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= 045812
         (105 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>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 = 82.8 bits (203), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 41/104 (39%), Positives = 61/104 (58%), Gaps = 16/104 (15%)

Query: 17  GGLNREAMPRHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFA 76
             +N   +P+H+A+IMDGN RWA+Q+ +P   GH  G++++R++       GVK LT++A
Sbjct: 13  NNINAAQIPKHIAIIMDGNGRWAKQKKMPRIKGHYEGMQTVRKITRYASDLGVKYLTLYA 72

Query: 77  FSYDNWV----EVEFLMK------------LFEKSIKSELEGFI 104
           FS +NW     EV +LMK            L EK++K E  GFI
Sbjct: 73  FSTENWSRPKDEVNYLMKLPGDFLNTFLPELIEKNVKVETIGFI 116


>pdb|4H8E|A Chain A, Structure Of S. Aureus Undecaprenyl Diphosphate Synthase
           In Complex With Fpp And Sulfate
          Length = 256

 Score = 78.6 bits (192), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 40/117 (34%), Positives = 63/117 (53%), Gaps = 19/117 (16%)

Query: 3   LNRNNVILARGGVAGGLNREAMPRHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVE 62
           +N+ N I         L+   +P H+A+IMDGN RWA++R +P   GH  G+++++++  
Sbjct: 6   INKKNTI---NNYNEELDSSNIPEHIAIIMDGNGRWAKKRKMPRIKGHYEGMQTIKKITR 62

Query: 63  LCCRWGVKVLTVFAFSYDNWVEVE----------------FLMKLFEKSIKSELEGF 103
           +    GVK LT++AFS +NW   E                FL +L EK++K E  GF
Sbjct: 63  IASDIGVKYLTLYAFSTENWSRPESEVNYIMNLPVNFLKTFLPELIEKNVKVETIGF 119


>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 = 73.9 bits (180), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 55/83 (66%), Gaps = 4/83 (4%)

Query: 26  RHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFAFSYDNW--- 82
           +H+A+IMDGN RWA+ +    + GH+ GV++L+++   C    ++ LT++AFS +NW   
Sbjct: 17  KHLAIIMDGNGRWAKLKNKARAYGHKKGVKTLKDITIWCANHKLECLTLYAFSTENWKRP 76

Query: 83  -VEVEFLMKLFEKSIKSELEGFI 104
             EV+FLMK+ +K +K E   ++
Sbjct: 77  KSEVDFLMKMLKKYLKDERSTYL 99


>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 = 73.9 bits (180), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 31/82 (37%), Positives = 55/82 (67%), Gaps = 4/82 (4%)

Query: 26  RHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFAFSYDNWV-- 83
           +H+AV+MDGN RWAR +G  +  G+  GV+++++L+E+C    +  L++FAFS +NW   
Sbjct: 8   KHLAVVMDGNRRWARAKGFLAKLGYSQGVKTMQKLMEVCMEENISNLSLFAFSTENWKRP 67

Query: 84  --EVEFLMKLFEKSIKSELEGF 103
             E++F+ +L ++ +   LE F
Sbjct: 68  KDEIDFIFELLDRCLDEALEKF 89


>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 = 73.6 bits (179), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 37/84 (44%), Positives = 55/84 (65%), Gaps = 4/84 (4%)

Query: 26  RHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFAFSYDNW--- 82
           RHVA+IMDGN RWA+++G   + GH+AG +S+R  V      G++ LT++AFS +NW   
Sbjct: 19  RHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRP 78

Query: 83  -VEVEFLMKLFEKSIKSELEGFIR 105
             EV  LM+LF  ++ SE++   R
Sbjct: 79  AQEVSALMELFVWALDSEVKSLHR 102


>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 = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/84 (42%), Positives = 54/84 (64%), Gaps = 4/84 (4%)

Query: 26  RHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFAFSYDNW--- 82
           RHVA+IM GN RWA+++G   + GH+AG +S+R  V      G++ LT++AFS +NW   
Sbjct: 19  RHVAIIMAGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRP 78

Query: 83  -VEVEFLMKLFEKSIKSELEGFIR 105
             EV  LM+LF  ++ SE++   R
Sbjct: 79  AQEVSALMELFVWALDSEVKSLHR 102


>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 = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 35/84 (41%), Positives = 53/84 (63%), Gaps = 4/84 (4%)

Query: 26  RHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLTVFAFSYDNW--- 82
           RHVA+I DGN RWA+++G   + GH+AG +S+R  V      G++ LT++AFS +NW   
Sbjct: 19  RHVAIIXDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRP 78

Query: 83  -VEVEFLMKLFEKSIKSELEGFIR 105
             EV  L +LF  ++ SE++   R
Sbjct: 79  AQEVSALXELFVWALDSEVKSLHR 102


>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 = 61.2 bits (147), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/80 (40%), Positives = 47/80 (58%), Gaps = 4/80 (5%)

Query: 14  GVAGGLNREAMPRHVAVIMDGNVRWARQRGLPSSAGHEAGVRSLRELVELCCRWGVKVLT 73
             A  +  + +P HVA++MDGN RWA QRGL  + GH+ G   + ++       G+K L+
Sbjct: 45  AAAPRIPADRLPNHVAIVMDGNGRWATQRGLARTEGHKMGEAVVIDIACGAIELGIKWLS 104

Query: 74  VFAFSYDNWV----EVEFLM 89
           ++AFS +NW     EV FLM
Sbjct: 105 LYAFSTENWKRSPEEVRFLM 124


>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 = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 35/59 (59%), Gaps = 1/59 (1%)

Query: 24 MPRHVAVIMDGNVRWARQRGLPS-SAGHEAGVRSLRELVELCCRWGVKVLTVFAFSYDN 81
          +PRH+AV+ DGN RWAR  G    S G+  G   + E++  C   G+++ TV+  S +N
Sbjct: 3  LPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTEN 61


>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 = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 35/59 (59%), Gaps = 1/59 (1%)

Query: 24 MPRHVAVIMDGNVRWARQRGLPS-SAGHEAGVRSLRELVELCCRWGVKVLTVFAFSYDN 81
          +PRH+AV+ DGN RWAR  G    S G+  G   + E++  C   G+++ TV+  S +N
Sbjct: 2  LPRHIAVLCDGNRRWARSAGYDDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTEN 60


>pdb|3AXS|A Chain A, Complex Structure Of Trna Methyltransferase Trm1 From
           Aquifex Aeolicus With Sinefungin
 pdb|3AXT|A Chain A, Complex Structure Of Trna Methyltransferase Trm1 From
           Aquifex Aeolicus With S-Adenosyl-L-Methionine
          Length = 392

 Score = 31.2 bits (69), Expect = 0.15,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 38/63 (60%), Gaps = 1/63 (1%)

Query: 42  RGLPSSAGHEAGVRSL-RELVELCCRWGVKVLTVFAFSYDNWVEVEFLMKLFEKSIKSEL 100
           R L +   HE G+R L ++++EL  ++ + ++ +FA+S+ ++ ++ F+ +   + +   +
Sbjct: 179 RPLRNEFKHEVGIRILIKKVIELAAQYDIAMIPIFAYSHLHYFKLFFVKERGVEKVDKLI 238

Query: 101 EGF 103
           E F
Sbjct: 239 EQF 241


>pdb|2HNH|A Chain A, Crystal Structure Of The Catalytic Alpha Subunit Of E.
           Coli Replicative Dna Polymerase Iii
          Length = 910

 Score = 26.2 bits (56), Expect = 4.8,   Method: Composition-based stats.
 Identities = 10/39 (25%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 19  LNREAMPRHVAVIMDGNVRWARQRGLPSSAGHEAGVRSL 57
           +N+   P +  ++M+  ++W++  G+P   G  +G  SL
Sbjct: 332 INQMGFPGYFLIVME-FIQWSKDNGVPVGPGRGSGAGSL 369


>pdb|2Z3W|A Chain A, Prolyl Tripeptidyl Aminopeptidase Mutant E636a
 pdb|2Z3Z|A Chain A, Prolyl Tripeptidyl Aminopeptidase Mutant E636a Complexd
           With An Inhibitor
          Length = 706

 Score = 26.2 bits (56), Expect = 4.9,   Method: Composition-based stats.
 Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 4/29 (13%)

Query: 6   NNVILARGGVAGGLNREAMPRHVAVIMDG 34
           +N+ +ARGG  G    E M R +AV +DG
Sbjct: 141 HNLYIARGGKLG----EGMSRAIAVTIDG 165


>pdb|2DCM|A Chain A, The Crystal Structure Of S603a Mutated Prolyl Tripeptidyl
           Aminopeptidase Complexed With Substrate
          Length = 706

 Score = 26.2 bits (56), Expect = 4.9,   Method: Composition-based stats.
 Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 4/29 (13%)

Query: 6   NNVILARGGVAGGLNREAMPRHVAVIMDG 34
           +N+ +ARGG  G    E M R +AV +DG
Sbjct: 141 HNLYIARGGKLG----EGMSRAIAVTIDG 165


>pdb|2D5L|A Chain A, Crystal Structure Of Prolyl Tripeptidyl Aminopeptidase
           From Porphyromonas Gingivalis
 pdb|2EEP|A Chain A, Prolyl Tripeptidyl Aminopeptidase Complexed With An
           Inhibitor
          Length = 706

 Score = 26.2 bits (56), Expect = 4.9,   Method: Composition-based stats.
 Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 4/29 (13%)

Query: 6   NNVILARGGVAGGLNREAMPRHVAVIMDG 34
           +N+ +ARGG  G    E M R +AV +DG
Sbjct: 141 HNLYIARGGKLG----EGMSRAIAVTIDG 165


>pdb|1VBF|A Chain A, Crystal Structure Of Protein L-Isoaspartate
           O-Methyltransferase Homologue From Sulfolobus Tokodaii
 pdb|1VBF|B Chain B, Crystal Structure Of Protein L-Isoaspartate
           O-Methyltransferase Homologue From Sulfolobus Tokodaii
 pdb|1VBF|C Chain C, Crystal Structure Of Protein L-Isoaspartate
           O-Methyltransferase Homologue From Sulfolobus Tokodaii
 pdb|1VBF|D Chain D, Crystal Structure Of Protein L-Isoaspartate
           O-Methyltransferase Homologue From Sulfolobus Tokodaii
          Length = 231

 Score = 25.4 bits (54), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 9/27 (33%), Positives = 18/27 (66%)

Query: 79  YDNWVEVEFLMKLFEKSIKSELEGFIR 105
           YD++ ++EF +   E+ IKS L+  ++
Sbjct: 203 YDDYDDIEFRVNKLERQIKSILDNLVK 229


  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
   0.324    0.139    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,951,842
Number of Sequences: 62578
Number of extensions: 99399
Number of successful extensions: 278
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 263
Number of HSP's gapped (non-prelim): 17
length of query: 105
length of database: 14,973,337
effective HSP length: 70
effective length of query: 35
effective length of database: 10,592,877
effective search space: 370750695
effective search space used: 370750695
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)