RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13245
(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 = 199 bits (508), Expect = 1e-67
Identities = 102/130 (78%), Positives = 113/130 (86%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGK 60
M R +VL+DAL +INNAEK GKRQVLIRP SKVI+KFL VM KHGYIGEFE +DDHR+GK
Sbjct: 1 MTRSSVLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRSGK 60
Query: 61 IVVNLKGRLNKCGVISPRFDVPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEARRKH 120
IVV L GRLNKCGVISPRF+V I IEKWT NLLP+RQFGYV+LTTS GIMDHEEARRKH
Sbjct: 61 IVVQLNGRLNKCGVISPRFNVKIGDIEKWTANLLPARQFGYVILTTSAGIMDHEEARRKH 120
Query: 121 LGGKILGFFF 130
+ GKILGF +
Sbjct: 121 VSGKILGFVY 130
>2xzm_H Ribosomal protein S8 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_H
Length = 130
Score = 195 bits (497), Expect = 5e-66
Identities = 88/130 (67%), Positives = 112/130 (86%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGK 60
MV+VN+L++ LK + NAEK GK+QVL+RP SKV++KFL +M K+GYIGEFE++DDHR+ K
Sbjct: 1 MVKVNILAECLKDLVNAEKMGKKQVLLRPVSKVVLKFLRIMQKNGYIGEFEVIDDHRSKK 60
Query: 61 IVVNLKGRLNKCGVISPRFDVPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEARRKH 120
+VV L GR+NKCGVISPR+DVP+ EKWTNN+LPSRQFG VVLTT+ GI+ HEE R++H
Sbjct: 61 VVVELIGRINKCGVISPRYDVPLADFEKWTNNILPSRQFGNVVLTTTYGILTHEECRKRH 120
Query: 121 LGGKILGFFF 130
GGKILGFF+
Sbjct: 121 TGGKILGFFY 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 = 194 bits (496), Expect = 8e-66
Identities = 59/130 (45%), Positives = 89/130 (68%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGK 60
M ++ L++AL I+N E+ GK+ V I+P SK+I + L VM +GYIGEFE ++D RAG
Sbjct: 1 MSLMDPLANALNHISNCERVGKKVVYIKPASKLIGRVLKVMQDNGYIGEFEFIEDGRAGI 60
Query: 61 IVVNLKGRLNKCGVISPRFDVPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEARRKH 120
V L G++NKCG I PRF V EK+ LP+R FG ++++T+ G+M HEEA+++
Sbjct: 61 FKVELIGKINKCGAIKPRFPVKKFGYEKFEKRYLPARDFGILIVSTTQGVMSHEEAKKRG 120
Query: 121 LGGKILGFFF 130
LGG++L + +
Sbjct: 121 LGGRLLAYVY 130
>3bbn_H Ribosomal protein S8; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 134
Score = 63.3 bits (155), Expect = 4e-14
Identities = 28/135 (20%), Positives = 56/135 (41%), Gaps = 25/135 (18%)
Query: 7 LSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLK 66
++D + I NA+ K V I + + + ++++ G+I + +V+ L+
Sbjct: 6 IADIITCIRNADMNRKGTVRI-VSTNITENIVKILLREGFIENARKHQERNKYFLVLTLR 64
Query: 67 -GRLNKCGVISPRFDVPIRHIEKWTNNLLPSRQ--------------FGYVVLTTSGGIM 111
R K ++ ++ + + P + G +L+TS GIM
Sbjct: 65 HRRNKKGPYLNTF---HLKRVSR------PGLRIYSNYQRIPRILGGMGIAILSTSRGIM 115
Query: 112 DHEEARRKHLGGKIL 126
EAR + +GG+IL
Sbjct: 116 TDREARLEGIGGEIL 130
>1sei_A Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus
stearothermophilus} SCOP: d.140.1.1
Length = 130
Score = 62.9 bits (154), Expect = 5e-14
Identities = 35/129 (27%), Positives = 67/129 (51%), Gaps = 17/129 (13%)
Query: 7 LSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLK 66
++D L +I NA ++ + P SK+ + ++ + G+I ++E ++D++ G + + LK
Sbjct: 6 IADMLTAIRNANMVRHEKLEV-PASKIKREIAEILKREGFIRDYEYIEDNKQGILRIFLK 64
Query: 67 GRLNKCGVIS-------P--RFDVPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEAR 117
N+ VI+ P R V + + N L G +L+TS G++ +EAR
Sbjct: 65 YGPNE-RVITGLKRISKPGLRVYVKAHEVPRVLNGL------GIAILSTSQGVLTDKEAR 117
Query: 118 RKHLGGKIL 126
+K GG+I+
Sbjct: 118 QKGTGGEII 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 = 62.9 bits (154), Expect = 6e-14
Identities = 33/131 (25%), Positives = 58/131 (44%), Gaps = 13/131 (9%)
Query: 7 LSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLK 66
++D L I NA + K + P S+ + L ++ + G+I +E VD + V LK
Sbjct: 6 IADMLTRIRNATRVYKESTDV-PASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLK 64
Query: 67 GRLNKCGVISPRFDVPIRHIEK---------WTNNLLPSRQ--FGYVVLTTSGGIMDHEE 115
+ G V I HI + +P + G +L+TS G++ E
Sbjct: 65 YGPRRQGPDPRPEQV-IHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDRE 123
Query: 116 ARRKHLGGKIL 126
AR+ +GG+++
Sbjct: 124 ARKLGVGGELI 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 = 59.8 bits (146), Expect = 7e-13
Identities = 35/129 (27%), Positives = 58/129 (44%), Gaps = 18/129 (13%)
Query: 7 LSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLK 66
++D L I N + K V + P SK+ V V+ + G+I +F++ D + ++ + LK
Sbjct: 6 IADMLTRIRNGQAANKAAVTM-PSSKLKVAIANVLKEEGFIEDFKVEGDTK-PELELTLK 63
Query: 67 GRLNKCGVIS-------P--RFDVPIRHIEKWTNNLLPSRQFGYVVLTTSGGIMDHEEAR 117
K V+ P R + K L G V++TS G+M AR
Sbjct: 64 YFQGK-AVVESIQRVSRPGLRIYKRKDELPKVMAGL------GIAVVSTSKGVMTDRAAR 116
Query: 118 RKHLGGKIL 126
+ LGG+I+
Sbjct: 117 QAGLGGEII 125
>3rf2_A 30S ribosomal protein S8; RNA-binding protein, hyperthermophilic
bacterium, ribosome; 2.16A {Aquifex aeolicus}
Length = 168
Score = 50.6 bits (121), Expect = 6e-09
Identities = 27/159 (16%), Positives = 52/159 (32%), Gaps = 40/159 (25%)
Query: 7 LSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLK 66
++D +I NA R + + P SK+ + L V+ K G+I ++E + + + +K
Sbjct: 7 IADMFSAIKNAIMRRDDFLYV-PSSKLKERILDVLKKEGFIQDWEALKGEKYEEEYKKMK 65
Query: 67 GRLNKCGVISPRFDVPIRHIEKWTNNLL-------------------------PSRQ--- 98
K + + R+
Sbjct: 66 ELAEKSPNPKMKRYLKQLEEYNKGTQYPIKIYLKYLDPKKRKSAITNIVKVSKGGRRVYA 125
Query: 99 -----------FGYVVLTTSGGIMDHEEARRKHLGGKIL 126
G +++T G+M EARR GG+++
Sbjct: 126 GVRTMPYVKRGLGIAIVSTDAGVMTDHEARRMRKGGEVI 164
>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 = 32.1 bits (72), Expect = 0.038
Identities = 20/120 (16%), Positives = 45/120 (37%), Gaps = 16/120 (13%)
Query: 5 NVLSDA-LKSI---NNAEKRGKR--QVLIRPCSKVIVKFLTVMMKHGYIGEF-------E 51
++LS + I +A R L+ +++ KF+ +++ Y +F E
Sbjct: 44 SILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINY--KFLMSPIKTE 101
Query: 52 IVDDHRAGKIVVNLKGRLNKCGVISPRFDVP-IRHIEKWTNNLLPSRQFGYVVLTTSGGI 110
++ + + RL + +++V ++ K LL R V++ G
Sbjct: 102 QRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGS 161
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 28.9 bits (64), Expect = 0.36
Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 19/51 (37%)
Query: 51 EIVDDHRAGKIVVNLKGRLNKCG-VISPRF-DVPIRHIEKWTNNLLPSRQF 99
+IV+ G +V CG V+S + D E W R F
Sbjct: 33 KIVERFSEGDVVC------ALCGLVLSDKLVD---TRSE-W-------RTF 66
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 28.6 bits (63), Expect = 0.61
Identities = 10/55 (18%), Positives = 21/55 (38%)
Query: 4 VNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRA 58
++L+ K I + G + + ++ + + KH + DHRA
Sbjct: 680 QDILATYKKEIVVSNTAGGAPLRLCANLRMFPLLMHSLTKHMAFRSGIVPSDHRA 734
>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 = 1.0
Identities = 15/61 (24%), Positives = 21/61 (34%), Gaps = 12/61 (19%)
Query: 73 GVISPRFDVPIRHIEKWTNNLLPSRQ----FGYVVLT-TSGGIMDHEEARRKHLGGKILG 127
G + VP T + + Q F ++ T G D E L GK LG
Sbjct: 14 GSLEHVLLVP-------TASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLG 66
Query: 128 F 128
+
Sbjct: 67 Y 67
Score = 26.2 bits (57), Expect = 4.5
Identities = 23/138 (16%), Positives = 48/138 (34%), Gaps = 41/138 (29%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGE------FEIVD 54
+V N ++ +I+ ++GKR IR + ++ + G+ F+ ++
Sbjct: 1664 IVINNPVN---LTIHFGGEKGKR---IR------ENYSAMIFETIVDGKLKTEKIFKEIN 1711
Query: 55 DHRAGKIVVNLKGRLNKCGVISPRFDVP---------IRHIEKWTNNLLPSRQF------ 99
+H + KG L+ +F P ++ L+P+
Sbjct: 1712 EHSTSYTFRSEKGLLSA-----TQFTQPALTLMEKAAFEDLKSKG--LIPADATFAGHSL 1764
Query: 100 G-YVVLTTSGGIMDHEEA 116
G Y L + +M E
Sbjct: 1765 GEYAALASLADVMSIESL 1782
>1cbf_A Cobalt-precorrin-4 transmethylase; precorrin-4 methyltransferase,
cobalamin biosynth methyltransferase; HET: SAH; 2.40A
{Bacillus megaterium} SCOP: c.90.1.1 PDB: 2cbf_A*
Length = 285
Score = 25.6 bits (57), Expect = 5.7
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 51 EIVDDHRAGKIVVNLKG 67
++D R GK+VV +
Sbjct: 85 TMLDRMREGKMVVRVHT 101
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded
RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus
tokodaii} PDB: 3aly_A
Length = 149
Score = 25.4 bits (56), Expect = 5.8
Identities = 7/76 (9%), Positives = 26/76 (34%), Gaps = 16/76 (21%)
Query: 11 LKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGYIGEFEIVDDHRAGKIVVNLKGRLN 70
+ + + G +I+ S++++K + GE+++ +
Sbjct: 57 ICLMETMLRLGISSPIIKGDSQLVIKQMN--------GEYKVKAK--------RIIPLYE 100
Query: 71 KCGVISPRFDVPIRHI 86
K + + + + +
Sbjct: 101 KAIELKKKLNATLIWV 116
>3ndc_A Precorrin-4 C(11)-methyltransferase; SAH; HET: SAH; 2.00A
{Rhodobacter capsulatus} PDB: 3nei_A
Length = 264
Score = 25.2 bits (56), Expect = 7.1
Identities = 6/17 (35%), Positives = 8/17 (47%)
Query: 51 EIVDDHRAGKIVVNLKG 67
I + H AG+ V L
Sbjct: 68 TIAEAHAAGQDVARLHS 84
>4e16_A Precorrin-4 C(11)-methyltransferase; structural genomics, center
for structural genomics of infec diseases, csgid; 2.49A
{Clostridium difficile}
Length = 253
Score = 25.1 bits (56), Expect = 7.6
Identities = 4/17 (23%), Positives = 7/17 (41%)
Query: 51 EIVDDHRAGKIVVNLKG 67
+ + K VV L+
Sbjct: 69 VMREGIENNKSVVRLQT 85
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
0.326 0.143 0.429
Gapped
Lambda K H
0.267 0.0847 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,121,173
Number of extensions: 122676
Number of successful extensions: 316
Number of sequences better than 10.0: 1
Number of HSP's gapped: 309
Number of HSP's successfully gapped: 37
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: 40 (21.6 bits)
S2: 52 (23.6 bits)