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= 003851
         (791 letters)

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

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



>pdb|1RQ8|A Chain A, Solution Structure Of The Hypothetical Protein Sav1595
           From Staphylococcus Aureus, A Putative Rna Binding
           Protein
          Length = 104

 Score = 34.7 bits (78), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 23/88 (26%), Positives = 46/88 (52%), Gaps = 4/88 (4%)

Query: 661 ITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKGKSFAQVKQI 720
           +T +++  LR +  ++ P   +G+ GI +  I+ +    + REL+K+ V   +F   K++
Sbjct: 2   LTGKQKRYLRSLAHNIDPIFQIGKGGINENMIKQIDDTLENRELIKVHVLQNNFDDKKEL 61

Query: 721 AISLEAESGGVLVSLDKTPKGIAIIVYR 748
           A +L   +   LV +     G  I++YR
Sbjct: 62  AETLSEATRSELVQV----IGSMIVIYR 85


>pdb|1VIS|A Chain A, Crystal Structure Of Mevalonate Kinase
          Length = 324

 Score = 33.1 bits (74), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 36/144 (25%), Positives = 68/144 (47%), Gaps = 28/144 (19%)

Query: 181 GDYNKELKTDEVKIDANPIELSKDRHREVGSLNQKQIKGYHEVDDPSVLPWKRNTDRRRR 240
           G YNKELK DE+               ++G + +K+I+G   + D S + +K   + +  
Sbjct: 127 GFYNKELKDDEI--------------AKLGYMVEKEIQGKASITDTSTITYKGILEIKNN 172

Query: 241 SNTELAEKMIPEHELQRLRNISLRML--ERTKVGSAGITQ--ALVDSIHEKWK-----LD 291
                  K+  E E + L+N    ++  E+ K  +A +    A +++  E +K     +D
Sbjct: 173 K----FRKIKGEFE-EFLKNCKFLIVYAEKRKKKTAELVNEVAKIENKDEIFKEIDKVID 227

Query: 292 EVVKLKFEEPHSLQMKRTHEILER 315
           E +K+K +E     M + HE+L++
Sbjct: 228 EALKIKNKEDFGKLMTKNHELLKK 251


>pdb|1KKH|A Chain A, Crystal Structure Of The Methanococcus Jannaschii
           Mevalonate Kinase
          Length = 317

 Score = 33.1 bits (74), Expect = 0.59,   Method: Compositional matrix adjust.
 Identities = 36/144 (25%), Positives = 68/144 (47%), Gaps = 28/144 (19%)

Query: 181 GDYNKELKTDEVKIDANPIELSKDRHREVGSLNQKQIKGYHEVDDPSVLPWKRNTDRRRR 240
           G YNKELK DE+               ++G + +K+I+G   + D S + +K   + +  
Sbjct: 130 GFYNKELKDDEI--------------AKLGYMVEKEIQGKASITDTSTITYKGILEIKNN 175

Query: 241 SNTELAEKMIPEHELQRLRNISLRML--ERTKVGSAGITQ--ALVDSIHEKWK-----LD 291
                  K+  E E + L+N    ++  E+ K  +A +    A +++  E +K     +D
Sbjct: 176 K----FRKIKGEFE-EFLKNCKFLIVYAEKRKKKTAELVNEVAKIENKDEIFKEIDKVID 230

Query: 292 EVVKLKFEEPHSLQMKRTHEILER 315
           E +K+K +E     M + HE+L++
Sbjct: 231 EALKIKNKEDFGKLMTKNHELLKK 254


>pdb|3FXA|A Chain A, Crystal Structure Of A Putative Sugar-Phosphate Isomerase
           (Lmof2365_0531) From Listeria Monocytogenes Str. 4b
           F2365 At 1.60 A Resolution
 pdb|3FXA|B Chain B, Crystal Structure Of A Putative Sugar-Phosphate Isomerase
           (Lmof2365_0531) From Listeria Monocytogenes Str. 4b
           F2365 At 1.60 A Resolution
 pdb|3FXA|C Chain C, Crystal Structure Of A Putative Sugar-Phosphate Isomerase
           (Lmof2365_0531) From Listeria Monocytogenes Str. 4b
           F2365 At 1.60 A Resolution
 pdb|3FXA|D Chain D, Crystal Structure Of A Putative Sugar-Phosphate Isomerase
           (Lmof2365_0531) From Listeria Monocytogenes Str. 4b
           F2365 At 1.60 A Resolution
          Length = 201

 Score = 31.2 bits (69), Expect = 2.6,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 278 QALVDSIHEKWKLDEVVKLKFEEPHSLQ-MKRTHEILERRTGGLVIWRSGSSVVLFRGMA 336
           QA++D+IH+ W+ +     +  E  S + + +T E +   TG +V+   G+S V  + + 
Sbjct: 5   QAILDNIHQTWQEEANAISRLPEVTSEEALVKTVEKIAECTGKIVVAGCGTSGVAAKKLV 64

Query: 337 YKLPCVQ 343
           +   C++
Sbjct: 65  HSFNCIE 71


>pdb|1JO0|A Chain A, Structure Of Hi1333, A Hypothetical Protein From
           Haemophilus Influenzae With Structural Similarity To
           Rna-binding Proteins
 pdb|1JO0|B Chain B, Structure Of Hi1333, A Hypothetical Protein From
           Haemophilus Influenzae With Structural Similarity To
           Rna-binding Proteins
          Length = 98

 Score = 30.8 bits (68), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 12/52 (23%), Positives = 29/52 (55%)

Query: 660 TITNEERFLLRKMGLSMKPYLLLGRRGIYDGTIENMHLHWKYRELVKIIVKG 711
           T++ +++  L+ +   + P ++LG  G+ +G +  +     + EL+K+ V G
Sbjct: 2   TLSTKQKQFLKGLAHHLNPVVMLGGNGLTEGVLAEIENALNHHELIKVKVAG 53


  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
   0.317    0.133    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,455,291
Number of Sequences: 62578
Number of extensions: 839215
Number of successful extensions: 1969
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1962
Number of HSP's gapped (non-prelim): 8
length of query: 791
length of database: 14,973,337
effective HSP length: 107
effective length of query: 684
effective length of database: 8,277,491
effective search space: 5661803844
effective search space used: 5661803844
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)