RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy6027
         (531 letters)



>gnl|CDD|182084 PRK09800, PRK09800, putative hypoxanthine oxidase; Provisional.
          Length = 956

 Score = 33.3 bits (76), Expect = 0.36
 Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 2/43 (4%)

Query: 285 VQSQYSHLIVNCILAYLNDHHSSPSLIRAKIADALSKIISIAA 327
           VQS Y+      I+  L D  ++P+  R +I DALS + S  A
Sbjct: 96  VQSGYNDPAAALIITDLLDRIAAPT--REEIDDALSGLFSRDA 136


>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La.  This protein is induced
           by heat shock and other stresses in E. coli, B.
           subtilis, and other species. The yeast member,
           designated PIM1, is located in the mitochondrial matrix,
           required for mitochondrial function, and also induced by
           heat shock [Protein fate, Degradation of proteins,
           peptides, and glycopeptides].
          Length = 775

 Score = 31.1 bits (71), Expect = 1.9
 Identities = 18/102 (17%), Positives = 43/102 (42%), Gaps = 9/102 (8%)

Query: 438 QKTEILVFIISKVLSTTYRESNK-SEHTLVQ-NMFMKSLLMVSGKYTCLHISSAFPLAFL 495
            K +  +  +++ +  T+RE    S+    Q  +      +         ++++  L   
Sbjct: 116 DKDDEEIKALTREIKETFRELISLSKLFREQPALLSALEDIDEPGRLADFVAASLQLKEK 175

Query: 496 EPLLKILQSNDAEIRL-----LVNKEK--ARKKKKIESHVKK 530
           + L ++L++ + E RL     L+ KE    + + KI   V++
Sbjct: 176 DELQEVLETVNIEKRLKKALELLKKELELLKLQNKITKKVEE 217


>gnl|CDD|235720 PRK06156, PRK06156, hypothetical protein; Provisional.
          Length = 520

 Score = 30.3 bits (69), Expect = 2.8
 Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 4/35 (11%)

Query: 44  SPEKLDRIGEYLYQRASRDISRRRNGYVVIAMEAM 78
            P K+  +G+ LY R + D      G +V A+ AM
Sbjct: 136 DPFKVTLVGDRLYGRGTED----DKGAIVTALYAM 166


>gnl|CDD|225290 COG2441, COG2441, Predicted butyrate kinase [Energy production and
           conversion].
          Length = 374

 Score = 29.5 bits (66), Expect = 4.0
 Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 4/57 (7%)

Query: 88  QTLNLFVESFLKIVQKLLESLDPDLQILATNSFVRFANIEEDTPSYHRRYDFFVSKF 144
           +T N  +E  +K V  LL S  PD   L+     RF+ I         +     S +
Sbjct: 252 ETYNALIEGVVKDVFTLLPSTYPDAIYLSG----RFSRIPRFFSDVKEKLRDAFSSY 304


>gnl|CDD|100026 cd02185, AroH, Chorismate mutase (AroH) is one of at least five
           chorismate-utilizing enzymes present in microorganisms
           that catalyze the rearrangement of chorismate to
           prephenic acid, the first committed step in the
           biosynthesis of aromatic amino acids. In prokaryotes,
           chorismate mutase may be fused to prephenate
           dehydratase, prephenate dehydrogenase, or
           3-deoxy-D-arabino-heptulosonat-7-phosphate (DAHP) as
           part of a bifunctional enzyme.  The AroH domain forms a
           homotrimer with three-fold symmetry.
          Length = 117

 Score = 27.9 bits (63), Expect = 5.6
 Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 4/32 (12%)

Query: 166 IRGIQGVIRKTVSDDLVENIWESTH--MEKII 195
           +RGI+G    TV ++  E I E+T   +E+II
Sbjct: 1   VRGIRGAT--TVEENTAEEILEATRELLEEII 30


>gnl|CDD|224339 COG1421, COG1421, CRISPR system related protein [Defense
           mechanisms].
          Length = 137

 Score = 28.2 bits (63), Expect = 5.9
 Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 54  YLYQRASRDISRRRNGY--VVIAMEAMDQLLAACHSQTLNLFVESFLKIVQKLLESLDPD 111
             Y    R      N +  +V+ +  M   LA    +     +E   ++++++++ +D D
Sbjct: 51  KFYDYILRIDEENENSWKEIVLDLPKMKPQLAYAVGRDGKEALEGLYEVLEEMIDKIDDD 110

Query: 112 LQILATNSFVRFANIEEDTPSYHRRY 137
               A   F  F    E   +YH+ Y
Sbjct: 111 NDRNAFEKFKTFF---EAIVAYHKFY 133


>gnl|CDD|233253 TIGR01057, topA_arch, DNA topoisomerase I, archaeal.  This model
           describes topoisomerase I from archaea. These enzymes
           are involved in the control of DNA topology. DNA
           topoisomerase I belongs to the type I topoisomerases,
           which are ATP-independent [DNA metabolism, DNA
           replication, recombination, and repair].
          Length = 618

 Score = 29.0 bits (65), Expect = 7.1
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 312 RAKIADALSKIISIAASESIGPTVL-EVLYTTLTLLCIELISDDTVVDFIRVIMRIQEIA 370
           RA+I + L K   I   +SI  T L E +  TL   C E+IS++    F   +  I    
Sbjct: 488 RARIIETLYKRGYIEGKKSIKVTPLGEAVIETLQRYCPEIISEELTRRFESKLEDIMSGR 547

Query: 371 LTSTTLSDSQKYNLHALV 388
           +T   + D  K  L  ++
Sbjct: 548 ITKDEVIDEAKKRLRKIL 565


>gnl|CDD|107255 cd01542, PBP1_TreR_like, Ligand-binding domain of DNA transcription
           repressor specific for trehalose (TreR) which is a
           member of the LacI-GalR family of bacterial
           transcription regulators.  Ligand-binding domain of DNA
           transcription repressor specific for trehalose (TreR)
           which is a member of the LacI-GalR family of bacterial
           transcription regulators. The ligand-binding domain of
           TreR is structurally homologous to the periplasmic
           sugar-binding domain of ABC-type transporters and both
           domains contain the type I periplasmic binding
           protein-like fold. The LacI-GalR family repressors are
           composed of two functional domains: an N-terminal HTH
           (helix-turn-helix) domain, which is responsible for the
           DNA-binding specificity, and a C-terminal ligand-binding
           domain, which is homologous to the type I periplasmic
           binding proteins. As also observed in the periplasmic
           binding proteins, the C-terminal domain of the bacterial
           transcription repressor undergoes a conformational
           change upon ligand binding which in turn changes the DNA
           binding affinity of the repressor.
          Length = 259

 Score = 28.7 bits (65), Expect = 7.5
 Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 20/83 (24%)

Query: 50  RIGEYLYQRASRDIS-------------RRRNGYVVIAMEAMDQ--LLAACHSQTLNLFV 94
            +GEYL Q+  ++I+              R+ GY    ++A+ +  +      +T +   
Sbjct: 104 ELGEYLAQQGHKNIAYLGVSESDIAVGILRKQGY----LDALKEHGICPPNIVET-DFSY 158

Query: 95  ESFLKIVQKLLESLDPDLQILAT 117
           ES  +  Q+LLE   PD  + AT
Sbjct: 159 ESAYEAAQELLEPQPPDAIVCAT 181


>gnl|CDD|182613 PRK10644, PRK10644, arginine:agmatin antiporter; Provisional.
          Length = 445

 Score = 29.0 bits (65), Expect = 8.0
 Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 2/35 (5%)

Query: 362 VIMRIQEIALTSTTLSDSQKYNLHALVAALFTLVP 396
           V+M I +++  S   S  +++ L + V+ +FTLVP
Sbjct: 332 VLMTIFQLSSISPNAS--KEFGLVSSVSVIFTLVP 364


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.322    0.134    0.382 

Gapped
Lambda     K      H
   0.267   0.0720    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,112,096
Number of extensions: 2689087
Number of successful extensions: 2544
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2543
Number of HSP's successfully gapped: 22
Length of query: 531
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 430
Effective length of database: 6,457,848
Effective search space: 2776874640
Effective search space used: 2776874640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 61 (27.3 bits)