RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780292|ref|YP_003064705.1| 50S ribosomal protein L13
[Candidatus Liberibacter asiaticus str. psy62]
(155 letters)
>2zjr_G 50S ribosomal protein L13; ribosome, large ribosomal
subunit, ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} (G:)
Length = 174
Score = 170 bits (433), Expect = 6e-44
Identities = 63/147 (42%), Positives = 91/147 (61%), Gaps = 1/147 (0%)
Query: 4 TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
E+ W++VDA G+ +GRLA+ IA R+RGK++P +TP+ GD VV+INA++V
Sbjct: 29 VKTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQV 88
Query: 64 AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
A +GKK D K Y R+TGY GG+K TA+E L+ P +++ A+ MLP+G R
Sbjct: 89 ALTGKKLDDKVYTRYTGYQGGLKTETAREALSKH-PERVIEHAVFGMLPKGRQGRAMHTR 147
Query: 124 LHIYAEDHHPHEAQKPVFMDIAKMNPK 150
L +YA + HPH AQKP + + K
Sbjct: 148 LKVYAGETHPHSAQKPQVLKTQPLEVK 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* ... (J:)
Length = 142
Score = 168 bits (426), Expect = 4e-43
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 AVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARR-PERVIEIAVKGMLPKGPLGRAMFRK 121
Query: 124 LHIYAEDHHPHEAQKPVFMDI 144
L +YA + H H AQ+P +DI
Sbjct: 122 LKVYAGNEHNHAAQQPQVLDI 142
>3bbo_L Ribosomal protein L13; large ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea} (L:)
Length = 250
Score = 166 bits (422), Expect = 1e-42
Identities = 65/156 (41%), Positives = 97/156 (62%), Gaps = 4/156 (2%)
Query: 1 MIPTFFQKSSE---VEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVI 57
T++ KS++ +KKW +VDA LI+GR+AS IA+ +RGKN +YTPS D G V++
Sbjct: 96 WNTTWYPKSADHVPTDKKWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIV 155
Query: 58 INASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLA 117
+NA KVA SGKK QK Y RH+G PGG+K+ T ++ P I++ A+ MLP+G L
Sbjct: 156 VNADKVAVSGKKRTQKLYRRHSGRPGGLKEETFDQLQK-RIPERIIEHAVRGMLPKGRLG 214
Query: 118 RKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSR 153
R +L +Y HPH+AQ+P+ + + + +
Sbjct: 215 RYLFNHLKVYKGAEHPHQAQQPIDLPLRDKRIRVEK 250
>3f1f_N 50S ribosomal protein L13; RF2, ribosome, termination, tRNA;
3.00A {Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N
3f1h_N (N:)
Length = 163
Score = 165 bits (419), Expect = 3e-42
Identities = 65/144 (45%), Positives = 102/144 (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 +++LA P +L+ A+ MLP+GPL R+
Sbjct: 81 DKIRVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATH-PERVLEHAVKGMLPKGPLGRRL 139
Query: 121 MKNLHIYAEDHHPHEAQKPVFMDI 144
K L +YA HPH+AQ+P +++
Sbjct: 140 FKRLKVYAGPDHPHQAQRPEKLEV 163
>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial;
mitochondrial ribosome, large ribosomal subunit,
ribosomal RNA; 12.10A {Bos taurus} (H:17-148)
Length = 132
Score = 163 bits (413), Expect = 1e-41
Identities = 52/131 (39%), Positives = 81/131 (61%), Gaps = 1/131 (0%)
Query: 16 WILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTY 75
W L+D K G+LA+ ++RL+G +KP Y +D GDHVVI+N +AFSG K++QK Y
Sbjct: 2 WYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHIAFSGNKWEQKVY 61
Query: 76 YRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHE 135
HTGYPGG ++ TA ++ P I+K AI MLP+ R M+ LH++ +++ P +
Sbjct: 62 SSHTGYPGGFRQVTAAQLHLRD-PVAIVKLAIYGMLPKNLHRRTMMERLHLFPDEYIPED 120
Query: 136 AQKPVFMDIAK 146
K + ++ +
Sbjct: 121 ILKNLVEELPQ 131
>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1
protein, flexible fitting; 8.90A {Thermomyces
lanuginosus} PDB: 1s1i_M (M:1-141)
Length = 141
Score = 132 bits (333), Expect = 3e-32
Identities = 30/139 (21%), Positives = 56/139 (40%), Gaps = 14/139 (10%)
Query: 17 ILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYY 76
+++D KG +VGRLAS +A +L G +V++ A ++ SG+ + K Y
Sbjct: 1 VVIDGKGHLVGRLASVVAKQLLN------------GQKIVVVRAEELNISGEFFRNKLKY 48
Query: 77 RHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPR-GPLARKQMKNLHIYAEDHHPHE 135
T A P+ I KA+ M+ + ++ L ++ P++
Sbjct: 49 HDFLRKATAFNKTRGPFHFRA-PSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYD 107
Query: 136 AQKPVFMDIAKMNPKNSRR 154
+K V + A +
Sbjct: 108 KKKRVVVPQALRVLRLKPG 126
>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} (J:)
Length = 145
Score = 127 bits (320), Expect = 7e-31
Identities = 29/147 (19%), Positives = 56/147 (38%), Gaps = 18/147 (12%)
Query: 9 SSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGK 68
S ++VDA+ I+GR+ASQ+A A DG+ V ++NA + +G+
Sbjct: 2 SVAEFDADVIVDARDCIMGRVASQVA------------EQALDGETVAVVNAERAVITGR 49
Query: 69 KYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPR-GPLARKQMKNLHIY 127
+ Y G P I K+ I MLP R+ +++ +Y
Sbjct: 50 EEQIVEKYEKRVDIGN-----DNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVY 104
Query: 128 AEDHHPHEAQKPVFMDIAKMNPKNSRR 154
+ + + + + +++
Sbjct: 105 LGNPYDEDGEVLDGTSLDRLSNIKFVT 131
>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal
assembly, ribosome; 1.60A {Pyrococcus horikoshii} (A:)
Length = 142
Score = 122 bits (308), Expect = 2e-29
Identities = 30/138 (21%), Positives = 56/138 (40%), Gaps = 14/138 (10%)
Query: 18 LVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYR 77
+++A GLI+GRLAS++A L G+ VVI+NA K +G + + Y+
Sbjct: 3 IINADGLILGRLASRVAKMLLE------------GEEVVIVNAEKAVITGNREVIFSKYK 50
Query: 78 HTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPR-GPLARKQMKNLHIYAEDHHPHEA 136
+ I+++ I MLP RK + L +Y +
Sbjct: 51 QRTGLRTLTNPRRGPFYPKR-SDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQD 109
Query: 137 QKPVFMDIAKMNPKNSRR 154
++ + A ++ + +
Sbjct: 110 KQLETIVEAHVSRLSRPK 127
>2j01_N 50S ribosomal protein L13; ribosome, tRNA, paromomycin,
mRNA, translation; 2.8A {Thermus thermophilus}
(N:1-63,N:93-140)
Length = 111
Score = 118 bits (298), Expect = 4e-28
Identities = 49/141 (34%), Positives = 77/141 (54%), Gaps = 32/141 (22%)
Query: 4 TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
T+ K +VE +W+L+DA+G +GRLA++IA LRGK++P +TP+ GD VV++NA K+
Sbjct: 3 TYVPK--QVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI 60
Query: 64 AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
+ P +L+ A+ MLP+GPL R+ K
Sbjct: 61 RVTT------------------------------HPERVLEHAVKGMLPKGPLGRRLFKR 90
Query: 124 LHIYAEDHHPHEAQKPVFMDI 144
L +YA HPH+AQ+P +++
Sbjct: 91 LKVYAGPDHPHQAQRPEKLEV 111
>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S
ribosomal subunit, ribosomal protein/RNA complex; 8.70A
{Canis familiaris} (j:)
Length = 203
Score = 115 bits (290), Expect = 2e-27
Identities = 25/143 (17%), Positives = 54/143 (37%), Gaps = 14/143 (9%)
Query: 13 EKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQ 72
E + +++D +G ++GRLA+ +A ++ G VV++ + SG Y
Sbjct: 3 EVQVLVLDGRGHLLGRLAAIVAKQVLL------------GRKVVVVRCEGINISGNFYRN 50
Query: 73 KTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPR-GPLARKQMKNLHIYAEDH 131
K Y + +P+ I + + MLP + + L ++
Sbjct: 51 KLNYLAFLRKRMNTNPSRGPYDF-RAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIP 109
Query: 132 HPHEAQKPVFMDIAKMNPKNSRR 154
P++ +K + + A +
Sbjct: 110 PPYDKKKRMVVPAALKVVRLKPT 132
>2j01_N 50S ribosomal protein L13; ribosome, tRNA, paromomycin,
mRNA, translation; 2.8A {Thermus thermophilus}
(N:64-92)
Length = 29
Score = 35.1 bits (80), Expect = 0.004
Identities = 16/29 (55%), Positives = 23/29 (79%)
Query: 67 GKKYDQKTYYRHTGYPGGIKKTTAKEILA 95
GKK +QK Y R++GYPGG+KK +++LA
Sbjct: 1 GKKLEQKIYTRYSGYPGGLKKIPLEKMLA 29
>3c85_A Putative glutathione-regulated potassium-efflux system
protein KEFB; TRKA domain; HET: AMP; 1.90A {Vibrio
parahaemolyticus rimd 2210633} (A:)
Length = 183
Score = 26.2 bits (57), Expect = 2.4
Identities = 4/42 (9%), Positives = 9/42 (21%)
Query: 25 IVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFS 66
I + K V+I+ ++
Sbjct: 12 IYQHSGKWLQETAAEKLNQRDQLINPGHAQVLILGXGRIGTG 53
>1h2w_A Prolyl endopeptidase; hydrolase, prolyl oligopeptidase,
amnesia, alpha/ beta- hydrolase, beta-propeller, serine
protease; 1.39A {Sus scrofa} (A:378-428)
Length = 51
Score = 25.4 bits (56), Expect = 3.4
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 61 SKVAFSGKKYDQKTYYRHTGY--PGGI 85
S V +SG+K D + +Y+ T + PG I
Sbjct: 4 SVVGYSGQKKDTEIFYQFTSFLSPGII 30
>2h1q_A Hypothetical protein; ZP_00559375.1, structural genomics,
PSI-2, protein structure initiative; 2.01A
{Desulfitobacterium hafniense dcb-2} (A:)
Length = 270
Score = 25.2 bits (55), Expect = 4.4
Identities = 3/32 (9%), Positives = 8/32 (25%)
Query: 77 RHTGYPGGIKKTTAKEILAGASPTNILKKAIA 108
R + + N ++ +I
Sbjct: 66 RXPXLTQNLLGLPLRVAAGCVKSWNYVEASIG 97
>3h9e_A Glyceraldehyde-3-phosphate dehydrogenase, testis- specific;
oxidoreductase, structural genomics, structural genomics
consortium, SGC, cytoplasm; HET: NAD; 1.72A {Homo
sapiens} PDB: 2vyn_D* 2vyv_D* (A:1-155,A:321-346)
Length = 181
Score = 25.1 bits (54), Expect = 5.0
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 4/37 (10%)
Query: 39 GKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTY 75
G N+ Y P ++ NAS+ +S + D Y
Sbjct: 137 GVNENDYNPG----SMNIVSNASEYGYSHRVVDLLRY 169
>2hur_A NDK, nucleoside diphosphate kinase, NDP kinase; type II
tetramer, signaling protein,transferase; 1.62A
{Escherichia coli} (A:)
Length = 142
Score = 24.6 bits (53), Expect = 6.8
Identities = 11/50 (22%), Positives = 17/50 (34%), Gaps = 4/50 (8%)
Query: 101 NILKKAIARMLPRGPLARKQMKNLHIY---AEDHHPHEAQKPVFMDIAKM 147
N++ AR G K LH+ A + KP F + +
Sbjct: 17 NVIGNIFARFEAAG-FKIVGTKMLHLTVEQARGFYAEHDGKPFFDGLVEF 65
>2zb4_A Prostaglandin reductase 2; rossmann fold, alternative
splicing, cytoplasm, NADP, oxidoreductase; HET: NAP
5OP; 1.63A {Homo sapiens} PDB: 2zb7_A* 2zb8_A* 2w98_A*
2vna_A* 2w4q_A* 1vj1_A 2zb3_A* (A:133-318)
Length = 186
Score = 24.1 bits (51), Expect = 7.9
Identities = 12/71 (16%), Positives = 21/71 (29%)
Query: 13 EKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQ 72
K ++V G +A QI L + + + A + KK +
Sbjct: 28 SNKTMVVSGAAGACGSVAGQIGHFLGCSRVVGICGTHEKCILLTSELGFDAAINYKKDNV 87
Query: 73 KTYYRHTGYPG 83
R + G
Sbjct: 88 AEQLRESCPAG 98
>1vbk_A Hypothetical protein PH1313; structural genomics, riken
structural genomics/proteomics initiative, RSGI, NPPSFA;
1.90A {Pyrococcus horikoshii OT3} (A:173-291)
Length = 119
Score = 24.4 bits (53), Expect = 8.2
Identities = 6/47 (12%), Positives = 14/47 (29%)
Query: 1 MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTP 47
+ + K ++ + + S+I + P Y P
Sbjct: 71 SFDRVLKLIRDFGVKGVIKGLRPNDLNSEVSEITEDFKMFPVPVYYP 117
>2np9_A DPGC; protein inhibitor complex, oxidoreductase; HET: YE1;
2.45A {Streptomyces toyocaensis} PDB: 2pg8_A*
(A:148-237,A:286-402)
Length = 207
Score = 24.3 bits (52), Expect = 8.3
Identities = 6/22 (27%), Positives = 14/22 (63%)
Query: 103 LKKAIARMLPRGPLARKQMKNL 124
+++++ R+ LA ++M NL
Sbjct: 183 IERSLTRLDGDAVLANRRMLNL 204
>3c8u_A Fructokinase; YP_612366.1, putative fructose transport
system kinase, structural genomics, joint center for
structural genomics, JCSG; 1.95A {Silicibacter SP}
(A:1-61,A:124-208)
Length = 146
Score = 23.9 bits (52), Expect = 8.9
Identities = 8/30 (26%), Positives = 12/30 (40%)
Query: 29 LASQIALRLRGKNKPTYTPSADDGDHVVII 58
L++ +A L + P D V II
Sbjct: 38 LSNPLAAALSAQGLPAEVVPXDGFCRVAII 67
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.317 0.133 0.386
Gapped
Lambda K H
0.267 0.0641 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,214,118
Number of extensions: 52109
Number of successful extensions: 140
Number of sequences better than 10.0: 1
Number of HSP's gapped: 122
Number of HSP's successfully gapped: 22
Length of query: 155
Length of database: 4,956,049
Length adjustment: 81
Effective length of query: 74
Effective length of database: 2,217,844
Effective search space: 164120456
Effective search space used: 164120456
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: 51 (23.6 bits)