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= 013992
         (432 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 =  178 bits (451), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 120/358 (33%), Positives = 179/358 (50%), Gaps = 57/358 (15%)

Query: 23  SWKNPYVLRLAFSAGIGGLLFGYDTGVISGAL-----LYIRDDFKSVDRKTLLQESIVSM 77
            + + Y+  +   A +GGLLFGYDT VISG +     +++     S      L    V+ 
Sbjct: 4   QYNSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVAS 63

Query: 78  AVXXXXXXXXXXXWMNDRFGRRTSILVADFLFFVGAVIMAAAPNPG-------------- 123
           A+           + ++RFGRR S+ +A  LFF+  V  +A P  G              
Sbjct: 64  ALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGV-GSAWPELGFTSINPDNTVPVYL 122

Query: 124 -----ALITGRVFVGLGVGMASMTSPLYISEASPAKIRGALVSTNGFLITSGQFLSYLIN 178
                  +  R+  G+GVG+ASM SP+YI+E +PA IRG LVS N F I  GQ L Y +N
Sbjct: 123 AGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVN 182

Query: 179 LAFTRAPGT-------WRWMLGVAGIPALLQFILMLLLPESPRWLYRKGREEEAQAILRK 231
               R+          WR+M     IPALL  +L+  +PESPRWL  +G++E+A+ ILRK
Sbjct: 183 YFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRK 242

Query: 232 VYPAHEVETEIRDLKESVDXXXXXXXXXXXXNLVKLLKTRTVRRGLIAGVG-------LQ 284
           +         ++++K S+D                    +T  R L+ GVG       L 
Sbjct: 243 IMGNTLATQAVQEIKHSLDH-----------------GRKTGGRLLMFGVGVIVIGVMLS 285

Query: 285 VFQQFVGINTVMYYSPTIVQLSGFASNRTALLLSLVTSGLNAAGSIVSIYFIDRTGRK 342
           +FQQFVGIN V+YY+P + +  G AS   ALL +++   +N   ++++I  +D+ GRK
Sbjct: 286 IFQQFVGINVVLYYAPEVFKTLG-ASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRK 342


>pdb|3AL8|B Chain B, Plexin A2  SEMAPHORIN 6A COMPLEX
 pdb|3AL9|A Chain A, Mouse Plexin A2 Extracellular Domain
 pdb|3AL9|B Chain B, Mouse Plexin A2 Extracellular Domain
          Length = 539

 Score = 28.5 bits (62), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 9/19 (47%), Positives = 13/19 (68%)

Query: 400 CMKCLKASSPDCGFCASHS 418
           C +CL +  P CG+CA H+
Sbjct: 487 CGECLSSGDPHCGWCALHN 505


  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    0.136    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,408,126
Number of Sequences: 62578
Number of extensions: 354345
Number of successful extensions: 808
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 798
Number of HSP's gapped (non-prelim): 5
length of query: 432
length of database: 14,973,337
effective HSP length: 102
effective length of query: 330
effective length of database: 8,590,381
effective search space: 2834825730
effective search space used: 2834825730
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)