Citrus Sinensis ID: 026235

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-

MAQVSLFSLSSPFPASAVSSRLRLNRPLPFQFSRIQASSDATSASASNSNPKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIPVVAVASPSAVR

ccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccHHHHHHHHHHccccEEEcccEEEEEcccHHHHHHHHHccccccEEEEEcHHHHHHHHHHHHHcccccccEEEEcHHHHHHHHHHHHccccccEEEEccccccHHHHHHHcccccccccEEEEEccccccHHHHHHHHHcccEEEEEEEEEccccccccHHHHHHcccccEEEEEcccccc

cccEEEccccccccccccccccEccccccccccccccccccccccccccccEEEEEccccHHHHHHHHHHHccccEEEEEEEEEcccccHHHHHHHHHHHccccEEEEEcHHHHHHHHHHHHHccccccEEEEEcHHHHHHHHHHHHHccccccccccccccHHHHHHHHcccccccccEEEEccHHHHHHHHHHHHHHcccEEEEEEEEEccccccccHHHHHHHccccEEEEEcccccc

maqvslfslsspfpasavssrlrlnrplpfqfsriqassdatsasasnsnpkvvvtrergkNGKLIKALAKHRidclelpliqhaqgpdtdrlssvlnadtIFDWIiitspeagSVFLEAWKeagtpnvrigvvgAGTASIFEEVIQSSkcsldvafspskatGKILaselpkngkkkctvlypasakasNEIEEglsnrgfevvrlntyttepvhhvDQTVLKQAlsipvvavaspsavr

maqvslfslsspfpasavSSRLRLNRPLPFQFSRIQassdatsasasnsnpkvvvtrergknGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKilaselpkngkkkCTVLYPAsakasneieeglsnrgFEVVRLNTYTTEPVHHVDQTVLKqalsipvvavaspsavr

MAQvslfslsspfpasavssRLRLNRPLPFQFSRIQassdatsasasnsNPKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIpvvavaspsavR

**************************************************************GKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFS*******************KCTVLYP************LSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIPVVAV*******

**********SPF*ASA*S**LRLNRPLPFQ*******************PKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIPVVAVASPSAVR

MAQVSLFSLSSPFPASAVSSRLRLNRPLPFQFSRI******************VVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIPVVAVASPSAVR

***VSLFSLSSPFPASAVSSRLRLNRPLPFQFSR************SNSNPKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIPVVAVASP****

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

SSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

SSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		241	2.2.26 [Sep-21-2011]
O48721		321	Uroporphyrinogen-III synt	yes	no	0.788	0.591	0.717	2e-72
Q10QR9		302	Uroporphyrinogen-III synt	yes	no	0.817	0.652	0.686	1e-70
Q59294		504	Porphyrin biosynthesis pr	N/A	no	0.692	0.331	0.252	1e-05

>sp\|O48721\|HEM4_ARATH Uroporphyrinogen-III synthase, chloroplastic OS=Arabidopsis thaliana GN=UROS PE=2 SV=2	Back alignment and function desciption

 Score =  272 bits (695), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 137/191 (71%), Positives = 159/191 (83%), Gaps = 1/191 (0%)

Query: 51  PKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITS 110
           P+VVVTRERGKN ++IKAL K+ I  LELPLIQHA+GPD DRL+SVLN D  FDWIIITS
Sbjct: 65  PQVVVTRERGKNNQIIKALEKNGISSLELPLIQHARGPDFDRLASVLN-DKSFDWIIITS 123

Query: 111 PEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASE 170
           PEAGSVFLEAWK A +P V+IGVVGAGTA +FEE ++S+   L VAF+PSKATGK+LASE
Sbjct: 124 PEAGSVFLEAWKTASSPEVQIGVVGAGTARVFEEAMKSADGLLHVAFTPSKATGKVLASE 183

Query: 171 LPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIP 230
           LP+   K+ +VLYPAS KA N+I EGLS RGFEVVRLNTYTT PV  VD  +L+QALS P
Sbjct: 184 LPEKVGKRSSVLYPASLKAGNDIVEGLSKRGFEVVRLNTYTTVPVQSVDTVLLQQALSAP 243

Query: 231 VVAVASPSAVR 241
           V++VASPSAVR
Sbjct: 244 VLSVASPSAVR 254

Catalyzes cyclization of the linear tetrapyrrole, hydroxymethylbilane, to the macrocyclic uroporphyrinogen III, a precursor of tetrapyrroles such as chlorophyll, heme and phycobilins.
Arabidopsis thaliana (taxid: 3702)
EC: 4EC: .EC: 2EC: .EC: 1EC: .EC: 7EC: 5

>sp\|Q10QR9\|HEM4_ORYSJ Uroporphyrinogen-III synthase, chloroplastic OS=Oryza sativa subsp. japonica GN=UROS PE=2 SV=1	Back alignment and function description

>sp\|Q59294\|HEM4_CLOJO Porphyrin biosynthesis protein HemD OS=Clostridium josui GN=hemD PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		241
224137378		296	predicted protein [Populus trichocarpa]	0.792	0.645	0.837	3e-88
359492064		304	PREDICTED: uroporphyrinogen-III synthase	0.887	0.703	0.726	3e-82
356519166		297	PREDICTED: uroporphyrinogen-III synthase	0.796	0.646	0.768	6e-80
449470043		311	PREDICTED: uroporphyrinogen-III synthase	0.991	0.768	0.676	9e-80
356509718		300	PREDICTED: uroporphyrinogen-III synthase	0.796	0.64	0.757	2e-78
357465443		308	Uroporphyrinogen-III synthase [Medicago	0.817	0.639	0.728	5e-78
18694346		321	uroporphyrinogen III synthase [Arabidops	0.788	0.591	0.717	9e-71
18401160		321	Uroporphyrinogen-III synthase [Arabidops	0.788	0.591	0.717	9e-71
21592861		321	uroporphyrinogen III synthase [Arabidops	0.788	0.591	0.712	1e-70
218192221		302	hypothetical protein OsI_10298 [Oryza sa	0.817	0.652	0.691	4e-70

>gi\|224137378\|ref\|XP_002327111.1\| predicted protein [Populus trichocarpa] gi\|222835426\|gb\|EEE73861.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  330 bits (846), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 160/191 (83%), Positives = 177/191 (92%)

Query: 51  PKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITS 110
           PKVVVTRERGKNGKLIKALAK+ I CLELPLIQH QGPD+D+LSSVL AD+ FDWII+TS
Sbjct: 46  PKVVVTRERGKNGKLIKALAKYGISCLELPLIQHTQGPDSDKLSSVLCADSAFDWIIVTS 105

Query: 111 PEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASE 170
           PEAGSVFLEAWK AGTP V++GVVGAGTASIFEEV+QSS+ SLDVAF+PSKATGK+LASE
Sbjct: 106 PEAGSVFLEAWKVAGTPKVKLGVVGAGTASIFEEVMQSSERSLDVAFTPSKATGKVLASE 165

Query: 171 LPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIP 230
           LP+NG K+CTVLYPASAKASNEIE+GL NRGFEVVRLNTYTT PV HVD+ VLKQA+S P
Sbjct: 166 LPRNGNKRCTVLYPASAKASNEIEQGLYNRGFEVVRLNTYTTVPVGHVDEMVLKQAISAP 225

Query: 231 VVAVASPSAVR 241
           VVAVASPS+VR
Sbjct: 226 VVAVASPSSVR 236

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|359492064\|ref\|XP_002282338.2\| PREDICTED: uroporphyrinogen-III synthase, chloroplastic-like [Vitis vinifera] gi\|302142364\|emb\|CBI19567.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356519166\|ref\|XP_003528245.1\| PREDICTED: uroporphyrinogen-III synthase, chloroplastic-like [Glycine max]	Back alignment and taxonomy information

>gi\|449470043\|ref\|XP_004152728.1\| PREDICTED: uroporphyrinogen-III synthase, chloroplastic-like [Cucumis sativus] gi\|449496021\|ref\|XP_004160014.1\| PREDICTED: uroporphyrinogen-III synthase, chloroplastic-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|356509718\|ref\|XP_003523593.1\| PREDICTED: uroporphyrinogen-III synthase, chloroplastic-like [Glycine max]	Back alignment and taxonomy information

>gi\|357465443\|ref\|XP_003603006.1\| Uroporphyrinogen-III synthase [Medicago truncatula] gi\|355492054\|gb\|AES73257.1\| Uroporphyrinogen-III synthase [Medicago truncatula]	Back alignment and taxonomy information

>gi\|18694346\|emb\|CAC85287.1\| uroporphyrinogen III synthase [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi|18401160|ref|NP_565625.1| Uroporphyrinogen-III synthase [Arabidopsis thaliana] gi|75219491|sp|O48721.2|HEM4_ARATH RecName: Full=Uroporphyrinogen-III synthase, chloroplastic; Short=AtUROS; AltName: Full=Hydroxymethylbilane hydrolyase [cyclizing]; AltName: Full=Uroporphyrinogen-III cosynthase; Flags: Precursor gi|20196944|gb|AAC14502.2| expressed protein [Arabidopsis thaliana] gi|109946587|gb|ABG48472.1| At2g26540 [Arabidopsis thaliana] gi|330252760|gb|AEC07854.1| Uroporphyrinogen-III synthase [Arabidopsis thaliana]

Back alignment and taxonomy information

>gi\|21592861\|gb\|AAM64811.1\| uroporphyrinogen III synthase [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|218192221\|gb\|EEC74648.1\| hypothetical protein OsI_10298 [Oryza sativa Indica Group]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		241
TAIR\|locus:2066256		321	HEMD [Arabidopsis thaliana (ta	0.829	0.623	0.647	4.3e-61

TAIR\|locus:2066256 HEMD [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 625 (225.1 bits), Expect = 4.3e-61, P = 4.3e-61
 Identities = 132/204 (64%), Positives = 153/204 (75%)

Query:    27 PLPFQFSRIQXXXXXXXXXXXXXN--PKVVVTRERGKNGKLIKALAKHRIDCLELPLIQH 84
             P P + S I              N  P+VVVTRERGKN ++IKAL K+ I  LELPLIQH
Sbjct:    40 PSPIRNS-ISSSVSSSSSSVSSSNSIPQVVVTRERGKNNQIIKALEKNGISSLELPLIQH 98

Query:    85 AQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEE 144
             A+GPD DRL+SVLN D  FDWIIITSPEAGSVFLEAWK A +P V+IGVVGAGTA +FEE
Sbjct:    99 ARGPDFDRLASVLN-DKSFDWIIITSPEAGSVFLEAWKTASSPEVQIGVVGAGTARVFEE 157

Query:   145 VIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEV 204
              ++S+   L VAF+PSKATGK+LASELP+   K+ +VLYPAS KA N+I EGLS RGFEV
Sbjct:   158 AMKSADGLLHVAFTPSKATGKVLASELPEKVGKRSSVLYPASLKAGNDIVEGLSKRGFEV 217

Query:   205 VRLNTYTTEPVHHVDQTVLKQALS 228
             VRLNTYTT PV  VD  +L+QALS
Sbjct:   218 VRLNTYTTVPVQSVDTVLLQQALS 241


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.317   0.132   0.379    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      241       200   0.00087  111 3  11 22  0.50    32
                                                     31  0.45    35


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  594 (63 KB)
  Total size of DFA:  160 KB (2096 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  19.24u 0.24s 19.48t   Elapsed:  00:00:01
  Total cpu time:  19.24u 0.24s 19.48t   Elapsed:  00:00:01
  Start:  Fri May 10 04:01:58 2013   End:  Fri May 10 04:01:59 2013

GO:0004852 "uroporphyrinogen-III synthase activity" evidence=IEA;ISS;IDA

GO:0006779 "porphyrin-containing compound biosynthetic process" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0033014 "tetrapyrrole biosynthetic process" evidence=IEA

GO:0006780 "uroporphyrinogen III biosynthetic process" evidence=IDA

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q10QR9	HEM4_ORYSJ	4, ., 2, ., 1, ., 7, 5	0.6868	0.8174	0.6523	yes	no
O48721	HEM4_ARATH	4, ., 2, ., 1, ., 7, 5	0.7172	0.7883	0.5919	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	4.2.1	0.921
4th Layer	4.2.1.75	0.914

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	gw1.40.619.1	hypothetical protein (272 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	fgenesh4_pm.C_LG_VII000271	hydroxymethylbilane synthase (EC-2.5.1.61) (363 aa)	•	•	•	•	0.959
	fgenesh4_pg.C_LG_V000312	hydroxymethylbilane synthase (EC-2.5.1.61) (364 aa)	•	•	•	•	0.958
	estExt_fgenesh4_pg.C_LG_XIX0326	SubName- Full=Putative uncharacterized protein; (403 aa)	•	•	•	•	0.932
	gw1.182.88.1	uroporphyrinogen decarboxylase (EC-4.1.1.37) (357 aa)	•	•	•	•	0.932
	eugene3.00150799	glutamate-1-semialdehyde 2,1-aminomutase (EC-5.4.3.8) (479 aa)	•	•		•	0.574
	gw1.148.3.1	uroporphyrin-III C-methyltransferase (EC-2.1.1.107) (328 aa)	•			•	0.415
	estExt_Genewise1_v1.C_LG_II0707	glutamyl-tRNA reductase (EC-1.2.1.70) (469 aa)	•			•	0.400

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		241
cd06578		239	cd06578, HemD, Uroporphyrinogen-III synthase (HemD	4e-32
COG1587		248	COG1587, HemD, Uroporphyrinogen-III synthase [Coen	1e-27
PRK05928		249	PRK05928, hemD, uroporphyrinogen-III synthase; Rev	4e-24
pfam02602		230	pfam02602, HEM4, Uroporphyrinogen-III synthase Hem	1e-23
PRK06975		656	PRK06975, PRK06975, bifunctional uroporphyrinogen-	9e-09

>gnl\|CDD\|119440 cd06578, HemD, Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme	Back alignment and domain information

 Score =  117 bits (294), Expect = 4e-32
 Identities = 59/194 (30%), Positives = 85/194 (43%), Gaps = 13/194 (6%)

Query: 53  VVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPE 112
           V+VTR R +  +L   L     + LELPLI+     D +  +++ + D  +DW+I TSP 
Sbjct: 1   VLVTRPRPQADELAALLEALGAEVLELPLIEIEPLDDAELDAALADLDE-YDWLIFTSPN 59

Query: 113 AGSVFLEAWKEAGT---PNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILAS 169
           A   F EA +E G      ++I  VG  TA    E        L   F P +   + L  
Sbjct: 60  AVEAFFEALEELGLRALAGLKIAAVGPKTAEALRE------AGLTADFVPEEGDSEGLLE 113

Query: 170 ELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTV--LKQAL 227
            L     K   +L P   +A  ++ E L  RG EV  +  Y T P     + +  L++  
Sbjct: 114 LLELQDGKGKRILRPRGGRAREDLAEALRERGAEVDEVEVYRTVPPDLDAELLELLEEGA 173

Query: 228 SIPVVAVASPSAVR 241
            I  V   SPS VR
Sbjct: 174 -IDAVLFTSPSTVR 186

This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in the human uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria, a recessive inborn error of metabolism also known as Gunther disease. Length = 239

>gnl\|CDD\|224503 COG1587, HemD, Uroporphyrinogen-III synthase [Coenzyme metabolism]	Back alignment and domain information

>gnl\|CDD\|235647 PRK05928, hemD, uroporphyrinogen-III synthase; Reviewed	Back alignment and domain information

>gnl\|CDD\|217136 pfam02602, HEM4, Uroporphyrinogen-III synthase HemD	Back alignment and domain information

>gnl\|CDD\|235899 PRK06975, PRK06975, bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		241
PRK05752		255	uroporphyrinogen-III synthase; Validated	100.0
PRK08811		266	uroporphyrinogen-III synthase; Validated	100.0
COG1587		248	HemD Uroporphyrinogen-III synthase [Coenzyme metab	100.0
PRK07239		381	bifunctional uroporphyrinogen-III synthetase/respo	100.0
PRK09189		240	uroporphyrinogen-III synthase; Validated	100.0
PRK05928		249	hemD uroporphyrinogen-III synthase; Reviewed	100.0
PRK06975		656	bifunctional uroporphyrinogen-III synthetase/uropo	100.0
cd06578		239	HemD Uroporphyrinogen-III synthase (HemD) catalyze	99.97
PF02602		231	HEM4: Uroporphyrinogen-III synthase HemD; InterPro	99.97
PRK07168		474	bifunctional uroporphyrinogen-III methyltransferas	99.94
KOG4132		260	consensus Uroporphyrinogen III synthase UROS/HEM4	99.93
PRK05928		249	hemD uroporphyrinogen-III synthase; Reviewed	99.74
cd06578		239	HemD Uroporphyrinogen-III synthase (HemD) catalyze	99.7
PRK07239		381	bifunctional uroporphyrinogen-III synthetase/respo	99.68
PRK05752		255	uroporphyrinogen-III synthase; Validated	99.66
PRK09189		240	uroporphyrinogen-III synthase; Validated	99.62
PF02602		231	HEM4: Uroporphyrinogen-III synthase HemD; InterPro	99.62
COG1587		248	HemD Uroporphyrinogen-III synthase [Coenzyme metab	99.6
KOG4132		260	consensus Uroporphyrinogen III synthase UROS/HEM4	99.55
PRK08811		266	uroporphyrinogen-III synthase; Validated	99.54
PRK06975		656	bifunctional uroporphyrinogen-III synthetase/uropo	99.28
PRK07168		474	bifunctional uroporphyrinogen-III methyltransferas	98.27
PRK02261		137	methylaspartate mutase subunit S; Provisional	95.94
COG2185		143	Sbm Methylmalonyl-CoA mutase, C-terminal domain/su	95.21
TIGR02853		287	spore_dpaA dipicolinic acid synthetase, A subunit.	95.17
TIGR00640		132	acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal	94.65
PRK08306		296	dipicolinate synthase subunit A; Reviewed	94.35
COG1609		333	PurR Transcriptional regulators [Transcription]	94.2
cd06298		268	PBP1_CcpA_like Ligand-binding domain of the catabo	94.07
cd06295		275	PBP1_CelR Ligand binding domain of a transcription	94.06
cd06299		265	PBP1_LacI_like_13 Ligand-binding domain of DNA-bin	93.92
cd02072		128	Glm_B12_BD B12 binding domain of glutamate mutase	93.9
TIGR01501		134	MthylAspMutase methylaspartate mutase, S subunit.	93.77
cd06273		268	PBP1_GntR_like_1 This group includes the ligand-bi	92.95
PF00532		279	Peripla_BP_1: Periplasmic binding proteins and sug	92.84
cd06271		268	PBP1_AglR_RafR_like Ligand-binding domain of DNA t	92.6
cd01575		268	PBP1_GntR Ligand-binding domain of DNA transcripti	92.5
cd06272		261	PBP1_hexuronate_repressor_like Ligand-binding doma	92.0
cd06297		269	PBP1_LacI_like_12 Ligand-binding domain of unchara	91.92
cd06301		272	PBP1_rhizopine_binding_like Periplasmic binding pr	91.62
cd06310		273	PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-bi	91.57
cd06320		275	PBP1_allose_binding Periplasmic allose-binding dom	91.43
cd02071		122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	91.3
cd06283		267	PBP1_RegR_EndR_KdgR_like Ligand-binding domain of	90.87
TIGR01481		329	ccpA catabolite control protein A. Catabolite cont	90.83
cd06288		269	PBP1_sucrose_transcription_regulator Ligand-bindin	90.64
PRK10014		342	DNA-binding transcriptional repressor MalI; Provis	90.6
cd06354		265	PBP1_BmpA_PnrA_like Periplasmic binding domain of	90.57
PRK11790		409	D-3-phosphoglycerate dehydrogenase; Provisional	90.53
cd06286		260	PBP1_CcpB_like Ligand-binding domain of a novel tr	90.47
cd06294		270	PBP1_ycjW_transcription_regulator_like Ligand-bind	90.41
cd06305		273	PBP1_methylthioribose_binding_like Methylthioribos	90.35
cd01537		264	PBP1_Repressors_Sugar_Binding_like Ligand-binding	90.22
PF04392		294	ABC_sub_bind: ABC transporter substrate binding pr	90.14
cd06270		268	PBP1_GalS_like Ligand binding domain of DNA transc	89.99
cd06292		273	PBP1_LacI_like_10 Ligand-binding domain of unchara	89.98
cd01545		270	PBP1_SalR Ligand-binding domain of DNA transcripti	89.96
cd06281		269	PBP1_LacI_like_5 Ligand-binding domain of uncharac	89.94
PRK10423		327	transcriptional repressor RbsR; Provisional	89.91
cd00316		399	Oxidoreductase_nitrogenase The nitrogenase enzyme	89.85
cd06309		273	PBP1_YtfQ_like Periplasmic binding domain of ABC-t	89.79
cd06284		267	PBP1_LacI_like_6 Ligand-binding domain of an uncha	89.66
PRK15438		378	erythronate-4-phosphate dehydrogenase PdxB; Provis	89.48
cd01536		267	PBP1_ABC_sugar_binding_like Periplasmic sugar-bind	89.45
PRK10703		341	DNA-binding transcriptional repressor PurR; Provis	89.38
cd06285		265	PBP1_LacI_like_7 Ligand-binding domain of uncharac	89.36
cd06289		268	PBP1_MalI_like Ligand-binding domain of MalI, a tr	89.17
cd01542		259	PBP1_TreR_like Ligand-binding domain of DNA transc	89.16
cd06275		269	PBP1_PurR Ligand-binding domain of purine represso	89.01
cd06296		270	PBP1_CatR_like Ligand-binding domain of a LacI-lik	88.87
cd06279		283	PBP1_LacI_like_3 Ligand-binding domain of uncharac	88.72
cd06274		264	PBP1_FruR Ligand binding domain of DNA transcripti	87.73
PF03358		152	FMN_red: NADPH-dependent FMN reductase; InterPro:	87.67
PRK10569		191	NAD(P)H-dependent FMN reductase; Provisional	87.65
PLN02928		347	oxidoreductase family protein	87.62
cd02067		119	B12-binding B12 binding domain (B12-BD). This doma	87.48
cd06267		264	PBP1_LacI_sugar_binding_like Ligand binding domain	87.21
PRK11303		328	DNA-binding transcriptional regulator FruR; Provis	87.14
cd06278		266	PBP1_LacI_like_2 Ligand-binding domain of uncharac	86.86
cd01541		273	PBP1_AraR Ligand-binding domain of DNA transcripti	86.85
cd06282		266	PBP1_GntR_like_2 Ligand-binding domain of putative	86.45
cd06313		272	PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-bi	86.13
cd06314		271	PBP1_tmGBP Periplasmic sugar-binding domain of The	85.89
cd01574		264	PBP1_LacI Ligand-binding domain of DNA transcripti	85.77
cd06307		275	PBP1_uncharacterized_sugar_binding Periplasmic sug	85.7
cd06302		298	PBP1_LsrB_Quorum_Sensing Periplasmic binding domai	85.65
COG4822		265	CbiK Cobalamin biosynthesis protein CbiK, Co2+ che	85.64
cd06290		265	PBP1_LacI_like_9 Ligand-binding domain of uncharac	85.33
cd06318		282	PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-bi	85.31
cd06293		269	PBP1_LacI_like_11 Ligand-binding domain of unchara	84.48
cd06287		269	PBP1_LacI_like_8 Ligand-binding domain of uncharac	84.07
cd06316		294	PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-bi	83.49
PRK00257		381	erythronate-4-phosphate dehydrogenase; Validated	83.27
PRK02910		519	light-independent protochlorophyllide reductase su	83.18
TIGR02417		327	fruct_sucro_rep D-fructose-responsive transcriptio	83.05
cd06291		265	PBP1_Qymf_like Ligand binding domain of the lacI-l	82.77
cd06300		272	PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-bi	82.69
cd06323		268	PBP1_ribose_binding Periplasmic sugar-binding doma	82.42
PRK10537		393	voltage-gated potassium channel; Provisional	82.11
cd06319		277	PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-b	82.0
PRK14719		360	bifunctional RNAse/5-amino-6-(5-phosphoribosylamin	81.83
cd06308		270	PBP1_sensor_kinase_like Periplasmic binding domain	81.82
TIGR03567		171	FMN_reduc_SsuE FMN reductase, SsuE family. Members	81.76
PRK06756		148	flavodoxin; Provisional	81.48
PRK12480		330	D-lactate dehydrogenase; Provisional	80.74
PRK00107		187	gidB 16S rRNA methyltransferase GidB; Reviewed	80.67

>PRK05752 uroporphyrinogen-III synthase; Validated	Back alignment and domain information

Probab=100.00  E-value=1.2e-36  Score=265.55  Aligned_cols=188  Identities=22%  Similarity=0.215  Sum_probs=164.8

Q ss_pred             CCCCeEEEeCCCCChHHHHHHHHHCCCcEEEeceEEEeeCCCchHHHHHHhcCCCccEEEEeCHHHHHHHHHHHHhcCC-
Q 026235           48 NSNPKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGT-  126 (241)
Q Consensus        48 l~g~~VLitR~~~~~~~l~~~L~~~G~~v~~~P~~~~~~~~~~~~l~~~l~~l~~~d~IiFTS~~aV~~f~~~l~~~~~-  126 (241)
                      +.|++||||||..+...+.+.|+++|++++.+|++++++.++...+...+.++..||||||||+|||++|++.+.+.+. 
T Consensus         1 ~~g~~vlvTRp~~~~~~l~~~l~~~G~~~~~~P~i~i~p~~~~~~~~~~l~~l~~~d~iifTS~naV~~~~~~l~~~~~~   80 (255)
T PRK05752          1 MSGWRLLLTRPAEECAALAASLAEAGIFSSSLPLLAIEPLPETPEQRALLLELDRYCAVIVVSKPAARLGLELLDRYWPQ   80 (255)
T ss_pred             CCCCEEEECCcHHHHHHHHHHHHHcCCCEEEcCcEEEeeCCCCHHHHHHHhcCCCCCEEEEECHHHHHHHHHHHHhhCCC
Confidence            4689999999999999999999999999999999999998776667777778899999999999999999998876543 


Q ss_pred             -CCcEEEEeCHHHHHHHHHhhhccCCCCceeecCCCCCHHHHHHH--hhhC-CCCccEEEEEccCCCchhHHHHHHhCCC
Q 026235          127 -PNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASE--LPKN-GKKKCTVLYPASAKASNEIEEGLSNRGF  202 (241)
Q Consensus       127 -~~~~i~aIG~~Ta~~L~~~~~~~~~Gi~~~~~p~~~t~e~L~~~--l~~~-~~~~~~iL~~~g~~~~~~L~~~L~~~G~  202 (241)
                       ++++++|||++|+++|+++      |+.++++|..+++++|++.  +... ..++++||++||+.+++.|.+.|++.|+
T Consensus        81 ~~~~~~~aVG~~Ta~al~~~------G~~~~~~p~~~~se~Ll~~~~l~~~~~~~~~~vLi~rg~~~r~~L~~~L~~~G~  154 (255)
T PRK05752         81 PPQQPWFSVGAATAAILQDY------GLDVSYPEQGDDSEALLALPALRQALAVPDPRVLIMRGEGGRELLAERLREQGA  154 (255)
T ss_pred             CcCCEEEEECHHHHHHHHHc------CCCcccCCCCCCcHHHHhChhhhccccCCCCEEEEEccCccHHHHHHHHHHCCC
Confidence             4689999999999999999      9999998999999999976  3332 2357899999999999999999999999


Q ss_pred             eeeEeeeeeeecCCCChHHHHHHc--CCCCEEEEECCccCC
Q 026235          203 EVVRLNTYTTEPVHHVDQTVLKQA--LSIPVVAVASPSAVR  241 (241)
Q Consensus       203 ~V~~~~vY~~~~~~~~~~~~~~~l--~~id~IvFtSps~v~  241 (241)
                      +|.++.+|++.++......+.+.+  +.+|+|+|||+++++
T Consensus       155 ~v~~~~vY~~~~~~~~~~~~~~~~~~~~~d~v~ftS~~~~~  195 (255)
T PRK05752        155 SVDYLELYRRCLPDYPAGTLLQRVEAERLNGLVVSSGQGFE  195 (255)
T ss_pred             EEeEEEEEeecCCCCCHHHHHHHHHhCCCCEEEECCHHHHH
Confidence            999999999987766555555444  679999999999863

>PRK08811 uroporphyrinogen-III synthase; Validated	Back alignment and domain information

>COG1587 HemD Uroporphyrinogen-III synthase [Coenzyme metabolism]	Back alignment and domain information

>PRK07239 bifunctional uroporphyrinogen-III synthetase/response regulator domain protein; Validated	Back alignment and domain information

>PRK09189 uroporphyrinogen-III synthase; Validated	Back alignment and domain information

>PRK05928 hemD uroporphyrinogen-III synthase; Reviewed	Back alignment and domain information

>PRK06975 bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed	Back alignment and domain information

>cd06578 HemD Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme	Back alignment and domain information

>PF02602 HEM4: Uroporphyrinogen-III synthase HemD; InterPro: IPR003754 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []	Back alignment and domain information

>PRK07168 bifunctional uroporphyrinogen-III methyltransferase/uroporphyrinogen-III synthase; Reviewed	Back alignment and domain information

>KOG4132 consensus Uroporphyrinogen III synthase UROS/HEM4 [Coenzyme transport and metabolism]	Back alignment and domain information

>PRK05928 hemD uroporphyrinogen-III synthase; Reviewed	Back alignment and domain information

>cd06578 HemD Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme	Back alignment and domain information

>PRK07239 bifunctional uroporphyrinogen-III synthetase/response regulator domain protein; Validated	Back alignment and domain information

>PRK05752 uroporphyrinogen-III synthase; Validated	Back alignment and domain information

>PRK09189 uroporphyrinogen-III synthase; Validated	Back alignment and domain information

>PF02602 HEM4: Uroporphyrinogen-III synthase HemD; InterPro: IPR003754 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []	Back alignment and domain information

>COG1587 HemD Uroporphyrinogen-III synthase [Coenzyme metabolism]	Back alignment and domain information

>KOG4132 consensus Uroporphyrinogen III synthase UROS/HEM4 [Coenzyme transport and metabolism]	Back alignment and domain information

>PRK08811 uroporphyrinogen-III synthase; Validated	Back alignment and domain information

>PRK06975 bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed	Back alignment and domain information

>PRK07168 bifunctional uroporphyrinogen-III methyltransferase/uroporphyrinogen-III synthase; Reviewed	Back alignment and domain information

>PRK02261 methylaspartate mutase subunit S; Provisional	Back alignment and domain information

>COG2185 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid metabolism]	Back alignment and domain information

>TIGR02853 spore_dpaA dipicolinic acid synthetase, A subunit	Back alignment and domain information

>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain	Back alignment and domain information

>PRK08306 dipicolinate synthase subunit A; Reviewed	Back alignment and domain information

>COG1609 PurR Transcriptional regulators [Transcription]	Back alignment and domain information

>cd06298 PBP1_CcpA_like Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation	Back alignment and domain information

>cd06295 PBP1_CelR Ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators	Back alignment and domain information

>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia	Back alignment and domain information

>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm)	Back alignment and domain information

>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit	Back alignment and domain information

>cd06273 PBP1_GntR_like_1 This group includes the ligand-binding domain of putative DNA transcription repressors which are highly similar to that of the repressor specific for gluconate (GntR), a member of the LacI-GalR family of bacterial transcription regulators	Back alignment and domain information

>PF00532 Peripla_BP_1: Periplasmic binding proteins and sugar binding domain of LacI family; InterPro: IPR001761 This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators	Back alignment and domain information

>cd06271 PBP1_AglR_RafR_like Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators	Back alignment and domain information

>cd01575 PBP1_GntR Ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators	Back alignment and domain information

>cd06272 PBP1_hexuronate_repressor_like Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are a member of the LacI-GalR family of bacterial transcription regulators	Back alignment and domain information

>cd06297 PBP1_LacI_like_12 Ligand-binding domain of uncharacterized transcription regulators from Thermus thermophilus and close homologs	Back alignment and domain information

>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines	Back alignment and domain information

>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems	Back alignment and domain information

>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis	Back alignment and domain information

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain	Back alignment and domain information

>cd06283 PBP1_RegR_EndR_KdgR_like Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR	Back alignment and domain information

>TIGR01481 ccpA catabolite control protein A	Back alignment and domain information

>cd06288 PBP1_sucrose_transcription_regulator Ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors	Back alignment and domain information

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional	Back alignment and domain information

>cd06354 PBP1_BmpA_PnrA_like Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea	Back alignment and domain information

>PRK11790 D-3-phosphoglycerate dehydrogenase; Provisional	Back alignment and domain information

>cd06286 PBP1_CcpB_like Ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species	Back alignment and domain information

>cd06294 PBP1_ycjW_transcription_regulator_like Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors	Back alignment and domain information

>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily	Back alignment and domain information

>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems	Back alignment and domain information

>PF04392 ABC_sub_bind: ABC transporter substrate binding protein; InterPro: IPR007487 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems	Back alignment and domain information

>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism	Back alignment and domain information

>cd06292 PBP1_LacI_like_10 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors	Back alignment and domain information

>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators	Back alignment and domain information

>cd06281 PBP1_LacI_like_5 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors	Back alignment and domain information

>PRK10423 transcriptional repressor RbsR; Provisional	Back alignment and domain information

>cd00316 Oxidoreductase_nitrogenase The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia	Back alignment and domain information

>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems	Back alignment and domain information

>cd06284 PBP1_LacI_like_6 Ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria	Back alignment and domain information

>PRK15438 erythronate-4-phosphate dehydrogenase PdxB; Provisional	Back alignment and domain information

>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily	Back alignment and domain information

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional	Back alignment and domain information

>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors	Back alignment and domain information

>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria	Back alignment and domain information

>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators	Back alignment and domain information

>cd06275 PBP1_PurR Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli	Back alignment and domain information

>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation	Back alignment and domain information

>cd06279 PBP1_LacI_like_3 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors	Back alignment and domain information

>cd06274 PBP1_FruR Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs	Back alignment and domain information

>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1	Back alignment and domain information

>PRK10569 NAD(P)H-dependent FMN reductase; Provisional	Back alignment and domain information

>PLN02928 oxidoreductase family protein	Back alignment and domain information

>cd02067 B12-binding B12 binding domain (B12-BD)	Back alignment and domain information

>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily	Back alignment and domain information

>PRK11303 DNA-binding transcriptional regulator FruR; Provisional	Back alignment and domain information

>cd06278 PBP1_LacI_like_2 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors	Back alignment and domain information

>cd01541 PBP1_AraR Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators	Back alignment and domain information

>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators	Back alignment and domain information

>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems	Back alignment and domain information

>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs	Back alignment and domain information

>cd01574 PBP1_LacI Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators	Back alignment and domain information

>cd06307 PBP1_uncharacterized_sugar_binding Periplasmic sugar-binding domain of uncharacterized transport systems	Back alignment and domain information

>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs	Back alignment and domain information

>COG4822 CbiK Cobalamin biosynthesis protein CbiK, Co2+ chelatase [Coenzyme metabolism]	Back alignment and domain information

>cd06290 PBP1_LacI_like_9 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors	Back alignment and domain information

>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems	Back alignment and domain information

>cd06293 PBP1_LacI_like_11 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors	Back alignment and domain information

>cd06287 PBP1_LacI_like_8 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors	Back alignment and domain information

>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems	Back alignment and domain information

>PRK00257 erythronate-4-phosphate dehydrogenase; Validated	Back alignment and domain information

>PRK02910 light-independent protochlorophyllide reductase subunit B; Provisional	Back alignment and domain information

>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor	Back alignment and domain information

>cd06291 PBP1_Qymf_like Ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs	Back alignment and domain information

>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily	Back alignment and domain information

>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs	Back alignment and domain information

>PRK10537 voltage-gated potassium channel; Provisional	Back alignment and domain information

>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems	Back alignment and domain information

>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional	Back alignment and domain information

>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems	Back alignment and domain information

>TIGR03567 FMN_reduc_SsuE FMN reductase, SsuE family	Back alignment and domain information

>PRK06756 flavodoxin; Provisional	Back alignment and domain information

>PRK12480 D-lactate dehydrogenase; Provisional	Back alignment and domain information

>PRK00107 gidB 16S rRNA methyltransferase GidB; Reviewed	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		241
3re1_A		269	Uroporphyrinogen-III synthetase; HEMD-like family,	4e-32
3mw8_A		240	Uroporphyrinogen-III synthase; structural genomics	6e-30
1jr2_A		286	Uroporphyrinogen-III synthase; heme biosynthesis,	9e-29
1wcw_A		261	Uroporphyrinogen III synthase; congenital erythrop	7e-24
3p9z_A		229	Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2	5e-22
3d8t_A		286	Uroporphyrinogen-III synthase; heme biosynthesis,	2e-19

>3re1_A Uroporphyrinogen-III synthetase; HEMD-like family, uroporphyrinogen III synthase, HMB, lyase; 2.50A {Pseudomonas syringae PV} Length = 269	Back alignment and structure

 Score =  117 bits (295), Expect = 4e-32
 Identities = 40/200 (20%), Positives = 69/200 (34%), Gaps = 13/200 (6%)

Query: 49  SNPKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIII 108
           S  ++++TR   ++  L + LA   I    LPL++    P T    S++     +  +I+
Sbjct: 13  SAWRLLLTRPAEESAALARVLADAGIFSSSLPLLETEPLPLTPAQRSIIFELLNYSAVIV 72

Query: 109 TSPEAGSVFLEAWKEAG--TPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKI 166
            S  A  + +E   E     P      VG+ T  I  +        LD ++       + 
Sbjct: 73  VSKPAARLAIELIDEVWPQPPMQPWFSVGSATGQILLD------YGLDASWPEQGDDSEA 126

Query: 167 LASELP---KNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVL 223
           L                VL     +    + E L  RG  V  L  Y      H   T+L
Sbjct: 127 LLDHPRLKQAIAVPGSRVLIMRGNEGRELLAEQLRERGVGVDYLPLYRRYLPQHAPGTLL 186

Query: 224 K--QALSIPVVAVASPSAVR 241
           +  +   +  + V+S     
Sbjct: 187 QRVEVERLNGLVVSSGQGFE 206

PyMOL of 3re1

>3mw8_A Uroporphyrinogen-III synthase; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, lyase; 1.65A {Shewanella amazonensis} Length = 240	Back alignment and structure

>1jr2_A Uroporphyrinogen-III synthase; heme biosynthesis, HEAM biosynthesis, lyase; 1.84A {Homo sapiens} SCOP: c.113.1.1 Length = 286	Back alignment and structure

>1wcw_A Uroporphyrinogen III synthase; congenital erythropoietic porph structural genomics, riken structural genomics/proteomics initiative, RSGI; 1.30A {Thermus thermophilus} PDB: 1wd7_A 1wcx_A Length = 261	Back alignment and structure

>3p9z_A Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2, structural genomics, protein structure initiativ midwest center for structural genomics; HET: MSE; 2.10A {Helicobacter pylori} Length = 229	Back alignment and structure

>3d8t_A Uroporphyrinogen-III synthase; heme biosynthesis, lyase; 1.60A {Thermus thermophilus} PDB: 3d8r_A 3d8s_A 3d8n_A Length = 286	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		241
4es6_A		254	Uroporphyrinogen-III synthase; heme-biosynthesis,	100.0
3re1_A		269	Uroporphyrinogen-III synthetase; HEMD-like family,	100.0
3mw8_A		240	Uroporphyrinogen-III synthase; structural genomics	100.0
1wcw_A		261	Uroporphyrinogen III synthase; congenital erythrop	100.0
1jr2_A		286	Uroporphyrinogen-III synthase; heme biosynthesis,	100.0
3d8t_A		286	Uroporphyrinogen-III synthase; heme biosynthesis,	100.0
3p9z_A		229	Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2	99.96
3p9z_A		229	Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2	99.77
1jr2_A		286	Uroporphyrinogen-III synthase; heme biosynthesis,	99.76
4es6_A		254	Uroporphyrinogen-III synthase; heme-biosynthesis,	99.76
3re1_A		269	Uroporphyrinogen-III synthetase; HEMD-like family,	99.76
1wcw_A		261	Uroporphyrinogen III synthase; congenital erythrop	99.73
3mw8_A		240	Uroporphyrinogen-III synthase; structural genomics	99.72
3d8t_A		286	Uroporphyrinogen-III synthase; heme biosynthesis,	99.72
3d4o_A		293	Dipicolinate synthase subunit A; NP_243269.1, stru	95.31
2rir_A		300	Dipicolinate synthase, A chain; structural genomic	94.62
2qh8_A		302	Uncharacterized protein; conserved domain protein,	94.24
1ccw_A		137	Protein (glutamate mutase); coenzyme B12, radical	93.97
3gbv_A		304	Putative LACI-family transcriptional regulator; NY	93.63
3lft_A		295	Uncharacterized protein; ABC, ATPase, cassette, L-	93.6
3qk7_A		294	Transcriptional regulators; structural genomics, N	93.47
3k5p_A		416	D-3-phosphoglycerate dehydrogenase; niaid, ssgcid,	93.43
2yxb_A		161	Coenzyme B12-dependent mutase; alpha/beta, structu	93.4
3egc_A		291	Putative ribose operon repressor; structural genom	92.44
3gv0_A		288	Transcriptional regulator, LACI family; transcript	92.41
3g1w_A		305	Sugar ABC transporter; sugar-binding protein, baci	91.98
3l49_A		291	ABC sugar (ribose) transporter, periplasmic substr	91.66
1lss_A		140	TRK system potassium uptake protein TRKA homolog;	91.59
2pln_A		137	HP1043, response regulator; signaling protein; 1.8	91.27
3gt7_A		154	Sensor protein; structural genomics, signal receiv	91.08
3llv_A		141	Exopolyphosphatase-related protein; NAD(P)-binding	90.95
2fep_A		289	Catabolite control protein A; CCPA, transcriptiona	90.9
3c3k_A		285	Alanine racemase; structural genomics, protein str	90.58
3brq_A		296	HTH-type transcriptional regulator ASCG; transcrip	90.51
3c85_A		183	Putative glutathione-regulated potassium-efflux S	90.37
2hmt_A		144	YUAA protein; RCK, KTN, KTR, KTRA, ktrab, membrane	90.16
3d8u_A		275	PURR transcriptional regulator; APC91343.1, vibrio	90.09
3g85_A		289	Transcriptional regulator (LACI family); transcrip	89.77
3k4h_A		292	Putative transcriptional regulator; structural gen	89.27
3dbi_A		338	Sugar-binding transcriptional regulator, LACI FAM;	89.23
2g1u_A		155	Hypothetical protein TM1088A; structural genomics,	89.2
2rgy_A		290	Transcriptional regulator, LACI family; 11011J, NY	88.91
3k9c_A		289	Transcriptional regulator, LACI family protein; PS	88.79
3bbl_A		287	Regulatory protein of LACI family; protein structu	88.72
3h1g_A		129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	88.48
2o20_A		332	Catabolite control protein A; CCPA, transcriptiona	88.46
1dbq_A		289	Purine repressor; transcription regulation, DNA-bi	88.34
3e3m_A		355	Transcriptional regulator, LACI family; structural	88.23
3fwz_A		140	Inner membrane protein YBAL; TRKA-N domain, E.coli	88.21
3rot_A		297	ABC sugar transporter, periplasmic sugar binding;	88.09
2hsg_A		332	Glucose-resistance amylase regulator; CCPA, transc	88.03
3gl9_A		122	Response regulator; beta-sheet, surrounded by alph	87.91
3eod_A		130	Protein HNR; response regulator, phosphoprotein, t	87.83
2fvy_A		309	D-galactose-binding periplasmic protein; periplasm	87.67
3kke_A		303	LACI family transcriptional regulator; structural	87.17
3tb6_A		298	Arabinose metabolism transcriptional repressor; tr	87.01
1sc6_A		404	PGDH, D-3-phosphoglycerate dehydrogenase; alloster	86.92
3lte_A		132	Response regulator; structural genomics, PSI, prot	86.78
1id1_A		153	Putative potassium channel protein; RCK domain, E.	86.42
3kht_A		144	Response regulator; PSI-II, 11023K, structural gen	86.22
3hdv_A		136	Response regulator; PSI-II, structural genomics, P	85.23
3ksm_A		276	ABC-type sugar transport system, periplasmic COMP;	85.17
3huu_A		305	Transcription regulator like protein; PSI-II, NYSG	84.95
3kjx_A		344	Transcriptional regulator, LACI family; LACL famil	84.63
2gkg_A		127	Response regulator homolog; social motility, recei	84.52
1qpz_A		340	PURA, protein (purine nucleotide synthesis repress	83.64
3gyb_A		280	Transcriptional regulators (LACI-family transcript	82.95
3clk_A		290	Transcription regulator; 11017J, PSI-II, NYSGXRC,	82.93
3jvd_A		333	Transcriptional regulators; structural genomics, P	82.75
1y80_A		210	Predicted cobalamin binding protein; corrinoid, fa	82.72
2xij_A		762	Methylmalonyl-COA mutase, mitochondrial; isomerase	82.31
2i2x_B		258	MTAC, methyltransferase 1; TIM barrel and helix bu	82.19
3h75_A		350	Periplasmic sugar-binding domain protein; protein	82.12
3grc_A		140	Sensor protein, kinase; protein structure initiati	82.09
2j48_A		119	Two-component sensor kinase; pseudo-receiver, circ	81.7
3jtm_A		351	Formate dehydrogenase, mitochondrial; mitochondrio	81.7
3aek_A		437	Light-independent protochlorophyllide reductase S;	81.67
2zay_A		147	Response regulator receiver protein; structural ge	81.57
2h0a_A		276	TTHA0807, transcriptional regulator; repressor, st	81.42
2rdm_A		132	Response regulator receiver protein; structural ge	80.6
3cg4_A		142	Response regulator receiver domain protein (CHEY-;	80.57
3hs3_A		277	Ribose operon repressor; PSI-II, NYSGXRC, periplas	80.46
2amj_A		204	Modulator of drug activity B; oxidoreductase, mena	80.34
2cuk_A		311	Glycerate dehydrogenase/glyoxylate reductase; stru	80.32
2wm8_A		187	MDP-1, magnesium-dependent phosphatase 1; haloacid	80.2
2h3h_A		313	Sugar ABC transporter, periplasmic sugar-binding p	80.19

>4es6_A Uroporphyrinogen-III synthase; heme-biosynthesis, cytoplasmi; 2.22A {Pseudomonas aeruginosa}	Back alignment and structure

Probab=100.00  E-value=6.2e-39  Score=277.61  Aligned_cols=190  Identities=19%  Similarity=0.199  Sum_probs=167.0

Q ss_pred             CCCCCCeEEEeCCCCChHHHHHHHHHCCCcEEEeceEEEeeCCCchHHHHHHhcCCCccEEEEeCHHHHHHHHHHHHhcC
Q 026235           46 ASNSNPKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAG  125 (241)
Q Consensus        46 ~~l~g~~VLitR~~~~~~~l~~~L~~~G~~v~~~P~~~~~~~~~~~~l~~~l~~l~~~d~IiFTS~~aV~~f~~~l~~~~  125 (241)
                      .||.||+||+|||..+.+.+.+.|+++|++++.+|+|++++.++...+++.+.+++.||||||||+|+|++|++.+...+
T Consensus         2 ~~L~g~~vlvtRp~~~~~~l~~~L~~~G~~~~~~P~i~i~~~~~~~~l~~~l~~l~~~d~vifTS~~aV~~~~~~l~~~~   81 (254)
T 4es6_A            2 SHMSGWRLLLTRPDEECAALAASLGEAGVHSSSLPLLAIDPLEETPEQRTLMLDLDRYCAVVVVSKPAARLGLERLDRYW   81 (254)
T ss_dssp             ----CCEEEECSCHHHHHHHHHHHHHTTCEEEECCSCEEEECCCCHHHHHHHHTGGGCSEEEECSHHHHHHHHHHHHHHC
T ss_pred             CCCCCCEEEEeCChHHhHHHHHHHHHCCCcEEEeCCEEEeeCcChHHHHHHHHhccCCCEEEEECHHHHHHHHHHHHHhC
Confidence            57999999999999889999999999999999999999999887667777777788999999999999999999987654


Q ss_pred             C--CCcEEEEeCHHHHHHHHHhhhccCCCCceeecCCCCCHHHHHHHhh--h-CCCCccEEEEEccCCCchhHHHHHHhC
Q 026235          126 T--PNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELP--K-NGKKKCTVLYPASAKASNEIEEGLSNR  200 (241)
Q Consensus       126 ~--~~~~i~aIG~~Ta~~L~~~~~~~~~Gi~~~~~p~~~t~e~L~~~l~--~-~~~~~~~iL~~~g~~~~~~L~~~L~~~  200 (241)
                      .  ++++++|||++|+++|+++      |+.++++|+.+++++|++.+.  + ....+++||++||+.++++|.+.|+++
T Consensus        82 ~~~~~~~i~aVG~~Ta~~L~~~------G~~~~~~~~~~~~e~L~~~l~~~~~~~~~~~~vL~~rg~~~r~~L~~~L~~~  155 (254)
T 4es6_A           82 PQPPQQTWCSVGAATAAILEAY------GLDVTYPEQGDDSEALLALPAFQDSLRVHDPKVLIMRGEGGREFLAERLRGQ  155 (254)
T ss_dssp             SSCCSCEEEESSHHHHHHHHHH------TCCEECCSSCCSHHHHHTCHHHHHHTCSSSCEEEEEECSSCCCHHHHHHHHT
T ss_pred             CCcccCEEEEECHHHHHHHHHc------CCCcccCCCCCCHHHHHHhHhhcccccCCCCEEEEEcCCccHHHHHHHHHHC
Confidence            3  4589999999999999999      999999998899999999987  3 234678999999999999999999999


Q ss_pred             CCeeeEeeeeeeecCCCChHHHHHHc--CCCCEEEEECCccCC
Q 026235          201 GFEVVRLNTYTTEPVHHVDQTVLKQA--LSIPVVAVASPSAVR  241 (241)
Q Consensus       201 G~~V~~~~vY~~~~~~~~~~~~~~~l--~~id~IvFtSps~v~  241 (241)
                      |++|.++.+|++.+++....++.+.+  +.+|+|+||||++|+
T Consensus       156 G~~v~~~~vY~~~~~~~~~~~~~~~l~~~~~d~v~ftS~s~v~  198 (254)
T 4es6_A          156 GVQVDYLPLYRRRAPDYPAGELLARVRAERLNGLVVSSGQGLQ  198 (254)
T ss_dssp             TCEEEEEECEEEECCCCCTTHHHHHHHHTTCCEEECCSHHHHH
T ss_pred             CCEEEEEeEEEeeCCCCCHHHHHHHHHhCCCCEEEEcCHHHHH
Confidence            99999999999999887655554444  689999999999874

PyMOL of 4es6

>3re1_A Uroporphyrinogen-III synthetase; HEMD-like family, uroporphyrinogen III synthase, HMB, lyase; 2.50A {Pseudomonas syringae PV}	Back alignment and structure

>3mw8_A Uroporphyrinogen-III synthase; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, lyase; 1.65A {Shewanella amazonensis}	Back alignment and structure

>1wcw_A Uroporphyrinogen III synthase; congenital erythropoietic porph structural genomics, riken structural genomics/proteomics initiative, RSGI; 1.30A {Thermus thermophilus} PDB: 1wd7_A 1wcx_A	Back alignment and structure

>1jr2_A Uroporphyrinogen-III synthase; heme biosynthesis, HEAM biosynthesis, lyase; 1.84A {Homo sapiens} SCOP: c.113.1.1	Back alignment and structure

>3d8t_A Uroporphyrinogen-III synthase; heme biosynthesis, lyase; 1.60A {Thermus thermophilus} PDB: 3d8r_A 3d8s_A 3d8n_A	Back alignment and structure

>3p9z_A Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2, structural genomics, protein structure initiativ midwest center for structural genomics; HET: MSE; 2.10A {Helicobacter pylori}	Back alignment and structure

>3p9z_A Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2, structural genomics, protein structure initiativ midwest center for structural genomics; HET: MSE; 2.10A {Helicobacter pylori}	Back alignment and structure

>1jr2_A Uroporphyrinogen-III synthase; heme biosynthesis, HEAM biosynthesis, lyase; 1.84A {Homo sapiens} SCOP: c.113.1.1	Back alignment and structure

>4es6_A Uroporphyrinogen-III synthase; heme-biosynthesis, cytoplasmi; 2.22A {Pseudomonas aeruginosa}	Back alignment and structure

>3re1_A Uroporphyrinogen-III synthetase; HEMD-like family, uroporphyrinogen III synthase, HMB, lyase; 2.50A {Pseudomonas syringae PV}	Back alignment and structure

>1wcw_A Uroporphyrinogen III synthase; congenital erythropoietic porph structural genomics, riken structural genomics/proteomics initiative, RSGI; 1.30A {Thermus thermophilus} PDB: 1wd7_A 1wcx_A	Back alignment and structure

>3mw8_A Uroporphyrinogen-III synthase; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, lyase; 1.65A {Shewanella amazonensis}	Back alignment and structure

>3d8t_A Uroporphyrinogen-III synthase; heme biosynthesis, lyase; 1.60A {Thermus thermophilus} PDB: 3d8r_A 3d8s_A 3d8n_A	Back alignment and structure

>3d4o_A Dipicolinate synthase subunit A; NP_243269.1, structural GEN joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: MSE TAR; 2.10A {Bacillus halodurans}	Back alignment and structure

>2rir_A Dipicolinate synthase, A chain; structural genomics, APC1343, PSI-2, structure initiative; HET: MSE NAP; 2.79A {Bacillus subtilis}	Back alignment and structure

>1ccw_A Protein (glutamate mutase); coenzyme B12, radical reaction, TIM-barrel rossman-fold, isomerase; HET: CNC TAR; 1.60A {Clostridium cochlearium} SCOP: c.23.6.1 PDB: 1cb7_A* 1b1a_A 1i9c_A* 1be1_A 1fmf_A 1id8_A*	Back alignment and structure

>3gbv_A Putative LACI-family transcriptional regulator; NYSGXRC, PSI-II, 11231J, structur genomics, protein structure initiative; 2.20A {Bacteroides fragilis}	Back alignment and structure

>3lft_A Uncharacterized protein; ABC, ATPase, cassette, L-Trp, PSI, MCSG, structural genomics center for structural genomics; HET: MSE TRP; 1.35A {Streptococcus pneumoniae}	Back alignment and structure

>3qk7_A Transcriptional regulators; structural genomics, NEW YORK structural genomix research CO NYSGXRC, PSI-2, protein structur initiative; 2.70A {Yersinia pestis}	Back alignment and structure

>3k5p_A D-3-phosphoglycerate dehydrogenase; niaid, ssgcid, seattle structural genomics center for infect disease, brucellosis; 2.15A {Brucella melitensis biovar abortus}	Back alignment and structure

>2yxb_A Coenzyme B12-dependent mutase; alpha/beta, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix}	Back alignment and structure

>3egc_A Putative ribose operon repressor; structural genomics, unknown function, DNA-binding, transcri transcription regulation, PSI-2; 2.35A {Burkholderia thailandensis}	Back alignment and structure

>3gv0_A Transcriptional regulator, LACI family; transcription regulator, PSI-II, structural genomics structure initiative; 2.35A {Agrobacterium tumefaciens str}	Back alignment and structure

>3g1w_A Sugar ABC transporter; sugar-binding protein, bacillus halod target 11229F, transport protein, structural genomics; 2.02A {Bacillus halodurans c-125}	Back alignment and structure

>3l49_A ABC sugar (ribose) transporter, periplasmic substrate-binding subunit; sugar binding/transporter, structural genomics, PSI; HET: UNL; 2.30A {Rhodobacter sphaeroides}	Back alignment and structure

>1lss_A TRK system potassium uptake protein TRKA homolog; KTN domain, NAD, RCK domain, potassium transport, potassium channel, KTRA; HET: NAD; 2.30A {Methanocaldococcus jannaschii} SCOP: c.2.1.9	Back alignment and structure

>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A	Back alignment and structure

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB}	Back alignment and structure

>3llv_A Exopolyphosphatase-related protein; NAD(P)-binding, rossmann, PSI, M structural genomics; 1.70A {Archaeoglobus fulgidus}	Back alignment and structure

>2fep_A Catabolite control protein A; CCPA, transcriptional regulator; HET: SEP; 2.45A {Bacillus subtilis} PDB: 2nzu_G* 1sxh_A 1sxi_A 1sxg_A* 2nzv_G* 2oen_G*	Back alignment and structure

>3c3k_A Alanine racemase; structural genomics, protein structure initiative, NEW YORK research center for structural genomics, nysgxrc; 1.99A {Actinobacillus succinogenes}	Back alignment and structure

>3brq_A HTH-type transcriptional regulator ASCG; transcriptional repressor structure escherichia coli, struct genomics, PSI-2; HET: FRU; 2.00A {Escherichia coli}	Back alignment and structure

>3c85_A Putative glutathione-regulated potassium-efflux S protein KEFB; TRKA domain; HET: AMP; 1.90A {Vibrio parahaemolyticus rimd 2210633}	Back alignment and structure

>2hmt_A YUAA protein; RCK, KTN, KTR, KTRA, ktrab, membrane protein, ION transporter, symporter, transport protein; HET: NAI; 2.20A {Bacillus subtilis} SCOP: c.2.1.9 PDB: 2hms_A* 2hmu_A* 2hmv_A* 2hmw_A* 1lsu_A*	Back alignment and structure

>3d8u_A PURR transcriptional regulator; APC91343.1, vibrio parahaem RIMD 2210633, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.88A {Vibrio parahaemolyticus}	Back alignment and structure

>3g85_A Transcriptional regulator (LACI family); transcription regulator, PSI-II, structural genomics structure initiative; 1.84A {Clostridium acetobutylicum atcc 824}	Back alignment and structure

>3k4h_A Putative transcriptional regulator; structural genomics, protein structure INI NEW YORK structural genomix research consortium; HET: MAL; 2.80A {Bacillus cytotoxicus nvh 391-98}	Back alignment and structure

>3dbi_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative, PSI-2; HET: MSE; 2.45A {Escherichia coli K12}	Back alignment and structure

>2g1u_A Hypothetical protein TM1088A; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: AMP; 1.50A {Thermotoga maritima} PDB: 3l4b_A*	Back alignment and structure

>2rgy_A Transcriptional regulator, LACI family; 11011J, NYSGXRC, transctiptional regulator, SUG binding protein, structural genomics, PSI-2; 2.05A {Burkholderia phymatum}	Back alignment and structure

>3k9c_A Transcriptional regulator, LACI family protein; PSI-II, 11026W, structural genomics, PR structure initiative; 2.14A {Rhodococcus jostii}	Back alignment and structure

>3bbl_A Regulatory protein of LACI family; protein structure initiative II, PSI-II, NYSGXRC, transcript regulator, periplasmic binding protein; 2.35A {Chloroflexus aggregans}	Back alignment and structure

>3h1g_A Chemotaxis protein CHEY homolog; sulfate-bound CHEY, cytoplasm, flagellar rotatio magnesium, metal-binding, phosphoprotein; 1.70A {Helicobacter pylori} SCOP: c.23.1.1 PDB: 3gwg_A 3h1e_A 3h1f_A	Back alignment and structure

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}	Back alignment and structure

>1dbq_A Purine repressor; transcription regulation, DNA-binding regulatory protein; 2.20A {Escherichia coli} SCOP: c.93.1.1 PDB: 1jhz_A	Back alignment and structure

>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi}	Back alignment and structure

>3fwz_A Inner membrane protein YBAL; TRKA-N domain, E.coli, structural genomics, PSI-2, Pro structure initiative; HET: MSE AMP; 1.79A {Escherichia coli k-12}	Back alignment and structure

>3rot_A ABC sugar transporter, periplasmic sugar binding; nysgrc, PSI-biology, structural genomics; 1.91A {Legionella pneumophila subsp}	Back alignment and structure

>2hsg_A Glucose-resistance amylase regulator; CCPA, transcriptional regulator, transcription regulator; 2.50A {Bacillus megaterium} SCOP: a.35.1.5 c.93.1.1 PDB: 1rzr_G 2jcg_A 1zvv_A 3oqo_A* 3oqm_A* 3oqn_A*	Back alignment and structure

>3gl9_A Response regulator; beta-sheet, surrounded by alpha helices, BOTH sides, signaling protein; HET: BFD; 1.80A {Thermotoga maritima} SCOP: c.23.1.0 PDB: 3dgf_C 3dge_C	Back alignment and structure

>3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12}	Back alignment and structure

>2fvy_A D-galactose-binding periplasmic protein; periplasmic binding protien, hinge, chemotaxis, transport,; HET: BGC; 0.92A {Escherichia coli} SCOP: c.93.1.1 PDB: 1glg_A* 2fw0_A* 2gbp_A* 2qw1_A* 2hph_A* 2ipn_A* 2ipm_A* 2ipl_A* 1gca_A* 1gcg_A 3ga5_A* 3gbp_A*	Back alignment and structure

>3kke_A LACI family transcriptional regulator; structural genomics, DNA-binding, transcription regulation, PSI-2; 2.20A {Mycobacterium smegmatis str}	Back alignment and structure

>3tb6_A Arabinose metabolism transcriptional repressor; transcription regulation, arabinose binding, DNA binding Pro; HET: ARB; 2.21A {Bacillus subtilis}	Back alignment and structure

>1sc6_A PGDH, D-3-phosphoglycerate dehydrogenase; allosteric regulation phosphoglycerate dehydrogenase PGDH, oxidoreductase; HET: NAD; 2.09A {Escherichia coli} SCOP: c.2.1.4 c.23.12.1 d.58.18.1 PDB: 1psd_A* 1yba_A* 2p9c_A* 2p9e_A* 2pa3_A* 2p9g_A*	Back alignment and structure

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri}	Back alignment and structure

>1id1_A Putative potassium channel protein; RCK domain, E.coli potassium channel, BK channel, rossmann fold, membrane protein; 2.40A {Escherichia coli} SCOP: c.2.1.9	Back alignment and structure

>3kht_A Response regulator; PSI-II, 11023K, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.10A {Hahella chejuensis} SCOP: c.23.1.0	Back alignment and structure

>3hdv_A Response regulator; PSI-II, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.09A {Pseudomonas putida} SCOP: c.23.1.0	Back alignment and structure

>3ksm_A ABC-type sugar transport system, periplasmic COMP; periplasmic component, PSI- 11023L, structural genomics, protein structure initiative; HET: BDR; 1.90A {Hahella chejuensis}	Back alignment and structure

>3huu_A Transcription regulator like protein; PSI-II, NYSGXRC, LAC I, STR genomics, protein structure initiative; 1.95A {Staphylococcus haemolyticus}	Back alignment and structure

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}	Back alignment and structure

>2gkg_A Response regulator homolog; social motility, receiver domain, signalling, high resolutio signaling protein; 1.00A {Myxococcus xanthus} PDB: 2i6f_A 2nt4_A 2nt3_A	Back alignment and structure

>1qpz_A PURA, protein (purine nucleotide synthesis repressor); transcription regulation, DNA-binding, purine biosynthesis; HET: DNA HPA; 2.50A {Escherichia coli} SCOP: a.35.1.5 c.93.1.1 PDB: 1bdi_A* 1qp0_A* 1qp4_A* 1pnr_A* 1wet_A* 1zay_A* 1vpw_A* 2pue_A* 2puf_A* 2pug_A* 1bdh_A* 1qp7_A* 1qqa_A* 1qqb_A* 2puc_A* 2pua_A* 2pub_A* 2pud_A* 1jfs_A* 1jh9_A* ...	Back alignment and structure

>3gyb_A Transcriptional regulators (LACI-family transcriptional regulatory protein); protein structure initiative II(PSI II), nysgxrc; 1.60A {Corynebacterium glutamicum}	Back alignment and structure

>3clk_A Transcription regulator; 11017J, PSI-II, NYSGXRC, dimer, structural genomics, protein structure initiative; 2.08A {Lactobacillus plantarum WCFS1}	Back alignment and structure

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}	Back alignment and structure

>1y80_A Predicted cobalamin binding protein; corrinoid, factor IIIM, methyl transferase, structural genomics, PSI, protein structure initiative; HET: B1M; 1.70A {Moorella thermoacetica}	Back alignment and structure

>2xij_A Methylmalonyl-COA mutase, mitochondrial; isomerase, organic aciduria, vitamin B12; HET: B12 5AD BTB; 1.95A {Homo sapiens} PDB: 2xiq_A* 3bic_A	Back alignment and structure

>2i2x_B MTAC, methyltransferase 1; TIM barrel and helix bundle (MTAB), rossman fold and helix B (MTAC); HET: B13; 2.50A {Methanosarcina barkeri}	Back alignment and structure

>3h75_A Periplasmic sugar-binding domain protein; protein structure initiative II (PSI II), sugar binding PROT alpha/beta fold; 1.60A {Pseudomonas fluorescens pf-5}	Back alignment and structure

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP}	Back alignment and structure

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus}	Back alignment and structure

>3jtm_A Formate dehydrogenase, mitochondrial; mitochondrion, NAD, oxidoreductase, T peptide; 1.30A {Arabidopsis thaliana} PDB: 3n7u_A* 3naq_A	Back alignment and structure

>3aek_A Light-independent protochlorophyllide reductase S; iron/sulfur cluster, oxidoreductase, bacteriochlorophyll biosynthesis; HET: PMR; 2.30A {Rhodobacter capsulatus} PDB: 3aeq_A* 3aes_A* 3aer_A* 3aet_A 3aeu_A	Back alignment and structure

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans}	Back alignment and structure

>2h0a_A TTHA0807, transcriptional regulator; repressor, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.80A {Thermus thermophilus}	Back alignment and structure

>2rdm_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.76A {Sinorhizobium medicae}	Back alignment and structure

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1}	Back alignment and structure

>3hs3_A Ribose operon repressor; PSI-II, NYSGXRC, periplasmic binding protein, structural genomics, protein structure initiative; 1.60A {Lactobacillus acidophilus}	Back alignment and structure

>2amj_A Modulator of drug activity B; oxidoreductase, menadione, DT-diaphorase, montreal-kingston structural genomics initiative, BSGI; 1.80A {Escherichia coli} PDB: 2b3d_A*	Back alignment and structure

>2cuk_A Glycerate dehydrogenase/glyoxylate reductase; structural genomics, riken structur genomics/proteomics initiative, RSGI, NPPSFA; HET: NHE; 2.00A {Thermus thermophilus}	Back alignment and structure

>2wm8_A MDP-1, magnesium-dependent phosphatase 1; haloacid dehalogenase, protein phosphatase, hydrolase, magne metal-binding; 1.75A {Homo sapiens} PDB: 1u7o_A 1u7p_A	Back alignment and structure

>2h3h_A Sugar ABC transporter, periplasmic sugar-binding protein; glucose binding protein, periplasmic binding protein, GBP; HET: BGC; 1.70A {Thermotoga maritima} PDB: 2qvc_A* 3c6q_B*	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		241
d1wd7a_		254	c.113.1.1 (A:) Probable uroporphyrinogen-III synth	1e-15

>d1wd7a_ c.113.1.1 (A:) Probable uroporphyrinogen-III synthase {Thermus thermophilus [TaxId: 274]} Length = 254	Back information, alignment and structure


class: Alpha and beta proteins (a/b)
fold: HemD-like
superfamily: HemD-like
family: HemD-like
domain: Probable uroporphyrinogen-III synthase
species: Thermus thermophilus [TaxId: 274]

 Score = 72.1 bits (176), Expect = 1e-15
 Identities = 33/198 (16%), Positives = 52/198 (26%), Gaps = 19/198 (9%)

Query: 52  KVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSP 111
           +V     R +         K     L  P+    + P  +    V       D  + T+ 
Sbjct: 3   RVAYAGLR-RKEAFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRALAQGVDLFLATTG 61

Query: 112 EAGSVFLEAWKEAGTP------NVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGK 165
                 LEA K  G               GA  A   +      +  L         +  
Sbjct: 62  VGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALK------EAGLPPHAVGDGTSKS 115

Query: 166 ILASELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQ 225
           +L       G            K    +E  L+ RG+ V+ L  Y   P       + + 
Sbjct: 116 LLPLLPQGRGV----AALQLYGKPLPLLENALAERGYRVLPLMPYRHLPDPEGILRLEEA 171

Query: 226 ALSIPVVAV--ASPSAVR 241
            L   V A+   +   V 
Sbjct: 172 LLRGEVDALAFVAAIQVE 189

PyMOL of d1wd7a_

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		241
d1jr2a_		260	Uroporphyrinogen III synthase (U3S, HemD) {Human (	100.0
d1wd7a_		254	Probable uroporphyrinogen-III synthase {Thermus th	99.97
d1wd7a_		254	Probable uroporphyrinogen-III synthase {Thermus th	99.66
d1jr2a_		260	Uroporphyrinogen III synthase (U3S, HemD) {Human (	99.65
d1ccwa_		137	Glutamate mutase, small subunit {Clostridium cochl	95.85
d7reqa2		168	Methylmalonyl-CoA mutase alpha subunit, C-terminal	94.77
d1lssa_		132	Ktn Mja218 {Archaeon Methanococcus jannaschii [Tax	93.6
d1zesa1		121	PhoB receiver domain {Escherichia coli [TaxId: 562	93.43
d1vmea1		148	ROO-like flavoprotein TM0755, C-terminal domain {T	93.05
d1dcfa_		134	Receiver domain of the ethylene receptor {Thale cr	92.9
d1mb3a_		123	Cell division response regulator DivK {Caulobacter	92.13
d2a9pa1		117	DNA-binding response regulator MicA, N-terminal do	90.61
d1u0sy_		118	CheY protein {Thermotoga maritima [TaxId: 2336]}	89.79
d1id1a_		153	Rck domain from putative potassium channel Kch {Es	89.57
d2hmva1		134	Ktn bsu222 {Bacillus subtilis [TaxId: 1423]}	89.44
d1sbya1		254	Drosophila alcohol dehydrogenase {Fly (Drosophila	89.3
d1sc6a2		132	Phosphoglycerate dehydrogenase {Escherichia coli [	89.26
d2b4aa1		118	Hypothetical protein BH3024 {Bacillus halodurans [	88.9
d2qwxa1		230	Quinone reductase type 2 (menadione reductase) {Hu	88.51
d1w25a1		139	Response regulator PleD, receiver domain {Caulobac	87.87
d1peya_		119	Sporulation response regulator Spo0F {Bacillus sub	87.02
d1dxya2		131	D-2-hydroxyisocaproate dehydrogenase {Lactobacillu	86.51
d1k68a_		140	Response regulator for cyanobacterial phytochrome	85.92
d2pl1a1		119	PhoP receiver domain {Escherichia coli [TaxId: 562	85.4
d1pr9a_		244	Carbonyl reductase {Human (Homo sapiens) [TaxId: 9	84.98
d2qwxa1		230	Quinone reductase type 2 (menadione reductase) {Hu	84.64
d1jyea_		271	Lac-repressor (lacR) core (C-terminal domain) {Esc	84.44
d1gdha2		129	D-glycerate dehydrogenase {Hyphomicrobium methylov	84.4
d1f4pa_		147	Flavodoxin {Desulfovibrio vulgaris [TaxId: 881]}	83.8
d1ycga1		149	Nitric oxide reductase C-terminal domain {Moorella	82.84
d1vmea1		148	ROO-like flavoprotein TM0755, C-terminal domain {T	82.35
d1e5da1		152	Rubredoxin oxygen:oxidoreductase (ROO), C-terminal	81.62
d1ae1a_		258	Tropinone reductase {Jimsonweed (Datura stramonium	80.93
d1cyda_		242	Carbonyl reductase {Mouse (Mus musculus) [TaxId: 1	80.89
d1d4aa_		273	NAD(P)H:quinone reductase {Human (Homo sapiens) [T	80.77
d1xrsb1		160	D-lysine 5,6-aminomutase beta subunit KamE, C-term	80.64
d1ydga_		201	Trp repressor binding protein WrbA {Deinococcus ra	80.22
d1ja9a_		259	1,3,6,8-tetrahydroxynaphthalene reductase {Rice bl	80.17

>d1jr2a_ c.113.1.1 (A:) Uroporphyrinogen III synthase (U3S, HemD) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: HemD-like
superfamily: HemD-like
family: HemD-like
domain: Uroporphyrinogen III synthase (U3S, HemD)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.6e-32  Score=235.37  Aligned_cols=182  Identities=16%  Similarity=0.212  Sum_probs=156.9

Q ss_pred             CeEEEeCCCCCh---HHHHHHHHHCCCcEEEeceEEEeeCCCchHHHHHHhcCCCccEEEEeCHHHHHHHHHHHHhcCC-
Q 026235           51 PKVVVTRERGKN---GKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGT-  126 (241)
Q Consensus        51 ~~VLitR~~~~~---~~l~~~L~~~G~~v~~~P~~~~~~~~~~~~l~~~l~~l~~~d~IiFTS~~aV~~f~~~l~~~~~-  126 (241)
                      |.||+|||..+.   +++.+.|+++|+++..+|++++++.+ .+.+.+.+.++.+||||||||++||++|++.+.+.+. 
T Consensus         2 k~il~trp~~~~~~~d~~~~~L~~~G~~~~~~P~i~i~~~~-~~~~~~~l~~~~~~d~iifTS~~aV~~~~~~l~~~~~~   80 (260)
T d1jr2a_           2 KVLLLKDAKEDDCGQDPYIRELGLYGLEATLIPVLSFEFLS-LPSFSEKLSHPEDYGGLIFTSPRAVEAAELCLEQNNKT   80 (260)
T ss_dssp             EEEEEESSCCCBTTBCHHHHHHHTTTCEEEEEECEEEEECC-HHHHHHHHTCGGGCSEEEECCHHHHHHHHHHHHHTTCH
T ss_pred             cEEEecCCCCCcccccHHHHHHHhCCCcEEEECCEEEeeCC-hHHHHHHHhChhhccEEEEeCchHHHHHHHHHHhhCcc
Confidence            457999998643   68999999999999999999999864 4566677767789999999999999999998876542 


Q ss_pred             -----------CCcEEEEeCHHHHHHHHHhhhccCCCCceeecCCCCCHHHHHHHhhhCCCCccEEEEEccCCCchhHHH
Q 026235          127 -----------PNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEE  195 (241)
Q Consensus       127 -----------~~~~i~aIG~~Ta~~L~~~~~~~~~Gi~~~~~p~~~t~e~L~~~l~~~~~~~~~iL~~~g~~~~~~L~~  195 (241)
                                 ++++++|||++|+++|+++      |+.+++.+ .+++++|++.+......++++||+||+.++++|.+
T Consensus        81 ~~~~~~~~~~~~~~~i~aVG~~Ta~~l~~~------G~~~~~~~-~~~s~~l~~~~~~~~~~~~~il~~~g~~~~~~L~~  153 (260)
T d1jr2a_          81 EVWERSLKEKWNAKSVYVVGNATASLVSKI------GLDTEGET-CGNAEKLAEYICSRESSALPLLFPCGNLKREILPK  153 (260)
T ss_dssp             HHHHHHTHHHHHHSEEEECSHHHHHHHHHT------TCCCSCCS-CSSHHHHHHHHHTSCCCSSCEEEEESCGGGCCHHH
T ss_pred             hhhhhhhhhhhccCeEEEEcHHHHHHHHHc------CCCccccc-cccHHHHHHHHhhhcccCceEEEeeccccchHHHH
Confidence                       3579999999999999999      99987655 58999999998877666789999999999999999


Q ss_pred             HHHhCCCeeeEeeeeeeecCCCChHHHHHHc---CCCCEEEEECCccC
Q 026235          196 GLSNRGFEVVRLNTYTTEPVHHVDQTVLKQA---LSIPVVAVASPSAV  240 (241)
Q Consensus       196 ~L~~~G~~V~~~~vY~~~~~~~~~~~~~~~l---~~id~IvFtSps~v  240 (241)
                      .|+++|++|.++.+|++++.........+.+   +.+|+|+||||++|
T Consensus       154 ~L~~~g~~v~~~~~Y~~~~~~~~~~~~~~~l~~~~~~d~i~f~S~s~v  201 (260)
T d1jr2a_         154 ALKDKGIAMESITVYQTVAHPGIQGNLNSYYSQQGVPASITFFSPSGL  201 (260)
T ss_dssp             HHHTTTCCEEEEECEEEEECTTHHHHHHHHHHHHCSCSEEEESSHHHH
T ss_pred             HHHhcCCcceEEEeeeeeccccchHHHHHHHHhccCceEEeecCHHHH
Confidence            9999999999999999999887555544443   57999999999886

PyMOL of d1jr2a_

>d1wd7a_ c.113.1.1 (A:) Probable uroporphyrinogen-III synthase {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1wd7a_ c.113.1.1 (A:) Probable uroporphyrinogen-III synthase {Thermus thermophilus [TaxId: 274]}	Back information, alignment and structure

>d1jr2a_ c.113.1.1 (A:) Uroporphyrinogen III synthase (U3S, HemD) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ccwa_ c.23.6.1 (A:) Glutamate mutase, small subunit {Clostridium cochlearium [TaxId: 1494]}	Back information, alignment and structure

>d7reqa2 c.23.6.1 (A:561-728) Methylmalonyl-CoA mutase alpha subunit, C-terminal domain {Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]}	Back information, alignment and structure

>d1lssa_ c.2.1.9 (A:) Ktn Mja218 {Archaeon Methanococcus jannaschii [TaxId: 2190]}	Back information, alignment and structure

>d1zesa1 c.23.1.1 (A:3-123) PhoB receiver domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1vmea1 c.23.5.1 (A:251-398) ROO-like flavoprotein TM0755, C-terminal domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1dcfa_ c.23.1.2 (A:) Receiver domain of the ethylene receptor {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1mb3a_ c.23.1.1 (A:) Cell division response regulator DivK {Caulobacter crescentus [TaxId: 155892]}	Back information, alignment and structure

>d2a9pa1 c.23.1.1 (A:2-118) DNA-binding response regulator MicA, N-terminal domain {Streptococcus pneumoniae [TaxId: 1313]}	Back information, alignment and structure

>d1u0sy_ c.23.1.1 (Y:) CheY protein {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1id1a_ c.2.1.9 (A:) Rck domain from putative potassium channel Kch {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2hmva1 c.2.1.9 (A:7-140) Ktn bsu222 {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d1sbya1 c.2.1.2 (A:1-254) Drosophila alcohol dehydrogenase {Fly (Drosophila lebanonensis) [TaxId: 7225]}	Back information, alignment and structure

>d1sc6a2 c.23.12.1 (A:7-107,A:296-326) Phosphoglycerate dehydrogenase {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d2b4aa1 c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Bacillus halodurans [TaxId: 86665]}	Back information, alignment and structure

>d2qwxa1 c.23.5.3 (A:1-230) Quinone reductase type 2 (menadione reductase) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1w25a1 c.23.1.1 (A:2-140) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]}	Back information, alignment and structure

>d1peya_ c.23.1.1 (A:) Sporulation response regulator Spo0F {Bacillus subtilis [TaxId: 1423]}	Back information, alignment and structure

>d1dxya2 c.23.12.1 (A:1-100,A:300-330) D-2-hydroxyisocaproate dehydrogenase {Lactobacillus casei [TaxId: 1582]}	Back information, alignment and structure

>d1k68a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpA [TaxId: 1188]}	Back information, alignment and structure

>d2pl1a1 c.23.1.1 (A:1-119) PhoP receiver domain {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1pr9a_ c.2.1.2 (A:) Carbonyl reductase {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2qwxa1 c.23.5.3 (A:1-230) Quinone reductase type 2 (menadione reductase) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1jyea_ c.93.1.1 (A:) Lac-repressor (lacR) core (C-terminal domain) {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1gdha2 c.23.12.1 (A:2-100,A:292-321) D-glycerate dehydrogenase {Hyphomicrobium methylovorum [TaxId: 84]}	Back information, alignment and structure

>d1f4pa_ c.23.5.1 (A:) Flavodoxin {Desulfovibrio vulgaris [TaxId: 881]}	Back information, alignment and structure

>d1ycga1 c.23.5.1 (A:251-399) Nitric oxide reductase C-terminal domain {Moorella thermoacetica [TaxId: 1525]}	Back information, alignment and structure

>d1vmea1 c.23.5.1 (A:251-398) ROO-like flavoprotein TM0755, C-terminal domain {Thermotoga maritima [TaxId: 2336]}	Back information, alignment and structure

>d1e5da1 c.23.5.1 (A:251-402) Rubredoxin oxygen:oxidoreductase (ROO), C-terminal domain {Desulfovibrio gigas [TaxId: 879]}	Back information, alignment and structure

>d1ae1a_ c.2.1.2 (A:) Tropinone reductase {Jimsonweed (Datura stramonium), I [TaxId: 4076]}	Back information, alignment and structure

>d1cyda_ c.2.1.2 (A:) Carbonyl reductase {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1d4aa_ c.23.5.3 (A:) NAD(P)H:quinone reductase {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1xrsb1 c.23.6.1 (B:102-261) D-lysine 5,6-aminomutase beta subunit KamE, C-terminal domain {Clostridium sticklandii [TaxId: 1511]}	Back information, alignment and structure

>d1ydga_ c.23.5.8 (A:) Trp repressor binding protein WrbA {Deinococcus radiodurans [TaxId: 1299]}	Back information, alignment and structure

>d1ja9a_ c.2.1.2 (A:) 1,3,6,8-tetrahydroxynaphthalene reductase {Rice blast fungus (Magnaporthe grisea) [TaxId: 148305]}	Back information, alignment and structure