RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254781067|ref|YP_003065480.1| elongation factor P
[Candidatus Liberibacter asiaticus str. psy62]
         (189 letters)



>gnl|CDD|30580 COG0231, Efp, Translation elongation factor P (EF-P)/translation
           initiation factor 5A (eIF-5A) [Translation, ribosomal
           structure and biogenesis].
          Length = 131

 Score =  132 bits (333), Expect = 8e-32
 Identities = 47/131 (35%), Positives = 82/131 (62%)

Query: 1   MVKVIASAVRKGNVLDVDGKLYIVLVAKNFHPGKGTPITQVEMRRISDGVKVSNRWRTTE 60
           M  + AS +RKG  + +DG+ Y+V+   +  PGKG    +V+++ +  G KV   ++  +
Sbjct: 1   MAMISASELRKGLYIVIDGEPYVVVEISHVKPGKGGAFVRVKLKNLFTGKKVEKTFKADD 60

Query: 61  QVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEG 120
           +VE A VE +  Q+LY D + + FM+ ETY+Q  + ++ IGD   + +EGMEV++L++ G
Sbjct: 61  KVEVAIVERKTAQYLYIDGDFYVFMDLETYEQYELPKDQIGDAAKFLKEGMEVEVLLYNG 120

Query: 121 VALSVEVPRHV 131
             ++VE+P  V
Sbjct: 121 EPIAVELPNFV 131


>gnl|CDD|88435 cd04470, S1_EF-P_repeat_1, S1_EF-P_repeat_1: Translation elongation
           factor P (EF-P), S1-like RNA-binding domain, repeat 1.
           EF-P stimulates the peptidyltransferase activity in the
           prokaryotic 70S ribosome. EF-P enhances the synthesis of
           certain dipeptides with N-formylmethionyl-tRNA and
           puromycine in vitro. EF-P binds to both the 30S and 50S
           ribosomal subunits. EF-P binds near the streptomycine
           binding site of the 16S rRNA in the 30S subunit. EF-P
           interacts with domains 2 and 5 of the 23S rRNA. The L16
           ribosomal protein of the 50S or its N-terminal fragment
           are required for EF-P mediated peptide bond synthesis,
           whereas L11, L15, and L7/L12 are not required in this
           reaction, suggesting that EF-P may function at a
           different ribosomal site than most other translation
           factors. EF-P is essential for cell viability and is
           required for protein synthesis. EF-P is mainly present
           in bacteria. The EF-P homologs in archaea and eukaryotes
           are the initiation factors aIF5A and eIF5A,
           respectively. EF-P has 3 domains (domains I, II, and
           III). Domains II and III are S1-like domains. This CD
           includes domain II (the first S1 domain of EF_P).
           Domains II and III have structural homology to the eIF5A
           domain C, suggesting that domains II and III evolved by
           duplication..
          Length = 61

 Score = 81.3 bits (201), Expect = 2e-16
 Identities = 24/61 (39%), Positives = 42/61 (68%)

Query: 68  EDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVALSVEV 127
           E++  Q+LY+D + + FM+ ETY+Q+ + +E +GD   + +EGMEV +L + G  + VE+
Sbjct: 1   EEREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVIVLFYNGEPIGVEL 60

Query: 128 P 128
           P
Sbjct: 61  P 61


>gnl|CDD|144650 pfam01132, EFP, Elongation factor P (EF-P) OB domain. 
          Length = 55

 Score = 78.6 bits (195), Expect = 9e-16
 Identities = 20/55 (36%), Positives = 36/55 (65%)

Query: 69  DQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQEGMEVKLLIHEGVAL 123
            +  Q+LY+D + + FM+ ETY+Q+ + +E +GD   + +EGMEV +L + G  +
Sbjct: 1   RREMQYLYKDGDNYVFMDTETYEQIELPKEALGDAAKFLKEGMEVTVLFYNGEPI 55


>gnl|CDD|88469 cd05794, S1_EF-P_repeat_2, S1_EF-P_repeat_2: Translation elongation
           factor P (EF-P), S1-like RNA-binding domain, repeat 1.
           EF-P stimulates the peptidyltransferase activity in the
           prokaryotic 70S ribosome. EF-P enhances the synthesis of
           certain dipeptides with N-formylmethionyl-tRNA and
           puromycine in vitro. EF-P binds to both the 30S and 50S
           ribosomal subunits. EF-P binds near the streptomycine
           binding site of the 16S rRNA in the 30S subunit. EF-P
           interacts with domains 2 and 5 of the 23S rRNA. The L16
           ribosomal protein of the 50S or its N-terminal fragment
           are required for EF-P mediated peptide bond synthesis,
           whereas L11, L15, and L7/L12 are not required in this
           reaction, suggesting that EF-P may function at a
           different ribosomal site than most other translation
           factors. EF-P is essential for cell viability and is
           required for protein synthesis. EF-P is mainly present
           in bacteria. The EF-P homologs in archaea and eukaryotes
           are the initiation factors aIF5A and eIF5A,
           respectively. EF-P has 3 domains (domains I, II, and
           III). Domains II and III are S1-like domains. This CD
           includes domain III (the second S1 domain of EF_P).
           Domains II and III of have structural homology to the
           eIF5A domain C, suggesting that domains II and III
           evolved by duplication..
          Length = 56

 Score = 68.6 bits (168), Expect = 1e-12
 Identities = 22/56 (39%), Positives = 27/56 (48%)

Query: 131 VVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVILTEDNSYVER 186
           V   V +TEP  KG T ++  KPA L       VP  I  G+ I + T    YVER
Sbjct: 1   VELEVTETEPGVKGDTASSGTKPATLETGAEVQVPLFIKEGEKIKVDTRTGEYVER 56


>gnl|CDD|37159 KOG1948, KOG1948, KOG1948, Metalloproteinase-related collagenase pM5
            [Posttranslational modification, protein turnover,
            chaperones].
          Length = 1165

 Score = 29.2 bits (65), Expect = 0.66
 Identities = 11/49 (22%), Positives = 18/49 (36%)

Query: 60   EQVERAFVEDQRFQFLYQDQEGFHFMNPETYDQVTVSEEVIGDQKVYFQ 108
              +ER+F          +D +G +FM         ++ EV  D     Q
Sbjct: 970  SPIERSFPRSFTVSVGNEDVKGLNFMAFIQAKTTDITVEVGMDTNEELQ 1018


>gnl|CDD|133365 cd04165, GTPBP1_like, GTPBP1-like.  Mammalian GTP binding protein 1
           (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1
           are GTPases whose specific functions remain unknown.  In
           mouse, GTPBP1 is expressed in macrophages, in smooth
           muscle cells of various tissues and in some neurons of
           the cerebral cortex; GTPBP2 tissue distribution appears
           to overlap that of GTPBP1.  In human leukemia and
           macrophage cell lines, expression of both GTPBP1 and
           GTPBP2 is enhanced by interferon-gamma (IFN-gamma).  The
           chromosomal location of both genes has been identified
           in humans, with GTPBP1 located in chromosome 22q12-13.1
           and GTPBP2 located in chromosome 6p21-12.  Human
           glioblastoma multiforme (GBM), a highly-malignant
           astrocytic glioma and the most common cancer in the
           central nervous system, has been linked to chromosomal
           deletions and a translocation on chromosome 6.  The GBM
           translocation results in a fusion of GTPBP2 and PTPRZ1,
           a protein involved in oligodendrocyte differentiation,
           recovery, and survival.  This fusion product may
           contribute to the onset of GBM.
          Length = 224

 Score = 28.8 bits (65), Expect = 0.97
 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 118 HEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVIL 177
           H G+AL++ +P  VV T ID  P++  Q      K  +    +R    P     DD V+L
Sbjct: 130 HLGLALALNIPVFVVVTKIDLAPANILQETLKDLKRILKVPGVRK--LPVPVKSDDDVVL 187

Query: 178 TEDNSYVERV 187
              N   ER+
Sbjct: 188 AASNFSSERI 197


>gnl|CDD|35684 KOG0463, KOG0463, KOG0463, GTP-binding protein GP-1 [General
           function prediction only].
          Length = 641

 Score = 28.1 bits (62), Expect = 1.6
 Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 118 HEGVALSVEVPRHVVFTVIDTEPSSKGQTVTASYKPAILSNDIRTTVPPHINIGDDIVIL 177
           H G+AL++ VP  VV T ID  P++  Q         + S   R  +P  +   DD V+ 
Sbjct: 265 HLGLALALHVPVFVVVTKIDMCPANILQETMKLLTRLLKSPGCR-KLPVLVRSMDD-VVH 322

Query: 178 TEDNSYVERV 187
              N   ERV
Sbjct: 323 AAVNFPSERV 332


>gnl|CDD|176260 cd08300, alcohol_DH_class_III, class III alcohol dehydrogenases.
           Members identified as glutathione-dependent formaldehyde
           dehydrogenase(FDH), a member of the zinc
           dependent/medium chain alcohol dehydrogenase family.
           FDH converts formaldehyde and NAD(P) to formate and
           NAD(P)H. The initial step in this process the
           spontaneous formation of a S-(hydroxymethyl)glutathione
           adduct from formaldehyde and glutathione, followed by
           FDH-mediated oxidation (and detoxification) of the
           adduct to S-formylglutathione.  MDH family uses NAD(H)
           as a cofactor in the interconversion of alcohols and
           aldehydes or ketones. Like many zinc-dependent alcohol
           dehydrogenases (ADH) of the medium chain alcohol
           dehydrogenase/reductase family (MDR), these FDHs form
           dimers, with 4 zinc ions per dimer. The medium chain
           alcohol dehydrogenase family (MDR) have a
           NAD(P)(H)-binding domain in a Rossmann fold of a
           beta-alpha form. The N-terminal region typically has an
           all-beta catalytic domain. These proteins typically form
           dimers (typically higher plants, mammals) or tetramers
           (yeast, bacteria), and have 2 tightly bound zinc atoms
           per subunit.  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 have 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.  A GxGxxG motif after the first
           mononucleotide contact half allows the close contact of
           the coenzyme with the ADH backbone.  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 = 368

 Score = 26.4 bits (59), Expect = 4.8
 Identities = 9/31 (29%), Positives = 16/31 (51%)

Query: 69  DQRFQFLYQDQEGFHFMNPETYDQVTVSEEV 99
           D   +F  + +  +HFM   T+ + TV  E+
Sbjct: 120 DGTSRFSCKGKPIYHFMGTSTFSEYTVVAEI 150


>gnl|CDD|176645 cd05282, ETR_like, 2-enoyl thioester reductase-like.  2-enoyl
           thioester reductase (ETR) catalyzes the NADPH-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.
            Candida tropicalis enoyl thioester reductase (Etr1p)
           catalyzes the NADPH-dependent reduction of trans-2-enoyl
           thioesters in mitochondrial fatty acid synthesis. Etr1p
           forms homodimers with each subunit containing a
           nucleotide-binding Rossmann fold domain and a catalytic
           domain.
          Length = 323

 Score = 25.7 bits (57), Expect = 8.5
 Identities = 7/20 (35%), Positives = 11/20 (55%)

Query: 170 IGDDIVILTEDNSYVERVKK 189
           +G D VI +      +RVK+
Sbjct: 182 LGADEVIDSSPEDLAQRVKE 201


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.318    0.135    0.381 

Gapped
Lambda     K      H
   0.267   0.0876    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,205,434
Number of extensions: 109059
Number of successful extensions: 264
Number of sequences better than 10.0: 1
Number of HSP's gapped: 264
Number of HSP's successfully gapped: 14
Length of query: 189
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 101
Effective length of database: 4,362,145
Effective search space: 440576645
Effective search space used: 440576645
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.3 bits)