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= 040333
         (513 letters)

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

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



>pdb|4HG6|A Chain A, Structure Of A Cellulose Synthase - Cellulose
           Translocation Intermediate
          Length = 802

 Score = 94.7 bits (234), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 70/256 (27%), Positives = 116/256 (45%), Gaps = 28/256 (10%)

Query: 78  LGSSNFPVVLIQIPMFNEK-EVYKISIGAACGLSWPSDRLVIQVLDD--------STDPA 128
           L     P V I +P +NE  ++  +++ AA  + +P+    + + DD        S DP 
Sbjct: 134 LQPEELPTVDILVPSYNEPADMLSVTLAAAKNMIYPARLRTVVLCDDGGTDQRCMSPDPE 193

Query: 129 IKQMVEQ---ECQRWAAKGINIRYQIRENRTGYKAGALKEGLKRSY--------VKHCEY 177
           + Q  ++   E Q+   + + + Y  RE     KAG +   L+R            H   
Sbjct: 194 LAQKAQERRRELQQLC-RELGVVYSTRERNEHAKAGNMSAALERLKGELVVVFDADHVPS 252

Query: 178 PDYLRRAIPYLVQNSDIALVQARWRFVNA-----NECLLTRMQEMSLDYHFKVEQEVGSA 232
            D+L R + Y V++ D+ LVQ    F+N      N  L  R    +  ++ K+ + +   
Sbjct: 253 RDFLARTVGYFVEDPDLFLVQTPHFFINPDPIQRNLALGDRCPPENEMFYGKIHRGLDRW 312

Query: 233 THAFFGFNGTAGVWRIAAINEAGGWKDRTTVEDMDLAVRASLKGWKFVYLGDLQVKSELP 292
             AFF   G+A V R  A++EAGG+   T  ED + A+    +GWK +Y+    +    P
Sbjct: 313 GGAFF--CGSAAVLRRRALDEAGGFAGETITEDAETALEIHSRGWKSLYIDRAMIAGLQP 370

Query: 293 STFKAFRFQQHRWSCG 308
            TF +F  Q+ RW+ G
Sbjct: 371 ETFASFIQQRGRWATG 386


>pdb|3F4A|A Chain A, Structure Of Ygr203w, A Yeast Protein Tyrosine Phosphatase
           Of The Rhodanese Family
 pdb|3F4A|B Chain B, Structure Of Ygr203w, A Yeast Protein Tyrosine Phosphatase
           Of The Rhodanese Family
          Length = 169

 Score = 29.6 bits (65), Expect = 4.2,   Method: Composition-based stats.
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 114 DRLVIQVLDDSTDPAIKQMVEQECQRWAAKG--INIR--YQIRENR-TGYKAGALKEGLK 168
           + L  Q  D  +   +K +   E  RW  +G    +R  +Q+ + R + Y  G +K+G  
Sbjct: 15  ENLYFQGXDSYSITNVKYLDPTELHRWXQEGHTTTLREPFQVVDVRGSDYXGGHIKDGWH 74

Query: 169 RSYVKHCEYPDYLR 182
            +Y +  + P+YLR
Sbjct: 75  YAYSRLKQDPEYLR 88


>pdb|2BG9|E Chain E, Refined Structure Of The Nicotinic Acetylcholine Receptor
           At 4a Resolution
          Length = 370

 Score = 29.3 bits (64), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 5/45 (11%)

Query: 65  KRYNWQPIEDDVELGSSNFPVVLIQIPMFNEKEVYKISIGAACGL 109
           K YNWQ  +DD++     F +++ + P+F     Y I+I A C L
Sbjct: 185 KNYNWQLTKDDIDFQEIIFFLIIQRKPLF-----YIINIIAPCVL 224


>pdb|4AQ5|E Chain E, Gating Movement In Acetylcholine Receptor Analysed By
           Time- Resolved Electron Cryo-Microscopy (Closed Class)
 pdb|4AQ9|E Chain E, Gating Movement In Acetylcholine Receptor Analysed By
           Time-Resolved Electron Cryo-Microscopy (Open Class)
          Length = 488

 Score = 28.9 bits (63), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 25/45 (55%), Gaps = 5/45 (11%)

Query: 65  KRYNWQPIEDDVELGSSNFPVVLIQIPMFNEKEVYKISIGAACGL 109
           K YNWQ  +DD++     F +++ + P+F     Y I+I A C L
Sbjct: 192 KNYNWQLTKDDIDFQEIIFFLIIQRKPLF-----YIINIIAPCVL 231


  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
   0.327    0.141    0.441 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,690,361
Number of Sequences: 62578
Number of extensions: 529924
Number of successful extensions: 1161
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: 1159
Number of HSP's gapped (non-prelim): 4
length of query: 513
length of database: 14,973,337
effective HSP length: 103
effective length of query: 410
effective length of database: 8,527,803
effective search space: 3496399230
effective search space used: 3496399230
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 bits)