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= psy13859
         (108 letters)

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

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



>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
           Bound To Amppnp
          Length = 997

 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/86 (39%), Positives = 47/86 (54%), Gaps = 12/86 (13%)

Query: 20  SEEADNLNFGLVQVVYEWAM------------QKEGIIVRCIQQLSELLRSIKDGAKIFG 67
           +E  D   F ++ VVYEWA             + EG +VR I  L E+ R +K  + I G
Sbjct: 911 AEFLDRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKTASIIIG 970

Query: 68  ERDLPLKMDQAIQVIKRDIVFAPSLW 93
              L +KM +A ++IKRDIVFA SL+
Sbjct: 971 NSTLHMKMSRAQELIKRDIVFAASLY 996


>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
            Exosome
          Length = 1108

 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 12/76 (15%)

Query: 30   LVQVVYEWAMQK------------EGIIVRCIQQLSELLRSIKDGAKIFGERDLPLKMDQ 77
            L++VVYEW                EG ++R  ++L EL++ + D A   G   L  KM+ 
Sbjct: 1032 LMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEA 1091

Query: 78   AIQVIKRDIVFAPSLW 93
             +++I RDIV A SL+
Sbjct: 1092 VLKLIHRDIVSAGSLY 1107


>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
            Processing And Surveillance
 pdb|2XGJ|B Chain B, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
            Processing And Surveillance
          Length = 1010

 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 12/76 (15%)

Query: 30   LVQVVYEWAMQK------------EGIIVRCIQQLSELLRSIKDGAKIFGERDLPLKMDQ 77
            L++VVYEW                EG ++R  ++L EL++ + D A   G   L  KM+ 
Sbjct: 934  LMEVVYEWCRGATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEA 993

Query: 78   AIQVIKRDIVFAPSLW 93
             +++I RDIV A SL+
Sbjct: 994  VLKLIHRDIVSAGSLY 1009


>pdb|4AKF|A Chain A, Crystal Structure Of Vipd From Legionella Pneumophila
          Length = 577

 Score = 26.6 bits (57), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 11/43 (25%), Positives = 26/43 (60%), Gaps = 3/43 (6%)

Query: 26  LNFGLVQ---VVYEWAMQKEGIIVRCIQQLSELLRSIKDGAKI 65
           +N+G+++    +YE  + + GI++  +  +  L +S+KD  K+
Sbjct: 149 MNYGILKQKIALYEDKLSRAGIVINNVDDIINLTKSVKDLEKL 191


>pdb|3ZEN|D Chain D, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
 pdb|3ZEN|E Chain E, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
 pdb|3ZEN|F Chain F, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
 pdb|4B3Y|A Chain A, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
 pdb|4B3Y|B Chain B, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
 pdb|4B3Y|C Chain C, Cryo-em Structure Of The Mycobacterial Fatty Acid Synthase
          Length = 3089

 Score = 25.4 bits (54), Expect = 9.6,   Method: Composition-based stats.
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 49  IQQLSELLRSI---KDGAKIFGERDLPLKMDQAIQVIKRDIVFAPSLWTKLLVGGQP 102
           ++ L EL+ S     + A + GE +L L+   +  V+ R I F P  W + L   +P
Sbjct: 56  LETLEELVSSAGIESELATLAGEAELLLEPVASELVVVRPIGFEPLQWVRALAAEEP 112


  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
   0.319    0.137    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,204,330
Number of Sequences: 62578
Number of extensions: 105541
Number of successful extensions: 298
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 292
Number of HSP's gapped (non-prelim): 10
length of query: 108
length of database: 14,973,337
effective HSP length: 72
effective length of query: 36
effective length of database: 10,467,721
effective search space: 376837956
effective search space used: 376837956
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)