RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780798|ref|YP_003065211.1| possible lolA type protein
[Candidatus Liberibacter asiaticus str. psy62]
         (204 letters)



>gnl|CDD|32662 COG2834, LolA, Outer membrane lipoprotein-sorting protein [Cell
           envelope biogenesis, outer membrane].
          Length = 211

 Score = 73.1 bits (179), Expect = 5e-14
 Identities = 33/202 (16%), Positives = 78/202 (38%), Gaps = 11/202 (5%)

Query: 9   VIGVVILFFYSAIFPFNAAYPITKDQSVKKAIEHFLSIQTMQGTFLQ----EDAGYVMKG 64
           ++ ++ L    A+     +      ++  +  E    +++   +F Q           +G
Sbjct: 2   MLMMMKLLLALALLLLFLSACAQAGEAASQLKERLAKVKSYSASFTQTVESGSGKQTQEG 61

Query: 65  EFFMARPSKFYFKYSSPSSVSLISDGSNIAVYNAKLD----TWSVYPLRYMAFSVIFSNN 120
           + ++ RP+ F ++Y SP    ++SDG  + +Y+  L+    TW           ++ SN 
Sbjct: 62  KLWIKRPNLFRWEYESPDEQVIVSDGKTVWIYDPDLEQVTKTWLSEATGNTPLMLLLSNI 121

Query: 121 QHVIQESIQRVESNNSFITIFF---KDDFMGNMISVTFDRLSYRLLNWKIMDSSRRYSII 177
           + ++ E    +   +    +     K +   +   +  D+     L +++ D+  +   I
Sbjct: 122 KDLLNEYNVSLLGTSDVAYVLELTPKANLGNSKQRIIVDKEDGTPLRFELTDADGQTVTI 181

Query: 178 KILKYKENTVLDPKVFEIPYDK 199
                K N  LD  +F+    K
Sbjct: 182 TFSNVKNNPGLDDSLFKFTPPK 203


>gnl|CDD|146274 pfam03548, LolA, Outer membrane lipoprotein carrier protein LolA. 
          Length = 164

 Score = 62.0 bits (151), Expect = 1e-10
 Identities = 32/164 (19%), Positives = 63/164 (38%), Gaps = 13/164 (7%)

Query: 45  SIQTMQGTFLQED------AGYVMKGEFFMARPSKFYFKYSSPSSVSLISDGSNIAVYNA 98
            ++T    F+Q              G F++ RP  F ++Y +P    ++SDG  + +Y+ 
Sbjct: 2   KVKTFSADFVQTVTSGEGKVIQEGSGTFYIKRPGLFRWEYDAPDEQLIVSDGKTVWIYDP 61

Query: 99  KLDTWSVYPLRYMAFSVIFSN---NQHVIQESIQRVESNNSFITIFFKD---DFMGNMIS 152
            L+  ++Y L+    +  F     ++  +       E      T   K    D   + I 
Sbjct: 62  DLEQVTIYWLKQALSNTPFVLLLRDKIKLDGQYNVTEEEGDLDTFTLKPKAKDVGLSQIR 121

Query: 153 VTFDRLSYRLLNWKIMDSSRRYSIIKILKYKENTVLDPKVFEIP 196
           + FD+    L  + ++D   + + I     K N  L   +F+  
Sbjct: 122 IGFDKKGV-LRQFTVVDQDGQRTTITFSNVKTNPTLADDLFKFT 164


>gnl|CDD|36624 KOG1410, KOG1410, KOG1410, Nuclear transport receptor RanBP16
           (importin beta superfamily) [Nuclear structure,
           Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 1082

 Score = 28.0 bits (62), Expect = 1.9
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 7/61 (11%)

Query: 65  EFFMARPSKFYFKYSSPSSVSLISDGSN-IAVYNAKLDTW------SVYPLRYMAFSVIF 117
           E    R  +  F  SSP+ + L  + S  +++Y  ++          +Y  +Y   SV F
Sbjct: 770 ELVQNRSQRLKFDVSSPNGILLFRETSKMVSIYGNRILQLPEVSKDQIYAEKYKGISVCF 829

Query: 118 S 118
           S
Sbjct: 830 S 830


>gnl|CDD|39437 KOG4236, KOG4236, KOG4236, Serine/threonine protein kinase PKC
           mu/PKD and related proteins [Signal transduction
           mechanisms].
          Length = 888

 Score = 27.7 bits (61), Expect = 2.4
 Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 1/38 (2%)

Query: 96  YNAKLDTWSVYPLRYMAFSVIFS-NNQHVIQESIQRVE 132
           YN  LD WSV  + Y++ S  F  N    I + IQ   
Sbjct: 743 YNRSLDMWSVGVIIYVSLSGTFPFNEDEDINDQIQNAA 780


>gnl|CDD|29791 cd02892, SQCY_1, Squalene cyclase (SQCY) domain subgroup 1; found
           in class II terpene cyclases that have an alpha 6 -
           alpha 6 barrel fold. Squalene cyclase (SQCY)  and
           2,3-oxidosqualene cyclase (OSQCY) are integral membrane
           proteins that catalyze a cationic cyclization cascade
           converting linear triterpenes to fused ring compounds.
           This group contains bacterial SQCY which catalyzes the
           convertion of squalene to hopene or diplopterol and
           eukaryotic OSQCY which transforms the 2,3-epoxide of
           squalene to compounds such as, lanosterol in mammals and
           fungi or, cycloartenol in plants. Deletion of a single
           glycine residue of Alicyclobacillus acidocaldarius SQCY
           alters its substrate specificity into that of eukaryotic
           OSQCY. Both enzymes have a second minor domain, which
           forms an alpha-alpha barrel that is inserted into the
           major domain..
          Length = 634

 Score = 27.5 bits (61), Expect = 2.7
 Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 8/46 (17%)

Query: 35  SVKKAIEHFLSIQTMQGTFLQEDAGYVMKGEFFMARPSKFYFKYSS 80
           +V++ I++ L+ Q   G + QE+    + G  F      FY +Y +
Sbjct: 584 AVERGIKYLLNTQLPDGDWPQEE----ITGVGFP----NFYIRYHN 621


>gnl|CDD|73334 cd02889, SQCY, Squalene cyclase (SQCY) domain; found in class II
           terpene cyclases that have an alpha 6 - alpha 6 barrel
           fold. Squalene cyclase (SQCY) and 2,3-oxidosqualene
           cyclase (OSQCY) are integral membrane proteins that
           catalyze a cationic cyclization cascade converting
           linear triterpenes to fused ring compounds. Bacterial
           SQCY catalyzes the convertion of squalene to hopene or
           diplopterol. Eukaryotic OSQCY transforms the 2,3-epoxide
           of squalene to compounds such as, lanosterol (a
           metabolic precursor of cholesterol and steroid hormones)
           in mammals and fungi or, cycloartenol in plants.
           Deletion of a single glycine residue of Alicyclobacillus
           acidocaldarius SQCY alters its substrate specificity
           into that of eukaryotic OSQCY. Both enzymes have a
           second minor domain, which forms an alpha-alpha barrel
           that is inserted into the major domain. This group also
           contains SQCY-like archael sequences and some bacterial
           SQCY's which lack this minor domain..
          Length = 348

 Score = 27.1 bits (60), Expect = 3.6
 Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 8/48 (16%)

Query: 33  DQSVKKAIEHFLSIQTMQGTFLQEDAGYVMKGEFFMARPSKFYFKYSS 80
            ++VK+ +++ L+ Q   G + QE+    + G FF      FY +Y +
Sbjct: 296 SEAVKRGVKYLLNTQQEDGDWPQEE----ITGVFFKN----FYIRYHN 335


>gnl|CDD|173854 cd08489, PBP2_NikA, The substrate-binding component of an ABC-type
           nickel import system contains the type 2 periplasmic
           binding fold.  This family represents the periplasmic
           substrate-binding domain of nickel transport system,
           which functions in the import of nickel and in the
           control of chemotactic response away from nickel. The
           ATP-binding cassette (ABC) type nickel transport system
           is comprised of five subunits NikABCDE: the two
           pore-forming integral inner membrane proteins NikB and
           NikC; the two inner membrane-associated proteins with
           ATPase activity NikD and NikE; and the periplasmic
           nickel binding NikA, the initial nickel receptor. The
           oligopeptide-binding protein OppA and the
           dipeptide-binding protein DppA show significant sequence
           similarity to NikA. The DppA binds dipeptides and some
           tripeptides and is involved in chemotaxis toward
           dipeptides, whereas the OppA binds peptides of a wide
           range of lengths (2-35 amino acid residues) and plays a
           role in recycling of cell wall peptides, which precludes
           any involvement in chemotaxis. Most of other periplasmic
           binding proteins are comprised of only two globular
           subdomains corresponding to domains I and III of the
           dipeptide/oligopeptide binding proteins. The structural
           topology of these domains is most similar to that of the
           type 2 periplasmic binding proteins (PBP2), which are
           responsible for the uptake of a variety of substrates
           such as phosphate, sulfate, polysaccharides,
           lysine/arginine/ornithine, and histidine.  The PBP2 bind
           their ligand in the cleft between these domains in a
           manner resembling a Venus flytrap. After binding their
           specific ligand with high affinity, they can interact
           with a cognate membrane transport complex comprised of
           two integral membrane domains and two cytoplasmically
           located ATPase domains. This interaction triggers the
           ligand translocation across the cytoplasmic membrane
           energized by ATP hydrolysis.  Besides transport
           proteins, the PBP2 superfamily includes the
           ligand-binding domains from ionotropic glutamate
           receptors, LysR-type transcriptional regulators, and
           unorthodox sensor proteins involved in signal
           transduction.
          Length = 488

 Score = 26.8 bits (60), Expect = 3.9
 Identities = 6/19 (31%), Positives = 9/19 (47%)

Query: 24  FNAAYPITKDQSVKKAIEH 42
            N A     D  V++AI +
Sbjct: 247 LNTASEPLSDLKVREAINY 265


>gnl|CDD|144657 pfam01144, CoA_trans, Coenzyme A transferase. 
          Length = 217

 Score = 26.9 bits (60), Expect = 4.1
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 4/53 (7%)

Query: 145 DFMGNMISVTFDRLSYRLLNWKIMDSSRRYSIIKILKYKENTVLDPKVFEIPY 197
           D  GN   + F R +    N   + ++ + +I+++ +  E   L P    IP 
Sbjct: 160 DGEGN---LVF-RTTAGNFNGPAVAAAAKVTILEVEEIVEVGELLPLTVHIPG 208


>gnl|CDD|111555 pfam02669, KdpC, K+-transporting ATPase, c chain.  This family
           consists of K+-transporting ATPase, c chain, KdpC. KdpC
           forms strong interactions with the KdpA subunit, serving
           to assemble and stabilize the Kdp complex. It has been
           suggested that KdpC could be one of the connecting links
           between the energy providing subunit KdpB and the
           K+-transporting subunit KdpA. The K+ transport system
           actively transports K+ ions via ATP hydrolysis.
          Length = 188

 Score = 26.8 bits (59), Expect = 4.7
 Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 4/36 (11%)

Query: 66  FFMARPSKFYFKYSSPSSVSLISDGSNIAVYNAKLD 101
           +F +RPS   +           S GSN+A  N  L 
Sbjct: 64  YFHSRPSAINYSEYPTG----ASGGSNLAPSNPDLL 95


>gnl|CDD|147605 pfam05510, Sarcoglycan_2, Sarcoglycan alpha/epsilon.  Sarcoglycans
           are a subcomplex of transmembrane proteins which are
           part of the dystrophin-glycoprotein complex. They are
           expressed in the skeletal, cardiac and smooth muscle.
           Although numerous studies have been conducted on the
           sarcoglycan subcomplex in skeletal and cardiac muscle,
           the manner of the distribution and localisation of these
           proteins along the nonjunctional sarcolemma is not
           clear. This family contains alpha and epsilon members.
          Length = 398

 Score = 26.3 bits (58), Expect = 6.7
 Identities = 15/63 (23%), Positives = 22/63 (34%), Gaps = 10/63 (15%)

Query: 51  GTFLQEDAGYVMKGEFFMARPSKFYFKYSSPSSVSLISDGSNIAVYNAKLDTWSVYP--L 108
            T   +       G  F+      +F  S PS+V +         Y A L+ +   P  L
Sbjct: 19  STKSFKATVTATVGVLFVHTLEPAHFWVSFPSTVQV--------TYRATLNGYPDLPNWL 70

Query: 109 RYM 111
           RY 
Sbjct: 71  RYE 73


>gnl|CDD|173657 cd05113, PTKc_Btk_Bmx, Catalytic domain of the Protein Tyrosine
           Kinases, Bruton's tyrosine kinase and Bone marrow kinase
           on the X chromosome.  Protein Tyrosine Kinase (PTK)
           family; Bruton's tyrosine kinase (Btk) and Bone marrow
           kinase on the X chromosome (Bmx); 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. Btk and
           Bmx (also named Etk) are members of the Tec subfamily of
           proteins, which are cytoplasmic (or nonreceptor) tyr
           kinases with similarity to Src kinases in that they
           contain Src homology protein interaction domains (SH3,
           SH2) N-terminal to the catalytic tyr kinase domain.
           Unlike Src kinases, most Tec subfamily members (except
           Rlk) also contain an N-terminal pleckstrin homology (PH)
           domain, which binds the products of PI3K and allows
           membrane recruitment and activation. In addition, Btk
           contains the Tec homology (TH) domain with proline-rich
           and zinc-binding regions. Tec kinases are expressed
           mainly by haematopoietic cells. Btk is expressed in
           B-cells, and a variety of myeloid cells including mast
           cells, platelets, neutrophils, and dendrictic cells. It
           interacts with a variety of partners, from cytosolic
           proteins to nuclear transcription factors, suggesting a
           diversity of functions. Stimulation of a diverse array
           of cell surface receptors, including antigen engagement
           of the B-cell receptor (BCR), leads to PH-mediated
           membrane translocation of Btk and subsequent
           phosphorylation by Src kinase and activation. Btk plays
           an important role in the life cycle of B-cells including
           their development, differentiation, proliferation,
           survival, and apoptosis. Mutations in Btk cause the
           primary immunodeficiency disease, X-linked
           agammaglobulinaemia (XLA) in humans. Bmx is primarily
           expressed in bone marrow and the arterial endothelium,
           and plays an important role in ischemia-induced
           angiogenesis. It facilitates arterial growth, capillary
           formation, vessel maturation, and bone marrow-derived
           endothelial progenitor cell mobilization.
          Length = 256

 Score = 26.0 bits (57), Expect = 7.4
 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 5/83 (6%)

Query: 50  QGTFLQEDAG---YVMKGEFFMARPSKFYFKYSSPSSVSLISDGSNIAVYNAKLDTWSVY 106
           QG     D G   YV+  E+  +  SKF  ++S P  +      S   V+   +  W VY
Sbjct: 136 QGCVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLLYSKFSSKSDVWAFGVLMWEVY 195

Query: 107 PLRYMAFSVIFSNNQHVIQESIQ 129
            L  M +     NN   +++  Q
Sbjct: 196 SLGKMPYERF--NNSETVEKVSQ 216


>gnl|CDD|33688 COG3900, COG3900, Predicted periplasmic protein [Function unknown].
          Length = 262

 Score = 26.1 bits (57), Expect = 7.5
 Identities = 8/53 (15%), Positives = 16/53 (30%), Gaps = 1/53 (1%)

Query: 56  EDAGYVMKGEFFMARPSKFYFKYSSPSSVSLIS-DGSNIAVYNAKLDTWSVYP 107
           +   Y   G   ++RP K           +    DG    +    L+ ++   
Sbjct: 70  QKLQYSASGTLTVSRPDKLRSTRVGGFRDTEFYFDGKTFTLLGKNLNFYAQIE 122


  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
   0.325    0.138    0.401 

Gapped
Lambda     K      H
   0.267   0.0635    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,476,594
Number of extensions: 125366
Number of successful extensions: 417
Number of sequences better than 10.0: 1
Number of HSP's gapped: 414
Number of HSP's successfully gapped: 25
Length of query: 204
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 115
Effective length of database: 4,340,536
Effective search space: 499161640
Effective search space used: 499161640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.2 bits)