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!