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= 022765
         (292 letters)

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

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



>pdb|2PZK|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
           Wbmg In Complex With Nad
 pdb|2PZK|B Chain B, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
           Wbmg In Complex With Nad
 pdb|2PZL|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
           Wbmg In Complex With Nad And Udp
 pdb|2PZL|B Chain B, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
           Wbmg In Complex With Nad And Udp
 pdb|2PZM|A Chain A, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
           Wbmg In Complex With Nad And Udp
 pdb|2PZM|B Chain B, Crystal Structure Of The Bordetella Bronchiseptica Enzyme
           Wbmg In Complex With Nad And Udp
          Length = 330

 Score = 34.3 bits (77), Expect = 0.076,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 5/58 (8%)

Query: 133 DTFRLSKCVQIARLYLEDDD-----AVNAEAFINKASFLVSSSQQEVLNLQYKVCYAR 185
           D+F+ +  V  A  Y + DD     A N +  IN A     +  + +LN Q  +CY R
Sbjct: 85  DSFKPTHVVHSAAAYKDPDDWAEDAATNVQGSINVAKAASKAGVKRLLNFQTALCYGR 142


>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
           Factor  3b
          Length = 96

 Score = 28.1 bits (61), Expect = 5.2,   Method: Composition-based stats.
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 119 LSGIDLDSGMRVIDDTFRLSKCVQIARLYLEDDDAVNAE--AFINKASFLVSSSQQEVLN 176
           +  +D +   +++ DTF     +      + D D  N++  AFIN ASF  S +  E +N
Sbjct: 10  IGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMN 69

Query: 177 LQY 179
            QY
Sbjct: 70  GQY 72


>pdb|3U44|A Chain A, Crystal Structure Of Addab-Dna Complex
 pdb|3U4Q|A Chain A, Structure Of Addab-Dna Complex At 2.8 Angstroms
          Length = 1232

 Score = 27.7 bits (60), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 85/194 (43%), Gaps = 24/194 (12%)

Query: 24  ILSSVISSNDIVQAKKFIDHMLSDDVPLVVSRQLLQTF-----AQELGRLEPETQKEIAN 78
           + ++  S    V  ++ I  + +++ P+ V R L+ TF     A+   R+    +KE+  
Sbjct: 28  VAAAAGSGKTAVLVERMIRKITAEENPIDVDRLLVVTFTNASAAEMKHRIAEALEKELVQ 87

Query: 79  YTLAQIQPRVVSFEEQV-LIIREKLADLYESEQQWSKAAQMLSGIDLDSGMRVIDDTFRL 137
                 +P  +    Q+ L+ R  ++ L+    Q  K    L  IDLD G R+ D T   
Sbjct: 88  ------RPGSLHIRRQLSLLNRASISTLHSFCLQVLKKYYYL--IDLDPGFRIADQTEGE 139

Query: 138 SKCVQIARLYLEDDDAVNAEAFINKASFLVS--SSQQEVLNLQYKVC----YARILDLKR 191
               ++     ED+ A   +AF      LV   ++ +  L+LQ+ V     Y+R      
Sbjct: 140 LIGDEVLDELFEDEYAKGEKAFFE----LVDRYTTDRHDLDLQFLVKQVYEYSRSHPNPE 195

Query: 192 KFLEAALRYYDISQ 205
            +LE+ +  YD+S+
Sbjct: 196 AWLESFVHLYDVSE 209


>pdb|3O53|A Chain A, Crystal Structure Of Lrim1 Leucine-Rich Repeat Domain
 pdb|3O53|B Chain B, Crystal Structure Of Lrim1 Leucine-Rich Repeat Domain
          Length = 317

 Score = 27.3 bits (59), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 38/92 (41%), Gaps = 19/92 (20%)

Query: 123 DLDSGMRVIDDTFRLSKCVQIARLYLEDDDAVNAEAFINKASFLVSSSQQEVLNLQYKVC 182
           DLD G R           VQ   L L + D VN       A    SS   E LNLQY   
Sbjct: 137 DLDEGCR---------SRVQYLDLKLNEIDTVNF------AELAASSDTLEHLNLQYNFI 181

Query: 183 YARILDLKRKFLEAALRYYDISQIQKRQIGDE 214
           Y    D+K + + A L+  D+S  +   +G E
Sbjct: 182 Y----DVKGQVVFAKLKTLDLSSNKLAFMGPE 209


  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
   0.319    0.132    0.354 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,106,314
Number of Sequences: 62578
Number of extensions: 250520
Number of successful extensions: 626
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 626
Number of HSP's gapped (non-prelim): 9
length of query: 292
length of database: 14,973,337
effective HSP length: 98
effective length of query: 194
effective length of database: 8,840,693
effective search space: 1715094442
effective search space used: 1715094442
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: 51 (24.3 bits)