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= 039177
         (453 letters)

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

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



>pdb|2E7U|A Chain A, Crystal Structure Of Glutamate-1-Semialdehyde
           2,1-Aminomutase From Thermus Thermophilus Hb8
          Length = 424

 Score = 34.7 bits (78), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 38/163 (23%), Positives = 63/163 (38%), Gaps = 28/163 (17%)

Query: 236 GIKPDIVCYTMVLNGVIVQEDYVKAEELFDELLVLGLVPDVYTYNVYINGLCKQNNV--E 293
           G+KPD+V    +L G +    Y    E+ +++  LG         VY  G    N +   
Sbjct: 256 GLKPDLVTLGKILGGGLPAAAYAGRREIMEKVAPLG--------PVYQAGTLSGNPLAMA 307

Query: 294 AGIKMIACMEELGSKPDVITYNTLLQALCKVRELNRLRELVKEMKWKGIVLNLQTYSIMI 353
           AG+  +  +EE    P    Y   L A  +      L+E++KE   KG+   +     MI
Sbjct: 308 AGLATLELLEE---NPGYYAYLEDLGARLEA----GLKEVLKE---KGLPHTVNRVGSMI 357

Query: 354 DGLASKGDIIEACGLLEEALNKGLCTQSSMFDETICGLCQRGL 396
               ++G ++               T + +F     GL  RG+
Sbjct: 358 TVFFTEGPVV--------TFQDARRTDTELFKRFFHGLLDRGI 392


>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Ca
          Length = 501

 Score = 30.8 bits (68), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 19/55 (34%), Positives = 28/55 (50%)

Query: 209 YTNVIRSLVKKEKVFDALGILNQMKSDGIKPDIVCYTMVLNGVIVQEDYVKAEEL 263
           +TN  R  V K+    A  ++ QMK+ GI+P +  Y   L G   + D  KA E+
Sbjct: 108 FTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162


>pdb|4DNG|A Chain A, Crystal Structure Of Putative Aldehyde Dehydrogenase From
           Bacillus Subtilis Subsp. Subtilis Str. 168
 pdb|4DNG|B Chain B, Crystal Structure Of Putative Aldehyde Dehydrogenase From
           Bacillus Subtilis Subsp. Subtilis Str. 168
          Length = 485

 Score = 30.4 bits (67), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 2/82 (2%)

Query: 157 LNCMINDGFCVDGKTCSLILSSVCEQRDLSSDELLGFVQEMKKLGFCFGMVDYTNVIRSL 216
           ++  I   F   G+ C +I++ +   +D+  + +  F   +K+L +     D   V+  L
Sbjct: 272 VDAAIFGKFIHQGQIC-MIINRIIVHQDVYDEFVEKFTARVKQLPYG-DQTDPKTVVGPL 329

Query: 217 VKKEKVFDALGILNQMKSDGIK 238
           + + ++  AL I+ Q K+DGI+
Sbjct: 330 INERQIEKALEIIEQAKTDGIE 351


>pdb|2PJU|A Chain A, Crystal Structure Of Propionate Catabolism Operon
           Regulatory Protein Prpr
 pdb|2PJU|B Chain B, Crystal Structure Of Propionate Catabolism Operon
           Regulatory Protein Prpr
 pdb|2PJU|C Chain C, Crystal Structure Of Propionate Catabolism Operon
           Regulatory Protein Prpr
 pdb|2PJU|D Chain D, Crystal Structure Of Propionate Catabolism Operon
           Regulatory Protein Prpr
          Length = 225

 Score = 30.0 bits (66), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 13/66 (19%)

Query: 186 SSDELLGFVQEMKKLGFCFGMVDYTNVIRSLVKKEKVF-------------DALGILNQM 232
           S  ++L F+ +  KL    G+V Y   I +LV  +K F             DA G +N++
Sbjct: 91  SGYDVLQFLAKAGKLTSSIGVVTYQETIPALVAFQKTFNLRLDQRSYITEEDARGQINEL 150

Query: 233 KSDGIK 238
           K++G +
Sbjct: 151 KANGTE 156


>pdb|3C8M|A Chain A, Crystal Structure Of Homoserine Dehydrogenase From
           Thermoplasma Volcanium
          Length = 331

 Score = 28.5 bits (62), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 25/45 (55%)

Query: 227 GILNQMKSDGIKPDIVCYTMVLNGVIVQEDYVKAEELFDELLVLG 271
           GIL+Q +S G    +V  T ++NG    E  +K+ +  D LL LG
Sbjct: 243 GILDQDRSFGKNERLVTETGIVNGKPSAESRIKSLDSNDYLLTLG 287


>pdb|3JSA|A Chain A, Homoserine Dehydrogenase From Thermoplasma Volcanium
           Complexed With Nad
          Length = 328

 Score = 28.5 bits (62), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 25/45 (55%)

Query: 227 GILNQMKSDGIKPDIVCYTMVLNGVIVQEDYVKAEELFDELLVLG 271
           GIL+Q +S G    +V  T ++NG    E  +K+ +  D LL LG
Sbjct: 240 GILDQDRSFGKNERLVTETGIVNGKPSAESRIKSLDSNDYLLTLG 284


  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    0.138    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,084,681
Number of Sequences: 62578
Number of extensions: 464453
Number of successful extensions: 1095
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1089
Number of HSP's gapped (non-prelim): 8
length of query: 453
length of database: 14,973,337
effective HSP length: 102
effective length of query: 351
effective length of database: 8,590,381
effective search space: 3015223731
effective search space used: 3015223731
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: 53 (25.0 bits)