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= 038076
         (345 letters)

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

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



>pdb|1JCF|A Chain A, Mreb From Thermotoga Maritima, Trigonal
 pdb|1JCG|A Chain A, Mreb From Thermotoga Maritima, Amppnp
 pdb|2WUS|A Chain A, Bacterial Actin Mreb Assembles In Complex With Cell Shape
           Protein Rodz
 pdb|2WUS|B Chain B, Bacterial Actin Mreb Assembles In Complex With Cell Shape
           Protein Rodz
          Length = 344

 Score = 35.0 bits (79), Expect = 0.069,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 44/78 (56%), Gaps = 9/78 (11%)

Query: 140 PNGPIAIYGLGGGTAAHLMLDL-----WPSLKLEGWEIDEILIDKVRDYFGLSDLEKPTA 194
           P+G + +  +GGGT    ++ L     W S+++ G E+DE ++  VR+ + ++  E+   
Sbjct: 146 PSGNM-VVDIGGGTTEVAVISLGSIVTWESIRIAGDEMDEAIVQYVRETYRVAIGER--- 201

Query: 195 TGGVLQVHIGDVFSPSED 212
           T   +++ IG+VF   E+
Sbjct: 202 TAERVKIEIGNVFPSKEN 219


>pdb|1JCE|A Chain A, Mreb From Thermotoga Maritima
          Length = 344

 Score = 33.9 bits (76), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 8/69 (11%)

Query: 149 LGGGTAAHLMLDL-----WPSLKLEGWEIDEILIDKVRDYFGLSDLEKPTATGGVLQVHI 203
           +GGGT    ++ L     W S+++ G E DE ++  VR+ + ++  E+   T   +++ I
Sbjct: 154 IGGGTTEVAVISLGSIVTWESIRIAGDEXDEAIVQYVRETYRVAIGER---TAERVKIEI 210

Query: 204 GDVFSPSED 212
           G+VF   E+
Sbjct: 211 GNVFPSKEN 219


>pdb|1POI|B Chain B, Crystal Structure Of Glutaconate Coenzyme A-transferase
           From Acidaminococcus Fermentans To 2.55 Angstoms
           Resolution
 pdb|1POI|D Chain D, Crystal Structure Of Glutaconate Coenzyme A-transferase
           From Acidaminococcus Fermentans To 2.55 Angstoms
           Resolution
          Length = 260

 Score = 28.9 bits (63), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 25/104 (24%), Positives = 46/104 (44%), Gaps = 13/104 (12%)

Query: 161 LWPSLKLEGWEIDEIL--IDKVRDYFGLSDLEKPTATGGVLQVHIGDVFSPSEDASGRYA 218
           +WP+++  G+EI+E L   +++  + G + ++     G V    IGD   P    +G   
Sbjct: 79  IWPNVRFVGFEINEYLHKANRLIAFIGGAQID---PYGNVNSTSIGDYHHPKTRFTGSGG 135

Query: 219 GIVVDLFSEGKVLPQLEEVATWLKLKDRLMPNGRFMVNCGGIDG 262
              +  +S   ++ Q E        K R M    ++ + G IDG
Sbjct: 136 ANGIATYSNTIIMMQHE--------KRRFMNKIDYVTSPGWIDG 171


>pdb|1C8O|A Chain A, 2.9 A Structure Of Cleaved Viral Serpin Crma
          Length = 300

 Score = 28.1 bits (61), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 30/113 (26%), Positives = 41/113 (36%), Gaps = 20/113 (17%)

Query: 132 FVSLPAIVPNGPIAIYGLGGGTAAHLMLDLWPSLKLEGWEIDEILIDKVRDYFGLSDLEK 191
           F+S P+I     I  YG  G TA  L             +  E   DK +D      + K
Sbjct: 17  FISPPSISSVLTILYYGANGSTAEQLS------------KYVEKEADKNKDDISFKSMNK 64

Query: 192 -----PTATGGVLQVHIGDVFSPSEDASGRYAGIV---VDLFSEGKVLPQLEE 236
                           IGD F   +    R    +   VD+F+EGK+ P L+E
Sbjct: 65  VYGRYSAVFKDSFLRKIGDNFQTVDFTDSRTVDAINKSVDIFTEGKINPLLDE 117


  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
   0.318    0.135    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,957,975
Number of Sequences: 62578
Number of extensions: 431744
Number of successful extensions: 795
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 794
Number of HSP's gapped (non-prelim): 4
length of query: 345
length of database: 14,973,337
effective HSP length: 100
effective length of query: 245
effective length of database: 8,715,537
effective search space: 2135306565
effective search space used: 2135306565
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)