RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 031095
(166 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 = 177 bits (451), Expect = 5e-58
Identities = 151/164 (92%), Positives = 161/164 (98%)
Query: 1 MPPKFDPSQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT 60
MPPK DP+QVVDV+VRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT
Sbjct: 1 MPPKLDPTQVVDVFVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT 60
Query: 61 VKLTVQNRQAKVAVVPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPR 120
VKLTVQNRQAKV+VVPSAAALVIKALKEPERDRKK KNIKH+GNI+LDDVIEIA+IMR R
Sbjct: 61 VKLTVQNRQAKVSVVPSAAALVIKALKEPERDRKKVKNIKHSGNISLDDVIEIARIMRNR 120
Query: 121 SMAKELSGTVKEILGTCVSVGCTVDGKDPKDLQQEINDGDVEIP 164
SMAKE++GTVKEILGTCVSVGCTVDGKDPKDLQQEI+DG+VEIP
Sbjct: 121 SMAKEMAGTVKEILGTCVSVGCTVDGKDPKDLQQEISDGEVEIP 164
>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 (421), Expect = 1e-53
Identities = 116/164 (70%), Positives = 140/164 (85%), Gaps = 1/164 (0%)
Query: 1 MPPKFDPSQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT 60
MPPKFDP+++ VY+R TGGEVGA S+LAPKIGPLGLSPKK+G+DIAK T DWKGLR+T
Sbjct: 1 MPPKFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKAT-GDWKGLRIT 59
Query: 61 VKLTVQNRQAKVAVVPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPR 120
VKLT+QNRQA++ VVPSA+AL+IKALKEP RDRKK KNIKH+GNIT D+++ IA+ MR R
Sbjct: 60 VKLTIQNRQAQIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHR 119
Query: 121 SMAKELSGTVKEILGTCVSVGCTVDGKDPKDLQQEINDGDVEIP 164
S+A+ELSGT+KEILGT SVGC VDG+ P D+ +IN G VE P
Sbjct: 120 SLARELSGTIKEILGTAQSVGCNVDGRHPHDIIDDINSGAVECP 163
>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 = 155 bits (393), Expect = 3e-49
Identities = 38/153 (24%), Positives = 81/153 (52%), Gaps = 7/153 (4%)
Query: 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQA-- 70
+ V V GGE L P++GP + + + ++I +T + G V V + + +
Sbjct: 5 IEVLVPGGEANPGPPLGPELGPTPVDVQAVVQEINDQT-AAFDGTEVPVTVKYDDDGSFE 63
Query: 71 -KVAVVPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGT 129
+V V P+A + +A E + + ++++D V +IA+ P ++ +L+
Sbjct: 64 IEVGVPPTAELIKDEAGFETGSGEPQEDFV---ADLSVDQVKQIAEQKHPDLLSYDLTNA 120
Query: 130 VKEILGTCVSVGCTVDGKDPKDLQQEINDGDVE 162
KE++GTC S+G T++G++P++ ++ I+ G+ +
Sbjct: 121 AKEVVGTCTSLGVTIEGENPREFKERIDAGEYD 153
>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 = 128 bits (321), Expect = 1e-37
Identities = 32/158 (20%), Positives = 66/158 (41%), Gaps = 3/158 (1%)
Query: 1 MPPKFDPSQVVD--VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLR 58
M PK ++ V + + + G+ A + P +G G++ +D T D G
Sbjct: 66 MAPKPGKAKKVIGVIKLALEAGKATPAPPVGPALGSKGVNIMAFCKDYNART-ADKPGFV 124
Query: 59 VTVKLTVQNRQAKVAVVPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMR 118
+ V++TV + ++ ++ + A V+ K ++ G IT+D + IA
Sbjct: 125 IPVEITVFDDKSFTFILKTPPASVLLLKASGAEKGSKDPQMEKVGKITIDQLRGIATEKL 184
Query: 119 PRSMAKELSGTVKEILGTCVSVGCTVDGKDPKDLQQEI 156
P + ++ I GT ++G +D ++E+
Sbjct: 185 PDLNCTTIESAMRIIAGTAANMGIDIDPPILVKKKKEV 222
>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 = 118 bits (298), Expect = 8e-36
Identities = 61/86 (70%), Positives = 73/86 (84%), Gaps = 1/86 (1%)
Query: 1 MPPKFDPSQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVT 60
PPKFDP++V VY+R TGGEVGA S+LAPKIGPLGLSPKK+G+DIAK T DWKGLR+T
Sbjct: 7 GPPKFDPNEVKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKAT-GDWKGLRIT 65
Query: 61 VKLTVQNRQAKVAVVPSAAALVIKAL 86
VKLT+QNRQA++ VVPSA+AL +
Sbjct: 66 VKLTIQNRQAQIEVVPSASALSGPSS 91
>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 = 109 bits (273), Expect = 2e-31
Identities = 28/139 (20%), Positives = 51/139 (36%), Gaps = 1/139 (0%)
Query: 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKV 72
V +++ G A + P +G G + + + T + V V++T+ ++
Sbjct: 7 VKLQLPAGAATPAPPVGPALGQHGANIMEFVKAFNAAT-ANMGDAIVPVEITIYADRSFT 65
Query: 73 AVVPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKE 132
V + A + + G IT + V+EIAK P +L +
Sbjct: 66 FVTKTPPASYLIRKAAGLEKGAHKPGREKVGRITWEQVLEIAKQKMPDLNTTDLEAAARM 125
Query: 133 ILGTCVSVGCTVDGKDPKD 151
I G+ S+G V G
Sbjct: 126 IAGSARSMGVEVVGAPEVK 144
>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 = 101 bits (253), Expect = 2e-28
Identities = 28/133 (21%), Positives = 53/133 (39%)
Query: 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKV 72
V ++V G + + P +G G++ + + +T KGL + V +TV ++
Sbjct: 8 VKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFT 67
Query: 73 AVVPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKE 132
V + A V+ + N G I+ + EIA+ ++ +
Sbjct: 68 FVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRS 127
Query: 133 ILGTCVSVGCTVD 145
I GT S+G V+
Sbjct: 128 IEGTARSMGLVVE 140
>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 = 97.1 bits (241), Expect = 1e-26
Identities = 30/133 (22%), Positives = 54/133 (40%), Gaps = 1/133 (0%)
Query: 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKV 72
+ +++ G+ A + P +G G++ + + ET D G+ + V +TV ++
Sbjct: 8 IKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAET-ADKAGMILPVVITVYEDKSFT 66
Query: 73 AVVPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKE 132
++ + A + K G +T + EIAK P A L +K
Sbjct: 67 FIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKI 126
Query: 133 ILGTCVSVGCTVD 145
I GT S+G V
Sbjct: 127 IEGTAKSMGIEVV 139
>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 = 86.0 bits (212), Expect = 3e-22
Identities = 27/137 (19%), Positives = 49/137 (35%), Gaps = 4/137 (2%)
Query: 13 VYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKV 72
+ V G L P +G G+S + ++ + T +G+ + K+ V+ +
Sbjct: 8 IRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDIKEGIPLPTKILVKPDRTFE 67
Query: 73 AVVPSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKI----MRPRSMAKELSG 128
+ + + G +TL V EIA+I LS
Sbjct: 68 IKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEIARIKAQDEAFALQDVPLSS 127
Query: 129 TVKEILGTCVSVGCTVD 145
V+ I+G+ S+G V
Sbjct: 128 VVRSIIGSARSLGIRVV 144
>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 = 49.1 bits (117), Expect = 8e-09
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 2/70 (2%)
Query: 76 PSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILG 135
P AA L+ KA + +N I D V EIA++ P A + ++ I G
Sbjct: 8 PPAAVLLKKAAGIESGSGEPNRNK--VATIKRDKVREIAELKMPDLNAASIEAAMRMIEG 65
Query: 136 TCVSVGCTVD 145
T S+G V+
Sbjct: 66 TARSMGIVVE 75
>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 = 44.8 bits (105), Expect = 4e-06
Identities = 25/174 (14%), Positives = 46/174 (26%), Gaps = 51/174 (29%)
Query: 5 FDPSQVVDVYVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKLT 64
P +V + ++ P LS I E I ++ W +
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS--IIAESI-RDGLATWDNWK-----H 349
Query: 65 VQNRQAKVAVVPSAAALVIKALKEPERDRK---------KTKNIKHN------GNITLDD 109
V + + S L EP RK + +I ++ D
Sbjct: 350 VNCDKLTTIIESSLNVL------EPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD 403
Query: 110 VIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVDGKDPKDLQQEINDGDVEI 163
V+ + + S+ + K PK+ I +E+
Sbjct: 404 VMVVVNKLHKYSLVE----------------------KQPKESTISIPSIYLEL 435
>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 = 39.4 bits (92), Expect = 3e-05
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 76 PSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMAKELSGTVKEILG 135
P AA L+ KA + +N I D V EIA++ P A + ++ I G
Sbjct: 3 PPAAVLLKKAAGIESGSGEPNRNKVAT--IKRDKVREIAELKMPDLNAASIEAAMRMIEG 60
Query: 136 TCVSVG 141
T S+G
Sbjct: 61 TARSMG 66
>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 = 42.3 bits (99), Expect = 3e-05
Identities = 35/192 (18%), Positives = 65/192 (33%), Gaps = 51/192 (26%)
Query: 5 FDPSQVVDVYVRVTGGEVGAASS-LAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKL 63
PS + D + E G S L+ L+ +++ + + K + G +V + L
Sbjct: 319 LPPSILEDS---LENNE-GVPSPMLSIS----NLTQEQVQDYVNKTNSHLPAGKQVEISL 370
Query: 64 TVQN--RQAKVAVV---PSA-AALV-----IKAL------KEPERDRKKTKNIKHN-GNI 105
N + VV P + L KA + P +RK + +
Sbjct: 371 V--NGAKNL---VVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLK--FSNRFLPV 423
Query: 106 T-------LDDVIEIAKIMRPRSMAKELSGTVKEILGTCVSVGCTVDGKDPKDLQQEIN- 157
L + I + + +S K+ + + V T DG D + L I+
Sbjct: 424 ASPFHSHLLVPASD--LINK-DLVKNNVSFNAKD-IQ--IPVYDTFDGSDLRVLSGSISE 477
Query: 158 ---DGDVEIPLD 166
D + +P+
Sbjct: 478 RIVDCIIRLPVK 489
Score = 42.0 bits (98), Expect = 4e-05
Identities = 22/129 (17%), Positives = 48/129 (37%), Gaps = 33/129 (25%)
Query: 5 FDPSQVVD-VYVR-------VTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDW-- 54
+V+ V+ R V E+G ++ G + ++P ++ ++E +
Sbjct: 1777 MSIESLVEVVFYRGMTMQVAVPRDELGRSN-----YGMIAINPGRVAASFSQEALQYVVE 1831
Query: 55 -----KGLRV-TVKLTVQNRQ-----AKVAVVPSAAALVIKALKEPERDRKKTKNIKHNG 103
G V V V+N+Q A+ V+ +K +K I+
Sbjct: 1832 RVGKRTGWLVEIVNYNVENQQYVAAGDLRAL--DTVTNVLNFIKL-----QKIDIIELQK 1884
Query: 104 NITLDDVIE 112
+++L++V
Sbjct: 1885 SLSLEEVEG 1893
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.8 bits (74), Expect = 0.032
Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 12/72 (16%)
Query: 38 SPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKVAVVPSAAALVIKALKEPE-----RD 92
++ ++ E+ + W+ + + +Q A V KA K+ E +
Sbjct: 76 QADRLTQE--PESIRKWREEQ---RKRLQELDAASKV--MEQEWREKAKKDLEEWNQRQS 128
Query: 93 RKKTKNIKHNGN 104
+ KN +N
Sbjct: 129 EQVEKNKINNRI 140
>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 = 31.8 bits (71), Expect = 0.045
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 14/42 (33%)
Query: 48 KETAKDWKGLRVTVKLTVQNRQAKVAVVP-SAAALVIKALKE 88
K+ K K L+ ++KL SA AL IKA E
Sbjct: 19 KQALK--K-LQASLKL----------YADDSAPALAIKATME 47
>2j58_A WZA, outer membrane lipoprotein WZA; membrane protein; 2.26A
{Escherichia coli} PDB: 2w8i_A 2w8h_A*
Length = 359
Score = 27.6 bits (61), Expect = 2.1
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 30 PKIGPL---GLSPKKIGEDIAKETAKDWKGLRVTVKLTVQNRQAKVAVV 75
P IG + G + ++ +DI + +V V + R KV V
Sbjct: 109 PYIGKVQVAGKTVSQVRQDITSRLTTYIESPQVDVSI-AAFRSQKVYVT 156
>2cy7_A Cysteine protease APG4B; papain-like fold, autophagy, hydrolase;
1.90A {Homo sapiens} SCOP: d.3.1.22 PDB: 2d1i_A 2zzp_A
2z0d_A 2z0e_A
Length = 396
Score = 26.8 bits (58), Expect = 4.1
Identities = 8/48 (16%), Positives = 21/48 (43%)
Query: 76 PSAAALVIKALKEPERDRKKTKNIKHNGNITLDDVIEIAKIMRPRSMA 123
P+ A V+K L + +I + + ++++ + + P + A
Sbjct: 148 PNTVAQVLKKLAVFDTWSSLAVHIAMDNTVVMEEIRRLCRTSVPCAGA 195
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
0.313 0.133 0.373
Gapped
Lambda K H
0.267 0.0837 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,613,796
Number of extensions: 155461
Number of successful extensions: 482
Number of sequences better than 10.0: 1
Number of HSP's gapped: 473
Number of HSP's successfully gapped: 36
Length of query: 166
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 79
Effective length of database: 4,272,666
Effective search space: 337540614
Effective search space used: 337540614
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (24.0 bits)