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= psy3814
         (69 letters)

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

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



>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form
 pdb|2ZAN|A Chain A, Crystal Structure Of Mouse Skd1VPS4B ATP-Form
 pdb|2ZAO|A Chain A, Crystal Structure Of Mouse Skd1VPS4B ADP-Form
          Length = 444

 Score = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 21/33 (63%), Positives = 28/33 (84%)

Query: 34  MQANLEGAIVMEKPNVKWTDVAGLEAAKKQKKK 66
           +Q  L+GAIV+E+PNVKW+DVAGLE AK+  K+
Sbjct: 116 LQNQLQGAIVIERPNVKWSDVAGLEGAKEALKE 148


>pdb|2QP9|X Chain X, Crystal Structure Of S.Cerevisiae Vps4
 pdb|2QPA|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence
          Of Adp
 pdb|2QPA|B Chain B, Crystal Structure Of S.Cerevisiae Vps4 In The Presence
          Of Adp
 pdb|2QPA|C Chain C, Crystal Structure Of S.Cerevisiae Vps4 In The Presence
          Of Adp
          Length = 355

 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 19/33 (57%), Positives = 24/33 (72%)

Query: 34 MQANLEGAIVMEKPNVKWTDVAGLEAAKKQKKK 66
          ++  L  AI+ EKPNVKW DVAGLE AK+  K+
Sbjct: 33 LRGALSSAILSEKPNVKWEDVAGLEGAKEALKE 65


>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b
          Length = 322

 Score = 41.2 bits (95), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/26 (69%), Positives = 23/26 (88%)

Query: 41 AIVMEKPNVKWTDVAGLEAAKKQKKK 66
          AIV+E+PNVKW+DVAGLE AK+  K+
Sbjct: 1  AIVIERPNVKWSDVAGLEGAKEALKE 26


>pdb|3EIH|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence
          Of Atpgammas
 pdb|3EIH|B Chain B, Crystal Structure Of S.Cerevisiae Vps4 In The Presence
          Of Atpgammas
 pdb|3EIH|C Chain C, Crystal Structure Of S.Cerevisiae Vps4 In The Presence
          Of Atpgammas
          Length = 340

 Score = 40.4 bits (93), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/33 (57%), Positives = 24/33 (72%)

Query: 34 MQANLEGAIVMEKPNVKWTDVAGLEAAKKQKKK 66
          ++  L  AI+ EKPNVKW DVAGLE AK+  K+
Sbjct: 18 LRGALSSAILSEKPNVKWEDVAGLEGAKEALKE 50


>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound
          State
          Length = 322

 Score = 38.9 bits (89), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 18/26 (69%), Positives = 21/26 (80%)

Query: 41 AIVMEKPNVKWTDVAGLEAAKKQKKK 66
          AI+ EKPNVKW DVAGLE AK+  K+
Sbjct: 7  AILSEKPNVKWEDVAGLEGAKEALKE 32


>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer
          Length = 331

 Score = 35.8 bits (81), Expect = 0.007,   Method: Composition-based stats.
 Identities = 16/22 (72%), Positives = 18/22 (81%)

Query: 45 EKPNVKWTDVAGLEAAKKQKKK 66
          EKPNVKW DVAGLE AK+  K+
Sbjct: 20 EKPNVKWEDVAGLEGAKEALKE 41


>pdb|3CF0|A Chain A, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|B Chain B, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|C Chain C, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|D Chain D, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|E Chain E, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|F Chain F, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|G Chain G, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|H Chain H, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|I Chain I, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|J Chain J, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|K Chain K, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|L Chain L, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|M Chain M, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF0|N Chain N, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
          Length = 301

 Score = 27.3 bits (59), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 43 VMEKPNVKWTDVAGLEAAKKQ 63
          V+E P V W D+ GLE  K++
Sbjct: 6  VVEVPQVTWEDIGGLEDVKRE 26


>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
 pdb|3CF1|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
 pdb|3CF1|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
 pdb|3CF2|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
 pdb|3CF2|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
 pdb|3CF2|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
 pdb|3CF2|D Chain D, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
 pdb|3CF3|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF3|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADP
 pdb|3CF3|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADP
          Length = 806

 Score = 26.9 bits (58), Expect = 2.7,   Method: Composition-based stats.
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 43  VMEKPNVKWTDVAGLEAAKKQ 63
           V+E P V W D+ GLE  K++
Sbjct: 468 VVEVPQVTWEDIGGLEDVKRE 488


>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A
          Length = 816

 Score = 26.9 bits (58), Expect = 2.8,   Method: Composition-based stats.
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 43  VMEKPNVKWTDVAGLEAAKKQ 63
           V+E P V W D+ GLE  K++
Sbjct: 468 VVEVPQVTWEDIGGLEDVKRE 488


>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent
          Protease, Ftsh
 pdb|2R62|B Chain B, Crystal Structure Of Helicobacter Pylori Atp Dependent
          Protease, Ftsh
 pdb|2R65|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent
          Protease, Ftsh Adp Complex
 pdb|2R65|B Chain B, Crystal Structure Of Helicobacter Pylori Atp Dependent
          Protease, Ftsh Adp Complex
 pdb|2R65|C Chain C, Crystal Structure Of Helicobacter Pylori Atp Dependent
          Protease, Ftsh Adp Complex
 pdb|2R65|D Chain D, Crystal Structure Of Helicobacter Pylori Atp Dependent
          Protease, Ftsh Adp Complex
 pdb|2R65|E Chain E, Crystal Structure Of Helicobacter Pylori Atp Dependent
          Protease, Ftsh Adp Complex
          Length = 268

 Score = 26.2 bits (56), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 11/19 (57%), Positives = 16/19 (84%)

Query: 45 EKPNVKWTDVAGLEAAKKQ 63
          EKPNV++ D+AG E AK++
Sbjct: 4  EKPNVRFKDMAGNEEAKEE 22


  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
   0.309    0.123    0.342 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,206,362
Number of Sequences: 62578
Number of extensions: 21046
Number of successful extensions: 55
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 41
Number of HSP's gapped (non-prelim): 14
length of query: 69
length of database: 14,973,337
effective HSP length: 39
effective length of query: 30
effective length of database: 12,532,795
effective search space: 375983850
effective search space used: 375983850
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 45 (21.9 bits)