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= 041786
         (260 letters)

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

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



>pdb|3RJV|A Chain A, Crystal Structure Of A Putative Sel1 Repeat Protein
           (Kpn_04481) From Klebsiella Pneumoniae Subsp. Pneumoniae
           At 1.65 A Resolution
          Length = 212

 Score = 32.7 bits (73), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 120 DKRTHTILVNAWCSSGKMREAQEFLQELSDKGFNPPVRSAKQMVNKMIKQGSVPDLETF- 178
           D+R    L + W SSG  ++A+ + Q+ + +G    +    Q+  +  +Q   P      
Sbjct: 17  DRRAQYYLADTWVSSGDYQKAEYWAQKAAAQGDGDALALLAQLKIRNPQQADYPQARQLA 76

Query: 179 NSLIETICKSGEL 191
              +E   KSGE+
Sbjct: 77  EKAVEAGSKSGEI 89


>pdb|4IFU|A Chain A, Crystal Structure Of Treponema Pallidum Tp0796 Fad
           Processing Protein, Apo Form
 pdb|4IFW|A Chain A, Crystal Structure Of Treponema Pallidum Tp0796 Fad
           Processing Protein, Adp Inhibited Form
 pdb|4IFX|A Chain A, Crystal Structure Of Treponema Pallidum Tp0796 Fad
           Processing Protein, Fad Substrate Bound Form
 pdb|4IFZ|A Chain A, Crystal Structure Of Treponema Pallidum Tp0796 Fad
           Processing Protein, Mn(ii)-amp Product Bound Form
 pdb|4IG1|A Chain A, Crystal Structure Of Treponema Pallidum Tp0796 Fad
           Processing Protein, Mg(ii)-amp Product Bound Form
          Length = 340

 Score = 29.3 bits (64), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 25/107 (23%), Positives = 46/107 (42%), Gaps = 19/107 (17%)

Query: 143 FLQELSDKGFNPPVRSAKQMVNKMIKQGSVPDLETFNSLIETICKSGELGLCADVNTN-- 200
           F  E S   FNP + +  ++ N    + +VPD +     + T C   ++ L A V+    
Sbjct: 88  FFAEKSGGAFNPALGAVVKLWNIGFDRAAVPDPDALKEAL-TRCDFRQVHLRAGVSVGAP 146

Query: 201 ----------KISIPAVSKEFMIDEAFRLL------CNLVEDGHKLF 231
                     ++ + A++K F+ D+  +LL        LV+ G  +F
Sbjct: 147 HTVQLAQAGMQLDLGAIAKGFLADKIVQLLTAHALDSALVDLGGNIF 193


>pdb|3MT5|A Chain A, Crystal Structure Of The Human Bk Gating Apparatus
          Length = 726

 Score = 28.5 bits (62), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 11/38 (28%), Positives = 21/38 (55%)

Query: 126 ILVNAWCSSGKMREAQEFLQELSDKGFNPPVRSAKQMV 163
           IL N +C+     +A   ++ +S K ++P +R   QM+
Sbjct: 85  ILANKYCADPDAEDASNIMRVISIKNYHPKIRIITQML 122


>pdb|3U6N|A Chain A, Open Structure Of The Bk Channel Gating Ring
 pdb|3U6N|B Chain B, Open Structure Of The Bk Channel Gating Ring
 pdb|3U6N|C Chain C, Open Structure Of The Bk Channel Gating Ring
 pdb|3U6N|D Chain D, Open Structure Of The Bk Channel Gating Ring
 pdb|3U6N|E Chain E, Open Structure Of The Bk Channel Gating Ring
 pdb|3U6N|F Chain F, Open Structure Of The Bk Channel Gating Ring
 pdb|3U6N|G Chain G, Open Structure Of The Bk Channel Gating Ring
 pdb|3U6N|H Chain H, Open Structure Of The Bk Channel Gating Ring
          Length = 696

 Score = 28.5 bits (62), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 11/38 (28%), Positives = 21/38 (55%)

Query: 126 ILVNAWCSSGKMREAQEFLQELSDKGFNPPVRSAKQMV 163
           IL N +C+     +A   ++ +S K ++P +R   QM+
Sbjct: 85  ILANKYCADPDAEDASNIMRVISIKNYHPKIRIITQML 122


>pdb|3NAF|A Chain A, Structure Of The Intracellular Gating Ring From The Human
           High- Conductance Ca2+ Gated K+ Channel (Bk Channel)
          Length = 798

 Score = 28.1 bits (61), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 11/38 (28%), Positives = 21/38 (55%)

Query: 126 ILVNAWCSSGKMREAQEFLQELSDKGFNPPVRSAKQMV 163
           IL N +C+     +A   ++ +S K ++P +R   QM+
Sbjct: 135 ILANKYCADPDAEDASNIMRVISIKNYHPKIRIITQML 172


  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
   0.323    0.136    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,342,994
Number of Sequences: 62578
Number of extensions: 275918
Number of successful extensions: 564
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 561
Number of HSP's gapped (non-prelim): 9
length of query: 260
length of database: 14,973,337
effective HSP length: 97
effective length of query: 163
effective length of database: 8,903,271
effective search space: 1451233173
effective search space used: 1451233173
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 50 (23.9 bits)