Query         T0578 3NAT, Enterococcus faecalis, 164 residues
Match_columns 164
No_of_seqs    24 out of 26
Neff          3.3 
Searched_HMMs 11830
Date          Sun Jun 13 15:18:04 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0578.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0578.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF11217 DUF3013:  Protein of u 100.0       0       0  493.1  16.6  160    4-163     1-160 (160)
  2 PF11536 DUF3226:  Protein of u  22.2      20  0.0017   14.4   2.3   21   84-104    53-73  (239)
  3 PF10911 DUF2717:  Protein of u  20.8      22  0.0018   14.2   3.0   29   91-124    41-69  (77)
  4 PF01967 MoaC:  MoaC family;  I  20.5      22  0.0019   14.2   2.3   38   22-59     68-105 (136)
  5 PF09816 EAF:  RNA polymerase I  16.1      21  0.0018   14.2   1.2   17   69-85     78-94  (109)
  6 PF12202 OSR1_C:  Oxidative-str  12.7      34  0.0029   13.0   1.5   20   32-51     18-37  (38)
  7 PF07063 DUF1338:  Protein of u  10.4      19  0.0016   14.6  -0.4   16   56-72     41-56  (111)
  8 PF05396 Phage_T7_Capsid:  Phag   8.0      52  0.0044   12.0   2.6   36   95-130    12-47  (123)
  9 PF05894 Podovirus_Gp16:  Podov   8.0      48  0.0041   12.1   0.8   29   73-104     5-33  (333)
 10 PF10850 DUF2653:  Protein of u   8.0     6.2 0.00053   17.4  -3.7   41   60-103     5-45  (91)

No 1  
>PF11217 DUF3013:  Protein of unknown function (DUF3013)
Probab=100.00  E-value=0  Score=493.14  Aligned_cols=160  Identities=52%  Similarity=0.873  Sum_probs=159.4

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEEEEEEEEEEECCCCEEEECCCCEECCCCCEEEECEEEEECCCCCCCC
Q ss_conf             14434899999988730455323772057650799999999746442057515660025762122024477755424532
Q T0578             4 MKKATMLTYLEEQLEKHLGDYEVGLDWDRKNHTIEVIVRLYAENNEQVAIDDVDGTLSEEEFIEFEDGLLFYNPQKSVVD   83 (164)
Q Consensus         4 Mak~~~L~~Lee~ldk~~~~yD~~ldWDKknHaiEv~~~l~aen~~~~e~~D~~G~~s~e~iI~fED~ILfynp~Ks~fd   83 (164)
                      |||+|||+||+|+|+||+|+||++||||||||+|||+|+|+|||+++++|+|++|++|+|+||+||||||||||+||+||
T Consensus         1 Mak~~~L~~Lee~ldk~dF~~D~~l~WDKknhaiEv~f~l~aen~~~~e~~D~~G~~s~e~ii~feDaiLfYnp~Ks~fd   80 (160)
T PF11217_consen    1 MAKFGFLDVLEEELDKHDFDYDYALNWDKKNHAIEVEFTLEAENKAGVETEDDEGEVSDEDIIEFEDAILFYNPAKSGFD   80 (160)
T ss_pred             CCCCCHHHHHHHHHHHCCCCCCEEECCCCCCCEEEEEEEEEEECCCCEEEECCCCCCCCCCCEEEEEEEEEECCCCCCCC
T ss_conf             95110899999999744687524732466673699999999834456167868882537885565678999765214687


Q ss_pred             CCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             21237873247422235899999999999998412578888636997203677408899998873011122333246899
Q T0578            84 DEEYLVTIPYEGKKGLRKAVLDGFIHYLKVVLDEGQSDLLDFLSDETAEVFELHWEPADFEAMIKKVAETEKEQWIAYPS  163 (164)
Q Consensus        84 ~ddYLa~iPy~gKkG~s~~~l~~f~~yLq~vld~G~sDLmDFl~D~s~e~F~L~Wd~~~fe~~~~~~~e~~~~~~~~YPk  163 (164)
                      ++||||||||+|||||||++++||++|||+||++|||||||||+|+++++|+|+||+++|++++++++++++++||||||
T Consensus        81 addYL~~iPf~gKkG~s~~~l~~f~~yL~~v~d~G~sDLmDFl~D~~~e~F~L~Wd~~~Fe~~~~~l~e~~~~~~~~YPk  160 (160)
T PF11217_consen   81 ADDYLAVIPFDGKKGLSREFLDYFAQYLQDVADEGQSDLMDFLADDDDEEFELNWDDEAFEAGIAELEETEPRQFYPYPK  160 (160)
T ss_pred             HHHEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             33307862458644420999999999999998715788998746986001788638899998986200234323366998


No 2  
>PF11536 DUF3226:  Protein of unknown function (DUF3226); PDB: 2p62_A.
Probab=22.21  E-value=20  Score=14.39  Aligned_cols=21  Identities=38%  Similarity=0.716  Sum_probs=17.7

Q ss_pred             CCCCEEEECCCCCCCHHHHHH
Q ss_conf             212378732474222358999
Q T0578            84 DEEYLVTIPYEGKKGLRKAVL  104 (164)
Q Consensus        84 ~ddYLa~iPy~gKkG~s~~~l  104 (164)
                      ++-|||+||-+||.|+-+...
T Consensus        53 d~v~Lavi~seG~~~v~~~L~   73 (239)
T PF11536_consen   53 DDVYLAVIHSEGKSGVKRNLK   73 (239)
T ss_dssp             TTEEEEEE------SHHHHHH
T ss_pred             CCEEEEEEECCCHHHHHHHHH
T ss_conf             786999983777044799999


No 3  
>PF10911 DUF2717:  Protein of unknown function (DUF2717)
Probab=20.77  E-value=22  Score=14.21  Aligned_cols=29  Identities=31%  Similarity=0.426  Sum_probs=20.7

Q ss_pred             ECCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             3247422235899999999999998412578888
Q T0578            91 IPYEGKKGLRKAVLDGFIHYLKVVLDEGQSDLLD  124 (164)
Q Consensus        91 iPy~gKkG~s~~~l~~f~~yLq~vld~G~sDLmD  124 (164)
                      |..--+.|+|-+|..+|..=||--     |++||
T Consensus        41 i~~Lr~~G~SE~~IaGfl~Gl~~a-----S~~ld   69 (77)
T PF10911_consen   41 IRDLRQAGYSEAFIAGFLKGLQYA-----SRTLD   69 (77)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHHH-----HHHHH
T ss_conf             999988477399999999999999-----99999


No 4  
>PF01967 MoaC:  MoaC family;  InterPro: IPR002820   The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cisdithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism , .    In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which coverts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner . MoCF is the active co-factor in eukaryotic and some prokaryotic molybdoenzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdoenzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF . Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 () of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) .   This entry contain the molybdenum cofactor biosynthesis protein MoaC.; GO: 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 2ide_D 2iih_A 2ekn_C 2ohd_F 1eks_A 1ekr_A 2eey_A.
Probab=20.54  E-value=22  Score=14.19  Aligned_cols=38  Identities=11%  Similarity=0.290  Sum_probs=30.5

Q ss_pred             CCCCEEEEECCCCEEEEEEEEEEEECCCCEEEECCCCE
Q ss_conf             55323772057650799999999746442057515660
Q T0578            22 GDYEVGLDWDRKNHTIEVIVRLYAENNEQVAIDDVDGT   59 (164)
Q Consensus        22 ~~yD~~ldWDKknHaiEv~~~l~aen~~~~e~~D~~G~   59 (164)
                      ..-++.++|+-..+.|++..+--...+-|+|++--.|.
T Consensus        68 ~~v~v~~~~~~~~~~v~i~~~v~t~~kTGVEMEALtav  105 (136)
T PF01967_consen   68 TGVDVDFEVDDDENSVEIRATVKTTGKTGVEMEALTAV  105 (136)
T ss_dssp             CEEEEEEEEECCCTEEEEEEEEEEEE----HHHHHHHH
T ss_pred             CEEEEEEEECCCCCEEEEEEEEEEECCCCCCHHHHHHH
T ss_conf             26899999858885899999999835886128999999


No 5  
>PF09816 EAF:  RNA polymerase II transcription elongation factor
Probab=16.12  E-value=21  Score=14.24  Aligned_cols=17  Identities=18%  Similarity=0.440  Sum_probs=12.8

Q ss_pred             ECEEEEECCCCCCCCCC
Q ss_conf             02447775542453221
Q T0578            69 EDGLLFYNPQKSVVDDE   85 (164)
Q Consensus        69 ED~ILfynp~Ks~fd~d   85 (164)
                      .|+||+|||....|--+
T Consensus        78 ~~~VLifD~~~~~f~Le   94 (109)
T PF09816_consen   78 KECVLIFDPETKAFVLE   94 (109)
T ss_pred             CEEEEEEECCCCEEEEE
T ss_conf             54999995999979999


No 6  
>PF12202 OSR1_C:  Oxidative-stress-responsive kinase 1 C terminal; PDB: 2v3s_B.
Probab=12.65  E-value=34  Score=13.04  Aligned_cols=20  Identities=30%  Similarity=0.413  Sum_probs=13.9

Q ss_pred             CCCEEEEEEEEEEEECCCCE
Q ss_conf             76507999999997464420
Q T0578            32 RKNHTIEVIVRLYAENNEQV   51 (164)
Q Consensus        32 KknHaiEv~~~l~aen~~~~   51 (164)
                      |.|++|+-+|.+.-..+++|
T Consensus        18 keneaI~F~F~~~~D~~e~v   37 (38)
T PF12202_consen   18 KENEAIEFEFDLGKDTAEEV   37 (38)
T ss_dssp             --EEEEEEEE----------
T ss_pred             CCCCCEEEEEECCCCCCCCC
T ss_conf             55664789885388880405


No 7  
>PF07063 DUF1338:  Protein of unknown function (DUF1338);  InterPro: IPR009770   This entry represents the C terminus (approximately 100 residues) of a number of hypothetical bacterial proteins of unknown function.; PDB: 2rjb_C.
Probab=10.43  E-value=19  Score=14.56  Aligned_cols=16  Identities=31%  Similarity=0.569  Sum_probs=13.0

Q ss_pred             CCCEECCCCCEEEECEE
Q ss_conf             56600257621220244
Q T0578            56 VDGTLSEEEFIEFEDGL   72 (164)
Q Consensus        56 ~~G~~s~e~iI~fED~I   72 (164)
                      +.|.+.-+||| |||-.
T Consensus        41 ~~G~v~~ePIv-YEDFL   56 (111)
T PF07063_consen   41 ASGLVQAEPIV-YEDFL   56 (111)
T ss_dssp             H---EEEEE-----S--
T ss_pred             HCCCCCCCCCC-HHCCC
T ss_conf             87981316700-00247


No 8  
>PF05396 Phage_T7_Capsid:  Phage T7 capsid assembly protein;  InterPro: IPR008768   This family contains the capsid assembly protein (scaffolding protein) of bacteriophage T7.; GO: 0019069 viral capsid assembly
Probab=8.00  E-value=52  Score=11.97  Aligned_cols=36  Identities=11%  Similarity=0.339  Sum_probs=30.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCC
Q ss_conf             422235899999999999998412578888636997
Q T0578            95 GKKGLRKAVLDGFIHYLKVVLDEGQSDLLDFLSDET  130 (164)
Q Consensus        95 gKkG~s~~~l~~f~~yLq~vld~G~sDLmDFl~D~s  130 (164)
                      .+-|++|+|++.++.=-+-++++=-+-.|.+.-+.+
T Consensus        12 a~aGYsr~fVDsyI~GQEAL~~Qyv~sv~~yaGG~e   47 (123)
T PF05396_consen   12 AKAGYSRQFVDSYIRGQEALAEQYVNSVVEYAGGRE   47 (123)
T ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
T ss_conf             984873889999988999999999999999815699


No 9  
>PF05894 Podovirus_Gp16:  Podovirus DNA encapsidation protein (Gp16);  InterPro: IPR008784 This family consists of several DNA encapsidation protein (Gp16) sequences from the phi-29-like viruses. Gene product 16 catalyses the in vivo and in vitro genome-encapsidation reaction .; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=7.99  E-value=48  Score=12.14  Aligned_cols=29  Identities=38%  Similarity=0.613  Sum_probs=0.0

Q ss_pred             EEECCCCCCCCCCCCEEEECCCCCCCHHHHHH
Q ss_conf             77755424532212378732474222358999
Q T0578            73 LFYNPQKSVVDDEEYLVTIPYEGKKGLRKAVL  104 (164)
Q Consensus        73 Lfynp~Ks~fd~ddYLa~iPy~gKkG~s~~~l  104 (164)
                      +||+|+|..--+.---.+|   |.+|+-|.|+
T Consensus         5 ~~~~p~k~lsyd~~~~~vi---G~RgvGKtfa   33 (333)
T PF05894_consen    5 LYYNPQKMLSYDRILNFVI---GARGVGKTFA   33 (333)
T ss_pred             CCCCHHHHHHHCCEEEEEE---CCCCCCHHHH
T ss_conf             0369889730161248898---1565452467


No 10 
>PF10850 DUF2653:  Protein of unknown function (DUF2653)
Probab=7.96  E-value=6.2  Score=17.44  Aligned_cols=41  Identities=22%  Similarity=0.490  Sum_probs=0.0

Q ss_pred             ECCCCCEEEECEEEEECCCCCCCCCCCCEEEECCCCCCCHHHHH
Q ss_conf             02576212202447775542453221237873247422235899
Q T0578            60 LSEEEFIEFEDGLLFYNPQKSVVDDEEYLVTIPYEGKKGLRKAV  103 (164)
Q Consensus        60 ~s~e~iI~fED~ILfynp~Ks~fd~ddYLa~iPy~gKkG~s~~~  103 (164)
                      .|+.+||   +|||.|--.|....-+|-.|-+-|+-.-|++.++
T Consensus         5 i~eqdII---nAvC~~~A~~r~i~PedV~veL~ydd~tGf~AEv   45 (91)
T PF10850_consen    5 ISEQDII---NAVCLYIADQRQIYPEDVEVELSYDDDTGFSAEV   45 (91)
T ss_pred             CCHHHHH---HHHHHHHHHHCCCCCCCEEEEEEEECCCCCEEEE
T ss_conf             0588999---9999988864357850279999971677803899


Done!