RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781074|ref|YP_003065487.1| uracil-DNA glycosylase
[Candidatus Liberibacter asiaticus str. psy62]
         (227 letters)



>gnl|CDD|31036 COG0692, Ung, Uracil DNA glycosylase [DNA replication,
           recombination, and repair].
          Length = 223

 Score =  327 bits (839), Expect = 2e-90
 Identities = 123/223 (55%), Positives = 160/223 (71%), Gaps = 1/223 (0%)

Query: 4   VKIHESWKSLLENHFQSEHMRNLKEFLLSEKRKGKRIFPRGSHYFRAFDITPFNKVKVVI 63
            K+  SWK  L+  F+  + + L EFL  E   GK I+P     F AF +TPF+ VKVVI
Sbjct: 1   SKLELSWKEFLKPEFKKPYFQELLEFLKQEYASGKTIYPPKEDIFNAFRLTPFDDVKVVI 60

Query: 64  LGQDPYHNYGQAHGLCFSVPLGIRIPPSLVNVYKELQEDVN-FIPPTHGFLEHWGHEGVL 122
           LGQDPYH  GQAHGL FSVP G++IPPSL N+YKEL+ D+  F  P HG L  W  +GVL
Sbjct: 61  LGQDPYHGPGQAHGLSFSVPPGVKIPPSLKNIYKELEADLGGFPIPNHGDLTSWAEQGVL 120

Query: 123 LLNAVLTVEEGRAASHRGRGWEQFTDSVIDLISNNHQNIVFMLWGASAQKKQDVLDHKRH 182
           LLN VLTV  G+A SH G+GWE FTD+VI  ++   + +VF+LWG+ AQKK+ ++D+K+H
Sbjct: 121 LLNTVLTVRAGQANSHAGKGWETFTDAVIKALNERREPVVFVLWGSHAQKKKKLIDNKKH 180

Query: 183 LVLKAAHPSPLSASHGFFGCRHFSKANRYLQEHGKTTVNWQIP 225
           L+L+A HPSPLSA  GFFGC+HFSKAN +L++HGK  ++W +P
Sbjct: 181 LILEAPHPSPLSAHRGFFGCKHFSKANEWLEKHGKKPIDWSLP 223


>gnl|CDD|38205 KOG2994, KOG2994, KOG2994, Uracil DNA glycosylase [Replication,
           recombination and repair].
          Length = 297

 Score =  285 bits (730), Expect = 7e-78
 Identities = 118/225 (52%), Positives = 146/225 (64%), Gaps = 2/225 (0%)

Query: 1   MEGVKIHESWKSLLENHFQSEHMRNLKEFLLSEKRKGKRIFPRGSHYFRAFDITPFNKVK 60
           +E   I ESW   L+  F   +   LK FL  E R    +FP     F    +TPF+KVK
Sbjct: 73  LEERTIGESWFKHLKGEFGKPYFIKLKGFLAEE-RNSYTVFPPPHQIFTWTRLTPFDKVK 131

Query: 61  VVILGQDPYHNYGQAHGLCFSVPLGIRIPPSLVNVYKELQEDV-NFIPPTHGFLEHWGHE 119
           VVI+GQDPYHN  QAHGL FSV  G+  PPSL N+YKEL  D+ +F+ P HG L  W  +
Sbjct: 132 VVIIGQDPYHNPNQAHGLSFSVQPGVPPPPSLKNIYKELSSDIEDFVIPKHGDLSGWAKQ 191

Query: 120 GVLLLNAVLTVEEGRAASHRGRGWEQFTDSVIDLISNNHQNIVFMLWGASAQKKQDVLDH 179
           GVLLLNAVLTV   +A SH   GWE FTD+V+ +I+   + +VF+LWG  AQKK  ++D 
Sbjct: 192 GVLLLNAVLTVRAHQANSHAKIGWETFTDAVVQVINQQSKGLVFLLWGRYAQKKGKLIDR 251

Query: 180 KRHLVLKAAHPSPLSASHGFFGCRHFSKANRYLQEHGKTTVNWQI 224
           K+H VL  AHPSPLSA  GFFGCRHFSK N  L+E GK  ++WQ+
Sbjct: 252 KKHHVLTTAHPSPLSAYRGFFGCRHFSKTNELLEESGKKPIDWQV 296


>gnl|CDD|146005 pfam03167, UDG, Uracil DNA glycosylase superfamily. 
          Length = 147

 Score = 82.0 bits (203), Expect = 1e-16
 Identities = 39/166 (23%), Positives = 59/166 (35%), Gaps = 35/166 (21%)

Query: 58  KVKVVILGQDPYHNYGQAHGLCFSVPLGIRIPPSLVNVYKELQEDVNFIPPTHGFLEHWG 117
             KV+I+G+ P      A GL F+   G      L  +  E                   
Sbjct: 7   NAKVLIVGEAPGPG-EDATGLPFAGRAG----NLLWRILAEA---------------GLA 46

Query: 118 HEGVLLLNAV---LTVEEGRAASHRGRGWEQFTDSVIDLISNNHQNIVFMLWGASAQK-- 172
            EGV L N V     V      S     W      +++ ++     +V +L G +A K  
Sbjct: 47  REGVYLTNVVKCPRPVGRKPTRSEIAACWPY----LLEELALLRPKVVVLL-GKTAAKAF 101

Query: 173 -----KQDVLDHKRHLVLKAAHPSPLSASHGFFGCRHFSKANRYLQ 213
                K+ + +     VL   HPSPL+ + GF     F +A   L+
Sbjct: 102 LGLGKKESLFEGGGIPVLPLPHPSPLNRNPGFKRPEAFREALEDLK 147


>gnl|CDD|35558 KOG0337, KOG0337, KOG0337, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 529

 Score = 31.9 bits (72), Expect = 0.14
 Identities = 26/127 (20%), Positives = 42/127 (33%), Gaps = 5/127 (3%)

Query: 96  YKELQEDVNFIPPTHGFLEHWGHEGVLLLNAVLTVEEGRAASHRGRGWEQFTDSVIDLIS 155
           +  L E+ + I  T G L H G E  L L++V  V    A      G+++    ++  + 
Sbjct: 134 FILLNENPDIIIATPGRLLHLGVEMTLTLSSVEYVVFDEADRLFEMGFQEQLHEILSRLP 193

Query: 156 NNHQNIVF--MLWGASAQKKQDVLDHKRHLVLKAAHPSPLSASHGFFGCRHFSKAN---R 210
            + Q ++F   L        +  L     + L             FF  R   K      
Sbjct: 194 ESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLKVRFFRVRKAEKEAALLS 253

Query: 211 YLQEHGK 217
            L    K
Sbjct: 254 ILGGRIK 260


>gnl|CDD|133168 cd05036, PTKc_ALK_LTK, Catalytic domain of the Protein Tyrosine
           Kinases, Anaplastic Lymphoma Kinase and Leukocyte
           Tyrosine Kinase.  Protein Tyrosine Kinase (PTK) family;
           Anaplastic Lymphoma Kinase (ALK) and Leukocyte Tyrosine
           (tyr) Kinase (LTK); catalytic (c) domain. The PTKc
           family is part of a larger superfamily that includes the
           catalytic domains of other kinases such as protein
           serine/threonine kinases, RIO kinases, and
           phosphoinositide 3-kinase (PI3K). PTKs catalyze the
           transfer of the gamma-phosphoryl group from ATP to tyr
           residues in protein substrates. ALK and LTK are orphan
           receptor tyr kinases (RTKs) whose ligands are not yet
           well-defined. RTKs contain an extracellular
           ligand-binding domain, a transmembrane region, and an
           intracellular tyr kinase domain. They are usually
           activated through ligand binding, which causes
           dimerization and autophosphorylation of the
           intracellular tyr kinase catalytic domain. ALK appears
           to play an important role in mammalian neural
           development as well as visceral muscle differentiation
           in Drosophila. ALK is aberrantly expressed as fusion
           proteins, due to chromosomal translocations, in about
           60% of anaplastic large cell lymphomas (ALCLs). ALK
           fusion proteins are also found in rare cases of diffuse
           large B cell lymphomas (DLBCLs). LTK is mainly expressed
           in B lymphocytes and neuronal tissues. It is important
           in cell proliferation and survival. Transgenic mice
           expressing TLK display retarded growth and high
           mortality rate. In addition, a polymorphism in mouse and
           human LTK is implicated in the pathogenesis of systemic
           lupus erythematosus.
          Length = 277

 Score = 27.4 bits (61), Expect = 3.3
 Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 12/71 (16%)

Query: 157 NHQNIVFMLWGASAQKKQ-----------DVLDHKRHLVLKAAHPSPLSASHGFFGCRHF 205
           NHQNIV ++ G S ++             D+    R    +   PS L+     F  R  
Sbjct: 67  NHQNIVRLI-GVSFERLPRFILLELMAGGDLKSFLRENRPRPERPSSLTMKDLLFCARDV 125

Query: 206 SKANRYLQEHG 216
           +K  +YL+E+ 
Sbjct: 126 AKGCKYLEENH 136


>gnl|CDD|112256 pfam03431, RNA_replicase_B, RNA replicase, beta-chain.  This family
           is of Leviviridae RNA replicases. The replicase is also
           known as RNA dependent RNA polymerase.
          Length = 539

 Score = 27.1 bits (60), Expect = 4.1
 Identities = 8/13 (61%), Positives = 9/13 (69%)

Query: 44  GSHYFRAFDITPF 56
           G HYF   D+TPF
Sbjct: 374 GKHYFAGVDVTPF 386


>gnl|CDD|30531 COG0182, COG0182, Predicted translation initiation factor 2B
           subunit, eIF-2B alpha/beta/delta family [Translation,
           ribosomal structure and biogenesis].
          Length = 346

 Score = 26.8 bits (59), Expect = 4.7
 Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 4/42 (9%)

Query: 23  MRNLKEFLLSEKRKGKRIFPRGSH-YFRAFDITPFNKVKVVI 63
            R+ +E L      G RI P G   Y  AFD+TP   +  +I
Sbjct: 288 ERDPEEVLEVG---GVRIAPEGVEAYNPAFDVTPPELITGII 326


>gnl|CDD|113810 pfam05053, Menin, Menin.  MEN1, the gene responsible for multiple
           endocrine neoplasia type 1, is a tumour suppressor gene
           that encodes a protein called Menin which may be an
           atypical GTPase stimulated by nm23.
          Length = 618

 Score = 26.5 bits (58), Expect = 6.2
 Identities = 10/17 (58%), Positives = 13/17 (76%)

Query: 18  FQSEHMRNLKEFLLSEK 34
           F SE M+ +KE LL+EK
Sbjct: 561 FYSEKMKGMKELLLAEK 577


>gnl|CDD|37292 KOG2081, KOG2081, KOG2081, Nuclear transport regulator
           [Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 559

 Score = 26.4 bits (58), Expect = 6.4
 Identities = 8/19 (42%), Positives = 10/19 (52%)

Query: 206 SKANRYLQEHGKTTVNWQI 224
            KAN +L    K+   WQI
Sbjct: 2   EKANNWLGNFQKSNDAWQI 20


>gnl|CDD|113049 pfam04262, Glu_cys_ligase, Glutamate-cysteine ligase.  Family of
           bacterial f glutamate-cysteine ligases (EC:6.3.2.2) that
           carry out the first step of the glutathione biosynthesis
           pathway.
          Length = 377

 Score = 26.6 bits (59), Expect = 6.4
 Identities = 18/68 (26%), Positives = 26/68 (38%), Gaps = 16/68 (23%)

Query: 3   GVKIHESWKSLLENHFQSEHMRNLKEF--LLSEKRKGKR-------IFPRGSHY--FRAF 51
           G+K    W+ L  N  Q E      E    +  KR  K        +  RG  Y   R+ 
Sbjct: 274 GIKKDGEWRQLNTNLLQIE-----NELYAPIRPKRVTKSGERPLDALARRGVEYIEVRSL 328

Query: 52  DITPFNKV 59
           D+ PF+ +
Sbjct: 329 DVNPFSPI 336


>gnl|CDD|143452 cd07134, ALDH_AlkH-like, Pseudomonas putida Aldehyde dehydrogenase
           AlkH-like.  Aldehyde dehydrogenase AlkH (locus name
           P12693, EC=1.2.1.3) of the alkBFGHJKL operon that allows
           Pseudomonas putida to metabolize alkanes and the
           aldehyde dehydrogenase AldX of Bacillus subtilis (locus
           P46329, EC=1.2.1.3), and similar sequences, are present
           in this CD.
          Length = 433

 Score = 26.4 bits (59), Expect = 7.0
 Identities = 16/82 (19%), Positives = 29/82 (35%), Gaps = 16/82 (19%)

Query: 148 DSVIDLISNNHQNIVFMLWGASAQKKQDVLDHK-------RHLVLKAAHP---------S 191
           D VI+ I+   + +   ++         VL            +VL   +P         S
Sbjct: 352 DEVIEYINAKPKPLALYVFSKDKANVNKVLARTSSGGVVVNDVVLHFLNPNLPFGGVNNS 411

Query: 192 PLSASHGFFGCRHFSKANRYLQ 213
            + + HG +G + FS     L+
Sbjct: 412 GIGSYHGVYGFKAFSHERAVLR 433


>gnl|CDD|37070 KOG1859, KOG1859, KOG1859, Leucine-rich repeat proteins [General
           function prediction only].
          Length = 1096

 Score = 26.2 bits (57), Expect = 7.2
 Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 4/58 (6%)

Query: 21  EHMRNLKEFLLSEKRKGKRIFPRGSHYFRAFDITPFNKVKVVILGQDPYHNYGQAHGL 78
           E ++ + +FL   K       P          I PF  ++V+ L          A GL
Sbjct: 74  EQLQRILDFLQKTKVLKLLPSP-ARDPTEPISIFPFRSLRVLELRGCDLS---TAKGL 127


  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
   0.322    0.138    0.436 

Gapped
Lambda     K      H
   0.267   0.0565    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,996,697
Number of extensions: 156377
Number of successful extensions: 353
Number of sequences better than 10.0: 1
Number of HSP's gapped: 349
Number of HSP's successfully gapped: 14
Length of query: 227
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 137
Effective length of database: 4,318,927
Effective search space: 591692999
Effective search space used: 591692999
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 (21.9 bits)
S2: 56 (25.7 bits)