RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780147|ref|YP_003064560.1| 50S ribosomal protein L11
[Candidatus Liberibacter asiaticus str. psy62]
(142 letters)
>3ofq_I 50S ribosomal protein L11; protein biosynthesis, ribosomes, RNA,
tRNA, transfer, antibi EXIT, peptidyl, ribosomal
subunit, large; 3.10A {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 = 167 bits (423), Expect = 1e-42
Identities = 77/141 (54%), Positives = 95/141 (67%)
Query: 2 AKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTC 61
AK V VKLQ+ +G A PSPPVGPA+GQ G+ IM FCKAFNA T+ +EKG+PIP +T
Sbjct: 1 AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITV 60
Query: 62 YKDKSFTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAID 121
Y D+SFTF PP + LKK GIKSGS P K+ G I+R +++IAQ K DM D
Sbjct: 61 YADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGAD 120
Query: 122 IEGAMRMVEGSACSMGISVVD 142
IE R +EG+A SMG+ V D
Sbjct: 121 IEAMTRSIEGTARSMGLVVED 141
>1mms_A Protein (ribosomal protein L11); RNA-protein complex, RNA,
ribosome, translocation, thiostrepton; 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 = 159 bits (405), Expect = 1e-40
Identities = 72/141 (51%), Positives = 97/141 (68%), Gaps = 1/141 (0%)
Query: 2 AKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTC 61
AK V+ +KLQ+ +G A P+PPVGPA+GQ G+ IM FCK FNA T G+ +P +T
Sbjct: 1 AKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADK-AGMILPVVITV 59
Query: 62 YKDKSFTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAID 121
Y+DKSFTF + PP SF LKK GI+ GS P ++ G +TR+ I +IA+ KM D+ A
Sbjct: 60 YEDKSFTFIIKTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANS 119
Query: 122 IEGAMRMVEGSACSMGISVVD 142
+E AM+++EG+A SMGI VVD
Sbjct: 120 LEAAMKIIEGTAKSMGIEVVD 140
>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 = 157 bits (399), Expect = 8e-40
Identities = 65/141 (46%), Positives = 86/141 (60%), Gaps = 1/141 (0%)
Query: 1 MAKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVT 60
AK V ++KL +E+G A P+PPVGPA+G G+ IMAFCK +NA T G IP +T
Sbjct: 72 KAKKVIGVIKLALEAGKATPAPPVGPALGSKGVNIMAFCKDYNARTADK-PGFVIPVEIT 130
Query: 61 CYKDKSFTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAI 120
+ DKSFTF + PP S L K G + GSK P E G IT + +R IA K+ D+
Sbjct: 131 VFDDKSFTFILKTPPASVLLLKASGAEKGSKDPQMEKVGKITIDQLRGIATEKLPDLNCT 190
Query: 121 DIEGAMRMVEGSACSMGISVV 141
IE AMR++ G+A +MGI +
Sbjct: 191 TIESAMRIIAGTAANMGIDID 211
>3i1n_I 50S ribosomal protein L11; ribosome structure, protein-RNA complex,
acetylation, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA- binding, methylation; 3.19A
{Escherichia coli k-12} PDB: 1vs8_I 3e1b_5 3e1d_5 1vs6_I
3i1p_I 3i1r_I 3i1t_I 3i20_I 3i22_I 2qam_I* 1p85_G 1p86_G
2awb_I 2aw4_I 2i2v_I 2j28_I 2i2t_I* 2qao_I* 2qba_I*
2qbc_I* ...
Length = 142
Score = 154 bits (391), Expect = 6e-39
Identities = 78/142 (54%), Positives = 96/142 (67%)
Query: 1 MAKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVT 60
MAK V VKLQ+ +G A PSPPVGPA+GQ G+ IM FCKAFNA T+ +EKG+PIP +T
Sbjct: 1 MAKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVIT 60
Query: 61 CYKDKSFTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAI 120
Y D+SFTF PP + LKK GIKSGS P K+ G I+R +++IAQ K DM
Sbjct: 61 VYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGA 120
Query: 121 DIEGAMRMVEGSACSMGISVVD 142
DIE R +EG+A SMG+ V D
Sbjct: 121 DIEAMTRSIEGTARSMGLVVED 142
>2ftc_G L11MT, MRP-L11, 39S ribosomal protein L11, mitochondrial;
mitochondrial ribosome, large ribosomal subunit,
ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_G
Length = 145
Score = 148 bits (374), Expect = 5e-37
Identities = 54/143 (37%), Positives = 88/143 (61%), Gaps = 4/143 (2%)
Query: 3 KVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCY 62
V +++ + +G A P PP+GP +GQ G+ I FCK FN T+ +++GIP+PT +
Sbjct: 2 PEVGGVIRAIVRAGLAMPGPPLGPVLGQRGVSINQFCKEFNERTKDIKEGIPLPTKILVK 61
Query: 63 KDKSFTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQD----MG 118
D++F + QP VS+FLK GI+ G++ GKE G +T +++ +IA++K QD +
Sbjct: 62 PDRTFEIKIGQPTVSYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEIARIKAQDEAFALQ 121
Query: 119 AIDIEGAMRMVEGSACSMGISVV 141
+ + +R + GSA S+GI VV
Sbjct: 122 DVPLSSVVRSIIGSARSLGIRVV 144
>1vq8_I 50S ribosomal protein L11P; 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: 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 = 146 bits (370), Expect = 2e-36
Identities = 36/137 (26%), Positives = 71/137 (51%), Gaps = 1/137 (0%)
Query: 5 VSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKD 64
++ +++ + G A P PP+GP +G + + A + N T G +P TV D
Sbjct: 1 MAGTIEVLVPGGEANPGPPLGPELGPTPVDVQAVVQEINDQTAAF-DGTEVPVTVKYDDD 59
Query: 65 KSFTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEG 124
SF + PP + +K E G ++GS P ++ ++ + +++IA+ K D+ + D+
Sbjct: 60 GSFEIEVGVPPTAELIKDEAGFETGSGEPQEDFVADLSVDQVKQIAEQKHPDLLSYDLTN 119
Query: 125 AMRMVEGSACSMGISVV 141
A + V G+ S+G+++
Sbjct: 120 AAKEVVGTCTSLGVTIE 136
>3egv_B 50S ribosomal protein L11, ribosomal protein L11 methyltransferase;
post-translational modification, multiple
methyltransferase, cytoplasm; 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 3cjt_B*
3f1f_K 3f1h_K ...
Length = 146
Score = 145 bits (368), Expect = 3e-36
Identities = 68/139 (48%), Positives = 91/139 (65%), Gaps = 1/139 (0%)
Query: 3 KVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCY 62
K V +VKLQ+ +G+A P+PPVGPA+GQ G IM F KAFNAAT M +P +T Y
Sbjct: 1 KKVVAVVKLQLPAGAATPAPPVGPALGQHGANIMEFVKAFNAATANM-GDAIVPVEITIY 59
Query: 63 KDKSFTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDI 122
D+SFTF PP S+ ++K G++ G+ PG+E G IT E + +IA+ KM D+ D+
Sbjct: 60 ADRSFTFVTKTPPASYLIRKAAGLEKGAHKPGREKVGRITWEQVLEIAKQKMPDLNTTDL 119
Query: 123 EGAMRMVEGSACSMGISVV 141
E A RM+ GSA SMG+ VV
Sbjct: 120 EAAARMIAGSARSMGVEVV 138
>2zkr_i 60S ribosomal protein L12; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris} PDB: 1s1i_K
Length = 165
Score = 133 bits (336), Expect = 2e-32
Identities = 27/134 (20%), Positives = 52/134 (38%), Gaps = 1/134 (0%)
Query: 7 RIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKS 66
++V L+ G + + P IG G+ AT KG+ I +T ++
Sbjct: 11 KVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDW-KGLRITVKLTIQNRQA 69
Query: 67 FTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAM 126
+ + + K + G+IT + I IA+ A ++ G +
Sbjct: 70 QIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVNIARQMRHRSLARELSGTI 129
Query: 127 RMVEGSACSMGISV 140
+ + G+A S+G +V
Sbjct: 130 KEILGTAQSVGCNV 143
>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 = 97.0 bits (242), Expect = 1e-21
Identities = 38/72 (52%), Positives = 46/72 (63%), Gaps = 1/72 (1%)
Query: 3 KVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCY 62
K V +VKLQ+ +G A P+PPVGPA+GQ G IM F KAFNAAT M +P +T Y
Sbjct: 2 KKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANM-GDAIVPVEITIY 60
Query: 63 KDKSFTFTMSQP 74
D+SFTF P
Sbjct: 61 ADRSFTFVTKTP 72
>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 = 94.0 bits (234), Expect = 1e-20
Identities = 38/76 (50%), Positives = 50/76 (65%)
Query: 67 FTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAM 126
FTF PP + LKK GI+SGS P + +I R+ +R+IA+LKM D+ A IE AM
Sbjct: 1 FTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAM 60
Query: 127 RMVEGSACSMGISVVD 142
RM+EG+A SMGI V +
Sbjct: 61 RMIEGTARSMGIVVEN 76
>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 = 90.8 bits (226), Expect = 1e-19
Identities = 34/65 (52%), Positives = 45/65 (69%)
Query: 74 PPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGSA 133
PP + LKK GI+SGS P + +I R+ +R+IA+LKM D+ A IE AMRM+EG+A
Sbjct: 3 PPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTA 62
Query: 134 CSMGI 138
SMGI
Sbjct: 63 RSMGI 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 = 79.0 bits (195), Expect = 3e-16
Identities = 16/79 (20%), Positives = 28/79 (35%), Gaps = 3/79 (3%)
Query: 7 RIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKS 66
++V L+ G + + P IG G+ AT KG+ I +T +++
Sbjct: 17 KVVYLRCTGGEVGATSALAPKIGPLGLSPKKVGDDIAKATGDW-KGLRITVKLT-IQNRQ 74
Query: 67 FTFTMSQPPVSFFLKKEVG 85
+ P S G
Sbjct: 75 AQIEVV-PSASALSGPSSG 92
>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 = 31.8 bits (72), Expect = 0.064
Identities = 32/219 (14%), Positives = 60/219 (27%), Gaps = 98/219 (44%)
Query: 8 IVKLQIESGSAKPSP----------PVGPAIGQ------------------------AGI 33
I++ +E+ PSP V + + +G
Sbjct: 323 ILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSG- 381
Query: 34 PIMAFCKAFN-------AATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVS--F------ 78
P + N A + + IP + ++ F+ PV+ F
Sbjct: 382 PPQSLY-GLNLTLRKAKAPSGLDQSRIP-------FSERKLKFSNRFLPVASPFHSHLLV 433
Query: 79 ---------FLKKEVGIKSGS-KLP------GK---ESCGSITRENIRKIAQLKMQ---- 115
+K V + ++P G GSI+ + I +L ++
Sbjct: 434 PASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETT 493
Query: 116 ---------DMGAIDIEG----AMRMVEGSACSMGISVV 141
D G G R +G+ G+ V+
Sbjct: 494 TQFKATHILDFGPGGASGLGVLTHRNKDGT----GVRVI 528
Score = 26.1 bits (57), Expect = 3.4
Identities = 8/32 (25%), Positives = 14/32 (43%), Gaps = 7/32 (21%)
Query: 56 PTTVTCYKDKSFTFTMSQPPVSFF----LKKE 83
P T++ S + P SFF L+++
Sbjct: 8 PLTLS---HGSLEHVLLVPTASFFIASQLQEQ 36
>1jlx_A Agglutinin, amaranthin, ACA; complex (lectin/saccharide),
T-disaccharide homodimer, bivalent, lectin; HET: GAL
A2G; 2.20A {Amaranthus caudatus} SCOP: b.42.3.1 b.42.3.1
PDB: 1jly_A
Length = 303
Score = 27.2 bits (60), Expect = 1.2
Identities = 7/26 (26%), Positives = 16/26 (61%)
Query: 93 PGKESCGSITRENIRKIAQLKMQDMG 118
PG +C + +N+ + A L++ ++G
Sbjct: 275 PGFINCMNAATQNVDETAILEIIELG 300
>1g4w_R Protein tyrosine phosphatase SPTP; virulence factor, GTPase
activating protein, 4-helix bundle, disorder, signaling
protein; 2.20A {Salmonella typhimurium} SCOP: a.24.11.1
c.45.1.2 PDB: 1g4u_S
Length = 383
Score = 27.1 bits (59), Expect = 1.6
Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 3/64 (4%)
Query: 12 QIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATE-GMEKGIPIPTTVTCYKDKSFTFT 70
+IE+G+ P GP +G A + + N T+ + G+P+P + K
Sbjct: 129 KIEAGAPMPQTMSGPTLGLARFAVSSI--PINQQTQVKLSDGMPVPVNTLTFDGKPVALA 186
Query: 71 MSQP 74
S P
Sbjct: 187 GSYP 190
>1xkn_A Putative peptidyl-arginine deiminase; alpha-beta protein, NESG,
structural genomics, protein structure initiative, PSI;
1.60A {Chlorobium tepidum tls} SCOP: d.126.1.6
Length = 355
Score = 25.1 bits (54), Expect = 6.5
Identities = 7/38 (18%), Positives = 17/38 (44%)
Query: 57 TTVTCYKDKSFTFTMSQPPVSFFLKKEVGIKSGSKLPG 94
TT C + + ++ + + L++ +GI+ L
Sbjct: 170 TTTACLLNPNRNPSLGKAEIEAQLRRYLGIEKVLWLGD 207
>1zcd_A Na(+)/H(+) antiporter 1; membrane protein; 3.45A {Escherichia coli}
PDB: 3fi1_A
Length = 388
Score = 24.5 bits (53), Expect = 8.6
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 23 PVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTT 58
PV AIG +P + + AFN A +G IP
Sbjct: 97 PVIAAIGGMIVPALLYL-AFNYADPITREGWAIPAA 131
>2a1v_A Conserved hypothetical protein; structural genomics, PSI, protein
structure initiative; 2.15A {Deinococcus radiodurans}
SCOP: d.198.3.1
Length = 144
Score = 24.6 bits (53), Expect = 8.8
Identities = 5/37 (13%), Positives = 10/37 (27%)
Query: 35 IMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTM 71
+ + C + E Y KS + +
Sbjct: 13 LRSVCDELPHSLETFPFDDETLVFKVGYLSKSRMYAL 49
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
0.317 0.133 0.379
Gapped
Lambda K H
0.267 0.0546 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,177,158
Number of extensions: 50193
Number of successful extensions: 122
Number of sequences better than 10.0: 1
Number of HSP's gapped: 114
Number of HSP's successfully gapped: 23
Length of query: 142
Length of database: 5,693,230
Length adjustment: 83
Effective length of query: 59
Effective length of database: 3,680,978
Effective search space: 217177702
Effective search space used: 217177702
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 (21.7 bits)
S2: 52 (24.2 bits)