RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13939
(86 letters)
>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 = 70.6 bits (173), Expect = 5e-18
Identities = 28/61 (45%), Positives = 40/61 (65%), Gaps = 1/61 (1%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
+YSWR P G+WF+Q LC L + G L+++ I+TRV+ RVA ES +D H++KQ
Sbjct: 23 YYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSD-DPHFHEKKQ 81
Query: 86 I 86
I
Sbjct: 82 I 82
>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 = 69.6 bits (170), Expect = 2e-17
Identities = 27/61 (44%), Positives = 42/61 (68%), Gaps = 1/61 (1%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
+YSWR+ ++G+WFIQ LC L KL+ + I+TRV+R+VA + ES++ + H +KQ
Sbjct: 28 YYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSF-DATFHAKKQ 86
Query: 86 I 86
I
Sbjct: 87 I 87
>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 = 68.0 bits (166), Expect = 6e-17
Identities = 27/61 (44%), Positives = 42/61 (68%), Gaps = 1/61 (1%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
+YSWR+ ++G+WFIQ LC L KL+ + I+TRV+R+VA + ES++ + H +KQ
Sbjct: 29 YYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSF-DATFHAKKQ 87
Query: 86 I 86
I
Sbjct: 88 I 88
>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 = 67.2 bits (164), Expect = 2e-16
Identities = 12/61 (19%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
+ R+ + G+W+I+ L Q ++ + + ++ +V+ + D E Y + H+ K+
Sbjct: 27 TAAMRNTKRGSWYIEALAQVFSERACDMHVADMLVKVNALIK-DREGYAP-GTEFHRCKE 84
Query: 86 I 86
+
Sbjct: 85 M 85
>3rjm_B Caspase-2; caspase-2, caspase, hydrolase-hydrolase inhibitor;
HET: 3PX; 2.55A {Homo sapiens}
Length = 117
Score = 66.1 bits (161), Expect = 5e-16
Identities = 12/61 (19%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
+ R+ + G+W+I+ L Q ++ + + ++ +V+ + D E Y + H+ K+
Sbjct: 28 TAAMRNTKRGSWYIEALAQVFSERACDMHVADMLVKVNALIK-DREGYAP-GTEFHRCKE 85
Query: 86 I 86
+
Sbjct: 86 M 86
>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 = 63.6 bits (155), Expect = 2e-15
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 8/62 (12%)
Query: 26 FYSWRHPENGTWFIQCLCQELAD-SGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQK 84
S+R+P GTW+IQ LCQ L + D+L+I+T V+ V+ + + K
Sbjct: 25 CVSYRNPAEGTWYIQSLCQSLRERCPRGDDILTILTEVNYEVSNKDDKK-------NMGK 77
Query: 85 QI 86
Q+
Sbjct: 78 QM 79
>3sir_A Caspase; hydrolase; 2.68A {Drosophila melanogaster} PDB: 3sip_A
Length = 259
Score = 67.1 bits (163), Expect = 2e-15
Identities = 32/61 (52%), Positives = 43/61 (70%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
FYSWR+ G+WF+Q LC ELA +G +LD+L+++T V +RVA+D ES HQQKQ
Sbjct: 182 FYSWRNTTRGSWFMQSLCAELAANGKRLDILTLLTFVCQRVAVDFESCTPDTPEMHQQKQ 241
Query: 86 I 86
I
Sbjct: 242 I 242
>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 = 67.5 bits (164), Expect = 2e-15
Identities = 28/61 (45%), Positives = 44/61 (72%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
++SWR+ G+WF+Q LC+EL +GT+ D+L+++T V ++VALD ES + HQQKQ
Sbjct: 192 YFSWRNTTRGSWFMQALCEELRYAGTERDILTLLTFVCQKVALDFESNAPDSAMMHQQKQ 251
Query: 86 I 86
+
Sbjct: 252 V 252
>2nn3_C Caspase-1; cysteine protease, hydrolase; 3.00A {Spodoptera
frugiperda}
Length = 310
Score = 67.1 bits (163), Expect = 3e-15
Identities = 28/61 (45%), Positives = 44/61 (72%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
++SWR+ G+WF+Q LC+EL +GT+ D+L+++T V ++VALD ES + HQQKQ
Sbjct: 220 YFSWRNTTRGSWFMQALCEELRYAGTERDILTLLTFVCQKVALDFESNAPDSAMMHQQKQ 279
Query: 86 I 86
+
Sbjct: 280 V 280
>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 = 61.6 bits (150), Expect = 1e-14
Identities = 12/41 (29%), Positives = 18/41 (43%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRV 66
SWRHP G+ FI L + + + D+ I +V
Sbjct: 21 NVSWRHPTMGSVFIGRLIEHMQEYACSCDVEEIFRKVRFSF 61
>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 = 63.2 bits (153), Expect = 7e-14
Identities = 27/61 (44%), Positives = 42/61 (68%), Gaps = 1/61 (1%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
+YSWR+ ++G+WFIQ LC L KL+ + I+TRV+R+VA + ES++ + H +KQ
Sbjct: 203 YYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSF-DATFHAKKQ 261
Query: 86 I 86
I
Sbjct: 262 I 262
>3e4c_A Caspase-1; zymogen, inflammasome, ICE, IL-1B, innate immunity,
apoptosis, hydrolase, protease protease; 2.05A {Homo
sapiens}
Length = 302
Score = 62.8 bits (152), Expect = 1e-13
Identities = 12/42 (28%), Positives = 18/42 (42%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVA 67
SWRHP G+ FI L + + + D+ I +V
Sbjct: 235 NVSWRHPTMGSVFIGRLIEHMQEYACSCDVEEIFRKVRFSFE 276
>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 = 61.8 bits (149), Expect = 3e-13
Identities = 28/61 (45%), Positives = 40/61 (65%), Gaps = 1/61 (1%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
+YSWR P G+WF+Q LC L + G L+++ I+TRV+ RVA ES +D H++KQ
Sbjct: 231 YYSWRSPGRGSWFVQALCSILEEHGKDLEIMQILTRVNDRVARHFESQSD-DPHFHEKKQ 289
Query: 86 I 86
I
Sbjct: 290 I 290
>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 = 60.8 bits (147), Expect = 5e-13
Identities = 27/61 (44%), Positives = 42/61 (68%), Gaps = 1/61 (1%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
+YSWR+ ++G+WFIQ LC L KL+ + I+TRV+R+VA + ES++ + H +KQ
Sbjct: 175 YYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSF-DATFHAKKQ 233
Query: 86 I 86
I
Sbjct: 234 I 234
>2fp3_A Caspase NC; apoptosis, initiator caspase activation, dimerization,
active site conformation, hydrolysis/apoptosis complex;
2.50A {Drosophila melanogaster}
Length = 316
Score = 60.6 bits (146), Expect = 1e-12
Identities = 14/49 (28%), Positives = 22/49 (44%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYN 74
+ + R + G+W+IQ CQ +AD DL I+ + S V
Sbjct: 243 YVTHRDLDTGSWYIQKFCQVMADHAHDTDLEDILKKTSEAVGNKRTKKG 291
>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 = 60.2 bits (145), Expect = 1e-12
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
+YS R NG+W+IQ LC+ L G+ L+ ++T V+R+V+ + S +KQ
Sbjct: 193 YYSHRETVNGSWYIQDLCEMLGKYGSSLEFTELLTLVNRKVSQRRVDFCKDPS-AIGKKQ 251
Query: 86 I 86
+
Sbjct: 252 V 252
>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 = 57.0 bits (137), Expect = 1e-11
Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 7/61 (11%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
+ + + ++QCL Q+L + LL + ++ + D S ++K
Sbjct: 203 SLLEQSHSSPSLYLQCLSQKLRQERKR-PLLDLHIELNGYMY-DWNSRVS-----AKEKY 255
Query: 86 I 86
Sbjct: 256 Y 256
>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 = 56.7 bits (136), Expect = 2e-11
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 11/61 (18%)
Query: 26 FYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQKQ 85
F SWR P++G+W+++ L DL S++ RV+ V++ KQ
Sbjct: 212 FVSWRDPKSGSWYVETLDDIFEQWAHSEDLQSLLLRVANAVSVK-----------GIYKQ 260
Query: 86 I 86
+
Sbjct: 261 M 261
>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 = 50.9 bits (121), Expect = 2e-09
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 8/62 (12%)
Query: 26 FYSWRHPENGTWFIQCLCQELAD-SGTKLDLLSIMTRVSRRVALDMESYNDLLSWQHQQK 84
S+R+P GTW+IQ LCQ L + D+L+I+T V+ V+ + + K
Sbjct: 193 CVSYRNPAEGTWYIQSLCQSLRERCPRGDDILTILTEVNYEVSNKDDKK-------NMGK 245
Query: 85 QI 86
Q+
Sbjct: 246 QM 247
>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 = 0.55
Identities = 7/30 (23%), Positives = 14/30 (46%), Gaps = 6/30 (20%)
Query: 14 FDEEDDDDVFVSFYSWRHPE---NGTWFIQ 40
F E ++ + Y++R + + T F Q
Sbjct: 1707 FKEINEH---STSYTFRSEKGLLSATQFTQ 1733
>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP
regulatory protein, structural genomi 2, protein
structure initiative; 2.20A {Ruegeria pomeroyi} PDB:
3h3z_A*
Length = 237
Score = 25.3 bits (56), Expect = 2.4
Identities = 10/38 (26%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 30 RHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVA 67
R PE + L +L+ L T ++RVA
Sbjct: 123 RDPEICISILATTFGHLHSLVAQLEQLKAQT-GAQRVA 159
>3apo_A DNAJ homolog subfamily C member 10; PDI family, thioredoxin,
endoplasmic reticulum, oxidoreducta; 2.40A {Mus
musculus}
Length = 780
Score = 25.5 bits (55), Expect = 2.7
Identities = 7/35 (20%), Positives = 11/35 (31%), Gaps = 11/35 (31%)
Query: 14 FDEEDDDDVFVSFYS-WRHPENGTWFIQCLCQELA 47
F D + V F++ W P + L
Sbjct: 450 FPASDKEPWLVDFFAPWSPP----------SRALL 474
>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity,
CRP, CLP, C-DI-GMP receptor, quorum SENS binding,
transcription; 2.30A {Xanthomonas campestris PV}
Length = 230
Score = 25.0 bits (55), Expect = 3.3
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 20 DDVFVSFYSWRHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVA 67
+F + S P L + L D+ K L+ + V+ R+
Sbjct: 119 QQLFQTSLSPDAPRILYAIGVQLSKRLLDTTRKASRLAFLD-VTDRIV 165
>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix,
transcription factor, CAMP-B proteins, CAMP receptor
protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP:
a.4.5.4 b.82.3.2
Length = 207
Score = 24.9 bits (55), Expect = 3.8
Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 30 RHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVA 67
+ E + L + K+ L+ + V+ RVA
Sbjct: 106 QDSEILYTLGSQMADRLRKTTRKVGDLAFLD-VTGRVA 142
>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix,
homodimer, transcription regulator; 3.60A {Pseudomonas
aeruginosa}
Length = 227
Score = 24.9 bits (55), Expect = 4.0
Identities = 6/38 (15%), Positives = 13/38 (34%), Gaps = 1/38 (2%)
Query: 30 RHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVA 67
+ + L L +++ LS+ + RV
Sbjct: 122 DNTPLALALLAKLSTRLHQRIDEIETLSLKN-ATHRVV 158
>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics,
porphyromona gingivalis, PSI, protein structure
initiative; 1.90A {Porphyromonas gingivalis} SCOP:
a.4.5.4 b.82.3.2
Length = 232
Score = 24.5 bits (54), Expect = 4.2
Identities = 8/38 (21%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 30 RHPENGTWFIQCLCQELADSGTKLDLLSIMTRVSRRVA 67
+ +F++ L +EL + + L+ V R+A
Sbjct: 122 GNTSFCRYFLKALAKELGYAERRTVTLTQKH-VRGRLA 158
>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 = 24.4 bits (52), Expect = 5.6
Identities = 18/118 (15%), Positives = 38/118 (32%), Gaps = 35/118 (29%)
Query: 4 DYELSKMYYK---------------FDEEDDDDVFVSFYSWR---------HPENGTWFI 39
D+E + Y+ FD +D D+ S S +GT +
Sbjct: 8 DFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRL 67
Query: 40 -QCLC-------QELADSGTKLD---LLSIMTRVSRRVALDMESYNDLLSWQHQQKQI 86
L Q+ + +++ L+S + R+ ++ Y + + Q+
Sbjct: 68 FWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125
>1oah_A Cytochrome C nitrite reductase; nitrogen cycle, respiratory nitrite
ammonification; HET: HEM; 2.3A {Desulfovibrio
desulfuricans} SCOP: a.138.1.3
Length = 519
Score = 24.2 bits (51), Expect = 9.1
Identities = 5/31 (16%), Positives = 10/31 (32%)
Query: 6 ELSKMYYKFDEEDDDDVFVSFYSWRHPENGT 36
++ + Y + D F W H +
Sbjct: 262 DMYQYYKGHGAKGPDGKPGPFVDWVHAASKV 292
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 0.134 0.422
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: 1,407,154
Number of extensions: 68421
Number of successful extensions: 222
Number of sequences better than 10.0: 1
Number of HSP's gapped: 219
Number of HSP's successfully gapped: 36
Length of query: 86
Length of database: 6,701,793
Length adjustment: 54
Effective length of query: 32
Effective length of database: 5,194,059
Effective search space: 166209888
Effective search space used: 166209888
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: 51 (23.9 bits)