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= 018342
         (357 letters)

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

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



>pdb|4B4A|A Chain A, Structure Of The Tatc Core Of The Twin Arginine Protein
           Translocation System
          Length = 249

 Score =  110 bits (276), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 74/232 (31%), Positives = 121/232 (52%), Gaps = 10/232 (4%)

Query: 132 DHLEELRQRIFVSVLA--VGAAILGCFAYSKELIMFLEAPVKSE--GVRFLQLAPGEFFF 187
           +HL ELR R+ +S++A  +G+ I   F ++K +   L+ P+      V  + L+P E  F
Sbjct: 5   EHLRELRYRLIISIIAFLIGSGI--AFYFAKYVFEILKEPILKSYPEVELITLSPTEPLF 62

Query: 188 TTLKVSGYCGLLLGSPVILYEIIAFVLPGLTRAERRFLGPIVLGSSVLFYAGIAFSYWVL 247
             +K+S   G ++ SPVILY+   F+ P L   E+R   P++LGS +LF  G  F+Y+++
Sbjct: 63  ILIKISLAVGFIIASPVILYQFWRFIEPALYSHEKRAFIPLLLGSILLFXLGALFAYFIV 122

Query: 248 TPAALNFF--VNYAEGVVESLWSIDQYFEFVLVLMFSTGLSFQVPVIXXXXXXXXXXTSD 305
            P AL F   + + + +     S+D Y  FVL L+ + G++F+ P++          T +
Sbjct: 123 LPLALKFLLGLGFTQLLATPYLSVDXYISFVLKLVVAFGIAFEXPIVLYVLQKAGVITPE 182

Query: 306 QMLSIWRYXXXXXXXXXXXLTPSTDPVTQMLLAAPLLGLYFGGAWMVKLTGR 357
           Q+ S  +Y           + P  D  TQ+L A PLL LY    ++ KL  R
Sbjct: 183 QLASFRKYFIVIAFVIGAIIAP--DVSTQVLXAIPLLLLYEISIFLGKLATR 232


>pdb|3NEK|A Chain A, Crystal Structure Of A Nitrogen Repressor-Like Protein
           Mj0159 From Methanococcus Jannaschii
 pdb|3NEK|B Chain B, Crystal Structure Of A Nitrogen Repressor-Like Protein
           Mj0159 From Methanococcus Jannaschii
          Length = 238

 Score = 28.9 bits (63), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 15/52 (28%), Positives = 23/52 (44%)

Query: 42  RFGVSRSRRRFEDALVCFAAFDGDDARDNQPELGSSGGVGSAVEDRPDVTDI 93
           RFG+     R +   +C    DG   R++ P +   GG+    ED+    DI
Sbjct: 75  RFGIVEENDRIKIQTICAVTLDGIFLRNSVPLIPKYGGILEITEDKERFIDI 126


  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
   0.324    0.140    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,712,405
Number of Sequences: 62578
Number of extensions: 380331
Number of successful extensions: 727
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 722
Number of HSP's gapped (non-prelim): 4
length of query: 357
length of database: 14,973,337
effective HSP length: 100
effective length of query: 257
effective length of database: 8,715,537
effective search space: 2239893009
effective search space used: 2239893009
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)