RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2448
         (151 letters)



>gnl|CDD|172808 PRK14332, PRK14332, (dimethylallyl)adenosine tRNA
           methylthiotransferase; Provisional.
          Length = 449

 Score = 27.3 bits (60), Expect = 3.3
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 6/52 (11%)

Query: 76  GSELCEAVTMINSYFPEDIVRYYSPRCTD------HLLAKVDQFTPQVSLPL 121
            ++    + M+      + +R+ SP   D       L+AK  +F P + LPL
Sbjct: 217 STDFAGLIQMLLDETTIERIRFTSPHPKDFPDHLLSLMAKNPRFCPNIHLPL 268


>gnl|CDD|214840 smart00829, PKS_ER, Enoylreductase.  Enoylreductase in Polyketide
           synthases.
          Length = 287

 Score = 27.4 bits (62), Expect = 3.5
 Identities = 11/33 (33%), Positives = 18/33 (54%)

Query: 17  FLSNVSFSFVDLLLYESPPEILLPALKQLCKIF 49
           F  NVS+  VDL   E  P+ +   L ++ ++F
Sbjct: 219 FRPNVSYHAVDLDALEEGPDRIRELLAEVLELF 251


>gnl|CDD|222996 PHA03131, PHA03131, dUTPase; Provisional.
          Length = 286

 Score = 26.9 bits (60), Expect = 4.0
 Identities = 20/71 (28%), Positives = 27/71 (38%), Gaps = 8/71 (11%)

Query: 74  PAGSELCEAVTMINSYFPEDIVRYYSPRCTDHLL----AKV----DQFTPQVSLPLITCA 125
           PAGS +C+ V M   + P       S RC    +    A+V        P  S   +  +
Sbjct: 208 PAGSRICQVVFMHKDHLPSFFNPLLSARCLGPRILFRWARVSFEDIPKDPCTSSKTLRQS 267

Query: 126 PDTPSDMSLGD 136
            D  SD S G 
Sbjct: 268 EDGDSDPSRGT 278


>gnl|CDD|224444 COG1527, NtpC, Archaeal/vacuolar-type H+-ATPase subunit C [Energy
           production and conversion].
          Length = 346

 Score = 26.9 bits (60), Expect = 4.7
 Identities = 12/44 (27%), Positives = 16/44 (36%), Gaps = 5/44 (11%)

Query: 62  AGGLKRVQALKPPAG-----SELCEAVTMINSYFPEDIVRYYSP 100
           AG  + +  L  P G       L EA TM       +   Y +P
Sbjct: 113 AGDPEEISDLLIPLGDFETLLTLAEAKTMEEVVETLEGTTYLAP 156


>gnl|CDD|176179 cd05195, enoyl_red, enoyl reductase of polyketide synthase.
           Putative enoyl reductase of polyketide synthase.
           Polyketide synthases produce polyketides in step by step
           mechanism that is similar to fatty acid synthesis. Enoyl
           reductase reduces a double to single bond. Erythromycin
           is one example of a polyketide generated by 3 complex
           enzymes (megasynthases). 2-enoyl thioester reductase
           (ETR) catalyzes the NADPH-dependent dependent conversion
           of trans-2-enoyl acyl carrier protein/coenzyme A
           (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis.
           2-enoyl thioester reductase activity has been linked in 
           Candida tropicalis as essential in maintaining
           mitiochondrial respiratory function. This ETR family is
           a part of the medium chain dehydrogenase/reductase
           family, but lack the zinc coordination sites
           characteristic of the alcohol dehydrogenases in this
           family. NAD(P)(H)-dependent oxidoreductases are the
           major enzymes in the interconversion of alcohols and
           aldehydes or ketones. Alcohol dehydrogenase in the liver
           converts ethanol and NAD+ to acetaldehyde and NADH,
           while in yeast and some other microorganisms ADH
           catalyzes the conversion acetaldehyde to ethanol in
           alcoholic fermentation.   ADH is a member of the medium
           chain alcohol dehydrogenase family (MDR), which has a
           NAD(P)(H)-binding domain in a Rossmann fold of a
           beta-alpha form.  The NAD(H)-binding region is comprised
           of 2 structurally similar halves, each of which contacts
           a mononucleotide. The N-terminal catalytic domain has a
           distant homology  to GroES. These proteins typically
           form dimers (typically higher plants, mammals) or
           tetramers (yeast, bacteria), and have 2 tightly bound
           zinc atoms per subunit, a catalytic zinc at the active
           site, and a structural zinc in a lobe of the catalytic
           domain. NAD(H) binding occurs in the cleft between the
           catalytic  and coenzyme-binding domains, at the active
           site, and coenzyme binding induces a conformational
           closing of this cleft. Coenzyme binding typically
           precedes and contributes to substrate binding.
          Length = 293

 Score = 26.4 bits (59), Expect = 6.3
 Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 2/42 (4%)

Query: 10  NSGLQIS-FLSNVSFSFVDLL-LYESPPEILLPALKQLCKIF 49
           NS L +  FL NVSFS VDL  L    PE+L   L+++ ++ 
Sbjct: 216 NSKLGMRPFLRNVSFSSVDLDQLARERPELLRELLREVLELL 257


>gnl|CDD|220610 pfam10165, Ric8, Guanine nucleotide exchange factor synembryn.
          Ric8 is involved in the EGL-30 neurotransmitter
          signalling pathway. It is a guanine nucleotide exchange
          factor that regulates neurotransmitter secretion.
          Length = 439

 Score = 26.1 bits (58), Expect = 7.7
 Identities = 11/36 (30%), Positives = 18/36 (50%)

Query: 35 PEILLPALKQLCKIFPVDLKARRVFVSAGGLKRVQA 70
           ++   ALK LC    +  KAR++FV  G  + +  
Sbjct: 43 EDVRREALKCLCNALFLSPKARQLFVDLGLGEGLAE 78


>gnl|CDD|111047 pfam02108, FliH, Flagellar assembly protein FliH. 
          Length = 128

 Score = 25.6 bits (57), Expect = 8.3
 Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 4/55 (7%)

Query: 35  PEILLPALKQLCKIFPVDLKARRVFVSAGGLKRVQALKP----PAGSELCEAVTM 85
           PE++L  +++     PV      + ++   L  V+          G  L    ++
Sbjct: 49  PELILALVREALAALPVLSGKVTLRLNPDDLALVEEHLGDELKARGWRLVADPSL 103


>gnl|CDD|129570 TIGR00478, tly, hemolysin TlyA family protein.  Hemolysins are
          exotoxins that attack blood cell membranes and cause
          cell rupture, often by forming a pore in the membrane.
          At least two members of this protein family have been
          characterized indirectly as pore-forming hemolysins,
          one from the spirochete Serpula (Treponema)
          hyodysenteriae and one from Mycobacterium tuberculosis.
          However, homology domains in this protein suggest
          methyltransferase activity (pfam01728) and RNA-binding
          activity (pfam01479) [Unknown function, General].
          Length = 228

 Score = 25.9 bits (57), Expect = 8.9
 Identities = 9/23 (39%), Positives = 14/23 (60%)

Query: 50 PVDLKARRVFVSAGGLKRVQALK 72
           ++L    +FVS GG K  +AL+
Sbjct: 46 KIELLQNPLFVSRGGEKLKEALE 68


>gnl|CDD|225969 COG3435, COG3435, Gentisate 1,2-dioxygenase [Secondary
          metabolites biosynthesis, transport, and catabolism].
          Length = 351

 Score = 25.8 bits (57), Expect = 9.7
 Identities = 12/48 (25%), Positives = 25/48 (52%)

Query: 29 LLYESPPEILLPALKQLCKIFPVDLKARRVFVSAGGLKRVQALKPPAG 76
          L+ + P    +PAL +  +I P+ L++  +  +   ++RV  L+ P  
Sbjct: 35 LVPKEPKPDCVPALWKYEEIRPLLLRSGELISAREAVRRVIYLENPGL 82


  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
   0.319    0.136    0.404 

Gapped
Lambda     K      H
   0.267   0.0902    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,868,343
Number of extensions: 711233
Number of successful extensions: 597
Number of sequences better than 10.0: 1
Number of HSP's gapped: 597
Number of HSP's successfully gapped: 14
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 (21.7 bits)
S2: 54 (24.3 bits)