RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780712|ref|YP_003065125.1| 30S ribosomal protein S16
[Candidatus Liberibacter asiaticus str. psy62]
(116 letters)
>3bn0_A 30S ribosomal protein S16; ribonucleoprotein, ribosome; 2.00A
{Aquifex aeolicus} SCOP: d.27.1.1
Length = 112
Score = 119 bits (300), Expect = 1e-28
Identities = 37/115 (32%), Positives = 59/115 (51%), Gaps = 5/115 (4%)
Query: 1 MTLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQ 60
M ++IRLA G K YRIVV +++SPR+GK+I+ LGT++P + E+++
Sbjct: 1 MAVRIRLAKFGRKHHPIYRIVVMDAKSPREGKYIDILGTYDPKRKV----LINVYPEKVK 56
Query: 61 HWMSKGAQPTDRILFFLDKAGLIKR-SPQNNPKKSQPKKKALERLASKKNADEHA 114
W+ KG + + R L G++K P+ K E+ SKK+ A
Sbjct: 57 EWVLKGVELSHRAKAILWNHGILKEVVPEGYEMKRVGDYYVFEKRESKKSKGGEA 111
>3ofo_P 30S ribosomal protein S16; protein biosynthesis, ribosomes, RNA,
tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 1p6g_P
1p87_P* 1vs7_P* 2avy_P 2aw7_P 1vs5_P 2i2u_P 2i2p_P*
2qan_P* 2qb9_P* 2qbb_P* 2qbd_P 2qbf_P 2qbh_P* 2qbj_P*
2qou_P* 2qow_P* 2qoy_P* 2qp0_P* 2vho_P ...
Length = 82
Score = 111 bits (279), Expect = 4e-26
Identities = 30/78 (38%), Positives = 51/78 (65%), Gaps = 1/78 (1%)
Query: 3 LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHW 62
+ IRLA G+K R Y++VVA+SR+ R+G+FIE++G +NP + E ++ +RI HW
Sbjct: 2 VTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNP-IASEKEEGTRLDLDRIAHW 60
Query: 63 MSKGAQPTDRILFFLDKA 80
+ +GA +DR+ + +
Sbjct: 61 VGQGATISDRVAALIKEV 78
>3mr8_P 30S ribosomal protein S16; ribosome, termination, RF1, amber,
STOP UAG; 3.62A {Thermus thermophilus} PDB: 1pnx_P
1voq_P 1vos_P 1vov_P 1vox_P 1voz_P 1pns_P 3ms0_P
3fic_P* 1emw_A 1fjg_P* 1hnw_P* 1hnx_P* 1hnz_P* 1hr0_P
1i94_P* 1i95_P* 1i96_P* 1i97_P* 1ibk_P* ...
Length = 83
Score = 106 bits (266), Expect = 2e-24
Identities = 38/83 (45%), Positives = 56/83 (67%), Gaps = 2/83 (2%)
Query: 3 LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHW 62
+KIRLA GSK HYRIVV ++R RDGK+IEK+G ++P + L+ ++ ER ++W
Sbjct: 2 VKIRLARFGSKHNPHYRIVVTDARRKRDGKYIEKIGYYDPRKTTPDWLK--VDVERARYW 59
Query: 63 MSKGAQPTDRILFFLDKAGLIKR 85
+S GAQPTD L +AG+ ++
Sbjct: 60 LSVGAQPTDTARRLLRQAGVFRQ 82
>1jgq_S 30S ribosomal protein S16; ribosome assembly, protein synthesis,
LIFE; HET: 2MG H2U M2G OMC OMG YG PSU 5MC 7MG 5MU 1MA
4SU; 5.00A {Thermus thermophilus} SCOP: i.1.1.1 PDB:
1jgo_S* 1jgp_S* 1gix_S* 1ml5_S* 1emw_A 1fjg_P* 1hnw_P*
1hnx_P* 1hnz_P* 1hr0_P 1i94_P* 1i95_P* 1i96_P* 1i97_P*
1ibk_P* 1ibl_P* 1ibm_P 1j5e_P 1n32_P* 1n33_P* ...
Length = 91
Score = 105 bits (265), Expect = 2e-24
Identities = 39/90 (43%), Positives = 56/90 (62%), Gaps = 5/90 (5%)
Query: 3 LKIRLACGGSKSRH---HYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERI 59
+KIRLA GSK HYRIVV ++R RDGK+IEK+G ++P K P ++ ER
Sbjct: 2 VKIRLARFGSKHNPHYPHYRIVVTDARRKRDGKYIEKIGYYDP--RKTTPDWLKVDVERA 59
Query: 60 QHWMSKGAQPTDRILFFLDKAGLIKRSPQN 89
++W+S GAQPTD L +AG+ ++ +
Sbjct: 60 RYWLSVGAQPTDTARRLLRQAGVFRQEARE 89
>3i1m_P 30S ribosomal protein S16; ribosome structure, protein-RNA
complex, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA-binding, antibiotic resistance; 3.19A
{Escherichia coli k-12} PDB: 1p6g_P 1p87_P* 1vs7_P*
2avy_P 2aw7_P 1vs5_P 2i2u_P 2i2p_P* 2qan_P* 2qb9_P*
2qbb_P* 2qbd_P 2qbf_P 2qbh_P* 2qbj_P* 2qou_P* 2qow_P*
2qoy_P* 2qp0_P* 2vho_P ...
Length = 82
Score = 100 bits (251), Expect = 7e-23
Identities = 30/78 (38%), Positives = 51/78 (65%), Gaps = 1/78 (1%)
Query: 3 LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHW 62
+ IRLA G+K R Y++VVA+SR+ R+G+FIE++G +NP + E ++ +RI HW
Sbjct: 2 VTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNP-IASEKEEGTRLDLDRIAHW 60
Query: 63 MSKGAQPTDRILFFLDKA 80
+ +GA +DR+ + +
Sbjct: 61 VGQGATISDRVAALIKEV 78
>3bbn_P Ribosomal protein S16; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea}
Length = 88
Score = 98.3 bits (245), Expect = 4e-22
Identities = 30/92 (32%), Positives = 49/92 (53%), Gaps = 5/92 (5%)
Query: 3 LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHW 62
+K+RL G K R YRIV + RS R+G+ ++K+G ++P + +N I +
Sbjct: 2 VKLRLKRCGRKQRAVYRIVAIDVRSRREGRDLQKVGFYDPIKSQT-----YLNVPAILDF 56
Query: 63 MSKGAQPTDRILFFLDKAGLIKRSPQNNPKKS 94
+ KGAQPT+ + L +A + K N K +
Sbjct: 57 LEKGAQPTETVYDILKRAEVFKEFRLNQTKFN 88
>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 = 33.4 bits (75), Expect = 0.013
Identities = 10/20 (50%), Positives = 15/20 (75%), Gaps = 2/20 (10%)
Query: 97 KKKALERL-AS-KKNADEHA 114
+K+AL++L AS K AD+ A
Sbjct: 18 EKQALKKLQASLKLYADDSA 37
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 2006
Score = 29.9 bits (67), Expect = 0.15
Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 23/83 (27%)
Query: 48 NPLRFTMNF-----ERIQHWMS--------KGAQPTDRIL----------FFLDKAGLIK 84
NP+ T++F +RI+ S G T++I F + GL+
Sbjct: 1668 NPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLS 1727
Query: 85 RSPQNNPKKSQPKKKALERLASK 107
+ P + +K A E L SK
Sbjct: 1728 ATQFTQPALTLMEKAAFEDLKSK 1750
>2ae0_X Membrane-bound lytic murein transglycosylase A; double-PSI
beta-barrel, small mixed parallel/antiparallel six
stranded beta barrel; 2.00A {Escherichia coli} SCOP:
b.52.1.4 PDB: 2pjj_A 2pic_A 2pi8_A* 2gae_A
Length = 345
Score = 25.2 bits (55), Expect = 4.2
Identities = 5/28 (17%), Positives = 11/28 (39%)
Query: 51 RFTMNFERIQHWMSKGAQPTDRILFFLD 78
+ + +Q W+ G + F +D
Sbjct: 56 NQSNVYNAVQEWLRAGGDTRNMRQFGID 83
>2pbe_A AAD6, aminoglycoside 6-adenylyltransferase; NYSGXRC, aminoglycoside
6-adenyltransferase, PSI-2, structural genomics; 2.65A
{Bacillus subtilis} SCOP: a.160.1.5 d.218.1.13
Length = 294
Score = 24.8 bits (54), Expect = 5.0
Identities = 7/55 (12%), Positives = 18/55 (32%), Gaps = 6/55 (10%)
Query: 47 ENPLRFTMNF---ERIQHWMSKGAQPTDRILFFLDKAGLIKRSPQNNPKKSQPKK 98
E+ + + + + + ++L DK I N ++ K+
Sbjct: 97 EDGNKLDLTLIPIREAEDYFANNDGLV-KVLL--DKDSFINYKVTPNDRQYWIKR 148
>1kqn_A Nmnat, nicotinamide mononucleotide adenylyl transferase;
nucleotidyltransferase superfamily; HET: NAD; 2.20A
{Homo sapiens} SCOP: c.26.1.3 PDB: 1kqo_A* 1kr2_A*
1kku_A 1gzu_A*
Length = 279
Score = 24.4 bits (52), Expect = 6.9
Identities = 6/28 (21%), Positives = 12/28 (42%)
Query: 86 SPQNNPKKSQPKKKALERLASKKNADEH 113
SP + K + A R+ + A ++
Sbjct: 49 SPVGDAYKKKGLIPAYHRVIMAELATKN 76
>1gqp_A DOC1/APC10; cell cycle, APC10/DOC1, APC/cyclosome,
ubiquitination, E3 ubiquitin ligase, beta sandwich,
jelly roll; 2.2A {Saccharomyces cerevisiae} SCOP:
b.18.1.9
Length = 221
Score = 23.9 bits (51), Expect = 8.7
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 34 IEKLGTWNPTLPKE-NPLRFTMNFERIQHWMSKGAQP 69
+ L W P+ K NP+ F ++ W S G QP
Sbjct: 55 VTHLALWKPSSFKLGNPVDFALDDNYDTFWQSDGGQP 91
>1u09_A Polyprotein; protein-DNA complex, RNA-dependent RNA polymerase,
transferase; 1.91A {Foot-and-mouth disease virus c-s8c1}
SCOP: e.8.1.4 PDB: 1wne_A 2e9r_X* 2e9t_A* 2e9z_A* 2ec0_A
2f8e_X* 2d7s_A*
Length = 476
Score = 23.8 bits (51), Expect = 9.3
Identities = 5/46 (10%), Positives = 15/46 (32%), Gaps = 8/46 (17%)
Query: 29 RDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRIL 74
R G + P + + E I + ++ ++++
Sbjct: 388 RHFHMDYGTGFYKPVMASK-------TLEAILSF-ARRGTIQEKLI 425
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.317 0.131 0.396
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,042,711
Number of extensions: 45193
Number of successful extensions: 130
Number of sequences better than 10.0: 1
Number of HSP's gapped: 123
Number of HSP's successfully gapped: 19
Length of query: 116
Length of database: 5,693,230
Length adjustment: 79
Effective length of query: 37
Effective length of database: 3,777,954
Effective search space: 139784298
Effective search space used: 139784298
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: 41 (21.7 bits)
S2: 50 (23.0 bits)