RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 040226
(137 letters)
>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 = 167 bits (424), Expect = 2e-53
Identities = 84/117 (71%), Positives = 100/117 (85%)
Query: 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
M ISKKRK VADGVF+AELNE TRELAE+GYSGVEVRVTP +TE+IIRATRTQ+VLG
Sbjct: 1 MVALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLG 60
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRR 117
E GRRI ELT +VQKRFK+ ++ LYAE+V +RGL A+AQAES+++KLL GLA+RR
Sbjct: 61 ENGRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRR 117
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 243
Score = 165 bits (419), Expect = 1e-52
Identities = 106/119 (89%), Positives = 108/119 (90%)
Query: 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
MA QISKKRKFVADG+F AELNE LTRELAEDGYSGVEVRVTP RTEIII ATRTQNVLG
Sbjct: 1 MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG 60
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYI 119
EKGRRIRELT+VVQKRF FPE SVELYAEKV RGLCAIAQAESLRYKLLGGLAVRR
Sbjct: 61 EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRAC 119
>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 = 164 bits (417), Expect = 2e-52
Identities = 108/119 (90%), Positives = 113/119 (94%)
Query: 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
MATQISKK+KFV+DGVF+AELNE+LTRELAEDGYSGVEVRVTP+RTEIIIRATRTQNVLG
Sbjct: 1 MATQISKKKKFVSDGVFYAELNEMLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLG 60
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYI 119
EKGRRIRELTSVVQKRF F EN VELYAEKV NRGLCAIAQAESLRYKLLGGLAVRR
Sbjct: 61 EKGRRIRELTSVVQKRFNFLENGVELYAEKVVNRGLCAIAQAESLRYKLLGGLAVRRAC 119
>2xzm_C KH domain containing protein; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_C
Length = 243
Score = 155 bits (394), Expect = 7e-49
Identities = 55/117 (47%), Positives = 84/117 (71%)
Query: 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60
I+KK+KFVADGVF AEL+ ++ L + GY+G+EVR TP +TEI I+AT+ Q V+G
Sbjct: 4 TTRAINKKKKFVADGVFNAELHSFFSKSLQDAGYAGIEVRRTPTKTEIRIKATKPQQVIG 63
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRR 117
+G++ +ELT +QKRF + ++ ++++AE + +GLCA AQ E++ YKLL + VR
Sbjct: 64 VEGKKHKELTQFLQKRFGYSDDQIQIWAEPIKFKGLCASAQVEAMNYKLLKDVPVRL 120
>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 = 126 bits (319), Expect = 2e-39
Identities = 70/89 (78%), Positives = 72/89 (80%)
Query: 12 VADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTS 71
F AELNE LTRELAEDGYSGVEVRVTP RTEIII ATRTQNVLGEKGRRIRELT+
Sbjct: 3 SGSSGFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTA 62
Query: 72 VVQKRFKFPENSVELYAEKVNNRGLCAIA 100
VVQKRF FPE SVELYAEKV RG +
Sbjct: 63 VVQKRFGFPEGSVELYAEKVATRGSGPSS 91
>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 = 34.9 bits (79), Expect = 0.003
Identities = 12/44 (27%), Positives = 21/44 (47%), Gaps = 15/44 (34%)
Query: 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAI-AQAE 103
EK + +++L + S++LYA+ + L AI A E
Sbjct: 18 EK-QALKKL-----------QASLKLYADD-SAPAL-AIKATME 47
>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 = 32.7 bits (74), Expect = 0.026
Identities = 16/57 (28%), Positives = 21/57 (36%), Gaps = 20/57 (35%)
Query: 13 ADGVFFAELNEVLTRELAEDGYSGVE-VRVTPVRTEIIIRATRTQNVLGEKGRRIRE 68
AD F G+S ++ V P + I GEKG+RIRE
Sbjct: 1649 ADNHFKDTY-----------GFSILDIVINNP--VNLTIHFG------GEKGKRIRE 1686
Score = 29.2 bits (65), Expect = 0.43
Identities = 21/122 (17%), Positives = 29/122 (23%), Gaps = 47/122 (38%)
Query: 25 LTRELAEDGYSGVEV---RVTPVRTEIIIRA-----TRTQN--------------VLGEK 62
+ E DG E + T R+ + TQ L K
Sbjct: 1691 MIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSK 1750
Query: 63 GRR-------------------------IRELTSVVQKRFKFPENSVELYAEKVNNRGLC 97
G I L VV R + +V +N G+
Sbjct: 1751 GLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMI 1810
Query: 98 AI 99
AI
Sbjct: 1811 AI 1812
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 218
Score = 31.0 bits (71), Expect = 0.079
Identities = 14/111 (12%), Positives = 40/111 (36%), Gaps = 5/111 (4%)
Query: 7 KKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRI 66
K R + + + +G + +E++ ++II + ++ + + +
Sbjct: 38 KIRDCI-----KNYVQKNTKTSSGVEGIARIEIQKRIDLIQVIIHMGFPKLLIENRPQGV 92
Query: 67 RELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRR 117
+L VQK + + ++ AE + +L ++ R+
Sbjct: 93 EDLKINVQKELNCVNRKLNIAITRIAKPYGDPNILAEFIAGQLKSRVSFRK 143
>1wpw_A 3-isopropylmalate dehydrogenase; oxidoreductase; 2.80A {Sulfolobus
tokodaii} SCOP: c.77.1.1
Length = 336
Score = 27.9 bits (63), Expect = 1.0
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 6/43 (13%)
Query: 24 VLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRI 66
++ RE ED Y G E V+ + TR RI
Sbjct: 113 LIVRENTEDLYKGFEHIVSDGVAVGMKIITR------FASERI 149
>3blx_A Isocitrate dehydrogenase [NAD] subunit 1; TCA cycle, oxidative
metabolism, allostery, decarboxylase, allosteric enzyme,
magnesium; 2.70A {Saccharomyces cerevisiae} PDB: 3blw_A
3blv_A*
Length = 349
Score = 26.8 bits (60), Expect = 2.7
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 6/43 (13%)
Query: 24 VLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRI 66
++ RE E +SG+E P E + TR K RI
Sbjct: 126 IVIRENTEGEFSGLEHESVPGVVESLKVMTR------PKTERI 162
>2ab1_A Hypothetical protein; HS.95870, DUF498, structural genomics,
protein structure INI PSI, center for eukaryotic
structural genomics, CESG; 2.59A {Homo sapiens} SCOP:
c.103.1.1 PDB: 2q4q_A
Length = 122
Score = 26.0 bits (57), Expect = 3.0
Identities = 8/31 (25%), Positives = 12/31 (38%), Gaps = 7/31 (22%)
Query: 36 GVEVRVTPVRTEIIIRATRTQNVLGEKGRRI 66
V V T +A + N L +G R+
Sbjct: 91 DVRVLQTE-------QAVKEYNALVAQGVRV 114
>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 = 26.1 bits (58), Expect = 3.8
Identities = 24/95 (25%), Positives = 41/95 (43%), Gaps = 3/95 (3%)
Query: 23 EVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPEN 82
+L +EL G + V++ + + + V+G G RIR L + K
Sbjct: 41 GLLEKELYSAGLARVDIERAADNVAVTVHVAKPGVVIGRGGERIRVLREELAKLTG---K 97
Query: 83 SVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRR 117
+V L ++V N L A A+ + ++ AVRR
Sbjct: 98 NVALNVQEVQNPNLSAPLVAQRVAEQIERRFAVRR 132
>1wyu_A Glycine dehydrogenase (decarboxylating) subunit 1; alpha(2)beta(2)
tetramer, riken structural genomics/proteomi initiative,
RSGI; HET: PLP; 2.10A {Thermus thermophilus} SCOP:
c.67.1.7 PDB: 1wyt_A* 1wyv_A*
Length = 438
Score = 26.4 bits (59), Expect = 3.9
Identities = 8/61 (13%), Positives = 17/61 (27%), Gaps = 5/61 (8%)
Query: 1 MATQISKKRKFVADGVFFAELNEVL-TRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVL 59
+A + + + + E VL E G ++ P+ + V
Sbjct: 143 LALRETGRMGVLVSQGVHPEYRAVLRAY--LE--AVGAKLLTLPLEGGRTPLPEVGEEVG 198
Query: 60 G 60
Sbjct: 199 A 199
>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 = 3.9
Identities = 23/95 (24%), Positives = 40/95 (42%), Gaps = 3/95 (3%)
Query: 23 EVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPEN 82
+ LT+ELA+ S + + + I R V+G+KG + +L VV
Sbjct: 40 QYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAG---V 96
Query: 83 SVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRR 117
++ +V L A A+S+ +L + RR
Sbjct: 97 PAQINIAEVRKPELDAKLVADSITSQLERRVMFRR 131
>3blx_B Isocitrate dehydrogenase [NAD] subunit 2; TCA cycle, oxidative
metabolism, allostery, decarboxylase, allosteric enzyme,
magnesium; 2.70A {Saccharomyces cerevisiae} PDB: 3blw_B*
3blv_B
Length = 354
Score = 26.0 bits (58), Expect = 4.0
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 6/43 (13%)
Query: 24 VLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRI 66
VL RE E YSG+E V P + I TR + R+
Sbjct: 132 VLIRENTEGEYSGIEHIVCPGVVQSIKLITR------DASERV 168
>3tva_A Xylose isomerase domain protein TIM barrel; structural genomics,
PSI-biology, midwest center for structu genomics, MCSG;
HET: MSE; 2.15A {Planctomyces limnophilus}
Length = 290
Score = 25.9 bits (57), Expect = 4.8
Identities = 7/51 (13%), Positives = 13/51 (25%), Gaps = 1/51 (1%)
Query: 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTS 71
L L + V+V T A + G ++ +
Sbjct: 23 LGVHL-EVAQDLKVPTVQVHAPHPHTRTREHAQAFRAKCDAAGIQVTVIFG 72
>2a3l_A AMP deaminase, AMPD; atampd, AT2G38280, adenosine 5'-monophosphate
deaminase, COF 5'-phosphate, structural genomics; HET:
CF5; 3.34A {Arabidopsis thaliana} SCOP: c.1.9.1
Length = 701
Score = 26.2 bits (57), Expect = 5.2
Identities = 7/28 (25%), Positives = 12/28 (42%)
Query: 14 DGVFFAELNEVLTRELAEDGYSGVEVRV 41
G F E+ + + +L Y E R+
Sbjct: 349 QGRFLGEITKQVFSDLEASKYQMAEYRI 376
>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 = 5.3
Identities = 23/95 (24%), Positives = 40/95 (42%), Gaps = 3/95 (3%)
Query: 23 EVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPEN 82
+ LT+ELA+ S + + + I R V+G+KG + +L VV
Sbjct: 41 QYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAG---V 97
Query: 83 SVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRR 117
++ +V L A A+S+ +L + RR
Sbjct: 98 PAQINIAEVRKPELDAKLVADSITSQLERRVMFRR 132
>3obe_A Sugar phosphate isomerase/epimerase; structural genomics, joint
center for structural genomics, J protein structure
initiative; HET: MSE; 1.70A {Parabacteroides
distasonis}
Length = 305
Score = 25.4 bits (55), Expect = 6.8
Identities = 6/23 (26%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 17 FFAELNEVLTRELAEDGYSGVEV 39
++ L LA+ GY+ +E+
Sbjct: 34 LLQDMPNGL-NRLAKAGYTDLEI 55
>3ty4_A Probable homoisocitrate dehydrogenase; B-hydroxyacid oxidative
decarboxylase, amino-acid biosynthes lysine
biosynthesis; 1.55A {Schizosaccharomyces pombe} PDB:
3ty3_A
Length = 366
Score = 25.3 bits (56), Expect = 7.3
Identities = 9/31 (29%), Positives = 12/31 (38%)
Query: 24 VLTRELAEDGYSGVEVRVTPVRTEIIIRATR 54
V+ RE E Y E V + + A R
Sbjct: 127 VIVRENTECLYVKEERMVQNTPGKRVAEAIR 157
>2d4v_A Isocitrate dehydrogenase; alpha and beta protein,
isocitrate/isopropylmalate dehydrogenase-like fold,
oxidoreductase; HET: FLC NAD; 1.90A {Acidithiobacillus
thiooxidans}
Length = 429
Score = 25.4 bits (56), Expect = 7.8
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 24 VLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRF 77
V+ RE +ED Y+G+E E IIR R + +G R + +++ K
Sbjct: 150 VIFRENSEDIYAGIEWPAGSPEAEKIIRFLREE--MGVTKIRFPDSSAIGIKPV 201
>2d1c_A Isocitrate dehydrogenase; structural genomics, NPPSFA, national
project protein structural and functional analyses; HET:
NAP CIT; 1.80A {Thermus thermophilus}
Length = 496
Score = 25.4 bits (56), Expect = 8.8
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 24 VLTRELAEDGYSGVEVRVTP 43
V+ RE ED Y+G+E TP
Sbjct: 134 VVVRENVEDLYAGIEHMQTP 153
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 0.137 0.368
Gapped
Lambda K H
0.267 0.0659 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,026,328
Number of extensions: 116900
Number of successful extensions: 305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 305
Number of HSP's successfully gapped: 31
Length of query: 137
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 53
Effective length of database: 4,356,429
Effective search space: 230890737
Effective search space used: 230890737
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: 52 (24.0 bits)