The Burnham Institute
Version 3 Proteins from 2002-10-01
A bioinformatics resource for apoptosis researchers
About
Domains
Proteins
Structures
BLAST

Database Version Information (and sources)

Database Version 3
NCBI "nr" database 2002-10-01 (date current nr database was downloaded from NCBI)
FPS compilation date 2002-12-16 Date that all proteins were sorted into FPS based categories
Pfam database version 7.7 Used to calculate domains on 2753 proteins
Pfscan database version 17.27 Used to calculate domains on 1941 proteins

Statistics over whole Database

Count Statistic
3138 Proteins in the database
970 SwissProt proteins in the database
89 Unigene proteins in the database
1292 NCBI RefSeq proteins in the database
336 Total Species represented in the database

Top 12 Species represented in the DB

Proteins Species ID Organism Name
688 9606 Homo sapiens
443 10090 Mus musculus
411 3702 Arabidopsis thaliana
202 6239 Caenorhabditis elegans
155 7227 Drosophila melanogaster
129 10116 Rattus norvegicus
82 180454 Anopheles gambiae str.
70 39947 Oryza sativa (japonica
60 9031 Gallus gallus
40 7955 Danio rerio
38 4006 Linum usitatissimum
31 8355 Xenopus laevis

Statistics over whole Database: Domains

Count Statistic
13 Apoptotic domains (not preliminary)
12 Pfam domains linked to Apoptotic domains
8 Pfscan domains linked to Apoptotic domains
1965 Proteins with FPS based domains Expectation value < 0.001

Correspondence between Profiles/Domains

Apoptotic Domain PFAM PFSCAN Customized PSIBLAST Profiles
ID Name Status ID Name ID Name Count
1 Death Effector Domain primary PF01335 DED PS50168 DED 7
2 CAspase Recruitment Domain primary PF00619 CARD PS50209 CARD 11
3 Death Domain primary PF00531 death PS50017 DEATH_DOMAIN 10
4 Caspase Small Subunit primary PF00655 ICE_p10 PS50207 CASPASE_P10 8
5 Caspase Large Subunit primary PF00656 ICE_p20 PS50208 CASPASE_P20 9
6 CIDE N-terminal Domain   PF02017 CIDE-N     3
7 BAG Domain   PF02179 BAG     6
8 TRAF Domain   PF00917 MATH     5
9 NB-ARC Domain primary PF00931 NB-ARC     3
10 BIR Domain primary PF00653 BIR PS50143 BIR_REPEAT_2 7
11 Bcl-2 Domain primary PF00452 Bcl-2 PS50062 BCL2_FAMILY 12
12 N-TRADD preliminary          
13 Smac/DIABLO preliminary          
14 AIF/PCD-8 C-term Motif primary         1
15 TNFReceptor C6 primary PF00020 TNFR_c6 PS50050 TNFR_NGFR_2 2
16 BH3 motif preliminary         13

Proteins Counts per Domain via different methods

ID Name PSI BLAST FPS PFAM PFSCAN
Expectation value cutoff: 0.01 0.001 0.01 0.01
1 Death Effector Domain 108 113 81 87
2 CAspase Recruitment Domain 183 197 127 178
3 Death Domain 282 289 253 192
4 Caspase Small Subunit 193 209 197 197
5 Caspase Large Subunit 303 265 221 244
6 CIDE N-terminal Domain 51 52 52 0
7 BAG Domain 43 37 42 0
8 TRAF Domain 364 189 284 0
9 NB-ARC Domain 842 533 398 0
10 BIR Domain 179 183 165 175
11 Bcl-2 Domain 238 234 163 199
12 N-TRADD 0 0 0 0
13 Smac/DIABLO 0 0 0 0
14 AIF/PCD-8 C-term Motif 20 20 0 0
15 TNFReceptor C6 503 105 73 61
16 BH3 motif 56 0 0 0

Statistics over whole Database: Families

No proteins defining across FPS families

Families and defining domains

Domains
Family Protein 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Caspase-8 Group 14731648 XX X X
Caspase-8 Group 14731585 XX X X
c-FLIP 12643551 XX X
c-FLIP 14731493 XX X
v-FLIP 1914847 XX
v-FLIP 9629092 XX
v-FLIP 13095651 XX
v-FLIP 9628077 XX
FADD 4505229 X X
FADD 6753812 X X
BAP29/BAP31 6753162 X
BAP29/BAP31 5031675 X
DEDD 4758144 X
DEDD 6755835 X
PEA-15 2498751 X
PEA-15 2498752 X
RAIDD 6753516 X X
RAIDD 4503031 X X
CED-3 1168879 X X X
CED-3 5305337 X X X
CED-3 1168878 X X X
Caspase-1 4757914 X X X
Caspase-1 266322 X X X
Caspase-1 14770290 X X X
Caspase-1 4502577 X X X
Caspase-2 14741608 X X X
Family Protein 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Caspase-2 2506262 X X X
Caspase-9 7656963 X X X
Caspase-9 12644321 X X X
DRONC 4633107 X X X
APAF-1 6857755 X X
APAF-1 4502123 X X
CARD-12 14324113 X X
CARD4 5174617 X X
CED-4 231729 X X
cIAP-1/cIAP-2 4502141 X XXX
cIAP-1/cIAP-2 4502139 X XXX
ARC 4505419 X
ASC-1 10835256 X
ASC-1 12963605 X
ASC-1 7673624 X
Bcl-10 6753166 X
Bcl-10 4502379 X
CARD-14 13129124 X
CARD-8 7662404 X
CARDIAK/RIP-2-Kinase 4506537 X
Viral E10 9628080 X
mda-5 11545922 X
Paracaspase 11596375 X X
Paracaspase 5803078 X X
Death Receptor 6 11559850 X X
Death Receptor 6 7657039 X X
Family Protein 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Death Receptor-5, TNFSF 10a 4507559 X X
FASL-Receptor 4507583 X X
FASL-Receptor 1706766 X X
NGF-Receptor 6981272 X X
NGF-Receptor 4505393 X X
TNF-R1 1729987 X X
TNF-R1 4507575 X X
TNF-R1 6981664 X X
TNF-R1 135960 X X
Ankyrin 1703310 X
Ankyrin 10947038 X
Ankyrin 1168457 X
DAP-Kinase 4826684 X
E1 1177584 X
IRAK 14768299 X
IRAK 4504719 X
MyD88 2827757 X
NF-kappaB 6679044 X
NF-kappaB 547761 X
NF-kappaB 125241 X
PELLE 585366 X
PIDD 10130019 X
PIDD 12083587 X
RIP-Kinase 4506539 X
RIP-Kinase 6677753 X
TRADD 13378137 X
Family Protein 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
UNC-5 345372 X
UNC-5 6678505 X
UNC-5 4507837 X
ectodysplasin-1 6753714 X
Caspase-14 6753280 X X
Caspase-14 6912286 X X
Caspase-3, -7 Group 1169072 X X
Caspase-3, -7 Group 4502581 X X
Caspase-6 1708949 X X
Caspase-6 6753286 X X
Caspy 12007504 X X
Type 1 C. elegans Caspase 11359738 X X
Type 1 Drosophila Caspase 12643987 X X
Type 2 C. elegans Caspase 11359739 X X
Type 2 Drosophila Caspase 8575823 X X
Type 3 Drosophila Caspase 7290067 X X
Type 4 Drosophila Caspase 7300162 X X
CIDE-A/B 6753422 X
CIDE-A/B 4557465 X
Caspase Activated DNA-ase 6681185 X
Caspase Activated DNA-ase 4758150 X
DREP-1 3114590 X
Drosophila CAD 8809672 X
Fat Specific Protein-27 2829467 X
ICAD 9087146 X
ICAD 4758148 X
Family Protein 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
viral CIDE 9635288 X
BAG-5 6631077 XX
mammalian Bag-3 7304915 XX
BAG-1 5915764 X
BAG-1 14742147 X
SODD 6631075 X
Yeast Bag Protein 7491412 X
Meprin 2827776 X
Meprin 5031909 X
Meprin 6678862 X
Meprin 5174551 X
Plant TRAF 6862923 X
TRAF-1 & -2 10863939 X
TRAF-1 & -2 731003 X
TRAF-1 & -2 5032193 X
TRAF-3 & -5 4507679 X
TRAF-3 & -5 11321603 X
TRAF-3 & -5 1549146 X
TRAF-4 6678427 X
TRAF-4 4759252 X
TRAF-6 6678429 X
TRAF-6 7513262 X
Type-1 C. elegans Traf 7331732 X
Type-1 Drosophila TRAF 4959432 X
RPS2 13661831 X
Drosophila IAP 2497244 XXX
Family Protein 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
NAIP 4758752 XXX
NAIP 6679008 XXX
XIAP 4502143 XXX
Baculoviral IAP 9627769 XX
BRUCE 10442822 X
KIAP 14769864 X
Survivin / IAP-4 6753090 X
Survivin / IAP-4 4502145 X
Bcl-2 231633 XX
Bcl-2 12741054 XX
MCL-1 6678824 XX
MCL-1 730000 XX
A-1 4757840 X
A-1 11024684 X
BAK 4502363 X
BAK 6671612 X
BAX 6680770 X
BAX 14760604 X
BHP1 9188120 X
BHP1 9187970 X
BHP2 14041180 X
BID 4557361 X
BID 6680782 X
BOK 10092610 X
BOK 7949082 X
BOK 6724090 X
Family Protein 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Bcl-X 14772457 X
Bcl-X 6753170 X
Bcl-w 6680774 X
Bcl-w 4757842 X
Boo/Diva 7304927 X
Boo/Diva 9966783 X
CED-9 1168880 X
CED-9 1168881 X
E1B 19k 119041 X
E1B 19k 9626623 X
MIL-1 7662506 X
AIF / PCD-8 6755004 X
AIF / PCD-8 4757732 X
Family Protein 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

No families with inconsistent domain definitions

Statistics on Alternative Splice Forms/Minor Variants of Proteins

Protein "variant" records (FPS matches with Expect < 0.001)
Variant Level Count of Protein Ave Sequence Length Description
-1 395 334.5584 Suppressed Variants
0 503 450.8576 Shown but cannot be representative of others
1 1067 503.4262 Shown and can be representative of others