RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13938
(245 letters)
>2nn3_C Caspase-1; cysteine protease, hydrolase; 3.00A {Spodoptera
frugiperda}
Length = 310
Score = 160 bits (405), Expect = 3e-48
Identities = 84/188 (44%), Positives = 114/188 (60%), Gaps = 16/188 (8%)
Query: 8 MPVAKDSAEYNMSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY 67
MPV +++ YNM+H RG A++FNH+ F + ++ R G+ D NL LGF+V+V+
Sbjct: 44 MPVDRNAPYYNMNHKHRGMAIIFNHEHFDIHSLKSRTGTNVDSDNLSKVLKTLGFKVTVF 103
Query: 68 TNPEFREITEILSNLSQEDHSDADCLVITVLTHGLGEQ-----------KLWLPFTADKC 116
N + EI + + ++ DHSDADCL++ VLT G LW FTADKC
Sbjct: 104 PNLKSEEINKFIQQTAEMDHSDADCLLVAVLTAGELGMLYAKDTHYKPDNLWYYFTADKC 163
Query: 117 RTLAGKPKIFFIQACRGTKLDGGVRLVSRANTETDAGVNA-YKIPSYADFLIAYSTVEDS 175
TLAGKPK+FFIQAC+G +LDGG+ L TETD + Y+IP +ADFLIA+STV
Sbjct: 164 PTLAGKPKLFFIQACQGDRLDGGITLSR---TETDGSPSTSYRIPVHADFLIAFSTVPGY 220
Query: 176 LLACRGTK 183
+ R T
Sbjct: 221 -FSWRNTT 227
>3sir_A Caspase; hydrolase; 2.68A {Drosophila melanogaster} PDB: 3sip_A
Length = 259
Score = 159 bits (402), Expect = 3e-48
Identities = 78/184 (42%), Positives = 113/184 (61%), Gaps = 14/184 (7%)
Query: 12 KDSAEYNMSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPE 71
+ +AEYNM H RG AL+FNH+ F++ + R G+ D +NL L FEV+VY +
Sbjct: 8 RHAAEYNMRHKNRGMALIFNHEHFEVPTLKSRAGTNVDCENLTRVLKQLDFEVTVYKDCR 67
Query: 72 FREITEILSNLSQEDHSDADCLVITVLTHGLGE-----------QKLWLPFTADKCRTLA 120
+++I + + ++HSD+DC+++ +L+HG +W FTA+ C +LA
Sbjct: 68 YKDILRTIEYSASQNHSDSDCILVAILSHGEMGYIYAKDTQYKLDNIWSFFTANHCPSLA 127
Query: 121 GKPKIFFIQACRGTKLDGGVRLVSRANTETDA-GVNAYKIPSYADFLIAYSTVEDSLLAC 179
GKPK+FFIQAC+G +LDGGV + R+ TETD +YKIP +ADFLIAYSTV +
Sbjct: 128 GKPKLFFIQACQGDRLDGGV-TMQRSQTETDGDSSMSYKIPVHADFLIAYSTVPGF-YSW 185
Query: 180 RGTK 183
R T
Sbjct: 186 RNTT 189
>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 = 155 bits (393), Expect = 8e-47
Identities = 85/188 (45%), Positives = 115/188 (61%), Gaps = 16/188 (8%)
Query: 8 MPVAKDSAEYNMSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVY 67
MPV +++ YNM+H RG A++FNH+ F + ++ R G+ D NL LGF+V+V+
Sbjct: 16 MPVDRNAPYYNMNHKHRGMAIIFNHEHFDIHSLKSRTGTNVDSDNLSKVLKTLGFKVTVF 75
Query: 68 TNPEFREITEILSNLSQEDHSDADCLVITVLTHGLGE-----------QKLWLPFTADKC 116
N + EI + + ++ DHSDADCL++ VLTHG LW FTADKC
Sbjct: 76 PNLKSEEINKFIQQTAEMDHSDADCLLVAVLTHGELGMLYAKDTHYKPDNLWYYFTADKC 135
Query: 117 RTLAGKPKIFFIQACRGTKLDGGVRLVSRANTETDAGVNA-YKIPSYADFLIAYSTVEDS 175
TLAGKPK+FFIQAC+G +LDGG+ L TETD + Y+IP +ADFLIA+STV
Sbjct: 136 PTLAGKPKLFFIQACQGDRLDGGITLSR---TETDGSPSTSYRIPVHADFLIAFSTVPGY 192
Query: 176 LLACRGTK 183
+ R T
Sbjct: 193 -FSWRNTT 199
>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 = 146 bits (371), Expect = 6e-45
Identities = 50/137 (36%), Positives = 73/137 (53%), Gaps = 12/137 (8%)
Query: 16 EYNMSHPRRGRALVFNHDEF-QMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFRE 74
Y M +P G ++ N+ F + MT R G+ D NL F L +EV + E
Sbjct: 8 SYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREE 67
Query: 75 ITEILSNLSQEDHSDADCLVITVLTHG-----------LGEQKLWLPFTADKCRTLAGKP 123
I E++ ++S+EDHS V +L+HG + +K+ F D+CR+L GKP
Sbjct: 68 IVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKP 127
Query: 124 KIFFIQACRGTKLDGGV 140
K+F IQACRGT+LD G+
Sbjct: 128 KLFIIQACRGTELDCGI 144
>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 = 146 bits (370), Expect = 2e-44
Identities = 49/147 (33%), Positives = 80/147 (54%), Gaps = 12/147 (8%)
Query: 7 PMPVAKDSAEYNMSHPRRGRALVFNHDEF-QMDNMTPRPGSGADVKNLEAAFYALGFEVS 65
+ +YNM+ + G+ ++ N+ F ++ M R G+ D + L F +LGF+V
Sbjct: 27 TTRDRVPTYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVI 86
Query: 66 VYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLGE-----------QKLWLPFTAD 114
VY + ++ ++L S+EDH++A C +L+HG + L F D
Sbjct: 87 VYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGD 146
Query: 115 KCRTLAGKPKIFFIQACRGTKLDGGVR 141
+C+TL KPK+FFIQACRGT+LD G++
Sbjct: 147 RCKTLLEKPKLFFIQACRGTELDDGIQ 173
>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 = 149 bits (378), Expect = 2e-44
Identities = 68/198 (34%), Positives = 94/198 (47%), Gaps = 22/198 (11%)
Query: 7 PMPVAKDSAEYNMSHPRRGRALVFNHDEFQMD-NMTPRPGSGADVKNLEAAFYALGFEVS 65
+ + +Y M H RRG AL+FNH+ F + R G+ AD NL F LGFEV
Sbjct: 4 KREMFDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDLGFEVK 63
Query: 66 VYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLGEQ-----------KLWLPFTAD 114
+ + + E+ + +S H+DADC V L+HG G L F D
Sbjct: 64 CFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTGLFKGD 123
Query: 115 KCRTLAGKPKIFFIQACRGTKLDGGVRLVSRANTETDA---------GVNAYKIPSYADF 165
KC +L GKPKIF IQACRG + D V + + +T+ + Y +P+ ADF
Sbjct: 124 KCHSLVGKPKIFIIQACRGNQHDVPVIPLDVVDNQTEKLDTNITEVDAASVYTLPAGADF 183
Query: 166 LIAYSTVEDSLLACRGTK 183
L+ YS E + R T
Sbjct: 184 LMCYSVAEGY-YSHRETV 200
>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 = 148 bits (375), Expect = 2e-44
Identities = 65/180 (36%), Positives = 91/180 (50%), Gaps = 17/180 (9%)
Query: 16 EYNMSHPRRGRALVFNHDEFQ-MDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFRE 74
Y M +P G ++ N+ F MT R G+ D NL F L +EV + E
Sbjct: 8 SYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREE 67
Query: 75 ITEILSNLSQEDHSDADCLVITVLTHG-----------LGEQKLWLPFTADKCRTLAGKP 123
I E++ ++S+EDHS V +L+HG + +K+ F D+CR+L GKP
Sbjct: 68 IVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKP 127
Query: 124 KIFFIQACRGTKLDGGVRLVSRANTETDAGVNAYKIPSYADFLIAYSTVEDSLLACRGTK 183
K+F IQACRGT+LD G+ S D + +KIP ADFL AYST + R +K
Sbjct: 128 KLFIIQACRGTELDCGIATDS----GVDDDMACHKIPVEADFLYAYSTAPGY-YSWRNSK 182
>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 = 149 bits (377), Expect = 4e-44
Identities = 66/189 (34%), Positives = 97/189 (51%), Gaps = 14/189 (7%)
Query: 7 PMPVAKDSAEYNMSHPRRGRALVFNHDEFQMD-NMTPRPGSGADVKNLEAAFYALGFEVS 65
+ +YNM+ + G+ ++ N+ F M R G+ D + L F +LGF+V
Sbjct: 52 TTRDRVPTYQYNMNFEKLGKCIIINNKNFDKVTGMGVRNGTDKDAEALFKCFRSLGFDVI 111
Query: 66 VYTNPEFREITEILSNLSQEDHSDADCLVITVLTHG-----------LGEQKLWLPFTAD 114
VY + ++ ++L S+EDH++A C +L+HG + L F D
Sbjct: 112 VYNDCSCAKMQDLLKKASEEDHTNAACFACILLSHGEENVIYGKDGVTPIKDLTAHFRGD 171
Query: 115 KCRTLAGKPKIFFIQACRGTKLDGGVRLVSRANTETDAGVNAYKIPSYADFLIAYSTVED 174
+ +TL KPK+FFIQACRGT+LD G++ S +TDA YKIP ADFL AYSTV
Sbjct: 172 RSKTLLEKPKLFFIQACRGTELDDGIQADSGPINDTDANPR-YKIPVEADFLFAYSTVPG 230
Query: 175 SLLACRGTK 183
+ R
Sbjct: 231 Y-YSWRSPG 238
>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 = 148 bits (374), Expect = 8e-44
Identities = 64/191 (33%), Positives = 92/191 (48%), Gaps = 17/191 (8%)
Query: 5 EVPMPVAKDSAEYNMSHPRRGRALVFNHDEFQ-MDNMTPRPGSGADVKNLEAAFYALGFE 63
E Y M +P G ++ N+ F MT R G+ D NL F L +E
Sbjct: 25 ESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYE 84
Query: 64 VSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHG-----------LGEQKLWLPFT 112
V + EI E++ ++S+EDHS V +L+HG + +K+ F
Sbjct: 85 VRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFR 144
Query: 113 ADKCRTLAGKPKIFFIQACRGTKLDGGVRLVSRANTETDAGVNAYKIPSYADFLIAYSTV 172
D+CR+L GKPK+F IQACRGT+LD G+ ++ D + +KIP ADFL A ST
Sbjct: 145 GDRCRSLTGKPKLFIIQACRGTELDCGIET----DSGVDDDMACHKIPVEADFLYACSTA 200
Query: 173 EDSLLACRGTK 183
+ R +K
Sbjct: 201 PGY-YSWRNSK 210
>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 = 142 bits (358), Expect = 7e-43
Identities = 46/148 (31%), Positives = 68/148 (45%), Gaps = 20/148 (13%)
Query: 17 YNMSHPRRGRALVFNHDEF--------QMDNMTPRPGSGADVKNLEAAFYALGFEVSVYT 68
Y M RG L+ N+ F ++ ++ R G+ D L F L FE+ +
Sbjct: 16 YQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHD 75
Query: 69 NPEFREITEILSNLSQEDHSDADCLVITVLTHGLGE------------QKLWLPFTADKC 116
+ +I EIL DHS+ DC + +L+HG +L FT KC
Sbjct: 76 DCTVEQIYEILKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKC 135
Query: 117 RTLAGKPKIFFIQACRGTKLDGGVRLVS 144
+LAGKPK+FFIQAC+G G+ + +
Sbjct: 136 PSLAGKPKVFFIQACQGDNYQKGIPVET 163
>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 = 142 bits (358), Expect = 2e-41
Identities = 53/207 (25%), Positives = 85/207 (41%), Gaps = 41/207 (19%)
Query: 17 YNMSHPRRGRALVFNHDEF-QMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREI 75
Y +S G L+ N+ F + + R GS D + L F +L F V V + +++
Sbjct: 14 YILSMEPCGHCLIINNVNFCRESGLRTRTGSNIDCEKLRRRFSSLHFMVEVKGDLTAKKM 73
Query: 76 TEILSNLSQEDHSDADCLVITVLTHGLGE-------------------QKLWLPFTADKC 116
L L+++DH DC V+ +L+HG +K+ F C
Sbjct: 74 VLALLELARQDHGALDCCVVVILSHGCQASHLQFPGAVYGTDGCPVSVEKIVNIFNGTSC 133
Query: 117 RTLAGKPKIFFIQACRGTKLDGGVRLVSRANTETDAGVNA-------------------- 156
+L GKPK+FFIQAC G + D G + S + + G N
Sbjct: 134 PSLGGKPKLFFIQACGGEQKDHGFEVASTSPEDESPGSNPEPDATPFQEGLRTFDQLDAI 193
Query: 157 YKIPSYADFLIAYSTVEDSLLACRGTK 183
+P+ +D ++YST ++ R K
Sbjct: 194 SSLPTPSDIFVSYSTFPGF-VSWRDPK 219
>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 = 136 bits (343), Expect = 2e-40
Identities = 44/143 (30%), Positives = 66/143 (46%), Gaps = 14/143 (9%)
Query: 12 KDSAEYNMSHPRRGRALVFNHDEFQMD-NMTPRPGSGADVKNLEAAFYALGFEVSVYTNP 70
Y + RG ALV ++ F + + R G D L F LG++V V +
Sbjct: 21 HFQLAYRLQSRPRGLALVLSNVHFTGEKELEFRSGGDVDHSTLVTLFKLLGYDVHVLCDQ 80
Query: 71 EFREITEILSNLSQ-EDHSDADCLVITVLTHGLGE------------QKLWLPFTADKCR 117
+E+ E L N +Q H D ++ +L+HG+ Q+++ F C
Sbjct: 81 TAQEMQEKLQNFAQLPAHRVTDSCIVALLSHGVEGAIYGVDGKLLQLQEVFQLFDNANCP 140
Query: 118 TLAGKPKIFFIQACRGTKLDGGV 140
+L KPK+FFIQACRG + D GV
Sbjct: 141 SLQNKPKMFFIQACRGDETDRGV 163
>3p45_A Caspase-6; protease, huntington'S disease, physio PH, competitive
inhibition, hydrolase; 2.53A {Homo sapiens}
Length = 179
Score = 136 bits (343), Expect = 2e-40
Identities = 58/151 (38%), Positives = 75/151 (49%), Gaps = 12/151 (7%)
Query: 2 EDIEVPMPVAKDSAEYNMSHPRRGRALVFNHDEFQMD-NMTPRPGSGADVKNLEAAFYAL 60
D + + +Y M H RRG AL+FNH+ F + R G+ AD NL F L
Sbjct: 22 TDAFYKREMFDPAEKYKMDHRRRGIALIFNHERFFWHLTLPERRGTCADRDNLTRRFSDL 81
Query: 61 GFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITVLTHGLGE-----------QKLWL 109
GFEV + + + E+ + +S H+DADC V L+HG G Q L
Sbjct: 82 GFEVKCFNDLKAEELLLKIHEVSTVSHADADCFVCVFLSHGEGNHIYAYDAKIEIQTLTG 141
Query: 110 PFTADKCRTLAGKPKIFFIQACRGTKLDGGV 140
F DKC +L GKPKIF IQACRG + D V
Sbjct: 142 LFKGDKCHSLVGKPKIFIIQACRGNQHDVPV 172
>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 = 135 bits (342), Expect = 4e-39
Identities = 40/197 (20%), Positives = 69/197 (35%), Gaps = 35/197 (17%)
Query: 1 MEDIEVPMPVAKDSAEYNMSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYAL 60
+++ E +P + Y M G L+ + + + L F +L
Sbjct: 20 IQESEAFLPQSIPEERYKMKSKPLGICLIIDCIGN-------------ETELLRDTFTSL 66
Query: 61 GFEVSVYTNPEFREITEILSNLS-QEDHSDADCLVITVLTHGLGE--------------Q 105
G+EV + + I++IL + +H D D V +++ G +
Sbjct: 67 GYEVQKFLHLSMHGISQILGQFACMPEHRDYDSFVCVLVSRGGSQSVYGVDQTHSGLPLH 126
Query: 106 KLWLPFTADKCRTLAGKPKIFFIQAC---RGTKLDGGVRLV----SRANTETDAGVNAYK 158
+ F D C LAGKPK+FFIQ G + + V +
Sbjct: 127 HIRRMFMGDSCPYLAGKPKMFFIQNYVVSEGQLENSSLLEVDGPAMKNVEFKAQKRGLCT 186
Query: 159 IPSYADFLIAYSTVEDS 175
+ ADF + T + S
Sbjct: 187 VHREADFFWSLCTADMS 203
>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 = 135 bits (340), Expect = 7e-39
Identities = 54/183 (29%), Positives = 81/183 (44%), Gaps = 25/183 (13%)
Query: 17 YNMSHPRRGRALVFNHDEF--------QMDNMTPRPGSGADVKNLEAAFYALGFEVSVYT 68
Y M RG L+ N+ F ++ ++ R G+ D L F L FE+ +
Sbjct: 10 YQMKSKPRGYCLIINNHNFAKAREKVPKLHSIRDRNGTHLDAGALTTTFEELHFEIKPHD 69
Query: 69 NPEFREITEILSNLSQEDHSDADCLVITVLTHG------------LGEQKLWLPFTADKC 116
+ +I EIL DHS+ DC + +L+HG +L FT KC
Sbjct: 70 DCTVEQIYEILKIYQLMDHSNMDCFICCILSHGDKGIIYGTDGQEAPIYELTSQFTGLKC 129
Query: 117 RTLAGKPKIFFIQACRGTKLDGGVRLVSRANT-----ETDAGVNAYKIPSYADFLIAYST 171
+LAGKPK+FFIQAC+G G+ + + + + IP ADFL+ +T
Sbjct: 130 PSLAGKPKVFFIQACQGDNYQKGIPVETASEEQPYLEMALSSPQTRYIPDEADFLLGMAT 189
Query: 172 VED 174
V +
Sbjct: 190 VNN 192
>3e4c_A Caspase-1; zymogen, inflammasome, ICE, IL-1B, innate immunity,
apoptosis, hydrolase, protease protease; 2.05A {Homo
sapiens}
Length = 302
Score = 135 bits (340), Expect = 2e-38
Identities = 42/204 (20%), Positives = 72/204 (35%), Gaps = 31/204 (15%)
Query: 8 MPVAKDSAEYNMSH--PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVS 65
+ K + Y + R AL+ ++EF D++ R G+ D+ + LG+ V
Sbjct: 42 IWKQKSAEIYPIMDKSSRTRLALIICNEEF--DSIPRRTGAEVDITGMTMLLQNLGYSVD 99
Query: 66 VYTNPEFREITEILSNLSQE-DHSDADCLVITVLTHGLGE-----------------QKL 107
V N ++T L + +H +D + ++HG+ E +
Sbjct: 100 VKKNLTASDMTTELEAFAHRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQLNAI 159
Query: 108 WLPFTADKCRTLAGKPKIFFIQACRGTKLDGGVRLVSRA--------NTETDAGVNAYKI 159
+ C +L KPK+ IQA RG S TE K
Sbjct: 160 FNMLNTKNCPSLKDKPKVIIIQAARGDSPGVVWFKDSVGVSGNLSLPTTEEFEDDAIKKA 219
Query: 160 PSYADFLIAYSTVEDSLLACRGTK 183
DF+ S+ D+ ++ R
Sbjct: 220 HIEKDFIAFCSSTPDN-VSWRHPT 242
>2fp3_A Caspase NC; apoptosis, initiator caspase activation, dimerization,
active site conformation, hydrolysis/apoptosis complex;
2.50A {Drosophila melanogaster}
Length = 316
Score = 134 bits (337), Expect = 5e-38
Identities = 44/205 (21%), Positives = 70/205 (34%), Gaps = 35/205 (17%)
Query: 12 KDSAEYNMSH-PRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALGFEVSVYTNP 70
Y M RG L+ N ++ D R G+ D K+L F L F + Y N
Sbjct: 48 AILGTYKMQSRFNRGVLLMVNIMDYP-DQNRRRIGAEKDSKSLIHLFQELNFTIFPYGNV 106
Query: 71 EFREITEILSNLSQEDH-SDADCLVITVLTHG----------------LGEQKLWLPFTA 113
+ ++L+ ++ + + +C V+ ++THG + QK+ F
Sbjct: 107 NQDQFFKLLTMVTSSSYVQNTECFVMVLMTHGNSVEGKEKVEFRDGSVVDMQKIKDHFQT 166
Query: 114 DKCRTLAGKPKIFFIQACRGTKLDGGVRLVSRANTETDAGVNA---------------YK 158
KC L KPK+ RG + D G E
Sbjct: 167 AKCPYLVNKPKVLMFPFARGDEYDLGHPKNQGNLMEPVYTAQEEKWPDTQTEGIPSPSTN 226
Query: 159 IPSYADFLIAYSTVEDSLLACRGTK 183
+PS AD L+ Y+ + R
Sbjct: 227 VPSLADTLVCYANTPGY-VTHRDLD 250
>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 = 125 bits (314), Expect = 4e-36
Identities = 33/156 (21%), Positives = 58/156 (37%), Gaps = 20/156 (12%)
Query: 2 EDIEVPMPVAKDSAEYNMSHPRRGRALVFNHDEFQMDNMTPRPGSGADVKNLEAAFYALG 61
E + + + R AL+ ++EF D++ R G+ D+ + LG
Sbjct: 21 EAQRIWKQKSAEIYPIMDKSSRTRLALIICNEEF--DSIPRRTGAEVDITGMTMLLQNLG 78
Query: 62 FEVSVYTNPEFREITEILSNLSQE-DHSDADCLVITVLTHGLGE---------------- 104
+ V V N ++T L + +H +D + ++HG+ E
Sbjct: 79 YSVDVKKNLTASDMTTELEAFAHRPEHKTSDSTFLVFMSHGIREGICGKKHSEQVPDILQ 138
Query: 105 -QKLWLPFTADKCRTLAGKPKIFFIQACRGTKLDGG 139
++ C +L KPK+ IQACRG
Sbjct: 139 LNAIFNMLNTKNCPSLKDKPKVIIIQACRGDSPGVV 174
>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 = 49.7 bits (118), Expect = 4e-07
Identities = 47/246 (19%), Positives = 67/246 (27%), Gaps = 87/246 (35%)
Query: 41 TPRPGSGA---DVKNLEAAFYAL--G-------FE--VSVYTNPE------FREITEILS 80
+ + A V A A+ G FE +Y + E LS
Sbjct: 137 FDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLS 196
Query: 81 NLSQEDHSDADCLVITVLTHGLGEQKLWL--PFTADKCRTLAGK----PKIFFIQ----- 129
L DA+ V T GL WL P L P I IQ
Sbjct: 197 ELI-RTTLDAE----KVFTQGL-NILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYV 250
Query: 130 -ACRGTKLD-GGVR-----------------LVSRANTETDAGVNAYKIPSYADFLI--- 167
+ G +R ++ ++ V+ K + F I
Sbjct: 251 VTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVL-FFIGVR 309
Query: 168 ---AY-------STVEDSL----------LACRGTKLDGGVRLVSRANTETDAG------ 201
AY S +EDSL L+ + V++ N+ AG
Sbjct: 310 CYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEIS 369
Query: 202 -VNAYK 206
VN K
Sbjct: 370 LVNGAK 375
Score = 43.9 bits (103), Expect = 3e-05
Identities = 43/234 (18%), Positives = 74/234 (31%), Gaps = 75/234 (32%)
Query: 9 PVAK---DSAEYNMSHPRRGRALVFNHDEFQMDN---MTPRPGSGADVKNLEAAFYALGF 62
A+ + A+ +H + F+ + ++N +T G G K + + A+ F
Sbjct: 1640 KAAQDVWNRAD---NHFKD--TYGFSILDIVINNPVNLTIHFG-GEKGKRIRENYSAMIF 1693
Query: 63 EV----SVYTNPEFREITEILSNLSQEDHSDADCLVITVLT------------------- 99
E + T F+EI E ++ + S+ L T T
Sbjct: 1694 ETIVDGKLKTEKIFKEINEHSTSYTFR--SEKGLLSATQFTQPALTLMEKAAFEDLKSKG 1751
Query: 100 ----------HGLGEQKLWLPFTADKCRTLAGKPKIFFIQACRGTKLDGGVRLVS-RANT 148
H LGE + A LA + I++ V +V R T
Sbjct: 1752 LIPADATFAGHSLGE------YAA-----LASLADVMSIES--------LVEVVFYRGMT 1792
Query: 149 ETDA------GVNAYKIPSYADFLIAYSTVEDSLLA-CRGTKLDGGVRLVSRAN 195
A G + Y + + +A S +++L G LV N
Sbjct: 1793 MQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTG-WLVEIVN 1845
>3uoa_B Mucosa-associated lymphoid tissue lymphoma transl protein 1;
paracaspase, lymphoma, NF-KB signalling, caspase fold,
immun fold, hydrolase-hydrolase inhibitor complex; 1.75A
{Homo sapiens} PDB: 3uo8_B 3v55_A 3v4l_A* 3v4o_A*
Length = 390
Score = 43.7 bits (102), Expect = 3e-05
Identities = 20/152 (13%), Positives = 37/152 (24%), Gaps = 31/152 (20%)
Query: 38 DNMTPRPGSGADVKNLEAAFYALGFEVSVYTNPEFREITEILSNLSQEDHSDADCLVITV 97
DV L L F+V + E+ + ++
Sbjct: 17 REHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLL-LDKGVYGLLYY 75
Query: 98 LTHGL--GEQKLWLPFTA----------------DKCRTLAGKPKIFFIQACRGTKLDGG 139
HG +P A + +F + CR
Sbjct: 76 AGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRK------ 129
Query: 140 VRLVSRANTETDAGVNAYKIPSYADFLIAYST 171
+T ++A K+ A+ + Y+T
Sbjct: 130 ----RNDYDDTIPILDALKVT--ANIVFGYAT 155
>2xzd_B Caspase-3; hydrolase-protein binding complex, de novo protein,
apoptosi ankyrin repeat protein, ribosome display; 2.10A
{Homo sapiens} PDB: 2xzt_B 2y0b_B
Length = 118
Score = 41.4 bits (97), Expect = 3e-05
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 196 TETDAGVNAYKIPSYADFLIAYSTVEDCKLC 226
+ D + +KIP ADFL AYST
Sbjct: 1 SGVDDDMACHKIPVEADFLYAYSTAPGYYSW 31
Score = 40.7 bits (95), Expect = 5e-05
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 148 TETDAGVNAYKIPSYADFLIAYSTVED 174
+ D + +KIP ADFL AYST
Sbjct: 1 SGVDDDMACHKIPVEADFLYAYSTAPG 27
>2dko_B Caspase-3; low barrier hydrogen bond, caspase, drug design,
radiation D tetrahedral intermediate, protease; 1.06A
{Homo sapiens} PDB: 2c2k_B* 2c2m_B* 2c2o_B* 2c1e_B*
2cdr_B* 2cnk_B* 2cnl_B* 2cnn_B* 2cno_B* 2cjy_B 1pau_B
1re1_B* 1rhk_B* 1rhm_B* 1rhq_B* 1rhr_B* 1rhu_B* 1rhj_B*
1i3o_B* 3edq_B ...
Length = 103
Score = 40.6 bits (95), Expect = 4e-05
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 196 TETDAGVNAYKIPSYADFLIAYSTVEDCKLC 226
+ D + +KIP ADFL AYST
Sbjct: 2 SGVDDDMACHKIPVEADFLYAYSTAPGYYSW 32
Score = 40.2 bits (94), Expect = 6e-05
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 148 TETDAGVNAYKIPSYADFLIAYSTVED 174
+ D + +KIP ADFL AYST
Sbjct: 2 SGVDDDMACHKIPVEADFLYAYSTAPG 28
>2ql9_B Caspase-7; cysteine protease, apoptosis, thiol protease, zymogen,
hydro hydrolase inhibitor complex; HET: CIT; 2.14A {Homo
sapiens} PDB: 2ql7_B* 2ql5_B* 2qlb_B* 2qlf_B 2qlj_B*
3edr_B 3ibc_B 3ibf_B 1i51_B
Length = 97
Score = 37.9 bits (88), Expect = 4e-04
Identities = 13/19 (68%), Positives = 13/19 (68%)
Query: 205 YKIPSYADFLIAYSTVEDC 223
YKIP ADFL AYSTV
Sbjct: 5 YKIPVEADFLFAYSTVPGY 23
Score = 37.5 bits (87), Expect = 5e-04
Identities = 13/18 (72%), Positives = 13/18 (72%)
Query: 157 YKIPSYADFLIAYSTVED 174
YKIP ADFL AYSTV
Sbjct: 5 YKIPVEADFLFAYSTVPG 22
>1qtn_B Caspase-8; apoptosis, dithiane-DIOL, caspase, cysteine-protease,
hydrol hydrolase inhibitor complex; 1.20A {Homo sapiens}
SCOP: c.17.1.1 PDB: 3kjn_B* 3kjq_B* 2y1l_B 1f9e_B*
1qdu_B*
Length = 95
Score = 37.4 bits (87), Expect = 5e-04
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 157 YKIPSYADFLIAYSTVEDSLLACRGTK 183
IP ADFL+ +TV + ++ R
Sbjct: 7 RYIPDEADFLLGMATVNNC-VSYRNPA 32
Score = 37.1 bits (86), Expect = 6e-04
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 205 YKIPSYADFLIAYSTVEDCK 224
IP ADFL+ +TV +C
Sbjct: 7 RYIPDEADFLLGMATVNNCV 26
>1pyo_B Caspase-2; apoptosis, caspase, alpha-beta, thiol protease,
hydrolase-HY inhibitor complex; 1.65A {Homo sapiens}
SCOP: c.17.1.1 PDB: 2p2c_B 3r5j_B 3r6g_B 3r7b_B 3r7n_B
3r7s_B 3r6l_B
Length = 105
Score = 37.1 bits (86), Expect = 6e-04
Identities = 5/31 (16%), Positives = 13/31 (41%), Gaps = 3/31 (9%)
Query: 194 ANTETDAGVNAYKIPSYADFLIAYSTVEDCK 224
A E ++P+ +D + Y+ ++
Sbjct: 1 AGKEKLP---KMRLPTRSDMICGYACLKGTA 28
Score = 36.3 bits (84), Expect = 0.001
Identities = 5/29 (17%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 146 ANTETDAGVNAYKIPSYADFLIAYSTVED 174
A E ++P+ +D + Y+ ++
Sbjct: 1 AGKEKLP---KMRLPTRSDMICGYACLKG 26
>3rjm_B Caspase-2; caspase-2, caspase, hydrolase-hydrolase inhibitor; HET:
3PX; 2.55A {Homo sapiens}
Length = 117
Score = 37.2 bits (86), Expect = 8e-04
Identities = 3/28 (10%), Positives = 12/28 (42%)
Query: 197 ETDAGVNAYKIPSYADFLIAYSTVEDCK 224
+ ++P+ +D + Y+ ++
Sbjct: 2 AGKEKLPKMRLPTRSDMICGYACLKGTA 29
Score = 36.8 bits (85), Expect = 0.001
Identities = 7/35 (20%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 149 ETDAGVNAYKIPSYADFLIAYSTVEDSLLACRGTK 183
+ ++P+ +D + Y+ ++ + A R TK
Sbjct: 2 AGKEKLPKMRLPTRSDMICGYACLKGT-AAMRNTK 35
>1sc3_B Interleukin-1 beta convertase; malonate-bound caspase-1, hydrolase;
1.80A {Homo sapiens} SCOP: c.17.1.1 PDB: 1ice_B 1bmq_B*
1rwm_B* 1rwk_B* 1rwo_B* 1rwp_B* 1rwv_B* 1rww_B* 1rwn_B*
1sc1_B 1rwx_B 1sc4_B 2h4y_B* 2hbq_B* 2hbr_B* 3ns7_B*
3d6f_B* 3d6h_B* 3d6m_B* 2h4w_B* ...
Length = 88
Score = 34.6 bits (80), Expect = 0.004
Identities = 5/18 (27%), Positives = 7/18 (38%)
Query: 157 YKIPSYADFLIAYSTVED 174
K DF+ S+ D
Sbjct: 3 KKAHIEKDFIAFCSSTPD 20
Score = 34.6 bits (80), Expect = 0.004
Identities = 5/18 (27%), Positives = 7/18 (38%)
Query: 205 YKIPSYADFLIAYSTVED 222
K DF+ S+ D
Sbjct: 3 KKAHIEKDFIAFCSSTPD 20
>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast
structural genomics consortium (NESG), target HR3102A,
PSI-2; NMR {Homo sapiens}
Length = 86
Score = 26.7 bits (60), Expect = 2.4
Identities = 10/17 (58%), Positives = 12/17 (70%), Gaps = 2/17 (11%)
Query: 46 SGADVKNL--EAAFYAL 60
SGA+VK + EA YAL
Sbjct: 46 SGAEVKGVCTEAGMYAL 62
>2we8_A Xanthine dehydrogenase; oxidoreductase; 2.30A {Mycobacterium
smegmatis} PDB: 2we7_A
Length = 386
Score = 28.3 bits (63), Expect = 2.5
Identities = 15/72 (20%), Positives = 25/72 (34%), Gaps = 16/72 (22%)
Query: 45 GSGADVKNLEAAFYALGFEVSV------YTNPE-FREITEI--------LSNLSQEDHSD 89
G+ + LG+ V+V + F E+ L+ ++ D
Sbjct: 211 GAIDFAAAVAQQGAFLGYRVTVCDARPVFATTARFPTADEVVVDWPHRYLAAQAEAGAID 270
Query: 90 ADCLVITVLTHG 101
A +V VLTH
Sbjct: 271 ARTVVC-VLTHD 281
>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium, NESG; 2.10A {Homo sapiens}
Length = 78
Score = 26.3 bits (59), Expect = 2.6
Identities = 10/17 (58%), Positives = 12/17 (70%), Gaps = 2/17 (11%)
Query: 46 SGADVKNL--EAAFYAL 60
SGA+VK + EA YAL
Sbjct: 38 SGAEVKGVCTEAGMYAL 54
>3prn_A Porin; integral membrane protein, pore eyelet mutant, membra
protein; HET: C8E; 1.90A {Rhodobacter blasticus} SCOP:
f.4.3.1 PDB: 1bh3_A* 1prn_A* 7prn_A* 6prn_A* 5prn_A*
2prn_A* 8prn_A* 1h6s_1
Length = 289
Score = 26.3 bits (57), Expect = 9.6
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 158 KIPSYADFLIAYSTVEDSLLACRGTKLDGGVRLVSRANTETDAGV 202
+ Y F + Y ED + T + +R+ TETD GV
Sbjct: 3 SLNGYGRFGLQYV--EDRGVGLEDTIISSRLRINIVGTTETDQGV 45
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
0.319 0.136 0.403
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: 3,687,369
Number of extensions: 212267
Number of successful extensions: 508
Number of sequences better than 10.0: 1
Number of HSP's gapped: 463
Number of HSP's successfully gapped: 55
Length of query: 245
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 154
Effective length of database: 4,160,982
Effective search space: 640791228
Effective search space used: 640791228
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 (21.7 bits)
S2: 56 (25.8 bits)