254781037

254781037

porphobilinogen deaminase

GeneID in NCBI database:8210060Locus tag:CLIBASIA_04695
Protein GI in NCBI database:254781037Protein Accession:YP_003065450.1
Gene range:-(1040348, 1041271)Protein Length:307aa
Gene description:porphobilinogen deaminase
COG prediction:[H] Porphobilinogen deaminase
KEGG prediction:hemC; porphobilinogen deaminase (EC:2.5.1.61); K01749 hydroxymethylbilane synthase [EC:2.5.1.61]
SEED prediction:Porphobilinogen deaminase (EC 2.5.1.61)
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
TMHMMnone TM-Helix
TOPPRED1 TM-Helix
HMMTOPnone 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-------
MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAELDGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIRFISNKNVFNF
cccccEEEEccccHHHHHHHHHHHHHHHHHccccccEEEEEEEEEEccHHccccHHHHccccccHHHHHHHHHcccccEEEEccccccccccccEEEEEEcccccccEEEEEcccccHHHcccccEEEccHHHHHHHHHHHccccEEEEccccHHHHHHHHHcccccHHHHHHHHHHHcccccHHcccccHHHccccccccEEEEEEccccHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccccccEEEEEEEEccEEEEEEEEEcccccEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHcc
ccccEEEEEccccHHHHHHHHHHHHHHHHHccccccEEEEEEEEccccEEccccHHcccccccHHHHHHHHHHcccccEEEEcccccccccccccEEEEEcccccccHHEEccccccHHHcccccEEEcHHHHHHHHHHHHccccEEEEccccHHHHHHHHccccHHHHHHHHHHHHHcccHHHHHHHccHccccccccccEEEEEEcccHHHHHHHHHHcccHHHHHHHHHHHHHHHHHcccccccEEEEEEEEccEEEEEEEEEcccccEEEEEcccccHHHHHHHHHHHHHHHHHcccHHHccc
mekkpfrigtrcsplALAHAFETRSslmdvhkipphniviiplstkgdritnrtlteiggkglfTEEIEKKLISGEIDCAVHSAKDMPTKLLKglqisaylpredirDVFISHTAQSLKDLALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEKVIKEILniedfppspgqgaiciethvnnpkAQELVKVInhedtwdsvNCERAFLAELDGSCKSAIAGFAYCKGSTLYFYGIVLAsdgkifhevsrngnrcdainIGRDAAQYIRFISNKNVFNF
mekkpfrigtrcsplaLAHAFETRSSLMDVHKIPPHNIViiplstkgdritnrtlteiggkglftEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHSVIGTSSLRRKALLlrwrsdisvidfrGKIETrlnklnnnkAHAILLAYAGIKRLKKEKVIKEILNiedfppspGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAELDGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIRFISNKNVFNF
MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAELDGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIRFISNKNVFNF
***KPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAELDGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIRFISNKNVFNF
MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAELDGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIRFISNKNVFNF
**KKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAELDGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIRFISNKNVFNF
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MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAELDGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIRFISNKNVFNF
MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAELDGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIRFISNKNVFNF
MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAELDGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIRFISNKNVFNF

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

Original result of BLAST against C. L. asiaticus genome

No hits with e-value below 0.05

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

Original result of PSI-BLAST first 2 iterations

IdentityAlignment graphLength Definition Round E-value
Target307 porphobilinogen deaminase [Candidatus Liberibacter asia
315122376307 porphobilinogen deaminase [Candidatus Liberibacter sola 1 1e-145
325294021309 Porphobilinogen deaminase [Agrobacterium sp. H13-3] Len 1 9e-98
15889908309 porphobilinogen deaminase [Agrobacterium tumefaciens st 1 2e-95
190893753309 porphobilinogen deaminase [Rhizobium etli CIAT 652] Len 1 8e-93
86359485309 porphobilinogen deaminase [Rhizobium etli CFN 42] Lengt 1 1e-92
209551271309 porphobilinogen deaminase [Rhizobium leguminosarum bv. 1 9e-92
241206704309 porphobilinogen deaminase [Rhizobium leguminosarum bv. 1 4e-91
222150055309 porphobilinogen deaminase [Agrobacterium vitis S4] Leng 1 5e-91
116254224309 porphobilinogen deaminase [Rhizobium leguminosarum bv. 1 2e-90
222087476322 porphobilinogen deaminase [Agrobacterium radiobacter K8 1 2e-90
>gi|315122376|ref|YP_004062865.1| porphobilinogen deaminase [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 307 Back     alignment and organism information
 Score =  518 bits (1334), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 243/307 (79%), Positives = 276/307 (89%)

Query: 1   MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGG 60
           ME+K F+IGTR SPLALAHAFETRS LM VHKIP   I ++PLSTKGDRITNRTLTEIGG
Sbjct: 1   MEEKDFKIGTRRSPLALAHAFETRSYLMSVHKIPLEKIFVVPLSTKGDRITNRTLTEIGG 60

Query: 61  KGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKD 120
           KGLFTEEIE+KLISGEID AVHSAKDMPTKLLKGL+ISAYLPRED+RDVFISHTAQSL D
Sbjct: 61  KGLFTEEIERKLISGEIDFAVHSAKDMPTKLLKGLRISAYLPREDVRDVFISHTAQSLND 120

Query: 121 LALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLK 180
           LA++S++GTSSLRRKALLLRWR+D+S+IDFRGKIETRL KL N +A A+LLAYAGIKRLK
Sbjct: 121 LAVNSIVGTSSLRRKALLLRWRADLSIIDFRGKIETRLTKLKNKQADAMLLAYAGIKRLK 180

Query: 181 KEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAEL 240
           KE V+KEILN+EDFPPSPGQGAICIETH+NN +A EL   INH +TWD+V+CERAFLAEL
Sbjct: 181 KESVVKEILNLEDFPPSPGQGAICIETHMNNTRAHELATAINHRETWDTVSCERAFLAEL 240

Query: 241 DGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIRFIS 300
           DGSCKSAIAGF+YCKG +LYFYG +L  DGKIFHEVS++GN CDAI IGRDA ++IR I+
Sbjct: 241 DGSCKSAIAGFSYCKGQSLYFYGTILTPDGKIFHEVSKSGNCCDAIQIGRDAGRHIRLIA 300

Query: 301 NKNVFNF 307
           +K +FN 
Sbjct: 301 DKTIFNL 307



Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|325294021|ref|YP_004279885.1| Porphobilinogen deaminase [Agrobacterium sp. H13-3] Length = 309 Back     alignment and organism information
>gi|15889908|ref|NP_355589.1| porphobilinogen deaminase [Agrobacterium tumefaciens str. C58] Length = 309 Back     alignment and organism information
>gi|190893753|ref|YP_001980295.1| porphobilinogen deaminase [Rhizobium etli CIAT 652] Length = 309 Back     alignment and organism information
>gi|86359485|ref|YP_471377.1| porphobilinogen deaminase [Rhizobium etli CFN 42] Length = 309 Back     alignment and organism information
>gi|209551271|ref|YP_002283188.1| porphobilinogen deaminase [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 309 Back     alignment and organism information
>gi|241206704|ref|YP_002977800.1| porphobilinogen deaminase [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 309 Back     alignment and organism information
>gi|222150055|ref|YP_002551012.1| porphobilinogen deaminase [Agrobacterium vitis S4] Length = 309 Back     alignment and organism information
>gi|116254224|ref|YP_770062.1| porphobilinogen deaminase [Rhizobium leguminosarum bv. viciae 3841] Length = 309 Back     alignment and organism information
>gi|222087476|ref|YP_002546013.1| porphobilinogen deaminase [Agrobacterium radiobacter K84] Length = 322 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

Original result of RPS-BLAST against CDD database part I

Original result of RPS-BLASTagainst CDD database part II

IdentityAlignment graphLength Definition E-value
Target307 porphobilinogen deaminase [Candidatus Liberibacter asia
PRK00072295 PRK00072, hemC, porphobilinogen deaminase; Reviewed 1e-104
TIGR00212292 TIGR00212, hemC, porphobilinogen deaminase 8e-84
cd00494292 cd00494, HMBS, Hydroxymethylbilane synthase (HMBS), als 1e-76
PLN02691351 PLN02691, PLN02691, porphobilinogen deaminase 2e-76
KOG2892320 KOG2892, KOG2892, KOG2892, Porphobilinogen deaminase [C 3e-59
COG0181307 COG0181, HemC, Porphobilinogen deaminase [Coenzyme meta 1e-88
pfam01379213 pfam01379, Porphobil_deam, Porphobilinogen deaminase, d 4e-61
PRK01066231 PRK01066, PRK01066, porphobilinogen deaminase; Provisio 7e-26
pfam0390074 pfam03900, Porphobil_deamC, Porphobilinogen deaminase, 3e-11
>gnl|CDD|178840 PRK00072, hemC, porphobilinogen deaminase; Reviewed Back     alignment and domain information
>gnl|CDD|161767 TIGR00212, hemC, porphobilinogen deaminase Back     alignment and domain information
>gnl|CDD|29604 cd00494, HMBS, Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12 Back     alignment and domain information
>gnl|CDD|178294 PLN02691, PLN02691, porphobilinogen deaminase Back     alignment and domain information
>gnl|CDD|38103 KOG2892, KOG2892, KOG2892, Porphobilinogen deaminase [Coenzyme transport and metabolism] Back     alignment and domain information
>gnl|CDD|30530 COG0181, HemC, Porphobilinogen deaminase [Coenzyme metabolism] Back     alignment and domain information
>gnl|CDD|144826 pfam01379, Porphobil_deam, Porphobilinogen deaminase, dipyromethane cofactor binding domain Back     alignment and domain information
>gnl|CDD|167150 PRK01066, PRK01066, porphobilinogen deaminase; Provisional Back     alignment and domain information
>gnl|CDD|146500 pfam03900, Porphobil_deamC, Porphobilinogen deaminase, C-terminal domain Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

Original result of HHsearch against CDD database

IdentityAlignment graphLength Definition Probability
Target 307 porphobilinogen deaminase [Candidatus Liberibacter asia
TIGR00212312 hemC porphobilinogen deaminase; InterPro: IPR000860 Tet 100.0
PRK00072300 hemC porphobilinogen deaminase; Reviewed 100.0
COG0181307 HemC Porphobilinogen deaminase [Coenzyme metabolism] 100.0
cd00494292 HMBS Hydroxymethylbilane synthase (HMBS), also known as 100.0
KOG2892320 consensus 100.0
pfam01379213 Porphobil_deam Porphobilinogen deaminase, dipyromethane 100.0
PRK01066234 porphobilinogen deaminase; Provisional 100.0
PRK09861272 cytoplasmic membrane lipoprotein-28; Provisional 96.66
PRK10797302 glutamate and aspartate transporter subunit; Provisiona 96.33
PRK11063271 metQ DL-methionine transporter substrate-binding subuni 94.03
pfam03180236 Lipoprotein_9 NLPA lipoprotein. This family of bacteria 93.41
COG1464268 NlpA ABC-type metal ion transport system, periplasmic c 91.18
pfam0390074 Porphobil_deamC Porphobilinogen deaminase, C-terminal d 99.82
PRK11260264 cystine transporter subunit; Provisional 95.85
PRK09959 1197 hybrid sensory histidine kinase in two-component regula 94.84
cd00134218 PBPb Bacterial periplasmic transport systems use membra 92.81
pfam00497224 SBP_bac_3 Bacterial extracellular solute-binding protei 92.37
COG0834275 HisJ ABC-type amino acid transport/signal transduction 92.27
PRK10859 507 putative transglycosylase; Provisional 95.16
pfam09084216 NMT1 NMT1/THI5 like. This family contains the NMT1 and 94.43
>TIGR00212 hemC porphobilinogen deaminase; InterPro: IPR000860 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway Back     alignment and domain information
>PRK00072 hemC porphobilinogen deaminase; Reviewed Back     alignment and domain information
>COG0181 HemC Porphobilinogen deaminase [Coenzyme metabolism] Back     alignment and domain information
>cd00494 HMBS Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12 Back     alignment and domain information
>KOG2892 consensus Back     alignment and domain information
>pfam01379 Porphobil_deam Porphobilinogen deaminase, dipyromethane cofactor binding domain Back     alignment and domain information
>PRK01066 porphobilinogen deaminase; Provisional Back     alignment and domain information
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional Back     alignment and domain information
>PRK10797 glutamate and aspartate transporter subunit; Provisional Back     alignment and domain information
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional Back     alignment and domain information
>pfam03180 Lipoprotein_9 NLPA lipoprotein Back     alignment and domain information
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism] Back     alignment and domain information
>pfam03900 Porphobil_deamC Porphobilinogen deaminase, C-terminal domain Back     alignment and domain information
>PRK11260 cystine transporter subunit; Provisional Back     alignment and domain information
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional Back     alignment and domain information
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions Back     alignment and domain information
>pfam00497 SBP_bac_3 Bacterial extracellular solute-binding proteins, family 3 Back     alignment and domain information
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms] Back     alignment and domain information
>PRK10859 putative transglycosylase; Provisional Back     alignment and domain information
>pfam09084 NMT1 NMT1/THI5 like 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

Original result of PSI-BLAST

IdentityAlignment graphLength Definition E-value
Target307 porphobilinogen deaminase [Candidatus Liberibacter asia
1pda_A313 Structure Of Porphobilinogen Deaminase Reveals A Fl 3e-75
2ypn_A313 Hydroxymethylbilane Synthase Length = 313 3e-75
1ypn_A313 Reduced Form Hydroxymethylbilane Synthase (K59q Mut 1e-74
1ah5_A313 Reduced Form Selenomethionine-Labelled Hydroxymethy 2e-73
3ecr_A364 Structure Of Human Porphobilinogen Deaminase Length 1e-60
3eq1_A361 The Crystal Structure Of Human Porphobilinogen Deam 6e-60
>gi|157833452|pdb|1PDA|A Chain A, Structure Of Porphobilinogen Deaminase Reveals A Flexible Multidomain Polymerase With A Single Catalytic Site Length = 313 Back     alignment and structure 
 Score =  286 bits (732), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 114/305 (37%), Positives = 166/305 (54%), Gaps = 2/305 (0%)

Query: 1   MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGG 60
           M     RI TR SPLAL  A   +  LM  H  P   + ++P+ T+GD I +  L ++GG
Sbjct: 1   MLDNVLRIATRQSPLALWQAHYVKDKLMASH--PGLVVELVPMVTRGDVILDTPLAKVGG 58

Query: 61  KGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKD 120
           KGLF +E+E  L+    D AVHS KD+P +  +GL +     RED RD F+S+   SL  
Sbjct: 59  KGLFVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDA 118

Query: 121 LALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLK 180
           L   S++GTSSLRR+  L   R D+ +   RG + TRL+KL+N +  AI+LA AG+KRL 
Sbjct: 119 LPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLG 178

Query: 181 KEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAEL 240
            E  I+  L  E   P+ GQGA+ IE  +++ + +EL+  +NH +T   V  ERA    L
Sbjct: 179 LESRIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRL 238

Query: 241 DGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIRFIS 300
           +G+C+  I  +A      ++  G+V A DG       R G   DA  +G   A+ +    
Sbjct: 239 EGACQVPIGSYAELIDGEIWLRGLVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNG 298

Query: 301 NKNVF 305
            + + 
Sbjct: 299 AREIL 303
gi|4388845|pdb|2YPN|A Chain A, Hydroxymethylbilane Synthase Length = 313 Back     alignment and structure
>gi|157834325|pdb|1YPN|A Chain A, Reduced Form Hydroxymethylbilane Synthase (K59q Mutant) Crystal Structure After 2 Hours In A Flow Cell Determined By Time-Resolved Laue Diffraction Length = 313 Back     alignment and structure
>gi|157829875|pdb|1AH5|A Chain A, Reduced Form Selenomethionine-Labelled Hydroxymethylbilane Synthase Determined By Mad Length = 313 Back     alignment and structure
>gi|208435725|pdb|3ECR|A Chain A, Structure Of Human Porphobilinogen Deaminase Length = 364 Back     alignment and structure
>gi|224510663|pdb|3EQ1|A Chain A, The Crystal Structure Of Human Porphobilinogen Deaminase At 2.8a Resolution Length = 361 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

IdentityAlignment graphLength Definition E-value
Target307 porphobilinogen deaminase [Candidatus Liberibacter asia
1gtk_A313 Porphobilinogen deaminase; lyase, biosynthesis of linea 3e-73
3ecr_A364 Porphobilinogen deaminase; heme biosynthesis, porphobil 6e-52
>1gtk_A Porphobilinogen deaminase; lyase, biosynthesis of linear tetrapyrrole, all alpha/beta; HET: DPM; 1.66A {Escherichia coli} SCOP: c.94.1.1 d.50.2.1 PDB: 1ah5_A* 2ypn_A* 1ypn_A* 1pda_A* Length = 313 Back     alignment and structure
 Score =  270 bits (691), Expect = 3e-73
 Identities = 113/297 (38%), Positives = 162/297 (54%), Gaps = 2/297 (0%)

Query: 1   MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGG 60
           M     RI TR SPLAL  A   +  LM  H  P   + ++P+ T+GD I +  L ++GG
Sbjct: 1   MLDNVLRIATRQSPLALWQAHYVKDKLMASH--PGLVVELVPMVTRGDVILDTPLAKVGG 58

Query: 61  KGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKD 120
           KGLF +E+E  L+    D AVHS KD+P +  +GL +     RED RD F+S+   SL  
Sbjct: 59  KGLFVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDA 118

Query: 121 LALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLK 180
           L   S++GTSSLRR+  L   R D+ +   RG + TRL+KL+N +  AI+LA AG+KRL 
Sbjct: 119 LPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLG 178

Query: 181 KEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAEL 240
            E  I+  L  E   P+ GQGA+ IE  +++ + +EL+  +NH +T   V  ERA    L
Sbjct: 179 LESRIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRL 238

Query: 241 DGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIR 297
           +G C+  I  +A      ++   +V A DG       R G   DA  +G   A+ + 
Sbjct: 239 EGGCQVPIGSYAELIDGEIWLRALVGAPDGSQIIRGERRGAPQDAEQMGISLAEELL 295
>3ecr_A Porphobilinogen deaminase; heme biosynthesis, porphobilinogen hinge, alternative splicing, cytoplasm, disease mutation, porphyrin biosynthesis; HET: DPM; 2.18A {Homo sapiens} PDB: 3eq1_A* Length = 364 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target307 porphobilinogen deaminase [Candidatus Liberibacter asia
1gtk_A313 Porphobilinogen deaminase; lyase, biosynthesis of linea 100.0
3ecr_A364 Porphobilinogen deaminase; heme biosynthesis, porphobil 100.0
3gxa_A275 Outer membrane lipoprotein GNA1946; periplasmic, L-meth 98.0
1p99_A295 Hypothetical protein PG110; structural genomics, PSI, p 97.96
3ir1_A245 Outer membrane lipoprotein GNA1946; D-methionine cultur 97.92
3k2d_A237 ABC-type metal ION transport system, periplasmic; alpha 97.62
1xs5_A241 29 kDa protein, membrane lipoprotein TPN32; periplasmic 97.49
3del_B242 Arginine binding protein; alpha and beta protein (A/B), 94.64
2vha_A287 Periplasmic binding transport protein; periplasmic bind 93.72
3hv1_A268 Polar amino acid ABC uptake transporter substrate bindi 92.86
2ozz_A231 Hypothetical protein YHFZ; alpha-beta structure, struct 97.4
2x26_A308 Periplasmic aliphatic sulphonates-binding protein; tran 97.03
1wdn_A226 GLNBP, glutamine binding protein; closed form, complex, 94.81
3g41_A246 Amino acid ABC transporter, periplasmic amino acid-bind 93.23
3hn0_A283 Nitrate transport protein; YP_001302749.1, structural g 96.28
2pyy_A228 Ionotropic glutamate receptor bacterial homologue; GLUR 90.83
3ksx_A324 Nitrate transport protein; SSUA, alkanesulfonate-bindin 90.71
2a5s_A284 N-methyl-D-aspartate receptor nmdar2A subunit, NMDA rec 95.77
2iee_A271 ORF2, probable ABC transporter extracellular-binding pr 94.32
3h7m_A234 Sensor protein; histidine kinase sensor domain, kinase, 91.93
3ix1_A302 N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine prote 91.13
2v25_A259 Major cell-binding factor; antigen, adhesin, aspartate, 93.95
1xt8_A292 Putative amino-acid transporter periplasmic solute-bind 93.05
3mpk_A267 Virulence sensor protein BVGS; venus flytrap, sensor do 92.9
2czl_A272 Hypothetical protein TTHA1568; conserved hypothetical p 91.87
>1gtk_A Porphobilinogen deaminase; lyase, biosynthesis of linear tetrapyrrole, all alpha/beta; HET: DPM; 1.66A {Escherichia coli} SCOP: c.94.1.1 d.50.2.1 PDB: 1ah5_A* 2ypn_A* 1ypn_A* 1pda_A* Back     alignment and structure
Probab=100.00  E-value=0  Score=776.72  Aligned_cols=304  Identities=37%  Similarity=0.566  Sum_probs=300.1

Q ss_pred             CCCCCEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCCCHHHCCCHHHHHHHHHHHHHCCCCEEE
Q ss_conf             99882899707988889999999999997408998338999997327411587556748622699999999870983699
Q gi|254781037|r    1 MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCA   80 (307)
Q Consensus         1 M~~~~i~IgtR~S~LAl~Qa~~v~~~L~~~~~~p~~~~ei~~i~T~GD~~~~~~l~~~g~kg~Ftkele~aLl~g~iDiA   80 (307)
                      |++|+||||||+|+||+|||++|+++|++.+  |++++||++|+|+||+++++||+++||||+||||||++|++|+||||
T Consensus         1 mm~~~IrIgtR~S~LAl~Qa~~v~~~L~~~~--p~~~~ei~~i~T~GD~~~~~~l~~~ggkg~F~kele~aLl~g~iDiA   78 (313)
T 1gtk_A            1 MLDNVLRIATRQSPLALWQAHYVKDKLMASH--PGLVVELVPMVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIA   78 (313)
T ss_dssp             --CCEEEEEECCSHHHHHHHHHHHHHHHHHC--TTCEEEEEECC-----------------CTTHHHHHHHHHTTSCSEE
T ss_pred             CCCCCEEEEECCCHHHHHHHHHHHHHHHHHC--CCCEEEEEEEECCCCCCCCCCHHHCCCCEEEHHHHHHHHHCCCCCEE
T ss_conf             9988669995884999999999999999758--99729999996348434687477728863017999999863876489


Q ss_pred             EECCCCCCCCCCCCCEEEEECCCCCCCEEEEECCCCCCCCCCCCCEEECCCCCHHHHHHHHHCCCCCHHHCCCHHHHHHH
Q ss_conf             74034321110122101222365683105665243243324567322047530288899842377310330767999998
Q gi|254781037|r   81 VHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNK  160 (307)
Q Consensus        81 VHSlKDlP~~~~~~l~i~a~~~R~d~rD~lv~~~~~~l~~lp~~a~IGTsS~RR~aql~~~~p~l~~~~iRGNv~TRl~K  160 (307)
                      ||||||||+++|+||.|+||++|+|||||||+++++++.+||+|++|||||+||++|++++|||++|++|||||+|||+|
T Consensus        79 VHSlKDlP~~~~~gl~i~av~~R~d~rD~li~~~~~~l~~lp~g~~IGTsS~RR~aql~~~~pdl~i~~iRGNVdTRl~K  158 (313)
T 1gtk_A           79 VHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSK  158 (313)
T ss_dssp             EEEGGGSCSCCCTTEEEEEECCCCCCCEEEECSSCSSGGGCCTTCEEECCCHHHHHHHHHHCTTSEEECCCSCHHHHHHH
T ss_pred             EEECCCCCCCCCCCCEEEEEECCCCHHHHHCCCCCCCHHHCCCCCEEECCCHHHHHHHHHHCCCCCEEECCCCHHHHHHH
T ss_conf             75136577546998569999567888887503763556248998988318888999999868999377564769999999


Q ss_pred             HHCCCCCEEEEEHHHHHHCCCCCCCCCCCCHHHCCCCCCCCEEEEEEECCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             63787655630145454216211222336866735854320789998527612455677623978888878899999871
Q gi|254781037|r  161 LNNNKAHAILLAYAGIKRLKKEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVINHEDTWDSVNCERAFLAEL  240 (307)
Q Consensus       161 l~~g~~DaiilA~Agl~RL~l~~~i~~~l~~~~~~PA~gQGaIaIe~r~~d~~i~~il~~Ind~~T~~~v~aER~fL~~L  240 (307)
                      |++|+|||||||+|||+|||+.+.++++|++++|+|||||||||||||++|.++.++++.|||++|+.|+.+||+||+.|
T Consensus       159 L~~g~~DaiILA~AGl~RLgl~~~~~~~l~~~~~~PA~gQGaiave~r~~d~~~~~~l~~in~~~t~~~~~aER~fL~~L  238 (313)
T 1gtk_A          159 LDNGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRL  238 (313)
T ss_dssp             HHTTSCSEEEEEHHHHHHTTCGGGCSEECCTTTSCCCTTTTCEEEEEETTCHHHHHHHGGGCCHHHHHHHHHHHHHHHHH
T ss_pred             HHCCCCCEEEEECCHHCCCCCCCCCEEECCCHHCCCCCCCCEEEEEECCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             76789778986400121012113304861602046641001256655178588999998744578999999999999985


Q ss_pred             CCCCCCCEEEEEEEECCEEEEEEEEECCCCCEEEEEEEECCHHHHHHHHHHHHHHHHHHCCHHHCC
Q ss_conf             776488528999999998999999986998789999984398889999999999999706056337
Q gi|254781037|r  241 DGSCKSAIAGFAYCKGSTLYFYGIVLASDGKIFHEVSRNGNRCDAINIGRDAAQYIRFISNKNVFN  306 (307)
Q Consensus       241 ~GgC~~PIGa~A~i~~~~l~l~a~v~s~DG~~~i~~~~~g~~~~a~~LG~~la~~Ll~~g~k~iLn  306 (307)
                      +|||++|||+||++++++++|+|+|+|+||++.+..+.+|+.++++++|+++|++|+++||+++|+
T Consensus       239 ~ggC~sPIga~A~~~~~~l~l~~~v~s~DG~~~i~~~~~g~~~~a~~lG~~la~~Ll~~Ga~ell~  304 (313)
T 1gtk_A          239 EGGCQVPIGSYAELIDGEIWLRALVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREILA  304 (313)
T ss_dssp             TCCTTSCEEEEEEEETTEEEEEEEEECTTSSCEEEEEEEECGGGHHHHHHHHHHHHHHTTHHHHHH
T ss_pred             CCCCCCCEEEEEEEECCEEEEEEEEECCCCCEEEEEEEEECHHHHHHHHHHHHHHHHHHCHHHHHH
T ss_conf             899998649999998999999999998899789999998478999999999999999848999999
>3ecr_A Porphobilinogen deaminase; heme biosynthesis, porphobilinogen hinge, alternative splicing, cytoplasm, disease mutation, porphyrin biosynthesis; HET: DPM; 2.18A {Homo sapiens} PDB: 3eq1_A* Back     alignment and structure
>3gxa_A Outer membrane lipoprotein GNA1946; periplasmic, L-methionine bingding, protein binding; 2.25A {Neisseria meningitidis} Back     alignment and structure
>1p99_A Hypothetical protein PG110; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; 1.70A {Staphylococcus aureus subsp} SCOP: c.94.1.1 Back     alignment and structure
>3ir1_A Outer membrane lipoprotein GNA1946; D-methionine cultured, protein binding; 2.15A {Neisseria meningitidis} Back     alignment and structure
>3k2d_A ABC-type metal ION transport system, periplasmic; alpha/beta domain, immune system; 2.60A {Vibrio vulnificus} Back     alignment and structure
>1xs5_A 29 kDa protein, membrane lipoprotein TPN32; periplasmic binding protein, methionine, membrane protein; 1.85A {Treponema pallidum} SCOP: c.94.1.1 Back     alignment and structure
>3del_B Arginine binding protein; alpha and beta protein (A/B), periplasmic protein, protein binding, transport protein; 1.92A {Chlamydia trachomatis} Back     alignment and structure
>2vha_A Periplasmic binding transport protein; periplasmic binding protein, ligand binding, ultrahigh resolution; HET: GLU; 1.00A {Shigella flexneri} PDB: 2ia4_A* Back     alignment and structure
>3hv1_A Polar amino acid ABC uptake transporter substrate binding protein; protein structure initiative II(PSI II), nysgxrc; 1.90A {Streptococcus thermophilus lmg 18311} Back     alignment and structure
>2ozz_A Hypothetical protein YHFZ; alpha-beta structure, structural genomics, PSI-2, protein structure initiative; 2.30A {Shigella flexneri 2A} SCOP: c.94.1.1 Back     alignment and structure
>2x26_A Periplasmic aliphatic sulphonates-binding protein; transport protein; 1.75A {Escherichia coli} Back     alignment and structure
>1wdn_A GLNBP, glutamine binding protein; closed form, complex, peptide, complex (binding protein/peptide); 1.94A {Escherichia coli} SCOP: c.94.1.1 PDB: 1ggg_A Back     alignment and structure
>3hn0_A Nitrate transport protein; YP_001302749.1, structural genomics, joint center for structural genomics, JCSG; 1.75A {Parabacteroides distasonis} Back     alignment and structure
>2pyy_A Ionotropic glutamate receptor bacterial homologue; GLUR0 ligand binding domain, transport protein; HET: GLU; 2.10A {Nostoc punctiforme pcc 73102} Back     alignment and structure
>3ksx_A Nitrate transport protein; SSUA, alkanesulfonate-binding protein, periplasmic-binding P transport protein; HET: MPO; 1.70A {Xanthomonas axonopodis PV} PDB: 3e4r_A* 3ksj_A* Back     alignment and structure
>2a5s_A N-methyl-D-aspartate receptor nmdar2A subunit, NMDA receptor nmdar2A; protein-ligand complex, metal transport,membrane protein; HET: GLU; 1.70A {Rattus norvegicus} SCOP: c.94.1.1 PDB: 2a5t_B* Back     alignment and structure
>2iee_A ORF2, probable ABC transporter extracellular-binding protein YCKB; SR574, NESG, X-RAY, structural genomics, PSI-2; 2.20A {Bacillus subtilis} Back     alignment and structure
>3h7m_A Sensor protein; histidine kinase sensor domain, kinase, phosphoprotein, transferase; 2.40A {Geobacter sulfurreducens} Back     alignment and structure
>3ix1_A N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine protein; periplasmic N-formyl-4-amino-5-aminomethyl-2-methylpyrimidin protein; HET: NFM; 2.40A {Bacillus halodurans c-125} Back     alignment and structure
>2v25_A Major cell-binding factor; antigen, adhesin, aspartate, glutamate, transport, ABC transport, virulence factor, receptor; 1.49A {Campylobacter jejuni} Back     alignment and structure
>1xt8_A Putative amino-acid transporter periplasmic solute-binding protein; ABC transport, cysteine uptake, spine, structural genomics; 2.00A {Campylobacter jejuni} SCOP: c.94.1.1 Back     alignment and structure
>3mpk_A Virulence sensor protein BVGS; venus flytrap, sensor domain, signaling protein; 2.04A {Bordetella pertussis} PDB: 3mpl_A Back     alignment and structure
>2czl_A Hypothetical protein TTHA1568; conserved hypothetical protein, extremely thermoph bacteria, structural genomics, NPPSFA; HET: CME TLA XPE; 1.55A {Thermus thermophilus HB8} SCOP: c.94.1.1 PDB: 2dbp_A* 3a3u_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

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

IdentityAlignment graphLength Definition E-value
Target 307 porphobilinogen deaminase [Candidatus Liberibacter asia
d1pdaa1217 c.94.1.1 (A:3-219) Porphobilinogen deaminase (hydroxyme 8e-43
d1pdaa288 d.50.2.1 (A:220-307) Porphobilinogen deaminase (hydroxy 4e-15
>d1pdaa1 c.94.1.1 (A:3-219) Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain {Escherichia coli [TaxId: 562]} Length = 217 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score =  167 bits (425), Expect = 8e-43
 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 2/218 (0%)

Query: 4   KPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGL 63
              RI TR SPLAL  A   +  LM  H  P   + ++P+ T+GD I +  L ++GGKGL
Sbjct: 2   NVLRIATRQSPLALWQAHYVKDKLMASH--PGLVVELVPMVTRGDVILDTPLAKVGGKGL 59

Query: 64  FTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLAL 123
           F +E+E  L+    D AVHS KD+P +  +GL +     RED RD F+S+   SL  L  
Sbjct: 60  FVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPA 119

Query: 124 HSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEK 183
            S++GTSSLRR+  L   R D+ +   RG + TRL+KL+N +  AI+LA AG+KRL  E 
Sbjct: 120 GSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLES 179

Query: 184 VIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVI 221
            I+  L  E   P+ GQGA+ IE  +++ + +EL+  +
Sbjct: 180 RIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAAL 217
>d1pdaa2 d.50.2.1 (A:220-307) Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain {Escherichia coli [TaxId: 562]} Length = 88 Back     information, alignment and structure

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

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

IdentityAlignment graphLength Definition Probability
Target307 porphobilinogen deaminase [Candidatus Liberibacter asia
d1pdaa1217 Porphobilinogen deaminase (hydroxymethylbilane synthase 100.0
d1p99a_255 Putative lipoprotein (NlpA family) {Staphylococcus aure 97.44
d1pdaa288 Porphobilinogen deaminase (hydroxymethylbilane synthase 99.89
d1xs5a_240 Putative lipoprotein (NlpA family) {Treponema pallidum 97.89
d2ozza1228 Hypothetical protein YhfZ {Shigella flexneri [TaxId: 62 97.13
d1xt8a1248 Putative amino-acid transporter CjaA {Campylobacter jej 94.74
d2czla1270 Hypothetical protein TTHA1568 {Thermus thermophilus [Ta 93.39
>d1pdaa1 c.94.1.1 (A:3-219) Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Periplasmic binding protein-like II
superfamily: Periplasmic binding protein-like II
family: Phosphate binding protein-like
domain: Porphobilinogen deaminase (hydroxymethylbilane synthase), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=0  Score=580.54  Aligned_cols=217  Identities=41%  Similarity=0.643  Sum_probs=212.7

Q ss_pred             CCCEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             88289970798888999999999999740899833899999732741158755674862269999999987098369974
Q gi|254781037|r    3 KKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCAVH   82 (307)
Q Consensus         3 ~~~i~IgtR~S~LAl~Qa~~v~~~L~~~~~~p~~~~ei~~i~T~GD~~~~~~l~~~g~kg~Ftkele~aLl~g~iDiAVH   82 (307)
                      +|.||||||+|+||+|||++|.+.|++.+  |++++||++|+|+||++++.||+++||||+||+|||++|++|++|||||
T Consensus         1 ~~~IrIgtR~S~LAl~Qa~~v~~~L~~~~--p~~~~ei~~i~T~GD~~~~~~l~~~ggkg~Ftkele~~Ll~~~iDiAVH   78 (217)
T d1pdaa1           1 DNVLRIATRQSPLALWQAHYVKDKLMASH--PGLVVELVPMVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIAVH   78 (217)
T ss_dssp             CCEEEEEECCSHHHHHHHHHHHHHHHHHC--TTCEEEEEECCCHHHHC---------CCCTTTHHHHHHHHTTSCSEEEE
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHHHHHC--CCCCEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEHH
T ss_conf             98479996885999999999999999858--9981899998625876230344342016799999999997076435035


Q ss_pred             CCCCCCCCCCCCCEEEEECCCCCCCEEEEECCCCCCCCCCCCCEEECCCCCHHHHHHHHHCCCCCHHHCCCHHHHHHHHH
Q ss_conf             03432111012210122236568310566524324332456732204753028889984237731033076799999863
Q gi|254781037|r   83 SAKDMPTKLLKGLQISAYLPREDIRDVFISHTAQSLKDLALHSVIGTSSLRRKALLLRWRSDISVIDFRGKIETRLNKLN  162 (307)
Q Consensus        83 SlKDlP~~~~~~l~i~a~~~R~d~rD~lv~~~~~~l~~lp~~a~IGTsS~RR~aql~~~~p~l~~~~iRGNv~TRl~Kl~  162 (307)
                      ||||||+++|++|.|+|+++|+||||+||+++++++++||+|++|||||+||++|++++||+++|++|||||+|||+||.
T Consensus        79 S~KDlP~~~~~~l~i~a~~~R~d~rD~li~~~~~~l~~l~~~~~IGTsS~RR~aql~~~~p~l~~~~iRGNv~TRl~Kl~  158 (217)
T d1pdaa1          79 SMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLD  158 (217)
T ss_dssp             EGGGSCSCCCTTEEEEEECCCCCCCEEEECSSCSSTTTSCTTCEEECCCHHHHHHHHHHCTTSEEECCCSCHHHHHHHHH
T ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCCCCHHHCCCCCEECCCCHHHHHHHHHHCCCCCEEECCCCHHHHHHHHH
T ss_conf             33144532577651213335677300100467477736789998234651179999876888754664142343888856


Q ss_pred             CCCCCEEEEEHHHHHHCCCCCCCCCCCCHHHCCCCCCCCEEEEEEECCCCHHHHHHHHH
Q ss_conf             78765563014545421621122233686673585432078999852761245567762
Q gi|254781037|r  163 NNKAHAILLAYAGIKRLKKEKVIKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVI  221 (307)
Q Consensus       163 ~g~~DaiilA~Agl~RL~l~~~i~~~l~~~~~~PA~gQGaIaIe~r~~d~~i~~il~~I  221 (307)
                      +|+|||+|||+|||+||++.++++++|++++|+||||||+||||||++|.++.+++++|
T Consensus       159 ~g~~DaiILA~AGL~RL~l~~~i~~~l~~~~~~PA~gQGaiaIe~r~~d~~~~~il~~i  217 (217)
T d1pdaa1         159 NGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAAL  217 (217)
T ss_dssp             TTSCSEEEEEHHHHHHTTCGGGCSEECCTTTSCCCTTTTCEEEEEETTCHHHHHHHGGG
T ss_pred             CCCCCEEEEEHHHHHHCCCCHHEEEECCHHHCCCHHHHHHEEEEECCCCHHHHHHHHCC
T ss_conf             56867899555678654733301577585544794865054889817999999998549
>d1p99a_ c.94.1.1 (A:) Putative lipoprotein (NlpA family) {Staphylococcus aureus [TaxId: 1280]} Back     information, alignment and structure
>d1pdaa2 d.50.2.1 (A:220-307) Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1xs5a_ c.94.1.1 (A:) Putative lipoprotein (NlpA family) {Treponema pallidum [TaxId: 160]} Back     information, alignment and structure
>d2ozza1 c.94.1.1 (A:1-228) Hypothetical protein YhfZ {Shigella flexneri [TaxId: 623]} Back     information, alignment and structure
>d1xt8a1 c.94.1.1 (A:10-257) Putative amino-acid transporter CjaA {Campylobacter jejuni [TaxId: 197]} Back     information, alignment and structure
>d2czla1 c.94.1.1 (A:3-272) Hypothetical protein TTHA1568 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against MMDB70 database

IdentityAlignment graphLength Definition E-value
Target 307 porphobilinogen deaminase [Candidatus Liberibacter
1gtk_A_1-103_194-219129 (A:1-103,A:194-219) Porphobilinogen deaminase; lya 4e-32
3ecr_A_1-120_217-241145 (A:1-120,A:217-241) Porphobilinogen deaminase; hem 2e-29
1gtk_A_104-19390 (A:104-193) Porphobilinogen deaminase; lyase, bios 1e-23
3ecr_A_121-21696 (A:121-216) Porphobilinogen deaminase; heme biosyn 1e-21
1gtk_A_220-31394 (A:220-313) Porphobilinogen deaminase; lyase, bios 8e-17
3ecr_A_242-364123 (A:242-364) Porphobilinogen deaminase; heme biosyn 9e-16
>1gtk_A (A:1-103,A:194-219) Porphobilinogen deaminase; lyase, biosynthesis of linear tetrapyrrole, all alpha/beta; HET: DPM; 1.66A {Escherichia coli}Length = 129 Back     alignment and structure
 Score =  132 bits (335), Expect = 4e-32
 Identities = 43/105 (40%), Positives = 59/105 (56%), Gaps = 2/105 (1%)

Query: 1   MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGG 60
           M     RI TR SPLAL  A   +  LM  H  P   + ++P+ T+GD I +  L ++GG
Sbjct: 1   MLDNVLRIATRQSPLALWQAHYVKDKLMASH--PGLVVELVPMVTRGDVILDTPLAKVGG 58

Query: 61  KGLFTEEIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPRED 105
           KGLF +E+E  L+    D AVHS KD+P +  +GL +     RED
Sbjct: 59  KGLFVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICERED 103
>3ecr_A (A:1-120,A:217-241) Porphobilinogen deaminase; heme biosynthesis, porphobilinogen hinge, alternative splicing, cytoplasm, disease mutation, porphyrin biosynthesis; HET: DPM; 2.18A {Homo sapiens} PDB: 3eq1_A*Length = 145 Back     alignment and structure
>1gtk_A (A:104-193) Porphobilinogen deaminase; lyase, biosynthesis of linear tetrapyrrole, all alpha/beta; HET: DPM; 1.66A {Escherichia coli}Length = 90 Back     alignment and structure
>3ecr_A (A:121-216) Porphobilinogen deaminase; heme biosynthesis, porphobilinogen hinge, alternative splicing, cytoplasm, disease mutation, porphyrin biosynthesis; HET: DPM; 2.18A {Homo sapiens} PDB: 3eq1_A*Length = 96 Back     alignment and structure
>1gtk_A (A:220-313) Porphobilinogen deaminase; lyase, biosynthesis of linear tetrapyrrole, all alpha/beta; HET: DPM; 1.66A {Escherichia coli}Length = 94 Back     alignment and structure
>3ecr_A (A:242-364) Porphobilinogen deaminase; heme biosynthesis, porphobilinogen hinge, alternative splicing, cytoplasm, disease mutation, porphyrin biosynthesis; HET: DPM; 2.18A {Homo sapiens} PDB: 3eq1_A*Length = 123 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

IdentityAlignment graphLength Definition Probability
Target307 porphobilinogen deaminase [Candidatus Liberibacter asia
1gtk_A_1-103_194-219129 Porphobilinogen deaminase; lyase, biosynthesis of 100.0
3ecr_A_1-120_217-241145 Porphobilinogen deaminase; heme biosynthesis, porp 100.0
1gtk_A_104-19390 Porphobilinogen deaminase; lyase, biosynthesis of 100.0
3ecr_A_121-21696 Porphobilinogen deaminase; heme biosynthesis, porp 100.0
1gtk_A_220-31394 Porphobilinogen deaminase; lyase, biosynthesis of 99.88
3ecr_A_242-364123 Porphobilinogen deaminase; heme biosynthesis, porp 99.85
>1gtk_A (A:1-103,A:194-219) Porphobilinogen deaminase; lyase, biosynthesis of linear tetrapyrrole, all alpha/beta; HET: DPM; 1.66A {Escherichia coli} Back     alignment and structure
Probab=100.00  E-value=7e-43  Score=297.53  Aligned_cols=104  Identities=41%  Similarity=0.653  Sum_probs=102.3

Q ss_pred             CCCCCEEEEECCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCCCHHHCCCHHHHHHHHHHHHHCCCCEEE
Q ss_conf             99882899707988889999999999997408998338999997327411587556748622699999999870983699
Q gi|254781037|r    1 MEKKPFRIGTRCSPLALAHAFETRSSLMDVHKIPPHNIVIIPLSTKGDRITNRTLTEIGGKGLFTEEIEKKLISGEIDCA   80 (307)
Q Consensus         1 M~~~~i~IgtR~S~LAl~Qa~~v~~~L~~~~~~p~~~~ei~~i~T~GD~~~~~~l~~~g~kg~Ftkele~aLl~g~iDiA   80 (307)
                      |++++|+||||+|+||++||++|++.|++.|  |++++||++|+|+||+++++||+++||||+||||||++|++|++|+|
T Consensus         1 Mm~~~i~IGTR~S~LAl~Qt~~V~~~L~~~~--P~~~~eiv~i~T~GD~~~~~~L~~~ggKGlFtkELe~aLl~g~iDiA   78 (129)
T 1gtk_A            1 MLDNVLRIATRQSPLALWQAHYVKDKLMASH--PGLVVELVPMVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIA   78 (129)
T ss_dssp             --CCEEEEEECCSHHHHHHHHHHHHHHHHHC--TTCEEEEEECC-----------------CTTHHHHHHHHHTTSCSEE
T ss_pred             CCCCCEEEEECCCHHHHHHHHHHHHHHHHHC--CCCEEEEEEEECCCCCCCCCCHHHCCCCEEEHHHHHHHHHCCCCCEE
T ss_conf             9988679996885999999999999999758--99718999996327434687577738862543899999871877689


Q ss_pred             EECCCCCCCCCCCCCEEEEECCCCCC
Q ss_conf             74034321110122101222365683
Q gi|254781037|r   81 VHSAKDMPTKLLKGLQISAYLPREDI  106 (307)
Q Consensus        81 VHSlKDlP~~~~~~l~i~a~~~R~d~  106 (307)
                      ||||||||+.+|+||.|+|+++|+||
T Consensus        79 VHSlKDlPt~l~~gl~iaAv~~ReD~  104 (129)
T 1gtk_A           79 VHSMKDVPVEFPQGLGLVTICEREDP  104 (129)
T ss_dssp             EEEGGGSCSCCCTTEEEEEECCCCCC
T ss_pred             EEECCCCCCHHCCCCEEEECCCCCCC
T ss_conf             84035477221188158502556775
>3ecr_A (A:1-120,A:217-241) Porphobilinogen deaminase; heme biosynthesis, porphobilinogen hinge, alternative splicing, cytoplasm, disease mutation, porphyrin biosynthesis; HET: DPM; 2.18A {Homo sapiens} PDB: 3eq1_A* Back     alignment and structure
>1gtk_A (A:104-193) Porphobilinogen deaminase; lyase, biosynthesis of linear tetrapyrrole, all alpha/beta; HET: DPM; 1.66A {Escherichia coli} Back     alignment and structure
>3ecr_A (A:121-216) Porphobilinogen deaminase; heme biosynthesis, porphobilinogen hinge, alternative splicing, cytoplasm, disease mutation, porphyrin biosynthesis; HET: DPM; 2.18A {Homo sapiens} PDB: 3eq1_A* Back     alignment and structure
>1gtk_A (A:220-313) Porphobilinogen deaminase; lyase, biosynthesis of linear tetrapyrrole, all alpha/beta; HET: DPM; 1.66A {Escherichia coli} Back     alignment and structure
>3ecr_A (A:242-364) Porphobilinogen deaminase; heme biosynthesis, porphobilinogen hinge, alternative splicing, cytoplasm, disease mutation, porphyrin biosynthesis; HET: DPM; 2.18A {Homo sapiens} PDB: 3eq1_A* Back     alignment and structure