RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14481
(179 letters)
>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical
domain, RNA binding protein; NMR {Saccharomyces
cerevisiae} SCOP: a.144.1.1
Length = 92
Score = 124 bits (312), Expect = 1e-37
Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 2/88 (2%)
Query: 94 QEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMY--PELAGKITGMLLEIDNAELLYMLEH 151
P + Q+Q+Q LGE+L+ + E AGKITGM+L++ E+ +LE
Sbjct: 4 GSPRNANDNNQFYQQKQRQALGEQLYKKVSAKTSNEEAAGKITGMILDLPPQEVFPLLES 63
Query: 152 NESLKSKVEEAVAVLQAHQAKQAAVKKE 179
+E + +EA A ++ + +Q ++
Sbjct: 64 DELFEQHYKEASAAYESFKKEQEQQTEQ 91
>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding
protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1
Length = 85
Score = 119 bits (300), Expect = 5e-36
Identities = 36/84 (42%), Positives = 51/84 (60%)
Query: 88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
+ Q ST+LA P++QK +LGERL+ I + P A K+TGMLLE+DN E+L
Sbjct: 1 GSSLASQGQNLSTVLANLTPEQQKNVLGERLYNHIVAINPAAAAKVTGMLLEMDNGEILN 60
Query: 148 MLEHNESLKSKVEEAVAVLQAHQA 171
+L+ L +KV+EA+ VL H
Sbjct: 61 LLDTPGLLDAKVQEALEVLNRHMN 84
>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding
protein; NMR {Triticum aestivum}
Length = 85
Score = 115 bits (289), Expect = 3e-34
Identities = 33/82 (40%), Positives = 55/82 (67%)
Query: 91 VQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLE 150
+ ++ LA + P+ Q+ MLGE L+PL+ ++ + A K+TGMLLE+D E+L++LE
Sbjct: 3 LGSPIGALASALANSPPETQRMMLGENLYPLVDQLEHDQAAKVTGMLLEMDQTEVLHLLE 62
Query: 151 HNESLKSKVEEAVAVLQAHQAK 172
++LK+KV EA+ VL++ Q
Sbjct: 63 SPDALKAKVAEAMEVLRSAQQH 84
>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo
sapiens} SCOP: a.144.1.1 PDB: 3ntw_A
Length = 61
Score = 105 bits (264), Expect = 9e-31
Identities = 30/60 (50%), Positives = 44/60 (73%)
Query: 110 QKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHNESLKSKVEEAVAVLQAH 169
+Q LGERL+P +Q M P A KITGMLLE+ A+LL +L +SL+++V+EA+ ++ AH
Sbjct: 1 HRQALGERLYPRVQAMQPAFASKITGMLLELSPAQLLLLLASEDSLRARVDEAMELIIAH 60
>3kuj_A Polyadenylate-binding protein 1; protein-protein complex,
methylation, mRNA processing, mRNA nucleus,
phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo
sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A 3pkn_A
2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A
Length = 88
Score = 105 bits (263), Expect = 2e-30
Identities = 66/83 (79%), Positives = 75/83 (90%)
Query: 93 GQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLYMLEHN 152
PLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+MLE
Sbjct: 3 LGSPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESP 62
Query: 153 ESLKSKVEEAVAVLQAHQAKQAA 175
ESL+SKV+EAVAVLQAHQAK+AA
Sbjct: 63 ESLRSKVDEAVAVLQAHQAKEAA 85
>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding
protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A
1jh4_A
Length = 144
Score = 105 bits (262), Expect = 1e-29
Identities = 74/88 (84%), Positives = 83/88 (94%)
Query: 88 AVHVQGQEPLTSTMLAAAQPQEQKQMLGERLFPLIQRMYPELAGKITGMLLEIDNAELLY 147
AVHVQGQEPLT++MLA+A PQEQKQMLGERLFPLIQ M+P LAGKITGMLLEIDN+ELL+
Sbjct: 44 AVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLH 103
Query: 148 MLEHNESLKSKVEEAVAVLQAHQAKQAA 175
MLE ESL+SKV+EAVAVLQAHQAK+AA
Sbjct: 104 MLESPESLRSKVDEAVAVLQAHQAKEAA 131
>2k9y_A Ephrin type-A receptor 2; receptor tyrosine kinase, membrane
protein, dimeric transmembrane domain, ephrin receptor,
ATP-binding, glycoprotein; NMR {Homo sapiens}
Length = 41
Score = 32.2 bits (73), Expect = 0.008
Identities = 15/37 (40%), Positives = 24/37 (64%), Gaps = 1/37 (2%)
Query: 25 SGEGGVNVAMISGISFGALALVTLFGAVSFIMYRRYR 61
S EG N+A+I G++ G + L+ L G V F ++RR +
Sbjct: 6 SPEGSGNLAVIGGVAVGVVLLLVLAG-VGFFIHRRRK 41
>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 = 33.9 bits (77), Expect = 0.027
Identities = 23/122 (18%), Positives = 40/122 (32%), Gaps = 40/122 (32%)
Query: 78 SGYID-DSTLRAVHVQGQ---------EPLTSTM-LAAAQPQEQKQMLG-ERLFPLIQRM 125
+ + +S + V +G E S + A P E L +++R
Sbjct: 1774 ADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVER- 1832
Query: 126 YPELAGKITGMLLEIDNAELLYMLEHNES---------LKSKVEEAVAVLQAHQAKQAAV 176
GK TG L+EI N +N L++ ++ VL +
Sbjct: 1833 ----VGKRTGWLVEIVN--------YNVENQQYVAAGDLRA-LDTVTNVL-----NFIKL 1874
Query: 177 KK 178
+K
Sbjct: 1875 QK 1876
>1cd1_A CD1, MCD1D.1; immunology, MHC, TCR, glycoprotein, signal,
immunoglobulin fold, T-cell; 2.67A {Mus musculus} SCOP:
b.1.1.2 d.19.1.1
Length = 315
Score = 28.0 bits (63), Expect = 1.5
Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 18 EDLSNPWSGEGGVNVAMISGISFGALALVTLFGAVSFIMYRRYRWNKP 65
+D+ W V +I I L ++ + GAV + ++RR +
Sbjct: 270 QDIILYWDARQ-APVGLIVFI---VLIMLVVVGAVVYYIWRRRSAYQD 313
>3e6q_A Putative 5-carboxymethyl-2-hydroxymuconate isomer; structural
genomics, APC7683, isomerase, PSI-2, protein STRU
initiative; HET: GOL IMD; 1.75A {Pseudomonas aeruginosa}
Length = 146
Score = 27.6 bits (61), Expect = 1.7
Identities = 6/34 (17%), Positives = 13/34 (38%)
Query: 107 PQEQKQMLGERLFPLIQRMYPELAGKITGMLLEI 140
+Q LGE L ++ + + +E+
Sbjct: 94 DAATRQALGESLCEVLAGAVAGGGEEGVQVSVEV 127
>3nqh_A Glycosyl hydrolase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; 2.11A {Bacteroides thetaiotaomicron}
Length = 441
Score = 27.7 bits (61), Expect = 2.5
Identities = 11/59 (18%), Positives = 20/59 (33%), Gaps = 5/59 (8%)
Query: 15 AHAEDLSNPWSGEGGVNVAMISGISFG---ALALVTLFGAVSFIMYRRYRWNKPQTLSD 70
A + PW+ +G A +++ G + M+ RW+ P S
Sbjct: 217 FTAPSVKGPWTRQG--LFAPEGSLTYNSQTTFVFPLKCGEDTIPMFMGDRWSYPHQASA 273
>3cps_A Glyceraldehyde 3-phosphate dehydrogenase; GAPDH, glycolysis,
malaria, structural genomics; HET: NAD; 1.90A
{Cryptosporidium parvum iowa II} PDB: 1vsv_A* 1vsu_A*
3chz_A 3cie_A* 3cif_A* 3sth_A*
Length = 354
Score = 27.1 bits (61), Expect = 3.8
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 127 PELAGKITGM 136
P L GK+TGM
Sbjct: 240 PALNGKLTGM 249
>1gad_O D-glyceraldehyde-3-phosphate dehydrogenase; oxidoreductase
(aldehyde(D)-NAD+(A)); HET: NAD; 1.80A {Escherichia
coli} SCOP: c.2.1.3 d.81.1.1 PDB: 1dc4_A* 1dc3_A 1dc6_A*
1dc5_A* 1s7c_A* 1gae_O* 2vyn_A* 2vyv_A*
Length = 330
Score = 26.7 bits (60), Expect = 4.2
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 127 PELAGKITGM 136
PEL GK+TGM
Sbjct: 219 PELNGKLTGM 228
>3ids_C GAPDH, glyceraldehyde-3-phosphate dehydrogenase, glycoso;
irreversible inhibitor, protein-ligand complex,X-RAY,
glycol NAD, oxireductase; HET: NAD; 1.80A {Trypanosoma
cruzi} PDB: 1ml3_A* 1qxs_C* 3dmt_A* 1k3t_A* 2x0n_A*
1gga_O* 1i32_A* 1a7k_A* 1i33_A* 1gyp_A* 1gyq_A*
Length = 359
Score = 26.8 bits (60), Expect = 4.4
Identities = 6/10 (60%), Positives = 7/10 (70%)
Query: 127 PELAGKITGM 136
P GK+TGM
Sbjct: 237 PSTQGKLTGM 246
>3h9e_O Glyceraldehyde-3-phosphate dehydrogenase, testis-; oxidoreductase,
structural genomics, structural genomics CON SGC,
glycolysis, NAD; HET: NAD; 1.72A {Homo sapiens} PDB:
3pfw_O* 2vyn_D* 2vyv_D*
Length = 346
Score = 26.8 bits (60), Expect = 4.6
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 127 PELAGKITGM 136
PEL GK+TGM
Sbjct: 226 PELKGKLTGM 235
>2f33_A Calbindin; EF-hand, Ca2+-binding, metal binding protein; NMR
{Rattus norvegicus} PDB: 2g9b_A
Length = 263
Score = 26.8 bits (59), Expect = 4.7
Identities = 9/41 (21%), Positives = 14/41 (34%)
Query: 76 DSSGYIDDSTLRAVHVQGQEPLTSTMLAAAQPQEQKQMLGE 116
D SG+I+ L+ E T+ + ML
Sbjct: 115 DHSGFIETEELKNFLKDLLEKANKTVDDTKLAEYTDLMLKL 155
>3pym_A GAPDH 3, glyceraldehyde-3-phosphate dehydrogenase 3; NAD(P)-binding
rossmann-fold domain, alpha and beta protein,
oxidoreductase; HET: NAD; 2.00A {Saccharomyces
cerevisiae} PDB: 2i5p_O*
Length = 332
Score = 26.7 bits (60), Expect = 4.9
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 127 PELAGKITGM 136
PEL GK+TGM
Sbjct: 220 PELQGKLTGM 229
>2b4r_O Glyceraldehyde-3-phosphate dehydrogenase; SGPP, structural
genomics, PSI, structural genomi pathogenic protozoa
consortium; HET: NAD AES; 2.25A {Plasmodium falciparum}
SCOP: c.2.1.3 d.81.1.1 PDB: 2b4t_O* 1ywg_O*
Length = 345
Score = 26.4 bits (59), Expect = 5.0
Identities = 7/10 (70%), Positives = 9/10 (90%)
Query: 127 PELAGKITGM 136
PEL GK+TG+
Sbjct: 233 PELNGKLTGV 242
>3e5r_O PP38, glyceraldehyde-3-phosphate dehydrogenase, cytosolic; GAPDH,
RICE, oxidoreductase, cytoplasm, glycolysis, NAD; HET:
NAD; 2.30A {Oryza sativa subsp} PDB: 3e6a_O
Length = 337
Score = 26.4 bits (59), Expect = 5.8
Identities = 7/10 (70%), Positives = 9/10 (90%)
Query: 127 PELAGKITGM 136
P+L GK+TGM
Sbjct: 224 PDLNGKLTGM 233
>3p3b_A Mandelate racemase/muconate lactonizing protein; enolase
superfamily fold, galacturonate dehydratase, D-tartr
galacturonate, lyase; HET: TAR; 1.65A {Geobacillus SP}
PDB: 3ops_A* 3n4f_A* 3qpe_A*
Length = 392
Score = 26.2 bits (58), Expect = 6.5
Identities = 3/21 (14%), Positives = 7/21 (33%)
Query: 18 EDLSNPWSGEGGVNVAMISGI 38
L + + G + A +
Sbjct: 75 RRLLDLFDDRGRLREAYRLQL 95
>1u8f_O GAPDH, glyceraldehyde-3-phosphate dehydrogenase, liver; rossmann
fold, oxidoreductase, mammalian GAPDH; HET: NAD; 1.75A
{Homo sapiens} SCOP: c.2.1.3 d.81.1.1 PDB: 1znq_O*
1j0x_O* 3gpd_R* 1dss_G* 1crw_G* 1szj_G* 1ihx_A* 1ihy_A*
1gpd_G* 4gpd_1
Length = 335
Score = 26.0 bits (58), Expect = 7.5
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 127 PELAGKITGM 136
PEL GK+TGM
Sbjct: 222 PELNGKLTGM 231
>3mp7_A Preprotein translocase subunit SECY; protein transport, membrane
protein complex, preprotein TRAN membrane insertion,;
2.90A {Pyrococcus furiosus}
Length = 482
Score = 26.1 bits (58), Expect = 8.5
Identities = 5/34 (14%), Positives = 11/34 (32%), Gaps = 1/34 (2%)
Query: 24 WSGEGGVNVAMISGISFGALALVTLFGAVSFIMY 57
G G V + + L ++ L ++
Sbjct: 131 LGGAFG-RVGVDVTYAIAVLMILQLAMGGIVLII 163
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.315 0.130 0.370
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,684,464
Number of extensions: 151949
Number of successful extensions: 385
Number of sequences better than 10.0: 1
Number of HSP's gapped: 384
Number of HSP's successfully gapped: 29
Length of query: 179
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 92
Effective length of database: 4,272,666
Effective search space: 393085272
Effective search space used: 393085272
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (24.4 bits)