RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6350
         (189 letters)



>gnl|CDD|143944 pfam00178, Ets, Ets-domain. 
          Length = 85

 Score = 88.1 bits (219), Expect = 3e-23
 Identities = 26/50 (52%), Positives = 37/50 (74%)

Query: 94  DREYCPRYIKWTNRERGVFKLVDSKAVSRLWGLHKNKPDMNYETMGRALR 143
             +    +I+WT R++G FKLVD + V+RLWG+ KNKP+MNY+ + RALR
Sbjct: 13  TDQDNRDFIRWTGRDKGEFKLVDPEEVARLWGIRKNKPNMNYDKLSRALR 62


>gnl|CDD|197710 smart00413, ETS, erythroblast transformation specific domain.
           variation of the helix-turn-helix motif.
          Length = 87

 Score = 86.2 bits (214), Expect = 1e-22
 Identities = 28/46 (60%), Positives = 34/46 (73%)

Query: 98  CPRYIKWTNRERGVFKLVDSKAVSRLWGLHKNKPDMNYETMGRALR 143
               IKWT+R+ G FKLVD + V+RLWG  KNKP+MNYE + RALR
Sbjct: 17  NSDIIKWTDRDEGEFKLVDPEEVARLWGQRKNKPNMNYEKLSRALR 62


>gnl|CDD|219117 pfam06638, Strabismus, Strabismus protein.  This family consists of
           several strabismus (STB) or Van Gogh-like (VANGL)
           proteins 1 and 2. The exact function of this family is
           unknown. It is thought, however that STB1 gene and STB2
           may be potent tumour suppressor gene candidates.
          Length = 507

 Score = 32.4 bits (74), Expect = 0.11
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 4/70 (5%)

Query: 35  GPSPTRPAIPTSVIQAAA---TSSHDDLYFLELGFQQRVKK-KIRRVKSEGTPGTGAKRK 90
           GP+    +   ++I AAA    SSH++ Y+ E  +++RV+K K R V +     T  KR 
Sbjct: 299 GPTSNSTSQSRALIAAAARRRDSSHNERYYEEAEYERRVRKRKARLVVAVEEAFTHIKRL 358

Query: 91  SREDREYCPR 100
             ED    P 
Sbjct: 359 QEEDENKKPA 368


>gnl|CDD|238527 cd01094, Alkanesulfonate_monoxygenase, Alkanesulfonate monoxygenase
           is the monoxygenase of a two-component system that
           catalyzes the conversion of alkanesulfonates to the
           corresponding aldehyde and sulfite. Alkanesulfonate
           monoxygenase (SsuD) has an absolute requirement for
           reduced flavin mononucleotide (FMNH2), which is provided
           by the NADPH-dependent FMN oxidoreductase (SsuE).
          Length = 244

 Score = 29.6 bits (67), Expect = 0.78
 Identities = 20/83 (24%), Positives = 31/83 (37%), Gaps = 13/83 (15%)

Query: 18  THNGYYHYNNGGFVMPPGPSPTRPAI-----PTSVIQAAATSSHDDLYFLELGFQQRVKK 72
              G ++     F+ P  P    P I       + I+ AA   H D+YF       +V +
Sbjct: 148 DFEGKFYRFKNAFLRPKPPQQPHPPIYFGGSSEAAIEFAAR--HADVYFTWGEPPAQVAE 205

Query: 73  KIRRVKSEGTPGTGAKRKSREDR 95
            I RV++       A    R+ R
Sbjct: 206 AIARVRAA------AAAAGRDVR 222


>gnl|CDD|217769 pfam03867, FTZ, Fushi tarazu (FTZ), N-terminal region.  This region
           contains the important motif (LXXLL) necessary for the
           interaction of FTZ with the nuclear receptor FTZ-F1. FTZ
           is thought to represents a category of LXXLL
           motif-dependent co-activators for nuclear receptors.
          Length = 264

 Score = 29.4 bits (65), Expect = 1.1
 Identities = 13/49 (26%), Positives = 20/49 (40%)

Query: 7   NYGGYMPPPSNTHNGYYHYNNGGFVMPPGPSPTRPAIPTSVIQAAATSS 55
           NY  +    S + + YY   +    +   P P  P IP  VI+ +   S
Sbjct: 53  NYYAHYSQESYSESCYYANYHHQPTLDTVPQPQVPTIPEPVIETSPVKS 101


>gnl|CDD|221818 pfam12868, DUF3824, Domain of unknwon function (DUF3824).  This
          is a repeating domain found in fungal proteins. It is
          proline-rich, and the function is not known.
          Length = 135

 Score = 27.2 bits (60), Expect = 3.1
 Identities = 12/40 (30%), Positives = 15/40 (37%), Gaps = 2/40 (5%)

Query: 13 PPPSNTHNGYYHYNNGGFVMPPGPSPTRPAIPTSVIQAAA 52
           PP +    Y + N   F  PPG +P  P  P      A 
Sbjct: 62 SPPVSDPRYYPNSNY--FPPPPGSTPVPPPGPQPGYNPAD 99


>gnl|CDD|181109 PRK07769, PRK07769, long-chain-fatty-acid--CoA ligase; Validated.
          Length = 631

 Score = 28.2 bits (63), Expect = 3.3
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 2   DLVPDNYGG-YMPPPSNTHN-GYYHYNNGGFVMPPGPSPTRPAIPTSVIQ 49
           D VPD  G  ++PP +N     Y  Y +G   +P G   T   +PT+V+Q
Sbjct: 162 DAVPDEVGATWVPPEANEDTIAYLQYTSGSTRIPAGVQITHLNLPTNVLQ 211


>gnl|CDD|226097 COG3567, COG3567, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 452

 Score = 27.2 bits (60), Expect = 5.9
 Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 10/57 (17%)

Query: 113 KLVDSKAVSRLWG---LHKN-------KPDMNYETMGRALRSSVVLTRLRTKCTQKQ 159
           K+  + A +RL+G   L           P      M  +L+S  VL R R      Q
Sbjct: 101 KVRKALAWARLYGGAVLFIGVHGQNPSLPLDPTSIMPGSLKSLTVLDRWRVALGSGQ 157


>gnl|CDD|133399 cd04772, HTH_TioE_rpt1, First Helix-Turn-Helix DNA binding domain
          of the regulatory protein TioE.  Putative
          helix-turn-helix (HTH) regulatory protein, TioE, and
          related proteins. TioE is part of the thiocoraline gene
          cluster, which is involved in the biosynthesis of the
          antitumor thiocoraline from the marine actinomycete,
          Micromonospora. These proteins share the N-terminal DNA
          binding domain with other transcription regulators of
          the MerR superfamily that promote transcription by
          reconfiguring the spacer between the -35 and -10
          promoter elements. Proteins in this family are unique
          within the MerR superfamily in that they are composed
          of just two adjacent MerR-like N-terminal domains; this
          CD contains the N-terminal or first repeat (rpt1) of
          these tandem MerR-like domain proteins.
          Length = 99

 Score = 25.8 bits (57), Expect = 6.3
 Identities = 8/18 (44%), Positives = 10/18 (55%)

Query: 10 GYMPPPSNTHNGYYHYNN 27
          G +PP   T NGY  Y +
Sbjct: 24 GLIPPAERTANGYRIYTD 41


>gnl|CDD|239215 cd02864, Heme_Cu_Oxidase_III_1, Heme-copper oxidase subunit III
           subfamily.  Heme-copper oxidases are transmembrane
           protein complexes in the respiratory chains of
           prokaryotes and mitochondria which couple the reduction
           of molecular oxygen to water to, proton pumping across
           the membrane. The heme-copper oxidase superfamily is
           diverse in terms of electron donors, subunit
           composition, and heme types.  This superfamily includes
           cytochrome c and ubiquinol oxidases.  Bacterial oxidases
           typically contain 3 or 4 subunits in contrast to the 13
           subunit bovine cytochrome c oxidase (CcO). Subunits I,
           II, and III of mammalian CcO are encoded within the
           mitochondrial genome and the remaining 10 subunits are
           encoded within the nuclear genome. Subunits I, II and
           III of ubiquinol oxidase are homologous to the
           corresponding subunits in CcO.  Although not required
           for catalytic activity, subunit III is believed to play
           a role in assembly of the multimer complex. Rhodobacter
           CcO subunit III stabilizes the integrity of the
           binuclear center in subunit I.  It has been proposed
           that Archaea acquired heme-copper oxidases through gene
           transfer from Gram-positive bacteria.
          Length = 202

 Score = 26.7 bits (59), Expect = 7.6
 Identities = 8/21 (38%), Positives = 14/21 (66%)

Query: 164 DVPLVFSSIMGHVLTSVIGTI 184
           ++PLV  +IM  +L +  GT+
Sbjct: 57  NIPLVLIAIMTFILITSSGTM 77


>gnl|CDD|133383 cd01108, HTH_CueR, Helix-Turn-Helix DNA binding domain of
          CueR-like transcription regulators.  Helix-turn-helix
          (HTH) transcription regulators CueR and ActP, copper
          efflux regulators. In Bacillus subtilis, copper induced
          CueR regulates the copZA operon, preventing copper
          toxicity. In Rhizobium leguminosarum, ActP controls
          copper homeostasis; it detects cytoplasmic copper
          stress and activates transcription in response to
          increasing copper concentrations. These proteins are
          comprised of two distinct domains that harbor the
          regulatory (effector-binding) site and the active
          (DNA-binding) site. Their conserved N-terminal domains
          contain winged HTH motifs that mediate DNA binding,
          while the C-terminal domains have two conserved
          cysteines that define a monovalent copper ion binding
          site. These proteins share the N-terminal DNA binding
          domain with other transcription regulators of the MerR
          superfamily that promote transcription by reconfiguring
          the spacer between the -35 and -10 promoter elements.
          Length = 127

 Score = 26.0 bits (58), Expect = 8.3
 Identities = 10/18 (55%), Positives = 12/18 (66%)

Query: 10 GYMPPPSNTHNGYYHYNN 27
          G +PPPS + NGY  YN 
Sbjct: 24 GLIPPPSRSDNGYRVYNQ 41


  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
   0.317    0.133    0.403 

Gapped
Lambda     K      H
   0.267   0.0751    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,561,748
Number of extensions: 845920
Number of successful extensions: 694
Number of sequences better than 10.0: 1
Number of HSP's gapped: 694
Number of HSP's successfully gapped: 17
Length of query: 189
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 98
Effective length of database: 6,901,388
Effective search space: 676336024
Effective search space used: 676336024
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 (21.6 bits)
S2: 56 (25.3 bits)