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= 039271
         (609 letters)

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

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



>pdb|2XUT|A Chain A, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|B Chain B, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter.
 pdb|2XUT|C Chain C, Crystal Structure Of A Proton Dependent Oligopeptide (Pot)
           Family Transporter
          Length = 524

 Score = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 44/173 (25%), Positives = 73/173 (42%), Gaps = 30/173 (17%)

Query: 61  LLANQGLATLAFFGVGVNLVLFLTRVL------QQENANAANNVSKWTGTVYMCSLIGAF 114
           ++A++     +F+G+   L  FL   L      +   A A +    +   VY   L+G +
Sbjct: 17  IIASEACERFSFYGMRNILTPFLMTALLLSIPEELRGAVAKDVFHSFVIGVYFFPLLGGW 76

Query: 115 LSDSYWGRYLTCAVFQXXXXXXXXXXXXXXXXMIKPTGCGDGFISCKPLSSIFAAIFYLS 174
           ++D ++G+Y T                            G  F++    S      FY  
Sbjct: 77  IADRFFGKYNTILWLSLIYC------------------VGHAFLAIFEHS---VQGFYTG 115

Query: 175 IYLIAFGYGGHQPTLATFGADQFDESKPKERQSKTLFFCYFYFFLNVGSLFSN 227
           ++LIA G GG +P +++F  DQFD+S     Q     F  FYF +N GS F++
Sbjct: 116 LFLIALGSGGIKPLVSSFMGDQFDQSNKSLAQKA---FDMFYFTINFGSFFAS 165



 Score = 41.6 bits (96), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 92/237 (38%), Gaps = 37/237 (15%)

Query: 350 VEEAKCVLKMLPIWLCTIIYSVVFTQMASLFVEQGDVMNSHIGEFRLPAASMSAFDICSV 409
           V+  + VL++L ++     +  +F Q AS ++ Q    N  +       A M A +   V
Sbjct: 292 VDGVRSVLRILVLFALVTPFWSLFDQKASTWILQA---NDMVKPQWFEPAMMQALNPLLV 348

Query: 410 LICTGIYRKILVPVAGKLNGNPKGLSELQRXXXXXXXXXXXXXXXXXTEIQRLKYISPG- 468
           ++       +L P   ++      L ++                     I  L +I  G 
Sbjct: 349 MLLIPFNNFVLYPAIERMGVKLTALRKM----------------GAGIAITGLSWIVVGT 392

Query: 469 -----EKASSLSIFWQIPQYVLVGASEVFMYVGQLEFFNGQAPDGIKSFGSSLCMASISF 523
                +  S+LSIFWQI  Y L+   EV +    LEF   QAP  +K    S    S++ 
Sbjct: 393 IQLMMDGGSALSIFWQILPYALLTFGEVLVSATGLEFAYSQAPKAMKGTIMSFWTLSVTV 452

Query: 524 GNYVSSLLVVMVMGITAKGDKPGWIPDDLNTGH----MDRFYFL-LAVLTAFDFVIY 575
           GN     L V++  ++ K   P      + TG        F+F   A+L A  F +Y
Sbjct: 453 GN-----LWVLLANVSVK--SPTVTEQIVQTGMSVTAFQMFFFAGFAILAAIVFALY 502


>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd
          Finger Protein 3
          Length = 120

 Score = 31.2 bits (69), Expect = 1.8,   Method: Composition-based stats.
 Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 3  SVLNSTNQITLK-VTDENISTGQAQAANKNNKDEKKLTSFIRKNLIHEKNK 52
          SV +S   I +K +TD N+   + +AA    K EK+L SF R      KNK
Sbjct: 15 SVRHSLKDILMKRLTDSNLKVPEEKAAKVATKIEKELFSFFRDTDAKYKNK 65


>pdb|3SF4|A Chain A, Crystal Structure Of The Complex Between The Conserved
           Cell Polarity Proteins Inscuteable And Lgn
 pdb|3SF4|B Chain B, Crystal Structure Of The Complex Between The Conserved
           Cell Polarity Proteins Inscuteable And Lgn
 pdb|3SF4|C Chain C, Crystal Structure Of The Complex Between The Conserved
           Cell Polarity Proteins Inscuteable And Lgn
          Length = 406

 Score = 31.2 bits (69), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 26/59 (44%), Gaps = 4/59 (6%)

Query: 156 GFISCKPLSSIFA----AIFYLSIYLIAFGYGGHQPTLATFGADQFDESKPKERQSKTL 210
           G    K LS+I++    A FYL  Y  A  Y  H  TLA    DQ  E+K       TL
Sbjct: 39  GTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTL 97


>pdb|3RO2|A Chain A, Structures Of The LgnNUMA COMPLEX
          Length = 338

 Score = 30.8 bits (68), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 26/59 (44%), Gaps = 4/59 (6%)

Query: 156 GFISCKPLSSIFA----AIFYLSIYLIAFGYGGHQPTLATFGADQFDESKPKERQSKTL 210
           G    K LS+I++    A FYL  Y  A  Y  H  TLA    DQ  E+K       TL
Sbjct: 35  GTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTL 93


>pdb|4G2V|A Chain A, Structure Complex Of Lgn Binding With Frmpd1
          Length = 340

 Score = 30.8 bits (68), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 26/59 (44%), Gaps = 4/59 (6%)

Query: 156 GFISCKPLSSIFA----AIFYLSIYLIAFGYGGHQPTLATFGADQFDESKPKERQSKTL 210
           G    K LS+I++    A FYL  Y  A  Y  H  TLA    DQ  E+K       TL
Sbjct: 37  GTEDLKTLSAIYSQLGNAYFYLHDYAKALEYHHHDLTLARTIGDQLGEAKASGNLGNTL 95


  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    0.138    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,206,539
Number of Sequences: 62578
Number of extensions: 622134
Number of successful extensions: 1014
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1008
Number of HSP's gapped (non-prelim): 8
length of query: 609
length of database: 14,973,337
effective HSP length: 105
effective length of query: 504
effective length of database: 8,402,647
effective search space: 4234934088
effective search space used: 4234934088
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)