RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7546
(150 letters)
>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 = 110 bits (277), Expect = 7e-32
Identities = 36/131 (27%), Positives = 62/131 (47%), Gaps = 14/131 (10%)
Query: 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVI 79
+ +RLL+ + GS+IGK G ++ ++R + A + + + PERI+T+ K
Sbjct: 4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAF 63
Query: 80 EEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGT 139
++ L+E + + +RL+V SQ G +IGKGG
Sbjct: 64 AMIIDKLEE--------------DISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGC 109
Query: 140 KIKELRDTFDA 150
KIKE+R++ A
Sbjct: 110 KIKEIRESTGA 120
Score = 55.2 bits (133), Expect = 1e-10
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 15 RGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP---ERILTIFAE 71
V LRL++P+ GS+IGKGG I +R A V V P ER +TI
Sbjct: 83 AASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITIAGI 142
Query: 72 LENGLKVIEEVLPALDE 88
++ ++ ++++ + E
Sbjct: 143 PQSIIECVKQICVVMLE 159
>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 = 109 bits (273), Expect = 3e-31
Identities = 37/139 (26%), Positives = 58/139 (41%), Gaps = 10/139 (7%)
Query: 17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG-----PERILTIFAE 71
+ L++LIPS AGS+IGKGG I +L+ + A++ + ER+ I
Sbjct: 2 LGSQYFLKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYPGTTERVCLIQGT 61
Query: 72 LENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAG 131
+E V + + E+ Q K +++IV S AG
Sbjct: 62 IEALNAVHGFIAEKIREMPQNVAKTEPVSILQPQTTVNPDR-----ANQVKIIVPNSTAG 116
Query: 132 CIIGKGGTKIKELRDTFDA 150
IIGKGG +K + + A
Sbjct: 117 LIIGKGGATVKAIMEQSGA 135
Score = 56.0 bits (135), Expect = 9e-11
Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV---PDCPGP-ERILTIFAE 71
++++++P+ AG +IGKGG+ + + A V + PD R++T+ E
Sbjct: 99 NPDRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQKPDGINLQNRVVTVSGE 158
Query: 72 LENGLKVIEEVLPALDEIRQ 91
E K +E ++ + E Q
Sbjct: 159 PEQNRKAVELIIQKIQEDPQ 178
>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 = 103 bits (259), Expect = 4e-29
Identities = 35/134 (26%), Positives = 48/134 (35%), Gaps = 3/134 (2%)
Query: 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV--PDCPGPERILTIFAELENGLK 77
+ + IP G VIG+ G I +++ND + D PERI I +
Sbjct: 2 SHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTPERIAQITGPPDRAQH 61
Query: 78 VIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYD-IRLIVHQSQAGCIIGK 136
E + L ++ G G G G G IV + G IIGK
Sbjct: 62 AAEIITDLLRSVQAGNPGGPGPGGRGRGRGQGNWNMGPPGGLQEFNFIVPTGKTGLIIGK 121
Query: 137 GGTKIKELRDTFDA 150
GG IK + A
Sbjct: 122 GGETIKSISQQSGA 135
Score = 51.4 bits (123), Expect = 4e-09
Identities = 17/82 (20%), Positives = 29/82 (35%), Gaps = 12/82 (14%)
Query: 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP-----ERILTIFA 70
E ++P+ G +IGKGG I + A + + P P ++ TI
Sbjct: 99 PPGGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNADPNMKLFTIRG 158
Query: 71 ELENGLKVIEEVLPALDEIRQK 92
+ + A I +K
Sbjct: 159 TPQQ-------IDYARQLIEEK 173
>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 = 97.9 bits (244), Expect = 5e-27
Identities = 31/134 (23%), Positives = 52/134 (38%), Gaps = 22/134 (16%)
Query: 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP---ERILTIFAELENGL 76
+++ IP++ G++IGK G +I +L AS+ + P R++ I E
Sbjct: 2 QEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPETPDSKVRMVIITGPPEAQF 61
Query: 77 KVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGK 136
K + L E G + + + V S AG +IGK
Sbjct: 62 KAQGRIYGKLKE-------------------ENFFGPKEEVKLETHIRVPASAAGRVIGK 102
Query: 137 GGTKIKELRDTFDA 150
GG + EL++ A
Sbjct: 103 GGKTVNELQNLTAA 116
Score = 55.9 bits (135), Expect = 8e-11
Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP----ERILTI--- 68
+E + +P+ AG VIGKGG + L+N A V VP P + I+ I
Sbjct: 80 KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPRDQTPDENDQVIVKIIGH 139
Query: 69 FAELENGLKVIEEVLPALDEIRQK 92
F + + I ++L + + QK
Sbjct: 140 FYASQMAQRKIRDILAQVKQQHQK 163
Score = 40.5 bits (95), Expect = 4e-05
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 117 DDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
+ +++ + G IIGK G IK+L A
Sbjct: 1 EQEMVQVFIPAQAVGAIIGKKGQHIKQLSRFASA 34
>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 = 94.1 bits (234), Expect = 2e-25
Identities = 27/132 (20%), Positives = 49/132 (37%), Gaps = 17/132 (12%)
Query: 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV----PDCPGPERILTIFAELENGLKV 78
++IP+ AG VIGKGG I +L+ + + ++ L I + +
Sbjct: 4 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGDPYKVQQA 63
Query: 79 IEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGG 138
E V+ L + G G + I + V + G +IG+ G
Sbjct: 64 CEMVMDIL-------------RERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSG 110
Query: 139 TKIKELRDTFDA 150
IK++++
Sbjct: 111 EMIKKIQNDAGV 122
Score = 55.2 bits (133), Expect = 2e-10
Identities = 18/92 (19%), Positives = 32/92 (34%), Gaps = 2/92 (2%)
Query: 1 MEFFIQQLSNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP 60
+ Q + G + + +P G VIG+ G I +++ND +
Sbjct: 71 LRERDQGGFGDRNEYGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDD 130
Query: 61 G--PERILTIFAELENGLKVIEEVLPALDEIR 90
G PE+I I + + L +R
Sbjct: 131 GTGPEKIAHIMGPPDRCEHAARIINDLLQSLR 162
>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 = 73.5 bits (181), Expect = 2e-18
Identities = 19/69 (27%), Positives = 37/69 (53%)
Query: 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVI 79
+ +RLL+ + GS+IGK G ++ ++R + A + + + PERI+T+ K
Sbjct: 4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFKAF 63
Query: 80 EEVLPALDE 88
++ L+E
Sbjct: 64 AMIIDKLEE 72
Score = 45.7 bits (109), Expect = 1e-07
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 118 DYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
IRL++H + G IIGK G +K++R+ A
Sbjct: 4 TLTIRLLMHGKEVGSIIGKKGESVKKMREESGA 36
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 106
Score = 51.3 bits (123), Expect = 1e-09
Identities = 24/99 (24%), Positives = 36/99 (36%), Gaps = 2/99 (2%)
Query: 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV--PDCPGPERILTIFAELE 73
G + + +P G VIG+ G I +++ND + D GPE+I I +
Sbjct: 6 GSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGPEKIAHIMGPPD 65
Query: 74 NGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGGGVG 112
+ L +R GG G G G G
Sbjct: 66 RCEHAARIINDLLQSLRSGPPGPPGGPGMPPGGRGRGRG 104
Score = 39.0 bits (91), Expect = 7e-05
Identities = 9/38 (23%), Positives = 19/38 (50%)
Query: 109 GGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRD 146
G + + I + V + G +IG+ G IK++++
Sbjct: 1 GAMATGSRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQN 38
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo
sapiens}
Length = 85
Score = 50.0 bits (120), Expect = 2e-09
Identities = 18/75 (24%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV----PDCPGPERILTI--- 68
GG N ++IP+ AG VIGKGG I +L+ + + ++ L I
Sbjct: 9 GGQNGTVQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNTNVDKPLRIIGD 68
Query: 69 FAELENGLKVIEEVL 83
+++ +++ ++L
Sbjct: 69 PYKVQQACEMVMDIL 83
Score = 39.6 bits (93), Expect = 2e-05
Identities = 12/42 (28%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 106 YNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDT 147
++ GG ++ +++ +AG +IGKGG IK+L++
Sbjct: 3 FHDNANGG--QNGTVQEIMIPAGKAGLVIGKGGETIKQLQER 42
>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 = 50.5 bits (121), Expect = 3e-09
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 4/85 (4%)
Query: 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV----PDCPGPERILTIFAE 71
GP + ++IP+ AG VIGKGG I +L+ + + P G ++ L I +
Sbjct: 10 DGPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNTGADKPLRITGD 69
Query: 72 LENGLKVIEEVLPALDEIRQKYGKG 96
+ E VL + + G
Sbjct: 70 PYKVQQAKEMVLELIRDQGSGPSSG 94
Score = 41.2 bits (97), Expect = 7e-06
Identities = 15/42 (35%), Positives = 25/42 (59%)
Query: 105 GYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRD 146
G +G G G + +++ S+AG +IGKGG IK+L++
Sbjct: 1 GSSGSSGHGDGPGNAVQEIMIPASKAGLVIGKGGETIKQLQE 42
>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 = 50.1 bits (120), Expect = 4e-09
Identities = 19/80 (23%), Positives = 26/80 (32%)
Query: 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKV 78
+ IP VIGK G + L + +P P + I E K
Sbjct: 15 TQASATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKA 74
Query: 79 IEEVLPALDEIRQKYGKGRG 98
EVL E ++ G G
Sbjct: 75 RHEVLLISAEQDKRSGPSSG 94
Score = 31.2 bits (71), Expect = 0.036
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 102 GGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
G G +G V L + + + + +IGK G K+++L
Sbjct: 1 GSSGSSGDIVARL-QTQASATVAIPKEHHRFVIGKNGEKLQDLELKTAT 48
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 107
Score = 48.3 bits (115), Expect = 2e-08
Identities = 21/101 (20%), Positives = 37/101 (36%), Gaps = 8/101 (7%)
Query: 17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP-----ERILTI--- 68
E+ IP+ G VIG+GG N+ + A V + P ++ I
Sbjct: 3 MAPGGEMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNGDPNFKLFIIRGS 62
Query: 69 FAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGGDGYNGG 109
++++ ++IEE + G G +N G
Sbjct: 63 PQQIDHAKQLIEEKIEGPLCPVGPGPGGPGPAGPMGPFNPG 103
Score = 38.3 bits (89), Expect = 1e-04
Identities = 6/26 (23%), Positives = 13/26 (50%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRD 146
+ + + G +IG+GG +K +
Sbjct: 9 MTFSIPTHKCGLVIGRGGENVKAINQ 34
>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 = 47.3 bits (113), Expect = 3e-08
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERILTI 68
+ L IP+ + G +IG+ G+NI +R A + + + R +TI
Sbjct: 2 LGSQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTI 55
Score = 36.1 bits (84), Expect = 4e-04
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
L + + GCIIG+ G I E+R
Sbjct: 8 HELTIPNNLIGCIIGRQGANINEIR 32
>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA
binding protein/DNA complex; 1.60A {Homo sapiens}
Length = 76
Score = 46.9 bits (112), Expect = 3e-08
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERILTI 68
L IP+ + G +IG+ G+ I +R A + + + +R +TI
Sbjct: 2 AQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTI 54
Score = 35.3 bits (82), Expect = 9e-04
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDT 147
L + GCIIG+ G KI E+R
Sbjct: 7 HELTIPNDLIGCIIGRQGAKINEIRQM 33
>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 = 46.9 bits (112), Expect = 4e-08
Identities = 19/54 (35%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 17 GPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERILTI 68
G + ++ IP +AGS+IGKGG I ++R++ AS+ + + +RI+TI
Sbjct: 10 GGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 63
Score = 43.5 bits (103), Expect = 1e-06
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 107 NGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELR 145
+ G LG ++ + + AG IIGKGG +IK++R
Sbjct: 2 SHMSYGDLGGPIITTQVTIPKDLAGSIIGKGGQRIKQIR 40
>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 = 46.9 bits (112), Expect = 5e-08
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERILTI 68
+ ++ IP +AGS+IGKGG I ++R++ AS+ + + +RI+TI
Sbjct: 2 AMGPIITTQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLEGSEDRIITI 56
Score = 36.9 bits (86), Expect = 2e-04
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
++ + + AG IIGKGG +IK++R
Sbjct: 9 TQVTIPKDLAGSIIGKGGQRIKQIR 33
>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 = 46.6 bits (111), Expect = 7e-08
Identities = 22/97 (22%), Positives = 38/97 (39%), Gaps = 9/97 (9%)
Query: 9 SNFKRFRGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPG--PERIL 66
S + + + +P + G +IG+GG I+R++ + + + G PER
Sbjct: 3 SGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSGGLPERSC 62
Query: 67 TIFAELENGLKVIEEVLPALDEIRQKYGKGRGGEDGG 103
+ E+ V A + Q KGR G G
Sbjct: 63 MLTGTPES-------VQSAKRLLDQIVEKGRSGPSSG 92
Score = 33.6 bits (77), Expect = 0.004
Identities = 10/43 (23%), Positives = 16/43 (37%)
Query: 105 GYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDT 147
G +G + V G IIG+GG +I ++
Sbjct: 1 GSSGSSGHQQQRSVMTEEYKVPDGMVGFIIGRGGEQISRIQQE 43
>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 = 45.3 bits (108), Expect = 1e-07
Identities = 10/51 (19%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP-----ERILTI 68
+ + +P + G+++GKGG + + A + + R +TI
Sbjct: 5 VEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTI 55
Score = 38.8 bits (91), Expect = 4e-05
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRD 146
+ + V ++ G I+GKGG + E ++
Sbjct: 5 VEMAVPENLVGAILGKGGKTLVEYQE 30
>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 = 45.4 bits (108), Expect = 1e-07
Identities = 10/51 (19%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 23 LRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGP-----ERILTI 68
+ + +P + G+++GKGG + + A + + R +TI
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLPGTRNRRVTI 55
Score = 38.5 bits (90), Expect = 8e-05
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDT 147
+ + V ++ G I+GKGG + E ++
Sbjct: 5 VEIAVPENLVGAILGKGGKTLVEYQEL 31
>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 = 45.2 bits (107), Expect = 3e-07
Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 3/83 (3%)
Query: 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVP---DCPGPERILTIFAELENG 75
+L + + + +IG+ G+ I ++R + ++ P D P+ +TI +N
Sbjct: 15 RSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITITGYEKNT 74
Query: 76 LKVIEEVLPALDEIRQKYGKGRG 98
+ +L + E+ Q G G
Sbjct: 75 EAARDAILRIVGELEQMSGPSSG 97
Score = 29.4 bits (66), Expect = 0.15
Identities = 8/32 (25%), Positives = 14/32 (43%)
Query: 119 YDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
+ + + V IIG+ G I ++R D
Sbjct: 17 FKLSVTVDPKYHPKIIGRKGAVITQIRLEHDV 48
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo
sapiens} SCOP: d.51.1.1 PDB: 1vih_A
Length = 71
Score = 44.3 bits (105), Expect = 3e-07
Identities = 15/63 (23%), Positives = 31/63 (49%)
Query: 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIE 80
+ + I + +IGK G+NI R+++ +K SV +P ++ I + + +
Sbjct: 5 DYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKR 64
Query: 81 EVL 83
E+L
Sbjct: 65 ELL 67
Score = 26.9 bits (60), Expect = 0.93
Identities = 8/37 (21%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 114 LGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
+ + DY + + + +IGK G I ++D +
Sbjct: 1 INRMDY-VEINIDHKFHRHLIGKSGANINRIKDQYKV 36
>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 = 44.6 bits (105), Expect = 4e-07
Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 8/87 (9%)
Query: 16 GGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENG 75
+++ +P RV G V+G G+ I R++ + P E + + EN
Sbjct: 5 SSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPG-RDKEPVFAVTGMPEN- 62
Query: 76 LKVIEEVLPALDEIRQKYGKGRGGEDG 102
V A +EI G G
Sbjct: 63 ------VDRAREEIEAHITLRSGPSSG 83
Score = 28.0 bits (62), Expect = 0.48
Identities = 9/41 (21%), Positives = 15/41 (36%)
Query: 110 GVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
G G I++ V G ++G G IK ++
Sbjct: 1 GSSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHT 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 = 44.4 bits (105), Expect = 6e-07
Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 1/82 (1%)
Query: 18 PNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCP-GPERILTIFAELENGL 76
V + + RV +IG G I ++ ++FK + P +T+ EN
Sbjct: 14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGAPDPNCVTVTGLPENVE 73
Query: 77 KVIEEVLPALDEIRQKYGKGRG 98
+ I+ +L +E G G
Sbjct: 74 EAIDHILNLEEEYLADSGPSSG 95
Score = 26.7 bits (59), Expect = 1.5
Identities = 7/35 (20%), Positives = 13/35 (37%)
Query: 116 KDDYDIRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
+ + + IIG G I+++ D F
Sbjct: 14 EQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKV 48
>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 = 43.2 bits (102), Expect = 1e-06
Identities = 16/73 (21%), Positives = 35/73 (47%)
Query: 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIE 80
V + + +P + VIG+ GS I ++ ++F+ ++ VP I+ I N +
Sbjct: 17 VTIEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPELQSDIIAITGLAANLDRAKA 76
Query: 81 EVLPALDEIRQKY 93
+L + E++ +
Sbjct: 77 GLLERVKELQAEQ 89
Score = 28.6 bits (64), Expect = 0.39
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFDA 150
I + V +IG+ G+ I+++ D F+
Sbjct: 19 IEVEVPFDLHRYVIGQKGSGIRKMMDEFEV 48
>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 = 41.7 bits (98), Expect = 5e-06
Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 7/90 (7%)
Query: 21 VELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV----PDCPGPERILTIF---AELE 73
V +L +P R G +IG+GG I + A +T R++ I E+
Sbjct: 15 VFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVA 74
Query: 74 NGLKVIEEVLPALDEIRQKYGKGRGGEDGG 103
+I E + +E+R++ G G
Sbjct: 75 AAKHLILEKVSEDEELRKRIAHSASGPSSG 104
Score = 35.2 bits (81), Expect = 0.002
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDT 147
+L V Q G IIG+GG I+ +
Sbjct: 17 EQLSVPQRSVGRIIGRGGETIRSICKA 43
>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 = 41.2 bits (96), Expect = 2e-05
Identities = 23/123 (18%), Positives = 41/123 (33%), Gaps = 35/123 (28%)
Query: 24 RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVL 83
+ ++ + G IG G+NI + R VT D I+ E ++ +K L
Sbjct: 7 QFIVREDLMGLAIGTHGANIQQARK--VPGVTAIDLDEDTCTFHIYGEDQDAVKKARSFL 64
Query: 84 PALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKIKE 143
+ + + V ++ G +IGK G I+E
Sbjct: 65 ---------------------------------EFAEDVIQVPRNLVGKVIGKNGKLIQE 91
Query: 144 LRD 146
+ D
Sbjct: 92 IVD 94
Score = 29.2 bits (65), Expect = 0.31
Identities = 10/38 (26%), Positives = 15/38 (39%)
Query: 15 RGGPNDVELRLLIPSRVAGSVIGKGGSNIARLRNDFKA 52
R E + +P + G VIGK G I + +
Sbjct: 61 RSFLEFAEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGV 98
>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 = 39.0 bits (91), Expect = 6e-05
Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 1/81 (1%)
Query: 19 NDVELRLLIPSRVAGSVIGKGGSNIARLRNDF-KASVTVPDCPGPERILTIFAELENGLK 77
N E+ + IP+++ S+IG G I + + + P + I + K
Sbjct: 15 NIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEK 74
Query: 78 VIEEVLPALDEIRQKYGKGRG 98
+++L +E + K G G
Sbjct: 75 AKKQLLHLAEEKQTKSGPSSG 95
>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 = 34.1 bits (78), Expect = 0.004
Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 2/72 (2%)
Query: 27 IPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPAL 86
PS + +IGK G N+A++ V + + E +T+ E+ E++ +
Sbjct: 33 APSWLHRFIIGKKGQNLAKITQQMP-KVHI-EFTEGEDKITLEGPTEDVSVAQEQIEGMV 90
Query: 87 DEIRQKYGKGRG 98
++ + G G
Sbjct: 91 KDLINRSGPSSG 102
>3n89_A Defective in GERM LINE development protein 3, ISO; KH domains, RNA
binding, cell cycle; 2.79A {Caenorhabditis elegans}
Length = 376
Score = 34.5 bits (78), Expect = 0.008
Identities = 14/76 (18%), Positives = 26/76 (34%), Gaps = 2/76 (2%)
Query: 18 PNDVELRLLIPSRVAGSVIGKGG--SNIARLRNDFKASVTVPDCPGPERILTIFAELENG 75
P V L + S+ + G N+A + + + +PD FA+
Sbjct: 27 PTRVTLNMEFESQYYSLMTSDNGDHENVASIMAETNTLIQLPDRSVGGTTPDPFAQQVTI 86
Query: 76 LKVIEEVLPALDEIRQ 91
+V A +R+
Sbjct: 87 TGYFGDVDRARMLMRR 102
>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 = 32.0 bits (72), Expect = 0.055
Identities = 19/125 (15%), Positives = 33/125 (26%), Gaps = 7/125 (5%)
Query: 24 RLLIPSRVAGSVIGKGGSNIARLRNDFKASVTV--PDCPGPERILTIFAELENGLKVIEE 81
+ IP +IGK G + K +T+ + K +
Sbjct: 37 YVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDI 96
Query: 82 VLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIGKGGTKI 141
V A+ R +G + L G IIG+ G
Sbjct: 97 V-LAIGRGFSPERAFRLLNEG----EYLEIINLTDIIIGNEKNALPRVRGRIIGRKGRTR 151
Query: 142 KELRD 146
+ + +
Sbjct: 152 QIIEE 156
>2xzm_C KH domain containing protein; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_C
Length = 243
Score = 31.6 bits (72), Expect = 0.062
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
+ + ++ +IG G K KEL
Sbjct: 49 TEIRIKATKPQQVIGVEGKKHKELT 73
Score = 28.1 bits (63), Expect = 1.1
Identities = 6/26 (23%), Positives = 7/26 (26%)
Query: 33 GSVIGKGGSNIARLRNDFKASVTVPD 58
VIG G L + D
Sbjct: 59 QQVIGVEGKKHKELTQFLQKRFGYSD 84
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 243
Score = 31.7 bits (72), Expect = 0.063
Identities = 6/25 (24%), Positives = 15/25 (60%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
+I+ ++ ++G+ G +I+EL
Sbjct: 46 TEIIILATRTQNVLGEKGRRIRELT 70
Score = 27.8 bits (62), Expect = 1.1
Identities = 5/19 (26%), Positives = 9/19 (47%)
Query: 33 GSVIGKGGSNIARLRNDFK 51
+V+G+ G I L +
Sbjct: 56 QNVLGEKGRRIRELTAVVQ 74
>3iz6_B 40S ribosomal protein S3 (S3P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
1s1h_C 3jyv_C*
Length = 227
Score = 31.2 bits (71), Expect = 0.077
Identities = 6/25 (24%), Positives = 15/25 (60%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
+I+ ++ ++G+ G +I+EL
Sbjct: 46 TEIIIRATRTQNVLGEKGRRIRELT 70
Score = 27.8 bits (62), Expect = 1.4
Identities = 5/26 (19%), Positives = 11/26 (42%)
Query: 33 GSVIGKGGSNIARLRNDFKASVTVPD 58
+V+G+ G I L + + +
Sbjct: 56 QNVLGEKGRRIRELTSVVQKRFNFLE 81
>3u5c_D RP13, YS3, 40S ribosomal protein S3; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_B 3o30_C 3o2z_C 3u5g_D 1s1h_C
3jyv_C*
Length = 240
Score = 31.3 bits (71), Expect = 0.082
Identities = 6/25 (24%), Positives = 14/25 (56%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
+I+ ++ ++G+ G +I EL
Sbjct: 46 TEVIIRATRTQDVLGENGRRINELT 70
Score = 27.8 bits (62), Expect = 1.1
Identities = 5/26 (19%), Positives = 8/26 (30%)
Query: 33 GSVIGKGGSNIARLRNDFKASVTVPD 58
V+G+ G I L +
Sbjct: 56 QDVLGENGRRINELTLLVQKRFKYAP 81
>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 = 31.6 bits (71), Expect = 0.11
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 12/60 (20%)
Query: 39 GGSNIARLRNDFKASVTVPDCPGPERILTIFAEL-ENGLKVI----EEVL-------PAL 86
GG R+R ++ A + G + IF E+ E+ + +L PAL
Sbjct: 1677 GGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPAL 1736
Score = 31.2 bits (70), Expect = 0.12
Identities = 18/93 (19%), Positives = 32/93 (34%), Gaps = 23/93 (24%)
Query: 20 DVELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVP-------DCPG--PE---RILT 67
+E LL+P+ ++L+ F + P D P E + L
Sbjct: 15 SLEHVLLVPTASF--------FIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLG 66
Query: 68 IFAEL--ENGLKVIEEVLP-ALDEIRQKYGKGR 97
+ L + + ++VL L E Y +G
Sbjct: 67 YVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGN 99
Score = 26.9 bits (59), Expect = 3.2
Identities = 14/61 (22%), Positives = 19/61 (31%), Gaps = 23/61 (37%)
Query: 113 GLGKDDYD-----------------------IRLIVHQSQAGCIIGKGGTKIKELRDTFD 149
G+G D Y I IV + I GG K K +R+ +
Sbjct: 1630 GMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYS 1689
Query: 150 A 150
A
Sbjct: 1690 A 1690
>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 = 31.4 bits (70), Expect = 0.11
Identities = 24/129 (18%), Positives = 40/129 (31%), Gaps = 19/129 (14%)
Query: 2 EFFIQQLSN--FKRFRGGPNDVE-LRLLIPSRVAGSVIGKGGSNIAR-----LRNDFK-- 51
+ LS + V L +++ K + + LR ++K
Sbjct: 40 DMPKSILSKEEIDHIIMSKDAVSGTLRLF-----WTLLSKQEEMVQKFVEEVLRINYKFL 94
Query: 52 ASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDEIR-QKYGKGRGG--EDGGDGYNG 108
S + P + ++ E + L +V + R Q Y K R E
Sbjct: 95 MSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVL 154
Query: 109 -GGVGGLGK 116
GV G GK
Sbjct: 155 IDGVLGSGK 163
>3r8n_C 30S ribosomal protein S3; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2gyb_C 2gy9_C* 2ykr_C 3fih_C* 2wwl_C 3oar_C
3oaq_C 3ofb_C 3ofa_C 3ofp_C 3ofx_C 3ofy_C 3ofo_C 3r8o_C
4a2i_C
Length = 206
Score = 30.6 bits (70), Expect = 0.12
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRD 146
IR+ +H ++ G +IGK G +++LR
Sbjct: 63 IRVTIHTARPGIVIGKKGEDVEKLRK 88
Score = 27.1 bits (61), Expect = 1.8
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 33 GSVIGKGGSNIARLRNDFK 51
G VIGK G ++ +LR
Sbjct: 73 GIVIGKKGEDVEKLRKVVA 91
>3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C
3i1q_C 3i1s_C 3i1z_C 3i21_C 3izv_G* 3izw_G* 3kc4_C
3or9_C 3ora_C 3sfs_C* 3uoq_C* 2qal_C* 1p6g_C 1p87_C
2aw7_C ...
Length = 233
Score = 30.7 bits (70), Expect = 0.14
Identities = 10/26 (38%), Positives = 18/26 (69%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRD 146
IR+ +H ++ G +IGK G +++LR
Sbjct: 64 IRVTIHTARPGIVIGKKGEDVEKLRK 89
Score = 27.2 bits (61), Expect = 2.0
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 33 GSVIGKGGSNIARLRNDFK 51
G VIGK G ++ +LR
Sbjct: 74 GIVIGKKGEDVEKLRKVVA 92
>2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C*
1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F*
1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C
1xmo_C* 1xmq_C* 1xnq_C* ...
Length = 239
Score = 30.3 bits (69), Expect = 0.16
Identities = 10/26 (38%), Positives = 19/26 (73%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRD 146
+ + VH ++ G +IG+GG +I+ LR+
Sbjct: 64 VAVTVHVAKPGVVIGRGGERIRVLRE 89
Score = 27.2 bits (61), Expect = 2.2
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 33 GSVIGKGGSNIARLRNDFK 51
G VIG+GG I LR +
Sbjct: 74 GVVIGRGGERIRVLREELA 92
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 218
Score = 30.2 bits (69), Expect = 0.16
Identities = 5/25 (20%), Positives = 13/25 (52%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELR 145
I++I+H +I +++L+
Sbjct: 72 IQVIIHMGFPKLLIENRPQGVEDLK 96
Score = 26.4 bits (59), Expect = 3.7
Identities = 2/17 (11%), Positives = 6/17 (35%)
Query: 33 GSVIGKGGSNIARLRND 49
+I + L+ +
Sbjct: 82 KLLIENRPQGVEDLKIN 98
>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 = 0.30
Identities = 6/17 (35%), Positives = 10/17 (58%), Gaps = 1/17 (5%)
Query: 71 ELENGLKVIE-EVLPAL 86
+L+ LK+ + PAL
Sbjct: 24 KLQASLKLYADDSAPAL 40
>1wf3_A GTP-binding protein; GTPase, riken structural genomics/prote
initiative, RSGI, structural genomics, hydrolase; HET:
GNP; 1.88A {Thermus thermophilus} SCOP: c.37.1.8
d.52.3.1
Length = 301
Score = 29.3 bits (67), Expect = 0.46
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 116 KDDYDIRLIVH---QSQAGCIIGKGGTKIKE 143
I+ I++ SQ +IG+GG KIKE
Sbjct: 225 NGVLYIKAILYVERPSQKAIVIGEGGRKIKE 255
>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA,
30S ribosome ASSE GTP-binding, nucleotide-binding; HET:
GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*
Length = 308
Score = 29.0 bits (66), Expect = 0.48
Identities = 8/32 (25%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 115 GKDDYDIRLIVH---QSQAGCIIGKGGTKIKE 143
+ I+ + ++ IIGK G ++KE
Sbjct: 234 NPNMLVIKGEIIVDRENLKPIIIGKKGQRLKE 265
>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like,
hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8
d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X
Length = 301
Score = 29.0 bits (66), Expect = 0.51
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 3/31 (9%)
Query: 116 KDDYDIRLIVH---QSQAGCIIGKGGTKIKE 143
+ YDI ++ + Q +IG G KIK
Sbjct: 226 RGGYDINGLILVEREGQKKMVIGNKGAKIKT 256
>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural
genomics, structural GEN consortium, SGC, rRNA,
ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}
Length = 245
Score = 28.3 bits (64), Expect = 0.80
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 43 IARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEEVLPALDE 88
I LRN K V D P P + F +L+ K+ +L + +
Sbjct: 4 INFLRNKHKIHVQGTDLPDP---IATFQQLDQEYKINSRLLQNILD 46
>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 = 27.7 bits (61), Expect = 1.3
Identities = 20/140 (14%), Positives = 43/140 (30%), Gaps = 26/140 (18%)
Query: 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFAELENGLKVIEE 81
+ + + G+VIG G A + +TV + E
Sbjct: 5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITVDTENSMVIVEP-----EAEGIPPVN 59
Query: 82 VLPALDEIRQKYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLI-----------VHQSQA 130
++ A + ++ G+ L ++D + ++ +
Sbjct: 60 LMKAAEVVKAI----------SLGFPPEKAFRLLEEDQILVVVDLKQVVGDSQNHLKRIK 109
Query: 131 GCIIGKGGTKIKELRDTFDA 150
G IIG+GG + + + D
Sbjct: 110 GRIIGEGGRARRTIEEMTDT 129
>2cpq_A FragIle X mental retardation syndrome related protein 1, isoform
B'; KH domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.51.1.1
Length = 91
Score = 26.2 bits (57), Expect = 2.3
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 24 RLLIPSRVAGSVIGKGGSNIARLRND 49
++ + G IG GSNI + R
Sbjct: 18 EFVVREDLMGLAIGTHGSNIQQARKV 43
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 27.1 bits (60), Expect = 2.9
Identities = 25/135 (18%), Positives = 43/135 (31%), Gaps = 20/135 (14%)
Query: 22 ELRLLIPSRVAGSVIGKGGSNIARLRNDFKASVTVPDCPGPERILTIFA-ELENGLKVIE 80
+ + +V I + G +L A++ +P R + A ++ G
Sbjct: 944 QFKHQHGDKVDIFEIPETGEYSVKLLKG--ATLYIPK---ALRFDRLVAGQIPTGWNAKT 998
Query: 81 EVLPALDEIRQ-----KYGKGRGGEDGGDGYNGGGVGGLGKDDYDIRLIVHQSQAGCIIG 135
+ D I Q + E G+ D Y++ VH S+ G G
Sbjct: 999 YGISD-DIISQVDPITLFVLVSVVEAFIAS-------GI-TDPYEMYKYVHVSEVGNCSG 1049
Query: 136 KGGTKIKELRDTFDA 150
G + LR F
Sbjct: 1050 SGMGGVSALRGMFKD 1064
>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken
structural genomics/proteomics initiative, RSGI,
ribosome; NMR {Homo sapiens} SCOP: d.52.3.1
Length = 92
Score = 25.2 bits (55), Expect = 4.5
Identities = 6/29 (20%), Positives = 15/29 (51%)
Query: 121 IRLIVHQSQAGCIIGKGGTKIKELRDTFD 149
+I+ ++ ++G+ G +I+EL
Sbjct: 37 TEIIILATRTQNVLGEKGRRIRELTAVVQ 65
>2hhl_A CTD small phosphatase-like protein; CTD phosphatase, keggins anion,
structural genomics, PSI, protein structure initiative;
HET: KEG; 2.10A {Homo sapiens}
Length = 195
Score = 25.8 bits (57), Expect = 4.9
Identities = 8/28 (28%), Positives = 11/28 (39%), Gaps = 3/28 (10%)
Query: 4 FIQQLSNF---KRFRGGPNDVELRLLIP 28
+I N + + D EL LIP
Sbjct: 150 YIFHPENAVPVQSWFDDMTDTELLDLIP 177
>2ght_A Carboxy-terminal domain RNA polymerase II polypeptide A small
phosphatase 1; protein-peptide complex, HAD superfamily,
hydrolase; HET: SEP; 1.80A {Homo sapiens} PDB: 2ghq_A*
3pgl_A* 1t9z_A* 1ta0_A* 3l0c_A 3l0y_A 3l0b_A* 2q5e_A
Length = 181
Score = 25.4 bits (56), Expect = 7.3
Identities = 6/28 (21%), Positives = 11/28 (39%), Gaps = 3/28 (10%)
Query: 4 FIQQLSNF---KRFRGGPNDVELRLLIP 28
++ N + +D EL L+P
Sbjct: 137 YVFHPDNAVPVASWFDNMSDTELHDLLP 164
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.318 0.145 0.425
Gapped
Lambda K H
0.267 0.0837 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,514,286
Number of extensions: 161603
Number of successful extensions: 514
Number of sequences better than 10.0: 1
Number of HSP's gapped: 495
Number of HSP's successfully gapped: 101
Length of query: 150
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 65
Effective length of database: 4,328,508
Effective search space: 281353020
Effective search space used: 281353020
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 (21.6 bits)
S2: 53 (24.0 bits)