RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4335
(152 letters)
>3u5c_C Guanine nucleotide-binding protein subunit beta-L protein (ASC1,
RACK1); translation, ribosome, ribosomal, ribosomal R
ribosomal protein, eukaryotic ribosome, RNA-protein C;
3.00A {Saccharomyces cerevisiae} PDB: 3izb_E 3o30_B
3o2z_B 3u5g_C 3jyv_E* 1s1h_E
Length = 254
Score = 192 bits (489), Expect = 8e-63
Identities = 72/113 (63%), Positives = 93/113 (82%), Gaps = 1/113 (0%)
Query: 8 RDGKIQSLEQIYLFSLPIKEFEIIDFFIGSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAI 67
+ GKI ++E+I+L SLP+KEF+IID + L+DEV+ I PVQKQTRAGQRTRFKA V +
Sbjct: 46 KAGKITTIEEIFLHSLPVKEFQIIDTLLPG-LQDEVMNIKPVQKQTRAGQRTRFKAVVVV 104
Query: 68 GDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHTVPCK 120
GDSNGH+GLG+K +KEVA AIR II+AKLSV+P+RRGYWG +G+PH++ K
Sbjct: 105 GDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATK 157
>3iz6_E 40S ribosomal protein S2 (S5P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
2zkq_e 1s1h_E
Length = 274
Score = 186 bits (473), Expect = 4e-60
Identities = 85/113 (75%), Positives = 101/113 (89%), Gaps = 1/113 (0%)
Query: 8 RDGKIQSLEQIYLFSLPIKEFEIIDFFIGSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAI 67
++G+ +E+IYL SLP+KE +I++ + LKDEV+KI PVQKQTRAGQRTRFKAFV +
Sbjct: 55 KEGRFSKIEEIYLHSLPVKEHQIVETLVPG-LKDEVMKITPVQKQTRAGQRTRFKAFVVV 113
Query: 68 GDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHTVPCK 120
GD+NGH+GLGVKC+KEVATAIRGAIILAKLSVVPVRRGYWGNKIG+PHTVPCK
Sbjct: 114 GDNNGHVGLGVKCAKEVATAIRGAIILAKLSVVPVRRGYWGNKIGQPHTVPCK 166
>2xzm_E Ribosomal protein S5 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_E
Length = 296
Score = 180 bits (458), Expect = 1e-57
Identities = 74/121 (61%), Positives = 90/121 (74%), Gaps = 8/121 (6%)
Query: 8 RDGKIQSLEQIYLFSLPIKEFEIIDFFIG--------SSLKDEVLKIMPVQKQTRAGQRT 59
+ GKI SL++I+ +S+PIKE EIID F L +EVL+I PVQKQT+AGQRT
Sbjct: 38 KYGKISSLDEIFKYSIPIKEPEIIDHFYPKNKDVQAEHKLMEEVLQITPVQKQTQAGQRT 97
Query: 60 RFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHTVPC 119
RFK FV +GDSNGHIGLG K +KEV AI+GAI AKL++VPVR+GYWGNKI HT+P
Sbjct: 98 RFKGFVVVGDSNGHIGLGWKVAKEVQGAIKGAITHAKLNMVPVRKGYWGNKIANAHTIPQ 157
Query: 120 K 120
K
Sbjct: 158 K 158
>1pkp_A Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} SCOP:
d.14.1.1 d.50.1.2 PDB: 1eg0_B 1dv4_E* 1qd7_D
Length = 150
Score = 53.7 bits (130), Expect = 4e-10
Identities = 29/72 (40%), Positives = 40/72 (55%), Gaps = 2/72 (2%)
Query: 36 GSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILA 95
L++ V+ + V K + G+R RF A V +GD NGH+G G ++EV AIR AI A
Sbjct: 8 KLELEERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIEDA 67
Query: 96 K--LSVVPVRRG 105
K L VP+
Sbjct: 68 KKNLIEVPIVGT 79
>3i1m_E 30S ribosomal protein S5; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1vs7_E* 1vs5_E 3i1o_E 3i1q_E 3i1s_E
3i1z_E 3i21_E 3izv_I* 3izw_I* 3kc4_E 3or9_E 3ora_E
3sfs_E* 3uoq_E*
Length = 167
Score = 54.1 bits (131), Expect = 4e-10
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 36 GSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILA 95
L+++++ + V K + G+ F A +GD NG +G G ++EV AI+ A+ A
Sbjct: 8 AGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKA 67
Query: 96 K--LSVVPVRRG 105
+ + V + G
Sbjct: 68 RRNMINVALNNG 79
>3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 308
Score = 55.6 bits (134), Expect = 4e-10
Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 2/72 (2%)
Query: 36 GSSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILA 95
++ V+++ V K + G+ RF+A V +GD G +G+GV +KEV +A++ A + A
Sbjct: 149 RDGFEENVVQVRRVTKVVKGGKHMRFRAIVVVGDKKGQVGVGVGKAKEVVSAVQKAAVDA 208
Query: 96 K--LSVVPVRRG 105
+ + VP+ +
Sbjct: 209 RRNIITVPMTKY 220
>3r8n_E 30S ribosomal protein S5; protein biosynthesis, RNA, tRNA, transfer
RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia
coli} PDB: 2ykr_E 3fih_E* 3iy8_E 2wwl_E 3oar_E 3oaq_E
3ofb_E 3ofa_E 3ofp_E 3ofx_E 3ofy_E 3ofo_E 3r8o_E 4a2i_E
2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E ...
Length = 150
Score = 53.7 bits (130), Expect = 5e-10
Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 39 LKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAK-- 96
L+++++ + V K + G+ F A +GD NG +G G ++EV AI+ A+ A+
Sbjct: 2 LQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRN 61
Query: 97 LSVVPVRRG 105
+ V + G
Sbjct: 62 MINVALNNG 70
>2vqe_E 30S ribosomal protein S5; tRNA-binding, rRNA-binding,
metal-binding, zinc-finger, translation; HET: TM2 PAR;
2.5A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1fka_E
1gix_H* 1hnw_E* 1hnx_E* 1hnz_E* 1hr0_E 1ibk_E* 1ibl_E*
1ibm_E 1jgo_H* 1jgp_H* 1jgq_H* 1ml5_H* 1xmo_E* 1xmq_E*
1xnq_E* 1xnr_E* 1yl4_H 2b64_E* 2b9m_E* ...
Length = 162
Score = 53.7 bits (130), Expect = 6e-10
Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 37 SSLKDEVLKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAK 96
+ +++++ I + G+R RF A V +GD G +GLG + EV A++ A A+
Sbjct: 4 TDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYAR 63
Query: 97 --LSVVPVRRG 105
+ VP++ G
Sbjct: 64 RNMVEVPLQNG 74
>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 = 39.3 bits (91), Expect = 3e-04
Identities = 26/137 (18%), Positives = 47/137 (34%), Gaps = 36/137 (26%)
Query: 14 SLEQIYLFSLPIKEFEIIDFFIGSSLKDEVLKIMPVQKQTRAGQR---------TRFKAF 64
SLE ++ +P FFI S L+++ KI+P + A +F +
Sbjct: 15 SLE--HVLLVPTA-----SFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGY 67
Query: 65 VAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVRRGY-WGNKIGKPHTVPCKRLT 123
V+ +G +V L + Y GN I H + K L
Sbjct: 68 VSSLVEPSKVGQ----FDQV----------LNLCLTEFENCYLEGNDI---HALAAKLLQ 110
Query: 124 HGDQQIPGGRKSKVLSS 140
D + + +++ +
Sbjct: 111 ENDTTLV--KTKELIKN 125
>1ozh_A ALS, acetolactate synthase, catabolic; acetohydroxyacid synthase,
thiamin diphosphate, lyase; HET: PGE HE3; 2.00A
{Klebsiella pneumoniae} SCOP: c.31.1.3 c.36.1.5 c.36.1.9
PDB: 1ozg_A* 1ozf_A*
Length = 566
Score = 29.8 bits (68), Expect = 0.36
Identities = 17/97 (17%), Positives = 32/97 (32%), Gaps = 15/97 (15%)
Query: 12 IQSLEQIYLFSLPIKEFEIIDFFIGSSLKDEVLKIMPVQKQTRAGQR---TRFKA--FVA 66
LE + +D M ++ + QR F F A
Sbjct: 454 SMELETAVRLKANVLHLIWVDNGYN----------MVAIQEEKKYQRLSGVEFGPMDFKA 503
Query: 67 IGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVR 103
+S G G V+ ++ + +R A+ + +VV +
Sbjct: 504 YAESFGAKGFAVESAEALEPTLRAAMDVDGPAVVAIP 540
>2pan_A Glyoxylate carboligase; thiamin-diphosphate (THDP),
thimain-dependent enzymes, FAD, lyase; HET: FAD TDP 1PE;
2.70A {Escherichia coli}
Length = 616
Score = 29.5 bits (67), Expect = 0.40
Identities = 10/39 (25%), Positives = 16/39 (41%)
Query: 64 FVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPV 102
V + + G + V +++A A A L VPV
Sbjct: 534 HVKVAEGLGCKAIRVFKPEDIAPAFEQAKALMAQYRVPV 572
>2fki_A Protein YJBR; NESG, GFT-alpha-beta, structural genomics, PSI,
protein structure initiative, northeast structural
genomics consortium; NMR {Escherichia coli} SCOP:
d.198.3.1
Length = 126
Score = 27.9 bits (62), Expect = 0.82
Identities = 6/28 (21%), Positives = 12/28 (42%)
Query: 62 KAFVAIGDSNGHIGLGVKCSKEVATAIR 89
F + + + +K S E+A +R
Sbjct: 34 VLFAMVKEVENRPAVSLKTSPELAELLR 61
>2a1v_A Conserved hypothetical protein; structural genomics, PSI, protein
structure initiative; 2.15A {Deinococcus radiodurans}
SCOP: d.198.3.1
Length = 144
Score = 27.6 bits (61), Expect = 1.1
Identities = 6/38 (15%), Positives = 15/38 (39%)
Query: 54 RAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGA 91
+ G ++ + + + + L +K E +R A
Sbjct: 37 KVGYLSKSRMYALTDITQDPLRLSLKVDPERGEELRQA 74
>2iht_A Carboxyethylarginine synthase; thiamin diphosphate complex,
transferase; HET: MSE TPP; 2.00A {Streptomyces
clavuligerus} SCOP: c.31.1.3 c.36.1.5 c.36.1.9 PDB:
1upb_A* 1upc_A* 1upa_A* 2ihu_A* 2ihv_A*
Length = 573
Score = 27.9 bits (63), Expect = 1.4
Identities = 10/40 (25%), Positives = 19/40 (47%)
Query: 64 FVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVR 103
FVA+ ++NG +E+ A+R L + ++ V
Sbjct: 519 FVALAEANGVDATRATNREELLAALRKGAELGRPFLIEVP 558
>1yrz_A Xylan beta-1,4-xylosidase; structural genomics, nysgxrc target
T1997, PSI, structure initiative; 2.00A {Bacillus
halodurans} SCOP: b.29.1.23 b.67.2.1
Length = 528
Score = 26.8 bits (59), Expect = 3.2
Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 7/46 (15%)
Query: 44 LKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIR 89
L+ P Q AG V D+ H+ L V +E ++
Sbjct: 389 LEYQPESFQHMAG-------LVIYYDTEDHVYLHVTWHEEKGKCLQ 427
>1yif_A Beta-1,4-xylosidase; glycosidase, xylan, structural genomics, PSI,
protein structure initiative; 1.80A {Bacillus subtilis}
SCOP: b.29.1.23 b.67.2.1
Length = 533
Score = 26.8 bits (59), Expect = 3.4
Identities = 9/75 (12%), Positives = 20/75 (26%), Gaps = 16/75 (21%)
Query: 44 LKIMPVQKQTRAGQRTRFKAFVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVR 103
++ P Q AG V ++ L V +E+ + +
Sbjct: 395 VEFYPENFQQAAG-------LVNYYNTENWTALQVTHDEELGRILE---------LTICD 438
Query: 104 RGYWGNKIGKPHTVP 118
+ + +P
Sbjct: 439 NFSFSQPLNNKIVIP 453
>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 = 26.7 bits (58), Expect = 3.7
Identities = 12/86 (13%), Positives = 23/86 (26%), Gaps = 20/86 (23%)
Query: 76 LGVKCSKEVATAIRG-----AIILAKLSVVPVRRGYWGNKIGKPHTVPCKRLTHG----- 125
L + + +II + W + V C +LT
Sbjct: 311 LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKH-------VNCDKLTTIIESSL 363
Query: 126 DQQIPGGRKS--KVLSS-PENLKVTS 148
+ P + LS P + + +
Sbjct: 364 NVLEPAEYRKMFDRLSVFPPSAHIPT 389
>1v5e_A Pyruvate oxidase; oxidoreductase, flavoprotein; HET: FAD; 1.60A
{Aerococcus viridans} SCOP: c.31.1.3 c.36.1.5 c.36.1.9
PDB: 2dji_A* 1v5f_A* 1v5g_A*
Length = 590
Score = 26.8 bits (60), Expect = 3.7
Identities = 5/29 (17%), Positives = 13/29 (44%)
Query: 64 FVAIGDSNGHIGLGVKCSKEVATAIRGAI 92
+ I ++ G G V +++ + A+
Sbjct: 494 YAKIAEAQGAKGFTVSRIEDMDRVMAEAV 522
>3eya_A Pyruvate dehydrogenase [cytochrome]; pyruvate oxidase,
membrane-associated flavoprotein dehydrogenase,
interactions with lipids cell membrane; HET: TDP FAD;
2.50A {Escherichia coli} PDB: 3ey9_A*
Length = 549
Score = 25.9 bits (58), Expect = 5.6
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 64 FVAIGDSNGHIGLGVKCSKEVATAIRGAI 92
F I ++ G G+ V+ + EV A++ A
Sbjct: 487 FARIAEACGITGIRVEKASEVDEALQRAF 515
>2pgn_A Cyclohexane-1,2-dione hydrolase (CDH); three alpha/beta domains;
HET: P6G FAD TPP; 1.20A {Azoarcus SP} PDB: 2pgo_A*
Length = 589
Score = 26.0 bits (58), Expect = 6.0
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 64 FVAIGDSNGHIGLGVKCSKEVATAIRGAI 92
+V I + G G V+ + ++A A++ AI
Sbjct: 505 WVGIAKAFGAYGESVRETGDIAGALQRAI 533
>1ybh_A Acetolactate synthase, chloroplast; acetohydroxyacid synthase,
herbicide, sulfonylurea, thiamin diphosphate, FAD,
inhibitor; HET: CIE NHE FAD P22; 2.50A {Arabidopsis
thaliana} SCOP: c.31.1.3 c.36.1.5 c.36.1.9 PDB: 1yhy_A*
1yhz_A* 1yi0_A* 1yi1_A* 1z8n_A* 3ea4_A* 3e9y_A*
Length = 590
Score = 25.9 bits (58), Expect = 6.7
Identities = 4/29 (13%), Positives = 10/29 (34%)
Query: 64 FVAIGDSNGHIGLGVKCSKEVATAIRGAI 92
+ + G V ++ AI+ +
Sbjct: 516 MLLFAAACGIPAARVTKKADLREAIQTML 544
>4feg_A Pyruvate oxidase; carbanion, structure activity relationship,
oxidation-reduct umpolung, thiamine diphosphate,
reaction intermediate; HET: TDM FAD GOL; 1.09A
{Lactobacillus plantarum} PDB: 4fee_A* 1y9d_A* 2ez9_A*
2ez4_A* 2ez8_A* 2ezt_A* 2ezu_A* 1pow_A* 1pox_A*
Length = 603
Score = 26.0 bits (58), Expect = 6.9
Identities = 6/32 (18%), Positives = 10/32 (31%)
Query: 64 FVAIGDSNGHIGLGVKCSKEVATAIRGAIILA 95
F I D V +++ A +A
Sbjct: 502 FSKIADGVHMQAFRVNKIEQLPDVFEQAKAIA 533
>2q28_A Oxalyl-COA decarboxylase; lyase, oxalate degradation, thiami
diphosphate, lyase; HET: TPP ADP MES; 1.74A {Escherichia
coli} PDB: 2q27_A* 2q29_A*
Length = 564
Score = 25.6 bits (57), Expect = 8.1
Identities = 8/40 (20%), Positives = 18/40 (45%)
Query: 64 FVAIGDSNGHIGLGVKCSKEVATAIRGAIILAKLSVVPVR 103
+ + D+ +G V + E+ A+ I K +++ V
Sbjct: 502 YDKLMDAFRGVGYNVTTTDELRHALTTGIQSRKPTIINVV 541
>1q6z_A BFD, BFDC, benzoylformate decarboxylase; lyase, carbon-carbon,
mandelate catabolism, T thiazolone diphosphate,
inhibitor, high resolution; HET: TZD; 1.00A {Pseudomonas
putida} SCOP: c.31.1.3 c.36.1.5 c.36.1.9 PDB: 1po7_A*
1pi3_A* 3fsj_X* 1mcz_A* 1bfd_A* 2fwn_A* 3fzn_A* 2fn3_A*
2v3w_A* 1yno_A* 3f6b_X* 3f6e_X*
Length = 528
Score = 25.6 bits (57), Expect = 8.4
Identities = 5/29 (17%), Positives = 13/29 (44%)
Query: 64 FVAIGDSNGHIGLGVKCSKEVATAIRGAI 92
F A+ G L +++ +++ A+
Sbjct: 483 FRALAKGYGVQALKADNLEQLKGSLQEAL 511
>1dlj_A UDP-glucose dehydrogenase; rossmann fold, ternary complex,
crystallographic dimer, oxidoreductase; HET: NAI UGA;
1.80A {Streptococcus pyogenes} SCOP: a.100.1.4 c.2.1.6
c.26.3.1 PDB: 1dli_A*
Length = 402
Score = 25.6 bits (57), Expect = 8.6
Identities = 12/64 (18%), Positives = 27/64 (42%), Gaps = 21/64 (32%)
Query: 82 KEVATAIRGAIILAKLSVVPVRRGYWGNKIGKPHTVPCKRLTHGDQQIPGGRKSKVLSSP 141
KEV + A ++ K S +P+ G+ ++ ++ + +++ SP
Sbjct: 102 KEVLSVNSHATLIIK-STIPI--GF-ITEM-------RQKF----------QTDRIIFSP 140
Query: 142 ENLK 145
E L+
Sbjct: 141 EFLR 144
>1t9b_A Acetolactate synthase, mitochondrial; acetohydroxyacid synthase,
herbicide, sulfonylurea, thiamin diphosphate, FAD,
inhibitor; HET: 1CS P25 FAD NSP P22 YF3; 2.20A
{Saccharomyces cerevisiae} SCOP: c.31.1.3 c.36.1.5
c.36.1.9 PDB: 1n0h_A* 1t9a_A* 1t9c_A* 1t9d_A* 1jsc_A*
Length = 677
Score = 25.7 bits (57), Expect = 9.0
Identities = 7/29 (24%), Positives = 16/29 (55%)
Query: 64 FVAIGDSNGHIGLGVKCSKEVATAIRGAI 92
F+ + ++ G GL VK +E+ ++ +
Sbjct: 595 FIKLAEAMGLKGLRVKKQEELDAKLKEFV 623
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 0.138 0.406
Gapped
Lambda K H
0.267 0.0799 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,276,437
Number of extensions: 128980
Number of successful extensions: 243
Number of sequences better than 10.0: 1
Number of HSP's gapped: 240
Number of HSP's successfully gapped: 30
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 (24.1 bits)