Query 041783
Match_columns 225
No_of_seqs 148 out of 1106
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 10:37:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041783.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041783hhsearch_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 7.5E-41 1.6E-45 282.0 15.7 168 12-203 46-214 (222)
2 PF04117 Mpv17_PMP22: Mpv17 / 99.9 1.6E-25 3.6E-30 155.4 4.8 68 135-202 1-68 (68)
3 PF03818 MadM: Malonate/sodium 53.0 33 0.00071 22.9 4.1 36 7-42 3-38 (60)
4 cd02577 PSTD1 PSTD1: Pseudouri 30.7 44 0.00095 29.9 2.7 30 173-202 228-258 (319)
5 PF09396 Thrombin_light: Throm 25.2 27 0.00058 22.3 0.2 16 200-215 31-46 (49)
6 PF13268 DUF4059: Protein of u 20.3 39 0.00084 23.4 0.3 28 182-209 17-44 (72)
7 TIGR00799 mtp Golgi 4-transmem 19.5 1.1E+02 0.0025 26.2 2.9 17 186-203 200-216 (258)
8 PF00140 Sigma70_r1_2: Sigma-7 17.1 72 0.0016 18.8 0.9 17 4-20 3-19 (37)
9 PF03821 Mtp: Golgi 4-transmem 16.9 1.2E+02 0.0026 25.9 2.6 16 186-201 176-191 (233)
10 PF07960 CBP4: CBP4; InterPro 15.9 91 0.002 24.1 1.4 25 67-91 3-29 (128)
No 1
>KOG1944 consensus Peroxisomal membrane protein MPV17 and related proteins [General function prediction only]
Probab=100.00 E-value=7.5e-41 Score=282.03 Aligned_cols=168 Identities=35% Similarity=0.636 Sum_probs=157.0
Q ss_pred HhhCchHHHHHHHHHHH-HHhHHHHHhhhhhhhhhhcccCCCCCcccCCCCCCCccchHHHHHHHHHhccccchhhHHHH
Q 041783 12 LAVHPVKTQVVSSGLIW-GFGDVAAQSITHLTAQNRLHNQNEKSTEDTGNGNNELKLNWNRVAKTSFFGFAFVGPVGHFW 90 (225)
Q Consensus 12 l~~~Pl~t~~~ts~~l~-~~gD~iaQ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~D~~R~~r~~~~G~~~~gP~~h~w 90 (225)
...+|++++.++++.+. .+||+++|.++..++. . ...+|+.|++||+++|+++.||.+|+|
T Consensus 46 ~~~~~~l~~~i~~~~~~~~~~d~~~q~~~~~~~~-----------------~-~~~~d~~rtlr~~~~G~~f~gp~~~~W 107 (222)
T KOG1944|consen 46 FSLYPLLTKAITTSLLLAAAGDVISQSLEGRSKK-----------------L-FQTLDLTRTLRMGIFGFLFVGPTLHYW 107 (222)
T ss_pred hhhhhHHHHHHHHHHHHHHhchhhhhhhhhhccc-----------------c-cccccHHHHHHHHhhhhheeccchhHH
Confidence 35688888888888888 9999999999987531 0 357999999999999988999999999
Q ss_pred HHHHHHhhhhhccCCCCChHHHHHHHHHhhhhhhhHHHHHHHHHHHhhcCCChhhHHHHHHHhhHHHHHhccccchhhhh
Q 041783 91 YEGLDRFIRNRFLMQPNSPRFVATKVAIDGGLFGPLDLLVFFSYMGFAAGKSFPQVKEDVKRDFLPALILEGGLWPLLQV 170 (225)
Q Consensus 91 y~~Ld~~~~~~~~~~~~~~~~v~~Kv~~Dq~i~~P~~~~~F~~~~~~l~G~s~~~~~~~lk~~~~~~l~~~~~~Wp~~q~ 170 (225)
|..||+.+| .++..++++|+++||++++|+.+.+||.+++++||++.+++.++++++++|+++++|++||++|+
T Consensus 108 y~~L~~~~p------~~~~~~~~~kvl~dql~~~P~~~~~ff~~~~~legk~~~~~~~~~~~~~~p~l~~~~~~WP~~q~ 181 (222)
T KOG1944|consen 108 YRLLSKLFP------KKTLITVVKKVLLDQLVFAPLFIVVFFLLMGLLEGKTNEEAKAKLKRKFWPTLKANWMVWPLVQF 181 (222)
T ss_pred HHHHHHHcc------CccHHHHHHHHHHhhhhhchHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhheecchhhe
Confidence 999999997 57889999999999999999999999999999999999999999999999999999999999999
Q ss_pred hheeeecCCcchhhhhHHHHHHHHHHHHhhhCC
Q 041783 171 ANFRFVPVPYQLLYVNIFCLLDSCFLSWIEQQE 203 (225)
Q Consensus 171 inF~~VP~~~Rvlf~n~v~~~Wn~yLS~~~~~~ 203 (225)
+||++||+++|++++|+++++||+|||+++++.
T Consensus 182 inF~~VP~~~rvl~~~~vsl~W~~~Ls~~~~~~ 214 (222)
T KOG1944|consen 182 INFRLVPLQYRVLFVNIVSLVWNTYLSYKNASL 214 (222)
T ss_pred eeeEEccccceehhhhhHHHHHHHHHHHHhhcc
Confidence 999999999999999999999999999999998
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=1.6e-25 Score=155.44 Aligned_cols=68 Identities=40% Similarity=0.824 Sum_probs=66.4
Q ss_pred HHhhcCCChhhHHHHHHHhhHHHHHhccccchhhhhhheeeecCCcchhhhhHHHHHHHHHHHHhhhC
Q 041783 135 MGFAAGKSFPQVKEDVKRDFLPALILEGGLWPLLQVANFRFVPVPYQLLYVNIFCLLDSCFLSWIEQQ 202 (225)
Q Consensus 135 ~~~l~G~s~~~~~~~lk~~~~~~l~~~~~~Wp~~q~inF~~VP~~~Rvlf~n~v~~~Wn~yLS~~~~~ 202 (225)
|+++||+++++++++++++|+++++++|++|||+|++||.|||+++|++|+|+++++||+|||+++|+
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 67899999999999999999999999999999999999999999999999999999999999999986
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=52.95 E-value=33 Score=22.94 Aligned_cols=36 Identities=14% Similarity=0.093 Sum_probs=32.2
Q ss_pred HHHHHHhhCchHHHHHHHHHHHHHhHHHHHhhhhhh
Q 041783 7 WYQNCLAVHPVKTQVVSSGLIWGFGDVAAQSITHLT 42 (225)
Q Consensus 7 ~Y~~~l~~~Pl~t~~~ts~~l~~~gD~iaQ~~~~~~ 42 (225)
...+.++++.|+|..+.-|+++.++..++-.++..|
T Consensus 3 ~i~~vl~~ngLitaFa~vG~~m~~S~~lS~~LT~Gr 38 (60)
T PF03818_consen 3 MIEKVLTKNGLITAFAVVGIIMWVSYWLSKKLTRGR 38 (60)
T ss_pred HHHHHHhhCchHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 346789999999999999999999999999998765
No 4
>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=30.70 E-value=44 Score=29.86 Aligned_cols=30 Identities=20% Similarity=0.269 Sum_probs=25.7
Q ss_pred eeeecCCcchhhhhHH-HHHHHHHHHHhhhC
Q 041783 173 FRFVPVPYQLLYVNIF-CLLDSCFLSWIEQQ 202 (225)
Q Consensus 173 F~~VP~~~Rvlf~n~v-~~~Wn~yLS~~~~~ 202 (225)
|.-+|...|.+|++.. |.+||-.+|..-..
T Consensus 228 l~~iP~~lr~myvhAYQSylfN~~lS~Ri~~ 258 (319)
T cd02577 228 FLALPKNLRRMFVHAYQSYLFNEILSERIEE 258 (319)
T ss_pred HHhcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3469999999999986 99999999987753
No 5
>PF09396 Thrombin_light: Thrombin light chain; InterPro: IPR018992 Thrombin is a Na+-activated, allosteric serine protease that functions in blood homeostasis, inflammation and wound healing []. Thrombin (or coagulation factor II) is an enzyme that cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, and (in complex with thrombomodulin) protein C []. Sodium binding is the major driving force behind the procoagulant, prothrombotic and signaling functions of the enzyme, but is dispensable for cleavage of the anticoagulant protein C []. Prothrombin is activated on the surface of a phospholipid membrane where factor Xa removes the activation peptide and cleaves the remaining part into light and heavy chains. This domain corresponds to the light chain of thrombin. ; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis, 0007596 blood coagulation, 0005576 extracellular region; PDB: 3HKI_D 2OCV_A 3EDX_A 3HK6_C 2PV9_A 2PUX_A 3HK3_A 1HRT_L 1TOC_G 1ETT_L ....
Probab=25.17 E-value=27 Score=22.29 Aligned_cols=16 Identities=19% Similarity=0.470 Sum_probs=11.0
Q ss_pred hhCCCcccchhhhccc
Q 041783 200 EQQEDAPWKQWIKSFL 215 (225)
Q Consensus 200 ~~~~~~~~~~~~~~~~ 215 (225)
.+.++..|+|+|.||.
T Consensus 31 k~~~D~~E~ELleSY~ 46 (49)
T PF09396_consen 31 KSKKDKTEKELLESYI 46 (49)
T ss_dssp GT---TTHHHHHHHHH
T ss_pred hcccccCHHHHHHHHh
Confidence 4567889999999985
No 6
>PF13268 DUF4059: Protein of unknown function (DUF4059)
Probab=20.35 E-value=39 Score=23.42 Aligned_cols=28 Identities=11% Similarity=0.016 Sum_probs=21.5
Q ss_pred hhhhhHHHHHHHHHHHHhhhCCCcccch
Q 041783 182 LLYVNIFCLLDSCFLSWIEQQEDAPWKQ 209 (225)
Q Consensus 182 vlf~n~v~~~Wn~yLS~~~~~~~~~~~~ 209 (225)
.+++-+++.+|..+=...+..+.+.|||
T Consensus 17 ~i~V~~~~~~wi~~Ra~~~~DKT~~eRQ 44 (72)
T PF13268_consen 17 SILVLLVSGIWILWRALRKKDKTAKERQ 44 (72)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCcHHHHH
Confidence 4556678899999888777777777775
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=19.49 E-value=1.1e+02 Score=26.16 Aligned_cols=17 Identities=18% Similarity=0.387 Sum_probs=11.6
Q ss_pred hHHHHHHHHHHHHhhhCC
Q 041783 186 NIFCLLDSCFLSWIEQQE 203 (225)
Q Consensus 186 n~v~~~Wn~yLS~~~~~~ 203 (225)
-+++++||||=. ++++.
T Consensus 200 YlI~cVWrCYky-l~~rn 216 (258)
T TIGR00799 200 YMFKCVWNCYKY-IKNMN 216 (258)
T ss_pred HHHHHHHHHHHH-hhccc
Confidence 457899999954 44443
No 8
>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=17.11 E-value=72 Score=18.81 Aligned_cols=17 Identities=18% Similarity=0.235 Sum_probs=13.2
Q ss_pred HHHHHHHHHhhCchHHH
Q 041783 4 LWKWYQNCLAVHPVKTQ 20 (225)
Q Consensus 4 l~~~Y~~~l~~~Pl~t~ 20 (225)
.++.|.+-+.++||+|.
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 46789999999999874
No 9
>PF03821 Mtp: Golgi 4-transmembrane spanning transporter; InterPro: IPR004687 LAPTM4 and 5 are lysosome-associated transmembrane proteins, found in mammals, insects and nematodes. ; GO: 0016021 integral to membrane
Probab=16.94 E-value=1.2e+02 Score=25.93 Aligned_cols=16 Identities=6% Similarity=0.177 Sum_probs=11.3
Q ss_pred hHHHHHHHHHHHHhhh
Q 041783 186 NIFCLLDSCFLSWIEQ 201 (225)
Q Consensus 186 n~v~~~Wn~yLS~~~~ 201 (225)
=+++++|+||--....
T Consensus 176 Y~i~CVW~CYKyl~~r 191 (233)
T PF03821_consen 176 YMISCVWRCYKYLKAR 191 (233)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 3478999999655443
No 10
>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=15.87 E-value=91 Score=24.14 Aligned_cols=25 Identities=32% Similarity=0.371 Sum_probs=19.1
Q ss_pred chHHHHHHHHHhcccc--chhhHHHHH
Q 041783 67 LNWNRVAKTSFFGFAF--VGPVGHFWY 91 (225)
Q Consensus 67 ~D~~R~~r~~~~G~~~--~gP~~h~wy 91 (225)
..|.|-++|.++|+++ .||.++.|-
T Consensus 3 ~~w~~W~K~~~~G~~ii~~G~~l~~y~ 29 (128)
T PF07960_consen 3 PNWRRWAKMLVAGAVIIGGGPALVKYT 29 (128)
T ss_pred chHHHHHHHHHhcceeEeechHHheec
Confidence 5688999999999876 477766654
Done!