254780161

254780161

phytoene synthase protein

GeneID in NCBI database:8209138Locus tag:CLIBASIA_00220
Protein GI in NCBI database:254780161Protein Accession:YP_003064574.1
Gene range:-(44016, 44915)Protein Length:299aa
Gene description:phytoene synthase protein
COG prediction:[I] Phytoene/squalene synthetase
KEGG prediction:phytoene synthase protein; K02291 phytoene synthase [EC:2.5.1.32]
SEED prediction:Phytoene synthase (EC 2.5.1.32)
Pathway involved in KEGG:Carotenoid biosynthesis
Subsystem involved in SEED:- none -
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
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-------30
MVLKFLTKNTRKEEKIFSRDSLFVLRNLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRDMRLQWWKDIFESSTKGLIAESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATMILDSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPAFIPVSITESVLKHAQNHGFKIVSHSHTPNQLVRPWYMLSSSIKKRF
ccEEEcccccccHHHHHHHHHHHHHHHHHHccccHHHHHHHccHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHccccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHccc
cccHccccHHHHHHHHccccHHHHHHHHHHcccHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHccHHHHcccEEccHHHHHHccccHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHccHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHccc
mvlkfltkntrkeekifsrdslfvlrnlrdidydRYLACllspplyriSLSFLYYFHTELMRVRdtarnpitrdMRLQWWKDIFESSTkgliaesisPFSVELLSIVrqydlpnqyFLDMIEahffdsyndsifdckqFEHYAFRISSRLIHLATMILDSERYSASLRVIKYAGIAQFIGQLICQlpihyhrgqlyfpldilgavgldresflsgqnsdRISLAIKIFAELGLKYLFKAREEMRyilpdvfpafipvSITESVLKHAQnhgfkivshshtpnqlvrpwymlsSSIKKRF
mvlkfltkntrkeekifsrdslfvlrnLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMrvrdtarnpitrdmRLQWWKDIFESSTKGLIAESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATMILDSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPAFIPVSITESVLKHAQNHGFKIvshshtpnqlvrpwymlsssikkrf
MVLKFLTKNTRKEEKIFSRDSLFVLRNLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRDMRLQWWKDIFESSTKGLIAESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATMILDSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPAFIPVSITESVLKHAQNHGFKIVSHSHTPNQLVRPWYMLSSSIKKRF
******************RDSLFVLRNLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRDMRLQWWKDIFESSTKGLIAESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATMILDSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPAFIPVSITESVLKHAQNHGFKIVSHSHTPNQLVRPWYMLSSSIKKRF
MVLKFLTKNTRKEEKIFSRDSLFVLRNLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRDMRLQWWKDIFESSTKGLIAESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATMILDSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPAFIPVSITESVLKHAQNHGFKIVSHSHTPNQLVRPWYMLSSSIKKRF
**LKFLTKNTRKEEKIFSRDSLFVLRNLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRDMRLQWWKDIFESSTKGLIAESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATMILDSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPAFIPVSITESVLKHAQNHGFKIVSHSHTPNQLVRPWYMLSSSIKKRF
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MVLKFLTKNTRKEEKIFSRDSLFVLRNLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRDMRLQWWKDIFESSTKGLIAESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATMILDSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPAFIPVSITESVLKHAQNHGFKIVSHSHTPNQLVRPWYMLSSSIKKRF
MVLKFLTKNTRKEEKIFSRDSLFVLRNLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRDMRLQWWKDIFESSTKGLIAESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATMILDSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPAFIPVSITESVLKHAQNHGFKIVSHSHTPNQLVRPWYMLSSSIKKRF
MVLKFLTKNTRKEEKIFSRDSLFVLRNLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRDMRLQWWKDIFESSTKGLIAESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATMILDSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPAFIPVSITESVLKHAQNHGFKIVSHSHTPNQLVRPWYMLSSSIKKRF

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

Original result of BLAST against C. L. asiaticus genome

No hits with e-value below 0.05

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

Original result of PSI-BLAST first 2 iterations

IdentityAlignment graphLength Definition Round E-value
Target299 phytoene synthase protein [Candidatus Liberibacter asia
315122666254 phytoene synthase protein [Candidatus Liberibacter sola 1 1e-91
222085796286 phytoene synthase protein [Agrobacterium radiobacter K8 1 2e-59
190891523285 phytoene synthase protein [Rhizobium etli CIAT 652] Len 1 5e-57
15965294280 putative phytoene synthase protein [Sinorhizobium melil 1 9e-56
241204426285 Squalene/phytoene synthase [Rhizobium leguminosarum bv. 1 4e-55
218510623383 phytoene synthase protein [Rhizobium etli Brasil 5] Len 1 1e-54
227821946279 hypothetical protein NGR_c13830 [Sinorhizobium fredii N 1 2e-54
116251817280 phytoene synthase [Rhizobium leguminosarum bv. viciae 3 1 2e-54
209549099285 phytoene synthase protein [Rhizobium leguminosarum bv. 1 7e-54
325292956281 phytoene synthase [Agrobacterium sp. H13-3] Length = 28 1 9e-54
>gi|315122666|ref|YP_004063155.1| phytoene synthase protein [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 254 Back     alignment and organism information
 Score =  340 bits (873), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 166/248 (66%), Positives = 200/248 (80%)

Query: 18  SRDSLFVLRNLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRDMRL 77
           ++D LF L NLRD+D DRYLACLLSP   RI L+ LY F+ EL RVRD A NP+  ++RL
Sbjct: 3   AQDHLFSLHNLRDMDRDRYLACLLSPSHLRIPLAILYSFNAELARVRDLASNPLAGEIRL 62

Query: 78  QWWKDIFESSTKGLIAESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCK 137
           QWWKDIFESS   +++ES SP S++L+SI+ QY LP Q+F DMIEA FFD YNDSIFDCK
Sbjct: 63  QWWKDIFESSRDNILSESKSPLSIKLVSIINQYALPYQFFFDMIEARFFDPYNDSIFDCK 122

Query: 138 QFEHYAFRISSRLIHLATMILDSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYF 197
           Q E YAF+I+S LIHLATMIL  ++    + VIK+AGIAQFIG+LI  L  H +RGQLY 
Sbjct: 123 QLEIYAFKIASSLIHLATMILSDKKNFDIIDVIKHAGIAQFIGELILLLSKHCNRGQLYL 182

Query: 198 PLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPAFIPV 257
           PLDILGAVGLDRESF SG+N++RISL IKIFAELGL++L KAR+EM +I PD+FPAFIPV
Sbjct: 183 PLDILGAVGLDRESFFSGENNERISLVIKIFAELGLEHLVKARKEMNHISPDIFPAFIPV 242

Query: 258 SITESVLK 265
           SITE++LK
Sbjct: 243 SITENILK 250



Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222085796|ref|YP_002544326.1| phytoene synthase protein [Agrobacterium radiobacter K84] Length = 286 Back     alignment and organism information
>gi|190891523|ref|YP_001978065.1| phytoene synthase protein [Rhizobium etli CIAT 652] Length = 285 Back     alignment and organism information
>gi|15965294|ref|NP_385647.1| putative phytoene synthase protein [Sinorhizobium meliloti 1021] Length = 280 Back     alignment and organism information
>gi|241204426|ref|YP_002975522.1| Squalene/phytoene synthase [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 285 Back     alignment and organism information
>gi|218510623|ref|ZP_03508501.1| phytoene synthase protein [Rhizobium etli Brasil 5] Length = 383 Back     alignment and organism information
>gi|227821946|ref|YP_002825916.1| hypothetical protein NGR_c13830 [Sinorhizobium fredii NGR234] Length = 279 Back     alignment and organism information
>gi|116251817|ref|YP_767655.1| phytoene synthase [Rhizobium leguminosarum bv. viciae 3841] Length = 280 Back     alignment and organism information
>gi|209549099|ref|YP_002281016.1| phytoene synthase protein [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 285 Back     alignment and organism information
>gi|325292956|ref|YP_004278820.1| phytoene synthase [Agrobacterium sp. H13-3] Length = 281 Back     alignment and organism information

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

Conserved Domains in CDD Database Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Original result of RPS-BLASTagainst CDD database part II

IdentityAlignment graphLength Definition E-value
Target299 phytoene synthase protein [Candidatus Liberibacter asia
COG1562288 COG1562, ERG9, Phytoene/squalene synthetase [Lipid meta 9e-25
cd00683265 cd00683, Trans_IPPS_HH, Trans-Isoprenyl Diphosphate Syn 1e-04
pfam00494262 pfam00494, SQS_PSY, Squalene/phytoene synthase 5e-30
KOG4411292 KOG4411, KOG4411, KOG4411, Phytoene/squalene synthetase 1e-16
>gnl|CDD|31750 COG1562, ERG9, Phytoene/squalene synthetase [Lipid metabolism] Back     alignment and domain information
>gnl|CDD|173831 cd00683, Trans_IPPS_HH, Trans-Isoprenyl Diphosphate Synthases, head-to-head Back     alignment and domain information
>gnl|CDD|144184 pfam00494, SQS_PSY, Squalene/phytoene synthase Back     alignment and domain information
>gnl|CDD|39612 KOG4411, KOG4411, KOG4411, Phytoene/squalene synthetase [Lipid transport and metabolism] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

Original result of HHsearch against CDD database

IdentityAlignment graphLength Definition Probability
Target 299 phytoene synthase protein [Candidatus Liberibacter asia
TIGR03465266 HpnD squalene synthase HpnD. The genes of this family a 100.0
TIGR03464266 HpnC squalene synthase HpnC. This family of genes are m 100.0
cd00683265 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases (Tr 100.0
pfam00494262 SQS_PSY Squalene/phytoene synthase. 100.0
COG1562288 ERG9 Phytoene/squalene synthetase [Lipid metabolism] 100.0
KOG4411292 consensus 100.0
TIGR01559350 squal_synth farnesyl-diphosphate farnesyltransferase; I 99.87
KOG1459413 consensus 99.61
KOG1459413 consensus 99.58
cd00867236 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases (Trans 99.72
cd00385243 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, C 99.63
cd00685298 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases (Tr 95.53
PRK10581299 geranyltranstransferase; Provisional 95.35
PRK10888323 octaprenyl diphosphate synthase; Provisional 92.41
KOG0776384 consensus 91.93
>TIGR03465 HpnD squalene synthase HpnD Back     alignment and domain information
>TIGR03464 HpnC squalene synthase HpnC Back     alignment and domain information
>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS), head-to-head (HH) (1'-1) condensation reaction Back     alignment and domain information
>pfam00494 SQS_PSY Squalene/phytoene synthase Back     alignment and domain information
>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism] Back     alignment and domain information
>KOG4411 consensus Back     alignment and domain information
>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase; InterPro: IPR006449 This family of sequences describe farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes Back     alignment and domain information
>KOG1459 consensus Back     alignment and domain information
>KOG1459 consensus Back     alignment and domain information
>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate Back     alignment and domain information
>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1; Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate Back     alignment and domain information
>cd00685 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS), head-to-tail (HT) (1'-4) condensation reactions Back     alignment and domain information
>PRK10581 geranyltranstransferase; Provisional Back     alignment and domain information
>PRK10888 octaprenyl diphosphate synthase; Provisional Back     alignment and domain information
>KOG0776 consensus Back     alignment and domain information

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

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

Original result of PSI-BLAST

IdentityAlignment graphLength Definition E-value
Target299 phytoene synthase protein [Candidatus Liberibacter asia
2zco_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 2e-39
3adz_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 4e-39
3ae0_A293 Crystal Structure Of The C(30) Carotenoid Dehydrosq 5e-39
3lee_A340 Crystal Structure Of The Human Squalene Synthase Co 1e-13
1ezf_A340 Crystal Structure Of Human Squalene Synthase Length 1e-13
>gi|169791834|pdb|2ZCO|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Length = 293 Back     alignment and structure 
 Score =  167 bits (422), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 28/278 (10%), Positives = 90/278 (32%), Gaps = 2/278 (0%)

Query: 14  EKIFSRDSLFVLRNLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITR 73
             +   +  +  + ++        A  L P   R ++  +Y    ++    D   +    
Sbjct: 7   MTMMDMNFKYCHKIMKKHSKSFSYAFDLLPEDQRKAVWAIYAVCRKIDDSIDVYGDIQFL 66

Query: 74  DMRLQWWKDIFESSTKGLIAESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSI 133
           +   +  + I +   +    +S     + L  + +  ++  Q F ++I+  + D +    
Sbjct: 67  NQIKEDIQSIEKYPYEYHHFQSDRRIMMALQHVAQHKNIAFQSFYNLIDTVYKDQHFTMF 126

Query: 134 FDCKQFEHYAFRISSRLIHLATMILDSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRG 193
               +   Y + ++  +  + T IL       +  V +  G +  +  ++  +   +   
Sbjct: 127 ETDAELFGYCYGVAGTVGEVLTPILSDHETHQTYDVARRLGESLQLINILRDVGEDFENE 186

Query: 194 QLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPA 253
           ++YF    L    +D         ++      + +A +  K      ++++    +  P 
Sbjct: 187 RIYFSKQRLKQYEVDIAEVYQNGVNNHYIDLWEYYAAIAEKDFRDVMDQIKVFSIEAQPI 246

Query: 254 F-IPVSITESVLKHAQNHGFKIVSHSHTPNQLVRPWYM 290
             +   I   +L   +   +  +       +  +    
Sbjct: 247 IELAARIYIEILDEVRQANY-TLHERVFVEKRKKAKLF 283
>gi|312597217|pdb|3ADZ|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed With Intermediate Pspp Length = 293 Back     alignment and structure
>gi|312597218|pdb|3AE0|A Chain A, Crystal Structure Of The C(30) Carotenoid Dehydrosqualene Synthase From Staphylococcus Aureus Complexed With Geranylgeranyl Thiopyrophosphate Length = 293 Back     alignment and structure
>gi|313754278|pdb|3LEE|A Chain A, Crystal Structure Of The Human Squalene Synthase Complexed With Bph- 652 Length = 340 Back     alignment and structure
>gi|11514495|pdb|1EZF|A Chain A, Crystal Structure Of Human Squalene Synthase Length = 340 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

IdentityAlignment graphLength Definition E-value
Target299 phytoene synthase protein [Candidatus Liberibacter asia
1ezf_A340 Farnesyl-diphosphate farnesyltransferase; isoprenoid sy 3e-18
2zco_A293 Dehydrosqualene synthase; CRTM, carotenoid biosynthesis 1e-10
>1ezf_A Farnesyl-diphosphate farnesyltransferase; isoprenoid synthase fold, all alpha-helix; HET: IN0; 2.15A {Homo sapiens} SCOP: a.128.1.2 Length = 340 Back     alignment and structure
 Score = 87.7 bits (217), Expect = 3e-18
 Identities = 20/238 (8%), Positives = 58/238 (24%), Gaps = 23/238 (9%)

Query: 36  YLACLLSPPLYRISLSFLYYFHTELMRVRDT-----ARNPITRDMRLQWWKDIFESSTKG 90
                      R ++   Y      +R  DT       +   +   L  +          
Sbjct: 25  AAVIQALDGEMRNAVCIFYLV----LRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWR 80

Query: 91  LIA---------ESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEH 141
            +          E     S+E  ++  +Y          +     +  +  +   ++++ 
Sbjct: 81  FMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDK 140

Query: 142 YAFRISSRLIHLATMIL-----DSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLY 196
           Y   ++  +    + +      +              G+      +I         G+ +
Sbjct: 141 YCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREF 200

Query: 197 FPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPAF 254
           +P ++          F   +N D     +       L ++      +  +       F
Sbjct: 201 WPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNF 258
>2zco_A Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation; 1.58A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A* Length = 293 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target299 phytoene synthase protein [Candidatus Liberibacter asia
2zco_A293 Dehydrosqualene synthase; CRTM, carotenoid biosynthesis 100.0
1ezf_A340 Farnesyl-diphosphate farnesyltransferase; isoprenoid sy 100.0
3n3d_A335 Geranylgeranyl pyrophosphate synthase; isoprenyl diphos 96.38
3lmd_A360 Geranylgeranyl pyrophosphate synthase; isoprenyl diphos 96.21
3ipi_A295 Geranyltranstransferase; isoprene biosynthesis, helical 96.19
2q80_A301 Geranylgeranyl pyrophosphate synthetase; isoprenoid pat 95.19
1wy0_A342 Geranylgeranyl pyrophosphate synthetase; structural gen 93.53
3mzv_A341 Decaprenyl diphosphate synthase; transferase, structura 93.36
3oyr_A345 Trans-isoprenyl diphosphate synthase; isoprenyl synthas 92.65
3nf2_A352 Putative polyprenyl synthetase; isoprenyl diphosphate s 91.97
3pde_A309 Farnesyl-diphosphate synthase; isoprenyl diphosphate sy 90.16
1ps1_A337 Pentalenene synthase; antibiotic biosynthesis, sesquite 95.98
3lk5_A380 Geranylgeranyl pyrophosphate synthase; structural genom 93.99
1v4e_A299 Octoprenyl-diphosphate synthase; trans-type prenyltrans 92.44
2e8v_A340 Geranylgeranyl pyrophosphate synthetase; prenyltransfer 92.27
1uby_A367 FPS, farnesyl diphosphate synthase; transferase, isopre 90.2
>2zco_A Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation; 1.58A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A* Back     alignment and structure
Probab=100.00  E-value=0  Score=420.12  Aligned_cols=280  Identities=10%  Similarity=0.093  Sum_probs=254.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHH---HHHHHHHHHHHHHH
Q ss_conf             068999999999999985281387998859988806899999999999776036788258999---99999999997740
Q gi|254780161|r   13 EEKIFSRDSLFVLRNLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRDM---RLQWWKDIFESSTK   89 (299)
Q Consensus        13 ~~~~~~~d~~~c~~~lr~~d~~~y~a~~~lP~~~R~~~~alyaf~re~d~i~d~~~~~~~~~~---rL~~w~~~l~~~~~   89 (299)
                      ..+++++|++||.+++|++++|||++++|||+++|++++++|+|||.+|||+|+..++.....   ++++|.....   .
T Consensus         6 ~~~~~~~~~~~C~~i~r~~~~sF~~a~~~Lp~~~r~~~~alYaf~R~~Ddi~D~~~~~~~~~~~~~~l~~~~~~~~---~   82 (293)
T 2zco_A            6 AMTMMDMNFKYCHKIMKKHSKSFSYAFDLLPEDQRKAVWAIYAVCRKIDDSIDVYGDIQFLNQIKEDIQSIEKYPY---E   82 (293)
T ss_dssp             -CCHHHHHHHHHHHHHHHHCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHGGGTTSSSHHHHHHHHHHHHHHHCTT---S
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH---H
T ss_conf             7766999999999999863966999998789999999999999999988630078966779999999999998677---6


Q ss_pred             CCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             17898689899999999986189989999999999853058888998999998644337999999984034303455766
Q gi|254780161|r   90 GLIAESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATMILDSERYSASLRV  169 (299)
Q Consensus        90 ~~~~~~~~Pv~~aL~~~~~~~~l~~~~l~~lid~~~~Dl~~~~~~t~~~L~~Y~~~~ag~vg~l~~~i~~~~~~~~~~~~  169 (299)
                      .....+.|||..+|.+++++++++++++.++|+||++|++.++|+|++||+.||++|||+||+|++.+++..+.....+.
T Consensus        83 ~~~~~~~~pv~~al~~~~~~~~l~~~~~~~li~g~~~Dl~~~~~~t~~dL~~Y~~~vAg~VG~l~~~il~~~~~~~~~~~  162 (293)
T 2zco_A           83 YHHFQSDRRIMMALQHVAQHKNIAFQSFYNLIDTVYKDQHFTMFETDAELFGYCYGVAGTVGEVLTPILSDHETHQTYDV  162 (293)
T ss_dssp             CCCCSSCHHHHHHHHHHHTTSCCCHHHHHHHHHHHHHGGGCCCCSSHHHHHHHHHHHTHHHHHHHHHHHCSSCCHHHHHH
T ss_pred             HCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHCCCCCCHHHHH
T ss_conf             42688887999999999998499856899999999986243568999999999871302199999999615220027999


Q ss_pred             HHHHHHHHHHHHHHHCCHHHHHCCCCCCCHHHHHHCCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             88999999899887224787634887346789996399977852468998799999999999999999999644528999
Q gi|254780161|r  170 IKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPD  249 (299)
Q Consensus       170 a~~lG~A~ql~niLRdi~~d~~~gr~yLP~~~l~~~gv~~e~l~~~~~~~~~~~~~~~~~~~A~~~l~~a~~~~~~lp~~  249 (299)
                      |.++|.|+|+||||||+++|+++||+|||.|+|.+||++++++.++..++++++++.+++++|+.||.+|+.++..+|++
T Consensus       163 A~~lG~AlQltNiLRDi~eD~~~gR~YlP~e~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~a~~~~~~a~~~~~~lp~~  242 (293)
T 2zco_A          163 ARRLGESLQLINILRDVGEDFENERIYFSKQRLKQYEVDIAEVYQNGVNNHYIDLWEYYAAIAEKDFRDVMDQIKVFSIE  242 (293)
T ss_dssp             HHHHHHHHHHHHHHHCHHHHHHTTCCCSCHHHHHHTTCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHTGGGSCTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCEECCHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
T ss_conf             99999999999999715989977984288999988599999985576205899989999999999999999868758998


Q ss_pred             HHHH-HHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             9999-9999999999999996888724589868966799999999862
Q gi|254780161|r  250 VFPA-FIPVSITESVLKHAQNHGFKIVSHSHTPNQLVRPWYMLSSSIK  296 (299)
Q Consensus       250 ~r~~-~l~~~~~~~~L~~l~~~~~~v~~~~~~~~~~~~~~~l~r~~~~  296 (299)
                      .+++ .+++.+|..+|++|++++|+ |..|+.+|+++|.|++++...+
T Consensus       243 ~r~~v~~a~~~y~~il~~i~~~~~~-~~~R~~vs~~~K~~l~~~~~~~  289 (293)
T 2zco_A          243 AQPIIELAARIYIEILDEVRQANYT-LHERVFVEKRKKAKLFHEINSK  289 (293)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTTC-SSSCCCCCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCC-CCCCCEECHHHHHHHHHHHHHH
T ss_conf             7899999999999999999938998-8789851799999999999998
>1ezf_A Farnesyl-diphosphate farnesyltransferase; isoprenoid synthase fold, all alpha-helix; HET: IN0; 2.15A {Homo sapiens} SCOP: a.128.1.2 Back     alignment and structure
>3n3d_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.40A {Lactobacillus brevis} Back     alignment and structure
>3lmd_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, protein structure initiative, nysgrc; 1.90A {Corynebacterium glutamicum} Back     alignment and structure
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle, protein structure initiative II (PSI II), structural genomics, nysgxrc; 1.90A {Methanosarcina mazei} Back     alignment and structure
>2q80_A Geranylgeranyl pyrophosphate synthetase; isoprenoid pathway, isopentenyl transferase, structural genomics, structural genomics consortium, SGC; HET: GRG; 2.70A {Homo sapiens} SCOP: a.128.1.1 Back     alignment and structure
>1wy0_A Geranylgeranyl pyrophosphate synthetase; structural genomics, riken structural genomics/proteomics initiative, RSGI, transferase; 2.20A {Pyrococcus horikoshii OT3} Back     alignment and structure
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics, PSI-2, protein structure initiative; 1.90A {Rhodobacter capsulatus} Back     alignment and structure
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI, protein structure initiative; HET: IPE; 2.00A {Caulobacter crescentus} Back     alignment and structure
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative, nysgrc; 2.20A {Streptomyces coelicolor} Back     alignment and structure
>3pde_A Farnesyl-diphosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, PR structure initiative; HET: IPE; 1.75A {Lactobacillus brevis} PDB: 3m9u_A* Back     alignment and structure
>1ps1_A Pentalenene synthase; antibiotic biosynthesis, sesquiterpene cyclase, lyase; 2.60A {Streptomyces SP} SCOP: a.128.1.4 PDB: 1hm7_A 1hm4_A Back     alignment and structure
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein structure initiative; 1.90A {Corynebacterium glutamicum} Back     alignment and structure
>1v4e_A Octoprenyl-diphosphate synthase; trans-type prenyltransferase, thermophilic; 2.28A {Thermotoga maritima} SCOP: a.128.1.1 PDB: 1v4j_A 1wkz_A 1vg2_A 1wl3_A 1wl0_A 1wl2_A 1v4h_A 1v4i_A 1v4k_A 2azl_A 1wl1_A 1vg4_A 1vg3_A 1vg6_A 1vg7_A Back     alignment and structure
>2e8v_A Geranylgeranyl pyrophosphate synthetase; prenyltransferase, farnesyl pyrophosphate, bisphosphonate; HET: GRG; 1.80A {Saccharomyces cerevisiae} PDB: 2e8t_A* 2e8u_A* 2dh4_A* 2e8w_A* 2e8x_A* 2e90_A* 2e91_A* 2e92_A* 2e93_A* 2e94_A* 2e95_A* 2z4v_A* 2z4w_A* 2z4x_A* 2z4y_A* 2z4z_A* 2z50_A* 2z52_A* 2z78_A* 2z7h_A* ... Back     alignment and structure
>1uby_A FPS, farnesyl diphosphate synthase; transferase, isoprene biosynthesis, cholesterol biosynthesis; HET: DMA; 2.40A {Gallus gallus} SCOP: a.128.1.1 PDB: 1ubw_A* 1ubv_A* 1ubx_A* 1fps_A Back     alignment and structure

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

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

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

IdentityAlignment graphLength Definition E-value
Target 299 phytoene synthase protein [Candidatus Liberibacter asia
d1ezfa_333 a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) 4e-16
>d1ezfa_ a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) [TaxId: 9606]} Length = 333 Back     information, alignment and structure

class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Squalene synthase
domain: Squalene synthase
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 79.0 bits (194), Expect = 4e-16
 Identities = 21/246 (8%), Positives = 59/246 (23%), Gaps = 23/246 (9%)

Query: 28  LRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDT-----ARNPITRDMRLQWWKD 82
           L                  R ++   Y      +R  DT       +   +   L  +  
Sbjct: 10  LNQTSRSFAAVIQALDGEMRNAVCIFYLV----LRALDTLEDDMTISVEKKVPLLHNFHS 65

Query: 83  IFESSTKGLIA---------ESISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSI 133
                    +          E     S+E  ++  +Y          +     +  +  +
Sbjct: 66  FLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHV 125

Query: 134 FDCKQFEHYAFRISSRLIHLATMIL-----DSERYSASLRVIKYAGIAQFIGQLICQLPI 188
              ++++ Y   ++  +    + +      +              G+      +I     
Sbjct: 126 TSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLE 185

Query: 189 HYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILP 248
               G+ ++P ++          F   +N D     +       L ++      +  +  
Sbjct: 186 DQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRN 245

Query: 249 DVFPAF 254
                F
Sbjct: 246 QSVFNF 251

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

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

IdentityAlignment graphLength Definition Probability
Target299 phytoene synthase protein [Candidatus Liberibacter asia
d1ezfa_333 Squalene synthase {Human (Homo sapiens) [TaxId: 9606]} 100.0
d1ps1a_311 Pentalenene synthase {Streptomyces sp., UC5319 [TaxId: 96.4
d1v4ea_280 Octoprenyl-diphosphate synthase {Thermotoga maritima [T 94.84
d1fpsa_348 Farnesyl diphosphate synthase (geranyltranstransferase) 92.86
d1rqja_299 Farnesyl diphosphate synthase (geranyltranstransferase) 92.06
d2q80a1291 Geranylgeranyl pyrophosphate synthetase {Human (Homo sa 93.77
>d1ezfa_ a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
class: All alpha proteins
fold: Terpenoid synthases
superfamily: Terpenoid synthases
family: Squalene synthase
domain: Squalene synthase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=0  Score=359.03  Aligned_cols=275  Identities=8%  Similarity=0.048  Sum_probs=230.0

Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHHHCCCC--CC
Q ss_conf             9999999999852813879988599888068999999999997760367882-58999999999999977401789--86
Q gi|254780161|r   19 RDSLFVLRNLRDIDYDRYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNP-ITRDMRLQWWKDIFESSTKGLIA--ES   95 (299)
Q Consensus        19 ~d~~~c~~~lr~~d~~~y~a~~~lP~~~R~~~~alyaf~re~d~i~d~~~~~-~~~~~rL~~w~~~l~~~~~~~~~--~~   95 (299)
                      +++++|.++++++|+|||+++++||+++|++++++|+|||.+|+|+|+...+ ..+...|.+|++.+.....+...  ..
T Consensus         1 ~sl~~C~~~l~~~SrSF~~a~~~Lp~~~R~~v~~lYafcR~~DdI~D~~~~~~~~k~~~L~~~~~~l~~~~~~~~~~~~~   80 (333)
T d1ezfa_           1 NSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEK   80 (333)
T ss_dssp             CHHHHHHHHHHHHCSSHHHHHHTSCTHHHHHHHHHHHHHHHHHHHHHCTTSCHHHHHHHHHHHHHHTTCTTCCCCCCCST
T ss_pred             CHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             95999999998439419999987899999999999999998555473899998999999999999998744201035820


Q ss_pred             CC-------HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCH-----
Q ss_conf             89-------899999999986189989999999999853058888998999998644337999999984034303-----
Q gi|254780161|r   96 IS-------PFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATMILDSERY-----  163 (299)
Q Consensus        96 ~~-------Pv~~aL~~~~~~~~l~~~~l~~lid~~~~Dl~~~~~~t~~~L~~Y~~~~ag~vg~l~~~i~~~~~~-----  163 (299)
                      .+       ||..++..+...+..+...+.+.+++++.|....+++|++||+.|||+|||+||+|++.+++..+.     
T Consensus        81 ~~~ll~~~~~v~~~~~~l~~~~~~~i~~~~~~m~~gm~d~~~~~~~t~~dL~~Ycy~VAG~VG~~l~~l~~~~~~~~~~~  160 (333)
T d1ezfa_          81 DRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLV  160 (333)
T ss_dssp             THHHHHTHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTSCCCSHHHHHHHHHHHTHHHHHHHHHHHHHHTSSCHHH
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCH
T ss_conf             27888604499999999898845125779999826478872676899999999999999999999999957677763007


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCCHHHHHHCCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             45576688999999899887224787634887346789996399977852468998799999999999999999999644
Q gi|254780161|r  164 SASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEM  243 (299)
Q Consensus       164 ~~~~~~a~~lG~A~ql~niLRdi~~d~~~gr~yLP~~~l~~~gv~~e~l~~~~~~~~~~~~~~~~~~~A~~~l~~a~~~~  243 (299)
                      +...+.|.++|.|+|+||||||+++|+++||||||.++|.+||++++++.+++.++++..++.+++++|+.||.+|.+++
T Consensus       161 ~~~~~~A~~lG~AlQltNIlRDi~eD~~~gR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~~~~l~~~A~~~~~~a~~y~  240 (333)
T d1ezfa_         161 GEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYL  240 (333)
T ss_dssp             HHCHHHHHHHHHHHHHHHHHHTHHHHHHHTCCCSCHHHHTTTCSSGGGGGSGGGHHHHHHHHHHHHHHHHTTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCHHHHHHCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999898899735789968967777799988399999997420317899999999999999999999999


Q ss_pred             HHCCHHHHHHH-HHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             52899999999-999999999999996888724589868966799999999
Q gi|254780161|r  244 RYILPDVFPAF-IPVSITESVLKHAQNHGFKIVSHSHTPNQLVRPWYMLSS  293 (299)
Q Consensus       244 ~~lp~~~r~~~-l~~~~~~~~L~~l~~~~~~v~~~~~~~~~~~~~~~l~r~  293 (299)
                      ..+|.+.+..| +...++..+.-++.++|+++|++++.++...+..++.++
T Consensus       241 ~~lp~~~~~~~~~~~~~~a~~tl~~~~~~~~~~~~~vkisr~~~~~l~~~~  291 (333)
T d1ezfa_         241 SRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDA  291 (333)
T ss_dssp             HTCCCHHHHHHHHHHHHHHHHHHHHHTTCGGGGTSCCCC----------CT
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHCCCCEEEEHHHHHHHHHHH
T ss_conf             878922589999999999999999997391531798576499999999980
>d1ps1a_ a.128.1.4 (A:) Pentalenene synthase {Streptomyces sp., UC5319 [TaxId: 1931]} Back     information, alignment and structure
>d1v4ea_ a.128.1.1 (A:) Octoprenyl-diphosphate synthase {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d1fpsa_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Chicken (Gallus gallus) [TaxId: 9031]} Back     information, alignment and structure
>d1rqja_ a.128.1.1 (A:) Farnesyl diphosphate synthase (geranyltranstransferase) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2q80a1 a.128.1.1 (A:6-296) Geranylgeranyl pyrophosphate synthetase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against MMDB70 database

IdentityAlignment graphLength Definition E-value
Target 299 phytoene synthase protein [Candidatus Liberibacter
2zco_A_106-239134 (A:106-239) Dehydrosqualene synthase; CRTM, carote 7e-16
1ezf_A_132-340209 (A:132-340) Farnesyl-diphosphate farnesyltransfera 6e-13
1ezf_A_1-131131 (A:1-131) Farnesyl-diphosphate farnesyltransferase 3e-10
2zco_A_1-105_240-293159 (A:1-105,A:240-293) Dehydrosqualene synthase; CRTM 5e-07
>2zco_A (A:106-239) Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation; 1.58A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A*Length = 134 Back     alignment and structure
 Score = 78.9 bits (194), Expect = 7e-16
 Identities = 16/134 (11%), Positives = 47/134 (35%)

Query: 113 PNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATMILDSERYSASLRVIKY 172
             Q F ++I+  + D +        +   Y + ++  +  + T IL       +  V + 
Sbjct: 1   AFQSFYNLIDTVYKDQHFTMFETDAELFGYCYGVAGTVGEVLTPILSDHETHQTYDVARR 60

Query: 173 AGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRESFLSGQNSDRISLAIKIFAELG 232
            G +  +  ++  +   +   ++YF    L    +D         ++      + +A + 
Sbjct: 61  LGESLQLINILRDVGEDFENERIYFSKQRLKQYEVDIAEVYQNGVNNHYIDLWEYYAAIA 120

Query: 233 LKYLFKAREEMRYI 246
            K      ++++  
Sbjct: 121 EKDFRDVMDQIKVF 134
>1ezf_A (A:132-340) Farnesyl-diphosphate farnesyltransferase; isoprenoid synthase fold, all alpha-helix; HET: IN0; 2.15A {Homo sapiens}Length = 209 Back     alignment and structure
>1ezf_A (A:1-131) Farnesyl-diphosphate farnesyltransferase; isoprenoid synthase fold, all alpha-helix; HET: IN0; 2.15A {Homo sapiens}Length = 131 Back     alignment and structure
>2zco_A (A:1-105,A:240-293) Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation; 1.58A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A*Length = 159 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

IdentityAlignment graphLength Definition Probability
Target299 phytoene synthase protein [Candidatus Liberibacter asia
1ezf_A_132-340209 Farnesyl-diphosphate farnesyltransferase; isopreno 100.0
2zco_A_1-105_240-293159 Dehydrosqualene synthase; CRTM, carotenoid biosynt 95.46
2zco_A_106-239134 Dehydrosqualene synthase; CRTM, carotenoid biosynt 99.97
1v4e_A_125-299175 Octoprenyl-diphosphate synthase; trans-type prenyl 97.55
2q80_A_109-281173 Geranylgeranyl pyrophosphate synthetase; isoprenoi 96.65
3ipi_A_295 Geranyltranstransferase; isoprene biosynthesis, he 96.37
3lmd_A_360 Geranylgeranyl pyrophosphate synthase; isoprenyl d 95.98
2her_A_368 Fragment, farnesyl pyrophosphate synthase; farnesy 94.35
1wy0_A_342 Geranylgeranyl pyrophosphate synthetase; structura 91.16
1rqj_A_299 Geranyltranstransferase; bisphosphonate, isoprenyl 90.74
1ezf_A_1-131131 Farnesyl-diphosphate farnesyltransferase; isopreno 99.89
2zco_A_1-105_240-293159 Dehydrosqualene synthase; CRTM, carotenoid biosynt 99.84
2azj_A_133-289157 Geranylgeranyl pyrophosphate synthetase; hexpps, t 94.43
2ftz_A_131-266136 Geranyltranstransferase; TM0161, structural genomi 92.32
2j1p_A_293 Geranylgeranyl pyrophosphate synthetase; transfera 91.14
1di1_A_300 Aristolochene synthase; sesquiterpene cyclase, iso 94.0
5eau_A_261-527267 5-EPI-aristolochene synthase; isoprenoid synthase, 92.57
1ps1_A_337 Pentalenene synthase; antibiotic biosynthesis, ses 93.94
2e8v_A_195-340146 Geranylgeranyl pyrophosphate synthetase; prenyltra 90.93
2qis_A_241-374134 Farnesyl pyrophosphate synthetase; trans-prenyltra 90.08
>1ezf_A (A:132-340) Farnesyl-diphosphate farnesyltransferase; isoprenoid synthase fold, all alpha-helix; HET: IN0; 2.15A {Homo sapiens} Back     alignment and structure
Probab=100.00  E-value=1.1e-33  Score=246.76  Aligned_cols=165  Identities=7%  Similarity=0.040  Sum_probs=153.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHCCCCC-----HHHHHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCCHHHHHHCCC
Q ss_conf             899899999864433799999998403430-----345576688999999899887224787634887346789996399
Q gi|254780161|r  133 IFDCKQFEHYAFRISSRLIHLATMILDSER-----YSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGL  207 (299)
Q Consensus       133 ~~t~~~L~~Y~~~~ag~vg~l~~~i~~~~~-----~~~~~~~a~~lG~A~ql~niLRdi~~d~~~gr~yLP~~~l~~~gv  207 (299)
                      .+|++||+.||++|||+||+|++.+++...     .+...+.+.|+|.|+|+||||||+++|+++||+|||.|+|.+||+
T Consensus         1 i~t~~eL~~Yc~~vAg~vg~l~~~il~~~~~~~~~~~~~~~~A~~lG~AlqltniLRDi~~D~~~gr~yLP~e~L~~~gv   80 (209)
T 1ezf_A            1 VTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVK   80 (209)
T ss_dssp             CCSHHHHHHHHHHHTHHHHHHHHHHHHHHTSSCHHHHHCHHHHHHHHHHHHHHHHHHTHHHHHHHTCCCSCHHHHTTTCS
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCHHHHHHCCC
T ss_conf             89999999999980269999999996768875120598999999999999999999976989957975686999988599


Q ss_pred             CHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH-HHHHHHHHHHHHHCCCCCCCCCCCCCHHHH
Q ss_conf             9778524689987999999999999999999996445289999999999-999999999999688872458986896679
Q gi|254780161|r  208 DRESFLSGQNSDRISLAIKIFAELGLKYLFKAREEMRYILPDVFPAFIP-VSITESVLKHAQNHGFKIVSHSHTPNQLVR  286 (299)
Q Consensus       208 ~~e~l~~~~~~~~~~~~~~~~~~~A~~~l~~a~~~~~~lp~~~r~~~l~-~~~~~~~L~~l~~~~~~v~~~~~~~~~~~~  286 (299)
                      +++++.+++.+++++.++++++++|+.||.+|+++.+.+|+..++++.+ ..++..+|.+++++||++|++++.++++++
T Consensus        81 ~~e~l~~~~~~~~~~~~~~~l~~~A~~~l~~a~~~~~~lp~~~~~~~~~~~~~~~~~L~~l~~~~~~~~~~r~~~~~~~~  160 (209)
T 1ezf_A           81 KLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQA  160 (209)
T ss_dssp             SGGGGGSGGGHHHHHHHHHHHHHHHHTTHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHTTCGGGGTSCCCC-----
T ss_pred             CHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEHHHH
T ss_conf             99998577688999999999999999999999999987896147899999999999999999679401278705509999


Q ss_pred             HHHHHHHHHHC
Q ss_conf             99999998627
Q gi|254780161|r  287 PWYMLSSSIKK  297 (299)
Q Consensus       287 ~~~l~r~~~~~  297 (299)
                      .|++|++.+++
T Consensus       161 ~~l~~~a~~~~  171 (209)
T 1ezf_A          161 VTLMMDATNMP  171 (209)
T ss_dssp             -----CTTSHH
T ss_pred             HHHHHHCCCHH
T ss_conf             99999648789
>2zco_A (A:1-105,A:240-293) Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation; 1.58A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A* Back     alignment and structure
>2zco_A (A:106-239) Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation; 1.58A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A* Back     alignment and structure
>1v4e_A (A:125-299) Octoprenyl-diphosphate synthase; trans-type prenyltransferase, thermophilic; 2.28A {Thermotoga maritima} Back     alignment and structure
>2q80_A (A:109-281) Geranylgeranyl pyrophosphate synthetase; isoprenoid pathway, isopentenyl transferase, structural genomics, structural genomics consortium, SGC; HET: GRG; 2.70A {Homo sapiens} Back     alignment and structure
>3ipi_A (A:) Geranyltranstransferase; isoprene biosynthesis, helical bundle, protein structure initiative II (PSI II), structural genomics, nysgxrc; 1.90A {Methanosarcina mazei} Back     alignment and structure
>3lmd_A (A:) Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate synthase, structural genomics, PSI, protein structure initiative, nysgrc; 1.90A {Corynebacterium glutamicum} Back     alignment and structure
>1wy0_A (A:) Geranylgeranyl pyrophosphate synthetase; structural genomics, riken structural genomics/proteomics initiative, RSGI, transferase; 2.20A {Pyrococcus horikoshii OT3} Back     alignment and structure
>1rqj_A (A:) Geranyltranstransferase; bisphosphonate, isoprenyl synthase; HET: IPR RIS; 1.95A {Escherichia coli} Back     alignment and structure
>1ezf_A (A:1-131) Farnesyl-diphosphate farnesyltransferase; isoprenoid synthase fold, all alpha-helix; HET: IN0; 2.15A {Homo sapiens} Back     alignment and structure
>2zco_A (A:1-105,A:240-293) Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation; 1.58A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A* Back     alignment and structure
>2azj_A (A:133-289) Geranylgeranyl pyrophosphate synthetase; hexpps, trans-prenyltransferase; 2.40A {Sulfolobus solfataricus} PDB: 2azk_A Back     alignment and structure
>2ftz_A (A:131-266) Geranyltranstransferase; TM0161, structural genomics, joint center for structural genomics, JCSG, protein structure initiative, PSI; HET: MLY; 1.90A {Thermotoga maritima MSB8} Back     alignment and structure
>2j1p_A (A:) Geranylgeranyl pyrophosphate synthetase; transferase, isoprene biosynthesis, multifunctional enzyme, carotenoid biosynthesis; HET: GRG; 1.8A {Sinapis alba} PDB: 2j1o_A Back     alignment and structure
>1di1_A (A:) Aristolochene synthase; sesquiterpene cyclase, isoprenoid biosynthesis; 2.50A {Penicillium roqueforti} Back     alignment and structure
>5eau_A (A:261-527) 5-EPI-aristolochene synthase; isoprenoid synthase, natural products biosynthesis, isoprenoid cyclase; HET: FFF; 2.15A {Nicotiana tabacum} Back     alignment and structure
>1ps1_A (A:) Pentalenene synthase; antibiotic biosynthesis, sesquiterpene cyclase, lyase; 2.60A {Streptomyces SP} Back     alignment and structure
>2e8v_A (A:195-340) Geranylgeranyl pyrophosphate synthetase; prenyltransferase, farnesyl pyrophosphate, bisphosphonate; HET: GRG; 1.80A {Saccharomyces cerevisiae} PDB: 2e8t_A* 2e8u_A* 2dh4_A* 2e8w_A* 2e8x_A* 2e90_A* 2e91_A* 2e92_A* 2e93_A* 2e94_A* 2e95_A* 2z4v_A* 2z4w_A* 2z4x_A* 2z4y_A* 2z4z_A* 2z50_A* 2z52_A* 2z78_A* 2z7h_A* ... Back     alignment and structure
>2qis_A (A:241-374) Farnesyl pyrophosphate synthetase; trans-prenyltransferase, structural genomics, structural genomics consortium, SGC; HET: RIS; 1.80A {Homo sapiens} PDB: 1yv5_A* 1yq7_A* 2opm_A* 2opn_A* 3cp6_A* 2rah_A* 2vf6_A* 1zw5_A* 3b7l_A* 2f94_F* 2f89_F* 2f7m_F* 2f8z_F* 2f8c_F* 2f92_F* 2f9k_F* Back     alignment and structure