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= 005563
         (691 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 = 75.9 bits (185), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 47/116 (40%), Positives = 73/116 (62%), Gaps = 10/116 (8%)

Query: 141 LFEKMLSASDAGRIGRLVLPKKCAEAYFP-PISQ--PEGLPLKVQDSKGKEWIFQFRFWP 197
           LFEK ++ SD G++ RLV+PK  AE +FP P S    +G+ L  +D  GK W F++ +W 
Sbjct: 13  LFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYW- 71

Query: 198 NNNSRMYVL-EGVTPCIQNMQLQAGDIVTFSRLEPEG-KLVMGFRKASSASASDQD 251
            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: 368 DNVGEKIQWVQCEDCSKWRKVPANA----RLPSKWTCSGNLWDPERSVCSVAQELREEQL 423
           D+   +  WV+C+DC KWR++PA+        S+W C  N  D   + CS +QE+  E++
Sbjct: 20  DSYSTESAWVRCDDCFKWRRIPASVVGSIDESSRWICMNNS-DKRFADCSKSQEMSNEEI 78

Query: 424 -EDLIAPNNPASSKKLKAAKQ 443
            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: 609 SPGSD-SGSMIRLLQDATEKYLRQQ---RLSSSGVNTSSVDNEGLQGGVTGEKISNGITL 664
           S G+D +G M RLL        +QQ   R+++SG+ T   +   L G + G +    + L
Sbjct: 20  SFGADPAGGMTRLLYSPEWLETQQQFKKRMAASGLETRFDEVGNLYGRLNGTEYPQEVVL 79

Query: 665 DGSHQDT 671
            GSH DT
Sbjct: 80  SGSHIDT 86


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

 Score = 29.3 bits (64), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 19/31 (61%)

Query: 47  HFGLAVSYASPSETNSQIGVSGSHLRPVVQP 77
           H+G+A  YA  +     IG+S ++ RP+V P
Sbjct: 127 HYGIAGYYALXAAEEGXIGISXTNSRPLVAP 157


  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: 21,037,597
Number of Sequences: 62578
Number of extensions: 885663
Number of successful extensions: 1791
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: 1786
Number of HSP's gapped (non-prelim): 7
length of query: 691
length of database: 14,973,337
effective HSP length: 106
effective length of query: 585
effective length of database: 8,340,069
effective search space: 4878940365
effective search space used: 4878940365
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 55 (25.8 bits)