Query T0540 FAIM-NTD, Human, 90 residues
Match_columns 90
No_of_seqs 29 out of 31
Neff 2.4
Searched_HMMs 11830
Date Fri May 21 18:06:10 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0540.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0540.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06905 FAIM1: Fas apoptotic 100.0 0 0 350.3 0.0 90 1-90 1-91 (177)
2 PF09038 53-BP1_Tudor: Tumour 57.1 3.3 0.00028 20.1 2.9 70 4-85 9-96 (122)
3 PF11605 Vps36_ESCRT-II: Vacuo 52.2 0.64 5.4E-05 24.3 -1.4 38 4-41 17-57 (92)
4 PF04057 Rep-A_N: Replication 43.9 9.1 0.00077 17.5 3.4 16 5-20 38-53 (102)
5 PF12294 DUF3626: Protein of u 43.0 3.9 0.00033 19.6 1.4 39 9-50 20-58 (297)
6 PF03888 MucB_RseB: MucB/RseB 39.3 6.1 0.00051 18.5 1.9 74 12-85 50-162 (314)
7 PF00840 Glyco_hydro_7: Glycos 28.1 9.2 0.00078 17.4 1.3 47 17-66 90-140 (434)
8 PF04765 DUF616: Protein of un 19.3 15 0.0013 16.2 1.0 12 74-85 153-164 (306)
9 PF08685 GON: GON domain; Int 17.9 17 0.0015 15.8 1.1 10 37-46 103-112 (201)
10 PF07608 DUF1571: Protein of u 15.1 30 0.0026 14.4 1.8 15 23-37 43-57 (213)
No 1
>PF06905 FAIM1: Fas apoptotic inhibitory molecule (FAIM1); InterPro: IPR010695 This family consists of several fas apoptotic inhibitory molecule (FAIM) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology .; GO: 0043066 negative regulation of apoptosis; PDB: 2kd2_A.
Probab=100.00 E-value=0 Score=350.30 Aligned_cols=90 Identities=82% Similarity=1.315 Sum_probs=88.7
Q ss_pred CC-CEEEEEEEECCCCCEEEEEEECCCCCCEEEEECCEEEEEECCCEEECCCEEEEECCCCCEEEEEEECCCCCCEEEEE
Q ss_conf 96-42778664138980699984167767189996893887311311112731330178656489998427996358999
Q T0540 1 MT-DLVAVWDVALSDGVHKIEFEHGTTSGKRVVYVDGKEEIRKEWMFKLVGKETFYVGAAKTKATINIDAISGFAYEYTL 79 (90)
Q Consensus 1 m~-dvvA~W~V~L~dgvhkIeFEHGTtsGKRvi~VDgkei~RrdWMFkLVG~E~F~ig~~~~k~~I~Id~~~gf~yeYtL 79 (90)
|| |+||+||||||||+|+||||||||||||||||||||++||||||||||+|+|.+|++++||+|+|||+|||+|||||
T Consensus 1 m~~divA~W~v~l~d~vhkIefEHGTTsGKRvi~VdgkEvlRrdWMFKLVG~etF~vg~~~~k~~I~Ida~sGFaYEYsL 80 (177)
T PF06905_consen 1 MSGDIVAVWDVALSDGVHKIEFEHGTTSGKRVIWVDGKEVLRRDWMFKLVGKETFKVGSSDTKATINIDAISGFAYEYSL 80 (177)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCCCEEEEEEEECCCCEEEEEEECCCCCCCEEEEECCEEEEEHHHHHHHCCCCEEECCCCCCEEEEEEECCCCCEEEEEE
T ss_conf 96526899987058965899985066566089999886633123344200630285067662679999606882189999
Q ss_pred EECCEEHHHCC
Q ss_conf 86885213249
Q T0540 80 EINGKSLKKYM 90 (90)
Q Consensus 80 ~v~GKsl~kFi 90 (90)
+||||||+||+
T Consensus 81 ~IdGKsl~kf~ 91 (177)
T PF06905_consen 81 EIDGKSLKKFT 91 (177)
T ss_dssp -----------
T ss_pred EECCEEHHHHH
T ss_conf 99999889987
No 2
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 . ; PDB: 1xni_J 2g3r_A 2ig0_A 1ssf_A.
Probab=57.13 E-value=3.3 Score=20.11 Aligned_cols=70 Identities=24% Similarity=0.436 Sum_probs=46.8
Q ss_pred EEEEEEE-----------ECCCCCEEEEEEECCCC---CCEEEEEC----CEEEEEECCCEEECCCEEEEECCCCCEEEE
Q ss_conf 2778664-----------13898069998416776---71899968----938873113111127313301786564899
Q T0540 4 LVAVWDV-----------ALSDGVHKIEFEHGTTS---GKRVVYVD----GKEEIRKEWMFKLVGKETFYVGAAKTKATI 65 (90)
Q Consensus 4 vvA~W~V-----------~L~dgvhkIeFEHGTts---GKRvi~VD----gkei~RrdWMFkLVG~E~F~ig~~~~k~~I 65 (90)
++|.|.- .++++-+.|-||-|+-+ +|++|-+| |.||+ -|.++|.|..|-- +.
T Consensus 9 V~ArWSs~kyfY~GkI~~~~~~~ry~v~FdDG~~~~i~~kdiiv~d~LPvg~~V~------A~~eDeyf~~GvI--~~-- 78 (122)
T PF09038_consen 9 VMARWSSNKYFYPGKITRDKGNGRYMVLFDDGDECEILAKDIIVCDPLPVGTEVL------ALTEDEYFEPGVI--KG-- 78 (122)
T ss_dssp EEEESST---BB---EEEE-----EEEE-----EEEE----EEEESSS-TTB--E------ECCTTCTSE---B------
T ss_pred EEEEECCCCCEECCEEECCCCCCEEEEEECCCCEEEECCCCEEEEECCCCCCEEE------EECCCCEECCCEE--EE--
T ss_conf 9999703783505368535789889999658851132138379994245884467------6116742043379--93--
Q ss_pred EEECCCCCCEEEEEEECCEE
Q ss_conf 98427996358999868852
Q T0540 66 NIDAISGFAYEYTLEINGKS 85 (90)
Q Consensus 66 ~Id~~~gf~yeYtL~v~GKs 85 (90)
---.+=...|..+.||.+
T Consensus 79 --h~~~~~E~~Y~Ve~dG~~ 96 (122)
T PF09038_consen 79 --HKKDSGEVYYSVEKDGQT 96 (122)
T ss_dssp ---EE----EEEEEE----E
T ss_pred --ECCCCCCEEEEEEECCCE
T ss_conf --117898488999965872
No 3
>PF11605 Vps36_ESCRT-II: Vacuolar protein sorting protein 36 Vps36; PDB: 2cay_B 2hth_B 2dx5_A.
Probab=52.22 E-value=0.64 Score=24.30 Aligned_cols=38 Identities=29% Similarity=0.551 Sum_probs=29.9
Q ss_pred EEEEEEEECCCCCEEE-EEEECCC--CCCEEEEECCEEEEE
Q ss_conf 2778664138980699-9841677--671899968938873
Q T0540 4 LVAVWDVALSDGVHKI-EFEHGTT--SGKRVVYVDGKEEIR 41 (90)
Q Consensus 4 vvA~W~V~L~dgvhkI-eFEHGTt--sGKRvi~VDgkei~R 41 (90)
+-..=.|.|.||-.|+ .|+-|+. |-+|+||+|..+.-+
T Consensus 17 v~~q~~VgLY~G~~K~~~~q~G~l~LTshRliw~d~~~~~~ 57 (92)
T PF11605_consen 17 VYVQDGVGLYDGKQKIPNFQNGRLYLTSHRLIWVDSADPTK 57 (92)
T ss_dssp EEEES--EEE----CSTT-----EEEESSEEEE--SSGHCH
T ss_pred EEEECCCCEECCCCCCCCCCCCEEEEEEEEEEEECCCCCCE
T ss_conf 99706832063873360331558999954799957988740
No 4
>PF04057 Rep-A_N: Replication factor-A protein 1, N-terminal domain; InterPro: IPR007199 Replication factor-a protein 1 (RPA1) forms a multiprotein complex with RPA2 and RPA3 that binds single-stranded DNA and functions in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian Virus 40 origin of replication .; GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus; PDB: 1ewi_A 2b3g_A 2b29_A.
Probab=43.86 E-value=9.1 Score=17.46 Aligned_cols=16 Identities=38% Similarity=0.538 Sum_probs=12.4
Q ss_pred EEEEEEECCCCCEEEE
Q ss_conf 7786641389806999
Q T0540 5 VAVWDVALSDGVHKIE 20 (90)
Q Consensus 5 vA~W~V~L~dgvhkIe 20 (90)
.-++.+-||||.|.+.
T Consensus 38 ~~RyR~~lSDG~~~~~ 53 (102)
T PF04057_consen 38 QERYRIVLSDGVYYIQ 53 (102)
T ss_dssp --EEEEEEE---EEEE
T ss_pred CCEEEEEEECCHHHHH
T ss_conf 6369999997068887
No 5
>PF12294 DUF3626: Protein of unknown function (DUF3626)
Probab=42.97 E-value=3.9 Score=19.63 Aligned_cols=39 Identities=36% Similarity=0.624 Sum_probs=27.7
Q ss_pred EEECCCCCEEEEEEECCCCCCEEEEECCEEEEEECCCEEECC
Q ss_conf 641389806999841677671899968938873113111127
Q T0540 9 DVALSDGVHKIEFEHGTTSGKRVVYVDGKEEIRKEWMFKLVG 50 (90)
Q Consensus 9 ~V~L~dgvhkIeFEHGTtsGKRvi~VDgkei~RrdWMFkLVG 50 (90)
+.-+.||+++-+||-||..|-..-+--|. |-.|-=++-|
T Consensus 20 ~~l~~dG~y~sQFeTg~SnGglta~pGG~---R~~WE~r~Fg 58 (297)
T PF12294_consen 20 EALLRDGVYRSQFETGTSNGGLTAHPGGD---RWRWERRLFG 58 (297)
T ss_pred HHHHHCCCEEEEEEECCCCCCCCCCCCCC---HHHHHHHHHC
T ss_conf 99986683534345202489868888971---8889988606
No 6
>PF03888 MucB_RseB: MucB/RseB family; InterPro: IPR005588 The members of this family are regulators of the anti-sigma E protein RseD.; PDB: 2p4b_C 2v43_C 2v42_B.
Probab=39.30 E-value=6.1 Score=18.51 Aligned_cols=74 Identities=20% Similarity=0.352 Sum_probs=45.8
Q ss_pred CCCCCEEEEEEECCCCCC---EEEEECC--EEEEEECCCEEECC--CEEEEECC--------------------------
Q ss_conf 389806999841677671---8999689--38873113111127--31330178--------------------------
Q T0540 12 LSDGVHKIEFEHGTTSGK---RVVYVDG--KEEIRKEWMFKLVG--KETFYVGA-------------------------- 58 (90)
Q Consensus 12 L~dgvhkIeFEHGTtsGK---Rvi~VDg--kei~RrdWMFkLVG--~E~F~ig~-------------------------- 58 (90)
-.+++.-...-|+..-|+ |+...|| .|++|++=+-.-+. .+.|.+.+
T Consensus 50 ~~~~i~s~ri~H~~~~~~e~e~L~~LdG~~rEviR~~~~v~~~~p~~~~~~l~~~~~~~~~P~~~~~~~~l~~~Y~~~~~ 129 (314)
T PF03888_consen 50 RGGSIESMRIRHAVIDGKEYERLEQLDGPPREVIRRGDEVSCFEPDQKPVSLESRHIPDSFPLLPADFSQLAEYYDFRLG 129 (314)
T ss_dssp S----EEEEEEEEEETTEEEEEEEE------EEEE----EEEE------EEE-----TTSS-GGG--HHHHTTTEEEEE-
T ss_pred ECCCEEEEEEEEEECCCEEEEEEEECCCCCEEEEEECCEEEEECCCCCEEEEECCCCCCCCCCCCCCHHHHHHCCCEEEC
T ss_conf 69917789999991399699999953899659999899999991798218982676677666566797788535767987
Q ss_pred -----CCCE-EEEEEECCCCCCEEEEEEECCEE
Q ss_conf -----6564-89998427996358999868852
Q T0540 59 -----AKTK-ATINIDAISGFAYEYTLEINGKS 85 (90)
Q Consensus 59 -----~~~k-~~I~Id~~~gf~yeYtL~v~GKs 85 (90)
|+.. -.|+|.|--++.|.|.||+|-+|
T Consensus 130 G~~RVAGR~a~vi~l~PkD~~RYgy~lWiD~et 162 (314)
T PF03888_consen 130 GRSRVAGRPAQVIRLVPKDDYRYGYRLWIDEET 162 (314)
T ss_dssp --EEETTEEEEEEEEEE------EEEEEEETTT
T ss_pred CCCEECCCEEEEEEEEECCCCCEEEEEEEECCC
T ss_conf 985087865899999845998327999996488
No 7
>PF00840 Glyco_hydro_7: Glycosyl hydrolase family 7; InterPro: IPR001722 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families , , . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site . Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'. Glycoside hydrolase family 7 GH7 from CAZY comprises enzymes with several known activities; endoglucanase (3.2.1.4 from EC); cellobiohydrolase (3.2.1.91 from EC). These enzymes were formerly known as cellulase family C. Exoglucanases and cellobiohydrolases play a role in the conversion of cellulose to glucose by cutting the dissaccharide cellobiose from the nonreducing end of the cellulose polymer chain. Structurally, cellulases and xylanases generally consist of a catalytic domain joined to a cellulose-binding domain (CBD) via a linker region that is rich in proline and/or hydroxy-amino acids. In type I exoglucanases, the CBD domain is found at the C-terminal extremity of these enzyme (this short domain forms a hairpin loop structure stabilised by 2 disulphide bridges).; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1egn_A 1cel_A 2cel_B 1q2e_B 2v3i_A 2v3r_A 6cel_A 1dy4_A 3cel_A 7cel_A ....
Probab=28.08 E-value=9.2 Score=17.44 Aligned_cols=47 Identities=28% Similarity=0.425 Sum_probs=32.8
Q ss_pred EEEEEEE---CCCCCCEEEEECCEEEEEECCCEEECCCE-EEEECCCCCEEEEE
Q ss_conf 6999841---67767189996893887311311112731-33017865648999
Q T0540 17 HKIEFEH---GTTSGKRVVYVDGKEEIRKEWMFKLVGKE-TFYVGAAKTKATIN 66 (90)
Q Consensus 17 hkIeFEH---GTtsGKRvi~VDgkei~RrdWMFkLVG~E-~F~ig~~~~k~~I~ 66 (90)
-+..|-. ++.-|-||-..+...- -=||+|.|+| +|.|.-++.-|-++
T Consensus 90 L~l~fvt~~~~~nvgsRvYLm~~~~~---Y~mf~Ll~~EftFDVD~S~lpCGlN 140 (434)
T PF00840_consen 90 LTLKFVTKGSSKNVGSRVYLMADDTK---YQMFKLLNNEFTFDVDVSNLPCGLN 140 (434)
T ss_dssp EEEESSECTSSEE---EEEEEEETTE---E-BE--TTEEEEEEEETTT-----E
T ss_pred EEEEEEECCCCCCCCCEEEEECCCCC---EEEEEECCCEEEEEEECCCCCCCCC
T ss_conf 78886836765554642799637883---6657852867889863577876553
No 8
>PF04765 DUF616: Protein of unknown function (DUF616); InterPro: IPR006852 This is a family of uncharacterised proteins.
Probab=19.33 E-value=15 Score=16.19 Aligned_cols=12 Identities=42% Similarity=0.894 Sum_probs=9.0
Q ss_pred CEEEEEEECCEE
Q ss_conf 358999868852
Q T0540 74 AYEYTLEINGKS 85 (90)
Q Consensus 74 ~yeYtL~v~GKs 85 (90)
.|.||+|||||.
T Consensus 153 ~y~ySIWIDgki 164 (306)
T PF04765_consen 153 NYDYSIWIDGKI 164 (306)
T ss_pred CCCEEEEEEEEE
T ss_conf 774799996334
No 9
>PF08685 GON: GON domain; InterPro: IPR012314 Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. The ADAMTSs (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) are a family of zinc dependent metalloproteinases that play important roles in a variety of normal and pathological conditions. These enzymes show a complex domain organization including signal sequence, propeptide, metalloproteinase domain (see PDOC50215 from PROSITEDOC), disintegrin-like domain (see PDOC00351 from PROSITEDOC), central TS-1 motif (see PDOC50092 from PROSITEDOC), cysteine-rich region, and a variable number of TS-like repeats at the C-terminal region. The GON domain is an approximately 200-residue module, whose presence is the hallmark of a subfamily of structurally and evolutionarily related ADAMTSs, called GON- ADAMTSs. The GON domain is characterised by the presence of several conserved cysteine residues and is likely to be globular , . Some proteins known to contain a GON domain are listed below: Mammalian ADAMTS-9 Mammalian ADAMTS-20 Caenorhabditis elegans gon-1, a protease required for gonadal morphogenesis Proteins containing the GON domain belong to MEROPS peptidase subfamily M12B (adamalysin, clan MA).; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0005578 proteinaceous extracellular matrix
Probab=17.95 E-value=17 Score=15.80 Aligned_cols=10 Identities=30% Similarity=0.594 Sum_probs=4.1
Q ss_pred EEEEEECCCE
Q ss_conf 3887311311
Q T0540 37 KEEIRKEWMF 46 (90)
Q Consensus 37 kei~RrdWMF 46 (90)
-.|.+-|+-|
T Consensus 103 l~i~~~D~tF 112 (201)
T PF08685_consen 103 LRIIRNDFTF 112 (201)
T ss_pred CEEEECCCEE
T ss_conf 5799566058
No 10
>PF07608 DUF1571: Protein of unknown function (DUF1571); InterPro: IPR011465 This is a family of paralogous proteins from Rhodopirellula baltica.
Probab=15.07 E-value=30 Score=14.36 Aligned_cols=15 Identities=33% Similarity=0.862 Sum_probs=12.2
Q ss_pred ECCCCCCEEEEECCE
Q ss_conf 167767189996893
Q T0540 23 HGTTSGKRVVYVDGK 37 (90)
Q Consensus 23 HGTtsGKRvi~VDgk 37 (90)
-|+..|++|||+.|+
T Consensus 43 ~~~~~GrEvIY~e~~ 57 (213)
T PF07608_consen 43 PGAHAGREVIYDEGQ 57 (213)
T ss_pred CCCCCCCEEEEECCC
T ss_conf 998788389996366
Done!