RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7547
(138 letters)
>3u5e_H L8, RP24, YL11, 60S ribosomal protein L9-A; translation,
ribosome, ribosomal R ribosomal protein, STM1,
eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae}
PDB: 3izc_F 1s1i_H 3izs_F* 3j16_F 3o5h_I 3o58_I 3u5i_H
3jyw_H
Length = 191
Score = 62.0 bits (151), Expect = 5e-13
Identities = 18/41 (43%), Positives = 27/41 (65%)
Query: 1 MVNKRVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDFT 41
VN +++KV G +K +AA+RTV S + NM+ GVTK +
Sbjct: 47 KVNNQLIKVAVHNGGRKHVAALRTVKSLVDNMITGVTKGYK 87
>1vq8_E 50S ribosomal protein L6P; 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: d.141.1.1 d.141.1.1 PDB:
1vq4_E* 1vq5_E* 1vq6_E* 1vq7_E* 1s72_E* 1vq9_E* 1vqk_E*
1vql_E* 1vqm_E* 1vqn_E* 1vqo_E* 1vqp_E* 1yhq_E* 1yi2_E*
1yij_E* 1yit_E* 1yj9_E* 1yjn_E* 1yjw_E* 2otj_E* ...
Length = 178
Score = 61.0 bits (149), Expect = 9e-13
Identities = 12/40 (30%), Positives = 20/40 (50%)
Query: 2 VNKRVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDFT 41
V+ + +E K ++ + T SHI NM GVT+ +
Sbjct: 43 VDGDTVVIESDEDNAKTMSTIGTFQSHIENMFHGVTEGWE 82
>3iz5_F 60S ribosomal protein L9 (L6P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
PDB: 3izr_F
Length = 190
Score = 59.3 bits (144), Expect = 5e-12
Identities = 18/40 (45%), Positives = 28/40 (70%)
Query: 2 VNKRVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDFT 41
R L+V+ WFGT++ +AA+RT SH+ N++ GVTK +
Sbjct: 49 EGGRKLQVDAWFGTRRTMAAIRTAISHVQNLITGVTKGYR 88
>4a17_E RPL9, 60S ribosomal protein L9; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_E 4a1c_E 4a1e_E
Length = 188
Score = 58.5 bits (142), Expect = 9e-12
Identities = 12/41 (29%), Positives = 25/41 (60%)
Query: 1 MVNKRVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDFT 41
+K++ W ++KE A ++++ S I NM++GVT+ +
Sbjct: 47 KPTADNVKLQIWQASRKERAVLQSIASQIKNMIRGVTEGYK 87
>2zkr_e 60S ribosomal protein L9; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 192
Score = 58.1 bits (141), Expect = 1e-11
Identities = 22/39 (56%), Positives = 31/39 (79%)
Query: 3 NKRVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDFT 41
K+ L+V+KW+G +KE+A VRT+CSH+ NM+KGVT F
Sbjct: 51 KKKRLRVDKWWGNRKELATVRTICSHVQNMIKGVTLGFR 89
>2cql_A OK/SW-CL.103, 60S ribosomal protein L9; N-terminal domain, alpha
and beta (A+B), structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: d.141.1.1
Length = 100
Score = 55.4 bits (134), Expect = 3e-11
Identities = 21/39 (53%), Positives = 30/39 (76%)
Query: 3 NKRVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDFT 41
K+ L+V+KW+G +KE+A VRT+CSH+ NM+KGVT
Sbjct: 58 KKKRLRVDKWWGNRKELATVRTICSHVQNMIKGVTLGSG 96
>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein
structure initiative; NMR {Salmonella typhimurium}
Length = 61
Score = 27.8 bits (63), Expect = 0.31
Identities = 7/25 (28%), Positives = 13/25 (52%), Gaps = 5/25 (20%)
Query: 15 TKKEIAA-----VRTVCSHISNMLK 34
T I+ ++TV +H NM++
Sbjct: 15 TNHGISEKLHISIKTVETHRMNMMR 39
>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory
proteins, LUXR family, structural genomics; 2.04A
{Bacteroides thetaiotaomicron vpi-5482}
Length = 258
Score = 27.3 bits (60), Expect = 1.7
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 5/25 (20%)
Query: 15 TKKEIAA-----VRTVCSHISNMLK 34
+ KEIAA V TV H N+L+
Sbjct: 214 SSKEIAATLYISVNTVNRHRQNILE 238
>1p1x_A Deoxyribose-phosphate aldolase; alpha-beta barrel, TIM barrel,
lyase; 0.99A {Escherichia coli} SCOP: c.1.10.1 PDB:
1jcl_A 1jcj_A* 1ktn_A 3npv_B 3npu_A 3npw_A 3nq2_A 3npx_A
3nq8_A 3q2d_A* 3nr0_A 3nqv_A
Length = 260
Score = 26.1 bits (58), Expect = 3.7
Identities = 7/35 (20%), Positives = 13/35 (37%), Gaps = 1/35 (2%)
Query: 1 MV-NKRVLKVEKWFGTKKEIAAVRTVCSHISNMLK 34
+V R L + A + C+ + +LK
Sbjct: 104 VVFPYRALMAGNEQVGFDLVKACKEACAAANVLLK 138
>1xdt_R Hbegf, heparin-binding epidermal growth factor; complex
(toxin-growth factor), diphtheria toxin, receptor, H
binding epidermal growth factor; 2.65A {Homo sapiens}
SCOP: g.3.11.1
Length = 79
Score = 25.1 bits (54), Expect = 3.7
Identities = 17/58 (29%), Positives = 20/58 (34%)
Query: 20 AAVRTVCSHISNMLKGVTKDFTIFTNRCLSRRCYSCAGGNCSYKMTSSYPSIICPPGY 77
A+ T K K + CL + C G C Y PS IC PGY
Sbjct: 13 QALATPNKEEHGKRKKKGKGLGKKRDPCLRKYKDFCIHGECKYVKELRAPSCICHPGY 70
>1iox_A Betacellulin; EGF-like fold, hormone/growth factor complex; NMR
{Homo sapiens} SCOP: g.3.11.1 PDB: 1ip0_A
Length = 50
Score = 24.4 bits (53), Expect = 5.0
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 45 NRCLSRRCYSCAGGNCSYKMTSSYPSIICPPGY 77
+RC + + C G C + + PS +C GY
Sbjct: 6 SRCPKQYKHYCIKGRCRFVVAEQTPSCVCDEGY 38
>1nkw_E 50S ribosomal protein L6; ribosome, large subunit, X- RAY
structure, peptidyl-transferase, peptide bond formation;
3.10A {Deinococcus radiodurans} SCOP: i.1.1.2 PDB:
1sm1_E*
Length = 212
Score = 25.2 bits (56), Expect = 6.4
Identities = 5/15 (33%), Positives = 11/15 (73%)
Query: 27 SHISNMLKGVTKDFT 41
+ ++N +KGV+ +T
Sbjct: 97 TLVANAVKGVSDGYT 111
>2zjr_E 50S ribosomal protein L6; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: d.141.1.1 d.141.1.1 PDB: 1nwx_E*
1xbp_E* 2zjp_E* 2zjq_E 1nwy_E 3cf5_E* 3dll_E* 3pio_E*
3pip_E* 1pnu_E 1pny_E 1vor_H 1vou_H 1vow_H 1voy_H
1vp0_H
Length = 185
Score = 25.1 bits (56), Expect = 7.7
Identities = 5/15 (33%), Positives = 11/15 (73%)
Query: 27 SHISNMLKGVTKDFT 41
+ ++N +KGV+ +T
Sbjct: 70 TLVANAVKGVSDGYT 84
>3r8s_G 50S ribosomal protein L6; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
1p85_E 1p86_E 2awb_G 2aw4_G 2i2v_G 2j28_G 2i2t_G*
2qao_G* 2qba_G* 2qbc_G* 2qbe_G 2qbg_G 2qbi_G* 2qbk_G*
2qov_G 2qox_G 2qoz_G* 2qp1_G* 2rdo_G 2vhm_G ...
Length = 176
Score = 25.1 bits (56), Expect = 8.4
Identities = 6/15 (40%), Positives = 12/15 (80%)
Query: 27 SHISNMLKGVTKDFT 41
+ +++M+ GVT+ FT
Sbjct: 69 ALLNSMVIGVTEGFT 83
>3v2d_H 50S ribosomal protein L6; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus}
PDB: 1vsp_F 2hgj_H 2hgq_H 2hgu_H 1vsa_F 2j03_H 2jl6_H
2jl8_H 2v47_H 2v49_H 2wdi_H 2wdj_H 2wdl_H 2wdn_H 2wh2_H
2wh4_H 2wrj_H 2wrl_H 2wro_H 2wrr_H ...
Length = 180
Score = 24.8 bits (55), Expect = 8.8
Identities = 5/15 (33%), Positives = 12/15 (80%)
Query: 27 SHISNMLKGVTKDFT 41
+ I+N +KGV++ ++
Sbjct: 70 TLIANAVKGVSEGYS 84
>1rl6_A Protein (ribosomal protein L6); RNA-binding protein, gentamicin
resistance, alpha/beta protein; 2.00A {Geobacillus
stearothermophilus} SCOP: d.141.1.1 d.141.1.1 PDB:
1giy_H 1ml5_h* 1c04_B 1yl3_H 2b66_H 2b9n_H 2b9p_H
1eg0_J 487d_J
Length = 177
Score = 24.8 bits (55), Expect = 8.8
Identities = 6/15 (40%), Positives = 12/15 (80%)
Query: 27 SHISNMLKGVTKDFT 41
S ++NM++GV+K +
Sbjct: 69 SLLANMVEGVSKGYE 83
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
0.322 0.132 0.421
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,012,740
Number of extensions: 104057
Number of successful extensions: 387
Number of sequences better than 10.0: 1
Number of HSP's gapped: 382
Number of HSP's successfully gapped: 75
Length of query: 138
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 54
Effective length of database: 4,356,429
Effective search space: 235247166
Effective search space used: 235247166
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (23.8 bits)