Query gi|254781181|ref|YP_003065594.1| hypothetical protein CLIBASIA_05440 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 85 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Mon May 30 05:47:11 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781181.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR00737 nifR3_yhdG putative 80.5 0.26 6.6E-06 28.4 -1.2 16 20-35 101-116 (336) 2 TIGR02053 MerA mercuric reduct 74.4 2.2 5.6E-05 23.4 2.1 62 22-83 42-106 (494) 3 KOG0819 consensus 64.5 14 0.00036 19.0 4.8 47 13-81 21-67 (321) 4 PRK10415 tRNA-dihydrouridine s 47.8 6.4 0.00016 20.9 0.5 15 20-34 94-108 (321) 5 PRK10550 tRNA-dihydrouridine s 47.5 5.6 0.00014 21.2 0.1 16 20-35 92-107 (312) 6 PRK11815 tRNA-dihydrouridine s 45.1 8.5 0.00022 20.2 0.8 14 20-33 94-107 (333) 7 cd02911 arch_FMN Archeal FMN-b 44.6 6.3 0.00016 20.9 0.0 14 20-33 101-114 (233) 8 COG0042 tRNA-dihydrouridine sy 43.5 7 0.00018 20.6 0.1 15 21-35 97-111 (323) 9 pfam01207 Dus Dihydrouridine s 37.7 10 0.00026 19.8 0.2 13 22-34 85-97 (309) 10 cd02801 DUS_like_FMN Dihydrour 35.9 12 0.00031 19.4 0.3 15 20-34 84-98 (231) 11 TIGR02625 YiiL_rotase L-rhamno 31.4 14 0.00035 19.0 0.1 22 55-76 3-24 (102) 12 TIGR02392 rpoH_proteo alternat 31.1 22 0.00056 18.0 1.0 21 55-75 11-31 (279) 13 COG1365 Predicted ATPase (PP-l 31.0 22 0.00055 18.0 1.0 29 2-33 181-217 (255) 14 TIGR01329 cysta_beta_ly_E cyst 24.5 15 0.00038 18.9 -0.8 36 22-58 151-186 (415) 15 KOG2613 consensus 23.0 32 0.00081 17.1 0.7 33 34-66 257-289 (502) 16 pfam10792 DUF2605 Protein of u 20.7 69 0.0017 15.3 2.0 25 55-79 34-58 (99) No 1 >TIGR00737 nifR3_yhdG putative TIM-barrel protein, nifR3 family; InterPro: IPR004652 This family represents one branch of COG0042 from COG (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family) and includes NifR3 itself, from Rhodobacter capsulatus. Members of this family catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes , and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. ; GO: 0016491 oxidoreductase activity, 0050660 FAD binding, 0008033 tRNA processing. Probab=80.50 E-value=0.26 Score=28.42 Aligned_cols=16 Identities=44% Similarity=0.779 Sum_probs=12.1 Q ss_pred HHHHCCCHHHHHHHHH Q ss_conf 9954297099999999 Q gi|254781181|r 20 ILKNFGCPLKRIVKVQ 35 (85) Q Consensus 20 ilknfgcplkrivkvq 35 (85) |=-|||||.++|.|-. T Consensus 101 IDiN~GCP~~Kitk~~ 116 (336) T TIGR00737 101 IDINMGCPVPKITKKG 116 (336) T ss_pred EEECCCCCCCCCCCCC T ss_conf 8536765488421676 No 2 >TIGR02053 MerA mercuric reductase; InterPro: IPR011796 This entry represents the mercuric reductase found in the mer operon for the detoxification of mercury compounds. MerA is a FAD-containing flavoprotein which reduces Hg(II) to Hg(0) utilizing NADPH .; GO: 0016152 mercury (II) reductase activity, 0045340 mercury ion binding, 0050660 FAD binding, 0050661 NADP binding, 0006118 electron transport, 0050787 detoxification of mercury ion. Probab=74.39 E-value=2.2 Score=23.37 Aligned_cols=62 Identities=26% Similarity=0.390 Sum_probs=30.9 Q ss_pred HHCCC-HHHHHHHHHHHHHHHHHHH--HHCCHHHCCCEEEEEEHHHHHHHHHHHHHHHHHHHEEC Q ss_conf 54297-0999999999867752112--31116660460658702669999999885330020215 Q gi|254781181|r 22 KNFGC-PLKRIVKVQKQAKSLANAS--QKLTVDQIDNSIMFLYPEQRQELAKRYKEKYNDVLIHL 83 (85) Q Consensus 22 knfgc-plkrivkvqkqakslanas--qkltvdqidnsimflypeqrqelakrykekyndvlihl 83 (85) -|+|| |-|....--+-++--.+.+ -++.-....-+.--|.-.++.-...--+|||-|||-.. T Consensus 42 VNVGCVPSK~llraa~~~~~a~~~~~f~g~~~~~~~v~~~~ll~~~~~~V~eLR~eKY~~vl~~y 106 (494) T TIGR02053 42 VNVGCVPSKILLRAAEVAHYARKPPFFVGLLAATVEVDFEELLEQKREVVEELRKEKYEDVLSSY 106 (494) T ss_pred EEECCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 85232745899999988767634777777535434423899999988999998776789998517 No 3 >KOG0819 consensus Probab=64.55 E-value=14 Score=19.00 Aligned_cols=47 Identities=32% Similarity=0.434 Sum_probs=36.5 Q ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCHHHCCCEEEEEEHHHHHHHHHHHHHHHHHHHE Q ss_conf 999999999542970999999999867752112311166604606587026699999998853300202 Q gi|254781181|r 13 VAVVIRLILKNFGCPLKRIVKVQKQAKSLANASQKLTVDQIDNSIMFLYPEQRQELAKRYKEKYNDVLI 81 (85) Q Consensus 13 vavvirlilknfgcplkrivkvqkqakslanasqkltvdqidnsimflypeqrqelakrykekyndvli 81 (85) -|-.+|--+|.|||--+-|+.+- ++-| -+|||+..+-||+.|+.-|| T Consensus 21 DAe~L~kA~kG~Gtde~aII~iL------~~Rs----------------n~QRq~I~~ayk~~ygkDLi 67 (321) T KOG0819 21 DAEQLRKAMKGFGTDEQAIIDIL------THRS----------------NAQRQLIRAAYKTMYGKDLI 67 (321) T ss_pred HHHHHHHHHHCCCCCHHHHHHHH------HCCC----------------HHHHHHHHHHHHHHHHHHHH T ss_conf 89999998716797799999999------7247----------------99999999999998737899 No 4 >PRK10415 tRNA-dihydrouridine synthase B; Provisional Probab=47.83 E-value=6.4 Score=20.87 Aligned_cols=15 Identities=40% Similarity=0.791 Sum_probs=11.5 Q ss_pred HHHHCCCHHHHHHHH Q ss_conf 995429709999999 Q gi|254781181|r 20 ILKNFGCPLKRIVKV 34 (85) Q Consensus 20 ilknfgcplkrivkv 34 (85) |=-|+|||.++++|- T Consensus 94 IDiN~GCP~~kV~k~ 108 (321) T PRK10415 94 IDINMGCPAKKVNRK 108 (321) T ss_pred EEEECCCCHHHHCCC T ss_conf 943189998997079 No 5 >PRK10550 tRNA-dihydrouridine synthase C; Provisional Probab=47.48 E-value=5.6 Score=21.16 Aligned_cols=16 Identities=31% Similarity=0.509 Sum_probs=11.6 Q ss_pred HHHHCCCHHHHHHHHH Q ss_conf 9954297099999999 Q gi|254781181|r 20 ILKNFGCPLKRIVKVQ 35 (85) Q Consensus 20 ilknfgcplkrivkvq 35 (85) |=-|||||-+.+++-. T Consensus 92 IDlN~GCP~~~V~k~g 107 (312) T PRK10550 92 VDLNCGCPSKTVNGSG 107 (312) T ss_pred EEEECCCCHHHHCCCC T ss_conf 6254799978966899 No 6 >PRK11815 tRNA-dihydrouridine synthase A; Provisional Probab=45.09 E-value=8.5 Score=20.18 Aligned_cols=14 Identities=43% Similarity=0.809 Sum_probs=10.3 Q ss_pred HHHHCCCHHHHHHH Q ss_conf 99542970999999 Q gi|254781181|r 20 ILKNFGCPLKRIVK 33 (85) Q Consensus 20 ilknfgcplkrivk 33 (85) |=-|+|||-+++.+ T Consensus 94 IDlN~GCP~~kV~~ 107 (333) T PRK11815 94 INLNVGCPSDRVQN 107 (333) T ss_pred ECCCCCCCHHHHHC T ss_conf 35238998688732 No 7 >cd02911 arch_FMN Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent flavin oxidoreductase (oxidored) FMN-binding family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN. The specific function of this group is unknown. Probab=44.59 E-value=6.3 Score=20.89 Aligned_cols=14 Identities=21% Similarity=0.332 Sum_probs=9.9 Q ss_pred HHHHCCCHHHHHHH Q ss_conf 99542970999999 Q gi|254781181|r 20 ILKNFGCPLKRIVK 33 (85) Q Consensus 20 ilknfgcplkrivk 33 (85) |=-|+|||-+.++| T Consensus 101 IDiN~GCP~~kV~~ 114 (233) T cd02911 101 LEINAHCRQPEMVE 114 (233) T ss_pred EEEECCCCCHHHCC T ss_conf 99979999289837 No 8 >COG0042 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis] Probab=43.51 E-value=7 Score=20.62 Aligned_cols=15 Identities=40% Similarity=0.623 Sum_probs=11.2 Q ss_pred HHHCCCHHHHHHHHH Q ss_conf 954297099999999 Q gi|254781181|r 21 LKNFGCPLKRIVKVQ 35 (85) Q Consensus 21 lknfgcplkrivkvq 35 (85) =-|+|||-+++++-. T Consensus 97 DlN~GCP~~~V~~~g 111 (323) T COG0042 97 DLNCGCPSPKVVKGG 111 (323) T ss_pred EEECCCCCHHHHCCC T ss_conf 876899928980898 No 9 >pfam01207 Dus Dihydrouridine synthase (Dus). Members of this family catalyse the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria. Probab=37.74 E-value=10 Score=19.78 Aligned_cols=13 Identities=38% Similarity=0.928 Sum_probs=10.1 Q ss_pred HHCCCHHHHHHHH Q ss_conf 5429709999999 Q gi|254781181|r 22 KNFGCPLKRIVKV 34 (85) Q Consensus 22 knfgcplkrivkv 34 (85) -|+|||-+++++- T Consensus 85 lN~GCP~~~v~~~ 97 (309) T pfam01207 85 INMGCPAKKVTRG 97 (309) T ss_pred EECCCCHHHHCCC T ss_conf 5189999998789 No 10 >cd02801 DUS_like_FMN Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present. Probab=35.88 E-value=12 Score=19.37 Aligned_cols=15 Identities=40% Similarity=0.711 Sum_probs=10.9 Q ss_pred HHHHCCCHHHHHHHH Q ss_conf 995429709999999 Q gi|254781181|r 20 ILKNFGCPLKRIVKV 34 (85) Q Consensus 20 ilknfgcplkrivkv 34 (85) |=-|+|||-+++++- T Consensus 84 IDlN~GCP~~~v~~~ 98 (231) T cd02801 84 IDLNMGCPSPKVTKG 98 (231) T ss_pred EEEECCCCHHHHCCC T ss_conf 998389996997089 No 11 >TIGR02625 YiiL_rotase L-rhamnose 1-epimerase; InterPro: IPR013448 This entry contains rhamnose mutarotase from Escherichia coli, previously designated YiiL as an uncharacterised protein, and close homologs associated with rhamnose dissimilation operons in other bacterial genomes. Mutarotase is a term for an epimerase that changes optical activity. This enzyme was shown experimentally to interconvert alpha and beta stereoisomers of the pyranose form of L-rhamnose . The crystal structure of this small (104 amino acid) protein shows a locally asymmetric dimer with active site residues of His, Tyr, and Trp .. Probab=31.37 E-value=14 Score=19.03 Aligned_cols=22 Identities=32% Similarity=0.708 Sum_probs=18.4 Q ss_pred CEEEEEEHHHHHHHHHHHHHHH Q ss_conf 6065870266999999988533 Q gi|254781181|r 55 NSIMFLYPEQRQELAKRYKEKY 76 (85) Q Consensus 55 nsimflypeqrqelakrykeky 76 (85) .+||.+||....|-.||-.|-+ T Consensus 3 afvM~v~PD~h~EY~kRH~eiW 24 (102) T TIGR02625 3 AFVMYVYPDAHEEYKKRHNEIW 24 (102) T ss_pred CEEEEECCCCHHHHHCCCCCCC T ss_conf 2021014888466640688556 No 12 >TIGR02392 rpoH_proteo alternative sigma factor RpoH; InterPro: IPR012759 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the proteobacterial clade of sigma factors called RpoH. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0008270 zinc ion binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent, 0009408 response to heat. Probab=31.05 E-value=22 Score=17.95 Aligned_cols=21 Identities=52% Similarity=0.683 Sum_probs=9.0 Q ss_pred CEEEEEEHHHHHHHHHHHHHH Q ss_conf 606587026699999998853 Q gi|254781181|r 55 NSIMFLYPEQRQELAKRYKEK 75 (85) Q Consensus 55 nsimflypeqrqelakrykek 75 (85) |++-.|-||+-++||+||.|. T Consensus 11 n~~P~L~~EEE~~LA~r~r~~ 31 (279) T TIGR02392 11 NRIPMLTAEEEQELAKRLREE 31 (279) T ss_pred HHCCCCCHHHHHHHHHHHHHC T ss_conf 717899988999999986542 No 13 >COG1365 Predicted ATPase (PP-loop superfamily) [General function prediction only] Probab=30.96 E-value=22 Score=17.97 Aligned_cols=29 Identities=48% Similarity=0.854 Sum_probs=16.4 Q ss_pred CCCHHHHHHHHHHHHHHHHHH--------HCCCHHHHHHH Q ss_conf 876111330399999999995--------42970999999 Q gi|254781181|r 2 HQPSFLVSYPLVAVVIRLILK--------NFGCPLKRIVK 33 (85) Q Consensus 2 hqpsflvsyplvavvirlilk--------nfgcplkrivk 33 (85) |-|+|+. +.-.-.|-|++ +|||||-+++. T Consensus 181 nlPAflA---ltK~Elr~il~~~~~e~~~kygCPll~e~h 217 (255) T COG1365 181 NLPAFLA---LTKDELRSILKWNGYELEMKYGCPLLREVH 217 (255) T ss_pred CCHHHHH---HCCHHHHHHHHHCCCCCHHCCCCCHHHHHH T ss_conf 2588885---171999999871384300115883589998 No 14 >TIGR01329 cysta_beta_ly_E cystathionine beta-lyase; InterPro: IPR006238 This group of sequences represent cystathionine beta-lyase (alternate name: beta-cystathionase), one of several pyridoxal-dependent enzymes of cysteine, methionine, and homocysteine metabolism. This enzyme is involved in the biosynthesis of Met from Cys.. Probab=24.54 E-value=15 Score=18.87 Aligned_cols=36 Identities=28% Similarity=0.418 Sum_probs=21.7 Q ss_pred HHCCCHHHHHHHHHHHHHHHHHHHHHCCHHHCCCEEE Q ss_conf 5429709999999998677521123111666046065 Q gi|254781181|r 22 KNFGCPLKRIVKVQKQAKSLANASQKLTVDQIDNSIM 58 (85) Q Consensus 22 knfgcplkrivkvqkqakslanasqkltvdqidnsim 58 (85) ..=--||-|||...+-+..--..+.+-+| -|||++| T Consensus 151 ESPTNPl~~ivDI~~i~~~ah~~~~~~~V-~vDNtmm 186 (415) T TIGR01329 151 ESPTNPLIKIVDIRKIAEAAHALNEDALV-VVDNTMM 186 (415) T ss_pred CCCCCCCCEEECHHHHHHHHHHCCCCCEE-EEECCCC T ss_conf 38889862463378999999850897189-9822204 No 15 >KOG2613 consensus Probab=22.98 E-value=32 Score=17.08 Aligned_cols=33 Identities=36% Similarity=0.457 Sum_probs=26.2 Q ss_pred HHHHHHHHHHHHHHCCHHHCCCEEEEEEHHHHH Q ss_conf 999867752112311166604606587026699 Q gi|254781181|r 34 VQKQAKSLANASQKLTVDQIDNSIMFLYPEQRQ 66 (85) Q Consensus 34 vqkqakslanasqkltvdqidnsimflypeqrq 66 (85) -.|.|+||.|-||-.-+..+.|+|-|+-|..-| T Consensus 257 pkkva~~lGNi~qlvvc~kVs~~I~llDP~tlq 289 (502) T KOG2613 257 PKKVAQSLGNISQLVVCTKVSNTITLLDPRTLQ 289 (502) T ss_pred CHHHHHHCCCCCCEEEEEEECCCEEEECCCCEE T ss_conf 788997508854359999704834986775002 No 16 >pfam10792 DUF2605 Protein of unknown function (DUF2605). This family is conserved in Cyanobacteria. The function is not known. Probab=20.69 E-value=69 Score=15.25 Aligned_cols=25 Identities=40% Similarity=0.642 Sum_probs=20.8 Q ss_pred CEEEEEEHHHHHHHHHHHHHHHHHH Q ss_conf 6065870266999999988533002 Q gi|254781181|r 55 NSIMFLYPEQRQELAKRYKEKYNDV 79 (85) Q Consensus 55 nsimflypeqrqelakrykekyndv 79 (85) ..|-|+-|+++++|..|-++....| T Consensus 34 e~~~fls~~eq~~Ll~Rv~~aq~ev 58 (99) T pfam10792 34 EPISFMSPEEQQALLERVKEAQKEV 58 (99) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHH T ss_conf 9832289999999999999999999 Done!