RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780144|ref|YP_003064557.1| 50S ribosomal protein L12P
[Candidatus Liberibacter asiaticus str. psy62]
(126 letters)
>2j01_L 50S ribosomal protein L7; ribosome, tRNA, paromomycin, mRNA,
translation; 2.8A {Thermus thermophilus} PDB: 2j03_L
Length = 125
Score = 106 bits (266), Expect = 2e-24
Identities = 67/127 (52%), Positives = 87/127 (68%), Gaps = 4/127 (3%)
Query: 1 MSNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVA-PVAAEAGSAASEKTEFE 59
+IE I E+LS T++E +L L++ WGV+A+APV+V A P A A + A EKTEF+
Sbjct: 2 ALDIERIKEELSQATVLELKQLIDALKEAWGVTAAAPVAVAAAPAAGAAAAPAEEKTEFD 61
Query: 60 VVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDA 119
V+LK KK+ VIKE+RAIT LGLKEAK+L E +K G+SK EA E+KKKLE
Sbjct: 62 VILKEAGA--KKLEVIKELRAITGLGLKEAKDLAEK-GGPVKEGVSKQEAEEIKKKLEAV 118
Query: 120 GATVELR 126
GA VEL+
Sbjct: 119 GAVVELK 125
>2zjq_5 50S ribosomal protein L7/L12; ribosome, ribosomal subunit,
thiopeptide antibiotics, complex, translational
regulation, molecular switch; 3.30A {Deinococcus
radiodurans} SCOP: d.45.1.1
Length = 122
Score = 105 bits (263), Expect = 4e-24
Identities = 60/126 (47%), Positives = 83/126 (65%), Gaps = 5/126 (3%)
Query: 1 MSNIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEV 60
+ ++++++L LT++E A+L L++ WGV+A+ VS A A AA EKTEF+V
Sbjct: 2 AYDKQALIDQLGQLTIMELADLIDGLKETWGVTAAVAVS--GGGAGAASPAAEEKTEFDV 59
Query: 61 VLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAG 120
VL D KI VIKE+R IT LGLKEAK++ E LK G++KDEA +MK +LE AG
Sbjct: 60 VLI--DAGASKINVIKEIRGITGLGLKEAKDMSE-KGGVLKEGVAKDEAEKMKAQLEAAG 116
Query: 121 ATVELR 126
A VEL+
Sbjct: 117 ARVELK 122
>1dd3_A 50S ribosomal protein L7/L12; dimer formation, flexibility, hinge
region, four-helix- bundle, five-helix- bundle,
alpha-beta structure; 2.00A {Thermotoga maritima} SCOP:
a.108.1.1 d.45.1.1 PDB: 1dd4_A* 1giy_I 1yl3_I
Length = 128
Score = 104 bits (261), Expect = 6e-24
Identities = 71/129 (55%), Positives = 92/129 (71%), Gaps = 7/129 (5%)
Query: 3 NIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAAS--EKTEFEV 60
I+ I+E + LT+ E AEL K+LE ++GV+A+APV+V A A A + A+ EKTEF+V
Sbjct: 2 TIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAVAAAPVAGAAAGAAQEEKTEFDV 61
Query: 61 VLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESA---PKSLKTGLSKDEANEMKKKLE 117
VLK F KI VIK VR IT LGLKEAK+LVE A +K+G+SK+EA E+KKKLE
Sbjct: 62 VLKSFGQ--NKIQVIKVVREITGLGLKEAKDLVEKAGSPDAVIKSGVSKEEAEEIKKKLE 119
Query: 118 DAGATVELR 126
+AGA VEL+
Sbjct: 120 EAGAEVELK 128
>2ftc_E Mitochondrial ribosomal protein L7/12, mitochondrial 39S ribosomal
protein L3; mitochondrial ribosome, large ribosomal
subunit, ribosomal RNA; 12.10A {Bos taurus}
Length = 137
Score = 97.6 bits (243), Expect = 8e-22
Identities = 37/134 (27%), Positives = 64/134 (47%), Gaps = 12/134 (8%)
Query: 4 IESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSV------------VAPVAAEAGSA 51
I+ +V+ ++SLTL+E ++L++ L+K + + + A E
Sbjct: 3 IQQLVQDIASLTLLEISDLNELLKKTLKIQDVGLMPMGGMVPGAAPAPTAPEAAEEDVPK 62
Query: 52 ASEKTEFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANE 111
E+T F V L K + + + + L +AK+LVES P+ +K ++K EA +
Sbjct: 63 QKERTHFTVRLTEAKPVDKVKLIKEIKNYVQGINLVQAKKLVESLPQEIKANVAKAEAEK 122
Query: 112 MKKKLEDAGATVEL 125
+K LE G TV L
Sbjct: 123 IKAALEAVGGTVVL 136
>1rqu_A L8, 50S ribosomal protein L7/L12; ribosome,; NMR {Escherichia coli}
SCOP: a.108.1.1 d.45.1.1 PDB: 1rqv_A 2gya_3 2gyc_3
Length = 120
Score = 92.9 bits (231), Expect = 2e-20
Identities = 61/122 (50%), Positives = 87/122 (71%), Gaps = 6/122 (4%)
Query: 5 ESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVLKG 64
+ I+E ++++++++ EL +E+++GVSA+A V VAA AA EKTEF+V+LK
Sbjct: 5 DQIIEAVAAMSVMDVVELISAMEEKFGVSAAAAV----AVAAGPVEAAEEKTEFDVILK- 59
Query: 65 FDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLEDAGATVE 124
K+AVIK VR T LGLKEAK+LVESAP +LK G+SKD+A +KK LE+AGA VE
Sbjct: 60 -AAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEEAGAEVE 118
Query: 125 LR 126
++
Sbjct: 119 VK 120
>1ctf_A Ribosomal protein L7/L12; 1.70A {Escherichia coli} SCOP: d.45.1.1
PDB: 1rqs_A 2bcw_B
Length = 74
Score = 79.7 bits (197), Expect = 2e-16
Identities = 47/76 (61%), Positives = 58/76 (76%), Gaps = 2/76 (2%)
Query: 51 AASEKTEFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEAN 110
AA EKTEF+V+LK K+AVIK VR T LGLKEAK+LVESAP +LK G+SKD+A
Sbjct: 1 AAEEKTEFDVILKAAGA--NKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAE 58
Query: 111 EMKKKLEDAGATVELR 126
+KK LE+AGA VE++
Sbjct: 59 ALKKALEEAGAEVEVK 74
>1dd4_C 50S ribosomal protein L7/L12; dimer formation, flexibility, hinge
region, four-helix- bundle, five-helix- bundle,
alpha-beta structure; HET: TBR; 2.40A {Thermotoga
maritima} SCOP: a.108.1.1
Length = 40
Score = 38.0 bits (88), Expect = 6e-04
Identities = 19/38 (50%), Positives = 29/38 (76%)
Query: 3 NIESIVEKLSSLTLIEAAELSKRLEKEWGVSASAPVSV 40
I+ I+E + LT+ E AEL K+LE ++GV+A+APV+V
Sbjct: 2 TIDEIIEAIEKLTVSELAELVKKLEDKFGVTAAAPVAV 39
>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 = 33.0 bits (75), Expect = 0.019
Identities = 14/55 (25%), Positives = 19/55 (34%), Gaps = 16/55 (29%)
Query: 4 IESIVEKLSSLT-LIEAAE--LSKRLE-KEW--------GVS--ASAPVSVVAPV 44
I+ E LS L AE ++ L EW S P+S P+
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISC--PL 240
>3err_A Fusion protein of microtubule binding domain from mouse cytoplasmic
dynein and seryl-tRNA...; coiled coil, ligase; HET: AMP;
2.27A {Mus musculus}
Length = 536
Score = 28.8 bits (64), Expect = 0.33
Identities = 11/61 (18%), Positives = 25/61 (40%), Gaps = 1/61 (1%)
Query: 54 EKTEFEVVLKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMK 113
+ E +L + K+ VI + + L + + V A ++K+ + K E++
Sbjct: 23 VALDLEALLAVDEQLHKQQEVIADKQMSVKEDLDKVEPAVIEAQNAVKS-IKKQHLVEVR 81
Query: 114 K 114
Sbjct: 82 S 82
>3ga7_A Acetyl esterase; phosphoserine, IDP00896, cytoplasm, hydrolase,
serine esterase, structural genomics; HET: SEP MSE;
1.55A {Salmonella typhimurium}
Length = 326
Score = 27.8 bits (60), Expect = 0.65
Identities = 3/20 (15%), Positives = 9/20 (45%)
Query: 107 DEANEMKKKLEDAGATVELR 126
D++ + + L+ E +
Sbjct: 269 DDSRLLHQTLQAHQQPCEYK 288
>2o7r_A CXE carboxylesterase; alpha/beta hydrolase; 1.40A {Actinidia
eriantha} PDB: 2o7v_A
Length = 338
Score = 27.7 bits (60), Expect = 0.77
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 107 DEANEMKKKLEDAGATVELR 126
D E+ ++LE G V +
Sbjct: 280 DRQMELAERLEKKGVDVVAQ 299
>3k6k_A Esterase/lipase; alpha/beta hydrolase fold; 2.20A {Uncultured
bacterium} PDB: 3dnm_A
Length = 322
Score = 27.3 bits (59), Expect = 1.0
Identities = 5/20 (25%), Positives = 12/20 (60%)
Query: 107 DEANEMKKKLEDAGATVELR 126
++ + ++ AG +VEL+
Sbjct: 255 SDSTTLAERAGAAGVSVELK 274
>3ebl_A Gibberellin receptor GID1; alpha/beta hydrolase, lipase,
gibberellin signaling pathway, hydrolase, nucleus,
hydrolase receptor; HET: GA4; 1.90A {Oryza sativa subsp}
PDB: 3ed1_A*
Length = 365
Score = 26.7 bits (58), Expect = 1.7
Identities = 4/20 (20%), Positives = 7/20 (35%)
Query: 107 DEANEMKKKLEDAGATVELR 126
D L + G V++
Sbjct: 299 DRQLAYADALREDGHHVKVV 318
>1jkm_A Brefeldin A esterase; serine hydrolase, degradation of brefeldin A,
alpha/beta hydrolase family; 1.85A {Bacillus subtilis}
SCOP: c.69.1.2
Length = 361
Score = 26.5 bits (57), Expect = 1.9
Identities = 7/20 (35%), Positives = 9/20 (45%)
Query: 107 DEANEMKKKLEDAGATVELR 126
DE ++L AG V R
Sbjct: 303 DEGIAFARRLARAGVDVAAR 322
>2wir_A Pesta, alpha/beta hydrolase fold-3 domain protein;
hyperthermophilic enzyme, esterase, tertiary ALCO
alpha/beta hydrolase fold; 2.00A {Pyrobaculum
calidifontis}
Length = 313
Score = 26.4 bits (57), Expect = 2.0
Identities = 4/20 (20%), Positives = 5/20 (25%)
Query: 107 DEANEMKKKLEDAGATVELR 126
DE L+ G
Sbjct: 258 DEGELYAHLLKTRGVRAVAV 277
>3d7r_A Esterase; alpha/beta fold, hydrolase; 2.01A {Staphylococcus aureus
subsp}
Length = 326
Score = 26.3 bits (57), Expect = 2.1
Identities = 1/20 (5%), Positives = 6/20 (30%)
Query: 107 DEANEMKKKLEDAGATVELR 126
+ ++ + +E
Sbjct: 271 PDMKLFEQMMLQHHQYIEFY 290
>2ifu_A Gamma-SNAP; membrane fusion, snare complex disassembly, protein
structure initiative, PSI, center for eukaryotic
structural genomics, CESG; HET: MSE; 2.60A {Danio rerio}
Length = 307
Score = 26.1 bits (56), Expect = 2.4
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 86 LKEAKELVESAPKSLKTGLSKDEAN 110
+ EA E + A K LKT K + +
Sbjct: 7 ISEAHEHIAKAEKYLKTSFMKWKPD 31
>2zsh_A Probable gibberellin receptor GID1L1; plant hormone receptor,
gibberellin, gibberellin signaling pathway, hydrolase,
nucleus, receptor, developmental protein; HET: GA3;
1.80A {Arabidopsis thaliana} PDB: 2zsi_A*
Length = 351
Score = 25.9 bits (56), Expect = 2.6
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 106 KDEANEMKKKLEDAGATVELR 126
+D + L+ AG V+L
Sbjct: 299 RDWQLAYAEGLKKAGQEVKLM 319
>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency
decline, transcription-coupled DNA repair, ATP-binding,
DNA damage, DNA repair; 1.95A {Escherichia coli} PDB:
2b2n_A*
Length = 483
Score = 25.7 bits (55), Expect = 2.8
Identities = 16/70 (22%), Positives = 25/70 (35%), Gaps = 18/70 (25%)
Query: 41 VAPVAAEAGSAASEKTEFEVVL---KGFDDPKKKIAVIKEV---------------RAIT 82
+AP AS++ + ++ GF D + +A+I E R I
Sbjct: 407 IAPQRIMRLDEASDRGRYLMIGAAEHGFVDTVRNLALICESDLLGERVARRRQDSRRTIN 466
Query: 83 DLGLKEAKEL 92
LK A L
Sbjct: 467 PDTLKLAAAL 476
>3k5i_A Phosphoribosyl-aminoimidazole carboxylase; purine biosynthesis,
ATP-grAsp, lyase; HET: NHE ADP AIR; 2.00A {Aspergillus
clavatus} PDB: 3k5h_A*
Length = 403
Score = 25.7 bits (55), Expect = 3.0
Identities = 10/67 (14%), Positives = 19/67 (28%), Gaps = 14/67 (20%)
Query: 16 LIEAAELSKRLEKEWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVLKGFDDPKKKIAVI 75
L+E+A + V + A+ A V F + + +
Sbjct: 39 LVESA-------NRLNIQ-------VNVLDADNSPAKQISAHDGHVTGSFKEREAVRQLA 84
Query: 76 KEVRAIT 82
K +T
Sbjct: 85 KTCDVVT 91
>1umd_A E1-alpha, 2-OXO acid dehydrogenase alpha subunit; alpha(2)beta(2)
tetramer, structural genomics; HET: TDP; 1.90A {Thermus
thermophilus} SCOP: c.36.1.11 PDB: 1um9_A* 1umc_A*
1umb_A*
Length = 367
Score = 25.7 bits (55), Expect = 3.1
Identities = 12/55 (21%), Positives = 28/55 (50%)
Query: 63 KGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLE 117
+G + + + V +E+RA + GLKEA+E P+ + + ++ + ++
Sbjct: 307 RGLWNEEWEEDVREEIRAELERGLKEAEEAGPVPPEWMFEDVFAEKPWHLLRQEA 361
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 25.3 bits (54), Expect = 3.9
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 6/30 (20%)
Query: 5 ESI----VEKLSSLTLIEAAELSKRLEKEW 30
ESI E+ L ++AA SK +E+EW
Sbjct: 85 ESIRKWREEQRKRLQELDAA--SKVMEQEW 112
>2vi8_A Serine hydroxymethyltransferase; SHMT, E53Q, FTHF, enzyme memory,
pyridoxal phosphate, one-carbon metabolism,
PLP-dependent enzymes; HET: PLP; 1.67A {Bacillus
stearothermophilus} PDB: 2vi9_A* 2via_A* 2vib_A* 1kkj_A*
1kkp_A* 1kl1_A* 1kl2_A* 1yjs_A* 1yjz_A* 1yjy_A* 2vgu_A*
2vgs_A* 2vgt_A* 2vgv_A* 2vgw_A* 2vmr_A* 2vms_A* 2vmt_A*
2vmu_A* 2vmq_A* ...
Length = 405
Score = 25.3 bits (55), Expect = 4.5
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 61 VLKGFDDPKKKIAVIKEVRAITD 83
VLK + + V A+TD
Sbjct: 383 VLKNVGSEQALEEARQRVAALTD 405
>1acc_A PA, anthrax protective antigen; toxin, calcium-binding; 2.10A
{Bacillus anthracis} SCOP: f.11.1.1 PDB: 1t6b_X* 1tzo_A
1tzn_A 3etb_J
Length = 735
Score = 24.9 bits (54), Expect = 4.8
Identities = 15/109 (13%), Positives = 27/109 (24%), Gaps = 27/109 (24%)
Query: 29 EWGVSASAPVSVVAPVAAEAGSAASEKTEFEVVLKGFDDPKKKIAVIKEVRAITDLGLKE 88
W A + E + DP + D+ LKE
Sbjct: 476 NWSEVLPQIQETTARIIFNGKD--LNLVERRIAAVNPSDPLET--------TKPDMTLKE 525
Query: 89 AKELVESAPKSLKTG---------------LSKDEANEMKKKLEDAGAT 122
A ++ + G + + +K +L + AT
Sbjct: 526 ALKIAFGFNE--PNGNLQYQGKDITEFDFNFDQQTSQNIKNQLAELNAT 572
>2xnk_A DNA topoisomerase 2-binding protein 1; phosphorylation,
protein-protein interaction; HET: DNA; 2.60A {Homo
sapiens} PDB: 2xnh_A*
Length = 292
Score = 24.8 bits (53), Expect = 6.6
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 102 TGLSKDEANEMKKKLEDAGATV 123
T L K++ E+ K ++ G V
Sbjct: 116 TSLEKEKREEVHKYVQMMGGRV 137
>1w85_A Pyruvate dehydrogenase E1 component, alpha subunit; dehydrogenase,
multienzyme complex, oxidoreductase; HET: TDP; 2.0A
{Geobacillus stearothermophilus} SCOP: c.36.1.11 PDB:
3duf_A* 3dv0_A* 3dva_A* 1w88_A*
Length = 368
Score = 24.4 bits (52), Expect = 6.9
Identities = 10/55 (18%), Positives = 26/55 (47%)
Query: 63 KGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLKTGLSKDEANEMKKKLE 117
KG +++ VI++ + +K+A E + L + + ++ +K++ E
Sbjct: 306 KGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPFNLKEQYE 360
>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli K12}
Length = 671
Score = 24.4 bits (52), Expect = 7.7
Identities = 15/69 (21%), Positives = 23/69 (33%), Gaps = 7/69 (10%)
Query: 62 LKGFDDPKKKIAVIKEVRAITDLGLKEAKELVESAPKSLK------TG-LSKDEANEMKK 114
+ F + VI E+ A E TG LS+ ++ K
Sbjct: 560 VHNFFAEESNRNVISELLAEGVHWPAPIVINAEEIDSPFAGKTVVLTGSLSQMSRDDAKA 619
Query: 115 KLEDAGATV 123
+L + GA V
Sbjct: 620 RLVELGAKV 628
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
0.304 0.122 0.305
Gapped
Lambda K H
0.267 0.0450 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 944,825
Number of extensions: 40847
Number of successful extensions: 183
Number of sequences better than 10.0: 1
Number of HSP's gapped: 169
Number of HSP's successfully gapped: 50
Length of query: 126
Length of database: 5,693,230
Length adjustment: 81
Effective length of query: 45
Effective length of database: 3,729,466
Effective search space: 167825970
Effective search space used: 167825970
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 51 (24.1 bits)