RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11409
(320 letters)
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 108 bits (272), Expect = 9e-30
Identities = 75/95 (78%), Positives = 84/95 (88%)
Query: 63 PHYDHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVDED 122
P D +EITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ+ESSVQ LIDAC+ ++
Sbjct: 18 PDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDG 77
Query: 123 KCYLCVSSPTIKDKPVQIRPWKLTDADFVLDASMP 157
K YLCVSSPTIKDKPVQIRPW L+D+DFV+D+
Sbjct: 78 KLYLCVSSPTIKDKPVQIRPWNLSDSDFVMDSGPS 112
Score = 43.8 bits (103), Expect = 6e-06
Identities = 27/112 (24%), Positives = 44/112 (39%), Gaps = 14/112 (12%)
Query: 154 ASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGV--CYAGIDTDPELKYPKGAGRVAF 211
+S RK VFVGG+P + E+ R +G + + PKG + F
Sbjct: 2 SSGSSGSRK-VFVGGLPPDIDEDEITASFRR-FGPLVVDWPHKAESKSYFPPKGYAFLLF 59
Query: 212 ASQASYIAAISARFVQLQHGEI--------DKRVEVKPYVLDDQ--MCDECQ 253
++S A I A + + DK V+++P+ L D + D
Sbjct: 60 QEESSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIRPWNLSDSDFVMDSGP 111
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 44.2 bits (105), Expect = 1e-05
Identities = 24/145 (16%), Positives = 45/145 (31%), Gaps = 20/145 (13%)
Query: 96 PKGYAFLLFQDESSVQQLIDACIVDEDKCYLCVSSPTIKDKPVQIRPWKLTDADFVLDAS 155
+G+ F+ + V DA + + + V+ K +
Sbjct: 54 SRGFGFVTYATVEEV----DAAMNARPH--------KVDGRVVEP---KRAVSREDSQRP 98
Query: 156 MPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQA 215
K +FVGG+ + L ++ YG + I TD +G V F
Sbjct: 99 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQ-YGKIEVIEIMTDRGSGKKRGFAFVTFDDHD 157
Query: 216 SYIAAISARFVQLQHGEIDKRVEVK 240
S + ++ + EV+
Sbjct: 158 SVDKIVIQKYHTVN----GHNCEVR 178
Score = 39.2 bits (92), Expect = 7e-04
Identities = 24/87 (27%), Positives = 40/87 (45%), Gaps = 8/87 (9%)
Query: 156 MPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQA 215
P RK +F+GG+ L ++ +G + + DP K +G G V +A+
Sbjct: 9 EPEQLRK-LFIGGLSFETTDESLRSHFEQ-WGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 216 SYIAAISARFVQLQHGEID-KRVEVKP 241
AA++AR H ++D + VE K
Sbjct: 67 EVDAAMNAR----PH-KVDGRVVEPKR 88
Score = 32.3 bits (74), Expect = 0.13
Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 16/77 (20%)
Query: 66 DHEEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVDEDKC 124
+ + F ++G + ++ S +G+AF+ F D SV D ++ +
Sbjct: 117 EEHHLRDYFEQYGKIEVIEIMTDRGSG---KKRGFAFVTFDDHDSV----DKIVIQKYH- 168
Query: 125 YLCVSSPTIKDKPVQIR 141
T+ ++R
Sbjct: 169 -------TVNGHNCEVR 178
>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 = 42.3 bits (100), Expect = 2e-05
Identities = 18/88 (20%), Positives = 41/88 (46%), Gaps = 5/88 (5%)
Query: 154 ASMPLDPR--KTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAF 211
+ +P D KTVF+ + + L ++ + +G + Y + P+ ++ KG F
Sbjct: 6 SGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQ-FGDLKYVRVVLHPDTEHSKGCAFAQF 64
Query: 212 ASQASYIAAISARFVQLQHG--EIDKRV 237
+Q + ++A ++ + G ++D R
Sbjct: 65 MTQEAAQKCLAAASLEAEGGGLKLDGRQ 92
Score = 27.7 bits (62), Expect = 2.4
Identities = 11/56 (19%), Positives = 24/56 (42%), Gaps = 12/56 (21%)
Query: 66 DHEEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
+ E + ++FG +V+ +++ KG AF F + + Q+ + A
Sbjct: 28 EEEALGEVLQQFGDLKYVRVVLH----PDTEH---SKGCAFAQFMTQEAAQKCLAA 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 = 42.5 bits (101), Expect = 4e-05
Identities = 26/145 (17%), Positives = 53/145 (36%), Gaps = 27/145 (18%)
Query: 96 PKGYAFLLFQDESSVQQLIDACIVDEDKCYLCVSSPTIKDKPVQIRPWKLTDADFVLDAS 155
+G+ FL F+ SSV D + + + K + +
Sbjct: 44 SRGFGFLSFEKPSSV----DEVVKTQHI---------LDGKVIDPKRAI---------PR 81
Query: 156 MPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQA 215
D +FVGG+ ++ E + +G + A + D + +G G V + S
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQ-WGTIIDAQLMLDKDTGQSRGFGFVTYDSAD 140
Query: 216 SYIAAISARFVQLQHGEIDKRVEVK 240
+ +F+ + D+++E+K
Sbjct: 141 AVDRVCQNKFIDFK----DRKIEIK 161
Score = 36.0 bits (84), Expect = 0.006
Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 9/84 (10%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
+ K +F+GG+ L + YG V I DP +G G ++F +S
Sbjct: 2 ESCK-MFIGGLNWDTTEDNLREYFGK-YGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVD 59
Query: 219 AAISARFVQLQHGEID-KRVEVKP 241
+ + H +D K ++ K
Sbjct: 60 EVVKTQ-----H-ILDGKVIDPKR 77
Score = 31.3 bits (72), Expect = 0.18
Identities = 6/50 (12%), Positives = 20/50 (40%), Gaps = 4/50 (8%)
Query: 66 DHEEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLI 114
+E F ++G ++ ++ +G+ F+ + +V ++
Sbjct: 100 RPKEFEEFFSQWGTIIDAQLMLDKDTG---QSRGFGFVTYDSADAVDRVC 146
>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 = 44.3 bits (104), Expect = 4e-05
Identities = 49/281 (17%), Positives = 77/281 (27%), Gaps = 110/281 (39%)
Query: 1 MLANLVEILGGRSPYISAGLDDASLLDDFLLLLSRALVPNLGPNDILKLSFP-SPPQFPL 59
L+ L+ + GL+ L++ P+ P+ LS P S PL
Sbjct: 194 TLSELIRTTLDAEKVFTQGLNILEWLEN----------PSNTPDKDYLLSIPIS---CPL 240
Query: 60 QG---TPHY---------DHEEITASFR----RFGPLVV--------DWP------HKA- 88
G HY E+ + + LV W KA
Sbjct: 241 IGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAI 300
Query: 89 --------ESKSYFPPKGYAFLLFQDES-----------SVQQLIDACI---VDEDKCYL 126
+P + +D S+ L + V++ +L
Sbjct: 301 TVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHL 360
Query: 127 CVSSPTIKDKPVQIRPWKLTDADFVLDASMPLDPRKTVFVGGVPRPLKALELAMIMDRLY 186
P K V+I L + + V V G P+ L L L + R
Sbjct: 361 ----PA--GKQVEI---SLVNG-----------AKNLV-VSGPPQSLYGLNLTL---R-- 394
Query: 187 GGVCYAGIDTDPELKYPKGA--GRVAFASQASYIAAISARF 225
+ K P G R+ F+ + S RF
Sbjct: 395 ------------KAKAPSGLDQSRIPFSERK---LKFSNRF 420
Score = 30.8 bits (69), Expect = 0.80
Identities = 9/39 (23%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 218 IAAISARFVQLQHGEIDKRVEVKP---YVLDDQMCDECQ 253
+ A S R + L HG ++ + V P + + Q+ ++
Sbjct: 1 MDAYSTRPLTLSHGSLEHVLLV-PTASFFIASQLQEQFN 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 = 40.4 bits (95), Expect = 3e-04
Identities = 30/165 (18%), Positives = 64/165 (38%), Gaps = 26/165 (15%)
Query: 66 DHEEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVD 120
+ I +F FGP + D K KG+AF+ ++ + Q ++
Sbjct: 41 GEDTIRQAFAPFGPIKSIDMSWD---SVTMKH----KGFAFVEYEVPEAAQLALEQ---- 89
Query: 121 EDKCYLCVSSPTIKDKPVQI-RPWKLTDADFVLDASM-PLDPRKTVFVGGVPRPLKALEL 178
++S + + +++ RP + A ++D ++V V + L ++
Sbjct: 90 -------MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 142
Query: 179 AMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+ + +G + A + DP KG G + + S A+S+
Sbjct: 143 KSVFEA-FGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
>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 = 41.0 bits (95), Expect = 4e-04
Identities = 23/170 (13%), Positives = 48/170 (28%), Gaps = 7/170 (4%)
Query: 153 DASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFA 212
D + D KT+FV V +L + YG + + P+G + +
Sbjct: 94 DPNAQGDAFKTLFVARVNYDTTESKLRREFEV-YGPIKRIHMVYSKRSGKPRGYAFIEYE 152
Query: 213 SQASYIAAISARFVQLQHGEIDKRVEVKPYVLDDQMCDECQGVRCGGKFAPFFCANVCCL 272
+ +A +ID R + + GG +
Sbjct: 153 HERDMHSAYK----HADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNI 208
Query: 273 QYYCEHCWATIHSKPGRE--FHKPLVKEGAYDSLQTRTRVSQTSSEGRSG 320
++ + +PG H+ ++ + + + RS
Sbjct: 209 RHSGRDDTSRYDERPGPSPLPHRDRDRDRERERRERSRERDKERERRRSR 258
Score = 31.7 bits (71), Expect = 0.31
Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 5/69 (7%)
Query: 74 FRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQ---LIDACIVDEDKCYLCVSS 130
F +GP + H SK P+GYAF+ ++ E + D +D + + V
Sbjct: 123 FEVYGP--IKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180
Query: 131 PTIKDKPVQ 139
Sbjct: 181 GRTVKGWRP 189
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 40.2 bits (93), Expect = 7e-04
Identities = 31/180 (17%), Positives = 53/180 (29%), Gaps = 56/180 (31%)
Query: 20 LDD---ASLLDDF-----LLLLSRALVPNLGPNDILKLSFPSPPQFPLQGTPHYDHEEIT 71
L + A + F +LL +R D L T H + +
Sbjct: 250 LLNVQNAKAWNAFNLSCKILLTTR----FKQVTDFLSA----------ATTTHISLDHHS 295
Query: 72 ASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQL-IDACIVDEDKCYLCVSS 130
+ E KS +L + Q L + + + + S
Sbjct: 296 MTL-----------TPDEVKSLLL----KYL----DCRPQDLPREVLTTNPRRLSIIAES 336
Query: 131 PTIKDKPVQIRPWKLTDAD---FVLDASM----PLDPRK-----TVFVGGVPRPLKALEL 178
I+D WK + D ++++S+ P + RK +VF P L L
Sbjct: 337 --IRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL 394
>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 = 39.3 bits (91), Expect = 7e-04
Identities = 24/196 (12%), Positives = 49/196 (25%), Gaps = 29/196 (14%)
Query: 66 DHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA---CIVDED 122
+ + + F +G + + K G A + D +V + I +
Sbjct: 18 NCDRVFNVFCLYGNVE-------KVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQ 70
Query: 123 KCYLCVSSPTIKDKPVQIRPWKLTDADFVLDASMPLDPRK--------------TVFVGG 168
K +CVS + + S +
Sbjct: 71 KMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFN 130
Query: 169 VPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISARFVQL 228
P + I D G + +G + + S++ + + L
Sbjct: 131 APLEVTEENFFEICDE-LGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGF----L 185
Query: 229 QHGEIDKRVEVKPYVL 244
H ++ PY L
Sbjct: 186 NHYQMKNPNGPYPYTL 201
>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 = 37.2 bits (87), Expect = 9e-04
Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 1/64 (1%)
Query: 160 PRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIA 219
P + V++G +P ++ + G V + DP+ KG + F S +
Sbjct: 1 PSRVVYLGSIPYDQTEEQILDLCSN-VGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 59
Query: 220 AISA 223
A+
Sbjct: 60 AVRN 63
Score = 28.4 bits (64), Expect = 1.1
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
E+I GP++ + ++ KGYAF+ F+D S +
Sbjct: 17 EQILDLCSNVGPVINLKMMFDPQTGR---SKGYAFIEFRDLESSASAVRN 63
>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 = 35.7 bits (83), Expect = 0.002
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 1/65 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
+ TV+V +P L +L I + YG V I D + + KG + F + S
Sbjct: 14 PSKSTVYVSNLPFSLTNNDLYRIFSK-YGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 219 AAISA 223
A
Sbjct: 73 NCTRA 77
Score = 26.8 bits (60), Expect = 3.2
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 96 PKGYAFLLFQDESSVQQLIDA 116
KG AF+LF D+ S Q A
Sbjct: 57 SKGVAFILFLDKDSAQNCTRA 77
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 36.2 bits (84), Expect = 0.002
Identities = 14/64 (21%), Positives = 21/64 (32%), Gaps = 1/64 (1%)
Query: 160 PRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIA 219
P K V + ++ L + + YG V I P + G RV F S
Sbjct: 5 PLKEVTFARLNDNVRETFLKDMCRK-YGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE 63
Query: 220 AISA 223
+
Sbjct: 64 TVKN 67
Score = 27.4 bits (61), Expect = 3.2
Identities = 7/52 (13%), Positives = 18/52 (34%), Gaps = 4/52 (7%)
Query: 66 DHEEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
+ R++G + V+ ++ G A +LF ++ +
Sbjct: 19 RETFLKDMCRKYGEVEEVEILLHPRTRK---HLGLARVLFTSTRGAKETVKN 67
>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 = 35.7 bits (83), Expect = 0.003
Identities = 26/78 (33%), Positives = 32/78 (41%), Gaps = 8/78 (10%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
P KT+FV G+ L + G A I TD E KG G V F S+
Sbjct: 13 QPSKTLFVKGLSEDTTEETLK----ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAK 68
Query: 219 AAISARFVQLQHGEIDKR 236
AA A ++ GEID
Sbjct: 69 AAKEA----MEDGEIDGN 82
>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 = 35.8 bits (83), Expect = 0.003
Identities = 15/63 (23%), Positives = 22/63 (34%), Gaps = 1/63 (1%)
Query: 160 PRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIA 219
+TVF + ++ +L G V I +D + KG V F S
Sbjct: 24 DARTVFCMQLAARIRPRDLEDFFSA-VGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 82
Query: 220 AIS 222
AI
Sbjct: 83 AIG 85
Score = 28.1 bits (63), Expect = 1.9
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 96 PKGYAFLLFQDESSVQQLI 114
KG A++ F + SV I
Sbjct: 66 SKGIAYVEFCEIQSVPLAI 84
>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 = 36.0 bits (84), Expect = 0.006
Identities = 29/166 (17%), Positives = 65/166 (39%), Gaps = 28/166 (16%)
Query: 63 PHYDHEEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
+ +++ F ++G ++ D + +S KG F+ F + + +A
Sbjct: 13 RTWSEKDLRELFEQYGAVYEINVLRD-RSQNPPQS----KGCCFVTFYTRKAALEAQNA- 66
Query: 118 IVDEDKCYLCVSSPTIKDKPVQIRPWKLTDADFVLDASMPLDPRKTVFVGGVPRPLKALE 177
+ K P+Q++P AD + + ++ RK +F+G + + +
Sbjct: 67 -LHNMKVL------PGMHHPIQMKP-----ADS--EKNNAVEDRK-LFIGMISKKCTEND 111
Query: 178 LAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+ ++ +G + I P+ +G V F ++A AI A
Sbjct: 112 IRVMFSS-FGQIEECRILRGPD-GLSRGCAFVTFTTRAMAQTAIKA 155
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 34.5 bits (80), Expect = 0.006
Identities = 20/88 (22%), Positives = 34/88 (38%), Gaps = 8/88 (9%)
Query: 154 ASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFAS 213
+ D K +FVGG+ +L + +G V I DP +G G + F
Sbjct: 5 SKNEEDAGK-MFVGGLSWDTSKKDLKDYFTK-FGEVVDCTIKMDPNTGRSRGFGFILFKD 62
Query: 214 QASYIAAISARFVQLQHGEID-KRVEVK 240
AS + + H +D + ++ K
Sbjct: 63 AASVEKVLDQKE----H-RLDGRVIDPK 85
>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 = 35.5 bits (82), Expect = 0.007
Identities = 16/85 (18%), Positives = 27/85 (31%), Gaps = 5/85 (5%)
Query: 153 DASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFA 212
DP + V G+ +L + + YG + I D + + +G V F
Sbjct: 38 GNRANPDPNCCLGVFGLSLYTTERDLREVFSK-YGPIADVSIVYDQQSRRSRGFAFVYFE 96
Query: 213 SQASYIAAISARFVQLQHGEIDKRV 237
+ A E+D R
Sbjct: 97 NVDDAKEAKER----ANGMELDGRR 117
>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 = 34.4 bits (80), Expect = 0.007
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 1/63 (1%)
Query: 160 PRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIA 219
++++VG V A EL G V I D +PKG + F+ + S
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHG-CGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63
Query: 220 AIS 222
+++
Sbjct: 64 SLA 66
Score = 26.7 bits (60), Expect = 3.1
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 12/52 (23%)
Query: 68 EEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLI 114
EE+ A F G ++ D S PKG+A++ F D+ SV+ +
Sbjct: 21 EELEAHFHGCGSVNRVTILCD----KFSGH---PKGFAYIEFSDKESVRTSL 65
>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 = 34.7 bits (80), Expect = 0.009
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 162 KTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAI 221
++V+VG V A +L G + I D +PKG + FA + S AA+
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSS-CGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
Query: 222 S 222
+
Sbjct: 96 A 96
Score = 29.3 bits (66), Expect = 0.67
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLI 114
+++ A F G + + S PKGYA++ F + +SV +
Sbjct: 51 QDLEAHFSSCGSINRITILCDKFSGH---PKGYAYIEFAERNSVDAAV 95
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 34.5 bits (80), Expect = 0.009
Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 8/89 (8%)
Query: 153 DASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFA 212
+ M K +F+GG+ L + +G V + DP K +G G V F
Sbjct: 18 GSHMGSSGCK-MFIGGLSWQTTQEGLREYFGQ-FGEVKECLVMRDPLTKRSRGFGFVTFM 75
Query: 213 SQASYIAAISARFVQLQHGEID-KRVEVK 240
QA ++ H E+D K ++ K
Sbjct: 76 DQAGVDKVLAQSR----H-ELDSKTIDPK 99
>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 = 34.9 bits (81), Expect = 0.013
Identities = 18/162 (11%), Positives = 43/162 (26%), Gaps = 36/162 (22%)
Query: 66 DHEEITASFRRFGPL----VVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVDE 121
E+ + VVD + + + ++ F+ +++ ++
Sbjct: 26 SVAELKVAISELFAKNDLAVVD---VRTGTN----RKFGYVDFESAEDLEKALE------ 72
Query: 122 DKCYLCVSSPTIKDKPVQIRPWKLTDADFVLDASMPLDPRKTVFVGGVPRPLKALELAMI 181
+ V KL S + +T+ + + EL +
Sbjct: 73 -----------LTGLKVFGNEIKLEKPK--GRDSKKVRAARTLLAKNLSFNITEDELKEV 119
Query: 182 MDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+ I + KG + F S+A +
Sbjct: 120 FED------ALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 155
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 33.7 bits (77), Expect = 0.013
Identities = 12/51 (23%), Positives = 21/51 (41%), Gaps = 11/51 (21%)
Query: 68 EEITASFRRFG--PLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
++ + R G PL + W P+ AFL + D ++ QQ +
Sbjct: 34 SDLKRALRELGSVPLRLTWQ---------GPRRRAFLHYPDSAAAQQAVSC 75
>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 = 33.4 bits (77), Expect = 0.020
Identities = 20/85 (23%), Positives = 30/85 (35%), Gaps = 9/85 (10%)
Query: 162 KTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAI 221
++VFVG +P +L I G V + D E PKG G + Q + ++A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSE-VGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 222 SARFVQLQHGEIDKRV----EVKPY 242
L E R
Sbjct: 68 RN----LNGREFSGRALRVDNAASE 88
Score = 26.5 bits (59), Expect = 5.8
Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 4/50 (8%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
E++ F GP+V + E+ PKGY F +QD+ + +
Sbjct: 23 EQLKDIFSEVGPVVSFRLVYDRETGK---PKGYGFCEYQDQETALSAMRN 69
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 33.2 bits (76), Expect = 0.021
Identities = 11/78 (14%), Positives = 22/78 (28%), Gaps = 17/78 (21%)
Query: 63 PHYDHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVDED 122
++ + + FGP+ P K A + F+D ++
Sbjct: 31 DGVVEADLVEALQEFGPIS--------YVVVMPKKRQALVEFEDVLGACNAVN------- 75
Query: 123 KCYLCVSSPTIKDKPVQI 140
Y + I P +
Sbjct: 76 --YAADNQIYIAGHPAFV 91
>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 = 34.5 bits (79), Expect = 0.021
Identities = 21/183 (11%), Positives = 52/183 (28%), Gaps = 31/183 (16%)
Query: 66 DHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA---CIVDED 122
+ + F +G + K F K A + D + Q + +
Sbjct: 17 TPQSLFILFGVYGDVQ-------RVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGK 69
Query: 123 KCYLCVSSPTIKDKPVQIRPWKLTDADF------------VLDASMPLDPRKTVFVGGVP 170
+ +S P + + + D+ + P T+ + +P
Sbjct: 70 PIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIP 129
Query: 171 RPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISARFVQLQH 230
+ +L ++ GGV + + + + S + A+ L +
Sbjct: 130 PSVSEEDLKVLFSS-NGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALID----LHN 180
Query: 231 GEI 233
++
Sbjct: 181 HDL 183
>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 = 33.9 bits (78), Expect = 0.022
Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 5/75 (6%)
Query: 153 DASMPLDPR----KTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGR 208
D P R +FV GV ++ YG + ++ D Y KG
Sbjct: 10 DGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAE-YGEIKNIHLNLDRRTGYLKGYTL 68
Query: 209 VAFASQASYIAAISA 223
V + + AA+
Sbjct: 69 VEYETYKEAQAAMEG 83
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 33.1 bits (76), Expect = 0.024
Identities = 22/89 (24%), Positives = 34/89 (38%), Gaps = 12/89 (13%)
Query: 154 ASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGA-GRVAFA 212
S ++VFV G PR + + +L+ +G V +D D KG V
Sbjct: 1 GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLA-FGPVASVVMDKD------KGVFAIVEMG 53
Query: 213 SQASYIAAISARFVQLQHGEIDKRVEVKP 241
+ A +S L G R+ V+P
Sbjct: 54 DVGAREAVLSQSQHSL-GG---HRLRVRP 78
>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 = 33.0 bits (76), Expect = 0.024
Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 5/78 (6%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
D T+ V + L + ++ YG V I +P K P+G V F +
Sbjct: 11 DGMITLKVDNLTYRTSPDSLRRVFEK-YGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQ 69
Query: 219 AAISARFVQLQHGEIDKR 236
A +A + E+D R
Sbjct: 70 DAEAA----MDGAELDGR 83
>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 = 34.1 bits (79), Expect = 0.025
Identities = 24/129 (18%), Positives = 40/129 (31%), Gaps = 26/129 (20%)
Query: 97 KGYAFLLFQDESSVQQLIDACIVDEDKCYLCVSSPTIKDKPVQIRPWKLTDADFVLDASM 156
K +AFL F+ Q A D + + ++IR
Sbjct: 51 KNFAFLEFRSVDETTQ---AMAFDGII---------FQGQSLKIRRPH---------DYQ 89
Query: 157 PLDPRKTVFVGGVPRPLKALELAMIMDRL--YGGVCYAGIDTDPELKYPKGAGRVAFASQ 214
PL +F+GG+P L + + L +G + + D KG +
Sbjct: 90 PLPGAHKLFIGGLP---NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 146
Query: 215 ASYIAAISA 223
AI+
Sbjct: 147 NVTDQAIAG 155
Score = 30.7 bits (70), Expect = 0.43
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 12/59 (20%)
Query: 63 PHYDHEEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
+ + +++ FGP LV D A S KGYAF + D + Q I
Sbjct: 104 NYLNDDQVKELLTSFGPLKAFNLVKD---SATGLS----KGYAFCEYVDINVTDQAIAG 155
>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 = 32.6 bits (75), Expect = 0.029
Identities = 13/65 (20%), Positives = 23/65 (35%), Gaps = 1/65 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
DP + V G+ +L + + YG + I D + + +G V F +
Sbjct: 13 DPNCCLGVFGLSLYTTERDLREVFSK-YGPIADVSIVYDQQSRRSRGFAFVYFENVDDAK 71
Query: 219 AAISA 223
A
Sbjct: 72 EAKER 76
>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 = 0.033
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 2/71 (2%)
Query: 153 DASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFA 212
D K +F+G +PR L +L + + +G + + D KG + +
Sbjct: 6 SGMKDHDAIK-LFIGQIPRNLDEKDLKPLFEE-FGKIYELTVLKDRFTGMHKGCAFLTYC 63
Query: 213 SQASYIAAISA 223
+ S + A SA
Sbjct: 64 ERESALKAQSA 74
>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 = 31.7 bits (73), Expect = 0.039
Identities = 12/78 (15%), Positives = 28/78 (35%), Gaps = 7/78 (8%)
Query: 164 VFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+FVGG+ ++ +G V + D + +G + F + +
Sbjct: 2 IFVGGLSPDTPEEKIREYFGG-FGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 224 RFVQLQHGEID-KRVEVK 240
++ H + + E+K
Sbjct: 61 KY----H-NVGLSKCEIK 73
Score = 26.7 bits (60), Expect = 2.5
Identities = 11/50 (22%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
E+I F FG + ++ P ++ +G+ F+ F++E V+++++
Sbjct: 14 EKIREYFGGFGEVESIELPMDNKTNK---RRGFCFITFKEEEPVKKIMEK 60
>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 = 34.2 bits (79), Expect = 0.039
Identities = 23/169 (13%), Positives = 46/169 (27%), Gaps = 36/169 (21%)
Query: 63 PHYDHEEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
P ++ R FG LV + +S KGY F + + S +
Sbjct: 105 PSLTQQQFEELVRPFGSLERCFLVYS---ERTGQS----KGYGFAEYMKKDSAARAKSDL 157
Query: 118 IVDEDKCYLCVSSPTIKDKPVQIRPWKLTDADFVLDASMPLDPRKTVFVGGVPRPLKALE 177
KP+ R + D + L + + V +P ++
Sbjct: 158 ----------------LGKPLGPRTLYVHWTD-AGQLTPALLHSRCLCVDRLPPGFNDVD 200
Query: 178 LAMIMDRL---YGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+ R + + + + KG + + + A
Sbjct: 201 A---LCRALSAVHSPTFCQLACGQDGQ-LKGFAVLEYETAEMAEEAQQQ 245
Score = 33.8 bits (78), Expect = 0.061
Identities = 21/158 (13%), Positives = 47/158 (29%), Gaps = 36/158 (22%)
Query: 66 DHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVDEDKCY 125
++E+ + K KG AF+ + + I+A
Sbjct: 35 TNQEVHDLLSDYELKYCF-----VDKY----KGTAFVTLLNGEQAEAAINA--------- 76
Query: 126 LCVSSPTIKDKPVQIRPWKLTDADFVLDASMPLDPRKTVFVGGVPRPLKALELAMIMDRL 185
++++ + ++ + TDA + V +P L + ++
Sbjct: 77 --FHQSRLRERELSVQ-LQPTDA--------------LLCVANLPPSLTQQQFEELVRP- 118
Query: 186 YGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+G + + KG G + + S A S
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
>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 = 32.7 bits (75), Expect = 0.042
Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 8/89 (8%)
Query: 153 DASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFA 212
+ K +FVGG+P L + +G + A + TD + +G G V A
Sbjct: 10 GSQKDTTFTK-IFVGGLPYHTTDASLRKYFEG-FGDIEEAVVITDRQTGKSRGYGFVTMA 67
Query: 213 SQASYIAAISARFVQLQHGEID-KRVEVK 240
+A+ A + ID ++ V
Sbjct: 68 DRAAAERACKDP-----NPIIDGRKANVN 91
>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 = 32.6 bits (75), Expect = 0.043
Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 1/64 (1%)
Query: 160 PRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIA 219
+FV + + E+ YG + ++ D + KG V + + +A
Sbjct: 25 EGWILFVTSIHEEAQEDEIQEKFCD-YGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 83
Query: 220 AISA 223
A A
Sbjct: 84 AKEA 87
>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 105
Score = 32.6 bits (75), Expect = 0.044
Identities = 21/90 (23%), Positives = 34/90 (37%), Gaps = 8/90 (8%)
Query: 153 DASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFA 212
+ S + K +FVGG+ L + YG V I D +G G V F
Sbjct: 9 NNSGADEIGK-LFVGGLDWSTTQETLRSYFSQ-YGEVVDCVIMKDKTTNQSRGFGFVKFK 66
Query: 213 SQASYIAAISARFVQLQHGEID-KRVEVKP 241
+++R H +D + ++ KP
Sbjct: 67 DPNCVGTVLASRP----H-TLDGRNIDPKP 91
>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 = 0.044
Identities = 8/79 (10%), Positives = 21/79 (26%), Gaps = 17/79 (21%)
Query: 63 PHYDHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVDED 122
++ + +FG + P K A + F++ S ++ +
Sbjct: 25 ESVVEADLVEALEKFGTI--------CYVMMMPFKRQALVEFENIDSAKECVT------- 69
Query: 123 KCYLCVSSPTIKDKPVQIR 141
+ I +
Sbjct: 70 --FAADVPVYIAGQQAFFN 86
Score = 27.1 bits (60), Expect = 3.4
Identities = 11/70 (15%), Positives = 25/70 (35%), Gaps = 7/70 (10%)
Query: 154 ASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFAS 213
+ + V V G+ + +L +++ +G +CY + K V F +
Sbjct: 8 SHHKVSVSPVVHVRGLCESVVEADLVEALEK-FGTICYVMMMPF------KRQALVEFEN 60
Query: 214 QASYIAAISA 223
S ++
Sbjct: 61 IDSAKECVTF 70
>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 = 33.3 bits (76), Expect = 0.046
Identities = 13/65 (20%), Positives = 23/65 (35%), Gaps = 1/65 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
+ ++ V + L + ++ YG V I D K +G V F +
Sbjct: 68 EGMTSLKVDNLTYRTSPDTLRRVFEK-YGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 219 AAISA 223
A+ A
Sbjct: 127 DAMDA 131
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 31.7 bits (73), Expect = 0.048
Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 7/78 (8%)
Query: 164 VFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+FVGG+ ++ ++ +G V A + D +G G V F S+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQ-FGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
Query: 224 RFVQLQHGEID-KRVEVK 240
F H EI+ K VE K
Sbjct: 61 HF----H-EINNKMVECK 73
>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 = 32.2 bits (74), Expect = 0.048
Identities = 27/88 (30%), Positives = 40/88 (45%), Gaps = 8/88 (9%)
Query: 154 ASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFAS 213
S K +FVGG+P EL + +G V + D E + P+G G + F
Sbjct: 4 GSSGSKSNK-IFVGGIPHNCGETELREYFKK-FGVVTEVVMIYDAEKQRPRGFGFITFED 61
Query: 214 QASYIAAISARFVQLQHGEID-KRVEVK 240
+ S A++ F H +I K+VEVK
Sbjct: 62 EQSVDQAVNMHF----H-DIMGKKVEVK 84
Score = 26.0 bits (58), Expect = 7.6
Identities = 16/52 (30%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 66 DHEEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
E+ F++FG + V + AE + P+G+ F+ F+DE SV Q ++
Sbjct: 23 GETELREYFKKFGVVTEVVMIYDAEKQR---PRGFGFITFEDEQSVDQAVNM 71
>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 = 33.8 bits (78), Expect = 0.055
Identities = 18/168 (10%), Positives = 49/168 (29%), Gaps = 30/168 (17%)
Query: 63 PHYDHEEITASFRRFGPLVVD--WPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC--- 117
P Y I + + + P + S + +A++ + + ++
Sbjct: 127 PSYTQRNIRDLLQDINVVALSIRLPSLRFNTS----RRFAYIDVTSKEDARYCVEKLNGL 182
Query: 118 IVDEDKCYLCVSSPTIKDKPVQIRPWKLTDADFVLDASMPLDPRKTVFVGGVPRPLKALE 177
++ VS+P K K + + + + + L+
Sbjct: 183 KIEGYTLVTKVSNPLEKSKR----------------TDSATLEGREIMIRNLST--ELLD 224
Query: 178 LAMIMDRL--YGGVCYAGIDTD-PELKYPKGAGRVAFASQASYIAAIS 222
++ + +G + I E + + F ++ S A+
Sbjct: 225 ENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ 272
Score = 31.5 bits (72), Expect = 0.30
Identities = 15/205 (7%), Positives = 46/205 (22%), Gaps = 52/205 (25%)
Query: 66 DHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVDEDKCY 125
+ ++ F+ GP++ + K+ +A + F I
Sbjct: 54 NQNKVYKYFKHCGPIIHVDVADSLKKN----FRFARIEFARYDGALAAITKT-------- 101
Query: 126 LCVSSPTIKDKPVQIRPWKLTDADFVLDASMPLDPRKTVFVGGVPRPLKALELAMIMDRL 185
+ + + T+++ P + ++
Sbjct: 102 ----HKVVGQNEIIVSHLT----------------ECTLWMTNFPPSYTQRNIRDLLQD- 140
Query: 186 YGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAI-----------------SARFVQL 228
V + + + S+ + S +
Sbjct: 141 INVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKS 200
Query: 229 QHGEIDKRVEVKPYV--LDDQMCDE 251
+ + + + L ++ DE
Sbjct: 201 KRTDSATLEGREIMIRNLSTELLDE 225
>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 31.8 bits (73), Expect = 0.067
Identities = 18/85 (21%), Positives = 30/85 (35%), Gaps = 9/85 (10%)
Query: 157 PLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQAS 216
+ V G+P +L +G V + D + + KG G V F +
Sbjct: 12 VQKTSD-LIVLGLPWKTTEQDLKEYFST-FGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69
Query: 217 YIAAISARFVQLQHGEID-KRVEVK 240
+ +S R H ID + + K
Sbjct: 70 QVKVMSQR-----H-MIDGRWCDCK 88
>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 = 31.9 bits (73), Expect = 0.071
Identities = 17/72 (23%), Positives = 25/72 (34%), Gaps = 9/72 (12%)
Query: 160 PRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAG--------IDTDPELKYPKGAGRVAF 211
T+FV G+ + +A + G + + TD E KG V+F
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQ-IGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 70
Query: 212 ASQASYIAAISA 223
S AAI
Sbjct: 71 DDPPSAKAAIDW 82
Score = 30.4 bits (69), Expect = 0.21
Identities = 12/57 (21%), Positives = 19/57 (33%), Gaps = 6/57 (10%)
Query: 66 DHEEITASFRRFGPLVVDWPHKAES-KSYF-----PPKGYAFLLFQDESSVQQLIDA 116
E + F++ G + + Y KG A + F D S + ID
Sbjct: 26 TIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW 82
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 31.4 bits (72), Expect = 0.076
Identities = 7/46 (15%), Positives = 16/46 (34%), Gaps = 10/46 (21%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQ 112
+ F RFG + +D +A++ ++ + Q
Sbjct: 32 AALAREFDRFGSIRTIDHV---------KGDSFAYIQYESLDAAQA 68
Score = 28.7 bits (65), Expect = 0.79
Identities = 12/64 (18%), Positives = 21/64 (32%), Gaps = 7/64 (10%)
Query: 160 PRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIA 219
P ++VGG+ LA DR +G + + + S + A
Sbjct: 16 PTTRLWVGGLGPNTSLAALAREFDR-FGSIRTIDHVKG------DSFAYIQYESLDAAQA 68
Query: 220 AISA 223
A +
Sbjct: 69 ACAK 72
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 31.6 bits (72), Expect = 0.080
Identities = 19/95 (20%), Positives = 26/95 (27%), Gaps = 9/95 (9%)
Query: 157 PLDPRKTVFVGGVPR--PLKALELAMIMDRL---YGGVCYAGIDTDPELKYPKGAGRVAF 211
PL + + V G P K L + L G V D KG V
Sbjct: 2 PLGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVEC 61
Query: 212 ASQASYIAAISARFVQLQHGEIDKRVEVKPYVLDD 246
S I +D + + Y + D
Sbjct: 62 GSMNDAKKIIK----SFHGKRLDLKHRLFLYTMKD 92
>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 = 32.5 bits (74), Expect = 0.083
Identities = 12/64 (18%), Positives = 23/64 (35%), Gaps = 1/64 (1%)
Query: 160 PRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIA 219
+FV + + E+ YG + ++ D + KG V + + +A
Sbjct: 71 EGWILFVTSIHEEAQEDEIQEKFCD-YGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 129
Query: 220 AISA 223
A A
Sbjct: 130 AKEA 133
Score = 27.1 bits (60), Expect = 5.3
Identities = 9/50 (18%), Positives = 18/50 (36%), Gaps = 4/50 (8%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
+EI F +G + + + KGYA + ++ +A
Sbjct: 87 DEIQEKFCDYGEIKNIHLNLDRRTGF---SKGYALVEYETHKQALAAKEA 133
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 31.5 bits (72), Expect = 0.088
Identities = 13/65 (20%), Positives = 22/65 (33%), Gaps = 1/65 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
+FV GV ++ YG + ++ D Y KG V + +
Sbjct: 21 VEGWILFVTGVHEEATEEDIHDKFAE-YGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79
Query: 219 AAISA 223
AA+
Sbjct: 80 AAMEG 84
>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 = 31.4 bits (72), Expect = 0.092
Identities = 11/65 (16%), Positives = 23/65 (35%), Gaps = 1/65 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
++VG + + L I + +G + + D + KG G + F+
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEP-FGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 219 AAISA 223
A+
Sbjct: 62 RALEQ 66
>2jun_A Midline-1; B-BOX, TRIM, ring finger, alternative splicing, coiled
coil, cytoplasm, cytoskeleton, disease mutation, ligase,
metal-binding; NMR {Homo sapiens}
Length = 101
Score = 31.5 bits (71), Expect = 0.097
Identities = 10/61 (16%), Positives = 17/61 (27%), Gaps = 4/61 (6%)
Query: 248 MCDECQGVRCGGKFAPFFCANVCCLQYYCEHCWATIHSKPGREFHKPLVKEGAYDSLQTR 307
+C C + A C C YC+ C H L++ ++
Sbjct: 5 LCQFCDQ--DPAQDAVKTCVT--CEVSYCDECLKATHPNKKPFTGHRLIEPIPDSHIRGL 60
Query: 308 T 308
Sbjct: 61 M 61
>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 = 31.6 bits (72), Expect = 0.10
Identities = 15/80 (18%), Positives = 28/80 (35%), Gaps = 9/80 (11%)
Query: 153 DASMPLDPRK--TVFVGGVPRPLKALELA-------MIMDRLYGGVCYAGIDTDPELKYP 203
+ P + ++V G+ + +LA ++ G I D E P
Sbjct: 5 SSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKP 64
Query: 204 KGAGRVAFASQASYIAAISA 223
KG V++ + AA+
Sbjct: 65 KGDATVSYEDPPTAKAAVEW 84
Score = 29.7 bits (67), Expect = 0.52
Identities = 7/57 (12%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 66 DHEEITASFRRFGPLVVDWPHKAESKSYFP------PKGYAFLLFQDESSVQQLIDA 116
+++ F++ G + ++ + PKG A + ++D + + ++
Sbjct: 28 TLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEW 84
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 31.6 bits (72), Expect = 0.10
Identities = 18/71 (25%), Positives = 25/71 (35%), Gaps = 7/71 (9%)
Query: 160 PRKTVFVGGVPRPLKALELA-------MIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFA 212
T+FV G+ + +A +I G + TD E KG V+F
Sbjct: 6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65
Query: 213 SQASYIAAISA 223
S AAI
Sbjct: 66 DPPSAKAAIDW 76
Score = 28.9 bits (65), Expect = 0.98
Identities = 11/58 (18%), Positives = 19/58 (32%), Gaps = 8/58 (13%)
Query: 66 DHEEITASFRRFGPLVVDWPHKAESKSYFP-------PKGYAFLLFQDESSVQQLIDA 116
E + F++ G + + + KG A + F D S + ID
Sbjct: 20 TIESVADYFKQIGIIKTN-KKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDW 76
>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 = 31.1 bits (71), Expect = 0.11
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 1/65 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
+FVGG+ L + + YG + + D E + +G G V F +
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSK-YGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 219 AAISA 223
A+ A
Sbjct: 69 DAMMA 73
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 30.5 bits (70), Expect = 0.12
Identities = 20/78 (25%), Positives = 32/78 (41%), Gaps = 7/78 (8%)
Query: 164 VFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+F+GG+ L + +G V + DP K +G G V F QA ++
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQ-FGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 224 RFVQLQHGEID-KRVEVK 240
H E+D K ++ K
Sbjct: 62 SR----H-ELDSKTIDPK 74
>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics,
RRM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 116
Score = 31.5 bits (72), Expect = 0.12
Identities = 26/89 (29%), Positives = 39/89 (43%), Gaps = 8/89 (8%)
Query: 154 ASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFAS 213
RK +F+GG+ L ++ +G + + DP K +G G V F+S
Sbjct: 21 KREKEQFRK-LFIGGLSFETTEESLRNYYEQ-WGKLTDCVVMRDPASKRSRGFGFVTFSS 78
Query: 214 QASYIAAISARFVQLQHGEID-KRVEVKP 241
A AA++AR H ID + VE K
Sbjct: 79 MAEVDAAMAARP----H-SIDGRVVEPKR 102
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 31.6 bits (72), Expect = 0.12
Identities = 15/78 (19%), Positives = 27/78 (34%), Gaps = 5/78 (6%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
+ ++ V + L + ++ YG V I D K +G V F +
Sbjct: 45 EGMTSLKVDNLTYRTSPDTLRRVFEK-YGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 103
Query: 219 AAISARFVQLQHGEIDKR 236
A+ A + +D R
Sbjct: 104 DAMDA----MDGAVLDGR 117
>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 = 31.8 bits (73), Expect = 0.15
Identities = 35/166 (21%), Positives = 55/166 (33%), Gaps = 33/166 (19%)
Query: 63 PHYDHEEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
E+ A FR GP ++ D S GYAF+ F E Q+ I
Sbjct: 13 QDMTDRELYALFRAIGPINTCRIMRD---YKTGYS----YGYAFVDFTSEMDSQRAIK-- 63
Query: 118 IVDEDKCYLCVSSPTIKDKPVQIRPWKLTDADFVLDASMPLDPRKTVFVGGVPRPLKALE 177
+ V+ + K++ A ++V +PR + +
Sbjct: 64 --------------VLNGITVRNKRLKVSYAR----PGGESIKDTNLYVTNLPRTITDDQ 105
Query: 178 LAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
L I + YG + I D P+G V + + AISA
Sbjct: 106 LDTIFGK-YGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 150
>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 = 31.5 bits (72), Expect = 0.21
Identities = 23/129 (17%), Positives = 41/129 (31%), Gaps = 6/129 (4%)
Query: 97 KGYAFLLFQDESSVQQLIDACIVDEDKCYLCVSSPTIKDKPVQIRPWKLTDADFVLDASM 156
K +AFL F+ Q + + L + P + V+ +
Sbjct: 51 KNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVV 110
Query: 157 PLDPRKTVFVGGVPRPLKALELAMIMDRL--YGGVCYAGIDTDPELKYPKGAGRVAFASQ 214
P K +F+GG+P L + + L +G + + D KG +
Sbjct: 111 PDSAHK-LFIGGLP---NYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 166
Query: 215 ASYIAAISA 223
AI+
Sbjct: 167 NVTDQAIAG 175
>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 = 30.4 bits (69), Expect = 0.27
Identities = 14/81 (17%), Positives = 30/81 (37%), Gaps = 8/81 (9%)
Query: 156 MPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQA 215
+P + + +++ +P + A E+ I + YG + + PE +G V +
Sbjct: 3 LPPEVNRILYIRNLPYKITAEEMYDIFGK-YGPIRQIRVGNTPE---TRGTAYVVYEDIF 58
Query: 216 SYIAAISARFVQLQHGEIDKR 236
A+ L + R
Sbjct: 59 DAKNAVDH----LSGFNVSNR 75
Score = 28.9 bits (65), Expect = 0.90
Identities = 10/51 (19%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
EE+ F ++GP+ + + E++ G A+++++D + +D
Sbjct: 23 EEMYDIFGKYGPIRQIRVGNTPETR------GTAYVVYEDIFDAKNAVDHL 67
>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 = 30.5 bits (69), Expect = 0.28
Identities = 19/90 (21%), Positives = 31/90 (34%), Gaps = 15/90 (16%)
Query: 34 SRALVPNLGPNDILKLSFPSP-PQFPLQGTPHY------DHEEITASFRRFGPLVVDWPH 86
S LVP + S P + P +G Y + +F FG ++
Sbjct: 11 SSGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGEDMTPTLLRGAFSPFGNII----- 65
Query: 87 KAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
S PP+ AF+ ++ S Q +
Sbjct: 66 ---DLSMDPPRNCAFVTYEKMESADQAVAE 92
>2d8v_A Zinc finger FYVE domain-containing protein 19; zfyve19, ZF- B_BOX,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
g.43.1.1
Length = 67
Score = 29.2 bits (65), Expect = 0.34
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 10/46 (21%)
Query: 248 MCDECQGVRCGGKFAPFFCANVCCLQYYCEHCWATIHSKPGREFHK 293
+C+E +RC G C YC C+ H + H+
Sbjct: 13 ICNEDATLRCAG----------CDGDLYCARCFREGHDNFDLKEHQ 48
>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 = 30.5 bits (69), Expect = 0.41
Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 5/80 (6%)
Query: 157 PLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQAS 216
L T++VG + ++ + + G + + D K G V + S+A
Sbjct: 35 LLKKSCTLYVGNLSFYTTEEQIYELFSK-SGDIKKIIMGLDKMKKTACGFCFVEYYSRAD 93
Query: 217 YIAAISARFVQLQHGEIDKR 236
A+ + +D R
Sbjct: 94 AENAMRY----INGTRLDDR 109
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 30.1 bits (68), Expect = 0.42
Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 1/65 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
++ ++VGG+ + L +G + I D E + +G V F
Sbjct: 61 TTKRVLYVGGLAEEVDDKVLHAAFIP-FGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 119
Query: 219 AAISA 223
AAI
Sbjct: 120 AAIDN 124
>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 = 0.44
Identities = 16/96 (16%), Positives = 27/96 (28%), Gaps = 30/96 (31%)
Query: 153 DASMPLDPRKTVFVGGVP------------RPLKALELAMIMDRLYGGVCYAGIDTDPEL 200
+ +P P T F+G +P R L + + +
Sbjct: 11 RSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPE------------ 58
Query: 201 KYPKGAGRVAFASQASYIAAISARFVQLQHGEIDKR 236
KG G F S ++A+ L + R
Sbjct: 59 -RLKGFGYAEFEDLDSLLSAL-----SLNEESLGNR 88
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 29.5 bits (67), Expect = 0.47
Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 1/65 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
++ ++VGG+ + L +G + I D E + +G V F
Sbjct: 10 TTKRVLYVGGLAEEVDDKVLHAAFIP-FGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 68
Query: 219 AAISA 223
AAI
Sbjct: 69 AAIDN 73
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 29.2 bits (66), Expect = 0.52
Identities = 10/50 (20%), Positives = 20/50 (40%), Gaps = 5/50 (10%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
EE+ + G + + K KG A++ +++ES Q +
Sbjct: 32 EELEEICKAHGTVKDLRLVTNRAGKP----KGLAYVEYENESQASQAVMK 77
Score = 28.0 bits (63), Expect = 1.3
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 2/64 (3%)
Query: 160 PRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIA 219
+ +F+ G+P EL I +G V + T+ K PKG V + +++
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKA-HGTVKDLRLVTNRAGK-PKGLAYVEYENESQASQ 73
Query: 220 AISA 223
A+
Sbjct: 74 AVMK 77
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP,
RBD, poly(U) binding, tandem, acetylation, cytopla
nucleus; 2.70A {Saccharomyces cerevisiae}
Length = 166
Score = 30.2 bits (69), Expect = 0.52
Identities = 21/129 (16%), Positives = 40/129 (31%), Gaps = 23/129 (17%)
Query: 97 KGYAFLLFQDESSVQQLIDACIVDEDKCYLCVSSPTIKDKPVQIRPWKLTDADFVLDASM 156
YAF+ + + T+ K ++ K+ A
Sbjct: 41 VNYAFVEYHQSHDANIALQ----------------TLNGKQIENNIVKINWAFQ--SQQS 82
Query: 157 PLDPRKTVFVGGVPRPL--KALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQ 214
D +FVG + + + L A + + + D + +G G V+F SQ
Sbjct: 83 SSDDTFNLFVGDLNVNVDDETLRNAF---KDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQ 139
Query: 215 ASYIAAISA 223
A+ +
Sbjct: 140 DDAQNAMDS 148
>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 = 29.6 bits (67), Expect = 0.53
Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 1/65 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
++VG + + L I + +G + + D E KG G + F+
Sbjct: 24 AGPMRLYVGSLHFNITEDMLRGIFEP-FGRIESIQLMMDSETGRSKGYGFITFSDSECAK 82
Query: 219 AAISA 223
A+
Sbjct: 83 KALEQ 87
>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 = 30.2 bits (67), Expect = 0.55
Identities = 9/81 (11%), Positives = 22/81 (27%), Gaps = 17/81 (20%)
Query: 63 PHYDHEEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVDE 121
++I G ++ + KG F++F S ++ ++
Sbjct: 119 TDATLDDIKEWLEDKGQVLNIQMRRTLHKAF----KGSIFVVFDSIESAKKFVET----- 169
Query: 122 DKCYLCVSSPTIKDKPVQIRP 142
K+ + I
Sbjct: 170 -------PGQKYKETDLLILF 183
>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 = 28.6 bits (65), Expect = 0.69
Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 2/70 (2%)
Query: 154 ASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFAS 213
SM ++ ++VGG+ + L +G + I D E + +G V F
Sbjct: 1 GSMA-TTKRVLYVGGLAEEVDDKVLHAAFIP-FGDITDIQIPLDYETEKHRGFAFVEFEL 58
Query: 214 QASYIAAISA 223
AAI
Sbjct: 59 AEDAAAAIDN 68
>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 = 28.8 bits (65), Expect = 0.72
Identities = 10/51 (19%), Positives = 19/51 (37%), Gaps = 8/51 (15%)
Query: 66 DHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
+ +F FG ++ S PP+ AF+ ++ S Q +
Sbjct: 26 TPTLLRGAFSPFGNII--------DLSMDPPRNCAFVTYEKMESADQAVAE 68
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 29.0 bits (65), Expect = 0.74
Identities = 10/69 (14%), Positives = 23/69 (33%), Gaps = 4/69 (5%)
Query: 153 DASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFA 212
S R + + +P +L + ++ ++T G G + F
Sbjct: 20 HMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDF----DGTGALEFP 75
Query: 213 SQASYIAAI 221
S+ + A+
Sbjct: 76 SEEILVEAL 84
>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 = 29.0 bits (65), Expect = 0.76
Identities = 9/47 (19%), Positives = 18/47 (38%)
Query: 63 PHYDHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESS 109
EEI + V+D A + +G+AF+ ++ +
Sbjct: 18 KMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRA 64
>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 = 28.3 bits (64), Expect = 0.78
Identities = 14/74 (18%), Positives = 29/74 (39%), Gaps = 5/74 (6%)
Query: 164 VFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+++ G+ +L + YG + D KG G V F S ++ A++A
Sbjct: 8 LYIRGLQPGTTDQDLVKLCQP-YGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66
Query: 224 RFVQLQHGEIDKRV 237
L+ + ++
Sbjct: 67 ----LKASGVQAQM 76
>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 = 30.0 bits (68), Expect = 0.79
Identities = 19/85 (22%), Positives = 36/85 (42%), Gaps = 20/85 (23%)
Query: 63 PHYDHEEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
P +E + +F +FGP +VVD + G F+ F + ++ ++ C
Sbjct: 106 PVVSNELLEQAFSQFGPVEKAVVVVD-----DRGR---ATGKGFVEFAAKPPARKALERC 157
Query: 118 IVDEDKCYLCVSSPTIKDKPVQIRP 142
D +L ++P +PV + P
Sbjct: 158 ---GDGAFLLTTTP----RPVIVEP 175
Score = 28.9 bits (65), Expect = 1.8
Identities = 21/149 (14%), Positives = 44/149 (29%), Gaps = 36/149 (24%)
Query: 97 KGYAFLLFQDESSVQQLIDACIVDEDKCYLCVSSPTIKDKPVQIRPWKLTDADFVLDASM 156
+G+ F+ + + + + ++ RP ++ A
Sbjct: 58 RGFGFIRLESRTLAEIAKA----------------ELDGTILKSRPLRIRFA-------- 93
Query: 157 PLDPRKTVFVGGVPRPL--KALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQ 214
+ V + + + LE A +G V A + D + G G V FA++
Sbjct: 94 --THGAALTVKNLSPVVSNELLEQAF---SQFGPVEKAVVVVDDRGR-ATGKGFVEFAAK 147
Query: 215 ASYIAAISARFVQLQHGEIDKRVEVKPYV 243
A+ G +P +
Sbjct: 148 PPARKALER----CGDGAFLLTTTPRPVI 172
>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 = 28.8 bits (65), Expect = 0.80
Identities = 14/52 (26%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 66 DHEEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
E + F + GPL V E K K + F+ F+ SV I
Sbjct: 29 REEILYELFLQAGPLTKVTICKDREGKP----KSFGFVCFKHPESVSYAIAL 76
>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 = 29.5 bits (67), Expect = 0.85
Identities = 33/166 (19%), Positives = 58/166 (34%), Gaps = 33/166 (19%)
Query: 63 PHYDHEEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
+ EE + F G LV D K +S GY F+ + D ++ I+
Sbjct: 12 QNMTQEEFRSLFGSIGEIESCKLVRD---KITGQS----LGYGFVNYIDPKDAEKAIN-- 62
Query: 118 IVDEDKCYLCVSSPTIKDKPVQIRPWKLTDADFVLDASMPLDPRKTVFVGGVPRPLKALE 177
T+ +Q + K++ A S ++V G+P+ + E
Sbjct: 63 --------------TLNGLRLQTKTIKVSYAR----PSSASIRDANLYVSGLPKTMTQKE 104
Query: 178 LAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
L + + YG + + I D +G G + F + AI
Sbjct: 105 LEQLFSQ-YGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 28.5 bits (64), Expect = 0.96
Identities = 16/90 (17%), Positives = 35/90 (38%), Gaps = 11/90 (12%)
Query: 162 KTVFVGGVPR--PLKALELAMIMDRL---YGGVCYAGIDTDPELKYPKGAGRVAFASQAS 216
+ V VP+ P + +L ++ ++ +G + E KG + +AS A
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPAH 73
Query: 217 YIAAISARFVQLQHGEIDKRVEVKPYVLDD 246
+ A+ ++DK+ + + D
Sbjct: 74 AVDAVK----NADGYKLDKQHTFRVNLFTD 99
Score = 28.2 bits (63), Expect = 1.2
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 68 EEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
I F +FG + D+ + + K+ KGY FL + + +
Sbjct: 36 NVIHKIFSKFGKITNDFYPEEDGKT----KGYIFLEYASPAHAVDAVKN 80
>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 = 28.4 bits (64), Expect = 1.1
Identities = 15/82 (18%), Positives = 26/82 (31%), Gaps = 10/82 (12%)
Query: 155 SMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQ 214
S + +T+ + + EL + + I + KG + F S+
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFED------ALEIRLVSQDGKSKGIAYIEFKSE 63
Query: 215 ASYIAAISARFVQLQHGEIDKR 236
A + Q EID R
Sbjct: 64 ADAEKNLEE----KQGAEIDGR 81
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 27.8 bits (63), Expect = 1.2
Identities = 8/38 (21%), Positives = 15/38 (39%)
Query: 186 YGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+ + D + +G G V+F SQ A+ +
Sbjct: 25 FPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 27.9 bits (63), Expect = 1.2
Identities = 17/70 (24%), Positives = 20/70 (28%), Gaps = 3/70 (4%)
Query: 154 ASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFAS 213
S +FV +P L G V YA I + KG G V F S
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKF-NECGHVLYADIKMEN--GKSKGCGVVKFES 57
Query: 214 QASYIAAISA 223
A
Sbjct: 58 PEVAERACRM 67
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 28.2 bits (63), Expect = 1.3
Identities = 13/86 (15%), Positives = 28/86 (32%), Gaps = 19/86 (22%)
Query: 57 FPLQGTPHYDHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
FP T ++I G ++ + K++ KG F++F S ++ ++
Sbjct: 19 FPTDAT----LDDIKEWLEDKGQVLNIQMRRTLHKAF---KGSIFVVFDSIESAKKFVET 71
Query: 117 CIVDEDKCYLCVSSPTIKDKPVQIRP 142
K+ + I
Sbjct: 72 ------------PGQKYKETDLLILF 85
>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding
protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi}
SCOP: d.58.7.1
Length = 139
Score = 28.6 bits (64), Expect = 1.4
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
D + + V +P + ++L + +R YG + I D E + +G G V F S +S
Sbjct: 40 DVLRNLMVNYIPTTVDEVQLRQLFER-YGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQ 98
Query: 219 AAISA 223
AI+
Sbjct: 99 QAIAG 103
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 28.0 bits (63), Expect = 1.6
Identities = 15/69 (21%), Positives = 26/69 (37%), Gaps = 2/69 (2%)
Query: 154 ASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFAS 213
+P +P T +VG +P ++ I L + + D + KG V F
Sbjct: 8 KELPTEPPYTAYVGNLPFNTVQGDIDAIFKDL--SIRSVRLVRDKDTDKFKGFCYVEFDE 65
Query: 214 QASYIAAIS 222
S A++
Sbjct: 66 VDSLKEALT 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 = 28.0 bits (63), Expect = 1.6
Identities = 16/96 (16%), Positives = 28/96 (29%), Gaps = 30/96 (31%)
Query: 153 DASMPLDPRKTVFVGGVP------------RPLKALELAMIMDRLYGGVCYAGIDTDPEL 200
+ +P P T F+G +P R L + + +
Sbjct: 7 GSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPE------------ 54
Query: 201 KYPKGAGRVAFASQASYIAAISARFVQLQHGEIDKR 236
KG G F S ++A+S L + +
Sbjct: 55 -RLKGFGYAEFEDLDSLLSALS-----LNEESLGNK 84
Score = 26.1 bits (58), Expect = 6.4
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 4/46 (8%)
Query: 68 EEITASFRRFGPLVVDWP-HKAESKSYFPPKGYAFLLFQDESSVQQ 112
E I FR V P + + KG+ + F+D S+
Sbjct: 30 ESIKEFFRGLNISAVRLPREPSNPER---LKGFGYAEFEDLDSLLS 72
>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 = 28.0 bits (63), Expect = 1.7
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
E++ F +GPL + +P + +K PKG+AF+ F +
Sbjct: 23 EDLEKLFSAYGPLSELHYPIDSLTKK---PKGFAFVTFMFPEHAVKAYAE 69
Score = 27.6 bits (62), Expect = 1.9
Identities = 13/65 (20%), Positives = 20/65 (30%), Gaps = 1/65 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
+FV + +L + YG + D K PKG V F +
Sbjct: 6 SGSGRLFVRNLSYTSSEEDLEKLFSA-YGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64
Query: 219 AAISA 223
A +
Sbjct: 65 KAYAE 69
>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 = 27.9 bits (62), Expect = 1.8
Identities = 8/59 (13%), Positives = 17/59 (28%), Gaps = 4/59 (6%)
Query: 62 TPHYDHEEITAS---FRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
+ E+ F +FG + V + P A++ + + I
Sbjct: 24 SQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQC 82
>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain,
structural genomics, NPPSFA; NMR {Mus musculus} PDB:
2rne_A 2dh7_A
Length = 115
Score = 27.7 bits (62), Expect = 1.9
Identities = 16/76 (21%), Positives = 28/76 (36%), Gaps = 7/76 (9%)
Query: 154 ASMPLDPRK------TVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAG 207
+S +K VFVG + + ++ +G + A + D KG G
Sbjct: 2 SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAP-FGRISDARVVKDMATGKSKGYG 60
Query: 208 RVAFASQASYIAAISA 223
V+F ++ AI
Sbjct: 61 FVSFFNKWDAENAIQQ 76
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 27.4 bits (61), Expect = 2.0
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 68 EEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
I F +FG + D+ + + K+ KGY FL + + +
Sbjct: 22 NVIHKIFSKFGKITNDFYPEEDGKT----KGYIFLEYASPAHAVDAVKN 66
>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 = 27.6 bits (62), Expect = 2.1
Identities = 11/65 (16%), Positives = 23/65 (35%), Gaps = 1/65 (1%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
D T+ V + + +L + +G + + D KG ++F +
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRP-FGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 71
Query: 219 AAISA 223
AI+
Sbjct: 72 RAIAG 76
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 27.1 bits (61), Expect = 2.2
Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 6/75 (8%)
Query: 162 KTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAI 221
+ ++VG + + ++ + + +G V + D E K PKG G V ++ AI
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQ-FGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAI 59
Query: 222 SARFVQLQHGEIDKR 236
+ L + + R
Sbjct: 60 AK----LDNTDFMGR 70
>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 = 27.6 bits (62), Expect = 2.3
Identities = 10/52 (19%), Positives = 22/52 (42%), Gaps = 6/52 (11%)
Query: 66 DHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
E + F + + V + ++ KGYAF+ F ++ +++C
Sbjct: 28 TEETLQEVFEKATFIKV---PQNQNGK---SKGYAFIEFASFEDAKEALNSC 73
>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 = 27.2 bits (61), Expect = 2.3
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 9/48 (18%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLI 114
+E+ F ++G ++ V P P + +AF+ F D+ Q L
Sbjct: 20 DELREFFSQYGDVMDVFIPK--------PFRAFAFVTFADDQIAQSLC 59
>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 = 27.2 bits (61), Expect = 2.4
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 13/56 (23%)
Query: 66 DHEEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
D EI + F R+G ++ D S KGY F+ F ++ VQ+++++
Sbjct: 22 DETEIRSFFARYGSVKEVKIITD----RTGVS----KGYGFVSFYNDVDVQKIVES 69
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 28.4 bits (64), Expect = 2.5
Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 14/59 (23%)
Query: 63 PHYDHEEITASFRRFGP-----LVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
D++ + +F FG +V D E+ S KGY F+ F+ + + ++ I+
Sbjct: 113 KSIDNKALYDTFSAFGNILSCKVVCD-----ENGS----KGYGFVHFETQEAAERAIEK 162
>2ffw_A Midline-1; B-BOX, ring finger, zinc-finger, ligase; NMR {Homo
sapiens}
Length = 78
Score = 27.0 bits (59), Expect = 2.6
Identities = 10/41 (24%), Positives = 13/41 (31%), Gaps = 4/41 (9%)
Query: 248 MCDECQGVRCGGKFAPFFCANVCCLQYYCEHCWATIHSKPG 288
+C C + A C V C YC+ C H
Sbjct: 32 LCQFCDQDP--AQDAVKTC--VTCEVSYCDECLKATHPNKK 68
>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 = 27.5 bits (61), Expect = 2.7
Identities = 19/86 (22%), Positives = 32/86 (37%), Gaps = 7/86 (8%)
Query: 157 PLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQAS 216
P + V++ G+P + + +L I P K G G V F ++A
Sbjct: 21 PHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK-ATGEGFVEFRNEAD 79
Query: 217 YIAAISARFVQLQHGEIDKR-VEVKP 241
Y AA+ + R ++V P
Sbjct: 80 YKAAL-----CRHKQYMGNRFIQVHP 100
>2hr7_A Insulin receptor; hormone receptor, leucine rich repeat,
transferase; HET: NAG BMA MAN FUC P33; 2.32A {Homo
sapiens}
Length = 486
Score = 28.7 bits (63), Expect = 2.7
Identities = 9/39 (23%), Positives = 13/39 (33%)
Query: 242 YVLDDQMCDECQGVRCGGKFAPFFCANVCCLQYYCEHCW 280
VL+ +EC + G C + E CW
Sbjct: 145 IVLNKDDNEECGDICPGTAKGKTNCPATVINGQFVERCW 183
>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 = 28.5 bits (63), Expect = 2.8
Identities = 12/55 (21%), Positives = 25/55 (45%)
Query: 62 TPHYDHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
T E++T + G + E+++ KG+A + E+S ++L+D
Sbjct: 77 TWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDL 131
>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 = 2.9
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 8/55 (14%)
Query: 66 DHEEITASFRRFGPL-VVD---WPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
+++ R G VV+ ++A +S KGYA ++ E+SV +L++
Sbjct: 68 TDQQLIQVIRSIGVYDVVELKFAENRANGQS----KGYAEVVVASENSVHKLLEL 118
>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA
binding domain, RBD, RNA splicing, apoptosis,
phosphoprotein, RNA-binding; 1.95A {Homo sapiens}
Length = 87
Score = 26.7 bits (60), Expect = 3.0
Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 1/67 (1%)
Query: 157 PLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQAS 216
PL VFVG + + +A +G + A + D KG G V+F ++
Sbjct: 2 PLGSHFHVFVGDLSPEITTAAIAAAFAP-FGRISDARVVKDMATGKSKGYGFVSFFNKWD 60
Query: 217 YIAAISA 223
AI
Sbjct: 61 AENAIQQ 67
>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 = 27.6 bits (61), Expect = 3.1
Identities = 7/71 (9%), Positives = 23/71 (32%), Gaps = 7/71 (9%)
Query: 153 DASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFA 212
D+ P + + + +P + E+ + +G V + K +
Sbjct: 23 DSRSAGVPSRVIHIRKLPIDVTEGEVISLGLP-FGKVTNLLMLKG------KNQAFIEMN 75
Query: 213 SQASYIAAISA 223
++ + ++
Sbjct: 76 TEEAANTMVNY 86
>1y02_A CARP2, FYVE-ring finger protein sakura; zinc-binding module,
phosphoinositide binding, caspase regulation, metal
binding protein; 1.80A {Homo sapiens} SCOP: a.140.2.1
g.50.1.1
Length = 120
Score = 27.0 bits (59), Expect = 3.7
Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 4/45 (8%)
Query: 245 DDQMCDECQGVRCGGKFAPFFCANVC--CLQYYCEHCWATIHSKP 287
+ C+ CG FA C C + +C C + + + P
Sbjct: 15 PTGLEPSCK--SCGAHFANTARKQTCLDCKKNFCMTCSSQVGNGP 57
>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 = 27.3 bits (60), Expect = 3.8
Identities = 16/94 (17%), Positives = 33/94 (35%), Gaps = 20/94 (21%)
Query: 68 EEITASFRRF----GPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDACIVDEDK 123
E++ G V + + E + G AF+ E V+ + +D+
Sbjct: 59 EDVQNFLSDCTIHDGAAGVHFIYTREGR----QSGEAFVELGSEDDVK-----MALKKDR 109
Query: 124 CYLCVSSPTIKDKPVQIRPWKLTDADFVLDASMP 157
+ + +++ T+ D+VL S P
Sbjct: 110 ES-------MGHRYIEVFKSHRTEMDWVLKHSGP 136
>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 = 26.9 bits (60), Expect = 4.0
Identities = 8/53 (15%), Positives = 19/53 (35%), Gaps = 8/53 (15%)
Query: 68 EEITASFRRFGPL---VVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDAC 117
++ + F RF + + + +G AF+ F ++ Q +
Sbjct: 40 RDLVSLFARFQEKKGPPIQFRMM-TGRM----RGQAFITFPNKEIAWQALHLV 87
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 26.7 bits (59), Expect = 4.2
Identities = 6/64 (9%), Positives = 21/64 (32%), Gaps = 7/64 (10%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
P + + + +P + E+ + +G V + K + ++ +
Sbjct: 14 VPSRVIHIRKLPIDVTEGEVISLGLP-FGKVTNLLMLKG------KNQAFIEMNTEEAAN 66
Query: 219 AAIS 222
++
Sbjct: 67 TMVN 70
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 26.9 bits (60), Expect = 4.9
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 186 YGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+G V A + D + K G V+F + S AI A
Sbjct: 64 FGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101
>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 = 26.5 bits (59), Expect = 5.2
Identities = 15/82 (18%), Positives = 26/82 (31%), Gaps = 6/82 (7%)
Query: 159 DPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYI 218
+ V +P + E+ + + + P G VAF S+
Sbjct: 13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGM-PTGEAMVAFESRDEAT 71
Query: 219 AAISARFVQLQHGEIDKR-VEV 239
AA+ L I R V++
Sbjct: 72 AAVI----DLNDRPIGSRKVKL 89
>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 = 26.5 bits (59), Expect = 5.3
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 186 YGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+G V A + D + K G V++ + S AAI +
Sbjct: 49 FGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA
recognition motif, G-tract, G-quadruplex, alternative
splicing, RNA binding protein; NMR {Homo sapiens} PDB:
2kg0_A
Length = 126
Score = 26.8 bits (59), Expect = 5.8
Identities = 23/91 (25%), Positives = 30/91 (32%), Gaps = 9/91 (9%)
Query: 153 DASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFA 212
S V + G+P E+ L + DPE K G V FA
Sbjct: 34 SNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGK-ITGEAFVQFA 92
Query: 213 SQASYIAAISARFVQLQHGE-IDKR-VEVKP 241
SQ A+ +H E I R +EV
Sbjct: 93 SQELAEKALG------KHKERIGHRYIEVFK 117
>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 = 26.0 bits (58), Expect = 6.0
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 9/48 (18%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLI 114
EE+ F ++G +V V P P + +AF+ F D+ Q L
Sbjct: 26 EELQQFFCQYGEVVDVFIPK--------PFRAFAFVTFADDKVAQSLC 65
>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 = 26.7 bits (59), Expect = 6.2
Identities = 15/91 (16%), Positives = 31/91 (34%), Gaps = 11/91 (12%)
Query: 153 DASMPLDPRKTVFVGGVPRPLKALELAMIMDRLYGGVCYAGIDTDPELKYPKGAGRVAFA 212
+ ++ V + G+P ++ L I+ P+ + G V FA
Sbjct: 38 EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL--NPVRVHIEIGPDGR-VTGEADVEFA 94
Query: 213 SQASYIAAISARFVQLQHGE-IDKR-VEVKP 241
+ +AA+S + R +E+
Sbjct: 95 THEEAVAAMSK------DRANMQHRYIELFL 119
Score = 26.3 bits (58), Expect = 8.3
Identities = 7/45 (15%), Positives = 12/45 (26%), Gaps = 4/45 (8%)
Query: 68 EEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQ 112
+I F P+ V + + G A + F
Sbjct: 61 NDIYNFFSPLNPVRVHIEIGPDGR----VTGEADVEFATHEEAVA 101
>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 = 26.8 bits (59), Expect = 6.3
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 9/41 (21%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDE 107
E+ +F +GPL V P G+AF+ F+D
Sbjct: 88 TELERAFGYYGPLRSVWVARN--------PPGFAFVEFEDP 120
>4esj_A Type-2 restriction enzyme DPNI; restriction endonuclease-DNA
complex, type IIM, type IIE, RE enzyme, DPNI; HET: DNA
6MA; 2.05A {Streptococcus pneumoniae}
Length = 257
Score = 27.2 bits (60), Expect = 6.7
Identities = 13/54 (24%), Positives = 20/54 (37%)
Query: 256 RCGGKFAPFFCANVCCLQYYCEHCWATIHSKPGREFHKPLVKEGAYDSLQTRTR 309
CG F N +YC HC K + + +GAY ++ R +
Sbjct: 39 NCGNNPLNHFENNRPVADFYCNHCSEEFELKSKKGNFSSTINDGAYATMMKRVQ 92
>3ung_C CMR2DHD; ferredoxin fold, nucleotide-binding, polymerase, CMR
complex function; HET: ADP; 2.31A {Pyrococcus furiosus}
PDB: 3ur3_C 4doz_A
Length = 693
Score = 27.7 bits (60), Expect = 6.7
Identities = 8/58 (13%), Positives = 17/58 (29%), Gaps = 1/58 (1%)
Query: 59 LQGTPHYDHEEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
++G+ H+ H + + + + + K L VQ I
Sbjct: 1 MRGSHHHHHHGMASMTGGQQMGRDLYDDDDKDHPFTSVKDPTLLRI-KIVPVQPFIAN 57
>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 = 26.1 bits (58), Expect = 6.8
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 184 RLYGGVCYAGIDTDPELKYPKGAGRVAFASQASYIAAISA 223
+ G V A I D + K +G G V F + AIS
Sbjct: 37 SMAGVVVRADILEDKDGK-SRGIGTVTFEQSIEAVQAISM 75
>1wew_A DNA-binding family protein; structural genomics, PHD domain, riken
structural genomics/proteomics initiative, RSGI, DNA
binding protein; NMR {Arabidopsis thaliana} SCOP:
g.50.1.2
Length = 78
Score = 25.4 bits (55), Expect = 7.4
Identities = 12/45 (26%), Positives = 14/45 (31%), Gaps = 1/45 (2%)
Query: 245 DDQMCDECQGVRC-GGKFAPFFCANVCCLQYYCEHCWATIHSKPG 288
+D C Q V C P +YCE C T G
Sbjct: 34 EDPRCHVWQHVGCVILPDKPMDGNPPLPESFYCEICRLTSGPSSG 78
>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 = 26.1 bits (58), Expect = 8.1
Identities = 8/50 (16%), Positives = 21/50 (42%), Gaps = 7/50 (14%)
Query: 68 EEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQDESSVQQLIDA 116
++I F ++G + +D ++ +AF+ F+D + +
Sbjct: 37 KDIEDVFYKYGAIRDIDLKNRRG------GPPFAFVEFEDPRDAEDAVYG 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
0.322 0.140 0.439
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: 5,012,956
Number of extensions: 307051
Number of successful extensions: 946
Number of sequences better than 10.0: 1
Number of HSP's gapped: 913
Number of HSP's successfully gapped: 160
Length of query: 320
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 226
Effective length of database: 4,077,219
Effective search space: 921451494
Effective search space used: 921451494
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 (21.9 bits)
S2: 57 (25.7 bits)