RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780470|ref|YP_003064883.1| translation initiation factor
IF-1 [Candidatus Liberibacter asiaticus str. psy62]
         (110 letters)



>gnl|CDD|88417 cd04451, S1_IF1, S1_IF1: Translation Initiation Factor IF1, S1-like
           RNA-binding domain. IF1 contains an S1-like RNA-binding
           domain, which is found in a wide variety of
           RNA-associated proteins. Translation initiation includes
           a number of interrelated steps preceding the formation
           of the first peptide bond. In Escherichia coli, the
           initiation mechanism requires, in addition to mRNA,
           fMet-tRNA, and ribosomal subunits,  the presence of
           three additional proteins (initiation factors IF1, IF2,
           and IF3) and at least one GTP molecule. The three
           initiation factors influence both the kinetics and the
           stability of ternary complex formation. IF1 is the
           smallest of the three factors. IF1 enhances the rate of
           70S ribosome subunit association and dissociation and
           the interaction of 30S ribosomal subunit with IF2 and
           IF3. It stimulates 30S complex formation. In addition,
           by binding to the A-site of the 30S ribosomal subunit,
           IF1 may contribute to the fidelity of the selection of
           the initiation site of the mRNA..
          Length = 64

 Score = 73.6 bits (181), Expect = 1e-14
 Identities = 36/102 (35%), Positives = 51/102 (50%), Gaps = 38/102 (37%)

Query: 7   LEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLD 66
           +E  G+V+E LPNA FRV+L                      E+G E             
Sbjct: 1   IEMEGVVTEALPNAMFRVEL----------------------ENGHE------------- 25

Query: 67  NAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108
              V+A+ +G+MR + IRI  GD+VKV ++PYD+T+ RI YR
Sbjct: 26  ---VLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRIVYR 64


>gnl|CDD|176953 CHL00010, infA, translation initiation factor 1.
          Length = 78

 Score = 73.1 bits (180), Expect = 2e-14
 Identities = 36/111 (32%), Positives = 52/111 (46%), Gaps = 40/111 (36%)

Query: 1   MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60
           M KE  +E  G+V+E LPN  FRV+L                                  
Sbjct: 1   MKKENKIEMEGLVTESLPNGMFRVRL---------------------------------- 26

Query: 61  PISYLDN-AVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110
                DN   V+ Y +G++R++ IRI  GD+VKV ++PYD+T+ RI YR +
Sbjct: 27  -----DNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLR 72


>gnl|CDD|30710 COG0361, InfA, Translation initiation factor 1 (IF-1) [Translation,
           ribosomal structure and biogenesis].
          Length = 75

 Score = 72.5 bits (178), Expect = 2e-14
 Identities = 35/110 (31%), Positives = 50/110 (45%), Gaps = 38/110 (34%)

Query: 1   MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60
           M K + +E  G V E+LPN  FRV+L                                  
Sbjct: 1   MAKPDEIEMEGTVIEMLPNGRFRVEL---------------------------------- 26

Query: 61  PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110
                +    +A+ +G+MRK+RIRI  GD V V ++PYD+T+ RI YR+K
Sbjct: 27  ----ENGHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYRYK 72


>gnl|CDD|110196 pfam01176, eIF-1a, Translation initiation factor 1A / IF-1.  This
           family includes both the eukaryotic translation factor
           eIF-1A and the bacterial translation initiation factor
           IF-1.
          Length = 65

 Score = 55.2 bits (134), Expect = 4e-09
 Identities = 29/101 (28%), Positives = 38/101 (37%), Gaps = 39/101 (38%)

Query: 8   EFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDN 67
           E  G V+E+L N  F V+L                              DG         
Sbjct: 4   EMIGQVTEMLGNGRFEVEL-----------------------------EDGH-------- 26

Query: 68  AVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108
              +A+  G+ RK RI I  GD V V ++PYD  + RI YR
Sbjct: 27  -ERLAHIPGKRRK-RIWILRGDFVLVELSPYDKVKGRIIYR 65


>gnl|CDD|30879 COG0533, QRI7, Metal-dependent proteases with possible chaperone
           activity [Posttranslational modification, protein
           turnover, chaperones].
          Length = 342

 Score = 27.1 bits (60), Expect = 1.1
 Identities = 10/24 (41%), Positives = 11/24 (45%)

Query: 66  DNAVVIAYTAGRMRKHRIRISLGD 89
           DNA +IAY      K    IS  D
Sbjct: 302 DNAAMIAYAGLLRYKAGRFISPLD 325


>gnl|CDD|119407 cd02696, MurNAc-LAA, N-acetylmuramoyl-L-alanine amidase or
          MurNAc-LAA (also known as peptidoglycan aminohydrolase,
          NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan
          amidase; EC 3.5.1.28) is an autolysin that hydrolyzes
          the amide bond between N-acetylmuramoyl and L-amino
          acids in certain cell wall glycopeptides. These
          proteins are Zn-dependent peptidases with highly
          conserved residues involved in cation co-ordination.
          MurNAc-LAA in this family is one of several
          peptidoglycan hydrolases (PGHs) found in bacterial and
          bacteriophage or prophage genomes that are involved in
          the degradation of the peptidoglycan. In Escherichia
          coli, there are five MurNAc-LAAs present: AmiA, AmiB,
          AmiC and AmiD that are periplasmic, and AmpD that is
          cytoplasmic. Three of these (AmiA, AmiB and AmiC)
          belong to this family, the other two (AmiD and AmpD) do
          not. E. coli AmiA, AmiB and AmiC play an important role
          in cleaving the septum to release daughter cells after
          cell division. In general, bacterial MurNAc-LAAs are
          members of the bacterial autolytic system and carry a
          signal peptide in their N-termini that allows their
          transport across the cytoplasmic membrane. However, the
          bacteriophage MurNAc-LAAs are endolysins since these
          phage-encoded enzymes break down bacterial
          peptidoglycan at the terminal stage of the phage
          reproduction cycle. As opposed to autolysins, almost
          all endolysins have no signal peptides and their
          translocation through the cytoplasmic membrane is
          thought to proceed with the help of phage-encoded holin
          proteins. The amidase catalytic module is fused to
          another functional module (cell wall binding module or
          CWBM) either at the N- or C-terminus, which is
          responsible for high affinity binding of the protein to
          the cell wall..
          Length = 172

 Score = 27.1 bits (61), Expect = 1.2
 Identities = 9/30 (30%), Positives = 16/30 (53%)

Query: 3  KEETLEFSGIVSELLPNANFRVKLITNDDD 32
          K+  L  +  +++LL  A  +V L  +DD 
Sbjct: 24 KDINLAIALKLAKLLEAAGAKVVLTRDDDT 53


>gnl|CDD|88466 cd05791, S1_CSL4, S1_CSL4: CSL4, S1-like RNA-binding domain.
           S1-like RNA-binding domains are found in a wide variety
           of RNA-associated proteins. ScCSL4 protein is a subunit
           of the exosome complex. The exosome plays a central role
           in 3' to 5' RNA processing and degradation in eukarytes
           and archaea. Its functions include the removal of
           incorrectly processed RNA and the maintenance of proper
           levels of mRNA, rRNA and a number of small RNA species.
           In S. cerevisiae, the exosome includes nine core
           components, six of which are homologous to bacterial
           RNase PH. These form a hexameric ring structure. The
           other three subunits (RrP4, Rrp40, and Csl4) contain an
           S1 RNA binding domain and are part of the "S1 pore
           structure"..
          Length = 92

 Score = 26.3 bits (58), Expect = 1.8
 Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 2/48 (4%)

Query: 62  ISYLDNAVVIAYTAGRMRKHRIRISLGDKVKV--AMNPYDMTRARITY 107
           I  +    +     G +RK  IR +  DKV++     P D+ RA++  
Sbjct: 26  ILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVIS 73


>gnl|CDD|144931 pfam01520, Amidase_3, N-acetylmuramoyl-L-alanine amidase.  This
          enzyme domain cleaves the amide bond between
          N-acetylmuramoyl and L-amino acids in bacterial cell
          walls.
          Length = 172

 Score = 26.0 bits (58), Expect = 2.1
 Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 1/36 (2%)

Query: 3  KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCK 38
          K+  L+ +  +++LL  A   V L T DDDS     
Sbjct: 23 KDLNLDIALRLAKLLEAAGVEVVL-TRDDDSFVSLS 57


>gnl|CDD|107371 cd06376, PBP1_mGluR_groupIII, Ligand-binding domain of the group
           III metabotropic glutamate receptor.  Ligand-binding
           domain of the group III metabotropic glutamate receptor,
           a family which contains mGlu4R, mGluR6R, mGluR7, and
           mGluR8; all of which inhibit adenylyl cyclase. The
           metabotropic glutamate receptor is a member of the
           family C of G-protein-coupled receptors that transduce
           extracellular signals into G-protein activation and
           ultimately into intracellular responses. The mGluRs are
           classified into three groups which comprise eight
           subtypes.
          Length = 463

 Score = 25.2 bits (55), Expect = 4.5
 Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 1   MPKE-ETLEFSGIVSELLPNANFR-VKLITNDDD 32
           +P+E    EF  I+  LL   N R V +  N+DD
Sbjct: 210 IPREPRPGEFDKIIKRLLETPNARAVIIFANEDD 243


>gnl|CDD|173846 cd01157, MCAD, Medium chain acyl-CoA dehydrogenase.  MCADs are
           mitochondrial beta-oxidation enzymes, which catalyze the
           alpha,beta dehydrogenation of the corresponding medium
           chain acyl-CoA by FAD, which becomes reduced. The
           reduced form of MCAD is reoxidized in the oxidative
           half-reaction by electron-transferring flavoprotein
           (ETF), from which the electrons are transferred to the
           mitochondrial respiratory chain coupled with ATP
           synthesis. MCAD is a  homotetramer.
          Length = 378

 Score = 24.9 bits (54), Expect = 4.6
 Identities = 11/33 (33%), Positives = 16/33 (48%)

Query: 70  VIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTR 102
            I +   R+ K  + I  G   K+AM  +D TR
Sbjct: 209 GITFEDVRVPKENVLIGEGAGFKIAMGAFDKTR 241


>gnl|CDD|143211 cd05734, Ig7_DSCAM, Seventh immunoglobulin (Ig)-like domain of
          Down Syndrome Cell Adhesion molecule (DSCAM).
          Ig7_DSCAM: the seventh immunoglobulin (Ig)-like domain
          of Down Syndrome Cell Adhesion molecule (DSCAM). DSCAM
          is a cell adhesion molecule expressed largely in the
          developing nervous system. The gene encoding DSCAM is
          located at human chromosome 21q22, the locus associated
          with the mental retardation phenotype of Down Syndrome.
          DSCAM is predicted to be the largest member of the IG
          superfamily. It has been demonstrated that DSCAM can
          mediate cation-independent homophilic intercellular
          adhesion.
          Length = 79

 Score = 24.5 bits (53), Expect = 7.0
 Identities = 10/36 (27%), Positives = 20/36 (55%)

Query: 15 ELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSES 50
          +LL N +  +K +  +D     CK+ + V ++ S+S
Sbjct: 39 QLLSNGSLLIKHVLEEDSGYYLCKVSNDVGADASKS 74


>gnl|CDD|36570 KOG1356, KOG1356, KOG1356, Putative transcription factor 5qNCA,
           contains JmjC domain [Transcription].
          Length = 889

 Score = 24.2 bits (52), Expect = 7.5
 Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 4/63 (6%)

Query: 30  DDDSSADCKLDSKVKSNFSESGSESGNDGVDPISYLDNAVV----IAYTAGRMRKHRIRI 85
            D+S   C+     +  F++ G       + P  Y   A+     I+ +  R+     + 
Sbjct: 131 KDESPVFCRFYEFRRLQFTKKGVLRVQGFLSPDQYDPEAISLWGPISGSDSRLDTETAKY 190

Query: 86  SLG 88
            L 
Sbjct: 191 ILA 193


  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
   0.315    0.132    0.365 

Gapped
Lambda     K      H
   0.267   0.0768    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,211,932
Number of extensions: 52385
Number of successful extensions: 128
Number of sequences better than 10.0: 1
Number of HSP's gapped: 127
Number of HSP's successfully gapped: 19
Length of query: 110
Length of database: 6,263,737
Length adjustment: 76
Effective length of query: 34
Effective length of database: 4,621,453
Effective search space: 157129402
Effective search space used: 157129402
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 (21.5 bits)
S2: 51 (23.3 bits)