Query         537021.9.peg.455_1
Match_columns 37
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Tue May 24 23:55:33 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_455.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam11654 DUF2665 Protein of u  78.2     1.4 3.5E-05   23.9   1.9   32    3-34     10-44  (47)
  2 COG5582 Uncharacterized conser  33.3      42  0.0011   16.6   2.8   29    7-35     12-41  (182)
  3 pfam06936 Selenoprotein_S Sele  24.2      54  0.0014   16.0   2.0   15    3-17     41-55  (190)
  4 pfam12004 DUF3498 Domain of un  21.3      43  0.0011   16.5   1.0   14   16-32    429-442 (489)
  5 cd02554 PseudoU_synth_RluF Pse  19.8     5.5 0.00014   20.9  -3.8   14    9-22      1-14  (164)
  6 PRK03636 hypothetical protein;  18.3      99  0.0025   14.7   2.8   31    7-37     11-42  (179)
  7 cd02553 PseudoU_synth_RsuA Pse  14.2     8.7 0.00022   20.0  -3.9   15    9-23      1-15  (167)
  8 KOG3789 consensus               13.3 1.4E+02  0.0035   14.0   2.2   17   21-37    119-135 (396)
  9 pfam08864 UPF0302 UPF0302 doma  13.0 1.4E+02  0.0035   14.0   2.9   31    7-37      5-36  (106)
 10 TIGR01127 ilvA_1Cterm threonin  12.4      82  0.0021   15.1   0.7   14    8-21    242-255 (381)

No 1  
>pfam11654 DUF2665 Protein of unknown function (DUF2665). Some members in this family are annotated as Non classical export proteins, however no specific function is known.
Probab=78.21  E-value=1.4  Score=23.94  Aligned_cols=32  Identities=44%  Similarity=0.678  Sum_probs=26.0

Q ss_pred             HHHHHH---HHHHHHHHCCHHHHHHHHHHHHHHHH
Q ss_conf             799999---99999752241789999999846776
Q 537021.9.peg.4    3 LLAIII---VYFLFEKRKGIICGRLLNMLLEEKSF   34 (37)
Q Consensus         3 llaiii---vyflfekrkgiicgrllnmlleeksf   34 (37)
                      ++||.|   -|+++|.|.|---|+-||-|+..|-.
T Consensus        10 ~~ai~iG~~sYyl~E~r~gRp~Gh~LneL~~kk~~   44 (47)
T pfam11654        10 ILAISIGVASYYLYERRTGRPQGHTLNELLKKRWN   44 (47)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf             89999988899887630379999638999999876


No 2  
>COG5582 Uncharacterized conserved protein [Function unknown]
Probab=33.31  E-value=42  Score=16.56  Aligned_cols=29  Identities=28%  Similarity=0.382  Sum_probs=22.4

Q ss_pred             HHHHHHHH-HHCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999997-522417899999998467763
Q 537021.9.peg.4    7 IIVYFLFE-KRKGIICGRLLNMLLEEKSFL   35 (37)
Q Consensus         7 iivyflfe-krkgiicgrllnmlleeksfl   35 (37)
                      .|-|||++ .-|.-+|-++||.++...+.+
T Consensus        12 FirwfL~q~qlK~Rea~wvLnYl~~hd~ll   41 (182)
T COG5582          12 FIRWFLNQYQLKRREAVWVLNYLMSHDALL   41 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999988888999999999998259999


No 3  
>pfam06936 Selenoprotein_S Selenoprotein S (SelS). This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. The function of this family is unknown.
Probab=24.19  E-value=54  Score=16.01  Aligned_cols=15  Identities=33%  Similarity=0.651  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHHHC
Q ss_conf             799999999997522
Q 537021.9.peg.4    3 LLAIIIVYFLFEKRK   17 (37)
Q Consensus         3 llaiiivyflfekrk   17 (37)
                      |+.+|++|+++.|-.
T Consensus        41 L~~~v~ly~l~qkL~   55 (190)
T pfam06936        41 LLGCVGIYLLIQKLR   55 (190)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999999999999871


No 4  
>pfam12004 DUF3498 Domain of unknown function (DUF3498). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 433 to 538 amino acids in length. This domain is found associated with pfam00616, pfam00168. This domain has two conserved sequence motifs: DLQ and PLSFQNP.
Probab=21.26  E-value=43  Score=16.54  Aligned_cols=14  Identities=57%  Similarity=0.762  Sum_probs=8.4

Q ss_pred             HCCHHHHHHHHHHHHHH
Q ss_conf             22417899999998467
Q 537021.9.peg.4   16 RKGIICGRLLNMLLEEK   32 (37)
Q Consensus        16 rkgiicgrllnmlleek   32 (37)
                      -||||| ||  |..||.
T Consensus       429 MKsIIs-RL--MaVEEE  442 (489)
T pfam12004       429 MKSIIS-RL--MAVEEE  442 (489)
T ss_pred             HHHHHH-HH--HHHHHH
T ss_conf             999999-99--989999


No 5  
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Probab=19.81  E-value=5.5  Score=20.93  Aligned_cols=14  Identities=43%  Similarity=0.828  Sum_probs=11.2

Q ss_pred             HHHHHHHHCCHHHH
Q ss_conf             99999752241789
Q 537021.9.peg.4    9 VYFLFEKRKGIICG   22 (37)
Q Consensus         9 vyflfekrkgiicg   22 (37)
                      ||++|.|-+|++|.
T Consensus         1 vYillnKP~G~v~s   14 (164)
T cd02554           1 VYIAYNKPVGIDCT   14 (164)
T ss_pred             CEEEEECCCCEEEC
T ss_conf             99999899982838


No 6  
>PRK03636 hypothetical protein; Provisional
Probab=18.31  E-value=99  Score=14.72  Aligned_cols=31  Identities=26%  Similarity=0.465  Sum_probs=24.7

Q ss_pred             HHHHHHHH-HHCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             99999997-52241789999999846776369
Q 537021.9.peg.4    7 IIVYFLFE-KRKGIICGRLLNMLLEEKSFLSN   37 (37)
Q Consensus         7 iivyflfe-krkgiicgrllnmlleeksflsn   37 (37)
                      -|.|||+. .-|.-+|-++||.++....+|.+
T Consensus        11 Fi~wfL~~y~lK~Re~~wiLnyl~~~~~lL~~   42 (179)
T PRK03636         11 FIRWFLNNYQLKRRECVWILNYLMSHDQLMEK   42 (179)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHCHHHHHH
T ss_conf             99999985332211799999999707998866


No 7  
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).  No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
Probab=14.17  E-value=8.7  Score=19.96  Aligned_cols=15  Identities=33%  Similarity=1.008  Sum_probs=10.1

Q ss_pred             HHHHHHHHCCHHHHH
Q ss_conf             999997522417899
Q 537021.9.peg.4    9 VYFLFEKRKGIICGR   23 (37)
Q Consensus         9 vyflfekrkgiicgr   23 (37)
                      ||++|.|.+|.+|.+
T Consensus         1 VYillnKP~G~v~t~   15 (167)
T cd02553           1 VYLMLNKPAGVVCAT   15 (167)
T ss_pred             CEEEEECCCCEEECC
T ss_conf             999998899979698


No 8  
>KOG3789 consensus
Probab=13.34  E-value=1.4e+02  Score=14.04  Aligned_cols=17  Identities=47%  Similarity=0.546  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHHHHHCC
Q ss_conf             89999999846776369
Q 537021.9.peg.4   21 CGRLLNMLLEEKSFLSN   37 (37)
Q Consensus        21 cgrllnmlleeksflsn   37 (37)
                      |++.|-+|-||-+|||+
T Consensus       119 la~yl~~LE~e~~flS~  135 (396)
T KOG3789         119 LAEYLIVLEEESKFLSN  135 (396)
T ss_pred             HHHHHHHHHHHHHHHCC
T ss_conf             99999999988776358


No 9  
>pfam08864 UPF0302 UPF0302 domain. This family is known as UPF0302. It is currently uncharacterized.
Probab=13.00  E-value=1.4e+02  Score=13.99  Aligned_cols=31  Identities=26%  Similarity=0.299  Sum_probs=24.1

Q ss_pred             HHHHHHHH-HHCCHHHHHHHHHHHHHHHHHCC
Q ss_conf             99999997-52241789999999846776369
Q 537021.9.peg.4    7 IIVYFLFE-KRKGIICGRLLNMLLEEKSFLSN   37 (37)
Q Consensus         7 iivyflfe-krkgiicgrllnmlleeksflsn   37 (37)
                      -|.|||+. .-|.-+|-++||-++....+|.+
T Consensus         5 Fi~wfL~~y~~K~re~~wiLnyl~~~~~lL~~   36 (106)
T pfam08864         5 FIEWFLNNYQLKRREAVWILNYLKSHDHLLER   36 (106)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHCHHHHHH
T ss_conf             99999974332321699999999628988854


No 10 
>TIGR01127 ilvA_1Cterm threonine dehydratase; InterPro: IPR005789    Serine and threonine dehydratases ,  are functionally and structurally related pyridoxal-phosphate dependent enzymes. L-serine dehydratase () and D-serine dehydratase () catalyze the dehydratation of L-serine (respectively D-serine) into ammonia and pyruvate. Threonine dehydratase () (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism. Threonine synthase () is also a pyridoxal-phosphate enzyme, it catalyzes the transformation of homoserine-phosphate into threonine. It has been shown  that threonine synthase is distantly related to the serine/threonine dehydratases. In all these enzymes, the pyridoxal-phosphate group is attached to a lysine residue.    A form of threonine dehydratase with two copies of the C-terminal domain  is described by . This model describes a phylogenetically distinct which branches with the catabolic threonine dehydratase of E. coli; many members are designated as catabolic for this reason. However, the catabolic form lacks any  domain. Many members of this model are found in species with other isoleucine biosynthetic enzymes.; GO: 0004794 L-threonine ammonia-lyase activity.
Probab=12.41  E-value=82  Score=15.11  Aligned_cols=14  Identities=21%  Similarity=0.335  Sum_probs=9.9

Q ss_pred             HHHHHHHHHCCHHH
Q ss_conf             99999975224178
Q 537021.9.peg.4    8 IVYFLFEKRKGIIC   21 (37)
Q Consensus         8 ivyflfekrkgiic   21 (37)
                      -+|||||+.|=+.=
T Consensus       242 A~~~LLEr~Ki~aE  255 (381)
T TIGR01127       242 AILLLLERAKIVAE  255 (381)
T ss_pred             HHHHHHCCCCEEEC
T ss_conf             99998607747882


Done!