RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 024440
(267 letters)
>3bbo_H Ribosomal protein L5; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.2
Length = 220
Score = 373 bits (961), Expect = e-133
Identities = 164/219 (74%), Positives = 194/219 (88%)
Query: 46 AAGGIVLVEKSEAEKTGRLKTTYLEKIVPLLREEFSYTNIHQVPKIEKIVVNCGIGDAAQ 105
AAG V V+K+EAE RLKT Y+EK+VPLL+EEFSY+NI +VPK+ KIVVNCGIGDA+Q
Sbjct: 1 AAGTAVFVDKAEAETINRLKTNYIEKMVPLLKEEFSYSNILEVPKVVKIVVNCGIGDASQ 60
Query: 106 NAKGLEAAMNDLALITGQRPVKTRARNSIATFKIREGEPLGIAVTLRGNMMYSFLDRLIN 165
NAKGL+AA+N+LALITGQRPVKT+A+ SIA FK+REG LGIAVTLRGN+MYSFLDRLIN
Sbjct: 61 NAKGLDAAINELALITGQRPVKTKAKTSIAGFKVREGMTLGIAVTLRGNLMYSFLDRLIN 120
Query: 166 LGLPRTRDFQGVNPNSFDGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTAKTDKE 225
L LPRTRDFQGVNPNSFDGHGNYS+G +EQSVFPEI+ + +GK +G+DVCITTTAKTDKE
Sbjct: 121 LALPRTRDFQGVNPNSFDGHGNYSVGFREQSVFPEIKPEIVGKARGMDVCITTTAKTDKE 180
Query: 226 GQRLLALMGMPFREGGGPANLIRKKKLKAHHFDSKSKGK 264
+LL+LMGMPFREG GP+ L+RKKKLK+HHFD+K +
Sbjct: 181 AYKLLSLMGMPFREGSGPSTLVRKKKLKSHHFDAKKGRR 219
>1mji_A 50S ribosomal protein L5; ribosomal protein - 5S rRNA complex,
ribosome; 2.50A {Thermus thermophilus} SCOP: d.77.1.1
PDB: 2hgj_G 2hgq_G 2hgu_G 2j01_G 2j03_G 2jl6_G 2jl8_G
2v47_G 2v49_G 2wdi_G 2wdj_G 2wdl_G 2wdn_G 2wh2_G 2wh4_G
2wrj_G 2wrl_G 2wro_G 2wrr_G 2x9s_G ...
Length = 182
Score = 314 bits (808), Expect = e-110
Identities = 91/179 (50%), Positives = 135/179 (75%)
Query: 61 TGRLKTTYLEKIVPLLREEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALI 120
LK Y E++ P L F Y N+ +VP++EK+V+N G+G+A ++A+ LE A +LALI
Sbjct: 4 DVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALI 63
Query: 121 TGQRPVKTRARNSIATFKIREGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPN 180
TGQ+P TRA+ SI+ FK+R+G P+G+ VTLR + M+ FL++L+N+ LPR RDF+G+NPN
Sbjct: 64 TGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLNPN 123
Query: 181 SFDGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTAKTDKEGQRLLALMGMPFRE 239
SFDG GNY++G++EQ +FPEI YD + +G+D+ + TTA+TD+E + LL L+G PFR+
Sbjct: 124 SFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFRK 182
>1iq4_A 50S ribosomal protein L5; rRNA-binding, RNP motif, RNA binding
PROT; 1.80A {Geobacillus stearothermophilus} SCOP:
d.77.1.1
Length = 179
Score = 314 bits (808), Expect = e-110
Identities = 104/177 (58%), Positives = 138/177 (77%)
Query: 63 RLKTTYLEKIVPLLREEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITG 122
RLK YL ++VP L +F+Y +I QVPKIEKIV+N G+GDA QN K L++A+ +L LI G
Sbjct: 3 RLKEKYLNEVVPALMSKFNYKSIMQVPKIEKIVINMGVGDAVQNPKALDSAVEELTLIAG 62
Query: 123 QRPVKTRARNSIATFKIREGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSF 182
QRPV TRA+ SIA F++R+G P+G VTLRG MY FLD+LI++ LPR RDF+GV+ SF
Sbjct: 63 QRPVVTRAKKSIAGFRLRQGMPIGAKVTLRGERMYEFLDKLISVSLPRARDFRGVSKKSF 122
Query: 183 DGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTAKTDKEGQRLLALMGMPFRE 239
DG GNY++G+KEQ +FPEI YD + K +G+D+ I TTA TD+E + LLAL+GMPF++
Sbjct: 123 DGRGNYTLGIKEQLIFPEIDYDKVNKVRGMDIVIVTTANTDEEARELLALLGMPFQK 179
>3r8s_F 50S ribosomal protein L5; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 3oat_F*
3ofc_F* 3ofz_F* 3ofr_F 3r8t_F 3i1n_F 1vs8_F 1vs6_F
1vt2_F 3i1p_F 3i1r_F 3i1t_F 3i20_F 3i22_F 3iyx_F 3iyy_F
3izt_G* 3izu_G* 3kcr_F 3orb_F* ...
Length = 177
Score = 312 bits (802), Expect = e-109
Identities = 90/176 (51%), Positives = 129/176 (73%)
Query: 63 RLKTTYLEKIVPLLREEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITG 122
+L Y +++V L EF+Y ++ QVP++EKI +N G+G+A + K L+ A DLA I+G
Sbjct: 2 KLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISG 61
Query: 123 QRPVKTRARNSIATFKIREGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSF 182
Q+P+ T+AR S+A FKIR+G P+G VTLRG M+ F +RLI + +PR RDF+G++ SF
Sbjct: 62 QKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSF 121
Query: 183 DGHGNYSIGVKEQSVFPEIRYDALGKPKGIDVCITTTAKTDKEGQRLLALMGMPFR 238
DG GNYS+GV+EQ +FPEI YD + + +G+D+ ITTTAK+D+EG+ LLA PFR
Sbjct: 122 DGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR 177
>1vq8_D 50S ribosomal protein L5P; 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.77.1.1 PDB: 1vq4_D*
1vq5_D* 1vq6_D* 1vq7_D* 1s72_D* 1vq9_D* 1vqk_D* 1vql_D*
1vqm_D* 1vqn_D* 1vqo_D* 1vqp_D* 1yhq_D* 1yi2_D* 1yij_D*
1yit_D* 1yj9_D* 1yjn_D* 1yjw_D* 2otj_D* ...
Length = 177
Score = 204 bits (522), Expect = 7e-67
Identities = 54/165 (32%), Positives = 80/165 (48%), Gaps = 17/165 (10%)
Query: 73 VPLLREEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARN 132
+ E + + P+IEK+VV+ GIG ++ L A + L ITGQ PV+T+A+
Sbjct: 1 MSSESESGGDFHEMREPRIEKVVVHMGIGHGGRD---LANAEDILGEITGQMPVRTKAKR 57
Query: 133 SIATFKIREGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSIGV 192
++ F IREG+P+G VTLR M FL + + + FD GN+S GV
Sbjct: 58 TVGEFDIREGDPIGAKVTLRDEMAEEFLQTALP--------LAELATSQFDDTGNFSFGV 109
Query: 193 KEQSVFPEIRYDALGKPKGIDVCIT------TTAKTDKEGQRLLA 231
+E + FP YD G+DV + AK DK + +
Sbjct: 110 EEHTEFPSQEYDPSIGIYGLDVTVNLVRPGYRVAKRDKASRSIPT 154
>3iz5_e 60S ribosomal protein L7 (L30P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_e
Length = 244
Score = 199 bits (509), Expect = 6e-65
Identities = 13/163 (7%), Positives = 38/163 (23%), Gaps = 10/163 (6%)
Query: 76 LREEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIA 135
+ E + + + +++ + Q + A A T +
Sbjct: 1 MASEAAKVAVPEKVILKRRREEVWAAEKKQK---VAAEKIKAAENTKVIYARAEQYAGEY 57
Query: 136 TFKIREGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSIGVKEQ 195
+ +E L ++G S + + + ++ +
Sbjct: 58 EAQDKELVQLKREARMKGGFYVSPEAKPL-----FVVRIR-GINAMHPKTKKILQLLRLR 111
Query: 196 SVFPEIRYDALGKPKGIDVCITTTAKTDKEGQRLLALMGMPFR 238
+F + + K + T + R
Sbjct: 112 QIF-NGVFLKVNKATINMLRRVEPYVTYGYPNLKSVRELIYKR 153
>4a17_D L21, RPL11, 60S ribosomal protein L11; eukaryotic ribosome,
ribosome, eukaryotic initiation factor 60S, translation,
large ribosomal subunit; 3.52A {Tetrahymena thermophila}
PDB: 4a1a_D 4a1c_D 4a1e_D
Length = 172
Score = 197 bits (502), Expect = 6e-64
Identities = 40/157 (25%), Positives = 69/157 (43%), Gaps = 10/157 (6%)
Query: 82 YTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIRE 141
N + KI K+V+NC +G++ L A L ++GQ PV +RAR +I +F I+
Sbjct: 5 KENKMREVKIAKLVINCCVGESGDK---LTKAAKVLKDLSGQEPVFSRARYTIRSFGIKR 61
Query: 142 GEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSIGVKEQSVFPEI 201
E + + VT+RG+ L R + + R +F GN+ G++E +
Sbjct: 62 NEKMAVHVTIRGDKARDILTRGLKVKEMELRK------KNFSNTGNFGFGIQEHIDL-GM 114
Query: 202 RYDALGKPKGIDVCITTTAKTDKEGQRLLALMGMPFR 238
+YD G+D + + +R A +
Sbjct: 115 KYDPSTGIFGMDFYVVLERPGTRVARRRRATSRVGNN 151
>2zkr_d 60S ribosomal protein L11; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 178
Score = 181 bits (462), Expect = 7e-58
Identities = 35/162 (21%), Positives = 72/162 (44%), Gaps = 10/162 (6%)
Query: 77 REEFSYTNIHQVPKIEKIVVNCGIGDAAQNAKGLEAAMNDLALITGQRPVKTRARNSIAT 136
+++ N + +I K+ +N +G++ L A L +TGQ PV ++AR ++ +
Sbjct: 3 QDQGEKENPMRELRIRKLCLNICVGESGDR---LTRAAKVLEQLTGQTPVFSKARYTVRS 59
Query: 137 FKIREGEPLGIAVTLRGNMMYSFLDRLINLGLPRTRDFQGVNPNSFDGHGNYSIGVKEQS 196
F IR E + + T+RG L++ + + R+++ + N+F GN+ G++E
Sbjct: 60 FGIRRNEKIAVHCTVRGAKAEEILEKGL-----KVREYE-LRKNNFSDTGNFGFGIQEHI 113
Query: 197 VFPEIRYDALGKPKGIDVCITTTAKTDKEGQRLLALMGMPFR 238
I+YD G+D + + + +
Sbjct: 114 DL-GIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAK 154
>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 = 30.0 bits (67), Expect = 1.00
Identities = 24/158 (15%), Positives = 52/158 (32%), Gaps = 57/158 (36%)
Query: 15 H--GRFPALSSSSYVRPTYPNPINVNGVVSVKAAAG-----GIVLVEKSEAEKTGRLKTT 67
H G + AL+S + V+S+++ G+ + ++ GR +
Sbjct: 1762 HSLGEYAALASLA-------------DVMSIESLVEVVFYRGMTMQVAVPRDELGR--SN 1806
Query: 68 YL------EKIVPLLREEFSYTNIHQVPKIEKI---------VVN---------CGIGDA 103
Y ++ +E + V +E++ +VN GD
Sbjct: 1807 YGMIAINPGRVAASFSQE----ALQYV--VERVGKRTGWLVEIVNYNVENQQYVAA-GDL 1859
Query: 104 AQNAKGLEAAMNDLALITGQRPVKTRARNSIATFKIRE 141
+ L+ N L I Q+ + S++ ++
Sbjct: 1860 ----RALDTVTNVLNFIKLQKIDIIELQKSLSLEEVEG 1893
Score = 28.9 bits (64), Expect = 2.1
Identities = 20/108 (18%), Positives = 36/108 (33%), Gaps = 30/108 (27%)
Query: 190 IGVKEQSVFP------EIRYDAL----GKP------KGIDVC-----ITTTAKTDKEGQR 228
IGV+ +P I D+L G P + + T G++
Sbjct: 306 IGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQ 365
Query: 229 L-LALMGMP--FREGGGPANL------IRKKKLKAHHFDSKSKGKSRR 267
+ ++L+ G P +L +RK K + S+ R+
Sbjct: 366 VEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERK 413
>3abq_A Ethanolamine ammonia-lyase heavy chain; (beta/alpha)8 fold, cobalt,
cobalamin; HET: B12; 2.05A {Escherichia coli} PDB:
3abo_A* 3abr_A* 3abs_A* 3any_A* 3ao0_A*
Length = 453
Score = 27.8 bits (62), Expect = 3.8
Identities = 12/41 (29%), Positives = 14/41 (34%), Gaps = 10/41 (24%)
Query: 206 LGKPKGIDVCITTTAKTDKEGQRLLA----------LMGMP 236
G G D C T A D+ L +MGMP
Sbjct: 355 SGISMGCDCCYTNHADADQNLNENLMILLATAGCNYIMGMP 395
>2qez_A Ethanolamine ammonia-lyase heavy chain; ethanol ammonia lyase large
subunit (EUTB), structural genomics; HET: MSE; 2.15A
{Listeria monocytogenes serotype 4B}
Length = 455
Score = 27.8 bits (62), Expect = 3.9
Identities = 12/41 (29%), Positives = 16/41 (39%), Gaps = 10/41 (24%)
Query: 206 LGKPKGIDVCITTTAKTDKEGQRLLA----------LMGMP 236
G G DVC T K D+ L+ +MG+P
Sbjct: 356 TGISMGCDVCYTNHMKADQNDVENLSVLLTAAGCNFIMGIP 396
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
0.317 0.135 0.387
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,124,416
Number of extensions: 257577
Number of successful extensions: 519
Number of sequences better than 10.0: 1
Number of HSP's gapped: 507
Number of HSP's successfully gapped: 18
Length of query: 267
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 175
Effective length of database: 4,133,061
Effective search space: 723285675
Effective search space used: 723285675
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.2 bits)