RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5901
         (122 letters)



>gnl|CDD|178421 PLN02826, PLN02826, dihydroorotate dehydrogenase.
          Length = 409

 Score = 58.2 bits (141), Expect = 4e-11
 Identities = 19/48 (39%), Positives = 26/48 (54%)

Query: 43 PILFKFDAETAHNIAIWTAKYKLLPKSVYEDPPQLASQVWNLKFPNPL 90
          P+    D ETAH++AI  A   L+P+    DP  L  +VW   F NP+
Sbjct: 40 PLFRLLDPETAHSLAISAAARGLVPREKRPDPSVLGVEVWGRTFSNPI 87


>gnl|CDD|235388 PRK05286, PRK05286, dihydroorotate dehydrogenase 2; Reviewed.
          Length = 344

 Score = 54.8 bits (133), Expect = 5e-10
 Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 7/61 (11%)

Query: 37 YNNVLLPILFKFDAETAHNIAIWTAK-------YKLLPKSVYEDPPQLASQVWNLKFPNP 89
          Y  +  P+LFK D ETAH + I   K         LL + +    P+L   V  L FPNP
Sbjct: 2  YYPLARPLLFKLDPETAHELTIRALKRASRTPLLSLLRQRLTYTDPRLPVTVMGLTFPNP 61

Query: 90 L 90
          +
Sbjct: 62 V 62


>gnl|CDD|240089 cd04738, DHOD_2_like, Dihydroorotate dehydrogenase (DHOD) class
          2. DHOD catalyzes the oxidation of (S)-dihydroorotate
          to orotate. This is the fourth step and the only redox
          reaction in the de novo biosynthesis of UMP, the
          precursor of all pyrimidine nucleotides. DHOD requires
          FMN as co-factor. DHOD divides into class 1 and class 2
          based on their amino acid sequences, their cellular
          location and their natural electron acceptor used to
          reoxidize the flavin group. Members of class 1 are
          cytosolic enzymes and multimers, while class 2 enzymes
          are membrane associated, monomeric and use respiratory
          quinones as their physiological electron acceptors.
          Length = 327

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 22/51 (43%), Positives = 29/51 (56%), Gaps = 3/51 (5%)

Query: 43 PILFKFDAETAHNIAIWTAKYKLLPKSVYE---DPPQLASQVWNLKFPNPL 90
          P+LF  D ETAH +AI   K  L P  +     D P+L  +V+ L FPNP+
Sbjct: 2  PLLFLLDPETAHRLAIRALKLGLGPPLLLLLVYDDPRLEVEVFGLTFPNPV 52


>gnl|CDD|233243 TIGR01036, pyrD_sub2, dihydroorotate dehydrogenase, subfamily 2. 
          This model describes enzyme protein dihydroorotate
          dehydrogenase exclusively for subfamily 2. It includes
          members from bacteria, yeast, plants etc. The
          subfamilies 1 and 2 share extensive homology,
          particularly toward the C-terminus. This subfamily has
          a longer N-terminal region [Purines, pyrimidines,
          nucleosides, and nucleotides, Pyrimidine ribonucleotide
          biosynthesis].
          Length = 336

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 6/52 (11%)

Query: 45 LFKFDAETAHNIAIWTAK------YKLLPKSVYEDPPQLASQVWNLKFPNPL 90
          LF+ D E AH       +      +  L +S+     +L   V  L FPNPL
Sbjct: 8  LFQLDPERAHEFTFQQLRLITGTPFLALLRSLVGAKDKLPVTVLGLTFPNPL 59


>gnl|CDD|225157 COG2248, COG2248, Predicted hydrolase (metallo-beta-lactamase
           superfamily) [General function prediction only].
          Length = 304

 Score = 26.6 bits (59), Expect = 3.6
 Identities = 10/31 (32%), Positives = 14/31 (45%)

Query: 78  ASQVWNLKFPNPLAELRTQKPTEVSIQGPPT 108
           AS V        L  +  ++P  + I GPPT
Sbjct: 182 ASDVQGPINDEALEFILEKRPDVLIIGGPPT 212


>gnl|CDD|193205 pfam12729, 4HB_MCP_1, Four helix bundle sensory module for signal
          transduction.  This family is a four helix bundle that
          operates as a ubiquitous sensory module in prokaryotic
          signal-transduction. The 4HB_MCP is always found
          between two predicted transmembrane helices indicating
          that it detects only extracellular signals. In many
          cases the domain is associated with a cytoplasmic HAMP
          domain suggesting that most proteins carrying the
          bundle might share the mechanism of transmembrane
          signalling which is well-characterized in E coli
          chemoreceptors.
          Length = 181

 Score = 26.4 bits (59), Expect = 3.9
 Identities = 13/35 (37%), Positives = 20/35 (57%)

Query: 10 LVSLAAVSSGSFALFSGINIYQNNENYYNNVLLPI 44
          L++L  +  G   L+S   I +N+E  Y + LLPI
Sbjct: 14 LLALLLIIVGIVGLYSLKKINKNSETMYEDRLLPI 48


>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
          Length = 987

 Score = 26.5 bits (58), Expect = 4.1
 Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 5/68 (7%)

Query: 48  FDAETAHNIAIW-TAKYKLLPKSVYEDPPQLASQVWNLKFPNPLAELRTQKPTEVSIQGP 106
           F AE    +  W   ++K       +DP   A +VW+ +    +A+    K   V+ +  
Sbjct: 234 FHAEAGEYLGKWFDPQWK----KASDDPEARADRVWSEREARAIADAVRGKAATVTEESK 289

Query: 107 PTVSISGV 114
           PT   S +
Sbjct: 290 PTTQASPL 297


>gnl|CDD|217347 pfam03063, Prismane, Prismane/CO dehydrogenase family.  This family
           includes both hybrid-cluster proteins and the beta chain
           of carbon monoxide dehydrogenase. The hybrid-cluster
           proteins contain two Fe/S centres - a [4Fe-4S] cubane
           cluster, and a hybrid [4Fe-2S-2O] cluster. The
           physiological role of this protein is as yet unknown,
           although a role in nitrate/nitrite respiration has been
           suggested. The prismane protein from Escherichia coli
           was shown to contain hydroxylamine reductase activity
           (NH2OH + 2e + 2 H+ -> NH3 + H2O). This activity is
           rather low. Hydroxylamine reductase activity was also
           found in CO-dehydrogenase in which the active site Ni
           was replaced by Fe. The CO dehydrogenase contains a
           Ni-3Fe-2S-3O centre.
          Length = 505

 Score = 25.9 bits (58), Expect = 6.8
 Identities = 19/77 (24%), Positives = 26/77 (33%), Gaps = 18/77 (23%)

Query: 10  LVSLA-------AVSSGSFALFSGINIYQNNENYYNNVLLPILFKFDAETAHNIAIWTAK 62
           L S A       AV+ G   L  GINI+          L P    F +     +     +
Sbjct: 439 LASSAPEWYEQKAVAIGLTLLALGINIH----------LGPTPPAFGSPNVLKVLTENFE 488

Query: 63  YKLLPKS-VYEDPPQLA 78
             +     V EDP + A
Sbjct: 489 DLIGGIFTVEEDPKKAA 505


  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
   0.314    0.132    0.388 

Gapped
Lambda     K      H
   0.267   0.0774    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,124,941
Number of extensions: 515760
Number of successful extensions: 350
Number of sequences better than 10.0: 1
Number of HSP's gapped: 347
Number of HSP's successfully gapped: 15
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
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: 42 (22.0 bits)
S2: 53 (24.1 bits)