Citrus Sinensis ID: 031564

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------
Protein Sequence
MQKAKSLDKFSRSALSPLMSNSKESLGVAKFASIGVNSLKGGNLDYTREKKFSRKQVRNVSCTNLNGYLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALFSE
Secondary Structure (PSIPRED)
ccHHHHHHHccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccHHHHHHcccccccEEEEEEccccccccccccccHHHHHHHHHHHHHccccEEEEEcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHcHccHccccccccccccccccccccccccccccccccHccccccccccccEccccccHHHHHHHccccccccHHHHHHHcHHHccccccEEEEEEEcccccccccccccccHHHHHHHHHHHHccccEEEEEEccccccHHHHHHHHHcc
Coil and Loop (DISEMBL)
mqkaksldkfsrsalsplmsnskeslgVAKFASIGVnslkggnldytrEKKFSRKQVRNvsctnlngylskahysssctdnstkDLTSkllgrvpgfVKIVevgprdglqneknivPAVVKVELIKLLVssglpvveatsfvspkwvpqVADALFSE
Flexible Loop (DISEMBL)
mqkaksldkfsrsalsplmsnskeSLGVAKFAsigvnslkggnldytrekkfsrkqvrnvscTNLNGYLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVevgprdglqnekniVPAVVKVELIKLLVSSGLPVveatsfvspkwvpQVADALFSE
Low Complexity Region (SEG)
MQKAKSLDKFSRSALSPLMSNSKESLGVAKFASIGVNSLKGGNLDYTREKKFSRKQVRNVSCTNLNGYLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALFSE
Disordered region (IsUnstruct)
***************************VAKFASIGVNSLKGGNLDYTREKKFSRKQVRNVSCTNLNGYLSKAHYSSSCT****KDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA****
Disordered Region (DISOPRED)
*********FS**************LG************************FSRKQVRN***T*****************************RVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALFS*
Disordered Region (DISEMBL)
***********RSALSPLMSNSKESLGVAKFASIGVNSLKGGNLDYTREKKFSRKQVRNVSCTNLNGYLSKAH**********KDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALFSE
Disordered Region (DISPRO)
****************************AKFASIGV*****************RKQVRNVSCTNLNGYLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALFS*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooo
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MQKAKSLDKFSRSALSPLMSNSKESLGVAKFASIGVNSLKGGNLDYTREKKFSRKQVRNVSCTNLNGYLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALFSE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	157	2.2.26 [Sep-21-2011]
O81027	468	Hydroxymethylglutaryl-CoA	yes	no	0.687	0.230	0.550	4e-27
Q29448	325	Hydroxymethylglutaryl-CoA	yes	no	0.394	0.190	0.758	4e-21
P38060	325	Hydroxymethylglutaryl-CoA	yes	no	0.458	0.221	0.638	5e-21
P97519	325	Hydroxymethylglutaryl-CoA	yes	no	0.394	0.190	0.725	8e-21
A8WG57	335	3-hydroxymethyl-3-methylg	no	no	0.394	0.185	0.709	4e-19
P35915	298	Hydroxymethylglutaryl-CoA	yes	no	0.369	0.194	0.706	5e-19
Q8HXZ6	325	Hydroxymethylglutaryl-CoA	N/A	no	0.452	0.218	0.619	1e-18
Q5R9E1	325	Hydroxymethylglutaryl-CoA	yes	no	0.452	0.218	0.605	1e-18
P35914	325	Hydroxymethylglutaryl-CoA	yes	no	0.452	0.218	0.605	1e-18
Q8TB92	370	3-hydroxymethyl-3-methylg	no	no	0.414	0.175	0.666	1e-17

>sp|O81027|HMGCL_ARATH Hydroxymethylglutaryl-CoA lyase, mitochondrial OS=Arabidopsis thaliana GN=HMGCL PE=1 SV=2

 Score =  120 bits (301), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 65/118 (55%), Positives = 82/118 (69%), Gaps = 10/118 (8%)

Query: 46  YTREKKFSRKQVRNVS----CTNLNGYLSKAH------YSSSCTDNSTKDLTSKLLGRVP 95
           +TR+        RN+S     + ++G L ++       YS+   +N T  +++K+   +P
Sbjct: 106 HTRKLSEGEHMFRNISFAGRTSTVSGTLRESKSFKEQKYSTFSNENGTSHISNKISKGIP 165

Query: 96  GFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
            FVKIVEVGPRDGLQNEKNIVP  VKVELI+ LVSSGLPVVEATSFVSPKWVPQ+ADA
Sbjct: 166 KFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPKWVPQLADA 223

Involved in the catabolism of branched amino acids such as leucine.
Arabidopsis thaliana (taxid: 3702)
EC: 4EC: .EC: 1EC: .EC: 3EC: .EC: 4

>sp|Q29448|HMGCL_BOVIN Hydroxymethylglutaryl-CoA lyase, mitochondrial OS=Bos taurus GN=HMGCL PE=2 SV=2

 Score =  100 bits (249), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 47/62 (75%), Positives = 53/62 (85%)

Query: 91  LGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQV 150
           +G  P  VKIVEVGPRDGLQNEKNIVP  VK++LI +L  +GLPVVEATSFVSPKWVPQ+
Sbjct: 26  VGTFPKQVKIVEVGPRDGLQNEKNIVPTPVKIKLIDMLSEAGLPVVEATSFVSPKWVPQM 85

Query: 151 AD 152
           AD
Sbjct: 86  AD 87

Key enzyme in ketogenesis (ketone body formation). Terminal step in leucine catabolism.

Bos taurus (taxid: 9913)

EC: 4

EC: .

EC: 1

EC: .

EC: 3

EC: .

EC: 4

>sp|P38060|HMGCL_MOUSE Hydroxymethylglutaryl-CoA lyase, mitochondrial OS=Mus musculus GN=Hmgcl PE=1 SV=2

 Score =  100 bits (248), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 46/72 (63%), Positives = 58/72 (80%)

Query: 81  NSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS 140
            S + +++  +G +P  VKIVEVGPRDGLQNEK+IVP  VK+ LI +L  +GLPV+EATS
Sbjct: 16  TSLRAVSTSSMGTLPKQVKIVEVGPRDGLQNEKSIVPTPVKIRLIDMLSEAGLPVIEATS 75

Query: 141 FVSPKWVPQVAD 152
           FVSPKWVPQ+AD
Sbjct: 76  FVSPKWVPQMAD 87

Key enzyme in ketogenesis (ketone body formation). Terminal step in leucine catabolism.

Mus musculus (taxid: 10090)

EC: 4

EC: .

EC: 1

EC: .

EC: 3

EC: .

EC: 4

>sp|P97519|HMGCL_RAT Hydroxymethylglutaryl-CoA lyase, mitochondrial OS=Rattus norvegicus GN=Hmgcl PE=2 SV=1

 Score = 99.4 bits (246), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 45/62 (72%), Positives = 54/62 (87%)

Query: 91  LGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQV 150
           +G +P  VKIVEVGPRDGLQNEK+IVP  VK++LI +L  +GLPV+EATSFVSPKWVPQ+
Sbjct: 26  MGTLPKRVKIVEVGPRDGLQNEKSIVPTPVKIKLIDMLSEAGLPVIEATSFVSPKWVPQM 85

Query: 151 AD 152
           AD
Sbjct: 86  AD 87

Key enzyme in ketone body formation (ketogenesis). Terminal step in leucine catabolism.

Rattus norvegicus (taxid: 10116)

EC: 4

EC: .

EC: 1

EC: .

EC: 3

EC: .

EC: 4

>sp|A8WG57|HMGC2_DANRE 3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic OS=Danio rerio GN=hmgcll1 PE=2 SV=1

 Score = 93.6 bits (231), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 44/62 (70%), Positives = 52/62 (83%)

Query: 91  LGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQV 150
           L ++P +VKIVEVGPRDGLQNEK IVP  VK++LI LL  +GLPV+EATSFVS KWV Q+
Sbjct: 36  LPKLPVYVKIVEVGPRDGLQNEKEIVPTEVKIQLIDLLSQTGLPVIEATSFVSSKWVAQM 95

Query: 151 AD 152
           AD
Sbjct: 96  AD 97

Involved in the catabolism of branched amino acids such as leucine.

Danio rerio (taxid: 7955)

EC: 4

EC: .

EC: 1

EC: .

EC: 3

EC: .

EC: 4

>sp|P35915|HMGCL_CHICK Hydroxymethylglutaryl-CoA lyase, mitochondrial OS=Gallus gallus GN=HMGCL PE=1 SV=1

 Score = 93.6 bits (231), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 41/58 (70%), Positives = 50/58 (86%)

Query: 95  PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVAD 152
           P  VK+VEVGPRDGLQNEK++VP  VK+ LI +L  +GLPV+EATSFVSP+WVPQ+AD
Sbjct: 3   PQRVKVVEVGPRDGLQNEKSVVPTPVKIRLIDMLSETGLPVIEATSFVSPRWVPQMAD 60

Key enzyme in ketogenesis (ketone body formation). Terminal step in leucine catabolism.

Gallus gallus (taxid: 9031)

EC: 4

EC: .

EC: 1

EC: .

EC: 3

EC: .

EC: 4

>sp|Q8HXZ6|HMGCL_MACFA Hydroxymethylglutaryl-CoA lyase, mitochondrial OS=Macaca fascicularis GN=HMGCL PE=2 SV=1

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 44/71 (61%), Positives = 56/71 (78%)

Query: 82  STKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSF 141
           S + +++  +  +P  VKIVEVGPRDGLQNEKNIV   VK++LI +L  +GL V+EATSF
Sbjct: 17  SLRAVSTSSMDTLPKQVKIVEVGPRDGLQNEKNIVSTPVKIKLIDMLSEAGLSVIEATSF 76

Query: 142 VSPKWVPQVAD 152
           VSPKWVPQ+AD
Sbjct: 77  VSPKWVPQMAD 87

Key enzyme in ketogenesis (ketone body formation). Terminal step in leucine catabolism.

Macaca fascicularis (taxid: 9541)

EC: 4

EC: .

EC: 1

EC: .

EC: 3

EC: .

EC: 4

>sp|Q5R9E1|HMGCL_PONAB Hydroxymethylglutaryl-CoA lyase, mitochondrial OS=Pongo abelii GN=HMGCL PE=2 SV=1

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 43/71 (60%), Positives = 55/71 (77%)

Query: 82  STKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSF 141
           S + +++  +G +P  VKIVEVGPRDGLQNEKNIV   VK++LI +L  +GL V+E TSF
Sbjct: 17  SLRAVSTSSMGTLPKRVKIVEVGPRDGLQNEKNIVSTPVKIKLIDMLSEAGLSVIETTSF 76

Query: 142 VSPKWVPQVAD 152
           VSPKWVPQ+ D
Sbjct: 77  VSPKWVPQMGD 87

Key enzyme in ketogenesis (ketone body formation). Terminal step in leucine catabolism.

Pongo abelii (taxid: 9601)

EC: 4

EC: .

EC: 1

EC: .

EC: 3

EC: .

EC: 4

>sp|P35914|HMGCL_HUMAN Hydroxymethylglutaryl-CoA lyase, mitochondrial OS=Homo sapiens GN=HMGCL PE=1 SV=2

 Score = 92.0 bits (227), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 43/71 (60%), Positives = 55/71 (77%)

Query: 82  STKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSF 141
           S + +++  +G +P  VKIVEVGPRDGLQNEKNIV   VK++LI +L  +GL V+E TSF
Sbjct: 17  SLRAVSTSSMGTLPKRVKIVEVGPRDGLQNEKNIVSTPVKIKLIDMLSEAGLSVIETTSF 76

Query: 142 VSPKWVPQVAD 152
           VSPKWVPQ+ D
Sbjct: 77  VSPKWVPQMGD 87

Key enzyme in ketogenesis (ketone body formation). Terminal step in leucine catabolism.

Homo sapiens (taxid: 9606)

EC: 4

EC: .

EC: 1

EC: .

EC: 3

EC: .

EC: 4

>sp|Q8TB92|HMGC2_HUMAN 3-hydroxymethyl-3-methylglutaryl-CoA lyase, cytoplasmic OS=Homo sapiens GN=HMGCLL1 PE=1 SV=3

 Score = 89.0 bits (219), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 44/66 (66%), Positives = 52/66 (78%), Gaps = 1/66 (1%)

Query: 87  TSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKW 146
           TS+L G +P FVKIVEVGPRDGLQNEK IVP  +K+E I  L  +GL V+E TSFVS +W
Sbjct: 68  TSQLSG-LPEFVKIVEVGPRDGLQNEKVIVPTDIKIEFINRLSQTGLSVIEVTSFVSSRW 126

Query: 147 VPQVAD 152
           VPQ+AD
Sbjct: 127 VPQMAD 132

Involved in the catabolism of branched amino acids such as leucine.

Homo sapiens (taxid: 9606)

EC: 4

EC: .

EC: 1

EC: .

EC: 3

EC: .

EC: 4

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	157
297741659	398	unnamed protein product [Vitis vinifera]	0.738	0.291	0.579	9e-32
359481554	427	PREDICTED: hydroxymethylglutaryl-CoA lya	0.738	0.271	0.579	9e-32
255552523	377	hydroxymethylglutaryl-CoA lyase, putativ	0.547	0.228	0.720	6e-29
356571909	412	PREDICTED: hydroxymethylglutaryl-CoA lya	0.783	0.298	0.544	2e-28
224105993	429	predicted protein [Populus trichocarpa]	0.630	0.230	0.653	2e-27
147769707	268	hypothetical protein VITISV_010123 [Viti	0.910	0.533	0.441	3e-27
225435868	432	PREDICTED: hydroxymethylglutaryl-CoA lya	0.547	0.199	0.686	6e-27
356574064	435	PREDICTED: hydroxymethylglutaryl-CoA lya	0.974	0.351	0.414	1e-25
30683260	433	Hydroxymethylglutaryl-CoA lyase [Arabido	0.687	0.249	0.550	2e-25
18401240	468	Hydroxymethylglutaryl-CoA lyase [Arabido	0.687	0.230	0.550	2e-25

>gi|297741659|emb|CBI32791.3| unnamed protein product [Vitis vinifera]

 Score =  141 bits (356), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 80/138 (57%), Positives = 94/138 (68%), Gaps = 22/138 (15%)

Query: 36  VNSLKGGNLDYTREKKFSRKQVRNVSCTN-LN-------------------GYLSKAHYS 75
           ++S K  N +YT E    R+Q+RNVS  + LN                    YL+   YS
Sbjct: 19  LHSPKNSNYEYTEEVCPWRRQMRNVSRGDFLNRTPANMSRNHRVFRSVPDACYLTDRPYS 78

Query: 76  SSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPV 135
           S C D  T+D  +KLL  +PGFVKIVEVGPRDGLQNEK+IVP VVKVELIK+LVSSGLP+
Sbjct: 79  SHCNDECTRD--NKLLRSMPGFVKIVEVGPRDGLQNEKDIVPTVVKVELIKMLVSSGLPI 136

Query: 136 VEATSFVSPKWVPQVADA 153
           VEATSFVSPKWVPQ+ADA
Sbjct: 137 VEATSFVSPKWVPQLADA 154

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359481554|ref|XP_002282814.2| PREDICTED: hydroxymethylglutaryl-CoA lyase, mitochondrial [Vitis vinifera]

 Score =  141 bits (356), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 80/138 (57%), Positives = 94/138 (68%), Gaps = 22/138 (15%)

Query: 36  VNSLKGGNLDYTREKKFSRKQVRNVSCTN-LN-------------------GYLSKAHYS 75
           ++S K  N +YT E    R+Q+RNVS  + LN                    YL+   YS
Sbjct: 48  LHSPKNSNYEYTEEVCPWRRQMRNVSRGDFLNRTPANMSRNHRVFRSVPDACYLTDRPYS 107

Query: 76  SSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPV 135
           S C D  T+D  +KLL  +PGFVKIVEVGPRDGLQNEK+IVP VVKVELIK+LVSSGLP+
Sbjct: 108 SHCNDECTRD--NKLLRSMPGFVKIVEVGPRDGLQNEKDIVPTVVKVELIKMLVSSGLPI 165

Query: 136 VEATSFVSPKWVPQVADA 153
           VEATSFVSPKWVPQ+ADA
Sbjct: 166 VEATSFVSPKWVPQLADA 183

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255552523|ref|XP_002517305.1| hydroxymethylglutaryl-CoA lyase, putative [Ricinus communis] gi|223543568|gb|EEF45098.1| hydroxymethylglutaryl-CoA lyase, putative [Ricinus communis]

 Score =  132 bits (331), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 62/86 (72%), Positives = 70/86 (81%)

Query: 68  YLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKL 127
           +LS  HY+S   D S  D   KLL  VP +VKIVEVGPRDGLQNEK++VP  +KVELIK+
Sbjct: 48  HLSNRHYTSHSNDKSVGDFVDKLLRYVPEYVKIVEVGPRDGLQNEKDVVPTAIKVELIKM 107

Query: 128 LVSSGLPVVEATSFVSPKWVPQVADA 153
           LVSSGLPVVEATSFVSPKWVPQ+ADA
Sbjct: 108 LVSSGLPVVEATSFVSPKWVPQLADA 133

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356571909|ref|XP_003554113.1| PREDICTED: hydroxymethylglutaryl-CoA lyase, mitochondrial-like [Glycine max]

 Score =  130 bits (327), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 74/136 (54%), Positives = 88/136 (64%), Gaps = 13/136 (9%)

Query: 31  FASIGVNSLKGGNLDYTREKK--FSRKQVRNVS-CTNLNG----------YLSKAHYSSS 77
           F S GV S     +  TRE K  F +  V+ +S C N             Y+   H++S 
Sbjct: 33  FPSHGVESPHVREITNTREVKNDFDKYHVKGLSRCLNWTSRSNANSQASCYVVNRHFASD 92

Query: 78  CTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVE 137
           C D  +K+ +SKLL  +P +VKIVEVG RDGLQNEK I+P  VKVELIKLLVSSGL VVE
Sbjct: 93  CNDICSKEFSSKLLTSIPDYVKIVEVGARDGLQNEKAIIPTNVKVELIKLLVSSGLSVVE 152

Query: 138 ATSFVSPKWVPQVADA 153
           ATSFVSPKWVPQ+ADA
Sbjct: 153 ATSFVSPKWVPQLADA 168

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224105993|ref|XP_002314006.1| predicted protein [Populus trichocarpa] gi|222850414|gb|EEE87961.1| predicted protein [Populus trichocarpa]

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 66/101 (65%), Positives = 73/101 (72%), Gaps = 2/101 (1%)

Query: 53  SRKQVRNVSCTNLNGYLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNE 112
           S+  V   SC +   Y     YSS   D   +D+T+K L  +P FVKIVEVGPRDGLQNE
Sbjct: 87  SKNVVSGSSCDSR--YFPDHQYSSKSNDKDIRDITNKFLKGIPKFVKIVEVGPRDGLQNE 144

Query: 113 KNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
           KNIVP  VKVELI  LVSSGLPVVEATSFVSPKWVPQ+ADA
Sbjct: 145 KNIVPTDVKVELIHRLVSSGLPVVEATSFVSPKWVPQLADA 185

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147769707|emb|CAN74167.1| hypothetical protein VITISV_010123 [Vitis vinifera]

 Score =  126 bits (316), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 76/172 (44%), Positives = 93/172 (54%), Gaps = 29/172 (16%)

Query: 7   LDKFSRSALSPLMSNSKESLGVAKFASIGVNSLKGGNLD-----YTREKKFSRKQVRNVS 61
           L +FS +A  P      E +G+      G       N +     YTRE    ++Q R  S
Sbjct: 21  LQRFSSNACRP----RAEDMGMGSCWIDGRTCSSSNNCNEDYEGYTREAFQWKRQTRETS 76

Query: 62  ---------------C----TNLNGYLSKAH-YSSSCTDNSTKDLTSKLLGRVPGFVKIV 101
                          C    ++ + + S  H Y   C +   + + +K LG +P FVKIV
Sbjct: 77  QGDSLKRRTSSQGRSCMVYGSSCDSWYSSDHQYGFQCNNKGVRGMANKFLGGIPKFVKIV 136

Query: 102 EVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
           EVGPRDGLQNEKNIVP  VKVELI  LVS GLPVVEATSFVSPKWVPQ+ADA
Sbjct: 137 EVGPRDGLQNEKNIVPTAVKVELIHRLVSCGLPVVEATSFVSPKWVPQLADA 188

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225435868|ref|XP_002263865.1| PREDICTED: hydroxymethylglutaryl-CoA lyase, mitochondrial [Vitis vinifera] gi|296083893|emb|CBI24281.3| unnamed protein product [Vitis vinifera]

 Score =  125 bits (314), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 59/86 (68%), Positives = 65/86 (75%)

Query: 68  YLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKL 127
           Y S   Y   C +   + + +K LG +P FVKIVEVGPRDGLQNEKNIVP  VKVELI  
Sbjct: 103 YSSDHQYGFQCNNKGVRGMANKFLGGIPKFVKIVEVGPRDGLQNEKNIVPTAVKVELIHR 162

Query: 128 LVSSGLPVVEATSFVSPKWVPQVADA 153
           LVS GLPVVEATSFVSPKWVPQ+ADA
Sbjct: 163 LVSCGLPVVEATSFVSPKWVPQLADA 188

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356574064|ref|XP_003555172.1| PREDICTED: hydroxymethylglutaryl-CoA lyase, mitochondrial-like [Glycine max]

 Score =  120 bits (302), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 73/176 (41%), Positives = 95/176 (53%), Gaps = 23/176 (13%)

Query: 1   MQKAKSLDKFSRSALSPLMSNSKESLG---VAKFASIGVNSLKGGNLDYTREKKFSRKQV 57
           M     + +FS +A  P + N    LG   +   +    NS    + +YT E    R+Q 
Sbjct: 16  MSTIDRIQRFSSAACCPRVDNFNLGLGNCWIEGRSCSTSNSCNEDSEEYTEETFPWRRQR 75

Query: 58  RNVS--------------------CTNLNGYLSKAHYSSSCTDNSTKDLTSKLLGRVPGF 97
           R++S                      + + Y S   YS    +N+ +D+  K +  +P F
Sbjct: 76  RDLSRGDTFSQKSMTMGRNSMKFGMIDNSFYTSDYQYSPQNNNNNVQDMAYKFMKGIPNF 135

Query: 98  VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
           VKIVEVGPRDGLQNEKNIVP  VK+ELI  L SSGL V+EATSFVSPKWVPQ+ADA
Sbjct: 136 VKIVEVGPRDGLQNEKNIVPTDVKIELIHRLASSGLSVIEATSFVSPKWVPQLADA 191

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30683260|ref|NP_850087.1| Hydroxymethylglutaryl-CoA lyase [Arabidopsis thaliana] gi|22136060|gb|AAM91612.1| putative hydroxymethylglutaryl-CoA lyase [Arabidopsis thaliana] gi|23197746|gb|AAN15400.1| putative hydroxymethylglutaryl-CoA lyase [Arabidopsis thaliana] gi|330252794|gb|AEC07888.1| Hydroxymethylglutaryl-CoA lyase [Arabidopsis thaliana]

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 65/118 (55%), Positives = 82/118 (69%), Gaps = 10/118 (8%)

Query: 46  YTREKKFSRKQVRNVS----CTNLNGYLSKAH------YSSSCTDNSTKDLTSKLLGRVP 95
           +TR+        RN+S     + ++G L ++       YS+   +N T  +++K+   +P
Sbjct: 71  HTRKLSEGEHMFRNISFAGRTSTVSGTLRESKSFKEQKYSTFSNENGTSHISNKISKGIP 130

Query: 96  GFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
            FVKIVEVGPRDGLQNEKNIVP  VKVELI+ LVSSGLPVVEATSFVSPKWVPQ+ADA
Sbjct: 131 KFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPKWVPQLADA 188

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18401240|ref|NP_565629.1| Hydroxymethylglutaryl-CoA lyase [Arabidopsis thaliana] gi|75100042|sp|O81027.2|HMGCL_ARATH RecName: Full=Hydroxymethylglutaryl-CoA lyase, mitochondrial; Short=HL; Short=HMG-CoA lyase; AltName: Full=3-hydroxy-3-methylglutarate-CoA lyase gi|11935189|gb|AAG42010.1|AF327420_1 putative hydroxymethylglutaryl-CoA lyase [Arabidopsis thaliana] gi|13194812|gb|AAK15568.1|AF349521_1 putative hydroxymethylglutaryl-CoA lyase [Arabidopsis thaliana] gi|20197286|gb|AAC32247.2| putative hydroxymethylglutaryl-CoA lyase [Arabidopsis thaliana] gi|330252796|gb|AEC07890.1| Hydroxymethylglutaryl-CoA lyase [Arabidopsis thaliana]

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 65/118 (55%), Positives = 82/118 (69%), Gaps = 10/118 (8%)

Query: 46  YTREKKFSRKQVRNVS----CTNLNGYLSKAH------YSSSCTDNSTKDLTSKLLGRVP 95
           +TR+        RN+S     + ++G L ++       YS+   +N T  +++K+   +P
Sbjct: 106 HTRKLSEGEHMFRNISFAGRTSTVSGTLRESKSFKEQKYSTFSNENGTSHISNKISKGIP 165

Query: 96  GFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
            FVKIVEVGPRDGLQNEKNIVP  VKVELI+ LVSSGLPVVEATSFVSPKWVPQ+ADA
Sbjct: 166 KFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPKWVPQLADA 223

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	157
TAIR|locus:2039548	468	AT2G26800 [Arabidopsis thalian	0.687	0.230	0.567	1.1e-25
UNIPROTKB|Q29448	325	HMGCL "Hydroxymethylglutaryl-C	0.426	0.206	0.701	2.7e-20
MGI|MGI:96158	325	Hmgcl "3-hydroxy-3-methylgluta	0.452	0.218	0.647	3.5e-20
RGD|620554	325	Hmgcl "3-hydroxymethyl-3-methy	0.452	0.218	0.647	4.4e-20
UNIPROTKB|I3LIL5	325	HMGCL "Uncharacterized protein	0.452	0.218	0.605	1.9e-19
ZFIN|ZDB-GENE-040426-958	340	hmgcl "3-hydroxymethyl-3-methy	0.375	0.173	0.745	6.5e-19
DICTYBASE|DDB_G0283813	406	hmgL "hydroxymethylglutaryl-Co	0.649	0.251	0.504	8.8e-19
ZFIN|ZDB-GENE-080220-15	335	hmgcll1 "3-hydroxymethyl-3-met	0.394	0.185	0.709	1.4e-18
UNIPROTKB|F1NWD1	298	HMGCL "Hydroxymethylglutaryl-C	0.369	0.194	0.706	2.2e-18
UNIPROTKB|F1P1E7	301	HMGCL "Hydroxymethylglutaryl-C	0.369	0.192	0.706	2.2e-18

TAIR|locus:2039548 AT2G26800 [Arabidopsis thaliana (taxid:3702)]

 Score = 294 (108.6 bits), Expect = 1.1e-25, P = 1.1e-25
 Identities = 67/118 (56%), Positives = 83/118 (70%)

Query:    46 YTREKKFSRKQVRNVS----CTNLNGYL--SKAH----YSSSCTDNSTKDLTSKLLGRVP 95
             +TR+        RN+S     + ++G L  SK+     YS+   +N T  +++K+   +P
Sbjct:   106 HTRKLSEGEHMFRNISFAGRTSTVSGTLRESKSFKEQKYSTFSNENGTSHISNKISKGIP 165

Query:    96 GFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
              FVKIVEVGPRDGLQNEKNIVP  VKVELI+ LVSSGLPVVEATSFVSPKWVPQ+ADA
Sbjct:   166 KFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPKWVPQLADA 223

GO:0003824 "catalytic activity" evidence=IEA

GO:0004419 "hydroxymethylglutaryl-CoA lyase activity" evidence=ISS;IDA

GO:0005739 "mitochondrion" evidence=ISM;IDA

GO:0006551 "leucine metabolic process" evidence=ISS

UNIPROTKB|Q29448 HMGCL "Hydroxymethylglutaryl-CoA lyase, mitochondrial" [Bos taurus (taxid:9913)]

 Score = 240 (89.5 bits), Expect = 2.7e-20, P = 2.7e-20
 Identities = 47/67 (70%), Positives = 56/67 (83%)

Query:    86 LTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPK 145
             +++  +G  P  VKIVEVGPRDGLQNEKNIVP  VK++LI +L  +GLPVVEATSFVSPK
Sbjct:    21 VSTSSVGTFPKQVKIVEVGPRDGLQNEKNIVPTPVKIKLIDMLSEAGLPVVEATSFVSPK 80

Query:   146 WVPQVAD 152
             WVPQ+AD
Sbjct:    81 WVPQMAD 87

GO:0046951 "ketone body biosynthetic process" evidence=ISS

GO:0004419 "hydroxymethylglutaryl-CoA lyase activity" evidence=ISS

GO:0046872 "metal ion binding" evidence=ISS

GO:0005777 "peroxisome" evidence=IEA

GO:0005759 "mitochondrial matrix" evidence=IEA

GO:0051262 "protein tetramerization" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0030145 "manganese ion binding" evidence=IEA

GO:0009790 "embryo development" evidence=IEA

GO:0007005 "mitochondrion organization" evidence=IEA

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0005102 "receptor binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

MGI|MGI:96158 Hmgcl "3-hydroxy-3-methylglutaryl-Coenzyme A lyase" [Mus musculus (taxid:10090)]

 Score = 239 (89.2 bits), Expect = 3.5e-20, P = 3.5e-20
 Identities = 46/71 (64%), Positives = 58/71 (81%)

Query:    82 STKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSF 141
             S + +++  +G +P  VKIVEVGPRDGLQNEK+IVP  VK+ LI +L  +GLPV+EATSF
Sbjct:    17 SLRAVSTSSMGTLPKQVKIVEVGPRDGLQNEKSIVPTPVKIRLIDMLSEAGLPVIEATSF 76

Query:   142 VSPKWVPQVAD 152
             VSPKWVPQ+AD
Sbjct:    77 VSPKWVPQMAD 87

GO:0000062 "fatty-acyl-CoA binding" evidence=ISO

GO:0000287 "magnesium ion binding" evidence=ISO

GO:0003824 "catalytic activity" evidence=IEA

GO:0004419 "hydroxymethylglutaryl-CoA lyase activity" evidence=ISO

GO:0005102 "receptor binding" evidence=ISO

GO:0005739 "mitochondrion" evidence=ISO;IDA

GO:0005743 "mitochondrial inner membrane" evidence=IDA

GO:0005777 "peroxisome" evidence=ISO

GO:0006637 "acyl-CoA metabolic process" evidence=ISO

GO:0007005 "mitochondrion organization" evidence=IMP

GO:0009790 "embryo development" evidence=IMP

GO:0016829 "lyase activity" evidence=IEA

GO:0030145 "manganese ion binding" evidence=ISO

GO:0031406 "carboxylic acid binding" evidence=ISO

GO:0042803 "protein homodimerization activity" evidence=ISO

GO:0046872 "metal ion binding" evidence=ISO

GO:0046951 "ketone body biosynthetic process" evidence=ISO

GO:0051262 "protein tetramerization" evidence=ISO

RGD|620554 Hmgcl "3-hydroxymethyl-3-methylglutaryl-CoA lyase" [Rattus norvegicus (taxid:10116)]

 Score = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 46/71 (64%), Positives = 58/71 (81%)

Query:    82 STKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSF 141
             S +  ++  +G +P  VKIVEVGPRDGLQNEK+IVP  VK++LI +L  +GLPV+EATSF
Sbjct:    17 SLRAASTSSMGTLPKRVKIVEVGPRDGLQNEKSIVPTPVKIKLIDMLSEAGLPVIEATSF 76

Query:   142 VSPKWVPQVAD 152
             VSPKWVPQ+AD
Sbjct:    77 VSPKWVPQMAD 87

GO:0000062 "fatty-acyl-CoA binding" evidence=IPI

GO:0000287 "magnesium ion binding" evidence=IEA;ISO

GO:0001889 "liver development" evidence=IEP

GO:0004419 "hydroxymethylglutaryl-CoA lyase activity" evidence=ISO;ISS;IDA

GO:0005102 "receptor binding" evidence=IEA;ISO

GO:0005739 "mitochondrion" evidence=ISO;IDA

GO:0005743 "mitochondrial inner membrane" evidence=IEA;ISO

GO:0005759 "mitochondrial matrix" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA;ISO

GO:0006637 "acyl-CoA metabolic process" evidence=IDA

GO:0007005 "mitochondrion organization" evidence=IEA;ISO

GO:0007584 "response to nutrient" evidence=IEP

GO:0009790 "embryo development" evidence=IEA;ISO

GO:0030145 "manganese ion binding" evidence=IEA;ISO

GO:0031406 "carboxylic acid binding" evidence=IPI

GO:0042594 "response to starvation" evidence=IEP

GO:0042803 "protein homodimerization activity" evidence=IEA;ISO

GO:0046872 "metal ion binding" evidence=ISO;ISS

GO:0046951 "ketone body biosynthetic process" evidence=ISO;IDA

GO:0051262 "protein tetramerization" evidence=IEA;ISO

GO:0070542 "response to fatty acid" evidence=IEP

UNIPROTKB|I3LIL5 HMGCL "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 43/71 (60%), Positives = 56/71 (78%)

Query:    82 STKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSF 141
             S + +++  +G  P  VKIVEVGPRDGLQNEKNI+P   K++L+ +L  +GLPV+E TSF
Sbjct:    17 SLRAVSTSSVGTFPKRVKIVEVGPRDGLQNEKNIIPTPTKIKLVDMLSETGLPVIEVTSF 76

Query:   142 VSPKWVPQVAD 152
             VSPKWVPQ+AD
Sbjct:    77 VSPKWVPQMAD 87

GO:0051262 "protein tetramerization" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0030145 "manganese ion binding" evidence=IEA

GO:0009790 "embryo development" evidence=IEA

GO:0007005 "mitochondrion organization" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0005102 "receptor binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0004419 "hydroxymethylglutaryl-CoA lyase activity" evidence=IEA

ZFIN|ZDB-GENE-040426-958 hmgcl "3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase (hydroxymethylglutaricaciduria)" [Danio rerio (taxid:7955)]

 Score = 227 (85.0 bits), Expect = 6.5e-19, P = 6.5e-19
 Identities = 44/59 (74%), Positives = 50/59 (84%)

Query:    94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVAD 152
             +P  VKIVEVGPRDGLQNEK IVP  VK+ LI +L  +GLPV+EATSFVSPKWVPQ+AD
Sbjct:    44 LPERVKIVEVGPRDGLQNEKTIVPTEVKIRLIDMLSEAGLPVIEATSFVSPKWVPQMAD 102

GO:0004419 "hydroxymethylglutaryl-CoA lyase activity" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0016829 "lyase activity" evidence=IEA

DICTYBASE|DDB_G0283813 hmgL "hydroxymethylglutaryl-CoA lyase" [Dictyostelium discoideum (taxid:44689)]

 Score = 230 (86.0 bits), Expect = 8.8e-19, P = 8.8e-19
 Identities = 53/105 (50%), Positives = 68/105 (64%)

Query:    50 KKFSR--KQVRNVSCTNLNGYLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRD 107
             K FS+  K +  +   N N   +    +++  +N  K   ++  G  P +VKIVEVGPRD
Sbjct:     5 KIFSKATKSILTLGIKNNNINRTFISLNNNNKENEFKRFQNRF-GPFPEYVKIVEVGPRD 63

Query:   108 GLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVAD 152
             GLQNEK IVP V K++LI  L  +GL VVEATSFVSPKWVPQ+AD
Sbjct:    64 GLQNEKIIVPTVDKIQLINRLAQTGLSVVEATSFVSPKWVPQMAD 108

GO:0008152 "metabolic process" evidence=IEA

GO:0004419 "hydroxymethylglutaryl-CoA lyase activity" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0016829 "lyase activity" evidence=IEA

ZFIN|ZDB-GENE-080220-15 hmgcll1 "3-hydroxymethyl-3-methylglutaryl-CoA lyase-like 1" [Danio rerio (taxid:7955)]

 Score = 224 (83.9 bits), Expect = 1.4e-18, P = 1.4e-18
 Identities = 44/62 (70%), Positives = 52/62 (83%)

Query:    91 LGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQV 150
             L ++P +VKIVEVGPRDGLQNEK IVP  VK++LI LL  +GLPV+EATSFVS KWV Q+
Sbjct:    36 LPKLPVYVKIVEVGPRDGLQNEKEIVPTEVKIQLIDLLSQTGLPVIEATSFVSSKWVAQM 95

Query:   151 AD 152
             AD
Sbjct:    96 AD 97

GO:0003824 "catalytic activity" evidence=IEA

GO:0004419 "hydroxymethylglutaryl-CoA lyase activity" evidence=IEA;ISS

GO:0048471 "perinuclear region of cytoplasm" evidence=ISS

GO:0046951 "ketone body biosynthetic process" evidence=ISS

GO:0005829 "cytosol" evidence=ISS

GO:0016020 "membrane" evidence=IEA;ISS

GO:0046872 "metal ion binding" evidence=IEA;ISS

GO:0005783 "endoplasmic reticulum" evidence=IEA;ISS

GO:0005737 "cytoplasm" evidence=IEA

GO:0016829 "lyase activity" evidence=IEA

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA

UNIPROTKB|F1NWD1 HMGCL "Hydroxymethylglutaryl-CoA lyase, mitochondrial" [Gallus gallus (taxid:9031)]

 Score = 222 (83.2 bits), Expect = 2.2e-18, P = 2.2e-18
 Identities = 41/58 (70%), Positives = 50/58 (86%)

Query:    95 PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVAD 152
             P  VK+VEVGPRDGLQNEK++VP  VK+ LI +L  +GLPV+EATSFVSP+WVPQ+AD
Sbjct:     3 PQRVKVVEVGPRDGLQNEKSVVPTPVKIRLIDMLSETGLPVIEATSFVSPRWVPQMAD 60

GO:0004419 "hydroxymethylglutaryl-CoA lyase activity" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0005102 "receptor binding" evidence=IEA

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA

GO:0007005 "mitochondrion organization" evidence=IEA

GO:0009790 "embryo development" evidence=IEA

GO:0030145 "manganese ion binding" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0051262 "protein tetramerization" evidence=IEA

UNIPROTKB|F1P1E7 HMGCL "Hydroxymethylglutaryl-CoA lyase, mitochondrial" [Gallus gallus (taxid:9031)]

 Score = 222 (83.2 bits), Expect = 2.2e-18, P = 2.2e-18
 Identities = 41/58 (70%), Positives = 50/58 (86%)

Query:    95 PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVAD 152
             P  VK+VEVGPRDGLQNEK++VP  VK+ LI +L  +GLPV+EATSFVSP+WVPQ+AD
Sbjct:     6 PQRVKVVEVGPRDGLQNEKSVVPTPVKIRLIDMLSETGLPVIEATSFVSPRWVPQMAD 63

GO:0004419 "hydroxymethylglutaryl-CoA lyase activity" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0005102 "receptor binding" evidence=IEA

GO:0005743 "mitochondrial inner membrane" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA

GO:0007005 "mitochondrion organization" evidence=IEA

GO:0009790 "embryo development" evidence=IEA

GO:0030145 "manganese ion binding" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0051262 "protein tetramerization" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	157
PLN02746	347	PLN02746, PLN02746, hydroxymethylglutaryl-CoA lyas	2e-41
cd07938	274	cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-	3e-31
PRK05692	287	PRK05692, PRK05692, hydroxymethylglutaryl-CoA lyas	2e-29
cd03174	265	cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyas	7e-17
COG0119	409	COG0119, LeuA, Isopropylmalate/homocitrate/citrama	5e-09
pfam00682	236	pfam00682, HMGL-like, HMGL-like	5e-06

>gnl|CDD|178347 PLN02746, PLN02746, hydroxymethylglutaryl-CoA lyase

 Score =  140 bits (355), Expect = 2e-41
 Identities = 60/86 (69%), Positives = 67/86 (77%)

Query: 68  YLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKL 127
              +  YSSS  +     + +KLL  +P FVKIVEVGPRDGLQNEKNIVP  VKVELI+ 
Sbjct: 17  SFKEHQYSSSSNEVGVAHMHNKLLKGLPKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQR 76

Query: 128 LVSSGLPVVEATSFVSPKWVPQVADA 153
           LVSSGLPVVEATSFVSPKWVPQ+ADA
Sbjct: 77  LVSSGLPVVEATSFVSPKWVPQLADA 102

Length = 347

>gnl|CDD|163676 cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain

 Score =  112 bits (283), Expect = 3e-31
 Identities = 37/54 (68%), Positives = 43/54 (79%)

Query: 100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
           IVEVGPRDGLQNEK  +P   K+ELI  L ++GL  +E TSFVSPKWVPQ+ADA
Sbjct: 1   IVEVGPRDGLQNEKTFIPTEDKIELIDALSAAGLRRIEVTSFVSPKWVPQMADA 54

3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes the cleavage of HMG-CoA to acetyl-CoA and acetoacetate, one of the terminal steps in ketone body generation and leucine degradation, and is a key enzyme in the pathway that supplies metabolic fuel to extrahepatic tissues. Mutations in HMGL cause a human autosomal recessive disorder called primary metabolic aciduria that affects ketogenesis and leucine catabolism and can be fatal due to an inability to tolerate hypoglycemia. HMGL has a TIM barrel domain with a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. The cleavage of HMG-CoA requires the presence of a divalent cation like Mg2+ or Mn2+, and the reaction is thought to involve general acid/base catalysis. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM". Length = 274

>gnl|CDD|180206 PRK05692, PRK05692, hydroxymethylglutaryl-CoA lyase; Provisional

 Score =  108 bits (271), Expect = 2e-29
 Identities = 38/59 (64%), Positives = 44/59 (74%)

Query: 95  PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
           P  VKIVEVGPRDGLQNEK  +P   K+ LI  L ++GL  +E  SFVSPKWVPQ+ADA
Sbjct: 2   PKRVKIVEVGPRDGLQNEKRFIPTADKIALIDRLSAAGLSYIEVASFVSPKWVPQMADA 60

Length = 287

>gnl|CDD|163674 cd03174, DRE_TIM_metallolyase, DRE-TIM metallolyase superfamily

 Score = 74.4 bits (184), Expect = 7e-17
 Identities = 19/53 (35%), Positives = 28/53 (52%)

Query: 101 VEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
            +   RDGLQ+E        K+E+ + L  +G+  +E  S  SPK VPQ+ D 
Sbjct: 1   TDTTLRDGLQSEGATFSTEDKLEIAEALDEAGVDSIEVGSGASPKAVPQMEDD 53

The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM". Length = 265

>gnl|CDD|223197 COG0119, LeuA, Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]

 Score = 53.4 bits (129), Expect = 5e-09
 Identities = 14/57 (24%), Positives = 22/57 (38%)

Query: 98  VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADAL 154
           V I +   RDG Q          K+ + K L   G+  +EA   V+     +   A+
Sbjct: 3   VIIFDTTLRDGEQAPGVSFSVEEKIRIAKALDDLGVDYIEAGFPVASPGDFEFVRAI 59

Length = 409

>gnl|CDD|201390 pfam00682, HMGL-like, HMGL-like

 Score = 44.2 bits (105), Expect = 5e-06
 Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 1/48 (2%)

Query: 107 DGLQNEKNIVPAVVKVELIKLLVSSGLPVVEAT-SFVSPKWVPQVADA 153
           DG Q          K+ + + L  +G+  +E    F+SP     V   
Sbjct: 1   DGEQALGAAFSVEEKLAIARALDEAGVDEIEVGFPFMSPTDFESVRAI 48

This family contains a diverse set of enzymes. These include various aldolases and a region of pyruvate carboxylase. Length = 236

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	157
KOG2368	316	consensus Hydroxymethylglutaryl-CoA lyase [Energy	99.94
PLN02746	347	hydroxymethylglutaryl-CoA lyase	99.91
PRK05692	287	hydroxymethylglutaryl-CoA lyase; Provisional	99.79
cd07938	274	DRE_TIM_HMGL 3-hydroxy-3-methylglutaryl-CoA lyase,	99.72
cd07945	280	DRE_TIM_CMS Leptospira interrogans citramalate syn	99.56
cd07948	262	DRE_TIM_HCS Saccharomyces cerevisiae homocitrate s	99.48
cd07942	284	DRE_TIM_LeuA Mycobacterium tuberculosis LeuA3 and	99.4
cd07941	273	DRE_TIM_LeuA3 Desulfobacterium autotrophicum LeuA3	99.39
cd07947	279	DRE_TIM_Re_CS Clostridium kluyveri Re-citrate synt	99.36
cd03174	265	DRE_TIM_metallolyase DRE-TIM metallolyase superfam	99.34
PLN02321	632	2-isopropylmalate synthase	99.34
PRK03739	552	2-isopropylmalate synthase; Validated	99.33
COG0119	409	LeuA Isopropylmalate/homocitrate/citramalate synth	99.33
PLN03228	503	methylthioalkylmalate synthase; Provisional	99.32
TIGR02090	363	LEU1_arch isopropylmalate/citramalate/homocitrate	99.31
PRK11858	378	aksA trans-homoaconitate synthase; Reviewed	99.27
TIGR00970	564	leuA_yeast 2-isopropylmalate synthase, yeast type.	99.26
TIGR00977	526	LeuA_rel 2-isopropylmalate synthase/homocitrate sy	99.26
cd07943	263	DRE_TIM_HOA 4-hydroxy-2-oxovalerate aldolase, N-te	99.25
cd07940	268	DRE_TIM_IPMS 2-isopropylmalate synthase (IPMS), N-	99.23
PRK12344	524	putative alpha-isopropylmalate/homocitrate synthas	99.22
PRK09389	488	(R)-citramalate synthase; Provisional	99.21
PRK00915	513	2-isopropylmalate synthase; Validated	99.18
TIGR02660	365	nifV_homocitr homocitrate synthase NifV. This fami	99.13
TIGR00973	494	leuA_bact 2-isopropylmalate synthase, bacterial ty	99.08
TIGR03217	333	4OH_2_O_val_ald 4-hydroxy-2-oxovalerate aldolase.	99.05
PRK12331	448	oxaloacetate decarboxylase; Provisional	98.99
PRK08195	337	4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic ac	98.99
PRK14041	467	oxaloacetate decarboxylase; Provisional	98.93
cd07939	259	DRE_TIM_NifV Streptomyces rubellomurinus FrbC and	98.89
TIGR02146	344	LysS_fung_arch homocitrate synthase. This model in	98.87
PRK14847	333	hypothetical protein; Provisional	98.73
TIGR01108	582	oadA oxaloacetate decarboxylase alpha subunit. Thi	98.69
PRK09282	592	pyruvate carboxylase subunit B; Validated	98.52
cd07937	275	DRE_TIM_PC_TC_5S Pyruvate carboxylase and Transcar	98.44
cd07944	266	DRE_TIM_HOA_like 4-hydroxy-2-oxovalerate aldolase-	98.32
PRK12330	499	oxaloacetate decarboxylase; Provisional	98.01
PRK14040	593	oxaloacetate decarboxylase; Provisional	98.01
KOG2367	560	consensus Alpha-isopropylmalate synthase/homocitra	97.9
PRK12581	468	oxaloacetate decarboxylase; Provisional	97.44
PRK12999	1146	pyruvate carboxylase; Reviewed	97.39
PRK14042	596	pyruvate carboxylase subunit B; Provisional	95.98
COG5016	472	Pyruvate/oxaloacetate carboxyltransferase [Energy	90.57
PF04481	242	DUF561: Protein of unknown function (DUF561); Inte	80.94

>KOG2368 consensus Hydroxymethylglutaryl-CoA lyase [Energy production and conversion; Amino acid transport and metabolism]

Probab=99.94  E-value=1.8e-27  Score=204.13  Aligned_cols=73  Identities=64%  Similarity=0.925  Sum_probs=69.7

Q ss_pred             cchhhHhhhhcCCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccC
Q 031564           82 STKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADAL  154 (157)
Q Consensus        82 ~~~~~~~~~~~~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~  154 (157)
                      ..+.++++.+...|++|+|+|||||||||||+.++||+.|++||++|+++|++.||.||||||||||||||+.
T Consensus         3 ~~~~~s~~a~~t~~~~vkiVEVGpRDGLQnEk~~vpt~vKveLI~~Lse~Gl~~vEtTSFVSpKWVPQl~D~~   75 (316)
T KOG2368|consen    3 PNRLLSNRAYSTAPKRVKIVEVGPRDGLQNEKNIVPTEVKVELIDRLSECGLQVVETTSFVSPKWVPQLADHN   75 (316)
T ss_pred             hhHHHHhhhhhcccceeEEEEecCcccccccCccCCchHHHHHHHHHHHcCCceeeeecccCccccccccchH
Confidence            4577889999999999999999999999999999999999999999999999999999999999999999963

>PLN02746 hydroxymethylglutaryl-CoA lyase

Probab=99.91  E-value=3.1e-25  Score=192.76  Aligned_cols=89  Identities=67%  Similarity=0.966  Sum_probs=86.4

Q ss_pred             ccccccccccCCCCcccchhhHhhhhcCCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCC
Q 031564           66 NGYLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPK  145 (157)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK  145 (157)
                      .|+++.+||++..+..+++.+++|+..+||++|+|+|||||||+|+++..+|+++|++|+++|.++||++||+|||||||
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~~~V~I~DtTlRDG~Q~~g~~~s~e~Ki~ia~~L~~~GV~~IEvGs~vspk   94 (347)
T PLN02746         15 SWSFKEHQYSSSSNEVGVAHMHNKLLKGLPKFVKIVEVGPRDGLQNEKNIVPTSVKVELIQRLVSSGLPVVEATSFVSPK   94 (347)
T ss_pred             ccchhhhccccccccccccccccchhhcCCCceEEEECCCCccCcCCCCCCCHHHHHHHHHHHHHcCCCEEEECCCcCcc
Confidence            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccccccC
Q 031564          146 WVPQVADAL  154 (157)
Q Consensus       146 ~VPQMADa~  154 (157)
                      |||||+|++
T Consensus        95 ~vPqmad~~  103 (347)
T PLN02746         95 WVPQLADAK  103 (347)
T ss_pred             cccccccHH
Confidence            999999863

>PRK05692 hydroxymethylglutaryl-CoA lyase; Provisional

Probab=99.79  E-value=1.4e-19  Score=152.17  Aligned_cols=60  Identities=63%  Similarity=1.016  Sum_probs=58.0

Q ss_pred             CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564           94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA  153 (157)
Q Consensus        94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa  153 (157)
                      ||..|.|+|++||||+|+++..+||++|++|++.|.++||++||+||||+|||+|||+|+
T Consensus         1 m~~~v~I~D~TlRDG~Q~~~~~~s~e~k~~ia~~L~~~Gv~~IEvgsf~~p~~~p~~~d~   60 (287)
T PRK05692          1 LPKRVKIVEVGPRDGLQNEKRFIPTADKIALIDRLSAAGLSYIEVASFVSPKWVPQMADA   60 (287)
T ss_pred             CCCceEEEECCCCccccCcCCCcCHHHHHHHHHHHHHcCCCEEEeCCCcCcccccccccH
Confidence            477899999999999999999999999999999999999999999999999999999986

>cd07938 DRE_TIM_HMGL 3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain

Probab=99.72  E-value=4.8e-18  Score=141.66  Aligned_cols=55  Identities=67%  Similarity=1.036  Sum_probs=53.4

Q ss_pred             EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccC
Q 031564          100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADAL  154 (157)
Q Consensus       100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~  154 (157)
                      |+|++||||+|+++..+|+++|+++++.|.++||++||+|||++||++|||+|.+
T Consensus         1 i~D~TlRDG~Q~~~~~~s~e~K~~i~~~L~~~Gv~~IEvGs~~~~~~~p~~~d~~   55 (274)
T cd07938           1 IVEVGPRDGLQNEKTFIPTEDKIELIDALSAAGLRRIEVTSFVSPKWVPQMADAE   55 (274)
T ss_pred             CeeCCCCCCCcCCCCCcCHHHHHHHHHHHHHcCCCEEEeCCCCCcccccccCCHH
Confidence            6899999999999999999999999999999999999999999999999999975

3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes the cleavage of HMG-CoA to acetyl-CoA and acetoacetate, one of the terminal steps in ketone body generation and leucine degradation, and is a key enzyme in the pathway that supplies metabolic fuel to extrahepatic tissues. Mutations in HMGL cause a human autosomal recessive disorder called primary metabolic aciduria that affects ketogenesis and leucine catabolism and can be fatal due to an inability to tolerate hypoglycemia. HMGL has a TIM barrel domain with a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. The cleavage of HMG-CoA requires the presence of a divalent cation like Mg2+ or Mn2+, and the reaction is thought to involve general acid/base catalysis. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropy

>cd07945 DRE_TIM_CMS Leptospira interrogans citramalate synthase (CMS) and related proteins, N-terminal catalytic TIM barrel domain

Probab=99.56  E-value=8e-16  Score=129.14  Aligned_cols=53  Identities=25%  Similarity=0.241  Sum_probs=49.9

Q ss_pred             EeccCccccCCCCCCCHHHHHHHHHHH-HhCCCCeeeeecc-cCC---CccccccccC
Q 031564          102 EVGPRDGLQNEKNIVPAVVKVELIKLL-VSSGLPVVEATSF-VSP---KWVPQVADAL  154 (157)
Q Consensus       102 EVGpRDGLQne~~~vpTe~KIeLI~~L-~~AGv~~IEvgSF-VsP---K~VPQMADa~  154 (157)
                      |||||||+|+++..+|+++|++|+++| .++||+.||+||| |||   ++||||+|+.
T Consensus         2 D~TlRDG~Q~~~~~~s~e~K~~i~~~L~~~~Gv~~IEvg~~~~s~~e~~av~~~~~~~   59 (280)
T cd07945           2 DTTLRDGEQTSGVSFSPSEKLNIAKILLQELKVDRIEVASARVSEGEFEAVQKIIDWA   59 (280)
T ss_pred             CCCCCCcCcCCCCccCHHHHHHHHHHHHHHhCCCEEEecCCCCCHHHHHHHHHHHHHh
Confidence            799999999999999999999999997 5669999999999 999   9999999853

Citramalate synthase (CMS) catalyzes the conversion of pyruvate and acetyl-CoA to (R)-citramalate in the first dedicated step of the citramalate pathway. Citramalate is only found in Leptospira interrogans and a few other microorganisms. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center con

>cd07948 DRE_TIM_HCS Saccharomyces cerevisiae homocitrate synthase and related proteins, catalytic TIM barrel domain

Probab=99.48  E-value=2.8e-14  Score=118.84  Aligned_cols=52  Identities=31%  Similarity=0.366  Sum_probs=50.1

Q ss_pred             EEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564           99 KIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA  153 (157)
Q Consensus        99 ~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa  153 (157)
                      .|.|||||||+|+++..+|+++|++|+++|.++||+.||+|+   |+++|||+++
T Consensus         2 ~I~D~TLRDG~Q~~~~~~s~~~k~~i~~~L~~~Gv~~IEvG~---P~~~~~~~~~   53 (262)
T cd07948           2 KIIDSTLREGEQFANAFFDTEDKIEIAKALDAFGVDYIELTS---PAASPQSRAD   53 (262)
T ss_pred             EEEECCCCCcCcCCCCCCCHHHHHHHHHHHHHcCCCEEEEEC---CCCCHHHHHH
Confidence            699999999999999999999999999999999999999997   9999999875

Homocitrate synthase (HCS) catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate, the first step in the lysine biosynthesis pathway. This family includes the Yarrowia lipolytica LYS1 protein as well as the Saccharomyces cerevisiae LYS20 and LYS21 proteins. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. Th

>cd07942 DRE_TIM_LeuA Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain

Probab=99.40  E-value=1.5e-13  Score=116.52  Aligned_cols=49  Identities=31%  Similarity=0.426  Sum_probs=46.4

Q ss_pred             EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccCC
Q 031564          100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALF  155 (157)
Q Consensus       100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~~  155 (157)
                      -++||||||+|+++..+|+++|++|+++|.++||++||+| |      |||+|+++
T Consensus         4 ~~d~tlRDG~Q~~g~~~s~~~Ki~ia~~L~~~Gv~~IE~g-f------P~~~~~e~   52 (284)
T cd07942           4 WCSVDLRDGNQALAEPMSVEQKLRFFKLLVKIGFKEIEVG-F------PSASQTDF   52 (284)
T ss_pred             ccCCCCCCcCCCCCCCCCHHHHHHHHHHHHHcCCCEEEEe-C------CCCCHHHH
Confidence            4689999999999999999999999999999999999999 7      99999874

Alpha-isopropylmalate synthase (LeuA), a key enzyme in leucine biosynthesis, catalyzes the first committed step in the pathway, converting acetyl-CoA and alpha-ketoisovalerate to alpha-isopropyl malate and CoA. Although the reaction catalyzed by LeuA is similar to that of the Arabidopsis thaliana IPMS1 protein, the two fall into phylogenetically distinct families within the same superfamily. LeuA has and N-terminal TIM barrel catalytic domain, a helical linker domain, and a C-terminal regulatory domain. LeuA forms a homodimer in which the linker domain of one monomer sits over the catalytic domain of the other, inserting residues into the active site that may be important for catalysis. Homologs of LeuA are found in bacteria as well as fungi. This family includes alpha-isopropylmalate synthases I (LEU4) and II (LEU9) from Saccharomyces cerevisiae. This family belong

>cd07941 DRE_TIM_LeuA3 Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain

Probab=99.39  E-value=1.6e-13  Score=113.69  Aligned_cols=52  Identities=23%  Similarity=0.213  Sum_probs=50.0

Q ss_pred             EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec-ccCCCccc------ccc
Q 031564          100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS-FVSPKWVP------QVA  151 (157)
Q Consensus       100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS-FVsPK~VP------QMA  151 (157)
                      |.|||||||+|+++..+++++|++++++|.++||++||+|+ |++|+.+|      ||+
T Consensus         1 i~D~TLRDG~Q~~~~~~s~e~k~~i~~~L~~~Gv~~IE~G~~~~~~~~~~~~~~~~~~~   59 (273)
T cd07941           1 IYDTTLRDGTQGEGISFSVEDKLRIARKLDELGVDYIEGGWPGSNPKDTEFFARAKKLK   59 (273)
T ss_pred             CCcCCCCCcCCCCCCCCCHHHHHHHHHHHHHcCCCEEEecCCcCCHHHHHHHHHHHHcC
Confidence            57999999999999999999999999999999999999999 99999999      776

Desulfobacterium autotrophicum LeuA3 is sequence-similar to alpha-isopropylmalate synthase (LeuA) but its exact function is unknown. Members of this family have an N-terminal TIM barrel domain that belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of in

>cd07947 DRE_TIM_Re_CS Clostridium kluyveri Re-citrate synthase and related proteins, catalytic TIM barrel domain

Probab=99.36  E-value=5.8e-13  Score=112.40  Aligned_cols=45  Identities=20%  Similarity=0.207  Sum_probs=43.1

Q ss_pred             eEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCC-----CCeeeeecccC
Q 031564           98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSG-----LPVVEATSFVS  143 (157)
Q Consensus        98 V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AG-----v~~IEvgSFVs  143 (157)
                      |.|+|||||||+|+++.+ |+++|++|+++|.++|     |++||++||++
T Consensus         1 i~i~d~tlRDG~Q~~~~~-~~~~Kv~i~~~L~~~G~~~~~v~~IE~~s~~~   50 (279)
T cd07947           1 IWITDTTFRDGQQARPPY-TVEQIVKIYDYLHELGGGSGVIRQTEFFLYTE   50 (279)
T ss_pred             CEEEeCCCCCcCCCCCCC-CHHHHHHHHHHHHHcCCCCCccceEEecCcCh
Confidence            579999999999999987 9999999999999999     99999999986

Re-citrate synthase (Re-CS) is a Clostridium kluyveri enzyme that converts acetyl-CoA and oxaloacetate to citrate. In most organisms, this reaction is catalyzed by Si-citrate synthase which is Si-face stereospecific with respect to C-2 of oxaloacetate, and phylogenetically unrelated to Re-citrate synthase. Re-citrate synthase is also found in a few other strictly anaerobic organisms. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with

>cd03174 DRE_TIM_metallolyase DRE-TIM metallolyase superfamily

Probab=99.34  E-value=1.2e-12  Score=103.80  Aligned_cols=53  Identities=36%  Similarity=0.456  Sum_probs=50.9

Q ss_pred             EEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564          101 VEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA  153 (157)
Q Consensus       101 vEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa  153 (157)
                      .|+++|||+|.....+++++|+++++.|.++||+.||+|++++++++||+.|.
T Consensus         1 ~D~tlRDG~q~~~~~~s~e~~~~i~~~L~~~GV~~IEvg~~~~~~~~p~~~~~   53 (265)
T cd03174           1 TDTTLRDGLQSEGATFSTEDKLEIAEALDEAGVDSIEVGSGASPKAVPQMEDD   53 (265)
T ss_pred             CCCCCCCcccCCCCCCCHHHHHHHHHHHHHcCCCEEEeccCcCccccccCCCH
Confidence            38999999999999999999999999999999999999999999999999874

The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM".

>PLN02321 2-isopropylmalate synthase

Probab=99.34  E-value=1.1e-12  Score=122.40  Aligned_cols=51  Identities=27%  Similarity=0.502  Sum_probs=49.7

Q ss_pred             CCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec-ccCCC
Q 031564           95 PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS-FVSPK  145 (157)
Q Consensus        95 P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS-FVsPK  145 (157)
                      |+.|.|.||+||||+|+++..+++++|++|+++|.++||+.||+|+ |+||+
T Consensus        84 ~~~V~I~DtTLRDGeQ~~g~~~s~eeKl~Ia~~L~~lGVd~IEvGfP~~Sp~  135 (632)
T PLN02321         84 PNYVRIFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDIIEAGFPIASPD  135 (632)
T ss_pred             CCceEEEECCCCccccCCCCCCCHHHHHHHHHHHHHcCCCEEEEeCcCCCcc
Confidence            7889999999999999999999999999999999999999999999 79998

>PRK03739 2-isopropylmalate synthase; Validated

Probab=99.33  E-value=1.1e-12  Score=119.89  Aligned_cols=55  Identities=25%  Similarity=0.331  Sum_probs=51.7

Q ss_pred             CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccCC
Q 031564           94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALF  155 (157)
Q Consensus        94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~~  155 (157)
                      +.....|+|+|||||+|+++..+++++|++|+++|.++||++||+| |      |||++++|
T Consensus        27 ~~~~~~i~dttLRDGeQ~~gv~~s~~~Ki~ia~~L~~~GV~~IE~G-f------P~~s~~e~   81 (552)
T PRK03739         27 ITKAPIWCSVDLRDGNQALIEPMSPERKLRMFDLLVKIGFKEIEVG-F------PSASQTDF   81 (552)
T ss_pred             cCCCCeEeeCCCCCcCcCCCCCCCHHHHHHHHHHHHHcCCCEEEEE-C------CCcChHHH
Confidence            5667889999999999999999999999999999999999999999 6      99998875

>COG0119 LeuA Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]

Probab=99.33  E-value=9.7e-13  Score=116.96  Aligned_cols=57  Identities=25%  Similarity=0.142  Sum_probs=54.7

Q ss_pred             ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564           97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA  153 (157)
Q Consensus        97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa  153 (157)
                      .|.|.|+|||||.|+++..+++++|++|+++|.++|++.||+|+++++++.+|+..+
T Consensus         2 ~v~i~DtTLRDG~Q~~g~~~s~e~Ki~Ia~~Ld~lGv~~IE~g~p~~s~~~~~~~~~   58 (409)
T COG0119           2 KVIIFDTTLRDGEQAPGVSFSVEEKIRIAKALDDLGVDYIEAGFPVASPGDFEFVRA   58 (409)
T ss_pred             CcEEEeCCCCcCCcCCCCcCCHHHHHHHHHHHHHcCCCEEEEeCCcCChhhHHHHHH
Confidence            589999999999999999999999999999999999999999999999999998754

>PLN03228 methylthioalkylmalate synthase; Provisional

Probab=99.32  E-value=1.1e-12  Score=119.30  Aligned_cols=56  Identities=20%  Similarity=0.303  Sum_probs=52.7

Q ss_pred             CCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564           95 PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA  153 (157)
Q Consensus        95 P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa  153 (157)
                      +..|.|.|+|||||+|+++..+++++|++|+++|.++||+.||+|+   |++.|+++++
T Consensus        82 ~~~V~I~DtTLRDGeQ~~gv~fs~eeKi~Ia~~L~~~GVd~IEvG~---Pa~s~~e~e~  137 (503)
T PLN03228         82 KNYVRVLDTTLRDGEQSPGGSLTPPQKLEIARQLAKLRVDIMEVGF---PGSSEEEFEA  137 (503)
T ss_pred             CCCeEEEeCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCEEEEeC---CCCCHHHHHH
Confidence            5689999999999999999999999999999999999999999998   8888888764

>TIGR02090 LEU1_arch isopropylmalate/citramalate/homocitrate synthases

Probab=99.31  E-value=2e-12  Score=111.66  Aligned_cols=56  Identities=29%  Similarity=0.260  Sum_probs=52.8

Q ss_pred             eEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCC-------Ccccccccc
Q 031564           98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSP-------KWVPQVADA  153 (157)
Q Consensus        98 V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsP-------K~VPQMADa  153 (157)
                      |.|.|+|||||.|+.+..+++++|+++++.|.++||+.||+|+|+++       +.+|++++.
T Consensus         1 i~i~DtTLRDG~Q~~~~~~s~~~k~~ia~~L~~~Gv~~IEvG~p~~~~~~~e~i~~i~~~~~~   63 (363)
T TIGR02090         1 VYIFDTTLRDGEQTPGVSLTVEQKVEIARKLDELGVDVIEAGFPIASEGEFEAIKKISQEGLN   63 (363)
T ss_pred             CEEEeCCCCCcCCCCCCCCCHHHHHHHHHHHHHcCCCEEEEeCCCCChHHHHHHHHHHhcCCC
Confidence            57999999999999999999999999999999999999999999999       888888753

Methanogens, then should and aparrently do contain all three of these enzymes. Unfortunately, phylogenetic trees do not resolve into three unambiguous clades, making assignment of function to particular genes problematic. Other archaea which lack a threonine dehydratase (mainly Euryarchaeota) should contain both a CimA and a LeuA gene. This is true of, for example, archaeoglobus fulgidis, but not for the Pyrococci which have none in this clade, but one in TIGR00973 and one in TIGRT00977 which may fulfill these roles. Other species which have only one hit to this model and lack threonine dehydratase are very likely LeuA enzymes.

>PRK11858 aksA trans-homoaconitate synthase; Reviewed

Probab=99.27  E-value=4.4e-12  Score=109.99  Aligned_cols=54  Identities=26%  Similarity=0.367  Sum_probs=50.2

Q ss_pred             CCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccCC
Q 031564           95 PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALF  155 (157)
Q Consensus        95 P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~~  155 (157)
                      |++|.|.|+|||||.|.++..+++++|++++++|.++||+.||+|       +|+|++.+|
T Consensus         2 ~~~v~I~DtTLRDG~Q~~~~~~s~e~k~~ia~~L~~~GV~~IE~G-------~p~~~~~~~   55 (378)
T PRK11858          2 PKDIEIVDTTLRDGEQTPGVVFTNEEKLAIARMLDEIGVDQIEAG-------FPAVSEDEK   55 (378)
T ss_pred             CCeeEEEeCCCCccCcCCCCCCCHHHHHHHHHHHHHhCCCEEEEe-------CCCcChHHH
Confidence            567999999999999999999999999999999999999999998       688887764

>TIGR00970 leuA_yeast 2-isopropylmalate synthase, yeast type

Probab=99.26  E-value=4.3e-12  Score=116.27  Aligned_cols=51  Identities=24%  Similarity=0.282  Sum_probs=48.6

Q ss_pred             CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCC
Q 031564           94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPK  145 (157)
Q Consensus        94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK  145 (157)
                      +.....|+|++||||+|+++..+++++|++|+++|.++||++||+| |++|+
T Consensus        23 ~~~~~~~~DtTLRDG~Q~~g~~~s~e~Ki~ia~~L~~~Gvd~IE~G-fp~~s   73 (564)
T TIGR00970        23 ITRAPRWLSTDLRDGNQALPDPMSPARKRRYFDLLVRIGFKEIEVG-FPSAS   73 (564)
T ss_pred             cCcCCeEecCCCCccccCCCCCCCHHHHHHHHHHHHHcCCCEEEEe-CCCCC
Confidence            5566889999999999999999999999999999999999999999 99998

A larger family of homologous proteins includes homocitrate synthase, distinct lineages of 2-isopropylmalate synthase, several distinct, uncharacterized, orthologous sets in the Archaea, and other related enzymes. This model describes a family of 2-isopropylmalate synthases as found in yeasts and in a minority of studied bacteria.

>TIGR00977 LeuA_rel 2-isopropylmalate synthase/homocitrate synthase family protein

Probab=99.26  E-value=4.3e-12  Score=115.43  Aligned_cols=55  Identities=22%  Similarity=0.164  Sum_probs=52.9

Q ss_pred             ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeee-cccCCCcccccc
Q 031564           97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEAT-SFVSPKWVPQVA  151 (157)
Q Consensus        97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvg-SFVsPK~VPQMA  151 (157)
                      .|.|.|+|||||.|.++..+++++|++|+++|.++||+.||+| .++||+.+|+++
T Consensus         1 ~V~I~DtTLRDG~Q~~g~~~s~eeKl~Ia~~L~~~GVd~IE~G~p~~s~~d~~~v~   56 (526)
T TIGR00977         1 SLWLYDTTLRDGAQREGVSFSLEDKIRIAERLDDLGIHYIEGGWPGANPKDVQFFW   56 (526)
T ss_pred             CeEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCEEEEeCCCCChHHHHHHH
Confidence            4899999999999999999999999999999999999999999 799999999887

This model represents uncharacterized proteins related to 2-isopropylmalate synthases and homocitrate synthases but phylogenetically distint. Each species represented in the seed alignment also has a member of a known family of 2-isopropylmalate synthases.

>cd07943 DRE_TIM_HOA 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain

Probab=99.25  E-value=8.5e-12  Score=102.19  Aligned_cols=56  Identities=20%  Similarity=0.232  Sum_probs=50.8

Q ss_pred             eEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeee-----cccCCCcccccccc
Q 031564           98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEAT-----SFVSPKWVPQVADA  153 (157)
Q Consensus        98 V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvg-----SFVsPK~VPQMADa  153 (157)
                      |.|.|||+|||+|..+..+++++|+++++.|.++||+.||+|     ..++++++|+++|.
T Consensus         1 i~i~D~TlRDG~Q~~~~~~~~~~k~~i~~~L~~~Gv~~iEvg~~~~~~~~~~~~~~~~~~~   61 (263)
T cd07943           1 VYIHDVTLRDGMHAVRHQFTLEQVRAIARALDAAGVPLIEVGHGDGLGGSSLNYGFAAHTD   61 (263)
T ss_pred             CEEEeCCCCcCcccCCeecCHHHHHHHHHHHHHcCCCEEEeecCCCCCCcccccCCCCCCh
Confidence            679999999999999999999999999999999999999999     44555888998873

4-hydroxy 2-ketovalerate aldolase (Also known as 4-hydroxy-2-ketovalerate aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA)) converts 4-hydroxy-2-oxopentanoate to acetaldehyde and pyruvate, the penultimate step in the meta-cleavage pathway for the degradation of phenols, cresols and catechol. This family includes the Escherichia coli MhpE aldolase, the Pseudomonas DmpG aldolase, and the Burkholderia xenovorans BphI pyruvate aldolase. In Pseudomonas, the DmpG aldolase tightly associates with a dehydrogenase (DmpF ) and is inactive without it. HOA has a canonical TIM-barrel fold with a C-terminal extension that forms a funnel leading to the active site. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate

>cd07940 DRE_TIM_IPMS 2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain

Probab=99.23  E-value=5.8e-12  Score=103.39  Aligned_cols=45  Identities=31%  Similarity=0.341  Sum_probs=43.3

Q ss_pred             EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeeccc-CC
Q 031564          100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFV-SP  144 (157)
Q Consensus       100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFV-sP  144 (157)
                      |+|||||||+|+....+++++|++++++|.++||+.||+|+|+ +|
T Consensus         1 i~D~TlRDG~Q~~~~~~~~~~k~~i~~~L~~~Gv~~iEvg~~~~~~   46 (268)
T cd07940           1 IFDTTLRDGEQTPGVSLTPEEKLEIARQLDELGVDVIEAGFPAASP   46 (268)
T ss_pred             CCCCCCCccccCCCCCCCHHHHHHHHHHHHHcCCCEEEEeCCCCCH
Confidence            5799999999999999999999999999999999999999998 67

2-isopropylmalate synthase (IPMS) catalyzes an aldol-type condensation of acetyl-CoA and 2-oxoisovalerate yielding 2-isopropylmalate and CoA, the first committed step in leucine biosynthesis. This family includes the Arabidopsis thaliana IPMS1 and IPMS2 proteins, the Glycine max GmN56 protein, and the Brassica insularis BatIMS protein. This family also includes a group of archeal IPMS-like proteins represented by the Methanocaldococcus jannaschii AksA protein. AksA catalyzes the condensation of alpha-ketoglutarate and acetyl-CoA to form trans-homoaconitate, one of 13 steps in the conversion of alpha-ketoglutarate and acetylCoA to alpha-ketosuberate, a precursor to coenzyme B and biotin. AksA also catalyzes the condensation of alpha-ketoadipate or alpha-ketopimelate with acetylCoA to form, respectively, the (R)-homocitrate homologs (R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and (R)-2-h

>PRK12344 putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional

Probab=99.22  E-value=1.3e-11  Score=112.04  Aligned_cols=56  Identities=20%  Similarity=0.203  Sum_probs=52.9

Q ss_pred             CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec-ccCCC------cccc
Q 031564           94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS-FVSPK------WVPQ  149 (157)
Q Consensus        94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS-FVsPK------~VPQ  149 (157)
                      ||.+|.|.|++||||.|.++..+++++|+++++.|.++||+.||+|+ +++|+      ++++
T Consensus         2 ~~~~V~I~DtTLRDG~Q~~g~~~s~e~Kl~ia~~L~~~Gvd~IEvG~p~as~~d~~~~~~i~~   64 (524)
T PRK12344          2 MMERIELYDTTLRDGAQGEGISFSVEDKLRIARKLDELGVDYIEGGWPGSNPKDTEFFKRAKE   64 (524)
T ss_pred             CCCceEEEeCCCCCcCcCCCCCCCHHHHHHHHHHHHHcCCCEEEEcCCcCChhHHHHHHHHHH
Confidence            57789999999999999999999999999999999999999999999 88998      7776

>PRK09389 (R)-citramalate synthase; Provisional

Probab=99.21  E-value=1.6e-11  Score=110.51  Aligned_cols=56  Identities=27%  Similarity=0.317  Sum_probs=51.7

Q ss_pred             ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCC-------ccccccc
Q 031564           97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPK-------WVPQVAD  152 (157)
Q Consensus        97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK-------~VPQMAD  152 (157)
                      +|.|.|++||||.|.++..+++++|++++++|.++||+.||+|+|++++       .+++++.
T Consensus         2 ~i~I~DtTLRDG~Q~~g~~~s~e~K~~ia~~L~~~Gv~~IE~G~p~~~~~d~e~v~~i~~~~~   64 (488)
T PRK09389          2 MVRILDTTLRDGEQTPGVSLTPEEKLEIARKLDELGVDVIEAGSAITSEGEREAIKAVTDEGL   64 (488)
T ss_pred             ceEEEeCCCCCcCCCCCCCcCHHHHHHHHHHHHHcCCCEEEEeCCcCCHHHHHHHHHHHhcCC
Confidence            4899999999999999999999999999999999999999999999987       6766543

>PRK00915 2-isopropylmalate synthase; Validated

Probab=99.18  E-value=3e-11  Score=108.97  Aligned_cols=52  Identities=29%  Similarity=0.283  Sum_probs=48.5

Q ss_pred             CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec-ccCCC
Q 031564           94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS-FVSPK  145 (157)
Q Consensus        94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS-FVsPK  145 (157)
                      ||..|.|.|++||||.|.++..+++++|++++++|.++||+.||+|+ ++||+
T Consensus         1 m~~~v~I~DtTLRDG~Q~~g~~~s~e~K~~ia~~L~~~Gv~~IE~G~p~~s~~   53 (513)
T PRK00915          1 MMDRVIIFDTTLRDGEQSPGASLTVEEKLQIAKQLERLGVDVIEAGFPASSPG   53 (513)
T ss_pred             CCCCcEEEECCCCcCCCCCCCCCCHHHHHHHHHHHHHcCCCEEEEcCCCCChH
Confidence            46789999999999999999999999999999999999999999998 56764

>TIGR02660 nifV_homocitr homocitrate synthase NifV

Probab=99.13  E-value=5.3e-11  Score=102.52  Aligned_cols=51  Identities=24%  Similarity=0.293  Sum_probs=47.6

Q ss_pred             eEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccCC
Q 031564           98 VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADALF  155 (157)
Q Consensus        98 V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~~  155 (157)
                      |.|.|+|+|||.|.....+++++|+++++.|.++||+.||+|       +|+|++.+|
T Consensus         2 v~i~D~TLRDG~Q~~~~~~s~~~k~~ia~~L~~~Gv~~IEvG-------~p~~~~~~~   52 (365)
T TIGR02660         2 VIINDTTLRDGEQAPGVAFTAAEKLAIARALDEAGVDELEVG-------IPAMGEEER   52 (365)
T ss_pred             cEEEeCCCCCcCcCCCCCCCHHHHHHHHHHHHHcCCCEEEEe-------CCCCCHHHH
Confidence            789999999999999999999999999999999999999998       678877654

This family consists of the NifV clade of homocitrate synthases, most of which are found in operons for nitrogen fixation. Members are closely homologous to enzymes that include 2-isopropylmalate synthase, (R)-citramalate synthase, and homocitrate synthases associated with other processes. The homocitrate made by this enzyme becomes a part of the iron-molybdenum cofactor of nitrogenase.

>TIGR00973 leuA_bact 2-isopropylmalate synthase, bacterial type

Probab=99.08  E-value=1.4e-10  Score=104.47  Aligned_cols=49  Identities=24%  Similarity=0.242  Sum_probs=46.7

Q ss_pred             ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCC
Q 031564           97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPK  145 (157)
Q Consensus        97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK  145 (157)
                      +|.|.|+|+|||.|.++..+++++|++++++|.++||+.||+|+|++++
T Consensus         1 ~v~I~DtTLRDG~Q~~g~~~s~e~K~~ia~~L~~~GV~~IEvG~p~~s~   49 (494)
T TIGR00973         1 RIIIFDTTLRDGEQSPGASLTVEEKLQIALALERLGVDIIEAGFPVSSP   49 (494)
T ss_pred             CeEEEECCCCccCcCCCCCcCHHHHHHHHHHHHHcCCCEEEEECCCCCH
Confidence            4889999999999999999999999999999999999999999998864

A larger family of homologous proteins includes homocitrate synthase, distinct lineages of 2-isopropylmalate synthase, several distinct, uncharacterized, orthologous sets in the Archaea, and other related enzymes. This model describes a family of 2-isopropylmalate synthases found primarily in Bacteria. The homologous families in the Archaea may represent isozymes and/or related enzymes.

>TIGR03217 4OH_2_O_val_ald 4-hydroxy-2-oxovalerate aldolase

Probab=99.05  E-value=2.3e-10  Score=98.62  Aligned_cols=56  Identities=20%  Similarity=0.181  Sum_probs=51.5

Q ss_pred             ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeee--------cccC-CCccccccc
Q 031564           97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEAT--------SFVS-PKWVPQVAD  152 (157)
Q Consensus        97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvg--------SFVs-PK~VPQMAD  152 (157)
                      +|.|.|||+|||.|.....+++++|++++++|.++||+.||+|        ||.. +.++|++.+
T Consensus         2 ~i~i~D~TLRDG~q~~~~~f~~~~~~~ia~~Ld~aGV~~IEvg~g~gl~g~s~~~G~~~~~~~e~   66 (333)
T TIGR03217         2 KLYITDVTLRDGMHAIRHQFTIEQVRAIAAALDEAGVDAIEVTHGDGLGGSSFNYGFSAHTDLEY   66 (333)
T ss_pred             CcEEEECCCCCCCcCCCCcCCHHHHHHHHHHHHHcCCCEEEEecCCCCCCccccCCCCCCChHHH
Confidence            5899999999999999999999999999999999999999997        8886 788887653

Members of this protein family are 4-hydroxy-2-oxovalerate aldolase, also called 4-hydroxy-2-ketovalerate aldolase and 2-oxo-4-hydroxypentanoate aldolase. This enzyme, part of the pathway for the meta-cleavage of catechol, produces pyruvate and acetaldehyde. Acetaldehyde is then converted by acetaldehyde dehydrogenase (acylating) (DmpF; EC 1.2.1.10) to acetyl-CoA. The two enzymes are tightly associated.

>PRK12331 oxaloacetate decarboxylase; Provisional

Probab=98.99  E-value=5.6e-10  Score=100.27  Aligned_cols=50  Identities=22%  Similarity=0.256  Sum_probs=47.2

Q ss_pred             CceEEEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeeee---------cccCCC
Q 031564           96 GFVKIVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEAT---------SFVSPK  145 (157)
Q Consensus        96 ~~V~IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEvg---------SFVsPK  145 (157)
                      ++|.|+|+|+|||.|++ ...++|++|+++++.|.++|+..||++         +|++|+
T Consensus         2 ~~V~I~DtTlRDG~Qs~~~~~~~t~dkl~ia~~Ld~~Gv~~IE~~ggatf~~~~~f~~e~   61 (448)
T PRK12331          2 TKIKITETVLRDGQQSLIATRMTTEEMLPILEKLDNAGYHSLEMWGGATFDACLRFLNED   61 (448)
T ss_pred             CccEEEECCCCccccCcCCcccCHHHHHHHHHHHHHcCCCEEEecCCccchhhhccCCCC
Confidence            46999999999999998 779999999999999999999999999         899986

>PRK08195 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated

Probab=98.99  E-value=8.1e-10  Score=95.30  Aligned_cols=53  Identities=25%  Similarity=0.286  Sum_probs=48.9

Q ss_pred             CceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeee--------ccc-CCCccc
Q 031564           96 GFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEAT--------SFV-SPKWVP  148 (157)
Q Consensus        96 ~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvg--------SFV-sPK~VP  148 (157)
                      ++|.|.|||+|||.|.....+++++|++++++|.++||+.||+|        ||+ .+.++|
T Consensus         2 ~~i~I~D~TLRDG~q~~~~~f~~~~~~~i~~~L~~aGv~~IEvg~~~g~g~~s~~~g~~~~~   63 (337)
T PRK08195          2 KKIYISDVTLRDGMHAVRHQYTLEQVRAIARALDAAGVPVIEVTHGDGLGGSSFNYGFGAHT   63 (337)
T ss_pred             CceEEEECCCCCcCcCCCCccCHHHHHHHHHHHHHcCCCEEEeecCCCCCCccccCCCCCCC
Confidence            46999999999999999999999999999999999999999997        887 776665

>PRK14041 oxaloacetate decarboxylase; Provisional

Probab=98.93  E-value=1.2e-09  Score=98.86  Aligned_cols=49  Identities=18%  Similarity=0.207  Sum_probs=46.1

Q ss_pred             ceEEEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeee---------ecccCCC
Q 031564           97 FVKIVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEA---------TSFVSPK  145 (157)
Q Consensus        97 ~V~IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEv---------gSFVsPK  145 (157)
                      +|.|.||++|||.|++ ...++|++|++++++|.++|+..||+         ++|++|+
T Consensus         2 ~V~I~DtTlRDG~Qs~~~~~~~t~dkl~Ia~~Ld~~Gv~~IE~~ggatfd~~~~Fl~e~   60 (467)
T PRK14041          2 KVMFVDTTLRDGHQSLIATRMRTEDMLPALEAFDRMGFYSMEVWGGATFDVCVRFLNEN   60 (467)
T ss_pred             ceEEEECCCCccccCcCCccCCHHHHHHHHHHHHHcCCCEEEecCCccchhhhcccCCC
Confidence            4899999999999998 58999999999999999999999999         7899876

>cd07939 DRE_TIM_NifV Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain

Probab=98.89  E-value=1.5e-09  Score=88.89  Aligned_cols=42  Identities=21%  Similarity=0.200  Sum_probs=39.9

Q ss_pred             EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecc
Q 031564          100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSF  141 (157)
Q Consensus       100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSF  141 (157)
                      |.|||||||+|+....+++++|+++++.|.++||+.||+|..
T Consensus         1 i~D~TlRDG~Q~~~~~~~~~~k~~i~~~L~~~Gv~~iE~g~p   42 (259)
T cd07939           1 INDTTLRDGEQAPGVAFSREEKLAIARALDEAGVDEIEVGIP   42 (259)
T ss_pred             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHcCCCEEEEecC
Confidence            579999999999999999999999999999999999999954

FrbC (NifV) of Streptomyces rubellomurinus catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate and CoA, a reaction similar to one catalyzed by homocitrate synthase. The gene encoding FrbC is one of several genes required for the biosynthesis of FR900098, a potent antimalarial antibiotic. This protein is also required for assembly of the nitrogenase MoFe complex but its exact role is unknown. This family also includes the NifV proteins of Heliobacterium chlorum and Gluconacetobacter diazotrophicus, which appear to be orthologous to FrbC. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarbox

>TIGR02146 LysS_fung_arch homocitrate synthase

Probab=98.87  E-value=1.4e-09  Score=90.06  Aligned_cols=51  Identities=25%  Similarity=0.246  Sum_probs=47.3

Q ss_pred             EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564          100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA  153 (157)
Q Consensus       100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa  153 (157)
                      |.|+++|||.|++...+++++|+++++.|.++|++.||+|+   |++.||++++
T Consensus         1 i~D~TlRDG~q~~~~~~~~~~ki~i~~~l~~~Gv~~iE~g~---p~~~~~~~~~   51 (344)
T TIGR02146         1 IIDSTLREGEQFPGANFSTEQKIEIAKALDEFGIDYIEVTH---PAASKQSRID   51 (344)
T ss_pred             CCCCCCCccCcCCCCCCCHHHHHHHHHHHHHcCCCEEEEeC---CCCCHHHHHH
Confidence            57899999999999999999999999999999999999998   8889988643

This model includes the yeast LYS21 gene which carries out the first step of the alpha-aminoadipate (AAA) lysine biosynthesis pathway. A related pathway is found in Thermus thermophilus. This enzyme is closely related to 2-isopropylmalate synthase (LeuA) and citramalate synthase (CimA), both of which are present in the euryarchaeota. Some archaea have a separate homocitrate synthase (AksA) which also synthesizes longer homocitrate analogs.

>PRK14847 hypothetical protein; Provisional

Probab=98.73  E-value=1.6e-08  Score=88.80  Aligned_cols=59  Identities=22%  Similarity=0.273  Sum_probs=52.2

Q ss_pred             CcccchhhHhhhhcCCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec
Q 031564           79 TDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS  140 (157)
Q Consensus        79 ~~~~~~~~~~~~~~~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS  140 (157)
                      -....|.-+.|.....|.   |.|+++|||.|..+..++.++|++|+++|.++||+.||||.
T Consensus        17 ~~~~~~~w~~~~~~~~p~---~~DTTLRDGeQ~pGv~fs~eeKl~IA~~L~~lGVd~IEvG~   75 (333)
T PRK14847         17 ADHAERAWPARRPAAAPI---WMSTDLRDGNQALIEPMDGARKLRLFEQLVAVGLKEIEVAF   75 (333)
T ss_pred             CCCccCCCcccccCCCCc---eecCCCCccCCCCCCCCCHHHHHHHHHHHHHcCCCEEEeeC
Confidence            345556667777777776   99999999999999999999999999999999999999996

>TIGR01108 oadA oxaloacetate decarboxylase alpha subunit

Probab=98.69  E-value=1.5e-08  Score=93.71  Aligned_cols=46  Identities=20%  Similarity=0.156  Sum_probs=43.1

Q ss_pred             EEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeeee---------cccCCC
Q 031564          100 IVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEAT---------SFVSPK  145 (157)
Q Consensus       100 IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEvg---------SFVsPK  145 (157)
                      |.|+++|||+|++ ...++|++|+++++.|.++|+..||++         +|++++
T Consensus         1 I~DtTlRDG~Qs~~~~~~~t~dkl~ia~~L~~~Gv~~IE~~GGatfd~~~~f~~e~   56 (582)
T TIGR01108         1 ITDVVLRDAHQSLFATRMRTEDMLPIAEKLDDVGYWSLEVWGGATFDACIRFLNED   56 (582)
T ss_pred             CccCCCCccccccCCccCCHHHHHHHHHHHHHcCCCEEEecCCcccccccccCCCC
Confidence            6799999999998 679999999999999999999999998         888876

This model describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea. The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane.

>PRK09282 pyruvate carboxylase subunit B; Validated

Probab=98.52  E-value=1.3e-07  Score=87.72  Aligned_cols=44  Identities=20%  Similarity=0.098  Sum_probs=41.6

Q ss_pred             CceEEEEeccCccccCCC-CCCCHHHHHHHHHHHHhCCCCeeeee
Q 031564           96 GFVKIVEVGPRDGLQNEK-NIVPAVVKVELIKLLVSSGLPVVEAT  139 (157)
Q Consensus        96 ~~V~IvEVGpRDGLQne~-~~vpTe~KIeLI~~L~~AGv~~IEvg  139 (157)
                      ++|.|.|+++|||.|+.. ..++|++|++++..|.++|+..||++
T Consensus         2 ~~v~i~DtTlRDG~Qs~~atr~~t~d~l~ia~~l~~~G~~~iE~~   46 (592)
T PRK09282          2 KKVKITDTTLRDAHQSLLATRMRTEDMLPIAEKLDKVGFWSLEVW   46 (592)
T ss_pred             CccEEEECCCCccccccCCccCCHHHHHHHHHHHHHcCCCEEEec
Confidence            459999999999999985 68999999999999999999999998

>cd07937 DRE_TIM_PC_TC_5S Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain

Probab=98.44  E-value=1e-07  Score=79.48  Aligned_cols=41  Identities=17%  Similarity=0.139  Sum_probs=39.1

Q ss_pred             EEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeeeec
Q 031564          100 IVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEATS  140 (157)
Q Consensus       100 IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEvgS  140 (157)
                      |.|+|+|||.|.. +..+++++|++++..|.++||+.||+|.
T Consensus         1 i~DtTlRDG~Qs~~~~~~~~~~~~~ia~~L~~~Gv~~iE~G~   42 (275)
T cd07937           1 ITDTTLRDAHQSLLATRMRTEDMLPIAEALDEAGFFSLEVWG   42 (275)
T ss_pred             CCcCcccchhhchhceeccHHHHHHHHHHHHHcCCCEEEccC
Confidence            5799999999998 8999999999999999999999999996

This family includes the carboxyltransferase domains of pyruvate carboxylase (PC) and the transcarboxylase (TC) 5S subunit. Transcarboxylase 5S is a cobalt-dependent metalloenzyme subunit of the biotin-dependent transcarboxylase multienzyme complex. Transcarboxylase 5S transfers carbon dioxide from the 1.3S biotin to pyruvate in the second of two carboxylation reactions catalyzed by TC. The first reaction involves the transfer of carbon dioxide from methylmalonyl-CoA to the 1.3S biotin, and is catalyzed by the 12S subunit. These two steps allow a carboxylate group to be transferred from oxaloacetate to propionyl-CoA to yield pyruvate and methylmalonyl-CoA. The catalytic domain of transcarboxylase 5S has a canonical TIM-barrel fold with a large C-terminal extension that forms a funnel leading to the active site. Transcarboxylase 5S forms a homodimer and there are six dimers per complex

>cd07944 DRE_TIM_HOA_like 4-hydroxy-2-oxovalerate aldolase-like, N-terminal catalytic TIM barrel domain

Probab=98.32  E-value=5.9e-07  Score=74.94  Aligned_cols=44  Identities=20%  Similarity=0.144  Sum_probs=41.1

Q ss_pred             EEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccC
Q 031564          100 IVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVS  143 (157)
Q Consensus       100 IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVs  143 (157)
                      |.|+|+|||.|.....+++++|++++..|.++||+.||+|.-.+
T Consensus         1 i~D~TLRDG~q~~~~~f~~~~~~~ia~~L~~~GVd~IEvG~~~~   44 (266)
T cd07944           1 ILDCTLRDGGYVNNWDFGDEFVKAIYRALAAAGIDYVEIGYRSS   44 (266)
T ss_pred             CccCCcccCccccCccCCHHHHHHHHHHHHHCCCCEEEeecCCC
Confidence            57999999999999999999999999999999999999997544

This family of bacterial enzymes is sequence-similar to 4-hydroxy-2-oxovalerate aldolase (HOA) but its exact function is unknown. This family includes the Bacteroides vulgatus Bvu_2661 protein and belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues t

>PRK12330 oxaloacetate decarboxylase; Provisional

Probab=98.01  E-value=7.7e-06  Score=75.26  Aligned_cols=46  Identities=20%  Similarity=0.133  Sum_probs=43.1

Q ss_pred             CCCceEEEEeccCccccCCC-CCCCHHHHHHHHHHHHhCCCCeeeee
Q 031564           94 VPGFVKIVEVGPRDGLQNEK-NIVPAVVKVELIKLLVSSGLPVVEAT  139 (157)
Q Consensus        94 ~P~~V~IvEVGpRDGLQne~-~~vpTe~KIeLI~~L~~AGv~~IEvg  139 (157)
                      |++.|.|.|+++|||.|... .-++|++|+.++..|.++|+..||++
T Consensus         1 ~~~~i~i~DTTLRDG~QSl~atr~~t~d~l~ia~~ld~~G~~siE~~   47 (499)
T PRK12330          1 MPRKIGVTELALRDAHQSLMATRMAMEDMVGACEDIDNAGYWSVECW   47 (499)
T ss_pred             CCCCcEEEECCccchhhcccCccCCHHHHHHHHHHHHhcCCCEEEec
Confidence            45679999999999999976 89999999999999999999999997

>PRK14040 oxaloacetate decarboxylase; Provisional

Probab=98.01  E-value=7.9e-06  Score=76.14  Aligned_cols=45  Identities=18%  Similarity=0.039  Sum_probs=42.3

Q ss_pred             CCceEEEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeeee
Q 031564           95 PGFVKIVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEAT  139 (157)
Q Consensus        95 P~~V~IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEvg  139 (157)
                      .++|.|.|+++|||.|.. ...++|++|+.++..|.++|+..||++
T Consensus         2 ~k~v~i~DtTLRDG~Qs~~~tr~~~~d~l~ia~~ld~~G~~siE~~   47 (593)
T PRK14040          2 SKPLAITDVVLRDAHQSLFATRLRLDDMLPIAAKLDKVGYWSLESW   47 (593)
T ss_pred             CCccEEEECCcccccccccccccCHHHHHHHHHHHHHcCCCEEEec
Confidence            457999999999999999 779999999999999999999999994

>KOG2367 consensus Alpha-isopropylmalate synthase/homocitrate synthase [Amino acid transport and metabolism]

Probab=97.90  E-value=1.4e-05  Score=74.54  Aligned_cols=50  Identities=22%  Similarity=0.363  Sum_probs=46.8

Q ss_pred             CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccC
Q 031564           94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVS  143 (157)
Q Consensus        94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVs  143 (157)
                      .|..|++.+.++|||.|..+.++.+++|+++.++|...||+.||+|+=|.
T Consensus        54 ~~n~vr~~dttLRdGeQs~ga~~~~~qK~eiar~L~~~gvd~IEv~fP~a  103 (560)
T KOG2367|consen   54 DVNYVRVLDTTLRDGEQSPGAFLTTEQKLEIARQLAKLGVDIIEVGFPVA  103 (560)
T ss_pred             CcCcceeecccccccccCCCCcCCcHHHHHHHHHHHhcCcCEEEecCccc
Confidence            46789999999999999999999999999999999999999999998554

>PRK12581 oxaloacetate decarboxylase; Provisional

Probab=97.44  E-value=0.0002  Score=65.77  Aligned_cols=46  Identities=22%  Similarity=0.180  Sum_probs=41.9

Q ss_pred             CCCceEEEEeccCccccC-CCCCCCHHHHHHHHHHHHhCCCCeeeee
Q 031564           94 VPGFVKIVEVGPRDGLQN-EKNIVPAVVKVELIKLLVSSGLPVVEAT  139 (157)
Q Consensus        94 ~P~~V~IvEVGpRDGLQn-e~~~vpTe~KIeLI~~L~~AGv~~IEvg  139 (157)
                      |.++|.|.|+++|||-|. ..+-+.|++.+.++..|.++|+..||++
T Consensus         9 ~~~~v~i~DtTlRDg~QSl~atr~~t~d~l~ia~~ld~~G~~siE~w   55 (468)
T PRK12581          9 MQQQVAITETVLRDGHQSLMATRLSIEDMLPVLTILDKIGYYSLECW   55 (468)
T ss_pred             cCCceEEEECCccchhhhccccCCCHHHHHHHHHHHHhcCCCEEEec
Confidence            345799999999999999 5666999999999999999999999995

>PRK12999 pyruvate carboxylase; Reviewed

Probab=97.39  E-value=0.0002  Score=71.13  Aligned_cols=46  Identities=15%  Similarity=0.005  Sum_probs=43.5

Q ss_pred             CCceEEEEeccCccccCC-CCCCCHHHHHHHHHHHHhC--CCCeeeeec
Q 031564           95 PGFVKIVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSS--GLPVVEATS  140 (157)
Q Consensus        95 P~~V~IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~A--Gv~~IEvgS  140 (157)
                      .++|.|.|+++|||.|.. ..-+.|++|+.++..|.++  |+..||++.
T Consensus       530 ~~~v~i~DtTlRDg~Qs~~atr~~~~d~l~ia~~l~~~~~g~~siE~~g  578 (1146)
T PRK12999        530 QKRVLLTDTTFRDAHQSLLATRVRTKDLLRIAPATARLLPNLFSLEMWG  578 (1146)
T ss_pred             cCCcEEEECCcchhhhccccccCCHHHHHHHHHHHHHHhCCCCEEEeeC
Confidence            457999999999999997 7999999999999999999  999999996

>PRK14042 pyruvate carboxylase subunit B; Provisional

Probab=95.98  E-value=0.0092  Score=56.30  Aligned_cols=45  Identities=16%  Similarity=0.042  Sum_probs=41.7

Q ss_pred             CceEEEEeccCcccc-CCCCCCCHHHHHHHHHHHHhCCCCeeeeec
Q 031564           96 GFVKIVEVGPRDGLQ-NEKNIVPAVVKVELIKLLVSSGLPVVEATS  140 (157)
Q Consensus        96 ~~V~IvEVGpRDGLQ-ne~~~vpTe~KIeLI~~L~~AGv~~IEvgS  140 (157)
                      ++|.|.|+++|||-| ...+-+.|++=+.++..|.++|+..||++.
T Consensus         2 ~~~~i~DttlRDg~QSl~atr~~t~d~~~ia~~~d~~g~~siE~~g   47 (596)
T PRK14042          2 SKTFITDVTLRDAHQCLIATRMRTEDMLPICNKMDDVGFWAMEVWG   47 (596)
T ss_pred             CceEEEECCcchhhhhhhhcCCCHHHHHHHHHHHHhcCCCEEEeeC
Confidence            469999999999999 678899999999999999999999999974

>COG5016 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]

Probab=90.57  E-value=0.13  Score=48.03  Aligned_cols=44  Identities=20%  Similarity=0.129  Sum_probs=39.7

Q ss_pred             CceEEEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeeee
Q 031564           96 GFVKIVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEAT  139 (157)
Q Consensus        96 ~~V~IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEvg  139 (157)
                      ..|.|.|+.+|||.|+. .+-+.|++=+-+++.|.++|+-.+|+.
T Consensus         4 k~i~itdt~lRDghQSl~ATRmrt~DmlPi~e~lD~~G~~slE~W   48 (472)
T COG5016           4 KKIKITDTVLRDGHQSLLATRMRTEDMLPIAEALDKVGYWSLEVW   48 (472)
T ss_pred             ceeeeEeeeechHHHHHHHHHHhHHhhHHHHHHHHhcCeeEEEec
Confidence            56999999999999997 446889999999999999999999985

>PF04481 DUF561: Protein of unknown function (DUF561); InterPro: IPR007570 Protein in this entry are of unknown function and are found in cyanobacteria and the chloroplasts of algae

Probab=80.94  E-value=2.3  Score=37.02  Aligned_cols=60  Identities=20%  Similarity=0.315  Sum_probs=47.3

Q ss_pred             ccccccccccCCCCcccchhhHhhhhcCCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeee
Q 031564           66 NGYLSKAHYSSSCTDNSTKDLTSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEA  138 (157)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEv  138 (157)
                      ++|-.++.|+.    .++-.++.+.+.-+|+- .+.=+        .|+++|.++-++|...|.++|++-|+-
T Consensus        92 sFY~qGr~f~a----~eVL~Lt~~tR~LLP~~-~LsVT--------VPHiL~ld~Qv~LA~~L~~~GaDiIQT  151 (242)
T PF04481_consen   92 SFYAQGRRFSA----EEVLALTRETRSLLPDI-TLSVT--------VPHILPLDQQVQLAEDLVKAGADIIQT  151 (242)
T ss_pred             HHHhcCCeecH----HHHHHHHHHHHHhCCCC-ceEEe--------cCccccHHHHHHHHHHHHHhCCcEEEc
Confidence            66666777654    47778888888888883 33322        579999999999999999999999974

As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	157
2cw6_A	298	Crystal Structure Of Human Hmg-Coa Lyase: Insights		2e-18
3mp4_A	298	Crystal Structure Of Human Lyase R41m Mutant Length		1e-17
1ydn_A	295	Crystal Structure Of The Hmg-Coa Lyase From Brucell		2e-13
2ftp_A	302	Crystal Structure Of Hydroxymethylglutaryl-Coa Lyas		5e-13
1ydo_A	307	Crystal Structure Of The Bacillis Subtilis Hmg-Coa		1e-10

>pdb|2CW6|A Chain A, Crystal Structure Of Human Hmg-Coa Lyase: Insights Into Catalysis And The Molecular Basis For Hydroxymethylglutaric Aciduria Length = 298

Iteration: 1
 Score = 88.2 bits (217), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 41/59 (69%), Positives = 48/59 (81%)
Query: 94  VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVAD 152
           +P  VKIVEVGPRDGLQNEKNIV   VK++LI +L  +GL V+E TSFVSPKWVPQ+ D
Sbjct: 2   LPKRVKIVEVGPRDGLQNEKNIVSTPVKIKLIDMLSEAGLSVIETTSFVSPKWVPQMGD 60

>pdb|3MP4|A Chain A, Crystal Structure Of Human Lyase R41m Mutant Length = 298

Iteration: 1
 Score = 85.5 bits (210), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 40/59 (67%), Positives = 47/59 (79%)
Query: 94  VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVAD 152
           +P  VKIVEVGP DGLQNEKNIV   VK++LI +L  +GL V+E TSFVSPKWVPQ+ D
Sbjct: 2   LPKRVKIVEVGPMDGLQNEKNIVSTPVKIKLIDMLSEAGLSVIETTSFVSPKWVPQMGD 60

>pdb|1YDN|A Chain A, Crystal Structure Of The Hmg-Coa Lyase From Brucella Melitensis, Northeast Structural Genomics Target Lr35. Length = 295

Iteration: 1
 Score = 71.6 bits (174), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/56 (60%), Positives = 39/56 (69%)
Query: 98  VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
           V+IVE   RDGLQNEK  VP   K+ LI  L   G   +EATSFVSPKWVPQ+AD+
Sbjct: 5   VEIVEXAARDGLQNEKRFVPTADKIALINRLSDCGYARIEATSFVSPKWVPQLADS 60

>pdb|2FTP|A Chain A, Crystal Structure Of Hydroxymethylglutaryl-Coa Lyase From Pseudomonas Aeruginosa Length = 302

Iteration: 1
 Score = 70.1 bits (170), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 32/58 (55%), Positives = 42/58 (72%)
Query: 94  VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVA 151
           +P  V++VEVGPRDGLQNEK  +    K+ L+  L ++GL  +E  SFVSPKWVPQ+A
Sbjct: 5   LPKKVRLVEVGPRDGLQNEKQPIEVADKIRLVDDLSAAGLDYIEVGSFVSPKWVPQMA 62

>pdb|1YDO|A Chain A, Crystal Structure Of The Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target Sr181. Length = 307

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 37/60 (61%)
Query: 95  PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADAL 154
           P  V I EVGPRDGLQNE   +    K+  I  L  +GL  +E TSFV PKW+P + DA+
Sbjct: 4   PKKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDAI 63

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	157
2ftp_A	302	Hydroxymethylglutaryl-COA lyase; structural genomi	1e-34
2cw6_A	298	Hydroxymethylglutaryl-COA lyase, mitochondrial; HM	1e-34
1ydn_A	295	Hydroxymethylglutaryl-COA lyase; TIM-barrel protei	2e-34
1ydo_A	307	HMG-COA lyase; TIM-barrel protein, structural geno	2e-34

>2ftp_A Hydroxymethylglutaryl-COA lyase; structural genomics, PSI, protein structure initiativ midwest center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa} Length = 302

 Score =  121 bits (306), Expect = 1e-34
 Identities = 32/59 (54%), Positives = 42/59 (71%)

Query: 95  PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
           P  V++VEVGPRDGLQNEK  +    K+ L+  L ++GL  +E  SFVSPKWVPQ+A +
Sbjct: 6   PKKVRLVEVGPRDGLQNEKQPIEVADKIRLVDDLSAAGLDYIEVGSFVSPKWVPQMAGS 64

>2cw6_A Hydroxymethylglutaryl-COA lyase, mitochondrial; HMG-COA lyase, ketogenic enzyme; HET: 3HG; 2.10A {Homo sapiens} PDB: 3mp3_A* 3mp4_A 3mp5_A* Length = 298

 Score =  121 bits (306), Expect = 1e-34
 Identities = 41/59 (69%), Positives = 47/59 (79%)

Query: 95  PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
           P  VKIVEVGPRDGLQNEKNIV   VK++LI +L  +GL V+E TSFVSPKWVPQ+ D 
Sbjct: 3   PKRVKIVEVGPRDGLQNEKNIVSTPVKIKLIDMLSEAGLSVIETTSFVSPKWVPQMGDH 61

>1ydn_A Hydroxymethylglutaryl-COA lyase; TIM-barrel protein, structural genomics, PSI, protein struct initiative; 2.30A {Brucella melitensis} Length = 295

 Score =  120 bits (304), Expect = 2e-34
 Identities = 34/59 (57%), Positives = 40/59 (67%)

Query: 95  PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
              V+IVE+  RDGLQNEK  VP   K+ LI  L   G   +EATSFVSPKWVPQ+AD+
Sbjct: 2   AEHVEIVEMAARDGLQNEKRFVPTADKIALINRLSDCGYARIEATSFVSPKWVPQLADS 60

>1ydo_A HMG-COA lyase; TIM-barrel protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG,; 2.71A {Bacillus subtilis subsp} Length = 307

 Score =  121 bits (305), Expect = 2e-34
 Identities = 30/59 (50%), Positives = 36/59 (61%)

Query: 95  PGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
           P  V I EVGPRDGLQNE   +    K+  I  L  +GL  +E TSFV PKW+P + DA
Sbjct: 4   PKKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDA 62

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	157
1ydo_A	307	HMG-COA lyase; TIM-barrel protein, structural geno	99.78
2cw6_A	298	Hydroxymethylglutaryl-COA lyase, mitochondrial; HM	99.76
2ftp_A	302	Hydroxymethylglutaryl-COA lyase; structural genomi	99.73
1ydn_A	295	Hydroxymethylglutaryl-COA lyase; TIM-barrel protei	99.7
3ble_A	337	Citramalate synthase from leptospira interrogans;	99.6
3dxi_A	320	Putative aldolase; TIM barrel, 11107N, PSI2, NYSGX	99.58
3ivs_A	423	Homocitrate synthase, mitochondrial; TIM barrel, m	99.51
3eeg_A	325	2-isopropylmalate synthase; 11106D, beta barrel, P	99.48
1nvm_A	345	HOA, 4-hydroxy-2-oxovalerate aldolase; sequestered	99.43
3ewb_X	293	2-isopropylmalate synthase; LEUA, structural genom	99.43
3rmj_A	370	2-isopropylmalate synthase; LEUA, truncation, neis	99.39
2ztj_A	382	Homocitrate synthase; (beta/alpha)8 TIM barrel, su	99.36
3hq1_A	644	2-isopropylmalate synthase; LEUA, mycobacterium tu	99.26
2nx9_A	464	Oxaloacetate decarboxylase 2, subunit alpha; carbo	99.0
1rqb_A	539	Transcarboxylase 5S subunit; TIM-barrel, carbamyla	98.91
3bg3_A	718	Pyruvate carboxylase, mitochondrial; TIM barrel, A	98.16
3hbl_A	1150	Pyruvate carboxylase; TIM barrel, ligase; HET: BTI	98.1
2qf7_A	1165	Pyruvate carboxylase protein; multi-domain, multi-	97.75

>1ydo_A HMG-COA lyase; TIM-barrel protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG,; 2.71A {Bacillus subtilis subsp}

Probab=99.78  E-value=7.5e-20  Score=152.84  Aligned_cols=62  Identities=48%  Similarity=0.770  Sum_probs=59.5

Q ss_pred             CCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccC
Q 031564           93 RVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADAL  154 (157)
Q Consensus        93 ~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~  154 (157)
                      .||.+|+|.|||||||+|+++..+++++|++|+++|.++|++.||+|||++|||||||+|++
T Consensus         2 ~~~~~v~i~DtTlRDG~Q~~~~~~~~e~k~~i~~~L~~~Gv~~IE~g~~~~~~~~p~~~d~~   63 (307)
T 1ydo_A            2 PYPKKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDAI   63 (307)
T ss_dssp             CCCSBCEEEECHHHHTGGGSSSCCCHHHHHHHHHHHHTTTCSEEEEEECSCTTTCGGGTTHH
T ss_pred             CCCCceEEEECCCCCCcCCCCCCCCHHHHHHHHHHHHHcCCCEEEECCCcCcccccccCCHH
Confidence            37889999999999999999999999999999999999999999999999999999999864

>2cw6_A Hydroxymethylglutaryl-COA lyase, mitochondrial; HMG-COA lyase, ketogenic enzyme; HET: 3HG; 2.10A {Homo sapiens} PDB: 3mp3_A* 3mp4_A 3mp5_A*

Probab=99.76  E-value=3.3e-19  Score=146.43  Aligned_cols=62  Identities=66%  Similarity=1.035  Sum_probs=59.2

Q ss_pred             CCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccC
Q 031564           93 RVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADAL  154 (157)
Q Consensus        93 ~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~  154 (157)
                      .+|++|+|.|||||||+|+++..+++++|++|+++|.++|++.||+|+|++|||+|||+|.+
T Consensus         1 ~~~~~v~i~D~tlRDG~Q~~~~~~~~e~k~~i~~~L~~~Gv~~IE~g~~~~~~~~p~~~d~~   62 (298)
T 2cw6_A            1 TLPKRVKIVEVGPRDGLQNEKNIVSTPVKIKLIDMLSEAGLSVIETTSFVSPKWVPQMGDHT   62 (298)
T ss_dssp             CCCSBCEEEECTTTHHHHTCSSCCCHHHHHHHHHHHHHTTCSEECCEECCCTTTCGGGTTHH
T ss_pred             CCCCceEEEECCCCcccCCCCCCCCHHHHHHHHHHHHHcCcCEEEECCCcCcccccccCCHH
Confidence            37889999999999999999999999999999999999999999999999999999999853

>2ftp_A Hydroxymethylglutaryl-COA lyase; structural genomics, PSI, protein structure initiativ midwest center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=99.73  E-value=2e-18  Score=142.35  Aligned_cols=61  Identities=52%  Similarity=0.867  Sum_probs=58.9

Q ss_pred             CCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564           93 RVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA  153 (157)
Q Consensus        93 ~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa  153 (157)
                      .||++|+|.|+|||||+|+++..+++++|++++++|.++|++.||+|+|++|+++|||+|.
T Consensus         4 ~~~~~v~i~D~tlRDG~Q~~~~~~~~e~k~~i~~~L~~~Gv~~IE~g~~~~~~~~~~~~d~   64 (302)
T 2ftp_A            4 NLPKKVRLVEVGPRDGLQNEKQPIEVADKIRLVDDLSAAGLDYIEVGSFVSPKWVPQMAGS   64 (302)
T ss_dssp             CCCSBCEEEECTTTHHHHTSSSCCCHHHHHHHHHHHHHTTCSEEEEEECSCTTTCGGGTTH
T ss_pred             CCCCCcEEEeCCCCCCccCCCCCCCHHHHHHHHHHHHHcCcCEEEECCCcCccccccccCH
Confidence            4789999999999999999999999999999999999999999999999999999999875

>1ydn_A Hydroxymethylglutaryl-COA lyase; TIM-barrel protein, structural genomics, PSI, protein struct initiative; 2.30A {Brucella melitensis}

Probab=99.70  E-value=8.8e-18  Score=136.96  Aligned_cols=60  Identities=57%  Similarity=0.882  Sum_probs=57.2

Q ss_pred             CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564           94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA  153 (157)
Q Consensus        94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa  153 (157)
                      +|++|.|.|||||||+|+++..+++++|++++++|.++|++.||+|+|++|+++|||+|.
T Consensus         1 ~~~~v~i~d~tlRDG~Q~~~~~~~~e~k~~i~~~L~~~Gv~~IE~g~~~~~~~~p~~~~~   60 (295)
T 1ydn_A            1 MAEHVEIVEMAARDGLQNEKRFVPTADKIALINRLSDCGYARIEATSFVSPKWVPQLADS   60 (295)
T ss_dssp             -CCBCEEEECTTTHHHHTSSSCCCHHHHHHHHHHHTTTTCSEEEEEECSCTTTCGGGTTH
T ss_pred             CCCceEEEECCCCccccCCCCCcCHHHHHHHHHHHHHcCcCEEEEccCcCccccccccCH
Confidence            578999999999999999999999999999999999999999999999999999999864

>3ble_A Citramalate synthase from leptospira interrogans; TIM barrel, licmsn, substrate specificity, acyltransferase, amino-acid biosynthesis; 2.00A {Leptospira interrogans} PDB: 3blf_A 3bli_A*

Probab=99.60  E-value=1.3e-16  Score=134.21  Aligned_cols=63  Identities=24%  Similarity=0.248  Sum_probs=55.1

Q ss_pred             hcCCCCceEEEEeccCccccCCCCCCCHHHHHHHHH-HHHhCCCCeeeeecccC-C---Ccccccccc
Q 031564           91 LGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIK-LLVSSGLPVVEATSFVS-P---KWVPQVADA  153 (157)
Q Consensus        91 ~~~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~-~L~~AGv~~IEvgSFVs-P---K~VPQMADa  153 (157)
                      |..+|++|.|.|||||||+|++...++|++|++|++ +|.++|++.||+|+|++ |   ++||||+++
T Consensus        13 ~~~~~~~v~I~DtTlRDG~Q~~~~~~~~~~k~~i~~~~L~~~Gv~~IE~g~~~~~~~~~~~v~~~~~~   80 (337)
T 3ble_A           13 MTKVETRLEILDVTLRDGEQTRGVSFSTSEKLNIAKFLLQKLNVDRVEIASARVSKGELETVQKIMEW   80 (337)
T ss_dssp             ------CCEEEECHHHHHTTSTTCCCCHHHHHHHHHHHHHTTCCSEEEEEETTSCTTHHHHHHHHHHH
T ss_pred             cccCCCceEEEECCCCCCCCCCCCCcCHHHHHHHHHHHHHHcCCCEEEEeCCCCChhHHHHHHHHHhh
Confidence            344788999999999999999999999999999999 99999999999999995 8   899999984

>3dxi_A Putative aldolase; TIM barrel, 11107N, PSI2, NYSGXRC, structural genomics, protein structure initiative; 2.04A {Bacteroides vulgatus atcc 8482}

Probab=99.58  E-value=5.9e-16  Score=131.19  Aligned_cols=57  Identities=14%  Similarity=-0.006  Sum_probs=53.9

Q ss_pred             ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcc----cccccc
Q 031564           97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWV----PQVADA  153 (157)
Q Consensus        97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~V----PQMADa  153 (157)
                      +|+|.|||||||+|+++..++|++|++++++|.++|++.||+|+||+|+|+    |||++.
T Consensus         2 ~V~I~DtTlRDG~Qs~~~~~~~~~k~~ia~~L~~aGv~~IEvg~~~~p~~~f~~~~~~~~~   62 (320)
T 3dxi_A            2 SLKILDCTLRDGGYYTNWDFNSKIVDAYILAMNELPIDYLEVGYRNKPSKEYMGKFGYTPV   62 (320)
T ss_dssp             -CEEEECHHHHHGGGGTTCCCHHHHHHHHHHHHTTTCCEEEEEECCSCCSSCCCHHHHCCH
T ss_pred             eEEEEECCcCccccCCCCcCCHHHHHHHHHHHHHhCCCEEEEecccCCccccccccccChH
Confidence            589999999999999999999999999999999999999999999999997    999863

>3ivs_A Homocitrate synthase, mitochondrial; TIM barrel, metalloprotein, transferase, claisen condensatio acid biosynthesis; 2.24A {Schizosaccharomyces pombe} PDB: 3ivt_A* 3ivu_A* 3mi3_A*

Probab=99.51  E-value=8.1e-15  Score=129.03  Aligned_cols=56  Identities=25%  Similarity=0.237  Sum_probs=53.2

Q ss_pred             CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccc
Q 031564           94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVAD  152 (157)
Q Consensus        94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMAD  152 (157)
                      ++.+|.|.|||||||+|+++..+++++|++|+++|.++||+.||+|+   |+++||+++
T Consensus        36 ~~~~V~I~DtTLRDG~Q~~~~~~s~eeKl~Ia~~L~~~Gv~~IEvG~---P~asp~d~~   91 (423)
T 3ivs_A           36 RVNNFSIIESTLREGEQFANAFFDTEKKIQIAKALDNFGVDYIELTS---PVASEQSRQ   91 (423)
T ss_dssp             CTTSCEEEECTTTGGGGSTTCCCCHHHHHHHHHHHHHHTCSEEEECC---TTSCHHHHH
T ss_pred             CCCcEEEEECCCCCCCCCCCCCcCHHHHHHHHHHHHHcCCCEEEEee---cccCHHHHH
Confidence            57789999999999999999999999999999999999999999997   899999865

>3eeg_A 2-isopropylmalate synthase; 11106D, beta barrel, PSI-II, structural genomics, protein structure initiative; 2.78A {Cytophaga hutchinsonii atcc 33406}

Probab=99.48  E-value=9.9e-15  Score=122.98  Aligned_cols=50  Identities=24%  Similarity=0.174  Sum_probs=39.6

Q ss_pred             CCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeeccc
Q 031564           93 RVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFV  142 (157)
Q Consensus        93 ~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFV  142 (157)
                      .||++|.|.|||||||+|+++..+||++|++|+++|.++|++.||+|+|+
T Consensus         2 ~~~~~v~I~DttlRDG~Q~~~~~~~~~~Kl~ia~~L~~~Gv~~IE~g~p~   51 (325)
T 3eeg_A            2 SLGKRIFVFDTTLRDGEQVPGCQLNTEEKIIVAKALDELGVDVIEAGFPV   51 (325)
T ss_dssp             --CEECEEEECGGGCC-------CCTTHHHHHHHHHHHHTCSEEEEECTT
T ss_pred             CCCCceEEEECCCCCcccCCCCCCCHHHHHHHHHHHHHcCCCEEEEeCCC
Confidence            47899999999999999999999999999999999999999999999864

>1nvm_A HOA, 4-hydroxy-2-oxovalerate aldolase; sequestered tunnel, substrate channeling; HET: NAD; 1.70A {Pseudomonas SP} SCOP: a.5.7.1 c.1.10.5

Probab=99.43  E-value=6.1e-14  Score=117.74  Aligned_cols=60  Identities=13%  Similarity=0.009  Sum_probs=55.4

Q ss_pred             CCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeee----cc-cCCCccccccc
Q 031564           93 RVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEAT----SF-VSPKWVPQVAD  152 (157)
Q Consensus        93 ~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvg----SF-VsPK~VPQMAD  152 (157)
                      ..+++|.|.|||||||+|+++..+++++|++++++|.++|++.||+|    +| .+|+|.||++|
T Consensus         4 ~~~~~v~i~DttlRDG~Q~~~~~~~~e~k~~i~~~L~~~Gvd~IEvG~~~g~p~ssp~~g~~~~~   68 (345)
T 1nvm_A            4 NPSKKLYISDVTLRDGSHAIRHQYTLDDVRAIARALDKAKVDSIEVAHGDGLQGSSFNYGFGRHT   68 (345)
T ss_dssp             CCCCBCEEEECTTTHHHHHTTTCCCHHHHHHHHHHHHHHTCSEEECSCTTSTTCCBTTTBCCSSC
T ss_pred             CCCCCcEEEECCCCcccCCCCCCCCHHHHHHHHHHHHHcCCCEEEEecCCCCCCCCCcccCCCCC
Confidence            34568999999999999999999999999999999999999999998    66 58999999986

>3ewb_X 2-isopropylmalate synthase; LEUA, structural genomics, unknown function, amino-acid biosynthesis; 2.10A {Listeria monocytogenes str}

Probab=99.43  E-value=6.2e-14  Score=116.44  Aligned_cols=50  Identities=22%  Similarity=0.185  Sum_probs=41.3

Q ss_pred             CceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccc
Q 031564           96 GFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVP  148 (157)
Q Consensus        96 ~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VP  148 (157)
                      ++|+|+|||||||+|+++..+||++|++|+++|.++||+.||+|++   +++|
T Consensus         4 ~~v~I~DttlRDG~Q~~~~~~~~~~K~~i~~~L~~~Gv~~IE~g~p---~~~~   53 (293)
T 3ewb_X            4 KKIQFFDTTLRDGEQTPGVNFDVKEKIQIALQLEKLGIDVIEAGFP---ISSP   53 (293)
T ss_dssp             EEEEEEECTTTCCC-----CCCHHHHHHHHHHHHHHTCSEEEEECG---GGCH
T ss_pred             CeeEEEECCCCCcCcCCCCCCCHHHHHHHHHHHHHcCCCEEEEeCC---CCCc
Confidence            4699999999999999999999999999999999999999999974   4555

>3rmj_A 2-isopropylmalate synthase; LEUA, truncation, neisseria MENI TIM barrel, catalytic domain, dimer, leucine biosynthesis, ketoisovalerate; 1.95A {Neisseria meningitidis}

Probab=99.39  E-value=2.6e-13  Score=116.59  Aligned_cols=50  Identities=22%  Similarity=0.241  Sum_probs=47.5

Q ss_pred             CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccC
Q 031564           94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVS  143 (157)
Q Consensus        94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVs  143 (157)
                      +|++|.|.|||||||+|+++..+++++|++|+++|.++|++.||+|+|++
T Consensus         9 ~~~~v~I~DtTLRDG~Q~~~~~~~~~~Kl~ia~~L~~~Gv~~IE~g~p~~   58 (370)
T 3rmj_A            9 QTNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAA   58 (370)
T ss_dssp             -CCBCEEEECCCCCCTTSTTCCCCHHHHHHHHHHHHHHTCSEEEEEEGGG
T ss_pred             CCCCEEEEECCCCccccCCCCCcCHHHHHHHHHHHHHcCCCEEEEeCCCC
Confidence            68899999999999999999999999999999999999999999999774

>2ztj_A Homocitrate synthase; (beta/alpha)8 TIM barrel, substrate complex, amino-acid BIOS lysine biosynthesis, transferase; HET: AKG; 1.80A {Thermus thermophilus} PDB: 2ztk_A* 2zyf_A* 3a9i_A*

Probab=99.36  E-value=3e-13  Score=115.72  Aligned_cols=54  Identities=33%  Similarity=0.340  Sum_probs=51.3

Q ss_pred             ceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccccccc
Q 031564           97 FVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA  153 (157)
Q Consensus        97 ~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa  153 (157)
                      +|.|.|+|||||+|++...+++++|++++++|.++|++.||+|+   |+++||++|+
T Consensus         3 ~v~I~DtTLRDG~Q~~~~~~~~~~k~~ia~~L~~~Gv~~IE~g~---p~~~~~~~~~   56 (382)
T 2ztj_A            3 EWKIIDSTLREGEQFEKANFSTQDKVEIAKALDEFGIEYIEVTT---PVASPQSRKD   56 (382)
T ss_dssp             CCEEEEEEETGGGGSTTCCCCHHHHHHHHHHHHHHTCSEEEECC---TTSCHHHHHH
T ss_pred             ceEEEECCCCcccCCCCCCcCHHHHHHHHHHHHHcCcCEEEEcC---CcCCHHHHHH
Confidence            59999999999999999999999999999999999999999996   9999998754

>3hq1_A 2-isopropylmalate synthase; LEUA, mycobacterium tuberculosis inhibition, bromopyruvate, amino-acid biosynthesis; HET: FLC; 1.70A {Mycobacterium tuberculosis} PDB: 1sr9_A 3hpz_A 3hps_A* 3fig_A 3u6w_A 3hpx_A

Probab=99.26  E-value=2.6e-12  Score=118.86  Aligned_cols=53  Identities=23%  Similarity=0.195  Sum_probs=49.6

Q ss_pred             CCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCcccc
Q 031564           94 VPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQ  149 (157)
Q Consensus        94 ~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQ  149 (157)
                      +.+.++|+|||||||+|+++..+++++|++|+++|.++||++||+|+   |++.|+
T Consensus        68 ~~~~p~i~DtTLRDGeQ~~g~~~s~eeKl~Ia~~L~~lGVd~IEaGf---P~asp~  120 (644)
T 3hq1_A           68 IDRAPLWCAVDLRDGNQALIDPMSPARKRRMFDLLVRMGYKEIEVGF---PSASQT  120 (644)
T ss_dssp             CCSCCEEEECCCCCCGGGCSSCCCHHHHHHHHHHHHHHTCSEEEEEC---TTTCHH
T ss_pred             cCCCCEEEECCCCccccCCCCCCCHHHHHHHHHHHHHcCCCEEEEeC---CCCChh
Confidence            56678899999999999999999999999999999999999999999   888775

>2nx9_A Oxaloacetate decarboxylase 2, subunit alpha; carboxyltransferase structure, B enzymes, Zn2+ binding site, TIM-barrel fold, lyase; 1.70A {Vibrio cholerae}

Probab=99.00  E-value=3.4e-11  Score=106.75  Aligned_cols=53  Identities=19%  Similarity=0.036  Sum_probs=46.6

Q ss_pred             cCCCCceEEEEeccCccccCCC-CCCCHHHHHHHHHHHHhCCCCeeeeec---ccCC
Q 031564           92 GRVPGFVKIVEVGPRDGLQNEK-NIVPAVVKVELIKLLVSSGLPVVEATS---FVSP  144 (157)
Q Consensus        92 ~~~P~~V~IvEVGpRDGLQne~-~~vpTe~KIeLI~~L~~AGv~~IEvgS---FVsP  144 (157)
                      ..-+++|.|.|+|||||.|++. ..++|++|++++++|.++|++.||+|+   |++|
T Consensus         2 ~~~~~~V~I~DtTLRDG~Qs~~~~~~~~~dkl~Ia~~L~~~Gv~~IE~g~~atF~~~   58 (464)
T 2nx9_A            2 TQAIKRVGVTDVVLRDAHQSLFATRLRIDDMLPIAQQLDQIGYWSLECWGGATFDSC   58 (464)
T ss_dssp             --CCCCCEEEECTTTHHHHHHSTTCCCGGGTGGGHHHHHTSCCSEEEEEETTHHHHH
T ss_pred             CCCCCCcEEEECCccccccCCCCcCCCHHHHHHHHHHHHHcCCCEEEeCcCccccch
Confidence            3456789999999999999985 589999999999999999999999998   7654

>1rqb_A Transcarboxylase 5S subunit; TIM-barrel, carbamylated lysine, transfera; HET: KCX; 1.90A {Propionibacterium freudenreichii subspshermanii} SCOP: a.5.7.2 c.1.10.5 PDB: 1rqe_A 1rqh_A* 1rr2_A* 1u5j_A* 1s3h_A*

Probab=98.91  E-value=9.9e-11  Score=105.94  Aligned_cols=50  Identities=24%  Similarity=0.093  Sum_probs=45.8

Q ss_pred             CCceEEEEeccCccccCCC-CCCCHHHHHHHHHHHHhCCCCeeeeec---ccCC
Q 031564           95 PGFVKIVEVGPRDGLQNEK-NIVPAVVKVELIKLLVSSGLPVVEATS---FVSP  144 (157)
Q Consensus        95 P~~V~IvEVGpRDGLQne~-~~vpTe~KIeLI~~L~~AGv~~IEvgS---FVsP  144 (157)
                      |.+|.|.|||||||.|++. ..++|++|++|+++|.++|++.||+|+   |++|
T Consensus        22 ~~~V~I~DtTLRDG~Qs~~~~~~~tedKl~Ia~~L~~~Gv~~IE~G~patF~~~   75 (539)
T 1rqb_A           22 PREVGITELVLRDAHQSLMATRMAMEDMVGACADIDAAGYWSVECWGGATYDSC   75 (539)
T ss_dssp             SEECEEEECTTTHHHHHHSTTCCCGGGTGGGHHHHHHTTCSEEEEEETTHHHHH
T ss_pred             CCceEEEECCCCchhccCCCCCCCHHHHHHHHHHHHHcCCCEEEeCcccccccc
Confidence            4679999999999999995 589999999999999999999999998   6654

>3bg3_A Pyruvate carboxylase, mitochondrial; TIM barrel, ATP-binding, biotin, disease mutation, gluconeogenesis, ligase, lipid synthesis, manganese; HET: KCX BTI; 2.80A {Homo sapiens} PDB: 3bg9_A

Probab=98.16  E-value=7.2e-07  Score=83.08  Aligned_cols=45  Identities=13%  Similarity=-0.006  Sum_probs=40.8

Q ss_pred             CCceEEEEeccCccccCCCCC-CCHHHHHHHHHHHHhC--CCCeeeee
Q 031564           95 PGFVKIVEVGPRDGLQNEKNI-VPAVVKVELIKLLVSS--GLPVVEAT  139 (157)
Q Consensus        95 P~~V~IvEVGpRDGLQne~~~-vpTe~KIeLI~~L~~A--Gv~~IEvg  139 (157)
                      +++|.|.|+++|||.|++... +++++|++++++|.++  |+..||+|
T Consensus       100 ~~~I~I~DTTLRDG~Qs~~~~r~~~edkl~Ia~~Ld~~Gvg~~~IE~g  147 (718)
T 3bg3_A          100 HPGLLLMDTTFRDAHQSLLATRVRTHDLKKIAPYVAHNFSKLFSMENW  147 (718)
T ss_dssp             CCSCEEEECTTTHHHHHHSTTCCCHHHHHHHHHHHHHHCTTCSEEEEE
T ss_pred             cCCeEEeecCCChhhCCCCCcCCCHHHHHHHHHHHHHhcCCCcEEEec
Confidence            457999999999999999754 9999999999999998  57779998

>3hbl_A Pyruvate carboxylase; TIM barrel, ligase; HET: BTI ADP; 2.71A {Staphylococcus aureus subsp} PDB: 3bg5_A* 3ho8_A* 4hnu_A* 4hnt_A* 4hnv_A* 3hb9_A*

Probab=98.10  E-value=6.3e-07  Score=86.52  Aligned_cols=55  Identities=13%  Similarity=-0.043  Sum_probs=46.9

Q ss_pred             CCceEEEEeccCccccCCCCC-CCHHHHHHHHHHHHhC--CCCeeeee---cccCCCcccccc
Q 031564           95 PGFVKIVEVGPRDGLQNEKNI-VPAVVKVELIKLLVSS--GLPVVEAT---SFVSPKWVPQVA  151 (157)
Q Consensus        95 P~~V~IvEVGpRDGLQne~~~-vpTe~KIeLI~~L~~A--Gv~~IEvg---SFVsPK~VPQMA  151 (157)
                      +++|.|.|+|+|||.|++... ++|++|++++++|.++  |+..||+.   +|..  .+|+|.
T Consensus       530 ~~~v~I~DtTlRDG~Qs~~~~r~~~~~kl~ia~~L~~~~~G~~~lE~~Gga~~e~--~~~~~~  590 (1150)
T 3hbl_A          530 QDDVLLTDTTFRDAHQSLLATRVRTKDMINIASKTADVFKDGFSLEMWGGATFDV--AYNFLK  590 (1150)
T ss_dssp             CSSBEEEECTTTHHHHHHSTTCCCHHHHHHHHHHHHHHTTTCSEEEEEETTHHHH--HHHTSC
T ss_pred             CCceEEEECccchhhccCCCcCCCHHHHHHHHHHHHHhhCCCcEEeecCCceEEe--cccccC
Confidence            567999999999999999886 9999999999999999  99999996   4433  355553

>2qf7_A Pyruvate carboxylase protein; multi-domain, multi-functional, biotin-dependent, ligase; HET: KCX COA AGS; 2.00A {Rhizobium etli} PDB: 3tw6_A* 3tw7_A*

Probab=97.75  E-value=7.8e-06  Score=79.03  Aligned_cols=44  Identities=16%  Similarity=0.048  Sum_probs=39.5

Q ss_pred             CCceEEEEeccCccccCCCC-CCCHHHHHHHHHHHHhCC--CCeeee
Q 031564           95 PGFVKIVEVGPRDGLQNEKN-IVPAVVKVELIKLLVSSG--LPVVEA  138 (157)
Q Consensus        95 P~~V~IvEVGpRDGLQne~~-~vpTe~KIeLI~~L~~AG--v~~IEv  138 (157)
                      +++|.|.|+++|||.|++.. .+++++|++++++|.++|  +..||+
T Consensus       548 ~~~v~i~DtTLRDG~Qs~~~~~~~~~dkl~ia~~L~~~gv~~~~iE~  594 (1165)
T 2qf7_A          548 EKRVLLTDTTMRDGHQSLLATRMRTYDIARIAGTYSHALPNLLSLEC  594 (1165)
T ss_dssp             CSSCEEEECTTTHHHHHHHTTCCCHHHHHHHHHHHHHHCTTCSEEEE
T ss_pred             CCceEEEecccccccccCCcccCCHHHHHHHHHHHHHhCCCceEEEe
Confidence            45799999999999999975 699999999999999995  556998

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	157
d1rqba2	303	c.1.10.5 (A:4-306) Transcarboxylase 5S subunit, N-	1e-12
d1sr9a2	310	c.1.10.5 (A:61-370) 2-isopropylmalate synthase Leu	3e-11
d1nvma2	289	c.1.10.5 (A:2-290) 4-hydroxy-2-oxovalerate aldolas	4e-09

>d1rqba2 c.1.10.5 (A:4-306) Transcarboxylase 5S subunit, N-terminal domain {Propionibacterium freudenreichii shermanii [TaxId: 1752]} Length = 303

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: HMGL-like
domain: Transcarboxylase 5S subunit, N-terminal domain
species: Propionibacterium freudenreichii shermanii [TaxId: 1752]

 Score = 61.5 bits (148), Expect = 1e-12
 Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 1/60 (1%)

Query: 95  PGFVKIVEVGPRDGLQN-EKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADA 153
           P  V I E+  RD  Q+     +     V     + ++G   VE     +     +  + 
Sbjct: 8   PREVGITELVLRDAHQSLMATRMAMEDMVGACADIDAAGYWSVECWGGATYDSCIRFLNE 67

>d1sr9a2 c.1.10.5 (A:61-370) 2-isopropylmalate synthase LeuA, catalytic domain {Mycobacterium tuberculosis [TaxId: 1773]} Length = 310

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: HMGL-like
domain: 2-isopropylmalate synthase LeuA, catalytic domain
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 57.7 bits (138), Expect = 3e-11
 Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 4/66 (6%)

Query: 88  SKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS-FVSPKW 146
            +++ R P       V  RDG Q   + +    K  +  LLV  G   +E      S   
Sbjct: 5   DRVIDRAP---LWCAVDLRDGNQALIDPMSPARKRRMFDLLVRMGYKEIEVGFPSASQTD 61

Query: 147 VPQVAD 152
              V +
Sbjct: 62  FDFVRE 67

>d1nvma2 c.1.10.5 (A:2-290) 4-hydroxy-2-oxovalerate aldolase DmpG, catalytic domain {Pseudomonas sp. [TaxId: 306]} Length = 289

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: HMGL-like
domain: 4-hydroxy-2-oxovalerate aldolase DmpG, catalytic domain
species: Pseudomonas sp. [TaxId: 306]

 Score = 51.5 bits (122), Expect = 4e-09
 Identities = 7/48 (14%), Positives = 17/48 (35%)

Query: 98  VKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPK 145
           + I +V  RDG    ++         + + L  + +  +E       +
Sbjct: 8   LYISDVTLRDGSHAIRHQYTLDDVRAIARALDKAKVDSIEVAHGDGLQ 55

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	157
d1rqba2	303	Transcarboxylase 5S subunit, N-terminal domain {Pr	99.68
d1sr9a2	310	2-isopropylmalate synthase LeuA, catalytic domain	99.42
d1nvma2	289	4-hydroxy-2-oxovalerate aldolase DmpG, catalytic d	99.39

>d1rqba2 c.1.10.5 (A:4-306) Transcarboxylase 5S subunit, N-terminal domain {Propionibacterium freudenreichii shermanii [TaxId: 1752]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: HMGL-like
domain: Transcarboxylase 5S subunit, N-terminal domain
species: Propionibacterium freudenreichii shermanii [TaxId: 1752]

Probab=99.68  E-value=1.1e-18  Score=137.53  Aligned_cols=65  Identities=17%  Similarity=-0.026  Sum_probs=59.8

Q ss_pred             hhcCCCCceEEEEeccCccccCC-CCCCCHHHHHHHHHHHHhCCCCeeeeecccCCCccccccccC
Q 031564           90 LLGRVPGFVKIVEVGPRDGLQNE-KNIVPAVVKVELIKLLVSSGLPVVEATSFVSPKWVPQVADAL  154 (157)
Q Consensus        90 ~~~~~P~~V~IvEVGpRDGLQne-~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK~VPQMADa~  154 (157)
                      +-..+|++|.|.|||||||+|++ +..++|++|+++++.|.++|++.||+|+|++|+++|||++..
T Consensus         3 ~~~~~p~~i~I~D~tlRDG~Qs~~~~~~~~~~ki~i~~~L~~~Gv~~IEvg~~~~~~~~~~~~~~~   68 (303)
T d1rqba2           3 IEVSEPREVGITELVLRDAHQSLMATRMAMEDMVGACADIDAAGYWSVECWGGATYDSCIRFLNED   68 (303)
T ss_dssp             CCCCCSEECEEEECTTTHHHHHHSTTCCCGGGTGGGHHHHHHTTCSEEEEEETTHHHHHHHTSCCC
T ss_pred             ccCCCCCeeEEEECCCcccccCCCCcCCCHHHHHHHHHHHHHcCCCEEEeCCCcChHHHHHHhcCc
Confidence            44678999999999999999985 667999999999999999999999999999999999998753

>d1sr9a2 c.1.10.5 (A:61-370) 2-isopropylmalate synthase LeuA, catalytic domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: HMGL-like
domain: 2-isopropylmalate synthase LeuA, catalytic domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.42  E-value=1.6e-14  Score=111.77  Aligned_cols=56  Identities=25%  Similarity=0.301  Sum_probs=47.9

Q ss_pred             HhhhhcCCCCceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeec-ccCCC
Q 031564           87 TSKLLGRVPGFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATS-FVSPK  145 (157)
Q Consensus        87 ~~~~~~~~P~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgS-FVsPK  145 (157)
                      +.|.+..-|   ++.|||+|||+|++...++|++|+++++.|.++|++.||+|+ +++|+
T Consensus         4 ~~~~~~~~~---~~~D~tLRDG~Q~~~~~~~~~~k~~i~~~L~~aGv~~IEvG~p~~s~~   60 (310)
T d1sr9a2           4 PDRVIDRAP---LWCAVDLRDGNQALIDPMSPARKRRMFDLLVRMGYKEIEVGFPSASQT   60 (310)
T ss_dssp             GGCCCCSCC---EEEECTTTHHHHTCSSCCCHHHHHHHHHHHHHHTCSEEEEECTTTCHH
T ss_pred             ccccccCCC---eeeECCCCccCcCCCCCCCHHHHHHHHHHHHHcCCCEEEEeCCcCCHH
Confidence            344444444   677999999999999999999999999999999999999998 66665

>d1nvma2 c.1.10.5 (A:2-290) 4-hydroxy-2-oxovalerate aldolase DmpG, catalytic domain {Pseudomonas sp. [TaxId: 306]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: HMGL-like
domain: 4-hydroxy-2-oxovalerate aldolase DmpG, catalytic domain
species: Pseudomonas sp. [TaxId: 306]

Probab=99.39  E-value=6.9e-14  Score=109.02  Aligned_cols=50  Identities=14%  Similarity=0.048  Sum_probs=47.1

Q ss_pred             CceEEEEeccCccccCCCCCCCHHHHHHHHHHHHhCCCCeeeeecccCCC
Q 031564           96 GFVKIVEVGPRDGLQNEKNIVPAVVKVELIKLLVSSGLPVVEATSFVSPK  145 (157)
Q Consensus        96 ~~V~IvEVGpRDGLQne~~~vpTe~KIeLI~~L~~AGv~~IEvgSFVsPK  145 (157)
                      ++|.|.|||||||+|+.+..+|+++|+++++.|.++||+.||+|++++|+
T Consensus         6 kkI~I~D~TlRDG~Q~~~~~~s~e~k~~i~~~L~~~Gv~~IEvG~~~~~~   55 (289)
T d1nvma2           6 KKLYISDVTLRDGSHAIRHQYTLDDVRAIARALDKAKVDSIEVAHGDGLQ   55 (289)
T ss_dssp             CBCEEEECTTTHHHHHTTTCCCHHHHHHHHHHHHHHTCSEEECSCTTSTT
T ss_pred             CCeEEEECCcccccCCCCCCCCHHHHHHHHHHHHHcCCCEEEeCCCcCcc
Confidence            46999999999999999999999999999999999999999999877664