RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780305|ref|YP_003064718.1| hypothetical protein
CLIBASIA_00950 [Candidatus Liberibacter asiaticus str. psy62]
         (95 letters)



>gnl|CDD|31101 COG0758, Smf, Predicted Rossmann fold nucleotide-binding protein
           involved in DNA uptake [DNA replication, recombination,
           and repair / Intracellular trafficking and secretion].
          Length = 350

 Score = 45.0 bits (106), Expect = 4e-06
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 6   IEQNFFSSQSDTNHTKNINITHYPEYTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVY 65
           I++      S  +  + +N      Y     + +  +L + P  ID +   TG+    V 
Sbjct: 269 IKEGAKLVTSAEDILEELNALLVLLYPY-TFLALLANLGDEPKEIDRLASCTGLTIAQVL 327

Query: 66  LVLLELDLAGRLCHHPEGKVSL 87
             LLEL+L G++     G   L
Sbjct: 328 AWLLELELEGKVKRLGGGYYRL 349


>gnl|CDD|143853 pfam00071, Ras, Ras family.  Includes sub-families Ras, Rab, Rac,
           Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
           GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
           pfam00063. As regards Rab GTPases, these are important
           regulators of vesicle formation, motility and fusion.
           They share a fold in common with all Ras GTPases: this
           is a six-stranded beta-sheet surrounded by five
           alpha-helices.
          Length = 162

 Score = 25.5 bits (57), Expect = 3.1
 Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)

Query: 40  KQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLA 74
           + S  NV   +++I+ H     P+V LV  + DL 
Sbjct: 84  RDSFENVKKWLEEILRHADDNVPIV-LVGNKCDLE 117


>gnl|CDD|73064 cd02658, Peptidase_C19B, A subfamily of Peptidase C19. Peptidase
           C19 contains ubiquitinyl hydrolases. They are
           intracellular peptidases that remove ubiquitin molecules
           from polyubiquinated peptides by cleavage of isopeptide
           bonds. They hydrolyze bonds involving the carboxyl group
           of the C-terminal Gly residue of ubiquitin. The purpose
           of the de-ubiquitination is thought to be editing of the
           ubiquitin conjugates, which could rescue them from
           degradation, as well as recycling of the ubiquitin. The
           ubiquitin/proteasome system is responsible for most
           protein turnover in the mammalian cell, and with over 50
           members, family C19 is one of the largest families of
           peptidases in the human genome..
          Length = 311

 Score = 25.3 bits (55), Expect = 4.4
 Identities = 17/75 (22%), Positives = 25/75 (33%), Gaps = 6/75 (8%)

Query: 5   QIEQNFFSSQSDTNHTKNINITHYPEYTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVV 64
            IE    + +  T  TK      +P+Y      R +   N VP  +D  I       P  
Sbjct: 192 TIEDFCSTCKEKTTATKTTGFKTFPDYLVINMKRFQLLENWVPKKLDVPIDVPEELGPGK 251

Query: 65  YLVLLELDLAGRLCH 79
           Y      +L   + H
Sbjct: 252 Y------ELIAFISH 260


>gnl|CDD|143409 cd07090, ALDH_F9_TMBADH, NAD+-dependent
           4-trimethylaminobutyraldehyde dehydrogenase, ALDH family
           9A1.  NAD+-dependent, 4-trimethylaminobutyraldehyde
           dehydrogenase (TMABADH, EC=1.2.1.47), also known as
           aldehyde dehydrogenase family 9 member A1 (ALDH9A1) in
           humans, is a cytosolic tetramer which catalyzes the
           oxidation of gamma-aminobutyraldehyde involved in
           4-aminobutyric acid (GABA) biosynthesis  and also
           oxidizes betaine aldehyde
           (gamma-trimethylaminobutyraldehyde) which is involved in
           carnitine biosynthesis.
          Length = 457

 Score = 25.0 bits (55), Expect = 4.8
 Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 52  DIIHHTGIEAPVVYLVLLELDLAGRLCHHPE-GKVSLTMHLPS 93
           +I+   G+   V  +V    +    LC HP+  KVS T  +P+
Sbjct: 164 EILTEAGLPDGVFNVVQGGGETGQLLCEHPDVAKVSFTGSVPT 206


>gnl|CDD|37096 KOG1885, KOG1885, KOG1885, Lysyl-tRNA synthetase (class II)
           [Translation, ribosomal structure and biogenesis].
          Length = 560

 Score = 24.9 bits (54), Expect = 5.7
 Identities = 8/13 (61%), Positives = 11/13 (84%)

Query: 23  INITHYPEYTQCE 35
           I++TH PE+T CE
Sbjct: 308 IDLTHNPEFTTCE 320


>gnl|CDD|63868 cd04399, RhoGAP_fRGD2, RhoGAP_fRGD2: RhoGAP (GTPase-activator
          protein [GAP] for Rho-like small GTPases) domain of
          fungal RGD2-like proteins. Yeast Rgd2 is a GAP protein
          for Cdc42 and Rho5. Small GTPases cluster into distinct
          families, and all act as molecular switches, active in
          their GTP-bound form but inactive when GDP-bound. The
          Rho family of GTPases activates effectors involved in a
          wide variety of developmental processes, including
          regulation of cytoskeleton formation, cell
          proliferation and the JNK signaling pathway. GTPases
          generally have a low intrinsic GTPase hydrolytic
          activity but there are family-specific groups of GAPs
          that enhance the rate of GTP hydrolysis by several
          orders of magnitude..
          Length = 212

 Score = 24.5 bits (53), Expect = 7.6
 Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 4/37 (10%)

Query: 39 IKQSLNNVPIHIDDIIHHTGIEAPVVY----LVLLEL 71
          ++  LN       ++I     E   V     L LLEL
Sbjct: 56 LRNLLNKPKKPDKEVIILKKFEPSTVASVLKLYLLEL 92


>gnl|CDD|29807 cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS)
           alpha chain catalytic core domain. PheRS belongs to
           class II aminoacyl-tRNA synthetases (aaRS) based upon
           its structure and the presence of three characteristic
           sequence motifs. This domain is primarily responsible
           for ATP-dependent formation of the enzyme bound
           aminoacyl-adenylate. While class II aaRSs generally
           aminoacylate the 3'-OH ribose of the appropriate tRNA,
           PheRS is an exception in that it attaches the amino acid
           at the 2'-OH group, like class I aaRSs.  PheRS is an
           alpha-2/ beta-2 tetramer..
          Length = 218

 Score = 23.9 bits (52), Expect = 8.8
 Identities = 8/23 (34%), Positives = 13/23 (56%)

Query: 22  NINITHYPEYTQCERVRIKQSLN 44
            I+ TH PE+ Q E + + + L 
Sbjct: 94  EIDATHLPEFHQIEGLVVDKGLT 116


>gnl|CDD|29820 cd00775, LysRS_core, Lys_tRNA synthetase (LysRS) class II core
           domain.  Class II LysRS is a dimer which attaches a
           lysine to the 3' OH group of ribose of the appropriate
           tRNA. Its assignment to class II aaRS is based upon its
           structure and the presence of three characteristic
           sequence motifs in the core domain. It is found in
           eukaryotes as well as some prokaryotes and archaea.
           However, LysRS belongs to class I aaRS's  in some
           prokaryotes and archaea. The catalytic core domain is
           primarily responsible for the ATP-dependent formation of
           the enzyme bound aminoacyl-adenylate..
          Length = 329

 Score = 24.0 bits (52), Expect = 9.7
 Identities = 7/13 (53%), Positives = 10/13 (76%)

Query: 23  INITHYPEYTQCE 35
           I++TH PE+T  E
Sbjct: 91  IDLTHNPEFTMIE 103


  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
   0.320    0.136    0.415 

Gapped
Lambda     K      H
   0.267   0.0832    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,194,543
Number of extensions: 53153
Number of successful extensions: 108
Number of sequences better than 10.0: 1
Number of HSP's gapped: 108
Number of HSP's successfully gapped: 9
Length of query: 95
Length of database: 6,263,737
Length adjustment: 63
Effective length of query: 32
Effective length of database: 4,902,370
Effective search space: 156875840
Effective search space used: 156875840
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: 51 (23.2 bits)