RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy882
(253 letters)
>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 = 93.0 bits (232), Expect = 8e-24
Identities = 25/91 (27%), Positives = 50/91 (54%), Gaps = 3/91 (3%)
Query: 12 RSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIR 69
+R + + L++ L + +T+D L F +G+I + ++D+ TG +GVA++R
Sbjct: 79 YARPGGESIKDTNLYVTNL-PRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 137
Query: 70 FSKTSEAAKAVEEMNGEFLPNHSKPIKVLIA 100
++K EA +A+ +N S+P+ V +A
Sbjct: 138 YNKREEAQEAISALNNVIPEGGSQPLSVRLA 168
Score = 75.3 bits (186), Expect = 4e-17
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 2/72 (2%)
Query: 31 KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPN 90
+D+T+ +L F G I R ++D TG S G A++ F+ ++ +A++ +NG + N
Sbjct: 13 QDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN 72
Query: 91 HSKPIKVLIAAK 102
K +KV A
Sbjct: 73 --KRLKVSYARP 82
Score = 27.5 bits (62), Expect = 2.9
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 220 QTLHGAEMYGSRLKVMEADPPK 241
+ L+G + RLKV A P
Sbjct: 63 KVLNGITVRNKRLKVSYARPGG 84
>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 = 90.0 bits (224), Expect = 1e-22
Identities = 29/92 (31%), Positives = 48/92 (52%), Gaps = 5/92 (5%)
Query: 12 RSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIR 69
E N+ +LFI + K TE+D+R FS FG I+E R ++ G S+G A++
Sbjct: 85 ADSEKNNAVEDRKLFIGMI-SKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVT 142
Query: 70 FSKTSEAAKAVEEMNG-EFLPNHSKPIKVLIA 100
F+ + A A++ M+ + + S P+ V A
Sbjct: 143 FTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFA 174
Score = 73.0 bits (180), Expect = 3e-16
Identities = 34/160 (21%), Positives = 52/160 (32%), Gaps = 46/160 (28%)
Query: 31 KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGE--SKGVAYIRFSKTSEAAKAVEEMNG-EF 87
+ +E DLR+ F +G + EI ++DR+ SKG ++ F A +A ++ +
Sbjct: 13 RTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKV 72
Query: 88 LPNHSKPIKVLIAAKLEFKEGYRG------------------------GQKIS------- 116
LP PI++ A E GQ
Sbjct: 73 LPGMHHPIQM-KPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP 131
Query: 117 ---------VQYTSPQSAAYARDKFHGFAYPPGI--PMVV 145
V +T+ A A H G PMVV
Sbjct: 132 DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV 171
>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 = 89.2 bits (222), Expect = 2e-22
Identities = 31/91 (34%), Positives = 51/91 (56%), Gaps = 3/91 (3%)
Query: 12 RSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIR 69
+R + + L++ L K +T+ +L Q FS +G I R + D+ TG S+GV +IR
Sbjct: 78 YARPSSASIRDANLYVSGL-PKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIR 136
Query: 70 FSKTSEAAKAVEEMNGEFLPNHSKPIKVLIA 100
F K EA +A++ +NG+ ++PI V A
Sbjct: 137 FDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 74.1 bits (183), Expect = 1e-16
Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 31 KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPN 90
+++T+++ R F G I+ + V+D+ TG+S G ++ + +A KA+ +NG L
Sbjct: 12 QNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQT 71
Query: 91 HSKPIKVLIA 100
K IKV A
Sbjct: 72 --KTIKVSYA 79
Score = 27.5 bits (62), Expect = 3.2
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 220 QTLHGAEMYGSRLKVMEADPPK 241
TL+G + +KV A P
Sbjct: 62 NTLNGLRLQTKTIKVSYARPSS 83
>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
PDB: 2dgq_A
Length = 106
Score = 87.0 bits (216), Expect = 3e-22
Identities = 28/89 (31%), Positives = 46/89 (51%), Gaps = 6/89 (6%)
Query: 13 SREYNDEPPHSRLFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIR 69
+ +LFI G +++ E DL+ F FG I E+ +KDR TG KG A++
Sbjct: 4 GSSGMKDHDAIKLFI--GQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 70 FSKTSEAAKAVEEMNG-EFLPNHSKPIKV 97
+ + A KA ++ + LP ++PI+V
Sbjct: 62 YCERESALKAQSALHEQKTLPGMNRPIQV 90
>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 = 88.4 bits (220), Expect = 5e-22
Identities = 27/103 (26%), Positives = 48/103 (46%), Gaps = 8/103 (7%)
Query: 1 MDRNYRINTHDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRN 58
++ +I R +Y P +LFI L + +D +++ + FG ++ VKD
Sbjct: 76 QGQSLKIR---RPHDYQPLPGAHKLFIGGL-PNYLNDDQVKELLTSFGPLKAFNLVKDSA 131
Query: 59 TGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAA 101
TG SKG A+ + + +A+ +NG L K + V A+
Sbjct: 132 TGLSKGYAFCEYVDINVTDQAIAGLNGMQL--GDKKLLVQRAS 172
Score = 54.2 bits (131), Expect = 3e-09
Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 13/82 (15%)
Query: 24 RLFILCG---KDVTEDDLRQGFSPFGNIQEIRC-----VKDRNTGESKGVAYIRFSKTSE 75
RL++ G +TE+ + F+ + + V + K A++ F E
Sbjct: 6 RLYV--GNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 76 AAKAVEEMNGEFLPNHSKPIKV 97
+A+ +G + +K+
Sbjct: 64 TTQAM-AFDGIIF--QGQSLKI 82
>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 = 85.7 bits (213), Expect = 7e-22
Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 5/82 (6%)
Query: 18 DEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSE 75
H +F+ L ++T + F+PFG I + R VKD TG+SKG ++ F +
Sbjct: 2 PLGSHFHVFVGDL-SPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD 60
Query: 76 AAKAVEEMNGEFLPNHSKPIKV 97
A A+++M G++L + I+
Sbjct: 61 AENAIQQMGGQWL--GGRQIRT 80
>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 = 87.2 bits (217), Expect = 1e-21
Identities = 26/102 (25%), Positives = 52/102 (50%), Gaps = 6/102 (5%)
Query: 3 RNYRINTHDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTG 60
+IN +S++ + + + LF+ L +V ++ LR F F + + D TG
Sbjct: 69 NIVKINWAFQSQQSSSDDTFN-LFVGDL-NVNVDDETLRNAFKDFPSYLSGHVMWDMQTG 126
Query: 61 ESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAK 102
S+G ++ F+ +A A++ M G+ L + +P+++ AAK
Sbjct: 127 SSRGYGFVSFTSQDDAQNAMDSMQGQDL--NGRPLRINWAAK 166
Score = 64.9 bits (159), Expect = 3e-13
Identities = 17/66 (25%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+TED L+Q F G I I+ + D+ ++ A++ + ++ +A A++ +NG+ + N
Sbjct: 11 AITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIEN- 68
Query: 92 SKPIKV 97
+K+
Sbjct: 69 -NIVKI 73
Score = 26.3 bits (59), Expect = 6.8
Identities = 8/39 (20%), Positives = 17/39 (43%), Gaps = 9/39 (23%)
Query: 216 VEFS---------QTLHGAEMYGSRLKVMEADPPKGDRN 245
VE+ QTL+G ++ + +K+ A + +
Sbjct: 46 VEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSS 84
>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification,
transcription regulation, structural genomics,
structural genomics consortium; 1.30A {Homo sapiens}
Length = 110
Score = 84.4 bits (209), Expect = 3e-21
Identities = 15/87 (17%), Positives = 35/87 (40%), Gaps = 3/87 (3%)
Query: 19 EPPHSRLFILC-GKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAA 77
+ P + +V E L+ +G ++E+ + T + G+A + F+ T A
Sbjct: 3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAK 62
Query: 78 KAVEEMNGEFLPNHSKPIKVLIAAKLE 104
+ V+ ++ + I + K +
Sbjct: 63 ETVKNLHLTSV--MGNIIHAQLDIKGQ 87
>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 = 83.5 bits (207), Expect = 6e-21
Identities = 26/86 (30%), Positives = 46/86 (53%), Gaps = 3/86 (3%)
Query: 17 NDEPPHSRLFILC-GKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSE 75
+ +LF+ K +E+D+ + F PFG I E ++ + G SKG A+++FS +E
Sbjct: 10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTE 68
Query: 76 AAKAVEEMNG-EFLPNHSKPIKVLIA 100
A A+ ++G + +P S + V A
Sbjct: 69 AQAAIHALHGSQTMPGASSSLVVKFA 94
>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 = 83.6 bits (207), Expect = 8e-21
Identities = 28/87 (32%), Positives = 49/87 (56%), Gaps = 5/87 (5%)
Query: 13 SREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRF 70
S + D H +F+ L ++T +D++ F+PFG I + R VKD TG+SKG ++ F
Sbjct: 6 SGQKKDTSNHFHVFVGDL-SPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
Query: 71 SKTSEAAKAVEEMNGEFLPNHSKPIKV 97
+A A+++M G++L + I+
Sbjct: 65 FNKWDAENAIQQMGGQWL--GGRQIRT 89
>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A
{Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A
Length = 216
Score = 85.8 bits (213), Expect = 2e-20
Identities = 22/92 (23%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
Query: 13 SREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRF 70
+ + +R+++ + +D+++DD++ F FG I+ +D TG+ KG +I +
Sbjct: 116 DQLAEEARAFNRIYVASV-HQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEY 174
Query: 71 SKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAK 102
K + AV MN L + ++V A
Sbjct: 175 EKAQSSQDAVSSMNLFDL--GGQYLRVGKAVT 204
Score = 77.4 bits (191), Expect = 2e-17
Identities = 27/89 (30%), Positives = 44/89 (49%), Gaps = 7/89 (7%)
Query: 12 RSREYNDEPPHSRLFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYI 68
++ SR+++ G ++ ED +RQ F+PFG I+ I D T + KG A++
Sbjct: 18 AAQRQGALAIMSRVYV--GSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75
Query: 69 RFSKTSEAAKAVEEMNGEFLPNHSKPIKV 97
+ A A+E+MN L + IKV
Sbjct: 76 EYEVPEAAQLALEQMNSVML--GGRNIKV 102
>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition
motif, bruno; NMR {Drosophila melanogaster}
Length = 118
Score = 80.1 bits (198), Expect = 2e-19
Identities = 26/85 (30%), Positives = 41/85 (48%), Gaps = 5/85 (5%)
Query: 18 DEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSE 75
+ P LFI L ++ T+ DL F PFGN+ + D+ T SK ++ F
Sbjct: 36 EGPEGCNLFIYHLP-QEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94
Query: 76 AAKAVEEMNGEFLPNHSKPIKVLIA 100
A A++ MNG + +K +KV +
Sbjct: 95 AQVAIKAMNGFQV--GTKRLKVQLK 117
>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 = 78.7 bits (195), Expect = 3e-19
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+V ++ LR F F + + D TG S+G ++ F+ +A A++ M G+ L +
Sbjct: 12 NVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL--N 69
Query: 92 SKPIKV 97
+P+++
Sbjct: 70 GRPLRI 75
>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 = 81.6 bits (202), Expect = 4e-19
Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 7/89 (7%)
Query: 17 NDEPPHSRLFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKT 73
+LFI G + +D +++ + FG ++ VKD TG SKG A+ +
Sbjct: 109 VVPDSAHKLFI--GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDI 166
Query: 74 SEAAKAVEEMNGEFLPNHSKPIKVLIAAK 102
+ +A+ +NG L K + V A+
Sbjct: 167 NVTDQAIAGLNGMQL--GDKKLLVQRASV 193
Score = 55.0 bits (133), Expect = 2e-09
Identities = 14/105 (13%), Positives = 32/105 (30%), Gaps = 8/105 (7%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRC-----VKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGE 86
+TE+ + F+ + + V + K A++ F E +A+ +G
Sbjct: 15 GITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGI 73
Query: 87 FLPNHSKPIKVLIAAKLEFKEGYRGGQKISVQYTSPQSAAYARDK 131
+ +K+ + G + V + K
Sbjct: 74 IFQG--QSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHK 116
>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 = 83.1 bits (206), Expect = 4e-19
Identities = 21/103 (20%), Positives = 42/103 (40%), Gaps = 5/103 (4%)
Query: 17 NDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTS 74
+P + L + L +T+ + PFG+++ V TG+SKG + + K
Sbjct: 90 QLQPTDALLCVANL-PPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKD 148
Query: 75 EAAKAVEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRGGQKISV 117
AA+A ++ G+ L + + V + + + V
Sbjct: 149 SAARAKSDLLGKPL--GPRTLYVHWTDAGQLTPALLHSRCLCV 189
Score = 75.0 bits (185), Expect = 4e-16
Identities = 17/104 (16%), Positives = 35/104 (33%), Gaps = 7/104 (6%)
Query: 2 DRNYRINTHDRSREYNDEPPHSRLFI--LCGKDVTEDD-LRQGFSPFGNIQEIRCVKDRN 58
R ++ D + L + L + D L + S + + +
Sbjct: 164 PRTLYVHWTDAGQLTPALLHSRCLCVDRL-PPGFNDVDALCRALSAVHSPTFCQLACGQ- 221
Query: 59 TGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAK 102
G+ KG A + + A +A ++ +G L ++V A
Sbjct: 222 DGQLKGFAVLEYETAEMAEEAQQQADGLSL--GGSHLRVSFCAP 263
Score = 60.0 bits (146), Expect = 7e-11
Identities = 13/83 (15%), Positives = 27/83 (32%), Gaps = 14/83 (16%)
Query: 18 DEPPHSRLFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTS 74
++ I DVT ++ S + +K + KG A++
Sbjct: 18 QFRNRRKILI--RGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGE 68
Query: 75 EAAKAVEEMNGEFLPNHSKPIKV 97
+A A+ + L + + V
Sbjct: 69 QAEAAINAFHQSRLRE--RELSV 89
>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA
binding protein, structure, protein-RNA complex, RNA
stem-loop, structural protein/RNA complex; NMR {Homo
sapiens}
Length = 116
Score = 78.5 bits (194), Expect = 6e-19
Identities = 38/107 (35%), Positives = 55/107 (51%), Gaps = 6/107 (5%)
Query: 18 DEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSE 75
+ +LFI L ++ E L+ F G I E+ +KDR T +S+G A+I F ++
Sbjct: 3 EADHPGKLFIGGL-NRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPAD 60
Query: 76 AAKAVEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRGGQKISVQYTSP 122
A A ++MNG+ L H K IKV A K F+ G R S + SP
Sbjct: 61 AKNAAKDMNGKSL--HGKAIKVEQAKKPSFQSGGRRRPPASSRNRSP 105
>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 = 78.0 bits (193), Expect = 8e-19
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 7/86 (8%)
Query: 18 DEPPHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTS 74
RLF+ +E+DL + FS +G + E+ D T + KG A++ F
Sbjct: 4 GSSGSGRLFV--RNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61
Query: 75 EAAKAVEEMNGEFLPNHSKPIKVLIA 100
A KA E++G+ + + VL +
Sbjct: 62 HAVKAYAEVDGQVF--QGRMLHVLPS 85
>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation,
RRM domain, transcr; NMR {Homo sapiens}
Length = 140
Score = 79.1 bits (195), Expect = 9e-19
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 18 DEPPHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTS 74
L++ G +V + L F PFG+I +I+ D T + +G A++ F
Sbjct: 59 SATTKRVLYV--GGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 116
Query: 75 EAAKAVEEMNGEFLPNHSKPIKV 97
+AA A++ MN L + I+V
Sbjct: 117 DAAAAIDNMNESEL--FGRTIRV 137
>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 = 78.1 bits (193), Expect = 1e-18
Identities = 25/90 (27%), Positives = 42/90 (46%), Gaps = 5/90 (5%)
Query: 13 SREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRF 70
+ + P + LFI L ++ + DL Q F PFGN+ + D+ T SK ++ +
Sbjct: 16 AGSQKEGPEGANLFIYHL-PQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSY 74
Query: 71 SKTSEAAKAVEEMNGEFLPNHSKPIKVLIA 100
A A++ MNG + K +KV +
Sbjct: 75 DNPVSAQAAIQSMNGFQI--GMKRLKVQLK 102
>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 = 77.3 bits (191), Expect = 1e-18
Identities = 25/66 (37%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
D E DL++ F PFG+I I KD+ TG+SKG A+I F + +AA+A+ ++G
Sbjct: 26 DTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGY--D 83
Query: 92 SKPIKV 97
+ V
Sbjct: 84 HLILNV 89
>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 = 76.9 bits (190), Expect = 2e-18
Identities = 32/86 (37%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 20 PPHSRLFI--LCGKDVTEDDLRQGFSPFGNI-QEIRCVKDRNTGESKGVAYIRFSKTSEA 76
S +FI L ++ E L FS FG I Q + ++D +TG SKG A+I F+ +
Sbjct: 3 SGSSGIFIGNLD-PEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 77 AKAVEEMNGEFLPNHSKPIKVLIAAK 102
A+E MNG++L ++PI V A K
Sbjct: 62 DAAIEAMNGQYL--CNRPITVSYAFK 85
>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 = 76.5 bits (189), Expect = 2e-18
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 7/84 (8%)
Query: 20 PPHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEA 76
P S +++ +T +DL + FS +G + ++ +KD++T +SKGVA+I F A
Sbjct: 14 PSKSTVYV--SNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71
Query: 77 AKAVEEMNGEFLPNHSKPIKVLIA 100
+N + L + IK IA
Sbjct: 72 QNCTRAINNKQL--FGRVIKASIA 93
>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation
factors PAIP1 and PAIP2, translation-RNA complex; 2.00A
{Homo sapiens} PDB: 1cvj_A*
Length = 213
Score = 79.2 bits (196), Expect = 3e-18
Identities = 31/117 (26%), Positives = 47/117 (40%), Gaps = 12/117 (10%)
Query: 2 DRNYRIN--THDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDR 57
+ RI D S + +FI L K + L FS FGNI + V D
Sbjct: 84 GKPVRIMWSQRDPSLRKSG---VGNIFIKNL-DKSIDNKALYDTFSAFGNILSCKVVCD- 138
Query: 58 NTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRGGQK 114
SKG ++ F A +A+E+MNG L + + + V + +E G +
Sbjct: 139 -ENGSKGYGFVHFETQEAAERAIEKMNGMLL--NDRKVFVGRFKSRKEREAELGARA 192
Score = 75.8 bits (187), Expect = 8e-17
Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 7/83 (8%)
Query: 18 DEPPHSRLFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTS 74
P + L++ G DVTE L + FSP G I IR +D T S G AY+ F + +
Sbjct: 11 PSYPMASLYV--GDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPA 68
Query: 75 EAAKAVEEMNGEFLPNHSKPIKV 97
+A +A++ MN + + KP+++
Sbjct: 69 DAERALDTMNFDVIKG--KPVRI 89
>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 = 75.3 bits (186), Expect = 6e-18
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
T+ DL + P+G I + + D+ T + KG ++ F S A KAV + +
Sbjct: 16 GTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGV--Q 73
Query: 92 SKPIKV 97
++ K
Sbjct: 74 AQMAKQ 79
>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 = 76.2 bits (188), Expect = 6e-18
Identities = 25/94 (26%), Positives = 38/94 (40%), Gaps = 5/94 (5%)
Query: 6 RINTHDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESK 63
I YN P+ L++ L VTE DL F+ F + TG +
Sbjct: 9 EIRKIPMFSSYNPGEPNKVLYLKNLS-PRVTERDLVSLFARFQEKKGPPIQFRMMTGRMR 67
Query: 64 GVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKV 97
G A+I F A +A+ +NG L + K + +
Sbjct: 68 GQAFITFPNKEIAWQALHLVNGYKL--YGKILVI 99
>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 = 74.9 bits (185), Expect = 7e-18
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+V + L F PFG+I +I+ D T + +G A++ F +AA A++ MN L
Sbjct: 18 EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL--F 75
Query: 92 SKPIKV 97
+ I+V
Sbjct: 76 GRTIRV 81
>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 = 75.8 bits (187), Expect = 8e-18
Identities = 23/96 (23%), Positives = 39/96 (40%), Gaps = 6/96 (6%)
Query: 13 SREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRF 70
E + L+I L + E +L PFG + R ++D ++G S+GV + R
Sbjct: 16 QMAKQQEQDPTNLYISNL-PLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARM 73
Query: 71 SKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAKLEFK 106
T + + NG+F+ + P L K
Sbjct: 74 ESTEKCEAVIGHFNGKFI--KTPPGVSAPTEPLLCK 107
>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 95
Score = 74.5 bits (184), Expect = 1e-17
Identities = 26/92 (28%), Positives = 43/92 (46%), Gaps = 7/92 (7%)
Query: 9 THDRSREYNDEPPHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGV 65
+ S + P+ L + TE DLR+ FS +G I ++ V D+ + S+G
Sbjct: 2 SSGSSGNRANPDPNCCLGV--FGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGF 59
Query: 66 AYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKV 97
A++ F +A +A E NG L + I+V
Sbjct: 60 AFVYFENVDDAKEAKERANGMEL--DGRRIRV 89
>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 = 74.6 bits (184), Expect = 2e-17
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 3/82 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+V + L F PFG+I +I+ D T + +G A++ F +AA A++ MN L
Sbjct: 23 EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL--F 80
Query: 92 SKPIKVLIAAKLEFK-EGYRGG 112
+ I+V +A + K G G
Sbjct: 81 GRTIRVNLAKPMRIKESGPSSG 102
Score = 26.4 bits (59), Expect = 3.7
Identities = 8/43 (18%), Positives = 17/43 (39%), Gaps = 9/43 (20%)
Query: 216 VEFS---------QTLHGAEMYGSRLKVMEADPPKGDRNRKRQ 249
VEF ++ +E++G ++V A P + +
Sbjct: 59 VEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGPSS 101
>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 = 74.2 bits (183), Expect = 2e-17
Identities = 28/90 (31%), Positives = 43/90 (47%), Gaps = 9/90 (10%)
Query: 11 DRSREYNDEPPHSRLFILCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRF 70
S E + L++ G+D+T LR FSPFGNI ++ + A++ +
Sbjct: 4 GSSGERRAPRKGNTLYV-YGEDMTPTLLRGAFSPFGNIIDLS------MDPPRNCAFVTY 56
Query: 71 SKTSEAAKAVEEMNGEFLPNHSKPIKVLIA 100
K A +AV E+NG + S +KV IA
Sbjct: 57 EKMESADQAVAELNGTQV--ESVQLKVNIA 84
>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 = 73.4 bits (181), Expect = 4e-17
Identities = 29/66 (43%), Positives = 42/66 (63%), Gaps = 2/66 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
++TED LR F PFG I I +KD +TG SKG +I FS + A +A+E++NG L
Sbjct: 16 NITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFEL--A 73
Query: 92 SKPIKV 97
+P++V
Sbjct: 74 GRPMRV 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 = 75.3 bits (186), Expect = 4e-17
Identities = 21/104 (20%), Positives = 38/104 (36%), Gaps = 11/104 (10%)
Query: 1 MDRNYRINTHDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRN 58
++ L L ++TED+L++ F I
Sbjct: 79 FGNEIKLEKPKGRDSKKVRAAR-TLLAKNL-SFNITEDELKEVFEDALEI-----RLVSQ 131
Query: 59 TGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAK 102
G+SKG+AYI F ++A K +EE G + + + + +
Sbjct: 132 DGKSKGIAYIEFKSEADAEKNLEEKQGAEI--DGRSVSLYYTGE 173
Score = 63.4 bits (155), Expect = 1e-12
Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 7/85 (8%)
Query: 15 EYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSK 72
E ++ LFI L + + +L+ S ++ V D TG ++ Y+ F
Sbjct: 6 EGSESTTPFNLFIGNL-NPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYVDFES 63
Query: 73 TSEAAKAVEEMNGEFLPNHSKPIKV 97
+ KA+ E+ G + IK+
Sbjct: 64 AEDLEKAL-ELTGLKV--FGNEIKL 85
>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A
{Homo sapiens} SCOP: d.58.7.1
Length = 106
Score = 73.4 bits (181), Expect = 5e-17
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ TE+D+ F+ +G I+ I DR TG KG + + EA A+E +NG+ L
Sbjct: 34 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL--M 91
Query: 92 SKPIKV 97
+PI V
Sbjct: 92 GQPISV 97
>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 = 73.0 bits (180), Expect = 7e-17
Identities = 30/95 (31%), Positives = 47/95 (49%), Gaps = 7/95 (7%)
Query: 10 HDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAY 67
S + L++ L + ++ LR+ FSPFG I + + + G SKG +
Sbjct: 3 SGSSGDRITRYQVVNLYVKNL-DDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGF 59
Query: 68 IRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAK 102
+ FS EA KAV EMNG + +KP+ V +A +
Sbjct: 60 VCFSSPEEATKAVTEMNGRIV--ATKPLYVALAQR 92
>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural
genomi center for structural genomics, JCSG, protein
structure INI PSI-biology; 2.54A {Homo sapiens} PDB:
1no8_A
Length = 107
Score = 73.1 bits (180), Expect = 7e-17
Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
V++ D+++ F+ FG +++ DR +G S G A + F + ++A KA+++ NG L
Sbjct: 40 GVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPL--D 96
Query: 92 SKPIKVLIA 100
+P+ + +
Sbjct: 97 GRPMNIQLV 105
>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}
Length = 95
Score = 72.7 bits (179), Expect = 7e-17
Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 7/88 (7%)
Query: 19 EPPHSRLFI--LCGKDVTEDDLRQGFSPFGN--IQEIRCVKDRNTGESKGVAYIRFSKTS 74
+ + + D + SP+ + + IR +KD+ T +++G A+++ S
Sbjct: 6 HHHMDTIILRNIA-PHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAM 64
Query: 75 EAAKAVEEMNGEFLPNH--SKPIKVLIA 100
+A++ ++ + P K I V A
Sbjct: 65 DASQLLQILQSLHPPLKIDGKTIGVDFA 92
>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 = 72.6 bits (179), Expect = 8e-17
Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ D LR+ F +G + ++ ++ +T +G A++RF +A A M+G L
Sbjct: 24 RTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAEL--D 81
Query: 92 SKPIKVLIA 100
+ ++V +A
Sbjct: 82 GRELRVQVA 90
>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 = 72.7 bits (179), Expect = 9e-17
Identities = 30/66 (45%), Positives = 42/66 (63%), Gaps = 2/66 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
++TED LR F PFG I+ I+ + D TG SKG +I FS + A KA+E++NG L
Sbjct: 37 NITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFEL--A 94
Query: 92 SKPIKV 97
+P+KV
Sbjct: 95 GRPMKV 100
>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 = 72.3 bits (178), Expect = 9e-17
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
D TE+ + S G + ++ + D TG SKG A+I F +A AV +NG L
Sbjct: 13 DQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL--G 70
Query: 92 SKPIKV 97
S+ +K
Sbjct: 71 SRFLKC 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 = 72.8 bits (179), Expect = 1e-16
Identities = 18/69 (26%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
V++ D+++ F+ FG +++ DR +G S G A + F + ++A KA+++ G L
Sbjct: 46 GVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPL--D 102
Query: 92 SKPIKVLIA 100
+P+ + +
Sbjct: 103 GRPMDIQLV 111
>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM
domaim, RDB, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 100
Score = 71.9 bits (177), Expect = 1e-16
Identities = 25/92 (27%), Positives = 47/92 (51%), Gaps = 8/92 (8%)
Query: 12 RSREYNDEPPHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYI 68
Y+ +LFI T+++L + G ++++R V +R G+ KG+AY+
Sbjct: 7 GVFRYSTSLEKHKLFI--SGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYV 63
Query: 69 RFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIA 100
+ S+A++AV +M+G + IKV I+
Sbjct: 64 EYENESQASQAVMKMDGMTI--KENIIKVAIS 93
>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 = 72.0 bits (177), Expect = 2e-16
Identities = 16/69 (23%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 32 DVTEDDLRQGFSPFG-NIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPN 90
+ E+ + + F+ G + ++ +++R TG G ++ F+ + A K + ++NG+ LP
Sbjct: 20 YMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPG 79
Query: 91 H--SKPIKV 97
+K K+
Sbjct: 80 ATPAKRFKL 88
>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 = 72.5 bits (178), Expect = 2e-16
Identities = 28/92 (30%), Positives = 44/92 (47%), Gaps = 12/92 (13%)
Query: 12 RSREYNDEPPHS---RLFILCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYI 68
RS + + L++ G+D+T LR FSPFGNI ++ + A++
Sbjct: 26 RSDSFPERRAPRKGNTLYV-YGEDMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFV 78
Query: 69 RFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIA 100
+ K A +AV E+NG + S +KV IA
Sbjct: 79 TYEKMESADQAVAELNGTQV--ESVQLKVNIA 108
Score = 25.5 bits (56), Expect = 9.3
Identities = 6/23 (26%), Positives = 10/23 (43%)
Query: 220 QTLHGAEMYGSRLKVMEADPPKG 242
L+G ++ +LKV A
Sbjct: 91 AELNGTQVESVQLKVNIARKQPM 113
>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 = 72.0 bits (177), Expect = 2e-16
Identities = 29/96 (30%), Positives = 42/96 (43%), Gaps = 16/96 (16%)
Query: 8 NTHDRSRE--YNDEPPH-SRLFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGE 61
NT E N P ++ G +T+ +RQ FSPFG I EIR +
Sbjct: 8 NTKQLRFEDVVNQSSPKNCTVYC--GGIASGLTDQLMRQTFSPFGQIMEIRVFPE----- 60
Query: 62 SKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKV 97
KG +++RFS AA A+ +NG + +K
Sbjct: 61 -KGYSFVRFSTHESAAHAIVSVNGTTI--EGHVVKC 93
>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 = 72.5 bits (178), Expect = 2e-16
Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
TE DLR+ FS +G I ++ V D+ + S+G A++ F +A +A E NG L
Sbjct: 57 YTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL--D 114
Query: 92 SKPIKVLIA 100
+ I+V +
Sbjct: 115 GRRIRVDFS 123
>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 = 71.0 bits (175), Expect = 3e-16
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 8/85 (9%)
Query: 20 PPHSRLFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRN-TGESKGVAYIRFSKTSE 75
+++ I G ++VT+D + + FS +G I+ I +R SKG AY+ F E
Sbjct: 2 MKPTKVHI--GRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDE 59
Query: 76 AAKAVEEMNGEFLPNHSKPIKVLIA 100
A KA++ M+G + + I
Sbjct: 60 AEKALKHMDGGQI--DGQEITATAV 82
>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 = 75.3 bits (184), Expect = 3e-16
Identities = 26/155 (16%), Positives = 54/155 (34%), Gaps = 12/155 (7%)
Query: 18 DEPPHSRLFI--LCGKDVTEDDLRQG----FSPFGNIQEIRCVKDRNTGESKGVAYIRFS 71
+ P+ ++I L + + +D+L++ FS FG I +I + + + +G A++ F
Sbjct: 5 ETRPNHTIYINNL-NEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFK 60
Query: 72 KTSEAAKAVEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRGGQKISVQYTSPQSAAYARDK 131
+ S A A+ M G + KP+++ A G + + +++
Sbjct: 61 EVSSATNALRSMQGFPF--YDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQET 118
Query: 132 FHGFAYPPGIPMVVVPDFSYGLPRNGASALGGNAA 166
G V G
Sbjct: 119 PATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRI 153
Score = 61.0 bits (147), Expect = 3e-11
Identities = 18/100 (18%), Positives = 35/100 (35%), Gaps = 6/100 (6%)
Query: 3 RNYRINTHDRSREYNDEPPHSRLFILCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGES 62
+ + P H ++ E L F+ F +E+R V R
Sbjct: 189 QLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----- 243
Query: 63 KGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAK 102
+A++ F +A A + + G + + +K+ A K
Sbjct: 244 HDIAFVEFDNEVQAGAARDALQGFKITQ-NNAMKISFAKK 282
>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 = 71.2 bits (175), Expect = 3e-16
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ ED++++ F +G I+ I DR TG SKG A + + +A A E +NG +
Sbjct: 37 EAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI--M 94
Query: 92 SKPIKV 97
+ I+V
Sbjct: 95 GQTIQV 100
>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 = 72.1 bits (177), Expect = 3e-16
Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
V E LRQ F +G I+ ++ V DR T +S+G +++F S A +A+ +NG + N
Sbjct: 53 TVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN- 111
Query: 92 SKPIKV 97
K +KV
Sbjct: 112 -KRLKV 116
>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 = 71.1 bits (175), Expect = 3e-16
Identities = 22/103 (21%), Positives = 41/103 (39%), Gaps = 10/103 (9%)
Query: 11 DRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYI 68
+ E ++ LFI L + + +L+ S ++ V D TG ++ Y+
Sbjct: 6 EDPVEGSESTTPFNLFIGNL-NPNKSVAELKVAISELFAKNDLA-VVDVRTGTNRKFGYV 63
Query: 69 RFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRG 111
F + KA+ E+ G + IK+ ++G RG
Sbjct: 64 DFESAEDLEKAL-ELTGLKV--FGNEIKLEKPKG---RDGTRG 100
>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 = 70.7 bits (174), Expect = 4e-16
Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 7/82 (8%)
Query: 19 EPPHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSE 75
+LF+ G D E L Q FS +G I E+ VKDR T S+G ++ F +
Sbjct: 9 ASDEGKLFV--GGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDD 66
Query: 76 AAKAVEEMNGEFLPNHSKPIKV 97
A A+ MNG+ + + I+V
Sbjct: 67 AKDAMMAMNGKSV--DGRQIRV 86
>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 = 70.4 bits (173), Expect = 5e-16
Identities = 18/72 (25%), Positives = 34/72 (47%), Gaps = 5/72 (6%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGE---SKGVAYIRFSKTSEAAKAVEEMNGEFL 88
TE+ L+ FS G I+ K +N S G ++ + K +A KA++++ G +
Sbjct: 16 STTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTV 75
Query: 89 PNHSKPIKVLIA 100
++V I+
Sbjct: 76 --DGHKLEVRIS 85
>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 = 72.2 bits (177), Expect = 5e-16
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ D LR+ F +G + ++ +DR T ES+G A++RF +A A++ M+G L
Sbjct: 81 RTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL--D 138
Query: 92 SKPIKVLIA 100
+ ++V +A
Sbjct: 139 GRELRVQMA 147
>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 = 70.4 bits (173), Expect = 6e-16
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
V+E L + F G + KDR TG+ +G ++ F +A A++ M+ L +
Sbjct: 26 KVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKL--Y 83
Query: 92 SKPIKV 97
KPI+V
Sbjct: 84 GKPIRV 89
Score = 30.7 bits (70), Expect = 0.15
Identities = 7/43 (16%), Positives = 16/43 (37%), Gaps = 9/43 (20%)
Query: 216 VEFS---------QTLHGAEMYGSRLKVMEADPPKGDRNRKRQ 249
VEF + + ++YG ++V +A + +
Sbjct: 62 VEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSS 104
>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 = 73.2 bits (179), Expect = 7e-16
Identities = 26/137 (18%), Positives = 47/137 (34%), Gaps = 7/137 (5%)
Query: 32 DVTEDDLRQGFSPFG--NIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLP 89
T++DL + G +I EI+ ++R G+SKG A + + + K ++ + L
Sbjct: 79 WTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKREL- 137
Query: 90 NHSKPIKVLIAAKLEFKEGYRGGQKISVQYTSPQSAAYARDKFHGFAYPPGIPMVVVPDF 149
H + V K + +K S Q + + G + P
Sbjct: 138 -HGQNPVVTPVNKQFLSQFEMQSRK---TTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRG 193
Query: 150 SYGLPRNGASALGGNAA 166
+ G G A
Sbjct: 194 RFPGAVPGGDRFPGPAG 210
>3sde_A Paraspeckle component 1; RRM, anti parallel right handed
coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A
{Homo sapiens} PDB: 3sde_B
Length = 261
Score = 74.0 bits (182), Expect = 7e-16
Identities = 30/134 (22%), Positives = 51/134 (38%), Gaps = 9/134 (6%)
Query: 17 NDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTS 74
+ L + L V+ + L Q FS FG +++ V D + G + G ++ F+
Sbjct: 91 RFATHGAALTVKNL-SPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKP 148
Query: 75 EAAKAVEEMN-GEFLPNHSKPIKVLIAAKLEFKEGYRGGQKISVQYTSPQSAAYARDKFH 133
A KA+E G FL + +I +E + G + +Q T R++
Sbjct: 149 PARKALERCGDGAFLLT--TTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYH--KEREQPP 204
Query: 134 GFAYPPGIPMVVVP 147
FA P
Sbjct: 205 RFAQPGTFEFEYAS 218
Score = 62.0 bits (151), Expect = 1e-11
Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 11/87 (12%)
Query: 13 SREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRF 70
RLF+ L D+TE+D ++ F +G E+ +DR G +IR
Sbjct: 13 KPGEKTYTQRCRLFVGNL-PTDITEEDFKRLFERYGEPSEVFINRDR------GFGFIRL 65
Query: 71 SKTSEAAKAVEEMNGEFLPNHSKPIKV 97
+ A A E++G L S+P+++
Sbjct: 66 ESRTLAEIAKAELDGTIL--KSRPLRI 90
>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 104
Score = 70.0 bits (172), Expect = 9e-16
Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 6/88 (6%)
Query: 18 DEPPHSRLFI--LCGKDVTEDDLRQGFS-PFGNIQEIRCVKDRNTGESKGVAYIRFSKTS 74
P LF+ L DV + L + F + + + + V D+ TG SKG +++F+
Sbjct: 5 SSGPEYSLFVGDL-TPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDEL 62
Query: 75 EAAKAVEEMNGEFLPNHSKPIKVLIAAK 102
E +A+ E G SKP+++ +A
Sbjct: 63 EQKRALTECQGAVGLG-SKPVRLSVAIP 89
>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding
protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A
Length = 135
Score = 70.9 bits (174), Expect = 9e-16
Identities = 24/93 (25%), Positives = 44/93 (47%), Gaps = 7/93 (7%)
Query: 11 DRSREYNDEPPHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAY 67
R D + L + + D LR+ F +G + ++ +DR T ES+G A+
Sbjct: 36 SYGRPPPDVEGMTSLKV--DNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAF 93
Query: 68 IRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIA 100
+RF +A A++ M+G L + ++V +A
Sbjct: 94 VRFHDKRDAEDAMDAMDGAVL--DGRELRVQMA 124
>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 = 69.6 bits (171), Expect = 1e-15
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
V E+ L + F G + ++ KDR G+ K ++ F + A+ +NG L +
Sbjct: 27 RVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRL--Y 83
Query: 92 SKPIKVLIAA 101
+PI V +
Sbjct: 84 GRPINVSGPS 93
>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 = 69.6 bits (171), Expect = 1e-15
Identities = 24/100 (24%), Positives = 49/100 (49%), Gaps = 19/100 (19%)
Query: 18 DEPPHSRLFI--LCGKDVTEDDLRQG----FSPFGNIQEIRCVKDRNTGESKGVAYIRFS 71
+ P+ ++I L + + +D+L++ FS FG I +I + + + +G A++ F
Sbjct: 4 ETRPNHTIYINNL-NEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFK 59
Query: 72 KTSEAAKAVEEMNGEFLPNHSKPIKVLIA-------AKLE 104
+ S A A+ M G + KP+++ A AK++
Sbjct: 60 EVSSATNALRSMQGFPF--YDKPMRIQYAKTDSDIIAKMK 97
>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 = 70.1 bits (172), Expect = 1e-15
Identities = 27/84 (32%), Positives = 42/84 (50%), Gaps = 3/84 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ TE+D+ F+ +G I+ I DR TG KG + + EA A+E +NG+ L
Sbjct: 33 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL--M 90
Query: 92 SKPIKVLIAA-KLEFKEGYRGGQK 114
+PI V + K RGG++
Sbjct: 91 GQPISVDWCFVRGPPKGKRRGGRR 114
>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 = 69.6 bits (171), Expect = 2e-15
Identities = 25/84 (29%), Positives = 38/84 (45%), Gaps = 4/84 (4%)
Query: 31 KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPN 90
K + L FS FGNI + V D N SKG ++ F A +A+E+MNG L
Sbjct: 15 KSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLL-- 70
Query: 91 HSKPIKVLIAAKLEFKEGYRGGQK 114
+ + + V + +E G +
Sbjct: 71 NDRKVFVGRFKSRKEREAELGARA 94
>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 = 70.2 bits (172), Expect = 2e-15
Identities = 31/115 (26%), Positives = 45/115 (39%), Gaps = 17/115 (14%)
Query: 7 INTHDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRC-----VKDRNT 59
+ T R Y P+ R+++ L K V E DL+ F + + ++
Sbjct: 30 METLSVFRSYEPGEPNCRIYVKNL-AKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKE 88
Query: 60 GESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIA-------AKLEFKE 107
G KG A+I AAKA++E NG L KP+ V A E K
Sbjct: 89 GRMKGQAFIGLPNEKAAAKALKEANGYVL--FGKPMVVQFARSARPKQDPKEGKR 141
>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 = 70.6 bits (173), Expect = 2e-15
Identities = 19/55 (34%), Positives = 30/55 (54%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGE 86
+ ED++++ F +G I+ I DR TG SKG A + + +A A E +NG
Sbjct: 83 EAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGA 137
>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 = 68.9 bits (169), Expect = 3e-15
Identities = 23/95 (24%), Positives = 39/95 (41%), Gaps = 9/95 (9%)
Query: 13 SREYNDEPPHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIR 69
S +D +FI D E+ L + FG+++ +R V +T SKG A+ +
Sbjct: 6 SGLPSDVTEGKTVFI--RNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQ 63
Query: 70 FSKTSEAAKAVEEMNGEFLPN----HSKPIKVLIA 100
F A K + + E + +KV +A
Sbjct: 64 FMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLA 98
>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 = 72.3 bits (178), Expect = 3e-15
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 33 VTEDDLRQGFSPFGNIQEIRCVKDR-NTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ E+ LR+ F FG+I++I + + A++ F A +A+ +MN L
Sbjct: 223 LDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLL--G 279
Query: 92 SKPIKVLIAAK 102
++ I V +A K
Sbjct: 280 NREISVSLADK 290
Score = 71.2 bits (175), Expect = 1e-14
Identities = 14/91 (15%), Positives = 31/91 (34%), Gaps = 5/91 (5%)
Query: 23 SRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAV 80
L++ T+ ++R + + S+ AYI + +A V
Sbjct: 118 CTLWMTNFP-PSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 176
Query: 81 EEMNGEFLPNHSKPIKVLIAAKLEFKEGYRG 111
E++NG + + ++ LE +
Sbjct: 177 EKLNGLKI--EGYTLVTKVSNPLEKSKRTDS 205
Score = 67.3 bits (165), Expect = 2e-13
Identities = 20/137 (14%), Positives = 38/137 (27%), Gaps = 37/137 (27%)
Query: 31 KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPN 90
K ++ + + F G I + ++ A I F++ A A+ + +
Sbjct: 51 KSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKTHKVV--- 105
Query: 91 HSKPIKV--LIAAKL----------------EFKEGYRGGQKIS--------------VQ 118
I V L L ++ I +
Sbjct: 106 GQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYID 165
Query: 119 YTSPQSAAYARDKFHGF 135
TS + A Y +K +G
Sbjct: 166 VTSKEDARYCVEKLNGL 182
>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 = 68.2 bits (167), Expect = 6e-15
Identities = 22/69 (31%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
T DL FS G+I I + D+ +G KG AYI F+ + A M+
Sbjct: 47 GSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA-ERNSVDAAVAMDETVF--R 103
Query: 92 SKPIKVLIA 100
+ IKVL
Sbjct: 104 GRTIKVLPK 112
>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 = 67.2 bits (165), Expect = 6e-15
Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNG-EFLPN 90
T ++L F G++ + + D+ +G KG AYI FS E+ + ++ F
Sbjct: 17 GATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFS-DKESVRTSLALDESLF--- 72
Query: 91 HSKPIKVLIA 100
+ IKV+
Sbjct: 73 RGRQIKVIPK 82
>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 = 67.7 bits (166), Expect = 7e-15
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ DL FS G ++++R + DRN+ SKG+AY+ F ++ + G+ L
Sbjct: 36 RIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF-CEIQSVPLAIGLTGQRL--L 92
Query: 92 SKPIKVLIA 100
PI V +
Sbjct: 93 GVPIIVQAS 101
>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA
recognition, stress granules, nucleus, RNA-binding,
transcription; NMR {Saccharomyces cerevisiae}
Length = 101
Score = 66.9 bits (164), Expect = 1e-14
Identities = 17/86 (19%), Positives = 30/86 (34%), Gaps = 14/86 (16%)
Query: 16 YNDEPPHSR-LFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFS 71
PP +I G TE DL F FG I + + + KG +I++
Sbjct: 20 IRSAPPRVTTAYI--GNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYD 71
Query: 72 KTSEAAKAVEEMNGEFLPNHSKPIKV 97
+AA + + + ++
Sbjct: 72 THEQAAVCIVALANFPF--QGRNLRT 95
>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 = 66.1 bits (162), Expect = 2e-14
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 9/85 (10%)
Query: 15 EYNDEPPHSRLFILCG--KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSK 72
Y P +RL++ G + + L + F FG+I+ I VK + AYI++
Sbjct: 10 GYGKANPTTRLWV-GGLGPNTSLAALAREFDRFGSIRTIDHVKGDSF------AYIQYES 62
Query: 73 TSEAAKAVEEMNGEFLPNHSKPIKV 97
A A +M G L + ++V
Sbjct: 63 LDAAQAACAKMRGFPLGGPDRRLRV 87
>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 = 69.0 bits (168), Expect = 2e-14
Identities = 18/106 (16%), Positives = 37/106 (34%), Gaps = 3/106 (2%)
Query: 1 MDRNYRINTHDRSREYNDEPPHSRLFIL-CGKDVTEDDLRQGFSPFGNIQEIRCVKDRNT 59
RN R +T +++ + + P + L +VTE++ + G +
Sbjct: 102 ESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK 161
Query: 60 GESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAKLEF 105
E + + S+A + + +N + N KL F
Sbjct: 162 SERSSSGLLEWDSKSDALETLGFLNHYQMKN--PNGPYPYTLKLCF 205
Score = 59.7 bits (144), Expect = 4e-11
Identities = 18/123 (14%), Positives = 46/123 (37%), Gaps = 13/123 (10%)
Query: 20 PPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAA 77
L + L + D + F +GN+++++ +K + G A + +
Sbjct: 2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVD 56
Query: 78 KAVEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRGGQKISVQYTSPQSAAYARDKFHGFAY 137
+A+ +N F+ + + V ++ + G G + S ++ + + F+
Sbjct: 57 RAITHLNNNFM--FGQKMNVCVSKQPAIMPGQSYGLEDG----SCSYKDFSESRNNRFST 110
Query: 138 PPG 140
P
Sbjct: 111 PEQ 113
>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 = 66.6 bits (163), Expect = 2e-14
Identities = 19/83 (22%), Positives = 42/83 (50%), Gaps = 3/83 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
V L++ FS G + ++D++ G+S+G+ + F ++ EA +A+ NG+ L
Sbjct: 26 KVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAISMFNGQLL--F 82
Query: 92 SKPIKVLIAAKLEFKEGYRGGQK 114
+P+ V + + K + ++
Sbjct: 83 DRPMHVKMDERALPKGDFFPPER 105
>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 = 65.7 bits (161), Expect = 2e-14
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 32 DVTEDDLRQGFSPFG--NIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLP 89
T++DL + G +I EI+ ++R G+SKG A + + + K ++ + L
Sbjct: 12 WTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKREL- 70
Query: 90 NHSKPIKVLIA 100
H + V +
Sbjct: 71 -HGQNPVVTPS 80
>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein
complex, coexpression, heterotetramer, mRNA maturation,
mRNA cleavage; 1.92A {Homo sapiens}
Length = 156
Score = 67.6 bits (165), Expect = 3e-14
Identities = 19/111 (17%), Positives = 40/111 (36%), Gaps = 24/111 (21%)
Query: 32 DVTEDDLRQGFSPFG--NIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLP 89
T+ L Q G ++ E++ ++R G+SKG A + + + K +E + G+ L
Sbjct: 66 WTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVL- 124
Query: 90 NHSKPIKVLIAAKLEFKEGYRGGQKISVQYTSPQSAAYARDKFHGFAYPPG 140
G+K+ V+ + Q+ + +
Sbjct: 125 ---------------------NGEKVDVRPATRQNLSQFEAQARKRECVRV 154
>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 = 65.7 bits (161), Expect = 3e-14
Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 10/81 (12%)
Query: 8 NTHDRSREYNDEPPHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKG 64
+ + L ++TED+L++ F I G+SKG
Sbjct: 2 HMLEDPCTSKKVRAARTLLA--KNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKG 54
Query: 65 VAYIRFSKTSEAAKAVEEMNG 85
+AYI F ++A K +EE G
Sbjct: 55 IAYIEFKSEADAEKNLEEKQG 75
>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A
{Saccharomyces cerevisiae} PDB: 3ns5_A
Length = 100
Score = 65.5 bits (160), Expect = 4e-14
Identities = 13/55 (23%), Positives = 25/55 (45%)
Query: 31 KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNG 85
V + L FS G + + D TG++KG ++ ++A K ++ +G
Sbjct: 22 VPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR
{Homo sapiens}
Length = 116
Score = 65.9 bits (161), Expect = 4e-14
Identities = 32/108 (29%), Positives = 49/108 (45%), Gaps = 16/108 (14%)
Query: 18 DEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQE--------IRCVKDRNTGESKGVAY 67
D ++ +F+ L G++VT + + F G I+ I DR TG+ KG A
Sbjct: 3 DNSDNNTIFVQGL-GENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61
Query: 68 IRFSKTSEAAKAVEEMNG-EFLPNHSKPIKVLIAA-KLEFKEGYRGGQ 113
+ F A A++ +G EF N PIKV A + +F G G+
Sbjct: 62 VSFDDPPSAKAAIDWFDGKEFSGN---PIKVSFATRRADFNRGGGNGR 106
Score = 26.6 bits (59), Expect = 3.6
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 220 QTLHGAEMYGSRLKVMEADPPKGDRNRK 247
G E G+ +KV A + D NR
Sbjct: 75 DWFDGKEFSGNPIKVSFAT-RRADFNRG 101
>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP
domain, MIF4G domain, RNA maturation, RNA export,
nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP:
d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B
3fey_B 1h6k_X
Length = 156
Score = 67.1 bits (164), Expect = 4e-14
Identities = 25/118 (21%), Positives = 48/118 (40%), Gaps = 13/118 (11%)
Query: 5 YRINTHDRSREYNDEP--PHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNT 59
YR E ++ L++ G TE+ + + FS G+I++I D+
Sbjct: 20 YRDQHFRGDNEEQEKLLKKSCTLYV--GNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMK 77
Query: 60 GESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAKLE----FKEGYRGGQ 113
+ G ++ + ++A A+ +NG L + I+ A + + G GGQ
Sbjct: 78 KTACGFCFVEYYSRADAENAMRYINGTRLDDR--IIRTDWDAGFKEGRQYGRGRSGGQ 133
>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain.,
transport protein; NMR {Mus musculus}
Length = 177
Score = 67.2 bits (164), Expect = 5e-14
Identities = 20/76 (26%), Positives = 46/76 (60%), Gaps = 4/76 (5%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
V++ D+++ F+ FG +++ DR +G S G A + F + ++A KA+++ G L
Sbjct: 99 GVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPL--D 155
Query: 92 SKPIKV-LIAAKLEFK 106
+P+ + L+A++++ +
Sbjct: 156 GRPMDIQLVASQIDLE 171
>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 = 65.0 bits (159), Expect = 6e-14
Identities = 26/91 (28%), Positives = 40/91 (43%), Gaps = 13/91 (14%)
Query: 13 SREYNDEPPHSRLFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIR 69
S SRLF+ G D+TE+++R+ F +G E+ KD KG +IR
Sbjct: 6 SGGEKTFTQRSRLFV--GNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIR 57
Query: 70 FSKTSEAAKAVEEMNGEFLPNHSKPIKVLIA 100
+ A A E++ L K ++V A
Sbjct: 58 LETRTLAEIAKVELDNMPL--RGKQLRVRFA 86
>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 = 65.0 bits (159), Expect = 7e-14
Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 9/84 (10%)
Query: 17 NDEPPHSRLFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKT 73
D+ L++ G +DVTE + Q FS G + + + + + ++ F +
Sbjct: 10 EDDGQPRTLYV--GNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEH 65
Query: 74 SEAAKAVEEMNGEFLPNHSKPIKV 97
+AA A+ MNG + K +KV
Sbjct: 66 RDAAAALAAMNGRKI--LGKEVKV 87
Score = 26.4 bits (59), Expect = 4.5
Identities = 9/40 (22%), Positives = 16/40 (40%), Gaps = 9/40 (22%)
Query: 216 VEFS---------QTLHGAEMYGSRLKVMEADPPKGDRNR 246
VEF ++G ++ G +KV A P ++
Sbjct: 60 VEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSSQKSG 99
>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 = 64.6 bits (158), Expect = 8e-14
Identities = 18/54 (33%), Positives = 27/54 (50%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNG 85
+ TE+ L+ FS G + R V DR TG+ KG + + A A+ +NG
Sbjct: 19 EATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNG 72
>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 = 64.6 bits (158), Expect = 9e-14
Identities = 26/95 (27%), Positives = 40/95 (42%), Gaps = 17/95 (17%)
Query: 18 DEPPHSRLFILCG---KDVTEDDLRQGFSPFGNIQE--------IRCVKDRNTGESKGVA 66
++ +F+ ++VT + + F G I+ I DR TG+ KG A
Sbjct: 9 SHSDNNTIFV--QGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 66
Query: 67 YIRFSKTSEAAKAVEEMNG-EFLPNHSKPIKVLIA 100
+ F A A++ +G EF N PIKV A
Sbjct: 67 TVSFDDPPSAKAAIDWFDGKEFSGN---PIKVSFA 98
>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 109
Score = 64.6 bits (158), Expect = 1e-13
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ DLRQ F FG I ++ + + SKG ++ F +++A +A E+++G +
Sbjct: 40 RFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVV--E 95
Query: 92 SKPIKV 97
+ I+V
Sbjct: 96 GRKIEV 101
>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed
protein, RRM, U1A, RNA binding protein; NMR {Homo
sapiens}
Length = 127
Score = 64.9 bits (158), Expect = 1e-13
Identities = 19/101 (18%), Positives = 37/101 (36%), Gaps = 12/101 (11%)
Query: 6 RINTHDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQG----FSPFGNIQEIRCVKDRNT 59
+++ D P + I + +V ++ L+ S G+I +I +
Sbjct: 13 HMDSPDLGSTPPHTEPSQVVLITNI-NPEVPKEKLQALLYALASSQGDILDIVV---DLS 68
Query: 60 GESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIA 100
++ G AYI F+ A VE G P+ + +
Sbjct: 69 DDNSGKAYIVFATQESAQAFVEAFQGYPF--QGNPLVITFS 107
>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 = 63.8 bits (156), Expect = 2e-13
Identities = 19/89 (21%), Positives = 34/89 (38%), Gaps = 11/89 (12%)
Query: 12 RSREYNDEPPHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYI 68
S L + TE+ L++ F I+ V G+SKG A+I
Sbjct: 5 SSGNSTWSGESKTLVL--SNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFI 58
Query: 69 RFSKTSEAAKAVEEMNGEFLPNHSKPIKV 97
F+ +A +A+ N + + I++
Sbjct: 59 EFASFEDAKEALNSCNKREI--EGRAIRL 85
>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 = 63.5 bits (155), Expect = 2e-13
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ DLRQ F FG I ++ + + SKG ++ F +++A +A E+++G +
Sbjct: 26 RFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVV--E 81
Query: 92 SKPIKV 97
+ I+V
Sbjct: 82 GRKIEV 87
>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 = 65.8 bits (160), Expect = 4e-13
Identities = 22/127 (17%), Positives = 49/127 (38%), Gaps = 9/127 (7%)
Query: 18 DEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSE 75
+S L + L + VT L F +G++Q ++ + + K A ++ + ++
Sbjct: 30 AGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQ 84
Query: 76 AAKAVEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRGGQKISVQYTSPQSAAYARDKFHGF 135
A A+ +NG L I + ++ + Q ++ Y + + + F
Sbjct: 85 AQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNF 144
Query: 136 --AYPPG 140
+PP
Sbjct: 145 QNIFPPS 151
Score = 62.3 bits (151), Expect = 6e-12
Identities = 19/96 (19%), Positives = 40/96 (41%), Gaps = 6/96 (6%)
Query: 3 RNYRINTHDRSREYNDEPPHSRLFIL-CGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGE 61
+R N PP + L + V+E+DL+ FS G + + ++
Sbjct: 132 PLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD--- 188
Query: 62 SKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKV 97
+ +A I+ EA +A+ +++ L + ++V
Sbjct: 189 -RKMALIQMGSVEEAVQALIDLHNHDLGE-NHHLRV 222
>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 = 62.3 bits (152), Expect = 6e-13
Identities = 26/82 (31%), Positives = 42/82 (51%), Gaps = 10/82 (12%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
VTE+ L + FS FG ++ ++ + K A+I F + A KA+EEMNG+ L
Sbjct: 22 TVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEEMNGKDL--E 71
Query: 92 SKPIKVLIAAKLEFKEGYRGGQ 113
+ I+++ A + K R Q
Sbjct: 72 GENIEIVFAKPPDQKRKERKAQ 93
Score = 26.1 bits (58), Expect = 4.8
Identities = 7/44 (15%), Positives = 20/44 (45%), Gaps = 9/44 (20%)
Query: 216 VEFS---------QTLHGAEMYGSRLKVMEADPPKGDRNRKRQR 250
+ F + ++G ++ G ++++ A PP R ++ +
Sbjct: 50 IHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQ 93
>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 = 62.7 bits (153), Expect = 6e-13
Identities = 24/114 (21%), Positives = 47/114 (41%), Gaps = 9/114 (7%)
Query: 8 NTHDRSREYNDEPPHSR-LFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESK 63
++ + + +F+ G T+ LR+ F FG+I+E + DR TG+S+
Sbjct: 2 SSGSSGMHGSQKDTTFTKIFV--GGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSR 59
Query: 64 GVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRGGQKISV 117
G ++ + + A +A ++ N + V +A + G I V
Sbjct: 60 GYGFVTMADRAAAERACKDPNPII---DGRKANVNLAYLGAKPRSLQTGFAIGV 110
>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 = 62.3 bits (152), Expect = 7e-13
Identities = 17/91 (18%), Positives = 38/91 (41%), Gaps = 9/91 (9%)
Query: 12 RSREYNDEPPHSRLFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDR-NTGESKGVAY 67
S + + S++ + + ++R+ FS FG ++ +R K TG +G +
Sbjct: 5 SSGQVPKKQTTSKILV--RNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62
Query: 68 IRFSKTSEAAKAVEEM-NGEFLPNHSKPIKV 97
+ F +A KA + + L + + +
Sbjct: 63 VDFITKQDAKKAFNALCHSTHLYG--RRLVL 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 = 61.9 bits (151), Expect = 8e-13
Identities = 22/83 (26%), Positives = 41/83 (49%), Gaps = 5/83 (6%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ E ++R F+ +G+++E++ + DR TG SKG ++ F + K VE F H
Sbjct: 20 RMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQI-NF---H 74
Query: 92 SKPIKVLIAAKLEFKEGYRGGQK 114
K +K+ A + + Y +
Sbjct: 75 GKKLKLGPAIRKQNLSTYHVQPR 97
>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 = 61.1 bits (149), Expect = 1e-12
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 9/68 (13%)
Query: 31 KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEM-NGEFLP 89
+TE DLR F FG I+ I V+ + A+I+F+ A A E+ N +
Sbjct: 22 DTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIV- 74
Query: 90 NHSKPIKV 97
+ + + V
Sbjct: 75 -NGRRLNV 81
>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding
proteins, RNA binding protein/SS-DNA binding protein
complex; NMR {Helicobacter pylori}
Length = 90
Score = 61.0 bits (149), Expect = 1e-12
Identities = 11/54 (20%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNG 85
T + +++ FS FG + ++ + DR T + KG ++ ++A+ +++
Sbjct: 12 SATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKLDN 64
Score = 29.1 bits (66), Expect = 0.37
Identities = 9/42 (21%), Positives = 14/42 (33%), Gaps = 8/42 (19%)
Query: 216 VEFS--------QTLHGAEMYGSRLKVMEADPPKGDRNRKRQ 249
VE L + G ++V EA+P K +
Sbjct: 48 VEMQEESVSEAIAKLDNTDFMGRTIRVTEANPKKSLEHHHHH 89
>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} PDB:
2dh9_A
Length = 92
Score = 61.1 bits (149), Expect = 1e-12
Identities = 21/82 (25%), Positives = 31/82 (37%), Gaps = 7/82 (8%)
Query: 31 KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPN 90
D T L+ F+ G++ + G+SKG ++F A +A MNG L
Sbjct: 18 FDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKL-- 73
Query: 91 HSKPIKVLIAAKLEFKEGYRGG 112
+ I V I G G
Sbjct: 74 SGREIDVRID---RNASGPSSG 92
>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 = 61.3 bits (149), Expect = 2e-12
Identities = 26/91 (28%), Positives = 36/91 (39%), Gaps = 13/91 (14%)
Query: 32 DVTEDDLRQGFSPFGNIQE--------IRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEM 83
VT DDL F G ++ I D+ TG+ KG A + + A AVE
Sbjct: 26 SVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWF 85
Query: 84 NG-EFLPNHSKPIKVLIA-AKLEFKEGYRGG 112
+G +F +KV +A K G G
Sbjct: 86 DGKDF---QGSKLKVSLARKKPPMNSGPSSG 113
>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 = 60.7 bits (148), Expect = 2e-12
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 10/82 (12%)
Query: 19 EPPHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSE 75
P LF+ D TE+ L++ F R V DR TG SKG ++ F+ +
Sbjct: 12 SQPSKTLFV--KGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEED 66
Query: 76 AAKAVEEMNGEFLPNHSKPIKV 97
A A E M + + +
Sbjct: 67 AKAAKEAMEDGEI--DGNKVTL 86
>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein,
ribosome biogenesis, RNA-binding, rRNA processing; NMR
{Saccharomyces cerevisiae} PDB: 2osq_A
Length = 108
Score = 61.2 bits (149), Expect = 2e-12
Identities = 25/92 (27%), Positives = 48/92 (52%), Gaps = 13/92 (14%)
Query: 13 SREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRF 70
E ++RLF+ DV E +L + F PFG ++E++ + G A++ F
Sbjct: 22 HHRQEGELSNTRLFVRPF-PLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEF 72
Query: 71 SKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAK 102
+ AAKA+EE++G+ ++P++V+ +
Sbjct: 73 EEAESAAKAIEEVHGKSF--ANQPLEVVYSKL 102
>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 = 60.8 bits (148), Expect = 2e-12
Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 8/69 (11%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+E+ + + F+ R K + A++ FS +A +A++ +NG+ L
Sbjct: 26 STSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVL--D 77
Query: 92 SKPIKVLIA 100
PI+V +A
Sbjct: 78 GSPIEVTLA 86
>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 = 60.6 bits (147), Expect = 3e-12
Identities = 12/82 (14%), Positives = 32/82 (39%), Gaps = 5/82 (6%)
Query: 20 PPHSRLFI--LCGKDVTEDDLRQGFSPFG-NIQEIRCVKD-RNTGESKGVAYIRFSKTSE 75
+ RLFI + K +++ + + + ++ + +++G A++ +
Sbjct: 6 SGNCRLFIGGIP-KMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRA 64
Query: 76 AAKAVEEMNGEFLPNHSKPIKV 97
AA A ++ + I V
Sbjct: 65 AAMARRKLMPGRIQLWGHQIAV 86
>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 = 62.2 bits (151), Expect = 4e-12
Identities = 19/96 (19%), Positives = 40/96 (41%), Gaps = 6/96 (6%)
Query: 3 RNYRINTHDRSREYNDEPPHSRLFIL-CGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGE 61
+R N PP + L + V+E+DL+ FS G + + + +
Sbjct: 101 PLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF----KFFQK 156
Query: 62 SKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKV 97
+ +A I+ EA +A+ +++ L + ++V
Sbjct: 157 DRKMALIQMGSVEEAVQALIDLHNHDLGE-NHHLRV 191
Score = 61.8 bits (150), Expect = 7e-12
Identities = 26/124 (20%), Positives = 54/124 (43%), Gaps = 13/124 (10%)
Query: 22 HSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKA 79
+S L + L + VT L F +G++Q ++ + + K A ++ + ++A A
Sbjct: 3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLA 57
Query: 80 VEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRG--GQKISVQYTSPQSAAYARDKFHGF-- 135
+ +NG L H KPI++ ++ + G Q ++ Y + + + F
Sbjct: 58 MSHLNGHKL--HGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQN 115
Query: 136 AYPP 139
+PP
Sbjct: 116 IFPP 119
>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein,
translation; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 103
Score = 59.4 bits (144), Expect = 7e-12
Identities = 13/58 (22%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 30 GKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEF 87
D T DD+++ G + I+ + + KG ++ F A K VE ++
Sbjct: 20 PTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKY 76
>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain,
RBD, structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 96
Score = 59.0 bits (143), Expect = 9e-12
Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ + L +G ++ V + V + +S +A +A++++NG L N
Sbjct: 26 HLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQALDKLNGFQLEN- 81
Query: 92 SKPIKV 97
+KV
Sbjct: 82 -FTLKV 86
>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 = 59.2 bits (144), Expect = 9e-12
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 17 NDEPPHSR-LFILCG--KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKT 73
+ L +L G TE DL++ FS FG + ++ KD TG SKG ++RF++
Sbjct: 9 KRAVQKTSDLIVL-GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 67
Query: 74 SEAAKAVEEMN 84
K + + +
Sbjct: 68 ETQVKVMSQRH 78
>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 = 59.3 bits (144), Expect = 1e-11
Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+T +++ F +G I++IR T E++G AY+ + +A AV+ ++G + N
Sbjct: 19 KITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVDHLSGFNVSN- 74
Query: 92 SKPIKVLIAA 101
+ + VL
Sbjct: 75 -RYLVVLYYN 83
>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif,
RRM, transcription termination, NUC phosphoprotein; NMR
{Saccharomyces cerevisiae}
Length = 96
Score = 58.0 bits (141), Expect = 2e-11
Identities = 26/100 (26%), Positives = 46/100 (46%), Gaps = 12/100 (12%)
Query: 15 EYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSK 72
E ++ PP SRLFI L K+V+++DL + FSP+G+I +I +I+F
Sbjct: 3 EMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDN 54
Query: 73 TSEAAKAVEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRGG 112
A+E + E K + + +++ + G
Sbjct: 55 PQSVRDAIECESQEMN--FGKKLILEVSSSNARPQFDHGD 92
>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 = 57.6 bits (140), Expect = 2e-11
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 11/68 (16%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNG--EFLP 89
VT DDLRQ F G A++ + + A +A+E ++G E
Sbjct: 19 AVTADDLRQLFGDRKL------PLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVEL-- 70
Query: 90 NHSKPIKV 97
H K ++V
Sbjct: 71 -HGKIMEV 77
>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 = 59.5 bits (145), Expect = 3e-11
Identities = 15/77 (19%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 17 NDEPPHSRLFI-LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSE 75
+++ ++F+ G DV + + FS +G I + + + D++TG+S+G ++ + +++
Sbjct: 82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY-DSAD 140
Query: 76 AAKAVEEMNGEFLPNHS 92
A V + +
Sbjct: 141 AVDRVCQNKFIDFKDRK 157
Score = 58.3 bits (142), Expect = 8e-11
Identities = 18/53 (33%), Positives = 32/53 (60%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMN 84
D TED+LR+ F +G + +++ +KD TG S+G ++ F K S + V+ +
Sbjct: 14 DTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH 66
>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding
domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: d.58.7.1
Length = 98
Score = 57.7 bits (140), Expect = 3e-11
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
V+ D++ F + I C+K G G A + F EA AV ++N +
Sbjct: 26 TVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI--G 83
Query: 92 SKPIKVLIAAK 102
S+ +K+++ +
Sbjct: 84 SRKVKLVLGSG 94
>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 103
Score = 57.7 bits (140), Expect = 3e-11
Identities = 23/108 (21%), Positives = 45/108 (41%), Gaps = 12/108 (11%)
Query: 11 DRSREYNDEP--PHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGV 65
+ P P ++ G + + D+ F I+ +R V+D++T + KG
Sbjct: 2 SSGSSGKELPTEPPYTAYV--GNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGF 58
Query: 66 AYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAA-KLEFKEGYRGG 112
Y+ F ++ K +G L + + ++V IA + + K G G
Sbjct: 59 CYVEFD-EVDSLKEALTYDGALLGD--RSLRVDIAEGRKQDKSGPSSG 103
Score = 28.8 bits (65), Expect = 0.60
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 8/41 (19%)
Query: 216 VEFSQ--------TLHGAEMYGSRLKVMEADPPKGDRNRKR 248
VEF + T GA + L+V A+ K D++
Sbjct: 61 VEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKSGPS 101
>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP
A1, RNA-recognition motif, RNA- binding, UP1, RNA
binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1
d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A
1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A*
1up1_A
Length = 196
Score = 59.2 bits (144), Expect = 5e-11
Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 12 RSREYNDEPPHSRLFIL-CGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRF 70
+S + +LFI + T++ LR F +G + + ++D NT S+G ++ +
Sbjct: 3 KSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 62
Query: 71 SKTSEAAKAVEE 82
+ E A+
Sbjct: 63 ATVEEVDAAMNA 74
Score = 58.5 bits (142), Expect = 1e-10
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 13 SREYNDEPPHS----RLFI-LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAY 67
SRE + P ++F+ +D E LR F +G I+ I + DR +G+ +G A+
Sbjct: 91 SREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAF 150
Query: 68 IRFSKTSEAAKAVEE 82
+ F K V +
Sbjct: 151 VTFDDHDSVDKIVIQ 165
>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; 2.00A {Homo sapiens} PDB:
2ek6_A
Length = 95
Score = 55.8 bits (135), Expect = 1e-10
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 2/71 (2%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
V+ D++ F + I C+K G G A + F EA AV ++N +
Sbjct: 26 TVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI--G 83
Query: 92 SKPIKVLIAAK 102
S+ +K+ +
Sbjct: 84 SRKVKLSGPSS 94
>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic
initiation factor 3 complex, RNA recognition motif; NMR
{Homo sapiens}
Length = 105
Score = 55.5 bits (134), Expect = 2e-10
Identities = 12/55 (21%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 31 KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNG 85
+ ++ + + FS FG I G++KG ++ ++ + A AV+ +G
Sbjct: 31 LEKLKNVIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNADG 83
>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3,
eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo
sapiens}
Length = 81
Score = 55.1 bits (133), Expect = 2e-10
Identities = 13/62 (20%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 31 KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNG-EFLP 89
+ ++ + + FS FG I G++KG ++ ++ + A AV+ +G +
Sbjct: 17 LEKLKNVIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK 74
Query: 90 NH 91
H
Sbjct: 75 QH 76
>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like,
structural genomics, joint center for struc genomics,
JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A
Length = 87
Score = 54.5 bits (132), Expect = 3e-10
Identities = 15/56 (26%), Positives = 27/56 (48%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEF 87
D ++ DL+ F+ FG + + D NTG S+G +I F + K +++
Sbjct: 22 DTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRL 77
>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 = 55.3 bits (133), Expect = 3e-10
Identities = 18/113 (15%), Positives = 36/113 (31%), Gaps = 20/113 (17%)
Query: 16 YNDEPPHSRLFILCGK---DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSK 72
L + G V+ + L G + + + K ++ R+
Sbjct: 19 ETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRT 72
Query: 73 TSEAAKAVEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRGGQKISVQYTSPQSA 125
T E+ +A +NG+ + + L +E VQ++ P S
Sbjct: 73 TEESKRAYVTLNGKEVVDDLGQKITLYLNFVE-----------KVQWSGPSSG 114
Score = 26.8 bits (59), Expect = 3.9
Identities = 5/47 (10%), Positives = 15/47 (31%), Gaps = 6/47 (12%)
Query: 117 VQYTSPQSAAYARDKFHGFAYPPGIPMVVVPDFSY------GLPRNG 157
+Y + + + A +G + + ++ P +G
Sbjct: 68 ARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWSGPSSG 114
>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A
Length = 75
Score = 54.0 bits (131), Expect = 4e-10
Identities = 11/54 (20%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNG 85
+ T +D++ F FG + + + D+ T +G ++ F ++ + + V E++
Sbjct: 10 NTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF-ESEDIVEKVCEIHF 62
>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A
Length = 110
Score = 54.3 bits (131), Expect = 6e-10
Identities = 21/100 (21%), Positives = 43/100 (43%), Gaps = 12/100 (12%)
Query: 3 RNYRINTHDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTG 60
+ ++ + + + + + +SR+FI L V + D+ FS +G +
Sbjct: 8 MSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV------- 60
Query: 61 ESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIA 100
KG A++++S A AV NG L + + + +A
Sbjct: 61 -HKGYAFVQYSNERHARAAVLGENGRVL--AGQTLDINMA 97
Score = 25.8 bits (57), Expect = 8.4
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 222 LHGAEMYGSRLKVMEADPPKGDRNR 246
+G + G L + A PK DR+
Sbjct: 82 ENGRVLAGQTLDINMAGEPKPDRSG 106
>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 = 54.1 bits (131), Expect = 6e-10
Identities = 14/66 (21%), Positives = 28/66 (42%), Gaps = 3/66 (4%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ E +LR+ F FG + E+ + D +G +I F ++ M+ +
Sbjct: 21 NCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE-DEQSVDQAVNMHFHDI--M 77
Query: 92 SKPIKV 97
K ++V
Sbjct: 78 GKKVEV 83
>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 = 53.3 bits (129), Expect = 7e-10
Identities = 14/51 (27%), Positives = 25/51 (49%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEE 82
D E+ +R+ F FG ++ I D T + +G +I F + K +E+
Sbjct: 10 DTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>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 = 54.0 bits (130), Expect = 8e-10
Identities = 13/76 (17%), Positives = 32/76 (42%), Gaps = 5/76 (6%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
E+D+R F + + +KD G + G ++F + +A+ + N +
Sbjct: 27 SAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLM--I 81
Query: 92 SKPIKVLIAAKLEFKE 107
+ ++V A + ++
Sbjct: 82 QRYVEVSPATERQWVA 97
>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 = 54.0 bits (130), Expect = 1e-09
Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 3/79 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+T+ D+ Q + V N G+ G A ++F K + A+ E ++ + L +
Sbjct: 26 SITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQF-KNEDDARKSERLHRKKL--N 82
Query: 92 SKPIKVLIAAKLEFKEGYR 110
+ V + + +E +
Sbjct: 83 GREAFVHVVTLEDMREIEK 101
>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold,
protein binding, nucleus; 2.04A {Homo sapiens}
Length = 100
Score = 53.2 bits (128), Expect = 1e-09
Identities = 17/92 (18%), Positives = 28/92 (30%), Gaps = 9/92 (9%)
Query: 8 NTHDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGV 65
+ + + + P + I L V E DL + FG I + + +
Sbjct: 7 HHMENYDDPHKTPASPVVHIRGLI-DGVVEADLVEALQEFGPISYVVVMPKKRQ------ 59
Query: 66 AYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKV 97
A + F A AV + P V
Sbjct: 60 ALVEFEDVLGACNAVNYAADNQIYIAGHPAFV 91
>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 = 53.4 bits (129), Expect = 1e-09
Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 6/75 (8%)
Query: 14 REYNDEPPHSR-LFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIR 69
E R LFI G + TE+ LR + +G + + ++D + S+G ++
Sbjct: 18 ERKKREKEQFRKLFI--GGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 75
Query: 70 FSKTSEAAKAVEEMN 84
FS +E A+
Sbjct: 76 FSSMAEVDAAMAARP 90
>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 = 52.7 bits (127), Expect = 2e-09
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 12/86 (13%)
Query: 17 NDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTS 74
SRLFI L K+V+++DL + FSP+G+I +I +I+F
Sbjct: 17 RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQ 68
Query: 75 EAAKAVEEMNGEFLPNHSKPIKVLIA 100
A+E + E K + + ++
Sbjct: 69 SVRDAIEXESQEMN--FGKKLILEVS 92
>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR
{Mus musculus} SCOP: d.58.7.1
Length = 77
Score = 52.1 bits (126), Expect = 2e-09
Identities = 13/51 (25%), Positives = 26/51 (50%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEE 82
T++ LR+ F FG ++E ++D T S+G ++ F + K + +
Sbjct: 11 QTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
>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 = 52.9 bits (127), Expect = 2e-09
Identities = 11/72 (15%), Positives = 32/72 (44%), Gaps = 8/72 (11%)
Query: 32 DVTEDDL---RQGFSPFGNIQEIRCVKDRNTGESK---GVAYIRFSKTSEAAKAVEEMNG 85
+ + ++ + F FG I ++ + S+ AY+ + ++ +A +A++ +N
Sbjct: 26 RLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNN 85
Query: 86 EFLPNHSKPIKV 97
+ + +K
Sbjct: 86 VVV--DGRTLKA 95
>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 = 53.7 bits (129), Expect = 2e-09
Identities = 18/100 (18%), Positives = 43/100 (43%), Gaps = 10/100 (10%)
Query: 3 RNYRINTHDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTG 60
+ H + P ++++ L G + + +L + F +G ++ + ++
Sbjct: 54 VTEGSHHHHHHMHRDSCPLDCKVYVGNL-GNNGNKTELERAFGYYGPLRSVWVARN---- 108
Query: 61 ESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIA 100
G A++ F +AA AV E++G L ++V ++
Sbjct: 109 -PPGFAFVEFEDPRDAADAVRELDGRTL--CGCRVRVELS 145
>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 = 52.4 bits (126), Expect = 2e-09
Identities = 13/76 (17%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+++++ Q FS + + G S G A+++F + E A+ + + E +
Sbjct: 26 GCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF-ASQEIAEKALKKHKERI--G 82
Query: 92 SKPIKVLIAAKLEFKE 107
+ I++ +++ E +
Sbjct: 83 HRYIEIFKSSRAEVRT 98
>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding
protein; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 105
Score = 51.8 bits (124), Expect = 5e-09
Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 10/91 (10%)
Query: 9 THDRSREYNDEPPHSRLFILCG--KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVA 66
+H + P SR+ + DVTE ++ PFG + + +K +N A
Sbjct: 4 SHHHHHHGSGVP--SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQ------A 55
Query: 67 YIRFSKTSEAAKAVEEMNGEFLPNHSKPIKV 97
+I + A V +PI +
Sbjct: 56 FIEMNTEEAANTMVNYYTSVTPVLRGQPIYI 86
>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 = 51.7 bits (124), Expect = 5e-09
Identities = 16/95 (16%), Positives = 30/95 (31%), Gaps = 8/95 (8%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
++++ FS FG++ + E A + F + EA KA + H
Sbjct: 21 GTLAAEIQETFSRFGSLGRVL------LPEGGITAIVEFLEPLEARKAFRHLAYSKF--H 72
Query: 92 SKPIKVLIAAKLEFKEGYRGGQKISVQYTSPQSAA 126
P+ + A F + Q +
Sbjct: 73 HVPLYLEWAPIGVFGAAPQKKDSQHEQPAEKAESG 107
>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 = 51.5 bits (124), Expect = 6e-09
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 6/75 (8%)
Query: 14 REYNDEPPHSRLFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRF 70
R + ++FI G T++ LR+ F FG ++E ++D T S+G ++ F
Sbjct: 17 RGSHMGSSGCKMFI--GGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
Query: 71 SKTSEAAKAVEEMNG 85
V +
Sbjct: 75 -MDQAGVDKVLAQSR 88
>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 = 51.1 bits (123), Expect = 6e-09
Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 10/81 (12%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
T +LR F G + E V K A++ K ++A A+ ++NG+ +
Sbjct: 20 ACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEV--K 69
Query: 92 SKPIKVLIAAKLEFKEGYRGG 112
K I V ++ K + K G G
Sbjct: 70 GKRINVELSTKGQKKSGPSSG 90
>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 = 51.1 bits (123), Expect = 7e-09
Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 7/81 (8%)
Query: 9 THDRSREYNDEPPHSR-LFILCG---KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKG 64
+ S N LF+ G T++ LR FS +G + + +KD+ T +S+G
Sbjct: 2 SSGSSGMNNSGADEIGKLFV--GGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRG 59
Query: 65 VAYIRFSKTSEAAKAVEEMNG 85
+++F V
Sbjct: 60 FGFVKFK-DPNCVGTVLASRP 79
>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A
{Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A
Length = 240
Score = 53.6 bits (128), Expect = 7e-09
Identities = 24/103 (23%), Positives = 40/103 (38%), Gaps = 18/103 (17%)
Query: 31 KDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPN 90
E +R FS G+I IR V+ SK +++F + A A E M+
Sbjct: 153 PAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSN----- 201
Query: 91 HSKPIKVLIAAKLEFKEGYRGGQKISVQY--TSPQSAAYARDK 131
+ L+ + + R G + V++ P AA R +
Sbjct: 202 -----QTLLLPSDKEWDDRREGTGLLVKWANEDPDPAAQKRLQ 239
>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 = 51.8 bits (124), Expect = 7e-09
Identities = 10/83 (12%), Positives = 31/83 (37%), Gaps = 3/83 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ + F +++ + G++ G ++ F ++ A+ + +++
Sbjct: 36 EAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYM--G 92
Query: 92 SKPIKVLIAAKLEFKEGYRGGQK 114
++ I+V K E +K
Sbjct: 93 NRFIQVHPITKKGMLEKIDMIRK 115
>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 = 53.3 bits (127), Expect = 8e-09
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 30 GKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEF 87
D T DD+++ G + I+ + KG ++ F A K VE ++
Sbjct: 118 PTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVETPGQKY 174
>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 = 51.4 bits (123), Expect = 1e-08
Identities = 14/76 (18%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
T++++ Q FS + + G+ G A+++F+ + E A+ + E +
Sbjct: 53 GCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFA-SQELAEKALGKHKERI--G 109
Query: 92 SKPIKVLIAAKLEFKE 107
+ I+V +++ E +
Sbjct: 110 HRYIEVFKSSQEEVRS 125
>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 = 50.8 bits (122), Expect = 1e-08
Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 6/82 (7%)
Query: 6 RINTHDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESK 63
+ R+++ L D+ D+ F +G I++I R
Sbjct: 6 SGMSGGGVIRGPAGNNDCRIYVGNL-PPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GP 61
Query: 64 GVAYIRFSKTSEAAKAVEEMNG 85
A++ F +A AV +G
Sbjct: 62 PFAFVEFEDPRDAEDAVYGRDG 83
>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 = 49.9 bits (120), Expect = 2e-08
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNT-GESKGVAYIRFSKTSEAAKAVEEMNGEFLPN 90
DVTE+ +++ F I +R ++ + KG Y F ++ + +N E L N
Sbjct: 30 DVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFE-DLDSLLSALSLNEESLGN 87
Query: 91 HSKPIKVLIAA 101
+ I+V +A
Sbjct: 88 --RRIRVDVAD 96
>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA
complex, RNA binding protein/RNA complex; NMR {Homo
sapiens} SCOP: d.58.7.1
Length = 119
Score = 50.7 bits (121), Expect = 2e-08
Identities = 15/66 (22%), Positives = 25/66 (37%), Gaps = 6/66 (9%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
DVTE ++ PFG + + +K +N A+I + A V
Sbjct: 42 DVTEGEVISLGLPFGKVTNLLMLKGKNQ------AFIEMNTEEAANTMVNYYTSVTPVLR 95
Query: 92 SKPIKV 97
+PI +
Sbjct: 96 GQPIYI 101
>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 = 50.0 bits (120), Expect = 2e-08
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKD-RNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPN 90
DVTE+ +++ F I +R ++ N KG Y F ++ + +N E L N
Sbjct: 26 DVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFE-DLDSLLSALSLNEESLGN 83
Query: 91 HSKPIKVLIAA 101
K I+V +A
Sbjct: 84 --KRIRVDVAD 92
Score = 27.6 bits (62), Expect = 1.7
Identities = 7/42 (16%), Positives = 14/42 (33%), Gaps = 8/42 (19%)
Query: 216 VEFSQ--------TLHGAEMYGSRLKVMEADPPKGDRNRKRQ 249
EF +L+ + R++V AD + +
Sbjct: 62 AEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSGPSS 103
>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 = 49.8 bits (119), Expect = 2e-08
Identities = 12/66 (18%), Positives = 19/66 (28%), Gaps = 6/66 (9%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
V E DL + FG I + + K A + F A + V +
Sbjct: 26 SVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIA 79
Query: 92 SKPIKV 97
+
Sbjct: 80 GQQAFF 85
>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 = 50.6 bits (121), Expect = 2e-08
Identities = 16/82 (19%), Positives = 30/82 (36%), Gaps = 5/82 (6%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
TE+D+ FSP + + G G A + F+ EA A+ + +
Sbjct: 57 KATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANM--Q 111
Query: 92 SKPIKVLIAAKLEFKEGYRGGQ 113
+ I++ + + G Q
Sbjct: 112 HRYIELFLNSTTGASNGAYSSQ 133
>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 = 48.8 bits (117), Expect = 4e-08
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+VTE ++ + +P IR V++ + G G ++ FS E +A+ + N E++
Sbjct: 21 NVTEKNVMEFLAPL-KPVAIRIVRNAH-GNKTGYIFVDFSNEEEVKQAL-KCNREYM--G 75
Query: 92 SKPIKVL 98
+ I+V
Sbjct: 76 GRYIEVF 82
>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein;
NMR {Homo sapiens}
Length = 101
Score = 48.4 bits (116), Expect = 6e-08
Identities = 12/81 (14%), Positives = 35/81 (43%), Gaps = 7/81 (8%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ +L + FS +G ++ + ++ G A++ F +A AV ++G+ +
Sbjct: 11 GAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVI--C 63
Query: 92 SKPIKVLIAAKLEFKEGYRGG 112
++V ++ + + +
Sbjct: 64 GSRVRVELSTGMPRRSRFDRP 84
>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: d.58.7.1
Length = 101
Score = 48.7 bits (116), Expect = 6e-08
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 6/66 (9%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+VTE ++ PFG + I +K K A++ + A V +
Sbjct: 26 EVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLR 79
Query: 92 SKPIKV 97
++PI +
Sbjct: 80 NQPIYI 85
>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 = 47.4 bits (113), Expect = 2e-07
Identities = 13/73 (17%), Positives = 29/73 (39%), Gaps = 5/73 (6%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
TE+D+ FSP N + + G G A + F+ +A A+ + +
Sbjct: 26 RATENDIYNFFSPL-NPMRVHIEIGPD-GRVTGEADVEFATHEDAVAAM-AKDKANM--Q 80
Query: 92 SKPIKVLIAAKLE 104
+ +++ + +
Sbjct: 81 HRYVELFLNSTAG 93
>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide
binding, RNA recognition motif; 1.40A {Homo sapiens}
PDB: 3zzz_A
Length = 130
Score = 48.1 bits (114), Expect = 2e-07
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 4/66 (6%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
VT D L Q FS FG + +I N + A ++++ A A ++G+ + N
Sbjct: 39 PVTLDVLHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVSAQHAKLSLDGQNIYNA 94
Query: 92 SKPIKV 97
+++
Sbjct: 95 CCTLRI 100
Score = 27.3 bits (60), Expect = 3.0
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 117 VQYTSPQSAAYARDKFHGFA-YPPGIPMVVVPDFS 150
+QY P SA +A+ G Y + + DFS
Sbjct: 71 LQYADPVSAQHAKLSLDGQNIYNACCTLRI--DFS 103
>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 = 46.6 bits (111), Expect = 2e-07
Identities = 8/69 (11%), Positives = 21/69 (30%), Gaps = 9/69 (13%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
D ++ + +K +K A++ +A A++ +
Sbjct: 16 DSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSF--R 66
Query: 92 SKPIKVLIA 100
K + V +
Sbjct: 67 GKDLIVQLQ 75
>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 = 50.8 bits (121), Expect = 2e-07
Identities = 40/202 (19%), Positives = 62/202 (30%), Gaps = 69/202 (34%)
Query: 41 GFSPFGNIQE-IRCVKDRNTGESKGV---AYIRFSKTSEAAKAVEEMNGEFLPNHSKPIK 96
GF+P G ++ ++ TG S+G+ I + + E F + K I
Sbjct: 257 GFTP-GELRSYLKGA----TGHSQGLVTAVAIAETDSWE----------SFFVSVRKAIT 301
Query: 97 VLIAAKLEFKEGYRGGQKISVQYTSPQSAAYARDKFHGFAYPPGIPMVVVPDFSYGLPR- 155
VL F G R + P + + + P PM+ + L +
Sbjct: 302 VL------FFIGVRCYEAYPNTSLPPSILEDSLE--NNEGVPS--PMLSIS----NLTQE 347
Query: 156 ---------NGASALGGNAALSVVDSK------GALQSLTKALAQATSLLR--SAGLSTD 198
N G +S+V+ G QSL L LR A D
Sbjct: 348 QVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSL-YGLNLT---LRKAKAPSGLD 403
Query: 199 SRFISRLRLDDFIYYILVEFSQ 220
SR + FS+
Sbjct: 404 Q---SR-----------IPFSE 411
Score = 37.7 bits (87), Expect = 0.003
Identities = 34/197 (17%), Positives = 63/197 (31%), Gaps = 48/197 (24%)
Query: 72 KTSEAAKAV-EEMNGEFLPNHSKPIKVLIA---AKLEFKEGYRGGQKISVQYTSPQSAAY 127
KTS+AA+ V + F + I ++ L G G++I Y++
Sbjct: 1637 KTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETI 1696
Query: 128 ARDKFHGFAYPPGIPMVVVPDFSYGLPRNG---------ASALGGNAALSVVDSKGALQ- 177
K I +++ + A L AA + SKG +
Sbjct: 1697 VDGKLKTEKIFKEIN-EHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPA 1755
Query: 178 -------SL---TKALAQATSLLRSAGLSTDSRFISRLRLDDFIYYILVEF-SQTLHGA- 225
SL ALA + A + + ++ + +V + T+ A
Sbjct: 1756 DATFAGHSLGEYA-ALA-S-----LADV---------MSIESLVE--VVFYRGMTMQVAV 1797
Query: 226 ---EMYGSRLKVMEADP 239
E+ S ++ +P
Sbjct: 1798 PRDELGRSNYGMIAINP 1814
>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 = 47.6 bits (113), Expect = 2e-07
Identities = 12/88 (13%), Positives = 31/88 (35%), Gaps = 7/88 (7%)
Query: 32 DVTEDDLRQGFSPF---GNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFL 88
+ +D++ S + + + R G G A++ + + K + + E +
Sbjct: 28 SCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELE-SEDDVKLALKKDRESM 85
Query: 89 PNHSKPIKVLIAAKLEFKEGYRGGQKIS 116
+ I+V + + E + S
Sbjct: 86 --GHRYIEVFKSHRTEMDWVLKHSGPNS 111
>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 = 46.5 bits (111), Expect = 3e-07
Identities = 13/69 (18%), Positives = 27/69 (39%), Gaps = 10/69 (14%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
T +LR F +G + E V K A++ + +A +A+ ++
Sbjct: 21 TCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEF--Q 70
Query: 92 SKPIKVLIA 100
K + V ++
Sbjct: 71 GKRMHVQLS 79
>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 47.2 bits (112), Expect = 3e-07
Identities = 14/80 (17%), Positives = 30/80 (37%), Gaps = 8/80 (10%)
Query: 32 DVTEDDLRQGFSPFGNIQE----IRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEF 87
T +++ F I I V + G G A++ F+ E A+ + +
Sbjct: 34 TATAEEVVAFFGQHCPITGGKEGILFVTYPD-GRPTGDAFVLFA-CEEYAQNALRKHKDL 91
Query: 88 LPNHSKPIKVLIAAKLEFKE 107
L + I++ + E ++
Sbjct: 92 L--GKRYIELFRSTAAEVQQ 109
>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 = 46.4 bits (110), Expect = 4e-07
Identities = 14/88 (15%), Positives = 32/88 (36%), Gaps = 7/88 (7%)
Query: 32 DVTEDDLRQGFSPF---GNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFL 88
T +D+ FS I + +R+ G+ +G A I + + + E + ++
Sbjct: 22 SCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEME-SEQDVQKALEKHRMYM 79
Query: 89 PNHSKPIKVLIAAKLEFKEGYRGGQKIS 116
+ ++V + + Q S
Sbjct: 80 --GQRYVEVYEINNEDVDALMKSLQVKS 105
>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 = 47.3 bits (112), Expect = 4e-07
Identities = 12/102 (11%), Positives = 30/102 (29%), Gaps = 10/102 (9%)
Query: 11 DRSREYNDEPPHSRLFILCGK---DVTEDDLRQGFSPF---GNIQEIRCVKDRNTGESKG 64
R + + +D++ S + + R G G
Sbjct: 31 GRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSG 89
Query: 65 VAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAKLEFK 106
A++ + + K + + E + + I+V + + E
Sbjct: 90 EAFVEL-GSEDDVKMALKKDRESM--GHRYIEVFKSHRTEMD 128
>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 = 46.0 bits (110), Expect = 4e-07
Identities = 9/54 (16%), Positives = 21/54 (38%), Gaps = 8/54 (14%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNG 85
+ TE ++R F +G + E + K ++ + A A+ ++
Sbjct: 19 EATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHH 64
Score = 25.2 bits (56), Expect = 8.2
Identities = 4/25 (16%), Positives = 10/25 (40%)
Query: 222 LHGAEMYGSRLKVMEADPPKGDRNR 246
LH +++G + V + +
Sbjct: 62 LHHYKLHGVNINVEASKNKSKASSG 86
>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 = 49.5 bits (117), Expect = 4e-07
Identities = 16/61 (26%), Positives = 30/61 (49%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
D TE LR+ F +G I+ I V + +G+ +G A+I + + A + +G+ +
Sbjct: 113 DTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGR 172
Query: 92 S 92
Sbjct: 173 R 173
>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 = 47.4 bits (112), Expect = 4e-07
Identities = 17/99 (17%), Positives = 35/99 (35%), Gaps = 9/99 (9%)
Query: 4 NYRINTHDRSREYNDEPPHSRLFILCG-----KDVTEDDLRQGFSPFGNIQEIRCVKDRN 58
N + + + + VT D L Q FS FG + +I N
Sbjct: 24 NLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN 83
Query: 59 TGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKV 97
+ A ++++ A A ++G+ + N +++
Sbjct: 84 QFQ----ALLQYADPVSAQHAKLSLDGQNIYNACCTLRI 118
Score = 26.2 bits (57), Expect = 8.3
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 3/35 (8%)
Query: 117 VQYTSPQSAAYARDKFHGFA-YPPGIPMVVVPDFS 150
+QY P SA +A+ G Y + + DFS
Sbjct: 89 LQYADPVSAQHAKLSLDGQNIYNACCTLRI--DFS 121
>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 = 46.0 bits (109), Expect = 6e-07
Identities = 13/56 (23%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEF 87
+ E+ + +G ++E+ V D G Y++F + +A KAV ++N +
Sbjct: 38 EFFEEVFTEMEEKYGEVEEMN-VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRW 92
>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 112
Score = 46.1 bits (109), Expect = 7e-07
Identities = 11/92 (11%), Positives = 31/92 (33%), Gaps = 8/92 (8%)
Query: 8 NTHDRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGV 65
+ + + + L ++ + + P+G I+ ++ ++
Sbjct: 11 EGKPDQKFDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQ------ 64
Query: 66 AYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKV 97
A+I +A V+ + L + +KV
Sbjct: 65 AFIEMETREDAMAMVDHCLKKALWFQGRCVKV 96
>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 114
Score = 44.6 bits (105), Expect = 2e-06
Identities = 16/72 (22%), Positives = 28/72 (38%), Gaps = 6/72 (8%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKD--RNTGESKGVAYIRFSKTSEAAKAVEE----MNG 85
D+ ED++ F FG + K ++ KG A++ F + S ++
Sbjct: 19 DIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGK 78
Query: 86 EFLPNHSKPIKV 97
+L S IK
Sbjct: 79 LYLCVSSPTIKD 90
>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 = 43.1 bits (102), Expect = 6e-06
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 35 EDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNG 85
+DD+ + + G + I D+N+ + G Y++ + A AV ++G
Sbjct: 31 KDDVIEECNKHGGVIHIYV--DKNSAQ--GNVYVKCPSIAAAIAAVNALHG 77
Score = 25.8 bits (57), Expect = 6.8
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 114 KISVQYTSPQSAAYARDKFHG 134
+ V+ S +A A + HG
Sbjct: 57 NVYVKCPSIAAAIAAVNALHG 77
>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 = 42.2 bits (100), Expect = 8e-06
Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 7/68 (10%)
Query: 17 NDEPPHSR-LFIL-CGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTS 74
+ H +F+ C +D+T ++L+Q F +G + ++ K + A++ F+
Sbjct: 5 HHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDK 59
Query: 75 EAAKAVEE 82
A E
Sbjct: 60 VAQSLCGE 67
>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 94
Score = 41.9 bits (99), Expect = 1e-05
Identities = 12/83 (14%), Positives = 23/83 (27%), Gaps = 8/83 (9%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
V L + F FG + + KD+ A + + +
Sbjct: 19 GVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREAVLSQSQHSL---G 70
Query: 92 SKPIKVLIAAKLEFKEGYRGGQK 114
++V + EF+ K
Sbjct: 71 GHRLRVRPREQKEFQSPASKSPK 93
>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 = 42.0 bits (99), Expect = 2e-05
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 35 EDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNG 85
+DLR S FG I+++ GVA + F EA ++ ++G
Sbjct: 40 REDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDG 86
Score = 26.2 bits (58), Expect = 5.4
Identities = 6/21 (28%), Positives = 8/21 (38%)
Query: 114 KISVQYTSPQSAAYARDKFHG 134
SV + P+ A Y G
Sbjct: 66 VASVSFRDPEEADYCIQTLDG 86
>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 = 40.7 bits (96), Expect = 3e-05
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 23 SRLFIL-CGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVE 81
S +F+ C D+TED+LR+ FS +G++ ++ K + A++ F+ A
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG 60
Query: 82 EM 83
E
Sbjct: 61 ED 62
>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD,
structural genomics, NPPSFA; NMR {Mus musculus}
Length = 124
Score = 41.2 bits (96), Expect = 4e-05
Identities = 25/124 (20%), Positives = 37/124 (29%), Gaps = 12/124 (9%)
Query: 4 NYRINTHDRSREYNDEPPHSRLFILCG-----KDVTEDDLRQGFSPFGNIQEIRCVKDRN 58
+ D+P +L +T D L +P G +Q I K
Sbjct: 3 SGSSGKRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRN- 61
Query: 59 TGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRGGQKISVQ 118
A + F A KA +NG + +K+ A+ R S
Sbjct: 62 ----GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY-ARPTRLNVIRNDND-SWD 115
Query: 119 YTSP 122
YT P
Sbjct: 116 YTKP 119
Score = 27.0 bits (59), Expect = 3.7
Identities = 6/30 (20%), Positives = 12/30 (40%), Gaps = 1/30 (3%)
Query: 117 VQYTSPQSAAYARDKFHGFA-YPPGIPMVV 145
V++ S A A+ +G Y + +
Sbjct: 67 VEFESVLCAQKAKAALNGADIYAGCCTLKI 96
>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 = 40.2 bits (94), Expect = 7e-05
Identities = 10/53 (18%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 35 EDDLRQGFSPFGNIQEIRCVKDRN--TGESKGVAYIRFSKTSEAAKAVEEMNG 85
+D+R S +G ++ I + + G ++ F+ + KA++ + G
Sbjct: 29 VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG 81
>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 = 38.9 bits (91), Expect = 1e-04
Identities = 9/71 (12%), Positives = 25/71 (35%), Gaps = 8/71 (11%)
Query: 32 DVTEDDLRQGFSPFGNIQEIR-----CVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGE 86
+TE+ + F+ + + V + K A++ F ++ + +G
Sbjct: 17 GITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF-RSVDETTQAMAFDGI 75
Query: 87 FLPNHSKPIKV 97
+ +K+
Sbjct: 76 IFQG--QSLKI 84
>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 = 39.0 bits (91), Expect = 2e-04
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 35 EDDLRQGFSPFGNIQEIRCVKDRNTG----ESKGVAYIRFSKTSEAAKAVEEMNG 85
E ++ + FG + + +++ E ++ FS SE KA++ +NG
Sbjct: 39 EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNG 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 = 38.3 bits (89), Expect = 3e-04
Identities = 14/98 (14%), Positives = 27/98 (27%), Gaps = 7/98 (7%)
Query: 2 DRNYRINTHDRSREYNDEPPHS-RLFIL-CGKDVTEDDLRQGFSPFGNIQEIRCVKDRNT 59
++ R + P R+ + + + DL+ NT
Sbjct: 7 HHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLET---TFSSVNT 63
Query: 60 GESKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKV 97
+ G + F +A+E +N I V
Sbjct: 64 RDFDGTGALEFPSEEILVEALERLNNIEFRGS--VITV 99
>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM
domain, RBD, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 97
Score = 35.6 bits (82), Expect = 0.002
Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 10/78 (12%)
Query: 11 DRSREYNDEPPHSRLFI--LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGE-SKGVAY 67
S P + +++ L +D DL++ G V R T + + A+
Sbjct: 8 PGSPPGEGAPLAADVYVGNL-PRDARVSDLKRALRELG------SVPLRLTWQGPRRRAF 60
Query: 68 IRFSKTSEAAKAVEEMNG 85
+ + ++ A +AV + G
Sbjct: 61 LHYPDSAAAQQAVSCLQG 78
>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens}
PDB: 2peh_A
Length = 105
Score = 35.2 bits (81), Expect = 0.003
Identities = 9/56 (16%), Positives = 23/56 (41%), Gaps = 1/56 (1%)
Query: 31 KDVTEDDLRQGFSPFGNIQEIRCVKDRNTG-ESKGVAYIRFSKTSEAAKAVEEMNG 85
+ E + ++ +G + + + + ++ F + A KAV ++NG
Sbjct: 23 DEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNG 78
>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A,
mirnas, P-bodies, argonaute, mRNA decay; NMR
{Drosophila melanogaster}
Length = 89
Score = 34.3 bits (78), Expect = 0.005
Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 6/59 (10%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPN 90
+ LR G + ++G+A +++ EA KA +N L N
Sbjct: 18 QIDGPTLRTLCMQHGPLVSFH------PYLNQGIALCKYTTREEANKAQMALNNCVLAN 70
>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national
project on protein structural and functional analyses;
NMR {Mus musculus} SCOP: d.58.7.1
Length = 102
Score = 33.7 bits (77), Expect = 0.010
Identities = 16/70 (22%), Positives = 23/70 (32%), Gaps = 6/70 (8%)
Query: 28 LCGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEF 87
L Q PFG I + N A+I + T +A AV+
Sbjct: 23 FQRGKNLRYQLLQLVEPFGVISNHLILNKINE------AFIEMATTEDAQAAVDYYTTTP 76
Query: 88 LPNHSKPIKV 97
KP++V
Sbjct: 77 ALVFGKPVRV 86
>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 = 32.8 bits (75), Expect = 0.022
Identities = 8/54 (14%), Positives = 19/54 (35%), Gaps = 7/54 (12%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNG 85
+ DL+ G++ +D G + F + + AV +++
Sbjct: 26 SGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDN 72
>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 = 32.5 bits (74), Expect = 0.033
Identities = 9/60 (15%), Positives = 21/60 (35%), Gaps = 7/60 (11%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFLPNH 91
+ DL+ G++ +D G + F + + AV +++ +H
Sbjct: 27 SGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSH 79
>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 100
Score = 32.1 bits (72), Expect = 0.045
Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 9/69 (13%)
Query: 29 CGKDVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFL 88
++D L + +G + + + G A + F+ A AV+ G
Sbjct: 25 SKGGYSKDVLLRLLQKYGEVLNLVLSSKK-----PGTAVVEFATVKAAELAVQNEVG--- 76
Query: 89 PNHSKPIKV 97
P+K+
Sbjct: 77 -LVDNPLKI 84
>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 = 33.6 bits (76), Expect = 0.053
Identities = 22/132 (16%), Positives = 44/132 (33%), Gaps = 32/132 (24%)
Query: 21 PHSRLFIL-CGKD--VTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAA 77
L + G V+ + L G + + +K ++ R+ T E+
Sbjct: 17 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALL------MPPNKPYSFARYRTTEESK 70
Query: 78 KAVEEMNGEFLPNHSKPIKVLIAAKLEFKEGYRGGQKISVQYTSPQSAAYARDKFHGFAY 137
+A +NG+ + + GQKI++ + + A
Sbjct: 71 RAYVTLNGKEVVD-------------------DLGQKITLYLNFVEKV--QWKELRPQAL 109
Query: 138 PPGIPMVVVPDF 149
PPG+ +VV +
Sbjct: 110 PPGL--MVVEEI 119
>2l2q_A PTS system, cellobiose-specific IIB component (CE;
cellobiose-specific phosphotransferase IIB component,
struct genomics; NMR {Borrelia burgdorferi}
Length = 109
Score = 30.5 bits (69), Expect = 0.19
Identities = 13/56 (23%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 121 SPQSAAYARDKFHGFAYPPGIPMVVVPDFSYGLPRNGASALGGNAALSVVDSKGAL 176
+PQ + + + + P GIP+ ++ YG NG L A++ ++K ++
Sbjct: 58 APQ-SRFNKKRLEEITKPKGIPIEIINTIDYG-TMNGEKVL--QLAINAFNNKSSV 109
>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 = 32.1 bits (72), Expect = 0.19
Identities = 21/148 (14%), Positives = 36/148 (24%), Gaps = 61/148 (41%)
Query: 3 RNYRINTHDRSREYNDEPPHSRLFI------------L----------------CGK--- 31
R+ R R YND ++ + L GK
Sbjct: 107 MMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWV 166
Query: 32 --DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEM------ 83
DV Q F + ++ + +E +
Sbjct: 167 ALDVCLSYKVQCKMDF------------------KIFWLNLKNCNSPETVLEMLQKLLYQ 208
Query: 84 ---NGEFLPNHSKPIKVLI-AAKLEFKE 107
N +HS IK+ I + + E +
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRR 236
>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 = 31.8 bits (72), Expect = 0.23
Identities = 12/105 (11%), Positives = 21/105 (20%), Gaps = 14/105 (13%)
Query: 7 INTHDRSREYND--EPPHSRL------FILCGKDVTEDDLRQGFSPFGNIQEIRCVKDRN 58
+ D E R + + + I +R
Sbjct: 1271 LKLEAEEIPSEDQNEFLLERTREIHNEAESQLRAAQQQWGNDFYKRDPRIAPLRGALATY 1330
Query: 59 TGESKGVAYIRFSKTSEAA------KAVEEMNGEFLPNHSKPIKV 97
+ F TS A + EM + P+
Sbjct: 1331 GLTIDDLGVASFHGTSTKANDKNESATINEMMKHLGRSEGNPVIG 1375
>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 = 0.72
Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 2/43 (4%)
Query: 62 SKGVAYIRFSKTSEAAKAVEEMNGEFLPNHSKPIKVLIAAKLE 104
+ A +RF A +A + M E + I V K
Sbjct: 45 TGCSAILRFINQDSAERAQKRMENEDV--FGNRIIVSFTPKNR 85
>3nbm_A PTS system, lactose-specific IIBC components; PTS_IIB_LACTOSE,
phosphoenolpyruvate:carbohydrate system, P-
phosphorylation; HET: MSE; 1.30A {Streptococcus
pneumoniae}
Length = 108
Score = 28.6 bits (64), Expect = 0.74
Identities = 10/42 (23%), Positives = 16/42 (38%), Gaps = 2/42 (4%)
Query: 121 SPQSAAYARDKFHGFAYPPGIPMVVVPDFSYG-LPRNGASAL 161
+PQ + A GI +V Y L ++ + AL
Sbjct: 60 APQ-VRSYYREMKVDAERLGIQIVATRGMEYIHLTKSPSKAL 100
>4fgs_A Probable dehydrogenase protein; PSI-biology, nysgrc, structural
genomics, NEW YORK structura genomics research
consortium, three layer; 1.76A {Rhizobium etli}
Length = 273
Score = 28.7 bits (65), Expect = 1.9
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 1/27 (3%)
Query: 159 SALGGNAALSV-VDSKGALQSLTKALA 184
+ G A SV SK AL+S +
Sbjct: 162 AGSTGTPAFSVYAASKAALRSFARNWI 188
>1ooe_A Dihydropteridine reductase; structural genomics, PSI, protein
structure initiative, southeast collaboratory for
structural genomics; HET: MES; 1.65A {Caenorhabditis
elegans} SCOP: c.2.1.2
Length = 236
Score = 28.4 bits (64), Expect = 2.2
Identities = 9/29 (31%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 158 ASALGGNAALSV-VDSKGALQSLTKALAQ 185
A+A+G ++ +K A+ LT +LA
Sbjct: 131 AAAMGPTPSMIGYGMAKAAVHHLTSSLAA 159
>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural
genomics/proteomics initiative, RSGI, RNA binding
protein; NMR {Mus musculus} SCOP: d.58.7.1
Length = 104
Score = 27.3 bits (60), Expect = 2.4
Identities = 7/25 (28%), Positives = 16/25 (64%)
Query: 113 QKISVQYTSPQSAAYARDKFHGFAY 137
+++ + +++P SAA AR + H +
Sbjct: 47 KRVRINFSNPLSAADARLRLHKTEF 71
>1dhr_A Dihydropteridine reductase; oxidoreductase(acting on NADH or
NADPH); HET: NAD; 2.30A {Rattus norvegicus} SCOP:
c.2.1.2 PDB: 1dir_A* 1hdr_A*
Length = 241
Score = 28.1 bits (63), Expect = 2.4
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 158 ASALGGNAALSV-VDSKGALQSLTKALAQ 185
+AL G + +KGA+ L ++LA
Sbjct: 135 KAALDGTPGMIGYGMAKGAVHQLCQSLAG 163
>1geg_A Acetoin reductase; SDR family, oxidoreductase; HET: GLC NAD; 1.70A
{Klebsiella pneumoniae} SCOP: c.2.1.2
Length = 256
Score = 28.3 bits (64), Expect = 2.5
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 156 NGAS--ALGGNAALSV-VDSKGALQSLTKALA 184
N S GN L+V SK A++ LT+ A
Sbjct: 136 NACSQAGHVGNPELAVYSSSKFAVRGLTQTAA 167
>3gem_A Short chain dehydrogenase; structural genomics, APC65077,
oxidoreductase, PSI-2, protein structure initiative;
1.83A {Pseudomonas syringae PV}
Length = 260
Score = 27.9 bits (63), Expect = 2.7
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 172 SKGALQSLTKALAQA 186
+K L+SLT + A
Sbjct: 173 TKAGLESLTLSFAAR 187
>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, alternative
splicing, FBP interacting repressor, RRM, electron
transport; 2.20A {Escherichia coli O157}
Length = 222
Score = 27.9 bits (62), Expect = 2.7
Identities = 13/60 (21%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 32 DVTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVA----YIRFSKTSEAAKAVEEMNGEF 87
D E ++ + FG + + +++ E ++ FS SE KA++ +NG +
Sbjct: 140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW 199
>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone
methyltransferase, RRM fold, telomere, nuclear protein;
3.0A {Saccharomyces cerevisiae}
Length = 136
Score = 27.4 bits (60), Expect = 2.8
Identities = 10/62 (16%), Positives = 21/62 (33%), Gaps = 8/62 (12%)
Query: 33 VTEDDLRQGFSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSE--------AAKAVEEMN 84
+ + ++ F +G I D N+ V I+++ + A AV +
Sbjct: 18 IQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHE 77
Query: 85 GE 86
Sbjct: 78 SS 79
>3ijr_A Oxidoreductase, short chain dehydrogenase/reducta; structural
genomics, infectious D center for structural genomics of
infectious diseases; HET: NAD; 2.05A {Bacillus anthracis
str} PDB: 3i3o_A*
Length = 291
Score = 27.9 bits (63), Expect = 2.9
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 7/35 (20%)
Query: 156 NGAS--ALGGNAALSVVD---SKGALQSLTKALAQ 185
N AS A GN L +D +KGA+ + T++L+Q
Sbjct: 180 NTASIVAYEGNETL--IDYSATKGAIVAFTRSLSQ 212
>4eso_A Putative oxidoreductase; NADP, structural genomics, PSI-biology,
NEW structural genomics research consortium, nysgrc;
HET: MSE NAP; 1.91A {Sinorhizobium meliloti} PDB: 3vc7_A
Length = 255
Score = 27.9 bits (63), Expect = 3.0
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 159 SALGGNAALSV-VDSKGALQSLTKALAQ 185
+ GG+ +SV SK AL S LA
Sbjct: 141 ADEGGHPGMSVYSASKAALVSFASVLAA 168
>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken
structural genomics/proteomics initiative, RSGI,
protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1
Length = 119
Score = 27.0 bits (59), Expect = 3.2
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 7/47 (14%)
Query: 42 FSPFGNIQEIRCVKDRNTGESKGVAYIRFSKTSEAAKAVEEMNGEFL 88
F+ +GNI + N +IR+ +A KA+ + +G
Sbjct: 44 FAQYGNILKHVMSNTGNW------MHIRYQSKLQARKALSK-DGRIF 83
>2ag5_A DHRS6, dehydrogenase/reductase (SDR family) member 6;
protein-CO-factor complex, structural genomics,
structural G consortium, SGC, oxidoreductase; HET: NAD;
1.84A {Homo sapiens} SCOP: c.2.1.2
Length = 246
Score = 27.8 bits (63), Expect = 3.2
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 158 ASALGGNAALSV-VDSKGALQSLTKALA 184
AS++ G V +K A+ LTK++A
Sbjct: 135 ASSVKGVVNRCVYSTTKAAVIGLTKSVA 162
>3a28_C L-2.3-butanediol dehydrogenase; chiral substrate recognition,
oxidoreductase; HET: NAD; 2.00A {Brevibacterium
saccharolyticum}
Length = 258
Score = 27.9 bits (63), Expect = 3.3
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 156 NGASALG--GNAALSV-VDSKGALQSLTKALAQ 185
N AS G LS +K A++ LT+A AQ
Sbjct: 138 NAASIAAIQGFPILSAYSTTKFAVRGLTQAAAQ 170
>2wsb_A Galactitol dehydrogenase; oxidoreductase, SDR, rossmann fold,
tagatose; HET: NAD; 1.25A {Rhodobacter sphaeroides} PDB:
2wdz_A* 3lqf_A*
Length = 254
Score = 27.5 bits (62), Expect = 3.5
Identities = 13/35 (37%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 156 NGASALG--GNAALSVVD---SKGALQSLTKALAQ 185
N S G N SKGA+ LT+ALA
Sbjct: 141 NLGSMSGTIVNRPQFASSYMASKGAVHQLTRALAA 175
>1spx_A Short-chain reductase family member (5L265); parallel beta-sheet of
seven strands in the order 3214567; 2.10A
{Caenorhabditis elegans} SCOP: c.2.1.2
Length = 278
Score = 27.2 bits (61), Expect = 4.7
Identities = 7/28 (25%), Positives = 10/28 (35%), Gaps = 1/28 (3%)
Query: 158 ASALGGNAALSV-VDSKGALQSLTKALA 184
AS L +K A+ T+ A
Sbjct: 150 ASGLHATPDFPYYSIAKAAIDQYTRNTA 177
>3uxy_A Short-chain dehydrogenase/reductase SDR; structural genomics,
PSI-biology, NEW YORK structural genomi research
consortium, nysgrc; HET: NAD; 2.10A {Rhodobacter
sphaeroides}
Length = 266
Score = 27.1 bits (61), Expect = 4.7
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 3/33 (9%)
Query: 156 NGAS--ALGGNAALSV-VDSKGALQSLTKALAQ 185
N AS L ++ +K AL SLT+ +
Sbjct: 150 NVASCWGLRPGPGHALYCLTKAALASLTQCMGM 182
>4e4y_A Short chain dehydrogenase family protein; structural genomics, the
center for structural genomics of I diseases, csgid,
niaid; 1.80A {Francisella tularensis subsp}
Length = 244
Score = 27.1 bits (61), Expect = 4.9
Identities = 8/27 (29%), Positives = 11/27 (40%), Gaps = 1/27 (3%)
Query: 159 SALGGNAALSV-VDSKGALQSLTKALA 184
SKGA+ +TK+LA
Sbjct: 129 QCFIAKPNSFAYTLSKGAIAQMTKSLA 155
>2x3l_A ORN/Lys/Arg decarboxylase family protein; lyase; HET: LLP; 2.00A
{Staphylococcus aureus}
Length = 446
Score = 27.1 bits (60), Expect = 5.7
Identities = 6/9 (66%), Positives = 8/9 (88%)
Query: 137 YPPGIPMVV 145
YPPGIP++
Sbjct: 402 YPPGIPIIF 410
>3zv4_A CIS-2,3-dihydrobiphenyl-2,3-DIOL dehydrogenase; oxidoreductase,
short chain dehydrogenase/oxidoreductase, SD comamonas
testosteroni; 1.80A {Pandoraea pnomenusa} PDB: 2y99_A*
3zv3_A 2y93_A 3zv5_A* 3zv6_A* 1bdb_A*
Length = 281
Score = 27.2 bits (61), Expect = 5.8
Identities = 5/27 (18%), Positives = 11/27 (40%), Gaps = 1/27 (3%)
Query: 159 SALGGNAALSV-VDSKGALQSLTKALA 184
+ N + +K A+ L + +A
Sbjct: 144 AGFYPNGGGPLYTATKHAVVGLVRQMA 170
>4e6p_A Probable sorbitol dehydrogenase (L-iditol 2-dehyd; NAD(P)-binding,
structural genomics, PSI-biology; HET: MSE; 2.10A
{Sinorhizobium meliloti} PDB: 1k2w_A
Length = 259
Score = 27.1 bits (61), Expect = 5.9
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 156 NGASALG--GNAALSV-VDSKGALQSLTKALA 184
N AS G G A +++ +K A+ SLT++
Sbjct: 139 NMASQAGRRGEALVAIYCATKAAVISLTQSAG 170
>1cyd_A Carbonyl reductase; short-chain dehydrogenase, oxidoreductase; HET:
NAP; 1.80A {Mus musculus} SCOP: c.2.1.2
Length = 244
Score = 26.7 bits (60), Expect = 6.7
Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 156 NGASALG--GNAALSV-VDSKGALQSLTKALA 184
N +S + L +KGA+ LTKA+A
Sbjct: 133 NVSSMVAHVTFPNLITYSSTKGAMTMLTKAMA 164
>2dkn_A 3-alpha-hydroxysteroid dehydrogenase; oxidoreductase, rossmann
fold; HET: NAI; 1.80A {Pseudomonas SP}
Length = 255
Score = 26.8 bits (60), Expect = 7.0
Identities = 6/26 (23%), Positives = 10/26 (38%)
Query: 159 SALGGNAALSVVDSKGALQSLTKALA 184
+ G L+ SK A+ L +
Sbjct: 143 AEQQGQTHLAYAGSKYAVTCLARRNV 168
>4g81_D Putative hexonate dehydrogenase; enzyme function initiative, EFI,
structural genomics, dehydr oxidoreductase; 1.90A
{Salmonella enterica subsp}
Length = 255
Score = 26.7 bits (60), Expect = 7.0
Identities = 5/13 (38%), Positives = 10/13 (76%)
Query: 172 SKGALQSLTKALA 184
+KG ++ LT ++A
Sbjct: 162 AKGGIKMLTCSMA 174
>1ae1_A Tropinone reductase-I; oxidoreductase, tropane alkaloid
biosynthesis, reduction of tropinone to tropine,
short-chain dehydrogenase; HET: NAP; 2.40A {Datura
stramonium} SCOP: c.2.1.2
Length = 273
Score = 26.7 bits (60), Expect = 7.0
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 172 SKGALQSLTKALA 184
SKGA+ +TK+LA
Sbjct: 174 SKGAINQMTKSLA 186
>2ae2_A Protein (tropinone reductase-II); oxidoreductase, tropane alkaloid
biosynthesis, reduction of tropinone to pseudotropine;
HET: NAP PTO; 1.90A {Datura stramonium} SCOP: c.2.1.2
PDB: 2ae1_A* 1ipe_A* 1ipf_A*
Length = 260
Score = 26.7 bits (60), Expect = 7.2
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 172 SKGALQSLTKALA 184
+KGA+ LT+ LA
Sbjct: 162 TKGAMDQLTRCLA 174
>3n74_A 3-ketoacyl-(acyl-carrier-protein) reductase; seattle structural
genomics center for infectious disease, S brucellosis;
2.20A {Brucella melitensis biovar abortus}
Length = 261
Score = 26.7 bits (60), Expect = 7.6
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 156 NGAS--ALGGNAALSV-VDSKGALQSLTKALA 184
N AS A L+ +KG + S+TKALA
Sbjct: 144 NVASTGAGRPRPNLAWYNATKGWVVSVTKALA 175
>1c4k_A Protein (ornithine decarboxylase); lyase; HET: PLP GTP; 2.70A
{Lactobacillus SP} SCOP: c.23.1.4 c.67.1.5 d.125.1.1
PDB: 1ord_A*
Length = 730
Score = 27.0 bits (59), Expect = 7.6
Identities = 5/9 (55%), Positives = 6/9 (66%)
Query: 137 YPPGIPMVV 145
YPPG+ V
Sbjct: 660 YPPGVFCVA 668
>3vmm_A Alanine-anticapsin ligase BACD; ATP-grAsp domain, amino acid
ligase, ATP binding; HET: ADP P0D; 2.50A {Bacillus
subtilis}
Length = 474
Score = 26.8 bits (59), Expect = 7.7
Identities = 15/119 (12%), Positives = 35/119 (29%), Gaps = 41/119 (34%)
Query: 119 YTSPQSAAYARDKF--------HGFAYPP-----------------GIPMVVVPDFSYGL 153
Q+A ARDK G G P+++ P +Y
Sbjct: 128 GAGVQAAENARDKNKMRDAFNKAGVKSIKNKRVTTLEDFRAALEEIGTPLILKP--TYLA 185
Query: 154 PRNGASALGGNAALSVVDSKGALQS-LTKALAQATSLLRSAGLSTDSRFISRLRLDDFI 211
+ ++++ + + S+ ++ ++ FI ++F+
Sbjct: 186 ---------SSIGVTLITDTETAEDEFNRVNDYLKSINVPKAVTFEAPFI----AEEFL 231
>3ucx_A Short chain dehydrogenase; ssgcid, seattle structural genomics
center for infectious DI dehydrogenase, oxidoreductase;
HET: 1PE; 1.85A {Mycobacterium smegmatis}
Length = 264
Score = 26.7 bits (60), Expect = 8.0
Identities = 6/28 (21%), Positives = 11/28 (39%), Gaps = 1/28 (3%)
Query: 159 SALGGNAALSV-VDSKGALQSLTKALAQ 185
A +K AL ++++ LA
Sbjct: 149 VVRHSQAKYGAYKMAKSALLAMSQTLAT 176
>1yde_A Retinal dehydrogenase/reductase 3; oxidoreductase, structural
genomics, structural genomics CON SGC; 2.40A {Homo
sapiens} SCOP: c.2.1.2
Length = 270
Score = 26.4 bits (59), Expect = 8.3
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 156 NGAS--ALGGNAALSV-VDSKGALQSLTKALA 184
N +S G A V +KGA+ ++TKALA
Sbjct: 138 NISSLVGAIGQAQAVPYVATKGAVTAMTKALA 169
>3uf0_A Short-chain dehydrogenase/reductase SDR; gluconate, gluconate
5-dehydratase, NAD(P) dependent, enzyme initiative, EFI,
oxidoreductase; HET: NAP; 2.00A {Beutenbergia cavernae}
Length = 273
Score = 26.4 bits (59), Expect = 8.5
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 172 SKGALQSLTKALA 184
SK A+ LT+ALA
Sbjct: 181 SKHAVVGLTRALA 193
>1vl8_A Gluconate 5-dehydrogenase; TM0441, structural genomics, JCSG
structure initiative, PSI, joint center for structural
GENO oxidoreductase; HET: NAP; 2.07A {Thermotoga
maritima} SCOP: c.2.1.2
Length = 267
Score = 26.3 bits (59), Expect = 8.5
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 172 SKGALQSLTKALAQ 185
SKG + SLTKALA+
Sbjct: 175 SKGGVASLTKALAK 188
>3ak4_A NADH-dependent quinuclidinone reductase; SDR, (R)-3-quinuclidinol,
chiral alcohol, oxidoreductase; HET: NAD; 2.00A
{Agrobacterium tumefaciens}
Length = 263
Score = 26.4 bits (59), Expect = 8.8
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 156 NGASALG--GNAALSV-VDSKGALQSLTKALAQ 185
N AS G L+ SK A+ T+ALA+
Sbjct: 143 NTASLAAKVGAPLLAHYSASKFAVFGWTQALAR 175
>3r3s_A Oxidoreductase; structural genomics, csgid, center for structural
genomics O infectious diseases, 3-layer(ABA) sandwich,
rossmann fold; HET: NAD; 1.25A {Salmonella enterica
subsp}
Length = 294
Score = 26.4 bits (59), Expect = 8.8
Identities = 8/35 (22%), Positives = 17/35 (48%), Gaps = 7/35 (20%)
Query: 156 NGAS--ALGGNAALSVVD---SKGALQSLTKALAQ 185
+S A + L +D +K A+ + ++ LA+
Sbjct: 183 TTSSIQAYQPSPHL--LDYAATKAAILNYSRGLAK 215
>4dqx_A Probable oxidoreductase protein; structural genomics, PSI-biology,
NEW YORK structural genomi research consortium, nysgrc;
2.00A {Rhizobium etli}
Length = 277
Score = 26.4 bits (59), Expect = 9.2
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 156 NGAS--ALGGNAALSV-VDSKGALQSLTKALA 184
N S A A + V SKGA+ SLT+A+A
Sbjct: 157 NTTSYTATSAIADRTAYVASKGAISSLTRAMA 188
>2cfc_A 2-(R)-hydroxypropyl-COM dehydrogenase; NAD, oxidoreductase; HET:
NAD KPC; 1.8A {Xanthobacter autotrophicus}
Length = 250
Score = 26.3 bits (59), Expect = 9.3
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 156 NGAS--ALGGNAALSV-VDSKGALQSLTKALA 184
N AS +L S SKGA+ LTK++A
Sbjct: 139 NIASVASLVAFPGRSAYTTSKGAVLQLTKSVA 170
>2vyc_A Biodegradative arginine decarboxylase; pyridoxal phosphate,
PLP-dependent E lyase, acid resistance; HET: LLP; 2.4A
{Escherichia coli}
Length = 755
Score = 26.6 bits (58), Expect = 9.4
Identities = 7/10 (70%), Positives = 9/10 (90%)
Query: 136 AYPPGIPMVV 145
YPPGIPM++
Sbjct: 696 PYPPGIPMLL 705
>3orf_A Dihydropteridine reductase; alpha-beta-alpha sandwich, rossmann
fold, oxidoreductase (AC NADH), NADH binding,
oxidoreductase; HET: NAD; 2.16A {Dictyostelium
discoideum}
Length = 251
Score = 26.5 bits (59), Expect = 9.5
Identities = 7/27 (25%), Positives = 12/27 (44%), Gaps = 1/27 (3%)
Query: 159 SALGGNAALSV-VDSKGALQSLTKALA 184
+AL + + +K A + K LA
Sbjct: 147 AALNRTSGMIAYGATKAATHHIIKDLA 173
>2zat_A Dehydrogenase/reductase SDR family member 4; alpha/beta,
oxidoreductase; HET: NAP; 1.50A {Sus scrofa} PDB:
3o4r_A*
Length = 260
Score = 26.3 bits (59), Expect = 10.0
Identities = 11/28 (39%), Positives = 11/28 (39%), Gaps = 1/28 (3%)
Query: 159 SALGGNAALSV-VDSKGALQSLTKALAQ 185
A L SK AL LTK LA
Sbjct: 153 GAYHPFPNLGPYNVSKTALLGLTKNLAV 180
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
0.318 0.135 0.388
Gapped
Lambda K H
0.267 0.0850 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,832,336
Number of extensions: 226908
Number of successful extensions: 1065
Number of sequences better than 10.0: 1
Number of HSP's gapped: 950
Number of HSP's successfully gapped: 313
Length of query: 253
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 162
Effective length of database: 4,160,982
Effective search space: 674079084
Effective search space used: 674079084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.1 bits)