RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15221
(70 letters)
>3bbn_U Ribosomal protein S21; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 190
Score = 75.3 bits (184), Expect = 4e-19
Identities = 21/68 (30%), Positives = 36/68 (52%)
Query: 1 MTIIRVKENEPFEVAIRRFKRTIEKTGLLTDLRAREFYEKPTTVRKRKLAAAIKRHYKRI 60
+ V +NEP E + RF+R + + G++ + + R F+E VRKRK A KR+ +R
Sbjct: 96 NVQVVVDDNEPEERLLNRFRREVMRAGVIQECKRRRFFENTQDVRKRKTREAAKRNRRRR 155
Query: 61 RSQQLPKK 68
+ +
Sbjct: 156 PQARFTPQ 163
>3i1m_U 30S ribosomal protein S21; ribosome structure, protein-RNA
complex, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA-binding, antibiotic resistance; 3.19A
{Escherichia coli k-12} PDB: 1vs7_U* 2avy_U 2aw7_U
2vho_U 2vhp_U 3df1_U* 3df3_U* 3e1a_Q 3e1c_Q 1vs5_U
3i1o_U 3i1q_U 3i1s_U 3i1z_U 3i21_U 3izv_Y* 3izw_Y*
3kc4_U 3or9_U 3ora_U ...
Length = 71
Score = 70.2 bits (172), Expect = 2e-18
Identities = 38/68 (55%), Positives = 53/68 (77%)
Query: 1 MTIIRVKENEPFEVAIRRFKRTIEKTGLLTDLRAREFYEKPTTVRKRKLAAAIKRHYKRI 60
M +I+V+ENEPF+VA+RRFKR+ EK G+L ++R REFYEKPTT RKR A+A+KRH K++
Sbjct: 1 MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKL 60
Query: 61 RSQQLPKK 68
+ +
Sbjct: 61 ARENARRT 68
>3r8n_U 30S ribosomal protein S21; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_U 3fih_U* 2wwl_U 3oar_U
3oaq_U 3ofb_U 3ofa_U 3ofp_U 3ofx_U 3ofy_U 3ofo_U 3r8o_U
4a2i_U
Length = 51
Score = 63.2 bits (154), Expect = 8e-16
Identities = 34/51 (66%), Positives = 44/51 (86%)
Query: 4 IRVKENEPFEVAIRRFKRTIEKTGLLTDLRAREFYEKPTTVRKRKLAAAIK 54
I+V+ENEPF+VA+RRFKR+ EK G+L ++R REFYEKPTT RKR A+A+K
Sbjct: 1 IKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVK 51
>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding
loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori}
SCOP: c.37.1.20
Length = 376
Score = 27.2 bits (61), Expect = 0.40
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 46 KRKLAAAIKRHYKRIRSQQLPKK 68
K+ + A+ HYKR+ ++ KK
Sbjct: 30 KKVFSVAVYNHYKRLSFKEKLKK 52
>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+
molecular machine, hexamer, asymmetric,, ATP-BIN
chaperone, metal-binding; HET: ADP; 3.25A {Escherichia
coli} PDB: 3hte_A
Length = 363
Score = 27.2 bits (61), Expect = 0.40
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 46 KRKLAAAIKRHYKRIRSQQ 64
K+ LA A+ HYKR+R+
Sbjct: 24 KKVLAVAVYNHYKRLRNGD 42
>4dn7_A ABC transporter, ATP-binding protein; structural genomics,
protein structure initiative, NEW YORK structural
genomix research consortium; HET: 1PE; 1.60A
{Methanosarcina maze}
Length = 429
Score = 26.1 bits (58), Expect = 0.79
Identities = 7/62 (11%), Positives = 18/62 (29%), Gaps = 4/62 (6%)
Query: 3 IIRVKENEPFEVAIRRFKRTIEKTGLLTDLRAREFYEKPTTVRKRK----LAAAIKRHYK 58
+ + E + R +K D ++ E + + L K+
Sbjct: 19 YFQSMQTEQVSLKKRAESAAEKKAAFGEDFELEKYEEGSKVSKPIEDLQSLDEESKKTLL 78
Query: 59 RI 60
++
Sbjct: 79 QV 80
>1gtm_A Glutamate dehydrogenase; oxidoreductase, NAD, NADP; 2.20A
{Pyrococcus furiosus} SCOP: c.2.1.7 c.58.1.1 PDB:
1bvu_A 1euz_A
Length = 419
Score = 25.5 bits (57), Expect = 1.2
Identities = 5/28 (17%), Positives = 14/28 (50%)
Query: 8 ENEPFEVAIRRFKRTIEKTGLLTDLRAR 35
E +P+E+ I++ +R + + +
Sbjct: 2 EADPYEIVIKQLERAAQYMEISEEALEF 29
>1v9l_A Glutamate dehydrogenase; protein-NAD complex, oxidoreductase;
HET: NAD; 2.80A {Pyrobaculum islandicum} SCOP: c.2.1.7
c.58.1.1
Length = 421
Score = 25.5 bits (57), Expect = 1.3
Identities = 5/30 (16%), Positives = 10/30 (33%)
Query: 6 VKENEPFEVAIRRFKRTIEKTGLLTDLRAR 35
++ E + K+ +E G D
Sbjct: 1 MERTGFLEYVLNYVKKGVELGGFPEDFYKI 30
>3aog_A Glutamate dehydrogenase; NAD(H), oxidoreducta; HET: GLU; 2.10A
{Thermus thermophilus HB27} PDB: 3aoe_A
Length = 440
Score = 24.4 bits (54), Expect = 3.1
Identities = 7/29 (24%), Positives = 12/29 (41%)
Query: 7 KENEPFEVAIRRFKRTIEKTGLLTDLRAR 35
K+ P+E+ + R + G L L
Sbjct: 27 KDGGPWEIFTEQVDRVVPYLGRLAPLAES 55
>2tmg_A Protein (glutamate dehydrogenase); metabolic role, mutant,
oxidoreductase; 2.90A {Thermotoga maritima} SCOP:
c.2.1.7 c.58.1.1 PDB: 1b26_A 1b3b_A
Length = 415
Score = 24.4 bits (54), Expect = 3.5
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 8 ENEPFEVAIRRFKRTIEKTGLLTDLRAR 35
E +E+A+ +F R L +DL
Sbjct: 2 EKSLYEMAVEQFNRAASLMDLESDLAEV 29
>1qs0_A 2-oxoisovalerate dehydrogenase alpha-subunit; heterotetramer, THDP
cofactor, oxidoreductase; HET: TDP; 2.40A {Pseudomonas
putida} SCOP: c.36.1.11 PDB: 2bp7_A
Length = 407
Score = 24.3 bits (53), Expect = 3.8
Identities = 8/52 (15%), Positives = 17/52 (32%), Gaps = 4/52 (7%)
Query: 16 IRRFKRTIEKTGLLTDLRAREFYEKPTTVRKRKLAAAIKRHYKRIRSQQLPK 67
I R K+ + K G ++ + + + + AA K +
Sbjct: 335 IARLKQHLIKIGHWSEEEHQATTAE----FEAAVIAAQKEAEQYGTLANGHI 382
>3gwm_A Holo-[acyl-carrier-protein] synthase; HOMO-trimer, 9-stand pseudo
beta barrel protein, cytoplasm, fatty acid
biosynthesis; 1.70A {Mycobacterium smegmatis} PDB:
3h7q_A* 3ne3_B 3ne1_A 3hqj_A*
Length = 129
Score = 23.3 bits (51), Expect = 6.9
Identities = 6/27 (22%), Positives = 11/27 (40%), Gaps = 3/27 (11%)
Query: 14 VAIRRFKRTIEKTGLLTDLRAREFYEK 40
V+I F +++ G + A F
Sbjct: 10 VSIPDFAEQVDRPG---TVFAETFTPG 33
>1xpm_A 3-hydroxy-3-methylglutaryl COA synthase; HMG-COA synthase, HMGS,
coenzyme A, thiolase fold, condensing enzyme; HET: HMG
CAA; 1.60A {Staphylococcus aureus subsp} SCOP: c.95.1.2
c.95.1.2 PDB: 1xpl_A* 1xpk_A* 1tvz_A 1txt_A*
Length = 396
Score = 23.6 bits (51), Expect = 8.1
Identities = 11/70 (15%), Positives = 20/70 (28%), Gaps = 4/70 (5%)
Query: 4 IRVKENEPFEVAIRRF----KRTIEKTGLLTDLRAREFYEKPTTVRKRKLAAAIKRHYKR 59
V + IR F ++ G A + P T +K +I +
Sbjct: 194 PLVDGALSKDAYIRSFQQSWNEYAKRQGKSLADFASLCFHVPFTKMGKKALESIIDNADE 253
Query: 60 IRSQQLPKKM 69
++L
Sbjct: 254 TTQERLRSGY 263
>1umd_A E1-alpha, 2-OXO acid dehydrogenase alpha subunit; alpha(2)beta(2)
tetramer, structural genomics; HET: TDP; 1.90A {Thermus
thermophilus} SCOP: c.36.1.11 PDB: 1um9_A* 1umc_A*
1umb_A*
Length = 367
Score = 23.4 bits (51), Expect = 8.4
Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 8/49 (16%)
Query: 7 KENEPFEVAIRRFKRTIEKTGLLTDLRAREFYEKPTTVRKRKLAAAIKR 55
++ +P I RF+R +E GL + + E+ + +L +K
Sbjct: 292 RKKDP----IPRFRRFLEARGLWNEEWEEDVREE----IRAELERGLKE 332
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
0.325 0.136 0.374
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,100,647
Number of extensions: 55798
Number of successful extensions: 205
Number of sequences better than 10.0: 1
Number of HSP's gapped: 205
Number of HSP's successfully gapped: 20
Length of query: 70
Length of database: 6,701,793
Length adjustment: 40
Effective length of query: 30
Effective length of database: 5,584,953
Effective search space: 167548590
Effective search space used: 167548590
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.4 bits)