RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 030918
(169 letters)
>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 = 137 bits (345), Expect = 2e-42
Identities = 68/120 (56%), Positives = 85/120 (70%), Gaps = 2/120 (1%)
Query: 51 IQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAV 108
IQ +T L+V DN+GA+ +MCI+ LKG K A +GD IVASVKEA+P G VK+G VV AV
Sbjct: 2 IQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKAV 61
Query: 109 VVRAAMQHGRFDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHL 168
VVR + R DGS +RFDDNA V++N EP GTRVFGPV ELR K + I++LA +
Sbjct: 62 VVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPEV 121
>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 = 132 bits (334), Expect = 7e-41
Identities = 62/117 (52%), Positives = 79/117 (67%), Gaps = 2/117 (1%)
Query: 51 IQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAV 108
IQ + LKV DNSGA+ V+ I+ L G R+ A +GD +VA+VK+A P G VKKGQVV AV
Sbjct: 2 IQQESRLKVADNSGAREVLVIKVLGGSGRRYANIGDVVVATVKDATPGGVVKKGQVVKAV 61
Query: 109 VVRAAMQHGRFDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLA 165
VVR R DGS +RFD+NA V++ P GTR+FGPV ELR K + I++LA
Sbjct: 62 VVRTKRGVRRPDGSYIRFDENACVIIRDDKSPRGTRIFGPVARELRDKDFMKIISLA 118
>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 = 130 bits (329), Expect = 4e-40
Identities = 65/120 (54%), Positives = 82/120 (68%), Gaps = 3/120 (2%)
Query: 51 IQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAV 108
IQ +T+L V DNSGA+ VMCI+ L G R+ A +GD I ++KEA+P GKVKKG V+ AV
Sbjct: 2 IQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKAV 61
Query: 109 VVRAAMQHGRFDGSEVRFDDNAVVLVNKAGE-PTGTRVFGPVPHELRRKKHVSILTLAEH 167
VVR R DGS +RFD NA VL+N E P GTR+FGPV ELR +K + I++LA
Sbjct: 62 VVRTKKGVRRPDGSVIRFDGNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAPE 121
>3bbo_M Ribosomal protein L14; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 121
Score = 126 bits (317), Expect = 3e-38
Identities = 53/117 (45%), Positives = 80/117 (68%), Gaps = 3/117 (2%)
Query: 51 IQMRTVLKVVDNSGAKTVMCIQPLKG--RKVARLGDTIVASVKEAMPTGKVKKGQVVHAV 108
IQ +T L V DNSGA+ +MCI+ + R+ AR+GD IVA +KEA+P +++ +V+ AV
Sbjct: 2 IQPQTHLNVADNSGARELMCIRIIGASNRRYARIGDVIVAVIKEAIPNTPLERSEVIRAV 61
Query: 109 VVRAAMQHGRFDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLA 165
VVR + R +G +R+DDNA V++++ G P GTR+FG + EL R+K I++LA
Sbjct: 62 VVRTCKELKRDNGMIIRYDDNAAVIIDQEGNPKGTRIFGAIAREL-RQKFAKIVSLA 117
>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 = 112 bits (282), Expect = 8e-33
Identities = 36/121 (29%), Positives = 58/121 (47%), Gaps = 10/121 (8%)
Query: 51 IQMRTVLKVVDNSGAKTVMCIQPLKG------RKVARLGDTIVASVKEAMPTGKVKKGQV 104
+ + ++ DNSGA+ + I A LGD ++A+VK+ P + +V
Sbjct: 17 LPVGAIMNCADNSGARNLYIIAVKGSGSRLNRLPAASLGDMVMATVKKGKPE---LRKKV 73
Query: 105 VHAVVVRAAMQHGRFDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTL 164
+ A+VVR A R DG + F+DNA V+ N GE G+ + GPV E + +
Sbjct: 74 MPAIVVRQAKSWRRRDGVFLYFEDNAGVIANPKGEMKGSAITGPVGKEC-ADLWPRVASN 132
Query: 165 A 165
+
Sbjct: 133 S 133
>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 = 110 bits (276), Expect = 6e-32
Identities = 39/129 (30%), Positives = 64/129 (49%), Gaps = 10/129 (7%)
Query: 43 LSQQQRTFIQMRTVLKVVDNSGAKTVMCIQPLKGRK------VARLGDTIVASVKEAMPT 96
L ++ +++ DN+GA+ + I A LGD I SV + P
Sbjct: 4 LGADVTQGLEKGSLITCADNTGARELKVISVHGYSGTKNRLPKAGLGDKITVSVTKGTP- 62
Query: 97 GKVKKGQVVHAVVVRAAMQHGRFDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRK 156
+ QV+ AVVVR R DG+ V+F+DNA V+V++ +P GT + GP+ E+ +
Sbjct: 63 --EMRRQVLEAVVVRQRKPIRRPDGTRVKFEDNAAVIVDENEDPRGTELKGPIAREV-AQ 119
Query: 157 KHVSILTLA 165
+ S+ + A
Sbjct: 120 RFGSVASAA 128
>2v3m_A NAF1; ribosomal protein, GAR1, snoRNP, phosphorylation,
hypothetical protein; 2.74A {Saccharomyces cerevisiae}
Length = 131
Score = 29.9 bits (67), Expect = 0.23
Identities = 8/42 (19%), Positives = 15/42 (35%), Gaps = 7/42 (16%)
Query: 124 VRFDDNAVVLVNKAGEPTGTRVFGPVPH-------ELRRKKH 158
++ D+ L ++ G + F P EL+ H
Sbjct: 88 IKLPDSKKNLFDELKVRLGEKAFIVTPDAHWIDTFELKHHHH 129
>2je8_A Beta-mannosidase; glycoside hydrolase, hydrolase; HET: B3P; 1.7A
{Bacteroides thetaiotaomicron} SCOP: b.1.4.1 b.1.4.1
b.1.4.1 b.18.1.5 c.1.8.3 PDB: 2vr4_A* 2vl4_A* 2vmf_A*
2vo5_A* 2vot_A* 2vqt_A* 2vjx_A* 2vqu_A* 2wbk_A*
Length = 848
Score = 29.3 bits (65), Expect = 0.71
Identities = 17/118 (14%), Positives = 36/118 (30%), Gaps = 13/118 (11%)
Query: 52 QMRTVLKVVDNSG---AKTVMCIQPLKGRKVARLGDTIVASVKEAMPTGKVKKGQVVHAV 108
+ L + D SG A++V + K ++ + + + + +
Sbjct: 731 RSFLKLILKDKSGHQVAESVHFFRKTKDLQLPPTSVSYQMKQTDGKCELTLFSSMLAKDI 790
Query: 109 VVRAAMQHGRFDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAE 166
+ R+ DN L+ GE + P + V+I + E
Sbjct: 791 FIET-------PLQGARYSDNFFDLL--PGERKKVIITSPRIKKGEELP-VNIKHIRE 838
>3fov_A UPF0102 protein RPA0323; structural genomics, APC7380, PSI-2,
protein structure initi midwest center for structural
genomics, MCSG; 1.88A {Rhodopseudomonas palustris}
Length = 134
Score = 28.0 bits (63), Expect = 0.84
Identities = 16/76 (21%), Positives = 26/76 (34%), Gaps = 24/76 (31%)
Query: 79 VARLGDTIV-ASVK---------EAMPTGKVKKGQVVHAVVVRAA----MQHGRFDGSEV 124
VA+ + VK A+ + + +V AA +H SE+
Sbjct: 56 VAQRDALVAFVEVKARGNVDDAAYAVTPRQQSR-------IVAAAEAWLSRHPEHAMSEL 108
Query: 125 RFDDNAVVLVNKAGEP 140
RFD +L+ P
Sbjct: 109 RFD---AILIAPNTAP 121
>3nrf_A APAG protein; structural genomics, joint center for structural
genomics, J protein structure initiative, PSI-2, unknown
function; 1.50A {Pseudomonas aeruginosa} PDB: 3sb3_A
Length = 106
Score = 27.5 bits (60), Expect = 1.2
Identities = 14/74 (18%), Positives = 24/74 (32%), Gaps = 8/74 (10%)
Query: 60 VDNSGAKTV----MCIQPLKGRKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAMQ 115
+ N+ + C+ + DT V E + +K G V + A+
Sbjct: 35 LVNAAKSEISLKNSCLVAQSAAGQSFRLDT----VDEELTADTLKPGASVEGDAIFASED 90
Query: 116 HGRFDGSEVRFDDN 129
+ S VR D
Sbjct: 91 DAVYGASLVRLSDR 104
>3by7_A Uncharacterized protein; metagenomics, structural genomics, joint
center for structur genomics, JCSG, protein structure
initiative; 2.60A {Uncultured marine organism}
Length = 100
Score = 26.6 bits (59), Expect = 2.2
Identities = 9/30 (30%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 78 KVARL--GDTIVASVKEAMPTGKVKKGQVV 105
K+ RL G+ I+ ++ E+ +KK V+
Sbjct: 6 KIMRLVTGEDIIGNISESQGLITIKKAFVI 35
>2z0s_A Probable exosome complex RNA-binding protein 1; alpha/beta
protein, cytoplasm, structural genomics, NPPSFA; 3.20A
{Aeropyrum pernix} SCOP: b.40.4.5 d.51.1.1
Length = 235
Score = 27.4 bits (60), Expect = 2.3
Identities = 8/38 (21%), Positives = 16/38 (42%)
Query: 55 TVLKVVDNSGAKTVMCIQPLKGRKVARLGDTIVASVKE 92
TV+ ++ G LK V + GD ++ ++
Sbjct: 39 TVVGLLREKGDGGGRAFVKLKEIYVPQAGDVVIGLIQS 76
>4e9o_X D8L antigen, IMV membrane protein; CAH alpha fold, VP7 motif, beta
sheet, cell surface chondroi binding, viral entry,
chondroitin sulfate; 1.42A {Vaccinia virus} PDB: 4etq_X
Length = 269
Score = 27.1 bits (60), Expect = 3.0
Identities = 6/42 (14%), Positives = 13/42 (30%), Gaps = 7/42 (16%)
Query: 43 LSQQQRTFIQMRTVLKVVDNSGAKTVMC-----IQPLKGRKV 79
+ Q + RT+L + ++ G + L
Sbjct: 191 IHSDQ--LSKFRTLLSLSNHEGKPHYITENYRNPYKLNDDTE 230
>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis,
ATP-binding, hydrogen ION TRA hydrolase, ION transport;
2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D
3j0j_D*
Length = 464
Score = 27.0 bits (60), Expect = 3.1
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 12/52 (23%)
Query: 118 RFDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKHVSILTLAEHLA 169
F+ + +V+ +NKA +PT R+ P LT+AE+LA
Sbjct: 207 EFERTGAL--SRSVLFLNKADDPTIERILTP----------RMALTVAEYLA 246
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 26.8 bits (59), Expect = 4.5
Identities = 8/42 (19%), Positives = 19/42 (45%), Gaps = 7/42 (16%)
Query: 12 VILVGRSLLGGLGNNLSGLSSTSHEMASGNFLSQQQRTFIQM 53
+++ G + +G G+ + T EM + S + ++M
Sbjct: 820 IVVTGFAEVGPWGS-----ARTRWEMEAFGEFSLE--GCVEM 854
>3e5r_O PP38, glyceraldehyde-3-phosphate dehydrogenase, cytosolic; GAPDH,
RICE, oxidoreductase, cytoplasm, glycolysis, NAD; HET:
NAD; 2.30A {Oryza sativa subsp} PDB: 3e6a_O
Length = 337
Score = 26.4 bits (59), Expect = 5.2
Identities = 5/20 (25%), Positives = 13/20 (65%)
Query: 116 HGRFDGSEVRFDDNAVVLVN 135
HG++ S+++ D+ +L+
Sbjct: 53 HGQWKHSDIKIKDSKTLLLG 72
>2dho_A Isopentenyl-diphosphate delta-isomerase 1; alpha/beta protein;
1.60A {Homo sapiens} PDB: 2i6k_A* 2icj_A 2ick_A*
Length = 235
Score = 25.9 bits (56), Expect = 6.5
Identities = 4/24 (16%), Positives = 10/24 (41%)
Query: 120 DGSEVRFDDNAVVLVNKAGEPTGT 143
D +V+ +L+++ G
Sbjct: 18 DKQQVQLLAEMCILIDENDNKIGA 41
>3kfu_F Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase; ASPRS, gatcab,
ATP-binding, aminoacyl-tRNA synthetase, ligas
nucleotide-binding, protein biosynthesis, ligase-RNA
comple; HET: H2U 5MU PSU; 3.00A {Thermus thermophilus}
Length = 466
Score = 26.0 bits (58), Expect = 6.6
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 7/32 (21%)
Query: 114 MQHGRFDGSEVRFDDNAVVLVNKAGEPTGTRV 145
+ G+ R D N V V + GEP GT+V
Sbjct: 180 PEEGKL-----RADVN--VSVRRVGEPLGTKV 204
>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase,
A1AO, ATP synthesis, hydrogen ION transport, ION
transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A*
3b2q_A* 2rkw_A* 3eiu_A*
Length = 469
Score = 25.8 bits (57), Expect = 8.8
Identities = 20/71 (28%), Positives = 27/71 (38%), Gaps = 21/71 (29%)
Query: 108 VVVRAAM-QHGR--------FDGSEVRFDDNAVVLVNKAGEPTGTRVFGPVPHELRRKKH 158
VV AAM F+ + + AVV +N A +P R+ P
Sbjct: 186 AVVFAAMGITNEEAQYFMSDFEKTGAL--ERAVVFLNLADDPAVERIVTP---------- 233
Query: 159 VSILTLAEHLA 169
LT AE+LA
Sbjct: 234 RMALTAAEYLA 244
>3uif_A Sulfonate ABC transporter, periplasmic sulfonate- protein SSUA;
structural genomics; 2.60A {Methylobacillus flagellatus}
Length = 348
Score = 25.6 bits (56), Expect = 9.2
Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 21/63 (33%)
Query: 55 TVLKVVDNSGAKTVMCIQPLKGRKVARLGDTIVASVKEAMPTGKVKKGQVVHAVVVRAAM 114
+ L V NS AK++ + LKG+K+A + +G+
Sbjct: 101 SYLVVPKNSTAKSI---KDLKGKKIA------------------LHRGRPWELAFSNLLQ 139
Query: 115 QHG 117
G
Sbjct: 140 SEG 142
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
0.319 0.132 0.369
Gapped
Lambda K H
0.267 0.0814 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,507,685
Number of extensions: 147662
Number of successful extensions: 376
Number of sequences better than 10.0: 1
Number of HSP's gapped: 368
Number of HSP's successfully gapped: 32
Length of query: 169
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 82
Effective length of database: 4,272,666
Effective search space: 350358612
Effective search space used: 350358612
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: 54 (24.4 bits)