RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780239|ref|YP_003064652.1| 30S ribosomal protein S13
[Candidatus Liberibacter asiaticus str. psy62]
(122 letters)
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Oryza sativa} (M:)
Length = 145
Score = 116 bits (292), Expect = 1e-27
Identities = 48/111 (43%), Positives = 60/111 (54%), Gaps = 12/111 (10%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
RI GV IP KRV +L YIHGIG S+ I L + L E EVI +R+
Sbjct: 46 CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDN-KVTKDLSEEEVIILRK-- 102
Query: 61 EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRK 111
+R + I+RL ++ CYRG+RH+ GLPVRGQRT N RT K
Sbjct: 103 ---------EKRFNRVAIERLKEIRCYRGIRHKLGLPVRGQRTKNNCRTLK 144
>2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S
ribosomal subunit, ribosomal protein/RNA complex; 8.70A
{Canis familiaris} PDB: 1s1h_M (m:1-88)
Length = 88
Score = 87.8 bits (218), Expect = 4e-19
Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
+ R+ NI +++ A+ I G+G + + + K I +R +L E EV ++ +
Sbjct: 12 ILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIM 71
Query: 61 EQDYQVEGD---LRR 72
+ Q + L R
Sbjct: 72 QNPRQYKIPDWFLNR 86
>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6;
tRNA-binding, rRNA-binding, metal-binding, zinc-finger,
translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}
(M:1-64)
Length = 64
Score = 82.3 bits (204), Expect = 2e-17
Identities = 31/64 (48%), Positives = 42/64 (65%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
MARIAGV IPR KRV AL YI+GIG +++ K I P RV L E+EV+++R+ +
Sbjct: 1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV 60
Query: 61 EQDY 64
E +
Sbjct: 61 ENTW 64
>3i1m_M 30S ribosomal protein S13; ribosome structure, protein-RNA
complex, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA-binding, antibiotic resistance; 3.19A
{Escherichia coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F
1vs5_M 3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M*
1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M*
2qb9_M* 2qbb_M* 2qbd_M ... (M:1-63)
Length = 63
Score = 78.1 bits (193), Expect = 3e-16
Identities = 22/62 (35%), Positives = 35/62 (56%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
MARIAG+NIP K V AL I+G+G S+ I I + ++ +L E ++ +R +
Sbjct: 1 MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEV 60
Query: 61 EQ 62
+
Sbjct: 61 AK 62
>2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein,
decatenation, ATPase, drug design, DNA-binding,
magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus
shibatae} (B:229-310)
Length = 82
Score = 75.5 bits (186), Expect = 3e-15
Identities = 10/72 (13%), Positives = 25/72 (34%), Gaps = 4/72 (5%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
+ + + IG ++ I + P ++V L E E+ ++ +
Sbjct: 13 IKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVET- 71
Query: 61 EQDYQVEGDLRR 72
++ + D R
Sbjct: 72 ---FKKDEDFRS 80
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae} (B:1772-1800,B:1916-2006)
Length = 120
Score = 31.7 bits (72), Expect = 0.038
Identities = 8/27 (29%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 73 TVA--MNIKRLMDLGCYRGLRHRRGLP 97
++A M+I+ L+++ YRG+ + +P
Sbjct: 1 SLADVMSIESLVEVVFYRGMTMQVAVP 27
>3gzu_A Inner capsid protein VP2; 7RP, DLP, metal- binding,
virion, zinc, core protein, RNA-binding, icosaderal
virus; 3.80A {Rotavirus A} (A:102-180,A:753-767)
Length = 94
Score = 27.3 bits (60), Expect = 0.66
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 40 PPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVA 75
R ++V+SE I AI QD + EG +RR +A
Sbjct: 10 KNSRDAGKVVDSETASICDAIFQDEETEGAVRRFIA 45
>3fqi_A Protein DOM3Z, DOM-3 homolog Z; hydrolase, protein binding;
HET: EPE; 2.01A {Mus musculus} PDB: 3fqj_A* (A:)
Length = 417
Score = 25.1 bits (54), Expect = 3.8
Identities = 5/35 (14%), Positives = 9/35 (25%)
Query: 88 RGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122
H + + H R K+ + K
Sbjct: 4 SHHHHHHSSGLVPRSGHMEPRGTKRKAEKTEVEKP 38
>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex,
DNA repair, beta sandwich, zinc finger, helix two-turns
helix, hydrolase/DNA complex; HET: PED; 2.10A
{Escherichia coli} (A:129-225)
Length = 97
Score = 24.7 bits (54), Expect = 4.7
Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 3/55 (5%)
Query: 11 RAKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62
+ + L + G+G + + I P+R L +E + + I+
Sbjct: 21 KKTAIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIKA 75
>1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix
two-turns helix; 2.00A {Sulfolobus shibatae}
(A:230-311)
Length = 82
Score = 24.3 bits (53), Expect = 6.6
Identities = 8/41 (19%), Positives = 19/41 (46%)
Query: 22 IHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62
IG ++ I + P ++V L E E+ ++ + ++
Sbjct: 34 FQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK 74
>3ip3_A Oxidoreductase, putative; structural genomics, PSI-2,
protein structure initiative, NEW YORK SGX research
center for structural genomics; 2.14A {Thermotoga
maritima} (A:130-337)
Length = 208
Score = 24.2 bits (51), Expect = 7.0
Identities = 6/52 (11%), Positives = 13/52 (25%), Gaps = 4/52 (7%)
Query: 40 PPERRVHQLVES----EVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCY 87
P +LV E+ + D + + +G +
Sbjct: 4 PHFLTAKKLVSEGAVGEIRLVNTQKSYKLGQRPDFYKKRETYGGTIPWVGIH 55
>1w36_C RECC, exodeoxyribonuclease V gamma chain; recombination,
helicase, hydrolase, DNA repair; HET: DNA; 3.1A
{Escherichia coli} (C:463-584)
Length = 122
Score = 24.0 bits (52), Expect = 7.6
Identities = 7/34 (20%), Positives = 15/34 (44%)
Query: 29 SSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62
S+D+ L +P + E + +RQ + +
Sbjct: 4 VSEDVLALLDVPVLAARFDITEEGLRYLRQWVNE 37
>1bg6_A N-(1-D-carboxylethyl)-L-norvaline dehydrogenase; L)
stereospecific opine dehydrogenase, oxidoreductase;
1.80A {Arthrobacter} (A:196-359)
Length = 164
Score = 24.0 bits (52), Expect = 8.2
Identities = 7/39 (17%), Positives = 13/39 (33%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAI 39
+ R V P V+ + + F+ KL +
Sbjct: 113 LGRAVNVPTPLIDAVLDLISSLIDTDFRKEGRTLEKLGL 151
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta
protein, ATP-binding, nucleotide-binding, hydrolase;
2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*
(A:1-149)
Length = 149
Score = 23.6 bits (51), Expect = 8.6
Identities = 7/34 (20%), Positives = 12/34 (35%), Gaps = 2/34 (5%)
Query: 19 LCYIHGIGFKSSQDICNKLAIPP--ERRVHQLVE 50
L + GIGF ++ + RR+
Sbjct: 46 LTEVEGIGFLTADKLWQARGGALDDPRRLTAAAV 79
>1xd7_A YWNA; structural genomics, protein structure initiative,
winged helix DNA binding, hypothetical protein, PSI;
2.30A {Bacillus subtilis subsp} (A:)
Length = 145
Score = 23.7 bits (51), Expect = 9.1
Identities = 10/58 (17%), Positives = 21/58 (36%), Gaps = 3/58 (5%)
Query: 11 RAKRVVRALCYIHGIGFKSSQDICNKLAIPP---ERRVHQLVESEVIQIRQAIEQDYQ 65
R + L I SS+ I + + P R + L +++++ R +
Sbjct: 7 RLAVAIHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKADILTSRAGVPGASL 64
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
0.326 0.141 0.416
Gapped
Lambda K H
0.267 0.0413 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 946,051
Number of extensions: 39683
Number of successful extensions: 321
Number of sequences better than 10.0: 1
Number of HSP's gapped: 319
Number of HSP's successfully gapped: 25
Length of query: 122
Length of database: 4,956,049
Length adjustment: 73
Effective length of query: 49
Effective length of database: 2,488,284
Effective search space: 121925916
Effective search space used: 121925916
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)