254780333

254780333

alanine racemase

GeneID in NCBI database:8209318Locus tag:CLIBASIA_01090
Protein GI in NCBI database:254780333Protein Accession:YP_003064746.1
Gene range:+(228006, 229118)Protein Length:370aa
Gene description:alanine racemase
COG prediction:[M] Alanine racemase
KEGG prediction:alanine racemase; K01775 alanine racemase [EC:5.1.1.1]
SEED prediction:Alanine racemase (EC 5.1.1.1)
Pathway involved in KEGG:D-Alanine metabolism [PATH:las00473]
Subsystem involved in SEED:Pyruvate Alanine Serine Interconversions;
Alanine 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
TOPPRED3 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-------310-------320-------330-------340-------350-------360-------370
MHSNEFLRLKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEEGVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYALQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTLISHYKGIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKINKSHPMQTVVTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLVRIGTRYAKFYT
ccccccEEEEEEHHHHHHHHHHHHHHccccEEEEEEEEccccccHHHHHHHHHHccccEEEEccHHHHHHHHHccccccEEEEccccHHHHHHHHHcccEEEEccHHHHHHHHHHHHHccccEEEEEEEcccccccccHHHHHHHHHHHHHcccccEEEEEEEcccccccccHHHHHHHHHHHHHHHccccccEEEEEHHHHHccccccccEEEccEEEEcccccccccccccEEEEEEEEEEEEEEEccccEEccccEEEccccEEEEEEEccccccHHHHccccccccccccccccEEEEccEEEEEEEccccccEEEEcccccccccccEEEEEcccccHHHHHHHHccccEEEEccccccccEEEc
cccccccEEEEcHHHHHHHHHHHHHHccccEEEEEEEEccccccHHHHHHHHHHcccccHHHEEHHHHHHHHHccccccEEEEccccHHHHHHHHHcccEEEEccHHHHHHHHHHHccccccEEEEEEccccccccccHHHHHHHHHHHHHcccccEEEEEEEccccccccccHHHHHHHHHHHHHHccccccEEHcccHHHHcccccccccccccEEEEccccccccccccccEEEEEEEEEEEEEcccccccccccEEEEccccEEEEEEEEccccccccccccccccccccccccEEEEccEEEEEEEEEEccEEEEEcccccccccccEEEEEcccccHHHHHHHHccccEEEEEccccccccEcc
MHSNEFLRLKIDLTALKNNWHSMNALSGNARTAAVvkdnayglgcekiapalynagvqdFFVTSVEEGVKLRLYTPQARIFVLYgihpgqekiifdtnlipvissvpqltfysklmscgvshpyalqvdtgfnrlGLSLQEALDFTHNSFNKKLGQLSLIISHLacaddpsshvnsVQLERFRTLISHYKGIEAslasssgillgpnyhfqltrpgislyggtdkinkshpmqtVVTAEARIILIRKALAGELvsyggqkkltrDSLIAVAAIGyadgypltlsgldsehspsvflggkgfikgyMVPILGKITMDMTMFDITDSLSIEVGDYiqifgpdiklddvalasgttnYDLLVRIGTRYAKFYT
MHSNEFLRLKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEEGVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYALQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTLISHYKGIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKINKSHPMQTVVTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALAsgttnydllvrIGTRYAKFYT
MHSNEFLRLKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEEGVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYALQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTLISHYKgieaslasssgillgPNYHFQLTRPGISLYGGTDKINKSHPMQTVVTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLVRIGTRYAKFYT
***NEFL*LKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEEGVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYALQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTLISHYKGIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKINKSHPMQTVVTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLVRIGTRYAKFYT
MHSNEFLRLKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEEGVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYALQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTLISHYKGIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKINKSHPMQTVVTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLVRIGTRYAKFYT
****EFLRLKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEEGVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYALQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTLISHYKGIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKINKSHPMQTVVTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLVRIGTRYAK*Y*
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MHSNEFLRLKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEEGVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYALQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTLISHYKGIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKINKSHPMQTVVTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLVRIGTRYAKFYT
MHSNEFLRLKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEEGVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYALQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTLISHYKGIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKINKSHPMQTVVTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLVRIGTRYAKFYT
MHSNEFLRLKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEEGVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYALQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTLISHYKGIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKINKSHPMQTVVTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLVRIGTRYAKFYT

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
Target370 alanine racemase [Candidatus Liberibacter asiaticus str
315122242348 alanine racemase [Candidatus Liberibacter solanacearum 1 1e-159
325292459391 Alanine racemase [Agrobacterium sp. H13-3] Length = 391 1 1e-100
241203930389 alanine racemase [Rhizobium leguminosarum bv. trifolii 1 1e-100
222148127387 alanine racemase [Agrobacterium vitis S4] Length = 387 1 1e-99
222085428387 alanine racemase [Agrobacterium radiobacter K84] Length 1 2e-99
15888423391 alanine racemase [Agrobacterium tumefaciens str. C58] L 1 2e-99
116251316389 alanine racemase [Rhizobium leguminosarum bv. viciae 38 1 4e-99
227821452409 alanine racemase [Sinorhizobium fredii NGR234] Length = 1 3e-97
327187996386 putative alanine racemase [Rhizobium etli CNPAF512] Len 1 5e-95
209548649388 alanine racemase [Rhizobium leguminosarum bv. trifolii 1 3e-93
>gi|315122242|ref|YP_004062731.1| alanine racemase [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 348 Back     alignment and organism information
 Score =  565 bits (1457), Expect = e-159,   Method: Compositional matrix adjust.
 Identities = 279/348 (80%), Positives = 307/348 (88%)

Query: 23  MNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEEGVKLRLYTPQARIFV 82
           MN LSG ARTAAVVKDNAYGLG EKIA  LYN+GVQDFFV  V EGVKLR Y P+A+IFV
Sbjct: 1   MNVLSGCARTAAVVKDNAYGLGFEKIAQTLYNSGVQDFFVAHVGEGVKLRAYVPKAKIFV 60

Query: 83  LYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYALQVDTGFNRLGLSLQEA 142
           LYGIHPG+EKI+FD NLIPVISS  QLTFY KLMS G SHPYALQVDTGFNRLGLSLQEA
Sbjct: 61  LYGIHPGEEKILFDANLIPVISSSQQLTFYLKLMSNGFSHPYALQVDTGFNRLGLSLQEA 120

Query: 143 LDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTLISHYKGIEASLASSSGI 202
           L+F  N  NKK  +LSLI+SHLAC++DP S +NS QLE+F TL+  YKGIEASLASS+GI
Sbjct: 121 LNFAKNFSNKKSDKLSLIMSHLACSEDPVSLMNSSQLEQFLTLMKSYKGIEASLASSAGI 180

Query: 203 LLGPNYHFQLTRPGISLYGGTDKINKSHPMQTVVTAEARIILIRKALAGELVSYGGQKKL 262
           LLG NYHFQLTRPGISLYGGT  INK +PMQTVVTAEARIILIR+A AGE++SYGGQKKL
Sbjct: 181 LLGENYHFQLTRPGISLYGGTPAINKLNPMQTVVTAEARIILIREAAAGEVISYGGQKKL 240

Query: 263 TRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGYMVPILGKITMDMTMFDI 322
            R+SLIAVAAIGYADGYPLTLSG+D EH+ + F GGKGFIKGYMVPILGKITMD+TMFDI
Sbjct: 241 KRNSLIAVAAIGYADGYPLTLSGIDLEHNQAQFPGGKGFIKGYMVPILGKITMDITMFDI 300

Query: 323 TDSLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLVRIGTRYAKFYT 370
           TDS+ IE GDYI++FGP+IKLDDVALAS TTNYDLLVRIGTRYA+FYT
Sbjct: 301 TDSIGIEAGDYIEVFGPNIKLDDVALASRTTNYDLLVRIGTRYARFYT 348


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|325292459|ref|YP_004278323.1| Alanine racemase [Agrobacterium sp. H13-3] Length = 391 Back     alignment and organism information
>gi|241203930|ref|YP_002975026.1| alanine racemase [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 389 Back     alignment and organism information
>gi|222148127|ref|YP_002549084.1| alanine racemase [Agrobacterium vitis S4] Length = 387 Back     alignment and organism information
>gi|222085428|ref|YP_002543958.1| alanine racemase [Agrobacterium radiobacter K84] Length = 387 Back     alignment and organism information
>gi|15888423|ref|NP_354104.1| alanine racemase [Agrobacterium tumefaciens str. C58] Length = 391 Back     alignment and organism information
>gi|116251316|ref|YP_767154.1| alanine racemase [Rhizobium leguminosarum bv. viciae 3841] Length = 389 Back     alignment and organism information
>gi|227821452|ref|YP_002825422.1| alanine racemase [Sinorhizobium fredii NGR234] Length = 409 Back     alignment and organism information
>gi|327187996|gb|EGE55226.1| putative alanine racemase [Rhizobium etli CNPAF512] Length = 386 Back     alignment and organism information
>gi|209548649|ref|YP_002280566.1| alanine racemase [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 388 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
Target370 alanine racemase [Candidatus Liberibacter asiaticus str
cd00430367 cd00430, PLPDE_III_AR, Type III Pyridoxal 5-phosphate ( 4e-87
PRK00053363 PRK00053, alr, alanine racemase; Reviewed 8e-77
cd06827354 cd06827, PLPDE_III_AR_proteobact, Type III Pyridoxal 5- 3e-62
TIGR00492367 TIGR00492, alr, alanine racemase 1e-59
cd06825368 cd06825, PLPDE_III_VanT, Type III Pyridoxal 5-phosphate 3e-48
PRK03646355 PRK03646, dadX, alanine racemase; Reviewed 2e-45
PRK11930822 PRK11930, PRK11930, putative bifunctional UDP-N-acetylm 1e-41
PRK13340406 PRK13340, PRK13340, alanine racemase; Reviewed 8e-40
cd06826365 cd06826, PLPDE_III_AR2, Type III Pyridoxal 5-phosphate 2e-27
COG0787360 COG0787, Alr, Alanine racemase [Cell envelope biogenesi 4e-91
pfam01168216 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal 2e-40
pfam00842125 pfam00842, Ala_racemase_C, Alanine racemase, C-terminal 5e-35
>gnl|CDD|143481 cd00430, PLPDE_III_AR, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase Back     alignment and domain information
>gnl|CDD|178827 PRK00053, alr, alanine racemase; Reviewed Back     alignment and domain information
>gnl|CDD|143500 cd06827, PLPDE_III_AR_proteobact, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases Back     alignment and domain information
>gnl|CDD|129583 TIGR00492, alr, alanine racemase Back     alignment and domain information
>gnl|CDD|143498 cd06825, PLPDE_III_VanT, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, VanT and similar proteins Back     alignment and domain information
>gnl|CDD|179622 PRK03646, dadX, alanine racemase; Reviewed Back     alignment and domain information
>gnl|CDD|183386 PRK11930, PRK11930, putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional Back     alignment and domain information
>gnl|CDD|183984 PRK13340, PRK13340, alanine racemase; Reviewed Back     alignment and domain information
>gnl|CDD|143499 cd06826, PLPDE_III_AR2, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2 Back     alignment and domain information
>gnl|CDD|31130 COG0787, Alr, Alanine racemase [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>gnl|CDD|144675 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain Back     alignment and domain information
>gnl|CDD|144438 pfam00842, Ala_racemase_C, Alanine racemase, C-terminal domain Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 370 alanine racemase [Candidatus Liberibacter asiaticus str
PRK11930824 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D 100.0
PRK00053360 alr alanine racemase; Reviewed 100.0
TIGR00492383 alr alanine racemase; InterPro: IPR000821 Alanine racem 100.0
cd06827354 PLPDE_III_AR_proteobact Type III Pyridoxal 5-phosphate 100.0
cd06825368 PLPDE_III_VanT Type III Pyridoxal 5-phosphate (PLP)-Dep 100.0
PRK13340404 alanine racemase; Reviewed 100.0
cd00430367 PLPDE_III_AR Type III Pyridoxal 5-phosphate (PLP)-Depen 100.0
PRK03646355 dadX alanine racemase; Reviewed 100.0
COG0787360 Alr Alanine racemase [Cell envelope biogenesis, outer m 100.0
cd06826365 PLPDE_III_AR2 Type III Pyridoxal 5-phosphate (PLP)-Depe 100.0
cd06821361 PLPDE_III_D-TA Type III Pyridoxal 5-phosphate (PLP)-Dep 99.93
cd06812374 PLPDE_III_DSD_D-TA_like_1 Type III Pyridoxal 5-phosphat 99.9
cd06813388 PLPDE_III_DSD_D-TA_like_2 Type III Pyridoxal 5-phosphat 99.85
cd06817389 PLPDE_III_DSD Type III Pyridoxal 5-phosphate (PLP)-Depe 99.85
cd06814379 PLPDE_III_DSD_D-TA_like_3 Type III Pyridoxal 5-phosphat 99.85
COG0019394 LysA Diaminopimelate decarboxylase [Amino acid transpor 99.57
PRK11165412 diaminopimelate decarboxylase; Provisional 99.3
PRK08961865 bifunctional aspartate kinase/diaminopimelate decarboxy 99.25
TIGR01048431 lysA diaminopimelate decarboxylase; InterPro: IPR002986 99.11
cd06815353 PLPDE_III_AR_like_1 Type III Pyridoxal 5-phosphate (PLP 100.0
cd06820353 PLPDE_III_LS_D-TA_like Type III Pyridoxal 5-phosphate ( 99.94
COG3457353 Predicted amino acid racemase [Amino acid transport and 99.93
cd06818382 PLPDE_III_cryptic_DSD Type III Pyridoxal 5-phosphate (P 99.92
cd06819358 PLPDE_III_LS_D-TA Type III Pyridoxal 5-phosphate (PLP)- 99.91
cd07376345 PLPDE_III_DSD_D-TA_like Type III Pyridoxal 5-phosphate 99.84
cd06843377 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP 99.73
COG3616368 Predicted amino acid aldolase or racemase [Amino acid t 99.69
cd06828373 PLPDE_III_DapDC Type III Pyridoxal 5-phosphate (PLP)-De 99.67
cd06810368 PLPDE_III_ODC_DapDC_like Type III Pyridoxal 5-phosphate 99.67
cd06839382 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP 99.66
cd06841379 PLPDE_III_MccE_like Type III Pyridoxal 5-phosphate (PLP 99.65
cd06840368 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate 99.62
cd06831394 PLPDE_III_ODC_like_AZI Type III Pyridoxal 5-phosphate ( 99.61
TIGR03099398 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, exosort 99.58
cd00622362 PLPDE_III_ODC Type III Pyridoxal 5-phosphate (PLP)-Depe 99.53
cd06836379 PLPDE_III_ODC_DapDC_like_1 Type III Pyridoxal 5-phospha 99.53
cd06829346 PLPDE_III_CANSDC Type III Pyridoxal 5-phosphate (PLP)-D 99.39
pfam01168216 Ala_racemase_N Alanine racemase, N-terminal domain. 100.0
cd06808211 PLPDE_III Type III Pyridoxal 5-phosphate (PLP)-Dependen 100.0
cd06824224 PLPDE_III_Yggs_like Pyridoxal 5-phosphate (PLP)-binding 99.39
cd00635222 PLPDE_III_YBL036c_like Type III Pyridoxal 5-phosphate ( 99.33
COG0325228 Predicted enzyme with a TIM-barrel fold [General functi 99.25
cd06822227 PLPDE_III_YBL036c_euk Pyridoxal 5-phosphate (PLP)-bindi 99.22
TIGR00044250 TIGR00044 conserved hypothetical protein TIGR00044; Int 98.4
KOG3157244 consensus 98.29
pfam00842125 Ala_racemase_C Alanine racemase, C-terminal domain. 100.0
cd06842423 PLPDE_III_Y4yA_like Type III Pyridoxal 5-phosphate (PLP 99.55
pfam02784245 Orn_Arg_deC_N Pyridoxal-dependent decarboxylase, pyrido 99.07
cd06830409 PLPDE_III_ADC Type III Pyridoxal 5-phosphate (PLP)-Depe 98.68
TIGR01047403 nspC carboxynorspermidine decarboxylase; InterPro: IPR0 97.95
cd06811382 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP 99.37
KOG0622448 consensus 98.35
TIGR02090371 LEU1_arch isopropylmalate/citramalate/homocitrate synth 94.97
TIGR00693210 thiE thiamine-phosphate pyrophosphorylase; InterPro: IP 92.6
>PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional Back     alignment and domain information
>PRK00053 alr alanine racemase; Reviewed 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
>cd06827 PLPDE_III_AR_proteobact Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases 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
>PRK13340 alanine racemase; Reviewed Back     alignment and domain information
>cd00430 PLPDE_III_AR Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase 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
>cd06826 PLPDE_III_AR2 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2 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
>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
>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
>cd06817 PLPDE_III_DSD Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Eukaryotic D-Serine Dehydratase 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
>COG0019 LysA Diaminopimelate decarboxylase [Amino acid transport and metabolism] 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
>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
>cd06815 PLPDE_III_AR_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1 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
>COG3457 Predicted amino acid racemase [Amino acid transport and metabolism] 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
>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
>cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE Back     alignment and domain information
>COG3616 Predicted amino acid aldolase or racemase [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
>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
>cd06839 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk 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
>cd06840 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase 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
>TIGR03099 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, exosortase system type 1 associated Back     alignment and domain information
>cd00622 PLPDE_III_ODC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase 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
>cd06829 PLPDE_III_CANSDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase 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
>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
>COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only] 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
>pfam00842 Ala_racemase_C Alanine racemase, C-terminal domain Back     alignment and domain information
>cd06842 PLPDE_III_Y4yA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Y4yA Back     alignment and domain information
>pfam02784 Orn_Arg_deC_N Pyridoxal-dependent decarboxylase, pyridoxal binding domain Back     alignment and domain information
>cd06830 PLPDE_III_ADC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase Back     alignment and domain information
>TIGR01047 nspC carboxynorspermidine decarboxylase; InterPro: IPR005730 Carboxynorspermidine synthase, mediates the nicotinamide-nucleotide-linked reduction of the Schiff base H2N(CH2)3N = CHCH2CH(NH2)COOH Back     alignment and domain information
>cd06811 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX Back     alignment and domain information
>KOG0622 consensus Back     alignment and domain information
>TIGR02090 LEU1_arch isopropylmalate/citramalate/homocitrate synthases; InterPro: IPR011830 Methanogenic archaea contain three closely related homologs of the 2-isopropylmalate synthases (LeuA) represented by IPR005671 from INTERPRO Back     alignment and domain information
>TIGR00693 thiE thiamine-phosphate pyrophosphorylase; InterPro: IPR003733 Thiamine monophosphate synthase (TMP) (2 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
Target370 alanine racemase [Candidatus Liberibacter asiaticus str
1rcq_A357 The 1.45 A Crystal Structure Of Alanine Racemase Fr 1e-77
1epv_A387 Alanine Racemase With Bound Inhibitor Derived From 4e-77
1sft_A388 Alanine Racemase Length = 388 5e-77
2sfp_A388 Alanine Racemase With Bound Propionate Inhibitor Le 6e-77
2odo_A357 Crystal Structure Of Pseudomonas Fluorescens Alanin 8e-77
1xqk_A388 Effect Of A Y265f Mutant On The Transamination Base 1e-76
3b8w_A379 Crystal Structure Of Escherichia Coli Alaine Racema 2e-76
3b8v_A379 Crystal Structure Of Escherichia Coli Alaine Racema 2e-76
2rjg_A379 Crystal Structure Of Biosynthetic Alaine Racemase F 2e-76
1xfc_A384 The 1.9 A Crystal Structure Of Alanine Racemase Fro 2e-76
3b8u_A379 Crystal Structure Of Escherichia Coli Alaine Racema 2e-76
3b8t_A379 Crystal Structure Of Escherichia Coli Alaine Racema 1e-75
3kw3_A376 Crystal Structure Of Alanine Racemase From Bartonel 7e-74
2dy3_A361 Crystal Structure Of Alanine Racemase From Coryneba 3e-71
3e5p_A371 Crystal Structure Of Alanine Racemase From E.Faecal 1e-70
1vfh_A386 Crystal Structure Of Alanine Racemase From D-Cyclos 4e-70
3ha1_A397 Alanine Racemase From Bacillus Anthracis (Ames) Len 6e-70
3oo2_A385 2.37 Angstrom Resolution Crystal Structure Of An Al 1e-69
2vd9_A391 The Crystal Structure Of Alanine Racemase From Baci 2e-67
3mub_A367 The Crystal Structure Of Alanine Racemase From Stre 7e-66
2vd8_A391 The Crystal Structure Of Alanine Racemase From Baci 2e-65
3hur_A395 Crystal Structure Of Alanine Racemase From Oenococc 7e-58
3co8_A380 Crystal Structure Of Alanine Racemase From Oenococc 9e-44
>gi|49258690|pdb|1RCQ|A Chain A, The 1.45 A Crystal Structure Of Alanine Racemase From A Pathogenic Bacterium, Pseudomonas Aeruginosa, Contains Both Internal And External Aldimine Forms Length = 357 Back     alignment and structure
 Score =  295 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 102/369 (27%), Positives = 160/369 (43%), Gaps = 18/369 (4%)

Query: 5   EFLRLKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTS 64
              R  IDL AL++N+      +G AR  AV+K +AYG G  + A AL       F V  
Sbjct: 2   RPARALIDLQALRHNYRLAREATG-ARALAVIKADAYGHGAVRCAEALAAE-ADGFAVAC 59

Query: 65  VEEGVKLRLYTPQARIFVLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPY 124
           +EEG++LR    +  I +L G     E  +   +    +          +  S       
Sbjct: 60  IEEGLELREAGIRQPILLLEGFFEASELELIVAHDFWCVVHCAWQLEAIERASLARPLNV 119

Query: 125 ALQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRT 184
            L +D+G +R+G   ++                 +++SH + AD+        QL  F  
Sbjct: 120 WLXMDSGMHRVGFFPEDFRAAHERLRASGKVAKIVMMSHFSRADELDCPRTEEQLAAFSA 179

Query: 185 LISHYKGIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKINKS---HPMQTVVTAEAR 241
                +G E SL +S  +L  P       RPGI LYG T           ++ V+T E++
Sbjct: 180 ASQGLEG-EISLRNSPAVLGWPKVPSDWVRPGILLYGATPFERAHPLADRLRPVMTLESK 238

Query: 242 IILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGF 301
           +I +R   AGE V YG +    R   I V A+GYADGYP                G   F
Sbjct: 239 VISVRDLPAGEPVGYGARYSTERRQRIGVVAMGYADGYPRHA-----------ADGTLVF 287

Query: 302 IKGYMVPILGKITMDMTMFDITDSLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLVRI 361
           I G    ++G+++MDM   D+TD     +G  ++++GP++ +  +A   G+  Y LL  +
Sbjct: 288 IDGKPGRLVGRVSMDMLTVDLTDHPQAGLGSRVELWGPNVPVGALAAQFGSIPYQLLCNL 347

Query: 362 GTRYAKFYT 370
             R  + Y+
Sbjct: 348 -KRVPRVYS 355


>gi|28373266|pdb|1EPV|A Chain A, Alanine Racemase With Bound Inhibitor Derived From D- Cycloserine Length = 387 Back     alignment and structure
>gi|1942328|pdb|1SFT|A Chain A, Alanine Racemase Length = 388 Back     alignment and structure
>gi|4558012|pdb|2SFP|A Chain A, Alanine Racemase With Bound Propionate Inhibitor Length = 388 Back     alignment and structure
>gi|167013239|pdb|2ODO|A Chain A, Crystal Structure Of Pseudomonas Fluorescens Alanine Racemase Length = 357 Back     alignment and structure
>gi|60594046|pdb|1XQK|A Chain A, Effect Of A Y265f Mutant On The Transamination Based Cycloserine Inactivation Of Alanine Racemase Length = 388 Back     alignment and structure
>gi|193885285|pdb|3B8W|A Chain A, Crystal Structure Of Escherichia Coli Alaine Racemase Mutant E221p Length = 379 Back     alignment and structure
>gi|193885281|pdb|3B8V|A Chain A, Crystal Structure Of Escherichia Coli Alaine Racemase Mutant E221k Length = 379 Back     alignment and structure
>gi|193885202|pdb|2RJG|A Chain A, Crystal Structure Of Biosynthetic Alaine Racemase From Escherichia Coli Length = 379 Back     alignment and structure
>gi|75765474|pdb|1XFC|A Chain A, The 1.9 A Crystal Structure Of Alanine Racemase From Mycobacterium Tuberculosis Contains A Conserved Entryway Into The Active Site Length = 384 Back     alignment and structure
>gi|193885277|pdb|3B8U|A Chain A, Crystal Structure Of Escherichia Coli Alaine Racemase Mutant E221a Length = 379 Back     alignment and structure
>gi|193885273|pdb|3B8T|A Chain A, Crystal Structure Of Escherichia Coli Alaine Racemase Mutant P219a Length = 379 Back     alignment and structure
>gi|281500991|pdb|3KW3|A Chain A, Crystal Structure Of Alanine Racemase From Bartonella Henselae With Covalently Bound Pyridoxal Phosphate Length = 376 Back     alignment and structure
gi|158428171|pdb|2DY3|A Chain A, Crystal Structure Of Alanine Racemase From Corynebacterium Glutamicum Length = 361 Back     alignment and structure
>gi|256032536|pdb|3E5P|A Chain A, Crystal Structure Of Alanine Racemase From E.Faecalis Length = 371 Back     alignment and structure
>gi|55670437|pdb|1VFH|A Chain A, Crystal Structure Of Alanine Racemase From D-Cycloserine Producing Streptomyces Lavendulae Length = 386 Back     alignment and structure
>gi|258588448|pdb|3HA1|A Chain A, Alanine Racemase From Bacillus Anthracis (Ames) Length = 397 Back     alignment and structure
>gi|308198664|pdb|3OO2|A Chain A, 2.37 Angstrom Resolution Crystal Structure Of An Alanine Racemase (Alr) From Staphylococcus Aureus Subsp. Aureus Col Length = 385 Back     alignment and structure
>gi|188595863|pdb|2VD9|A Chain A, The Crystal Structure Of Alanine Racemase From Bacillus Anthracis (Ba0252) With Bound L-Ala-P Length = 391 Back     alignment and structure
>gi|332639567|pdb|3MUB|A Chain A, The Crystal Structure Of Alanine Racemase From Streptococcus Pneumoniae Length = 367 Back     alignment and structure
>gi|188595861|pdb|2VD8|A Chain A, The Crystal Structure Of Alanine Racemase From Bacillus Anthracis (Ba0252) Length = 391 Back     alignment and structure
>gi|254221103|pdb|3HUR|A Chain A, Crystal Structure Of Alanine Racemase From Oenococcus Oeni Length = 395 Back     alignment and structure
>gi|178847612|pdb|3CO8|A Chain A, Crystal Structure Of Alanine Racemase From Oenococcus Oeni Length = 380 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target370 alanine racemase [Candidatus Liberibacter asiaticus str
3kw3_A376 Alanine racemase; niaid, ssgcid, seattle structural gen 5e-75
3oo2_A385 Alanine racemase 1; infectious diseases, center for str 1e-72
3hur_A395 Alanine racemase; structural genomics, isomerase, pyrid 4e-65
2rjg_A379 Alanine racemase; alpha/beta barrel, cell shape, cell W 5e-62
1bd0_A388 Alanine racemase; isomerase, pyridoxal phosphate, alani 1e-61
2vd8_A391 Alanine racemase; pyridoxal 5'-phosphate, peptidoglycan 2e-61
1vfs_A386 Alanine racemase; TIM-barrel, greek-KEY motief, isomera 1e-60
2dy3_A361 Alanine racemase; alpha/beta barrel, isomerase; HET: PL 2e-60
1rcq_A357 Catabolic alanine racemase DADX; alpha-beta barrel, bet 6e-60
3e5p_A371 Alanine racemase; ALR, PLP, SCP, isomerase, pyridoxal p 2e-59
1xfc_A384 Alanine racemase; alpha-beta barrel, beta-structure for 4e-57
3co8_A380 Alanine racemase; protein structure initiative II, PSI- 7e-56
3llx_A376 Predicted amino acid aldolase or racemase; structural g 6e-12
3cpg_A282 Uncharacterized protein; unknown protein, TIM barrel, m 2e-07
>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} Length = 376 Back     alignment and structure
 Score =  276 bits (707), Expect = 5e-75
 Identities = 119/365 (32%), Positives = 189/365 (51%), Gaps = 14/365 (3%)

Query: 8   RLKIDLTALKNNWHSMNALSGNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEE 67
              ID+ A+  N+ ++         +AVVK NAYGLG  KIAPALY AG + FFV  +EE
Sbjct: 22  IATIDVRAIVANYRTLAQHVAPTECSAVVKANAYGLGAHKIAPALYQAGCRTFFVAQIEE 81

Query: 68  GVKLRLYTPQARIFVLYGIHPGQ-EKIIFDTNLIPVISSVPQLT-FYSKLMSCGVSHPYA 125
            ++L+   P+  +  L    P + E+ +  + +IP+++S   +  + +         P  
Sbjct: 82  ALQLKAVLPENVMIALLNGFPHKAEEFVAQSGIIPLLNSWSTIEDWQTLCQKKNKKFPAI 141

Query: 126 LQVDTGFNRLGLSLQEALDFTHNSFNKKLGQLSLIISHLACADDPSSHVNSVQLERFRTL 185
           +QVDT  +RLGL  +E      N    +  ++  I+SHLA  +D S   N+ QL  F+ +
Sbjct: 142 IQVDTNMSRLGLDKKELQKLIKNPTIFEKAEIKYILSHLANGEDASHSSNNKQLAAFKRV 201

Query: 186 ISHYKGIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKINKSHPMQTVVTAEARIILI 245
           ++     + S A+S GI LG +++F L RPGI+LYG         P++ VV  EA+++  
Sbjct: 202 LAQLPTCKVSFANSGGIFLGSDFYFDLVRPGIALYGVDPHGKHPTPLKAVVKVEAQVLQS 261

Query: 246 RKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGY 305
           R   AG  V Y       R S +A  +IGYADG+P  LS             G  +  G+
Sbjct: 262 RFIDAGIPVGYRESFMTRRPSTLATISIGYADGWPRILSN-----------KGTVYFNGH 310

Query: 306 MVPILGKITMDMTMFDITD-SLSIEVGDYIQIFGPDIKLDDVALASGTTNYDLLVRIGTR 364
            +PI+G I+MD  + D TD     + GD++++ GP   L+ V+  + T  +++L  +G R
Sbjct: 311 KLPIVGHISMDSIIVDATDLDKKPQRGDWVELIGPHQPLEKVSTDTNTIPHEILTSLGKR 370

Query: 365 YAKFY 369
           Y + Y
Sbjct: 371 YKRIY 375


>3oo2_A Alanine racemase 1; infectious diseases, center for structural of infectious diseases (csgid); 2.37A {Staphylococcus aureus subsp} Length = 385 Back     alignment and structure
>3hur_A Alanine racemase; structural genomics, isomerase, pyridoxal phosphate, PSI-2, protein structure initiative; 2.50A {Oenococcus oeni psu-1} Length = 395 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* Length = 379 Back     alignment and structure
>1bd0_A Alanine racemase; isomerase, pyridoxal phosphate, alanine phosphonate; HET: IN5; 1.60A {Bacillus 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* Length = 388 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* Length = 391 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* Length = 386 Back     alignment and structure
>2dy3_A Alanine racemase; alpha/beta barrel, isomerase; HET: PLP; 2.10A {Corynebacterium glutamicum} Length = 361 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* Length = 357 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* Length = 371 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} Length = 384 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} Length = 380 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} Length = 376 Back     alignment and structure
>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

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target370 alanine racemase [Candidatus Liberibacter asiaticus str
2vd8_A391 Alanine racemase; pyridoxal 5'-phosphate, peptidoglycan 100.0
2dy3_A361 Alanine racemase; alpha/beta barrel, isomerase; HET: PL 100.0
2rjg_A379 Alanine racemase; alpha/beta barrel, cell shape, cell W 100.0
1vfs_A386 Alanine racemase; TIM-barrel, greek-KEY motief, isomera 100.0
1rcq_A357 Catabolic alanine racemase DADX; alpha-beta barrel, bet 100.0
3kw3_A376 Alanine racemase; niaid, ssgcid, seattle structural gen 100.0
1bd0_A388 Alanine racemase; isomerase, pyridoxal phosphate, alani 100.0
3oo2_A385 Alanine racemase 1; infectious diseases, center for str 100.0
1xfc_A384 Alanine racemase; alpha-beta barrel, beta-structure for 100.0
3co8_A380 Alanine racemase; protein structure initiative II, PSI- 100.0
3e5p_A371 Alanine racemase; ALR, PLP, SCP, isomerase, pyridoxal p 100.0
3hur_A395 Alanine racemase; structural genomics, isomerase, pyrid 100.0
2plj_A419 Lysine/ornithine decarboxylase; type IV decarboxylase, 99.75
3gwq_A426 D-serine deaminase; YP_556991.1, structural genomics, j 100.0
3llx_A376 Predicted amino acid aldolase or racemase; structural g 100.0
2p3e_A420 Diaminopimelate decarboxylase; southeast collaboratory 99.74
3btn_A448 Antizyme inhibitor 1; TIM-like A/B barrel domain and A 99.72
2qgh_A425 Diaminopimelate decarboxylase; lyase; HET: PLP LYS; 2.3 99.7
2oo0_A471 ODC, ornithine decarboxylase; beta-alpha barrel, sheet, 99.69
7odc_A424 Protein (ornithine decarboxylase); pyridoxal-5'-phospha 99.63
1f3t_A425 ODC, ornithine decarboxylase; beta-alpha-barrel, modifi 99.63
3n2b_A441 Diaminopimelate decarboxylase; LYSA, lyase, structural 99.58
2o0t_A467 Diaminopimelate decarboxylase; PLP binding enzyme, lysi 99.48
2j66_A428 BTRK, decarboxylase; butirosin, AHBA biosynthesis, lyas 99.43
1twi_A434 Diaminopimelate decarboxylase; antibiotic resistance, l 99.41
2nva_A372 Arginine decarboxylase, A207R protein; PLP, TIM barrel, 99.4
3mt1_A365 Putative carboxynorspermidine decarboxylase prote; PSI2 99.39
1knw_A425 Diaminopimelate decarboxylase; pyridoxal-phosphate, dec 99.23
2yxx_A386 Diaminopimelate decarboxylase; TM1517, TIM beta/alpha b 99.21
3n29_A418 Carboxynorspermidine decarboxylase; lyase; HET: PLP; 1. 99.14
1w8g_A234 YGGS, hypothetical UPF0001 protein YGGS; structural gen 99.33
3cpg_A282 Uncharacterized protein; unknown protein, TIM barrel, m 99.26
1ct5_A256 Protein (yeast hypothetical protein, selenoMet); TIM ba 99.04
3nzp_A 619 Arginine decarboxylase; alpha-beta protein, structural 98.5
3nzq_A 666 ADC, biosynthetic arginine decarboxylase; alpha-beta pr 98.48
3n2o_A 648 ADC, biosynthetic arginine decarboxylase; lyase; HET: P 98.2
>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
Probab=100.00  E-value=0  Score=773.22  Aligned_cols=353  Identities=24%  Similarity=0.368  Sum_probs=329.5

Q ss_pred             CCCCEEEEEEHHHHHHHHHHHHHHC-CCCEEEEEEECCCCCCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHCCCCCEE
Q ss_conf             8885099986889999999998628-997599999328665798999999998799899985599999999838985267
Q gi|254780333|r    3 SNEFLRLKIDLTALKNNWHSMNALS-GNARTAAVVKDNAYGLGCEKIAPALYNAGVQDFFVTSVEEGVKLRLYTPQARIF   81 (370)
Q Consensus         3 ~~~~~~leIdl~al~~Ni~~i~~~~-~~~~i~aVVKanAYGhG~~~va~~l~~~Gv~~faVa~~~EA~~lR~~g~~~~Il   81 (370)
                      -+|.+|+|||++||+||++.+|++. +++++||||||||||||+.+|++.+.++||++|||++++||++||++|++.|||
T Consensus         8 ~~r~t~~EIdl~al~~N~~~i~~~~~~~~~i~aVVKanAYGhG~~~va~~l~~~Gi~~faVa~~~EA~~LR~~gi~~~Il   87 (391)
T 2vd8_A            8 FYRDTWVEVDLDAIYNNVTHIXEFIPSDVEIFAVVKGNAYGHDYVPVAXIALEAGATRLAVAFLDEALVLRRAGITAPIL   87 (391)
T ss_dssp             CCSSCEEEEEHHHHHHHHHHHHHHSCTTCEEEEECHHHHHTTCHHHHHHHHHHTTCCEEEESSHHHHHHHHHTTCCSCEE
T ss_pred             CCCCEEEEEEHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCHHHHHHHHHHCCCCEEEEEEHHHHHHHHHCCCCCCEE
T ss_conf             88988999859999999999997479998799999150264788999999998698999991699999999719999779


Q ss_pred             EECCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCHH-HHHHHHHHHHHHHCCCHHHH
Q ss_conf             30689746988887542101348998999988887608877616761266676556988-99999988886310001243
Q gi|254780333|r   82 VLYGIHPGQEKIIFDTNLIPVISSVPQLTFYSKLMSCGVSHPYALQVDTGFNRLGLSLQ-EALDFTHNSFNKKLGQLSLI  160 (370)
Q Consensus        82 vl~~~~~~~~~~~~~~~i~~~i~s~~~l~~l~~~~~~~~~~~vhlkiDTGM~R~G~~~~-e~~~~~~~~~~~~~~~i~gi  160 (370)
                      +|+++.+++++.+.++++++++++.+++..+.++.+.+++.++|||+||||||+||.++ |+.++++.+..+++++++|+
T Consensus        88 vl~~~~~~~~~~~~~~~~~~~i~s~~~l~~~~~~~~~~~~~~vhlkiDTGM~RlG~~~~~e~~~~~~~i~~~~~l~i~Gi  167 (391)
T 2vd8_A           88 VLGPSPPRDINVAAENDVALTVFQXEWVDEAIXLWDGSSTMXYHINFDSGMGRIGIRERXELXGFLXSLEGAPFLELEGV  167 (391)
T ss_dssp             ECSCCCGGGHHHHHHTTEEEECCCHHHHHHHHHHCCSSCCEEEEEEBCSSCCSSSBCCHHHHHHHHHHHTTCTTEEEEEE
T ss_pred             EEECCCHHHHHHHHHCCCCEEECHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             97488825655654205320340599999999986046864899996379886788741468999999972899650367


Q ss_pred             HCCCCCCCCCCCHHHHHHHHHHHHHHHHHC-----CCCHHHCCCCHHCCCCCCCCHHHCCCCCCCCCCCCCC----CCCC
Q ss_conf             201243333466788999999999975434-----8860111641100477322202048735306787767----5567
Q gi|254780333|r  161 ISHLACADDPSSHVNSVQLERFRTLISHYK-----GIEASLASSSGILLGPNYHFQLTRPGISLYGGTDKIN----KSHP  231 (370)
Q Consensus       161 ~THfa~ad~~~~~~~~~Q~~~F~~~~~~~~-----~~~~h~~nS~~~l~~p~~~~d~vR~Gi~lYG~~~~~~----~~~~  231 (370)
                      ||||++||+++.+++..|+++|.++++.++     +...|++||+|++++|+.++||||||++|||++|...    .+.+
T Consensus       168 ~THfa~ad~~~~~~~~~Q~~~F~~~~~~~~~~~~~~~~~h~anS~a~l~~~~~~~d~VR~Gi~lYG~~p~~~~~~~~~~~  247 (391)
T 2vd8_A          168 YTHFATADEVETSYFDXQYNTFLEQLSWLXEFGVDPXFVHTANSAATLRFQGITFNAVRIGIAMYGLSPSVEIRPFLPFX  247 (391)
T ss_dssp             ECCCSSTTSSSCHHHHHHHHHHHHHHHHHHHTTCCCCSEECCCHHHHTTCTTCCTTEEEESTTTTTCCSCTTTGGGCSSC
T ss_pred             EECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCHHHHCCCCCCCCCEECCCCEECCCCCCCCCCCCCCC
T ss_conf             61227677654056789999999999999862898320552276766467523577340682014777763324455534


Q ss_pred             CCCEEEEEEEEEEEEEECCCCCCCCCCCCCCCCCCEEEEECCCCCCCEECCCCCCCCCCCCCCCCCCEEEECCEEEEEEE
Q ss_conf             64100123688632671489834665653467764179712330026010236854334443232886999999950770
Q gi|254780333|r  232 MQTVVTAEARIILIRKALAGELVSYGGQKKLTRDSLIAVAAIGYADGYPLTLSGLDSEHSPSVFLGGKGFIKGYMVPILG  311 (370)
Q Consensus       232 l~pv~~l~s~i~~ir~l~~G~~VgYg~~~~~~~~~~iavipiGYaDG~pr~ls~~~~~~~~~~~~~~~vli~G~~~pivG  311 (370)
                      |||+|+|+|+|++||++++|++||||++|++++|++|||||+||||||||.+||            ++|+|+|++|||+|
T Consensus       248 Lkpv~~l~s~v~~i~~~~~G~~VgYg~~~~a~~~~~iavv~iGYaDG~~r~~~~------------~~v~i~G~~~pivG  315 (391)
T 2vd8_A          248 LEPALSLHTXVAHIKQVIXGDGISYNVTYRTXTEEWIATVAIGYADGWLRRLQG------------FEVLVNGXRVPIVG  315 (391)
T ss_dssp             CCCCEEEEEEEEEEEEECTTCEESGGGCEECSSSEEEEEESCCGGGTCCGGGTT------------CEEEETTEEEEEES
T ss_pred             CCEEEEEEEECCEEEECCCCCCCCCCCEEECCCCEEEEEECEEECCCCCCCCCC------------CEEEECCEECCEEE
T ss_conf             322166541001069846999778676275136648988441806862304679------------88999998874745


Q ss_pred             ECCCCCEEEECCCCCCCCCCCEEEEECCC----CCHHHHHHHHCCCCEEEECCCCCCCCCCC
Q ss_conf             04256479966887787888789997888----89989999817946042154888736445
Q gi|254780333|r  312 KITMDMTMFDITDSLSIEVGDYIQIFGPD----IKLDDVALASGTTNYDLLVRIGTRYAKFY  369 (370)
Q Consensus       312 rv~MD~~~vdvt~~~~~~~GD~V~l~G~~----i~~~~~A~~~gti~yEil~~i~~RvpRiY  369 (370)
                      ||||||+|||+|+  ++++||+|+|||++    ++++++|+++|||+||++|+|++|+||+|
T Consensus       316 ri~MD~~~VDv~~--~v~~GD~v~l~G~~~~~~i~~~~~a~~~gti~yEil~~l~~Rv~R~y  375 (391)
T 2vd8_A          316 RVTMDQFMIHLPC--EVPLGTXVTLIGRQGDEYISATEVAEYSGTINYEIITTISFRVPRIF  375 (391)
T ss_dssp             CCCSSCEEEEESS--CCCTTCEEEEEEEETTEEECHHHHHHHTTSCHHHHHHTSCTTSCEEE
T ss_pred             EECCCEEEEECCC--CCCCCCEEEEECCCCCCCCCHHHHHHHHCCCCCHHHHCCCCCCCEEE
T ss_conf             7546437998999--99999989997799987889999999878961368608788887599



>2dy3_A Alanine racemase; alpha/beta barrel, isomerase; HET: PLP; 2.10A {Corynebacterium glutamicum} 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
>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
>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
>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
>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
>3oo2_A Alanine racemase 1; infectious diseases, center for structural of infectious diseases (csgid); 2.37A {Staphylococcus aureus subsp} 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
>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
>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
>3hur_A Alanine racemase; structural genomics, isomerase, pyridoxal phosphate, PSI-2, protein structure initiative; 2.50A {Oenococcus oeni psu-1} 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
>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
>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
>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
>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
>2qgh_A Diaminopimelate decarboxylase; lyase; HET: PLP LYS; 2.30A {Helicobacter pylori} PDB: 3c5q_A* Back     alignment and structure