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= 010873
         (498 letters)

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

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



>pdb|1UL4|A Chain A, Solution Structure Of The Dna-Binding Domain Of Squamosa
           Promoter Binding Protein-Like 4
          Length = 94

 Score =  113 bits (282), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 53/83 (63%), Positives = 63/83 (75%)

Query: 171 TSSCSQTPLCQVYGCNKDLSSSKDYHKRHKVCDVHSKTPKVIVNGNEQRFCQQCSRFHLL 230
           +S  S   LCQV  C  D+  +K YH+RHKVC+VH+K   V ++G  QRFCQQCSRFH L
Sbjct: 2   SSGSSGLRLCQVDRCTADMKEAKLYHRRHKVCEVHAKASSVFLSGLNQRFCQQCSRFHDL 61

Query: 231 AEFDDSKRSCRRRLAGHNERRRK 253
            EFD++KRSCRRRLAGHNERRRK
Sbjct: 62  QEFDEAKRSCRRRLAGHNERRRK 84


>pdb|1UL5|A Chain A, Solution Structure Of The Dna-binding Domain Of Squamosa
           Promoter Binding Protein-like 7
          Length = 88

 Score = 90.9 bits (224), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 41/76 (53%), Positives = 53/76 (69%), Gaps = 1/76 (1%)

Query: 180 CQVYGCNKDLSSSKDYHKRHKVCDVHSKTPKVIVNGNEQRFCQQCSRFHLLAEFDDSKRS 239
           CQV  C  D+S  K YHKRH+VC   +    V+++G  +R+CQQC +FHLL +FD+ KRS
Sbjct: 6   CQVPDCEADISELKGYHKRHRVCLRCATASFVVLDGENKRYCQQCGKFHLLPDFDEGKRS 65

Query: 240 CRRRLAGHNERR-RKP 254
           CRR+L  HN RR RKP
Sbjct: 66  CRRKLERHNNRRKRKP 81


>pdb|1WJ0|A Chain A, Solution Structure Of The Dna-Binding Domain Of Squamosa
           Promoter Binding Protein-Like 12 Lacking The Second
           Zinc- Binding Site
          Length = 60

 Score = 86.3 bits (212), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 36/55 (65%), Positives = 41/55 (74%)

Query: 180 CQVYGCNKDLSSSKDYHKRHKVCDVHSKTPKVIVNGNEQRFCQQCSRFHLLAEFD 234
           CQV  C  DLS  KDYH+RHKVC++HSK    +V G  QRFCQQCSRFH+L EFD
Sbjct: 6   CQVDNCGADLSKVKDYHRRHKVCEIHSKATTALVGGIMQRFCQQCSRFHVLEEFD 60


>pdb|2PGX|A Chain A, Crystal Structure Of Upf0341 Protein Yhiq From E. Coli,
           Northeast Structural Genomics Target Er585
          Length = 258

 Score = 31.2 bits (69), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 277 SFVYPDMLPGGILFPERYEPVKQIKFSERPPYSPQLAVPNTNEQLLTKS---SLYQGN 331
           S V PD+   G+L P R    K++   +RP Y+P LA   T   ++TK     +Y G 
Sbjct: 192 SLVGPDLDADGLLEPARLLATKRV-VVKRPDYAPPLANVATPNAVVTKGHRFDIYAGT 248


>pdb|2OYR|A Chain A, Crystal Structure Of Upf0341 Protein (Yhiq) From Shigella
           Flexneri In Complex With S-Adenosyl Homocysteine,
           Northeast Structural Genomics Target Sfr275
          Length = 258

 Score = 31.2 bits (69), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 277 SFVYPDMLPGGILFPERYEPVKQIKFSERPPYSPQLAVPNTNEQLLTKS---SLYQGN 331
           S V PD+   G+L P R    K++   +RP Y+P LA   T   ++TK     +Y G 
Sbjct: 192 SLVGPDLDADGLLEPARLLATKRV-VVKRPDYAPPLANVATPNAVVTKGHRFDIYAGT 248


>pdb|2PKW|A Chain A, Crystal Structure Of Upf0341 Protein Yhiq From Salmonella
           Typhimurium, Northeast Structural Genomics Consortium
           Target Str221
          Length = 260

 Score = 30.8 bits (68), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 32/70 (45%), Gaps = 10/70 (14%)

Query: 277 SFVYPDMLPGGILFPERYEPVKQIKFSERPPYSPQLAVPNTNEQLLTKSSLYQGNKKQHR 336
           S V PD+   G+L P R    K++   +RP Y+P LA   T   ++TK          HR
Sbjct: 192 SLVGPDLDADGLLEPARQLATKRV-VVKRPDYAPPLADVATPNAIVTKG---------HR 241

Query: 337 LAIPLDTALT 346
             I   T LT
Sbjct: 242 FDIYAGTPLT 251


  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
   0.316    0.131    0.393 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,333,225
Number of Sequences: 62578
Number of extensions: 566481
Number of successful extensions: 1045
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: 1042
Number of HSP's gapped (non-prelim): 6
length of query: 498
length of database: 14,973,337
effective HSP length: 103
effective length of query: 395
effective length of database: 8,527,803
effective search space: 3368482185
effective search space used: 3368482185
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)