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= 011839
         (476 letters)

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

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



>pdb|4FE9|A Chain A, Crystal Structure Of Susf From Bacteroides
           Thetaiotaomicron
          Length = 470

 Score = 31.2 bits (69), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 18/64 (28%), Positives = 35/64 (54%)

Query: 204 RDESAALNMKRASLEERLKLLEADKDSWTQMESVSKETIAGLSVDITQLRMQVVELEESR 263
            D ++A  MK+ +L+E L +LEA+ +S +  +      I G  +D T+     V+ ++S 
Sbjct: 162 WDGNSAQQMKKDALDENLYILEAEIESTSNFKIFPASAINGNDIDWTKALGSSVDGDDSG 221

Query: 264 NNLL 267
           +N +
Sbjct: 222 DNFV 225


>pdb|2IUJ|A Chain A, Crystal Structure Of Soybean Lipoxygenase-B
          Length = 853

 Score = 30.4 bits (67), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 11/31 (35%), Positives = 22/31 (70%)

Query: 222 KLLEADKDSWTQMESVSKETIAGLSVDITQL 252
           K+++ DK +W   E  ++ETIAGL+ ++ ++
Sbjct: 344 KVMQVDKSAWMTDEEFARETIAGLNPNVIKI 374


>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
           Activator-Dependent Transcription Initiation Complex
          Length = 1413

 Score = 29.6 bits (65), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 42/93 (45%), Gaps = 8/93 (8%)

Query: 190 LQKEAALEQKISQLRDESAALN--MKRASLEERLKLLEADKDSWTQMESVSKETIAGLSV 247
           L K   LEQ+  QLR+E    N   KR  L +R+KLLEA   S  + E +    +  L  
Sbjct: 188 LLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPP 247

Query: 248 DITQL------RMQVVELEESRNNLLQENRQLK 274
           D+  L      R    +L +    ++  N +LK
Sbjct: 248 DLRPLVPLDGGRFATSDLNDLYRRVINRNNRLK 280


>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
 pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
           Holoenzyme
 pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
           Holoenzyme
          Length = 1407

 Score = 29.6 bits (65), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 42/93 (45%), Gaps = 8/93 (8%)

Query: 190 LQKEAALEQKISQLRDESAALN--MKRASLEERLKLLEADKDSWTQMESVSKETIAGLSV 247
           L K   LEQ+  QLR+E    N   KR  L +R+KLLEA   S  + E +    +  L  
Sbjct: 188 LLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPP 247

Query: 248 DITQL------RMQVVELEESRNNLLQENRQLK 274
           D+  L      R    +L +    ++  N +LK
Sbjct: 248 DLRPLVPLDGGRFATSDLNDLYRRVINRNNRLK 280


>pdb|1ZXJ|A Chain A, Crystal Structure Of The Hypthetical Mycoplasma Protein,
           Mpn555
 pdb|1ZXJ|B Chain B, Crystal Structure Of The Hypthetical Mycoplasma Protein,
           Mpn555
 pdb|1ZXJ|C Chain C, Crystal Structure Of The Hypthetical Mycoplasma Protein,
           Mpn555
 pdb|1ZXJ|D Chain D, Crystal Structure Of The Hypthetical Mycoplasma Protein,
           Mpn555
          Length = 218

 Score = 28.5 bits (62), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 28/106 (26%), Positives = 52/106 (49%), Gaps = 8/106 (7%)

Query: 68  AESANLAEAERQHLLQ----REAMAILEETVKHLRNERESHIQKEATLEGTVQQLQNECD 123
           AE  N+ E  ++ ++Q        AI E+ +K  +    +H+QKE  +E T + ++N   
Sbjct: 109 AELKNVMEGLKRDVIQGAEDNTVQAIAEKIIK--KALVFNHLQKEWKVEITDEVVKNVIS 166

Query: 124 LYKEKVQATLEETIQQLQRQNDLR--MQKEATLEETIKQLRNQNDL 167
           LY EK   ++ E +   Q+   +R  + +E  + ETI   +   +L
Sbjct: 167 LYYEKTNQSVREYLDDKQKFEGVRTALLEERMVLETINHFKFHFNL 212


  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
   0.307    0.124    0.320 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,012,300
Number of Sequences: 62578
Number of extensions: 391624
Number of successful extensions: 1298
Number of sequences better than 100.0: 55
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 47
Number of HSP's that attempted gapping in prelim test: 1257
Number of HSP's gapped (non-prelim): 84
length of query: 476
length of database: 14,973,337
effective HSP length: 102
effective length of query: 374
effective length of database: 8,590,381
effective search space: 3212802494
effective search space used: 3212802494
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 53 (25.0 bits)