Query         gi|255764492|ref|YP_003065069.2| hypothetical protein CLIBASIA_02715 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 56
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 21:22:29 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 255764492.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00636 PduO_Nterm ATP:cob(I  34.0      15 0.00038   19.0   0.6   17   16-32     28-45  (184)
  2 COG5154 BRX1 RNA-binding prote  30.8      18 0.00047   18.5   0.6   29   25-53     36-65  (283)
  3 TIGR01225 hutH histidine ammon  24.8      52  0.0013   16.2   2.0   20   11-30    351-370 (529)
  4 TIGR01389 recQ ATP-dependent D  20.9      35  0.0009   17.0   0.5   50    3-52    527-577 (607)
  5 COG4800 Predicted transcriptio  17.5   1E+02  0.0026   14.6   2.6   28   14-41     20-50  (170)
  6 PRK03661 competence damage-ind  10.9      76  0.0019   15.3   0.1   21    2-22     17-42  (164)
  7 PRK03657 competence damage-ind  10.7   1E+02  0.0026   14.6   0.7   21    2-22     23-48  (170)
  8 KOG2971 consensus               10.1 1.2E+02   0.003   14.3   0.8   29   25-53     55-84  (299)
  9 pfam00570 HRDC HRDC domain. Th   9.4      59  0.0015   15.9  -0.9   28   24-51     13-40  (68)
 10 pfam03289 Pox_I1 Poxvirus prot   8.9 1.1E+02  0.0027   14.5   0.2   21   22-42      9-29  (312)

No 1  
>TIGR00636 PduO_Nterm ATP:cob(I)alamin adenosyltransferase; InterPro: IPR002779   ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2.5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) . Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type , EutT-type  and PduO-type . Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution.    This entry represents EutT- and PduO-type ATP:cob(I)alamin adenosyltransferases. PduO functions to convert cobalamin to AdoCbl for 1,2-propanediol degradation , while EutT produces AdoCbl for ethanolamine utilisation . ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid ac-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process.
Probab=33.98  E-value=15  Score=18.99  Aligned_cols=17  Identities=47%  Similarity=0.569  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHH-HHHHCC
Q ss_conf             88899776446-543058
Q gi|255764492|r   16 KSTVDELNSIS-SRRQNI   32 (56)
Q Consensus        16 kstvdelnsis-srrqni   32 (56)
                      -.|+|||||.- --++.+
T Consensus        28 ~G~~DELNS~iG~a~~~~   45 (184)
T TIGR00636        28 YGTVDELNSFIGVARSHL   45 (184)
T ss_pred             HCCHHHHHHHHHHHHHHC
T ss_conf             254257988999999853


No 2  
>COG5154 BRX1 RNA-binding protein required for 60S ribosomal subunit biogenesis [Translation, ribosomal structure and biogenesis]
Probab=30.80  E-value=18  Score=18.50  Aligned_cols=29  Identities=38%  Similarity=0.487  Sum_probs=19.9

Q ss_pred             HHHHHHCCCHHHHHHHHH-HCCCCCCCHHH
Q ss_conf             465430587578768876-38222015265
Q gi|255764492|r   25 ISSRRQNIPPSSVISDLV-VHPHEKKEPKK   53 (56)
Q Consensus        25 issrrqnippssvisdlv-vhphekkepkk   53 (56)
                      +|||.-+.--...+.||+ .-||+|||+|-
T Consensus        36 lSsRGvsyr~RHL~~Dls~l~phskke~Kl   65 (283)
T COG5154          36 LSSRGVSYRIRHLMKDLSRLVPHSKKEQKL   65 (283)
T ss_pred             EECCCCHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             932772387999999898747664100013


No 3  
>TIGR01225 hutH histidine ammonia-lyase; InterPro: IPR005921    Histidine ammonia-lyase deaminates histidine to urocanic acid, the first step in histidine degradation. It is closely related to phenylalanine ammonia-lyase. ; GO: 0004397 histidine ammonia-lyase activity, 0006548 histidine catabolic process, 0005737 cytoplasm.
Probab=24.84  E-value=52  Score=16.18  Aligned_cols=20  Identities=35%  Similarity=0.411  Sum_probs=17.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHH
Q ss_conf             03578888997764465430
Q gi|255764492|r   11 TGDKIKSTVDELNSISSRRQ   30 (56)
Q Consensus        11 tgdkikstvdelnsissrrq   30 (56)
                      +-|-++.-+-||-+||-||-
T Consensus       351 a~D~LAiA~aELg~IsERRi  370 (529)
T TIGR01225       351 ALDFLAIAIAELGAISERRI  370 (529)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             99899999998876878989


No 4  
>TIGR01389 recQ ATP-dependent DNA helicase RecQ; InterPro: IPR006293   The ATP-dependent DNA helicase RecQ (3.6.1 from EC) is involved in genome maintenance . All homologues tested to date unwind paired DNA, translocating in a 3' to 5' direction and several have a preference for forked or 4-way DNA structures (e.g. Holliday junctions) or for G-quartet DNA. The yeast protein, Sgs1, is present in numerous foci that coincide with sites of de novo synthesis DNA, such as the replication fork, and protein levels peak during S-phase.    A model has been proposed for Sgs1p action in the S-phase checkpoint response, both as a 'sensor' for damage during replication and a 'resolvase' for structures that arise at paused forks, such as the four-way 'chickenfoot' structure. The action of Sgs1p may serve to maintain the proper amount and integrity of ss DNA that is necessary for the binding of RPA (replication protein A, the eukaryotic ss DNA-binding protein)DNA pol complexes. Sgs1p would thus function by detecting (or resolving) aberrant DNA structures, and would thus contribute to the full activation of the DNA-dependent protein kinase, Mec1p and the effector kinase, Rad53p. Its ability to bind both the large subunit of RPA and the RecA-like protein Rad51p, place it in a unique position to resolve inappropriate fork structures that can occur when either the leading or lagging strand synthesis is stalled. Thus, RecQ helicases integrate checkpoint activation and checkpoint response. ; GO: 0004003 ATP-dependent DNA helicase activity, 0006310 DNA recombination, 0009432 SOS response.
Probab=20.85  E-value=35  Score=17.03  Aligned_cols=50  Identities=24%  Similarity=0.393  Sum_probs=37.1

Q ss_pred             CCCCCCCCCHH-HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCHH
Q ss_conf             22253200035-788889977644654305875787688763822201526
Q gi|255764492|r    3 IQNNLTSCTGD-KIKSTVDELNSISSRRQNIPPSSVISDLVVHPHEKKEPK   52 (56)
Q Consensus         3 iqnnltsctgd-kikstvdelnsissrrqnippssvisdlvvhphekkepk   52 (56)
                      .+++|+.-.-+ ..=+..-+|-.--++++||||-.|.||-+..---++-|+
T Consensus       527 ~~~~l~~~~d~~~LF~~Lr~lR~~~A~~~~VPPYvIF~D~TL~E~ae~~P~  577 (607)
T TIGR01389       527 QQKELSVEVDDLALFEALRELRKELAQEENVPPYVIFSDSTLREMAEKRPA  577 (607)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCHHHHHHHHHCCC
T ss_conf             230012440458999999999999998648992898184579999973552


No 5  
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=17.48  E-value=1e+02  Score=14.62  Aligned_cols=28  Identities=32%  Similarity=0.402  Sum_probs=18.3

Q ss_pred             HHHHHHHHHHH---HHHHHHCCCHHHHHHHH
Q ss_conf             78888997764---46543058757876887
Q gi|255764492|r   14 KIKSTVDELNS---ISSRRQNIPPSSVISDL   41 (56)
Q Consensus        14 kikstvdelns---issrrqnippssvisdl   41 (56)
                      -.+.-.|||+-   --+.|.|||+|+...-|
T Consensus        20 ~l~~~l~Elglt~~eFak~anIP~StLYKil   50 (170)
T COG4800          20 CLQKLLDELGLTPSEFAKRANIPLSTLYKIL   50 (170)
T ss_pred             HHHHHHHHCCCCHHHHHHHCCCCHHHHHHHH
T ss_conf             9999999819998999887099899999998


No 6  
>PRK03661 competence damage-inducible protein A; Validated
Probab=10.92  E-value=76  Score=15.32  Aligned_cols=21  Identities=29%  Similarity=0.548  Sum_probs=14.5

Q ss_pred             CCCCCCC-----CCCHHHHHHHHHHH
Q ss_conf             3222532-----00035788889977
Q gi|255764492|r    2 LIQNNLT-----SCTGDKIKSTVDEL   22 (56)
Q Consensus         2 liqnnlt-----sctgdkikstvdel   22 (56)
                      |+++++|     ||||..|-+..-..
T Consensus        17 L~~~~~tis~AEScTGGlias~lt~v   42 (164)
T PRK03661         17 LKARGATVTTAESCTGGWVAKVITDI   42 (164)
T ss_pred             HHHCCCEEEEEHHHHHHHHHHHHHCC
T ss_conf             99879989973322528999999768


No 7  
>PRK03657 competence damage-inducible protein A; Validated
Probab=10.70  E-value=1e+02  Score=14.65  Aligned_cols=21  Identities=43%  Similarity=0.662  Sum_probs=14.8

Q ss_pred             CCCCCCC-----CCCHHHHHHHHHHH
Q ss_conf             3222532-----00035788889977
Q gi|255764492|r    2 LIQNNLT-----SCTGDKIKSTVDEL   22 (56)
Q Consensus         2 liqnnlt-----sctgdkikstvdel   22 (56)
                      |+++++|     ||||..|-+..-..
T Consensus        23 L~~~~ltis~AEScTGGlias~lt~i   48 (170)
T PRK03657         23 LIAQQLRLTTAESCTGGKLASALCAA   48 (170)
T ss_pred             HHHCCCEEEEEHHHHHHHHHHHHHCC
T ss_conf             99879999986202538999999768


No 8  
>KOG2971 consensus
Probab=10.05  E-value=1.2e+02  Score=14.31  Aligned_cols=29  Identities=31%  Similarity=0.517  Sum_probs=19.4

Q ss_pred             HHHHHHCCCHHHHHHHHH-HCCCCCCCHHH
Q ss_conf             465430587578768876-38222015265
Q gi|255764492|r   25 ISSRRQNIPPSSVISDLV-VHPHEKKEPKK   53 (56)
Q Consensus        25 issrrqnippssvisdlv-vhphekkepkk   53 (56)
                      +|||+-+.---..+-|++ .-||+++++|-
T Consensus        55 ~ssRgis~R~RhLm~di~~Llph~k~dsk~   84 (299)
T KOG2971          55 LSSRGISFRTRHLMKDISSLLPHSKKDSKL   84 (299)
T ss_pred             EECCCCHHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf             942784177999999899856554343044


No 9  
>pfam00570 HRDC HRDC domain. The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains.
Probab=9.38  E-value=59  Score=15.88  Aligned_cols=28  Identities=25%  Similarity=0.446  Sum_probs=18.2

Q ss_pred             HHHHHHHCCCHHHHHHHHHHCCCCCCCH
Q ss_conf             4465430587578768876382220152
Q gi|255764492|r   24 SISSRRQNIPPSSVISDLVVHPHEKKEP   51 (56)
Q Consensus        24 sissrrqnippssvisdlvvhphekkep   51 (56)
                      .--+++.|+||..|++|-+..---++-|
T Consensus        13 ~~~A~~~~~~~~~I~~d~~L~~ia~~~P   40 (68)
T pfam00570        13 DELAREEDVPPYVIFSDATLLEIAEKLP   40 (68)
T ss_pred             HHHHHHCCCCCCEEECHHHHHHHHHHCC
T ss_conf             9999971998424477999999998784


No 10 
>pfam03289 Pox_I1 Poxvirus protein I1.
Probab=8.90  E-value=1.1e+02  Score=14.54  Aligned_cols=21  Identities=43%  Similarity=0.480  Sum_probs=10.6

Q ss_pred             HHHHHHHHHCCCHHHHHHHHH
Q ss_conf             764465430587578768876
Q gi|255764492|r   22 LNSISSRRQNIPPSSVISDLV   42 (56)
Q Consensus        22 lnsissrrqnippssvisdlv   42 (56)
                      |||||.|--..--.+-|+|.|
T Consensus         9 lNsIsA~aLKaYl~skI~e~V   29 (312)
T pfam03289         9 LNSISARALKAYLTSKINEIV   29 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             526419999999998899999


Done!