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= 009268
         (538 letters)

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

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



>pdb|1PW4|A Chain A, Crystal Structure Of The Glycerol-3-Phosphate Transporter
           From E.Coli
          Length = 451

 Score = 77.4 bits (189), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 108/486 (22%), Positives = 197/486 (40%), Gaps = 71/486 (14%)

Query: 47  HASRKPSSIVKSVLCPDPLKGPKKKPWPI--GEFFVRQEFVGLDRNVSTAKGWDPFNGTH 104
           H +R P++ +      DP    ++  W I  G FF    +  + +N + A    P+    
Sbjct: 9   HKARLPAAEI------DPTY--RRLRWQIFLGIFFGYAAYYLVRKNFALAM---PYLVEQ 57

Query: 105 GTSKLGEIDLAFLA---CYSVGMFVAGHLGDTLDLRLFLTTGMVGSGIFVGLFGMGYF-L 160
           G S+ G++  A       Y    F+ G + D  + R+FL  G++ +   V LF MG+   
Sbjct: 58  GFSR-GDLGFALSGISIAYGFSKFIMGSVSDRSNPRVFLPAGLILAAA-VMLF-MGFVPW 114

Query: 161 DIHAFGFYLIMQMVAGLFQATGWPSVVAVIGNWFGKRKRGLIMGVWN-AHTSVGNISGSL 219
              +     ++  + G FQ  GWP     + +W+ +++RG I+ VWN AH   G I   L
Sbjct: 115 ATSSIAVMFVLLFLCGWFQGMGWPPCGRTMVHWWSQKERGGIVSVWNCAHNVGGGIPPLL 174

Query: 220 LAASVLDYG-WGWSFILPGASIVMGGIIVYLFLAAYPEDVGFP----YANDPIPSSERLP 274
               +  +  W  +  +P    ++  +  +  +   P+  G P    Y ND        P
Sbjct: 175 FLLGMAWFNDWHAALYMPAFCAILVALFAFAMMRDTPQSCGLPPIEEYKND-------YP 227

Query: 275 NDEESHMQKGKTAAVENNSGIRYGSGSRTSVGLFQACLIPGVIPF--AFCLFFAKLVAYT 332
           +D     ++  TA                   +F   ++P  + +  A    F  L+ Y 
Sbjct: 228 DDYNEKAEQELTAK-----------------QIFMQYVLPNKLLWYIAIANVFVYLLRYG 270

Query: 333 FLYWLPFYLSQTEIGGEYLSVKTAGNLSTLFDVXXXXXXXXXXXXSDKL--KARATTAAT 390
            L W P YL +     ++ ++  +     L++             SDK+    R  T   
Sbjct: 271 ILDWSPTYLKEV----KHFALDKSSWAYFLYEYAGIPGTLLCGWMSDKVFRGNRGATGVF 326

Query: 391 FMYAAIPSMLLYRTYGSVSQTVNIVLMMVAGLFVNGPYALITTAVSADLGTHSSVRGDSR 450
           FM     + ++Y    + + TV+++ M+V G  + GP  LI        G H+      +
Sbjct: 327 FMTLVTIATIVYWMNPAGNPTVDMICMIVIGFLIYGPVMLI--------GLHALELAPKK 378

Query: 451 ALATVTAIIDGTGSVGAALGP-LLTGF-LSTQGWDAVFIMLMVGALIAGLLLSRLVIAEI 508
           A  T        G +G ++    + G+ +   GWD  F++++ G+++A +L   L++  I
Sbjct: 379 AAGTAAGFTGLFGYLGGSVAASAIVGYTVDFFGWDGGFMVMIGGSILAVIL---LIVVMI 435

Query: 509 TEKIRR 514
            EK R 
Sbjct: 436 GEKRRH 441


>pdb|3S6N|2 Chain 2, Crystal Structure Of The Gemin2-Binding Domain Of Smn,
           Gemin2 In Complex With Smd1D2FEG FROM HUMAN
          Length = 280

 Score = 30.8 bits (68), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 160 LDIHAFGFYLIMQMVAGLFQATGWPSVVAVIGNWFGKRKRGLIMGVW 206
           +D    GF  ++ +V+ + QAT   SV+  + NWFG+R     +G W
Sbjct: 169 IDYVQIGFPPLLSIVSRMNQATVT-SVLEYLSNWFGERDFTPELGRW 214


>pdb|2LEH|A Chain A, Solution Structure Of The Core Smn-Gemin2 Complex
          Length = 189

 Score = 30.4 bits (67), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 160 LDIHAFGFYLIMQMVAGLFQATGWPSVVAVIGNWFGKRKRGLIMGVW 206
           +D    GF  ++ +V+ + QAT   SV+  + NWFG+R     +G W
Sbjct: 75  IDYVQIGFPPLLSIVSRMNQATV-TSVLEYLSNWFGERDFTPELGRW 120


  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
   0.323    0.139    0.430 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,277,602
Number of Sequences: 62578
Number of extensions: 623787
Number of successful extensions: 1277
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1271
Number of HSP's gapped (non-prelim): 11
length of query: 538
length of database: 14,973,337
effective HSP length: 103
effective length of query: 435
effective length of database: 8,527,803
effective search space: 3709594305
effective search space used: 3709594305
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)