RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11848
         (184 letters)



>gnl|CDD|216332 pfam01151, ELO, GNS1/SUR4 family.  Members of this family are
           involved in long chain fatty acid elongation systems
           that produce the 26-carbon precursors for ceramide and
           sphingolipid synthesis. Predicted to be integral
           membrane proteins, in eukaryotes they are probably
           located on the endoplasmic reticulum. Yeast ELO3 affects
           plasma membrane H+-ATPase activity, and may act on a
           glucose-signaling pathway that controls the expression
           of several genes that are transcriptionally regulated by
           glucose such as PMA1.
          Length = 244

 Score =  124 bits (314), Expect = 1e-35
 Identities = 62/187 (33%), Positives = 90/187 (48%), Gaps = 25/187 (13%)

Query: 12  FLMESPIPTLVMVGIYLYIVVFLGPWIMANRKPFKLKTVLIVYNAAQVIFSLAMLWEHLM 71
            L+ SP P ++++ +YL   VFLGP IM NRKPF LK +LIV+N   V+ SL   +  L 
Sbjct: 1   PLLSSPWPVILIIVLYLV-FVFLGPKIMRNRKPFDLKRLLIVHNLFLVLLSLYGFYGLLA 59

Query: 72  SGWLLDYSYKCQPVDYSHNPTALRHLMSGWLLDYSY----------------KCQPVD-- 113
                   Y    V YS +P A+R  + G+                      K + +   
Sbjct: 60  GAGWGRGLYLALCVCYSFDPGAIRMGLVGFWYWLFLSKFLELLDTVFLVLRKKQRQLSFL 119

Query: 114 --YSHNPTALRVSFWVIIECFNQGGHGTFSNLINNIVHVIMYFYYMVSAMGPEYQKYLWW 171
             Y H    L   +  +   +  GGH  F  L+N+ VHVIMYFYY ++A+G      +WW
Sbjct: 120 HVYHHATMLL---YSWLGLKYGPGGHFWFIALLNSFVHVIMYFYYFLAALGAR-GLPVWW 175

Query: 172 KRHLTTL 178
           K+++T L
Sbjct: 176 KKYITQL 182


>gnl|CDD|217553 pfam03430, TATR, Trans-activating transcriptional regulator.  This
           family of trans-activating transcriptional regulator
           (TATR), also known as intermediate early protein 1, are
           common to the Nucleopolyhedroviruses.
          Length = 571

 Score = 32.2 bits (73), Expect = 0.13
 Identities = 14/56 (25%), Positives = 21/56 (37%), Gaps = 12/56 (21%)

Query: 137 HGTFSNLINNIVHVIMY-----FYYMVSAMGPEYQKYLWWK-------RHLTTLTV 180
              F   + N  ++ MY     F  ++ +MG    K L  K       R L TL +
Sbjct: 310 KDVFQTTLINHFNLDMYYAQTTFVTLMQSMGESKSKMLLNKLYEMIQDRSLFTLPI 365


>gnl|CDD|217262 pfam02875, Mur_ligase_C, Mur ligase family, glutamate ligase
          domain.  This family contains a number of related
          ligase enzymes which have EC numbers 6.3.2.*. This
          family includes: MurC, MurD, MurE, MurF, Mpl and FolC.
          MurC, MurD, Mure and MurF catalyze consecutive steps in
          the synthesis of peptidoglycan. Peptidoglycan consists
          of a sheet of two sugar derivatives, with one of these
          N-acetylmuramic acid attaching to a small pentapeptide.
          The pentapeptide is is made of L-alanine, D-glutamic
          acid, Meso-diaminopimelic acid and D-alanyl alanine.
          The peptide moiety is synthesised by successively
          adding these amino acids to UDP-N-acetylmuramic acid.
          MurC transfers the L-alanine, MurD transfers the
          D-glutamate, MurE transfers the diaminopimelic acid,
          and MurF transfers the D-alanyl alanine. This family
          also includes Folylpolyglutamate synthase that
          transfers glutamate to folylpolyglutamate.
          Length = 88

 Score = 26.9 bits (60), Expect = 2.8
 Identities = 6/13 (46%), Positives = 8/13 (61%)

Query: 85 VDYSHNPTALRHL 97
           DY+HNP A+   
Sbjct: 18 DDYAHNPDAMEAA 30



 Score = 26.2 bits (58), Expect = 4.7
 Identities = 6/12 (50%), Positives = 8/12 (66%)

Query: 112 VDYSHNPTALRV 123
            DY+HNP A+  
Sbjct: 18  DDYAHNPDAMEA 29


>gnl|CDD|185330 PRK15432, PRK15432, autoinducer 2 ABC transporter permease LsrC;
          Provisional.
          Length = 344

 Score = 27.8 bits (62), Expect = 3.6
 Identities = 11/40 (27%), Positives = 23/40 (57%)

Query: 26 IYLYIVVFLGPWIMANRKPFKLKTVLIVYNAAQVIFSLAM 65
            L IV+        +R+   L+T+ +V+++AQ++  LA+
Sbjct: 13 ALLAIVLLFVLLGFLDRQYLSLQTLTMVFSSAQILILLAI 52


>gnl|CDD|227665 COG5373, COG5373, Predicted membrane protein [Function unknown].
          Length = 931

 Score = 27.9 bits (62), Expect = 3.9
 Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 7/60 (11%)

Query: 11  WFLMESPIPTLVMVGIYLYIVVFLGPWIMANRKPFKLKTVLIVYNAAQVIFSLAMLWEHL 70
            F     +  L  VG  L+ +++  P + A+ +PF    +++          +A+ W   
Sbjct: 292 RFRAWRVLNLLAFVGTGLWGLLYYTPALGASTEPFLFLLLVMYA-------GIALRWPGR 344


>gnl|CDD|237444 PRK13607, PRK13607, proline dipeptidase; Provisional.
          Length = 443

 Score = 27.2 bits (61), Expect = 6.0
 Identities = 11/18 (61%), Positives = 11/18 (61%)

Query: 110 QPVDYSHNPTALRVSFWV 127
           QPVDY HN   L  SFW 
Sbjct: 84  QPVDYWHNVEPLPESFWT 101


>gnl|CDD|206292 pfam14123, DUF4290, Domain of unknown function (DUF4290).  This
           family of proteins is functionally uncharacterized. This
           family of proteins is found in bacteria. Proteins in
           this family are typically between 200 and 221 amino
           acids in length. There are two conserved sequence
           motifs: EYGR and KLWD.
          Length = 177

 Score = 26.4 bits (59), Expect = 6.8
 Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 14/46 (30%)

Query: 65  MLWEHL--MSGWLLDYSY------------KCQPVDYSHNPTALRH 96
            LW+HL  MS + LD               K +P+ Y  N    RH
Sbjct: 62  KLWDHLFIMSDFKLDVDSPYPIPSKEKLAKKPEPLPYPQNRIKYRH 107


>gnl|CDD|201962 pfam01773, Nucleos_tra2_N, Na+ dependent nucleoside transporter
          N-terminus.  This family consists of nucleoside
          transport proteins. Rat CNT 2 is a purine-specific
          Na+-nucleoside cotransporter localised to the bile
          canalicular membrane. Rat CNT 1 is a a Na+-dependent
          nucleoside transporter selective for pyrimidine
          nucleosides and adenosine it also transports the
          anti-viral nucleoside analogues AZT and ddC. This
          alignment covers the N terminus of this family.
          Length = 75

 Score = 25.0 bits (56), Expect = 8.7
 Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 3/40 (7%)

Query: 30 IVVFLG-PWIM-ANRKPFKLKTVLIVYNAAQVIFSLAMLW 67
          IVV L   +++  NRK    +TV     A Q++ +L +L 
Sbjct: 3  IVVLLLIAFLLSENRKAINWRTVGGGL-ALQLLLALFVLK 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
   0.328    0.140    0.479 

Gapped
Lambda     K      H
   0.267   0.0811    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,705,075
Number of extensions: 888720
Number of successful extensions: 1038
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1034
Number of HSP's successfully gapped: 30
Length of query: 184
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 93
Effective length of database: 6,901,388
Effective search space: 641829084
Effective search space used: 641829084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 56 (25.2 bits)