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= 016120
         (394 letters)

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

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



>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp
          Length = 262

 Score = 32.0 bits (71), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 154 NRMQQLPPGDNGFDISDKCNE-IIHLLSEGQPRLDINEFERGREELF 199
            R+ +L PG +G DI++ CNE  +H   EG   +    FE   E + 
Sbjct: 204 QRLAELTPGFSGADIANICNEAALHAAREGHTSVHTLNFEYAVERVL 250


>pdb|2ZW9|A Chain A, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZW9|B Chain B, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZWA|A Chain A, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZWA|B Chain B, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZZK|A Chain A, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
 pdb|2ZZK|B Chain B, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
           Tyw4
          Length = 695

 Score = 30.8 bits (68), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 38/172 (22%), Positives = 73/172 (42%), Gaps = 12/172 (6%)

Query: 195 REELFDLLIEGPSGLAVVAILDSSGFDKTVFTADTYNNDHVKFYFDCLAWVRVSIAYDFG 254
           R  L  ++ + P    +V +    G+D   F     NN   + Y D ++++ +  + D  
Sbjct: 93  RSRLNSIIEQTPQDKKIVVVNLGCGYDPLPFQLLDTNNIQSQQYHDRVSFIDIDYS-DLL 151

Query: 255 KMLDDIIKSVMPPSRVSVIIGEDYQLKKSILRDYLTNKKYFIVLDDVFDNSEIWSDLEEL 314
           K+  ++IK++   S++ + + ED         D+LT  KY     D+ D+    + L E 
Sbjct: 152 KIKIELIKTIPELSKI-IGLSEDKDYVDDSNVDFLTTPKYLARPCDLNDSKMFSTLLNEC 210

Query: 315 LPDDENGSRVLIT----------VTDPDLLASLEMENGEKIRRDSVLFGGPL 356
              D N  +V +            +D  + A+ +MEN   I  + ++  GP 
Sbjct: 211 QLYDPNVVKVFVAEVSLAYMKPERSDSIIEATSKMENSHFIILEQLIPKGPF 262


>pdb|2HLP|A Chain A, Crystal Structure Of The E267r Mutant Of A Halophilic
           Malate Dehydrogenase In The Apo Form
 pdb|2HLP|B Chain B, Crystal Structure Of The E267r Mutant Of A Halophilic
           Malate Dehydrogenase In The Apo Form
          Length = 303

 Score = 28.9 bits (63), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 25/89 (28%), Positives = 45/89 (50%), Gaps = 6/89 (6%)

Query: 303 DNSEIWSDLEELLPDDENGSRVLITVTDP-DLLASLEMENGEKIRRDSVLFGGPLIRLKH 361
           DN+ I  D++  L D+ N   + +T ++P DLL     E G++ R   + FGG   RL  
Sbjct: 94  DNAPIMEDIQSSL-DEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGG---RLDS 149

Query: 362 EAWQFFILHYGSMPLENYLQGEAIPTVGD 390
             +++ +      P++N ++G  +   GD
Sbjct: 150 ARFRYVLSEEFDAPVQN-VEGTILGEHGD 177


>pdb|2J5K|A Chain A, 2.0 A Resolution Structure Of The Wild Type Malate
           Dehydrogenase From Haloarcula Marismortui (radiation
           Damage Series)
 pdb|2J5K|B Chain B, 2.0 A Resolution Structure Of The Wild Type Malate
           Dehydrogenase From Haloarcula Marismortui (radiation
           Damage Series)
 pdb|2J5K|C Chain C, 2.0 A Resolution Structure Of The Wild Type Malate
           Dehydrogenase From Haloarcula Marismortui (radiation
           Damage Series)
 pdb|2J5K|D Chain D, 2.0 A Resolution Structure Of The Wild Type Malate
           Dehydrogenase From Haloarcula Marismortui (radiation
           Damage Series)
 pdb|2J5Q|A Chain A, 2.15 A Resolution Structure Of The Wild Type Malate
           Dehydrogenase From Haloarcula Marismortui After First
           Radiation Burn (Radiation Damage Series)
 pdb|2J5Q|B Chain B, 2.15 A Resolution Structure Of The Wild Type Malate
           Dehydrogenase From Haloarcula Marismortui After First
           Radiation Burn (Radiation Damage Series)
 pdb|2J5Q|C Chain C, 2.15 A Resolution Structure Of The Wild Type Malate
           Dehydrogenase From Haloarcula Marismortui After First
           Radiation Burn (Radiation Damage Series)
 pdb|2J5Q|D Chain D, 2.15 A Resolution Structure Of The Wild Type Malate
           Dehydrogenase From Haloarcula Marismortui After First
           Radiation Burn (Radiation Damage Series)
 pdb|2J5R|A Chain A, 2.25 A Resolution Structure Of The Wild Type Malate
           Dehydrogenase From Haloarcula Marismortui After Second
           Radiation Burn (Radiation Damage Series)
 pdb|2J5R|B Chain B, 2.25 A Resolution Structure Of The Wild Type Malate
           Dehydrogenase From Haloarcula Marismortui After Second
           Radiation Burn (Radiation Damage Series)
 pdb|2J5R|C Chain C, 2.25 A Resolution Structure Of The Wild Type Malate
           Dehydrogenase From Haloarcula Marismortui After Second
           Radiation Burn (Radiation Damage Series)
 pdb|2J5R|D Chain D, 2.25 A Resolution Structure Of The Wild Type Malate
           Dehydrogenase From Haloarcula Marismortui After Second
           Radiation Burn (Radiation Damage Series)
          Length = 304

 Score = 28.9 bits (63), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 303 DNSEIWSDLEELLPDDENGSRVLITVTDP-DLLASLEMENGEKIRRDSVLFGGPLIRLKH 361
           DN+ I  D++  L D+ N   + +T ++P DLL     E G++ R   + FGG   RL  
Sbjct: 95  DNAPIMEDIQSSL-DEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGG---RLDS 150

Query: 362 EAWQFFILHYGSMPLEN 378
             +++ +      P++N
Sbjct: 151 ARFRYVLSEEFDAPVQN 167


>pdb|1HLP|A Chain A, Structural Features Stabilizing Halophilic Malate
           Dehydrogenase From An Archaebacterium
 pdb|1HLP|B Chain B, Structural Features Stabilizing Halophilic Malate
           Dehydrogenase From An Archaebacterium
 pdb|1D3A|A Chain A, Crystal Structure Of The Wild Type Halophilic Malate
           Dehydrogenase In The Apo Form
 pdb|1D3A|B Chain B, Crystal Structure Of The Wild Type Halophilic Malate
           Dehydrogenase In The Apo Form
          Length = 303

 Score = 28.9 bits (63), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 303 DNSEIWSDLEELLPDDENGSRVLITVTDP-DLLASLEMENGEKIRRDSVLFGGPLIRLKH 361
           DN+ I  D++  L D+ N   + +T ++P DLL     E G++ R   + FGG   RL  
Sbjct: 94  DNAPIMEDIQSSL-DEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGG---RLDS 149

Query: 362 EAWQFFILHYGSMPLEN 378
             +++ +      P++N
Sbjct: 150 ARFRYVLSEEFDAPVQN 166


>pdb|2X0R|A Chain A, R207s,R292s Mutant Of Malate Dehydrogenase From The
           Halophilic Archaeon Haloarcula Marismortui (Holo Form)
 pdb|2X0R|B Chain B, R207s,R292s Mutant Of Malate Dehydrogenase From The
           Halophilic Archaeon Haloarcula Marismortui (Holo Form)
          Length = 304

 Score = 28.9 bits (63), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 303 DNSEIWSDLEELLPDDENGSRVLITVTDP-DLLASLEMENGEKIRRDSVLFGGPLIRLKH 361
           DN+ I  D++  L D+ N   + +T ++P DLL     E G++ R   + FGG   RL  
Sbjct: 95  DNAPIMEDIQSSL-DEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGG---RLDS 150

Query: 362 EAWQFFILHYGSMPLEN 378
             +++ +      P++N
Sbjct: 151 ARFRYVLSEEFDAPVQN 167


>pdb|1O6Z|A Chain A, 1.95 A Resolution Structure Of (r207s,r292s) Mutant Of
           Malate Dehydrogenase From The Halophilic Archaeon
           Haloarcula Marismortui (holo Form)
 pdb|1O6Z|B Chain B, 1.95 A Resolution Structure Of (r207s,r292s) Mutant Of
           Malate Dehydrogenase From The Halophilic Archaeon
           Haloarcula Marismortui (holo Form)
 pdb|1O6Z|C Chain C, 1.95 A Resolution Structure Of (r207s,r292s) Mutant Of
           Malate Dehydrogenase From The Halophilic Archaeon
           Haloarcula Marismortui (holo Form)
 pdb|1O6Z|D Chain D, 1.95 A Resolution Structure Of (r207s,r292s) Mutant Of
           Malate Dehydrogenase From The Halophilic Archaeon
           Haloarcula Marismortui (holo Form)
          Length = 303

 Score = 28.9 bits (63), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 39/77 (50%), Gaps = 5/77 (6%)

Query: 303 DNSEIWSDLEELLPDDENGSRVLITVTDP-DLLASLEMENGEKIRRDSVLFGGPLIRLKH 361
           DN+ I  D++  L D+ N   + +T ++P DLL     E G++ R   + FGG   RL  
Sbjct: 94  DNAPIMEDIQSSL-DEHNDDYISLTTSNPVDLLNRHLYEAGDRSREQVIGFGG---RLDS 149

Query: 362 EAWQFFILHYGSMPLEN 378
             +++ +      P++N
Sbjct: 150 ARFRYVLSEEFDAPVQN 166


  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
   0.323    0.142    0.417 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,316,745
Number of Sequences: 62578
Number of extensions: 460407
Number of successful extensions: 1096
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1091
Number of HSP's gapped (non-prelim): 7
length of query: 394
length of database: 14,973,337
effective HSP length: 101
effective length of query: 293
effective length of database: 8,652,959
effective search space: 2535316987
effective search space used: 2535316987
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)