RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 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} (A:)
Length = 112
Score = 112 bits (283), Expect = 1e-26
Identities = 34/116 (29%), Positives = 58/116 (50%), Gaps = 6/116 (5%)
Query: 1 MTLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQ 60
M ++IRLA G K YRIVV +++SPR+GK+I+ LGT++P + E+++
Sbjct: 1 MAVRIRLAKFGRKHHPIYRIVVMDAKSPREGKYIDILGTYDPKRKV----LINVYPEKVK 56
Query: 61 HWMSKGAQPTDRILFFLDKAGLIKRSPQNNPKKSQPKKKAL--ERLASKKNADEHA 114
W+ KG + + R L G++K + + + +R + K E A
Sbjct: 57 EWVLKGVELSHRAKAILWNHGILKEVVPEGYEMKRVGDYYVFEKRESKKSKGGEAA 112
>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 ... (P:)
Length = 82
Score = 107 bits (268), Expect = 7e-25
Identities = 30/80 (37%), Positives = 51/80 (63%), Gaps = 1/80 (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 MSKGAQPTDRILFFLDKAGL 82
+ +GA +DR+ + +
Sbjct: 61 VGQGATISDRVAALIKEVNK 80
>3bbn_P Ribosomal protein S16; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea} (P:)
Length = 88
Score = 104 bits (262), Expect = 3e-24
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 VKLRLKRCGRKQRAVYRIVAIDVRSRREGRDLQKVGFYDP-----IKSQTYLNVPAILDF 56
Query: 63 MSKGAQPTDRILFFLDKAGLIKRSPQNNPKKS 94
+ KGAQPT+ + L +A + K N K +
Sbjct: 57 LEKGAQPTETVYDILKRAEVFKEFRLNQTKFN 88
>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} (S:)
Length = 91
Score = 102 bits (255), Expect = 2e-23
Identities = 39/91 (42%), Positives = 56/91 (61%), Gaps = 5/91 (5%)
Query: 3 LKIRLACGGSKSRHHY---RIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERI 59
+KIRLA GSK HY RIVV ++R RDGK+IEK+G ++P K P ++ ER
Sbjct: 2 VKIRLARFGSKHNPHYPHYRIVVTDARRKRDGKYIEKIGYYDPR--KTTPDWLKVDVERA 59
Query: 60 QHWMSKGAQPTDRILFFLDKAGLIKRSPQNN 90
++W+S GAQPTD L +AG+ ++ +
Sbjct: 60 RYWLSVGAQPTDTARRLLRQAGVFRQEAREG 90
>3ia1_A THIO-disulfide isomerase/thioredoxin; oxidoreductase, PSI-2,
NYSGXRC, structural genomics, protein structure
initiative; 1.76A {Thermus thermophilus HB27} (A:)
Length = 154
Score = 28.7 bits (63), Expect = 0.31
Identities = 7/62 (11%), Positives = 16/62 (25%)
Query: 52 FTMNFERIQHWMSKGAQPTDRILFFLDKAGLIKRSPQNNPKKSQPKKKALERLASKKNAD 111
+ +R ++ F +D+ G + + L A +
Sbjct: 91 LASDRDRPHEVAARFKVLGQPWTFVVDREGKVVALFAGRAGREALLDALLLAGADLEGHH 150
Query: 112 EH 113
H
Sbjct: 151 HH 152
>2exh_A Beta-D-xylosidase; glykosidase, hydrolsase, family43,
hydrolase; HET: MES; 1.88A {Geobacillus
stearothermophilus} (A:67-236)
Length = 170
Score = 25.5 bits (55), Expect = 2.7
Identities = 9/47 (19%), Positives = 17/47 (36%), Gaps = 10/47 (21%)
Query: 4 KIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPL 50
L +R+++ +A S S G + + +NPL
Sbjct: 131 YYYLLTAEGGTRYNHAATIARSTSL--------YGPY--EVHPDNPL 167
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase
holoenzyme, streptolydigin, antibiotic, transcription
regulation; HET: STD; 2.40A {Thermus thermophilus}
(C:14-143,C:324-461)
Length = 268
Score = 25.0 bits (54), Expect = 3.5
Identities = 9/53 (16%), Positives = 14/53 (26%), Gaps = 8/53 (15%)
Query: 38 GTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKAGLIKRSPQNN 90
+ + NPL + RI G ++AG R
Sbjct: 196 SQLSQFKDETNPLSSLRHKRRISALGPGG--------LTRERAGFDVRDVHRT 240
>1yrz_A Xylan beta-1,4-xylosidase; structural genomics, nysgxrc
target T1997, PSI, protein structure initiative; 2.00A
{Bacillus halodurans c-125} (A:68-237)
Length = 170
Score = 24.4 bits (52), Expect = 6.2
Identities = 7/47 (14%), Positives = 13/47 (27%), Gaps = 10/47 (21%)
Query: 4 KIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPL 50
L + + + +A S+S G + PL
Sbjct: 131 YYYLLVAEGGTEYEHAATLARSQSI--------DGPY--ETDPSYPL 167
>3h6g_A Glutamate receptor, ionotropic kainate 2; membrane protein
glycoprotein, cell junction, cell membrane,
glycoprotein, ION transport; HET: NAG TLA; 2.70A {Rattus
norvegicus} PDB: 3h6h_A* (A:121-276,A:352-395)
Length = 200
Score = 23.6 bits (50), Expect = 9.7
Identities = 8/28 (28%), Positives = 16/28 (57%), Gaps = 5/28 (17%)
Query: 34 IEKLGTWNPTLPKENPLRFTMNF-ERIQ 60
+EK+GTW+P + L T + +++
Sbjct: 173 LEKIGTWDPA----SGLNMTESQKGKLE 196
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.317 0.131 0.396
Gapped
Lambda K H
0.267 0.0453 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 924,150
Number of extensions: 38353
Number of successful extensions: 122
Number of sequences better than 10.0: 1
Number of HSP's gapped: 117
Number of HSP's successfully gapped: 11
Length of query: 116
Length of database: 4,956,049
Length adjustment: 69
Effective length of query: 47
Effective length of database: 2,623,504
Effective search space: 123304688
Effective search space used: 123304688
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 (23.7 bits)