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= 019729
         (336 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 =  102 bits (254), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 87/281 (30%), Positives = 130/281 (46%), Gaps = 56/281 (19%)

Query: 94  ANVGAMVGAIASGQIAEYIGRKGSLMIAAVPNII-----GWLIISFSK---DSSF----- 140
           A +G ++G    G  +   GR+ SL IAAV   I      W  + F+    D++      
Sbjct: 64  ALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLA 123

Query: 141 -----LFMGRLLEGFGVGVISYTVPVYIAEIAPQNMRGSLGSVNQLSVTIGIMLAYLLGL 195
                  + R++ G GVG+ S   P+YIAE+AP ++RG L S NQ ++  G +L Y +  
Sbjct: 124 GYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNY 183

Query: 196 FV------------NWRVLAVLGVLPCTLLIPGLFFIPESPRWLAKMGMTEDFESSLQVL 243
           F+             WR +     +P  L +  L+ +PESPRWL   G  E  E  L+ +
Sbjct: 184 FIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKI 243

Query: 244 RGFDTDISIEVNEIKRSVASSSRRTAIRFAELKRKRYWFPLMIGIGLLVL-------QQL 296
            G +T  +  V EIK S+    R+T  R            LM G+G++V+       QQ 
Sbjct: 244 MG-NTLATQAVQEIKHSL-DHGRKTGGRL-----------LMFGVGVIVIGVMLSIFQQF 290

Query: 297 SGINGVLFYSSNIFANAGKINISLDVIL---PIVEALNSTY 334
            GIN VL+Y+  +F   G    S D+ L    IV  +N T+
Sbjct: 291 VGINVVLYYAPEVFKTLGA---STDIALLQTIIVGVINLTF 328


>pdb|2D6F|A Chain A, Crystal Structure Of Glu-Trna(Gln) Amidotransferase In The
           Complex With Trna(Gln)
 pdb|2D6F|B Chain B, Crystal Structure Of Glu-Trna(Gln) Amidotransferase In The
           Complex With Trna(Gln)
          Length = 435

 Score = 35.4 bits (80), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 33/139 (23%), Positives = 63/139 (45%), Gaps = 33/139 (23%)

Query: 124 PNIIGWLIISFSKDSSFLFMGRLLEGFGVGVISYT-VPVYIAEIAPQNMRGSLGSVNQLS 182
           P+II W +          + G ++EG G+G    T +PV             +G  + + 
Sbjct: 315 PDIIKWHLDEG-------YRGIVIEGTGLGHCPDTLIPV-------------IGEAHDMG 354

Query: 183 VTIGIMLAYLLG-----LFVNWRVLAVLGVLPCTLLIPGLFFIPESPRWLAKMGMTEDFE 237
           V + +    L G     ++   R L   GV+PC  ++P + ++     W+  +G T+D E
Sbjct: 355 VPVAMTSQCLNGRVNMNVYSTGRRLLQAGVIPCDDMLPEVAYVKMC--WV--LGQTDDPE 410

Query: 238 SSLQVLRGFDTDISIEVNE 256
            + +++R    +I+ E+NE
Sbjct: 411 MAREMMR---ENIAGEINE 426


>pdb|1VSW|A Chain A, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|B Chain B, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|C Chain C, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|D Chain D, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|E Chain E, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|F Chain F, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|G Chain G, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|H Chain H, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|I Chain I, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|J Chain J, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|K Chain K, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|L Chain L, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|M Chain M, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|N Chain N, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|O Chain O, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|P Chain P, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|Q Chain Q, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|R Chain R, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|S Chain S, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|T Chain T, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|U Chain U, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|V Chain V, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|W Chain W, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|X Chain X, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|Y Chain Y, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|Z Chain Z, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|1 Chain 1, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|2 Chain 2, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|3 Chain 3, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSW|4 Chain 4, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|A Chain A, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|B Chain B, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|C Chain C, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|D Chain D, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|E Chain E, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|F Chain F, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|G Chain G, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|H Chain H, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|I Chain I, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|J Chain J, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|K Chain K, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|L Chain L, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|M Chain M, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|N Chain N, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|O Chain O, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|P Chain P, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|Q Chain Q, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|R Chain R, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|S Chain S, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|T Chain T, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|U Chain U, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|V Chain V, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|W Chain W, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|X Chain X, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|Y Chain Y, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|Z Chain Z, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|1 Chain 1, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|2 Chain 2, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|3 Chain 3, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|1VSX|4 Chain 4, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|A Chain A, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|B Chain B, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|C Chain C, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|D Chain D, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|E Chain E, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|F Chain F, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|G Chain G, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|H Chain H, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|I Chain I, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|J Chain J, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|K Chain K, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|L Chain L, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|M Chain M, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|N Chain N, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|O Chain O, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|P Chain P, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|Q Chain Q, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|R Chain R, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|S Chain S, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|T Chain T, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|U Chain U, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|V Chain V, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|W Chain W, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|X Chain X, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|Y Chain Y, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|Z Chain Z, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|1 Chain 1, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|2 Chain 2, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|3 Chain 3, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
 pdb|3JV8|4 Chain 4, Crystal Structure Of Lumazine Synthase From Bacillus
           Anthracis
          Length = 153

 Score = 31.2 bits (69), Expect = 0.89,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 28/57 (49%)

Query: 214 IPGLFFIPESPRWLAKMGMTEDFESSLQVLRGFDTDISIEVNEIKRSVASSSRRTAI 270
           +PG F IP   + +A  G  +   +   V+RG  T      NE+ + VAS S +T I
Sbjct: 52  VPGAFEIPLIAKKMANSGKYDAVITLGTVIRGATTHYDYVCNEVAKGVASLSLQTDI 108


>pdb|3ZEF|B Chain B, Crystal Structure Of Prp8:aar2 Complex: Second Crystal Form
            At 3.1 Angstrom Resolution
 pdb|3ZEF|E Chain E, Crystal Structure Of Prp8:aar2 Complex: Second Crystal Form
            At 3.1 Angstrom Resolution
          Length = 1531

 Score = 28.9 bits (63), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 77   ISDLKLTISEFSIFGSLANVGAMVGAIASGQIAEYIGRKGSLMIAAVPNI 126
            ISD+K+ ++ F I+G  A     V  I +  +   +G  GS+ I+ +P+I
Sbjct: 1314 ISDVKIQVAAF-IYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDI 1362


>pdb|4I43|B Chain B, Crystal Structure Of Prp8:aar2 Complex
          Length = 1564

 Score = 28.9 bits (63), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 77   ISDLKLTISEFSIFGSLANVGAMVGAIASGQIAEYIGRKGSLMIAAVPNI 126
            ISD+K+ ++ F I+G  A     V  I +  +   +G  GS+ I+ +P+I
Sbjct: 1347 ISDVKIQVAAF-IYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDI 1395


>pdb|3SBG|A Chain A, Crystal Structure Of A Prp8 C-Terminal Fragment
          Length = 565

 Score = 28.5 bits (62), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 77  ISDLKLTISEFSIFGSLANVGAMVGAIASGQIAEYIGRKGSLMIAAVPNI 126
           ISD+K+ ++ F I+G  A     V  I +  +   +G  GS+ I+ +P+I
Sbjct: 364 ISDVKIQVAAF-IYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDI 412


>pdb|2OG4|A Chain A, Structure Of An Expanded Jab1-mpn-like Domain Of Splicing
           Factor Prp8p From Yeast
          Length = 254

 Score = 28.1 bits (61), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 77  ISDLKLTISEFSIFGSLANVGAMVGAIASGQIAEYIGRKGSLMIAAVPNI 126
           ISD+K+ ++ F I+G  A     V  I +  +   +G  GS+ I+ +P+I
Sbjct: 53  ISDVKIQVAAF-IYGMSAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDI 101


  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
   0.324    0.140    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,375,991
Number of Sequences: 62578
Number of extensions: 307280
Number of successful extensions: 560
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: 553
Number of HSP's gapped (non-prelim): 11
length of query: 336
length of database: 14,973,337
effective HSP length: 99
effective length of query: 237
effective length of database: 8,778,115
effective search space: 2080413255
effective search space used: 2080413255
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.6 bits)