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= psy13362
         (216 letters)

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

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



>pdb|3CJH|B Chain B, Tim8-Tim13 Complex
 pdb|3CJH|D Chain D, Tim8-Tim13 Complex
 pdb|3CJH|F Chain F, Tim8-Tim13 Complex
 pdb|3CJH|H Chain H, Tim8-Tim13 Complex
 pdb|3CJH|J Chain J, Tim8-Tim13 Complex
 pdb|3CJH|L Chain L, Tim8-Tim13 Complex
          Length = 64

 Score = 48.1 bits (113), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 2/60 (3%)

Query: 151 LEREKAKMTAQM--FEFNDICWDKCMTDKPGQRLDSKTETCIVNCVDRFIDISMFIANRL 208
           LE E +K   QM   +F +IC+ KC+       L S+ E C+ NCV+RF+D ++ I N L
Sbjct: 1   LEGENSKQKVQMSIHQFTNICFKKCVESVNDSNLSSQEEQCLSNCVNRFLDTNIRIVNGL 60



 Score = 38.5 bits (88), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 27/49 (55%), Gaps = 2/49 (4%)

Query: 2  LEREKAKMTAQM--FEFNDICWDKCMTDKPGQRLDSKTETCIVNCVDSF 48
          LE E +K   QM   +F +IC+ KC+       L S+ E C+ NCV+ F
Sbjct: 1  LEGENSKQKVQMSIHQFTNICFKKCVESVNDSNLSSQEEQCLSNCVNRF 49


>pdb|3EH1|A Chain A, Crystal Structure Of The Human Copii-Coat Protein Sec24b
          Length = 751

 Score = 28.5 bits (62), Expect = 2.9,   Method: Composition-based stats.
 Identities = 10/23 (43%), Positives = 15/23 (65%)

Query: 44  CVDSFPVFHHFNKPSQIERLNFD 66
           C+  +P FH+ + PSQ E+L  D
Sbjct: 370 CIYYYPSFHYTHNPSQAEKLQKD 392


>pdb|2EX0|A Chain A, Crystal Structure Of Multifunctional Sialyltransferase
           From Pasteurella Multocida
 pdb|2EX0|B Chain B, Crystal Structure Of Multifunctional Sialyltransferase
           From Pasteurella Multocida
 pdb|2IHJ|A Chain A, Crystal Structure Of Multifunctional Sialyltransferase
           From Pasteurella Multocida With Cmp-3f-Neu5ac Bound
 pdb|2IHK|A Chain A, Crystal Structure Of Multifunctional Sialyltransferase
           From Pasteurella Multocida With
           Cmp-3f(Equatorial)-Neu5ac Bound
 pdb|2IHZ|A Chain A, Crystal Structure Of Multifunctional Sialyltransferase
           From Pasteurella Multocida With Cmp-3f-Neu5ac And
           Alpha-Lactose Bound
 pdb|2IIQ|A Chain A, Crystal Structure Of Pasteurella Multocida
           Sialyltransferase In An Open Conformation With Cmp Bound
 pdb|2IIQ|B Chain B, Crystal Structure Of Pasteurella Multocida
           Sialyltransferase In An Open Conformation With Cmp Bound
          Length = 399

 Score = 27.3 bits (59), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 51  FHHFNKPSQIERLN-FDDGSISTSGLKANSNKDLEDFLMLEREKAKMTAQTGSTCFISPR 109
           F H ++ S I++LN +DDGS+    L+   NKD+   +    ++      TG   F +P 
Sbjct: 101 FKHLDRVS-IQQLNLYDDGSMEYVDLEKEENKDISAEIKQAEKQLSHYLLTGKIKFDNPT 159

Query: 110 V 110
           +
Sbjct: 160 I 160


>pdb|2ILV|A Chain A, Crystal Structure Of Multifunctional Sialyltransferase
           From Pasteurella Multocida With Cmp And Alpha-lactose
           Bound
          Length = 400

 Score = 27.3 bits (59), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 51  FHHFNKPSQIERLN-FDDGSISTSGLKANSNKDLEDFLMLEREKAKMTAQTGSTCFISPR 109
           F H ++ S I++LN +DDGS+    L+   NKD+   +    ++      TG   F +P 
Sbjct: 102 FKHLDRVS-IQQLNLYDDGSMEYVDLEKEENKDISAEIKQAEKQLSHYLLTGKIKFDNPT 160

Query: 110 V 110
           +
Sbjct: 161 I 161


>pdb|2EX1|A Chain A, Crystal Structure Of Mutifunctional Sialyltransferase From
           Pasteurella Multocida With Cmp Bound
          Length = 399

 Score = 26.9 bits (58), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 51  FHHFNKPSQIERLN-FDDGSISTSGLKANSNKDLEDFLMLEREKAKMTAQTGSTCFISPR 109
           F H ++ S I++LN +DDGS+    L+   NKD+   +    ++      TG   F +P 
Sbjct: 101 FAHLDRVS-IQQLNLYDDGSMEYVDLEKEENKDISAEIKQAEKQLSHYLLTGKIKFDNPT 159

Query: 110 V 110
           +
Sbjct: 160 I 160


  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    0.135    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,032,070
Number of Sequences: 62578
Number of extensions: 234704
Number of successful extensions: 358
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 353
Number of HSP's gapped (non-prelim): 14
length of query: 216
length of database: 14,973,337
effective HSP length: 95
effective length of query: 121
effective length of database: 9,028,427
effective search space: 1092439667
effective search space used: 1092439667
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)