Citrus Sinensis ID: 024727

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-------250-------260---

MAQVSLFSLSSPFPASAVSSRLRLNRPLPFQFSRIQASSDATSASASNSNPKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIPVVAVASPSAVRSSWVNLISDTEQWSNSVACIAG

cccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccHHHHHHHHHHccccEEEEccEEEEEcccHHHHHHHHHccccccEEEEEcHHHHHHHHHHHHHccccccEEEEEcHHHHHHHHHHHHccccccEEEEccccccHHHHHHHcccccccccEEEEEcccccHHHHHHHHHHcccEEEEEEEEcccccccccHHHHHHcccccEEEEEcHHHHHHHHHHccccccccccEEEEEcc

cccEEEccccccccccccccEEEccccccccccccccccccccccccccccEEEEEccccHHHHHHHHHHHccccEEEEEEEEEcccccHHHHHHHHHHHccccEEEEEcHHHHHHHHHHHHHccccccEEEEEcHHHHHHHHHHHHcccccccccccccccHHHHHHHHccHHcccccEEEEccHHHHHHHHHHHHHHcccEEEEEEEEEcccccccHHHHHHHHccccEEEEEcHHHHHHHHHHHHcccHccccEEEEEcc

maqvslfslsspfpasavssrlrlnrplpfqfsriqassdatsasasnsnpkvvvtrergkNGKLIKALAKHRidclelpliqhaqgpdtdrlssvlnadtIFDWIiitspeagSVFLEAWKeagtpnvrigvvgAGTASIFEEVIQSSkcsldvafspskatGKILaselpkngkkkctvlypasakasNEIEEglsnrgfevvrlntyttepvhhvDQTVLKQAlsipvvavaspsAVRSSWVNLISDteqwsnsvaciag

maqvslfslsspfpasavSSRLRLNRPLPFQFSRIQassdatsasasnsnpkvvvtrergknGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKilaselpkngkkkCTVLYPAsakasneieeglsnrgFEVVRLNTYTTEPVHHVDQTVLKQALSIPVVAVASPSAVRSSWVNLisdteqwsnsvaciag

MAQvslfslsspfpasavssRLRLNRPLPFQFSRIQassdatsasasnsNPKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQalsipvvavaspsavrsswvNLISDTEQWSNSVACIAG

**************************************************************GKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFS*******************KCTVLYP************LSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIPVVAVASPSAVRSSWVNLISDTEQWSNSVAC***

*********SSPFPASA*S**LRLNRPLPF********************PKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIPVVAVASPSAVRSSWVNLISDTEQWSNSVACIAG

MAQVSLFSLSSPFPASAVSSRLRLNRPLPFQFSRI******************VVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIPVVAVASPSAVRSSWVNLISDTEQWSNSVACIAG

***VSLFSLSSPFPASAVSSRLRLNRPLPFQFS***************SNPKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGTPNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEEGLSNRGFEVVRLNTYTTEPVHHVDQTVLKQALSIPVVAVASPSAVRSSWVNLISDTEQWSNSVACIAG

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooo

SSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

SSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		263	2.2.26 [Sep-21-2011]
O48721		321	Uroporphyrinogen-III synt	yes	no	0.798	0.654	0.702	6e-80
Q10QR9		302	Uroporphyrinogen-III synt	yes	no	0.825	0.718	0.662	5e-77
Q59294		504	Porphyrin biosynthesis pr	N/A	no	0.775	0.404	0.238	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 =  297 bits (760), Expect = 6e-80,   Method: Compositional matrix adjust.
 Identities = 149/212 (70%), Positives = 175/212 (82%), Gaps = 2/212 (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 VVAVASPSAVRSSWVNLISDTEQWSNSVACIA 262
           V++VASPSAVR +W++LI + EQWSN VACI 
Sbjct: 244 VLSVASPSAVR-AWLHLIQNEEQWSNYVACIG 274

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		263
224137378		296	predicted protein [Populus trichocarpa]	0.802	0.712	0.811	1e-95
359492064		304	PREDICTED: uroporphyrinogen-III synthase	0.889	0.769	0.712	7e-90
449470043		311	PREDICTED: uroporphyrinogen-III synthase	0.984	0.832	0.667	6e-87
356519166		297	PREDICTED: uroporphyrinogen-III synthase	0.802	0.710	0.753	2e-86
356509718		300	PREDICTED: uroporphyrinogen-III synthase	0.802	0.703	0.744	8e-85
357465443		308	Uroporphyrinogen-III synthase [Medicago	0.821	0.701	0.718	2e-84
18694346		321	uroporphyrinogen III synthase [Arabidops	0.798	0.654	0.702	4e-78
18401160		321	Uroporphyrinogen-III synthase [Arabidops	0.798	0.654	0.702	4e-78
21592861		321	uroporphyrinogen III synthase [Arabidops	0.798	0.654	0.698	5e-78
297825849		305	hypothetical protein ARALYDRAFT_481514 [	0.798	0.688	0.698	2e-77

>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 =  355 bits (910), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 172/212 (81%), Positives = 194/212 (91%), Gaps = 1/212 (0%)

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 VVAVASPSAVRSSWVNLISDTEQWSNSVACIA 262
           VVAVASPS+VR +W NLI ++E+W+NSVACI 
Sbjct: 226 VVAVASPSSVR-AWANLIPESEEWNNSVACIG 256

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\|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\|356519166\|ref\|XP_003528245.1\| PREDICTED: uroporphyrinogen-III synthase, chloroplastic-like [Glycine max]	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\|297825849\|ref\|XP_002880807.1\| hypothetical protein ARALYDRAFT_481514 [Arabidopsis lyrata subsp. lyrata] gi\|297326646\|gb\|EFH57066.1\| hypothetical protein ARALYDRAFT_481514 [Arabidopsis lyrata subsp. lyrata]	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		263
TAIR\|locus:2066256		321	HEMD [Arabidopsis thaliana (ta	0.882	0.722	0.599	2.9e-64

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

 Score = 655 (235.6 bits), Expect = 2.9e-64, P = 2.9e-64
 Identities = 142/237 (59%), Positives = 163/237 (68%)

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 VRLNTYTTEPVHHVDQTVLKQXXXXXXXXXXXXXXXXXXXXNLISDTEQWSNSVACI 261
             VRLNTYTT PV  VD TVL Q                    +LI + EQWSN VACI
Sbjct:   218 VRLNTYTTVPVQSVD-TVLLQQALSAPVLSVASPSAVRAWLHLIQNEEQWSNYVACI 273


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        0.316   0.131   0.381    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      263       213   0.00084  112 3  11 22  0.40    33
                                                     31  0.49    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:  595 (63 KB)
  Total size of DFA:  176 KB (2102 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:  18.16u 0.18s 18.34t   Elapsed:  00:00:01
  Total cpu time:  18.16u 0.18s 18.34t   Elapsed:  00:00:01
  Start:  Mon May 20 18:13:42 2013   End:  Mon May 20 18:13:43 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	0.6621	0.8250	0.7185	yes	no
O48721	HEM4_ARATH	4, ., 2, ., 1, ., 7, 5	0.7028	0.7984	0.6542	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	0.963
4th Layer	4.2.1.75	0.946

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	Alignment Graph	Length	Definition	E-value
Query		263
cd06578		239	cd06578, HemD, Uroporphyrinogen-III synthase (HemD	5e-33
COG1587		248	COG1587, HemD, Uroporphyrinogen-III synthase [Coen	3e-28
pfam02602		230	pfam02602, HEM4, Uroporphyrinogen-III synthase Hem	7e-26
PRK05928		249	PRK05928, hemD, uroporphyrinogen-III synthase; Rev	4e-25
PRK06975		656	PRK06975, PRK06975, bifunctional uroporphyrinogen-	1e-08

>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 =  120 bits (302), Expect = 5e-33
 Identities = 62/217 (28%), Positives = 93/217 (42%), Gaps = 17/217 (7%)

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 SIPVVAVASPSAVRSSWVNLISDTEQWSNS---VACI 261
            I  V   SPS VR + + L+    +       +A I
Sbjct: 174 -IDAVLFTSPSTVR-NLLELLGKEGRALLKNVKIAAI 208

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

>gnl\|CDD\|235647 PRK05928, hemD, uroporphyrinogen-III synthase; Reviewed	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		263
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	100.0
PF02602		231	HEM4: Uroporphyrinogen-III synthase HemD; InterPro	100.0
PRK07168		474	bifunctional uroporphyrinogen-III methyltransferas	99.98
KOG4132		260	consensus Uroporphyrinogen III synthase UROS/HEM4	99.94
PRK05928		249	hemD uroporphyrinogen-III synthase; Reviewed	99.7
cd06578		239	HemD Uroporphyrinogen-III synthase (HemD) catalyze	99.65
PRK07239		381	bifunctional uroporphyrinogen-III synthetase/respo	99.61
PRK05752		255	uroporphyrinogen-III synthase; Validated	99.58
PF02602		231	HEM4: Uroporphyrinogen-III synthase HemD; InterPro	99.55
COG1587		248	HemD Uroporphyrinogen-III synthase [Coenzyme metab	99.54
PRK09189		240	uroporphyrinogen-III synthase; Validated	99.54
KOG4132		260	consensus Uroporphyrinogen III synthase UROS/HEM4	99.47
PRK08811		266	uroporphyrinogen-III synthase; Validated	99.47
PRK06975		656	bifunctional uroporphyrinogen-III synthetase/uropo	99.18
PRK07168		474	bifunctional uroporphyrinogen-III methyltransferas	98.71
cd06298		268	PBP1_CcpA_like Ligand-binding domain of the catabo	96.79
cd06295		275	PBP1_CelR Ligand binding domain of a transcription	96.79
cd06299		265	PBP1_LacI_like_13 Ligand-binding domain of DNA-bin	96.6
cd01575		268	PBP1_GntR Ligand-binding domain of DNA transcripti	96.56
cd06273		268	PBP1_GntR_like_1 This group includes the ligand-bi	96.42
cd06297		269	PBP1_LacI_like_12 Ligand-binding domain of unchara	96.42
cd06270		268	PBP1_GalS_like Ligand binding domain of DNA transc	96.27
cd06286		260	PBP1_CcpB_like Ligand-binding domain of a novel tr	96.22
cd06271		268	PBP1_AglR_RafR_like Ligand-binding domain of DNA t	96.17
cd06272		261	PBP1_hexuronate_repressor_like Ligand-binding doma	96.14
cd06296		270	PBP1_CatR_like Ligand-binding domain of a LacI-lik	96.13
cd06283		267	PBP1_RegR_EndR_KdgR_like Ligand-binding domain of	96.1
cd06294		270	PBP1_ycjW_transcription_regulator_like Ligand-bind	96.06
cd06305		273	PBP1_methylthioribose_binding_like Methylthioribos	96.05
COG1609		333	PurR Transcriptional regulators [Transcription]	96.04
cd06301		272	PBP1_rhizopine_binding_like Periplasmic binding pr	96.02
cd01542		259	PBP1_TreR_like Ligand-binding domain of DNA transc	95.99
cd06274		264	PBP1_FruR Ligand binding domain of DNA transcripti	95.89
cd06288		269	PBP1_sucrose_transcription_regulator Ligand-bindin	95.89
cd06279		283	PBP1_LacI_like_3 Ligand-binding domain of uncharac	95.85
cd06285		265	PBP1_LacI_like_7 Ligand-binding domain of uncharac	95.79
cd01545		270	PBP1_SalR Ligand-binding domain of DNA transcripti	95.79
cd06292		273	PBP1_LacI_like_10 Ligand-binding domain of unchara	95.7
cd06309		273	PBP1_YtfQ_like Periplasmic binding domain of ABC-t	95.69
TIGR01481		329	ccpA catabolite control protein A. Catabolite cont	95.65
cd06320		275	PBP1_allose_binding Periplasmic allose-binding dom	95.62
cd06281		269	PBP1_LacI_like_5 Ligand-binding domain of uncharac	95.61
cd06289		268	PBP1_MalI_like Ligand-binding domain of MalI, a tr	95.57
cd01574		264	PBP1_LacI Ligand-binding domain of DNA transcripti	95.54
cd06275		269	PBP1_PurR Ligand-binding domain of purine represso	95.51
cd06290		265	PBP1_LacI_like_9 Ligand-binding domain of uncharac	95.5
cd06310		273	PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-bi	95.49
PRK02261		137	methylaspartate mutase subunit S; Provisional	95.49
cd06316		294	PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-bi	95.47
cd06313		272	PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-bi	95.43
cd01537		264	PBP1_Repressors_Sugar_Binding_like Ligand-binding	95.43
PRK10423		327	transcriptional repressor RbsR; Provisional	95.42
cd06284		267	PBP1_LacI_like_6 Ligand-binding domain of an uncha	95.26
PRK10014		342	DNA-binding transcriptional repressor MalI; Provis	95.17
PRK10703		341	DNA-binding transcriptional repressor PurR; Provis	95.16
cd06293		269	PBP1_LacI_like_11 Ligand-binding domain of unchara	95.15
cd01541		273	PBP1_AraR Ligand-binding domain of DNA transcripti	95.14
cd06278		266	PBP1_LacI_like_2 Ligand-binding domain of uncharac	95.14
cd06267		264	PBP1_LacI_sugar_binding_like Ligand binding domain	95.1
PRK11303		328	DNA-binding transcriptional regulator FruR; Provis	94.86
cd06282		266	PBP1_GntR_like_2 Ligand-binding domain of putative	94.67
cd06354		265	PBP1_BmpA_PnrA_like Periplasmic binding domain of	94.63
cd06302		298	PBP1_LsrB_Quorum_Sensing Periplasmic binding domai	94.6
PF04392		294	ABC_sub_bind: ABC transporter substrate binding pr	94.58
PF00532		279	Peripla_BP_1: Periplasmic binding proteins and sug	94.56
cd06318		282	PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-bi	94.5
cd06314		271	PBP1_tmGBP Periplasmic sugar-binding domain of The	94.48
cd06308		270	PBP1_sensor_kinase_like Periplasmic binding domain	94.46
PF13407		257	Peripla_BP_4: Periplasmic binding protein domain;	94.42
COG2185		143	Sbm Methylmalonyl-CoA mutase, C-terminal domain/su	94.29
TIGR00640		132	acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal	94.27
cd06307		275	PBP1_uncharacterized_sugar_binding Periplasmic sug	94.07
cd02072		128	Glm_B12_BD B12 binding domain of glutamate mutase	94.07
cd01536		267	PBP1_ABC_sugar_binding_like Periplasmic sugar-bind	93.94
TIGR02853		287	spore_dpaA dipicolinic acid synthetase, A subunit.	93.93
cd06323		268	PBP1_ribose_binding Periplasmic sugar-binding doma	93.77
cd06321		271	PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-b	93.75
PRK10653		295	D-ribose transporter subunit RbsB; Provisional	93.68
PRK09526		342	lacI lac repressor; Reviewed	93.59
cd06312		271	PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-bi	93.58
cd06291		265	PBP1_Qymf_like Ligand binding domain of the lacI-l	93.57
cd06276		247	PBP1_FucR_like Ligand-binding domain of a transcri	93.55
cd06287		269	PBP1_LacI_like_8 Ligand-binding domain of uncharac	93.49
cd06319		277	PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-b	93.42
cd06277		268	PBP1_LacI_like_1 Ligand-binding domain of uncharac	93.22
TIGR01501		134	MthylAspMutase methylaspartate mutase, S subunit.	93.17
cd06322		267	PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-b	93.14
cd01391		269	Periplasmic_Binding_Protein_Type_1 Type 1 periplas	93.13
cd06280		263	PBP1_LacI_like_4 Ligand-binding domain of uncharac	93.11
PRK08306		296	dipicolinate synthase subunit A; Reviewed	93.07
cd02071		122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	93.07
cd01539		303	PBP1_GGBP Periplasmic glucose/galactose-binding pr	93.01
cd01544		270	PBP1_GalR Ligand-binding domain of DNA transcripti	92.93
TIGR02417		327	fruct_sucro_rep D-fructose-responsive transcriptio	92.88
PRK09492		315	treR trehalose repressor; Provisional	92.86
cd06300		272	PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-bi	92.84
PRK10401		346	DNA-binding transcriptional regulator GalS; Provis	92.83
PRK10727		343	DNA-binding transcriptional regulator GalR; Provis	92.69
cd01538		288	PBP1_ABC_xylose_binding Periplasmic xylose-binding	92.2
cd06317		275	PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-bi	92.08
PRK14987		331	gluconate operon transcriptional regulator; Provis	91.11
cd06304		260	PBP1_BmpA_like Periplasmic binding component of a	90.94
PRK09701		311	D-allose transporter subunit; Provisional	90.44
COG4822		265	CbiK Cobalamin biosynthesis protein CbiK, Co2+ che	90.41
cd06324		305	PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-b	90.25
cd06306		268	PBP1_TorT-like TorT-like proteins, a periplasmic b	90.05
PRK15408		336	autoinducer 2-binding protein lsrB; Provisional	90.02
PRK11041		309	DNA-binding transcriptional regulator CytR; Provis	89.67
cd06303		280	PBP1_LuxPQ_Quorum_Sensing Periplasmic binding prot	89.37
PRK10339		327	DNA-binding transcriptional repressor EbgR; Provis	88.39
COG2984		322	ABC-type uncharacterized transport system, peripla	88.3
cd02067		119	B12-binding B12 binding domain (B12-BD). This doma	87.82
cd01543		265	PBP1_XylR Ligand-binding domain of DNA transcripti	87.51
PRK02910		519	light-independent protochlorophyllide reductase su	87.45
PF10087		97	DUF2325: Uncharacterized protein conserved in bact	86.97
PRK10569		191	NAD(P)H-dependent FMN reductase; Provisional	86.63
cd06311		274	PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-bi	86.47
TIGR03567		171	FMN_reduc_SsuE FMN reductase, SsuE family. Members	86.32
PF03358		152	FMN_red: NADPH-dependent FMN reductase; InterPro:	86.03
PRK06756		148	flavodoxin; Provisional	86.01
TIGR00853		95	pts-lac PTS system, lactose/cellobiose family IIB	85.95
PRK11790		409	D-3-phosphoglycerate dehydrogenase; Provisional	85.75
cd01540		289	PBP1_arabinose_binding Periplasmic L-arabinose-bin	85.55
cd00316		399	Oxidoreductase_nitrogenase The nitrogenase enzyme	85.31
PRK15395		330	methyl-galactoside ABC transporter galactose-bindi	84.7
cd06341		341	PBP1_ABC_ligand_binding_like_7 Type I periplasmic	84.3
PF03808		172	Glyco_tran_WecB: Glycosyl transferase WecB/TagA/Cp	83.96
cd05564		96	PTS_IIB_chitobiose_lichenan PTS_IIB_chitobiose_lic	83.93
TIGR02637		302	RhaS rhamnose ABC transporter, rhamnose-binding pr	83.75
PRK15438		378	erythronate-4-phosphate dehydrogenase PdxB; Provis	83.66
TIGR02955		295	TMAO_TorT TMAO reductase system periplasmic protei	83.05
cd06325		281	PBP1_ABC_uncharacterized_transporter Type I peripl	82.15
PF06506		176	PrpR_N: Propionate catabolism activator; InterPro:	82.08
PF03358		152	FMN_red: NADPH-dependent FMN reductase; InterPro:	81.54

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

Probab=100.00  E-value=5.1e-39  Score=282.97  Aligned_cols=209  Identities=21%  Similarity=0.171  Sum_probs=182.4

Q ss_pred             CCCCeEEEeCCCCChHHHHHHHHhCCCcEEEeceEEeeeCCCchHHHHHHhcCCCccEEEEeCHHHHHHHHHHHHHcCC-
Q 024727           48 NSNPKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGT-  126 (263)
Q Consensus        48 l~g~~ILitr~~~~~~~l~~~L~~~G~~v~~~p~~~~~~~~~~~~l~~~l~~l~~~d~IiFTS~~aV~~~~~~l~~~~~-  126 (263)
                      +.|++||||||.++.+++.+.|+++|++++.+|+++++|.++...++..+..+..||||||||+|||++|++.+.+.+. 
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            4699999999999999999999999999999999999998776667777778899999999999999999999876654 


Q ss_pred             -CCcEEEEeChhHHHHHHHhhhhcCCCCceeecCCCCCHHHHHHH--hccC-CCCCcEEEEEcCCCCchhHHHHHHhCCC
Q 024727          127 -PNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASE--LPKN-GKKKCTVLYPASAKASNEIEEGLSNRGF  202 (263)
Q Consensus       127 -~~~~i~aVG~~Ta~~L~~~~~~~~~G~~~~~~p~~~t~e~L~~~--l~~~-~~~~~~vL~~~g~~~~~~L~~~L~~~G~  202 (263)
                       .+.+++|||++|+++|+++      |+.++++|..+++++|++.  +.+. ..++++||++||+++++.|.+.|++.|+
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             3689999999999999999      9999998999999999976  3332 2367899999999999999999999999


Q ss_pred             eeeEEeeeccccCCCChHHHHHHh--CCCCEEEEeCHHHHHHHHHHhccccC--CCCceEEEECC
Q 024727          203 EVVRLNTYTTEPVHHVDQTVLKQA--LSIPVVAVASPSAVRSSWVNLISDTE--QWSNSVACIAG  263 (263)
Q Consensus       203 ~v~~~~vY~~~~~~~~~~~~~~~l--~~~d~vvFtS~s~v~~~~~~~~~~~~--~~~~~i~~IGp  263 (263)
                      +|.++++|++.......+.+.+.+  +.+|+|+|||+++++ +|+++++...  +.+.+++||||
T Consensus       155 ~v~~~~vY~~~~~~~~~~~~~~~~~~~~~d~v~ftS~~~~~-~~~~~~~~~~~~~~~~~~~~ig~  218 (255)
T PRK05752        155 SVDYLELYRRCLPDYPAGTLLQRVEAERLNGLVVSSGQGFE-HLQQLAGADWPELARLPLFVPSP  218 (255)
T ss_pred             EEeEEEEEeecCCCCCHHHHHHHHHhCCCCEEEECCHHHHH-HHHHHhChhHHHhcCceEEEeCH
Confidence            999999999987766555544444  579999999999999 9999886532  35789999996

>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

>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

>PRK09189 uroporphyrinogen-III synthase; Validated	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

>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

>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

>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

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

>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

>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

>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

>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

>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

>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

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

>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines	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

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

>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

>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

>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

>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

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

>TIGR01481 ccpA catabolite control protein A	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

>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

>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

>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

>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

>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

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

>PRK02261 methylaspartate mutase subunit S; Provisional	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

>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems	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

>PRK10423 transcriptional repressor RbsR; Provisional	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

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

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional	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

>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

>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

>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

>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

>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

>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

>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

>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

>cd06318 PBP1_ABC_sugar_binding_like_9 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

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

>PF13407 Peripla_BP_4: Periplasmic binding protein domain; PDB: 3BRS_B 3GBP_A 3GA5_A 1GCG_A 1GCA_A 3H75_A 3D02_A 3L49_B 3EJW_B 3T95_A	Back alignment and domain information

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

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

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

>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm)	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

>TIGR02853 spore_dpaA dipicolinic acid synthetase, A subunit	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

>cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems	Back alignment and domain information

>PRK10653 D-ribose transporter subunit RbsB; Provisional	Back alignment and domain information

>PRK09526 lacI lac repressor; Reviewed	Back alignment and domain information

>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems	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

>cd06276 PBP1_FucR_like Ligand-binding domain of a transcription repressor, FucR, which functions as a molecular sensor of L-fucose availability	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

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

>cd06277 PBP1_LacI_like_1 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

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

>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems	Back alignment and domain information

>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily	Back alignment and domain information

>cd06280 PBP1_LacI_like_4 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

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

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

>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species	Back alignment and domain information

>cd01544 PBP1_GalR Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism	Back alignment and domain information

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

>PRK09492 treR trehalose repressor; Provisional	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

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional	Back alignment and domain information

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional	Back alignment and domain information

>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the 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

>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems	Back alignment and domain information

>PRK14987 gluconate operon transcriptional regulator; Provisional	Back alignment and domain information

>cd06304 PBP1_BmpA_like Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria	Back alignment and domain information

>PRK09701 D-allose transporter subunit; Provisional	Back alignment and domain information

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

>cd06324 PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems	Back alignment and domain information

>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria	Back alignment and domain information

>PRK15408 autoinducer 2-binding protein lsrB; Provisional	Back alignment and domain information

>PRK11041 DNA-binding transcriptional regulator CytR; Provisional	Back alignment and domain information

>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs	Back alignment and domain information

>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional	Back alignment and domain information

>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]	Back alignment and domain information

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

>cd01543 PBP1_XylR Ligand-binding domain of DNA transcription repressor specific for xylose (XylR)	Back alignment and domain information

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

>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function	Back alignment and domain information

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

>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems	Back alignment and domain information

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

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

>PRK06756 flavodoxin; Provisional	Back alignment and domain information

>TIGR00853 pts-lac PTS system, lactose/cellobiose family IIB component	Back alignment and domain information

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

>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily	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

>PRK15395 methyl-galactoside ABC transporter galactose-binding periplasmic protein MglB; Provisional	Back alignment and domain information

>cd06341 PBP1_ABC_ligand_binding_like_7 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions	Back alignment and domain information

>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli	Back alignment and domain information

>cd05564 PTS_IIB_chitobiose_lichenan PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS)	Back alignment and domain information

>TIGR02637 RhaS rhamnose ABC transporter, rhamnose-binding protein	Back alignment and domain information

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

>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT	Back alignment and domain information

>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions	Back alignment and domain information

>PF06506 PrpR_N: Propionate catabolism activator; InterPro: IPR010524 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []	Back alignment and domain information

>PF03358 FMN_red: NADPH-dependent FMN reductase; InterPro: IPR005025 NADPH-dependent FMN reductase (1	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		263
3re1_A		269	Uroporphyrinogen-III synthetase; HEMD-like family,	3e-34
1jr2_A		286	Uroporphyrinogen-III synthase; heme biosynthesis,	3e-31
3mw8_A		240	Uroporphyrinogen-III synthase; structural genomics	1e-30
1wcw_A		261	Uroporphyrinogen III synthase; congenital erythrop	5e-25
3p9z_A		229	Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2	2e-23
3d8t_A		286	Uroporphyrinogen-III synthase; heme biosynthesis,	2e-20

>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 =  123 bits (311), Expect = 3e-34
 Identities = 42/221 (19%), Positives = 74/221 (33%), Gaps = 14/221 (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--QALSIPVVAVASPSAVRSSWVNLISDTEQWSNSVACIA 262
           +  +   +  + V+S        + L  D+      +    
Sbjct: 187 QRVEVERLNGLVVSSGQGFE-HLLQLAGDSWPDLAGLPLFV 226

PyMOL of 3re1

>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

>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

>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		263
4es6_A		254	Uroporphyrinogen-III synthase; heme-biosynthesis,	100.0
3d8t_A		286	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
1jr2_A		286	Uroporphyrinogen-III synthase; heme biosynthesis,	100.0
1wcw_A		261	Uroporphyrinogen III synthase; congenital erythrop	100.0
3p9z_A		229	Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2	99.97
3p9z_A		229	Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2	99.72
1jr2_A		286	Uroporphyrinogen-III synthase; heme biosynthesis,	99.72
3re1_A		269	Uroporphyrinogen-III synthetase; HEMD-like family,	99.71
4es6_A		254	Uroporphyrinogen-III synthase; heme-biosynthesis,	99.7
1wcw_A		261	Uroporphyrinogen III synthase; congenital erythrop	99.67
3d8t_A		286	Uroporphyrinogen-III synthase; heme biosynthesis,	99.67
3mw8_A		240	Uroporphyrinogen-III synthase; structural genomics	99.66
3gbv_A		304	Putative LACI-family transcriptional regulator; NY	96.4
3gv0_A		288	Transcriptional regulator, LACI family; transcript	96.23
3qk7_A		294	Transcriptional regulators; structural genomics, N	96.18
3l49_A		291	ABC sugar (ribose) transporter, periplasmic substr	96.11
3g1w_A		305	Sugar ABC transporter; sugar-binding protein, baci	95.89
3egc_A		291	Putative ribose operon repressor; structural genom	95.74
3d8u_A		275	PURR transcriptional regulator; APC91343.1, vibrio	95.7
3brq_A		296	HTH-type transcriptional regulator ASCG; transcrip	95.55
3bbl_A		287	Regulatory protein of LACI family; protein structu	95.47
2fep_A		289	Catabolite control protein A; CCPA, transcriptiona	95.43
3k9c_A		289	Transcriptional regulator, LACI family protein; PS	95.41
3g85_A		289	Transcriptional regulator (LACI family); transcrip	95.4
3k4h_A		292	Putative transcriptional regulator; structural gen	95.38
3rot_A		297	ABC sugar transporter, periplasmic sugar binding;	95.26
3c3k_A		285	Alanine racemase; structural genomics, protein str	95.17
2rgy_A		290	Transcriptional regulator, LACI family; 11011J, NY	95.14
3dbi_A		338	Sugar-binding transcriptional regulator, LACI FAM;	95.03
2o20_A		332	Catabolite control protein A; CCPA, transcriptiona	94.83
1dbq_A		289	Purine repressor; transcription regulation, DNA-bi	94.79
3h75_A		350	Periplasmic sugar-binding domain protein; protein	94.77
2fvy_A		309	D-galactose-binding periplasmic protein; periplasm	94.76
3d4o_A		293	Dipicolinate synthase subunit A; NP_243269.1, stru	94.65
3clk_A		290	Transcription regulator; 11017J, PSI-II, NYSGXRC,	94.63
3ksm_A		276	ABC-type sugar transport system, periplasmic COMP;	94.62
3e3m_A		355	Transcriptional regulator, LACI family; structural	94.55
3lft_A		295	Uncharacterized protein; ABC, ATPase, cassette, L-	94.34
3gyb_A		280	Transcriptional regulators (LACI-family transcript	94.34
3kke_A		303	LACI family transcriptional regulator; structural	94.29
3huu_A		305	Transcription regulator like protein; PSI-II, NYSG	93.9
2qh8_A		302	Uncharacterized protein; conserved domain protein,	93.89
2rir_A		300	Dipicolinate synthase, A chain; structural genomic	93.81
3o74_A		272	Fructose transport system repressor FRUR; dual tra	93.8
2hsg_A		332	Glucose-resistance amylase regulator; CCPA, transc	93.72
3l6u_A		293	ABC-type sugar transport system periplasmic compo;	93.6
2h3h_A		313	Sugar ABC transporter, periplasmic sugar-binding p	93.57
3tb6_A		298	Arabinose metabolism transcriptional repressor; tr	93.57
2h0a_A		276	TTHA0807, transcriptional regulator; repressor, st	93.51
3jvd_A		333	Transcriptional regulators; structural genomics, P	93.44
3kjx_A		344	Transcriptional regulator, LACI family; LACL famil	93.26
1qpz_A		340	PURA, protein (purine nucleotide synthesis repress	93.14
1ccw_A		137	Protein (glutamate mutase); coenzyme B12, radical	93.01
2x7x_A		325	Sensor protein; transferase, sensor histidine kina	92.4
3jy6_A		276	Transcriptional regulator, LACI family; NYSGXRC, P	92.28
3hcw_A		295	Maltose operon transcriptional repressor; RNA-bind	92.26
2yxb_A		161	Coenzyme B12-dependent mutase; alpha/beta, structu	92.16
2dri_A		271	D-ribose-binding protein; sugar transport; HET: RI	92.08
3cs3_A		277	Sugar-binding transcriptional regulator, LACI FAM;	92.05
2iks_A		293	DNA-binding transcriptional dual regulator; escher	91.9
2ioy_A		283	Periplasmic sugar-binding protein; ribose binding	91.85
3hs3_A		277	Ribose operon repressor; PSI-II, NYSGXRC, periplas	91.79
3k5p_A		416	D-3-phosphoglycerate dehydrogenase; niaid, ssgcid,	91.6
3m9w_A		313	D-xylose-binding periplasmic protein; xylose bindi	91.43
2vk2_A		306	YTFQ, ABC transporter periplasmic-binding protein	91.17
3e61_A		277	Putative transcriptional repressor of ribose OPER;	90.96
2hqb_A		296	Transcriptional activator of COMK gene; berkeley s	90.76
4fe7_A		412	Xylose operon regulatory protein; HTH_ARAC, helix-	90.69
1gud_A		288	ALBP, D-allose-binding periplasmic protein; peripl	90.53
2rjo_A		332	Twin-arginine translocation pathway signal protei;	90.43
3bil_A		348	Probable LACI-family transcriptional regulator; st	90.23
2hmt_A		144	YUAA protein; RCK, KTN, KTR, KTRA, ktrab, membrane	89.95
2pln_A		137	HP1043, response regulator; signaling protein; 1.8	89.92
3d02_A		303	Putative LACI-type transcriptional regulator; peri	89.71
2g1u_A		155	Hypothetical protein TM1088A; structural genomics,	89.5
2qu7_A		288	Putative transcriptional regulator; structural gen	89.47
2fn9_A		290	Ribose ABC transporter, periplasmic ribose-bindin;	88.48
3llv_A		141	Exopolyphosphatase-related protein; NAD(P)-binding	88.47
1lss_A		140	TRK system potassium uptake protein TRKA homolog;	88.27
1jye_A		349	Lactose operon repressor; gene regulation, protein	88.01
3brs_A		289	Periplasmic binding protein/LACI transcriptional;	87.97
3fwz_A		140	Inner membrane protein YBAL; TRKA-N domain, E.coli	87.39
3h5o_A		339	Transcriptional regulator GNTR; transcription regu	87.11
3miz_A		301	Putative transcriptional regulator protein, LACI f	87.01
1id1_A		153	Putative potassium channel protein; RCK domain, E.	86.59
3h5t_A		366	Transcriptional regulator, LACI family; DNA-depend	86.01
1tjy_A		316	Sugar transport protein; protein-ligand complex, s	86.0
1jx6_A		342	LUXP protein; protein-ligand complex, signaling pr	85.12
3c85_A		183	Putative glutathione-regulated potassium-efflux S	84.17
3td9_A		366	Branched chain amino acid ABC transporter, peripl	84.13
3gt7_A		154	Sensor protein; structural genomics, signal receiv	84.06
4eyg_A		368	Twin-arginine translocation pathway signal; PSI-bi	83.11
3lkv_A		302	Uncharacterized conserved domain protein; ATPase b	82.98
2amj_A		204	Modulator of drug activity B; oxidoreductase, mena	81.77
2fqx_A		318	Membrane lipoprotein TMPC; ABC transport system, l	81.77
4evq_A		375	Putative ABC transporter subunit, substrate-bindi	81.61
2q62_A		247	ARSH; alpha/beta, flavoprotein; 1.80A {Sinorhizobi	81.32
4imr_A		275	3-oxoacyl-(acyl-carrier-protein) reductase; oxidor	80.92
2fzv_A		279	Putative arsenical resistance protein; flavin bind	80.82
1mio_B		458	Nitrogenase molybdenum iron protein (beta chain);	80.39
3eod_A		130	Protein HNR; response regulator, phosphoprotein, t	80.27
2vzf_A		197	NADH-dependent FMN reductase; oxidoreductase; 2.50	80.07

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

Probab=100.00  E-value=1.7e-41  Score=296.61  Aligned_cols=211  Identities=18%  Similarity=0.159  Sum_probs=185.0

Q ss_pred             CCCCCCeEEEeCCCCChHHHHHHHHhCCCcEEEeceEEeeeCCCchHHHHHHhcCCCccEEEEeCHHHHHHHHHHHHHcC
Q 024727           46 ASNSNPKVVVTRERGKNGKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAG  125 (263)
Q Consensus        46 ~~l~g~~ILitr~~~~~~~l~~~L~~~G~~v~~~p~~~~~~~~~~~~l~~~l~~l~~~d~IiFTS~~aV~~~~~~l~~~~  125 (263)
                      .||.|++||+|||..+.+++.+.|+++|++++.+|+|++++.++...++..+..+..||||||||+|+|++|++.+...+
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            58999999999999889999999999999999999999999887667788887788999999999999999999988765


Q ss_pred             CC--CcEEEEeChhHHHHHHHhhhhcCCCCceeecCCCCCHHHHHHHhc--c-CCCCCcEEEEEcCCCCchhHHHHHHhC
Q 024727          126 TP--NVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELP--K-NGKKKCTVLYPASAKASNEIEEGLSNR  200 (263)
Q Consensus       126 ~~--~~~i~aVG~~Ta~~L~~~~~~~~~G~~~~~~p~~~t~e~L~~~l~--~-~~~~~~~vL~~~g~~~~~~L~~~L~~~  200 (263)
                      .+  +++++|||++|+++|+++      |+.++++|+.+++++|++.+.  + ...++++||++||+.++++|.+.|+++
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            43  589999999999999999      999999998999999998886  3 244689999999999999999999999


Q ss_pred             CCeeeEEeeeccccCCCChHHHHHHh--CCCCEEEEeCHHHHHHHHHHhcccc--CCCCceEEEECC
Q 024727          201 GFEVVRLNTYTTEPVHHVDQTVLKQA--LSIPVVAVASPSAVRSSWVNLISDT--EQWSNSVACIAG  263 (263)
Q Consensus       201 G~~v~~~~vY~~~~~~~~~~~~~~~l--~~~d~vvFtS~s~v~~~~~~~~~~~--~~~~~~i~~IGp  263 (263)
                      |++|.++++|++.+.+...+.+.+.+  +.+|+|+||||++++ +|++++++.  .+.+++++||||
T Consensus       156 G~~v~~~~vY~~~~~~~~~~~~~~~l~~~~~d~v~ftS~s~v~-~~~~~~~~~~~~l~~~~~~aIG~  221 (254)
T 4es6_A          156 GVQVDYLPLYRRRAPDYPAGELLARVRAERLNGLVVSSGQGLQ-NLYQLAAADWPEIGRLPLFVPSP  221 (254)
T ss_dssp             TCEEEEEECEEEECCCCCTTHHHHHHHHTTCCEEECCSHHHHH-HHHHHHGGGHHHHTTSCEEESSH
T ss_pred             CCEEEEEeEEEeeCCCCCHHHHHHHHHhCCCCEEEEcCHHHHH-HHHHHhhHHHHHHhCCeEEEECH
Confidence            99999999999999887655554444  589999999999999 999998753  145799999996

PyMOL of 4es6

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

>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

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

>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

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

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

>3d8t_A Uroporphyrinogen-III synthase; heme biosynthesis, lyase; 1.60A {Thermus thermophilus} PDB: 3d8r_A 3d8s_A 3d8n_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

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

>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

>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

>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

>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

>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

>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

>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

>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

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

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

>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

>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

>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

>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

>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

>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

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

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

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

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

>3o74_A Fructose transport system repressor FRUR; dual transcriptional regulator, DNA, transcription; 2.00A {Pseudomonas putida} PDB: 3o75_A*	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

>3l6u_A ABC-type sugar transport system periplasmic compo; structural genomics, nysgrc, target 11006S, PSI-2, protein S initiative; 1.90A {Exiguobacterium sibiricum}	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

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

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

>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

>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

>2x7x_A Sensor protein; transferase, sensor histidine kinase; HET: FRU; 2.64A {Bacteroides thetaiotaomicron}	Back alignment and structure

>3jy6_A Transcriptional regulator, LACI family; NYSGXRC, PSI-II, protein S initiative, structural genomics; 1.97A {Lactobacillus brevis}	Back alignment and structure

>3hcw_A Maltose operon transcriptional repressor; RNA-binding, PSI-2, NYSGXRC, STRU genomics, protein structure initiative; 2.20A {Staphylococcus aureus subsp}	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

>2dri_A D-ribose-binding protein; sugar transport; HET: RIP; 1.60A {Escherichia coli} SCOP: c.93.1.1 PDB: 1urp_A* 1ba2_A 1dbp_A* 1drj_A* 1drk_A* 2gx6_A*	Back alignment and structure

>3cs3_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative; 2.40A {Enterococcus faecalis}	Back alignment and structure

>2iks_A DNA-binding transcriptional dual regulator; escherichia coli structural genomics, PSI-2, protein structure initiative; 1.85A {Escherichia coli}	Back alignment and structure

>2ioy_A Periplasmic sugar-binding protein; ribose binding protein, thermophilic proteins; HET: RIP; 1.90A {Thermoanaerobacter tengcongensis}	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

>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

>3m9w_A D-xylose-binding periplasmic protein; xylose binding protein, conformational changes, SUGA protein; 2.15A {Escherichia coli} PDB: 3m9x_A* 3ma0_A*	Back alignment and structure

>2vk2_A YTFQ, ABC transporter periplasmic-binding protein YTFQ; transport protein, galactofuranose; HET: GZL; 1.20A {Escherichia coli}	Back alignment and structure

>3e61_A Putative transcriptional repressor of ribose OPER; structural genomics, DNA-binding, transcripti regulation, PSI-2; 2.00A {Staphylococcus saprophyticus subsp}	Back alignment and structure

>2hqb_A Transcriptional activator of COMK gene; berkeley structure genomics center target 1957B, structural genomics, PSI; 2.70A {Bacillus halodurans}	Back alignment and structure

>4fe7_A Xylose operon regulatory protein; HTH_ARAC, helix-turn-helix, PBP, periplasmic binding protein binding transcription regulator, DNA xylose; HET: XYS; 2.90A {Escherichia coli} PDB: 4fe4_A	Back alignment and structure

>1gud_A ALBP, D-allose-binding periplasmic protein; periplasmic binding protein, X-RAY crystallography, hinge bending, conformational change; 1.7A {Escherichia coli} SCOP: c.93.1.1 PDB: 1gub_A 1rpj_A*	Back alignment and structure

>2rjo_A Twin-arginine translocation pathway signal protei; PSI-2, NYSGXRC, twin arginine translocation pathway signal P structural genomics; HET: GAL; 2.05A {Burkholderia phytofirmans}	Back alignment and structure

>3bil_A Probable LACI-family transcriptional regulator; structural genomics, unknown function, PSI-2, protein structure initiative; 2.50A {Corynebacterium glutamicum atcc 13032}	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

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

>3d02_A Putative LACI-type transcriptional regulator; periplasmic sugar-binding protein, structura genomics; HET: MSE GOL; 1.30A {Klebsiella pneumoniae subsp}	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

>2qu7_A Putative transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 2.30A {Staphylococcus saprophyticus subsp}	Back alignment and structure

>2fn9_A Ribose ABC transporter, periplasmic ribose-bindin; RBP, ribose binding protein, periplasmic binding protein, thermophilic proteins; 1.40A {Thermotoga maritima} PDB: 2fn8_A*	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

>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

>1jye_A Lactose operon repressor; gene regulation, protein stability, protein DNA-binding, transcription; 1.70A {Escherichia coli} SCOP: c.93.1.1 PDB: 1lbi_A 1lbg_A* 1lbh_A 1jyf_A 3edc_A 1efa_A* 1jwl_A* 2pe5_A* 1tlf_A* 2p9h_A* 2paf_A* 1cjg_A* 1l1m_A 1osl_A 2kei_A* 2kej_A* 2kek_A* 2bjc_A 1lqc_A 1lcc_A* ...	Back alignment and structure

>3brs_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; 2.00A {Clostridium phytofermentans}	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

>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum}	Back alignment and structure

>3miz_A Putative transcriptional regulator protein, LACI family; LACL family, protein structure initiative II (PSI II), NYSGXRC, structural genomics; 1.91A {Rhizobium etli}	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

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}	Back alignment and structure

>1tjy_A Sugar transport protein; protein-ligand complex, signaling protein; HET: PAV; 1.30A {Salmonella typhimurium} SCOP: c.93.1.1 PDB: 1tm2_A 3t95_A* 3ejw_A*	Back alignment and structure

>1jx6_A LUXP protein; protein-ligand complex, signaling protein; HET: AI2; 1.50A {Vibrio harveyi} SCOP: c.93.1.1 PDB: 1zhh_A* 2hj9_A*	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

>3td9_A Branched chain amino acid ABC transporter, peripl amino acid-binding protein; leucine binding, structural genomics; HET: MSE PHE; 1.90A {Thermotoga maritima}	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

>4eyg_A Twin-arginine translocation pathway signal; PSI-biology, MCSG, midwest center for structural genomics, transporter; HET: VNL; 1.86A {Rhodopseudomonas palustris} PDB: 4ey3_A* 3t0n_A* 4eyk_A*	Back alignment and structure

>3lkv_A Uncharacterized conserved domain protein; ATPase binding cassette, PSI, MCSG, structural genomics, Pro structure initiative; HET: PHE; 2.20A {Vibrio cholerae}	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

>2fqx_A Membrane lipoprotein TMPC; ABC transport system, ligand-binding protein, guanosine, TP0319, transport protein; HET: GMP; 1.70A {Treponema pallidum} PDB: 2fqw_A* 2fqy_A*	Back alignment and structure

>4evq_A Putative ABC transporter subunit, substrate-bindi component; structural genomics, PSI-biology, midwest center for structu genomics; HET: MSE PHB; 1.40A {Rhodopseudomonas palustris} PDB: 4evr_A	Back alignment and structure

>2q62_A ARSH; alpha/beta, flavoprotein; 1.80A {Sinorhizobium meliloti}	Back alignment and structure

>4imr_A 3-oxoacyl-(acyl-carrier-protein) reductase; oxidoreductase, nicotinamide adenine dinucleotide phosphate, structural genomics; HET: NAP; 1.96A {Agrobacterium fabrum}	Back alignment and structure

>2fzv_A Putative arsenical resistance protein; flavin binding protein, structural genomics, PSI, protein ST initiative; 1.70A {Shigella flexneri 2A} SCOP: c.23.5.4	Back alignment and structure

>1mio_B Nitrogenase molybdenum iron protein (beta chain); HET: HCA CFM CLP; 3.00A {Clostridium pasteurianum} SCOP: c.92.2.3	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

>2vzf_A NADH-dependent FMN reductase; oxidoreductase; 2.50A {Edta-degrading bacterium BNC1} PDB: 2vzh_A* 2vzj_A*	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		263
d1wd7a_		254	c.113.1.1 (A:) Probable uroporphyrinogen-III synth	1e-16

>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 = 74.8 bits (183), Expect = 1e-16
 Identities = 34/224 (15%), Positives = 56/224 (25%), Gaps = 26/224 (11%)

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--ASPSAVRSSWVNLISDTEQWSNS------VACI 261
            L   V A+   +   V         D +    +         +
Sbjct: 172 LLRGEVDALAFVAAIQVE-FLFEGAKDPKALREALNTRVKALAV 214

PyMOL of d1wd7a_

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		263
d1jr2a_		260	Uroporphyrinogen III synthase (U3S, HemD) {Human (	100.0
d1wd7a_		254	Probable uroporphyrinogen-III synthase {Thermus th	100.0
d1jr2a_		260	Uroporphyrinogen III synthase (U3S, HemD) {Human (	99.59
d1wd7a_		254	Probable uroporphyrinogen-III synthase {Thermus th	99.58
d1ccwa_		137	Glutamate mutase, small subunit {Clostridium cochl	95.43
d1jyea_		271	Lac-repressor (lacR) core (C-terminal domain) {Esc	94.9
d7reqa2		168	Methylmalonyl-CoA mutase alpha subunit, C-terminal	94.27
d1jx6a_		338	Quorum-sensing signal (autoinducer-2) binding prot	93.7
d2nzug1		275	Glucose-resistance amylase regulator CcpA, C-termi	92.28
d1lssa_		132	Ktn Mja218 {Archaeon Methanococcus jannaschii [Tax	90.94
d1sbya1		254	Drosophila alcohol dehydrogenase {Fly (Drosophila	89.91
d1vmea1		148	ROO-like flavoprotein TM0755, C-terminal domain {T	89.4
d2dria_		271	D-ribose-binding protein {Escherichia coli, strain	88.93
d1vmea1		148	ROO-like flavoprotein TM0755, C-terminal domain {T	88.64
d1byka_		255	Trehalose repressor, C-terminal domain {Escherichi	88.54
d2qwxa1		230	Quinone reductase type 2 (menadione reductase) {Hu	87.87
d1dbqa_		282	Purine repressor (PurR), C-terminal domain {Escher	87.5
d1id1a_		153	Rck domain from putative potassium channel Kch {Es	85.37
d2hmva1		134	Ktn bsu222 {Bacillus subtilis [TaxId: 1423]}	84.13
d1sc6a2		132	Phosphoglycerate dehydrogenase {Escherichia coli [	83.95
d1f4pa_		147	Flavodoxin {Desulfovibrio vulgaris [TaxId: 881]}	83.62
d1pr9a_		244	Carbonyl reductase {Human (Homo sapiens) [TaxId: 9	83.46
d1guda_		288	D-allose-binding protein {Escherichia coli [TaxId:	83.39
d1xg5a_		257	Putative dehydrogenase ARPG836 (MGC4172) {Human (H	82.42
d1zesa1		121	PhoB receiver domain {Escherichia coli [TaxId: 562	81.87

>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=3.9e-35  Score=254.46  Aligned_cols=204  Identities=16%  Similarity=0.185  Sum_probs=175.3

Q ss_pred             CeEEEeCCCCCh---HHHHHHHHhCCCcEEEeceEEeeeCCCchHHHHHHhcCCCccEEEEeCHHHHHHHHHHHHHcCC-
Q 024727           51 PKVVVTRERGKN---GKLIKALAKHRIDCLELPLIQHAQGPDTDRLSSVLNADTIFDWIIITSPEAGSVFLEAWKEAGT-  126 (263)
Q Consensus        51 ~~ILitr~~~~~---~~l~~~L~~~G~~v~~~p~~~~~~~~~~~~l~~~l~~l~~~d~IiFTS~~aV~~~~~~l~~~~~-  126 (263)
                      +.||+|||.++.   +.+.+.|+++|++++.+|++++++.+ .+.+...+.++.+||||||||++||++|++.+.+.+. 
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            568999997543   68999999999999999999999864 4566777777889999999999999999999887653 


Q ss_pred             -----------CCcEEEEeChhHHHHHHHhhhhcCCCCceeecCCCCCHHHHHHHhccCCCCCcEEEEEcCCCCchhHHH
Q 024727          127 -----------PNVRIGVVGAGTASIFEEVIQSSKCSLDVAFSPSKATGKILASELPKNGKKKCTVLYPASAKASNEIEE  195 (263)
Q Consensus       127 -----------~~~~i~aVG~~Ta~~L~~~~~~~~~G~~~~~~p~~~t~e~L~~~l~~~~~~~~~vL~~~g~~~~~~L~~  195 (263)
                                 ++++++|||++|+++|+++      |+.+++.+ .+++++|++.+......++++++++|+.++++|.+
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      99987654 68999999998877767899999999999999999


Q ss_pred             HHHhCCCeeeEEeeeccccCCCChHHHHHHh---CCCCEEEEeCHHHHHHHHHHhccccC---CCCceEEEECC
Q 024727          196 GLSNRGFEVVRLNTYTTEPVHHVDQTVLKQA---LSIPVVAVASPSAVRSSWVNLISDTE---QWSNSVACIAG  263 (263)
Q Consensus       196 ~L~~~G~~v~~~~vY~~~~~~~~~~~~~~~l---~~~d~vvFtS~s~v~~~~~~~~~~~~---~~~~~i~~IGp  263 (263)
                      .|++.|++|.++.+|++.+.....+.+.+.+   ..+|+|+|||+++++ .|++++++..   +.+++++||||
T Consensus       154 ~L~~~g~~v~~~~~Y~~~~~~~~~~~~~~~l~~~~~~d~i~f~S~s~v~-~~~~~~~~~~~~~~~~~~i~~IG~  226 (260)
T d1jr2a_         154 ALKDKGIAMESITVYQTVAHPGIQGNLNSYYSQQGVPASITFFSPSGLT-YSLKHIQELSGDNIDQIKFAAIGP  226 (260)
T ss_dssp             HHHTTTCCEEEEECEEEEECTTHHHHHHHHHHHHCSCSEEEESSHHHHH-HHHHHHHHHHGGGGGGSEEEESSH
T ss_pred             HHHhcCCcceEEEeeeeeccccchHHHHHHHHhccCceEEeecCHHHHH-HHHHHHHHhhhccccCcEEEEECH
Confidence            9999999999999999998877655444433   478999999999999 9999886532   45789999996

PyMOL of d1jr2a_

>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

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

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

>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

>d1jx6a_ c.93.1.1 (A:) Quorum-sensing signal (autoinducer-2) binding protein LuxP {Vibrio harveyi [TaxId: 669]}	Back information, alignment and structure

>d2nzug1 c.93.1.1 (G:58-332) Glucose-resistance amylase regulator CcpA, C-terminal domain {Bacillus megaterium [TaxId: 1404]}	Back information, alignment and structure

>d1lssa_ c.2.1.9 (A:) Ktn Mja218 {Archaeon Methanococcus jannaschii [TaxId: 2190]}	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

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

>d2dria_ c.93.1.1 (A:) D-ribose-binding protein {Escherichia coli, strain k-12 [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

>d1byka_ c.93.1.1 (A:) Trehalose repressor, C-terminal domain {Escherichia coli [TaxId: 562]}	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

>d1dbqa_ c.93.1.1 (A:) Purine repressor (PurR), C-terminal domain {Escherichia coli [TaxId: 562]}	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

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

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

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

>d1guda_ c.93.1.1 (A:) D-allose-binding protein {Escherichia coli [TaxId: 562]}	Back information, alignment and structure

>d1xg5a_ c.2.1.2 (A:) Putative dehydrogenase ARPG836 (MGC4172) {Human (Homo sapiens) [TaxId: 9606]}	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