RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16369
         (101 letters)



>gnl|CDD|236550 PRK09529, PRK09529, bifunctional acetyl-CoA decarbonylase/synthase
           complex subunit alpha/beta; Reviewed.
          Length = 711

 Score = 28.8 bits (65), Expect = 0.42
 Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 4/30 (13%)

Query: 67  VALKFGGIPAGETNGMRGY----MLTFVIA 92
            AL FGG+  G+   +  Y    +  FV A
Sbjct: 208 AALIFGGVEPGDYEELLDYTKERVPAFVNA 237


>gnl|CDD|237756 PRK14559, PRK14559, putative protein serine/threonine phosphatase;
           Provisional.
          Length = 645

 Score = 26.6 bits (59), Expect = 2.9
 Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 5/34 (14%)

Query: 17  VETSTSYSRPRHYPLTDM---RENE--KPGIDSF 45
           VE   +Y+RP  Y LT     R+N   +P I   
Sbjct: 535 VEPQIAYARPDAYQLTQALGPRDNSAIQPDIQFL 568


>gnl|CDD|187737 cd09616, Peptidase_C12_UCH_L1_L3, Cysteine peptidase C12
          containing ubiquitin carboxyl-terminal hydrolase (UCH)
          families L1 and L3.  This ubiquitin C-terminal
          hydrolase (UCH) family includes UCH-L1 and UCH-L3, the
          two members sharing around 53% sequence identity as
          well as conserved catalytic residues. Both enzymes
          hydrolyze carboxyl terminal esters and amides of
          ubiquitin (Ub). UCH-L1, in dimeric form, has additional
          enzymatic activity as a ubiquitin ligase. It is highly
          abundant in the brain, constituting up to 2% of total
          protein, and is expressed exclusively in neurons and
          testes. Abnormal expression of UCH-L1 has been shown to
          correlate with several forms of cancer, including
          several primary lung tumors, lung tumor cell lines, and
          colorectal cancers. Mutations in the UCH-L1 gene have
          been linked to susceptibility to and protection from
          Parkinson's disease (PD); dysfunction of the hydrolase
          activity can lead to an accumulation of
          alpha-synuclein, which is linked to Parkinson's disease
          (PD), while accumulation of neurofibrillary tangles is
          linked to Alzheimer's disease (AD).  UCH-L3 hydrolyzes
          isopeptide bonds at the C-terminal glycine of either Ub
          or Nedd8, a ubiquitin-like protein. It can also
          interact with Lys48-linked Ub dimers to protect them
          from degradation while inhibiting its hydrolase
          activity at the same time.  Unlike UCH-L1, neither
          dimerization nor ligase activity have been observed for
          UCH-L3. It has been shown that levels of Nedd8 and the
          apoptotic protein p53 and Bax are elevated in UCH-L3
          knockout mice upon cryptorchid injury, possibly
          contributing to profound germ cell loss via apoptosis.
          Length = 222

 Score = 26.1 bits (58), Expect = 3.2
 Identities = 6/29 (20%), Positives = 10/29 (34%)

Query: 29 YPLTDMRENEKPGIDSFGKPDSHGDPEDV 57
          +P+T   E  +   +   K       E V
Sbjct: 51 FPITKAYEEFRKEEEEEIKEKGQEVSESV 79


>gnl|CDD|238250 cd00443, ADA_AMPD, Adenosine/AMP deaminase. Adenosine deaminases
           (ADAs) are present in pro- and eukaryotic organisms and
           catalyze  the zinc dependent irreversible deamination of
           adenosine nucleosides to inosine nucleosides and
           ammonia. The eukaryotic AMP deaminase catalyzes a
           similar reaction leading to the hydrolytic removal of an
           amino group at the 6 position of the adenine nucleotide
           ring, a branch point in the adenylate catabolic pathway.
          Length = 305

 Score = 26.2 bits (58), Expect = 3.4
 Identities = 11/43 (25%), Positives = 16/43 (37%), Gaps = 7/43 (16%)

Query: 41  GIDSFGKPDSHGDPEDVKKNQAKIYSVALKFGGIP----AGET 79
           GID  G      +P    ++    Y  A + G +      GET
Sbjct: 138 GIDLVGDESKGENP---LRDFYSYYEYARRLGLLGLTLHCGET 177


>gnl|CDD|232817 TIGR00081, purC, phosphoribosylaminoimidazole-succinocarboxamide
           synthase.  Alternate name: SAICAR synthetase purine de
           novo biosynthesis. E.coli example noted as homotrimer.
           Check length. Longer versions may be multifunctional
           enzymes [Purines, pyrimidines, nucleosides, and
           nucleotides, Purine ribonucleotide biosynthesis].
          Length = 237

 Score = 25.8 bits (57), Expect = 4.6
 Identities = 9/28 (32%), Positives = 15/28 (53%)

Query: 27  RHYPLTDMRENEKPGIDSFGKPDSHGDP 54
           +   + +  E E+P ++   KPD  GDP
Sbjct: 105 KRLGIPEGLELEQPLVEFIFKPDEVGDP 132


>gnl|CDD|215543 PLN03028, PLN03028, pyrophosphate--fructose-6-phosphate
           1-phosphotransferase; Provisional.
          Length = 610

 Score = 25.5 bits (56), Expect = 7.0
 Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 4/33 (12%)

Query: 30  PLTDM----RENEKPGIDSFGKPDSHGDPEDVK 58
           P+T M    R +  PG    GKP  H  P D+K
Sbjct: 476 PITAMMSVKRWSRGPGASQIGKPAIHPAPVDLK 508


>gnl|CDD|237681 PRK14342, PRK14342, lipoate-protein ligase B; Provisional.
          Length = 213

 Score = 24.8 bits (55), Expect = 7.4
 Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 4/30 (13%)

Query: 41  GIDSFGKPDSHGDPEDVKKNQAKIYSVALK 70
           GI++  KPD+ G    V  +  KI S+ L+
Sbjct: 117 GIEAHAKPDAPG----VYVDGKKIASLGLR 142


>gnl|CDD|238898 cd01917, ACS_2, Acetyl-CoA synthase (ACS), also known as acetyl-CoA
           decarbonylase, is found in acetogenic and methanogenic
           organisms and is responsible for the synthesis and
           breakdown of acetyl-CoA.  ACS forms a heterotetramer
           with carbon monoxide dehydrogenase (CODH) consisting of
           two ACS and two CODH subunits. CODH reduces carbon
           dioxide to carbon monoxide and ACS then synthesizes
           acetyl-CoA from carbon monoxide, CoA, and a methyl group
           donated by another protein (CoFeSP).  ACS has three
           structural domains, an N-terminal rossman fold domain
           with a helical region at its N-terminus which interacts
           with CODH, and two alpha + beta fold domains.  A Ni-Fe-S
           center referred to as the A-cluster is located in the
           C-terminal domain. A large cavity exists between the
           three domains which may bind CoA.
          Length = 287

 Score = 25.2 bits (55), Expect = 7.7
 Identities = 10/26 (38%), Positives = 14/26 (53%)

Query: 69  LKFGGIPAGETNGMRGYMLTFVIAYI 94
           L FGGI  G+   +R Y    V A++
Sbjct: 201 LMFGGIEPGKREEIRDYQRRRVRAFV 226


  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    0.137    0.401 

Gapped
Lambda     K      H
   0.267   0.0692    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,218,838
Number of extensions: 434083
Number of successful extensions: 307
Number of sequences better than 10.0: 1
Number of HSP's gapped: 307
Number of HSP's successfully gapped: 14
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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: 53 (24.3 bits)