Query 041618
Match_columns 129
No_of_seqs 100 out of 117
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 09:00:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041618.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041618hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05553 DUF761: Cotton fibre 99.6 1.7E-15 3.6E-20 94.6 4.6 34 87-121 1-34 (38)
2 PF02898 NO_synthase: Nitric o 54.6 8.8 0.00019 34.3 2.0 33 87-119 5-37 (372)
3 PF11485 DUF3211: Protein of u 46.8 26 0.00057 27.1 3.4 23 89-111 110-132 (136)
4 COG4443 Uncharacterized protei 45.8 11 0.00025 26.8 1.1 22 40-62 28-49 (72)
5 COG4362 Nitric oxide synthase, 40.8 22 0.00048 31.5 2.3 21 89-109 5-25 (355)
6 cd00795 NOS_oxygenase_euk Nitr 33.3 38 0.00083 30.8 2.7 22 87-108 51-72 (412)
7 cd02987 Phd_like_Phd Phosducin 27.1 93 0.002 23.8 3.5 23 89-115 30-52 (175)
8 PF07240 Turandot: Stress-indu 24.2 1E+02 0.0022 22.3 3.1 21 87-107 28-48 (85)
9 TIGR03687 pupylate_cterm ubiqu 22.0 90 0.0019 19.4 2.1 14 91-104 16-29 (33)
10 KOG3446 NADH:ubiquinone oxidor 19.9 70 0.0015 23.9 1.6 13 95-107 32-44 (97)
No 1
>PF05553 DUF761: Cotton fibre expressed protein; InterPro: IPR008480 This family consists of several plant proteins of unknown function. Three of the sequences from Gossypium hirsutum (Upland cotton) in this family are described as G. hirsutum fibre expressed proteins []. The remaining sequences, found in Arabidopsis thaliana, are uncharacterised.
Probab=99.59 E-value=1.7e-15 Score=94.62 Aligned_cols=34 Identities=53% Similarity=0.870 Sum_probs=32.0
Q ss_pred CchhHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 041618 87 SEDDIDKRAEMFIANFHRQLQIERQISLELRYCRA 121 (129)
Q Consensus 87 ~dd~ID~rAE~FI~kF~~QmrLQRq~Sl~lRY~~~ 121 (129)
++++||++||+||++||+||||||++|++ ||+++
T Consensus 1 ~~~evd~rAe~FI~~f~~qlrlqr~~S~~-ry~em 34 (38)
T PF05553_consen 1 SDDEVDRRAEEFIAKFREQLRLQRQESLQ-RYQEM 34 (38)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH
Confidence 47899999999999999999999999996 99986
No 2
>PF02898 NO_synthase: Nitric oxide synthase, oxygenase domain; InterPro: IPR004030 Nitric oxide synthase (1.14.13.39 from EC) (NOS) enzymes produce nitric oxide (NO) by catalysing a five-electron oxidation of a guanidino nitrogen of L-arginine (L-Arg). Oxidation of L-Arg to L-citrulline occurs via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine as an intermediate. 2 mol of O(2) and 1.5 mol of NADPH are consumed per mole of NO formed []. Arginine-derived NO synthesis has been identified in mammals, fish, birds, invertebrates, plants, and bacteria []. Best studied are mammals, where three distinct genes encode NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3) []. iNOS and nNOS are soluble and found predominantly in the cytosol, while eNOS is membrane associated. The enzymes exist as homodimers, each monomer consisting of two major domains: an N-terminal oxygenase domain, which belongs to the class of haem-thiolate proteins, and a C-terminal reductase domain, which is homologous to NADPH:P450 reductase (1.6.2.4 from EC). The interdomain linker between the oxygenase and reductase domains contains a calmodulin (CaM)-binding sequence. NOSs are the only enzymes known to simultaneously require five bound cofactors animal NOS isozymes are catalytically self-sufficient. The electron flow in the NO synthase reaction is: NADPH --> FAD --> FMN --> haem --> O(2). eNOS localisation to endothelial membranes is mediated by cotranslational N-terminal myristoylation and post-translational palmitoylation []. The subcellular localisation of nNOS in skeletal muscle is mediated by anchoring of nNOS to dystrophin. nNOS contains an additional N-terminal domain, the PDZ domain []. Some bacteria, like Bacillus halodurans, Bacillus subtilis or Deinococcus radiodurans, contain homologs of NOS oxygenase domain. The pattern is directed against the N-terminal haem binding site. This entry represents the oxygenase domain of NOS.; GO: 0004517 nitric-oxide synthase activity, 0006809 nitric oxide biosynthetic process, 0055114 oxidation-reduction process; PDB: 2FBZ_X 2AMO_A 2AN0_A 1M7V_A 2FC1_A 2FC2_B 1M7Z_A 2AN2_A 2ORS_A 1QW5_B ....
Probab=54.64 E-value=8.8 Score=34.26 Aligned_cols=33 Identities=21% Similarity=0.291 Sum_probs=24.6
Q ss_pred CchhHhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 041618 87 SEDDIDKRAEMFIANFHRQLQIERQISLELRYC 119 (129)
Q Consensus 87 ~dd~ID~rAE~FI~kF~~QmrLQRq~Sl~lRY~ 119 (129)
..|+|-..|++||..||..++-+..+...-|-.
T Consensus 5 ~~e~l~~~A~~Fi~~~y~e~~~~~~~~~~~Rl~ 37 (372)
T PF02898_consen 5 SKEELLEEAKEFIDQYYSELKRSGSEAHERRLE 37 (372)
T ss_dssp THHHHHHHHHHHHHHHHHHTTSTTCHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHhcCCccchHHHHHHH
Confidence 468999999999999999877554444444443
No 3
>PF11485 DUF3211: Protein of unknown function (DUF3211); InterPro: IPR021578 This archaeal family of proteins has no known function. ; PDB: 2EJX_A.
Probab=46.83 E-value=26 Score=27.12 Aligned_cols=23 Identities=30% Similarity=0.361 Sum_probs=20.9
Q ss_pred hhHhHHHHHHHHHHHHHHHHHHH
Q 041618 89 DDIDKRAEMFIANFHRQLQIERQ 111 (129)
Q Consensus 89 d~ID~rAE~FI~kF~~QmrLQRq 111 (129)
--++++-+.|.++|.+.+||+|-
T Consensus 110 ~~i~~~i~~f~~~ldE~IRlERI 132 (136)
T PF11485_consen 110 FFISKWIEKFKKNLDEEIRLERI 132 (136)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhhhHHHHHHhH
Confidence 46889999999999999999985
No 4
>COG4443 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.77 E-value=11 Score=26.81 Aligned_cols=22 Identities=32% Similarity=0.356 Sum_probs=19.0
Q ss_pred cccccCCCCCccccccCCCCCCC
Q 041618 40 RRLSFNDRPGLRACTDDNYADES 62 (129)
Q Consensus 40 rrlSFn~~pgL~~~~d~~~~d~~ 62 (129)
-|+|||.||-=-|. -+|+|||.
T Consensus 28 n~vSwNg~~~KyDi-R~Wspdh~ 49 (72)
T COG4443 28 NRVSWNGRPPKYDI-RAWSPDHS 49 (72)
T ss_pred hhcccCCCCCcCcc-cccCcchh
Confidence 48999999988885 48999998
No 5
>COG4362 Nitric oxide synthase, oxygenase domain [Inorganic ion transport and metabolism / Amino acid transport and metabolism]
Probab=40.76 E-value=22 Score=31.45 Aligned_cols=21 Identities=24% Similarity=0.434 Sum_probs=17.4
Q ss_pred hhHhHHHHHHHHHHHHHHHHH
Q 041618 89 DDIDKRAEMFIANFHRQLQIE 109 (129)
Q Consensus 89 d~ID~rAE~FI~kF~~QmrLQ 109 (129)
+.+-..|++||.|||++|-|.
T Consensus 5 ~~L~~ea~aFl~~~yeE~g~~ 25 (355)
T COG4362 5 AVLTPEARAFLRRFYEEMGIE 25 (355)
T ss_pred hhhCHHHHHHHHHHHHHhCcc
Confidence 456678999999999999854
No 6
>cd00795 NOS_oxygenase_euk Nitric oxide synthase (NOS) eukaryotic oxygenase domain. NOS produces nitric oxide (NO) by catalyzing a five-electron heme-based oxidation of a guanidine nitrogen of L-arginine to L-citrulline via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine (NHA) as an intermediate. In mammals, there are three distinct NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3) . Nitric oxide synthases are homodimers. In eukaryotes, each monomer has an N-terminal oxygenase domain, which binds to the substrate L-Arg, zinc, and to the cofactors heme and 5.6.7.8-(6R)-tetrahydrobiopterin (BH4) . Eukaryotic NOS's also have a C-terminal electron supplying reductase region, which is homologous to cytochrome P450 reductase and binds NADH, FAD and FMN.
Probab=33.33 E-value=38 Score=30.76 Aligned_cols=22 Identities=14% Similarity=0.357 Sum_probs=18.6
Q ss_pred CchhHhHHHHHHHHHHHHHHHH
Q 041618 87 SEDDIDKRAEMFIANFHRQLQI 108 (129)
Q Consensus 87 ~dd~ID~rAE~FI~kF~~QmrL 108 (129)
..+++-..|++||..||..++.
T Consensus 51 ~~e~l~~eA~~Fi~~~y~e~~~ 72 (412)
T cd00795 51 PKEELLPQAKDFINQYYSSIKR 72 (412)
T ss_pred CHHHHHHHHHHHHHHHHHhhcC
Confidence 4577889999999999987764
No 7
>cd02987 Phd_like_Phd Phosducin (Phd)-like family, Phd subfamily; Phd is a cytosolic regulator of G protein functions. It specifically binds G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane. This impedes the formation of a functional G protein trimer (G protein alphabetagamma), thereby inhibiting G protein-mediated signal transduction. Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=27.14 E-value=93 Score=23.78 Aligned_cols=23 Identities=30% Similarity=0.442 Sum_probs=11.9
Q ss_pred hhHhHHHHHHHHHHHHHHHHHHHHHHH
Q 041618 89 DDIDKRAEMFIANFHRQLQIERQISLE 115 (129)
Q Consensus 89 d~ID~rAE~FI~kF~~QmrLQRq~Sl~ 115 (129)
|++|.-.|+|+. ++|-||...++
T Consensus 30 d~~~~~~e~~l~----~~R~~R~~el~ 52 (175)
T cd02987 30 DDDDEDKEEFLQ----QYREQRMQEMH 52 (175)
T ss_pred hhhhhhHHHHHH----HHHHHHHHHHH
Confidence 444444444554 45555666665
No 8
>PF07240 Turandot: Stress-inducible humoral factor Turandot; InterPro: IPR010825 This family consists of several Drosophila species specific Turandot proteins. The Turandot A (TotA) gene encodes a humoral factor, which is secreted from the fat body and accumulates in the body fluids. TotA is strongly induced upon bacterial challenge, as well as by other types of stress such as high temperature, mechanical pressure, dehydration, UV irradiation, and oxidative agents. It is also upregulated during metamorphosis and at high age. Flies that overexpress TotA show prolonged survival and retain normal activity at otherwise lethal temperatures. Although TotA is only induced by severe stress, it responds to a much wider range of stimuli than heat shock genes such as hsp70 or immune genes such as Cecropin A1 [].
Probab=24.21 E-value=1e+02 Score=22.32 Aligned_cols=21 Identities=14% Similarity=0.264 Sum_probs=17.6
Q ss_pred CchhHhHHHHHHHHHHHHHHH
Q 041618 87 SEDDIDKRAEMFIANFHRQLQ 107 (129)
Q Consensus 87 ~dd~ID~rAE~FI~kF~~Qmr 107 (129)
...+...++|.||++|.++-.
T Consensus 28 L~~~~r~~~d~~i~~y~~~~~ 48 (85)
T PF07240_consen 28 LTPQDRQRIDRFIRRYKEENN 48 (85)
T ss_pred CCHHHHHHHHHHHHHHHHHhh
Confidence 467888999999999998753
No 9
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=21.98 E-value=90 Score=19.39 Aligned_cols=14 Identities=29% Similarity=0.627 Sum_probs=11.0
Q ss_pred HhHHHHHHHHHHHH
Q 041618 91 IDKRAEMFIANFHR 104 (129)
Q Consensus 91 ID~rAE~FI~kF~~ 104 (129)
+..-||+|.+.|-|
T Consensus 16 Le~NAe~FV~~fVQ 29 (33)
T TIGR03687 16 LESNAEEFVRGFVQ 29 (33)
T ss_pred HHHhHHHHHHHHHH
Confidence 34579999999975
No 10
>KOG3446 consensus NADH:ubiquinone oxidoreductase NDUFA2/B8 subunit [Energy production and conversion]
Probab=19.89 E-value=70 Score=23.95 Aligned_cols=13 Identities=23% Similarity=0.473 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHH
Q 041618 95 AEMFIANFHRQLQ 107 (129)
Q Consensus 95 AE~FI~kF~~Qmr 107 (129)
..+||+|||-.+|
T Consensus 32 vR~fvEk~Y~~lK 44 (97)
T KOG3446|consen 32 VREFVEKFYVNLK 44 (97)
T ss_pred HHHHHHHhhhhhh
Confidence 4689999999987
Done!