Query 030708
Match_columns 173
No_of_seqs 135 out of 947
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 03:24:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030708.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030708hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1944 Peroxisomal membrane p 100.0 1.1E-39 2.3E-44 263.9 11.3 144 1-150 69-214 (222)
2 PF04117 Mpv17_PMP22: Mpv17 / 99.9 2.2E-26 4.8E-31 153.9 4.9 68 82-149 1-68 (68)
3 TIGR02163 napH_ ferredoxin-typ 27.7 1.5E+02 0.0032 24.3 5.1 83 16-101 4-102 (255)
4 PF07960 CBP4: CBP4; InterPro 22.4 58 0.0013 24.3 1.6 26 13-38 2-29 (128)
5 PRK04307 putative disulfide ox 22.2 74 0.0016 25.9 2.3 55 92-149 160-214 (218)
6 PF12191 stn_TNFRSF12A: Tumour 21.5 31 0.00067 25.7 0.0 10 162-171 112-121 (129)
7 PF02375 JmjN: jmjN domain; I 21.2 27 0.00057 19.9 -0.3 8 159-166 1-8 (34)
8 PF15128 T_cell_tran_alt: T-ce 21.1 2.7E+02 0.0058 19.4 4.5 38 30-74 4-41 (92)
9 PF10960 DUF2762: Protein of u 17.0 1.7E+02 0.0037 19.4 2.8 25 59-83 4-28 (71)
10 cd02577 PSTD1 PSTD1: Pseudouri 16.9 1.5E+02 0.0032 25.4 3.1 28 121-148 229-257 (319)
No 1
>KOG1944 consensus Peroxisomal membrane protein MPV17 and related proteins [General function prediction only]
Probab=100.00 E-value=1.1e-39 Score=263.89 Aligned_cols=144 Identities=35% Similarity=0.653 Sum_probs=136.6
Q ss_pred CCccccccCC--CCcccHHHHHHHhHhcccccchHHHHHHHHHHHHhhhhcCCCCCcHHHHHHHHHHhhhhhhhHHHHHH
Q 030708 1 MCLTGQDADE--KFKVNWKRVAVTSSFGFGFVGPVGHFWYEGLDRFIRLKLQLPPKSARFVATKVAMDSIIFGPLDLFVF 78 (173)
Q Consensus 1 ~cq~~~~~~~--~~~~D~~Rt~~~~~~G~~~~gP~~h~wy~~Ld~~~~~~~~~~~~~~~~~~~Kv~~DQ~v~~P~~~~~F 78 (173)
++|...++.+ .+++|+.|++||+++|+++.||.+|+||+.||+++| .++..++++|+++||++++|+.+.+|
T Consensus 69 ~~q~~~~~~~~~~~~~d~~rtlr~~~~G~~f~gp~~~~Wy~~L~~~~p------~~~~~~~~~kvl~dql~~~P~~~~~f 142 (222)
T KOG1944|consen 69 ISQSLEGRSKKLFQTLDLTRTLRMGIFGFLFVGPTLHYWYRLLSKLFP------KKTLITVVKKVLLDQLVFAPLFIVVF 142 (222)
T ss_pred hhhhhhhhcccccccccHHHHHHHHhhhhheeccchhHHHHHHHHHcc------CccHHHHHHHHHHhhhhhchHHHHHH
Confidence 3566666655 589999999999999988999999999999999996 56889999999999999999999999
Q ss_pred HHHHHhcCCCChHHHHHHHHhchHHHHHhccccchHHHhhhheeecCccchhhhhHhHHHHHHHHHHhhccc
Q 030708 79 FTYMGFSTGKNVAQVKEDLKRDFLPALVLEGGIWPIVQVANFRYVPVRYQLLYVNIFCLLDSAFLSWVEQQK 150 (173)
Q Consensus 79 ~~~~~~leg~s~~~~~~~l~~~~~~~~~~~~~vWp~~q~iNF~~vP~~~Rvlf~n~v~~~Wn~~LS~~~~~~ 150 (173)
+.+|+++||++.+++.++++++++|+++++|++||++|++||.+||+++|++++|+++++||+|||+++++.
T Consensus 143 f~~~~~legk~~~~~~~~~~~~~~p~l~~~~~~WP~~q~inF~~VP~~~rvl~~~~vsl~W~~~Ls~~~~~~ 214 (222)
T KOG1944|consen 143 FLLMGLLEGKTNEEAKAKLKRKFWPTLKANWMVWPLVQFINFRLVPLQYRVLFVNIVSLVWNTYLSYKNASL 214 (222)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHhhhheecchhheeeeEEccccceehhhhhHHHHHHHHHHHHhhcc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999997
No 2
>PF04117 Mpv17_PMP22: Mpv17 / PMP22 family ; InterPro: IPR007248 The 22 kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore-forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesised on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information []. Mpv17 is a closely related peroxisomal protein involved in the development of early-onset glomerulosclerosis []. A member of this family found in Saccharomyces cerevisiae (Baker's yeast) is an integral membrane protein of the inner mitochondrial membrane and has been suggested to play a role in mitochondrial function during heat shock [].; GO: 0016021 integral to membrane
Probab=99.93 E-value=2.2e-26 Score=153.95 Aligned_cols=68 Identities=40% Similarity=0.820 Sum_probs=66.4
Q ss_pred HHhcCCCChHHHHHHHHhchHHHHHhccccchHHHhhhheeecCccchhhhhHhHHHHHHHHHHhhcc
Q 030708 82 MGFSTGKNVAQVKEDLKRDFLPALVLEGGIWPIVQVANFRYVPVRYQLLYVNIFCLLDSAFLSWVEQQ 149 (173)
Q Consensus 82 ~~~leg~s~~~~~~~l~~~~~~~~~~~~~vWp~~q~iNF~~vP~~~Rvlf~n~v~~~Wn~~LS~~~~~ 149 (173)
|+++||+|++++++++|++++++++++|++|||+|++||.+||+++|++|+|+|+++||+|||+++|+
T Consensus 1 Mg~l~g~s~~~~~~~l~~~~~~~~~~~~~~Wp~~~~vnF~~vP~~~Rv~~~~~v~~~W~~~LS~~~~r 68 (68)
T PF04117_consen 1 MGLLEGKSWEEIKEKLKRDYWPTLKASWKFWPPAQIVNFRYVPPHYRVLFVNVVSFFWNTYLSYIANR 68 (68)
T ss_pred CCcccCCCHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHhcccChhhhhhhhhhHHHHHHHHHHHHhcC
Confidence 57899999999999999999999999999999999999999999999999999999999999999985
No 3
>TIGR02163 napH_ ferredoxin-type protein, NapH/MauN family. Most members of this family are the NapH protein, found next to NapG,in operons that encode the periplasmic nitrate reductase. Some species with this reductase lack NapC but accomplish electron transfer to NapAB in some other manner, likely to involve NapH, NapG, and/or some other protein. A few members of this protein are designated MauN and are found in methylamine utilization operons in species that appear to lack a periplasmic nitrate reductase.
Probab=27.73 E-value=1.5e+02 Score=24.31 Aligned_cols=83 Identities=16% Similarity=0.266 Sum_probs=49.9
Q ss_pred HHHHHHHhHhcccccchHHHHHH--HHHH--HHhhhhcCCCCCcHHHHHHHHHHhhhhhhhHHHHHHH--HHHHhcCCC-
Q 030708 16 WKRVAVTSSFGFGFVGPVGHFWY--EGLD--RFIRLKLQLPPKSARFVATKVAMDSIIFGPLDLFVFF--TYMGFSTGK- 88 (173)
Q Consensus 16 ~~Rt~~~~~~G~~~~gP~~h~wy--~~Ld--~~~~~~~~~~~~~~~~~~~Kv~~DQ~v~~P~~~~~F~--~~~~~leg~- 88 (173)
+||+...++...++.||..+.|. +-|. +.++. +|-.+.-.++.-++.-+.+..+++....+ ...+++-|+
T Consensus 4 ~r~~~~~~~~~lf~~~~~~~~~~~~G~l~~s~~~~~---~~l~dP~~~lq~~~a~~~~~~~~~~~~~iv~~~~~l~~GR~ 80 (255)
T TIGR02163 4 LRRLVQLSILGLFLLGPYAGVWILKGNLSSSRLLGT---IPLSDPLITLQILLAGHSPPTNALIGALIIVAFYALFGGRA 80 (255)
T ss_pred HHHHHHHHHHHHHHcchhhcceEEEecchHHHhcCC---ccCcCHHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHhccc
Confidence 68899999999988899887775 3343 33321 23344455555666666666666555543 333566665
Q ss_pred ---------ChHHHHHHHHhch
Q 030708 89 ---------NVAQVKEDLKRDF 101 (173)
Q Consensus 89 ---------s~~~~~~~l~~~~ 101 (173)
.+.|..++++++.
T Consensus 81 fCgwiCP~g~~~el~~~l~~k~ 102 (255)
T TIGR02163 81 FCSWVCPVNLVTDFAAWLRRKL 102 (255)
T ss_pred ceeccCCchHHHHHHHHHHHhh
Confidence 3456666665543
No 4
>PF07960 CBP4: CBP4; InterPro: IPR012420 The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase [, ]. This family appears to be fungal specific.
Probab=22.44 E-value=58 Score=24.32 Aligned_cols=26 Identities=27% Similarity=0.266 Sum_probs=19.8
Q ss_pred cccHHHHHHHhHhcccc--cchHHHHHH
Q 030708 13 KVNWKRVAVTSSFGFGF--VGPVGHFWY 38 (173)
Q Consensus 13 ~~D~~Rt~~~~~~G~~~--~gP~~h~wy 38 (173)
...|.|.++|.++|+++ .||++..|-
T Consensus 2 ~~~w~~W~K~~~~G~~ii~~G~~l~~y~ 29 (128)
T PF07960_consen 2 PPNWRRWAKMLVAGAVIIGGGPALVKYT 29 (128)
T ss_pred CchHHHHHHHHHhcceeEeechHHheec
Confidence 45789999999999864 477766554
No 5
>PRK04307 putative disulfide oxidoreductase; Provisional
Probab=22.18 E-value=74 Score=25.86 Aligned_cols=55 Identities=13% Similarity=0.056 Sum_probs=42.7
Q ss_pred HHHHHHHhchHHHHHhccccchHHHhhhheeecCccchhhhhHhHHHHHHHHHHhhcc
Q 030708 92 QVKEDLKRDFLPALVLEGGIWPIVQVANFRYVPVRYQLLYVNIFCLLDSAFLSWVEQQ 149 (173)
Q Consensus 92 ~~~~~l~~~~~~~~~~~~~vWp~~q~iNF~~vP~~~Rvlf~n~v~~~Wn~~LS~~~~~ 149 (173)
...+++++.+...|..+|..+|.-+++| +|.-.-+.|....-+.=..++|++...
T Consensus 160 ~~l~~~q~~~~~~y~~gwyl~p~w~f~~---Maq~~~~~f~~~~~~l~~~~~~~~~~~ 214 (218)
T PRK04307 160 VTLSSVQQWFVDLYSEGWYLLPPWHFMN---MAQACLLAFGLCLVLLVVMSGAWALKL 214 (218)
T ss_pred chhHHHHHHHhhhccccccccccHHHhh---HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4567788888899999999999999965 788777777776666666666665554
No 6
>PF12191 stn_TNFRSF12A: Tumour necrosis factor receptor stn_TNFRSF12A_TNFR domain; InterPro: IPR022316 The tumour necrosis factor (TNF) receptor (TNFR) superfamily comprises more than 20 type-I transmembrane proteins. Family members are defined based on similarity in their extracellular domain - a region that contains many cysteine residues arranged in a specific repetitive pattern []. The cysteines allow formation of an extended rod-like structure, responsible for ligand binding []. Upon receptor activation, different intracellular signalling complexes are assembled for different members of the TNFR superfamily, depending on their intracellular domains and sequences []. Activation of TNFRs can therefore induce a range of disparate effects, including cell proliferation, differentiation, survival, or apoptotic cell death, depending upon the receptor involved []. TNFRs are widely distributed and play important roles in many crucial biological processes, such as lymphoid and neuronal development, innate and adaptive immunity, and maintenance of cellular homeostasis []. Drugs that manipulate their signalling have potential roles in the prevention and treatment of many diseases, such as viral infections, coronary heart disease, transplant rejection, and immune disease []. TNF receptor 12 (also known as TWEAK receptor, and fibroblast growth factor-inducible-14 (Fn14)) has been implicated in endothelial cell growth and migration []. The receptor may also play a role in cell-matrix interactions [].; PDB: 2KN0_A 2RPJ_A 2KMZ_A 2EQP_A.
Probab=21.46 E-value=31 Score=25.71 Aligned_cols=10 Identities=50% Similarity=1.029 Sum_probs=0.0
Q ss_pred ccccccCCCC
Q 030708 162 HSLEERGGKG 171 (173)
Q Consensus 162 ~~~~~~~~~~ 171 (173)
+|-|||||.|
T Consensus 112 tPIeeTgg~~ 121 (129)
T PF12191_consen 112 TPIEETGGEG 121 (129)
T ss_dssp ----------
T ss_pred CcccccCCCC
Confidence 4999999987
No 7
>PF02375 JmjN: jmjN domain; InterPro: IPR003349 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with JmjC (see IPR003347 from INTERPRO).; PDB: 2XML_A 2W2I_C 3DXT_A 3DXU_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=21.15 E-value=27 Score=19.91 Aligned_cols=8 Identities=25% Similarity=0.194 Sum_probs=3.6
Q ss_pred cccccccc
Q 030708 159 TSFHSLEE 166 (173)
Q Consensus 159 ~~~~~~~~ 166 (173)
|++|||+|
T Consensus 1 Pvf~Pt~e 8 (34)
T PF02375_consen 1 PVFYPTME 8 (34)
T ss_dssp EEE---HH
T ss_pred CcccCCHH
Confidence 67888876
No 8
>PF15128 T_cell_tran_alt: T-cell leukemia translocation-altered
Probab=21.06 E-value=2.7e+02 Score=19.38 Aligned_cols=38 Identities=16% Similarity=0.210 Sum_probs=30.5
Q ss_pred cchHHHHHHHHHHHHhhhhcCCCCCcHHHHHHHHHHhhhhhhhHH
Q 030708 30 VGPVGHFWYEGLDRFIRLKLQLPPKSARFVATKVAMDSIIFGPLD 74 (173)
Q Consensus 30 ~gP~~h~wy~~Ld~~~~~~~~~~~~~~~~~~~Kv~~DQ~v~~P~~ 74 (173)
.+.+..++.++++.+- ..+.+..+.|+++--++.+-+.
T Consensus 4 ~d~~~sf~sef~~dW~-------a~Dmrv~ifkllL~WlvlsLl~ 41 (92)
T PF15128_consen 4 LDSLLSFLSEFVDDWE-------ANDMRVQIFKLLLGWLVLSLLA 41 (92)
T ss_pred HHHHHHHHHHHHHHHH-------hccHHHHHHHHHHHHHHHHHHH
Confidence 3556778889998887 5688999999999988887764
No 9
>PF10960 DUF2762: Protein of unknown function (DUF2762); InterPro: IPR024405 BhlA is a SP-beta prophage-derived protein found in Bacillus subtilis [, ] and other Bacilli. A related protein, UviB, has also been described in Clostridia, where it is believed to be involved in bacteriocin secretion or immunity [, ].
Probab=16.97 E-value=1.7e+02 Score=19.44 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=19.8
Q ss_pred HHHHHHHhhhhhhhHHHHHHHHHHH
Q 030708 59 VATKVAMDSIIFGPLDLFVFFTYMG 83 (173)
Q Consensus 59 ~~~Kv~~DQ~v~~P~~~~~F~~~~~ 83 (173)
-+.|+++.|-+||-++...+++.+-
T Consensus 4 ei~k~~~sQG~fA~LFv~Ll~yvlK 28 (71)
T PF10960_consen 4 EIIKLALSQGIFAVLFVWLLFYVLK 28 (71)
T ss_pred HHHHHHHHcCcHHHHHHHHHHHHHH
Confidence 3678999999999988777766554
No 10
>cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD.
Probab=16.89 E-value=1.5e+02 Score=25.41 Aligned_cols=28 Identities=18% Similarity=0.150 Sum_probs=22.6
Q ss_pred eeecCccchhhhhH-hHHHHHHHHHHhhc
Q 030708 121 RYVPVRYQLLYVNI-FCLLDSAFLSWVEQ 148 (173)
Q Consensus 121 ~~vP~~~Rvlf~n~-v~~~Wn~~LS~~~~ 148 (173)
.-+|...|.+|++. -|.+||-.+|..-.
T Consensus 229 ~~iP~~lr~myvhAYQSylfN~~lS~Ri~ 257 (319)
T cd02577 229 LALPKNLRRMFVHAYQSYLFNEILSERIE 257 (319)
T ss_pred HhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35999999988875 58999999996543
Done!