Query         gi|254781192|ref|YP_003065605.1| hypothetical protein CLIBASIA_05495 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 198
No_of_seqs    108 out of 241
Neff          7.6 
Searched_HMMs 39220
Date          Mon May 30 07:03:48 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781192.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam10991 DUF2815 Protein of u 100.0       0       0  301.1  17.6  177    2-188     1-179 (181)
  2 PHA00458 single-stranded DNA-b 100.0 8.7E-35 2.2E-39  224.4  15.3  180    4-193     7-204 (230)
  3 pfam10927 DUF2738 Protein of u  79.4     4.7 0.00012   19.9  10.2   65  101-170   141-206 (246)
  4 smart00425 TBOX Domain first f  34.7      24 0.00062   15.7   1.8   36    4-40     23-58  (190)
  5 cd00182 TBOX T-box DNA binding  29.8      32 0.00081   15.0   1.7   35    4-39     24-58  (188)
  6 pfam00907 T-box T-box. The T-b  28.2      36 0.00092   14.6   1.8   35    4-39     22-56  (183)
  7 TIGR00492 alr alanine racemase  17.8      69  0.0018   13.0   2.1   41  133-173   224-277 (383)
  8 CHL00123 rps6 ribosomal protei  17.5      70  0.0018   12.9   4.8   51   28-80      7-58  (97)
  9 TIGR02874 spore_ytfJ sporulati  17.2      62  0.0016   13.3   1.1   23  143-165    73-95  (132)
 10 pfam07157 DNA_circ_N DNA circu  15.9      77   0.002   12.7   3.8   43    9-51     30-74  (93)

No 1  
>pfam10991 DUF2815 Protein of unknown function (DUF2815). This is a phage related family of proteins with unknown function.
Probab=100.00  E-value=0  Score=301.11  Aligned_cols=177  Identities=37%  Similarity=0.637  Sum_probs=153.9

Q ss_pred             CEE-EEEEEEEEEEECCCCCCCC-CCCCEEEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             436-7317999415305862466-77840899999776668999999999999998540341001134555455676300
Q gi|254781192|r    2 AKV-LIKGRLSYPQLHEPRAYGD-KGDEVYSADILFSKTDNEQCDKLEQAIREAGEEKFGGSNMSALIERMKRTGRYPLK   79 (198)
Q Consensus         2 ~kv-t~~gr~~y~~L~~Pd~~~~-~~~~~Ys~~l~i~k~d~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~p~~   79 (198)
                      ||| |.++||||||||+|++..+ .++++|||+|||||+|..++++|+++|++++++.|+++...   .+.+..+++|+|
T Consensus         1 tkv~t~~VRlSy~~l~ep~~~~~~~ge~KYs~t~lipK~d~~ti~~I~~AI~~a~~~~~~~k~~g---~~~~~~~k~plr   77 (181)
T pfam10991         1 TKVKTGNVRLSYANLFEPKSIENGQGEPKYSASFIIPKSDTETIKAIKAAIKAAAEEGWGKKADG---KKIPATLKTPLR   77 (181)
T ss_pred             CEEEECCEEEECCCCCCCCCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCC---CCCCCCCCCCCC
T ss_conf             90586748898431046643446898623689999857988999999999999998754100357---725765656311


Q ss_pred             CCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEECCCCEEEEEEECC
Q ss_conf             48665444433345411155489705787768658936886823666653136628999999978762797569988552
Q gi|254781192|r   80 DGDQKISTSLKPEAYEVYAGQYYITPKNKKVRPRLVDRHVQEVTENIQEVFYSGCHVNAIISVYAYTFQGTKGVTFTLTG  159 (198)
Q Consensus        80 dgD~~~~~~~~~~~~~~~~g~~~~~~~~~~~~P~v~Ds~g~~l~~~~~~~I~sGs~v~v~~~~~pY~~~~g~GVsl~L~a  159 (198)
                      |||...+.     ..++|+|+|++++++ +.+|.|+|++.+||+.+ ..+||||||+|+++++|+|++++|+||+|.|++
T Consensus        78 DGD~~~~~-----d~~~y~g~~~inA~s-k~~P~vvD~~~~pi~~~-~~evYSGcy~rasi~~~ayn~~gnKGI~~gL~~  150 (181)
T pfam10991        78 DGDLERPF-----DDEAYAGHYFINASS-KTRPLIVDRNVRPLALD-EGEVYSGCYANASINFYAYNNNGNKGIAAGLNN  150 (181)
T ss_pred             CCCCCCCC-----CCCCCCCCEEEECCC-CCCCCEECCCCCCCCCC-CCCEECCEEEEEEEEEEEEECCCCCEEEEEECC
T ss_conf             58746656-----575548758996578-87991663876524467-785764528999998988826899248885020


Q ss_pred             EEEEECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             58974156466776754346555665422
Q gi|254781192|r  160 VQFVKDDTRWGGQLRASSSDFESYEEETA  188 (198)
Q Consensus       160 VQ~i~~~e~~gg~~~~~~d~f~~~~~~~~  188 (198)
                      ||+++++||+||++.+++++|++.+++++
T Consensus       151 VQk~~DGE~lGgg~~sae~dF~~~~~~~~  179 (181)
T pfam10991       151 VQFVRDGEPLGGGRVAAEDDFDALADEDE  179 (181)
T ss_pred             EEEECCCCCCCCCCCCHHHHHCCCCCCCC
T ss_conf             69701687146787672565045442335


No 2  
>PHA00458 single-stranded DNA-binding protein
Probab=100.00  E-value=8.7e-35  Score=224.35  Aligned_cols=180  Identities=19%  Similarity=0.191  Sum_probs=119.2

Q ss_pred             EEEEEEEE-EEEECCCC----CCCCCCCCEEEEEEEECCCCH---HHHHHHHHHHHHHHHHHCC----CCCCCCC--CCC
Q ss_conf             67317999-41530586----246677840899999776668---9999999999999985403----4100113--455
Q gi|254781192|r    4 VLIKGRLS-YPQLHEPR----AYGDKGDEVYSADILFSKTDN---EQCDKLEQAIREAGEEKFG----GSNMSAL--IER   69 (198)
Q Consensus         4 vt~~gr~~-y~~L~~Pd----~~~~~~~~~Ys~~l~i~k~d~---~~~~~i~~~i~~~~~~~~~----~~~~~~~--~~~   69 (198)
                      +|+.|.+. ||||++||    ++|++ +|+|||+|+|+++|+   ++|+.|+++++++......    ++.+.+.  .+.
T Consensus         7 tTP~G~a~~Yp~LtkPD~g~~t~fne-~G~YKv~L~v~~ddp~aq~li~~ie~~~e~a~a~a~e~~~~n~~k~~~gKkp~   85 (230)
T PHA00458          7 TTPVGTAEPYAYIAKPDFGNEGFGNP-RGVYKVDLTVSNDDPRCQKMIDEIVKAHEEAYAAAVEEYEANPPKVQRGKKPL   85 (230)
T ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCCC-CCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCC
T ss_conf             46874301352235887575554488-97168999835753778999999999999999999988652431110256678


Q ss_pred             CCCCCCCCEECCCCCCCCCCCCCCCCCCC--CEEEECCCCCCCCCEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEE--
Q ss_conf             54556763004866544443334541115--54897057877686589368868236666531366289999999787--
Q gi|254781192|r   70 MKRTGRYPLKDGDQKISTSLKPEAYEVYA--GQYYITPKNKKVRPRLVDRHVQEVTENIQEVFYSGCHVNAIISVYAY--  145 (198)
Q Consensus        70 ~~~~~~~p~~dgD~~~~~~~~~~~~~~~~--g~~~~~~~~~~~~P~v~Ds~g~~l~~~~~~~I~sGs~v~v~~~~~pY--  145 (198)
                      .+....+|+.+..+     +....+..++  +...++++++.++|.||||+|+||++  .+.|||||++||++.+.||  
T Consensus        86 ~pye~d~p~~d~e~-----G~~~FkfK~kas~~~kKtge~~~~~~~l~Dskgkpi~~--~p~I~gGS~lKV~~~l~PY~~  158 (230)
T PHA00458         86 KPYEGDMPFFDNGD-----GTVTFKFKCYASYQDKKTGENKPIVLRVVDSKGKRIED--VPIIGGGSKLKVKFSLFPYKW  158 (230)
T ss_pred             CCCCCCCCCCCCCC-----CEEEEEEEEEECCCCCCCCCCCCCCEEEEECCCCCCCC--CCCCCCCCEEEEEEEEECCCC
T ss_conf             75335687533788-----72899999630246433586242451688688988888--875568867899899841332


Q ss_pred             ECCCCEEEEEEECCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             627975699885525897415646677675434655566542234776
Q gi|254781192|r  146 TFQGTKGVTFTLTGVQFVKDDTRWGGQLRASSSDFESYEEETASIDEL  193 (198)
Q Consensus       146 ~~~~g~GVsl~L~aVQ~i~~~e~~gg~~~~~~d~f~~~~~~~~~~~~~  193 (198)
                      +.+.|+||||||.+||||+|+|+.||  .++..+|+++++++++.+..
T Consensus       159 ~~~~GagvslrL~avQvieLve~~g~--g~~~~g~~~ee~Gyva~e~~  204 (230)
T PHA00458        159 NAAVGASVKLQLESVMLVELAEFGGG--GEDDWADEEEEDGYVASESP  204 (230)
T ss_pred             CCCCCEEEEEEEEEEEEEEEEECCCC--CCCCCCCCCCCCCEECCCCC
T ss_conf             57664247988622279985320677--76556763323854346653


No 3  
>pfam10927 DUF2738 Protein of unknown function (DUF2738). This is a viral family of proteins with unknown function.
Probab=79.37  E-value=4.7  Score=19.87  Aligned_cols=65  Identities=22%  Similarity=0.153  Sum_probs=39.1

Q ss_pred             EEECCCCCCCCCEEE-CCCCCCCCCCCCCCCCCCCEEEEEEEEEEEECCCCEEEEEEECCEEEEECCCCCC
Q ss_conf             897057877686589-3688682366665313662899999997876279756998855258974156466
Q gi|254781192|r  101 YYITPKNKKVRPRLV-DRHVQEVTENIQEVFYSGCHVNAIISVYAYTFQGTKGVTFTLTGVQFVKDDTRWG  170 (198)
Q Consensus       101 ~~~~~~~~~~~P~v~-Ds~g~~l~~~~~~~I~sGs~v~v~~~~~pY~~~~g~GVsl~L~aVQ~i~~~e~~g  170 (198)
                      ...++++.++--.+| |..|+++.-++  .|++=|.+..++.+-.-.-+.  -||++|+.+-+| ++|+++
T Consensus       141 li~s~K~~kf~T~F~k~~~g~~~~i~D--~i~~~C~v~a~l~iESIfiG~--K~SiQlKi~~vl-ivE~l~  206 (246)
T pfam10927       141 LIYSAKAKKFVTGFFKDVEGQEVKIPD--IIKGRCRVIADLRVESIFIGA--KPSIQLKIVDVL-IVEPLG  206 (246)
T ss_pred             HHHCCCCCCEEEEEEECCCCCCCCHHH--HHHCCEEEEEEEEEEEEEECC--CEEEEEEEEEEE-EECCCH
T ss_conf             551067882689987315798556434--442505786766787788647--036899988888-842321


No 4  
>smart00425 TBOX Domain first found  in the mice T locus (Brachyury) protein.
Probab=34.67  E-value=24  Score=15.65  Aligned_cols=36  Identities=25%  Similarity=0.302  Sum_probs=26.7

Q ss_pred             EEEEEEEEEEEECCCCCCCCCCCCEEEEEEEECCCCH
Q ss_conf             6731799941530586246677840899999776668
Q gi|254781192|r    4 VLIKGRLSYPQLHEPRAYGDKGDEVYSADILFSKTDN   40 (198)
Q Consensus         4 vt~~gr~~y~~L~~Pd~~~~~~~~~Ys~~l~i~k~d~   40 (198)
                      ||.+||-.||.|.=--+..++ +..|.+.|-+..-|.
T Consensus        23 vTk~GRrmFP~l~~~vsGLdp-~~~Y~v~l~~~~~D~   58 (190)
T smart00425       23 VTKSGRRMFPTLKYKVSGLDP-NALYSVLMDLVPVDD   58 (190)
T ss_pred             EECCCCCCCCCEEEEEECCCC-CCCEEEEEEEEECCC
T ss_conf             933883458735999978895-732699999998758


No 5  
>cd00182 TBOX T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family.  Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors.
Probab=29.84  E-value=32  Score=14.97  Aligned_cols=35  Identities=23%  Similarity=0.295  Sum_probs=25.9

Q ss_pred             EEEEEEEEEEEECCCCCCCCCCCCEEEEEEEECCCC
Q ss_conf             673179994153058624667784089999977666
Q gi|254781192|r    4 VLIKGRLSYPQLHEPRAYGDKGDEVYSADILFSKTD   39 (198)
Q Consensus         4 vt~~gr~~y~~L~~Pd~~~~~~~~~Ys~~l~i~k~d   39 (198)
                      ||..||-.||.|.=--+..++ ...|.+.+-+..-|
T Consensus        24 ITk~GRrMFP~l~~~vsGLdp-~~~Y~v~ld~~~~D   58 (188)
T cd00182          24 ITKSGRRMFPTLKVKVSGLDP-NALYSVLMDLVPVD   58 (188)
T ss_pred             EECCCCCCCCCEEEEEECCCC-CCCEEEEEEEEECC
T ss_conf             903874568735999968995-74179999999876


No 6  
>pfam00907 T-box T-box. The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for development of the specific tissues they are expressed in, and mutations in T-box genes are implicated in human conditions such as DiGeorge syndrome and X-linked cleft palate, which feature malformations.
Probab=28.22  E-value=36  Score=14.63  Aligned_cols=35  Identities=26%  Similarity=0.355  Sum_probs=26.2

Q ss_pred             EEEEEEEEEEEECCCCCCCCCCCCEEEEEEEECCCC
Q ss_conf             673179994153058624667784089999977666
Q gi|254781192|r    4 VLIKGRLSYPQLHEPRAYGDKGDEVYSADILFSKTD   39 (198)
Q Consensus         4 vt~~gr~~y~~L~~Pd~~~~~~~~~Ys~~l~i~k~d   39 (198)
                      ||..||-.||.|.=--+..++ ...|++.+-+..-|
T Consensus        22 ITk~GRrMFP~l~~~vsGLdp-~~~Y~v~ld~~~~D   56 (183)
T pfam00907        22 ITKSGRRMFPTLKVSVSGLDP-NALYSVLLDFVPVD   56 (183)
T ss_pred             EECCCCCCCCCEEEEEECCCC-CCCEEEEEEEEECC
T ss_conf             933883458744999979994-73179999999876


No 7  
>TIGR00492 alr alanine racemase; InterPro: IPR000821 Alanine racemase catalyses the pyridoxal-dependent conversion of L-alanine into D-alanine, a key component of bacterial peptidoglycan . In Escherichia coli and Salmonella typhimurium, there are two alanine racemase isoforms, alr is a biosynthetic form required for cell wall formation; and dadB functions in L-alanine catabolism. By contrast with dadB and alr, both of which are monomeric enzymes, the alanine racemase of Bacillaceae are homodimers. In Pseudomonas putida, a broad-specificity amino acid racemase is structurally and functionally related to alanine racemase. The 3D-structure of the dimeric alanine racemase from Bacillus stearothermophilus has been determined to a resolution of 1.9 A . Each monomer comprises two domains, with an eight-stranded alpha/beta barrel at the N-terminus, and a C-terminal beta-strand domain. In the dimer, the mouth of the alpha/beta barrel of one monomer faces the second domain of the other monomer. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the barrel mouth and is covalently linked via an aldimine linkage to Lys39. Several other residues are involved in anchoring the PLP, for example, Arg219 forms a hydrogen bond with the pyridine nitrogen of the cofactor, which is assumed to influence electron delocalisation in PLP-alanine intermediates; Arg136 donates a hydrogen bond to the phenolic oxygen of PLP, and may be involved in substrate binding and stabilisation of intermediates; and Tyr265' is postulated to be a 2 proton donor to the carbanion intermediate .; GO: 0008784 alanine racemase activity, 0006522 alanine metabolic process.
Probab=17.84  E-value=69  Score=12.98  Aligned_cols=41  Identities=17%  Similarity=0.019  Sum_probs=29.6

Q ss_pred             CCEEEEEEEEEEEECCC--CEE----------EEEEECCEEEEECCC-CCCCCC
Q ss_conf             62899999997876279--756----------998855258974156-466776
Q gi|254781192|r  133 GCHVNAIISVYAYTFQG--TKG----------VTFTLTGVQFVKDDT-RWGGQL  173 (198)
Q Consensus       133 Gs~v~v~~~~~pY~~~~--g~G----------Vsl~L~aVQ~i~~~e-~~gg~~  173 (198)
                      =..||..+-+|.+++..  +.+          ++.+|..|+-++.|| +.|-|+
T Consensus       224 fd~vRpGIiLYG~~Ps~~~~~~~~~~L~PVlsL~s~i~~vr~~k~Ger~VsYG~  277 (383)
T TIGR00492       224 FDMVRPGIILYGLYPSADMKDGAPLGLKPVLSLKSKIIQVRTVKKGERPVSYGG  277 (383)
T ss_pred             EEEEECCHHHHCCCCCHHCCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCCCE
T ss_conf             114421435321476200145543475031267899999874058897424672


No 8  
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=17.54  E-value=70  Score=12.94  Aligned_cols=51  Identities=12%  Similarity=0.111  Sum_probs=32.0

Q ss_pred             EEEEEEEECCC-CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEC
Q ss_conf             08999997766-689999999999999985403410011345554556763004
Q gi|254781192|r   28 VYSADILFSKT-DNEQCDKLEQAIREAGEEKFGGSNMSALIERMKRTGRYPLKD   80 (198)
Q Consensus        28 ~Ys~~l~i~k~-d~~~~~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~p~~d   80 (198)
                      +|.+.+|+.++ +.++++.+.+.+.+..++.-+.-.....+.  ...+.||++.
T Consensus         7 ~YE~~~I~~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG--~R~LAY~I~k   58 (97)
T CHL00123          7 KYETMYILKPDLNEEELLKWIENYKKLLTKRGAKNIIVQNRG--RRKLAYKIKK   58 (97)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEE--CCCCCCCCCC
T ss_conf             211999989999989999999999999986897799998056--3000351566


No 9  
>TIGR02874 spore_ytfJ sporulation protein YtfJ; InterPro: IPR014229   Proteins in this entry, exemplified by YtfJ of Bacillus subtilis, are encoded by bacterial genomes if, and only if, the species is capable of endospore formation. YtfJ was confirmed in spores of B. subtilis; it appears to be expressed in the forespore under control of SigF ..
Probab=17.20  E-value=62  Score=13.25  Aligned_cols=23  Identities=9%  Similarity=0.118  Sum_probs=13.6

Q ss_pred             EEEECCCCEEEEEEECCEEEEEC
Q ss_conf             78762797569988552589741
Q gi|254781192|r  143 YAYTFQGTKGVTFTLTGVQFVKD  165 (198)
Q Consensus       143 ~pY~~~~g~GVsl~L~aVQ~i~~  165 (198)
                      +|+-=+.|+|||++.-|-.||+.
T Consensus        73 ~PFGGGSGaGVS~~PvAFLvig~   95 (132)
T TIGR02874        73 LPFGGGSGAGVSVKPVAFLVIGS   95 (132)
T ss_pred             CCCCCCCCCCEEECCEEEEEECC
T ss_conf             88867688873513158998778


No 10 
>pfam07157 DNA_circ_N DNA circulation protein N-terminus. This family represents the N-terminus (approximately 100 residues) of a number of phage DNA circulation proteins.
Probab=15.88  E-value=77  Score=12.69  Aligned_cols=43  Identities=21%  Similarity=0.190  Sum_probs=29.6

Q ss_pred             EEEEEEECCCCCCCCCCC-CEEEEEEEECCCCH-HHHHHHHHHHH
Q ss_conf             999415305862466778-40899999776668-99999999999
Q gi|254781192|r    9 RLSYPQLHEPRAYGDKGD-EVYSADILFSKTDN-EQCDKLEQAIR   51 (198)
Q Consensus         9 r~~y~~L~~Pd~~~~~~~-~~Ys~~l~i~k~d~-~~~~~i~~~i~   51 (198)
                      .-.||+-..|+.-.-+.. -.|+++.++=-+|. .+.+++.++++
T Consensus        30 ~HeyP~rD~~~vEDlG~~~r~~~i~a~~~G~dy~~~~~~Ll~ale   74 (93)
T pfam07157        30 LHEYPLRDTGYTEDLGKKLRRYTISALVVGDDYFTQRDRLLDALE   74 (93)
T ss_pred             EECCCCCCCCCCCCCCCCCCEEEEEEEEECCCHHHHHHHHHHHHC
T ss_conf             873788887550014766667899999999859999999999970


Done!