RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780239|ref|YP_003064652.1| 30S ribosomal protein S13
[Candidatus Liberibacter asiaticus str. psy62]
(122 letters)
>3ofp_M 30S ribosomal protein S13; protein biosynthesis, ribosomes, RNA,
tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_M*
2wwl_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M
2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M 2qbf_M 2qbh_M*
2qbj_M* 2qou_M* 2qow_M* 2qoy_M* 2qp0_M* ...
Length = 113
Score = 146 bits (370), Expect = 1e-36
Identities = 62/111 (55%), Positives = 79/111 (71%), Gaps = 1/111 (0%)
Query: 2 ARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61
ARIAG+NIP K V AL I+G+G S+ I I + ++ +L E ++ +R +
Sbjct: 1 ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA 60
Query: 62 QDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKK 112
+ + VEGDLRR ++M+IKRLMDLGCYRGLRHRRGLPVRGQRT TNARTRK
Sbjct: 61 K-FVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKG 110
>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} SCOP:
a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M
1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P*
1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M*
1xmq_M* ...
Length = 126
Score = 138 bits (350), Expect = 2e-34
Identities = 72/122 (59%), Positives = 89/122 (72%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
MARIAGV IPR KRV AL YI+GIG +++ K I P RV L E+EV+++R+ +
Sbjct: 1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV 60
Query: 61 EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVAR 120
E +++EG+LR VA NIKRLMD+GCYRGLRHRRGLPVRGQRT TNARTRK K +
Sbjct: 61 ENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGK 120
Query: 121 KR 122
K+
Sbjct: 121 KK 122
>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 ...
Length = 118
Score = 133 bits (337), Expect = 8e-33
Identities = 64/116 (55%), Positives = 80/116 (68%), Gaps = 1/116 (0%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
MARIAG+NIP K V AL I+G+G S+ I I + ++ +L E ++ +R +
Sbjct: 1 MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEV 60
Query: 61 EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKG 116
+ VEGDLRR ++M+IKRLMDLGCYRGLRHRRGLPVRGQRT TNARTRK K
Sbjct: 61 AKFV-VEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKP 115
>2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris} PDB: 1s1h_M
Length = 152
Score = 126 bits (317), Expect = 2e-30
Identities = 35/144 (24%), Positives = 62/144 (43%), Gaps = 25/144 (17%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
+ R+ NI +++ A+ I G+G + + + K I +R +L E EV ++ +
Sbjct: 12 ILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIM 71
Query: 61 EQDYQ----------------------VEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPV 98
+ Q + L + +++RL + +RGLRH GL V
Sbjct: 72 QNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRV 131
Query: 99 RGQRTHTNARTRKKFGKGGVARKR 122
RGQ T T R + GV++K+
Sbjct: 132 RGQHTKTTGRRGRTV---GVSKKK 152
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Oryza sativa}
Length = 145
Score = 117 bits (295), Expect = 6e-28
Identities = 43/111 (38%), Positives = 57/111 (51%), Gaps = 12/111 (10%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
RI GV IP KRV +L YIHGIG S+ I L + +
Sbjct: 46 CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDNKV------------TKDLS 93
Query: 61 EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRK 111
E++ + +R + I+RL ++ CYRG+RH+ GLPVRGQRT N RT K
Sbjct: 94 EEEVIILRKEKRFNRVAIERLKEIRCYRGIRHKLGLPVRGQRTKNNCRTLK 144
>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 = 31.5 bits (71), Expect = 0.051
Identities = 29/169 (17%), Positives = 50/169 (29%), Gaps = 79/169 (46%)
Query: 4 IAGVNIPRAKRVV----RALC----YIHGIGFKSSQDICNKLAIP-PERRVHQLVESEVI 54
I+ VN + VV ++L + S D ++ IP ER++
Sbjct: 368 ISLVNGAKN-LVVSGPPQSLYGLNLTLRKAKAPSGLDQ-SR--IPFSERKL-------KF 416
Query: 55 QIR-----------------QAIEQDYQVEG------DLR------------RTVAMNI- 78
R I +D D++ R ++ +I
Sbjct: 417 SNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSIS 476
Query: 79 KRLMDLGCYRGLRHRRGLPVRGQR------TH--TNARTRKKFGKGGVA 119
+R++D LPV+ + TH FG GG +
Sbjct: 477 ERIVDCIIR--------LPVKWETTTQFKATHILD-------FGPGGAS 510
Score = 31.1 bits (70), Expect = 0.074
Identities = 19/113 (16%), Positives = 33/113 (29%), Gaps = 42/113 (37%)
Query: 1 MARIAGVNIPRAKRVVRAL-CYIHGIGFKSSQDICNKLAIPPERRVH-QLVESEVIQIRQ 58
M I+ + + + Y+ + N +P ++V LV +
Sbjct: 338 MLSISN--LTQE-----QVQDYV---------NKTNS-HLPAGKQVEISLVNGA----KN 376
Query: 59 AIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGL---------R----HRRGLPV 98
+ V G + +N+ L GL R R LPV
Sbjct: 377 LV-----VSGPPQSLYGLNL-TLRKAKAPSGLDQSRIPFSERKLKFSNRFLPV 423
Score = 25.3 bits (55), Expect = 4.1
Identities = 9/31 (29%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 76 MNIKRLMDLGCYRGLRHRRGLPVRGQRTHTN 106
M+I+ L+++ YRG+ + +P R + +N
Sbjct: 1777 MSIESLVEVVFYRGMTMQVAVP-RDELGRSN 1806
>3nt1_A Prostaglandin-endoperoxide synthase 2; prostaglandin H2 synthase,
cyclooxygenase-2, naproxen, oxido; HET: NAG BOG NPS HEM;
1.73A {Mus musculus} PDB: 3ntb_A* 1pxx_A* 3pgh_A*
1cx2_A* 4cox_A* 5cox_A* 6cox_A* 3hs5_A* 3hs6_A* 3hs7_A*
3krk_A* 1ddx_A* 1cvu_A*
Length = 587
Score = 28.4 bits (63), Expect = 0.39
Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 2/62 (3%)
Query: 38 AIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIK--RLMDLGCYRGLRHRRG 95
+I E + Q VES QI + V ++ +I R M R R
Sbjct: 381 SILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFS 440
Query: 96 LP 97
L
Sbjct: 441 LK 442
>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 = 28.4 bits (62), Expect = 0.42
Identities = 7/32 (21%), Positives = 16/32 (50%), Gaps = 8/32 (25%)
Query: 57 RQAIEQDYQVEGDLR-----RTVAMNIKRLMD 83
+QA+++ ++ L+ A+ IK M+
Sbjct: 19 KQALKK---LQASLKLYADDSAPALAIKATME 47
>1q4g_A Prostaglandin G/H synthase 1; cyclooxygenase, non-steroidal
anti-inflammatory drug, peroxidase, prostaglandin
synthase, EGF-like domain; HET: BOG NAG NDG BMA MAN BFL
HEM; 2.00A {Ovis aries} SCOP: a.93.1.2 g.3.11.1 PDB:
1diy_A* 2ayl_A* 3kk6_A* 2oyu_P* 2oye_P* 1eqg_A* 1cqe_A*
1eqh_A* 1igz_A* 1igx_A* 1fe2_A* 1pge_A* 1pgf_A* 1pgg_A*
1pth_A* 1u67_A* 1ht8_A* 1ebv_A* 1ht5_A* 1prh_A*
Length = 553
Score = 28.3 bits (63), Expect = 0.52
Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 2/71 (2%)
Query: 29 SSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIK--RLMDLGC 86
S + ++ + V LV++ Q I ++ + IK R++ L
Sbjct: 372 SYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDVIKESRVLRLQP 431
Query: 87 YRGLRHRRGLP 97
+ R R G+
Sbjct: 432 FNEYRKRFGMK 442
>3gzu_A Inner capsid protein VP2; 7RP, DLP, metal- binding, virion, zinc,
core protein, RNA-binding, icosaderal virus; 3.80A
{Rotavirus A}
Length = 800
Score = 27.7 bits (61), Expect = 0.68
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 40 PPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVA 75
R ++V+SE I AI QD + EG +RR +A
Sbjct: 111 KNSRDAGKVVDSETASICDAIFQDEETEGAVRRFIA 146
>1xd7_A YWNA; structural genomics, protein structure initiative, winged
helix DNA binding, hypothetical protein, PSI; 2.30A
{Bacillus subtilis subsp} SCOP: a.4.5.55
Length = 145
Score = 26.9 bits (59), Expect = 1.2
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
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 26.7 bits (58), Expect = 1.3
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 72 RTVAMNIKRLMDLGCYRGLRHRRGLPVR 99
R + NI R+M GC + + RG+ R
Sbjct: 594 RIMLTNILRMM--GCVKKQKSARGIETR 619
>1cvu_A Prostaglandin H2 synthase-2; COX-2, cyclooxygenase, prostaglandin,
arachidonate, endoperoxide, oxidoreductase; HET: NAG MAN
BOG ACD; 2.40A {Mus musculus} SCOP: a.93.1.2 g.3.11.1
PDB: 3pgh_A* 1cx2_A* 4cox_A* 5cox_A* 6cox_A* 1pxx_A*
1ddx_A*
Length = 552
Score = 26.7 bits (59), Expect = 1.3
Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 2/61 (3%)
Query: 39 IPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKR--LMDLGCYRGLRHRRGL 96
I E + Q VES QI + V ++ +I + M R R L
Sbjct: 382 ILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSL 441
Query: 97 P 97
Sbjct: 442 K 442
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein,
ATP-binding, nucleotide-binding, hydrolase; 2.20A
{Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*
Length = 574
Score = 26.4 bits (57), Expect = 1.8
Identities = 7/29 (24%), Positives = 12/29 (41%), Gaps = 2/29 (6%)
Query: 19 LCYIHGIGFKSSQDICNKLAIPP--ERRV 45
L + GIGF ++ + RR+
Sbjct: 46 LTEVEGIGFLTADKLWQARGGALDDPRRL 74
>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal
helicase, DNA repair,, DNA binding protein/DNA complex;
3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2
c.37.1.19 c.37.1.19 PDB: 2p6u_A
Length = 702
Score = 26.0 bits (56), Expect = 2.1
Identities = 10/54 (18%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNK----LAIPPERRVHQLVE 50
+ RI + RA+++ A G ++++DI ++ ++VE
Sbjct: 634 LVRIRHIGRVRARKLYNA-------GIRNAEDIVRHREKVASLIGRGIAERVVE 680
>2cfm_A Thermostable DNA ligase; protein-nucleotide complex, cell cycle,
cell division, DNA damage, DNA recombination, DNA
repair, DNA replication; HET: AMP; 1.8A {Pyrococcus
furiosus}
Length = 561
Score = 26.0 bits (56), Expect = 2.3
Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 8/56 (14%)
Query: 33 ICNKLAIPPERRVHQLVESEVIQI--------RQAIEQDYQVEGDLRRTVAMNIKR 80
I ++ + R + E +I+ + IE+ + GDL ++A+ +K+
Sbjct: 45 ILGEVFPEWDERELGVGEKLLIKAVAMATGIDAKEIEESVKDTGDLGESIALAVKK 100
>1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG,
8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET:
DRZ ANG; 1.90A {Homo sapiens} SCOP: a.96.1.3 d.129.1.2
PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A*
1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A*
2nol_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* 1yqm_A*
...
Length = 317
Score = 25.5 bits (55), Expect = 3.7
Identities = 20/118 (16%), Positives = 32/118 (27%), Gaps = 26/118 (22%)
Query: 7 VNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESE------------VI 54
NI R +V LC G D+ + VE+ V
Sbjct: 142 NNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVS 201
Query: 55 QIRQAIEQDYQVEGDLRRTVAMN----IKRLMDLGCY----------RGLRHRRGLPV 98
+AI ++ L++ + K L L L + +PV
Sbjct: 202 ASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPV 259
>1k3x_A Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia
coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1k3w_A*
1q39_A 2ea0_A* 2oq4_A* 1q3c_A 2opf_A* 1q3b_A*
Length = 262
Score = 24.4 bits (52), Expect = 6.0
Identities = 7/62 (11%), Positives = 24/62 (38%)
Query: 13 KRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRR 72
++ ++ G+G +I ++ + + L +++ + A+ + + R
Sbjct: 154 AGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRG 213
Query: 73 TV 74
V
Sbjct: 214 QV 215
>2qsb_A UPF0147 protein TA0600; structural genomics, four-helix bundle,
PSI-2, protein structure initiative; HET: MSE; 1.30A
{Thermoplasma acidophilum dsm 1728} SCOP: a.29.14.1
Length = 89
Score = 24.0 bits (52), Expect = 9.3
Identities = 10/42 (23%), Positives = 20/42 (47%)
Query: 42 ERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMD 83
RV Q + +EV+ + + QD V ++R+ + +L
Sbjct: 4 MVRVDQNLFNEVMYLLDELSQDITVPKNVRKVAQDSKAKLSQ 45
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
0.326 0.141 0.416
Gapped
Lambda K H
0.267 0.0690 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,062,662
Number of extensions: 45151
Number of successful extensions: 238
Number of sequences better than 10.0: 1
Number of HSP's gapped: 234
Number of HSP's successfully gapped: 32
Length of query: 122
Length of database: 5,693,230
Length adjustment: 81
Effective length of query: 41
Effective length of database: 3,729,466
Effective search space: 152908106
Effective search space used: 152908106
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 (23.1 bits)