Citrus Sinensis ID: 028137

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210---
Protein Sequence
MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYIIQSELRYSSTMIVIFFIILAIIFSYLSSTRASK
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHccHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHEHHHHHHHHHHHHHHHccHHHHccEEEEccHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
MGLFLQKTNIIRDYLEDineipkcrmfwprEIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYdfsnilkpkinkndpnatkTLSRVEAIQKACMdsgvlnkrksYIIQSELRYSSTMIVIFFIILAIIFSYLSSTRASK
Flexible Loop (DISEMBL)
mglflqktnIIRDYLEDineipkcrmfwprEIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTakvidrtnnmtDVYLAFYDfsnilkpkinkndpnaTKTLSRVEAIQKacmdsgvlnkrKSYIIQSELRYSSTMIVIFFIILAIIFSYLSSTRASK
Low Complexity Region (SEG)
MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYIIQSELRYSSTMiviffiilaiifSYLSSTRASK
Disordered region (IsUnstruct)
**LFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKIN********TLSRVEAIQKACMDSGVLNKRKSYIIQSELRYSSTMIVIFFIILAIIFSYL*******
Disordered Region (DISOPRED)
MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKAC*********************STMIVIFFIILAIIFSYLSSTR***
Disordered Region (DISEMBL)
MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYIIQSELRYSSTMIVIFFIILAIIFSYLSSTRASK
Disordered Region (DISPRO)
*GLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYIIQSELRYSSTMIVIFFIILAIIFSYLSST****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHoooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYIIQSELRYSSTMIVIFFIILAIIFSYLSSTRASK
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	213	2.2.26 [Sep-21-2011]
P53800	411	Squalene synthase OS=Nico	N/A	no	0.990	0.513	0.796	5e-91
P53799	410	Squalene synthase OS=Arab	yes	no	0.971	0.504	0.740	8e-90
Q9SDW9	461	Squalene synthase OS=Botr	N/A	no	0.784	0.362	0.549	5e-49
Q54DR1	416	Squalene synthase OS=Dict	yes	no	0.779	0.399	0.508	3e-46
Q02769	416	Squalene synthase OS=Ratt	yes	no	0.924	0.473	0.437	3e-45
P53798	416	Squalene synthase OS=Mus	yes	no	0.924	0.473	0.437	4e-45
Q32KR6	417	Squalene synthase OS=Bos	yes	no	0.924	0.472	0.447	2e-44
G0Y287	465	Botryococcus squalene syn	N/A	no	0.784	0.359	0.523	3e-44
Q5R6U3	417	Squalene synthase OS=Pong	yes	no	0.924	0.472	0.427	7e-44
P37268	417	Squalene synthase OS=Homo	yes	no	0.924	0.472	0.427	7e-44

>sp|P53800|FDFT_NICBE Squalene synthase OS=Nicotiana benthamiana PE=2 SV=1

 Score =  333 bits (854), Expect = 5e-91,   Method: Compositional matrix adjust.
 Identities = 168/211 (79%), Positives = 185/211 (87%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINE+PKCRMFWPREIWSKYVNKLE+LKYE+NS KAVQCLNDMV
Sbjct: 201 MGLFLQKTNIIRDYLEDINEVPKCRMFWPREIWSKYVNKLEELKYEDNSAKAVQCLNDMV 260

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL HVEDCL YMSALRD +IFRFCAIPQ+MAIGTLA+CY+NIEVFRGVVKMRRGLTAK
Sbjct: 261 TNALPHVEDCLTYMSALRDPSIFRFCAIPQVMAIGTLAMCYDNIEVFRGVVKMRRGLTAK 320

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           VIDRT  + DVY AF+DFS +LK K+N NDPNATKTL R+E I K C DSG LNKRKSYI
Sbjct: 321 VIDRTRTIADVYGAFFDFSCMLKSKVNNNDPNATKTLKRLEVILKTCRDSGTLNKRKSYI 380

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSSTRA 211
           I+SE  YS  +IV+ FIILAII + LS  R+
Sbjct: 381 IRSEPNYSPVLIVVIFIILAIILAQLSGNRS 411

Nicotiana benthamiana (taxid: 4100)
EC: 2EC: .EC: 5EC: .EC: 1EC: .EC: 2EC: 1

>sp|P53799|FDFT_ARATH Squalene synthase OS=Arabidopsis thaliana GN=SQS1 PE=2 SV=1

 Score =  329 bits (844), Expect = 8e-90,   Method: Compositional matrix adjust.
 Identities = 154/208 (74%), Positives = 182/208 (87%), Gaps = 1/208 (0%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINEIPK RMFWPREIW KY +KLEDLKYEEN++K+VQCLN+MV
Sbjct: 203 MGLFLQKTNIIRDYLEDINEIPKSRMFWPREIWGKYADKLEDLKYEENTNKSVQCLNEMV 262

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNALMH+EDCLKYM +LRD +IFRFCAIPQIMAIGTLALCYNN +VFRGVVK+RRGLTAK
Sbjct: 263 TNALMHIEDCLKYMVSLRDPSIFRFCAIPQIMAIGTLALCYNNEQVFRGVVKLRRGLTAK 322

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           VIDRT  M DVY AFYDFS +LK K++KNDPNA+KTL+R+EA+QK C D+GVL  RKSY 
Sbjct: 323 VIDRTKTMADVYGAFYDFSCMLKTKVDKNDPNASKTLNRLEAVQKLCRDAGVLQNRKSY- 381

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSS 208
           +  + + +S  I++  I+LAI+F+YL +
Sbjct: 382 VNDKGQPNSVFIIMVVILLAIVFAYLRA 409

Arabidopsis thaliana (taxid: 3702)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|Q9SDW9|BSS_BOTBR Squalene synthase OS=Botryococcus braunii GN=BSS PE=1 SV=1

 Score =  194 bits (492), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 95/173 (54%), Positives = 116/173 (67%), Gaps = 6/173 (3%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDY EDINE+P  RMFWPREIW KY N L + K   N   A+ CLN+MV
Sbjct: 208 MGLFLQKTNIIRDYFEDINELPAPRMFWPREIWGKYANNLAEFKDPANKAAAMCCLNEMV 267

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRG---VVKMRRGL 117
           T+AL H   CL+YMS + D  IF FCAIPQ MA GTL+LCYNN  +F G    VK+RRG 
Sbjct: 268 TDALRHAVYCLQYMSMIEDPQIFNFCAIPQTMAFGTLSLCYNNYTIFTGPKAAVKLRRGT 327

Query: 118 TAKVIDRTNNMTDVYLAFYDFSNILKPKIN---KNDPNATKTLSRVEAIQKAC 167
           TAK++  +NNM  +Y  F +F+  L+ + N     DP+ T TL  +  I+ AC
Sbjct: 328 TAKLMYTSNNMFAMYRHFLNFAEKLEVRCNTETSEDPSVTTTLEHLHKIKAAC 380

Converts farnesyl diphosphate into squalene but has no botryococcene synthase activity.

Botryococcus braunii (taxid: 38881)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|Q54DR1|FDFT_DICDI Squalene synthase OS=Dictyostelium discoideum GN=fdfT PE=3 SV=1

 Score =  184 bits (468), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 87/171 (50%), Positives = 120/171 (70%), Gaps = 5/171 (2%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINE    R+FWPR++W++Y   LE+ K  +    A+ CLND++
Sbjct: 207 MGLFLQKTNIIRDYLEDINEK---RIFWPRDVWARYTLHLENFKEAKYQIPALHCLNDLI 263

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL H    L YMS L++  +  FCAIPQ+MAIGTL  CYNN  VF GVVK+R+G  A 
Sbjct: 264 TNALSHALIALDYMSRLKNPQVINFCAIPQVMAIGTLNACYNNYNVFTGVVKIRKGQRAL 323

Query: 121 VID--RTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMD 169
           ++D  ++  +T  Y  F+ F+N ++ K+  NDP+A KT+  +E+I+K C++
Sbjct: 324 IVDAIQSKGLTATYELFFKFANEMRHKVPPNDPSAKKTIQHLESIEKLCIE 374

Dictyostelium discoideum (taxid: 44689)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|Q02769|FDFT_RAT Squalene synthase OS=Rattus norvegicus GN=Fdft1 PE=2 SV=1

 Score =  181 bits (459), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 91/208 (43%), Positives = 127/208 (61%), Gaps = 11/208 (5%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLED  E    R FWP+E+W KYV KLED    EN D AV+CLN+++
Sbjct: 207 MGLFLQKTNIIRDYLEDQQE---GRQFWPQEVWGKYVKKLEDFVKPENVDVAVKCLNELI 263

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL H+ D + Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+GVVK+R+G    
Sbjct: 264 TNALQHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNHQVFKGVVKIRKGQAVT 323

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           ++    NM  V    Y +   +  ++  +DP+A+K    +  I+   + +  L  R    
Sbjct: 324 LMMDATNMPAVKAIIYQYIEEIYHRVPNSDPSASKAKQLISNIRTQSLPNCQLISRS--- 380

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSS 208
                 YS   +    ++ A+ + YLS+
Sbjct: 381 -----HYSPIYLSFIMLLAALSWQYLST 403

Critical branch point enzyme of isoprenoid biosynthesis that is thought to regulate the flux of isoprene intermediates through the sterol pathway.

Rattus norvegicus (taxid: 10116)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|P53798|FDFT_MOUSE Squalene synthase OS=Mus musculus GN=Fdft1 PE=2 SV=2

 Score =  181 bits (459), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 91/208 (43%), Positives = 127/208 (61%), Gaps = 11/208 (5%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLED  E    R FWP+E+W +Y+ KLED    EN D AVQCLN+++
Sbjct: 207 MGLFLQKTNIIRDYLEDQQE---GRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELI 263

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TN L H+ D L Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+GVVK+R+G    
Sbjct: 264 TNTLQHIPDVLTYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQAVT 323

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           ++    NM  V    Y +   +  +I  +DP+++KT   +  I+   + +  L  R    
Sbjct: 324 LMMDATNMPAVKAIIYQYIEEIYHRIPNSDPSSSKTKQVISKIRTQNLPNCQLISRS--- 380

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSS 208
                 YS   +    ++ A+ + YLS+
Sbjct: 381 -----HYSPIYLSFIMLLAALSWQYLST 403

Critical branch point enzyme of isoprenoid biosynthesis that is thought to regulate the flux of isoprene intermediates through the sterol pathway.

Mus musculus (taxid: 10090)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|Q32KR6|FDFT_BOVIN Squalene synthase OS=Bos taurus GN=FDFT1 PE=2 SV=1

 Score =  178 bits (452), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 93/208 (44%), Positives = 125/208 (60%), Gaps = 11/208 (5%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLED  E    R FWP+E WSKYV KL D    EN D AVQCLN+++
Sbjct: 207 MGLFLQKTNIIRDYLEDQRE---GREFWPQETWSKYVKKLGDFAKPENIDLAVQCLNELI 263

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TN L H+ D + Y+S LR+ +IF FCAIPQ+MAI TLA CYNN +VF+GVVK+R+G    
Sbjct: 264 TNTLHHIPDVITYLSRLRNQSIFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQAVT 323

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           ++    NM  V    + +   +  +I  +DP +TKT   +  I+   + +  L  R    
Sbjct: 324 LMMDATNMPAVKAIIHQYMEEIYHRIPNSDPCSTKTQQIISTIRTQNLPNCQLVSRS--- 380

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSS 208
                 YS   +    ++ A+ + YLS+
Sbjct: 381 -----HYSPIYLSFVMLLAALSWQYLST 403

Critical branch point enzyme of isoprenoid biosynthesis that is thought to regulate the flux of isoprene intermediates through the sterol pathway.

Bos taurus (taxid: 9913)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|G0Y287|BOSS_BOTBR Botryococcus squalene synthase OS=Botryococcus braunii GN=SSL-2 PE=1 SV=1

 Score =  178 bits (451), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 89/170 (52%), Positives = 105/170 (61%), Gaps = 3/170 (1%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MG FLQKTN+IRDYLEDINE P  RMFWPREIW KY  +L D K   N   AVQCLN MV
Sbjct: 204 MGQFLQKTNVIRDYLEDINEEPAPRMFWPREIWGKYAQELADFKDPANEKAAVQCLNHMV 263

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           T+AL H E  L  +  L++  I R C IP++M + TL LCYNN +VFRGVVKMRRG TAK
Sbjct: 264 TDALRHCEIGLNVIPLLQNIGILRSCLIPEVMGLRTLTLCYNNPQVFRGVVKMRRGETAK 323

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKIN---KNDPNATKTLSRVEAIQKAC 167
           +     +    Y  +   +N L+ K       DP    TL  V  IQK+C
Sbjct: 324 LFMSIYDKRSFYQTYLRLANELEAKCKGEASGDPMVATTLKHVHGIQKSC 373

Produces squalene when coexpressed with SSL-1 and bisfarnesyl ether and a very small amount of squalene when incubated alone in the presence of NADPH.

Botryococcus braunii (taxid: 38881)

EC: 1

EC: .

EC: 3

EC: .

EC: 1

EC: .

EC: 9

EC: 6

>sp|Q5R6U3|FDFT_PONAB Squalene synthase OS=Pongo abelii GN=FDFT1 PE=2 SV=1

 Score =  176 bits (447), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 89/208 (42%), Positives = 126/208 (60%), Gaps = 11/208 (5%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLED       R FWP+E+WS+YV KL D    EN D AVQCLN+++
Sbjct: 207 MGLFLQKTNIIRDYLEDQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELI 263

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL H+ D + Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+G VK+R+G    
Sbjct: 264 TNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVT 323

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           ++    NM  V    Y +   +  +I  +DP+++KT   +  I+   + +  L  R    
Sbjct: 324 LMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRTQNLPNCQLISRS--- 380

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSS 208
                 YS   +    ++ A+ + YL++
Sbjct: 381 -----HYSPIYLSFVMLLAALSWQYLTT 403

Critical branch point enzyme of isoprenoid biosynthesis that is thought to regulate the flux of isoprene intermediates through the sterol pathway.

Pongo abelii (taxid: 9601)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

EC: 1

>sp|P37268|FDFT_HUMAN Squalene synthase OS=Homo sapiens GN=FDFT1 PE=1 SV=1

 Score =  176 bits (447), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 89/208 (42%), Positives = 126/208 (60%), Gaps = 11/208 (5%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLED       R FWP+E+WS+YV KL D    EN D AVQCLN+++
Sbjct: 207 MGLFLQKTNIIRDYLEDQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELI 263

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL H+ D + Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+G VK+R+G    
Sbjct: 264 TNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVT 323

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           ++    NM  V    Y +   +  +I  +DP+++KT   +  I+   + +  L  R    
Sbjct: 324 LMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRTQNLPNCQLISRS--- 380

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSS 208
                 YS   +    ++ A+ + YL++
Sbjct: 381 -----HYSPIYLSFVMLLAALSWQYLTT 403

Homo sapiens (taxid: 9606)

EC: 2

EC: .

EC: 5

EC: .

EC: 1

EC: .

EC: 2

EC: 1

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
386649283	392	squalene synthase [Azadirachta indica]	0.995	0.540	0.872	1e-105
255641455	413	unknown [Glycine max]	0.985	0.508	0.809	2e-98
414073181	387	squalene synthase, partial [Eriobotrya j	0.981	0.540	0.813	4e-98
351726622	413	squalene synthase [Glycine max] gi|24635	0.985	0.508	0.809	5e-98
327243159	415	squalene synthase [Eleutherococcus senti	0.981	0.503	0.823	6e-98
432139331	414	squalene synthase [Camellia oleifera]	0.995	0.512	0.806	1e-97
225427738	413	PREDICTED: squalene synthase [Vitis vini	0.985	0.508	0.819	1e-97
259014869	415	squalene synthase [Panax ginseng]	0.976	0.501	0.827	2e-97
327243161	415	squalene synthase [Eleutherococcus senti	0.981	0.503	0.819	6e-97
356538706	413	PREDICTED: squalene synthase-like [Glyci	0.985	0.508	0.795	6e-97

>gi|386649283|gb|AFJ15526.1| squalene synthase [Azadirachta indica]

 Score =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 185/212 (87%), Positives = 198/212 (93%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINEIPK RMFWPREIWSKYVNKLEDLKYEENS KAVQCLNDMV
Sbjct: 180 MGLFLQKTNIIRDYLEDINEIPKSRMFWPREIWSKYVNKLEDLKYEENSVKAVQCLNDMV 239

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL HVEDCLKYMSALRD AIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK
Sbjct: 240 TNALNHVEDCLKYMSALRDPAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 299

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
            IDRTN M DVY AFYDFS +LKPKIN+NDPNATKTLSRVEAIQKACM+SG+LN+RKSYI
Sbjct: 300 AIDRTNKMADVYGAFYDFSCMLKPKINENDPNATKTLSRVEAIQKACMESGLLNRRKSYI 359

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSSTRAS 212
           IQ E +Y++TMI++ FIILAIIF+YLS+ R +
Sbjct: 360 IQREPKYNTTMIIMLFIILAIIFAYLSANRPN 391

Source: Azadirachta indica

Species: Azadirachta indica

Genus: Azadirachta

Family: Meliaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255641455|gb|ACU21003.1| unknown [Glycine max]

 Score =  364 bits (934), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 170/210 (80%), Positives = 190/210 (90%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINEIPK RMFWPR+IWS+YVNKLEDLKYEENS KAVQCLNDMV
Sbjct: 201 MGLFLQKTNIIRDYLEDINEIPKSRMFWPRQIWSEYVNKLEDLKYEENSVKAVQCLNDMV 260

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNALMH EDCLKYM+ALRD  IFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK
Sbjct: 261 TNALMHAEDCLKYMAALRDPPIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 320

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           VIDRT  M DVY AF+DF+++L+PK++KNDPNATKTLSR+EAIQK C +SG+L+KRKSYI
Sbjct: 321 VIDRTKTMADVYGAFFDFASMLEPKVDKNDPNATKTLSRLEAIQKTCRESGLLSKRKSYI 380

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSSTR 210
           +  E  Y STMIVI  I+++IIF+YLS+  
Sbjct: 381 VNDESGYGSTMIVILVIMVSIIFAYLSANH 410

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|414073181|gb|AFI33135.2| squalene synthase, partial [Eriobotrya japonica]

 Score =  362 bits (930), Expect = 4e-98,   Method: Compositional matrix adjust.
 Identities = 170/209 (81%), Positives = 191/209 (91%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINEIPK RMFWPR+IWSKYVNKLEDLKYEENS+KAVQCLNDMV
Sbjct: 176 MGLFLQKTNIIRDYLEDINEIPKSRMFWPRQIWSKYVNKLEDLKYEENSEKAVQCLNDMV 235

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL+H+EDCLKYM+ALRD AIF+FCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTA+
Sbjct: 236 TNALIHMEDCLKYMAALRDPAIFKFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAE 295

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           VIDRT +M DVY AF+DFS+IL  K++KNDPNATK+LSRVEA+QK C DSG L+KRKSYI
Sbjct: 296 VIDRTKSMDDVYGAFFDFSSILNSKVDKNDPNATKSLSRVEAVQKLCRDSGALSKRKSYI 355

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSST 209
              E  Y+ST+IV  FIILAII++Y S++
Sbjct: 356 ANREQSYNSTLIVALFIILAIIYAYFSAS 384

Source: Eriobotrya japonica

Species: Eriobotrya japonica

Genus: Eriobotrya

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351726622|ref|NP_001236365.1| squalene synthase [Glycine max] gi|2463569|dbj|BAA22559.1| squalene synthase [Glycine max]

 Score =  362 bits (930), Expect = 5e-98,   Method: Compositional matrix adjust.
 Identities = 170/210 (80%), Positives = 190/210 (90%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINEIPK RMFWPR+IWS+YVNKLEDLKYEENS KAVQCLNDMV
Sbjct: 201 MGLFLQKTNIIRDYLEDINEIPKSRMFWPRQIWSEYVNKLEDLKYEENSVKAVQCLNDMV 260

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNALMH EDCLKYM+ALRD  IFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK
Sbjct: 261 TNALMHPEDCLKYMAALRDPPIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 320

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           VIDRT  M DVY AF+DF+++L+PK++KNDPNATKTLSR+EAIQK C +SG+L+KRKSYI
Sbjct: 321 VIDRTKTMADVYGAFFDFASMLEPKVDKNDPNATKTLSRLEAIQKTCRESGLLSKRKSYI 380

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSSTR 210
           +  E  Y STMIVI  I+++IIF+YLS+  
Sbjct: 381 VNDESGYGSTMIVILVIMVSIIFAYLSANH 410

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|327243159|gb|AEA41712.1| squalene synthase [Eleutherococcus senticosus] gi|327243163|gb|AEA41714.1| squalene synthase [Eleutherococcus senticosus] gi|327243167|gb|AEA41716.1| squalene synthase [Eleutherococcus senticosus]

 Score =  362 bits (928), Expect = 6e-98,   Method: Compositional matrix adjust.
 Identities = 173/210 (82%), Positives = 194/210 (92%), Gaps = 1/210 (0%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINEIPK RMFWPR+IWSKYV+KLEDLKYEENS KAVQCLNDMV
Sbjct: 201 MGLFLQKTNIIRDYLEDINEIPKSRMFWPRQIWSKYVDKLEDLKYEENSGKAVQCLNDMV 260

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL+HVEDCLKYMS LRD AIFRFCAIPQIMAIGTLALCYNNI+VFRGVVK+RRGLTAK
Sbjct: 261 TNALLHVEDCLKYMSDLRDPAIFRFCAIPQIMAIGTLALCYNNIQVFRGVVKLRRGLTAK 320

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVL-NKRKSY 179
           VIDRTN M+DVY AF+DFS +LK K++ NDPNATKTLSR+EAIQK+C +SG L  KRKSY
Sbjct: 321 VIDRTNTMSDVYGAFFDFSCMLKSKVDNNDPNATKTLSRLEAIQKSCKNSGALTTKRKSY 380

Query: 180 IIQSELRYSSTMIVIFFIILAIIFSYLSST 209
           II++E  Y+ST+IVI FIILAI+++YLSS+
Sbjct: 381 IIENESGYNSTLIVILFIILAILYAYLSSS 410

Source: Eleutherococcus senticosus

Species: Eleutherococcus senticosus

Genus: Eleutherococcus

Family: Araliaceae

Order: Apiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|432139331|gb|AGB05603.1| squalene synthase [Camellia oleifera]

 Score =  361 bits (926), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 171/212 (80%), Positives = 192/212 (90%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINEIPK RMFWPR+IWSKYVNKLEDLK +ENS KAV+CLNDMV
Sbjct: 201 MGLFLQKTNIIRDYLEDINEIPKSRMFWPRQIWSKYVNKLEDLKDKENSVKAVECLNDMV 260

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL+HVEDCL YMSALRD +IFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK
Sbjct: 261 TNALIHVEDCLTYMSALRDPSIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 320

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           VIDRT  M+DVY AF+DFS +LK K+NK+DPNA K LSR+EAIQK C +SG LNKRKSYI
Sbjct: 321 VIDRTKTMSDVYGAFFDFSCMLKSKVNKSDPNAMKALSRLEAIQKICRESGTLNKRKSYI 380

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSSTRAS 212
           ++SE RY+ST++ + FIILAI+F+YLS+ R S
Sbjct: 381 VKSEPRYNSTLVFVLFIILAILFAYLSANRPS 412

Source: Camellia oleifera

Species: Camellia oleifera

Genus: Camellia

Family: Theaceae

Order: Ericales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225427738|ref|XP_002266150.1| PREDICTED: squalene synthase [Vitis vinifera] gi|297744746|emb|CBI38008.3| unnamed protein product [Vitis vinifera]

 Score =  360 bits (925), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 172/210 (81%), Positives = 190/210 (90%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINEIPK RMFWPREIWSKYVNKLEDLK EENS KAVQCLNDMV
Sbjct: 201 MGLFLQKTNIIRDYLEDINEIPKSRMFWPREIWSKYVNKLEDLKEEENSIKAVQCLNDMV 260

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL+H+EDCL YMSAL+  AIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK
Sbjct: 261 TNALIHMEDCLTYMSALQSPAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 320

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           VIDRT  M+DVY AF+DFS +LK K++KNDPNATK LSR+EA+QK C +SG L KRKSY+
Sbjct: 321 VIDRTKAMSDVYGAFFDFSCMLKSKVDKNDPNATKALSRLEAVQKICRESGALTKRKSYV 380

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSSTR 210
           I+SE RY+S +IV FFIIL+IIF+YLS+ R
Sbjct: 381 IRSEPRYNSALIVAFFIILSIIFAYLSANR 410

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|259014869|gb|ACV88718.1| squalene synthase [Panax ginseng]

 Score =  360 bits (924), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 173/209 (82%), Positives = 192/209 (91%), Gaps = 1/209 (0%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINEIPK RMFWPR+IWSKYV+KLEDLKYEENS KAVQCLNDMV
Sbjct: 201 MGLFLQKTNIIRDYLEDINEIPKSRMFWPRQIWSKYVDKLEDLKYEENSGKAVQCLNDMV 260

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL+HVEDCLKYMS LRD AIFRFCAIPQIM+IGTLALCYNNI+VFRGVVKMRRGLTAK
Sbjct: 261 TNALLHVEDCLKYMSDLRDPAIFRFCAIPQIMSIGTLALCYNNIQVFRGVVKMRRGLTAK 320

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVL-NKRKSY 179
           VIDRTN M+DVY AF+DFS +LK K++ NDPNATKTLSR+EAIQK C +SG L  KRKSY
Sbjct: 321 VIDRTNTMSDVYGAFFDFSCMLKSKVDNNDPNATKTLSRLEAIQKICKNSGALTTKRKSY 380

Query: 180 IIQSELRYSSTMIVIFFIILAIIFSYLSS 208
           II++E  Y+ST+IVI FIILAI+++YLSS
Sbjct: 381 IIENESGYNSTLIVILFIILAILYAYLSS 409

Source: Panax ginseng

Species: Panax ginseng

Genus: Panax

Family: Araliaceae

Order: Apiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|327243161|gb|AEA41713.1| squalene synthase [Eleutherococcus senticosus] gi|327243165|gb|AEA41715.1| squalene synthase [Eleutherococcus senticosus] gi|327243169|gb|AEA41717.1| squalene synthase [Eleutherococcus senticosus]

 Score =  358 bits (920), Expect = 6e-97,   Method: Compositional matrix adjust.
 Identities = 172/210 (81%), Positives = 193/210 (91%), Gaps = 1/210 (0%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINEIPK RMFWPR+IWS YV+KLEDLKYEENS KAVQCLNDMV
Sbjct: 201 MGLFLQKTNIIRDYLEDINEIPKSRMFWPRQIWSIYVDKLEDLKYEENSGKAVQCLNDMV 260

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL+HVEDCLKYMS LRD AIFRFCAIPQIMAIGTLALCYNNI+VFRGVVK+RRGLTAK
Sbjct: 261 TNALLHVEDCLKYMSDLRDPAIFRFCAIPQIMAIGTLALCYNNIQVFRGVVKLRRGLTAK 320

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVL-NKRKSY 179
           VIDRTN M+DVY AF+DFS +LK K++ NDPNATKTLSR+EAIQK+C +SG L  KRKSY
Sbjct: 321 VIDRTNTMSDVYGAFFDFSCMLKSKVDNNDPNATKTLSRLEAIQKSCKNSGALTTKRKSY 380

Query: 180 IIQSELRYSSTMIVIFFIILAIIFSYLSST 209
           II++E  Y+ST+IVI FIILAI+++YLSS+
Sbjct: 381 IIENESGYNSTLIVILFIILAILYAYLSSS 410

Source: Eleutherococcus senticosus

Species: Eleutherococcus senticosus

Genus: Eleutherococcus

Family: Araliaceae

Order: Apiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356538706|ref|XP_003537842.1| PREDICTED: squalene synthase-like [Glycine max]

 Score =  358 bits (920), Expect = 6e-97,   Method: Compositional matrix adjust.
 Identities = 167/210 (79%), Positives = 189/210 (90%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINEIPK RMFWPR+IWSKYVNKLEDLKYEENS KAVQCLNDMV
Sbjct: 201 MGLFLQKTNIIRDYLEDINEIPKSRMFWPRQIWSKYVNKLEDLKYEENSVKAVQCLNDMV 260

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNALMH EDCL YM+ALRD  IFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK
Sbjct: 261 TNALMHAEDCLTYMAALRDPPIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 320

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
           VIDRT  M DVY AF+DF+++L+ K++KNDPNATK LSR+EAIQK C +SG+L+KRKSYI
Sbjct: 321 VIDRTTTMADVYGAFFDFASMLESKVDKNDPNATKALSRLEAIQKTCRESGLLSKRKSYI 380

Query: 181 IQSELRYSSTMIVIFFIILAIIFSYLSSTR 210
           ++ E  Y STMI++  I+++IIFSYLS++ 
Sbjct: 381 VKDESGYGSTMIIVLVIMVSIIFSYLSASH 410

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
TAIR|locus:2139514	410	SQS1 "squalene synthase 1" [Ar	0.845	0.439	0.805	6.2e-78
TAIR|locus:2139534	413	SQS2 "squalene synthase 2" [Ar	0.840	0.433	0.731	6.3e-69
UNIPROTKB|F1NFJ9	418	FDFT1 "Uncharacterized protein	0.826	0.421	0.508	6.4e-44
DICTYBASE|DDB_G0292072	416	fdfT "farnesyl-diphosphate far	0.779	0.399	0.514	8.1e-44
RGD|61834	416	Fdft1 "farnesyl diphosphate fa	0.826	0.423	0.480	6.6e-42
MGI|MGI:102706	416	Fdft1 "farnesyl diphosphate fa	0.826	0.423	0.480	8.4e-42
UNIPROTKB|Q32KR6	417	FDFT1 "Squalene synthase" [Bos	0.826	0.422	0.491	9.6e-41
UNIPROTKB|Q6IE76	417	fdft1 "FDFT1 protein" [Bos tau	0.826	0.422	0.491	9.6e-41
UNIPROTKB|E2R6N6	417	FDFT1 "Uncharacterized protein	0.826	0.422	0.474	9.6e-41
UNIPROTKB|B3KQ95	306	FDFT1 "Squalene synthase" [Hom	0.826	0.575	0.474	2e-40

TAIR|locus:2139514 SQS1 "squalene synthase 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 784 (281.0 bits), Expect = 6.2e-78, P = 6.2e-78
 Identities = 145/180 (80%), Positives = 164/180 (91%)

Query:     1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
             MGLFLQKTNIIRDYLEDINEIPK RMFWPREIW KY +KLEDLKYEEN++K+VQCLN+MV
Sbjct:   203 MGLFLQKTNIIRDYLEDINEIPKSRMFWPREIWGKYADKLEDLKYEENTNKSVQCLNEMV 262

Query:    61 TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
             TNALMH+EDCLKYM +LRD +IFRFCAIPQIMAIGTLALCYNN +VFRGVVK+RRGLTAK
Sbjct:   263 TNALMHIEDCLKYMVSLRDPSIFRFCAIPQIMAIGTLALCYNNEQVFRGVVKLRRGLTAK 322

Query:   121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
             VIDRT  M DVY AFYDFS +LK K++KNDPNA+KTL+R+EA+QK C D+GVL  RKSY+
Sbjct:   323 VIDRTKTMADVYGAFYDFSCMLKTKVDKNDPNASKTLNRLEAVQKLCRDAGVLQNRKSYV 382

GO:0004310 "farnesyl-diphosphate farnesyltransferase activity" evidence=IEA;ISS;IDA

GO:0008610 "lipid biosynthetic process" evidence=IEA

GO:0009058 "biosynthetic process" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0016765 "transferase activity, transferring alkyl or aryl (other than methyl) groups" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0006084 "acetyl-CoA metabolic process" evidence=RCA

GO:0006598 "polyamine catabolic process" evidence=RCA

GO:0009698 "phenylpropanoid metabolic process" evidence=RCA

GO:0016126 "sterol biosynthetic process" evidence=RCA;TAS

GO:0016132 "brassinosteroid biosynthetic process" evidence=RCA

GO:0042398 "cellular modified amino acid biosynthetic process" evidence=RCA

GO:0005789 "endoplasmic reticulum membrane" evidence=TAS

TAIR|locus:2139534 SQS2 "squalene synthase 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 699 (251.1 bits), Expect = 6.3e-69, P = 6.3e-69
 Identities = 131/179 (73%), Positives = 155/179 (86%)

Query:     2 GLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVT 61
             GLFLQKTNII+DYLEDINE PK RMFWPREIW KYV+KLED K EE + KAVQCLN+MVT
Sbjct:   204 GLFLQKTNIIKDYLEDINERPKSRMFWPREIWGKYVDKLEDFKNEEKATKAVQCLNEMVT 263

Query:    62 NALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKV 121
             NAL HVEDCLK +++LRD AIF+ CAIPQI+AIGTLALCYNN++VFRGVV++RRGL AKV
Sbjct:   264 NALNHVEDCLKSLASLRDPAIFQSCAIPQIVAIGTLALCYNNVQVFRGVVRLRRGLIAKV 323

Query:   122 IDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSYI 180
             IDRT  M DVY AFYDFS +L+ K++ NDPNA KTL+R+E I+K C ++G L+KRKSY+
Sbjct:   324 IDRTKTMDDVYGAFYDFSCMLQTKVDNNDPNAMKTLNRLETIKKFCKENGGLHKRKSYV 382

GO:0004310 "farnesyl-diphosphate farnesyltransferase activity" evidence=IEA;IGI;ISS;IDA

GO:0008610 "lipid biosynthetic process" evidence=IEA

GO:0009058 "biosynthetic process" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0016126 "sterol biosynthetic process" evidence=ISS

UNIPROTKB|F1NFJ9 FDFT1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 463 (168.0 bits), Expect = 6.4e-44, P = 6.4e-44
 Identities = 91/179 (50%), Positives = 117/179 (65%)

Query:     1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
             MGLFLQKTNIIRDYLED  E    R FWPRE+WS+Y  KL DL   EN D AVQC+N+++
Sbjct:   208 MGLFLQKTNIIRDYLEDQLE---GREFWPREVWSRYTKKLSDLTKPENIDMAVQCMNELI 264

Query:    61 TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
             TNAL HV D L Y+S L++ ++F FCAIPQ+MAI TLA CYNN +VFRGVVK+R+G    
Sbjct:   265 TNALRHVPDVLTYLSRLKNQSVFNFCAIPQVMAIATLAACYNNKQVFRGVVKIRKGQAVT 324

Query:   121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSY 179
             ++    NM  V    Y +   +  KI   DP++ KT   + +I+   + SG +  R  Y
Sbjct:   325 LMMDATNMQSVKAIMYQYVEEIYQKIPSTDPSSNKTQQIIASIRAMSLPSGPMASRHHY 383

GO:0004310 "farnesyl-diphosphate farnesyltransferase activity" evidence=IEA

GO:0008610 "lipid biosynthetic process" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

DICTYBASE|DDB_G0292072 fdfT "farnesyl-diphosphate farnesyltransferase" [Dictyostelium discoideum (taxid:44689)]

 Score = 462 (167.7 bits), Expect = 8.1e-44, P = 8.1e-44
 Identities = 88/171 (51%), Positives = 121/171 (70%)

Query:     1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
             MGLFLQKTNIIRDYLEDINE  K R+FWPR++W++Y   LE+ K  +    A+ CLND++
Sbjct:   207 MGLFLQKTNIIRDYLEDINE--K-RIFWPRDVWARYTLHLENFKEAKYQIPALHCLNDLI 263

Query:    61 TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
             TNAL H    L YMS L++  +  FCAIPQ+MAIGTL  CYNN  VF GVVK+R+G  A 
Sbjct:   264 TNALSHALIALDYMSRLKNPQVINFCAIPQVMAIGTLNACYNNYNVFTGVVKIRKGQRAL 323

Query:   121 VID--RTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMD 169
             ++D  ++  +T  Y  F+ F+N ++ K+  NDP+A KT+  +E+I+K C++
Sbjct:   324 IVDAIQSKGLTATYELFFKFANEMRHKVPPNDPSAKKTIQHLESIEKLCIE 374

GO:0016765 "transferase activity, transferring alkyl or aryl (other than methyl) groups" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA;ISS

GO:0009058 "biosynthetic process" evidence=IEA

GO:0008610 "lipid biosynthetic process" evidence=IEA

GO:0004310 "farnesyl-diphosphate farnesyltransferase activity" evidence=IEA;ISS

GO:0051996 "squalene synthase activity" evidence=IEA

GO:0006695 "cholesterol biosynthetic process" evidence=IEA;ISS

GO:0055114 "oxidation-reduction process" evidence=IEA

GO:0016491 "oxidoreductase activity" evidence=IEA

GO:0016126 "sterol biosynthetic process" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0008299 "isoprenoid biosynthetic process" evidence=IEA

GO:0008203 "cholesterol metabolic process" evidence=IEA

GO:0008202 "steroid metabolic process" evidence=IEA

GO:0008152 "metabolic process" evidence=IEA

GO:0006694 "steroid biosynthetic process" evidence=IEA

GO:0006629 "lipid metabolic process" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0003824 "catalytic activity" evidence=IEA

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

RGD|61834 Fdft1 "farnesyl diphosphate farnesyl transferase 1" [Rattus norvegicus (taxid:10116)]

 Score = 444 (161.4 bits), Expect = 6.6e-42, P = 6.6e-42
 Identities = 86/179 (48%), Positives = 116/179 (64%)

Query:     1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
             MGLFLQKTNIIRDYLED  E    R FWP+E+W KYV KLED    EN D AV+CLN+++
Sbjct:   207 MGLFLQKTNIIRDYLEDQQE---GRQFWPQEVWGKYVKKLEDFVKPENVDVAVKCLNELI 263

Query:    61 TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
             TNAL H+ D + Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+GVVK+R+G    
Sbjct:   264 TNALQHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNHQVFKGVVKIRKGQAVT 323

Query:   121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSY 179
             ++    NM  V    Y +   +  ++  +DP+A+K    +  I+   + +  L  R  Y
Sbjct:   324 LMMDATNMPAVKAIIYQYIEEIYHRVPNSDPSASKAKQLISNIRTQSLPNCQLISRSHY 382

GO:0004310 "farnesyl-diphosphate farnesyltransferase activity" evidence=IDA;IMP

GO:0005783 "endoplasmic reticulum" evidence=ISO

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA

GO:0006695 "cholesterol biosynthetic process" evidence=IMP;TAS

GO:0008299 "isoprenoid biosynthetic process" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016491 "oxidoreductase activity" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

GO:0045338 "farnesyl diphosphate metabolic process" evidence=IMP

GO:0051996 "squalene synthase activity" evidence=IEA

MGI|MGI:102706 Fdft1 "farnesyl diphosphate farnesyl transferase 1" [Mus musculus (taxid:10090)]

 Score = 443 (161.0 bits), Expect = 8.4e-42, P = 8.4e-42
 Identities = 86/179 (48%), Positives = 116/179 (64%)

Query:     1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
             MGLFLQKTNIIRDYLED  E    R FWP+E+W +Y+ KLED    EN D AVQCLN+++
Sbjct:   207 MGLFLQKTNIIRDYLEDQQE---GRKFWPQEVWGRYIKKLEDFAKPENVDVAVQCLNELI 263

Query:    61 TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
             TN L H+ D L Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+GVVK+R+G    
Sbjct:   264 TNTLQHIPDVLTYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQAVT 323

Query:   121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSY 179
             ++    NM  V    Y +   +  +I  +DP+++KT   +  I+   + +  L  R  Y
Sbjct:   324 LMMDATNMPAVKAIIYQYIEEIYHRIPNSDPSSSKTKQVISKIRTQNLPNCQLISRSHY 382

GO:0003824 "catalytic activity" evidence=IEA

GO:0004310 "farnesyl-diphosphate farnesyltransferase activity" evidence=ISO

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0006629 "lipid metabolic process" evidence=IEA

GO:0006694 "steroid biosynthetic process" evidence=IEA

GO:0006695 "cholesterol biosynthetic process" evidence=ISO

GO:0008152 "metabolic process" evidence=IEA

GO:0008202 "steroid metabolic process" evidence=IEA

GO:0008203 "cholesterol metabolic process" evidence=IEA

GO:0008299 "isoprenoid biosynthetic process" evidence=IEA

GO:0008610 "lipid biosynthetic process" evidence=IEA

GO:0009058 "biosynthetic process" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0016126 "sterol biosynthetic process" evidence=IEA

GO:0016491 "oxidoreductase activity" evidence=IEA

GO:0016740 "transferase activity" evidence=IEA

GO:0016765 "transferase activity, transferring alkyl or aryl (other than methyl) groups" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" evidence=ISO

GO:0045338 "farnesyl diphosphate metabolic process" evidence=ISO

GO:0051996 "squalene synthase activity" evidence=IEA

GO:0055114 "oxidation-reduction process" evidence=IEA

UNIPROTKB|Q32KR6 FDFT1 "Squalene synthase" [Bos taurus (taxid:9913)]

 Score = 433 (157.5 bits), Expect = 9.6e-41, P = 9.6e-41
 Identities = 88/179 (49%), Positives = 114/179 (63%)

Query:     1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
             MGLFLQKTNIIRDYLED  E    R FWP+E WSKYV KL D    EN D AVQCLN+++
Sbjct:   207 MGLFLQKTNIIRDYLEDQRE---GREFWPQETWSKYVKKLGDFAKPENIDLAVQCLNELI 263

Query:    61 TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
             TN L H+ D + Y+S LR+ +IF FCAIPQ+MAI TLA CYNN +VF+GVVK+R+G    
Sbjct:   264 TNTLHHIPDVITYLSRLRNQSIFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQAVT 323

Query:   121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSY 179
             ++    NM  V    + +   +  +I  +DP +TKT   +  I+   + +  L  R  Y
Sbjct:   324 LMMDATNMPAVKAIIHQYMEEIYHRIPNSDPCSTKTQQIISTIRTQNLPNCQLVSRSHY 382

GO:0005789 "endoplasmic reticulum membrane" evidence=IEA

GO:0051996 "squalene synthase activity" evidence=IEA

GO:0004310 "farnesyl-diphosphate farnesyltransferase activity" evidence=IEA

GO:0016491 "oxidoreductase activity" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0008299 "isoprenoid biosynthetic process" evidence=IEA

GO:0006695 "cholesterol biosynthetic process" evidence=IEA

UNIPROTKB|Q6IE76 fdft1 "FDFT1 protein" [Bos taurus (taxid:9913)]

 Score = 433 (157.5 bits), Expect = 9.6e-41, P = 9.6e-41
 Identities = 88/179 (49%), Positives = 114/179 (63%)

Query:     1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
             MGLFLQKTNIIRDYLED  E    R FWP+E WSKYV KL D    EN D AVQCLN+++
Sbjct:   207 MGLFLQKTNIIRDYLEDQRE---GREFWPQETWSKYVKKLGDFAKPENIDLAVQCLNELI 263

Query:    61 TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
             TN L H+ D + Y+S LR+ +IF FCAIPQ+MAI TLA CYNN +VF+GVVK+R+G    
Sbjct:   264 TNTLHHIPDVITYLSRLRNQSIFNFCAIPQVMAIATLAACYNNQQVFKGVVKIRKGQAVT 323

Query:   121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSY 179
             ++    NM  V    + +   +  +I  +DP +TKT   +  I+   + +  L  R  Y
Sbjct:   324 LMMDATNMPAVKAIIHQYMEEIYHRIPNSDPCSTKTQQIISTIRTQNLPNCQLVSRSHY 382

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0008610 "lipid biosynthetic process" evidence=IEA

GO:0004310 "farnesyl-diphosphate farnesyltransferase activity" evidence=IEA

UNIPROTKB|E2R6N6 FDFT1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 433 (157.5 bits), Expect = 9.6e-41, P = 9.6e-41
 Identities = 85/179 (47%), Positives = 115/179 (64%)

Query:     1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
             MGLFLQKTNIIRDYLED  E    R FWP+E+WSKYV KL D    +N D AVQCLN+++
Sbjct:   207 MGLFLQKTNIIRDYLEDQRE---GREFWPQEVWSKYVKKLGDFAKPQNIDSAVQCLNELI 263

Query:    61 TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
             TNAL H+   + Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+G+VK+R+G    
Sbjct:   264 TNALHHIPHVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGIVKIRKGQAVT 323

Query:   121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSY 179
             ++    NM  V    Y +   +  +I  +DP++ KT   +  I+   + +  L  R  Y
Sbjct:   324 LMMDATNMPAVKAIIYQYMEEIYHRIPSSDPSSGKTRQIISTIRTQNLPNCQLISRSHY 382

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0008610 "lipid biosynthetic process" evidence=IEA

GO:0004310 "farnesyl-diphosphate farnesyltransferase activity" evidence=IEA

UNIPROTKB|B3KQ95 FDFT1 "Squalene synthase" [Homo sapiens (taxid:9606)]

 Score = 430 (156.4 bits), Expect = 2.0e-40, P = 2.0e-40
 Identities = 85/179 (47%), Positives = 115/179 (64%)

Query:     1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
             MGLFLQKTNIIRDYLED       R FWP+E+WS+YV KL D    EN D AVQCLN+++
Sbjct:    96 MGLFLQKTNIIRDYLEDQQG---GREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELI 152

Query:    61 TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
             TNAL H+ D + Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+G VK+R+G    
Sbjct:   153 TNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVT 212

Query:   121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKACMDSGVLNKRKSY 179
             ++    NM  V    Y +   +  +I  +DP+++KT   +  I+   + +  L  R  Y
Sbjct:   213 LMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRTQNLPNCQLISRSHY 271

GO:0008610 "lipid biosynthetic process" evidence=IEA

GO:0016021 "integral to membrane" evidence=IEA

GO:0004310 "farnesyl-diphosphate farnesyltransferase activity" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IEA

GO:0045338 "farnesyl diphosphate metabolic process" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P53799	FDFT_ARATH	2, ., 5, ., 1, ., 2, 1	0.7403	0.9718	0.5048	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	2.5.1	0.921
4th Layer	2.5.1.21	0.914

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00035946001	SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (413 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00033429001	SubName- Full=Chromosome chr19 scaffold_66, whole genome shotgun sequence; (341 aa)				•		•	•		0.972
	GSVIVG00012453001	SubName- Full=Chromosome chr7 scaffold_382, whole genome shotgun sequence; (522 aa)				•		•	•		0.949
	GSVIVG00015002001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (523 aa)				•		•	•		0.949
	GSVIVG00038545001	SubName- Full=Chromosome chr3 scaffold_95, whole genome shotgun sequence; (524 aa)				•		•	•		0.948
	GSVIVG00038547001	SubName- Full=Chromosome chr3 scaffold_95, whole genome shotgun sequence; (522 aa)				•		•	•		0.948
	GSVIVG00007515001	SubName- Full=Chromosome chr7 scaffold_192, whole genome shotgun sequence; (245 aa)						•	•		0.811
	GSVIVG00024111001	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (311 aa)						•	•		0.809
	GSVIVG00036415001	SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (255 aa)						•			0.800
	GSVIVG00036188001	SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence (Chromosome undetermine [...] (341 aa)						•			0.800
	GSVIVG00027313001	SubName- Full=Chromosome chr19 scaffold_4, whole genome shotgun sequence; (298 aa)						•			0.800

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	213
TIGR01559	337	TIGR01559, squal_synth, farnesyl-diphosphate farne	6e-94
cd00683	265	cd00683, Trans_IPPS_HH, Trans-Isoprenyl Diphosphat	9e-36
pfam00494	262	pfam00494, SQS_PSY, Squalene/phytoene synthase	4e-20
COG1562	288	COG1562, ERG9, Phytoene/squalene synthetase [Lipid	5e-19
cd00385	243	cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynth	2e-08
cd00867	236	cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate S	4e-05

>gnl|CDD|188157 TIGR01559, squal_synth, farnesyl-diphosphate farnesyltransferase

 Score =  277 bits (710), Expect = 6e-94
 Identities = 106/167 (63%), Positives = 126/167 (75%), Gaps = 3/167 (1%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLEDINE    RMFWPREIWSKY  KL D K  ENSDKA+QCLN++V
Sbjct: 174 MGLFLQKTNIIRDYLEDINE---GRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELV 230

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL H  DCL Y+S LRD +IF FCAIPQ+MAI TLALCYNN +VF+G VK+R+G T K
Sbjct: 231 TNALHHATDCLTYLSRLRDQSIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTTVK 290

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQKAC 167
           +I  + NM  VY  FY ++  +  KI+ NDPN +KTL  +  I++ C
Sbjct: 291 LILDSTNMPAVYDIFYRYARKIYHKIDPNDPNFSKTLIIISKIEQQC 337

This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family. Length = 337

>gnl|CDD|173831 cd00683, Trans_IPPS_HH, Trans-Isoprenyl Diphosphate Synthases, head-to-head

 Score =  126 bits (318), Expect = 9e-36
 Identities = 36/120 (30%), Positives = 51/120 (42%), Gaps = 5/120 (4%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           +GL LQ TNI+RD  ED       R++ PRE  +++   LEDL   ENS      L  ++
Sbjct: 151 LGLALQLTNILRDVGEDARR---GRIYLPREELARFGVTLEDLLAPENSPAFRALLRRLI 207

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
             A  H  + L  ++AL      RFC     M   T+             V++R     K
Sbjct: 208 ARARAHYREALAGLAAL--PRRSRFCVRAAAMLYRTILDEIEARGYDVLSVRVRVPKARK 265

These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes the condensation reaction of two molecules of geranylgeranyl diphosphate to produce phytoene, a precursor of beta-carotene. These enzymes produce the triterpene and tetraterpene precursors for many diverse sterol and carotenoid end products and are widely distributed among eukareya, bacteria, and archaea. Length = 265

>gnl|CDD|215948 pfam00494, SQS_PSY, Squalene/phytoene synthase

 Score = 85.1 bits (211), Expect = 4e-20
 Identities = 25/116 (21%), Positives = 46/116 (39%), Gaps = 4/116 (3%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           +G+ LQ TNI+RD  ED     + R++ P +  +++    EDL     S      + ++ 
Sbjct: 148 LGIALQLTNILRDVGEDAR---RGRVYLPADWLARFGVSPEDLLRGRPSPALRALIRELA 204

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCY-NNIEVFRGVVKMRR 115
             A  H+ +    ++ L          +   +    L        +V R  VK+ R
Sbjct: 205 ARARAHLAEARALLALLPPRRARLAVLLAAALYRAILDRLEAAGYDVLRRRVKLSR 260

Length = 262

>gnl|CDD|224478 COG1562, ERG9, Phytoene/squalene synthetase [Lipid metabolism]

 Score = 82.8 bits (205), Expect = 5e-19
 Identities = 25/128 (19%), Positives = 48/128 (37%), Gaps = 3/128 (2%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           +GL LQ  NI+RD  ED     + R++ P E  +++     DL      D   + +    
Sbjct: 161 LGLALQLVNILRDVGEDRR---RGRVYLPAEELARFGVSEADLLAGRVDDAFRELMRFEA 217

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
             A  H+ +  + + AL   A     A   + A    A+  +  +V      + +     
Sbjct: 218 DRARDHLAEARRGLPALPGRAQLAVLAAALLYAYLLDAIEADPADVLSQRAVLPKLRKLW 277

Query: 121 VIDRTNNM 128
           ++ +    
Sbjct: 278 LLLKAWLR 285

Length = 288

>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes, Class 1

 Score = 52.9 bits (127), Expect = 2e-08
 Identities = 19/94 (20%), Positives = 33/94 (35%), Gaps = 3/94 (3%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           +GL  Q TN + DY  D       +   P     +Y    EDL   E S    + L ++ 
Sbjct: 152 LGLAFQLTNDLLDYEGDAERGEG-KCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELA 210

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAI 94
             A   +++  + +  L    + R      +   
Sbjct: 211 KLAEEALKELNELI--LSLPDVPRALLALALNLY 242

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. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoterpenes, diterpenes, and sesquiterpenes, are formed from their respective linear isoprenoid diphosphates by class I terpene cyclases. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Cyclization of these 30- and 40-carbon linear forms are catalyzed by class II cyclases. Both the isoprenoid chain elongation reactions and the class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Generally, the enzymes in this family exhibit an all-trans reaction pathway, an exception, is the cis-trans terpene cyclase, trichodiene synthase. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD. Length = 243

>gnl|CDD|173836 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate Synthases

 Score = 42.7 bits (101), Expect = 4e-05
 Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 7/54 (12%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKC-------RMFWPREIWSKYVNKLEDLKYEE 47
           +GL  Q T+ + D   D  E+ K        R+  P  +  +   +  +  Y  
Sbjct: 158 LGLAFQLTDDLLDVFGDAEELGKVGSDLREGRITLPVILARERAAEYAEEAYAA 211

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. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Mechanistically and structurally distinct, cis-IPPS are not included in this CD. Length = 236

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	213
TIGR01559	336	squal_synth farnesyl-diphosphate farnesyltransfera	100.0
KOG1459	413	consensus Squalene synthetase [Lipid transport and	100.0
COG1562	288	ERG9 Phytoene/squalene synthetase [Lipid metabolis	99.92
TIGR03465	266	HpnD squalene synthase HpnD. The genes of this fam	99.92
TIGR03464	266	HpnC squalene synthase HpnC. This family of genes	99.91
PLN02632	334	phytoene synthase	99.9
PF00494	267	SQS_PSY: Squalene/phytoene synthase; InterPro: IPR	99.9
cd00683	265	Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthase	99.9
cd00385	243	Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzym	98.18
cd00867	236	Trans_IPPS Trans-Isoprenyl Diphosphate Synthases.	98.12
KOG4411	292	consensus Phytoene/squalene synthetase [Lipid tran	97.67
KOG1459	413	consensus Squalene synthetase [Lipid transport and	95.73

>TIGR01559 squal_synth farnesyl-diphosphate farnesyltransferase

Probab=100.00  E-value=7.6e-56  Score=403.07  Aligned_cols=164  Identities=64%  Similarity=1.071  Sum_probs=162.4

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH   80 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~   80 (213)
                      ||+|||+|||||||+||++   +||+|||+|+|++||++.+|+.+|++++++.+|+++|+.+|+.||++|+.|++.++++
T Consensus       173 lG~aLQlTNIlRDv~ED~~---~GR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~lv~~A~~~~~~al~yl~~l~~~  249 (336)
T TIGR01559       173 MGLFLQKTNIIRDYLEDIN---EGRMFWPREIWSKYAKKLGDFKKPENSDKALQCLNELVTNALHHATDCLTYLSRLRDQ  249 (336)
T ss_pred             HHHHHHHHHHHHHHHhHHh---CCCCCCCHHHHHHcCCCHHHhcCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence            7999999999999999998   7999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhHHHHHHHHHHHHHHcCCCCCCCccccCHHHHHHHHHHhCChHHHHHHHHHHHHhhccccCCCCCCHHHHHHHH
Q 028137           81 AIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRV  160 (213)
Q Consensus        81 s~f~fcaip~~maiatL~~i~~n~~Vf~~rVKi~r~~~~~l~~~~~~~~~v~~~f~~~~~~i~~k~~~~dp~~~~~~~~~  160 (213)
                      ++|+||+||++||++||++|++|++||+++|||||++++++|++|+|+.+|+.+|++|+++|++|++|+||||.+|++.|
T Consensus       250 ~~~~fcaip~~mAi~TL~~~~~n~~~~~~~VKi~r~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~dp~~~~~~~~~  329 (336)
T TIGR01559       250 SIFNFCAIPQVMAIATLALCYNNPQVFQGNVKIRKGTTVKLILDSTNMPAVYDIFYRYARKIYHKIDPNDPNFSKTLIII  329 (336)
T ss_pred             chhHHHHHHHHHHHHHHHHHhcChhhcCCCceecHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHh
Q 028137          161 EAIQKAC  167 (213)
Q Consensus       161 ~~i~~~~  167 (213)
                      ++|+|+|
T Consensus       330 ~~~~~~~  336 (336)
T TIGR01559       330 SKIEQQC  336 (336)
T ss_pred             HHHHHhC
Confidence            9999997

This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family.

>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism]

Probab=100.00  E-value=1.1e-49  Score=361.71  Aligned_cols=199  Identities=51%  Similarity=0.818  Sum_probs=186.7

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH   80 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~   80 (213)
                      ||+|||+|||||||.||..   .||.|||+|||++|..+++|+..|+|++.+++|+++|+++|+.|.++++.|++.++.+
T Consensus       199 ~glfLqktnIirdy~ed~~---d~r~Fwp~eIwg~y~d~L~d~~~~en~dl~l~Cln~m~tnaL~hv~d~l~yls~l~~q  275 (413)
T KOG1459|consen  199 MGLFLQKTNIIRDYLEDPV---DGRPFWPREIWGKYMDKLKDFRYPENDDLALQCLNEMVTNALMHVPDVLTYLSKLRTQ  275 (413)
T ss_pred             cchHHHHhHHHHHHHhccc---cCCccChHHHHHHHHHHHHhhhCccchhHHHHHHHHHHHHHhhccHHHHHHHhhcccH
Confidence            7999999999999999999   6999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhHHHHHHHHHHHHHHcCCCCCCCccccCHHHHHHHHHHhCChHHHHHHHHHHHHhhccccCCCCCC-----HHH
Q 028137           81 AIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINKNDPN-----ATK  155 (213)
Q Consensus        81 s~f~fcaip~~maiatL~~i~~n~~Vf~~rVKi~r~~~~~l~~~~~~~~~v~~~f~~~~~~i~~k~~~~dp~-----~~~  155 (213)
                      |+|+||||||+||++||++|+||.+||+|+||||||.++.+|+.++|+.+|+.+|++|.++|+.|++++|||     ..+
T Consensus       276 svfnfcaipqimai~Tlal~~nn~dvfrG~VklrkGl~~~~I~~~k~~~~v~~~f~~y~~~i~~k~d~~dpnflklsask  355 (413)
T KOG1459|consen  276 SVFNFCAIPQIMAIATLALCYNNEDVFRGNVKLRKGLAVELILASKTMDKVRNIFYMYLRDIRMKFDEADPNFLKLSASK  355 (413)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCHhHhccceeecCCchHHHHHhcccHHHHHHHHHHHHHHHHhhCCccCCCchhhhhhh
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999     667


Q ss_pred             HHHHHHHHHHHhhhccccccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHhh
Q 028137          156 TLSRVEAIQKACMDSGVLNKRKSYIIQSELRYSSTMIVIFFIILAIIFSYLSS  208 (213)
Q Consensus       156 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  208 (213)
                      |.+..+++.+.|.+.+.++++..+..+      +..+.++++++|+.|+|...
T Consensus       356 ~~qv~esl~~~~~~~~il~n~~~~f~k------~~~v~~V~~i~al~~ay~~~  402 (413)
T KOG1459|consen  356 TEQVWESLLLYRRPDEILANRYNNFTK------RIYVGFVKKIAALPLAYAKS  402 (413)
T ss_pred             HHHHHHHHHHhhccccccccccccccc------hhHHHHHHHHHHHHHHHHHH
Confidence            777788888899999999988554211      56677889999999999854

>COG1562 ERG9 Phytoene/squalene synthetase [Lipid metabolism]

Probab=99.92  E-value=1.5e-25  Score=200.69  Aligned_cols=124  Identities=20%  Similarity=0.161  Sum_probs=119.6

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH   80 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~   80 (213)
                      ||+|+|+||||||++||..   +||+|||+|+|++||++.+|+.++.+++.+..|+++++.+|+.|+.+|..+++.+|.+
T Consensus       161 lG~A~QlvNilRdv~eD~~---~GrvylP~e~l~~~g~~~~d~~~~~~~~~~~~~~~~~~~~ar~~~~~a~~~~~~lp~~  237 (288)
T COG1562         161 LGLALQLVNILRDVGEDRR---RGRVYLPAEELARFGVSEADLLAGRVDDAFRELMRFEADRARDHLAEARRGLPALPGR  237 (288)
T ss_pred             HHHHHHHHHHHHHhHHHHh---CCcccCCHHHHHHhCCCHHHHHcccchhHHHHHHHHHHHHHHHHHHHHHHhhhhCCcc
Confidence            6999999999999999999   8999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhHHHHHHHHHHHHHHcCCCCCCCccccCHHHHHHHHHHhCC
Q 028137           81 AIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNN  127 (213)
Q Consensus        81 s~f~fcaip~~maiatL~~i~~n~~Vf~~rVKi~r~~~~~l~~~~~~  127 (213)
                      +.+.||++|+++++.+.++..++.+||+++++++++++++++.++..
T Consensus       238 ~~~~~~~~~~~~~~~~~~i~a~~~~vl~~~~~l~~~~~~~~~~~~~~  284 (288)
T COG1562         238 AQLAVLAAALLYAYLLDAIEADPADVLSQRAVLPKLRKLWLLLKAWL  284 (288)
T ss_pred             ccchhhHHHHHHHHHHHHHHccchhhhccCcccCcchHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999987753

>TIGR03465 HpnD squalene synthase HpnD

Probab=99.92  E-value=1.2e-24  Score=190.70  Aligned_cols=121  Identities=21%  Similarity=0.167  Sum_probs=113.5

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH   80 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~   80 (213)
                      +|.|||+||||||+.||++   +||+|||.|+|.+||++.+|+..+++++++..++++++.+|+.||.+|..++..+|..
T Consensus       142 lG~AlqltnilRdv~eD~~---~gR~ylP~~~l~~~gv~~~~l~~~~~~~~~~~~~~~l~~~A~~~l~~a~~~~~~~p~~  218 (266)
T TIGR03465       142 LGRALQLTNILRDVGEDAR---RGRIYLPAEELQRFGVPAADILEGRYSPALAALCRFQAERARAHYAEADALLPACDRR  218 (266)
T ss_pred             HHHHHHHHHHHHHhHHHHh---CCCeecCHHHHHHcCCCHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhCCHh
Confidence            6999999999999999999   8999999999999999999999999999999999999999999999999999999976


Q ss_pred             hhhhhhhHHHHHHHHHHHHH-HcCCCCCCCccccCHHHHHHHHHHh
Q 028137           81 AIFRFCAIPQIMAIGTLALC-YNNIEVFRGVVKMRRGLTAKVIDRT  125 (213)
Q Consensus        81 s~f~fcaip~~maiatL~~i-~~n~~Vf~~rVKi~r~~~~~l~~~~  125 (213)
                      +. .+|.++..++.++|..+ .+|++||++++++++.++.+++.++
T Consensus       219 ~~-~~~~~~~~~~~~iL~~i~~~~~~~~~~r~~~~~~~k~~~~~~~  263 (266)
T TIGR03465       219 AQ-RAARAMAAIYRALLDEIEADGFQVLRQRVSLTPLRKLWIALRT  263 (266)
T ss_pred             hh-HHHHHHHHHHHHHHHHHHHCCCCCCCCCCcCCHHHHHHHHHHH
Confidence            53 47888999999999988 5789999999999999999988765

The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.

>TIGR03464 HpnC squalene synthase HpnC

Probab=99.91  E-value=2.3e-24  Score=189.45  Aligned_cols=121  Identities=17%  Similarity=0.083  Sum_probs=110.8

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH   80 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~   80 (213)
                      +|.|||+|||+||++||++   +||+|||.|++.+||++.+|+..+..++++.+++.+++.+|+.||.+|..++..+|..
T Consensus       143 lG~AlQltniLRDl~eD~~---~gR~YLP~~~l~~~Gv~~edl~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~  219 (266)
T TIGR03464       143 ICTALQLINFWQDVGVDYR---KGRVYLPRDDLARFGVSEEDLAAGRATPALRELMAFEVSRTRALLDRGAPLAARVDGR  219 (266)
T ss_pred             HHHHHHHHHHHHhhHHHHh---cCCccCCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHh
Confidence            6999999999999999999   8999999999999999999999999999999999999999999999999999999876


Q ss_pred             hhhhhhhHHHHHHHHHHHHH-HcCCCCCCCccccCHHHHHHHHHHh
Q 028137           81 AIFRFCAIPQIMAIGTLALC-YNNIEVFRGVVKMRRGLTAKVIDRT  125 (213)
Q Consensus        81 s~f~fcaip~~maiatL~~i-~~n~~Vf~~rVKi~r~~~~~l~~~~  125 (213)
                      +. .++..+..++.++|..+ .++++||++++++++.++.+++.++
T Consensus       220 ~~-~~~~~~~~~y~~iL~~l~~~~~~~~~~r~~~~~~~kl~~~~~a  264 (266)
T TIGR03464       220 LG-LELALIVRGGLRILEKIERQGYDVLRERPKLGKFDWAGLLLRA  264 (266)
T ss_pred             hh-HHHHHHHHHHHHHHHHHHHcCCCCCCCCCcCCHHHHHHHHHHH
Confidence            53 35566677777899888 5799999999999999999998764

This family of genes are members of a superfamily (pfam00494) of phytoene and squalene synthases which catalyze the head-t0-head condensation of polyisoprene pyrophosphates. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnD gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated.

>PLN02632 phytoene synthase

Probab=99.90  E-value=8.9e-24  Score=192.18  Aligned_cols=121  Identities=18%  Similarity=0.146  Sum_probs=110.2

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH   80 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~   80 (213)
                      ||.|||+|||+||++||++   +||+|||.|+|.+||++.+|+..+.+++++.+++.+++.+|+.||.+|..++..+|..
T Consensus       203 lG~AlQltNILRDv~eD~~---~GRvYLP~e~L~~~Gv~~edl~~~~~~~~~~~l~~~~~~~Ar~~~~~a~~~l~~lp~~  279 (334)
T PLN02632        203 LGIANQLTNILRDVGEDAR---RGRVYLPQDELAQFGLTDEDIFAGKVTDKWRAFMKFQIKRARMYFAEAEEGVSELDPA  279 (334)
T ss_pred             HHHHHHHHHHHHHHHHHHh---CCceeCCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHhHhhCCHH
Confidence            6999999999999999998   8999999999999999999999999999999999999999999999999999999987


Q ss_pred             hhhhhhhHHHHHHHHHHHHH-HcCCCCCCCccccCHHHHHHHHHHh
Q 028137           81 AIFRFCAIPQIMAIGTLALC-YNNIEVFRGVVKMRRGLTAKVIDRT  125 (213)
Q Consensus        81 s~f~fcaip~~maiatL~~i-~~n~~Vf~~rVKi~r~~~~~l~~~~  125 (213)
                      +. ..+.++..++-++|..+ .+|++||++|+.+++.++++++.++
T Consensus       280 ~r-~~v~~a~~~y~~iL~~i~~~~~~v~~~R~~l~~~~Kl~~~~~~  324 (334)
T PLN02632        280 SR-WPVWASLLLYRQILDAIEANDYDNFTKRAYVGKWKKLLALPLA  324 (334)
T ss_pred             hH-HHHHHHHHHHHHHHHHHHHcCCCcCCCCCccCHHHHHHHHHHH
Confidence            63 24456666666789888 6799999999999999999988655

>PF00494 SQS_PSY: Squalene/phytoene synthase; InterPro: IPR002060 Squalene synthase 2

Probab=99.90  E-value=8.6e-24  Score=183.64  Aligned_cols=114  Identities=25%  Similarity=0.296  Sum_probs=93.5

Q ss_pred             CcchHHHHHhhhchHhh-hhcCCCCcccccHHHHHhhcCChhhhcccc-ccHHHHHHHHHHHHHHHHHHHHHHHhHHccc
Q 028137            1 MGLFLQKTNIIRDYLED-INEIPKCRMFWPREIWSKYVNKLEDLKYEE-NSDKAVQCLNDMVTNALMHVEDCLKYMSALR   78 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED-~~e~p~GRiY~P~eil~k~g~~~~dl~~~~-~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~   78 (213)
                      +|.|||+||||||++|| +.   +||+|||.|+|.+||++++|+..+. .++++..++.+++.+|+.|+.+|..++..++
T Consensus       150 lG~alql~nilRd~~~D~~~---~gR~ylP~d~l~~~gv~~~dl~~~~~~~~~~~~~~~~~~~~A~~~l~~a~~~~~~l~  226 (267)
T PF00494_consen  150 LGRALQLTNILRDIPEDALR---RGRIYLPLDDLRRFGVTPEDLLAGRPRSERLRALIRELAARARAHLDEARAGLSALP  226 (267)
T ss_dssp             HHHHHHHHHHHHTHHHH-HH---TT---S-HHHHHHTTSSHHHHHHHG-GGHHHHHHHHHHHHHHHHHHHHHHHGGGGS-
T ss_pred             HHHHHHHHHHHHHhHHHHHh---cccccCCchhHHHcCCCHHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            59999999999999999 78   7999999999999999999998876 7777999999999999999999999999996


Q ss_pred             hhhhhhhhhHHHHHHHHHHHHH-HcCCC-CCCCccccCHHH
Q 028137           79 DHAIFRFCAIPQIMAIGTLALC-YNNIE-VFRGVVKMRRGL  117 (213)
Q Consensus        79 ~~s~f~fcaip~~maiatL~~i-~~n~~-Vf~~rVKi~r~~  117 (213)
                      ++..+.+|.+|..++.++|+.+ .+|++ ||++|++++|++
T Consensus       227 ~~~~~~~~~~~~~~~~~~l~~l~~~~~~~v~~~r~~~~~~r  267 (267)
T PF00494_consen  227 PPRARPAVAAAAALYRAILDKLERNGYDPVFQRRVKVSKWR  267 (267)
T ss_dssp             -TTHHHHHHHHHHHHHHHHHHHHHTTT--GSSS-----HH-
T ss_pred             CHhhhHHHHHHHHHHHHHHHHHHcCCCcccCCCCCcCCCCC
Confidence            6666778999999999999988 56888 899999999974

5.1.21 from EC (farnesyl-diphosphate farnesyltransferase) (SQS) and Phytoene synthase 2.5.1.32 from EC (PSY) share a number of functional similarities. These similarities are also reflected at the level of their primary structure [, , ]. In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. SQS catalyzes the conversion of two molecules of farnesyl diphosphate (FPP) into squalene. It is the first committed step in the cholesterol biosynthetic pathway. The reaction carried out by SQS is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of FPP to form presqualene diphosphate; this intermediate is then rearranged in a NADP-dependent reduction, to form squalene: 2 FPP -> presqualene diphosphate + NADP -> squalene SQS is found in eukaryotes. In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS seems to be membrane-bound. PSY catalyzes the conversion of two molecules of geranylgeranyl diphosphate (GGPP) into phytoene. It is the second step in the biosynthesis of carotenoids from isopentenyl diphosphate. The reaction carried out by PSY is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of GGPP to form prephytoene diphosphate; this intermediate is then rearranged to form phytoene. 2 GGPP -> prephytoene diphosphate -> phytoene PSY is found in all organisms that synthesize carotenoids: plants and photosynthetic bacteria as well as some non- photosynthetic bacteria and fungi. In bacteria PSY is encoded by the gene crtB. In plants PSY is localized in the chloroplast.; GO: 0016740 transferase activity, 0009058 biosynthetic process; PDB: 3NRI_A 3NPR_A 2ZCR_A 2ZCP_B 4F6V_A 4EA0_A 3ACW_A 4F6X_A 3VJE_B 3ACX_A ....

>cd00683 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head

Probab=99.90  E-value=9.7e-24  Score=184.35  Aligned_cols=112  Identities=31%  Similarity=0.421  Sum_probs=103.4

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH   80 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~   80 (213)
                      +|.|||+||||||++||++   +||+|||.|+|.+||++.+|+..+..++++.+++.+++..|+.||..|..++..+|..
T Consensus       151 lG~AlqltnilRdv~eD~~---~gR~YlP~d~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~  227 (265)
T cd00683         151 LGLALQLTNILRDVGEDAR---RGRIYLPREELARFGVTLEDLLAPENSPAFRALLRRLIARARAHYREALAGLAALPRR  227 (265)
T ss_pred             HHHHHHHHHHHHHHHHHHc---cCCCcCCHHHHHHcCCCHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHh
Confidence            6999999999999999998   8999999999999999999999999999999999999999999999999999999976


Q ss_pred             hhhhhhhHHHHHHHH-HHHHH-HcCCCCCCCccccCHHH
Q 028137           81 AIFRFCAIPQIMAIG-TLALC-YNNIEVFRGVVKMRRGL  117 (213)
Q Consensus        81 s~f~fcaip~~maia-tL~~i-~~n~~Vf~~rVKi~r~~  117 (213)
                      +  ++|++|+++.+. +|..+ .+++++|++++.+++.+
T Consensus       228 ~--~~~~~~~~~~y~~il~~i~~~~~~~~~~r~~~~~~~  264 (265)
T cd00683         228 S--RFCVRAAAMLYRTILDEIEARGYDVLSVRVRVPKAR  264 (265)
T ss_pred             h--HHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Confidence            5  689999999876 56677 57899999999888754

These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes

>cd00385 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1

Probab=98.18  E-value=2e-06  Score=69.98  Aligned_cols=77  Identities=23%  Similarity=0.210  Sum_probs=66.3

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccc
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALR   78 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~   78 (213)
                      +|.++|++|.++|+..|.... .||+++|...+.+++.+.+++......+...++++.+...+..++.+..+....++
T Consensus       152 ~g~~~ql~nDl~~~~~e~~~~-~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~  228 (243)
T cd00385         152 LGLAFQLTNDLLDYEGDAERG-EGKCTLPVLYALEYGVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILSLP  228 (243)
T ss_pred             HHHHHHHHHHHHhccCCHHHh-CCchHHHHHHHHHhCChhhHHHHHHHCChHHHHHHHHHHHHHHHHHHHhcCCCCcH
Confidence            589999999999999999821 18999999999999999988888887888888888888888888888888777664

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. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoter

>cd00867 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases

Probab=98.12  E-value=3.2e-06  Score=71.79  Aligned_cols=53  Identities=19%  Similarity=0.122  Sum_probs=41.2

Q ss_pred             CcchHHHHHhhhchHhhh----------hcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHH
Q 028137            1 MGLFLQKTNIIRDYLEDI----------NEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDC   70 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~----------~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~a   70 (213)
                      +|+|+|++|++||+.+|.          .   .||+|||.+.+                      .+.+...+..++..+
T Consensus       158 lG~a~Qi~dd~~D~~~d~~~~gk~~~D~~---~gr~tlp~~~~----------------------~~~~~~~~~~~~~~~  212 (236)
T cd00867         158 LGLAFQLTDDLLDVFGDAEELGKVGSDLR---EGRITLPVILA----------------------RERAAEYAEEAYAAL  212 (236)
T ss_pred             HHHHHHHHHHhccccCChHHHCccHHHHH---cCCchHHHHHH----------------------HHHHHHHHHHHHHHH
Confidence            699999999999999888          6   69999999977                      445555666666666


Q ss_pred             HHhHHccc
Q 028137           71 LKYMSALR   78 (213)
Q Consensus        71 l~yl~~l~   78 (213)
                      ..+....+
T Consensus       213 ~~~~~~~~  220 (236)
T cd00867         213 EALPPSLP  220 (236)
T ss_pred             HhCCCCch
Confidence            66655543

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. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates

>KOG4411 consensus Phytoene/squalene synthetase [Lipid transport and metabolism]

Probab=97.67  E-value=0.00028  Score=62.57  Aligned_cols=104  Identities=15%  Similarity=0.158  Sum_probs=83.8

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhh-ccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccch
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDL-KYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRD   79 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl-~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~   79 (213)
                      +|.|--+.|.||-..=-..   +|-.|+|.|+++.||++..|+ .+....++...|..+++..|-+|..+|.+....+|.
T Consensus       164 lGkA~gia~llrs~p~~~~---r~~~~iPadv~~lhGvtq~~il~~k~~~~g~~~~~fd~as~an~hL~~AR~l~~kVP~  240 (292)
T KOG4411|consen  164 LGKAYGIANLLRSTPPLLA---RGIVLIPADVMSLHGVTQLDILYKKKKLDGMVGMTFDLASEANRHLIDARSLIEKVPK  240 (292)
T ss_pred             HhHHHHHHHHHHhccHHHh---CCCccccHHHHHHcCCCHHHHHhhccchhhhhhHHHHHHHHHHHHHHHHHhHhhhCCH
Confidence            5888889999999999888   899999999999999999665 456667889999999999999999999999999988


Q ss_pred             hhhhhhhhHHHHHHHHHHHHH-HcCCCCCCC
Q 028137           80 HAIFRFCAIPQIMAIGTLALC-YNNIEVFRG  109 (213)
Q Consensus        80 ~s~f~fcaip~~maiatL~~i-~~n~~Vf~~  109 (213)
                      +.  +......+---.+|+.+ .+|+++|+.
T Consensus       241 ~v--rp~ll~tv~td~~l~~l~k~nfdi~~p  269 (292)
T KOG4411|consen  241 AV--RPALLATVTTDYILKTLEKNNFDIYSP  269 (292)
T ss_pred             HH--HHHHHHhhhHHHHHHHHHHccccccCH
Confidence            75  22222222223457666 689999985

>KOG1459 consensus Squalene synthetase [Lipid transport and metabolism]

Probab=95.73  E-value=0.011  Score=55.48  Aligned_cols=102  Identities=11%  Similarity=-0.010  Sum_probs=74.1

Q ss_pred             cchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchhh
Q 028137            2 GLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDHA   81 (213)
Q Consensus         2 GlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~s   81 (213)
                      |.+=|.||+++|..||+-   +||+++|+      |.+.+++....+.++....+-....++...++++....-.+.-.+
T Consensus       285 qimai~Tlal~~nn~dvf---rG~Vklrk------Gl~~~~I~~~k~~~~v~~~f~~y~~~i~~k~d~~dpnflklsask  355 (413)
T KOG1459|consen  285 QIMAIATLALCYNNEDVF---RGNVKLRK------GLAVELILASKTMDKVRNIFYMYLRDIRMKFDEADPNFLKLSASK  355 (413)
T ss_pred             HHHHHHHHHHHhcCHhHh---ccceeecC------CchHHHHHhcccHHHHHHHHHHHHHHHHhhCCccCCCchhhhhhh
Confidence            566789999999999999   89999999      888899999999999999999999999888887766644443222


Q ss_pred             hhhhhhHHHHHHH----HHHHHH-HcCCCCCCCccccCHHHH
Q 028137           82 IFRFCAIPQIMAI----GTLALC-YNNIEVFRGVVKMRRGLT  118 (213)
Q Consensus        82 ~f~fcaip~~mai----atL~~i-~~n~~Vf~~rVKi~r~~~  118 (213)
                            +-++++-    .....+ .|.++.|++++.+..-.+
T Consensus       356 ------~~qv~esl~~~~~~~~il~n~~~~f~k~~~v~~V~~  391 (413)
T KOG1459|consen  356 ------TEQVWESLLLYRRPDEILANRYNNFTKRIYVGFVKK  391 (413)
T ss_pred             ------HHHHHHHHHHhhccccccccccccccchhHHHHHHH
Confidence                  1223322    223444 345577877666655443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	213
3lee_A	340	Crystal Structure Of The Human Squalene Synthase Co		3e-44
3vj8_A	343	Crystal Structure Of The Human Squalene Synthase Le		3e-44
1ezf_A	340	Crystal Structure Of Human Squalene Synthase Length		3e-44

>pdb|3LEE|A Chain A, Crystal Structure Of The Human Squalene Synthase Complexed With Bph- 652 Length = 340

Iteration: 1
 Score =  174 bits (441), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 82/164 (50%), Positives = 110/164 (67%), Gaps = 3/164 (1%)
Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLED       R FWP+E+WS+YV KL D    EN D AVQCLN+++
Sbjct: 177 MGLFLQKTNIIRDYLEDQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELI 233
Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL H+ D + Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+G VK+R+G    
Sbjct: 234 TNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVT 293
Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQ 164
           ++    NM  V    Y +   +  +I  +DP+++KT   +  I+
Sbjct: 294 LMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIR 337

>pdb|3VJ8|A Chain A, Crystal Structure Of The Human Squalene Synthase Length = 343

Iteration: 1
 Score =  174 bits (441), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 82/164 (50%), Positives = 110/164 (67%), Gaps = 3/164 (1%)
Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLED       R FWP+E+WS+YV KL D    EN D AVQCLN+++
Sbjct: 180 MGLFLQKTNIIRDYLEDQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELI 236
Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL H+ D + Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+G VK+R+G    
Sbjct: 237 TNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVT 296
Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQ 164
           ++    NM  V    Y +   +  +I  +DP+++KT   +  I+
Sbjct: 297 LMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIR 340

>pdb|1EZF|A Chain A, Crystal Structure Of Human Squalene Synthase Length = 340

Iteration: 1
 Score =  174 bits (441), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 82/164 (50%), Positives = 110/164 (67%), Gaps = 3/164 (1%)
Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLED       R FWP+E+WS+YV KL D    EN D AVQCLN+++
Sbjct: 177 MGLFLQKTNIIRDYLEDQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELI 233
Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL H+ D + Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+G VK+R+G    
Sbjct: 234 TNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVT 293
Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQ 164
           ++    NM  V    Y +   +  +I  +DP+++KT   +  I+
Sbjct: 294 LMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIR 337

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	213
3vj8_A	343	Squalene synthase; farnesyl-diphosphate farnesyltr	1e-68

>3vj8_A Squalene synthase; farnesyl-diphosphate farnesyltransferase, head-TO-head synth cholesterol biosynthesis, oxidoreductase, transferase; 1.52A {Homo sapiens} PDB: 3vj9_A 3vja_A 3vjb_A 3vjc_A* 3asx_A* 3lee_A* 3q2z_A* 3q30_A* 1ezf_A* Length = 343

 Score =  212 bits (542), Expect = 1e-68
 Identities = 82/165 (49%), Positives = 110/165 (66%), Gaps = 3/165 (1%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLED       R FWP+E+WS+YV KL D    EN D AVQCLN+++
Sbjct: 180 MGLFLQKTNIIRDYLEDQQG---GREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELI 236

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL H+ D + Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+G VK+R+G    
Sbjct: 237 TNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVT 296

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQK 165
           ++    NM  V    Y +   +  +I  +DP+++KT   +  I+ 
Sbjct: 297 LMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRT 341

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	213
3vj8_A	343	Squalene synthase; farnesyl-diphosphate farnesyltr	100.0
3acx_A	293	Dehydrosqualene synthase; CRTM, carotenoid biosynt	99.94
4hd1_A	294	Squalene synthase HPNC; MCSG, structural genomics,	99.92

>3vj8_A Squalene synthase; farnesyl-diphosphate farnesyltransferase, head-TO-head synth cholesterol biosynthesis, oxidoreductase, transferase; 1.52A {Homo sapiens} PDB: 3vj9_A 3vja_A 3vjb_A 3vjc_A* 3v66_A* 3lee_A* 3q2z_A* 3q30_A* 3asx_A* 1ezf_A*

Probab=100.00  E-value=3.8e-45  Score=331.46  Aligned_cols=163  Identities=50%  Similarity=0.900  Sum_probs=160.1

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH   80 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~   80 (213)
                      ||.|||+||||||++||++   +||+|||+|+|++||++.+|+..+.+++++.+|+++++.+|+.||.+|+.|++.++++
T Consensus       180 lG~AlQltNilRDv~eD~~---~gR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~l~~l~~~A~~~~~~a~~~~~~L~~~  256 (343)
T 3vj8_A          180 MGLFLQKTNIIRDYLEDQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQ  256 (343)
T ss_dssp             HHHHHHHHHHHHTHHHHHH---TTCCCSCHHHHTTTCSSGGGGGSGGGHHHHHHHHHHHHHHHHTTHHHHHHHHHTCCCH
T ss_pred             HHHHHHHHHHHHHhHHHHh---CCCeeCCHHHHHHcCCCHHHHhcccCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcc
Confidence            6999999999999999999   8999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhHHHHHHHHHHHHHHcCCCCCCCccccCHHHHHHHHHHhCChHHHHHHHHHHHHhhccccCCCCCCHHHHHHHH
Q 028137           81 AIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRV  160 (213)
Q Consensus        81 s~f~fcaip~~maiatL~~i~~n~~Vf~~rVKi~r~~~~~l~~~~~~~~~v~~~f~~~~~~i~~k~~~~dp~~~~~~~~~  160 (213)
                      ++++||++|++||++||+.|++|++||+++|||+|+++++++++++|+++|+.+|++|+++|++|++|+||||.+|.++|
T Consensus       257 ~~~~~~~ip~~lA~~tL~~i~~~~~v~~~rvkisr~~~~~l~~ra~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  336 (343)
T 3vj8_A          257 SVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQII  336 (343)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCGGGGTSCCCCCHHHHHHHHHHCSSHHHHHHHHHHHHHHHHTTCCTTCTTHHHHHHHH
T ss_pred             chhhHHHHHHHHHHHHHHHHHhCCccccCCCcccHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhCCCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHH
Q 028137          161 EAIQKA  166 (213)
Q Consensus       161 ~~i~~~  166 (213)
                      ++|++.
T Consensus       337 ~~~~~~  342 (343)
T 3vj8_A          337 STIRTQ  342 (343)
T ss_dssp             HHHHHC
T ss_pred             HHHHhc
Confidence            999873

>3acx_A Dehydrosqualene synthase; CRTM, carotenoid biosynthesis, staphyloxanthin biosynthesis, transferase, head-TO-head condensation, inhibitor; HET: 673; 1.31A {Staphylococcus aureus} PDB: 2zcp_A* 2zcq_A* 2zcr_A* 2zcs_A* 2zy1_A* 3acw_A* 2zco_A* 3acy_A* 3npr_A* 3nri_A* 3tfn_A* 3tfp_A* 3tfv_A* 3adz_A* 3lgz_B* 3vjd_A* 3vje_A* 3ae0_A* 4ea2_A* 4e9u_A* ...

Probab=99.94  E-value=2.9e-27  Score=208.68  Aligned_cols=120  Identities=17%  Similarity=0.212  Sum_probs=113.1

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH   80 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~   80 (213)
                      ||.|||+||||||++||++   +||+|||.|+|.+||++.+|+..+.+++++.+++++++.+|+.||.+|..+++.+|.+
T Consensus       166 lG~AlQltNilRDv~eD~~---~gR~YLP~d~l~~~gv~~e~l~~~~~~~~~~~~~~~l~~~A~~~~~~a~~~~~~lp~~  242 (293)
T 3acx_A          166 LGESLQLINILRDVGEDFE---NERIYFSKQRLKQYEVDIAEVYQNGVNNHYIDLWEYYAAIAEKDFRDVMDQIKVFSIE  242 (293)
T ss_dssp             HHHHHHHHHHHHCHHHHHH---TTCCCSCHHHHHHHTCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHTGGGSCTT
T ss_pred             HHHHHHHHHHHHHHHHHHh---CCcEEeCHHHHHHcCCCHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHhHHhCCHH
Confidence            6999999999999999999   8999999999999999999999999999999999999999999999999999999988


Q ss_pred             hhhhhhhHHHHHHHHHHHHHH-cCCCCCCCccccCHHHHHHHHHHh
Q 028137           81 AIFRFCAIPQIMAIGTLALCY-NNIEVFRGVVKMRRGLTAKVIDRT  125 (213)
Q Consensus        81 s~f~fcaip~~maiatL~~i~-~n~~Vf~~rVKi~r~~~~~l~~~~  125 (213)
                      +. .+|.++..++.++|+.+. +|++ |++++++++.++++++.++
T Consensus       243 ~r-~~~~~~~~~~~~iL~~i~~~~~~-~~~r~~v~~~~k~~~~~~a  286 (293)
T 3acx_A          243 AQ-PIIELAARIYIEILDEVRQANYT-LHERVFVEKRKKAKLFHEI  286 (293)
T ss_dssp             HH-HHHHHHHHHHHHHHHHHHHTTTC-SSSCCCCCHHHHHHHHHHH
T ss_pred             HH-HHHHHHHHHHHHHHHHHHhCCCC-CCCCceeCHHHHHHHHHHH
Confidence            74 477788999999999985 7899 9999999999999999875

>4hd1_A Squalene synthase HPNC; MCSG, structural genomics, PSI-biology, midwest center for S genomics, transferase; 2.40A {Alicyclobacillus acidocaldarius subsp}

Probab=99.92  E-value=1.9e-25  Score=197.64  Aligned_cols=121  Identities=16%  Similarity=0.162  Sum_probs=92.8

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH   80 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~   80 (213)
                      ||.|||+|||+||++||++   +||+|||.|+|.+||++++|+..+..++++.+++.+++.+|+.||++|..++..+|..
T Consensus       161 lG~AlQltNilRDv~eD~~---~gR~YlP~~~l~~~gv~~~dl~~~~~~~~~~~~~~~~~~~A~~~~~~a~~~~~~lp~~  237 (294)
T 4hd1_A          161 TCTALQVANHMQDIDRDLA---LGRIYVPRADLEQFGATLDDIRARRATDGVRRCIALEVDRAQALFDEGRRLESLVPPR  237 (294)
T ss_dssp             HHHHHHHHHHHHTHHHHHH---TTCBCSCHHHHHTTTCCHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHGGGGGSSCHH
T ss_pred             HHHHHHHHHHHHhchhhhc---cCceeCCHHHHHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHH
Confidence            5999999999999999999   8999999999999999999999999999999999999999999999999999999987


Q ss_pred             hhhhhhhHHHHHHHHHHHHHH-cCCCCCCCccccCHHHHHHHHHHh
Q 028137           81 AIFRFCAIPQIMAIGTLALCY-NNIEVFRGVVKMRRGLTAKVIDRT  125 (213)
Q Consensus        81 s~f~fcaip~~maiatL~~i~-~n~~Vf~~rVKi~r~~~~~l~~~~  125 (213)
                      +.+ .+.++..++.++|..+. +|+++|++|+++++.++++++.++
T Consensus       238 ~r~-~~~~~~~~y~~il~~i~~~~~~~~~~R~~vs~~~Kl~l~~~a  282 (294)
T 4hd1_A          238 LAR-QLKLYRLGGEAILAAIRRQGYNPFAGRPVVSGKQKLRIALSV  282 (294)
T ss_dssp             HHH-HHHHHHHHHHHHHHHHHTTTTCCC------------------
T ss_pred             HHH-HHHHHHHHHHHHHHHHHhCCCCCCCCCCccCHHHHHHHHHHH
Confidence            632 34455566667898884 689999999999999999998875

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	213
d1ezfa_	333	a.128.1.2 (A:) Squalene synthase {Human (Homo sapi	2e-52

>d1ezfa_ a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) [TaxId: 9606]} Length = 333

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

 Score =  169 bits (429), Expect = 2e-52
 Identities = 82/165 (49%), Positives = 110/165 (66%), Gaps = 3/165 (1%)

Query: 1   MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMV 60
           MGLFLQKTNIIRDYLED       R FWP+E+WS+YV KL D    EN D AVQCLN+++
Sbjct: 170 MGLFLQKTNIIRDYLEDQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELI 226

Query: 61  TNALMHVEDCLKYMSALRDHAIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAK 120
           TNAL H+ D + Y+S LR+ ++F FCAIPQ+MAI TLA CYNN +VF+G VK+R+G    
Sbjct: 227 TNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVT 286

Query: 121 VIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRVEAIQK 165
           ++    NM  V    Y +   +  +I  +DP+++KT   +  I+ 
Sbjct: 287 LMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQIISTIRT 331

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	213
d1ezfa_	333	Squalene synthase {Human (Homo sapiens) [TaxId: 96	100.0

>d1ezfa_ a.128.1.2 (A:) Squalene synthase {Human (Homo sapiens) [TaxId: 9606]}

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=1.6e-44  Score=323.48  Aligned_cols=161  Identities=51%  Similarity=0.911  Sum_probs=148.7

Q ss_pred             CcchHHHHHhhhchHhhhhcCCCCcccccHHHHHhhcCChhhhccccccHHHHHHHHHHHHHHHHHHHHHHHhHHccchh
Q 028137            1 MGLFLQKTNIIRDYLEDINEIPKCRMFWPREIWSKYVNKLEDLKYEENSDKAVQCLNDMVTNALMHVEDCLKYMSALRDH   80 (213)
Q Consensus         1 lGlaLQlTNILRDv~ED~~e~p~GRiY~P~eil~k~g~~~~dl~~~~~~~~~~~ll~~lv~~A~~h~~~al~yl~~l~~~   80 (213)
                      ||+|||+||||||+.||++   +||+|||+|+|.+||++++|+.++++++++..++++|+.+|+.||++|++|+..+|.+
T Consensus       170 lG~AlQltNIlRDi~eD~~---~gR~YlP~e~l~~~g~~~~dl~~~~~~~~~~~~~~~l~~~A~~~~~~a~~y~~~lp~~  246 (333)
T d1ezfa_         170 MGLFLQKTNIIRDYLEDQQ---GGREFWPQEVWSRYVKKLGDFAKPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQ  246 (333)
T ss_dssp             HHHHHHHHHHHHTHHHHHH---HTCCCSCHHHHTTTCSSGGGGGSGGGHHHHHHHHHHHHHHHHTTHHHHHHHHHTCCCH
T ss_pred             HHHHHHHHHHHHhhHHHHh---CCcEECCHHHHHHcCCCHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCch
Confidence            6999999999999999999   8999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhhHHHHHHHHHHHHHHcCCCCCCCccccCHHHHHHHHHHhCChHHHHHHHHHHHHhhccccCCCCCCHHHHHHHH
Q 028137           81 AIFRFCAIPQIMAIGTLALCYNNIEVFRGVVKMRRGLTAKVIDRTNNMTDVYLAFYDFSNILKPKINKNDPNATKTLSRV  160 (213)
Q Consensus        81 s~f~fcaip~~maiatL~~i~~n~~Vf~~rVKi~r~~~~~l~~~~~~~~~v~~~f~~~~~~i~~k~~~~dp~~~~~~~~~  160 (213)
                      +.|.||++|++|+..||+++++|+++|+++|||||+++++||++++|+.+++.+|++|++.+++|++|+|||+.+|.+.|
T Consensus       247 ~~~~~~~~~~~~a~~tl~~~~~~~~~~~~~vkisr~~~~~l~~~~~~~~~~~~~f~~~~~~~~~k~~~~dp~~~~~~~~~  326 (333)
T d1ezfa_         247 SVFNFCAIPQVMAIATLAACYNNQQVFKGAVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIPDSDPSSSKTRQII  326 (333)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCGGGGTSCCCC----------CTTSHHHHHHHHHHHHHHHHHHCCTTSTTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHcCchhcCCCeEeeHHHHHHHHHHhccHHHHHHHHHHHHHhhcccCCCCCCChHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHH
Q 028137          161 EAIQ  164 (213)
Q Consensus       161 ~~i~  164 (213)
                      ++|+
T Consensus       327 ~~~~  330 (333)
T d1ezfa_         327 STIR  330 (333)
T ss_dssp             HHHH
T ss_pred             HHhh
Confidence            9995