RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 031787
(153 letters)
>3iz6_M 40S ribosomal protein S18 (S13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 152
Score = 243 bits (622), Expect = 3e-84
Identities = 133/151 (88%), Positives = 145/151 (96%)
Query: 3 SLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSA 62
SL+A E+FQHILRVLNTNVDGKQKIMFALTSIKG+GRR +NIVCKKAD+DMNKRAGELSA
Sbjct: 2 SLIAGEEFQHILRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELSA 61
Query: 63 AELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHR 122
E+D LM VV NPRQFK+PDWFLNR+KDYKDG++SQVVSNA+DMKLRDDLERLKKIRNHR
Sbjct: 62 EEMDRLMAVVHNPRQFKVPDWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIRNHR 121
Query: 123 GLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 153
GLRHYWG+RVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 122 GLRHYWGVRVRGQHTKTTGRRGKTVGVSKKR 152
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_M
Length = 155
Score = 236 bits (604), Expect = 1e-81
Identities = 81/147 (55%), Positives = 106/147 (72%)
Query: 7 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 66
DF++I R+LNTN+DGK+ ALT I+GIGRR A I+CK +D N RAG L+ + +
Sbjct: 8 ESDFKYIHRILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGLLTEDQCN 67
Query: 67 NLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRH 126
+ ++A+P IP W LNR D+KDGK Q+ SN LD K+R+DLERLKKI++HRGLRH
Sbjct: 68 KITDLIADPEAHGIPTWLLNRINDFKDGKNYQMASNTLDTKMREDLERLKKIKSHRGLRH 127
Query: 127 YWGLRVRGQHTKTTGRRGKTVGVSKKR 153
+WGL+VRGQHTKT+GR G GV +K
Sbjct: 128 FWGLKVRGQHTKTSGRHGVVCGVVRKN 154
>3u5c_S 40S ribosomal protein S18-A, 40S ribosomal protein S17-A;
translation, ribosome, ribosomal, ribosomal R ribosomal
protein, eukaryotic ribosome, RNA-protein C; 3.00A
{Saccharomyces cerevisiae} PDB: 3izb_M 3o30_L 3o2z_L
3u5g_S 1s1h_M 3jyv_M* 2zkq_m
Length = 146
Score = 220 bits (562), Expect = 2e-75
Identities = 95/144 (65%), Positives = 117/144 (81%), Gaps = 2/144 (1%)
Query: 3 SLVANE--DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGEL 60
SLV E FQHILR+LNTNVDG KI++ALT+IKG+GRR +N+VCKKADVD++KRAGEL
Sbjct: 2 SLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGEL 61
Query: 61 SAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRN 120
+ EL+ ++ ++ NP +KIP WFLNRQ D DGK ++N ++ KLRDDLERLKKIR
Sbjct: 62 TQEELERIVQIMQNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRA 121
Query: 121 HRGLRHYWGLRVRGQHTKTTGRRG 144
HRG+RH+WGLRVRGQHTKTTGRR
Sbjct: 122 HRGIRHFWGLRVRGQHTKTTGRRR 145
>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP:
a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M
1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P*
1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M*
1xmq_M* ...
Length = 126
Score = 73.3 bits (181), Expect = 9e-18
Identities = 41/142 (28%), Positives = 64/142 (45%), Gaps = 26/142 (18%)
Query: 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74
R+ + +++ ALT I GIG+ A +K ++ R +L+ AE+ L V
Sbjct: 3 RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV-- 60
Query: 75 PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 134
+ +K + L ++ +++RL I +RGLRH GL VRG
Sbjct: 61 -------------ENTWK-------LEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRG 100
Query: 135 QHTKTTGR--RG--KTVGVSKK 152
Q T+T R +G KTV KK
Sbjct: 101 QRTRTNARTRKGPRKTVAGKKK 122
>3r8n_M 30S ribosomal protein S13; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_M 3oaq_M 3ofa_M 3ofx_M
3ofo_M 3r8o_M 4a2i_M 3i1m_M 1vs7_M* 3e1a_F 3e1c_F 1vs5_M
3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 3iyx_M 3iyy_M 3izv_Q*
...
Length = 114
Score = 72.1 bits (178), Expect = 2e-17
Identities = 39/129 (30%), Positives = 59/129 (45%), Gaps = 25/129 (19%)
Query: 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74
R+ N+ + + ALTSI G+G+ + + A + + + ELS ++D L VA
Sbjct: 2 RIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAK 61
Query: 75 PRQFKI-PDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVR 133
F + D L R+ ++ +K RL + +RGLRH GL VR
Sbjct: 62 ---FVVEGD--LRRE-------------ISMSIK------RLMDLGCYRGLRHRRGLPVR 97
Query: 134 GQHTKTTGR 142
GQ TKT R
Sbjct: 98 GQRTKTNAR 106
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 145
Score = 64.3 bits (157), Expect = 3e-14
Identities = 35/128 (27%), Positives = 54/128 (42%), Gaps = 34/128 (26%)
Query: 15 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 74
R+ + +++ ++L I GIGR + + + D NK +LS E+ L
Sbjct: 48 RIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFD-NKVTKDLSEEEVIIL------ 100
Query: 75 PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 134
R+ R N + ++ RLK+IR +RG+RH GL VRG
Sbjct: 101 -RK-------EKRF-------------NRVAIE------RLKEIRCYRGIRHKLGLPVRG 133
Query: 135 QHTKTTGR 142
Q TK R
Sbjct: 134 QRTKNNCR 141
>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 = 34.4 bits (78), Expect = 0.011
Identities = 26/159 (16%), Positives = 48/159 (30%), Gaps = 47/159 (29%)
Query: 1 MKSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCK------KADVD-- 52
KS+++ E+ HI+ + +F K +V K + +
Sbjct: 42 PKSILSKEEIDHIIMS--KDAVSGTLRLFWTLLSKQ-----EEMVQKFVEEVLRINYKFL 94
Query: 53 MNKRAGELSAAELDNLMVVVANPRQF----KIPDWFLNRQKDYKDGKYSQVVSNALDMKL 108
M+ E + M + R + + ++R + Y KL
Sbjct: 95 MSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYL--------------KL 140
Query: 109 RDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTV 147
R L L+ +N + + G G GKT
Sbjct: 141 RQALLELRPAKN---------VLIDGV----LG-SGKTW 165
Score = 27.5 bits (60), Expect = 2.1
Identities = 20/133 (15%), Positives = 45/133 (33%), Gaps = 26/133 (19%)
Query: 2 KSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 61
SLV + + + + + ++ K K+ + + R + + D + L
Sbjct: 414 YSLVEKQPKESTISIPSIYLELKVKLE----NEYALHRSIVDHYNIPKTFDSDD----LI 465
Query: 62 AAELDNL--------MVVVANPRQFKI-PDWFLN----RQKDYKDGKYSQVVSNALDMKL 108
LD + + +P + + FL+ QK D + L+
Sbjct: 466 PPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILN--- 522
Query: 109 RDDLERLKKIRNH 121
L++LK + +
Sbjct: 523 --TLQQLKFYKPY 533
>2i0z_A NAD(FAD)-utilizing dehydrogenases; structural genomics, PSI-2,
protein structure initiative, midwest center for
structural genomics, MCSG; HET: FAD; 1.84A {Bacillus
cereus} SCOP: c.3.1.8 e.74.1.1
Length = 447
Score = 33.7 bits (78), Expect = 0.018
Identities = 13/59 (22%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 10 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 68
FQ +L+ + + K+ I L + R + +K ++D +++AG++S ++ L
Sbjct: 308 FQRMLKQMKED--PKKGIKNVLKGY--VPERYFLFLLEKNEIDGSEQAGQVSHEKIRAL 362
>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 = 30.4 bits (68), Expect = 0.21
Identities = 14/69 (20%), Positives = 24/69 (34%), Gaps = 30/69 (43%)
Query: 13 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 72
++ ++N NV+ +Q V AG+L A LD + V+
Sbjct: 1840 LVEIVNYNVENQQ------------------YVA----------AGDLRA--LDTVTNVL 1869
Query: 73 ANPRQFKIP 81
+ KI
Sbjct: 1870 NFIKLQKID 1878
Score = 29.6 bits (66), Expect = 0.50
Identities = 17/96 (17%), Positives = 35/96 (36%), Gaps = 28/96 (29%)
Query: 1 MKSL--VANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAG 58
M S+ + E Q + N+++ +++ +L G + N+V +G
Sbjct: 338 MLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV----NGAK--NLVV----------SG 381
Query: 59 ELSAAELDNLMVVV------ANPRQFKIPDWFLNRQ 88
L L + + + Q +IP F R+
Sbjct: 382 --PPQSLYGLNLTLRKAKAPSGLDQSRIP--FSERK 413
>2hnh_A DNA polymerase III alpha subunit; DNA replication,
nucleotidyltransferase, beta, PHP, transferase; HET:
DNA; 2.30A {Escherichia coli} PDB: 2hqa_A*
Length = 910
Score = 28.6 bits (65), Expect = 0.95
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 17/56 (30%)
Query: 21 VDGKQKIMFALTSIKGIGRR-LANIV---------------CKKADV-DMNKRAGE 59
V+ +I++ + +IKG+G + I+ C + D +N+R E
Sbjct: 825 VNDDGEIVYGIGAIKGVGEGPIEAIIEARNKGGYFRELFDLCARTDTKKLNRRVLE 880
>4dcm_A Ribosomal RNA large subunit methyltransferase G; 23S rRNA
(guanine1835-N2)-methyltransferase; HET: SAM; 2.30A
{Escherichia coli}
Length = 375
Score = 27.9 bits (62), Expect = 1.5
Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 6/68 (8%)
Query: 37 IGRRLANIVCKKA--DVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDG 94
IG L + + VD + A S ++ M + +F I + +
Sbjct: 236 IGLTLLDKNPQAKVVFVDESPMAVASSRLNVETNMPEALDRCEFMINNAL----SGVEPF 291
Query: 95 KYSQVVSN 102
+++ V+ N
Sbjct: 292 RFNAVLCN 299
>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C, DNA
polymerase III; HET: DGT; 2.39A {Geobacillus
kaustophilus} PDB: 3f2c_A* 3f2d_A*
Length = 1041
Score = 27.7 bits (62), Expect = 1.9
Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 18/54 (33%)
Query: 21 VDGKQKIMFALTSIKGIGRRLA-NIV--------------CKKADVDMNKRAGE 59
+DG ++ +I G+G +A IV ++ + +K E
Sbjct: 960 IDGN-SLIPPFNAIPGLGTNVAQAIVRAREEGEFLSKEDLQQRGKL--SKTLLE 1010
>2zkr_l 60S ribosomal protein L27A; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 148
Score = 27.0 bits (59), Expect = 2.1
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 114 RLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 153
RL+K R RG G G+H K G RG G+ R
Sbjct: 4 RLRKTRKLRGHVS-HGHGRIGKHRKHPGGRGNAGGMHHHR 42
>3o58_Y 60S ribosomal protein L28; ribosomal RNA and proteins, ribosome;
4.00A {Saccharomyces cerevisiae} PDB: 3o5h_Y 3izc_O
3izs_O 3u5e_a 3u5i_a 1s1i_V 3jyw_V
Length = 149
Score = 26.6 bits (58), Expect = 2.6
Identities = 15/41 (36%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 114 RLKKIRNHRGLR-HYWGLRVRGQHTKTTGRRGKTVGVSKKR 153
R K R HRG G G+H K G RG G R
Sbjct: 4 RFTKTRKHRGHVSAGKGR--IGKHRKHPGGRGMAGGEHHHR 42
>3doa_A Fibrinogen binding protein; structural genomics, MCSG., protein
structure initiative, midwest center for structural
genomics; 2.81A {Staphylococcus aureus subsp}
Length = 288
Score = 26.9 bits (59), Expect = 3.2
Identities = 7/62 (11%), Positives = 19/62 (30%), Gaps = 2/62 (3%)
Query: 7 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 66
+ +L+ ++ N K + L +G + N + + + E +
Sbjct: 173 DITGAEVLKYIDFNAGNIAKQL--LNQFEGFSPLITNEIVSRRQFMTSSTLPEAFDEVMA 230
Query: 67 NL 68
Sbjct: 231 ET 232
>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP
complex, calcium stimulation, RECA, DMC1; HET: DNA ANP;
1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11
PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A*
3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A*
3etl_A* 4dc9_A* 2gdj_A*
Length = 322
Score = 25.3 bits (55), Expect = 8.8
Identities = 12/73 (16%), Positives = 27/73 (36%), Gaps = 1/73 (1%)
Query: 53 MNKRAGEL-SAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDD 111
+ + L A+L N +V+V N K +F ++ + ++
Sbjct: 234 LGRHMATLNKLADLFNCVVLVTNQVSAKPDAFFGMAEQAIGGHIVGHAATFRFFVRKGKG 293
Query: 112 LERLKKIRNHRGL 124
+R+ K+ + L
Sbjct: 294 DKRVAKLYDSPHL 306
>3eag_A UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-ME diaminopimelate
ligase; UDP-N-acetylmuramate:L-alanyl-G
glutamyl-MESO-diaminopimelate ligase; 2.55A {Neisseria
meningitidis MC58}
Length = 326
Score = 25.3 bits (56), Expect = 9.6
Identities = 15/55 (27%), Positives = 19/55 (34%), Gaps = 17/55 (30%)
Query: 99 VVSNALDMKLRDDLERLKKIRNHR-------------GLRHYWGLRVRGQHTKTT 140
V+ N R ++ I N L H+W L V G H KTT
Sbjct: 71 VIGNVAK---RGMDV-VEAILNLGLPYISGPQWLSENVLHHHWVLGVAGTHGKTT 121
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 0.136 0.394
Gapped
Lambda K H
0.267 0.0600 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,345,398
Number of extensions: 134084
Number of successful extensions: 469
Number of sequences better than 10.0: 1
Number of HSP's gapped: 465
Number of HSP's successfully gapped: 40
Length of query: 153
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 68
Effective length of database: 4,328,508
Effective search space: 294338544
Effective search space used: 294338544
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: 53 (24.5 bits)