Query 034663
Match_columns 88
No_of_seqs 41 out of 43
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 05:12:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034663.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034663hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06364 DUF1068: Protein of u 100.0 5.4E-36 1.2E-40 222.7 2.3 74 4-80 3-76 (176)
2 KOG1823 DRIM (Down-regulated i 98.1 5.6E-07 1.2E-11 82.6 -1.2 72 6-80 1195-1267(1364)
3 PF01462 LRRNT: Leucine rich r 37.2 16 0.00034 19.4 0.6 15 53-67 13-27 (28)
4 PF14946 DUF4501: Domain of un 33.6 16 0.00034 28.1 0.3 28 17-51 20-47 (180)
5 smart00013 LRRNT Leucine rich 33.4 25 0.00055 18.9 1.0 18 52-69 12-29 (33)
6 PF14342 DUF4396: Domain of un 30.6 22 0.00047 25.5 0.6 37 2-38 102-138 (139)
7 PF11027 DUF2615: Protein of u 29.5 35 0.00075 23.8 1.4 30 8-38 55-84 (103)
8 PF06463 Mob_synth_C: Molybden 25.4 38 0.00082 23.3 1.0 30 25-54 46-76 (128)
9 PF04703 FaeA: FaeA-like prote 22.1 46 0.001 20.9 0.9 9 26-34 53-61 (62)
10 PF06869 DUF1258: Protein of u 20.6 40 0.00088 27.0 0.5 17 38-54 199-215 (258)
11 PF10999 DUF2839: Protein of u 20.0 51 0.0011 21.5 0.8 18 14-31 50-67 (68)
No 1
>PF06364 DUF1068: Protein of unknown function (DUF1068); InterPro: IPR010471 This family consists of several hypothetical plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Probab=100.00 E-value=5.4e-36 Score=222.70 Aligned_cols=74 Identities=62% Similarity=1.093 Sum_probs=68.5
Q ss_pred CchhHHHHHHHHHHHHhheeeeCCcceeeehhhhccccCCCCCCCCCcccCCCCCCCccccccCCCcCccCCCCCCC
Q 034663 4 NQAAIAKVGLSLLGLCLFGYIVGPPLYWHFMEGLDAVSHSSAATCPPCVCDCSSQPLLSIPDGLGNASITGYFPYQN 80 (88)
Q Consensus 4 ~~~~~lr~~Lvllav~~a~yIvGPpLYW~~~e~l~~~~~sss~sCppC~CDCss~~Ll~ip~gL~N~S~~DC~k~~~ 80 (88)
.+++++||+|||||+++++||+|||||||++|+++++ ++++||||+||||++||++||+||+|+||+||||+|.
T Consensus 3 ~s~~~lr~~l~llal~~a~yivGP~LYWh~~~~~~~~---s~~sCppC~CDCs~~~ll~ip~gl~N~S~~DC~k~dP 76 (176)
T PF06364_consen 3 PSPAALRVVLVLLALCLAGYIVGPPLYWHLSEGLAAV---SSSSCPPCDCDCSSQPLLSIPPGLSNLSFTDCGKHDP 76 (176)
T ss_pred CChhHHHHHHHHHHHHHHhheeCchHHHHHHHhhhcc---cCCCCCCCCCCCCCHHHHHhcccccccchHhhccCCh
Confidence 3567999999999999999999999999999999864 4568999999999999999999999999999999984
No 2
>KOG1823 consensus DRIM (Down-regulated in metastasis)-like proteins [Defense mechanisms]
Probab=98.05 E-value=5.6e-07 Score=82.62 Aligned_cols=72 Identities=22% Similarity=0.406 Sum_probs=62.5
Q ss_pred hhHHHHHHHHHHHHhheeeeCCcceeeehhhhccccCCCCCCCCCcccCCCCC-CCccccccCCCcCccCCCCCCC
Q 034663 6 AAIAKVGLSLLGLCLFGYIVGPPLYWHFMEGLDAVSHSSAATCPPCVCDCSSQ-PLLSIPDGLGNASITGYFPYQN 80 (88)
Q Consensus 6 ~~~lr~~Lvllav~~a~yIvGPpLYW~~~e~l~~~~~sss~sCppC~CDCss~-~Ll~ip~gL~N~S~~DC~k~~~ 80 (88)
.+-.+..+++.+.....+|.||++||++++++++.. +.+||+|.|||.++ .+.++.|++.+...+|||..+.
T Consensus 1195 l~~~~~~~~l~~qv~~~li~~~~l~~~~~~~~~~~~---~~~~~~c~~e~~~~~~~~~~~p~~~~~i~~~~~~~d~ 1267 (1364)
T KOG1823|consen 1195 LRSSKFDLVLGAQVAKNLIFGPALLWNLRENLEALI---SEICPACRCECMEKKACSQLLPLFALVIDEDCGQVDD 1267 (1364)
T ss_pred HccCcHHHHHHHHHhhheeecHHHHHHHHhhcchhh---hhhhhhhhhhhhhhhhhhhhcchhhhccchhhcccCc
Confidence 344567899999999999999999999999997653 23499999999877 8999999999999999999874
No 3
>PF01462 LRRNT: Leucine rich repeat N-terminal domain; InterPro: IPR000372 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. LRRs are often flanked by cysteine-rich domains: an N-terminal LRR domain and a C-terminal LRR domain (IPR000483 from INTERPRO). This entry represents the N-terminal LRR domain. ; PDB: 3E6J_A 1W8A_A 2V9S_C 2V9T_B 3TWI_D 3ZYN_A 3ZYO_A 1OOK_G 1QYY_G 1SQ0_B ....
Probab=37.25 E-value=16 Score=19.36 Aligned_cols=15 Identities=40% Similarity=0.840 Sum_probs=10.3
Q ss_pred cCCCCCCCccccccC
Q 034663 53 CDCSSQPLLSIPDGL 67 (88)
Q Consensus 53 CDCss~~Ll~ip~gL 67 (88)
=||+.+.|.+||.+|
T Consensus 13 V~C~~~~L~~vP~~l 27 (28)
T PF01462_consen 13 VDCSGRGLTAVPSDL 27 (28)
T ss_dssp EEETTSS-SSS-STS
T ss_pred eECCCCCCCccCCCC
Confidence 378888999999865
No 4
>PF14946 DUF4501: Domain of unknown function (DUF4501)
Probab=33.62 E-value=16 Score=28.08 Aligned_cols=28 Identities=29% Similarity=0.656 Sum_probs=20.0
Q ss_pred HHHhheeeeCCcceeeehhhhccccCCCCCCCCCc
Q 034663 17 GLCLFGYIVGPPLYWHFMEGLDAVSHSSAATCPPC 51 (88)
Q Consensus 17 av~~a~yIvGPpLYW~~~e~l~~~~~sss~sCppC 51 (88)
+-|-..-.+||.-|||.+| ..+.+|-.|
T Consensus 20 aSCpg~slCgPGcyr~~~e-------dgs~sCv~c 47 (180)
T PF14946_consen 20 ASCPGTSLCGPGCYRHWNE-------DGSVSCVQC 47 (180)
T ss_pred ccCCCCCccCCcceeeecC-------CCCeEEEEc
Confidence 4455667899999999987 234567655
No 5
>smart00013 LRRNT Leucine rich repeat N-terminal domain.
Probab=33.41 E-value=25 Score=18.87 Aligned_cols=18 Identities=33% Similarity=0.556 Sum_probs=14.4
Q ss_pred ccCCCCCCCccccccCCC
Q 034663 52 VCDCSSQPLLSIPDGLGN 69 (88)
Q Consensus 52 ~CDCss~~Ll~ip~gL~N 69 (88)
.-||+.+.|..||.++-.
T Consensus 12 ~V~C~~~~L~~vP~~iP~ 29 (33)
T smart00013 12 AVDCSGRGLTEVPLDLPP 29 (33)
T ss_pred EeEeCCCCcCccCCCCCc
Confidence 457888899999998764
No 6
>PF14342 DUF4396: Domain of unknown function (DUF4396)
Probab=30.63 E-value=22 Score=25.45 Aligned_cols=37 Identities=11% Similarity=0.053 Sum_probs=29.5
Q ss_pred CcCchhHHHHHHHHHHHHhheeeeCCcceeeehhhhc
Q 034663 2 AVNQAAIAKVGLSLLGLCLFGYIVGPPLYWHFMEGLD 38 (88)
Q Consensus 2 ~~~~~~~lr~~Lvllav~~a~yIvGPpLYW~~~e~l~ 38 (88)
+++++..+-|....+|+.....+-=|.-||+++++..
T Consensus 102 ~~~~~~~~FW~~m~iam~~GF~~a~P~N~wli~~g~K 138 (139)
T PF14342_consen 102 AMPPDDPLFWFMMQIAMLAGFLTAYPVNWWLIKKGIK 138 (139)
T ss_pred cCCCcchHHHHHHHHHHHHHHHHhcchHHHHHHhcCC
Confidence 4566777788888888887777778999999998763
No 7
>PF11027 DUF2615: Protein of unknown function (DUF2615); InterPro: IPR020309 This entry represents a group of uncharacterised protein from the Metazoa, including CD034 (or C4orf34) and YQF4 (or C34C12.4).
Probab=29.52 E-value=35 Score=23.81 Aligned_cols=30 Identities=10% Similarity=0.077 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHhheeeeCCcceeeehhhhc
Q 034663 8 IAKVGLSLLGLCLFGYIVGPPLYWHFMEGLD 38 (88)
Q Consensus 8 ~lr~~Lvllav~~a~yIvGPpLYW~~~e~l~ 38 (88)
..-+.++|+.+++++|++.|. -+|-.++..
T Consensus 55 ~~~~~~~w~~~A~~ly~~RP~-s~R~~~~~~ 84 (103)
T PF11027_consen 55 MFMMMMLWMVLAMALYLLRPS-SLRSRSADG 84 (103)
T ss_pred HHHHHHHHHHHHHHHHHcCch-hhcCCCCCC
Confidence 566789999999999999998 344443343
No 8
>PF06463 Mob_synth_C: Molybdenum Cofactor Synthesis C; InterPro: IPR010505 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cis-dithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism [, ]. In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which converts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner []. MoCF is the active co-factor in eukaryotic and some prokaryotic molybdo-enzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdo-enzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF []. Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 (Q39054 from SWISSPROT) of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) []. This entry represents MoaA, which belongs to a family of enzymes involved in the synthesis of metallo-cofactors (IPR000385 from INTERPRO). Each subunit of the MoaA dimer is comprised of an N-terminal SAM domain (IPR007197 from INTERPRO) that contains the [4Fe-4S] cluster typical for this family of enzymes, as well as an additional [4Fe-4S] cluster in the C-terminal domain that is unique to MoaA proteins []. The unique Fe site of the C-terminal [4Fe-4S] cluster is thought to be involved in the binding and activation of 5'-GTP. Mutations in the human MoCF biosynthesis proteins MOCS1, MOCS2 or GEPH cause MoCF Deficiency type A (MOCOD), causing the loss of activity of MoCF-containing enzymes, resulting in neurological abnormalities and death [].; GO: 0051539 4 iron, 4 sulfur cluster binding, 0006777 Mo-molybdopterin cofactor biosynthetic process, 0019008 molybdopterin synthase complex; PDB: 2FB2_A 2FB3_A 1TV8_B 1TV7_A.
Probab=25.44 E-value=38 Score=23.33 Aligned_cols=30 Identities=30% Similarity=0.629 Sum_probs=13.9
Q ss_pred eCCcceeeehhhhccccCCCCCCCCCcc-cC
Q 034663 25 VGPPLYWHFMEGLDAVSHSSAATCPPCV-CD 54 (88)
Q Consensus 25 vGPpLYW~~~e~l~~~~~sss~sCppC~-CD 54 (88)
.||+-||++..+-+.+-=-++.|.|.|. |+
T Consensus 46 ~~pa~~y~~~g~~g~vG~I~~~s~~FC~~CN 76 (128)
T PF06463_consen 46 NGPARYYRIPGGKGRVGFISPVSNPFCSSCN 76 (128)
T ss_dssp T-SSEEEEETTT--EEEEE-TTTS--GGG--
T ss_pred CCcceEEEECCCCcEEEEEeCCCCCCCCcCC
Confidence 7999999996654221001345677775 54
No 9
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=22.06 E-value=46 Score=20.89 Aligned_cols=9 Identities=33% Similarity=1.018 Sum_probs=6.9
Q ss_pred CCcceeeeh
Q 034663 26 GPPLYWHFM 34 (88)
Q Consensus 26 GPpLYW~~~ 34 (88)
|.+.||+++
T Consensus 53 G~~~~W~l~ 61 (62)
T PF04703_consen 53 GKSTYWRLN 61 (62)
T ss_dssp SSS-EEEES
T ss_pred Ccceeeeec
Confidence 888999985
No 10
>PF06869 DUF1258: Protein of unknown function (DUF1258); InterPro: IPR009667 This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to Caenorhabditis elegans. Note that this family contains a number of conserved cysteine and histidine residues.
Probab=20.59 E-value=40 Score=27.01 Aligned_cols=17 Identities=29% Similarity=0.593 Sum_probs=13.3
Q ss_pred ccccCCCCCCCCCcccC
Q 034663 38 DAVSHSSAATCPPCVCD 54 (88)
Q Consensus 38 ~~~~~sss~sCppC~CD 54 (88)
+...|+++.|||.|.|.
T Consensus 199 g~r~H~s~~SC~ycls~ 215 (258)
T PF06869_consen 199 GMRGHSSSGSCFYCLSQ 215 (258)
T ss_pred cccccccccceeeEecC
Confidence 44578899999998864
No 11
>PF10999 DUF2839: Protein of unknown function (DUF2839); InterPro: IPR021262 This bacterial family of unknown function appear to be restricted to Cyanobacteria.
Probab=20.03 E-value=51 Score=21.50 Aligned_cols=18 Identities=22% Similarity=0.573 Sum_probs=13.8
Q ss_pred HHHHHHhheeeeCCccee
Q 034663 14 SLLGLCLFGYIVGPPLYW 31 (88)
Q Consensus 14 vllav~~a~yIvGPpLYW 31 (88)
++.++.+++-++||..+|
T Consensus 50 ~l~~~wi~vrfiGp~~gw 67 (68)
T PF10999_consen 50 ILVLIWIIVRFIGPAFGW 67 (68)
T ss_pred HHHHHHHHHHhhcchhee
Confidence 455566777889999998
Done!