RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy7228
         (151 letters)



>gnl|CDD|203730 pfam07700, HNOB, Heme NO binding.  The HNOB (Heme NO Binding)
           domain, is a predominantly alpha-helical domain and
           binds heme via a covalent linkage to histidine. The HNOB
           domain is predicted to function as a heme-dependent
           sensor for gaseous ligands, and transduce diverse
           downstream signals, in both bacteria and animals.
          Length = 171

 Score = 96.2 bits (240), Expect = 6e-26
 Identities = 34/59 (57%), Positives = 41/59 (69%), Gaps = 1/59 (1%)

Query: 4   RNFVNF-QNLDALHDHLGTLYPGMRAPSFRCTETDDGALVLHYYSDRPGLEHIVIGIVK 61
           RN  +F Q+LD +H  +  LYPG R PSFRCTE  DG LVLHY S R GL H V+G++K
Sbjct: 92  RNLRDFLQSLDNIHVEVTKLYPGARPPSFRCTEESDGGLVLHYRSKRTGLYHYVLGLLK 150


>gnl|CDD|143636 cd07302, CHD, cyclase homology domain.  Catalytic domains of the
           mononucleotidyl cyclases (MNC's), also called cyclase
           homology domains (CHDs), are part of the class III
           nucleotidyl cyclases. This class includes eukaryotic and
           prokaryotic adenylate cyclases (AC's) and guanylate
           cyclases (GC's). They seem to share a common catalytic
           mechanism in their requirement for two magnesium ions to
           bind the polyphosphate moiety of the nucleotide.
          Length = 177

 Score = 40.3 bits (95), Expect = 7e-05
 Identities = 13/27 (48%), Positives = 17/27 (62%)

Query: 117 EDPQFQFEYRGPVTMKGKSEPMEVWFL 143
            D  F+FE  G V +KGKS P+ V+ L
Sbjct: 151 GDAGFEFEELGEVELKGKSGPVRVYRL 177


>gnl|CDD|201086 pfam00211, Guanylate_cyc, Adenylate and Guanylate cyclase catalytic
           domain. 
          Length = 184

 Score = 35.3 bits (82), Expect = 0.005
 Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 5/42 (11%)

Query: 104 SDFVSRLLCSPDNEDPQFQFEYRGPVTMKGKSEPMEVWFLSR 145
           S+   RLL        QF+F  RG V +KGK + ME +FL+ 
Sbjct: 148 SEETYRLL----KTREQFEFTERGEVEVKGKGK-METYFLNG 184


>gnl|CDD|225025 COG2114, CyaA, Adenylate cyclase, family 3 (some proteins contain
           HAMP domain) [Signal transduction mechanisms].
          Length = 227

 Score = 30.6 bits (69), Expect = 0.21
 Identities = 8/46 (17%), Positives = 15/46 (32%), Gaps = 6/46 (13%)

Query: 102 ITSDFVSRLLCSPDNEDPQFQFEYRGPVTMKGKSEPMEVWFLSRGK 147
           ++      +       D    F   G   +KG + P+ V+ L    
Sbjct: 178 LSEATYDLV------RDLVDLFSGLGSHRLKGLARPVRVYQLCHRS 217


>gnl|CDD|217467 pfam03274, Foamy_BEL, Foamy virus BEL 1/2 protein. 
          Length = 222

 Score = 28.3 bits (63), Expect = 1.6
 Identities = 9/40 (22%), Positives = 16/40 (40%), Gaps = 1/40 (2%)

Query: 113 SPDNEDPQ-FQFEYRGPVTMKGKSEPMEVWFLSRGKEYIV 151
              +  P  F+  Y   +      EPM +W+   GK ++ 
Sbjct: 97  EQSHTAPTYFEVYYECKMCDTVIHEPMPIWWDPSGKLWMK 136


>gnl|CDD|226864 COG4457, SrfB, Uncharacterized protein conserved in bacteria,
           putative virulence factor [Function unknown].
          Length = 1014

 Score = 27.9 bits (62), Expect = 2.7
 Identities = 11/31 (35%), Positives = 14/31 (45%)

Query: 111 LCSPDNEDPQFQFEYRGPVTMKGKSEPMEVW 141
           L   D   P   F+ RGPV +  +  P E W
Sbjct: 891 LDKADASLPDAHFDLRGPVRLGFRQLPNERW 921


>gnl|CDD|219447 pfam07520, SrfB, Virulence factor SrfB.  This family includes
           homologues of SsrAB is a two-component regulatory system
           encoded within the Salmonella pathogenicity island
           SPI-2. Among the products of genes activated by SsrAB
           within epithelial and macrophage cells is Salmonella
           typhimurium srfB. Homologues are found in several other
           proteobacteria.
          Length = 999

 Score = 26.9 bits (60), Expect = 5.3
 Identities = 13/31 (41%), Positives = 16/31 (51%)

Query: 111 LCSPDNEDPQFQFEYRGPVTMKGKSEPMEVW 141
           L +PD E P   FE RGPV +  +    E W
Sbjct: 880 LDAPDAELPDAHFELRGPVRLGFRQLDNERW 910


>gnl|CDD|129265 TIGR00161, TIGR00161, TIGR00161 family protein.  This model
           represents one out of two closely related ortholgous
           sets of proteins that, so far, are found only in the
           Archaea. This ortholog set includes MJ0106 from
           Methanococcus jannaschii and AF1251 from Archaeoglobus
           fulgidus, but not MJ1210 or AF0525 [Hypothetical
           proteins, Conserved].
          Length = 238

 Score = 26.3 bits (58), Expect = 6.9
 Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 7/60 (11%)

Query: 19  LGTLYPGMRAPSFRCTETDDGALVLHYYSDRPGLEHIVIGIVK--VSW---NKHQLTCTF 73
           L  LY G+  P  R  E  DG ++    SD      +V  +    V W   N  +   +F
Sbjct: 57  LAVLYKGVAIPPVRIYEGKDGIVLFL--SDFIIPPAVVYDMTNAIVEWMVRNNSRELISF 114


  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
   0.321    0.139    0.427 

Gapped
Lambda     K      H
   0.267   0.0750    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,708,713
Number of extensions: 680699
Number of successful extensions: 451
Number of sequences better than 10.0: 1
Number of HSP's gapped: 451
Number of HSP's successfully gapped: 12
Length of query: 151
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 63
Effective length of database: 7,034,450
Effective search space: 443170350
Effective search space used: 443170350
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.5 bits)