RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4355
         (71 letters)



>gnl|CDD|215646 pfam00001, 7tm_1, 7 transmembrane receptor (rhodopsin family).
          This family contains, amongst other G-protein-coupled
          receptors (GCPRs), members of the opsin family, which
          have been considered to be typical members of the
          rhodopsin superfamily. They share several motifs,
          mainly the seven transmembrane helices, GCPRs of the
          rhodopsin superfamily. All opsins bind a chromophore,
          such as 11-cis-retinal. The function of most opsins
          other than the photoisomerases is split into two steps:
          light absorption and G-protein activation.
          Photoisomerases, on the other hand, are not coupled to
          G-proteins - they are thought to generate and supply
          the chromophore that is used by visual opsins.
          Length = 251

 Score = 44.2 bits (105), Expect = 4e-07
 Identities = 13/41 (31%), Positives = 21/41 (51%)

Query: 24 AAILLEKNLQSVANYLIVSLAVADLMVACLVMPLGAVYELN 64
            IL  K L++  N  +++LAVADL+    + P    Y + 
Sbjct: 1  LVILRTKKLRTPTNIFLLNLAVADLLFLLTLPPWALYYLVG 41


>gnl|CDD|192535 pfam10320, 7TM_GPCR_Srsx, Serpentine type 7TM GPCR chemoreceptor
          Srsx.  Chemoreception is mediated in Caenorhabditis
          elegans by members of the seven-transmembrane
          G-protein-coupled receptor class (7TM GPCRs) of
          proteins which are of the serpentine type. Srsx is a
          solo family amongst the superfamilies of
          chemoreceptors. Chemoperception is one of the central
          senses of soil nematodes like C. elegans which are
          otherwise 'blind' and 'deaf'.
          Length = 257

 Score = 27.9 bits (63), Expect = 0.36
 Identities = 12/41 (29%), Positives = 19/41 (46%)

Query: 19 NVFVIAAILLEKNLQSVANYLIVSLAVADLMVACLVMPLGA 59
          NV +I     +K L+S  +YLI    +ADL+     +    
Sbjct: 8  NVIMIILTFKKKKLRSKCSYLICVQCLADLLCLSGEIIFVV 48


>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
           subunit (SR-beta), together with SR-alpha, forms the
           heterodimeric signal recognition particle (SRP).  Signal
           recognition particle receptor, beta subunit (SR-beta).
           SR-beta and SR-alpha form the heterodimeric signal
           recognition particle (SRP or SR) receptor that binds SRP
           to regulate protein translocation across the ER
           membrane. Nascent polypeptide chains are synthesized
           with an N-terminal hydrophobic signal sequence that
           binds SRP54, a component of the SRP. SRP directs
           targeting of the ribosome-nascent chain complex (RNC) to
           the ER membrane via interaction with the SR, which is
           localized to the ER membrane. The RNC is then
           transferred to the protein-conducting channel, or
           translocon, which facilitates polypeptide translation
           across the ER membrane or integration into the ER
           membrane. SR-beta is found only in eukaryotes; it is
           believed to control the release of the signal sequence
           from SRP54 upon binding of the ribosome to the
           translocon. High expression of SR-beta has been observed
           in human colon cancer, suggesting it may play a role in
           the development of this type of cancer.
          Length = 202

 Score = 25.0 bits (55), Expect = 3.3
 Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 7/40 (17%)

Query: 20  VFVIAAILLEKNLQSVANYL-------IVSLAVADLMVAC 52
           VFV+ +   +KN++ VA +L               +++AC
Sbjct: 76  VFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPILIAC 115


>gnl|CDD|184957 PRK14995, PRK14995, methyl viologen resistance protein SmvA;
          Provisional.
          Length = 495

 Score = 24.7 bits (54), Expect = 4.8
 Identities = 13/41 (31%), Positives = 24/41 (58%)

Query: 20 VFVIAAILLEKNLQSVANYLIVSLAVADLMVACLVMPLGAV 60
          V  +AA  L   L +  N L+  + +  L++A +V+P+GA+
Sbjct: 24 VLHVAAPTLSMTLGASGNELLWIIDIYSLVMAGMVLPMGAL 64


  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    0.137    0.392 

Gapped
Lambda     K      H
   0.267   0.0710    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,473,170
Number of extensions: 257947
Number of successful extensions: 317
Number of sequences better than 10.0: 1
Number of HSP's gapped: 317
Number of HSP's successfully gapped: 13
Length of query: 71
Length of database: 10,937,602
Length adjustment: 41
Effective length of query: 30
Effective length of database: 9,119,088
Effective search space: 273572640
Effective search space used: 273572640
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: 40 (21.6 bits)
S2: 53 (24.2 bits)