RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781163|ref|YP_003065576.1| hypothetical protein
CLIBASIA_05350 [Candidatus Liberibacter asiaticus str. psy62]
         (214 letters)



>gnl|CDD|176858 cd07816, Bet_v1-like, Ligand-binding bet_v_1 domain of major pollen
           allergen of white birch (Betula verrucosa), Bet v 1, and
           related proteins.  This family includes the ligand
           binding domain of Bet v 1 (the major pollen allergen of
           white birch, Betula verrucosa) and related proteins. In
           addition to birch Bet v 1, this family includes other
           plant intracellular pathogenesis-related class 10
           (PR-10) proteins, norcoclaurine synthases (NCSs),
           cytokinin binding proteins (CSBPs), major latex proteins
           (MLPs), and ripening-related proteins. It belongs to the
           SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
           superfamily of proteins that bind hydrophobic ligands.
           SRPBCC domains have a deep hydrophobic ligand-binding
           pocket. Members of this family binds a diverse range of
           ligands. Bet v 1 can bind brassinosteroids, cytokinins,
           flavonoids and fatty acids. Hyp-1, a PR-10 from
           Hypericum perforatum/St. John's wort, catalyzes the
           condensation of two molecules of emodin to the bioactive
           naphthodianthrone hypericin. NCSs catalyze the
           condensation of dopamine and 4-hydroxyphenylacetaldehyde
           to (S)-norcoclaurine, the first committed step in the
           biosynthesis of benzylisoquinoline alkaloids such as
           morphine. The role of MLPs is unclear; however, they are
           associated with fruit and flower development and in
           pathogen defense responses. A number of PR-10 proteins
           in this subgroup, including Bet v 1, have in vitro RNase
           activity, the biological significance of which is
           unclear. Bet v 1 family proteins have a conserved
           glycine-rich P (phosphate-binding)-loop proximal to the
           entrance of the ligand-binding pocket. However, its
           conformation differs from that of the canonical P-loop
           structure found in nucleotide-binding proteins. Several
           PR-10 members including Bet v1 are allergenic.
           Cross-reactivity of Bet v 1 with homologs from plant
           foods results in birch-fruit syndrome.
          Length = 148

 Score = 32.9 bits (76), Expect = 0.058
 Identities = 18/46 (39%), Positives = 20/46 (43%), Gaps = 7/46 (15%)

Query: 148 FTHFKEYIDEVDKILMRYG---IEGIPLTDFDHEKIKSYLTHIKIV 190
             + KE ID VD+    Y    IEG  L D      KSY   IK V
Sbjct: 61  VKYVKERIDAVDEENKTYKYTVIEGDVLKD----GYKSYKVEIKFV 102


>gnl|CDD|73095 cd04595, CBS_pair_DHH_polyA_Pol_assoc, This cd contains two tandem
           repeats of the cystathionine beta-synthase (CBS pair)
           domains associated with an upstream DHH domain which
           performs a phosphoesterase function and a downstream
           polyA polymerase domain. CBS is a small domain
           originally identified in cystathionine beta-synthase and
           subsequently found in a wide range of different
           proteins. CBS domains usually come in tandem repeats,
           which associate to form a so-called Bateman domain or a
           CBS pair which is reflected in this model. The interface
           between the two CBS domains forms a cleft that is a
           potential ligand binding site. The CBS pair coexists
           with a variety of other functional domains. It has been
           proposed that the CBS domain may play a regulatory role,
           although its exact function is unknown..
          Length = 110

 Score = 30.5 bits (69), Expect = 0.31
 Identities = 7/31 (22%), Positives = 18/31 (58%), Gaps = 2/31 (6%)

Query: 155 IDEVDKILMRYGIEGIPLTDFDHEKIKSYLT 185
           I+E  ++L+RYG   +P+   +  ++   ++
Sbjct: 13  IEEARELLLRYGHTALPV--VEGGRVVGIIS 41


>gnl|CDD|32643 COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport
           and metabolism].
          Length = 394

 Score = 30.2 bits (68), Expect = 0.44
 Identities = 24/76 (31%), Positives = 33/76 (43%), Gaps = 12/76 (15%)

Query: 31  SAEQRKLWSLLRYWSVEFWELLCRTFLWLLCLGFFTLFAY--WFFGEKFSYDVSIKIVLA 88
               R L  LLR   V     L  TFL+    G F L+ Y   F      + VS     A
Sbjct: 198 PGPLRTLLRLLRRPGV--LLGLLATFLF--MTGHFALYTYIRPFLESVAGFSVS-----A 248

Query: 89  INVLLFSFVIA-LLGN 103
           ++++L +F IA  +GN
Sbjct: 249 VSLVLLAFGIAGFIGN 264


>gnl|CDD|112133 pfam03304, Mlp, Mlp lipoprotein family.  The Mlp (for Multicopy
           Lipoprotein) family of lipoproteins is found in Borrelia
           species. This family were previously known as 2.9
           lipoprotein genes. These surface expressed genes may
           represent new candidate vaccinogens for Lyme disease.
           Members of this family generally are downstream of four
           ORFs called A,B,C and D that are involved in hemolytic
           activity.
          Length = 150

 Score = 30.2 bits (68), Expect = 0.49
 Identities = 22/77 (28%), Positives = 28/77 (36%), Gaps = 20/77 (25%)

Query: 131 EKISQKNVEKDFFNS------KFFTHFKEYID---EVDKILMRYGIEGIPLTDFDHEKIK 181
           EK   K+ E+  F         F    KE +    +  K L           + D  KIK
Sbjct: 50  EKPKSKSDEELLFEKLSDDQKTFLDWLKEALGAFGKFYKFL-----------ESDKSKIK 98

Query: 182 SYLTHIKIVRDCLKKDN 198
           S LTHIK   DC   + 
Sbjct: 99  SALTHIKGELDCCNGNP 115


>gnl|CDD|37761 KOG2550, KOG2550, KOG2550, IMP dehydrogenase/GMP reductase
           [Nucleotide transport and metabolism].
          Length = 503

 Score = 29.2 bits (65), Expect = 0.92
 Identities = 25/88 (28%), Positives = 34/88 (38%), Gaps = 4/88 (4%)

Query: 107 EMAKDIAQL--FTLIDNIENGYGQYLEKISQKNVEKDFFNSKFFTHFKEYIDEVDKILMR 164
           EMA  +A L     I +      Q       KN E  F N+         + EV +   +
Sbjct: 77  EMAIAMALLGGIGFIHHNCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEVKEAKEK 136

Query: 165 YGIEGIPLTDFDHEKIKSYLTHIKIVRD 192
           +G  GIP+T+    K  S L  I   RD
Sbjct: 137 HGFSGIPVTEDG--KRGSKLVGIITSRD 162


>gnl|CDD|36975 KOG1764, KOG1764, KOG1764, 5'-AMP-activated protein kinase, gamma
           subunit [Energy production and conversion].
          Length = 381

 Score = 28.8 bits (64), Expect = 1.2
 Identities = 21/130 (16%), Positives = 45/130 (34%), Gaps = 20/130 (15%)

Query: 80  DVSIKIVLAINVLLFSFVIALLGNPNIEMAKDIAQLFTLID--NIENGYGQYLEKISQKN 137
           D  + +  A N L+ + V A     +    +    + T+ D   +   Y +    +    
Sbjct: 82  DTKLSVKKAFNALVQNGVRAAPLWDS--KKQQFVGMLTITDFITVLLRYYKSKSSLDNIE 139

Query: 138 VEKDFFNSK----------FFTHFKEYID------EVDKILMRYGIEGIPLTDFDHEKIK 181
           V +D   SK                  I       +   +L++  I  +P+ D +  ++ 
Sbjct: 140 VLEDSQLSKRREVECLLKETLKPPFVSISPESSLLDAVLLLIKSRIHRVPVIDPETGEVL 199

Query: 182 SYLTHIKIVR 191
             LT  +I++
Sbjct: 200 YILTQRRILK 209


>gnl|CDD|37313 KOG2102, KOG2102, KOG2102, Exosomal 3'-5' exoribonuclease complex,
           subunit Rrp44/Dis3 [Translation, ribosomal structure and
           biogenesis].
          Length = 941

 Score = 28.1 bits (62), Expect = 2.0
 Identities = 11/59 (18%), Positives = 18/59 (30%), Gaps = 4/59 (6%)

Query: 143 FNSKFFTHF----KEYIDEVDKILMRYGIEGIPLTDFDHEKIKSYLTHIKIVRDCLKKD 197
             S  +THF    + Y D +    +         T  D   + S   +    +   KK 
Sbjct: 775 LASPLYTHFTSPIRRYADIIVHRQLAAAFLERSPTAPDRPNLSSLAANCNERKKAAKKA 833


>gnl|CDD|39018 KOG3814, KOG3814, KOG3814, Signaling protein van gogh/strabismus
           [Signal transduction mechanisms].
          Length = 531

 Score = 27.7 bits (61), Expect = 2.7
 Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 14/85 (16%)

Query: 27  GLFDSAEQRKLWSLLRYWSVEFWEL----LCRTFLW---LLCLGFFTLFAYW-FFGEK-- 76
           GL  S   + L  L+  W++ F+      + R F+    LL L F  +FAYW F+  +  
Sbjct: 156 GLLISMAFKLLILLIGIWAL-FFRKAMADMPRVFVVRALLLVLVFLIVFAYWLFYIVRIL 214

Query: 77  FSYDVSIKIVLAINVLLFSFVIALL 101
                + K ++       S V ALL
Sbjct: 215 DERYRNYKGIVQYAT---SLVDALL 236


>gnl|CDD|144171 pfam00478, IMPDH, IMP dehydrogenase / GMP reductase domain.  This
           family is involved in biosynthesis of guanosine
           nucleotide. Members of this family contain a TIM barrel
           structure. In the inosine monophosphate dehydrogenases 2
           CBS domains pfam00571 are inserted in the TIM barrel.
           This family is a member of the common phosphate binding
           site TIM barrel family.
          Length = 467

 Score = 27.6 bits (62), Expect = 3.0
 Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 136 KNVEKDFFNSKFFTHFKEYIDEVDKILMRYGIEGIPLTDFDHEKIKSYLTHIKIVRD 192
           K  E  F            + E  ++  RYGI G+P+T  +  K+   L  I+  RD
Sbjct: 82  KRFESGFITDPVTVSPDTTVAEALELKERYGISGVPVT--EDGKLLGGLVGIRTSRD 136


>gnl|CDD|36273 KOG1055, KOG1055, KOG1055, GABA-B ion channel receptor subunit
           GABABR1 and related subunits, G-protein coupled receptor
           superfamily [Inorganic ion transport and metabolism,
           Amino acid transport and metabolism, Signal transduction
           mechanisms].
          Length = 865

 Score = 26.9 bits (59), Expect = 4.0
 Identities = 11/28 (39%), Positives = 13/28 (46%)

Query: 45  SVEFWELLCRTFLWLLCLGFFTLFAYWF 72
           SV  +  LC    W+L LGF   F   F
Sbjct: 529 SVNAFPFLCTARTWILGLGFTLAFGAMF 556


>gnl|CDD|144229 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6.  RNA
           polymerases catalyse the DNA dependent polymerisation of
           RNA. Prokaryotes contain a single RNA polymerase
           compared to three in eukaryotes (not including
           mitochondrial. and chloroplast polymerases). This domain
           represents the hybrid binding domain and the wall
           domain. The hybrid binding domain binds the nascent RNA
           strand / template DNA strand in the Pol II transcription
           elongation complex. This domain contains the important
           structural motifs, switch 3 and the flap loop and binds
           an active site metal ion. This domain is also involved
           in binding to Rpb1 and Rpb3. Many of the bacterial
           members contain large insertions within this domain, as
           region known as dispensable region 2 (DRII).
          Length = 373

 Score = 27.1 bits (61), Expect = 4.0
 Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 3/52 (5%)

Query: 133 ISQKNVEKDFFNSKFFTHFKEYIDEVDKILMRYGIEGIPLTDFDHEKIKSYL 184
           I++ +V++  F S    H KEY  E  K  +    E         E+    L
Sbjct: 92  INKSSVDRGLFTS---IHIKEYEIEARKTKLGPIEEITRDPPNVSEEAYRKL 140


>gnl|CDD|36500 KOG1286, KOG1286, KOG1286, Amino acid transporters [Amino acid
           transport and metabolism].
          Length = 554

 Score = 26.8 bits (59), Expect = 4.8
 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 3/47 (6%)

Query: 59  LLCLGFFTLFAYWFFGEKFSYDVSIKIVLAINVLLFSFVIALLGNPN 105
           +L +  F + AY     +FS     KI+ A+  ++ + VI   G P 
Sbjct: 166 ILIINLFGVLAY--GEVEFSL-AFNKILTAVGFIILAIVIIAGGGPA 209


>gnl|CDD|38951 KOG3747, KOG3747, KOG3747, Concentrative Na+-nucleoside
           cotransporter CNT1/CNT2 [Nucleotide transport and
           metabolism, Inorganic ion transport and metabolism].
          Length = 602

 Score = 26.8 bits (59), Expect = 5.0
 Identities = 18/81 (22%), Positives = 26/81 (32%), Gaps = 24/81 (29%)

Query: 43  YWSVEFWELLCRTFLWLLCLGFFTLFAYWFF----------------GEKFSYDVSIK-- 84
            W +    L  +  L LL L        W F                G  F +  +I   
Sbjct: 203 NWRIVTSGLGLQFLLGLLVLR--WPTGRWIFQWLGEQVQIFLEYAQAGASFVFGDNICDL 260

Query: 85  IVLAINVL----LFSFVIALL 101
            V A  +L     FS V+++L
Sbjct: 261 AVFAFAILPIIIFFSAVVSIL 281


>gnl|CDD|153334 cd07650, F-BAR_Syp1p_like, The F-BAR (FES-CIP4 Homology and
           Bin/Amphiphysin/Rvs) domain of yeast Syp1 protein.
           F-BAR domains are dimerization modules that bind and
           bend membranes and are found in proteins involved in
           membrane dynamics and actin reorganization. Syp1p is
           associated with septins, a family of GTP-binding
           proteins that serve as elements of septin filaments,
           which are required for cell morphogenesis and division.
           Syp1p regulates cell-cycle dependent septin cytoskeletal
           dynamics in yeast. It contains an N-terminal F-BAR
           domain and a C-terminal domain of unknown function named
           SAFF which is also present in FCH domain Only (FCHO)
           proteins and endophilin interacting protein 1. F-BAR
           domains form banana-shaped dimers with a
           positively-charged concave surface that binds to
           negatively-charged lipid membranes. They can induce
           membrane deformation in the form of long tubules.
          Length = 228

 Score = 26.5 bits (59), Expect = 5.2
 Identities = 7/32 (21%), Positives = 15/32 (46%)

Query: 110 KDIAQLFTLIDNIENGYGQYLEKISQKNVEKD 141
            ++A        +E  Y Q L K++++N   +
Sbjct: 22  TELADWLQERRRLERQYVQGLRKLARRNEPLN 53


>gnl|CDD|33694 COG3907, COG3907, PAP2 (acid phosphatase) superfamily protein
           [General function prediction only].
          Length = 249

 Score = 26.1 bits (57), Expect = 6.6
 Identities = 9/16 (56%), Positives = 10/16 (62%)

Query: 55  TFLWLLCLGFFTLFAY 70
           T  WL+ LGFF LF  
Sbjct: 224 TICWLVALGFFYLFFV 239


>gnl|CDD|73050 cd03291, ABCC_CFTR1, The CFTR subfamily domain 1.  The cystic
           fibrosis transmembrane regulator (CFTR), the product of
           the gene mutated in patients with cystic fibrosis, has
           adapted the ABC transporter structural motif to form a
           tightly regulated anion channel at the apical surface of
           many epithelia.  Use of the term assembly of a
           functional ion channel implies the coming together of
           subunits, or at least smaller not-yet functional
           components of the active whole.  In fact, on the basis
           of current knowledge only the CFTR polypeptide itself is
           required to form an ATP- and protein kinase A-dependent
           low-conductance chloride channel of the type present in
           the apical membrane of many epithelial cells.  CFTR
           displays the typical organization (IM-ABC)2 and carries
           a characteristic hydrophilic R-domain that separates
           IM1-ABC1 from IM2-ABC2..
          Length = 282

 Score = 26.1 bits (57), Expect = 6.9
 Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 3/41 (7%)

Query: 123 ENGYGQYLEKISQKNVEKDFFN---SKFFTHFKEYIDEVDK 160
           + G+G+ LEK  Q+N ++   +   + FF++       V K
Sbjct: 14  DEGFGELLEKAKQENNDRKHSSDDNNLFFSNLCLVGAPVLK 54


>gnl|CDD|110588 pfam01594, UPF0118, Domain of unknown function DUF20.  This
           transmembrane region is found in putative permeases and
           predicted transmembrane proteins it has no known
           function. It is not clear what source suggested that
           these proteins may be permeases and this information
           should be treated with caution.
          Length = 327

 Score = 26.0 bits (58), Expect = 7.5
 Identities = 11/83 (13%), Positives = 27/83 (32%), Gaps = 8/83 (9%)

Query: 56  FLWLLCLGFFTLFAY-----WFFGEKFSYDVSIKIVLAINVLLFSFVIALLGNPNIEMAK 110
            L  L +     +       +         ++I +VL + ++    +  LL    I    
Sbjct: 21  LLVPLLIALVLAYLLNPVVRFLKRRGIPRSLAILLVLLLFLVALVLLGLLLIPLLIIQ-- 78

Query: 111 DIAQLFTLIDNIENGYGQYLEKI 133
            + QL   +    +    +L ++
Sbjct: 79  -LTQLIKSLPQYIDSLLNWLNEL 100


>gnl|CDD|176956 CHL00013, rpoA, RNA polymerase alpha subunit.
          Length = 327

 Score = 26.1 bits (58), Expect = 7.8
 Identities = 20/71 (28%), Positives = 28/71 (39%), Gaps = 13/71 (18%)

Query: 141 DFFNSKFFTHFKE---YIDEVDKILMRYGIEGIPLTDFDHEKIKSYLTHIKI------VR 191
           D F    F H +E    ++  +  +         LTD    K +  L  I I      VR
Sbjct: 216 DLFIP--FLHAEEENLKLENNENRVTLLFTFHDRLTDLKKNKKEIALKQIFIEQLELSVR 273

Query: 192 --DCLKKDNIH 200
             +CLK+ NIH
Sbjct: 274 AYNCLKRANIH 284


>gnl|CDD|146277 pfam03552, Cellulose_synt, Cellulose synthase.  Cellulose, an
           aggregate of unbranched polymers of beta-1,4-linked
           glucose residues, is the major component of wood and
           thus paper, and is synthesized by plants, most algae,
           some bacteria and fungi, and even some animals. The
           genes that synthesize cellulose in higher plants differ
           greatly from the well-characterized genes found in
           Acetobacter and Agrobacterium sp. More correctly
           designated as 'cellulose synthase catalytic subunits',
           plant cellulose synthase (CesA) proteins are integral
           membrane proteins, approximately 1,000 amino acids in
           length. There are a number of highly conserved residues,
           including several motifs shown to be necessary for
           processive glycosyltransferase activity.
          Length = 716

 Score = 25.9 bits (57), Expect = 8.1
 Identities = 27/101 (26%), Positives = 40/101 (39%), Gaps = 18/101 (17%)

Query: 113 AQLFTLIDNIENGYGQYLEKISQKNVEKDFFNSKFFTHFKEYIDEVDKILMRYGIEGIPL 172
           A +F L D  E    +    +SQ ++EK F  S  F         +   LM  G  G+P 
Sbjct: 334 APIFNLEDIDEGDEDEKSSLMSQLSLEKRFGQSPVF---------IASTLMEEG--GVPR 382

Query: 173 TDFDHEKIKSYLTHIKIVRDCLKKDNIHYAKELRNDWI-GS 212
           +      +K  +  I     C  +D   + KE+   WI GS
Sbjct: 383 SPLPATLVKEAIHVIS----CGYEDKTEWGKEI--GWIYGS 417


>gnl|CDD|31481 COG1290, QcrB, Cytochrome b subunit of the bc complex [Energy
           production and conversion].
          Length = 381

 Score = 26.0 bits (57), Expect = 8.6
 Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 5/69 (7%)

Query: 38  WSLLRYWSVEFWELLCRTFLWLLCLGFFTLFAYWFFGEKFSYDVSIKIVLAINVLLFSFV 97
           W  + YW       L     ++      T    W FG     D ++    A++VLL   +
Sbjct: 145 WDQMSYWGATVITNLFSAIPFI-----GTWLVQWLFGGFSVSDPTLNRFFALHVLLLPAI 199

Query: 98  IALLGNPNI 106
           I  L   ++
Sbjct: 200 ILALVGLHL 208


>gnl|CDD|48065 cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like :
           N-terminal DNA binding fragment found in eukaryotic DNA
           topoisomerase (topo) IB proteins similar to the
           monomeric yeast and human topo I.  Topo I enzymes are
           divided into:  topo type IA (bacterial) and type IB
           (eukaryotic). Topo I relaxes superhelical tension in
           duplex DNA by creating a single-strand nick, the broken
           strand can then rotate around the unbroken strand to
           remove DNA supercoils and, the nick is religated,
           liberating topo I. These enzymes regulate the
           topological changes that accompany DNA replication,
           transcription and other nuclear processes.  Human topo I
           is the target of a diverse set of anticancer drugs
           including camptothecins (CPTs). CPTs bind to the topo
           I-DNA complex and inhibit religation of the
           single-strand nick, resulting in the accumulation of
           topo I-DNA adducts.  This family may represent more than
           one structural domain..
          Length = 215

 Score = 25.6 bits (56), Expect = 9.2
 Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 3/39 (7%)

Query: 126 YGQYLEKISQKNVEKDFFNSKFFTHFKEYIDEVDKILMR 164
           Y + LE        K+ F   FF  FK+ + + +K++++
Sbjct: 45  YAKMLE---HDYATKEIFQKNFFKDFKKVMTKEEKVIIK 80


  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
   0.327    0.143    0.450 

Gapped
Lambda     K      H
   0.267   0.0711    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,847,001
Number of extensions: 159493
Number of successful extensions: 850
Number of sequences better than 10.0: 1
Number of HSP's gapped: 847
Number of HSP's successfully gapped: 93
Length of query: 214
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 124
Effective length of database: 4,318,927
Effective search space: 535546948
Effective search space used: 535546948
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (25.0 bits)