Query         537021.9.peg.1140_1
Match_columns 90
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Wed May 25 08:34:31 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_1140.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam03753 HHV6-IE Human herpes  50.3      24  0.0006   17.4   5.1   57   17-73    187-260 (993)
  2 pfam00798 Arena_glycoprot Aren  37.2      38 0.00096   16.1   4.7   26   60-85     14-39  (473)
  3 KOG3518 consensus               35.9      39   0.001   16.0   5.2   39   13-51    208-248 (521)
  4 pfam08647 BRE1 BRE1 E3 ubiquit  26.6      55  0.0014   15.1   2.4   26   20-45     65-90  (96)
  5 pfam07423 DUF1510 Protein of u  22.0      69  0.0018   14.4   3.4   27   41-81      6-32  (214)
  6 KOG3918 consensus               20.4      74  0.0019   14.2   5.4   59   28-89     10-68  (129)
  7 pfam05961 Chordopox_A13L Chord  20.3      75  0.0019   14.2   2.4   20   66-85      7-26  (68)
  8 pfam04834 Adeno_E3_14_5 Early   19.6      77   0.002   14.1   2.3   32   56-88     21-52  (97)
  9 TIGR01584 citF citrate lyase,   19.1      17 0.00044   18.3  -1.4   48   22-78     38-85  (496)
 10 pfam02270 TFIIF_beta Transcrip  19.0      80   0.002   14.0   2.7   47   24-72    198-244 (260)

No 1  
>pfam03753 HHV6-IE Human herpesvirus 6 immediate early protein. The proteins in this family are poorly characterized, but an investigation has indicated that the immediate early protein is required the down-regulation of MHC class I expression in dendritic cells. Human herpesvirus 6 immediate early protein is also referred to as U90.
Probab=50.33  E-value=24  Score=17.41  Aligned_cols=57  Identities=39%  Similarity=0.497  Sum_probs=43.0

Q ss_pred             HHHHCCC-CHHHHHHHHHHHHHHHHHHHH-------HCHHHH---------HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9973686-336778999999999999986-------278999---------99999999999998668999998
Q 537021.9.peg.1   17 EFCTNSN-SKQDCLISQFKLFEKHYREQQ-------KGVNEI---------LDILKSVKWLFSALKNIAIAVTS   73 (90)
Q Consensus        17 efctnsn-skqdclisqfklfekhyreqq-------kgvnei---------ldilksvkwlfsalkniaiavts   73 (90)
                      +||...| -|||-|-+.+...|+|-|.-|       |..|.|         |.|--..|-|..|.||+++||-.
T Consensus       187 ~Fc~k~N~lKq~LLE~knEIiE~n~knmq~~q~FAiKQMNQiFMd~CDktFLKih~NCkNLI~AAKNlg~avLQ  260 (993)
T pfam03753       187 AFCIKTNKLKQDLLECKNEIIEKNSKNMQTMQDFAIKQMNQIFMDMCDKTFLKIHFNCKNLIEAAKNLGAAVLQ  260 (993)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             89999888999998515799874268899999999999999998660776777520278899998888898887


No 2  
>pfam00798 Arena_glycoprot Arenavirus glycoprotein.
Probab=37.22  E-value=38  Score=16.12  Aligned_cols=26  Identities=38%  Similarity=0.516  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99998668999998999999997166
Q 537021.9.peg.1   60 LFSALKNIAIAVTSLTAIIYGLLNIK   85 (90)
Q Consensus        60 lfsalkniaiavtsltaiiygllnik   85 (90)
                      .+...-|||+.+.|+-||+-|+.|+-
T Consensus        14 ii~EalNIaLIavsiiailKGv~Nlw   39 (473)
T pfam00798        14 IIQEALNIALIAVSLIAIIKGVVNLW   39 (473)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999979999999999999999999


No 3  
>KOG3518 consensus
Probab=35.95  E-value=39  Score=15.99  Aligned_cols=39  Identities=33%  Similarity=0.604  Sum_probs=28.8

Q ss_pred             HHHHHHHHCCCCHHHHH--HHHHHHHHHHHHHHHHCHHHHH
Q ss_conf             99999973686336778--9999999999999862789999
Q 537021.9.peg.1   13 EEFIEFCTNSNSKQDCL--ISQFKLFEKHYREQQKGVNEIL   51 (90)
Q Consensus        13 eefiefctnsnskqdcl--isqfklfekhyreqqkgvneil   51 (90)
                      |.+||+|||-..--..|  .-|-|+..|.++|.|...|.-|
T Consensus       208 e~yieyctny~rmmatl~~~~q~~ilaka~qerq~al~hsl  248 (521)
T KOG3518         208 EDYIEYCTNYHRMMATLTECMQNKILAKAFQERQEALKHSL  248 (521)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             89999972237789999999875899999999999874456


No 4  
>pfam08647 BRE1 BRE1 E3 ubiquitin ligase. BRE1 is an E3 ubiquitin ligase that has been shown to act as a transcriptional activator through direct activator interactions.
Probab=26.61  E-value=55  Score=15.08  Aligned_cols=26  Identities=35%  Similarity=0.370  Sum_probs=19.7

Q ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             36863367789999999999999862
Q 537021.9.peg.1   20 TNSNSKQDCLISQFKLFEKHYREQQK   45 (90)
Q Consensus        20 tnsnskqdclisqfklfekhyreqqk   45 (90)
                      ...++|+.|+|+|++=.|+.||-.-.
T Consensus        65 ~~q~~Ks~e~i~ql~e~E~~~~~~i~   90 (96)
T pfam08647        65 NTQLNKSSELISQLKDLENELRRRIK   90 (96)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98886789999998989999999999


No 5  
>pfam07423 DUF1510 Protein of unknown function (DUF1510). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=22.03  E-value=69  Score=14.45  Aligned_cols=27  Identities=33%  Similarity=0.609  Sum_probs=16.9

Q ss_pred             HHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99862789999999999999999866899999899999999
Q 537021.9.peg.1   41 REQQKGVNEILDILKSVKWLFSALKNIAIAVTSLTAIIYGL   81 (90)
Q Consensus        41 reqqkgvneildilksvkwlfsalkniaiavtsltaiiygl   81 (90)
                      |.|.+-.|-||              ||||++..|+-+|.+.
T Consensus         6 r~k~Rk~n~vL--------------NiaI~iV~llIiiva~   32 (214)
T pfam07423         6 RQKRRKINRVL--------------NIAIGIVVVLIIIVAY   32 (214)
T ss_pred             HHHHHHHHHHH--------------HHHHHHHHHHHHHHHH
T ss_conf             77776453455--------------7999999999999766


No 6  
>KOG3918 consensus
Probab=20.39  E-value=74  Score=14.23  Aligned_cols=59  Identities=29%  Similarity=0.351  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             78999999999999986278999999999999999986689999989999999971665531
Q 537021.9.peg.1   28 CLISQFKLFEKHYREQQKGVNEILDILKSVKWLFSALKNIAIAVTSLTAIIYGLLNIKGWFK   89 (90)
Q Consensus        28 clisqfklfekhyreqqkgvneildilksvkwlfsalkniaiavtsltaiiygllnikgwfk   89 (90)
                      .+|+-|.|-.--|...|...--   -|..-.|.--.+.-++-.|-||.+.|||...|.|-||
T Consensus        10 ~~i~lfaLaHaAfSAAqHR~Yl---RLTEqe~~sLP~DivlQTvisli~~iYgi~~iag~Fk   68 (129)
T KOG3918          10 TIISLFALAHAAFSAAQHRFYL---RLTEQEFISLPSDIVLQTVISLIALIYGISFIAGPFK   68 (129)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH---HHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_conf             9999999999998888878898---6200200128599999999999999985798704077


No 7  
>pfam05961 Chordopox_A13L Chordopoxvirus A13L protein. This family consists of A13L proteins from the Chordopoxviruses. A13L or p8 is one of the three most abundant membrane proteins of the intracellular mature Vaccinia virus.
Probab=20.27  E-value=75  Score=14.22  Aligned_cols=20  Identities=35%  Similarity=0.595  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             68999998999999997166
Q 537021.9.peg.1   66 NIAIAVTSLTAIIYGLLNIK   85 (90)
Q Consensus        66 niaiavtsltaiiygllnik   85 (90)
                      -+.|.|.-..+|+||+.|-|
T Consensus         7 Li~ICVavi~lIvYgiYnkk   26 (68)
T pfam05961         7 LVIICVAIIGLIVYGIYNKK   26 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHCC
T ss_conf             99999999999999885134


No 8  
>pfam04834 Adeno_E3_14_5 Early E3 14.5 kDa protein. The E3B 14.5 kDa was first identified in Human adenovirus type 5. It is an integral membrane protein oriented with its C terminus in the cytoplasm. It functions to down-regulate the epidermal growth factor receptor and prevent tumour necrosis factor cytolysis. It achieves this through the interaction with E3 10.4 kDa protein.
Probab=19.64  E-value=77  Score=14.13  Aligned_cols=32  Identities=25%  Similarity=0.508  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999998668999998999999997166553
Q 537021.9.peg.1   56 SVKWLFSALKNIAIAVTSLTAIIYGLLNIKGWF   88 (90)
Q Consensus        56 svkwlfsalkniaiavtsltaiiygllnikgwf   88 (90)
                      +.-|+....--...+-|-+.-.||..+++ ||-
T Consensus        21 ~~~wl~~i~~v~Vf~~T~~sl~iYp~~d~-GWn   52 (97)
T pfam04834        21 PSAWLYIIGIVLVFVCTFFSLQIYPCLDF-GWN   52 (97)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHEEEC-CCC
T ss_conf             70299999999999998888766430512-547


No 9  
>TIGR01584 citF citrate lyase, alpha subunit; InterPro: IPR006472   These sequences, from both Gram-positive and Gram-negative bacteria, represent the alpha subunit of the holoenzyme citrate lyase composed of alpha (2.8.3.10 from EC), beta, and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The alpha subunit catalyzes the reaction Acetyl-CoA + citrate = acetate + (3S)-citryl-CoA. The protein from Lactococcus lactis subsp. lactis has been experimentally characterised . ; GO: 0008814 citrate CoA-transferase activity, 0006084 acetyl-CoA metabolic process, 0005737 cytoplasm, 0009346 citrate lyase complex.
Probab=19.07  E-value=17  Score=18.31  Aligned_cols=48  Identities=33%  Similarity=0.516  Sum_probs=36.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             863367789999999999999862789999999999999999866899999899999
Q 537021.9.peg.1   22 SNSKQDCLISQFKLFEKHYREQQKGVNEILDILKSVKWLFSALKNIAIAVTSLTAII   78 (90)
Q Consensus        22 snskqdclisqfklfekhyreqqkgvneildilksvkwlfsalkniaiavtsltaii   78 (90)
                      |--|.---||    |..|+|+-.-=||+.+++.-..     -.||..+|+.|||...
T Consensus        38 sGlKDGMTiS----FHHhfR~GDyvvn~Vm~~Ia~~-----G~KdL~LA~SSL~~~h   85 (496)
T TIGR01584        38 SGLKDGMTIS----FHHHFREGDYVVNMVMKIIAEM-----GIKDLTLAPSSLTSAH   85 (496)
T ss_pred             CCCCCCCCCH----HHHHCCCCCEEEHHHHHHHHHC-----CCCCCCCCCCCHHHHC
T ss_conf             4886887101----2332068875305679999963-----8874420433033312


No 10 
>pfam02270 TFIIF_beta Transcription initiation factor IIF, beta subunit. Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter.
Probab=18.98  E-value=80  Score=14.04  Aligned_cols=47  Identities=30%  Similarity=0.309  Sum_probs=30.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3367789999999999999862789999999999999999866899999
Q 537021.9.peg.1   24 SKQDCLISQFKLFEKHYREQQKGVNEILDILKSVKWLFSALKNIAIAVT   72 (90)
Q Consensus        24 skqdclisqfklfekhyreqqkgvneildilksvkwlfsalkniaiavt   72 (90)
                      .+.+-|---|++||+|--=--|+..++.+  ..+.||=..|+.||+-+.
T Consensus       198 ~k~eLld~LF~~Fek~~yWslK~L~~~t~--QPe~yLKEiL~~Ia~lnk  244 (260)
T pfam02270       198 PKNELLDLLFKAFEKHQYWSLKDLKERTK--QPEAYLKEILDEIAVLNK  244 (260)
T ss_pred             CHHHHHHHHHHHHHHCCCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHC
T ss_conf             68899999999875445766999987754--919999999999988863


Done!