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= 008961
         (547 letters)

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

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



>pdb|1WID|A Chain A, Solution Structure Of The B3 Dna-Binding Domain Of Rav1
          Length = 130

 Score = 68.2 bits (165), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 44/118 (37%), Positives = 71/118 (60%), Gaps = 10/118 (8%)

Query: 2   LSASDAGRIGRLVLPKKCAEAYFP-PISQ--PEGLPLKVQDSKGKEWIFQFRFWPNNNSR 58
           ++ SD G++ RLV+PK  AE +FP P S    +G+ L  +D  GK W F++ +W  N+S+
Sbjct: 18  VTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYW--NSSQ 75

Query: 59  MYVL-EGVTPCIQNMQLQAGDIVTFSRLEPEG-KLVMGFRKASSASASDQDNEANKAG 114
            YVL +G +  ++   L+AGD+V+FSR   +  +L +G++   S S SD D     +G
Sbjct: 76  SYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWK---SRSGSDLDASGPSSG 130


>pdb|2L7P|A Chain A, Ashh2 A Cw Domain
          Length = 100

 Score = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 6/73 (8%)

Query: 232 WVQCEDCSKWRKVPANA----RLPSKWTCSGNLWDPERSVCSVAQELREEQL-EDLIAPN 286
           WV+C+DC KWR++PA+        S+W C  N  D   + CS +QE+  E++ E+L    
Sbjct: 28  WVRCDDCFKWRRIPASVVGSIDESSRWICMNNS-DKRFADCSKSQEMSNEEINEELGIGQ 86

Query: 287 NPASSKKLKAAKQ 299
           + A +    AAK+
Sbjct: 87  DEADAYDCDAAKR 99


>pdb|1Z2L|A Chain A, Crystal Structure Of Allantoate-Amidohydrolase From E.Coli
           K12 In Complex With Substrate Allantoate
 pdb|1Z2L|B Chain B, Crystal Structure Of Allantoate-Amidohydrolase From E.Coli
           K12 In Complex With Substrate Allantoate
          Length = 423

 Score = 31.2 bits (69), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 4/67 (5%)

Query: 465 SPGSD-SGSMIRLLQDATEKYLRQQ---RLSSSGVNTSSVDNEGLQGGVTGEKISNGITL 520
           S G+D +G M RLL        +QQ   R+++SG+ T   +   L G + G +    + L
Sbjct: 20  SFGADPAGGMTRLLYSPEWLETQQQFKKRMAASGLETRFDEVGNLYGRLNGTEYPQEVVL 79

Query: 521 DGSHQDT 527
            GSH DT
Sbjct: 80  SGSHIDT 86


>pdb|2YNS|A Chain A, Rimp_alpha_b54nls
 pdb|2YNS|B Chain B, Rimp_alpha_b54nls
 pdb|4B8O|A Chain A, Rimp_alpha_sv40tagnls
 pdb|4B8P|A Chain A, Rimp_alpha_a89nls
 pdb|4B8P|B Chain B, Rimp_alpha_a89nls
          Length = 490

 Score = 29.3 bits (64), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 24/103 (23%), Positives = 51/103 (49%), Gaps = 7/103 (6%)

Query: 391 ETSRKKQQQQKLPVPEKSADDDPLSCSKTGNNSPNEKKVVSEGSDDDSSRIKSSTSPFKG 450
           ET+  K ++Q +  P+   DDD  + +  G++ P    +    SDD++ +++++T  F+ 
Sbjct: 6   ETAAAKFERQHMDSPDLGTDDDDKAMADIGSSLP--AMIGGVYSDDNNLQLEATTQ-FRK 62

Query: 451 QIDLNIQPEREEELSPGSDSGSMIRLLQDATEKYLRQQRLSSS 493
            + +   P  EE +     SG + R +Q  T +   Q +  ++
Sbjct: 63  LLSIERSPPIEEVIQ----SGVVPRFVQFLTREDFPQLQFEAA 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
   0.310    0.128    0.370 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,426,571
Number of Sequences: 62578
Number of extensions: 671720
Number of successful extensions: 1574
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1570
Number of HSP's gapped (non-prelim): 7
length of query: 547
length of database: 14,973,337
effective HSP length: 104
effective length of query: 443
effective length of database: 8,465,225
effective search space: 3750094675
effective search space used: 3750094675
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (25.4 bits)