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!