RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 033325
(122 letters)
>3r8s_G 50S ribosomal protein L6; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_E
1p86_E 2awb_G 2aw4_G 2i2v_G 2j28_G 2i2t_G* 2qao_G*
2qba_G* 2qbc_G* 2qbe_G 2qbg_G 2qbi_G* 2qbk_G* 2qov_G
2qox_G 2qoz_G* 2qp1_G* 2rdo_G 2vhm_G ...
Length = 176
Score = 113 bits (285), Expect = 2e-33
Identities = 39/97 (40%), Positives = 58/97 (59%), Gaps = 2/97 (2%)
Query: 24 FFRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPPAVRVFCLKNNVVCCCGLDKHR 83
F + L++VGVGY RA +G ++ L LG+ H V+ +P + C + G DK
Sbjct: 82 FTKKLQLVGVGY--RAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQV 139
Query: 84 VHQFAASVRSCKPPEPFKGKGIMYTDEVIKKKVGKKK 120
+ Q AA +R+ + PEP+KGKG+ Y DEV++ K KKK
Sbjct: 140 IGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK 176
>2zjr_E 50S ribosomal protein L6; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: d.141.1.1 d.141.1.1 PDB: 1nwx_E*
1xbp_E* 2zjp_E* 2zjq_E 1nwy_E 3cf5_E* 3dll_E* 3pio_E*
3pip_E* 1pnu_E 1pny_E 1vor_H 1vou_H 1vow_H 1voy_H 1vp0_H
Length = 185
Score = 111 bits (281), Expect = 1e-32
Identities = 32/101 (31%), Positives = 50/101 (49%), Gaps = 4/101 (3%)
Query: 24 FFRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPPAVRVFCLKNNVVCCCGLDKHR 83
+ L++ GVG+ RA+ G+ L + +GY H V + P V + + G+DK
Sbjct: 83 YTINLELRGVGF--RAKLTGKALEMNIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQL 140
Query: 84 VHQFAASVRSCKPPEPFKGKGIMYTDEVIKKKVGK--KKSK 122
V Q AA+VR + P+ + GKG+ + E I K GK
Sbjct: 141 VGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATGG 181
>3v2d_H 50S ribosomal protein L6; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_F 2hgj_H 2hgq_H 2hgu_H 1vsa_F 2j03_H 2jl6_H 2jl8_H
2v47_H 2v49_H 2wdi_H 2wdj_H 2wdl_H 2wdn_H 2wh2_H 2wh4_H
2wrj_H 2wrl_H 2wro_H 2wrr_H ...
Length = 180
Score = 111 bits (280), Expect = 2e-32
Identities = 34/99 (34%), Positives = 52/99 (52%), Gaps = 2/99 (2%)
Query: 24 FFRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPPAVRVFCLKNNVVCCCGLDKHR 83
+ + L I G+GY RA GR L L +G+ H V + P + + V G+DK +
Sbjct: 83 YSKELLIKGIGY--RARLVGRALELTVGFSHPVVVEPPEGITFEVPEPTRVRVSGIDKQK 140
Query: 84 VHQFAASVRSCKPPEPFKGKGIMYTDEVIKKKVGKKKSK 122
V Q AA++R+ + P + KGI Y E ++ K GK +K
Sbjct: 141 VGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAK 179
>1nkw_E 50S ribosomal protein L6; ribosome, large subunit, X- RAY
structure, peptidyl-transferase, peptide bond formation;
3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB:
1sm1_E*
Length = 212
Score = 112 bits (282), Expect = 2e-32
Identities = 32/101 (31%), Positives = 50/101 (49%), Gaps = 4/101 (3%)
Query: 24 FFRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPPAVRVFCLKNNVVCCCGLDKHR 83
+ L++ GVG+ RA+ G+ L + +GY H V + P V + + G+DK
Sbjct: 110 YTINLELRGVGF--RAKLTGKALEMNIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQL 167
Query: 84 VHQFAASVRSCKPPEPFKGKGIMYTDEVIKKKVGK--KKSK 122
V Q AA+VR + P+ + GKG+ + E I K GK
Sbjct: 168 VGQVAANVRKVRKPDAYHGKGVRFVGEQIALKAGKAGATGG 208
>3bbo_I Ribosomal protein L6; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 223
Score = 111 bits (280), Expect = 4e-32
Identities = 43/99 (43%), Positives = 66/99 (66%), Gaps = 2/99 (2%)
Query: 24 FFRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPPAVRVFCLKNNVVCCCGLDKHR 83
F + L +VGVGY RA +G+ L L LG+ H V++ +P +++V +N + G DK
Sbjct: 126 FEKKLILVGVGY--RATVDGKELVLNLGFSHPVKMQIPDSLKVKVEENTRITVSGYDKSE 183
Query: 84 VHQFAASVRSCKPPEPFKGKGIMYTDEVIKKKVGKKKSK 122
+ QFAA+VR +PPEP+KGKG+ Y+DE++++K GK K
Sbjct: 184 IGQFAATVRKWRPPEPYKGKGVKYSDEIVRRKEGKAGKK 222
>1rl6_A Protein (ribosomal protein L6); RNA-binding protein, gentamicin
resistance, alpha/beta protein; 2.00A {Geobacillus
stearothermophilus} SCOP: d.141.1.1 d.141.1.1 PDB:
1giy_H 1ml5_h* 1c04_B 1yl3_H 2b66_H 2b9n_H 2b9p_H 1eg0_J
487d_J
Length = 177
Score = 109 bits (275), Expect = 9e-32
Identities = 38/95 (40%), Positives = 58/95 (61%), Gaps = 2/95 (2%)
Query: 24 FFRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPPAVRVFCLKNNVVCCCGLDKHR 83
+ + L++VGVGY RA +G+ L L +GY H VE+ + + + G DK R
Sbjct: 82 YEKALELVGVGY--RASKQGKKLVLSVGYSHPVEIEPEEGLEIEVPSQTKIIVKGADKQR 139
Query: 84 VHQFAASVRSCKPPEPFKGKGIMYTDEVIKKKVGK 118
V + AA++R+ +PPEP+KGKGI Y E+++ K GK
Sbjct: 140 VGELAANIRAVRPPEPYKGKGIRYEGELVRLKEGK 174
>1vq8_E 50S ribosomal protein L6P; 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.141.1.1 d.141.1.1 PDB:
1vq4_E* 1vq5_E* 1vq6_E* 1vq7_E* 1s72_E* 1vq9_E* 1vqk_E*
1vql_E* 1vqm_E* 1vqn_E* 1vqo_E* 1vqp_E* 1yhq_E* 1yi2_E*
1yij_E* 1yit_E* 1yj9_E* 1yjn_E* 1yjw_E* 2otj_E* ...
Length = 178
Score = 73.4 bits (181), Expect = 1e-17
Identities = 15/94 (15%), Positives = 29/94 (30%), Gaps = 4/94 (4%)
Query: 28 LKIVGVGYKARAEAEGRLLYLK--LGYVHDVELTVPPAVRVFCLKNNVVCCCGLDKHRVH 85
+++ + + EG + ++ LG T+ V + G D V
Sbjct: 85 MEVFYSHFPMQVNVEGDEVVIENFLGEKAPRRTTIHGDTDVEIDGEELT-VSGPDIEAVG 143
Query: 86 QFAASVRSCKPPEPFKGKGIMYTDEVIKKKVGKK 119
Q AA + K + I +K +
Sbjct: 144 QTAADIEQLTRIND-KDVRVFQDGVYITRKPNRG 176
>2zkr_e 60S ribosomal protein L9; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 192
Score = 57.0 bits (138), Expect = 2e-11
Identities = 18/107 (16%), Positives = 37/107 (34%), Gaps = 11/107 (10%)
Query: 24 FFRFLKIVGVGYKA--RAEAEGRLLYLKL----GYVHDVELTVPPAVRVFCLKNNVVCCC 77
F ++ V + + G L+ ++ Y+ V + A V + + +
Sbjct: 88 FRYKMRSVYAHFPINVVIQENGSLVEIRNFLGEKYIRRVRMRPGVACSVSQAQKDELILE 147
Query: 78 GLDKHRVHQFAASVRSCKPPEPFKGKGIMYTDEVI--KKKVGKKKSK 122
G D V AA ++ K K I + I +K +++
Sbjct: 148 GNDIELVSNSAALIQQ---ATTVKNKDIRKFLDGIYVSEKGTVQQAD 191
>3iz5_F 60S ribosomal protein L9 (L6P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_F
Length = 190
Score = 47.7 bits (114), Expect = 6e-08
Identities = 13/90 (14%), Positives = 28/90 (31%), Gaps = 9/90 (10%)
Query: 22 AKFFRFLKIVGVGYKARAEAEGRLLYLK----LGYVHDVELTVPPAVRVFCLKN--NVVC 75
+ ++ V + A ++ LG ++ + V + + + +
Sbjct: 85 KGYRYKMRFVYAHFPINASITNSNTAIEIRNFLGEKKVRKVDMLEGVTILRSEKVKDELV 144
Query: 76 CCGLDKHRVHQFAASVRSCKPPEPFKGKGI 105
G D V + AA + K K I
Sbjct: 145 LDGNDIELVSRSAALINQKCHV---KNKDI 171
>4a17_E RPL9, 60S ribosomal protein L9; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_E 4a1c_E 4a1e_E
Length = 188
Score = 45.8 bits (109), Expect = 3e-07
Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 11/90 (12%)
Query: 23 KFFRFLKIVGVGYKA--RAEAEGRLLYLK--LGYVHDVELTVPP--AVRVFCLKNNVVCC 76
+ +K+ + +G + +K LG + P + + N +
Sbjct: 85 GYKFKMKLAFAHFPIQEAVAKDGSSIEIKHFLGEKRIRRIQALPGVKISRKDEEKNTLTL 144
Query: 77 CGLDKHRVHQFAASVR-SCKPPEPFKGKGI 105
G+D + V Q A + SC K K I
Sbjct: 145 QGIDLNNVSQTCALIHQSCLV----KEKDI 170
>3u5e_H L8, RP24, YL11, 60S ribosomal protein L9-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3izc_F
1s1i_H 3izs_F* 3j16_F 3o5h_I 3o58_I 3u5i_H 3jyw_H
Length = 191
Score = 42.3 bits (100), Expect = 6e-06
Identities = 14/86 (16%), Positives = 27/86 (31%), Gaps = 11/86 (12%)
Query: 28 LKIVGVGYKA------RAEAEGRLLYLKLGYVHDVELTVPPAVRVFCLKN--NVVCCCGL 79
++ V + + A+ + LG + V V + N + + G
Sbjct: 90 MRYVYAHFPINVNIVEKDGAKFIEVRNFLGDKKIRNVPVRDGVTIEFSTNVKDEIVLSGN 149
Query: 80 DKHRVHQFAASVRSCKPPEPFKGKGI 105
V Q AA ++ + K I
Sbjct: 150 SVEDVSQNAADLQQIC---RVRNKDI 172
>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 = 0.051
Identities = 30/130 (23%), Positives = 47/130 (36%), Gaps = 38/130 (29%)
Query: 15 FTLTRMEAKFFRFLKIVGVGYKARAE----AEGRLLYLK-LGYV-HDVE----------L 58
F ++++ +F + L G+ A E AE L K LGYV VE L
Sbjct: 28 FIASQLQEQFNKILPEPTEGFAADDEPTTPAE---LVGKFLGYVSSLVEPSKVGQFDQVL 84
Query: 59 TVPPAVRVF---CLKNNVVCCCGLDKHRVHQFAASVRSCKPPEPFKGKGIM--YTD--EV 111
+ + F L+ N D +H AA + K K ++ Y +
Sbjct: 85 NL--CLTEFENCYLEGN-------D---IHALAAKLLQENDTTLVKTKELIKNYITARIM 132
Query: 112 IKKKVGKKKS 121
K+ KK +
Sbjct: 133 AKRPFDKKSN 142
Score = 29.2 bits (65), Expect = 0.36
Identities = 12/73 (16%), Positives = 28/73 (38%), Gaps = 11/73 (15%)
Query: 35 YKARAEAEGRLLYLKLGY-VHDV--ELTVPPAVRVFCLKNNV------VCCCGLDKHRVH 85
+ + +A L ++ G ++ ++PP++ L+NN + L + +V
Sbjct: 293 FVSVRKAITVLFFI--GVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQ 350
Query: 86 QFAASVRSCKPPE 98
+ S P
Sbjct: 351 DYVNKTNSHLPAG 363
>3hi7_A Amiloride-sensitive amine oxidase; oxidoreductase, copper amine
oxidase, topaquinone, TPQ, DIAM oxidase, DAO, human,
glycoprotein, heparin-binding; HET: TPQ NAG BMA; 1.80A
{Homo sapiens} PDB: 3hig_A* 3hii_A* 3k5t_A* 3mph_A*
Length = 731
Score = 26.4 bits (57), Expect = 3.3
Identities = 11/47 (23%), Positives = 14/47 (29%), Gaps = 8/47 (17%)
Query: 58 LTVPPAVRVFCLKNNVVCCCGLDKHRVHQFAASVRSCKPPEPFKGKG 104
L V V+ N V ++ R C P PF G
Sbjct: 688 LASRDTVIVWPRDNGPNY--------VQRWIPEDRDCSMPPPFSYNG 726
>2q0y_A GCN5-related N-acetyltransferase; YP_295895.1, acetyltransferase
(GNAT) family, structural genomics, joint center for ST
genomics; HET: MSE; 1.80A {Ralstonia eutropha JMP134}
Length = 153
Score = 24.8 bits (54), Expect = 6.8
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 39 AEAEGRLLYLKLGYVHDVELTVP 61
A G+ LY ++G+ E++ P
Sbjct: 128 ATEMGQPLYARMGWSPTTEMSKP 150
>1yfo_A D1, receptor protein tyrosine phosphatase alpha; hydrolase, signal
transduction, glycoprotein, phosphorylation, signal;
2.25A {Mus musculus} SCOP: c.45.1.2
Length = 302
Score = 25.3 bits (56), Expect = 6.9
Identities = 6/24 (25%), Positives = 10/24 (41%)
Query: 64 VRVFCLKNNVVCCCGLDKHRVHQF 87
VR FC++ + + QF
Sbjct: 170 VRKFCIQQVGDVTNRKPQRLITQF 193
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
0.327 0.143 0.451
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,886,775
Number of extensions: 102673
Number of successful extensions: 271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 255
Number of HSP's successfully gapped: 27
Length of query: 122
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 40
Effective length of database: 4,412,271
Effective search space: 176490840
Effective search space used: 176490840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.5 bits)