RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8860
(374 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 = 225 bits (577), Expect = 9e-74
Identities = 72/155 (46%), Positives = 107/155 (69%)
Query: 122 GKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFTAINNSRIAKSM 181
K P+ +P V+V +N IT+KG G L + N+ V +K+ N L F + +
Sbjct: 4 AKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQ 63
Query: 182 SGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICE 241
+GT R+++N+M+IGVT+GF KKLQL+GVG+RA ++ N +NL LGFSHP+ +++P I E
Sbjct: 64 AGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAE 123
Query: 242 TPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276
P+QTEI++KG +KQ +G VAA++R Y +PEPYKG
Sbjct: 124 CPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKG 158
>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 = 220 bits (562), Expect = 2e-71
Identities = 68/155 (43%), Positives = 101/155 (65%)
Query: 122 GKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFTAINNSRIAKSM 181
GK PI IP V VT+N N +T+KGP G L + + + I + NV+ T ++ + +++
Sbjct: 4 GKKPIEIPAGVTVTVNGNTVTVKGPKGELTRTFHPDMTITVEGNVITVTRPSDEKHHRAL 63
Query: 182 SGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICE 241
GT RS++ NM+ GV+KG+EK L+L+GVG+RA + L L +G+SHP+ + + E
Sbjct: 64 HGTTRSLLANMVEGVSKGYEKALELVGVGYRASKQGKKLVLSVGYSHPVEIEPEEGLEIE 123
Query: 242 TPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276
PSQT+I++KG +KQ VG +AA IR PEPYKG
Sbjct: 124 VPSQTKIIVKGADKQRVGELAANIRAVRPPEPYKG 158
>3bbo_I Ribosomal protein L6; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 223
Score = 220 bits (563), Expect = 5e-71
Identities = 64/177 (36%), Positives = 92/177 (51%), Gaps = 4/177 (2%)
Query: 104 VIISTASGIITDRKARSM---GKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNI 160
G + GK PI +P NV + L + +KGPLG L V +
Sbjct: 26 STPFAQVGYSSKTIECKESRIGKQPIAVPSNVTIALEGQDLKVKGPLGELALTYPREVEL 85
Query: 161 K-NDSNVLYFTAINNSRIAKSMSGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKNY 219
+S L +R A M G R++ +NM++GV+KGFEKKL L+GVG+RA ++
Sbjct: 86 TKEESGFLRVKKTVETRRANQMHGLFRTLTDNMVVGVSKGFEKKLILVGVGYRATVDGKE 145
Query: 220 LNLILGFSHPILYKIPFDIICETPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276
L L LGFSHP+ +IP + + T I + G +K +G AA +R++ PEPYKG
Sbjct: 146 LVLNLGFSHPVKMQIPDSLKVKVEENTRITVSGYDKSEIGQFAATVRKWRPPEPYKG 202
>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 = 213 bits (545), Expect = 6e-69
Identities = 54/155 (34%), Positives = 89/155 (57%)
Query: 122 GKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFTAINNSRIAKSM 181
G++PI +P V V + ++ +KGP G L+ + + + + V+ ++ R KS+
Sbjct: 5 GRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERRHKSL 64
Query: 182 SGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICE 241
G R++I N + GV++G+ K+L + G+G+RA++ L L +GFSHP++ + P I E
Sbjct: 65 HGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEGITFE 124
Query: 242 TPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276
P T + + GI+KQ VG VAA IR KP Y
Sbjct: 125 VPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHE 159
>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 = 214 bits (547), Expect = 9e-69
Identities = 55/163 (33%), Positives = 89/163 (54%), Gaps = 3/163 (1%)
Query: 117 KARSM---GKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFTAIN 173
K +M GK PI +P V V +KGP G L N + ++ D + L +
Sbjct: 24 KEDNMSRIGKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPS 83
Query: 174 NSRIAKSMSGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYK 233
+++ +++ G R+++ N + GV+ G+ L+L GVGFRAK+ L + +G+SHP++ +
Sbjct: 84 DAQKHRALHGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIE 143
Query: 234 IPFDIICETPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276
P + P T I + GI+KQ VG VAA +R+ KP+ Y G
Sbjct: 144 PPAGVTFAVPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHG 186
>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 = 212 bits (542), Expect = 2e-68
Identities = 53/155 (34%), Positives = 86/155 (55%)
Query: 122 GKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIKNDSNVLYFTAINNSRIAKSM 181
GK PI +P V V +KGP G L N + ++ D + L ++++ +++
Sbjct: 5 GKQPIAVPSGVTVNAQDGVFKVKGPKGELTVPYNTELTVRQDGDQLLVERPSDAQKHRAL 64
Query: 182 SGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKNYLNLILGFSHPILYKIPFDIICE 241
G R+++ N + GV+ G+ L+L GVGFRAK+ L + +G+SHP++ + P +
Sbjct: 65 HGLTRTLVANAVKGVSDGYTINLELRGVGFRAKLTGKALEMNIGYSHPVIIEPPAGVTFA 124
Query: 242 TPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276
P T I + GI+KQ VG VAA +R+ KP+ Y G
Sbjct: 125 VPEPTRIDVSGIDKQLVGQVAANVRKVRKPDAYHG 159
>1s03_H 30S ribosomal protein S8; protein-RNA complex, SPC operon,
transcription-RN; 2.70A {Escherichia coli} SCOP:
d.140.1.1 PDB: 1p6g_H 1p87_H 2avy_H 2aw7_H 2i2p_H 2i2u_H
2qal_H* 2qan_H* 2qb9_H* 2qbb_H* 2qbd_H 2qbf_H 2qbh_H*
2qbj_H* 2qou_H* 2qow_H* 2qoy_H* 2qp0_H* 2vho_H 2vhp_H
...
Length = 129
Score = 187 bits (478), Expect = 2e-59
Identities = 70/121 (57%), Positives = 92/121 (76%), Gaps = 2/121 (1%)
Query: 2 SMSDPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFEL 61
SM DPIADMLT IRNGQ NK + MPSSK+K+AIA VLK+EG+I+DF + K EL
Sbjct: 1 SMQDPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEG--DTKPEL 58
Query: 62 KILLKYYMNRPVIECLKRVSRPGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKARSM 121
++ LKY+ + V+E ++RVSRPGLRIYK KD +PK+M GLG+ ++ST+ G++TDR AR
Sbjct: 59 ELTLKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQA 118
Query: 122 G 122
G
Sbjct: 119 G 119
>1sei_A Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus
stearothermophilus} SCOP: d.140.1.1
Length = 130
Score = 183 bits (467), Expect = 7e-58
Identities = 59/120 (49%), Positives = 87/120 (72%), Gaps = 1/120 (0%)
Query: 3 MSDPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELK 62
M+DPIADMLT IRN +V +K+ +P+SKIK IA++LK EG+I+D+ I+ + L+
Sbjct: 2 MTDPIADMLTAIRNANMVRHEKLEVPASKIKREIAEILKREGFIRDYEYIE-DNKQGILR 60
Query: 63 ILLKYYMNRPVIECLKRVSRPGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKARSMG 122
I LKY N VI LKR+S+PGLR+Y +P+++NGLG+ I+ST+ G++TD++AR G
Sbjct: 61 IFLKYGPNERVITGLKRISKPGLRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQKG 120
>2vqe_H 30S ribosomal protein S8, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP:
d.140.1.1 PDB: 1eg0_E* 1fka_H 1gix_K* 1hnw_H* 1hnx_H*
1hnz_H* 1hr0_H 1ibk_H* 1ibl_H* 1ibm_H 1j5e_H 1jgo_K*
1jgp_K* 1jgq_K* 1ml5_K* 1n32_H* 1n33_H* 1n34_H 1n36_H
1pns_H ...
Length = 138
Score = 178 bits (453), Expect = 1e-55
Identities = 51/128 (39%), Positives = 78/128 (60%), Gaps = 9/128 (7%)
Query: 3 MSDPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELK 62
++DPIADMLT IRN V K+ +P+S+ K I ++L EG+IK + + K L+
Sbjct: 2 LTDPIADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVD-VDGKPYLR 60
Query: 63 ILLKYYMNR--------PVIECLKRVSRPGLRIYKNKDNIPKIMNGLGLVIISTASGIIT 114
+ LKY R VI ++R+S+PG R+Y IP++ GLG+ I+ST+ G++T
Sbjct: 61 VYLKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLT 120
Query: 115 DRKARSMG 122
DR+AR +G
Sbjct: 121 DREARKLG 128
>3bbn_H Ribosomal protein S8; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 134
Score = 173 bits (441), Expect = 6e-54
Identities = 52/124 (41%), Positives = 78/124 (62%), Gaps = 5/124 (4%)
Query: 3 MSDPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELK 62
D IAD++T IRN + K + + S+ I I K+L EG+I++ + +NK+ L
Sbjct: 2 GKDTIADIITCIRNADMNRKGTVRIVSTNITENIVKILLREGFIENARKHQ-ERNKYFLV 60
Query: 63 ILLKYYMNR--PVIE--CLKRVSRPGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKA 118
+ L++ N+ P + LKRVSRPGLRIY N IP+I+ G+G+ I+ST+ GI+TDR+A
Sbjct: 61 LTLRHRRNKKGPYLNTFHLKRVSRPGLRIYSNYQRIPRILGGMGIAILSTSRGIMTDREA 120
Query: 119 RSMG 122
R G
Sbjct: 121 RLEG 124
>3rf2_A 30S ribosomal protein S8; RNA-binding protein, hyperthermophilic
bacterium, ribosome; 2.16A {Aquifex aeolicus}
Length = 168
Score = 166 bits (423), Expect = 7e-51
Identities = 49/158 (31%), Positives = 75/158 (47%), Gaps = 36/158 (22%)
Query: 1 MSMSDPIADMLTYIRNGQIVNKKKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFK---- 56
MS DPIADM + I+N + + +PSSK+K I VLK EG+I+D+ +K K
Sbjct: 1 MSAVDPIADMFSAIKNAIMRRDDFLYVPSSKLKERILDVLKKEGFIQDWEALKGEKYEEE 60
Query: 57 -----------------------------NKFELKILLKYYMNR---PVIECLKRVSRPG 84
++ +KI LKY + I + +VS+ G
Sbjct: 61 YKKMKELAEKSPNPKMKRYLKQLEEYNKGTQYPIKIYLKYLDPKKRKSAITNIVKVSKGG 120
Query: 85 LRIYKNKDNIPKIMNGLGLVIISTASGIITDRKARSMG 122
R+Y +P + GLG+ I+ST +G++TD +AR M
Sbjct: 121 RRVYAGVRTMPYVKRGLGIAIVSTDAGVMTDHEARRMR 158
>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 = 165 bits (420), Expect = 3e-50
Identities = 37/162 (22%), Positives = 72/162 (44%), Gaps = 7/162 (4%)
Query: 121 MGKMPIFIPPNVEVTLNSNKITLKGPLGILKQN-KNNLVNIKNDSNVLYFTAINNSRIAK 179
M ++ + IP +V+ + IT++G G + + +++ D + + + ++
Sbjct: 1 MPRVELEIPEDVDAEQDHLDITVEGDNGSVTRRLWYPDIDVSVDGDTVVIESDEDNAKTM 60
Query: 180 SMSGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKN----YLNLILGFSHPILYKIP 235
S GT +S I NM GVT+G+E +++ F ++ + LG P I
Sbjct: 61 STIGTFQSHIENMFHGVTEGWEYGMEVFYSHFPMQVNVEGDEVVIENFLGEKAPRRTTIH 120
Query: 236 FDIICETPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKGI 277
D E E+ + G + +AVG AA+I + + K +
Sbjct: 121 GDTDVEIDG-EELTVSGPDIEAVGQTAADIEQLTRIND-KDV 160
>1i6u_A 30S ribosomal protein S8P; protein-RNA interactions, ribosome, RNA,
X-RAY crystallography; 2.60A {Methanocaldococcus
jannaschii} SCOP: d.140.1.1
Length = 130
Score = 158 bits (401), Expect = 5e-48
Identities = 36/124 (29%), Positives = 64/124 (51%), Gaps = 6/124 (4%)
Query: 1 MSMSDPIADMLTYIRNGQIVNKKKI-IMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKF 59
MS+ DP+A+ L +I N + V KK + I P+SK+ + KV++D GYI +F I+
Sbjct: 1 MSLMDPLANALNHISNCERVGKKVVYIKPASKLIGRVLKVMQDNGYIGEFEFIE-DGRAG 59
Query: 60 ELKILLKYYMNR-PVIECLKRVSRPGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKA 118
K+ L +N+ I+ V + G ++ G++I+ST G+++ +A
Sbjct: 60 IFKVELIGKINKCGAIKPRFPVKKFGYEKFE---KRYLPARDFGILIVSTTQGVMSHEEA 116
Query: 119 RSMG 122
+ G
Sbjct: 117 KKRG 120
>3u5c_W 40S ribosomal protein S22-A; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_H 3o30_O 3o2z_O 3u5g_W 1s1h_H 3jyv_H* 3iz6_H 2zkq_h
Length = 130
Score = 151 bits (384), Expect = 2e-45
Identities = 32/123 (26%), Positives = 61/123 (49%), Gaps = 4/123 (3%)
Query: 1 MSMSDPIADMLTYIRNGQIVNKKK-IIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKF 59
M+ S +AD L I N + K++ +I PSSK+ I +V++ GYI +F I ++
Sbjct: 1 MTRSSVLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRSG- 59
Query: 60 ELKILLKYYMNRPVIECLKRVSRPGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKAR 119
++ + L +N+ + + + G + +P G VI++T++GI+ +AR
Sbjct: 60 KIVVQLNGRLNKCGVISPRFNVKIGDIEKWTANLLPA--RQFGYVILTTSAGIMDHEEAR 117
Query: 120 SMG 122
Sbjct: 118 RKH 120
>2xzm_H Ribosomal protein S8 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_H
Length = 130
Score = 149 bits (378), Expect = 1e-44
Identities = 28/124 (22%), Positives = 58/124 (46%), Gaps = 6/124 (4%)
Query: 1 MSMSDPIADMLTYIRNGQIVNKKK-IIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKF 59
M + +A+ L + N + + KK+ ++ P SK+ + ++++ GYI +F +I ++K
Sbjct: 1 MVKVNILAECLKDLVNAEKMGKKQVLLRPVSKVVLKFLRIMQKNGYIGEFEVIDDHRSK- 59
Query: 60 ELKILLKYYMNR-PVIECLKRVSRPGLRIYKNKDNIPKIMNGLGLVIISTASGIITDRKA 118
++ + L +N+ VI V + N G V+++T GI+T +
Sbjct: 60 KVVVELIGRINKCGVISPRYDVPLADFEKWTNNILPS---RQFGNVVLTTTYGILTHEEC 116
Query: 119 RSMG 122
R
Sbjct: 117 RKRH 120
>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 = 147 bits (372), Expect = 5e-43
Identities = 34/166 (20%), Positives = 73/166 (43%), Gaps = 15/166 (9%)
Query: 123 KMPIFIPPNVEVTLNSNKITLKGPLGILKQ--NKNNLVNIKNDSNVLYFTAINNSRIAKS 180
+ I +P V V++ S + + GP G L + ++ K ++ ++ N R +
Sbjct: 7 EQQIEVPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNGGRKHVA 66
Query: 181 MSGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKNY--------LNLILGFSHPILY 232
T++S+++NMI GVTKG++ K++ + F + + LG
Sbjct: 67 ALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGDKKIRNV 126
Query: 233 KIPFDIICE--TPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276
+ + E T + EI++ G + + V AA++++ + +
Sbjct: 127 PVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICR---VRN 169
>3r8s_O 50S ribosomal protein L18; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3fik_O 2wwq_O 3oat_O* 3oas_O* 3ofd_O 3ofc_O 3ofr_O*
3ofz_O* 3og0_O 3ofq_O 3r8t_O 3i1n_O 1p85_M 1p86_M 1vs8_O
1vs6_O 2aw4_O 2awb_O 1vt2_O 2i2v_O ...
Length = 116
Score = 143 bits (364), Expect = 9e-43
Identities = 49/100 (49%), Positives = 73/100 (73%), Gaps = 5/100 (5%)
Query: 276 GINRLMVHRTNLHIYANIIS-SNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQR 334
G RL+VHRT HIYA +I+ + +++L++AST+EK + +L GN AA+ +G+
Sbjct: 21 GATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIA----EQLKYTGNKDAAAAVGKA 76
Query: 335 IAKKALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLNF 374
+A++AL+ GI V+FDRSGF+YHGR++ LADAAR+ GL F
Sbjct: 77 VAERALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF 116
>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 = 142 bits (359), Expect = 4e-41
Identities = 34/162 (20%), Positives = 61/162 (37%), Gaps = 11/162 (6%)
Query: 121 MGKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNL---VNIKNDSNVLYFTAINNSRI 177
+ + IP V V + + +T++GP G L +N +L + L A +R
Sbjct: 5 LASETMEIPEGVTVQVAAKVVTVEGPRGKLTRNFKHLNLDFQLLEGGRKLQVDAWFGTRR 64
Query: 178 AKSMSGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIEKNYLNLI------LGFSHPIL 231
+ T S + N+I GVTKG+ K++ + F N LG
Sbjct: 65 TMAAIRTAISHVQNLITGVTKGYRYKMRFVYAHFPINASITNSNTAIEIRNFLGEKKVRK 124
Query: 232 YKIPFDIICE--TPSQTEILIKGINKQAVGHVAAEIRRYYKP 271
+ + + E+++ G + + V AA I +
Sbjct: 125 VDMLEGVTILRSEKVKDELVLDGNDIELVSRSAALINQKCHV 166
>2zkr_e 60S ribosomal protein L9; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 192
Score = 139 bits (352), Expect = 6e-40
Identities = 36/170 (21%), Positives = 69/170 (40%), Gaps = 19/170 (11%)
Query: 121 MGKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKN----NLVNIKNDSNVLYFTAINNSR 176
+ + IP NV++TL + +KGP G L+++ N L + L +R
Sbjct: 5 LSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKWWGNR 64
Query: 177 IAKSMSGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIE----------KNYLNLILGF 226
+ T+ S + NMI GVT GF K++ + F + +N+L +
Sbjct: 65 KELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLG--EKY 122
Query: 227 SHPILYKIPFDIICETPSQTEILIKGINKQAVGHVAAEIRRYYKPEPYKG 276
+ + + E++++G + + V + AA I+ + K
Sbjct: 123 IRRVRMRPGVACSVSQAQKDELILEGNDIELVSNSAALIQ---QATTVKN 169
>3bbo_Q Ribosomal protein L18; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 161
Score = 135 bits (341), Expect = 8e-39
Identities = 45/97 (46%), Positives = 58/97 (59%), Gaps = 3/97 (3%)
Query: 279 RLMVHRTNLHIYANIIS-SNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAK 337
RL V R+N H+Y +I S L SAST++K + L+ A +G+ IA
Sbjct: 67 RLCVFRSNKHLYVQVIDDSKMHTLASASTMQKSISEELDYS--SSPTIEVAKKVGEVIAS 124
Query: 338 KALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLNF 374
L+ GITKVAFDR G+ YHGR+K LADAAR+ GL F
Sbjct: 125 ACLEKGITKVAFDRGGYPYHGRVKALADAAREKGLQF 161
>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 = 133 bits (337), Expect = 8e-38
Identities = 32/161 (19%), Positives = 66/161 (40%), Gaps = 10/161 (6%)
Query: 121 MGKMPIFIPPNVEVTLNSNKITLKGPLGILKQ--NKNNLVNIKNDSNVLYFTAINNSRIA 178
+ ++ + IP V +T + +KGPLG +K+ ++ K ++ + SR
Sbjct: 5 LTEVNVPIPDKVTITAKQRVVEVKGPLGTIKRAFRYASVDIQKPTADNVKLQIWQASRKE 64
Query: 179 KSMSGTMRSIINNMIIGVTKGFEKKLQLIGVGFRAKIE------KNYLNLILGFSHPILY 232
+++ ++ S I NMI GVT+G++ K++L F + + LG
Sbjct: 65 RAVLQSIASQIKNMIRGVTEGYKFKMKLAFAHFPIQEAVAKDGSSIEIKHFLGEKRIRRI 124
Query: 233 KIPFDIICETPSQ--TEILIKGINKQAVGHVAAEIRRYYKP 271
+ + + + ++GI+ V A I +
Sbjct: 125 QALPGVKISRKDEEKNTLTLQGIDLNNVSQTCALIHQSCLV 165
>1ovy_A 50S ribosomal protein L18; ribosome; NMR {Geobacillus
stearothermophilus} SCOP: c.55.4.1
Length = 120
Score = 130 bits (330), Expect = 1e-37
Identities = 48/97 (49%), Positives = 63/97 (64%), Gaps = 7/97 (7%)
Query: 279 RLMVHRTNLHIYANIIS-SNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAK 337
RL V R+N HIYA II + + ++SASTL+KE L N AA +G+ +AK
Sbjct: 30 RLSVFRSNKHIYAQIIDDTKSATIVSASTLDKEF------GLDSTNNIEAAKKVGELVAK 83
Query: 338 KALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLNF 374
+AL+ GI +V FDR G+ YHGR+K LADAAR+ GL F
Sbjct: 84 RALEKGIKQVVFDRGGYLYHGRVKALADAAREAGLEF 120
>2zjr_L 50S ribosomal protein L18; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.55.4.1 PDB: 1sm1_M* 2zjp_L* 2zjq_L
1nkw_M 3cf5_L* 3dll_L* 3pio_L* 3pip_L* 1nwy_M* 1nwx_M*
1xbp_M* 1pnu_M 1pny_M 1vor_P 1vou_P 1vow_P 1voy_P 1vp0_P
Length = 114
Score = 127 bits (321), Expect = 2e-36
Identities = 40/97 (41%), Positives = 58/97 (59%), Gaps = 11/97 (11%)
Query: 279 RLMVHRTNLHIYANIIS-SNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAK 337
RL V+R++ HIYA II S + L +AS+ + G T A+ +G+ +A
Sbjct: 28 RLSVYRSSKHIYAQIIDDSRGQTLAAASSAALK----------SGNKTDTAAAVGKALAA 77
Query: 338 KALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLNF 374
A + GI +V FDR ++YHGR+K LADAAR+ GL+F
Sbjct: 78 AAAEKGIKQVVFDRGSYKYHGRVKALADAAREGGLDF 114
>3v2d_S 50S ribosomal protein L18; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_M 2hgj_R 2hgq_R 2hgu_R 1vsa_M 2j03_S 2jl6_S 2jl8_S
2v47_S 2v49_S 2wdi_S 2wdj_S 2wdl_S 2wdn_S 2wh2_S 2wh4_S
2wrj_S 2wrl_S 2wro_S 2wrr_S ...
Length = 112
Score = 126 bits (320), Expect = 3e-36
Identities = 43/97 (44%), Positives = 59/97 (60%), Gaps = 10/97 (10%)
Query: 279 RLMVHRTNLHIYANIIS-SNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIAK 337
RL V R+ HIYA II L+SAS+L ++ KG T A +G+ +A+
Sbjct: 25 RLSVFRSLKHIYAQIIDDEKGVTLVSASSLALKL---------KGNKTEVARQVGRALAE 75
Query: 338 KALKIGITKVAFDRSGFRYHGRIKFLADAARKNGLNF 374
KAL +GI +VAFDR ++YHGR+K LA+ AR+ GL F
Sbjct: 76 KALALGIKQVAFDRGPYKYHGRVKALAEGAREGGLEF 112
>1vq8_N 50S ribosomal protein L18P; 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: c.55.4.1 PDB: 1vq4_N*
1vq5_N* 1vq6_N* 1vq7_N* 1s72_N* 1vq9_N* 1vqk_N* 1vql_N*
1vqm_N* 1vqn_N* 1vqo_N* 1vqp_N* 1yhq_N* 1yi2_N* 1yij_N*
1yit_N* 1yj9_N* 1yjn_N* 1yjw_N* 2otj_N* ...
Length = 187
Score = 89.1 bits (221), Expect = 3e-21
Identities = 19/103 (18%), Positives = 40/103 (38%), Gaps = 9/103 (8%)
Query: 276 GINRLMVHRTNLHIYANIISSNA---KILISASTLEKEVRLTLNTKLGKGGNTFAASIIG 332
G RL+ ++N H+ A +++ L SA + + GN +A + G
Sbjct: 31 GKPRLVARKSNKHVRAQLVTLGPNGDDTLASAHSSDLAEYG----WEAPTGNMPSAYLTG 86
Query: 333 QRIAKKALKIGITKVAFDR--SGFRYHGRIKFLADAARKNGLN 373
+A + G+ + D + ++ + + A GL+
Sbjct: 87 LLAGLRAQEAGVEEAVLDIGLNSPTPGSKVFAIQEGAIDAGLD 129
>2cql_A OK/SW-CL.103, 60S ribosomal protein L9; N-terminal domain, alpha
and beta (A+B), structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.141.1.1
Length = 100
Score = 84.3 bits (209), Expect = 2e-20
Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 4/86 (4%)
Query: 121 MGKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKN----NLVNIKNDSNVLYFTAINNSR 176
+ + IP NV++TL + +KGP G L+++ N L + L +R
Sbjct: 12 LSNQTVDIPENVDITLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKWWGNR 71
Query: 177 IAKSMSGTMRSIINNMIIGVTKGFEK 202
+ T+ S + NMI GVT G
Sbjct: 72 KELATVRTICSHVQNMIKGVTLGSGP 97
>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 = 52.2 bits (124), Expect = 2e-07
Identities = 40/364 (10%), Positives = 99/364 (27%), Gaps = 94/364 (25%)
Query: 29 SSKIKIAIAKVLKD--EGYIKDF-------FIIKCFKNKFELKILLK--------YYMNR 71
+ + + +L + ++ +F + E+ ++ +
Sbjct: 11 TGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKE-EIDHIIMSKDAVSGTLRL-- 67
Query: 72 PVIECLKRVSRPGLRIYKN------KDNIPKIMNGLGLVIISTA--SGIITDRKARSMGK 123
L + + + N +M+ + + + + +++ R
Sbjct: 68 --FWTLLS---KQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYND 122
Query: 124 MPIFIPPNV----EVT--------LNSNK-ITLKGPLGILKQN------KNNLVNIKNDS 164
+F NV L K + + G LG K + V K D
Sbjct: 123 NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182
Query: 165 NVLYFTAINNSRIAKSMSGTMRSIINNMIIGVTKGFEKKL-QLIGVGFRAKIEKNYL-NL 222
+ + N + + ++ ++ + + + + R + L L
Sbjct: 183 KIFWLNLKNCNSPETVLE-----MLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRL 237
Query: 223 ILGFSHP----IL-----YKI--PFDIICETPSQTEILIKGINKQAVGHVAAEIRRYYKP 271
+ + +L K F++ C+ IL+ KQ ++A +
Sbjct: 238 LKSKPYENCLLVLLNVQNAKAWNAFNLSCK------ILLTTRFKQVTDFLSAATTTHISL 291
Query: 272 EPYKGINRLMVHRTNLHIYANIISSNAKILISASTLEKEVRLTLNTKLGKGGNTFAASII 331
+ + + + + L +EV N SII
Sbjct: 292 DH---HSMTLTPDEVKSLLLKYLD------CRPQDLPREV---------LTTNPRRLSII 333
Query: 332 GQRI 335
+ I
Sbjct: 334 AESI 337
Score = 51.0 bits (121), Expect = 4e-07
Identities = 57/397 (14%), Positives = 126/397 (31%), Gaps = 117/397 (29%)
Query: 5 DPIADMLTYI-------RNGQIVNKKKI--IMPSSKIKIAIAKVLKDEGYI--------- 46
P YI + Q+ K + + P K++ A+ + L+ +
Sbjct: 104 QPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLE-LRPAKNVLIDGVLGSG 162
Query: 47 KDFFIIK-C----FKNKFELKILLKYYMNRPVIECLKRVSRPGLRIYKNKDNIPKIMNGL 101
K + + C + K + KI +++N LK + P + + +++ L
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKI---FWLN------LKNCNSP--------ETVLEMLQKL 205
Query: 102 GLVIISTASGIITDRKARSMGKMPIFIPPNVEVTLNSNKITLKGPLGILKQNKNNLVNIK 161
I N+++ ++S + L+ L K +N L+ +
Sbjct: 206 LYQI-------------DPNWTSRSDHSSNIKLRIHSIQAELRR-LLKSKPYENCLL-VL 250
Query: 162 NDSNVLYFTAINNSRIAKSMSG------TMR--SIINNMIIGVTKGFEKKLQLIGVGFRA 213
+ + N++ + + T R + + + L +
Sbjct: 251 LN--------VQNAKAWNAFNLSCKILLTTRFKQVTD--FLSAATTTHISLDHHSMTLTP 300
Query: 214 KIEKNYLNLILGFS-----------HPILYKIPFDIICETPSQTEILIKGINKQAVGHV- 261
K+ L L +P I + I + + + K +N + +
Sbjct: 301 DEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNW-KHVNCDKLTTII 359
Query: 262 --------AAEIRRYYKPEPYKGINRLMVHRTNLHIYANIISSNAKILISASTLEKEVRL 313
AE R+ + RL V + HI ++S ++ + +V +
Sbjct: 360 ESSLNVLEPAEYRKMFD--------RLSVFPPSAHIPTILLS----LIWFDVI-KSDVMV 406
Query: 314 TLNTKLGKGGNTFAASIIGQRIAKKALKIGITKVAFD 350
+N KL K S++ ++ K I I + +
Sbjct: 407 VVN-KLHK------YSLVEKQ--PKESTISIPSIYLE 434
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.3 bits (67), Expect = 0.51
Identities = 7/26 (26%), Positives = 12/26 (46%), Gaps = 3/26 (11%)
Query: 255 KQAVGHVAAEIRRYYKPE--PYKGIN 278
KQA+ + A + + Y + P I
Sbjct: 19 KQALKKLQASL-KLYADDSAPALAIK 43
>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 = 30.8 bits (69), Expect = 0.99
Identities = 20/101 (19%), Positives = 30/101 (29%), Gaps = 18/101 (17%)
Query: 68 YMNRPVIECL-KR-----VSRPGLRIYK-NKDNIPK---IMNGL--GLVIISTASGIITD 115
Y + + R G I +N P I G G I S +I +
Sbjct: 1636 YKTSKAAQDVWNRADNHFKDTYGFSILDIVINN-PVNLTIHFGGEKGKRIRENYSAMIFE 1694
Query: 116 RKARSMGKM-PIFIPPNVEVTLNSNKITLKGPLGILKQNKN 155
K IF E+ +S T + G+L +
Sbjct: 1695 TIVDGKLKTEKIF----KEINEHSTSYTFRSEKGLLSATQF 1731
>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase,
A1AO, ATP synthesis, hydrogen ION transport, ION
transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A*
3b2q_A* 2rkw_A* 3eiu_A*
Length = 469
Score = 28.5 bits (64), Expect = 4.1
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 3 MSDPIADMLTYIRNGQIV 20
++ PI D+ YI GQIV
Sbjct: 319 ITHPIPDLSGYITEGQIV 336
>3led_A 3-oxoacyl-acyl carrier protein synthase III; structural genomics,
PSI-2, protein structure initiative; HET: MSE; 1.45A
{Rhodopseudomonas palustris}
Length = 392
Score = 27.7 bits (62), Expect = 6.3
Identities = 12/85 (14%), Positives = 28/85 (32%), Gaps = 27/85 (31%)
Query: 277 INRLMVHRTNLHIYANIISSNAKILISASTLEKEVRLTLNTKLGKGGNTFAASIIGQRIA 336
+ R+ +H+ N+ N+ + ++ E + L+ NT +A I
Sbjct: 311 LKRMWLHQANI----NMNEIIGRKVLGRDPTRDENVIILD----DYANTSSAGSI----- 357
Query: 337 KKALKIGITKVAFDRSGFRYHGRIK 361
+AF ++ +
Sbjct: 358 ----------IAFH----KHQDDMA 368
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C
4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Length = 395
Score = 27.8 bits (61), Expect = 7.4
Identities = 5/48 (10%), Positives = 12/48 (25%)
Query: 23 KKIIMPSSKIKIAIAKVLKDEGYIKDFFIIKCFKNKFELKILLKYYMN 70
+I+ + + + Y D K E + +
Sbjct: 108 IEIVDAKKVPSTPMMTIYLTDEYKHDKEKALEVARKLEYTKIENVVSS 155
>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis,
ATP-binding, hydrogen ION TRA hydrolase, ION transport;
2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D
3j0j_D*
Length = 464
Score = 27.4 bits (61), Expect = 8.9
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 3 MSDPIADMLTYIRNGQIV 20
+ PI D+ YI GQI
Sbjct: 321 RTHPIPDLTGYITEGQIQ 338
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
0.322 0.139 0.391
Gapped
Lambda K H
0.267 0.0510 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,672,134
Number of extensions: 354771
Number of successful extensions: 895
Number of sequences better than 10.0: 1
Number of HSP's gapped: 840
Number of HSP's successfully gapped: 49
Length of query: 374
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 279
Effective length of database: 4,049,298
Effective search space: 1129754142
Effective search space used: 1129754142
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: 58 (26.6 bits)