RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 047908
(94 letters)
>3r8s_L 50S ribosomal protein L15; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3fik_L 2wwq_L 3oat_L* 3oas_L* 3ofd_L 3ofc_L 3ofr_L*
3ofz_L* 3og0_L 3ofq_L 3r8t_L 3i1n_L 1p85_J 1p86_J 1vs8_L
1vs6_L 2aw4_L 2awb_L 1vt2_L 2i2v_L ...
Length = 143
Score = 52.5 bits (127), Expect = 2e-10
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 10/77 (12%)
Query: 1 PVGLGKIAYLINAGKIDSHELITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVS 60
+ L +A + ++ + TLK A IG QI + +++ G ++ P+ +
Sbjct: 75 EIRLSDLAKVEG-------GVVDLNTLKAANIIGIQI-EFAKVILAG--EVTTPVTVRGL 124
Query: 61 RVTVRAKAAVEAAGGSV 77
RVT A+AA+EAAGG +
Sbjct: 125 RVTKGARAAIEAAGGKI 141
>2zjr_I 50S ribosomal protein L15; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.12.1.1 PDB: 1nwx_J* 1nwy_J* 1sm1_J*
1xbp_J* 2zjp_I* 2zjq_I 1nkw_J 3cf5_I* 3dll_I* 3pio_I*
3pip_I* 1pnu_J 1pny_J 1vor_M 1vou_M 1vow_M 1voy_M 1vp0_M
Length = 156
Score = 48.7 bits (117), Expect = 8e-09
Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 10/77 (12%)
Query: 1 PVGLGKIAYLINAGKIDSHELITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVS 60
V L ++ L + TL+ + ++ V+L+ G +I + + V
Sbjct: 74 VVKLSQLQDLEDTT-------FDRDTLEAYRLVRRKN-RPVKLLASG--EISRAVTVHVD 123
Query: 61 RVTVRAKAAVEAAGGSV 77
+ A AVEAAGG V
Sbjct: 124 AASAAAIKAVEAAGGRV 140
>3bbo_N Ribosomal protein L15; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 257
Score = 49.1 bits (117), Expect = 1e-08
Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 5/70 (7%)
Query: 11 INAGKIDSHELITMKTLKDAGAIGKQIE---DGVRLMGRGAEKIKWPIHLEVSRVTVRAK 67
I E ++++TLK I ++++ G ++ + ++ + AK
Sbjct: 150 IENAGFQDGEEVSLETLKAKRVINPSGRERKLPLKILADG--ELSKKLTIKAGAFSTSAK 207
Query: 68 AAVEAAGGSV 77
+E AG S+
Sbjct: 208 EKLEYAGCSL 217
>3v2d_P 50S ribosomal protein L15; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_J 2hgj_O 2hgq_O 2hgu_O 1vsa_J 2j03_P 2jl6_P 2jl8_P
2v47_P 2v49_P 2wdi_P 2wdj_P 2wdl_P 2wdn_P 2wh2_P 2wh4_P
2wrj_P 2wrl_P 2wro_P 2wrr_P ...
Length = 150
Score = 44.8 bits (107), Expect = 2e-07
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 6/68 (8%)
Query: 11 INAGKIDSHE-LITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRAKAA 69
+N + E +T + L AG + K ++++G G K P+ + + A
Sbjct: 83 VNLKDLARFEGEVTPELLVRAGLLKKG--YRLKILGEGEAK---PLKVVAHAFSKSALEK 137
Query: 70 VEAAGGSV 77
++AAGG
Sbjct: 138 LKAAGGEP 145
>1vq8_L 50S ribosomal protein L15P; 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: c.12.1.1 PDB: 1vq4_L*
1vq5_L* 1vq6_L* 1vq7_L* 1s72_L* 1vq9_L* 1vqk_L* 1vql_L*
1vqm_L* 1vqn_L* 1vqo_L* 1vqp_L* 1yhq_L* 1yi2_L* 1yij_L*
1yit_L* 1yj9_L* 1yjn_L* 1yjw_L* 2otj_L* ...
Length = 165
Score = 35.2 bits (81), Expect = 0.001
Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 3/71 (4%)
Query: 7 IAYLINAGKIDSHELITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRA 66
+ L + + ++D D V+++G G +++ + L + A
Sbjct: 74 VTLLAADDVAEVEDGGFRVDVRDVVEEADD-ADYVKVLGAG--QVRHELTLIADDFSEGA 130
Query: 67 KAAVEAAGGSV 77
+ VE AGGSV
Sbjct: 131 REKVEGAGGSV 141
>3iz5_O 60S ribosomal protein L27A (L15P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_O
Length = 144
Score = 32.7 bits (74), Expect = 0.007
Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 11 INAGKIDSH-ELITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRAKAA 69
+N ++ S A I +++G+G + PI ++ ++ A+
Sbjct: 73 VNVERLWSMVPAEAGAGAGKAPVIDVTQFGYTKVLGKGMLPPERPIVVKAKLISKVAEKK 132
Query: 70 VEAAGGSV 77
++AAGG+V
Sbjct: 133 IKAAGGAV 140
>2ze3_A DFA0005; organic waste LEFT-OVER decomposition, alkaliphilic,
ICL/PEPM superfamily, alpha-ketoglutarate LIG isomerase;
HET: AKG; 1.65A {Deinococcus ficus}
Length = 275
Score = 29.9 bits (68), Expect = 0.090
Identities = 10/51 (19%), Positives = 16/51 (31%), Gaps = 8/51 (15%)
Query: 23 TMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAA 73
T++ G G +ED L ++ R +AA A
Sbjct: 97 TVEHFAALGVAGVNLEDATGLTPTE--------LYDLDSQLRRIEAARAAI 139
>2qiw_A PEP phosphonomutase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; HET: P6G; 1.80A {Corynebacterium glutamicum atcc
13032}
Length = 255
Score = 29.2 bits (66), Expect = 0.15
Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 8/51 (15%)
Query: 23 TMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAA 73
+ + +AGA+G +ED V G+ + AA +AA
Sbjct: 98 LIAQILEAGAVGINVEDVVHSEGKRV----REAQEHADYI----AAARQAA 140
>4a17_K L29, RPL27A, 60S ribosomal protein L27A; eukaryotic ribosome,
ribosome, eukaryotic initiation factor 60S, translation,
large ribosomal subunit; 3.52A {Tetrahymena thermophila}
PDB: 4a1a_K 4a1c_K 4a1e_K
Length = 149
Score = 27.4 bits (60), Expect = 0.53
Identities = 10/71 (14%), Positives = 22/71 (30%), Gaps = 4/71 (5%)
Query: 11 INAGKIDSH----ELITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRA 66
+N K+ S K + + G + P+ ++ + A
Sbjct: 75 VNIDKLWSLVSDATRQKYAEDKKKVPVIDVTKAGFFKVLGKGRLPNQPVVVKAKYFSKTA 134
Query: 67 KAAVEAAGGSV 77
+ + A GG+
Sbjct: 135 ERRIVAVGGAC 145
>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 = 27.3 bits (60), Expect = 0.79
Identities = 11/62 (17%), Positives = 17/62 (27%), Gaps = 24/62 (38%)
Query: 30 AGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAA-GGSVRRVHYNKLGLR 88
A + IE V + V R A + R +Y G+
Sbjct: 1774 ADVM--SIESLVEV------------------VFYRGMTMQVAVPRDELGRSNY---GMI 1810
Query: 89 AL 90
A+
Sbjct: 1811 AI 1812
>3p0w_A Mandelate racemase/muconate lactonizing protein; structural
genomics, PSI-2, protein structure initiative; HET: GKR;
1.71A {Ralstonia pickettii} PDB: 3nxl_A
Length = 470
Score = 24.9 bits (54), Expect = 5.1
Identities = 15/72 (20%), Positives = 24/72 (33%), Gaps = 2/72 (2%)
Query: 7 IAYLINAGKIDSHELITMKTLKDAGAIGKQIEDGVRLMGRGAEKIKWPIHLEVSRVTVRA 66
+ YL A D + + AI + E G K+K + + A
Sbjct: 178 LPYLEGANGADDWLRLRHEAAMTPAAIARLAEAATERYGFADFKLK--GGVMPGAEEMEA 235
Query: 67 KAAVEAAGGSVR 78
AA++A R
Sbjct: 236 IAAIKARFPHAR 247
>3pj0_A LMO0305 protein; structural genomics, joint center for structural
genomics, J protein structure initiative, PSI-biology,
lyase; HET: LLP MSE; 1.80A {Listeria monocytogenes}
Length = 359
Score = 24.2 bits (53), Expect = 9.3
Identities = 11/43 (25%), Positives = 15/43 (34%)
Query: 38 EDGVRLMGRGAEKIKWPIHLEVSRVTVRAKAAVEAAGGSVRRV 80
E GV + G EK EVS A+ + R +
Sbjct: 313 ETGVGISGYLQEKSADVCAFEVSVGDAFAEIPAKNLELVFRCL 355
>2ra5_A Putative transcriptional regulator; beta structure, UTRA domain,
structural genomics, PSI-2, protein structure
initiative; HET: SRT; 2.40A {Streptomyces coelicolor
A3} SCOP: d.190.1.2
Length = 247
Score = 24.2 bits (53), Expect = 9.4
Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 4/28 (14%)
Query: 56 HLEVSRVTVRAKAAVE--AAGGSVRRVH 81
L +SR TVR A++ G + R
Sbjct: 49 RLGLSRPTVR--QAIQSLVDKGLLVRRR 74
>2zkr_l 60S ribosomal protein L27A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 148
Score = 23.9 bits (51), Expect = 9.8
Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 7/73 (9%)
Query: 11 INAGKIDSH-ELITMKTLKDAGAIGKQIEDGV-----RLMGRGAEKIKWPIHLEVSRVTV 64
+N K + T I D V +++G+G + K P+ ++ +
Sbjct: 73 VNLDKPWTLVSEQTRVNAAKNKTGVAPIIDVVRSGYYKVLGKG-KLPKQPVIVKAKFFSR 131
Query: 65 RAKAAVEAAGGSV 77
RA+ +++ GG+
Sbjct: 132 RAEEKIKSVGGAC 144
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
0.318 0.137 0.389
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,491,862
Number of extensions: 84437
Number of successful extensions: 256
Number of sequences better than 10.0: 1
Number of HSP's gapped: 252
Number of HSP's successfully gapped: 51
Length of query: 94
Length of database: 6,701,793
Length adjustment: 61
Effective length of query: 33
Effective length of database: 4,998,612
Effective search space: 164954196
Effective search space used: 164954196
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: 51 (23.4 bits)