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= 026975
         (230 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 (275), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 76/232 (32%), Positives = 123/232 (53%), Gaps = 10/232 (4%)

Query: 5   DHLEELRQRIFVSVLA--VGAAILGCFAYSKELIMFLEAPV-KS-EGVRFLQLAPGEFFF 60
           +HL ELR R+ +S++A  +G+ I   F ++K +   L+ P+ KS   V  + L+P E  F
Sbjct: 5   EHLRELRYRLIISIIAFLIGSGI--AFYFAKYVFEILKEPILKSYPEVELITLSPTEPLF 62

Query: 61  TTLKVSGYCGLLLGSPVILYEIIAFVLPGLTRAERRFLGPIVLGSSVLFYAGIAFSYWVL 120
             +K+S   G ++ SPVILY+   F+ P L   E+R   P++LGS +LF  G  F+Y+++
Sbjct: 63  ILIKISLAVGFIIASPVILYQFWRFIEPALYSHEKRAFIPLLLGSILLFXLGALFAYFIV 122

Query: 121 TPAALNFF--VNYAEGVVESLWSIDQYFEFVLVLMFSTGLSFQVPVIXXXXXXXXXXTSD 178
            P AL F   + + + +     S+D Y  FVL L+ + G++F+ P++          T +
Sbjct: 123 LPLALKFLLGLGFTQLLATPYLSVDXYISFVLKLVVAFGIAFEXPIVLYVLQKAGVITPE 182

Query: 179 QMLSIWRYXXXXXXXXXXXLTPSTDPVTQMLLAAPLLGLYFGGAWMVKLTGR 230
           Q+ S  +Y           + P  D  TQ+L A PLL LY    ++ KL  R
Sbjct: 183 QLASFRKYFIVIAFVIGAIIAP--DVSTQVLXAIPLLLLYEISIFLGKLATR 232


>pdb|2I5Q|A Chain A, Crystal Structure Of Apo L-Rhamnonate Dehydratase From
           Escherichia Coli
 pdb|2I5Q|B Chain B, Crystal Structure Of Apo L-Rhamnonate Dehydratase From
           Escherichia Coli
          Length = 415

 Score = 29.6 bits (65), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 24/92 (26%), Positives = 37/92 (40%), Gaps = 21/92 (22%)

Query: 1   MSIFDHLEELRQRIFVSVLAV-----------------GAAILGCFAYSKELIMFLEAPV 43
           MS +   E+LRQ   ++VL                    A  +GCF   K L  F+E   
Sbjct: 51  MSKYRDYEQLRQSFGINVLGTLVVEVEAENGQTGFAVSTAGEMGCFIVEKHLNRFIEGKC 110

Query: 44  KSEGVRFLQLAPGEFFFTTLKVSGYCGLLLGS 75
            S+    ++L   +    TL  SG  GL++ +
Sbjct: 111 VSD----IKLIHDQMLNATLYYSGSGGLVMNT 138


  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
   0.329    0.144    0.441 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,864,217
Number of Sequences: 62578
Number of extensions: 202633
Number of successful extensions: 449
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 445
Number of HSP's gapped (non-prelim): 2
length of query: 230
length of database: 14,973,337
effective HSP length: 96
effective length of query: 134
effective length of database: 8,965,849
effective search space: 1201423766
effective search space used: 1201423766
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)