RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780801|ref|YP_003065214.1| hypothetical protein
CLIBASIA_03460 [Candidatus Liberibacter asiaticus str. psy62]
         (222 letters)



>gnl|CDD|129155 TIGR00044, TIGR00044, pyridoxal phosphate enzyme, YggS family.
           Members of this protein family include YggS from
           Escherichia coli and YBL036C, an uncharacterized
           pyridoxal protein of Saccharomyces cerevisiae.
          Length = 229

 Score =  134 bits (339), Expect = 1e-32
 Identities = 78/223 (34%), Positives = 109/223 (48%), Gaps = 10/223 (4%)

Query: 6   KLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKW 65
            L+  K KIE +     R    V L+AVSK   +  I++A   GQ  F EN +QE  +K 
Sbjct: 7   YLEDIKTKIEAANTHVNRNPSKVKLLAVSKTKPASAIQIAYDAGQRAFGENYVQELVEKI 66

Query: 66  IPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQ 125
             L     ++  FIG LQSNK   +V  FD + T+   K A  L+ +  K    L V +Q
Sbjct: 67  KLLEDLGKLEWHFIGPLQSNKDRLVVENFDWVHTIDSLKIAKKLNEQREKLQPPLNVLLQ 126

Query: 126 VNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPH----------FY 175
           +N   E  KSGI P +  +  I   +   L + GLM I     + +            F+
Sbjct: 127 INISDEESKSGIQPEELLELAIQIEELKHLKLRGLMTIGAPTDSHEDQEENFRFMKLLFW 186

Query: 176 LLSEIARECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGER 218
            + + +    +  LSMGM+ DFE AIA+GAT VRIG+ IFG R
Sbjct: 187 QIKQDSPFGTIDTLSMGMSDDFEEAIAAGATMVRIGTAIFGAR 229


>gnl|CDD|178827 PRK00053, alr, alanine racemase; Reviewed.
          Length = 363

 Score = 35.9 bits (84), Expect = 0.008
 Identities = 12/59 (20%), Positives = 30/59 (50%), Gaps = 5/59 (8%)

Query: 106 ASLLSLEMIKQSRF---LPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLM 161
            SL  LE ++++     L V+++++TG  + + G+ P + +  +        + +EG+ 
Sbjct: 103 HSLEQLEALEKAELGKPLKVHLKIDTG--MHRLGVRPEEAEAALERLLACPNVRLEGIF 159


>gnl|CDD|129583 TIGR00492, alr, alanine racemase.  This enzyme interconverts
           L-alanine and D-alanine. Its primary function is to
           generate D-alanine for cell wall formation. With
           D-alanine-D-alanine ligase, it makes up the D-alanine
           branch of the peptidoglycan biosynthetic route. It is a
           monomer with one pyridoxal phosphate per subunit. In E.
           coli, the ortholog is duplicated so that a second
           isozyme, DadX, is present. DadX, a paralog of the
           biosynthetic Alr, is induced by D- or L-alanine and is
           involved in catabolism.
          Length = 367

 Score = 31.2 bits (71), Expect = 0.19
 Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 89  EIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVIL 148
           +I++ +D+  TV   +    L   ++K+ + L V+++++TG  + + G+ P++   FV  
Sbjct: 89  KILAAWDLTTTVHSVEQLQALEEALLKEPKRLKVHLKIDTG--MNRLGVKPDEAALFVQK 146

Query: 149 CRQKYQ-LNVEGLM 161
            RQ  + L +EG+ 
Sbjct: 147 LRQLKKFLELEGIF 160


>gnl|CDD|181127 PRK07807, PRK07807, inosine 5-monophosphate dehydrogenase;
           Validated.
          Length = 479

 Score = 30.6 bits (70), Expect = 0.29
 Identities = 11/18 (61%), Positives = 15/18 (83%)

Query: 195 RDFELAIASGATSVRIGS 212
           RD  LA+A+GA++V IGS
Sbjct: 343 RDVALALAAGASNVMIGS 360


>gnl|CDD|184518 PRK14119, gpmA, phosphoglyceromutase; Provisional.
          Length = 228

 Score = 30.2 bits (68), Expect = 0.39
 Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%)

Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQS-NK 86
          L E+K++WIP+ K W +  R  G LQ  NK
Sbjct: 69 LTESKQQWIPVYKSWRLNERHYGGLQGLNK 98


>gnl|CDD|152009 pfam11573, Med23, Mediator complex subunit 23.  Med23 is one of the
           subunits of the Tail portion of the Mediator complex
           that regulates RNA polymerase II activity. Med23 is
           required for heat-shock-specific gene expression, and
           has been shown to mediate transcriptional activation of
           E1A in mice.
          Length = 1341

 Score = 29.8 bits (67), Expect = 0.52
 Identities = 28/145 (19%), Positives = 60/145 (41%), Gaps = 17/145 (11%)

Query: 1   MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQE 60
           M    K  + ++ ++    +A++ +    +  + + V  K I   + C + + +E    E
Sbjct: 57  MEQEEKESLVRELLKMVHHVAEKNRYERVVDVLLRYVHQKIIPATMLCEEGLISEKLFYE 116

Query: 61  AKKKWIPLRKEWDVQLRFIGSLQSNKVSEIV-----SLFDVIETVSREKTASLLSLEMI- 114
             + WI   +++ +  + IG +    V EI+            +VS E    LL++E + 
Sbjct: 117 CSRFWI---EKFKLIRKVIGGVDYKGVREIMKYILEKALRFPYSVSPEIVPQLLAVEEVI 173

Query: 115 -----KQSRFLPVYIQVNTGYEIQK 134
                + +  LP Y  +N   EI +
Sbjct: 174 LHIFDRNANLLPAYFTLN---EIMR 195


>gnl|CDD|130370 TIGR01303, IMP_DH_rel_1, IMP dehydrogenase family protein.  This
           model represents a family of proteins, often annotated
           as a putative IMP dehydrogenase, related to IMP
           dehydrogenase and GMP reductase and restricted to the
           high GC Gram-positive bacteria. All species in which a
           member is found so far (Corynebacterium glutamicum,
           Mycobacterium tuberculosis, Streptomyces coelicolor,
           etc.) also have IMP dehydrogenase as described by
           TIGRFAMs entry TIGR01302.
          Length = 475

 Score = 29.9 bits (67), Expect = 0.52
 Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 13/72 (18%)

Query: 159 GLMCIPPAM-GNPKPHFYLLSEIARECKLTKLSMGM--------TRDFELAIASGATSVR 209
           G MC    M G  +P F  + E A E +  KL   +         RD  LA+A+GA++V 
Sbjct: 298 GAMCTTRMMTGVGRPQFSAVLECAAEAR--KLGGHVWADGGVRHPRDVALALAAGASNVM 355

Query: 210 IGSGIFG--ERP 219
           +GS   G  E P
Sbjct: 356 VGSWFAGTYESP 367


>gnl|CDD|184519 PRK14120, gpmA, phosphoglyceromutase; Provisional.
          Length = 249

 Score = 30.0 bits (68), Expect = 0.56
 Identities = 11/26 (42%), Positives = 16/26 (61%)

Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83
          L  A + WIP+R+ W +  R  G+LQ
Sbjct: 72 LDAADRLWIPVRRSWRLNERHYGALQ 97


>gnl|CDD|130325 TIGR01258, pgm_1, phosphoglycerate mutase, BPG-dependent, family
          1.  Most members of this family are phosphoglycerate
          mutase (EC 5.4.2.1). This enzyme interconverts
          2-phosphoglycerate and 3-phosphoglycerate. The enzyme
          is transiently phosphorylated on an active site
          histidine by 2,3-diphosphoglyerate, which is both
          substrate and product. Some members of this family have
          are phosphoglycerate mutase as a minor activity and act
          primarily as a bisphoglycerate mutase, interconverting
          2,3-diphosphoglycerate and 1,3-diphosphoglycerate (EC
          5.4.2.4). This model is designated as a subfamily for
          this reason. The second and third paralogs in S.
          cerevisiae are somewhat divergent and apparently
          inactive (see PUBMED:9544241) but are also part of this
          subfamily phylogenetically.
          Length = 245

 Score = 29.7 bits (67), Expect = 0.64
 Identities = 11/26 (42%), Positives = 16/26 (61%)

Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83
          L E  + WIP++K W +  R  G+LQ
Sbjct: 68 LDELDQLWIPVKKSWRLNERHYGALQ 93


>gnl|CDD|180614 PRK06546, PRK06546, pyruvate dehydrogenase; Provisional.
          Length = 578

 Score = 28.0 bits (63), Expect = 2.1
 Identities = 12/19 (63%), Positives = 13/19 (68%)

Query: 199 LAIASGATSVRIGSGIFGE 217
           LAIAS   S +IGSG F E
Sbjct: 96  LAIASHIPSAQIGSGFFQE 114


>gnl|CDD|185556 PTZ00326, PTZ00326, phenylalanyl-tRNA synthetase alpha chain;
           Provisional.
          Length = 494

 Score = 28.0 bits (63), Expect = 2.2
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 62  KKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLP 121
           KKKWI L K  D ++     L  + V  +  L  ++   S+ +      L+ +K+ +   
Sbjct: 112 KKKWIKLNKG-DKKVFLSRKLVDSVVDTVRLLLKIVAKGSQAEKIDSKELKELKKRKL-- 168

Query: 122 VYIQVNTGYEIQK 134
             ++    + + K
Sbjct: 169 ATLEKIKYFVVTK 181


>gnl|CDD|172606 PRK14116, gpmA, phosphoglyceromutase; Provisional.
          Length = 228

 Score = 28.0 bits (62), Expect = 2.2
 Identities = 11/26 (42%), Positives = 16/26 (61%)

Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83
          L+E+ + WIP  K W +  R  G+LQ
Sbjct: 69 LEESDQLWIPETKTWRLNERHYGALQ 94


>gnl|CDD|148843 pfam07467, BLIP, Beta-lactamase inhibitor (BLIP).  The structure of
           BLIP reveals two structural domains, which form a polar,
           concave surface that docks onto a predominantly polar,
           convex protrusion on beta-lactamase. The ability of BLIP
           to adapt to a variety of class A beta-lactamases is
           thought to be due to flexibility between these two
           domains.
          Length = 183

 Score = 27.6 bits (61), Expect = 2.5
 Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 1/34 (2%)

Query: 185 KLTKLSMGMTRDFELAIASGATSVRIGSGIFGER 218
           K T++  GMTR     IA    +   G G FG+ 
Sbjct: 35  KYTQIQFGMTRQQVWDIAGAEQNCETG-GSFGDS 67


>gnl|CDD|172608 PRK14118, gpmA, phosphoglyceromutase; Provisional.
          Length = 227

 Score = 27.6 bits (61), Expect = 2.6
 Identities = 11/26 (42%), Positives = 16/26 (61%)

Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83
          L+E+ + WIP  K W +  R  G+LQ
Sbjct: 68 LEESNQLWIPQVKNWRLNERHYGALQ 93


>gnl|CDD|178757 PLN03218, PLN03218, maturation of RBCL 1; Provisional.
          Length = 1060

 Score = 27.2 bits (60), Expect = 3.5
 Identities = 46/200 (23%), Positives = 73/200 (36%), Gaps = 42/200 (21%)

Query: 31  VAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPL--------------RKEWDVQL 76
           V   ++  S  + VA   G +  A   LQ+A+K+ I L               K W   L
Sbjct: 645 VKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKAL 704

Query: 77  RFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSG 136
                ++S K+   VS  + + T   E      +LE++                E+++ G
Sbjct: 705 ELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLS---------------EMKRLG 749

Query: 137 IMPNQTKDFVIL--CRQKYQLNVEGLMCIPPAMGNP-KPHFYLLSEIARECKLTKLSMGM 193
           + PN     ++L    +K   +V GL  +  A  +  KP+  +   I   C         
Sbjct: 750 LCPNTITYSILLVASERKDDADV-GLDLLSQAKEDGIKPNLVMCRCITGLCL-------- 800

Query: 194 TRDFELAIASGATSVRIGSG 213
            R FE A A G   V   SG
Sbjct: 801 -RRFEKACALGEPVVSFDSG 819


>gnl|CDD|132434 TIGR03393, indolpyr_decarb, indolepyruvate decarboxylase, Erwinia
           family.  A family of closely related, thiamine
           pyrophosphate-dependent enzymes includes indolepyruvate
           decarboxylase (EC 4.1.1.74), phenylpyruvate
           decarboxylase (EC 4.1.1.43), pyruvate decarboxylase (EC
           4.1.1.1), branched-chain alpha-ketoacid decarboxylase,
           etc.. Members of this group of homologs may overlap in
           specificity. Within the larger family, this model
           represents a clade of bacterial indolepyruvate
           decarboxylases, part of a pathway for biosynthesis of
           the plant hormone indole-3-acetic acid. Typically, these
           species interact with plants, as pathogens or as
           beneficial, root-associated bacteria.
          Length = 539

 Score = 26.4 bits (58), Expect = 5.5
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 80  GSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIK 115
              +  +VSE   L DV+E V+  +  SL+ + + K
Sbjct: 493 PQSECWRVSEAEQLADVLEKVAAHERLSLIEVVLPK 528


>gnl|CDD|148471 pfam06872, EspG, EspG protein.  This family consists of several
           EspG like proteins from Citrobacter rodentium and
           Escherichia coli. EspG is secreted by the type III
           secretory system and is translocated into host
           epithelial cells. EspG is homologous with Shigella
           flexneri protein VirA and can rescue invasion in a
           Shigella virA mutant, indicating that these proteins are
           functionally equivalent in Shigella. EspG plays an
           accessory but as yet undefined role in EPEC virulence
           that may involve intestinal colonisation.
          Length = 336

 Score = 26.4 bits (58), Expect = 6.8
 Identities = 16/67 (23%), Positives = 22/67 (32%), Gaps = 3/67 (4%)

Query: 114 IKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPH 173
           I QS    +Y+  +TG  I      PN         R  Y++   G  C    +      
Sbjct: 269 ISQSSGGAIYVTSHTGVLIMAPEDRPNGVGMLTN--RTSYEVP-AGTKCEIEELVRAIKP 325

Query: 174 FYLLSEI 180
            Y  SE 
Sbjct: 326 RYASSET 332


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.320    0.134    0.378 

Gapped
Lambda     K      H
   0.267   0.0725    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,354,946
Number of extensions: 197507
Number of successful extensions: 360
Number of sequences better than 10.0: 1
Number of HSP's gapped: 358
Number of HSP's successfully gapped: 26
Length of query: 222
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 132
Effective length of database: 4,049,753
Effective search space: 534567396
Effective search space used: 534567396
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 (21.8 bits)
S2: 55 (25.0 bits)