RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 039384
(104 letters)
>1f75_A Undecaprenyl pyrophosphate synthetase; parallel beta sheet, NEW
fold for isoprenoid synthase, peptidoglycan synthesis,
transferase; 2.20A {Micrococcus luteus} SCOP: c.101.1.1
Length = 249
Score = 68.3 bits (168), Expect = 2e-15
Identities = 24/61 (39%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 22 VQEYCEDKLDGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLW 81
VQ E G +L ++I E +++F A PDP++ IR+SGE R SNFL+W
Sbjct: 158 VQLIAERYKSGEISL-DEISETHF------NEYLFTANMPDPELLIRTSGEERLSNFLIW 210
Query: 82 Q 82
Q
Sbjct: 211 Q 211
>2d2r_A Undecaprenyl pyrophosphate synthase; prenyltransferase,
transferase; 1.88A {Helicobacter pylori} PDB: 2dtn_A
Length = 245
Score = 67.1 bits (165), Expect = 4e-15
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 8/61 (13%)
Query: 22 VQEYCEDKLDGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLW 81
+ E + E+ I + P+ D+ +R+ GE R SNFLLW
Sbjct: 153 FKSLLESPPSN--ISLLESLENEI------SNRLDTRNLPEVDLLLRTGGEMRLSNFLLW 204
Query: 82 Q 82
Q
Sbjct: 205 Q 205
>3qas_B Undecaprenyl pyrophosphate synthase; alpha-helix, isoprenoid
biosynthesis, transferase; 1.70A {Escherichia coli} PDB:
1jp3_A* 1v7u_A* 1x06_A* 1x07_A* 2e98_A* 2e99_A* 2e9a_A*
2e9c_A* 2e9d_A* 1ueh_A 1x09_A* 1x08_A*
Length = 253
Score = 67.2 bits (165), Expect = 5e-15
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 22 VQEYCEDKLDGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLW 81
V++ E G+ ++IDE+ + +H+ M D+ IR+ GE R SNFLLW
Sbjct: 155 VRQLAEKVQQGNLQP-DQIDEEML------NQHVCMHELAPVDLVIRTGGEHRISNFLLW 207
Query: 82 Q 82
Q
Sbjct: 208 Q 208
>2vg0_A Short-chain Z-isoprenyl diphosphate synthetase; peptidoglycan
synthesis, cell WALL biogenesis/degradation, secreted,
cell shape; HET: GPP; 1.7A {Mycobacterium tuberculosis}
PDB: 2vfw_A* 2vg1_A*
Length = 227
Score = 66.0 bits (162), Expect = 8e-15
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 9/77 (11%)
Query: 22 VQEYCEDKLDG---SQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNF 78
V+ +L ++ L + + + I ++++ + PDPD+ IR+SGE R S F
Sbjct: 139 VRALLSKELANGATAEELVDAVTVEGI------SENLYTSGQPDPDLVIRTSGEQRLSGF 192
Query: 79 LLWQTSNCSLYSPAALW 95
LLWQ++ ++ A W
Sbjct: 193 LLWQSAYSEMWFTEAHW 209
>2vg3_A Undecaprenyl pyrophosphate synthetase; transferase, cell WALL
biogenesis/degradation, cell cycle, P transferase; HET:
GPP; 1.8A {Mycobacterium tuberculosis} PDB: 2vg2_A*
2vg4_A
Length = 284
Score = 66.5 bits (163), Expect = 9e-15
Identities = 20/45 (44%), Positives = 27/45 (60%), Gaps = 6/45 (13%)
Query: 38 EKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQ 82
E+I E TI +H+ PD D+ +R+SGE R SNF+LWQ
Sbjct: 208 ERITESTI------ARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQ 246
>3ugs_B Undecaprenyl pyrophosphate synthase; niaid, csgid, structural
genomics, center for structural GEN infectious diseases;
HET: FFT; 2.46A {Campylobacter jejuni}
Length = 225
Score = 61.7 bits (151), Expect = 3e-13
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 8/46 (17%)
Query: 37 KEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQ 82
K +++E+ + +++ + D D+ +R R SNFLLWQ
Sbjct: 151 KLELNEENL------TQNLDLP--LDVDLMLRVGNAKRLSNFLLWQ 188
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 34.9 bits (79), Expect = 0.001
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 38 EKIDEDTIKKLVDVEKHMFMAVAPD--PDITIRSSGE 72
EK +KKL + + + A D P + I+++ E
Sbjct: 18 EK---QALKKL---QASLKL-YADDSAPALAIKATME 47
>4ew6_A D-galactose-1-dehydrogenase protein; nysgrc, PSI-biology,
structural genomics, NEW YORK structura genomics
research consortium, two domain; 2.30A {Rhizobium etli}
Length = 330
Score = 27.0 bits (60), Expect = 1.3
Identities = 9/40 (22%), Positives = 16/40 (40%)
Query: 32 GSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSG 71
+A K + TIK + + K P+ D ++ G
Sbjct: 146 AVEAAKAFLASTTIKSVHVIWKEDVRHWHPNQDWIWQAGG 185
>1iru_A 20S proteasome; cell cycle, immune response, proteolysis,
ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP:
d.153.1.4 PDB: 3unb_G* 3une_G 3unf_G* 3unh_G
Length = 246
Score = 25.6 bits (57), Expect = 2.9
Identities = 3/21 (14%), Positives = 10/21 (47%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
+D T+ L + +++ +
Sbjct: 61 LDSSTVTHLFKITENIGCVMT 81
>1iru_E 20S proteasome; cell cycle, immune response, proteolysis,
ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP:
d.153.1.4 PDB: 3unb_D* 3une_D 3unf_D* 3unh_D
Length = 241
Score = 25.6 bits (57), Expect = 3.2
Identities = 5/21 (23%), Positives = 16/21 (76%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
++ +I+K+V+++ H+ A++
Sbjct: 59 MEPSSIEKIVEIDAHIGCAMS 79
>1ryp_B 20S proteasome; multicatalytic proteinase, protein degradation,
antigen processing, hydrolase, protease; 1.90A
{Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1fnt_B
1g0u_A* 1jd2_A* 1g65_A 1z7q_B 2f16_A* 2fak_A* 2fny_A*
2gpl_A* 2zcy_A* 3bdm_A* 3d29_A* 3dy3_A* 3dy4_A* 3e47_A*
3gpj_A* 3gpt_A* 3gpw_A* 3hye_A* 3mg0_A* ...
Length = 250
Score = 25.7 bits (57), Expect = 3.3
Identities = 2/21 (9%), Positives = 8/21 (38%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
+T+ K+ + + +
Sbjct: 56 AMSETLSKVSLLTPDIGAVYS 76
>1ryp_A 20S proteasome; multicatalytic proteinase, protein degradation,
antigen processing, hydrolase, protease; 1.90A
{Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_G*
1g65_G 1vsy_A 2f16_G* 2fak_G* 2fny_G* 2gpl_G* 3d29_G*
3dy3_G* 3dy4_G* 3e47_G* 3gpj_G* 3gpt_G* 3gpw_G* 3hye_G*
3l5q_A 3mg0_G* 3mg4_G* 3oeu_G* 3oev_G* ...
Length = 243
Score = 25.6 bits (57), Expect = 3.4
Identities = 4/21 (19%), Positives = 10/21 (47%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
+D T+ + + + + M V
Sbjct: 55 LDPTTVSYIFCISRTIGMVVN 75
>1yar_A Proteasome alpha subunit; proteasome 20S, PA26 proteasome
activator 11S, hydrolase-HYD activator complex; 1.90A
{Thermoplasma acidophilum} SCOP: d.153.1.4 PDB: 1ya7_A
1pma_A 3c91_A 3c92_A 3ipm_A 2ku1_A 2ku2_A 1yau_A 3jrm_A
3jse_A 3jtl_A
Length = 233
Score = 25.3 bits (56), Expect = 3.5
Identities = 3/21 (14%), Positives = 14/21 (66%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
I++++I+K+ ++ ++ +
Sbjct: 59 IEQNSIEKIQLIDDYVAAVTS 79
>1iru_D 20S proteasome; cell cycle, immune response, proteolysis,
ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP:
d.153.1.4 PDB: 3unf_C* 3une_C* 3unh_C 3unb_C*
Length = 248
Score = 25.3 bits (56), Expect = 3.7
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
DE T++K+ ++ ++ MA A
Sbjct: 54 QDERTVRKICALDDNVCMAFA 74
>1iru_G 20S proteasome; cell cycle, immune response, proteolysis,
ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP:
d.153.1.4 PDB: 3unb_F* 3une_F 3unf_F* 3unh_F
Length = 254
Score = 25.4 bits (56), Expect = 3.7
Identities = 9/21 (42%), Positives = 16/21 (76%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
+E + K+L +V++H+ MAVA
Sbjct: 58 YEEGSNKRLFNVDRHVGMAVA 78
>4gcn_A Protein STI-1; structural genomics, PSI-biology, midwest center for
structu genomics, MCSG, tetratricopeptide repeat domain;
HET: PGE; 1.85A {Caenorhabditis elegans}
Length = 127
Score = 24.9 bits (55), Expect = 4.0
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 33 SQALKEKIDEDTIKKLVDVEK 53
++L E D + +KK+ ++EK
Sbjct: 107 HRSLSEFRDPELVKKVKELEK 127
>1ryp_E 20S proteasome; multicatalytic proteinase, protein degradation,
antigen processing, hydrolase, protease; 1.90A
{Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_D*
1g65_D 2f16_D* 2fak_D* 2fny_D* 2gpl_D* 3d29_D* 3dy3_D*
3dy4_D* 3e47_D* 3gpj_D* 3gpt_D* 3gpw_D* 3hye_D* 3mg0_D*
3mg4_D* 3okj_D* 3shj_D* 3tdd_D* 2z5c_C ...
Length = 242
Score = 25.3 bits (56), Expect = 4.1
Identities = 6/21 (28%), Positives = 18/21 (85%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
++ D+I+K+V++++H+ A++
Sbjct: 51 LESDSIEKIVEIDRHIGCAMS 71
>1iru_B 20S proteasome; cell cycle, immune response, proteolysis,
ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP:
d.153.1.4 PDB: 3unb_A* 3une_A 3unf_A* 3unh_A
Length = 233
Score = 25.2 bits (56), Expect = 4.1
Identities = 5/21 (23%), Positives = 12/21 (57%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
DE ++ K+ + KH+ + +
Sbjct: 56 YDERSVHKVEPITKHIGLVYS 76
>1ryp_G 20S proteasome; multicatalytic proteinase, protein degradation,
antigen processing, hydrolase, protease; 1.90A
{Saccharomyces cerevisiae} SCOP: d.153.1.4 PDB: 1jd2_F*
1g65_F 1vsy_G 2f16_F* 2fak_F* 2fny_F* 2gpl_F* 3d29_F*
3dy3_F* 3dy4_F* 3e47_F* 3gpj_F* 3gpt_F* 3gpw_F* 3hye_F*
3l5q_L 3mg0_F* 3mg4_F* 3okj_F* 3shj_F* ...
Length = 244
Score = 25.3 bits (56), Expect = 4.4
Identities = 3/21 (14%), Positives = 9/21 (42%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
+ K+ V++H+ +
Sbjct: 55 LVPQKNVKIQVVDRHIGCVYS 75
>1j2p_A Alpha-ring, proteasome alpha subunit; hydrolase; 2.60A
{Archaeoglobus fulgidus} SCOP: d.153.1.4 PDB: 1j2q_A*
Length = 246
Score = 25.0 bits (55), Expect = 4.6
Identities = 6/21 (28%), Positives = 16/21 (76%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
+++DTI+K+ +++H+ A +
Sbjct: 59 LEKDTIEKIYKIDEHICAATS 79
>3h4p_A Proteasome subunit alpha; core particle, cytoplasm, hydrolase,
protease, threonine protease; 4.10A {Methanocaldococcus
jannaschii}
Length = 264
Score = 25.0 bits (55), Expect = 5.2
Identities = 4/21 (19%), Positives = 12/21 (57%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
+ +I+K+ ++ H+ A +
Sbjct: 63 VKIRSIEKIFQIDDHVAAATS 83
>3nzj_F Proteasome component C1; ubiquitin, protein degradation,
N-terminal nucleophilic HYDR 19S regulatory particle;
HET: TY5 TRO MES; 2.40A {Saccharomyces cerevisiae} PDB:
1z7q_G* 3nzw_F* 3nzx_F* 3un4_F* 3un8_F* 3bdm_F* 1fnt_G*
2zcy_F*
Length = 288
Score = 24.6 bits (54), Expect = 6.8
Identities = 3/21 (14%), Positives = 9/21 (42%)
Query: 40 IDEDTIKKLVDVEKHMFMAVA 60
+ K+ V++H+ +
Sbjct: 59 LVPQKNVKIQVVDRHIGCVYS 79
>3mvk_A Protein FUCU, protein RBSD; PSI, MCSG, structural genomics, midwest
center for structura genomics, protein structure
initiative; HET: PGE; 1.65A {Bifidobacterium longum
subsp}
Length = 148
Score = 24.4 bits (52), Expect = 7.0
Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 30 LDGSQALKEKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRP-SNFLL 80
D L ++ DE + +E+ F A + I SGE+ +N +L
Sbjct: 89 WDVYAGLIKEHDERGADAIGSLERFAFYEQAKNAYCVIA-SGESAQYANLIL 139
>1xl7_A COT, peroxisomal carnitine O-octanoyltransferase;
selenomethionine, hepes; HET: EPE; 2.00A {Mus musculus}
SCOP: c.43.1.3 c.43.1.3 PDB: 1xl8_A* 1xmd_A* 1xmc_A*
Length = 612
Score = 24.4 bits (52), Expect = 8.8
Identities = 7/34 (20%), Positives = 17/34 (50%)
Query: 17 LPVPDVQEYCEDKLDGSQALKEKIDEDTIKKLVD 50
LPVP ++E + L+ + + + +++V
Sbjct: 23 LPVPALEESLKKYLESVKPFANEDEYKKTEEIVQ 56
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
0.315 0.132 0.389
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,585,957
Number of extensions: 83416
Number of successful extensions: 172
Number of sequences better than 10.0: 1
Number of HSP's gapped: 172
Number of HSP's successfully gapped: 30
Length of query: 104
Length of database: 6,701,793
Length adjustment: 69
Effective length of query: 35
Effective length of database: 4,775,244
Effective search space: 167133540
Effective search space used: 167133540
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: 42 (22.0 bits)
S2: 51 (23.4 bits)