Query         537021.9.peg.348_1
Match_columns 42
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Tue May 24 18:31:40 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_348.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 smart00115 CASc Caspase, inter  43.0      10 0.00027   19.9   0.9   28    2-29     27-54  (241)
  2 TIGR01648 hnRNP-R-Q hnRNP-R, Q  36.8      16 0.00042   18.9   1.2   14   28-41    131-144 (611)
  3 TIGR01422 phosphonatase phosph  32.0      40   0.001   16.9   2.5   22    1-22     71-92  (199)
  4 pfam03526 Microcin Colicin E1   29.8      47  0.0012   16.6   2.6   26    3-30     23-49  (55)
  5 pfam06589 CRA Circumsporozoite  24.0      75  0.0019   15.6   2.7   24    7-30      4-27  (157)
  6 cd00032 CASc Caspase, interleu  21.6      39 0.00099   17.0   0.9   28    2-29     29-56  (243)
  7 pfam04827 Plant_tran Plant tra  18.8      89  0.0023   15.2   2.2   35    4-38    160-199 (211)
  8 cd08003 WGR_PARP2_like WGR dom  16.7   1E+02  0.0026   14.9   2.2   18    5-22     62-79  (103)
  9 PRK12773 flhB flagellar biosyn  16.2 1.2E+02  0.0029   14.6   2.6   23    5-27    194-216 (649)
 10 TIGR02121 Na_Pro_sym sodium/pr  15.5      41   0.001   16.9  -0.2   30    3-32    316-346 (517)

No 1  
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=42.97  E-value=10  Score=19.92  Aligned_cols=28  Identities=25%  Similarity=0.484  Sum_probs=23.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             7246799999999999745654144531
Q 537021.9.peg.3    2 NSDKDVERIFAVFKKIFFEKSIGKNLNG   29 (42)
Q Consensus         2 nsdkdverifavfkkiffeksigknlng   29 (42)
                      ++++|++++-.+|+++-|+-.+..|+..
T Consensus        27 Gs~~D~~~L~~~f~~LgF~V~~~~nlt~   54 (241)
T smart00115       27 GTDVDAENLTELFQSLGYEVHVKNNLTA   54 (241)
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEECCCCH
T ss_conf             8389999999999978998999238999


No 2  
>TIGR01648 hnRNP-R-Q hnRNP-R, Q splicing factor family; InterPro: IPR006535   Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q  and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein) . These proteins contain three RNA recognition domains and a somewhat variable C-terminal domain. .
Probab=36.77  E-value=16  Score=18.92  Aligned_cols=14  Identities=50%  Similarity=0.992  Sum_probs=12.6

Q ss_pred             CCCEEEEEEEEEEC
Q ss_conf             31100101100112
Q 537021.9.peg.3   28 NGAILNVCCIVDVC   41 (42)
Q Consensus        28 ngailnvccivdvc   41 (42)
                      ||-.|-|||-||-|
T Consensus       131 pGrlLGVC~SVdNc  144 (611)
T TIGR01648       131 PGRLLGVCISVDNC  144 (611)
T ss_pred             CCCEEEEEEEEECC
T ss_conf             88513378787057


No 3  
>TIGR01422 phosphonatase phosphonoacetaldehyde hydrolase; InterPro: IPR006323   These sequences represent an enzyme that catalyzes the cleavage of the carbon phosphorous bond of a phosphonate. The mechanism depends on the substrate having a carbonyl one carbon away from the cleavage position. This enzyme is a member of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases, and contains a modified version of the conserved catalytic motifs of that superfamily: the first motif is usually DxDx(T/V), here it is DxAxT, and in the third motif the normal conserved lysine is instead an arginine. Additionally, the enzyme contains a unique conserved catalytic lysine (B. cereus pos. 53) which is involved in the binding and activation of the substrate through the formation of a Schiff base . The substrate of this enzyme is the product of 2-aminoethylphosphonate (AEP) transaminase, phosphonoacetaldehyde. This degradation pathway for AEP may be related to its toxic properties which are utilised by microorganisms as a chemical warfare agent..
Probab=32.03  E-value=40  Score=16.93  Aligned_cols=22  Identities=23%  Similarity=0.477  Sum_probs=19.6

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             9724679999999999974565
Q 537021.9.peg.3    1 LNSDKDVERIFAVFKKIFFEKS   22 (42)
Q Consensus         1 lnsdkdverifavfkkiffeks   22 (42)
                      |-++.|+..|++-|..|.|+|-
T Consensus        71 lp~~~Di~aiYe~F~pl~ia~~   92 (199)
T TIGR01422        71 LPTEADIQAIYEEFMPLQIAKV   92 (199)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHH
T ss_conf             9977458999986168999986


No 4  
>pfam03526 Microcin Colicin E1 (microcin) immunity protein.
Probab=29.84  E-value=47  Score=16.61  Aligned_cols=26  Identities=46%  Similarity=0.544  Sum_probs=18.2

Q ss_pred             CHHHHHHHHHHH-HHHHHHHHHCCCCCCC
Q ss_conf             246799999999-9997456541445311
Q 537021.9.peg.3    3 SDKDVERIFAVF-KKIFFEKSIGKNLNGA   30 (42)
Q Consensus         3 sdkdverifavf-kkiffeksigknlnga   30 (42)
                      |.+-+|.|+--| ||-||++  |||||.+
T Consensus        23 SkyaiEhiafkfikk~Ff~~--rknln~~   49 (55)
T pfam03526        23 SKYAIEHIAFKFIKKEFFVT--RKNLNSE   49 (55)
T ss_pred             HHHHHHHHHHHHHHHHHHHH--HHHCCCC
T ss_conf             89999999999999999998--7511459


No 5  
>pfam06589 CRA Circumsporozoite-related antigen (CRA). This family consists of several circumsporozoite-related antigen (CRA) or exported protein-1 (EXP1) sequences found specifically in Plasmodium species. The function of this family is unknown.
Probab=24.01  E-value=75  Score=15.58  Aligned_cols=24  Identities=38%  Similarity=0.682  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             999999999997456541445311
Q 537021.9.peg.3    7 VERIFAVFKKIFFEKSIGKNLNGA   30 (42)
Q Consensus         7 verifavfkkiffeksigknlnga   30 (42)
                      ..-||-.|--||-..+.|+|.||.
T Consensus         4 ls~~FllF~~il~~~a~g~n~Ng~   27 (157)
T pfam06589         4 LSIIFLLFSLILVNDALGKNKNGK   27 (157)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             999999999999737763555688


No 6  
>cd00032 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
Probab=21.61  E-value=39  Score=17.03  Aligned_cols=28  Identities=25%  Similarity=0.481  Sum_probs=22.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             7246799999999999745654144531
Q 537021.9.peg.3    2 NSDKDVERIFAVFKKIFFEKSIGKNLNG   29 (42)
Q Consensus         2 nsdkdverifavfkkiffeksigknlng   29 (42)
                      .+++|++++-.+|+++-|+-.+..|++.
T Consensus        29 Gs~~D~~~L~~~f~~Lgf~V~~~~nlt~   56 (243)
T cd00032          29 GTDVDAENLTKLFESLGYEVEVKNNLTA   56 (243)
T ss_pred             CHHHHHHHHHHHHHHCCCEEEEEECCCH
T ss_conf             7399999999999988998999608999


No 7  
>pfam04827 Plant_tran Plant transposon protein. This family contains plant transposases which are putative members of the PIF / Ping-Pong family.
Probab=18.84  E-value=89  Score=15.19  Aligned_cols=35  Identities=34%  Similarity=0.520  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHHH--HHHCC-CCC--CCEEEEEEEE
Q ss_conf             46799999999999745--65414-453--1100101100
Q 537021.9.peg.3    4 DKDVERIFAVFKKIFFE--KSIGK-NLN--GAILNVCCIV   38 (42)
Q Consensus         4 dkdverifavfkkiffe--ksigk-nln--gailnvcciv   38 (42)
                      -++|||.|.+.|.-|--  +.+-. +.+  -.|...|||.
T Consensus       160 R~vVEraFGvLk~RfriL~~~~~~~~~~~~~~Ii~AC~iL  199 (211)
T pfam04827       160 RKDVERAFGVLQARFKIVATPARLWNQSDLSNIMTACIIL  199 (211)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             9999999999999999851864568877899999999987


No 8  
>cd08003 WGR_PARP2_like WGR domain of poly(ADP-ribose) polymerases. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent synthesis of ADP-ribose polymers and their addition to various nuclear proteins. Higher eukaryotes contain several PARPs and and there may be up to 17 human PARP-like proteins, with three of them (PARP-1, PARP-2, and PARP-3) containing a WGR domain. The synthesis of poly-ADP-ribose requires multiple enzymatic activities for initiation, trans-ADP-ribosylation, elongation, branching, and release of the polymer from the enzyme. This subfamily is composed of human PARP-2 and similar proteins. Similar to PARP-1, PARP-2 is ubiquitously expressed and it
Probab=16.74  E-value=1e+02  Score=14.88  Aligned_cols=18  Identities=33%  Similarity=0.671  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             679999999999974565
Q 537021.9.peg.3    5 KDVERIFAVFKKIFFEKS   22 (42)
Q Consensus         5 kdverifavfkkiffeks   22 (42)
                      .+.|.....|+++|.+|+
T Consensus        62 ~~l~~A~~~F~kkF~~KT   79 (103)
T cd08003          62 SDLEQAKSLFEKKFLDKT   79 (103)
T ss_pred             CCHHHHHHHHHHHHHHHH
T ss_conf             889999999999999863


No 9  
>PRK12773 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=16.24  E-value=1.2e+02  Score=14.62  Aligned_cols=23  Identities=39%  Similarity=0.905  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             67999999999997456541445
Q 537021.9.peg.3    5 KDVERIFAVFKKIFFEKSIGKNL   27 (42)
Q Consensus         5 kdverifavfkkiffeksigknl   27 (42)
                      ...||.|...||.||.|...|..
T Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~  216 (649)
T PRK12773        194 RTIERFFSIIKKLFFKKKFSKSF  216 (649)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHH
T ss_conf             99999999999999887503225


No 10 
>TIGR02121 Na_Pro_sym sodium/proline symporter; InterPro: IPR011851    This family consists of the sodium/proline symporter (proline permease) from a number of Gram-negative and Gram-positive bacteria and from the archaeal genus Methanosarcina. ; GO: 0005298 proline:sodium symporter activity, 0031402 sodium ion binding, 0006814 sodium ion transport, 0015824 proline transport, 0016021 integral to membrane.
Probab=15.51  E-value=41  Score=16.93  Aligned_cols=30  Identities=40%  Similarity=0.538  Sum_probs=24.3

Q ss_pred             CHHHH-HHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             24679-9999999999745654144531100
Q 537021.9.peg.3    3 SDKDV-ERIFAVFKKIFFEKSIGKNLNGAIL   32 (42)
Q Consensus         3 sdkdv-erifavfkkiffeksigknlngail   32 (42)
                      .|++- |+||-++-++.|.-=|+-=|=-|||
T Consensus       316 ~d~~~yE~iFI~~~~~LFhP~iaG~LLaAIL  346 (517)
T TIGR02121       316 ADPKAYETIFIVLSQILFHPWIAGILLAAIL  346 (517)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             4787511568989988733568999999999


Done!