RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy39
(195 letters)
>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 = 154 bits (392), Expect = 1e-48
Identities = 41/166 (24%), Positives = 82/166 (49%), Gaps = 6/166 (3%)
Query: 20 RMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRS 79
I +P G A+PGPPLGP LG V++ ++ N++T +G +P +K + D S
Sbjct: 3 GTIEVLVPGGEANPGPPLGPELGPTPVDVQAVVQEINDQTAA-FDGTEVPVTVKYDDDGS 61
Query: 80 YKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEY 139
+++ + PPT+ +K AG G +P ++ L++ + +IA+ K D L
Sbjct: 62 FEIEVGVPPTAELIKDEAGFETGSGEPQEDFVADLSVDQVKQIAEQKHPDL--LSYDLTN 119
Query: 140 ICTSVIGSARSVGIEVVDKLDAEEYQQFLEERKIIVAEQKKELEEA 185
V+G+ S+G+ + + + E+++ ++ + + +A
Sbjct: 120 AAKEVVGTCTSLGVTIEGE-NPREFKERIDAGEY--DDVFAAEAQA 162
>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 = 131 bits (330), Expect = 1e-38
Identities = 56/155 (36%), Positives = 86/155 (55%), Gaps = 3/155 (1%)
Query: 14 KAVDNFRMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIK 73
KA +I+ + AG A+P PP+GP LG +GVNI FCKD+N +T D K G +P I
Sbjct: 72 KAKKVIGVIKLALEAGKATPAPPVGPALGSKGVNIMAFCKDYNARTAD-KPGFVIPVEIT 130
Query: 74 VNPDRSYKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFE 133
V D+S+ I+ PP S L +A+G KG P E GK+T+ + IA K D
Sbjct: 131 VFDDKSFTFILKTPPASVLLLKASGAEKGSKDPQMEKVGKITIDQLRGIATEKLPDL--N 188
Query: 134 CETLEYICTSVIGSARSVGIEVVDKLDAEEYQQFL 168
C T+E + G+A ++GI++ + ++ ++ +
Sbjct: 189 CTTIESAMRIIAGTAANMGIDIDPPILVKKKKEVI 223
>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 = 125 bits (315), Expect = 2e-37
Identities = 56/144 (38%), Positives = 83/144 (57%), Gaps = 3/144 (2%)
Query: 20 RMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRS 79
+++ +PAG A+P PP+GP LG+ G NI F K FN T + +P I + DRS
Sbjct: 5 AVVKLQLPAGAATPAPPVGPALGQHGANIMEFVKAFNAATAN-MGDAIVPVEITIYADRS 63
Query: 80 YKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEY 139
+ + PP SY +++AAG+ KG KPG+E G++T + + EIAK K D LE
Sbjct: 64 FTFVTKTPPASYLIRKAAGLEKGAHKPGREKVGRITWEQVLEIAKQKMPDL--NTTDLEA 121
Query: 140 ICTSVIGSARSVGIEVVDKLDAEE 163
+ GSARS+G+EVV + ++
Sbjct: 122 AARMIAGSARSMGVEVVGAPEVKD 145
>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 = 122 bits (308), Expect = 2e-36
Identities = 57/138 (41%), Positives = 86/138 (62%), Gaps = 2/138 (1%)
Query: 20 RMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRS 79
++ + AG+A+P PP+GP LG++GVNI FCK FN KT +++GLP+P I V DRS
Sbjct: 6 AYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRS 65
Query: 80 YKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEY 139
+ + PP + LK+AAG+ G KP K+ GK++ + EIA+ K+ D +E
Sbjct: 66 FTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADM--TGADIEA 123
Query: 140 ICTSVIGSARSVGIEVVD 157
+ S+ G+ARS+G+ V D
Sbjct: 124 MTRSIEGTARSMGLVVED 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 = 116 bits (292), Expect = 6e-34
Identities = 67/138 (48%), Positives = 88/138 (63%), Gaps = 3/138 (2%)
Query: 20 RMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRS 79
I+ +PAG A+P PP+GP LG+ GVNI FCK FN +T D K G+ LP I V D+S
Sbjct: 6 AQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETAD-KAGMILPVVITVYEDKS 64
Query: 80 YKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEY 139
+ II PP S+ LK+AAG+ KG +P ++I GK+T K I EIAK K D +LE
Sbjct: 65 FTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDL--NANSLEA 122
Query: 140 ICTSVIGSARSVGIEVVD 157
+ G+A+S+GIEVVD
Sbjct: 123 AMKIIEGTAKSMGIEVVD 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 = 115 bits (288), Expect = 3e-33
Identities = 80/139 (57%), Positives = 106/139 (76%), Gaps = 2/139 (1%)
Query: 20 RMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRS 79
+IR + AGLA PGPPLGP LG+RGV+I FCK+FNE+TKD+KEG+PLPT+I V PDR+
Sbjct: 6 GVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDIKEGIPLPTKILVKPDRT 65
Query: 80 YKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFE--CETL 137
+++ I +P SY+LK AAG+ KG + GKE+ G +TLKH+YEIA+IK++D AF L
Sbjct: 66 FEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEIARIKAQDEAFALQDVPL 125
Query: 138 EYICTSVIGSARSVGIEVV 156
+ S+IGSARS+GI VV
Sbjct: 126 SSVVRSIIGSARSLGIRVV 144
>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 = 111 bits (279), Expect = 1e-31
Identities = 32/167 (19%), Positives = 65/167 (38%), Gaps = 7/167 (4%)
Query: 13 KKAVDNFRMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRI 72
K + + G L P +G G++ +D ++T +GL + ++
Sbjct: 4 KLDPTQVVDVFVRVTGGEVGAASSLAPKIGPLGLSPKKIGEDIAKETAKDWKGLRVTVKL 63
Query: 73 KVNPDRSYKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIG--GKLTLKHIYEIAKIKSEDS 130
V + P + + +A + K K I G ++L + EIA+I S
Sbjct: 64 TV--QNRQAKVSVVPSAAALVIKALKEPERDRKKVKNIKHSGNISLDDVIEIARIMRNRS 121
Query: 131 AFECETLEYICTSVIGSARSVGIEVVDKLDAEEYQQFLEERKIIVAE 177
+ + ++G+ SVG VD D ++ QQ + + ++ +
Sbjct: 122 --MAKEMAGTVKEILGTCVSVGCT-VDGKDPKDLQQEISDGEVEIPS 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 = 106 bits (265), Expect = 2e-29
Identities = 26/165 (15%), Positives = 53/165 (32%), Gaps = 4/165 (2%)
Query: 13 KKAVDNFRMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRI 72
K + +++ G L P +G G++ D + T D K GL + ++
Sbjct: 4 KFDPNEIKVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWK-GLRITVKL 62
Query: 73 KVNPDRSYKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAF 132
+ ++ ++ + + G +T I IA+ S
Sbjct: 63 TIQNRQAQIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRS-- 120
Query: 133 ECETLEYICTSVIGSARSVGIEVVDKLDAEEYQQFLEERKIIVAE 177
L ++G+A+SVG VD + + +
Sbjct: 121 LARELSGTIKEILGTAQSVGCN-VDGRHPHDIIDDINSGAVECPA 164
>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 = 79.9 bits (197), Expect = 2e-20
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 80 YKLIIHKPPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEY 139
+ I PP + LK+AAG+ G +P + + + EIA++K D ++E
Sbjct: 1 FTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDL--NAASIEA 58
Query: 140 ICTSVIGSARSVGIEVVD 157
+ G+ARS+GI V +
Sbjct: 59 AMRMIEGTARSMGIVVEN 76
>3cjs_B 50S ribosomal protein L11, ribosomal protein L11
methyltransferase; S-adenosyl-L-methionine dependent
methyltransferase; 1.37A {Thermus thermophilus} SCOP:
d.47.1.1 PDB: 3cju_B* 2bcw_A
Length = 72
Score = 77.3 bits (190), Expect = 2e-19
Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 20 RMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRS 79
+++ +PAG A+P PP+GP LG+ G NI F K FN T + +P I + DRS
Sbjct: 6 AVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATAN-MGDAIVPVEITIYADRS 64
Query: 80 YKLIIHKP 87
+ + P
Sbjct: 65 FTFVTKTP 72
>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 = 72.9 bits (179), Expect = 9e-18
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 87 PPTSYYLKQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEYICTSVIG 146
PP + LK+AAG+ G +P + + + EIA++K D ++E + G
Sbjct: 3 PPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPD--LNAASIEAAMRMIEG 60
Query: 147 SARSVGI 153
+ARS+GI
Sbjct: 61 TARSMGI 67
>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 = 44.6 bits (105), Expect = 8e-07
Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 3/79 (3%)
Query: 20 RMIRTNIPAGLASPGPPLGPTLGERGVNIATFCKDFNEKTKDLKEGLPLPTRIKVNPDRS 79
+++ G L P +G G++ D + T D K GL + ++ + +R
Sbjct: 17 KVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDWK-GLRITVKLTIQ-NRQ 74
Query: 80 YKLIIHKPPTSYYLKQAAG 98
++ + P S ++G
Sbjct: 75 AQIEVV-PSASALSGPSSG 92
>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 = 33.7 bits (76), Expect = 0.038
Identities = 29/182 (15%), Positives = 57/182 (31%), Gaps = 48/182 (26%)
Query: 44 RGVNIATFCKDFNEKTKDLKEGLPLPTRIK-----VNPDRSYKLIIHKPPTSYYLKQAAG 98
V A FN K L L TR K ++ + + + + +
Sbjct: 251 LNVQNAKAWNAFNLSCKIL-----LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS 305
Query: 99 M-AKGV-MKPGK---EIGGKLTLKHIYEIAKIKSEDSA-------FECETLEYICTSVIG 146
+ K + +P E+ + IA+ + A C+ L T++I
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNPR-RLSIIAESIRDGLATWDNWKHVNCDKL----TTIIE 360
Query: 147 SARSVGIEVVDKLDAEEYQQ-------FLEERKI------IV-AEQKKELEEAKEAKMLR 192
S+ ++ L+ EY++ F I ++ + K K+ +
Sbjct: 361 SS-------LNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK 413
Query: 193 TS 194
S
Sbjct: 414 YS 415
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.1 bits (67), Expect = 0.36
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 154 EVVDKLDAEEYQQFLEERKIIVAEQKKELEEAKEAK 189
E + K EE ++ L+E A + E E ++AK
Sbjct: 85 ESIRKW-REEQRKRLQELD--AASKVMEQEWREKAK 117
Score = 25.9 bits (56), Expect = 8.3
Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 3/40 (7%)
Query: 153 IEVVDKLDAEE--YQQFLEERKIIVAEQKKELEEAKEAKM 190
I D+L E +++ EE++ + E + E +
Sbjct: 74 IAQADRLTQEPESIRKWREEQRKRLQE-LDAASKVMEQEW 112
>2wsk_A Glycogen debranching enzyme; carbohydrate metabolism, hydrolase,
glycosidase, ISO-amylase glycosyl hydrolase, glycogen
metabolism; 2.25A {Escherichia coli k-12}
Length = 657
Score = 29.1 bits (66), Expect = 0.94
Identities = 8/25 (32%), Positives = 10/25 (40%), Gaps = 2/25 (8%)
Query: 32 SPGP--PLGPTLGERGVNIATFCKD 54
+ G PLG +GVN F
Sbjct: 5 AIGKPAPLGAHYDGQGVNFTLFSAH 29
>3r4c_A Hydrolase, haloacid dehalogenase-like hydrolase; haloalkanoate
dehalogenase enzyme superfamily, phosphohydrol
hydrolase; 1.82A {Bacteroides thetaiotaomicron}
Length = 268
Score = 26.3 bits (59), Expect = 6.0
Identities = 14/79 (17%), Positives = 27/79 (34%), Gaps = 7/79 (8%)
Query: 115 TLKHIYEIAKIKSEDSAFECETLEYICTS-----VIGSARSVGIEVVDKLDAEEYQQFLE 169
+ E+A+ D A E E + + V A V V +D EE + E
Sbjct: 96 DFRKSMELAR--EFDFAVALELNEGVFVNRLTPTVEQIAGIVEHPVPPVVDIEEMFERKE 153
Query: 170 ERKIIVAEQKKELEEAKEA 188
++ ++ ++
Sbjct: 154 CCQLCFYFDEEAEQKVMPL 172
>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome
segregation, cell adhesion, kleisin, MIT cell cycle;
HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP:
c.37.1.12
Length = 430
Score = 26.6 bits (59), Expect = 7.0
Identities = 15/98 (15%), Positives = 35/98 (35%), Gaps = 5/98 (5%)
Query: 94 KQAAGMAKGVMKPGKEIGGKLTLKHIYEIAKIKSEDSAFECETLEYICTSVIGSARSVGI 153
+ AA + + +E+ G + K YE K K E + + G ++
Sbjct: 156 QIAAQSPVELSRMFEEVSGSIQYKKEYEELKEKIEKLSKSATESIKNRRRIHGELKTYKS 215
Query: 154 E----VVDKLDAEEYQQFLEERKIIVAEQKKELEEAKE 187
+ Y + E R ++ + ++L+ ++
Sbjct: 216 PGLEVLFQGPRGSRYDE-AEGRFEVINNETEQLKAEEK 252
>1ygy_A PGDH, D-3-phosphoglycerate dehydrogenase; oxidoreductase, serine
biosy structural genomics, PSI, protein structure
initiative; HET: TAR; 2.30A {Mycobacterium tuberculosis}
SCOP: c.2.1.4 c.23.12.1 d.58.18.1 d.81.2.2 PDB: 3dc2_A*
3ddn_A*
Length = 529
Score = 26.1 bits (58), Expect = 9.2
Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 14/60 (23%)
Query: 4 AGKVFSKNVKK---AVDNFRMIRTNIPAG-------LASPG--PPLGPTLGERGVNIATF 51
+G ++ + + ++ G + PG +G LG GVNI
Sbjct: 428 SGTLYGPQLSQKIVQINGRHF--DLRAQGINLIIHYVDRPGALGKIGTLLGTAGVNIQAA 485
>2qyw_A Vesicle transport through interaction with T-SNAR homolog; HABC
domain, protein transport, endocytosis; 2.00A {Mus
musculus} PDB: 2v8s_V
Length = 102
Score = 25.0 bits (54), Expect = 9.5
Identities = 7/34 (20%), Positives = 16/34 (47%)
Query: 154 EVVDKLDAEEYQQFLEERKIIVAEQKKELEEAKE 187
++ + EE+K +V + ++ +EA E
Sbjct: 30 DLQGVPERLLGTAGTEEKKKLVRDFDEKQQEANE 63
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 0.133 0.372
Gapped
Lambda K H
0.267 0.0535 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,994,539
Number of extensions: 179411
Number of successful extensions: 452
Number of sequences better than 10.0: 1
Number of HSP's gapped: 430
Number of HSP's successfully gapped: 36
Length of query: 195
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 106
Effective length of database: 4,216,824
Effective search space: 446983344
Effective search space used: 446983344
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 (21.9 bits)
S2: 55 (25.4 bits)