Citrus Sinensis ID: 029918

Local Sequence Feature Prediction

Prediction and (Method)Result
Residue Number Marker
Protein Sequence ?
Secondary Structure (PSIPRED) ?
Secondary Structure Prediction (SSPRO) ?
Coil and Loop (DISEMBL) ?
Flexible Loop (DISEMBL) ?
Low Complexity Region (SEG) ?
Disordered region (IsUnstruct) ?
Disordered Region (DISOPRED) ?
Disordered Region (DISEMBL) ?
Disordered Region (DISPRO) ?
Transmembrane Helix (TMHMM) ?
Transmembrane Helix (HMMTOP) ?
Transmembrane Helix (MEMSAT) ?
TM Helix, Signal Peptide (MEMSAT_SVM) ?
TM Helix, Signal Peptide (Phobius) ?
Signal Peptide (SignalP HMM Mode) ?
Signal Peptide (SignalP NN Mode) ?
Coiled Coils (COILS) ?
Positional Conservation ?
 
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-----
MKNQEHEEERKRRENHINEQVEAETMAASAATDGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFIKCSWSHSCLLMI
cccccccHHccccccccccHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEcccccHHHHHHHHHHccccccHHHHHHHHHHHHccccccEEEEEcccccccccccccccccccEEEEccHHHHHHHHHHHHHHccccccEEEEEEEccccccccccccccHHHHHHHHc
cccccHHHHHHHccccHHHHHcccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEEEccccHHHHHHHHHHcHHHHcHHHHHHHHHHHHHcccccEEEEEcccccccHHHHHHccccccEEEEHcHHHHHHHHHHHHccccccccEEEEEEEEcccccccccccccHHHHEEHcc
MKNQEHEEERKRRENHINEQVEAETMAASAATDGVAATALRSVIQRVHQAaerssrppdriRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAaqlpddlewhfignlqsnkvkpllagvpnlamvesvdnEKIAGRLNRMVETMGRKPLKVLVQVNTSgeeygecfikcswshscllmi
mknqeheeerkrrenhineqvEAETMAASAATDGVAATALRSVIQRVHqaaerssrppdririvavsktkpvsvIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMvetmgrkplKVLVQVNTSGEEYGECFIKCSWSHSCLLMI
MknqeheeerkrrenhineQVEAEtmaasaatdgvaataLRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFIKCSWSHSCLLMI
************************************************************IRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFIKCSWSHSCLL**
**************************************ALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMV*TMGRKPLKVLVQVNTSGEEYGECFIKCSWSHSCLLMI
**************NHINEQVEAETMAASAATDGVAATALRSVIQ************PDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFIKCSWSHSCLLMI
*********************************GVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGE*YGECFIKCSWSHSC*L**
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MKxxxxxxxxxxxxxxxxxxxxxETMAASAATDGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFIKCSWSHSCLLMI
no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST ?

Original result of BLAST against SWISS-PROT Database

ID ?Alignment graph ?Length ? Definition ? RBH(Q2H) ? RBH(H2Q) ? Q cover ? H cover ? Identity ? E-value ?
Query185 2.2.26 [Sep-21-2011]
Q9Z2Y8 274 Proline synthase co-trans no no 0.691 0.467 0.481 2e-26
O94903 275 Proline synthase co-trans yes no 0.756 0.509 0.469 3e-26
Q5R4Z1 275 Proline synthase co-trans yes no 0.756 0.509 0.463 7e-26
Q3T0G5 273 Proline synthase co-trans yes no 0.745 0.505 0.463 1e-25
Q9P6Q1237 UPF0001 protein C644.09 O yes no 0.567 0.443 0.504 3e-23
Q9CPD5233 UPF0001 protein PM0112 OS yes no 0.670 0.532 0.473 6e-23
P38197257 UPF0001 protein YBL036C O yes no 0.578 0.416 0.518 3e-22
Q1ZXI6255 Proline synthase co-trans yes no 0.686 0.498 0.429 1e-21
P52055233 UPF0001 protein in pilT-p N/A no 0.6 0.476 0.491 1e-21
P44506237 UPF0001 protein HI_0090 O yes no 0.670 0.523 0.442 3e-21
>sp|Q9Z2Y8|PROSC_MOUSE Proline synthase co-transcribed bacterial homolog protein OS=Mus musculus GN=Prosc PE=1 SV=1 Back     alignment and function desciption
 Score =  118 bits (295), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 66/137 (48%), Positives = 94/137 (68%), Gaps = 9/137 (6%)

Query: 39  ALRSVIQRVHQAAERSSR--PPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVE 96
           ALR+V +RV Q+  R  R  P  + R+VAVSKTKP  ++ + Y  G R FGENYVQE++E
Sbjct: 16  ALRAVNERVQQSVARRPRDLPAIQPRLVAVSKTKPADMVIEAYGHGQRTFGENYVQELLE 75

Query: 97  KAAQLP-----DDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMG 151
           KA+         +++WHFIG+LQ   V  L+A VPNL+M+E+VD+ K+A ++N   +  G
Sbjct: 76  KASNPKILSSCPEIKWHFIGHLQKQNVNKLMA-VPNLSMLETVDSVKLADKVNSSWQKKG 134

Query: 152 -RKPLKVLVQVNTSGEE 167
             +PLKV+VQ+NTSGE+
Sbjct: 135 PTEPLKVMVQINTSGED 151

Mus musculus (taxid: 10090)
>sp|O94903|PROSC_HUMAN Proline synthase co-transcribed bacterial homolog protein OS=Homo sapiens GN=PROSC PE=1 SV=1 Back     alignment and function description
>sp|Q5R4Z1|PROSC_PONAB Proline synthase co-transcribed bacterial homolog protein OS=Pongo abelii GN=PROSC PE=2 SV=1 Back     alignment and function description
>sp|Q3T0G5|PROSC_BOVIN Proline synthase co-transcribed bacterial homolog protein OS=Bos taurus GN=PROSC PE=2 SV=1 Back     alignment and function description
>sp|Q9P6Q1|YKC9_SCHPO UPF0001 protein C644.09 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC644.09 PE=3 SV=1 Back     alignment and function description
>sp|Q9CPD5|Y112_PASMU UPF0001 protein PM0112 OS=Pasteurella multocida (strain Pm70) GN=PM0112 PE=3 SV=1 Back     alignment and function description
>sp|P38197|YBD6_YEAST UPF0001 protein YBL036C OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=YBL036C PE=1 SV=1 Back     alignment and function description
>sp|Q1ZXI6|PROSC_DICDI Proline synthase co-transcribed bacterial homolog protein OS=Dictyostelium discoideum GN=prosc PE=3 SV=2 Back     alignment and function description
>sp|P52055|YPI1_VIBAL UPF0001 protein in pilT-proC intergenic region OS=Vibrio alginolyticus PE=3 SV=1 Back     alignment and function description
>sp|P44506|Y090_HAEIN UPF0001 protein HI_0090 OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) GN=HI_0090 PE=1 SV=1 Back     alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST ?

Original result of BLAST against Nonredundant Database

GI ?Alignment Graph ?Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query185
359483335264 PREDICTED: proline synthase co-transcrib 0.832 0.583 0.748 7e-61
302144100 311 unnamed protein product [Vitis vinifera] 0.832 0.495 0.748 1e-60
449479493246 PREDICTED: proline synthase co-transcrib 0.767 0.577 0.763 1e-57
297844046242 alanine racemase family protein [Arabido 0.745 0.570 0.778 4e-57
18391333257 putative pyridoxal phosphate-dependent e 0.789 0.568 0.738 3e-55
30682530255 putative pyridoxal phosphate-dependent e 0.789 0.572 0.738 3e-55
356567318244 PREDICTED: proline synthase co-transcrib 0.767 0.581 0.732 3e-55
356527077252 PREDICTED: proline synthase co-transcrib 0.767 0.563 0.718 3e-55
356527075244 PREDICTED: proline synthase co-transcrib 0.767 0.581 0.718 4e-55
147861921245 hypothetical protein VITISV_024616 [Viti 0.751 0.567 0.762 7e-55
>gi|359483335|ref|XP_002263767.2| PREDICTED: proline synthase co-transcribed bacterial homolog protein-like [Vitis vinifera] Back     alignment and taxonomy information
 Score =  238 bits (608), Expect = 7e-61,   Method: Compositional matrix adjust.
 Identities = 116/155 (74%), Positives = 135/155 (87%), Gaps = 1/155 (0%)

Query: 13  RENHINEQVEAETMAASAATDGVAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPV 72
           R+    E+ E  +MAASA  DGVAA ALRSV+ RV QAAERS R P +IR+VAVSKTK V
Sbjct: 7   RDGERAEEAEQSSMAASA-MDGVAAAALRSVLHRVQQAAERSGRGPHQIRVVAVSKTKSV 65

Query: 73  SVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVE 132
           S+IR+VY++GHRCFGENYVQEI+EKA QLP+D+EWHFIGNLQSNKVKPLL GVPNLA+VE
Sbjct: 66  SLIREVYDSGHRCFGENYVQEIIEKAPQLPEDIEWHFIGNLQSNKVKPLLTGVPNLAVVE 125

Query: 133 SVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEE 167
           +VD+EKIA RL+RMV T+GRKPLKV+VQVNTSGEE
Sbjct: 126 TVDDEKIADRLDRMVATIGRKPLKVMVQVNTSGEE 160

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota
>gi|302144100|emb|CBI23205.3| unnamed protein product [Vitis vinifera] Back     alignment and taxonomy information
>gi|449479493|ref|XP_004155614.1| PREDICTED: proline synthase co-transcribed bacterial homolog protein-like [Cucumis sativus] Back     alignment and taxonomy information
>gi|297844046|ref|XP_002889904.1| alanine racemase family protein [Arabidopsis lyrata subsp. lyrata] gi|297335746|gb|EFH66163.1| alanine racemase family protein [Arabidopsis lyrata subsp. lyrata] Back     alignment and taxonomy information
>gi|18391333|ref|NP_563897.1| putative pyridoxal phosphate-dependent enzyme, YBL036C type [Arabidopsis thaliana] gi|16226282|gb|AAL16123.1|AF428291_1 At1g11930/F12F1_20 [Arabidopsis thaliana] gi|21436037|gb|AAM51596.1| At1g11930/F12F1_20 [Arabidopsis thaliana] gi|332190696|gb|AEE28817.1| putative pyridoxal phosphate-dependent enzyme, YBL036C type [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|30682530|ref|NP_849649.1| putative pyridoxal phosphate-dependent enzyme, YBL036C type [Arabidopsis thaliana] gi|3157934|gb|AAC17617.1| Similar to hypothetical protein F09E5.8 gb|U37429 from C. elegans. ESTs gb|T42019 and gb|N97000 come from this gene [Arabidopsis thaliana] gi|332190697|gb|AEE28818.1| putative pyridoxal phosphate-dependent enzyme, YBL036C type [Arabidopsis thaliana] Back     alignment and taxonomy information
>gi|356567318|ref|XP_003551868.1| PREDICTED: proline synthase co-transcribed bacterial homolog protein-like [Glycine max] Back     alignment and taxonomy information
>gi|356527077|ref|XP_003532140.1| PREDICTED: proline synthase co-transcribed bacterial homolog protein-like isoform 2 [Glycine max] Back     alignment and taxonomy information
>gi|356527075|ref|XP_003532139.1| PREDICTED: proline synthase co-transcribed bacterial homolog protein-like isoform 1 [Glycine max] Back     alignment and taxonomy information
>gi|147861921|emb|CAN80917.1| hypothetical protein VITISV_024616 [Vitis vinifera] Back     alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST ?

Original result of BLAST against Gene Ontology (AMIGO)

ID ? Alignment graph ? Length ? Definition ? Q cover ? H cover ? Identity ? E-value ?
Query185
UNIPROTKB|Q0DKP7214 Os05g0150000 "Os05g0150000 pro 0.691 0.598 0.75 8.5e-49
TAIR|locus:2008910257 AT1G11930 [Arabidopsis thalian 0.691 0.498 0.765 2.3e-48
UNIPROTKB|A8HP79251 CHLREDRAFT_116897 "Predicted p 0.697 0.513 0.583 1.9e-35
MGI|MGI:1891207 274 Prosc "proline synthetase co-t 0.686 0.463 0.485 2.5e-26
UNIPROTKB|E1C516 276 PROSC "Uncharacterized protein 0.686 0.460 0.5 4e-26
UNIPROTKB|E5RG77152 PROSC "Proline synthase co-tra 0.686 0.835 0.492 4e-26
UNIPROTKB|O94903 275 PROSC "Proline synthase co-tra 0.686 0.461 0.492 4e-26
UNIPROTKB|F1RX84 275 PROSC "Uncharacterized protein 0.686 0.461 0.5 5.2e-26
UNIPROTKB|Q3T0G5 273 PROSC "Proline synthase co-tra 0.681 0.461 0.488 8.4e-26
RGD|1308962 275 Prosc "proline synthetase co-t 0.686 0.461 0.470 2.9e-25
UNIPROTKB|Q0DKP7 Os05g0150000 "Os05g0150000 protein" [Oryza sativa Japonica Group (taxid:39947)] Back     alignment and assigned GO terms
 Score = 509 (184.2 bits), Expect = 8.5e-49, P = 8.5e-49
 Identities = 96/128 (75%), Positives = 113/128 (88%)

Query:    40 LRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAA 99
             LRSV+ R  QAA RS R P+ +R+VAVSKTKPV VIR VY+AGHRCFGENYVQE+++KA+
Sbjct:     9 LRSVLSRAQQAAARSGRAPESVRVVAVSKTKPVGVIRGVYDAGHRCFGENYVQELIDKAS 68

Query:   100 QLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLV 159
             QLP+D+EWHFIGNLQSNK + LLAGVPNL MVESVD++KIA RL+R+V  +GRKPLKVLV
Sbjct:    69 QLPEDIEWHFIGNLQSNKARALLAGVPNLDMVESVDDQKIANRLDRVVADLGRKPLKVLV 128

Query:   160 QVNTSGEE 167
             QVNTSGEE
Sbjct:   129 QVNTSGEE 136
GO:0030170 "pyridoxal phosphate binding" evidence=ISS
TAIR|locus:2008910 AT1G11930 [Arabidopsis thaliana (taxid:3702)] Back     alignment and assigned GO terms
UNIPROTKB|A8HP79 CHLREDRAFT_116897 "Predicted protein" [Chlamydomonas reinhardtii (taxid:3055)] Back     alignment and assigned GO terms
MGI|MGI:1891207 Prosc "proline synthetase co-transcribed" [Mus musculus (taxid:10090)] Back     alignment and assigned GO terms
UNIPROTKB|E1C516 PROSC "Uncharacterized protein" [Gallus gallus (taxid:9031)] Back     alignment and assigned GO terms
UNIPROTKB|E5RG77 PROSC "Proline synthase co-transcribed bacterial homolog protein" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|O94903 PROSC "Proline synthase co-transcribed bacterial homolog protein" [Homo sapiens (taxid:9606)] Back     alignment and assigned GO terms
UNIPROTKB|F1RX84 PROSC "Uncharacterized protein" [Sus scrofa (taxid:9823)] Back     alignment and assigned GO terms
UNIPROTKB|Q3T0G5 PROSC "Proline synthase co-transcribed bacterial homolog protein" [Bos taurus (taxid:9913)] Back     alignment and assigned GO terms
RGD|1308962 Prosc "proline synthetase co-transcribed homolog (bacterial)" [Rattus norvegicus (taxid:10116)] Back     alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries ?

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server ?

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software ?

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING ?

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST ?

Original result of RPS-BLAST against CDD database part I

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query185
cd06822227 cd06822, PLPDE_III_YBL036c_euk, Pyridoxal 5-phosph 5e-65
cd00635222 cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxa 3e-52
COG0325228 COG0325, COG0325, Predicted enzyme with a TIM-barr 2e-51
cd06824224 cd06824, PLPDE_III_Yggs_like, Pyridoxal 5-phosphat 2e-48
TIGR00044229 TIGR00044, TIGR00044, pyridoxal phosphate enzyme, 2e-35
pfam01168217 pfam01168, Ala_racemase_N, Alanine racemase, N-ter 1e-12
cd06808211 cd06808, PLPDE_III, Type III Pyridoxal 5-phosphate 6e-09
>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 
 Score =  198 bits (507), Expect = 5e-65
 Identities = 78/131 (59%), Positives = 104/131 (79%), Gaps = 4/131 (3%)

Query: 40  LRSVIQRVHQAAERSSR--PPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEK 97
           L + ++R+ QA +R+S+  P  + R+VAVSKTKP  +I++ Y+AG R FGENYVQE++EK
Sbjct: 1   LIANLKRIRQAVKRASKKLPASKPRLVAVSKTKPAELIKEAYDAGQRHFGENYVQELIEK 60

Query: 98  AAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMG-RKPLK 156
           A  LP D++WHFIG+LQSNKVK  L  VPNL MVE+VD+EK+A +LN+  E +G R+PLK
Sbjct: 61  APDLPIDIKWHFIGHLQSNKVK-KLLKVPNLYMVETVDSEKLADKLNKAWEKLGEREPLK 119

Query: 157 VLVQVNTSGEE 167
           V+VQVNTSGEE
Sbjct: 120 VMVQVNTSGEE 130

This subfamily contains mostly uncharacterized eukaryotic proteins with similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Some members of this subfamily are also referred to as PROSC (Proline synthetase co-transcribed bacterial homolog). Length = 227
>gnl|CDD|143483 cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins Back     alignment and domain information
>gnl|CDD|223402 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|129155 TIGR00044, TIGR00044, pyridoxal phosphate enzyme, YggS family Back     alignment and domain information
>gnl|CDD|216340 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain Back     alignment and domain information
>gnl|CDD|143484 cd06808, PLPDE_III, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Back     alignment and domain information

Conserved Domains Detected by HHsearch ?

Original result of HHsearch against CDD database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query 185
COG0325228 Predicted enzyme with a TIM-barrel fold [General f 100.0
cd06822227 PLPDE_III_YBL036c_euk Pyridoxal 5-phosphate (PLP)- 100.0
KOG3157244 consensus Proline synthetase co-transcribed protei 100.0
TIGR00044229 pyridoxal phosphate enzyme, YggS family. Members o 100.0
cd06824224 PLPDE_III_Yggs_like Pyridoxal 5-phosphate (PLP)-bi 99.97
cd00635222 PLPDE_III_YBL036c_like Type III Pyridoxal 5-phosph 99.85
cd06815 353 PLPDE_III_AR_like_1 Type III Pyridoxal 5-phosphate 99.6
cd00430 367 PLPDE_III_AR Type III Pyridoxal 5-phosphate (PLP)- 99.6
PF01168218 Ala_racemase_N: Alanine racemase, N-terminal domai 99.6
TIGR00492 367 alr alanine racemase. This enzyme interconverts L- 99.37
cd06821 361 PLPDE_III_D-TA Type III Pyridoxal 5-phosphate (PLP 99.29
PRK00053 363 alr alanine racemase; Reviewed 99.29
cd06808211 PLPDE_III Type III Pyridoxal 5-phosphate (PLP)-Dep 99.21
cd06820 353 PLPDE_III_LS_D-TA_like Type III Pyridoxal 5-phosph 99.18
cd07376 345 PLPDE_III_DSD_D-TA_like Type III Pyridoxal 5-phosp 99.12
cd06811 382 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate 99.05
PRK13340 406 alanine racemase; Reviewed 98.54
cd06819 358 PLPDE_III_LS_D-TA Type III Pyridoxal 5-phosphate ( 98.47
cd06818 382 PLPDE_III_cryptic_DSD Type III Pyridoxal 5-phospha 98.44
cd06826 365 PLPDE_III_AR2 Type III Pyridoxal 5-phosphate (PLP) 98.31
cd06843 377 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate 98.15
cd06827 354 PLPDE_III_AR_proteobact Type III Pyridoxal 5-phosp 98.13
cd06839 382 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate 98.09
cd06810 368 PLPDE_III_ODC_DapDC_like Type III Pyridoxal 5-phos 98.06
cd06828 373 PLPDE_III_DapDC Type III Pyridoxal 5-phosphate (PL 97.97
TIGR01048 417 lysA diaminopimelate decarboxylase. This family co 97.91
cd06825 368 PLPDE_III_VanT Type III Pyridoxal 5-phosphate (PLP 97.79
cd06817 389 PLPDE_III_DSD Type III Pyridoxal 5-phosphate (PLP) 97.76
PRK11930 822 putative bifunctional UDP-N-acetylmuramoyl-tripept 97.72
cd06814 379 PLPDE_III_DSD_D-TA_like_3 Type III Pyridoxal 5-pho 97.68
cd06812 374 PLPDE_III_DSD_D-TA_like_1 Type III Pyridoxal 5-pho 97.62
PRK03646 355 dadX alanine racemase; Reviewed 97.53
cd06813 388 PLPDE_III_DSD_D-TA_like_2 Type III Pyridoxal 5-pho 97.44
cd06842 423 PLPDE_III_Y4yA_like Type III Pyridoxal 5-phosphate 97.44
PLN02537 410 diaminopimelate decarboxylase 97.23
TIGR03099 398 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, ex 96.87
cd06841 379 PLPDE_III_MccE_like Type III Pyridoxal 5-phosphate 96.81
COG3457 353 Predicted amino acid racemase [Amino acid transpor 96.72
cd00622 362 PLPDE_III_ODC Type III Pyridoxal 5-phosphate (PLP) 95.47
COG0787 360 Alr Alanine racemase [Cell envelope biogenesis, ou 95.46
COG3616 368 Predicted amino acid aldolase or racemase [Amino a 91.13
TIGR03619246 F420_Rv2161c probable F420-dependent oxidoreductas 89.75
PRK11165 420 diaminopimelate decarboxylase; Provisional 82.01
TIGR01047 380 nspC carboxynorspermidine decarboxylase. This prot 81.38
COG0019 394 LysA Diaminopimelate decarboxylase [Amino acid tra 80.68
>COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only] Back     alignment and domain information 
Probab=100.00  E-value=2.2e-58  Score=392.45  Aligned_cols=147  Identities=46%  Similarity=0.626  Sum_probs=140.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCC--CceEEEEec
Q 029918           35 VAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPD--DLEWHFIGN  112 (185)
Q Consensus        35 ~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~--~i~WHfIG~  112 (185)
                      ++.+||..|+++|.++|.++||+|++|+|||||||+|+++|++||++|+|+||||||||+.+|++.|++  +|.|||||+
T Consensus         2 ~i~~nl~~v~~~I~~a~~~a~R~~~~V~LvAVSK~~~~~~I~~~~~aG~r~fGENrvQe~~~K~~~l~~~~~i~WHfIG~   81 (228)
T COG0325           2 DIKENLAAVRERIAAAAERAGRNPGSVTLVAVSKTVPAEDIREAYEAGQRHFGENRVQEALDKIEALKDLPDIEWHFIGP   81 (228)
T ss_pred             cHHHHHHHHHHHHHHHHHHcCCCCCcEEEEEEeCCCCHHHHHHHHHcCChhhcchHHHHHHHHHHhcCcCCCeEEEEech
Confidence            478999999999999999999999999999999999999999999999999999999999999999987  499999999


Q ss_pred             ccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCccccc------------ccCCcccc
Q 029918          113 LQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECF------------IKCSWSHS  180 (185)
Q Consensus       113 LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~------------~~~~~l~l  180 (185)
                      |||||+|+++   ++|+|||||||+|||.+|++++...+ ++++||||||+|+|+||||+            ..||+|.+
T Consensus        82 LQsNK~k~v~---~~~~~ihSlDr~klA~~l~kra~~~~-~~l~v~iQVNi~~E~sK~G~~~~e~~~~~~~~~~~~~L~l  157 (228)
T COG0325          82 LQSNKVKLVA---ENFDWIHSLDRLKLAKELNKRALELP-KPLNVLIQVNISGEESKSGVPPEELDELAQEVQELPNLEL  157 (228)
T ss_pred             hhhhHHHHHH---hhcceeeecCHHHHHHHHHHHHHhCC-CCceEEEEEecCCccccCCCCHHHHHHHHHHHHhCCCCeE
Confidence            9999999999   89999999999999999999887654 58999999999999999996            36999999


Q ss_pred             cccCC
Q 029918          181 CLLMI  185 (185)
Q Consensus       181 ~g~m~  185 (185)
                      .|||+
T Consensus       158 ~GLM~  162 (228)
T COG0325         158 RGLMT  162 (228)
T ss_pred             eEEEe
Confidence            99996

>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
>KOG3157 consensus Proline synthetase co-transcribed protein [General function prediction only] Back     alignment and domain information
>TIGR00044 pyridoxal phosphate enzyme, YggS family 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
>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
>PF01168 Ala_racemase_N: Alanine racemase, N-terminal domain; InterPro: IPR001608 Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine Back     alignment and domain information
>TIGR00492 alr alanine racemase 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
>PRK00053 alr alanine racemase; Reviewed Back     alignment and domain information
>cd06808 PLPDE_III Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes 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
>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
>cd06811 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX Back     alignment and domain information
>PRK13340 alanine racemase; Reviewed 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
>cd06818 PLPDE_III_cryptic_DSD Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bacterial Cryptic D-Serine Dehydratase 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
>cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE 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
>cd06839 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk 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
>cd06828 PLPDE_III_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase Back     alignment and domain information
>TIGR01048 lysA diaminopimelate decarboxylase 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
>cd06817 PLPDE_III_DSD Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Eukaryotic D-Serine Dehydratase 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
>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
>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
>PRK03646 dadX alanine racemase; Reviewed 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
>cd06842 PLPDE_III_Y4yA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Y4yA Back     alignment and domain information
>PLN02537 diaminopimelate decarboxylase Back     alignment and domain information
>TIGR03099 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, exosortase system type 1 associated Back     alignment and domain information
>cd06841 PLPDE_III_MccE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE Back     alignment and domain information
>COG3457 Predicted amino acid racemase [Amino acid transport and metabolism] Back     alignment and domain information
>cd00622 PLPDE_III_ODC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase Back     alignment and domain information
>COG0787 Alr Alanine racemase [Cell envelope biogenesis, outer membrane] Back     alignment and domain information
>COG3616 Predicted amino acid aldolase or racemase [Amino acid transport and metabolism] Back     alignment and domain information
>TIGR03619 F420_Rv2161c probable F420-dependent oxidoreductase, Rv2161c family Back     alignment and domain information
>PRK11165 diaminopimelate decarboxylase; Provisional Back     alignment and domain information
>TIGR01047 nspC carboxynorspermidine decarboxylase Back     alignment and domain information
>COG0019 LysA Diaminopimelate decarboxylase [Amino acid transport and metabolism] Back     alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST ?

Original result of BLAST against Protein Data Bank

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query185
1b54_A257 Crystal Structure Of A Yeast Hypothetical Protein-A 8e-23
1ct5_A256 Crystal Structure Of Yeast Hypothetical Protein Ybl 1e-22
1w8g_A234 Crystal Structure Of E. Coli K-12 Yggs Length = 234 1e-19
3sy1_A245 Crystal Structure Of Engineered Protein. Northeast 1e-16
3r79_A244 Crystal Structure Of An Uncharactertized Protein Fr 3e-16
3cpg_A282 Crystal Structure Of An Unknown Protein From Bifido 3e-12
>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 
Iteration: 1

 Score =  102 bits (255), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 57/110 (51%), Positives = 75/110 (68%), Gaps = 3/110 (2%)
Query: 60  RIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNKVK 119
           +I ++ VSK KP S I+ +Y+ G R FGENYVQE++EKA  LPDD++WHFIG LQ+NK K
Sbjct: 41  KILLLVVSKLKPASDIQILYDHGVREFGENYVQELIEKAKLLPDDIKWHFIGGLQTNKCK 100
Query: 120 PLLAGVPNLAMVESVDNEKIAGRLN--RMVETMGRKPLKVLVQVNTSGEE 167
             LA VPNL  VE++D+ K A +LN  R        P+   VQ+NTS E+
Sbjct: 101 D-LAKVPNLYSVETIDSLKKAKKLNESRAKFQPDCNPILCNVQINTSHED 149
>pdb|1CT5|A Chain A, Crystal Structure Of Yeast Hypothetical Protein Ybl036c-Selenomet Crystal Length = 256 Back     alignment and structure
>pdb|1W8G|A Chain A, Crystal Structure Of E. Coli K-12 Yggs Length = 234 Back     alignment and structure
>pdb|3SY1|A Chain A, Crystal Structure Of Engineered Protein. Northeast Structural Genomics Consortium Target Or70 Length = 245 Back     alignment and structure
>pdb|3R79|A Chain A, Crystal Structure Of An Uncharactertized Protein From Agrobacterium Tumefaciens Length = 244 Back     alignment and structure
>pdb|3CPG|A Chain A, Crystal Structure Of An Unknown Protein From Bifidobacterium Adolescentis Length = 282 Back     alignment and structure

Structure Templates Detected by RPS-BLAST ?

Original result of RPS-BLAST against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query185
1ct5_A256 Protein (yeast hypothetical protein, selenoMet); T 1e-65
3sy1_A245 UPF0001 protein YGGS; engineered protein, structur 6e-61
3cpg_A282 Uncharacterized protein; unknown protein, TIM barr 1e-56
3r79_A244 Uncharacterized protein; PSI-biology, structural g 6e-56
>1ct5_A Protein (yeast hypothetical protein, selenoMet); TIM barrel, pyridoxal-5'-phosphate, selenomethionine, structural genomics, PSI; HET: PLP; 2.00A {Saccharomyces cerevisiae} SCOP: c.1.6.2 PDB: 1b54_A* Length = 256 Back     alignment and structure
 Score =  200 bits (512), Expect = 1e-65
 Identities = 60/149 (40%), Positives = 84/149 (56%), Gaps = 5/149 (3%)

Query: 23  AETMAASAATDGVAATALRSVIQRVHQAAE--RSSRPPDRIRIVAVSKTKPVSVIRQVYE 80
           +  +               SV + V+  A+    +    +I ++ VSK KP S I+ +Y+
Sbjct: 1   STGITYDEDRKTQLIAQYESVREVVNAEAKNVHVNENASKILLLVVSKLKPASDIQILYD 60

Query: 81  AGHRCFGENYVQEIVEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIA 140
            G R FGENYVQE++EKA  LPDD++WHFIG LQ+NK K  LA VPNL  VE++D+ K A
Sbjct: 61  HGVREFGENYVQELIEKAKLLPDDIKWHFIGGLQTNKCK-DLAKVPNLYSVETIDSLKKA 119

Query: 141 GRLNRMVETMGR--KPLKVLVQVNTSGEE 167
            +LN           P+   VQ+NTS E+
Sbjct: 120 KKLNESRAKFQPDCNPILCNVQINTSHED 148
>3sy1_A UPF0001 protein YGGS; engineered protein, structural genomics, PSI-biology, protei structure initiative; HET: MES; 1.47A {Escherichia coli} PDB: 1w8g_A* Length = 245 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
>3r79_A Uncharacterized protein; PSI-biology, structural genomics, NEW YORK structural genomi research consortium, TIM barrel; HET: PLP; 1.90A {Agrobacterium tumefaciens} Length = 244 Back     alignment and structure

Structure Templates Detected by HHsearch ?

Original result of HHsearch against PDB70 database

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query185
3r79_A244 Uncharacterized protein; PSI-biology, structural g 100.0
3sy1_A245 UPF0001 protein YGGS; engineered protein, structur 100.0
1ct5_A256 Protein (yeast hypothetical protein, selenoMet); T 100.0
3cpg_A282 Uncharacterized protein; unknown protein, TIM barr 99.96
3kw3_A 376 Alanine racemase; niaid, ssgcid, seattle structura 99.71
3e5p_A 371 Alanine racemase; ALR, PLP, SCP, isomerase, pyrido 99.66
1rcq_A 357 Catabolic alanine racemase DADX; alpha-beta barrel 99.65
1xfc_A 384 Alanine racemase; alpha-beta barrel, beta-structur 99.65
1vfs_A 386 Alanine racemase; TIM-barrel, greek-KEY motief, is 99.64
2rjg_A 379 Alanine racemase; alpha/beta barrel, cell shape, c 99.64
4a3q_A 382 Alanine racemase 1; isomerase, PLP-dependent enzym 99.63
3co8_A 380 Alanine racemase; protein structure initiative II, 99.63
4ecl_A 374 Serine racemase, vantg; antibiotic resistance, van 99.62
2vd8_A 391 Alanine racemase; pyridoxal 5'-phosphate, peptidog 99.59
3hur_A 395 Alanine racemase; structural genomics, isomerase, 99.58
2dy3_A 361 Alanine racemase; alpha/beta barrel, isomerase; HE 99.57
3mub_A 367 Alanine racemase; alpha/beta barrel, extended beta 99.56
3gwq_A 426 D-serine deaminase; structural genomics, joint cen 99.55
1bd0_A 388 Alanine racemase; isomerase, pyridoxal phosphate, 99.53
1twi_A 434 Diaminopimelate decarboxylase; antibiotic resistan 99.46
2p3e_A 420 Diaminopimelate decarboxylase; southeast collabora 99.46
3llx_A 376 Predicted amino acid aldolase or racemase; structu 99.4
2j66_A 428 BTRK, decarboxylase; butirosin, AHBA biosynthesis, 99.33
3anu_A 376 D-serine dehydratase; PLP-dependent fold-type III 99.32
2qgh_A 425 Diaminopimelate decarboxylase; lyase; HET: PLP LYS 99.28
2o0t_A 467 Diaminopimelate decarboxylase; PLP binding enzyme, 99.14
3vab_A 443 Diaminopimelate decarboxylase 1; structural genomi 98.22
3n2b_A 441 Diaminopimelate decarboxylase; LYSA, lyase, struct 98.2
2nva_A 372 Arginine decarboxylase, A207R protein; PLP, TIM ba 97.95
2plj_A 419 Lysine/ornithine decarboxylase; type IV decarboxyl 97.61
2yxx_A 386 Diaminopimelate decarboxylase; TM1517, TIM beta/al 97.12
7odc_A 424 Protein (ornithine decarboxylase); pyridoxal-5'-ph 97.06
3n29_A 418 Carboxynorspermidine decarboxylase; lyase; HET: PL 96.88
3nzq_A 666 ADC, biosynthetic arginine decarboxylase; alpha-be 96.64
3nzp_A 619 Arginine decarboxylase; alpha-beta protein, struct 96.37
3mt1_A 365 Putative carboxynorspermidine decarboxylase prote; 96.13
3n2o_A 648 ADC, biosynthetic arginine decarboxylase; lyase; H 96.01
1f3t_A 425 ODC, ornithine decarboxylase; beta-alpha-barrel, m 95.35
3btn_A 448 Antizyme inhibitor 1; TIM-like A/B barrel domain a 94.28
2oo0_A 471 ODC, ornithine decarboxylase; beta-alpha barrel, s 94.1
1knw_A 425 Diaminopimelate decarboxylase; pyridoxal-phosphate 91.2
>3r79_A Uncharacterized protein; PSI-biology, structural genomics, NEW YORK structural genomi research consortium, TIM barrel; HET: PLP; 1.90A {Agrobacterium tumefaciens} Back     alignment and structure
Probab=100.00  E-value=2.1e-43  Score=300.77  Aligned_cols=147  Identities=39%  Similarity=0.430  Sum_probs=139.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHcCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCC---CCceEEEEe
Q 029918           35 VAATALRSVIQRVHQAAERSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLP---DDLEWHFIG  111 (185)
Q Consensus        35 ~i~~nl~~V~~rI~~a~~~~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~---~~i~WHfIG  111 (185)
                      .|.+||+.|+++|+++|.++||+|++|+|+||||++|++.|++++++|+++|||||+||+.+|.+.++   ++|.|||||
T Consensus         5 ~i~~nl~~v~~~i~~a~~~~~r~~~~v~l~AVvKahga~~i~~~~~~G~~~fgen~vqEa~~kr~~~~~~~~~i~wh~iG   84 (244)
T 3r79_A            5 EIEARLEDVRQRIADVAEKSGRKAADVALVAVSKTFDAEAIQPVIDAGQRVFGENRVQEAQGKWPALKEKTSDIELHLIG   84 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCCGGGSEEEEECTTCCHHHHHHHHHTTCCEEEESCHHHHHHHHHHHHHHSTTCEEEECS
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCCCCcEEEEEECCcCHHHHHHHHHCCCCEEEEeeHHHHHHHHHhccccCCCeEEEecC
Confidence            58899999999999999999999999999999999999999999999999999999999999998875   379999999


Q ss_pred             cccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcCCCCccEEEEEeCCCCCcccccc------------cCCccc
Q 029918          112 NLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMGRKPLKVLVQVNTSGEEYGECFI------------KCSWSH  179 (185)
Q Consensus       112 ~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~~~~l~VLIQVNis~E~sKsG~~------------~~~~l~  179 (185)
                      +||+||+++++   +.+++||||||+++|++|++.+.+.+ ++++|+|||||++|.+|+|+.            .||+|+
T Consensus        85 ~lq~nk~~~~v---~~~~~i~sVds~~~a~~L~~~a~~~g-~~~~V~LqVdtG~e~~R~Gv~~ee~~~l~~~i~~l~~L~  160 (244)
T 3r79_A           85 PLQSNKAADAV---ALFDVVESIDREKIARALSEECARQG-RSLRFYVQVNTGLEPQKAGIDPRETVAFVAFCRDELKLP  160 (244)
T ss_dssp             CCCGGGHHHHH---HHCSEEEEECSHHHHHHHHHHHHHHT-CCCEEEEEBCTTCCTTSCSBCHHHHHHHHHHHHHTSCCC
T ss_pred             CCCHHHHHHHH---HHCCEEEeeCCHHHHHHHHHHHHHcC-CCceEEEEEECCCCcCCCCCCHHHHHHHHHHHHcCCCCE
Confidence            99999999999   67899999999999999999998775 689999999999999999973            599999


Q ss_pred             ccccCC
Q 029918          180 SCLLMI  185 (185)
Q Consensus       180 l~g~m~  185 (185)
                      +.||||
T Consensus       161 l~GlmT  166 (244)
T 3r79_A          161 VEGLMC  166 (244)
T ss_dssp             CCEEEC
T ss_pred             EEEEEe
Confidence            999997
>3sy1_A UPF0001 protein YGGS; engineered protein, structural genomics, PSI-biology, protei structure initiative; HET: MES; 1.47A {Escherichia coli} PDB: 1w8g_A* Back     alignment and structure
>1ct5_A Protein (yeast hypothetical protein, selenoMet); TIM barrel, pyridoxal-5'-phosphate, selenomethionine, structural genomics, PSI; HET: PLP; 2.00A {Saccharomyces cerevisiae} SCOP: c.1.6.2 PDB: 1b54_A* 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} Back     alignment and structure
>3kw3_A Alanine racemase; niaid, ssgcid, seattle structural genomics center for infect disease, iodide SOAK, LLP, CAT-scratch DI isomerase; HET: LLP; 2.04A {Bartonella henselae} Back     alignment and structure
>3e5p_A Alanine racemase; ALR, PLP, SCP, isomerase, pyridoxal phosph; HET: PLP EPE 2PE; 2.50A {Enterococcus faecalis} PDB: 3e6e_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
>1xfc_A Alanine racemase; alpha-beta barrel, beta-structure for C-terminal domain, INT aldimine form, isomerase; HET: PLP; 1.90A {Mycobacterium tuberculosis} 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
>2rjg_A Alanine racemase; alpha/beta barrel, cell shape, cell WALL biogenesis/degradat 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
>4a3q_A Alanine racemase 1; isomerase, PLP-dependent enzymes; HET: PLP; 2.15A {Staphylococcus aureus} PDB: 3oo2_A Back     alignment and structure
>3co8_A Alanine racemase; protein structure initiative II, PSI-II, PLP, TIM barrel, structural genomics, NEW YORK SGX center for structural genomics; HET: PLP; 1.70A {Oenococcus oeni} Back     alignment and structure
>4ecl_A Serine racemase, vantg; antibiotic resistance, vancomycin resistance, center for STR genomics of infectious diseases (csgid); HET: MSE; 2.02A {Enterococcus faecalis} 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
>3hur_A Alanine racemase; structural genomics, isomerase, pyridoxal phosphate, PSI-2, protein structure initiative; 2.50A {Oenococcus oeni psu-1} Back     alignment and structure
>2dy3_A Alanine racemase; alpha/beta barrel, isomerase; HET: PLP; 2.10A {Corynebacterium glutamicum} Back     alignment and structure
>3gwq_A D-serine deaminase; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, lyase; HET: MSE; 2.00A {Burkholderia xenovorans LB400} 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* 3uw6_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
>2p3e_A Diaminopimelate decarboxylase; southeast collaboratory for struct genomics, riken spring-8 center; 1.99A {Aquifex aeolicus} Back     alignment and structure
>3llx_A Predicted amino acid aldolase or racemase; structural genomics, joint center for structural genomics, J protein structure initiative; HET: LLP TRS; 1.50A {Idiomarina loihiensis} Back     alignment and structure
>2j66_A BTRK, decarboxylase; butirosin, AHBA biosynthesis, lyase; HET: PLP; 1.65A {Bacillus circulans} Back     alignment and structure
>3anu_A D-serine dehydratase; PLP-dependent fold-type III enzyme, PL binding, zinc binding, lyase; HET: PLP; 1.90A {Gallus gallus} PDB: 3anv_A* 3awn_A* 3awo_A* Back     alignment and structure
>2qgh_A Diaminopimelate decarboxylase; lyase; HET: PLP LYS; 2.30A {Helicobacter pylori} PDB: 3c5q_A* Back     alignment and structure
>2o0t_A Diaminopimelate decarboxylase; PLP binding enzyme, lysine biosynthesis, STRU genomics, TB structural genomics consortium, TBSGC; HET: LLP; 2.33A {Mycobacterium tuberculosis} PDB: 1hkv_A* 1hkw_A Back     alignment and structure
>3vab_A Diaminopimelate decarboxylase 1; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: LLP; 2.10A {Brucella melitensis BV} 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
>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
>2plj_A Lysine/ornithine decarboxylase; type IV decarboxylase, beta/alpha barrel, beta barrel, lyase; HET: P3T; 1.70A {Vibrio vulnificus} PDB: 2plk_A* Back     alignment and structure
>2yxx_A Diaminopimelate decarboxylase; TM1517, TIM beta/alpha barrel fold, lyase, structural genomi NPPSFA; HET: PLP; 1.70A {Thermotoga maritima} Back     alignment and structure
>7odc_A Protein (ornithine decarboxylase); pyridoxal-5'-phosphate, PLP, group IV decarboxylase, polyami 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
>3n29_A Carboxynorspermidine decarboxylase; lyase; HET: PLP; 1.90A {Campylobacter jejuni subsp} Back     alignment and structure
>3nzq_A ADC, biosynthetic arginine decarboxylase; alpha-beta protein, structural genomics, PSI-biology, protei structure initiative; 3.10A {Escherichia coli} Back     alignment and structure
>3nzp_A Arginine decarboxylase; alpha-beta protein, structural genomics, PSI-biology, protei structure initiative; HET: PLP; 3.00A {Campylobacter jejuni subsp} Back     alignment and structure
>3mt1_A Putative carboxynorspermidine decarboxylase prote; PSI2, MCSG, structural genomics; 2.50A {Sinorhizobium meliloti} Back     alignment and structure
>3n2o_A ADC, biosynthetic arginine decarboxylase; lyase; HET: PLP; 2.30A {Vibrio vulnificus} 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
>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
>2oo0_A ODC, ornithine decarboxylase; beta-alpha barrel, sheet, lyase; HET: PLP; 1.90A {Homo sapiens} Back     alignment and structure
>1knw_A Diaminopimelate decarboxylase; pyridoxal-phosphate, decarboxylation, lysin barrel, lyase; HET: PLP MES; 2.10A {Escherichia coli} SCOP: b.49.2.3 c.1.6.1 PDB: 1ko0_A* Back     alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST ?

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

ID ?Alignment Graph ?Length ? Definition ? E-value ?
Query 185
d1ct5a_244 c.1.6.2 (A:) "Hypothetical" protein ybl036c {Baker 2e-19
>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 = 80.3 bits (197), Expect = 2e-19
 Identities = 59/135 (43%), Positives = 81/135 (60%), Gaps = 5/135 (3%)

Query: 37  ATALRSVIQRVHQAAE--RSSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEI 94
                SV + V+  A+    +    +I ++ VSK KP S I+ +Y+ G R FGENYVQE+
Sbjct: 14  IAQYESVREVVNAEAKNVHVNENASKILLLVVSKLKPASDIQILYDHGVREFGENYVQEL 73

Query: 95  VEKAAQLPDDLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNR--MVETMGR 152
           +EKA  LPDD++WHFIG LQ+NK    LA VPNL  VE++D+ K A +LN          
Sbjct: 74  IEKAKLLPDDIKWHFIGGLQTNKC-KDLAKVPNLYSVETIDSLKKAKKLNESRAKFQPDC 132

Query: 153 KPLKVLVQVNTSGEE 167
            P+   VQ+NTS E+
Sbjct: 133 NPILCNVQINTSHED 147

Homologous Domains Detected by HHsearch ?

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

ID ?Alignment Graph ?Length ? Definition ? Probability ?
Query185
d1ct5a_244 "Hypothetical" protein ybl036c {Baker's yeast (Sac 100.0
d1vfsa2237 Alanine racemase {Streptomyces lavendulae [TaxId: 98.42
d1bd0a2233 Alanine racemase {Bacillus stearothermophilus [Tax 98.39
d1rcqa2226 Alanine racemase {Pseudomonas aeruginosa [TaxId: 2 97.8
d1hkva2265 Diaminopimelate decarboxylase LysA {Mycobacterium 94.34
d1twia2 264 Diaminopimelate decarboxylase LysA {Archaeon Metha 93.28
>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=4.8e-55  Score=371.95  Aligned_cols=159  Identities=39%  Similarity=0.564  Sum_probs=138.4

Q ss_pred             hcccccChHHHHHHHHHHHHHHHHHHHH--cCCCCCCeEEEEeecCCCHHHHHHHHHcCCcccccccHHHHHHHHhcCCC
Q 029918           26 MAASAATDGVAATALRSVIQRVHQAAER--SSRPPDRIRIVAVSKTKPVSVIRQVYEAGHRCFGENYVQEIVEKAAQLPD  103 (185)
Q Consensus        26 m~~~~~~~~~i~~nl~~V~~rI~~a~~~--~gR~p~~V~LvAVSKt~p~e~I~~a~~~G~r~FGENrvQEl~~K~~~L~~  103 (185)
                      |+..+.+..+|..||+.|+++|+.+|+.  +||+|.+|+|||||||+|+++|+.||++|+++|||||+||+.+|++.||+
T Consensus         3 m~~d~~r~~ei~~~~~~i~~~I~~~~~~~~~~r~~~~V~LiaVsK~~~~~~I~~~~~~G~~~fGENrvQE~~~K~~~l~~   82 (244)
T d1ct5a_           3 ITYDEDRKTQLIAQYESVREVVNAEAKNVHVNENASKILLLVVSKLKPASDIQILYDHGVREFGENYVQELIEKAKLLPD   82 (244)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHHHHTC-------CCEEEEECTTSCHHHHHHHHHHTCCEEEECCHHHHHHHHHHSCT
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCceEEEEEECCCCHHHHHHHHHcCCchhhcchhhhhhhhcccccc
Confidence            5555555788999999999999999986  89999999999999999999999999999999999999999999999999


Q ss_pred             CceEEEEecccccchHHHhhcCCCccEEEecCcHHHHHHHHHHHHhcC--CCCccEEEEEeCCCCCcccccc--------
Q 029918          104 DLEWHFIGNLQSNKVKPLLAGVPNLAMVESVDNEKIAGRLNRMVETMG--RKPLKVLVQVNTSGEEYGECFI--------  173 (185)
Q Consensus       104 ~i~WHfIG~LQsNKvk~~~~~~~~~~~IhSVDs~kLA~~L~k~a~~~~--~~~l~VLIQVNis~E~sKsG~~--------  173 (185)
                      +++|||||||||||||++++ ..++++||||||+++|++|++.+.+.+  ..+++||||||+++|++|+|+.        
T Consensus        83 ~i~wHfIG~LQsNKvk~i~~-~~~~~~I~svds~kla~~l~~~~~~~~~~~~~~~~~iQVNi~~e~~KsG~~~~~~l~~~  161 (244)
T d1ct5a_          83 DIKWHFIGGLQTNKCKDLAK-VPNLYSVETIDSLKKAKKLNESRAKFQPDCNPILCNVQINTSHEDQKSGLNNEAEIFEV  161 (244)
T ss_dssp             TCEEEECSCCCGGGHHHHHH-CTTEEEEEEECSHHHHHHHHHHHHHHCTTSCCEEEEEEBCCSSSCCSSSBCCHHHHHHH
T ss_pred             ceeeeeecccccchHHHHHH-hcccccccccccccchhHHHHHHhhhhcccCcceeEEeeecccccccCCCCcHHHHHHH
Confidence            99999999999999999983 234588999999999999999887643  2368899999999999999982        


Q ss_pred             -------cCCcccccccCC
Q 029918          174 -------KCSWSHSCLLMI  185 (185)
Q Consensus       174 -------~~~~l~l~g~m~  185 (185)
                             .|++|++.|||+
T Consensus       162 ~~~~~~~~~~~l~l~GLM~  180 (244)
T d1ct5a_         162 IDFFLSEECKYIKLNGLMT  180 (244)
T ss_dssp             HHHHHSTTCCSEEEEEEEC
T ss_pred             HHHHHHHhcccchhccccc
Confidence                   589999999997
>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
>d1hkva2 c.1.6.1 (A:46-310) Diaminopimelate decarboxylase LysA {Mycobacterium tuberculosis [TaxId: 1773]} 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