RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy72
         (202 letters)



>gnl|CDD|150427 pfam09752, DUF2048, Uncharacterized conserved protein (DUF2048).
           The proteins in this family are conserved from plants to
           vertebrates. The function is unknown.
          Length = 337

 Score = 32.4 bits (74), Expect = 0.13
 Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 5/31 (16%)

Query: 169 FSWCRENGYGPLFPCILLGTGSSLGPGMAMM 199
             W    GYGPL   +   TG S+G  MA +
Sbjct: 164 LHWLEREGYGPL--GV---TGLSMGGHMAAL 189


>gnl|CDD|236634 PRK09926, PRK09926, putative chaperone protein EcpD; Provisional.
          Length = 246

 Score = 31.6 bits (72), Expect = 0.21
 Identities = 18/41 (43%), Positives = 22/41 (53%), Gaps = 6/41 (14%)

Query: 5   LFIR--NLKGSTSSVMKNLKGSALWNGEQGRSSL--DNSTP 41
           LF R   LKG+ S     LK S  W G +G++SL   N TP
Sbjct: 144 LFYRPDGLKGNPSEAPLALKWS--WAGSEGKASLRVTNPTP 182


>gnl|CDD|173876 cd08511, PBP2_NikA_DppA_OppA_like_5, The substrate-binding
           component of an uncharacterized ABC-type
           nickel/dipeptide/oligopeptide-like import system
           contains the type 2 periplasmic binding fold.  This
           family represents the substrate-binding domain of an
           uncharacterized ATP-binding cassette (ABC) type
           nickel/dipeptide/oligopeptide-like transporter. The
           oligopeptide-binding protein OppA and the
           dipeptide-binding protein DppA show significant sequence
           similarity to NikA, the initial nickel receptor. The
           DppA binds dipeptides and some tripeptides and is
           involved in chemotaxis toward dipeptides, whereas the
           OppA binds peptides of a wide range of lengths (2-35
           amino acid residues) and plays a role in recycling of
           cell wall peptides, which precludes any involvement in
           chemotaxis. Most of other periplasmic binding proteins
           are comprised of only two globular subdomains
           corresponding to domains I and III of the
           dipeptide/oligopeptide binding proteins. The structural
           topology of these domains is most similar to that of the
           type 2 periplasmic binding proteins (PBP2), which are
           responsible for the uptake of a variety of substrates
           such as phosphate, sulfate, polysaccharides,
           lysine/arginine/ornithine, and histidine.  The PBP2 bind
           their ligand in the cleft between these domains in a
           manner resembling a Venus flytrap. After binding their
           specific ligand with high affinity, they can interact
           with a cognate membrane transport complex comprised of
           two integral membrane domains and two cytoplasmically
           located ATPase domains. This interaction triggers the
           ligand translocation across the cytoplasmic membrane
           energized by ATP hydrolysis.  Besides transport
           proteins, the PBP2 superfamily includes the
           ligand-binding domains from ionotropic glutamate
           receptors, LysR-type transcriptional regulators,  and
           unorthodox sensor proteins involved in signal
           transduction.
          Length = 467

 Score = 29.2 bits (66), Expect = 1.6
 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 3/54 (5%)

Query: 30  EQGRSSLDNSTPKESYSAAGEIFLIKVPISFYSFARTSTWLIATSATVALLPIV 83
           E+ R+S D +  K  Y+ A +I    +P  +        + IA S  V  L   
Sbjct: 410 EKARASADPAERKALYNQAAKILADDLPYIYLYH---QPYYIAASKKVRGLVPY 460


>gnl|CDD|117240 pfam08667, BetR, BetR domain.  This family includes an N-terminal
          helix-turn-helix domain.
          Length = 146

 Score = 26.7 bits (59), Expect = 5.5
 Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 1/26 (3%)

Query: 7  IRNLKG-STSSVMKNLKGSALWNGEQ 31
          I N+ G S S   + LKGS  WN  Q
Sbjct: 28 IANILGLSFSQAYRKLKGSIPWNLAQ 53


>gnl|CDD|181186 PRK07983, PRK07983, exodeoxyribonuclease X; Provisional.
          Length = 219

 Score = 27.0 bits (60), Expect = 5.6
 Identities = 13/57 (22%), Positives = 20/57 (35%)

Query: 104 TRPFSWLIFAFQGVNFENVEHHHPLKKILDTGHYSPVYVAHKVPANVACGPHTHGSW 160
            RP S    A   +    V     ++ ++   + S  YVAH    +    P   G W
Sbjct: 40  DRPISPQAMAIHRITEAMVADKPWIEDVIPHYYGSEWYVAHNASFDRRVLPEMPGEW 96


>gnl|CDD|220799 pfam10536, PMD, Plant mobile domain.  This domain was identified by
           Babu and colleagues in a variety of transposases.
          Length = 357

 Score = 27.4 bits (61), Expect = 5.9
 Identities = 20/103 (19%), Positives = 27/103 (26%), Gaps = 25/103 (24%)

Query: 25  ALWNGEQGRSSLDNSTPKESYSAAGEIFLIKVPISFYSFARTSTWLIATSATVALLPIVF 84
           A W G   R S     P               P           W   T + V   P +F
Sbjct: 215 ARWCGRGSRHS----RPARDLKEYRAELDRLKPDDV-------VWRPYTDSLVNERPPLF 263

Query: 85  ESQRFEVQEMQRNQQKQWSTRPFSWLIFAFQGVNFENVEHHHP 127
                   E  +     W T     L+       F++VE + P
Sbjct: 264 LP------EDCKEDLSFWRTV--CPLVG------FDSVEWYLP 292


>gnl|CDD|131636 TIGR02587, TIGR02587, putative integral membrane protein TIGR02587.
            Members of this family are found in Nostoc sp. PCC
           7120, Agrobacterium tumefaciens, Sinorhizobium meliloti,
           and Gloeobacter violaceus in a conserved two-gene
           neighborhood. This family, as defined, includes some
           members of COG4711 but is narrower and strictly
           bacterial. Members appear to span the membrane seven
           times [Cell envelope, Other].
          Length = 271

 Score = 27.1 bits (60), Expect = 7.3
 Identities = 21/111 (18%), Positives = 40/111 (36%), Gaps = 21/111 (18%)

Query: 23  GSALWNGEQGRSSLDNSTPKESYSA----AGEIFLIKVPISFYSF------------ART 66
           G+AL   + G ++ +NS  +   ++      E+F + V   F SF             + 
Sbjct: 116 GAALARQQLGDTNQNNSLSEGKQNSEYGYLAELFAMLVGALFLSFNIAPTEEVPLIAYKI 175

Query: 67  STW--LIATSATVALL-PIVFESQRFEVQEMQRNQQKQWSTRPFSWLIFAF 114
           S         A++ ++   V++   F  Q  +R Q K    R        +
Sbjct: 176 SPPHIFALILASLVIMHAFVYQLG-FRGQH-KRRQGKGIFQRFLRETTIGY 224


>gnl|CDD|205395 pfam13214, DUF4022, Protein of unknown function (DUF4022).  This
           family of proteins is functionally uncharacterized. This
           family of proteins is found in bacteria. Proteins in
           this family are typically between 73 and 85 amino acids
           in length.
          Length = 83

 Score = 25.7 bits (56), Expect = 8.0
 Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 3/34 (8%)

Query: 162 SLYLCLTFSWCRENG--YGPLFPCILLGTGSSLG 193
           S+ +C ++ W + NG  Y  L   +LLGT S LG
Sbjct: 36  SIEIC-SYGWKKSNGIKYSCLLLSLLLGTASILG 68


  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    0.134    0.431 

Gapped
Lambda     K      H
   0.267   0.0587    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,060,072
Number of extensions: 877027
Number of successful extensions: 717
Number of sequences better than 10.0: 1
Number of HSP's gapped: 716
Number of HSP's successfully gapped: 15
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
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: 56 (25.7 bits)