Query psy2991
Match_columns 71
No_of_seqs 17 out of 19
Neff 2.2
Searched_HMMs 46136
Date Fri Aug 16 22:42:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2991.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2991hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08615 RNase_H2_suC: Ribonuc 66.4 3 6.4E-05 27.2 0.9 9 40-48 2-10 (137)
2 KOG3469|consensus 47.0 4.1 8.8E-05 28.1 -1.0 24 31-54 37-60 (112)
3 PF10324 7TM_GPCR_Srw: Serpent 40.8 0.94 2E-05 31.7 -4.9 27 29-55 189-215 (318)
4 PF15613 WHIM2: WSTF, HB1, Itc 40.1 22 0.00047 20.1 1.5 23 23-45 5-38 (38)
5 PF03181 BURP: BURP domain; I 36.2 19 0.00041 26.5 1.1 11 11-21 175-185 (216)
6 PF09770 PAT1: Topoisomerase I 26.7 21 0.00047 29.5 0.0 12 23-34 384-395 (808)
7 cd00852 NifB NifB belongs to a 24.3 67 0.0015 19.6 1.9 26 44-69 5-30 (106)
8 PF02932 Neur_chan_memb: Neuro 23.8 4.9 0.00011 23.9 -3.2 14 42-55 2-15 (237)
9 PF04673 Cyclase_polyket: Poly 19.5 45 0.00097 22.5 0.4 12 33-44 33-44 (97)
10 PF06990 Gal-3-0_sulfotr: Gala 19.0 28 0.0006 27.3 -0.7 23 36-58 68-90 (402)
No 1
>PF08615 RNase_H2_suC: Ribonuclease H2 non-catalytic subunit (Ylr154p-like); InterPro: IPR013924 Whereas bacterial and archaeal RNases H2 are active as single polypeptides, the Saccharomyces cerevisiae (Baker's yeast) homologue, Rnh2Ap, when expressed in Escherichia coli, fails to produce an active RNase H2. For RNase H2 activity three proteins are required [Rnh2Ap (Rnh201p), Ydr279p (Rnh202p) and Ylr154p (Rnh203p)]. Deletion of any one of the proteins or mutations in the catalytic site in Rnh2A leads to loss of RNase H2 activity []. RNase H2 is an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. It participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. This entry represents the non-catalytic C subunit of RNase H2, which in S. cerevisiae is Q12338 from SWISSPROT (Ylr154p/Rnh203p).; PDB: 3PUF_L 3P56_C 3P5J_C 3KIO_C.
Probab=66.41 E-value=3 Score=27.21 Aligned_cols=9 Identities=33% Similarity=0.508 Sum_probs=7.2
Q ss_pred Eeeecccee
Q psy2991 40 VHTGPCISL 48 (71)
Q Consensus 40 Vhl~PC~sL 48 (71)
+|++||.+-
T Consensus 2 ~hlLPc~I~ 10 (137)
T PF08615_consen 2 AHLLPCKIH 10 (137)
T ss_dssp EEEESSEES
T ss_pred ceeEeeEec
Confidence 799999763
No 2
>KOG3469|consensus
Probab=46.98 E-value=4.1 Score=28.13 Aligned_cols=24 Identities=13% Similarity=0.146 Sum_probs=20.6
Q ss_pred EEEEEEEEEEeeeccceeeeehee
Q psy2991 31 AYYTFRVLFVHTGPCISLVVEKEK 54 (71)
Q Consensus 31 ~Yf~FRVlFVhl~PC~sLVvLnil 54 (71)
.-.|+++-|.-.+||+.|..+|.-
T Consensus 37 s~~Wkkit~~~alP~~al~~~n~y 60 (112)
T KOG3469|consen 37 SRTWKKITFFVALPAVALAMYNAY 60 (112)
T ss_pred hhhhhheeeeeeccHHHHHHHHHH
Confidence 457889999999999999998854
No 3
>PF10324 7TM_GPCR_Srw: Serpentine type 7TM GPCR chemoreceptor Srw; InterPro: IPR019427 G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). The nematode Caenorhabditis elegans has only 14 types of chemosensory neuron, yet is able to sense and respond to several hundred different chemicals because each neuron detects several stimuli []. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf' []. Chemoreception in C. elegans is mediated by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs). More than 1300 potential chemoreceptor genes have been identified in C. elegans, which are generally prefixed sr for serpentine receptor. The receptor superfamilies include Sra (Sra, Srb, Srab, Sre), Str (Srh, Str, Sri, Srd, Srj, Srm, Srn) and Srg (Srx, Srt, Srg, Sru, Srv, Srxa), as well as the families Srw, Srz, Srbc, Srsx and Srr [, , ]. Many of these proteins have homologues in Caenorhabditis briggsae. This entry represents serpentine receptor class w (Srw), which is a solo family amongst the superfamilies of chemoreceptors. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz [].
Probab=40.76 E-value=0.94 Score=31.71 Aligned_cols=27 Identities=26% Similarity=0.498 Sum_probs=22.3
Q ss_pred EEEEEEEEEEEEeeeccceeeeeheee
Q psy2991 29 FTAYYTFRVLFVHTGPCISLVVEKEKF 55 (71)
Q Consensus 29 yt~Yf~FRVlFVhl~PC~sLVvLnil~ 55 (71)
+..|++.++++.+++||..+..++++.
T Consensus 189 ~~~~~~~~gi~~kiiP~il~~ilti~L 215 (318)
T PF10324_consen 189 FRIYFFIDGIFFKIIPCILLPILTILL 215 (318)
T ss_pred HHHHHHhhhhHhhhhhHHHHHHHHHHH
Confidence 346778899999999999998888753
No 4
>PF15613 WHIM2: WSTF, HB1, Itc1p, MBD9 motif 2
Probab=40.10 E-value=22 Score=20.08 Aligned_cols=23 Identities=39% Similarity=0.543 Sum_probs=17.7
Q ss_pred EeeeEEEEEEEEE-----------EEEEEeeecc
Q psy2991 23 LSVDFYFTAYYTF-----------RVLFVHTGPC 45 (71)
Q Consensus 23 vs~d~Yyt~Yf~F-----------RVlFVhl~PC 45 (71)
++.|=|+.-|+|| ..+||=..||
T Consensus 5 LG~DR~~NrYwwf~~s~~~~~~~~~~~~v~~~~~ 38 (38)
T PF15613_consen 5 LGKDRYGNRYWWFSSSSSNSQYYNGGRFVEQGPD 38 (38)
T ss_pred ccccCCCceEEEEecccccCCCCCceEEEEeCCC
Confidence 5788899999999 5666666665
No 5
>PF03181 BURP: BURP domain; InterPro: IPR004873 The BURP domain is a ~230-residue module, which has been named for the four members of the group initially identified, BNM2, USP, RD22, and PG1beta. It is found in the C-terminal part of a number of plant cell wall proteins, which are defined not only by the BURP domain, but also by the overall similarity in their modular construction. The BURP domain proteins consists of either three or four modules: (i) an N-terminal hydrophobic domain - a presumptive transit peptide, joined to (ii) a short conserved segment or other short segment, (iii) an optional segment consisting of repeated units which is unique to each member, and (iv) the C-terminal BURP domain. Although the BURP domain proteins share primary structural features, their expression patterns and the conditions under which they are expressed differ. The presence of the conserved BURP domain in diverse plant proteins suggests an important and fundamental functional role for this domain []. It is possible that the BURP domain represents a general motif for localization of proteins within the cell wall matrix. The other structural domains associated with the BURP domain may specify other target sites for intermolecular interactions []. Some proteins known to contain a BURP domain are listed below [, , ]: Brassica protein BNM2, which is expressed during the induction of microspore embryogenesis. Field bean USPs, abundant non-storage seed proteins with unknown function. Soybean USP-like proteins ADR6 (or SALI5-4A), an auxin-repressible, aluminium-inducible protein and SALI3-2, a protein that is up-regulated by aluminium. Soybean seed coat BURP-domain protein 1 (SCB1). It might play a role in the differentiation of the seed coat parenchyma cells. Arabidopsis RD22 drought induced protein. Maize ZRP2, a protein of unknown function in cortex parenchyma. Tomato PG1beta, the beta-subunit of polygalacturonase isozyme 1 (PG1), which is expressed in ripening fruits. Cereal RAFTIN. It is essential specifically for the maturation phase of pollen development.
Probab=36.17 E-value=19 Score=26.45 Aligned_cols=11 Identities=9% Similarity=0.259 Sum_probs=9.7
Q ss_pred eeecccccceE
Q psy2991 11 ELLPEHAAWVT 21 (71)
Q Consensus 11 ~chve~A~WV~ 21 (71)
.||.+++.|-.
T Consensus 175 vCH~DTS~W~p 185 (216)
T PF03181_consen 175 VCHLDTSGWNP 185 (216)
T ss_pred EEecCCCCCCc
Confidence 69999999964
No 6
>PF09770 PAT1: Topoisomerase II-associated protein PAT1; InterPro: IPR019167 Proteins in this entry are necessary for accurate chromosome transmission during cell division []. ; PDB: 2XER_C 2XES_B 2XEQ_D.
Probab=26.68 E-value=21 Score=29.53 Aligned_cols=12 Identities=33% Similarity=0.822 Sum_probs=0.0
Q ss_pred EeeeEEEEEEEE
Q psy2991 23 LSVDFYFTAYYT 34 (71)
Q Consensus 23 vs~d~Yyt~Yf~ 34 (71)
..+|+||+.|+-
T Consensus 384 y~eDfYYQVY~~ 395 (808)
T PF09770_consen 384 YNEDFYYQVYSQ 395 (808)
T ss_dssp ------------
T ss_pred cccccccccccc
Confidence 468999999986
No 7
>cd00852 NifB NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of nitrogen fixation in bacteria. This domain is sometimes found fused to a N-terminal domain (the Radical SAM domain) in nifB-like proteins.
Probab=24.33 E-value=67 Score=19.59 Aligned_cols=26 Identities=15% Similarity=0.184 Sum_probs=19.7
Q ss_pred ccceeeeeheeeeeeeeEEEeeeccC
Q psy2991 44 PCISLVVEKEKFRWSSFFLLYDFETS 69 (71)
Q Consensus 44 PC~sLVvLnil~~~~~~~~~~~~~~~ 69 (71)
|..--..+|-=|.++.+|.+||.++.
T Consensus 5 ~s~~~~~V~~HFG~a~~F~Iydv~~~ 30 (106)
T cd00852 5 ASKGGGRVNQHFGHATEFQIYEVSGS 30 (106)
T ss_pred ECCCCCEehhhccCCCEEEEEEEcCC
Confidence 44344567788999999999998763
No 8
>PF02932 Neur_chan_memb: Neurotransmitter-gated ion-channel transmembrane region ion channel family signature gamma-aminobutyric acid (GABA) receptor signature nicotinic acetylcholine receptor signature; InterPro: IPR006029 Neurotransmitter ligand-gated ion channels are transmembrane receptor-ion channel complexes that open transiently upon binding of specific ligands, allowing rapid transmission of signals at chemical synapses [, ]. Five of these ion channel receptor families have been shown to form a sequence-related superfamily: Nicotinic acetylcholine receptor (AchR), an excitatory cation channel in vertebrates and invertebrates; in vertebrate motor endplates it is composed of alpha, beta, gamma and delta/epsilon subunits; in neurons it is composed of alpha and non-alpha (or beta) subunits []. Glycine receptor, an inhibitory chloride ion channel composed of alpha and beta subunits []. Gamma-aminobutyric acid (GABA) receptor, an inhibitory chloride ion channel; at least four types of subunits (alpha, beta, gamma and delta) are known []. Serotonin 5HT3 receptor, of which there are seven major types (5HT3-5HT7) []. Glutamate receptor, an excitatory cation channel of which at least three types have been described (kainate, N-methyl-D-aspartate (NMDA) and quisqualate) []. These receptors possess a pentameric structure (made up of varying subunits), surrounding a central pore. All known sequences of subunits from neurotransmitter-gated ion-channels are structurally related. They are composed of a large extracellular glycosylated N-terminal ligand-binding domain, followed by three hydrophobic transmembrane regions which form the ionic channel, followed by an intracellular region of variable length. A fourth hydrophobic region is found at the C-terminal of the sequence [, ]. This domain represents four transmembrane helices of a variety of neurotransmitter-gated ion-channels.; GO: 0006811 ion transport, 0016020 membrane; PDB: 1DXZ_A 3MRA_A 1EQ8_C 1OED_C 2PR9_P 1A11_A 1CEK_A 2BG9_E 2KSR_A 2K59_B ....
Probab=23.79 E-value=4.9 Score=23.92 Aligned_cols=14 Identities=36% Similarity=0.325 Sum_probs=10.8
Q ss_pred eeccceeeeeheee
Q psy2991 42 TGPCISLVVEKEKF 55 (71)
Q Consensus 42 l~PC~sLVvLnil~ 55 (71)
.+||+.+++|+.+-
T Consensus 2 ~~P~~li~~~s~~~ 15 (237)
T PF02932_consen 2 IIPCILIVVLSWLS 15 (237)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred eehHHHHHHHHHhh
Confidence 37999999988553
No 9
>PF04673 Cyclase_polyket: Polyketide synthesis cyclase; InterPro: IPR006765 Aromatic polyketides are assembled by a type II (iterative) polyketide synthase in bacteria. Iterative type II polyketide synthases produce polyketide chains of variable but defined length from a specific starter unit and a number of extender units. They also specify the initial regiospecific folding and cyclization pattern of nascent polyketides either through the action of a cyclase (CYC) subunit or through the combined action of site-specific ketoreductase and CYC subunits. Additional CYCs and other modifications may be necessary to produce linear aromatic polyketides. This family represents a number of cyclases involved in polyketide synthesis in a number of actinobacterial species. TcmI (P39890 from SWISSPROT) catalyses an aromatic rearrangement in the biosynthetic pathaway of tetracenomycin C from Streptomyces coelicolor. The protein is a homodimer where each subunit forms a beta-alpha-beta fold belonging to the ferrodoxin fold superfamily []. Four strands of antiparallel sheets and a layer of alpha helices create a cavity which was proposed to be the active site. This structure shows strong topological similarity to a polyketide monoxygenase (Q53908 from SWISSPROT) from S. coelicolor which functions in the actinorhodin biosynthesic pathway []. It was suggested, therefore, that this fold is well suited to serve as a framework for rearrangements and chemical modification of polyaromatic substrates.; GO: 0030639 polyketide biosynthetic process; PDB: 1TUW_A.
Probab=19.53 E-value=45 Score=22.53 Aligned_cols=12 Identities=25% Similarity=0.562 Sum_probs=10.2
Q ss_pred EEEEEEEEeeec
Q psy2991 33 YTFRVLFVHTGP 44 (71)
Q Consensus 33 f~FRVlFVhl~P 44 (71)
|.|+.|++||+=
T Consensus 33 f~~~dLY~HLiE 44 (97)
T PF04673_consen 33 FSFHDLYFHLIE 44 (97)
T ss_dssp EEETTEEEEEEE
T ss_pred eeeCCEEEEEEe
Confidence 788999999973
No 10
>PF06990 Gal-3-0_sulfotr: Galactose-3-O-sulfotransferase ; InterPro: IPR009729 This family consists of several mammalian galactose-3-O-sulphotransferase proteins. Gal-3-O-sulphotransferase is thought to play a critical role in 3'-sulphation of N-acetyllactosamine in both O- and N-glycans [].; GO: 0001733 galactosylceramide sulfotransferase activity, 0009058 biosynthetic process, 0005794 Golgi apparatus, 0016021 integral to membrane
Probab=18.98 E-value=28 Score=27.34 Aligned_cols=23 Identities=26% Similarity=0.392 Sum_probs=21.2
Q ss_pred EEEEEeeeccceeeeeheeeeee
Q psy2991 36 RVLFVHTGPCISLVVEKEKFRWS 58 (71)
Q Consensus 36 RVlFVhl~PC~sLVvLnil~~~~ 58 (71)
+|+|+++==|+|=++.||++|+.
T Consensus 68 nIvFlKTHKTgSSTv~nIL~Rfg 90 (402)
T PF06990_consen 68 NIVFLKTHKTGSSTVQNILFRFG 90 (402)
T ss_pred eEEEEecCCcccHHHHHHHHHHH
Confidence 58999999999999999999974
Done!