RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2141
(173 letters)
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 130 bits (330), Expect = 8e-39
Identities = 72/116 (62%), Positives = 93/116 (80%)
Query: 7 VQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ 66
++VGRPSN+ QAQ +ID++ EEA+ +NRIYVAS+H DL+++DIKSVFEAFG IK L +
Sbjct: 100 IKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLAR 159
Query: 67 GSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGP 122
+ +HKGYGFIEYE Q+S +A+SSMNLFDLGGQYLRVG+A+TPP L + P
Sbjct: 160 DPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATP 215
Score = 84.7 bits (210), Expect = 5e-21
Identities = 34/103 (33%), Positives = 51/103 (49%)
Query: 26 TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
+ +R+YV SI+ +L E+ I+ F FGPIK + S +HKG+ F+EYE +
Sbjct: 22 QGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPE 81
Query: 86 ASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
A+ A+ MN LGG+ ++VGR A A
Sbjct: 82 AAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124
>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 = 108 bits (272), Expect = 1e-30
Identities = 25/103 (24%), Positives = 49/103 (47%), Gaps = 11/103 (10%)
Query: 7 VQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ 66
+++ RP + +++++ + L ++ +K + +FGP+K L +
Sbjct: 80 LKIRRPHDYQPLPG-----------AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVK 128
Query: 67 GSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
S+ KGY F EY +++AI+ +N LG + L V RA
Sbjct: 129 DSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 171
Score = 68.8 bits (169), Expect = 2e-15
Identities = 19/92 (20%), Positives = 39/92 (42%), Gaps = 6/92 (6%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS---SPH--RHKGYGFIEYETKQASN 88
R+YV +I +TEE + F A + G+ + + K + F+E+ + +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 89 EAISSMNLFDLGGQYLRVGRAITPPNALHSSK 120
+A+ + + GQ L++ R + K
Sbjct: 66 QAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHK 96
>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 = 108 bits (272), Expect = 2e-30
Identities = 26/105 (24%), Positives = 48/105 (45%)
Query: 5 PHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL 64
+ + S P T +++++ + L ++ +K + +FGP+K L
Sbjct: 87 DYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNL 146
Query: 65 QQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
+ S+ KGY F EY +++AI+ +N LG + L V RA
Sbjct: 147 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA 191
Score = 69.7 bits (171), Expect = 2e-15
Identities = 20/98 (20%), Positives = 41/98 (41%), Gaps = 6/98 (6%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS-----SPHRHKGYGFIEYETKQAS 87
R+YV +I +TEE + F A + G+ ++ K + F+E+ + +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 88 NEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
+A+ + + GQ L++ R S+ P+
Sbjct: 65 TQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVY 101
>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 = 93.9 bits (234), Expect = 5e-24
Identities = 23/91 (25%), Positives = 36/91 (39%), Gaps = 2/91 (2%)
Query: 26 TEEAKLYNRIYVASIHPDLTEED-IKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETK 84
T + V + P + D + A +C+L G + KG+ +EYET
Sbjct: 178 TPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQD-GQLKGFAVLEYETA 236
Query: 85 QASNEAISSMNLFDLGGQYLRVGRAITPPNA 115
+ + EA + LGG +LRV P
Sbjct: 237 EMAEEAQQQADGLSLGGSHLRVSFCAPGPPG 267
Score = 87.3 bits (217), Expect = 2e-21
Identities = 23/95 (24%), Positives = 38/95 (40%)
Query: 27 EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
+ + VA++ P LT++ + + FG ++ C L + KGYGF EY K +
Sbjct: 90 QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS 149
Query: 87 SNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKG 121
+ A S + LG + L V
Sbjct: 150 AARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHS 184
Score = 83.1 bits (206), Expect = 7e-20
Identities = 15/96 (15%), Positives = 40/96 (41%), Gaps = 7/96 (7%)
Query: 19 QSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGF 78
+ ++ + + +I + + D+T +++ + + +KYC + ++KG F
Sbjct: 9 RKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD------KYKGTAF 61
Query: 79 IEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
+ + + AI++ + L + L V T
Sbjct: 62 VTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDAL 97
>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 = 86.9 bits (216), Expect = 4e-23
Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 9/92 (9%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
+R++V ++ PD+TEE+++ +FE +G + + KG+GFI ET+ + A
Sbjct: 15 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETRTLAEIAK 68
Query: 92 SSMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
++ L G+ LRV A + + GP+
Sbjct: 69 VELDNMPLRGKQLRVRFACHSAS---LTSGPS 97
>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 = 87.0 bits (216), Expect = 5e-23
Identities = 21/103 (20%), Positives = 42/103 (40%), Gaps = 6/103 (5%)
Query: 12 PSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH 71
S + D + + + +Y I LT++ ++ F FG I ++
Sbjct: 5 SSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------ 58
Query: 72 RHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
KGY F+ + T +++ AI S+N + G ++ P+
Sbjct: 59 PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD 101
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 85.1 bits (211), Expect = 2e-22
Identities = 29/97 (29%), Positives = 42/97 (43%), Gaps = 10/97 (10%)
Query: 12 PSNMPQAQSVIDEITEEAKLYNR-IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSP 70
P PQA +D I A Y+ +I TE D+ +F+ FG I K
Sbjct: 9 PQVNPQA---VDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY----- 60
Query: 71 HRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVG 107
KG FI+Y+T + + I ++ F G+ LR G
Sbjct: 61 -PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG 96
>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 = 84.1 bits (209), Expect = 3e-22
Identities = 18/83 (21%), Positives = 40/83 (48%), Gaps = 1/83 (1%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQG-SSPHRHKGYGFIEYETKQASNEAI 91
++++ + ++T++ I +F +G IK + PH KGY ++E+E + +A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 92 SSMNLFDLGGQYLRVGRAITPPN 114
M+ + GQ + + P
Sbjct: 65 KHMDGGQIDGQEITATAVLAPWP 87
>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 = 87.7 bits (218), Expect = 4e-22
Identities = 25/91 (27%), Positives = 42/91 (46%), Gaps = 2/91 (2%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
I++ ++ + + + F AFG I CK+ + KGYGF+ +ET++A+ AI
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIE 161
Query: 93 SMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
MN L + + VGR + A
Sbjct: 162 KMNGMLLNDRKVFVGRFKSRKEREAELGARA 192
Score = 76.5 bits (189), Expect = 5e-18
Identities = 22/87 (25%), Positives = 42/87 (48%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+YV +HPD+TE + F GPI ++ + R GY ++ ++ + A+ +M
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 95 NLFDLGGQYLRVGRAITPPNALHSSKG 121
N + G+ +R+ + P+ S G
Sbjct: 78 NFDVIKGKPVRIMWSQRDPSLRKSGVG 104
>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 = 83.4 bits (207), Expect = 7e-22
Identities = 25/76 (32%), Positives = 41/76 (53%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+Y+ SI D TEE I + GP+ K+ R KGY FIE+ ++S A+ +
Sbjct: 4 VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63
Query: 94 MNLFDLGGQYLRVGRA 109
+N + LG ++L+ G +
Sbjct: 64 LNGYQLGSRFLKCGYS 79
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 82.7 bits (205), Expect = 2e-21
Identities = 23/104 (22%), Positives = 43/104 (41%), Gaps = 8/104 (7%)
Query: 11 RPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSP 70
S + S + E R++V D+ E ++ +F FGP+K K+
Sbjct: 10 HSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL----- 64
Query: 71 HRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
G+ F+E+E +++ +AI ++ Q L V + P
Sbjct: 65 ---NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLPAK 105
>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 = 82.7 bits (205), Expect = 2e-21
Identities = 29/96 (30%), Positives = 56/96 (58%)
Query: 14 NMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRH 73
+ A ++ + + + + R+YV S+H ++TE+ ++ +FE FG I+ +L S R
Sbjct: 8 HSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRS 67
Query: 74 KGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
KGYGFI + + + +A+ +N F+L G+ ++VG
Sbjct: 68 KGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV 103
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 83.3 bits (206), Expect = 3e-21
Identities = 21/84 (25%), Positives = 42/84 (50%)
Query: 26 TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
A +YV + ++ ++ + + F FG I ++ +H+G+ F+E+E +
Sbjct: 57 GGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 116
Query: 86 ASNEAISSMNLFDLGGQYLRVGRA 109
+ AI +MN +L G+ +RV A
Sbjct: 117 DAAAAIDNMNESELFGRTIRVNLA 140
>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger,
CYP33, MLL, RNA binding protein, ALT splicing, mRNA
processing, mRNA splicing; 1.85A {Homo sapiens} PDB:
2kyx_A 3lpy_A*
Length = 85
Score = 80.3 bits (199), Expect = 1e-20
Identities = 20/77 (25%), Positives = 41/77 (53%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+YV + ++ ++ + + F FG I ++ +H+G+ F+E+E + + AI
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 93 SMNLFDLGGQYLRVGRA 109
+MN +L G+ +RV A
Sbjct: 68 NMNESELFGRTIRVNLA 84
>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 = 82.2 bits (203), Expect = 1e-20
Identities = 23/82 (28%), Positives = 39/82 (47%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
++V SIH + E++I+ F +G IK L KGY +EYET + + A
Sbjct: 73 WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132
Query: 93 SMNLFDLGGQYLRVGRAITPPN 114
++N ++ GQ ++V
Sbjct: 133 ALNGAEIMGQTIQVDWCFVKGP 154
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 80.0 bits (198), Expect = 3e-20
Identities = 28/83 (33%), Positives = 39/83 (46%), Gaps = 2/83 (2%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
++V +H + TEEDI F +G IK L KGY +EYET + + A+
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
Query: 93 SMNLFDLGGQYLRVGRAIT--PP 113
+N DL GQ + V PP
Sbjct: 84 GLNGQDLMGQPISVDWCFVRGPP 106
>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 = 79.6 bits (197), Expect = 3e-20
Identities = 23/76 (30%), Positives = 39/76 (51%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++V SIH + E++I+ F +G IK L KGY +EYET + + A +
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87
Query: 94 MNLFDLGGQYLRVGRA 109
+N ++ GQ ++V
Sbjct: 88 LNGAEIMGQTIQVDWC 103
>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 = 77.2 bits (191), Expect = 2e-19
Identities = 28/77 (36%), Positives = 46/77 (59%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+ +YV S+H ++TE+ ++ +FE FG I L + S R KGYGFI + + + A+
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 93 SMNLFDLGGQYLRVGRA 109
+N F+L G+ +RVG
Sbjct: 66 QLNGFELAGRPMRVGHV 82
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 76.8 bits (190), Expect = 3e-19
Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 2/77 (2%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+I+V ++ D T + +K F G + Y ++ + + KG G +++E+ + + A
Sbjct: 9 CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMEN--GKSKGCGVVKFESPEVAERACR 66
Query: 93 SMNLFDLGGQYLRVGRA 109
MN L G+ + V
Sbjct: 67 MMNGMKLSGREIDVRID 83
>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 = 76.9 bits (190), Expect = 3e-19
Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 8/83 (9%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
R++V + P+ + + F+ FG I+ + + +I+YE+ A+ A +
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACA 71
Query: 93 SMNLFDLGGQY--LRVGRAITPP 113
M F LGG LRV A + P
Sbjct: 72 KMRGFPLGGPDRRLRVDFAKSGP 94
>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 = 76.6 bits (189), Expect = 4e-19
Identities = 19/91 (20%), Positives = 43/91 (47%), Gaps = 5/91 (5%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
R++V++I + D++ +F FG I ++ + KG+GF+ +E ++ A
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRARE 73
Query: 93 SMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
++ + G+ + V A ++ GP+
Sbjct: 74 KLHGTVVEGRKIEVNNATARVM---TNSGPS 101
>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 = 76.6 bits (189), Expect = 5e-19
Identities = 22/101 (21%), Positives = 42/101 (41%), Gaps = 8/101 (7%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
++V ++ +TEE ++ F FG ++ K K Y FI ++ + + +A+
Sbjct: 11 VKVLFVRNLANTVTEEILEKAFSQFGKLERVKK--------LKDYAFIHFDERDGAVKAM 62
Query: 92 SSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTA 132
MN DL G+ + + A P K + S +
Sbjct: 63 EEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103
>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 = 76.2 bits (188), Expect = 5e-19
Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 8/88 (9%)
Query: 27 EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
+ N +YV D+T ++ F FG I + + F+ YE ++
Sbjct: 10 RAPRKGNTLYVY--GEDMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMES 61
Query: 87 SNEAISSMNLFDLGGQYLRVGRAITPPN 114
+++A++ +N + L+V A P
Sbjct: 62 ADQAVAELNGTQVESVQLKVNIARKQPM 89
>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 = 76.6 bits (189), Expect = 6e-19
Identities = 24/106 (22%), Positives = 47/106 (44%), Gaps = 7/106 (6%)
Query: 28 EAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETK 84
EA ++++ ++ + E+ +K+VF GPI L + + +G+ FI +E
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTS----KSRGFAFITFENP 58
Query: 85 QASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMP 130
+ A MN L G+ ++V +A P + P S+ +
Sbjct: 59 ADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRS 104
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 76.7 bits (189), Expect = 7e-19
Identities = 22/111 (19%), Positives = 41/111 (36%), Gaps = 11/111 (9%)
Query: 2 QHFPHVQVGRPS---NMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGP 58
H H P P +S + N +YV D+T ++ F FG
Sbjct: 6 HHHHHSSGLVPRGSHMGPFRRSDSFPERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGN 63
Query: 59 IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
I + + F+ YE +++++A++ +N + L+V A
Sbjct: 64 IIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 108
>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 = 77.2 bits (190), Expect = 8e-19
Identities = 14/80 (17%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++YV ++ + + +++ F +GP++ + G+ F+E+E + + +A+
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRE 129
Query: 94 MNLFDLGGQYLRVGRAITPP 113
++ L G +RV +
Sbjct: 130 LDGRTLCGCRVRVELSNGEK 149
>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 = 75.7 bits (187), Expect = 9e-19
Identities = 17/78 (21%), Positives = 37/78 (47%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+ +YV+++ LT D+ +F +G + + + + KG FI + K ++
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 93 SMNLFDLGGQYLRVGRAI 110
++N L G+ ++ AI
Sbjct: 77 AINNKQLFGRVIKASIAI 94
>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 = 75.8 bits (187), Expect = 1e-18
Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ---QGSSPHRHKGYGFIEYETKQASNE 89
+ +++ +++ TEE +K VF G IK C + + G+GF+EY+ + + +
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 90 AISSMNLFDLGGQYLRVGRA 109
A+ + + G L V +
Sbjct: 66 ALKQLQGHTVDGHKLEVRIS 85
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 75.4 bits (186), Expect = 1e-18
Identities = 15/83 (18%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
++++++ + T+E+++ + +A G +K +L + + KG ++EYE + +++A+
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAVM 76
Query: 93 SMNLFDLGGQYLRVGRAITPPNA 115
M+ + ++V + + P++
Sbjct: 77 KMDGMTIKENIIKVAISNSGPSS 99
>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 = 75.3 bits (186), Expect = 1e-18
Identities = 21/84 (25%), Positives = 43/84 (51%)
Query: 26 TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
+ A +YV + ++ ++ + + F FG I ++ +H+G+ F+E+E +
Sbjct: 6 SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65
Query: 86 ASNEAISSMNLFDLGGQYLRVGRA 109
+ AI +MN +L G+ +RV A
Sbjct: 66 DAAAAIDNMNESELFGRTIRVNLA 89
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 75.4 bits (186), Expect = 1e-18
Identities = 16/95 (16%), Positives = 41/95 (43%), Gaps = 5/95 (5%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++YV ++ + +++ F +GP++ + G+ F+E+E + + +A+
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRG 56
Query: 94 MNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSH 128
++ + G +RV + P + PA
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLL 91
>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 = 76.8 bits (190), Expect = 1e-18
Identities = 19/75 (25%), Positives = 39/75 (52%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+ V + D+T+ ++ ++F A GPI C++ + GY F+++ ++ S AI +
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 95 NLFDLGGQYLRVGRA 109
N + + L+V A
Sbjct: 66 NGITVRNKRLKVSYA 80
Score = 64.1 bits (157), Expect = 1e-13
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKL----QQGSSPHRHKGYGFIEYETKQASNEA 90
+YV ++ +T++ + ++F +G I + G +G F+ Y ++ + EA
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP----RGVAFVRYNKREEAQEA 147
Query: 91 ISSMN--LFDLGGQYLRVGRA 109
IS++N + + G Q L V A
Sbjct: 148 ISALNNVIPEGGSQPLSVRLA 168
>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 = 75.4 bits (186), Expect = 2e-18
Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 3/77 (3%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
RIYV ++ PD+ +DI+ VF +G I+ L+ + F+E+E + + +A+
Sbjct: 23 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVY 79
Query: 93 SMNLFDLGGQYLRVGRA 109
+ +D G LRV
Sbjct: 80 GRDGYDYDGYRLRVEFP 96
>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 = 75.4 bits (186), Expect = 2e-18
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 5/93 (5%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+Y+ ++ P +TE D+ S+F F K +Q R +G FI + K+ + +A+
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 93 SMNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
+N + L G+ L + + PS
Sbjct: 86 LVNGYKLYGKILVIEFGKNK-----KQRSSGPS 113
>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 = 74.6 bits (184), Expect = 2e-18
Identities = 16/80 (20%), Positives = 39/80 (48%), Gaps = 7/80 (8%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNE 89
++V ++ + EE + +F GP+ + ++G + K +GF+ ++ ++ +
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG----KPKSFGFVCFKHPESVSY 72
Query: 90 AISSMNLFDLGGQYLRVGRA 109
AI+ +N L G+ + V
Sbjct: 73 AIALLNGIRLYGRPINVSGP 92
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 74.5 bits (184), Expect = 2e-18
Identities = 20/77 (25%), Positives = 34/77 (44%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+ V + TE D++ VF +GPI + R +G+ F+ +E + EA
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
Query: 93 SMNLFDLGGQYLRVGRA 109
N +L G+ +RV
Sbjct: 76 RANGMELDGRRIRVSGP 92
>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 = 76.5 bits (189), Expect = 3e-18
Identities = 16/100 (16%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 10 GRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSS 69
G + + + +++ + + ++ ++TE+++K VFE I+ Q G S
Sbjct: 80 GNEIKLEKPKG---RDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-QDGKS 135
Query: 70 PHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
KG +IE++++ + + + ++ G+ + +
Sbjct: 136 ----KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT 171
Score = 68.8 bits (169), Expect = 2e-15
Identities = 10/95 (10%), Positives = 43/95 (45%), Gaps = 3/95 (3%)
Query: 20 SVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFI 79
S + E +E +N +++ +++P+ + ++K + + ++ +G++
Sbjct: 2 SHMVEGSESTTPFN-LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-GTNRKFGYV 59
Query: 80 EYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
++E+ + +A+ + + G +++ + +
Sbjct: 60 DFESAEDLEKAL-ELTGLKVFGNEIKLEKPKGRDS 93
>1x4e_A RNA binding motif, single-stranded interacting protein 2;
structural genomics, RRM domain, NPPSFA; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 85
Score = 74.1 bits (183), Expect = 3e-18
Identities = 15/76 (19%), Positives = 40/76 (52%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+Y+ + P T++D+ + + +G I K + ++ KGYGF+++++ A+ +A+++
Sbjct: 7 GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66
Query: 94 MNLFDLGGQYLRVGRA 109
+ + Q +
Sbjct: 67 LKASGVQAQMAKQSGP 82
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 74.7 bits (184), Expect = 3e-18
Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 2/77 (2%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
R++V++I + D++ +F FG I ++ + KG+GF+ +E ++ A
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII--FNERGSKGFGFVTFENSADADRARE 87
Query: 93 SMNLFDLGGQYLRVGRA 109
++ + G+ + V A
Sbjct: 88 KLHGTVVEGRKIEVNNA 104
>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 = 73.8 bits (182), Expect = 4e-18
Identities = 19/90 (21%), Positives = 39/90 (43%), Gaps = 9/90 (10%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+YV ++ +EE I+ F P +++ + + Y F+ + ++ + EA+ ++
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKAL 71
Query: 95 NLFDLGGQYLRVGRAITPPNALHSSKGPAP 124
N L G + V A S GP+
Sbjct: 72 NGKVLDGSPIEVTLAKPVDK---DSSGPSS 98
>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 = 74.2 bits (183), Expect = 4e-18
Identities = 21/83 (25%), Positives = 38/83 (45%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
I V ++ D E D++ +F FG I L + + + KG+ FI + ++ + AI+
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75
Query: 93 SMNLFDLGGQYLRVGRAITPPNA 115
++ F L V A N+
Sbjct: 76 GVSGFGYDHLILNVEWAKPSTNS 98
>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 = 73.4 bits (181), Expect = 6e-18
Identities = 23/90 (25%), Positives = 48/90 (53%), Gaps = 11/90 (12%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++++ ++ + TE++I+S+FE +G + C + K YGF+ E K A+ +AI +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDKTAAEDAIRN 61
Query: 94 MNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
++ + L G + V + +S GP+
Sbjct: 62 LHHYKLHGVNINVEASKNKSK---ASSGPS 88
>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 101
Score = 73.9 bits (182), Expect = 6e-18
Identities = 23/78 (29%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
+ ++++ TEE ++ VFE IK + Q G S KGY FIE+ + + + EA+
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKS----KGYAFIEFASFEDAKEAL 70
Query: 92 SSMNLFDLGGQYLRVGRA 109
+S N ++ G+ +R+
Sbjct: 71 NSCNKREIEGRAIRLELQ 88
>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 = 74.3 bits (183), Expect = 7e-18
Identities = 14/77 (18%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
++ V+++ +++ DI+ +F FG +K + S R G + +E + + +A+
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMK 94
Query: 93 SMNLFDLGGQYLRVGRA 109
L G+ + +
Sbjct: 95 QYKGVPLDGRPMDIQLV 111
>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 = 74.3 bits (183), Expect = 7e-18
Identities = 30/96 (31%), Positives = 41/96 (42%), Gaps = 1/96 (1%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
++V +H + TEEDI F +G IK L KGY +EYET + + A+
Sbjct: 23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82
Query: 93 SMNLFDLGGQYLRVGRAIT-PPNALHSSKGPAPSTS 127
+N DL GQ + V P G S S
Sbjct: 83 GLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSRS 118
>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 = 73.1 bits (180), Expect = 7e-18
Identities = 17/95 (17%), Positives = 42/95 (44%), Gaps = 12/95 (12%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
N++Y+ ++ P +T +D++ +F ++ GY F++Y + + AI
Sbjct: 9 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNWAIRAIE 62
Query: 93 SMN-LFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
+++ +L G+ + V + + PS+
Sbjct: 63 TLSGKVELHGKIMEVDYS-VSK----KLRSSGPSS 92
>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 = 75.3 bits (186), Expect = 8e-18
Identities = 27/108 (25%), Positives = 47/108 (43%), Gaps = 14/108 (12%)
Query: 8 QVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL--- 64
+ P M A S + E+ KL+ + I TE DI+ +F +FG I+ C++
Sbjct: 75 GMHHPIQMKPADSEKNNAVEDRKLF----IGMISKKCTENDIRVMFSSFGQIEECRILRG 130
Query: 65 QQGSSPHRHKGYGFIEYETKQASNEAISSMN---LFDLGGQYLRVGRA 109
G S +G F+ + T+ + AI +M+ + + V A
Sbjct: 131 PDGLS----RGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
Score = 71.1 bits (175), Expect = 3e-16
Identities = 14/77 (18%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ--GSSPHRHKGYGFIEYETKQASNEAIS 92
++V + +E+D++ +FE +G + + + +P + KG F+ + T++A+ EA +
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 93 SMNLFDLGGQYLRVGRA 109
+++ + +
Sbjct: 66 ALHNMKVLPGMHHPIQM 82
>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation,
RNA-binding, EIF4G-binding translation; 1.90A {Homo
sapiens} PDB: 4f26_A 2k8g_A
Length = 115
Score = 73.8 bits (182), Expect = 8e-18
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
I++ ++ + + + F AFG I CK+ + KGYGF+ +ET++A+ AI M
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVC--DENGSKGYGFVHFETQEAAERAIEKM 65
Query: 95 NLFDLGGQYLRVGRAI 110
N L + + VGR
Sbjct: 66 NGMLLNDRKVFVGRFK 81
>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 = 73.5 bits (181), Expect = 9e-18
Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
++ V+++ +++ DI+ +F FG +K + S R G + +E K + +A+
Sbjct: 30 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALKAMK 88
Query: 93 SMNLFDLGGQYLRVGRA 109
N L G+ + +
Sbjct: 89 QYNGVPLDGRPMNIQLV 105
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 73.6 bits (181), Expect = 9e-18
Identities = 15/77 (19%), Positives = 37/77 (48%), Gaps = 3/77 (3%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+Y+ ++ +T E++ +F +GPI+ ++ +G ++ YE + A+ +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 95 NLFDLGGQYLRVGRAIT 111
+ F++ +YL V
Sbjct: 68 SGFNVSNRYLVVLYYNA 84
>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 = 74.5 bits (184), Expect = 1e-17
Identities = 21/75 (28%), Positives = 43/75 (57%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+ V + ++T+E+ +S+F + G I+ CKL + + GYGF+ Y + + +AI+++
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 95 NLFDLGGQYLRVGRA 109
N L + ++V A
Sbjct: 65 NGLRLQTKTIKVSYA 79
Score = 64.1 bits (157), Expect = 1e-13
Identities = 16/78 (20%), Positives = 37/78 (47%), Gaps = 2/78 (2%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+YV+ + +T+++++ +F +G I ++ +G GFI ++ + + EAI
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
Query: 94 MN--LFDLGGQYLRVGRA 109
+N + + V A
Sbjct: 150 LNGQKPSGATEPITVKFA 167
>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 = 72.1 bits (178), Expect = 1e-17
Identities = 17/82 (20%), Positives = 39/82 (47%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
++V ++ ++ +E +++ F+ F + +GYGF+ + ++ + A+
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
Query: 93 SMNLFDLGGQYLRVGRAITPPN 114
SM DL G+ LR+ A +
Sbjct: 62 SMQGQDLNGRPLRINWAAKLEH 83
>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 = 72.4 bits (178), Expect = 2e-17
Identities = 23/96 (23%), Positives = 47/96 (48%), Gaps = 8/96 (8%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++++ I +L E+D+K +FE FG I + + HKG F+ Y ++++ +A S+
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 94 MN---LFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
++ + ++V A + S G PS+
Sbjct: 75 LHEQKTLPGMNRPIQVKPADS-----ESRGGSGPSS 105
>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 = 72.8 bits (179), Expect = 2e-17
Identities = 29/94 (30%), Positives = 46/94 (48%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++V + P++T EDIK+ F FG I ++ + + + KGYGF+ + K + AI
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 94 MNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTS 127
M LGG+ +R A P A S+ S
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQS 110
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 72.4 bits (178), Expect = 2e-17
Identities = 9/74 (12%), Positives = 33/74 (44%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+ A ++ ++ E +K + +G ++ ++ +H G + + + + + E +
Sbjct: 7 KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
Query: 93 SMNLFDLGGQYLRV 106
+++L + G +
Sbjct: 67 NLHLTSVMGNIIHA 80
>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 = 71.9 bits (177), Expect = 3e-17
Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 2/80 (2%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+YV ++ D+TE I +F GP K CK+ + + Y F+E+ + + A+++M
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKM--ITEHTSNDPYCFVEFYEHRDAAAALAAM 75
Query: 95 NLFDLGGQYLRVGRAITPPN 114
N + G+ ++V A TP +
Sbjct: 76 NGRKILGKEVKVNWATTPSS 95
>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 = 71.4 bits (176), Expect = 3e-17
Identities = 22/76 (28%), Positives = 38/76 (50%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++V + P++T I + F FG I ++ + + + KGYGF+ + K + AI
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 94 MNLFDLGGQYLRVGRA 109
M LGG+ +R A
Sbjct: 68 MGGQWLGGRQIRTNWA 83
>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 = 76.8 bits (188), Expect = 3e-17
Identities = 20/71 (28%), Positives = 37/71 (52%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
+ ++VA ++ D TE ++ FE +GPIK + + +GY FIEYE ++ + A
Sbjct: 102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 92 SSMNLFDLGGQ 102
+ + G+
Sbjct: 162 KHADGKKIDGR 172
>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 = 71.5 bits (176), Expect = 5e-17
Identities = 27/99 (27%), Positives = 44/99 (44%), Gaps = 4/99 (4%)
Query: 27 EEAKL-YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
E K+ N ++V I + E +I+S F +G +K K+ + KGYGF+ +
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDV 61
Query: 86 ASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAP 124
+ + S F G+ L++G AI N P P
Sbjct: 62 DVQKIVESQINFH--GKKLKLGPAIRKQNLSTYHVQPRP 98
>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 = 74.7 bits (184), Expect = 5e-17
Identities = 23/106 (21%), Positives = 46/106 (43%), Gaps = 9/106 (8%)
Query: 9 VGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS 68
+G ++ ++ R++V ++ D+TEED K +FE +G +
Sbjct: 2 MGFTIDIKSFLKPGEK---TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFIN--- 55
Query: 69 SPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
R +G+GFI E++ + A + ++ L + LR+ A
Sbjct: 56 ---RDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAA 98
Score = 66.6 bits (163), Expect = 6e-14
Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 12/83 (14%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNE 89
+ V ++ P ++ E ++ F FGP++ + +G R G GF+E+ K + +
Sbjct: 97 AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRG----RATGKGFVEFAAKPPARK 152
Query: 90 AISSMNLFDLGGQYLRVGRAITP 112
A+ G +L + P
Sbjct: 153 ALERCG----DGAFL-LTTTPRP 170
>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 = 71.1 bits (175), Expect = 7e-17
Identities = 20/75 (26%), Positives = 43/75 (57%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+YV + ++E + +F GP+ + + +H+GYGF+E+ +++ ++ AI M
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 95 NLFDLGGQYLRVGRA 109
++ L G+ +RV +A
Sbjct: 78 DMIKLYGKPIRVNKA 92
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 70.0 bits (172), Expect = 9e-17
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 7/74 (9%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+YV + +TE D+++ F FG I+ + Q + FI++ T+QA+ A
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKS 68
Query: 95 -NLFDLGGQYLRVG 107
N + G+ L V
Sbjct: 69 FNKLIVNGRRLNVK 82
>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 = 70.7 bits (174), Expect = 9e-17
Identities = 17/93 (18%), Positives = 42/93 (45%), Gaps = 5/93 (5%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+ V ++ + + ++ VFE +G + + + +G+ F+ + ++ + +A ++
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 94 MNLFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
M+ +L G+ LRV A PS+
Sbjct: 75 MDGAELDGRELRVQVARYGRR-----DLSGPSS 102
>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 = 70.8 bits (174), Expect = 1e-16
Identities = 18/75 (24%), Positives = 38/75 (50%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+++ + + ++D+ +F FG + K+ + K +GF+ Y+ ++ AI SM
Sbjct: 28 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 95 NLFDLGGQYLRVGRA 109
N F +G + L+V
Sbjct: 88 NGFQIGMKRLKVQLK 102
>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 = 69.9 bits (172), Expect = 1e-16
Identities = 20/92 (21%), Positives = 41/92 (44%), Gaps = 14/92 (15%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+I+V ++ T ++++S+FE G + C + K Y F+ E + + AI+
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDV--------VKDYAFVHMEKEADAKAAIAQ 62
Query: 94 MNLFDLGGQYLRVGRAITPPNALHSSKGPAPS 125
+N ++ G+ + V + K PS
Sbjct: 63 LNGKEVKGKRINVELSTKGQ------KKSGPS 88
>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 = 69.6 bits (171), Expect = 2e-16
Identities = 20/91 (21%), Positives = 45/91 (49%), Gaps = 11/91 (12%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+++V +I P T +++++ FE +GP+ C + K Y F+ E + + EAI
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDI--------VKDYAFVHMERAEDAVEAIR 62
Query: 93 SMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
++ + G+ + V + + ++ GP+
Sbjct: 63 GLDNTEFQGKRMHVQLSTSRL---RTASGPS 90
>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 = 70.5 bits (173), Expect = 2e-16
Identities = 23/102 (22%), Positives = 52/102 (50%)
Query: 8 QVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQG 67
Q+ + Q ++ E + + V I + E ++ +FE +GPI+ K+
Sbjct: 18 QLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCD 77
Query: 68 SSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
+ +GYGF+++++ ++ +AI+ +N F++ + L+V A
Sbjct: 78 RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119
>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 = 69.7 bits (171), Expect = 2e-16
Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 6/88 (6%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+++ ++ D EE + V + FG +KY ++ KG F ++ T++A+ + +++
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAA 76
Query: 94 MNL------FDLGGQYLRVGRAITPPNA 115
+L L G+ L+V A+T A
Sbjct: 77 ASLEAEGGGLKLDGRQLKVDLAVTRDEA 104
>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure
genomics, RRM domain, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 70.0 bits (172), Expect = 2e-16
Identities = 12/78 (15%), Positives = 33/78 (42%), Gaps = 7/78 (8%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQASNEAI 91
+Y++++ + E++++++ + FG + ++ G+S +G GF E+ + I
Sbjct: 28 LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTS----RGVGFARMESTEKCEAVI 83
Query: 92 SSMNLFDLGGQYLRVGRA 109
N +
Sbjct: 84 GHFNGKFIKTPPGVSAPT 101
>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 = 69.6 bits (171), Expect = 3e-16
Identities = 19/82 (23%), Positives = 42/82 (51%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+++V + D E+ ++ VF +G I + + R +G+GF+ +E + +A+
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72
Query: 93 SMNLFDLGGQYLRVGRAITPPN 114
+MN + G+ +RV +A +
Sbjct: 73 AMNGKSVDGRQIRVDQAGKSSD 94
>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 = 73.1 bits (180), Expect = 3e-16
Identities = 12/76 (15%), Positives = 29/76 (38%), Gaps = 3/76 (3%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+ V ++ + + F+ GPI + + S ++ + IE+ + AI+
Sbjct: 44 VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD--SLKKNFRFARIEFARYDGALAAITKT 101
Query: 95 NLFDLGGQYLRVGRAI 110
+ +G + V
Sbjct: 102 H-KVVGQNEIIVSHLT 116
Score = 70.8 bits (174), Expect = 3e-15
Identities = 8/77 (10%), Positives = 30/77 (38%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+++ + P T+ +I+ + + + + + + +I+ +K+ + +
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177
Query: 93 SMNLFDLGGQYLRVGRA 109
+N + G L +
Sbjct: 178 KLNGLKIEGYTLVTKVS 194
Score = 65.0 bits (159), Expect = 2e-13
Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 35 IYVASIHPDLTEED-IKSVFEAFGPIKYCKLQQGSSPH-RHKGYGFIEYETKQASNEAIS 92
I + ++ +L +E+ ++ FE FG I+ + G H + F+ +E K ++ A+
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL- 271
Query: 93 SMNLFDLGGQYLRVGRA 109
MN LG + + V A
Sbjct: 272 QMNRSLLGNREISVSLA 288
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 71.0 bits (174), Expect = 4e-16
Identities = 14/79 (17%), Positives = 36/79 (45%), Gaps = 1/79 (1%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
++ V+++ +++ DI+ +F FG +K + S R G + +E + + +A+
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS-GRSLGTADVHFERRADALKAMK 147
Query: 93 SMNLFDLGGQYLRVGRAIT 111
L G+ + + +
Sbjct: 148 QYKGVPLDGRPMDIQLVAS 166
>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 = 68.8 bits (169), Expect = 4e-16
Identities = 15/89 (16%), Positives = 41/89 (46%), Gaps = 5/89 (5%)
Query: 26 TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
+++ + + ++ ++TE+++K VFE I+ Q G S KG +IE++++
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-QDGKS----KGIAYIEFKSEA 64
Query: 86 ASNEAISSMNLFDLGGQYLRVGRAITPPN 114
+ + + ++ G+ + +
Sbjct: 65 DAEKNLEEKQGAEIDGRSVSLYYTGEKGG 93
>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 = 68.9 bits (169), Expect = 4e-16
Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 33 NRIYVASIHPDL-TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
+R+++ +++ L + D++++F +G + C + HKGY F++Y ++ + A+
Sbjct: 28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAV 79
Query: 92 SSMNLFDLGGQYLRVGRAITPPN 114
N L GQ L + A P
Sbjct: 80 LGENGRVLAGQTLDINMAGEPKP 102
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 69.3 bits (170), Expect = 5e-16
Identities = 18/75 (24%), Positives = 37/75 (49%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+++ + + T+ D+ S F FG + K+ K +GF+ ++ ++ AI +M
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 95 NLFDLGGQYLRVGRA 109
N F +G + L+V
Sbjct: 103 NGFQVGTKRLKVQLK 117
>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 = 68.4 bits (168), Expect = 7e-16
Identities = 24/77 (31%), Positives = 42/77 (54%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
++V +I + TEE +K +F GP+ +L + KGYGF EY+ ++ + A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 93 SMNLFDLGGQYLRVGRA 109
++N + G+ LRV A
Sbjct: 69 NLNGREFSGRALRVDNA 85
>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 = 69.9 bits (172), Expect = 7e-16
Identities = 18/80 (22%), Positives = 39/80 (48%), Gaps = 1/80 (1%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+YV ++ +TE+ +K F+ GPI K+ + +++ Y F+EY +N A+ ++
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTL 61
Query: 95 NLFDLGGQYLRVGRAITPPN 114
N + +++ A
Sbjct: 62 NGKQIENNIVKINWAFQSQQ 81
Score = 68.7 bits (169), Expect = 2e-15
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 8/80 (10%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKL----QQGSSPHRHKGYGFIEYETKQASNE 89
++V ++ ++ +E +++ F+ F + Q GSS +GYGF+ + ++ +
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSS----RGYGFVSFTSQDDAQN 144
Query: 90 AISSMNLFDLGGQYLRVGRA 109
A+ SM DL G+ LR+ A
Sbjct: 145 AMDSMQGQDLNGRPLRINWA 164
>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 = 69.0 bits (169), Expect = 7e-16
Identities = 22/79 (27%), Positives = 37/79 (46%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+ V + TE D++ VF +GPI + R +G+ F+ +E + EA
Sbjct: 47 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106
Query: 93 SMNLFDLGGQYLRVGRAIT 111
N +L G+ +RV +IT
Sbjct: 107 RANGMELDGRRIRVDFSIT 125
>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 103
Score = 67.6 bits (166), Expect = 1e-15
Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 6/78 (7%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKL--QQGSSPHRHKGYGFIEYETKQASNEAI 91
+YV ++ + +E ++ F FG I K+ + G S KG+GF+ + + + + +A+
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRS----KGFGFVCFSSPEEATKAV 72
Query: 92 SSMNLFDLGGQYLRVGRA 109
+ MN + + L V A
Sbjct: 73 TEMNGRIVATKPLYVALA 90
>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 107
Score = 67.7 bits (166), Expect = 1e-15
Identities = 21/79 (26%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQ-GSSPHRHKGYGFIEYETKQASNEAI 91
++I V +I + +I+ +F FG +K +L + + H+G+GF+++ TKQ + +A
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Query: 92 SSM-NLFDLGGQYLRVGRA 109
+++ + L G+ L + A
Sbjct: 76 NALCHSTHLYGRRLVLEWA 94
>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 = 67.3 bits (165), Expect = 2e-15
Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 4/83 (4%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+++V ++ +EED+ +F+ FG I C + +G KG F+++ + + AI
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDG-SSKGCAFVKFSSHTEAQAAIH 74
Query: 93 SMN---LFDLGGQYLRVGRAITP 112
+++ L V A T
Sbjct: 75 ALHGSQTMPGASSSLVVKFADTD 97
>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 96
Score = 67.2 bits (165), Expect = 2e-15
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYC-KLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
I++ ++ P++ E+ + F AFG I K+ + KGY FI + + AS+ AI
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 93 SMNLFDLGGQYLRVGRAI 110
+MN L + + V A
Sbjct: 67 AMNGQYLCNRPITVSYAF 84
>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 = 67.3 bits (165), Expect = 2e-15
Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 7/87 (8%)
Query: 26 TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYE 82
+ +L + ++VA++ + + +K VF G + + + G S +G G + +E
Sbjct: 9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKS----RGIGTVTFE 64
Query: 83 TKQASNEAISSMNLFDLGGQYLRVGRA 109
+ +AIS N L + + V
Sbjct: 65 QSIEAVQAISMFNGQLLFDRPMHVKMD 91
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 67.8 bits (166), Expect = 3e-15
Identities = 20/88 (22%), Positives = 44/88 (50%), Gaps = 2/88 (2%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+ V ++ + + ++ VFE +G + + + +G+ F+ + K+ + +A+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 93 SMNLFDLGGQYLRVGRAIT--PPNALHS 118
+M+ L G+ LRV A PP++ HS
Sbjct: 108 AMDGAVLDGRELRVQMARYGRPPDSHHS 135
>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear
ribonucleoprotein, R binding domain, RNA binding
protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1
PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A*
3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P*
3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A*
...
Length = 97
Score = 66.5 bits (163), Expect = 3e-15
Identities = 15/81 (18%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 33 NRIYVASIHPDLTEEDIK----SVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASN 88
+ IY+ +++ + ++++K ++F FG I + + + +G F+ ++ ++
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSSAT 65
Query: 89 EAISSMNLFDLGGQYLRVGRA 109
A+ SM F + +R+ A
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 99
Score = 66.5 bits (163), Expect = 3e-15
Identities = 17/77 (22%), Positives = 39/77 (50%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
R++V ++ +EED++ +F A+GP+ S + KG+ F+ + + + +A +
Sbjct: 9 GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
Query: 93 SMNLFDLGGQYLRVGRA 109
++ G+ L V +
Sbjct: 69 EVDGQVFQGRMLHVLPS 85
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 66.5 bits (163), Expect = 3e-15
Identities = 14/75 (18%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 33 NRIYVASIHP-DLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
+R+++ ++ ++++ED+ +F +G I + +GFI+++ Q+ +AI
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 62
Query: 92 SSMNLFDLGGQYLRV 106
+ G+ L +
Sbjct: 63 ECESQEMNFGKKLIL 77
>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 = 66.7 bits (163), Expect = 4e-15
Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 13/102 (12%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH--------RHKGYGFIEYETK 84
+ IYV ++ +T +D+ F+ G +K K H + KG + YE
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 85 QASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
+ A+ + D G L+V A P PS+
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVSLARKKPP-----MNSGPSS 112
>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA
recognition, alternative conformation binding protein;
HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A
Length = 87
Score = 65.9 bits (161), Expect = 4e-15
Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 6/80 (7%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGS-----SPHRHKGYGFIEYETKQASN 88
R+YV +I +TEE + F A + G+ ++ K + F+E+ + +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 89 EAISSMNLFDLGGQYLRVGR 108
+A+ + + GQ L++ R
Sbjct: 68 QAM-AFDGIIFQGQSLKIRR 86
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 66.3 bits (162), Expect = 5e-15
Identities = 12/78 (15%), Positives = 31/78 (39%), Gaps = 1/78 (1%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+ S + ++ + S+F G + + + + KG+ F+E + + + I
Sbjct: 13 GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
Query: 93 SMNLFDLGGQY-LRVGRA 109
S + L ++ L +
Sbjct: 73 SFHGKRLDLKHRLFLYTM 90
>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 = 67.6 bits (165), Expect = 5e-15
Identities = 20/88 (22%), Positives = 44/88 (50%), Gaps = 2/88 (2%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+ V ++ + + ++ VFE +G + + + +G+ F+ + K+ + +A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 93 SMNLFDLGGQYLRVGRAIT--PPNALHS 118
+M+ L G+ LRV A PP++ HS
Sbjct: 131 AMDGAVLDGRELRVQMARYGRPPDSHHS 158
>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 = 67.1 bits (164), Expect = 6e-15
Identities = 18/82 (21%), Positives = 32/82 (39%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+YV ++ TEE I +F G IK + G+ F+EY ++ + A+
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 93 SMNLFDLGGQYLRVGRAITPPN 114
+N L + +R
Sbjct: 100 YINGTRLDDRIIRTDWDAGFKE 121
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 65.5 bits (160), Expect = 7e-15
Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
++ + +I P L E + S+ +G ++ C+ + + Y +K + +A+
Sbjct: 16 RKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQ---VNTDSETAVVNVTYSSKDQARQALD 72
Query: 93 SMNLFDLGGQYLRV 106
+N F L L+V
Sbjct: 73 KLNGFQLENFTLKV 86
>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 = 65.4 bits (160), Expect = 9e-15
Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH--------RHKGYGFIEYETK 84
N I+V + ++T E + F+ G IK K + + KG + ++
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 85 QASNEAISSMNLFDLGGQYLRVGRA 109
++ AI + + G ++V A
Sbjct: 74 PSAKAAIDWFDGKEFSGNPIKVSFA 98
>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
1wi6_A
Length = 88
Score = 64.7 bits (158), Expect = 1e-14
Identities = 17/91 (18%), Positives = 36/91 (39%), Gaps = 10/91 (10%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+ I V ++ D +++ + + + +KYC + R+K F+ + + AI
Sbjct: 6 SGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQ 58
Query: 93 SMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
+ + G+ L V P GP+
Sbjct: 59 MFHQYSFRGKDLIVQLQ---PTDALLCSGPS 86
>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 = 65.0 bits (159), Expect = 1e-14
Identities = 14/75 (18%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 33 NRIYVASI-HPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
+R+++ ++ ++++ED+ +F +G I + +GFI+++ Q+ +AI
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAI 74
Query: 92 SSMNLFDLGGQYLRV 106
+ G+ L +
Sbjct: 75 EXESQEMNFGKKLIL 89
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 65.1 bits (159), Expect = 2e-14
Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 8/85 (9%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPH--------RHKGYGFIEYETK 84
N I+V + ++T E + F+ G IK K + + KG + ++
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 85 QASNEAISSMNLFDLGGQYLRVGRA 109
++ AI + + G ++V A
Sbjct: 68 PSAKAAIDWFDGKEFSGNPIKVSFA 92
>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 = 64.8 bits (158), Expect = 2e-14
Identities = 17/99 (17%), Positives = 35/99 (35%), Gaps = 6/99 (6%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGP-IKYCKL-QQGSSPHRHKGYGFIEYETKQASNEA 90
R+++ I E+I + + + +++G+ F+EYE+ +A+ A
Sbjct: 9 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68
Query: 91 ISSMNL--FDLGGQYLRVGRAITP--PNALHSSKGPAPS 125
+ L G + V A + PS
Sbjct: 69 RRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGPS 107
>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 = 66.7 bits (162), Expect = 3e-14
Identities = 11/75 (14%), Positives = 31/75 (41%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
N ++ + ++TEE+ + + G + ++ S G +E+++K + E +
Sbjct: 123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182
Query: 92 SSMNLFDLGGQYLRV 106
+N + +
Sbjct: 183 GFLNHYQMKNPNGPY 197
Score = 49.7 bits (118), Expect = 5e-08
Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 6/96 (6%)
Query: 35 IYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+ V + + + + +VF +G ++ K G +E A + AI+
Sbjct: 7 LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKF-----MKSKPGAAMVEMADGYAVDRAITH 61
Query: 94 MNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHM 129
+N + GQ + V + P S G +
Sbjct: 62 LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSY 97
>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 = 63.8 bits (156), Expect = 4e-14
Identities = 6/76 (7%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+++ +++P+ + ++K + + ++ +G++++E+ + +A+
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-GTNRKFGYVDFESAEDLEKAL-E 76
Query: 94 MNLFDLGGQYLRVGRA 109
+ + G +++ +
Sbjct: 77 LTGLKVFGNEIKLEKP 92
>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 = 64.1 bits (156), Expect = 4e-14
Identities = 14/85 (16%), Positives = 30/85 (35%), Gaps = 6/85 (7%)
Query: 33 NRIYVASIHPDLTEEDI---KSVFEAFGPIKYCKL---QQGSSPHRHKGYGFIEYETKQA 86
N ++V + L + ++ F FG I + + ++ Y +
Sbjct: 16 NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75
Query: 87 SNEAISSMNLFDLGGQYLRVGRAIT 111
+ AI +N + G+ L+ T
Sbjct: 76 ALRAIQCVNNVVVDGRTLKASLGTT 100
>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 = 64.1 bits (156), Expect = 9e-14
Identities = 25/119 (21%), Positives = 47/119 (39%), Gaps = 5/119 (4%)
Query: 8 QVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ-- 65
+ GR S + E + RIYV ++ + E+D+K +F + +
Sbjct: 21 EKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIM 80
Query: 66 ---QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKG 121
+ R KG FI ++A+ +A+ N + L G+ + V A + +G
Sbjct: 81 FDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSARPKQDPKEG 139
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 62.1 bits (151), Expect = 2e-13
Identities = 14/80 (17%), Positives = 35/80 (43%), Gaps = 3/80 (3%)
Query: 28 EAKLYNR-IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
+ + NR +Y+ D T +DIK E G + ++++ KG F+ +++ ++
Sbjct: 6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIES 64
Query: 87 SNEAISSMNLFDLGGQYLRV 106
+ + + + L +
Sbjct: 65 AKKFVETPGQ-KYKETDLLI 83
>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 = 63.3 bits (155), Expect = 3e-13
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+I+V I PD+ ++ + F +G I +L + +G+GF+ Y++ A +
Sbjct: 88 GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC- 146
Query: 93 SMNLFDLGGQYLRVGRAI 110
D + + + RA
Sbjct: 147 QNKFIDFKDRKIEIKRAE 164
Score = 53.7 bits (130), Expect = 1e-09
Identities = 18/87 (20%), Positives = 46/87 (52%), Gaps = 2/87 (2%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++++ ++ D TE++++ F +G + K+ + + R +G+GF+ +E + +E + +
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 94 MNLFDLGGQYLRVGRAITPPNALHSSK 120
++ D G+ + RAI + K
Sbjct: 65 QHILD--GKVIDPKRAIPRDEQDKTGK 89
>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 = 60.6 bits (148), Expect = 5e-13
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
IYV ++ T E +K +F FG + KL + KG+GF+E + + +EAI+
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAIAK 61
Query: 94 MNLFDLGGQYLRVGRA 109
++ D G+ +RV A
Sbjct: 62 LDNTDFMGRTIRVTEA 77
>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 = 61.2 bits (149), Expect = 5e-13
Identities = 18/104 (17%), Positives = 41/104 (39%), Gaps = 1/104 (0%)
Query: 11 RPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSP 70
S + +D ++ E + ++ + + D++ F A G ++ ++ +
Sbjct: 4 GSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNS 63
Query: 71 HRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPN 114
R KG ++E+ Q+ AI + L G + V + N
Sbjct: 64 RRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAEKN 106
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 61.5 bits (149), Expect = 9e-13
Identities = 17/107 (15%), Positives = 41/107 (38%), Gaps = 2/107 (1%)
Query: 5 PHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGP--IKYC 62
P Q P + +++ + +YV S T++ + V + G +
Sbjct: 28 PVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVEL 87
Query: 63 KLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
K + + + KGY + ++ + ++ + + L G+ + V A
Sbjct: 88 KFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPA 134
>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 = 60.5 bits (147), Expect = 1e-12
Identities = 17/104 (16%), Positives = 43/104 (41%), Gaps = 1/104 (0%)
Query: 6 HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
H ++ + + ++ +YV ++ T +D+++ F + G I +
Sbjct: 10 HSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITIL 69
Query: 66 QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
KGY +IE+ + + + A+ +M+ G+ ++V
Sbjct: 70 CDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK 112
>2div_A TRNA selenocysteine associated protein; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 99
Score = 59.6 bits (145), Expect = 1e-12
Identities = 13/73 (17%), Positives = 27/73 (36%), Gaps = 1/73 (1%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFG-PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+++ + P + E I F G + K+ + GY F+E+ + + +
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
Query: 94 MNLFDLGGQYLRV 106
+N L G
Sbjct: 72 INGKPLPGATPAK 84
>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain,
poly(A) site recognition, RNA, nuclear, RNA BIND
protein; 2.70A {Homo sapiens} PDB: 3p6y_C
Length = 90
Score = 59.5 bits (145), Expect = 1e-12
Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 2/78 (2%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGP--IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
+Y+ ++ T+ED+ + G I K + + + KG+ + ++ +S + +
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 92 SSMNLFDLGGQYLRVGRA 109
+ +L GQ V +
Sbjct: 63 DLLPKRELHGQNPVVTPS 80
>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 = 59.4 bits (145), Expect = 1e-12
Identities = 14/76 (18%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
IYV ++ T E++++ F G + + KG+ +IE+ K++ ++ +
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-A 66
Query: 94 MNLFDLGGQYLRVGRA 109
++ G+ ++V
Sbjct: 67 LDESLFRGRQIKVIPK 82
>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.58.7.1
Length = 108
Score = 59.8 bits (145), Expect = 1e-12
Identities = 19/99 (19%), Positives = 37/99 (37%), Gaps = 12/99 (12%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
NR+ V+ + P + +D+K G + Y + G G +E+ K+ A+
Sbjct: 16 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGVVEFVRKEDMTYAVR 68
Query: 93 SMNLFDLGGQ-----YLRVGRAITPPNALHSSKGPAPST 126
++ Y+RV + S+ PS+
Sbjct: 69 KLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSS 107
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 59.4 bits (144), Expect = 2e-12
Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 8/74 (10%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
++V + + E D+ E FG I Y + K +E+E ++ E ++
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFENIDSAKECVTFA 71
Query: 95 NL--FDLGGQYLRV 106
+ GQ
Sbjct: 72 ADVPVYIAGQQAFF 85
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 59.4 bits (144), Expect = 2e-12
Identities = 15/108 (13%), Positives = 32/108 (29%), Gaps = 8/108 (7%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
I ++ +I+ F FG + L +G +E+ + +A
Sbjct: 11 TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG------GITAIVEFLEPLEARKAFR 64
Query: 93 SMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTAAAVAAAAA 140
+ L + A P ++ S P A + ++
Sbjct: 65 HLAYSKFHHVPLYLEWA--PIGVFGAAPQKKDSQHEQPAEKAESGPSS 110
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 58.7 bits (142), Expect = 3e-12
Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 5/83 (6%)
Query: 27 EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
E A L +YV ++ D D+K G + QG + F+ Y A
Sbjct: 14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP-----RRRAFLHYPDSAA 68
Query: 87 SNEAISSMNLFDLGGQYLRVGRA 109
+ +A+S + LG LRV A
Sbjct: 69 AQQAVSCLQGLRLGTDTLRVALA 91
>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase,
SR protein, PRE-mRNA splicing, at binding, chromosome
partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP:
d.58.7.1 PDB: 2o3d_A 1wg4_A
Length = 115
Score = 59.1 bits (143), Expect = 3e-12
Identities = 18/98 (18%), Positives = 36/98 (36%), Gaps = 12/98 (12%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
NR+ V+ + P + +D+K G + Y + G G +E+ K+ A+
Sbjct: 17 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADV-------YRDGTGVVEFVRKEDMTYAVR 69
Query: 93 SMNLFDLGGQ-----YLRVGRAITPPNALHSSKGPAPS 125
++ Y+RV + S+ + S
Sbjct: 70 KLDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRS 107
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 58.1 bits (141), Expect = 4e-12
Identities = 10/83 (12%), Positives = 34/83 (40%), Gaps = 6/83 (7%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFG--PIKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
+ I + +I P + I + + + +L + +++G+ F++ + +++
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69
Query: 91 ISSMN----LFDLGGQYLRVGRA 109
+ + + G+ + V A
Sbjct: 70 LQILQSLHPPLKIDGKTIGVDFA 92
>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 = 57.7 bits (140), Expect = 8e-12
Identities = 11/83 (13%), Positives = 33/83 (39%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
I V ++ ++ ++I F + I + + G + +E++ + A+
Sbjct: 16 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75
Query: 93 SMNLFDLGGQYLRVGRAITPPNA 115
+N +G + +++ P +
Sbjct: 76 DLNDRPIGSRKVKLVLGSGPSSG 98
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 58.4 bits (141), Expect = 9e-12
Identities = 12/88 (13%), Positives = 39/88 (44%), Gaps = 7/88 (7%)
Query: 33 NRIYVASIHPDLTEEDIK----SVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASN 88
+ + +I+P++ +E ++ ++ + G I + + G +I + T++++
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQ 86
Query: 89 EAISSMNLFDLGGQYLRVGRAITPPNAL 116
+ + + G L + + TP + +
Sbjct: 87 AFVEAFQGYPFQGNPLVITFSETPQSQV 114
>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 = 59.6 bits (145), Expect = 1e-11
Identities = 14/78 (17%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+I+V I D E ++ FE +G I+ ++ + +G+ F+ ++ + ++ +
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV- 163
Query: 93 SMNLFDLGGQYLRVGRAI 110
+ G V +A+
Sbjct: 164 IQKYHTVNGHNCEVRKAL 181
Score = 45.7 bits (109), Expect = 1e-06
Identities = 19/87 (21%), Positives = 46/87 (52%), Gaps = 1/87 (1%)
Query: 24 EITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYET 83
E +E + ++++ + + T+E ++S FE +G + C + + + R +G+GF+ Y T
Sbjct: 5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT 64
Query: 84 KQASNEAISSMNLFDLGGQYLRVGRAI 110
+ + A+ + + G+ + RA+
Sbjct: 65 VEEVDAAM-NARPHKVDGRVVEPKRAV 90
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 60.1 bits (145), Expect = 1e-11
Identities = 16/108 (14%), Positives = 39/108 (36%), Gaps = 6/108 (5%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGP--IKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
+Y+ ++ T+ED+ + G I K + + + KG+ + ++ +S +
Sbjct: 69 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 128
Query: 91 ISSMNLFDLGGQYLRVG----RAITPPNALHSSKGPAPSTSHMPTAAA 134
+ + +L GQ V + ++ + S A
Sbjct: 129 MDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGP 176
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 57.1 bits (138), Expect = 1e-11
Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 8/74 (10%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+++ + + E D+ + FGPI Y + K +E+E + A++
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVNYA 77
Query: 95 NL--FDLGGQYLRV 106
+ G V
Sbjct: 78 ADNQIYIAGHPAFV 91
>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 = 56.9 bits (138), Expect = 2e-11
Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 8/95 (8%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
++V + D TEE +K E+F ++ KG+GF+++ +++ + A
Sbjct: 15 SKTLFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 92 SSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
+M ++ G + + A G PS+
Sbjct: 72 EAMEDGEIDGNKVTLDWAKPKGE-----GGSGPSS 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 = 55.8 bits (135), Expect = 3e-11
Identities = 11/81 (13%), Positives = 32/81 (39%), Gaps = 8/81 (9%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKY----CKLQQGSSPHRHKGYGFIEYETKQASN 88
I V ++ ++ ++I F + I ++G G + +E++ +
Sbjct: 16 TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKG----MPTGEAMVAFESRDEAT 71
Query: 89 EAISSMNLFDLGGQYLRVGRA 109
A+ +N +G + +++
Sbjct: 72 AAVIDLNDRPIGSRKVKLSGP 92
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 55.7 bits (135), Expect = 5e-11
Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 2/82 (2%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
YV ++ + + DI ++F+ I+ +L + + KG+ ++E++ + EA+
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL- 73
Query: 93 SMNLFDLGGQYLRVGRAITPPN 114
+ + LG + LRV A
Sbjct: 74 TYDGALLGDRSLRVDIAEGRKQ 95
>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 = 56.1 bits (135), Expect = 5e-11
Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 9/71 (12%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+ + ++ + V E G + + +K Y F Y T + S A ++
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMP------PNKPYSFARYRTTEESKRAYVTL 83
Query: 95 N---LFDLGGQ 102
N + D GQ
Sbjct: 84 NGKEVVDDLGQ 94
>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 = 55.3 bits (134), Expect = 6e-11
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 1/81 (1%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++ ++ D+TEE IK F ++ S+P R KG+G+ E+E + A+ S
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 75
Query: 94 MNLFDLGGQYLRVGRAITPPN 114
+N LG + +RV A +
Sbjct: 76 LNEESLGNKRIRVDVADQAQD 96
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 54.6 bits (132), Expect = 1e-10
Identities = 18/89 (20%), Positives = 29/89 (32%), Gaps = 6/89 (6%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++V+ + + F AFGP+ + + +E A +S
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVM-----DKDKGVFAIVEMGDVGAREAVLSQ 64
Query: 94 MNLFDLGGQYLRVGRAITPPNALHSSKGP 122
LGG LRV +SK P
Sbjct: 65 SQH-SLGGHRLRVRPREQKEFQSPASKSP 92
>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein
biosynthesis, RNA recognition motif, RNA binding domain,
RRM, RBD, RNP; NMR {Homo sapiens}
Length = 100
Score = 54.6 bits (132), Expect = 1e-10
Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 1/81 (1%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++ ++ D+TEE IK F ++ S+P R KG+G+ E+E + A+ S
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-S 79
Query: 94 MNLFDLGGQYLRVGRAITPPN 114
+N LG + +RV A +
Sbjct: 80 LNEESLGNRRIRVDVADQAQD 100
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 54.7 bits (132), Expect = 1e-10
Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 9/94 (9%)
Query: 23 DEITEEAKLYNRIYVASI------HPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGY 76
D E + + I V ++ + + I +F FG I + + KGY
Sbjct: 6 DRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGY 63
Query: 77 GFIEYETKQASNEAISSMNLFDLGGQY-LRVGRA 109
F+EY + + +A+ + + + L Q+ RV
Sbjct: 64 IFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLF 97
>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 = 56.4 bits (136), Expect = 2e-10
Identities = 14/98 (14%), Positives = 38/98 (38%), Gaps = 6/98 (6%)
Query: 35 IYVASIHPD-LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+ V++++P+ +T + + +F +G ++ K+ K ++ + A+S
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKIL-----FNKKENALVQMADGNQAQLAMSH 60
Query: 94 MNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPT 131
+N L G+ +R+ + L +
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYG 98
Score = 54.5 bits (131), Expect = 8e-10
Identities = 16/75 (21%), Positives = 38/75 (50%), Gaps = 5/75 (6%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+++++I P ++EED+K +F + G + + + I+ + + + +A+
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQALI 176
Query: 93 SMNLFDLG-GQYLRV 106
++ DLG +LRV
Sbjct: 177 DLHNHDLGENHHLRV 191
>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 = 53.4 bits (129), Expect = 3e-10
Identities = 26/94 (27%), Positives = 50/94 (53%), Gaps = 6/94 (6%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
N+I+V I + E +++ F+ FG + + + R +G+GFI +E +Q+ ++A+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV- 69
Query: 93 SMNLFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
+M+ D+ G+ + V RA SK PS+
Sbjct: 70 NMHFHDIMGKKVEVKRAEPRD-----SKSSGPSS 98
>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A
Length = 282
Score = 56.4 bits (135), Expect = 3e-10
Identities = 18/106 (16%), Positives = 44/106 (41%), Gaps = 7/106 (6%)
Query: 33 NRIYVASIHPDLTEEDIKS----VFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASN 88
+ IY+ +++ + ++++K +F FG I + + + +G F+ ++ ++
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRS---LKMRGQAFVIFKEVSSAT 66
Query: 89 EAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTAAA 134
A+ SM F + +R+ A T + + KG
Sbjct: 67 NALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRK 112
Score = 49.1 bits (116), Expect = 1e-07
Identities = 11/79 (13%), Positives = 32/79 (40%), Gaps = 6/79 (7%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
+ +++ ++ + E + +F F K +L G F+E++ + + A
Sbjct: 207 NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAAR 261
Query: 92 SSMNLFDL-GGQYLRVGRA 109
++ F + +++ A
Sbjct: 262 DALQGFKITQNNAMKISFA 280
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 53.7 bits (129), Expect = 4e-10
Identities = 17/74 (22%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS-- 92
I++ + D+TE ++ S+ FG + + + K FIE T++A+N ++
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYY 72
Query: 93 SMNLFDLGGQYLRV 106
+ L GQ + +
Sbjct: 73 TSVTPVLRGQPIYI 86
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 53.7 bits (129), Expect = 4e-10
Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 5/82 (6%)
Query: 33 NRIYVASIHPDLTEEDIKSVF-EAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
RI + ++ + +D+K + E + + G G +E+ +++ EA+
Sbjct: 29 YRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEAL 84
Query: 92 SSMNLFDLGGQYLRVGRAITPP 113
+N + G + V R PP
Sbjct: 85 ERLNNIEFRGSVITVERDDNPP 106
>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 = 52.2 bits (126), Expect = 6e-10
Identities = 15/92 (16%), Positives = 36/92 (39%), Gaps = 10/92 (10%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
+ ++V D+TE++++ F +G + + P + + F+ + Q +
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQSLC 59
Query: 92 SSMNLFDLGGQYLRVGRAITPPNALHSSKGPA 123
+ G + + A N S+ GP+
Sbjct: 60 GEDLIIK--GISVHISNAEPKHN---SNSGPS 86
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 52.0 bits (125), Expect = 7e-10
Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 9/81 (11%)
Query: 33 NRIYVASI------HPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
+ I V ++ + + I +F FG I + + KGY F+EY +
Sbjct: 2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAH 59
Query: 87 SNEAISSMNLFDLGGQY-LRV 106
+ +A+ + + + L Q+ RV
Sbjct: 60 AVDAVKNADGYKLDKQHTFRV 80
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 52.5 bits (126), Expect = 8e-10
Identities = 11/74 (14%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+++ + ++TE ++ ++ FG + + + K F+E T++A+ ++
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILM------LKGKNQAFLELATEEAAITMVNYY 71
Query: 95 NL--FDLGGQYLRV 106
+ L Q + +
Sbjct: 72 SAVTPHLRNQPIYI 85
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 52.3 bits (126), Expect = 8e-10
Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 10/98 (10%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGP-IKYCKL---QQGSSPHRHKGYGFIEYETKQASNE 89
++V + PD+ + + F P + K+ Q G S KGYGF+++ +
Sbjct: 11 SLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVS----KGYGFVKFTDELEQKR 66
Query: 90 AISSMN-LFDLGGQYLRVGRAITPPNALHSSKGPAPST 126
A++ LG + +R+ A P + PS+
Sbjct: 67 ALTECQGAVGLGSKPVRLSVA-IPKASRVKPVESGPSS 103
>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 = 52.6 bits (126), Expect = 1e-09
Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 8/76 (10%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
I++ + D+TE ++ S+ FG + + + K FIE T++A+N ++
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVN 85
Query: 93 --SMNLFDLGGQYLRV 106
+ L GQ + +
Sbjct: 86 YYTSVTPVLRGQPIYI 101
>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 = 54.2 bits (130), Expect = 1e-09
Identities = 17/130 (13%), Positives = 42/130 (32%), Gaps = 6/130 (4%)
Query: 3 HFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPD-LTEEDIKSVFEAFGPIKY 61
H H I + + V++++P+ +T + + +F +G ++
Sbjct: 5 HHHHHHSSGLVPRGSHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQR 64
Query: 62 CKLQQGSSPHRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKG 121
K+ K ++ + A+S +N L G+ +R+ + L
Sbjct: 65 VKIL-----FNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQ 119
Query: 122 PAPSTSHMPT 131
+
Sbjct: 120 EDQGLTKDYG 129
Score = 52.7 bits (126), Expect = 4e-09
Identities = 16/76 (21%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
+++++I P ++EED+K +F + G + + + I+ + + + +A+
Sbjct: 151 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQAL 206
Query: 92 SSMNLFDLG-GQYLRV 106
++ DLG +LRV
Sbjct: 207 IDLHNHDLGENHHLRV 222
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 54.0 bits (129), Expect = 2e-09
Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 6/87 (6%)
Query: 31 LYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
+ + + P E I+ VF G I + K GF++++ + + A
Sbjct: 142 IDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRY------VESKNCGFVKFKYQANAEFA 195
Query: 91 ISSMNLFDLGGQYLRVGRAITPPNALH 117
+M+ L + L
Sbjct: 196 KEAMSNQTLLLPSDKEWDDRREGTGLL 222
>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 = 51.1 bits (123), Expect = 2e-09
Identities = 10/85 (11%), Positives = 30/85 (35%), Gaps = 7/85 (8%)
Query: 26 TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
++++V D+T E+++ F +G + + P + + F+ + +
Sbjct: 5 HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFI-----PKPFRAFAFVTFADDK 59
Query: 86 ASNEAISSMNLFDLGGQYLRVGRAI 110
+ + G + + A
Sbjct: 60 VAQSLCGEDLIIK--GISVHISNAE 82
>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 = 50.8 bits (122), Expect = 5e-09
Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 1/83 (1%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
+ +I+V + T+ ++ FE FG I+ + + +GYGF+ + A+ A
Sbjct: 17 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76
Query: 92 SSMNLFDLGGQYLRVGRAITPPN 114
N + G+ V A
Sbjct: 77 KDPNP-IIDGRKANVNLAYLGAK 98
>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 = 49.0 bits (118), Expect = 8e-09
Identities = 16/76 (21%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+I+V + PD EE I+ F FG ++ +L + ++ +G+ FI ++ ++ + +
Sbjct: 1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
Query: 94 MNLFDLGGQYLRVGRA 109
++G + A
Sbjct: 61 KYH-NVGLSKCEIKVA 75
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 49.6 bits (118), Expect = 1e-08
Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 33 NRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ--QGSSPHRHKGYGFIEYETKQASNEA 90
+++V + PD+ E++I + F FGP+ + S KGY F+ ++ + +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 91 ISSMNLFDLGGQYLRV 106
I + D G YL V
Sbjct: 69 IDACLEED-GKLYLCV 83
>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 = 48.8 bits (117), Expect = 2e-08
Identities = 17/101 (16%), Positives = 38/101 (37%), Gaps = 8/101 (7%)
Query: 27 EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQA 86
+ + + V + TE+D+K F FG + ++++ KG+GF+ + +
Sbjct: 10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET 69
Query: 87 SNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTS 127
+ +S ++ D GR + +S
Sbjct: 70 QVKVMSQRHMID--------GRWCDCKLPNSKQSQDSGPSS 102
>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 = 49.0 bits (117), Expect = 2e-08
Identities = 8/78 (10%), Positives = 28/78 (35%), Gaps = 1/78 (1%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
++ +I +T+ D+ E + + + G ++++ + + ++
Sbjct: 15 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE 74
Query: 92 SSMNLFDLGGQYLRVGRA 109
++ L G+ V
Sbjct: 75 -RLHRKKLNGREAFVHVV 91
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 47.8 bits (115), Expect = 2e-08
Identities = 18/76 (23%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+I+V + + T ED+K FE FG + L + +RH+G+GF+ +E++ +
Sbjct: 1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59
Query: 94 MNLFDLGGQYLRVGRA 109
++ ++ + + +A
Sbjct: 60 IHFHEINNKMVECKKA 75
>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 = 50.2 bits (119), Expect = 3e-08
Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 2/75 (2%)
Query: 32 YNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAI 91
+Y+ D T +DIK E G + ++++ KG F+ +++ +++ + +
Sbjct: 109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFV 167
Query: 92 SSMNLFDLGGQYLRV 106
+ L +
Sbjct: 168 ETPGQ-KYKETDLLI 181
>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 = 48.3 bits (115), Expect = 4e-08
Identities = 10/75 (13%), Positives = 32/75 (42%), Gaps = 1/75 (1%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+ + + T+E+I F + + G F+++ +++ + +A+
Sbjct: 45 VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL-GK 103
Query: 95 NLFDLGGQYLRVGRA 109
+ +G +Y+ V ++
Sbjct: 104 HKERIGHRYIEVFKS 118
>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM
domain, riken structural genomics/proteomics initiative,
RSGI; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 46.3 bits (110), Expect = 2e-07
Identities = 9/75 (12%), Positives = 32/75 (42%), Gaps = 1/75 (1%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+ + + ++E+I F + R G F+++ +++ + +A+
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KK 76
Query: 95 NLFDLGGQYLRVGRA 109
+ +G +Y+ + ++
Sbjct: 77 HKERIGHRYIEIFKS 91
>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 91
Score = 45.4 bits (108), Expect = 2e-07
Identities = 16/83 (19%), Positives = 38/83 (45%), Gaps = 7/83 (8%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGP--IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+ + ++TE+++ P I+ + G GY F+++ ++ +A+
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHG----NKTGYIFVDFSNEEEVKQAL- 67
Query: 93 SMNLFDLGGQYLRVGRAITPPNA 115
N +GG+Y+ V R + P++
Sbjct: 68 KCNREYMGGRYIEVFREKSGPSS 90
>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 109
Score = 45.9 bits (109), Expect = 3e-07
Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 7/77 (9%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGP--IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+ V + E D++ F + K G R+ G G +++ + Q + EA+
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVG----RNNGNGLVKFLSPQDTFEAL- 73
Query: 93 SMNLFDLGGQYLRVGRA 109
N + +Y+ V A
Sbjct: 74 KRNRMLMIQRYVEVSPA 90
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 46.0 bits (109), Expect = 4e-07
Identities = 18/89 (20%), Positives = 40/89 (44%), Gaps = 5/89 (5%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+++ + TE DI + F P++ ++ G R G +E+ T + + A+ S
Sbjct: 49 VHMRGLPYKATENDIYNFFSPLNPVR-VHIEIGPD-GRVTGEADVEFATHEEAVAAM-SK 105
Query: 95 NLFDLGGQYLRVGRAITPP--NALHSSKG 121
+ ++ +Y+ + T N +SS+
Sbjct: 106 DRANMQHRYIELFLNSTTGASNGAYSSQV 134
>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 = 44.5 bits (106), Expect = 6e-07
Identities = 13/70 (18%), Positives = 35/70 (50%)
Query: 26 TEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ 85
++ + +++V + D +++D+K F FG + C ++ + R +G+GFI ++
Sbjct: 5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAA 64
Query: 86 ASNEAISSMN 95
+ + +
Sbjct: 65 SVEKVLDQKE 74
>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 124
Score = 44.8 bits (106), Expect = 9e-07
Identities = 11/79 (13%), Positives = 29/79 (36%), Gaps = 9/79 (11%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGP----IKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
+Y+ + + + + F+ I G + G GF+E+ + A
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNG----KATGEGFVEFRNEADYKAA 83
Query: 91 ISSMNLFDLGGQYLRVGRA 109
+ + +G ++++V
Sbjct: 84 L-CRHKQYMGNRFIQVHPI 101
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 43.2 bits (103), Expect = 1e-06
Identities = 13/76 (17%), Positives = 37/76 (48%), Gaps = 1/76 (1%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++++ + T+E ++ F FG +K C + + R +G+GF+ + + ++ + +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60
Query: 94 MNLFDLGGQYLRVGRA 109
+ +L + + A
Sbjct: 61 QSRHELDSKTIDPKVA 76
>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H';
structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 42.8 bits (101), Expect = 3e-06
Identities = 13/74 (17%), Positives = 31/74 (41%), Gaps = 7/74 (9%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGP--IKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+++ + TE DI + F P + G R G +E+ T + + A+
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDG----RVTGEADVEFATHEDAVAAM- 72
Query: 93 SMNLFDLGGQYLRV 106
+ + ++ +Y+ +
Sbjct: 73 AKDKANMQHRYVEL 86
>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 = 45.0 bits (106), Expect = 4e-06
Identities = 31/163 (19%), Positives = 52/163 (31%), Gaps = 35/163 (21%)
Query: 19 QSVIDEITEE-AKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGY- 76
Q D+ EE LY Y L + IK E + + + +G
Sbjct: 163 QGNTDDYFEELRDLYQ-TY-----HVLVGDLIKFSAETLSEL--IRTTLDAEKVFTQGLN 214
Query: 77 --GFIEYETKQASNEAIS----SMNLFDLG--GQYLRVGRA--ITPPNALHSSKGPAPST 126
++E + + + S L + Y+ + TP KG +T
Sbjct: 215 ILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKG---AT 271
Query: 127 SH---MPTAAAVAAAAATAKIQAMDGGATNAVGVLSKLSQVFF 166
H + TA A+A + ++ A+ VL FF
Sbjct: 272 GHSQGLVTAVAIAETDS---WESFFVSVRKAITVL------FF 305
Score = 31.2 bits (70), Expect = 0.20
Identities = 33/177 (18%), Positives = 57/177 (32%), Gaps = 37/177 (20%)
Query: 2 QHFPHVQVGR---PSNMPQAQSVI---DEITEEAKLYNRI--YVAS-IHPD---LTEEDI 49
F + +P+ DE T A+L + YV+S + P ++ +
Sbjct: 25 ASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVL 84
Query: 50 KSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQ-ASNEAISSMNLFDLGGQYLRVGR 108
F Y L+ G+ H E +T + E I + Y+
Sbjct: 85 NLCLTEFE-NCY--LE-GNDIHALAAKLLQENDTTLVKTKELIKN---------YIT--- 128
Query: 109 AITPPNALHSSKGPAPSTSHMPTAAAVAAAAATAKIQAMDGGATNAVGVLSKLSQVF 165
A +K P S +A A A++ A+ GG N +L ++
Sbjct: 129 ------ARIMAKRPFDKKS--NSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLY 177
Score = 29.6 bits (66), Expect = 0.60
Identities = 22/127 (17%), Positives = 33/127 (25%), Gaps = 63/127 (49%)
Query: 2 QHFPHVQV-------------GRPSNM--------PQAQSVIDEITEEAK--------LY 32
+ +P+ + G PS M Q Q +++ L
Sbjct: 312 EAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV 371
Query: 33 N--RIYVASIHP-DL-------------TEEDI--------KSVFEA-FGPIKYCKLQQG 67
N + V S P L + D K F F P+
Sbjct: 372 NGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPV-------- 423
Query: 68 SSP-HRH 73
+SP H H
Sbjct: 424 ASPFHSH 430
Score = 25.8 bits (56), Expect = 9.9
Identities = 20/158 (12%), Positives = 40/158 (25%), Gaps = 72/158 (45%)
Query: 23 DEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYE 82
+ E + ++ I ++ E F Q + P
Sbjct: 1689 SAMIFETIVDGKLKTEKIFKEINEHSTSYTFR--SEKGLLSATQFTQP------------ 1734
Query: 83 TKQASNEAI--SSMNLFDLGGQYLRVGRAITPPNAL---HS----SKGPAPSTSHMPTAA 133
A+ F + L+ + + P +A HS +
Sbjct: 1735 -------ALTLMEKAAF----EDLK-SKGLIPADATFAGHSLGEYA-------------- 1768
Query: 134 AVAAAAATAKIQAMDGGATNAVGVLS-----KLSQVFF 166
A+A+ A V+S ++ VF+
Sbjct: 1769 ALASLA----------------DVMSIESLVEV--VFY 1788
>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 = 42.6 bits (101), Expect = 4e-06
Identities = 15/88 (17%), Positives = 45/88 (51%), Gaps = 1/88 (1%)
Query: 23 DEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYE 82
+ E + + ++++ + + TEE +++ +E +G + C + + + R +G+GF+ +
Sbjct: 18 ERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFS 77
Query: 83 TKQASNEAISSMNLFDLGGQYLRVGRAI 110
+ + A+ + + G+ + RA+
Sbjct: 78 SMAEVDAAM-AARPHSIDGRVVEPKRAV 104
>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 = 42.2 bits (100), Expect = 6e-06
Identities = 12/77 (15%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+++V + T+E ++S F +G + C + + + ++ +G+GF++++ + +
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-A 76
Query: 94 MNLFDLGGQYLRVGRAI 110
L G+ +
Sbjct: 77 SRPHTLDGRNIDPKPCT 93
>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 = 41.5 bits (98), Expect = 1e-05
Identities = 13/77 (16%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
++++ + T+E ++ F FG +K C + + R +G+GF+ + + ++ + +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 85
Query: 94 MNLFDLGGQYLRVGRAI 110
+ +L + + A
Sbjct: 86 QSRHELDSKTIDPKVAF 102
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 112
Score = 39.9 bits (93), Expect = 5e-05
Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 35 IYVASI-HPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
I+++++ H ++ + + E +G IK L R K FIE ET++ + +
Sbjct: 28 IHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL------MRMKSQAFIEMETREDAMAMVD 80
>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding
factor, RNA binding domain, STRU genomics, joint center
for structural genomics, JCSG; NMR {Homo sapiens}
Length = 107
Score = 39.1 bits (91), Expect = 8e-05
Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 11/93 (11%)
Query: 23 DEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGP------IKYCKLQQGSSPHRHKGY 76
++ EE I + T ED+ + F I + + G + +G
Sbjct: 2 SKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDG----KRRGD 57
Query: 77 GFIEYETKQASNEAISSMNLFDLGGQYLRVGRA 109
IE E++Q +A+ + +G +Y+ V
Sbjct: 58 ALIEMESEQDVQKAL-EKHRMYMGQRYVEVYEI 89
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 39.1 bits (91), Expect = 9e-05
Identities = 14/78 (17%), Positives = 31/78 (39%), Gaps = 4/78 (5%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ---QGSSPHRHKGYGFIEYETKQASNEAI 91
+ + + T E++ + F PI K R G F+ + ++ + A+
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 92 SSMNLFDLGGQYLRVGRA 109
+ LG +Y+ + R+
Sbjct: 86 -RKHKDLLGKRYIELFRS 102
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 38.9 bits (90), Expect = 2e-04
Identities = 17/103 (16%), Positives = 39/103 (37%), Gaps = 7/103 (6%)
Query: 7 VQVGRPSNMPQAQSVIDEIT-EEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQ 65
VQ G + A +V + RI V ++ +T + + +F FG +
Sbjct: 2 VQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKII-- 59
Query: 66 QGSSPHRHKGYGFIEYETKQASNEAISSMNLFDL--GGQYLRV 106
+ ++ ++Y ++ A S++ ++ LR+
Sbjct: 60 --TFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI 100
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA
binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB:
2adb_A
Length = 164
Score = 38.5 bits (89), Expect = 2e-04
Identities = 12/75 (16%), Positives = 31/75 (41%), Gaps = 6/75 (8%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
RI V ++ +T + + +F FG + + ++ ++Y ++ A S
Sbjct: 48 RIIVENLFYPVTLDVLHQIFSKFGTVLKII----TFTKNNQFQALLQYADPVSAQHAKLS 103
Query: 94 MNLFDL--GGQYLRV 106
++ ++ LR+
Sbjct: 104 LDGQNIYNACCTLRI 118
>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens} SCOP: d.58.7.1
Length = 96
Score = 36.9 bits (85), Expect = 4e-04
Identities = 14/85 (16%), Positives = 38/85 (44%), Gaps = 7/85 (8%)
Query: 35 IYVASIHPDLTEEDIK----SVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEA 90
+ V++I L+ ++++ F G +K +L + ++ ++ E Q + A
Sbjct: 12 VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHT---DYQLKAVVQMENLQDAIGA 68
Query: 91 ISSMNLFDLGGQYLRVGRAITPPNA 115
++S++ + +G + + V A
Sbjct: 69 VNSLHRYKIGSKKILVSLATGASGP 93
>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 = 36.9 bits (85), Expect = 8e-04
Identities = 11/78 (14%), Positives = 30/78 (38%), Gaps = 11/78 (14%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGP------IKYCKLQQGSSPHRHKGYGFIEYETKQASN 88
+ + + + ED+++ + + ++G R G F+E ++
Sbjct: 47 VKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREG----RQSGEAFVELGSEDDVK 102
Query: 89 EAISSMNLFDLGGQYLRV 106
A+ + +G +Y+ V
Sbjct: 103 MAL-KKDRESMGHRYIEV 119
>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus}
Length = 118
Score = 36.1 bits (83), Expect = 0.001
Identities = 12/78 (15%), Positives = 31/78 (39%), Gaps = 11/78 (14%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFG------PIKYCKLQQGSSPHRHKGYGFIEYETKQASN 88
+ + + + ED+++ + + ++G R G F+E E++
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREG----RQSGEAFVELESEDDVK 75
Query: 89 EAISSMNLFDLGGQYLRV 106
A+ + +G +Y+ V
Sbjct: 76 LAL-KKDRESMGHRYIEV 92
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 35.0 bits (80), Expect = 0.003
Identities = 10/73 (13%), Positives = 30/73 (41%), Gaps = 5/73 (6%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+ + + +T + + +V G + Q+ R+ +E+E+ + +A ++
Sbjct: 27 LLSIQNPLYPITVDVLYTVCNPVGKV-----QRIVIFKRNGIQAMVEFESVLCAQKAKAA 81
Query: 94 MNLFDLGGQYLRV 106
+N D+ +
Sbjct: 82 LNGADIYAGCCTL 94
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 36.3 bits (83), Expect = 0.003
Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 6/52 (11%)
Query: 44 LTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSMN 95
++ + V E G + +K Y F Y T + S A ++N
Sbjct: 32 VSRNQLLPVLEKCGLVDAL------LMPPNKPYSFARYRTTEESKRAYVTLN 77
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding
protein, RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 34.8 bits (80), Expect = 0.003
Identities = 8/52 (15%), Positives = 21/52 (40%), Gaps = 2/52 (3%)
Query: 46 EEDIKSVFEAFGPIKYCKLQQGS--SPHRHKGYGFIEYETKQASNEAISSMN 95
ED++ +G +K ++ + G F+E+ + +A+ +
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT 80
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 34.5 bits (79), Expect = 0.004
Identities = 10/84 (11%), Positives = 32/84 (38%), Gaps = 2/84 (2%)
Query: 13 SNMPQAQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEA-FGPIKYCKLQQGSSPH 71
N+ + + + + H D E++ + E +G ++ + H
Sbjct: 7 LNIYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDH 66
Query: 72 RHKGYGFIEYETKQASNEAISSMN 95
G ++++ ++ + +A+ +N
Sbjct: 67 -LVGNVYVKFRREEDAEKAVIDLN 89
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila
melanogaster}
Length = 89
Score = 33.1 bits (75), Expect = 0.008
Identities = 9/70 (12%), Positives = 30/70 (42%), Gaps = 6/70 (8%)
Query: 35 IYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISSM 94
+ + ++ + ++++ GP+ + ++G +Y T++ +N+A ++
Sbjct: 10 LLLKNLTAQIDGPTLRTLCMQHGPLVSFHP------YLNQGIALCKYTTREEANKAQMAL 63
Query: 95 NLFDLGGQYL 104
N L +
Sbjct: 64 NNCVLANTTI 73
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project
on protein structural and functional analyses; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 102
Score = 32.9 bits (75), Expect = 0.011
Identities = 12/64 (18%), Positives = 22/64 (34%), Gaps = 8/64 (12%)
Query: 45 TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS--SMNLFDLGGQ 102
+ + E FG I + FIE T + + A+ + + G+
Sbjct: 29 LRYQLLQLVEPFGVISNHLIL------NKINEAFIEMATTEDAQAAVDYYTTTPALVFGK 82
Query: 103 YLRV 106
+RV
Sbjct: 83 PVRV 86
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 31.7 bits (71), Expect = 0.031
Identities = 7/48 (14%), Positives = 21/48 (43%), Gaps = 5/48 (10%)
Query: 45 TEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAIS 92
+++ + + + +G + L + G +E+ T +A+ A+
Sbjct: 30 SKDVLLRLLQKYGEVLNLVL-----SSKKPGTAVVEFATVKAAELAVQ 72
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 31.6 bits (72), Expect = 0.038
Identities = 10/73 (13%), Positives = 25/73 (34%), Gaps = 14/73 (19%)
Query: 23 DEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYE 82
+ ++ + N I ED++ FG I+ L G + +
Sbjct: 27 MDFEDDPLVLNEI----------REDLRVECSKFGQIRKLLLFDRHP----DGVASVSFR 72
Query: 83 TKQASNEAISSMN 95
+ ++ I +++
Sbjct: 73 DPEEADYCIQTLD 85
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif,
RRM, RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 31.3 bits (71), Expect = 0.053
Identities = 9/54 (16%), Positives = 20/54 (37%), Gaps = 4/54 (7%)
Query: 46 EEDIKSVFEAFGPIKYCKL----QQGSSPHRHKGYGFIEYETKQASNEAISSMN 95
E ++ FG + + Q F+E+ +++AI ++N
Sbjct: 39 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALN 92
>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 121
Score = 30.7 bits (69), Expect = 0.11
Identities = 17/72 (23%), Positives = 29/72 (40%), Gaps = 9/72 (12%)
Query: 35 IYVASIHPDLTE-EDIKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQASNEAISS 93
+ + D T ED+ +F G IK+ +G+ G I + K+ + EA+
Sbjct: 21 LKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKE------GIILF--KEKAKEALGK 72
Query: 94 MNLFDLGGQYLR 105
+ G LR
Sbjct: 73 AKDANNGNLQLR 84
>3ghp_A Cellulosomal scaffoldin adaptor protein B; linker segments, beta
barrel, alpha helix, beta flaps, structural protein;
2.49A {Acetivibrio cellulolyticus}
Length = 227
Score = 30.6 bits (68), Expect = 0.19
Identities = 13/65 (20%), Positives = 26/65 (40%)
Query: 79 IEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTAAAVAAA 138
+ +E + I+ LF+ G ++ G + P ++S+ + + PTA A
Sbjct: 135 VVFEDSETMPNGITGTTLFNWYGNRIQSGYFVIQPGEINSAPIATATPTTKPTAFASTMP 194
Query: 139 AATAK 143
T
Sbjct: 195 TVTLT 199
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain,
RNA- binding, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 104
Score = 29.5 bits (66), Expect = 0.21
Identities = 18/98 (18%), Positives = 34/98 (34%), Gaps = 14/98 (14%)
Query: 35 IYVASIHPDLTEEDIKSVFEAF-----GPIKYCKLQQGSSPHRHKGYGFIEYETKQASNE 89
+ V + P + +E + FE GP+ + R G + + +
Sbjct: 11 VEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ--------RLGCGGVLTFREPADAER 62
Query: 90 AISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTS 127
++ + +L G L + A A +G P TS
Sbjct: 63 VLAQADH-ELHGAQLSLRPAPPRAPARLLLQGLPPGTS 99
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics,
joint center for struc genomics, JCSG, protein
structure initiative, PSI-biology; HET: MSE CIT; 0.95A
{Mus musculus} PDB: 2lq5_A
Length = 114
Score = 28.8 bits (65), Expect = 0.41
Identities = 5/52 (9%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 46 EEDIKSVFEAFGPIKYCKLQQGSSPHRHKGYG--FIEYETKQASNEAISSMN 95
++D+ G + + + ++ G +++ + A+ A+++++
Sbjct: 31 KDDVIEECNKHGGVIHIYV------DKNSAQGNVYVKCPSIAAAIAAVNALH 76
>3jz0_A Lincosamide nucleotidyltransferase; alpha-beta structure,
transferase-antibiotic CO; HET: APC CLY; 2.00A
{Enterococcus faecium} PDB: 3jyy_A*
Length = 287
Score = 28.7 bits (63), Expect = 0.98
Identities = 8/34 (23%), Positives = 14/34 (41%)
Query: 2 QHFPHVQVGRPSNMPQAQSVIDEITEEAKLYNRI 35
H V R S+M + + +I + + RI
Sbjct: 8 HHHSSGLVPRGSHMLKQKELIANVKNLTESDERI 41
>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 = 28.7 bits (63), Expect = 1.1
Identities = 14/115 (12%), Positives = 38/115 (33%), Gaps = 22/115 (19%)
Query: 19 QSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAFGPIKYCKL----QQGS------ 68
+ V D ++ A I + LT +++KS+ + + L +
Sbjct: 275 KQVTDFLS--AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI 332
Query: 69 -------SPHRHKGYGFIEYETKQASNEA-ISSMNLFDLGGQYLRVGRAITPPNA 115
+ + + E+ ++ + + + R+ ++ PP+A
Sbjct: 333 IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL--SVFPPSA 385
>2zue_A Arginyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP-binding,
cytoplasm, ligase, nucleotide-binding, protein
biosynthesis, ligase/RNA complex; HET: ANP; 2.00A
{Pyrococcus horikoshii} PDB: 2zuf_A
Length = 629
Score = 28.5 bits (64), Expect = 1.2
Identities = 15/63 (23%), Positives = 24/63 (38%), Gaps = 10/63 (15%)
Query: 18 AQSVIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFE--AFGPIKYCKLQQGSSPHRHKG 75
VI E + A R + +P L++E+ V E G I+Y ++ K
Sbjct: 437 VDEVIQEAVKRA----RELIEEKNPALSDEEKAEVAEKVGIGAIRYNLIKY----SPDKK 488
Query: 76 YGF 78
F
Sbjct: 489 IIF 491
>2v9l_A Rhamnulose-1-phosphate aldolase; entropy index, metal-binding,
oligomerization, zinc, lyase, class II, cytoplasm; HET:
PGO; 1.23A {Escherichia coli} PDB: 2uyv_A* 1ojr_A
2v9g_A* 1gt7_A* 2v9n_A* 2uyu_A* 2v9m_A* 2v9o_A 2v9e_A
2v9f_A 2v9i_A 2v29_A 2v2a_A* 2v2b_A
Length = 274
Score = 28.0 bits (62), Expect = 1.4
Identities = 9/53 (16%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 6 HVQVGRPSNMPQAQSVIDEITEEAKLYNRIYVASIHPD-LTEEDIKSVFEAFG 57
H G + + +ID + A++ ++Y ++ E++ ++ + FG
Sbjct: 212 HGVFGSGPTLDETFGLIDTAEKSAQVLVKVYSMGGMKQTISREELIALGKRFG 264
>3io1_A Aminobenzoyl-glutamate utilization protein; peptidase_M20D
superfamily, protein structure initiative II, NYSGXRC,
structural genomics; 2.50A {Klebsiella pneumoniae subsp}
Length = 445
Score = 27.7 bits (62), Expect = 2.3
Identities = 18/88 (20%), Positives = 30/88 (34%), Gaps = 8/88 (9%)
Query: 71 HRHKGYGFIEYETKQASNEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMP 130
H H G++E+ T + + + G L +GR + ++ P T
Sbjct: 24 HLHAESGWLEFRTASKVADILDGL------GYQLALGRDVIDADSRMG--LPDEETLARA 75
Query: 131 TAAAVAAAAATAKIQAMDGGATNAVGVL 158
A A + A +GG V L
Sbjct: 76 FERAREQGAPERWLPAFEGGFAGVVATL 103
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex,
box H/ACA, snoRNP, pseudouridine synthase, RNA
modification; 1.95A {Methanocaldococcus jannaschii}
SCOP: b.122.1.1 d.265.1.2
Length = 357
Score = 27.3 bits (61), Expect = 2.4
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 21 VIDEITEEAKLYNRIYVASIHPDLTEEDIKSVFEAF-GPIK 60
I K Y + + +H D +EEDI VF+ F G I
Sbjct: 119 TIPMWHIPPKEY--VCLMHLHRDASEEDILRVFKEFTGRIY 157
>2aus_C Pseudouridine synthase; isomerase, structural protein,
isomerase-structural protein; 2.10A {Pyrococcus abyssi}
PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A*
2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A
Length = 334
Score = 27.2 bits (61), Expect = 3.0
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 36 YVASI--HPDLTEEDIKSVFEAF-GPI 59
YVA + H D+ E+ I++V + F G I
Sbjct: 110 YVALMHLHGDVPEDKIRAVMKEFEGEI 136
>1mdo_A ARNB aminotransferase; type 1 aminotransferase fold; HET: MSE PMP;
1.70A {Salmonella typhimurium} SCOP: c.67.1.4 PDB:
1mdx_A* 1mdz_A*
Length = 393
Score = 27.1 bits (61), Expect = 3.1
Identities = 13/34 (38%), Positives = 15/34 (44%), Gaps = 4/34 (11%)
Query: 40 IHPDLTEEDIKSVFEAFGPIKYCKLQQGSSPHRH 73
+ PD+TE D V A I QGS H H
Sbjct: 363 LFPDMTESDFDRVITALHQI----AGQGSHHHHH 392
>4e4t_A Phosphoribosylaminoimidazole carboxylase, ATPase; structural
genomics, seattle structural genomics center for
infectious disease, ssgcid; 1.55A {Burkholderia
ambifaria} PDB: 3uvz_A
Length = 419
Score = 26.8 bits (60), Expect = 4.3
Identities = 12/46 (26%), Positives = 15/46 (32%), Gaps = 7/46 (15%)
Query: 113 PNALHSSKGPAPSTSHMPTAAAVAAAAATAKIQAMDGGATNAVGVL 158
L + PAP+ A AA A + VGVL
Sbjct: 245 NGILALTIVPAPAADTARVEEAQQAAVRIAD--TLGY-----VGVL 283
>2j5a_A 30S ribosomal protein S6; ribonucleoprotein, RIBO protein S6,
RNA-binding, rRNA-binding, protein folding; 2.3A
{Aquifex aeolicus} SCOP: d.58.14.1
Length = 110
Score = 25.7 bits (57), Expect = 4.5
Identities = 8/27 (29%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 30 KLYNRIYVASIHPDLTEEDIKSVFEAF 56
+ Y ++ + P L+EE++K FE
Sbjct: 8 RYYETVFA--VKPTLSEEEMKKKFEQV 32
>3aw8_A PURK, phosphoribosylaminoimidazole carboxylase, ATPase; structural
genomics, riken structural genomics/proteomics in RSGI,
ATP grAsp; HET: AMP; 2.60A {Thermus thermophilus}
Length = 369
Score = 26.4 bits (59), Expect = 5.9
Identities = 15/43 (34%), Positives = 18/43 (41%), Gaps = 7/43 (16%)
Query: 116 LHSSKGPAPSTSHMPTAAAVAAAAATAKIQAMDGGATNAVGVL 158
L S PAP S A A A ++A+D VGVL
Sbjct: 208 LRLSLAPAPGAS--EALQKKAEAYALRAMEALDY-----VGVL 243
>3lcr_A Tautomycetin biosynthetic PKS; alpha-beta hydrolase, thioesterase,
polyketide synthase, phosphopantetheine, transferase,
hydrolase; 2.00A {Streptomyces SP}
Length = 319
Score = 26.4 bits (58), Expect = 6.2
Identities = 14/84 (16%), Positives = 26/84 (30%), Gaps = 5/84 (5%)
Query: 95 NLFDLGGQYLRVGRAITPPNALHSSKGPAPSTSHMPTAAAVAAAAATAKIQAMDGGATNA 154
+ DLG + L + A T + A + A AA +++ D A
Sbjct: 9 SGVDLGTENLYFQSNAAQSDYFGELFLQAMRTGELAQAQQLMAGAAQLRLKYGDPAGPEA 68
Query: 155 VGVLSKLSQ-----VFFFFAFSHA 173
V + +L + +
Sbjct: 69 VPEIVRLGRGQLGPQLILVCPTVM 92
>3uqy_S Hydrogenase-1 small chain; membrane-bound hydrogenase,
oxidoreductase; HET: LMT; 1.47A {Escherichia coli} PDB:
3usc_S* 3use_S*
Length = 335
Score = 26.2 bits (57), Expect = 6.2
Identities = 8/32 (25%), Positives = 13/32 (40%), Gaps = 3/32 (9%)
Query: 129 MPTAAAVAA---AAATAKIQAMDGGATNAVGV 157
A+A+ A A+ +QA T A +
Sbjct: 103 AAGASAIIAWGTCASWGCVQAARPNPTQATPI 134
>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural
genomics, structural consortium, SGC, alternative
initiation, ATP-binding, devel protein; 2.80A {Homo
sapiens}
Length = 175
Score = 26.0 bits (58), Expect = 6.3
Identities = 9/47 (19%), Positives = 20/47 (42%), Gaps = 11/47 (23%)
Query: 19 QSVI--------DEITEEAKLYNRIY-VASIHPDLTEEDIKSVFEAF 56
Q++I +T ++ + V+ + +LT E S+ + F
Sbjct: 36 QAIIFCQTRRNAKWLTV--EMIQDGHQVSLLSGELTVEQRASIIQRF 80
>1o69_A Aminotransferase; structural genomics, unknown function; HET:
X04; 1.84A {Campylobacter jejuni} SCOP: c.67.1.4 PDB:
1o62_A 1o61_A*
Length = 394
Score = 25.7 bits (57), Expect = 8.9
Identities = 5/23 (21%), Positives = 12/23 (52%), Gaps = 2/23 (8%)
Query: 34 RIYVASIHPDLTEEDIKSVFEAF 56
R +++ P + ++K + E F
Sbjct: 2 RFFLSP--PHMGGNELKYIEEVF 22
>3nwy_A Uridylate kinase; allosterically activated form, AAK fold, UMP
kinase, transfe; HET: GTP UDP; 2.54A {Mycobacterium
tuberculosis}
Length = 281
Score = 25.8 bits (56), Expect = 8.9
Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 4/56 (7%)
Query: 111 TPPNALHSSKGPAPSTSHMPTAAAVAAAAATAKIQAMDGGATNAVG----VLSKLS 162
+ + H S G P SHM A A+ + + + + VL KL
Sbjct: 3 SSHHHHHHSSGLVPRGSHMTEPDVAGAPASKPEPASTGAASAAQLSGYSRVLLKLG 58
>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 25.0 bits (54), Expect = 9.2
Identities = 15/100 (15%), Positives = 33/100 (33%), Gaps = 11/100 (11%)
Query: 33 NRIYVASIHPDLTEED-----IKSVFEAFGPIKYCKLQQGSSPHRHKGYGFIEYETKQAS 87
+ + + D+ E +S+F + Q S R I + ++
Sbjct: 6 SGLIACVANDDVFSESETRAKFESLFRTYDKD--TTFQYFKSFKR----VRINFSNPLSA 59
Query: 88 NEAISSMNLFDLGGQYLRVGRAITPPNALHSSKGPAPSTS 127
+A ++ + G+ +++ A T P P S
Sbjct: 60 ADARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKS 99
>1qi9_A Protein (vanadium bromoperoxidase); haloperoxidase, oxidoreductase;
2.05A {Ascophyllum nodosum} SCOP: a.111.1.2
Length = 556
Score = 25.9 bits (56), Expect = 9.5
Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 7/79 (8%)
Query: 73 HKGYGFIEYETKQASNEAISSMNLFD-----LGGQYLRVGRAITPPNA--LHSSKGPAPS 125
H G ++ + A + I + +L +G + P A GPA S
Sbjct: 60 HDDLGQVDADAFAALEDCILNGDLSICEDVPVGNSEGDPVGRLVNPTAAFAIDISGPAFS 119
Query: 126 TSHMPTAAAVAAAAATAKI 144
+ +P + + A++
Sbjct: 120 ATTIPPVPTLPSPELAAQL 138
>2ywe_A GTP-binding protein LEPA; G domain, beta-barrel, ferredoxin-like
domain, structural GE NPPSFA; 2.05A {Aquifex aeolicus}
PDB: 2ywf_A* 2ywg_A* 2ywh_A*
Length = 600
Score = 25.9 bits (58), Expect = 9.7
Identities = 5/22 (22%), Positives = 11/22 (50%)
Query: 6 HVQVGRPSNMPQAQSVIDEITE 27
++V P + P +I+ + E
Sbjct: 384 VIEVRNPMDFPDNAGLIEYVEE 405
>1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG,
structure initiative, PSI, joint center for structural
GENO translation; 1.70A {Thermotoga maritima} SCOP:
d.58.14.1
Length = 140
Score = 25.1 bits (55), Expect = 9.8
Identities = 6/27 (22%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 30 KLYNRIYVASIHPDLTEEDIKSVFEAF 56
++Y +++ I P++ EE+ +++ E
Sbjct: 19 RIYESMFI--IAPNVPEEERENLVERV 43
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.130 0.375
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,616,687
Number of extensions: 152515
Number of successful extensions: 1110
Number of sequences better than 10.0: 1
Number of HSP's gapped: 925
Number of HSP's successfully gapped: 252
Length of query: 173
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 86
Effective length of database: 4,272,666
Effective search space: 367449276
Effective search space used: 367449276
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.5 bits)