RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781031|ref|YP_003065444.1| exsB protein [Candidatus
Liberibacter asiaticus str. psy62]
         (240 letters)



>gnl|CDD|30948 COG0603, COG0603, Predicted PP-loop superfamily ATPase [General
           function prediction only].
          Length = 222

 Score =  223 bits (569), Expect = 4e-59
 Identities = 93/234 (39%), Positives = 128/234 (54%), Gaps = 29/234 (12%)

Query: 11  ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70
           A++L SGG DS+TCL+WA      V  L+FDYGQR++ ELE      K++ +        
Sbjct: 5   AVVLLSGGLDSTTCLAWAKKEGYEVHALTFDYGQRHRKELEAA----KELAKK------- 53

Query: 71  LG-EDHILPLAILGDISHSSLTKNVAMKIQDNN----LPNTFVPGRNIIFLVFAATLAYR 125
           LG   HI+ + +LG+I  S+LT +     +       +P TFVP RN+IFL  AA  A  
Sbjct: 54  LGVPHHIIDVDLLGEIGGSALTDDSIDVPKYEFAEEEIPATFVPARNLIFLSIAAAYAEA 113

Query: 126 LGITNIVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHV-TVHTPLMWLKKYETWKLA 184
           LG   I+IGV E D+SGYPDCR + I A+  A+NLG E  V  +H PLM L K E  KLA
Sbjct: 114 LGADAIIIGVNEEDFSGYPDCRPEFIEALNEALNLGTEKGVRIIHAPLMELTKAEIVKLA 173

Query: 185 QDIGGQDLVNLILEESHTCYLGKRDKRYEWGYGCNSCPACYLRQKGWMEFKEKY 238
            ++G      + LE + +CY G        G  C  C +C LR++ + E   + 
Sbjct: 174 DELG------VPLELTWSCYNG------GEGDHCGECESCVLRERAFKEAGLED 215


>gnl|CDD|73293 cd01995, ExsB, ExsB is a transcription regulator related protein.
           It is a subfamily of a Adenosine nucleotide binding
           superfamily of proteins. This protein family is
           represented by a single member in nearly every completed
           large (> 1000 genes) prokaryotic genome. In Rhizobium
           meliloti, a species in which the exo genes make
           succinoglycan, a symbiotically important
           exopolysaccharide, exsB is located nearby and affects
           succinoglycan levels, probably through polar effects on
           exsA expression or the same polycistronic mRNA. In
           Arthrobacter viscosus, the homologous gene is designated
           ALU1 and is associated with an aluminum tolerance
           phenotype. The function is unknown.
          Length = 169

 Score =  200 bits (509), Expect = 4e-52
 Identities = 81/223 (36%), Positives = 107/223 (47%), Gaps = 55/223 (24%)

Query: 11  ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70
           A++L SGG DS+TCL+WA      V  LSFDYGQR+  E E      K I E        
Sbjct: 2   AVVLLSGGLDSTTCLAWAKKEGYEVHALSFDYGQRHAKEEEAA----KLIAEK------- 50

Query: 71  LGEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGITN 130
                      LG                    P+T+VP RN+IFL  AA  A  LG   
Sbjct: 51  -----------LG--------------------PSTYVPARNLIFLSIAAAYAEALGAEA 79

Query: 131 IVIGVCETDYSGYPDCRHDTIRAIETAINLGMESHVTVHTPLMWLKKYETWKLAQDIGGQ 190
           I+IGV   DYSGYPDCR + I A+  A+NLG E+ + +H PL+ L K E  +L  ++G  
Sbjct: 80  IIIGVNAEDYSGYPDCRPEFIEAMNKALNLGTENGIKIHAPLIDLSKAEIVRLGGELG-- 137

Query: 191 DLVNLILEESHTCYLGKRDKRYEWGYGCNSCPACYLRQKGWME 233
               + LE + +CY G           C  C +C LR++ + E
Sbjct: 138 ----VPLELTWSCYNGGE-------KHCGECDSCLLRKRAFEE 169


>gnl|CDD|73292 cd01986, Alpha_ANH_like, Adenine nucleotide alpha hydrolases
          superfamily  including N type ATP PPases and ATP
          sulphurylases. The domain forms a apha/beta/apha fold
          which  binds to Adenosine group...
          Length = 103

 Score = 37.1 bits (85), Expect = 0.004
 Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 11 ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70
           L+ FSGG+DSS   +       +V  ++ D+G   ++E    +  ++   E   +    
Sbjct: 1  VLVAFSGGKDSSVAAALLKKLGYQVIAVTVDHGISPRLEDAKEIA-KEAREEAAKRIAKE 59

Query: 71 LGEDHILPLAILGDIS 86
           G + I       D++
Sbjct: 60 KGAETIATGTRRDDVA 75


>gnl|CDD|109807 pfam00764, Arginosuc_synth, Arginosuccinate synthase.  This
          family contains a PP-loop motif.
          Length = 389

 Score = 36.2 bits (84), Expect = 0.008
 Identities = 12/32 (37%), Positives = 20/32 (62%)

Query: 13 LLFSGGQDSSTCLSWALDRFDRVETLSFDYGQ 44
          L +SGG D+S C+ W  +++  V  ++ D GQ
Sbjct: 2  LAYSGGLDTSVCIPWLKEKYYEVIAVAVDVGQ 33


>gnl|CDD|30186 cd01999, Argininosuccinate_Synthase, Argininosuccinate synthase.
          The Argininosuccinate synthase is a urea cycle enzyme
          that catalyzes the penultimate step in arginine
          biosynthesis: the ATP-dependent ligation of citrulline
          to aspartate to form argininosuccinate, AMP and
          pyrophosphate .  In humans, a defect in the AS gene
          causes citrullinemia, a genetic disease characterized
          by severe vomiting spells and mental retardation. AS is
          a homotetrameric enzyme of chains of about 400
          amino-acid residues. An arginine seems to be important
          for the enzyme's catalytic mechanism. The sequences of
          AS from various prokaryotes, archaebacteria and
          eukaryotes show significant similarity.
          Length = 385

 Score = 33.2 bits (76), Expect = 0.071
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 5/53 (9%)

Query: 12 LLLFSGGQDSSTCLSWALDRF-DRVETLSFDYGQRNKVELECRLCVRKKIVEL 63
          +L +SGG D+S  L W  ++    V  ++ D GQ  +        + +K ++L
Sbjct: 2  VLAYSGGLDTSVILKWLKEKGGYEVIAVTADVGQPEEEIEA----IEEKALKL 50


>gnl|CDD|30486 COG0137, ArgG, Argininosuccinate synthase [Amino acid transport
          and metabolism].
          Length = 403

 Score = 30.9 bits (70), Expect = 0.29
 Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 12 LLLFSGGQDSSTCLSWALDRFDR-VETLSFDYGQ 44
          +L +SGG D+S  + W  ++    V  ++ D GQ
Sbjct: 8  VLAYSGGLDTSVAIKWLKEKGGAEVIAVTADVGQ 41


>gnl|CDD|30386 COG0037, MesJ, Predicted ATPase of the PP-loop superfamily
          implicated in cell cycle control [Cell division and
          chromosome partitioning].
          Length = 298

 Score = 30.6 bits (68), Expect = 0.35
 Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 2/48 (4%)

Query: 12 LLLFSGGQDSSTCLSWALDRFDR--VETLSFDYGQRNKVELECRLCVR 57
          L+  SGG+DS   L    +   R  VE +  D+G R   + E  L  +
Sbjct: 25 LVAVSGGKDSLALLHLLKELGRRIEVEAVHVDHGLRGYSDQEAELVEK 72


>gnl|CDD|145913 pfam03016, Exostosin, Exostosin family.  The EXT family is a family
           of tumour suppressor genes. Mutations of EXT1 on 8q24.1,
           EXT2 on 11p11-13, and EXT3 on 19p have been associated
           with the autosomal dominant disorder known as hereditary
           multiple exostoses (HME). This is the most common known
           skeletal dysplasia. The chromosomal locations of other
           EXT genes suggest association with other forms of
           neoplasia. EXT1 and EXT2 have both been shown to encode
           a heparan sulphate polymerase with both D-glucuronyl
           (GlcA) and N-acetyl-D-glucosaminoglycan (GlcNAC)
           transferase activities. The nature of the defect in
           heparan sulphate biosynthesis in HME is unclear.
          Length = 289

 Score = 30.5 bits (69), Expect = 0.39
 Identities = 12/65 (18%), Positives = 23/65 (35%), Gaps = 10/65 (15%)

Query: 59  KIVELMPKWKDSLGEDHILPLAILGDISHSSLTKN--------VAMKIQDNNLPNTFVPG 110
           K +  +P W  S G DHI+  +       S+  +         + +          F PG
Sbjct: 86  KWLSSLPYWNRSGGRDHIIVNS--HPFGGSAFDRLPALNNPTILVVLAGGGFSERQFRPG 143

Query: 111 RNIIF 115
           +++  
Sbjct: 144 KDVPL 148


>gnl|CDD|144677 pfam01171, ATP_bind_3, PP-loop family.  This family of proteins
          belongs to the PP-loop superfamily.
          Length = 182

 Score = 27.6 bits (62), Expect = 2.9
 Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 16/75 (21%)

Query: 12 LLLFSGGQDSSTCLSWALDRF-----DRVETLSFDYGQRNKVELE----CRLCVRKKI-- 60
          L+  SGG D S  L + L +        +     D+G R + + E      LC +  I  
Sbjct: 3  LVAVSGGPD-SMALLYLLKKLKPKFGIDLTAAHVDHGLREESDREAQFVKELCRQLNIPL 61

Query: 61 ----VELMPKWKDSL 71
              V++  K   +L
Sbjct: 62 EVLRVDVAKKSGLNL 76


>gnl|CDD|146412 pfam03759, PRONE, PRONE (Plant-specific Rop nucleotide
          exchanger).  This is a functional guanine exchange
          factor (GEF) of plant Rho GTPase.
          Length = 360

 Score = 27.7 bits (62), Expect = 3.1
 Identities = 10/33 (30%), Positives = 17/33 (51%)

Query: 34 RVETLSFDYGQRNKVELECRLCVRKKIVELMPK 66
          R+E L+ +     + E++  L V   IVE +P 
Sbjct: 51 RLEPLAPEKKAMWRREMDWLLSVTDYIVEFVPS 83


>gnl|CDD|30167 cd01712, ThiI, ThiI is required for thiazole synthesis in the
           thiamine biosynthesis pathway. It belongs to the
           Adenosine Nucleotide Hydrolysis suoerfamily and
           predicted to bind to Adenosine nucleotide..
          Length = 177

 Score = 27.5 bits (61), Expect = 3.8
 Identities = 41/183 (22%), Positives = 60/183 (32%), Gaps = 34/183 (18%)

Query: 11  ALLLFSGGQDSSTCLSWALDRFDRVETLSFDYGQRNKVELECRLCVRKKIVELMPKWKDS 70
           AL L SGG DS       + R   V+ L F+ G     +       R+K+ +L  K    
Sbjct: 2   ALALLSGGIDSPVAAWLLMKRGIEVDALHFNSGPFTSEK------AREKVEDLARKLAR- 54

Query: 71  LGEDHILPLAILGDISHSSLTKNVAMKIQDNNLPNTFVPGRNIIFLVFAATLAYRLGITN 130
               H L + I        +                       +    A  LA  LG   
Sbjct: 55  YSPGHKLVVIIFTFFVQKEIYGYG-----KEKYRCILC---KRMMYRIAEKLAEELGADA 106

Query: 131 IVIGVCETDYSGYPDCRHDTI--RAIETAINLGMESHVT---VHTPLMWLKKYETWKLAQ 185
           IV G              +++   A +T  NL + S  T   +  PL+   K E   +A+
Sbjct: 107 IVTG--------------ESLGQVASQTLENLLVISSGTDLPILRPLIGFDKEEIIGIAR 152

Query: 186 DIG 188
            IG
Sbjct: 153 RIG 155


>gnl|CDD|73291 cd01984, AANH_like, Adenine nucleotide alpha hydrolases
          superfamily  including N type ATP PPases, ATP
          sulphurylases Universal Stress Response protein and
          electron transfer flavoprotein (ETF). The domain forms
          a apha/beta/apha fold which  binds to Adenosine
          nucleotide..
          Length = 86

 Score = 26.9 bits (59), Expect = 4.4
 Identities = 10/38 (26%), Positives = 14/38 (36%), Gaps = 1/38 (2%)

Query: 11 ALLLFSGGQDSSTCLSWALDRFDR-VETLSFDYGQRNK 47
           L+  SGG DSS  L  A        E ++       +
Sbjct: 1  ILVALSGGLDSSVLLHLAKRLKSGGPEVVALVVVAFVR 38


>gnl|CDD|176542 cd08600, GDPD_EcGlpQ_like, Glycerophosphodiester phosphodiesterase
           domain of Escherichia coli (GlpQ) and similar proteins. 
           This subfamily corresponds to the glycerophosphodiester
           phosphodiesterase domain (GDPD) present in Escherichia
           coli periplasmic glycerophosphodiester phosphodiesterase
           (GP-GDE, EC 3.1.4.46), GlpQ, and similar proteins.
           GP-GDE plays an essential role in the metabolic pathway
           of E. coli. It catalyzes the degradation of
           glycerophosphodiesters to produce
           sn-glycerol-3-phosphate (G3P) and the corresponding
           alcohols, which are major sources of carbon and
           phosphate. E. coli possesses two major G3P uptake
           systems: Glp and Ugp, which contain genes coding for two
           different GP-GDEs. GlpQ gene from the E. coli glp operon
           codes for a periplasmic phosphodiesterase GlpQ, which is
           the prototype of this family. GlpQ is a dimeric enzyme
           that hydrolyzes periplasmic glycerophosphodiesters, such
           as glycerophosphocholine (GPC),
           glycerophosphoethanolanmine (GPE),
           glycerophosphoglycerol (GPG), glycerophosphoinositol
           (GPI), and glycerophosphoserine (GPS), to the
           corresponding alcohols and G3P, which is subsequently
           transported into the cell through the GlpT transport
           system. Ca2+ is required for the enzymatic activity of
           GlpQ.  This family also includes a surface-exposed
           lipoprotein, protein D (HPD), from Haemophilus influenza
           Type b and nontypeable strains, which shows very high
           sequence similarity with E. coli GlpQ. HPD has been
           characterized as a human immunoglobulin D-binding
           protein with glycerophosphodiester phosphodiesterase
           activity. It can hydrolyze phosphatidylcholine from host
           membranes to produce free choline on the
           lipopolysaccharides on the surface of pathogenic
           bacteria.
          Length = 318

 Score = 27.0 bits (60), Expect = 5.0
 Identities = 9/37 (24%), Positives = 20/37 (54%), Gaps = 2/37 (5%)

Query: 35  VETLSFDYGQRNKVELECRLCVRKKIVELMP--KWKD 69
           ++T   +  +R K EL  ++ +  K+V+L+    W +
Sbjct: 177 LQTFDPNELKRIKNELLPKMGMDLKLVQLIAYTDWGE 213


>gnl|CDD|31794 COG1606, COG1606, ATP-utilizing enzymes of the PP-loop
          superfamily [General function prediction only].
          Length = 269

 Score = 26.8 bits (59), Expect = 5.1
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 7/70 (10%)

Query: 1  MNDIIKKAPSALLLFSGGQDSSTCLSWALDRF-DRVETLSFDYGQRNKVELE------CR 53
          +   IK+    ++ FSGG DSS     A +   D V  ++ D     + E+E        
Sbjct: 10 LKKAIKEKKKVVVAFSGGVDSSLLAKLAKEALGDNVVAVTVDSPYIPRREIEEAKNIAKE 69

Query: 54 LCVRKKIVEL 63
          + +R + +++
Sbjct: 70 IGIRHEFIKM 79


>gnl|CDD|32300 COG2117, COG2117, Predicted subunit of
          tRNA(5-methylaminomethyl-2-thiouridylate)
          methyltransferase, contains the PP-loop ATPase domain
          [Translation, ribosomal structure and biogenesis].
          Length = 198

 Score = 26.8 bits (59), Expect = 5.3
 Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 2/32 (6%)

Query: 13 LLFSGGQDSSTCLSWALDRFD-RVETLSFDYG 43
          +LFSGG+DSS   +  LD+    VE ++ ++G
Sbjct: 5  VLFSGGKDSSLA-ALILDKLGYEVELVTVNFG 35


>gnl|CDD|32285 COG2102, COG2102, Predicted ATPases of PP-loop superfamily
          [General function prediction only].
          Length = 223

 Score = 26.3 bits (58), Expect = 7.2
 Identities = 11/25 (44%), Positives = 14/25 (56%)

Query: 14 LFSGGQDSSTCLSWALDRFDRVETL 38
          L+SGG+DS   L  AL+    V  L
Sbjct: 6  LYSGGKDSFYALYLALEEGHEVVYL 30


>gnl|CDD|30178 cd01991, Asn_Synthase_B_C, The C-terminal domain of Asparagine
          Synthase B. This domain is always found associated
          n-terminal amidotransferase domain. Family members that
          contain this domain catalyse the conversion of
          aspartate to asparagine. Asparagine synthetase B
          catalyzes the assembly of asparagine from aspartate,
          Mg(2+)ATP, and glutamine. The three-dimensional
          architecture of the N-terminal domain of asparagine
          synthetase B is similar to that observed for glutamine
          phosphoribosylpyrophosphate amidotransferase while the
          molecular motif of the C-domain is reminiscent to that
          observed for GMP synthetase ..
          Length = 269

 Score = 26.2 bits (57), Expect = 7.2
 Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)

Query: 13 LLFSGGQDSSTCLSWALDRF--DRVETLSFDYGQRNKVELE 51
          +L SGG DSS  ++    R   + V+T S  +G     E E
Sbjct: 20 VLLSGGLDSSL-VAALAARLLPEPVKTFSIGFGFEGSDERE 59


>gnl|CDD|145198 pfam01902, ATP_bind_4, ATP-binding region.  This family of
          proteins probably binds ATP. This domain is about 200
          amino acids long with a strongly conserved motif SGGKD
          at the N terminus.In some members of this family, this
          domain is associated with pfam01042.
          Length = 219

 Score = 26.3 bits (58), Expect = 7.3
 Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 1/25 (4%)

Query: 14 LFSGGQDSSTCLSWALDRFDRVETL 38
          L+SGG+DS+  L WAL   + V  L
Sbjct: 6  LYSGGKDSNYALYWALKEIE-VPYL 29


>gnl|CDD|38147 KOG2936, KOG2936, KOG2936, Uncharacterized conserved protein
          [Function unknown].
          Length = 301

 Score = 26.4 bits (58), Expect = 7.3
 Identities = 10/59 (16%), Positives = 22/59 (37%), Gaps = 8/59 (13%)

Query: 21 SSTCLSWALDRFDR----VETLSFD----YGQRNKVELECRLCVRKKIVELMPKWKDSL 71
             C  W+ +  ++    V +LS        + + ++ E R+  RK  +  +      L
Sbjct: 15 EKNCSPWSKEYLNQKLSGVSSLSGPFSCKITEVSSIDGEARVNQRKGKLISLFDLSIEL 73


>gnl|CDD|147621 pfam05544, Pro_racemase, Proline racemase.  This family consists of
           proline racemase (EC 5.1.1.4) proteins which catalyse
           the interconversion of L- and D-proline in bacteria.
           This family also contains several similar eukaryotic
           proteins including a sequence with B-cell mitogenic
           properties which has been characterized as a
           co-factor-independent proline racemase.
          Length = 325

 Score = 26.1 bits (58), Expect = 8.4
 Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 7/38 (18%)

Query: 141 SGYPD-CRHDTIRAIETAINLGM------ESHVTVHTP 171
           SGY   C H+TI  +   +  G+      E+ + + TP
Sbjct: 77  SGYLPMCGHNTIGVVTVLLETGIVPPQEPETRLNLETP 114


>gnl|CDD|144131 pfam00420, Oxidored_q2, NADH-ubiquinone/plastoquinone
           oxidoreductase chain 4L. 
          Length = 96

 Score = 26.3 bits (59), Expect = 8.4
 Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 4/31 (12%)

Query: 112 NIIFLVFAATLAYRLG----ITNIVIGVCET 138
            ++ ++F+  LA  L     +T +V   CE 
Sbjct: 39  FLLLVLFSLLLADPLPQALPLTLLVFAACEA 69


  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
   0.322    0.138    0.438 

Gapped
Lambda     K      H
   0.267   0.0736    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,022,433
Number of extensions: 153143
Number of successful extensions: 385
Number of sequences better than 10.0: 1
Number of HSP's gapped: 378
Number of HSP's successfully gapped: 25
Length of query: 240
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 149
Effective length of database: 4,297,318
Effective search space: 640300382
Effective search space used: 640300382
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 (21.9 bits)
S2: 56 (25.3 bits)