Query psy13053
Match_columns 242
No_of_seqs 222 out of 658
Neff 5.8
Searched_HMMs 46136
Date Fri Aug 16 18:15:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13053.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13053hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14955 MRP-S24: Mitochondria 100.0 1.3E-36 2.8E-41 245.7 1.2 116 19-134 1-130 (136)
2 KOG1101|consensus 99.9 6.6E-25 1.4E-29 182.2 6.0 80 109-196 14-93 (147)
3 smart00238 BIR Baculoviral inh 99.9 2.6E-22 5.6E-27 146.3 5.5 69 110-188 2-70 (71)
4 PF00653 BIR: Inhibitor of Apo 99.9 1.2E-22 2.6E-27 148.4 2.6 69 113-188 1-70 (70)
5 cd00022 BIR Baculoviral inhibi 99.9 4.1E-22 8.9E-27 144.5 5.0 68 111-188 1-68 (69)
6 KOG1101|consensus 99.1 2E-11 4.3E-16 101.7 2.2 67 42-113 11-92 (147)
7 smart00238 BIR Baculoviral inh 99.1 1.9E-11 4.2E-16 88.8 1.4 57 45-106 1-70 (71)
8 cd00022 BIR Baculoviral inhibi 99.1 3.1E-11 6.7E-16 87.2 1.5 55 47-106 1-68 (69)
9 PF00653 BIR: Inhibitor of Apo 99.0 4.1E-11 8.9E-16 87.4 0.8 52 49-105 1-69 (70)
10 PF07967 zf-C3HC: C3HC zinc fi 93.7 0.062 1.3E-06 43.7 3.0 44 112-165 9-54 (133)
11 PF11682 DUF3279: Protein of u 81.6 0.86 1.9E-05 37.4 1.6 52 133-193 16-75 (128)
12 KOG3497|consensus 70.9 1.6 3.4E-05 31.5 0.3 15 154-168 4-19 (69)
13 PF08600 Rsm1: Rsm1-like; Int 53.4 6.4 0.00014 30.1 0.9 50 138-191 4-65 (91)
14 COG1644 RPB10 DNA-directed RNA 49.5 6.9 0.00015 28.3 0.5 13 154-166 4-16 (63)
15 KOG4765|consensus 47.8 9.2 0.0002 36.8 1.2 97 102-208 46-159 (419)
16 PLN00032 DNA-directed RNA poly 47.6 7.6 0.00016 28.8 0.5 13 154-166 4-16 (71)
17 PRK04016 DNA-directed RNA poly 45.0 9.1 0.0002 27.6 0.5 13 154-166 4-16 (62)
18 PF01194 RNA_pol_N: RNA polyme 40.6 7.3 0.00016 27.9 -0.5 12 155-166 5-16 (60)
19 PF03604 DNA_RNApol_7kD: DNA d 22.7 24 0.00053 22.0 -0.3 14 151-164 14-27 (32)
No 1
>PF14955 MRP-S24: Mitochondrial ribosome subunit S24
Probab=100.00 E-value=1.3e-36 Score=245.75 Aligned_cols=116 Identities=67% Similarity=1.114 Sum_probs=112.3
Q ss_pred hhhhcceeEeeccCCCccccccCCCCchhhhhhccccCcCccccCCCCCCccCCCceEE--------------EEEEecc
Q psy13053 19 KHVQAARYKTSKKGDKPLTYEMSGPPHTIAHIKSWNSWNTCNMLDGLRPSETAVEDEFI--------------QIIIKRQ 84 (242)
Q Consensus 19 ~~~~~~~~~~~~~~~~~ltye~a~~~~~i~RlkSF~~Wpt~na~aGF~y~~tg~~D~v~--------------~v~ikr~ 84 (242)
.||||||||+|++|++|||||||++||+|+++|||+||||+|+++|...+++..+|+|+ +|+|||+
T Consensus 1 qk~~agr~r~t~~~~kplTYE~a~~Ph~Ig~rKsW~S~~T~nL~g~~~~~e~~~eD~fIRkFi~GTf~~~l~sEiiIKRr 80 (136)
T PF14955_consen 1 QKNRAGRYRVTPKGDKPLTYEMANPPHYIGHRKSWNSWHTSNLEGENRASERTVEDVFIRKFIRGTFPGLLASEIIIKRR 80 (136)
T ss_pred CCcccceEEecCCCCCccchhhcCCCcEEeeeeeeccccccccccCCCCcchhhHHHHHHHhccCCCchhcchhhhhhhc
Confidence 38999999999999999999999999999999999999999999999999999999999 9999999
Q ss_pred CCcccchhhhhhccCCCceeecccchHHhhhhhccCCcccccccccccCC
Q psy13053 85 HNIIRIGGIVERAIHPRKIYFLIGYTEELLSFWLQCPVKLELQTVENKCT 134 (242)
Q Consensus 85 gD~~~ia~~~Hrr~sP~C~y~ligytEerLstF~kwPvk~e~q~ve~k~t 134 (242)
+|.|+||++..++++|+.+|||+||+|++||.|++||+++++|+++++.+
T Consensus 81 ~N~I~Ia~~~~~~l~~~k~YFL~GYtEelLS~~lkcpVKlelqtv~~k~d 130 (136)
T PF14955_consen 81 HNVIRIAGIVLRRLQPRKIYFLIGYTEELLSHWLKCPVKLELQTVESKKD 130 (136)
T ss_pred ccEEEEeEeeeccCCceeEEEehhhhHHHHHHHHCCCeEEEEEEcCCCCc
Confidence 99999999999999999999999999999999999999999999987654
No 2
>KOG1101|consensus
Probab=99.91 E-value=6.6e-25 Score=182.25 Aligned_cols=80 Identities=40% Similarity=0.808 Sum_probs=72.0
Q ss_pred chHHhhhhhccCCcccccccccccCChhhhhhcCceecCCCCCCCcEEEeecCCccCCccCCCCcHHHHhccCCCCcccc
Q psy13053 109 YTEELLSFWLQCPVKLELQTVENKCTPENMATAGFYSISKLRNDTSVKCFCCLKELDGWESMDDPWEEHKRHQKDCPYIK 188 (242)
Q Consensus 109 ytEerLstF~kwPvk~e~q~ve~k~t~~~LA~AGFyytg~~~~~D~v~Cf~C~~~l~~We~~DdP~~EH~r~sp~C~fv~ 188 (242)
..+.||.||.+||... + -+++|+.||+|||||+| ..|.|+||+|+++|.+|+++||||+||++|+|.|.|++
T Consensus 14 ~~~aRl~TF~~Wp~~~-~----~~c~p~~lA~AGFy~~g---~~D~~~Cf~C~~~L~~We~~DDPW~EH~k~~p~C~F~~ 85 (147)
T KOG1101|consen 14 REEARLKTFKNWPYSD-M----DKCTPEQLAEAGFYYTG---KQDCVKCFFCSGGLDDWEPGDDPWEEHAKWSPECEFLK 85 (147)
T ss_pred HHHHHHhhhhcCCCCC-C----CCcCHHHHHhCCceeeC---CCCceECcccCcccccCCCCCCcHHHHHhhCCCCceee
Confidence 4467899999999752 1 16899999999999999 78999999999999999999999999999999999999
Q ss_pred cccccccc
Q psy13053 189 LNTVEQQW 196 (242)
Q Consensus 189 ~~k~~~~~ 196 (242)
..|+.+.+
T Consensus 86 ~~k~~e~~ 93 (147)
T KOG1101|consen 86 LKKGREFL 93 (147)
T ss_pred cccchhhh
Confidence 99997553
No 3
>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=99.86 E-value=2.6e-22 Score=146.26 Aligned_cols=69 Identities=46% Similarity=0.918 Sum_probs=63.0
Q ss_pred hHHhhhhhccCCcccccccccccCChhhhhhcCceecCCCCCCCcEEEeecCCccCCccCCCCcHHHHhccCCCCcccc
Q psy13053 110 TEELLSFWLQCPVKLELQTVENKCTPENMATAGFYSISKLRNDTSVKCFCCLKELDGWESMDDPWEEHKRHQKDCPYIK 188 (242)
Q Consensus 110 tEerLstF~kwPvk~e~q~ve~k~t~~~LA~AGFyytg~~~~~D~v~Cf~C~~~l~~We~~DdP~~EH~r~sp~C~fv~ 188 (242)
.+.|++||.+||... ...++.||+|||||+| .+|.|+|++|+++|.+|+++||||+||++++|+|+||+
T Consensus 2 ~~~R~~sF~~w~~~~-------~~~~~~LA~~Gfyy~~---~~d~v~C~~C~~~l~~w~~~d~p~~~H~~~~p~C~fv~ 70 (71)
T smart00238 2 EEARLKTFQNWPYNS-------KLTPEQLAEAGFYYTG---VGDEVKCFFCGGELDNWEPGDDPWEEHKKWSPNCPFVR 70 (71)
T ss_pred HHHHHHHHHcCCCCc-------cCCHHHHHHcCCeECC---CCCEEEeCCCCCCcCCCCCCCCHHHHHhHhCcCCcCcc
Confidence 367899999999632 3479999999999999 79999999999999999999999999999999999986
No 4
>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=99.86 E-value=1.2e-22 Score=148.37 Aligned_cols=69 Identities=45% Similarity=0.938 Sum_probs=57.6
Q ss_pred hhhhhc-cCCcccccccccccCChhhhhhcCceecCCCCCCCcEEEeecCCccCCccCCCCcHHHHhccCCCCcccc
Q psy13053 113 LLSFWL-QCPVKLELQTVENKCTPENMATAGFYSISKLRNDTSVKCFCCLKELDGWESMDDPWEEHKRHQKDCPYIK 188 (242)
Q Consensus 113 rLstF~-kwPvk~e~q~ve~k~t~~~LA~AGFyytg~~~~~D~v~Cf~C~~~l~~We~~DdP~~EH~r~sp~C~fv~ 188 (242)
||.||. +||..... ...++++||+|||||+| .+|+|+|++|++.|.+|+++||||+||++++|+|+|++
T Consensus 1 Rl~SF~~~wp~~~~~----~~~~~~~LA~aGFyy~~---~~d~v~C~~C~~~l~~w~~~Ddp~~~H~~~sp~C~f~k 70 (70)
T PF00653_consen 1 RLKSFRSNWPHSNDH----DPVSPEKLARAGFYYTG---TGDRVRCFYCGLELDNWEPNDDPWEEHKRHSPNCPFVK 70 (70)
T ss_dssp HHHGGTTGSSTTTTT----SSSHHHHHHHTTEEEES---STTEEEETTTTEEEES-STT--HHHHHHHHSTTBHHHH
T ss_pred ChhHHCCcccCcccc----CCCCHHHHHHCCCEEcC---CCCEEEEeccCCEEeCCCCCCCHHHHHHHHCcCCeecC
Confidence 689996 59953211 24689999999999999 79999999999999999999999999999999999974
No 5
>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=99.85 E-value=4.1e-22 Score=144.45 Aligned_cols=68 Identities=49% Similarity=0.957 Sum_probs=62.7
Q ss_pred HHhhhhhccCCcccccccccccCChhhhhhcCceecCCCCCCCcEEEeecCCccCCccCCCCcHHHHhccCCCCcccc
Q psy13053 111 EELLSFWLQCPVKLELQTVENKCTPENMATAGFYSISKLRNDTSVKCFCCLKELDGWESMDDPWEEHKRHQKDCPYIK 188 (242)
Q Consensus 111 EerLstF~kwPvk~e~q~ve~k~t~~~LA~AGFyytg~~~~~D~v~Cf~C~~~l~~We~~DdP~~EH~r~sp~C~fv~ 188 (242)
+.|++||.+||... ...+++||+|||||+| .+|.|+|++|++.|.+|+++|+|++||++++|+|+|++
T Consensus 1 ~~R~~TF~~w~~~~-------~~~~~~La~~Gfyy~~---~~d~v~C~~C~~~~~~w~~~d~p~~~H~~~~p~C~fv~ 68 (69)
T cd00022 1 EARLKTFKNWPISL-------KVTPEKLAEAGFYYTG---RGDEVKCFFCGLELKNWEPGDDPWEEHKRWSPNCPFVL 68 (69)
T ss_pred ChHHHHHHcCCCCc-------cCCHHHHHHcCCeEcC---CCCEEEeCCCCCCccCCCCCCCHHHHHhHhCcCCcCcc
Confidence 46899999999862 3479999999999999 78999999999999999999999999999999999986
No 6
>KOG1101|consensus
Probab=99.12 E-value=2e-11 Score=101.72 Aligned_cols=67 Identities=12% Similarity=0.066 Sum_probs=57.2
Q ss_pred CCCchhhhhhccccCcCcc---------ccCCCCCCccCCCceEE------EEEEeccCCcccchhhhhhccCCCceeec
Q psy13053 42 GPPHTIAHIKSWNSWNTCN---------MLDGLRPSETAVEDEFI------QIIIKRQHNIIRIGGIVERAIHPRKIYFL 106 (242)
Q Consensus 42 ~~~~~i~RlkSF~~Wpt~n---------a~aGF~y~~tg~~D~v~------~v~ikr~gD~~~ia~~~Hrr~sP~C~y~l 106 (242)
.+..+.+||+||.+||.++ |+||||| +|.+|.|+ ++.-+..+|+| +.+|.+|+|.|.|++
T Consensus 11 ~~~~~~aRl~TF~~Wp~~~~~~c~p~~lA~AGFy~--~g~~D~~~Cf~C~~~L~~We~~DDP---W~EH~k~~p~C~F~~ 85 (147)
T KOG1101|consen 11 KMAREEARLKTFKNWPYSDMDKCTPEQLAEAGFYY--TGKQDCVKCFFCSGGLDDWEPGDDP---WEEHAKWSPECEFLK 85 (147)
T ss_pred hHHHHHHHHhhhhcCCCCCCCCcCHHHHHhCCcee--eCCCCceECcccCcccccCCCCCCc---HHHHHhhCCCCceee
Confidence 3558899999999999774 9999999 99999999 55555699999 999999999999998
Q ss_pred ccchHHh
Q psy13053 107 IGYTEEL 113 (242)
Q Consensus 107 igytEer 113 (242)
.....+.
T Consensus 86 ~~k~~e~ 92 (147)
T KOG1101|consen 86 LKKGREF 92 (147)
T ss_pred cccchhh
Confidence 6665443
No 7
>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=99.11 E-value=1.9e-11 Score=88.79 Aligned_cols=57 Identities=16% Similarity=0.143 Sum_probs=48.2
Q ss_pred chhhhhhccccCcC-cc------ccCCCCCCccCCCceEE----EEEEe--ccCCcccchhhhhhccCCCceeec
Q psy13053 45 HTIAHIKSWNSWNT-CN------MLDGLRPSETAVEDEFI----QIIIK--RQHNIIRIGGIVERAIHPRKIYFL 106 (242)
Q Consensus 45 ~~i~RlkSF~~Wpt-~n------a~aGF~y~~tg~~D~v~----~v~ik--r~gD~~~ia~~~Hrr~sP~C~y~l 106 (242)
++++|++||.+||. .. |++|||| +|..|.|+ ++.|. ..+|+| ..+|.+++|.|+|++
T Consensus 1 ~~~~R~~sF~~w~~~~~~~~~~LA~~Gfyy--~~~~d~v~C~~C~~~l~~w~~~d~p---~~~H~~~~p~C~fv~ 70 (71)
T smart00238 1 SEEARLKTFQNWPYNSKLTPEQLAEAGFYY--TGVGDEVKCFFCGGELDNWEPGDDP---WEEHKKWSPNCPFVR 70 (71)
T ss_pred CHHHHHHHHHcCCCCccCCHHHHHHcCCeE--CCCCCEEEeCCCCCCcCCCCCCCCH---HHHHhHhCcCCcCcc
Confidence 36899999999995 22 9999999 99999999 44444 488888 999999999999984
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=99.09 E-value=3.1e-11 Score=87.25 Aligned_cols=55 Identities=18% Similarity=0.222 Sum_probs=47.3
Q ss_pred hhhhhccccCcCc-c------ccCCCCCCccCCCceEE----EEEEe--ccCCcccchhhhhhccCCCceeec
Q psy13053 47 IAHIKSWNSWNTC-N------MLDGLRPSETAVEDEFI----QIIIK--RQHNIIRIGGIVERAIHPRKIYFL 106 (242)
Q Consensus 47 i~RlkSF~~Wpt~-n------a~aGF~y~~tg~~D~v~----~v~ik--r~gD~~~ia~~~Hrr~sP~C~y~l 106 (242)
++|++||.+||.+ . |++|||| +|..|.|+ +++|. ..+|+| ..+|++++|+|+|++
T Consensus 1 ~~R~~TF~~w~~~~~~~~~~La~~Gfyy--~~~~d~v~C~~C~~~~~~w~~~d~p---~~~H~~~~p~C~fv~ 68 (69)
T cd00022 1 EARLKTFKNWPISLKVTPEKLAEAGFYY--TGRGDEVKCFFCGLELKNWEPGDDP---WEEHKRWSPNCPFVL 68 (69)
T ss_pred ChHHHHHHcCCCCccCCHHHHHHcCCeE--cCCCCEEEeCCCCCCccCCCCCCCH---HHHHhHhCcCCcCcc
Confidence 4799999999986 2 9999999 99999999 55554 488888 999999999999974
No 9
>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=99.05 E-value=4.1e-11 Score=87.36 Aligned_cols=52 Identities=15% Similarity=0.224 Sum_probs=42.7
Q ss_pred hhhccc-cCcCcc----------ccCCCCCCccCCCceEE----EEEEec--cCCcccchhhhhhccCCCceee
Q psy13053 49 HIKSWN-SWNTCN----------MLDGLRPSETAVEDEFI----QIIIKR--QHNIIRIGGIVERAIHPRKIYF 105 (242)
Q Consensus 49 RlkSF~-~Wpt~n----------a~aGF~y~~tg~~D~v~----~v~ikr--~gD~~~ia~~~Hrr~sP~C~y~ 105 (242)
||+||. +||+.. |++|||| ++..|.|+ +++|.. .+|+| +.+|++++|+|+|+
T Consensus 1 Rl~SF~~~wp~~~~~~~~~~~~LA~aGFyy--~~~~d~v~C~~C~~~l~~w~~~Ddp---~~~H~~~sp~C~f~ 69 (70)
T PF00653_consen 1 RLKSFRSNWPHSNDHDPVSPEKLARAGFYY--TGTGDRVRCFYCGLELDNWEPNDDP---WEEHKRHSPNCPFV 69 (70)
T ss_dssp HHHGGTTGSSTTTTTSSSHHHHHHHTTEEE--ESSTTEEEETTTTEEEES-STT--H---HHHHHHHSTTBHHH
T ss_pred ChhHHCCcccCccccCCCCHHHHHHCCCEE--cCCCCEEEEeccCCEEeCCCCCCCH---HHHHHHHCcCCeec
Confidence 899996 599532 9999999 99999999 555554 88889 99999999999986
No 10
>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=93.69 E-value=0.062 Score=43.66 Aligned_cols=44 Identities=23% Similarity=0.252 Sum_probs=37.0
Q ss_pred Hhhhhhc--cCCcccccccccccCChhhhhhcCceecCCCCCCCcEEEeecCCccC
Q psy13053 112 ELLSFWL--QCPVKLELQTVENKCTPENMATAGFYSISKLRNDTSVKCFCCLKELD 165 (242)
Q Consensus 112 erLstF~--kwPvk~e~q~ve~k~t~~~LA~AGFyytg~~~~~D~v~Cf~C~~~l~ 165 (242)
+||+||. +|..++. ..+|-.+|.-||...+ .|.++|-.|+..|.
T Consensus 9 ~RL~Tf~~~~W~~kp~------~lspl~cA~~GW~~~~----~d~l~C~~C~~~l~ 54 (133)
T PF07967_consen 9 RRLETFKSLTWFPKPP------WLSPLECARRGWICVS----KDMLKCESCGARLC 54 (133)
T ss_pred HHHHHcccccccCCCc------ccCHHHHHHcCCCcCC----CCEEEeCCCCCEEE
Confidence 4789996 5866543 4699999999999987 99999999999776
No 11
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=81.63 E-value=0.86 Score=37.37 Aligned_cols=52 Identities=27% Similarity=0.496 Sum_probs=39.1
Q ss_pred CChhhhhhcCceecCCCCCCCcEEEeecCCccCCc--cCCCCcHHHHhccC------CCCccccccccc
Q psy13053 133 CTPENMATAGFYSISKLRNDTSVKCFCCLKELDGW--ESMDDPWEEHKRHQ------KDCPYIKLNTVE 193 (242)
Q Consensus 133 ~t~~~LA~AGFyytg~~~~~D~v~Cf~C~~~l~~W--e~~DdP~~EH~r~s------p~C~fv~~~k~~ 193 (242)
.++.+.+.+ +.|...|.+||..|.-= .....||-||...+ -.|+|+.-.+.+
T Consensus 16 v~A~~a~~~---------~~~~~tC~~Cg~~L~lh~~~~~~~pWFEH~~~~~~~~~l~~C~yl~pe~k~ 75 (128)
T PF11682_consen 16 VGARTAASA---------PYDHWTCHSCGCPLILHPGTDTEPPWFEHDQHSLAENGLMQCPYLDPEEKE 75 (128)
T ss_pred EehhhhhhC---------CCCeEEEecCCceEEEecCCcCCCCccccCccccChhhcccCceECcccch
Confidence 356666666 68999999999988732 45678999999765 249999876654
No 12
>KOG3497|consensus
Probab=70.87 E-value=1.6 Score=31.53 Aligned_cols=15 Identities=40% Similarity=1.185 Sum_probs=12.1
Q ss_pred cEEEeecCCccCC-cc
Q psy13053 154 SVKCFCCLKELDG-WE 168 (242)
Q Consensus 154 ~v~Cf~C~~~l~~-We 168 (242)
.++||.||+.+.+ |+
T Consensus 4 PiRCFtCGKvig~KWe 19 (69)
T KOG3497|consen 4 PIRCFTCGKVIGDKWE 19 (69)
T ss_pred eeEeeeccccccccHH
Confidence 3799999999974 54
No 13
>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=53.44 E-value=6.4 Score=30.07 Aligned_cols=50 Identities=30% Similarity=0.607 Sum_probs=32.9
Q ss_pred hhhcCceecCCCCCCCcEEEeecCCccCCccCC------------CCcHHHHhccCCCCccccccc
Q psy13053 138 MATAGFYSISKLRNDTSVKCFCCLKELDGWESM------------DDPWEEHKRHQKDCPYIKLNT 191 (242)
Q Consensus 138 LA~AGFyytg~~~~~D~v~Cf~C~~~l~~We~~------------DdP~~EH~r~sp~C~fv~~~k 191 (242)
||--|+=... ......+.|-+|...|.=|.-- =||.+||+.+ ||++....
T Consensus 4 lAl~GW~~~~-~~~~~~~~C~~C~Rr~GLW~f~~~~ss~~~~~~~~d~~~eHr~~---CPwv~~~~ 65 (91)
T PF08600_consen 4 LALCGWQGLS-DSRLGLLSCSYCFRRLGLWMFKSKESSDSDPMSPFDPLEEHREY---CPWVNPST 65 (91)
T ss_pred EEEeCCCCCC-CCCcCeEEccccCcEeeeeecccCccCCCCcCCCCCCccccccc---CCccCCcc
Confidence 4555662222 1122489999999998877321 3788899876 88887654
No 14
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=49.45 E-value=6.9 Score=28.26 Aligned_cols=13 Identities=38% Similarity=0.897 Sum_probs=11.1
Q ss_pred cEEEeecCCccCC
Q psy13053 154 SVKCFCCLKELDG 166 (242)
Q Consensus 154 ~v~Cf~C~~~l~~ 166 (242)
.|+||.||..|.+
T Consensus 4 PiRCFsCGkvi~~ 16 (63)
T COG1644 4 PVRCFSCGKVIGH 16 (63)
T ss_pred ceEeecCCCCHHH
Confidence 3899999999973
No 15
>KOG4765|consensus
Probab=47.85 E-value=9.2 Score=36.84 Aligned_cols=97 Identities=21% Similarity=0.136 Sum_probs=60.0
Q ss_pred ceeecccchHHhhhhhc--cCCcccccccccccCChhhhhhcCceecCCCCCCCcEEEeecCCccCC------ccCC---
Q psy13053 102 KIYFLIGYTEELLSFWL--QCPVKLELQTVENKCTPENMATAGFYSISKLRNDTSVKCFCCLKELDG------WESM--- 170 (242)
Q Consensus 102 C~y~ligytEerLstF~--kwPvk~e~q~ve~k~t~~~LA~AGFyytg~~~~~D~v~Cf~C~~~l~~------We~~--- 170 (242)
|.++-.+.--.||.||. +|-.++. ..++-..|..|+.... .|.++|-+|+.-|.- |+.+
T Consensus 46 ~k~wdred~lrRl~Tfks~tWygkp~------~iS~lnCA~~GWv~vd----~D~lkCe~C~a~L~~s~pq~s~s~d~~n 115 (419)
T KOG4765|consen 46 CKPWDREDLLRRLATFKSRTWYGKPF------EISPLNCAKYGWVCVD----CDMLKCESCGAFLCASLPQQSFSFDRYN 115 (419)
T ss_pred cCcccHHHHHHHHHhccCchhccCCc------ccchHHHhhcCeeecc----CCeeehhhhhhHHhccCCccccChHHHH
Confidence 44443333345689986 7777653 3589999999999987 999999999997752 3322
Q ss_pred CCcHHHHhc----cCCCCccccccccc--ccccHHHHHHHHHHH
Q psy13053 171 DDPWEEHKR----HQKDCPYIKLNTVE--QQWTLEEWIDLQQAM 208 (242)
Q Consensus 171 DdP~~EH~r----~sp~C~fv~~~k~~--~~~~~~~~~~l~~~~ 208 (242)
.-+-.-|++ |...|++....-++ -++++.+=++|++..
T Consensus 116 ~~~ek~~kkLetaHe~~C~W~~~s~pe~i~e~p~~~p~~lV~r~ 159 (419)
T KOG4765|consen 116 QRCEKFKKKLETAHEKFCPWRDSSCPERIVELPLDEPADLVGRR 159 (419)
T ss_pred hHHHHHHHHHHHHHhhcCcCCCCCCchhhccCCCccHHHHHHHH
Confidence 112222332 34567776554443 345555555555433
No 16
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=47.60 E-value=7.6 Score=28.77 Aligned_cols=13 Identities=38% Similarity=0.928 Sum_probs=11.2
Q ss_pred cEEEeecCCccCC
Q psy13053 154 SVKCFCCLKELDG 166 (242)
Q Consensus 154 ~v~Cf~C~~~l~~ 166 (242)
-|+||.||+.+.+
T Consensus 4 PVRCFTCGkvig~ 16 (71)
T PLN00032 4 PVRCFTCGKVIGN 16 (71)
T ss_pred ceeecCCCCCcHH
Confidence 3899999999973
No 17
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=45.04 E-value=9.1 Score=27.64 Aligned_cols=13 Identities=38% Similarity=0.887 Sum_probs=11.4
Q ss_pred cEEEeecCCccCC
Q psy13053 154 SVKCFCCLKELDG 166 (242)
Q Consensus 154 ~v~Cf~C~~~l~~ 166 (242)
.|+||.||+.+.+
T Consensus 4 PvRCFTCGkvi~~ 16 (62)
T PRK04016 4 PVRCFTCGKVIAE 16 (62)
T ss_pred CeEecCCCCChHH
Confidence 4899999999984
No 18
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=40.64 E-value=7.3 Score=27.94 Aligned_cols=12 Identities=42% Similarity=0.994 Sum_probs=9.6
Q ss_pred EEEeecCCccCC
Q psy13053 155 VKCFCCLKELDG 166 (242)
Q Consensus 155 v~Cf~C~~~l~~ 166 (242)
|+||.||..+.+
T Consensus 5 VRCFTCGkvi~~ 16 (60)
T PF01194_consen 5 VRCFTCGKVIGN 16 (60)
T ss_dssp SS-STTTSBTCG
T ss_pred eecCCCCCChhH
Confidence 789999999983
No 19
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=22.67 E-value=24 Score=21.99 Aligned_cols=14 Identities=14% Similarity=0.501 Sum_probs=11.0
Q ss_pred CCCcEEEeecCCcc
Q psy13053 151 NDTSVKCFCCLKEL 164 (242)
Q Consensus 151 ~~D~v~Cf~C~~~l 164 (242)
..|.++|.+||-.+
T Consensus 14 ~~~~irC~~CG~RI 27 (32)
T PF03604_consen 14 PGDPIRCPECGHRI 27 (32)
T ss_dssp TSSTSSBSSSS-SE
T ss_pred CCCcEECCcCCCeE
Confidence 67899999999754
Done!