RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2945
(134 letters)
>2y69_F Cytochrome C oxidase subunit 5B; electron transport, complex IV,
proton pumps, membrane prote; HET: TPO HEA CHD PEK PGV
DMU; 1.95A {Bos taurus}
Length = 129
Score = 121 bits (305), Expect = 6e-37
Identities = 39/91 (42%), Positives = 54/91 (59%), Gaps = 2/91 (2%)
Query: 42 ELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICE 101
+P + ATGLE+ +LA DP+N+ K GTK P VPS RIVGCICE
Sbjct: 36 GVPTDEEQATGLEREVMLAAR-KGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICE 94
Query: 102 EESPSINWMWLYEGKPKRCM-CGHWFKLVYK 131
E++ ++ W WL++G+ +RC CG +KLV
Sbjct: 95 EDNSTVIWFWLHKGEAQRCPSCGTHYKLVPH 125
>1v54_F VI, cytochrome C oxidase polypeptide VB; oxidoreductase; HET: FME
TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus}
SCOP: g.41.5.3 PDB: 1oco_F* 1occ_F* 1ocz_F* 1ocr_F*
1v55_F* 2dyr_F* 2dys_F* 2eij_F* 2eik_F* 2eil_F* 2eim_F*
2ein_F* 2occ_F* 2ybb_Q* 2zxw_F* 3abk_F* 3abl_F* 3abm_F*
3ag1_F* 3ag2_F* ...
Length = 98
Score = 120 bits (302), Expect = 7e-37
Identities = 39/92 (42%), Positives = 54/92 (58%), Gaps = 2/92 (2%)
Query: 42 ELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICE 101
+P + ATGLE+ +LA DP+N+ K GTK P VPS RIVGCICE
Sbjct: 5 GVPTDEEQATGLEREVMLAAR-KGQDPYNILAPKATSGTKEDPNLVPSITNKRIVGCICE 63
Query: 102 EESPSINWMWLYEGKPKRCM-CGHWFKLVYKA 132
E++ ++ W WL++G+ +RC CG +KLV
Sbjct: 64 EDNSTVIWFWLHKGEAQRCPSCGTHYKLVPHQ 95
>2odx_A Cytochrome C oxidase polypeptide IV; all beta-protein,
metallo-protein, oxidoreductase; NMR {Saccharomyces
cerevisiae}
Length = 80
Score = 92.5 bits (230), Expect = 5e-26
Identities = 20/70 (28%), Positives = 28/70 (40%), Gaps = 3/70 (4%)
Query: 67 DPFNVK-IRKRGLGTKTQPTEVPSAFEARIVGCI-CEEESPSINWMWLYEGKPKRCM-CG 123
D F+ K + GT P + S + R VGC S +I W+ + RC CG
Sbjct: 4 DVFDTKPLDSSRKGTMKDPIIIESYDDYRYVGCTGSPAGSHTIMWLKPTVNEVARCWECG 63
Query: 124 HWFKLVYKAP 133
+KL
Sbjct: 64 SVYKLNPVGV 73
>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 = 31.4 bits (70), Expect = 0.079
Identities = 13/97 (13%), Positives = 29/97 (29%), Gaps = 14/97 (14%)
Query: 35 WNKNDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGTKTQPTEVPSAFEAR 94
W D + + L K L+ + P + I L K + A
Sbjct: 396 WFDVIKS---DVMVVVNKLHKYSLVEK---QPKESTISIPSIYLELKVKLENEY-ALHRS 448
Query: 95 IVGCICEEESPSINWMWLYEGKPKRCMCGHWFK-LVY 130
IV + +I + + + +++ + +
Sbjct: 449 IV------DHYNIPKTFDSDDLIPPYLDQYFYSHIGH 479
Score = 29.8 bits (66), Expect = 0.31
Identities = 14/85 (16%), Positives = 27/85 (31%), Gaps = 13/85 (15%)
Query: 37 KNDLDELPDPLDLATGLEKRELLAELAGDPDPFNVKIRKRGLGT-KTQPTEVPSAFEARI 95
++ D D D+ + +E + + D + R T ++ E+ F
Sbjct: 30 VDNFD-CKDVQDMPKSILSKEEIDHIIMSKDAVS-GTL-RLFWTLLSKQEEMVQKFV--- 83
Query: 96 VGCICEEESPSINWMWLYEGKPKRC 120
EE IN+ +L
Sbjct: 84 ------EEVLRINYKFLMSPIKTEQ 102
Score = 26.4 bits (57), Expect = 4.0
Identities = 24/121 (19%), Positives = 37/121 (30%), Gaps = 41/121 (33%)
Query: 6 RSLVLSPNTRYLARSVTATGNSFSTCAQRWNKNDLDELPDPLDLATGLEKRELLAELAGD 65
+ L+ TR+ + VT ++ +T LD L E+ + L
Sbjct: 267 KILLT---TRF--KQVTDFLSAATTTHIS-----LDHHSM------TLTPDEVKSLLL-- 308
Query: 66 PDPFNVKIRKRGLGTKTQ--PTEV----PSAFEARIVGCICEEESPSIN-W-MWLYEGKP 117
K L + Q P EV P R + I E + W W +
Sbjct: 309 ------KY----LDCRPQDLPREVLTTNP-----RRLSIIAESIRDGLATWDNWKHVNCD 353
Query: 118 K 118
K
Sbjct: 354 K 354
>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 = 0.16
Identities = 21/108 (19%), Positives = 35/108 (32%), Gaps = 33/108 (30%)
Query: 6 RSLVLS-PNTRYLARSVTATGNSFSTCAQRWNKND--LDELPDPLDLATGLEKRELLAEL 62
R L LS + + + SF +Q + LP+P + ++ AEL
Sbjct: 7 RPLTLSHGSLEH---VLLVPTASFFIASQLQ---EQFNKILPEPTEGFAADDEPTTPAEL 60
Query: 63 AGDPDPFNVKIRKRGLG---TKTQPTEVPS----------AFEARIVG 97
G F LG + +P++V FE +
Sbjct: 61 VGK---F--------LGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLE 97
>3ooi_A Histone-lysine N-methyltransferase, H3 lysine-36 lysine-20
specific; SET domain, S-adenosyl-L methionine; HET: SAM;
1.75A {Homo sapiens}
Length = 232
Score = 29.3 bits (66), Expect = 0.33
Identities = 21/80 (26%), Positives = 30/80 (37%), Gaps = 14/80 (17%)
Query: 54 EKRELLAELAGD--PDPFNVKIRKRGLGTKTQPTEVPSAFEARIVGCICEEESPS----- 106
E R+L + D P P+ I+ + Q +A + I C C+ +
Sbjct: 3 ELRQLQEDRKNDKKPPPY-KHIKVNRPIGRVQI---FTADLSEIPRCNCKATDENPCGID 58
Query: 107 ---INWMWLYEGKPKRCMCG 123
IN M LYE P C G
Sbjct: 59 SECINRMLLYECHPTVCPAG 78
>3nt1_A Prostaglandin-endoperoxide synthase 2; prostaglandin H2 synthase,
cyclooxygenase-2, naproxen, oxido; HET: NAG BOG NPS HEM;
1.73A {Mus musculus} PDB: 3ln1_A* 3mqe_A* 3ln0_A*
3ntb_A* 3q7d_A* 1pxx_A* 3pgh_A* 1cx2_A* 4cox_A* 5cox_A*
6cox_A* 3qh0_A* 3qmo_A* 4e1g_A* 3olu_A* 3olt_A* 3hs5_A*
3hs6_A* 3hs7_A* 3krk_A* ...
Length = 587
Score = 27.8 bits (61), Expect = 1.1
Identities = 13/67 (19%), Positives = 21/67 (31%), Gaps = 8/67 (11%)
Query: 5 FRSLVLSPNTRYLARSVTATGNSFSTCAQRWNKNDLDELPDPLDLATGLEKRELLAELAG 64
++S N Y R++ + T ELPD ++ + R
Sbjct: 105 YKSWEAFSNLSYYTRALPPVADDCPTPMGVKGNK---ELPDSKEVLEKVLLRR-----EF 156
Query: 65 DPDPFNV 71
PDP
Sbjct: 157 IPDPQGS 163
>1a1w_A FADD protein; apoptosis, death effector domain; NMR {Homo
sapiens} SCOP: a.77.1.4 PDB: 1a1z_A
Length = 91
Score = 25.9 bits (57), Expect = 2.4
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 31 CAQRWNKNDLDELPDPLDLATGLEKRELLAE 61
C R K L+ + LDL + L ++ L
Sbjct: 27 CLGRVGKRKLERVQSGLDLFSMLLEQNDLEP 57
>3qs7_E FL cytokine receptor; immunoglobulin-like domain, four-helical
bundle cytokine, CY receptor complex, extracellular
complex; HET: NAG; 4.30A {Homo sapiens}
Length = 423
Score = 26.6 bits (58), Expect = 3.1
Identities = 9/48 (18%), Positives = 15/48 (31%), Gaps = 1/48 (2%)
Query: 71 VKIRKRGLGTKTQPTEVPSAFEARIVGCICE-EESPSINWMWLYEGKP 117
V I ++G T +E + + P I W + K
Sbjct: 319 VTIVEKGFINATNSSEDYEIDQYEEFCFSVRFKAYPQIRCTWTFSRKS 366
>2jx3_A Protein DEK; alpha helix, SAF/SAP motif, DNA binding, chromosomal
rearrangement, DNA-binding, nucleus, phosphorylation,
proto oncogene; NMR {Homo sapiens}
Length = 131
Score = 25.7 bits (56), Expect = 3.6
Identities = 6/32 (18%), Positives = 13/32 (40%)
Query: 32 AQRWNKNDLDELPDPLDLATGLEKRELLAELA 63
+++ L + + LDL EL+ +
Sbjct: 72 LKKFRNAMLKSICEVLDLERSGVNSELVKRIL 103
>2kbz_A GP15, 15 protein (bacteriophage SPP1 complete nucleotide
sequence); three alpha-helix bundle, viral protein; NMR
{Bacillus phage SPP1}
Length = 99
Score = 25.5 bits (55), Expect = 3.8
Identities = 10/60 (16%), Positives = 20/60 (33%), Gaps = 3/60 (5%)
Query: 32 AQRWNKNDLDELPDPLDLATGLEKRELLAELA-GDPDPFNVKIRKRGLGTKTQPTEVPSA 90
A+ N + + +G+ +A+ A + R + TE+PS
Sbjct: 29 AKDECHNPFIDKDGNESIPSGVLI--FVAKAAQFYMTNAGLTGRSMDTVSYNFATEIPST 86
>1k8k_B ARP2, actin-like protein 2; beta-propeller, structural protein;
2.00A {Bos taurus} SCOP: c.55.1.1 PDB: 1tyq_B* 1u2v_B*
2p9i_B* 2p9l_B 2p9n_B* 2p9p_B* 2p9s_B* 2p9u_B* 3dxk_B*
3dxm_B* 3rse_B 2p9k_B*
Length = 394
Score = 25.1 bits (55), Expect = 8.7
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 14 TRYLARSVTATGNSFSTCAQRWNKNDLDE 42
TRYL + + G +F+ A + E
Sbjct: 190 TRYLIKLLLLRGYAFNHSADFETVRMIKE 218
>3c8d_A Enterochelin esterase; alpha-beta-alpha sandwich, IROD, iron
aquisition, structural genomics, PSI-2, protein
structure initiative; HET: CIT; 1.80A {Shigella flexneri
2a str} SCOP: b.1.18.20 c.69.1.2 PDB: 2b20_A 3c87_A*
3c8h_A 3mga_A*
Length = 403
Score = 25.0 bits (54), Expect = 9.7
Identities = 23/88 (26%), Positives = 32/88 (36%), Gaps = 14/88 (15%)
Query: 3 VFFRSLVLSPNTRYLARSVTATGNSFSTCAQRWNKNDLDELPDPLDLATGLEKRELLAEL 62
V+ + L+ N R S C ++D+ P P L R+LL
Sbjct: 79 VWQWTTQLNANWR------------GSYCFIPTERDDIFSAPSPDRLELREGWRKLLP-- 124
Query: 63 AGDPDPFNVKIRKRGLGTKTQPTEVPSA 90
DP N + K GLG E+P A
Sbjct: 125 QAIADPLNPQSWKGGLGHAVSALEMPQA 152
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
0.320 0.136 0.439
Gapped
Lambda K H
0.267 0.0537 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,147,690
Number of extensions: 118309
Number of successful extensions: 245
Number of sequences better than 10.0: 1
Number of HSP's gapped: 239
Number of HSP's successfully gapped: 18
Length of query: 134
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 51
Effective length of database: 4,384,350
Effective search space: 223601850
Effective search space used: 223601850
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 (21.8 bits)
S2: 52 (24.2 bits)