RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13318
(100 letters)
>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 = 74.4 bits (183), Expect = 9e-19
Identities = 17/60 (28%), Positives = 30/60 (50%)
Query: 12 HNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
H +Q + NL+VNY+P T+ + +++ LF G +ES K++ D+ T
Sbjct: 22 LQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETR 81
>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 = 71.8 bits (177), Expect = 1e-17
Identities = 33/41 (80%), Positives = 37/41 (90%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
SKTNLIVNYLPQ MTQEE +SLF S+GE+ESCKL+RDK TG
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITG 41
Score = 48.3 bits (116), Expect = 1e-08
Identities = 19/47 (40%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 26 PSNEESK-TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
PS+ + NL V+ LP+TMTQ+E++ LFS G + + +++ D+ TG
Sbjct: 81 PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTG 127
>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 = 69.1 bits (170), Expect = 1e-16
Identities = 22/41 (53%), Positives = 31/41 (75%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S TNLIVNYLPQ MT E+ +LF ++G + +C+++RD TG
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTG 42
Score = 47.2 bits (113), Expect = 4e-08
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 26 PSNEESK-TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
P E K TNL V LP+T+T +++ ++F G + ++RDK TG
Sbjct: 82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTG 128
>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 = 65.7 bits (161), Expect = 4e-15
Identities = 9/40 (22%), Positives = 22/40 (55%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
+ V +P+T ++++++ LF G V ++RD++
Sbjct: 4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNP 43
Score = 48.0 bits (115), Expect = 2e-08
Identities = 11/48 (22%), Positives = 25/48 (52%)
Query: 22 ASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
A +N L + + + T+ +++ +FSS G++E C+++R
Sbjct: 85 ADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD 132
>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 = 62.3 bits (152), Expect = 3e-14
Identities = 14/59 (23%), Positives = 24/59 (40%)
Query: 13 NSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ A+ + NL + +LPQ +++ +F G V S K+ DK T
Sbjct: 6 SGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTN 64
>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 = 63.8 bits (156), Expect = 4e-14
Identities = 11/51 (21%), Positives = 20/51 (39%)
Query: 21 SASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ + +L V L +T+ + FS G + S ++ RD T
Sbjct: 4 GSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITR 54
Score = 40.3 bits (95), Expect = 2e-05
Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 20 NSASQTPSNEESK-TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
+ + PS +S N+ + L +++ + + FS+ G + SCK++ D
Sbjct: 90 MWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD 138
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA
recognition motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 61.2 bits (149), Expect = 6e-14
Identities = 16/69 (23%), Positives = 27/69 (39%)
Query: 3 AMPQQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESC 62
+ + + + +A+ NL + +LPQ T ++ S F G V S
Sbjct: 11 SALSTSPLASVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISA 70
Query: 63 KLIRDKTTG 71
K+ DK T
Sbjct: 71 KVFIDKQTS 79
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 54.4 bits (131), Expect = 2e-11
Identities = 12/57 (21%), Positives = 24/57 (42%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELSVV 76
+ +S + + L + +P + E + SL G VESC+ + + + V
Sbjct: 3 SGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNV 59
>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 = 57.0 bits (138), Expect = 2e-11
Identities = 13/48 (27%), Positives = 19/48 (39%)
Query: 21 SASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
+ L V LP +T+E+ K LF GE + RD+
Sbjct: 11 FLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR 58
Score = 42.0 bits (99), Expect = 5e-06
Identities = 10/37 (27%), Positives = 16/37 (43%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
L V L ++ E ++ FS G VE ++ D
Sbjct: 97 AALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR 133
>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-11
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 30 ESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ L V LP ++TQ++ + L G +E C L+ + TG
Sbjct: 93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTG 134
Score = 50.7 bits (122), Expect = 4e-09
Identities = 10/49 (20%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 23 SQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
T ++ +++ LP +T +E+ L S ++ C + + K T
Sbjct: 13 EHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTA 60
Score = 42.7 bits (101), Expect = 3e-06
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 16 VNSHNSASQTPSNEESKTNLIVNYLPQTMTQEE-MKSLFSSVGEVESCKLIRDKT 69
V+ ++ TP+ S+ L V+ LP + + S+V C+L +
Sbjct: 169 VHWTDAGQLTPALLHSR-CLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQD 222
>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 = 53.3 bits (129), Expect = 4e-11
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ L + L T +++ L G++ S K I DKTT
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTN 44
>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 = 53.5 bits (129), Expect = 6e-11
Identities = 14/53 (26%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT-TG 71
+ +S +++ + ++V +P Q E++ LFS+ GE+++ +L + T TG
Sbjct: 3 SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTG 55
>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 = 52.6 bits (127), Expect = 2e-10
Identities = 15/53 (28%), Positives = 30/53 (56%)
Query: 17 NSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
S A E+ TNL ++ LP +M ++E++++ G+V S +++RD +
Sbjct: 10 ASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS 62
>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 = 51.9 bits (125), Expect = 2e-10
Identities = 17/46 (36%), Positives = 29/46 (63%)
Query: 26 PSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
P+ + S ++ V +P T+E++K +FS VG V S +L+ D+ TG
Sbjct: 2 PAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETG 47
>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 = 51.5 bits (124), Expect = 3e-10
Identities = 12/53 (22%), Positives = 24/53 (45%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
+ +S + + V L + + +++ LF G + L +DKTTG+
Sbjct: 3 SGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQ 55
>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 = 51.2 bits (123), Expect = 4e-10
Identities = 10/52 (19%), Positives = 27/52 (51%)
Query: 21 SASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
S+ + + L + +P+ + ++++K LF G++ +++D+ TG
Sbjct: 2 SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGM 53
>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 = 50.3 bits (121), Expect = 8e-10
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 21 SASQTPSNEESK-TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S S ++ + L V L + +T+ + LFS +G +SCK+I + T+
Sbjct: 3 SGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN 54
>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 = 51.4 bits (124), Expect = 9e-10
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
L V L + +T++ +K F G + + K++ DK
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN 37
Score = 40.2 bits (95), Expect = 1e-05
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 20 NSASQTPSNEESKT-NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
N A Q+ + T NL V L + E +++ F S ++ D TG
Sbjct: 74 NWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTG 126
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 50.4 bits (121), Expect = 1e-09
Identities = 14/55 (25%), Positives = 25/55 (45%)
Query: 17 NSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+S +S + + T + V LP T ++ F G++E +I D+ TG
Sbjct: 2 SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTG 56
>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 = 50.0 bits (120), Expect = 1e-09
Identities = 11/49 (22%), Positives = 22/49 (44%)
Query: 21 SASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
+S + S L V L + ++E++ LF G ++ C ++R
Sbjct: 4 GSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD 52
>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 = 49.9 bits (120), Expect = 1e-09
Identities = 15/55 (27%), Positives = 30/55 (54%)
Query: 18 SHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
S S+ + SK+ + V+ LP ++T ++ +FS G+V +++DK T +
Sbjct: 2 SSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRK 56
>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 = 48.4 bits (116), Expect = 3e-09
Identities = 10/47 (21%), Positives = 27/47 (57%)
Query: 22 ASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
+S + +++ T L V L T+T+ ++++ F GE+ + +++ +
Sbjct: 2 SSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ 48
>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 = 48.4 bits (116), Expect = 4e-09
Identities = 12/53 (22%), Positives = 23/53 (43%)
Query: 18 SHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTT 70
S S+ P+ EE+ + V L + +E + LF G + + +D+
Sbjct: 2 SSGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG 54
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 48.4 bits (116), Expect = 5e-09
Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 1/62 (1%)
Query: 7 QNGSLHNSSVNSHNSASQTPSNEE-SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLI 65
+ H+S + S E S T L V P + + E+ +F G ++ K++
Sbjct: 5 HHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL 64
Query: 66 RD 67
Sbjct: 65 NG 66
>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 = 48.1 bits (115), Expect = 7e-09
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 27 SNEESKTNLIVNYLPQTMTQEEMKSLFSSVGE-VESCKLIRDKTTG 71
+ +L + L M + + F+++GE V S K+IR++ TG
Sbjct: 4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTG 49
>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 = 47.3 bits (113), Expect = 2e-08
Identities = 7/51 (13%), Positives = 20/51 (39%)
Query: 21 SASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+S PS+ + + L +E + + G+++ +++ T
Sbjct: 4 GSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTE 54
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 46.9 bits (112), Expect = 2e-08
Identities = 12/50 (24%), Positives = 26/50 (52%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
+S S K L ++ LP + T+EE++ + + G V+ +L+ ++
Sbjct: 5 SSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA 54
>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 = 46.5 bits (111), Expect = 2e-08
Identities = 14/46 (30%), Positives = 22/46 (47%)
Query: 22 ASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
S S L V L T+T+E ++ FS G++E K ++D
Sbjct: 1 GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD 46
>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 = 48.4 bits (116), Expect = 3e-08
Identities = 8/51 (15%), Positives = 20/51 (39%)
Query: 18 SHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
+ A++ + T ++V LP++ Q ++ F G + +
Sbjct: 27 TSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSL 77
Score = 40.0 bits (94), Expect = 3e-05
Identities = 6/41 (14%), Positives = 14/41 (34%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
++ L + P + TQ ++ L + V +
Sbjct: 116 TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFN 156
Score = 40.0 bits (94), Expect = 3e-05
Identities = 7/52 (13%), Positives = 18/52 (34%), Gaps = 1/52 (1%)
Query: 24 QTPSNEESKTNLIVNYLPQTMTQEE-MKSLFSSVGEVESCKLIRDKTTGELS 74
+T S +++ L + E ++ F G +E + + +
Sbjct: 202 RTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFN 253
>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 = 46.5 bits (111), Expect = 3e-08
Identities = 9/52 (17%), Positives = 20/52 (38%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
E + L + +++ FS+VG+V ++I D+ +
Sbjct: 13 EPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSR 64
>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 = 3e-08
Identities = 9/52 (17%), Positives = 21/52 (40%)
Query: 21 SASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
S+ + + + L V+ L + + ++ +F G V + R+ T
Sbjct: 2 SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKA 53
>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 = 47.7 bits (114), Expect = 3e-08
Identities = 15/51 (29%), Positives = 23/51 (45%)
Query: 21 SASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S S++P E L + L T E ++S F G + C ++RD T
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTK 52
Score = 43.1 bits (102), Expect = 2e-06
Identities = 9/49 (18%), Positives = 23/49 (46%)
Query: 23 SQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
SQ P + + V + + + ++ F G++E +++ D+ +G
Sbjct: 95 SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSG 143
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 46.1 bits (110), Expect = 4e-08
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 2/61 (3%)
Query: 13 NSSVNSHNSASQTPSNEESK--TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTT 70
+S P + S L V + + T+E++ F+ GE+++ L D+ T
Sbjct: 2 REDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRT 61
Query: 71 G 71
G
Sbjct: 62 G 62
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 47.7 bits (114), Expect = 4e-08
Identities = 10/63 (15%), Positives = 24/63 (38%)
Query: 9 GSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
S+ SA+Q + + V + + ++ ++ F+ G ++S + D
Sbjct: 5 ASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDS 64
Query: 69 TTG 71
T
Sbjct: 65 VTM 67
Score = 44.2 bits (105), Expect = 7e-07
Identities = 14/60 (23%), Positives = 30/60 (50%)
Query: 12 HNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
++ + Q + + V + Q ++ +++KS+F + G+++S L RD TTG
Sbjct: 105 PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTG 164
>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 = 45.7 bits (109), Expect = 5e-08
Identities = 14/49 (28%), Positives = 24/49 (48%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
+ +S ++ L V LP +T+EEM+ LF G+ + +DK
Sbjct: 3 SGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK 51
>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 = 45.2 bits (108), Expect = 6e-08
Identities = 11/43 (25%), Positives = 20/43 (46%)
Query: 29 EESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
E ++ V + T EE+++ F G V ++ DK +G
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSG 45
>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 = 6e-08
Identities = 13/70 (18%), Positives = 30/70 (42%)
Query: 3 AMPQQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESC 62
Q + + + + + +S L + LP + +++K L +S G +++
Sbjct: 85 PHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF 144
Query: 63 KLIRDKTTGE 72
L++D TG
Sbjct: 145 NLVKDSATGL 154
Score = 30.0 bits (68), Expect = 0.081
Identities = 5/29 (17%), Positives = 11/29 (37%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
+P +T+E M F++ +
Sbjct: 12 IPFGITEEAMMDFFNAQMRLGGLTQAPGN 40
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 45.4 bits (108), Expect = 7e-08
Identities = 9/53 (16%), Positives = 26/53 (49%)
Query: 17 NSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
+ +S + E+ L+V+ L ++ +++ LF+ G ++ + D++
Sbjct: 14 DLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS 66
>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 = 46.0 bits (109), Expect = 9e-08
Identities = 14/72 (19%), Positives = 29/72 (40%)
Query: 1 MDAMPQQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVE 60
+D + + +V + + E T+L V+ L + + ++ +F G V
Sbjct: 39 VDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVG 98
Query: 61 SCKLIRDKTTGE 72
+ RD+ T E
Sbjct: 99 DVYIPRDRYTKE 110
>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 = 45.4 bits (108), Expect = 1e-07
Identities = 9/53 (16%), Positives = 25/53 (47%)
Query: 17 NSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
+ +S E+ L+V+ L ++ +++ LF+ G ++ + D++
Sbjct: 20 DLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS 72
>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 = 44.9 bits (107), Expect = 1e-07
Identities = 9/40 (22%), Positives = 21/40 (52%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTT 70
N+ + L +++ + + FS+ G + SCK++ D+
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG 43
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 46.0 bits (109), Expect = 1e-07
Identities = 9/53 (16%), Positives = 25/53 (47%)
Query: 17 NSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
+ +S E+ L+V+ L ++ +++ LF+ G ++ + D++
Sbjct: 73 DLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS 125
>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 = 46.0 bits (109), Expect = 1e-07
Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 1/72 (1%)
Query: 1 MDAMPQQNGSLHNSSVNSHNSASQ-TPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEV 59
D+ ++ + N + + P L V + + ++E++ F GE+
Sbjct: 40 SDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEI 99
Query: 60 ESCKLIRDKTTG 71
++ L D+ TG
Sbjct: 100 KNIHLNLDRRTG 111
>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 = 45.7 bits (109), Expect = 2e-07
Identities = 9/50 (18%), Positives = 18/50 (36%), Gaps = 2/50 (4%)
Query: 22 ASQT-PSNEES-KTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
S +E + NL + L + E+K S + ++ +T
Sbjct: 1 GSHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT 50
Score = 34.1 bits (79), Expect = 0.003
Identities = 9/67 (13%), Positives = 22/67 (32%), Gaps = 6/67 (8%)
Query: 6 QQNGS-LHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKL 64
+ G + + + + + L+ L +T++E+K +F E+
Sbjct: 72 ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL--- 128
Query: 65 IRDKTTG 71
G
Sbjct: 129 --VSQDG 133
>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 = 44.1 bits (105), Expect = 2e-07
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+P T+E++ L S+VG V + K++ D TG
Sbjct: 10 IPYDQTEEQILDLCSNVGPVINLKMMFDPQTG 41
>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 = 44.2 bits (105), Expect = 2e-07
Identities = 11/52 (21%), Positives = 23/52 (44%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ +S S + V L + +++ + LF G V + + +D+ TG
Sbjct: 3 SGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTG 54
>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 = 45.3 bits (108), Expect = 2e-07
Identities = 11/50 (22%), Positives = 22/50 (44%)
Query: 23 SQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
L + LP + +++K L +S G +++ L++D TG
Sbjct: 85 PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGL 134
Score = 29.1 bits (66), Expect = 0.15
Identities = 8/37 (21%), Positives = 14/37 (37%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
S L V +P +T+E M F++ +
Sbjct: 3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPG 39
>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 = 44.3 bits (105), Expect = 3e-07
Identities = 9/61 (14%), Positives = 23/61 (37%)
Query: 12 HNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ + +N + L V L T+ +++ +FS G + ++ D+ +
Sbjct: 26 GGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSR 85
Query: 72 E 72
Sbjct: 86 R 86
>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 = 43.7 bits (104), Expect = 3e-07
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 34 NLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
N+ V L + T E++K LFS G+V + KLI D+ T
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETK 40
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 43.8 bits (104), Expect = 3e-07
Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 3/46 (6%)
Query: 23 SQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
P T + +P T+ ++ LF + G + K +K
Sbjct: 21 RSAPPR---VTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK 63
>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 = 43.8 bits (104), Expect = 3e-07
Identities = 11/55 (20%), Positives = 22/55 (40%)
Query: 17 NSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ P L V + + ++E++ F GE+++ L D+ TG
Sbjct: 11 EDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTG 65
>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 = 4e-07
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 1/60 (1%)
Query: 13 NSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
SV + E L V + + T+E++ F+ GE+++ L D+ TG
Sbjct: 4 YDSVEQDGDEPGPQRSVEG-WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 62
>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 = 43.9 bits (104), Expect = 4e-07
Identities = 12/58 (20%), Positives = 25/58 (43%)
Query: 14 SSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ S E K ++ V + T +++++ FSS G + ++ DK +G
Sbjct: 18 YTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSG 75
>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 = 43.0 bits (102), Expect = 4e-07
Identities = 10/53 (18%), Positives = 24/53 (45%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
+ +S +N + L V L T+ +++ +FS G + ++ D+ +
Sbjct: 3 SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRR 55
>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 = 43.4 bits (103), Expect = 5e-07
Identities = 16/52 (30%), Positives = 29/52 (55%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ +S + ++LIV LP T++++K FS+ GEV ++ +D TG
Sbjct: 3 SGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTG 54
>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 = 43.1 bits (102), Expect = 5e-07
Identities = 13/51 (25%), Positives = 23/51 (45%)
Query: 21 SASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
A+ L V L +T++ ++ +F G +ES +L+ D TG
Sbjct: 15 MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETG 65
>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 = 43.0 bits (102), Expect = 5e-07
Identities = 9/50 (18%), Positives = 21/50 (42%)
Query: 22 ASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+S + +K L V L + + + + + F G++ ++ D T
Sbjct: 2 SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETE 51
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 43.2 bits (102), Expect = 6e-07
Identities = 7/41 (17%), Positives = 16/41 (39%)
Query: 32 KTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
+ L + + +K + GEVE +++ T +
Sbjct: 6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRK 46
>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 = 43.1 bits (102), Expect = 7e-07
Identities = 10/50 (20%), Positives = 21/50 (42%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
+ +S + + V L + +++K +FS G V ++ DK
Sbjct: 3 SGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD 52
>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 = 42.6 bits (101), Expect = 7e-07
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ L + L + T+E +K +FS VG ++SC + + K
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKA 44
>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 = 42.5 bits (101), Expect = 7e-07
Identities = 9/45 (20%), Positives = 19/45 (42%)
Query: 27 SNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S +K L V L + + + + + F G++ ++ D T
Sbjct: 2 SMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETE 46
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 43.2 bits (102), Expect = 8e-07
Identities = 11/66 (16%), Positives = 23/66 (34%), Gaps = 1/66 (1%)
Query: 6 QQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLI 65
N + + S S S + L V L + + + + + F G++ ++
Sbjct: 38 CVNCTERHVDGGSGGSGGSGGSATTKRV-LYVGGLAEEVDDKVLHAAFIPFGDITDIQIP 96
Query: 66 RDKTTG 71
D T
Sbjct: 97 LDYETE 102
>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 = 42.6 bits (101), Expect = 8e-07
Identities = 9/50 (18%), Positives = 23/50 (46%)
Query: 22 ASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+S + + L V L ++ ++ +FS G++ +++D+ T
Sbjct: 2 SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQ 51
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 43.2 bits (102), Expect = 8e-07
Identities = 14/60 (23%), Positives = 25/60 (41%)
Query: 13 NSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
S + P + E T+L V+ L + + ++ +F G V + RD+ T E
Sbjct: 28 QQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE 87
>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 = 42.2 bits (100), Expect = 1e-06
Identities = 11/49 (22%), Positives = 20/49 (40%)
Query: 19 HNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
+ +S NL V L + E ++ FS G + S K++ +
Sbjct: 2 SSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME 50
>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 = 42.3 bits (100), Expect = 1e-06
Identities = 11/52 (21%), Positives = 27/52 (51%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ +S + + ++ V L +T E++K+ F+ G + ++++D TG
Sbjct: 3 SGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATG 54
>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 = 1e-06
Identities = 12/44 (27%), Positives = 22/44 (50%)
Query: 26 PSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
P + + V + M + E++S F+ G V+ K+I D+T
Sbjct: 3 PEGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT 46
>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 = 41.8 bits (99), Expect = 1e-06
Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 25 TPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ S+ + L V L T ++E+++ LFS+ G + D T
Sbjct: 3 SGSSGSGR--LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTK 47
>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA
complex, RRM, RBD, RNA binding protein- complex; NMR
{Mus musculus}
Length = 109
Score = 41.9 bits (99), Expect = 2e-06
Identities = 17/63 (26%), Positives = 27/63 (42%)
Query: 9 GSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
GS H+ +S + S + + L TQE ++ F GEV+ C ++RD
Sbjct: 2 GSSHHHHHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDP 61
Query: 69 TTG 71
T
Sbjct: 62 LTK 64
>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding,
RNA processing, mRNA processing, nonsense-mediated mRNA
decay, cleavage; NMR {Saccharomyces cerevisiae} PDB:
2km8_C
Length = 167
Score = 42.9 bits (102), Expect = 2e-06
Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 29 EESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ES + + L T++ ++ F G V K+++D TG
Sbjct: 1 KESCK-MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATG 42
Score = 42.5 bits (101), Expect = 2e-06
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 25 TPSNEESKTNLI-VNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
P +E+ KT I V + + +E + FS G + +L+ DK TG
Sbjct: 79 IPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTG 126
>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 = 41.6 bits (98), Expect = 2e-06
Identities = 12/61 (19%), Positives = 25/61 (40%), Gaps = 8/61 (13%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVES--------CKLIRDKTTG 71
+ +S P + + + V L ++T +++ F G V+ + DK TG
Sbjct: 3 SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 62
Query: 72 E 72
+
Sbjct: 63 K 63
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 41.3 bits (97), Expect = 3e-06
Identities = 7/42 (16%), Positives = 18/42 (42%)
Query: 28 NEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
N+ ++ + P T +++K G+V + ++ R
Sbjct: 7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH 48
>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 = 41.0 bits (97), Expect = 3e-06
Identities = 10/39 (25%), Positives = 23/39 (58%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ L V L +T++ ++ +F G++++ L++D TG
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTG 44
>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 = 41.1 bits (97), Expect = 3e-06
Identities = 20/54 (37%), Positives = 28/54 (51%)
Query: 18 SHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S S+ S + L V L + TQE ++S FS GEV C +++DKTT
Sbjct: 2 SSGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTN 55
>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 = 3e-06
Identities = 9/48 (18%), Positives = 17/48 (35%)
Query: 24 QTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ S+ + V +P + E++ F G V +I D
Sbjct: 2 SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQ 49
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 40.5 bits (96), Expect = 3e-06
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
L T E++K F G+V+ L+ DKTT
Sbjct: 7 LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTN 38
>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 = 41.3 bits (97), Expect = 3e-06
Identities = 12/46 (26%), Positives = 18/46 (39%)
Query: 26 PSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S+ SKT ++ LP E++ FS G + L T
Sbjct: 4 GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITA 49
>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 = 41.2 bits (97), Expect = 3e-06
Identities = 11/41 (26%), Positives = 17/41 (41%)
Query: 30 ESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTT 70
E L + LP +T EEM +F G + ++ T
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET 46
>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 = 41.2 bits (97), Expect = 3e-06
Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 13 NSSVNSHNSASQTPSNEES--KTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
SS N+ + N+ S + + +T + M+ FS G++ ++ +K
Sbjct: 4 GSSGNTKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK 61
>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 = 41.1 bits (97), Expect = 3e-06
Identities = 7/51 (13%), Positives = 24/51 (47%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTT 70
+ +S ++ + L V+ +P +++ +F G++ ++I ++
Sbjct: 3 SGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG 53
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 40.6 bits (96), Expect = 4e-06
Identities = 9/41 (21%), Positives = 15/41 (36%)
Query: 27 SNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
S + V LP T + +K F+ G V + +
Sbjct: 3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME 43
>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 = 40.8 bits (96), Expect = 4e-06
Identities = 13/60 (21%), Positives = 23/60 (38%), Gaps = 9/60 (15%)
Query: 22 ASQTPSNEESKTNLI-VNYLPQTMTQEEMKSLFSSVGEVES--------CKLIRDKTTGE 72
+ S N I V L + +T E + F +G +++ L D+ TG+
Sbjct: 2 GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61
>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 = 39.8 bits (94), Expect = 5e-06
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
L +E+++ F GEVES +L D T
Sbjct: 7 LSPDTPEEKIREYFGGFGEVESIELPMDNKTN 38
>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 = 40.2 bits (95), Expect = 5e-06
Identities = 14/46 (30%), Positives = 22/46 (47%)
Query: 26 PSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
NEE + V L +++++K F+ GEV C + D TG
Sbjct: 5 SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTG 50
>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 = 40.7 bits (96), Expect = 5e-06
Identities = 14/63 (22%), Positives = 25/63 (39%), Gaps = 5/63 (7%)
Query: 14 SSVNSHNSASQTP-----SNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
SS +S + P + E L + L +T+ ++ SLF+ E + +
Sbjct: 2 SSGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM 61
Query: 69 TTG 71
TG
Sbjct: 62 MTG 64
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 40.0 bits (94), Expect = 6e-06
Identities = 9/48 (18%), Positives = 20/48 (41%), Gaps = 3/48 (6%)
Query: 27 SNEESKTNLIVNYLPQTMTQEEMKSLFSSVG--EVESCKLIRDKTTGE 72
+ T +I+ + + + + S V + +LI+DK T +
Sbjct: 5 HHHHMDT-IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQ 51
>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 = 40.9 bits (96), Expect = 8e-06
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
++ Q ++S T L V L T+E++ LFS G+++ + DK
Sbjct: 28 DNEEQEKLLKKSCT-LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKT 79
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 40.0 bits (94), Expect = 9e-06
Identities = 10/57 (17%), Positives = 25/57 (43%)
Query: 12 HNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
H+SS + N+ L V+ +P +++ +F G++ ++I ++
Sbjct: 9 HHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE 65
>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 = 1e-05
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
L TQE ++ F GEV+ C ++RD T
Sbjct: 8 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTK 39
>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 = 39.5 bits (93), Expect = 1e-05
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 22 ASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
S S + S T L V + T T +E+++ F G V C +++D
Sbjct: 1 GSSGSSGKAS-TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD 45
>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 = 38.3 bits (90), Expect = 2e-05
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 27 SNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIR 66
S L + LP+ T++E++SLF G+V C +I+
Sbjct: 3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIK 42
>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 = 38.8 bits (91), Expect = 3e-05
Identities = 9/40 (22%), Positives = 20/40 (50%)
Query: 30 ESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
+ L + L + ++ +K++F G + LI+D+T
Sbjct: 5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT 44
>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 = 38.8 bits (91), Expect = 3e-05
Identities = 12/65 (18%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 13 NSSVNSHNSASQTPSNEESKTN------LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIR 66
+S + +T E K L + L T+E +++ + G++ C ++R
Sbjct: 2 SSGSSGMEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMR 61
Query: 67 DKTTG 71
D +
Sbjct: 62 DPASK 66
>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 = 37.9 bits (89), Expect = 3e-05
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
NL V L + E +++ F S ++ D TG
Sbjct: 2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTG 40
>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 = 38.0 bits (89), Expect = 4e-05
Identities = 7/50 (14%), Positives = 21/50 (42%)
Query: 19 HNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
+ +S S L V L + ++E ++ F+++ ++ + +
Sbjct: 2 SSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR 51
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 38.1 bits (89), Expect = 4e-05
Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 8/49 (16%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVES--------CKLIRDKTTGEL 73
+ V L + +T E + F +G +++ L D+ TG+L
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 56
>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 = 37.6 bits (88), Expect = 6e-05
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 22 ASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
S S K + V + T +E++SLF G V C +++D
Sbjct: 1 GSSGSSGNTWK--IFVGNVSAACTSQELRSLFERRGRVIECDVVKD 44
>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 = 37.5 bits (87), Expect = 8e-05
Identities = 11/48 (22%), Positives = 25/48 (52%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
+ +S P + S+ ++V+ LP + + +++K G+V + RD
Sbjct: 3 SGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD 50
>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 = 36.8 bits (86), Expect = 1e-04
Identities = 8/44 (18%), Positives = 23/44 (52%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELS 74
T + + L + +T++ + +FS+ G+++ + ++ LS
Sbjct: 3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLS 46
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 36.9 bits (86), Expect = 1e-04
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 18 SHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S S+ + E T + N LP Q ++ ++F + + S +L+RDK T
Sbjct: 2 SSGSSGKELPTEPPYTAYVGN-LPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTD 53
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 37.1 bits (86), Expect = 1e-04
Identities = 11/56 (19%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 16 VNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ + S S+ + + LP +T+ E+ SL G+V + +++ K
Sbjct: 1 MRGSHHHHHHGSGVPSRV-IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQA 55
>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 = 36.4 bits (85), Expect = 1e-04
Identities = 9/41 (21%), Positives = 20/41 (48%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S ++ V L +T + + F+ G + ++++D TG
Sbjct: 5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATG 45
>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 = 37.4 bits (86), Expect = 2e-04
Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 30 ESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELSVVANSIFAP----EL 85
+S ++ M + + ++F G VE K ++ K + +A+ L
Sbjct: 3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHL 62
Query: 86 NG 87
N
Sbjct: 63 NN 64
Score = 33.9 bits (77), Expect = 0.003
Identities = 8/60 (13%), Positives = 18/60 (30%), Gaps = 1/60 (1%)
Query: 12 HNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
N+ ++ A++ S N P +T+E + +G +
Sbjct: 104 RNNRFSTPEQAAKNRIQHPSNVLHFFN-APLEVTEENFFEICDELGVKRPTSVKVFSGKS 162
>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 = 36.1 bits (84), Expect = 2e-04
Identities = 12/55 (21%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 18 SHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
S S+ T + LP +T+E +K F + + + +L R+ + E
Sbjct: 2 SSGSSGSRLPKSPPYT-AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPE 54
>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 = 2e-04
Identities = 6/60 (10%), Positives = 17/60 (28%), Gaps = 5/60 (8%)
Query: 12 HNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
H+ N + S + + L + + ++ G + ++ K
Sbjct: 6 HHHMENYDDPHKTPASP-----VVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQA 60
>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 = 36.0 bits (83), Expect = 3e-04
Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 6 QQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLI 65
+G + S + ++ PS + + LP +T+ E+ SL G+V + ++
Sbjct: 10 HSSGLVPRGSHMGDSRSAGVPSR-----VIHIRKLPIDVTEGEVISLGLPFGKVTNLLML 64
Query: 66 RDKTTG 71
+ K
Sbjct: 65 KGKNQA 70
>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 = 36.0 bits (83), Expect = 4e-04
Identities = 10/42 (23%), Positives = 22/42 (52%)
Query: 26 PSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRD 67
P + S+ ++V+ LP + + +++K G+V + RD
Sbjct: 10 PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD 51
>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 = 4e-04
Identities = 10/61 (16%), Positives = 24/61 (39%), Gaps = 2/61 (3%)
Query: 9 GSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
GS +S ++ N + + + V LP + ++++ +F G + L +
Sbjct: 1 GSSGSSGMSGGGVIRGPAGNNDCR--IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR 58
Query: 69 T 69
Sbjct: 59 G 59
>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 = 35.6 bits (82), Expect = 4e-04
Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 18 SHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S S+ S+ L + LP +T+ E+ +L G+V + +++ K
Sbjct: 2 SSGSSGDKMDGAPSRV-LHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQA 54
>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 = 35.3 bits (82), Expect = 5e-04
Identities = 6/39 (15%), Positives = 13/39 (33%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
T L V L + + F G + + ++ +
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFA 56
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 35.1 bits (81), Expect = 5e-04
Identities = 9/36 (25%), Positives = 19/36 (52%)
Query: 36 IVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
++ + ++ + SLFS G+V + + D+ TG
Sbjct: 16 VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATG 51
>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 = 35.2 bits (81), Expect = 6e-04
Identities = 7/54 (12%), Positives = 18/54 (33%), Gaps = 1/54 (1%)
Query: 18 SHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S S+ S + V L +++ + ++ G + ++ K
Sbjct: 2 SSGSSGSHHKVSVSPV-VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQA 54
>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 = 36.2 bits (83), Expect = 6e-04
Identities = 10/72 (13%), Positives = 22/72 (30%), Gaps = 3/72 (4%)
Query: 2 DAMPQQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVG--EV 59
D M ++ + + L + L T E++ S+G ++
Sbjct: 39 DYMDTLPPTVGDDVGKGAAPNVVYTYTGKR-IALYIGNLTWWTTDEDLTEAVHSLGVNDI 97
Query: 60 ESCKLIRDKTTG 71
K ++ G
Sbjct: 98 LEIKFFENRANG 109
>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 = 36.0 bits (82), Expect = 6e-04
Identities = 8/69 (11%), Positives = 24/69 (34%)
Query: 1 MDAMPQQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVE 60
+ + + + S + N+ ++ + P T +++K G+V
Sbjct: 78 LMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVL 137
Query: 61 SCKLIRDKT 69
+ ++ R
Sbjct: 138 NIQMRRTLH 146
>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 = 34.9 bits (81), Expect = 7e-04
Identities = 10/55 (18%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 18 SHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
H+ ++ + + LP +T+E +K F + + +L R+ + E
Sbjct: 5 HHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRG-LNISAVRLPREPSNPE 58
>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 = 34.5 bits (80), Expect = 7e-04
Identities = 8/42 (19%), Positives = 17/42 (40%), Gaps = 2/42 (4%)
Query: 32 KTNLIVNYLPQTMTQEEMKSLFSSVG--EVESCKLIRDKTTG 71
+ L + L T E++ S+G ++ K ++ G
Sbjct: 1 RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANG 42
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 34.6 bits (80), Expect = 8e-04
Identities = 7/31 (22%), Positives = 14/31 (45%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRDKTT 70
P+ + ++ F + G V S + +DK
Sbjct: 16 FPRGVDSAQLSEYFLAFGPVASVVMDKDKGV 46
>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 = 34.6 bits (80), Expect = 8e-04
Identities = 12/54 (22%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 18 SHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S S+ + + ESKT L+++ L + T+E ++ +F ++ + G
Sbjct: 2 SSGSSGNSTWSGESKT-LVLSNLSYSATEETLQEVFEKATFIK----VPQNQNG 50
>2bz2_A Negative elongation factor E; NELF E, RNA recognition motif,
alternative splicing, nuclear protein, phosphorylation,
repeat, repressor; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2jx2_A
Length = 121
Score = 34.7 bits (80), Expect = 0.001
Identities = 7/59 (11%), Positives = 15/59 (25%), Gaps = 2/59 (3%)
Query: 10 SLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
+ + + L V MT ++ FS G + + +
Sbjct: 17 RGSHMGPFRRSDSFPERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR 73
>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 = 35.6 bits (81), Expect = 0.001
Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 11/70 (15%)
Query: 10 SLHNSSVNSHNSASQTPSNEESKTNL---IVNYLP---QTMTQEEMKSLFSSV----GEV 59
+LH S V+ +N S++ L +++ + + E +LF V +
Sbjct: 444 ALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFL 503
Query: 60 ESCKLIRDKT 69
E K+ D T
Sbjct: 504 EQ-KIRHDST 512
Score = 35.6 bits (81), Expect = 0.001
Identities = 13/70 (18%), Positives = 30/70 (42%), Gaps = 2/70 (2%)
Query: 28 NEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELSVVANSIFAPELNG 87
+ + T++ +++ T+T +E+KSL + L R+ T + SI A +
Sbjct: 282 SAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRL--SIIAESIRD 339
Query: 88 LHSQTERSRK 97
+ + +
Sbjct: 340 GLATWDNWKH 349
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 35.0 bits (80), Expect = 0.001
Identities = 12/66 (18%), Positives = 25/66 (37%)
Query: 7 QNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIR 66
Q+G+L ++ + A + + +IV L +T + + +FS G V
Sbjct: 3 QSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT 62
Query: 67 DKTTGE 72
+
Sbjct: 63 KNNQFQ 68
>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 = 34.2 bits (79), Expect = 0.001
Identities = 12/55 (21%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 13 NSSVNSHNSASQTPSNEESKTNLIVNYLP-QTMTQEEMKSLFSSVGEVESCKLIR 66
+S + H+S+ P K+ L + LP + +++E++ +FS G + +
Sbjct: 3 SSHHHHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 57
>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A
Length = 229
Score = 35.4 bits (81), Expect = 0.001
Identities = 13/64 (20%), Positives = 27/64 (42%), Gaps = 1/64 (1%)
Query: 5 PQQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKL 64
+G + S A + + L+ N P+ +T + + LF G+V+ K+
Sbjct: 9 HHSSGLVPRGSHMGRI-AIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKI 67
Query: 65 IRDK 68
+ +K
Sbjct: 68 LFNK 71
Score = 29.6 bits (66), Expect = 0.11
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 1/66 (1%)
Query: 6 QQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLI 65
+ G+ S + S T L ++ +P ++++E++K LFSS G V
Sbjct: 126 KDYGNSPLHRFKKPGSKNFQNIFPPSAT-LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF 184
Query: 66 RDKTTG 71
K
Sbjct: 185 FQKDRK 190
>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 = 33.8 bits (78), Expect = 0.002
Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 3/52 (5%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ +S + + L V L + T+E +K F +++ D+ TG
Sbjct: 3 SGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETG 51
>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 = 33.7 bits (78), Expect = 0.002
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
MT++E++ FS G+V + +
Sbjct: 13 CTGDMTEDELREFFSQYGDVMDVFIPKPF 41
>3n9u_C Cleavage and polyadenylation specificity factor S;
protein-protein complex, coexpression, heterotetramer,
mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 34.5 bits (79), Expect = 0.002
Identities = 8/69 (11%), Positives = 21/69 (30%), Gaps = 2/69 (2%)
Query: 5 PQQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVG--EVESC 62
P + + + + + V T +++ + S+G +V
Sbjct: 28 PVRQEPSPKPNNKTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVEL 87
Query: 63 KLIRDKTTG 71
K ++ G
Sbjct: 88 KFAENRANG 96
>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 = 34.4 bits (78), Expect = 0.003
Identities = 7/38 (18%), Positives = 18/38 (47%)
Query: 35 LIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGE 72
L V + T+ +++ F G ++ ++ K +G+
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGK 142
>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 = 33.0 bits (76), Expect = 0.003
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
+ MT EE++ F GEV + +
Sbjct: 19 CTEDMTAEELQQFFCQYGEVVDVFIPKPF 47
>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 = 33.2 bits (76), Expect = 0.003
Identities = 7/40 (17%), Positives = 14/40 (35%), Gaps = 1/40 (2%)
Query: 30 ESKTNLIVNYLPQTMTQEEMKSLFSSVGE-VESCKLIRDK 68
L + +P+ +EE+ + V E V +
Sbjct: 6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASA 45
>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP,
RNA, spicing, translation; NMR {Homo sapiens} SCOP:
d.58.7.1 d.58.7.1
Length = 198
Score = 34.1 bits (78), Expect = 0.003
Identities = 11/37 (29%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 33 TNLIV-NYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
+ L+V N P+ +T + + LF G+V+ K++ +K
Sbjct: 4 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK 40
Score = 28.3 bits (63), Expect = 0.29
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 1/55 (1%)
Query: 17 NSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S + S T L ++ +P ++++E++K LFSS G V K
Sbjct: 106 KKPGSKNFQNIFPPSAT-LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK 159
>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 = 32.6 bits (75), Expect = 0.005
Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 1/46 (2%)
Query: 26 PSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S + NL + L + E+K S + + D TG
Sbjct: 11 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLA-VVDVRTG 55
>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 = 33.7 bits (76), Expect = 0.005
Identities = 8/48 (16%), Positives = 19/48 (39%), Gaps = 4/48 (8%)
Query: 26 PSNEESKTNLIVNYLPQTMTQEEMKS----LFSSVGEVESCKLIRDKT 69
+ +N L + + ++E+K +FS G++ + R
Sbjct: 3 VPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK 50
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 33.0 bits (75), Expect = 0.006
Identities = 9/69 (13%), Positives = 25/69 (36%), Gaps = 4/69 (5%)
Query: 4 MPQQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMK----SLFSSVGEV 59
M + + TP + E +++ + + +E+++ +L SS G++
Sbjct: 1 MKETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDI 60
Query: 60 ESCKLIRDK 68
+
Sbjct: 61 LDIVVDLSD 69
>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 = 32.0 bits (73), Expect = 0.007
Identities = 10/41 (24%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 31 SKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ ++V LPQ +E+ L ++ C + R+K T
Sbjct: 4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVDRNKRTA 43
>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 = 31.6 bits (72), Expect = 0.009
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 13/61 (21%)
Query: 40 LPQTMTQEEMKSLFSSV-----------GEVESCKLIRDKTTG--ELSVVANSIFAPELN 86
+P +T+E M F++ V + ++ +DK E V + A +
Sbjct: 14 IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFD 73
Query: 87 G 87
G
Sbjct: 74 G 74
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 31.9 bits (72), Expect = 0.010
Identities = 5/32 (15%), Positives = 14/32 (43%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
LP + ++E+ + F G + + ++
Sbjct: 16 LPPDIDEDEITASFRRFGPLVVDWPHKAESKS 47
>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 = 31.5 bits (72), Expect = 0.012
Identities = 6/43 (13%), Positives = 16/43 (37%)
Query: 26 PSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
S L + L +T ++++ LF + +++
Sbjct: 2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS 44
>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 = 31.5 bits (72), Expect = 0.012
Identities = 8/52 (15%), Positives = 15/52 (28%), Gaps = 2/52 (3%)
Query: 20 NSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
+ +S L V MT ++ FS G + + +
Sbjct: 3 SGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCA 52
>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 = 32.2 bits (73), Expect = 0.012
Identities = 8/65 (12%), Positives = 20/65 (30%)
Query: 3 AMPQQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESC 62
+ + + H+ + + V L + E++ F G + S
Sbjct: 44 TYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSV 103
Query: 63 KLIRD 67
+ R+
Sbjct: 104 WVARN 108
>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 = 31.0 bits (71), Expect = 0.015
Identities = 8/47 (17%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 26 PSNEESKTNLIVNYLPQTMTQEEMK----SLFSSVGEVESCKLIRDK 68
+ +N L + + ++E+K ++FS G++ + R
Sbjct: 2 VPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL 48
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 31.1 bits (71), Expect = 0.016
Identities = 6/28 (21%), Positives = 13/28 (46%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRD 67
L + E++ FS G + + + R+
Sbjct: 8 LGTGAGKGELERAFSYYGPLRTVWIARN 35
>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 = 31.1 bits (71), Expect = 0.017
Identities = 9/51 (17%), Positives = 17/51 (33%), Gaps = 5/51 (9%)
Query: 21 SASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
T + L+ L +T++E+K +F E+ G
Sbjct: 5 EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDG 50
>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 114
Score = 31.4 bits (71), Expect = 0.019
Identities = 4/30 (13%), Positives = 14/30 (46%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
L +++ ++ + G V++ + +K
Sbjct: 35 LGNGVSRNQLLPVLEKCGLVDALLMPPNKP 64
>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 = 29.9 bits (68), Expect = 0.052
Identities = 9/40 (22%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 34 NLIVNYLPQTMTQEEMKSLFSSVGEVESC-KLIRDKTTGE 72
+ + L + ++ + FS+ G + K++RD TG
Sbjct: 7 GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGN 46
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 30.4 bits (68), Expect = 0.057
Identities = 9/61 (14%), Positives = 21/61 (34%), Gaps = 20/61 (32%)
Query: 44 MTQEEMKSLFSSVGEVES-------CK-----LIRDKTTGEL------SVVANSIF--AP 83
MT+E + G + CK ++ + G++ V+++ +
Sbjct: 2 MTRESIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRS 61
Query: 84 E 84
E
Sbjct: 62 E 62
>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 = 29.7 bits (67), Expect = 0.073
Identities = 13/61 (21%), Positives = 27/61 (44%), Gaps = 8/61 (13%)
Query: 14 SSVNSHNSASQTPSNEESKTN-------LIVNYLP-QTMTQEEMKSLFSSVGEVESCKLI 65
SS +S S SN +K + + + L + + +++++FS G V C +
Sbjct: 2 SSGSSGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH 61
Query: 66 R 66
+
Sbjct: 62 K 62
>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 = 29.1 bits (65), Expect = 0.10
Identities = 8/45 (17%), Positives = 16/45 (35%), Gaps = 4/45 (8%)
Query: 32 KTNLI-VNYLPQTMTQEEM---KSLFSSVGEVESCKLIRDKTTGE 72
+ NL+ V L Q + E+ F G++ + +
Sbjct: 14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAG 58
>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif,
RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1
PDB: 2adb_A
Length = 164
Score = 29.3 bits (65), Expect = 0.12
Identities = 12/67 (17%), Positives = 25/67 (37%)
Query: 6 QQNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLI 65
Q+G+L ++ + A + + +IV L +T + + +FS G V
Sbjct: 20 VQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITF 79
Query: 66 RDKTTGE 72
+
Sbjct: 80 TKNNQFQ 86
>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 = 28.9 bits (65), Expect = 0.12
Identities = 11/54 (20%), Positives = 21/54 (38%), Gaps = 1/54 (1%)
Query: 18 SHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S S+ +P + + LP ++EE+ FS + V + + G
Sbjct: 2 SSGSSGNSPDTANDGF-VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQG 54
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 29.8 bits (66), Expect = 0.13
Identities = 6/37 (16%), Positives = 17/37 (45%)
Query: 32 KTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
L +L + ++ +FS +G+++ + + K
Sbjct: 143 DGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESK 179
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.1 bits (64), Expect = 0.15
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 19/48 (39%)
Query: 46 QEEMKSLFSSVGEVESCKLIRDKTTGELSVVANSIFAPELNGLHSQTE 93
++ +K L +S+ KL D + AP L + + E
Sbjct: 19 KQALKKLQASL------KLYADDS------------APAL-AIKATME 47
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 28.6 bits (64), Expect = 0.17
Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 17 NSHNSASQTPSNEESK--TNLIVNYLPQTMTQEEMKSLFSSVGEV 59
+S +S +P E + ++ V LP+ ++K +G V
Sbjct: 2 SSGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV 46
>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 = 28.6 bits (64), Expect = 0.17
Identities = 10/53 (18%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 17 NSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKT 69
+S +S P N + + V+ +P + + +++ F + V++ L++D
Sbjct: 2 SSGSSGKPLPINPDDLY-VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV 52
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 28.5 bits (63), Expect = 0.33
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 19/55 (34%)
Query: 16 VNSHNSASQ------TPSNEESKTNLIVNY----------LPQTMTQEEMKS-LF 53
VN +N +Q ++ TN++ N+ L ++++ EE++ LF
Sbjct: 1844 VN-YNVENQQYVAAGDLRALDTVTNVL-NFIKLQKIDIIELQKSLSLEEVEGHLF 1896
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 28.1 bits (62), Expect = 0.34
Identities = 9/64 (14%), Positives = 24/64 (37%), Gaps = 2/64 (3%)
Query: 7 QNGSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIR 66
+GS + + + PS L + +T + + ++ + VG+V+ + +
Sbjct: 2 SSGS--SGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK 59
Query: 67 DKTT 70
Sbjct: 60 RNGI 63
>3rfa_A Ribosomal RNA large subunit methyltransferase N; radical SAM,
S-adenosylmethionine, iron sulfur cluster,
oxidoreductase; HET: SAM; 2.05A {Escherichia coli} PDB:
3rf9_A*
Length = 404
Score = 27.2 bits (61), Expect = 0.90
Identities = 7/37 (18%), Positives = 18/37 (48%), Gaps = 6/37 (16%)
Query: 22 ASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGE 58
+ + ++ K NL+ + +++M+ F +GE
Sbjct: 7 TPENVTTKDGKINLL------DLNRQQMREFFKDLGE 37
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 26.4 bits (59), Expect = 0.92
Identities = 9/42 (21%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 26 PSNEESKTNLIVNYLP-QTMTQEEMKSLFSSVGEVESCKLIR 66
N K+ L + LP + +++E++ +FS G + +
Sbjct: 4 MHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN 45
>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 = 26.7 bits (59), Expect = 0.94
Identities = 9/46 (19%), Positives = 15/46 (32%)
Query: 26 PSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTG 71
S E+ + + LP + + F + VE I G
Sbjct: 19 RSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNG 64
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 26.8 bits (59), Expect = 1.0
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 9 GSLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVE 60
GS +S + N +Q S E + + LP T T EE+ + F +
Sbjct: 1 GSSGSSGGGTSNEVAQFLSKENQVI-VRMRGLPFTATAEEVVAFFGQHCPIT 51
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 112
Score = 26.1 bits (57), Expect = 1.3
Identities = 7/56 (12%), Positives = 16/56 (28%)
Query: 13 NSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
E + + N + + L G++++ L+R K
Sbjct: 7 GKKPEGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK 62
>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator,
structural genomics, PSI-2, protei structure
initiative; NMR {Homo sapiens}
Length = 97
Score = 25.9 bits (57), Expect = 1.4
Identities = 4/38 (10%), Positives = 15/38 (39%), Gaps = 2/38 (5%)
Query: 23 SQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVE 60
+ +++ LP +T+E+++ + +
Sbjct: 2 GHHHHHHSHM--VVIRRLPPGLTKEQLEEQLRPLPAHD 37
>3rdw_A Putative arsenate reductase; structural genomics, center for
structural genomics of infec diseases, csgid,
oxidoreductase; 2.20A {Yersinia pestis}
Length = 121
Score = 26.1 bits (58), Expect = 1.7
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 36 IVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDK 68
+V YL + +++K L +G ++ +L+R K
Sbjct: 34 VVLYLETPPSVDKLKELLQQLGFSDARQLMRTK 66
>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein,
N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP:
d.58.7.4
Length = 91
Score = 25.1 bits (55), Expect = 2.4
Identities = 6/28 (21%), Positives = 17/28 (60%)
Query: 33 TNLIVNYLPQTMTQEEMKSLFSSVGEVE 60
+ +++ LP T+T+E+++ + E +
Sbjct: 2 SKVVIRRLPPTLTKEQLQEHLQPMPEHD 29
>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C, DNA
polymerase III; HET: DGT; 2.39A {Geobacillus
kaustophilus} PDB: 3f2c_A* 3f2d_A*
Length = 1041
Score = 25.7 bits (57), Expect = 2.7
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 22 ASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGE 58
SQ +N ++ L Y T EM FS +G
Sbjct: 346 HSQGGANPLNRHELPDVYF---RTTNEMLDCFSFLGP 379
>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 = 25.2 bits (55), Expect = 2.9
Identities = 10/54 (18%), Positives = 19/54 (35%), Gaps = 8/54 (14%)
Query: 27 SNEESKTNLIV--NYLPQTMTQEEMKSLFSS---VGEVESCKLIRD---KTTGE 72
EE ++ LP + T E++ + FS + + K G+
Sbjct: 4 LEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGD 57
>3etf_A Putative succinate-semialdehyde dehydrogenase; center for ST
genomics of infectious diseases, oxidoreductase, csgid;
1.85A {Salmonella typhimurium} PDB: 3efv_A
Length = 462
Score = 25.2 bits (56), Expect = 4.0
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESC 62
+ Q +T+E K + + EV
Sbjct: 71 MAQCITREMGKPIKQARAEVTKS 93
>3ros_A NAD-dependent aldehyde dehydrogenase; nysgrc, PSI-biology,
structural genomics, NEW YORK structura genomics
research consortium; 1.88A {Lactobacillus acidophilus}
Length = 484
Score = 25.2 bits (56), Expect = 4.1
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 40 LPQTMTQEEMKSLFSSVGEVESC 62
L + MT E K L S EVE C
Sbjct: 68 LAKMMTLEMGKLLSESKEEVELC 90
>1f2t_B RAD50 ABC-ATPase; DNA double-strand break repair, replication;
1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB:
1f2u_B* 1us8_B*
Length = 148
Score = 24.7 bits (54), Expect = 4.8
Identities = 5/44 (11%), Positives = 14/44 (31%), Gaps = 2/44 (4%)
Query: 32 KTNLIVNYLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGELSV 75
K L E +F+ E + +++ ++ +
Sbjct: 3 KALAREAALS--KIGELASEIFAEFTEGKYSEVVVRAEENKVRL 44
>1ng6_A Hypothetical protein YQEY; structural genomics, domain GATB/YQEY,
PFAM02637, DUF186, PSI, protein structure initiative;
1.40A {Bacillus subtilis} SCOP: a.182.1.1
Length = 148
Score = 24.9 bits (55), Expect = 5.1
Identities = 5/25 (20%), Positives = 18/25 (72%)
Query: 28 NEESKTNLIVNYLPQTMTQEEMKSL 52
+ + +++ YLP+ +++EE++++
Sbjct: 79 KVQKELDILEVYLPEQLSEEELRTI 103
>3k7b_A Protein A33; C-type lectin-like domain, homodimer, poxvirus, EEV,
EV, VIR protein; 2.10A {Vaccinia virus WR}
Length = 96
Score = 24.4 bits (52), Expect = 5.3
Identities = 5/52 (9%), Positives = 20/52 (38%), Gaps = 1/52 (1%)
Query: 10 SLHNSSVNSHNSASQTPSNEESKTNLIVNYLPQTMTQEEMKSLFSSVGEVES 61
+++ N +S P+ + +++Y+ T + + + + +
Sbjct: 29 MFSDAAANCTAESSTLPNKSDVMITWLIDYVEDTWG-SDGNPITKTTSDYQD 79
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 24.3 bits (53), Expect = 5.6
Identities = 8/51 (15%), Positives = 20/51 (39%), Gaps = 7/51 (13%)
Query: 24 QTPSNEESKTNLI-VNYLPQT------MTQEEMKSLFSSVGEVESCKLIRD 67
P + ++I V+ +PQ + + +FS G++ + +
Sbjct: 6 DRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE 56
>2a3v_A Site-specific recombinase INTI4; protein-DNA complex,
recombination; HET: DNA; 2.80A {Vibrio cholerae o1
biovar eltor str}
Length = 320
Score = 24.5 bits (54), Expect = 7.2
Identities = 7/35 (20%), Positives = 15/35 (42%), Gaps = 7/35 (20%)
Query: 39 YLPQTMTQEEMKSLFSSVGEVESCKLIRDKTTGEL 73
LP +T++E++ L V + + +L
Sbjct: 101 KLPVVLTRDEIRRLLEIVD-------PKHQLPIKL 128
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
0.305 0.118 0.311
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: 1,166,360
Number of extensions: 50565
Number of successful extensions: 270
Number of sequences better than 10.0: 1
Number of HSP's gapped: 261
Number of HSP's successfully gapped: 194
Length of query: 100
Length of database: 6,701,793
Length adjustment: 66
Effective length of query: 34
Effective length of database: 4,859,007
Effective search space: 165206238
Effective search space used: 165206238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 51 (23.4 bits)