RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13211
         (89 letters)



>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain. 
          Length = 26

 Score = 29.7 bits (67), Expect = 0.022
 Identities = 13/24 (54%), Positives = 17/24 (70%)

Query: 23 RNHYRKHTGRKPFKCVVCKQFFAT 46
          R H R HTG KP+KC VC + F++
Sbjct: 3  RRHMRTHTGEKPYKCPVCGKSFSS 26


>gnl|CDD|223911 COG0841, AcrB, Cation/multidrug efflux pump [Defense mechanisms].
          Length = 1009

 Score = 28.3 bits (64), Expect = 0.40
 Identities = 5/18 (27%), Positives = 8/18 (44%)

Query: 19  IHIIRNHYRKHTGRKPFK 36
           I ++ N  R   G  P +
Sbjct: 401 IVVVENIERHMRGLPPRE 418


>gnl|CDD|104216 PRK09903, PRK09903, putative transporter YfdV; Provisional.
          Length = 314

 Score = 27.3 bits (60), Expect = 0.86
 Identities = 10/31 (32%), Positives = 18/31 (58%)

Query: 38  VVCKQFFATYSGAYQHLRRTHGQESCSSLKA 68
           V+   FF ++ G Y+  +RTH + +  +L A
Sbjct: 74  VIVGCFFFSWFGCYKFFKRTHAEAAVCALIA 104


>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
           Zn-finger [General function prediction only].
          Length = 493

 Score = 25.8 bits (56), Expect = 3.4
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 6/55 (10%)

Query: 13  QVRMFRIHIIRNHYRKHTGRKPFK----CVVCKQFFATYSGAYQHLRRTHGQESC 63
           ++R+FR   +R+H       + FK    C+ CK +F       +H R  H  E+C
Sbjct: 195 EIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKIYFYDDDELRRHCRLRH--EAC 247


>gnl|CDD|100083 cd06162, S2P-M50_PDZ_SREBP, Sterol regulatory element-binding
           protein (SREBP) Site-2 protease (S2P), a zinc
           metalloprotease (MEROPS family M50A), regulates
           intramembrane proteolysis (RIP) of SREBP and is part of
           a signal transduction mechanism involved in sterol and
           lipid metabolism. In sterol-depleted mammalian cells, a
           two-step proteolytic process releases the N-terminal
           domains of SREBPs from membranes of the endoplasmic
           reticulum (ER). These domains translocate into the
           nucleus, where they activate genes of cholesterol and
           fatty acid biosynthesis. The first cleavage occurs at
           Site-1 within the ER lumen to generate an intermediate
           that is subsequently released from the membrane by
           cleavage at Site-2, which lies within the first
           transmembrane domain. It is the second proteolytic step
           that is carried out by the SREBP Site-2 protease (S2P)
           which is present in this CD family.  This group appears
           to be limited to eumetazoan proteins and contains one
           PDZ domain.
          Length = 277

 Score = 25.4 bits (56), Expect = 3.7
 Identities = 10/31 (32%), Positives = 14/31 (45%), Gaps = 4/31 (12%)

Query: 43  FFATYSGAYQHLRRTHGQESCSSLKALRKLR 73
           FF  Y GAY  L   H       +  +++LR
Sbjct: 163 FFIIYPGAYVDLFTDHLN----LISPVQQLR 189


>gnl|CDD|131452 TIGR02399, salt_tol_Pase, glucosylglycerol 3-phosphatase.  Proteins
           in this family are glucosylglycerol-phosphate
           phosphatase, with the gene symbol stpA (Salt Tolerance
           Protein A). A motif characteristic of acid phosphatases
           is found, but otherwise this family shows little
           sequence similarity to other phosphatases. This enzyme
           acts on the glucosylglycerol phosphate, product of
           glucosylglycerol phosphate synthase and immediate
           precursor of the osmoprotectant glucosylglycerol.
          Length = 389

 Score = 25.6 bits (56), Expect = 4.5
 Identities = 9/39 (23%), Positives = 14/39 (35%), Gaps = 9/39 (23%)

Query: 5   GKTKSTDIQVRMFR--------IHIIRNHYRKHTGRKPF 35
           G   +TDIQ  M +        + ++       TG  P 
Sbjct: 221 GDIGTTDIQF-MLKGAVKEAGVLFLLNKFIYDSTGIAPL 258


>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
          Length = 619

 Score = 25.1 bits (56), Expect = 5.1
 Identities = 8/10 (80%), Positives = 8/10 (80%)

Query: 67  KALRKLRGPK 76
           KALRKLR P 
Sbjct: 599 KALRKLRHPS 608


>gnl|CDD|177931 PLN02294, PLN02294, cytochrome c oxidase subunit Vb.
          Length = 174

 Score = 24.8 bits (54), Expect = 6.3
 Identities = 7/13 (53%), Positives = 9/13 (69%)

Query: 33  KPFKCVVCKQFFA 45
           K F+C VC Q+F 
Sbjct: 140 KSFECPVCTQYFE 152


>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
          Length = 1486

 Score = 24.9 bits (55), Expect = 7.3
 Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 6/27 (22%)

Query: 30   TGRKPFKCVVCKQFFATYSGAYQHLRR 56
              ++P + V   QF   Y   YQHLR 
Sbjct: 1177 DPKRPERKV---QF---YIAVYQHLRE 1197


  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
   0.327    0.137    0.427 

Gapped
Lambda     K      H
   0.267   0.0655    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,380,446
Number of extensions: 327692
Number of successful extensions: 421
Number of sequences better than 10.0: 1
Number of HSP's gapped: 421
Number of HSP's successfully gapped: 17
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
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: 53 (24.3 bits)