RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6417
(194 letters)
>3i1m_R 30S ribosomal protein S18; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_R* 1vs5_R 3i1o_R 3i1q_R 3i1s_R
3i1z_R 3i21_R 3izv_V* 3izw_V* 3kc4_R 3or9_R 3ora_R
3sfs_R* 3uoq_R* 2qal_R* 1p6g_R 1p87_R 2aw7_R 2avy_R
2i2u_R ...
Length = 75
Score = 36.4 bits (85), Expect = 4e-04
Identities = 6/31 (19%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 155 FQKEKVVCILCKMKIKP-DYKNIKLLSQFVS 184
+ + + C ++ DYK+I L +++
Sbjct: 4 YFRRRKFCRFTAEGVQEIDYKDIATLKNYIT 34
>2vqe_R 30S ribosomal protein S18; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: a.4.8.1 PDB: 1fka_R
1fjg_R 1gix_U* 1hnw_R* 1hnx_R* 1hnz_R* 1hr0_R 1ibk_R*
1ibl_R* 1ibm_R 1j5e_R 1jgo_U* 1jgp_U* 1jgq_U* 1ml5_U*
1n32_R* 1n33_R* 1n34_R 1n36_R 1xmo_R* ...
Length = 88
Score = 35.8 bits (83), Expect = 0.001
Identities = 8/42 (19%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 144 SNKPAEDLKNPFQKEKVVCILCKMKIKP-DYKNIKLLSQFVS 184
+ KP ++ + ++ + DY+N+++L +F+S
Sbjct: 5 NAKPKKEAQRRPSRKAK-VKATLGEFDLRDYRNVEVLKRFLS 45
>3bbn_R Ribosomal protein S18; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 103
Score = 33.1 bits (76), Expect = 0.011
Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 142 EASNKPAEDLKNPFQKEKVVCILCKMKIKPDYKNIKLLSQFVS 184
+ S +P K F++ ++ I +I DY+N+ L+S+F+S
Sbjct: 2 DKSKRPFIKSKRSFRR-RLPPIQSGDRI--DYRNMSLISRFIS 41
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 33.3 bits (75), Expect = 0.047
Identities = 21/157 (13%), Positives = 49/157 (31%), Gaps = 41/157 (26%)
Query: 42 LEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEV--------NMARVYN--W 91
+Y D ++ +A N + D + + E+ ++ W
Sbjct: 14 HQYQYKD---ILSVFEDAFVDNFD-CKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFW 69
Query: 92 DV--KRRNQLKMGLEKSNRLRQMTRPVY---LSSTRFESKSTNN-----IYEIDFTLGDP 141
+ K+ ++ +E ++ R Y +S + E + + I + D D
Sbjct: 70 TLLSKQEEMVQKFVE------EVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN 123
Query: 142 EASNK-------PAEDLKNPFQK---EKVVCILCKMK 168
+ K P L+ + K V ++ +
Sbjct: 124 QVFAKYNVSRLQPYLKLRQALLELRPAKNV-LIDGVL 159
Score = 31.4 bits (70), Expect = 0.19
Identities = 28/161 (17%), Positives = 51/161 (31%), Gaps = 53/161 (32%)
Query: 52 LVQKNIEAAKKNL-SYIEHDLDFLRDQFTT----TEVNMA-------RVYN-------WD 92
L+ K E +K + + + FL T + R+YN ++
Sbjct: 71 LLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN 130
Query: 93 VKRR---NQLKMGLEKSNRLRQMTR-PVY--------------LSSTRFESKSTNNIYEI 134
V R +L+ L + LR + S + + K I+ +
Sbjct: 131 VSRLQPYLKLRQALLE---LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWL 187
Query: 135 DFTLGDPEASNKPAEDLKNPFQKEKVVCILCKMKIKPDYKN 175
L + N P L+ QK L +I P++ +
Sbjct: 188 --NLKN---CNSPETVLE-MLQK------LL-YQIDPNWTS 215
>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 = 31.2 bits (70), Expect = 0.24
Identities = 20/148 (13%), Positives = 44/148 (29%), Gaps = 50/148 (33%)
Query: 31 KVCLWLGANVMLEYNLTDATA-LVQKNIEAAKKNLSYIEHDLDFLRDQFTTTEVNMARVY 89
V ++G Y T +++ ++E + S M +
Sbjct: 301 TVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSP------------------MLSIS 342
Query: 90 NWDVKRRNQLKMGLEKSNRLRQMTRPVYLS---STRFESKSTNNIYEIDFTL-GDPEA-- 143
N + Q++ + K+N + V +S + + + G P++
Sbjct: 343 NLT---QEQVQDYVNKTNSHLPAGKQVEISLVNGAK------------NLVVSGPPQSLY 387
Query: 144 -------SNKPAEDL---KNPFQKEKVV 161
K L + PF + K+
Sbjct: 388 GLNLTLRKAKAPSGLDQSRIPFSERKLK 415
Score = 28.9 bits (64), Expect = 1.4
Identities = 14/45 (31%), Positives = 16/45 (35%), Gaps = 11/45 (24%)
Query: 113 TRPVYLSSTRFESKSTNNIYEIDFTLGDPEASNKPAEDLKNPFQK 157
TRP+ LS E L P AS A L+ F K
Sbjct: 6 TRPLTLSHGSLE-----------HVLLVPTASFFIASQLQEQFNK 39
>2ct5_A Zinc finger BED domain containing protein 1; DREF homolog, putative
C-like transposable element, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: g.37.1.6
Length = 73
Score = 28.7 bits (63), Expect = 0.36
Identities = 5/26 (19%), Positives = 9/26 (34%)
Query: 145 NKPAEDLKNPFQKEKVVCILCKMKIK 170
Q +K+ C +C +I
Sbjct: 15 GFDTNAEGCILQWKKIYCRICMAQIA 40
>3r8n_R 30S ribosomal protein S18; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_R 3fih_R* 3iy8_R 2wwl_R
3oar_R 3oaq_R 3ofb_R 3ofa_R 3ofp_R 3ofx_R 3ofy_R 3ofo_R
3r8o_R 4a2i_R
Length = 55
Score = 26.7 bits (60), Expect = 0.93
Identities = 5/15 (33%), Positives = 10/15 (66%)
Query: 170 KPDYKNIKLLSQFVS 184
+ DYK+I L +++
Sbjct: 1 EIDYKDIATLKNYIT 15
>3mq2_A 16S rRNA methyltransferase; methyltranferase, ribosomal, antibiotic
resistance, aminoglycoside, S-adenosyl-L-methionine;
HET: SAH; 1.69A {Streptomyces SP}
Length = 218
Score = 28.1 bits (62), Expect = 1.6
Identities = 16/99 (16%), Positives = 30/99 (30%), Gaps = 9/99 (9%)
Query: 17 IEAAKKNSSIPPTDKVCLWLGANVMLEYNLTDATALVQKNIEAAKKNLSYIEHDLDFLRD 76
+ A++N S L + + + K + NL Y+ + L
Sbjct: 43 YKVARQNPSR-------LVVALDADKSRMEKISAKAAAKPAKGGLPNLLYLWATAERLPP 95
Query: 77 QFTTTEVNMARVYNWDVKRRNQLKMGLEKSNRLRQMTRP 115
E++ + W R L E + + RP
Sbjct: 96 LSGVGELH--VLMPWGSLLRGVLGSSPEMLRGMAAVCRP 132
>3pzl_A Agmatine ureohydrolase; structural genomics, PSI-2, protein
structure initiative, NE SGX research center for
structural genomics; 2.70A {Thermoplasma volcanium GSS1}
Length = 313
Score = 27.9 bits (63), Expect = 2.3
Identities = 10/56 (17%), Positives = 25/56 (44%), Gaps = 12/56 (21%)
Query: 65 SYIEHDLDFLRDQFTTTEVNMARVYNWDVKRRNQLKMGLEKS-NRLRQMTRPVYLS 119
S + + + ++ + ++DVK+ G++K + + +R VY+S
Sbjct: 183 SVSREEFEDPDFR------KVSFISSFDVKK-----NGIDKYIEEVDRKSRRVYIS 227
>2pk8_A Uncharacterized protein PF0899; structural genomics, uncharacte
protein, PSI, protein structure initiative; 1.85A
{Pyrococcus furiosus dsm 3638} SCOP: d.274.1.1
Length = 103
Score = 26.6 bits (58), Expect = 2.7
Identities = 10/39 (25%), Positives = 17/39 (43%)
Query: 132 YEIDFTLGDPEASNKPAEDLKNPFQKEKVVCILCKMKIK 170
+ D L EA N + LK ++E + +KI+
Sbjct: 34 FNPDIILFGREAYNFLSNLLKKEMEEEGPFTHVSNIKIE 72
>2v1n_A KIN17, protein KIN homolog; nuclear protein, winged helix motif;
NMR {Homo sapiens}
Length = 111
Score = 25.6 bits (56), Expect = 6.9
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 71 LDFLRDQFTTTEVNMARVYNWDVKRRNQLKMGLEKSNRLRQMTRPVYLSST 121
L+ LR +F T V+ VYN + R + M + L T+ +L
Sbjct: 28 LELLRRRFGTKRVHNNIVYNEYISHREHIHMNATQWETLTDFTK--WLGRE 76
>3rv1_A K. polysporus DCR1; RNAse III enzyme, RNA binding protein; 1.98A
{Vanderwaltozyma polyspora}
Length = 246
Score = 25.9 bits (57), Expect = 9.0
Identities = 10/66 (15%), Positives = 21/66 (31%), Gaps = 8/66 (12%)
Query: 125 SKSTNNIYEIDFTLGDPEASNKPAEDLKNPFQKEKVVCILCKMKIKPDY---KNIKLLSQ 181
+ N ++ + N+ + DL + FQ + + Y + L +
Sbjct: 48 DYTILNTPTLN--VAKTLLGNRYSLDLIDLFQSHDFKDSNTDVDMFIKYPVVYDENLENL 105
Query: 182 FVSAFT 187
AF
Sbjct: 106 ---AFM 108
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 0.131 0.377
Gapped
Lambda K H
0.267 0.0638 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,795,954
Number of extensions: 152999
Number of successful extensions: 340
Number of sequences better than 10.0: 1
Number of HSP's gapped: 337
Number of HSP's successfully gapped: 19
Length of query: 194
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 106
Effective length of database: 4,244,745
Effective search space: 449942970
Effective search space used: 449942970
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: 55 (25.2 bits)