RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780122|ref|YP_003064535.1| hypothetical protein
CLIBASIA_00005 [Candidatus Liberibacter asiaticus str. psy62]
         (123 letters)



>gnl|CDD|180235 PRK05752, PRK05752, uroporphyrinogen-III synthase; Validated.
          Length = 255

 Score = 28.9 bits (65), Expect = 0.31
 Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 7/90 (7%)

Query: 26  PDISIE-MQISENQRYLDEEISQCNAVVDVFKRSDSTILDKLDAM---DDLKTYISLLQA 81
           P ++IE +  +  QR L  E+ +  AV+ V K +    L+ LD        + + S+  A
Sbjct: 33  PLLAIEPLPETPEQRALLLELDRYCAVIVVSKPAARLGLELLDRYWPQPPQQPWFSVGAA 92

Query: 82  TAKNLKSL-LKEYWEESLDGEDDEEIYEHP 110
           TA  L+   L   + E   G+D E +   P
Sbjct: 93  TAAILQDYGLDVSYPEQ--GDDSEALLALP 120


>gnl|CDD|149408 pfam08336, P4Ha_N, Prolyl 4-Hydroxylase alpha-subunit, N-terminal
           region.  The members of this family are eukaryotic
           proteins, and include all three isoforms of the prolyl
           4-hydroxylase alpha subunit. This enzyme (EC:1.14.11.2)
           is important in the post-translational modification of
           collagen, as it catalyses the formation of
           4-hydroxyproline. In vertebrates, the complete enzyme is
           an alpha2-beta2 tetramer; the beta-subunit is identical
           to protein disulphide isomerase. The function of the
           N-terminal region featured in this family does not seem
           to be known.
          Length = 134

 Score = 28.0 bits (63), Expect = 0.68
 Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 69  MDDLKTYISLLQATAKNLKSLLKEYWEESLDGEDDEEIY-EHP 110
           +D+L  YI  L+     LK  L E   E    + D E Y  +P
Sbjct: 17  IDNLDDYIEALEEKLDTLKRFLDELKREHEKAKSDPEEYLGNP 59


>gnl|CDD|180458 PRK06194, PRK06194, hypothetical protein; Provisional.
          Length = 287

 Score = 27.3 bits (61), Expect = 1.1
 Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 1/31 (3%)

Query: 10  DEINEN-FYFHSHPNADPDISIEMQISENQR 39
           D I    FY +SHP A   +   M+    QR
Sbjct: 248 DAIRAGRFYIYSHPQALASVRTRMEDIVQQR 278


>gnl|CDD|177564 PHA03237, PHA03237, envelope glycoprotein M; Provisional.
          Length = 424

 Score = 25.9 bits (57), Expect = 3.0
 Identities = 12/57 (21%), Positives = 27/57 (47%), Gaps = 4/57 (7%)

Query: 67  DAMDDLKTYISLLQATAKNLKSLLKEYW----EESLDGEDDEEIYEHPDQEHREDYY 119
                +K Y++ ++   +  KSL+++       E  + +D+E IY+    E   ++Y
Sbjct: 367 TVQQKVKRYLNRVRGGRRRPKSLVEDERGLLLTEDSETDDEEPIYDVVYSEFESEWY 423


>gnl|CDD|117067 pfam08490, DUF1744, Domain of unknown function (DUF1744).  This
           domain is found on the epsilon catalytic subunit of DNA
           polymerase. It is found C terminal to pfam03104 and
           pfam00136.
          Length = 396

 Score = 25.7 bits (57), Expect = 3.4
 Identities = 9/24 (37%), Positives = 17/24 (70%)

Query: 77  SLLQATAKNLKSLLKEYWEESLDG 100
           +   A  + LKS++KE+W+++L G
Sbjct: 258 AFSSAALRVLKSMVKEWWDDALSG 281


>gnl|CDD|162490 TIGR01691, enolase-ppase, 2,3-diketo-5-methylthio-1-phosphopentane
           phosphatase.  This enzyme is the enolase-phosphatase of
           methionine salvage, a pathway that regenerates
           methionine from methylthioadenosine (MTA).
           Adenosylmethionine (AdoMet) is a donor of different
           moieties for various processes, including methylation
           reactions. Use of AdoMet for spermidine biosynthesis,
           which leads to polyamine biosynthesis, leaves MTA as a
           by-product that must be cleared. In Bacillus subtilis
           and related species, this single protein is replaced by
           separate enzymes with enolase and phosphatase
           activities.
          Length = 220

 Score = 25.2 bits (55), Expect = 4.5
 Identities = 5/31 (16%), Positives = 12/31 (38%)

Query: 83  AKNLKSLLKEYWEESLDGEDDEEIYEHPDQE 113
           A  L+S + + +E ++     E      +  
Sbjct: 27  ASRLESFVNDNYESTIVENLRELGKTPEELI 57


>gnl|CDD|177920 PLN02281, PLN02281, chlorophyllide a oxygenase.
          Length = 536

 Score = 25.1 bits (54), Expect = 5.4
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 41  LDEEISQCNAVVDVFKRSDSTILDKLDAMDDL 72
           L EE+S+ +  V + +   ST LDKL  M++L
Sbjct: 133 LQEELSKAHQQVHISEARVSTALDKLAHMEEL 164


>gnl|CDD|150226 pfam09481, CRISPR_Cse1, CRISPR-associated protein Cse1
           (CRISPR_cse1).  Clusters of short DNA repeats with
           non-homologous spacers, which are found at regular
           intervals in the genomes of phylogenetically distinct
           prokaryotic species, comprise a family with recognisable
           features. This family is known as CRISPR (short for
           Clustered, Regularly Interspaced Short Palindromic
           Repeats). A number of protein families appear only in
           association with these repeats and are designated Cas
           (CRISPR-Associated) proteins. This entry, represented by
           CT1972 from Chlorobaculum tepidum, is found in the
           CRISPR/Cas subtype Ecoli regions of many bacteria (most
           of which are mesophiles), and not in Archaea. It is
           designated Cse1.
          Length = 475

 Score = 25.0 bits (55), Expect = 5.7
 Identities = 11/63 (17%), Positives = 23/63 (36%)

Query: 59  DSTILDKLDAMDDLKTYISLLQATAKNLKSLLKEYWEESLDGEDDEEIYEHPDQEHREDY 118
            + +L   D    +K  +   +  A+ L+S LKE W         ++ +        E +
Sbjct: 374 PAALLSDEDLRAQIKEAVDAAEEAARALRSALKEAWFALGKDAKGDKSFVDLAGRAEERF 433

Query: 119 YAN 121
           +  
Sbjct: 434 WQR 436


>gnl|CDD|183823 PRK12901, secA, preprotein translocase subunit SecA; Reviewed.
          Length = 1112

 Score = 24.2 bits (53), Expect = 8.4
 Identities = 17/49 (34%), Positives = 23/49 (46%)

Query: 70  DDLKTYISLLQATAKNLKSLLKEYWEESLDGEDDEEIYEHPDQEHREDY 118
           D+ K YI    A        LK    ESLD ++ E+IY   D+  +E Y
Sbjct: 47  DEFKQYIKEAVADIDAKIEELKAEAIESLDIDEREDIYAQIDKLEKEAY 95


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.313    0.132    0.377 

Gapped
Lambda     K      H
   0.267   0.0602    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,054,183
Number of extensions: 115438
Number of successful extensions: 237
Number of sequences better than 10.0: 1
Number of HSP's gapped: 236
Number of HSP's successfully gapped: 39
Length of query: 123
Length of database: 5,994,473
Length adjustment: 82
Effective length of query: 41
Effective length of database: 4,222,617
Effective search space: 173127297
Effective search space used: 173127297
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (23.7 bits)