RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780500|ref|YP_003064913.1| hypothetical protein
CLIBASIA_01935 [Candidatus Liberibacter asiaticus str. psy62]
         (159 letters)



>gnl|CDD|32737 COG2913, SmpA, Small protein A (tmRNA-binding) [Translation,
           ribosomal structure and biogenesis].
          Length = 147

 Score = 46.9 bits (111), Expect = 2e-06
 Identities = 29/119 (24%), Positives = 53/119 (44%), Gaps = 6/119 (5%)

Query: 37  GSISGASLDMSAISLVSQGSSRSHVIESLGSPSFSILHNGNRSQSFYYVSQKKKWFPVKF 96
               G  LD  A+  +  G ++  V+  LG+PS     + N    +YYV Q+++      
Sbjct: 34  DINQGNVLDQDAVDQLKVGMTKDQVLYLLGTPSLVDTFDTNT---WYYVFQQQR--RGVA 88

Query: 97  LSPKIMEYIVLKITFGEKGVVSSVSMERL-PNRRFNPNPHTIPAPIQTADGFLRRLLNP 154
             P+I+E   L + F + GVV+S+++ +    + F     T P P +      + + N 
Sbjct: 89  FGPEIVEQKTLTVYFDKDGVVTSIAVYKPADGKAFEAVNRTTPTPGKELTFLQQLVGNR 147


>gnl|CDD|146803 pfam04355, SmpA_OmlA, SmpA / OmlA family.  Lipoprotein Bacterial
           outer membrane lipoprotein, possibly involved in in
           maintaining the structural integrity of the cell
           envelope. Lipid attachment site is a conserved N
           terminal cysteine residue. Sometimes found adjacent to
           the OmpA domain (pfam00691).
          Length = 71

 Score = 41.4 bits (98), Expect = 1e-04
 Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 10/77 (12%)

Query: 44  LDMSAISLVSQGSSRSHVIESLGSPSFSILHNGNRSQSFYYVSQKKKWFPVKFLSPKIME 103
           +    +  +  G ++  V   LG+PS       N    +YYV   ++           +E
Sbjct: 4   VTQEDVDQLKPGMTKEQVRYLLGTPSLEDTFGPNT---WYYVYNFRR-------GGGAVE 53

Query: 104 YIVLKITFGEKGVVSSV 120
             VL + F + G+V ++
Sbjct: 54  QQVLAVYFDDDGLVRNI 70


>gnl|CDD|133174 cd05042, PTKc_Aatyk, Catalytic domain of the Protein Tyrosine
           Kinases, Apoptosis-associated tyrosine kinases.  Protein
           Tyrosine Kinase (PTK) family; Apoptosis-associated
           tyrosine kinase (Aatyk) subfamily; catalytic (c) domain.
           The Aatyk subfamily is also referred to as the lemur
           tyrosine kinase (Lmtk) subfamily. It consists of Aatyk1
           (Lmtk1), Aatyk2 (Lmtk2, Brek), Aatyk3 (Lmtk3), and
           similar proteins. 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 tyrosine (tyr) residues in protein substrates.
           Aatyk proteins are mostly receptor tyr kinases (RTKs)
           containing a transmembrane segment and a long C-terminal
           cytoplasmic tail with a catalytic domain. Aatyk1 does
           not contain a transmembrane segment and is a cytoplasmic
           (or nonreceptor) kinase. Aatyk proteins are classified
           as tyr kinases based on overall sequence similarity and
           the phylogenetic tree. However, analysis of catalytic
           residues suggests that Aatyk proteins may be
           multispecific kinases, functioning also as
           serine/threonine kinases. They are involved in neural
           differentiation, nerve growth factor (NGF) signaling,
           apoptosis, and spermatogenesis.
          Length = 269

 Score = 31.4 bits (71), Expect = 0.11
 Identities = 6/21 (28%), Positives = 16/21 (76%)

Query: 83  YYVSQKKKWFPVKFLSPKIME 103
           YY+++     P+++L+P+++E
Sbjct: 155 YYITKDCHAVPLRWLAPELVE 175


>gnl|CDD|133322 cd04122, Rab14, Rab14 subfamily.  Rab14 GTPases are localized to
           biosynthetic compartments, including the rough ER, the
           Golgi complex, and the trans-Golgi network, and to
           endosomal compartments, including early endosomal
           vacuoles and associated vesicles.  Rab14 is believed to
           function in both the biosynthetic and recycling pathways
           between the Golgi and endosomal compartments.  Rab14 has
           also been identified on GLUT4 vesicles, and has been
           suggested to help regulate GLUT4 translocation.  In
           addition, Rab14 is believed to play a role in the
           regulation of phagocytosis.  GTPase activating proteins
           (GAPs) interact with GTP-bound Rab and accelerate the
           hydrolysis of GTP to GDP. Guanine nucleotide exchange
           factors (GEFs) interact with GDP-bound Rabs to promote
           the formation of the GTP-bound state.  Rabs are further
           regulated by guanine nucleotide dissociation inhibitors
           (GDIs), which facilitate Rab recycling by masking
           C-terminal lipid binding and promoting cytosolic
           localization.  Most Rab GTPases contain a lipid
           modification site at the C-terminus, with sequence
           motifs CC, CXC, or CCX. Lipid binding is essential for
           membrane attachment, a key feature of most Rab proteins.
            Due to the presence of truncated sequences in this CD,
           the lipid modification site is not available for
           annotation.
          Length = 166

 Score = 29.4 bits (66), Expect = 0.49
 Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 1/35 (2%)

Query: 104 YIVLKITFGEKGVVSSVSMERLPNRRFNPN-PHTI 137
           YI   I  G+ GV  S  + +   ++F  + PHTI
Sbjct: 1   YIFKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTI 35


>gnl|CDD|173646 cd05087, PTKc_Aatyk1_Aatyk3, Catalytic domain of the Protein
           Tyrosine Kinases, Apoptosis-associated tyrosine kinases
           1 and 3.  Protein Tyrosine Kinase (PTK) family;
           Apoptosis-associated tyrosine kinase 1 (Aatyk1) and
           Aatyk3; 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 tyrosine (tyr)
           residues in protein substrates. Aatyk1 and Aatyk3 are
           members of the Aatyk subfamily of proteins. Aatyk3 is a
           receptor kinase containing a transmembrane segment and a
           long C-terminal cytoplasmic tail with a catalytic
           domain. Aatyk1 has a similar domain arrangement but
           without the transmembrane segment and is thus, a
           cytoplasmic (or nonreceptor) kinase. The expression of
           Aatyk1 (also referred simply as Aatyk) is upregulated
           during growth arrest and apoptosis in myeloid cells.
           Aatyk1 has been implicated in neural differentiation,
           and is a regulator of the Na-K-2Cl cotransporter, a
           membrane protein involved in cell proliferation and
           survival, epithelial transport, and blood pressure
           control. The function of Aatyk3 is still unknown.
          Length = 269

 Score = 27.6 bits (61), Expect = 1.5
 Identities = 8/34 (23%), Positives = 22/34 (64%), Gaps = 2/34 (5%)

Query: 70  FSILHNGNRSQSFYYVSQKKKWFPVKFLSPKIME 103
           + + HN  +    YYV+  + W P+++++P++++
Sbjct: 144 YGLSHNKYKED--YYVTPDQLWVPLRWIAPELVD 175


>gnl|CDD|112512 pfam03702, UPF0075, Uncharacterized protein family (UPF0075).
          The proteins is this family are about 370 amino acids
          long and have no known function.
          Length = 363

 Score = 27.7 bits (62), Expect = 1.6
 Identities = 12/32 (37%), Positives = 18/32 (56%)

Query: 37 GSISGASLDMSAISLVSQGSSRSHVIESLGSP 68
          G +SG SLD    +LV  G ++  ++ S  SP
Sbjct: 5  GLMSGTSLDGVDAALVDIGLTKIELLASHSSP 36


>gnl|CDD|34081 COG4372, COG4372, Uncharacterized protein conserved in bacteria
           with the myosin-like domain [Function unknown].
          Length = 499

 Score = 27.4 bits (60), Expect = 2.0
 Identities = 10/30 (33%), Positives = 12/30 (40%)

Query: 125 LPNRRFNPNPHTIPAPIQTADGFLRRLLNP 154
            P R+F      IPAP Q +DG        
Sbjct: 426 SPARQFRARRPGIPAPAQNSDGAAPTWSTF 455


>gnl|CDD|37454 KOG2243, KOG2243, KOG2243, Ca2+ release channel (ryanodine receptor)
            [Signal transduction mechanisms].
          Length = 5019

 Score = 27.0 bits (59), Expect = 2.8
 Identities = 18/92 (19%), Positives = 28/92 (30%), Gaps = 8/92 (8%)

Query: 53   SQGSSRSHV------IESLGSPSFSILHNGNRSQSFYYVSQKKKWFPVKFLSPKIMEYIV 106
             Q S R++       +        S + NG    + Y V    K FP  F         +
Sbjct: 1505 GQRSGRNNNDLEIGCLVDAAMGLLSFIANGKELGTCYQVEPNTKLFPAVFAQATSPN--L 1562

Query: 107  LKITFGEKGVVSSVSMERLPNRRFNPNPHTIP 138
             +   G+      +S     +   NP P   P
Sbjct: 1563 FQFELGKIKNAMPLSAAIFKSEEKNPVPQCPP 1594


>gnl|CDD|48183 cd03372, TPP_ComE, Thiamine pyrophosphate (TPP) family, ComE
          subfamily, TPP-binding module; composed of proteins
          similar to Methanococcus jannaschii sulfopyruvate
          decarboxylase beta subunit (ComE). M. jannaschii
          sulfopyruvate decarboxylase (ComDE) is a dodecamer of
          six alpha (D) subunits and six (E) beta subunits, which
          catalyzes the decarboxylation of sulfopyruvic acid to
          sulfoacetaldehyde in the coenzyme M pathway. ComDE
          requires TPP and divalent metal cation cofactors..
          Length = 179

 Score = 26.7 bits (59), Expect = 3.2
 Identities = 10/36 (27%), Positives = 17/36 (47%)

Query: 48 AISLVSQGSSRSHVIESLGSPSFSILHNGNRSQSFY 83
          AI  +        V+ ++G PS  +   G+R  +FY
Sbjct: 4  AIKTLIADLKDELVVSNIGFPSKELYAAGDRPLNFY 39


>gnl|CDD|109982 pfam00947, Pico_P2A, Picornavirus core protein 2A.  This protein is
           a protease, involved in cleavage of the polyprotein.
          Length = 127

 Score = 26.2 bits (58), Expect = 4.1
 Identities = 8/21 (38%), Positives = 13/21 (61%)

Query: 83  YYVSQKKKWFPVKFLSPKIME 103
           YY   + K++PV F  P ++E
Sbjct: 45  YYCKSRNKYYPVTFTGPTLIE 65


>gnl|CDD|39713 KOG4513, KOG4513, KOG4513, Phosphoglycerate mutase [Carbohydrate
           transport and metabolism].
          Length = 531

 Score = 25.4 bits (55), Expect = 7.2
 Identities = 8/32 (25%), Positives = 10/32 (31%)

Query: 51  LVSQGSSRSHVIESLGSPSFSILHNGNRSQSF 82
           L   G    H  E+      +   NG R   F
Sbjct: 334 LAHNGVRTFHCAETEKFAHVTFFFNGGREGYF 365


>gnl|CDD|173624 cd00192, PTKc, Catalytic domain of Protein Tyrosine Kinases.
           Protein Tyrosine Kinase (PTK) family, catalytic domain.
           This PTKc family is part of a larger superfamily that
           includes the catalytic domains of protein
           serine/threonine kinases, RIO kinases, aminoglycoside
           phosphotransferase, choline kinase, and phosphoinositide
           3-kinase (PI3K). PTKs catalyze the transfer of the
           gamma-phosphoryl group from ATP to tyrosine (tyr)
           residues in protein substrates. They can be classified
           into receptor and non-receptor tyr kinases. PTKs play
           important roles in many cellular processes including,
           lymphocyte activation, epithelium growth and
           maintenance, metabolism control, organogenesis
           regulation, survival, proliferation, differentiation,
           migration, adhesion, motility, and morphogenesis.
           Receptor tyr kinases (RTKs) are integral membrane
           proteins which contain an extracellular ligand-binding
           region, a transmembrane segment, and an intracellular
           tyr kinase domain. RTKs are usually activated through
           ligand binding, which causes dimerization and
           autophosphorylation of the intracellular tyr kinase
           catalytic domain, leading to intracellular signaling.
           Some RTKs are orphan receptors with no known ligands.
           Non-receptor (or cytoplasmic) tyr kinases are
           distributed in different intracellular compartments and
           are usually multi-domain proteins containing a catalytic
           tyr kinase domain as well as various regulatory domains
           such as SH3 and SH2. PTKs are usually autoinhibited and
           require a mechanism for activation. In many PTKs, the
           phosphorylation of tyr residues in the activation loop
           is essential for optimal activity. Aberrant expression
           of PTKs is associated with many development
           abnormalities and cancers.
          Length = 262

 Score = 25.2 bits (56), Expect = 8.2
 Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 10/41 (24%)

Query: 83  YYVSQKKKWFPVKFLSPKIMEYIVLKITFGEK------GVV 117
           YY  +     P+++++P   E +   I F  K      GV+
Sbjct: 160 YYRKKTGGKLPIRWMAP---ESLKDGI-FTSKSDVWSFGVL 196


>gnl|CDD|146137 pfam03345, DDOST_48kD, Oligosaccharyltransferase 48 kDa subunit
           beta.  Members of this family are involved in
           asparagine-linked protein glycosylation. In particular,
           dolichyl-diphosphooligosaccharide-protein
           glycosyltransferase (DDOST), also known as
           oligosaccharyltransferase EC:2.4.1.119, transfers the
           high-mannose sugar GlcNAc(2)-Man(9)-Glc(3) from a
           dolichol-linked donor to an asparagine acceptor in a
           consensus Asn-X-Ser/Thr motif. In most eukaryotes, the
           DDOST complex is composed of three subunits, which in
           humans are described as a 48kD subunit, ribophorin I,
           and ribophorin II. However, the yeast DDOST appears to
           consist of six subunits (alpha, beta, gamma, delta,
           epsilon, zeta). The yeast beta subunit is a 45kD
           polypeptide, previously discovered as the Wbp1 protein,
           with known sequence similarity to the human 48kD subunit
           and the other orthologues. This family includes the
           48kD-like subunits from several eukaryotes; it also
           includes the yeast DDOST beta subunit Wbp1.
          Length = 439

 Score = 25.3 bits (56), Expect = 8.2
 Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 2/34 (5%)

Query: 106 VLKITFGEKGV--VSSVSMERLPNRRFNPNPHTI 137
           + K  F EKGV  V  V+        +NP  +TI
Sbjct: 264 LTKWVFKEKGVLKVGKVTHHLAGEPSYNPEIYTI 297


>gnl|CDD|144920 pfam01504, PIP5K, Phosphatidylinositol-4-phosphate 5-Kinase.
          This family contains a region from the common kinase
          core found in the type I
          phosphatidylinositol-4-phosphate 5-kinase (PIP5K)
          family as described in. The family consists of various
          type I, II and III PIP5K enzymes. PIP5K catalyses the
          formation of phosphoinositol-4,5-bisphosphate via the
          phosphorylation of phosphatidylinositol-4-phosphate a
          precursor in the phosphinositide signaling pathway.
          Length = 257

 Score = 25.3 bits (56), Expect = 8.5
 Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 1/31 (3%)

Query: 63 ESLGSPS-FSILHNGNRSQSFYYVSQKKKWF 92
          +SL S    S L +G +S SF+Y S+  ++ 
Sbjct: 1  KSLCSLDTLSELSSGGKSGSFFYKSRDGRFI 31


>gnl|CDD|37906 KOG2695, KOG2695, KOG2695, WD40 repeat protein [General function
           prediction only].
          Length = 425

 Score = 25.0 bits (54), Expect = 8.6
 Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 15/53 (28%)

Query: 82  FYYVSQKKKWFPVKFLSPKIMEYIVLKITFGEKGVVSSVSMERL-PNRRFNPN 133
           +YY S+KK++F +   S                   +  + ERL P +RF   
Sbjct: 10  YYYNSEKKRYFRIS--SG------------QSTPSSNIYTKERLKPGKRFENI 48


>gnl|CDD|31154 COG0812, MurB, UDP-N-acetylmuramate dehydrogenase [Cell envelope
           biogenesis, outer membrane].
          Length = 291

 Score = 25.2 bits (55), Expect = 8.8
 Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 10/60 (16%)

Query: 103 EYIVLKITF-GEKGVVSSVS--MERLPNRRFNPNPHTIPAPIQTADGFLRRLLNPNGRSA 159
             +VL + F   KG    +   M  +  RR    P  +P    +A  F +   NP G  A
Sbjct: 170 YLVVLSVEFKLTKGDPEDILAAMCAIRRRRELKQPIDLP----SAGSFFK---NPVGDFA 222


  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    0.137    0.399 

Gapped
Lambda     K      H
   0.267   0.0665    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,980,167
Number of extensions: 97951
Number of successful extensions: 265
Number of sequences better than 10.0: 1
Number of HSP's gapped: 265
Number of HSP's successfully gapped: 29
Length of query: 159
Length of database: 6,263,737
Length adjustment: 86
Effective length of query: 73
Effective length of database: 4,405,363
Effective search space: 321591499
Effective search space used: 321591499
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: 53 (24.3 bits)