RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3067
(141 letters)
>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 = 80.2 bits (198), Expect = 1e-20
Identities = 18/60 (30%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIF 97
K D+ QF +G+ + N + ++ D NG+ G+A VQF +++ A + + H++++ R F
Sbjct: 29 KMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAF 87
>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 = 77.9 bits (192), Expect = 6e-20
Identities = 39/60 (65%), Positives = 46/60 (76%), Gaps = 1/60 (1%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
K++I QFF GLEI+ NG+TL D GR TGEA+VQF +E AE AL+KHKERIGHRYI
Sbjct: 28 SKEEIVQFFSGLEIVPNGMTLPVDF-QGRSTGEAFVQFASQEIAEKALKKHKERIGHRYI 86
Score = 25.1 bits (55), Expect = 5.3
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 11 DRYIEVFKVRRQEM 24
RYIE+FK R E+
Sbjct: 83 HRYIEIFKSSRAEV 96
>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 = 78.0 bits (192), Expect = 1e-19
Identities = 20/61 (32%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+ + FF L+I+ + I + P NG+ TGE +V+F ++ + AL +HK+ +G+R+I
Sbjct: 38 ENKHVIDFFKKLDIVEDSIYIAYGP-NGKATGEGFVEFRNEADYKAALCRHKQYMGNRFI 96
Query: 97 F 97
Sbjct: 97 Q 97
Score = 25.2 bits (55), Expect = 7.0
Identities = 5/22 (22%), Positives = 12/22 (54%)
Query: 11 DRYIEVFKVRRQEMDWKLQHTG 32
+R+I+V + ++ M K+
Sbjct: 93 NRFIQVHPITKKGMLEKIDMIR 114
>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 = 76.1 bits (187), Expect = 5e-19
Identities = 40/60 (66%), Positives = 46/60 (76%), Gaps = 1/60 (1%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
K++I QFF GLEI+ NGITL DP G+ TGEA+VQF +E AE AL KHKERIGHRYI
Sbjct: 55 TKEEIVQFFSGLEIVPNGITLPVDP-EGKITGEAFVQFASQELAEKALGKHKERIGHRYI 113
Score = 24.8 bits (54), Expect = 8.6
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 11 DRYIEVFKVRRQEM 24
RYIEVFK ++E+
Sbjct: 110 HRYIEVFKSSQEEV 123
>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 = 74.4 bits (183), Expect = 1e-18
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
++D+ FF GL + + + L++D GR G V+F+ + AL++++ + RY+
Sbjct: 29 MENDVRDFFHGLRV--DAVHLLKDH-VGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYV 85
>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 = 73.5 bits (181), Expect = 2e-18
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRY 95
D+I FF G ++I + L + G PTGEA V F ++ A A+ + IG R
Sbjct: 28 SIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRK 86
Query: 96 I 96
+
Sbjct: 87 V 87
>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 = 73.1 bits (180), Expect = 3e-18
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRY 95
D+I FF G ++I + L + G PTGEA V F ++ A A+ + IG R
Sbjct: 28 SIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRK 86
Query: 96 I 96
+
Sbjct: 87 V 87
>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 = 73.2 bits (180), Expect = 3e-18
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
++DI FF L + + + P +GR TGEA V+F E A A+ K K + HRY+
Sbjct: 28 TENDIYNFFSPLNPMR--VHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYV 84
>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 = 72.7 bits (179), Expect = 4e-18
Identities = 17/61 (27%), Positives = 35/61 (57%), Gaps = 3/61 (4%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+ ++ +F L+ ++ I +V + +G TG +V F ++E + AL+ ++E +G RYI
Sbjct: 23 TEKNVMEFLAPLKPVA--IRIVRNA-HGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYI 79
Query: 97 F 97
Sbjct: 80 E 80
>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 = 69.5 bits (170), Expect = 3e-16
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
++DI FF L + + + P +GR TGEA V+F E A A+ K + + HRYI
Sbjct: 59 TENDIYNFFSPLNPVR--VHIEIGP-DGRVTGEADVEFATHEEAVAAMSKDRANMQHRYI 115
Score = 25.2 bits (55), Expect = 6.3
Identities = 5/50 (10%), Positives = 12/50 (24%), Gaps = 1/50 (2%)
Query: 82 LALQKHKERIGHRYIFFTGHRYTVQHRAPRCETSIPVSSSTHKPGRHHTL 131
+ H + H ++ + S T + H +
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMASMT-GGQQMGRGSGDSEFTVQSTTGHCV 49
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens}
Length = 123
Score = 68.8 bits (168), Expect = 4e-16
Identities = 26/63 (41%), Positives = 38/63 (60%), Gaps = 4/63 (6%)
Query: 37 KKDDIAQFFDGLEIISN---GITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGH 93
+++ FF I+ GI V P +GRPTG+A+V F +E A+ AL+KHK+ +G
Sbjct: 36 TAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRKHKDLLGK 94
Query: 94 RYI 96
RYI
Sbjct: 95 RYI 97
Score = 29.9 bits (67), Expect = 0.14
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 11 DRYIEVFKVRRQEMDWKLQHTGIVEG 36
RYIE+F+ E+ L G
Sbjct: 94 KRYIELFRSTAAEVQQVLNRFSSASG 119
>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 = 68.0 bits (166), Expect = 4e-16
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 37 KKDDIAQFFDGLEIIS--NGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHR 94
+D+ FF I + NGI + + +G+ G+A ++ ++ + AL+KH+ +G R
Sbjct: 24 TMEDVLNFFSDCRIRNGENGIHFLLNR-DGKRRGDALIEMESEQDVQKALEKHRMYMGQR 82
Query: 95 YI 96
Y+
Sbjct: 83 YV 84
Score = 31.0 bits (70), Expect = 0.045
Identities = 5/23 (21%), Positives = 15/23 (65%)
Query: 11 DRYIEVFKVRRQEMDWKLQHTGI 33
RY+EV+++ +++D ++ +
Sbjct: 81 QRYVEVYEINNEDVDALMKSLQV 103
>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 = 66.9 bits (163), Expect = 2e-15
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 37 KKDDIAQFFDGLEIIS--NGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHR 94
+D+ F I G+ + GR +GEA+V+ ++ +LAL+K +E +GHR
Sbjct: 30 SIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLALKKDRESMGHR 88
Query: 95 YI 96
YI
Sbjct: 89 YI 90
Score = 31.8 bits (72), Expect = 0.026
Identities = 15/22 (68%), Positives = 17/22 (77%)
Query: 11 DRYIEVFKVRRQEMDWKLQHTG 32
RYIEVFK R EMDW L+H+G
Sbjct: 87 HRYIEVFKSHRTEMDWVLKHSG 108
>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 = 66.6 bits (162), Expect = 3e-15
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 37 KKDDIAQFFDGLEIISN--GITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHR 94
+D+ F I G+ + GR +GEA+V+ ++ ++AL+K +E +GHR
Sbjct: 57 SVEDVQNFLSDCTIHDGAAGVHFIYTR-EGRQSGEAFVELGSEDDVKMALKKDRESMGHR 115
Query: 95 YI 96
YI
Sbjct: 116 YI 117
Score = 33.1 bits (75), Expect = 0.013
Identities = 15/22 (68%), Positives = 17/22 (77%)
Query: 11 DRYIEVFKVRRQEMDWKLQHTG 32
RYIEVFK R EMDW L+H+G
Sbjct: 114 HRYIEVFKSHRTEMDWVLKHSG 135
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 45.0 bits (107), Expect = 3e-07
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
DI F L I S + LV D + G YV+F + ++ + AL +G R +
Sbjct: 30 GDIDAIFKDLSIRS--VRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSL 85
>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 = 42.6 bits (101), Expect = 2e-06
Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFN-GRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+ I +FF GL I + + L +P N R G Y +F D ++ AL ++E +G+R I
Sbjct: 34 ESIKEFFRGLNISA--VRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRI 90
>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 = 42.2 bits (100), Expect = 3e-06
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFN-GRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+ I +FF GL I + + L +P N R G Y +F D ++ AL ++E +G++ I
Sbjct: 30 ESIKEFFRGLNISA--VRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRI 86
>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 = 41.2 bits (97), Expect = 1e-05
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 39 DDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
D+ FF + ++ + ++ D + R G AYV+F + ++ LA+ +R+ I
Sbjct: 40 RDLEDFFSAVGKVRD--VRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPI 96
>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 = 39.0 bits (92), Expect = 4e-05
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+++ F G ++ +T++ D F+G P G AY++F DKE+ +L
Sbjct: 21 EELEAHFHGCGSVNR-VTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
>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 = 38.8 bits (91), Expect = 5e-05
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 38 KDDIAQFF-------DGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+ +A +F + I L D G+ GEA V F D +A+ A+
Sbjct: 27 IESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAID 81
>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 = 39.3 bits (92), Expect = 5e-05
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 39 DDIAQFFDGLEIISNG-------ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
DD+A FF ++ I + D G+P G+A V + D TA+ A++
Sbjct: 30 DDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVE 83
>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 = 38.9 bits (91), Expect = 8e-05
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
D+ F I+ IT++ D F+G P G AY++F ++ + + A+ + R I
Sbjct: 50 AQDLEAHFSSCGSINR-ITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTI 107
>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 = 38.1 bits (89), Expect = 1e-04
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 4/50 (8%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+ I++ F G ++S + ++ + G P G +V+F D TAE L K
Sbjct: 24 NFISRAFATMGETVMS--VKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 36.6 bits (85), Expect = 5e-04
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 38 KDDIAQFFDGLEIISNG-------ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+ +A +F + II I L D G+ GEA V F D +A+ A+
Sbjct: 21 IESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAID 75
>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 = 37.7 bits (88), Expect = 5e-04
Identities = 9/62 (14%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 38 KDDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRY 95
+ + + LV G+ G + +++ K++A A + +G R
Sbjct: 109 QQQFEELVRPFGSLER--CFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRT 166
Query: 96 IF 97
++
Sbjct: 167 LY 168
Score = 30.3 bits (69), Expect = 0.16
Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 8/48 (16%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
++ E+ F + G A+V ++ E AE A+
Sbjct: 37 QEVHDLLSDYELKY--------CFVDKYKGTAFVTLLNGEQAEAAINA 76
Score = 29.2 bits (66), Expect = 0.36
Identities = 9/35 (25%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 63 NGRPTGEAYVQFVDKETAELALQK-HKERIGHRYI 96
+G+ G A +++ E AE A Q+ +G ++
Sbjct: 222 DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHL 256
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 37.1 bits (85), Expect = 0.001
Identities = 22/109 (20%), Positives = 37/109 (33%), Gaps = 12/109 (11%)
Query: 3 HCRTGEVSDRYIEVFKVRRQEMDW---KLQHTGIVEGKKDDIAQFFDGLEIISNGITLVE 59
H + E +R +F++ + + K++H I L+ I
Sbjct: 480 HLKNIEHPERM-TLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYIC-DN 537
Query: 60 DPFNGRPTGEAYVQFVDKETAELALQKHKE--RIG----HRYIFFTGHR 102
DP R A + F+ K L K+ + RI IF H+
Sbjct: 538 DPKYERLV-NAILDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHK 585
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 35.4 bits (82), Expect = 0.002
Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 11/95 (11%)
Query: 39 DDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRYI 96
D I Q F I S I + D + G A+V++ E A+LAL++ + +G R I
Sbjct: 43 DTIRQAFAPFGPIKS--IDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNI 100
Query: 97 FFTGHRYTVQHRAPRCETSIPVSSSTHKPGRHHTL 131
V + + + + + +
Sbjct: 101 K-------VGRPSNIGQAQPIIDQLAEEARAFNRI 128
Score = 29.6 bits (67), Expect = 0.26
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
DDI F+ G +I S TL DP G+ G ++++ ++++ A+
Sbjct: 140 DDIKSVFEAFG-KIKS--ATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186
>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 = 35.5 bits (81), Expect = 0.002
Identities = 15/103 (14%), Positives = 33/103 (32%), Gaps = 11/103 (10%)
Query: 39 DDIAQFFD---GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRY 95
+D+ + +I+ I E+ NG+ G A V + +++ + +R
Sbjct: 83 EDLTEAVHSLGVNDILE--IKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKR----- 135
Query: 96 IFFTGHRYTVQHRAPRCETSIPVSSSTHKPGRHHTLDGPNGGG 138
G V + + + S + +G G
Sbjct: 136 -ELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPP 177
>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 = 33.7 bits (78), Expect = 0.003
Identities = 12/48 (25%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 39 DDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+ I + +I+ + ++ DP GR G A+++F D E++ A++
Sbjct: 17 EQILDLCSNVGPVIN--LKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 33.4 bits (77), Expect = 0.005
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 3/49 (6%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
D I ++N I L++D + G A+VQ A LQ
Sbjct: 24 DSIMTALSPYASLAVNN-IRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
>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 = 34.6 bits (80), Expect = 0.005
Identities = 12/99 (12%), Positives = 28/99 (28%), Gaps = 6/99 (6%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGE----AYVQFVDKETAELALQKHKERIGHR 94
+ + FF+ + +P + A+++F + A+ +
Sbjct: 19 EAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQ 78
Query: 95 YIF--FTGHRYTVQHRAPRCETSIPVSSSTHKPGRHHTL 131
+ + + +P ST P H L
Sbjct: 79 SLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKL 117
Score = 32.3 bits (74), Expect = 0.033
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 57 LVEDPFNGRPTGEAYVQFVDKETAELALQK 86
LV+D G G A+ ++VD + A+
Sbjct: 146 LVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
>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 = 33.2 bits (76), Expect = 0.006
Identities = 6/51 (11%), Positives = 17/51 (33%), Gaps = 4/51 (7%)
Query: 39 DDIAQFFDGLEIISNGITLVEDP----FNGRPTGEAYVQFVDKETAELALQ 85
+ + FF+ + +P + A+++F + A+
Sbjct: 21 EAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA 71
>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 = 33.1 bits (76), Expect = 0.008
Identities = 12/55 (21%), Positives = 19/55 (34%)
Query: 57 LVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTVQHRAPR 111
+V P G A+ QF+ +E A+ L + G + V R
Sbjct: 47 VVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTR 101
>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 = 33.0 bits (76), Expect = 0.009
Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 2/58 (3%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
++ L ++ V D G YV F E E AL+ ++ I
Sbjct: 32 AELKVAISELFAKNDLA--VVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEI 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 = 32.2 bits (74), Expect = 0.013
Identities = 11/49 (22%), Positives = 29/49 (59%), Gaps = 5/49 (10%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+D+ + F G +++ +T+++D + G A++ F+DK++A+ +
Sbjct: 31 NDLYRIFSKYG-KVVK--VTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 32.2 bits (74), Expect = 0.014
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+DI F G EI + I L D G G V++ + A+ A++
Sbjct: 38 EDIHDKFAEYG-EIKN--IHLNLDRRTGYLKGYTLVEYETYKEAQAAME 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 = 32.6 bits (74), Expect = 0.018
Identities = 8/51 (15%), Positives = 18/51 (35%), Gaps = 5/51 (9%)
Query: 39 DDIAQFFD---GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+ Q +++ + E+ NG+ G A V + + L+
Sbjct: 70 QQLIQVIRSIGVYDVVE--LKFAENRANGQSKGYAEVVVASENSVHKLLEL 118
>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 = 31.9 bits (73), Expect = 0.021
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
D+I + F G EI + I L D G G A V++ + A A +
Sbjct: 41 DEIQEKFCDYG-EIKN--IHLNLDRRTGFSKGYALVEYETHKQALAAKE 86
>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 = 32.1 bits (73), Expect = 0.026
Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 2/59 (3%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRYI 96
+ I + F I I + D G +V++ + AE A++ + R+ R I
Sbjct: 54 EQIYELFSKSGDIKK-IIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRII 111
>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 = 32.4 bits (73), Expect = 0.028
Identities = 5/48 (10%), Positives = 15/48 (31%), Gaps = 1/48 (2%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
++ + D L + ++ + +++ K A L
Sbjct: 138 ENFFEICDELGVKRP-TSVKVFSGKSERSSSGLLEWDSKSDALETLGF 184
Score = 26.2 bits (57), Expect = 3.4
Identities = 8/72 (11%), Positives = 19/72 (26%), Gaps = 2/72 (2%)
Query: 67 TGEAYVQFVDKETAELALQK-HKERIGHRYIFFTGHRYT-VQHRAPRCETSIPVSSSTHK 124
G A V+ D + A+ + + + + + + S
Sbjct: 42 PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFS 101
Query: 125 PGRHHTLDGPNG 136
R++ P
Sbjct: 102 ESRNNRFSTPEQ 113
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 31.2 bits (71), Expect = 0.030
Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 9/75 (12%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFF 98
DDI ++ + + N I + + G +V F E+A+ ++ ++ +
Sbjct: 26 DDIKEWLEDKGQVLN-IQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQK-------Y 76
Query: 99 TGHRYTVQHRAPRCE 113
+ +
Sbjct: 77 KETDLLILFKDDYFA 91
>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 = 31.4 bits (72), Expect = 0.032
Identities = 9/31 (29%), Positives = 13/31 (41%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+ D +P G A+V F+ E A A
Sbjct: 38 LHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 31.5 bits (71), Expect = 0.034
Identities = 8/47 (17%), Positives = 17/47 (36%), Gaps = 4/47 (8%)
Query: 61 PFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTVQH 107
F +A +Q+ D +A+ A K + + I+ +
Sbjct: 60 TFTKNNQFQALLQYADPVSAQHA----KLSLDGQNIYNACCTLRIDF 102
>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 = 31.1 bits (71), Expect = 0.037
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
D + F+ G I S I L+ D GR G ++ F D E A+ AL++
Sbjct: 41 DMLRGIFEPFG-RIES--IQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA
binding domain, RBD, RNP, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 95
Score = 31.0 bits (71), Expect = 0.040
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
D + F+ G +I + I L++D GR G ++ F D E A AL+
Sbjct: 20 DMLRGIFEPFG-KIDN--IVLMKDSDTGRSKGYGFITFSDSECARRALE 65
>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 = 31.7 bits (72), Expect = 0.042
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
D+I + F I N I L D G G A V++ + A A +
Sbjct: 87 DEIQEKFCDYGEIKN-IHLNLDRRTGFSKGYALVEYETHKQALAAKE 132
>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 = 30.6 bits (70), Expect = 0.047
Identities = 8/36 (22%), Positives = 17/36 (47%)
Query: 51 ISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
I ++ DP G G A++ F + ++ A++
Sbjct: 32 ILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
>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 = 31.4 bits (72), Expect = 0.051
Identities = 12/59 (20%), Positives = 19/59 (32%), Gaps = 2/59 (3%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIF 97
++ L ++ V D G YV F E E AL+ ++ I
Sbjct: 28 AELKVAISELFAKND--LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIK 84
Score = 29.5 bits (67), Expect = 0.28
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 56 TLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+ +G+ G AY++F + AE L++
Sbjct: 125 EIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 155
>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 = 31.4 bits (72), Expect = 0.055
Identities = 9/33 (27%), Positives = 15/33 (45%)
Query: 54 GITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
LV+D G G A+ ++VD + A+
Sbjct: 123 AFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Score = 29.9 bits (68), Expect = 0.16
Identities = 6/62 (9%), Positives = 17/62 (27%), Gaps = 4/62 (6%)
Query: 39 DDIAQFF----DGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHR 94
+ + FF + V + A+++F + A+ +
Sbjct: 19 EAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQ 78
Query: 95 YI 96
+
Sbjct: 79 SL 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 = 31.5 bits (72), Expect = 0.061
Identities = 11/37 (29%), Positives = 21/37 (56%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+ A++ F +K++AE ALQ ++ +G+R I
Sbjct: 247 QKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREI 283
Score = 30.0 bits (68), Expect = 0.20
Identities = 10/60 (16%), Positives = 24/60 (40%), Gaps = 5/60 (8%)
Query: 39 DDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIF 97
+ + ++F II + + + + A ++F + A A+ K + +G I
Sbjct: 56 NKVYKYFKHCGPIIH--VDVADS--LKKNFRFARIEFARYDGALAAITKTHKVVGQNEII 111
>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 = 31.5 bits (72), Expect = 0.063
Identities = 14/37 (37%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 49 EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
I+S I + D R G AYV F AE AL
Sbjct: 41 PILS--IRVCRDMITRRSLGYAYVNFQQPADAERALD 75
>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 = 31.0 bits (71), Expect = 0.075
Identities = 13/60 (21%), Positives = 21/60 (35%), Gaps = 5/60 (8%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+ +FF G II L+ D G+ G +V + + + Q R I
Sbjct: 102 KEFEEFFSQWG-TIID--AQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKI 158
Score = 26.7 bits (60), Expect = 1.9
Identities = 7/30 (23%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELALQK-HK 88
DP GR G ++ F + + ++ H
Sbjct: 38 DPATGRSRGFGFLSFEKPSSVDEVVKTQHI 67
>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 = 30.3 bits (69), Expect = 0.076
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
I L +D G+ G A++ F +E A A+
Sbjct: 45 IYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76
>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 = 31.0 bits (71), Expect = 0.078
Identities = 7/30 (23%), Positives = 14/30 (46%)
Query: 57 LVEDPFNGRPTGEAYVQFVDKETAELALQK 86
++ D G G +V F ++ A+ A+
Sbjct: 119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Score = 27.9 bits (63), Expect = 0.81
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 63 NGRPTGEAYVQFVDKETAELALQK 86
N + A+V++ A +ALQ
Sbjct: 37 NNKNVNYAFVEYHQSHDANIALQT 60
>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 = 30.3 bits (69), Expect = 0.079
Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+ D+ F + G + GR G+A++ F +KE A AL
Sbjct: 38 TERDLVSLFARFQEKK-GPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86
>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 = 30.3 bits (69), Expect = 0.082
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+ + +P P G A+V+F D+ A+ A
Sbjct: 43 VYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
>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 = 29.9 bits (68), Expect = 0.087
Identities = 9/51 (17%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 39 DDIAQFFD---GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+D+ + +I+ I E+ NG+ G A V + +++ +
Sbjct: 16 EDLTEAVHSLGVNDILE--IKFFENRANGQSKGFALVGVGSEASSKKLMDL 64
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 30.5 bits (69), Expect = 0.095
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
I + D + G A+V+F E A A+
Sbjct: 93 IQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
>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 = 30.0 bits (68), Expect = 0.11
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+DI F G EI + I L D G G V++ + A+ A++
Sbjct: 37 EDIHDKFAEYG-EIKN--IHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82
>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 = 30.2 bits (69), Expect = 0.12
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELALQK 86
D GRP G A+V++ +E A+ A+
Sbjct: 124 DKLTGRPRGVAFVRYNKREEAQEAISA 150
Score = 27.5 bits (62), Expect = 1.0
Identities = 12/79 (15%), Positives = 31/79 (39%), Gaps = 11/79 (13%)
Query: 39 DDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRYI 96
++ F + I + ++ D G G A+V F + ++ A++ + + ++ +
Sbjct: 18 RELYALFRAIGPINT--CRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75
Query: 97 FFTGHRYTVQHRAPRCETS 115
V + P E+
Sbjct: 76 K-------VSYARPGGESI 87
>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif,
systemic lupus erythematosus, phosphoprotein, RNA
maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1
PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A
Length = 193
Score = 30.6 bits (68), Expect = 0.13
Identities = 10/58 (17%), Positives = 24/58 (41%), Gaps = 2/58 (3%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
DDI ++ + + N I + + G +V F E+A+ ++ ++ +
Sbjct: 124 DDIKEWLEDKGQVLN-IQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDL 179
>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 = 30.5 bits (68), Expect = 0.13
Identities = 10/54 (18%), Positives = 19/54 (35%), Gaps = 4/54 (7%)
Query: 54 GITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTVQH 107
G L F +A +Q+ D +A+ A K + + I+ +
Sbjct: 71 GTVLKIITFTKNNQFQALLQYADPVSAQHA----KLSLDGQNIYNACCTLRIDF 120
>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 = 29.4 bits (67), Expect = 0.14
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
I + D + G A+V+F E A A+
Sbjct: 37 IQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
>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 = 30.3 bits (69), Expect = 0.15
Identities = 11/60 (18%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+ +F+ G +I I ++ D +G+ G A+V F D ++ + + + +
Sbjct: 119 HHLRDYFEQYG-KIEV--IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNC 175
Score = 30.0 bits (68), Expect = 0.20
Identities = 12/70 (17%), Positives = 25/70 (35%), Gaps = 7/70 (10%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTVQHRAPRCET 114
++ DP R G +V + E + A+ ++ R + + R ++
Sbjct: 43 CVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVV-------EPKRAVSREDS 95
Query: 115 SIPVSSSTHK 124
P + T K
Sbjct: 96 QRPGAHLTVK 105
>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA
splicing, adenine, mRNA processing, nucleus,
phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo
sapiens} PDB: 2f9d_A 2f9j_A 2fho_B
Length = 115
Score = 29.6 bits (67), Expect = 0.16
Identities = 9/57 (15%), Positives = 15/57 (26%), Gaps = 6/57 (10%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTVQHRAPR 111
I + G AYV + D A+ A+ + V +
Sbjct: 35 IRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFN------VSNRYLVVLYYNAN 85
>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 = 29.2 bits (66), Expect = 0.17
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 5/48 (10%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+ + + F+ V NG+ G A+++F E A+ AL
Sbjct: 30 ETLQEVFE-----KATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNS 72
>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 = 29.1 bits (66), Expect = 0.19
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 39 DDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+ + F + ++S LV D G+P G + ++ D+ETA A++
Sbjct: 23 EQLKDIFSEVGPVVS--FRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 30.0 bits (68), Expect = 0.21
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 63 NGRPTGEAYVQFVDKETAELALQK 86
GR TG+ +V+F K A AL++
Sbjct: 133 RGRATGKGFVEFAAKPPARKALER 156
>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 = 28.7 bits (65), Expect = 0.27
Identities = 9/32 (28%), Positives = 19/32 (59%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+++V D + R G A+V F + + A+ A ++
Sbjct: 45 VSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
>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 = 29.4 bits (66), Expect = 0.28
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
D + + F+ + + + + D + G A+V+F DK AE A+
Sbjct: 85 DTLRRVFEKYGRVGD-VYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex,
AU-rich element, transcription/RNA complex; 1.80A {Homo
sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H
1d8z_A 1d9a_A 3hi9_A
Length = 167
Score = 29.1 bits (66), Expect = 0.30
Identities = 7/31 (22%), Positives = 15/31 (48%)
Query: 56 TLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
++ D G G +++F + AE A++
Sbjct: 119 RILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149
Score = 28.7 bits (65), Expect = 0.47
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 39 DDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRYI 96
++ F + EI S LV D G+ G +V ++D + AE A+ + R+ + I
Sbjct: 17 EEFRSLFGSIGEIES--CKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74
>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 = 28.8 bits (65), Expect = 0.31
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 39 DDIAQFFDGL-EIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
D+ F+ +I +T+++D F G G A++ + ++E+A A
Sbjct: 28 KDLKPLFEEFGKIYE--LTVLKDRFTGMHKGCAFLTYCERESALKAQS 73
>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 = 28.9 bits (65), Expect = 0.31
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 57 LVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+V+D G+ G +V F +K AE A+Q
Sbjct: 47 VVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
>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 = 28.4 bits (64), Expect = 0.35
Identities = 7/30 (23%), Positives = 13/30 (43%)
Query: 57 LVEDPFNGRPTGEAYVQFVDKETAELALQK 86
L +G A+V + D+ A A++
Sbjct: 34 LPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63
>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 = 27.9 bits (63), Expect = 0.38
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 54 GITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+V+D G+ G +V F +K AE A+Q
Sbjct: 35 DARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
>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 = 28.0 bits (63), Expect = 0.43
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+ + + FDG +V D G G +V F +E A+ A +
Sbjct: 30 ETLKESFDGSV----RARIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 28.0 bits (63), Expect = 0.45
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 63 NGRPTGEAYVQFVDKETAELALQK 86
G+P G AYV++ ++ A A+ K
Sbjct: 54 AGKPKGLAYVEYENESQASQAVMK 77
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 28.6 bits (64), Expect = 0.45
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRYI 96
+ + D + G A+V+F DK AE A+ + R +
Sbjct: 77 VYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL 119
>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 = 28.0 bits (63), Expect = 0.48
Identities = 8/31 (25%), Positives = 18/31 (58%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+ +D G+ G +V+F+ +E A+ A++
Sbjct: 45 THMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 28.7 bits (64), Expect = 0.50
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 57 LVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+ D +GR G A V F + A A+++
Sbjct: 120 VDYDR-SGRSLGTADVHFERRADALKAMKQ 148
>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 = 28.3 bits (63), Expect = 0.55
Identities = 9/49 (18%), Positives = 21/49 (42%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
K ++ D + + GR G+A++ +++ A AL++
Sbjct: 63 KYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKE 111
>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 = 28.2 bits (63), Expect = 0.62
Identities = 9/32 (28%), Positives = 19/32 (59%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+++V D + R G A+V F + + A+ A ++
Sbjct: 76 VSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
>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 = 27.6 bits (62), Expect = 0.62
Identities = 6/31 (19%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
++ + + P +V+F + A AL
Sbjct: 45 CKMITEHTSNDPYC--FVEFYEHRDAAAALA 73
>2c5u_A RNA ligase, T4 RNA ligase 1; nucleotidyl transferase, ATP-binding;
HET: APC; 2.21A {Bacteriophage T4}
Length = 375
Score = 28.6 bits (63), Expect = 0.65
Identities = 15/96 (15%), Positives = 33/96 (34%), Gaps = 8/96 (8%)
Query: 10 SDRYIEVFKVRRQEMDWKLQHTGIVEGKKDDIAQFFDGLEIISNGITLVEDPFNG----- 64
SD Y+ + + + + I++G DD+ + E I E +
Sbjct: 244 SDWYVSLHSTKSSLDNPEKLFKTIIDGASDDLKAMYADDEYSYRKIEAFETTYLKYLDRA 303
Query: 65 -RPTGEAYVQFVDKETAELAL--QKHKERIGHRYIF 97
+ + + K+ A+ Q + G ++F
Sbjct: 304 LFLVLDCHNKHCGKDRKTYAMEAQGVAKGAGMDHLF 339
>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 = 27.6 bits (62), Expect = 0.65
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 64 GRPTGEAYVQFVDKETAELALQ 85
G+ G AY++F + AE L+
Sbjct: 50 GKSKGIAYIEFKSEADAEKNLE 71
>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 = 27.7 bits (62), Expect = 0.74
Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 38 KDDIAQFFD--GLEIISNGITLVEDP-FNGRPTGEAYVQFVDKETAELALQ 85
+ +I + F G E+ + + L + G G +V F+ K+ A+ A
Sbjct: 29 QREIRELFSTFG-ELKT--VRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 27.4 bits (61), Expect = 0.75
Identities = 8/48 (16%), Positives = 16/48 (33%), Gaps = 4/48 (8%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+ + ++ + + D T V + K+ A AL K
Sbjct: 30 EVLDSLLVQYGVVESCEQVNTDS----ETAVVNVTYSSKDQARQALDK 73
>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD,
RNP, poly(U) binding, nucleus, RNA-binding, binding
protein; 1.60A {Saccharomyces cerevisiae}
Length = 83
Score = 27.1 bits (61), Expect = 0.76
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 57 LVEDPFNGRPTGEAYVQFVDKETAELALQ 85
++ D G G +V F ++ A+ A+
Sbjct: 33 VMWDMQTGSSRGYGFVSFTSQDDAQNAMD 61
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 27.0 bits (60), Expect = 0.76
Identities = 7/43 (16%), Positives = 16/43 (37%), Gaps = 5/43 (11%)
Query: 63 NGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTV 105
+G+ G ++++ A A++ Y H + V
Sbjct: 43 DGKTKGYIFLEYASPAHAVDAVKN-----ADGYKLDKQHTFRV 80
>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 = 27.3 bits (61), Expect = 0.97
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 63 NGRPTGEAYVQFVDKETAELALQK 86
+GR G A V F + A A+++
Sbjct: 72 SGRSLGTADVHFERRADALKAMKQ 95
>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 = 1.0
Identities = 8/42 (19%), Positives = 17/42 (40%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
I L D + G ++ F ++E + ++K +G
Sbjct: 29 IELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKC 70
>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 = 26.6 bits (59), Expect = 1.2
Identities = 8/39 (20%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 58 VEDPFNGRPTGEAYVQFVDKETAELALQK--HKERIGHR 94
++ + R A+V ++ E A+ A+Q G
Sbjct: 31 LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKD 69
>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM
domain, RNA- binding, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 104
Score = 26.8 bits (59), Expect = 1.2
Identities = 5/32 (15%), Positives = 10/32 (31%)
Query: 65 RPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
R + F + AE L + + +
Sbjct: 45 RLGCGGVLTFREPADAERVLAQADHELHGAQL 76
>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 = 26.7 bits (60), Expect = 1.3
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 38 KDDIAQFFD--GLEIISNGITLVEDPFN-GRPTGEAYVQFVDKETAELALQ 85
KD I + F G +I I + + + G AYV+F + + AE AL+
Sbjct: 18 KDHIMEIFSTYG-KIKM--IDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 102
Score = 26.8 bits (60), Expect = 1.3
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
I + D + G A+V+F E A A+
Sbjct: 42 IQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 26.3 bits (59), Expect = 1.4
Identities = 9/42 (21%), Positives = 17/42 (40%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
L+ D R G +V F ++ E + H I ++ +
Sbjct: 29 AMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMV 70
>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 = 26.8 bits (60), Expect = 1.4
Identities = 8/32 (25%), Positives = 16/32 (50%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
I + + + G+A+V F + +A AL+
Sbjct: 39 ILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
>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 = 27.7 bits (61), Expect = 1.4
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 6/56 (10%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGH 93
+D+ F SNG + F + A +Q E A AL H +G
Sbjct: 166 EDLKVLFS-----SNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGE 216
>3giw_A Protein of unknown function DUF574; rossmann-fold protein,
structural genomics, joint center for structural
genomics, JCSG; HET: MSE UNL; 1.45A {Streptomyces
avermitilis} PDB: 3go4_A*
Length = 277
Score = 27.6 bits (61), Expect = 1.5
Identities = 10/42 (23%), Positives = 20/42 (47%)
Query: 19 VRRQEMDWKLQHTGIVEGKKDDIAQFFDGLEIISNGITLVED 60
V R ++ ++ + + +FF+GLE++ GI V
Sbjct: 210 VGRVAREYAARNMPMRLRTHAEAEEFFEGLELVEPGIVQVHK 251
>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 = 26.8 bits (59), Expect = 1.5
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 58 VEDPFNGRPTGEAYVQFVDKETAELALQK 86
V D G YV+F +E AE A+
Sbjct: 59 VCDNLGDHLVGNVYVKFRREEDAEKAVID 87
>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 = 26.5 bits (59), Expect = 1.6
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 63 NGRPTGEAYVQFVDKETAELALQK 86
+GR G A V F K A A+++
Sbjct: 66 SGRSLGTADVHFERKADALKAMKQ 89
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 26.6 bits (59), Expect = 1.8
Identities = 5/40 (12%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRYIFF 98
+G+ G ++++ A A++ ++ ++ F
Sbjct: 54 PEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR 93
>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus,
phosphorylation, ribonucleoprotein, ribosome
biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae}
PDB: 2osr_A
Length = 111
Score = 26.7 bits (59), Expect = 1.8
Identities = 6/33 (18%), Positives = 11/33 (33%)
Query: 54 GITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
T G ++F +E AL++
Sbjct: 54 LETTFSSVNTRDFDGTGALEFPSEEILVEALER 86
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 26.8 bits (59), Expect = 1.8
Identities = 7/32 (21%), Positives = 17/32 (53%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
I + + +G+AY+ F +E+A+ ++
Sbjct: 60 ILDIVVDLSDDNSGKAYIVFATQESAQAFVEA 91
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 26.1 bits (58), Expect = 2.2
Identities = 3/28 (10%), Positives = 10/28 (35%), Gaps = 1/28 (3%)
Query: 70 AYVQFVDKETAELALQK-HKERIGHRYI 96
++++ E A + + R +
Sbjct: 66 CFIKYDTHEQAAVCIVALANFPFQGRNL 93
>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 = 26.1 bits (58), Expect = 2.2
Identities = 5/17 (29%), Positives = 10/17 (58%)
Query: 70 AYVQFVDKETAELALQK 86
++V+F E+A A+
Sbjct: 64 SFVRFSTHESAAHAIVS 80
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 27.1 bits (60), Expect = 2.4
Identities = 10/46 (21%), Positives = 17/46 (36%), Gaps = 8/46 (17%)
Query: 62 FNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTVQH 107
NG G Y +VD +T E + + +Y ++H
Sbjct: 864 HNGNLKGRPYTGWVDSKTKEPV---DDKDVKAKY-----ETSILEH 901
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 25.5 bits (57), Expect = 2.5
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
DP R G +V F+D+ + L + + + + I
Sbjct: 35 DPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTI 71
>2qe6_A Uncharacterized protein TFU_2867; putative methyltransferase,
structural genomics, joint cente structural genomics,
JCSG; HET: NEP SAM; 1.95A {Thermobifida fusca}
Length = 274
Score = 26.8 bits (59), Expect = 2.6
Identities = 6/32 (18%), Positives = 12/32 (37%), Gaps = 3/32 (9%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEA 70
++I + F E++ G+ RP
Sbjct: 225 EEIERQFGDFELVEPGVVYTAL---WRPDEPV 253
>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 = 25.7 bits (57), Expect = 2.6
Identities = 7/17 (41%), Positives = 13/17 (76%)
Query: 70 AYVQFVDKETAELALQK 86
A++QF ++ AE+A +K
Sbjct: 51 AFIQFATRQAAEVAAEK 67
>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 = 26.2 bits (58), Expect = 2.6
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 5/49 (10%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
++D+ E G F+ P G A V F D E A+ +Q
Sbjct: 40 REDLRV-----ECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQT 83
>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 = 25.6 bits (57), Expect = 2.8
Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 5/49 (10%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
D+ + G +I+S + D + G +V F A+ A+
Sbjct: 20 QDLVKLCQPYG-KIVS--TKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
>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 = 26.1 bits (58), Expect = 2.8
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 57 LVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+V+D R G +V F + + A+ A+
Sbjct: 44 VVKDRETQRSRGFGFVTFENIDDAKDAMM 72
>1pj3_A NAD-dependent malic enzyme, mitochondrial; oxidative decarboxylase,
oxidoreductase; HET: NAD; 2.10A {Homo sapiens} SCOP:
c.2.1.7 c.58.1.3 PDB: 1pj2_A* 1do8_A* 1pj4_A* 1qr6_A*
1efl_A* 1pjl_A* 1efk_A* 1gz4_A* 1gz3_A*
Length = 564
Score = 26.6 bits (59), Expect = 3.1
Identities = 8/30 (26%), Positives = 14/30 (46%), Gaps = 5/30 (16%)
Query: 53 NGITLVEDPF-----NGRPTGEAYVQFVDK 77
+ I L++DPF R + Y +D+
Sbjct: 188 DNIALLKDPFYMGLYQKRDRTQQYDDLIDE 217
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 25.6 bits (57), Expect = 3.2
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 63 NGRPTGEAYVQFVDKETAELALQK 86
NG+ G V+F E AE A +
Sbjct: 44 NGKSKGCGVVKFESPEVAERACRM 67
>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 = 25.6 bits (57), Expect = 3.8
Identities = 9/42 (21%), Positives = 21/42 (50%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
+ ++ D RP G ++ F D+++ + A+ H I + +
Sbjct: 40 VVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKV 81
>1gq2_A Malic enzyme; oxidoreductase, pigeon liver, NADP-dependent,
NAD-NADP selectivity, decarboxylase, malate, Mn2+; HET:
NAP; 2.5A {Columba livia} SCOP: c.2.1.7 c.58.1.3 PDB:
2aw5_A
Length = 555
Score = 26.5 bits (59), Expect = 3.9
Identities = 9/30 (30%), Positives = 16/30 (53%), Gaps = 5/30 (16%)
Query: 53 NGITLVEDPF-----NGRPTGEAYVQFVDK 77
+ TL++DP + R G+AY +D+
Sbjct: 186 DNETLLKDPLYIGLRHKRIRGQAYDDLLDE 215
>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 = 26.0 bits (58), Expect = 3.9
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+DI F G +I ++ P +G G A+V F + A+ A++
Sbjct: 110 NDIRVMFSSFG-QIEE--CRILRGP-DGLSRGCAFVTFTTRAMAQTAIKA 155
>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 = 26.0 bits (56), Expect = 4.4
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 63 NGRPTGEAYVQFVDKETAELALQ 85
+ + G+A+V F + +A AL+
Sbjct: 48 SLKMRGQAFVIFKEVSSATNALR 70
>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 = 24.8 bits (55), Expect = 4.7
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
DP GR G ++ F D + E L + + R+ R I
Sbjct: 46 DPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVI 82
>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 = 25.6 bits (56), Expect = 5.2
Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 5/48 (10%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK 86
+D+ F SNG + F + A +Q E A AL
Sbjct: 135 EDLKVLFS-----SNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALID 177
>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 = 25.3 bits (56), Expect = 5.3
Identities = 9/35 (25%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELAL-QKHK 88
+ + +D G G +V+F + ET + Q+H
Sbjct: 45 VQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHM 79
>1o0s_A NAD-ME, NAD-dependent malic enzyme; oxidoreductase, oxidative
decarboxylase, rossmann fold, MAla dehydrogenase; HET:
NAI; 2.00A {Ascaris suum} SCOP: c.2.1.7 c.58.1.3 PDB:
1llq_A*
Length = 605
Score = 25.9 bits (57), Expect = 5.5
Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 5/30 (16%)
Query: 53 NGITLVEDPF-----NGRPTGEAYVQFVDK 77
N + L+ DPF + R G+ Y +D
Sbjct: 224 NNMDLLNDPFYIGLRHKRVRGKDYDTLLDN 253
>1nko_A Sialic acid binding IG-like lectin 7; immunoglobulin, siglec7,
immune system; 1.45A {Homo sapiens} SCOP: b.1.1.1 PDB:
2g5r_A* 1o7v_A* 2df3_A* 1o7s_A* 2hrl_A*
Length = 132
Score = 25.3 bits (55), Expect = 6.3
Identities = 13/88 (14%), Positives = 32/88 (36%), Gaps = 4/88 (4%)
Query: 38 KDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIF 97
+ + +N V++ R + + L+++ + RY F
Sbjct: 49 RAGNDISWKAPVATNNPAWAVQEETRDRFH---LLGDPQTKNCTLSIRDARMSDAGRY-F 104
Query: 98 FTGHRYTVQHRAPRCETSIPVSSSTHKP 125
F + ++ + S+ V++ TH+P
Sbjct: 105 FRMEKGNIKWNYKYDQLSVNVTALTHRP 132
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 25.0 bits (54), Expect = 6.4
Identities = 8/43 (18%), Positives = 16/43 (37%), Gaps = 4/43 (9%)
Query: 65 RPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTVQH 107
R +A V+F A+ A K + I+ +++
Sbjct: 60 RNGIQAMVEFESVLCAQKA----KAALNGADIYAGCCTLKIEY 98
>1iqz_A Ferredoxin; iron-sulfer protein, ultlahigh resolution analysis,
geometry of [4Fe-4S] cluster, electron transport; 0.92A
{Bacillus thermoproteolyticus} SCOP: d.58.1.4 PDB:
1ir0_A 1wtf_A*
Length = 81
Score = 24.4 bits (53), Expect = 6.6
Identities = 5/13 (38%), Positives = 9/13 (69%)
Query: 55 ITLVEDPFNGRPT 67
I + ++PF+G P
Sbjct: 66 IKVADEPFDGDPN 78
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 24.8 bits (54), Expect = 6.7
Identities = 8/49 (16%), Positives = 18/49 (36%), Gaps = 6/49 (12%)
Query: 37 KKDDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+ D+ + L + +T P A++ + D A+ A+
Sbjct: 32 RVSDLKRALRELGSVPLRLTW------QGPRRRAFLHYPDSAAAQQAVS 74
>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 = 24.5 bits (54), Expect = 7.1
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQ 85
+T+ +D G+P +V F E+ A+
Sbjct: 46 VTICKDR-EGKPKSFGFVCFKHPESVSYAIA 75
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 24.6 bits (54), Expect = 7.7
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 8/52 (15%)
Query: 70 AYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTVQHRAPRCETSIPVSSS 121
A V+ D E L + + +G GHR V+ R + E P S S
Sbjct: 48 AIVEMGDVGAREAVLSQSQHSLG-------GHRLRVRPREQK-EFQSPASKS 91
>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 = 24.5 bits (54), Expect = 8.1
Identities = 5/31 (16%), Positives = 11/31 (35%)
Query: 64 GRPTGEAYVQFVDKETAELALQKHKERIGHR 94
G G +V F + + ++ G +
Sbjct: 47 GVSKGYGFVSFYNDVDVQKIVESQINFHGKK 77
>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 = 24.6 bits (54), Expect = 8.7
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 7/58 (12%)
Query: 55 ITLVEDPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYIFFTGHRYTVQH-RAPR 111
I ++ A+V+F D AE A+ R G+ + G+R V+ R+ R
Sbjct: 49 IRDIDLKNRRGGPPFAFVEFEDPRDAEDAV---YGRDGYD---YDGYRLRVEFPRSGR 100
>3h7f_A Serine hydroxymethyltransferase 1; cytoplasm, one-carbon
metabolism, pyridoxal phosphate, structural genomics;
HET: LLP; 1.50A {Mycobacterium tuberculosis}
Length = 447
Score = 25.3 bits (56), Expect = 8.7
Identities = 8/20 (40%), Positives = 10/20 (50%), Gaps = 5/20 (25%)
Query: 118 VSSSTHKPGRHHTLDGPNGG 137
VS++ HK TL G G
Sbjct: 242 VSTTVHK-----TLGGGRSG 256
>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 = 24.7 bits (54), Expect = 8.8
Identities = 5/28 (17%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 70 AYVQFVDKETAELALQK-HKERIGHRYI 96
A+V + E+A+ A+ + + ++ +
Sbjct: 76 AFVTYEKMESADQAVAELNGTQVESVQL 103
>3na5_A Phosphoglucomutase; isomerase, metal binding; HET: BTB; 1.70A
{Salmonella enterica subsp} PDB: 3olp_A 2fuv_A*
Length = 570
Score = 25.3 bits (56), Expect = 8.8
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 39 DDIAQFFDGLEIISNGITLVEDPFNGRPTGEAYVQ 73
+ +A D I G+TL DP G +G Y +
Sbjct: 237 EGLADIVDMAAIQKAGLTLGVDPLGG--SGIEYWK 269
>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 = 24.5 bits (54), Expect = 8.9
Identities = 9/37 (24%), Positives = 17/37 (45%)
Query: 60 DPFNGRPTGEAYVQFVDKETAELALQKHKERIGHRYI 96
DP R G +V F+D+ + L + + + + I
Sbjct: 60 DPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTI 96
>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 = 24.7 bits (54), Expect = 9.2
Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 15/92 (16%)
Query: 39 DDIAQFFD--GLEIISNGITLVEDPFNGRPTGEAYVQFVDKETAELALQK-HKERIGHRY 95
+ Q F+ G I S + +V D + G +V+F +A+ A+ + I ++
Sbjct: 57 VQLRQLFERYG-PIES--VKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKR 113
Query: 96 IFFTGHRYTVQHRAPRCETSIPVSSSTHKPGR 127
+ V A + P + G
Sbjct: 114 L-------KVALAASGHQR--PGIAGAVGDGN 136
>1te5_A Conserved hypothetical protein; glutamine amidotransferase,
amidotransferase, structural genomics, PSI, protein
structure initiative; 2.00A {Pseudomonas aeruginosa
PAO1} SCOP: d.153.1.1
Length = 257
Score = 25.1 bits (54), Expect = 9.3
Identities = 14/91 (15%), Positives = 23/91 (25%), Gaps = 8/91 (8%)
Query: 1 MGHCR---TGEVSDRYIEVFKVRRQEMDWKLQHTGIVEGKKDDIAQFF-----DGLEIIS 52
+GH R G+V F W H G + + + D
Sbjct: 75 IGHIRQANVGKVGLSNTHPFIRELGGRYWTFAHNGQLADFQPKPGFYRPVGETDSEAAFC 134
Query: 53 NGITLVEDPFNGRPTGEAYVQFVDKETAELA 83
+ + V F E + + E
Sbjct: 135 DLLNRVRRAFPEPVPVEVLLPVLISACDEYR 165
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
0.319 0.138 0.424
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,318,708
Number of extensions: 131464
Number of successful extensions: 440
Number of sequences better than 10.0: 1
Number of HSP's gapped: 421
Number of HSP's successfully gapped: 187
Length of query: 141
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 57
Effective length of database: 4,356,429
Effective search space: 248316453
Effective search space used: 248316453
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 (21.8 bits)
S2: 52 (23.8 bits)