RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4594
         (82 letters)



>gnl|CDD|215208 PLN02366, PLN02366, spermidine synthase.
          Length = 308

 Score = 84.3 bits (209), Expect = 2e-21
 Identities = 30/46 (65%), Positives = 35/46 (76%), Gaps = 2/46 (4%)

Query: 28  FGTALILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIFTVGG 73
           +G  L+LDG+IQ TE DE +Y EMI  LPLCS PNPKKVL+  VGG
Sbjct: 57  YGKVLVLDGVIQLTERDECAYQEMITHLPLCSIPNPKKVLV--VGG 100


>gnl|CDD|216573 pfam01564, Spermine_synth, Spermine/spermidine synthase.
          Spermine and spermidine are polyamines. This family
          includes spermidine synthase that catalyzes the fifth
          (last) step in the biosynthesis of spermidine from
          arginine, and spermine synthase.
          Length = 240

 Score = 77.3 bits (191), Expect = 4e-19
 Identities = 33/48 (68%), Positives = 37/48 (77%), Gaps = 2/48 (4%)

Query: 26 KEFGTALILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIFTVGG 73
          K FG  L+LDG +Q TE DEF Y EMIA +PLCSHPNPKKVLI  +GG
Sbjct: 39 KTFGKILVLDGRVQLTERDEFIYHEMIAHVPLCSHPNPKKVLI--IGG 84


>gnl|CDD|188048 TIGR00417, speE, spermidine synthase.  the SpeE subunit of
          spermidine synthase catalysesthe reaction (putrescine +
          S-adenosylmethioninamine = spermidine +
          5'-methylthioadenosine) and is involved in polyamine
          biosynthesis and in the biosynthesis of spermidine from
          arganine. The region between residues 77 and 120 of the
          seed alignment is thought to be involved in binding to
          decarboxylated SAM [Central intermediary metabolism,
          Polyamine biosynthesis].
          Length = 271

 Score = 77.9 bits (192), Expect = 4e-19
 Identities = 27/48 (56%), Positives = 35/48 (72%), Gaps = 2/48 (4%)

Query: 26 KEFGTALILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIFTVGG 73
          + FG  L+LDG++Q TE DEF Y EMI  +PL +HPNPK VL+  +GG
Sbjct: 36 EAFGNVLVLDGVVQTTERDEFIYHEMITHVPLFTHPNPKHVLV--IGG 81


>gnl|CDD|234843 PRK00811, PRK00811, spermidine synthase; Provisional.
          Length = 283

 Score = 75.6 bits (187), Expect = 3e-18
 Identities = 27/48 (56%), Positives = 33/48 (68%), Gaps = 2/48 (4%)

Query: 26 KEFGTALILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIFTVGG 73
           EFG  L LDG +  TE DEF Y EM+  +PL +HPNPK+VLI  +GG
Sbjct: 40 PEFGRLLALDGCVMTTERDEFIYHEMMTHVPLFAHPNPKRVLI--IGG 85


>gnl|CDD|223498 COG0421, SpeE, Spermidine synthase [Amino acid transport and
          metabolism].
          Length = 282

 Score = 75.1 bits (185), Expect = 4e-18
 Identities = 28/48 (58%), Positives = 38/48 (79%), Gaps = 2/48 (4%)

Query: 26 KEFGTALILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIFTVGG 73
          ++FG  L+LDG++Q TE DEF Y EM+A +PL +HPNPK+VLI  +GG
Sbjct: 40 EDFGKVLVLDGVVQLTERDEFIYHEMLAHVPLLAHPNPKRVLI--IGG 85


>gnl|CDD|178418 PLN02823, PLN02823, spermine synthase.
          Length = 336

 Score = 58.2 bits (141), Expect = 8e-12
 Identities = 26/51 (50%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 26  KEFGTALILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIFTVG-GST 75
           K FG  LI+DG +Q  E DEF Y E +    L  HPNPK V I   G GST
Sbjct: 67  KPFGKVLIIDGKMQSAEADEFVYHESLVHPALLHHPNPKTVFIMGGGEGST 117


>gnl|CDD|134311 PRK00536, speE, spermidine synthase; Provisional.
          Length = 262

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 8/21 (38%), Positives = 13/21 (61%)

Query: 49 SEMIAFLPLCSHPNPKKVLIF 69
          SE++A +  C+    K+VLI 
Sbjct: 59 SELLAHMGGCTKKELKEVLIV 79


>gnl|CDD|235139 PRK03612, PRK03612, spermidine synthase; Provisional.
          Length = 521

 Score = 30.2 bits (69), Expect = 0.075
 Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 2/42 (4%)

Query: 32  LILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIFTVGG 73
           L L+G +Q +  DE+ Y E +    + +   P++VL+  +GG
Sbjct: 267 LYLNGRLQFSSRDEYRYHEALVHPAMAASARPRRVLV--LGG 306


>gnl|CDD|224288 COG1369, POP5, RNase P/RNase MRP subunit POP5 [Translation,
           ribosomal structure and biogenesis].
          Length = 124

 Score = 29.6 bits (67), Expect = 0.097
 Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 3/39 (7%)

Query: 36  GIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIFTVGGS 74
           GI++C          + A L L    N K+V+I  +G S
Sbjct: 68  GIVRC---RREYVDLVRAALMLAREVNGKRVIIVVLGVS 103


>gnl|CDD|226713 COG4262, COG4262, Predicted spermidine synthase with an N-terminal
           membrane domain [General function prediction only].
          Length = 508

 Score = 29.8 bits (67), Expect = 0.10
 Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)

Query: 32  LILDGIIQCTEFDEFSYSEMIAFLPLCSHPNPKKVLIFTVGG 73
           L LDG +Q +  DE+ Y E + +  L S    + VL+  +GG
Sbjct: 259 LYLDGGLQFSTRDEYRYHESLVYPALSSVRGARSVLV--LGG 298


>gnl|CDD|152817 pfam12382, Peptidase_A2E, Retrotransposon peptidase.  This is a
           small family of fungal retroviral aspartyl peptidases.
          Length = 137

 Score = 27.0 bits (59), Expect = 0.91
 Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 12/65 (18%)

Query: 5   DKKVRVLSYPNKPF---------YPSSSNRKEFGTALILDGIIQCTEF---DEFSYSEMI 52
           ++ VR    P +P+         YP+  NRK     + L+GI   TEF    +FS+   I
Sbjct: 63  EETVRAHKLPTRPWLKSVIYGGVYPNKINRKTIKLIINLNGISIKTEFLVVKKFSHPAAI 122

Query: 53  AFLPL 57
           +F  L
Sbjct: 123 SFTTL 127


>gnl|CDD|197274 cd09177, PLDc_RE_NgoFVII, Putative catalytic domain of type II
           restriction enzyme NgoFVII and similar proteins.
           Putative catalytic domain of type II restriction enzyme
           NgoFVII (EC 3.1.21.4), which shows high sequence
           similarity to type IIs restriction endonuclease BfiI.
           Type II restriction endonucleases are components of
           restriction modification (RM) systems that protect
           bacteria and archaea against invading foreign DNA. They
           usually function as homodimers or homotetramers that
           cleave DNA at defined sites of 4 to 8 bp in length, and
           they require Mg2+, not ATP or GTP, for catalysis. The
           prototype of this subfamily is the NgoFVII restriction
           endonuclease from Neisseria gonorrhoeae. It plays an
           essential role in the endonucleolytic cleavage of DNA to
           give specific double-stranded fragments with terminal
           5'-phosphates. It recognizes the double-stranded
           sequence GCSGC and cleaves after G-4. Members of this
           subfamily contain one copy of the conserved HKD motif
           (H-x-K-x(4)-D, where x represents any amino acid
           residue) per protein chain and have been classified into
           the phospholipase D (PLD, EC 3.1.4.4) superfamily.
          Length = 143

 Score = 26.2 bits (58), Expect = 1.5
 Identities = 7/29 (24%), Positives = 17/29 (58%)

Query: 18  FYPSSSNRKEFGTALILDGIIQCTEFDEF 46
            + ++S R+++ T++IL+ I +  E    
Sbjct: 111 IWLTASTRRQYETSVILEDISEPAEIQLH 139


>gnl|CDD|234084 TIGR03007, pepcterm_ChnLen, polysaccharide chain length determinant
           protein, PEP-CTERM locus subfamily.  Members of this
           protein family belong to the family of polysaccharide
           chain length determinant proteins (pfam02706). All are
           found in species that encode the PEP-CTERM/exosortase
           system predicted to act in protein sorting in a number
           of Gram-negative bacteria, and are found near the epsH
           homolog that is the putative exosortase gene [Cell
           envelope, Biosynthesis and degradation of surface
           polysaccharides and lipopolysaccharides].
          Length = 498

 Score = 25.8 bits (57), Expect = 2.9
 Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 2/38 (5%)

Query: 1   MSGDDKKV--RVLSYPNKPFYPSSSNRKEFGTALILDG 36
           M   DK V  R++  P  P  PS  NR     A +L G
Sbjct: 387 MEVQDKAVSFRIIDPPIVPSKPSGPNRPLLMLAGLLGG 424


>gnl|CDD|216192 pfam00920, ILVD_EDD, Dehydratase family. 
          Length = 521

 Score = 25.5 bits (57), Expect = 2.9
 Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 2/29 (6%)

Query: 27 EFGTALILDGIIQCTEFDEFS--YSEMIA 53
          EFGT  + DGI   TE   +S    E+IA
Sbjct: 40 EFGTIAVCDGITMGTEGMRYSLPSRELIA 68


>gnl|CDD|143414 cd07095, ALDH_SGSD_AstD, N-succinylglutamate 5-semialdehyde
           dehydrogenase, AstD-like.  N-succinylglutamate
           5-semialdehyde dehydrogenase or succinylglutamic
           semialdehyde dehydrogenase (SGSD, E. coli AstD,
           EC=1.2.1.71) involved in L-arginine degradation via the
           arginine succinyltransferase (AST) pathway and catalyzes
           the NAD+-dependent reduction of succinylglutamate
           semialdehyde into succinylglutamate.
          Length = 431

 Score = 25.7 bits (57), Expect = 3.3
 Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 2/33 (6%)

Query: 25  RKEFGTALILDGIIQCTEFDEFSYSEMIAFLPL 57
           R   GTA +  GII  T+  +    E+  F PL
Sbjct: 312 RLVAGTAFLSPGIIDVTDAADVPDEEI--FGPL 342


>gnl|CDD|223578 COG0504, PyrG, CTP synthase (UTP-ammonia lyase) [Nucleotide
           transport and metabolism].
          Length = 533

 Score = 25.2 bits (56), Expect = 4.5
 Identities = 6/19 (31%), Positives = 10/19 (52%)

Query: 1   MSGDDKKVRVLSYPNKPFY 19
            S D   V ++  P+ PF+
Sbjct: 481 TSPDGGLVEIVELPDHPFF 499


>gnl|CDD|198317 cd03208, GST_C_Alpha, C-terminal, alpha helical domain of Class
          Alpha Glutathione S-transferases.  Glutathione
          S-transferase (GST) C-terminal domain family, Class
          Alpha subfamily; GSTs are cytosolic dimeric proteins
          involved in cellular detoxification by catalyzing the
          conjugation of glutathione (GSH) with a wide range of
          endogenous and xenobiotic alkylating agents, including
          carcinogens, therapeutic drugs, environmental toxins,
          and products of oxidative stress. The GST fold contains
          an N-terminal thioredoxin-fold domain and a C-terminal
          alpha helical domain, with an active site located in a
          cleft between the two domains. GSH binds to the
          N-terminal domain while the hydrophobic substrate
          occupies a pocket in the C-terminal domain. The class
          Alpha subfamily is composed of vertebrate GSTs which
          can form homodimer and heterodimers. There are at least
          six types of class Alpha GST subunits in rats, four of
          which have human counterparts, resulting in many
          possible isoenzymes with different activities, tissue
          distribution and substrate specificities. Human GSTA1-1
          and GSTA2-2 show high GSH peroxidase activity. GSTA3-3
          catalyzes the isomerization of intermediates in steroid
          hormone biosynthesis. GSTA4-4 preferentially catalyzes
          the GSH conjugation of alkenals.
          Length = 135

 Score = 24.2 bits (53), Expect = 9.2
 Identities = 9/32 (28%), Positives = 12/32 (37%), Gaps = 1/32 (3%)

Query: 50 EMIAFLPLCSHPNPKKVLIFTVGGSTVQYSFP 81
          EMI  LP       +  L      +  +Y FP
Sbjct: 19 EMIMMLPFLPPEEKEAKLALIKEKAKNRY-FP 49


  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    0.139    0.422 

Gapped
Lambda     K      H
   0.267   0.0524    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,181,855
Number of extensions: 325665
Number of successful extensions: 255
Number of sequences better than 10.0: 1
Number of HSP's gapped: 255
Number of HSP's successfully gapped: 18
Length of query: 82
Length of database: 10,937,602
Length adjustment: 51
Effective length of query: 31
Effective length of database: 8,675,548
Effective search space: 268941988
Effective search space used: 268941988
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 (21.8 bits)
S2: 53 (24.7 bits)