RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780292|ref|YP_003064705.1| 50S ribosomal protein L13
[Candidatus Liberibacter asiaticus str. psy62]
(155 letters)
>3ofq_J 50S ribosomal protein L13; protein biosynthesis, ribosomes, RNA,
tRNA, transfer, antibi EXIT, peptidyl, ribosomal
subunit, large; 3.10A {Escherichia coli} PDB: 1p85_H
1p86_H 1vs8_J 1vs6_J 2aw4_J 2awb_J 2gya_H 2gyc_H 1vt2_J
2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J 2qbg_J
2qbi_J* 2qbk_J* 2qov_J 2qox_J ...
Length = 142
Score = 179 bits (456), Expect = 2e-46
Identities = 65/141 (46%), Positives = 94/141 (66%), Gaps = 1/141 (0%)
Query: 4 TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
TF K V++ W +VDA G +GRLA+++A RLRGK+K YTP D GD+++++NA KV
Sbjct: 3 TFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKV 62
Query: 64 AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
A +G K K YY HTG+ GGIK+ T +E++A P +++ A+ MLP+GPL R +
Sbjct: 63 AVTGNKRTDKVYYHHTGHIGGIKQATFEEMIA-RRPERVIEIAVKGMLPKGPLGRAMFRK 121
Query: 124 LHIYAEDHHPHEAQKPVFMDI 144
L +YA + H H AQ+P +DI
Sbjct: 122 LKVYAGNEHNHAAQQPQVLDI 142
>3f1f_N 50S ribosomal protein L13; RF2, ribosome, termination, tRNA; 3.00A
{Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N 3f1h_N
Length = 163
Score = 176 bits (448), Expect = 2e-45
Identities = 64/144 (44%), Positives = 101/144 (70%), Gaps = 3/144 (2%)
Query: 1 MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINA 60
++ T+ K +VE +W+L+DA+G +GRLA++IA LRGK++P +TP+ GD VV++NA
Sbjct: 23 LVKTYVPK--QVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNA 80
Query: 61 SKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQ 120
K+ +GKK +QK Y R++GYPGG+KK +++L P +L+ A+ MLP+GPL R+
Sbjct: 81 DKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKML-ATHPERVLEHAVKGMLPKGPLGRRL 139
Query: 121 MKNLHIYAEDHHPHEAQKPVFMDI 144
K L +YA HPH+AQ+P +++
Sbjct: 140 FKRLKVYAGPDHPHQAQRPEKLEV 163
>3bbo_L Ribosomal protein L13; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 250
Score = 168 bits (426), Expect = 6e-43
Identities = 65/153 (42%), Positives = 97/153 (63%), Gaps = 4/153 (2%)
Query: 4 TFFQKSSE---VEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINA 60
T++ KS++ +KKW +VDA LI+GR+AS IA+ +RGKN +YTPS D G V+++NA
Sbjct: 99 TWYPKSADHVPTDKKWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVVNA 158
Query: 61 SKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQ 120
KVA SGKK QK Y RH+G PGG+K+ T ++ P I++ A+ MLP+G L R
Sbjct: 159 DKVAVSGKKRTQKLYRRHSGRPGGLKEETFDQL-QKRIPERIIEHAVRGMLPKGRLGRYL 217
Query: 121 MKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSR 153
+L +Y HPH+AQ+P+ + + + +
Sbjct: 218 FNHLKVYKGAEHPHQAQQPIDLPLRDKRIRVEK 250
>2zjr_G 50S ribosomal protein L13; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.21.1.1 PDB: 1nwx_H* 1nwy_H* 1sm1_H*
1xbp_H* 2zjp_G* 2zjq_G 1nkw_H 3cf5_G* 3dll_G* 1pnu_H
1pny_H 1vor_K 1vou_K 1vow_K 1voy_K 1vp0_K
Length = 174
Score = 152 bits (384), Expect = 4e-38
Identities = 63/141 (44%), Positives = 91/141 (64%), Gaps = 1/141 (0%)
Query: 10 SEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKK 69
E+ W++VDA G+ +GRLA+ IA R+RGK++P +TP+ GD VV+INA++VA +GKK
Sbjct: 35 KNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKK 94
Query: 70 YDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAE 129
D K Y R+TGY GG+K TA+E L+ P +++ A+ MLP+G R L +YA
Sbjct: 95 LDDKVYTRYTGYQGGLKTETAREALSK-HPERVIEHAVFGMLPKGRQGRAMHTRLKVYAG 153
Query: 130 DHHPHEAQKPVFMDIAKMNPK 150
+ HPH AQKP + + K
Sbjct: 154 ETHPHSAQKPQVLKTQPLEVK 174
>3i1n_J 50S ribosomal protein L13; ribosome structure, protein-RNA complex,
acetylation, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA- binding, methylation; 3.19A
{Escherichia coli k-12} PDB: 1p85_H 1p86_H 1vs8_J 2aw4_J
2awb_J 2gya_H 2gyc_H 1vs6_J 2i2v_J 2i2t_J* 2qao_J*
2qba_J* 2qbc_J* 2qbe_J 2qbg_J 2qbi_J* 2qbk_J* 2qov_J
2qox_J 2qoz_J* ...
Length = 142
Score = 145 bits (366), Expect = 5e-36
Identities = 65/141 (46%), Positives = 94/141 (66%), Gaps = 1/141 (0%)
Query: 4 TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
TF K V++ W +VDA G +GRLA+++A RLRGK+K YTP D GD+++++NA KV
Sbjct: 3 TFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKV 62
Query: 64 AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
A +G K K YY HTG+ GGIK+ T +E++A P +++ A+ MLP+GPL R +
Sbjct: 63 AVTGNKRTDKVYYHHTGHIGGIKQATFEEMIA-RRPERVIEIAVKGMLPKGPLGRAMFRK 121
Query: 124 LHIYAEDHHPHEAQKPVFMDI 144
L +YA + H H AQ+P +DI
Sbjct: 122 LKVYAGNEHNHAAQQPQVLDI 142
>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
1s1i_M
Length = 178
Score = 144 bits (364), Expect = 9e-36
Identities = 29/140 (20%), Positives = 59/140 (42%), Gaps = 18/140 (12%)
Query: 17 ILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYY 76
+++D KG +VGRLAS +A +L G +V++ A ++ SG+ + K Y
Sbjct: 1 VVIDGKGHLVGRLASVVAKQLLN------------GQKIVVVRAEELNISGEFFRNKLKY 48
Query: 77 RHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHE 135
T +P+ I KA+ M+ + + ++ L ++ P++
Sbjct: 49 HDFLRKATAFNKTRGPFHF-RAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYD 107
Query: 136 AQKPV----FMDIAKMNPKN 151
+K V + + ++ P
Sbjct: 108 KKKRVVVPQALRVLRLKPGR 127
>2j01_N 50S ribosomal protein L13; ribosome, tRNA, paromomycin, mRNA,
translation; 2.8A {Thermus thermophilus} SCOP: c.21.1.1
PDB: 2hgq_M 2hgj_M 2hgu_M 2j03_N 2jl6_N 2jl8_N 2v47_N
2v49_N 2wdi_N 2wdj_N 2wdl_N 2wdn_N 2wh2_N 2wh4_N 3hux_N
3huz_N 3fin_N 1vsp_H
Length = 140
Score = 143 bits (361), Expect = 2e-35
Identities = 62/135 (45%), Positives = 96/135 (71%), Gaps = 1/135 (0%)
Query: 10 SEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKK 69
+VE +W+L+DA+G +GRLA++IA LRGK++P +TP+ GD VV++NA K+ +GKK
Sbjct: 7 KQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKK 66
Query: 70 YDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAE 129
+QK Y R++GYPGG+KK +++L P +L+ A+ MLP+GPL R+ K L +YA
Sbjct: 67 LEQKIYTRYSGYPGGLKKIPLEKML-ATHPERVLEHAVKGMLPKGPLGRRLFKRLKVYAG 125
Query: 130 DHHPHEAQKPVFMDI 144
HPH+AQ+P +++
Sbjct: 126 PDHPHQAQRPEKLEV 140
>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial;
mitochondrial ribosome, large ribosomal subunit,
ribosomal RNA; 12.10A {Bos taurus}
Length = 148
Score = 137 bits (347), Expect = 7e-34
Identities = 53/138 (38%), Positives = 84/138 (60%), Gaps = 1/138 (0%)
Query: 7 QKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFS 66
Q+ + + W L+D K G+LA+ ++RL+G +KP Y +D GDHVVI+N +AFS
Sbjct: 9 QQWATFARIWYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHIAFS 68
Query: 67 GKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHI 126
G K++QK Y HTGYPGG ++ TA ++ P I+K AI MLP+ R M+ LH+
Sbjct: 69 GNKWEQKVYSSHTGYPGGFRQVTAAQL-HLRDPVAIVKLAIYGMLPKNLHRRTMMERLHL 127
Query: 127 YAEDHHPHEAQKPVFMDI 144
+ +++ P + K + ++
Sbjct: 128 FPDEYIPEDILKNLVEEL 145
>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly,
ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1
Length = 142
Score = 119 bits (300), Expect = 2e-28
Identities = 30/138 (21%), Positives = 58/138 (42%), Gaps = 14/138 (10%)
Query: 18 LVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYR 77
+++A GLI+GRLAS++A L +G+ VVI+NA K +G + + Y+
Sbjct: 3 IINADGLILGRLASRVAKML------------LEGEEVVIVNAEKAVITGNREVIFSKYK 50
Query: 78 HTGYPGGIKKTTAKEILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHEA 136
+ I+++ I MLP + RK + L +Y +
Sbjct: 51 QRTGLRTLTNPRRGPFYPK-RSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQD 109
Query: 137 QKPVFMDIAKMNPKNSRR 154
++ + A ++ + +
Sbjct: 110 KQLETIVEAHVSRLSRPK 127
>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 203
Score = 118 bits (296), Expect = 8e-28
Identities = 27/145 (18%), Positives = 59/145 (40%), Gaps = 16/145 (11%)
Query: 13 EKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQ 72
E + +++D +G ++GRLA+ +A ++ G VV++ + SG Y
Sbjct: 3 EVQVLVLDGRGHLLGRLAAIVAKQV------------LLGRKVVVVRCEGINISGNFYRN 50
Query: 73 KTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDH 131
K Y + +P+ I + + MLP + + + L ++
Sbjct: 51 KLNYLAFLRKRMNTNPSRGPYDF-RAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIP 109
Query: 132 HPHEAQKPVFMDIA--KMNPKNSRR 154
P++ +K + + A + K +R+
Sbjct: 110 PPYDKKKRMVVPAALKVVRLKPTRK 134
>1vq8_J 50S ribosomal protein L13P; ribosome 50S, protein-protein complex,
RNA-RNA complex, protein-RNA complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} SCOP: c.21.1.1 PDB:
1giy_M 1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K*
1kqs_I* 1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K*
1q81_K* 1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ...
Length = 145
Score = 110 bits (277), Expect = 1e-25
Identities = 27/139 (19%), Positives = 57/139 (41%), Gaps = 18/139 (12%)
Query: 14 KKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQK 73
++VDA+ I+GR+ASQ+A + DG+ V ++NA + +G++
Sbjct: 7 DADVIVDARDCIMGRVASQVAEQA------------LDGETVAVVNAERAVITGREEQIV 54
Query: 74 TYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHH 132
Y G + P I K+ I MLP + R+ +++ +Y + +
Sbjct: 55 EKYEKRVDIGNDNGYFYPK-----RPDGIFKRTIRGMLPHKKQRGREAFESVRVYLGNPY 109
Query: 133 PHEAQKPVFMDIAKMNPKN 151
+ + + +++
Sbjct: 110 DEDGEVLDGTSLDRLSNIK 128
>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 = 35.4 bits (80), Expect = 0.006
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 7/32 (21%)
Query: 117 ARKQMK-NLHIYAEDHHPHEAQKPVFMDIAKM 147
A K+++ +L +YA+D P A K A M
Sbjct: 21 ALKKLQASLKLYADDSAPALAIK------ATM 46
Score = 29.2 bits (64), Expect = 0.37
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 21/49 (42%)
Query: 13 EKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINAS 61
EK+ + K L Q +L+L Y ADD + I A+
Sbjct: 18 EKQAL----KKL-------QASLKL-------Y---ADDSAPALAIKAT 45
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 31.1 bits (70), Expect = 0.11
Identities = 24/117 (20%), Positives = 38/117 (32%), Gaps = 53/117 (45%)
Query: 33 IALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYR--------HTGYPGG 84
+ L LR K K A G ++ S++ FS +K K R H+
Sbjct: 389 LNLTLR-KAK------APSG-----LDQSRIPFSERK--LKFSNRFLPVASPFHSHL--- 431
Query: 85 IKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVF 141
L AS ++ K + + N+ A+D Q PV+
Sbjct: 432 ---------LVPASD--LINKDLVK------------NNVSFNAKD-----IQIPVY 460
>3khk_A Type I restriction-modification system methylation subunit;
structural genomics, PSI-2, protein structure
initiative; 2.55A {Methanosarcina mazei}
Length = 544
Score = 25.6 bits (55), Expect = 5.1
Identities = 7/30 (23%), Positives = 13/30 (43%)
Query: 40 KNKPTYTPSADDGDHVVIINASKVAFSGKK 69
K+K D V+ I+A K+ + +
Sbjct: 445 KDKNAKNGKRDRRGQVLFIDARKLGYMKDR 474
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.317 0.133 0.386
Gapped
Lambda K H
0.267 0.0622 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,373,441
Number of extensions: 62423
Number of successful extensions: 176
Number of sequences better than 10.0: 1
Number of HSP's gapped: 159
Number of HSP's successfully gapped: 19
Length of query: 155
Length of database: 5,693,230
Length adjustment: 84
Effective length of query: 71
Effective length of database: 3,656,734
Effective search space: 259628114
Effective search space used: 259628114
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 (21.7 bits)
S2: 52 (24.0 bits)