RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8001
(172 letters)
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 110 bits (277), Expect = 1e-31
Identities = 51/148 (34%), Positives = 71/148 (47%), Gaps = 1/148 (0%)
Query: 25 STEHDDIDLYDDVTLQPFPEHTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTE 84
+ +LY P P SP + + +YVG+ +WWTT+
Sbjct: 10 GVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTD 69
Query: 85 ADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKP 144
+ IRSIGV D +++KF EN +NGQSKG+ V + SE S+ ++E LP L+G K
Sbjct: 70 QQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKV 129
Query: 145 MVAYPTRNVLYQFEAQNPLRSRSRRSYR 172
V TR L QFEAQ + R R
Sbjct: 130 DVRPATRQNLSQFEAQ-ARKRECVRVPR 156
>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 = 108 bits (271), Expect = 4e-30
Identities = 59/156 (37%), Positives = 82/156 (52%), Gaps = 13/156 (8%)
Query: 27 EHDDIDLYDDVTLQPFPEHTGRSPARYRHHRYSHHHSQATSSSH------------CNLY 74
HD IDLYDDV + P + R LY
Sbjct: 14 GHDQIDLYDDV-ISPSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIALY 72
Query: 75 VGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERL 134
+GNLTWWTT+ D+++A+ S+GV D +++KFFEN +NGQSKGF V +GSE S +M+ L
Sbjct: 73 IGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLL 132
Query: 135 PTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRRS 170
P ELHG+ P+V + L QFE Q+ ++S +
Sbjct: 133 PKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQM 168
>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 = 97.7 bits (244), Expect = 2e-27
Identities = 42/79 (53%), Positives = 58/79 (73%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
LY+GNLTWWTT+ D+++A+ S+GV D +++KFFEN +NGQSKGF V +GSE S +M
Sbjct: 3 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62
Query: 132 ERLPTLELHGRKPMVAYPT 150
+ LP ELHG+ P+V
Sbjct: 63 DLLPKRELHGQNPVVTPSN 81
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 59.3 bits (144), Expect = 2e-12
Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 8/94 (8%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCT 118
HHH + + N+ T + A+ +++ ++ Q++GF
Sbjct: 2 GHHHHHHMD----TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAF 57
Query: 119 VTLGSEESMSLVMERL----PTLELHGRKPMVAY 148
V L S S +++ L P L++ G+ V +
Sbjct: 58 VQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDF 91
>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 = 58.9 bits (143), Expect = 2e-12
Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 1/86 (1%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
S +S +L++G+L + E +S A ++G + VK N G G+C V
Sbjct: 2 SSGSSGMAASLWMGDLEPYMDENFISRAFATMGET-VMSVKIIRNRLTGIPAGYCFVEFA 60
Query: 123 SEESMSLVMERLPTLELHGRKPMVAY 148
+ + ++ L G P +
Sbjct: 61 DLATAEKCLHKINGKPLPGATPAKRF 86
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 57.2 bits (139), Expect = 9e-12
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 4/79 (5%)
Query: 65 ATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
+ SS C ++V NL + T + D G + D+K NG+SKG V S
Sbjct: 3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKM----ENGKSKGCGVVKFESP 58
Query: 125 ESMSLVMERLPTLELHGRK 143
E + ++L GR+
Sbjct: 59 EVAERACRMMNGMKLSGRE 77
>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 = 57.3 bits (139), Expect = 1e-11
Identities = 18/90 (20%), Positives = 33/90 (36%), Gaps = 6/90 (6%)
Query: 60 HHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGV------PDFIDVKFFENASNGQS 113
HHH + S + ++V L T ++D + IG+ + + + G+
Sbjct: 3 HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62
Query: 114 KGFCTVTLGSEESMSLVMERLPTLELHGRK 143
KG TV+ S ++ E G
Sbjct: 63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNP 92
>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 = 57.4 bits (139), Expect = 2e-11
Identities = 20/111 (18%), Positives = 38/111 (34%), Gaps = 4/111 (3%)
Query: 43 PEHTGRSPARYRHHRYSHHHS-QATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFID 101
+ GR P +++H + + L V NL + ++AD+ + G
Sbjct: 7 GQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAA 66
Query: 102 VKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAYPTRN 152
V + +G+S G V M++ + L GR +
Sbjct: 67 VDYDR---SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ 114
>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 = 55.7 bits (135), Expect = 4e-11
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 2/89 (2%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
++A +C L V L+ +TTE D+ + G DV + + +S+GF V
Sbjct: 8 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYG--PIADVSIVYDQQSRRSRGFAFVYFE 65
Query: 123 SEESMSLVMERLPTLELHGRKPMVAYPTR 151
+ + ER +EL GR+ V+ P+
Sbjct: 66 NVDDAKEAKERANGMELDGRRIRVSGPSS 94
>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 = 55.3 bits (134), Expect = 6e-11
Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 2/82 (2%)
Query: 62 HSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTL 121
S +S L+VG L++ T E + G +V ++ +S+GF VT
Sbjct: 4 GSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYG--QISEVVVVKDRETQRSRGFGFVTF 61
Query: 122 GSEESMSLVMERLPTLELHGRK 143
+ + M + + GR+
Sbjct: 62 ENIDDAKDAMMAMNGKSVDGRQ 83
>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 = 55.1 bits (133), Expect = 9e-11
Identities = 17/88 (19%), Positives = 30/88 (34%), Gaps = 6/88 (6%)
Query: 62 HSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGV------PDFIDVKFFENASNGQSKG 115
S + +YV L T D++D + GV + + + G+ KG
Sbjct: 7 GDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKG 66
Query: 116 FCTVTLGSEESMSLVMERLPTLELHGRK 143
TV+ + +E + G K
Sbjct: 67 DATVSYEDPPTAKAAVEWFDGKDFQGSK 94
>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 = 56.0 bits (135), Expect = 1e-10
Identities = 24/100 (24%), Positives = 37/100 (37%), Gaps = 2/100 (2%)
Query: 43 PEHTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDV 102
+ S R +H R + + C LYVGNL+++TTE + + G D +
Sbjct: 12 DSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSG--DIKKI 69
Query: 103 KFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGR 142
+ + GFC V S M + L R
Sbjct: 70 IMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDR 109
>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 = 54.5 bits (132), Expect = 1e-10
Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 2/80 (2%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
S +++ LYVG L + + A G D D++ + + +GF V
Sbjct: 5 SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFG--DITDIQIPLDYETEKHRGFAFVEFE 62
Query: 123 SEESMSLVMERLPTLELHGR 142
E + ++ + EL GR
Sbjct: 63 LAEDAAAAIDNMNESELFGR 82
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 55.1 bits (133), Expect = 1e-10
Identities = 16/91 (17%), Positives = 34/91 (37%), Gaps = 6/91 (6%)
Query: 64 QATSSSHCNLYVGNLTWWTTEADMSDAIRSIGV------PDFIDVKFFENASNGQSKGFC 117
+ +S + ++V L T ++D + IG+ + + + G+ KG
Sbjct: 1 EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60
Query: 118 TVTLGSEESMSLVMERLPTLELHGRKPMVAY 148
TV+ S ++ E G V++
Sbjct: 61 TVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 91
>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 = 54.8 bits (132), Expect = 2e-10
Identities = 16/98 (16%), Positives = 27/98 (27%), Gaps = 2/98 (2%)
Query: 51 ARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASN 110
+ + NL V + E + G VK +
Sbjct: 23 QQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYG--PIESVKIVCDRET 80
Query: 111 GQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAY 148
QS+G+ V S S + L + ++ VA
Sbjct: 81 RQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL 118
>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA
recognition motif, vincu alpha-actinin, nucleus, RNA
binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E
Length = 284
Score = 56.5 bits (137), Expect = 3e-10
Identities = 13/91 (14%), Positives = 27/91 (29%), Gaps = 9/91 (9%)
Query: 62 HSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTL 121
H++ + + + L T ++ D + + + KG VTL
Sbjct: 14 HTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYEL---KYCF------VDKYKGTAFVTL 64
Query: 122 GSEESMSLVMERLPTLELHGRKPMVAYPTRN 152
+ E + L R+ V +
Sbjct: 65 LNGEQAEAAINAFHQSRLRERELSVQLQPTD 95
Score = 52.3 bits (126), Expect = 9e-09
Identities = 17/86 (19%), Positives = 27/86 (31%), Gaps = 2/86 (2%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
+ L V NL T+ + +R G + GQSKG+ ++S
Sbjct: 92 QPTDALLCVANLPPSLTQQQFEELVRPFG--SLERCFLVYSERTGQSKGYGFAEYMKKDS 149
Query: 127 MSLVMERLPTLELHGRKPMVAYPTRN 152
+ L L R V +
Sbjct: 150 AARAKSDLLGKPLGPRTLYVHWTDAG 175
Score = 43.0 bits (102), Expect = 1e-05
Identities = 22/102 (21%), Positives = 38/102 (37%), Gaps = 10/102 (9%)
Query: 72 NLYVGNLTWWTTEAD-MSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLV 130
L V L + D + A+ ++ P + +GQ KGF + + E
Sbjct: 186 CLCVDRLPPGFNDVDALCRALSAVHSP--TFCQLACG-QDGQLKGFAVLEYETAEMAEEA 242
Query: 131 MERLPTLELHGRKPMVAY-----PTRNVLY-QFEAQNPLRSR 166
++ L L G V++ P R++L AQ +R
Sbjct: 243 QQQADGLSLGGSHLRVSFCAPGPPGRSMLAALIAAQATALNR 284
>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 = 53.8 bits (130), Expect = 3e-10
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 2/79 (2%)
Query: 64 QATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGS 123
Q S+ LYVG+L + TE + G ++ ++ G+SKG+ +T
Sbjct: 20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFG--RIESIQLMMDSETGRSKGYGFITFSD 77
Query: 124 EESMSLVMERLPTLELHGR 142
E +E+L EL GR
Sbjct: 78 SECAKKALEQLNGFELAGR 96
>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 = 54.3 bits (131), Expect = 3e-10
Identities = 24/103 (23%), Positives = 42/103 (40%), Gaps = 2/103 (1%)
Query: 46 TGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFF 105
+ + H ++A +C L V L+ +TTE D+ + G DV
Sbjct: 22 ASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYG--PIADVSIV 79
Query: 106 ENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAY 148
+ + +S+GF V + + ER +EL GR+ V +
Sbjct: 80 YDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF 122
>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 = 53.0 bits (128), Expect = 4e-10
Identities = 17/81 (20%), Positives = 30/81 (37%), Gaps = 2/81 (2%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
S + S +YV NL + T D+ G + V ++ +SKG +
Sbjct: 9 SGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYG--KVVKVTIMKDKDTRKSKGVAFILFL 66
Query: 123 SEESMSLVMERLPTLELHGRK 143
++S + +L GR
Sbjct: 67 DKDSAQNCTRAINNKQLFGRV 87
>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 = 52.5 bits (127), Expect = 4e-10
Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 2/83 (2%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
SS LY+ L TT+ D+ + G + K + + + KG+ V S +
Sbjct: 2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYG--KIVSTKAILDKTTNKCKGYGFVDFDSPSA 59
Query: 127 MSLVMERLPTLELHGRKPMVAYP 149
+ L + + + P
Sbjct: 60 AQKAVTALKASGVQAQMAKQSGP 82
>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 = 52.5 bits (127), Expect = 5e-10
Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 2/78 (2%)
Query: 65 ATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
+ +++ LYVG L + + A G D D++ + + +GF V
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFG--DITDIQIPLDYETEKHRGFAFVEFELA 59
Query: 125 ESMSLVMERLPTLELHGR 142
E + ++ + EL GR
Sbjct: 60 EDAAAAIDNMNESELFGR 77
>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 = 52.7 bits (127), Expect = 7e-10
Identities = 20/99 (20%), Positives = 37/99 (37%), Gaps = 5/99 (5%)
Query: 48 RSPARYRHHRYSHHHSQATSSSH-CNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFE 106
+ P +++H + L V NL + ++AD+ + G V +
Sbjct: 6 QLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR 65
Query: 107 NASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPM 145
+G+S G V + M++ + L GR PM
Sbjct: 66 ---SGRSLGTADVHFERKADALKAMKQYNGVPLDGR-PM 100
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 52.3 bits (126), Expect = 1e-09
Identities = 17/90 (18%), Positives = 37/90 (41%), Gaps = 3/90 (3%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCT 118
S +TS L++ L + T+ ++ + ++ G D++ N + G+ KG
Sbjct: 6 SGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHG--TVKDLRLVTNRA-GKPKGLAY 62
Query: 119 VTLGSEESMSLVMERLPTLELHGRKPMVAY 148
V +E S + ++ + + VA
Sbjct: 63 VEYENESQASQAVMKMDGMTIKENIIKVAI 92
>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 = 53.0 bits (128), Expect = 2e-09
Identities = 19/84 (22%), Positives = 33/84 (39%), Gaps = 4/84 (4%)
Query: 68 SSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESM 127
+S+ NL V L T+ ++ R+IG + + G S G+ V SE
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPI--NTCRIMRDYKTGYSYGYAFVDFTSEMDS 58
Query: 128 SLVMERLPTLELHGR--KPMVAYP 149
++ L + + + K A P
Sbjct: 59 QRAIKVLNGITVRNKRLKVSYARP 82
Score = 40.6 bits (96), Expect = 6e-05
Identities = 17/84 (20%), Positives = 27/84 (32%), Gaps = 4/84 (4%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
S NLYV NL T+ + G + + G+ +G V E
Sbjct: 86 SIKDTNLYVTNLPRTITDDQLDTIFGKYG--SIVQKNILRDKLTGRPRGVAFVRYNKREE 143
Query: 127 MSLVMERLPTLELHGR-KPM-VAY 148
+ L + G +P+ V
Sbjct: 144 AQEAISALNNVIPEGGSQPLSVRL 167
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 52.1 bits (125), Expect = 2e-09
Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 2/84 (2%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCT 118
S ++++ LYVG L + + A G D D++ + + +GF
Sbjct: 52 GSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFG--DITDIQIPLDYETEKHRGFAF 109
Query: 119 VTLGSEESMSLVMERLPTLELHGR 142
V E + ++ + EL GR
Sbjct: 110 VEFELAEDAAAAIDNMNESELFGR 133
>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 = 51.2 bits (123), Expect = 3e-09
Identities = 19/108 (17%), Positives = 36/108 (33%), Gaps = 3/108 (2%)
Query: 65 ATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
+ L++G L T E + G +V ++ + +S+GF +T +
Sbjct: 2 VEADHPGKLFIGGLNRETNEKMLKAVFGKHG--PISEVLLIKDRT-SKSRGFAFITFENP 58
Query: 125 ESMSLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRRSYR 172
+ + LHG+ V + + P S RS
Sbjct: 59 ADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPS 106
>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 = 52.1 bits (125), Expect = 3e-09
Identities = 24/128 (18%), Positives = 39/128 (30%), Gaps = 7/128 (5%)
Query: 21 GEHVSTEHDDIDLYDDVTLQPFPEHTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTW 80
E V ++ + + D T HH +L V NLT+
Sbjct: 26 AEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHH-----HHMDVEGMTSLKVDNLTY 80
Query: 81 WTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELH 140
T+ + G DV + +S+GF V + M+ + L
Sbjct: 81 RTSPDTLRRVFEKYG--RVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD 138
Query: 141 GRKPMVAY 148
GR+ V
Sbjct: 139 GRELRVQM 146
>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 = 50.6 bits (122), Expect = 3e-09
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
SS LYVG+L + TE + G ++ +++ G+SKG+ +T E
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFG--KIDNIVLMKDSDTGRSKGYGFITFSDSEC 59
Query: 127 MSLVMERLPTLELHGR 142
+E+L EL GR
Sbjct: 60 ARRALEQLNGFELAGR 75
>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 = 50.9 bits (122), Expect = 3e-09
Identities = 17/87 (19%), Positives = 42/87 (48%), Gaps = 4/87 (4%)
Query: 65 ATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASN-GQSKGFCTVTLGS 123
+ SS +C L++G + ++ + I + +DV + +A++ +++GF V S
Sbjct: 3 SGSSGNCRLFIGGIPKMKKREEILEEIAKVT-EGVLDVIVYASAADKMKNRGFAFVEYES 61
Query: 124 EESMSLVMERL--PTLELHGRKPMVAY 148
+ ++ +L ++L G + V +
Sbjct: 62 HRAAAMARRKLMPGRIQLWGHQIAVDW 88
>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 = 50.7 bits (122), Expect = 4e-09
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 4/84 (4%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
S++ NL++GNL + A++ AI + + + G ++ F V S E
Sbjct: 14 STTPFNLFIGNLNPNKSVAELKVAISELFA---KNDLAVVDVRTGTNRKFGYVDFESAED 70
Query: 127 MSLVMERLPTLELHGRKPMVAYPT 150
+ +E L L++ G + + P
Sbjct: 71 LEKALE-LTGLKVFGNEIKLEKPK 93
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 52.2 bits (125), Expect = 4e-09
Identities = 19/120 (15%), Positives = 37/120 (30%), Gaps = 4/120 (3%)
Query: 35 DDVTLQPFPEHTGRSPARYRHHRY-SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRS 93
P +++H + S + L V NL + ++AD+ +
Sbjct: 52 GGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAE 111
Query: 94 IGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAYPTRNV 153
G V + +G+S G V M++ + L GR + +
Sbjct: 112 FGTLKKAAVDYDR---SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI 168
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 52.7 bits (127), Expect = 4e-09
Identities = 19/88 (21%), Positives = 36/88 (40%), Gaps = 2/88 (2%)
Query: 64 QATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGS 123
Q + +YVG++ + E + A G + ++ + KGF V
Sbjct: 22 QGALAIMSRVYVGSIYYELGEDTIRQAFAPFG--PIKSIDMSWDSVTMKHKGFAFVEYEV 79
Query: 124 EESMSLVMERLPTLELHGRKPMVAYPTR 151
E+ L +E++ ++ L GR V P+
Sbjct: 80 PEAAQLALEQMNSVMLGGRNIKVGRPSN 107
Score = 47.7 bits (114), Expect = 2e-07
Identities = 10/82 (12%), Positives = 29/82 (35%), Gaps = 2/82 (2%)
Query: 62 HSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTL 121
+ + +YV ++ ++ D+ + G + + G+ KG+ +
Sbjct: 117 QLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFG--KIKSATLARDPTTGKHKGYGFIEY 174
Query: 122 GSEESMSLVMERLPTLELHGRK 143
+S + + +L G+
Sbjct: 175 EKAQSSQDAVSSMNLFDLGGQY 196
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 50.0 bits (120), Expect = 9e-09
Identities = 24/99 (24%), Positives = 37/99 (37%), Gaps = 10/99 (10%)
Query: 51 ARYRHHRYS------HHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKF 104
+ + HH S H + S L+V N+ + + D+ G +DV+
Sbjct: 4 SHHHHHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFG--KILDVEI 61
Query: 105 FENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRK 143
N SKGF VT + E+L + GRK
Sbjct: 62 IFN--ERGSKGFGFVTFENSADADRAREKLHGTVVEGRK 98
>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 = 51.0 bits (123), Expect = 1e-08
Identities = 21/83 (25%), Positives = 29/83 (34%), Gaps = 4/83 (4%)
Query: 69 SHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMS 128
S NL V L T+ + SIG + K + GQS G+ V +
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIG--EIESCKLVRDKITGQSLGYGFVNYIDPKDAE 58
Query: 129 LVMERLPTLELHGR--KPMVAYP 149
+ L L L + K A P
Sbjct: 59 KAINTLNGLRLQTKTIKVSYARP 81
Score = 38.3 bits (90), Expect = 3e-04
Identities = 14/84 (16%), Positives = 24/84 (28%), Gaps = 4/84 (4%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
S NLYV L T+ ++ G I + + G S+G +
Sbjct: 85 SIRDANLYVSGLPKTMTQKELEQLFSQYG--RIITSRILVDQVTGVSRGVGFIRFDKRIE 142
Query: 127 MSLVMERL--PTLELHGRKPMVAY 148
++ L V +
Sbjct: 143 AEEAIKGLNGQKPSGATEPITVKF 166
>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 = 49.2 bits (118), Expect = 1e-08
Identities = 16/80 (20%), Positives = 27/80 (33%), Gaps = 6/80 (7%)
Query: 64 QATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGS 123
S L + NL++ TE + + + NG+SKG+ + S
Sbjct: 9 STWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQ------NGKSKGYAFIEFAS 62
Query: 124 EESMSLVMERLPTLELHGRK 143
E + E+ GR
Sbjct: 63 FEDAKEALNSCNKREIEGRA 82
>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 = 49.2 bits (118), Expect = 1e-08
Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 4/81 (4%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
+ + S+ L+V N+ + + D+ G +DV+ N SKGF VT
Sbjct: 8 NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFG--KILDVEIIFN--ERGSKGFGFVTFE 63
Query: 123 SEESMSLVMERLPTLELHGRK 143
+ E+L + GRK
Sbjct: 64 NSADADRAREKLHGTVVEGRK 84
>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 = 48.7 bits (117), Expect = 2e-08
Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
SH +++VG+L+ T A ++ A G D + ++ + G+SKG+ V+ ++
Sbjct: 3 LGSHFHVFVGDLSPEITTAAIAAAFAPFG--RISDARVVKDMATGKSKGYGFVSFFNKWD 60
Query: 127 MSLVMERLPTLELHGR 142
++++ L GR
Sbjct: 61 AENAIQQMGGQWLGGR 76
>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 = 50.3 bits (121), Expect = 2e-08
Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 7/92 (7%)
Query: 57 RYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGF 116
+ L NL++ TE ++ + +++ +G+SKG
Sbjct: 86 EKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQ--DGKSKGI 138
Query: 117 CTVTLGSEESMSLVMERLPTLELHGRKPMVAY 148
+ SE +E E+ GR + Y
Sbjct: 139 AYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY 170
Score = 49.5 bits (119), Expect = 3e-08
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCT 118
SH + S++ NL++GNL + A++ AI + D+ + G ++ F
Sbjct: 2 SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAK--NDLAVVDVR-TGTNRKFGY 58
Query: 119 VTLGSEESMSLVMERLPTLELHGRKPMVAYPTR 151
V S E + +E L L++ G + + P
Sbjct: 59 VDFESAEDLEKALE-LTGLKVFGNEIKLEKPKG 90
>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 = 48.8 bits (117), Expect = 2e-08
Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 2/79 (2%)
Query: 65 ATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
A S +++VGN+ + TE + D +G + + + G+ KG+ +
Sbjct: 3 AVDRSLRSVFVGNIPYEATEEQLKDIFSEVG--PVVSFRLVYDRETGKPKGYGFCEYQDQ 60
Query: 125 ESMSLVMERLPTLELHGRK 143
E+ M L E GR
Sbjct: 61 ETALSAMRNLNGREFSGRA 79
>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 = 48.8 bits (117), Expect = 2e-08
Identities = 18/113 (15%), Positives = 33/113 (29%), Gaps = 5/113 (4%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCT 118
+ ++V NL + + + G + E+ +G+S+G T
Sbjct: 4 GSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAG--VVVRADILEDK-DGKSRGIGT 60
Query: 119 VTLGSEESMSLVMERLPTLELHGRKPMVAYPTRNVLYQ--FEAQNPLRSRSRR 169
VT + L R V R + F + P +S
Sbjct: 61 VTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSS 113
>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 = 48.9 bits (117), Expect = 2e-08
Identities = 18/80 (22%), Positives = 40/80 (50%), Gaps = 2/80 (2%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
+ +S+H +++VG+L+ T D+ A G D + ++ + G+SKG+ V+
Sbjct: 8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFG--RISDARVVKDMATGKSKGYGFVSFF 65
Query: 123 SEESMSLVMERLPTLELHGR 142
++ ++++ L GR
Sbjct: 66 NKWDAENAIQQMGGQWLGGR 85
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 49.4 bits (118), Expect = 2e-08
Identities = 23/136 (16%), Positives = 39/136 (28%), Gaps = 19/136 (13%)
Query: 41 PFPEHTGRSPARYRH----HRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGV 96
P + + S+ +L V NLT+ T+ + G
Sbjct: 14 LVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYG- 72
Query: 97 PDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAYPTRNVLYQ 156
DV + +S+GF V + M+ + L GR+ V
Sbjct: 73 -RVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ--------- 122
Query: 157 FEAQNPLRSRSRRSYR 172
A+ R S+
Sbjct: 123 -MAR---YGRPPDSHH 134
>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 = 48.6 bits (116), Expect = 3e-08
Identities = 21/116 (18%), Positives = 36/116 (31%), Gaps = 12/116 (10%)
Query: 57 RYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGF 116
+ S + V L + D+ D +R G + DV G
Sbjct: 2 SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY---------RDGT 52
Query: 117 CTVTLGSEESMSLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRRSYR 172
V +E M+ + +L + + AY + ++P RSR S
Sbjct: 53 GVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR---VKVDGPRSPSYGRSRSSGP 105
>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 = 48.0 bits (115), Expect = 3e-08
Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 7/77 (9%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
L NL++ TE ++ + +++ +G+SKG + SE +
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQ--DGKSKGIAYIEFKSEADAEKNL 70
Query: 132 ERLPTLELHGRKPMVAY 148
E E+ GR + Y
Sbjct: 71 EEKQGAEIDGRSVSLYY 87
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 48.5 bits (116), Expect = 3e-08
Identities = 11/97 (11%), Positives = 24/97 (24%), Gaps = 2/97 (2%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
+ L E + D R G + +V+ + + G V S +
Sbjct: 8 EVTFARLNDNVRETFLKDMCRKYG--EVEEVEILLHPRTRKHLGLARVLFTSTRGAKETV 65
Query: 132 ERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSR 168
+ L + G + + +
Sbjct: 66 KNLHLTSVMGNIIHAQLDIKGQQRMKYYELIVNGSYT 102
>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 = 48.0 bits (115), Expect = 3e-08
Identities = 21/82 (25%), Positives = 31/82 (37%), Gaps = 5/82 (6%)
Query: 62 HSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTL 121
A S L+V L+ TTE + ++ + + + G SKGF V
Sbjct: 7 GPNARSQPSKTLFVKGLSEDTTEETLKESFDGS-----VRARIVTDRETGSSKGFGFVDF 61
Query: 122 GSEESMSLVMERLPTLELHGRK 143
SEE E + E+ G K
Sbjct: 62 NSEEDAKAAKEAMEDGEIDGNK 83
>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 = 47.6 bits (114), Expect = 5e-08
Identities = 20/88 (22%), Positives = 29/88 (32%), Gaps = 5/88 (5%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFF---ENASNGQSKGFCTVTLGS 123
SS L++ NL + TTE + +G A S GF V
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVG--AIKSCTISKKKNKAGVLLSMGFGFVEYKK 59
Query: 124 EESMSLVMERLPTLELHGRKPMVAYPTR 151
E +++L + G K V R
Sbjct: 60 PEQAQKALKQLQGHTVDGHKLEVRISER 87
>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 = 47.7 bits (114), Expect = 5e-08
Identities = 16/87 (18%), Positives = 27/87 (31%), Gaps = 7/87 (8%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCT 118
S S L++G + E D+ G ++ ++ G KG
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFG--KIYELTVLKDRFTGMHKGCAF 59
Query: 119 VTLGSEESMSLVMERLPTLELHGRKPM 145
+T ES LH +K +
Sbjct: 60 LTYCERESALKAQS-----ALHEQKTL 81
>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 = 50.0 bits (120), Expect = 5e-08
Identities = 14/82 (17%), Positives = 35/82 (42%), Gaps = 2/82 (2%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
+ C L++ N T+ ++ D ++ I + ++ + S+ F + + S+E
Sbjct: 114 HLTECTLWMTNFPPSYTQRNIRDLLQDIN-VVALSIRL-PSLRFNTSRRFAYIDVTSKED 171
Query: 127 MSLVMERLPTLELHGRKPMVAY 148
+E+L L++ G +
Sbjct: 172 ARYCVEKLNGLKIEGYTLVTKV 193
Score = 47.7 bits (114), Expect = 4e-07
Identities = 13/107 (12%), Positives = 35/107 (32%), Gaps = 5/107 (4%)
Query: 49 SPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENA 108
SPA + + + + V NL + + + G I V ++
Sbjct: 20 SPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCG--PIIHVDVADS- 76
Query: 109 SNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAYPTRNVLY 155
++ F + + + + + + + +V++ T L+
Sbjct: 77 -LKKNFRFARIEFARYDGALAAITKTHKV-VGQNEIIVSHLTECTLW 121
Score = 37.3 bits (87), Expect = 0.001
Identities = 10/96 (10%), Positives = 32/96 (33%), Gaps = 15/96 (15%)
Query: 63 SQATSSSHCNLYVGNLTW-WTTEADMSDA------IRSIGVPDFIDVKFFENASNGQSKG 115
+ + + + + NL+ E + ++ I I +P + +
Sbjct: 203 TDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIP-------AGQKEHSFNNC 255
Query: 116 FCTVTLGSEESMSLVMERLPTLELHGRKPMVAYPTR 151
+ +++S ++ + L R+ V+ +
Sbjct: 256 CAFMVFENKDSAERALQ-MNRSLLGNREISVSLADK 290
>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 = 47.7 bits (114), Expect = 6e-08
Identities = 22/104 (21%), Positives = 39/104 (37%), Gaps = 8/104 (7%)
Query: 43 PEHTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDV 102
+G+SP R S A + ++ L D+ D ++G DV
Sbjct: 3 SGSSGKSPVREPVDNLSPEERDART-----VFCMQLAARIRPRDLEDFFSAVG--KVRDV 55
Query: 103 KFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMV 146
+ + ++ +SKG V +S+ L + L L G +V
Sbjct: 56 RIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIV 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 = 47.6 bits (114), Expect = 6e-08
Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 2/76 (2%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
+ + + V NL+ T E D+ + R G + ++ + GQSKGF ++ E
Sbjct: 12 ADDNATIRVTNLSEDTRETDLQELFRPFG--SISRIYLAKDKTTGQSKGFAFISFHRRED 69
Query: 127 MSLVMERLPTLELHGR 142
+ + +
Sbjct: 70 AARAIAGVSGFGYDHL 85
>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 = 47.2 bits (113), Expect = 7e-08
Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 2/72 (2%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLV 130
+Y+G++ + TE + D ++G I++K + G+SKG+ + ES +
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPV--INLKMMFDPQTGRSKGYAFIEFRDLESSASA 60
Query: 131 MERLPTLELHGR 142
+ L +L R
Sbjct: 61 VRNLNGYQLGSR 72
>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 = 46.8 bits (112), Expect = 7e-08
Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 1/76 (1%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
S +++G LT T+ + + + G ID+ E SKG+ V + +
Sbjct: 1 SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMP-VERMHPHLSKGYAYVEFENPDE 59
Query: 127 MSLVMERLPTLELHGR 142
++ + ++ G+
Sbjct: 60 AEKALKHMDGGQIDGQ 75
>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 = 47.3 bits (113), Expect = 8e-08
Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 3/76 (3%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLV 130
LY+ NL+ TE D+ + G+ +G +T ++E
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQ--EKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQA 83
Query: 131 MERLPTLELHGRKPMV 146
+ + +L+G+ +V
Sbjct: 84 LHLVNGYKLYGK-ILV 98
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 47.4 bits (113), Expect = 8e-08
Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 2/86 (2%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
Q CNL++ +L T+ D++ G + I K F + SK F V+
Sbjct: 33 KQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFG--NVISAKVFIDKQTSLSKCFGFVSFD 90
Query: 123 SEESMSLVMERLPTLELHGRKPMVAY 148
+ +S + ++ + ++ ++ V
Sbjct: 91 NPDSAQVAIKAMNGFQVGTKRLKVQL 116
>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 = 46.8 bits (112), Expect = 9e-08
Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 3/71 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++GNL + TE + + R + + + N + KGF +S+ +
Sbjct: 22 AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSN--PERLKGFGYAEFEDLDSLLSALS 79
Query: 133 RLPTLELHGRK 143
L L R+
Sbjct: 80 -LNEESLGNRR 89
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome biogenesis,
RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A
Length = 111
Score = 47.1 bits (112), Expect = 9e-08
Identities = 20/100 (20%), Positives = 30/100 (30%), Gaps = 11/100 (11%)
Query: 49 SPARYRHHRYSHH----HSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIG-VPDFIDVK 103
S + HH H + + + NL + D+ D R F V
Sbjct: 3 SSHHHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVN 62
Query: 104 FFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRK 143
G + SEE + +ERL +E G
Sbjct: 63 T------RDFDGTGALEFPSEEILVEALERLNNIEFRGSV 96
>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 = 46.9 bits (112), Expect = 1e-07
Identities = 18/85 (21%), Positives = 31/85 (36%), Gaps = 15/85 (17%)
Query: 64 QATSSSHCNLYVGNLTWWTTEADMSDA------IRSIGVPDFIDVKFFENASNGQSKGFC 117
A + ++VGNL E + + + + + D G+ K F
Sbjct: 10 PAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTIC--KD-------REGKPKSFG 60
Query: 118 TVTLGSEESMSLVMERLPTLELHGR 142
V ES+S + L + L+GR
Sbjct: 61 FVCFKHPESVSYAIALLNGIRLYGR 85
>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 = 46.4 bits (111), Expect = 1e-07
Identities = 23/101 (22%), Positives = 36/101 (35%), Gaps = 14/101 (13%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
N+YVGNL + T + + G +VK + + KGF V + E +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFG--KVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AI 59
Query: 132 ERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRRSYR 172
+L + GR V EA P +S +
Sbjct: 60 AKLDNTDFMGRTIRVT----------EAN-PKKSLEHHHHH 89
>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 = 47.5 bits (113), Expect = 1e-07
Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 11/85 (12%)
Query: 71 CNLYVGNLTWWTTEADMSDA------IRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
C +YV NL E D+ S D++ + G+ KG + L +E
Sbjct: 46 CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKE---GRMKGQAFIGLPNE 102
Query: 125 ESMSLVMERLPTLELHGRKPM-VAY 148
++ + ++ L G KPM V +
Sbjct: 103 KAAAKALKEANGYVLFG-KPMVVQF 126
>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 = 46.4 bits (111), Expect = 1e-07
Identities = 17/80 (21%), Positives = 22/80 (27%), Gaps = 2/80 (2%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
S L V NLT+ T+ + G DV +GF V
Sbjct: 6 SGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYG--RVGDVYIPREPHTKAPRGFAFVRFH 63
Query: 123 SEESMSLVMERLPTLELHGR 142
+ EL GR
Sbjct: 64 DRRDAQDAEAAMDGAELDGR 83
>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 = 47.5 bits (114), Expect = 2e-07
Identities = 17/94 (18%), Positives = 42/94 (44%), Gaps = 2/94 (2%)
Query: 58 YSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFC 117
++ Q++S NL+VG+L + + +A + ++ + G S+G+
Sbjct: 75 WAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFP--SYLSGHVMWDMQTGSSRGYG 132
Query: 118 TVTLGSEESMSLVMERLPTLELHGRKPMVAYPTR 151
V+ S++ M+ + +L+GR + + +
Sbjct: 133 FVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK 166
Score = 40.6 bits (96), Expect = 5e-05
Identities = 13/70 (18%), Positives = 27/70 (38%), Gaps = 3/70 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
LYVGNL TE + + G ++K + N ++ + V ++ ++
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPI--ANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59
Query: 133 RLPTLELHGR 142
L ++
Sbjct: 60 TLNGKQIENN 69
>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 = 46.1 bits (110), Expect = 2e-07
Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 2/78 (2%)
Query: 65 ATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
+ SS L+V NL++ ++E D+ + G ++ + ++ + KGF VT
Sbjct: 3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYG--PLSELHYPIDSLTKKPKGFAFVTFMFP 60
Query: 125 ESMSLVMERLPTLELHGR 142
E + GR
Sbjct: 61 EHAVKAYAEVDGQVFQGR 78
>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 = 45.6 bits (109), Expect = 2e-07
Identities = 15/71 (21%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
NL+VG+L + + +A + ++ + G S+G+ V+ S++ M
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFP--SYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 132 ERLPTLELHGR 142
+ + +L+GR
Sbjct: 61 DSMQGQDLNGR 71
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 45.7 bits (109), Expect = 3e-07
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 4/71 (5%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
YVGNL + T + D+ + + + V+ + + KGFC V +S+ +
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLSI---RSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74
Query: 133 RLPTLELHGRK 143
L R
Sbjct: 75 -YDGALLGDRS 84
>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 = 45.7 bits (109), Expect = 3e-07
Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 2/78 (2%)
Query: 65 ATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
+ + +YVG L +E + + G ++ ++ GQ +G+ V SE
Sbjct: 10 SERNQDATVYVGGLDEKVSEPLLWELFLQAG--PVVNTHMPKDRVTGQHQGYGFVEFLSE 67
Query: 125 ESMSLVMERLPTLELHGR 142
E ++ + ++L+G+
Sbjct: 68 EDADYAIKIMDMIKLYGK 85
>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 = 45.8 bits (109), Expect = 3e-07
Identities = 15/90 (16%), Positives = 35/90 (38%), Gaps = 8/90 (8%)
Query: 65 ATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
+ + +++ NL++ + E + + ++ G D V+ + SKG ++
Sbjct: 10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFG--DLKYVRVVLHPDTEHSKGCAFAQFMTQ 67
Query: 125 ESMSLVMERLPT------LELHGRKPMVAY 148
E+ + L+L GR+ V
Sbjct: 68 EAAQKCLAAASLEAEGGGLKLDGRQLKVDL 97
>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 = 45.8 bits (109), Expect = 3e-07
Identities = 15/86 (17%), Positives = 32/86 (37%), Gaps = 2/86 (2%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
SQ NL++ +L + D+ G + + K F + SK F V+
Sbjct: 18 SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFG--NVVSAKVFIDKQTNLSKCFGFVSYD 75
Query: 123 SEESMSLVMERLPTLELHGRKPMVAY 148
+ S ++ + ++ ++ V
Sbjct: 76 NPVSAQAAIQSMNGFQIGMKRLKVQL 101
>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 = 46.8 bits (112), Expect = 3e-07
Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 2/82 (2%)
Query: 62 HSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTL 121
H L++G L + + + + + S G ++++ G SKG+
Sbjct: 86 HDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFG--PLKAFNLVKDSATGLSKGYAFCEY 143
Query: 122 GSEESMSLVMERLPTLELHGRK 143
+ L ++L +K
Sbjct: 144 VDINVTDQAIAGLNGMQLGDKK 165
Score = 41.1 bits (97), Expect = 4e-05
Identities = 14/63 (22%), Positives = 21/63 (33%), Gaps = 3/63 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFE---NASNGQSKGFCTVTLGSEESMSL 129
LYVGN+ + TE M D + + Q K F + S + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66
Query: 130 VME 132
M
Sbjct: 67 AMA 69
>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 = 46.9 bits (112), Expect = 3e-07
Identities = 16/110 (14%), Positives = 35/110 (31%), Gaps = 2/110 (1%)
Query: 41 PFPEHTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFI 100
P + S S L++G L + + + + + S G
Sbjct: 85 PHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFG--PLK 142
Query: 101 DVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAYPT 150
++++ G SKG+ + L ++L +K +V +
Sbjct: 143 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 192
Score = 44.6 bits (106), Expect = 2e-06
Identities = 18/95 (18%), Positives = 30/95 (31%), Gaps = 4/95 (4%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFE---NASNGQSKGFCTVTLGSEESM 127
LYVGN+ + TE M D + + Q K F + S +
Sbjct: 5 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 128 SLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNP 162
+ M + G+ + P ++NP
Sbjct: 65 TQAMA-FDGIIFQGQSLKIRRPHDYQPLPGMSENP 98
>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 = 45.3 bits (108), Expect = 4e-07
Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 3/86 (3%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIG-VPDFIDVKFFENASNGQSKGFCTVTLGSEE 125
SS +++GNL E + D + G + K + G SKG+ + S +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQ--TPKIMRDPDTGNSKGYAFINFASFD 59
Query: 126 SMSLVMERLPTLELHGRKPMVAYPTR 151
+ +E + L R V+Y +
Sbjct: 60 ASDAAIEAMNGQYLCNRPITVSYAFK 85
>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 = 45.6 bits (108), Expect = 4e-07
Identities = 21/107 (19%), Positives = 36/107 (33%), Gaps = 12/107 (11%)
Query: 66 TSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEE 125
+ S + V L + D+ D +R G + DV G V +E
Sbjct: 12 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADV---------YRDGTGVVEFVRKE 62
Query: 126 SMSLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRRSYR 172
M+ + +L + + AY + ++P RSR R
Sbjct: 63 DMTYAVRKLDNTKFRSHEGETAYIR---VKVDGPRSPSYGRSRSRSR 106
>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 = 44.9 bits (107), Expect = 4e-07
Identities = 20/107 (18%), Positives = 36/107 (33%), Gaps = 20/107 (18%)
Query: 65 ATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
+ SS L++GNL TE ++ G D+ K + V + +
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII----------KNYGFVHIEDK 52
Query: 125 ESMSLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRRSY 171
+ + L +LHG V ++N ++ S S
Sbjct: 53 TAAEDAIRNLHHYKLHGVNINVE----------ASKNKSKASSGPSS 89
>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 = 45.4 bits (108), Expect = 5e-07
Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 3/85 (3%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCT 118
S H ++ ++VG L + TT+A + G D + + G+S+G+
Sbjct: 6 SGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFG--DIEEAVVITDRQTGKSRGYGF 63
Query: 119 VTLGSEESMSLVMERLPTLELHGRK 143
VT+ + + + GRK
Sbjct: 64 VTMADRAAAERACKDPNP-IIDGRK 87
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 45.0 bits (107), Expect = 5e-07
Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 8/80 (10%)
Query: 64 QATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGS 123
++ Y+GN+ + TEAD+ ++ G +D K + KG C + +
Sbjct: 21 RSAPPRVTTAYIGNIPHFATEADLIPLFQNFG--FILDFKHY------PEKGCCFIKYDT 72
Query: 124 EESMSLVMERLPTLELHGRK 143
E ++ + L GR
Sbjct: 73 HEQAAVCIVALANFPFQGRN 92
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo
sapiens} SCOP: d.58.7.1
Length = 106
Score = 44.9 bits (107), Expect = 6e-07
Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 2/78 (2%)
Query: 65 ATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
S L+V + TE D+ D G + ++ + G KG+ V +
Sbjct: 18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYG--EIKNIHLNLDRRTGYLKGYTLVEYETY 75
Query: 125 ESMSLVMERLPTLELHGR 142
+ ME L +L G+
Sbjct: 76 KEAQAAMEGLNGQDLMGQ 93
>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 = 46.5 bits (111), Expect = 6e-07
Identities = 16/94 (17%), Positives = 35/94 (37%), Gaps = 2/94 (2%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCT 118
+ A S +LYVG+L TEA + + G + ++ + +S G+
Sbjct: 4 GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAG--PILSIRVCRDMITRRSLGYAY 61
Query: 119 VTLGSEESMSLVMERLPTLELHGRKPMVAYPTRN 152
V ++ + + G+ + + R+
Sbjct: 62 VNFQQPADAERALDTMNFDVIKGKPVRIMWSQRD 95
Score = 39.2 bits (92), Expect = 2e-04
Identities = 18/94 (19%), Positives = 36/94 (38%), Gaps = 4/94 (4%)
Query: 58 YSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFC 117
+S S N+++ NL + D + G + + K + SKG+
Sbjct: 91 WSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFG--NILSCKVVCD--ENGSKGYG 146
Query: 118 TVTLGSEESMSLVMERLPTLELHGRKPMVAYPTR 151
V ++E+ +E++ + L+ RK V
Sbjct: 147 FVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 180
>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 = 44.2 bits (105), Expect = 7e-07
Identities = 20/80 (25%), Positives = 31/80 (38%), Gaps = 10/80 (12%)
Query: 65 ATSSSHCN-LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGS 123
++ SS N LY+GNL+ T D+ +P V G+ V
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV--------LLKSGYAFVDYPD 53
Query: 124 EESMSLVMERL-PTLELHGR 142
+ +E L +ELHG+
Sbjct: 54 QNWAIRAIETLSGKVELHGK 73
>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 = 44.2 bits (105), Expect = 1e-06
Identities = 13/71 (18%), Positives = 27/71 (38%), Gaps = 3/71 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++GNL + TE + + R + + + N + KGF +S+ +
Sbjct: 18 AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSN--PERLKGFGYAEFEDLDSLLSALS 75
Query: 133 RLPTLELHGRK 143
L L ++
Sbjct: 76 -LNEESLGNKR 85
>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 = 44.7 bits (106), Expect = 1e-06
Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 3/72 (4%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
++YVGN+ + +T D+ S G + + +G KG+ + S+ +
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCG--SINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95
Query: 132 ERLPTLELHGRK 143
+ GR
Sbjct: 96 A-MDETVFRGRT 106
>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 = 43.8 bits (104), Expect = 1e-06
Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 8/80 (10%)
Query: 64 QATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGS 123
+ T + L+VGNL TE +M G +V + KGF + L +
Sbjct: 9 EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYG--KAGEVFIH------KDKGFGFIRLET 60
Query: 124 EESMSLVMERLPTLELHGRK 143
+ L + L G++
Sbjct: 61 RTLAEIAKVELDNMPLRGKQ 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 = 43.7 bits (104), Expect = 1e-06
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 3/72 (4%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
++YVGN+ + T ++ G V + +G KGF + +ES+ +
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCG--SVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 132 ERLPTLELHGRK 143
L GR+
Sbjct: 66 A-LDESLFRGRQ 76
>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 = 43.8 bits (104), Expect = 1e-06
Identities = 12/83 (14%), Positives = 31/83 (37%), Gaps = 4/83 (4%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKF-FENASNGQSKGFCTVTL 121
+ + V N+ + + ++ + + G + V+ + G +GF V
Sbjct: 8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFG--ELKTVRLPKKMTGTGAHRGFGFVDF 65
Query: 122 GSEESMSLVMERLP-TLELHGRK 143
+++ L + L+GR+
Sbjct: 66 ITKQDAKKAFNALCHSTHLYGRR 88
>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 = 43.7 bits (104), Expect = 2e-06
Identities = 21/88 (23%), Positives = 30/88 (34%), Gaps = 4/88 (4%)
Query: 64 QATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGS 123
+ T NLYV NL + + A G K G+SKGF V S
Sbjct: 9 RITRYQVVNLYVKNLDDGIDDERLRKAFSPFG--TITSAKVMME--GGRSKGFGFVCFSS 64
Query: 124 EESMSLVMERLPTLELHGRKPMVAYPTR 151
E + + + + + VA R
Sbjct: 65 PEEATKAVTEMNGRIVATKPLYVALAQR 92
>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 = 43.9 bits (104), Expect = 2e-06
Identities = 22/103 (21%), Positives = 36/103 (34%), Gaps = 7/103 (6%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
L+V + TE D+ D G + ++ + G KG+ V + + M
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYG--EIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 132 ERLPTLELHGRKPMV--AYPTRNVLYQFEAQNPLRSRSRRSYR 172
E L +L G+ V + + R RSR R
Sbjct: 82 EGLNGQDLMGQPISVDWCFVRGP---PKGKRRGGRRRSRSPDR 121
>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 = 44.1 bits (104), Expect = 2e-06
Identities = 20/128 (15%), Positives = 45/128 (35%), Gaps = 8/128 (6%)
Query: 43 PEHTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDV 102
+G+SP+ + R S++ + +Y+ L + + D + + + + +
Sbjct: 3 SGSSGKSPSGQKRSR-----SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVE-DSI 56
Query: 103 KFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNP 162
NG++ G V +E + R + R V T+ + +
Sbjct: 57 YIAYGP-NGKATGEGFVEFRNEADYKAALCR-HKQYMGNRFIQVHPITKKGMLEKIDMIR 114
Query: 163 LRSRSRRS 170
R +S S
Sbjct: 115 KRLQSGPS 122
>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 = 44.4 bits (105), Expect = 2e-06
Identities = 15/100 (15%), Positives = 30/100 (30%), Gaps = 2/100 (2%)
Query: 44 EHTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVK 103
E S L+V ++ E ++ + G + ++
Sbjct: 46 EAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYG--EIKNIH 103
Query: 104 FFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRK 143
+ G SKG+ V + + E L E+ G+
Sbjct: 104 LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT 143
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 43.2 bits (102), Expect = 2e-06
Identities = 13/75 (17%), Positives = 26/75 (34%), Gaps = 4/75 (5%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
++Y+ T D+ + + G I ++ + KG V S ES +
Sbjct: 13 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH---KAFKGSIFVVFDSIESAKKFV 69
Query: 132 ERLPTLELHGRKPMV 146
E P + ++
Sbjct: 70 E-TPGQKYKETDLLI 83
>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 43.6 bits (103), Expect = 2e-06
Identities = 22/111 (19%), Positives = 43/111 (38%), Gaps = 3/111 (2%)
Query: 60 HHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTV 119
+S+ ++ N+ + T+ D+ + I V + V + +NGQ G V
Sbjct: 5 SSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDE-NAVHVLVD-NNGQGLGQALV 62
Query: 120 TLGSEESMSLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRRS 170
+E+ +L+GR+ V T + + E P + +S S
Sbjct: 63 QFKNEDDARKSERLHRK-KLNGREAFVHVVTLEDMREIEKNPPAQGKSGPS 112
>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 = 43.0 bits (102), Expect = 2e-06
Identities = 15/81 (18%), Positives = 30/81 (37%), Gaps = 10/81 (12%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
S +S + ++VGN++ T ++ G DV K + V +
Sbjct: 2 SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV----------KDYAFVHME 51
Query: 123 SEESMSLVMERLPTLELHGRK 143
E + +L E+ G++
Sbjct: 52 KEADAKAAIAQLNGKEVKGKR 72
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding
domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 98
Score = 43.1 bits (102), Expect = 3e-06
Identities = 13/78 (16%), Positives = 27/78 (34%), Gaps = 4/78 (5%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIG-VPDFIDVKFFENASNGQSKGFCTVTLGSEE 125
+ V N+ + + ++ D +P + +K+ E G G V S +
Sbjct: 12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEK---GMPTGEAMVAFESRD 68
Query: 126 SMSLVMERLPTLELHGRK 143
+ + L + RK
Sbjct: 69 EATAAVIDLNDRPIGSRK 86
>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 = 44.5 bits (106), Expect = 3e-06
Identities = 19/83 (22%), Positives = 31/83 (37%), Gaps = 19/83 (22%)
Query: 68 SSHCNLYVGNLTWWTTEADMSD------AIRSIGVP-DFIDVKFFENASNGQSKGFCTVT 120
S ++VG + +E D+ + A+ I V D + + QSKG C VT
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRD-------RSQNPPQSKGCCFVT 53
Query: 121 LGSEESMSLVMERLPTLELHGRK 143
+ ++ LH K
Sbjct: 54 FYTRKAALEAQN-----ALHNMK 71
Score = 34.9 bits (81), Expect = 0.005
Identities = 14/79 (17%), Positives = 29/79 (36%), Gaps = 8/79 (10%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
+ L++G ++ TE D+ S G + + +G S+G VT +
Sbjct: 92 AVEDRKLFIGMISKKCTENDIRVMFSSFGQ--IEECRILRG-PDGLSRGCAFVTFTTRAM 148
Query: 127 MSLVMERLPTLELHGRKPM 145
++ +H + M
Sbjct: 149 AQTAIK-----AMHQAQTM 162
>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 = 44.1 bits (105), Expect = 3e-06
Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 3/72 (4%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
++VG + + + G ID + + GQS+GF VT S +++ V
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQWG--TIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC 146
Query: 132 ERLPTLELHGRK 143
+ ++ RK
Sbjct: 147 Q-NKFIDFKDRK 157
Score = 37.1 bits (87), Expect = 9e-04
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLV 130
C +++G L W TTE ++ + G D+K ++ + G+S+GF ++ S+ V
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYG--TVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 131 ME 132
++
Sbjct: 62 VK 63
>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 = 42.7 bits (101), Expect = 3e-06
Identities = 14/82 (17%), Positives = 29/82 (35%), Gaps = 4/82 (4%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIG-VPDFIDVKFFENASNGQSKGFCTVTL 121
S + + V N+ + + ++ D +P + +K+ E G G V
Sbjct: 8 SSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEK---GMPTGEAMVAF 64
Query: 122 GSEESMSLVMERLPTLELHGRK 143
S + + + L + RK
Sbjct: 65 ESRDEATAAVIDLNDRPIGSRK 86
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 43.1 bits (102), Expect = 3e-06
Identities = 17/83 (20%), Positives = 28/83 (33%), Gaps = 17/83 (20%)
Query: 72 NLYVGNLTWWTTEADMSD------AIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEE 125
LY+ NL + T +M D IR I V + +++G V
Sbjct: 10 ILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN-----------TPETRGTAYVVYEDIF 58
Query: 126 SMSLVMERLPTLELHGRKPMVAY 148
++ L + R +V Y
Sbjct: 59 DAKNAVDHLSGFNVSNRYLVVLY 81
>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 = 43.1 bits (102), Expect = 3e-06
Identities = 14/79 (17%), Positives = 29/79 (36%), Gaps = 8/79 (10%)
Query: 64 QATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGS 123
+S +C +Y G + T+ M G ++++ F KG+ V +
Sbjct: 19 NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFG--QIMEIRVF------PEKGYSFVRFST 70
Query: 124 EESMSLVMERLPTLELHGR 142
ES + + + + G
Sbjct: 71 HESAAHAIVSVNGTTIEGH 89
>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 = 44.7 bits (106), Expect = 3e-06
Identities = 20/93 (21%), Positives = 31/93 (33%), Gaps = 10/93 (10%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
+ T + C L+VGNL TE D G + +V + +GF + L
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFERYG--EPSEVFI------NRDRGFGFIRLE 66
Query: 123 SEESMSLVMERLPTLELHGR--KPMVAYPTRNV 153
S + L L R + A +
Sbjct: 67 SRTLAEIAKAELDGTILKSRPLRIRFATHGAAL 99
Score = 37.4 bits (87), Expect = 0.001
Identities = 14/86 (16%), Positives = 28/86 (32%), Gaps = 6/86 (6%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
++ L V NL+ + + A G + G++ G V ++
Sbjct: 93 ATHGAALTVKNLSPVVSNELLEQAFSQFG--PVEKAVVVVD-DRGRATGKGFVEFAAKPP 149
Query: 127 MSLVMERL---PTLELHGRKPMVAYP 149
+ER L +P++ P
Sbjct: 150 ARKALERCGDGAFLLTTTPRPVIVEP 175
>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 = 42.7 bits (101), Expect = 4e-06
Identities = 18/88 (20%), Positives = 28/88 (31%), Gaps = 8/88 (9%)
Query: 58 YSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFC 117
S++ L+VG L +E D+ + G + +G SKG
Sbjct: 3 SGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFG--VIDECTVLRG-PDGSSKGCA 59
Query: 118 TVTLGSEESMSLVMERLPTLELHGRKPM 145
V S + LHG + M
Sbjct: 60 FVKFSSHTEAQAAIH-----ALHGSQTM 82
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 42.3 bits (100), Expect = 5e-06
Identities = 19/95 (20%), Positives = 33/95 (34%), Gaps = 13/95 (13%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
S +S +L+VG+LT + + + + P K + G SKG+ V
Sbjct: 2 SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVY-PSCRGGKVVLD-QTGVSKGYGFVKFT 59
Query: 123 SEESMSLVMERLPTLELHGR-----KPM-VAYPTR 151
E + E G KP+ ++
Sbjct: 60 DELEQKRALT-----ECQGAVGLGSKPVRLSVAIP 89
>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 = 42.3 bits (100), Expect = 5e-06
Identities = 14/78 (17%), Positives = 29/78 (37%), Gaps = 2/78 (2%)
Query: 65 ATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
S L+V ++ E ++ + G + ++ + G SKG+ V +
Sbjct: 21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYG--EIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 125 ESMSLVMERLPTLELHGR 142
+ E L E+ G+
Sbjct: 79 KQALAAKEALNGAEIMGQ 96
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 41.7 bits (98), Expect = 7e-06
Identities = 15/90 (16%), Positives = 28/90 (31%), Gaps = 5/90 (5%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
L + N+ + + GV V+ E + VT S++
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGV-----VESCEQVNTDSETAVVNVTYSSKDQ 66
Query: 127 MSLVMERLPTLELHGRKPMVAYPTRNVLYQ 156
+++L +L VAY + Q
Sbjct: 67 ARQALDKLNGFQLENFTLKVAYIPDEMAAQ 96
>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 = 41.8 bits (99), Expect = 7e-06
Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
++VG + E ++ G +VK + + G SKG+ V+ ++ + ++
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYG--SVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIV 67
Query: 132 ERLPTLELHGRK 143
E + HG+K
Sbjct: 68 ES--QINFHGKK 77
>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 = 41.9 bits (99), Expect = 8e-06
Identities = 16/85 (18%), Positives = 31/85 (36%), Gaps = 3/85 (3%)
Query: 64 QATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGS 123
+ NLY+ NL E ++ + ++ G I + + S+G S+G + S
Sbjct: 19 KQQEQDPTNLYISNLPLSMDEQELENMLKPFG--QVISTRILRD-SSGTSRGVGFARMES 75
Query: 124 EESMSLVMERLPTLELHGRKPMVAY 148
E V+ + + A
Sbjct: 76 TEKCEAVIGHFNGKFIKTPPGVSAP 100
>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 = 41.0 bits (97), Expect = 1e-05
Identities = 15/82 (18%), Positives = 36/82 (43%), Gaps = 3/82 (3%)
Query: 62 HSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTL 121
S ++ S ++VG + E ++ + + G +V +A + +GF +T
Sbjct: 2 SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFG--VVTEVVMIYDAEKQRPRGFGFITF 59
Query: 122 GSEESMSLVMERLPTLELHGRK 143
E+S+ + + ++ G+K
Sbjct: 60 EDEQSVDQAVN-MHFHDIMGKK 80
>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 = 40.5 bits (95), Expect = 2e-05
Identities = 13/78 (16%), Positives = 27/78 (34%), Gaps = 11/78 (14%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPD-FIDVKFFENASNGQSKGFCTVTLGSEE 125
SS + V NL + ++ D ++ + ++D +K VTL + E
Sbjct: 2 SSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDR----------NKRTAFVTLLNGE 51
Query: 126 SMSLVMERLPTLELHGRK 143
++ G+
Sbjct: 52 QAQNAIQMFHQYSFRGKD 69
>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 = 42.2 bits (99), Expect = 2e-05
Identities = 15/109 (13%), Positives = 33/109 (30%), Gaps = 9/109 (8%)
Query: 40 QPFPEHTGRSPARYRHHRYSHHHSQATSSSH---CNLYVGNLTWWTTEADMSDAIRSIGV 96
+ + HR+ S+ + L++ N+ +E D+ S G
Sbjct: 87 GQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG 146
Query: 97 PDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPM 145
+ F + + + +GS E + L +L +
Sbjct: 147 --VVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHL 189
Score = 34.1 bits (78), Expect = 0.012
Identities = 18/102 (17%), Positives = 28/102 (27%), Gaps = 8/102 (7%)
Query: 69 SHCNLYVGNL-TWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESM 127
+ L V NL T + G D VK N K V +
Sbjct: 2 GNSVLLVSNLNPERVTPQSLFILFGVYG--DVQRVKILFN-----KKENALVQMADGNQA 54
Query: 128 SLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRR 169
L M L +LHG+ + + + ++
Sbjct: 55 QLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKD 96
>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 = 40.7 bits (96), Expect = 2e-05
Identities = 19/80 (23%), Positives = 28/80 (35%), Gaps = 8/80 (10%)
Query: 64 QATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGS 123
+ T SS LYV NL T+E + +I VK + + + V +
Sbjct: 9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK--------KIRDYAFVHFSN 60
Query: 124 EESMSLVMERLPTLELHGRK 143
E M+ L L G
Sbjct: 61 REDAVEAMKALNGKVLDGSP 80
>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 = 40.1 bits (94), Expect = 2e-05
Identities = 15/73 (20%), Positives = 24/73 (32%), Gaps = 4/73 (5%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFE---NASNGQSKGFCTVTLGSEESMSL 129
LYVGN+ + TE M D + + Q K F + S + +
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68
Query: 130 VMERLPTLELHGR 142
M + G+
Sbjct: 69 AMA-FDGIIFQGQ 80
>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 = 40.7 bits (96), Expect = 2e-05
Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 4/82 (4%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
N+++ NL + D + G + + K + SKG+ V ++E+
Sbjct: 2 PLGSGNIFIKNLDKSIDNKALYDTFSAFG--NILSCKVVCD--ENGSKGYGFVHFETQEA 57
Query: 127 MSLVMERLPTLELHGRKPMVAY 148
+E++ + L+ RK V
Sbjct: 58 AERAIEKMNGMLLNDRKVFVGR 79
Score = 31.8 bits (73), Expect = 0.039
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 2/40 (5%)
Query: 49 SPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMS 88
+ R R + ++A + N+Y+ N +T A S
Sbjct: 78 GRFKSRKEREAELGARAKEFT--NVYIKNFGPGSTRAAAS 115
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 39.4 bits (93), Expect = 3e-05
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++VG L+ TT D+ G D + + + +GF VT SE+ + V E
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFG--KVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
Query: 133 RLPTLELHGRK 143
+ E++ +
Sbjct: 60 -IHFHEINNKM 69
>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 = 39.9 bits (94), Expect = 3e-05
Identities = 19/108 (17%), Positives = 36/108 (33%), Gaps = 20/108 (18%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
S ++ + L+VGN++ T ++ G D+ K + V +
Sbjct: 3 SGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV----------KDYAFVHME 52
Query: 123 SEESMSLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRRS 170
E + L E G++ V + + LR+ S S
Sbjct: 53 RAEDAVEAIRGLDNTEFQGKRMHVQ----------LSTSRLRTASGPS 90
>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 = 39.4 bits (93), Expect = 4e-05
Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++VG L+ T E + + G + ++ + + +GFC +T EE + +ME
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFG--EVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
Query: 133 RLPTLELHGRK 143
+ + K
Sbjct: 60 K-KYHNVGLSK 69
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 77
Score = 39.0 bits (92), Expect = 4e-05
Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 3/73 (4%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLV 130
C +++G L+W TT+ + + G + + + +S+GF VT + + V
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFG--EVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58
Query: 131 MERLPTLELHGRK 143
+ + EL +
Sbjct: 59 LAQSRH-ELDSKT 70
>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 = 40.7 bits (96), Expect = 6e-05
Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 3/71 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++VG + T E + D G ++ + +G+ +GF VT +S+ ++
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYG--KIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164
Query: 133 RLPTLELHGRK 143
++G
Sbjct: 165 -QKYHTVNGHN 174
Score = 38.8 bits (91), Expect = 3e-04
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 3/77 (3%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
L++G L++ TT+ + G D + + +S+GF VT + E
Sbjct: 10 PEQLRKLFIGGLSFETTDESLRSHFEQWG--TLTDCVVMRDPNTKRSRGFGFVTYATVEE 67
Query: 127 MSLVMERLPTLELHGRK 143
+ M P ++ GR
Sbjct: 68 VDAAMNARPH-KVDGRV 83
>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 = 40.8 bits (95), Expect = 7e-05
Identities = 15/115 (13%), Positives = 32/115 (27%), Gaps = 5/115 (4%)
Query: 40 QPFPEHTGRSPARYRHHRYS---HHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGV 96
+ + + R++R+S L+ N TE + + +GV
Sbjct: 90 LEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGV 149
Query: 97 PDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAYPTR 151
VK F + + S+ + L ++ Y +
Sbjct: 150 KRPTSVKVFSG--KSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLK 202
Score = 27.4 bits (60), Expect = 2.2
Identities = 13/95 (13%), Positives = 29/95 (30%), Gaps = 8/95 (8%)
Query: 68 SSHCNLYVGNL-TWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
+ L V L + + G + VKF ++ G V + +
Sbjct: 2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYG--NVEKVKFMKS-----KPGAAMVEMADGYA 54
Query: 127 MSLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQN 161
+ + L + G+K V + + ++
Sbjct: 55 VDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYG 89
>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 = 10/71 (14%), Positives = 26/71 (36%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
+ + L W T D+ + + + + F +G+ +G + +
Sbjct: 4 LEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEME 63
Query: 123 SEESMSLVMER 133
SE+ + +E+
Sbjct: 64 SEQDVQKALEK 74
>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 = 38.8 bits (91), Expect = 1e-04
Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 3/85 (3%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCT 118
S + + + L+VG L W TT+ + G + +D ++ + QS+GF
Sbjct: 5 SSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYG--EVVDCVIMKDKTTNQSRGFGF 62
Query: 119 VTLGSEESMSLVMERLPTLELHGRK 143
V + V+ P L GR
Sbjct: 63 VKFKDPNCVGTVLASRPH-TLDGRN 86
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 97
Score = 38.3 bits (89), Expect = 1e-04
Identities = 14/83 (16%), Positives = 26/83 (31%), Gaps = 7/83 (8%)
Query: 66 TSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEE 125
+ ++YVGNL +D+ A+R +G + + +
Sbjct: 15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVPL-------RLTWQGPRRRAFLHYPDSA 67
Query: 126 SMSLVMERLPTLELHGRKPMVAY 148
+ + L L L VA
Sbjct: 68 AAQQAVSCLQGLRLGTDTLRVAL 90
>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 = 38.1 bits (89), Expect = 2e-04
Identities = 9/71 (12%), Positives = 31/71 (43%), Gaps = 4/71 (5%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
S ++ ++ + + + TE ++ + + + + ++ N ++G G+ V
Sbjct: 3 SGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKP---VAIRIVRN-AHGNKTGYIFVDFS 58
Query: 123 SEESMSLVMER 133
+EE + ++
Sbjct: 59 NEEEVKQALKC 69
>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 = 38.2 bits (89), Expect = 2e-04
Identities = 12/75 (16%), Positives = 25/75 (33%), Gaps = 4/75 (5%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCT 118
S + + V + + E D+ D + V V ++ G++ G
Sbjct: 5 SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRV---DAVHLLKDH-VGRNNGNGL 60
Query: 119 VTLGSEESMSLVMER 133
V S + ++R
Sbjct: 61 VKFLSPQDTFEALKR 75
>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 = 37.8 bits (88), Expect = 2e-04
Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 4/71 (5%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
S S++ +++ L + TE D+ + + + V +G+ G V
Sbjct: 8 SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNP---MRVHIEIG-PDGRVTGEADVEFA 63
Query: 123 SEESMSLVMER 133
+ E M +
Sbjct: 64 THEDAVAAMAK 74
>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 = 37.6 bits (88), Expect = 3e-04
Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 4/85 (4%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCT 118
+ +L V L W TTE D+ + + G + + V+ ++ G SKGF
Sbjct: 4 GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFG--EVLMVQVKKDLKTGHSKGFGF 61
Query: 119 VTLGSEESMSLVMERLPTLELHGRK 143
V E+ VM + + GR
Sbjct: 62 VRFTEYETQVKVMSQRHM--IDGRW 84
>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 = 38.7 bits (89), Expect = 4e-04
Identities = 15/105 (14%), Positives = 37/105 (35%), Gaps = 9/105 (8%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSI--GVPDFIDVKFFENASNGQSKGFCTVTLGSEESMS 128
+Y+ NL + ++ ++ +I +D+ + + +G V S +
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 66
Query: 129 LVMERLPTLELHGRKPMV---AYPTRNVLYQFEAQNPLRSRSRRS 170
+ + + KPM A +++ + + R R R
Sbjct: 67 NALRSMQGFPFYD-KPMRIQYAKTDSDIIAKMKGTFVERDRKREK 110
Score = 34.1 bits (77), Expect = 0.013
Identities = 16/140 (11%), Positives = 35/140 (25%), Gaps = 9/140 (6%)
Query: 10 GMGPTDTNTSPGEHVSTEHDDIDLYDDVTLQPFPEHTGRSPARYRHHRYSHHHSQATSSS 69
P + PG+ + + P + +
Sbjct: 148 TQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQP-LSENPP 206
Query: 70 HCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSL 129
+ L++ NL T E +S F +V+ V +E
Sbjct: 207 NHILFLTNLPEETNELMLSMLFNQFPG--FKEVRLVPG-----RHDIAFVEFDNEVQAGA 259
Query: 130 VMERLPTLELHGRKPM-VAY 148
+ L ++ M +++
Sbjct: 260 ARDALQGFKITQNNAMKISF 279
>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 = 37.6 bits (87), Expect = 4e-04
Identities = 12/61 (19%), Positives = 26/61 (42%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
+ + L W + D+ + + + D + F G+ G V L SE+ + L ++
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79
Query: 133 R 133
+
Sbjct: 80 K 80
>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 = 37.3 bits (87), Expect = 5e-04
Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L++G L++ TTE + + G D + ++ +S+GF VT S + M
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWG--KLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 133 RLPTLELHGRK 143
P + GR
Sbjct: 88 ARPH-SIDGRV 97
>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 = 37.0 bits (86), Expect = 5e-04
Identities = 14/88 (15%), Positives = 23/88 (26%), Gaps = 10/88 (11%)
Query: 56 HRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKG 115
R + LYV T + A G + ID+ +
Sbjct: 25 RRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFG--NIIDLSMDPP------RN 74
Query: 116 FCTVTLGSEESMSLVMERLPTLELHGRK 143
VT ES + L ++ +
Sbjct: 75 CAFVTYEKMESADQAVAELNGTQVESVQ 102
>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 = 38.1 bits (88), Expect = 6e-04
Identities = 21/131 (16%), Positives = 34/131 (25%), Gaps = 10/131 (7%)
Query: 40 QPFPEHTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWT-TEADMSDAIRSIGVPD 98
+G P R + + + L V NL T + G D
Sbjct: 6 HHHHHSSGLVPRGSHMGRIAI--PGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYG--D 61
Query: 99 FIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAYPTRNVLYQFE 158
VK N K V + L M L +LHG+ + +
Sbjct: 62 VQRVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPR 116
Query: 159 AQNPLRSRSRR 169
+ ++
Sbjct: 117 EGQEDQGLTKD 127
Score = 37.7 bits (87), Expect = 7e-04
Identities = 15/109 (13%), Positives = 33/109 (30%), Gaps = 9/109 (8%)
Query: 40 QPFPEHTGRSPARYRHHRYSHHHSQATSSSH---CNLYVGNLTWWTTEADMSDAIRSIGV 96
+ + HR+ S+ + L++ N+ +E D+ S G
Sbjct: 118 GQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG 177
Query: 97 PDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPM 145
+ F + + + +GS E + L +L +
Sbjct: 178 --VVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHL 220
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 37.1 bits (86), Expect = 7e-04
Identities = 15/94 (15%), Positives = 30/94 (31%), Gaps = 5/94 (5%)
Query: 41 PFPEHTGRSPARYRHHRYSHH-HSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDF 99
P H + R S S++ +++ L + TE D+ + +
Sbjct: 16 PRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNP--- 72
Query: 100 IDVKFFENASNGQSKGFCTVTLGSEESMSLVMER 133
+ V +G+ G V + E M +
Sbjct: 73 VRVHIEIGP-DGRVTGEADVEFATHEEAVAAMSK 105
>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 = 37.2 bits (86), Expect = 8e-04
Identities = 19/96 (19%), Positives = 30/96 (31%), Gaps = 10/96 (10%)
Query: 48 RSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFEN 107
+ + HH + H S C +YVGNL + ++ A G + V
Sbjct: 54 VTEGSHHHHHHMHRDSCPLD---CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVA---- 106
Query: 108 ASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRK 143
GF V + + L L G +
Sbjct: 107 ---RNPPGFAFVEFEDPRDAADAVRELDGRTLCGCR 139
>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 = 9e-04
Identities = 13/89 (14%), Positives = 28/89 (31%)
Query: 45 HTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKF 104
S + + + L W + D+ + + + D
Sbjct: 19 SHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVH 78
Query: 105 FENASNGQSKGFCTVTLGSEESMSLVMER 133
F G+ G V LGSE+ + + +++
Sbjct: 79 FIYTREGRQSGEAFVELGSEDDVKMALKK 107
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 35.9 bits (83), Expect = 0.001
Identities = 16/99 (16%), Positives = 32/99 (32%), Gaps = 11/99 (11%)
Query: 52 RYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNG 111
+ HH ++ T +S +++ L EAD+ +A++ G ++ V
Sbjct: 4 HHHHHMENYDDPHKTPASPV-VHIRGLIDGVVEADLVEALQEFGPISYVVV--------M 54
Query: 112 QSKGFCTVTLGSEESMSLVMERLPT--LELHGRKPMVAY 148
K V + + + G V Y
Sbjct: 55 PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNY 93
>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 = 36.4 bits (84), Expect = 0.001
Identities = 12/96 (12%), Positives = 31/96 (32%), Gaps = 9/96 (9%)
Query: 45 HTGRSPARYRH-------HRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVP 97
H+ R H + + A S++ + + L + T+ ++ + +
Sbjct: 10 HSSGLVPRGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIV 69
Query: 98 DFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMER 133
+ + G+ G V S+E + +
Sbjct: 70 P-NGITLPVDP-EGKITGEAFVQFASQELAEKALGK 103
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 36.1 bits (84), Expect = 0.001
Identities = 18/105 (17%), Positives = 32/105 (30%), Gaps = 14/105 (13%)
Query: 44 EHTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVK 103
H+ R H H Q S+ L+V E+++++ G + +
Sbjct: 9 HHSSGLVPRGSHMH----HRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL 64
Query: 104 FFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAY 148
GF V ES + +E + + V Y
Sbjct: 65 ----------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY 99
>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2,
alternate splicing factor)...; structure genomics, SURP
domain, splicing factor SF2; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 109
Score = 35.8 bits (83), Expect = 0.001
Identities = 15/79 (18%), Positives = 24/79 (30%), Gaps = 5/79 (6%)
Query: 65 ATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSE 124
++ C +YVGNL D+ D G ID+K + F V
Sbjct: 17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLK-----NRRGGPPFAFVEFEDP 71
Query: 125 ESMSLVMERLPTLELHGRK 143
+ + G +
Sbjct: 72 RDAEDAVYGRDGYDYDGYR 90
>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 = 35.9 bits (83), Expect = 0.001
Identities = 10/75 (13%), Positives = 28/75 (37%), Gaps = 3/75 (4%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCT 118
S +S T++ + + L + ++ ++ + + + G+S G
Sbjct: 5 SSGNSPDTANDGF-VRLRGLPFGCSKEEIVQFFSGLEIVP--NGMTLPVDFQGRSTGEAF 61
Query: 119 VTLGSEESMSLVMER 133
V S+E +++
Sbjct: 62 VQFASQEIAEKALKK 76
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 35.2 bits (82), Expect = 0.001
Identities = 18/71 (25%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
++VG L+W T++ D+ D G + +D + + G+S+GF + S+ V++
Sbjct: 14 MFVGGLSWDTSKKDLKDYFTKFG--EVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD 71
Query: 133 RLPTLELHGRK 143
+ L GR
Sbjct: 72 QKEH-RLDGRV 81
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 36.0 bits (83), Expect = 0.001
Identities = 9/82 (10%), Positives = 28/82 (34%), Gaps = 9/82 (10%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSI----GVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
+ + N+ + + + ++ G D +D+ + + G + ++ES
Sbjct: 30 QVVLITNINPEVPKEKLQALLYALASSQG--DILDIVVDL---SDDNSGKAYIVFATQES 84
Query: 127 MSLVMERLPTLELHGRKPMVAY 148
+E G ++ +
Sbjct: 85 AQAFVEAFQGYPFQGNPLVITF 106
>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 = 36.7 bits (84), Expect = 0.001
Identities = 13/105 (12%), Positives = 28/105 (26%), Gaps = 4/105 (3%)
Query: 42 FPEHTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFID 101
E + + ++Y+ T D+ + + G I
Sbjct: 81 ISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQ 140
Query: 102 VKFFENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMV 146
++ + KG V S ES +E + ++
Sbjct: 141 MRRTLH---KAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLI 181
>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 = 35.7 bits (83), Expect = 0.002
Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 3/82 (3%)
Query: 62 HSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTL 121
SS C +++G L+W TT+ + + G + + + +S+GF VT
Sbjct: 17 RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFG--EVKECLVMRDPLTKRSRGFGFVTF 74
Query: 122 GSEESMSLVMERLPTLELHGRK 143
+ + V+ + EL +
Sbjct: 75 MDQAGVDKVLAQSRH-ELDSKT 95
>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 = 34.9 bits (81), Expect = 0.002
Identities = 19/110 (17%), Positives = 32/110 (29%), Gaps = 20/110 (18%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
+ + L+V NL TE + A G VK K + +
Sbjct: 4 GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFG--KLERVKK--------LKDYAFIHFD 53
Query: 123 SEESMSLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRRSYR 172
+ ME + +L G + A+ P + R R +
Sbjct: 54 ERDGAVKAMEEMNGKDLEGENIEIV----------FAKPPDQKRKERKAQ 93
>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 = 34.5 bits (80), Expect = 0.002
Identities = 14/83 (16%), Positives = 23/83 (27%), Gaps = 11/83 (13%)
Query: 62 HSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIG-VPDFIDVKFFENASNGQSKGFCTVT 120
S ++VG T T ++ G V D K + F VT
Sbjct: 3 GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK--------PFRAFAFVT 54
Query: 121 LGSEESMSLVMERLPTLELHGRK 143
++ + L + G
Sbjct: 55 FADDKVAQSLCGE--DLIIKGIS 75
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 34.7 bits (80), Expect = 0.002
Identities = 10/69 (14%), Positives = 27/69 (39%), Gaps = 2/69 (2%)
Query: 74 YVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVMER 133
+ + + ++ G ++++F + + G++KGF V GS +++
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKV--VNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73
Query: 134 LPTLELHGR 142
L +
Sbjct: 74 FHGKRLDLK 82
>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 = 34.6 bits (80), Expect = 0.003
Identities = 13/81 (16%), Positives = 22/81 (27%), Gaps = 10/81 (12%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
+ LYV T + A G + ID+ + VT
Sbjct: 8 ERRAPRKGNTLYVYGED--MTPTLLRGAFSPFG--NIIDLSMD------PPRNCAFVTYE 57
Query: 123 SEESMSLVMERLPTLELHGRK 143
ES + L ++ +
Sbjct: 58 KMESADQAVAELNGTQVESVQ 78
>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 = 34.1 bits (79), Expect = 0.004
Identities = 16/78 (20%), Positives = 26/78 (33%), Gaps = 11/78 (14%)
Query: 67 SSSHCNLYVGNLTWWTTEADMSDAIRSIG-VPDFIDVKFFENASNGQSKGFCTVTLGSEE 125
SS ++VG T TE ++ + G V D K + F VT ++
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK--------PFRAFAFVTFADDQ 53
Query: 126 SMSLVMERLPTLELHGRK 143
+ L + G
Sbjct: 54 IAQSLCGE--DLIIKGIS 69
>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 = 34.1 bits (79), Expect = 0.004
Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 11/83 (13%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSI----GVPDFIDVKFFENASNGQSKGFCTVTLGSEES 126
+Y+ NL + ++ ++ +I G +D+ + + +G V S
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFG--QILDILVSR---SLKMRGQAFVIFKEVSS 63
Query: 127 MSLVMERLPTLELHGRKPM-VAY 148
+ + + + KPM + Y
Sbjct: 64 ATNALRSMQGFPFYD-KPMRIQY 85
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 33.8 bits (78), Expect = 0.006
Identities = 18/101 (17%), Positives = 28/101 (27%), Gaps = 16/101 (15%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
+YVGNL + ++ A G + + GF V +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIA-------RNPPGFAFVEFEDPRDAEDAV 54
Query: 132 ERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRRSYR 172
L + G + V + P RSR R
Sbjct: 55 RGLDGKVICGSRVRV---------ELSTGMPRRSRFDRPPA 86
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 33.3 bits (76), Expect = 0.008
Identities = 14/102 (13%), Positives = 33/102 (32%), Gaps = 17/102 (16%)
Query: 49 SPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENA 108
+ + HH S S +++ L TE ++ G N
Sbjct: 2 RGSHHHHHHGSGVPS-------RVIHIRKLPIDVTEGEVISLGLPFGKV--------TNL 46
Query: 109 SNGQSKGFCTVTLGSEESMSLVMERLPT--LELHGRKPMVAY 148
+ K + + +EE+ + ++ + L G+ + +
Sbjct: 47 LMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF 88
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 114
Score = 33.0 bits (75), Expect = 0.012
Identities = 12/63 (19%), Positives = 25/63 (39%)
Query: 71 CNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLV 130
++VG L E +++ + R G E+ S KG+ + E S+ +
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68
Query: 131 MER 133
++
Sbjct: 69 IDA 71
>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 = 33.0 bits (76), Expect = 0.013
Identities = 14/80 (17%), Positives = 24/80 (30%), Gaps = 4/80 (5%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
LYVGNL+ TE + IG K ++ F V
Sbjct: 8 MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIG--PCKSCKMITEHTSNDPYCF--VEFY 63
Query: 123 SEESMSLVMERLPTLELHGR 142
+ + + ++ G+
Sbjct: 64 EHRDAAAALAAMNGRKILGK 83
>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription
termination, RNA processi recognition, RRM; HET: CAF;
1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A
Length = 97
Score = 32.7 bits (75), Expect = 0.014
Identities = 17/93 (18%), Positives = 33/93 (35%), Gaps = 11/93 (11%)
Query: 55 HHRYSHHHSQATSSSHCNLYVGNLTWWT-TEADMSDAIRSIGVPDFIDVKFFENASNGQS 113
HH +S S L++GNL ++ D+ G I++K
Sbjct: 7 HHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK---------- 56
Query: 114 KGFCTVTLGSEESMSLVMERLPTLELHGRKPMV 146
F + + +S+ +E G+K ++
Sbjct: 57 NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL 89
>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics,
RRM domain, riken structural genomics/proteomics
initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 32.8 bits (75), Expect = 0.016
Identities = 14/93 (15%), Positives = 31/93 (33%), Gaps = 10/93 (10%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVM 131
++V L EAD+ +A+ G ++ + K V + +S +
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMM--------PFKRQALVEFENIDSAKECV 68
Query: 132 ERLPT--LELHGRKPMVAYPTRNVLYQFEAQNP 162
+ + G++ Y T + + P
Sbjct: 69 TFAADVPVYIAGQQAFFNYSTSKRITRPGNSGP 101
>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 85
Score = 32.2 bits (74), Expect = 0.016
Identities = 14/84 (16%), Positives = 30/84 (35%), Gaps = 9/84 (10%)
Query: 61 HHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVT 120
S + LYVG L TE D+ + G + + + + +
Sbjct: 3 SGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFG--EIRTITVVQR------QQCAFIQ 54
Query: 121 LGSEESMSLVMERLPT-LELHGRK 143
+ ++ + E+ L ++GR+
Sbjct: 55 FATRQAAEVAAEKSFNKLIVNGRR 78
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 32.6 bits (74), Expect = 0.019
Identities = 13/113 (11%), Positives = 33/113 (29%), Gaps = 11/113 (9%)
Query: 41 PFPEHTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFI 100
H S + A S +++ L TE ++ G +
Sbjct: 3 SSHHHHHHSSGLVPRGSHMGDSRSAGVPSR-VIHIRKLPIDVTEGEVISLGLPFGKVTNL 61
Query: 101 DVKFFENASNGQSKGFCTVTLGSEESMSLVMERLPT--LELHGRKPMVAYPTR 151
+ + K + + +EE+ + ++ + L G+ + +
Sbjct: 62 LM--------LKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNH 106
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 32.6 bits (74), Expect = 0.022
Identities = 11/85 (12%), Positives = 26/85 (30%), Gaps = 2/85 (2%)
Query: 51 ARYRHHRYSHHHSQATSSSHCN-LYVGNLTWWTTEADMSDAIRSIG-VPDFIDVKFFENA 108
+ S+ +Q S + + + L + T ++ + + F
Sbjct: 3 SGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY 62
Query: 109 SNGQSKGFCTVTLGSEESMSLVMER 133
+G+ G V EE + +
Sbjct: 63 PDGRPTGDAFVLFACEEYAQNALRK 87
>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 = 32.1 bits (73), Expect = 0.026
Identities = 10/83 (12%), Positives = 26/83 (31%), Gaps = 4/83 (4%)
Query: 73 LYVGNLTWWTTEADM---SDAIRSIGVPDFIDV-KFFENASNGQSKGFCTVTLGSEESMS 128
++V L+ + ++ + G + + A + VT E
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77
Query: 129 LVMERLPTLELHGRKPMVAYPTR 151
++ + + + GR + T
Sbjct: 78 RAIQCVNNVVVDGRTLKASLGTT 100
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 32.2 bits (73), Expect = 0.028
Identities = 14/111 (12%), Positives = 34/111 (30%), Gaps = 13/111 (11%)
Query: 45 HTGRSPARYRHHRYSHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKF 104
+G S A++ R+ + + ++ + G L + + + G +
Sbjct: 2 SSGSSGAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCG--LVDALLM 59
Query: 105 FENASNGQSKGFCTVTLGSEESMSLVMERLPTLELHGRKPMVAYPTRNVLY 155
N K + + E L+G++ + + LY
Sbjct: 60 PPN------KPYSFARYRTTEESKRAYV-----TLNGKEVVDDLGQKITLY 99
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 31.5 bits (72), Expect = 0.030
Identities = 12/73 (16%), Positives = 23/73 (31%), Gaps = 10/73 (13%)
Query: 72 NLYVGNLTWWTTEADMSDAIRSIG-VPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLV 130
+++V A +S+ + G V + K F V +G + V
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDK--------DKGVFAIVEMGDVGAREAV 61
Query: 131 MERLPTLELHGRK 143
+ L G +
Sbjct: 62 LS-QSQHSLGGHR 73
>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 = 33.3 bits (75), Expect = 0.031
Identities = 16/113 (14%), Positives = 38/113 (33%), Gaps = 2/113 (1%)
Query: 60 HHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTV 119
H+ A + L+V + + TTE+ + G I + + +G+ +G+ +
Sbjct: 92 HNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHM--VYSKRSGKPRGYAFI 149
Query: 120 TLGSEESMSLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRRSYR 172
E M + ++ GR+ +V + + +
Sbjct: 150 EYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRG 202
>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 = 31.7 bits (72), Expect = 0.032
Identities = 12/81 (14%), Positives = 24/81 (29%), Gaps = 10/81 (12%)
Query: 73 LYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSLVME 132
L++ L TE ++ G N + K + L +EE+ ++
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFG--------KVTNILMLKGKNQAFLELATEEAAITMVN 69
Query: 133 RLPT--LELHGRKPMVAYPTR 151
L + + Y
Sbjct: 70 YYSAVTPHLRNQPIYIQYSNH 90
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 29.3 bits (66), Expect = 0.21
Identities = 13/87 (14%), Positives = 28/87 (32%), Gaps = 14/87 (16%)
Query: 64 QATSSSHCNLYVGNLTWWTTE--ADMSDAIRSI----G--VPDFIDVKFFENASNGQSKG 115
Q + V N+ + + + I I G DF + +G++KG
Sbjct: 9 QEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE------DGKTKG 62
Query: 116 FCTVTLGSEESMSLVMERLPTLELHGR 142
+ + S ++ +L +
Sbjct: 63 YIFLEYASPAHAVDAVKNADGYKLDKQ 89
>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif,
RRM, RNA binding domain, RBD, RNP, structural genomics;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 111
Score = 29.4 bits (66), Expect = 0.28
Identities = 10/80 (12%), Positives = 20/80 (25%), Gaps = 8/80 (10%)
Query: 63 SQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLG 122
S ++ S + NL T A++ + G + + + V
Sbjct: 3 SGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP--------EGGITAIVEFL 54
Query: 123 SEESMSLVMERLPTLELHGR 142
L + H
Sbjct: 55 EPLEARKAFRHLAYSKFHHV 74
>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition
motif, RRM, RNA binding domain, RBD, RNP, structural
genomics; NMR {Mus musculus} SCOP: d.58.7.1
Length = 97
Score = 28.4 bits (64), Expect = 0.47
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 72 NLYVGNLTWWTTEAD 86
L+VG L T+ A
Sbjct: 19 RLWVGGLGPNTSLAA 33
>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 = 28.1 bits (63), Expect = 0.60
Identities = 18/109 (16%), Positives = 30/109 (27%), Gaps = 21/109 (19%)
Query: 63 SQATSSSHCNLYVGNLTW-WTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTL 121
S + +++GNL ++D+ G V KG+ V
Sbjct: 20 KNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH----------KGYAFVQY 69
Query: 122 GSEESMSLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRRS 170
+E + L G+ + A P RS S
Sbjct: 70 SNERHARAAVLGENGRVLAGQTLDINM----------AGEPKPDRSGPS 108
>2dkz_A Hypothetical protein LOC64762; cell-free protein synthesis, protein
regulation, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 84
Score = 27.2 bits (60), Expect = 0.91
Identities = 8/36 (22%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 77 NLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQ 112
+L+ + E ++S ++R IG+ + + F +G
Sbjct: 14 DLSGLSIE-EVSKSLRFIGLSEDVISFFVTEKIDGN 48
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 26.0 bits (58), Expect = 2.8
Identities = 14/83 (16%), Positives = 30/83 (36%), Gaps = 11/83 (13%)
Query: 71 CNLYVGNL-TWWTTEADMSDAIRSIGVPDFIDVKFFENASNGQSKGFCTVTLGSEESMSL 129
L++GNL ++ D+ G I++K F + + +S+
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK----------NAFGFIQFDNPQSVRD 60
Query: 130 VMERLPTLELHGRKPMVAYPTRN 152
+E G+K ++ + N
Sbjct: 61 AIECESQEMNFGKKLILEVSSSN 83
>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 = 27.1 bits (59), Expect = 3.8
Identities = 8/51 (15%), Positives = 18/51 (35%), Gaps = 1/51 (1%)
Query: 119 VTLGSEESMSLVMERLPTLELHGRKPMVAYPTRNVLYQFEAQNPLRSRSRR 169
+ L + S V+E L L + + + + +++ RR
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI-HSIQAELRR 236
>2h7w_A Chagasin; beta-strands, immunoglobulin-fold, hydrolase inhibitor;
1.70A {Trypanosoma cruzi} SCOP: b.1.26.1 PDB: 2nnr_A
2oul_B 3cbj_B 3cbk_B 3e1z_A 2fo8_A 2nqd_A*
Length = 131
Score = 25.8 bits (56), Expect = 5.5
Identities = 11/53 (20%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 59 SHHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVPDFIDVKFFENASNG 111
S HH SS + G+++ T+A + + V + ++++ N + G
Sbjct: 3 SSHHHHHHSSGENLYFQGHMSHKVTKAHNGATLT-VAVGELVEIQLPSNPTTG 54
>2w57_A Ferric uptake regulation protein; gene regulation, transcription
regulation, transport, iron, repressor, DNA-binding,
transcription; 2.60A {Vibrio cholerae}
Length = 150
Score = 25.3 bits (56), Expect = 8.0
Identities = 10/65 (15%), Positives = 17/65 (26%), Gaps = 25/65 (38%)
Query: 19 SPGEHVSTEHDDIDLYDDV--------------TLQPFPE-------HTGRSPARYRHHR 57
+H+S E +LY + L F + H + +
Sbjct: 29 PECQHISAE----ELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVFELST 84
Query: 58 YSHHH 62
HH
Sbjct: 85 QHHHD 89
>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM,
XRRM, RNA binding protein; 2.50A {Tetrahymena
thermophila} PDB: 4erd_A
Length = 129
Score = 25.4 bits (55), Expect = 8.1
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 60 HHHSQATSSSHCNLYVGNLTWWTTEADMSDAIRSIGVP---DFID 101
HHH + +C + + N+ T +A++ A+R +G D+ID
Sbjct: 2 HHHHHHSIKQNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYID 46
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 0.132 0.404
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: 2,732,327
Number of extensions: 150741
Number of successful extensions: 793
Number of sequences better than 10.0: 1
Number of HSP's gapped: 658
Number of HSP's successfully gapped: 203
Length of query: 172
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 85
Effective length of database: 4,272,666
Effective search space: 363176610
Effective search space used: 363176610
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)