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= psy1734
         (610 letters)

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

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



>pdb|3M8J|A Chain A, Crystal Structure Of E.Coli Focb At 1.4 A Resolution
 pdb|3M8J|B Chain B, Crystal Structure Of E.Coli Focb At 1.4 A Resolution
          Length = 111

 Score = 31.2 bits (69), Expect = 1.8,   Method: Composition-based stats.
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 425 LSSLRFMRKIIAMKDDFYNRYIIKGHLFQPVIDTFNRNKGRYN-LLDSAEDIKVLCSHVV 483
           +SS+   R I+AMKD     Y++ GH  + V + +  N G ++  L     + VL + + 
Sbjct: 41  ISSIHSDRVILAMKD-----YLVSGHSRKDVCEKYQMNNGYFSTTLGRLTRLNVLVARLA 95

Query: 484 ETYGDELESI 493
             Y D + +I
Sbjct: 96  PYYTDSVSAI 105


>pdb|3BGH|A Chain A, Crystal Structure Of Putative Neuraminyllactose-Binding
           Hemagglutinin Homolog From Helicobacter Pylori
 pdb|3BGH|B Chain B, Crystal Structure Of Putative Neuraminyllactose-Binding
           Hemagglutinin Homolog From Helicobacter Pylori
          Length = 236

 Score = 29.6 bits (65), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 49/93 (52%), Gaps = 14/93 (15%)

Query: 12  TLLLESKIQTDT----AYQKQQDT-----LIVWSERDNYDLALSFQEKAGC-DEIWEKIC 61
            +L+E KI+ +     +YQK+ +      L  + ER  Y ++  F++ +    +I EK  
Sbjct: 39  VVLIEPKIEINKVIPESYQKEFEKSLFLQLSSFLERKGYSVS-QFKDASEIPQDIKEKAL 97

Query: 62  QVQGKDPSVEITQDIIEESE---DERFDDMSDG 91
            V   D +V I +DI+EES+   +E+  DMS G
Sbjct: 98  LVLRMDGNVAILEDIVEESDALSEEKVIDMSSG 130



 Score = 29.6 bits (65), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 49/93 (52%), Gaps = 14/93 (15%)

Query: 252 TLLLESKIQTDT----AYQKQQDT-----LIVWSERDNYDLALSFQEKAGC-DEIWEKIC 301
            +L+E KI+ +     +YQK+ +      L  + ER  Y ++  F++ +    +I EK  
Sbjct: 39  VVLIEPKIEINKVIPESYQKEFEKSLFLQLSSFLERKGYSVS-QFKDASEIPQDIKEKAL 97

Query: 302 QVQGKDPSVEITQDIIEESE---DERFDDMSDG 331
            V   D +V I +DI+EES+   +E+  DMS G
Sbjct: 98  LVLRMDGNVAILEDIVEESDALSEEKVIDMSSG 130


>pdb|1G5C|A Chain A, Crystal Structure Of The 'cab' Type Beta Class Carbonic
           Anhydrase From Methanobacterium Thermoautotrophicum
 pdb|1G5C|B Chain B, Crystal Structure Of The 'cab' Type Beta Class Carbonic
           Anhydrase From Methanobacterium Thermoautotrophicum
 pdb|1G5C|C Chain C, Crystal Structure Of The 'cab' Type Beta Class Carbonic
           Anhydrase From Methanobacterium Thermoautotrophicum
 pdb|1G5C|D Chain D, Crystal Structure Of The 'cab' Type Beta Class Carbonic
           Anhydrase From Methanobacterium Thermoautotrophicum
 pdb|1G5C|E Chain E, Crystal Structure Of The 'cab' Type Beta Class Carbonic
           Anhydrase From Methanobacterium Thermoautotrophicum
 pdb|1G5C|F Chain F, Crystal Structure Of The 'cab' Type Beta Class Carbonic
           Anhydrase From Methanobacterium Thermoautotrophicum
          Length = 170

 Score = 28.9 bits (63), Expect = 8.5,   Method: Composition-based stats.
 Identities = 16/41 (39%), Positives = 26/41 (63%), Gaps = 2/41 (4%)

Query: 72  ITQDIIEESEDERFDDMSD--GSPPIELPPCEINRLEEIKE 110
           I +DI+ E++D RF D+SD   SP + +  C  +RL ++ E
Sbjct: 2   IIKDILRENQDFRFRDLSDLKHSPKLCIITCMDSRLIDLLE 42



 Score = 28.9 bits (63), Expect = 8.5,   Method: Composition-based stats.
 Identities = 16/41 (39%), Positives = 26/41 (63%), Gaps = 2/41 (4%)

Query: 312 ITQDIIEESEDERFDDMSD--GSPPIELPPCEINRLEEIKE 350
           I +DI+ E++D RF D+SD   SP + +  C  +RL ++ E
Sbjct: 2   IIKDILRENQDFRFRDLSDLKHSPKLCIITCMDSRLIDLLE 42


  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    0.134    0.388 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,930,890
Number of Sequences: 62578
Number of extensions: 660320
Number of successful extensions: 1614
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1612
Number of HSP's gapped (non-prelim): 7
length of query: 610
length of database: 14,973,337
effective HSP length: 105
effective length of query: 505
effective length of database: 8,402,647
effective search space: 4243336735
effective search space used: 4243336735
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: 54 (25.4 bits)