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= 003937
         (785 letters)

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

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



>pdb|3UGM|A Chain A, Structure Of Tal Effector Pthxo1 Bound To Its Dna Target
          Length = 1047

 Score = 32.3 bits (72), Expect = 0.96,   Method: Compositional matrix adjust.
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 11/70 (15%)

Query: 486 IVALAQHGLGEEAIQLFERMLEL-----GIKPDHITYVGVLTACTHGG--LVEQGQRYYN 538
           +VA+A HG G++A++  +R+L +     G+ PD +  +    A   GG   +E  QR   
Sbjct: 294 VVAIASHGGGKQALETVQRLLPVLCQAHGLTPDQVVAI----ASHDGGKQALETVQRLLP 349

Query: 539 MMKNVHKIKP 548
           ++   H + P
Sbjct: 350 VLCQAHGLTP 359



 Score = 30.0 bits (66), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 25/106 (23%), Positives = 47/106 (44%), Gaps = 12/106 (11%)

Query: 451 NALITMYSKAGNINAARRVFNLIHWRQETVSWTS-MIVALAQHGLGEEAIQLFERMLEL- 508
           + ++ + S  G   A   V  L+    +    T   +VA+A H  G++A++  +R+L + 
Sbjct: 292 DQVVAIASHGGGKQALETVQRLLPVLCQAHGLTPDQVVAIASHDGGKQALETVQRLLPVL 351

Query: 509 ----GIKPDHITYVGVLTACTHGG--LVEQGQRYYNMMKNVHKIKP 548
               G+ PD +  +    A   GG   +E  QR   ++   H + P
Sbjct: 352 CQAHGLTPDQVVAI----ASNGGGKQALETVQRLLPVLCQAHGLTP 393



 Score = 30.0 bits (66), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 12/70 (17%)

Query: 486 IVALAQHGLGEEAIQLFERMLEL-----GIKPDHITYVGVLTACTHGG--LVEQGQRYYN 538
           +VA+A +G G++A++  +R+L +     G+ PD +  +      ++GG   +E  QR   
Sbjct: 362 VVAIASNGGGKQALETVQRLLPVLCQAHGLTPDQVVAIA-----SNGGKQALETVQRLLP 416

Query: 539 MMKNVHKIKP 548
           ++   H + P
Sbjct: 417 VLCQAHGLTP 426



 Score = 29.6 bits (65), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 11/72 (15%)

Query: 484 SMIVALAQHGLGEEAIQLFERMLEL-----GIKPDHITYVGVLTACTHGG--LVEQGQRY 536
           + +VA+A H  G++A++  +R+L +     G+ PD +  +    A   GG   +E  QR 
Sbjct: 224 AQVVAIASHDGGKQALETMQRLLPVLCQAHGLPPDQVVAI----ASNIGGKQALETVQRL 279

Query: 537 YNMMKNVHKIKP 548
             ++   H + P
Sbjct: 280 LPVLCQAHGLTP 291


>pdb|1W3B|A Chain A, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
           Reveals Structural Similarities To Importin Alpha.
 pdb|1W3B|B Chain B, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
           Reveals Structural Similarities To Importin Alpha
          Length = 388

 Score = 32.3 bits (72), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 37/171 (21%), Positives = 69/171 (40%), Gaps = 16/171 (9%)

Query: 351 TLLDGYIKIGDIGPARRIFD----------SLRDRDVVAWTAMLVGYEQNGLNKDAVELF 400
             LD YI +G++    RIFD          SL     V    +   Y + GL   A++ +
Sbjct: 201 NFLDAYINLGNVLKEARIFDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTY 260

Query: 401 RSMVREGPK-PNNYTXXXXXXXXXXXXXXDHGKQIHASALRSGEASSLSVSNALITMYSK 459
           R  +   P  P+ Y                  +  + +ALR     + S++N L  +  +
Sbjct: 261 RRAIELQPHFPDAYCNLANALKEKGSVA--EAEDCYNTALRLCPTHADSLNN-LANIKRE 317

Query: 460 AGNINAARRVFN--LIHWRQETVSWTSMIVALAQHGLGEEAIQLFERMLEL 508
            GNI  A R++   L  + +   + +++   L Q G  +EA+  ++  + +
Sbjct: 318 QGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRI 368


>pdb|2WQH|A Chain A, Crystal Structure Of Ctpr3y3
          Length = 125

 Score = 32.0 bits (71), Expect = 1.5,   Method: Composition-based stats.
 Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 10/94 (10%)

Query: 53  SLMNFYAKT----ESISYAKKVFDEMPVKTLCSWNTILSAYAKQGRLDLACEVFN----L 104
           +L N Y K     E+I Y +K  +  P     +W  + +AY KQG  D A E +     L
Sbjct: 14  NLGNAYYKQGDYDEAIEYYQKALELYP-NNAEAWYNLGNAYYKQGDYDEAIEYYQKALEL 72

Query: 105 MPNRDSVSWTTIIVTYNEIGRFKNAIRMFVEMVQ 138
            PN ++ +W  +   Y + G +  AI  + + ++
Sbjct: 73  YPN-NAEAWYNLGNAYYKQGDYDEAIEYYQKALE 105


>pdb|2FO7|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
           (Trigonal Crystal Form)
 pdb|2HYZ|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
           (Orthorombic Crystal Form)
          Length = 136

 Score = 31.2 bits (69), Expect = 2.4,   Method: Composition-based stats.
 Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 10/94 (10%)

Query: 53  SLMNFYAKT----ESISYAKKVFDEMPVKTLCSWNTILSAYAKQGRLDLACEVFN----L 104
           +L N Y K     E+I Y +K   E+  ++  +W  + +AY KQG  D A E +     L
Sbjct: 6   NLGNAYYKQGDYDEAIEYYQKAL-ELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALEL 64

Query: 105 MPNRDSVSWTTIIVTYNEIGRFKNAIRMFVEMVQ 138
            P R + +W  +   Y + G +  AI  + + ++
Sbjct: 65  DP-RSAEAWYNLGNAYYKQGDYDEAIEYYQKALE 97


>pdb|3GWQ|A Chain A, Crystal Structure Of A Putative D-serine Deaminase
           (bxe_a4060) From Burkholderia Xenovorans Lb400 At 2.00 A
           Resolution
 pdb|3GWQ|B Chain B, Crystal Structure Of A Putative D-serine Deaminase
           (bxe_a4060) From Burkholderia Xenovorans Lb400 At 2.00 A
           Resolution
          Length = 426

 Score = 30.8 bits (68), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 466 ARRVFNLIHWRQETVSWTSMIVALAQHGLGEEAIQLFERMLELGIKPDHITYVGVLTACT 525
           A RV + + W Q  V+     V LA HG    A QLF R LE G     +     + A  
Sbjct: 53  ADRVEHNLKWXQAFVA--EYGVKLAPHGKTTXAPQLFRRQLETGAWGITLATAHQVRAAY 110

Query: 526 HGGL 529
           HGG+
Sbjct: 111 HGGV 114


>pdb|1NA0|A Chain A, Design Of Stable Alpha-Helical Arrays From An Idealized
           Tpr Motif
 pdb|1NA0|B Chain B, Design Of Stable Alpha-Helical Arrays From An Idealized
           Tpr Motif
          Length = 125

 Score = 30.0 bits (66), Expect = 5.0,   Method: Composition-based stats.
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 62  ESISYAKKVFDEMPVKTLCSWNTILSAYAKQGRLDLACEVFN----LMPNRDSVSWTTII 117
           E+I Y +K   E+      +W  + +AY KQG  D A E +     L PN ++ +W  + 
Sbjct: 27  EAIEYYQKAL-ELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPN-NAEAWYNLG 84

Query: 118 VTYNEIGRFKNAIRMFVEMVQ 138
             Y + G +  AI  + + ++
Sbjct: 85  NAYYKQGDYDEAIEYYQKALE 105


  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
   0.321    0.134    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,459,698
Number of Sequences: 62578
Number of extensions: 887560
Number of successful extensions: 2257
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2169
Number of HSP's gapped (non-prelim): 101
length of query: 785
length of database: 14,973,337
effective HSP length: 107
effective length of query: 678
effective length of database: 8,277,491
effective search space: 5612138898
effective search space used: 5612138898
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)