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= 043499
         (396 letters)

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

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



>pdb|4I1K|A Chain A, Crystal Structure Of Vrn1 (residues 208-341)
 pdb|4I1K|B Chain B, Crystal Structure Of Vrn1 (residues 208-341)
          Length = 146

 Score = 81.3 bits (199), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 45/125 (36%), Positives = 72/125 (57%), Gaps = 4/125 (3%)

Query: 275 SEGHRYLSVEERQSLVTAVRLFKPQNPSFVDILRSKKRY--SYMYVPSKFSKKHLIRGTR 332
           S   R ++ EER+  + A + F+P NP F  +LR    Y    MY+PS F++K+L   + 
Sbjct: 21  SARKRTVTAEERERAINAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISG 80

Query: 333 SIKLQDSDGKEWPAQLTWSSG-CGIKGGWPAFSKYKNLKQGHVCVFELIKAKDILLKVSI 391
            IK+Q ++ K+WP +  + +G      GW  F+   NL +G VCVFEL++ +D +LKV+ 
Sbjct: 81  FIKVQLAE-KQWPVRCLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTA 139

Query: 392 HASSE 396
              +E
Sbjct: 140 FRVNE 144


>pdb|1YEL|A Chain A, Structure Of The Hypothetical Arabidopsis Thaliana Protein
           At1g16640.1
          Length = 104

 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 44/83 (53%)

Query: 85  KKLRIPRKFVKRFGDELSAVATLNVPNGRVWQVGLRKDGRKIWLQDGWDNFAEYHSIAVG 144
           K L IP  F + F         L   +GR W V ++K G K++L  GW+NF + +++  G
Sbjct: 22  KSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDG 81

Query: 145 YFLVFKYAKNSTFDVLVFDMTAC 167
            +L F Y ++ TF V+++    C
Sbjct: 82  KYLQFIYDRDRTFYVIIYGHNMC 104


>pdb|1OIW|A Chain A, X-ray Structure Of The Small G Protein Rab11a In Complex
           With Gtpgammas
 pdb|1OIX|A Chain A, X-Ray Structure Of The Small G Protein Rab11a In Complex
           With Gdp And Pi
          Length = 191

 Score = 29.3 bits (64), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 28/102 (27%), Positives = 47/102 (46%), Gaps = 6/102 (5%)

Query: 62  AGGNRRAETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNG-RVWQVGLR 120
           A G R  E  + FKV+L       K  +  +F +   + L + +T+ V    R  QV  +
Sbjct: 18  AMGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFN-LESKSTIGVEFATRSIQVDGK 76

Query: 121 KDGRKIWLQDGWDNF----AEYHSIAVGYFLVFKYAKNSTFD 158
               +IW   G + +    + Y+  AVG  LV+  AK+ T++
Sbjct: 77  TIKAQIWDTAGLERYRAITSAYYRGAVGALLVYDIAKHLTYE 118


>pdb|1WID|A Chain A, Solution Structure Of The B3 Dna-Binding Domain Of Rav1
          Length = 130

 Score = 28.9 bits (63), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 12/85 (14%)

Query: 316 MYVPSKFSKKHL--------IRGTRSIKLQDSDGKEWPAQLT-WSSGCG--IKGGWPAFS 364
           + +P   ++KH         ++G   +  +D +GK W  + + W+S     +  GW  F 
Sbjct: 29  LVIPKHHAEKHFPLPSSNVSVKGVL-LNFEDVNGKVWRFRYSYWNSSQSYVLTKGWSRFV 87

Query: 365 KYKNLKQGHVCVFELIKAKDILLKV 389
           K KNL+ G V  F     +D  L +
Sbjct: 88  KEKNLRAGDVVSFSRSNGQDQQLYI 112


>pdb|1OIV|A Chain A, X-Ray Structure Of The Small G Protein Rab11a In Complex
           With Gdp
 pdb|1OIV|B Chain B, X-Ray Structure Of The Small G Protein Rab11a In Complex
           With Gdp
          Length = 191

 Score = 28.5 bits (62), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 28/102 (27%), Positives = 47/102 (46%), Gaps = 6/102 (5%)

Query: 62  AGGNRRAETSHFFKVILPSTVQEKKLRIPRKFVKRFGDELSAVATLNVPNG-RVWQVGLR 120
           A G R  E  + FKV+L       K  +  +F +   + L + +T+ V    R  QV  +
Sbjct: 18  AMGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFN-LESKSTIGVEFATRSIQVDGK 76

Query: 121 KDGRKIWLQDGWDNF----AEYHSIAVGYFLVFKYAKNSTFD 158
               +IW   G + +    + Y+  AVG  LV+  AK+ T++
Sbjct: 77  TIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYE 118


  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    0.134    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,978,886
Number of Sequences: 62578
Number of extensions: 496143
Number of successful extensions: 1052
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1045
Number of HSP's gapped (non-prelim): 8
length of query: 396
length of database: 14,973,337
effective HSP length: 101
effective length of query: 295
effective length of database: 8,652,959
effective search space: 2552622905
effective search space used: 2552622905
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)