RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9398
(154 letters)
>3r8n_I 30S ribosomal protein S9; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2ykr_I 3fih_I* 3iy8_I 2wwl_I 3oar_I 3oaq_I
3ofb_I 3ofa_I 3ofp_I 3ofx_I 3ofy_I 3ofo_I 3r8o_I 4a2i_I
2qal_I* 1p6g_I 1p87_I 2aw7_I 2avy_I 2i2u_I ...
Length = 127
Score = 128 bits (324), Expect = 2e-39
Identities = 48/83 (57%), Positives = 61/83 (73%)
Query: 68 NYKYGTGRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMVISQPLKLTKHTKTFDI 127
N YGTGRRKS+ ARVFIK G+GK+ IN+ ++YF R+T MV+ QPL+L + D+
Sbjct: 1 NQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDL 60
Query: 128 KINVRGGGESGQYGAVRHGITRA 150
I V+GGG SGQ GA+RHGITRA
Sbjct: 61 YITVKGGGISGQAGAIRHGITRA 83
>2vqe_I 30S ribosomal protein S9, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.14.1.1
PDB: 1gix_L* 1hnw_I* 1hnx_I* 1hnz_I* 1hr0_I 1i94_I*
1i95_I* 1i96_I* 1i97_I* 1ibk_I* 1ibl_I* 1ibm_I 1j5e_I
1jgo_L* 1jgp_L* 1jgq_L* 1ml5_L* 1n32_I* 1n33_I* 1n34_I
...
Length = 128
Score = 126 bits (318), Expect = 2e-38
Identities = 37/80 (46%), Positives = 51/80 (63%)
Query: 71 YGTGRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMVISQPLKLTKHTKTFDIKIN 130
YGTGRRK A+ARVF++ G+GK+T+N ++YF + +PL+ FD I
Sbjct: 5 YGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFDAYIT 64
Query: 131 VRGGGESGQYGAVRHGITRA 150
VRGGG+SGQ A++ GI RA
Sbjct: 65 VRGGGKSGQIDAIKLGIARA 84
>3bbn_I Ribosomal protein S9; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 197
Score = 126 bits (317), Expect = 2e-37
Identities = 32/84 (38%), Positives = 43/84 (51%), Gaps = 1/84 (1%)
Query: 68 NYKYGTGRRKSAIARVFIKIGSGKMTINRIPADKYF-SRKTGLMVISQPLKLTKHTKTFD 126
GTGRRK AIARV ++ G+GK IN A +Y L + PL + +D
Sbjct: 70 QTVIGTGRRKCAIARVVLQEGTGKFIINYRDAKEYLQGNPLWLQYVKTPLATLGYETNYD 129
Query: 127 IKINVRGGGESGQYGAVRHGITRA 150
+ + GGG SGQ A+ G+ RA
Sbjct: 130 VFVKAHGGGLSGQAQAISLGVARA 153
>3iz6_I 40S ribosomal protein S16 (S9P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 149
Score = 110 bits (276), Expect = 8e-32
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 3/84 (3%)
Query: 69 YKYGTGRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMVISQPLKLTK--HTKTFD 126
GR+K+A+A + K G G + +N +P + + + +P+ L K D
Sbjct: 12 TVQCFGRKKTAVAVSYCKPGRGLIKVNGVPIE-LIRPEMLRLKAFEPILLAGRSRFKDID 70
Query: 127 IKINVRGGGESGQYGAVRHGITRA 150
++I VRGGG++ Q A+R I +A
Sbjct: 71 MRIRVRGGGKTSQIYAIRQAIAKA 94
>2zkq_i 40S ribosomal protein S16E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 146
Score = 109 bits (274), Expect = 2e-31
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 70 KYGTGRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMVISQPLKL-TKHTKTFDIK 128
GR+K+A A K G+G + +N P + R ++ L L + DI+
Sbjct: 10 VQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAGVDIR 69
Query: 129 INVRGGGESGQYGAVRHGITRA 150
+ V+GGG Q A+R I++A
Sbjct: 70 VRVKGGGHVAQIYAIRQSISKA 91
>3u5c_Q RP61R, 40S ribosomal protein S16-A; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_I 3o30_J 3o2z_J 3u5g_Q 1s1h_I
3jyv_I*
Length = 143
Score = 107 bits (269), Expect = 7e-31
Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 3/86 (3%)
Query: 67 VNYKYGTGRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMVISQPLKLTK--HTKT 124
V G++KSA A +K G G + +N P + + +PL L
Sbjct: 4 VPSVQTFGKKKSATAVAHVKAGKGLIKVNGSPIT-LVEPEILRFKVYEPLLLVGLDKFSN 62
Query: 125 FDIKINVRGGGESGQYGAVRHGITRA 150
DI++ V GGG Q A+R I +
Sbjct: 63 IDIRVRVTGGGHVSQVYAIRQAIAKG 88
>2xzm_I RPS16E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_I
Length = 145
Score = 106 bits (268), Expect = 1e-30
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 3/82 (3%)
Query: 71 YGTGRRKSAIARVFIKIGSGKMTINRIPADKYFSRKTGLMVISQPLKL--TKHTKTFDIK 128
GR+K+A+A ++ G G + +N P D + I +P+ L + DI+
Sbjct: 10 QTFGRKKNAVAVASVRPGKGLLKVNGSPIDMIN-PQILQAKIYEPILLLGQQKFANLDIR 68
Query: 129 INVRGGGESGQYGAVRHGITRA 150
I VRG G + Q A+R +++
Sbjct: 69 IRVRGSGYTSQVYAIRQALSKG 90
>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 = 97.2 bits (243), Expect = 6e-27
Identities = 36/92 (39%), Positives = 48/92 (52%), Gaps = 28/92 (30%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHID------------------------- 36
W LIDA+ K LGR+A+KIA LRGKH+ ++TP++
Sbjct: 13 WVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIY 72
Query: 37 ---TGYPGGIRKINFLKMQEDFPGRVLQKAVK 65
+GYPGG++KI KM P RVL+ AVK
Sbjct: 73 TRYSGYPGGLKKIPLEKMLATHPERVLEHAVK 104
>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 = 97.2 bits (243), Expect = 6e-27
Identities = 34/92 (36%), Positives = 48/92 (52%), Gaps = 28/92 (30%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHID------------------------- 36
W+++DA K LGR+A+++A LRGKHK EYTPH+D
Sbjct: 15 WYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVY 74
Query: 37 ---TGYPGGIRKINFLKMQEDFPGRVLQKAVK 65
TG+ GGI++ F +M P RV++ AVK
Sbjct: 75 YHHTGHIGGIKQATFEEMIARRPERVIEIAVK 106
>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 = 97.3 bits (243), Expect = 1e-26
Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 28/92 (30%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHID------------------------- 36
W ++DA LGR+A+ IA +RGKH+ ++TP++
Sbjct: 41 WVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVY 100
Query: 37 ---TGYPGGIRKINFLKMQEDFPGRVLQKAVK 65
TGY GG++ + P RV++ AV
Sbjct: 101 TRYTGYQGGLKTETAREALSKHPERVIEHAVF 132
>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 = 96.9 bits (242), Expect = 2e-26
Identities = 36/92 (39%), Positives = 48/92 (52%), Gaps = 28/92 (30%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHID------------------------- 36
W LIDA+ K LGR+A+KIA LRGKH+ ++TP++
Sbjct: 36 WVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKIRVTGKKLEQKIY 95
Query: 37 ---TGYPGGIRKINFLKMQEDFPGRVLQKAVK 65
+GYPGG++KI KM P RVL+ AVK
Sbjct: 96 TRYSGYPGGLKKIPLEKMLATHPERVLEHAVK 127
>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 = 97.6 bits (243), Expect = 6e-26
Identities = 28/92 (30%), Positives = 49/92 (53%), Gaps = 28/92 (30%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHID------------------------- 36
W+++DA + ILGR+AS IA+++RGK+ YTP +D
Sbjct: 114 WYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVVNADKVAVSGKKRTQKLY 173
Query: 37 ---TGYPGGIRKINFLKMQEDFPGRVLQKAVK 65
+G PGG+++ F ++Q+ P R+++ AV+
Sbjct: 174 RRHSGRPGGLKEETFDQLQKRIPERIIEHAVR 205
>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 = 94.2 bits (235), Expect = 1e-25
Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 28/92 (30%)
Query: 2 WFLIDAKNKILGRVASKIAVYLRGKHKTEYTPHID------------------------- 36
W+L+D K + G++A+ ++ L+G HK Y D
Sbjct: 18 WYLLDGKMQPPGKLAAMASIRLQGLHKPVYHALSDCGDHVVIMNTRHIAFSGNKWEQKVY 77
Query: 37 ---TGYPGGIRKINFLKMQEDFPGRVLQKAVK 65
TGYPGG R++ ++ P +++ A+
Sbjct: 78 SSHTGYPGGFRQVTAAQLHLRDPVAIVKLAIY 109
>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 = 57.7 bits (139), Expect = 4e-11
Identities = 21/104 (20%), Positives = 37/104 (35%), Gaps = 17/104 (16%)
Query: 2 WFLIDAKNKILGRVASKIAVYLR----------------GKHKTEYTPHIDTGYPGGIRK 45
+ID K ++GR+AS +A L G+ + D
Sbjct: 6 VVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRKATAFN 65
Query: 46 INFLKMQEDFPGRVLQKAVKVVNYKYGTGRRKSAIARVFIKIGS 89
P R+ KA++ + + T R K+A+ R+ + G
Sbjct: 66 KTRGPFHFRAPSRIFYKALRGM-VSHKTARGKAALERLKVFEGI 108
>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly,
ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1
Length = 142
Score = 56.1 bits (136), Expect = 6e-11
Identities = 11/78 (14%), Positives = 27/78 (34%), Gaps = 16/78 (20%)
Query: 4 LIDAKNKILGRVASKIAVYLR----------------GKHKTEYTPHIDTGYPGGIRKIN 47
+I+A ILGR+AS++A L G + ++ + +
Sbjct: 3 IINADGLILGRLASRVAKMLLEGEEVVIVNAEKAVITGNREVIFSKYKQRTGLRTLTNPR 62
Query: 48 FLKMQEDFPGRVLQKAVK 65
++++ ++
Sbjct: 63 RGPFYPKRSDEIVRRTIR 80
>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 = 56.5 bits (136), Expect = 1e-10
Identities = 19/104 (18%), Positives = 42/104 (40%), Gaps = 17/104 (16%)
Query: 2 WFLIDAKNKILGRVASKIAVYLR----------------GKHKTEYTPHIDTGYPGGIRK 45
++DA++ +LGR+AS +A L G + ++ K
Sbjct: 11 RVVVDARHHMLGRLASIVAKELLNGQRVVVVRCEEICMSGGLVRQKMKYLRFLRKRMNTK 70
Query: 46 INFLKMQEDFPGRVLQKAVKVVNYKYGTGRRKSAIARVFIKIGS 89
+ + P ++L + ++ + + T R ++A+AR+ G
Sbjct: 71 PSHGPIHFRAPAKILWRTIRGM-IPHKTARGEAALARLKAYEGV 113
>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 = 56.1 bits (135), Expect = 1e-10
Identities = 16/80 (20%), Positives = 24/80 (30%), Gaps = 16/80 (20%)
Query: 2 WFLIDAKNKILGRVASKIAVYLR----------------GKHKTEYTPHIDTGYPGGIRK 45
+IDAK +LGR+AS +A L G +
Sbjct: 5 LVVIDAKGHLLGRLASYVAKELLSGQRIVVVRTEAINISGSLFRNRVKFSEFLNKWMNHN 64
Query: 46 INFLKMQEDFPGRVLQKAVK 65
P R+ +AV+
Sbjct: 65 PRRGVQHFRAPSRIFWRAVR 84
>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
1s1i_M
Length = 178
Score = 53.6 bits (129), Expect = 9e-10
Identities = 21/102 (20%), Positives = 37/102 (36%), Gaps = 17/102 (16%)
Query: 4 LIDAKNKILGRVASKIAVYLR----------------GKHKTEYTPHIDTGYPGGIRKIN 47
+ID K ++GR+AS +A L G+ + D
Sbjct: 2 VIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRKATAFNKT 61
Query: 48 FLKMQEDFPGRVLQKAVKVVNYKYGTGRRKSAIARVFIKIGS 89
P R+ KA++ + + T R K+A+ R+ + G
Sbjct: 62 RGPFHFRAPSRIFYKALRGM-VSHKTARGKAALERLKVFEGI 102
>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 = 51.1 bits (123), Expect = 5e-09
Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 20/80 (25%)
Query: 2 WFLIDAKNKILGRVASKIAVYLR----------------GKHKTEYTPHIDTGYPGGIRK 45
++DA++ I+GRVAS++A G+ + + G
Sbjct: 9 DVIVDARDCIMGRVASQVAEQALDGETVAVVNAERAVITGREEQIVEKYEKRVDIGNDNG 68
Query: 46 INFLKMQEDFPGRVLQKAVK 65
+ K P + ++ ++
Sbjct: 69 YFYPK----RPDGIFKRTIR 84
>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 203
Score = 50.8 bits (121), Expect = 1e-08
Identities = 16/105 (15%), Positives = 38/105 (36%), Gaps = 19/105 (18%)
Query: 2 WFLIDAKNKILGRVASKIAVYLR----------------GKHKTEYTPHIDTGYPGGIRK 45
++D + +LGR+A+ +A + G ++
Sbjct: 6 VLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLNYLAFLRKRMNTN 65
Query: 46 INFLKMQEDFPGRVLQKAVK-VVNYKYGTGRRKSAIARVFIKIGS 89
+ P R+ + V+ ++ +K T R ++A+ R+ + G
Sbjct: 66 PSRGPYDFRAPSRIFWRTVRGMLPHK--TKRGQAALDRLKVFDGI 108
>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 = 38.5 bits (89), Expect = 4e-04
Identities = 22/77 (28%), Positives = 30/77 (38%), Gaps = 31/77 (40%)
Query: 72 GTG---RRKSAIAR-VFIKIGSGKMTINRIPADKYFSRKTGL----MVISQPLKLTKHTK 123
G G + S A+ V+ NR AD +F G +VI+ P+ LT H
Sbjct: 1630 GMGMDLYKTSKAAQDVW----------NR--ADNHFKDTYGFSILDIVINNPVNLTIH-- 1675
Query: 124 TFDIKINVRGGGESGQY 140
F GGE G+
Sbjct: 1676 -F--------GGEKGKR 1683
Score = 34.3 bits (78), Expect = 0.012
Identities = 22/102 (21%), Positives = 34/102 (33%), Gaps = 29/102 (28%)
Query: 16 ASKIAVYLRGKHKTEYTPHIDTGY-PGGIRKINFLKMQEDFPGRVLQKAVK--------- 65
++ V+ RG P + G G+ IN ++ F LQ V+
Sbjct: 1782 LVEV-VFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWL 1840
Query: 66 --VVNYK-----Y---GTGRRKSAIARV-----FIKIGSGKM 92
+VNY Y G A+ V FIK+ +
Sbjct: 1841 VEIVNYNVENQQYVAAGD---LRALDTVTNVLNFIKLQKIDI 1879
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 0.140 0.411
Gapped
Lambda K H
0.267 0.0586 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,430,606
Number of extensions: 144038
Number of successful extensions: 253
Number of sequences better than 10.0: 1
Number of HSP's gapped: 237
Number of HSP's successfully gapped: 35
Length of query: 154
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 69
Effective length of database: 4,328,508
Effective search space: 298667052
Effective search space used: 298667052
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: 53 (24.5 bits)