RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780446|ref|YP_003064859.1| hypothetical protein
CLIBASIA_01655 [Candidatus Liberibacter asiaticus str. psy62]
         (171 letters)



>gnl|CDD|144199 pfam00519, PPV_E1_C, Papillomavirus helicase.  This protein is a
           DNA helicase that is required for initiation of viral
           DNA replication. This protein forms a complex with the
           E2 protein pfam00508.
          Length = 432

 Score = 29.4 bits (67), Expect = 0.49
 Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 4/36 (11%)

Query: 48  VNKDGKFKPIGYLPSDRLKVFEFKYPCLYKEDQEQV 83
           V  D ++K   YL S R+ VFEF  P  + E+   V
Sbjct: 362 VKADDRYK---YLHS-RITVFEFPNPFPFDENGNPV 393


>gnl|CDD|146172 pfam03393, Pneumo_matrix, Pneumovirus matrix protein. 
          Length = 252

 Score = 29.5 bits (66), Expect = 0.55
 Identities = 11/16 (68%), Positives = 13/16 (81%)

Query: 140 AIPNAKIAPYQGIILL 155
           AI NAKI PY G+IL+
Sbjct: 188 AITNAKIIPYAGLILV 203


>gnl|CDD|73019 cd03260, ABC_PstB_phosphate_transporter, Phosphate uptake is of
           fundamental importance in the cell physiology of
           bacteria because phosphate is required as a nutrient.
           The Pst system of E. coli comprises four distinct
           subunits encoded by the pstS, pstA, pstB, and pstC
           genes.  The PstS protein is a phosphate-binding protein
           located in the periplasmic space. P stA and PstC are
           hydrophobic and they form the transmembrane portion of
           the Pst system.  PstB is the catalytic subunit, which
           couples the energy of ATP hydrolysis to the import of
           phosphate across cellular membranes through the Pst
           system, often referred as ABC-protein.  PstB belongs to
           one of the largest superfamilies of proteins
           characterized by a highly conserved adenosine
           triphosphate (ATP) binding cassette (ABC), which is also
           a nucleotide binding domain (NBD)..
          Length = 227

 Score = 28.6 bits (64), Expect = 0.88
 Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 11/55 (20%)

Query: 118 GIGKNSNSVASTLIRCMGLKELAIPNAKIAPYQGIILLDDRKINEIQNN--WIRC 170
           G GK      STL+R +      IP    AP +G +LLD + I ++  +   +R 
Sbjct: 36  GCGK------STLLRLLNRLNDLIPG---APDEGEVLLDGKDIYDLDVDVLELRR 81


>gnl|CDD|73053 cd03294, ABC_Pro_Gly_Bertaine, This family comprises the glycine
           betaine/L-proline ATP binding subunit in bacteria and
           its equivalents in archaea.  This transport system
           belong to the larger ATP-Binding Cassette (ABC)
           transporter superfamily.  The characteristic feature of
           these transporters is the obligatory coupling of ATP
           hydrolysis to substrate translocation.  ABC transporters
           are a subset of nucleotide hydrolases that contain a
           signature motif, Q-loop, and H-loop/switch region, in
           addition to, the Walker A motif/P-loop and Walker B
           motif commonly found in a number of ATP- and GTP-binding
           and hydrolyzing proteins..
          Length = 269

 Score = 28.2 bits (63), Expect = 1.1
 Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 8/41 (19%)

Query: 123 SNSVASTLIRCMGLKELAIPNAKIAPYQGIILLDDRKINEI 163
           S S  STL+RC+        N  I P  G +L+D + I  +
Sbjct: 59  SGSGKSTLLRCI--------NRLIEPTSGKVLIDGQDIAAM 91


>gnl|CDD|73021 cd03262, ABC_HisP_GlnQ_permeases, HisP and GlnQ are the ATP-binding
           components of the bacterial periplasmic histidine and
           glutamine permeases, repectively.  Histidine permease is
           a multisubunit complex containing the HisQ and HisM
           integral membrane subunits and two copies of HisP.  HisP
           has properties intermediate between those of integral
           and peripheral membrane proteins and is accessible from
           both sides of the membrane, presumably by its
           interaction with HisQ and HisM.  The two HisP subunits
           form a homodimer within the complex.  The domain
           structure of the amino acid uptake systems is typical
           for prokaryote extracellular solute binding
           protein-dependent uptake systems.  All of the amino acid
           uptake systems also have at least one, and in a few
           cases, two extracellular solute binding proteins located
           in the periplasm of Gram-negative bacteria, or attached
           to the cell membrane of Gram-positive bacteria.  The
           best-studied member of the PAAT (polar amino acid
           transport) family is the HisJQMP system of S.
           typhimurium, where HisJ is the extracellular solute
           binding proteins and HisP is the ABC protein..
          Length = 213

 Score = 28.2 bits (63), Expect = 1.3
 Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 8/48 (16%)

Query: 123 SNSVASTLIRCMGLKELAIPNAKIAPYQGIILLDDRKINEIQNNWIRC 170
           S S  STL+RC+ L E         P  G I++D  K+ + + N    
Sbjct: 35  SGSGKSTLLRCINLLE--------EPDSGTIIIDGLKLTDDKKNINEL 74


>gnl|CDD|35278 KOG0055, KOG0055, KOG0055, Multidrug/pheromone exporter, ABC
           superfamily [Secondary metabolites biosynthesis,
           transport and catabolism].
          Length = 1228

 Score = 27.9 bits (62), Expect = 1.6
 Identities = 7/22 (31%), Positives = 11/22 (50%)

Query: 148 PYQGIILLDDRKINEIQNNWIR 169
           P  G +L+D   I  +   W+R
Sbjct: 405 PTSGEVLIDGEDIRNLNLKWLR 426


>gnl|CDD|73056 cd03297, ABC_ModC_molybdenum_transporter, ModC is an ABC-type
           transporter and the ATPase component of a molybdate
           transport system that also includes the periplasmic
           binding protein ModA and the membrane protein ModB. ABC
           transporters are a large family of proteins involved in
           the transport of a wide variety of different compounds,
           like sugars, ions, peptides and more complex organic
           molecules. The nucleotide binding domain shows the
           highest similarity between all members of the family.
           ABC transporters are a subset of nucleotide hydrolases
           that contain a signature motif, Q-loop, and
           H-loop/switch region, in addition to, the Walker A
           motif/P-loop and Walker B motif commonly found in a
           number of ATP- and GTP-binding and hydrolyzing
           proteins..
          Length = 214

 Score = 27.9 bits (62), Expect = 1.6
 Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 10/55 (18%)

Query: 113 PYPFLGIGKNSNSVASTLIRCM-GLKELAIPNAKIAPYQGIILLDDRKINEIQNN 166
                GI   S +  STL+RC+ GL++         P  G I+L+   + + +  
Sbjct: 22  NEEVTGIFGASGAGKSTLLRCIAGLEK---------PDGGTIVLNGTVLFDSRKK 67


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

 Score = 27.0 bits (59), Expect = 3.1
 Identities = 19/70 (27%), Positives = 28/70 (40%), Gaps = 6/70 (8%)

Query: 25   FAHRLLVVFDSNKEFVAELDGLVVNKDGKFKP----IGYLPSDRLKVFE--FKYPCLYKE 78
            F  +++   D   EF+AE D +     G+  P    I +     L + +  FK  CLY  
Sbjct: 2942 FLKKIIKYVDEAHEFIAEFDAIGSRGKGEHFPRDQEIKFFAKVLLPLIDQYFKNHCLYFL 3001

Query: 79   DQEQVVLCSS 88
                  LCS 
Sbjct: 3002 SAALKPLCSG 3011


>gnl|CDD|73017 cd03258, ABC_MetN_methionine_transporter, MetN (also known as YusC)
           is an ABC-type transporter encoded by metN of the metNPQ
           operon in Bacillus subtilis that is involved in
           methionine transport.  Other members of this system
           include the MetP permease and  the MetQ substrate
           binding protein.  ABC transporters are a subset of
           nucleotide hydrolases that contain a signature motif,
           Q-loop, and H-loop/switch region, in addition to, the
           Walker A motif/P-loop and Walker B motif commonly found
           in a number of ATP- and GTP-binding and hydrolyzing
           proteins..
          Length = 233

 Score = 26.7 bits (59), Expect = 3.4
 Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 8/53 (15%)

Query: 117 LGIGKNSNSVASTLIRCMGLKELAIPNAKIAPYQGIILLDDRKINEIQNNWIR 169
            GI   S +  STLIRC+   E         P  G +L+D   +  +    +R
Sbjct: 34  FGIIGRSGAGKSTLIRCINGLE--------RPTSGSVLVDGTDLTLLSGKELR 78


>gnl|CDD|31330 COG1135, AbcC, ABC-type metal ion transport system, ATPase
           component [Inorganic ion transport and metabolism].
          Length = 339

 Score = 26.4 bits (58), Expect = 4.7
 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 8/53 (15%)

Query: 117 LGIGKNSNSVASTLIRCMGLKELAIPNAKIAPYQGIILLDDRKINEIQNNWIR 169
            GI   S +  STL+R + L E         P  G + +D + +  +    +R
Sbjct: 35  FGIIGYSGAGKSTLLRLINLLE--------RPTSGSVFVDGQDLTALSEAELR 79


>gnl|CDD|176034 cd08388, C2A_Synaptotagmin-4-11, C2A domain first repeat present in
           Synaptotagmins 4 and 11.  Synaptotagmin is a
           membrane-trafficking protein characterized by a
           N-terminal transmembrane region, a linker, and 2
           C-terminal C2 domains.  Synaptotagmins 4 and 11, class 4
           synaptotagmins, are located in the brain.  Their
           functions are unknown. They are distinguished from the
           other synaptotagmins by having and Asp to Ser
           substitution in their C2A domains. Previously all
           synaptotagmins were thought to be calcium sensors in the
           regulation of neurotransmitter release and hormone
           secretion, but it has been shown that not all of them
           bind calcium.  Of the 17 identified synaptotagmins only
           8 bind calcium (1-3, 5-7, 9, 10).  The function of the
           two C2 domains that bind calcium are: regulating the
           fusion step of synaptic vesicle exocytosis (C2A) and
           binding to phosphatidyl-inositol-3,4,5-triphosphate
           (PIP3) in the absence of calcium ions and to
           phosphatidylinositol bisphosphate (PIP2) in their
           presence (C2B).  C2B also regulates also the recycling
           step of synaptic vesicles.  C2 domains fold into an
           8-standed beta-sandwich that can adopt 2 structural
           arrangements: Type I and Type II, distinguished by a
           circular permutation involving their N- and C-terminal
           beta strands. Many C2 domains are Ca2+-dependent
           membrane-targeting modules that bind a wide variety of
           substances including bind phospholipids, inositol
           polyphosphates, and intracellular proteins.  Most C2
           domain proteins are either signal transduction enzymes
           that contain a single C2 domain, such as protein kinase
           C, or membrane trafficking proteins which contain at
           least two C2 domains, such as synaptotagmin 1.  However,
           there are a few exceptions to this including RIM
           isoforms and some splice variants of piccolo/aczonin and
           intersectin which only have a single C2 domain.  C2
           domains with a calcium binding region have negatively
           charged residues, primarily aspartates, that serve as
           ligan