RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 032911
(130 letters)
>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 = 191 bits (488), Expect = 1e-64
Identities = 103/130 (79%), Positives = 117/130 (90%)
Query: 1 MVRVSVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGK 60
M R SVL DAL ++ NAEK GKRQV+IRPSSKVIIKFL VMQKHGYIGEFEY+DDHR+GK
Sbjct: 1 MTRSSVLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRSGK 60
Query: 61 IVVELNGRLNKCGVISPRFDVGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKN 120
IVV+LNGRLNKCGVISPRF+V + +IE WTA LLP+RQFGY++LTTSAGIMDHEEARRK+
Sbjct: 61 IVVQLNGRLNKCGVISPRFNVKIGDIEKWTANLLPARQFGYVILTTSAGIMDHEEARRKH 120
Query: 121 VGGKVLGFFY 130
V GK+LGF Y
Sbjct: 121 VSGKILGFVY 130
>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 = 188 bits (479), Expect = 3e-63
Identities = 60/130 (46%), Positives = 90/130 (69%)
Query: 1 MVRVSVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGK 60
M + L +AL + N E+ GK+ V I+P+SK+I + L VMQ +GYIGEFE+++D RAG
Sbjct: 1 MSLMDPLANALNHISNCERVGKKVVYIKPASKLIGRVLKVMQDNGYIGEFEFIEDGRAGI 60
Query: 61 IVVELNGRLNKCGVISPRFDVGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKN 120
VEL G++NKCG I PRF V E + R LP+R FG ++++T+ G+M HEEA+++
Sbjct: 61 FKVELIGKINKCGAIKPRFPVKKFGYEKFEKRYLPARDFGILIVSTTQGVMSHEEAKKRG 120
Query: 121 VGGKVLGFFY 130
+GG++L + Y
Sbjct: 121 LGGRLLAYVY 130
>2xzm_H Ribosomal protein S8 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_H
Length = 130
Score = 184 bits (470), Expect = 7e-62
Identities = 82/130 (63%), Positives = 109/130 (83%)
Query: 1 MVRVSVLNDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGK 60
MV+V++L + LK + NAEK GK+QV++RP SKV++KFL +MQK+GYIGEFE +DDHR+ K
Sbjct: 1 MVKVNILAECLKDLVNAEKMGKKQVLLRPVSKVVLKFLRIMQKNGYIGEFEVIDDHRSKK 60
Query: 61 IVVELNGRLNKCGVISPRFDVGVKEIEGWTARLLPSRQFGYIVLTTSAGIMDHEEARRKN 120
+VVEL GR+NKCGVISPR+DV + + E WT +LPSRQFG +VLTT+ GI+ HEE R+++
Sbjct: 61 VVVELIGRINKCGVISPRYDVPLADFEKWTNNILPSRQFGNVVLTTTYGILTHEECRKRH 120
Query: 121 VGGKVLGFFY 130
GGK+LGFFY
Sbjct: 121 TGGKILGFFY 130
>3bbn_H Ribosomal protein S8; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 134
Score = 58.3 bits (142), Expect = 3e-12
Identities = 28/125 (22%), Positives = 48/125 (38%), Gaps = 23/125 (18%)
Query: 16 NAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVELN-GRLNKCGV 74
NA+ K V I S+ + + ++ + G+I + +V+ L R K
Sbjct: 15 NADMNRKGTVRI-VSTNITENIVKILLREGFIENARKHQERNKYFLVLTLRHRRNKKGPY 73
Query: 75 ISP-----------RFDVGVKEIEGWTARLLPSRQ--FGYIVLTTSAGIMDHEEARRKNV 121
++ R + I P G +L+TS GIM EAR + +
Sbjct: 74 LNTFHLKRVSRPGLRIYSNYQRI--------PRILGGMGIAILSTSRGIMTDREARLEGI 125
Query: 122 GGKVL 126
GG++L
Sbjct: 126 GGEIL 130
>1sei_A Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus
stearothermophilus} SCOP: d.140.1.1
Length = 130
Score = 57.1 bits (139), Expect = 8e-12
Identities = 30/124 (24%), Positives = 62/124 (50%), Gaps = 25/124 (20%)
Query: 16 NAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVEL---NG----- 67
NA ++ + P+SK+ + ++++ G+I ++EY++D++ G + + L
Sbjct: 15 NANMVRHEKLEV-PASKIKREIAEILKREGFIRDYEYIEDNKQGILRIFLKYGPNERVIT 73
Query: 68 ---RLNKCGVISPRFDVGVKEIEGWTARLLPSRQ--FGYIVLTTSAGIMDHEEARRKNVG 122
R++K G+ R V E+ P G +L+TS G++ +EAR+K G
Sbjct: 74 GLKRISKPGL---RVYVKAHEV--------PRVLNGLGIAILSTSQGVLTDKEARQKGTG 122
Query: 123 GKVL 126
G+++
Sbjct: 123 GEII 126
>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 = 56.4 bits (137), Expect = 2e-11
Identities = 35/129 (27%), Positives = 55/129 (42%), Gaps = 27/129 (20%)
Query: 16 NAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVEL-------NGR 68
NA + K + P+S+ + L ++ + G+I +E VD + V L
Sbjct: 15 NATRVYKESTDV-PASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKYGPRRQGPD 73
Query: 69 LNKCGVIS-------P--RFDVGVKEIEGWTARLLPSRQ--FGYIVLTTSAGIMDHEEAR 117
VI P R VGVKEI P + G +L+TS G++ EAR
Sbjct: 74 PRPEQVIHHIRRISKPGRRVYVGVKEI--------PRVRRGLGIAILSTSKGVLTDREAR 125
Query: 118 RKNVGGKVL 126
+ VGG+++
Sbjct: 126 KLGVGGELI 134
>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 = 55.5 bits (135), Expect = 4e-11
Identities = 29/124 (23%), Positives = 56/124 (45%), Gaps = 26/124 (20%)
Query: 16 NAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVEL---NG----- 67
N + K V + PSSK+ + V+++ G+I +F+ D + ++ + L G
Sbjct: 15 NGQAANKAAVTM-PSSKLKVAIANVLKEEGFIEDFKVEGDTK-PELELTLKYFQGKAVVE 72
Query: 68 ---RLNKCGVISPRFDVGVKEIEGWTARLLPSRQ--FGYIVLTTSAGIMDHEEARRKNVG 122
R+++ G+ R E+ P G V++TS G+M AR+ +G
Sbjct: 73 SIQRVSRPGL---RIYKRKDEL--------PKVMAGLGIAVVSTSKGVMTDRAARQAGLG 121
Query: 123 GKVL 126
G+++
Sbjct: 122 GEII 125
>3rf2_A 30S ribosomal protein S8; RNA-binding protein, hyperthermophilic
bacterium, ribosome; 2.16A {Aquifex aeolicus}
Length = 168
Score = 47.5 bits (113), Expect = 6e-08
Identities = 28/150 (18%), Positives = 52/150 (34%), Gaps = 40/150 (26%)
Query: 16 NAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIGEFEYVDDHRAGKIVVELNGRLNKCGVI 75
NA R + + PSSK+ + L V++K G+I ++E + + + ++ K
Sbjct: 16 NAIMRRDDFLYV-PSSKLKERILDVLKKEGFIQDWEALKGEKYEEEYKKMKELAEKSPNP 74
Query: 76 SPRFDVGVKEIEGWTARLL-------------------------PSRQ------------ 98
+ + E + R+
Sbjct: 75 KMKRYLKQLEEYNKGTQYPIKIYLKYLDPKKRKSAITNIVKVSKGGRRVYAGVRTMPYVK 134
Query: 99 --FGYIVLTTSAGIMDHEEARRKNVGGKVL 126
G +++T AG+M EARR GG+V+
Sbjct: 135 RGLGIAIVSTDAGVMTDHEARRMRKGGEVI 164
>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 = 0.070
Identities = 24/155 (15%), Positives = 42/155 (27%), Gaps = 51/155 (32%)
Query: 11 LKSMYNAEKRGKRQVMIRPSSKVI-------IKFLLVM--QKHG----YIGE----FE-Y 52
+K+ A KR + +S + + + + Q G Y E ++ Y
Sbjct: 123 IKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQ--GNTDDYFEELRDLYQTY 180
Query: 53 ---VDD--HRAGKIVVELNGRLNKCGVISPR-FDVGVKEIEGW--TARLLPSR------- 97
V D + + + EL + + + I W P +
Sbjct: 181 HVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLN-----ILEWLENPSNTPDKDYLLSIP 235
Query: 98 ---------QFG-YIVLTTSAGIMDHEEARRKNVG 122
Q Y+V G E R G
Sbjct: 236 ISCPLIGVIQLAHYVVTAKLLG-FTPGELRSYLKG 269
Score = 26.9 bits (59), Expect = 2.4
Identities = 26/133 (19%), Positives = 43/133 (32%), Gaps = 42/133 (31%)
Query: 8 NDALKSMYNAEKRGKRQVMIRPSSKVIIKFLLVMQKHGYIG-EFEYVDDHRAG--KIVVE 64
N +++ ++GKR IR Y FE + D + KI E
Sbjct: 1668 NPVNLTIHFGGEKGKR---IR---------------ENYSAMIFETIVDGKLKTEKIFKE 1709
Query: 65 LNGRLNKC------GVIS------PR-FDVGVKEIEGWTAR-LLPSRQF------G-YIV 103
+N G++S P + E ++ L+P+ G Y
Sbjct: 1710 INEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAA 1769
Query: 104 LTTSAGIMDHEEA 116
L + A +M E
Sbjct: 1770 LASLADVMSIESL 1782
>1h2i_A RAD52, DNA repair protein RAD52 homolog; DNA-binding protein, DNA
recombination; HET: DNA; 2.7A {Homo sapiens} SCOP:
d.50.1.3 PDB: 1kn0_A
Length = 209
Score = 27.1 bits (59), Expect = 1.8
Identities = 18/58 (31%), Positives = 21/58 (36%), Gaps = 5/58 (8%)
Query: 47 IGEFEYVDDHRAGKIVVELNGRLNKCGVISPRFDVG---VKEIEGWTARLLPSRQFGY 101
G+ +Y I L RL IS R G V IEG L + FGY
Sbjct: 26 FGQCQY-TAEEYQAIQKALRQRLGP-EYISSRMAGGGQKVCYIEGHRVINLANEMFGY 81
>2cud_A SRC-like-adapter; SH3 domain, negative mitogenesis regulator,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 79
Score = 24.7 bits (54), Expect = 4.7
Identities = 6/19 (31%), Positives = 8/19 (42%)
Query: 84 KEIEGWTARLLPSRQFGYI 102
E W A L + + YI
Sbjct: 47 DEGGWWKAISLSTGRESYI 65
>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 = 25.6 bits (55), Expect = 6.6
Identities = 9/77 (11%), Positives = 25/77 (32%), Gaps = 19/77 (24%)
Query: 44 HGYIGEFEYVD-DHRAGKIVVELNGRLNKCGVISPRF--DVGVKEIEGWTARLLPSRQFG 100
H + +FE + ++ I+ V F + K+++ +L +
Sbjct: 3 HHHHMDFETGEHQYQYKDILS----------VFEDAFVDNFDCKDVQDMPKSILSKEEID 52
Query: 101 YIVLTTSAGIMDHEEAR 117
+I+ + +
Sbjct: 53 HII------MSKDAVSG 63
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 0.141 0.411
Gapped
Lambda K H
0.267 0.0834 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,081,811
Number of extensions: 122816
Number of successful extensions: 250
Number of sequences better than 10.0: 1
Number of HSP's gapped: 248
Number of HSP's successfully gapped: 18
Length of query: 130
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 47
Effective length of database: 4,384,350
Effective search space: 206064450
Effective search space used: 206064450
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: 41 (22.0 bits)
S2: 52 (23.6 bits)