RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6163
(137 letters)
>3u5e_V L17A, YL32, 60S ribosomal protein L23-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3izc_M
1s1i_R 3izs_M* 3j16_I 3o5h_U 3o58_U 3u5i_V 2x7n_C 3jyw_R
2zkr_k 3iz5_M 3izr_M 4a17_J 4a1a_J 4a1c_J 4a1e_J
Length = 137
Score = 117 bits (295), Expect = 3e-35
Identities = 90/118 (76%), Positives = 103/118 (87%)
Query: 7 GGSAGAKFRISLALPVGAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVK 66
G+ G KFRISL LPVGA++NCADN+GA+NL++IAV+G RLNRLPAA GDM +ATVK
Sbjct: 4 NGAQGTKFRISLGLPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPAASLGDMVMATVK 63
Query: 67 KGKPELRKKVMPAVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPVAKE 124
KGKPELRKKVMPA+V+RQ K +RRRDGVF+YFEDNAGVI N KGEMKGSAITGPV KE
Sbjct: 64 KGKPELRKKVMPAIVVRQAKSWRRRDGVFLYFEDNAGVIANPKGEMKGSAITGPVGKE 121
>1vq8_K 50S ribosomal protein L14P; 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: b.39.1.1 PDB: 1vq4_K*
1vq5_K* 1vq6_K* 1vq7_K* 1s72_K* 1vq9_K* 1vqk_K* 1vql_K*
1vqm_K* 1vqn_K* 1vqo_K* 1vqp_K* 1yhq_K* 1yi2_K* 1yij_K*
1yit_K* 1yj9_K* 1yjn_K* 1yjw_K* 2otj_K* ...
Length = 132
Score = 111 bits (278), Expect = 1e-32
Identities = 56/114 (49%), Positives = 76/114 (66%)
Query: 11 GAKFRISLALPVGAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKKGKP 70
++ L G++I CADNTGA+ L VI+V G G NRLP AG GD +V KG P
Sbjct: 3 ALGADVTQGLEKGSLITCADNTGARELKVISVHGYSGTKNRLPKAGLGDKITVSVTKGTP 62
Query: 71 ELRKKVMPAVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPVAKE 124
E+R++V+ AVV+RQRKP RR DG + FEDNA VIV+ + +G+ + GP+A+E
Sbjct: 63 EMRRQVLEAVVVRQRKPIRRPDGTRVKFEDNAAVIVDENEDPRGTELKGPIARE 116
>3bbo_M Ribosomal protein L14; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 121
Score = 92.0 bits (228), Expect = 2e-25
Identities = 39/106 (36%), Positives = 60/106 (56%), Gaps = 7/106 (6%)
Query: 22 VGAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKKGKPE---LRKKVMP 78
+N ADN+GA+ L I + G R A GD+ VA +K+ P R +V+
Sbjct: 4 PQTHLNVADNSGARELMCIRIIGASNR----RYARIGDVIVAVIKEAIPNTPLERSEVIR 59
Query: 79 AVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPVAKE 124
AVV+R K +R +G+ I ++DNA VI++ +G KG+ I G +A+E
Sbjct: 60 AVVVRTCKELKRDNGMIIRYDDNAAVIIDQEGNPKGTRIFGAIARE 105
>1whi_A Ribosomal protein L14; rRNA-binding; 1.50A {Geobacillus
stearothermophilus} SCOP: b.39.1.1 PDB: 1giy_N 1ml5_n*
1c04_D 1yl3_N 2b66_O 2b9n_O 2b9p_O 487d_M
Length = 122
Score = 91.6 bits (227), Expect = 4e-25
Identities = 42/106 (39%), Positives = 62/106 (58%), Gaps = 7/106 (6%)
Query: 22 VGAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKKGKPE---LRKKVMP 78
+ + ADN+GA+ + VI V G GR A GD+ VATVK P + +V+
Sbjct: 4 QESRLKVADNSGAREVLVIKVLGGSGR----RYANIGDVVVATVKDATPGGVVKKGQVVK 59
Query: 79 AVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPVAKE 124
AVV+R ++ RR DG +I F++NA VI+ + +G+ I GPVA+E
Sbjct: 60 AVVVRTKRGVRRPDGSYIRFDENACVIIRDDKSPRGTRIFGPVARE 105
>3v2d_O 50S ribosomal protein L14; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2j03_O 2jl6_O 2jl8_O 2v47_O 2v49_O 2wdi_O 2wdj_O 2wdl_O
2wdn_O 2wh2_O 2wh4_O 2wrj_O 2wrl_O 2wro_O 2wrr_O 2x9s_O
2x9u_O 2xg0_O 2xg2_O 2xqe_O ...
Length = 122
Score = 90.1 bits (223), Expect = 2e-24
Identities = 42/106 (39%), Positives = 59/106 (55%), Gaps = 7/106 (6%)
Query: 22 VGAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKKGKPELRKK---VMP 78
+ ADNTGA+ + I V A GD+ VA+VK+ P K V+
Sbjct: 4 PQTYLEVADNTGARKIMCIRVLKGSNA----KYATVGDVIVASVKEAIPRGAVKEGDVVK 59
Query: 79 AVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEMKGSAITGPVAKE 124
AVV+R +K +R DG I F+DNA VI+NN+ E +G+ + GPVA+E
Sbjct: 60 AVVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARE 105
>3r8s_K 50S ribosomal protein L14; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3oat_K* 3oas_K* 3ofd_K 3ofc_K 3ofr_K* 3ofz_K* 3og0_K
3ofq_K 3r8t_K 3i1n_K 1p85_I 1p86_I 1vs8_K 1vs6_K 2aw4_K
2awb_K 1vt2_K 2i2v_K 2i2t_K* 2qao_K* ...
Length = 122
Score = 87.8 bits (217), Expect = 1e-23
Identities = 40/107 (37%), Positives = 57/107 (53%), Gaps = 8/107 (7%)
Query: 22 VGAVINCADNTGAKNLFVIAVQGVKGRLNRLPAAGSGDMFVATVKKGKPELR---KKVMP 78
++N ADN+GA+ + I V G R G GD+ T+K+ P + V+
Sbjct: 4 EQTMLNVADNSGARRVMCIKVLGGSHRRYA----GVGDIIKITIKEAIPRGKVKKGDVLK 59
Query: 79 AVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEM-KGSAITGPVAKE 124
AVV+R +K RR DG I F+ NA V++NN E G+ I GPV +E
Sbjct: 60 AVVVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRE 106
>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 = 41.2 bits (96), Expect = 3e-05
Identities = 25/107 (23%), Positives = 35/107 (32%), Gaps = 29/107 (27%)
Query: 18 LALPVGAVINCADNT-GA-------KNLFVIAVQGVKGRLNR-LPAAG--------SGDM 60
+LP + + +N G NL VQ + N LPA
Sbjct: 317 TSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKN 376
Query: 61 FVATVKKGKPE--------LRKKVMPAVVIRQRKPFRRRDGVFIY-F 98
V + G P+ LRK P+ + + R PF R F F
Sbjct: 377 LVVS---GPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF 420
>3h9w_A Diguanylate cyclase with PAS/PAC sensor; alpha-beta protein.,
structural genomics, PSI-2, protein STR initiative;
1.90A {Marinobacter aquaeolei}
Length = 115
Score = 27.2 bits (61), Expect = 0.95
Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 13/62 (20%)
Query: 70 PELRKKVMPAV--VIRQRKPF------RRRDGVFIYFEDNAGVIVNNKGE---MKGSA-- 116
PE ++ V+ RDG +++ D V+ ++ GE + G
Sbjct: 46 PEDQEWVVNFCVKQSECGVDHEADYRALHRDGHYVWIRDVVHVVRDDSGEVEALIGFMFD 105
Query: 117 IT 118
I+
Sbjct: 106 IS 107
>3f1p_A Endothelial PAS domain-containing protein 1; PAS domain,
heterodimer, internal cavity, activator, angiogenesis,
congenital erythrocytosis; 1.17A {Homo sapiens} PDB:
3f1o_A* 3f1n_A 3h7w_A* 3h82_A* 1p97_A 2a24_A
Length = 117
Score = 26.4 bits (59), Expect = 1.9
Identities = 7/39 (17%), Positives = 14/39 (35%), Gaps = 4/39 (10%)
Query: 72 LRKKVMPAVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKG 110
K + + R + G +++ E VI N +
Sbjct: 64 CTKGQVVSGQYR----MLAKHGGYVWLETQGTVIYNPRN 98
>2kdk_A ARYL hydrocarbon receptor nuclear translocator-LI 2; circadian
clock, PAS domain, transcription, activator, biolo
rhythms, DNA-binding, nucleus; NMR {Homo sapiens}
Length = 121
Score = 25.7 bits (57), Expect = 4.2
Identities = 6/24 (25%), Positives = 10/24 (41%)
Query: 88 FRRRDGVFIYFEDNAGVIVNNKGE 111
FR +DG F+ + N +
Sbjct: 81 FRAKDGSFVTLKSQWFSFTNPDTK 104
>1lcy_A HTRA2 serine protease; apoptosis, PDZ domain, caspase activation,
binding, hydrolase; 2.00A {Homo sapiens} SCOP: b.36.1.4
b.47.1.1
Length = 325
Score = 26.1 bits (58), Expect = 4.3
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 13/45 (28%)
Query: 74 KKVMPAVV---IRQRKPFRRRD-------GVFIYFEDNAGVIVNN 108
+K PAVV I R PF R+ G + G+IV N
Sbjct: 22 EKTAPAVVYIEILDRHPFLGREVPISNGSGFVV---AADGLIVTN 63
>3lgi_A Protease DEGS; stress-sensor, HTRA, PDZ OMP, hydrolase, serine PR;
1.65A {Escherichia coli} PDB: 2qf3_A 2qf0_A 2rce_A*
3lh3_A* 3b8j_A 2qgr_A 3lh1_A 3lgy_A 3lgu_A 3lgv_A 3lgw_A
3lgt_A 2r3u_A
Length = 237
Score = 25.3 bits (56), Expect = 6.8
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 74 KKVMPAVV-IRQRKPFRRRDGVFIYFEDNAGVIVNNKG 110
++ PAVV + R +GVI++ +G
Sbjct: 27 RRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRG 64
>2vlg_A Sporulation kinase A; histidine kinase, two-component regulatory
system, two-component signal transduction, transferase,
phosphorylation, SCOD; 1.7A {Bacillus subtilis}
Length = 111
Score = 24.7 bits (54), Expect = 7.1
Identities = 3/27 (11%), Positives = 10/27 (37%)
Query: 88 FRRRDGVFIYFEDNAGVIVNNKGEMKG 114
F ++D ++ E ++ +
Sbjct: 73 FIKKDHTIVWVEAAVEIVTTRAERTER 99
>3cpf_A Eukaryotic translation initiation factor 5A-1; structural genomics
consortium, leukemia, apoptosis, SGC, HY initiation
factor, nucleus; 2.50A {Homo sapiens}
Length = 138
Score = 25.0 bits (54), Expect = 8.4
Identities = 7/39 (17%), Positives = 16/39 (41%)
Query: 75 KVMPAVVIRQRKPFRRRDGVFIYFEDNAGVIVNNKGEMK 113
+ P+ +R D I +D ++ + GE++
Sbjct: 58 DICPSTHNMDVPNIKRNDFQLIGIQDGYLSLLQDSGEVR 96
>3e8t_A Takeout 1, takeout-like protein 1; transport protein; HET: UQ8;
1.30A {Epiphyas postvittana} PDB: 3e8w_A*
Length = 220
Score = 24.9 bits (54), Expect = 9.1
Identities = 11/64 (17%), Positives = 22/64 (34%), Gaps = 8/64 (12%)
Query: 45 VKGRLNRLPAAGSGDMFV------ATVK-KGKPELRKKVMPAVVIRQRKP-FRRRDGVFI 96
GR+ LP G G M + + + E + + V+ ++ F +D
Sbjct: 99 AGGRILILPITGDGQMKLKLKNIHIHLVVSYEMEKDAEGVDHVIFKKYTVTFDVKDNAQF 158
Query: 97 YFED 100
+
Sbjct: 159 GLTN 162
>3num_A Serine protease HTRA1; DEGP, hydrolase; 2.75A {Homo sapiens} PDB:
3nzi_A 3nwu_A 2ytw_A 2joa_A
Length = 332
Score = 24.9 bits (55), Expect = 9.3
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 11/47 (23%)
Query: 71 ELRKKVMPAVV---IRQRKPFRRRDGV------FIYFEDNAGVIVNN 108
++ +K+ PAVV + ++ PF +R+ FI ED G+IV N
Sbjct: 18 DVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSED--GLIVTN 62
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
0.321 0.139 0.407
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,141,439
Number of extensions: 128199
Number of successful extensions: 311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 306
Number of HSP's successfully gapped: 27
Length of query: 137
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 53
Effective length of database: 4,356,429
Effective search space: 230890737
Effective search space used: 230890737
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 (21.8 bits)
S2: 52 (23.8 bits)