RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 031813
(152 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 = 247 bits (632), Expect = 7e-86
Identities = 134/152 (88%), Positives = 146/152 (96%)
Query: 1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
MSL+A E+FQHILRVLNTNVDGKQKIMFALTSIKG+GRR +NIVCKKAD+DMNKRAGELS
Sbjct: 1 MSLIAGEEFQHILRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELS 60
Query: 61 AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
A E+D LM VV NPRQFK+PDWFLNR+KDYKDG++SQVVSNA+DMKLRDDLERLKKIRNH
Sbjct: 61 AEEMDRLMAVVHNPRQFKVPDWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIRNH 120
Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
RGLRHYWG+RVRGQHTKTTGRRGKTVGVSKKR
Sbjct: 121 RGLRHYWGVRVRGQHTKTTGRRGKTVGVSKKR 152
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_M
Length = 155
Score = 239 bits (612), Expect = 7e-83
Identities = 84/154 (54%), Positives = 109/154 (70%), Gaps = 2/154 (1%)
Query: 1 MSLVA--NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGE 58
MS V DF++I R+LNTN+DGK+ ALT I+GIGRR A I+CK +D N RAG
Sbjct: 1 MSFVIEKESDFKYIHRILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGL 60
Query: 59 LSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118
L+ + + + ++A+P IP W LNR D+KDGK Q+ SN LD K+R+DLERLKKI+
Sbjct: 61 LTEDQCNKITDLIADPEAHGIPTWLLNRINDFKDGKNYQMASNTLDTKMREDLERLKKIK 120
Query: 119 NHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
+HRGLRH+WGL+VRGQHTKT+GR G GV +K
Sbjct: 121 SHRGLRHFWGLKVRGQHTKTSGRHGVVCGVVRKN 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 = 224 bits (572), Expect = 8e-77
Identities = 96/145 (66%), Positives = 118/145 (81%), Gaps = 2/145 (1%)
Query: 1 MSLVANE--DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGE 58
MSLV E FQHILR+LNTNVDG KI++ALT+IKG+GRR +N+VCKKADVD++KRAGE
Sbjct: 1 MSLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGE 60
Query: 59 LSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118
L+ EL+ ++ ++ NP +KIP WFLNRQ D DGK ++N ++ KLRDDLERLKKIR
Sbjct: 61 LTQEELERIVQIMQNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIR 120
Query: 119 NHRGLRHYWGLRVRGQHTKTTGRRG 143
HRG+RH+WGLRVRGQHTKTTGRR
Sbjct: 121 AHRGIRHFWGLRVRGQHTKTTGRRR 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 = 73.7 bits (182), Expect = 7e-18
Identities = 41/142 (28%), Positives = 64/142 (45%), Gaps = 26/142 (18%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
R+ + +++ ALT I GIG+ A +K ++ R +L+ AE+ L V
Sbjct: 3 RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV-- 60
Query: 74 PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
+ +K + L ++ +++RL I +RGLRH GL VRG
Sbjct: 61 -------------ENTWK-------LEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRG 100
Query: 134 QHTKTTGR--RG--KTVGVSKK 151
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 = 72.5 bits (179), Expect = 1e-17
Identities = 39/129 (30%), Positives = 59/129 (45%), Gaps = 25/129 (19%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
R+ N+ + + ALTSI G+G+ + + A + + + ELS ++D L VA
Sbjct: 2 RIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAK 61
Query: 74 PRQFKI-PDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVR 132
F + D L R+ ++ +K RL + +RGLRH GL VR
Sbjct: 62 ---FVVEGD--LRRE-------------ISMSIK------RLMDLGCYRGLRHRRGLPVR 97
Query: 133 GQHTKTTGR 141
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 = 64.7 bits (158), Expect = 3e-14
Identities = 35/128 (27%), Positives = 54/128 (42%), Gaps = 34/128 (26%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
R+ + +++ ++L I GIGR + + + D NK +LS E+ L
Sbjct: 48 RIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFD-NKVTKDLSEEEVIIL------ 100
Query: 74 PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
R+ R N + ++ RLK+IR +RG+RH GL VRG
Sbjct: 101 -RK-------EKRF-------------NRVAIE------RLKEIRCYRGIRHKLGLPVRG 133
Query: 134 QHTKTTGR 141
Q TK R
Sbjct: 134 QRTKNNCR 141
>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 = 0.017
Identities = 13/59 (22%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67
FQ +L+ + + K+ I L + R + +K ++D +++AG++S ++ L
Sbjct: 308 FQRMLKQMKED--PKKGIKNVLKGY--VPERYFLFLLEKNEIDGSEQAGQVSHEKIRAL 362
>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 = 32.1 bits (72), Expect = 0.071
Identities = 34/157 (21%), Positives = 55/157 (35%), Gaps = 31/157 (19%)
Query: 2 SLVANEDFQHIL----RVL-NTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRA 56
+ V N D + + +L +D I+ + ++ G RL + K + + K
Sbjct: 28 AFVDNFDCKDVQDMPKSILSKEEID---HIIMSKDAVSGT-LRLFWTLLSKQEEMVQKFV 83
Query: 57 GELSAAELDNLMVVVAN-PRQFKIPDWFLNRQKD--YKDG----KYSQVVSNALDMKLRD 109
E+ LM + RQ + Q+D Y D KY V +KLR
Sbjct: 84 EEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY-NVSRLQPYLKLRQ 142
Query: 110 DLERLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTV 146
L L+ +N + + G G GKT
Sbjct: 143 ALLELRPAKN---------VLIDGV----LG-SGKTW 165
Score = 26.7 bits (58), Expect = 3.8
Identities = 9/45 (20%), Positives = 16/45 (35%), Gaps = 9/45 (20%)
Query: 80 PDWFLN----RQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
FL+ QK D + L+ L++LK + +
Sbjct: 494 RMVFLDFRFLEQKIRHDSTAWNASGSILN-----TLQQLKFYKPY 533
>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 = 0.13
Identities = 15/96 (15%), Positives = 35/96 (36%), Gaps = 29/96 (30%)
Query: 1 MSLVANEDFQHI---LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAG 57
M ++N + + + N+++ +++ +L G + N+V +G
Sbjct: 338 MLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV----NGAK--NLVV----------SG 381
Query: 58 ELSAAELDNLMVVV------ANPRQFKIPDWFLNRQ 87
L L + + + Q +IP F R+
Sbjct: 382 --PPQSLYGLNLTLRKAKAPSGLDQSRIP--FSERK 413
Score = 30.4 bits (68), Expect = 0.22
Identities = 14/69 (20%), Positives = 24/69 (34%), Gaps = 30/69 (43%)
Query: 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71
++ ++N NV+ +Q V AG+L A LD + V+
Sbjct: 1840 LVEIVNYNVENQQ------------------YVA----------AGDLRA--LDTVTNVL 1869
Query: 72 ANPRQFKIP 80
+ KI
Sbjct: 1870 NFIKLQKID 1878
>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 = 0.93
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 17/56 (30%)
Query: 20 VDGKQKIMFALTSIKGIGRR-LANIV---------------CKKADV-DMNKRAGE 58
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: 36 IGRRLANIVCKKA--DVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDG 93
IG L + + VD + A S ++ M + +F I + +
Sbjct: 236 IGLTLLDKNPQAKVVFVDESPMAVASSRLNVETNMPEALDRCEFMINNAL----SGVEPF 291
Query: 94 KYSQVVSN 101
+++ V+ N
Sbjct: 292 RFNAVLCN 299
>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 = 1.8
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 113 RLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
RL+K R RG G G+H K G RG G+ R
Sbjct: 4 RLRKTRKLRGHVS-HGHGRIGKHRKHPGGRGNAGGMHHHR 42
>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 = 1.8
Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 18/54 (33%)
Query: 20 VDGKQKIMFALTSIKGIGRRLA-NIV--------------CKKADVDMNKRAGE 58
+DG ++ +I G+G +A IV ++ + +K E
Sbjct: 960 IDGN-SLIPPFNAIPGLGTNVAQAIVRAREEGEFLSKEDLQQRGKL--SKTLLE 1010
>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 = 27.0 bits (59), Expect = 2.2
Identities = 15/41 (36%), Positives = 16/41 (39%), Gaps = 3/41 (7%)
Query: 113 RLKKIRNHRGLR-HYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
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: 6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65
+ +L+ ++ N K + L +G + N + + + E +
Sbjct: 173 DITGAEVLKYIDFNAGNIAKQL--LNQFEGFSPLITNEIVSRRQFMTSSTLPEAFDEVMA 230
Query: 66 NL 67
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 = 8.9
Identities = 12/73 (16%), Positives = 27/73 (36%), Gaps = 1/73 (1%)
Query: 52 MNKRAGEL-SAAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDD 110
+ + L A+L N +V+V N K +F ++ + ++
Sbjct: 234 LGRHMATLNKLADLFNCVVLVTNQVSAKPDAFFGMAEQAIGGHIVGHAATFRFFVRKGKG 293
Query: 111 LERLKKIRNHRGL 123
+R+ K+ + L
Sbjct: 294 DKRVAKLYDSPHL 306
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 0.395
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: 2,337,137
Number of extensions: 133524
Number of successful extensions: 467
Number of sequences better than 10.0: 1
Number of HSP's gapped: 464
Number of HSP's successfully gapped: 40
Length of query: 152
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 67
Effective length of database: 4,328,508
Effective search space: 290010036
Effective search space used: 290010036
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)