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= 040949
         (490 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 =  165 bits (418), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 139/501 (27%), Positives = 228/501 (45%), Gaps = 61/501 (12%)

Query: 14  YVVVCWILAAFGGLMFGYDIG-ISGGVTAMDDFLIKFFPEVYKRKLHAREDNYCKYDNQI 72
           Y+    ++A  GGL+FGYD   ISG V +++   +            A ++      N +
Sbjct: 9   YIFSITLVATLGGLLFGYDTAVISGTVESLNTVFV------------APQNLSESAANSL 56

Query: 73  LQLFTSSLYLAALFASFVASKVCTKFGRKPTILVASS-FFLAGAGISSGALNXXXXXXXX 131
           L    +S  +  +    +      +FGR+ ++ +A+  FF++G G +   L         
Sbjct: 57  LGFCVASALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDN 116

Query: 132 XXXXXXXXXXNEAV-----------------PLFLSEIAPVQHRGAVNILFQLFVTIGIF 174
                      E V                 P++++E+AP   RG +    Q  +  G  
Sbjct: 117 TVPVYLAGYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQL 176

Query: 175 LANLVNYGTAK------LHPHGWRVSLALAGVPAIFLFIGSIVITETPTSLIERGNEVAG 228
           L   VNY  A+      L+  GWR   A   +PA+   +    + E+P  L+ RG +   
Sbjct: 177 LVYCVNYFIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQA 236

Query: 229 HKALKKIRGVEDVNAEYEQIKLASDIARQVKHPFKELMKRSSMPPLIIGVLLQVFQQFTG 288
              L+KI G        ++IK + D  R+     + LM    +  ++IGV+L +FQQF G
Sbjct: 237 EGILRKIMGNTLATQAVQEIKHSLDHGRKTGG--RLLMFGVGV--IVIGVMLSIFQQFVG 292

Query: 289 INAIMFYAPVLFQTVGFKNDASLLSSVITGTVNVLSTLVSIYAVDKVGRRKLLLQACVQM 348
           IN +++YAP +F+T+G   D +LL ++I G +N+  T+++I  VDK GR+ L +   + M
Sbjct: 293 INVVLYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGM 352

Query: 349 FISQSTIGGMLLVHLKATSNTLTTTQAGFVVFLVCLF-VMAFAWSWGPLGWLIPSETFPL 407
            I   ++G               T   G V  L  LF V AFA SWGP+ W++ SE FP 
Sbjct: 353 AIGMFSLG-----------TAFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPN 401

Query: 408 ETRTAGFAFAVSSNMFFTFLIAQAFLSMMCH--MRAYIFFFFAGWIL-VMG-LFALFL-- 461
             R    A AV++     + ++  F  M  +  + A+    F+ WI   MG L ALF+  
Sbjct: 402 AIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWK 461

Query: 462 -LPETKGVPIDVMVERVWKKH 481
            +PETKG  ++ + E +W+  
Sbjct: 462 FVPETKGKTLEEL-EALWEPE 481


>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 428

 Score = 29.3 bits (64), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 7/53 (13%)

Query: 244 EYEQIKLASD-IARQVKHPFKEL------MKRSSMPPLIIGVLLQVFQQFTGI 289
           EYE + L  D I  + +H  +EL      +KR    PL+IG  L+   Q TGI
Sbjct: 57  EYELLTLQEDYIKDEQRHLKRELKRAQEEVKRIQSVPLVIGQFLEPIDQNTGI 109


>pdb|3RNV|A Chain A, Structure Of The Autocatalytic Cysteine Protease Domain Of
           Potyvirus Helper-Component Proteinase
          Length = 158

 Score = 28.9 bits (63), Expect = 7.5,   Method: Composition-based stats.
 Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 8/82 (9%)

Query: 33  IGISGGVTAMDDFLIKFFPEVYKRKLHAREDNYCKYDNQILQLFTSSLYLAALFASFVAS 92
           IG SG    +D       PE+ + K++  ++ YC  +  +  L       A  F   V  
Sbjct: 17  IGNSGDPKYID------LPEIEENKMYIAKEGYCYINIFLAMLVNVKESQAKEFTKVVRD 70

Query: 93  KVCTKFGRKPTIL-VASS-FFL 112
           K+  + G+ PT+L VA++ +FL
Sbjct: 71  KLVGELGKWPTLLDVATACYFL 92


  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
   0.328    0.141    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,421,376
Number of Sequences: 62578
Number of extensions: 451145
Number of successful extensions: 1381
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1375
Number of HSP's gapped (non-prelim): 4
length of query: 490
length of database: 14,973,337
effective HSP length: 103
effective length of query: 387
effective length of database: 8,527,803
effective search space: 3300259761
effective search space used: 3300259761
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (25.0 bits)