RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780645|ref|YP_003065058.1| hypothetical protein
CLIBASIA_02660 [Candidatus Liberibacter asiaticus str. psy62]
         (91 letters)



>gnl|CDD|35409 KOG0188, KOG0188, KOG0188, Alanyl-tRNA synthetase [Translation,
           ribosomal structure and biogenesis].
          Length = 895

 Score = 28.0 bits (62), Expect = 0.52
 Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 9/63 (14%)

Query: 23  LQKDLNHIRQIINEGD--FKSAAVKMRILVESFLRKLSEKESISIPGSIKARKNCWNLST 80
           L++D  H+  IINE +  F     + R L +   R+L    S +IPG        W L  
Sbjct: 350 LKRDPQHVIDIINEEEAQFLKTLDRGRKLFDRVAREL--GSSKTIPG-----DVAWRLYD 402

Query: 81  STG 83
           + G
Sbjct: 403 TYG 405


>gnl|CDD|35620 KOG0399, KOG0399, KOG0399, Glutamate synthase [Amino acid transport
           and metabolism].
          Length = 2142

 Score = 27.6 bits (61), Expect = 0.74
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 5/66 (7%)

Query: 24  QKDLNHIRQIINEGDFKSAAVK--MRILVESFLRKLSEKESISIPGSIKARKNCWNLSTS 81
           + +LN +  I+ EG   SAA+   + +LV S  R L E   + +P   +A +N  N+   
Sbjct: 339 KDELNKLLPIVEEGGSDSAALDNVLELLVRSGGRSLPEAVMMMVP---EAWQNDKNMDPE 395

Query: 82  TGAYLR 87
             A+  
Sbjct: 396 KKAFYD 401


>gnl|CDD|35098 COG5539, COG5539, Predicted cysteine protease (OTU family)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 306

 Score = 27.3 bits (60), Expect = 1.0
 Identities = 10/62 (16%), Positives = 23/62 (37%)

Query: 6   TPPSKKSKGAQVKENLGLQKDLNHIRQIINEGDFKSAAVKMRILVESFLRKLSEKESISI 65
              S   +   V E++  Q D + + Q        ++  K+R +V   +    +  + +I
Sbjct: 100 FEKSVSQQSINVLEDMPGQDDNSRLFQAERYSLRDASVAKLREVVSLEVLSNPDLYNPAI 159

Query: 66  PG 67
             
Sbjct: 160 LE 161


>gnl|CDD|185748 cd09235, V_Alix, Middle V-domain of mammalian Alix and related
          domains are dimerization and protein interaction
          modules.  This family contains the middle V-shaped (V)
          domain of mammalian Alix (apoptosis-linked gene-2
          interacting protein X) and related domains. It belongs
          to the V_Alix_like superfamily which includes the
          V-domains of Bro1 and Rim20 (also known as PalA) from
          Saccharomyces cerevisiae, mammalian 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),
          is part of the ESCRT (Endosomal Sorting Complexes
          Required for Transport) system, and participates in
          membrane remodeling processes, including the budding of
          enveloped viruses, vesicle budding inside late
          endosomal multivesicular bodies (MVBs), the abscission
          reactions of mammalian cell division, and in apoptosis.
          The Alix V-domain is a dimerization domain, and
          contains a binding site, partially conserved in the
          V_Alix_like superfamily, for the retroviral late
          assembly (L) domain YPXnL motif. In addition to the
          V-domain, Alix also has an N-terminal Bro1-like domain,
          which binds components of the ESCRT-III complex, in
          particular CHMP4. The Bro1-like domain of Alix can also
          bind to human immunodeficiency virus type 1 (HIV-1)
          nucleocapsid. Alix also has a C-terminal proline-rich
          region (PRR) that binds multiple partners including
          Tsg101 (tumor susceptibility gene 101, a component of
          ESCRT-1), and the apoptotic protein ALG-2.
          Length = 339

 Score = 25.3 bits (56), Expect = 3.2
 Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 4/30 (13%)

Query: 7  PPSKKSKGAQVKENLGLQKDLNHIRQIINE 36
          P S   K   V E  G+Q     I Q+I E
Sbjct: 55 PQSLLEKSRTVIEKGGIQT----IDQLIKE 80


>gnl|CDD|147094 pfam04762, IKI3, IKI3 family.  Members of this family are
           components of the elongator multi-subunit component of a
           novel RNA polymerase II holoenzyme for transcriptional
           elongation. This region contains WD40 like repeats.
          Length = 918

 Score = 25.0 bits (55), Expect = 4.7
 Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 11/40 (27%)

Query: 27  LNHIRQIINEGDFKSAAVKMR-------ILV----ESFLR 55
           L  IR++++   +K A +  R       IL     E FL 
Sbjct: 688 LAGIRKLLDAKRYKDAFLTCRTHRIDLNILHDYDPELFLD 727


>gnl|CDD|37296 KOG2085, KOG2085, KOG2085, Serine/threonine protein phosphatase 2A,
           regulatory subunit [Signal transduction mechanisms].
          Length = 457

 Score = 24.5 bits (53), Expect = 5.9
 Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 3/48 (6%)

Query: 2   HYDFTPPSKKSKGAQVKEN--LGLQKDLNHIRQIINEGDFKSAAVKMR 47
            +DF  P K  KG ++K    L L  D+   R  I+E  + S  VKM 
Sbjct: 70  LFDFNDPLKDLKGKEIKRQTLLELVDDVISRRGKISEEVY-SEVVKMF 116


>gnl|CDD|31726 COG1537, PelA, Predicted RNA-binding proteins [General function
          prediction only].
          Length = 352

 Score = 24.0 bits (52), Expect = 8.9
 Identities = 16/65 (24%), Positives = 25/65 (38%), Gaps = 4/65 (6%)

Query: 26 DLNHIRQIINEGDFKSAAVKMRILVESFLRKLSEKESISIPGSIKARKNCWNLSTSTGAY 85
          DL H+  II +GD   A    R   +     +  K+   IP ++  +             
Sbjct: 22 DLWHLYNIIEKGDKVFAKTTRR---DESSDVIRSKKGERIPMTLGIKVEKIEFDKFAN-R 77

Query: 86 LRIRG 90
          LRI+G
Sbjct: 78 LRIKG 82


>gnl|CDD|176668 cd07244, FosA, FosA, a Fosfomycin resistance protein, catalyzes
          the addition of glutathione to the antibiotic
          fosfomycin, making it inactive.  This subfamily family
          contains FosA, a fosfomycin resistant protein.
          Fosfomycin inhibits the enzyme
          UDP-N-acetylglucosamine-3-enolpyruvyltransferase
          (MurA), which catalyzes the first committed step in
          bacterial cell wall biosynthesis. FosA, catalyzes the
          addition of glutathione to the antibiotic fosfomycin,
          (1R,2S)-epoxypropylphosphonic acid, making it inactive.
          FosA is a Mn(II) dependent enzyme. It is evolutionarily
          related to glyoxalase I and type I extradiol
          dioxygenases.
          Length = 121

 Score = 23.9 bits (52), Expect = 10.0
 Identities = 20/71 (28%), Positives = 28/71 (39%), Gaps = 12/71 (16%)

Query: 5  FTPPSKKSKGA-----------QVKENLGLQKDLNHIRQIINEGDFKSAAVKMRIL-VES 52
          F    +  KGA            V  N+G  KD  H    ++E DF S   K+R   V+ 
Sbjct: 25 FKLHVRWDKGAYLEAGDLWLCLSVDANVGPAKDYTHYAFSVSEEDFASLKEKLRQAGVKE 84

Query: 53 FLRKLSEKESI 63
          +    SE +S 
Sbjct: 85 WKENTSEGDSF 95


  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
   0.316    0.131    0.371 

Gapped
Lambda     K      H
   0.267   0.0733    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 999,633
Number of extensions: 39973
Number of successful extensions: 115
Number of sequences better than 10.0: 1
Number of HSP's gapped: 115
Number of HSP's successfully gapped: 13
Length of query: 91
Length of database: 6,263,737
Length adjustment: 60
Effective length of query: 31
Effective length of database: 4,967,197
Effective search space: 153983107
Effective search space used: 153983107
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 (21.6 bits)
S2: 51 (23.4 bits)