RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14680
(78 letters)
>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 = 61.9 bits (151), Expect = 7e-15
Identities = 18/43 (41%), Positives = 31/43 (72%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
+++ VP GAI+GKGG+T+ + Q+ TG++I++SK +F P
Sbjct: 4 LVEMAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP 46
>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 = 64.1 bits (156), Expect = 7e-15
Identities = 29/42 (69%), Positives = 39/42 (92%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
+K+L+PSYAAG+IIGKGG+TI Q+QK+TG+ IK+SK+ DFYP
Sbjct: 8 LKVLIPSYAAGSIIGKGGQTIVQLQKETGATIKLSKSKDFYP 49
Score = 54.1 bits (130), Expect = 6e-11
Identities = 18/41 (43%), Positives = 29/41 (70%)
Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
D Q+KI+VP+ AG IIGKGG T+ I + +G+ +++S+
Sbjct: 101 DRANQVKIIVPNSTAGLIIGKGGATVKAIMEQSGAWVQLSQ 141
>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 = 61.6 bits (150), Expect = 1e-14
Identities = 19/43 (44%), Positives = 31/43 (72%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
++I VP GAI+GKGG+T+ + Q+ TG++I++SK +F P
Sbjct: 4 LVEIAVPENLVGAILGKGGKTLVEYQELTGARIQISKKGEFLP 46
>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 = 63.0 bits (153), Expect = 2e-14
Identities = 16/46 (34%), Positives = 25/46 (54%)
Query: 12 GVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
G I + +P +A G +IG+ GE I +IQ D G +I+ + P
Sbjct: 1 GSHMIDVPIPRFAVGIVIGRNGEMIKKIQNDAGVRIQFKPDDGTTP 46
Score = 51.4 bits (123), Expect = 5e-10
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
G+ + +VP+ G IIGKGGETI I + +G++I++ +
Sbjct: 101 GGLQEFNFIVPTGKTGLIIGKGGETIKSISQQSGARIELQRNPPPNA 147
>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 = 58.1 bits (141), Expect = 2e-13
Identities = 13/43 (30%), Positives = 30/43 (69%)
Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53
+ I++L+ G+IIGK GE++ ++++++G++I +S+ N
Sbjct: 2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN 44
>2hh3_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 106
Score = 59.0 bits (143), Expect = 2e-13
Identities = 15/43 (34%), Positives = 25/43 (58%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
I + VP ++ G +IG+ GE I +IQ D G +I+ + + P
Sbjct: 12 GIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDGTGP 54
>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 = 59.4 bits (144), Expect = 4e-13
Identities = 16/42 (38%), Positives = 26/42 (61%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
+I++P+ AG +IGKGGETI Q+Q+ G K+ + +
Sbjct: 4 QEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGSQNT 45
Score = 53.3 bits (128), Expect = 1e-10
Identities = 14/45 (31%), Positives = 25/45 (55%)
Query: 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
+ I + VP ++ G +IG+ GE I +IQ D G +I+ + +
Sbjct: 87 SRIGGGIDVPVPRHSVGVVIGRSGEMIKKIQNDAGVRIQFKQDDG 131
>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 = 57.4 bits (139), Expect = 6e-13
Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 10 ADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
G +I++P+ AG +IGKGGETI Q+Q+ G K+ M +
Sbjct: 11 GPGNAVQEIMIPASKAGLVIGKGGETIKQLQERAGVKMVMIQDGPQNT 58
>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 = 59.0 bits (143), Expect = 6e-13
Identities = 13/43 (30%), Positives = 30/43 (69%)
Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAN 53
+ I++L+ G+IIGK GE++ ++++++G++I +S+ N
Sbjct: 2 NVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGN 44
Score = 52.1 bits (125), Expect = 3e-10
Identities = 14/54 (25%), Positives = 32/54 (59%)
Query: 11 DGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITL 64
++++VP+ G++IGKGG I +I++ TG++++++ + IT+
Sbjct: 86 RPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTERAITI 139
>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 = 58.2 bits (141), Expect = 1e-12
Identities = 13/39 (33%), Positives = 24/39 (61%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
+++ +P+ A GAIIGK G+ I Q+ + + IK++
Sbjct: 5 VQVFIPAQAVGAIIGKKGQHIKQLSRFASASIKIAPPET 43
Score = 52.1 bits (125), Expect = 3e-10
Identities = 14/43 (32%), Positives = 28/43 (65%)
Query: 9 RADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSK 51
+ + + I VP+ AAG +IGKGG+T+ ++Q T +++ + +
Sbjct: 80 KEEVKLETHIRVPASAAGRVIGKGGKTVNELQNLTAAEVVVPR 122
>2opv_A KHSRP protein; KH domain, RNA binding protein, KSRP; NMR {Homo
sapiens}
Length = 85
Score = 55.8 bits (135), Expect = 2e-12
Identities = 16/40 (40%), Positives = 26/40 (65%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
+I++P+ AG +IGKGGETI Q+Q+ G K+ + +
Sbjct: 15 VQEIMIPAGKAGLVIGKGGETIKQLQERAGVKMILIQDGS 54
>2hh2_A KH-type splicing regulatory protein; KH-RNA binding domain, RNA
binding protein; NMR {Homo sapiens}
Length = 107
Score = 55.6 bits (134), Expect = 3e-12
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYP 57
++ +P++ G +IG+GGE + I + TG+ +++S+
Sbjct: 8 EMTFSIPTHKCGLVIGRGGENVKAINQQTGAFVEISRQLPPNG 50
>1zzk_A Heterogeneous nuclear ribonucleoprotein K; KH domian, alpha-beta
fold, DNA binding protein; 0.95A {Homo sapiens} SCOP:
d.51.1.1 PDB: 1zzj_A 1zzi_A
Length = 82
Score = 55.0 bits (133), Expect = 4e-12
Identities = 15/39 (38%), Positives = 27/39 (69%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
++ +P AG+IIGKGG+ I QI+ ++G+ IK+ + +
Sbjct: 9 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE 47
>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 = 54.6 bits (132), Expect = 5e-12
Identities = 15/39 (38%), Positives = 27/39 (69%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
++ +P AG+IIGKGG+ I QI+ ++G+ IK+ + +
Sbjct: 16 TQVTIPKDLAGSIIGKGGQRIKQIRHESGASIKIDEPLE 54
>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 = 53.8 bits (130), Expect = 1e-11
Identities = 11/39 (28%), Positives = 25/39 (64%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
++ +P+ G IIG+ G I +I++ +G++IK++ +
Sbjct: 8 HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE 46
>2p2r_A Poly(RC)-binding protein 2; protein-DNA complex, RNA and DNA
binding protein/DNA complex; 1.60A {Homo sapiens}
Length = 76
Score = 52.7 bits (127), Expect = 2e-11
Identities = 11/40 (27%), Positives = 25/40 (62%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
++ +P+ G IIG+ G I +I++ +G++IK++ +
Sbjct: 6 SHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVE 45
>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 = 52.4 bits (126), Expect = 5e-11
Identities = 15/39 (38%), Positives = 26/39 (66%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
+ VP G IIG+GGE I++IQ+++G KI+++ +
Sbjct: 17 EEYKVPDGMVGFIIGRGGEQISRIQQESGCKIQIAPDSG 55
>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 = 50.6 bits (121), Expect = 4e-10
Identities = 17/40 (42%), Positives = 25/40 (62%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
++ VP + G IIG+GGETI I K +G+KI K ++
Sbjct: 16 FEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE 55
>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 = 46.9 bits (111), Expect = 7e-09
Identities = 13/49 (26%), Positives = 22/49 (44%)
Query: 6 PFIRADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
+ G I++ VP G ++G G TI +IQ+ T + I +
Sbjct: 2 SSGSSGGQTTIQVRVPYRVVGLVVGPKGATIKRIQQRTHTYIVTPGRDK 50
>2cte_A Vigilin; K homology type I domain, RNA-binding, cell sterol
metabolism, beta-alpha-alpha-beta-BETA-alpha structure,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.51.1.1
Length = 94
Score = 46.6 bits (111), Expect = 8e-09
Identities = 10/39 (25%), Positives = 21/39 (53%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
+ +P +IGK GE + ++ T +KI++ + +D
Sbjct: 19 ATVAIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDD 57
>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 = 46.4 bits (110), Expect = 1e-08
Identities = 12/50 (24%), Positives = 21/50 (42%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPVYQVITL 64
++ + V IIG+ G I QI+ + I+ +D IT+
Sbjct: 18 KLSVTVDPKYHPKIIGRKGAVITQIRLEHDVNIQFPDKDDGNQPQDQITI 67
>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 = 46.6 bits (110), Expect = 5e-08
Identities = 11/42 (26%), Positives = 20/42 (47%)
Query: 17 KILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKANDFYPV 58
+ +P +IGK G+T +I+K T +KI + +
Sbjct: 37 YVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWI 78
Score = 30.4 bits (68), Expect = 0.035
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 20 VPSYAAGAIIGKGGETIAQIQKDTGSKIKM 49
G IIG+ G T I++ +G+ + +
Sbjct: 135 ALPRVRGRIIGRKGRTRQIIEEMSGASVSV 164
>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 = 42.5 bits (100), Expect = 4e-07
Identities = 8/39 (20%), Positives = 16/39 (41%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
I++ VP +IG+ G I ++ + I +
Sbjct: 19 IEVEVPFDLHRYVIGQKGSGIRKMMDEFEVNIHVPAPEL 57
>1vig_A Vigilin; RNA-binding protein, ribonucleoprotein; NMR {Homo
sapiens} SCOP: d.51.1.1 PDB: 1vih_A
Length = 71
Score = 41.6 bits (98), Expect = 6e-07
Identities = 7/39 (17%), Positives = 18/39 (46%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
++I + +IGK G I +I+ +++ ++
Sbjct: 7 VEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSE 45
>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 = 41.9 bits (98), Expect = 2e-06
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKM 49
+I + V GA+IG GE A+I + TG+ I +
Sbjct: 5 RIYVKVKPERLGAVIGPRGEVKAEIMRRTGTVITV 39
Score = 27.3 bits (60), Expect = 0.38
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 24 AAGAIIGKGGETIAQIQKDTGSKIKM 49
G IIG+GG I++ T + I +
Sbjct: 108 IKGRIIGEGGRARRTIEEMTDTYINV 133
>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 = 40.1 bits (94), Expect = 3e-06
Identities = 7/46 (15%), Positives = 17/46 (36%)
Query: 9 RADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGSKIKMSKAND 54
+ + + + IIG G+ I +I + I+ ++
Sbjct: 12 ELEQMVSEDVPLDHRVHARIIGARGKAIRKIMDEFKVDIRFPQSGA 57
>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 = 39.2 bits (91), Expect = 2e-05
Identities = 9/33 (27%), Positives = 12/33 (36%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKI 47
+ +V G IG G I Q +K G
Sbjct: 5 HEQFIVREDLMGLAIGTHGANIQQARKVPGVTA 37
Score = 33.4 bits (76), Expect = 0.002
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 14 CQIKILVPSYAAGAIIGKGGETIAQIQKDTG-SKIKMSKAND 54
+ I VP G +IGK G+ I +I +G ++++ N+
Sbjct: 67 AEDVIQVPRNLVGKVIGKNGKLIQEIVDKSGVVRVRIEAENE 108
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 38.6 bits (91), Expect = 4e-05
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
+IG GG+ I +I TG+K+
Sbjct: 582 REVIGSGGKVIREIVATTGAKV 603
>2cxc_A NUSA; transcription termination, RNA binding protein, archaeal
NUS domain, structural genomics, NPPSFA; 2.00A
{Aeropyrum pernix} PDB: 2cy1_A
Length = 144
Score = 37.7 bits (88), Expect = 6e-05
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGSKIK 48
+ LV AG IG+GG I +++ G I+
Sbjct: 38 LIFLVSEGEAGRAIGRGGRLIKLLREALGKNIE 70
Score = 25.7 bits (57), Expect = 1.5
Identities = 10/33 (30%), Positives = 15/33 (45%)
Query: 15 QIKILVPSYAAGAIIGKGGETIAQIQKDTGSKI 47
Q+ I V GA IGKGG+ + + +
Sbjct: 104 QVVIKVSEDDKGAAIGKGGKNVKRARLVLSKLF 136
>3u1k_A Polyribonucleotide nucleotidyltransferase 1, MITO; RNAse PH, KH
domain, exoribonuclease; HET: CIT; 2.13A {Homo sapiens}
Length = 630
Score = 38.3 bits (90), Expect = 6e-05
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
+G GG + ++Q +TG I
Sbjct: 579 AKFVGPGGYNLKKLQAETGVTI 600
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA
degradation, kinase, transferase; 2.60A {Escherichia
coli} PDB: 1sro_A
Length = 723
Score = 37.9 bits (89), Expect = 8e-05
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
+IGKGG I + ++TG+ I
Sbjct: 572 KDVIGKGGSVIRALTEETGTTI 593
>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 = 37.2 bits (87), Expect = 2e-04
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 26 GAIIGKGGETIAQIQKDTGSKI 47
G +IG + I QIQ+DTG++I
Sbjct: 610 GEVIGPKRQMINQIQEDTGAEI 631
>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 = 32.9 bits (75), Expect = 0.003
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 6/41 (14%)
Query: 15 QIKILVPSYAA------GAIIGKGGETIAQIQKDTGSKIKM 49
K+++P G +IG G T+ I+K+ +KI +
Sbjct: 8 SDKVMIPQDEYPEINFVGLLIGPRGNTLKNIEKECNAKIMI 48
>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 = 31.8 bits (72), Expect = 0.005
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 9 RADGVCQIKILVPSYAAGAIIGKGGETIAQIQKDTGS-KIKMSKAND 54
+A+ + PS+ IIGK G+ +A+I + I+ ++ D
Sbjct: 22 KANSFTVSSVAAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGED 68
>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 = 31.7 bits (72), Expect = 0.005
Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 16 IKILVPSYAAGAIIGKGGETIAQIQKDTGS-KIKMSKAND 54
+++ +P+ ++IG G I I ++ G I
Sbjct: 19 VEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGS 58
>2bl5_A MGC83862 protein, quaking protein; STAR proteins, GSG proteins,
RNA binding; NMR {Xenopus laevis} SCOP: d.51.1.1
Length = 140
Score = 31.5 bits (71), Expect = 0.010
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 6/39 (15%)
Query: 15 QIKILVPSYAA------GAIIGKGGETIAQIQKDTGSKI 47
Q K+ VP G I+G G T Q++ +TG KI
Sbjct: 3 QEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKI 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 = 28.0 bits (62), Expect = 0.20
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 25 AGAIIGKGGETIAQIQKDTGSKI 47
+ G G + IQ +TG+K+
Sbjct: 30 KEKVEGPGCSYLQHIQIETGAKV 52
>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 = 27.9 bits (63), Expect = 0.22
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 6/39 (15%)
Query: 17 KILVPSYAA--GAIIGKGGETI----AQIQKDTGSKIKM 49
I V + A G +IGK GE + + G ++
Sbjct: 62 SIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQI 100
>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 = 28.0 bits (63), Expect = 0.26
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 6/39 (15%)
Query: 17 KILVPSYAA--GAIIGKGGETI----AQIQKDTGSKIKM 49
I V + A G +IGK GE + + G ++
Sbjct: 63 SIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQI 101
>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 = 27.6 bits (62), Expect = 0.29
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 17 KILVPSYAA--GAIIGKGGETI----AQIQKDTGSKIKM 49
+ V + A G +IG+GGE I ++ K TG + +
Sbjct: 63 NVAVTVHVAKPGVVIGRGGERIRVLREELAKLTGKNVAL 101
>2xr1_A Cleavage and polyadenylation specificity factor 1 subunit;
hydrolase, metallo-beta-lactamase, beta-CAsp, RNA
processing; 2.59A {Methanosarcina mazei}
Length = 640
Score = 26.9 bits (60), Expect = 0.56
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 26 GAIIGKGGETIAQIQKDTGSKIKMSKA 52
G +IGK G T+ +I K G K+ +
Sbjct: 114 GLVIGKHGATLREITKQIGWIPKVVRT 140
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 218
Score = 26.4 bits (59), Expect = 0.79
Identities = 3/45 (6%), Positives = 15/45 (33%), Gaps = 6/45 (13%)
Query: 9 RADGVCQIKILVPSYAA--GAIIGKGGETIAQIQKDTGSKIKMSK 51
+ + Q+ I + +I + + ++ + ++
Sbjct: 67 KRIDLIQVII----HMGFPKLLIENRPQGVEDLKINVQKELNCVN 107
>3af5_A Putative uncharacterized protein PH1404; archaeal CPSF, beta-CAsp
family, KH domain, ribonuclease, ME beta-lactamase
superfamily, archaea; 2.60A {Pyrococcus horikoshii} PDB:
3af6_A*
Length = 651
Score = 26.1 bits (58), Expect = 1.3
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 26 GAIIGKGGETIAQIQKDTG 44
G +IGK GET+ I +
Sbjct: 119 GLVIGKNGETLRLITQKVK 137
>2ycb_A Beta-CAsp RNAse, cleavage and polyadenylation specificity factor;
hydrolase, KH, metallo-beta-lactamase; 3.10A
{Methanothermobacter thermautotrophicusorganism_taxid}
Length = 636
Score = 25.7 bits (57), Expect = 1.5
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 26 GAIIGKGGETIAQIQKDTG 44
G +IGK G T +I K+TG
Sbjct: 110 GLVIGKYGSTSREIVKNTG 128
>3i9v_3 NADH-quinone oxidoreductase subunit 3; electron transport,
respiratory chain, cell flavoprotein, FMN, iron,
iron-sulfur, membrane; HET: FMN; 3.10A {Thermus
thermophilus} PDB: 2ybb_3* 2fug_3* 3iam_3* 3ias_3*
3m9s_3*
Length = 783
Score = 25.2 bits (55), Expect = 2.6
Identities = 10/45 (22%), Positives = 15/45 (33%), Gaps = 12/45 (26%)
Query: 2 RLKSPFIRADGVCQIKILVP-------SYAAGAIIGKGGETIAQI 39
RLK+P +R +G LV + GE +
Sbjct: 305 RLKTPLVRKEGR-----LVEATWEEAFLALKEGLKEARGEEVGLY 344
>2xzm_C KH domain containing protein; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_C
Length = 243
Score = 24.7 bits (54), Expect = 3.4
Identities = 7/32 (21%), Positives = 10/32 (31%), Gaps = 6/32 (18%)
Query: 23 YAA--GAIIGKGGETI----AQIQKDTGSKIK 48
A +IG G+ +QK G
Sbjct: 54 KATKPQQVIGVEGKKHKELTQFLQKRFGYSDD 85
>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 = 24.7 bits (54), Expect = 3.8
Identities = 5/31 (16%), Positives = 12/31 (38%), Gaps = 2/31 (6%)
Query: 23 YAA--GAIIGKGGETIAQIQKDTGSKIKMSK 51
A ++G+ G I ++ + K +
Sbjct: 51 RATRTQDVLGENGRRINELTLLVQKRFKYAP 81
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 243
Score = 24.4 bits (53), Expect = 4.2
Identities = 8/28 (28%), Positives = 12/28 (42%), Gaps = 6/28 (21%)
Query: 23 YAA--GAIIGKGGETI----AQIQKDTG 44
A ++G+ G I A +QK G
Sbjct: 51 LATRTQNVLGEKGRRIRELTAVVQKRFG 78
>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 = 24.3 bits (53), Expect = 5.2
Identities = 4/33 (12%), Positives = 11/33 (33%), Gaps = 2/33 (6%)
Query: 23 YAA--GAIIGKGGETIAQIQKDTGSKIKMSKAN 53
A ++G+ G I ++ + +
Sbjct: 51 RATRTQNVLGEKGRRIRELTSVVQKRFNFLENG 83
>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 = 23.6 bits (52), Expect = 8.0
Identities = 5/12 (41%), Positives = 6/12 (50%)
Query: 28 IIGKGGETIAQI 39
+IG G I I
Sbjct: 246 VIGNKGAKIKTI 257
>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 = 23.6 bits (52), Expect = 8.6
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 28 IIGKGGETIAQI 39
+IG+GG I +I
Sbjct: 245 VIGEGGRKIKEI 256
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 0.138 0.395
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: 1,133,099
Number of extensions: 53391
Number of successful extensions: 127
Number of sequences better than 10.0: 1
Number of HSP's gapped: 127
Number of HSP's successfully gapped: 61
Length of query: 78
Length of database: 6,701,793
Length adjustment: 47
Effective length of query: 31
Effective length of database: 5,389,506
Effective search space: 167074686
Effective search space used: 167074686
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: 51 (23.2 bits)