BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 039384
(104 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2VFW|A Chain A, Rv1086 Native
pdb|2VFW|B Chain B, Rv1086 Native
pdb|2VG0|A Chain A, Rv1086 Citronelly Pyrophosphate Complex
pdb|2VG0|B Chain B, Rv1086 Citronelly Pyrophosphate Complex
Length = 227
Score = 50.4 bits (119), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 8/74 (10%)
Query: 30 LDGSQAL--KEKIDEDTIKKLVD------VEKHMFMAVAPDPDITIRSSGETRPSNFLLW 81
+D +AL KE + T ++LVD + ++++ + PDPD+ IR+SGE R S FLLW
Sbjct: 136 VDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLW 195
Query: 82 QTSNCSLYSPAALW 95
Q++ ++ A W
Sbjct: 196 QSAYSEMWFTEAHW 209
>pdb|2VG1|A Chain A, Rv1086 E,E-Farnesyl Diphosphate Complex
pdb|2VG1|B Chain B, Rv1086 E,E-Farnesyl Diphosphate Complex
Length = 228
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 8/74 (10%)
Query: 30 LDGSQAL--KEKIDEDTIKKLVD------VEKHMFMAVAPDPDITIRSSGETRPSNFLLW 81
+D +AL KE + T ++LVD + ++++ + PDPD+ IR+SGE R S FLLW
Sbjct: 137 VDAVRALLSKELANGATAEELVDAVTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLW 196
Query: 82 QTSNCSLYSPAALW 95
Q++ ++ A W
Sbjct: 197 QSAYSEMWFTEAHW 210
>pdb|4H8E|A Chain A, Structure Of S. Aureus Undecaprenyl Diphosphate Synthase
In Complex With Fpp And Sulfate
Length = 256
Score = 46.6 bits (109), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 25/45 (55%)
Query: 51 VEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
+ H+ PDP++ IR+SGE R SNFL+WQ S LW
Sbjct: 184 INNHLMTKDYPDPELLIRTSGEQRISNFLIWQVSYSEFIFNQKLW 228
>pdb|1F75|A Chain A, Crystal Structure Of Undecaprenyl Diphosphate Synthase
From Micrococcus Luteus B-P 26
pdb|1F75|B Chain B, Crystal Structure Of Undecaprenyl Diphosphate Synthase
From Micrococcus Luteus B-P 26
Length = 249
Score = 45.4 bits (106), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 26/43 (60%)
Query: 53 KHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
+++F A PDP++ IR+SGE R SNFL+WQ S W
Sbjct: 182 EYLFTANMPDPELLIRTSGEERLSNFLIWQCSYSEFVFIDEFW 224
>pdb|1UEH|A Chain A, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
With Triton X- 100, Magnesium And Sulfate
pdb|1UEH|B Chain B, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
With Triton X- 100, Magnesium And Sulfate
pdb|1V7U|A Chain A, Crystal Structure Of Undecaprenyl Pyrophosphate Synthase
With Farnesyl Pyrophosphate
pdb|1V7U|B Chain B, Crystal Structure Of Undecaprenyl Pyrophosphate Synthase
With Farnesyl Pyrophosphate
pdb|1X06|A Chain A, Crystal Structure Of Undecaprenyl Pyrophosphate Synthase
In Complex With Mg, Ipp And Fspp
pdb|1X07|A Chain A, Crystal Structure Of Undecaprenyl Pyrophosphate Synthase
In Complex With Mg And Ipp
pdb|2E98|A Chain A, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
With Bph-629
pdb|2E98|B Chain B, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
With Bph-629
pdb|2E99|A Chain A, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
With Bph-608
pdb|2E99|B Chain B, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
With Bph-608
pdb|2E9A|A Chain A, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
With Bph-628
pdb|2E9A|B Chain B, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
With Bph-628
pdb|2E9C|A Chain A, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
With Bph-675
pdb|2E9C|B Chain B, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
With Bph-675
pdb|2E9D|A Chain A, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
With Bph-676
pdb|2E9D|B Chain B, E. Coli Undecaprenyl Pyrophosphate Synthase In Complex
With Bph-676
pdb|3QAS|B Chain B, Structure Of Undecaprenyl Diphosphate Synthase
pdb|3QAS|A Chain A, Structure Of Undecaprenyl Diphosphate Synthase
pdb|3TH8|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase
Complexed With Bph-1063
pdb|3TH8|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase
Complexed With Bph-1063
pdb|3SGT|B Chain B, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
Synthase In Complex With Bph-1299
pdb|3SGT|A Chain A, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
Synthase In Complex With Bph-1299
pdb|3SGV|B Chain B, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
Synthase In Complex With Bph-1290
pdb|3SGV|A Chain A, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
Synthase In Complex With Bph-1290
pdb|3SGX|A Chain A, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
Synthase In Complex With Bph-1100
pdb|3SGX|B Chain B, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
Synthase In Complex With Bph-1100
pdb|3SH0|B Chain B, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
Synthase In Complex With Bph-1065
pdb|3SH0|A Chain A, Crystal Structure Of E. Coli Undecaprenyl Pyrophosphate
Synthase In Complex With Bph-1065
pdb|4H2J|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
Complex With Bph-1354
pdb|4H2J|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
Complex With Bph-1354
pdb|4H2M|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
Complex With Bph-1408
pdb|4H2M|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
Complex With Bph-1408
pdb|4H2O|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
Complex With Bph-1248
pdb|4H2O|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
Complex With Bph-1248
pdb|4H38|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
Complex With Bph-1297
pdb|4H38|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
Complex With Bph-1297
pdb|4H3A|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
Complex With Bph-1330
pdb|4H3A|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
Complex With Bph-1330
pdb|4H3C|A Chain A, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
Complex With Bph-987
pdb|4H3C|B Chain B, Structure Of E. Coli Undecaprenyl Diphosphate Synthase In
Complex With Bph-987
Length = 253
Score = 45.1 bits (105), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 28 DKLDGSQALKEKIDEDTIK-KLVDVE---KHMFMAVAPDPDITIRSSGETRPSNFLLWQT 83
D + G + L EK+ + ++ +D E +H+ M D+ IR+ GE R SNFLLWQ
Sbjct: 150 DIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQI 209
Query: 84 SNCSLYSPAALW 95
+ LY LW
Sbjct: 210 AYAELYFTDVLW 221
>pdb|1X08|A Chain A, Crystal Structure Of D26a Mutant Upps In Complex With Mg,
Ipp And Fspp
pdb|1X09|A Chain A, Crystal Structure Of The D26a Mutant Upps In Complex With
Magnesium And Isopentenyl Pyrophosphate
Length = 253
Score = 45.1 bits (105), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 28 DKLDGSQALKEKIDEDTIK-KLVDVE---KHMFMAVAPDPDITIRSSGETRPSNFLLWQT 83
D + G + L EK+ + ++ +D E +H+ M D+ IR+ GE R SNFLLWQ
Sbjct: 150 DIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQI 209
Query: 84 SNCSLYSPAALW 95
+ LY LW
Sbjct: 210 AYAELYFTDVLW 221
>pdb|2D2R|A Chain A, Crystal Structure Of Helicobacter Pylori Undecaprenyl
Pyrophosphate Synthase
pdb|2D2R|B Chain B, Crystal Structure Of Helicobacter Pylori Undecaprenyl
Pyrophosphate Synthase
pdb|2DTN|A Chain A, Crystal Structure Of Helicobacter Pylori Undecaprenyl
Pyrophosphate Synthase Complexed With Pyrophosphate
pdb|2DTN|B Chain B, Crystal Structure Of Helicobacter Pylori Undecaprenyl
Pyrophosphate Synthase Complexed With Pyrophosphate
Length = 245
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 23/35 (65%)
Query: 61 PDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
P+ D+ +R+ GE R SNFLLWQ+S L+ LW
Sbjct: 184 PEVDLLLRTGGEMRLSNFLLWQSSYAELFFTPILW 218
>pdb|1JP3|A Chain A, Structure Of E.Coli Undecaprenyl Pyrophosphate Synthase
pdb|1JP3|B Chain B, Structure Of E.Coli Undecaprenyl Pyrophosphate Synthase
Length = 253
Score = 42.7 bits (99), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 4/72 (5%)
Query: 28 DKLDGSQALKEKIDEDTIK-KLVDVE---KHMFMAVAPDPDITIRSSGETRPSNFLLWQT 83
D + G + L EK+ + ++ +D E +H+ D+ IR+ GE R SNFLLWQ
Sbjct: 150 DIVQGVRQLAEKVQQGNLQPDQIDEEXLNQHVCXHELAPVDLVIRTGGEHRISNFLLWQI 209
Query: 84 SNCSLYSPAALW 95
+ LY LW
Sbjct: 210 AYAELYFTDVLW 221
>pdb|2VG2|A Chain A, Rv2361 With Ipp
pdb|2VG2|B Chain B, Rv2361 With Ipp
pdb|2VG2|C Chain C, Rv2361 With Ipp
pdb|2VG2|D Chain D, Rv2361 With Ipp
pdb|2VG4|A Chain A, Rv2361 Native
pdb|2VG4|B Chain B, Rv2361 Native
pdb|2VG4|C Chain C, Rv2361 Native
pdb|2VG4|D Chain D, Rv2361 Native
pdb|2VG3|A Chain A, Rv2361 With Citronellyl Pyrophosphate
pdb|2VG3|B Chain B, Rv2361 With Citronellyl Pyrophosphate
pdb|2VG3|C Chain C, Rv2361 With Citronellyl Pyrophosphate
pdb|2VG3|D Chain D, Rv2361 With Citronellyl Pyrophosphate
Length = 284
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 38 EKIDEDTIKKLVDVEKHMFMAVAPDPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
E+I E TI + H+ PD D+ +R+SGE R SNF+LWQ + LW
Sbjct: 208 ERITESTIAR------HLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYAEYIFQDKLW 259
>pdb|3UGS|B Chain B, Crystal Structure Of A Probable Undecaprenyl Diphosphate
Synthase (Upps) From Campylobacter Jejuni
pdb|3UGS|A Chain A, Crystal Structure Of A Probable Undecaprenyl Diphosphate
Synthase (Upps) From Campylobacter Jejuni
Length = 225
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 62 DPDITIRSSGETRPSNFLLWQTSNCSLYSPAALW 95
D D+ +R R SNFLLWQ S +Y L+
Sbjct: 168 DVDLMLRVGNAKRLSNFLLWQCSYAEIYFSETLF 201
>pdb|2P02|A Chain A, Crystal Structure Of The Alpha Subunit Of Human S-
Adenosylmethionine Synthetase 2
Length = 396
Score = 28.5 bits (62), Expect = 1.0, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 12/58 (20%)
Query: 1 MHKSDDVQPLKINSLILPVPDVQEYCEDKLDGSQALKEKI----------DEDTIKKL 48
M V P++++++++ V +E C D++ ALKEK+ DEDTI L
Sbjct: 190 MQDRGAVLPIRVHTIVISVQHDEEVCLDEM--RDALKEKVIKAVVPAKYLDEDTIYHL 245
>pdb|1VPB|A Chain A, Crystal Structure Of A Putative Modulator Of Dna Gyrase
(Bt3649) From Bacteroides Thetaiotaomicron Vpi-5482 At
1.75 A Resolution
Length = 451
Score = 26.9 bits (58), Expect = 2.9, Method: Composition-based stats.
Identities = 15/26 (57%), Positives = 16/26 (61%), Gaps = 4/26 (15%)
Query: 64 DITIRSSGETRPSNFLLWQTSNCSLY 89
DITIR GE RPS + W S SLY
Sbjct: 195 DITIRGEGEARPSAY--WYES--SLY 216
>pdb|3P9D|D Chain D, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|3P9D|L Chain L, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|3P9E|DD Chain d, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|3P9E|LL Chain l, The Crystal Structure Of Yeast Cct Reveals Intrinsic
Asymmetry Of Eukaryotic Cytosolic Chaperonins
pdb|4D8Q|D Chain D, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
pdb|4D8Q|L Chain L, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
pdb|4D8R|DD Chain d, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
pdb|4D8R|LL Chain l, Molecular Architecture Of The Eukaryotic Chaperonin
TricCCT DERIVED By A Combination Of Chemical
Crosslinking And Mass-Spectrometry, Xl- Ms
Length = 528
Score = 26.2 bits (56), Expect = 4.5, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 18 PVPDVQEYCEDKLDGSQALKEKIDEDTIK 46
P+ D++ + ED+LD S L E+ID D K
Sbjct: 332 PIADIELFTEDRLD-SADLVEEIDSDGSK 359
>pdb|1KHR|A Chain A, Crystal Structure Of Vat(D) In Complex With Virginiamycin
And Coenzyme A
pdb|1KHR|B Chain B, Crystal Structure Of Vat(D) In Complex With Virginiamycin
And Coenzyme A
pdb|1KHR|C Chain C, Crystal Structure Of Vat(D) In Complex With Virginiamycin
And Coenzyme A
pdb|1KHR|D Chain D, Crystal Structure Of Vat(D) In Complex With Virginiamycin
And Coenzyme A
pdb|1KHR|E Chain E, Crystal Structure Of Vat(D) In Complex With Virginiamycin
And Coenzyme A
pdb|1KHR|F Chain F, Crystal Structure Of Vat(D) In Complex With Virginiamycin
And Coenzyme A
pdb|1KK4|A Chain A, Crystal Structure Of Vat(D) In Complex With Acetyl-Coa
pdb|1KK4|B Chain B, Crystal Structure Of Vat(D) In Complex With Acetyl-Coa
pdb|1KK4|C Chain C, Crystal Structure Of Vat(D) In Complex With Acetyl-Coa
pdb|1KK4|D Chain D, Crystal Structure Of Vat(D) In Complex With Acetyl-Coa
pdb|1KK4|E Chain E, Crystal Structure Of Vat(D) In Complex With Acetyl-Coa
pdb|1KK4|F Chain F, Crystal Structure Of Vat(D) In Complex With Acetyl-Coa
pdb|1KK5|A Chain A, Crystal Structure Of Vat(D) (Form Ii)
pdb|1KK5|B Chain B, Crystal Structure Of Vat(D) (Form Ii)
pdb|1KK5|C Chain C, Crystal Structure Of Vat(D) (Form Ii)
pdb|1KK5|D Chain D, Crystal Structure Of Vat(D) (Form Ii)
pdb|1KK5|E Chain E, Crystal Structure Of Vat(D) (Form Ii)
pdb|1KK5|F Chain F, Crystal Structure Of Vat(D) (Form Ii)
pdb|1KK6|A Chain A, Crystal Structure Of Vat(D) (Form I)
pdb|1KK6|B Chain B, Crystal Structure Of Vat(D) (Form I)
pdb|1KK6|C Chain C, Crystal Structure Of Vat(D) (Form I)
pdb|1MRL|A Chain A, Crystal Structure Of Streptogramin A Acetyltransferase
With Dalfopristin
pdb|1MRL|B Chain B, Crystal Structure Of Streptogramin A Acetyltransferase
With Dalfopristin
pdb|1MRL|C Chain C, Crystal Structure Of Streptogramin A Acetyltransferase
With Dalfopristin
pdb|1MR7|A Chain A, Crystal Structure Of Streptogramin A Acetyltransferase
pdb|1MR7|B Chain B, Crystal Structure Of Streptogramin A Acetyltransferase
pdb|1MR7|C Chain C, Crystal Structure Of Streptogramin A Acetyltransferase
pdb|1MR7|X Chain X, Crystal Structure Of Streptogramin A Acetyltransferase
pdb|1MR7|Y Chain Y, Crystal Structure Of Streptogramin A Acetyltransferase
pdb|1MR7|Z Chain Z, Crystal Structure Of Streptogramin A Acetyltransferase
pdb|3DHO|A Chain A, Structure Of Streptogramin Acetyltransferase In Complex
With An Inhibitor
pdb|3DHO|B Chain B, Structure Of Streptogramin Acetyltransferase In Complex
With An Inhibitor
pdb|3DHO|C Chain C, Structure Of Streptogramin Acetyltransferase In Complex
With An Inhibitor
pdb|3DHO|D Chain D, Structure Of Streptogramin Acetyltransferase In Complex
With An Inhibitor
pdb|3DHO|E Chain E, Structure Of Streptogramin Acetyltransferase In Complex
With An Inhibitor
pdb|3DHO|F Chain F, Structure Of Streptogramin Acetyltransferase In Complex
With An Inhibitor
Length = 209
Score = 25.0 bits (53), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 3 KSDDVQPLKINSLILPVPDVQEYCEDKLDGSQALKEKIDEDTIKKLVDVE 52
K D + NS++ V D+ Y + + +K++ D+DTI +L+D++
Sbjct: 133 KIGDGAIVAANSVV--VKDIAPYMLAGGNPANEIKQRFDQDTINQLLDIK 180
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.315 0.132 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,267,674
Number of Sequences: 62578
Number of extensions: 117586
Number of successful extensions: 374
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 361
Number of HSP's gapped (non-prelim): 17
length of query: 104
length of database: 14,973,337
effective HSP length: 69
effective length of query: 35
effective length of database: 10,655,455
effective search space: 372940925
effective search space used: 372940925
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)