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= psy16493
         (151 letters)

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

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



>pdb|2K27|A Chain A, Solution Structure Of Human Pax8 Paired Box Domain
          Length = 159

 Score = 82.0 bits (201), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 45/80 (56%), Positives = 56/80 (70%), Gaps = 8/80 (10%)

Query: 54  FRHYDIAQHVLHQQQGAVSKLLG------TLRPPGLIGGSKPKVATPAVVSKIEQYKREN 107
            R  DI++  L    G VSK+LG      ++RP G+IGGSKPKVATP VV KI  YKR+N
Sbjct: 42  VRPCDISRQ-LRVSHGCVSKILGRYYETGSIRP-GVIGGSKPKVATPKVVEKIGDYKRQN 99

Query: 108 PTIFAWEIRERLISEDVGVN 127
           PT+FAWEIR+RL++E V  N
Sbjct: 100 PTMFAWEIRDRLLAEGVCDN 119


>pdb|1K78|A Chain A, Pax5(1-149)+ets-1(331-440)+dna
 pdb|1K78|E Chain E, Pax5(1-149)+ets-1(331-440)+dna
 pdb|1K78|I Chain I, Pax5(1-149)+ets-1(331-440)+dna
 pdb|1MDM|A Chain A, Inhibited Fragment Of Ets-1 And Paired Domain Of Pax5
           Bound To Dna
          Length = 149

 Score = 81.6 bits (200), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 44/79 (55%), Positives = 54/79 (68%), Gaps = 6/79 (7%)

Query: 54  FRHYDIAQHVLHQQQGAVSKLLGTLR-----PPGLIGGSKPKVATPAVVSKIEQYKRENP 108
            R  DI++  L    G VSK+LG         PG+IGGSKPKVATP VV KI +YKR+NP
Sbjct: 49  VRPCDISRQ-LRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYKRQNP 107

Query: 109 TIFAWEIRERLISEDVGVN 127
           T+FAWEIR+RL++E V  N
Sbjct: 108 TMFAWEIRDRLLAERVCDN 126


>pdb|6PAX|A Chain A, Crystal Structure Of The Human Pax-6 Paired Domain-Dna
           Complex Reveals A General Model For Pax Protein-Dna
           Interactions
          Length = 133

 Score = 81.6 bits (200), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 45/79 (56%), Positives = 56/79 (70%), Gaps = 8/79 (10%)

Query: 55  RHYDIAQHVLHQQQGAVSKLLG------TLRPPGLIGGSKPKVATPAVVSKIEQYKRENP 108
           R  DI++ +L    G VSK+LG      ++RP   IGGSKP+VATP VVSKI QYK+E P
Sbjct: 35  RPCDISR-ILQVSNGCVSKILGRYYATGSIRPRA-IGGSKPRVATPEVVSKIAQYKQECP 92

Query: 109 TIFAWEIRERLISEDVGVN 127
           +IFAWEIR+RL+SE V  N
Sbjct: 93  SIFAWEIRDRLLSEGVCTN 111


>pdb|1PDN|C Chain C, Crystal Structure Of A Paired Domain-Dna Complex At 2.5
           Angstroms Resolution Reveals Structural Basis For Pax
           Developmental Mutations
          Length = 128

 Score = 71.6 bits (174), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 49/67 (73%), Gaps = 7/67 (10%)

Query: 64  LHQQQGAVSKLL------GTLRPPGLIGGSKPKVATPAVVSKIEQYKRENPTIFAWEIRE 117
           L    G VSK+L      G++RP G+IGGSKP++ATP + ++IE+YKR +P +F+WEIRE
Sbjct: 43  LRVSHGCVSKILNRYQETGSIRP-GVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIRE 101

Query: 118 RLISEDV 124
           +LI E V
Sbjct: 102 KLIREGV 108


>pdb|1ECR|A Chain A, Escherichia Coli Replication Terminator Protein (Tus)
           Complexed With Dna
 pdb|2EWJ|A Chain A, Escherichia Coli Replication Terminator Protein (Tus)
           Complexed With Dna- Locked Form
 pdb|2I05|A Chain A, Escherichia Coli Replication Terminator Protein (Tus)
           Complexed With Tera Dna
 pdb|2I06|A Chain A, Escherichia Coli Replication Terminator Protein (tus)
           Complexed With Dna- Locked Form
          Length = 309

 Score = 26.6 bits (57), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 47  NQQQRLLFRHYDIAQHVLHQQQGAVSKLLGTLRPPGLIGGSKPKVATPAVVSKIEQYKR 105
           N  Q L  RH+   +H+  QQQ         +R PG++      ++  A+VS I+   +
Sbjct: 64  NDAQSLALRHF---RHLFIQQQSENRSSKAAVRLPGVLCYQVDNLSQAALVSHIQHINK 119


>pdb|2UUU|A Chain A, Alkyldihydroxyacetonephosphate Synthase In P212121
 pdb|2UUU|B Chain B, Alkyldihydroxyacetonephosphate Synthase In P212121
 pdb|2UUU|C Chain C, Alkyldihydroxyacetonephosphate Synthase In P212121
 pdb|2UUU|D Chain D, Alkyldihydroxyacetonephosphate Synthase In P212121
 pdb|2UUV|A Chain A, Alkyldihydroxyacetonephosphate Synthase In P1
 pdb|2UUV|B Chain B, Alkyldihydroxyacetonephosphate Synthase In P1
 pdb|2UUV|C Chain C, Alkyldihydroxyacetonephosphate Synthase In P1
 pdb|2UUV|D Chain D, Alkyldihydroxyacetonephosphate Synthase In P1
          Length = 584

 Score = 26.2 bits (56), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 12/38 (31%), Positives = 19/38 (50%)

Query: 56 HYDIAQHVLHQQQGAVSKLLGTLRPPGLIGGSKPKVAT 93
          H D+ Q +     G   K L  L+P G I  + P+V++
Sbjct: 9  HIDLYQQIKWNGWGDTRKFLHQLKPSGTIAMTTPEVSS 46


  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    0.139    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,100,032
Number of Sequences: 62578
Number of extensions: 136934
Number of successful extensions: 314
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 309
Number of HSP's gapped (non-prelim): 8
length of query: 151
length of database: 14,973,337
effective HSP length: 90
effective length of query: 61
effective length of database: 9,341,317
effective search space: 569820337
effective search space used: 569820337
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)