RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14782
(97 letters)
>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 421
Score = 112 bits (281), Expect = 3e-31
Identities = 63/92 (68%), Positives = 75/92 (81%)
Query: 1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
MRNRRRIQRRGP ++Y +D G+ KAFR PG+ L++VSKLN+LKLAPGGHVGRF IWTES
Sbjct: 196 MRNRRRIQRRGPCIIYNEDNGIIKAFRKHPGITLLNVSKLNILKLAPGGHVGRFCIWTES 255
Query: 61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
AF+KLD LYG+W+ A LK Y+LP KM NT
Sbjct: 256 AFRKLDDLYGTWRKAASLKSNYNLPMHKMLNT 287
>4a17_C RPL4, ribosomal protein L3; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_C 4a1c_C 4a1e_C
Length = 410
Score = 110 bits (275), Expect = 2e-30
Identities = 56/93 (60%), Positives = 72/93 (77%), Gaps = 1/93 (1%)
Query: 1 MRNRRRIQRRGPLVVYGK-DRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTE 59
+RNRR RRGPLVVYG LT+A RNIPGV++ +V++LNLL+LAPGGHVGRF+IWTE
Sbjct: 201 LRNRRYKLRRGPLVVYGNEKSTLTRALRNIPGVDVCNVNRLNLLQLAPGGHVGRFIIWTE 260
Query: 60 SAFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
SAFKKL+ ++G++ T K GY L +P +AN
Sbjct: 261 SAFKKLNEIFGTYSTTGVQKSGYQLQRPLLANA 293
>2wwb_H 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel,
cotranslational protein translocation, protein
conducting channel; 6.48A {Triticum aestivum} PDB:
2wwa_H 2ww9_H 3izc_D 3izs_D 3o58_D 3o5h_D 3u5e_C 3u5i_C
1s1i_D 3jyw_D
Length = 362
Score = 107 bits (268), Expect = 9e-30
Identities = 54/93 (58%), Positives = 68/93 (73%), Gaps = 1/93 (1%)
Query: 1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
RNRR QRRGPLVVY +D G+ KA RN+PGVE +V+ LNLL+LAPG H+GRFVIWTE+
Sbjct: 194 YRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWTEA 253
Query: 61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANTK 93
AF KLD ++GS A K GY+LP ++ +
Sbjct: 254 AFTKLDQVWGSET-VASSKVGYTLPSHIISTSD 285
>3iz5_D 60S ribosomal protein L4 (L4P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_D
Length = 405
Score = 106 bits (266), Expect = 3e-29
Identities = 58/93 (62%), Positives = 76/93 (81%), Gaps = 1/93 (1%)
Query: 1 MRNRRRIQRRGPLVVYG-KDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTE 59
MRNRR I R+GPL+VYG + + KAFRN+PGV++ +V +LNLL LAPGGH+GRFVIWTE
Sbjct: 200 MRNRRYINRKGPLIVYGTEGSKIVKAFRNLPGVDVANVERLNLLDLAPGGHLGRFVIWTE 259
Query: 60 SAFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
SAFKKL+ +YG+++ + KKG+ LP+PKMAN
Sbjct: 260 SAFKKLEEVYGTFEAPSLKKKGFILPRPKMANA 292
>1vq8_C 50S ribosomal protein L4E; 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.22.1.1 PDB: 1k73_E*
1k8a_E* 1k9m_E* 1kc8_E* 1kd1_E* 1kqs_C* 1m1k_E* 1m90_E*
1n8r_E* 1nji_E* 1q7y_E* 1q81_E* 1q82_E* 1q86_E* 1qvf_C
1qvg_C 1s72_C* 1vq4_C* 1vq5_C* 1vq6_C* ...
Length = 246
Score = 80.5 bits (198), Expect = 3e-20
Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
R R+ + L V + A RN+ G ++ + S++N LAPGG GR ++TES
Sbjct: 181 ARGRKYRRPASILFVT--SDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTES 238
Query: 61 AFKKLD 66
A ++
Sbjct: 239 ALAEVA 244
>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C
1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E
2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E*
2qbk_E* 2qov_E 2qox_E 2qoz_E* ...
Length = 201
Score = 35.7 bits (83), Expect = 8e-04
Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 13 LVVYGK-DRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
L++ G+ D L A RN+ V++ + ++ + L V+ T A K+++ +
Sbjct: 147 LIITGELDENLFLAARNLHKVDVRDATGIDPVSLI----AFDKVVMTADAVKQVEEMLA 201
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 293
Score = 35.2 bits (81), Expect = 0.001
Identities = 13/64 (20%), Positives = 27/64 (42%), Gaps = 4/64 (6%)
Query: 13 LVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYGSW 72
+ + K+ RNI ++L++ LNL + +++TE + L+ YG
Sbjct: 207 FFLMDLVENVEKSGRNIRTLKLLTPRSLNLFDVL----NAEKLVFTEGTIQYLNQRYGVD 262
Query: 73 KTKA 76
+
Sbjct: 263 TLED 266
>2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.22.1.1 PDB: 1j5a_K* 1jzy_K* 1jzz_K*
1k01_K* 1nkw_C 1sm1_C* 2zjp_C* 2zjq_C 1jzx_K 3cf5_C*
3dll_C* 3pio_C* 3pip_C* 1nwy_C* 1nwx_C* 1xbp_C* 1pnu_C
1pny_C 1vor_F 1vou_F ...
Length = 205
Score = 34.5 bits (80), Expect = 0.002
Identities = 10/71 (14%), Positives = 29/71 (40%), Gaps = 10/71 (14%)
Query: 3 NRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLN---LLKLAPGGHVGRFVIWTE 59
+ + +++ D +A RN+ V ++ V+ +N +L+ ++
Sbjct: 138 KQNGLDGTEKVLLVTDDENTRRAARNVSWVSVLPVAGVNVYDILR-------HDRLVIDA 190
Query: 60 SAFKKLDALYG 70
+A + ++ G
Sbjct: 191 AALEIVEEEAG 201
>3v2d_F 50S ribosomal protein L4; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F
2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F
2wro_F 2wrr_F 2x9s_F 2x9u_F ...
Length = 210
Score = 33.4 bits (77), Expect = 0.005
Identities = 9/61 (14%), Positives = 25/61 (40%), Gaps = 10/61 (16%)
Query: 13 LVVYGKDRGLTKAFRNIPGVELISVSKLN---LLKLAPGGHVGRFVIWTESAFKKLDALY 69
+++ + + +A RN+P V ++ LN +++ ++ A++
Sbjct: 154 VLLVTGNELVRRAARNLPWVVTLAPEGLNVYDIVR-------TERLVMDLDAWEVFQNRI 206
Query: 70 G 70
G
Sbjct: 207 G 207
>2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S
ribosomal protein L3; mitochondrial ribosome, large
ribosomal subunit, ribosomal R ribosome; 12.10A {Bos
taurus} PDB: 3iy9_D
Length = 175
Score = 31.1 bits (71), Expect = 0.033
Identities = 9/50 (18%), Positives = 17/50 (34%), Gaps = 10/50 (20%)
Query: 19 DRGLTKAFRNIPGVELISVSKLN---LLKLAPGGHVGRFVIWTESAFKKL 65
+ + +A + LI LN +LK + ++ T L
Sbjct: 131 PQSIVEATSRLKTFNLIPAVGLNVHSMLK-------HQTLVLTLPTVAFL 173
>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 = 28.7 bits (63), Expect = 0.31
Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 16/74 (21%)
Query: 1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
M R I++R L Y ++ K N+ ++ + LL+L P +V
Sbjct: 107 MMTRMYIEQRDRL--YNDNQVFAK--YNVSRLQPYLKLRQALLELRPAKNVL-------- 154
Query: 61 AFKKLDALYGSWKT 74
+D + GS KT
Sbjct: 155 ----IDGVLGSGKT 164
>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon, gene
regulation; HET: CIT; 1.70A {Thermotoga maritima} SCOP:
c.22.1.1
Length = 225
Score = 27.8 bits (62), Expect = 0.55
Identities = 10/63 (15%), Positives = 20/63 (31%), Gaps = 11/63 (17%)
Query: 19 DRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRF-----------VIWTESAFKKLDA 67
+ + RN+P V++I N K ++ T K++
Sbjct: 163 YMNVKLSGRNLPDVKVIIADNPNNSKNGEKAVRIDGLNVFDMLKYDYLVLTRDMVSKIEE 222
Query: 68 LYG 70
+ G
Sbjct: 223 VLG 225
>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 = 26.8 bits (58), Expect = 0.90
Identities = 11/32 (34%), Positives = 13/32 (40%), Gaps = 9/32 (28%)
Query: 59 ESAFKKLDALYGSWKTKAPLKKGYSLPQPKMA 90
+ A KKL A S K A S P +A
Sbjct: 19 KQALKKLQA---SLKLYAD----DS--APALA 41
>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 = 25.4 bits (55), Expect = 3.9
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 7/34 (20%)
Query: 11 GPLVVYGKDRG---LTKAFRNIPGVELISVSKLN 41
GP G G LT ++ GV +I L+
Sbjct: 505 GP----GGASGLGVLTHRNKDGTGVRVIVAGTLD 534
>3edf_A FSPCMD, cyclomaltodextrinase; alpha-cyclodextrin complex,
glycosidase, hydrolase; HET: CE6 ACX; 1.65A
{Flavobacterium SP} PDB: 3edj_A* 3edk_A* 3ede_A 3edd_A*
1h3g_A
Length = 601
Score = 24.8 bits (54), Expect = 7.0
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 13 LVVYGKDRGLTKAFRNIPGVELISVSKLN-------LLKLAPGGHVGRFVIW 57
L+V+G+D G +A + PGV L+S +++ L++ P G F I
Sbjct: 25 LMVHGRDIGRMEAALDYPGVRLVSPTRVPNANYLFVDLEIGPEAQPGSFDIV 76
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
0.321 0.138 0.415
Gapped
Lambda K H
0.267 0.0485 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,463,567
Number of extensions: 74582
Number of successful extensions: 174
Number of sequences better than 10.0: 1
Number of HSP's gapped: 169
Number of HSP's successfully gapped: 17
Length of query: 97
Length of database: 6,701,793
Length adjustment: 63
Effective length of query: 34
Effective length of database: 4,942,770
Effective search space: 168054180
Effective search space used: 168054180
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: 51 (24.0 bits)