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!