RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781138|ref|YP_003065551.1| hypothetical protein
CLIBASIA_05200 [Candidatus Liberibacter asiaticus str. psy62]
         (178 letters)



>gnl|CDD|144569 pfam01028, Topoisom_I, Eukaryotic DNA topoisomerase I, catalytic
          core.  Topoisomerase I promotes the relaxation of DNA
          superhelical tension by introducing a transient
          single-stranded break in duplex DNA and are vital for
          the processes of replication, transcription, and
          recombination.
          Length = 244

 Score = 28.7 bits (65), Expect = 1.0
 Identities = 8/30 (26%), Positives = 16/30 (53%)

Query: 25 FKNFLHRIEVKINRALRLREMERKIVLSLV 54
          F   L +I  ++ + LR   + R+ VL++ 
Sbjct: 30 FGKALPKIRKRVTKDLRRSGLPRERVLAVA 59


>gnl|CDD|133156 cd05489, xylanase_inhibitor_I_like, TAXI-I inhibits degradation of
           xylan in the cell wall.  Xylanase inhibitor-I (TAXI-I)
           is a member of potent TAXI-type inhibitors of fungal and
           bacterial family 11 xylanases. Plants developed a
           diverse battery of defense mechanisms in response to
           continual challenges by a broad spectrum of pathogenic
           microorganisms. Their defense arsenal includes
           inhibitors of cell wall-degrading enzymes, which hinder
           a possible invasion and colonization by antagonists.
           Xylanases of fungal and bacterial pathogens are the key
           enzymes in the degradation of xylan in the cell wall.
           Plants secrete proteins that inhibit these degradation
           glycosidases, including xylanase. Surprisingly, TAXI-I
           displays structural homology with the pepsin-like family
           of aspartic proteases but is proteolytically
           nonfunctional, because one or more residues of the
           essential catalytic triad are absent. The structure of
           the TAXI-inhibitor, Aspergillus niger xylanase I
           complex, illustrates the ability of tight binding and
           inhibition with subnanomolar affinity and indicates the
           importance of the C-terminal end for the differences in
           xylanase specificity among different TAXI-type
           inhibitors. This family also contains pepsin-like
           aspartic proteinases homologous to TAXI-I. Unlike
           TAXI-I, they have active site aspartates and are
           functionally active. This family of aspartate proteases
           is classified by MEROPS as the peptidase family A1
           (pepsin A, clan AA).
          Length = 362

 Score = 27.3 bits (61), Expect = 2.4
 Identities = 11/47 (23%), Positives = 16/47 (34%), Gaps = 5/47 (10%)

Query: 56  GSAPLPDDYIEIRFLEDNKGNKLDHLPLSISLQKNKGYIITADSICV 102
           G  P             +    L + PL  + +K+  Y I   SI V
Sbjct: 169 GGGPYYL-----FPPPIDLSKSLSYTPLLTNPRKSGEYYIGVTSIAV 210


>gnl|CDD|185751 cd09238, V_Alix_like_1, Protein-interacting V-domain of an
          uncharacterized family of the V_Alix_like superfamily. 
          This domain family is comprised of uncharacterized
          plant proteins. It belongs to the V_Alix_like
          superfamily which includes the V-shaped (V) domains of
          Bro1 and Rim20 (also known as PalA) from Saccharomyces
          cerevisiae, mammalian Alix (apoptosis-linked gene-2
          interacting protein X), (His-Domain) type N23 protein
          tyrosine phosphatase (HD-PTP, also known as PTPN23),
          and related domains. Alix, also known as
          apoptosis-linked gene-2 interacting protein 1 (AIP1),
          participates in membrane remodeling processes during
          the budding of enveloped viruses, vesicle budding
          inside late endosomal multivesicular bodies (MVBs), and
          the abscission reactions of mammalian cell division. It
          also functions in apoptosis. HD-PTP functions in cell
          migration and endosomal trafficking, Bro1 in endosomal
          trafficking, and Rim20 in the response to the external
          pH via the Rim101 pathway. Alix, HD-PTP, Bro1, and
          Rim20 all interact with the ESCRT (Endosomal Sorting
          Complexes Required for Transport) system. The mammalian
          Alix V-domain (belonging to a different family)
          contains a binding site, partially conserved in the
          superfamily, for the retroviral late assembly (L)
          domain YPXnL motif. The Alix V-domain is also a
          dimerization domain. In addition to this V-domain,
          members of the V_Alix_Rim20_Bro1_like superfamily also
          have an N-terminal Bro1-like domain, which binds
          components of the ESCRT-III complex. The Bro1-like
          domains of Alix and HD-PTP can also bind to human
          immunodeficiency virus type 1 (HIV-1) nucleocapsid.
          Many members of the V_Alix_like superfamily also have a
          proline-rich region (PRR).
          Length = 339

 Score = 26.3 bits (58), Expect = 4.8
 Identities = 11/24 (45%), Positives = 14/24 (58%)

Query: 40 LRLREMERKIVLSLVEGSAPLPDD 63
          + LREME    L  ++G A LP D
Sbjct: 35 VALREMELPETLIALDGGASLPGD 58


>gnl|CDD|32880 COG3066, MutH, DNA mismatch repair protein [DNA replication,
           recombination, and repair].
          Length = 229

 Score = 25.7 bits (56), Expect = 6.8
 Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 22/72 (30%)

Query: 80  HLPLSISLQKNKGYI---------ITADS------------ICVLPISSEDVVL-YYYAC 117
            + +   L+++KG++          +A S            +  +PI +    L   + C
Sbjct: 37  GMVVPPDLKRDKGWVGMLLEIWLGASAGSKPEQDFAHLGVELKTIPIDALGRPLETTFVC 96

Query: 118 IPPLTENNPVNW 129
           + PLT N+ V W
Sbjct: 97  VAPLTGNSGVTW 108


>gnl|CDD|144733 pfam01249, Ribosomal_S21e, Ribosomal protein S21e. 
          Length = 81

 Score = 25.7 bits (57), Expect = 8.5
 Identities = 10/27 (37%), Positives = 16/27 (59%)

Query: 2  AKDFASLLIDVSHYVEKGGFTYLFKNF 28
          AKD AS+ I+++   E G +T  F  +
Sbjct: 26 AKDHASVQINIADVDENGRYTGEFTTY 52


  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
   0.321    0.139    0.409 

Gapped
Lambda     K      H
   0.267   0.0704    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,225,783
Number of extensions: 114704
Number of successful extensions: 220
Number of sequences better than 10.0: 1
Number of HSP's gapped: 220
Number of HSP's successfully gapped: 11
Length of query: 178
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 90
Effective length of database: 4,362,145
Effective search space: 392593050
Effective search space used: 392593050
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: 54 (24.6 bits)