RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy529
         (338 letters)



>gnl|CDD|173975 cd08210, RLP_RrRLP, Ribulose bisphosphate carboxylase like proteins
           (RLPs) similar to R.rubrum RLP.  RLP from Rhodospirillum
           rubrum plays a role in an uncharacterized sulfur salvage
           pathway and has been shown to catalyze a novel
           isomerization reaction that converts
           5-methylthio-d-ribulose 1-phosphate to a 3:1 mixture of
           1-methylthioxylulose 5-phosphate and
           1-methylthioribulose 5-phosphate.
          Length = 364

 Score = 34.9 bits (81), Expect = 0.046
 Identities = 22/65 (33%), Positives = 27/65 (41%), Gaps = 10/65 (15%)

Query: 48  VALQPYLSGLPDSEWLALQWVLLFDDFHLLPFL-HPAPQFSFKSNSRPSAYKADVLLAEL 106
           V + P L+GL     LA       +DF  LP L HPA  F+    S        +L   L
Sbjct: 222 VLIAPGLTGLDTFRELA-------EDFDFLPILAHPA--FAGAFVSSGDGISHALLFGTL 272

Query: 107 TRLPG 111
            RL G
Sbjct: 273 FRLAG 277


>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
          Length = 1374

 Score = 32.0 bits (72), Expect = 0.53
 Identities = 20/47 (42%), Positives = 23/47 (48%), Gaps = 2/47 (4%)

Query: 49  ALQPYLSGLPDSEWLALQWVL--LFDDFHLLPFLHPAPQFSFKSNSR 93
           AL+PY SG      L L+WV   + DD HL P    APQ      SR
Sbjct: 327 ALEPYRSGARSESNLELRWVSEKIKDDQHLFPSRGVAPQQQSSHVSR 373


>gnl|CDD|107252 cd01539, PBP1_GGBP, Periplasmic glucose/galactose-binding protein
           (GGBP) involved in chemotaxis towards, and active
           transport of, glucose and galactose in various bacterial
           species.  Periplasmic glucose/galactose-binding protein
           (GGBP) involved in chemotaxis towards, and active
           transport of, glucose and galactose in various bacterial
           species. GGBP is a member of the pentose/hexose
           sugar-binding protein family of the type I periplasmic
           binding protein superfamily which consists of two
           alpha/beta globular domains connected by a
           three-stranded hinge. This Venus flytrap-like domain
           undergoes transition from an open to a closed
           conformational state upon ligand binding. Moreover, the
           periplasmic GGBP is homologous to the ligand-binding
           domain of eukaryotic receptors such as glutamate
           receptor (GluR) and DNA-binding transcriptional
           repressors such as LacI and GalR.
          Length = 303

 Score = 30.3 bits (69), Expect = 1.3
 Identities = 10/36 (27%), Positives = 18/36 (50%)

Query: 177 NQQIGNEEVDRGANRDTHTQAINICSPDDLKTMVKK 212
           NQ   NE++D    +     A+N+  P   +T++ K
Sbjct: 42  NQSTQNEQIDTALAKGVDLLAVNLVDPTAAQTVINK 77


>gnl|CDD|234435 TIGR03994, rSAM_HemZ, coproporphyrinogen dehydrogenase HemZ.
           Members of this radical SAM protein family are HemZ, a
           protein involved in coproporphyrinogen III
           decarboxylation. Alternative names for this enzyme (EC
           1.3.99.22) include coproporphyrinogen dehydrogenase and
           oxygen-independent coproporphyrinogen III oxidase. The
           family is related to, but distinct from HemN, and in
           Bacillus subtilis was shown to be connected to peroxide
           stress and catalase formation [Biosynthesis of
           cofactors, prosthetic groups, and carriers, Heme,
           porphyrin, and cobalamin].
          Length = 401

 Score = 29.9 bits (68), Expect = 2.2
 Identities = 8/18 (44%), Positives = 9/18 (50%)

Query: 26  CLPGERLDLYTTEAGRPD 43
                 L  +T EAGRPD
Sbjct: 166 NFDLSHLREFTVEAGRPD 183


>gnl|CDD|236548 PRK09525, lacZ, beta-D-galactosidase; Reviewed.
          Length = 1027

 Score = 29.5 bits (67), Expect = 3.3
 Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 1/39 (2%)

Query: 166 LHRGTTIHITQNQQIGNEEVD-RGANRDTHTQAINICSP 203
           L  G T+  +     G E +D RGA  D  T  +N+ +P
Sbjct: 261 LWDGETLVASGTAPFGTEIIDERGAYADRVTLRLNVENP 299


>gnl|CDD|181598 PRK08965, PRK08965, putative monovalent cation/H+ antiporter
          subunit E; Reviewed.
          Length = 162

 Score = 27.8 bits (63), Expect = 5.7
 Identities = 15/37 (40%), Positives = 17/37 (45%), Gaps = 5/37 (13%)

Query: 44 RRRYVALQPYLSGLPDSEWLALQWVLLFDDFHLLPFL 80
            R +  QP LS      WLAL W+LL   F L   L
Sbjct: 1  MMRRLLPQPLLSL-----WLALVWLLLNGSFSLGNLL 32


>gnl|CDD|237195 PRK12767, PRK12767, carbamoyl phosphate synthase-like protein;
           Provisional.
          Length = 326

 Score = 28.3 bits (64), Expect = 6.3
 Identities = 11/28 (39%), Positives = 15/28 (53%)

Query: 230 KLKQIKPIISTWKTSQQSRRYDEVVLSR 257
              + +PII  +K     RRYDEVV+  
Sbjct: 293 LGGENEPIIGEYKEGLYMRRYDEVVIVE 320


  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
   0.321    0.136    0.426 

Gapped
Lambda     K      H
   0.267   0.0767    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,213,762
Number of extensions: 1617112
Number of successful extensions: 1229
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1229
Number of HSP's successfully gapped: 10
Length of query: 338
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 240
Effective length of database: 6,590,910
Effective search space: 1581818400
Effective search space used: 1581818400
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: 59 (26.4 bits)