254780812

254780812

uroporphyrinogen decarboxylase

GeneID in NCBI database:8209818Locus tag:CLIBASIA_03515
Protein GI in NCBI database:254780812Protein Accession:YP_003065225.1
Gene range:+(442927, 443967)Protein Length:346aa
Gene description:uroporphyrinogen decarboxylase
COG prediction:[H] Uroporphyrinogen-III decarboxylase
KEGG prediction:hemE; uroporphyrinogen decarboxylase (EC:4.1.1.37); K01599 uroporphyrinogen decarboxylase [EC:4.1.1.37]
SEED prediction:Uroporphyrinogen III decarboxylase (EC 4.1.1.37)
Pathway involved in KEGG:Porphyrin and chlorophyll metabolism [PATH:las00860]
Subsystem involved in SEED:Heme and Siroheme Biosynthesis;
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMM2 TM-Helix
TOPPRED2 TM-Helix
HMMTOP2 TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------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-------270-------280-------290-------300-------310-------320-------330-------340------
MNERKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRSEKI
ccccHHHHHHHHcccccccccEEEEcccccccHHHHHHHHHcccHHHHcccHHHEEEEEccHHHHccccEEEEEEcEEHHHHHcccEEEEEcccccEEcccccHHHHHHccccccccHHHHHHHHHHHHHHHHHcccccEEEEcccHHHHHHHHHccccccHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEcccHHHHHHHHHcccccEEEEcccccHHHHHHHccccEEEccccccHHcccHHHHHHHHHHHHHHHccccEEEEEcccccccccHHHHHHHHHHHHHccc
ccccccHHHHHHHccccccccEcccccccccccHHHHHHHcccccccccccHHHHHHHHHHHHHHHcccEEEcccccccHHHHccccEEEEcccEEcccccccHHHHHHcccccccHHHHcHHHHHHHHHHHHHcccccEEEEEEcHHHHHHHHHHcccccccHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEccHHHccHHHHHHHcHHHHHHHHHHHHHHHHHccEEEEcccccccHHHHHHHHcccEEEcccEEcHHHHHHHccEEEEEEEEcHHHHHccHHHHHHHHHHHHHHHccccEEEEEcccccccccHHHHHHHHHHHHHccc
MNERKQKILEVLqgnvinpppiwlmrqagrylpEYRQIRKKFKNFLdmcytpeytveltlqpirrynfdaaILFSDILVIADALGrnvrfvenegprmdpittqeIYLLNPNIDLFLNYLLPIFQSISILRKKLpnhitligfcgapWTVASYMISggfikdhgqnRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDthagclgehefeNYAARSVGRIISAVRrkypnakfisfAKGAGYMLKNYrrltdsnaigldwsvPLSFALELqkegpvqgnldpmrlvVGNQVMIDGVNAILDvlgsgpfifnlghgitpqvdpknVLDLVKTVRSEKI
MNERKQKILEVlqgnvinpppiwLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADALGRNVRFvenegprmdpITTQEIYLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGSGPFIFNLGhgitpqvdpknvLDLVKTVRSEKI
MNERKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRSEKI
***RKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRSE**
MNERKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRSEKI
**ERKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRSE**
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MNERKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRSEKI
MNERKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRSEKI
MNERKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRSEKI

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target346 uroporphyrinogen decarboxylase [Candidatus Liberibacter
315122035346 uroporphyrinogen decarboxylase [Candidatus Liberibacter 1 1e-169
227823859344 uroporphyrinogen decarboxylase [Sinorhizobium fredii NG 1 1e-126
307316113343 uroporphyrinogen decarboxylase [Sinorhizobium meliloti 1 1e-122
307302556343 uroporphyrinogen decarboxylase [Sinorhizobium meliloti 1 1e-121
116254466343 uroporphyrinogen decarboxylase [Rhizobium leguminosarum 1 1e-121
15890080344 uroporphyrinogen decarboxylase [Agrobacterium tumefacie 1 1e-121
222150249346 uroporphyrinogen decarboxylase [Agrobacterium vitis S4] 1 1e-121
150398400343 uroporphyrinogen decarboxylase [Sinorhizobium medicae W 1 1e-120
209551505340 uroporphyrinogen decarboxylase [Rhizobium leguminosarum 1 1e-120
218516998338 uroporphyrinogen decarboxylase [Rhizobium etli 8C-3] Le 1 1e-119
>gi|315122035|ref|YP_004062524.1| uroporphyrinogen decarboxylase [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 346 Back     alignment and organism information
 Score =  599 bits (1545), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 287/345 (83%), Positives = 314/345 (91%)

Query: 1   MNERKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTL 60
           MN++KQKIL+VL+GN+I PPPIWLMRQAGRYLPEYR+IRKK KNFL+MCYTPEY VE+T+
Sbjct: 1   MNKQKQKILQVLKGNIITPPPIWLMRQAGRYLPEYREIRKKNKNFLNMCYTPEYVVEITM 60

Query: 61  QPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYL 120
           QPI RY FDAAILFSDILVI DALGRNVRF+ENEGP+MDPIT +EIY LNPNID  LNYL
Sbjct: 61  QPIHRYKFDAAILFSDILVIPDALGRNVRFIENEGPKMDPITVKEIYGLNPNIDFILNYL 120

Query: 121 LPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWL 180
             IF+SISILRKKLPN+ITLIGFCGAPWTVASYMISG   KDH + R+FAYQN+ AFNWL
Sbjct: 121 SSIFKSISILRKKLPNNITLIGFCGAPWTVASYMISGCPTKDHTETRIFAYQNNHAFNWL 180

Query: 181 LDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNA 240
           LDFLSD+SAEYLIAQI +GVDVIQIFDTHAG LGE EFENYAA+ VGRIISAVR+K PNA
Sbjct: 181 LDFLSDISAEYLIAQIRSGVDVIQIFDTHAGFLGECEFENYAAKPVGRIISAVRKKCPNA 240

Query: 241 KFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALELQKEGPVQGNLDPMRLVVGNQV 300
           + I+FAKGAGYMLKNYR+LTDSNAI LDWSVPLSFA +LQKEGPVQGNLDPMRLVVGN+V
Sbjct: 241 QIITFAKGAGYMLKNYRQLTDSNAISLDWSVPLSFAFDLQKEGPVQGNLDPMRLVVGNKV 300

Query: 301 MIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRSEK 345
           M DGV AILD LGSGP IFNLGHGITPQVDPKNVLDLV+TVRS K
Sbjct: 301 MKDGVKAILDTLGSGPLIFNLGHGITPQVDPKNVLDLVETVRSGK 345


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|227823859|ref|YP_002827832.1| uroporphyrinogen decarboxylase [Sinorhizobium fredii NGR234] Length = 344 Back     alignment and organism information
>gi|307316113|ref|ZP_07595557.1| uroporphyrinogen decarboxylase [Sinorhizobium meliloti AK83] Length = 343 Back     alignment and organism information
>gi|307302556|ref|ZP_07582313.1| uroporphyrinogen decarboxylase [Sinorhizobium meliloti BL225C] Length = 343 Back     alignment and organism information
>gi|116254466|ref|YP_765604.1| uroporphyrinogen decarboxylase [Rhizobium leguminosarum bv. viciae 3841] Length = 343 Back     alignment and organism information
>gi|15890080|ref|NP_355761.1| uroporphyrinogen decarboxylase [Agrobacterium tumefaciens str. C58] Length = 344 Back     alignment and organism information
>gi|222150249|ref|YP_002551206.1| uroporphyrinogen decarboxylase [Agrobacterium vitis S4] Length = 346 Back     alignment and organism information
>gi|150398400|ref|YP_001328867.1| uroporphyrinogen decarboxylase [Sinorhizobium medicae WSM419] Length = 343 Back     alignment and organism information
>gi|209551505|ref|YP_002283422.1| uroporphyrinogen decarboxylase [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 340 Back     alignment and organism information
>gi|218516998|ref|ZP_03513838.1| uroporphyrinogen decarboxylase [Rhizobium etli 8C-3] Length = 338 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target346 uroporphyrinogen decarboxylase [Candidatus Liberibacter
PRK00115346 PRK00115, hemE, uroporphyrinogen decarboxylase; Validat 1e-124
TIGR01464338 TIGR01464, hemE, uroporphyrinogen decarboxylase 1e-107
COG0407352 COG0407, HemE, Uroporphyrinogen-III decarboxylase [Coen 1e-94
pfam01208337 pfam01208, URO-D, Uroporphyrinogen decarboxylase (URO-D 3e-90
PLN02433345 PLN02433, PLN02433, uroporphyrinogen decarboxylase 2e-76
KOG2872359 KOG2872, KOG2872, KOG2872, Uroporphyrinogen decarboxyla 2e-72
cd03465330 cd03465, URO-D_like, The URO-D _like protein superfamil 3e-25
cd00465306 cd00465, URO-D_CIMS_like, The URO-D_CIMS_like protein s 1e-21
cd03307326 cd03307, Mta_CmuA_like, MtaA_CmuA_like family 2e-14
PRK06252339 PRK06252, PRK06252, methylcobalamin:coenzyme M methyltr 2e-08
cd00717335 cd00717, URO-D, Uroporphyrinogen decarboxylase (URO-D) 1e-107
TIGR01463340 TIGR01463, mtaA_cmuA, methyltransferase, MtaA/CmuA fami 1e-06
>gnl|CDD|178875 PRK00115, hemE, uroporphyrinogen decarboxylase; Validated Back     alignment and domain information
>gnl|CDD|162374 TIGR01464, hemE, uroporphyrinogen decarboxylase Back     alignment and domain information
>gnl|CDD|30756 COG0407, HemE, Uroporphyrinogen-III decarboxylase [Coenzyme metabolism] Back     alignment and domain information
>gnl|CDD|144708 pfam01208, URO-D, Uroporphyrinogen decarboxylase (URO-D) Back     alignment and domain information
>gnl|CDD|178052 PLN02433, PLN02433, uroporphyrinogen decarboxylase Back     alignment and domain information
>gnl|CDD|38083 KOG2872, KOG2872, KOG2872, Uroporphyrinogen decarboxylase [Coenzyme transport and metabolism] Back     alignment and domain information
>gnl|CDD|48148 cd03465, URO-D_like, The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases Back     alignment and domain information
>gnl|CDD|73209 cd00465, URO-D_CIMS_like, The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases Back     alignment and domain information
>gnl|CDD|48142 cd03307, Mta_CmuA_like, MtaA_CmuA_like family Back     alignment and domain information
>gnl|CDD|180490 PRK06252, PRK06252, methylcobalamin:coenzyme M methyltransferase; Validated Back     alignment and domain information
>gnl|CDD|48141 cd00717, URO-D, Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors Back     alignment and domain information
>gnl|CDD|130530 TIGR01463, mtaA_cmuA, methyltransferase, MtaA/CmuA family Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 346 uroporphyrinogen decarboxylase [Candidatus Liberibacter
TIGR01464351 hemE uroporphyrinogen decarboxylase; InterPro: IPR00636 100.0
PRK00115347 hemE uroporphyrinogen decarboxylase; Validated 100.0
cd00717335 URO-D Uroporphyrinogen decarboxylase (URO-D) is a dimer 100.0
COG0407352 HemE Uroporphyrinogen-III decarboxylase [Coenzyme metab 100.0
KOG2872359 consensus 100.0
pfam01208337 URO-D Uroporphyrinogen decarboxylase (URO-D). 100.0
cd03307326 Mta_CmuA_like MtaA_CmuA_like family. MtaA/CmuA, also Mt 100.0
PRK06252339 methylcobalamin:coenzyme M methyltransferase; Validated 100.0
cd00465306 URO-D_CIMS_like The URO-D_CIMS_like protein superfamily 100.0
cd03465330 URO-D_like The URO-D _like protein superfamily includes 100.0
TIGR01463350 mtaA_cmuA methyltransferase, MtaA/CmuA family; InterPro 100.0
cd03308378 CmuA_CmuC_like CmuA_CmuC_like: uncharacterized protein 100.0
cd03309321 CmuC_like CmuC_like. Proteins similar to the putative c 99.62
PRK00957307 methionine synthase; Provisional 98.63
cd03311332 CIMS_C_terminal_like CIMS - Cobalamine-independent meth 98.55
cd03310321 CIMS_like CIMS - Cobalamine-independent methonine synth 98.51
PRK09121339 5-methyltetrahydropteroyltriglutamate--homocysteine met 98.5
PRK04326330 methionine synthase; Provisional 98.48
pfam01717324 Meth_synt_2 Cobalamin-independent synthase, Catalytic d 98.47
PRK06520370 5-methyltetrahydropteroyltriglutamate--homocysteine met 98.17
PRK01207343 methionine synthase; Provisional 98.02
COG0620330 MetE Methionine synthase II (cobalamin-independent) [Am 97.81
PRK08575320 5-methyltetrahydropteroyltriglutamate--homocysteine met 97.38
cd03312360 CIMS_N_terminal_like CIMS - Cobalamine-independent meth 96.22
TIGR01371778 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--h 95.59
PRK05222756 5-methyltetrahydropteroyltriglutamate--homocysteine S-m 93.22
PRK06233372 hypothetical protein; Provisional 98.0
KOG2263765 consensus 91.98
PRK08645 608 bifunctional homocysteine S-methyltransferase/5,10-meth 91.76
TIGR00693210 thiE thiamine-phosphate pyrophosphorylase; InterPro: IP 90.86
PRK05222 756 5-methyltetrahydropteroyltriglutamate--homocysteine S-m 96.46
TIGR01371 778 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--h 96.19
PRK13123256 consensus 91.82
TIGR01235 1169 pyruv_carbox pyruvate carboxylase; InterPro: IPR005930 96.2
PRK13116278 consensus 95.72
PRK13117268 consensus 94.7
PRK13114266 consensus 93.3
PRK13119261 consensus 92.95
PRK13121265 consensus 90.24
TIGR02090371 LEU1_arch isopropylmalate/citramalate/homocitrate synth 95.66
PRK12330 499 oxaloacetate decarboxylase; Provisional 94.75
COG5016 472 Pyruvate/oxaloacetate carboxyltransferase [Energy produ 94.34
PRK12331 463 oxaloacetate decarboxylase; Provisional 94.22
PRK12581 468 oxaloacetate decarboxylase; Provisional 93.94
TIGR01854241 lipid_A_lpxH UDP-2,3-diacylglucosamine hydrolase; Inter 93.89
PRK07535268 methyltetrahydrofolate:corrinoid/iron-sulfur protein me 93.78
PRK03170292 dihydrodipicolinate synthase; Provisional 93.55
TIGR00078276 nadC nicotinate-nucleotide pyrophosphorylase; InterPro: 92.88
PRK09282 580 pyruvate carboxylase subunit B; Validated 92.78
PRK08195337 4-hydroxy-2-ketovalerate aldolase; Validated 92.22
TIGR03217333 4OH_2_O_val_ald 4-hydroxy-2-oxovalerate aldolase. Membe 91.44
PRK05692287 hydroxymethylglutaryl-CoA lyase; Provisional 91.14
TIGR01108 616 oadA oxaloacetate decarboxylase alpha subunit; InterPro 95.51
COG0159265 TrpA Tryptophan synthase alpha chain [Amino acid transp 95.13
PRK13138264 consensus 94.53
pfam00290258 Trp_syntA Tryptophan synthase alpha chain. 93.28
PRK13131257 consensus 92.12
COG0796269 MurI Glutamate racemase [Cell envelope biogenesis, oute 90.81
pfam08267310 Meth_synt_1 Cobalamin-independent synthase, N-terminal 93.55
PRK12999 1147 pyruvate carboxylase; Reviewed 92.27
PRK13133267 consensus 91.73
PRK08318413 dihydropyrimidine dehydrogenase; Validated 91.03
>TIGR01464 hemE uroporphyrinogen decarboxylase; InterPro: IPR006361 This entry represents uroporphyrinogen decarboxylase (HemE), which catalyzes the fifth step in the heme biosynthetic pathway, converting uroporphyrinogen III to coproporphyrinogen III by decarboxylating the four acetate side chains of the substrate Back     alignment and domain information
>PRK00115 hemE uroporphyrinogen decarboxylase; Validated Back     alignment and domain information
>cd00717 URO-D Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors Back     alignment and domain information
>COG0407 HemE Uroporphyrinogen-III decarboxylase [Coenzyme metabolism] Back     alignment and domain information
>KOG2872 consensus Back     alignment and domain information
>pfam01208 URO-D Uroporphyrinogen decarboxylase (URO-D) Back     alignment and domain information
>cd03307 Mta_CmuA_like MtaA_CmuA_like family Back     alignment and domain information
>PRK06252 methylcobalamin:coenzyme M methyltransferase; Validated Back     alignment and domain information
>cd00465 URO-D_CIMS_like The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases Back     alignment and domain information
>cd03465 URO-D_like The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases Back     alignment and domain information
>TIGR01463 mtaA_cmuA methyltransferase, MtaA/CmuA family; InterPro: IPR006360 This entry represents a methyltransferase domain found in proteins which are involved in C1 metabolism in methanogenic archaea and methylotrophic bacteria Back     alignment and domain information
>cd03308 CmuA_CmuC_like CmuA_CmuC_like: uncharacterized protein family similar to uroporphyrinogen decarboxylase (URO-D) and the methyltransferases CmuA and CmuC Back     alignment and domain information
>cd03309 CmuC_like CmuC_like Back     alignment and domain information
>PRK00957 methionine synthase; Provisional Back     alignment and domain information
>cd03311 CIMS_C_terminal_like CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like Back     alignment and domain information
>cd03310 CIMS_like CIMS - Cobalamine-independent methonine synthase, or MetE Back     alignment and domain information
>PRK09121 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional Back     alignment and domain information
>PRK04326 methionine synthase; Provisional Back     alignment and domain information
>pfam01717 Meth_synt_2 Cobalamin-independent synthase, Catalytic domain Back     alignment and domain information
>PRK06520 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional Back     alignment and domain information
>PRK01207 methionine synthase; Provisional Back     alignment and domain information
>COG0620 MetE Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism] Back     alignment and domain information
>PRK08575 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional Back     alignment and domain information
>cd03312 CIMS_N_terminal_like CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like Back     alignment and domain information
>TIGR01371 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; InterPro: IPR006276 This group represents cobalamin-independent methionine synthase Back     alignment and domain information
>PRK05222 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional Back     alignment and domain information
>PRK06233 hypothetical protein; Provisional Back     alignment and domain information
>KOG2263 consensus Back     alignment and domain information
>PRK08645 bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein; Reviewed Back     alignment and domain information
>TIGR00693 thiE thiamine-phosphate pyrophosphorylase; InterPro: IPR003733 Thiamine monophosphate synthase (TMP) (2 Back     alignment and domain information
>PRK05222 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional Back     alignment and domain information
>TIGR01371 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; InterPro: IPR006276 This group represents cobalamin-independent methionine synthase Back     alignment and domain information
>PRK13123 consensus Back     alignment and domain information
>TIGR01235 pyruv_carbox pyruvate carboxylase; InterPro: IPR005930 In the postabsorptive state, blood glucose concentration is kept constant by a combination of glycogenolysis and gluconeogenesis Back     alignment and domain information
>PRK13116 consensus Back     alignment and domain information
>PRK13117 consensus Back     alignment and domain information
>PRK13114 consensus Back     alignment and domain information
>PRK13119 consensus Back     alignment and domain information
>PRK13121 consensus Back     alignment and domain information
>TIGR02090 LEU1_arch isopropylmalate/citramalate/homocitrate synthases; InterPro: IPR011830 Methanogenic archaea contain three closely related homologs of the 2-isopropylmalate synthases (LeuA) represented by IPR005671 from INTERPRO Back     alignment and domain information
>PRK12330 oxaloacetate decarboxylase; Provisional Back     alignment and domain information
>COG5016 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion] Back     alignment and domain information
>PRK12331 oxaloacetate decarboxylase; Provisional Back     alignment and domain information
>PRK12581 oxaloacetate decarboxylase; Provisional Back     alignment and domain information
>TIGR01854 lipid_A_lpxH UDP-2,3-diacylglucosamine hydrolase; InterPro: IPR010138 This entry represents LpxH, or UDP-2,3-diacylglucosamine hydrolase (or pyrophosphatase), which is an essential enzyme in Escherichia coli that catalyses the fourth step in lipid A biosynthesis Back     alignment and domain information
>PRK07535 methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase; Validated Back     alignment and domain information
>PRK03170 dihydrodipicolinate synthase; Provisional Back     alignment and domain information
>TIGR00078 nadC nicotinate-nucleotide pyrophosphorylase; InterPro: IPR004393 Nicotinate-nucleotide pyrophosphorylase (2 Back     alignment and domain information
>PRK09282 pyruvate carboxylase subunit B; Validated Back     alignment and domain information
>PRK08195 4-hydroxy-2-ketovalerate aldolase; Validated Back     alignment and domain information
>TIGR03217 4OH_2_O_val_ald 4-hydroxy-2-oxovalerate aldolase Back     alignment and domain information
>PRK05692 hydroxymethylglutaryl-CoA lyase; Provisional Back     alignment and domain information
>TIGR01108 oadA oxaloacetate decarboxylase alpha subunit; InterPro: IPR005776 This family describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea Back     alignment and domain information
>COG0159 TrpA Tryptophan synthase alpha chain [Amino acid transport and metabolism] Back     alignment and domain information
>PRK13138 consensus Back     alignment and domain information
>pfam00290 Trp_syntA Tryptophan synthase alpha chain Back     alignment and domain information
>PRK13131 consensus Back     alignment and domain information
>COG0796 MurI Glutamate racemase [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>pfam08267 Meth_synt_1 Cobalamin-independent synthase, N-terminal domain Back     alignment and domain information
>PRK12999 pyruvate carboxylase; Reviewed Back     alignment and domain information
>PRK13133 consensus Back     alignment and domain information
>PRK08318 dihydropyrimidine dehydrogenase; Validated Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target346 uroporphyrinogen decarboxylase [Candidatus Liberibacter
3cyv_A354 Crystal Structure Of Uroporphyrinogen Decarboxylase 1e-85
3gw0_A367 Urod Mutant G318r Length = 367 4e-82
2q71_A356 Uroporphyrinogen Decarboxylase G168r Single Mutant 3e-81
1r3r_A367 Uroporphyrinogen Decarboxylase With Mutation D86n L 3e-81
1uro_A367 Uroporphyrinogen Decarboxylase Length = 367 3e-81
1jph_A388 Ile260thr Mutant Of Human Urod, Human Uroporphyrino 3e-81
1r3w_A367 Uroporphyrinogen Decarboxylase Y164f Mutant In Comp 4e-81
3gw3_A367 Human Urod Mutant K297n Length = 367 4e-81
1jpi_A388 Phe232leu Mutant Of Human Urod, Human Uroporphyrino 4e-81
3gvv_A367 Single-Chain Urod Y164g (Gy) Mutation Length = 367 5e-81
1r3v_A367 Uroporphyrinogen Decarboxylase Single Mutant D86e I 7e-81
1r3s_A367 Uroporphyrinogen Decarboxylase Single Mutant D86g I 9e-81
1jpk_A388 Gly156asp Mutant Of Human Urod, Human Uroporphyrino 2e-80
2inf_A359 Crystal Structure Of Uroporphyrinogen Decarboxylase 7e-72
1j93_A353 Crystal Structure And Substrate Binding Modeling Of 1e-70
2eja_A338 Crystal Structure Of Uroporphyrinogen Decarboxylase 4e-70
gi|228311952|pdb|3CYV|A Chain A, Crystal Structure Of Uroporphyrinogen Decarboxylase From Shigella Flexineri: New Insights Into Its Catalytic Mechanism Length = 354 Back     alignment and structure
 Score =  321 bits (822), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 117/346 (33%), Positives = 178/346 (51%), Gaps = 4/346 (1%)

Query: 1   MNE-RKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELT 59
           M E +  + L  L    ++  P+W+MRQAGRYLPEY+  R +  +F+ +C   E   E+T
Sbjct: 1   MTELKNDRYLRALLRQPVDVTPVWMMRQAGRYLPEYKATRAQAGDFMSLCKNAELACEVT 60

Query: 60  LQPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNY 119
           LQP+RRY  DAAILFSDIL + DA+G  + F   EGPR     T +  +    I    + 
Sbjct: 61  LQPLRRYPLDAAILFSDILTVPDAMGLGLYFEAGEGPRFTSPVTCKADVDKLPIPDPEDE 120

Query: 120 LLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNW 179
           L  +  ++  +R +L   + LIGF G+PWT+A+YM+ GG  K     +   Y + +A + 
Sbjct: 121 LGYVMNAVRTIRHELKGEVPLIGFSGSPWTLATYMVEGGSSKAFTVIKKMMYADPQALHA 180

Query: 180 LLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPN 239
           LLD L+     YL AQI AG   + IFDT  G L   +++ ++   + +I+  + R+   
Sbjct: 181 LLDKLAKSVTLYLNAQIKAGAQAVMIFDTWGGVLTGRDYQQFSLYYMHKIVDGLLRENDG 240

Query: 240 AKFISF-AKGAGYMLKNYRRLTDSNAIGLDWSVPLSFA-LELQKEGPVQGNLDPMRLVVG 297
            +         G         T  +A+GLDW+  ++ A   +  +  +QGN+DP  L   
Sbjct: 241 RRVPVTLFTKGGGQWLEAMAETGCDALGLDWTTDIADARRRVGNKVALQGNMDPSMLYAP 300

Query: 298 NQVMIDGVNAILDVLGSG-PFIFNLGHGITPQVDPKNVLDLVKTVR 342
              + + V  IL   G G   +FNLGHGI   V P++    V+ V 
Sbjct: 301 PARIEEEVATILAGFGHGEGHVFNLGHGIHQDVPPEHAGVFVEAVH 346


>gi|251836950|pdb|3GW0|A Chain A, Urod Mutant G318r Length = 367 Back     alignment and structure
>gi|150261558|pdb|2Q71|A Chain A, Uroporphyrinogen Decarboxylase G168r Single Mutant Enzyme In Complex With Coproporphyrinogen-Iii Length = 356 Back     alignment and structure
>gi|40889567|pdb|1R3R|A Chain A, Uroporphyrinogen Decarboxylase With Mutation D86n Length = 367 Back     alignment and structure
gi|3660278|pdb|1URO|A Chain A, Uroporphyrinogen Decarboxylase Length = 367 Back     alignment and structure
>gi|18158958|pdb|1JPH|A Chain A, Ile260thr Mutant Of Human Urod, Human Uroporphyrinogen Iii Decarboxylase Length = 388 Back     alignment and structure
>gi|40889571|pdb|1R3W|A Chain A, Uroporphyrinogen Decarboxylase Y164f Mutant In Complex With Coproporphyrinogen-Iii Length = 367 Back     alignment and structure
>gi|251836951|pdb|3GW3|A Chain A, Human Urod Mutant K297n Length = 367 Back     alignment and structure
>gi|18158959|pdb|1JPI|A Chain A, Phe232leu Mutant Of Human Urod, Human Uroporphyrinogen Iii Decarboxylase Length = 388 Back     alignment and structure
>gi|251836949|pdb|3GVV|A Chain A, Single-Chain Urod Y164g (Gy) Mutation Length = 367 Back     alignment and structure
>gi|40889570|pdb|1R3V|A Chain A, Uroporphyrinogen Decarboxylase Single Mutant D86e In Complex With Coproporphyrinogen-I Length = 367 Back     alignment and structure
>gi|40889568|pdb|1R3S|A Chain A, Uroporphyrinogen Decarboxylase Single Mutant D86g In Complex With Coproporphyrinogen-I Length = 367 Back     alignment and structure
>gi|18158960|pdb|1JPK|A Chain A, Gly156asp Mutant Of Human Urod, Human Uroporphyrinogen Iii Decarboxylase Length = 388 Back     alignment and structure
>gi|118138487|pdb|2INF|A Chain A, Crystal Structure Of Uroporphyrinogen Decarboxylase From Bacillus Subtilis Length = 359 Back     alignment and structure
>gi|16975230|pdb|1J93|A Chain A, Crystal Structure And Substrate Binding Modeling Of The Uroporphyrinogen-Iii Decarboxylase From Nicotiana Tabacum: Implications For The Catalytic Mechanism Length = 353 Back     alignment and structure
gi|170292161|pdb|2EJA|A Chain A, Crystal Structure Of Uroporphyrinogen Decarboxylase From Aquifex Aeolicus Length = 338 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target346 uroporphyrinogen decarboxylase [Candidatus Liberibacter
1j93_A353 UROD, uroporphyrinogen decarboxylase; beta barrel, plas 9e-82
1r3s_A367 URO-D, uroporphyrinogen decarboxylase, UPD; uroporphyri 7e-78
2inf_A359 URO-D, UPD, uroporphyrinogen decarboxylase; (alpha-beta 1e-63
2eja_A338 URO-D, UPD, uroporphyrinogen decarboxylase; dimer, X-RA 2e-62
3cyv_A354 URO-D, UPD, uroporphyrinogen decarboxylase; alpha/beta 8e-62
>1j93_A UROD, uroporphyrinogen decarboxylase; beta barrel, plastidial enzyme, crystallographic dimer, lyase; 2.30A {Nicotiana tabacum} SCOP: c.1.22.1 Length = 353 Back     alignment and structure
 Score =  299 bits (765), Expect = 9e-82
 Identities = 97/339 (28%), Positives = 174/339 (51%), Gaps = 2/339 (0%)

Query: 8   ILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYN 67
           +L+ ++G  +  PP+WLMRQAGRY+  Y+ + +K+  F D     +  VE++LQP + + 
Sbjct: 15  LLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPWKVFR 74

Query: 68  FDAAILFSDILVIADALGRNVRFVENEGPRMDPITTQEIYLLNPNIDLFLNYLLPIFQSI 127
            D  ILFSDIL     +      ++ +GP +         +      +    +  + +++
Sbjct: 75  PDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEAL 134

Query: 128 SILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDFLSDV 187
           +ILRK++ N   ++GF GAP+T+ASY++ GG  K+  + +  A+   +  + LL   +  
Sbjct: 135 TILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATS 194

Query: 188 SAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAKFISFAK 247
            A+Y+  Q  +G   +QIFD+ A  L   +FE ++   + +I+ +V+  +PN   I +A 
Sbjct: 195 MAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYAS 254

Query: 248 GAGYMLKNYRRLTDSNAIGLDWSVPLSFALE-LQKEGPVQGNLDPMRLVVGNQVMIDGVN 306
           G+G +L     LT  + + LDW+V ++     L     +QGN+DP  L    + + + +N
Sbjct: 255 GSGGLL-ERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRIN 313

Query: 307 AILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRSEK 345
             +   G G  I NLGHGI      +N     +  +  +
Sbjct: 314 DTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGLR 352


>1r3s_A URO-D, uroporphyrinogen decarboxylase, UPD; uroporphyrinogen decarboxylase coproporphyrinogen, X-RAY crystallography, lyase; HET: 1CP; 1.65A {Homo sapiens} SCOP: c.1.22.1 PDB: 1r3t_A* 1r3r_A 1r3q_A* 1r3y_A* 1uro_A 3gvq_A 3gvr_A 1r3v_A* 3gvv_A 1jph_A 1r3w_A* 3gw3_A 1jpi_A 1jpk_A 3gw0_A 2q71_A* 2q6z_A* Length = 367 Back     alignment and structure
>2inf_A URO-D, UPD, uroporphyrinogen decarboxylase; (alpha-beta)8 barrel, eight parallel beta strands surrounded by eight alpha helices, lyase; 2.30A {Bacillus subtilis} Length = 359 Back     alignment and structure
>2eja_A URO-D, UPD, uroporphyrinogen decarboxylase; dimer, X-RAY diffraction, structural genomics, NPPSFA; 1.90A {Aquifex aeolicus} Length = 338 Back     alignment and structure
>3cyv_A URO-D, UPD, uroporphyrinogen decarboxylase; alpha/beta barrel, cytoplasm, lyase, porphyrin biosynthesis; 2.80A {Shigella flexneri} Length = 354 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target346 uroporphyrinogen decarboxylase [Candidatus Liberibacter
1r3s_A367 URO-D, uroporphyrinogen decarboxylase, UPD; uroporphyri 100.0
2inf_A359 URO-D, UPD, uroporphyrinogen decarboxylase; (alpha-beta 100.0
1j93_A353 UROD, uroporphyrinogen decarboxylase; beta barrel, plas 100.0
3cyv_A354 URO-D, UPD, uroporphyrinogen decarboxylase; alpha/beta 100.0
2eja_A338 URO-D, UPD, uroporphyrinogen decarboxylase; dimer, X-RA 100.0
1t7l_A766 5-methyltetrahydropteroyltriglutamate-- homocysteine me 98.41
2nq5_A755 5-methyltetrahydropteroyltriglutamate-- homocysteine me 98.31
1u1j_A765 5-methyltetrahydropteroyltriglutamate-- homocysteine me 98.23
1ypx_A375 Putative vitamin-B12 independent methionine synthase fa 98.19
1u1j_A 765 5-methyltetrahydropteroyltriglutamate-- homocysteine me 97.83
2nq5_A 755 5-methyltetrahydropteroyltriglutamate-- homocysteine me 97.38
3bg3_A 718 Pyruvate carboxylase, mitochondrial; TIM barrel, ATP-bi 95.28
3ble_A337 Citramalate synthase from leptospira interrogans; TIM b 93.66
2cw6_A298 Hydroxymethylglutaryl-COA lyase, mitochondrial; HMG-COA 93.48
2ftp_A302 Hydroxymethylglutaryl-COA lyase; structural genomics, P 93.02
1rqb_A 539 Transcarboxylase 5S subunit; TIM-barrel, carbamylated l 92.18
2wkj_A303 N-acetylneuraminate lyase; directed evolution, sialic a 92.02
2nx9_A 464 Oxaloacetate decarboxylase 2, subunit alpha; carboxyltr 91.79
1o4u_A285 Type II quinolic acid phosphoribosyltransferase; TM1645 91.31
3e96_A316 Dihydrodipicolinate synthase; structural genomics, nysg 91.12
1ydo_A307 HMG-COA lyase; TIM-barrel protein, structural genomics, 91.07
2tps_A227 Protein (thiamin phosphate synthase); thiamin biosynthe 90.72
1f6y_A262 5-methyltetrahydrofolate corrinoid/iron sulfur protein 90.42
>1r3s_A URO-D, uroporphyrinogen decarboxylase, UPD; uroporphyrinogen decarboxylase coproporphyrinogen, X-RAY crystallography, lyase; HET: 1CP; 1.65A {Homo sapiens} SCOP: c.1.22.1 PDB: 1r3t_A* 1r3r_A 1r3q_A* 1r3y_A* 1uro_A 3gvq_A 3gvr_A 1r3v_A* 3gvv_A 3gvw_A 1jph_A 1r3w_A* 3gw3_A 1jpi_A 1jpk_A 3gw0_A 2q71_A* 2q6z_A* Back     alignment and structure
Probab=100.00  E-value=0  Score=767.29  Aligned_cols=341  Identities=36%  Similarity=0.651  Sum_probs=320.8

Q ss_pred             CHHHHHHHHHCCCCCCCCCCHHHHHCCCCCHHHHHHHHHCCCHHHHHCCHHHHHHHHHHHHHHCCCCEEEECCCCEECCH
Q ss_conf             60579999966998999976146231234579999976155389984279999998721287629872652133200104
Q gi|254780812|r    3 ERKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIAD   82 (346)
Q Consensus         3 ~~~~~~l~al~g~~~~r~PVW~MrQAGrylpey~~~r~~~~~f~~~~~~pela~evtl~p~~r~~~DaaIlFsDIl~~~e   82 (346)
                      .+|+||++||+|++|||+||||||||||||||||++|+++ ||+|+|+|||+++|+|+||++|||+||||+|||||+++|
T Consensus        14 ~~ner~l~al~ge~vdr~PVW~MrQAGr~lpey~~~r~~~-~f~e~~~~pe~~aevtl~p~~~~~~Daai~fsDil~~~e   92 (367)
T 1r3s_A           14 LKNDTFLRAAWGEETDYTPVWCMRQAGRYLPEFRETRAAQ-DFFSTCRSPEACCELTLQPLRRFPLDAAIIFSGILVVPQ   92 (367)
T ss_dssp             CSCCHHHHHHHTCCCSSCCBCCTTSSSTTSHHHHHHHHTS-CHHHHHTCHHHHHHHHHHHHHHSCCSCEECCCCTTHHHH
T ss_pred             CCHHHHHHHHCCCCCCCCCEEEECCCCCCCHHHHHHHHCC-CHHHHHCCHHHHHHHHHHHHHHCCCCEEEECCCCCCCHH
T ss_conf             2408999997699899999875421222488999987129-998885799999999973998659766872365566868


Q ss_pred             HHCCCEEEECCCCCCCC-CCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             32443373168875222-33333554205670123443237877787642102453201111479999999961246776
Q gi|254780812|r   83 ALGRNVRFVENEGPRMD-PITTQEIYLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIK  161 (346)
Q Consensus        83 alG~~v~f~~~~GP~~~-p~~~~~~~~~~~~~~~~~~~l~~v~eAi~~~k~~l~~~~pLIGF~GgP~TlasYmieG~~sk  161 (346)
                      |||++++|.++.||+++ +....++.....+.+...+++++|++|++++|++|++++|||||+|||||||+||++|++++
T Consensus        93 alG~~v~f~~~~gp~~~~~~~~~~~~~~~~~~~~~~~~l~~v~eai~~~~~~l~~~vpliGf~ggP~Tla~yli~~~~~~  172 (367)
T 1r3s_A           93 ALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQRLAGRVPLIGFAGAPWTLMTYMVEGGGSS  172 (367)
T ss_dssp             HTTCCCEEETTTEEECSSCCCSGGGGGGSCCGGGHHHHTHHHHHHHHHHHHHHTTSSCEEEEEECHHHHHHHHHHSSCCS
T ss_pred             HHCCCCEECCCCCCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCHHHHHHHHHCCCCCC
T ss_conf             81986300489998878776637777651021113445069999999999870787871435055078999996266520


Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHCCHHHHHHHHCCCHHHHHHHHHHHC----
Q ss_conf             5246775301372228999999999999997777754981678438311006835677761272268999986308----
Q gi|254780812|r  162 DHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKY----  237 (346)
Q Consensus       162 ~~~~~~~~~~~~p~~~~~ll~~lt~~~~~yl~~Qi~aGad~iqIFDs~ag~Ls~~~f~~f~~p~~kkI~~~ik~~~----  237 (346)
                      ++.+++++|+++|+.+|++|+++|+++++|+++|+++|||+|||||||||+||+++|++|++||+++|++.+++++    
T Consensus       173 ~~~~~~~~~~~~p~~~~~ll~~~t~~~~~~~~~qi~aGad~i~ifds~a~~ls~~~~~~~~~~~~~~i~~~i~~~~~~~~  252 (367)
T 1r3s_A          173 TMAQAKRWLYQRPQASHQLLRILTDALVPYLVGQVVAGAQALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAG  252 (367)
T ss_dssp             SCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHTTCSEEEEEETTGGGSCHHHHHHHTHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             26789999862878899999999999999999998448966785153020099799999899999999999987452124


Q ss_pred             -CCCEEECCCCCCCCCHHHHHCCCCCCEEECCCCCCHHHHHH-HCCCEEEECCCCHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf             -86236024311000013420147872230467799899997-0798469688884677099889999999999973259
Q gi|254780812|r  238 -PNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALE-LQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGSG  315 (346)
Q Consensus       238 -~~vpiI~f~~g~~~~l~~~~~~~g~d~isiD~~~dl~~a~~-~~~~~~lqGNldP~~L~~~~e~i~~~~~~~l~~~~~~  315 (346)
                       .++|+||||++++..++.+.+ +|+|++|+||.+|+.++++ ++++++|||||||.+|++++|+|+++|+++|+.++++
T Consensus       253 ~~~~~~i~~~~~~~~~~~~~~~-~g~d~is~d~~~dl~~~~~~~~~~~~lqGNldP~~L~~~~e~i~~~~~~~l~~~~~~  331 (367)
T 1r3s_A          253 LAPVPMIIFAKDGHFALEELAQ-AGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCALYASEEEIGQLVKQMLDDFGPH  331 (367)
T ss_dssp             CCCCCEEEEETTCGGGHHHHTT-SSCSEEECCTTSCHHHHHHHHCSSSEEEEEECGGGGGSCHHHHHHHHHHHHHHHCSS
T ss_pred             CCCCCEEECCCCHHHHHHHHHH-HCCCCCCCCCCCCHHHHHHHHCCCCEEEECCCHHHHCCCHHHHHHHHHHHHHHCCCC
T ss_conf             6787402105541566899987-077712665556999999993899159808887998699999999999999980899


Q ss_pred             CCEEEECCCCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             928960897633668899999999997306
Q gi|254780812|r  316 PFIFNLGHGITPQVDPKNVLDLVKTVRSEK  345 (346)
Q Consensus       316 ~~I~nLGhGi~p~tp~eNv~~~v~~vr~~~  345 (346)
                      ||||||||||+|+||+|||++||++||+|+
T Consensus       332 ~~I~nlGhgI~p~tp~eNV~a~v~avr~y~  361 (367)
T 1r3s_A          332 RYIANLGHGLYPDMDPEHVGAFVDAVHKHS  361 (367)
T ss_dssp             SEEEEESSCCCTTCCHHHHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             969959998599999999999999999967



>2inf_A URO-D, UPD, uroporphyrinogen decarboxylase; (alpha-beta)8 barrel, eight parallel beta strands surrounded by eight alpha helices, lyase; 2.30A {Bacillus subtilis} Back     alignment and structure
>1j93_A UROD, uroporphyrinogen decarboxylase; beta barrel, plastidial enzyme, crystallographic dimer, lyase; 2.30A {Nicotiana tabacum} SCOP: c.1.22.1 Back     alignment and structure
>3cyv_A URO-D, UPD, uroporphyrinogen decarboxylase; alpha/beta barrel, cytoplasm, lyase, porphyrin biosynthesis; 2.80A {Shigella flexneri} Back     alignment and structure
>2eja_A URO-D, UPD, uroporphyrinogen decarboxylase; dimer, X-RAY diffraction, structural genomics, NPPSFA; 1.90A {Aquifex aeolicus} Back     alignment and structure
>1t7l_A 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; TIM barrel, methyltetrahydrofolate, zinc; 2.00A {Thermotoga maritima} PDB: 3bq5_A 3bq6_A 1xdj_A 1xr2_A* 1xpg_A* Back     alignment and structure
>2nq5_A 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; structural genomics, target 6426D, PSI; 1.90A {Streptococcus mutans} Back     alignment and structure
>1u1j_A 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; methionine, synthase, methyltetrahydrofolate; HET: C2F; 2.40A {Arabidopsis thaliana} SCOP: c.1.22.2 c.1.22.2 PDB: 1u1h_A* 1u1u_A 1u22_A* Back     alignment and structure
>1ypx_A Putative vitamin-B12 independent methionine synthase family protein; alpha-beta protein, whose fold resembles A TIM-barrel protein; 2.60A {Listeria monocytogenes egd-e} Back     alignment and structure
>1u1j_A 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; methionine, synthase, methyltetrahydrofolate; HET: C2F; 2.40A {Arabidopsis thaliana} SCOP: c.1.22.2 c.1.22.2 PDB: 1u1h_A* 1u1u_A 1u22_A* Back     alignment and structure
>2nq5_A 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; structural genomics, target 6426D, PSI; 1.90A {Streptococcus mutans} Back     alignment and structure
>3bg3_A Pyruvate carboxylase, mitochondrial; TIM barrel, ATP-binding, biotin, disease mutation, gluconeogenesis, ligase, lipid synthesis, manganese; HET: KCX BTI; 2.80A {Homo sapiens} PDB: 3bg9_A Back     alignment and structure
>3ble_A Citramalate synthase from leptospira interrogans; TIM barrel, licmsn, substrate specificity, acyltransferase, amino-acid biosynthesis; 2.00A {Leptospira interrogans} PDB: 3blf_A 3bli_A* Back     alignment and structure
>2cw6_A Hydroxymethylglutaryl-COA lyase, mitochondrial; HMG-COA lyase, ketogenic enzyme; HET: 3HG; 2.10A {Homo sapiens} PDB: 3mp3_A* 3mp4_A 3mp5_A* Back     alignment and structure
>2ftp_A Hydroxymethylglutaryl-COA lyase; structural genomics, PSI, protein structure initiative, midwest center for structural genomics; 2.40A {Pseudomonas aeruginosa PAO1} Back     alignment and structure
>1rqb_A Transcarboxylase 5S subunit; TIM-barrel, carbamylated lysine, transferase; HET: KCX; 1.90A {Propionibacterium freudenreichiisubsp} SCOP: a.5.7.2 c.1.10.5 PDB: 1rqe_A 1rqh_A* 1rr2_A* 1u5j_A* 1s3h_A* Back     alignment and structure
>2wkj_A N-acetylneuraminate lyase; directed evolution, sialic acid mimetics, aldolase, cytoplasm, schiff base, carbohydrate metabolism; HET: KPI PYR; 1.45A {Escherichia coli} PDB: 1hl2_A 1fdy_A 1fdz_A 1nal_1 Back     alignment and structure
>2nx9_A Oxaloacetate decarboxylase 2, subunit alpha; carboxyltransferase structure, biotin enzymes, Zn2+ binding site, TIM-barrel fold, lyase; 1.70A {Vibrio cholerae} Back     alignment and structure
>1o4u_A Type II quinolic acid phosphoribosyltransferase; TM1645, structural genomics, JCSG, PSI, protein structure initiative; 2.50A {Thermotoga maritima} SCOP: c.1.17.1 d.41.2.1 Back     alignment and structure
>3e96_A Dihydrodipicolinate synthase; structural genomics, nysgrc, target 9375C, operon, , PSI-2, protein structure initiative; 1.80A {Bacillus clausii ksm-k16} Back     alignment and structure
>1ydo_A HMG-COA lyase; TIM-barrel protein, structural genomics, PSI, protein structure initiative, northeast structural genomics consortium; 2.71A {Bacillus subtilis subsp} Back     alignment and structure
>2tps_A Protein (thiamin phosphate synthase); thiamin biosynthesis, TIM barrel; HET: TPS; 1.25A {Bacillus subtilis} SCOP: c.1.3.1 PDB: 1g4t_A* 1g6c_A* 1g4e_A* 1g69_A* 1g4s_A* 1g4p_A* 1g67_A* Back     alignment and structure
>1f6y_A 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase; carbon dioxide fixation, cobalamin; 2.20A {Moorella thermoacetica atcc 39073} SCOP: c.1.21.2 PDB: 2e7f_A* 2ogy_A* Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 346 uroporphyrinogen decarboxylase [Candidatus Liberibacter
d1r3sa_356 c.1.22.1 (A:) Uroporphyrinogen decarboxylase, UROD {Hum 3e-65
d1j93a_343 c.1.22.1 (A:) Uroporphyrinogen decarboxylase, UROD {Tob 2e-62
>d1r3sa_ c.1.22.1 (A:) Uroporphyrinogen decarboxylase, UROD {Human (Homo sapiens) [TaxId: 9606]} Length = 356 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: UROD/MetE-like
family: Uroporphyrinogen decarboxylase, UROD
domain: Uroporphyrinogen decarboxylase, UROD
species: Human (Homo sapiens) [TaxId: 9606]
 Score =  242 bits (618), Expect = 3e-65
 Identities = 121/349 (34%), Positives = 180/349 (51%), Gaps = 10/349 (2%)

Query: 1   MNERKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTL 60
            N+     L    G   +  P+W MRQAGRYLPE+R+ R   ++F   C +PE   ELTL
Sbjct: 5   KNDT---FLRAAWGEETDYTPVWCMRQAGRYLPEFRETRAA-QDFFSTCRSPEACCELTL 60

Query: 61  QPIRRYNFDAAILFSDILVIADALGRNVRFVENEGPRMD-PITTQEIYLLNPNIDLFLNY 119
           QP+RR+  DAAI+FS ILV+  ALG  V  V  +GP    P+  ++      + ++  + 
Sbjct: 61  QPLRRFPLDAAIIFSGILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASE 120

Query: 120 LLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNW 179
           L  +FQ+I++ R++L   + LIGF GAPWT+ +YM+ GG      Q + + YQ  +A + 
Sbjct: 121 LGYVFQAITLTRQRLAGRVPLIGFAGAPWTLMTYMVEGGGSSTMAQAKRWLYQRPQASHQ 180

Query: 180 LLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPN 239
           LL  L+D    YL+ Q+ AG   +Q+F++HAG LG   F  +A   +  +   V+ +   
Sbjct: 181 LLRILTDALVPYLVGQVVAGAQALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLRE 240

Query: 240 AKFISFAK----GAGYMLKNYRRLTDSNAIGLDWSVPLSFALE-LQKEGPVQGNLDPMRL 294
           A             G+             +GLDW+V    A E + K   +QGNLDP  L
Sbjct: 241 AGLAPVPMIIFAKDGHFALEELAQAGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCAL 300

Query: 295 VVGNQVMIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRS 343
               + +   V  +LD  G   +I NLGHG+ P +DP++V   V  V  
Sbjct: 301 YASEEEIGQLVKQMLDDFGPHRYIANLGHGLYPDMDPEHVGAFVDAVHK 349


>d1j93a_ c.1.22.1 (A:) Uroporphyrinogen decarboxylase, UROD {Tobacco (Nicotiana tabacum), UROD-III [TaxId: 4097]} Length = 343 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target346 uroporphyrinogen decarboxylase [Candidatus Liberibacter
d1r3sa_356 Uroporphyrinogen decarboxylase, UROD {Human (Homo sapie 100.0
d1j93a_343 Uroporphyrinogen decarboxylase, UROD {Tobacco (Nicotian 100.0
d1u1ha2365 5-methyltetrahydropteroyltriglutamate--homocysteine met 98.17
d1u1ha1394 5-methyltetrahydropteroyltriglutamate--homocysteine met 97.46
d2tpsa_226 Thiamin phosphate synthase {Bacillus subtilis [TaxId: 1 90.31
d1rqba2303 Transcarboxylase 5S subunit, N-terminal domain {Propion 90.14
>d1r3sa_ c.1.22.1 (A:) Uroporphyrinogen decarboxylase, UROD {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: UROD/MetE-like
family: Uroporphyrinogen decarboxylase, UROD
domain: Uroporphyrinogen decarboxylase, UROD
species: Human (Homo sapiens) [TaxId: 9606]
Probab=100.00  E-value=0  Score=773.84  Aligned_cols=342  Identities=36%  Similarity=0.654  Sum_probs=321.7

Q ss_pred             CCHHHHHHHHHCCCCCCCCCCHHHHHCCCCCHHHHHHHHHCCCHHHHHCCHHHHHHHHHHHHHHCCCCEEEECCCCEECC
Q ss_conf             76057999996699899997614623123457999997615538998427999999872128762987265213320010
Q gi|254780812|r    2 NERKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIA   81 (346)
Q Consensus         2 ~~~~~~~l~al~g~~~~r~PVW~MrQAGrylpey~~~r~~~~~f~~~~~~pela~evtl~p~~r~~~DaaIlFsDIl~~~   81 (346)
                      .-+|+|||+||+|+++||+||||||||||||||||++|++ +||+|+|+|||+++|+||||++|||+||||+|||||+++
T Consensus         3 ~~~ne~~l~al~g~~~dr~PVw~MrqAGRylpey~~~r~~-~~f~e~~~~pe~~ae~tl~p~~~~~~DaaiifsDil~~~   81 (356)
T d1r3sa_           3 ELKNDTFLRAAWGEETDYTPVWCMRQAGRYLPEFRETRAA-QDFFSTCRSPEACCELTLQPLRRFPLDAAIIFSGILVVP   81 (356)
T ss_dssp             CCSCCHHHHHHHTCCCSSCCBCCTTSSSTTSHHHHHHHHT-SCHHHHHTCHHHHHHHHHHHHHHSCCSCEECCCCTTHHH
T ss_pred             CCCHHHHHHHHCCCCCCCCCEEEEECCCCCCHHHHHHHHC-CCHHHHHCCHHHHHHHHHHHHHHCCCCEEEECCCCCHHH
T ss_conf             7644899999759989999988884454258899998712-899998559999999984489867954256224421013


Q ss_pred             HHHCCCEEEECCCCCCCC-CCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             432443373168875222-3333355420567012344323787778764210245320111147999999996124677
Q gi|254780812|r   82 DALGRNVRFVENEGPRMD-PITTQEIYLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFI  160 (346)
Q Consensus        82 ealG~~v~f~~~~GP~~~-p~~~~~~~~~~~~~~~~~~~l~~v~eAi~~~k~~l~~~~pLIGF~GgP~TlasYmieG~~s  160 (346)
                      +|||++|+|.+|.||+++ +....++.....+.+...+++++|+||++++|++|++++|||||+|||||||+||++|+++
T Consensus        82 ealG~~v~f~~~~gp~~~~~~~~~~~~~~~~~~~~~~~~l~~v~eai~~~~~~l~~~~pliGf~ggP~Tla~yli~~~~~  161 (356)
T d1r3sa_          82 QALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQRLAGRVPLIGFAGAPWTLMTYMVEGGGS  161 (356)
T ss_dssp             HHTTCCCEEETTTEEECSSCCCSGGGGGGSCCGGGHHHHTHHHHHHHHHHHHHHTTSSCEEEEEECHHHHHHHHHHSSCC
T ss_pred             HHCCCEEEECCCCCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHCCCC
T ss_conf             42286356448898667764332023321011000021448999999999987355656630320318889998721342


Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHCCHHHHHHHHCCCHHHHHHHHHHHC---
Q ss_conf             65246775301372228999999999999997777754981678438311006835677761272268999986308---
Q gi|254780812|r  161 KDHGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKY---  237 (346)
Q Consensus       161 k~~~~~~~~~~~~p~~~~~ll~~lt~~~~~yl~~Qi~aGad~iqIFDs~ag~Ls~~~f~~f~~p~~kkI~~~ik~~~---  237 (346)
                      +++.+.+.+|+++|+.+|++|+++|+.+++|+++|+++|||+|||||||||+||+++|++|+.||+++|++.+++++   
T Consensus       162 ~~~~~~~~~~~~~pe~~~~ll~~lt~~~~~~~~~qi~aGad~i~ifDs~a~~l~~~~~~~~~~~~~~~i~~~i~~~~~~~  241 (356)
T d1r3sa_         162 STMAQAKRWLYQRPQASHQLLRILTDALVPYLVGQVVAGAQALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREA  241 (356)
T ss_dssp             SSCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHTTCSEEEEEETTGGGSCHHHHHHHTHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             13788988763035778899999999889999998605665402035201213578888888999999999998751012


Q ss_pred             --CCCEEECCCCCCCCCHHHHHCCCCCCEEECCCCCCHHHHHH-HCCCEEEECCCCHHHHCCCHHHHHHHHHHHHHHHCC
Q ss_conf             --86236024311000013420147872230467799899997-079846968888467709988999999999997325
Q gi|254780812|r  238 --PNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALE-LQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGS  314 (346)
Q Consensus       238 --~~vpiI~f~~g~~~~l~~~~~~~g~d~isiD~~~dl~~a~~-~~~~~~lqGNldP~~L~~~~e~i~~~~~~~l~~~~~  314 (346)
                        .++|++|||++++..++.+.+ +|+|++|+||.+|+.++++ ++++++||||+||..|++++|+++++|+++|+.+++
T Consensus       242 ~~~~~~~i~~~~~~~~~l~~~~~-~g~d~is~D~~~~l~~~~~~~~~~i~lqGNldP~~L~~~~e~i~~~~~~~l~~~~~  320 (356)
T d1r3sa_         242 GLAPVPMIIFAKDGHFALEELAQ-AGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCALYASEEEIGQLVKQMLDDFGP  320 (356)
T ss_dssp             TCCCCCEEEEETTCGGGHHHHTT-SSCSEEECCTTSCHHHHHHHHCSSSEEEEEECGGGGGSCHHHHHHHHHHHHHHHCS
T ss_pred             CCCCCEEEECCHHHHHHHHHHHC-CCCCCCCCCCCCCHHHHHHHHCCCEEEEECCCHHHHCCCHHHHHHHHHHHHHHHCC
T ss_conf             47773021010447878888742-48561254235799999998489832882888899859999999999999998189


Q ss_pred             CCCEEEECCCCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             9928960897633668899999999997306
Q gi|254780812|r  315 GPFIFNLGHGITPQVDPKNVLDLVKTVRSEK  345 (346)
Q Consensus       315 ~~~I~nLGhGi~p~tp~eNv~~~v~~vr~~~  345 (346)
                      +||||||||||+|+||+|||++||++||+|+
T Consensus       321 ~~~I~nlGhGI~p~tp~env~a~v~~vr~~~  351 (356)
T d1r3sa_         321 HRYIANLGHGLYPDMDPEHVGAFVDAVHKHS  351 (356)
T ss_dssp             SSEEEEESSCCCTTCCHHHHHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             9948969997598999999999999999968



>d1j93a_ c.1.22.1 (A:) Uroporphyrinogen decarboxylase, UROD {Tobacco (Nicotiana tabacum), UROD-III [TaxId: 4097]} Back     information, alignment and structure
>d1u1ha2 c.1.22.2 (A:396-760) 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase MetE {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d1u1ha1 c.1.22.2 (A:2-395) 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase MetE {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Back     information, alignment and structure
>d2tpsa_ c.1.3.1 (A:) Thiamin phosphate synthase {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1rqba2 c.1.10.5 (A:4-306) Transcarboxylase 5S subunit, N-terminal domain {Propionibacterium freudenreichii shermanii [TaxId: 1752]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 346 uroporphyrinogen decarboxylase [Candidatus Liberib
1r3s_A_367 (A:) URO-D, uroporphyrinogen decarboxylase, UPD; u 2e-67
2eja_A_338 (A:) URO-D, UPD, uroporphyrinogen decarboxylase; d 3e-66
1j93_A_353 (A:) UROD, uroporphyrinogen decarboxylase; beta ba 3e-65
2inf_A_1-330330 (A:1-330) URO-D, UPD, uroporphyrinogen decarboxyla 1e-64
3cyv_A_354 (A:) URO-D, UPD, uroporphyrinogen decarboxylase; a 1e-62
1t7l_A_392-766375 (A:392-766) 5-methyltetrahydropteroyltriglutamate- 4e-30
2nq5_A_415-755341 (A:415-755) 5-methyltetrahydropteroyltriglutamate- 4e-27
1u1j_A_1-10_129-393275 (A:1-10,A:129-393) 5-methyltetrahydropteroyltriglu 1e-29
2nq5_A_1-66_130-390327 (A:1-66,A:130-390) 5-methyltetrahydropteroyltriglu 1e-28
>1r3s_A (A:) URO-D, uroporphyrinogen decarboxylase, UPD; uroporphyrinogen decarboxylase coproporphyrinogen, X-RAY crystallography, lyase; HET: 1CP; 1.65A {Homo sapiens}Length = 367 Back     alignment and structure
 Score =  250 bits (639), Expect = 2e-67
 Identities = 124/346 (35%), Positives = 181/346 (52%), Gaps = 9/346 (2%)

Query: 5   KQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIR 64
               L    G   +  P+W MRQAGRYLPE+R+ R    +F   C +PE   ELTLQP+R
Sbjct: 16  NDTFLRAAWGEETDYTPVWCMRQAGRYLPEFRETRAAQ-DFFSTCRSPEACCELTLQPLR 74

Query: 65  RYNFDAAILFSDILVIADALGRNVRFVENEGPRM-DPITTQEIYLLNPNIDLFLNYLLPI 123
           R+  DAAI+FS ILV+  ALG  V  V  +GP   +P+  ++      + ++  + L  +
Sbjct: 75  RFPLDAAIIFSGILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYV 134

Query: 124 FQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKDHGQNRVFAYQNSRAFNWLLDF 183
           FQ+I++ R++L   + LIGF GAPWT+ +YM+ GG      Q + + YQ  +A + LL  
Sbjct: 135 FQAITLTRQRLAGRVPLIGFAGAPWTLMTYMVEGGGSSTMAQAKRWLYQRPQASHQLLRI 194

Query: 184 LSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKYPNAK-- 241
           L+D    YL+ Q+ AG   +Q+F++HAG LG   F  +A   +  +   V+ +   A   
Sbjct: 195 LTDALVPYLVGQVVAGAQALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGLA 254

Query: 242 ---FISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALEL-QKEGPVQGNLDPMRLVVG 297
               I FAK   + L           +GLDW+V    A E   K   +QGNLDP  L   
Sbjct: 255 PVPMIIFAKDGHFAL-EELAQAGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCALYAS 313

Query: 298 NQVMIDGVNAILDVLGSGPFIFNLGHGITPQVDPKNVLDLVKTVRS 343
            + +   V  +LD  G   +I NLGHG+ P +DP++V   V  V  
Sbjct: 314 EEEIGQLVKQMLDDFGPHRYIANLGHGLYPDMDPEHVGAFVDAVHK 359


>2eja_A (A:) URO-D, UPD, uroporphyrinogen decarboxylase; dimer, X-RAY diffraction, structural genomics, NPPSFA; 1.90A {Aquifex aeolicus}Length = 338 Back     alignment and structure
>1j93_A (A:) UROD, uroporphyrinogen decarboxylase; beta barrel, plastidial enzyme, crystallographic dimer, lyase; 2.30A {Nicotiana tabacum}Length = 353 Back     alignment and structure
>2inf_A (A:1-330) URO-D, UPD, uroporphyrinogen decarboxylase; (alpha-beta)8 barrel, eight parallel beta strands surrounded by eight alpha helices, lyase; 2.30A {Bacillus subtilis}Length = 330 Back     alignment and structure
>3cyv_A (A:) URO-D, UPD, uroporphyrinogen decarboxylase; alpha/beta barrel, cytoplasm, lyase, porphyrin biosynthesis; 2.80A {Shigella flexneri}Length = 354 Back     alignment and structure
>1t7l_A (A:392-766) 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; TIM barrel, methyltetrahydrofolate, zinc; 2.00A {Thermotoga maritima} PDB: 3bq5_A 3bq6_A 1xdj_A 1xr2_A* 1xpg_A*Length = 375 Back     alignment and structure
>2nq5_A (A:415-755) 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; structural genomics, target 6426D, PSI; 1.90A {Streptococcus mutans}Length = 341 Back     alignment and structure
>1u1j_A (A:1-10,A:129-393) 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; methionine, synthase, methyltetrahydrofolate; HET: C2F; 2.40A {Arabidopsis thaliana}Length = 275 Back     alignment and structure
>2nq5_A (A:1-66,A:130-390) 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; structural genomics, target 6426D, PSI; 1.90A {Streptococcus mutans}Length = 327 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target346 uroporphyrinogen decarboxylase [Candidatus Liberibacter
1r3s_A_367 URO-D, uroporphyrinogen decarboxylase, UPD; uropor 100.0
1j93_A_353 UROD, uroporphyrinogen decarboxylase; beta barrel, 100.0
2eja_A_338 URO-D, UPD, uroporphyrinogen decarboxylase; dimer, 100.0
2inf_A_1-330330 URO-D, UPD, uroporphyrinogen decarboxylase; (alpha 100.0
3cyv_A_354 URO-D, UPD, uroporphyrinogen decarboxylase; alpha/ 100.0
1t7l_A_392-766375 5-methyltetrahydropteroyltriglutamate-- homocystei 100.0
2nq5_A_415-755341 5-methyltetrahydropteroyltriglutamate-- homocystei 100.0
1u1j_A_1-10_129-393275 5-methyltetrahydropteroyltriglutamate-- homocystei 99.95
2nq5_A_1-66_130-390327 5-methyltetrahydropteroyltriglutamate-- homocystei 99.95
1t7l_A_1-391391 5-methyltetrahydropteroyltriglutamate-- homocystei 98.92
1ypx_A_375 Putative vitamin-B12 independent methionine syntha 98.2
1u1j_A_394-411_488-681212 5-methyltetrahydropteroyltriglutamate-- homocystei 97.08
3bg3_A_66-396_510-576398 Pyruvate carboxylase, mitochondrial; TIM barrel, A 95.22
1rqb_A_1-308_422-472359 Transcarboxylase 5S subunit; TIM-barrel, carbamyla 94.57
2ftp_A_302 Hydroxymethylglutaryl-COA lyase; structural genomi 94.33
1vr6_A_86-350265 Phospho-2-dehydro-3-deoxyheptonate aldolase; TM034 94.31
1zco_A_262 2-dehydro-3-deoxyphosphoheptonate aldolase; arabin 93.84
3ble_A_337 Citramalate synthase from leptospira interrogans; 93.11
2nx9_A_1-291_403-464353 Oxaloacetate decarboxylase 2, subunit alpha; carbo 92.72
3bi8_A_291 Dihydrodipicolinate synthase; TIM-barrel, amino-ac 92.62
1ydn_A_295 Hydroxymethylglutaryl-COA lyase; TIM-barrel protei 92.43
1nvm_A_1-273273 HOA, 4-hydroxy-2-oxovalerate aldolase; sequestered 92.11
2cw6_A_298 Hydroxymethylglutaryl-COA lyase, mitochondrial; HM 91.55
2qf7_A_513-842_963-1020388 Pyruvate carboxylase protein; multi-domain, multi- 90.63
1vs1_A_276 3-deoxy-7-phosphoheptulonate synthase; (beta/alpha 94.32
1ad1_A_266 DHPS, dihydropteroate synthetase; transferase, APO 92.79
1pii_A_241-452212 N-(5'phosphoribosyl)anthranilate isomerase; bifunc 91.89
3hbl_A_495-825_946-1003389 Pyruvate carboxylase; TIM barrel, ligase; HET: BTI 91.15
2vp8_A_318 Dihydropteroate synthase 2; RV1207, transferase, f 90.8
1ydo_A_307 HMG-COA lyase; TIM-barrel protein, structural geno 92.09
2ojp_A_292 DHDPS, dihydrodipicolinate synthase; dimer, lysine 90.19
>1r3s_A (A:) URO-D, uroporphyrinogen decarboxylase, UPD; uroporphyrinogen decarboxylase coproporphyrinogen, X-RAY crystallography, lyase; HET: 1CP; 1.65A {Homo sapiens} Back     alignment and structure
Probab=100.00  E-value=0  Score=497.36  Aligned_cols=340  Identities=36%  Similarity=0.656  Sum_probs=319.2

Q ss_pred             HHHHHHHHHCCCCCCCCCCHHHHHCCCCCHHHHHHHHHCCCHHHHHCCHHHHHHHHHHHHHHCCCCEEEECCCCEECCHH
Q ss_conf             05799999669989999761462312345799999761553899842799999987212876298726521332001043
Q gi|254780812|r    4 RKQKILEVLQGNVINPPPIWLMRQAGRYLPEYRQIRKKFKNFLDMCYTPEYTVELTLQPIRRYNFDAAILFSDILVIADA   83 (346)
Q Consensus         4 ~~~~~l~al~g~~~~r~PVW~MrQAGrylpey~~~r~~~~~f~~~~~~pela~evtl~p~~r~~~DaaIlFsDIl~~~ea   83 (346)
                      +++|+++|++|+++||+|||+++++|||+++|...+... +|.++|.+||+++|..+.+.++||+|++.+++|..+++++
T Consensus        15 ~rEr~~~al~~~~~DriPv~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~e~~a~~~~~~~~~~g~D~~~~~~~~~~~~e~   93 (367)
T 1r3s_A           15 KNDTFLRAAWGEETDYTPVWCMRQAGRYLPEFRETRAAQ-DFFSTCRSPEACCELTLQPLRRFPLDAAIIFSGILVVPQA   93 (367)
T ss_dssp             SCCHHHHHHHTCCCSSCCBCCTTSSSTTSHHHHHHHHTS-CHHHHHTCHHHHHHHHHHHHHHSCCSCEECCCCTTHHHHH
T ss_pred             CHHHHHHHHCCCCCCCCCEEEEECCCCCCHHHHHHHHCC-CHHHHHCCHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHH
T ss_conf             328999997699899999877614400389999987018-9999855999999999869997697679714654364798


Q ss_pred             HCCCEEEECCCCCCCC-CCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             2443373168875222-333335542056701234432378777876421024532011114799999999612467765
Q gi|254780812|r   84 LGRNVRFVENEGPRMD-PITTQEIYLLNPNIDLFLNYLLPIFQSISILRKKLPNHITLIGFCGAPWTVASYMISGGFIKD  162 (346)
Q Consensus        84 lG~~v~f~~~~GP~~~-p~~~~~~~~~~~~~~~~~~~l~~v~eAi~~~k~~l~~~~pLIGF~GgP~TlasYmieG~~sk~  162 (346)
                      +|+++.|.++.+|++. |+.+.++....+..+...++++++.+|++.++++.++++|++|+++||||++++++.|+..++
T Consensus        94 ~g~~i~~~~~~~p~~~~~i~~~~d~~~l~~~~~~~~~~~~~~~a~~~l~~~~~~~~~v~~~~~gP~~~~~~~~~~~~~~g  173 (367)
T 1r3s_A           94 LGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQRLAGRVPLIGFAGAPWTLMTYMVEGGGSST  173 (367)
T ss_dssp             TTCCCEEETTTEEECSSCCCSGGGGGGSCCGGGHHHHTHHHHHHHHHHHHHHTTSSCEEEEEECHHHHHHHHHHSSCCSS
T ss_pred             HCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCHHHHHHHHHCCCCCHH
T ss_conf             18852005899988876554167776510220013467999999999999716878733351541989999970554026


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCHHHCCHHHHHHHHCCCHHHHHHHHHHHC-----
Q ss_conf             246775301372228999999999999997777754981678438311006835677761272268999986308-----
Q gi|254780812|r  163 HGQNRVFAYQNSRAFNWLLDFLSDVSAEYLIAQIHAGVDVIQIFDTHAGCLGEHEFENYAARSVGRIISAVRRKY-----  237 (346)
Q Consensus       163 ~~~~~~~~~~~p~~~~~ll~~lt~~~~~yl~~Qi~aGad~iqIFDs~ag~Ls~~~f~~f~~p~~kkI~~~ik~~~-----  237 (346)
                      +......|+++||.++++++++|+.+++|+++|+++|||+|+++|+|++++||++|++|++||++++++.++++.     
T Consensus       174 ~~~~~~~l~~~Pe~v~~~l~~i~~~~~~~~~~~~e~g~d~i~~~d~~~~~ispe~~~e~~~P~~k~i~~~i~~~~~~~~~  253 (367)
T 1r3s_A          174 MAQAKRWLYQRPQASHQLLRILTDALVPYLVGQVVAGAQALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGL  253 (367)
T ss_dssp             CHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHTTCSEEEEEETTGGGSCHHHHHHHTHHHHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             88999998648788999999999999999999985368622440221123897999999999999999999985531146


Q ss_pred             CCCEEECCCCCCCCCHHHHHCCCCCCEEECCCCCCHHHHHH-HCCCEEEECCCCHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf             86236024311000013420147872230467799899997-07984696888846770998899999999999732599
Q gi|254780812|r  238 PNAKFISFAKGAGYMLKNYRRLTDSNAIGLDWSVPLSFALE-LQKEGPVQGNLDPMRLVVGNQVMIDGVNAILDVLGSGP  316 (346)
Q Consensus       238 ~~vpiI~f~~g~~~~l~~~~~~~g~d~isiD~~~dl~~a~~-~~~~~~lqGNldP~~L~~~~e~i~~~~~~~l~~~~~~~  316 (346)
                      ....++|+|+++.+.++.+.+ +|+|++++++.+|+.++++ .+++++++||+||.+|++++|+|+++|+++++.++++|
T Consensus       254 g~~~~~h~cg~~~~~l~~l~~-~g~d~~~~~~~~d~~~~~~~~g~~~~i~Gn~~~~ll~gt~eei~~~v~~~l~~~~~~g  332 (367)
T 1r3s_A          254 APVPMIIFAKDGHFALEELAQ-AGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCALYASEEEIGQLVKQMLDDFGPHR  332 (367)
T ss_dssp             CCCCEEEEETTCGGGHHHHTT-SSCSEEECCTTSCHHHHHHHHCSSSEEEEEECGGGGGSCHHHHHHHHHHHHHHHCSSS
T ss_pred             CCCCEEECCCCCHHHHHHHHH-CCCCEECCCCCCCHHHHHHHHCCCEEEEECCCHHHHCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             887423215550456899986-3887315656669899999809982488488879986999999999999999808999


Q ss_pred             CEEEECCCCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             28960897633668899999999997306
Q gi|254780812|r  317 FIFNLGHGITPQVDPKNVLDLVKTVRSEK  345 (346)
Q Consensus       317 ~I~nLGhGi~p~tp~eNv~~~v~~vr~~~  345 (346)
                      ||+|+||||+|+||+||+++|++++|+|.
T Consensus       333 ~Il~~gc~i~~~~p~eni~a~v~a~~e~g  361 (367)
T 1r3s_A          333 YIANLGHGLYPDMDPEHVGAFVDAVHKHS  361 (367)
T ss_dssp             EEEEESSCCCTTCCHHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             69959997499999999999999999967



>1j93_A (A:) UROD, uroporphyrinogen decarboxylase; beta barrel, plastidial enzyme, crystallographic dimer, lyase; 2.30A {Nicotiana tabacum} Back     alignment and structure
>2eja_A (A:) URO-D, UPD, uroporphyrinogen decarboxylase; dimer, X-RAY diffraction, structural genomics, NPPSFA; 1.90A {Aquifex aeolicus} Back     alignment and structure
>2inf_A (A:1-330) URO-D, UPD, uroporphyrinogen decarboxylase; (alpha-beta)8 barrel, eight parallel beta strands surrounded by eight alpha helices, lyase; 2.30A {Bacillus subtilis} Back     alignment and structure
>3cyv_A (A:) URO-D, UPD, uroporphyrinogen decarboxylase; alpha/beta barrel, cytoplasm, lyase, porphyrin biosynthesis; 2.80A {Shigella flexneri} Back     alignment and structure
>1t7l_A (A:392-766) 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; TIM barrel, methyltetrahydrofolate, zinc; 2.00A {Thermotoga maritima} PDB: 3bq5_A 3bq6_A 1xdj_A 1xr2_A* 1xpg_A* Back     alignment and structure
>2nq5_A (A:415-755) 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; structural genomics, target 6426D, PSI; 1.90A {Streptococcus mutans} Back     alignment and structure
>1u1j_A (A:1-10,A:129-393) 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; methionine, synthase, methyltetrahydrofolate; HET: C2F; 2.40A {Arabidopsis thaliana} Back     alignment and structure
>2nq5_A (A:1-66,A:130-390) 5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase; structural genomics, target 6426D, PSI; 1.90A {Streptococcus mutans} Back     alignment and structure