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= psy6142
         (483 letters)

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

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



>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 =  134 bits (336), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 126/456 (27%), Positives = 199/456 (43%), Gaps = 82/456 (17%)

Query: 40  LSALFGGMAGGPLIESLGRRTTILSTGLPFIVS----------FLLIALANGVPMILAG- 88
           +  + GG  GG      GRR ++    + F +S          F  I   N VP+ LAG 
Sbjct: 66  IGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGY 125

Query: 89  -------RCVAGFCVGIASLALPVYLGETVQPEVRGTLGLLPTFLGNIGILTCFIAGTFL 141
                  R + G  VG+AS+  P+Y+ E     +RG L     F    G L  +    F+
Sbjct: 126 VPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFI 185

Query: 142 ------NW-----YQLAFFGACIP-VPFLICMFLIPETPRWYIGRNKQKQARKALQWLRG 189
                 +W     ++  F   CIP + FL+ ++ +PE+PRW + R KQ+QA   L+ + G
Sbjct: 186 ARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMG 245

Query: 190 KDADISREFAEIEKMNNEGNAAEDENSTGCSEVFKAMYMRPLLISIGLMFFQQMSGINAV 249
            +   ++   EI+   + G       + G   +F    +  ++I + L  FQQ  GIN V
Sbjct: 246 -NTLATQAVQEIKHSLDHG-----RKTGGRLLMFG---VGVIVIGVMLSIFQQFVGINVV 296

Query: 250 LASLTVSLGSMIVGFASAYTSPAIPSMNQMGSRVSPTEEEDAGSTINENYCTIIVGVVNL 309
           L                 Y +P +     +G+           ST      TIIVGV+NL
Sbjct: 297 L-----------------YYAPEV--FKTLGA-----------STDIALLQTIIVGVINL 326

Query: 310 LSVLIATALIDRLGRKILLYISSTAMILTLATLGTFFYFKSTGSDVSELGWLPLLSFVVY 369
              ++A   +D+ GRK L  I +  M + + +LGT FY ++ G        + LLS + Y
Sbjct: 327 TFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGI-------VALLSMLFY 379

Query: 370 VIGFSIGFGSIPWLMMGEILPAKIRGSAASLATAFNWTCTFIVTKTF--NDLTALLGTHG 427
           V  F++ +G + W+++ EI P  IRG A ++A A  W   + V+ TF   D  + L  H 
Sbjct: 380 VAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHF 439

Query: 428 ----AXXXXXXXXXXXXXXXXXXXPETQGKSLEDIE 459
               +                   PET+GK+LE++E
Sbjct: 440 HNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELE 475



 Score = 30.8 bits (68), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 42/171 (24%), Positives = 72/171 (42%), Gaps = 40/171 (23%)

Query: 252 SLTVSLGSMIVGFASAYTSPAIPSMNQMGSRVSPTEEEDAGSTINENYCTIIVGVVNLLS 311
           +L  +LG ++ G+ +A  S  + S+N +   V+P    ++ +     +C        L+ 
Sbjct: 14  TLVATLGGLLFGYDTAVISGTVESLNTV--FVAPQNLSESAANSLLGFCV----ASALIG 67

Query: 312 VLIATAL----IDRLGRKILLYISSTAMILTLATLGTFFYFKSTGSDVSELGW------- 360
            +I  AL     +R GR+  L I++             F+    GS   ELG+       
Sbjct: 68  CIIGGALGGYCSNRFGRRDSLKIAA-----------VLFFISGVGSAWPELGFTSINPDN 116

Query: 361 -LPLL------SFVVYVI--GFSIGFGSI--PWLMMGEILPAKIRGSAASL 400
            +P+        FV+Y I  G  +G  S+  P + + E+ PA IRG   S 
Sbjct: 117 TVPVYLAGYVPEFVIYRIIGGIGVGLASMLSP-MYIAELAPAHIRGKLVSF 166


>pdb|3EG5|B Chain B, Crystal Structure Of Mdia1-Tsh Gbd-Fh3 In Complex With
           Cdc42-Gmppnp
 pdb|3EG5|D Chain D, Crystal Structure Of Mdia1-Tsh Gbd-Fh3 In Complex With
           Cdc42-Gmppnp
          Length = 383

 Score = 28.5 bits (62), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 32/129 (24%), Positives = 56/129 (43%), Gaps = 16/129 (12%)

Query: 175 NKQKQARKALQWLRGKDADISREFAEIEKMNNEGNAAEDENSTGCSEVFKAMYMRPLLIS 234
           N++KQ     Q LR KD  I RE   + +  +   A  ++  +  S +     +R  L  
Sbjct: 29  NEEKQ-----QPLREKDIVIKREM--VSQYLHTSKAGMNQKESSRSAMMYIQELRSGLRD 81

Query: 235 IGLMFFQQMSGINAVLASLTVSLGSMIVGFASAYTSPAIPSMNQMGSRVSPTEEEDAGST 294
           + L+         + L SL VSL S  V +   + +  + S+  +  R+   +EE +G+ 
Sbjct: 82  MHLL---------SCLESLRVSLTSHPVSWVQTFGAEGLASLLDILKRLHDEKEETSGNY 132

Query: 295 INENYCTII 303
            + N   II
Sbjct: 133 DSRNQHEII 141


  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    0.419 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,185,878
Number of Sequences: 62578
Number of extensions: 513148
Number of successful extensions: 956
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: 948
Number of HSP's gapped (non-prelim): 7
length of query: 483
length of database: 14,973,337
effective HSP length: 103
effective length of query: 380
effective length of database: 8,527,803
effective search space: 3240565140
effective search space used: 3240565140
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: 53 (25.0 bits)