RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 046142
(132 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 = 109 bits (274), Expect = 2e-31
Identities = 38/97 (39%), Positives = 59/97 (60%), Gaps = 2/97 (2%)
Query: 34 FLRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKNNVVCCCGLDKHR 93
F + L++VGVGY RA +G ++ L LG+ H V+ +P+ + C + G DK
Sbjct: 82 FTKKLQLVGVGY--RAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQV 139
Query: 94 VHQFAASVRSRKPPDPFKGKGIMCADEVIKKKVGKKK 130
+ Q AA +R+ + P+P+KGKG+ ADEV++ 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 = 107 bits (270), Expect = 1e-30
Identities = 33/101 (32%), Positives = 50/101 (49%), Gaps = 4/101 (3%)
Query: 34 FLRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKNNVVCCCGLDKHR 93
+ L++ GVG+ RA+ G+ L + +GY H V + P+ V + + G+DK
Sbjct: 83 YTINLELRGVGF--RAKLTGKALEMNIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQL 140
Query: 94 VHQFAASVRSRKPPDPFKGKGIMCADEVIKKKVGK--KKSK 132
V Q AA+VR + PD + 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 = 107 bits (269), Expect = 1e-30
Identities = 34/99 (34%), Positives = 52/99 (52%), Gaps = 2/99 (2%)
Query: 34 FLRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKNNVVCCCGLDKHR 93
+ + L I G+GY RA GR L L +G+ H V + P + + V G+DK +
Sbjct: 83 YSKELLIKGIGY--RARLVGRALELTVGFSHPVVVEPPEGITFEVPEPTRVRVSGIDKQK 140
Query: 94 VHQFAASVRSRKPPDPFKGKGIMCADEVIKKKVGKKKSK 132
V Q AA++R+ + P + KGI A 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 = 107 bits (270), Expect = 1e-30
Identities = 33/101 (32%), Positives = 50/101 (49%), Gaps = 4/101 (3%)
Query: 34 FLRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKNNVVCCCGLDKHR 93
+ L++ GVG+ RA+ G+ L + +GY H V + P+ V + + G+DK
Sbjct: 110 YTINLELRGVGF--RAKLTGKALEMNIGYSHPVIIEPPAGVTFAVPEPTRIDVSGIDKQL 167
Query: 94 VHQFAASVRSRKPPDPFKGKGIMCADEVIKKKVGK--KKSK 132
V Q AA+VR + PD + 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 = 107 bits (269), Expect = 3e-30
Identities = 40/99 (40%), Positives = 65/99 (65%), Gaps = 2/99 (2%)
Query: 34 FLRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKNNVVCCCGLDKHR 93
F + L +VGVGY RA +G+ L L LG+ H V++ +P ++++ +N + G DK
Sbjct: 126 FEKKLILVGVGY--RATVDGKELVLNLGFSHPVKMQIPDSLKVKVEENTRITVSGYDKSE 183
Query: 94 VHQFAASVRSRKPPDPFKGKGIMCADEVIKKKVGKKKSK 132
+ QFAA+VR +PP+P+KGKG+ +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 = 104 bits (263), Expect = 7e-30
Identities = 37/95 (38%), Positives = 57/95 (60%), Gaps = 2/95 (2%)
Query: 34 FLRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKNNVVCCCGLDKHR 93
+ + L++VGVGY RA +G+ L L +GY H VE+ + I + G DK R
Sbjct: 82 YEKALELVGVGY--RASKQGKKLVLSVGYSHPVEIEPEEGLEIEVPSQTKIIVKGADKQR 139
Query: 94 VHQFAASVRSRKPPDPFKGKGIMCADEVIKKKVGK 128
V + AA++R+ +PP+P+KGKGI 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 = 67.6 bits (166), Expect = 2e-15
Identities = 14/98 (14%), Positives = 31/98 (31%), Gaps = 4/98 (4%)
Query: 34 FLRFLKIVGVGYKARAEAEGRLLYLK--LGYVHDVELTVPSAVRIFCLKNNVVCCCGLDK 91
+ +++ + + EG + ++ LG T+ + + G D
Sbjct: 81 WEYGMEVFYSHFPMQVNVEGDEVVIENFLGEKAPRRTTIHGDTDVEIDGEELTVS-GPDI 139
Query: 92 HRVHQFAASVRSRKPPDPFKGKGIMCADEVIKKKVGKK 129
V Q AA + + K + I +K +
Sbjct: 140 EAVGQTAADIEQLTRIND-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 = 52.8 bits (127), Expect = 1e-09
Identities = 15/88 (17%), Positives = 30/88 (34%), Gaps = 9/88 (10%)
Query: 34 FLRFLKIVGVGYKA--RAEAEGRLLYLKL----GYVHDVELTVPSAVRIFCLKNNVVCCC 87
F ++ V + + G L+ ++ Y+ V + A + + + +
Sbjct: 88 FRYKMRSVYAHFPINVVIQENGSLVEIRNFLGEKYIRRVRMRPGVACSVSQAQKDELILE 147
Query: 88 GLDKHRVHQFAASVRSRKPPDPFKGKGI 115
G D V AA ++ K K I
Sbjct: 148 GNDIELVSNSAALIQQ---ATTVKNKDI 172
>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 = 45.8 bits (109), Expect = 4e-07
Identities = 14/90 (15%), Positives = 29/90 (32%), Gaps = 9/90 (10%)
Query: 32 AKFLRFLKIVGVGYKARAEAEGRLLYLK----LGYVHDVELTVPSAVRIFCLKN--NVVC 85
+ ++ V + A ++ LG ++ + V I + + +
Sbjct: 85 KGYRYKMRFVYAHFPINASITNSNTAIEIRNFLGEKKVRKVDMLEGVTILRSEKVKDELV 144
Query: 86 CCGLDKHRVHQFAASVRSRKPPDPFKGKGI 115
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 = 43.1 bits (102), Expect = 4e-06
Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 11/90 (12%)
Query: 33 KFLRFLKIVGVGYKA--RAEAEGRLLYLK--LGYVHDVELTVPSAVRI--FCLKNNVVCC 86
+ +K+ + +G + +K LG + V+I + N +
Sbjct: 85 GYKFKMKLAFAHFPIQEAVAKDGSSIEIKHFLGEKRIRRIQALPGVKISRKDEEKNTLTL 144
Query: 87 CGLDKHRVHQFAASVR-SRKPPDPFKGKGI 115
G+D + V Q A + S 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 = 40.8 bits (96), Expect = 2e-05
Identities = 15/90 (16%), Positives = 28/90 (31%), Gaps = 11/90 (12%)
Query: 34 FLRFLKIVGVGYKA------RAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKN--NVVC 85
+ ++ V + + A+ + LG + V V I N + +
Sbjct: 86 YKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGDKKIRNVPVRDGVTIEFSTNVKDEIV 145
Query: 86 CCGLDKHRVHQFAASVRSRKPPDPFKGKGI 115
G V Q AA ++ + K I
Sbjct: 146 LSGNSVEDVSQNAADLQQIC---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 = 37.3 bits (86), Expect = 7e-04
Identities = 37/160 (23%), Positives = 55/160 (34%), Gaps = 47/160 (29%)
Query: 1 MGANRTTPICNEDALNHMSNLCDKF---TLTWMEAKFLR--FLKIVGVGYKARA------ 49
M A T P+ L+H +L T ++ A L+ F KI+ + A
Sbjct: 1 MDAYSTRPL----TLSH-GSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPT 55
Query: 50 -EAEGRLLYLK-LGYV-HDVELTVPS--------AVRIF---CLKNNVVCCCGLDKHRVH 95
AE L K LGYV VE + + F L+ N D +H
Sbjct: 56 TPAE---LVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGN-------D---IH 102
Query: 96 QFAASVRSRKPPDPFKGKGIM----CADEVIKKKVGKKKS 131
AA + K K ++ A + K+ KK +
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSN 142
Score = 30.8 bits (69), Expect = 0.11
Identities = 18/93 (19%), Positives = 28/93 (30%), Gaps = 29/93 (31%)
Query: 28 TWME-----AKFLRFLKIVGVGYKARA-EAEGRLLYLKLGYVHD-VEL--TVPS---AVR 75
+W K + L +GV R EA L + D +E VPS ++
Sbjct: 288 SWESFFVSVRKAITVLFFIGV----RCYEAYPNT-SLPPSILEDSLENNEGVPSPMLSIS 342
Query: 76 IFCLKNNVVCCCGLDKHRVHQFAASVRSRKPPD 108
L + +V + S P
Sbjct: 343 ------------NLTQEQVQDYVNKTNSHLPAG 363
>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 = 26.7 bits (58), Expect = 3.2
Identities = 7/47 (14%), Positives = 16/47 (34%), Gaps = 3/47 (6%)
Query: 29 WMEAKFLRFLKIVGVGYKARAEAEGRLLYLKLG-YVHDVELTVPSAV 74
W + I+ AE R ++ +L + +P+ +
Sbjct: 347 WKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH--IPTIL 391
Score = 25.2 bits (54), Expect = 8.9
Identities = 14/86 (16%), Positives = 28/86 (32%), Gaps = 16/86 (18%)
Query: 22 CDKFTLTWMEAKFLRFLKIVGVGYKARAEAEGRLLYLKLGYVHDVELTVPSAVRIFCLKN 81
K TW+ K+ + + ++ +L L + E V ++ +
Sbjct: 161 SGK---TWVALDVCLSYKVQ-------CKMDFKIFWLNLKNCNSPET-VLEMLQKLLYQI 209
Query: 82 NVVCCCGLD-----KHRVHQFAASVR 102
+ D K R+H A +R
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQAELR 235
>2ixa_A Alpha-N-acetylgalactosaminidase; NAD, A-ECO conversion, hydrolase;
HET: NAD; 2.3A {Flavobacterium meningosepticum} PDB:
2ixb_A*
Length = 444
Score = 26.6 bits (58), Expect = 3.2
Identities = 3/22 (13%), Positives = 8/22 (36%)
Query: 88 GLDKHRVHQFAASVRSRKPPDP 109
G+D + F ++ +
Sbjct: 374 GMDYFLDNTFVECIKRNEAFPL 395
>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 = 7.0
Identities = 6/24 (25%), Positives = 10/24 (41%)
Query: 74 VRIFCLKNNVVCCCGLDKHRVHQF 97
VR FC++ + + QF
Sbjct: 170 VRKFCIQQVGDVTNRKPQRLITQF 193
>1peq_A Ribonucleoside-diphosphate reductase 2 alpha chain; stranded
alpha/beta barrel, protein-specificity-effector complex,
DTTP; HET: TTP; 2.80A {Salmonella typhimurium} SCOP:
a.98.1.1 c.7.1.2 PDB: 1peo_A* 1pem_A* 1peu_A* 2bq1_E*
Length = 714
Score = 25.3 bits (56), Expect = 7.3
Identities = 10/26 (38%), Positives = 12/26 (46%), Gaps = 10/26 (38%)
Query: 7 TP-ICNEDALN---------HMSNLC 22
P I ED +N +MSNLC
Sbjct: 363 YPYIMFEDTVNRANPIAGRINMSNLC 388
>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 = 8.2
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 49 AEAEGRLLYLKLGYVHDVELTVP 71
A G+ LY ++G+ E++ P
Sbjct: 128 ATEMGQPLYARMGWSPTTEMSKP 150
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
0.324 0.138 0.433
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: 2,027,482
Number of extensions: 110505
Number of successful extensions: 276
Number of sequences better than 10.0: 1
Number of HSP's gapped: 261
Number of HSP's successfully gapped: 24
Length of query: 132
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 49
Effective length of database: 4,384,350
Effective search space: 214833150
Effective search space used: 214833150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (23.9 bits)