Query 034862
Match_columns 81
No_of_seqs 126 out of 191
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 07:09:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034862.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034862hhsearch_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 1.4E-37 3E-42 196.0 5.1 60 22-81 1-60 (60)
2 PF09257 BCMA-Tall_bind: BCMA, 52.9 12 0.00025 22.2 1.7 20 27-46 17-36 (39)
3 PF00322 Endothelin: Endotheli 23.9 47 0.001 18.8 1.0 16 30-45 5-21 (31)
4 PF07699 GCC2_GCC3: GCC2 and G 22.7 1.1E+02 0.0024 17.1 2.5 28 50-77 10-41 (48)
5 PF15079 DUF4546: Domain of un 15.9 50 0.0011 25.4 0.0 20 40-59 169-189 (205)
6 smart00272 END Endothelin. 14.9 75 0.0016 17.2 0.5 16 30-45 1-17 (26)
7 PF11437 Vanabin-2: Vanadium-b 13.6 1.8E+02 0.0039 19.7 2.3 23 23-45 15-37 (94)
8 KOG1368 Threonine aldolase [Am 12.2 88 0.0019 26.2 0.5 9 54-62 77-85 (384)
9 PHA02637 TNF-alpha-receptor-li 11.8 78 0.0017 22.6 0.1 26 45-73 41-74 (127)
10 cd00150 PlantTI Plant trypsin 11.5 1.3E+02 0.0028 16.5 0.8 14 47-60 14-27 (27)
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=1.4e-37 Score=195.99 Aligned_cols=60 Identities=62% Similarity=1.528 Sum_probs=59.4
Q ss_pred CchHHhhHHHhcCCchhHHHHHHHhhcCcccccCCCCCCCCCCCCccccccccCCCCCCC
Q 034862 22 NCSQACNRRCKESSRKNMCHRACRTCCKRCHCVPPGTYGNKQACPCYASLRTHGNRPKCP 81 (81)
Q Consensus 22 ~C~~~C~~RCs~~~~~~~C~~~C~~CC~kC~CVP~GTyGnk~~CPCY~~m~t~~g~pKCP 81 (81)
||+++|++|||+++++++||+|||+||++|+|||||||||+|+||||+||+||+|+||||
T Consensus 1 ~C~~~C~~RCs~~~~~~~C~~~C~~CC~~C~CVP~GT~gn~~~CpCY~~m~t~~g~pKCP 60 (60)
T PF02704_consen 1 DCGGACSVRCSKASRKKRCMRACGTCCAKCKCVPPGTYGNKEECPCYRDMKTHGGKPKCP 60 (60)
T ss_pred CcchHHHHHHhccCCchHHHHHHHHHhccCcccCCCCCCCCccCCChhhhhccCCCCCCc
Confidence 699999999999999999999999999999999999999999999999999999999999
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=52.91 E-value=12 Score=22.15 Aligned_cols=20 Identities=30% Similarity=0.846 Sum_probs=15.8
Q ss_pred hhHHHhcCCchhHHHHHHHh
Q 034862 27 CNRRCKESSRKNMCHRACRT 46 (81)
Q Consensus 27 C~~RCs~~~~~~~C~~~C~~ 46 (81)
|--|||+..-+-.|-+||+.
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
>PF00322 Endothelin: Endothelin family; InterPro: IPR001928 Endothelins (ET's) are the most potent vasoconstrictors known [, , ]. They stimulate cardiac contraction, regulate release of vasoactive substances, and stimulate mitogenesis in blood vessels in primary culture. They also stimulate contraction in almost all other smooth muscles (e.g., uterus, bronchus, vas deferensa and stomach) and stimulate secretion in several tissues (e.g., kidney, liver and adrenals). Endothelin receptors have also been found in the brain, e.g. cerebral cortex, cerebellum and glial cells. Endothelins have been implicated in a variety of pathophysiological conditions associated with stress, including hypertension, myocardial infarction, subarachnoid haemorrhage and renal failure. Endothelins are synthesised by proteolysis of large preproendothelins, which are cleaved to 'big endothelins' before being processed to the mature peptide. Sarafotoxins (SRTX) and bibrotoxin (BTX) are cardiotoxins from the venom of snakes of the Atractaspis family, structurally and functionally [, ] similar to endothelin. As shown in the following schematic representation, these peptides which are 21 residues long contain two intramolecular disulphide bonds. +-------------+ | | CxCxxxxxxxCxxxCxxxxxx | | +-------+ 'C': conserved cysteine involved in a disulphide bond. ; GO: 0019229 regulation of vasoconstriction, 0005576 extracellular region; PDB: 1V6R_A 1T7H_A 1EDP_A 1EDN_A 3CMH_A 6CMH_A 1SRB_A 2LDF_A.
Probab=23.89 E-value=47 Score=18.77 Aligned_cols=16 Identities=31% Similarity=0.723 Sum_probs=11.6
Q ss_pred HHh-cCCchhHHHHHHH
Q 034862 30 RCK-ESSRKNMCHRACR 45 (81)
Q Consensus 30 RCs-~~~~~~~C~~~C~ 45 (81)
||| .+..-+.|+-||-
T Consensus 5 RCsC~s~~DkeC~yFCh 21 (31)
T PF00322_consen 5 RCSCASWKDKECVYFCH 21 (31)
T ss_dssp -ECCSSSTHHHHHHHHH
T ss_pred ceecCCCcchhhheeec
Confidence 888 4556778999985
No 4
>PF07699 GCC2_GCC3: GCC2 and GCC3; InterPro: IPR011641 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Tyrosine-protein kinases can transfer a phosphate group from ATP to a tyrosine residue in a protein. These enzymes can be divided into two main groups []: Receptor tyrosine kinases (RTK), which are transmembrane proteins involved in signal transduction; they play key roles in growth, differentiation, metabolism, adhesion, motility, death and oncogenesis []. RTKs are composed of 3 domains: an extracellular domain (binds ligand), a transmembrane (TM) domain, and an intracellular catalytic domain (phosphorylates substrate). The TM domain plays an important role in the dimerisation process necessary for signal transduction []. Cytoplasmic / non-receptor tyrosine kinases, which act as regulatory proteins, playing key roles in cell differentiation, motility, proliferation, and survival. For example, the Src-family of protein-tyrosine kinases []. This entry represents various ephrin type A and B receptors, which have tyrosine kinase activity.
Probab=22.70 E-value=1.1e+02 Score=17.09 Aligned_cols=28 Identities=32% Similarity=0.812 Sum_probs=19.6
Q ss_pred cccccCCCCCCCC---CCC-CccccccccCCC
Q 034862 50 RCHCVPPGTYGNK---QAC-PCYASLRTHGNR 77 (81)
Q Consensus 50 kC~CVP~GTyGnk---~~C-PCY~~m~t~~g~ 77 (81)
.|.=.|.|||-+. .+| +|-....|..-+
T Consensus 10 ~C~~Cp~GtYq~~~g~~~C~~Cp~g~~T~~~G 41 (48)
T PF07699_consen 10 KCQPCPKGTYQDEEGQTSCTPCPPGSTTSSEG 41 (48)
T ss_pred ccCCCCCCccCCccCCccCccCcCCCccCCcC
Confidence 3454689999754 578 898888775443
No 5
>PF15079 DUF4546: Domain of unknown function (DUF4546)
Probab=15.91 E-value=50 Score=25.38 Aligned_cols=20 Identities=40% Similarity=1.185 Sum_probs=15.3
Q ss_pred HHHHHHhhcCccc-ccCCCCC
Q 034862 40 CHRACRTCCKRCH-CVPPGTY 59 (81)
Q Consensus 40 C~~~C~~CC~kC~-CVP~GTy 59 (81)
-+-.|++||.+|. |..--+|
T Consensus 169 ~lH~C~tCcekcllCalk~n~ 189 (205)
T PF15079_consen 169 SLHQCRTCCEKCLLCALKNNY 189 (205)
T ss_pred chhhchhhhhhhhhhhccccc
Confidence 5667999999998 7765544
No 6
>smart00272 END Endothelin.
Probab=14.89 E-value=75 Score=17.17 Aligned_cols=16 Identities=31% Similarity=0.839 Sum_probs=8.9
Q ss_pred HHh-cCCchhHHHHHHH
Q 034862 30 RCK-ESSRKNMCHRACR 45 (81)
Q Consensus 30 RCs-~~~~~~~C~~~C~ 45 (81)
||+ .++.-+.|+-||-
T Consensus 1 RC~C~s~~Dk~C~~FCh 17 (26)
T smart00272 1 RCQCSSATDKACAYFCH 17 (26)
T ss_pred CcccCCCCChHHHHHhc
Confidence 444 3445556777763
No 7
>PF11437 Vanabin-2: Vanadium-binding protein 2; InterPro: IPR021544 The Vanadium binding protein, Vanabin2, contains four alpha-helices connected by nine disulphide bonds. Vanadium accumulates in Ascidians however the biological reason remains unclear []. ; PDB: 1VFI_A.
Probab=13.60 E-value=1.8e+02 Score=19.70 Aligned_cols=23 Identities=26% Similarity=0.956 Sum_probs=17.4
Q ss_pred chHHhhHHHhcCCchhHHHHHHH
Q 034862 23 CSQACNRRCKESSRKNMCHRACR 45 (81)
Q Consensus 23 C~~~C~~RCs~~~~~~~C~~~C~ 45 (81)
|...|..-|..+..+++|++.|.
T Consensus 15 Ck~~C~~~C~~~r~~~~C~~~C~ 37 (94)
T PF11437_consen 15 CKATCLESCAAARDKKLCMKNCK 37 (94)
T ss_dssp HHHHHHHHTTT-TTHHHHHHHHH
T ss_pred HHhHhhhHHhccCCchhHHHHcc
Confidence 56678888888888888998883
No 8
>KOG1368 consensus Threonine aldolase [Amino acid transport and metabolism]
Probab=12.22 E-value=88 Score=26.17 Aligned_cols=9 Identities=67% Similarity=1.058 Sum_probs=7.9
Q ss_pred cCCCCCCCC
Q 034862 54 VPPGTYGNK 62 (81)
Q Consensus 54 VP~GTyGnk 62 (81)
|||||-||.
T Consensus 77 v~SGTmgNl 85 (384)
T KOG1368|consen 77 VPSGTMGNL 85 (384)
T ss_pred ecccccccH
Confidence 899999985
No 9
>PHA02637 TNF-alpha-receptor-like protein; Provisional
Probab=11.80 E-value=78 Score=22.64 Aligned_cols=26 Identities=46% Similarity=1.170 Sum_probs=18.0
Q ss_pred HhhcCcccccCCCCCCC-------CCCC-Cccccccc
Q 034862 45 RTCCKRCHCVPPGTYGN-------KQAC-PCYASLRT 73 (81)
Q Consensus 45 ~~CC~kC~CVP~GTyGn-------k~~C-PCY~~m~t 73 (81)
+.||.+| |||||=. .-+| ||-..-.|
T Consensus 41 ~~CC~kC---PPGt~v~~~Ct~~t~T~C~PCp~GTYT 74 (127)
T PHA02637 41 NLCCLSC---PPGTYASRLCDIKTNTQCTPCGSGTFT 74 (127)
T ss_pred CeEcCCC---CCCCEEeCcCCCCCCcccccCCCCCee
Confidence 6789988 7887753 3477 77666544
No 10
>cd00150 PlantTI Plant trypsin inhibitors such as squash trypsin inhibitor. Plant proteinase inhibitors play important roles in natural plant defense. Proteinase inhibitors from squash seeds form an uniform family of small proteins cross-linked with three disulfide bridges.
Probab=11.47 E-value=1.3e+02 Score=16.54 Aligned_cols=14 Identities=36% Similarity=0.999 Sum_probs=9.4
Q ss_pred hcCcccccCCCCCC
Q 034862 47 CCKRCHCVPPGTYG 60 (81)
Q Consensus 47 CC~kC~CVP~GTyG 60 (81)
|-+.|.|++.|.-|
T Consensus 14 Cl~~CiC~~~G~CG 27 (27)
T cd00150 14 CLAECICLENGYCG 27 (27)
T ss_pred ccCCCEEccccccC
Confidence 45677888877543
Done!