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= 016653
         (385 letters)

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

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



>pdb|4B4T|R Chain R, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 429

 Score =  259 bits (661), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 149/411 (36%), Positives = 234/411 (56%), Gaps = 51/411 (12%)

Query: 13  LAHKRFLLTHPDVQDIEKVGLKGE-VFSMVKAHDMASFYETLVAESV------------- 58
           ++ K FLLT   V  IE+     E V + +K  +MA +Y+ L  E +             
Sbjct: 26  VSEKAFLLTQSKVS-IEQRKEAAEFVLAKIKEEEMAPYYKYLCEEYLVNNGQSDLEHDEK 84

Query: 59  -------LEMDQSVLDSMRTKIEDELKKLDDRI-------------ADAEENLGESEVRE 98
                  ++ DQ + + +  K E ++K+L+++I             A A  NLGE     
Sbjct: 85  SDSLNEWIKFDQELYNELCKKNESKIKELNEKIQKLEEDDEGELEQAQAWINLGE----- 139

Query: 99  AHLAKSLFYIQIGDKEKALEQLKVTESKTVAVGQKMDLVFYTLQLGFFYMDFDLISKSID 158
                  +Y QIGDK+ A + L  + SK ++ G K+D++    +LGFFY D   + + ++
Sbjct: 140 -------YYAQIGDKDNAEKTLGKSLSKAISTGAKIDVMLTIARLGFFYNDQLYVKEKLE 192

Query: 159 KAKSLFEEGGDWERKNRLKVYEGLYCMSTRNFKKAASLFLDSISTFTTYELFPYDTFIFY 218
              S+ E+GGDWER+NR K Y G++C++ RNFK+AA L +DS++TFT+ EL  Y++   Y
Sbjct: 193 AVNSMIEKGGDWERRNRYKTYYGIHCLAVRNFKEAAKLLVDSLATFTSIELTSYESIATY 252

Query: 219 TVLTSIISLDRVSLKQKVVDAPEILTVIGKIPYL---SEFLNSLYDCQYKSFFSAFAGLT 275
             +T + +L+R  LK KV+D+PE+L++I     L   S    SLY   Y S+F       
Sbjct: 253 ASVTGLFTLERTDLKSKVIDSPELLSLISTTAALQSISSLTISLYASDYASYFPYLLETY 312

Query: 276 EQIKLD-RYLYPHFRYYMREVRTVVYSQFLESYKSVTIEAMAKAFGVTVEFIDVELSRFI 334
             + +  +YL  H  +++RE+R  VY+Q LESYK++++++MA AFGV+V F+D +L +FI
Sbjct: 313 ANVLIPCKYLNRHADFFVREMRRKVYAQLLESYKTLSLKSMASAFGVSVAFLDNDLGKFI 372

Query: 335 AAGKLHCKIDKVAGVLETNRPDAKNALYQATIKQGDFLLNRIQKLSRVIDL 385
              +L+C ID+V G++ETNRPD KNA Y   +KQGD LL ++QK    + L
Sbjct: 373 PNKQLNCVIDRVNGIVETNRPDNKNAQYHLLVKQGDGLLTKLQKYGAAVRL 423


>pdb|1NYQ|A Chain A, Structure Of Staphylococcus Aureus Threonyl-Trna
           Synthetase Complexed With An Analogue Of Threonyl
           Adenylate
 pdb|1NYQ|B Chain B, Structure Of Staphylococcus Aureus Threonyl-Trna
           Synthetase Complexed With An Analogue Of Threonyl
           Adenylate
 pdb|1NYR|A Chain A, Structure Of Staphylococcus Aureus Threonyl-Trna
           Synthetase Complexed With Atp
 pdb|1NYR|B Chain B, Structure Of Staphylococcus Aureus Threonyl-Trna
           Synthetase Complexed With Atp
          Length = 645

 Score = 30.0 bits (66), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 3/55 (5%)

Query: 72  KIEDELKKLDDRIA--DAEENLGESEVREAHLAKSLFYIQIGDKEKALEQLKVTE 124
           +++DELK    R++  D  E +G  ++REA + K  + I +GDKE    Q+ V +
Sbjct: 564 QLQDELKSQGVRVSIDDRNEKMG-YKIREAQMQKIPYQIVVGDKEVENNQVNVRQ 617


  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
   0.321    0.136    0.379 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,037,334
Number of Sequences: 62578
Number of extensions: 388012
Number of successful extensions: 1061
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1049
Number of HSP's gapped (non-prelim): 16
length of query: 385
length of database: 14,973,337
effective HSP length: 101
effective length of query: 284
effective length of database: 8,652,959
effective search space: 2457440356
effective search space used: 2457440356
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)