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!