Query 035757
Match_columns 68
No_of_seqs 116 out of 145
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 06:07:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035757.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035757hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02601 beta-carotene hydroxy 100.0 1.2E-36 2.6E-41 228.7 -0.0 68 1-68 222-289 (303)
2 PF04116 FA_hydroxylase: Fatty 91.1 0.065 1.4E-06 32.3 0.0 31 3-38 84-114 (114)
3 PLN02434 fatty acid hydroxylas 79.8 1.8 4E-05 32.0 2.7 19 20-38 188-206 (237)
4 PF10890 DUF2741: Protein of u 44.5 11 0.00023 23.9 0.8 22 32-53 31-52 (72)
5 PF08352 oligo_HPY: Oligopepti 37.0 18 0.00039 20.3 0.8 21 17-37 9-29 (64)
6 COG3000 ERG3 Sterol desaturase 35.8 4.1 8.9E-05 29.6 -2.4 41 4-49 182-223 (271)
7 PF03915 AIP3: Actin interacti 28.8 19 0.00041 28.8 0.0 43 25-67 370-418 (424)
8 COG3080 FrdD Fumarate reductas 25.4 25 0.00054 24.1 0.1 9 30-38 77-85 (118)
9 PHA03293 deoxyribonuclease; Pr 17.5 86 0.0019 26.1 1.7 24 12-35 397-420 (523)
10 KOG0476 Cl- channel CLC-2 and 17.5 78 0.0017 28.2 1.5 27 9-36 347-373 (931)
No 1
>PLN02601 beta-carotene hydroxylase
Probab=100.00 E-value=1.2e-36 Score=228.66 Aligned_cols=68 Identities=81% Similarity=1.405 Sum_probs=66.4
Q ss_pred CeEEEEeceeeeccccCCccCCCHHHHHHHHHHHhhcCCCCCCeeeeEeeccchhhhhcccccccccC
Q 035757 1 MAYMFVHDGLVHRRFPVGPIAHVPYLRKVAAAHQLHHSEKFNGLPYGLFLGPQELEEVEGTEGLDKET 68 (68)
Q Consensus 1 iaYf~vHD~liH~R~~~~~~~~~~Y~rrl~~AH~~HH~~K~~g~~fGfl~~p~~l~~v~~~~~~~~~~ 68 (68)
|+||||||||||||||+++++||||+|+|++|||+||++|++|||||||++|+|||+|||+||||||+
T Consensus 222 iaYffVHDgLVHqRfp~~~~a~~~Y~rrl~~AHklHHa~Ke~Gv~FGfll~P~e~e~vgg~~el~~~~ 289 (303)
T PLN02601 222 MAYMFVHDGLVHKRFPVGPIANVPYLRKVAAAHQLHHTDKFKGVPYGLFLGPKEVEEVGGKEELEKEI 289 (303)
T ss_pred HHHHHHhhhhhccccccCCCCCCHHHHHHHHHHHhhccCCcCCccceEEeccHHHHhcCCHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999875
No 2
>PF04116 FA_hydroxylase: Fatty acid hydroxylase superfamily; InterPro: IPR006694 This superfamily includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways []. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain two copies of a HXHH motif. Members of this family are integral membrane proteins.; GO: 0005506 iron ion binding, 0016491 oxidoreductase activity, 0006633 fatty acid biosynthetic process, 0055114 oxidation-reduction process
Probab=91.11 E-value=0.065 Score=32.33 Aligned_cols=31 Identities=35% Similarity=0.599 Sum_probs=22.4
Q ss_pred EEEEeceeeeccccCCccCCCHHHHHHHHHHHhhcC
Q 035757 3 YMFVHDGLVHRRFPVGPIAHVPYLRKVAAAHQLHHS 38 (68)
Q Consensus 3 Yf~vHD~liH~R~~~~~~~~~~Y~rrl~~AH~~HH~ 38 (68)
|.+.|+++ .....+..+|++...+.|++||+
T Consensus 84 ~~~~H~~~-----~~~~~~~~~~~~~~~~~H~~HH~ 114 (114)
T PF04116_consen 84 YIFIHSGY-----HHRFPPRLRYLFVTPRHHDLHHS 114 (114)
T ss_pred HHHhhcCc-----cCCCCCcchhHhcCHHHHHhhCc
Confidence 34556666 23334667899999999999995
No 3
>PLN02434 fatty acid hydroxylase
Probab=79.83 E-value=1.8 Score=32.00 Aligned_cols=19 Identities=26% Similarity=0.270 Sum_probs=17.0
Q ss_pred cCCCHHHHHHHHHHHhhcC
Q 035757 20 IAHVPYLRKVAAAHQLHHS 38 (68)
Q Consensus 20 ~~~~~Y~rrl~~AH~~HH~ 38 (68)
+++++|+|++.+-|..||-
T Consensus 188 ~p~~~~~r~lkr~H~~HHf 206 (237)
T PLN02434 188 QPSTDVLRNLKKYHLNHHF 206 (237)
T ss_pred CcchHHHHHHHHHHHHHcC
Confidence 5668999999999999995
No 4
>PF10890 DUF2741: Protein of unknown function (DUF2741); InterPro: IPR020101 This entry represents subunit 8 of the Cytochrome b-c1 complex. The ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex) is part of the mitochondrial respiratory chain. This subunit, together with cytochrome b, binds to ubiquinone. In plants, the b-c1 complex contains 10 subunits: 3 respiratory subunits, 2 core proteins and 5 low-molecular weight proteins.
Probab=44.49 E-value=11 Score=23.92 Aligned_cols=22 Identities=32% Similarity=0.395 Sum_probs=19.2
Q ss_pred HHHhhcCCCCCCeeeeEeeccc
Q 035757 32 AHQLHHSEKFNGLPYGLFLGPQ 53 (68)
Q Consensus 32 AH~~HH~~K~~g~~fGfl~~p~ 53 (68)
.+++||..+|+.++=++|++|-
T Consensus 31 p~ki~hk~~enwv~a~~~~~p~ 52 (72)
T PF10890_consen 31 PKKIHHKFSENWVSATLFLVPL 52 (72)
T ss_pred HHHHHHHHhhcceeeEEEeeee
Confidence 5899998889999999999874
No 5
>PF08352 oligo_HPY: Oligopeptide/dipeptide transporter, C-terminal region; InterPro: IPR013563 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry features a region found towards the C terminus of oligopeptide ABC transporter ATP binding proteins, immediately following the ATP-binding domain (IPR003439 from INTERPRO). All characterised members appear able to be involved in the transport of oligopeptides or dipeptides. Some are important for sporulation or antibiotic resistance. Some dipeptide transporters also act on the haem precursor delta-aminolevulinic acid. ; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0015833 peptide transport
Probab=37.00 E-value=18 Score=20.35 Aligned_cols=21 Identities=24% Similarity=0.176 Sum_probs=16.1
Q ss_pred CCccCCCHHHHHHHHHHHhhc
Q 035757 17 VGPIAHVPYLRKVAAAHQLHH 37 (68)
Q Consensus 17 ~~~~~~~~Y~rrl~~AH~~HH 37 (68)
++..+.+||-|+|.+|.--..
T Consensus 9 i~~~P~HPYT~~Ll~a~p~~~ 29 (64)
T PF08352_consen 9 IFDNPRHPYTRALLAAVPSID 29 (64)
T ss_pred HHHCccCHHHHHHHHcCcchh
Confidence 346789999999999875443
No 6
>COG3000 ERG3 Sterol desaturase [Lipid metabolism]
Probab=35.81 E-value=4.1 Score=29.56 Aligned_cols=41 Identities=29% Similarity=0.555 Sum_probs=24.0
Q ss_pred EEEeceeeeccccCCccCCCHHHHHHHHHHHhhcCCCC-CCeeeeEe
Q 035757 4 MFVHDGLVHRRFPVGPIAHVPYLRKVAAAHQLHHSEKF-NGLPYGLF 49 (68)
Q Consensus 4 f~vHD~liH~R~~~~~~~~~~Y~rrl~~AH~~HH~~K~-~g~~fGfl 49 (68)
++.|.++.+. .+.+ ..+++-...+-|++||+. + ...|||..
T Consensus 182 ~~~H~~~~~~-~~~~---~~~~v~~~p~~H~lHH~~-~~~~~Nyg~~ 223 (271)
T COG3000 182 VLIHSNLDLP-LPLG---WLRYVFNTPRHHRLHHSK-DPYDKNYGVT 223 (271)
T ss_pred HHHhcCcccc-CCcc---cceeeecCchHHHHhccC-CCCCCcchhh
Confidence 3456666664 2222 223344556789999983 2 45889943
No 7
>PF03915 AIP3: Actin interacting protein 3; InterPro: IPR022782 This entry represents a domain found in yeast actin interacting protein 3 and bud site selection protein 6. In these proteins it is typically found towards the C terminus. It is also found in metazoan proteins, such as the mouse enhancer trap locus 4 protein. ; PDB: 3ONX_B 3OKQ_A.
Probab=28.78 E-value=19 Score=28.79 Aligned_cols=43 Identities=21% Similarity=0.318 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhhcCCCC--C----CeeeeEeeccchhhhhccccccccc
Q 035757 25 YLRKVAAAHQLHHSEKF--N----GLPYGLFLGPQELEEVEGTEGLDKE 67 (68)
Q Consensus 25 Y~rrl~~AH~~HH~~K~--~----g~~fGfl~~p~~l~~v~~~~~~~~~ 67 (68)
-+++|-+|=++==.+++ . ..--|=|+.-++|-+.||.||+||.
T Consensus 370 RLeAIerAEKlRqkele~~~~~~f~~EL~~FV~~~kLKksGG~eEvER~ 418 (424)
T PF03915_consen 370 RLEAIERAEKLRQKELEYRRVDEFQKELGNFVEEKKLKKSGGIEEVERL 418 (424)
T ss_dssp -------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccCcccccCCHHHHHHH
Confidence 45566666555443211 0 1234668899999999999999984
No 8
>COG3080 FrdD Fumarate reductase subunit D [Energy production and conversion]
Probab=25.38 E-value=25 Score=24.14 Aligned_cols=9 Identities=44% Similarity=0.903 Sum_probs=7.1
Q ss_pred HHHHHhhcC
Q 035757 30 AAAHQLHHS 38 (68)
Q Consensus 30 ~~AH~~HH~ 38 (68)
-.+|++||.
T Consensus 77 ~a~HRihHg 85 (118)
T COG3080 77 CALHRIHHG 85 (118)
T ss_pred HHHHHHHhh
Confidence 368999995
No 9
>PHA03293 deoxyribonuclease; Provisional
Probab=17.51 E-value=86 Score=26.06 Aligned_cols=24 Identities=8% Similarity=0.181 Sum_probs=19.8
Q ss_pred eccccCCccCCCHHHHHHHHHHHh
Q 035757 12 HRRFPVGPIAHVPYLRKVAAAHQL 35 (68)
Q Consensus 12 H~R~~~~~~~~~~Y~rrl~~AH~~ 35 (68)
.-+.|+|-||+++|+++|..-+.+
T Consensus 397 ~f~vpVFaNPRH~nFkQilvQ~YV 420 (523)
T PHA03293 397 ALEVPIFANPRHPNFKQILVQAYV 420 (523)
T ss_pred eeecccccCCCCcchHHHHHHHHH
Confidence 357799999999999999876654
No 10
>KOG0476 consensus Cl- channel CLC-2 and related proteins (CLC superfamily) [Inorganic ion transport and metabolism]
Probab=17.49 E-value=78 Score=28.19 Aligned_cols=27 Identities=22% Similarity=0.241 Sum_probs=21.4
Q ss_pred eeeeccccCCccCCCHHHHHHHHHHHhh
Q 035757 9 GLVHRRFPVGPIAHVPYLRKVAAAHQLH 36 (68)
Q Consensus 9 ~liH~R~~~~~~~~~~Y~rrl~~AH~~H 36 (68)
+.+|||+- +...||+|++++.+-|++=
T Consensus 347 VylhR~iv-lf~Rkn~~~~~~f~k~~ll 373 (931)
T KOG0476|consen 347 VYLHRRIV-LFLRKNRYAKKLFQKSRLL 373 (931)
T ss_pred eeeeeeee-eeehhhHHHHHHHhhCccH
Confidence 46789984 4578999999999988753
Done!