h94_A 3h9t_B
Length = 413
Score = 29.0 bits (65), Expect = 1.8
Identities = 11/49 (22%), Positives = 17/49 (34%), Gaps = 2/49 (4%)
Query: 75 KVTKSTL-EFVRLDGEIE-NRSKLLPVLARLDGRTIKLSGFADGLRVRA 121
VT+ L + N + V AR G K+ G +V+
Sbjct: 98 TVTRGPLTFAQSFPANVSYNEYQYAIVQARAAGFIDKVYPLTVGDKVQK 146
>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 = 27.6 bits (62), Expect = 2.0
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 11/49 (22%)
Query: 148 KPGERPDT-IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
K E+ T +Y+SNLP+ E L + + +G + I
Sbjct: 19 KQQEQDPTNLYISNLPLSM----------DEQELENMLKPFGQVISTRI 57
>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 = 28.3 bits (63), Expect = 2.1
Identities = 9/60 (15%), Positives = 18/60 (30%), Gaps = 11/60 (18%)
Query: 139 RDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
R + + +++ LP + +E + F +R V I I
Sbjct: 32 RGSGDSEFTVQSTTGHCVHMRGLP---YKA-------TENDIYNFFSPLNPVR-VHIEIG 80
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 27.2 bits (61), Expect = 2.1
Identities = 11/46 (23%), Positives = 16/46 (34%), Gaps = 10/46 (21%)
Query: 150 GERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
I++ NLP F + ML+ F G + DI
Sbjct: 5 SSGACQIFVRNLP---FDF-------TWKMLKDKFNECGHVLYADI 40
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 27.5 bits (61), Expect = 2.2
Identities = 5/41 (12%), Positives = 14/41 (34%), Gaps = 10/41 (24%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
I++ LP +E + + +G + + +
Sbjct: 18 VIHIRKLP----------IDVTEGEVISLGLPFGKVTNLLM 48
>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 = 27.8 bits (62), Expect = 2.4
Identities = 11/61 (18%), Positives = 22/61 (36%), Gaps = 11/61 (18%)
Query: 139 RDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPIN 198
+ + + ++ +P + E LR++F+ YG I V I +
Sbjct: 28 QHIPPTQMNPEPDVLRNLMVNYIP---TTV-------DEVQLRQLFERYGPIESVKI-VC 76
Query: 199 D 199
D
Sbjct: 77 D 77
>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 = 28.4 bits (63), Expect = 2.4
Identities = 19/98 (19%), Positives = 37/98 (37%), Gaps = 14/98 (14%)
Query: 102 RLDGRTIKLSGFADGLRVRATEAKPDFPTRHDWDSYF--RDAKNMNEMKPGERP--DTIY 157
+L G+ I+++ E + D D+ + R K ++ P T++
Sbjct: 96 KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLH 155
Query: 158 LSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
LSN+P SE L+ +F + G + +
Sbjct: 156 LSNIPPSV----------SEEDLKVLFSSNGGVVKGFK 183
>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 = 28.3 bits (64), Expect = 2.4
Identities = 6/57 (10%), Positives = 14/57 (24%), Gaps = 10/57 (17%)
Query: 140 DAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
D K ++ I++ + F +G I + +
Sbjct: 74 DPKRAIPRDEQDKTGKIFVGGIG---PDV-------RPKEFEEFFSQWGTIIDAQLM 120
>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 = 27.3 bits (61), Expect = 2.6
Identities = 7/52 (13%), Positives = 15/52 (28%), Gaps = 13/52 (25%)
Query: 144 MNEMKPGERP---DTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIRE 192
M +TI++ L + + + F+ G I+
Sbjct: 1 MGHHHHHHSHSDNNTIFVQGLG---ENV-------TIESVADYFKQIGIIKT 42
>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 = 28.5 bits (64), Expect = 2.8
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 14/54 (25%)
Query: 147 MKPGERPD----TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
+KPGE+ +++ NLP +E +R+F+ YG+ EV I
Sbjct: 12 LKPGEKTYTQRCRLFVGNLP----------TDITEEDFKRLFERYGEPSEVFIN 55
>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 = 27.5 bits (61), Expect = 3.0
Identities = 13/59 (22%), Positives = 18/59 (30%), Gaps = 10/59 (16%)
Query: 139 RDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPI 197
+PGE IY+ NL + E L+ +F Y D I
Sbjct: 31 ETLSVFRSYEPGEPNCRIYVKNLA---KHVQ-------EKDLKYIFGRYVDFSSETQRI 79
>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 = 27.6 bits (62), Expect = 3.3
Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 10/40 (25%)
Query: 156 IYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
+++ + K +E +R +F ++G I E I
Sbjct: 98 LFIGMISKKC----------TENDIRVMFSSFGQIEECRI 127
>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 = 26.8 bits (60), Expect = 4.0
Identities = 7/50 (14%), Positives = 15/50 (30%), Gaps = 10/50 (20%)
Query: 146 EMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDI 195
E P +++ NL + S A L+ ++ +
Sbjct: 10 EGSESTTPFNLFIGNLN---PNK-------SVAELKVAISELFAKNDLAV 49
>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 = 26.4 bits (59), Expect = 4.2
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 176 SEAMLRRVFQNYGDIREVDIP 196
+E LR F YGD+ +V IP
Sbjct: 18 TEDELREFFSQYGDVMDVFIP 38
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 27.3 bits (61), Expect = 5.1
Identities = 7/58 (12%), Positives = 20/58 (34%), Gaps = 10/58 (17%)
Query: 139 RDAKNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIP 196
+ + IY++++ S+ ++ VF+ +G I+ +
Sbjct: 111 AQPIIDQLAEEARAFNRIYVASVH---QDL-------SDDDIKSVFEAFGKIKSATLA 158
Score = 27.3 bits (61), Expect = 5.9
Identities = 9/54 (16%), Positives = 22/54 (40%), Gaps = 11/54 (20%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDPYRAQMKPY 208
+Y+ ++ + E +R+ F +G I+ +D+ D + K +
Sbjct: 30 RVYVGSIY---YEL-------GEDTIRQAFAPFGPIKSIDM-SWDSVTMKHKGF 72
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 26.5 bits (59), Expect = 5.3
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 176 SEAMLRRVFQNYGDIREVDIPINDP 200
++A LR+ F+ +GDI E + I D
Sbjct: 30 TDASLRKYFEGFGDIEEAVV-ITDR 53
>1qr0_A 4'-phosphopantetheinyl transferase SFP; protein-coenzyme A complex;
HET: COA; 1.90A {Bacillus subtilis} SCOP: d.150.1.1
d.150.1.1
Length = 228
Score = 26.8 bits (59), Expect = 8.6
Identities = 9/51 (17%), Positives = 19/51 (37%), Gaps = 6/51 (11%)
Query: 176 SEAMLRRVFQNYGDIREVDIPINDPYRAQMKPYISGMTLF----SHAQSLI 222
+ ++R V + + DI + + KP I + SH+ +
Sbjct: 47 GDVLVRSVISRQYQLDKSDIRFS--TQEYGKPCIPDLPDAHFNISHSGRWV 95
>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM,
splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo
sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*
Length = 437
Score = 27.1 bits (59), Expect = 9.3
Identities = 11/54 (20%), Positives = 26/54 (48%), Gaps = 11/54 (20%)
Query: 155 TIYLSNLPVKWFSTKARPNQPSEAMLRRVFQNYGDIREVDIPINDPYRAQMKPY 208
T++++ + + T +E+ LRR F+ YG I+ + + + + + Y
Sbjct: 104 TLFVARVN---YDT-------TESKLRREFEVYGPIKRIHM-VYSKRSGKPRGY 146
>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 = 26.9 bits (60), Expect = 9.4
Identities = 7/74 (9%), Positives = 12/74 (16%), Gaps = 23/74 (31%)
Query: 142 KNMNEMKPGERPDTIYLSNLPVKWFSTKARPNQPSEA----------------MLRRVFQ 185
++ G R +Y V W + L R
Sbjct: 155 SDLLGKPLGPRT--LY-----VHWTDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALS 207
Query: 186 NYGDIREVDIPIND 199
+
Sbjct: 208 AVHSPTFCQLACGQ 221
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
0.320 0.133 0.386
Gapped
Lambda K H
0.267 0.0811 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,574,512
Number of extensions: 271626
Number of successful extensions: 625
Number of sequences better than 10.0: 1
Number of HSP's gapped: 622
Number of HSP's successfully gapped: 116
Length of query: 305
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 212
Effective length of database: 4,105,140
Effective search space: 870289680
Effective search space used: 870289680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (25.6 bits)