Query 537021.9.peg.248_1
Match_columns 45
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Wed May 25 16:16:54 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i peg_248.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01341 aconitase_1 aconitat 59.9 6 0.00015 21.5 1.9 37 6-43 470-506 (896)
2 COG1048 AcnA Aconitase A [Ener 40.7 21 0.00054 18.7 2.2 38 5-43 448-485 (861)
3 PRK12881 acnA aconitate hydrat 34.9 27 0.00068 18.2 2.0 38 5-43 470-507 (896)
4 PTZ00092 aconitate hydratase; 29.6 37 0.00095 17.5 2.0 38 5-43 469-506 (887)
5 PRK09277 aconitate hydratase; 28.9 40 0.001 17.3 2.1 37 6-43 460-496 (884)
6 cd04934 ACT_AK-Hom3_1 CT domai 18.4 69 0.0017 16.1 1.6 20 3-22 4-23 (73)
7 COG5575 ORC2 Origin recognitio 12.2 1.6E+02 0.0041 14.3 2.3 30 4-36 258-287 (535)
8 pfam11090 DUF2833 Protein of u 10.6 89 0.0023 15.6 0.4 18 28-45 7-24 (86)
9 cd04912 ACT_AKiii-LysC-EC-like 9.6 1.6E+02 0.004 14.3 1.3 20 3-22 4-23 (75)
10 cd04933 ACT_AK1-AT_1 ACT domai 9.6 1.5E+02 0.0038 14.4 1.2 19 4-22 5-23 (78)
No 1
>TIGR01341 aconitase_1 aconitate hydratase 1; InterPro: IPR006249 Aconitase (aconitate hydratase; 4.2.1.3 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 bacterial aconitase A (AcnA), eukaryotic cytosolic aconitase (cAcn/IRP1), iron regulatory protein 2 (IRP2), and a few mitochondrial aconitases (certain mAcn proteins, but not the majority of these enzymes). More information about these proteins can be found at Protein of the Month: Aconitase .; GO: 0051539 4 iron 4 sulfur cluster binding, 0008152 metabolic process.
Probab=59.88 E-value=6 Score=21.50 Aligned_cols=37 Identities=35% Similarity=0.695 Sum_probs=34.1
Q ss_pred ECCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCEEE
Q ss_conf 10121355667788767656531266321120222134
Q 537021.9.peg.2 6 LQAGSLVATGFLEKIFVGNFLDSLSFPCFIGISCGACI 43 (45)
Q Consensus 6 lqagslvatgflekifvgnfldslsfpcfigiscgaci 43 (45)
|--||-|-|++|.|-=.-.+|+.|-|- .+|--|-.||
T Consensus 470 LAPGS~VVt~YL~~sGLlpYL~~LGF~-lVGYGCTTCI 506 (896)
T TIGR01341 470 LAPGSKVVTDYLAESGLLPYLEELGFN-LVGYGCTTCI 506 (896)
T ss_pred CCCCCHHHHHHHHHCCCCHHHHHCCCE-EEECCCCCCC
T ss_conf 087863589897430640368861972-7614432020
No 2
>COG1048 AcnA Aconitase A [Energy production and conversion]
Probab=40.71 E-value=21 Score=18.73 Aligned_cols=38 Identities=37% Similarity=0.673 Sum_probs=33.1
Q ss_pred EECCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCEEE
Q ss_conf 110121355667788767656531266321120222134
Q 537021.9.peg.2 5 FLQAGSLVATGFLEKIFVGNFLDSLSFPCFIGISCGACI 43 (45)
Q Consensus 5 flqagslvatgflekifvgnfldslsfpcfigiscgaci 43 (45)
.+-.||-|.+.+|+|-=.-..|+.+.|- ..|-.||.||
T Consensus 448 slAPGS~vV~~yL~~~Gl~~~L~~lGf~-iv~~gCttCI 485 (861)
T COG1048 448 SVAPGSKVVTEYLEKAGLLPYLEKLGFN-IVGYGCTTCI 485 (861)
T ss_pred EECCCCHHHHHHHHHCCCHHHHHHCCCE-EECCCCCCCC
T ss_conf 6578858999999975878899964978-8445564664
No 3
>PRK12881 acnA aconitate hydratase; Provisional
Probab=34.87 E-value=27 Score=18.23 Aligned_cols=38 Identities=39% Similarity=0.686 Sum_probs=32.9
Q ss_pred EECCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCEEE
Q ss_conf 110121355667788767656531266321120222134
Q 537021.9.peg.2 5 FLQAGSLVATGFLEKIFVGNFLDSLSFPCFIGISCGACI 43 (45)
Q Consensus 5 flqagslvatgflekifvgnfldslsfpcfigiscgaci 43 (45)
.+-.||-|.+-+||+-=.-..|+.+-|- ..|-.|+.||
T Consensus 470 slaPGSrvV~~yL~~~Gll~~L~~lGf~-vvgyGC~tCI 507 (896)
T PRK12881 470 SLAPGSKVVTEYLEKAGLLPYLEKLGFG-IVGYGCTTCI 507 (896)
T ss_pred EECCCHHHHHHHHHHCCCHHHHHHCCCE-EECCCCCCCC
T ss_conf 1688779999999986888889976968-9545553245
No 4
>PTZ00092 aconitate hydratase; Provisional
Probab=29.59 E-value=37 Score=17.47 Aligned_cols=38 Identities=37% Similarity=0.597 Sum_probs=32.6
Q ss_pred EECCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCEEE
Q ss_conf 110121355667788767656531266321120222134
Q 537021.9.peg.2 5 FLQAGSLVATGFLEKIFVGNFLDSLSFPCFIGISCGACI 43 (45)
Q Consensus 5 flqagslvatgflekifvgnfldslsfpcfigiscgaci 43 (45)
.+-.||-+.+.+||+-=.-..|+.+-|- ..|-.|+.||
T Consensus 469 slaPGS~vV~~yL~~~Gll~~L~~lGf~-vvg~gC~tCI 506 (887)
T PTZ00092 469 SLSPGSKVVTKYLEASGLQKYLEKLGFY-TTGYGCMTCI 506 (887)
T ss_pred EECCCHHHHHHHHHHCCCHHHHHHCCCE-EECCCCCCCC
T ss_conf 4688679999999986868899975968-9236785652
No 5
>PRK09277 aconitate hydratase; Validated
Probab=28.90 E-value=40 Score=17.31 Aligned_cols=37 Identities=41% Similarity=0.754 Sum_probs=31.4
Q ss_pred ECCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCEEE
Q ss_conf 10121355667788767656531266321120222134
Q 537021.9.peg.2 6 LQAGSLVATGFLEKIFVGNFLDSLSFPCFIGISCGACI 43 (45)
Q Consensus 6 lqagslvatgflekifvgnfldslsfpcfigiscgaci 43 (45)
+-.||-+.+-+||+-=.-..|+.+-|- ..|-.|+.||
T Consensus 460 laPGS~vV~~yL~~~GLl~~L~~lGf~-v~g~gC~tCI 496 (884)
T PRK09277 460 LAPGSKVVTEYLEKAGLLPYLEALGFN-LVGYGCTTCI 496 (884)
T ss_pred CCCCHHHHHHHHHHCCCHHHHHHCCCE-EECCCCCCCC
T ss_conf 388779999999986878899975978-9413342024
No 6
>cd04934 ACT_AK-Hom3_1 CT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydro
Probab=18.41 E-value=69 Score=16.14 Aligned_cols=20 Identities=35% Similarity=0.629 Sum_probs=15.1
Q ss_pred CEEECCCCHHHHHHHHHHHH
Q ss_conf 10110121355667788767
Q 537021.9.peg.2 3 INFLQAGSLVATGFLEKIFV 22 (45)
Q Consensus 3 inflqagslvatgflekifv 22 (45)
||.--.--+.+.|||.++|-
T Consensus 4 inI~Snrm~~ahGFLa~vF~ 23 (73)
T cd04934 4 INIHSNKKSLSHGFLARIFA 23 (73)
T ss_pred EEEECCCHHHHHHHHHHHHH
T ss_conf 99831501335178999999
No 7
>COG5575 ORC2 Origin recognition complex, subunit 2 [DNA replication, recombination, and repair]
Probab=12.16 E-value=1.6e+02 Score=14.26 Aligned_cols=30 Identities=37% Similarity=0.479 Sum_probs=18.0
Q ss_pred EEECCCCHHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf 011012135566778876765653126632112
Q 537021.9.peg.2 4 NFLQAGSLVATGFLEKIFVGNFLDSLSFPCFIG 36 (45)
Q Consensus 4 nflqagslvatgflekifvgnfldslsfpcfig 36 (45)
|.|--|---.+.||++.|.... -+||||+-
T Consensus 258 nLLFYG~GSK~~fL~~f~~~~L---P~~P~~~l 287 (535)
T COG5575 258 NLLFYGYGSKTAFLRKFFPSAL---PCFPIFYL 287 (535)
T ss_pred EEEEEECCCHHHHHHHHHHHHC---CCCCEEEE
T ss_conf 0899853736889999767745---77514666
No 8
>pfam11090 DUF2833 Protein of unknown function (DUF2833). This family of proteins with unknown function are found in the bacteriophage T7. Some of the members of this family are annotated as gene 13 protein.
Probab=10.65 E-value=89 Score=15.58 Aligned_cols=18 Identities=22% Similarity=0.233 Sum_probs=11.7
Q ss_pred HCCCCEEEEECCCEEEEC
Q ss_conf 126632112022213419
Q 537021.9.peg.2 28 SLSFPCFIGISCGACIFF 45 (45)
Q Consensus 28 slsfpcfigiscgaciff 45 (45)
.-.+|--||=+||.|+.|
T Consensus 7 ~~g~~~aiGGn~gd~vWF 24 (86)
T pfam11090 7 LGGLVLAIGGNQGDQVWF 24 (86)
T ss_pred ECCEEEEECCCCCCEEEE
T ss_conf 187899863776876999
No 9
>cd04912 ACT_AKiii-LysC-EC-like_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC) and plants, (Zea mays Ask1, Ask2, and Arabidopsis thaliana AK1). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Like the A. thaliana AK1 (AK1-AT), the E. coli AKIII (LysC) has two bound feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The lysine-sensitive plant isoenzyme is synergistically inhibited by S-adenosylmethionine. A homolog of this group appears to be the Saccharomyces cerevisiae AK (Hom3) which clusters with this group as well. Members of this CD
Probab=9.62 E-value=1.6e+02 Score=14.32 Aligned_cols=20 Identities=40% Similarity=0.581 Sum_probs=14.3
Q ss_pred CEEECCCCHHHHHHHHHHHH
Q ss_conf 10110121355667788767
Q 537021.9.peg.2 3 INFLQAGSLVATGFLEKIFV 22 (45)
Q Consensus 3 inflqagslvatgflekifv 22 (45)
||.--.+-+-+.|||.++|-
T Consensus 4 i~i~s~~m~~~~GFLa~vF~ 23 (75)
T cd04912 4 LNIKSNRMLGAHGFLAKVFE 23 (75)
T ss_pred EEEECCCHHHHCCHHHHHHH
T ss_conf 99845646656328999999
No 10
>cd04933 ACT_AK1-AT_1 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the first of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine. This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. Like the Escherichia coli AKIII (LysC), Arabidopsis AK1 binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. A loop in common is involved in the binding of both Lys and S-adenosylmethionine providing an explanation for the synergistic inhibition by these effectors. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=9.61 E-value=1.5e+02 Score=14.44 Aligned_cols=19 Identities=32% Similarity=0.506 Sum_probs=13.1
Q ss_pred EEECCCCHHHHHHHHHHHH
Q ss_conf 0110121355667788767
Q 537021.9.peg.2 4 NFLQAGSLVATGFLEKIFV 22 (45)
Q Consensus 4 nflqagslvatgflekifv 22 (45)
+.-...-+-+.|||.|+|-
T Consensus 5 ~i~S~rMl~a~GFLa~VF~ 23 (78)
T cd04933 5 DITSTRMLGQYGFLAKVFS 23 (78)
T ss_pred EEECHHHHHHCCHHHHHHH
T ss_conf 9834116777445999999
Done!