RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1775
(304 letters)
>1k1g_A SF1-BO isoform; splicing, branch point sequence, protein/RNA
recognition, complex E, KH domain, QUA2 homology; NMR
{Homo sapiens} SCOP: d.51.1.1
Length = 131
Score = 126 bits (317), Expect = 2e-36
Identities = 70/111 (63%), Positives = 88/111 (79%), Gaps = 2/111 (1%)
Query: 191 PPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGR 250
+V+DKVMIPQDE+P+INFVGLLIGPRGNTLK++EK+ AKI+IRGKGSVKEGKVGR
Sbjct: 2 AMATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGR 61
Query: 251 KDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPGADFI 301
KDGQ LPGE+EPLHA VTA+ ENVKKAV+++ ++ + P + +
Sbjct: 62 KDGQMLPGEDEPLHALVTANTMENVKKAVEQIRNIL--KQGIETPEDQNDL 110
>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA
binding; NMR {Xenopus laevis} SCOP: d.51.1.1
Length = 140
Score = 103 bits (258), Expect = 2e-27
Identities = 36/103 (34%), Positives = 60/103 (58%), Gaps = 7/103 (6%)
Query: 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRK--D 252
++ +K+ +P E+PD NFVG ++GPRG T K +E +TG KI++RGKGS+++ K +
Sbjct: 1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNRG 60
Query: 253 GQPLPGENEPLHAYVTAHNPEN-----VKKAVDRLVCLVSARP 290
NE LH +T + +N +K+AV+ + L+
Sbjct: 61 KPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVPAA 103
>2yqr_A KIAA0907 protein; structure genomics, KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 119
Score = 86.9 bits (215), Expect = 1e-21
Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 7/87 (8%)
Query: 195 KVNDKVMIPQDE-HPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDG 253
V DK+ + + P N + GP + L+ ++ +TGAK+ +RGKGS G +
Sbjct: 11 YVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGS------GCIEP 64
Query: 254 QPLPGENEPLHAYVTAHNPENVKKAVD 280
EP++ Y++ PE + A
Sbjct: 65 ASGREAFEPMYIYISHPKPEGLAAAKK 91
>2jzx_A Poly(RC)-binding protein 2; PCBP2, KH domains, RNA binding,
DNA-binding, nucleus, phosph ribonucleoprotein,
RNA-binding, RNA binding protein; NMR {Homo sapiens}
Length = 160
Score = 50.2 bits (120), Expect = 8e-08
Identities = 19/118 (16%), Positives = 42/118 (35%), Gaps = 24/118 (20%)
Query: 170 HDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEK 229
+I + + V ++++P + G LIG G +K + +
Sbjct: 63 FAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPA------SQCGSLIGKGGCKIKEIRE 116
Query: 230 DTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAH-NPENVKKAVDRLVCLV 286
TGA++ + G LP E +T P+++ + V ++ ++
Sbjct: 117 STGAQVQV--------------AGDMLPNSTERA---ITIAGIPQSIIECVKQICVVM 157
Score = 37.1 bits (86), Expect = 0.002
Identities = 12/39 (30%), Positives = 24/39 (61%), Gaps = 6/39 (15%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237
++++ E VG +IG +G ++K M +++GA+I I
Sbjct: 8 RLLMHGKE------VGSIIGKKGESVKKMREESGARINI 40
>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 94
Score = 46.6 bits (111), Expect = 4e-07
Identities = 19/105 (18%), Positives = 36/105 (34%), Gaps = 27/105 (25%)
Query: 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQ 254
+ + V IP++ H +IG G L+ +E T KI I
Sbjct: 16 QASATVAIPKEHH------RFVIGKNGEKLQDLELKTATKIQI----------------- 52
Query: 255 PLPGENEPLHAYVTAH-NPENVKKAVDRLVCLVSARPRARFPPGA 298
P P + + E ++KA ++ + + + + P
Sbjct: 53 PRPDDPSNQ---IKITGTKEGIEKARHEVLLISAEQDKRSGPSSG 94
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA
complex; NMR {Rous sarcoma virus}
Length = 61
Score = 45.3 bits (107), Expect = 5e-07
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 1/56 (1%)
Query: 41 GPRCTNCGASDHKSWLCPD-KPNITNSTLCSSCGGAGHIARDCREKRPGMGGPPAN 95
C CG+ H CP + + + C C G GH A+ CR++ G P
Sbjct: 4 RGLCYTCGSPGHYQAQCPKKRKSGNSRERCQLCNGMGHNAKQCRKRDGNQGQRPGK 59
>2anr_A Neuro-oncological ventral antigen 1; protein-RNA complex, KH
domain, hairpin, RNA-binding protein complex; HET: 5BU;
1.94A {Homo sapiens} PDB: 2ann_A*
Length = 178
Score = 46.8 bits (111), Expect = 1e-06
Identities = 22/108 (20%), Positives = 42/108 (38%), Gaps = 23/108 (21%)
Query: 185 PPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVK 244
P P K+++P + GL+IG G T+K++ + +GA + + K
Sbjct: 93 QPQTTVNPDRANQVKIIVPN------STAGLIIGKGGATVKAIMEQSGAWVQLSQKP--- 143
Query: 245 EGKVGRKDGQPLPGENEPLHAYVT-AHNPENVKKAVDRLVCLVSARPR 291
+ VT + PE +KAV+ ++ + P+
Sbjct: 144 ----------DGINLQNRV---VTVSGEPEQNRKAVELIIQKIQEDPQ 178
Score = 37.9 bits (88), Expect = 0.001
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 6/56 (10%)
Query: 191 PPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEG 246
P + KV+IP G +IG G T+ ++K+TGA I + G
Sbjct: 1 PLGSQYFLKVLIPSYA------AGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPG 50
>1x4m_A FAR upstream element binding protein 1; KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.51.1.1
Length = 94
Score = 44.3 bits (105), Expect = 2e-06
Identities = 23/113 (20%), Positives = 46/113 (40%), Gaps = 23/113 (20%)
Query: 186 PPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKE 245
+ ++MIP GL+IG G T+K +++ G K+++
Sbjct: 5 SSGHGDGPGNAVQEIMIPAS------KAGLVIGKGGETIKQLQERAGVKMVM-------- 50
Query: 246 GKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPGA 298
+DG G ++PL +T +P V++A + ++ L+ + P
Sbjct: 51 ----IQDGPQNTGADKPLR--ITG-DPYKVQQAKEMVLELIRDQGSG--PSSG 94
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding
protein, retrovirus, viral protein; NMR {Mason-pfizer
monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A
Length = 60
Score = 43.4 bits (102), Expect = 2e-06
Identities = 15/56 (26%), Positives = 19/56 (33%), Gaps = 4/56 (7%)
Query: 41 GPRCTNCGASDHKSWLCPDK----PNITNSTLCSSCGGAGHIARDCREKRPGMGGP 92
G C CG H + C + LC C H A +C+ K G P
Sbjct: 1 GGSCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKTDNQGNP 56
Score = 31.8 bits (72), Expect = 0.027
Identities = 10/32 (31%), Positives = 12/32 (37%)
Query: 69 CSSCGGAGHIARDCREKRPGMGGPPANTHRNR 100
C CG GH A++C E P R
Sbjct: 4 CFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPR 35
>1dtj_A RNA-binding neurooncological ventral antigen 2; KH domain,
alpha-beta fold RNA-binding motif, immune system; 2.00A
{Homo sapiens} SCOP: d.51.1.1 PDB: 1dt4_A
Length = 76
Score = 43.8 bits (104), Expect = 2e-06
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 194 IKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRK 251
+K ++ +P++ VG ++G G TL ++ TGA+I I KG G R+
Sbjct: 1 MKELVEMAVPEN------LVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRR 52
>2jvz_A KH type-splicing, FAR upstream element-binding protein 2; RNA
binding protein, KH domain, KSRP, posttranscriptional
regulation, mRNA decay; NMR {Homo sapiens}
Length = 164
Score = 45.5 bits (108), Expect = 3e-06
Identities = 16/115 (13%), Positives = 37/115 (32%), Gaps = 26/115 (22%)
Query: 170 HDLIQKMFKVNPEFKPPPDYKP-PVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSME 228
+++ + + + + I V +P+ + VG++IG G +K ++
Sbjct: 64 CEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPR------HSVGVVIGRSGEMIKKIQ 117
Query: 229 KDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVT-AHNPENVKKAVDRL 282
D G +I + Q E + P+ + A +
Sbjct: 118 NDAGVRIQFK---------------QDDGTGPEKI---AHIMGPPDRCEHAARII 154
Score = 44.4 bits (105), Expect = 8e-06
Identities = 22/102 (21%), Positives = 47/102 (46%), Gaps = 21/102 (20%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPG 258
++MIP + GL+IG G T+K +++ G K+I+ +DG
Sbjct: 5 EIMIPAGK------AGLVIGKGGETIKQLQERAGVKMIL------------IQDGSQNTN 46
Query: 259 ENEPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPGADF 300
++PL + +P V++A + ++ ++ R + F ++
Sbjct: 47 VDKPLR--IIG-DPYKVQQACEMVMDILRERDQGGFGDRNEY 85
>3krm_A Insulin-like growth factor 2 mRNA-binding protein 1; KH domain,
cell projection, cytoplasm, nucleus, phosphoprotein,
translation regulation; 2.75A {Homo sapiens}
Length = 163
Score = 45.1 bits (107), Expect = 4e-06
Identities = 17/124 (13%), Positives = 42/124 (33%), Gaps = 26/124 (20%)
Query: 170 HDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEK 229
I K F P + +K+ + +P + G +IG G T+ ++
Sbjct: 64 QGRIYGKLKEENFFGPKEE-----VKLETHIRVPA------SAAGRVIGKGGKTVNELQN 112
Query: 230 DTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDRLVCLVSAR 289
T A++++ P EN+ + + + + A ++ +++
Sbjct: 113 LTAAEVVV--------------PRDQTPDENDQVIVKIIG-HFYASQMAQRKIRDILAQV 157
Query: 290 PRAR 293
+
Sbjct: 158 KQQH 161
Score = 38.6 bits (90), Expect = 8e-04
Identities = 19/102 (18%), Positives = 30/102 (29%), Gaps = 22/102 (21%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPG 258
+V IP VG +IG +G +K + + A I I + P
Sbjct: 6 QVFIPAQA------VGAIIGKKGQHIKQLSRFASASIKIAPPET--------------PD 45
Query: 259 ENEPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPGADF 300
+ +T PE KA R+ +
Sbjct: 46 SKVRM-VIITG-PPEAQFKAQGRIYGKLKEENFFGPKEEVKL 85
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA
surveillance binds to TRF4P/AIR2P heterodimer; 2.70A
{Saccharomyces cerevisiae}
Length = 83
Score = 43.1 bits (101), Expect = 5e-06
Identities = 18/60 (30%), Positives = 22/60 (36%), Gaps = 16/60 (26%)
Query: 43 RCTNCGASDHKSWLCPDK-----PNITNSTL-----------CSSCGGAGHIARDCREKR 86
+CT C + H CP N C +CGG GH DC+EKR
Sbjct: 7 QCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKR 66
>1ec6_A RNA-binding protein NOVA-2; KH domain, alpha-beta fold, RNA-binding
motif, protein/RNA structure, RNA binding protein/RNA
complex; 2.40A {Homo sapiens} SCOP: d.51.1.1
Length = 87
Score = 43.1 bits (102), Expect = 5e-06
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 194 IKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRK 251
+K ++ +P++ VG ++G G TL ++ TGA+I I KG G R+
Sbjct: 1 MKELVEIAVPEN------LVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRR 52
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding,
exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Length = 124
Score = 43.2 bits (101), Expect = 9e-06
Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 16/60 (26%)
Query: 42 PRCTNCGASDHKSWLCPD----------------KPNITNSTLCSSCGGAGHIARDCREK 85
+CT C + H CP K ++ C +CGG GH DC+EK
Sbjct: 65 VQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEK 124
Score = 38.6 bits (89), Expect = 4e-04
Identities = 14/63 (22%), Positives = 18/63 (28%), Gaps = 13/63 (20%)
Query: 41 GPRCTNCGASDHKSWLCPDKP-------------NITNSTLCSSCGGAGHIARDCREKRP 87
P+C NC H CP + + CS C GH C K
Sbjct: 4 APKCNNCSQRGHLKKDCPHIICSYCGATDDHYSRHCPKAIQCSKCDEVGHYRSQCPHKWK 63
Query: 88 GMG 90
+
Sbjct: 64 KVQ 66
Score = 36.3 bits (83), Expect = 0.003
Identities = 11/65 (16%), Positives = 16/65 (24%), Gaps = 3/65 (4%)
Query: 40 EGPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCREKRPGMGGPPANTHRN 99
+ +C+ C H CP K C+ C H C N
Sbjct: 41 KAIQCSKCDEVGHYRSQCPHKWKKVQ---CTLCKSKKHSKERCPSIWRAYILVDDNEKAK 97
Query: 100 RAKID 104
+
Sbjct: 98 PKVLP 102
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA,
transcription-RNA complex; NMR {Homo sapiens}
Length = 74
Score = 41.9 bits (98), Expect = 1e-05
Identities = 16/56 (28%), Positives = 20/56 (35%), Gaps = 3/56 (5%)
Query: 37 RENEGPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCREKRPGMGGP 92
R ++G RC NCG DH + C P C C H+ C K
Sbjct: 20 RRSKGDRCYNCGGLDHHAKECKLPPQPKK---CHFCQSISHMVASCPLKAQQGPSA 72
>1wvn_A Poly(RC)-binding protein 1; KH domain, RNA binding domain, RNA
binding protein; 2.10A {Homo sapiens} SCOP: d.51.1.1
Length = 82
Score = 41.9 bits (99), Expect = 1e-05
Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 191 PPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237
P + ++ IP + +G +IG +G + + + +GA+I I
Sbjct: 1 PLGSQTTHELTIPNN------LIGCIIGRQGANINEIRQMSGAQIKI 41
>2ctm_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 95
Score = 41.7 bits (98), Expect = 2e-05
Identities = 19/91 (20%), Positives = 33/91 (36%), Gaps = 24/91 (26%)
Query: 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQP 255
V++ V + H +IG RG ++ + + I G+ V
Sbjct: 17 VSEDVPLDHRVH------ARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCV------- 63
Query: 256 LPGENEPLHAYVTAHNPENVKKAVDRLVCLV 286
VT PENV++A+D ++ L
Sbjct: 64 ----------TVTG-LPENVEEAIDHILNLE 83
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo
sapiens}
Length = 85
Score = 41.6 bits (98), Expect = 2e-05
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 6/48 (12%)
Query: 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGS 242
++MIP GL+IG G T+K +++ G K+I+ GS
Sbjct: 13 GTVQEIMIPAG------KAGLVIGKGGETIKQLQERAGVKMILIQDGS 54
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
Length = 63
Score = 40.7 bits (95), Expect = 2e-05
Identities = 15/61 (24%), Positives = 20/61 (32%), Gaps = 3/61 (4%)
Query: 39 NEGPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCREKRPGMGGPPANTHR 98
+ G RC NCG DH + C P C C H+ C K +
Sbjct: 5 SSGDRCYNCGGLDHHAKECKLPPQPKK---CHFCQSISHMVASCPLKAQQGPSAQGSGPS 61
Query: 99 N 99
+
Sbjct: 62 S 62
>1x4n_A FAR upstream element binding protein 1; KH domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
d.51.1.1 PDB: 2opu_A
Length = 92
Score = 41.3 bits (97), Expect = 2e-05
Identities = 10/53 (18%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 185 PPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237
++ + ++ +P VG +IG G + +++++G KI I
Sbjct: 4 GSSGHQQQRSVMTEEYKVPDG------MVGFIIGRGGEQISRIQQESGCKIQI 50
>1j4w_A FUSE binding protein; single-stranded DNA binding protein; HET:
DNA; NMR {Homo sapiens} SCOP: d.51.1.1 d.51.1.1
Length = 174
Score = 42.5 bits (100), Expect = 3e-05
Identities = 20/99 (20%), Positives = 36/99 (36%), Gaps = 22/99 (22%)
Query: 185 PPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVK 244
+ PP ++P GL+IG G T+KS+ + +GA+I +
Sbjct: 93 GNWNMGPPGGLQEFNFIVPTG------KTGLIIGKGGETIKSISQQSGARIEL------- 139
Query: 245 EGKVGRKDGQPLPGENEPLHAYVT-AHNPENVKKAVDRL 282
+++ P N L T P+ + A +
Sbjct: 140 -----QRNPPPNADPNMKL---FTIRGTPQQIDYARQLI 170
Score = 38.3 bits (89), Expect = 9e-04
Identities = 18/100 (18%), Positives = 34/100 (34%), Gaps = 23/100 (23%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPG 258
V IP+ VG++IG G +K ++ D G +I +
Sbjct: 6 DVPIPR------FAVGIVIGRNGEMIKKIQNDAGVRIQFK---------------PDDGT 44
Query: 259 ENEPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPGA 298
E + A +T P+ + A + + L+ +
Sbjct: 45 TPERI-AQITG-PPDRAQHAAEIITDLLRSVQAGNPGGPG 82
>2dgr_A Ring finger and KH domain-containing protein 1; structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 83
Score = 39.2 bits (91), Expect = 1e-04
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 6/48 (12%)
Query: 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGS 242
+ +V +P VGL++GP+G T+K +++ T I+ G+
Sbjct: 9 QTTIQVRVPYR------VVGLVVGPKGATIKRIQQRTHTYIVTPGRDK 50
>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta
fold, DNA binding protein; 0.95A {Homo sapiens} SCOP:
d.51.1.1 PDB: 1zzj_A 1zzi_A
Length = 82
Score = 38.8 bits (91), Expect = 1e-04
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237
+ +V IP+D G +IG G +K + ++GA I I
Sbjct: 6 IITTQVTIPKD------LAGSIIGKGGQRIKQIRHESGASIKI 42
>2ctk_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 104
Score = 39.4 bits (92), Expect = 2e-04
Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 6/49 (12%)
Query: 194 IKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGS 242
+ V +V +P D H +IG +G+ ++ M + I +
Sbjct: 15 VPVTIEVEVPFDLH------RYVIGQKGSGIRKMMDEFEVNIHVPAPEL 57
>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA
binding protein/DNA complex; 1.60A {Homo sapiens}
Length = 76
Score = 38.4 bits (90), Expect = 2e-04
Identities = 11/42 (26%), Positives = 22/42 (52%), Gaps = 6/42 (14%)
Query: 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237
+ ++ IP D +G +IG +G + + + +GA+I I
Sbjct: 5 TSHELTIPND------LIGCIIGRQGAKINEIRQMSGAQIKI 40
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 107
Score = 38.7 bits (90), Expect = 3e-04
Identities = 18/103 (17%), Positives = 30/103 (29%), Gaps = 22/103 (21%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPG 258
IP GL+IG G +K++ + TGA + I + P
Sbjct: 10 TFSIPTH------KCGLVIGRGGENVKAINQQTGAFVEI------------SRQLPPNGD 51
Query: 259 ENEPLHAYVTAH-NPENVKKAVDRLVCLVSARPRARFPPGADF 300
N L +P+ + A + + P
Sbjct: 52 PNFKL---FIIRGSPQQIDHAKQLIEEKIEGPLCPVGPGPGGP 91
>1j5k_A Heterogeneous nuclear ribonucleoprotein K; single-stranded DNA
binding protein, transcription factor, hnRNP K, CT
element, C-MYC oncogene; NMR {Homo sapiens} SCOP:
d.51.1.1 PDB: 1khm_A
Length = 89
Score = 38.1 bits (89), Expect = 3e-04
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 195 KVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237
+ +V IP+D G +IG G +K + ++GA I I
Sbjct: 13 IITTQVTIPKD------LAGSIIGKGGQRIKQIRHESGASIKI 49
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex,
PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus
musculus} PDB: 3trz_A* 3ts0_A*
Length = 148
Score = 38.8 bits (90), Expect = 4e-04
Identities = 16/57 (28%), Positives = 18/57 (31%), Gaps = 3/57 (5%)
Query: 31 LKKGTLRENEGPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCREKRP 87
R G RC NCG DH + C P C C H+ C K
Sbjct: 87 CIGSERRPKGGDRCYNCGGLDHHAKECKLPPQ---PKKCHFCQSINHMVASCPLKAQ 140
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 40.6 bits (96), Expect = 5e-04
Identities = 21/109 (19%), Positives = 33/109 (30%), Gaps = 35/109 (32%)
Query: 175 KMFKVNPEFKPPPDYKP--PVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTG 232
M K + P K PV++ V +P +GP G LK ++ +TG
Sbjct: 549 IMNKTISK--PRASRKENGPVVET---VQVPLS------KRAKFVGPGGYNLKKLQAETG 597
Query: 233 AKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDR 281
I + + V A P + +A D
Sbjct: 598 VTISQVDEETFS----------------------VFAPTPSAMHEARDF 624
>2e3u_A PH-DIM2P, hypothetical protein PH1566; PRE-ribosomal RNA processing
factor, RNA binding protein; 2.30A {Pyrococcus
horikoshii} PDB: 3aev_B
Length = 219
Score = 39.3 bits (91), Expect = 7e-04
Identities = 26/103 (25%), Positives = 36/103 (34%), Gaps = 15/103 (14%)
Query: 154 MNTREYRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFV 213
M + KK E D E D K + V IP+D +
Sbjct: 1 MGEEFEKLMKKFENVNKD---------GEIVEDEDEWEEFFKQEEYVKIPKD------RI 45
Query: 214 GLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPL 256
+LIG +G T K +EK T KI I + ++ PL
Sbjct: 46 AVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPL 88
Score = 36.6 bits (84), Expect = 0.005
Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 188 DYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGK 240
+I + D ++ + G +IG +G T + +E+ +GA + + GK
Sbjct: 116 GEYLEIINLTDIIIGNEKNAL-PRVRGRIIGRKGRTRQIIEEMSGASVSVYGK 167
>2axy_A Poly(RC)-binding protein 2; protein-DNA complex, DNA binding
protein-DNA complex; 1.70A {Homo sapiens} SCOP: d.51.1.1
PDB: 2pqu_A 2py9_A 1ztg_A 3vke_A*
Length = 73
Score = 36.5 bits (85), Expect = 7e-04
Identities = 12/39 (30%), Positives = 24/39 (61%), Gaps = 6/39 (15%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237
++++ E VG +IG +G ++K M +++GA+I I
Sbjct: 8 RLLMHGKE------VGSIIGKKGESVKKMREESGARINI 40
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo sapiens}
SCOP: d.51.1.1 PDB: 1vih_A
Length = 71
Score = 36.6 bits (85), Expect = 7e-04
Identities = 15/89 (16%), Positives = 29/89 (32%), Gaps = 25/89 (28%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPG 258
++ I H LIG G + ++ + I P
Sbjct: 8 EINIDHKFH------RHLIGKSGANINRIKDQYKVSVRI-------------------PP 42
Query: 259 ENEPLHAYVTAHNPENVKKAVDRLVCLVS 287
++E + +P+ V++A L+ L S
Sbjct: 43 DSEKSNLIRIEGDPQGVQQAKRELLELAS 71
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 39.4 bits (93), Expect = 0.001
Identities = 25/109 (22%), Positives = 38/109 (34%), Gaps = 35/109 (32%)
Query: 175 KMFKVNPEFKPPPDYKP--PVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTG 232
+M K P D P I+ + IP D + +IG G ++ + TG
Sbjct: 552 EMNKAMDA--PRADVGDFAPKIET---INIPTD------KIREVIGSGGKVIREIVATTG 600
Query: 233 AKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDR 281
AK+ I G VK V+A + +K A+D
Sbjct: 601 AKVDINDDGVVK----------------------VSASDGAKIKAAIDW 627
>1we8_A Tudor and KH domain containing protein; structural genomics, riken
structural genomics/proteomics initiative, RSGI, RNA
binding protein; NMR {Mus musculus} SCOP: d.51.1.1
Length = 104
Score = 36.7 bits (85), Expect = 0.001
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEG 246
V +++ +PQ VG +IG G T++S+ K +GAKI +
Sbjct: 15 VFEQLSVPQR------SVGRIIGRGGETIRSICKASGAKITCDKESEGTLL 59
>2qnd_A FMR1 protein; KH domain, eukaryotic KH domains, tandem KH domains,
type I domains, fragIle X mental retardation protein,
RNA BI protein; 1.90A {Homo sapiens} PDB: 2fmr_A
Length = 144
Score = 37.3 bits (86), Expect = 0.002
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 6/40 (15%)
Query: 198 DKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237
++ ++ +D +GL IG G ++ K G I
Sbjct: 6 EQFIVRED------LMGLAIGTHGANIQQARKVPGVTAID 39
Score = 31.1 bits (70), Expect = 0.20
Identities = 11/77 (14%), Positives = 29/77 (37%), Gaps = 11/77 (14%)
Query: 211 NFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAH 270
N VG +IG G ++ + +G + ++ ++ + +P E +
Sbjct: 76 NLVGKVIGKNGKLIQEIVDKSGVVRV----------RIEAENEKNVPQEEGMVPFVFVG- 124
Query: 271 NPENVKKAVDRLVCLVS 287
+++ A L ++
Sbjct: 125 TKDSIANATVLLDYHLN 141
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 106
Score = 36.3 bits (84), Expect = 0.002
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 6/39 (15%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIII 237
V +P+ VG++IG G +K ++ D G +I
Sbjct: 14 DVPVPRH------SVGVVIGRSGEMIKKIQNDAGVRIQF 46
>2bl6_A Nucleocapsid protein P11; lentivirus, polyprotein, core protein,
retrovirus zinc finger-like domains; NMR {Equine
infectious anemia virus}
Length = 37
Score = 32.6 bits (74), Expect = 0.009
Identities = 13/41 (31%), Positives = 16/41 (39%), Gaps = 6/41 (14%)
Query: 43 RCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAGHIARDCR 83
C NCG H S C +C C GH ++ CR
Sbjct: 2 TCYNCGKPGHLSSQCR------APKVCFKCKQPGHFSKQCR 36
Score = 26.8 bits (59), Expect = 1.0
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 69 CSSCGGAGHIARDCREKR 86
C +CG GH++ CR +
Sbjct: 3 CYNCGKPGHLSSQCRAPK 20
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 36.3 bits (85), Expect = 0.011
Identities = 21/109 (19%), Positives = 36/109 (33%), Gaps = 35/109 (32%)
Query: 175 KMFKVNPEFKPPPDYKP--PVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTG 232
M + P D P I + I D + +IG G+ ++++ ++TG
Sbjct: 542 VMEQAINA--PRGDISEFAPRIHT---IKINPD------KIKDVIGKGGSVIRALTEETG 590
Query: 233 AKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDR 281
I I G+V + A + E K A+ R
Sbjct: 591 TTIEIEDDGTV----------------------KIAATDGEKAKHAIRR 617
>1tua_A Hypothetical protein APE0754; structural genomics, protein
structure initiative, MCSG, four layers alpha-beta
sandwich, PSI; 1.50A {Aeropyrum pernix} SCOP: d.51.1.1
d.51.1.1
Length = 191
Score = 35.0 bits (80), Expect = 0.015
Identities = 18/104 (17%), Positives = 36/104 (34%), Gaps = 8/104 (7%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKEGKVGRKDGQPLPG 258
V + + +G +IGPRG + + TG I + + S+ + + P+
Sbjct: 7 YVKVKPE------RLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNL 60
Query: 259 EN--EPLHAYVTAHNPENVKKAVDRLVCLVSARPRARFPPGADF 300
E + A PE + ++ LV + +
Sbjct: 61 MKAAEVVKAISLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNH 104
Score = 35.0 bits (80), Expect = 0.016
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 188 DYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGK 240
D V+ + V Q+ I G +IG G +++E+ T I +
Sbjct: 86 DQILVVVDLKQVVGDSQNHLKRI--KGRIIGEGGRARRTIEEMTDTYINVGEY 136
>1dsq_A Nucleic acid binding protein P14; CCHC type zinc finger,
virus/viral protein; NMR {Mouse mammary tumor virus}
SCOP: g.40.1.1
Length = 26
Score = 31.6 bits (71), Expect = 0.017
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 68 LCSSCGGAGHIARDCREK 85
+C SCG GHI RDC+E+
Sbjct: 4 VCFSCGKTGHIKRDCKEE 21
>2ctl_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 97
Score = 32.1 bits (73), Expect = 0.051
Identities = 9/47 (19%), Positives = 15/47 (31%), Gaps = 6/47 (12%)
Query: 199 KVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGAKIIIRGKGSVKE 245
V + HP I IG +G + + + I K +
Sbjct: 20 SVTVDPKYHPKI------IGRKGAVITQIRLEHDVNIQFPDKDDGNQ 60
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide
transferase, ATP-GTP diphosphotransferase RNA
processing, RNA degradation; 2.5A {Streptomyces
antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4
d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A
Length = 757
Score = 33.3 bits (77), Expect = 0.091
Identities = 22/113 (19%), Positives = 40/113 (35%), Gaps = 32/113 (28%)
Query: 169 RHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSME 228
R ++ M + P +I V IP D+ +G +IGP+ + ++
Sbjct: 575 RLHILDVMMEAIDTPDEMSPNAPRIITVK----IPVDK------IGEVIGPKRQMINQIQ 624
Query: 229 KDTGAKIIIRGKGSVKEGKVGRKDGQPLPGENEPLHAYVTAHNPENVKKAVDR 281
+DTGA+I I G++ Y+ A + + A
Sbjct: 625 EDTGAEITIEDDGTI----------------------YIGAADGPAAEAARAT 655
>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 = 33.3 bits (75), Expect = 0.10
Identities = 19/165 (11%), Positives = 51/165 (30%), Gaps = 32/165 (19%)
Query: 154 MNTREYRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIK---VNDKVMIPQDEHPDI 210
+Y+ + L + + F N + K D ++ ++ +M +
Sbjct: 11 TGEHQYQYKDILS-----VFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTL 65
Query: 211 NFVGLLIGPRGNTLK-----SMEKDTG---AKIIIRGKGSVKEGKVGRKDGQPLPGENEP 262
L+ + ++ + + + I + ++ + L +N+
Sbjct: 66 RLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125
Query: 263 LHAYVTAHNPENV--KKAVDRL-VCLVSARPRARFPPGADFILNG 304
Y NV + +L L+ R P + +++G
Sbjct: 126 FAKY-------NVSRLQPYLKLRQALLELR------PAKNVLIDG 157
Score = 30.6 bits (68), Expect = 0.78
Identities = 28/199 (14%), Positives = 50/199 (25%), Gaps = 40/199 (20%)
Query: 58 PDKPNITNSTLC-----SSCGGAGHIARDCREKRPGMGGPPANTHRNRAKIDEEYMSLMA 112
P +I L + + P +T I Y+ L
Sbjct: 382 PPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTIS----IPSIYLELKV 437
Query: 113 ELGEGPPPDKRQRDNDSYRKNNTSGSLSPSPEP--IYSSDGKRMNTREYRTRKKLEEERH 170
+L + D+ + K S L P YS G + + ER
Sbjct: 438 KLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIG-------HHLKNIEHPERM 490
Query: 171 DLIQKMF--------KVNPEFKPPPDYKPPVIKVND-----KVMIPQDEHPD------IN 211
L + +F K+ + + + + D + ++
Sbjct: 491 TLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILD 550
Query: 212 FVGLLIGPRGNTLKSMEKD 230
F L N + S D
Sbjct: 551 F---LPKIEENLICSKYTD 566
Score = 28.7 bits (63), Expect = 3.1
Identities = 25/170 (14%), Positives = 52/170 (30%), Gaps = 44/170 (25%)
Query: 144 EPI-YSSDGKRMNTREYRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKP-PVIKVNDKVM 201
PI M TR Y E+ D +++ N F + P +K+ ++
Sbjct: 96 SPIKTEQRQPSMMTRMY-------IEQRD---RLYNDNQVFAKYNVSRLQPYLKLRQALL 145
Query: 202 IPQDEHPDINFVGLL-IGPRGNTLKS-MEKDT--GAKIIIRGKGSV---KEGKVGRKDG- 253
+ ++ G+L G K+ + D K+ + + +
Sbjct: 146 ELRP-AKNVLIDGVLGSG------KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV 198
Query: 254 ----QPL------PGENEPLHAYVTAHNPENVKKAVDRLV-------CLV 286
Q L + H+ +++ + RL+ CL+
Sbjct: 199 LEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL 248
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA
recognition, zinc finger, viral protein; NMR {Human
immunodeficiency virus type 2} SCOP: g.40.1.1
Length = 49
Score = 29.1 bits (65), Expect = 0.17
Identities = 16/48 (33%), Positives = 21/48 (43%), Gaps = 8/48 (16%)
Query: 43 RCTNCGASDHKSWLC--PDKPNITNSTLCSSCGGAGHIARDCREKRPG 88
RC NCG H + C P + C CG GH+ C E++ G
Sbjct: 8 RCWNCGKEGHSARQCRAPRRQG------CWKCGKTGHVMAKCPERQAG 49
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein,
metal binding protein; NMR {Synthetic}
Length = 39
Score = 27.9 bits (62), Expect = 0.42
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 69 CSSCGGAGHIARDCREKR 86
C +CG GH AR CR+ R
Sbjct: 3 CFNCGKPGHTARMCRQPR 20
Score = 27.5 bits (61), Expect = 0.60
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 8/44 (18%)
Query: 43 RCTNCGASDHKSWLC--PDKPNITNSTLCSSCGGAGHIARDCRE 84
C NCG H + +C P + C +CG H C +
Sbjct: 2 TCFNCGKPGHTARMCRQPRQEG------CWNCGSKEHRFAQCPK 39
>1gnf_A Transcription factor GATA-1; zinc finger, transcription
regulation; NMR {Mus musculus} SCOP: g.39.1.1 PDB:
1y0j_A 2l6y_A 2l6z_A
Length = 46
Score = 27.8 bits (62), Expect = 0.58
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 4/35 (11%)
Query: 39 NEGPRCTNCGASDHKSWLCPDKPNITNSTLCSSCG 73
+E C NCGA+ W + + T LC++CG
Sbjct: 2 SEARECVNCGATATPLW----RRDRTGHYLCNACG 32
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 30.0 bits (67), Expect = 0.66
Identities = 8/40 (20%), Positives = 10/40 (25%), Gaps = 14/40 (35%)
Query: 39 NEGPRCTNCGASDHKSWLCPDKPNI-----TNSTLCSSCG 73
N C C P I +C+ CG
Sbjct: 19 NIVLTCPECKV---------YPPKIVERFSEGDVVCALCG 49
Score = 26.9 bits (59), Expect = 7.0
Identities = 6/33 (18%), Positives = 7/33 (21%), Gaps = 8/33 (24%)
Query: 60 KPNITNSTLCSSCGGA-GHIARD-------CRE 84
PN+ C C I C
Sbjct: 15 GPNLNIVLTCPECKVYPPKIVERFSEGDVVCAL 47
>1nc8_A Nucleocapsid protein; HIV-2, RNA recognition, zinc finger, viral
protein; NMR {Human immunodeficiency virus 2} SCOP:
g.40.1.1 PDB: 2di2_A
Length = 29
Score = 27.2 bits (60), Expect = 0.68
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 69 CSSCGGAGHIARDCREKR 86
C +CG GH AR CR R
Sbjct: 9 CWNCGKEGHSARQCRAPR 26
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.5 bits (65), Expect = 0.89
Identities = 8/43 (18%), Positives = 15/43 (34%), Gaps = 14/43 (32%)
Query: 158 EYRTRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDKV 200
E + KKL+ L K++ D P + + +
Sbjct: 18 EKQALKKLQAS---L--KLYA--------DD-SAPALAIKATM 46
>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex;
NMR {Human immunodeficiency virus 1} SCOP: g.40.1.1
PDB: 1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A*
1bj6_A* 1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A
Length = 55
Score = 27.7 bits (61), Expect = 0.90
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 69 CSSCGGAGHIARDCREKR 86
C +CG GHIA++CR R
Sbjct: 15 CFNCGKEGHIAKNCRAPR 32
Score = 27.3 bits (60), Expect = 1.1
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 43 RCTNCGASDHKSWLC--PDKPNITNSTLCSSCGGAGHIARDCREKRP 87
+C NCG H + C P K C CG GH +DC E++
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKKG------CWKCGKEGHQMKDCTERQA 54
>2kae_A GATA-type transcription factor; zinc finger, GATA-type, DNA; NMR
{Caenorhabditis elegans}
Length = 71
Score = 27.9 bits (62), Expect = 0.98
Identities = 7/40 (17%), Positives = 15/40 (37%), Gaps = 3/40 (7%)
Query: 34 GTLRENEGPRCTNCGASDHKSWLCPDKPNITNSTLCSSCG 73
G+ + +C+NC ++ W C++C
Sbjct: 1 GSHMNKKSFQCSNCSVTETIRWRNIRSK---EGIQCNACF 37
>2uzg_A Ubiquitin carboxyl-terminal hydrolase 33; UBL conjugation
pathway, DE-ubiquitination, alternative splicing,
metal-binding, thiol protease; NMR {Homo sapiens} SCOP:
g.44.1.5
Length = 97
Score = 28.4 bits (63), Expect = 1.1
Identities = 9/44 (20%), Positives = 12/44 (27%), Gaps = 10/44 (22%)
Query: 33 KGTLRENEGPRCTNCGASDHKSWLCPDKPNITNSTLCSSCGGAG 76
K L + C +C W C L + C G
Sbjct: 17 KEDLIQKSLGTCQDCKVQGPNLWAC----------LENRCSYVG 50
>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 = 30.0 bits (67), Expect = 1.1
Identities = 48/309 (15%), Positives = 81/309 (26%), Gaps = 123/309 (39%)
Query: 76 GHIARDCREKRPGMGGPPANTHRNRAKIDEEYM------SLMAELGEGPPPDKRQRDN-- 127
G+++ + G N + Y+ +L A+L + +
Sbjct: 66 GYVSSLVEPSKVGQFDQVLNLCLTE--FENCYLEGNDIHALAAKLLQENDTTLVKTKELI 123
Query: 128 -DSYRKNNTSGSLSPSPEPIYS------SDGK-RM--------NTREYRTRKKLEEERH- 170
+ + P + S +G ++ NT +Y EE R
Sbjct: 124 KNYITARIMAKR--PFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDY-----FEELRDL 176
Query: 171 ---------DLIQKMFKV--------------------------NPEFKPPPDY---KP- 191
DLI+ + NP P DY P
Sbjct: 177 YQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPI 236
Query: 192 --PVIKVNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGA-KIIIRGKGSVKEGKV 248
P+I V Q H +V T K + G + ++G +G V
Sbjct: 237 SCPLIGVI------QLAH----YV--------VTAKLLGFTPGELRSYLKGATGHSQGLV 278
Query: 249 GRKDGQPLPGENEPLHAYVTAHNP------ENVKKAVDRLVCLVSAR-----PRARFPPG 297
A A +V+KA+ ++ + R P PP
Sbjct: 279 T---------------AVAIAETDSWESFFVSVRKAI-TVLFFIGVRCYEAYPNTSLPPS 322
Query: 298 --ADFILNG 304
D + N
Sbjct: 323 ILEDSLENN 331
>2eu9_A Dual specificity protein kinase CLK3; kinase domain, transferase;
1.53A {Homo sapiens} PDB: 2wu6_A* 2wu7_A* 3raw_A* 2exe_A
3nr9_A*
Length = 355
Score = 28.8 bits (65), Expect = 2.0
Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 11/89 (12%)
Query: 106 EYMSLMAELGEGPPPDKRQRDNDSYRKNNTSGSLSPSPEPIYSSDGKRM--NTREYRTRK 163
E++ +M ++ GP P +K G L SSDG+ + N + ++
Sbjct: 246 EHLVMMEKI-LGPIPSHMIH-RTRKQKYFYKGGL---VWDENSSDGRYVKENCKPLKSYM 300
Query: 164 KLEEERH----DLIQKMFKVNPEFKPPPD 188
+ H DL+++M + +P +
Sbjct: 301 LQDSLEHVQLFDLMRRMLEFDPAQRITLA 329
>2ctf_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 102
Score = 26.8 bits (59), Expect = 3.3
Identities = 10/54 (18%), Positives = 15/54 (27%), Gaps = 16/54 (29%)
Query: 196 VNDKVMIPQDEHPDINFVGLLIGPRGNTLKSMEKDTGA----------KIIIRG 239
V P H +IG +G L + + KI + G
Sbjct: 27 TVSSVAAPSWLH------RFIIGKKGQNLAKITQQMPKVHIEFTEGEDKITLEG 74
>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting,
protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP:
a.4.5.54 a.4.5.54
Length = 566
Score = 28.5 bits (62), Expect = 3.6
Identities = 20/177 (11%), Positives = 39/177 (22%), Gaps = 2/177 (1%)
Query: 2 ICDVTNFINYRLRKLAENCVPETWAFHPILKKGTLRENEGPRCTNCGASDHKSWLCPDKP 61
IC F N+ E C + K R + +
Sbjct: 182 ICPACTFANHPQIGNCEICGHRLPNASKVRSKLNRLNFHDSRVHIELEKNSLARNKSSHS 241
Query: 62 NITNSTLCSSCGGAGHIARDCREKRPGMGGPPANTHRNRAKIDEEYMSLMAELGEGPPPD 121
+++S S+ + R+ + ++ + D
Sbjct: 242 ALSSS--SSTGSSTEFVQLSFRKSDGVLFSQATERALENILTEKNKHIFNQNVVSVNGVD 299
Query: 122 KRQRDNDSYRKNNTSGSLSPSPEPIYSSDGKRMNTREYRTRKKLEEERHDLIQKMFK 178
R+ + N + SS K + DL + M
Sbjct: 300 MRKGASSHEYNNEVPFIETKLSRIGISSLEKSRENQLLNNDILFNNALTDLNKLMSL 356
>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U
mismatch, G-A MIS U mismatch, A-C mismatch, zinc
finger, NC, viral protein-RN; HET: AP7; NMR {Moloney
murine leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A
1wwe_A 1wwf_A 1wwg_A
Length = 56
Score = 25.5 bits (55), Expect = 4.6
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 69 CSSCGGAGHIARDCREKRPGMGGPPANT 96
C+ C GH A+DC +K G GP T
Sbjct: 26 CAYCKEKGHWAKDCPKKPRGPRGPRPQT 53
>3d00_A Tungsten formylmethanofuran dehydrogenase subunit; FWDE/GAPDH
domain-like fold, structural genomics, joint CENT
structural genomics; HET: MSE; 1.90A {Syntrophus
aciditrophicus}
Length = 191
Score = 27.3 bits (60), Expect = 4.9
Identities = 7/35 (20%), Positives = 11/35 (31%), Gaps = 5/35 (14%)
Query: 58 PDKPNITNSTLCSSCG-----GAGHIARDCREKRP 87
+K + LC C G + C+ P
Sbjct: 155 LEKKHKGKIVLCPQCREAYPAQDGELCLSCQGGSP 189
>3kvw_A DYRK2, dual specificity tyrosine-phosphorylation-regulat 2;
KI-(Y)-phosphorylation REG kinase 2, PSK-H2, kinase,
structural genomics consortium; HET: SEP PTR IRB; 2.28A
{Homo sapiens} PDB: 3k2l_A*
Length = 429
Score = 27.8 bits (62), Expect = 5.6
Identities = 15/94 (15%), Positives = 31/94 (32%), Gaps = 18/94 (19%)
Query: 106 EYMSLMAELGEGPPPDK------RQR---DNDSYRKNNTSGSLSPSPEPIYSSDGKRMNT 156
+ ++ M EL G P K R + + Y + T +LS + +R
Sbjct: 306 DQLACMIEL-LGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKL 364
Query: 157 REYRTRKKLEEERH--------DLIQKMFKVNPE 182
R ++ D +++ + +P
Sbjct: 365 RGPPESREWGNALKGCDDPLFLDFLKQCLEWDPA 398
>3llt_A Serine/threonine kinase-1, pflammer; lammer kinase, malaria,
structural GE structural genomics consortium, SGC,
transferase; HET: ANP; 2.50A {Plasmodium falciparum 3D7}
Length = 360
Score = 27.3 bits (61), Expect = 6.2
Identities = 16/97 (16%), Positives = 35/97 (36%), Gaps = 10/97 (10%)
Query: 96 THRNRAKIDEEYMSLMAELGEGPPPDK---RQRDNDSYRKNNTSGSLSPSPEPIYSSDGK 152
TH + E++++M + P P + + N PE S +
Sbjct: 261 THEHM-----EHLAMMESI-IQPIPKNMLYEATKTNGSKYVNKDELKLAWPENASSINSI 314
Query: 153 RMNTREYRTRKKLEEER-HDLIQKMFKVNPEFKPPPD 188
+ + K ++ E D + + +++P +P P
Sbjct: 315 KHVKKCLPLYKIIKHELFCDFLYSILQIDPTLRPSPA 351
>3lg3_A Isocitrate lyase; conserved, CD, proteomics evidence (cytopl
periplasmic), drug target functions; 1.40A {Yersinia
pestis} PDB: 1igw_A
Length = 435
Score = 27.3 bits (60), Expect = 6.5
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 169 RHDLIQKMFKVNPEFKPPPDYKPPVI 194
R D IQ + P K DY P++
Sbjct: 131 RADQIQWSNNIEPGSKGYTDYFLPIV 156
>3a99_A Proto-oncogene serine/threonine-protein kinase PI; PIM-1, P27KIP1,
peptide drug, prostate cancer, transferase; HET: ANP;
1.60A {Homo sapiens} PDB: 3bgq_A* 3bgp_A* 2obj_A*
3bgz_A* 3t9i_A* 3dcv_A* 1xws_A* 2xj1_A* 2xix_A* 2xiz_A*
2xj0_A* 2xiy_A* 2xj2_A* 3f2a_A* 1xr1_A* 1xqz_A* 3cy2_A*
3cxw_A* 3cy3_A* 2bik_B* ...
Length = 320
Score = 26.9 bits (60), Expect = 8.3
Identities = 5/33 (15%), Positives = 13/33 (39%)
Query: 150 DGKRMNTREYRTRKKLEEERHDLIQKMFKVNPE 182
+ + + R+++ E LI+ + P
Sbjct: 251 HDEEIIRGQVFFRQRVSSECQHLIRWCLALRPS 283
>2npp_B PP2A, B subunit, serine/threonine-protein phosphatase 2A 56 kDa RE
subunit gamma isoform; heat repeat, signaling protein,
hydrolase-hydrolase inhibito; HET: 1ZN; 3.30A {Homo
sapiens} SCOP: a.118.1.20
Length = 449
Score = 27.1 bits (59), Expect = 8.4
Identities = 12/64 (18%), Positives = 19/64 (29%), Gaps = 6/64 (9%)
Query: 161 TRKKLEEERHDLIQKMFKVNPEFKPPPDYKPPVIKVNDK-----VMIPQDEHPDINFVGL 215
R + E + + MF VN F+ P P D + H + +
Sbjct: 83 NRNVITEPIYPEVVHMFAVNM-FRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQLVYEFF 141
Query: 216 LIGP 219
L
Sbjct: 142 LRFL 145
>2fno_A AGR_PAT_752P; thioredoxin fold, GST C-terminal domain-like fold,
structura genomics, joint center for structural
genomics, JCSG; 2.00A {Agrobacterium tumefaciens} SCOP:
a.45.1.1 c.47.1.5
Length = 248
Score = 26.8 bits (59), Expect = 8.8
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 1/40 (2%)
Query: 166 EEERHDLIQKMFKVNPEFKPPPDYKPPVIKVND-KVMIPQ 204
+E D I+ + E +P PPV+ + I Q
Sbjct: 46 DEHDVDAIEGLMDCGAEKQPVAFMGPPVLIDRERNFAISQ 85
>1z57_A Dual specificity protein kinase CLK1; protein tyrosine kinase,
splicing, human, 10Z-hymendialdisine, structural
genomics; HET: DBQ; 1.70A {Homo sapiens} PDB: 2vag_A*
Length = 339
Score = 26.9 bits (60), Expect = 9.6
Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 11/89 (12%)
Query: 106 EYMSLMAELGEGPPPDKRQRDNDSYRKNNTSGSLSPSPEPIYSSDGKRM--NTREYRTRK 163
E++++M + GP P + RK L +SS G+ + + +
Sbjct: 241 EHLAMMERI-LGPLPKHMIQ-KTRKRKYFHHDRL---DWDEHSSAGRYVSRACKPLKEFM 295
Query: 164 KLEEERH----DLIQKMFKVNPEFKPPPD 188
++ H DLIQKM + +P +
Sbjct: 296 LSQDVEHERLFDLIQKMLEYDPAKRITLR 324
>3p23_A Serine/threonine-protein kinase/endoribonuclease; kinase domain,
kinase and RNAse function, ATP binding ssRNA
dephosphorylated, hydrolase; HET: ADP; 2.70A {Homo
sapiens}
Length = 432
Score = 27.0 bits (60), Expect = 9.7
Identities = 10/69 (14%), Positives = 19/69 (27%), Gaps = 18/69 (26%)
Query: 114 LGEGPPPDKRQRDNDSYRKNNTSGSLSPSPEPIYSSDGKRMNTREYRTRKKLEEERHDLI 173
+ EG P + + PE + +LI
Sbjct: 223 ISEGSHPFGKSLQRQANILLGACSLDCLHPEKHEDVIAR------------------ELI 264
Query: 174 QKMFKVNPE 182
+KM ++P+
Sbjct: 265 EKMIAMDPQ 273
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
0.315 0.136 0.422
Gapped
Lambda K H
0.267 0.0535 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,891,961
Number of extensions: 298772
Number of successful extensions: 946
Number of sequences better than 10.0: 1
Number of HSP's gapped: 923
Number of HSP's successfully gapped: 112
Length of query: 304
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 211
Effective length of database: 4,105,140
Effective search space: 866184540
Effective search space used: 866184540
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: 42 (22.0 bits)
S2: 57 (26.2 bits)