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= 005945
         (668 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 = 76.3 bits (186), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 47/116 (40%), Positives = 73/116 (62%), Gaps = 10/116 (8%)

Query: 118 LFEKMLSASDAGRIGRLVLPKKCAEAYFP-PISQ--PEGLPLKVQDSKGKEWIFQFRFWP 174
           LFEK ++ SD G++ RLV+PK  AE +FP P S    +G+ L  +D  GK W F++ +W 
Sbjct: 13  LFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYW- 71

Query: 175 NNNSRMYVL-EGVTPCIQNMQLQAGDIVTFSRLEPEG-KLVMGFRKASSASASDQD 228
            N+S+ YVL +G +  ++   L+AGD+V+FSR   +  +L +G++   S S SD D
Sbjct: 72  -NSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWK---SRSGSDLD 123


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

 Score = 44.7 bits (104), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 6/81 (7%)

Query: 345 DNVGEKIQWVQCEDCSKWRKVPANA----RLPSKWTCSGNLWDPERSVCSVAQELREEQL 400
           D+   +  WV+C+DC KWR++PA+        S+W C  N  D   + CS +QE+  E++
Sbjct: 20  DSYSTESAWVRCDDCFKWRRIPASVVGSIDESSRWICMNNS-DKRFADCSKSQEMSNEEI 78

Query: 401 -EDLIAPNNPASSKKLKAAKQ 420
            E+L    + A +    AAK+
Sbjct: 79  NEELGIGQDEADAYDCDAAKR 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 = 2.2,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 4/67 (5%)

Query: 586 SPGSD-SGSMIRLLQDATEKYLRQQ---RLSSSGVNTSSVDNEGLQGGVTGEKISNGITL 641
           S G+D +G M RLL        +QQ   R+++SG+ T   +   L G + G +    + L
Sbjct: 20  SFGADPAGGMTRLLYSPEWLETQQQFKKRMAASGLETRFDEVGNLYGRLNGTEYPQEVVL 79

Query: 642 DGSHQDT 648
            GSH DT
Sbjct: 80  SGSHIDT 86


>pdb|1V9N|A Chain A, Structure Of Malate Dehydrogenase From Pyrococcus
           Horikoshii Ot3
          Length = 360

 Score = 29.6 bits (65), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 19/31 (61%)

Query: 24  HFGLAVSYASPSETNSQIGVSGSHLRPVVQP 54
           H+G+A  YA  +     IG+S ++ RP+V P
Sbjct: 127 HYGIAGYYALXAAEEGXIGISXTNSRPLVAP 157


>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 = 28.9 bits (63), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 24/103 (23%), Positives = 51/103 (49%), Gaps = 7/103 (6%)

Query: 512 ETSRKKQQQQKLPVPEKSADDDPLSCSKTGNNSPNEKKVVSEGSDDDSSRIKSSTSPFKG 571
           ET+  K ++Q +  P+   DDD  + +  G++ P    +    SDD++ +++++T  F+ 
Sbjct: 6   ETAAAKFERQHMDSPDLGTDDDDKAMADIGSSLP--AMIGGVYSDDNNLQLEATTQ-FRK 62

Query: 572 QIDLNIQPEREEELSPGSDSGSMIRLLQDATEKYLRQQRLSSS 614
            + +   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    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,232,437
Number of Sequences: 62578
Number of extensions: 849329
Number of successful extensions: 1766
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1761
Number of HSP's gapped (non-prelim): 7
length of query: 668
length of database: 14,973,337
effective HSP length: 105
effective length of query: 563
effective length of database: 8,402,647
effective search space: 4730690261
effective search space used: 4730690261
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.8 bits)