Query 046458
Match_columns 960
No_of_seqs 162 out of 198
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 12:20:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046458.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046458hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4765 Uncharacterized conser 100.0 1.9E-66 4.2E-71 557.6 16.0 400 13-624 10-414 (419)
2 PF07967 zf-C3HC: C3HC zinc fi 100.0 3.5E-38 7.7E-43 300.2 12.8 127 79-205 1-132 (133)
3 PF08600 Rsm1: Rsm1-like; Int 98.5 6.1E-08 1.3E-12 88.9 4.3 47 863-913 44-90 (91)
4 KOG4765 Uncharacterized conser 98.5 1.2E-07 2.7E-12 104.9 5.2 83 865-954 334-417 (419)
5 PF08600 Rsm1: Rsm1-like; Int 97.4 2.9E-05 6.2E-10 71.6 -0.2 21 335-355 18-38 (91)
6 smart00238 BIR Baculoviral inh 95.8 0.0096 2.1E-07 51.4 3.7 46 85-133 2-48 (71)
7 PF00653 BIR: Inhibitor of Apo 95.8 0.011 2.4E-07 51.5 4.0 44 88-132 1-47 (70)
8 cd00022 BIR Baculoviral inhibi 95.5 0.013 2.7E-07 50.4 3.4 44 87-133 2-46 (69)
9 KOG1101 Apoptosis inhibitor IA 92.8 0.11 2.3E-06 52.5 3.8 50 82-133 12-63 (147)
10 smart00301 DM Doublesex DNA-bi 29.7 29 0.00062 30.5 1.3 18 157-174 18-35 (54)
No 1
>KOG4765 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.9e-66 Score=557.60 Aligned_cols=400 Identities=32% Similarity=0.433 Sum_probs=331.9
Q ss_pred CCCCcccCCCCCCCCCCCccccccccCCCCCCccccccccCCCCCCcccccCCCCCccCCCCCCCCCCChHHHHHHhhcC
Q 046458 13 DPTPAASSAGASSPAAPANVGSIDWSGHGHNSKAASVSCVGSQPPRTSLSTSAGGSILGSSRPSCRPWERGDLLRRLATF 92 (960)
Q Consensus 13 ~pt~~assag~ssp~~~~~~~~~~~~~~~~~~~~~s~~~v~~~~~~~s~st~~~g~~~~ss~p~yrPwDRedFLrRLaTF 92 (960)
+-|-.|..|+.+.+...++.++-||.|.++ ..+...|+|||||+||+||+||
T Consensus 10 p~~~~a~~~~ds~~~i~t~~~Ss~~~~~~~----------------------------k~s~~l~k~wdred~lrRl~Tf 61 (419)
T KOG4765|consen 10 PTTMEALEALDSLDEILTYARSSDILGKSL----------------------------KASKSLCKPWDREDLLRRLATF 61 (419)
T ss_pred CCcHHHHhhhcchhhhhhccccccccCccc----------------------------cccccccCcccHHHHHHHHHhc
Confidence 335567889999999998888888866543 3466789999999999999999
Q ss_pred CCCCccCCCCCCCHHHHHhhCCeeccCCeeEeccCCcEEEeecCC-CCCHHHHHHHHHHHHHHHhhhccCCCCCCCCCCC
Q 046458 93 KPSNWFGKPKLASSLACAQRGWMNIDVDRIACESCAACLSFVSVP-NWTPAEVEDAGQAFSKQLDDGHNINCPWRGNSCP 171 (960)
Q Consensus 93 k~snWf~KP~~LSPL~CArrGWvCvdkD~LkCesCga~Lvvkl~p-sld~~e~e~lvekys~qL~tgHk~~CPWR~~~CP 171 (960)
|..+||+||..|+|+.||+|||+|+++|+|+|+.|+++|++.+++ .|++++|++++++|+++|+++|+++||||.+.||
T Consensus 62 ks~tWygkp~~iS~lnCA~~GWv~vd~D~lkCe~C~a~L~~s~pq~s~s~d~~n~~~ek~~kkLetaHe~~C~W~~~s~p 141 (419)
T KOG4765|consen 62 KSRTWYGKPFEISPLNCAKYGWVCVDCDMLKCESCGAFLCASLPQQSFSFDRYNQRCEKFKKKLETAHEKFCPWRDSSCP 141 (419)
T ss_pred cCchhccCCcccchHHHhhcCeeeccCCeeehhhhhhHHhccCCccccChHHHHhHHHHHHHHHHHHHhhcCcCCCCCCc
Confidence 999999999999999999999999999999999999999999988 8999999999999999999999999999999999
Q ss_pred CcccccCCCChHHHHHHHHHHHHhhhcCCCCCCcccccccccccCCCcc-HHHHHhhccccccCccCCCccc---ccCcC
Q 046458 172 ESLVQFPPTPQSALIGGYKDRCDGLLQFQSLPIIATCAIEHMWVSRGPQ-IDRLLSQSQNLIVGEVDMKPEL---ENSRD 247 (960)
Q Consensus 172 dSIyrLPlt~psaLI~~fkeR~dsLl~l~~LP~is~saienM~l~e~~~-Id~~LSqLp~ll~~el~~~~~~---e~~~~ 247 (960)
++|++||++++.+||..|++|++.|+++..||.++|++|+.||+.+.++ |.++|.. +..++++++ .....
T Consensus 142 e~i~e~p~~~p~~lV~r~~dr~~~ll~~l~Lp~~~Ps~i~~mrle~v~e~l~~~la~------~~~d~~~der~t~~~g~ 215 (419)
T KOG4765|consen 142 ERIVELPLDEPADLVGRRLDRSSKLLQLLDLPAHSPSAIELMRLERVPEQLIRVLAE------AEDDHRTDERKTTIKGG 215 (419)
T ss_pred hhhccCCCccHHHHHHHHHhhhhhhhhhccCCCCCHHHhhhhhhhcchHhhhhhhhh------hcccccchhhccccccc
Confidence 9999999999999999999999999999999999999999999988655 5555543 233333331 11111
Q ss_pred ccchhhhHHHHHHHHhCCCCCCCCCCccccccccccccCCCCCCCccccccccCCCCCCccccccccccccCCCcccccc
Q 046458 248 GAFYLYSRAQKLISLCGWEPRWLPNVQDCEEHSAQSARDGCSFGPTEAQVQLTKDPGPSKNAISASAKRDTGKNKMFAVE 327 (960)
Q Consensus 248 ~a~~~~~raa~iLALcGWe~R~LPn~~dc~~~S~~sa~n~~~~~Pa~~~~~l~~~~~~s~~s~s~S~~~~~~~~~~~~~e 327 (960)
.+...+++++ ||+||||+ |+++.- . ++
T Consensus 216 s~~~~~~aaq-lislCGWe---------c~~~le-------------------~---------------------~p--- 242 (419)
T KOG4765|consen 216 SAIQLHVAAQ-LISLCGWE---------CSSSLE-------------------S---------------------MP--- 242 (419)
T ss_pred hHHHHHHHHH-HHhhcccc---------cccccc-------------------c---------------------Cc---
Confidence 2233566666 99999999 777650 0 11
Q ss_pred CCCCCCCCceecccccCccccccceecCCCccccCCCCCCCccccccccccccccccCccccccCCCccccccccccccc
Q 046458 328 SRPEYRSPLLDCSLCGATVRILDFLTVPRPARFAPNNIDIPDTSKKMGMTRGVSAASGISGWVAADDPEKEQTEDRDEVA 407 (960)
Q Consensus 328 s~~d~~S~vLdCslCGA~VgLW~F~tv~RP~~ls~~~i~~p~~~kk~~ltrgiSaaSgin~~~~~~~~e~eq~e~rdea~ 407 (960)
-.||||++||++||||+|+|++||+.++..+. ++|++|+|..-.|+
T Consensus 243 ------i~ll~Cs~C~r~vglw~f~t~~qp~~~s~~n~----------------~ts~~~~~~p~~g~------------ 288 (419)
T KOG4765|consen 243 ------ISLLDCSLCGRRVGLWGFQTEGQPIESSMTNL----------------DTSFGNTKSPITGL------------ 288 (419)
T ss_pred ------cceehhhhccceeeeccccccCCcchhhhhcc----------------ccccccccCCCCcc------------
Confidence 13999999999999999999999999885321 77888888774333
Q ss_pred ccccCccccccccceeEEecCCCCCcccCcccccccccccCCCccccccCCCCCCcCCccceeccCCCccccccccCCCC
Q 046458 408 TTDEGKLQQNTEFDLNLTIGGGLPFTQAGRTAISENVHDADMGRDLMIGQPAGSEVGDRAASYESRGPSSRKRSLEIGGS 487 (960)
Q Consensus 408 ~s~~~ks~~n~~~dlnlTiAGGpppT~~n~~~~~~~~~~~~~g~~l~i~qpsgSevgd~aasyesrgPs~rkrs~~~g~s 487 (960)
+.-.+.+|-|+++++++.|.+|+.++.-- ++.|+.|.-.+
T Consensus 289 -------lq~q~~~~~~~e~s~~rr~~~n~~~s~~t---p~~~~~l~s~~------------------------------ 328 (419)
T KOG4765|consen 289 -------LQGQPESLPLVEESIPRRTMTNSQDSIYT---PGSGQLLQSLR------------------------------ 328 (419)
T ss_pred -------cccccccchhhhhccchhhhhhccceeec---chhhhhhhccc------------------------------
Confidence 22335678889999999999998877654 34555443221
Q ss_pred CCCCccccccccccccceeecCCCccccccccccCCCccccccccccccCCCCCCCCCCCCCCCcccccccccCCCCCcc
Q 046458 488 SEDRPNLRMQQADSVEGTVIDRDGDEVTDSRQYSAGPSKRARELDIFDSNCSPYLRDSSGAGPSQSVGLEIHADGNRGSL 567 (960)
Q Consensus 488 ~~d~p~~~~q~ads~egtvid~d~~ev~d~~q~sa~~sKr~r~~~~~~~~~~~~~~~~sg~gps~~~~~~~~~d~n~~~~ 567 (960)
+++||.|.. .+.|+|+.+-.||+++..-.-+..+|+.++
T Consensus 329 -----------------------------------~~s~rs~~~------p~~~~rd~~~~~~~ts~k~~~e~~~~~~d~ 367 (419)
T KOG4765|consen 329 -----------------------------------DTSSRSFFD------PTSQHRDWCPWVNITSGKESRENGGTEPDA 367 (419)
T ss_pred -----------------------------------CccccccCC------ccccccccccccccccchhhhcCCCCCCCC
Confidence 678998865 567899999999999999999999999888
Q ss_pred cccCCcccccccccccccCccceeeecccccCCCCCcccccccCCCCCCCCccCCCc
Q 046458 568 FRQGSEQVIGVVSTRDSTRASSVIAMDTVCHSADDDSMESVENSPGGVDDVNFPSSS 624 (960)
Q Consensus 568 ~~~~~~~~~~~~~~rds~~assv~amdt~~h~~~e~SmeSVe~~p~d~~~v~~pss~ 624 (960)
|.. ..|..|+++ |+|+||++.||+++.|||++||++|.+++ ||+++.
T Consensus 368 f~p------a~pgwr~~l--s~l~ahk~scqpa~~dsm~~ve~~~~~fr--n~~~~~ 414 (419)
T KOG4765|consen 368 FAP------AEPGWRAVL--SILLAHKQSCQPAETDSMSLVEKSRKVFR--NFRQWE 414 (419)
T ss_pred CCC------CCCcHHHHH--HHHHHhhccCCCCCccchhhhhcchhhhh--hccccc
Confidence 877 667889998 99999999999999999999999999999 777754
No 2
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=100.00 E-value=3.5e-38 Score=300.16 Aligned_cols=127 Identities=46% Similarity=0.904 Sum_probs=122.7
Q ss_pred CCChHHHHHHhhcCCCCCccCCCCCCCHHHHHhhCCeeccCCeeEeccCCcEEEee---cCCCCCHHHHHHHHHHHHHHH
Q 046458 79 PWERGDLLRRLATFKPSNWFGKPKLASSLACAQRGWMNIDVDRIACESCAACLSFV---SVPNWTPAEVEDAGQAFSKQL 155 (960)
Q Consensus 79 PwDRedFLrRLaTFk~snWf~KP~~LSPL~CArrGWvCvdkD~LkCesCga~Lvvk---l~psld~~e~e~lvekys~qL 155 (960)
||||++||+||+||++.+||+||..||||+||+|||+|+++|+|+|+.|+++|+++ ....++.+.+++++++|.++|
T Consensus 1 P~~r~~~l~RL~Tf~~~~W~~kp~~lspl~cA~~GW~~~~~d~l~C~~C~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l 80 (133)
T PF07967_consen 1 PWDREDFLRRLETFKSLTWFPKPPWLSPLECARRGWICVSKDMLKCESCGARLCVKLSDSPPDLDSEVYKKLVEKYSEQL 80 (133)
T ss_pred CCCHHHHHHHHHHcccccccCCCcccCHHHHHHcCCCcCCCCEEEeCCCCCEEEEeccccchHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999 666778888999999999999
Q ss_pred hhhccCCCCCCCCCCC-CcccccCCCChHHHHHHHHHHHHhhhcC-CCCCCc
Q 046458 156 DDGHNINCPWRGNSCP-ESLVQFPPTPQSALIGGYKDRCDGLLQF-QSLPII 205 (960)
Q Consensus 156 ~tgHk~~CPWR~~~CP-dSIyrLPlt~psaLI~~fkeR~dsLl~l-~~LP~i 205 (960)
+++|+.+||||+++|| ++||+||++++.++|.+|++||++|+++ .+||++
T Consensus 81 ~~~H~~~CpWr~~~cpl~~~~~l~l~~~~~~l~~~~~r~~~L~~~~~~lP~~ 132 (133)
T PF07967_consen 81 VTGHKESCPWRNNSCPLDSLYRLPLTNPSALLEQFKERLDSLLQLSSQLPSL 132 (133)
T ss_pred HHhhhcCCCCCCCCCChhhhhcCCCCCHHHHHHHHHHHHHHHHhccccCCCC
Confidence 9999999999999999 9999999999999999999999999987 799997
No 3
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=98.55 E-value=6.1e-08 Score=88.95 Aligned_cols=47 Identities=34% Similarity=0.762 Sum_probs=34.7
Q ss_pred ccCCCCcccccCCcCCcccchhcccccCCCCCCCCcccccccchHhHHHHH
Q 046458 863 EATEFDPIAHHNQFCPWVNGNVAAAGCNGSGSSNSADAIALCGWQLTLDAL 913 (960)
Q Consensus 863 ~~~eFDPI~~H~~fCPWvn~~vaaAgc~~~~s~~~~~~~a~~GWqlTldAL 913 (960)
....|||+++||.||||||.........+.....+ ..+||++.+.+|
T Consensus 44 ~~~~~d~~~eHr~~CPwv~~~~q~~~~~~~~~~~~----~~~GW~~l~~~l 90 (91)
T PF08600_consen 44 PMSPFDPLEEHREYCPWVNPSTQSGTGRSSEAEQS----LSPGWKVLLQAL 90 (91)
T ss_pred cCCCCCCcccccccCCccCCcccccccccCCCCCC----cCcHHHHHHHHh
Confidence 34699999999999999997655444433333322 359999999998
No 4
>KOG4765 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.48 E-value=1.2e-07 Score=104.95 Aligned_cols=83 Identities=24% Similarity=0.406 Sum_probs=73.2
Q ss_pred CCCCcccccCCcCCcccchhcccccCCCCCCCCcccccccchHhHHHHHHHhhhcCCCCCccccCcccccccc-cCCCch
Q 046458 865 TEFDPIAHHNQFCPWVNGNVAAAGCNGSGSSNSADAIALCGWQLTLDALDTLRSLGHIPIQTVQSESAASLYK-DDHQTP 943 (960)
Q Consensus 865 ~eFDPI~~H~~fCPWvn~~vaaAgc~~~~s~~~~~~~a~~GWqlTldAL~~~~~~~~~~~~~~~S~saasl~k-dd~~~~ 943 (960)
..|||..|||++|||+|.+...+-..+++..++..++|+|||+.||.+|.++..--| +.+.-||.+ +||.+.
T Consensus 334 s~~~p~~~~rd~~~~~~~ts~k~~~e~~~~~~d~f~pa~pgwr~~ls~l~ahk~scq-------pa~~dsm~~ve~~~~~ 406 (419)
T KOG4765|consen 334 SFFDPTSQHRDWCPWVNITSGKESRENGGTEPDAFAPAEPGWRAVLSILLAHKQSCQ-------PAETDSMSLVEKSRKV 406 (419)
T ss_pred ccCCccccccccccccccccchhhhcCCCCCCCCCCCCCCcHHHHHHHHHHhhccCC-------CCCccchhhhhcchhh
Confidence 799999999999999999999999999999999999999999999999998744444 334578888 889999
Q ss_pred hhhhcccCCcc
Q 046458 944 GRKLLRRHSMS 954 (960)
Q Consensus 944 ~rkl~~~~s~~ 954 (960)
+|.++...|..
T Consensus 407 frn~~~~~s~~ 417 (419)
T KOG4765|consen 407 FRNFRQWESLC 417 (419)
T ss_pred hhhcccccccc
Confidence 99999888764
No 5
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=97.43 E-value=2.9e-05 Score=71.56 Aligned_cols=21 Identities=29% Similarity=0.480 Sum_probs=18.1
Q ss_pred CceecccccCccccccceecC
Q 046458 335 PLLDCSLCGATVRILDFLTVP 355 (960)
Q Consensus 335 ~vLdCslCGA~VgLW~F~tv~ 355 (960)
-+|.|.+|.++||||.|.+..
T Consensus 18 ~~~~C~~C~Rr~GLW~f~~~~ 38 (91)
T PF08600_consen 18 GLLSCSYCFRRLGLWMFKSKE 38 (91)
T ss_pred CeEEccccCcEeeeeecccCc
Confidence 389999999999999995543
No 6
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=95.81 E-value=0.0096 Score=51.43 Aligned_cols=46 Identities=26% Similarity=0.352 Sum_probs=38.2
Q ss_pred HHHHhhcCCCCCccCCCCCCCHHHHHhhCCeecc-CCeeEeccCCcEEEe
Q 046458 85 LLRRLATFKPSNWFGKPKLASSLACAQRGWMNID-VDRIACESCAACLSF 133 (960)
Q Consensus 85 FLrRLaTFk~snWf~KP~~LSPL~CArrGWvCvd-kD~LkCesCga~Lvv 133 (960)
+-+||+||+ +|-. +...++-..|+.|+...+ .|.++|..|+..|..
T Consensus 2 ~~~R~~sF~--~w~~-~~~~~~~~LA~~Gfyy~~~~d~v~C~~C~~~l~~ 48 (71)
T smart00238 2 EEARLKTFQ--NWPY-NSKLTPEQLAEAGFYYTGVGDEVKCFFCGGELDN 48 (71)
T ss_pred HHHHHHHHH--cCCC-CccCCHHHHHHcCCeECCCCCEEEeCCCCCCcCC
Confidence 357999999 8842 345788899999999998 889999999988654
No 7
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=95.79 E-value=0.011 Score=51.53 Aligned_cols=44 Identities=30% Similarity=0.505 Sum_probs=36.9
Q ss_pred HhhcCCCCCccC-C-CCCCCHHHHHhhCCeecc-CCeeEeccCCcEEE
Q 046458 88 RLATFKPSNWFG-K-PKLASSLACAQRGWMNID-VDRIACESCAACLS 132 (960)
Q Consensus 88 RLaTFk~snWf~-K-P~~LSPL~CArrGWvCvd-kD~LkCesCga~Lv 132 (960)
||+||.. +|-. + -..+++-..|+.||...+ .|+++|..|+..|.
T Consensus 1 Rl~SF~~-~wp~~~~~~~~~~~~LA~aGFyy~~~~d~v~C~~C~~~l~ 47 (70)
T PF00653_consen 1 RLKSFRS-NWPHSNDHDPVSPEKLARAGFYYTGTGDRVRCFYCGLELD 47 (70)
T ss_dssp HHHGGTT-GSSTTTTTSSSHHHHHHHTTEEEESSTTEEEETTTTEEEE
T ss_pred ChhHHCC-cccCccccCCCCHHHHHHCCCEEcCCCCEEEEeccCCEEe
Confidence 9999975 7852 2 135889999999999998 59999999999885
No 8
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=95.55 E-value=0.013 Score=50.44 Aligned_cols=44 Identities=30% Similarity=0.415 Sum_probs=36.0
Q ss_pred HHhhcCCCCCccCCCCCCCHHHHHhhCCeeccC-CeeEeccCCcEEEe
Q 046458 87 RRLATFKPSNWFGKPKLASSLACAQRGWMNIDV-DRIACESCAACLSF 133 (960)
Q Consensus 87 rRLaTFk~snWf~KP~~LSPL~CArrGWvCvdk-D~LkCesCga~Lvv 133 (960)
+||+||. +|-. +...++-..|+.||...+. |.++|..|+..|.-
T Consensus 2 ~R~~TF~--~w~~-~~~~~~~~La~~Gfyy~~~~d~v~C~~C~~~~~~ 46 (69)
T cd00022 2 ARLKTFK--NWPI-SLKVTPEKLAEAGFYYTGRGDEVKCFFCGLELKN 46 (69)
T ss_pred hHHHHHH--cCCC-CccCCHHHHHHcCCeEcCCCCEEEeCCCCCCccC
Confidence 6999998 7832 2357788999999999875 99999999987653
No 9
>KOG1101 consensus Apoptosis inhibitor IAP1 and related BIR domain proteins [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=92.84 E-value=0.11 Score=52.48 Aligned_cols=50 Identities=26% Similarity=0.416 Sum_probs=40.9
Q ss_pred hHHHHHHhhcCCCCCc-cCCCCCCCHHHHHhhCCeeccC-CeeEeccCCcEEEe
Q 046458 82 RGDLLRRLATFKPSNW-FGKPKLASSLACAQRGWMNIDV-DRIACESCAACLSF 133 (960)
Q Consensus 82 RedFLrRLaTFk~snW-f~KP~~LSPL~CArrGWvCvdk-D~LkCesCga~Lvv 133 (960)
...+..||+||+ +| +..=+..+|=+.|+.||+++++ |.++|-.|+..|..
T Consensus 12 ~~~~~aRl~TF~--~Wp~~~~~~c~p~~lA~AGFy~~g~~D~~~Cf~C~~~L~~ 63 (147)
T KOG1101|consen 12 MAREEARLKTFK--NWPYSDMDKCTPEQLAEAGFYYTGKQDCVKCFFCSGGLDD 63 (147)
T ss_pred HHHHHHHHhhhh--cCCCCCCCCcCHHHHHhCCceeeCCCCceECcccCccccc
Confidence 345678999999 88 4432279999999999999874 79999999998873
No 10
>smart00301 DM Doublesex DNA-binding motif.
Probab=29.73 E-value=29 Score=30.49 Aligned_cols=18 Identities=33% Similarity=0.909 Sum_probs=15.8
Q ss_pred hhccCCCCCCCCCCCCcc
Q 046458 157 DGHNINCPWRGNSCPESL 174 (960)
Q Consensus 157 tgHk~~CPWR~~~CPdSI 174 (960)
.+|+..|+|++-.|+.=.
T Consensus 18 KGHKr~C~~r~C~C~kC~ 35 (54)
T smart00301 18 KGHKPECPFRDCECEKCT 35 (54)
T ss_pred CCcCCCCCCCCCcCCCCc
Confidence 799999999999998643
Done!