RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780767|ref|YP_003065180.1| lipid-A-disaccharide synthase
[Candidatus Liberibacter asiaticus str. psy62]
         (383 letters)



>gnl|CDD|31106 COG0763, LpxB, Lipid A disaccharide synthetase [Cell envelope
           biogenesis, outer membrane].
          Length = 381

 Score =  363 bits (934), Expect = e-101
 Identities = 151/382 (39%), Positives = 221/382 (57%), Gaps = 7/382 (1%)

Query: 4   LKIAVIAGEISGDLLAGDLIKSLKEMVSYP-INLVGVGGPSLQKEGLVSLFDFSELSVIG 62
           LKIA+ AGE SGDLL   LIK+LK    YP +  VGVGG  ++ EGL SLFD  ELSV+G
Sbjct: 2   LKIALSAGEASGDLLGAGLIKALKA--RYPDVEFVGVGGEKMEAEGLESLFDMEELSVMG 59

Query: 63  IMQVVRHLPQFIFRINQTVELIVSSKPDVLLIVDNPDFTHRVAKRVRKKMPNLPIINYVC 122
            ++V+  LP+ +    + V  I+++KPDVL+++D+PDF  RVAK++RK  P + II+YV 
Sbjct: 60  FVEVLGRLPRLLKIRRELVRYILANKPDVLILIDSPDFNLRVAKKLRKAGPKIKIIHYVS 119

Query: 123 PSVWAWREGRARKMCAYINQVISILPFEKEVMQRLGGPPTTFVGHPLSSSPSILEVYSQR 182
           PSVWAWR  RA K+  Y++ +++ILPFE     + G  P T+VGHPL+    +L      
Sbjct: 120 PSVWAWRPKRAVKIAKYVDHLLAILPFEPAFYDKFGL-PCTYVGHPLADEIPLLPDREAA 178

Query: 183 NKQRNTPSQWKKILLLPGSRAQEIYKILPFFESAVASLVKRNPFFRFSLVTVSSQENLVR 242
            ++    +  K + LLPGSR  EI ++LP F  A   L  R P  +F L  V+++   + 
Sbjct: 179 REKLGIDADEKTLALLPGSRRSEIRRLLPPFVQAAQELKARYPDLKFVLPLVNAKYRRII 238

Query: 243 CIVSKWDIS-PEIIIDKEQKKQVFMTCNAAMAASGTVILELALCGIPVVSIYKSEWIVNF 301
               KW+++   +I+   +K++ F   +AA+AASGT  LE AL G P+V  YK + I  F
Sbjct: 239 EEALKWEVAGLSLILIDGEKRKAFAAADAALAASGTATLEAALAGTPMVVAYKVKPITYF 298

Query: 302 FI-FYIKTWTCALPNLIVDYPLVPEYFNSMIRSEALVRWIERLSQDTLQRRAMLHGFENL 360
                +K    +LPN++    +VPE        E L R +E L  +  +R A+   F  L
Sbjct: 299 IAKRLVKLPYVSLPNILAGREIVPELIQEDCTPENLARALEELLLNGDRREALKEKFREL 358

Query: 361 WDRMNTKKPAGHMAAEIVLQVL 382
              +    PA  +AA+ VL++L
Sbjct: 359 HQYLRE-DPASEIAAQAVLELL 379


>gnl|CDD|111570 pfam02684, LpxB, Lipid-A-disaccharide synthetase.  This is a family
           of lipid-A-disaccharide synthetases, EC:2.4.2.128. These
           enzymes catalyse the reaction:
           UDP-2,3-bis(3-hydroxytetradecanoyl) glucosamine +
           2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl
           1-phosphate <=> UDP +
           2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6
           -beta-D-2,
           3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl
           1-phosphate. These enzymes catalyse the fist
           disaccharide step in the synthesis of
           lipid-A-disaccharide.
          Length = 373

 Score =  224 bits (572), Expect = 4e-59
 Identities = 115/327 (35%), Positives = 187/327 (57%), Gaps = 13/327 (3%)

Query: 6   IAVIAGEISGDLLAGDLIKSLKEMVSYP-INLVGVGGPSLQKEGLVSLFDFSELSVIGIM 64
           I + AGE SGD+L G+LI++LKE   YP +  +GVGGP ++ EG  SL +  E+SV+G +
Sbjct: 1   IFLSAGEASGDILGGELIQNLKE--HYPNLRFIGVGGPKMEAEGFESLANMEEISVMGFI 58

Query: 65  QVVRHLPQFIFRINQTVELIVSSKPDVLLIVDNPDFTHRVAKRVRKKMPNLPIINYVCPS 124
           +V+  L + +    + V+ I+  KPD L+++D PDF  R+AK++RK  P L II+YV PS
Sbjct: 59  EVLGRLFKLLKIYQKVVKNILKKKPDTLILIDAPDFNLRLAKKLRKLGPKLKIIHYVSPS 118

Query: 125 VWAWREGRARKMCAYINQVISILPFEKEVMQRLGGPPTTFVGHPLSSSPSILEVYSQRNK 184
           VWAWR  RA+ +  Y + +++ILPFEK   Q+  G    +VGHPL      +++Y +R  
Sbjct: 119 VWAWRPKRAKIIAKYTDLLLAILPFEKGFFQKF-GLDCRYVGHPLLDE---IKLYKKRAS 174

Query: 185 QRNT--PSQWKKILLLPGSRAQEIYKILPFFESAVASLVKRNPFFRFSLVTVSSQENLVR 242
            +          + LLPGSR  EI ++LP  + A   L  + P  +  LV + +++   +
Sbjct: 175 AKELLIDHDEPILALLPGSRKGEIRRLLPPIQVAAQQLSSQFPNLKL-LVPLVNKKYEEQ 233

Query: 243 CIVSKWDISPEI--IIDKEQKKQVFMTCNAAMAASGTVILELALCGIPVVSIYKSEWIVN 300
              +    + ++  +    ++ +     +AA+A SGT  LE AL G P+V  Y+ + +  
Sbjct: 234 IEDTLALENCDVSLLEISGERYEAMFAADAALAKSGTATLEAALAGTPMVVAYRVKPLTF 293

Query: 301 FFIFYI-KTWTCALPNLIVDYPLVPEY 326
           F    + K    +LPN+I++  +VPE+
Sbjct: 294 FLAKRLVKIDYISLPNIILNREIVPEF 320


>gnl|CDD|99972 cd03799, GT1_amsK_like, This is a family of GT1
           glycosyltransferases found specifically in certain
           bacteria. amsK in Erwinia amylovora, has been reported
           to be involved in the biosynthesis of amylovoran, a
           exopolysaccharide acting as a virulence factor..
          Length = 355

 Score = 39.5 bits (93), Expect = 0.002
 Identities = 51/257 (19%), Positives = 79/257 (30%), Gaps = 81/257 (31%)

Query: 156 RLGGPPTTFVGH-PLSSSPSILEVY-------------SQRNKQ---RNTPSQWKKILLL 198
           RLGG P +F  H                          S+ N+Q   R       KI ++
Sbjct: 100 RLGGIPYSFTAHGKDIFRSPDAIDLDEKLARADFVVAISEYNRQQLIRLLGCDPDKIHVV 159

Query: 199 ------------PGSRAQEIYKIL-----------PFFESAVASLVKRNPFFRFSLVTVS 235
                       P     E  +IL            +   A+A L  R   FR  +V   
Sbjct: 160 HCGVDLERFPPRPPPPPGEPLRILSVGRLVEKKGLDYLLEALALLKDRGIDFRLDIVGDG 219

Query: 236 SQENLVRCIVSKWDI----------SPEIIIDKEQKKQVFM-----TCNAAMAASGTVIL 280
              + +  ++++  +          S E + +  +   +F+       +        V++
Sbjct: 220 PLRDELEALIAELGLEDRVTLLGAKSQEEVRELLRAADLFVLPSVTAADGDREGLPVVLM 279

Query: 281 ELALCGIPVVSIYKSEWIVNFFIFYIKTWTCALPNLIVD----YPLVPEYFNSMIRSEAL 336
           E    G+PV+S                T    +P L+ D      LVP         EAL
Sbjct: 280 EAMAMGLPVIS----------------TDVSGIPELVEDGETGL-LVPPG-----DPEAL 317

Query: 337 VRWIERLSQDTLQRRAM 353
              IERL  D   RR M
Sbjct: 318 ADAIERLLDDPELRREM 334


>gnl|CDD|30787 COG0438, RfaG, Glycosyltransferase [Cell envelope biogenesis, outer
           membrane].
          Length = 381

 Score = 30.8 bits (67), Expect = 0.62
 Identities = 45/261 (17%), Positives = 89/261 (34%), Gaps = 25/261 (9%)

Query: 113 PNLPIINYVCPSVWAWREGRARKMCAYINQVISILPFEKEVMQRLGGPPTTFVGHPLSSS 172
             LP +  +   +    +   + +    ++VI++ P  KE+++ LG P    V       
Sbjct: 124 LLLPRLLLLLGLLRLLLKRLKKALRLLADRVIAVSPALKELLEALGVPNKIVVIPN---- 179

Query: 173 PSILEVYSQRNKQRNTPSQWKKILLLPGSRAQEIYKILPFFESAVASLVKRNPFFRFSLV 232
             I        +    P   K ++L  G    E  K L     A A L KR P  +  +V
Sbjct: 180 -GIDTEKFAPARIGLLPEGGKFVVLYVGRLDPE--KGLDLLIEAAAKLKKRGPDIKLVIV 236

Query: 233 -TVSSQENLVRCIVSKWDISPEII----IDKEQKKQVFMTCNAAMAAS-----GTVILEL 282
                +   +  +  K  +   +     +  E+  ++  + +  +  S     G V+LE 
Sbjct: 237 GDGPERREELEKLAKKLGLEDNVKFLGYVPDEELAELLASADVFVLPSLSEGFGLVLLEA 296

Query: 283 ALCGIPVVSIYKSEWIVNFFIFYIKTWTCALPNLIVDYPLVPEYFNSMIRSEALVRWIER 342
              G PV++      I                 L+V    V E  +++ +        E 
Sbjct: 297 MAAGTPVIA-SDVGGIPEVVEDGET-------GLLVPPGDVEELADALEQLLEDPELREE 348

Query: 343 LSQDTLQRRAMLHGFENLWDR 363
           L +   +R      +E + ++
Sbjct: 349 LGEAARERVEEEFSWERIAEQ 369


>gnl|CDD|32002 COG1817, COG1817, Uncharacterized protein conserved in archaea
           [Function unknown].
          Length = 346

 Score = 30.6 bits (69), Expect = 0.71
 Identities = 45/250 (18%), Positives = 86/250 (34%), Gaps = 29/250 (11%)

Query: 53  FDFSELSVIGIMQVVRHLPQFIFRINQTVELIVSSKPDVLLIVDNPDFTHRVAKRVRKKM 112
           F +  +   G + +   L +   R+ +  ++I   KPDV +   +P+   RVA  +    
Sbjct: 49  FPYKSIGKHGGVTLKEKLLESAERVYKLSKIIAEFKPDVAIGKHSPELP-RVAFGL---- 103

Query: 113 PNLPIINYVCPSVWAWREGRARKMCAYINQVISILPFEKEVMQRLGGPPTTFVG------ 166
             +P I +V       +      +   I   I+    ++E +   G  P    G      
Sbjct: 104 -GIPSIIFVDNEHAEAQNKLTLPLADVI---ITPEAIDEEELLDFGADPNKISGYNGIAE 159

Query: 167 -HPLSSSPSILEVYSQRNKQRNTPSQWKKILLLPGSRAQEIYKILPFFESAVASLVKRNP 225
              +       EV  +   +         I++ P       Y       S +  L+K   
Sbjct: 160 LANVYGFVPDPEVLKELGLEEGETY----IVMRPEP-WGAHYDNGDRGISVLPDLIKE-- 212

Query: 226 FFRFSLVTVSSQENLVRCIVSKWD--ISPEIIIDKEQKKQVFMTCNAAMAASGTVILELA 283
             ++ +V +  ++     I   +   I P+  +D      +       + A GT+  E A
Sbjct: 213 LKKYGIVLIPREKEQ-AEIFEGYRNIIIPKKAVDT---LSLLYYATLVIGAGGTMAREAA 268

Query: 284 LCGIPVVSIY 293
           L G P +S Y
Sbjct: 269 LLGTPAISCY 278


>gnl|CDD|39368 KOG4166, KOG4166, KOG4166, Thiamine pyrophosphate-requiring enzyme
           [Amino acid transport and metabolism, Coenzyme transport
           and metabolism].
          Length = 675

 Score = 30.0 bits (67), Expect = 1.2
 Identities = 30/141 (21%), Positives = 58/141 (41%), Gaps = 28/141 (19%)

Query: 55  FSELSVIGIMQ-------VVRHLPQFIFRINQTVELIVSSKPDVLLIVDNP-DFTHRVAK 106
           F E  ++GI +       +V+ +     RI +  E+  S +P  +L VD P D T ++  
Sbjct: 200 FQEADIVGISRSCTKWNVMVKDVEDLPRRIEEAFEIATSGRPGPVL-VDLPKDVTAQLLI 258

Query: 107 RVRKKMPNLPIINYVCPSVWAWREGRA--RKMCAYINQVISILPFEKEVMQRLGGPPTTF 164
                 P +P    +  + +  R  +     + ++I Q+  ++   K+        P  +
Sbjct: 259 ------PPIPQAMRLPSNAYMSRMPKPPEDFVMSHIEQIARLISLAKK--------PVLY 304

Query: 165 VGHPL---SSSPSILEVYSQR 182
           VG      S  P +L  +S+R
Sbjct: 305 VGGGCLNSSDGPRLLGRFSER 325


>gnl|CDD|112806 pfam04007, DUF354, Protein of unknown function (DUF354).  Members
           of this family are around 350 amino acids in length.
           They are found in archaebacteria and have no known
           function.
          Length = 335

 Score = 29.7 bits (67), Expect = 1.3
 Identities = 11/29 (37%), Positives = 15/29 (51%)

Query: 268 CNAAMAASGTVILELALCGIPVVSIYKSE 296
            +  + A GT+  E AL G P VS Y  +
Sbjct: 249 SDLVIGAGGTMNREAALLGTPAVSCYPGK 277


>gnl|CDD|100003 cd05844, GT1_like_7, Glycosyltransferases catalyze the transfer of
           sugar moieties from activated donor molecules to
           specific acceptor molecules, forming glycosidic bonds.
           The acceptor molecule can be a lipid, a protein, a
           heterocyclic compound, or another carbohydrate residue.
           This group of glycosyltransferases is most closely
           related to the previously defined glycosyltransferase
           family 1 (GT1). The members of this family may transfer
           UDP, ADP, GDP, or CMP linked sugars. The diverse
           enzymatic activities among members of this family
           reflect a wide range of biological functions. The
           protein structure available for this family has the GTB
           topology, one of the two protein topologies observed for
           nucleotide-sugar-dependent glycosyltransferases. GTB
           proteins have distinct N- and C- terminal domains each
           containing a typical Rossmann fold. The two domains have
           high structural homology despite minimal sequence
           homology. The large cleft that separates the two domains
           includes the catalytic center and permits a high degree
           of flexibility..
          Length = 367

 Score = 29.9 bits (68), Expect = 1.3
 Identities = 7/16 (43%), Positives = 10/16 (62%)

Query: 276 GTVILELALCGIPVVS 291
             V+LE    G+PVV+
Sbjct: 284 PVVLLEAQASGVPVVA 299


>gnl|CDD|29750 cd01147, HemV-2, Metal binding protein HemV-2.  These proteins are
           predicted to function as initial receptors in ABC
           transport of metal ions.  They belong to the TroA
           superfamily of helical backbone metal receptor proteins
           that share a distinct fold and ligand binding mechanism.
            A typical TroA protein is comprised of two globular
           subdomains connected by a single helix and can bind the
           metal ion in the cleft between these domains. In
           addition, these proteins sometimes have a low complexity
           region containing a metal-binding histidine-rich motif
           (repetitive HDH sequence)..
          Length = 262

 Score = 28.3 bits (63), Expect = 3.5
 Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 14/93 (15%)

Query: 29  MVSYPINLVGVGGPSLQKEG---LVSLFDFSELSVIGIMQVVRHLPQFIFRINQTVELIV 85
            ++ P  +VGV       EG    ++  +  +L VIG         +         E I 
Sbjct: 21  ALAAPDKIVGVDDAEKSDEGRPYFLASPELKDLPVIG---------RGGRGNTPNYEKIA 71

Query: 86  SSKPDVLLIVDNPDFTHRVAKRVRKKMPNLPII 118
           + KPDV++ V + D    +A  ++KK   +P++
Sbjct: 72  ALKPDVVIDVGSDD-PTSIADDLQKKT-GIPVV 102


>gnl|CDD|32747 COG2923, DsrF, Uncharacterized protein involved in the oxidation
          of intracellular sulfur [Inorganic ion transport and
          metabolism].
          Length = 118

 Score = 28.3 bits (63), Expect = 3.9
 Identities = 14/43 (32%), Positives = 22/43 (51%)

Query: 7  AVIAGEISGDLLAGDLIKSLKEMVSYPINLVGVGGPSLQKEGL 49
           ++ G+    +LA D I + K +  Y I  V V   SL++ GL
Sbjct: 46 QLLPGQKPEAILARDYIATFKLLDLYDIEQVYVCEASLRERGL 88


>gnl|CDD|33760 COG3980, spsG, Spore coat polysaccharide biosynthesis protein,
           predicted glycosyltransferase [Cell envelope biogenesis,
           outer membrane].
          Length = 318

 Score = 28.0 bits (62), Expect = 4.2
 Identities = 10/45 (22%), Positives = 25/45 (55%), Gaps = 2/45 (4%)

Query: 254 IIIDKEQKKQVFMTCNAAMAASGTVILELALCGIP--VVSIYKSE 296
           + ID     ++    + A++A+G+ + E  L G+P  V+ + +++
Sbjct: 214 LYIDTNDMAELMKEADLAISAAGSTLYEALLLGVPSLVLPLAENQ 258


>gnl|CDD|34522 COG4913, COG4913, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 1104

 Score = 27.3 bits (60), Expect = 6.2
 Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 2/41 (4%)

Query: 305 YIKTWTCALPNLIVDYPLVPEYFNSM--IRSEALVRWIERL 343
             K  T AL  +  +   +PEY   +  +  +AL  ++ R 
Sbjct: 806 AKKEDTAALSEVGAELDDIPEYLARLQTLTEDALPEFLARF 846


>gnl|CDD|34079 COG4370, COG4370, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 412

 Score = 27.3 bits (60), Expect = 7.6
 Identities = 20/111 (18%), Positives = 36/111 (32%), Gaps = 15/111 (13%)

Query: 195 ILLLPGSRAQEIYKILPFFESAVASLVKRNPFFRF-----SLVTVSSQENLVRCIVSKWD 249
           I LLPGSR  E    L     ++ +L        F       + +     L       W 
Sbjct: 228 IALLPGSRVPEAQTNLAVILGSLCALPAMFALVVFWAAIAPELPLLLLWTLEE--RQGWQ 285

Query: 250 ISPE--------IIIDKEQKKQVFMTCNAAMAASGTVILELALCGIPVVSI 292
              +        + + ++    +    +AA+  +GT   +    G PV+  
Sbjct: 286 PLADRFGKDNCSLWLSQQSFADILHAADAALGMAGTATEQAVGLGKPVIGF 336


>gnl|CDD|112109 pfam03279, Lip_A_acyltrans, Bacterial lipid A biosynthesis
           acyltransferase. 
          Length = 295

 Score = 26.9 bits (60), Expect = 9.2
 Identities = 8/69 (11%), Positives = 21/69 (30%), Gaps = 5/69 (7%)

Query: 320 YPLVPEYFNSMIRSEALVRWIERLSQDTLQRRAMLHGFENLWDRMNTKKPA----GHMAA 375
             ++ +   S   +      +       + +R  + G EN+   +   +       H   
Sbjct: 73  EKIIDQSLASFGMAILETAELAFRPDSKIAKRTEVIGLENIKKALAQGRGVILLVPHFGN 132

Query: 376 -EIVLQVLG 383
            ++   VL 
Sbjct: 133 WDLPGLVLA 141


>gnl|CDD|163682 cd07944, DRE_TIM_HOA_like, 4-hydroxy-2-oxovalerate aldolase-like,
           N-terminal catalytic TIM barrel domain.  This family of
           bacterial enzymes is sequence-similar to
           4-hydroxy-2-oxovalerate aldolase (HOA) but its exact
           function is unknown.  This family includes the
           Bacteroides vulgatus Bvu_2661 protein and belongs to the
           DRE-TIM metallolyase superfamily.  DRE-TIM metallolyases
           include 2-isopropylmalate synthase (IPMS),
           alpha-isopropylmalate synthase (LeuA),
           3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
           synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
           aldolase, re-citrate synthase, transcarboxylase 5S,
           pyruvate carboxylase, AksA, and FrbC.  These members all
           share a conserved  triose-phosphate isomerase (TIM)
           barrel domain consisting of a core beta(8)-alpha(8)
           motif with the eight parallel beta strands forming an
           enclosed barrel surrounded by eight alpha helices.  The
           domain has a catalytic center containing a divalent
           cation-binding site formed by a cluster of invariant
           residues that cap the core of the barrel.  In addition,
           the catalytic site includes three invariant residues -
           an aspartate (D), an arginine (R), and a glutamate (E) -
           which is the basis for the domain name "DRE-TIM".
          Length = 266

 Score = 26.8 bits (60), Expect = 9.4
 Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 5/41 (12%)

Query: 77  INQTVELIVSSKPDVLLIVD-----NPDFTHRVAKRVRKKM 112
           + + +EL+   KPDV  IVD      P+   R+   +R  +
Sbjct: 140 LLELLELVNEIKPDVFYIVDSFGSMYPEDIKRIISLLRSNL 180


>gnl|CDD|29071 cd00156, REC, Signal receiver domain; originally thought to be
           unique to bacteria (CheY, OmpR, NtrC, and PhoB), now
           recently identified in eukaroytes ETR1 Arabidopsis
           thaliana; this domain receives the signal from the
           sensor partner in a two-component systems; contains a
           phosphoacceptor site that is phosphorylated by histidine
           kinase homologs; usually found N-terminal to a DNA
           binding effector domain; forms homodimers.
          Length = 113

 Score = 26.7 bits (59), Expect = 9.8
 Identities = 13/42 (30%), Positives = 26/42 (61%), Gaps = 2/42 (4%)

Query: 79  QTVELIVSSKPDVLLI-VDNPDFT-HRVAKRVRKKMPNLPII 118
           + + L+   KPD++L+ +  P      + +R+RK+ P++PII
Sbjct: 32  EALALLAEEKPDLILLDIMMPGMDGLELLRRIRKRGPDIPII 73


  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
   0.323    0.138    0.415 

Gapped
Lambda     K      H
   0.267   0.0690    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,828,333
Number of extensions: 263281
Number of successful extensions: 702
Number of sequences better than 10.0: 1
Number of HSP's gapped: 691
Number of HSP's successfully gapped: 31
Length of query: 383
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 287
Effective length of database: 4,189,273
Effective search space: 1202321351
Effective search space used: 1202321351
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (26.2 bits)