RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 045484
(179 letters)
>3bbo_E Ribosomal protein L2; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 269
Score = 94.1 bits (235), Expect = 4e-24
Identities = 34/77 (44%), Positives = 41/77 (53%), Gaps = 5/77 (6%)
Query: 97 HEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKW 156
K L +AG WLG+RPV+RGV MNPVDHP G GEGR TPWG P
Sbjct: 196 VNQKRLGRAGSKRWLGKRPVVRGVVMNPVDHPHGGGEGRAPIGRKS---PTTPWGYPALG 252
Query: 157 CKTASRKKKRKFSCLII 173
++ RK+ + II
Sbjct: 253 RRS--RKRNKYSDNFII 267
>3v2d_D 50S ribosomal protein L2; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_B 2hgj_D 2hgq_D 2hgu_D 1vsa_B 2j03_D 2jl6_D 2jl8_D
2v47_D 2v49_D 2wdi_D 2wdj_D 2wdl_D 2wdn_D 2wh2_D 2wh4_D
2wrj_D 2wrl_D 2wro_D 2wrr_D ...
Length = 276
Score = 94.1 bits (235), Expect = 4e-24
Identities = 38/77 (49%), Positives = 46/77 (59%), Gaps = 6/77 (7%)
Query: 97 HEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKW 156
H+ VL KAG+S WLG+RP +RG MNPVDHP G GEGR G +PWG K
Sbjct: 201 HKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGR-APRGRPPA---SPWGWQTKG 256
Query: 157 CKTASRKKKRKFSCLII 173
KT RK+++ S II
Sbjct: 257 LKT--RKRRKPSSRFII 271
>3r8s_C 50S ribosomal protein L2; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 3fik_C
2wwq_C 3oat_C* 3oas_C* 3ofd_C 3ofc_C 3ofr_C* 3ofz_C*
3og0_C 3ofq_C 3r8t_C 3i1n_C 1vs8_C 1vs6_C 2aw4_C 2awb_C
2vhm_C 2vhn_C 3bbx_C 3df2_C ...
Length = 271
Score = 88.3 bits (220), Expect = 6e-22
Identities = 36/70 (51%), Positives = 40/70 (57%), Gaps = 7/70 (10%)
Query: 97 HEAKVLRKAGQSHWLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKW 156
H +VL KAG + W G RP +RG MNPVDHP G GEGR + G H TPWG K
Sbjct: 199 HMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGR--NFGKHPV---TPWGVQTKG 253
Query: 157 CKTASRKKKR 166
KT R KR
Sbjct: 254 KKT--RSNKR 261
>1vq8_A 50S ribosomal protein L2P; 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: b.34.5.3 b.40.4.5 PDB:
1vq4_A* 1vq5_A* 1vq6_A* 1vq7_A* 1s72_A* 1vq9_A* 1vqk_A*
1vql_A* 1vqm_A* 1vqn_A* 1vqo_A* 1vqp_A* 1yhq_A* 1yi2_A*
1yij_A* 1yit_A* 1yj9_A* 1yjn_A* 1yjw_A* 2otj_A* ...
Length = 240
Score = 80.3 bits (199), Expect = 5e-19
Identities = 21/78 (26%), Positives = 30/78 (38%), Gaps = 9/78 (11%)
Query: 97 HEAKVLRKAGQSHWLGQR-----PVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWG 151
K KAG H + P +RGV MN VDHP G G + G S++
Sbjct: 165 RTDKPFVKAGNKHHKMKARGTKWPNVRGVAMNAVDHPFGGGGRQ--HPG--KPKSISRNA 220
Query: 152 KPCKWCKTASRKKKRKFS 169
P + + K+ +
Sbjct: 221 PPGRKVGDIASKRTGRGG 238
>3iz5_B 60S ribosomal protein L2 (L2P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_B 2zkr_a
Length = 261
Score = 79.2 bits (196), Expect = 2e-18
Identities = 20/82 (24%), Positives = 28/82 (34%), Gaps = 8/82 (9%)
Query: 97 HEAKVLRKAGQSHWL-----GQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWG 151
K + KAG ++ P +RGV MNPV+HP G G + P G
Sbjct: 174 RTEKPMLKAGNAYHKYRVKRNCWPKVRGVAMNPVEHPHGGGNHQH-IGHASTVRRDAPPG 232
Query: 152 KPCKWCKTASRKKKRKFSCLII 173
+ R+ R
Sbjct: 233 QKVGLIAA--RRTGRLRGQAAA 252
>4a17_A RPL8; eukaryotic ribosome, ribosome, eukaryotic initiation factor
60S, translation, large ribosomal subunit; 3.52A
{Tetrahymena thermophila} PDB: 4a1a_A 4a1c_A 4a1e_A
Length = 264
Score = 78.4 bits (194), Expect = 3e-18
Identities = 21/75 (28%), Positives = 29/75 (38%), Gaps = 11/75 (14%)
Query: 97 HEAKVLRKAGQSH-----WLGQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWG 151
K + KAG P +RGV MNPVDHP G G + G +++ W
Sbjct: 175 RTDKPILKAGNQFHKYARKRKSWPRVRGVAMNPVDHPHGGGNHQ--HIG--HPATVSKWA 230
Query: 152 KPCKWCKTASRKKKR 166
+ R +R
Sbjct: 231 SAGQKVGL--RAARR 243
>3jyw_B 60S ribosomal protein L2; eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
3izc_B 3izs_B 3o58_B 3o5h_B 3u5e_A 3u5i_A 1s1i_B
Length = 243
Score = 70.7 bits (174), Expect = 1e-15
Identities = 20/75 (26%), Positives = 28/75 (37%), Gaps = 11/75 (14%)
Query: 97 HEAKVLRKAGQSHWL-----GQRPVIRGVPMNPVDHPRGRGEGRGKSSGNHGRCSLTPWG 151
K L KAG++ P RGV MNPVDHP G G + G +++
Sbjct: 173 RVDKPLLKAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQ--HIG--KASTISRGA 228
Query: 152 KPCKWCKTASRKKKR 166
+ +R
Sbjct: 229 VSGQKAGL--IAARR 241
>1giy_D 50S ribosomal protein L2; ribosome assembly, protein synthesis,
LIFE; 5.50A {Thermus thermophilus} SCOP: i.1.1.1 PDB:
1ml5_d* 1yl3_D 2b66_D 2b9n_D 2b9p_D
Length = 178
Score = 54.4 bits (132), Expect = 7e-10
Identities = 16/39 (41%), Positives = 18/39 (46%), Gaps = 5/39 (12%)
Query: 97 HEAKVLRKAGQSHWLGQR-----PVIRGVPMNPVDHPRG 130
K KAG H + P +RGV MN VDHP G
Sbjct: 140 RTDKPFVKAGNKHHKMKARGTKWPNVRGVAMNAVDHPFG 178
>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 = 39.1 bits (90), Expect = 4e-04
Identities = 33/173 (19%), Positives = 58/173 (33%), Gaps = 28/173 (16%)
Query: 23 DTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPV-KLN----QLVMTL---I 74
+ R K+L + R S+ L N K N Q + L +
Sbjct: 85 EVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQAL 144
Query: 75 LKLEVACHLLVC-MLGPSSTTLSHEA----KVLRK-AGQSHWL--GQRPVIRGV--PMNP 124
L+L A ++L+ +LG T ++ + KV K + WL V +
Sbjct: 145 LELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK 204
Query: 125 VDHPRGRGEGRGKSSGNHGRCSLTPWGKPCKWCKTASR---KKKRKFSCLIIL 174
+ + + + S +H S + R K K +CL++L
Sbjct: 205 LLY---QIDPNWTSRSDHS--SNIK--LRIHSIQAELRRLLKSKPYENCLLVL 250
Score = 28.7 bits (63), Expect = 1.4
Identities = 23/163 (14%), Positives = 51/163 (31%), Gaps = 52/163 (31%)
Query: 7 VRQSEIDRRNQ------NLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNA 60
++ + NL N ++ + L +L +++ + +
Sbjct: 171 CLSYKVQCKMDFKIFWLNLKNCNSPETVLEML----QKLLYQIDPNWTSRSDHSSNIKLR 226
Query: 61 ISPVK--LNQLVMT-------LIL----------KLEVACHLLVC--------MLGPSST 93
I ++ L +L+ + L+L ++C +L+ L ++T
Sbjct: 227 IHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATT 286
Query: 94 T---LSHEAKVLRKAGQS-----HWLGQRP------VIRGVPM 122
T L H + L + +L RP V+ P
Sbjct: 287 THISLDHHSMTLTPD-EVKSLLLKYLDCRPQDLPREVLTTNPR 328
>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 = 0.13
Identities = 15/111 (13%), Positives = 42/111 (37%), Gaps = 17/111 (15%)
Query: 26 RDR-QKWLGA---EYAQLHRHSS--------LGFSA--LPFSTITLLNAISPVKLNQLVM 71
+++ K L +A ++ LG+ + + S + + + + L +
Sbjct: 34 QEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFEN 93
Query: 72 TLILKLEVACHLLVC-MLGPSSTTLSHEAKVLRKAGQSHWLGQRPVIRGVP 121
+ ++ H L +L + TTL ++++ + + +RP +
Sbjct: 94 CYLEGNDI--HALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSN 142
Score = 28.9 bits (64), Expect = 1.2
Identities = 14/89 (15%), Positives = 27/89 (30%), Gaps = 15/89 (16%)
Query: 28 RQKWLGAEYAQLHRHSSLGFSAL------PFSTITLLNAISPVKLNQLVMTLILKL---- 77
+ W A H + GFS L P + ++ + +I +
Sbjct: 1643 QDVW---NRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDG 1699
Query: 78 EVACHLLVCMLGPSST--TLSHEAKVLRK 104
++ + + ST T E +L
Sbjct: 1700 KLKTEKIFKEINEHSTSYTFRSEKGLLSA 1728
Score = 28.5 bits (63), Expect = 1.5
Identities = 35/213 (16%), Positives = 51/213 (23%), Gaps = 103/213 (48%)
Query: 9 QSEIDRRNQNLGNRDTERDRQKWLGAEYAQLHRHSSLGFSALPFSTITLLNAISPVKLNQ 68
Q +++ N +L Q+ I+L+N
Sbjct: 350 QDYVNKTNSHL--------------PAGKQVE--------------ISLVN--GA---KN 376
Query: 69 LVMTLILKLEVACHLLVCMLGPSSTTLSHEAKVLRKA------GQSHW-LGQR------- 114
LV++ GP +L LRKA QS +R
Sbjct: 377 LVVS----------------GPPQ-SLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNR 419
Query: 115 --PVIRGVP-----MNPV------DHPRGRGEGRGKS---------SGNHGRC------- 145
PV P + P D + K G+ R
Sbjct: 420 FLPV--ASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISE 477
Query: 146 SLTPW--GKPCKWCKTASRKKKRKFSCLIILSF 176
+ P KW T +F IL F
Sbjct: 478 RIVDCIIRLPVKWETTT------QFKATHILDF 504
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR
family, hydrolase; 2.35A {Escherichia coli} SCOP:
b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A
Length = 644
Score = 27.1 bits (61), Expect = 3.4
Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 5/40 (12%)
Query: 10 SEIDRRNQNLGNRDTERDRQKWLGAEYAQLHRHSSLGFSA 49
+E R N R ERD WL A + + + F+A
Sbjct: 532 AERRRLN-----RMAERDVGDWLYARFLKDKAGTDTRFAA 566
>1tdh_A NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS
finger, hydrolase; 2.10A {Homo sapiens} SCOP: a.156.1.2
b.113.1.1 g.39.1.8
Length = 364
Score = 26.5 bits (58), Expect = 6.2
Identities = 9/36 (25%), Positives = 12/36 (33%), Gaps = 2/36 (5%)
Query: 134 GRGKSSGNHGRCSLTPW--GKPCKWCKTASRKKKRK 167
G S R T W G P + +K+K
Sbjct: 264 GMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKSRKKK 299
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 0.135 0.438
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,575,850
Number of extensions: 136567
Number of successful extensions: 263
Number of sequences better than 10.0: 1
Number of HSP's gapped: 255
Number of HSP's successfully gapped: 18
Length of query: 179
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 92
Effective length of database: 4,272,666
Effective search space: 393085272
Effective search space used: 393085272
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 (22.0 bits)
S2: 54 (24.5 bits)