Query         537021.9.peg.80_1
Match_columns 37
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Mon May 23 07:40:57 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_80.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01116 ATPase-IIA1_Ca calci  28.1      26 0.00066   18.1   1.0   23    7-31    590-614 (800)
  2 TIGR02044 CueR Cu(I)-responsiv  27.7      53  0.0013   16.6   2.5   28    2-36     43-73  (127)
  3 COG5111 RPC34 DNA-directed RNA  25.8      63  0.0016   16.2   2.6   31    7-37     32-65  (301)
  4 pfam08874 DUF1835 Domain of un  20.0      66  0.0017   16.1   1.8   19   19-37     87-105 (115)
  5 KOG0202 consensus               14.7 1.1E+02  0.0028   14.9   1.9   24    7-32    725-750 (972)
  6 pfam11553 DUF3231 Protein of u   9.4 1.5E+02  0.0039   14.2   1.2   21    8-29    114-134 (166)
  7 pfam09456 RcsC RcsC Alpha-Beta   9.4   2E+02  0.0051   13.6   1.9   17   19-35      5-21  (92)
  8 COG2150 Predicted regulator of   8.9      73  0.0019   15.8  -0.6   17    8-24     21-37  (167)
  9 pfam00846 Hanta_nucleocap Hant   8.5 1.5E+02  0.0038   14.3   0.8   13   14-26    331-343 (428)
 10 pfam11707 Npa1 Ribosome 60S bi   8.4 2.2E+02  0.0057   13.4   1.7   16   19-35    127-142 (327)

No 1  
>TIGR01116 ATPase-IIA1_Ca calcium-translocating P-type ATPase, SERCA-type; InterPro: IPR005782    This model describes Ca2+ ATPases (3.6.3.8 from EC) from eukaryotes and includes significant representatives from plants. Plasma membrane Ca2+ ATPases are primarily responsible for extrusion of calcium from cytoplasmic milieu to outside, coupled to the hydrolyis of ATP. Besides Ca2+ ATPases, Na+/Ca2+ exchangers are also involved in the maintenance of Ca2+ homestasis in the cell. ; GO: 0005388 calcium-transporting ATPase activity, 0006816 calcium ion transport, 0016021 integral to membrane.
Probab=28.06  E-value=26  Score=18.12  Aligned_cols=23  Identities=48%  Similarity=0.920  Sum_probs=14.9

Q ss_pred             HHHHHH--HHHHHHHHHHHHHHHHHHH
Q ss_conf             688886--1276542135489999999
Q 537021.9.peg.8    7 TLLKAI--GFSVRNDMRNTCFIRYLLS   31 (37)
Q Consensus         7 tllkai--gfsvrndmrntcfirylls   31 (37)
                      |..+|.  |=+.-|.|.  -||||+.|
T Consensus       590 TIV~AV~EGR~IyNNmK--qFIRYmIS  614 (800)
T TIGR01116       590 TIVKAVEEGRAIYNNMK--QFIRYMIS  614 (800)
T ss_pred             HHHHHHCCCCHHHHCCH--HHHHHHHH
T ss_conf             46533104641331232--46566552


No 2  
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator; InterPro: IPR011789    This entry represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue .; GO: 0003677 DNA binding, 0005507 copper ion binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription.
Probab=27.73  E-value=53  Score=16.55  Aligned_cols=28  Identities=36%  Similarity=0.717  Sum_probs=19.4

Q ss_pred             CHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             54675688---886127654213548999999985027
Q 537021.9.peg.8    2 DVRKFTLL---KAIGFSVRNDMRNTCFIRYLLSLFRDK   36 (37)
Q Consensus         2 dvrkftll---kaigfsvrndmrntcfiryllslfrdk   36 (37)
                      +|..|+|+   +.+|||...       |+-||+||.|.
T Consensus        43 h~~~L~li~raR~~GFSLeE-------c~~ll~L~ndp   73 (127)
T TIGR02044        43 HVDELRLISRARSVGFSLEE-------CKELLSLWNDP   73 (127)
T ss_pred             HHHHHHHHHHHHHHCCCHHH-------HHHHHHHHCCC
T ss_conf             78888999999871898899-------99998752288


No 3  
>COG5111 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription]
Probab=25.75  E-value=63  Score=16.17  Aligned_cols=31  Identities=35%  Similarity=0.471  Sum_probs=24.5

Q ss_pred             HHHHHHHHHHHHHH---HHHHHHHHHHHHHHCCC
Q ss_conf             68888612765421---35489999999850279
Q 537021.9.peg.8    7 TLLKAIGFSVRNDM---RNTCFIRYLLSLFRDKK   37 (37)
Q Consensus         7 tllkaigfsvrndm---rntcfiryllslfrdkk   37 (37)
                      .|.+++|-+--+|.   -|.|.-|-|+++||++.
T Consensus        32 el~~qmg~~sltDl~s~ln~lL~r~li~l~rq~~   65 (301)
T COG5111          32 ELQMQMGKASLTDLASELNALLKRQLISLFRQKG   65 (301)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999854020888999999999876666774199


No 4  
>pfam08874 DUF1835 Domain of unknown function (DUF1835). This family of proteins are functionally uncharacterized.
Probab=19.99  E-value=66  Score=16.06  Aligned_cols=19  Identities=37%  Similarity=0.648  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHHHHHHCCC
Q ss_conf             2135489999999850279
Q 537021.9.peg.8   19 DMRNTCFIRYLLSLFRDKK   37 (37)
Q Consensus        19 dmrntcfiryllslfrdkk   37 (37)
                      ....-|..+|++++++||+
T Consensus        87 na~Dqlgl~~~~~~Lkd~~  105 (115)
T pfam08874        87 NAHDQLGLRYVLSLLKDKP  105 (115)
T ss_pred             CHHHHHHHHHHHHHHCCCC
T ss_conf             8798998999999854678


No 5  
>KOG0202 consensus
Probab=14.69  E-value=1.1e+02  Score=14.91  Aligned_cols=24  Identities=50%  Similarity=0.897  Sum_probs=15.8

Q ss_pred             HHHHHH--HHHHHHHHHHHHHHHHHHHH
Q ss_conf             688886--12765421354899999998
Q 537021.9.peg.8    7 TLLKAI--GFSVRNDMRNTCFIRYLLSL   32 (37)
Q Consensus         7 tllkai--gfsvrndmrntcfiryllsl   32 (37)
                      |.+.||  |-+.-|.|.|  ||||+||-
T Consensus       725 tIvaAVEEGr~IynNik~--Fir~~lSs  750 (972)
T KOG0202         725 TIVAAVEEGRAIYNNIKN--FIRYLLSS  750 (972)
T ss_pred             HHHHHHHHHHHHHHHHHH--HHHHHHHH
T ss_conf             999999976889999999--99999861


No 6  
>pfam11553 DUF3231 Protein of unknown function (DUF3231). This bacterial family of proteins has no known function.
Probab=9.37  E-value=1.5e+02  Score=14.19  Aligned_cols=21  Identities=38%  Similarity=0.513  Sum_probs=14.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8888612765421354899999
Q 537021.9.peg.8    8 LLKAIGFSVRNDMRNTCFIRYL   29 (37)
Q Consensus         8 llkaigfsvrndmrntcfiryl   29 (37)
                      ...|++.|.|+|.|.. |.+++
T Consensus       114 ~~~al~~s~R~Di~~~-f~~~~  134 (166)
T pfam11553       114 YGLALSMSLRNDIRLL-YSRCL  134 (166)
T ss_pred             HHHHHHHHHHHHHHHH-HHHHH
T ss_conf             9999999999999999-99999


No 7  
>pfam09456 RcsC RcsC Alpha-Beta-Loop (ABL). This domain is found in the C-terminus of the phospho-relay kinase RcsC between pfam00512 and pfam00072, and forms a discrete alpha/beta/loop structure.
Probab=9.35  E-value=2e+02  Score=13.61  Aligned_cols=17  Identities=24%  Similarity=0.385  Sum_probs=13.3

Q ss_pred             HHHHHHHHHHHHHHHHC
Q ss_conf             21354899999998502
Q 537021.9.peg.8   19 DMRNTCFIRYLLSLFRD   35 (37)
Q Consensus        19 dmrntcfiryllslfrd   35 (37)
                      +.||.+.-+||+++.+.
T Consensus         5 ~iRNa~Le~yL~~lL~~   21 (92)
T pfam09456         5 AIRNASLESFLERLLSY   21 (92)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             77788999999999997


No 8  
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=8.90  E-value=73  Score=15.84  Aligned_cols=17  Identities=35%  Similarity=0.468  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             88886127654213548
Q 537021.9.peg.8    8 LLKAIGFSVRNDMRNTC   24 (37)
Q Consensus         8 llkaigfsvrndmrntc   24 (37)
                      .|-..||||+|++.+.|
T Consensus        21 ~l~~~GisV~~g~~~~~   37 (167)
T COG2150          21 KLLESGISVKNGGKIYC   37 (167)
T ss_pred             HHHHHCEEECCCCCEEE
T ss_conf             99980836726983563


No 9  
>pfam00846 Hanta_nucleocap Hantavirus nucleocapsid protein.
Probab=8.46  E-value=1.5e+02  Score=14.29  Aligned_cols=13  Identities=54%  Similarity=0.782  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             2765421354899
Q 537021.9.peg.8   14 FSVRNDMRNTCFI   26 (37)
Q Consensus        14 fsvrndmrntcfi   26 (37)
                      ||+-.|||||-.-
T Consensus       331 fsilQDmRntImA  343 (428)
T pfam00846       331 FSILQDMRNTIMA  343 (428)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9999998877877


No 10 
>pfam11707 Npa1 Ribosome 60S biogenesis N-terminal. Npa1p is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits. The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre. The protein has also been referred to as Urb1, and this domain at the N-terminal is one of several conserved regions along the length.
Probab=8.35  E-value=2.2e+02  Score=13.38  Aligned_cols=16  Identities=38%  Similarity=0.675  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHHHHHC
Q ss_conf             21354899999998502
Q 537021.9.peg.8   19 DMRNTCFIRYLLSLFRD   35 (37)
Q Consensus        19 dmrntcfiryllslfrd   35 (37)
                      ++| ++||+|+||+++.
T Consensus       127 s~R-~~fI~F~lsfL~~  142 (327)
T pfam11707       127 SIR-RNFIRFALSFLSV  142 (327)
T ss_pred             CHH-HHHHHHHHHHHCC
T ss_conf             789-9999999999703


Done!