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= 029845
         (186 letters)

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

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



>pdb|3K11|A Chain A, Crystal Structure Of Putative Glycosyl Hydrolase
           (Np_813087.1) From Bacteroides Thetaiotaomicron Vpi-5482
           At 1.80 A Resolution
          Length = 445

 Score = 28.1 bits (61), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 99  NRIMNLHAPEWSGEVRNITYSADGKTVSVVYRVTIYGTDAEIFRESTGTALVDEQGYGDA 158
           N  ++L  P + G   ++T     K +  V+      T A +  ++TG  + D    GD 
Sbjct: 10  NTPLHLLQPAYQGTYGDLTPEQVKKDIDRVFAYIDKETPARVVDKNTGKVITDYTAXGDE 69

Query: 159 VQKAEAMAFRRACARFGL 176
            Q  E  AFR A   +G+
Sbjct: 70  AQ-LERGAFRLASYEWGV 86


>pdb|4H5I|A Chain A, Crystal Structure Of The Guanine Nucleotide Exchange
           Factor Sec12 (P1 Form)
 pdb|4H5I|B Chain B, Crystal Structure Of The Guanine Nucleotide Exchange
           Factor Sec12 (P1 Form)
 pdb|4H5J|A Chain A, Crystal Structure Of The Guanine Nucleotide Exchange
           Factor Sec12 (P64 Form)
 pdb|4H5J|B Chain B, Crystal Structure Of The Guanine Nucleotide Exchange
           Factor Sec12 (P64 Form)
          Length = 365

 Score = 26.9 bits (58), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 5/48 (10%)

Query: 108 EWSGEVRNITYSADGKTVSVVYRVTIYGTDAEIFRESTGTALVDEQGY 155
           E  GEV+++ +S DGK V+      I G+  E+    TG+ +  +  +
Sbjct: 174 ETRGEVKDLHFSTDGKVVAY-----ITGSSLEVISTVTGSCIARKTDF 216


>pdb|2CXH|A Chain A, Crystal Structure Of Probable Ribosomal Biogenesis Protein
           From Aeropyrum Pernix K1
          Length = 217

 Score = 26.6 bits (57), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 13/52 (25%), Positives = 27/52 (51%)

Query: 79  LIKIRVEDGFSMKYIPWHIVNRIMNLHAPEWSGEVRNITYSADGKTVSVVYR 130
           L+   ++ G ++++    ++     L  PE +G V  +  S D +TV+V +R
Sbjct: 141 LVARPLDSGVAVEFADAFVIAFHARLKPPEAAGYVEAVIESLDARTVAVTFR 192


>pdb|2PNZ|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
           Complexed With Udp And Gmp
 pdb|2PO0|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
           Complexed With Adp In Double Conformation
 pdb|2PO1|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
           Complexed With A Single Stranded 10-Mer Poly(A) Rna
 pdb|2PO2|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
           Complexed With Cdp
          Length = 277

 Score = 26.6 bits (57), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 18/32 (56%)

Query: 137 DAEIFRESTGTALVDEQGYGDAVQKAEAMAFR 168
           D E+  +   T   DE G+  AVQK+E  AF+
Sbjct: 215 DEELVMDGKITITTDETGHISAVQKSEGGAFK 246


  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
   0.317    0.133    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,677,876
Number of Sequences: 62578
Number of extensions: 176897
Number of successful extensions: 364
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: 361
Number of HSP's gapped (non-prelim): 6
length of query: 186
length of database: 14,973,337
effective HSP length: 93
effective length of query: 93
effective length of database: 9,153,583
effective search space: 851283219
effective search space used: 851283219
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)