Query 027921
Match_columns 217
No_of_seqs 157 out of 1015
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 03:30:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027921.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027921hhsearch_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 1E-41 2.2E-46 283.9 15.5 168 12-194 46-214 (222)
2 PF04117 Mpv17_PMP22: Mpv17 / 99.9 9.6E-26 2.1E-30 154.8 4.7 68 126-193 1-68 (68)
3 PF03818 MadM: Malonate/sodium 38.5 74 0.0016 21.0 4.0 37 7-43 3-39 (60)
4 PF00140 Sigma70_r1_2: Sigma-7 23.3 31 0.00066 20.2 0.2 17 4-20 3-19 (37)
5 cd02577 PSTD1 PSTD1: Pseudouri 17.5 1.3E+02 0.0028 26.6 3.0 29 165-193 229-258 (319)
6 TIGR02163 napH_ ferredoxin-typ 17.2 2.8E+02 0.0061 23.4 4.9 70 60-132 4-79 (255)
7 TIGR00799 mtp Golgi 4-transmem 16.5 96 0.0021 26.3 1.8 16 176-191 199-214 (258)
8 COG1369 POP5 RNase P/RNase MRP 15.5 1.5E+02 0.0033 22.5 2.5 51 161-212 18-68 (124)
9 PF09726 Macoilin: Transmembra 15.4 1.9E+02 0.0042 28.4 3.9 28 160-189 87-114 (697)
10 PF04854 DUF624: Protein of un 15.1 3.7E+02 0.0081 17.7 4.3 39 114-152 21-63 (77)
No 1
>KOG1944 consensus Peroxisomal membrane protein MPV17 and related proteins [General function prediction only]
Probab=100.00 E-value=1e-41 Score=283.91 Aligned_cols=168 Identities=36% Similarity=0.650 Sum_probs=157.9
Q ss_pred HhhCchHHHHHHHHHHH-HHHHHHHhhhhhhhhhhhhccccccccccchHHHHHHHHhhcccccchhHHHHHHHHHHHhh
Q 027921 12 LAVHPLKTQVISSGFLW-GVGDIAAQYITHATAKSRLQLSDADEKFKVNWKRVAVTSSFGFGFVGPVGHFWYEGLDRFIR 90 (217)
Q Consensus 12 l~~~Pl~tk~~ts~~l~-~~gD~laQ~~~~~~~~~~~~~~~~~~~~~~D~~R~~~~~~~G~~~~gP~~h~wy~~Ld~~~~ 90 (217)
...+|+++++++++.+. .+||+++|.++..... . ...+|+.|++||+++|+++.||.+|+||..||+++|
T Consensus 46 ~~~~~~l~~~i~~~~~~~~~~d~~~q~~~~~~~~--------~-~~~~d~~rtlr~~~~G~~f~gp~~~~Wy~~L~~~~p 116 (222)
T KOG1944|consen 46 FSLYPLLTKAITTSLLLAAAGDVISQSLEGRSKK--------L-FQTLDLTRTLRMGIFGFLFVGPTLHYWYRLLSKLFP 116 (222)
T ss_pred hhhhhHHHHHHHHHHHHHHhchhhhhhhhhhccc--------c-cccccHHHHHHHHhhhhheeccchhHHHHHHHHHcc
Confidence 35689999999998888 9999999999987531 0 468999999999999988999999999999999996
Q ss_pred hhcCCCCCchHHHHHHHHhhhhhhhhhHHHHHHHHHHhhCCCChHHHHHHHHhhhHHHHHhccccchhhhhhheeeecCc
Q 027921 91 LKLQLPPKSARFVATKVAMDSIIFGPLDLFVFFTYMGFSTGKNVAQVKEDLKRDFLPALVLEGGIWPIVQVANFRYVPVR 170 (217)
Q Consensus 91 ~~~~~~~~~~~~~~~Kvl~DQ~v~~P~~~~~f~~~~~~l~g~s~~~~~~~lk~~~~~~l~~~~~~Wp~~q~inF~~VP~~ 170 (217)
.++..++++|+++||++++|+.+.+||.+++++||++.+++.++++++++|++++||++||++|++||++||++
T Consensus 117 ------~~~~~~~~~kvl~dql~~~P~~~~~ff~~~~~legk~~~~~~~~~~~~~~p~l~~~~~~WP~~q~inF~~VP~~ 190 (222)
T KOG1944|consen 117 ------KKTLITVVKKVLLDQLVFAPLFIVVFFLLMGLLEGKTNEEAKAKLKRKFWPTLKANWMVWPLVQFINFRLVPLQ 190 (222)
T ss_pred ------CccHHHHHHHHHHhhhhhchHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhheecchhheeeeEEcccc
Confidence 56889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhhHHHHHHHHHHHHhhccc
Q 027921 171 YQLLYVNIFCLLDSAFLSWVEQQK 194 (217)
Q Consensus 171 ~Rvlf~n~v~~~W~~yLS~~~~~~ 194 (217)
+|++++|+++++||+|||+++++.
T Consensus 191 ~rvl~~~~vsl~W~~~Ls~~~~~~ 214 (222)
T KOG1944|consen 191 YRVLFVNIVSLVWNTYLSYKNASL 214 (222)
T ss_pred ceehhhhhHHHHHHHHHHHHhhcc
Confidence 999999999999999999999998
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=99.92 E-value=9.6e-26 Score=154.78 Aligned_cols=68 Identities=40% Similarity=0.820 Sum_probs=66.4
Q ss_pred HHhhCCCChHHHHHHHHhhhHHHHHhccccchhhhhhheeeecCccchhhhhHHHHHHHHHHHHhhcc
Q 027921 126 MGFSTGKNVAQVKEDLKRDFLPALVLEGGIWPIVQVANFRYVPVRYQLLYVNIFCLLDSAFLSWVEQQ 193 (217)
Q Consensus 126 ~~~l~g~s~~~~~~~lk~~~~~~l~~~~~~Wp~~q~inF~~VP~~~Rvlf~n~v~~~W~~yLS~~~~~ 193 (217)
|+++||++++++++++|++|+++++++|++|||+|++||+|||+++|++|+|+++++||+|||+++||
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 57899999999999999999999999999999999999999999999999999999999999999986
No 3
>PF03818 MadM: Malonate/sodium symporter MadM subunit; InterPro: IPR018402 The MSS family includes the monobasic malonate:Na+ symporter of Malonomonas rubra. It consists of two integral membrane proteins, MadL and MadM.The transporter is believed to catalyze the electroneutral reversible uptake of H+-malonate with one Na+, and both subunits have been shown to be essential for activity.
Probab=38.47 E-value=74 Score=21.00 Aligned_cols=37 Identities=16% Similarity=0.129 Sum_probs=32.6
Q ss_pred HHHHHHhhCchHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 027921 7 WYQNCLAVHPLKTQVISSGFLWGVGDIAAQYITHATA 43 (217)
Q Consensus 7 ~Y~~~l~~~Pl~tk~~ts~~l~~~gD~laQ~~~~~~~ 43 (217)
...+.++++.|+|.-..-|+++.++..++-++++.+-
T Consensus 3 ~i~~vl~~ngLitaFa~vG~~m~~S~~lS~~LT~Gri 39 (60)
T PF03818_consen 3 MIEKVLTKNGLITAFAVVGIIMWVSYWLSKKLTRGRI 39 (60)
T ss_pred HHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 3466789999999999999999999999999998753
No 4
>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....
Probab=23.31 E-value=31 Score=20.18 Aligned_cols=17 Identities=24% Similarity=0.278 Sum_probs=13.5
Q ss_pred HHHHHHHHHhhCchHHH
Q 027921 4 LWKWYQNCLAVHPLKTQ 20 (217)
Q Consensus 4 l~~~Y~~~l~~~Pl~tk 20 (217)
.++.|.+.+.++||+|.
T Consensus 3 ~l~~Yl~ei~~~~LLt~ 19 (37)
T PF00140_consen 3 SLRLYLKEIGRYPLLTA 19 (37)
T ss_dssp HHHHHHHHHHHS-EETT
T ss_pred HHHHHHHHHcCCCCCCH
Confidence 46789999999999875
No 5
>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=17.52 E-value=1.3e+02 Score=26.62 Aligned_cols=29 Identities=17% Similarity=0.164 Sum_probs=24.3
Q ss_pred eeecCccchhhhhH-HHHHHHHHHHHhhcc
Q 027921 165 RYVPVRYQLLYVNI-FCLLDSAFLSWVEQQ 193 (217)
Q Consensus 165 ~~VP~~~Rvlf~n~-v~~~W~~yLS~~~~~ 193 (217)
.-+|...|.+|++. -|.+||-.+|..-..
T Consensus 229 ~~iP~~lr~myvhAYQSylfN~~lS~Ri~~ 258 (319)
T cd02577 229 LALPKNLRRMFVHAYQSYLFNEILSERIEE 258 (319)
T ss_pred HhcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46999999998866 799999999987653
No 6
>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=17.20 E-value=2.8e+02 Score=23.37 Aligned_cols=70 Identities=14% Similarity=0.273 Sum_probs=41.4
Q ss_pred HHHHHHHHhhcccccchhHHHHH--HHHH--HHhhhhcCCCCCchHHHHHHHHhhhhhhhhhHHHHHH--HHHHhhCCC
Q 027921 60 WKRVAVTSSFGFGFVGPVGHFWY--EGLD--RFIRLKLQLPPKSARFVATKVAMDSIIFGPLDLFVFF--TYMGFSTGK 132 (217)
Q Consensus 60 ~~R~~~~~~~G~~~~gP~~h~wy--~~Ld--~~~~~~~~~~~~~~~~~~~Kvl~DQ~v~~P~~~~~f~--~~~~~l~g~ 132 (217)
+||+...++...++.||..+.|. +-|. ++++ . .|-.+...++.-++..+.+..+++....+ ...+++-|+
T Consensus 4 ~r~~~~~~~~~lf~~~~~~~~~~~~G~l~~s~~~~-~--~~l~dP~~~lq~~~a~~~~~~~~~~~~~iv~~~~~l~~GR 79 (255)
T TIGR02163 4 LRRLVQLSILGLFLLGPYAGVWILKGNLSSSRLLG-T--IPLSDPLITLQILLAGHSPPTNALIGALIIVAFYALFGGR 79 (255)
T ss_pred HHHHHHHHHHHHHHcchhhcceEEEecchHHHhcC-C--ccCcCHHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHhcc
Confidence 68888888888877889877775 3332 3332 1 12344455555566666655555554433 333566666
No 7
>TIGR00799 mtp Golgi 4-transmembrane spanning transporter. The proteins of the MET family have 4 TMS regions and are located in late endosomal or lysosomal membranes. Substrates of the mouse MTP transporter include thymidine, both nucleoside and nucleobase analogues, antibiotics, anthracyclines, ionophores and steroid hormones. MET transporters may be involved in the subcellular compartmentation of steroid hormones and other compounds.Drug sensitivity by mouse MET was regulated by compounds that inhibit lysosomal function, interface with intracellular cholesterol transport, or modulate the multidrug resistance phenotype of mammalian cells. Thus, MET family members may compartmentalize diverse hydrophobic molecules, thereby affecting cellular drug sensitivity,nucleoside/nucleobase availability and steroid hormone responses.
Probab=16.48 E-value=96 Score=26.27 Aligned_cols=16 Identities=13% Similarity=0.079 Sum_probs=11.2
Q ss_pred hhHHHHHHHHHHHHhh
Q 027921 176 VNIFCLLDSAFLSWVE 191 (217)
Q Consensus 176 ~n~v~~~W~~yLS~~~ 191 (217)
+-+++++||||=...+
T Consensus 199 aYlI~cVWrCYkyl~~ 214 (258)
T TIGR00799 199 VYMFKCVWNCYKYIKN 214 (258)
T ss_pred HHHHHHHHHHHHHhhc
Confidence 3468899999954433
No 8
>COG1369 POP5 RNase P/RNase MRP subunit POP5 [Translation, ribosomal structure and biogenesis]
Probab=15.50 E-value=1.5e+02 Score=22.50 Aligned_cols=51 Identities=12% Similarity=0.132 Sum_probs=42.3
Q ss_pred hhheeeecCccchhhhhHHHHHHHHHHHHhhccccccchhhhcccccccccC
Q 027921 161 VANFRYVPVRYQLLYVNIFCLLDSAFLSWVEQQKDAAWKQWFTSFHSLEERG 212 (217)
Q Consensus 161 ~inF~~VP~~~Rvlf~n~v~~~W~~yLS~~~~~~~~~~~~~~~~~~~~~~~~ 212 (217)
++.|..++. .-+-...+...+|+..++..-.-..+.-+.++-.|++-+.+|
T Consensus 18 Yiaf~vise-~~i~~~~l~~~I~~s~l~llG~~gta~~~~~lv~~~~~t~~G 68 (124)
T COG1369 18 YIAFEVISE-EEITRGELVRLIRRSLLSLLGDVGTAKANPRLVKYYFSTGTG 68 (124)
T ss_pred EEEEEEecc-ccCChhHHHHHHHHHHHHHcCcccccccceeEEEEeccCCce
Confidence 567777776 667788999999999999999988888889999888775554
No 9
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=15.37 E-value=1.9e+02 Score=28.44 Aligned_cols=28 Identities=7% Similarity=0.260 Sum_probs=16.5
Q ss_pred hhhheeeecCccchhhhhHHHHHHHHHHHH
Q 027921 160 QVANFRYVPVRYQLLYVNIFCLLDSAFLSW 189 (217)
Q Consensus 160 q~inF~~VP~~~Rvlf~n~v~~~W~~yLS~ 189 (217)
.+|.|.|||.++=+.+.+ .++|.-|+-+
T Consensus 87 d~~~~~~~p~~~~~~~~~--~~v~~~~~~~ 114 (697)
T PF09726_consen 87 DLICLFFIPVHWLFFAAS--TYVWVQYVWH 114 (697)
T ss_pred HHHHHHHHHHHHHHHHHh--HHHHHHHhhh
Confidence 677788888876444333 3555555443
No 10
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=15.07 E-value=3.7e+02 Score=17.72 Aligned_cols=39 Identities=15% Similarity=0.388 Sum_probs=22.0
Q ss_pred hhhhHHHHHHHHHHhhCCC-C---hHHHHHHHHhhhHHHHHhc
Q 027921 114 FGPLDLFVFFTYMGFSTGK-N---VAQVKEDLKRDFLPALVLE 152 (217)
Q Consensus 114 ~~P~~~~~f~~~~~~l~g~-s---~~~~~~~lk~~~~~~l~~~ 152 (217)
..|-..+.+.+.....+++ + +++-.+..|+++......+
T Consensus 21 igPA~~Al~~~~~~~~~~~~~~~~~~~f~~~fk~nf~~~~~~~ 63 (77)
T PF04854_consen 21 IGPATAALYYVVRKWVRDEEDSYLFRDFWRAFKQNFKQSLLLG 63 (77)
T ss_pred HHHHHHHHHHHHHHHHcCCccChHHHHHHHHHHHHHHHHHHHH
Confidence 5566666777777676766 2 2344455555555544433
Done!