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= psy4061
         (119 letters)

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

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



>pdb|2C9Y|A Chain A, Structure Of Human Adenylate Kinase 2
          Length = 242

 Score = 27.7 bits (60), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 12/32 (37%), Positives = 19/32 (59%)

Query: 46  LSGIPLLERSSDHKYRDNAKYQYYKKSTSPLI 77
           ++G PL+ RS D++     + Q Y   T+PLI
Sbjct: 168 ITGEPLIRRSDDNEKALKIRLQAYHTQTTPLI 199


>pdb|2WWB|A Chain A, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
           The Actively Translating Wheat Germ 80s Ribosome
          Length = 476

 Score = 27.7 bits (60), Expect = 1.7,   Method: Composition-based stats.
 Identities = 9/20 (45%), Positives = 13/20 (65%)

Query: 93  FILCCEYPLYDWMSEHPTDP 112
           F++CC+ PL+  MS    DP
Sbjct: 42  FLVCCQIPLFGIMSSDSADP 61


>pdb|3HNM|A Chain A, Crystal Structure Of Protein Bt_411 (Putative Chitobiase,
           Fragment 298-461) From Bacteroides Thetaiotaomicron,
           Northeast Structural Genomics Consortium Target Btr319d
 pdb|3HNM|B Chain B, Crystal Structure Of Protein Bt_411 (Putative Chitobiase,
           Fragment 298-461) From Bacteroides Thetaiotaomicron,
           Northeast Structural Genomics Consortium Target Btr319d
 pdb|3HNM|C Chain C, Crystal Structure Of Protein Bt_411 (Putative Chitobiase,
           Fragment 298-461) From Bacteroides Thetaiotaomicron,
           Northeast Structural Genomics Consortium Target Btr319d
 pdb|3HNM|D Chain D, Crystal Structure Of Protein Bt_411 (Putative Chitobiase,
           Fragment 298-461) From Bacteroides Thetaiotaomicron,
           Northeast Structural Genomics Consortium Target Btr319d
          Length = 172

 Score = 27.3 bits (59), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 5/46 (10%)

Query: 62  DNAKYQYYKKSTSPLIPIPPSVYVEVP----KFLKFILCCEYPLYD 103
           DN  +   K  TSP I   P+V  +VP    ++++F++   YP YD
Sbjct: 107 DNENWVKLKDWTSPKIG-EPNVNXDVPATQARYIRFVITDTYPTYD 151


>pdb|1AK2|A Chain A, Adenylate Kinase Isoenzyme-2
 pdb|2AK2|A Chain A, Adenylate Kinase Isoenzyme-2
          Length = 233

 Score = 26.9 bits (58), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 11/32 (34%), Positives = 19/32 (59%)

Query: 46  LSGIPLLERSSDHKYRDNAKYQYYKKSTSPLI 77
           ++G PL+ RS D+K     + + Y   T+PL+
Sbjct: 168 ITGEPLIRRSDDNKKALKIRLEAYHTQTTPLV 199


>pdb|3VF1|A Chain A, Structure Of A Calcium-Dependent 11r-Lipoxygenase Suggests
           A Mechanism For Ca-Regulation
 pdb|3VF1|B Chain B, Structure Of A Calcium-Dependent 11r-Lipoxygenase Suggests
           A Mechanism For Ca-Regulation
          Length = 698

 Score = 26.9 bits (58), Expect = 2.9,   Method: Composition-based stats.
 Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 37  IFITLIILFLSGIPLLERSSDHKYRDNAKYQYYKKSTSPLIPIPPSVY 84
           IFIT   + L GIP ++   D +Y       +Y K+   +IPI   +Y
Sbjct: 306 IFITDYKI-LEGIPTMDTPEDKRYITTPLGLFYLKNNDDIIPIAIQLY 352


  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
   0.325    0.143    0.473 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,942,007
Number of Sequences: 62578
Number of extensions: 146385
Number of successful extensions: 296
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 292
Number of HSP's gapped (non-prelim): 6
length of query: 119
length of database: 14,973,337
effective HSP length: 81
effective length of query: 38
effective length of database: 9,904,519
effective search space: 376371722
effective search space used: 376371722
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)