Query 027783
Match_columns 219
No_of_seqs 152 out of 1010
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 15:07:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027783.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027783hhsearch_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 7.1E-42 1.5E-46 285.3 15.4 168 12-196 46-214 (222)
2 PF04117 Mpv17_PMP22: Mpv17 / 99.9 6.1E-26 1.3E-30 156.0 4.9 68 128-195 1-68 (68)
3 PF03818 MadM: Malonate/sodium 49.2 38 0.00082 22.4 3.9 37 7-43 3-39 (60)
4 cd02577 PSTD1 PSTD1: Pseudouri 22.4 97 0.0021 27.4 3.3 30 166-195 228-258 (319)
5 PF00140 Sigma70_r1_2: Sigma-7 19.5 41 0.00088 19.7 0.2 17 4-20 3-19 (37)
6 PF04854 DUF624: Protein of un 17.0 3.3E+02 0.0072 18.0 4.5 37 116-152 21-61 (77)
7 TIGR02230 ATPase_gene1 F0F1-AT 16.5 3.8E+02 0.0083 19.5 4.8 31 62-92 39-71 (100)
8 PF11547 E3_UbLigase_EDD: E3 u 16.5 1.7E+02 0.0038 18.4 2.5 20 128-147 17-36 (53)
9 PF03806 ABG_transport: AbgT p 15.8 9.6E+02 0.021 22.8 8.7 54 21-74 208-265 (502)
10 PF07172 GRP: Glycine rich pro 15.4 1.7E+02 0.0038 21.0 2.7 26 14-39 4-29 (95)
No 1
>KOG1944 consensus Peroxisomal membrane protein MPV17 and related proteins [General function prediction only]
Probab=100.00 E-value=7.1e-42 Score=285.27 Aligned_cols=168 Identities=36% Similarity=0.650 Sum_probs=157.9
Q ss_pred HhhCchHHHHHHHHHHH-HHHHHHHhchhhhhhhhhhhcccccccccccchHHHHHHHHHhcccccchhHHHHHHHHHHH
Q 027783 12 LAVHPLKTQVISSGFLW-GVGDIAAQYITHATAKSRLQLSVTDADEKFKVNWKRVAVTSSFGFGFVGPVGHFWYEGLDRF 90 (219)
Q Consensus 12 l~~~Pl~tk~~ts~~l~-~~gD~laQ~~~~~~~~~~~~~~~~~~~~~~~~D~~Rt~~~~~~G~~~~gP~~h~wy~~Ld~~ 90 (219)
...+|+++++++++.+. .+||+++|.++..++. . ..++|+.|++||+++|+++.||.+|+||..||++
T Consensus 46 ~~~~~~l~~~i~~~~~~~~~~d~~~q~~~~~~~~----------~-~~~~d~~rtlr~~~~G~~f~gp~~~~Wy~~L~~~ 114 (222)
T KOG1944|consen 46 FSLYPLLTKAITTSLLLAAAGDVISQSLEGRSKK----------L-FQTLDLTRTLRMGIFGFLFVGPTLHYWYRLLSKL 114 (222)
T ss_pred hhhhhHHHHHHHHHHHHHHhchhhhhhhhhhccc----------c-cccccHHHHHHHHhhhhheeccchhHHHHHHHHH
Confidence 35688888999888888 9999999999987531 0 4689999999999999989999999999999999
Q ss_pred hhhhcCCCCCcHHHHHHHHHHhhhhhhhhHHHHHHHHHHhhCCCChHHHHHHHHHhhHHHHHhccccchHhhhhheeeec
Q 027783 91 IRLKLQLPPKSARFVATKVAMDSIIFGPLDLFVFFTYMGFSTGKNVAQVKEDLKRDFLPALVLEGGIWPIVQVANFRYVP 170 (219)
Q Consensus 91 ~~~~~~~~~~~~~~v~~Kvl~DQ~v~aP~~~~~f~~~~~~leg~s~~~~~~~lk~~~~~~l~~~~~vWp~~q~inF~~vP 170 (219)
+| .++..++++|+++||++++|+.+.+||.+|+++||++.+++.+++++++||++++||++||++|++||++||
T Consensus 115 ~p------~~~~~~~~~kvl~dql~~~P~~~~~ff~~~~~legk~~~~~~~~~~~~~~p~l~~~~~~WP~~q~inF~~VP 188 (222)
T KOG1944|consen 115 FP------KKTLITVVKKVLLDQLVFAPLFIVVFFLLMGLLEGKTNEEAKAKLKRKFWPTLKANWMVWPLVQFINFRLVP 188 (222)
T ss_pred cc------CccHHHHHHHHHHhhhhhchHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhheecchhheeeeEEcc
Confidence 96 568899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccchhhhhHHHHHHHHHHHhhhccc
Q 027783 171 VRYQLLYVNIFCLLDSAFLSWVEQQK 196 (219)
Q Consensus 171 ~~~Rvlf~n~v~~~W~~yLS~~~~~~ 196 (219)
+++|++++|+++++||+|||+++++.
T Consensus 189 ~~~rvl~~~~vsl~W~~~Ls~~~~~~ 214 (222)
T KOG1944|consen 189 LQYRVLFVNIVSLVWNTYLSYKNASL 214 (222)
T ss_pred ccceehhhhhHHHHHHHHHHHHhhcc
Confidence 99999999999999999999999998
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=6.1e-26 Score=155.98 Aligned_cols=68 Identities=40% Similarity=0.820 Sum_probs=66.5
Q ss_pred HHhhCCCChHHHHHHHHHhhHHHHHhccccchHhhhhheeeeccccchhhhhHHHHHHHHHHHhhhcc
Q 027783 128 MGFSTGKNVAQVKEDLKRDFLPALVLEGGIWPIVQVANFRYVPVRYQLLYVNIFCLLDSAFLSWVEQQ 195 (219)
Q Consensus 128 ~~~leg~s~~~~~~~lk~~~~~~l~~~~~vWp~~q~inF~~vP~~~Rvlf~n~v~~~W~~yLS~~~~~ 195 (219)
|+++||+|++++++++|++++++++++|++|||+|++||+|||+++|++|+|+|+++||+|||+++|+
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=49.22 E-value=38 Score=22.38 Aligned_cols=37 Identities=16% Similarity=0.129 Sum_probs=32.8
Q ss_pred HHHHHHhhCchHHHHHHHHHHHHHHHHHHhchhhhhh
Q 027783 7 WYQNCLAVHPLKTQVISSGFLWGVGDIAAQYITHATA 43 (219)
Q Consensus 7 ~Y~~~l~~~Pl~tk~~ts~~l~~~gD~laQ~~~~~~~ 43 (219)
.....++++.|+|.-+.-|+++.++..++-+++..+-
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 3567799999999999999999999999999998753
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=22.41 E-value=97 Score=27.38 Aligned_cols=30 Identities=20% Similarity=0.236 Sum_probs=24.8
Q ss_pred eeeeccccchhhhhH-HHHHHHHHHHhhhcc
Q 027783 166 FRYVPVRYQLLYVNI-FCLLDSAFLSWVEQQ 195 (219)
Q Consensus 166 F~~vP~~~Rvlf~n~-v~~~W~~yLS~~~~~ 195 (219)
|.-+|...|.+|++. -|.+||-.+|..-..
T Consensus 228 l~~iP~~lr~myvhAYQSylfN~~lS~Ri~~ 258 (319)
T cd02577 228 FLALPKNLRRMFVHAYQSYLFNEILSERIEE 258 (319)
T ss_pred HHhcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 346999999999876 789999999987653
No 5
>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=19.52 E-value=41 Score=19.67 Aligned_cols=17 Identities=24% Similarity=0.278 Sum_probs=13.0
Q ss_pred HHHHHHHHHhhCchHHH
Q 027783 4 LWKWYQNCLAVHPLKTQ 20 (219)
Q Consensus 4 l~~~Y~~~l~~~Pl~tk 20 (219)
..+.|.+-+.++||+|.
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 6
>PF04854 DUF624: Protein of unknown function, DUF624; InterPro: IPR006938 This family consists of uncharacterised or hypothetical bacterial proteins.
Probab=16.99 E-value=3.3e+02 Score=18.01 Aligned_cols=37 Identities=14% Similarity=0.381 Sum_probs=20.9
Q ss_pred hhhhHHHHHHHHHHhhCCC-C---hHHHHHHHHHhhHHHHH
Q 027783 116 FGPLDLFVFFTYMGFSTGK-N---VAQVKEDLKRDFLPALV 152 (219)
Q Consensus 116 ~aP~~~~~f~~~~~~leg~-s---~~~~~~~lk~~~~~~l~ 152 (219)
..|-..+.+.+.....+++ + +++-++.+|+++.....
T Consensus 21 igPA~~Al~~~~~~~~~~~~~~~~~~~f~~~fk~nf~~~~~ 61 (77)
T PF04854_consen 21 IGPATAALYYVVRKWVRDEEDSYLFRDFWRAFKQNFKQSLL 61 (77)
T ss_pred HHHHHHHHHHHHHHHHcCCccChHHHHHHHHHHHHHHHHHH
Confidence 4566666777777777776 2 23444445555544443
No 7
>TIGR02230 ATPase_gene1 F0F1-ATPase subunit, putative. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophic stretches and is presumed to be a subunit of the enzyme.
Probab=16.54 E-value=3.8e+02 Score=19.51 Aligned_cols=31 Identities=19% Similarity=0.195 Sum_probs=24.3
Q ss_pred HHHHHHHHHhcccccchhHHHHH--HHHHHHhh
Q 027783 62 WKRVAVTSSFGFGFVGPVGHFWY--EGLDRFIR 92 (219)
Q Consensus 62 ~~Rt~~~~~~G~~~~gP~~h~wy--~~Ld~~~~ 92 (219)
++....+++.|..+..|+.-.-| .+||+.++
T Consensus 39 ~~~l~~~g~IG~~~v~pil~G~~lG~WLD~~~~ 71 (100)
T TIGR02230 39 WEGLGMFGLIGWSVAIPTLLGVAVGIWLDRHYP 71 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 56677788888888888877666 77999995
No 8
>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.
Probab=16.50 E-value=1.7e+02 Score=18.44 Aligned_cols=20 Identities=20% Similarity=0.199 Sum_probs=15.4
Q ss_pred HHhhCCCChHHHHHHHHHhh
Q 027783 128 MGFSTGKNVAQVKEDLKRDF 147 (219)
Q Consensus 128 ~~~leg~s~~~~~~~lk~~~ 147 (219)
..+|+|+|.+-|.+++++.=
T Consensus 17 q~VLqgksR~vIirELqrTn 36 (53)
T PF11547_consen 17 QVVLQGKSRNVIIRELQRTN 36 (53)
T ss_dssp HHHSTTS-HHHHHHHHHHTT
T ss_pred HHHHcCCcHHHHHHHHHHhc
Confidence 46899999988999888743
No 9
>PF03806 ABG_transport: AbgT putative transporter family; InterPro: IPR004697 The p-aminobenzoyl-glutamate transporter family includes two putative transporters, the AbgT protein of Escherichia coli and MtrF of Neisseria gonorrhoeae. AbgT expression is apparently cryptic in wild type cells, but when present on a high copy number plasmid, or when expressed at higher levels due to mutation, it allows utilization of p-aminobenzoyl-glutamate as a source of p-aminobenzoate for p-aminobenzoate auxotrophs []. p-Aminobenzoate is a constituent of, and a precursor for, the biosynthesis of folic acid. It is not currently known if AbgT is naturally involved in transporting p-aminobenzoyl-glutamate, or if it only becomes involved when under altered regulation. MtrF is an inner membrane protein which, together with the MtrCDE efflux pump, is required for high-level resistance to hydrophobic antimicrobial agents in N. gonorrhoeae []. Its role in this process is not known, but it has been suggested that it may be a component of the efflux pump which is dispensible for basal activity, but required for high-level activity [].
Probab=15.78 E-value=9.6e+02 Score=22.79 Aligned_cols=54 Identities=11% Similarity=-0.045 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHHhchhhhhhhhhhhc-cccccc---ccccchHHHHHHHHHhccc
Q 027783 21 VISSGFLWGVGDIAAQYITHATAKSRLQL-SVTDAD---EKFKVNWKRVAVTSSFGFG 74 (219)
Q Consensus 21 ~~ts~~l~~~gD~laQ~~~~~~~~~~~~~-~~~~~~---~~~~~D~~Rt~~~~~~G~~ 74 (219)
++.+-++..++-.+..++.+.|-.+.... ++++.+ ..-+.+-+|.+|.+.+.++
T Consensus 208 ~aSt~~l~~v~~~vt~kivePrl~~~~~~~~~~~~~~~~~~Lt~~EkkgLr~Agi~~l 265 (502)
T PF03806_consen 208 IASTFVLTIVGTWVTEKIVEPRLGKYDGDADDDEIEEASSSLTPREKKGLRWAGIALL 265 (502)
T ss_pred HHHHHHHHHHHHHHhhhhhccccccccccccccccccccccCCHHHHHHHHHHHHHHH
Confidence 45556667777777777776554321111 111111 1234456788999888764
No 10
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=15.40 E-value=1.7e+02 Score=21.02 Aligned_cols=26 Identities=15% Similarity=0.127 Sum_probs=20.1
Q ss_pred hCchHHHHHHHHHHHHHHHHHHhchh
Q 027783 14 VHPLKTQVISSGFLWGVGDIAAQYIT 39 (219)
Q Consensus 14 ~~Pl~tk~~ts~~l~~~gD~laQ~~~ 39 (219)
|..|+--.+.+.+|..++|+.|..++
T Consensus 4 K~~llL~l~LA~lLlisSevaa~~~~ 29 (95)
T PF07172_consen 4 KAFLLLGLLLAALLLISSEVAARELE 29 (95)
T ss_pred hHHHHHHHHHHHHHHHHhhhhhHHhh
Confidence 33566667888999999999987773
Done!