RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13546
(109 letters)
>1wib_A 60S ribosomal protein L12; N-terminal domain, structural
genomics, riken structural genomics/proteomics
initiative, RSGI, ribosome; NMR {Mus musculus} SCOP:
d.47.1.1
Length = 92
Score = 130 bits (327), Expect = 4e-41
Identities = 69/85 (81%), Positives = 74/85 (87%)
Query: 1 MPPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITV 60
PPKFDP EVK VYLRC GGEVGATS+LAPKIGPLGLSPKKVGDDIAKATGDWKGL+ITV
Sbjct: 7 GPPKFDPNEVKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITV 66
Query: 61 CLTIQNRQAAISVVPSAASLIIKAL 85
LTIQNRQA I VVPSA++L +
Sbjct: 67 KLTIQNRQAQIEVVPSASALSGPSS 91
>2zkr_i 60S ribosomal protein L12; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris} PDB: 3izc_J 3izs_J 3j16_H* 3o5h_L 3jyw_K
1s1i_K
Length = 165
Score = 101 bits (253), Expect = 5e-29
Identities = 85/98 (86%), Positives = 90/98 (91%)
Query: 1 MPPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITV 60
MPPKFDP E+K VYLRC GGEVGATS+LAPKIGPLGLSPKKVGDDIAKATGDWKGL+ITV
Sbjct: 1 MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITV 60
Query: 61 CLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKND 98
LTIQNRQA I VVPSA++LIIKALKEPPRDRKK KN
Sbjct: 61 KLTIQNRQAQIEVVPSASALIIKALKEPPRDRKKQKNI 98
>3iz5_J 60S ribosomal protein L12 (L11P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_J
Length = 166
Score = 99.0 bits (246), Expect = 6e-28
Identities = 75/100 (75%), Positives = 86/100 (86%), Gaps = 1/100 (1%)
Query: 1 MPPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATG-DWKGLKIT 59
MPPK DPT+V V++R GGEVGA SSLAPKIGPLGLSPKK+G+DIAK T DWKGL++T
Sbjct: 1 MPPKLDPTQVVDVFVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT 60
Query: 60 VCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKNDW 99
V LT+QNRQA +SVVPSAA+L+IKALKEP RDRKKVKN
Sbjct: 61 VKLTVQNRQAKVSVVPSAAALVIKALKEPERDRKKVKNIK 100
>1vq8_I 50S ribosomal protein L11P; ribosome 50S, protein-protein
complex, RNA-RNA complex, PROT complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} SCOP: a.4.7.1 PDB:
1vq4_I* 1vq5_I* 1vq6_I* 1vq7_I* 1s72_I* 1vq9_I* 1vqk_I*
1vql_I* 1vqm_I* 1vqn_I* 1vqo_I* 1vqp_I* 1yhq_I* 1yi2_I*
1yij_I* 1yit_I* 1yj9_I* 1yjn_I* 1yjw_I* 2otl_I* ...
Length = 162
Score = 84.8 bits (210), Expect = 2e-22
Identities = 17/91 (18%), Positives = 35/91 (38%), Gaps = 3/91 (3%)
Query: 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQA 69
+ + GGE L P++GP + + V +I T + G ++ V + + +
Sbjct: 2 AGTIEVLVPGGEANPGPPLGPELGPTPVDVQAVVQEINDQTAAFDGTEVPVTVKYDDDGS 61
Query: 70 A---ISVVPSAASLIIKALKEPPRDRKKVKN 97
+ V P+A + +A E +
Sbjct: 62 FEIEVGVPPTAELIKDEAGFETGSGEPQEDF 92
>3bbo_K Ribosomal protein L11; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 224
Score = 63.3 bits (153), Expect = 1e-13
Identities = 16/99 (16%), Positives = 35/99 (35%), Gaps = 2/99 (2%)
Query: 1 MPPKFDPTE--VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKI 58
M PK + + + L G+ + P +G G++ D T D G I
Sbjct: 66 MAPKPGKAKKVIGVIKLALEAGKATPAPPVGPALGSKGVNIMAFCKDYNARTADKPGFVI 125
Query: 59 TVCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKN 97
V +T+ + ++ ++ + + ++ K
Sbjct: 126 PVEITVFDDKSFTFILKTPPASVLLLKASGAEKGSKDPQ 164
>3egv_B 50S ribosomal protein L11, ribosomal protein L11 methyltransferase;
post-translational modification, multiple
methyltransferase; HET: SAH 4MM; 1.75A {Thermus
thermophilus} SCOP: d.47.1.1 PDB: 2e34_A 2e35_A 2e36_A
2h8w_A 2hgj_L 2hgq_L 2hgu_L 2j01_K 2j03_K 2jl6_K 2jl8_K
2klm_A 2nxn_B 2wh2_K 2wh4_K 2wrj_K 2wrl_K 2x9s_K 2x9u_K
2xtg_K ...
Length = 146
Score = 60.8 bits (147), Expect = 3e-13
Identities = 16/92 (17%), Positives = 30/92 (32%), Gaps = 1/92 (1%)
Query: 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQA 69
V V L+ G + P +G G + + AT + + V +TI ++
Sbjct: 4 VAVVKLQLPAGAATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIVPVEITIYADRS 63
Query: 70 -AISVVPSAASLIIKALKEPPRDRKKVKNDWS 100
AS +I+ + K +
Sbjct: 64 FTFVTKTPPASYLIRKAAGLEKGAHKPGREKV 95
>1mms_A Protein (ribosomal protein L11); RNA-protein complex, RNA,
ribosome, translocation, thiostrep; 2.57A {Thermotoga
maritima} SCOP: a.4.7.1 d.47.1.1 PDB: 1mvr_L 1oln_A*
1giy_L 1mj1_L* 1ml5_l* 1yl3_L 2b66_K 2b9n_K 2b9p_K
2jq7_A* 2k3f_A 1eg0_K 1jqm_A 1jqs_A 1jqt_A 1r2w_A
1r2x_A 487d_L 1pn8_L 1pn7_L
Length = 140
Score = 52.1 bits (124), Expect = 6e-10
Identities = 10/89 (11%), Positives = 30/89 (33%)
Query: 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQA 69
++ L+ G+ + P +G G++ + T D G+ + V +T+ ++
Sbjct: 5 AAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKS 64
Query: 70 AISVVPSAASLIIKALKEPPRDRKKVKND 98
++ + + +
Sbjct: 65 FTFIIKTPPASFLLKKAAGIEKGSSEPKR 93
>3r8s_I 50S ribosomal protein L11; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1p85_G 1p86_G 2awb_I 2aw4_I 2i2v_I 2j28_I 2i2t_I*
2qao_I* 2qba_I* 2qbc_I* 2qbe_I 2qbg_I 2qbi_I* 2qbk_I*
2qov_I 2qox_I 2qoz_I* 2qp1_I* 2rdo_I 2vhm_I ...
Length = 141
Score = 51.3 bits (122), Expect = 1e-09
Identities = 14/93 (15%), Positives = 29/93 (31%), Gaps = 2/93 (2%)
Query: 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKI-TVCLTI-QNR 67
V L+ G + + P +G G++ + T + V +T+ +R
Sbjct: 5 QAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADR 64
Query: 68 QAAISVVPSAASLIIKALKEPPRDRKKVKNDWS 100
A++++K K D
Sbjct: 65 SFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKV 97
>2ftc_G L11MT, MRP-L11, 39S ribosomal protein L11, mitochondrial;
mitochondrial ribosome, large ribosomal subunit,
ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_G
Length = 145
Score = 48.7 bits (115), Expect = 1e-08
Identities = 14/95 (14%), Positives = 27/95 (28%), Gaps = 2/95 (2%)
Query: 7 PTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQN 66
P + G L P +G G+S + + + T D K +
Sbjct: 2 PEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDIKEGIPLPTKILVK 61
Query: 67 RQAA--ISVVPSAASLIIKALKEPPRDRKKVKNDW 99
I + S +KA + ++ +
Sbjct: 62 PDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEV 96
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 37.5 bits (86), Expect = 4e-04
Identities = 18/90 (20%), Positives = 27/90 (30%), Gaps = 15/90 (16%)
Query: 5 FDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTI 64
P EVK + L+ + P LS IA++ D T
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI------IAESIRDGLA-------TW 344
Query: 65 QN-RQAAISVVPSAASLIIKALKEPPRDRK 93
N + + + + L EP RK
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVL-EPAEYRK 373
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 34.3 bits (78), Expect = 0.004
Identities = 21/88 (23%), Positives = 31/88 (35%), Gaps = 31/88 (35%)
Query: 14 YLRCVGGEVGATSSLAPKIG------------PLGLSPKKVGDDIAKATGDWKGLKITVC 61
YL + S P IG LG +P ++ + ATG +GL +T
Sbjct: 230 YL------LSIPISC-PLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGL-VTA- 280
Query: 62 LTIQNRQAAISVVPSAAS---LIIKALK 86
AI+ S S + KA+
Sbjct: 281 -------VAIAETDSWESFFVSVRKAIT 301
Score = 32.7 bits (74), Expect = 0.016
Identities = 18/94 (19%), Positives = 36/94 (38%), Gaps = 24/94 (25%)
Query: 6 DPTEVKKVYLRCVGGEVGAT-----SSLAPKIGPLG-LSPKKVGDDIAKATGD--WKG-- 55
+P ++ GGE G S++ + G L +K+ +I + + ++
Sbjct: 1668 NPVN-LTIHF---GGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEK 1723
Query: 56 --LKITVCLTIQNRQAAISVVPSAASLIIKALKE 87
L T Q Q A++++ A + LK
Sbjct: 1724 GLLSAT-----QFTQPALTLM-EKA--AFEDLKS 1749
Score = 30.4 bits (68), Expect = 0.11
Identities = 27/136 (19%), Positives = 44/136 (32%), Gaps = 59/136 (43%)
Query: 15 LRCVGGEVGATSSLAPKI------------GPL----GLSPKKVGDDIAKATGDWKGLKI 58
+RC E +SL P I P+ L+ ++V D + K L
Sbjct: 308 VRCY--EAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTN---SHLP- 361
Query: 59 TVCLTIQNRQAAISVVPSAASLII----KAL-------------------KEPPRDRKKV 95
+Q IS+V A +L++ ++L + P +RK
Sbjct: 362 ------AGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLK 415
Query: 96 KNDWSWHMLP-----H 106
+S LP H
Sbjct: 416 ---FSNRFLPVASPFH 428
>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 = 27.2 bits (59), Expect = 0.87
Identities = 9/27 (33%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 63 TIQNRQAAISV-VP-SAASLIIKALKE 87
++ QA++ + SA +L IKA E
Sbjct: 21 ALKKLQASLKLYADDSAPALAIKATME 47
>2p18_A Glyoxalase II; metalloprotein, beta sandwich, alpha-helical domain,
hydrola; HET: SPD; 1.80A {Leishmania infantum} PDB:
2p1e_A*
Length = 311
Score = 25.9 bits (57), Expect = 3.1
Identities = 4/36 (11%), Positives = 12/36 (33%)
Query: 65 QNRQAAISVVPSAASLIIKALKEPPRDRKKVKNDWS 100
A V + I+ ++E + + ++
Sbjct: 49 TTHTLAAVDVNADYKPILTYIEEHLKQQGNADVTYT 84
>2zkr_5 60S ribosomal protein L10A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 212
Score = 25.4 bits (56), Expect = 3.6
Identities = 9/38 (23%), Positives = 14/38 (36%), Gaps = 4/38 (10%)
Query: 20 GEVGATSSLAPKIGPLGL--SPKKVGDDIAKATGDWKG 55
++G L +GP G P DD+ + K
Sbjct: 113 QDIG--RYLGTVLGPRGKMPEPLDPDDDVVEVIERMKN 148
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.316 0.135 0.423
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,673,519
Number of extensions: 84442
Number of successful extensions: 167
Number of sequences better than 10.0: 1
Number of HSP's gapped: 165
Number of HSP's successfully gapped: 18
Length of query: 109
Length of database: 6,701,793
Length adjustment: 73
Effective length of query: 36
Effective length of database: 4,663,560
Effective search space: 167888160
Effective search space used: 167888160
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: 51 (23.5 bits)