RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17945
(214 letters)
>2xzm_C KH domain containing protein; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_C
Length = 243
Score = 150 bits (381), Expect = 1e-45
Identities = 51/112 (45%), Positives = 75/112 (66%), Gaps = 2/112 (1%)
Query: 1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
++ GAKGCE+++SGKL+ QRAK+MKF G MI +G P NDY++ A RHV +QG++G+KV
Sbjct: 130 IQDGAKGCEIIISGKLKQQRAKTMKFKQGYMICTGQPKNDYIDVAVRHVFFKQGIMGVKV 189
Query: 61 KIMLPWD--STGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQVLDKPLAKLGE 110
KIMLP++ K G K P+PDNV + PK+ + + V + A+ +
Sbjct: 190 KIMLPYEPNPAKKFGVKTPIPDNVIIHPPKQITDDKEIRTAVEQQQPAQPEQ 241
Score = 58.2 bits (141), Expect = 1e-10
Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 116 VLGIKVKIMLPWD--STGKTGPKKPLPDNVNVLEPKEEVNPAFPQK 159
++G+KVKIMLP++ K G K P+PDNV + PK+ + +
Sbjct: 184 IMGVKVKIMLPYEPNPAKKFGVKTPIPDNVIIHPPKQITDDKEIRT 229
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 243
Score = 143 bits (362), Expect = 7e-43
Identities = 87/114 (76%), Positives = 95/114 (83%), Gaps = 1/114 (0%)
Query: 1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDP N YV+TA RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKV 186
Query: 61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQV-LDKPLAKLGEIPV 113
KIMLPWD TGK GPKKPLPD+V+++EPK+E+ PT P S+ KP PV
Sbjct: 187 KIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV 240
Score = 66.3 bits (162), Expect = 1e-13
Identities = 31/45 (68%), Positives = 38/45 (84%)
Query: 116 VLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQKK 160
VLGIKVKIMLPWD TGK GPKKPLPD+V+++EPK+E+ P P +
Sbjct: 181 VLGIKVKIMLPWDPTGKIGPKKPLPDHVSIVEPKDEILPTTPISE 225
>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 = 139 bits (351), Expect = 2e-41
Identities = 68/99 (68%), Positives = 74/99 (74%)
Query: 1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
MESGAKGCEV+VSGKLR QRAKSMKF DG MI SG P N+Y++ A RHVLLRQGVLGIKV
Sbjct: 127 MESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEYIDAAVRHVLLRQGVLGIKV 186
Query: 61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
KIML WD GK GP PLPD V + PKEE P+
Sbjct: 187 KIMLDWDPKGKLGPTTPLPDLVTIHPPKEENELRPPALV 225
Score = 63.6 bits (155), Expect = 1e-12
Identities = 26/42 (61%), Positives = 27/42 (64%)
Query: 116 VLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFP 157
VLGIKVKIML WD GK GP PLPD V + PKEE P
Sbjct: 181 VLGIKVKIMLDWDPKGKLGPTTPLPDLVTIHPPKEENELRPP 222
>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 = 128 bits (324), Expect = 3e-37
Identities = 64/99 (64%), Positives = 73/99 (73%), Gaps = 2/99 (2%)
Query: 1 MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
MESGAKGCEVVVSGKLR RAK+MKF DG +IHSG P ND+++TATRHVL+RQGVLGIKV
Sbjct: 127 MESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLGIKV 186
Query: 61 KIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPTIPSSQ 99
KIM D K LPD V ++EPKEE PS +
Sbjct: 187 KIM--RDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVK 223
Score = 52.1 bits (125), Expect = 2e-08
Identities = 22/45 (48%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 116 VLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQKK 160
VLGIKVKIM D K LPD V ++EPKEE P K
Sbjct: 181 VLGIKVKIM--RDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVK 223
>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 = 30.3 bits (69), Expect = 0.41
Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 20/97 (20%)
Query: 1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCN------DYVNTATRHVLLRQ 53
M GAKG +V VSG+L G + A++ + +G + P + DY T
Sbjct: 142 MRLGAKGIKVEVSGRLGGAEIARTEWYREGRV-----PLHTLRADIDY---NTSEAHTTY 193
Query: 54 GVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEE 90
GV+G+KV W G+ + + +
Sbjct: 194 GVIGVKV-----WIFKGEILGGMAAVEQPEKPAAQPK 225
>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 = 29.9 bits (68), Expect = 0.51
Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 20/97 (20%)
Query: 1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCN------DYVNTATRHVLLRQ 53
MESGAKG +V+VSG++ G ++A++ G + P + DY
Sbjct: 142 MESGAKGAKVIVSGRIGGAEQARTEWAAQGRV-----PLHTLRANIDY---GFALARTTY 193
Query: 54 GVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEE 90
GVLG+K + G+ + + + +E
Sbjct: 194 GVLGVKA-----YIFLGEVIGGQKPKARPELPKAEER 225
>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 = 28.6 bits (65), Expect = 0.99
Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 15/70 (21%)
Query: 1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCN------DYVNTATRHVLLRQ 53
M GAKG +V VSG+L G + A++ + +G + P + DY T
Sbjct: 141 MRLGAKGIKVEVSGRLGGAEIARTEWYREGRV-----PLHTLRADIDY---NTSEAHTTY 192
Query: 54 GVLGIKVKIM 63
GV+G+KV I
Sbjct: 193 GVIGVKVWIF 202
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 218
Score = 26.8 bits (60), Expect = 4.3
Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 19/69 (27%)
Query: 1 MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLM--------IHSGDPCNDYVNTATRHVLL 51
++ KG ++ ++G++ G + A+ +G + I DY V
Sbjct: 153 EQADTKGIQIQIAGRIDGKEIARIEWIREGRVPLQTIRAKI-------DY---CAYTVRT 202
Query: 52 RQGVLGIKV 60
GVLGIK+
Sbjct: 203 IYGVLGIKI 211
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 26.6 bits (58), Expect = 6.0
Identities = 13/100 (13%), Positives = 30/100 (30%), Gaps = 14/100 (14%)
Query: 40 DYVNTATRHVLLRQGVLGIK--VKIMLPWDSTGKTGPKKPLPDNVNVL----EPKEEVNP 93
+Y + + + + ++I+ + L EP E +
Sbjct: 123 NYSSEVKENSVDSDDKAKVPPLIRIVSGLEL------SDTKQKGKKFLVIAYEPFENIAI 176
Query: 94 TIPSSQVLDKPLAKLGEIPVASVLGIKVKIMLPWDSTGKT 133
+P +++L + V + K WD+ K
Sbjct: 177 ELPPNEILFSE-NNDMDNNNDGVDELNKKCTF-WDAISKL 214
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
0.314 0.135 0.402
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,190,922
Number of extensions: 179427
Number of successful extensions: 214
Number of sequences better than 10.0: 1
Number of HSP's gapped: 211
Number of HSP's successfully gapped: 14
Length of query: 214
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 124
Effective length of database: 4,188,903
Effective search space: 519423972
Effective search space used: 519423972
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: 42 (21.9 bits)
S2: 55 (25.5 bits)