RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1580
(267 letters)
>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins, RNA
binding; NMR {Xenopus laevis} SCOP: d.51.1.1
Length = 140
Score = 133 bits (335), Expect = 2e-39
Identities = 46/127 (36%), Positives = 81/127 (63%), Gaps = 7/127 (5%)
Query: 21 KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRI 80
++ ++ VPV+++P FNFVG++LGP+G + K+L+ +T ++ + G+GS+RD+ KEE+ R
Sbjct: 1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR- 59
Query: 81 SGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQ 140
G P + HL E+LHV IT A ++ A+ EV++ LVP + D +++ +
Sbjct: 60 -GKPNWEHLNEDLHVLITVEDAQNRAELKLKRAVEEVKKLLVP-----AAEGEDSLKKMK 113
Query: 141 MWEMQIL 147
+ E+ IL
Sbjct: 114 LMELAIL 120
>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 = 122 bits (307), Expect = 3e-35
Identities = 31/130 (23%), Positives = 66/130 (50%), Gaps = 11/130 (8%)
Query: 18 KPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEE 77
+V+ +V++P ++P+ NFVG L+GP+GN+LK ++++ ++ I G+GS+++ +
Sbjct: 3 MATRVSDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRK 62
Query: 78 LRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIR 137
E LH +T A + A+ ++R L + + +++R
Sbjct: 63 ----DGQMLPGEDEPLHALVT-----ANTMENVKKAVEQIRNILKQGIETP--EDQNDLR 111
Query: 138 QEQMWEMQIL 147
+ Q+ E+ L
Sbjct: 112 KMQLRELARL 121
>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 = 59.2 bits (143), Expect = 1e-11
Identities = 20/100 (20%), Positives = 36/100 (36%), Gaps = 14/100 (14%)
Query: 18 KPIKVTIRVIVPV-RDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEE 76
V ++ V + P FN K+ GP + L+ +Q +T ++ + G+GS
Sbjct: 8 GMHYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASG 67
Query: 77 ELRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAE 116
E +++ I+ P A L E
Sbjct: 68 R----------EAFEPMYIYISH---PKPEGLAAAKKLCE 94
>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 = 43.6 bits (103), Expect = 3e-06
Identities = 14/73 (19%), Positives = 28/73 (38%), Gaps = 11/73 (15%)
Query: 13 DITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDR 72
DI + + V +P H ++G G L+ L+ T T++ I
Sbjct: 8 DIVARLQTQASATVAIPKEHH------RFVIGKNGEKLQDLELKTATKIQIPRPDD---- 57
Query: 73 HKEEELRISGDPK 85
+++I+G +
Sbjct: 58 -PSNQIKITGTKE 69
>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 = 42.8 bits (101), Expect = 7e-06
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 19 PIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEEL 78
P +++P + G ++G G ++K+LQE +M ++ G ++ ++ L
Sbjct: 12 PGNAVQEIMIPA------SKAGLVIGKGGETIKQLQERAGVKMVMIQDGP-QNTGADKPL 64
Query: 79 RISGDPK 85
RI+GDP
Sbjct: 65 RITGDPY 71
>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 = 42.2 bits (99), Expect = 7e-06
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 12/68 (17%)
Query: 18 KPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEE 77
+ TI+V VP R VG ++GPKG ++KR+Q+ T T + R KE
Sbjct: 6 SGGQTTIQVRVPYR------VVGLVVGPKGATIKRIQQRTHTYI------VTPGRDKEPV 53
Query: 78 LRISGDPK 85
++G P+
Sbjct: 54 FAVTGMPE 61
>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 = 43.2 bits (102), Expect = 2e-05
Identities = 23/103 (22%), Positives = 41/103 (39%), Gaps = 9/103 (8%)
Query: 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISG 82
+++P G ++G G ++K+LQE +M ++ GS ++ LRI G
Sbjct: 3 VQEIMIPAG------KAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNV-DKPLRIIG 55
Query: 83 DPKFLHLLEELHVEITAFAPPAEAHARIAY--ALAEVRRFLVP 123
DP + E+ ++I R Y + VP
Sbjct: 56 DPYKVQQACEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVP 98
Score = 42.8 bits (101), Expect = 2e-05
Identities = 18/82 (21%), Positives = 27/82 (32%), Gaps = 9/82 (10%)
Query: 4 QEPHGRKMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAI 63
+ G I I V VP + VG ++G G +K++Q D R+
Sbjct: 73 ERDQGGFGDRNEYGSRIGGGIDVPVP------RHSVGVVIGRSGEMIKKIQNDAGVRIQF 126
Query: 64 LGRGSIRDRHKEEELRISGDPK 85
E+ I G P
Sbjct: 127 KQD---DGTGPEKIAHIMGPPD 145
>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 = 40.3 bits (95), Expect = 3e-05
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 20 IKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELR 79
+K + + VP N VG +LG G +L QE T R+ I +G + +
Sbjct: 1 MKELVEMAVPE------NLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVT 54
Query: 80 ISGDPK 85
I+G P
Sbjct: 55 ITGSPA 60
>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 = 44.3 bits (104), Expect = 3e-05
Identities = 28/133 (21%), Positives = 49/133 (36%), Gaps = 40/133 (30%)
Query: 2 KH-QEPHGRKMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTR 60
H ++ +G ++DI + P+ +TI H F G KG KR++E+
Sbjct: 1651 NHFKDTYGFSILDIVINNPVNLTI--------H--FG------GEKG---KRIRENY--- 1688
Query: 61 MAILGRGSIRDRHKEEELRISGDPK-----FLHLLEELHVEITAFAPPAEAHARI---AY 112
A++ + + K E++ + F L T F PA +
Sbjct: 1689 SAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS--ATQFTQPA-----LTLMEK 1741
Query: 113 ALAEV--RRFLVP 123
A E + L+P
Sbjct: 1742 AAFEDLKSKGLIP 1754
Score = 43.1 bits (101), Expect = 7e-05
Identities = 53/273 (19%), Positives = 93/273 (34%), Gaps = 71/273 (26%)
Query: 38 FVGKLLGPKGNSLKRLQEDTMTRMAILGRG-SIR-------DRHKEEELR---ISGDPKF 86
VG L+ +L L T+ + +G +I + ++ L IS P
Sbjct: 183 LVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISC-P-L 240
Query: 87 LHLLEELHVEITAFA---PPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMWE 143
+ +++ H +TA P E + + A + + ++ I + WE
Sbjct: 241 IGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVT----AVA------IAETDSWE 290
Query: 144 ---------MQILKEDG----GAASCSESSESSVNNPLLYAENT-SP---VENLTPPE-Y 185
+ +L G A + S + + L E SP + NLT +
Sbjct: 291 SFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQ 350
Query: 186 TLVDPAFNRIQPATEAINIPTKTMTTAALVNRKRPLLTAGSSRPTMSPT-------KRTV 238
V+ N PA + + I +LVN + L+ +G P S K
Sbjct: 351 DYVN-KTNSHLPAGKQVEI--------SLVNGAKNLVVSG---PPQSLYGLNLTLRKAKA 398
Query: 239 LSILTRARV--SQSKPTGV---LATSK--H-HY 263
S L ++R+ S+ K L + H H
Sbjct: 399 PSGLDQSRIPFSERKLKFSNRFLPVASPFHSHL 431
Score = 33.9 bits (77), Expect = 0.059
Identities = 26/171 (15%), Positives = 57/171 (33%), Gaps = 45/171 (26%)
Query: 99 AFAPPAEA-HARIAYALAEVRRF------LVPFT--RSLFQDYNDEIRQEQMWEMQILKE 149
A +A++ A+ F F R L+Q Y+ + ++K
Sbjct: 144 ALFRAVGEGNAQL-VAI-----FGGQGNTDDYFEELRDLYQTYHVLVG-------DLIKF 190
Query: 150 DGGAASCSESSESSVNNPLLYAEN-------TSPVENLTPPEYTLVDPAFNRIQPATEAI 202
A + SE ++++ ++ + +P + TP + L + I
Sbjct: 191 --SAETLSELIRTTLDAEKVFTQGLNILEWLENP--SNTPDKDYL----------LSIPI 236
Query: 203 NIPTKTMTTAA--LVNRKRPLLTAGSSRPTMSPTKRTVLSILTRARVSQSK 251
+ P + A +V K T G R + ++T ++++
Sbjct: 237 SCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETD 287
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo
sapiens}
Length = 85
Score = 39.6 bits (93), Expect = 6e-05
Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 21 KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRI 80
+++P G ++G G ++K+LQE +M ++ GS ++ + ++ LRI
Sbjct: 13 GTVQEIMIPA------GKAGLVIGKGGETIKQLQERAGVKMILIQDGS-QNTNVDKPLRI 65
Query: 81 SGDPK 85
GDP
Sbjct: 66 IGDPY 70
>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 = 39.2 bits (92), Expect = 9e-05
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 20 IKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELR 79
+K + + VP N VG +LG G +L QE T R+ I +G + +
Sbjct: 1 MKELVEIAVPE------NLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVT 54
Query: 80 ISGDPK 85
I+G P
Sbjct: 55 ITGSPA 60
>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 = 38.4 bits (90), Expect = 1e-04
Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 11/67 (16%)
Query: 18 KPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEE 77
K + +TIR+++ VG ++G KG S+K+++E++ R+ I E
Sbjct: 1 KNVTLTIRLLMHG------KEVGSIIGKKGESVKKMREESGARINISEGNC-----PERI 49
Query: 78 LRISGDP 84
+ ++G
Sbjct: 50 ITLAGPT 56
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo
sapiens} SCOP: d.51.1.1 PDB: 1vih_A
Length = 71
Score = 37.3 bits (87), Expect = 3e-04
Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 11/64 (17%)
Query: 22 VTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRIS 81
+ + + + H L+G G ++ R+++ + I D K +RI
Sbjct: 5 DYVEINIDHKFH------RHLIGKSGANINRIKDQYKVSVRI-----PPDSEKSNLIRIE 53
Query: 82 GDPK 85
GDP+
Sbjct: 54 GDPQ 57
>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 = 39.1 bits (91), Expect = 4e-04
Identities = 11/69 (15%), Positives = 22/69 (31%), Gaps = 6/69 (8%)
Query: 17 DKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEE 76
IVP G ++G G ++K + + + R+ + +
Sbjct: 99 PPGGLQEFNFIVPT------GKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMK 152
Query: 77 ELRISGDPK 85
I G P+
Sbjct: 153 LFTIRGTPQ 161
Score = 35.6 bits (82), Expect = 0.008
Identities = 16/65 (24%), Positives = 25/65 (38%), Gaps = 13/65 (20%)
Query: 22 VTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEE--LR 79
I V +P VG ++G G +K++Q D R+ D E +
Sbjct: 3 HMIDVPIPR------FAVGIVIGRNGEMIKKIQNDAGVRIQFK-----PDDGTTPERIAQ 51
Query: 80 ISGDP 84
I+G P
Sbjct: 52 ITGPP 56
>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 = 37.9 bits (88), Expect = 5e-04
Identities = 13/66 (19%), Positives = 27/66 (40%), Gaps = 11/66 (16%)
Query: 20 IKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELR 79
+ VTI V VP H ++G KG+ ++++ ++ + + D +
Sbjct: 15 VPVTIEVEVPFDLH------RYVIGQKGSGIRKMMDEFEVNIHVPAPELQSD-----IIA 63
Query: 80 ISGDPK 85
I+G
Sbjct: 64 ITGLAA 69
>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 = 38.3 bits (89), Expect = 7e-04
Identities = 14/81 (17%), Positives = 33/81 (40%), Gaps = 7/81 (8%)
Query: 5 EPHGRKMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAIL 64
EP T + +++IVP + G ++G G ++K + E + + +
Sbjct: 87 EPVSILQPQTTVNPDRANQVKIIVPN------STAGLIIGKGGATVKAIMEQSGAWVQLS 140
Query: 65 GRGSIRDRHKEEELRISGDPK 85
+ + + +SG+P+
Sbjct: 141 QKPDGINLQ-NRVVTVSGEPE 160
Score = 37.9 bits (88), Expect = 0.001
Identities = 11/64 (17%), Positives = 25/64 (39%), Gaps = 6/64 (9%)
Query: 21 KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRI 80
+ ++V++P G ++G G ++ +LQ++T + + E I
Sbjct: 5 QYFLKVLIPSY------AAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLI 58
Query: 81 SGDP 84
G
Sbjct: 59 QGTI 62
>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 = 38.3 bits (88), Expect = 0.002
Identities = 33/203 (16%), Positives = 58/203 (28%), Gaps = 80/203 (39%)
Query: 10 KMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSI 69
K++ TR K +VT + H + L P ++ + +
Sbjct: 267 KILLTTRFK--QVTDFLSAATTTHISLDHHSMTLTP---------DEVKSLLL------- 308
Query: 70 RDRHKEEELRISGDPKFLHL-LEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSL 128
K+L ++L E+ P + IA +R L
Sbjct: 309 ---------------KYLDCRPQDLPREVLTTNP--RRLSIIA---ESIRDGL------- 341
Query: 129 FQDYNDEIRQEQMWEMQILKEDGGAASCSESSESSVNNPLLYAENTSPVENLTPPEYTLV 188
D + ++ + ESS+N L P EY
Sbjct: 342 --ATWDNWKHVNCDKL------------TTIIESSLNV-------------LEPAEYR-- 372
Query: 189 DPAFNR--IQPATEAINIPTKTM 209
F+R + P + +IPT +
Sbjct: 373 -KMFDRLSVFP--PSAHIPTILL 392
Score = 30.2 bits (67), Expect = 0.77
Identities = 16/108 (14%), Positives = 41/108 (37%), Gaps = 22/108 (20%)
Query: 36 FNFVG-KL--LGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISGDPKFLHLLEE 92
F F+ K+ N+ + +T+ ++ + I D + E ++ FL +EE
Sbjct: 500 FRFLEQKIRHDSTAWNASGSIL-NTLQQLKFY-KPYICDNDPKYERLVNAILDFLPKIEE 557
Query: 93 LHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQ 140
++ + + + +R L+ ++ + + +Q Q
Sbjct: 558 -NLICS-------KYTDL------LRIALMAEDEAI---FEEAHKQVQ 588
>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 = 36.7 bits (85), Expect = 0.003
Identities = 20/107 (18%), Positives = 45/107 (42%), Gaps = 12/107 (11%)
Query: 18 KPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEE 77
K + +TIR+++ + VG ++G KG S+K+++E++ R+ I E
Sbjct: 1 KNVTLTIRLLMHGK------EVGSIIGKKGESVKKMREESGARINISEGNC-----PERI 49
Query: 78 LRISGDPK-FLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVP 123
+ ++G + ++ + ++ A R +VP
Sbjct: 50 ITLAGPTNAIFKAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVP 96
>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 = 36.3 bits (84), Expect = 0.004
Identities = 21/106 (19%), Positives = 34/106 (32%), Gaps = 20/106 (18%)
Query: 22 VTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRIS 81
++V +P + VG ++G KG +K+L + I + K + I+
Sbjct: 3 EMVQVFIPAQ------AVGAIIGKKGQHIKQLSRFASASIKIAPPET--PDSKVRMVIIT 54
Query: 82 GDP----KFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVP 123
G P K + E F P E VP
Sbjct: 55 GPPEAQFKAQGRIYGKLKEENFFGPKEEVKLET--------HIRVP 92
>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 = 34.8 bits (80), Expect = 0.004
Identities = 10/65 (15%), Positives = 26/65 (40%), Gaps = 8/65 (12%)
Query: 21 KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRI 80
+ V V + H K++G KG + +++ + + + ++++ I
Sbjct: 16 SFKLSVTVDPKYH------PKIIGRKGAVITQIRLEHDVNIQFPDKD--DGNQPQDQITI 67
Query: 81 SGDPK 85
+G K
Sbjct: 68 TGYEK 72
>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 = 34.4 bits (79), Expect = 0.006
Identities = 10/73 (13%), Positives = 30/73 (41%), Gaps = 10/73 (13%)
Query: 13 DITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDR 72
I + V+ V + R H +++G +G +++++ ++ + G+
Sbjct: 8 RIVGELEQMVSEDVPLDHRVH------ARIIGARGKAIRKIMDEFKVDIRFPQSGA---- 57
Query: 73 HKEEELRISGDPK 85
+ ++G P+
Sbjct: 58 PDPNCVTVTGLPE 70
>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 = 33.4 bits (77), Expect = 0.011
Identities = 9/64 (14%), Positives = 28/64 (43%), Gaps = 9/64 (14%)
Query: 21 KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRI 80
+ T + +P N +G ++G +G ++ +++ + ++ I + ++ I
Sbjct: 5 QTTHELTIPN------NLIGCIIGRQGANINEIRQMSGAQIKIANP---VEGSSGRQVTI 55
Query: 81 SGDP 84
+G
Sbjct: 56 TGSA 59
>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 = 31.5 bits (72), Expect = 0.050
Identities = 10/64 (15%), Positives = 28/64 (43%), Gaps = 9/64 (14%)
Query: 21 KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRI 80
+T +V +P + G ++G G +K+++ ++ + I + ++ + I
Sbjct: 13 IITTQVTIPK------DLAGSIIGKGGQRIKQIRHESGASIKIDEP---LEGSEDRIITI 63
Query: 81 SGDP 84
+G
Sbjct: 64 TGTQ 67
>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 = 31.2 bits (71), Expect = 0.066
Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 9/66 (13%)
Query: 19 PIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEEL 78
+T VP VG ++G G + R+Q+++ ++ I E
Sbjct: 12 RSVMTEEYKVPD------GMVGFIIGRGGEQISRIQQESGCKIQIAPD---SGGLPERSC 62
Query: 79 RISGDP 84
++G P
Sbjct: 63 MLTGTP 68
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 106
Score = 31.7 bits (72), Expect = 0.072
Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 9/62 (14%)
Query: 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISG 82
I V VP + VG ++G G +K++Q D R+ E+ I G
Sbjct: 12 GIDVPVPR------HSVGVVIGRSGEMIKKIQNDAGVRIQFKQD---DGTGPEKIAHIMG 62
Query: 83 DP 84
P
Sbjct: 63 PP 64
>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 = 31.5 bits (70), Expect = 0.17
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 13/34 (38%)
Query: 143 EMQILKEDGGAASCSESSESSVNNPLLYAENTSP 176
E Q LK+ ++S+ LYA++++P
Sbjct: 18 EKQALKK----------LQASLK---LYADDSAP 38
Score = 26.8 bits (58), Expect = 5.6
Identities = 7/25 (28%), Positives = 12/25 (48%), Gaps = 4/25 (16%)
Query: 90 LEELHVEITAFAP---PAEA-HARI 110
L++L + +A PA A A +
Sbjct: 22 LKKLQASLKLYADDSAPALAIKATM 46
>2z61_A Probable aspartate aminotransferase 2; amino acid aminotransferase,
kynurenine aminotransferase, MJ0684, cytoplasm; HET:
LLP; 2.20A {Methanococcus jannaschii}
Length = 370
Score = 32.1 bits (74), Expect = 0.19
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 89 LLEELHVEI---TAFAPPAEAHARIAYA 113
LL+E V + F + + RI+YA
Sbjct: 324 LLKEKFVALTPGIGFGSKGKNYIRISYA 351
>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 = 30.4 bits (68), Expect = 0.30
Identities = 11/90 (12%), Positives = 26/90 (28%), Gaps = 15/90 (16%)
Query: 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISG 82
+ IV + +G +G G ++++ ++ G +I I G
Sbjct: 5 HEQFIVRE------DLMGLAIGTHGANIQQARKVP-------GVTAIDLDEDTCTFHIYG 51
Query: 83 DPK--FLHLLEELHVEITAFAPPAEAHARI 110
+ + L P ++
Sbjct: 52 EDQDAVKKARSFLEFAEDVIQVPRNLVGKV 81
>1xi9_A Putative transaminase; alanine aminotransferase, southeast
collaboratory for structural genomics, secsg; HET: PLP;
2.33A {Pyrococcus furiosus} SCOP: c.67.1.1
Length = 406
Score = 31.4 bits (72), Expect = 0.31
Identities = 10/42 (23%), Positives = 14/42 (33%), Gaps = 4/42 (9%)
Query: 76 EELRISGDPKF-LHLLEELHVEI---TAFAPPAEAHARIAYA 113
E D +F L +L HV + F H R +
Sbjct: 342 EVGPWKNDKEFVLDVLHNAHVLFVHGSGFGEYGAGHFRAVFL 383
>2ctj_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 = 29.0 bits (65), Expect = 0.54
Identities = 17/84 (20%), Positives = 29/84 (34%), Gaps = 20/84 (23%)
Query: 22 VTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQED-TMTRMAILGRGSIRDRHKEEELRI 80
+ V +P + H L+G KG ++ + E+ + GS + + I
Sbjct: 17 AEVEVSIPAKLH------NSLIGTKGRLIRSIMEECGGVHIHFPVEGS-----GSDTVVI 65
Query: 81 SGDPK--------FLHLLEELHVE 96
G LHL EE +
Sbjct: 66 RGPSSDVEKAKKQLLHLAEEKQTK 89
>1gd9_A Aspartate aminotransferase; pyridoxal enzyme, temperature
dependence O substrate recognition; HET: PLP; 1.80A
{Pyrococcus horikoshii} SCOP: c.67.1.1 PDB: 1gde_A*
1dju_A*
Length = 389
Score = 30.2 bits (69), Expect = 0.66
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 3/28 (10%)
Query: 89 LLEELHVEI---TAFAPPAEAHARIAYA 113
+L+E V + +AF E + RI+YA
Sbjct: 339 MLKEARVAVVPGSAFGKAGEGYVRISYA 366
>1yx0_A Hypothetical protein YSNE; NESG, GFT structral genomics, SR220,
structural genomics, PSI, protein structure initiative;
NMR {Bacillus subtilis subsp} SCOP: d.108.1.1
Length = 159
Score = 29.0 bits (65), Expect = 0.89
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 83 DPKFLHLLEELHVEITAFAPPAEAHA 108
+ + L+ E +T +PP HA
Sbjct: 10 GRQVVSLVNEHLHSMTLMSPPESIHA 35
>3nra_A Aspartate aminotransferase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; HET: LLP; 2.15A {Rhodobacter sphaeroides}
Length = 407
Score = 29.5 bits (67), Expect = 1.2
Identities = 6/31 (19%), Positives = 12/31 (38%), Gaps = 3/31 (9%)
Query: 89 LLEELHVEI---TAFAPPAEAHARIAYALAE 116
L + V + T F+P R+ ++
Sbjct: 358 LRLQAGVVVTPGTEFSPHTADSVRLNFSQDH 388
>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 = 27.9 bits (62), Expect = 1.3
Identities = 12/64 (18%), Positives = 27/64 (42%), Gaps = 7/64 (10%)
Query: 22 VTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRIS 81
V ++ VP R VG+++G G +++ + + + ++ ++IS
Sbjct: 15 VFEQLSVPQR------SVGRIIGRGGETIRSICKASGAKITCDKESEGTLLL-SRLIKIS 67
Query: 82 GDPK 85
G K
Sbjct: 68 GTQK 71
>3lod_A Putative acyl-COA N-acyltransferase; structural genomics, PSI2,
MCSG, structure initiative; 2.50A {Klebsiella pneumoniae
subsp}
Length = 162
Score = 26.9 bits (60), Expect = 5.6
Identities = 7/41 (17%), Positives = 13/41 (31%), Gaps = 1/41 (2%)
Query: 83 DPKFLHLLEELHVEITAFAPPAEAHAR-IAYALAEVRRFLV 122
D +F+ L+ L P H ++ + L
Sbjct: 13 DAEFIALIAALDAWQETLYPAESNHLLDLSQLPPQTVIALA 53
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
0.317 0.132 0.376
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,080,257
Number of extensions: 243867
Number of successful extensions: 538
Number of sequences better than 10.0: 1
Number of HSP's gapped: 529
Number of HSP's successfully gapped: 50
Length of query: 267
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 175
Effective length of database: 4,133,061
Effective search space: 723285675
Effective search space used: 723285675
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 (21.6 bits)
S2: 56 (25.2 bits)