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= 048377
         (118 letters)

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

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



>pdb|1VLC|A Chain A, Crystal Structure Of 3-isopropylmalate Dehydrogenase
           (tm0556) From Thermotoga Maritima At 1.90 A Resolution
          Length = 366

 Score = 29.6 bits (65), Expect = 0.47,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 40  NQAAQIYNSKL-QSVVDSLSKEFPDSRFVYFDIYNPLNSLIQNPPQY 85
           ++A  +Y+S L + VV+ +++E+PD    +  + N    LI  P Q+
Sbjct: 198 DKANVLYSSMLWRKVVNEVAREYPDVELTHIYVDNAAMQLILKPSQF 244


>pdb|3U1H|A Chain A, Crystal Structure Of Ipmdh From The Last Common Ancestor
           Of Bacillus
 pdb|3U1H|B Chain B, Crystal Structure Of Ipmdh From The Last Common Ancestor
           Of Bacillus
          Length = 390

 Score = 28.9 bits (63), Expect = 0.75,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 40  NQAAQIYNSKL-QSVVDSLSKEFPDSRFVYFDIYNPLNSLIQNPPQY 85
           ++A  + +S+L + V + ++KE+PD    +  + N    LI+NP Q+
Sbjct: 210 DKANVLESSRLWREVAEEVAKEYPDVELEHMLVDNAAMQLIRNPRQF 256


>pdb|1CM7|A Chain A, 3-Isopropylmalate Dehydrogenase From Escherichia Coli
 pdb|1CM7|B Chain B, 3-Isopropylmalate Dehydrogenase From Escherichia Coli
          Length = 363

 Score = 27.3 bits (59), Expect = 1.9,   Method: Composition-based stats.
 Identities = 10/35 (28%), Positives = 20/35 (57%)

Query: 51  QSVVDSLSKEFPDSRFVYFDIYNPLNSLIQNPPQY 85
           + +V+ ++ E+PD    +  I N    LI++P Q+
Sbjct: 206 REIVNEIATEYPDVELAHMYIDNATMQLIKDPSQF 240


>pdb|1CNZ|A Chain A, 3-Isopropylmalate Dehydrogenase (Ipmdh) From Salmonella
           Typhimurium
 pdb|1CNZ|B Chain B, 3-Isopropylmalate Dehydrogenase (Ipmdh) From Salmonella
           Typhimurium
          Length = 363

 Score = 26.9 bits (58), Expect = 2.7,   Method: Composition-based stats.
 Identities = 10/35 (28%), Positives = 20/35 (57%)

Query: 51  QSVVDSLSKEFPDSRFVYFDIYNPLNSLIQNPPQY 85
           + +V+ ++K +PD    +  I N    LI++P Q+
Sbjct: 206 REIVNDVAKTYPDVELAHMYIDNATMQLIKDPSQF 240


>pdb|2EKC|A Chain A, Structural Study Of Project Id Aq_1548 From Aquifex
           Aeolicus Vf5
 pdb|2EKC|B Chain B, Structural Study Of Project Id Aq_1548 From Aquifex
           Aeolicus Vf5
          Length = 262

 Score = 26.6 bits (57), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 55  DSLSKEFPDSRFVYFDIYNPL 75
           ++L KEFPD  F+    YNP+
Sbjct: 86  ETLRKEFPDIPFLLMTYYNPI 106


>pdb|2D1C|A Chain A, Crystal Structure Of Tt0538 Protein From Thermus
           Thermophilus Hb8
 pdb|2D1C|B Chain B, Crystal Structure Of Tt0538 Protein From Thermus
           Thermophilus Hb8
          Length = 496

 Score = 26.2 bits (56), Expect = 5.0,   Method: Composition-based stats.
 Identities = 9/36 (25%), Positives = 21/36 (58%)

Query: 50  LQSVVDSLSKEFPDSRFVYFDIYNPLNSLIQNPPQY 85
           L+   + +++E+PD   V+  + N  + L++ P Q+
Sbjct: 202 LKRAFEQVAQEYPDIEAVHIIVDNAAHQLVKRPEQF 237


>pdb|3DMQ|A Chain A, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT
           Recycles Rna Polymerase During Transcription
 pdb|3DMQ|B Chain B, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT
           Recycles Rna Polymerase During Transcription
          Length = 968

 Score = 25.8 bits (55), Expect = 6.8,   Method: Composition-based stats.
 Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 1/42 (2%)

Query: 54  VDSLSKEFPDSRFVYFDIYNPLNSLIQNPPQY-GFEVADKGC 94
           +D+     P  R +Y  +YN L + + +P Q  GF+   K C
Sbjct: 629 LDAFEHTCPTGRTIYDSVYNDLINYLASPDQTEGFDDLIKNC 670


  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
   0.320    0.139    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,540,098
Number of Sequences: 62578
Number of extensions: 126291
Number of successful extensions: 322
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 316
Number of HSP's gapped (non-prelim): 10
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
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)