RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11114
         (88 letters)



>gnl|CDD|222140 pfam13452, zf-MaoC, Metal-binding domain of MaoC dehydratase. 
          Length = 132

 Score = 45.8 bits (109), Expect = 9e-08
 Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 11  EFDLSQVLHGEQYLTLHQPLPTYGDIVSRCKVIDVLDKGKHAGLFSTLVRD 61
             DLS++LHGEQ    H+P+    ++  R +V D+ DK K  G    +V +
Sbjct: 69  GIDLSRLLHGEQSFEYHRPIRAGDELTCRSRVADIYDK-KGNGALEFVVVE 118


>gnl|CDD|178455 PLN02864, PLN02864, enoyl-CoA hydratase.
          Length = 310

 Score = 46.7 bits (111), Expect = 2e-07
 Identities = 15/44 (34%), Positives = 29/44 (65%)

Query: 9   GKEFDLSQVLHGEQYLTLHQPLPTYGDIVSRCKVIDVLDKGKHA 52
           G  +D S +LHG+QY+ +++P+P+   + ++  +  + DKGK A
Sbjct: 86  GLNYDPSLLLHGQQYIEIYKPIPSSASVRNKVSIAGLHDKGKAA 129


>gnl|CDD|181214 PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated.
          Length = 329

 Score = 25.7 bits (57), Expect = 3.2
 Identities = 10/19 (52%), Positives = 14/19 (73%), Gaps = 3/19 (15%)

Query: 26  LHQPLPTYGDIVSRCKVID 44
            HQ LPT   I+SRC+V++
Sbjct: 150 KHQILPT---ILSRCQVVE 165


>gnl|CDD|217810 pfam03950, tRNA-synt_1c_C, tRNA synthetases class I (E and Q),
          anti-codon binding domain.  Other tRNA synthetase
          sub-families are too dissimilar to be included. This
          family includes only glutamyl and glutaminyl tRNA
          synthetases. In some organisms, a single glutamyl-tRNA
          synthetase aminoacylates both tRNA(Glu) and tRNA(Gln).
          Length = 174

 Score = 25.7 bits (57), Expect = 3.3
 Identities = 6/17 (35%), Positives = 9/17 (52%)

Query: 69 KFTVPLFPHDPSYGERE 85
          +  VP  P +P  G R+
Sbjct: 25 EAEVPNHPKNPELGTRK 41


>gnl|CDD|177641 PHA03413, PHA03413, putative internal core protein; Provisional.
          Length = 1304

 Score = 25.8 bits (56), Expect = 3.5
 Identities = 8/22 (36%), Positives = 13/22 (59%)

Query: 66  AISKFTVPLFPHDPSYGERESL 87
           AI K + P F  DP++   ++L
Sbjct: 80  AIRKASAPAFDEDPNFDAGQTL 101


>gnl|CDD|185613 PTZ00433, PTZ00433, tyrosine aminotransferase; Provisional.
          Length = 412

 Score = 25.5 bits (56), Expect = 4.0
 Identities = 9/46 (19%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 35 DIVSRCKVIDVLDKGKHAGLFSTLVRDQSRYAISKFTVPLFPHDPS 80
           I ++  +++ +D  +  G   T+   ++R A++ +    F H  S
Sbjct: 53 AIQTK-ALVEAVDSQECNGYPPTVGSPEAREAVATYWRNSFVHKES 97


>gnl|CDD|176799 cd08965, EcNei-like_N, N-terminal domain of Escherichia coli
          Nei/endonuclease VIII and related DNA glycosylases.
          This family contains the N-terminal domain of
          proteobacteria Nei and related DNA glycosylases. It
          includes Escherichia coli Nei, and belongs to the
          FpgNei_N, [N-terminal domain of Fpg
          (formamidopyrimidine-DNA glycosylase, MutM)_Nei
          (endonuclease VIII)] domain superfamily. DNA
          glycosylases maintain genome integrity by recognizing
          base lesions created by ionizing radiation, alkylating
          or oxidizing agents, and endogenous reactive oxygen
          species. They initiate the base-excision repair
          process, which is completed with the help of enzymes
          such as phosphodiesterases, AP endonucleases, DNA
          polymerases and DNA ligases. DNA glycosylases cleave
          the N-glycosyl bond between the sugar and the damaged
          base, creating an AP (apurinic/apyrimidinic) site. Most
          FpgNei DNA glycosylases use their N-terminal proline
          residue as the key catalytic nucleophile, and the
          reaction proceeds via a Schiff base intermediate.
          Escherichia coli Nei has been well studied, it is a DNA
          glycosylase/AP lyase that excises damaged pyrimidines,
          including 5-hydroxycytosine, 5-hydroxyuracil, and
          uracil glycol. In addition to this EcNei-like_N domain,
          enzymes belonging to this family contain a helix-two
          turn-helix (H2TH) domain and a canonical zinc-finger
          motif.
          Length = 115

 Score = 25.0 bits (55), Expect = 4.5
 Identities = 6/23 (26%), Positives = 8/23 (34%)

Query: 28 QPLPTYGDIVSRCKVIDVLDKGK 50
            L  Y   +    V  V  +GK
Sbjct: 30 PHLKEYEAQLKGQNVTRVETRGK 52


>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
           flavoprotein subunit [Energy production and conversion].
          Length = 562

 Score = 24.6 bits (54), Expect = 8.2
 Identities = 6/26 (23%), Positives = 12/26 (46%)

Query: 19  HGEQYLTLHQPLPTYGDIVSRCKVID 44
            GE+++  +   P Y ++  R  V  
Sbjct: 264 DGERFMERYGYAPKYKELAPRDVVSR 289


  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
   0.324    0.143    0.431 

Gapped
Lambda     K      H
   0.267   0.0729    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,515,114
Number of extensions: 356455
Number of successful extensions: 251
Number of sequences better than 10.0: 1
Number of HSP's gapped: 251
Number of HSP's successfully gapped: 17
Length of query: 88
Length of database: 10,937,602
Length adjustment: 56
Effective length of query: 32
Effective length of database: 8,453,778
Effective search space: 270520896
Effective search space used: 270520896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.2 bits)