RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13940
(88 letters)
>1qtn_A Caspase-8; apoptosis, dithiane-DIOL, caspase, cysteine-protease,
hydrol hydrolase inhibitor complex; 1.20A {Homo sapiens}
SCOP: c.17.1.1 PDB: 3kjn_A* 3kjq_A* 2y1l_A 2c2z_A
1qdu_A* 1f9e_A*
Length = 164
Score = 76.6 bits (188), Expect = 1e-19
Identities = 24/63 (38%), Positives = 32/63 (50%)
Query: 26 LGELSQEDHSDADCLVITVLTHGLGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKIF 85
L DHS+ DC + +L+HG + +L FT KC +LAGKPK+F
Sbjct: 86 LKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVF 145
Query: 86 FIQ 88
FIQ
Sbjct: 146 FIQ 148
>2dko_A Caspase-3; low barrier hydrogen bond, caspase, drug design,
radiation D tetrahedral intermediate, protease; 1.06A
{Homo sapiens} PDB: 1nme_A 2h5i_A 2h5j_A 2h65_A 2xyg_A*
2xyh_A 2xyp_A* 2xzd_A 2xzt_A 2y0b_A 3edq_A 1gfw_A
1re1_A* 1pau_A* 1rhk_A* 1rhm_A* 1rhq_A* 1rhr_A* 1rhu_A*
1rhj_A* ...
Length = 146
Score = 75.3 bits (185), Expect = 3e-19
Identities = 24/63 (38%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 26 LGELSQEDHSDADCLVITVLTHGLGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKIF 85
+ ++S+EDHS V +L+HG E ++ + P ++K+ F D+CR+L GKPK+F
Sbjct: 72 MRDVSKEDHSKRSSFVCVLLSHG-EEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLF 130
Query: 86 FIQ 88
IQ
Sbjct: 131 IIQ 133
>2ql9_A Caspase-7; cysteine protease, apoptosis, thiol protease, zymogen,
hydro hydrolase inhibitor complex; HET: CIT; 2.14A {Homo
sapiens} PDB: 2ql7_A* 2ql5_A* 2qlb_A* 2qlf_A 2qlj_A*
3edr_A 3ibc_A 3ibf_A 1i51_A
Length = 173
Score = 74.3 bits (182), Expect = 1e-18
Identities = 29/88 (32%), Positives = 46/88 (52%), Gaps = 7/88 (7%)
Query: 1 MKFKLVSQEDHSDADCLVITVLTHGLGELSQEDHSDADCLVITVLTHGLGERYLWAYDMP 60
+ F ++ D S A + L + S+EDH++A C +L+HG E ++ D
Sbjct: 81 LGFDVIVYNDCSCAKMQDL------LKKASEEDHTNAACFACILLSHG-EENVIYGKDGV 133
Query: 61 YFVEKLWLPFTADKCRTLAGKPKIFFIQ 88
++ L F D+C+TL KPK+FFIQ
Sbjct: 134 TPIKDLTAHFRGDRCKTLLEKPKLFFIQ 161
>3p45_A Caspase-6; protease, huntington'S disease, physio PH, competitive
inhibition, hydrolase; 2.53A {Homo sapiens}
Length = 179
Score = 73.3 bits (179), Expect = 4e-18
Identities = 28/63 (44%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 26 LGELSQEDHSDADCLVITVLTHGLGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKIF 85
+ E+S H+DADC V L+HG +++AYD ++ L F DKC +L GKPKIF
Sbjct: 100 IHEVSTVSHADADCFVCVFLSHG-EGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIF 158
Query: 86 FIQ 88
IQ
Sbjct: 159 IIQ 161
>1pyo_A Caspase-2; apoptosis, caspase, alpha-beta, thiol protease,
hydrolase-HY inhibitor complex; 1.65A {Homo sapiens}
SCOP: c.17.1.1 PDB: 3rjm_A* 2p2c_A 3r5j_A 3r6g_A 3r6l_A
3r7b_A 3r7n_A 3r7s_A
Length = 167
Score = 70.0 bits (171), Expect = 6e-17
Identities = 15/59 (25%), Positives = 27/59 (45%)
Query: 30 SQEDHSDADCLVITVLTHGLGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKIFFIQ 88
H D ++ +L+HG+ +++++ F C +L KPK+FFIQ
Sbjct: 94 QLPAHRVTDSCIVALLSHGVEGAIYGVDGKLLQLQEVFQLFDNANCPSLQNKPKMFFIQ 152
>2nn3_C Caspase-1; cysteine protease, hydrolase; 3.00A {Spodoptera
frugiperda}
Length = 310
Score = 70.2 bits (171), Expect = 3e-16
Identities = 35/63 (55%), Positives = 44/63 (69%), Gaps = 1/63 (1%)
Query: 26 LGELSQEDHSDADCLVITVLTHGLGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKIF 85
+ + ++ DHSDADCL++ VLT G L+A D Y + LW FTADKC TLAGKPK+F
Sbjct: 115 IQQTAEMDHSDADCLLVAVLTAG-ELGMLYAKDTHYKPDNLWYYFTADKCPTLAGKPKLF 173
Query: 86 FIQ 88
FIQ
Sbjct: 174 FIQ 176
>3h11_A CAsp8 and FADD-like apoptosis regulator; cell death, apoptosis,
caspase, alternative splicing, HOST- virus interaction,
polymorphism, cytoplasm, disease mutation; 1.90A {Homo
sapiens} PDB: 3h13_A
Length = 272
Score = 69.3 bits (169), Expect = 5e-16
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 30 SQEDHSDADCLVITVLTHGLGERYLWAYDMPY---FVEKLWLPFTADKCRTLAGKPKIFF 86
+H D D V +++ G G + ++ D + + + F D C LAGKPK+FF
Sbjct: 90 CMPEHRDYDSFVCVLVSRG-GSQSVYGVDQTHSGLPLHHIRRMFMGDSCPYLAGKPKMFF 148
Query: 87 IQ 88
IQ
Sbjct: 149 IQ 150
>3sir_A Caspase; hydrolase; 2.68A {Drosophila melanogaster} PDB: 3sip_A
Length = 259
Score = 68.6 bits (167), Expect = 7e-16
Identities = 27/63 (42%), Positives = 45/63 (71%), Gaps = 1/63 (1%)
Query: 26 LGELSQEDHSDADCLVITVLTHGLGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKIF 85
+ + ++HSD+DC+++ +L+HG Y++A D Y ++ +W FTA+ C +LAGKPK+F
Sbjct: 75 IEYSASQNHSDSDCILVAILSHG-EMGYIYAKDTQYKLDNIWSFFTANHCPSLAGKPKLF 133
Query: 86 FIQ 88
FIQ
Sbjct: 134 FIQ 136
>4ehd_A Caspase-3; caspase, apoptosis, allosteric inhibition; 1.58A {Homo
sapiens} PDB: 4ehk_A 4ehf_A 4ehn_A 1cp3_A 4ehh_A 4eha_A
4ehl_A 1i3o_A
Length = 277
Score = 68.6 bits (167), Expect = 8e-16
Identities = 24/63 (38%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 26 LGELSQEDHSDADCLVITVLTHGLGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKIF 85
+ ++S+EDHS V +L+HG E ++ + P ++K+ F D+CR+L GKPK+F
Sbjct: 100 MRDVSKEDHSKRSSFVCVLLSHG-EEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLF 158
Query: 86 FIQ 88
IQ
Sbjct: 159 IIQ 161
>3od5_A Caspase-6; caspase domain, apoptotic protease, hydrolase-hydrolase
INHI complex; 1.60A {Homo sapiens} PDB: 3k7e_A 3s70_A
3v6m_A 3v6l_A 3nr2_A 2wdp_A 3nkf_A 3s8e_A 3qnw_A*
3p4u_A* 3p45_B 3qnw_B* 3p4u_B*
Length = 278
Score = 67.5 bits (164), Expect = 2e-15
Identities = 28/63 (44%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 26 LGELSQEDHSDADCLVITVLTHGLGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKIF 85
+ E+S H+DADC V L+HG +++AYD ++ L F DKC +L GKPKIF
Sbjct: 77 IHEVSTVSHADADCFVCVFLSHG-EGNHIYAYDAKIEIQTLTGLFKGDKCHSLVGKPKIF 135
Query: 86 FIQ 88
IQ
Sbjct: 136 IIQ 138
>1m72_A Caspase-1; caspase, cysteine protease, hydrolase-hydrolase
inhibitor CO; 2.30A {Spodoptera frugiperda} SCOP:
c.17.1.1 PDB: 3sip_B
Length = 272
Score = 67.1 bits (163), Expect = 3e-15
Identities = 36/63 (57%), Positives = 45/63 (71%), Gaps = 1/63 (1%)
Query: 26 LGELSQEDHSDADCLVITVLTHGLGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKIF 85
+ + ++ DHSDADCL++ VLTHG L+A D Y + LW FTADKC TLAGKPK+F
Sbjct: 87 IQQTAEMDHSDADCLLVAVLTHG-ELGMLYAKDTHYKPDNLWYYFTADKCPTLAGKPKLF 145
Query: 86 FIQ 88
FIQ
Sbjct: 146 FIQ 148
>2j32_A Caspase-3; Pro-caspase3, thiol protease, hydrolase,
hydrolase-hydrolase inhibitor complex; 1.30A {Homo
sapiens} PDB: 2j30_A 3h0e_A* 2j33_A 3pd1_A 2j31_A 3pcx_A
1nms_A* 1nmq_A* 3deh_A* 3dei_A* 3dej_A* 3dek_A* 3pd0_A
3itn_A 1qx3_A
Length = 250
Score = 65.9 bits (160), Expect = 6e-15
Identities = 24/63 (38%), Positives = 39/63 (61%), Gaps = 1/63 (1%)
Query: 26 LGELSQEDHSDADCLVITVLTHGLGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKIF 85
+ ++S+EDHS V +L+HG E ++ + P ++K+ F D+CR+L GKPK+F
Sbjct: 72 MRDVSKEDHSKRSSFVCVLLSHG-EEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLF 130
Query: 86 FIQ 88
IQ
Sbjct: 131 IIQ 133
>1f1j_A Caspase-7 protease; caspase-7, cysteine protease, hydrolase,
apoptosis, hydrolas hydrolase inhibitor complex; 2.35A
{Homo sapiens} SCOP: c.17.1.1 PDB: 1kmc_A 3r5k_A 1i4o_A
1gqf_A 3h1p_A 1shj_A* 1k86_A 1k88_A 1shl_A*
Length = 305
Score = 64.5 bits (156), Expect = 3e-14
Identities = 28/88 (31%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 1 MKFKLVSQEDHSDADCLVITVLTHGLGELSQEDHSDADCLVITVLTHGLGERYLWAYDMP 60
+ F ++ D S A + L + S+EDH++A C +L+HG E ++ D
Sbjct: 106 LGFDVIVYNDCSCAKMQDL------LKKASEEDHTNAACFACILLSHG-EENVIYGKDGV 158
Query: 61 YFVEKLWLPFTADKCRTLAGKPKIFFIQ 88
++ L F D+ +TL KPK+FFIQ
Sbjct: 159 TPIKDLTAHFRGDRSKTLLEKPKLFFIQ 186
>1nw9_B Caspase 9, apoptosis-related cysteine protease; XIAP, caspase
inhibition, caspase activation, dimerization; 2.40A
{Homo sapiens} SCOP: c.17.1.1 PDB: 1jxq_A* 2ar9_A
Length = 277
Score = 64.0 bits (155), Expect = 4e-14
Identities = 27/70 (38%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 26 LGELSQEDHSDADCLVITVLTHGLGERYLWAYD-------MPYFVEKLWLPFTADKCRTL 78
L EL+++DH DC V+ +L+HG +L P VEK+ F C +L
Sbjct: 77 LLELARQDHGALDCCVVVILSHGCQASHLQFPGAVYGTDGCPVSVEKIVNIFNGTSCPSL 136
Query: 79 AGKPKIFFIQ 88
GKPK+FFIQ
Sbjct: 137 GGKPKLFFIQ 146
>3h11_B Caspase-8; cell death, apoptosis, caspase, alternative splicing,
HOST- virus interaction, polymorphism, cytoplasm,
disease mutation; 1.90A {Homo sapiens} PDB: 2k7z_A
1i4e_B 2fun_B 2c2z_B*
Length = 271
Score = 63.7 bits (154), Expect = 6e-14
Identities = 24/63 (38%), Positives = 32/63 (50%)
Query: 26 LGELSQEDHSDADCLVITVLTHGLGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKIF 85
L DHS+ DC + +L+HG + +L FT KC +LAGKPK+F
Sbjct: 80 LKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKCPSLAGKPKVF 139
Query: 86 FIQ 88
FIQ
Sbjct: 140 FIQ 142
>2h54_A Caspase-1; allosteric site, dimer interface, hydrolase; HET: PHQ;
1.80A {Homo sapiens} PDB: 1rwm_A* 1rwk_A* 1rwo_A*
1rwp_A* 1rwv_A* 1rww_A* 1rwn_A* 2h48_A* 2h4w_A* 1rwx_A*
2hbq_A* 2hby_A* 1ibc_A 3d6m_A* 2h4y_A* 2h51_A* 3d6f_A*
3d6h_A* 2hbz_A* 2hbr_A* ...
Length = 178
Score = 61.2 bits (148), Expect = 2e-13
Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 5/64 (7%)
Query: 30 SQEDHSDADCLVITVLTHG-----LGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKI 84
+ +H +D + ++HG G+++ + ++ C +L KPK+
Sbjct: 101 HRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQLNAIFNMLNTKNCPSLKDKPKV 160
Query: 85 FFIQ 88
IQ
Sbjct: 161 IIIQ 164
>2fp3_A Caspase NC; apoptosis, initiator caspase activation, dimerization,
active site conformation, hydrolysis/apoptosis complex;
2.50A {Drosophila melanogaster}
Length = 316
Score = 60.2 bits (145), Expect = 1e-12
Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 4/63 (6%)
Query: 30 SQEDHSDADCLVITVLTHGLGERY----LWAYDMPYFVEKLWLPFTADKCRTLAGKPKIF 85
S + +C V+ ++THG + ++K+ F KC L KPK+
Sbjct: 120 SSSYVQNTECFVMVLMTHGNSVEGKEKVEFRDGSVVDMQKIKDHFQTAKCPYLVNKPKVL 179
Query: 86 FIQ 88
Sbjct: 180 MFP 182
>3e4c_A Caspase-1; zymogen, inflammasome, ICE, IL-1B, innate immunity,
apoptosis, hydrolase, protease protease; 2.05A {Homo
sapiens}
Length = 302
Score = 58.6 bits (141), Expect = 5e-12
Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 5/64 (7%)
Query: 30 SQEDHSDADCLVITVLTHG-----LGERYLWAYDMPYFVEKLWLPFTADKCRTLAGKPKI 84
+ +H +D + ++HG G+++ + ++ C +L KPK+
Sbjct: 118 HRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQLNAIFNMLNTKNCPSLKDKPKV 177
Query: 85 FFIQ 88
IQ
Sbjct: 178 IIIQ 181
>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 = 25.6 bits (55), Expect = 2.8
Identities = 16/78 (20%), Positives = 27/78 (34%), Gaps = 17/78 (21%)
Query: 1 MKFKLVSQEDHSDADCLVITVLTHGLGELSQEDHSDADCLVITVLTHGLGERYLWAYDMP 60
+ S+ DHS L I + L L + +CL++ L + + +
Sbjct: 209 IDPNWTSRSDHSSNIKLRIHSIQAELRRL-LKSKPYENCLLV--LLN------VQ--N-- 255
Query: 61 YFVEKLWLPFTADKCRTL 78
K W F C+ L
Sbjct: 256 ---AKAWNAFNL-SCKIL 269
>3gdw_A Sigma-54 interaction domain protein; structural genomics, PSI-2,
protein structure initiative, M center for structural
genomics, MCSG; HET: MSE; 2.00A {Enterococcus faecalis}
Length = 139
Score = 23.6 bits (51), Expect = 8.7
Identities = 12/40 (30%), Positives = 15/40 (37%), Gaps = 15/40 (37%)
Query: 35 SDADCLVITVLTHG--------------LGERYLWAYDMP 60
S+A+ V VL HG LG A +MP
Sbjct: 1 SNANVGVF-VLMHGDSTASSMLKTAQELLGTSIGTAMNMP 39
>3ub6_A Chemoreceptor TLPB; homodimer, four-helix bundle, PAS domain,
membrane protein; 1.38A {Helicobacter pylori} PDB:
3ub7_A 3ub8_A 3ub9_A*
Length = 181
Score = 24.0 bits (52), Expect = 8.8
Identities = 3/43 (6%), Positives = 9/43 (20%)
Query: 17 LVITVLTHGLGELSQEDHSDADCLVITVLTHGLGERYLWAYDM 59
++ + + + G Y+ D
Sbjct: 35 ILEQGIHEYYKSFDNDTARKMALDYFKRINDDKGMIYMVVVDK 77
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 0.141 0.451
Gapped
Lambda K H
0.267 0.0520 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,324,213
Number of extensions: 65312
Number of successful extensions: 191
Number of sequences better than 10.0: 1
Number of HSP's gapped: 175
Number of HSP's successfully gapped: 30
Length of query: 88
Length of database: 6,701,793
Length adjustment: 56
Effective length of query: 32
Effective length of database: 5,138,217
Effective search space: 164422944
Effective search space used: 164422944
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 (23.9 bits)