RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11278
(238 letters)
>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA
binding, cell cycle; 2.79A {Caenorhabditis elegans}
Length = 376
Score = 181 bits (460), Expect = 8e-56
Identities = 45/225 (20%), Positives = 86/225 (38%), Gaps = 11/225 (4%)
Query: 1 MKLDVSYTDHSHIIGRGGLT--IKKVMEETGCHVHFPDSNRSVNAEK--SNQVSIAGSLL 56
+ ++ +S + G + +M ET + PD + + QV+I G
Sbjct: 32 LNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTITGYFG 91
Query: 57 GLERARYRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPK---LQPT 113
++RAR +R M P NV++ F + P+ + T
Sbjct: 92 DVDRARMLMRRNCHFTVFMALSKM-KMPLHELQAHVRQNPIQNVEMSFVDAPEKNGIVTT 150
Query: 114 LVMVKGCEKDVERVKEATTKLIEHMCG-SLANQTSVIMMMEISPQHHPIMEGPNAIN--L 170
+ + EK+ + EA +L E + S A + + + +S + + G ++ +
Sbjct: 151 YLRITAREKNQHELIEAAKRLNEILFRESPAPENNFTLHFTLSTYYVDQVLGSSSTAQLM 210
Query: 171 KTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
I +T I +P N+ + V GNID+V AR+ +
Sbjct: 211 PVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYI 255
Score = 75.4 bits (184), Expect = 5e-16
Identities = 23/175 (13%), Positives = 61/175 (34%), Gaps = 17/175 (9%)
Query: 1 MKLDVSYTDHSHIIGR--GGLTIKKVMEETGCHVHFPDSN-RSVNAEKSNQVSIAGSLLG 57
+ +S ++G + + ET + +P N R+ ++ + G++
Sbjct: 188 LHFTLSTYYVDQVLGSSSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDN 247
Query: 58 LERARYRVRELTPLIFCFEYP--LMGSTPNANSPFVQIIQEAYNVQVMFRNRPK------ 109
+ +AR + +L P+ CF M + + +I + + +
Sbjct: 248 VLKARRYIMDLLPISMCFNIKNTDMAEPSRVSDRNIHMIIDESGIILKMTPSVYEPADLL 307
Query: 110 ---LQPTLVMVKGCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPI 161
+ ++ E +++++ A K++ +A + S HH +
Sbjct: 308 SGEVPLNCASLRSKEFNIKKLYTAYQKVLSKKFDFIA---PQPNDYDNSIWHHSL 359
Score = 49.6 bits (117), Expect = 3e-07
Identities = 23/95 (24%), Positives = 42/95 (44%), Gaps = 3/95 (3%)
Query: 124 VERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPN--AINLKTIMAQTGAQI 181
+ ++K L ++ N T V + ME Q++ +M N N+ +IMA+T I
Sbjct: 6 IHQLKAQGLPLPSNIPMIEINPTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLI 65
Query: 182 VFPEANDPIIPVLKKSS-VTVSGNIDSVYLARQML 215
P+ + + VT++G V AR ++
Sbjct: 66 QLPDRSVGGTTPDPFAQQVTITGYFGDVDRARMLM 100
Score = 40.3 bits (93), Expect = 3e-04
Identities = 19/144 (13%), Positives = 48/144 (33%), Gaps = 23/144 (15%)
Query: 85 NANSPFVQIIQEAYNVQVMF-----RNRPKLQPTLVMVKGCEKDVERVKEATTKLIEHMC 139
++ + + +I+ + + RN + + V G +V + + L+
Sbjct: 204 SSTAQLMPVIERETTTIISYPCYNNRNETRGNIYEIKVVGNIDNVLKARRYIMDLL---- 259
Query: 140 GSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFP----EANDPIIPVLK 195
+ M I + N+ I+ ++G + E D + +
Sbjct: 260 -------PISMCFNIKNTDMAEPSRVSDRNIHMIIDESGIILKMTPSVYEPADLLSGEVP 312
Query: 196 KSSVTVSG---NIDSVYLARQMLV 216
+ ++ NI +Y A Q ++
Sbjct: 313 LNCASLRSKEFNIKKLYTAYQKVL 336
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo
sapiens} SCOP: d.51.1.1 PDB: 1vih_A
Length = 71
Score = 73.9 bits (182), Expect = 9e-18
Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 5/67 (7%)
Query: 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERA 61
++++ + H H+IG+ G I ++ ++ V P + EKSN + I G G+++A
Sbjct: 8 EINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDS-----EKSNLIRIEGDPQGVQQA 62
Query: 62 RYRVREL 68
+ + EL
Sbjct: 63 KRELLEL 69
Score = 47.3 bits (113), Expect = 8e-08
Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 152 MEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLA 211
+ I + H + G + N+ I Q + P ++ K + + + G+ V A
Sbjct: 9 INIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE------KSNLIRIEGDPQGVQQA 62
Query: 212 RQML 215
++ L
Sbjct: 63 KREL 66
>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 = 69.8 bits (171), Expect = 6e-16
Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+ + + H+ IIG G I+K+M+E + FP S A N V++ G +E
Sbjct: 19 EDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQS----GAPDPNCVTVTGLPENVEE 74
Query: 61 ARYRVRELT 69
A + L
Sbjct: 75 AIDHILNLE 83
Score = 50.2 bits (120), Expect = 1e-08
Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 7/81 (8%)
Query: 135 IEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVL 194
+ G L S + + + H + G ++ IM + I FP++ P
Sbjct: 6 SGRIVGELEQMVSEDV--PLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAP----- 58
Query: 195 KKSSVTVSGNIDSVYLARQML 215
+ VTV+G ++V A +
Sbjct: 59 DPNCVTVTGLPENVEEAIDHI 79
Score = 33.2 bits (76), Expect = 0.016
Identities = 11/44 (25%), Positives = 17/44 (38%)
Query: 94 IQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIEH 137
I + + V + F P V V G ++VE + L E
Sbjct: 42 IMDEFKVDIRFPQSGAPDPNCVTVTGLPENVEEAIDHILNLEEE 85
>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 = 69.5 bits (170), Expect = 9e-16
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 2/68 (2%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+ + V H IIGR G I ++ E ++ FPD + + +Q++I G E
Sbjct: 19 LSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDG--NQPQDQITITGYEKNTEA 76
Query: 61 ARYRVREL 68
AR + +
Sbjct: 77 ARDAILRI 84
Score = 46.7 bits (111), Expect = 3e-07
Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNID 206
S + + + P++HP + G + I + I FP+ +D + +T++G
Sbjct: 16 SFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDD---GNQPQDQITITGYEK 72
Query: 207 SVYLARQML 215
+ AR +
Sbjct: 73 NTEAARDAI 81
>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 = 69.1 bits (169), Expect = 1e-15
Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 5/68 (7%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
++++V + H ++IG+ G I+K+M+E ++H P +S+ ++I G L+R
Sbjct: 19 IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPE-----LQSDIIAITGLAANLDR 73
Query: 61 ARYRVREL 68
A+ + E
Sbjct: 74 AKAGLLER 81
Score = 45.2 bits (107), Expect = 9e-07
Identities = 11/74 (14%), Positives = 26/74 (35%), Gaps = 6/74 (8%)
Query: 142 LANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTV 201
L V + +E+ H + G ++ +M + I P + + +
Sbjct: 11 LEALVPVTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL------QSDIIAI 64
Query: 202 SGNIDSVYLARQML 215
+G ++ A+ L
Sbjct: 65 TGLAANLDRAKAGL 78
>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 = 67.4 bits (165), Expect = 4e-15
Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+ + H +IG+ G ++ + +T + P + + SNQ+ I G+ G+E+
Sbjct: 19 ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPD-----DPSNQIKITGTKEGIEK 73
Query: 61 ARYRVRELTP 70
AR+ V ++
Sbjct: 74 ARHEVLLISA 83
Score = 47.4 bits (113), Expect = 1e-07
Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 6/71 (8%)
Query: 145 QTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN 204
QT + I +HH + G N L+ + +T +I P +DP + + ++G
Sbjct: 14 QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDP------SNQIKITGT 67
Query: 205 IDSVYLARQML 215
+ + AR +
Sbjct: 68 KEGIEKARHEV 78
>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 = 65.2 bits (159), Expect = 4e-14
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 6/69 (8%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEE-TGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLE 59
+++ + H+ +IG G I+ +MEE G H+HFP S+ V I G +E
Sbjct: 19 VEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEG-----SGSDTVVIRGPSSDVE 73
Query: 60 RARYRVREL 68
+A+ ++ L
Sbjct: 74 KAKKQLLHL 82
Score = 39.0 bits (91), Expect = 1e-04
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 9/75 (12%)
Query: 142 LANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQ-TGAQIVFPEANDPIIPVLKKSSVT 200
LAN V + I + H + G +++IM + G I FP +V
Sbjct: 13 LANIAEVEV--SIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS------GSDTVV 64
Query: 201 VSGNIDSVYLARQML 215
+ G V A++ L
Sbjct: 65 IRGPSSDVEKAKKQL 79
Score = 27.1 bits (60), Expect = 1.8
Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 92 QIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIE 136
I++E V + F V+++G DVE+ K+ L E
Sbjct: 41 SIMEECGGVHIHFP-VEGSGSDTVVIRGPSSDVEKAKKQLLHLAE 84
>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 = 56.4 bits (136), Expect = 8e-11
Identities = 10/70 (14%), Positives = 28/70 (40%), Gaps = 9/70 (12%)
Query: 2 KLDVSYTDHSHIIGRGGLTIKKVMEE-TGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+ H IIG+ G + K+ ++ H+ F + +++++ G +
Sbjct: 30 SVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEG--------EDKITLEGPTEDVSV 81
Query: 61 ARYRVRELTP 70
A+ ++ +
Sbjct: 82 AQEQIEGMVK 91
Score = 32.6 bits (74), Expect = 0.029
Identities = 20/98 (20%), Positives = 36/98 (36%), Gaps = 16/98 (16%)
Query: 119 GCEKDVERVKEATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQ-T 177
G + E++ +A T++ AN + + H + G NL I Q
Sbjct: 4 GSSGEPEKLGQALTEVYA-----KANS-FTVSSVAAPSWLHRFIIGKKGQNLAKITQQMP 57
Query: 178 GAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
I F E D +T+ G + V +A++ +
Sbjct: 58 KVHIEFTEGED---------KITLEGPTEDVSVAQEQI 86
Score = 28.7 bits (64), Expect = 0.58
Identities = 8/45 (17%), Positives = 20/45 (44%), Gaps = 4/45 (8%)
Query: 92 QIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIE 136
+I Q+ V + F + + ++G +DV +E +++
Sbjct: 51 KITQQMPKVHIEF---TE-GEDKITLEGPTEDVSVAQEQIEGMVK 91
>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 = 52.1 bits (125), Expect = 8e-09
Identities = 11/68 (16%), Positives = 24/68 (35%), Gaps = 2/68 (2%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+++ + IIG+ G IK++ + + + V I G +
Sbjct: 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRM--VIITGPPEAQFK 62
Query: 61 ARYRVREL 68
A+ R+
Sbjct: 63 AQGRIYGK 70
Score = 47.8 bits (114), Expect = 3e-07
Identities = 14/68 (20%), Positives = 29/68 (42%), Gaps = 1/68 (1%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+ V + +IG+GG T+ ++ T V P ++ V I G +
Sbjct: 87 THIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQV-IVKIIGHFYASQM 145
Query: 61 ARYRVREL 68
A+ ++R++
Sbjct: 146 AQRKIRDI 153
Score = 46.3 bits (110), Expect = 1e-06
Identities = 16/141 (11%), Positives = 53/141 (37%), Gaps = 7/141 (4%)
Query: 90 FVQIIQEAYN--VQVMFRNRPKLQPTLVMVKGCEKDVERVKEA-TTKLIEHMCGSLANQT 146
++ + + +++ P + +V++ G + + + KL E +
Sbjct: 24 HIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQFKAQGRIYGKLKEENFFGPKEEV 83
Query: 147 SVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNID 206
+ + + + G + + T A++V P P + V + G+
Sbjct: 84 KLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTP--DENDQVIVKIIGHFY 141
Query: 207 SVYLARQML--VVSSVRPRRR 225
+ +A++ + +++ V+ + +
Sbjct: 142 ASQMAQRKIRDILAQVKQQHQ 162
Score = 34.4 bits (79), Expect = 0.015
Identities = 10/65 (15%), Positives = 22/65 (33%), Gaps = 3/65 (4%)
Query: 152 MEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLA 211
+ I Q + G ++K + A I P V ++G ++ + A
Sbjct: 7 VFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSK---VRMVIITGPPEAQFKA 63
Query: 212 RQMLV 216
+ +
Sbjct: 64 QGRIY 68
>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 = 51.3 bits (123), Expect = 2e-08
Identities = 23/156 (14%), Positives = 48/156 (30%), Gaps = 22/156 (14%)
Query: 2 KLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERA 61
++ + +IG+GG TIK++ E G + S N + I G +++A
Sbjct: 5 EIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDG-SQNTNVDKPLRIIGDPYKVQQA 63
Query: 62 RYRVRELTPLIFCFEYPLMGSTPNANSPFVQI--------------------IQEAYNVQ 101
V ++ + + + + IQ V+
Sbjct: 64 CEMVMDILRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVR 123
Query: 102 VMFRNRPKLQPT-LVMVKGCEKDVERVKEATTKLIE 136
+ F+ P + + G E L++
Sbjct: 124 IQFKQDDGTGPEKIAHIMGPPDRCEHAARIINDLLQ 159
Score = 49.4 bits (118), Expect = 9e-08
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 3/68 (4%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+ + V +IGR G IKK+ + G + F + + EK I G E
Sbjct: 93 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGT-GPEKI--AHIMGPPDRCEH 149
Query: 61 ARYRVREL 68
A + +L
Sbjct: 150 AARIINDL 157
Score = 44.0 bits (104), Expect = 7e-06
Identities = 15/132 (11%), Positives = 42/132 (31%), Gaps = 14/132 (10%)
Query: 94 IQEAYNVQVMFRNRPKLQPT---LVMVKGCEKDVERVKEATTKLIEHMC-------GSLA 143
+QE V+++ + + G V++ E ++
Sbjct: 27 LQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQACEMVMDILRERDQGGFGDRNEYG 86
Query: 144 NQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG 203
++ + + + ++ G + +K I G +I F + + + + G
Sbjct: 87 SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGT----GPEKIAHIMG 142
Query: 204 NIDSVYLARQML 215
D A +++
Sbjct: 143 PPDRCEHAARII 154
Score = 31.3 bits (71), Expect = 0.13
Identities = 10/65 (15%), Positives = 26/65 (40%), Gaps = 2/65 (3%)
Query: 152 MEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLA 211
+ I ++ G +K + + G +++ + V K + + G+ V A
Sbjct: 6 IMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKP--LRIIGDPYKVQQA 63
Query: 212 RQMLV 216
+M++
Sbjct: 64 CEMVM 68
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo
sapiens}
Length = 85
Score = 49.7 bits (119), Expect = 2e-08
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFP-DSNRSVNAEKSNQVSIAGSLLGLE 59
++ + +IG+GG TIK++ E G + D +++ N +K + I G ++
Sbjct: 16 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDK--PLRIIGDPYKVQ 73
Query: 60 RARYRVREL 68
+A V ++
Sbjct: 74 QACEMVMDI 82
Score = 32.3 bits (74), Expect = 0.022
Identities = 11/76 (14%), Positives = 28/76 (36%), Gaps = 2/76 (2%)
Query: 140 GSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSV 199
+ Q + + I ++ G +K + + G +++ + V K +
Sbjct: 6 NANGGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKP--L 63
Query: 200 TVSGNIDSVYLARQML 215
+ G+ V A +M+
Sbjct: 64 RIIGDPYKVQQACEMV 79
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 107
Score = 49.5 bits (118), Expect = 3e-08
Identities = 15/68 (22%), Positives = 25/68 (36%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
M + +IGRGG +K + ++TG V I GS ++
Sbjct: 9 MTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGSPQQIDH 68
Query: 61 ARYRVREL 68
A+ + E
Sbjct: 69 AKQLIEEK 76
Score = 33.3 bits (76), Expect = 0.018
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 164 GPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
G N+K I QTGA + P K + G+ + A+Q++
Sbjct: 23 GRGGENVKAINQQTGAFVEISRQLPPNGDPNFK-LFIIRGSPQQIDHAKQLI 73
>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 = 51.0 bits (122), Expect = 3e-08
Identities = 41/218 (18%), Positives = 67/218 (30%), Gaps = 57/218 (26%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+K+ + IIG+GG TI ++ +ETG + S I G++ L
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGTIEALNA 67
Query: 61 ARYRVRELTPLIFCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGC 120
+ E I+E LQP
Sbjct: 68 VHGFIAE-------------------------KIREMPQNVAKTEPVSILQP-------- 94
Query: 121 EKDVERVKEATTKLI--EHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTG 178
+ V + K+I G +I G +K IM Q+G
Sbjct: 95 QTTVNPDRANQVKIIVPNSTAG------LII--------------GKGGATVKAIMEQSG 134
Query: 179 AQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV 216
A + + P L+ VTVSG + A ++++
Sbjct: 135 AWVQL--SQKPDGINLQNRVVTVSGEPEQNRKAVELII 170
Score = 43.7 bits (103), Expect = 9e-06
Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+K+ V + IIG+GG T+K +ME++G V +N + V+++G +
Sbjct: 106 VKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQN-RVVTVSGEPEQNRK 164
Query: 61 ARYRVREL 68
A + +
Sbjct: 165 AVELIIQK 172
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 106
Score = 48.6 bits (116), Expect = 5e-08
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 3/68 (4%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+ + V +IGR G IKK+ + G + F + EK I G E
Sbjct: 13 IDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQF-KQDDGTGPEK--IAHIMGPPDRCEH 69
Query: 61 ARYRVREL 68
A + +L
Sbjct: 70 AARIINDL 77
Score = 29.8 bits (67), Expect = 0.28
Identities = 9/52 (17%), Positives = 19/52 (36%), Gaps = 4/52 (7%)
Query: 164 GPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
G + +K I G +I F + + + + G D A +++
Sbjct: 27 GRSGEMIKKIQNDAGVRIQFKQDD----GTGPEKIAHIMGPPDRCEHAARII 74
>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 = 5e-08
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 2/68 (2%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
++L V + +IG+GG IK++ E TG V + E+ ++IAG +
Sbjct: 91 LRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTER--AITIAGIPQSIIE 148
Query: 61 ARYRVREL 68
++ +
Sbjct: 149 CVKQICVV 156
Score = 45.5 bits (108), Expect = 2e-06
Identities = 15/68 (22%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
++L + + IIG+ G ++KK+ EE+G ++ + N E+ +++AG + +
Sbjct: 7 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN---CPER--IITLAGPTNAIFK 61
Query: 61 ARYRVREL 68
A + +
Sbjct: 62 AFAMIIDK 69
Score = 35.1 bits (81), Expect = 0.008
Identities = 16/128 (12%), Positives = 44/128 (34%), Gaps = 10/128 (7%)
Query: 94 IQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATTKLIE------HMCGSLANQTS 147
++E ++ + ++ + G + + +E + A++
Sbjct: 30 MREESGARINI-SEGNCPERIITLAGPTNAIFKAFAMIIDKLEEDISSSMTNSTAASRPP 88
Query: 148 VIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDS 207
V + + + + G +K I TGAQ+ P + ++T++G S
Sbjct: 89 VTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDML---PNSTERAITIAGIPQS 145
Query: 208 VYLARQML 215
+ + +
Sbjct: 146 IIECVKQI 153
Score = 32.1 bits (73), Expect = 0.069
Identities = 12/72 (16%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 145 QTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGN 204
++ + + + + + G ++K + ++GA+I E N P + +T++G
Sbjct: 2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCP------ERIITLAGP 55
Query: 205 IDSVYLARQMLV 216
++++ A M++
Sbjct: 56 TNAIFKAFAMII 67
>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 = 47.4 bits (113), Expect = 1e-07
Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 1/68 (1%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
++ + + +IG+GG TIK++ E G + + I G +++
Sbjct: 17 QEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGA-DKPLRITGDPYKVQQ 75
Query: 61 ARYRVREL 68
A+ V EL
Sbjct: 76 AKEMVLEL 83
Score = 33.2 bits (76), Expect = 0.016
Identities = 11/76 (14%), Positives = 29/76 (38%), Gaps = 2/76 (2%)
Query: 140 GSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSV 199
G + + + I ++ G +K + + G ++V + K +
Sbjct: 7 GHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKP--L 64
Query: 200 TVSGNIDSVYLARQML 215
++G+ V A++M+
Sbjct: 65 RITGDPYKVQQAKEMV 80
>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 = 46.4 bits (110), Expect = 1e-06
Identities = 15/67 (22%), Positives = 27/67 (40%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
V IIG+GG TIK + +++G + + +I G+ ++
Sbjct: 106 FNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRGTPQQIDY 165
Query: 61 ARYRVRE 67
AR + E
Sbjct: 166 ARQLIEE 172
Score = 46.0 bits (109), Expect = 1e-06
Identities = 30/203 (14%), Positives = 57/203 (28%), Gaps = 49/203 (24%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVRELTPLI 72
+IGR G IKK+ + G + F + + E+ I G + A + +L
Sbjct: 17 VIGRNGEMIKKIQNDAGVRIQFKPDDGTTP-ERI--AQITGPPDRAQHAAEIITDL---- 69
Query: 73 FCFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKDVERVKEATT 132
++ +Q R + +
Sbjct: 70 ------------------LRSVQAGNPGGPGPGGRGRGRG-------------------- 91
Query: 133 KLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIP 192
+ + ++ G +K+I Q+GA+I P
Sbjct: 92 ---QGNWNMGPPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNAD 148
Query: 193 VLKKSSVTVSGNIDSVYLARQML 215
K T+ G + ARQ++
Sbjct: 149 PNMK-LFTIRGTPQQIDYARQLI 170
>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 = 43.8 bits (104), Expect = 1e-06
Identities = 15/68 (22%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
++L + + IIG+ G ++KK+ EE+G ++ + N E+ +++AG + +
Sbjct: 7 IRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN---CPER--IITLAGPTNAIFK 61
Query: 61 ARYRVREL 68
A + +
Sbjct: 62 AFAMIIDK 69
Score = 29.2 bits (66), Expect = 0.23
Identities = 11/48 (22%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 169 NLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQMLV 216
++K + ++GA+I E N P + +T++G ++++ A M++
Sbjct: 26 SVKKMREESGARINISEGNCP------ERIITLAGPTNAIFKAFAMII 67
>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 = 43.8 bits (103), Expect = 2e-06
Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 6/68 (8%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+++ V Y ++G G TIK++ + T ++ P +K ++ G ++R
Sbjct: 12 IQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGR------DKEPVFAVTGMPENVDR 65
Query: 61 ARYRVREL 68
AR +
Sbjct: 66 AREEIEAH 73
Score = 34.2 bits (78), Expect = 0.005
Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 7/72 (9%)
Query: 144 NQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSG 203
+ + + + + ++ GP +K I +T IV P + K+ V+G
Sbjct: 6 SGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRD-------KEPVFAVTG 58
Query: 204 NIDSVYLARQML 215
++V AR+ +
Sbjct: 59 MPENVDRAREEI 70
>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 = 43.4 bits (103), Expect = 2e-06
Identities = 14/56 (25%), Positives = 28/56 (50%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
I+G+GG T+ + E TG + + ++ +V+I GS + A+Y + +
Sbjct: 17 ILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQAAQYLISQR 72
Score = 31.1 bits (71), Expect = 0.052
Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 164 GPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
G L TGA+I + + +P + VT++G+ + A+ ++
Sbjct: 19 GKGGKTLVEYQELTGARIQISKKGEF-LPGTRNRRVTITGSPAATQAAQYLI 69
>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 = 44.0 bits (104), Expect = 3e-06
Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
IIGRGG TI+ + + +G + + + I+G+ + A++ + E
Sbjct: 29 IIGRGGETIRSICKASGAKITCDKESEGTLLLSR-LIKISGTQKEVAAAKHLILEK 83
Score = 29.8 bits (67), Expect = 0.22
Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 2/76 (2%)
Query: 140 GSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSV 199
G L T V + + + + G +++I +GA+I + ++ +L +
Sbjct: 7 GILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEG--TLLLSRLI 64
Query: 200 TVSGNIDSVYLARQML 215
+SG V A+ ++
Sbjct: 65 KISGTQKEVAAAKHLI 80
>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 = 43.5 bits (103), Expect = 3e-06
Identities = 15/68 (22%), Positives = 32/68 (47%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
+++ V I+G+GG T+ + E TG + + ++ +V+I GS +
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTITGSPAATQA 64
Query: 61 ARYRVREL 68
A+Y + +
Sbjct: 65 AQYLISQR 72
Score = 30.8 bits (70), Expect = 0.094
Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 164 GPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
G L TGA+I + + +P + VT++G+ + A+ ++
Sbjct: 19 GKGGKTLVEYQELTGARIQISKKGEF-LPGTRNRRVTITGSPAATQAAQYLI 69
>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 = 40.5 bits (95), Expect = 4e-05
Identities = 12/56 (21%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
IIGRGG I ++ +E+GC + + + G+ ++ A+ + ++
Sbjct: 29 IIGRGGEQISRIQQESGCKIQIAPDS---GGLPERSCMLTGTPESVQSAKRLLDQI 81
Score = 32.0 bits (73), Expect = 0.030
Identities = 12/76 (15%), Positives = 30/76 (39%), Gaps = 4/76 (5%)
Query: 140 GSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSV 199
G ++ + ++ + G + I ++G +I + L + S
Sbjct: 7 GHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGG----LPERSC 62
Query: 200 TVSGNIDSVYLARQML 215
++G +SV A+++L
Sbjct: 63 MLTGTPESVQSAKRLL 78
>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 = 40.0 bits (94), Expect = 5e-05
Identities = 13/68 (19%), Positives = 32/68 (47%), Gaps = 3/68 (4%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLER 60
++ + IIG+GG IK++ E+G + + + + ++I G+ ++
Sbjct: 16 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQN 72
Query: 61 ARYRVREL 68
A+Y ++
Sbjct: 73 AQYLLQNS 80
Score = 26.9 bits (60), Expect = 2.2
Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 169 NLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
+K I ++GA I E + +T++G D + A+ +L
Sbjct: 35 RIKQIRHESGASIKIDEPL----EGSEDRIITITGTQDQIQNAQYLL 77
>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 = 39.2 bits (92), Expect = 9e-05
Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 3/57 (5%)
Query: 12 HIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
IIGR G I ++ + +G + + + + V+I GS + A+Y +
Sbjct: 19 CIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQ---VTITGSAASISLAQYLINAR 72
Score = 28.4 bits (64), Expect = 0.46
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 164 GPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
G N+ I +GAQI VT++G+ S+ LA+ ++
Sbjct: 22 GRQGANINEIRQMSGAQIKIANPV----EGSSGRQVTITGSAASISLAQYLI 69
>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 = 13/56 (23%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
IIG+GG IK++ E+G + + + + ++I G+ ++ A+Y ++
Sbjct: 21 IIGKGGQRIKQIRHESGASIKI---DEPLEGSEDRIITITGTQDQIQNAQYLLQNS 73
Score = 28.0 bits (63), Expect = 0.76
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 164 GPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
G +K I ++GA I E + +T++G D + A+ +L
Sbjct: 23 GKGGQRIKQIRHESGASIKIDEPL----EGSEDRIITITGTQDQIQNAQYLL 70
>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA
binding protein/DNA complex; 1.60A {Homo sapiens}
Length = 76
Score = 36.5 bits (85), Expect = 6e-04
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 12 HIIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRVREL 68
IIGR G I ++ + +G + + + V+I GS + A+Y +
Sbjct: 18 CIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQ---VTITGSAASISLAQYLINVR 71
Score = 28.8 bits (65), Expect = 0.39
Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 164 GPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
G + I +GAQI VT++G+ S+ LA+ ++
Sbjct: 21 GRQGAKINEIRQMSGAQIKIANPV----EGSTDRQVTITGSAASISLAQYLI 68
>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 = 39.6 bits (92), Expect = 6e-04
Identities = 35/223 (15%), Positives = 60/223 (26%), Gaps = 88/223 (39%)
Query: 23 KVMEETGCHVHFPDSNRSVNA-----EKSNQVSIAGSLLGLERA----RYRVRELTPLIF 73
+ ++ G P + A E + S+A + +E YR
Sbjct: 1745 EDLKSKG---LIPAD--ATFAGHSLGEYAALASLADVM-SIESLVEVVFYR--------- 1789
Query: 74 CFEYPLMGSTPNANSPFVQIIQEAYNVQVMFRNRPKLQPTLVMVKGCEKD-----VERVK 128
G T P ++ + Y M P + ++ VERV
Sbjct: 1790 -------GMTMQVAVPRDELGRSNY---GMIAINPGR-----VAASFSQEALQYVVERVG 1834
Query: 129 EATTKLIEHMCGSLANQTSVIMMMEISPQHHPIMEGPNAINLKTIMAQTGAQIVF---PE 185
+ T L+E + N N++ Q V
Sbjct: 1835 KRTGWLVE-----IVN-----------------------YNVE------NQQYVAAGDLR 1860
Query: 186 ANDPIIPVLKKSSVTVSGNIDSVYLARQMLVVSSVRPRRRLLL 228
A D + VL + ID + L + + S+ L
Sbjct: 1861 ALDTVTNVLNFIKL---QKIDIIELQKSL----SLEEVEGHLF 1896
Score = 31.9 bits (72), Expect = 0.17
Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 11/44 (25%)
Query: 21 IKKVMEETGCHVHFPDSNRSV---NAEKSNQVSIAGSLLGLERA 61
+++V + TG V + N E + Q AG L L+
Sbjct: 1830 VERVGKRTGWLV-------EIVNYNVE-NQQYVAAGDLRALDTV 1865
>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 = 36.9 bits (85), Expect = 0.002
Identities = 11/71 (15%), Positives = 26/71 (36%), Gaps = 3/71 (4%)
Query: 1 MKLDVSYTDHSHIIGRGGLTIKKVMEETGC-HVHFPDSNRSVNAEKSNQVS--IAGSLLG 57
+ V +IG+ G I+++++++G V N ++ V G+
Sbjct: 69 DVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKDS 128
Query: 58 LERARYRVREL 68
+ A +
Sbjct: 129 IANATVLLDYH 139
Score = 32.3 bits (73), Expect = 0.053
Identities = 6/32 (18%), Positives = 10/32 (31%)
Query: 10 HSHIIGRGGLTIKKVMEETGCHVHFPDSNRSV 41
IG G I++ + G D +
Sbjct: 15 MGLAIGTHGANIQQARKVPGVTAIDLDEDTCT 46
Score = 27.3 bits (60), Expect = 3.3
Identities = 11/69 (15%), Positives = 27/69 (39%), Gaps = 2/69 (2%)
Query: 149 IMMMEISPQHHPIMEGPNAINLKTIMAQTGA-QIVFPEANDPIIPV-LKKSSVTVSGNID 206
++++ + G N ++ I+ ++G ++ N+ +P G D
Sbjct: 68 EDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENEKNVPQEEGMVPFVFVGTKD 127
Query: 207 SVYLARQML 215
S+ A +L
Sbjct: 128 SIANATVLL 136
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 35.5 bits (83), Expect = 0.011
Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 10/58 (17%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRVRELT 69
+IG GG I++++ TG V+ V ++ S ++ A ++ +T
Sbjct: 584 VIGSGGKVIREIVATTGA---------KVDINDDGVVKVSASDGAKIKAAIDWIKSIT 632
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 35.6 bits (83), Expect = 0.012
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 10/58 (17%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRVRELT 69
+G GG +KK+ ETG +++ S+ + AR + E+
Sbjct: 581 FVGPGGYNLKKLQAETGV---------TISQVDEETFSVFAPTPSAMHEARDFITEIC 629
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 35.2 bits (82), Expect = 0.017
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 10/58 (17%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRVRELT 69
+IG+GG I+ + EETG ++ E V IA + + A R+ E+T
Sbjct: 574 VIGKGGSVIRALTEETGT---------TIEIEDDGTVKIAATDGEKAKHAIRRIEEIT 622
>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 = 35.3 bits (82), Expect = 0.017
Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 10/58 (17%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGS-LLGLERARYRVRELT 69
+IG I ++ E+TG + E + I + E AR + +
Sbjct: 612 VIGPKRQMINQIQEDTGA---------EITIEDDGTIYIGAADGPAAEAARATINGIA 660
>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 = 34.7 bits (79), Expect = 0.017
Identities = 18/143 (12%), Positives = 38/143 (26%), Gaps = 19/143 (13%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLGLERARYRV------- 65
+IG+ G T K++ + T + V + + ++ +
Sbjct: 48 LIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPE 107
Query: 66 ---RELTPLIFCFEYPLMGSTPNANSPFVQIIQEA---------YNVQVMFRNRPKLQPT 113
R L + L + ++ ++ M +
Sbjct: 108 RAFRLLNEGEYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTRQIIEEMSGASVSVYGK 167
Query: 114 LVMVKGCEKDVERVKEATTKLIE 136
V + G +E K A KL
Sbjct: 168 TVAIIGNPIQIEIAKTAIEKLAR 190
Score = 27.7 bits (61), Expect = 2.9
Identities = 8/51 (15%), Positives = 16/51 (31%), Gaps = 11/51 (21%)
Query: 164 GPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQM 214
G + I +GA + +V + GN + +A+
Sbjct: 145 GRKGRTRQIIEEMSGASVSVYG-----------KTVAIIGNPIQIEIAKTA 184
>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 = 32.3 bits (73), Expect = 0.082
Identities = 22/142 (15%), Positives = 41/142 (28%), Gaps = 18/142 (12%)
Query: 13 IIGRGGLTIKKVMEETGCHVHFPDSNRSVNAEKSNQVSIAGSLLG---LERARYR----- 64
+IG G ++M TG + N V E + +L+ + +A
Sbjct: 18 VIGPRGEVKAEIMRRTGTVITVDTENSMVIVEPEAEGIPPVNLMKAAEVVKAISLGFPPE 77
Query: 65 --VRELTPLIFCFEYPLMGSTPNANSPFVQIIQEA--------YNVQVMFRNRPKLQPTL 114
R L L ++ + +I ++ M +
Sbjct: 78 KAFRLLEEDQILVVVDLKQVVGDSQNHLKRIKGRIIGEGGRARRTIEEMTDTYINVGEYE 137
Query: 115 VMVKGCEKDVERVKEATTKLIE 136
V + G + K+A L E
Sbjct: 138 VAIIGDYERAMAAKQAIEMLAE 159
Score = 28.1 bits (62), Expect = 1.8
Identities = 9/52 (17%), Positives = 17/52 (32%), Gaps = 11/52 (21%)
Query: 164 GPNAINLKTIMAQTGAQIVFPEANDPIIPVLKKSSVTVSGNIDSVYLARQML 215
G +TI T I + + V + G+ + A+Q +
Sbjct: 114 GEGGRARRTIEEMTDTYI-----------NVGEYEVAIIGDYERAMAAKQAI 154
>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 = 29.4 bits (66), Expect = 0.41
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 13 IIGRGGLTIKKVMEETGCHV 32
+IG G T+K + +E +
Sbjct: 27 LIGPRGNTLKNIEKECNAKI 46
>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins,
RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1
Length = 140
Score = 29.2 bits (65), Expect = 0.57
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 13 IIGRGGLTIKKVMEETGCHV 32
I+G GLT K++ ETGC +
Sbjct: 22 ILGPRGLTAKQLEAETGCKI 41
>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 = 28.3 bits (63), Expect = 0.90
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 13 IIGRGGLTIKKVMEETGCHV 32
+ G G ++ + ETG V
Sbjct: 33 VEGPGCSYLQHIQIETGAKV 52
Score = 26.0 bits (57), Expect = 5.4
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 162 MEGPNAINLKTIMAQTGAQIV 182
+EGP L+ I +TGA++
Sbjct: 33 VEGPGCSYLQHIQIETGAKVF 53
>1nd6_A Prostatic acid phosphatase; PAP, prostate, phosphate, inhibi
hydrolase; HET: NAG MAN 1PE; 2.40A {Homo sapiens} SCOP:
c.60.1.2 PDB: 1nd5_A* 2hpa_A* 1cvi_A* 1rpa_A* 1rpt_A*
2l3h_A 2l77_A 2l79_A
Length = 354
Score = 28.6 bits (63), Expect = 2.1
Identities = 11/56 (19%), Positives = 21/56 (37%), Gaps = 6/56 (10%)
Query: 98 YNVQVMFRNRPKLQPTLVMVKGCEKD------VERVKEATTKLIEHMCGSLANQTS 147
Y V++ +RN + +P +M+ GC E V + C + +
Sbjct: 293 YFVEMYYRNETQHEPYPLMLPGCSPSCPLERFAELVGPVIPQDWSTECMTTNSHQG 348
>2ozl_A PDHE1-A type I, pyruvate dehydrogenase E1 component alpha subunit,
somatic form; pyruvate_dehydrogenase_complex, human,
multienzyme_complex_component; HET: TPP; 1.90A {Homo
sapiens} SCOP: c.36.1.11 PDB: 1ni4_A* 3exe_A* 3exi_A
3exh_A* 3exg_A 3exf_A*
Length = 365
Score = 28.0 bits (63), Expect = 2.8
Identities = 7/30 (23%), Positives = 14/30 (46%), Gaps = 6/30 (20%)
Query: 6 SYTDHSHIIGRGGLTIKKVMEE-----TGC 30
+Y H RG ++++++ E GC
Sbjct: 92 AYRAHGFTFTRGL-SVREILAELTGRKGGC 120
>1v4v_A UDP-N-acetylglucosamine 2-epimerase; UDP-GLCNAC, two domains,
homodimer, riken structural genomics/proteomics
initiative, RSGI; HET: MSE; 1.80A {Thermus thermophilus}
SCOP: c.87.1.3
Length = 376
Score = 27.5 bits (62), Expect = 4.2
Identities = 8/38 (21%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 195 KKSSVTVSGN--IDSVYLARQMLVVSSVRPRRRLLLIT 230
++ + V+G +D+V LA ++ + P + +T
Sbjct: 167 REEGILVTGQTGVDAVLLAAKLGRLPEGLPEGPYVTVT 204
>1kl7_A Threonine synthase; threonine synthesis, pyridoxal 5-phosphate,
beta-family, MON lyase; HET: PLP; 2.70A {Saccharomyces
cerevisiae} SCOP: c.79.1.1
Length = 514
Score = 27.4 bits (61), Expect = 5.4
Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 22/81 (27%)
Query: 166 NAINLKTIMAQ------TGAQIVFPEANDPIIPVLKKSSVTVS----GNIDSVYLARQML 215
N+IN I+AQ + Q + + + V G+I + Y A++M
Sbjct: 240 NSINWARILAQMTYYFYSFFQATNGKDSKKV-------KFVVPSGNFGDILAGYFAKKMG 292
Query: 216 VVSSVRPRRRLLLITIPNDII 236
+ P +L + T NDI+
Sbjct: 293 L-----PIEKLAIATNENDIL 308
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.50A {Vibrio
cholerae}
Length = 302
Score = 27.2 bits (61), Expect = 5.4
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 54 SLLGLERARYRVRELT 69
+LLGLE A+ + L
Sbjct: 258 ALLGLEGAQQKAHTLL 273
>1mut_A MUTT, nucleoside triphosphate pyrophosphohydrolase; DNA repair; NMR
{Escherichia coli} SCOP: d.113.1.1 PDB: 1ppx_A* 1pun_A*
1puq_A* 1pus_A* 1tum_A* 3a6s_A* 3a6t_A* 3a6u_A* 3a6v_A*
Length = 129
Score = 26.3 bits (59), Expect = 5.7
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 183 FPEANDPIIPVLKK 196
FP AN+P+I LK+
Sbjct: 115 FPPANEPVIAKLKR 128
>1rqj_A Geranyltranstransferase; bisphosphonate, isoprenyl synthase; HET:
IPR RIS; 1.95A {Escherichia coli} SCOP: a.128.1.1 PDB:
1rqi_A* 2for_A*
Length = 299
Score = 26.8 bits (60), Expect = 6.3
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 54 SLLGLERARYRVRELT 69
+LLGLE+AR + R+L
Sbjct: 252 ALLGLEQARKKARDLI 267
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics,
PSI, protein structure initiative, nysgrc; 2.30A
{Legionella pneumophila subsp}
Length = 313
Score = 26.8 bits (60), Expect = 6.5
Identities = 1/16 (6%), Positives = 5/16 (31%)
Query: 54 SLLGLERARYRVRELT 69
+L ++ +
Sbjct: 259 TLFNKQQLEEEIAVHY 274
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate
synthase; 1.94A {Methylococcus capsulatus}
Length = 324
Score = 26.8 bits (60), Expect = 6.8
Identities = 6/16 (37%), Positives = 10/16 (62%)
Query: 54 SLLGLERARYRVRELT 69
+LLGL A+ + E+
Sbjct: 258 ALLGLSGAKEKAEEMH 273
>3lsn_A Geranyltranstransferase; structural genomics, protein structure
initiative, NEW YORK structural genomix research
consortium, nysgxrc; HET: MSE; 1.35A {Pseudomonas
fluorescens} PDB: 3lji_A* 3p41_A*
Length = 304
Score = 26.8 bits (60), Expect = 7.3
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 54 SLLGLERARYRVRELT 69
+LLGL A+ EL
Sbjct: 252 ALLGLAAAKEYALELR 267
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid
diphosphate synthase; 2.00A {Clostridium perfringens}
Length = 324
Score = 26.5 bits (59), Expect = 7.8
Identities = 4/16 (25%), Positives = 9/16 (56%)
Query: 54 SLLGLERARYRVRELT 69
++ GLE + + +T
Sbjct: 280 TIFGLEECKKKCVNIT 295
>4f62_A Geranyltranstransferase; enzyme function initiative, structural
genomics; 2.10A {Marinomonas SP}
Length = 317
Score = 26.4 bits (59), Expect = 8.7
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 54 SLLGLERARYRVRELT 69
LLGL+ A+ V L
Sbjct: 251 KLLGLDGAKALVVRLH 266
>3m0g_A Farnesyl diphosphate synthase; structural genomics, protein
structure initiative, NYSGXRC, biosynthesis,
transferase, PSI-2; 1.90A {Rhodobacter capsulatus} PDB:
3lvs_A
Length = 297
Score = 26.4 bits (59), Expect = 9.5
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 54 SLLGLERARYRVRELT 69
SLLGL A+ R +L
Sbjct: 245 SLLGLAGAKSRAADLV 260
>2j1p_A Geranylgeranyl pyrophosphate synthetase; transferase, isoprene
biosynthesis, multifunctional enzyme, carotenoid
biosynthesis; HET: GRG; 1.8A {Sinapis alba} PDB: 2j1o_A
3kra_A 3krc_A* 3krf_A* 3kro_A* 3krp_A* 3oab_A* 3oac_A*
Length = 293
Score = 26.4 bits (59), Expect = 9.6
Identities = 6/16 (37%), Positives = 10/16 (62%)
Query: 54 SLLGLERARYRVRELT 69
L+GLE++R +L
Sbjct: 248 KLMGLEKSREFAEKLN 263
>3ayv_A Putative uncharacterized protein TTHB071; structural genomics,
riken structural genomics/proteomics in RSGI, TIM
barrel, unknown function; 1.85A {Thermus thermophilus}
PDB: 3ayt_A
Length = 254
Score = 26.3 bits (58), Expect = 9.7
Identities = 5/38 (13%), Positives = 12/38 (31%), Gaps = 4/38 (10%)
Query: 3 LDVSYTDHSHIIGRGGLTIKKVMEETGCHVHFPDSNRS 40
D + H+ + + H+H D++
Sbjct: 161 FDAA---HARVFS-RTPDPGPWLALAPEHLHLNDTDGV 194
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
0.320 0.134 0.382
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,514,799
Number of extensions: 198710
Number of successful extensions: 549
Number of sequences better than 10.0: 1
Number of HSP's gapped: 501
Number of HSP's successfully gapped: 113
Length of query: 238
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 147
Effective length of database: 4,160,982
Effective search space: 611664354
Effective search space used: 611664354
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.3 bits)