RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6375
(86 letters)
>3bbo_V Ribosomal protein L23; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 198
Score = 137 bits (345), Expect = 7e-43
Identities = 40/85 (47%), Positives = 62/85 (72%)
Query: 1 MDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP 60
+D + I++ P+ TE+A+K I D N+L+F V ++A+K I+ A+ + + V KVNTLIRP
Sbjct: 109 LDVYQILQSPIITEAAIKNIADENSLLFTVDVRADKKMIREAISNFFGVKVRKVNTLIRP 168
Query: 61 DGKKKAYVRLARDYDALDVANKIGI 85
DG KKAY+ L ++Y+A ++A KIGI
Sbjct: 169 DGTKKAYIMLNKEYNASELAKKIGI 193
>1vq8_S 50S ribosomal protein L23P; ribosome 50S, protein-protein
complex, RNA-RNA complex, PROT complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} SCOP: d.12.1.1 PDB:
1vq4_S* 1vq5_S* 1vq6_S* 1vq7_S* 1s72_S* 1vq9_S* 1vqk_S*
1vql_S* 1vqm_S* 1vqn_S* 1vqo_S* 1vqp_S* 1yhq_S* 1yi2_S*
1yij_S* 1yit_S* 1yj9_S* 1yjn_S* 1yjw_S* 2otj_S* ...
Length = 85
Score = 131 bits (332), Expect = 2e-42
Identities = 36/83 (43%), Positives = 56/83 (67%)
Query: 3 AFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDG 62
++++IK+P TE AM ++ N L F V +A+K + AV++ YD+ V +VNT DG
Sbjct: 2 SWDVIKHPHVTEKAMNDMDFQNKLQFAVDDRASKGEVADAVEEQYDVTVEQVNTQNTMDG 61
Query: 63 KKKAYVRLARDYDALDVANKIGI 85
+KKA VRL+ D DA +VA++IG+
Sbjct: 62 EKKAVVRLSEDDDAQEVASRIGV 84
>4a17_R RPL23A, 60S ribosomal protein L21; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_R 4a1c_R 4a1e_R
Length = 150
Score = 128 bits (323), Expect = 4e-40
Identities = 47/86 (54%), Positives = 64/86 (74%)
Query: 1 MDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP 60
+D +++K PLTTE AMKK+ED NT+VF VH ++ K IK+A +K+Y++ V VNTL
Sbjct: 65 LDNHSVVKTPLTTEKAMKKMEDENTMVFYVHNRSTKPQIKSAFEKLYNVKVRSVNTLNTI 124
Query: 61 DGKKKAYVRLARDYDALDVANKIGII 86
G KKAY+RLA D D+L +ANKIG+I
Sbjct: 125 TGNKKAYIRLAADSDSLTLANKIGLI 150
>3u5e_X 60S ribosomal protein L25; translation, ribosome, ribosomal R
ribosomal protein, STM1, eukaryotic ribosome; 3.00A
{Saccharomyces cerevisiae} PDB: 2wwa_K 2ww9_K 3izc_X
3izs_X 2wwb_K 3o5h_W 3o58_W 3u5i_X 1s1i_T 3jyw_T
Length = 142
Score = 126 bits (319), Expect = 1e-39
Identities = 52/86 (60%), Positives = 73/86 (84%)
Query: 1 MDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP 60
+D++ +I+ P+T+E+AMKK+ED N LVF V ++ANK+ IK AVK++Y+++V KVNTL+RP
Sbjct: 57 LDSYKVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRP 116
Query: 61 DGKKKAYVRLARDYDALDVANKIGII 86
+G KKAYVRL DYDALD+AN+IG I
Sbjct: 117 NGTKKAYVRLTADYDALDIANRIGYI 142
>3iz5_X 60S ribosomal protein L23A (L23P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_X 2go5_4 2j37_4
Length = 152
Score = 123 bits (310), Expect = 4e-38
Identities = 70/86 (81%), Positives = 76/86 (88%)
Query: 1 MDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP 60
+D + I+KYPLTTESAMKKIEDNNTLVFIV L+A+K IKAAVKKMYDI KVNTLIRP
Sbjct: 67 LDQYQILKYPLTTESAMKKIEDNNTLVFIVDLKADKKKIKAAVKKMYDIQAKKVNTLIRP 126
Query: 61 DGKKKAYVRLARDYDALDVANKIGII 86
DGKKKAYV+L DYDALDVANKIGII
Sbjct: 127 DGKKKAYVKLTPDYDALDVANKIGII 152
>2zkr_s 60S ribosomal protein L23A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 156
Score = 120 bits (303), Expect = 4e-37
Identities = 72/86 (83%), Positives = 80/86 (93%)
Query: 1 MDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP 60
+D + IIK+PLTTESAMKKIEDNNTLVFIV ++ANKH IK AVKK+YDI+VAKVNTLIRP
Sbjct: 71 LDHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRP 130
Query: 61 DGKKKAYVRLARDYDALDVANKIGII 86
DG+KKAYVRLA DYDALDVANKIGII
Sbjct: 131 DGEKKAYVRLAPDYDALDVANKIGII 156
>2zjr_Q 50S ribosomal protein L23; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: d.12.1.1 PDB: 1sm1_R* 2aar_R 2d3o_R
2zjp_Q* 2zjq_Q 1nkw_R 3cf5_Q* 3dll_Q* 3pio_Q* 3pip_Q*
1nwy_R* 1nwx_R* 1xbp_R* 1pnu_R 1pny_R 1vor_U 1vou_U
1vow_U 1voy_U 1vp0_U
Length = 95
Score = 69.5 bits (171), Expect = 1e-17
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 16/85 (18%)
Query: 1 MDAFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRP 60
M ++I++ P+ +E A +E F V +A K IK A+++ + + V ++T+ P
Sbjct: 1 MSHYDILQAPVISEKAYSAME-RGVYSFWVSPKATKTEIKDAIQQAFGVRVIGISTMNVP 59
Query: 61 DGK--------------KKAYVRLA 71
GK KKA VRLA
Sbjct: 60 -GKRKRVGRFIGQRNDRKKAIVRLA 83
>3tve_T 50S ribosomal protein L23; RNA, ribosome, tRNA, translation,
mRNA; 3.10A {Thermus thermophilus} PDB: 3pyr_T 3pyo_T
3pyv_T 3pyt_T 3tvh_T 1n88_A 1vsa_R 1vsp_R 2hgj_W 2hgq_W
2hgu_W 2j01_X 2j03_X 2jl6_X 2jl8_X 2v47_X 2v49_X 2wdi_X
2wdj_X 2wdl_X ...
Length = 92
Score = 67.2 bits (165), Expect = 1e-16
Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 16/87 (18%)
Query: 3 AFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDG 62
A+++I P+ +E A F VH +A K IK AV+ + + V KVNTL G
Sbjct: 2 AYDVILAPVLSEKAYAGFA-EGKYTFWVHPKATKTEIKNAVETAFKVKVVKVNTLHVR-G 59
Query: 63 K--------------KKAYVRLARDYD 75
K KKA V++A
Sbjct: 60 KKKRLGRYLGKRPDRKKAIVQVAPGQK 86
>3r8s_T 50S ribosomal protein L23; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3fik_T 2wwq_T 3oat_T* 3oas_T* 3ofd_T 3ofc_T 3ofr_T*
3ofz_T* 3og0_T 3ofq_T 3r8t_T 2j28_T 3e1b_M 3e1d_M
3iy9_T 3i1n_T 1p85_R 1p86_R 1vs8_T 1vs6_T ...
Length = 93
Score = 66.8 bits (164), Expect = 2e-16
Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 15/87 (17%)
Query: 3 AFNIIKYPLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTLIRPDG 62
+++ P +E A +E +NT+V V A K IKAAV+K++++ V VNTL+ G
Sbjct: 7 LLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVK-G 65
Query: 63 K--------------KKAYVRLARDYD 75
K KKAYV L +
Sbjct: 66 KVKRHGQRIGRRSDWKKAYVTLKEGQN 92
>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 = 28.1 bits (62), Expect = 0.31
Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 13/52 (25%)
Query: 32 LQANK-HHIKAAVKKMYDINVAKVNTLIRPDGKKKAYVRLARDYDALDVANK 82
L+ N H + A + + D + K LI+ Y A +A +
Sbjct: 96 LEGNDIHALAAKLLQENDTTLVKTKELIK------NY------ITARIMAKR 135
>3s21_A 3-oxoacyl-[ACP] synthase III; non-decarboxylative claisen
condensation reaction, transfera; HET: CER; 1.70A
{Xanthomonas campestris PV} PDB: 3s23_A* 3row_A 3s1z_A
3s20_A* 3fk5_A
Length = 345
Score = 27.2 bits (61), Expect = 0.65
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 28 FIVHLQANKHHIKAAVKKMYDINVAKV 54
F++H Q ++ H A VK I+ AKV
Sbjct: 269 FVIH-QVSRPHTAAFVKSF-GIDPAKV 293
>3lz8_A Putative chaperone DNAJ; structure genomics, structural genomics,
PSI-2, protein STRU initiative; 2.90A {Klebsiella
pneumoniae subsp} PDB: 2kqx_A
Length = 329
Score = 24.5 bits (54), Expect = 4.5
Identities = 8/11 (72%), Positives = 8/11 (72%)
Query: 64 KKAYVRLARDY 74
K AY RLAR Y
Sbjct: 46 KTAYRRLARKY 56
>2czd_A Orotidine 5'-phosphate decarboxylase; pyrimidine biosynthesis,
orotidine 5'-phosphate decarboxylas (ompdecase),
structural genomics; 1.60A {Pyrococcus horikoshii} SCOP:
c.1.2.3 PDB: 2cz5_A 2cze_A* 2czf_A*
Length = 208
Score = 24.2 bits (53), Expect = 7.4
Identities = 9/48 (18%), Positives = 17/48 (35%)
Query: 10 PLTTESAMKKIEDNNTLVFIVHLQANKHHIKAAVKKMYDINVAKVNTL 57
P T +K+ IVH + + A + I V +++
Sbjct: 64 PNTNRLIARKVFGAGADYVIVHTFVGRDSVMAVKELGEIIMVVEMSHP 111
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
0.321 0.135 0.375
Gapped
Lambda K H
0.267 0.0639 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,339,190
Number of extensions: 70116
Number of successful extensions: 211
Number of sequences better than 10.0: 1
Number of HSP's gapped: 206
Number of HSP's successfully gapped: 37
Length of query: 86
Length of database: 6,701,793
Length adjustment: 54
Effective length of query: 32
Effective length of database: 5,194,059
Effective search space: 166209888
Effective search space used: 166209888
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 (21.9 bits)
S2: 51 (23.6 bits)