RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5091
         (112 letters)



>gnl|CDD|203990 pfam08583, Cmc1, Cytochrome c oxidase biogenesis protein Cmc1
          like.  Cmc1 is a metallo-chaperone like protein which
          is known to localise to the inner mitochondrial
          membrane in Saccharomyces cerevisiae. It is essential
          for full expression of cytochrome c oxidase and
          respiration. Cmc1 contains two Cx9C motifs and is able
          to bind copper(I). Cmc1 is thought to play a role in
          mitochondrial copper trafficking and transfer to
          cytochrome c oxidase.
          Length = 69

 Score = 53.1 bits (128), Expect = 9e-11
 Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 3/67 (4%)

Query: 22 MRDIART---EKCAEFTEALEKCGRDNGWKGVFTCRKENEKMKECMAHWYHNEDFRKEVT 78
          M  + R    +KCAE  +AL +C +    K    C K+   M +C+  +  +E  R    
Sbjct: 1  MHPLLRKKARKKCAELIKALAECHKGRTLKAFGKCNKQKRAMNKCLKQYRKDEALRDREK 60

Query: 79 EMYLQQR 85
          + Y+++R
Sbjct: 61 DEYIKER 67


>gnl|CDD|214937 smart00957, SecA_DEAD, SecA DEAD-like domain.  SecA protein binds
          to the plasma membrane where it interacts with proOmpA
          to support translocation of proOmpA through the
          membrane. SecA protein achieves this translocation, in
          association with SecY protein, in an ATP dependent
          manner. This domain represents the N-terminal
          ATP-dependent helicase domain, which is related to the.
          Length = 380

 Score = 27.8 bits (63), Expect = 1.0
 Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 7/47 (14%)

Query: 1  MGDPNDKTLRKLEKDV-----LIEQM--MRDIARTEKCAEFTEALEK 40
           G  ND+ L++L K V     L  +M  + D     K AEF E L +
Sbjct: 5  FGSKNDRELKRLRKIVDQINALEPEMEALSDEELRAKTAEFKERLAE 51


>gnl|CDD|217570 pfam03457, HA, Helicase associated domain.  This short domain is
           found in multiple copies in bacterial helicase proteins.
           The domain is predicted to contain 3 alpha helices. The
           function of this domain may be to bind nucleic acid.
          Length = 61

 Score = 25.7 bits (57), Expect = 2.2
 Identities = 10/23 (43%), Positives = 15/23 (65%)

Query: 83  QQRTDYRKTGLSKKMRKELESLG 105
           +QR  YRK  LS +  + L++LG
Sbjct: 37  RQRRRYRKGKLSPERIELLDALG 59


>gnl|CDD|217373 pfam03115, Astro_capsid, Astrovirus capsid protein precursor.  This
           product is encoded by astrovirus ORF2, one of the three
           astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein
           undergoes an intracellular cleavage to form a 79kD
           protein. Subsequently, extracellular trypsin cleavage
           yields the three proteins forming the infectious virion.
          Length = 787

 Score = 26.7 bits (59), Expect = 2.9
 Identities = 8/30 (26%), Positives = 13/30 (43%)

Query: 4   PNDKTLRKLEKDVLIEQMMRDIARTEKCAE 33
             +KT R +  D+L   +    A +  C E
Sbjct: 738 LAEKTRRSVYMDLLYSGLRPSSAWSHACEE 767


>gnl|CDD|218124 pfam04518, Effector_1, Effector from type III secretion system.
           This is a family of effector proteins which are secreted
           by the type III secretion system. The precise function
           of this family is unknown.
          Length = 380

 Score = 26.1 bits (58), Expect = 4.2
 Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 2/33 (6%)

Query: 6   DKTLRKLEKDVLIEQMMRDIARTEKCAEFTEAL 38
           D+ L KLEK+   EQ+ RDI R E+       L
Sbjct: 200 DEALAKLEKE--KEQIRRDIKRCERAKAVLNKL 230


>gnl|CDD|221117 pfam11460, DUF3007, Protein of unknown function (DUF3007).  This is
           a family of uncharacterized proteins found in bacteria
           and eukaryotes.
          Length = 104

 Score = 25.4 bits (56), Expect = 5.6
 Identities = 11/35 (31%), Positives = 21/35 (60%), Gaps = 5/35 (14%)

Query: 73  FRKEVTEMYLQQRTDYRK---TGLSKKMRKELESL 104
              ++T  Y+QQR DYR+      +++++K  +SL
Sbjct: 58  VTGKMT--YMQQRRDYREAYDALTNEELQKRFDSL 90


>gnl|CDD|224295 COG1377, FlhB, Flagellar biosynthesis pathway, component FlhB [Cell
           motility and secretion / Intracellular trafficking and
           secretion].
          Length = 363

 Score = 25.6 bits (57), Expect = 5.9
 Identities = 8/27 (29%), Positives = 19/27 (70%), Gaps = 1/27 (3%)

Query: 2   GDPNDKT-LRKLEKDVLIEQMMRDIAR 27
           GDP  K+ +R++++++   +MM D+ +
Sbjct: 236 GDPEVKSRIRQMQREIARRRMMSDVPK 262


>gnl|CDD|99906 cd05564, PTS_IIB_chitobiose_lichenan, PTS_IIB_chitobiose_lichenan:
           subunit IIB of enzyme II (EII) of the
           N,N-diacetylchitobiose-specific and lichenan-specific
           phosphoenolpyruvate:carbohydrate phosphotransferase
           system (PTS). In these systems, EII is either a
           lichenan- or an N,N-diacetylchitobiose-specific permease
           with two cytoplasmic domains (IIA and IIB) and a
           transmembrane channel IIC domain. In the chitobiose
           system, these subunits are expressed as separate
           proteins from chbA, chbB, and chbC of the chb operon
           (formerly the cel (cellulose) operon). In the lichenan
           system, these subunits are expressed from licA, licB,
           and licC of the lic operon. The lic operon of Bacillus
           subtilis is required for the transport and degradation
           of oligomeric beta-glucosides, which are produced by
           extracellular enzymes on substrates such as lichenan or
           barley glucan. The lic operon is transcribed from a
           gammaA-dependent promoter and is inducible by lichenan,
           lichenan hydrolysate, and cellobiose. The IIB domain
           fold includes a central four-stranded parallel open
           twisted beta-sheet flanked by alpha-helices on both
           sides. The seven major PTS systems with this IIB fold
           include chitobiose/lichenan, ascorbate, lactose,
           galactitol, mannitol, fructose, and a sensory system
           with similarity to the bacterial bgl system.
          Length = 96

 Score = 24.4 bits (54), Expect = 10.0
 Identities = 8/19 (42%), Positives = 11/19 (57%)

Query: 93  LSKKMRKELESLGYEINIK 111
           L KKM+K  E  G +  I+
Sbjct: 15  LVKKMKKAAEKRGIDAEIE 33


  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
   0.316    0.132    0.393 

Gapped
Lambda     K      H
   0.267   0.0881    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,600,668
Number of extensions: 461147
Number of successful extensions: 592
Number of sequences better than 10.0: 1
Number of HSP's gapped: 589
Number of HSP's successfully gapped: 30
Length of query: 112
Length of database: 10,937,602
Length adjustment: 76
Effective length of query: 36
Effective length of database: 7,566,698
Effective search space: 272401128
Effective search space used: 272401128
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: 53 (23.9 bits)