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= psy1725
         (837 letters)

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

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



>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Xylose
 pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Glucose
 pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To
           6-Bromo-6-Deoxy-D-Glucose
          Length = 491

 Score = 59.3 bits (142), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 79/185 (42%), Gaps = 35/185 (18%)

Query: 222 LGMMLSSTFWGYVSDRYGRKQALTLCAVLLFYYGI--------LSSLAPSYTWMLFLRGL 273
           +G ++     GY S+R+GR+ +L + AVL F  G+         +S+ P  T  ++L G 
Sbjct: 66  IGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGY 125

Query: 274 V----------GFAIGCVPQSVTLY-AEFLPSKQRAKCVVLLDCFWALGACFEVLLALIV 322
           V          G  +G       +Y AE  P+  R K V     F      F  LL   V
Sbjct: 126 VPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLV----SFNQFAIIFGQLLVYCV 181

Query: 323 ------------MPTLGWKWLLALSTAPLLAFACICPWLPESARYHVASGQPEKALATLR 370
                       + T GW+++ A    P L F  +   +PES R+ ++ G+ E+A   LR
Sbjct: 182 NYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILR 241

Query: 371 EIAAD 375
           +I  +
Sbjct: 242 KIMGN 246



 Score = 36.2 bits (82), Expect = 0.083,   Method: Compositional matrix adjust.
 Identities = 17/53 (32%), Positives = 30/53 (56%)

Query: 538 MPTLGWKWLLALSTAPLLAFACICPWLPESARYHVASGQPEKALATLREIAAD 590
           + T GW+++ A    P L F  +   +PES R+ ++ G+ E+A   LR+I  +
Sbjct: 194 LNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGN 246


>pdb|1WZK|A Chain A, Thermoactinomyces Vulgaris R-47 Alpha-Amylase Ii (Tva Ii)
           Mutatnt D465n
 pdb|1WZK|B Chain B, Thermoactinomyces Vulgaris R-47 Alpha-Amylase Ii (Tva Ii)
           Mutatnt D465n
          Length = 585

 Score = 34.3 bits (77), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 745 TACVSFLFICT--QSRA-YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 790
           T  V ++F+ T  Q  A Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 77  TKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125



 Score = 31.6 bits (70), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 18/31 (58%)

Query: 434 YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 464
           Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 95  YFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125


>pdb|1WZM|A Chain A, Thermoactinomyces Vulgaris R-47 Alpha-amylase Ii (tva Ii)
           Mutatnt R469k
 pdb|1WZM|B Chain B, Thermoactinomyces Vulgaris R-47 Alpha-amylase Ii (tva Ii)
           Mutatnt R469k
          Length = 585

 Score = 34.3 bits (77), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 745 TACVSFLFICT--QSRA-YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 790
           T  V ++F+ T  Q  A Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 77  TKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125



 Score = 31.6 bits (70), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 18/31 (58%)

Query: 434 YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 464
           Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 95  YFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125


>pdb|1VFM|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Alpha- Amylase 2ALPHA-Cyclodextrin Complex
 pdb|1VFM|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Alpha- Amylase 2ALPHA-Cyclodextrin Complex
 pdb|1VFO|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Alpha- Amylase 2BETA-Cyclodextrin Complex
 pdb|1VFO|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Alpha- Amylase 2BETA-Cyclodextrin Complex
 pdb|1VFU|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Amylase 2GAMMA-Cyclodextrin Complex
 pdb|1VFU|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Amylase 2GAMMA-Cyclodextrin Complex
          Length = 585

 Score = 34.3 bits (77), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 745 TACVSFLFICT--QSRA-YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 790
           T  V ++F+ T  Q  A Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 77  TKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125



 Score = 31.6 bits (70), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 18/31 (58%)

Query: 434 YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 464
           Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 95  YFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125


>pdb|1JF6|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Alpha- Amylase Mutant F286y
 pdb|1JF6|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Alpha- Amylase Mutant F286y
          Length = 585

 Score = 34.3 bits (77), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 745 TACVSFLFICT--QSRA-YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 790
           T  V ++F+ T  Q  A Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 77  TKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125



 Score = 31.6 bits (70), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 18/31 (58%)

Query: 434 YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 464
           Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 95  YFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125


>pdb|1JL8|A Chain A, Complex Of Alpha-Amylase Ii (Tva Ii) From
           Thermoactinomyces Vulgaris R-47 With Beta-Cyclodextrin
           Based On A Co- Crystallization With Methyl
           Beta-Cyclodextrin
 pdb|1JL8|B Chain B, Complex Of Alpha-Amylase Ii (Tva Ii) From
           Thermoactinomyces Vulgaris R-47 With Beta-Cyclodextrin
           Based On A Co- Crystallization With Methyl
           Beta-Cyclodextrin
 pdb|1JIB|A Chain A, Complex Of Alpha-Amylase Ii (Tva Ii) From
           Thermoactinomyces Vulgaris R-47 With Maltotetraose Based
           On A Crystal Soaked With Maltohexaose.
 pdb|1JIB|B Chain B, Complex Of Alpha-Amylase Ii (Tva Ii) From
           Thermoactinomyces Vulgaris R-47 With Maltotetraose Based
           On A Crystal Soaked With Maltohexaose.
 pdb|1VB9|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Alpha- Amylase Ii (Tva Ii) Complexed With
           Transglycosylated Product
 pdb|1VB9|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Alpha- Amylase Ii (Tva Ii) Complexed With
           Transglycosylated Product
 pdb|2D2O|A Chain A, Structure Of A Complex Of Thermoactinomyces Vulgaris R-47
           Alpha-Amylase 2 With Maltohexaose Demonstrates The
           Important Role Of Aromatic Residues At The Reducing End
           Of The Substrate Binding Cleft
 pdb|2D2O|B Chain B, Structure Of A Complex Of Thermoactinomyces Vulgaris R-47
           Alpha-Amylase 2 With Maltohexaose Demonstrates The
           Important Role Of Aromatic Residues At The Reducing End
           Of The Substrate Binding Cleft
          Length = 585

 Score = 34.3 bits (77), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 745 TACVSFLFICT--QSRA-YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 790
           T  V ++F+ T  Q  A Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 77  TKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125



 Score = 31.6 bits (70), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 18/31 (58%)

Query: 434 YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 464
           Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 95  YFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125


>pdb|1WZL|A Chain A, Thermoactinomyces Vulgaris R-47 Alpha-Amylase Ii (Tva Ii)
           Mutatnt R469l
 pdb|1WZL|B Chain B, Thermoactinomyces Vulgaris R-47 Alpha-Amylase Ii (Tva Ii)
           Mutatnt R469l
          Length = 585

 Score = 34.3 bits (77), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 745 TACVSFLFICT--QSRA-YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 790
           T  V ++F+ T  Q  A Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 77  TKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125



 Score = 31.6 bits (70), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 18/31 (58%)

Query: 434 YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 464
           Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 95  YFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125


>pdb|1JF5|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Alpha- Amylase 2 Mutant F286a
 pdb|1JF5|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Alpha- Amylase 2 Mutant F286a
          Length = 585

 Score = 34.3 bits (77), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 745 TACVSFLFICT--QSRA-YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 790
           T  V ++F+ T  Q  A Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 77  TKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125



 Score = 31.6 bits (70), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 18/31 (58%)

Query: 434 YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 464
           Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 95  YFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125


>pdb|1BVZ|A Chain A, Alpha-Amylase Ii (Tvaii) From Thermoactinomyces Vulgaris
           R- 47
 pdb|1BVZ|B Chain B, Alpha-Amylase Ii (Tvaii) From Thermoactinomyces Vulgaris
           R- 47
 pdb|1JI2|A Chain A, Improved X-Ray Structure Of Thermoactinomyces Vulgaris
           R-47 Alpha-Amylase 2
 pdb|1JI2|B Chain B, Improved X-Ray Structure Of Thermoactinomyces Vulgaris
           R-47 Alpha-Amylase 2
 pdb|3A6O|A Chain A, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Alpha- Amylase 2ACARBOSE COMPLEX
 pdb|3A6O|B Chain B, Crystal Structure Of Thermoactinomyces Vulgaris R-47
           Alpha- Amylase 2ACARBOSE COMPLEX
          Length = 585

 Score = 34.3 bits (77), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 745 TACVSFLFICT--QSRA-YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 790
           T  V ++F+ T  Q  A Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 77  TKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125



 Score = 31.6 bits (70), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 18/31 (58%)

Query: 434 YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 464
           Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 95  YFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125


>pdb|1G1Y|A Chain A, Crystal Structure Of Alpha-Amylase Ii (Tvaii) From
           Thermoactinomyces Vulgaris R-47 And Beta-Cyclodextrin
           Complex
 pdb|1G1Y|B Chain B, Crystal Structure Of Alpha-Amylase Ii (Tvaii) From
           Thermoactinomyces Vulgaris R-47 And Beta-Cyclodextrin
           Complex
          Length = 585

 Score = 34.3 bits (77), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 745 TACVSFLFICT--QSRA-YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 790
           T  V ++F+ T  Q  A Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 77  TKRVKYVFLLTGPQGEAVYFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125



 Score = 31.6 bits (70), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/31 (48%), Positives = 18/31 (58%)

Query: 434 YLTVTLFVARGIIAGVFQAAYVYTPEVYPTP 464
           Y   T F A    AGVFQ AY++  EV+ TP
Sbjct: 95  YFGETGFSAERSKAGVFQYAYIHRSEVFTTP 125


>pdb|4HOL|A Chain A, Crystal Structure Of Porcine Aminopeptidase-N Complexed
           With Poly- Alanine
          Length = 908

 Score = 34.3 bits (77), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 23/47 (48%)

Query: 94  QWPSRGENMMGQELEMNSVSIVPDGRCPQIEAKAISCPFQWPSSGEN 140
            W  R EN+M Q  E+N++S       PQ E  A +   QW S  EN
Sbjct: 674 NWTERPENLMDQYSEINAISTACSNGLPQCENLAKTLFDQWMSDPEN 720


>pdb|4H5H|A Chain A, Crystal Structure Of Porcine Aminopeptidase-N Complexed
           With Cleaved Poly-Alanine
 pdb|4HOM|A Chain A, Crystal Structure Of Porcine Aminopeptidase-N Complexed
           With Substance P
          Length = 908

 Score = 34.3 bits (77), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 23/47 (48%)

Query: 94  QWPSRGENMMGQELEMNSVSIVPDGRCPQIEAKAISCPFQWPSSGEN 140
            W  R EN+M Q  E+N++S       PQ E  A +   QW S  EN
Sbjct: 674 NWTERPENLMDQYSEINAISTACSNGLPQCENLAKTLFDQWMSDPEN 720


>pdb|4FKE|A Chain A, Crystal Structure Of Porcine Aminopeptidase-N
 pdb|4FKH|A Chain A, Crystal Structure Of Porcine Aminopeptidase-N Complexed
           With Alanine
 pdb|4FKK|A Chain A, Crystal Structure Of Porcine Aminopeptidase-N Complexed
           With Bestatin
          Length = 909

 Score = 34.3 bits (77), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 23/47 (48%)

Query: 94  QWPSRGENMMGQELEMNSVSIVPDGRCPQIEAKAISCPFQWPSSGEN 140
            W  R EN+M Q  E+N++S       PQ E  A +   QW S  EN
Sbjct: 675 NWTERPENLMDQYSEINAISTACSNGLPQCENLAKTLFDQWMSDPEN 721


>pdb|4F5C|A Chain A, Crystal Structure Of The Spike Receptor Binding Domain Of
           A Porcine Respiratory Coronavirus In Complex With The
           Pig Aminopeptidase N Ectodomain
 pdb|4F5C|B Chain B, Crystal Structure Of The Spike Receptor Binding Domain Of
           A Porcine Respiratory Coronavirus In Complex With The
           Pig Aminopeptidase N Ectodomain
          Length = 959

 Score = 33.9 bits (76), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 23/47 (48%)

Query: 94  QWPSRGENMMGQELEMNSVSIVPDGRCPQIEAKAISCPFQWPSSGEN 140
            W  R EN+M Q  E+N++S       PQ E  A +   QW S  EN
Sbjct: 718 NWTERPENLMDQYSEINAISTACSNGLPQCENLAKTLFDQWMSDPEN 764


>pdb|2CRZ|A Chain A, Solution Structure Of The Fifth Fniii Domain Of Human
           Fibronectin Type Iii Domain Containing Protein 3a
          Length = 110

 Score = 29.3 bits (64), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 131 PFQWPSSGENMMGQELEMNSVSIVPDDTFTVS-QAVNAFGFGKFQAKLSLYT 181
           P +     E   G E+E    S++P  T++   +A N  GFG F  K  + T
Sbjct: 50  PIEKDEPREVYQGSEVECTVSSLLPGKTYSFRLRAANKMGFGPFSEKCDITT 101


  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
   0.326    0.136    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,577,463
Number of Sequences: 62578
Number of extensions: 816112
Number of successful extensions: 1879
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1837
Number of HSP's gapped (non-prelim): 45
length of query: 837
length of database: 14,973,337
effective HSP length: 107
effective length of query: 730
effective length of database: 8,277,491
effective search space: 6042568430
effective search space used: 6042568430
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 56 (26.2 bits)