RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13547
(165 letters)
>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 = 166 bits (422), Expect = 1e-53
Identities = 109/165 (66%), Positives = 138/165 (83%), Gaps = 1/165 (0%)
Query: 1 MPPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATG-DWKGLKIT 59
MPPK DPT+V V++R GGEVGA SSLAPKIGPLGLSPKK+G+DIAK T DWKGL++T
Sbjct: 1 MPPKLDPTQVVDVFVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT 60
Query: 60 VCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPR 119
V LT+QNRQA +SVVPSAA+L+IKALKEP RDRKKVKN+KH+GN+ +D++ I+R MR R
Sbjct: 61 VKLTVQNRQAKVSVVPSAAALVIKALKEPERDRKKVKNIKHSGNISLDDVIEIARIMRNR 120
Query: 120 SMARKFVGTVKEVLGTCQSVGATVEGRSARDIIEAIDNGEIEVPE 164
SMA++ GTVKE+LGTC SVG TV+G+ +D+ + I +GE+E+P
Sbjct: 121 SMAKEMAGTVKEILGTCVSVGCTVDGKDPKDLQQEISDGEVEIPS 165
>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 = 166 bits (420), Expect = 2e-53
Identities = 122/164 (74%), Positives = 140/164 (85%)
Query: 1 MPPKFDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITV 60
MPPKFDP E+K VYLRC GGEVGATS+LAPKIGPLGLSPKKVGDDIAKATGDWKGL+ITV
Sbjct: 1 MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWKGLRITV 60
Query: 61 CLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRS 120
LTIQNRQA I VVPSA++LIIKALKEPPRDRKK KN+KH+GN+ DEI NI+R MR RS
Sbjct: 61 KLTIQNRQAQIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRS 120
Query: 121 MARKFVGTVKEVLGTCQSVGATVEGRSARDIIEAIDNGEIEVPE 164
+AR+ GT+KE+LGT QSVG V+GR DII+ I++G +E P
Sbjct: 121 LARELSGTIKEILGTAQSVGCNVDGRHPHDIIDDINSGAVECPA 164
>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 = 149 bits (378), Expect = 5e-47
Identities = 38/155 (24%), Positives = 70/155 (45%), Gaps = 6/155 (3%)
Query: 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQA 69
+ + GGE L P++GP + + V +I T + G ++ V + + +
Sbjct: 2 AGTIEVLVPGGEANPGPPLGPELGPTPVDVQAVVQEINDQTAAFDGTEVPVTVKYDDDGS 61
Query: 70 A---ISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFV 126
+ V P+A + +A E + V ++ +D++ I+ P ++
Sbjct: 62 FEIEVGVPPTAELIKDEAGFETGSGEPQEDFV---ADLSVDQVKQIAEQKHPDLLSYDLT 118
Query: 127 GTVKEVLGTCQSVGATVEGRSARDIIEAIDNGEIE 161
KEV+GTC S+G T+EG + R+ E ID GE +
Sbjct: 119 NAAKEVVGTCTSLGVTIEGENPREFKERIDAGEYD 153
>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 = 128 bits (323), Expect = 1e-39
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
>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 = 111 bits (277), Expect = 3e-31
Identities = 24/157 (15%), Positives = 58/157 (36%), Gaps = 2/157 (1%)
Query: 1 MPPKFDPTE--VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKI 58
M PK + + + L G+ + P +G G++ D T D G I
Sbjct: 66 MAPKPGKAKKVIGVIKLALEAGKATPAPPVGPALGSKGVNIMAFCKDYNARTADKPGFVI 125
Query: 59 TVCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRP 118
V +T+ + ++ ++ + + ++ K ++ G + ID++ I+ P
Sbjct: 126 PVEITVFDDKSFTFILKTPPASVLLLKASGAEKGSKDPQMEKVGKITIDQLRGIATEKLP 185
Query: 119 RSMARKFVGTVKEVLGTCQSVGATVEGRSARDIIEAI 155
++ + GT ++G ++ + +
Sbjct: 186 DLNCTTIESAMRIIAGTAANMGIDIDPPILVKKKKEV 222
>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 = 99.0 bits (246), Expect = 3e-27
Identities = 25/139 (17%), Positives = 49/139 (35%), Gaps = 2/139 (1%)
Query: 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQA 69
V V L+ G + P +G G + + AT + + V +TI ++
Sbjct: 4 VAVVKLQLPAGAATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIVPVEITIYADRS 63
Query: 70 -AISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGT 128
AS +I+ + K K G + +++ I++ P
Sbjct: 64 FTFVTKTPPASYLIRKAAGLEKGAHKPGREK-VGRITWEQVLEIAKQKMPDLNTTDLEAA 122
Query: 129 VKEVLGTCQSVGATVEGRS 147
+ + G+ +S+G V G
Sbjct: 123 ARMIAGSARSMGVEVVGAP 141
>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 = 89.8 bits (222), Expect = 7e-24
Identities = 24/135 (17%), Positives = 51/135 (37%)
Query: 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQNRQA 69
++ L+ G+ + P +G G++ + T D G+ + V +T+ ++
Sbjct: 5 AAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKS 64
Query: 70 AISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTV 129
++ + + + K G V +I I++T P A +
Sbjct: 65 FTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAM 124
Query: 130 KEVLGTCQSVGATVE 144
K + GT +S+G V
Sbjct: 125 KIIEGTAKSMGIEVV 139
>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 = 84.8 bits (209), Expect = 7e-22
Identities = 20/136 (14%), Positives = 46/136 (33%), Gaps = 1/136 (0%)
Query: 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKI-TVCLTIQNRQ 68
V L+ G + + P +G G++ + T + V +T+ +
Sbjct: 5 QAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADR 64
Query: 69 AAISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGT 128
+ V + + ++ + N G + ++ I++T
Sbjct: 65 SFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAM 124
Query: 129 VKEVLGTCQSVGATVE 144
+ + GT +S+G VE
Sbjct: 125 TRSIEGTARSMGLVVE 140
>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 = 71.0 bits (173), Expect = 2e-16
Identities = 24/143 (16%), Positives = 45/143 (31%), Gaps = 7/143 (4%)
Query: 7 PTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTIQN 66
P + G L P +G G+S + + + T D K +
Sbjct: 2 PEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDIKEGIPLPTKILVK 61
Query: 67 RQAA--ISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRT----MRPRS 120
I + S +KA + ++ G V + +Y I+R
Sbjct: 62 PDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVA-GLVTLKHVYEIARIKAQDEAFAL 120
Query: 121 MARKFVGTVKEVLGTCQSVGATV 143
V+ ++G+ +S+G V
Sbjct: 121 QDVPLSSVVRSIIGSARSLGIRV 143
>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 = 45.2 bits (106), Expect = 3e-06
Identities = 19/141 (13%), Positives = 40/141 (28%), Gaps = 40/141 (28%)
Query: 5 FDPTEVKKVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITVCLTI 64
P EVK + L+ + P LS IA++ D T
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI------IAESIRDGLA-------TW 344
Query: 65 QN-RQAAISVVPSAASLIIKALKEPPRDRKKV--------KNVKHNGNVPI--------- 106
N + + + + L+ P + +K+ + ++P
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLE--PAEYRKMFDRLSVFPPSA----HIPTILLSLIWFD 398
Query: 107 ---DEIYNISRTMRPRSMARK 124
++ + + S+ K
Sbjct: 399 VIKSDVMVVVNKLHKYSLVEK 419
>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 = 43.9 bits (103), Expect = 8e-06
Identities = 21/125 (16%), Positives = 47/125 (37%), Gaps = 41/125 (32%)
Query: 10 VKKVYLRCVGGEVGATSSLAPKIGPLGLS--------PKKVG------------DDIAKA 49
V+ V+ R G T +A LG S P +V + + K
Sbjct: 1783 VEVVFYR------GMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKR 1836
Query: 50 TGDWKGLKITVCLTIQNRQAAIS-----VVPSAASLIIKALKEPPRDRKKVKNVKHNGNV 104
TG ++I V ++N+Q + + + ++ +K +K+ ++ ++
Sbjct: 1837 TGWL--VEI-VNYNVENQQYVAAGDLRAL--DTVTNVLNFIKL-----QKIDIIELQKSL 1886
Query: 105 PIDEI 109
++E+
Sbjct: 1887 SLEEV 1891
Score = 40.0 bits (93), Expect = 2e-04
Identities = 33/202 (16%), Positives = 65/202 (32%), Gaps = 71/202 (35%)
Query: 6 DPTEVKKVYLRCVGGEVG-----ATSSLAPKIGPLG-LSPKKVGDDIAKATGD--WKG-- 55
+P ++ GGE G S++ + G L +K+ +I + + ++
Sbjct: 1668 NPVN-LTIHF---GGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEK 1723
Query: 56 --LKITVCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPID------ 107
L T Q Q A++++ A + LK G +P D
Sbjct: 1724 GLLSAT-----QFTQPALTLM-EKA--AFEDLKS-------------KGLIPADATFAGH 1762
Query: 108 ---EIYN--------IS-----RTMRPRSMARKFVGTVKEVLGTCQSVGATVEGR----- 146
E Y +S + R M + E+ + + A GR
Sbjct: 1763 SLGE-YAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASF 1821
Query: 147 ---SARDIIEAI--DNGEI-EV 162
+ + ++E + G + E+
Sbjct: 1822 SQEALQYVVERVGKRTGWLVEI 1843
Score = 35.4 bits (81), Expect = 0.006
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 = 34.3 bits (78), Expect = 0.015
Identities = 28/131 (21%), Positives = 44/131 (33%), Gaps = 36/131 (27%)
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 TVCLTIQNRQAAISVVPSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRP 118
+Q IS+V A +L++ PP+ + P + SR P
Sbjct: 362 ------AGKQVEISLVNGAKNLVVSG---PPQSLYGLNLTLRKAKAPSGL--DQSRI--P 408
Query: 119 RSMARKFVGTV 129
S RK +
Sbjct: 409 FS-ERKLKFSN 418
>1hc8_A Ribosomal protein L11; ribosome, ribosomal RNA, tertiary structure,
RNA-protein; HET: GTP; 2.8A {Bacillus
stearothermophilus} SCOP: a.4.7.1 PDB: 1y39_A* 1aci_A
1fow_A 1fox_A 1foy_A 2fow_A
Length = 76
Score = 38.7 bits (90), Expect = 6e-05
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 2/70 (2%)
Query: 75 PSAASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEVLG 134
P AA L+ KA + +N + D++ I+ P A ++ + G
Sbjct: 8 PPAAVLLKKAAGIESGSGEPNRNK--VATIKRDKVREIAELKMPDLNAASIEAAMRMIEG 65
Query: 135 TCQSVGATVE 144
T +S+G VE
Sbjct: 66 TARSMGIVVE 75
>1qa6_A Ribosomal protein L11; ribosomal RNA, tertiary structur,E
RNA-protein interaction, minor groove binding,
antibiotic binding; 2.80A {Geobacillus
stearothermophilus} SCOP: a.4.7.1 PDB: 1c04_C
Length = 67
Score = 29.4 bits (66), Expect = 0.12
Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 75 PSAASLIIKA--LKEPPRDRKKVKNVKHNGNVPIDEIYNISRTMRPRSMARKFVGTVKEV 132
P AA L+ KA ++ + + K + D++ I+ P A ++ +
Sbjct: 3 PPAAVLLKKAAGIESGSGEPNRNKV----ATIKRDKVREIAELKMPDLNAASIEAAMRMI 58
Query: 133 LGTCQSVG 140
GT +S+G
Sbjct: 59 EGTARSMG 66
>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 = 28.0 bits (61), Expect = 1.0
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
>1i4j_A 50S ribosomal protein L22; mutant, erythromycin resistance, RNA
binding, RNA binding protein; 1.80A {Thermus
thermophilus} SCOP: d.55.1.1 PDB: 1bxe_A 1giy_S 1ml5_s*
1vsa_Q 1vsp_Q 1yl3_S 2b66_W 2b9n_W 2b9p_W 2hgj_V 2hgq_V
2hgu_V 2j01_W 2j03_W 2jl6_W 2jl8_W 2v47_W 2v49_W 2wdi_W
2wdj_W ...
Length = 110
Score = 25.9 bits (58), Expect = 3.8
Identities = 10/54 (18%), Positives = 18/54 (33%), Gaps = 14/54 (25%)
Query: 77 AASLIIKALKEPPRDRKKVKNVKHNGNVPIDEIYNISR-------TMRPRSMAR 123
A + K L+ N +N + D +Y + + PR+ R
Sbjct: 43 GAYFVAKVLES------AAANAVNNHDALEDRLY-VKAAYVDEGPAVLPRARGR 89
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
0.314 0.134 0.383
Gapped
Lambda K H
0.267 0.0518 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,568,514
Number of extensions: 149959
Number of successful extensions: 265
Number of sequences better than 10.0: 1
Number of HSP's gapped: 259
Number of HSP's successfully gapped: 21
Length of query: 165
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 79
Effective length of database: 4,300,587
Effective search space: 339746373
Effective search space used: 339746373
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: 42 (21.9 bits)
S2: 53 (24.7 bits)