Query         537021.9.peg.1080_1
Match_columns 110
No_of_seqs    50 out of 52
Neff          3.6 
Searched_HMMs 39220
Date          Wed May 25 08:31:38 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_1080.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam03237 Terminase_6 Terminas  92.8    0.22 5.5E-06   29.7   4.6   47    1-58      3-49  (380)
  2 COG3892 Uncharacterized protei  79.6     1.3 3.3E-05   25.1   2.1   21    9-30    186-206 (310)
  3 pfam09863 DUF2090 Uncharacteri  75.8       2   5E-05   24.1   2.2   25    6-31    190-214 (310)
  4 PRK13775 formimidoylglutamase;  65.0     1.6 4.2E-05   24.6  -0.2   41   25-65     10-58  (328)
  5 KOG2199 consensus               64.8     2.1 5.3E-05   23.9   0.3   29   20-52    243-271 (462)
  6 COG3411 Ferredoxin [Energy pro  55.7      11 0.00028   19.7   2.7   35   36-70     24-59  (64)
  7 TIGR01290 nifB nitrogenase cof  55.4     4.1  0.0001   22.2   0.5   12   23-34    152-164 (461)
  8 TIGR02713 allophanate_hyd allo  46.0     6.2 0.00016   21.2   0.1   38   56-104    79-118 (582)
  9 TIGR03435 Soli_TIGR03435 Solib  37.1      17 0.00042   18.7   1.2   40   18-60     50-89  (237)
 10 pfam10244 MRP-L51 Mitochondria  26.7      25 0.00064   17.6   0.7   35   54-88     13-48  (94)
 11 KOG0033 consensus               23.7      37 0.00095   16.6   1.1   45   25-69    181-238 (355)
 12 pfam00910 RNA_helicase RNA hel  22.4      74  0.0019   14.9   2.5   36    4-41      7-56  (105)
 13 TIGR02812 fadR_gamma fatty aci  22.2      43  0.0011   16.3   1.2   14   43-56     41-54  (275)
 14 PRK10528 multifunctional acyl-  20.2      42  0.0011   16.3   0.8   25   32-56     39-63  (191)
 15 TIGR00441 gmhA phosphoheptose   20.1      61  0.0016   15.3   1.6   23    7-36     48-70  (186)

No 1  
>pfam03237 Terminase_6 Terminase-like family. This family represents a group of terminase proteins.
Probab=92.76  E-value=0.22  Score=29.67  Aligned_cols=47  Identities=28%  Similarity=0.242  Sum_probs=36.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEECCCCEEEEECCCCHHHHHHHHHHHC
Q ss_conf             9521021247889999998638998501754555772799941453257876566650
Q 537021.9.peg.1    1 MAGNQLGKTLAGAAEAAMHLSGCYPSWWRGYRFLQPIVMVAGSVTYELTRDGIQRLLL   58 (110)
Q Consensus         1 mAgNr~GKT~~ga~E~A~HlTG~YP~WW~G~RF~~Pi~aWa~g~t~E~tRDivQ~~Ll   58 (110)
                      |+|.|.|||++.+.++.+|+...-+.           ..+..+.|..+.|++..+.+.
T Consensus         3 ~ggr~~GKT~~~~~~~~~~a~~~~~~-----------~~~i~~~t~~~~~~~~~~~~~   49 (380)
T pfam03237         3 LGSRQSGKTFAFAREALRHALGNGPK-----------NQIILSASKAQARLEFKKGII   49 (380)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHCCCC-----------CEEEEECCHHHHHHHHHHHHH
T ss_conf             26452528399999999999858997-----------289997999999999999999


No 2  
>COG3892 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.63  E-value=1.3  Score=25.13  Aligned_cols=21  Identities=43%  Similarity=0.953  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             4788999999863899850175
Q 537021.9.peg.1    9 TLAGAAEAAMHLSGCYPSWWRG   30 (110)
Q Consensus         9 T~~ga~E~A~HlTG~YP~WW~G   30 (110)
                      |+.-+.|--|.| |.|||||+=
T Consensus       186 t~~Raier~Y~l-Gv~PDWWKL  206 (310)
T COG3892         186 TVPRAIERFYNL-GVYPDWWKL  206 (310)
T ss_pred             HHHHHHHHHHHC-CCCCCCCCC
T ss_conf             899999999973-778640127


No 3  
>pfam09863 DUF2090 Uncharacterized protein conserved in bacteria (DUF2090). This domain, found in various prokaryotic carbohydrate kinases, has no known function.
Probab=75.80  E-value=2  Score=24.08  Aligned_cols=25  Identities=32%  Similarity=0.559  Sum_probs=18.5

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCE
Q ss_conf             21247889999998638998501754
Q 537021.9.peg.1    6 LGKTLAGAAEAAMHLSGCYPSWWRGY   31 (110)
Q Consensus         6 ~GKT~~ga~E~A~HlTG~YP~WW~G~   31 (110)
                      -..|+..+++--|-| |.|||||+=-
T Consensus       190 ~~~~~~~~i~r~Y~l-GI~PDWWKLe  214 (310)
T pfam09863       190 DDDTVARAIRRFYNL-GIKPDWWKLE  214 (310)
T ss_pred             CHHHHHHHHHHHHHC-CCCCCEEECC
T ss_conf             868999999999976-9998635458


No 4  
>PRK13775 formimidoylglutamase; Provisional
Probab=64.95  E-value=1.6  Score=24.55  Aligned_cols=41  Identities=12%  Similarity=0.143  Sum_probs=34.1

Q ss_pred             CCCCCCE--------EECCCCEEEEECCCCHHHHHHHHHHHCCCCCCCC
Q ss_conf             8501754--------5557727999414532578765666504646853
Q 537021.9.peg.1   25 PSWWRGY--------RFLQPIVMVAGSVTYELTRDGIQRLLLGEPMSPD   65 (110)
Q Consensus        25 P~WW~G~--------RF~~Pi~aWa~g~t~E~tRDivQ~~LlG~~~~~~   65 (110)
                      |+||+||        ||-..++.--......+.-+.++-.|||-|.|.+
T Consensus        10 ~~~w~gr~dd~~~~~r~~~~~~~~~l~~~~~~~~~~~dvailG~p~D~G   58 (328)
T PRK13775         10 TSYYHGGIDDDLYTAKWGMVMTFLDLNDSSLTPFEGTHFALIGFKSDKG   58 (328)
T ss_pred             HHHCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCEEEECCCCCCC
T ss_conf             3540777677654413056367521477446756799999982276667


No 5  
>KOG2199 consensus
Probab=64.81  E-value=2.1  Score=23.95  Aligned_cols=29  Identities=28%  Similarity=0.439  Sum_probs=16.2

Q ss_pred             HHCCCCCCCCCEEECCCCEEEEECCCCHHHHHH
Q ss_conf             638998501754555772799941453257876
Q 537021.9.peg.1   20 LSGCYPSWWRGYRFLQPIVMVAGSVTYELTRDG   52 (110)
Q Consensus        20 lTG~YP~WW~G~RF~~Pi~aWa~g~t~E~tRDi   52 (110)
                      |---||+||+|.--.- +   -.=.||-.|+|+
T Consensus       243 Ld~s~~~WWKG~~~~~-~---GlFPsnfVT~~l  271 (462)
T KOG2199         243 LDDSDPNWWKGENHRG-I---GLFPSNFVTADL  271 (462)
T ss_pred             CCCCCCCHHCCCCCCC-C---EECCHHHHHHHH
T ss_conf             0467821312445786-1---005466531222


No 6  
>COG3411 Ferredoxin [Energy production and conversion]
Probab=55.75  E-value=11  Score=19.68  Aligned_cols=35  Identities=29%  Similarity=0.232  Sum_probs=27.3

Q ss_pred             CCEEEEECCCCHHHHHHHHHHHC-CCCCCCCCCCCC
Q ss_conf             72799941453257876566650-464685323665
Q 537021.9.peg.1   36 PIVMVAGSVTYELTRDGIQRLLL-GEPMSPDQQGSG   70 (110)
Q Consensus        36 Pi~aWa~g~t~E~tRDivQ~~Ll-G~~~~~~~~GtG   70 (110)
                      |=..|-..++-|.-+.|+|.-|+ |+|.++.-+.++
T Consensus        24 pegvWY~~V~p~~a~rIv~~hl~~Gr~Ve~~~~~~~   59 (64)
T COG3411          24 PEGVWYTRVDPEDARRIVQSHLLGGRPVEELIYHTG   59 (64)
T ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCCCHHHCCCCC
T ss_conf             587468216989999999999767985123001578


No 7  
>TIGR01290 nifB nitrogenase cofactor biosynthesis protein NifB; InterPro: IPR005980    NifB is a protein required for the biosynthesis of the iron-molybdenum (or iron-vanadium) cofactor used by the nitrogen-fixing enzyme nitrogenase. Archaeal homologs lack most of the C-terminal region and are excluded from this model.; GO: 0009108 coenzyme biosynthetic process, 0009399 nitrogen fixation.
Probab=55.44  E-value=4.1  Score=22.20  Aligned_cols=12  Identities=33%  Similarity=0.692  Sum_probs=9.3

Q ss_pred             CCCC-CCCCEEEC
Q ss_conf             9985-01754555
Q 537021.9.peg.1   23 CYPS-WWRGYRFL   34 (110)
Q Consensus        23 ~YP~-WW~G~RF~   34 (110)
                      -||+ ||+|+||+
T Consensus       152 IYpWv~y~G~RY~  164 (461)
T TIGR01290       152 IYPWVAYEGKRYT  164 (461)
T ss_pred             ECCCEEECCCCCC
T ss_conf             0652332673335


No 8  
>TIGR02713 allophanate_hyd allophanate hydrolase; InterPro: IPR014085   Allophanate hydrolase catalyses the second reaction in an ATP-dependent two-step degradation of urea to ammonia and C02, following the action of the biotin-containing urea carboxylase. The yeast enzyme, a fusion of allophanate hydrolase to urea carboxylase, is designated urea amidolyase..
Probab=45.96  E-value=6.2  Score=21.17  Aligned_cols=38  Identities=24%  Similarity=0.473  Sum_probs=26.9

Q ss_pred             HHCCCCCCCCCCCCCCCCHHHHCCCEECCC--CCCCCEEEEEEEECCCCEE
Q ss_conf             650464685323665035777500145379--9997026999970588137
Q 537021.9.peg.1   56 LLLGEPMSPDQQGSGMIPANKVLNMTRRSN--IAGAYSTVTVRHLSGRDIG  104 (110)
Q Consensus        56 ~LlG~~~~~~~~GtG~IP~~~I~~ttr~~G--vpnavd~v~VrH~SGg~~~  104 (110)
                      +++|. .|=|.|=||+.-       ||.|+  ++|++|.   +|+|||+||
T Consensus        79 iv~GK-TNLDQFATGLVG-------TRSPYG~vrnAf~~---~yiSGGSSS  118 (582)
T TIGR02713        79 IVVGK-TNLDQFATGLVG-------TRSPYGAVRNAFDP---AYISGGSSS  118 (582)
T ss_pred             EEECC-CCCCHHHCCCCC-------CCCCCCCCCCCCCC---CCCCCCCHH
T ss_conf             04115-475301005687-------41387546888674---558897406


No 9  
>TIGR03435 Soli_TIGR03435 Solibacter paralogous family TIGR03435. This model describes a paralogous family of about 40 proteins found in Solibacter usitatus Ellin6076, one of the first three members of the Acidobacteria to be sequenced, and nowhere else. The family is well-diversified, with few pairs showing greater than 50 % pairwise identity. Two members of the family are longer, multidomain proteins with (two different) fused peptidase domains.
Probab=37.13  E-value=17  Score=18.66  Aligned_cols=40  Identities=30%  Similarity=0.370  Sum_probs=32.7

Q ss_pred             HHHHCCCCCCCCCEEECCCCEEEEECCCCHHHHHHHHHHHCCC
Q ss_conf             9863899850175455577279994145325787656665046
Q 537021.9.peg.1   18 MHLSGCYPSWWRGYRFLQPIVMVAGSVTYELTRDGIQRLLLGE   60 (110)
Q Consensus        18 ~HlTG~YP~WW~G~RF~~Pi~aWa~g~t~E~tRDivQ~~LlG~   60 (110)
                      |+++|  |+|=..-|||=--++ -.|.+.|+.|.-+|.+|--+
T Consensus        50 ~Qv~G--P~Wl~serfDI~AK~-p~g~~~~q~~~MLQ~LLaeR   89 (237)
T TIGR03435        50 YQVSG--PDWLDSERFDIVAKA-PAGATREQVRLMLQTLLAER   89 (237)
T ss_pred             CCCCC--CCCCCCCEEEEEEEC-CCCCCHHHHHHHHHHHHHHH
T ss_conf             40539--863456434179637-99999899999999999987


No 10 
>pfam10244 MRP-L51 Mitochondrial ribosomal subunit. MRP-L51 is a family of small proteins from the intact 55 S mitochondrial ribosome. It has otherwise been referred to as bMRP-64. The exact function of this family is not known.
Probab=26.67  E-value=25  Score=17.59  Aligned_cols=35  Identities=20%  Similarity=0.214  Sum_probs=27.7

Q ss_pred             HHHHCCCCCCCCCCCCCCC-CHHHHCCCEECCCCCC
Q ss_conf             6665046468532366503-5777500145379999
Q 537021.9.peg.1   54 QRLLLGEPMSPDQQGSGMI-PANKVLNMTRRSNIAG   88 (110)
Q Consensus        54 Q~~LlG~~~~~~~~GtG~I-P~~~I~~ttr~~Gvpn   88 (110)
                      .+.|||..+.-+-+|.+.+ |++.|.+-.+-.|+++
T Consensus        13 krAlFGqnDyIdILGd~~~hP~~l~~~P~WLRG~~G   48 (94)
T pfam10244        13 KRALFGQNDYIDILGDFKAHPKDLIYGPSWLRGWRG   48 (94)
T ss_pred             HHHHCCCCCCCCCCCCCCCCCHHHEECCHHHHCCCC
T ss_conf             775516752003127987680765038699963772


No 11 
>KOG0033 consensus
Probab=23.75  E-value=37  Score=16.61  Aligned_cols=45  Identities=16%  Similarity=0.130  Sum_probs=32.8

Q ss_pred             CCCCCCEEECCCCEEEEECC------------CCHHHHHHHHHHHCCCCCCCC-CCCC
Q ss_conf             85017545557727999414------------532578765666504646853-2366
Q 537021.9.peg.1   25 PSWWRGYRFLQPIVMVAGSV------------TYELTRDGIQRLLLGEPMSPD-QQGS   69 (110)
Q Consensus        25 P~WW~G~RF~~Pi~aWa~g~------------t~E~tRDivQ~~LlG~~~~~~-~~Gt   69 (110)
                      |+--.--++.+|+-.|++|+            ++|.+-|+-|.+.-|.++-|. +|-+
T Consensus       181 PEv~rkd~y~kpvDiW~cGViL~iLL~G~~PF~~e~~~rlye~I~~g~yd~~~~~w~~  238 (355)
T KOG0033         181 PEVLKKDPYSKPVDIWACGVILYILLVGYPPFWDEDQHRLYEQIKAGAYDYPSPEWDT  238 (355)
T ss_pred             HHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             7876238888961244454899999817889788748899999971566689643676


No 12 
>pfam00910 RNA_helicase RNA helicase. This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.
Probab=22.43  E-value=74  Score=14.87  Aligned_cols=36  Identities=31%  Similarity=0.592  Sum_probs=22.5

Q ss_pred             CCCCHHHHHHHHHHHHH---------HCCC-----CCCCCCEEECCCCEEEE
Q ss_conf             10212478899999986---------3899-----85017545557727999
Q 537021.9.peg.1    4 NQLGKTLAGAAEAAMHL---------SGCY-----PSWWRGYRFLQPIVMVA   41 (110)
Q Consensus         4 Nr~GKT~~ga~E~A~Hl---------TG~Y-----P~WW~G~RF~~Pi~aWa   41 (110)
                      ..+|||...-. +|-+|         ...|     .+||.|++ .++++.|-
T Consensus         7 ~G~GKS~~a~~-la~~~~~~~~~~~~~~~Y~~~~~~~~wdgY~-gq~vvi~D   56 (105)
T pfam00910         7 PGCGKSTLAKY-LARALLDHLGLPKKDSVYSRNPDDDFWDGYT-GQPVVIID   56 (105)
T ss_pred             CCCCHHHHHHH-HHHHHHHHHCCCCCCCEEECCCCCCCCCCCC-CCEEEEEE
T ss_conf             98988999999-9999999837787897796788776567889-98579996


No 13 
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178   Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process.
Probab=22.22  E-value=43  Score=16.25  Aligned_cols=14  Identities=43%  Similarity=0.480  Sum_probs=12.9

Q ss_pred             CCCCHHHHHHHHHH
Q ss_conf             14532578765666
Q 537021.9.peg.1   43 SVTYELTRDGIQRL   56 (110)
Q Consensus        43 g~t~E~tRDivQ~~   56 (110)
                      |||-=|.|.++||+
T Consensus        41 GVTRTTLREVLQRL   54 (275)
T TIGR02812        41 GVTRTTLREVLQRL   54 (275)
T ss_pred             CCCCCHHHHHHHHH
T ss_conf             76630378999887


No 14 
>PRK10528 multifunctional acyl-CoA thioesterase I and protease I and lysophospholipase L1; Provisional
Probab=20.24  E-value=42  Score=16.29  Aligned_cols=25  Identities=20%  Similarity=0.453  Sum_probs=18.8

Q ss_pred             EECCCCEEEEECCCCHHHHHHHHHH
Q ss_conf             5557727999414532578765666
Q 537021.9.peg.1   32 RFLQPIVMVAGSVTYELTRDGIQRL   56 (110)
Q Consensus        32 RF~~Pi~aWa~g~t~E~tRDivQ~~   56 (110)
                      ++.+....--+|+|+|||.+.++|.
T Consensus        39 ~l~~~~~viNaGvSGdTT~~gL~Rl   63 (191)
T PRK10528         39 KWQSKTSVVNASISGDTSQQGLARL   63 (191)
T ss_pred             HHHHCCCEEECCCCHHHHHHHHHHH
T ss_conf             9861894886687633254699998


No 15 
>TIGR00441 gmhA phosphoheptose isomerase; InterPro: IPR004515 Phosphoheptose isomerase is involved in lipopolysaccharide biosynthesis, and more specifically in the synthesis of glyceromannoheptose 7-phosphate. It may also have a role in virulence in Haemophilus ducreyi.; GO: 0008968 phosphoheptose isomerase activity, 0009244 lipopolysaccharide core region biosynthetic process, 0005737 cytoplasm.
Probab=20.11  E-value=61  Score=15.33  Aligned_cols=23  Identities=30%  Similarity=0.496  Sum_probs=19.5

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCEEECCC
Q ss_conf             124788999999863899850175455577
Q 537021.9.peg.1    7 GKTLAGAAEAAMHLSGCYPSWWRGYRFLQP   36 (110)
Q Consensus         7 GKT~~ga~E~A~HlTG~YP~WW~G~RF~~P   36 (110)
                      |-|.|-|+-.|--|||||       |++||
T Consensus        48 GgSaadAqHFAaEl~GRf-------~~eR~   70 (186)
T TIGR00441        48 GGSAADAQHFAAELVGRF-------KLERP   70 (186)
T ss_pred             CCCHHHHHHHHHHHHCCC-------CCCCC
T ss_conf             504335888999871640-------00267


Done!