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= 008555
         (561 letters)

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

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



>pdb|1V31|A Chain A, Solution Structure Of The SwibMDM2 DOMAIN OF THE
           Hypothetical Protein At5g14170 From Arabidopsis Thaliana
          Length = 93

 Score =  116 bits (291), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 53/72 (73%), Positives = 61/72 (84%)

Query: 344 PEKSKLSPSLMELLGIEVDTRPRIIAAIWHYVKVKKLQSPNDPSSFMCDPPLQKAFGEEK 403
           PEK KLS +LM++LGIEV+TRPRIIAAIWHYVK +KLQ+PNDPS F CD  LQK FGEEK
Sbjct: 9   PEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQKVFGEEK 68

Query: 404 IKFATISQKISQ 415
           +KF  +SQKIS 
Sbjct: 69  LKFTMVSQKISH 80


>pdb|1UHR|A Chain A, Solution Structure Of The Swib Domain Of Mouse Brg1-
           Associated Factor 60a
          Length = 93

 Score = 68.6 bits (166), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 31/70 (44%), Positives = 44/70 (62%)

Query: 344 PEKSKLSPSLMELLGIEVDTRPRIIAAIWHYVKVKKLQSPNDPSSFMCDPPLQKAFGEEK 403
           P + KL P L  LLGI   TRP II A+W Y+K  KLQ P++    +CD  LQ+ F  ++
Sbjct: 9   PPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVLCDKYLQQIFESQR 68

Query: 404 IKFATISQKI 413
           +KF+ I Q++
Sbjct: 69  MKFSEIPQRL 78


>pdb|3ND2|A Chain A, Structure Of Yeast Importin-Beta (Kap95p)
          Length = 861

 Score = 31.6 bits (70), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 243 TSPEKKTGEAPCWSLKLIGRILEDGQDPVLAGLMQKSDTLYPKFSSFFKKIT-IYLDQSL 301
           T PE  T EA  + +K++  +L D    ++AGL  K + L+P   + F+ I  +  D  L
Sbjct: 734 TKPENGTLEALDYQIKVLEAVL-DAYVGIVAGLHDKPEALFPYVGTIFQFIAQVAEDPQL 792

Query: 302 YPDN 305
           Y ++
Sbjct: 793 YSED 796


>pdb|2BPT|A Chain A, Structure Of The Nup1p:kap95p Complex
 pdb|2BKU|B Chain B, Kap95p:rangtp Complex
 pdb|2BKU|D Chain D, Kap95p:rangtp Complex
 pdb|3EA5|B Chain B, Kap95p Binding Induces The Switch Loops Of Rangdp To Adopt
           The Gtp- Bound Conformation: Implications For Nuclear
           Import Complex Assembly Dynamics
 pdb|3EA5|D Chain D, Kap95p Binding Induces The Switch Loops Of Rangdp To Adopt
           The Gtp- Bound Conformation: Implications For Nuclear
           Import Complex Assembly Dynamics
          Length = 861

 Score = 31.6 bits (70), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 243 TSPEKKTGEAPCWSLKLIGRILEDGQDPVLAGLMQKSDTLYPKFSSFFKKIT-IYLDQSL 301
           T PE  T EA  + +K++  +L D    ++AGL  K + L+P   + F+ I  +  D  L
Sbjct: 734 TKPENGTLEALDYQIKVLEAVL-DAYVGIVAGLHDKPEALFPYVGTIFQFIAQVAEDPQL 792

Query: 302 YPDN 305
           Y ++
Sbjct: 793 YSED 796


>pdb|1PFF|A Chain A, Crystal Structure Of Homocysteine Alpha-, Gamma-Lyase At
           1.8 Angstroms
 pdb|1PFF|B Chain B, Crystal Structure Of Homocysteine Alpha-, Gamma-Lyase At
           1.8 Angstroms
          Length = 331

 Score = 28.9 bits (63), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 32/102 (31%), Positives = 51/102 (50%), Gaps = 10/102 (9%)

Query: 195 TQLLEFEARVDSALARKKIDIQESLKNPPRVQKTLRMYVFNTFANQDETSPEKKTGEAPC 254
           T+++ FE   +  L  K IDI++++K   R QK + + V NTFA+   T+P     +   
Sbjct: 84  TRIVYFETPANPTL--KVIDIEDAVKQA-RKQKDILVIVDNTFASPILTNPLDLGVDIVV 140

Query: 255 WS-LKLIGRILEDGQDPVLAGLM-QKSDTLYPKFSSFFKKIT 294
            S  K I     +G   V+AGL+  ++D +    S   K IT
Sbjct: 141 HSATKYI-----NGHTDVVAGLVCSRADIIAKVKSQGIKDIT 177


  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
   0.316    0.131    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,756,559
Number of Sequences: 62578
Number of extensions: 494966
Number of successful extensions: 963
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 961
Number of HSP's gapped (non-prelim): 12
length of query: 561
length of database: 14,973,337
effective HSP length: 104
effective length of query: 457
effective length of database: 8,465,225
effective search space: 3868607825
effective search space used: 3868607825
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)