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!