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= 010112
         (518 letters)

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

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



>pdb|3EVZ|A Chain A, Crystal Strucure Of Methyltransferase From Pyrococcus
           Furiosus
          Length = 230

 Score = 32.3 bits (72), Expect = 0.74,   Method: Compositional matrix adjust.
 Identities = 14/36 (38%), Positives = 19/36 (52%)

Query: 179 GGIVALIVSSAFDHHFKAPPYSVDPVGSTAPEADYV 214
           GGI+  +V   FD  F APPY   P+G    E + +
Sbjct: 113 GGIIKGVVEGTFDVIFSAPPYYDKPLGRVLTEREAI 148


>pdb|3NH7|L Chain L, Crystal Structure Of The Neutralizing Fab Fragment Abd1556
           Bound To The Bmp Type I Receptor Ia
 pdb|3NH7|M Chain M, Crystal Structure Of The Neutralizing Fab Fragment Abd1556
           Bound To The Bmp Type I Receptor Ia
 pdb|3NH7|N Chain N, Crystal Structure Of The Neutralizing Fab Fragment Abd1556
           Bound To The Bmp Type I Receptor Ia
 pdb|3NH7|O Chain O, Crystal Structure Of The Neutralizing Fab Fragment Abd1556
           Bound To The Bmp Type I Receptor Ia
          Length = 213

 Score = 32.0 bits (71), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 65/175 (37%), Gaps = 33/175 (18%)

Query: 64  TLPPNVSAAVNGVA---LCGTLAGQLFFGWLGDKLGRKKVYGITLILMVISSIASGLS-- 118
           T PP+VS A    A     G   G  +  W   K G+  V    L++   S+  SG+   
Sbjct: 5   TQPPSVSVAPGQTARISCSGDSLGSKYVIWYQQKPGQAPV----LVIYDDSNRPSGIPER 60

Query: 119 FGKSAKGVIATLCFFRFWLGFGIGGDYPLSATIMSEYANKKTRGAFIAAVFAMQGFGILA 178
           F  S  G  ATL                +S T   + A+      +  + F M G G + 
Sbjct: 61  FSGSNSGNTATLT---------------ISGTQAEDEAD------YYCSTFTMSGNGTVF 99

Query: 179 GGIVALIVSSAFDHHFKAPPYSVDPVGSTAPEADYVWRIVLMVGALPAALTYYWR 233
           GG   L V         AP  ++ P  S   +A+    + L+    P A+T  W+
Sbjct: 100 GGGTKLTV---LGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWK 151


>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Xylose
 pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To D-Glucose
 pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
           Proton:xylose Symporter Xyle Bound To
           6-Bromo-6-Deoxy-D-Glucose
          Length = 491

 Score = 30.0 bits (66), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 1/80 (1%)

Query: 93  DKLGRKKVYGITLILMVISSIASGLSFGKSAKGVIATLCFFRFWLGFGIGGDYPLSATIM 152
           DK GRK +  I  + M I   + G +F   A G++A L    +   F +    P+   ++
Sbjct: 337 DKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGIVALLSMLFYVAAFAMSWG-PVCWVLL 395

Query: 153 SEYANKKTRGAFIAAVFAMQ 172
           SE      RG  +A   A Q
Sbjct: 396 SEIFPNAIRGKALAIAVAAQ 415


  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
   0.326    0.140    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,781,629
Number of Sequences: 62578
Number of extensions: 498793
Number of successful extensions: 1174
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1172
Number of HSP's gapped (non-prelim): 5
length of query: 518
length of database: 14,973,337
effective HSP length: 103
effective length of query: 415
effective length of database: 8,527,803
effective search space: 3539038245
effective search space used: 3539038245
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 bits)