RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= 537021.9.peg.1073_1
         (162 letters)



>gnl|CDD|145657 pfam02621, DUF178, Putative periplasminc binding protein (DUF178). 
           This family of proteins belong to the periplasmic
           binding protein clan.
          Length = 248

 Score = 28.3 bits (64), Expect = 1.0
 Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 3/32 (9%)

Query: 124 IAKNGDANKGVLIGEGALKVRNEKAVGVVADL 155
           + +  DA  G+LIG+ AL    E     V DL
Sbjct: 128 VLEGEDA--GLLIGDEALTYAREGLP-KVYDL 156


>gnl|CDD|48565 cd03016, PRX_1cys, Peroxiredoxin (PRX) family, 1-cys PRX subfamily;
           composed of PRXs containing only one conserved cysteine,
           which serves as the peroxidatic cysteine. They are
           homodimeric thiol-specific antioxidant (TSA) proteins
           that confer a protective role in cells by reducing and
           detoxifying hydrogen peroxide, peroxynitrite, and
           organic hydroperoxides. As with all other PRXs, a
           cysteine sulfenic acid intermediate is formed upon
           reaction of 1-cys PRX with its substrates. Having no
           resolving cysteine, the oxidized enzyme is resolved by
           an external small-molecule or protein reductant such as
           thioredoxin or glutaredoxin. Similar to typical 2-cys
           PRX, 1-cys PRX forms a functional dimeric unit with a
           B-type interface, as well as a decameric structure which
           is stabilized in the reduced form of the enzyme. Other
           oligomeric forms, tetramers and hexamers, have also been
           reported. Mammalian 1-cys PRX is localized cellularly in
           the cytosol and is expressed at high levels in brain,
           eye, testes and lung. The seed-specific plant 1-cys PRXs
           protect tissues from reactive oxygen species during
           desiccation and are also called rehydrins..
          Length = 203

 Score = 26.6 bits (59), Expect = 3.3
 Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 3/24 (12%)

Query: 85  MVHPNRVMASNAETARNAFLIDPN 108
           M+ P+   A +  T R  F+IDP+
Sbjct: 106 MIDPD---AGSTLTVRAVFIIDPD 126


>gnl|CDD|176652 cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3'-5'
           exonuclease domain of Bacillus stearothermophilus DNA
           polymerase I and similar family-A DNA polymerases.
           Bacillus stearothermophilus-like Polymerase I (Pol I), a
           subgroup of the family-A DNA polymerases, contains an
           inactive DnaQ-like 3'-5' exonuclease domain in the same
           polypeptide chain as the polymerase region. The
           exonuclease-like domain of these proteins possess the
           same fold as the Klenow fragment (KF) of Escherichia
           coli Pol I, but does not contain the four critical
           metal-binding residues necessary for activity. The
           function of this domain is unknown. It might act as a
           spacer between the polymerase and the 5'-3' exonuclease
           domains. Some members of this subgroup, such as those
           from Bacillus sphaericus and Thermus aquaticus, are
           thermostable DNA polymerases.
          Length = 178

 Score = 26.1 bits (58), Expect = 4.2
 Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 7/61 (11%)

Query: 98  TARNAFLIDPNM--LEFLWLRTIHEDKNIAKNG-DANKGVLIGEGALKVRNEKAVGVVAD 154
               A+ I   +  L+   L+   ED+ I K G DA K   +   ALK    +  GV  D
Sbjct: 29  NGGGAYYIPLELALLDLAALKEWLEDEKIPKVGHDA-KRAYV---ALKRHGIELAGVAFD 84

Query: 155 L 155
            
Sbjct: 85  T 85


>gnl|CDD|73148 cd02252, nylC_like, nylC-like family; composed of proteins with
           similarity to Flavobacterium endo-type
           6-aminohexanoate-oligomer hydrolase (EIII), the product
           of the nylon oligomer degradation gene, nylC. EIII is an
           amide hydrolase that catalyzes the degradation of
           highly-polymerized 6-aminohexanoate oligomers. Together
           with other nylon degradation enzymes, such as
           6-aminohexanoate cyclic dimer hydrolase (EI) and
           6-aminohexanoate dimer hydrolase (EII), EIII plays a
           role in the detoxification and biological removal of the
           synthetic by-products of nylon manufacture. EIII shows
           sequence similarity to L-aminopeptidase
           D-amidase/D-esterase (DmpA), an aminopeptidase that
           releases N-terminal D and L amino acids from peptide
           substrates. Like DmpA, EIII undergoes autocatalytic
           cleavage in front of a nucleophile to form a
           heterodimer. DmpA shows similarity in catalytic
           mechanism to N-terminal nucleophile (Ntn) hydrolases,
           which are enzymes that catalyze the cleavage of amide
           bonds through the nucleophilic attack of the side chain
           of an N-terminal serine, threonine, or cysteine..
          Length = 260

 Score = 26.3 bits (58), Expect = 4.4
 Identities = 9/33 (27%), Positives = 13/33 (39%), Gaps = 2/33 (6%)

Query: 70  IVATADIYDRPFGKVMVHPNRVMASNAETARNA 102
           IV  A ++D   G     P+  +   A  A  A
Sbjct: 97  IVPAAVLFDLGGGDKRWRPDAALGYAA--AEAA 127


>gnl|CDD|36751 KOG1538, KOG1538, KOG1538, Uncharacterized conserved protein WDR10,
           contains WD40 repeats [General function prediction
           only].
          Length = 1081

 Score = 25.8 bits (56), Expect = 5.8
 Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 3/42 (7%)

Query: 97  ETARNAFLIDPNMLEFLWLRTIHEDKNIAKNGDANKGVLIGE 138
           ETAR A++    + +  +L  I E +   K G+    +L+ +
Sbjct: 602 ETARKAYI---RVRDLRYLELISELEERKKRGETPNDLLLAD 640


>gnl|CDD|30426 COG0077, PheA, Prephenate dehydratase [Amino acid transport and
           metabolism].
          Length = 279

 Score = 25.2 bits (55), Expect = 10.0
 Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 7/60 (11%)

Query: 97  ETARNAFLIDPNMLEFLWLRTIHEDKNIAKNGDANKGVLIGEGALKVRNEKAVGVVADLF 156
           + AR  F    +  E L   TI +     +NG+A+ GV+  E ++    E +V    DL 
Sbjct: 17  QAARKLF---GSGAELLPCSTIEDVFKAVENGEADYGVVPIENSI----EGSVNETLDLL 69


>gnl|CDD|112220 pfam03395, Pox_P4A, Poxvirus P4A protein. 
          Length = 889

 Score = 25.2 bits (55), Expect = 10.0
 Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 3/68 (4%)

Query: 9   TQRTFSKQILDEVMQEGYQNGDNFRHIIVSPYVKSEFVRFMSDSNVASFRYATSGKSHNN 68
            +R F+ +I D+V  EG +    F  I  S Y     +  +       +    SG+S + 
Sbjct: 783 LERIFNARISDDVKAEGLEKYKAFSDISSSLYND---LIAIETIKALLYIIKRSGRSIDG 839

Query: 69  TIVATADI 76
           T +   ++
Sbjct: 840 TEIGPDEL 847


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.317    0.132    0.374 

Gapped
Lambda     K      H
   0.267   0.0625    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,826,084
Number of extensions: 87573
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 179
Number of HSP's successfully gapped: 11
Length of query: 162
Length of database: 6,263,737
Length adjustment: 86
Effective length of query: 76
Effective length of database: 4,405,363
Effective search space: 334807588
Effective search space used: 334807588
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.4 bits)