Query         gi|254780631|ref|YP_003065044.1| hypothetical protein CLIBASIA_02590 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 62
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Sun May 29 20:52:41 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780631.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 KOG1684 consensus               23.7      14 0.00035   19.1  -1.1   22   34-58     87-108 (401)
  2 COG3747 Phage terminase, small  17.5      45  0.0011   16.5   0.5   16   29-44     95-110 (160)
  3 TIGR02116 toxin_Txe_YoeB addic  14.8      73  0.0019   15.5   1.0   21   28-48     28-48  (82)
  4 KOG1114 consensus               14.7      72  0.0018   15.5   0.9   13   37-49    456-468 (1304)
  5 TIGR01340 aconitase_mito aconi  12.6      61  0.0015   15.9   0.1   50    4-57    427-476 (761)
  6 TIGR02960 SigX5 RNA polymerase  11.7      82  0.0021   15.2   0.5   12   30-41     45-56  (329)
  7 COG4115 Uncharacterized protei   8.2 1.6E+02  0.0041   13.7   0.9   26   23-48     27-52  (84)
  8 pfam12389 Peptidase_M73 Camely   7.3 1.5E+02  0.0038   13.9   0.4   14   26-39    169-182 (199)
  9 TIGR00058 Hemerythrin hemeryth   7.1 1.4E+02  0.0036   14.0   0.2    8    6-13     16-23  (116)
 10 PRK10753 transcriptional regul   6.9 1.7E+02  0.0043   13.6   0.5   21   36-56     56-76  (90)

No 1  
>KOG1684 consensus
Probab=23.65  E-value=14  Score=19.07  Aligned_cols=22  Identities=45%  Similarity=0.773  Sum_probs=15.9

Q ss_conf             3347545577667873587127764
Q gi|254780631|r   34 PFQGRSSRNPCQGGDIKAPETVVEI   58 (62)
Q Consensus        34 pfqgrssrnpcqggdikapetvvei   58 (62)
                      -..|-.+|--|-||||+   +++|+
T Consensus        87 Ilkgs~~raFCAGgDI~---~~ae~  108 (401)
T KOG1684          87 ILKGSGGRAFCAGGDIK---AVAES  108 (401)
T ss_pred             EEECCCCCEEECCCCHH---HHHHH
T ss_conf             99168986014586578---89887

No 2  
>COG3747 Phage terminase, small subunit [DNA replication, recombination, and repair]
Probab=17.51  E-value=45  Score=16.52  Aligned_cols=16  Identities=44%  Similarity=0.615  Sum_probs=12.0

Q ss_pred             CCCCCCCCCCCCCCCC
Q ss_conf             0002733475455776
Q gi|254780631|r   29 EKKRNPFQGRSSRNPC   44 (62)
Q Consensus        29 ekkrnpfqgrssrnpc   44 (62)
T Consensus        95 ~ii~~~~~g~~krNPa  110 (160)
T COG3747          95 FIITNQFSGRVKRNPA  110 (160)
T ss_pred             EEEECCCCCEECCCHH
T ss_conf             0121443450037858

No 3  
>TIGR02116 toxin_Txe_YoeB addiction module toxin, Txe/YoeB family; InterPro: IPR009614   The Axe-Txe pair in Enterococcus faecium and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This family describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by match to  ..
Probab=14.81  E-value=73  Score=15.46  Aligned_cols=21  Identities=33%  Similarity=0.683  Sum_probs=15.9

Q ss_conf             300027334754557766787
Q gi|254780631|r   28 NEKKRNPFQGRSSRNPCQGGD   48 (62)
Q Consensus        28 nekkrnpfqgrssrnpcqggd   48 (62)
T Consensus        28 ~~~~rdPf~g~gkpEpLk~~l   48 (82)
T TIGR02116        28 KDVKRDPFKGIGKPEPLKGDL   48 (82)
T ss_conf             985488960586789988788

No 4  
>KOG1114 consensus
Probab=14.69  E-value=72  Score=15.49  Aligned_cols=13  Identities=54%  Similarity=0.987  Sum_probs=9.9

Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             7545577667873
Q gi|254780631|r   37 GRSSRNPCQGGDI   49 (62)
Q Consensus        37 grssrnpcqggdi   49 (62)
T Consensus       456 tWsSRgP~~DG~l  468 (1304)
T KOG1114         456 TWSSRGPCLDGDL  468 (1304)
T ss_pred             CCCCCCCCCCCCC
T ss_conf             1346788767886

No 5  
>TIGR01340 aconitase_mito aconitate hydratase, mitochondrial; InterPro: IPR006248   Aconitase (aconitate hydratase; from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop , . Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) . Below is a description of some of the multi-functional activities associated with different aconitases.   Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway . The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA.    Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) , . As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated .   IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis . Although IRP2 is homologous to IRP1, IPR2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes . In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system.   Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica , . In S.enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress.   This entry represents mitochondrial aconitase (mAcn), as well as close homologues such as certain bacterial aconitase A (AcnA) enzymes.   More information about these proteins can be found at Protein of the Month: Aconitase .; GO: 0003994 aconitate hydratase activity, 0051539 4 iron 4 sulfur cluster binding, 0006099 tricarboxylic acid cycle.
Probab=12.60  E-value=61  Score=15.86  Aligned_cols=50  Identities=36%  Similarity=0.502  Sum_probs=35.1

Q ss_conf             300000233328334202102344300027334754557766787358712776
Q Consensus         4 csdnidrehkagieveknaittkdnekkrnpfqgrssrnpcqggdikapetvve   57 (62)
                      |--.-||+-..--.-|+|+|-|--|   || |.||---||----=+-.||-|+-
T Consensus       427 CIGQW~R~D~s~~kg~~N~I~tSyN---RN-F~gRND~N~~T~~Fl~SPelVtA  476 (761)
T ss_conf             8776553146325789751474036---67-66647467323100156789889

No 6  
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family; InterPro: IPR014305   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 group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution and represent a conserved family.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=11.73  E-value=82  Score=15.19  Aligned_cols=12  Identities=50%  Similarity=0.819  Sum_probs=9.3

Q ss_pred             CCCCCCCCCCCC
Q ss_conf             002733475455
Q gi|254780631|r   30 KKRNPFQGRSSR   41 (62)
Q Consensus        30 kkrnpfqgrssr   41 (62)
T Consensus        45 ~~~~~FeGrSS~   56 (329)
T TIGR02960        45 RAREKFEGRSSL   56 (329)
T ss_pred             HHCCCCCCCCCC
T ss_conf             100331577663

No 7  
>COG4115 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=8.20  E-value=1.6e+02  Score=13.73  Aligned_cols=26  Identities=35%  Similarity=0.555  Sum_probs=18.4

Q ss_conf             02344300027334754557766787
Q gi|254780631|r   23 ITTKDNEKKRNPFQGRSSRNPCQGGD   48 (62)
Q Consensus        23 ittkdnekkrnpfqgrssrnpcqggd   48 (62)
T Consensus        27 i~~Li~~i~rdPfkg~gkpEpLk~~~   52 (84)
T ss_conf             99999985159645679976576664

No 8  
>pfam12389 Peptidase_M73 Camelysin metallo-endopeptidase.
Probab=7.28  E-value=1.5e+02  Score=13.88  Aligned_cols=14  Identities=43%  Similarity=0.691  Sum_probs=0.0

Q ss_pred             CCCCCCCCCCCCCC
Q ss_conf             44300027334754
Q gi|254780631|r   26 KDNEKKRNPFQGRS   39 (62)
Q Consensus        26 kdnekkrnpfqgrs   39 (62)
T Consensus       169 vDn~~dQN~fQGDs  182 (199)
T pfam12389       169 VDDGKDQNEFQGDK  182 (199)
T ss_pred             EECCCCCCCCCCCE
T ss_conf             74886332005756

No 9  
>TIGR00058 Hemerythrin hemerythrin family non-heme iron proteins; InterPro: IPR002063   The hemerythrin family is composed of hemerythrin proteins found in invertebrates, and a broader collection of bacterial and archaeal homologues. Hemerythrin is an oxygen-binding protein found in the vascular system and coelemic fluid, or in muscles (myohemerythrin) in invertebrates . Many of the lhomologous proteins found in prokaryotes are multi-domain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (IPR000160 from INTERPRO) and methyl-accepting chemotaxis protein (MCP) signalling domain (IPR004089 from INTERPRO). Most hemerythrins are oxygen-carriers with a bound non-haem iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. The prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium.   Hemerythrins and myohemerythrins ,  are small proteins of about 110 to 129 amino acid residues that bind two iron atoms. They are left-twisted 4-alpha-helical bundles, which provide a hydrophobic pocket where dioxygen binds as a peroxo species, interacting with adjacent aliphatic side chains via van der Waals forces . In both hemerythrins and myohemerythrins, the active centre is a binuclear iron complex, bound directly to the protein via 7 amino acid side chains , 5 His, 1 Glu and 1 Asp . Ovohemerythrin , a yolk protein from the leech Theromyzon tessulatum seems to belong to this family of proteins, it may play a role in the detoxification of free iron after a blood meal .   This entry represents the hemerythrin family of proteins.; GO: 0005344 oxygen transporter activity, 0005506 iron ion binding, 0006810 transport.
Probab=7.13  E-value=1.4e+02  Score=13.99  Aligned_cols=8  Identities=75%  Similarity=1.215  Sum_probs=0.0

Q ss_pred             CCCCHHHH
Q ss_conf             00002333
Q gi|254780631|r    6 DNIDREHK   13 (62)
Q Consensus         6 dnidrehk   13 (62)
T Consensus        16 ~~LD~eHK   23 (116)
T TIGR00058        16 DNLDEEHK   23 (116)
T ss_pred             HHHHHHHH
T ss_conf             33327899

No 10 
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=6.94  E-value=1.7e+02  Score=13.62  Aligned_cols=21  Identities=38%  Similarity=0.572  Sum_probs=0.0

Q ss_conf             475455776678735871277
Q gi|254780631|r   36 QGRSSRNPCQGGDIKAPETVV   56 (62)
Q Consensus        36 qgrssrnpcqggdikapetvv   56 (62)
T Consensus        56 ~aR~grNP~TGe~i~Ipa~~v   76 (90)
T PRK10753         56 AERTGRNPQTGKEIKIAAANV   76 (90)
T ss_conf             781350819999898758764