RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780402|ref|YP_003064815.1|
3-deoxy-D-manno-octulosonic-acid transferase [Candidatus Liberibacter
asiaticus str. psy62]
         (440 letters)



>gnl|CDD|180233 PRK05749, PRK05749, 3-deoxy-D-manno-octulosonic-acid transferase;
           Reviewed.
          Length = 425

 Score =  459 bits (1183), Expect = e-130
 Identities = 165/424 (38%), Positives = 244/424 (57%), Gaps = 6/424 (1%)

Query: 8   ILLGIYRWGGIFFMPFLSVSLSLYRVFNRERGRKFGERLGYPT-ALRPIGPLIWFHASSV 66
           +L  +Y       +P + + L L      +  +++GER G+      P GPLIWFHA SV
Sbjct: 1   MLRLLYTALLYLALPLILLRLLLRSRKAPKYRKRWGERFGFRKPNPPPKGPLIWFHAVSV 60

Query: 67  GETMALIGLIPAIRSR--HVNVLLTTMTATSAKVARKYLGQYAIHQYAPLDIQPAVSRFL 124
           GET A I LI A+R R   + +L+TTMT T ++ A+   G    H+Y P D+  AV RFL
Sbjct: 61  GETRAAIPLIRALRKRYPDLPILVTTMTPTGSERAQALFGDDVEHRYLPYDLPGAVRRFL 120

Query: 125 KYWKPDCMILSESDIWPLTVFELSKQRIPQVLVNARMSRRSFKNWKTVLSFSKKIFSQFS 184
           ++W+P  +I+ E+++WP  + EL ++ IP VL NAR+S RSFK ++    F + +F    
Sbjct: 121 RFWRPKLVIIMETELWPNLIAELKRRGIPLVLANARLSERSFKRYQKFKRFYRLLFKNID 180

Query: 185 LVIVQSERYFRRYKELGAQK-LIVSGNLKIDTESLPCDKELLSLYQESIAG-RYTWAAIS 242
           LV+ QSE    R+  LGA+  + V+GNLK D E  P      +  +  +A  R  W A S
Sbjct: 181 LVLAQSEEDAERFLALGAKNEVTVTGNLKFDIEVPPELAARAATLRRQLAPNRPVWIAAS 240

Query: 243 TFEGEEDKAVYVH-NFIKCRTDVLTIIVPRHPRRCDAIERRLIAKGLKVARRSRGDVINA 301
           T EGEE+  +  H   +K   ++L I+VPRHP R   +E  L   GL   RRS+G+  +A
Sbjct: 241 THEGEEELVLDAHRALLKQFPNLLLILVPRHPERFKEVEELLKKAGLSYVRRSQGEPPSA 300

Query: 302 EVDIFLGDTIGEMGFYLRMTEIAFIGRSFCASGGQNPLEAAMLGCAILSGPNVENFRDIY 361
           + D+ LGDT+GE+G    + +IAF+G S    GG NPLE A  G  ++SGP+  NF++I+
Sbjct: 301 DTDVLLGDTMGELGLLYAIADIAFVGGSLVKRGGHNPLEPAAFGVPVISGPHTFNFKEIF 360

Query: 362 RRMVSSGAVRIVEEVGTLADMVYSLLSEPTIRYEMINAAINEVKKMQGPLKITLRSLDSY 421
            R++ +GA   VE+   LA  V  LL++P  R     A +  +K+ QG L+ TL+ L+ Y
Sbjct: 361 ERLLQAGAAIQVEDAEDLAKAVTYLLTDPDARQAYGEAGVAFLKQNQGALQRTLQLLEPY 420

Query: 422 VNPL 425
           + PL
Sbjct: 421 LPPL 424


>gnl|CDD|179146 PRK00865, PRK00865, glutamate racemase; Provisional.
          Length = 261

 Score = 32.8 bits (76), Expect = 0.18
 Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 13/48 (27%)

Query: 73  IGLIPAI-------RSRHVNVLLTTMTATSAKVARKYLGQYAIHQYAP 113
           +G++PAI       R+  + VL T  T  SA           I ++AP
Sbjct: 95  VGIVPAIKPAAALTRNGRIGVLATPGTVKSAAYRD------LIARFAP 136


>gnl|CDD|132039 TIGR02994, ectoine_eutE, ectoine utilization protein EutE.  Members
           of this family, part of the succinylglutamate
           desuccinylase / aspartoacylase family (pfam04952),
           belong to ectoine utilization operons, as found in
           Sinorhizobium meliloti 1021 (where it the operon is
           known to be induced by ectoine), Mesorhizobium loti,
           Silicibacter pomeroyi, Agrobacterium tumefaciens, and
           Pseudomonas putida.
          Length = 325

 Score = 30.5 bits (69), Expect = 0.88
 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 90  TMTATSAKVARKYLGQYAIHQYAPL-DIQPAVSRFLKYWKPDCMILSESD 138
           T +A + K+A++ +     H      +++ A + +L     DC I +E D
Sbjct: 214 TASARTIKIAKRGVRNVLRHAGILKGELEIAPTIWLDMPSDDCFIFAEDD 263


>gnl|CDD|180935 PRK07333, PRK07333, 2-octaprenyl-6-methoxyphenyl hydroxylase;
           Provisional.
          Length = 403

 Score = 30.3 bits (69), Expect = 1.1
 Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 9/48 (18%)

Query: 33  VFNRERGRKFGERLGYPTALRPIG-----PLIWFHASS-VGETMALIG 74
           VF  E  ++FG RLG    L+ +G     PL    A S V    AL+G
Sbjct: 242 VFEAELEQRFGHRLG---ELKVLGKRRAFPLGLTLARSFVAPRFALVG 286


>gnl|CDD|180314 PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed.
          Length = 455

 Score = 29.8 bits (68), Expect = 1.5
 Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 9/58 (15%)

Query: 239 AAISTFEGEEDKAVYVHNFIKCRTDVLTII---VPRHPRRCDAIERRLIAKGLKVARR 293
           +A+ST  G E  +  +   IK       +I    P+ P     I   L  +G+ VARR
Sbjct: 384 SAVSTDGGGEASSTAIRALIK------KLIAAENPKKPLSDSKIAELLKEQGIDVARR 435


>gnl|CDD|181663 PRK09126, PRK09126, hypothetical protein; Provisional.
          Length = 392

 Score = 29.1 bits (66), Expect = 2.5
 Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 9/47 (19%)

Query: 34  FNRERGRKFGERLGYPTALRPIG-----PLIWFHASS-VGETMALIG 74
           F  E   +F  RLG   A+R +      PL+  +A   V +  ALIG
Sbjct: 243 FAAEVTARFKGRLG---AMRLVSSRHAYPLVAVYAHRFVAKRFALIG 286


>gnl|CDD|185627 PTZ00448, PTZ00448, hypothetical protein; Provisional.
          Length = 373

 Score = 28.8 bits (64), Expect = 2.7
 Identities = 24/100 (24%), Positives = 45/100 (45%), Gaps = 14/100 (14%)

Query: 142 LTVFELSKQRIPQVLVNARMSRRSFKNWKTVLSFSKKI--FSQFSLVIVQSE-------- 191
           L  F++ K+RIP  +  A+M  +   +     + +KK+  F+ F +   +          
Sbjct: 155 LKAFDILKKRIPDQIERAKMMLKLSVDIVNKQNITKKLNEFNVFPISSEEKHNTYSITFL 214

Query: 192 ---RYFRRYKELGAQKLIVSGNLK-IDTESLPCDKELLSL 227
              RY+R   +L  + L++  N+K ID  S   + E + L
Sbjct: 215 CEPRYYREIDQLDCKLLLLDSNVKTIDKNSNQDNVEAIQL 254


>gnl|CDD|132132 TIGR03088, stp2, sugar transferase, PEP-CTERM/EpsH1 system
           associated.  Members of this family include a match to
           the pfam00534 Glycosyl transferases group 1 domain.
           Nearly all are found in species that encode the
           PEP-CTERM/exosortase system predicted to act in protein
           sorting in a number of Gram-negative bacteria. In
           particular, these transferases are found proximal to a
           particular variant of exosortase, EpsH1, which appears
           to travel with a conserved group of genes summarized by
           Genome Property GenProp0652. The nature of the sugar
           transferase reaction catalyzed by members of this clade
           is unknown and may conceivably be variable with respect
           to substrate by species, but we hypothesize a conserved
           substrate.
          Length = 374

 Score = 28.5 bits (64), Expect = 3.8
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 72  LIGLIPAIRSRHVNVLLTTMTATSAKVARKYLGQYAIHQYAPLD--IQPAVSRFLKYWKP 129
           LI  +PA R RH  V LT ++A   ++ R  +  YA+H+    D  + P + R L+  +P
Sbjct: 23  LINHLPADRYRHAVVALTEVSAFRKRIQRPDVAFYALHKQPGKDVAVYPQLYRLLRQLRP 82

Query: 130 D 130
           D
Sbjct: 83  D 83


>gnl|CDD|132616 TIGR03577, EF_0830, conserved hypothetical protein
           EF_0830/AHA_3911.  Members of this family of small
           (about 120 amino acid), relatively rare proteins are
           found in both Gram-positive (e.g. Enterococcus faecalis)
           and Gram-negative (e.g. Aeromonas hydrophila) bacteria,
           as part of a cluster of conserved proteins. The function
           is unknown.
          Length = 115

 Score = 27.9 bits (62), Expect = 5.0
 Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 8/59 (13%)

Query: 284 IAKGLKVARRSRGDVINAEVDIFLGDTIGEMGFYLRMTEIAFIGRSFCASGGQNPLEAA 342
           +AKG++ A      +     D+ LGD +          E A +G SFC SGG   + A 
Sbjct: 15  VAKGVEAAGGRAVVIPGMAADMKLGDVMK--------QENADLGISFCGSGGAGAITAQ 65


>gnl|CDD|161836 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5'
           exoribonucleases.  This model is defined to identify a
           pair of paralogous 3-prime exoribonucleases in E. coli,
           plus the set of proteins apparently orthologous to one
           or the other in other eubacteria. VacB was characterized
           originally as required for the expression of virulence
           genes, but is now recognized as the exoribonuclease
           RNase R (Rnr). Its paralog in E. coli and H. influenzae
           is designated exoribonuclease II (Rnb). Both are
           involved in the degradation of mRNA, and consequently
           have strong pleiotropic effects that may be difficult to
           disentangle. Both these proteins share domain-level
           similarity (RNB, S1) with a considerable number of other
           proteins, and full-length similarity scoring below the
           trusted cutoff to proteins associated with various
           phenotypes but uncertain biochemistry; it may be that
           these latter proteins are also 3-prime exoribonucleases.
          Length = 654

 Score = 27.8 bits (62), Expect = 5.7
 Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 159 ARMSRRSFKNWKTVLSFSKKIFSQFSLVIVQSERY--FRRYKELGAQKLI-VSGNLKIDT 215
           AR + R   +W        K+ ++FS  I    R+  F R  + G   LI +S    +  
Sbjct: 552 ARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLDDNGIDGLIHIS---TLHN 608

Query: 216 ESLPCDKELLSLYQES 231
           +    D+E ++L  + 
Sbjct: 609 DYYVFDQEKMALIGKG 624


>gnl|CDD|168170 PRK05677, PRK05677, long-chain-fatty-acid--CoA ligase; Validated.
          Length = 562

 Score = 27.8 bits (62), Expect = 6.1
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 11/54 (20%)

Query: 356 NFRDIYRRMVSSGAVR--IVEEVGTLADMVYSLLSEPTIRYEMINAAINEVKKM 407
           N   +  +++    V+  IV EV    DM+      P ++  +INA +  VKKM
Sbjct: 131 NMAHLAEKVLPKTGVKHVIVTEVA---DML------PPLKRLLINAVVKHVKKM 175


>gnl|CDD|184461 PRK14024, PRK14024, phosphoribosyl isomerase A; Provisional.
          Length = 241

 Score = 27.6 bits (62), Expect = 6.2
 Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 17/60 (28%)

Query: 339 LEAAMLGCA-----------ILSGPNVENFRDIYRR----MVSSGAVRIVEEVGTLADMV 383
           L++A  GC+            L+GPN+E  R++  R    +V+SG V  ++++  LA++V
Sbjct: 155 LDSA--GCSRYVVTDVTKDGTLTGPNLELLREVCARTDAPVVASGGVSSLDDLRALAELV 212


>gnl|CDD|132409 TIGR03366, HpnZ_proposed, putative phosphonate catabolism
           associated alcohol dehydrogenase.  This clade of
           zinc-binding alcohol dehydrogenases (members of
           pfam00107) are repeatedly associated with genes proposed
           to be involved with the catabolism of phosphonate
           compounds.
          Length = 280

 Score = 27.5 bits (61), Expect = 7.7
 Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 1/29 (3%)

Query: 97  KVARKYLGQYAIHQYAPLDIQPAVSRFLK 125
           +V R++L    +H Y P  +  AV RFL 
Sbjct: 232 QVVRRWLTIRGVHNYEPRHLDQAV-RFLA 259


>gnl|CDD|166839 PRK00178, tolB, translocation protein TolB; Provisional.
          Length = 430

 Score = 27.4 bits (61), Expect = 8.5
 Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 1/42 (2%)

Query: 189 QSERYFRRYKELGAQKLIVSGNLKIDTESLPCDKELLSLYQE 230
            SE  FR +K LGAQ ++V GN+      L     L ++  E
Sbjct: 84  ASEVIFRDWKALGAQYVMV-GNIVPAGGRLQVQYALFNVATE 124


>gnl|CDD|130031 TIGR00957, MRP_assoc_pro, multi drug resistance-associated protein
           (MRP).  This model describes multi drug
           resistance-associated protein (MRP) in eukaryotes. The
           multidrug resistance-associated protein is an integral
           membrane protein that causes multidrug resistance when
           overexpressed in mammalian cells. It belongs to ABC
           transporter superfamily. The protein topology and
           function was experimentally demonstrated by epitope
           tagging and immunofluorescence. Insertion of tags in the
           critical regions associated with drug efflux, abrogated
           its function. The C-terminal domain seem to highly
           conserved.
          Length = 1522

 Score = 27.2 bits (60), Expect = 9.3
 Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 6/69 (8%)

Query: 120 VSRFLKYWKPDCMI------LSESDIWPLTVFELSKQRIPQVLVNARMSRRSFKNWKTVL 173
           +SR   +W     +      L ESD+W L   + S+  +P ++ N +   +  +      
Sbjct: 210 LSRITFWWITGMAVYGYRQPLEESDLWSLNKEDTSEMVVPVLVENWKKECKKTRKQPVSA 269

Query: 174 SFSKKIFSQ 182
            + KK  S+
Sbjct: 270 VYGKKDPSK 278


  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
   0.325    0.139    0.414 

Gapped
Lambda     K      H
   0.267   0.0632    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 7,216,761
Number of extensions: 474775
Number of successful extensions: 1305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1298
Number of HSP's successfully gapped: 16
Length of query: 440
Length of database: 5,994,473
Length adjustment: 96
Effective length of query: 344
Effective length of database: 3,920,105
Effective search space: 1348516120
Effective search space used: 1348516120
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: 59 (26.7 bits)