RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12294
(123 letters)
>3u5c_C Guanine nucleotide-binding protein subunit beta-L protein (ASC1,
RACK1); translation, ribosome, ribosomal, ribosomal R
ribosomal protein, eukaryotic ribosome, RNA-protein C;
3.00A {Saccharomyces cerevisiae} PDB: 3izb_E 3o30_B
3o2z_B 3u5g_C 3jyv_E* 1s1h_E
Length = 254
Score = 104 bits (260), Expect = 8e-29
Identities = 36/53 (67%), Positives = 41/53 (77%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNF 81
TGKCGSV VRLIPAPRG+GIV +P KKLLQ+AG+ED YT + G T TL N
Sbjct: 158 TTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENT 210
>2xzm_E Ribosomal protein S5 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_E
Length = 296
Score = 104 bits (260), Expect = 1e-28
Identities = 36/53 (67%), Positives = 46/53 (86%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNF 81
+TGK GSV++RL+PAPRGTGIV AP+PKK+LQ AG++D YTS++G T T GNF
Sbjct: 159 ITGKSGSVRIRLVPAPRGTGIVAAPIPKKVLQFAGVQDIYTSSQGCTRTRGNF 211
>3iz6_E 40S ribosomal protein S2 (S5P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
2zkq_e 1s1h_E
Length = 274
Score = 103 bits (257), Expect = 3e-28
Identities = 41/53 (77%), Positives = 47/53 (88%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNF 81
VTGKCGSV VR++PAPRG+GIV A VPKK+LQ AGIED +TS+RGST TLGNF
Sbjct: 167 VTGKCGSVTVRMVPAPRGSGIVAARVPKKVLQFAGIEDVFTSSRGSTKTLGNF 219
>3i1m_E 30S ribosomal protein S5; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_E* 1vs5_E 3i1o_E 3i1q_E 3i1s_E
3i1z_E 3i21_E 3izv_I* 3izw_I* 3kc4_E 3or9_E 3ora_E
3sfs_E* 3uoq_E*
Length = 167
Score = 42.9 bits (102), Expect = 3e-06
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIV-GAPVPKKLLQMAGIEDCYTSARGST 75
V G +V + PA GTGI+ G + + +L++AG+ + A GST
Sbjct: 85 VKGVHTGSRVFMQPASEGTGIIAGGAM-RAVLEVAGVHNVLAKAYGST 131
>3r8n_E 30S ribosomal protein S5; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2ykr_E 3fih_E* 3iy8_E 2wwl_E 3oar_E 3oaq_E
3ofb_E 3ofa_E 3ofp_E 3ofx_E 3ofy_E 3ofo_E 3r8o_E 4a2i_E
2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E ...
Length = 150
Score = 42.5 bits (101), Expect = 3e-06
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIV-GAPVPKKLLQMAGIEDCYTSARGST 75
V G +V + PA GTGI+ G + + +L++AG+ + A GST
Sbjct: 76 VKGVHTGSRVFMQPASEGTGIIAGGAM-RAVLEVAGVHNVLAKAYGST 122
>1pkp_A Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} SCOP:
d.14.1.1 d.50.1.2 PDB: 1eg0_B 1dv4_E* 1qd7_D
Length = 150
Score = 42.1 bits (100), Expect = 4e-06
Identities = 18/48 (37%), Positives = 29/48 (60%), Gaps = 2/48 (4%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIV-GAPVPKKLLQMAGIEDCYTSARGST 75
V G G+ ++ L PA GTG++ G P + +L++AGI D + + GS
Sbjct: 85 VIGHFGAGEIILKPASEGTGVIAGGPA-RAVLELAGISDILSKSIGSN 131
>3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 308
Score = 43.3 bits (102), Expect = 4e-06
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIV-GAPVPKKLLQMAGIEDCYTSARGST 75
G+ +V L PA GTG++ G V + +L+MAG+E+ GS
Sbjct: 227 NEADYGAARVMLRPAAPGTGVIAGGAV-RTVLEMAGVENALGKQLGSN 273
>2vqe_E 30S ribosomal protein S5; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1fka_E
1gix_H* 1hnw_E* 1hnx_E* 1hnz_E* 1hr0_E 1ibk_E* 1ibl_E*
1ibm_E 1jgo_H* 1jgp_H* 1jgq_H* 1ml5_H* 1xmo_E* 1xmq_E*
1xnq_E* 1xnr_E* 1yl4_H 2b64_E* 2b9m_E* ...
Length = 162
Score = 42.1 bits (100), Expect = 5e-06
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIV-GAPVPKKLLQMAGIEDCYTSARGST 75
+ + G+ ++ L PA GTG++ GA + +L++AG+ D T GS
Sbjct: 80 IEVEFGASKIVLKPAAPGTGVIAGAVP-RAILELAGVTDILTKELGSR 126
>1z8r_A Coxsackievirus B4 polyprotein; beta barrel coordinated zinc ION,
hydrolase; NMR {Human coxsackievirus B4}
Length = 166
Score = 28.5 bits (64), Expect = 0.36
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 16 GILFCQHKVLGLIVTGKCGSV 36
GIL C+H V+GL+ G G V
Sbjct: 128 GILRCEHGVIGLVTMGGEGVV 148
>3p3c_A UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase;
lipid A biosynthesis, lipid A synthesis, LPXC, BAAB
sandwich hydrolase; HET: 3P3; 1.25A {Aquifex aeolicus}
PDB: 1xxe_A* 2jt2_A* 1p42_A* 1yh8_A* 1yhc_A* 3p76_A*
2ies_A* 2ier_A* 2o3z_A* 2j65_A* 2go3_A* 2go4_A*
Length = 274
Score = 28.6 bits (65), Expect = 0.50
Identities = 7/21 (33%), Positives = 11/21 (52%), Gaps = 2/21 (9%)
Query: 30 TGKCGSVQVRLIPAPRGTGIV 50
TG+ ++ + P GTGI
Sbjct: 19 TGE--YSKLIIHPEKEGTGIR 37
>3uhm_A UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase;
amidohydrolases, anti-bacterial agents, bacteria,
catalytic drug design; HET: RFN; 1.26A {Pseudomonas
aeruginosa} PDB: 2ves_A* 3u1y_A* 3p3e_A*
Length = 299
Score = 28.2 bits (64), Expect = 0.61
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 30 TGKCGSVQVRLIPAPRGTGIV 50
+G+ V + L PAP TGIV
Sbjct: 20 SGE--KVYLTLKPAPVDTGIV 38
>3p3g_A UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase;
lipid A biosynthesis, lipid A synthesis, LPXC, BAAB
sandwich hydrolase; HET: 3P3 UKW; 1.65A {Escherichia
coli} PDB: 3ps1_A* 3ps2_A* 3ps3_A* 3nzk_A*
Length = 300
Score = 28.2 bits (64), Expect = 0.66
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 30 TGKCGSVQVRLIPAPRGTGIV 50
TGK V + L PAP TG++
Sbjct: 20 TGK--KVTLTLRPAPANTGVI 38
>2hrv_A 2A cysteine proteinase; hydrolase (cysteine proteinase); 1.95A
{Human rhinovirus 2} SCOP: b.47.1.4
Length = 142
Score = 27.1 bits (60), Expect = 1.1
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 16 GILFCQHKVLGLIVTGKCGSV 36
G L C+H V+G++ G V
Sbjct: 108 GKLLCKHGVIGIVTAGGDNHV 128
>2rfq_A 3-HSA hydroxylase, oxygenase; rhodococcus SP. RHA1, structural
genomics protein structure initiative, midwest center
for structural genomics, MCSG; HET: 1PS; 1.65A
{Rhodococcus SP} PDB: 3aff_A 3afe_A
Length = 394
Score = 27.7 bits (62), Expect = 1.1
Identities = 9/32 (28%), Positives = 10/32 (31%)
Query: 14 TSGILFCQHKVLGLIVTGKCGSVQVRLIPAPR 45
+SG VLG V V PR
Sbjct: 142 SSGCDHASWAVLGGPVIKDGRPVDFVSFLIPR 173
>2jbr_A P-hydroxyphenylacetate hydroxylase C2 oxygenase C; flavoenzyme
hydroxylase, oxidoreductase; 2.3A {Acinetobacter
baumannii} PDB: 2jbs_A* 2jbt_A*
Length = 422
Score = 25.9 bits (57), Expect = 4.6
Identities = 6/32 (18%), Positives = 12/32 (37%)
Query: 14 TSGILFCQHKVLGLIVTGKCGSVQVRLIPAPR 45
+SG ++ ++G G+ PR
Sbjct: 170 SSGCDHAEYAIVGFNRFDADGNKIYSFGVIPR 201
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
0.320 0.135 0.409
Gapped
Lambda K H
0.267 0.0850 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,752,775
Number of extensions: 92354
Number of successful extensions: 115
Number of sequences better than 10.0: 1
Number of HSP's gapped: 110
Number of HSP's successfully gapped: 16
Length of query: 123
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 41
Effective length of database: 4,412,271
Effective search space: 180903111
Effective search space used: 180903111
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 (21.8 bits)
S2: 51 (23.2 bits)