RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780145|ref|YP_003064558.1| 50S ribosomal protein L10
[Candidatus Liberibacter asiaticus str. psy62]
(172 letters)
>2j01_J 50S ribosomal protein L10; ribosome, tRNA, paromomycin, mRNA,
translation; 2.8A {Thermus thermophilus} PDB: 2j03_J
3d5b_J 3d5d_J
Length = 173
Score = 119 bits (300), Expect = 3e-28
Identities = 42/173 (24%), Positives = 90/173 (52%), Gaps = 4/173 (2%)
Query: 1 MNRQGKSVEISELSKIFS-SSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVK 59
M + ++ L + + GS + +Y+G+ + LR+ +++ G + VAKN L++
Sbjct: 1 MPNKRNVELLATLKENLERAQGSFFLVNYQGLPAKETHALRQALKQNGARLFVAKNTLIR 60
Query: 60 IAIRDTSIRGISDLFVGQSLIVYSDSPVIAPKISVSFSNDNNEFR--VLGGVVEKGVLNQ 117
+A+++ + + D G S +V+ + PV A K V F+ N + V G+++ +L
Sbjct: 61 LALKELGLPEL-DGLQGPSAVVFYEDPVAAAKTLVQFAKSNPKGIPQVKSGLLQGQILTA 119
Query: 118 DSIKQIASLPDLEGIRAGIISAIQSNATRLVRLLGTPQTQVVRAISAFVDKNQ 170
++ +A LP ++ +RA ++ +Q+ LV +LG ++V + A+ +K
Sbjct: 120 KDVEALAELPTMDELRAELVGVLQAPMAELVGVLGGVARELVGILEAYAEKKA 172
>1zav_A 50S ribosomal protein L10; ribosome structure and function, L10-L12
complex structure, L10E structure, L7/12 ribosomal
stalk; 1.90A {Thermotoga maritima} SCOP: d.58.62.1 PDB:
1zaw_A 1zax_A
Length = 180
Score = 119 bits (299), Expect = 4e-28
Identities = 49/178 (27%), Positives = 90/178 (50%), Gaps = 7/178 (3%)
Query: 1 MNRQGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREA---GGGVKVAKNRL 57
+ RQ K + + E+S+IF + I+ A + G +VA + +LR ++RE G +V KN L
Sbjct: 3 LTRQQKELIVKEMSEIFKKTSLILFADFLGFTVADLTELRSRLREKYGDGARFRVVKNTL 62
Query: 58 VKIAIRDTSIRGISDLFVGQSLIVYSDS--PVIAPKISVSFSND--NNEFRVLGGVVEKG 113
+ +A+++ G + G + ++Y PV A KI +F D + R+ GG +E
Sbjct: 63 LNLALKNAEYEGYEEFLKGPTAVLYVTEGDPVEAVKIIYNFYKDKKADLSRLKGGFLEGK 122
Query: 114 VLNQDSIKQIASLPDLEGIRAGIISAIQSNATRLVRLLGTPQTQVVRAISAFVDKNQQ 171
+ ++ IA LP E + A ++ +++ T LV L +V ++A +K +
Sbjct: 123 KFTAEEVENIAKLPSKEELYAMLVGRVKAPITGLVFALSGILRNLVYVLNAIKEKKSE 180
>1vq8_G Acidic ribosomal protein P0 homolog; ribosome 50S, protein-protein
complex, RNA-RNA complex, protein-RNA complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} SCOP: j.84.1.1 PDB:
1k73_I* 1k8a_I* 1k9m_I* 1kc8_I* 1kd1_I* 1kqs_G* 1m1k_I*
1m90_I* 1n8r_I* 1nji_I* 1q7y_I* 1q81_I* 1q82_I* 1q86_I*
1qvf_G 1qvg_G 1s72_G* 1vq4_G* 1vq5_G* 1vq6_G* ...
Length = 348
Score = 74.9 bits (184), Expect = 8e-15
Identities = 19/98 (19%), Positives = 46/98 (46%), Gaps = 4/98 (4%)
Query: 3 RQGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAI 62
+ K E+ + ++ S S+ V + GI Q++D+R+ + ++V++N L++ A+
Sbjct: 13 PEWKQEEVDAIVEMIESYESVGVVNIAGIPSRQLQDMRRDLHG-TAELRVSRNTLLERAL 71
Query: 63 R--DTSIRGISDLFVGQSLIVY-SDSPVIAPKISVSFS 97
D + ++ GQ ++ D+P + +
Sbjct: 72 DDVDDGLEDLNGYITGQVGLIGTDDNPFSLFQELEASK 109
>3a1y_G Acidic ribosomal protein P0; stalk, ribosomal protein,helix SPIN,
ribonucleoprotein; 2.13A {Pyrococcus horikoshii}
Length = 284
Score = 71.8 bits (176), Expect = 7e-14
Identities = 20/100 (20%), Positives = 46/100 (46%), Gaps = 8/100 (8%)
Query: 1 MNRQGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKI 60
+ K E+ EL+K+ S I + + + +R+ +RE GG ++V++N L+++
Sbjct: 3 HVAEWKKKEVEELAKLIKSYPVIALVDVSSMPAYPLSQMRRLIRENGGLLRVSRNTLIEL 62
Query: 61 AIRDTS-------IRGISDLFVGQSLIVY-SDSPVIAPKI 92
AI+ + + + + + I+ + +P K
Sbjct: 63 AIKKAAKELGKPELEKLVEYIDRGAGILVTNMNPFKLYKF 102
>3jsy_A Acidic ribosomal protein P0 homolog; ribonucleoprotein; 1.60A
{Methanocaldococcus jannaschii}
Length = 213
Score = 63.1 bits (153), Expect = 4e-11
Identities = 13/93 (13%), Positives = 40/93 (43%), Gaps = 8/93 (8%)
Query: 6 KSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRDT 65
K E+ L + S + + + Q++++R K+R+ +++++N L+ A+++
Sbjct: 5 KIEEVKTLKGLIKSKPVVAIVDMMDVPAPQLQEIRDKIRD-KVKLRMSRNTLIIRALKEA 63
Query: 66 -------SIRGISDLFVGQSLIVYSDSPVIAPK 91
+ +++ + I+ +D
Sbjct: 64 AEELNNPKLAELANYVERGAAILVTDMNPFKLY 96
>3jyw_8 60S ribosomal protein LP0; eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus}
Length = 118
Score = 62.6 bits (152), Expect = 4e-11
Identities = 21/94 (22%), Positives = 41/94 (43%), Gaps = 6/94 (6%)
Query: 3 RQGKSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAI 62
R+ K+ ++L + S+ V +S Q+ ++RK++R V + KN +V+ AI
Sbjct: 3 REKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRG-RAVVLMGKNTMVRRAI 61
Query: 63 RDTS-----IRGISDLFVGQSLIVYSDSPVIAPK 91
R + G V+++ P+ K
Sbjct: 62 RGFLSDLPDFEKLLPFVKGYVGFVFTNEPLTEIK 95
>2zkr_g 60S acidic ribosomal protein P0; protein-RNA complex, 60S
ribosomal subunit, ribosomal protein/RNA complex; 8.70A
{Canis familiaris}
Length = 317
Score = 57.6 bits (139), Expect = 2e-09
Identities = 13/86 (15%), Positives = 31/86 (36%), Gaps = 6/86 (6%)
Query: 6 KSVEISELSKIFSSSGSIVVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRDT 65
KS ++ ++ + + Q++ +R +R V + KN +++ AIR
Sbjct: 10 KSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRG-KAVVLMGKNTMMRKAIRGH 68
Query: 66 S-----IRGISDLFVGQSLIVYSDSP 86
+ + G V++
Sbjct: 69 LENNPALEKLLPHIRGNVGFVFTKED 94
>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 = 0.029
Identities = 8/21 (38%), Positives = 14/21 (66%), Gaps = 3/21 (14%)
Query: 77 Q-SLIVYSD--SPVIAPKISV 94
Q SL +Y+D +P +A K ++
Sbjct: 26 QASLKLYADDSAPALAIKATM 46
>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 = 29.5 bits (66), Expect = 0.42
Identities = 17/127 (13%), Positives = 32/127 (25%), Gaps = 25/127 (19%)
Query: 63 RDT---SIRGISDLFVGQSLIVYSDSPVIAPKISVSF---------SNDNNEFR-VLGGV 109
++ + ++ F D P ++ F + +F VL
Sbjct: 34 QEQFNKILPEPTEGFAAD------DEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLC 87
Query: 110 V---EKGVLNQDSIKQ-IASLPDLEGIRAGIISAIQSNATRLVRLLGTPQTQVVRAISAF 165
+ E L + I A L + N + P + SA
Sbjct: 88 LTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSN--SAL 145
Query: 166 VDKNQQG 172
+G
Sbjct: 146 FRAVGEG 152
Score = 28.8 bits (64), Expect = 0.64
Identities = 31/167 (18%), Positives = 49/167 (29%), Gaps = 83/167 (49%)
Query: 7 SVEISELSKIFSSSGSIVVAHYK------GISVAQIKDLRKKMREAGG---GVKVAKNRL 57
S+ IS I G I +AHY G + + LR ++ A G G+ A
Sbjct: 233 SIPIS-CPLI----GVIQLAHYVVTAKLLGFTPGE---LRSYLKGATGHSQGLVTA---- 280
Query: 58 VKIAIRDT---------------------------------------------------S 66
V IA D+ S
Sbjct: 281 VAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLS 340
Query: 67 IRGISDLFVGQSLIVYSDSPVIAP---KISVSFSN--DNNEFRVLGG 108
I ++ V Q + ++S + P ++ +S N N V+ G
Sbjct: 341 ISNLTQEQV-QDYVNKTNSHL--PAGKQVEISLVNGAKN--L-VVSG 381
Score = 27.2 bits (60), Expect = 2.2
Identities = 15/88 (17%), Positives = 28/88 (31%), Gaps = 24/88 (27%)
Query: 80 IVYSDSPVIAPKISVS--FSN-DNNEFR---VLGGVVEKGVLNQDSIKQIASL-----PD 128
+ + P K S S F + + GG +G D +++ L
Sbjct: 130 RIMAKRPF--DKKSNSALFRAVGEGNAQLVAIFGG---QGN-TDDYFEELRDLYQTYHVL 183
Query: 129 LEGIRAGIISAIQSNATRLVRLLGTPQT 156
+ + I+ +A L L+ T
Sbjct: 184 VGDL-------IKFSAETLSELIRTTLD 204
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition,
helix-coil dynamics, inhibitor design, complex
(polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP:
a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A*
1taq_A* 1ktq_A* 5ktq_A* 3ktq_A* 1jxe_A* 4ktq_A* 1qtm_A*
2ktq_A* 1qss_A* 1qsy_A*
Length = 832
Score = 28.0 bits (61), Expect = 1.1
Identities = 3/42 (7%), Positives = 15/42 (35%)
Query: 30 GISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRDTSIRGIS 71
I + + ++ ++ V+ + ++ R + +
Sbjct: 683 AIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLF 724
>3cf4_A Acetyl-COA decarbonylase/synthase alpha subunit; methanomicrobia,
iron-nikel-sulfur, 4Fe-NI-4S, oxidoreductase; 2.00A
{Methanosarcina barkeri}
Length = 807
Score = 26.1 bits (57), Expect = 4.1
Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 24 VVAHYKGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRDTSIRGISDLFVG 76
++ + I+ QI + + MR G V A+ R + + + GI +G
Sbjct: 471 ILNVIEKIAQKQIAEEKGLMRAGRGQVSDAEIRAEGLNLVMGTTPGII-AIIG 522
>2egz_A 3-dehydroquinate dehydratase; aquifex aeolicus VF5, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; HET: TLA; 1.75A {Aquifex
aeolicus} PDB: 2ysw_A
Length = 219
Score = 26.1 bits (57), Expect = 4.8
Identities = 11/85 (12%), Positives = 25/85 (29%), Gaps = 15/85 (17%)
Query: 9 EISELSKIFSSSGSIVVAHY----KGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRD 64
+ +L I +G ++ Y I+++ ++ GG K+A
Sbjct: 96 LLVKLYNITKEAGKKLIISYHNFELTPPNWIIREVLREGYRYGGIPKIA----------- 144
Query: 65 TSIRGISDLFVGQSLIVYSDSPVIA 89
D+ + + I
Sbjct: 145 VKANSYEDVARLLCISRQVEGEKIL 169
>2tpt_A Thymidine phosphorylase; transferase, salvage pathway; 2.60A
{Escherichia coli K12} SCOP: a.46.2.1 c.27.1.1 d.41.3.1
PDB: 1azy_A 1tpt_A 1otp_A
Length = 440
Score = 25.5 bits (55), Expect = 5.8
Identities = 5/43 (11%), Positives = 17/43 (39%), Gaps = 1/43 (2%)
Query: 21 GSIVVAHY-KGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAI 62
++ + + +++ + L MR++G + L +
Sbjct: 40 AALAMTIFFHDMTMPERVSLTMAMRDSGTVLDWKSLHLNGPIV 82
>3f7c_A Protein of unknown function (DUF416); YP_958225.1, structural
genomics, joint center for structural genomics, JCSG;
HET: CIT; 2.00A {Marinobacter aquaeolei VT8}
Length = 200
Score = 25.5 bits (56), Expect = 7.1
Identities = 5/23 (21%), Positives = 10/23 (43%)
Query: 25 VAHYKGISVAQIKDLRKKMREAG 47
+ +Y+ A + +LR G
Sbjct: 168 LYYYRTPKEAFLAELRAGAANDG 190
>1vqu_A Anthranilate phosphoribosyltransferase 2; 17130499, structural
genomics, joint center for structural genomics, JCSG,
protein structure initiative; 1.85A {Nostoc SP}
Length = 374
Score = 25.3 bits (54), Expect = 7.2
Identities = 9/48 (18%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 21 GSIVVAHY-KGISVAQIKDLRKKMREAGGGVKVAKNRLVKIAIRDTSI 67
G+I+ A KG+S ++ + + ++ + I SI
Sbjct: 63 GAILTALNFKGVSADELTGMAEVLQSQSKMGTGENYSQLPITNSPFSI 110
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
0.316 0.133 0.349
Gapped
Lambda K H
0.267 0.0614 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,308,905
Number of extensions: 57892
Number of successful extensions: 212
Number of sequences better than 10.0: 1
Number of HSP's gapped: 206
Number of HSP's successfully gapped: 23
Length of query: 172
Length of database: 5,693,230
Length adjustment: 86
Effective length of query: 86
Effective length of database: 3,608,246
Effective search space: 310309156
Effective search space used: 310309156
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 (21.6 bits)
S2: 53 (24.4 bits)