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= psy8908
         (137 letters)

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

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



>pdb|2PTF|A Chain A, Crystal Structure Of Protein Mth_863 From Methanobacterium
           Thermoautotrophicum Bound To Fmn
 pdb|2PTF|B Chain B, Crystal Structure Of Protein Mth_863 From Methanobacterium
           Thermoautotrophicum Bound To Fmn
          Length = 233

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 3/47 (6%)

Query: 2   TENVENSLSNKMTSLSTSTSSFEPMISHDPRLNELATNMFKKTADYL 48
           T  VEN L+N   +++ +    +P+I  D  L +L  +MF    D+L
Sbjct: 72  TRTVENVLNNGRFTVNVT---LDPLIFTDSTLGDLEEDMFSHYRDFL 115


>pdb|3GAA|A Chain A, The Crystal Structure Of The Protein With Unknown Function
           From Thermoplasma Acidophilum
 pdb|3GAA|B Chain B, The Crystal Structure Of The Protein With Unknown Function
           From Thermoplasma Acidophilum
 pdb|3GAA|C Chain C, The Crystal Structure Of The Protein With Unknown Function
           From Thermoplasma Acidophilum
 pdb|3GAA|D Chain D, The Crystal Structure Of The Protein With Unknown Function
           From Thermoplasma Acidophilum
 pdb|3GAA|E Chain E, The Crystal Structure Of The Protein With Unknown Function
           From Thermoplasma Acidophilum
          Length = 252

 Score = 27.3 bits (59), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 24/88 (27%), Positives = 47/88 (53%), Gaps = 9/88 (10%)

Query: 57  ADYEVLEKMNNATITKYSDMKQITVNISF---SSARVPAYKQLIPQLEQIDQIYDSVLK- 112
           AD  ++  M    + +   +++IT  +SF   +S  +P    ++  +E I++ Y+  +K 
Sbjct: 159 ADSAIIAGMGGGILNE-CLVRKIT-GLSFITPTSVDIPDPGAVLSIIEAINKAYNLKIKT 216

Query: 113 --LEQAAYKLDHYAKRLEAKFKQL-EKQ 137
             LE+    LD   K++E ++K+L EKQ
Sbjct: 217 DLLEEQVKALDEQIKKIEEQYKELQEKQ 244


>pdb|2JFN|A Chain A, Crystal Structure Of Escherichia Coli Glutamate Racemase
           In Complex With L-Glutamate And Activator Udp-Murnac-Ala
          Length = 285

 Score = 26.9 bits (58), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 75  DMKQITVNISFSSARVPAYKQLIPQLEQ 102
           D K    NI+F  A  P  +QL+P L++
Sbjct: 245 DAKSADANIAFCMAMTPGAEQLLPVLQR 272


>pdb|1O7X|A Chain A, Citrate Synthase From Sulfolobus Solfataricus
 pdb|1O7X|B Chain B, Citrate Synthase From Sulfolobus Solfataricus
 pdb|1O7X|C Chain C, Citrate Synthase From Sulfolobus Solfataricus
 pdb|1O7X|D Chain D, Citrate Synthase From Sulfolobus Solfataricus
          Length = 377

 Score = 26.2 bits (56), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 8/88 (9%)

Query: 5   VENSLSNKMTSLSTSTSSFEPMI--SHDPRLNELATNMFKKTADYLIGELSSTQADYEVL 62
           V+N  ++K+ +       F   +  ++DPR       +FKK A  LI   +  +  +E+ 
Sbjct: 238 VQNWFNDKVVNQKNRLMGFGHRVYKTYDPR-----AKIFKKLALTLIERNADARRYFEIA 292

Query: 63  EKMNNATITKYSDMKQITVNISFSSARV 90
           +K+    I ++S  K I  N  F S  V
Sbjct: 293 QKLEELGIKQFSS-KGIYPNTDFYSGIV 319


>pdb|1R6F|A Chain A, The Structure Of Yersinia Pestis V-Antigen, An Essential
           Virulence Factor And Mediator Of Immunity Against Plague
          Length = 310

 Score = 25.4 bits (54), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 4/42 (9%)

Query: 29  HDPRLNELATNMFKKTADYLIGELSSTQADYEVLEKMNNATI 70
           HD  +N +  N++  T +    E+    A+Y++LEKM   TI
Sbjct: 165 HDKSINLMDKNLYGYTDE----EIFKASAEYKILEKMPQTTI 202


  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
   0.310    0.123    0.319 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,254,087
Number of Sequences: 62578
Number of extensions: 106897
Number of successful extensions: 282
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 279
Number of HSP's gapped (non-prelim): 14
length of query: 137
length of database: 14,973,337
effective HSP length: 89
effective length of query: 48
effective length of database: 9,403,895
effective search space: 451386960
effective search space used: 451386960
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 46 (22.3 bits)