Query 036249
Match_columns 68
No_of_seqs 62 out of 64
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 10:52:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036249.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036249hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00028 nitrate transmembrane 98.8 1.2E-09 2.6E-14 81.3 1.0 43 1-44 434-476 (476)
2 PF06989 BAALC_N: BAALC N-term 30.9 24 0.00051 21.2 0.7 22 7-29 1-22 (53)
3 PF10510 PIG-S: Phosphatidylin 29.1 25 0.00054 27.9 0.7 12 2-13 322-333 (517)
4 COG2993 CcoO Cbb3-type cytochr 23.1 25 0.00053 26.5 -0.3 25 3-29 98-122 (227)
5 PF09428 DUF2011: Fungal prote 21.2 40 0.00086 22.9 0.5 20 19-38 19-38 (131)
6 PF11033 ComJ: Competence prot 21.0 47 0.001 22.7 0.8 15 24-38 22-36 (125)
7 PF12368 DUF3650: Protein of u 19.4 67 0.0014 17.0 1.0 18 19-36 7-26 (28)
8 PF00573 Ribosomal_L4: Ribosom 16.8 1E+02 0.0023 21.6 1.8 45 2-51 65-112 (192)
9 PTZ00037 DnaJ_C chaperone prot 16.7 1.2E+02 0.0027 23.8 2.3 31 12-42 21-56 (421)
10 COG4171 SapC ABC-type antimicr 15.8 38 0.00082 26.3 -0.7 20 2-27 246-265 (296)
No 1
>PLN00028 nitrate transmembrane transporter; Provisional
Probab=98.81 E-value=1.2e-09 Score=81.27 Aligned_cols=43 Identities=60% Similarity=0.931 Sum_probs=39.3
Q ss_pred CCCcccceeccCCCCCcchhhhhhcccHHHHhhhccchhhhHHh
Q 036249 1 MPNVNNMKFLMNVVKSTEEYYYASEWNEEEKQKGLHQGSLRFAE 44 (68)
Q Consensus 1 fPqWGgM~~~p~~~~~teE~YY~sEwt~eE~~~Glh~~s~kFA~ 44 (68)
||+|+.|+. ....+..+||||.++|+++++.+|+|+.++||+|
T Consensus 434 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 476 (476)
T PLN00028 434 FPQWGGMFF-GPSKDAVEEDYYASEWTEEEKEKGLHQGSLKFAE 476 (476)
T ss_pred ccchhhhhc-CCCcccchhhhhhcccchhhhhcccccccccccC
Confidence 699999998 5556688899999999999999999999999986
No 2
>PF06989 BAALC_N: BAALC N-terminus; InterPro: IPR009728 This entry represents the mammalian BAALC proteins. BAALC (brain and acute leukaemia, cytoplasmic) is highly conserved among mammals, but is absent from lower organisms. Two isoforms are specifically expressed in neuroectoderm-derived tissues, but not in tumours or cancer cell lines of non-neural tissue origin. It has been shown that blasts from a subset of patients with acute leukaemia greatly overexpress eight different BAALC transcripts, resulting in five protein isoforms. Among patients with acute myeloid leukaemia, those overexpressing BAALC show distinctly poor prognosis, pointing to a key role of the BAALC products in leukaemia. It has been suggested that BAALC is a gene implicated in both neuroectodermal and hematopoietic cell functions [].; GO: 0005737 cytoplasm
Probab=30.87 E-value=24 Score=21.20 Aligned_cols=22 Identities=32% Similarity=0.490 Sum_probs=16.7
Q ss_pred ceeccCCCCCcchhhhhhcccHH
Q 036249 7 MKFLMNVVKSTEEYYYASEWNEE 29 (68)
Q Consensus 7 M~~~p~~~~~teE~YY~sEwt~e 29 (68)
|=|+.+..++.|..||-+ ||.|
T Consensus 1 mgcggsradaiepry~es-wtre 22 (53)
T PF06989_consen 1 MGCGGSRADAIEPRYYES-WTRE 22 (53)
T ss_pred CCCCccccccccchhhhh-hccc
Confidence 557778889999999975 5544
No 3
>PF10510 PIG-S: Phosphatidylinositol-glycan biosynthesis class S protein; InterPro: IPR019540 Phosphatidylinositol-glycan biosynthesis class S protein (PIG-S) is one of several key, core components of the glycosylphosphatidylinositol (GPI) trans-amidase complex that mediates GPI anchoring in the endoplasmic reticulum. Anchoring occurs when a protein's C-terminal GPI attachment signal peptide is replaced with a pre-assembled GPI []. Mammalian GPI transamidase consists of at least five components: Gaa1, Gpi8, PIG-S, PIG-T, and PIG-U, all five of which are required for its function. It is possible that Gaa1, Gpi8, PIG-S, and PIG-T form a tightly associated core that is only weakly associated with PIG-U. The exact function of PIG-S is unclear [].
Probab=29.10 E-value=25 Score=27.91 Aligned_cols=12 Identities=17% Similarity=0.183 Sum_probs=9.8
Q ss_pred CCcccceeccCC
Q 036249 2 PNVNNMKFLMNV 13 (68)
Q Consensus 2 PqWGgM~~~p~~ 13 (68)
|||||..+..+.
T Consensus 322 PqWGgv~I~N~~ 333 (517)
T PF10510_consen 322 PQWGGVVILNPP 333 (517)
T ss_pred CCcceEEEECCc
Confidence 999999985554
No 4
>COG2993 CcoO Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]
Probab=23.13 E-value=25 Score=26.51 Aligned_cols=25 Identities=8% Similarity=0.203 Sum_probs=17.7
Q ss_pred CcccceeccCCCCCcchhhhhhcccHH
Q 036249 3 NVNNMKFLMNVVKSTEEYYYASEWNEE 29 (68)
Q Consensus 3 qWGgM~~~p~~~~~teE~YY~sEwt~e 29 (68)
||||+-++|+-..+ -++|..+|-..
T Consensus 98 lWGSKRTGPDLaRV--G~ryS~dWH~~ 122 (227)
T COG2993 98 LWGSKRTGPDLARV--GGRYSDDWHRA 122 (227)
T ss_pred hhcCCccCcchhhh--ccccccHHHHH
Confidence 79999997764433 36788888543
No 5
>PF09428 DUF2011: Fungal protein of unknown function (DUF2011); InterPro: IPR018555 This is a family of fungal proteins whose function is unknown.
Probab=21.23 E-value=40 Score=22.86 Aligned_cols=20 Identities=30% Similarity=0.584 Sum_probs=15.9
Q ss_pred hhhhhhcccHHHHhhhccch
Q 036249 19 EYYYASEWNEEEKQKGLHQG 38 (68)
Q Consensus 19 E~YY~sEwt~eE~~~Glh~~ 38 (68)
..||.+.+++++....+..+
T Consensus 19 ~sYYfa~~~~~~~r~qf~~a 38 (131)
T PF09428_consen 19 LSYYFATYTEEERREQFEQA 38 (131)
T ss_pred CcceeCCCChHHHHHHHHHH
Confidence 78999999999965555555
No 6
>PF11033 ComJ: Competence protein J (ComJ); InterPro: IPR020354 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. The proteins in this entry play a role in the competence of cells to be transformed. They inhibit the activity of the DNA-entry nuclease. DNA-entry nuclease inhibitor is a subunit of a 75 kDa protein complex, which governs binding and entry of donor DNA. The complex is a tetramer of two subunits of the DNA-entry nuclease and two subunits of a competence-specific protein ComJ. Only the complex is able to bind ds- and ss-DNA []. It is found in the plasma membrane.
Probab=21.04 E-value=47 Score=22.74 Aligned_cols=15 Identities=20% Similarity=0.652 Sum_probs=13.0
Q ss_pred hcccHHHHhhhccch
Q 036249 24 SEWNEEEKQKGLHQG 38 (68)
Q Consensus 24 sEwt~eE~~~Glh~~ 38 (68)
.+||++..++|+...
T Consensus 22 ~dWtde~i~qG~a~~ 36 (125)
T PF11033_consen 22 IDWTDEDIEQGYAWA 36 (125)
T ss_pred cccCHhHHhCcceec
Confidence 589999999998654
No 7
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=19.44 E-value=67 Score=16.97 Aligned_cols=18 Identities=33% Similarity=0.396 Sum_probs=13.5
Q ss_pred hhhhhhc--ccHHHHhhhcc
Q 036249 19 EYYYASE--WNEEEKQKGLH 36 (68)
Q Consensus 19 E~YY~sE--wt~eE~~~Glh 36 (68)
..-|+.| +|++|++..|.
T Consensus 7 rNrYV~eh~ls~ee~~~RL~ 26 (28)
T PF12368_consen 7 RNRYVKEHGLSEEEVAERLA 26 (28)
T ss_pred chhhHHhcCCCHHHHHHHHH
Confidence 4568865 99999987664
No 8
>PF00573 Ribosomal_L4: Ribosomal protein L4/L1 family; InterPro: IPR002136 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes ribosomal L4/L1 from eukaryotes and plants and L4 from bacteria. L4 from yeast has been shown to bind rRNA []. These proteins have 246 (plant) to 427 (human) amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_D 1VSA_D 3D5D_F 3MS1_E 3F1F_F 3PYO_E 3MRZ_E 3F1H_F 3PYR_E 1VSP_D ....
Probab=16.80 E-value=1e+02 Score=21.60 Aligned_cols=45 Identities=18% Similarity=0.160 Sum_probs=28.7
Q ss_pred CCc--ccceeccCCCCCcchhhhhhcccHHHHhhhccch-hhhHHhhhhcccc
Q 036249 2 PNV--NNMKFLMNVVKSTEEYYYASEWNEEEKQKGLHQG-SLRFAENSRSERG 51 (68)
Q Consensus 2 PqW--GgM~~~p~~~~~teE~YY~sEwt~eE~~~Glh~~-s~kFA~nsrsErg 51 (68)
|+| ||+.|+|-. +.+|+. .-+..++..+|..+ +.|++++.-.-.+
T Consensus 65 P~~rgGg~afgPkp----~r~~~~-klnkK~r~lAl~~aLs~k~~~~~l~vvd 112 (192)
T PF00573_consen 65 PQWRGGGVAFGPKP----PRDYSY-KLNKKVRRLALRSALSAKAAEGNLIVVD 112 (192)
T ss_dssp TTSTTSSBSSSSSS----TSBCSH-HHHHHHHHHHHHHHHHHHHHTTHHHHCT
T ss_pred ceeeccEEecCCcc----ccccee-cCChHHHHHHHHHHHHHhhcccceEEee
Confidence 455 888884333 235554 34777888888766 7888877655444
No 9
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=16.69 E-value=1.2e+02 Score=23.83 Aligned_cols=31 Identities=13% Similarity=0.220 Sum_probs=22.7
Q ss_pred CCCCCcchhhhh-----hcccHHHHhhhccchhhhH
Q 036249 12 NVVKSTEEYYYA-----SEWNEEEKQKGLHQGSLRF 42 (68)
Q Consensus 12 ~~~~~teE~YY~-----sEwt~eE~~~Glh~~s~kF 42 (68)
.++.+...|||. ..-|.+|+++-+..-++|+
T Consensus 21 ~~~~~~~~d~Y~vLGV~~~As~~eIKkAYrkla~k~ 56 (421)
T PTZ00037 21 RKREVDNEKLYEVLNLSKDCTTSEIKKAYRKLAIKH 56 (421)
T ss_pred ccccccchhHHHHcCCCCCCCHHHHHHHHHHHHHHH
Confidence 344556789997 5778999999887666654
No 10
>COG4171 SapC ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]
Probab=15.75 E-value=38 Score=26.30 Aligned_cols=20 Identities=25% Similarity=0.504 Sum_probs=14.7
Q ss_pred CCcccceeccCCCCCcchhhhhhccc
Q 036249 2 PNVNNMKFLMNVVKSTEEYYYASEWN 27 (68)
Q Consensus 2 PqWGgM~~~p~~~~~teE~YY~sEwt 27 (68)
|.||.|+ +| .-|=-|++-||
T Consensus 246 pEWGAMl-----gD-sleLiY~APWT 265 (296)
T COG4171 246 PEWGAML-----GD-SLELIYVAPWT 265 (296)
T ss_pred chHHHHh-----cc-chheeeecccc
Confidence 7899999 33 33567888887
Done!