RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 032954
(130 letters)
>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly,
ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1
Length = 142
Score = 174 bits (443), Expect = 1e-57
Identities = 45/119 (37%), Positives = 64/119 (53%)
Query: 12 VVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKP 71
+++A +LGRLAS VAK LL G++VV V E+ ++G KY + R T P
Sbjct: 2 RIINADGLILGRLASRVAKMLLEGEEVVIVNAEKAVITGNREVIFSKYKQRTGLRTLTNP 61
Query: 72 SHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALK 130
GP + + +I RT+RGM+P KT RG A RLK Y G+P + + I +A
Sbjct: 62 RRGPFYPKRSDEIVRRTIRGMLPWKTDRGRKAFRRLKVYVGIPKEFQDKQLETIVEAHV 120
>1vq8_J 50S ribosomal protein L13P; 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.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 = 156 bits (398), Expect = 1e-50
Identities = 42/121 (34%), Positives = 67/121 (55%), Gaps = 6/121 (4%)
Query: 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNT 69
V+VDAR ++GR+AS VA++ L+G+ V V E ++G + KY KR++
Sbjct: 8 ADVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQIVEKY----EKRVDI 63
Query: 70 KPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDAL 129
+G + + P IF RT+RGM+PHK +RG A ++ Y G PYD+ ++ +L
Sbjct: 64 GNDNGYFYPKRPDGIFKRTIRGMLPHKKQRGREAFESVRVYLG--NPYDEDGEVLDGTSL 121
Query: 130 K 130
Sbjct: 122 D 122
>3iz5_K 60S ribosomal protein L13A (L13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_K
Length = 206
Score = 155 bits (394), Expect = 2e-49
Identities = 119/130 (91%), Positives = 124/130 (95%)
Query: 1 MVSGSGICAKRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYM 60
MVSGSG+CAKRVVVDARHHMLGRLASIVAKELLNGQ+VV VRCEEICMSGGLVRQKMKY+
Sbjct: 1 MVSGSGVCAKRVVVDARHHMLGRLASIVAKELLNGQRVVVVRCEEICMSGGLVRQKMKYL 60
Query: 61 RFLRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKV 120
RFLRKRMNTKPSHGPIHFRAPAKI WRT+RGMIPHKT RG AALARLKAYEGVP PYD+
Sbjct: 61 RFLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTARGEAALARLKAYEGVPPPYDRT 120
Query: 121 KRMVIPDALK 130
KRMVIPDALK
Sbjct: 121 KRMVIPDALK 130
>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
1s1i_M
Length = 178
Score = 152 bits (385), Expect = 2e-48
Identities = 69/119 (57%), Positives = 91/119 (76%)
Query: 12 VVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKP 71
VV+D + H++GRLAS+VAK+LLNGQK+V VR EE+ +SG R K+KY FLRK
Sbjct: 1 VVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRKATAFNK 60
Query: 72 SHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALK 130
+ GP HFRAP++IF++ +RGM+ HKT RG AAL RLK +EG+P PYDK KR+V+P AL+
Sbjct: 61 TRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQALR 119
>4a17_I RPL13A, 60S ribosomal protein L13A; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_I 4a1c_I 4a1e_I
Length = 198
Score = 150 bits (379), Expect = 3e-47
Identities = 75/124 (60%), Positives = 95/124 (76%)
Query: 7 ICAKRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKR 66
+ K VV+DA+ H+LGRLAS VAKELL+GQ++V VR E I +SG L R ++K+ FL K
Sbjct: 1 MFDKLVVIDAKGHLLGRLASYVAKELLSGQRIVVVRTEAINISGSLFRNRVKFSEFLNKW 60
Query: 67 MNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIP 126
MN P G HFRAP++IFWR VRGM+PHKT +GAAAL RLK +EG+P PYD+VK+ V+
Sbjct: 61 MNHNPRRGVQHFRAPSRIFWRAVRGMLPHKTPKGAAALERLKIFEGIPTPYDRVKKQVVV 120
Query: 127 DALK 130
DALK
Sbjct: 121 DALK 124
>3izc_K 60S ribosomal protein RPL16 (L13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_K
3o58_P 3o5h_P 3u5e_O 3u5i_O
Length = 199
Score = 147 bits (371), Expect = 5e-46
Identities = 69/121 (57%), Positives = 91/121 (75%)
Query: 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNT 69
VV+D + H++GRLAS+VAK+LLNGQK+V VR EE+ +SG R K+KY FLRK
Sbjct: 5 PVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRKATAF 64
Query: 70 KPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDAL 129
+ GP HFRAP++IF++ +RGM+ HKT RG AAL RLK +EG+P PYDK KR+V+P AL
Sbjct: 65 NKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQAL 124
Query: 130 K 130
+
Sbjct: 125 R 125
>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 203
Score = 140 bits (353), Expect = 2e-43
Identities = 80/121 (66%), Positives = 98/121 (80%)
Query: 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNT 69
+ +V+D R H+LGRLA+IVAK++L G+KVV VRCE I +SG R K+ Y+ FLRKRMNT
Sbjct: 5 QVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLNYLAFLRKRMNT 64
Query: 70 KPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDAL 129
PS GP FRAP++IFWRTVRGM+PHKTKRG AAL RLK ++G+P PYDK KRMV+P AL
Sbjct: 65 NPSRGPYDFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAAL 124
Query: 130 K 130
K
Sbjct: 125 K 125
>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial;
mitochondrial ribosome, large ribosomal subunit,
ribosomal R ribosome; 12.10A {Bos taurus}
Length = 148
Score = 50.7 bits (122), Expect = 4e-09
Identities = 25/119 (21%), Positives = 41/119 (34%), Gaps = 25/119 (21%)
Query: 12 VVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKY 59
++D + G+LA++ + L G VV + I SG QK+ Y
Sbjct: 19 YLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHIAFSGNKWEQKV-Y 77
Query: 60 MRF------LRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEG 112
R+ + +H R P I + GM+P K + RL +
Sbjct: 78 SSHTGYPGGFRQV-----TAAQLHLRDPVAIVKLAIYGMLP-KNLHRRTMMERLHLFPD 130
>3r8s_J 50S ribosomal protein L13; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {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 = 48.3 bits (116), Expect = 2e-08
Identities = 28/119 (23%), Positives = 50/119 (42%), Gaps = 25/119 (21%)
Query: 12 VVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKY 59
VVDA LGRLA+ +A+ L G ++ + +++ ++G K+ Y
Sbjct: 16 YVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKV-Y 74
Query: 60 MRF------LRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEG 112
+++ + + R P ++ V+GM+P K G A +LK Y G
Sbjct: 75 YHHTGHIGGIKQA-----TFEEMIARRPERVIEIAVKGMLP-KGPLGRAMFRKLKVYAG 127
>3v2d_N 50S ribosomal protein L13; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} 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 2wrj_N 2wrl_N
2wro_N 2wrr_N 2x9s_N 2x9u_N ...
Length = 140
Score = 48.3 bits (116), Expect = 2e-08
Identities = 34/119 (28%), Positives = 51/119 (42%), Gaps = 25/119 (21%)
Query: 12 VVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKY 59
V++DA LGRLA+ +A L G VV V ++I ++G + QK+ Y
Sbjct: 14 VLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI-Y 72
Query: 60 MRF------LRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEG 112
R+ L+K + P ++ V+GM+P K G RLK Y G
Sbjct: 73 TRYSGYPGGLKKI-----PLEKMLATHPERVLEHAVKGMLP-KGPLGRRLFKRLKVYAG 125
>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 = 48.0 bits (115), Expect = 4e-08
Identities = 34/119 (28%), Positives = 51/119 (42%), Gaps = 25/119 (21%)
Query: 12 VVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKY 59
V++DA LGRLA+ +A L G VV V ++I ++G + QK+ Y
Sbjct: 37 VLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKI-Y 95
Query: 60 MRF------LRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEG 112
R+ L+K + P ++ V+GM+P K G RLK Y G
Sbjct: 96 TRYSGYPGGLKKI-----PLEKMLATHPERVLEHAVKGMLP-KGPLGRRLFKRLKVYAG 148
>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* 3pio_G*
3pip_G* 1pnu_H 1pny_H 1vor_K 1vou_K 1vow_K 1voy_K 1vp0_K
Length = 174
Score = 47.6 bits (114), Expect = 7e-08
Identities = 32/119 (26%), Positives = 52/119 (43%), Gaps = 25/119 (21%)
Query: 12 VVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKY 59
VVVDA LGRLA+++A + G VV + ++ ++G + K+ Y
Sbjct: 42 VVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKV-Y 100
Query: 60 MRF------LRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEG 112
R+ L+ + + P ++ V GM+P K ++G A RLK Y G
Sbjct: 101 TRYTGYQGGLKTE-----TAREALSKHPERVIEHAVFGMLP-KGRQGRAMHTRLKVYAG 153
>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 = 46.7 bits (111), Expect = 2e-07
Identities = 34/119 (28%), Positives = 52/119 (43%), Gaps = 25/119 (21%)
Query: 12 VVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKY 59
VVDA +LGR+AS +A + G V+ V +++ +SG QK+ Y
Sbjct: 115 YVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVVNADKVAVSGKKRTQKL-Y 173
Query: 60 MRF------LRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEG 112
R L++ + + R P +I VRGM+P K + G LK Y+G
Sbjct: 174 RRHSGRPGGLKEE-----TFDQLQKRIPERIIEHAVRGMLP-KGRLGRYLFNHLKVYKG 226
>2btv_A T2A, T2B, protein (VP3 core protein); virus/viral protein,
icosahedral virus; 3.50A {Bluetongue virus} SCOP:
e.28.1.1
Length = 901
Score = 28.2 bits (62), Expect = 0.87
Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 1/68 (1%)
Query: 57 MKYMRFLRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAP 116
+ YM R ++N P+ P+ F+ + V T G A + PAP
Sbjct: 406 LLYMYNTRVQVNYGPTGEPLDFQIGRNQYDCNVFRADF-ATGTGYNGWATIDVEYRDPAP 464
Query: 117 YDKVKRMV 124
Y +R +
Sbjct: 465 YVHAQRYI 472
>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 = 27.2 bits (59), Expect = 1.3
Identities = 8/22 (36%), Positives = 9/22 (40%), Gaps = 5/22 (22%)
Query: 98 KRGAAAL-ARLKAYEGVP--AP 116
K+ L A LK Y AP
Sbjct: 19 KQALKKLQASLKLYA--DDSAP 38
>4ad9_A Lactb2, beta-lactamase-like protein 2; hydrolase, metallo-beta
lactamase, mitochondria; 2.60A {Homo sapiens}
Length = 289
Score = 27.5 bits (61), Expect = 1.5
Identities = 14/54 (25%), Positives = 20/54 (37%), Gaps = 6/54 (11%)
Query: 71 PSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPA-PYDKVKRM 123
P HGP+ A AKI + I H+ R L + + VK +
Sbjct: 198 PGHGPVIHNAEAKI-----QQYISHRNIREQQILTLFRENFEKSFTVMELVKII 246
>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 = 27.3 bits (60), Expect = 2.1
Identities = 25/133 (18%), Positives = 47/133 (35%), Gaps = 37/133 (27%)
Query: 9 AKRVVVDARHHM---LG-RLASIVA---KEL---LNGQKVVAVRCEEICMSGGLVRQ--- 55
A+ V A +H G + IV L G+K G +R+
Sbjct: 1642 AQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEK------------GKRIRENYS 1689
Query: 56 KMKYMRFLRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKR--------GAAALARL 107
M + + ++ T+ I+ + +R+ +G++ T+ AA L
Sbjct: 1690 AMIFETIVDGKLKTEKIFKEINEHST-SYTFRSEKGLL-SATQFTQPALTLMEKAAFEDL 1747
Query: 108 KAYEGVPAPYDKV 120
K+ +G+ P D
Sbjct: 1748 KS-KGL-IPADAT 1758
Score = 26.2 bits (57), Expect = 5.0
Identities = 23/125 (18%), Positives = 36/125 (28%), Gaps = 33/125 (26%)
Query: 2 VSGSGIC---AKRVVVDARHHML--GRLASIVAKELLNGQKVVAVRCEEICMSGG---LV 53
+S I VV A+ G L S + + Q +V I +
Sbjct: 236 ISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVA--IAETDSWESFF 293
Query: 54 RQKMKYMRFLRKRMNTKPSHGPIHFRAPAKIFWRTVRG--MIPHKTKRGAAALARLKAYE 111
K + L F+ VR P+ + + L+ E
Sbjct: 294 VSVRKAITVL---------------------FFIGVRCYEAYPNTSLPPSILEDSLENNE 332
Query: 112 GVPAP 116
GVP+P
Sbjct: 333 GVPSP 337
>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 = 26.7 bits (58), Expect = 3.0
Identities = 13/82 (15%), Positives = 22/82 (26%), Gaps = 41/82 (50%)
Query: 9 AKRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMN 68
AK V++ +LG + VA ++ KV + M
Sbjct: 150 AKNVLI---DGVLGSGKTWVALDVCLSYKV------QCKMDFK----------------- 183
Query: 69 TKPSHGPIHFRAPAKIFWRTVR 90
IFW ++
Sbjct: 184 ---------------IFWLNLK 190
>1z3i_X Similar to RAD54-like; recombination ATPase helicase,
recombination-DNA binding COM; 3.00A {Danio rerio} SCOP:
c.37.1.19 c.37.1.19
Length = 644
Score = 25.0 bits (55), Expect = 9.4
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 7/54 (12%)
Query: 17 RHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTK 70
++ R + I++K L + V V C ++ QK Y FL++ +
Sbjct: 292 NRCLIRRTSDILSKYLPVKIEQV-VCCN---LTP---LQKELYKLFLKQAKPVE 338
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
0.326 0.138 0.417
Gapped
Lambda K H
0.267 0.0639 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,161,353
Number of extensions: 123946
Number of successful extensions: 376
Number of sequences better than 10.0: 1
Number of HSP's gapped: 360
Number of HSP's successfully gapped: 29
Length of query: 130
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 47
Effective length of database: 4,384,350
Effective search space: 206064450
Effective search space used: 206064450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.0 bits)