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= 004728
         (733 letters)

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

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



>pdb|3O4L|D Chain D, Genetic And Structural Basis For Selection Of A Ubiquitous
           T Cell Receptor Deployed In Epstein-Barr Virus
          Length = 195

 Score = 30.8 bits (68), Expect = 2.5,   Method: Composition-based stats.
 Identities = 29/104 (27%), Positives = 46/104 (44%), Gaps = 4/104 (3%)

Query: 52  RRKVDQANRCRAQLRQAIADSEADLAAICSAMGERPVHIRQSDQTAESLKEELRRILPQV 111
           +RK    N+    L   IAD++   +AI     +    +   D T   +K  ++   P V
Sbjct: 54  QRKTVLLNKKDKHLSLRIADTQTGDSAIYFCAEDNNARLMFGDGTQLVVKPNIQNPDPAV 113

Query: 112 EEMRKRKSDRKK--QFVDVLEQIEMIKSEILGSTVYISSKTVVD 153
            ++R  KS  K    F D   Q  + +S+   S VYI+ K V+D
Sbjct: 114 YQLRDSKSSDKSVCLFTDFDSQTNVSQSK--DSDVYITDKCVLD 155


>pdb|4HPQ|C Chain C, Crystal Structure Of The Atg17-Atg31-Atg29 Complex
 pdb|4HPQ|F Chain F, Crystal Structure Of The Atg17-Atg31-Atg29 Complex
          Length = 413

 Score = 29.6 bits (65), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 25/90 (27%), Positives = 49/90 (54%), Gaps = 3/90 (3%)

Query: 108 LPQVEEMRKRKSDRKKQFVDVLEQIE--MIKSEILGSTVYISSKTVVDDADLSLRKLEEF 165
           L ++  +RK+  +  +Q+  +L +++  +++S + G     SSK   D    +L+  EEF
Sbjct: 137 LNEIPTIRKQVENITRQYQTMLAKVQSQLVESRMKGLRDEFSSK-FGDQCRENLKLNEEF 195

Query: 166 HRELHELQKEKSNRLKQVQDHLNTLSSLCS 195
             E  +L++E ++ LK   DH +  S+L S
Sbjct: 196 TNEADQLEQELADFLKSFTDHFDKCSALSS 225


>pdb|3HM6|X Chain X, Crystal Structure Of The Cytoplasmic Domain Of Human
           Plexin B1
          Length = 644

 Score = 29.3 bits (64), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 38/161 (23%), Positives = 72/161 (44%), Gaps = 29/161 (18%)

Query: 103 ELRRILPQVEEMRKRKSDR-KKQFVDVLEQIEMIKSEILGSTV-YISSKTVVDDADLSLR 160
           + +++  Q+E +     DR KK+F D++ ++  + S++LGS + ++  K   +      R
Sbjct: 30  DYKKVQIQLENLESSVRDRCKKEFTDLMTEMTDLTSDLLGSGIPFLDYKVYAE------R 83

Query: 161 KLEEFHRE--LHELQKEKSNRLKQVQDHLNTLSSLCS--VLGIDFKHTVSDIHPSFCENE 216
                HRE  LH       +R   V+  L  LS+L +  +    F HT+        E +
Sbjct: 84  IFFPGHRESPLHRDLGVPESRRPTVEQGLGQLSNLLNSKLFLTKFIHTL--------ETQ 135

Query: 217 GSMSISNDAI--ERLTIAIHKLREVKIQRMQKLQDLATTML 255
            + S  + A     LT+A+H        +++   D+  T+L
Sbjct: 136 RTFSARDRAYVASLLTVALHG-------KLEYFTDILRTLL 169


>pdb|3SUA|D Chain D, Crystal Structure Of The Intracellular Domain Of Plexin-B1
           In Complex With Rac1
 pdb|3SUA|E Chain E, Crystal Structure Of The Intracellular Domain Of Plexin-B1
           In Complex With Rac1
 pdb|3SUA|F Chain F, Crystal Structure Of The Intracellular Domain Of Plexin-B1
           In Complex With Rac1
          Length = 633

 Score = 29.3 bits (64), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 38/161 (23%), Positives = 72/161 (44%), Gaps = 29/161 (18%)

Query: 103 ELRRILPQVEEMRKRKSDR-KKQFVDVLEQIEMIKSEILGSTV-YISSKTVVDDADLSLR 160
           + +++  Q+E +     DR KK+F D++ ++  + S++LGS + ++  K   +      R
Sbjct: 19  DYKKVQIQLENLESSVRDRCKKEFTDLMTEMTDLTSDLLGSGIPFLDYKVYAE------R 72

Query: 161 KLEEFHRE--LHELQKEKSNRLKQVQDHLNTLSSLCS--VLGIDFKHTVSDIHPSFCENE 216
                HRE  LH       +R   V+  L  LS+L +  +    F HT+        E +
Sbjct: 73  IFFPGHRESPLHRDLGVPESRRPTVEQGLGQLSNLLNSKLFLTKFIHTL--------ETQ 124

Query: 217 GSMSISNDAI--ERLTIAIHKLREVKIQRMQKLQDLATTML 255
            + S  + A     LT+A+H        +++   D+  T+L
Sbjct: 125 RTFSARDRAYVASLLTVALHG-------KLEYFTDILRTLL 158


>pdb|3UK2|A Chain A, The Structure Of Pantothenate Synthetase From Burkholderia
           Thailandensis
 pdb|3UK2|B Chain B, The Structure Of Pantothenate Synthetase From Burkholderia
           Thailandensis
          Length = 283

 Score = 28.9 bits (63), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 27/91 (29%), Positives = 41/91 (45%), Gaps = 11/91 (12%)

Query: 8   LLQVETTCGSLLYELQIIWDEVGETDTDRDKMLLELEQECL-EVYRRKVDQANRCRAQLR 66
           L+ V   C  L   ++I+     ET  D D + L      L E  R +  +  +  A++R
Sbjct: 155 LMIVRRMCQQLALPVEIV---AAETVRDADGLALSSRNRYLSEAERAEAPELAKTLARVR 211

Query: 67  QAIADSEADLAAI-------CSAMGERPVHI 90
            A+ D E DLAAI        SA G +P ++
Sbjct: 212 DAVLDGERDLAAIERRAVAHLSARGWQPDYV 242


  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
   0.313    0.129    0.359 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,705,649
Number of Sequences: 62578
Number of extensions: 694503
Number of successful extensions: 1613
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 1605
Number of HSP's gapped (non-prelim): 26
length of query: 733
length of database: 14,973,337
effective HSP length: 106
effective length of query: 627
effective length of database: 8,340,069
effective search space: 5229223263
effective search space used: 5229223263
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.8 bits)