Query psy18229
Match_columns 111
No_of_seqs 194 out of 597
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 16:59:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy18229.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/18229hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3646|consensus 99.5 7.2E-15 1.6E-19 121.0 -0.3 49 1-49 306-354 (486)
2 PF02932 Neur_chan_memb: Neuro 98.7 3.4E-10 7.4E-15 78.9 -4.7 52 1-52 66-117 (237)
3 KOG3645|consensus 98.1 4.5E-07 9.8E-12 74.9 -0.5 50 1-50 311-361 (449)
4 TIGR00860 LIC Cation transport 98.1 2.8E-07 6E-12 76.3 -1.8 46 1-51 311-356 (459)
5 cd06533 Glyco_transf_WecG_TagA 40.7 11 0.00024 27.1 0.5 25 19-43 137-161 (171)
6 PF03808 Glyco_tran_WecB: Glyc 29.4 16 0.00035 26.2 -0.2 22 22-43 142-163 (172)
7 PF14202 TnpW: Transposon-enco 28.2 54 0.0012 18.1 1.8 28 9-36 8-35 (37)
8 TIGR00696 wecB_tagA_cpsF bacte 23.0 35 0.00077 24.9 0.6 25 20-44 139-163 (177)
9 PRK03692 putative UDP-N-acetyl 22.2 31 0.00068 26.5 0.2 24 21-44 197-220 (243)
10 PF00816 Histone_HNS: H-NS his 19.6 59 0.0013 20.9 1.0 11 25-35 77-87 (93)
No 1
>KOG3646|consensus
Probab=99.46 E-value=7.2e-15 Score=120.99 Aligned_cols=49 Identities=61% Similarity=1.227 Sum_probs=47.4
Q ss_pred CEeeheehheeeeEEEcccCCCCCCCCChhhHHhhhccccceeeeeCCC
Q psy18229 1 MFMVASSVVLTVVVLNYHHRTADSHEMPDWIRFLFLQWIPWILCMQRPH 49 (111)
Q Consensus 1 Mvlv~lSlv~Tv~VLn~h~r~~~~~~mP~WvR~l~L~~lp~lL~m~~p~ 49 (111)
|++|++|+++||+|||+|||+|++|+|++|+|.+||+|+||+|+|+||.
T Consensus 306 m~iv~~SvvfTv~vLn~h~R~p~~h~m~p~~r~vfL~wlpwll~M~rP~ 354 (486)
T KOG3646|consen 306 MFIVAASVVFTVIVLNLHHRTPETHEMSPWTRSVFLEWLPWLLRMKRPF 354 (486)
T ss_pred HHHHHhhheeEEEEEeeeccCccccccCHHHHHHHHHHHHHHHHhcCCC
Confidence 6889999999999999999999999999999999999999999999993
No 2
>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=98.69 E-value=3.4e-10 Score=78.94 Aligned_cols=52 Identities=44% Similarity=0.852 Sum_probs=22.4
Q ss_pred CEeeheehheeeeEEEcccCCCCCCCCChhhHHhhhccccceeeeeCCCCcc
Q psy18229 1 MFMVASSVVLTVVVLNYHHRTADSHEMPDWIRFLFLQWIPWILCMQRPHKKI 52 (111)
Q Consensus 1 Mvlv~lSlv~Tv~VLn~h~r~~~~~~mP~WvR~l~L~~lp~lL~m~~p~~~~ 52 (111)
|+++++++..|++++|+||+++..++||+|+|.++++++|+++||++++...
T Consensus 66 ~~v~~~~~~~avv~~~~~~~~~~~~~~~~~~r~~~l~~l~~~l~~~~~~~~~ 117 (237)
T PF02932_consen 66 MFVFSASLEFAVVVYNIHHRGPRTRPMPPWVRRLFLEKLARLLCMKRPSEKE 117 (237)
T ss_dssp HHHHHHHHHHHHHHHHHHHHSTTT-S--------------------------
T ss_pred chhhhHHHHhhhhhhhhcccccccccccchhHHHHhhhhhhhhhhccccccc
Confidence 4567889999999999999999899999999999999999999999987653
No 3
>KOG3645|consensus
Probab=98.12 E-value=4.5e-07 Score=74.89 Aligned_cols=50 Identities=50% Similarity=0.924 Sum_probs=47.1
Q ss_pred CEeeheehheeeeEEEcccCCCCCC-CCChhhHHhhhccccceeeeeCCCC
Q psy18229 1 MFMVASSVVLTVVVLNYHHRTADSH-EMPDWIRFLFLQWIPWILCMQRPHK 50 (111)
Q Consensus 1 Mvlv~lSlv~Tv~VLn~h~r~~~~~-~mP~WvR~l~L~~lp~lL~m~~p~~ 50 (111)
|+++++|++.|++++|+|||.+.++ +||.|++++++..+|+++++++++.
T Consensus 311 m~~~~~sv~~tv~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 361 (449)
T KOG3645|consen 311 MVLVTISVVVTVVILNLHHRSPTTHPPMPPWVRRVFLEKLPRLLLMSRPED 361 (449)
T ss_pred HHHHHHHHHHheeEEeeecccCCCCCCCchHHHHHHHHHHHHHHhcCCccc
Confidence 5788999999999999999999998 8999999999999999999998875
No 4
>TIGR00860 LIC Cation transporter family protein. selective while glycine receptors are anion selective).
Probab=98.11 E-value=2.8e-07 Score=76.26 Aligned_cols=46 Identities=30% Similarity=0.512 Sum_probs=42.2
Q ss_pred CEeeheehheeeeEEEcccCCCCCCCCChhhHHhhhccccceeeeeCCCCc
Q psy18229 1 MFMVASSVVLTVVVLNYHHRTADSHEMPDWIRFLFLQWIPWILCMQRPHKK 51 (111)
Q Consensus 1 Mvlv~lSlv~Tv~VLn~h~r~~~~~~mP~WvR~l~L~~lp~lL~m~~p~~~ 51 (111)
|++|++|++.|++|+|+|||++.+++ |.++++++|+++||++|++.
T Consensus 311 ~~~v~~sli~tv~V~~~~~~~~~~~~-----r~~~l~~l~~~l~~~~~~~~ 356 (459)
T TIGR00860 311 MAFVFLALLETAFVNYVHHKDPAQGK-----RHLLLERCAWRLCKQEPGED 356 (459)
T ss_pred HHHHHHHHHHHHhheeEEccCCCCCc-----eehHHhhchHHhcccCcccc
Confidence 56789999999999999999998876 99999999999999999764
No 5
>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Probab=40.66 E-value=11 Score=27.06 Aligned_cols=25 Identities=24% Similarity=0.597 Sum_probs=20.1
Q ss_pred cCCCCCCCCChhhHHhhhcccccee
Q psy18229 19 HRTADSHEMPDWIRFLFLQWIPWIL 43 (111)
Q Consensus 19 ~r~~~~~~mP~WvR~l~L~~lp~lL 43 (111)
+-+-..++.|.|++++-|+|+-+++
T Consensus 137 ~~aG~~~raP~w~~~~glEWlyRl~ 161 (171)
T cd06533 137 FLAGTVKRAPKWMQKLGLEWLYRLL 161 (171)
T ss_pred eccCCcccCcHHHHHhCchhHHhhh
Confidence 3344456889999999999999876
No 6
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=29.41 E-value=16 Score=26.21 Aligned_cols=22 Identities=32% Similarity=0.761 Sum_probs=18.6
Q ss_pred CCCCCCChhhHHhhhcccccee
Q psy18229 22 ADSHEMPDWIRFLFLQWIPWIL 43 (111)
Q Consensus 22 ~~~~~mP~WvR~l~L~~lp~lL 43 (111)
-...+.|+|++++-|+|+-+++
T Consensus 142 G~~~raP~w~~~~glEWlyRl~ 163 (172)
T PF03808_consen 142 GKVKRAPKWMRRLGLEWLYRLL 163 (172)
T ss_pred cCcCccCHHHHHcCcHHHHHHH
Confidence 3346899999999999998875
No 7
>PF14202 TnpW: Transposon-encoded protein TnpW
Probab=28.18 E-value=54 Score=18.11 Aligned_cols=28 Identities=25% Similarity=0.236 Sum_probs=20.7
Q ss_pred heeeeEEEcccCCCCCCCCChhhHHhhh
Q psy18229 9 VLTVVVLNYHHRTADSHEMPDWIRFLFL 36 (111)
Q Consensus 9 v~Tv~VLn~h~r~~~~~~mP~WvR~l~L 36 (111)
--|++++++||....+..|-.-+++++.
T Consensus 8 G~Tty~V~~~F~~~s~et~~DKi~rli~ 35 (37)
T PF14202_consen 8 GKTTYVVEVHFSETSKETMQDKIKRLIR 35 (37)
T ss_pred CCEEEEEEEEECCCccccHHHHHHHHHh
Confidence 4588999999977776677766666653
No 8
>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family. The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.
Probab=23.04 E-value=35 Score=24.92 Aligned_cols=25 Identities=20% Similarity=0.401 Sum_probs=20.1
Q ss_pred CCCCCCCCChhhHHhhhccccceee
Q psy18229 20 RTADSHEMPDWIRFLFLQWIPWILC 44 (111)
Q Consensus 20 r~~~~~~mP~WvR~l~L~~lp~lL~ 44 (111)
-+-..++-|+|++++=|+|+=+++.
T Consensus 139 ~aG~~~rAP~w~~~~gLEWlyRl~~ 163 (177)
T TIGR00696 139 FSGLVKRAPRWLMRLGLEWLYRLRM 163 (177)
T ss_pred cccCcCcCCHHHHHhCchHHHHhhh
Confidence 3444568999999999999988763
No 9
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=22.23 E-value=31 Score=26.54 Aligned_cols=24 Identities=25% Similarity=0.408 Sum_probs=19.7
Q ss_pred CCCCCCCChhhHHhhhccccceee
Q psy18229 21 TADSHEMPDWIRFLFLQWIPWILC 44 (111)
Q Consensus 21 ~~~~~~mP~WvR~l~L~~lp~lL~ 44 (111)
.-..++-|+|++++-|+|+=+++.
T Consensus 197 aG~~~RAP~w~~~~gLEWlyRl~~ 220 (243)
T PRK03692 197 TGHVKRAPKIWQNLGLEWLYRLLS 220 (243)
T ss_pred cCCcCcCcHHHHHhChHHHHHhHh
Confidence 334568999999999999998763
No 10
>PF00816 Histone_HNS: H-NS histone family Partial NMR structure.; InterPro: IPR001801 The histone-like nucleoid-structuring (H-NS) protein belongs to a family of bacterial proteins that play a role in the formation of nucleoid structure and affect gene expression under certain conditions [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2LEV_A 1HNS_A 1LR1_B 1HNR_A 1NI8_A 1OV9_A 2JR1_A 3NR7_A 2L93_A 2L92_A.
Probab=19.64 E-value=59 Score=20.89 Aligned_cols=11 Identities=18% Similarity=0.667 Sum_probs=9.0
Q ss_pred CCCChhhHHhh
Q psy18229 25 HEMPDWIRFLF 35 (111)
Q Consensus 25 ~~mP~WvR~l~ 35 (111)
+++|.|++-.+
T Consensus 77 Gr~P~Wl~~~~ 87 (93)
T PF00816_consen 77 GRRPKWLKEAL 87 (93)
T ss_dssp SSSSHHHHHHH
T ss_pred CCCCHHHHHHH
Confidence 68999998754
Done!