RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 046473
(120 letters)
>2xzm_C KH domain containing protein; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_C
Length = 243
Score = 132 bits (335), Expect = 4e-40
Identities = 48/109 (44%), Positives = 77/109 (70%)
Query: 1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
+QKRF + ++ ++++AE + +GLCA AQ E++ + L + ++A +++ +++ G
Sbjct: 74 QFLQKRFGYSDDQIQIWAEPIKFKGLCASAQVEAMNYKLLKDVPVRLAANYIIKSVIQDG 133
Query: 61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
AKGCE+I+SGKL+ QRA +MKFK GYMI +G P +YID AVRHV +Q
Sbjct: 134 AKGCEIIISGKLKQQRAKTMKFKQGYMICTGQPKNDYIDVAVRHVFFKQ 182
>3u5c_D RP13, YS3, 40S ribosomal protein S3; translation, ribosome,
ribosomal, ribosomal R ribosomal protein, eukaryotic
ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_B 3o30_C 3o2z_C 3u5g_D 1s1h_C
3jyv_C*
Length = 240
Score = 120 bits (303), Expect = 2e-35
Identities = 64/109 (58%), Positives = 85/109 (77%)
Query: 1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
VQKRFK+ ++ LYAE+V +RGL A+AQAES++ + L + + A YGV+R++MESG
Sbjct: 71 LLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVVRYVMESG 130
Query: 61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
AKGCEV+VSGKLRA RA +MKF DG++I SG PV ++ID+A RHVL RQ
Sbjct: 131 AKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQ 179
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 243
Score = 117 bits (296), Expect = 2e-34
Identities = 81/109 (74%), Positives = 88/109 (80%)
Query: 1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
+ VQKRF FPE SVELYAEKV RGLCAIAQAESLR + L + + ACYGVLRFIMESG
Sbjct: 71 AVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESG 130
Query: 61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
AKGCEV+VSGKLR QRA SMKF DG MI SG PV Y+D+AVRHVL RQ
Sbjct: 131 AKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQ 179
>3iz6_B 40S ribosomal protein S3 (S3P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
1s1h_C 3jyv_C*
Length = 227
Score = 117 bits (294), Expect = 4e-34
Identities = 88/109 (80%), Positives = 93/109 (85%)
Query: 1 SAVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRKEGLAVIVCKMACYGVLRFIMESG 60
S VQKRF F EN VELYAEKV NRGLCAIAQAESLR + L + + ACYGVLRF+MESG
Sbjct: 71 SVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESG 130
Query: 61 AKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVRHVLXRQ 109
AKGCEVIVSGKLRAQRA SMKFKDGYMISSG PV EYID+AVRHVL RQ
Sbjct: 131 AKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQ 179
>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken
structural genomics/proteomics initiative, RSGI,
ribosome; NMR {Homo sapiens} SCOP: d.52.3.1
Length = 92
Score = 48.3 bits (115), Expect = 7e-09
Identities = 19/30 (63%), Positives = 21/30 (70%)
Query: 1 SAVQKRFKFPENSVELYAEKVNNRGLCAIA 30
+ VQKRF FPE SVELYAEKV RG +
Sbjct: 62 AVVQKRFGFPEGSVELYAEKVATRGSGPSS 91
>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 = 38.9 bits (90), Expect = 1e-04
Identities = 18/91 (19%), Positives = 33/91 (36%), Gaps = 21/91 (23%)
Query: 3 VQKRFKFPENSVELYAEKVNNRGLCAI---AQAESLRKEGLAVIVCKMACYGVLRFIMES 59
V R + +V +N G+ AI A S +E L +V ++ +
Sbjct: 1786 VFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVG--------KRT 1837
Query: 60 G---------AKGCEVIVSGKLRA-QRATSM 80
G + + + +G LRA T++
Sbjct: 1838 GWLVEIVNYNVENQQYVAAGDLRALDTVTNV 1868
Score = 33.5 bits (76), Expect = 0.010
Identities = 14/66 (21%), Positives = 19/66 (28%), Gaps = 21/66 (31%)
Query: 26 LCAIAQAESLRKEGLAVIVCKMA-----------CY-GVLRFIMESGAKGCEVIVS--GK 71
L A E L+ +GL A V+ ES + +V G
Sbjct: 1738 LMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSI--ESLVE----VVFYRGM 1791
Query: 72 LRAQRA 77
Q A
Sbjct: 1792 T-MQVA 1796
Score = 29.2 bits (65), Expect = 0.30
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 51 GVLRFIMESGAKGCEVIVSGKLRAQRATSMKFK 83
GVL + G G VIV+G L FK
Sbjct: 513 GVLTHRNKDG-TGVRVIVAGTLDINPDDDYGFK 544
>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 = 29.9 bits (66), Expect = 0.13
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 4/32 (12%)
Query: 4 QKR-FKFPENSVELYAEKVNNRGLCAI-AQAE 33
+K+ K + S++LYA+ + L AI A E
Sbjct: 18 EKQALKKLQASLKLYADD-SAPAL-AIKATME 47
>3rko_M NADH-quinone oxidoreductase subunit M; complex I, proton pump,
membrane protein, Na ubiquinone, cytoplasmic membrane;
HET: LFA CA7; 3.00A {Escherichia coli}
Length = 509
Score = 27.7 bits (62), Expect = 1.00
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 40 LAVIVCKMACYGVLRFIME 58
LA I+ K A YG+LRF +
Sbjct: 259 LAGILLKTAAYGLLRFSLP 277
>3k8t_A Ribonucleoside-diphosphate reductase large chain; eukaryotic
ribonucleotide reductase, nucleotide analogs, all enzyme
ATP-binding; HET: DGT 2A5; 2.10A {Saccharomyces
cerevisiae} PDB: 1zyz_A 2cvs_A 2cvt_A* 2cvu_A* 2cvv_A*
1zzd_A* 2cvw_A* 2cvy_A* 2eud_A* 2zlf_A 2zlg_A* 2cvx_A*
3paw_A 3s87_A* 3s8b_A* 3s8c_A* 3s8a_A* 3tb9_A* 3tba_A*
Length = 888
Score = 26.4 bits (58), Expect = 3.1
Identities = 15/61 (24%), Positives = 23/61 (37%)
Query: 44 VCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYPVKEYIDSAVR 103
VC +A + FI S KL + + + + YPV+E S +R
Sbjct: 442 VCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMR 501
Query: 104 H 104
H
Sbjct: 502 H 502
>3r8n_C 30S ribosomal protein S3; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2gyb_C 2gy9_C* 2ykr_C 3fih_C* 2wwl_C 3oar_C
3oaq_C 3ofb_C 3ofa_C 3ofp_C 3ofx_C 3ofy_C 3ofo_C 3r8o_C
4a2i_C
Length = 206
Score = 25.9 bits (58), Expect = 3.3
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 57 MESGAKGCEVIVSGKL 72
M GAKG +V VSG+L
Sbjct: 141 MRLGAKGIKVEVSGRL 156
>3od1_A ATP phosphoribosyltransferase regulatory subunit; structural
genomics, PSI-2, protein structure initiative; 1.97A
{Bacillus halodurans}
Length = 400
Score = 26.1 bits (58), Expect = 3.7
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 28 AIAQAESLRKEGLAVIVCKMA 48
AI A R G AV++ +A
Sbjct: 351 AIELARKKRANGEAVVLQDLA 371
>3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C
3i1q_C 3i1s_C 3i1z_C 3i21_C 3izv_G* 3izw_G* 3kc4_C
3or9_C 3ora_C 3sfs_C* 3uoq_C* 2qal_C* 1p6g_C 1p87_C
2aw7_C ...
Length = 233
Score = 25.7 bits (57), Expect = 3.9
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 57 MESGAKGCEVIVSGKL 72
M GAKG +V VSG+L
Sbjct: 142 MRLGAKGIKVEVSGRL 157
>2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C*
1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F*
1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C
1xmo_C* 1xmq_C* 1xnq_C* ...
Length = 239
Score = 25.7 bits (57), Expect = 4.2
Identities = 12/16 (75%), Positives = 15/16 (93%)
Query: 57 MESGAKGCEVIVSGKL 72
MESGAKG +VIVSG++
Sbjct: 142 MESGAKGAKVIVSGRI 157
>4du5_A PFKB; structural genomics, PSI-biology, NEW YORK structural genomi
research consortium, nysgrc, transferase; 2.70A
{Polaromonas SP}
Length = 336
Score = 25.3 bits (56), Expect = 6.6
Identities = 14/68 (20%), Positives = 23/68 (33%), Gaps = 26/68 (38%)
Query: 32 AESLRKEGLAVIVCKMACYGVLRFIMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSG 91
A R+ G ++V K+ GA+G + G +G
Sbjct: 238 ARFYRQLGAKLVVVKL------------GAEGAYF--------------DGEAGSGRVAG 271
Query: 92 YPVKEYID 99
+PV E +D
Sbjct: 272 FPVAEVVD 279
>1vj7_A Bifunctional RELA/SPOT; HD domain, alpha beta 2-layer sandwich,
helix bundle, mangan PPG2':3'P, (P)PPGPP, PPGPP; HET:
GDP GPX; 2.10A {Streptococcus dysgalactiae subsp} SCOP:
a.211.1.1 d.218.1.8
Length = 393
Score = 25.2 bits (56), Expect = 7.1
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 6/25 (24%)
Query: 30 AQAESLRKEGLA------VIVCKMA 48
AE+ RK +A VI+ K+A
Sbjct: 119 QLAENHRKMLMAMSKDIRVILVKLA 143
>2q5c_A NTRC family transcriptional regulator; structural genomics, protein
structure initiative; HET: SO4 GOL; 1.49A {Clostridium
acetobutylicum atcc 824}
Length = 196
Score = 24.7 bits (54), Expect = 8.1
Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 56 IMESGAKGCEVIVSGKLRAQRATSMKFKDGYMISSGYP-VKEYIDSAVRHVLXRQ 109
I + + +++VSGK A G I+SG ++ I+ A+ + R
Sbjct: 135 ISKVKTENIKIVVSGKTVTDEAIKQGLY-GETINSGEESLRRAIEEALNLIEVRN 188
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 218
Score = 24.8 bits (55), Expect = 8.6
Identities = 3/16 (18%), Positives = 11/16 (68%)
Query: 57 MESGAKGCEVIVSGKL 72
++ KG ++ ++G++
Sbjct: 153 EQADTKGIQIQIAGRI 168
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
0.323 0.135 0.388
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,732,545
Number of extensions: 93009
Number of successful extensions: 164
Number of sequences better than 10.0: 1
Number of HSP's gapped: 159
Number of HSP's successfully gapped: 23
Length of query: 120
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 38
Effective length of database: 4,412,271
Effective search space: 167666298
Effective search space used: 167666298
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.3 bits)