Query         537021.9.peg.869_1
Match_columns 39
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Wed May 25 04:53:16 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_869.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG2991 Uncharacterized protei  35.7     8.8 0.00023   20.8  -0.4   32    3-35     40-73  (77)
  2 pfam11547 E3_UbLigase_EDD E3 u  29.1      42  0.0011   17.3   2.2   31    9-39      9-45  (51)
  3 TIGR00455 apsK adenylylsulfate  20.1      34 0.00086   17.8   0.3   11   27-37    137-147 (187)
  4 KOG1621 consensus               15.8      80  0.0021   15.8   1.4   20    3-22    234-253 (458)
  5 pfam04049 APC8 Anaphase promot  12.7   1E+02  0.0026   15.3   1.2   25   11-35      6-30  (133)
  6 PRK12301 bssS biofilm formatio  12.6 1.2E+02   0.003   15.0   1.5   21    7-27     53-73  (84)
  7 PHA00652 hypothetical protein   12.3 1.2E+02  0.0031   14.9   1.5   15    1-15      1-15  (128)
  8 TIGR02325 C_P_lyase_phnF phosp  11.8      98  0.0025   15.4   0.9   16    9-24      8-23  (240)
  9 COG2147 RPL19A Ribosomal prote  10.4 1.1E+02  0.0028   15.1   0.8   20   19-38    112-131 (150)
 10 TIGR01701 Fdhalpha-like oxidor  10.1      79   0.002   15.9  -0.0   16   17-32    425-445 (824)

No 1  
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.72  E-value=8.8  Score=20.82  Aligned_cols=32  Identities=28%  Similarity=0.479  Sum_probs=23.4

Q ss_pred             EHHHHHHHHHHHHHHHCCCH--HHCCHHHHHHHHH
Q ss_conf             22667579999999960501--3350256644554
Q 537021.9.peg.8    3 VLEKACDCYRQIEDILQGKI--AKCPVRGLYNKAK   35 (39)
Q Consensus         3 vlekacdcyrqiedilqgki--akcpvrglynkak   35 (39)
                      -+||.||| ++--|-.|-|.  ++-|-+--|+...
T Consensus        40 Gi~K~CdC-~~pCDt~~~kl~~~~e~ak~~~~~~f   73 (77)
T COG2991          40 GIEKVCDC-DEPCDTHKKKLDAGKEAAKAEYDAKF   73 (77)
T ss_pred             CCCHHCCC-CCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             52010599-99567898767742517888999988


No 2  
>pfam11547 E3_UbLigase_EDD E3 ubiquitin ligase EDD. EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated domain which binds ubiquitin. Ubiquitin is recognized by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins.
Probab=29.10  E-value=42  Score=17.33  Aligned_cols=31  Identities=42%  Similarity=0.476  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHCCCHHHCCHHHHH------HHHHHCCC
Q ss_conf             79999999960501335025664------45542249
Q 537021.9.peg.8    9 DCYRQIEDILQGKIAKCPVRGLY------NKAKNNLL   39 (39)
Q Consensus         9 dcyrqiedilqgkiakcpvrgly------nkaknnll   39 (39)
                      |-..|..-.||||-...-+|.|-      |-|-||||
T Consensus         9 ~Li~q~q~VLQgKSR~vIiRELQrtnLdVN~AVNNLL   45 (51)
T pfam11547         9 ELINQAQVVLQGKSRNVIIRELQRTNLDVNLAVNNLL   45 (51)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             9999999999553289999999981763999998874


No 3  
>TIGR00455 apsK adenylylsulfate kinase; InterPro: IPR002891 Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulphate. This domain contains an ATP binding P-loop motif .; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity transferring phosphorus-containing groups, 0000103 sulfate assimilation.
Probab=20.13  E-value=34  Score=17.81  Aligned_cols=11  Identities=55%  Similarity=0.987  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHC
Q ss_conf             25664455422
Q 537021.9.peg.8   27 VRGLYNKAKNN   37 (39)
Q Consensus        27 vrglynkaknn   37 (39)
                      +.|||.||.+-
T Consensus       137 PKGLYkKAR~G  147 (187)
T TIGR00455       137 PKGLYKKARNG  147 (187)
T ss_pred             CCCHHHHHHCC
T ss_conf             85023886468


No 4  
>KOG1621 consensus
Probab=15.80  E-value=80  Score=15.84  Aligned_cols=20  Identities=40%  Similarity=0.443  Sum_probs=16.1

Q ss_pred             EHHHHHHHHHHHHHHHCCCH
Q ss_conf             22667579999999960501
Q 537021.9.peg.8    3 VLEKACDCYRQIEDILQGKI   22 (39)
Q Consensus         3 vlekacdcyrqiedilqgki   22 (39)
                      ++||.-.-|-||||.||+--
T Consensus       234 ~vekdge~f~qieDLL~~F~  253 (458)
T KOG1621         234 EVEKDGEHFIQIEDLLQQFH  253 (458)
T ss_pred             HHHHCHHHHHHHHHHHHHCC
T ss_conf             34415267888999997437


No 5  
>pfam04049 APC8 Anaphase promoting complex subunit 8 / Cdc23. The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8).
Probab=12.65  E-value=1e+02  Score=15.28  Aligned_cols=25  Identities=28%  Similarity=0.434  Sum_probs=19.8

Q ss_pred             HHHHHHHHCCCHHHCCHHHHHHHHH
Q ss_conf             9999999605013350256644554
Q 537021.9.peg.8   11 YRQIEDILQGKIAKCPVRGLYNKAK   35 (39)
Q Consensus        11 yrqiedilqgkiakcpvrglynkak   35 (39)
                      -++|..-|+--+..|-.||||.-||
T Consensus         6 l~~ir~eL~~a~~ecs~RgL~qSaK   30 (133)
T pfam04049         6 LKELRNDLRKAIRELSERCLYQSAK   30 (133)
T ss_pred             HHHHHHHHHHHHHHHHHHCHHHHHH
T ss_conf             9999999999999999825598999


No 6  
>PRK12301 bssS biofilm formation regulatory protein BssS; Reviewed
Probab=12.63  E-value=1.2e+02  Score=14.98  Aligned_cols=21  Identities=38%  Similarity=0.397  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHCCCHHHCCH
Q ss_conf             757999999996050133502
Q 537021.9.peg.8    7 ACDCYRQIEDILQGKIAKCPV   27 (39)
Q Consensus         7 acdcyrqiedilqgkiakcpv   27 (39)
                      ..|.-||.-.||+..|||-.-
T Consensus        53 TTDVArQ~I~ILeAGIaKIEs   73 (84)
T PRK12301         53 TTDVARQFISILEAGIAKIES   73 (84)
T ss_pred             EHHHHHHHHHHHHHHHHHHCC
T ss_conf             168999999999977877324


No 7  
>PHA00652 hypothetical protein
Probab=12.32  E-value=1.2e+02  Score=14.92  Aligned_cols=15  Identities=40%  Similarity=0.694  Sum_probs=11.2

Q ss_pred             CEEHHHHHHHHHHHH
Q ss_conf             932266757999999
Q 537021.9.peg.8    1 MIVLEKACDCYRQIE   15 (39)
Q Consensus         1 mivlekacdcyrqie   15 (39)
                      |--.+.||.||.|.-
T Consensus         1 m~p~~ea~~~ydqm~   15 (128)
T PHA00652          1 MEPIEEATKCYDQML   15 (128)
T ss_pred             CCCHHHHHHHHHHHH
T ss_conf             973889986699999


No 8  
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF; InterPro: IPR012702    Members of this family are the PhnF protein associated with C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three-component ABC transporter, where IPR005769 from INTERPRO is the permease, IPR005770 from INTERPRO is the phosphonates binding protein, and IPR012693 from INTERPRO is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lyase complex. This protein (PhnF) is a predicted helix-turn-helix transcriptional regulatory protein of the broader GntR family, and is encoded in a gene cluster associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond. Its presence is apparently not required for phosphate utilisation to occur ..
Probab=11.77  E-value=98  Score=15.39  Aligned_cols=16  Identities=38%  Similarity=0.563  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHCCCHHH
Q ss_conf             7999999996050133
Q 537021.9.peg.8    9 DCYRQIEDILQGKIAK   24 (39)
Q Consensus         9 dcyrqiedilqgkiak   24 (39)
                      --||||+|-+...|+.
T Consensus         8 A~WR~IAd~i~~~i~~   23 (240)
T TIGR02325         8 ALWRQIADKIEQEIAA   23 (240)
T ss_pred             CHHHHHHHHHHHHHHC
T ss_conf             0147889999998632


No 9  
>COG2147 RPL19A Ribosomal protein L19E [Translation, ribosomal structure and biogenesis]
Probab=10.39  E-value=1.1e+02  Score=15.11  Aligned_cols=20  Identities=45%  Similarity=0.581  Sum_probs=16.8

Q ss_pred             CCCHHHCCHHHHHHHHHHCC
Q ss_conf             05013350256644554224
Q 537021.9.peg.8   19 QGKIAKCPVRGLYNKAKNNL   38 (39)
Q Consensus        19 qgkiakcpvrglynkaknnl   38 (39)
                      .|+|.+-.-|-||..||.+.
T Consensus       112 ~gkIdk~~YR~lY~~aKGg~  131 (150)
T COG2147         112 DGKIDKHTYRKLYRMAKGGA  131 (150)
T ss_pred             CCCCCHHHHHHHHHHHCCCC
T ss_conf             59868999999999971776


No 10 
>TIGR01701 Fdhalpha-like oxidoreductase alpha (molybdopterin) subunit; InterPro: IPR010046   This entry represents a well-defined clade of molybdopterin-dependent formate dehydrogenases, bacterial type , , , . It represents the alpha subunit, which contains a molybdopterin cofactor and generally associate with two other subunits which contain iron-sulphur clusters and cytochromes.; GO: 0008863 formate dehydrogenase activity, 0030151 molybdenum ion binding, 0051539 4 iron 4 sulfur cluster binding.
Probab=10.07  E-value=79  Score=15.88  Aligned_cols=16  Identities=56%  Similarity=1.184  Sum_probs=0.0

Q ss_pred             HHCCCHHH-----CCHHHHHH
Q ss_conf             96050133-----50256644
Q 537021.9.peg.8   17 ILQGKIAK-----CPVRGLYN   32 (39)
Q Consensus        17 ilqgkiak-----cpvrglyn   32 (39)
                      .|+|-|-|     |||||--|
T Consensus       425 Ll~G~IGK~GAG~cP~RGHSN  445 (824)
T TIGR01701       425 LLRGNIGKPGAGVCPIRGHSN  445 (824)
T ss_pred             HHCCCCCCCCCCCCCCCCCCC
T ss_conf             842577888886033447777


Done!