Query 035431
Match_columns 65
No_of_seqs 113 out of 190
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 02:56:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035431.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035431hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02704 GASA: Gibberellin reg 100.0 4.3E-38 9.3E-43 190.9 4.9 60 5-65 1-60 (60)
2 PF09257 BCMA-Tall_bind: BCMA, 60.1 8.2 0.00018 21.9 1.8 20 10-29 17-36 (39)
3 PF00097 zf-C3HC4: Zinc finger 26.3 41 0.00089 17.0 1.1 19 47-65 21-39 (41)
4 PF01754 zf-A20: A20-like zinc 20.4 82 0.0018 15.9 1.4 14 40-53 9-25 (25)
5 KOG1358 Serine palmitoyltransf 20.2 44 0.00096 27.4 0.6 13 35-47 128-140 (467)
6 PF01826 TIL: Trypsin Inhibito 18.3 4.6 0.0001 22.2 -3.9 39 4-46 8-46 (55)
7 PF08746 zf-RING-like: RING-li 17.3 79 0.0017 17.2 1.0 16 50-65 26-41 (43)
8 KOG1368 Threonine aldolase [Am 16.5 57 0.0012 26.1 0.5 9 37-45 77-85 (384)
9 smart00259 ZnF_A20 A20-like zi 16.2 81 0.0018 15.9 0.8 15 39-53 12-26 (26)
10 PRK14563 ribosome modulation f 15.9 55 0.0012 19.6 0.2 15 40-56 20-35 (55)
No 1
>PF02704 GASA: Gibberellin regulated protein; InterPro: IPR003854 This is the GASA gibberellin regulated cysteine rich protein family. The expression of these proteins is up-regulated by the plant hormone gibberellin, most of these proteins have some role in plant development. There are 12 cysteine residues conserved within the alignment giving the potential for these proteins to posses 6 disulphide bonds.
Probab=100.00 E-value=4.3e-38 Score=190.92 Aligned_cols=60 Identities=67% Similarity=1.474 Sum_probs=59.0
Q ss_pred cchHHHhHHHhcCCCCChHHHHHhhhcCcccccCCCCCCCcCCchhHHhhhhhcCCCCCCC
Q 035431 5 DCGGLCKQRCSLHSRPNLCNRACGTCCVRCKCVPPGTAGNRELCGSCYTDMTTHGNRTKCP 65 (65)
Q Consensus 5 ~C~~~C~~RCs~~~~~~~C~~~C~~CC~~C~CVP~GT~Gnk~~Cp~CY~~m~t~~g~~KCP 65 (65)
||+++|++|||+++++++||+|||+||++|+|||||||||+|+|| ||+||+||+|+||||
T Consensus 1 ~C~~~C~~RCs~~~~~~~C~~~C~~CC~~C~CVP~GT~gn~~~Cp-CY~~m~t~~g~pKCP 60 (60)
T PF02704_consen 1 DCGGACSVRCSKASRKKRCMRACGTCCAKCKCVPPGTYGNKEECP-CYRDMKTHGGKPKCP 60 (60)
T ss_pred CcchHHHHHHhccCCchHHHHHHHHHhccCcccCCCCCCCCccCC-ChhhhhccCCCCCCc
Confidence 799999999999999999999999999999999999999999996 999999999999998
No 2
>PF09257 BCMA-Tall_bind: BCMA, TALL-1 binding; InterPro: IPR015337 Cytokines can be grouped into a family on the basis of sequence, functional and structural similarities [, , ]. Tumor necrosis factor (TNF) (also known as TNF-alpha or cachectin) is a monocyte-derived cytotoxin that has been implicated in tumour regression, septic shock and cachexia [, ]. The protein is synthesised as a prohormone with an unusually long and atypical signal sequence, which is absent from the mature secreted cytokine []. A short hydrophobic stretch of amino acids serves to anchor the prohormone in lipid bilayers []. Both the mature protein and a partially-processed form of the hormone are secreted after cleavage of the propeptide []. There are a number of different families of TNF, but all these cytokines seem to form homotrimeric (or heterotrimeric in the case of LT-alpha/beta) complexes that are recognised by their specific receptors. Members of this entry, which are predominantly found in the tumour necrosis factor receptor superfamily member 17, BCMA, are required for binding to tumour necrosis factor ligand TALL-1 []. ; PDB: 2KN1_A 1OQD_R 1XU2_T.
Probab=60.06 E-value=8.2 Score=21.86 Aligned_cols=20 Identities=40% Similarity=0.953 Sum_probs=15.8
Q ss_pred HhHHHhcCCCCChHHHHHhh
Q 035431 10 CKQRCSLHSRPNLCNRACGT 29 (65)
Q Consensus 10 C~~RCs~~~~~~~C~~~C~~ 29 (65)
|.-|||+..-+-.|.+||+.
T Consensus 17 ChLRCsn~tPP~~Cq~YCna 36 (39)
T PF09257_consen 17 CHLRCSNNTPPLPCQRYCNA 36 (39)
T ss_dssp HHHHHTSSS--TTTHHHHHH
T ss_pred ceeecCCCCCCccchhhccc
Confidence 78899997778899999985
No 3
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=26.35 E-value=41 Score=16.97 Aligned_cols=19 Identities=26% Similarity=0.816 Sum_probs=14.9
Q ss_pred CchhHHhhhhhcCCCCCCC
Q 035431 47 LCGSCYTDMTTHGNRTKCP 65 (65)
Q Consensus 47 ~Cp~CY~~m~t~~g~~KCP 65 (65)
.|-.|...|....+..+||
T Consensus 21 fC~~C~~~~~~~~~~~~CP 39 (41)
T PF00097_consen 21 FCRDCLRKWLENSGSVKCP 39 (41)
T ss_dssp EEHHHHHHHHHHTSSSBTT
T ss_pred chHHHHHHHHHhcCCccCC
Confidence 5667888888777777787
No 4
>PF01754 zf-A20: A20-like zinc finger; InterPro: IPR002653 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 entry represents the zinc finger domain found in A20. A20 is an inhibitor of cell death that inhibits NF-kappaB activation via the tumour necrosis factor receptor associated factor pathway []. The zinc finger domains appear to mediate self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 2FIF_F 2FID_B 2C7N_C 2C7M_A 2L00_A 2KZY_A 2EQG_A 2EQE_A 3OJ3_J 3OJ4_C ....
Probab=20.43 E-value=82 Score=15.92 Aligned_cols=14 Identities=43% Similarity=1.044 Sum_probs=7.7
Q ss_pred CCCC---CcCCchhHHh
Q 035431 40 GTAG---NRELCGSCYT 53 (65)
Q Consensus 40 GT~G---nk~~Cp~CY~ 53 (65)
|.|| +.+.|-.||+
T Consensus 9 gf~Gs~~~~~~Cs~C~~ 25 (25)
T PF01754_consen 9 GFYGSPATNGLCSKCYR 25 (25)
T ss_dssp SSB-BGGGTTS-HHHHH
T ss_pred CCcccccccCcchhhcC
Confidence 5565 5577777774
No 5
>KOG1358 consensus Serine palmitoyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=20.19 E-value=44 Score=27.38 Aligned_cols=13 Identities=31% Similarity=0.677 Sum_probs=11.0
Q ss_pred cccCCCCCCCcCC
Q 035431 35 KCVPPGTAGNREL 47 (65)
Q Consensus 35 ~CVP~GT~Gnk~~ 47 (65)
.|.|.|.||+.|+
T Consensus 128 sCGPrGFYGt~Dv 140 (467)
T KOG1358|consen 128 SCGPRGFYGTIDV 140 (467)
T ss_pred CcCCCccccccee
Confidence 5889999998764
No 6
>PF01826 TIL: Trypsin Inhibitor like cysteine rich domain; InterPro: IPR002919 This domain is found in proteinase inhibitors as well as in many extracellular proteins. The domain typically contains ten cysteine residues that form five disulphide bonds. The cysteine residues that form the disulphide bonds are 1-7, 2-6, 3-5, 4-10 and 8-9. This inhibitor domain belongs to MEROPS inhibitor family I8 (clan IA). Proteins containing this domain inhibit peptidases belonging to families S1 (IPR001254 from INTERPRO), S8 (IPR000209 from INTERPRO), and M4 (IPR001570 from INTERPRO) [] and are restricted to the chordata, nematoda, arthropoda and echinodermata. Examples of proteins containing this domain are: chymotrypsin/elastase inhibitor from Ascaris suum (pig roundworm) Acp62F protein from Drosophila melanogaster Bombina trypsin inhibitor from Bombina maxima (large-webbed bell toad) Bombyx subtilisin inhibitor from Bombyx mori (silk moth) von Willebrand factor ; PDB: 2P3F_N 1HX2_A 1CCV_A 1EAI_D 2H9E_C 1COU_A 1ATE_A 1ATB_A 1ATD_A 1ATA_A ....
Probab=18.25 E-value=4.6 Score=22.22 Aligned_cols=39 Identities=33% Similarity=0.930 Sum_probs=25.2
Q ss_pred CcchHHHhHHHhcCCCCChHHHHHhhhcCcccccCCCCCCCcC
Q 035431 4 LDCGGLCKQRCSLHSRPNLCNRACGTCCVRCKCVPPGTAGNRE 46 (65)
Q Consensus 4 ~~C~~~C~~RCs~~~~~~~C~~~C~~CC~~C~CVP~GT~Gnk~ 46 (65)
.+|++.|...|+.......|.. .|=.-|.| |+|++-|.+
T Consensus 8 ~~C~~~C~~tC~~~~~~~~C~~---~C~~gC~C-~~G~v~~~~ 46 (55)
T PF01826_consen 8 SECGSPCPRTCDNPNNPEPCSE---PCVEGCFC-PPGYVRNDN 46 (55)
T ss_dssp ESSETSTTCBSSCTTTSSSCSS---S-ESEEEE-TTTEEEETT
T ss_pred CcccCCcCCcCCCCCCCcCcCC---CCCccCCC-CCCeeEcCC
Confidence 3688888888888777766663 33344666 557765444
No 7
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=17.25 E-value=79 Score=17.20 Aligned_cols=16 Identities=31% Similarity=0.910 Sum_probs=9.5
Q ss_pred hHHhhhhhcCCCCCCC
Q 035431 50 SCYTDMTTHGNRTKCP 65 (65)
Q Consensus 50 ~CY~~m~t~~g~~KCP 65 (65)
.|++....+...++||
T Consensus 26 ~C~~~y~r~~~~~~CP 41 (43)
T PF08746_consen 26 DCFKKYFRHRSNPKCP 41 (43)
T ss_dssp HHHHHHTTT-SS-B-T
T ss_pred HHHHHHHhcCCCCCCc
Confidence 3778877777776777
No 8
>KOG1368 consensus Threonine aldolase [Amino acid transport and metabolism]
Probab=16.50 E-value=57 Score=26.12 Aligned_cols=9 Identities=67% Similarity=1.036 Sum_probs=8.0
Q ss_pred cCCCCCCCc
Q 035431 37 VPPGTAGNR 45 (65)
Q Consensus 37 VP~GT~Gnk 45 (65)
|||||-||.
T Consensus 77 v~SGTmgNl 85 (384)
T KOG1368|consen 77 VPSGTMGNL 85 (384)
T ss_pred ecccccccH
Confidence 899999986
No 9
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=16.19 E-value=81 Score=15.93 Aligned_cols=15 Identities=27% Similarity=0.820 Sum_probs=9.8
Q ss_pred CCCCCCcCCchhHHh
Q 035431 39 PGTAGNRELCGSCYT 53 (65)
Q Consensus 39 ~GT~Gnk~~Cp~CY~ 53 (65)
.|+..+...|..||+
T Consensus 12 ~G~~~t~~~CskCy~ 26 (26)
T smart00259 12 FGNPATEGLCSKCFK 26 (26)
T ss_pred cCChhhcccCHhhcC
Confidence 444446778887874
No 10
>PRK14563 ribosome modulation factor; Provisional
Probab=15.92 E-value=55 Score=19.62 Aligned_cols=15 Identities=40% Similarity=1.010 Sum_probs=10.8
Q ss_pred CCCC-CcCCchhHHhhhh
Q 035431 40 GTAG-NRELCGSCYTDMT 56 (65)
Q Consensus 40 GT~G-nk~~Cp~CY~~m~ 56 (65)
|-.| +++.|| |.+..
T Consensus 20 Gv~GrSke~CP--y~~~~ 35 (55)
T PRK14563 20 GIAGRSKEMCP--YQTLD 35 (55)
T ss_pred hccCCCcccCC--CCCcH
Confidence 5566 899998 77653
Done!