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= 032425
         (141 letters)

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

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



>pdb|2ACI|A Chain A, Structure Of D166a Arginine Deiminase
 pdb|2ACI|B Chain B, Structure Of D166a Arginine Deiminase
 pdb|2ACI|C Chain C, Structure Of D166a Arginine Deiminase
 pdb|2ACI|D Chain D, Structure Of D166a Arginine Deiminase
          Length = 418

 Score = 29.3 bits (64), Expect = 0.76,   Method: Compositional matrix adjust.
 Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 3/89 (3%)

Query: 46  AGACGGKVTCFERDWLRT-DLNVIGFGLIGWLAPSSIPAINGKSLTGLFFESIGTELAHF 104
           A + G  +T   R WL + +   +   LIG +A   +PA  G ++  ++ E +G   + F
Sbjct: 96  ADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGH--SSF 153

Query: 105 PTPPPLTSQFWSVVVGYMALRVVPVPHFW 133
             PP   +QF      ++   V   P +W
Sbjct: 154 LLPPLPNTQFTRATTCWIYGGVTLNPMYW 182


>pdb|2AAF|A Chain A, Structure Of H278a Arginine Deiminase With L-Arginine
           Forming A S- Alkylthiouronium Reaction Intermediate
 pdb|2AAF|B Chain B, Structure Of H278a Arginine Deiminase With L-Arginine
           Forming A S- Alkylthiouronium Reaction Intermediate
 pdb|2AAF|C Chain C, Structure Of H278a Arginine Deiminase With L-Arginine
           Forming A S- Alkylthiouronium Reaction Intermediate
 pdb|2AAF|D Chain D, Structure Of H278a Arginine Deiminase With L-Arginine
           Forming A S- Alkylthiouronium Reaction Intermediate
          Length = 418

 Score = 28.5 bits (62), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 3/89 (3%)

Query: 46  AGACGGKVTCFERDWLRT-DLNVIGFGLIGWLAPSSIPAINGKSLTGLFFESIGTELAHF 104
           A + G  +T   R WL + +   +   LIG +A   +PA  G ++  ++ E +G   + F
Sbjct: 96  ADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGH--SSF 153

Query: 105 PTPPPLTSQFWSVVVGYMALRVVPVPHFW 133
             PP   +QF      ++   V   P +W
Sbjct: 154 LLPPLPNTQFTRDTTCWIYGGVTLNPMYW 182


>pdb|2A9G|A Chain A, Structure Of C406a Arginine Deiminase In Complex With
           L-Arginine
 pdb|2A9G|B Chain B, Structure Of C406a Arginine Deiminase In Complex With
           L-Arginine
 pdb|2A9G|C Chain C, Structure Of C406a Arginine Deiminase In Complex With
           L-Arginine
 pdb|2A9G|D Chain D, Structure Of C406a Arginine Deiminase In Complex With
           L-Arginine
          Length = 418

 Score = 28.5 bits (62), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 3/89 (3%)

Query: 46  AGACGGKVTCFERDWLRT-DLNVIGFGLIGWLAPSSIPAINGKSLTGLFFESIGTELAHF 104
           A + G  +T   R WL + +   +   LIG +A   +PA  G ++  ++ E +G   + F
Sbjct: 96  ADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGH--SSF 153

Query: 105 PTPPPLTSQFWSVVVGYMALRVVPVPHFW 133
             PP   +QF      ++   V   P +W
Sbjct: 154 LLPPLPNTQFTRDTTCWIYGGVTLNPMYW 182


>pdb|2ABR|A Chain A, Structure Of D280a Arginine Deiminase With L-Arginine
           Forming A S-Alkylthiouronium Reaction Intermediate
 pdb|2ABR|B Chain B, Structure Of D280a Arginine Deiminase With L-Arginine
           Forming A S-Alkylthiouronium Reaction Intermediate
 pdb|2ABR|C Chain C, Structure Of D280a Arginine Deiminase With L-Arginine
           Forming A S-Alkylthiouronium Reaction Intermediate
 pdb|2ABR|D Chain D, Structure Of D280a Arginine Deiminase With L-Arginine
           Forming A S-Alkylthiouronium Reaction Intermediate
          Length = 418

 Score = 28.5 bits (62), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 3/89 (3%)

Query: 46  AGACGGKVTCFERDWLRT-DLNVIGFGLIGWLAPSSIPAINGKSLTGLFFESIGTELAHF 104
           A + G  +T   R WL + +   +   LIG +A   +PA  G ++  ++ E +G   + F
Sbjct: 96  ADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGH--SSF 153

Query: 105 PTPPPLTSQFWSVVVGYMALRVVPVPHFW 133
             PP   +QF      ++   V   P +W
Sbjct: 154 LLPPLPNTQFTRDTTCWIYGGVTLNPMYW 182


>pdb|4BAC|A Chain A, Prototype Foamy Virus Strand Transfer Complexes On Product
           Dna
 pdb|4BAC|B Chain B, Prototype Foamy Virus Strand Transfer Complexes On Product
           Dna
          Length = 396

 Score = 27.7 bits (60), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 93  FFESIGTELAHFPTPPPLTSQFWSVVVGYMALRVVPVP 130
             + I T L H P+ PP +S+ WS VVG +    V  P
Sbjct: 298 LLQEIRTSLYH-PSTPPASSRSWSPVVGQLVQERVARP 334


>pdb|3L2Q|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Apo Form
 pdb|3L2Q|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Apo Form
 pdb|3L2R|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium
 pdb|3L2R|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium
 pdb|3L2U|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And Gs9137
           (Elvitegravir)
 pdb|3L2U|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And Gs9137
           (Elvitegravir)
 pdb|3L2V|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Manganese And Mk0518
           (Raltegravir)
 pdb|3L2V|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Manganese And Mk0518
           (Raltegravir)
 pdb|3L2W|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Manganese And Gs9137
           (Elvitegravir)
 pdb|3L2W|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Manganese And Gs9137
           (Elvitegravir)
 pdb|3OY9|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Manganese At 2.55 Resolution
 pdb|3OY9|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Manganese At 2.55 Resolution
 pdb|3OYA|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And Raltegravir At
           2.65 Resolution
 pdb|3OYA|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And Raltegravir At
           2.65 Resolution
 pdb|3OS0|A Chain A, Pfv Strand Transfer Complex (Stc) At 2.81 A Resolution
 pdb|3OS0|B Chain B, Pfv Strand Transfer Complex (Stc) At 2.81 A Resolution
 pdb|3OS1|A Chain A, Pfv Target Capture Complex (Tcc) At 2.97 A Resolution
 pdb|3OS1|B Chain B, Pfv Target Capture Complex (Tcc) At 2.97 A Resolution
 pdb|3OS2|A Chain A, Pfv Target Capture Complex (Tcc) At 3.32 A Resolution
 pdb|3OS2|B Chain B, Pfv Target Capture Complex (Tcc) At 3.32 A Resolution
 pdb|3OYB|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti Mk2048
 pdb|3OYB|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti Mk2048
 pdb|3OYC|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti Pica
 pdb|3OYC|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti Pica
 pdb|3OYD|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti Gs9160
 pdb|3OYD|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti Gs9160
 pdb|3OYE|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti
           Compound2
 pdb|3OYE|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti
           Compound2
 pdb|3OYF|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti
           L-870,810
 pdb|3OYF|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti
           L-870,810
 pdb|3OYG|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti
           Compound1 (Compoundg)
 pdb|3OYG|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti
           Compound1 (Compoundg)
 pdb|3OYH|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti Mk0536
 pdb|3OYH|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And The Insti Mk0536
 pdb|3S3M|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And Dolutegravir
           (SGSK1349572)
 pdb|3S3M|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv)
           Intasome In Complex With Magnesium And Dolutegravir
           (SGSK1349572)
 pdb|4E7H|A Chain A, Pfv Intasome Prior To 3'-Processing, Apo Form (Ui-Apo)
 pdb|4E7H|B Chain B, Pfv Intasome Prior To 3'-Processing, Apo Form (Ui-Apo)
 pdb|4E7I|A Chain A, Pfv Intasome Freeze-Trapped Prior To 3'-Processing,
           Mn-Bound Form (Ui- Mn)
 pdb|4E7I|B Chain B, Pfv Intasome Freeze-Trapped Prior To 3'-Processing,
           Mn-Bound Form (Ui- Mn)
 pdb|4E7J|A Chain A, Pfv Integrase Target Capture Complex, Apo Form (Tcc-Apo),
           At 3.15 A Resolution
 pdb|4E7J|B Chain B, Pfv Integrase Target Capture Complex, Apo Form (Tcc-Apo),
           At 3.15 A Resolution
 pdb|4E7K|A Chain A, Pfv Integrase Target Capture Complex (Tcc-Mn),
           Freeze-Trapped Prior To Strand Transfer, At 3.0 A
           Resolution
 pdb|4E7K|B Chain B, Pfv Integrase Target Capture Complex (Tcc-Mn),
           Freeze-Trapped Prior To Strand Transfer, At 3.0 A
           Resolution
 pdb|4E7L|A Chain A, Pfv Integrase Strand Transfer Complex (Stc-Mn) Following
           Reaction In Crystallo, At 3.0 A Resolution.
 pdb|4E7L|B Chain B, Pfv Integrase Strand Transfer Complex (Stc-Mn) Following
           Reaction In Crystallo, At 3.0 A Resolution.
 pdb|4BDY|A Chain A, Pfv Intasome With Inhibitor Xz-89
 pdb|4BDY|B Chain B, Pfv Intasome With Inhibitor Xz-89
 pdb|4BDZ|A Chain A, Pfv Intasome With Inhibitor Xz-90
 pdb|4BDZ|B Chain B, Pfv Intasome With Inhibitor Xz-90
 pdb|4BE0|A Chain A, Pfv Intasome With Inhibitor Xz-115
 pdb|4BE0|B Chain B, Pfv Intasome With Inhibitor Xz-115
 pdb|4BE1|A Chain A, Pfv Intasome With Inhibitor Xz-116
 pdb|4BE1|B Chain B, Pfv Intasome With Inhibitor Xz-116
 pdb|4BE2|A Chain A, Pfv Intasome With Inhibitor Xz-259
 pdb|4BE2|B Chain B, Pfv Intasome With Inhibitor Xz-259
          Length = 395

 Score = 27.7 bits (60), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 93  FFESIGTELAHFPTPPPLTSQFWSVVVGYMALRVVPVP 130
             + I T L H P+ PP +S+ WS VVG +    V  P
Sbjct: 297 LLQEIRTSLYH-PSTPPASSRSWSPVVGQLVQERVARP 333


>pdb|3OYM|A Chain A, Crystal Structure Of The Pfv N224h Mutant Intasome Bound
           To Manganese
 pdb|3OYM|B Chain B, Crystal Structure Of The Pfv N224h Mutant Intasome Bound
           To Manganese
 pdb|3OYN|A Chain A, Crystal Structure Of The Pfv N224h Mutant Intasome Bound
           To Magnesium And The Insti Mk2048
 pdb|3OYN|B Chain B, Crystal Structure Of The Pfv N224h Mutant Intasome Bound
           To Magnesium And The Insti Mk2048
 pdb|3S3O|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv) N224h
           Mutant Intasome In Complex With Magnesium And
           Dolutegravir (SGSK1349572)
 pdb|3S3O|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv) N224h
           Mutant Intasome In Complex With Magnesium And
           Dolutegravir (SGSK1349572)
          Length = 395

 Score = 27.7 bits (60), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 93  FFESIGTELAHFPTPPPLTSQFWSVVVGYMALRVVPVP 130
             + I T L H P+ PP +S+ WS VVG +    V  P
Sbjct: 297 LLQEIRTSLYH-PSTPPASSRSWSPVVGQLVQERVARP 333


>pdb|3OYK|A Chain A, Crystal Structure Of The Pfv S217h Mutant Intasome Bound
           To Manganese
 pdb|3OYK|B Chain B, Crystal Structure Of The Pfv S217h Mutant Intasome Bound
           To Manganese
 pdb|3OYL|A Chain A, Crystal Structure Of The Pfv S217h Mutant Intasome Bound
           To Magnesium And The Insti Mk2048
 pdb|3OYL|B Chain B, Crystal Structure Of The Pfv S217h Mutant Intasome Bound
           To Magnesium And The Insti Mk2048
 pdb|3S3N|A Chain A, Crystal Structure Of The Prototype Foamy Virus (Pfv) S217h
           Mutant Intasome In Complex With Magnesium And
           Dolutegravir (SGSK1349572)
 pdb|3S3N|B Chain B, Crystal Structure Of The Prototype Foamy Virus (Pfv) S217h
           Mutant Intasome In Complex With Magnesium And
           Dolutegravir (SGSK1349572)
          Length = 395

 Score = 27.7 bits (60), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 93  FFESIGTELAHFPTPPPLTSQFWSVVVGYMALRVVPVP 130
             + I T L H P+ PP +S+ WS VVG +    V  P
Sbjct: 297 LLQEIRTSLYH-PSTPPASSRSWSPVVGQLVQERVARP 333


>pdb|3OYI|A Chain A, Crystal Structure Of The Pfv S217q Mutant Intasome In
           Complex With Manganese
 pdb|3OYI|B Chain B, Crystal Structure Of The Pfv S217q Mutant Intasome In
           Complex With Manganese
 pdb|3OYJ|A Chain A, Crystal Structure Of The Pfv S217q Mutant Intasome In
           Complex With Magnesium And The Insti Mk2048
 pdb|3OYJ|B Chain B, Crystal Structure Of The Pfv S217q Mutant Intasome In
           Complex With Magnesium And The Insti Mk2048
          Length = 395

 Score = 27.7 bits (60), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 93  FFESIGTELAHFPTPPPLTSQFWSVVVGYMALRVVPVP 130
             + I T L H P+ PP +S+ WS VVG +    V  P
Sbjct: 297 LLQEIRTSLYH-PSTPPASSRSWSPVVGQLVQERVARP 333


>pdb|1RXX|A Chain A, Structure Of Arginine Deiminase
 pdb|1RXX|B Chain B, Structure Of Arginine Deiminase
 pdb|1RXX|C Chain C, Structure Of Arginine Deiminase
 pdb|1RXX|D Chain D, Structure Of Arginine Deiminase
          Length = 421

 Score = 27.3 bits (59), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 23/90 (25%), Positives = 39/90 (43%), Gaps = 3/90 (3%)

Query: 45  VAGACGGKVTCFERDWLRT-DLNVIGFGLIGWLAPSSIPAINGKSLTGLFFESIGTELAH 103
            A + G  +T   R WL + +   +   LIG +A   +PA  G ++   + E +G   + 
Sbjct: 98  TADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKXYREYLGH--SS 155

Query: 104 FPTPPPLTSQFWSVVVGYMALRVVPVPHFW 133
           F  PP   +QF      ++   V   P +W
Sbjct: 156 FLLPPLPNTQFTRDTTCWIYGGVTLNPXYW 185


  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
   0.323    0.139    0.465 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,927,222
Number of Sequences: 62578
Number of extensions: 151726
Number of successful extensions: 229
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 222
Number of HSP's gapped (non-prelim): 12
length of query: 141
length of database: 14,973,337
effective HSP length: 89
effective length of query: 52
effective length of database: 9,403,895
effective search space: 489002540
effective search space used: 489002540
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 bits)