Query 537021.9.peg.109_1 Match_columns 66 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 23 18:27:36 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_109.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam01858 RB_A Retinoblastoma- 49.8 20 0.0005 17.8 3.2 38 18-57 111-153 (192) 2 pfam09586 YfhO Bacterial membr 43.8 30 0.00077 16.8 4.9 43 4-46 196-238 (835) 3 pfam04910 DUF654 Protein of un 30.3 51 0.0013 15.6 2.9 35 15-58 149-183 (343) 4 KOG3858 consensus 21.0 23 0.00059 17.4 -0.4 33 19-53 8-40 (233) 5 KOG1010 consensus 19.2 85 0.0022 14.4 3.6 45 3-57 502-551 (920) 6 KOG2044 consensus 19.0 71 0.0018 14.8 1.8 30 37-66 152-183 (931) 7 pfam06139 BphX BphX-like. Fami 17.9 80 0.002 14.5 1.8 37 8-56 96-132 (136) 8 pfam08004 DUF1699 Protein of u 16.2 77 0.002 14.6 1.4 50 10-59 52-102 (131) 9 cd03061 GST_N_CLIC GST_N famil 14.7 84 0.0022 14.4 1.3 22 4-25 23-57 (91) 10 TIGR01239 galT_2 galactose-1-p 14.6 23 0.00058 17.4 -1.7 7 19-25 205-211 (502) No 1 >pfam01858 RB_A Retinoblastoma-associated protein A domain. This domain has the cyclin fold as predicted. Probab=49.79 E-value=20 Score=17.78 Aligned_cols=38 Identities=29% Similarity=0.647 Sum_probs=22.7 Q ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHH-----CCCCCHHHHHHH Q ss_conf 9999999998885102203568889987-----167048999757 Q 537021.9.peg.1 18 AQWFLQFSVSLLLSADISASVLFPVYWI-----LPGFDFRKILSL 57 (66) Q Consensus 18 aqwflqfsvslllsadisasvlfpvywi-----lpgfdfrkilsl 57 (66) -+-.+-.++.+.+-+.-+....|| || ++.|||-||... T Consensus 111 h~sLlACc~EvVl~~y~~~~~~FP--wiL~~~~i~af~f~KvIE~ 153 (192) T pfam01858 111 HRSLLACCLELVLATYKTTDLSFP--WILEVFGITAFDFYKVIES 153 (192) T ss_pred HHHHHHHHHHHHHHHCCCCCCCCC--HHHHHCCCCHHHHHHHHHH T ss_conf 999999999999999077767774--9998729977667667677 No 2 >pfam09586 YfhO Bacterial membrane protein YfhO. This protein is a conserved membrane protein. The yfhO gene is transcribed in Difco sporulation medium and the transcription is affected by the YvrGHb two-component system. Some members of this family have been annotated as glycosyl transferases of the PMT family. Probab=43.77 E-value=30 Score=16.79 Aligned_cols=43 Identities=37% Similarity=0.436 Sum_probs=36.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHC Q ss_conf 9999999999999999999999988851022035688899871 Q 537021.9.peg.1 4 LFCQRIFSITLSHFAQWFLQFSVSLLLSADISASVLFPVYWIL 46 (66) Q Consensus 4 lfcqrifsitlshfaqwflqfsvslllsadisasvlfpvywil 46 (66) -|+-|.+..+...+.+.+++|-.+-+++.-+||-++.|++.-+ T Consensus 196 Y~~~r~~~~~~k~~~~~~~~f~~~~llg~~lsav~llP~~~~l 238 (835) T pfam09586 196 YFLYRLIFKDIKSRWKQFLRFIISSLLSGGISAVVLLPTVLGL 238 (835) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999998620999999999999999999999999999999999 No 3 >pfam04910 DUF654 Protein of unknown function, DUF654. This family includes a number of poorly characterized eukaryotic proteins. Probab=30.29 E-value=51 Score=15.59 Aligned_cols=35 Identities=31% Similarity=0.548 Sum_probs=25.0 Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHHHH Q ss_conf 99999999999988851022035688899871670489997576 Q 537021.9.peg.1 15 SHFAQWFLQFSVSLLLSADISASVLFPVYWILPGFDFRKILSLR 58 (66) Q Consensus 15 shfaqwflqfsvslllsadisasvlfpvywilpgfdfrkilslr 58 (66) ++--+|+++|+-+.....+ .|.+|||-|-.-|+.. T Consensus 149 s~ey~~li~f~~~~~~~~~---------~~~lPn~afS~aLA~~ 183 (343) T pfam04910 149 AKEYEWLIDFSESPLASRN---------LSLLPNFAYSVALALF 183 (343) T ss_pred CCCHHHHHHHHHHHHCCCC---------HHHCCCHHHHHHHHHH T ss_conf 3537799999973530340---------6558487899999999 No 4 >KOG3858 consensus Probab=20.98 E-value=23 Score=17.38 Aligned_cols=33 Identities=30% Similarity=0.442 Sum_probs=21.2 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHH Q ss_conf 99999999888510220356888998716704899 Q 537021.9.peg.1 19 QWFLQFSVSLLLSADISASVLFPVYWILPGFDFRK 53 (66) Q Consensus 19 qwflqfsvslllsadisasvlfpvywilpgfdfrk 53 (66) |+|+-+. |..++--.+..+++|||.--.=-||. T Consensus 8 ~~~~ll~--l~~~~~~~~~~~~~VyWNSSNp~F~~ 40 (233) T KOG3858 8 LLFLLLI--LCPLGLAAGKNLHPVYWNSSNPRFRR 40 (233) T ss_pred HHHHHHH--HCCCCCCCCCCCCCEEECCCCCCEEC T ss_conf 8999987--60235576656542575478965216 No 5 >KOG1010 consensus Probab=19.22 E-value=85 Score=14.41 Aligned_cols=45 Identities=38% Similarity=0.708 Sum_probs=26.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH-----CCCCCHHHHHHH Q ss_conf 9999999999999999999999998885102203568889987-----167048999757 Q 537021.9.peg.1 3 KLFCQRIFSITLSHFAQWFLQFSVSLLLSADISASVLFPVYWI-----LPGFDFRKILSL 57 (66) Q Consensus 3 klfcqrifsitlshfaqwflqfsvslllsadisasvlfpvywi-----lpgfdfrkilsl 57 (66) +|.-|+||..+| +-+++.|.|-+-- ....|| || ++.|||-|++.+ T Consensus 502 ~LL~q~~Fh~sL-------lACclElVL~ty~-~~l~FP--wvle~~~l~aFdF~KVIE~ 551 (920) T KOG1010 502 KLLEQEIFHRSL-------LACCLELVLATYK-TDLSFP--WVLECFGLKAFDFYKVIES 551 (920) T ss_pred HHHHHHHHHHHH-------HHHHHHHHHHHHC-CCCCCC--HHHHHCCCCHHHHHHHHHH T ss_conf 998888999999-------9999999999817-898884--3565438858889999999 No 6 >KOG2044 consensus Probab=18.97 E-value=71 Score=14.82 Aligned_cols=30 Identities=40% Similarity=0.482 Sum_probs=22.7 Q ss_pred HHHHHHHHHCCCCCHHHHHH--HHHHHHHHCC Q ss_conf 56888998716704899975--7666542129 Q 537021.9.peg.1 37 SVLFPVYWILPGFDFRKILS--LRDYILCRLA 66 (66) Q Consensus 37 svlfpvywilpgfdfrkils--lrdyilcrla 66 (66) +--|----|-||-.|-..|+ ||-||-|||. T Consensus 152 ~e~fDSNcITPGTpFM~~La~aLrYyI~~rLn 183 (931) T KOG2044 152 KETFDSNCITPGTPFMDRLAKALRYYIHDRLN 183 (931) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC T ss_conf 14034575679976899999999999987622 No 7 >pfam06139 BphX BphX-like. Family of bacterial proteins located in the phenyl dioxygenase (bph) operon. The function of this family is unknown. Probab=17.85 E-value=80 Score=14.54 Aligned_cols=37 Identities=32% Similarity=0.554 Sum_probs=22.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCHHHHHH Q ss_conf 9999999999999999999888510220356888998716704899975 Q 537021.9.peg.1 8 RIFSITLSHFAQWFLQFSVSLLLSADISASVLFPVYWILPGFDFRKILS 56 (66) Q Consensus 8 rifsitlshfaqwflqfsvslllsadisasvlfpvywilpgfdfrkils 56 (66) .++||..||-|-||---. ..-.+-||.-|.--++-.+ T Consensus 96 D~YSivws~ea~~fgL~t------------l~iH~vwi~wgl~vwRa~~ 132 (136) T pfam06139 96 DFYSIVWSHEALWFGLTT------------LVIHVVWIVWGLRVWRAAS 132 (136) T ss_pred HHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHH T ss_conf 999999711689999999------------9999999999999998654 No 8 >pfam08004 DUF1699 Protein of unknown function (DUF1699). This family contains many archaeal proteins which have very conserved sequences. Probab=16.20 E-value=77 Score=14.62 Aligned_cols=50 Identities=18% Similarity=0.246 Sum_probs=38.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHH-HHHHHHHCCCCCHHHHHHHHH Q ss_conf 99999999999999999888510220356-888998716704899975766 Q 537021.9.peg.1 10 FSITLSHFAQWFLQFSVSLLLSADISASV-LFPVYWILPGFDFRKILSLRD 59 (66) Q Consensus 10 fsitlshfaqwflqfsvslllsadisasv-lfpvywilpgfdfrkilslrd 59 (66) +--|+|.+.+-|||..---|+..|....- -..-|+..|.-...||-+++. T Consensus 52 y~~tvSksi~mfLemq~I~LieGDVwGHrkDinEYy~i~~~viekI~el~~ 102 (131) T pfam08004 52 YYRTVSKSIEMFLEMQGIQLIEGDVWGHRKDINEYYTVSQSVIERIRELKA 102 (131) T ss_pred HHHHHHHHHHHHHHHHCEEEEECCCCCCCCCCHHHCCCCHHHHHHHHHHHH T ss_conf 999999999999987170466324422212333040147999999999997 No 9 >cd03061 GST_N_CLIC GST_N family, Chloride Intracellular Channel (CLIC) subfamily; composed of CLIC1-5, p64, parchorin and similar proteins. They are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated secretion, cell division and apoptosis. They can exist in both water-soluble and membrane-bound states, and are found in various vesicles and membranes. Biochemical studies of the C. elegans homolog, EXC-4, show that the membrane localization domain is present in the N-terminal part of the protein. The structure of soluble human CLIC1 reveals that it is monomeric and it adopts a fold similar to GSTs, containing an N-terminal domain with a TRX fold and a C-terminal alpha helical domain. Upon oxidation, the N-terminal domain of CLIC1 undergoes a structural change to form a non-covalent dimer stabilized by the formation of an intramolecular disulfide bond between two cysteines that are far apart in the reduced form. The CLI Probab=14.75 E-value=84 Score=14.43 Aligned_cols=22 Identities=23% Similarity=0.527 Sum_probs=14.3 Q ss_pred HHHHHHHHHH-------------HHHHHHHHHHHH Q ss_conf 9999999999-------------999999999999 Q 537021.9.peg.1 4 LFCQRIFSIT-------------LSHFAQWFLQFS 25 (66) Q Consensus 4 lfcqrifsit-------------lshfaqwflqfs 25 (66) .||||.|-+- +.+--+||+..+ T Consensus 23 PF~QR~~mvL~~Kgv~f~vt~VDl~~kPe~f~~~~ 57 (91) T cd03061 23 PFCQRLFMVLWLKGVVFNVTTVDMKRKPEDLKDLA 57 (91) T ss_pred HHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHC T ss_conf 77899999999749974589855466929999659 No 10 >TIGR01239 galT_2 galactose-1-phosphate uridylyltransferase; InterPro: IPR000766 Galactose-1-phosphate uridyl transferase 2.7.7.12 from EC (galT) catalyzes the transfer of an uridyldiphosphate group on galactose (or glucose) 1-phosphate. During the reaction, the uridyl moiety links to a histidine residue. In the Escherichia coli enzyme, it has been shown that two histidine residues separated by a single proline residue are essential for enzyme activity. On the basis of sequence similarities, two apparently unrelated families seem to exist. Class-I enzymes are found in eukaryotes as well as some bacteria such as E. coli or Streptomyces lividans, while class-II enzymes have been found so far only in bacteria such as Bacillus subtilis or Lactobacillus helveticus .; GO: 0008108 UDP-glucose:hexose-1-phosphate uridylyltransferase activity, 0006012 galactose metabolic process, 0005737 cytoplasm. Probab=14.62 E-value=23 Score=17.44 Aligned_cols=7 Identities=57% Similarity=1.170 Sum_probs=0.0 Q ss_pred HHHHHHH Q ss_conf 9999999 Q 537021.9.peg.1 19 QWFLQFS 25 (66) Q Consensus 19 qwflqfs 25 (66) +|++||| T Consensus 205 ~WGfQfS 211 (502) T TIGR01239 205 EWGFQFS 211 (502) T ss_pred CCCCCCC T ss_conf 6665358 Done!