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= psy7924
         (481 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 =  120 bits (302), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 83/285 (29%), Positives = 147/285 (51%), Gaps = 34/285 (11%)

Query: 187 IFFVGLMLLMPESPQFHLKKNRVKQAKESLQWFRGSEYDIDSEITDMQNSLEKERSDKVP 246
           + F+ L+  +PESP++ + + + +QA+  L+   G+     + + ++++SL+  R     
Sbjct: 211 LLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLATQA-VQEIKHSLDHGRKT--- 266

Query: 247 LMQAFSTPAAKRGLLIGLGVMFI-------QQFGGINAVVFYTVKIFKDAGSSLNPNLCX 299
                      R L+ G+GV+ I       QQF GIN V++Y  ++FK  G+S +  L  
Sbjct: 267 ---------GGRLLMFGVGVIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIALLQ 317

Query: 300 XXXX-XXXXXXXXXATMIVDRLGRRILLLVSAVIMALSTLTMGYYFYLKNSGSDVSNIGW 358
                         A M VD+ GR+ L ++ A+ MA+   ++G  FY +  G        
Sbjct: 318 TIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGI------- 370

Query: 359 LPLGSLCVFIIVFSLGFGPIPWMLVGEIFPSQIKGIAVSIACLFNWVSVLVVTKFF---- 414
           + L S+  ++  F++ +GP+ W+L+ EIFP+ I+G A++IA    W++   V+  F    
Sbjct: 371 VALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMD 430

Query: 415 GDVTLLLGGHGAF--WIFSVIAALGAVFTYILVPETKGKTLDEIQ 457
            +  L+   H  F  WI+  +  L A+F +  VPETKGKTL+E++
Sbjct: 431 KNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELE 475


>pdb|3E1Y|A Chain A, Crystal Structure Of Human Erf1ERF3 COMPLEX
 pdb|3E1Y|B Chain B, Crystal Structure Of Human Erf1ERF3 COMPLEX
 pdb|3E1Y|C Chain C, Crystal Structure Of Human Erf1ERF3 COMPLEX
 pdb|3E1Y|D Chain D, Crystal Structure Of Human Erf1ERF3 COMPLEX
          Length = 451

 Score = 30.4 bits (67), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 228 SEITDMQNSLEKERSDKVPLMQAFSTPAAKRGLLIGL-------GVMFIQQFGGINAVVF 280
           S  TD +   E E  + +PL++ F+    K G  + +       G  F++ FGGI  ++ 
Sbjct: 369 SHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILR 428

Query: 281 YTV 283
           Y V
Sbjct: 429 YRV 431


>pdb|2KTU|A Chain A, Human Erf1 C-Domain, "closed" Conformer
 pdb|2KTV|A Chain A, Human Erf1 C-Domain, "open" Conformer
          Length = 170

 Score = 30.4 bits (67), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 228 SEITDMQNSLEKERSDKVPLMQAFSTPAAKRGLLIGL-------GVMFIQQFGGINAVVF 280
           S  TD +   E E  + +PL++ F+    K G  + +       G  F++ FGGI  ++ 
Sbjct: 80  SHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILR 139

Query: 281 YTV 283
           Y V
Sbjct: 140 YRV 142


>pdb|1DT9|A Chain A, The Crystal Structure Of Human Eukaryotic Release Factor
           Erf1-Mechanism Of Stop Codon Recognition And
           Peptidyl-Trna Hydrolysis
          Length = 437

 Score = 30.4 bits (67), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 228 SEITDMQNSLEKERSDKVPLMQAFSTPAAKRGLLIGL-------GVMFIQQFGGINAVVF 280
           S  TD +   E E  + +PL++ F+    K G  + +       G  F++ FGGI  ++ 
Sbjct: 355 SHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILR 414

Query: 281 YTV 283
           Y V
Sbjct: 415 YRV 417


>pdb|3J2K|6 Chain 6, Cryo-Em Structure Of The Mammalian Erf1-Erf3-Associated
           Termination Complex
          Length = 411

 Score = 30.4 bits (67), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 228 SEITDMQNSLEKERSDKVPLMQAFSTPAAKRGLLIGL-------GVMFIQQFGGINAVVF 280
           S  TD +   E E  + +PL++ F+    K G  + +       G  F++ FGGI  ++ 
Sbjct: 346 SHFTDKETGQEHELIESMPLLEWFANNYKKFGATLEIVTDKSQEGSQFVKGFGGIGGILR 405

Query: 281 YTV 283
           Y V
Sbjct: 406 YRV 408


  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    0.140    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,860,780
Number of Sequences: 62578
Number of extensions: 493169
Number of successful extensions: 977
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 972
Number of HSP's gapped (non-prelim): 7
length of query: 481
length of database: 14,973,337
effective HSP length: 103
effective length of query: 378
effective length of database: 8,527,803
effective search space: 3223509534
effective search space used: 3223509534
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: 53 (25.0 bits)