254780801

254780801

hypothetical protein CLIBASIA_03460

GeneID in NCBI database:8209807Locus tag:CLIBASIA_03460
Protein GI in NCBI database:254780801Protein Accession:YP_003065214.1
Gene range:+(455896, 456564)Protein Length:222aa
Gene description:hypothetical protein
COG prediction:[R] Predicted enzyme with a TIM-barrel fold
KEGG prediction:hypothetical protein; K06997
SEED prediction:Hypothetical protein YggS, proline synthase co-transcribed bacterial homolog PROSC
Pathway involved in KEGG:not defined
Subsystem involved in SEED:- none -
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
TOPPREDnone 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--
MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEIARECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGERPCQT
ccHHHHHHHHHHHHHHHHHHccccHHHEEEEEEEccccHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHccccEEEEEccccHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccEEEEEEEcccccccccccHHHHHHHHHHHHHccccEEEEEEccccccccHHHHHHHHHHHHHHccccEEcccccHHHHHHHHccccEEEEcHHHcccccccc
ccHHHHHHHHHHHHHHHHHHHccccccEEEEEEEccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHccccEEEEEcccccccHHHHHHHccEEEcccHHHHHHHHHHHcccccccccEEEEEEcccccccccccHHHHHHHHHHHHHccccEEEEEEccccccccHHHHHHHHHHHHHcccccEEcccccccHHHHHHccccEEEEEHHHcccccccc
MSLGNKLQVFKQKIENSailakrpkdsVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMikqsrflpvyiQVNTGyeiqksgimpnqtKDFVILCRQKYQLNVEglmcippamgnpkphFYLLSEIARECKLTKLSMGMTRDFELAIASGatsvrigsgifgerpcqt
MSLGNKLQVFKQKIensailakrpkdsvSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRKEWDVQLRFIGslqsnkvseIVSLFDVIETVSREKTASllslemikqsrfLPVYIQVNTGYeiqksgimpnQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEIARECKLTKLSMGMTRDFELAIAsgatsvrigsgifgerpcqt
MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEIARECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGERPCQT
MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEIARECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGERP***
MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEIARECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGERPCQT
MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEIARECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGER****
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MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEIARECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGERPCQT
MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEIARECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGERPCQT
MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEIARECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGERPCQT

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
Target222 hypothetical protein CLIBASIA_03460 [Candidatus Liberib
315122023222 hypothetical protein CKC_01365 [Candidatus Liberibacter 1 8e-94
33326392219 hypothetical protein [Agrobacterium vitis] Length = 219 1 2e-61
222150238219 hypothetical protein Avi_4380 [Agrobacterium vitis S4] 1 5e-61
15967083219 hypothetical protein SMc02812 [Sinorhizobium meliloti 1 1 2e-60
116254455219 racemase [Rhizobium leguminosarum bv. viciae 3841] Leng 1 3e-60
190893971219 alanine racemase [Rhizobium etli CIAT 652] Length = 219 1 3e-60
86359693219 hypothetical protein RHE_CH04115 [Rhizobium etli CFN 42 1 7e-60
218510282219 putative alanine racemase protein [Rhizobium etli Brasi 1 8e-60
218461353219 putative alanine racemase protein [Rhizobium etli Kim 5 1 3e-59
222087921219 hypothetical protein Arad_4934 [Agrobacterium radiobact 1 3e-59
>gi|315122023|ref|YP_004062512.1| hypothetical protein CKC_01365 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 222 Back     alignment and organism information
 Score =  347 bits (889), Expect = 8e-94,   Method: Compositional matrix adjust.
 Identities = 169/221 (76%), Positives = 192/221 (86%)

Query: 1   MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQE 60
           MSL +KLQ FKQKI    +LAKR K SVSLVAVSKMVD + I+ ALSCGQ+IFAE+KLQE
Sbjct: 1   MSLEHKLQAFKQKIAYHEMLAKRLKGSVSLVAVSKMVDIQTIQSALSCGQIIFAESKLQE 60

Query: 61  AKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFL 120
           A+KKW  LRKEWD+QLRFIGSLQSNK+SEIVS FDVIETV REK ASLLS+EM KQ  FL
Sbjct: 61  AQKKWSFLRKEWDIQLRFIGSLQSNKISEIVSFFDVIETVDREKIASLLSIEMEKQKCFL 120

Query: 121 PVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEI 180
           P+YIQVNTG E QKSG+MPN+TKDF++LCRQKY+LNVEGLMCIPP   NP PHF LLS+I
Sbjct: 121 PIYIQVNTGCEKQKSGVMPNETKDFIVLCRQKYRLNVEGLMCIPPVTSNPGPHFCLLSKI 180

Query: 181 ARECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGERPCQ 221
           A+EC++TKLSMGMT+D++LAIA GATSVRIGSGIFGER  Q
Sbjct: 181 AKECEITKLSMGMTKDYDLAIAFGATSVRIGSGIFGERSYQ 221


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|33326392|gb|AAQ08613.1| hypothetical protein [Agrobacterium vitis] Length = 219 Back     alignment and organism information
>gi|222150238|ref|YP_002551195.1| hypothetical protein Avi_4380 [Agrobacterium vitis S4] Length = 219 Back     alignment and organism information
>gi|15967083|ref|NP_387436.1| hypothetical protein SMc02812 [Sinorhizobium meliloti 1021] Length = 219 Back     alignment and organism information
>gi|116254455|ref|YP_770293.1| racemase [Rhizobium leguminosarum bv. viciae 3841] Length = 219 Back     alignment and organism information
>gi|190893971|ref|YP_001980513.1| alanine racemase [Rhizobium etli CIAT 652] Length = 219 Back     alignment and organism information
>gi|86359693|ref|YP_471585.1| hypothetical protein RHE_CH04115 [Rhizobium etli CFN 42] Length = 219 Back     alignment and organism information
>gi|218510282|ref|ZP_03508160.1| putative alanine racemase protein [Rhizobium etli Brasil 5] Length = 219 Back     alignment and organism information
>gi|218461353|ref|ZP_03501444.1| putative alanine racemase protein [Rhizobium etli Kim 5] Length = 219 Back     alignment and organism information
>gi|222087921|ref|YP_002546459.1| hypothetical protein Arad_4934 [Agrobacterium radiobacter K84] Length = 219 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
Target222 hypothetical protein CLIBASIA_03460 [Candidatus Liberib
COG0325228 COG0325, COG0325, Predicted enzyme with a TIM-barrel fo 3e-58
cd06824224 cd06824, PLPDE_III_Yggs_like, Pyridoxal 5-phosphate (PL 2e-42
cd06822227 cd06822, PLPDE_III_YBL036c_euk, Pyridoxal 5-phosphate ( 4e-33
TIGR00044229 TIGR00044, TIGR00044, pyridoxal phosphate enzyme, YggS 1e-32
KOG3157244 KOG3157, KOG3157, KOG3157, Proline synthetase co-transc 7e-31
pfam01168216 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal 3e-27
cd00635222 cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-p 1e-64
>gnl|CDD|30673 COG0325, COG0325, Predicted enzyme with a TIM-barrel fold [General function prediction only] Back     alignment and domain information
>gnl|CDD|143497 cd06824, PLPDE_III_Yggs_like, Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins Back     alignment and domain information
>gnl|CDD|143496 cd06822, PLPDE_III_YBL036c_euk, Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins Back     alignment and domain information
>gnl|CDD|129155 TIGR00044, TIGR00044, pyridoxal phosphate enzyme, YggS family Back     alignment and domain information
>gnl|CDD|38367 KOG3157, KOG3157, KOG3157, Proline synthetase co-transcribed protein [General function prediction only] Back     alignment and domain information
>gnl|CDD|144675 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain Back     alignment and domain information
>gnl|CDD|143483 cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 222 hypothetical protein CLIBASIA_03460 [Candidatus Liberib
COG0325228 Predicted enzyme with a TIM-barrel fold [General functi 100.0
cd06824224 PLPDE_III_Yggs_like Pyridoxal 5-phosphate (PLP)-binding 100.0
cd00635222 PLPDE_III_YBL036c_like Type III Pyridoxal 5-phosphate ( 100.0
cd06822227 PLPDE_III_YBL036c_euk Pyridoxal 5-phosphate (PLP)-bindi 100.0
TIGR00044250 TIGR00044 conserved hypothetical protein TIGR00044; Int 100.0
KOG3157244 consensus 100.0
pfam01168216 Ala_racemase_N Alanine racemase, N-terminal domain. 99.98
cd06808211 PLPDE_III Type III Pyridoxal 5-phosphate (PLP)-Dependen 99.78
cd06815 353 PLPDE_III_AR_like_1 Type III Pyridoxal 5-phosphate (PLP 99.7
cd00430 367 PLPDE_III_AR Type III Pyridoxal 5-phosphate (PLP)-Depen 99.55
PRK00053 360 alr alanine racemase; Reviewed 99.39
PRK13340 404 alanine racemase; Reviewed 99.37
PRK11930 824 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D 99.37
cd06826 365 PLPDE_III_AR2 Type III Pyridoxal 5-phosphate (PLP)-Depe 99.32
cd06827 354 PLPDE_III_AR_proteobact Type III Pyridoxal 5-phosphate 99.31
PRK03646 355 dadX alanine racemase; Reviewed 99.29
COG0787 360 Alr Alanine racemase [Cell envelope biogenesis, outer m 99.27
cd06820 353 PLPDE_III_LS_D-TA_like Type III Pyridoxal 5-phosphate ( 99.24
cd06825 368 PLPDE_III_VanT Type III Pyridoxal 5-phosphate (PLP)-Dep 99.24
COG3457 353 Predicted amino acid racemase [Amino acid transport and 99.23
cd06821 361 PLPDE_III_D-TA Type III Pyridoxal 5-phosphate (PLP)-Dep 99.14
TIGR00492 383 alr alanine racemase; InterPro: IPR000821 Alanine racem 99.13
cd06819 358 PLPDE_III_LS_D-TA Type III Pyridoxal 5-phosphate (PLP)- 99.09
cd07376 345 PLPDE_III_DSD_D-TA_like Type III Pyridoxal 5-phosphate 99.05
cd06818 382 PLPDE_III_cryptic_DSD Type III Pyridoxal 5-phosphate (P 98.88
cd06813 388 PLPDE_III_DSD_D-TA_like_2 Type III Pyridoxal 5-phosphat 98.78
cd06812 374 PLPDE_III_DSD_D-TA_like_1 Type III Pyridoxal 5-phosphat 98.78
cd06814 379 PLPDE_III_DSD_D-TA_like_3 Type III Pyridoxal 5-phosphat 98.71
cd06817 389 PLPDE_III_DSD Type III Pyridoxal 5-phosphate (PLP)-Depe 98.54
COG3616 368 Predicted amino acid aldolase or racemase [Amino acid t 98.46
cd06811 382 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP 98.4
cd06843 377 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP 98.61
cd06839 382 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP 98.57
cd06830 409 PLPDE_III_ADC Type III Pyridoxal 5-phosphate (PLP)-Depe 98.44
TIGR01048 431 lysA diaminopimelate decarboxylase; InterPro: IPR002986 98.37
COG0019 394 LysA Diaminopimelate decarboxylase [Amino acid transpor 98.31
cd06828 373 PLPDE_III_DapDC Type III Pyridoxal 5-phosphate (PLP)-De 98.28
cd06841 379 PLPDE_III_MccE_like Type III Pyridoxal 5-phosphate (PLP 98.18
TIGR03099 398 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, exosort 98.12
cd06810 368 PLPDE_III_ODC_DapDC_like Type III Pyridoxal 5-phosphate 98.09
cd06842 423 PLPDE_III_Y4yA_like Type III Pyridoxal 5-phosphate (PLP 98.06
cd06840 368 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate 97.69
pfam02784245 Orn_Arg_deC_N Pyridoxal-dependent decarboxylase, pyrido 97.51
cd00622 362 PLPDE_III_ODC Type III Pyridoxal 5-phosphate (PLP)-Depe 97.5
PRK11165 412 diaminopimelate decarboxylase; Provisional 97.15
PRK08961 865 bifunctional aspartate kinase/diaminopimelate decarboxy 96.89
cd06836 379 PLPDE_III_ODC_DapDC_like_1 Type III Pyridoxal 5-phospha 96.87
cd06831 394 PLPDE_III_ODC_like_AZI Type III Pyridoxal 5-phosphate ( 96.7
KOG0622 448 consensus 92.53
COG1166 652 SpeA Arginine decarboxylase (spermidine biosynthesis) [ 91.0
cd06829 346 PLPDE_III_CANSDC Type III Pyridoxal 5-phosphate (PLP)-D 96.85
PRK00230231 orotidine 5'-phosphate decarboxylase; Reviewed 94.35
>COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only] Back     alignment and domain information
>cd06824 PLPDE_III_Yggs_like Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins Back     alignment and domain information
>cd00635 PLPDE_III_YBL036c_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins Back     alignment and domain information
>cd06822 PLPDE_III_YBL036c_euk Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins Back     alignment and domain information
>TIGR00044 TIGR00044 conserved hypothetical protein TIGR00044; InterPro: IPR011078 Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal) Back     alignment and domain information
>KOG3157 consensus Back     alignment and domain information
>pfam01168 Ala_racemase_N Alanine racemase, N-terminal domain Back     alignment and domain information
>cd06808 PLPDE_III Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Back     alignment and domain information
>cd06815 PLPDE_III_AR_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1 Back     alignment and domain information
>cd00430 PLPDE_III_AR Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase Back     alignment and domain information
>PRK00053 alr alanine racemase; Reviewed Back     alignment and domain information
>PRK13340 alanine racemase; Reviewed Back     alignment and domain information
>PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional Back     alignment and domain information
>cd06826 PLPDE_III_AR2 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2 Back     alignment and domain information
>cd06827 PLPDE_III_AR_proteobact Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases Back     alignment and domain information
>PRK03646 dadX alanine racemase; Reviewed Back     alignment and domain information
>COG0787 Alr Alanine racemase [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>cd06820 PLPDE_III_LS_D-TA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine Aldolase-like Back     alignment and domain information
>cd06825 PLPDE_III_VanT Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, VanT and similar proteins Back     alignment and domain information
>COG3457 Predicted amino acid racemase [Amino acid transport and metabolism] Back     alignment and domain information
>cd06821 PLPDE_III_D-TA Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme D-Threonine Aldolase Back     alignment and domain information
>TIGR00492 alr alanine racemase; InterPro: IPR000821 Alanine racemase catalyses the pyridoxal-dependent conversion of L-alanine into D-alanine, a key component of bacterial peptidoglycan Back     alignment and domain information
>cd06819 PLPDE_III_LS_D-TA Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase Back     alignment and domain information
>cd07376 PLPDE_III_DSD_D-TA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase Back     alignment and domain information
>cd06818 PLPDE_III_cryptic_DSD Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bacterial Cryptic D-Serine Dehydratase Back     alignment and domain information
>cd06813 PLPDE_III_DSD_D-TA_like_2 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 2 Back     alignment and domain information
>cd06812 PLPDE_III_DSD_D-TA_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 1 Back     alignment and domain information
>cd06814 PLPDE_III_DSD_D-TA_like_3 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 3 Back     alignment and domain information
>cd06817 PLPDE_III_DSD Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Eukaryotic D-Serine Dehydratase Back     alignment and domain information
>COG3616 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism] Back     alignment and domain information
>cd06811 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX Back     alignment and domain information
>cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE Back     alignment and domain information
>cd06839 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase Back     alignment and domain information
>cd06830 PLPDE_III_ADC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase Back     alignment and domain information
>TIGR01048 lysA diaminopimelate decarboxylase; InterPro: IPR002986 Pyridoxal-dependent decarboxylases that act on ornithine-, lysine-, arginine- and related substrates can be classified into different families on the basis of sequence similarity , Back     alignment and domain information
>COG0019 LysA Diaminopimelate decarboxylase [Amino acid transport and metabolism] Back     alignment and domain information
>cd06828 PLPDE_III_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase Back     alignment and domain information
>cd06841 PLPDE_III_MccE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE Back     alignment and domain information
>TIGR03099 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, exosortase system type 1 associated Back     alignment and domain information
>cd06810 PLPDE_III_ODC_DapDC_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Ornithine and Diaminopimelate Decarboxylases, and Related Enzymes Back     alignment and domain information
>cd06842 PLPDE_III_Y4yA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Y4yA Back     alignment and domain information
>cd06840 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase Back     alignment and domain information
>pfam02784 Orn_Arg_deC_N Pyridoxal-dependent decarboxylase, pyridoxal binding domain Back     alignment and domain information
>cd00622 PLPDE_III_ODC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase Back     alignment and domain information
>PRK11165 diaminopimelate decarboxylase; Provisional Back     alignment and domain information
>PRK08961 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional Back     alignment and domain information
>cd06836 PLPDE_III_ODC_DapDC_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Uncharacterized Proteins with similarity to Ornithine and Diaminopimelate Decarboxylases Back     alignment and domain information
>cd06831 PLPDE_III_ODC_like_AZI Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase-like Antizyme Inhibitor Back     alignment and domain information
>KOG0622 consensus Back     alignment and domain information
>COG1166 SpeA Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism] Back     alignment and domain information
>cd06829 PLPDE_III_CANSDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase Back     alignment and domain information
>PRK00230 orotidine 5'-phosphate decarboxylase; Reviewed 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
Target222 hypothetical protein CLIBASIA_03460 [Candidatus Liberib
1w8g_A234 Crystal Structure Of E. Coli K-12 Yggs Length = 234 1e-45
3r79_A244 Crystal Structure Of An Uncharactertized Protein Fr 6e-42
3cpg_A282 Crystal Structure Of An Unknown Protein From Bifido 9e-27
1b54_A257 Crystal Structure Of A Yeast Hypothetical Protein-A 3e-26
1ct5_A256 Crystal Structure Of Yeast Hypothetical Protein Ybl 2e-21
gi|112489681|pdb|1W8G|A Chain A, Crystal Structure Of E. Coli K-12 Yggs Length = 234 Back     alignment and structure
 Score =  187 bits (474), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 73/232 (31%), Positives = 111/232 (47%), Gaps = 11/232 (4%)

Query: 1   MS-LGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQ 59
           M+ + + L   + KI  +A    R  + ++L+AVSK   +  I  A+  GQ  F EN +Q
Sbjct: 1   MNDIAHNLAQVRDKISAAATRCGRSPEEITLLAVSKTKPASAIAEAIDAGQRQFGENYVQ 60

Query: 60  EAKKKWIPLRK--EWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQS 117
           E   K    ++     ++  FIG LQSNK   +   FD   T+ R + A+ L+ +   + 
Sbjct: 61  EGVDKIRHFQELGVTGLEWHFIGPLQSNKSRLVAEHFDWCHTIDRLRIATRLNDQRPAEL 120

Query: 118 RFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLL 177
             L V IQ+N   E  KSGI   +  +      +  +L + GLM IP         F + 
Sbjct: 121 PPLNVLIQINISDENSKSGIQLAELDELAAAVAELPRLRLRGLMAIPAPESEYVRQFEVA 180

Query: 178 SEIA--------RECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGERPCQ 221
            ++A        R   +  LS+GM+ D E AIA+G+T VRIG+ IFG R   
Sbjct: 181 RQMAVAFAGLKTRYPHIDTLSLGMSDDMEAAIAAGSTMVRIGTAIFGARDYS 232


>gi|327533820|pdb|3R79|A Chain A, Crystal Structure Of An Uncharactertized Protein From Agrobacterium Tumefaciens Length = 244 Back     alignment and structure
>gi|188036273|pdb|3CPG|A Chain A, Crystal Structure Of An Unknown Protein From Bifidobacterium Adolescentis Length = 282 Back     alignment and structure
gi|157830174|pdb|1B54|A Chain A, Crystal Structure Of A Yeast Hypothetical Protein-A Structure From Bnl's Human Proteome Project Length = 257 Back     alignment and structure
>gi|6137630|pdb|1CT5|A Chain A, Crystal Structure Of Yeast Hypothetical Protein Ybl036c- Selenomet Crystal Length = 256 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target222 hypothetical protein CLIBASIA_03460 [Candidatus Liberib
1ct5_A256 Protein (yeast hypothetical protein, selenoMet); TIM ba 5e-50
3cpg_A282 Uncharacterized protein; unknown protein, TIM barrel, m 3e-45
1w8g_A234 YGGS, hypothetical UPF0001 protein YGGS; structural gen 3e-36
>1ct5_A Protein (yeast hypothetical protein, selenoMet); TIM barrel, pyridoxal-5'-phosphate, selenomethionine, MAD, structural genomics, PSI; HET: PLP; 2.00A {Saccharomyces cerevisiae} SCOP: c.1.6.2 PDB: 1b54_A* Length = 256 Back     alignment and structure
 Score =  192 bits (490), Expect = 5e-50
 Identities = 66/237 (27%), Positives = 101/237 (42%), Gaps = 22/237 (9%)

Query: 3   LGNKLQVFKQKIENSA--ILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQE 60
           L  + +  ++ +   A  +        + L+ VSK+  +  I++    G   F EN +QE
Sbjct: 14  LIAQYESVREVVNAEAKNVHVNENASKILLLVVSKLKPASDIQILYDHGVREFGENYVQE 73

Query: 61  AKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSL--FDVIETVSREKTASLLSLEMIK--- 115
             +K   L    D++  FIG LQ+NK  ++  +     +ET+   K A  L+    K   
Sbjct: 74  LIEKAKLLPD--DIKWHFIGGLQTNKCKDLAKVPNLYSVETIDSLKKAKKLNESRAKFQP 131

Query: 116 QSRFLPVYIQVNTGYEIQKSGIMPNQTKDFV---ILCRQKYQLNVEGLMCIP-----PAM 167
               +   +Q+NT +E QKSG+        V    L  +   + + GLM I         
Sbjct: 132 DCNPILCNVQINTSHEDQKSGLNNEAEIFEVIDFFLSEECKYIKLNGLMTIGSWNVSHED 191

Query: 168 GNPKPHFYLLSEIARECK-----LTKLSMGMTRDFELAIASGATSVRIGSGIFGERP 219
                 F  L E  ++         KLSMGM+ DF  AI  G   VRIG+ IFG RP
Sbjct: 192 SKENRDFATLVEWKKKIDAKFGTSLKLSMGMSADFREAIRQGTAEVRIGTDIFGARP 248


>3cpg_A Uncharacterized protein; unknown protein, TIM barrel, monomer, structural genomics, PSI-2, protein structure initiative; 1.71A {Bifidobacterium adolescentis ATCC15703} Length = 282 Back     alignment and structure
>1w8g_A YGGS, hypothetical UPF0001 protein YGGS; structural genomics, hypothetical protein, putative enzyme with PLP-binding domain; HET: PLP ICT; 2.0A {Escherichia coli} Length = 234 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target222 hypothetical protein CLIBASIA_03460 [Candidatus Liberib
3cpg_A282 Uncharacterized protein; unknown protein, TIM barrel, m 100.0
1w8g_A234 YGGS, hypothetical UPF0001 protein YGGS; structural gen 100.0
1ct5_A256 Protein (yeast hypothetical protein, selenoMet); TIM ba 100.0
3kw3_A 376 Alanine racemase; niaid, ssgcid, seattle structural gen 99.58
1xfc_A 384 Alanine racemase; alpha-beta barrel, beta-structure for 99.57
3e5p_A 371 Alanine racemase; ALR, PLP, SCP, isomerase, pyridoxal p 99.46
2vd8_A 391 Alanine racemase; pyridoxal 5'-phosphate, peptidoglycan 99.46
1vfs_A 386 Alanine racemase; TIM-barrel, greek-KEY motief, isomera 99.45
1bd0_A 388 Alanine racemase; isomerase, pyridoxal phosphate, alani 99.42
3llx_A 376 Predicted amino acid aldolase or racemase; structural g 99.41
1rcq_A 357 Catabolic alanine racemase DADX; alpha-beta barrel, bet 99.39
2dy3_A 361 Alanine racemase; alpha/beta barrel, isomerase; HET: PL 99.36
3co8_A 380 Alanine racemase; protein structure initiative II, PSI- 99.32
3oo2_A 385 Alanine racemase 1; infectious diseases, center for str 99.24
3gwq_A 426 D-serine deaminase; YP_556991.1, structural genomics, j 99.24
3hur_A 395 Alanine racemase; structural genomics, isomerase, pyrid 99.24
2rjg_A 379 Alanine racemase; alpha/beta barrel, cell shape, cell W 99.11
2p3e_A 420 Diaminopimelate decarboxylase; southeast collaboratory 97.9
3n2o_A 648 ADC, biosynthetic arginine decarboxylase; lyase; HET: P 97.85
3nzq_A 666 ADC, biosynthetic arginine decarboxylase; alpha-beta pr 97.85
3n2b_A 441 Diaminopimelate decarboxylase; LYSA, lyase, structural 97.77
2qgh_A 425 Diaminopimelate decarboxylase; lyase; HET: PLP LYS; 2.3 97.59
3nzp_A 619 Arginine decarboxylase; alpha-beta protein, structural 97.59
2j66_A 428 BTRK, decarboxylase; butirosin, AHBA biosynthesis, lyas 97.19
2plj_A 419 Lysine/ornithine decarboxylase; type IV decarboxylase, 97.14
3btn_A 448 Antizyme inhibitor 1; TIM-like A/B barrel domain and A 96.54
1f3t_A 425 ODC, ornithine decarboxylase; beta-alpha-barrel, modifi 96.53
1twi_A 434 Diaminopimelate decarboxylase; antibiotic resistance, l 96.42
7odc_A 424 Protein (ornithine decarboxylase); pyridoxal-5'-phospha 96.12
2o0t_A 467 Diaminopimelate decarboxylase; PLP binding enzyme, lysi 95.86
2oo0_A 471 ODC, ornithine decarboxylase; beta-alpha barrel, sheet, 94.99
2nva_A 372 Arginine decarboxylase, A207R protein; PLP, TIM barrel, 94.37
3mt1_A 365 Putative carboxynorspermidine decarboxylase prote; PSI2 91.01
3n29_A 418 Carboxynorspermidine decarboxylase; lyase; HET: PLP; 1. 95.5
1h1y_A228 D-ribulose-5-phosphate 3-epimerase; oxidative pentose p 91.24
3ajx_A207 3-hexulose-6-phosphate synthase; HPS, OMPDC suprafamily 91.0
>3cpg_A Uncharacterized protein; unknown protein, TIM barrel, monomer, structural genomics, PSI-2, protein structure initiative; 1.71A {Bifidobacterium adolescentis ATCC15703} Back     alignment and structure
Probab=100.00  E-value=0  Score=587.51  Aligned_cols=220  Identities=30%  Similarity=0.403  Sum_probs=210.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCHHHCEEEEECCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCC-----------
Q ss_conf             989999999999999999819896441899871899999999999729810001210001111000001-----------
Q gi|254780801|r    2 SLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRK-----------   70 (222)
Q Consensus         2 ~i~~nl~~i~~~I~~a~~~~gR~~~~v~LiaVtK~~~~e~I~~~~~~G~~~fGENrvQE~~~K~~~l~~-----------   70 (222)
                      .|++||+.|+++|++||.++||+|++|+|||||||+|+++|.++|++|+++||||||||+.+|+..|++           
T Consensus        24 ~i~~nl~~V~~rI~~A~~~agR~p~~V~LiAVSK~~p~e~I~~a~~~G~r~FGENrvQE~~~K~~~l~~~~~~~~~~~~~  103 (282)
T 3cpg_A           24 EITDGVHRVLDRIAAAEEQAGREAGSVRLLAATKTRDIGEIMAAIDAGVRMIGENRPQEVTAKAEGLARRCAERGFSLGV  103 (282)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCCTTSSEEEEECTTCCHHHHHHHHHTTCCCEEESCHHHHHHHHHHHHHHHHHTTEEECC
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             99999999999999999982989366599999899899999999986997036870899999999987641000122222


Q ss_pred             --------CCCCCEEEECCCCCCHHHHHCCCCHHCCCCCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCCCCHH
Q ss_conf             --------258730230244320013201110000122222001344333333114303688970046656346570001
Q gi|254780801|r   71 --------EWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQT  142 (222)
Q Consensus        71 --------~~~i~wHfIG~LQsNKvk~i~~~~~~Ihsvds~~~a~~L~~~~~~~~~~~~vliQVN~~~e~~K~G~~p~el  142 (222)
                              ..+|+|||||||||||+|+++++|+|||||||+++|++|++++.+.+++++||||||+++|++|+||.|+++
T Consensus       104 ~~~~~~~~~~~I~WHfIG~LQsNKvk~iv~~~~~IhSVDs~kla~~l~~~a~~~~~~~~vlIQVNis~E~sK~G~~p~e~  183 (282)
T 3cpg_A          104 AGAAPDAAAEHIPFHLIGQLQSNKIGKVLPVVDTIESVDSIDLAEKISRRAVARGITVGVLLEVNESGEESKSGCDPAHA  183 (282)
T ss_dssp             C------CCEEECEEECSCCCGGGHHHHTTTCSEEEEECCHHHHHHHHHHHHHHTCCEEEEEEBCCSSCTTSSSBCGGGH
T ss_pred             CCCCCCCCCCCEEEEEECCCCHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCHHHH
T ss_conf             23444456777269994464200077765106466542564305889988762476616999962587756688787779


Q ss_pred             HHHHHHHHCCCCCCHHHHEECCCCCCCC---HHHHHHHHHHHHHC---------CCCEECCCCCHHHHHHHHHCCCEEEE
Q ss_conf             2223443104311001110115433452---05899999998875---------89472247773489999808988997
Q gi|254780801|r  143 KDFVILCRQKYQLNVEGLMCIPPAMGNP---KPHFYLLSEIAREC---------KLTKLSMGMTRDFELAIASGATSVRI  210 (222)
Q Consensus       143 ~~l~~~i~~~~~L~i~GLMti~p~~~d~---~~~F~~l~~l~~~~---------~~~~LSmGMS~D~~~Ai~~Gst~vRi  210 (222)
                      .++++.+..+++|+++|||||||++.|+   +++|..|+++++.+         ++++||||||+||++||++|||||||
T Consensus       184 ~~l~~~i~~~~~l~l~GLMti~p~~~d~~~~r~~F~~l~~l~d~l~~~~~~~~~~~~~LSMGMS~Dye~AIe~GST~VRI  263 (282)
T 3cpg_A          184 IRIAQKIGTLDGIELQGLMTIGAHVHDETVIRRGFSHLRKTRDLILASGEPGTDRCRELSMGMTGDMELAIAEGSTIVRV  263 (282)
T ss_dssp             HHHHHHHHTCTTEEEEEEECCCCCSSCHHHHHHHHHHHHHHHHHHHHHCCTTCTTCCEEECCCTTTHHHHHHTTCSEEEE
T ss_pred             HHHHHHHHHHCCHHCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEECHHHHHHHHHHHCCCCEEEC
T ss_conf             99999986510010221786368888877899999999999999998568877998988170077999999869997980


Q ss_pred             CHHHCCCCCCC
Q ss_conf             11323899999
Q gi|254780801|r  211 GSGIFGERPCQ  221 (222)
Q Consensus       211 Gs~iFG~R~~~  221 (222)
                      ||+|||+|.|.
T Consensus       264 GsaIFG~R~y~  274 (282)
T 3cpg_A          264 GTAIFGERAFI  274 (282)
T ss_dssp             STTTC------
T ss_pred             CCCCCCCCCCC
T ss_conf             86523498887



>1w8g_A YGGS, hypothetical UPF0001 protein YGGS; structural genomics, hypothetical protein, putative enzyme with PLP-binding domain; HET: PLP ICT; 2.0A {Escherichia coli} Back     alignment and structure
>1ct5_A Protein (yeast hypothetical protein, selenoMet); TIM barrel, pyridoxal-5'-phosphate, selenomethionine, MAD, structural genomics, PSI; HET: PLP; 2.00A {Saccharomyces cerevisiae} SCOP: c.1.6.2 PDB: 1b54_A* Back     alignment and structure
>3kw3_A Alanine racemase; niaid, ssgcid, seattle structural genomics center for infectious disease, iodide SOAK, LLP, CAT-scratch disease; HET: LLP; 2.04A {Bartonella henselae} Back     alignment and structure
>1xfc_A Alanine racemase; alpha-beta barrel, beta-structure for C-terminal domain, internal aldimine form, isomerase; HET: PLP; 1.90A {Mycobacterium tuberculosis} Back     alignment and structure
>3e5p_A Alanine racemase; ALR, PLP, SCP, isomerase, pyridoxal phosphate; HET: PLP EPE 2PE; 2.50A {Enterococcus faecalis} PDB: 3e6e_A* Back     alignment and structure
>2vd8_A Alanine racemase; pyridoxal 5'-phosphate, peptidoglycan synthesis, PLP, OPPF, L-alanine, isomerase, D- alanine, pyridoxal phosphate; HET: MLY LLP; 1.47A {Bacillus anthracis} PDB: 2vd9_A* 3ha1_A* Back     alignment and structure
>1vfs_A Alanine racemase; TIM-barrel, greek-KEY motief, isomerase; HET: KCX DCS; 1.90A {Streptomyces lavendulae} SCOP: b.49.2.2 c.1.6.1 PDB: 1vfh_A* 1vft_A* Back     alignment and structure
>1bd0_A Alanine racemase; isomerase, pyridoxal phosphate, alanine phosphonate; HET: IN5; 1.60A {Geobacillus stearothermophilus} SCOP: b.49.2.2 c.1.6.1 PDB: 1sft_A* 2sfp_A* 1l6g_A* 1niu_A* 1l6f_A* 1xql_A* 1xqk_A* 1epv_A* 1ftx_A* Back     alignment and structure
>3llx_A Predicted amino acid aldolase or racemase; structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: LLP TRS; 1.50A {Idiomarina loihiensis} Back     alignment and structure
>1rcq_A Catabolic alanine racemase DADX; alpha-beta barrel, beta-structure for C-terminal domain, internal/external aldimine forms, isomerase; HET: KCX PLP DLY; 1.45A {Pseudomonas aeruginosa} SCOP: b.49.2.2 c.1.6.1 PDB: 2odo_A* Back     alignment and structure
>2dy3_A Alanine racemase; alpha/beta barrel, isomerase; HET: PLP; 2.10A {Corynebacterium glutamicum} Back     alignment and structure
>3co8_A Alanine racemase; protein structure initiative II, PSI-II, NYSGXRC, PLP, TIM barrel, structural genomics; HET: PLP; 1.70A {Oenococcus oeni psu-1} Back     alignment and structure
>3oo2_A Alanine racemase 1; infectious diseases, center for structural of infectious diseases (csgid); 2.37A {Staphylococcus aureus subsp} Back     alignment and structure
>3gwq_A D-serine deaminase; YP_556991.1, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: MSE; 2.00A {Burkholderia xenovorans LB400} Back     alignment and structure
>3hur_A Alanine racemase; structural genomics, isomerase, pyridoxal phosphate, PSI-2, protein structure initiative; 2.50A {Oenococcus oeni psu-1} Back     alignment and structure
>2rjg_A Alanine racemase; alpha/beta barrel, cell shape, cell WALL biogenesis/degradation, isomerase, peptidoglycan synthesis, pyridoxal phosphate; HET: KCX PLP; 2.40A {Escherichia coli} PDB: 2rjh_A* 3b8v_A* 3b8u_A* 3b8t_A* 3b8w_A* Back     alignment and structure
>2p3e_A Diaminopimelate decarboxylase; southeast collaboratory for structural genomics, riken spring-8 center, riken genomic sciences center; 1.99A {Aquifex aeolicus VF5} Back     alignment and structure
>3n2o_A ADC, biosynthetic arginine decarboxylase; lyase; HET: PLP; 2.30A {Vibrio vulnificus} Back     alignment and structure
>3nzq_A ADC, biosynthetic arginine decarboxylase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; 3.10A {Escherichia coli} Back     alignment and structure
>3n2b_A Diaminopimelate decarboxylase; LYSA, lyase, structural genom center for structural genomics of infectious diseases, CSGI; 1.80A {Vibrio cholerae} Back     alignment and structure
>2qgh_A Diaminopimelate decarboxylase; lyase; HET: PLP LYS; 2.30A {Helicobacter pylori} PDB: 3c5q_A* Back     alignment and structure
>3nzp_A Arginine decarboxylase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: PLP; 3.00A {Campylobacter jejuni subsp} Back     alignment and structure
>2j66_A BTRK, decarboxylase; butirosin, AHBA biosynthesis, lyase; HET: PLP; 1.65A {Bacillus circulans} Back     alignment and structure
>2plj_A Lysine/ornithine decarboxylase; type IV decarboxylase, beta/alpha barrel, beta barrel, lyase; HET: P3T; 1.70A {Vibrio vulnificus CMCP6} PDB: 2plk_A* Back     alignment and structure
>3btn_A Antizyme inhibitor 1; TIM-like A/B barrel domain and A sheet domain, structural genomics, israel structural proteomics center, ISPC; 2.05A {Mus musculus} Back     alignment and structure
>1f3t_A ODC, ornithine decarboxylase; beta-alpha-barrel, modified greek KEY beta-sheet, lyase; HET: PLP; 2.00A {Trypanosoma brucei} SCOP: b.49.2.3 c.1.6.1 PDB: 1qu4_A* 1szr_C* 2tod_A* 1njj_A* Back     alignment and structure
>1twi_A Diaminopimelate decarboxylase; antibiotic resistance, lysine biosynthesis, structural genomics, NYSGXRC, PSI; HET: LYS PLP; 2.00A {Methanocaldococcus jannaschii} SCOP: b.49.2.3 c.1.6.1 PDB: 1tuf_A* Back     alignment and structure
>7odc_A Protein (ornithine decarboxylase); pyridoxal-5'-phosphate, PLP, group IV decarboxylase, polyamines, parasitical, chemotherapy target, putrescine; HET: PLP; 1.60A {Mus musculus} SCOP: b.49.2.3 c.1.6.1 PDB: 2on3_A 1d7k_A* Back     alignment and structure
>2o0t_A Diaminopimelate decarboxylase; PLP binding enzyme, lysine biosynthesis, structural genomics, TB structural genomics consortium; HET: LLP; 2.33A {Mycobacterium tuberculosis H37RV} PDB: 1hkv_A* 1hkw_A Back     alignment and structure
>2oo0_A ODC, ornithine decarboxylase; beta-alpha barrel, sheet, lyase; HET: PLP; 1.90A {Homo sapiens} Back     alignment and structure
>2nva_A Arginine decarboxylase, A207R protein; PLP, TIM barrel, eukaryotic ODC- like, lyase; HET: PL2; 1.80A {Paramecium bursaria chlorella virus 1} PDB: 2nv9_A* Back     alignment and structure
>3mt1_A Putative carboxynorspermidine decarboxylase prote; PSI2, MCSG, structural genomics; 2.50A {Sinorhizobium meliloti} Back     alignment and structure
>3n29_A Carboxynorspermidine decarboxylase; lyase; HET: PLP; 1.90A {Campylobacter jejuni subsp} Back     alignment and structure
>1h1y_A D-ribulose-5-phosphate 3-epimerase; oxidative pentose phosphate pathway, isomerase; 1.87A {Oryza sativa} SCOP: c.1.2.2 PDB: 1h1z_A Back     alignment and structure
>3ajx_A 3-hexulose-6-phosphate synthase; HPS, OMPDC suprafamily, LYA; 1.60A {Mycobacterium gastri} 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 222 hypothetical protein CLIBASIA_03460 [Candidatus Liberib
d1ct5a_244 c.1.6.2 (A:) "Hypothetical" protein ybl036c {Baker's ye 2e-27
>d1ct5a_ c.1.6.2 (A:) "Hypothetical" protein ybl036c {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 244 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: PLP-binding barrel
family: "Hypothetical" protein ybl036c
domain: "Hypothetical" protein ybl036c
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
 Score =  115 bits (289), Expect = 2e-27
 Identities = 56/234 (23%), Positives = 93/234 (39%), Gaps = 22/234 (9%)

Query: 3   LGNKLQVFKQKIENSA--ILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQE 60
           L  + +  ++ +   A  +        + L+ VSK+  +  I++    G   F EN +Q 
Sbjct: 13  LIAQYESVREVVNAEAKNVHVNENASKILLLVVSKLKPASDIQILYDHGVREFGENYVQ- 71

Query: 61  AKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRF- 119
            +          D++  FIG LQ+NK  ++  + ++    + +       L   +     
Sbjct: 72  -ELIEKAKLLPDDIKWHFIGGLQTNKCKDLAKVPNLYSVETIDSLKKAKKLNESRAKFQP 130

Query: 120 ----LPVYIQVNTGYEIQKSGIMP----NQTKDFVILCRQKY----QLNVEGLMCIPPAM 167
               +   +Q+NT +E QKSG+       +  DF +    KY     L   G   +    
Sbjct: 131 DCNPILCNVQINTSHEDQKSGLNNEAEIFEVIDFFLSEECKYIKLNGLMTIGSWNVSHED 190

Query: 168 GNPKPHFYLLSEIARECKL-----TKLSMGMTRDFELAIASGATSVRIGSGIFG 216
                 F  L E  ++         KLSMGM+ DF  AI  G   VRIG+ IFG
Sbjct: 191 SKENRDFATLVEWKKKIDAKFGTSLKLSMGMSADFREAIRQGTAEVRIGTDIFG 244


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

IdentityAlignment graphLength Definition Probability
Target222 hypothetical protein CLIBASIA_03460 [Candidatus Liberib
d1ct5a_244 "Hypothetical" protein ybl036c {Baker's yeast (Saccharo 100.0
d1vfsa2237 Alanine racemase {Streptomyces lavendulae [TaxId: 1914] 99.58
d1bd0a2233 Alanine racemase {Bacillus stearothermophilus [TaxId: 1 99.55
d1rcqa2226 Alanine racemase {Pseudomonas aeruginosa [TaxId: 287]} 99.47
d1twia2264 Diaminopimelate decarboxylase LysA {Archaeon Methanococ 97.68
d1hkva2265 Diaminopimelate decarboxylase LysA {Mycobacterium tuber 97.62
d1knwa2247 Diaminopimelate decarboxylase LysA {Escherichia coli [T 95.88
d1f3ta2240 Eukaryotic ornithine decarboxylase {Trypanosoma brucei 96.86
d7odca2240 Eukaryotic ornithine decarboxylase {Mouse (Mus musculus 95.98
>d1ct5a_ c.1.6.2 (A:) "Hypothetical" protein ybl036c {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: PLP-binding barrel
family: "Hypothetical" protein ybl036c
domain: "Hypothetical" protein ybl036c
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
Probab=100.00  E-value=0  Score=517.41  Aligned_cols=212  Identities=29%  Similarity=0.369  Sum_probs=194.1

Q ss_pred             HHHHHHHHHHHHHHHHHH--CCCCHHHCEEEEECCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEEEEC
Q ss_conf             899999999999999998--198964418998718999999999997298100012100011110000012587302302
Q gi|254780801|r    3 LGNKLQVFKQKIENSAIL--AKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPLRKEWDVQLRFIG   80 (222)
Q Consensus         3 i~~nl~~i~~~I~~a~~~--~gR~~~~v~LiaVtK~~~~e~I~~~~~~G~~~fGENrvQE~~~K~~~l~~~~~i~wHfIG   80 (222)
                      |..||+.|+++|+.+|+.  +||+|.+|+|||||||+|+++|+.+|++|+++|||||+||+.+|+..+++  +++|||||
T Consensus        13 i~~~~~~i~~~I~~~~~~~~~~r~~~~V~LiaVsK~~~~~~I~~~~~~G~~~fGENrvQE~~~K~~~l~~--~i~wHfIG   90 (244)
T d1ct5a_          13 LIAQYESVREVVNAEAKNVHVNENASKILLLVVSKLKPASDIQILYDHGVREFGENYVQELIEKAKLLPD--DIKWHFIG   90 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHTC-------CCEEEEECTTSCHHHHHHHHHHTCCEEEECCHHHHHHHHHHSCT--TCEEEECS
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCHHHHHHHHHCCCCHHHCCHHHHHHHHCCCCCC--CEEEEEEC
T ss_conf             9999999999999998876538997866999998999999999999849861200404556542012322--01212224


Q ss_pred             CCCCCHHHHHCCCC--HHCCCCCCCCHHHHHHHHHHHHCC---CEEEEEEEECCCCCCCCCCCCC-HHHHHHHHH--HCC
Q ss_conf             44320013201110--000122222001344333333114---3036889700466563465700-012223443--104
Q gi|254780801|r   81 SLQSNKVSEIVSLF--DVIETVSREKTASLLSLEMIKQSR---FLPVYIQVNTGYEIQKSGIMPN-QTKDFVILC--RQK  152 (222)
Q Consensus        81 ~LQsNKvk~i~~~~--~~Ihsvds~~~a~~L~~~~~~~~~---~~~vliQVN~~~e~~K~G~~p~-el~~l~~~i--~~~  152 (222)
                      ||||||+|++++++  |+||||||++++++|++.+.+.++   +++||||||+++|++|+||.|+ ++.++++.+  ..+
T Consensus        91 ~LQsNKvk~i~~~~~~~~I~svds~kla~~l~~~~~~~~~~~~~~~~~iQVNi~~e~~KsG~~~~~~l~~~~~~~~~~~~  170 (244)
T d1ct5a_          91 GLQTNKCKDLAKVPNLYSVETIDSLKKAKKLNESRAKFQPDCNPILCNVQINTSHEDQKSGLNNEAEIFEVIDFFLSEEC  170 (244)
T ss_dssp             CCCGGGHHHHHHCTTEEEEEEECSHHHHHHHHHHHHHHCTTSCCEEEEEEBCCSSSCCSSSBCCHHHHHHHHHHHHSTTC
T ss_pred             CCCCCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             55512399999733643333100012046777887653113576226776513666666787957899999999999755


Q ss_pred             CCCCHHHHEECCCCCCC-----CHHHHHHHHHHHHHCC-----CCEECCCCCHHHHHHHHHCCCEEEECHHHCC
Q ss_conf             31100111011543345-----2058999999988758-----9472247773489999808988997113238
Q gi|254780801|r  153 YQLNVEGLMCIPPAMGN-----PKPHFYLLSEIARECK-----LTKLSMGMTRDFELAIASGATSVRIGSGIFG  216 (222)
Q Consensus       153 ~~L~i~GLMti~p~~~d-----~~~~F~~l~~l~~~~~-----~~~LSmGMS~D~~~Ai~~Gst~vRiGs~iFG  216 (222)
                      ++|+++|||||||...+     ++.+|..++++++++.     ..+||||||+||++||++|||||||||+|||
T Consensus       171 ~~l~l~GLM~i~p~~~~~~~~~~~~~F~~l~~l~~~l~~~~~~~~~LSMGMS~Dye~AI~~GsT~VRIGs~iFG  244 (244)
T d1ct5a_         171 KYIKLNGLMTIGSWNVSHEDSKENRDFATLVEWKKKIDAKFGTSLKLSMGMSADFREAIRQGTAEVRIGTDIFG  244 (244)
T ss_dssp             CSEEEEEEECCCCCC---------HHHHHHHHHHHHHHHHHCCCCEEECCCTTTHHHHHHTTCSEEEESHHHHC
T ss_pred             CCCHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEECHHHHHHHHHHHCCCCEEECCCHHCC
T ss_conf             62102054333467888034578899999999999983537997977175454699999879997984723109



>d1vfsa2 c.1.6.1 (A:13-249) Alanine racemase {Streptomyces lavendulae [TaxId: 1914]} Back     information, alignment and structure
>d1bd0a2 c.1.6.1 (A:12-244) Alanine racemase {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1rcqa2 c.1.6.1 (A:8-233) Alanine racemase {Pseudomonas aeruginosa [TaxId: 287]} Back     information, alignment and structure
>d1twia2 c.1.6.1 (A:50-313) Diaminopimelate decarboxylase LysA {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1hkva2 c.1.6.1 (A:46-310) Diaminopimelate decarboxylase LysA {Mycobacterium tuberculosis [TaxId: 1773]} Back     information, alignment and structure
>d1knwa2 c.1.6.1 (A:32-278) Diaminopimelate decarboxylase LysA {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1f3ta2 c.1.6.1 (A:44-283) Eukaryotic ornithine decarboxylase {Trypanosoma brucei [TaxId: 5691]} Back     information, alignment and structure
>d7odca2 c.1.6.1 (A:44-283) Eukaryotic ornithine decarboxylase {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 222 hypothetical protein CLIBASIA_03460 [Candidatus Li
1ct5_A_256 (A:) Protein (yeast hypothetical protein, selenoMe 1e-31
3kw3_A_27-241215 (A:27-241) Alanine racemase; niaid, ssgcid, seattl 7e-27
3cpg_A_282 (A:) Uncharacterized protein; unknown protein, TIM 1e-23
2vd8_A_19-239221 (A:19-239) Alanine racemase; pyridoxal 5'-phosphat 6e-23
1w8g_A_234 (A:) YGGS, hypothetical UPF0001 protein YGGS; stru 7e-23
3llx_A_22-239218 (A:22-239) Predicted amino acid aldolase or racema 2e-21
2dy3_A_10-225216 (A:10-225) Alanine racemase; alpha/beta barrel, is 3e-21
2rjg_A_31-242212 (A:31-242) Alanine racemase; alpha/beta barrel, ce 3e-21
3hur_A_16-238_376-395243 (A:16-238,A:376-395) Alanine racemase; structural 9e-21
3e5p_A_15-235221 (A:15-235) Alanine racemase; ALR, PLP, SCP, isomer 2e-20
3co8_A_16-235220 (A:16-235) Alanine racemase; protein structure ini 3e-20
1bd0_A_15-232218 (A:15-232) Alanine racemase; isomerase, pyridoxal 5e-20
1xfc_A_19-240222 (A:19-240) Alanine racemase; alpha-beta barrel, be 8e-19
1vfs_A_15-237223 (A:15-237) Alanine racemase; TIM-barrel, greek-KEY 2e-18
1rcq_A_11-221211 (A:11-221) Catabolic alanine racemase DADX; alpha- 7e-18
3gwq_A_72-295224 (A:72-295) D-serine deaminase; YP_556991.1, struct 2e-17
>1ct5_A (A:) Protein (yeast hypothetical protein, selenoMet); TIM barrel, pyridoxal-5'-phosphate, selenomethionine, MAD, structural genomics, PSI; HET: PLP; 2.00A {Saccharomyces cerevisiae}Length = 256 Back     alignment and structure
 Score =  130 bits (328), Expect = 1e-31
 Identities = 55/231 (23%), Positives = 85/231 (36%), Gaps = 18/231 (7%)

Query: 7   LQVFKQKIENSAILA--KRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKK 64
            +  ++ +   A           + L+ VSK+  +  I++    G   F EN +QE  +K
Sbjct: 18  YESVREVVNAEAKNVHVNENASKILLLVVSKLKPASDIQILYDHGVREFGENYVQELIEK 77

Query: 65  WIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSL---EMIKQSRFLP 121
              L  +              K    V     +ET+   K A  L+    +       + 
Sbjct: 78  AKLLPDDIKWHFIGGLQTNKCKDLAKVPNLYSVETIDSLKKAKKLNESRAKFQPDCNPIL 137

Query: 122 VYIQVNTGYEIQKSGIMPNQTKDFV---ILCRQKYQLNVEGLMCIPPAMGNP-----KPH 173
             +Q+NT +E QKSG+        V    L  +   + + GL  I     +         
Sbjct: 138 CNVQINTSHEDQKSGLNNEAEIFEVIDFFLSEECKYIKLNGLXTIGSWNVSHEDSKENRD 197

Query: 174 FYLLSEIARECK-----LTKLSMGMTRDFELAIASGATSVRIGSGIFGERP 219
           F  L E  ++         KLS G + DF  AI  G   VRIG+ IFG RP
Sbjct: 198 FATLVEWKKKIDAKFGTSLKLSXGXSADFREAIRQGTAEVRIGTDIFGARP 248


>3kw3_A (A:27-241) Alanine racemase; niaid, ssgcid, seattle structural genomics center for infectious disease, iodide SOAK, LLP, CAT-scratch disease; HET: LLP; 2.04A {Bartonella henselae}Length = 215 Back     alignment and structure
>3cpg_A (A:) Uncharacterized protein; unknown protein, TIM barrel, monomer, structural genomics, PSI-2, protein structure initiative; 1.71A {Bifidobacterium adolescentis ATCC15703}Length = 282 Back     alignment and structure
>2vd8_A (A:19-239) Alanine racemase; pyridoxal 5'-phosphate, peptidoglycan synthesis, PLP, OPPF, L-alanine, isomerase, D- alanine, pyridoxal phosphate; HET: MLY LLP; 1.47A {Bacillus anthracis} PDB: 2vd9_A*Length = 221 Back     alignment and structure
>1w8g_A (A:) YGGS, hypothetical UPF0001 protein YGGS; structural genomics, hypothetical protein, putative enzyme with PLP-binding domain; HET: PLP ICT; 2.0A {Escherichia coli}Length = 234 Back     alignment and structure
>3llx_A (A:22-239) Predicted amino acid aldolase or racemase; structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: LLP TRS; 1.50A {Idiomarina loihiensis}Length = 218 Back     alignment and structure
>2dy3_A (A:10-225) Alanine racemase; alpha/beta barrel, isomerase; HET: PLP; 2.10A {Corynebacterium glutamicum}Length = 216 Back     alignment and structure
>2rjg_A (A:31-242) Alanine racemase; alpha/beta barrel, cell shape, cell WALL biogenesis/degradation, isomerase, peptidoglycan synthesis, pyridoxal phosphate; HET: KCX PLP; 2.40A {Escherichia coli} PDB: 2rjh_A* 3b8v_A* 3b8u_A* 3b8t_A* 3b8w_A*Length = 212 Back     alignment and structure
>3hur_A (A:16-238,A:376-395) Alanine racemase; structural genomics, isomerase, pyridoxal phosphate, PSI-2, protein structure initiative; 2.50A {Oenococcus oeni psu-1}Length = 243 Back     alignment and structure
>3e5p_A (A:15-235) Alanine racemase; ALR, PLP, SCP, isomerase, pyridoxal phosphate; HET: PLP EPE 2PE; 2.50A {Enterococcus faecalis} PDB: 3e6e_A*Length = 221 Back     alignment and structure
>3co8_A (A:16-235) Alanine racemase; protein structure initiative II, PSI-II, NYSGXRC, PLP, TIM barrel, structural genomics; HET: PLP; 1.70A {Oenococcus oeni psu-1}Length = 220 Back     alignment and structure
>1bd0_A (A:15-232) Alanine racemase; isomerase, pyridoxal phosphate, alanine phosphonate; HET: IN5; 1.60A {Bacillus stearothermophilus}Length = 218 Back     alignment and structure
>1xfc_A (A:19-240) Alanine racemase; alpha-beta barrel, beta-structure for C-terminal domain, internal aldimine form, isomerase; HET: PLP; 1.90A {Mycobacterium tuberculosis}Length = 222 Back     alignment and structure
>1vfs_A (A:15-237) Alanine racemase; TIM-barrel, greek-KEY motief, isomerase; HET: KCX DCS; 1.90A {Streptomyces lavendulae}Length = 223 Back     alignment and structure
>1rcq_A (A:11-221) Catabolic alanine racemase DADX; alpha-beta barrel, beta-structure for C-terminal domain, internal/external aldimine forms, isomerase; HET: KCX PLP DLY; 1.45A {Pseudomonas aeruginosa}Length = 211 Back     alignment and structure
>3gwq_A (A:72-295) D-serine deaminase; YP_556991.1, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: MSE; 2.00A {Burkholderia xenovorans LB400}Length = 224 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target222 hypothetical protein CLIBASIA_03460 [Candidatus Liberib
2vd8_A_19-239221 Alanine racemase; pyridoxal 5'-phosphate, peptidog 99.97
1ct5_A_256 Protein (yeast hypothetical protein, selenoMet); T 99.97
3cpg_A_282 Uncharacterized protein; unknown protein, TIM barr 99.96
1w8g_A_234 YGGS, hypothetical UPF0001 protein YGGS; structura 99.92
3kw3_A_27-241215 Alanine racemase; niaid, ssgcid, seattle structura 99.92
1rcq_A_11-221211 Catabolic alanine racemase DADX; alpha-beta barrel 99.91
3llx_A_22-239218 Predicted amino acid aldolase or racemase; structu 99.88
3co8_A_16-235220 Alanine racemase; protein structure initiative II, 99.86
1vfs_A_15-237223 Alanine racemase; TIM-barrel, greek-KEY motief, is 99.86
3e5p_A_15-235221 Alanine racemase; ALR, PLP, SCP, isomerase, pyrido 99.85
1xfc_A_19-240222 Alanine racemase; alpha-beta barrel, beta-structur 99.84
2rjg_A_31-242212 Alanine racemase; alpha/beta barrel, cell shape, c 99.82
1bd0_A_15-232218 Alanine racemase; isomerase, pyridoxal phosphate, 99.8
2dy3_A_10-225216 Alanine racemase; alpha/beta barrel, isomerase; HE 99.79
3hur_A_16-238_376-395243 Alanine racemase; structural genomics, isomerase, 99.66
2p3e_A_42-284243 Diaminopimelate decarboxylase; southeast collabora 99.47
3gwq_A_72-295224 D-serine deaminase; YP_556991.1, structural genomi 99.37
2plj_A_63-295233 Lysine/ornithine decarboxylase; type IV decarboxyl 98.66
2j66_A_40-274235 BTRK, decarboxylase; butirosin, AHBA biosynthesis, 98.4
2qgh_A_19-262244 Diaminopimelate decarboxylase; lyase; HET: PLP LYS 98.12
1twi_A_38-295258 Diaminopimelate decarboxylase; antibiotic resistan 98.58
2o0t_A_50-307258 Diaminopimelate decarboxylase; PLP binding enzyme, 98.32
2nva_A_25-257233 Arginine decarboxylase, A207R protein; PLP, TIM ba 97.84
1f3t_A_46-279234 ODC, ornithine decarboxylase; beta-alpha-barrel, m 97.81
1knw_A_34-273240 Diaminopimelate decarboxylase; pyridoxal-phosphate 96.98
2yxx_A_21-251231 Diaminopimelate decarboxylase; TM1517, TIM beta/al 96.9
3btn_A_61-276216 Antizyme inhibitor 1; TIM-like A/B barrel domain a 96.39
2oo0_A_71-289219 ODC, ornithine decarboxylase; beta-alpha barrel, s 95.48
7odc_A_61-279219 Protein (ornithine decarboxylase); pyridoxal-5'-ph 95.03
>2vd8_A (A:19-239) Alanine racemase; pyridoxal 5'-phosphate, peptidoglycan synthesis, PLP, OPPF, L-alanine, isomerase, D- alanine, pyridoxal phosphate; HET: MLY LLP; 1.47A {Bacillus anthracis} PDB: 2vd9_A* Back     alignment and structure
Probab=99.97  E-value=1.5e-30  Score=226.53  Aligned_cols=202  Identities=17%  Similarity=0.120  Sum_probs=172.5

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCHHHCEEEEEC----CCCCHHHHH-HHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCEE
Q ss_conf             89999999999999999819896441899871----899999999-9997298100012100011110000012587302
Q gi|254780801|r    3 LGNKLQVFKQKIENSAILAKRPKDSVSLVAVS----KMVDSKKIR-VALSCGQVIFAENKLQEAKKKWIPLRKEWDVQLR   77 (222)
Q Consensus         3 i~~nl~~i~~~I~~a~~~~gR~~~~v~LiaVt----K~~~~e~I~-~~~~~G~~~fGENrvQE~~~K~~~l~~~~~i~wH   77 (222)
                      |..|++.+++++          ++.++++||+    |++....|. .++++|++.||++++||+..+.....   +..||
T Consensus         3 l~~Ni~~i~~~~----------~~~~~~~avvK~~ayg~g~~~v~~~~~~~G~~~~~v~~~~Ea~~~~~~~~---~~~il   69 (221)
T 2vd8_A            3 IYNNVTHIXEFI----------PSDVEIFAVVXGNAYGHDYVPVAXIALEAGATRLAVAFLDEALVLRRAGI---TAPIL   69 (221)
T ss_dssp             HHHHHHHHHHHS----------CTTCEEEEECHHHHHTTCHHHHHHHHHHTTCCEEEESSHHHHHHHHHTTC---CSCEE
T ss_pred             HHHHHHHHHHHC----------CCCCEEEEEEEEECCCCCHHHHHHHHHHCCCCEEEEEEHHHHHHHHHHCC---CCCEE
T ss_conf             999999999747----------99987999993602658879999999987979999826999999997189---99868


Q ss_pred             EECCCCCCHHHHHCCCCHHCCCCCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCCCC-HHHHHHHHHHCCCCCC
Q ss_conf             302443200132011100001222220013443333331143036889700466563465700-0122234431043110
Q gi|254780801|r   78 FIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPN-QTKDFVILCRQKYQLN  156 (222)
Q Consensus        78 fIG~LQsNKvk~i~~~~~~Ihsvds~~~a~~L~~~~~~~~~~~~vliQVN~~~e~~K~G~~p~-el~~l~~~i~~~~~L~  156 (222)
                      ++|++|+++++.++. .+++++|||.+.++.|++.+. .+++++|+|+|+++  .+|.||.|+ ++.+++..+..+++|+
T Consensus        70 ~~~~~~~~~~~~~~~-~~~~~~v~s~~~~~~l~~~a~-~~~~~~v~i~id~g--~~R~G~~~~~~~~~l~~~i~~~~~l~  145 (221)
T 2vd8_A           70 VLGPSPPRDINVAAE-NDVALTVFQXEWVDEAIXLWD-GSSTMXYHINFDSG--MGRIGIRERXELXGFLXSLEGAPFLE  145 (221)
T ss_dssp             ECSCCCGGGHHHHHH-TTEEEECCCHHHHHHHHHHCC-SSCCEEEEEEBCSS--CCSSSBCCHHHHHHHHHHHTTCTTEE
T ss_pred             EECCCCHHHHHHHHC-CCCCCCCCCHHHHHHHHHHHH-CCCCEEEEEEECCC--CCCCCCCCHHHHHHHHHHHHHCCCCC
T ss_conf             865888355444430-354231033889999999862-35541699984156--67778783899999999997589975


Q ss_pred             HHHHEECCCCCCCC-----HHHHHHHHHHHHHC-----CCCEECCCCCHHHHHHHHHCCCEEEECHHHCCCCCCC
Q ss_conf             01110115433452-----05899999998875-----8947224777348999980898899711323899999
Q gi|254780801|r  157 VEGLMCIPPAMGNP-----KPHFYLLSEIAREC-----KLTKLSMGMTRDFELAIASGATSVRIGSGIFGERPCQ  221 (222)
Q Consensus       157 i~GLMti~p~~~d~-----~~~F~~l~~l~~~~-----~~~~LSmGMS~D~~~Ai~~Gst~vRiGs~iFG~R~~~  221 (222)
                      ++|+||+.+...++     +..|..+.++.+.+     ....+|+|||.+|..+.++|+|+||+|++|||.||++
T Consensus       146 l~Gi~th~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~S~~~~~~~~~~~~~vR~G~~lyG~~p~~  220 (221)
T 2vd8_A          146 LEGVYTHFATADEVETSYFDXQYNTFLEQLSWLXEFGVDPXFVHTANSAATLRFQGITFNAVRIGIAMYGLSPSV  220 (221)
T ss_dssp             EEEEECCCSSTTSSSCHHHHHHHHHHHHHHHHHHHTTCCCCSEECCCHHHHTTCTTCCTTEEEESTTTTTCCSCT
T ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHEEEHHHHHHHCCCCCCCCCCCCCCCEECCCCCC
T ss_conf             668776537565322156788999999999999860885010000102554348433565014574223367885



>1ct5_A (A:) Protein (yeast hypothetical protein, selenoMet); TIM barrel, pyridoxal-5'-phosphate, selenomethionine, MAD, structural genomics, PSI; HET: PLP; 2.00A {Saccharomyces cerevisiae} Back     alignment and structure
>3cpg_A (A:) Uncharacterized protein; unknown protein, TIM barrel, monomer, structural genomics, PSI-2, protein structure initiative; 1.71A {Bifidobacterium adolescentis ATCC15703} Back     alignment and structure
>1w8g_A (A:) YGGS, hypothetical UPF0001 protein YGGS; structural genomics, hypothetical protein, putative enzyme with PLP-binding domain; HET: PLP ICT; 2.0A {Escherichia coli} Back     alignment and structure
>3kw3_A (A:27-241) Alanine racemase; niaid, ssgcid, seattle structural genomics center for infectious disease, iodide SOAK, LLP, CAT-scratch disease; HET: LLP; 2.04A {Bartonella henselae} Back     alignment and structure
>1rcq_A (A:11-221) Catabolic alanine racemase DADX; alpha-beta barrel, beta-structure for C-terminal domain, internal/external aldimine forms, isomerase; HET: KCX PLP DLY; 1.45A {Pseudomonas aeruginosa} Back     alignment and structure
>3llx_A (A:22-239) Predicted amino acid aldolase or racemase; structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: LLP TRS; 1.50A {Idiomarina loihiensis} Back     alignment and structure
>3co8_A (A:16-235) Alanine racemase; protein structure initiative II, PSI-II, NYSGXRC, PLP, TIM barrel, structural genomics; HET: PLP; 1.70A {Oenococcus oeni psu-1} Back     alignment and structure
>1vfs_A (A:15-237) Alanine racemase; TIM-barrel, greek-KEY motief, isomerase; HET: KCX DCS; 1.90A {Streptomyces lavendulae} Back