RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4383
(89 letters)
>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 = 53.9 bits (130), Expect = 3e-11
Identities = 24/40 (60%), Positives = 31/40 (77%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+ G S+HKGYAF+Q+SN AR+A LGE+GR + GQTL
Sbjct: 53 GRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLAGQTL 92
Score = 49.7 bits (119), Expect = 1e-09
Identities = 23/40 (57%), Positives = 30/40 (75%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+HKGYAF+Q+SN AR+A LGE+GR + GQTL I+M
Sbjct: 60 VHKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE 99
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 51.8 bits (125), Expect = 2e-10
Identities = 13/40 (32%), Positives = 18/40 (45%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G + I++ + FIQF NP R A E G+ L
Sbjct: 36 GHIMQINIKNAFGFIQFDNPQSVRDAIECESQEMNFGKKL 75
Score = 48.0 bits (115), Expect = 5e-09
Identities = 11/40 (27%), Positives = 16/40 (40%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+ + FIQF NP R A E G+ L + +
Sbjct: 43 IKNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSS 82
>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 = 51.2 bits (123), Expect = 3e-10
Identities = 13/40 (32%), Positives = 18/40 (45%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G + I++ + FIQF NP R A E G+ L
Sbjct: 48 GHIMQINIKNAFGFIQFDNPQSVRDAIEXESQEMNFGKKL 87
Score = 47.3 bits (113), Expect = 7e-09
Identities = 11/40 (27%), Positives = 16/40 (40%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+ + FIQF NP R A E G+ L + +
Sbjct: 55 IKNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSS 94
>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 = 47.2 bits (113), Expect = 3e-08
Identities = 19/118 (16%), Positives = 36/118 (30%), Gaps = 51/118 (43%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL--------------------GIS----- 36
K +AF++F + + + + DG GQ+L G+
Sbjct: 50 DKNFAFLEFRSVDET-TQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLND 108
Query: 37 -------------------------MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+ KGYAF ++ + + A G +G + + L
Sbjct: 109 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 166
Score = 38.4 bits (90), Expect = 5e-05
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
I+ K +AF++F + + + + DG GQ+L
Sbjct: 47 INQDKNFAFLEFRSVDET-TQAMAFDGIIFQGQSL 80
>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 = 46.9 bits (112), Expect = 6e-08
Identities = 17/112 (15%), Positives = 34/112 (30%), Gaps = 44/112 (39%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS------------------------- 36
+ +A I+F+ A +A + + + V + +S
Sbjct: 80 NFRFARIEFARYDGALAA-ITKTHKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLL 138
Query: 37 ------------------MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
+ +A+I ++ DAR +G + G TLV
Sbjct: 139 QDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLV 190
Score = 36.5 bits (85), Expect = 3e-04
Identities = 9/33 (27%), Positives = 16/33 (48%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+ +A+I ++ DAR +G + G TL
Sbjct: 157 TSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTL 189
Score = 34.2 bits (79), Expect = 0.002
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
+ AF+ F N A A L + + + + VS
Sbjct: 253 NNCCAFMVFENKDSAERA-LQMNRSLLGNREISVSL 287
Score = 33.8 bits (78), Expect = 0.003
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
+ AF+ F N A A L + + + + +S+
Sbjct: 253 NNCCAFMVFENKDSAERA-LQMNRSLLGNREISVSL 287
>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 = 46.5 bits (111), Expect = 1e-07
Identities = 17/112 (15%), Positives = 29/112 (25%), Gaps = 44/112 (39%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM------------------------ 37
+KG AF+ N A +A + + L + +
Sbjct: 56 YKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEEL 115
Query: 38 --------------------HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY F ++ A A G+ + +TL
Sbjct: 116 VRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL 167
Score = 37.3 bits (87), Expect = 2e-04
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
KG+A +++ A A DG ++ G L +S
Sbjct: 225 LKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVS 259
Score = 36.9 bits (86), Expect = 2e-04
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
KG+A +++ A A DG ++ G L VS+
Sbjct: 225 LKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF 260
Score = 36.9 bits (86), Expect = 2e-04
Identities = 9/45 (20%), Positives = 16/45 (35%), Gaps = 1/45 (2%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYKLQYYN 78
+ +KG AF+ N A +A + + L V +
Sbjct: 53 VDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDAL 97
Score = 33.8 bits (78), Expect = 0.003
Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 9/54 (16%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSA 55
KGY F ++ A A G+ + +TL ++ +++ A
Sbjct: 136 SKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL---------YVHWTDAGQLTPA 180
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 42.3 bits (100), Expect = 9e-07
Identities = 10/38 (26%), Positives = 16/38 (42%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
G+AF++F A A G++ Q L + K
Sbjct: 65 NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKL 102
Score = 41.9 bits (99), Expect = 1e-06
Identities = 10/41 (24%), Positives = 17/41 (41%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G + + G+AF++F A A G++ Q L
Sbjct: 56 GPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFANQPLE 96
>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 = 41.4 bits (98), Expect = 1e-06
Identities = 8/41 (19%), Positives = 14/41 (34%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G+ L + K Y F+ + A A + G +
Sbjct: 33 GKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNIN 73
Score = 38.7 bits (91), Expect = 1e-05
Identities = 7/40 (17%), Positives = 13/40 (32%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+ K Y F+ + A A + G + + K
Sbjct: 40 IIKNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKN 79
>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 = 43.0 bits (102), Expect = 1e-06
Identities = 16/115 (13%), Positives = 32/115 (27%), Gaps = 48/115 (41%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMH----------------------- 38
++ + ++ F + D A L G V G + +
Sbjct: 53 NRKFGYVDFESAEDLEKA-LELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNI 111
Query: 39 ------------------------KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG A+I+F + DA + G + G+++
Sbjct: 112 TEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 166
Score = 34.9 bits (81), Expect = 9e-04
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL--GISMHKG 40
KG A+I+F + DA + G + G+++ + KG
Sbjct: 136 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG 175
>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 = 42.6 bits (100), Expect = 1e-06
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
G+AF++F +P DA A DGRT+ G + + + G
Sbjct: 109 PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG 147
Score = 41.8 bits (98), Expect = 3e-06
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+AF++F +P DA A DGRT+ G +
Sbjct: 109 PPGFAFVEFEDPRDAADAVRELDGRTLCGCRV 140
>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 = 40.8 bits (96), Expect = 3e-06
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 11/54 (20%)
Query: 17 RSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
R +G T +G A++ + + DA++A G V + LV
Sbjct: 36 RQIRVGNTPET-----------RGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLV 78
Score = 37.7 bits (88), Expect = 5e-05
Identities = 8/38 (21%), Positives = 18/38 (47%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+G A++ + + DA++A G V + L + +
Sbjct: 47 RGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNA 84
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin
modification, transcription regulation, structural
genomics, structural genomics consortium; 1.30A {Homo
sapiens}
Length = 110
Score = 40.5 bits (95), Expect = 4e-06
Identities = 7/36 (19%), Positives = 15/36 (41%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
H G A + F++ A+ +V+G + +
Sbjct: 47 HLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL 82
Score = 39.7 bits (93), Expect = 9e-06
Identities = 7/32 (21%), Positives = 14/32 (43%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
H G A + F++ A+ +V+G +
Sbjct: 47 HLGLARVLFTSTRGAKETVKNLHLTSVMGNII 78
>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 = 41.4 bits (98), Expect = 5e-06
Identities = 18/119 (15%), Positives = 34/119 (28%), Gaps = 54/119 (45%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL---------------------------- 33
GYAF+ F++ D++ A +G TV + L
Sbjct: 44 SYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITD 103
Query: 34 ------------------------GISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQT 68
G +G AF++++ +A+ A + G +
Sbjct: 104 DQLDTIFGKYGSIVQKNILRDKLTGRP--RGVAFVRYNKREEAQEAISALNNVIPEGGS 160
Score = 38.3 bits (90), Expect = 6e-05
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
GYAF+ F++ D++ A +G TV + L VSY
Sbjct: 44 SYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSY 79
>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 = 39.9 bits (94), Expect = 5e-06
Identities = 11/41 (26%), Positives = 21/41 (51%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G+ + + K YAF+ DA++A +G+ V G+ +
Sbjct: 34 GRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEVKGKRIN 74
Score = 38.0 bits (89), Expect = 3e-05
Identities = 10/40 (25%), Positives = 20/40 (50%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+ K YAF+ DA++A +G+ V G+ + + +
Sbjct: 41 VVKDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTK 80
>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 = 40.0 bits (94), Expect = 6e-06
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+ + YAF+ FSN DA A +G+ + G +
Sbjct: 47 VKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPI 81
Score = 39.6 bits (93), Expect = 7e-06
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
+ YAF+ FSN DA A +G+ + G + ++
Sbjct: 49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT 84
>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 = 8e-06
Identities = 11/40 (27%), Positives = 16/40 (40%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G + + K YAF+ DA A G D G+ +
Sbjct: 35 GPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEFQGKRM 74
Score = 38.4 bits (90), Expect = 2e-05
Identities = 10/40 (25%), Positives = 16/40 (40%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+ K YAF+ DA A G D G+ + + +
Sbjct: 42 IVKDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTS 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 = 40.2 bits (95), Expect = 1e-05
Identities = 21/120 (17%), Positives = 34/120 (28%), Gaps = 54/120 (45%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL--------------------------- 33
GY F+ + +P DA A +G + +T+
Sbjct: 42 QSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMT 101
Query: 34 -------------------------GISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQT 68
G+S +G FI+F +A A G +G+ G T
Sbjct: 102 QKELEQLFSQYGRIITSRILVDQVTGVS--RGVGFIRFDKRIEAEEAIKGLNGQKPSGAT 159
Score = 36.4 bits (85), Expect = 2e-04
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 37 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
GY F+ + +P DA A +G + +T+ VSY
Sbjct: 42 QSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSY 78
>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 = 40.4 bits (95), Expect = 1e-05
Identities = 17/109 (15%), Positives = 26/109 (23%), Gaps = 43/109 (39%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS-------------------------- 36
+G+ FI+ + A A DG + + L I
Sbjct: 58 RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAF 117
Query: 37 -----------------MHKGYAFIQFSNPHDARSACLGEDGRTVLGQT 68
G F++F+ AR A L T
Sbjct: 118 SQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTT 166
Score = 35.4 bits (82), Expect = 9e-04
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+ FI+ + A A DG + + L
Sbjct: 58 RGFGFIRLESRTLAEIAKAELDGTILKSRPL 88
Score = 29.3 bits (66), Expect = 0.11
Identities = 8/31 (25%), Positives = 11/31 (35%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQT 32
G F++F+ AR A L T
Sbjct: 136 ATGKGFVEFAAKPPARKALERCGDGAFLLTT 166
>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 = 39.2 bits (92), Expect = 1e-05
Identities = 12/38 (31%), Positives = 18/38 (47%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+AF++F +P DA A G DG G L + +
Sbjct: 61 PPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS 98
Score = 39.2 bits (92), Expect = 1e-05
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+AF++F +P DA A G DG G L
Sbjct: 61 PPFAFVEFEDPRDAEDAVYGRDGYDYDGYRL 91
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding
protein; NMR {Homo sapiens}
Length = 101
Score = 38.8 bits (91), Expect = 1e-05
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
G+AF++F +P DA A G DG+ + G +
Sbjct: 37 PGFAFVEFEDPRDAEDAVRGLDGKVICGSRV 67
Score = 38.8 bits (91), Expect = 1e-05
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+AF++F +P DA A G DG+ + G +
Sbjct: 37 PGFAFVEFEDPRDAEDAVRGLDGKVICGSRV 67
>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 = 39.6 bits (93), Expect = 2e-05
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KGYAF ++ + + A G +G + + L+
Sbjct: 155 SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLL 187
Score = 39.6 bits (93), Expect = 2e-05
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGYAF ++ + + A G +G + + L
Sbjct: 155 SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 186
Score = 38.5 bits (90), Expect = 6e-05
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
I+ K +AF++F + + + + DG GQ+L
Sbjct: 47 INQDKNFAFLEFRSVDET-TQAMAFDGIIFQGQSL 80
Score = 37.7 bits (88), Expect = 1e-04
Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGY 41
K +AF++F + + + + DG GQ+L I Y
Sbjct: 50 DKNFAFLEFRSVDET-TQAMAFDGIIFQGQSLKIRRPHDY 88
>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 = 39.4 bits (92), Expect = 2e-05
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGYA +++ A +A +G ++GQT+
Sbjct: 113 SKGYALVEYETHKQALAAKEALNGAEIMGQTI 144
Score = 39.4 bits (92), Expect = 2e-05
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGYA +++ A +A +G ++GQT+
Sbjct: 113 SKGYALVEYETHKQALAAKEALNGAEIMGQTI 144
>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 = 38.0 bits (89), Expect = 3e-05
Identities = 9/38 (23%), Positives = 14/38 (36%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+G AF+ F A +A G + + I K
Sbjct: 50 MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 87
Score = 37.6 bits (88), Expect = 4e-05
Identities = 8/36 (22%), Positives = 14/36 (38%), Gaps = 1/36 (2%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
+G AF+ F A +A G + + + Y
Sbjct: 50 MRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 85
>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 = 37.7 bits (88), Expect = 4e-05
Identities = 8/40 (20%), Positives = 14/40 (35%), Gaps = 1/40 (2%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYK 73
+ + AF+ + A A +G V L V+
Sbjct: 45 MDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA 84
Score = 37.3 bits (87), Expect = 6e-05
Identities = 7/32 (21%), Positives = 11/32 (34%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+ AF+ + A A +G V L
Sbjct: 48 PRNCAFVTYEKMESADQAVAELNGTQVESVQL 79
>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 = 37.7 bits (88), Expect = 4e-05
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+ KGY+F++FS A A + +G T+ G +
Sbjct: 57 VFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91
Score = 37.7 bits (88), Expect = 5e-05
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
KGY+F++FS A A + +G T+ G +
Sbjct: 59 PEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY 94
>4a8x_A RNA-binding protein with serine-rich domain 1; transcription,
splicing, RNA processing, nonsense mediated D NMD,
HDAC, histone deacetylation; 1.90A {Homo sapiens}
Length = 88
Score = 37.1 bits (87), Expect = 5e-05
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KGYA+++F NP +A A DG + GQ +
Sbjct: 46 SKGYAYVEFENPDEAEKALKHMDGGQIDGQEIT 78
Score = 37.1 bits (87), Expect = 5e-05
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGYA+++F NP +A A DG + GQ +
Sbjct: 46 SKGYAYVEFENPDEAEKALKHMDGGQIDGQEI 77
>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 = 37.6 bits (88), Expect = 5e-05
Identities = 11/40 (27%), Positives = 18/40 (45%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+ + K YAFI F A A +G+ + G+ +
Sbjct: 36 GKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENI 75
Score = 37.6 bits (88), Expect = 5e-05
Identities = 12/39 (30%), Positives = 17/39 (43%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
K YAFI F A A +G+ + G+ + I K
Sbjct: 43 KLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAK 81
>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 = 37.2 bits (87), Expect = 6e-05
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KG+ FI+ A A + D + G+ L +
Sbjct: 51 KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF 85
Score = 36.9 bits (86), Expect = 9e-05
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+ FI+ A A + D + G+ L
Sbjct: 51 KGFGFIRLETRTLAEIAKVELDNMPLRGKQL 81
>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 = 37.7 bits (88), Expect = 6e-05
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGYA +++ A +A +G ++GQT+
Sbjct: 68 KGYALVEYETHKQALAAKEALNGAEIMGQTI 98
Score = 37.7 bits (88), Expect = 6e-05
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGYA +++ A +A +G ++GQT+
Sbjct: 68 KGYALVEYETHKQALAAKEALNGAEIMGQTI 98
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 37.2 bits (87), Expect = 8e-05
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGY +++ +A++A G +G+ ++GQ +
Sbjct: 65 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 95
Score = 37.2 bits (87), Expect = 8e-05
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY +++ +A++A G +G+ ++GQ +
Sbjct: 65 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 95
>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 = 1e-04
Identities = 10/42 (23%), Positives = 16/42 (38%), Gaps = 2/42 (4%)
Query: 30 GQTLGISM--HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G + +SM + AF+ + A A +G V L
Sbjct: 62 GNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVESVQL 103
Score = 37.0 bits (86), Expect = 1e-04
Identities = 7/32 (21%), Positives = 11/32 (34%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+ AF+ + A A +G V L
Sbjct: 72 PRNCAFVTYEKMESADQAVAELNGTQVESVQL 103
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 37.2 bits (86), Expect = 1e-04
Identities = 9/38 (23%), Positives = 16/38 (42%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+ G A+I F+ A++ G G L I+ +
Sbjct: 71 NSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSE 108
Score = 36.0 bits (83), Expect = 3e-04
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
+ G A+I F+ A++ G G L +++
Sbjct: 71 NSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITF 106
>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 = 36.5 bits (85), Expect = 1e-04
Identities = 8/34 (23%), Positives = 15/34 (44%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQT 68
+A+IQ+ + A++AC G + G
Sbjct: 49 HVKGDSFAYIQYESLDAAQAACAKMRGFPLGGPD 82
Score = 36.1 bits (84), Expect = 1e-04
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQT 32
+A+IQ+ + A++AC G + G
Sbjct: 52 GDSFAYIQYESLDAAQAACAKMRGFPLGGPD 82
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 36.3 bits (84), Expect = 1e-04
Identities = 7/39 (17%), Positives = 17/39 (43%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
+ AF+ + + A+ A G + TL +++ +
Sbjct: 55 PRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQ 93
Score = 35.2 bits (81), Expect = 3e-04
Identities = 7/33 (21%), Positives = 13/33 (39%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
+ AF+ + + A+ A G + TL
Sbjct: 55 PRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLR 87
>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 = 36.1 bits (84), Expect = 1e-04
Identities = 9/37 (24%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVL-GQTLV 70
+ + GYAF+ + + + A A G+ L G+ +
Sbjct: 40 VLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIME 76
Score = 35.3 bits (82), Expect = 3e-04
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVL-GQTL 33
+ GYAF+ + + + A A G+ L G+ +
Sbjct: 42 LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIM 75
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 36.1 bits (84), Expect = 2e-04
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG A++++ N A A + DG T+ +
Sbjct: 58 KGLAYVEYENESQASQAVMKMDGMTIKENII 88
Score = 36.1 bits (84), Expect = 2e-04
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG A++++ N A A + DG T+ +
Sbjct: 58 KGLAYVEYENESQASQAVMKMDGMTIKENII 88
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 36.1 bits (84), Expect = 2e-04
Identities = 7/35 (20%), Positives = 11/35 (31%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG FI++ A + G+ L
Sbjct: 59 HYPEKGCCFIKYDTHEQAAVCIVALANFPFQGRNL 93
Score = 36.1 bits (84), Expect = 2e-04
Identities = 7/35 (20%), Positives = 11/35 (31%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
KG FI++ A + G+ L
Sbjct: 62 EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG 96
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 36.7 bits (85), Expect = 2e-04
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
H+G+AF++F DA +A + + G+T+
Sbjct: 104 HRGFAFVEFELAEDAAAAIDNMNESELFGRTI 135
Score = 36.7 bits (85), Expect = 2e-04
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
H+G+AF++F DA +A + + G+T+
Sbjct: 104 HRGFAFVEFELAEDAAAAIDNMNESELFGRTI 135
>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA
binding protein-RNA complex; 1.85A {Homo sapiens} PDB:
3nna_A 3nnc_A 2dhs_A 3nnh_A
Length = 175
Score = 36.8 bits (86), Expect = 2e-04
Identities = 8/43 (18%), Positives = 12/43 (27%)
Query: 34 GISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQY 76
KG F+ F A A VL +++
Sbjct: 42 NPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKP 84
Score = 34.9 bits (81), Expect = 0.001
Identities = 8/33 (24%), Positives = 9/33 (27%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG F+ F A A VL
Sbjct: 45 QSKGCCFVTFYTRKAALEAQNALHNMKVLPGMH 77
Score = 30.3 bits (69), Expect = 0.047
Identities = 6/18 (33%), Positives = 11/18 (61%)
Query: 2 HKGYAFIQFSNPHDARSA 19
+G AF+ F+ A++A
Sbjct: 135 SRGCAFVTFTTRAMAQTA 152
Score = 30.3 bits (69), Expect = 0.047
Identities = 6/18 (33%), Positives = 11/18 (61%)
Query: 38 HKGYAFIQFSNPHDARSA 55
+G AF+ F+ A++A
Sbjct: 135 SRGCAFVTFTTRAMAQTA 152
>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 = 36.2 bits (84), Expect = 2e-04
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGY +++ +A++A G +G+ ++GQ +
Sbjct: 64 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 94
Score = 36.2 bits (84), Expect = 2e-04
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY +++ +A++A G +G+ ++GQ +
Sbjct: 64 KGYTLVEYETYKEAQAAMEGLNGQDLMGQPI 94
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 36.9 bits (86), Expect = 2e-04
Identities = 9/32 (28%), Positives = 18/32 (56%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
HKG+AF+++ P A+ A + + G+ +
Sbjct: 69 HKGFAFVEYEVPEAAQLALEQMNSVMLGGRNI 100
Score = 36.9 bits (86), Expect = 2e-04
Identities = 9/32 (28%), Positives = 18/32 (56%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
HKG+AF+++ P A+ A + + G+ +
Sbjct: 69 HKGFAFVEYEVPEAAQLALEQMNSVMLGGRNI 100
Score = 35.0 bits (81), Expect = 0.001
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
HKGY FI++ ++ A + + GQ L
Sbjct: 166 HKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 197
Score = 35.0 bits (81), Expect = 0.001
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
HKGY FI++ ++ A + + GQ L
Sbjct: 166 HKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYL 197
>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 = 35.2 bits (82), Expect = 3e-04
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
H+G+AF++F DA +A + + G+T+
Sbjct: 48 HRGFAFVEFELAEDAAAAIDNMNESELFGRTI 79
Score = 35.2 bits (82), Expect = 3e-04
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
H+G+AF++F DA +A + + G+T+
Sbjct: 48 HRGFAFVEFELAEDAAAAIDNMNESELFGRTI 79
>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 = 35.4 bits (82), Expect = 3e-04
Identities = 7/34 (20%), Positives = 17/34 (50%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
G A + F + +A +A + + R + + + +S
Sbjct: 57 TGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLS 90
Score = 34.2 bits (79), Expect = 8e-04
Identities = 9/63 (14%), Positives = 20/63 (31%), Gaps = 11/63 (17%)
Query: 7 FIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLG 66
F + + E G G A + F + +A +A + + R +
Sbjct: 36 FYGYQVIPGSVCLKYNEKGM-----------PTGEAMVAFESRDEATAAVIDLNDRPIGS 84
Query: 67 QTL 69
+ +
Sbjct: 85 RKV 87
>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 = 36.7 bits (84), Expect = 3e-04
Identities = 12/41 (29%), Positives = 23/41 (56%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYA 42
+GYAFI++ + D SA DG+ + G+ + + + +G
Sbjct: 143 PRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRT 183
Score = 35.2 bits (80), Expect = 0.001
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+GYAFI++ + D SA DG+ + G+ +
Sbjct: 143 PRGYAFIEYEHERDMHSAYKHADGKKIDGRRV 174
>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 = 35.3 bits (82), Expect = 3e-04
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+ Y F++F DA +A +GR +LG+ +
Sbjct: 54 NDPYCFVEFYEHRDAAAALAAMNGRKILGKEV 85
Score = 35.3 bits (82), Expect = 3e-04
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+ Y F++F DA +A +GR +LG+ +
Sbjct: 54 NDPYCFVEFYEHRDAAAALAAMNGRKILGKEV 85
>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 = 35.3 bits (82), Expect = 3e-04
Identities = 7/38 (18%), Positives = 18/38 (47%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
G A + F + +A +A + + R + + + + + G
Sbjct: 57 TGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSG 94
Score = 34.6 bits (80), Expect = 6e-04
Identities = 6/31 (19%), Positives = 15/31 (48%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G A + F + +A +A + + R + + +
Sbjct: 57 TGEAMVAFESRDEATAAVIDLNDRPIGSRKV 87
>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 = 35.3 bits (82), Expect = 3e-04
Identities = 9/53 (16%), Positives = 20/53 (37%), Gaps = 9/53 (16%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSA 55
KG A+I+F + DA + G + G+++ + ++
Sbjct: 53 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSV---------SLYYTGEKGGTRG 96
Score = 34.9 bits (81), Expect = 5e-04
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KG A+I+F + DA + G + G+++
Sbjct: 53 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVS 84
>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 = 35.3 bits (82), Expect = 3e-04
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
G A + F DA A +G + G+ + I +
Sbjct: 70 LGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 104
Score = 33.4 bits (77), Expect = 0.002
Identities = 8/31 (25%), Positives = 13/31 (41%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G A + F DA A +G + G+ +
Sbjct: 70 LGTADVHFERKADALKAMKQYNGVPLDGRPM 100
>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 = 35.6 bits (82), Expect = 4e-04
Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 1/36 (2%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
A++ + DA A + V G+TL S
Sbjct: 62 PSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASL 97
Score = 34.5 bits (79), Expect = 9e-04
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
A++ + DA A + V G+TL
Sbjct: 62 PSASAYVTYIRSEDALRAIQCVNNVVVDGRTL 93
>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 = 34.9 bits (81), Expect = 4e-04
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG+AF+ F P A A DG+ G+ L
Sbjct: 50 KGFAFVTFMFPEHAVKAYAEVDGQVFQGRML 80
Score = 34.9 bits (81), Expect = 4e-04
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+AF+ F P A A DG+ G+ L
Sbjct: 50 KGFAFVTFMFPEHAVKAYAEVDGQVFQGRML 80
>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 = 34.9 bits (81), Expect = 4e-04
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGYAFI+F + + SA +G + + L
Sbjct: 43 SKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 74
Score = 34.9 bits (81), Expect = 4e-04
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGYAFI+F + + SA +G + + L
Sbjct: 43 SKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 74
>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 = 35.2 bits (81), Expect = 5e-04
Identities = 10/58 (17%), Positives = 16/58 (27%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGED 60
A ++F P +AR A L + F D++ E
Sbjct: 46 GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEK 103
Score = 34.8 bits (80), Expect = 7e-04
Identities = 7/31 (22%), Positives = 10/31 (32%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
A ++F P +AR A L
Sbjct: 46 GITAIVEFLEPLEARKAFRHLAYSKFHHVPL 76
>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 = 35.4 bits (82), Expect = 5e-04
Identities = 9/35 (25%), Positives = 14/35 (40%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
G A + F DA A G + G+ + I +
Sbjct: 76 LGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 110
Score = 33.5 bits (77), Expect = 0.003
Identities = 8/31 (25%), Positives = 12/31 (38%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G A + F DA A G + G+ +
Sbjct: 76 LGTADVHFERRADALKAMKQYKGVPLDGRPM 106
>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 = 35.7 bits (83), Expect = 5e-04
Identities = 17/104 (16%), Positives = 24/104 (23%), Gaps = 50/104 (48%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM------------------------ 37
GYA++ F P DA A + + G+ + I
Sbjct: 56 SLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSI 115
Query: 38 --------------------------HKGYAFIQFSNPHDARSA 55
KGY F+ F A A
Sbjct: 116 DNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERA 159
Score = 33.0 bits (76), Expect = 0.005
Identities = 9/32 (28%), Positives = 15/32 (46%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
GYA++ F P DA A + + G+ +
Sbjct: 56 SLGYAYVNFQQPADAERALDTMNFDVIKGKPV 87
Score = 30.3 bits (69), Expect = 0.046
Identities = 14/71 (19%), Positives = 22/71 (30%), Gaps = 9/71 (12%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDG 61
KGY F+ F A A +G + + + F+ R A LG
Sbjct: 142 SKGYGFVHFETQEAAERAIEKMNGMLLNDRKV---------FVGRFKSRKEREAELGARA 192
Query: 62 RTVLGQTLVSY 72
+ + Y
Sbjct: 193 KEFYPYDVPDY 203
>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 = 34.5 bits (80), Expect = 6e-04
Identities = 7/32 (21%), Positives = 14/32 (43%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
K + F+ F +P A +G + G+ +
Sbjct: 56 PKSFGFVCFKHPESVSYAIALLNGIRLYGRPI 87
Score = 34.5 bits (80), Expect = 6e-04
Identities = 7/32 (21%), Positives = 14/32 (43%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
K + F+ F +P A +G + G+ +
Sbjct: 56 PKSFGFVCFKHPESVSYAIALLNGIRLYGRPI 87
>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 = 34.3 bits (79), Expect = 6e-04
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
I+ K +AF++F + + + + DG GQ+L
Sbjct: 49 INQDKNFAFLEFRSVDET-TQAMAFDGIIFQGQSL 82
Score = 33.2 bits (76), Expect = 0.002
Identities = 9/32 (28%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
K +AF++F + + + + DG GQ+L
Sbjct: 52 DKNFAFLEFRSVDET-TQAMAFDGIIFQGQSL 82
>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 = 35.4 bits (81), Expect = 8e-04
Identities = 11/86 (12%), Positives = 29/86 (33%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDG 61
G A ++ ++ + A + + GQ + + + K A + + +C +D
Sbjct: 41 KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDF 100
Query: 62 RTVLGQTLVSYKLQYYNGCRYVSPTP 87
+ + N ++ S
Sbjct: 101 SESRNNRFSTPEQAAKNRIQHPSNVL 126
Score = 31.6 bits (71), Expect = 0.016
Identities = 3/42 (7%), Positives = 9/42 (21%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAF 43
+++ + DA + + F
Sbjct: 164 RSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLCF 205
Score = 28.1 bits (62), Expect = 0.27
Identities = 2/32 (6%), Positives = 8/32 (25%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+++ + DA + +
Sbjct: 164 RSSSGLLEWDSKSDALETLGFLNHYQMKNPNG 195
>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 = 34.1 bits (79), Expect = 0.001
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+G+AF++F + DA+ A DG + G+ L
Sbjct: 55 RGFAFVRFHDRRDAQDAEAAMDGAELDGREL 85
Score = 34.1 bits (79), Expect = 0.001
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+AF++F + DA+ A DG + G+ L
Sbjct: 55 RGFAFVRFHDRRDAQDAEAAMDGAELDGREL 85
>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP,
RBD, poly(U) binding, tandem, acetylation, cytopla
nucleus; 2.70A {Saccharomyces cerevisiae}
Length = 166
Score = 34.8 bits (81), Expect = 0.001
Identities = 8/32 (25%), Positives = 16/32 (50%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+ YAF+++ HDA A +G+ + +
Sbjct: 40 NVNYAFVEYHQSHDANIALQTLNGKQIENNIV 71
Score = 34.8 bits (81), Expect = 0.001
Identities = 8/32 (25%), Positives = 16/32 (50%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+ YAF+++ HDA A +G+ + +
Sbjct: 40 NVNYAFVEYHQSHDANIALQTLNGKQIENNIV 71
Score = 31.3 bits (72), Expect = 0.016
Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 11/50 (22%)
Query: 6 AFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSA 55
AF F + + G + +GY F+ F++ DA++A
Sbjct: 107 AFKDFPSYLSGHVMWDMQTGSS-----------RGYGFVSFTSQDDAQNA 145
Score = 29.4 bits (67), Expect = 0.086
Identities = 7/17 (41%), Positives = 13/17 (76%)
Query: 3 KGYAFIQFSNPHDARSA 19
+GY F+ F++ DA++A
Sbjct: 129 RGYGFVSFTSQDDAQNA 145
>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 = 34.2 bits (79), Expect = 0.001
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 9/54 (16%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSA 55
+G AFI F N A A +G + G+ L I+F RS+
Sbjct: 66 MRGQAFITFPNKEIAWQALHLVNGYKLYGKIL---------VIEFGKNKKQRSS 110
Score = 33.4 bits (77), Expect = 0.002
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
+G AFI F N A A +G + G+ LV
Sbjct: 66 MRGQAFITFPNKEIAWQALHLVNGYKLYGKILV 98
>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 = 33.7 bits (78), Expect = 0.001
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
H+G+AF++F DA +A + + G+T+
Sbjct: 53 HRGFAFVEFELAEDAAAAIDNMNESELFGRTI 84
Score = 33.7 bits (78), Expect = 0.001
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
H+G+AF++F DA +A + + G+T+
Sbjct: 53 HRGFAFVEFELAEDAAAAIDNMNESELFGRTI 84
>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 = 33.8 bits (78), Expect = 0.001
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 38 HKGYAFIQFSNPHDARSACLG-EDGRTVLGQTLV 70
H+G+ F+ F DA+ A + G+ LV
Sbjct: 57 HRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV 90
Score = 32.7 bits (75), Expect = 0.004
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 2 HKGYAFIQFSNPHDARSACLG-EDGRTVLGQTL 33
H+G+ F+ F DA+ A + G+ L
Sbjct: 57 HRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL 89
>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 103
Score = 33.7 bits (78), Expect = 0.002
Identities = 12/31 (38%), Positives = 13/31 (41%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG+AFI F DA A G G L
Sbjct: 57 KGFAFISFHRREDAARAIAGVSGFGYDHLIL 87
Score = 33.7 bits (78), Expect = 0.002
Identities = 12/31 (38%), Positives = 13/31 (41%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+AFI F DA A G G L
Sbjct: 57 KGFAFISFHRREDAARAIAGVSGFGYDHLIL 87
>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 = 33.8 bits (78), Expect = 0.002
Identities = 12/32 (37%), Positives = 22/32 (68%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+G+AFI F NP DA++A +G+++ G+ +
Sbjct: 47 SRGFAFITFENPADAKNAAKDMNGKSLHGKAI 78
Score = 33.8 bits (78), Expect = 0.002
Identities = 12/32 (37%), Positives = 22/32 (68%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+AFI F NP DA++A +G+++ G+ +
Sbjct: 47 SRGFAFITFENPADAKNAAKDMNGKSLHGKAI 78
>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 = 33.4 bits (77), Expect = 0.002
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGYAFI+F++ DA+ A + R + G+ +
Sbjct: 53 KGYAFIEFASFEDAKEALNSCNKREIEGRAI 83
Score = 33.4 bits (77), Expect = 0.002
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGYAFI+F++ DA+ A + R + G+ +
Sbjct: 53 KGYAFIEFASFEDAKEALNSCNKREIEGRAI 83
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 34.1 bits (78), Expect = 0.002
Identities = 6/32 (18%), Positives = 14/32 (43%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KGYA + ++ + G+ + G+ +
Sbjct: 99 KGYAEVVVASENSVHKLLELLPGKVLNGEKVD 130
Score = 33.4 bits (76), Expect = 0.003
Identities = 6/31 (19%), Positives = 14/31 (45%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGYA + ++ + G+ + G+ +
Sbjct: 99 KGYAEVVVASENSVHKLLELLPGKVLNGEKV 129
>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 = 33.4 bits (77), Expect = 0.002
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G+ F+++ P A+ A G TV G L
Sbjct: 50 MGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE 81
Score = 33.4 bits (77), Expect = 0.002
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
G+ F+++ P A+ A G TV G L
Sbjct: 50 MGFGFVEYKKPEQAQKALKQLQGHTVDGHKL 80
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 33.6 bits (77), Expect = 0.002
Identities = 9/40 (22%), Positives = 14/40 (35%), Gaps = 1/40 (2%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGY 41
KG F+ F + A+ + G+ L I Y
Sbjct: 51 FKGSIFVVFDSIESAKKF-VETPGQKYKETDLLILFKDDY 89
Score = 33.2 bits (76), Expect = 0.003
Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 9/56 (16%)
Query: 30 GQTLGISM-------HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYKLQYY 77
GQ L I M KG F+ F + A+ + G+ L + +K Y+
Sbjct: 36 GQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF-VETPGQKYKETDLLILFKDDYF 90
>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 = 33.7 bits (77), Expect = 0.002
Identities = 6/30 (20%), Positives = 17/30 (56%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQ 31
+K Y+F ++ +++ A + +G+ V+
Sbjct: 62 NKPYSFARYRTTEESKRAYVTLNGKEVVDD 91
Score = 33.7 bits (77), Expect = 0.002
Identities = 6/30 (20%), Positives = 17/30 (56%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQ 67
+K Y+F ++ +++ A + +G+ V+
Sbjct: 62 NKPYSFARYRTTEESKRAYVTLNGKEVVDD 91
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 34.1 bits (78), Expect = 0.002
Identities = 9/35 (25%), Positives = 14/35 (40%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
G A + F DA A G + G+ + I +
Sbjct: 129 LGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 163
Score = 32.1 bits (73), Expect = 0.011
Identities = 8/31 (25%), Positives = 12/31 (38%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G A + F DA A G + G+ +
Sbjct: 129 LGTADVHFERRADALKAMKQYKGVPLDGRPM 159
>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 = 33.6 bits (77), Expect = 0.002
Identities = 10/37 (27%), Positives = 16/37 (43%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
KG AFI N A A +G + G+ + + +
Sbjct: 92 KGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFAR 128
Score = 33.3 bits (76), Expect = 0.004
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KG AFI N A A +G + G+ +V
Sbjct: 92 KGQAFIGLPNEKAAAKALKEANGYVLFGKPMV 123
>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 = 33.4 bits (77), Expect = 0.002
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
H+GY F++F + DA A D + G+ +
Sbjct: 56 HQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI 87
Score = 33.4 bits (77), Expect = 0.002
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
H+GY F++F + DA A D + G+ +
Sbjct: 56 HQGYGFVEFLSEEDADYAIKIMDMIKLYGKPI 87
>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein
1; RRM domain, RBD, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 94
Score = 33.0 bits (76), Expect = 0.002
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG AFI F + A++ + + + G+ +
Sbjct: 58 KGVAFILFLDKDSAQNCTRAINNKQLFGRVI 88
Score = 33.0 bits (76), Expect = 0.002
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG AFI F + A++ + + + G+ +
Sbjct: 58 KGVAFILFLDKDSAQNCTRAINNKQLFGRVI 88
>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 = 34.1 bits (77), Expect = 0.002
Identities = 9/37 (24%), Positives = 14/37 (37%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+G AF+ F A +A G + + I K
Sbjct: 52 RGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAK 88
Score = 33.3 bits (75), Expect = 0.005
Identities = 8/35 (22%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
+G AF+ F A +A G + + + Y
Sbjct: 52 RGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY 86
Score = 26.8 bits (58), Expect = 0.93
Identities = 7/29 (24%), Positives = 11/29 (37%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLG 30
AF++F N A +A G +
Sbjct: 243 RHDIAFVEFDNEVQAGAARDALQGFKITQ 271
Score = 26.8 bits (58), Expect = 0.93
Identities = 7/29 (24%), Positives = 11/29 (37%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLG 66
AF++F N A +A G +
Sbjct: 243 RHDIAFVEFDNEVQAGAARDALQGFKITQ 271
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 33.1 bits (76), Expect = 0.003
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYK 73
K + F+ F NP A+ A +G V + L V K
Sbjct: 82 KCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK 117
Score = 32.3 bits (74), Expect = 0.005
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
K + F+ F NP A+ A +G V + L + + K
Sbjct: 82 KCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLKK 118
>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 = 33.0 bits (76), Expect = 0.003
Identities = 9/37 (24%), Positives = 15/37 (40%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
KGY F+ F A A +G + + + + K
Sbjct: 45 KGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK 81
Score = 31.8 bits (73), Expect = 0.009
Identities = 9/35 (25%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
KGY F+ F A A +G + + + V
Sbjct: 45 KGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 79
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 32.9 bits (76), Expect = 0.003
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+G+AF+ F N DA+ A +G + G+ +
Sbjct: 57 RGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Score = 32.9 bits (76), Expect = 0.003
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+AF+ F N DA+ A +G + G+ +
Sbjct: 57 RGFAFVYFENVDDAKEAKERANGMELDGRRI 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 = 32.5 bits (75), Expect = 0.003
Identities = 10/31 (32%), Positives = 13/31 (41%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGY F+ F +P A+ A V Q
Sbjct: 47 KGYGFVDFDSPSAAQKAVTALKASGVQAQMA 77
Score = 32.5 bits (75), Expect = 0.003
Identities = 10/31 (32%), Positives = 13/31 (41%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY F+ F +P A+ A V Q
Sbjct: 47 KGYGFVDFDSPSAAQKAVTALKASGVQAQMA 77
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 32.5 bits (75), Expect = 0.003
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KGY FI FS+ AR A +G + G+ +
Sbjct: 47 KGYGFITFSDSECARRALEQLNGFELAGRPMR 78
Score = 32.5 bits (75), Expect = 0.004
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGY FI FS+ AR A +G + G+ +
Sbjct: 47 KGYGFITFSDSECARRALEQLNGFELAGRPM 77
>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 113
Score = 32.8 bits (75), Expect = 0.003
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KG A + + +P A++A DG+ G L +S+
Sbjct: 65 KGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSL 99
Score = 32.0 bits (73), Expect = 0.007
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG A + + +P A++A DG+ G L
Sbjct: 65 KGDATVSYEDPPTAKAAVEWFDGKDFQGSKL 95
>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 = 32.7 bits (75), Expect = 0.004
Identities = 6/37 (16%), Positives = 16/37 (43%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+G + F +A A +G+ + + + + M +
Sbjct: 56 RGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDE 92
Score = 30.7 bits (70), Expect = 0.021
Identities = 5/31 (16%), Positives = 13/31 (41%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G + F +A A +G+ + + +
Sbjct: 56 RGIGTVTFEQSIEAVQAISMFNGQLLFDRPM 86
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 32.7 bits (75), Expect = 0.004
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 1 MHKGYAFIQFSNPHDARSA---------CLGEDGRTV 28
++G+AF+Q S+ DA L DG+T+
Sbjct: 51 QNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI 87
Score = 32.7 bits (75), Expect = 0.004
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 37 MHKGYAFIQFSNPHDARSA---------CLGEDGRTV 64
++G+AF+Q S+ DA L DG+T+
Sbjct: 51 QNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI 87
>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 = 32.7 bits (75), Expect = 0.004
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KGY FI FS+ A+ A +G + G+ +
Sbjct: 67 SKGYGFITFSDSECAKKALEQLNGFELAGRPMK 99
Score = 32.3 bits (74), Expect = 0.005
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGY FI FS+ A+ A +G + G+ +
Sbjct: 67 SKGYGFITFSDSECAKKALEQLNGFELAGRPM 98
>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 = 32.8 bits (75), Expect = 0.004
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+G+AF+ F N DA+ A +G + G+ +
Sbjct: 88 RGFAFVYFENVDDAKEAKERANGMELDGRRI 118
Score = 32.8 bits (75), Expect = 0.004
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+AF+ F N DA+ A +G + G+ +
Sbjct: 88 RGFAFVYFENVDDAKEAKERANGMELDGRRI 118
>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 = 33.3 bits (75), Expect = 0.004
Identities = 9/40 (22%), Positives = 14/40 (35%), Gaps = 1/40 (2%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGY 41
KG F+ F + A+ + G+ L I Y
Sbjct: 149 FKGSIFVVFDSIESAKKF-VETPGQKYKETDLLILFKDDY 187
Score = 32.1 bits (72), Expect = 0.013
Identities = 9/41 (21%), Positives = 17/41 (41%), Gaps = 2/41 (4%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYKLQYY 77
KG F+ F + A+ + G+ L + +K Y+
Sbjct: 149 FKGSIFVVFDSIESAKKF-VETPGQKYKETDLLILFKDDYF 188
>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 = 32.3 bits (74), Expect = 0.005
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYKLQY 76
GY F++F++ A +G+ + G T +KL Y
Sbjct: 52 AGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNY 90
Score = 30.0 bits (68), Expect = 0.032
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQT 32
GY F++F++ A +G+ + G T
Sbjct: 52 AGYCFVEFADLATAEKCLHKINGKPLPGAT 81
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 32.0 bits (73), Expect = 0.005
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDG 25
KGY F+++++P A A DG
Sbjct: 45 KTKGYIFLEYASPAHAVDAVKNADG 69
Score = 32.0 bits (73), Expect = 0.005
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 37 MHKGYAFIQFSNPHDARSACLGEDG 61
KGY F+++++P A A DG
Sbjct: 45 KTKGYIFLEYASPAHAVDAVKNADG 69
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 32.4 bits (74), Expect = 0.005
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
KG A + F +P A++A DG+ G + +S
Sbjct: 57 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 93
Score = 31.2 bits (71), Expect = 0.014
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG A + F +P A++A DG+ G +
Sbjct: 57 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPI 87
>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 = 32.3 bits (74), Expect = 0.005
Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYK 73
K + F+ + NP A++A +G + + L V K
Sbjct: 67 KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK 102
Score = 31.1 bits (71), Expect = 0.014
Identities = 8/37 (21%), Positives = 19/37 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
K + F+ + NP A++A +G + + L + + +
Sbjct: 67 KCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR 103
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 32.8 bits (75), Expect = 0.005
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+G+AF++F + DA A DG + G+ L
Sbjct: 89 RGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 119
Score = 32.8 bits (75), Expect = 0.005
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+AF++F + DA A DG + G+ L
Sbjct: 89 RGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 119
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 32.2 bits (74), Expect = 0.005
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG ++F +P A AC +G + G+ +
Sbjct: 48 KGCGVVKFESPEVAERACRMMNGMKLSGREI 78
Score = 32.2 bits (74), Expect = 0.005
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG ++F +P A AC +G + G+ +
Sbjct: 48 KGCGVVKFESPEVAERACRMMNGMKLSGREI 78
>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 = 32.5 bits (74), Expect = 0.006
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+G+AF++F + DA A DG + G+ L
Sbjct: 112 RGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 142
Score = 32.5 bits (74), Expect = 0.006
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+AF++F + DA A DG + G+ L
Sbjct: 112 RGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 142
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 32.0 bits (73), Expect = 0.006
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYK 73
+ +S+ AR A +G + TL V+Y
Sbjct: 54 TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI 89
Score = 30.5 bits (69), Expect = 0.024
Identities = 7/34 (20%), Positives = 14/34 (41%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
+ +S+ AR A +G + TL ++
Sbjct: 54 TAVVNVTYSSKDQARQALDKLNGFQLENFTLKVA 87
>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 = 31.9 bits (73), Expect = 0.007
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVL-GQTLGIS 36
+ AFIQF+ A A + ++ G+ L +
Sbjct: 48 QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK 82
Score = 31.5 bits (72), Expect = 0.009
Identities = 7/32 (21%), Positives = 13/32 (40%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLG 66
+ + AFIQF+ A A + ++
Sbjct: 44 VVQRQQCAFIQFATRQAAEVAAEKSFNKLIVN 75
>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 = 32.6 bits (74), Expect = 0.008
Identities = 9/38 (23%), Positives = 20/38 (52%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
K A +Q ++ + A+ A +G + G+ + I++ K
Sbjct: 40 KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK 77
Score = 31.4 bits (71), Expect = 0.019
Identities = 7/32 (21%), Positives = 16/32 (50%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
K A +Q ++ + A+ A +G + G+ +
Sbjct: 40 KKENALVQMADGNQAQLAMSHLNGHKLHGKPI 71
Score = 27.6 bits (61), Expect = 0.45
Identities = 7/35 (20%), Positives = 13/35 (37%), Gaps = 1/35 (2%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVL-GQTLGIS 36
+ A IQ + +A A + + L +S
Sbjct: 158 RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS 192
Score = 27.2 bits (60), Expect = 0.68
Identities = 8/36 (22%), Positives = 14/36 (38%), Gaps = 2/36 (5%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVL-GQTL-VSY 72
+ A IQ + +A A + + L VS+
Sbjct: 158 RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF 193
>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 = 32.7 bits (74), Expect = 0.008
Identities = 8/36 (22%), Positives = 19/36 (52%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
K A +Q ++ + A+ A +G + G+ + I++
Sbjct: 71 KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL 106
Score = 31.9 bits (72), Expect = 0.014
Identities = 7/32 (21%), Positives = 16/32 (50%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
K A +Q ++ + A+ A +G + G+ +
Sbjct: 71 KKENALVQMADGNQAQLAMSHLNGHKLHGKPI 102
Score = 26.9 bits (59), Expect = 0.95
Identities = 7/35 (20%), Positives = 13/35 (37%), Gaps = 1/35 (2%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVL-GQTLGIS 36
+ A IQ + +A A + + L +S
Sbjct: 189 RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS 223
Score = 26.1 bits (57), Expect = 1.6
Identities = 8/36 (22%), Positives = 14/36 (38%), Gaps = 2/36 (5%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVL-GQTL-VSY 72
+ A IQ + +A A + + L VS+
Sbjct: 189 RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF 224
>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 = 31.9 bits (73), Expect = 0.008
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KG+ F+ F N DA A G V G+ +
Sbjct: 54 SKGFGFVTFENSADADRAREKLHGTVVEGRKIE 86
Score = 31.5 bits (72), Expect = 0.010
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG+ F+ F N DA A G V G+ +
Sbjct: 54 SKGFGFVTFENSADADRAREKLHGTVVEGRKI 85
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 31.9 bits (73), Expect = 0.009
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KG+ F+ F N DA A G V G+ +
Sbjct: 69 KGFGFVTFENSADADRAREKLHGTVVEGRKIE 100
Score = 31.5 bits (72), Expect = 0.011
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG+ F+ F N DA A G V G+ +
Sbjct: 69 KGFGFVTFENSADADRAREKLHGTVVEGRKI 99
>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 = 32.4 bits (73), Expect = 0.009
Identities = 9/52 (17%), Positives = 20/52 (38%), Gaps = 4/52 (7%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARS 54
KG+A + + ++ R + GQ ++ QF + + +S
Sbjct: 112 KGFALVGVGSEASSKKLMDLLPKRELHGQNPVVT----PVNKQFLSQFEMQS 159
Score = 32.4 bits (73), Expect = 0.009
Identities = 7/32 (21%), Positives = 13/32 (40%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KG+A + + ++ R + GQ V
Sbjct: 112 KGFALVGVGSEASSKKLMDLLPKRELHGQNPV 143
>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 = 31.4 bits (72), Expect = 0.009
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
KG+ F+ FS+P +A A +GR V + L +++ +
Sbjct: 55 KGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ 91
Score = 31.0 bits (71), Expect = 0.017
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 34 GISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G S KG+ F+ FS+P +A A +GR V + L
Sbjct: 52 GRS--KGFGFVCFSSPEEATKAVTEMNGRIVATKPLY 86
>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 = 31.2 bits (71), Expect = 0.009
Identities = 8/36 (22%), Positives = 16/36 (44%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
+K AF+ N A++A + G+ L + +
Sbjct: 39 NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQL 74
Score = 31.2 bits (71), Expect = 0.011
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
+K AF+ N A++A + G+ L+
Sbjct: 39 NKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLI 71
>2la6_A RNA-binding protein FUS; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative, RNA recognition; NMR {Homo
sapiens}
Length = 99
Score = 31.5 bits (72), Expect = 0.009
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISM 37
KG A + F +P A++A DG+ G + +S
Sbjct: 63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97
Score = 31.5 bits (72), Expect = 0.011
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
KG A + F +P A++A DG+ G + VS+
Sbjct: 63 KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 31.5 bits (72), Expect = 0.010
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLG 30
KGY F++F++ + + A G LG
Sbjct: 51 KGYGFVKFTDELEQKRALTECQGAVGLG 78
Score = 31.5 bits (72), Expect = 0.010
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLG 66
KGY F++F++ + + A G LG
Sbjct: 51 KGYGFVKFTDELEQKRALTECQGAVGLG 78
>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: d.58.7.1
Length = 102
Score = 31.4 bits (72), Expect = 0.010
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+G+ F+ F N DA+ A + +G++V G+ +
Sbjct: 54 RGFGFVTFENIDDAKDAMMAMNGKSVDGRQI 84
Score = 31.4 bits (72), Expect = 0.010
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+G+ F+ F N DA+ A + +G++V G+ +
Sbjct: 54 RGFGFVTFENIDDAKDAMMAMNGKSVDGRQI 84
>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 = 31.6 bits (72), Expect = 0.010
Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLG 30
G A +QF N DAR + + + G
Sbjct: 56 GLGQALVQFKNEDDARKS-ERLHRKKLNG 83
Score = 31.6 bits (72), Expect = 0.010
Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLG 66
G A +QF N DAR + + + G
Sbjct: 56 GLGQALVQFKNEDDARKS-ERLHRKKLNG 83
>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 = 31.0 bits (71), Expect = 0.011
Identities = 7/32 (21%), Positives = 13/32 (40%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KG+A + + ++ R + GQ V
Sbjct: 45 KGFALVGVGSEASSKKLMDLLPKRELHGQNPV 76
Score = 30.2 bits (69), Expect = 0.025
Identities = 6/31 (19%), Positives = 12/31 (38%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG+A + + ++ R + GQ
Sbjct: 45 KGFALVGVGSEASSKKLMDLLPKRELHGQNP 75
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 31.2 bits (71), Expect = 0.012
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 14/63 (22%)
Query: 23 EDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQ-TLVSYKLQYYNGCR 81
EDG+T KGY F+++++P A A DG + Q T ++ +
Sbjct: 56 EDGKT-----------KGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFD--K 102
Query: 82 YVS 84
Y++
Sbjct: 103 YMT 105
Score = 29.7 bits (67), Expect = 0.049
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 3 KGYAFIQFSNPHDARSACLGEDG 25
KGY F+++++P A A DG
Sbjct: 61 KGYIFLEYASPAHAVDAVKNADG 83
>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 = 31.6 bits (72), Expect = 0.012
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYK 73
+GY F++F + A+ A G +G +L + L V+
Sbjct: 84 RGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA 119
Score = 30.5 bits (69), Expect = 0.033
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+GY F++F + A+ A G +G +L + L
Sbjct: 84 RGYGFVKFQSGSSAQQAIAGLNGFNILNKRL 114
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 31.6 bits (71), Expect = 0.014
Identities = 7/50 (14%), Positives = 18/50 (36%), Gaps = 7/50 (14%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHD 51
+ A ++F + A+ A +G + + I+++ P
Sbjct: 61 NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLK-------IEYARPTR 103
Score = 28.5 bits (63), Expect = 0.16
Identities = 5/30 (16%), Positives = 12/30 (40%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQ 67
+ A ++F + A+ A +G +
Sbjct: 61 NGIQAMVEFESVLCAQKAKAALNGADIYAG 90
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 30.9 bits (70), Expect = 0.018
Identities = 8/40 (20%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 37 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQ-TLVSYKLQ 75
KG+ F++ + +DA+ G+ + + L Y ++
Sbjct: 52 KTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMK 91
Score = 30.5 bits (69), Expect = 0.022
Identities = 6/25 (24%), Positives = 12/25 (48%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDG 25
KG+ F++ + +DA+ G
Sbjct: 52 KTKGFLFVECGSMNDAKKIIKSFHG 76
>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 = 30.7 bits (70), Expect = 0.018
Identities = 8/32 (25%), Positives = 17/32 (53%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KG+ F+ F++ DA++A + + G +
Sbjct: 54 KGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVT 85
Score = 30.7 bits (70), Expect = 0.021
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG+ F+ F++ DA++A + + G +
Sbjct: 54 KGFGFVDFNSEEDAKAAKEAMEDGEIDGNKV 84
>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 = 30.7 bits (70), Expect = 0.022
Identities = 6/37 (16%), Positives = 13/37 (35%), Gaps = 2/37 (5%)
Query: 34 GISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G S +G F + + + +G+ + V
Sbjct: 63 GTS--RGVGFARMESTEKCEAVIGHFNGKFIKTPPGV 97
Score = 30.3 bits (69), Expect = 0.027
Identities = 3/37 (8%), Positives = 12/37 (32%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
+G F + + + +G+ + + +
Sbjct: 66 RGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 102
>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 = 29.8 bits (68), Expect = 0.029
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 3 KGYAFIQFSNPHDARSA 19
KGY F+ F N DA +A
Sbjct: 48 KGYGFVSFFNKWDAENA 64
Score = 29.8 bits (68), Expect = 0.029
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 39 KGYAFIQFSNPHDARSA 55
KGY F+ F N DA +A
Sbjct: 48 KGYGFVSFFNKWDAENA 64
>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 = 29.8 bits (68), Expect = 0.030
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+GY F+ F++ DA++A G+ + G+ L
Sbjct: 43 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL 73
Score = 29.8 bits (68), Expect = 0.030
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+GY F+ F++ DA++A G+ + G+ L
Sbjct: 43 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL 73
>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 = 29.9 bits (68), Expect = 0.030
Identities = 8/30 (26%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 2 HKGYAFIQFSNPHDARSACLGE---DGRTV 28
+ +AF+ F++ A+S C + G +V
Sbjct: 47 FRAFAFVTFADDKVAQSLCGEDLIIKGISV 76
Score = 29.9 bits (68), Expect = 0.030
Identities = 8/30 (26%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 38 HKGYAFIQFSNPHDARSACLGE---DGRTV 64
+ +AF+ F++ A+S C + G +V
Sbjct: 47 FRAFAFVTFADDKVAQSLCGEDLIIKGISV 76
>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 = 29.9 bits (68), Expect = 0.032
Identities = 8/30 (26%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 2 HKGYAFIQFSNPHDARSACLGE---DGRTV 28
+ +AF+ F++ A+S C + G +V
Sbjct: 41 FRAFAFVTFADDQIAQSLCGEDLIIKGISV 70
Score = 29.9 bits (68), Expect = 0.032
Identities = 8/30 (26%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 38 HKGYAFIQFSNPHDARSACLGE---DGRTV 64
+ +AF+ F++ A+S C + G +V
Sbjct: 41 FRAFAFVTFADDQIAQSLCGEDLIIKGISV 70
>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 = 30.3 bits (69), Expect = 0.033
Identities = 10/31 (32%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGY F+ F N D + E G+ L
Sbjct: 50 KGYGFVSFYNDVDVQKIV--ESQINFHGKKL 78
Score = 30.3 bits (69), Expect = 0.033
Identities = 10/31 (32%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KGY F+ F N D + E G+ L
Sbjct: 50 KGYGFVSFYNDVDVQKIV--ESQINFHGKKL 78
>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 = 29.9 bits (68), Expect = 0.036
Identities = 7/30 (23%), Positives = 11/30 (36%), Gaps = 3/30 (10%)
Query: 2 HKGYAFIQFSNPHDARSACLGE---DGRTV 28
KG+ F++F+ DGR
Sbjct: 56 SKGFGFVRFTEYETQVKVMSQRHMIDGRWC 85
Score = 29.9 bits (68), Expect = 0.036
Identities = 7/30 (23%), Positives = 11/30 (36%), Gaps = 3/30 (10%)
Query: 38 HKGYAFIQFSNPHDARSACLGE---DGRTV 64
KG+ F++F+ DGR
Sbjct: 56 SKGFGFVRFTEYETQVKVMSQRHMIDGRWC 85
>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 = 29.9 bits (68), Expect = 0.038
Identities = 9/54 (16%), Positives = 17/54 (31%), Gaps = 10/54 (18%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSAC 56
+ + ++ F + D A L G V G + ++ D C
Sbjct: 58 RKFGYVDFESAEDLEKA-LELTGLKVFGNEI---------KLEKPKGRDGTRGC 101
>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 = 30.2 bits (69), Expect = 0.041
Identities = 11/115 (9%), Positives = 26/115 (22%), Gaps = 52/115 (45%)
Query: 2 HKGYAFIQFSNPHDARSACLGE---DGRTV------------------------------ 28
+G+ F+ F P + DG+ +
Sbjct: 44 SRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKE 103
Query: 29 -------LGQTLGISM--------HKGYAFIQFSNPHDARSACLGE----DGRTV 64
G + + +G+ F+ + + C + R +
Sbjct: 104 FEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKI 158
>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 = 29.9 bits (68), Expect = 0.042
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KGY F ++ + A SA +GR G+ L
Sbjct: 50 KGYGFCEYQDQETALSAMRNLNGREFSGRALR 81
Score = 29.9 bits (68), Expect = 0.045
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGY F ++ + A SA +GR G+ L
Sbjct: 50 KGYGFCEYQDQETALSAMRNLNGREFSGRAL 80
>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 29.8 bits (67), Expect = 0.045
Identities = 7/37 (18%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 2 HKGYAFIQFSNPHDARSA--CLGEDGRTVLGQTLGIS 36
++G+AF+++ + A A L + G + +
Sbjct: 51 NRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD 87
Score = 29.8 bits (67), Expect = 0.048
Identities = 7/35 (20%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 38 HKGYAFIQFSNPHDARSA--CLGEDGRTVLGQTLV 70
++G+AF+++ + A A L + G +
Sbjct: 51 NRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA 85
>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 = 29.7 bits (67), Expect = 0.049
Identities = 10/49 (20%), Positives = 16/49 (32%), Gaps = 11/49 (22%)
Query: 7 FIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSA 55
F + + + GR G AF+QF++ A A
Sbjct: 36 FSGLEIVPNGMTLPVDFQGR-----------STGEAFVQFASQEIAEKA 73
Score = 29.7 bits (67), Expect = 0.053
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 1 MHKGYAFIQFSNPHDARSA 19
G AF+QF++ A A
Sbjct: 55 RSTGEAFVQFASQEIAEKA 73
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
PDB: 2dgq_A
Length = 106
Score = 29.6 bits (67), Expect = 0.054
Identities = 9/29 (31%), Positives = 12/29 (41%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVL 29
MHKG AF+ + A A + L
Sbjct: 53 MHKGCAFLTYCERESALKAQSALHEQKTL 81
Score = 29.6 bits (67), Expect = 0.054
Identities = 9/29 (31%), Positives = 12/29 (41%)
Query: 37 MHKGYAFIQFSNPHDARSACLGEDGRTVL 65
MHKG AF+ + A A + L
Sbjct: 53 MHKGCAFLTYCERESALKAQSALHEQKTL 81
>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 = 29.3 bits (66), Expect = 0.059
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 2 HKGYAFIQFSNPHDARSA 19
G A ++F+ DA +A
Sbjct: 54 VTGEADVEFATHEDAVAA 71
Score = 29.3 bits (66), Expect = 0.059
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 38 HKGYAFIQFSNPHDARSA 55
G A ++F+ DA +A
Sbjct: 54 VTGEADVEFATHEDAVAA 71
>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 = 30.1 bits (67), Expect = 0.062
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 7/50 (14%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHD 51
++ A +Q+++P A+ A L DG+ + ++ I FS
Sbjct: 83 NQFQALLQYADPVSAQHAKLSLDGQNIYNA--CCTLR-----IDFSKLTS 125
Score = 28.1 bits (62), Expect = 0.28
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 27 TVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTV 64
TVL ++ A +Q+++P A+ A L DG+ +
Sbjct: 72 TVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNI 109
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 29.6 bits (66), Expect = 0.062
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 7/50 (14%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHD 51
++ A +Q+++P A+ A L DG+ + ++ I FS
Sbjct: 65 NQFQALLQYADPVSAQHAKLSLDGQNIYNA--CCTLR-----IDFSKLTS 107
Score = 27.7 bits (61), Expect = 0.30
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 27 TVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGR 62
TVL ++ A +Q+++P A+ A L DG+
Sbjct: 54 TVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQ 89
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 29.3 bits (66), Expect = 0.064
Identities = 8/49 (16%), Positives = 17/49 (34%), Gaps = 11/49 (22%)
Query: 2 HKGYAFIQFSNPHDARSA--CLGEDGRTVLGQTLGISMHKGYAFIQFSN 48
K A ++F + A +A ++ + G F+ +S
Sbjct: 56 KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPA---------FVNYST 95
Score = 26.6 bits (59), Expect = 0.57
Identities = 7/43 (16%), Positives = 15/43 (34%), Gaps = 5/43 (11%)
Query: 38 HKGYAFIQFSNPHDARSA--CLGEDGRTVLGQTLVSYKLQYYN 78
K A ++F + A +A ++ + G + Y
Sbjct: 56 KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPA---FVNYST 95
>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 = 29.4 bits (66), Expect = 0.070
Identities = 5/19 (26%), Positives = 9/19 (47%)
Query: 2 HKGYAFIQFSNPHDARSAC 20
+G A I+ + D + A
Sbjct: 54 RRGDALIEMESEQDVQKAL 72
Score = 29.4 bits (66), Expect = 0.070
Identities = 5/19 (26%), Positives = 9/19 (47%)
Query: 38 HKGYAFIQFSNPHDARSAC 56
+G A I+ + D + A
Sbjct: 54 RRGDALIEMESEQDVQKAL 72
>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 = 29.1 bits (66), Expect = 0.078
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSY 72
KGYAFI F++ + +A +G+ + + + VSY
Sbjct: 48 KGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY 82
Score = 28.7 bits (65), Expect = 0.087
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 3 KGYAFIQFSNPHDARSA 19
KGYAFI F++ + +A
Sbjct: 48 KGYAFINFASFDASDAA 64
>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 = 29.2 bits (66), Expect = 0.078
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 3 KGYAFIQFSNPHDARSA 19
KGY F+ F N DA +A
Sbjct: 57 KGYGFVSFFNKWDAENA 73
Score = 29.2 bits (66), Expect = 0.078
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 39 KGYAFIQFSNPHDARSA 55
KGY F+ F N DA +A
Sbjct: 57 KGYGFVSFFNKWDAENA 73
>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 = 29.3 bits (66), Expect = 0.078
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KGYA+I+F+ + +A + D G+T+
Sbjct: 78 KGYAYIEFAERNSVDAA-VAMDETVFRGRTIK 108
Score = 29.3 bits (66), Expect = 0.083
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KGYA+I+F+ + +A + D G+T+
Sbjct: 78 KGYAYIEFAERNSVDAA-VAMDETVFRGRTI 107
>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 = 29.4 bits (66), Expect = 0.079
Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 11/49 (22%)
Query: 7 FIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSA 55
F + D+ G +G+ G F++F N D ++A
Sbjct: 46 FKKLDIVEDSIYIAYGPNGK-----------ATGEGFVEFRNEADYKAA 83
Score = 28.7 bits (64), Expect = 0.12
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 3 KGYAFIQFSNPHDARSA 19
G F++F N D ++A
Sbjct: 67 TGEGFVEFRNEADYKAA 83
>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 = 29.6 bits (66), Expect = 0.080
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 1 MHKGYAFIQFSNPHDARSAC 20
G AF++ + D + A
Sbjct: 86 RQSGEAFVELGSEDDVKMAL 105
Score = 29.6 bits (66), Expect = 0.080
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 37 MHKGYAFIQFSNPHDARSAC 56
G AF++ + D + A
Sbjct: 86 RQSGEAFVELGSEDDVKMAL 105
>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 = 29.2 bits (66), Expect = 0.083
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVL 29
KG AF++FS+ +A++A G +
Sbjct: 55 SKGCAFVKFSSHTEAQAAIHALHGSQTM 82
Score = 29.2 bits (66), Expect = 0.083
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVL 65
KG AF++FS+ +A++A G +
Sbjct: 55 SKGCAFVKFSSHTEAQAAIHALHGSQTM 82
>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 = 29.6 bits (67), Expect = 0.087
Identities = 5/31 (16%), Positives = 12/31 (38%), Gaps = 4/31 (12%)
Query: 2 HKGYAFIQFSNPHDARSACLGE----DGRTV 28
+G+AF+ F + + + +G
Sbjct: 145 KRGFAFVTFDDHDSVDKIVIQKYHTVNGHNC 175
Score = 29.6 bits (67), Expect = 0.087
Identities = 5/31 (16%), Positives = 12/31 (38%), Gaps = 4/31 (12%)
Query: 38 HKGYAFIQFSNPHDARSACLGE----DGRTV 64
+G+AF+ F + + + +G
Sbjct: 145 KRGFAFVTFDDHDSVDKIVIQKYHTVNGHNC 175
Score = 27.3 bits (61), Expect = 0.58
Identities = 7/30 (23%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 3 KGYAFIQFSNPHDARSACLGE----DGRTV 28
+G+ F+ ++ + +A DGR V
Sbjct: 55 RGFGFVTYATVEEVDAAMNARPHKVDGRVV 84
Score = 27.3 bits (61), Expect = 0.58
Identities = 7/30 (23%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 39 KGYAFIQFSNPHDARSACLGE----DGRTV 64
+G+ F+ ++ + +A DGR V
Sbjct: 55 RGFGFVTYATVEEVDAAMNARPHKVDGRVV 84
>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 = 29.1 bits (65), Expect = 0.089
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 1 MHKGYAFIQFSNPHDARSAC 20
G AF++ + D + A
Sbjct: 59 RQSGEAFVELESEDDVKLAL 78
Score = 29.1 bits (65), Expect = 0.089
Identities = 5/20 (25%), Positives = 9/20 (45%)
Query: 37 MHKGYAFIQFSNPHDARSAC 56
G AF++ + D + A
Sbjct: 59 RQSGEAFVELESEDDVKLAL 78
>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 = 28.9 bits (65), Expect = 0.100
Identities = 9/54 (16%), Positives = 18/54 (33%), Gaps = 10/54 (18%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSA 55
+ G ++F +P D A L + M + Y + + +A
Sbjct: 55 NNGNGLVKFLSPQDTFEA-LKRNRML---------MIQRYVEVSPATERQWVAA 98
>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 = 28.8 bits (65), Expect = 0.100
Identities = 9/32 (28%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KG A+++F A +G G+ +LG ++
Sbjct: 67 KGIAYVEFCEIQSVPLA-IGLTGQRLLGVPII 97
Score = 28.8 bits (65), Expect = 0.12
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG A+++F A +G G+ +LG +
Sbjct: 67 KGIAYVEFCEIQSVPLA-IGLTGQRLLGVPI 96
>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 = 28.8 bits (65), Expect = 0.11
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 4/30 (13%)
Query: 3 KGYAFIQFSNPHDARSACLGE----DGRTV 28
+GY F+ ++ A AC DGR
Sbjct: 59 RGYGFVTMADRAAAERACKDPNPIIDGRKA 88
Score = 28.8 bits (65), Expect = 0.11
Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 4/30 (13%)
Query: 39 KGYAFIQFSNPHDARSACLGE----DGRTV 64
+GY F+ ++ A AC DGR
Sbjct: 59 RGYGFVTMADRAAAERACKDPNPIIDGRKA 88
>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 = 28.4 bits (64), Expect = 0.11
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 2 HKGYAFIQFSNPHDARSA 19
GY F+ FSN + + A
Sbjct: 49 KTGYIFVDFSNEEEVKQA 66
Score = 28.4 bits (64), Expect = 0.11
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 38 HKGYAFIQFSNPHDARSA 55
GY F+ FSN + + A
Sbjct: 49 KTGYIFVDFSNEEEVKQA 66
>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 96
Score = 28.5 bits (63), Expect = 0.11
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 3/58 (5%)
Query: 30 GQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL-VSYKLQYYNGCRYVSPT 86
G+ L I+ A ++F N A A + V G + VS+ + C P+
Sbjct: 39 GKVLSIT--GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRELCETSGPS 94
Score = 27.7 bits (61), Expect = 0.27
Identities = 8/37 (21%), Positives = 13/37 (35%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHK 39
A ++F N A A + V G + +S
Sbjct: 46 GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTP 82
>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA
recognition motif, RRM, RNA binding domain, RBD, RNP,
structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 104
Score = 28.8 bits (65), Expect = 0.12
Identities = 6/34 (17%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
KG+ + +F + SA L + ++ + + +
Sbjct: 57 KGFGYAEFEDLDSLLSA-LSLNEESLGNKRIRVD 89
Score = 28.4 bits (64), Expect = 0.16
Identities = 6/31 (19%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+ + +F + SA L + ++ + +
Sbjct: 57 KGFGYAEFEDLDSLLSA-LSLNEESLGNKRI 86
>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 = 28.4 bits (64), Expect = 0.12
Identities = 6/34 (17%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLGIS 36
KG+ + +F + SA L + ++ + + +
Sbjct: 61 KGFGYAEFEDLDSLLSA-LSLNEESLGNRRIRVD 93
Score = 28.4 bits (64), Expect = 0.16
Identities = 6/31 (19%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+ + +F + SA L + ++ + +
Sbjct: 61 KGFGYAEFEDLDSLLSA-LSLNEESLGNRRI 90
>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 = 28.5 bits (64), Expect = 0.15
Identities = 10/38 (26%), Positives = 13/38 (34%), Gaps = 6/38 (15%)
Query: 2 HKGYAFIQFSNPHDARSA------CLGEDGRTVLGQTL 33
KG AF QF A+ G + G+ L
Sbjct: 56 SKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL 93
Score = 28.5 bits (64), Expect = 0.15
Identities = 10/38 (26%), Positives = 13/38 (34%), Gaps = 6/38 (15%)
Query: 38 HKGYAFIQFSNPHDARSA------CLGEDGRTVLGQTL 69
KG AF QF A+ G + G+ L
Sbjct: 56 SKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQL 93
>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif,
G-tract, G-quadruplex, alternative splicing, RNA binding
protein; NMR {Homo sapiens} PDB: 2kg1_A
Length = 139
Score = 28.7 bits (64), Expect = 0.17
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 2 HKGYAFIQFSNPHDARSA 19
G A ++F+ +A +A
Sbjct: 85 VTGEADVEFATHEEAVAA 102
Score = 28.7 bits (64), Expect = 0.17
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 38 HKGYAFIQFSNPHDARSA 55
G A ++F+ +A +A
Sbjct: 85 VTGEADVEFATHEEAVAA 102
>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics,
PSI-biology, northeast structural genom consortium,
NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*
Length = 345
Score = 29.0 bits (64), Expect = 0.18
Identities = 11/56 (19%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACL 57
+K Y+F ++ +++ A + +G+ V+ LG + F++ + R L
Sbjct: 55 NKPYSFARYRTTEESKRAYVTLNGKEVVDD-LGQKITLYLNFVEKVQWKELRPQAL 109
Score = 28.6 bits (63), Expect = 0.26
Identities = 9/38 (23%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGR---TVLGQTLVSY 72
+K Y+F ++ +++ A + +G+ LGQ + Y
Sbjct: 55 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLY 92
>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 = 28.2 bits (63), Expect = 0.19
Identities = 9/49 (18%), Positives = 15/49 (30%), Gaps = 11/49 (22%)
Query: 2 HKGYAFIQFSNPHDARSA--CLGEDGRTVLGQTLGISMHKGYAFIQFSN 48
K A ++F N A+ + + GQ F +S
Sbjct: 50 FKRQALVEFENIDSAKECVTFAADVPVYIAGQQA---------FFNYST 89
Score = 27.1 bits (60), Expect = 0.43
Identities = 10/56 (17%), Positives = 17/56 (30%), Gaps = 5/56 (8%)
Query: 35 ISMHKGYAFIQFSNPHDARSA--CLGEDGRTVLGQTLVSYKLQYYNGCRYVSPTPT 88
+ K A ++F N A+ + + GQ Y R P +
Sbjct: 47 MMPFKRQALVEFENIDSAKECVTFAADVPVYIAGQQA---FFNYSTSKRITRPGNS 99
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 28.3 bits (63), Expect = 0.21
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 2 HKGYAFIQFSNPHDARSA 19
G AF+ F+ A++A
Sbjct: 67 PTGDAFVLFACEEYAQNA 84
Score = 28.3 bits (63), Expect = 0.21
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 38 HKGYAFIQFSNPHDARSA 55
G AF+ F+ A++A
Sbjct: 67 PTGDAFVLFACEEYAQNA 84
>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 = 28.3 bits (63), Expect = 0.23
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 2 HKGYAFIQFSNPHDARSA 19
G AF+QF++ A A
Sbjct: 83 ITGEAFVQFASQELAEKA 100
Score = 28.3 bits (63), Expect = 0.23
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 38 HKGYAFIQFSNPHDARSA 55
G AF+QF++ A A
Sbjct: 83 ITGEAFVQFASQELAEKA 100
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 27.7 bits (62), Expect = 0.24
Identities = 10/43 (23%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQYYNGCRY 82
G A + F +P +A DGR G+ + + ++G
Sbjct: 65 GVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ---AWDGTTD 104
Score = 25.8 bits (57), Expect = 1.5
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 4 GYAFIQFSNPHDARSACLGEDGR 26
G A + F +P +A DGR
Sbjct: 65 GVASVSFRDPEEADYCIQTLDGR 87
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 27.9 bits (62), Expect = 0.24
Identities = 9/43 (20%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQYYNGCRY 82
F++F A A + +GR G+ + + +YN ++
Sbjct: 57 VRIFLEFERVESAIKAVVDLNGRYFGGRVVKAC---FYNLDKF 96
Score = 25.9 bits (57), Expect = 1.4
Identities = 7/30 (23%), Positives = 13/30 (43%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
F++F A A + +GR G+ +
Sbjct: 57 VRIFLEFERVESAIKAVVDLNGRYFGGRVV 86
>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 = 27.5 bits (62), Expect = 0.25
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
KG+A+I+FS+ R++ L D G+ +
Sbjct: 48 KGFAYIEFSDKESVRTS-LALDESLFRGRQIK 78
Score = 27.1 bits (61), Expect = 0.32
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG+A+I+FS+ R++ L D G+ +
Sbjct: 48 KGFAYIEFSDKESVRTS-LALDESLFRGRQI 77
>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 = 28.2 bits (63), Expect = 0.27
Identities = 6/31 (19%), Positives = 16/31 (51%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
G+ F+++ + DA +A +G + + +
Sbjct: 81 CGFCFVEYYSRADAENAMRYINGTRLDDRII 111
Score = 28.2 bits (63), Expect = 0.27
Identities = 6/31 (19%), Positives = 16/31 (51%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G+ F+++ + DA +A +G + + +
Sbjct: 81 CGFCFVEYYSRADAENAMRYINGTRLDDRII 111
>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 = 27.1 bits (61), Expect = 0.37
Identities = 7/31 (22%), Positives = 12/31 (38%), Gaps = 4/31 (12%)
Query: 2 HKGYAFIQFSNPHDARSACLGE----DGRTV 28
+G+ FI F + + DGR +
Sbjct: 52 SRGFGFILFKDAASVEKVLDQKEHRLDGRVI 82
Score = 27.1 bits (61), Expect = 0.37
Identities = 7/31 (22%), Positives = 12/31 (38%), Gaps = 4/31 (12%)
Query: 38 HKGYAFIQFSNPHDARSACLGE----DGRTV 64
+G+ FI F + + DGR +
Sbjct: 52 SRGFGFILFKDAASVEKVLDQKEHRLDGRVI 82
>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 = 26.7 bits (60), Expect = 0.38
Identities = 4/31 (12%), Positives = 8/31 (25%), Gaps = 4/31 (12%)
Query: 2 HKGYAFIQFSNPHDARSACLGE----DGRTV 28
+G+ FI F + +
Sbjct: 40 RRGFCFITFKEEEPVKKIMEKKYHNVGLSKC 70
Score = 26.7 bits (60), Expect = 0.38
Identities = 4/31 (12%), Positives = 8/31 (25%), Gaps = 4/31 (12%)
Query: 38 HKGYAFIQFSNPHDARSACLGE----DGRTV 64
+G+ FI F + +
Sbjct: 40 RRGFCFITFKEEEPVKKIMEKKYHNVGLSKC 70
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 27.2 bits (61), Expect = 0.38
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 3 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
KG+ +++F + A L DG + ++L
Sbjct: 56 KGFCYVEFDEVDSLKEA-LTYDGALLGDRSL 85
Score = 27.2 bits (61), Expect = 0.38
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
KG+ +++F + A L DG + ++L
Sbjct: 56 KGFCYVEFDEVDSLKEA-LTYDGALLGDRSL 85
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 26.7 bits (60), Expect = 0.40
Identities = 5/31 (16%), Positives = 11/31 (35%), Gaps = 4/31 (12%)
Query: 2 HKGYAFIQFSNPHDARSACLGE----DGRTV 28
+G+ F+ F + D +T+
Sbjct: 41 SRGFGFVTFMDQAGVDKVLAQSRHELDSKTI 71
Score = 26.7 bits (60), Expect = 0.40
Identities = 5/31 (16%), Positives = 11/31 (35%), Gaps = 4/31 (12%)
Query: 38 HKGYAFIQFSNPHDARSACLGE----DGRTV 64
+G+ F+ F + D +T+
Sbjct: 41 SRGFGFVTFMDQAGVDKVLAQSRHELDSKTI 71
>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 = 26.8 bits (60), Expect = 0.53
Identities = 5/31 (16%), Positives = 11/31 (35%), Gaps = 4/31 (12%)
Query: 2 HKGYAFIQFSNPHDARSACLGE----DGRTV 28
+G+ F+ F + D +T+
Sbjct: 66 SRGFGFVTFMDQAGVDKVLAQSRHELDSKTI 96
Score = 26.8 bits (60), Expect = 0.53
Identities = 5/31 (16%), Positives = 11/31 (35%), Gaps = 4/31 (12%)
Query: 38 HKGYAFIQFSNPHDARSACLGE----DGRTV 64
+G+ F+ F + D +T+
Sbjct: 66 SRGFGFVTFMDQAGVDKVLAQSRHELDSKTI 96
>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 = 26.8 bits (60), Expect = 0.57
Identities = 7/31 (22%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 2 HKGYAFIQFSNPHDARSACLGE----DGRTV 28
+G+ F++F +P+ + DGR +
Sbjct: 57 SRGFGFVKFKDPNCVGTVLASRPHTLDGRNI 87
Score = 26.8 bits (60), Expect = 0.57
Identities = 7/31 (22%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 38 HKGYAFIQFSNPHDARSACLGE----DGRTV 64
+G+ F++F +P+ + DGR +
Sbjct: 57 SRGFGFVKFKDPNCVGTVLASRPHTLDGRNI 87
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 27.1 bits (59), Expect = 0.67
Identities = 7/39 (17%), Positives = 14/39 (35%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKG 40
K F++F +A A +T+L + +
Sbjct: 178 SKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRR 216
Score = 26.7 bits (58), Expect = 1.0
Identities = 7/35 (20%), Positives = 13/35 (37%)
Query: 35 ISMHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
K F++F +A A +T+L +
Sbjct: 175 YVESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSD 209
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 25.9 bits (58), Expect = 0.87
Identities = 6/31 (19%), Positives = 12/31 (38%), Gaps = 4/31 (12%)
Query: 2 HKGYAFIQFSNPHDARSACLGE----DGRTV 28
H+G+ F+ F + C + + V
Sbjct: 40 HRGFGFVTFESEDIVEKVCEIHFHEINNKMV 70
Score = 25.9 bits (58), Expect = 0.87
Identities = 6/31 (19%), Positives = 12/31 (38%), Gaps = 4/31 (12%)
Query: 38 HKGYAFIQFSNPHDARSACLGE----DGRTV 64
H+G+ F+ F + C + + V
Sbjct: 40 HRGFGFVTFESEDIVEKVCEIHFHEINNKMV 70
>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 = 26.5 bits (59), Expect = 0.96
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 4/30 (13%)
Query: 3 KGYAFIQFSNPHDARSACLGE----DGRTV 28
+G+ F+ FS+ + +A DGR V
Sbjct: 69 RGFGFVTFSSMAEVDAAMAARPHSIDGRVV 98
Score = 26.5 bits (59), Expect = 0.96
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 4/30 (13%)
Query: 39 KGYAFIQFSNPHDARSACLGE----DGRTV 64
+G+ F+ FS+ + +A DGR V
Sbjct: 69 RGFGFVTFSSMAEVDAAMAARPHSIDGRVV 98
>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 = 26.3 bits (58), Expect = 0.96
Identities = 5/33 (15%), Positives = 7/33 (21%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
G ++F D A D
Sbjct: 48 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEG 80
Score = 26.3 bits (58), Expect = 0.96
Identities = 5/33 (15%), Positives = 7/33 (21%)
Query: 37 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G ++F D A D
Sbjct: 48 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEG 80
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding
protein, RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 25.9 bits (57), Expect = 1.1
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQYYNGCRY 82
G F++F++ D + A G GR + +V+ Y + Y
Sbjct: 58 GCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTK---YCDPDSY 99
Score = 25.5 bits (56), Expect = 1.8
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGR 26
G F++F++ D + A G GR
Sbjct: 58 GCGKIFVEFTSVFDCQKAMQGLTGR 82
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 25.6 bits (56), Expect = 1.6
Identities = 4/34 (11%), Positives = 10/34 (29%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTLGI 35
G ++F + A + G + +
Sbjct: 66 FDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99
Score = 25.6 bits (56), Expect = 1.8
Identities = 4/32 (12%), Positives = 9/32 (28%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G ++F + A + G +
Sbjct: 66 FDGTGALEFPSEEILVEALERLNNIEFRGSVI 97
>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 = 25.6 bits (56), Expect = 1.7
Identities = 5/33 (15%), Positives = 7/33 (21%)
Query: 1 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
G ++F D A D
Sbjct: 49 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEG 81
Score = 25.6 bits (56), Expect = 1.7
Identities = 5/33 (15%), Positives = 7/33 (21%)
Query: 37 MHKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
G ++F D A D
Sbjct: 49 YRDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEG 81
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 25.5 bits (56), Expect = 1.9
Identities = 10/43 (23%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQYYNGCRY 82
F++FS + A +GR G+ +V+ Y+ R+
Sbjct: 72 VKIFVEFSIASETHKAIQALNGRWFAGRKVVAE---VYDQERF 111
Score = 24.3 bits (53), Expect = 5.4
Identities = 7/30 (23%), Positives = 13/30 (43%)
Query: 4 GYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
F++FS + A +GR G+ +
Sbjct: 72 VKIFVEFSIASETHKAIQALNGRWFAGRKV 101
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics,
joint center for struc genomics, JCSG, protein
structure initiative, PSI-biology; HET: MSE CIT; 0.95A
{Mus musculus} PDB: 2lq5_A
Length = 114
Score = 25.4 bits (56), Expect = 2.1
Identities = 8/43 (18%), Positives = 16/43 (37%), Gaps = 3/43 (6%)
Query: 40 GYAFIQFSNPHDARSACLGEDGRTVLGQTLVSYKLQYYNGCRY 82
G +++ + A +A GR G+ + + Y Y
Sbjct: 56 GNVYVKCPSIAAAIAAVNALHGRWFAGKMITA---AYVPLPTY 95
Score = 24.6 bits (54), Expect = 3.4
Identities = 5/23 (21%), Positives = 10/23 (43%)
Query: 4 GYAFIQFSNPHDARSACLGEDGR 26
G +++ + A +A GR
Sbjct: 56 GNVYVKCPSIAAAIAAVNALHGR 78
>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 = 24.5 bits (54), Expect = 3.8
Identities = 7/31 (22%), Positives = 11/31 (35%), Gaps = 4/31 (12%)
Query: 2 HKGYAFIQFSNPHDARSACLGE----DGRTV 28
+G+ FI F + A G+ V
Sbjct: 51 PRGFGFITFEDEQSVDQAVNMHFHDIMGKKV 81
Score = 24.5 bits (54), Expect = 3.8
Identities = 7/31 (22%), Positives = 11/31 (35%), Gaps = 4/31 (12%)
Query: 38 HKGYAFIQFSNPHDARSACLGE----DGRTV 64
+G+ FI F + A G+ V
Sbjct: 51 PRGFGFITFEDEQSVDQAVNMHFHDIMGKKV 81
>3pdu_A 3-hydroxyisobutyrate dehydrogenase family protein;
gamma-hydroxybutyrate dehydrogenase, succinic
semialdehyde R glyoxylate metabolism; HET: NAP; 1.89A
{Geobacter sulfurreducens}
Length = 287
Score = 24.8 bits (55), Expect = 5.0
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 9/45 (20%)
Query: 11 SNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFS--NPHDAR 53
++P AR C G +G VL + G +I S + +
Sbjct: 66 ADPAAAREVCFGANG--VLE-----GIGGGRGYIDMSTVDDETST 103
Score = 24.4 bits (54), Expect = 5.1
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 47 SNPHDARSACLGEDG 61
++P AR C G +G
Sbjct: 66 ADPAAAREVCFGANG 80
>3doj_A AT3G25530, dehydrogenase-like protein; gamma-hydroxybutyrate
dehydrogenase, 4-hydroxybutyrate dehydrogenase; 2.10A
{Arabidopsis thaliana}
Length = 310
Score = 24.5 bits (54), Expect = 5.1
Identities = 5/15 (33%), Positives = 7/15 (46%)
Query: 11 SNPHDARSACLGEDG 25
S+P A S + G
Sbjct: 86 SDPCAALSVVFDKGG 100
Score = 24.5 bits (54), Expect = 5.1
Identities = 5/15 (33%), Positives = 7/15 (46%)
Query: 47 SNPHDARSACLGEDG 61
S+P A S + G
Sbjct: 86 SDPCAALSVVFDKGG 100
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 24.1 bits (52), Expect = 5.4
Identities = 8/32 (25%), Positives = 14/32 (43%)
Query: 39 KGYAFIQFSNPHDARSACLGEDGRTVLGQTLV 70
G +++F DA A + + R GQ +
Sbjct: 68 VGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99
>2uyy_A N-PAC protein; long-chain dehydrogenase, cytokine; HET: NA7; 2.5A
{Homo sapiens}
Length = 316
Score = 24.5 bits (54), Expect = 5.6
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 11 SNPHDARSACLGEDG 25
S+P A+ LG G
Sbjct: 95 SDPKAAKDLVLGPSG 109
Score = 24.5 bits (54), Expect = 5.6
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 47 SNPHDARSACLGEDG 61
S+P A+ LG G
Sbjct: 95 SDPKAAKDLVLGPSG 109
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 23.8 bits (52), Expect = 6.0
Identities = 7/32 (21%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 2 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 33
+A ++ + AR A L + ++ G L
Sbjct: 44 KGVFAIVEMGD-VGAREAVLSQSQHSLGGHRL 74
Score = 23.8 bits (52), Expect = 6.0
Identities = 7/32 (21%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 38 HKGYAFIQFSNPHDARSACLGEDGRTVLGQTL 69
+A ++ + AR A L + ++ G L
Sbjct: 44 KGVFAIVEMGD-VGAREAVLSQSQHSLGGHRL 74
>3uw2_A Phosphoglucomutase/phosphomannomutase family PROT; structural
genomics, seattle structural genomics center for
infectious disease; 1.95A {Burkholderia thailandensis}
Length = 485
Score = 24.2 bits (53), Expect = 7.0
Identities = 6/23 (26%), Positives = 8/23 (34%)
Query: 4 GYAFIQFSNPHDARSACLGEDGR 26
G AF + + DGR
Sbjct: 50 GRAFGSEVRAQGGDAVVVARDGR 72
Score = 24.2 bits (53), Expect = 7.0
Identities = 6/23 (26%), Positives = 8/23 (34%)
Query: 40 GYAFIQFSNPHDARSACLGEDGR 62
G AF + + DGR
Sbjct: 50 GRAFGSEVRAQGGDAVVVARDGR 72
>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 = 24.2 bits (52), Expect = 7.3
Identities = 17/89 (19%), Positives = 27/89 (30%), Gaps = 21/89 (23%)
Query: 6 AFIQFSNPHDARSACLGEDGRTVLGQTLGISMHKGYAFIQFSNPHDARSACLGEDGRTVL 65
I+FS + D V Q L I +++ NP + +D L
Sbjct: 186 DLIKFSAETLSELIRTTLDAEKVFTQGLNI-----LEWLE--NPSNTPD----KD---YL 231
Query: 66 GQTLVSYKL-------QYYNGCRYVSPTP 87
+S L Y + + TP
Sbjct: 232 LSIPISCPLIGVIQLAHYVVTAKLLGFTP 260
>3pef_A 6-phosphogluconate dehydrogenase, NAD-binding;
gamma-hydroxybutyrate dehydrogenase, succinic
semialdehyde R geobacter metallireducens; HET: NAP;
2.07A {Geobacter metallireducens}
Length = 287
Score = 24.0 bits (53), Expect = 7.4
Identities = 5/15 (33%), Positives = 8/15 (53%)
Query: 11 SNPHDARSACLGEDG 25
++P A C G+ G
Sbjct: 66 ADPAAAEEVCFGKHG 80
Score = 24.0 bits (53), Expect = 7.4
Identities = 5/15 (33%), Positives = 8/15 (53%)
Query: 47 SNPHDARSACLGEDG 61
++P A C G+ G
Sbjct: 66 ADPAAAEEVCFGKHG 80
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.321 0.137 0.427
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: 1,352,072
Number of extensions: 66345
Number of successful extensions: 502
Number of sequences better than 10.0: 1
Number of HSP's gapped: 497
Number of HSP's successfully gapped: 392
Length of query: 89
Length of database: 6,701,793
Length adjustment: 57
Effective length of query: 32
Effective length of database: 5,110,296
Effective search space: 163529472
Effective search space used: 163529472
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.4 bits)