RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12005
(188 letters)
>1d4b_A CIDE B, human cell death-inducing effector B; alpha/beta roll,
apoptosis; NMR {Homo sapiens} SCOP: d.15.2.1
Length = 122
Score = 101 bits (253), Expect = 2e-28
Identities = 27/81 (33%), Positives = 45/81 (55%)
Query: 14 PCKVVDSNREKKIGIVALSLKDLMNRARLKLGMSSVVKVVLDLDGTEVDEEEYFSTLEKN 73
P +V D R + G+ A + ++L+ +A L ++ V+ +VL+ DGT VD E++F LE +
Sbjct: 37 PFRVCDHKRTIRKGLTAATRQELLAKALETLLLNGVLTLVLEEDGTAVDSEDFFQLLEDD 96
Query: 74 TSLMILSKNDKWTPRSETTAT 94
T LM+L W+P
Sbjct: 97 TCLMVLQSGQSWSPTRSGVLH 117
>2eel_A Cell death activator CIDE-A; CIDE-N domain, cell death- inducing
DFFA-like effector A, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 91
Score = 99.2 bits (247), Expect = 9e-28
Identities = 31/78 (39%), Positives = 49/78 (62%), Gaps = 1/78 (1%)
Query: 14 PCKVVDSNREKKIGIVALSLKDLMNRARLKLGMSS-VVKVVLDLDGTEVDEEEYFSTLEK 72
P +V + +R + G++A SL++L+++ L +++ +V +VL+ DGT VD EE+F TL
Sbjct: 11 PFRVSNHDRSSRRGVMASSLQELISKTLDALVIATGLVTLVLEEDGTVVDTEEFFQTLGD 70
Query: 73 NTSLMILSKNDKWTPRSE 90
NT MIL K KW P
Sbjct: 71 NTHFMILEKGQKWMPSGP 88
>1f2r_I Inhibitor of caspase-activated DNAse; alpha-beta roll,
protein-protein complex, DNA binding protein; NMR {Mus
musculus} SCOP: d.15.2.1
Length = 100
Score = 93.1 bits (231), Expect = 2e-25
Identities = 26/77 (33%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
Query: 14 PCKVVDSNREKKIGIVALSLKDLMNRARLKLGMSSV---VKVVLDLDGTEVDEEEYFSTL 70
PC + ++ + G+ A SL++L ++A L + + +VL DGT VD+++YF L
Sbjct: 20 PCLLRRNHSRDQHGVAASSLEELRSKACELLAIDKSLTPITLVLAEDGTIVDDDDYFLCL 79
Query: 71 EKNTSLMILSKNDKWTP 87
NT + L+ N+KWT
Sbjct: 80 PSNTKFVALACNEKWTY 96
>1v0d_A DNA fragmentation factor 40 kDa subunit; hydrolase, nuclease,
caspase-activated DNAse; HET: DNA; 2.6A {Mus musculus}
SCOP: d.4.1.7 PDB: 1f2r_C 1c9f_A 1ibx_A*
Length = 329
Score = 92.0 bits (228), Expect = 8e-23
Identities = 23/129 (17%), Positives = 49/129 (37%), Gaps = 2/129 (1%)
Query: 14 PCKVVDSNREKKIGIVALSLKDLMNRARLKLGMSSV-VKVVLDLDGTEVDEEEYFSTLEK 72
K+ + K G+ A S ++L+ + ++ + ++ L DGTEV ++ F L
Sbjct: 10 CVKLRALHSACKFGVAARSCQELLRKGCVRFQLPMPGSRLCLYEDGTEVT-DDCFPGLPN 68
Query: 73 NTSLMILSKNDKWTPRSETTATLTLERNETNNDVTGFLTKIHGNNGVSILGGLELELLSD 132
+ L++L+ + W NE + V + + + L +LL
Sbjct: 69 DAELLLLTAGETWHGYVSDITRFLSVFNEPHAGVIQAARQQLSDEQAPLRQKLLADLLHH 128
Query: 133 MDPESLTDI 141
+ +
Sbjct: 129 VSQNITAET 137
>1ibx_B Chimera of IGG binding protein G and DNA fragmentation factor 45;
DFF40, DFF45, protein-protein complex, CIDE, CIDE domain
complex; HET: DNA; NMR {Streptococcus SP} SCOP: d.15.2.1
Length = 145
Score = 87.6 bits (216), Expect = 1e-22
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 3/79 (3%)
Query: 14 PCKVVDSNREKKIGIVALSLKDLMNRARLKLGMSSV---VKVVLDLDGTEVDEEEYFSTL 70
PC + + ++ G+ A L+DL ++A L + V +VL DGT VD+++YF L
Sbjct: 65 PCLLRRNYSREQHGVAASCLEDLRSKACDILAIDKSLTPVTLVLAEDGTIVDDDDYFLCL 124
Query: 71 EKNTSLMILSKNDKWTPRS 89
NT + L+ N+KW +
Sbjct: 125 PSNTKFVALASNEKWAYNN 143
>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 = 44.1 bits (103), Expect = 1e-05
Identities = 37/215 (17%), Positives = 72/215 (33%), Gaps = 43/215 (20%)
Query: 1 MDYGLLEEDGIGLPCKVVDSN-----REKK------IGIVALSLKDLMNRAR--LKLG-- 45
L ++ L K +D RE + I+A S++D + +
Sbjct: 294 HSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCD 353
Query: 46 -MSSVVKVVLD-LDGTEVDEE-EYFSTLEKNTS-----LMILSKNDKWTPRSETTATLTL 97
++++++ L+ L+ E + + S + L ++ W ++
Sbjct: 354 KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLI-----WFDVIKSD----- 403
Query: 98 ERNETNNDVTGFLTKIHGNNGVSILGGLELELLSDMDPE-----SLTD--IIPDKLFLDQ 150
N L + + + LEL ++ E S+ D IP D
Sbjct: 404 VMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDD 463
Query: 151 F-KEVSSRYF-SNKNHHSKETK-SEKILHHRYVIL 182
+YF S+ HH K + E++ R V L
Sbjct: 464 LIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFL 498
Score = 33.7 bits (76), Expect = 0.034
Identities = 34/242 (14%), Positives = 65/242 (26%), Gaps = 90/242 (37%)
Query: 1 MDYG------LLEEDGIG-LPCK-VVD------SNRE-KKIGIVALSLKDLMNRARLKLG 45
Y + E+ + CK V D S E I + KD ++
Sbjct: 14 HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHI----IMSKDAVSGTLRLFW 69
Query: 46 M-----SSVVKV----VLDLD-------------GTEVDEEEYFSTLEK-NTSLMILSKN 82
+V+ VL ++ + Y ++ + +K
Sbjct: 70 TLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY 129
Query: 83 DKWTPRSETTATLT--LERNETNNDVTGFLTKIHG-----------------------NN 117
+ R + L L +V I G +
Sbjct: 130 N--VSRLQPYLKLRQALLELRPAKNVL-----IDGVLGSGKTWVALDVCLSYKVQCKMDF 182
Query: 118 GV------------SILGGLELELLSDMDPE--SLTDIIPD-KLFLDQFKEVSSRYFSNK 162
+ ++L L+ +LL +DP S +D + KL + + R +K
Sbjct: 183 KIFWLNLKNCNSPETVLEMLQ-KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK 241
Query: 163 NH 164
+
Sbjct: 242 PY 243
Score = 30.6 bits (68), Expect = 0.32
Identities = 20/126 (15%), Positives = 36/126 (28%), Gaps = 35/126 (27%)
Query: 47 SSVVKVVLDLDGTEVDEEEYFSTLEKNTSLMILSKNDKWTPRSETTATLTLERNETNNDV 106
V + T + + + TL + +L K+ L E TN
Sbjct: 275 KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLL---KYL--DCRPQDLPREVLTTNPRR 329
Query: 107 TGFLTKIHGNNGVSILGGLELELLSDM----------DPESLTDIIPDKLFLDQFK--EV 154
+SI+ E + D + + LT II + L+ + E
Sbjct: 330 ------------LSIIA----ESIRDGLATWDNWKHVNCDKLTTII--ESSLNVLEPAEY 371
Query: 155 SSRYFS 160
+
Sbjct: 372 RKMFDR 377
>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome
segregation, cell adhesion, kleisin, MIT cell cycle;
HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP:
c.37.1.12
Length = 430
Score = 30.8 bits (70), Expect = 0.21
Identities = 11/124 (8%), Positives = 41/124 (33%)
Query: 56 LDGTEVDEEEYFSTLEKNTSLMILSKNDKWTPRSETTATLTLERNETNNDVTGFLTKIHG 115
L+ + + + + I +++ R + +++ + ++ + K+
Sbjct: 135 LENENILIKAKNFLVFQGDVEQIAAQSPVELSRMFEEVSGSIQYKKEYEELKEKIEKLSK 194
Query: 116 NNGVSILGGLELELLSDMDPESLTDIIPDKLFLDQFKEVSSRYFSNKNHHSKETKSEKIL 175
+ SI + +++ ++ E R+ N + EK +
Sbjct: 195 SATESIKNRRRIHGELKTYKSPGLEVLFQGPRGSRYDEAEGRFEVINNETEQLKAEEKKI 254
Query: 176 HHRY 179
+++
Sbjct: 255 LNQF 258
>3idu_A Uncharacterized protein; all beta-protein, structural genomics,
PSI-2, protein structure initiative; 1.70A {Pyrococcus
furiosus} PDB: 2kl6_A
Length = 127
Score = 28.8 bits (64), Expect = 0.56
Identities = 15/74 (20%), Positives = 23/74 (31%), Gaps = 14/74 (18%)
Query: 47 SSVVKVVLDLDGTEVDEEEYFSTLEKNTSLMILSKNDKWTPRSETTATLTL--------- 97
KV + ++GT ++ L WTP E +
Sbjct: 49 VPSTKVRVYINGTLYKNWTVSLGPKEEKVLTF-----NWTPTQEGMYRINATVDEENTVV 103
Query: 98 ERNETNNDVTGFLT 111
E NE NN T ++
Sbjct: 104 ELNENNNVATFDVS 117
>1u7g_A Probable ammonium transporter; right handed helical bundle,
transmembrane helices, ammonia membrane protein, RH
protein, transport protein; HET: MSE BOG; 1.40A
{Escherichia coli} SCOP: f.44.1.1 PDB: 1u77_A* 1u7c_A*
1xqf_A 1xqe_A 2ns1_A* 2nop_A 2nmr_A 3c1g_A 3c1i_A*
3c1h_A* 2now_A 2npe_A 2npc_A 2npd_A 2npg_A 2npj_A
2nuu_A* 3c1j_A 2npk_A
Length = 385
Score = 29.1 bits (66), Expect = 0.93
Identities = 4/31 (12%), Positives = 13/31 (41%)
Query: 117 NGVSILGGLELELLSDMDPESLTDIIPDKLF 147
G + G + +L +++ ++ I +
Sbjct: 70 EGNNFFGNINWLMLKNIELTAVMGSIYQYIH 100
>2l0d_A Cell surface protein; structural genomics, northeast structural
genomics consortiu PSI-2, protein structure initiative;
NMR {Methanosarcina acetivorans}
Length = 114
Score = 27.8 bits (62), Expect = 1.1
Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 12/74 (16%)
Query: 47 SSVVKVVLDLDGTEVDEEEYFSTLEKNTSLMILSKNDKWTPRSETTATLTL--------- 97
S+ V L +DG VD + ++LE S + + + + TLT+
Sbjct: 35 STSFNVSLLVDGIVVDTQT-VTSLESENST-NVDFHWTL-DGTANSYTLTVNVDPENAVN 91
Query: 98 ERNETNNDVTGFLT 111
E NE+NN +T +
Sbjct: 92 EGNESNNTLTALVG 105
>2b82_A APHA, class B acid phosphatase; DDDD acid phosphatase, metallo-ENZ
hydrolase; HET: ADN; 1.25A {Escherichia coli} SCOP:
c.108.1.12 PDB: 2b8j_A* 2hf7_A 1rmt_A* 1n9k_A 1rmq_A
1n8n_A* 1rmy_A* 2g1a_A* 3cz4_A 2heg_A* 1z5g_A 1z5u_A*
1z88_A 2aut_A
Length = 211
Score = 28.3 bits (62), Expect = 1.2
Identities = 21/144 (14%), Positives = 43/144 (29%), Gaps = 13/144 (9%)
Query: 43 KLGMSSVVKVVLDLDGTEVDEEEYFSTLEKNTSLMILSKNDKWTPRSETTATLTLERNET 102
L + V D+D T + F +K S + +
Sbjct: 31 SLAGRPPMAVGFDIDDTVLFSSPGFWRGKKTFSPESEDYLKNPVFWEKMNN--GWDEFSI 88
Query: 103 NNDVTGFLTKIHGNNGVSILGGLELELLSDMDP---ESLTDIIPDKLFLDQFKEVSSRYF 159
+V L +H G +I ++ P E+++ + D + +
Sbjct: 89 PKEVARQLIDMHVRRGDAIF------FVTGRSPTKTETVSKTLADNFHIPATNMNPVIFA 142
Query: 160 SNKNHHSKETKSEKILHHRYVILF 183
+K + TKS+ + I +
Sbjct: 143 GDKP--GQNTKSQWLQDKNIRIFY 164
>1swv_A Phosphonoacetaldehyde hydrolase; HAD enzyme superfamily,
phosphonotase, metal binding; 2.30A {Bacillus cereus}
SCOP: c.108.1.3 PDB: 1sww_A 2iof_A* 2ioh_A 1rql_A
1rqn_A 2iof_K* 1rdf_A 1fez_A
Length = 267
Score = 28.3 bits (63), Expect = 1.6
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 7/28 (25%)
Query: 37 MNRARLKLGMSSVVKVVLDLDGTEVDEE 64
M+R +++ V+ GT VD
Sbjct: 1 MDRMKIEA-------VIFAWAGTTVDYG 21
>3iru_A Phoshonoacetaldehyde hydrolase like protein;
phosphonoacetaldehyde hydrolase like P structural
genomics, PSI-2, protein structure initiative; 2.30A
{Oleispira antarctica}
Length = 277
Score = 27.6 bits (61), Expect = 2.7
Identities = 5/15 (33%), Positives = 8/15 (53%)
Query: 52 VVLDLDGTEVDEEEY 66
++LD GT +D
Sbjct: 17 LILDWAGTTIDFGSL 31
>1oru_A YUAD protein; structural genomics, cytosolic hypothetical protein,
PSI, protein structure initiative, midwest center for
structural genomics; HET: MSE; 1.80A {Bacillus subtilis}
SCOP: b.58.1.2
Length = 195
Score = 27.3 bits (60), Expect = 2.8
Identities = 7/46 (15%), Positives = 12/46 (26%)
Query: 5 LLEEDGIGLPCKVVDSNREKKIGIVALSLKDLMNRARLKLGMSSVV 50
L +G PC + + A G+ +V
Sbjct: 122 ALLCEGENDPCIQPGEVIQSYYPDQPKLASAFVRHALGIRGIVCIV 167
>3m9l_A Hydrolase, haloacid dehalogenase-like family; HAD family
hydrolase, structural genomics, PSI, protein structure
initiative; HET: MSE; 1.60A {Pseudomonas fluorescens}
PDB: 2ybd_A* 3r09_A*
Length = 205
Score = 26.8 bits (60), Expect = 3.3
Identities = 7/26 (26%), Positives = 11/26 (42%), Gaps = 7/26 (26%)
Query: 37 MNRARLKLGMSSVVKVVLDLDGTEVD 62
M+ + +K V D+DGT
Sbjct: 1 MSLSEIKH-------WVFDMDGTLTI 19
>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 = 27.3 bits (60), Expect = 3.6
Identities = 6/30 (20%), Positives = 12/30 (40%)
Query: 15 CKVVDSNREKKIGIVALSLKDLMNRARLKL 44
V++ + +KI I+ L + L
Sbjct: 1866 TNVLNFIKLQKIDIIELQKSLSLEEVEGHL 1895
>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein,
ATPase, RNA binding protein; 3.00A {Methanocaldococcus
jannaschii} SCOP: c.37.1.19 c.37.1.19
Length = 367
Score = 27.1 bits (61), Expect = 3.6
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 6/31 (19%)
Query: 33 LKDLMNRARLKLGMSSVVKVVLDLDGTEVDE 63
+ D +NR L L +V +LD E DE
Sbjct: 134 ILDHINRGTLNL--KNVKYFILD----EADE 158
>1qyi_A ZR25, hypothetical protein; structural genomics, PSI, protein
structure initiative, NORT structural genomics
consortium, NESG; 2.50A {Staphylococcus aureus subsp}
SCOP: c.108.1.13
Length = 384
Score = 26.7 bits (58), Expect = 4.8
Identities = 11/48 (22%), Positives = 18/48 (37%)
Query: 51 KVVLDLDGTEVDEEEYFSTLEKNTSLMILSKNDKWTPRSETTATLTLE 98
K++ D+DG + EE F +++ K TLT
Sbjct: 3 KILFDVDGVFLSEERCFDVSALTVYELLMDKCYLGLHSHIDWETLTDN 50
>3bf0_A Protease 4; bacterial, hydrolase, inner membrane, membrane,
transmembrane; 2.55A {Escherichia coli} PDB: 3bez_A
Length = 593
Score = 26.8 bits (59), Expect = 5.2
Identities = 12/67 (17%), Positives = 31/67 (46%)
Query: 52 VVLDLDGTEVDEEEYFSTLEKNTSLMILSKNDKWTPRSETTATLTLERNETNNDVTGFLT 111
++LD+ G VD+ + K + ++ + +D+ S T+ + + + ++TG +
Sbjct: 34 LLLDISGVIVDKPDSSQRFSKLSRQLLGASSDRLQENSLFDIVNTIRQAKDDRNITGIVM 93
Query: 112 KIHGNNG 118
+ G
Sbjct: 94 DLKNFAG 100
>1ko7_A HPR kinase/phosphatase; protein kinase, phosphotransfer, protein
phosphatase, dual activity, product, substrate,
transferase, hydrolase; 1.95A {Staphylococcus xylosus}
SCOP: c.98.2.1 c.91.1.2
Length = 314
Score = 26.1 bits (57), Expect = 7.4
Identities = 6/38 (15%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 105 DVTGFLTKIHGNNGVSILGGLELELLSDMDPESLTDII 142
++ G+ + ++ + +LG EL + + E +
Sbjct: 37 EMAGYFSHYA-SDRIQLLGTTELSFYNLLPDEERKGRM 73
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 0.134 0.370
Gapped
Lambda K H
0.267 0.0827 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,844,660
Number of extensions: 161361
Number of successful extensions: 352
Number of sequences better than 10.0: 1
Number of HSP's gapped: 347
Number of HSP's successfully gapped: 30
Length of query: 188
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 100
Effective length of database: 4,244,745
Effective search space: 424474500
Effective search space used: 424474500
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: 54 (24.4 bits)