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= psy5288
         (186 letters)

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

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



>pdb|1QQE|A Chain A, Crystal Structure Of The Vesicular Transport Protein Sec17
          Length = 292

 Score = 92.4 bits (228), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 55/153 (35%), Positives = 88/153 (57%), Gaps = 1/153 (0%)

Query: 35  KTDEAIDLYVRAGNLFKLGKKWNDGGNAFLQAGTLHLKNNNKHDAGLCFVDAANCYKKS- 93
           K +EA DL V+A  +++L K+ N  G++FL+A     K  N+ +AG  +V+A  C+K   
Sbjct: 32  KFEEAADLCVQAATIYRLRKELNLAGDSFLKAADYQKKAGNEDEAGNTYVEAYKCFKSGG 91

Query: 94  NPAEAIKAIERAVEIHTDMGRFIMVAKHHENIAEIYEKELEDQEKAIDHYQHAADCYAGE 153
           N   A+ ++E A++I T  G+F   A     + EI E +L D  KAID Y+ A + YA +
Sbjct: 92  NSVNAVDSLENAIQIFTHRGQFRRGANFKFELGEILENDLHDYAKAIDCYELAGEWYAQD 151

Query: 154 ENKSSANKCLIKIANYSALTDHLDKAIKLYEQL 186
           ++ + +NKC IK A+  AL     +A  +Y +L
Sbjct: 152 QSVALSNKCFIKCADLKALDGQYIEASDIYSKL 184


>pdb|2IFU|A Chain A, Crystal Structure Of A Gamma-Snap From Danio Rerio
 pdb|2IFU|B Chain B, Crystal Structure Of A Gamma-Snap From Danio Rerio
 pdb|2IFU|C Chain C, Crystal Structure Of A Gamma-Snap From Danio Rerio
 pdb|2IFU|D Chain D, Crystal Structure Of A Gamma-Snap From Danio Rerio
          Length = 307

 Score = 34.7 bits (78), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 37/144 (25%), Positives = 56/144 (38%), Gaps = 3/144 (2%)

Query: 37  DEAIDLYVRAGNLFKLGKKWNDGGNAFLQAGTLHLKNNNKHDAGLCFVDAANCYKK-SNP 95
           D A   Y +A   FK  K+     +A+LQ    H  N +   A   F  A    K     
Sbjct: 33  DSAASEYAKAAVAFKNAKQLEQAKDAYLQEAEAHANNRSLFHAAKAFEQAGXXLKDLQRX 92

Query: 96  AEAIKAIERAVEIHTDMGRFIMVAKHHENIAEIYEKELEDQEKAIDHYQHAADCYAGEEN 155
            EA++ IE+A   + + G     A   +   ++ E    D  KA+  YQ AA  +  EE 
Sbjct: 93  PEAVQYIEKASVXYVENGTPDTAAXALDRAGKLXEPL--DLSKAVHLYQQAAAVFENEER 150

Query: 156 KSSANKCLIKIANYSALTDHLDKA 179
              A + + K +         D+A
Sbjct: 151 LRQAAELIGKASRLLVRQQKFDEA 174


>pdb|1WY2|A Chain A, Crystal Structure Of The Prolidase From Pyrococcus
           Horikoshii Ot3
 pdb|1WY2|B Chain B, Crystal Structure Of The Prolidase From Pyrococcus
           Horikoshii Ot3
          Length = 351

 Score = 28.1 bits (61), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 22/33 (66%)

Query: 109 HTDMGRFIMVAKHHENIAEIYEKELEDQEKAID 141
           ++D+ R I+V   +E   EIYE  LE Q+KA++
Sbjct: 221 NSDITRTIVVGSPNEKQKEIYEIVLEAQKKAVE 253


>pdb|3Q15|A Chain A, Crystal Structure Of Raph Complexed With Spo0f
 pdb|3Q15|B Chain B, Crystal Structure Of Raph Complexed With Spo0f
          Length = 378

 Score = 26.6 bits (57), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 5/67 (7%)

Query: 83  FVDAANCYKKSNPAEAIKAIERAVEIHTDM--GRFIMVAKHHENIAEIYEKELEDQEKAI 140
           FV A N     +  +A+  +E A+E+  D+   RFI ++    NIA  Y++  +DQ  A+
Sbjct: 186 FVIAGNYDDFKHYDKALPHLEAALELAMDIQNDRFIAISLL--NIANSYDRSGDDQ-MAV 242

Query: 141 DHYQHAA 147
           +H+Q AA
Sbjct: 243 EHFQKAA 249


  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
   0.314    0.130    0.372 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,000,869
Number of Sequences: 62578
Number of extensions: 186315
Number of successful extensions: 399
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 395
Number of HSP's gapped (non-prelim): 10
length of query: 186
length of database: 14,973,337
effective HSP length: 93
effective length of query: 93
effective length of database: 9,153,583
effective search space: 851283219
effective search space used: 851283219
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: 48 (23.1 bits)