RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780532|ref|YP_003064945.1| aminodeoxychorismate lyase
[Candidatus Liberibacter asiaticus str. psy62]
         (325 letters)



>gnl|CDD|145655 pfam02618, YceG, YceG-like family.  This family of proteins is
           found in bacteria. Proteins in this family are typically
           between 332 and 389 amino acids in length. This family
           was previously incorrectly annotated and names as
           aminodeoxychorismate lyase. The structure of YceG was
           solved by X-ray crystallography.
          Length = 287

 Score =  314 bits (807), Expect = 2e-86
 Identities = 118/292 (40%), Positives = 167/292 (57%), Gaps = 16/292 (5%)

Query: 36  TIFLVRNNMSLKEISKNLFNGGVIVNPYIFRYVTQFYFGSRGLKTGEYEIEKGSSMSQIA 95
            +  +    SL +I+  L   GVI +   FR   +       LK GEYE++ G S ++I 
Sbjct: 1   VVVTIPPGSSLSQIADILEEAGVIKSALAFRLYARLKGKDGNLKAGEYELKPGMSPAEIL 60

Query: 96  EKIMYGKVLMHSISFPEGFTVKQMARRLKDNPLLVGELPLE-----------LPLEGTLC 144
           EK++ GKV+ + ++ PEG T++Q+A RL     L  E  L            LPLEG L 
Sbjct: 61  EKLVSGKVVQYKVTIPEGLTLEQIAERLAKAGGLKKEEFLAFLEELGGELPSLPLEGYLF 120

Query: 145 PSTYNFPLGTHRSEILNQAMLKQKQVVDEVWEIRDVDHPIKSKEDLVILASIVEKETSRA 204
           P TY F  GT   EIL + + + ++V+ E W+ R    P+K+  + +ILASIVEKET  A
Sbjct: 121 PDTYEFDKGTSAEEILKRMVKRFEKVLAEAWQARAKGLPLKTPYEALILASIVEKETGVA 180

Query: 205 DERAHVASVFINRFSKSIRLQSDSTVIYGILEGDYDLTNRKISRSDFSIKTPYNSYLMNG 264
           +ER  +A VF NR  K +RLQSD TVIYG+ EGD      +++R D    +PYN+Y + G
Sbjct: 181 EERPKIAGVFYNRLKKGMRLQSDPTVIYGLGEGD-----GRLTRKDLRTDSPYNTYKIKG 235

Query: 265 LPPTAISNPGRLSLEAVAKPLHTEDLYFVGDGKGGHFFSTNFKDHTINVQKW 316
           LPP  I+NPG+ ++EA   P  T+ LYFV DG G H+FS    +H   V+K+
Sbjct: 236 LPPGPIANPGKAAIEAALNPAKTDYLYFVADGDGTHYFSKTLAEHNRAVRKY 287


>gnl|CDD|31747 COG1559, COG1559, Predicted periplasmic solute-binding protein
           [General function prediction only].
          Length = 342

 Score =  296 bits (759), Expect = 5e-81
 Identities = 130/334 (38%), Positives = 184/334 (55%), Gaps = 21/334 (6%)

Query: 2   LKFLIPLITIFLLAIG--VHIHVIRVYNATGPL-QNDTIFLVRNNMSLKEISKNLFNGGV 58
           LK L+ L+ + LL +G   +I ++  +  + PL +N     +    S+ EI   L    V
Sbjct: 9   LKTLLVLVLVLLLILGGVGYIGILYFFALSPPLGKNKKTVTIPPGSSVSEIGSELEKQKV 68

Query: 59  IVNPYIFRYVTQFYFGSRGLKTGEYEIEKGSSMSQIAEKIMYGKVLMHSISFPEGFTVKQ 118
           I N  +FR   ++   +  LK GEY +  G S + I + +  GK     ++ PEG+T+KQ
Sbjct: 69  IKNARVFRLYLKYNPAAGSLKAGEYRLRPGMSAADILKLLESGKSAQFKVTIPEGYTLKQ 128

Query: 119 MARRLKDNPLLVG--------ELPLELP------LEGTLCPSTYNFPLGTHRSEILNQAM 164
           +A++L + P+L G        E+   LP      LEG L P TY F  GT   +I+ + +
Sbjct: 129 IAKKLAEAPVLDGVLDGLAIAEIAARLPKLDKERLEGYLFPDTYEFTRGTSAEDIIKRMI 188

Query: 165 LKQKQVVDEVWEIRDVDHPIKSKEDLVILASIVEKETSRADERAHVASVFINRFSKSIRL 224
               + +DE WE R  D P K+  +L+ LASIVEKE +  +ER  +ASVF NR  K +RL
Sbjct: 189 KAMDKKLDEAWEKRADDLPGKTPYELLTLASIVEKEAAVDEERPKIASVFYNRLKKGMRL 248

Query: 225 QSDSTVIYGILEGDYDLTNRKISRSDFSIKTPYNSYLMNGLPPTAISNPGRLSLEAVAKP 284
           QSD TVIYG+           IS+ D  I TPYN+Y + GLPPT I+NPG  +L A   P
Sbjct: 249 QSDPTVIYGL----GKSHEGAISKKDLEIDTPYNTYKIKGLPPTPIANPGLAALRAALNP 304

Query: 285 LHTEDLYFVGDGKGGHFFSTNFKDHTINVQKWRK 318
             T+ LYFV DG GGH FS   ++H  NV+K+RK
Sbjct: 305 AKTDYLYFVADGDGGHVFSKTLEEHNANVEKYRK 338


>gnl|CDD|153433 cd08010, yceG_like, proteins similar to Escherichia coli yceG.  The
           gene product of Escherichia coli yceG has been
           erroneously annotated as an aminodeoxychorismate lyase.
           Its overexpression has been reported to cause abnormal
           biofilm architecture, and it has been reported to be
           part of a putative five-gene operon. It might function
           as a periplasmic solute-binding protein. The family also
           includes Streptomyces caeruleus NovB, an uncharacterized
           member of the novobiocin biosynthetic gene cluster.
          Length = 245

 Score =  243 bits (622), Expect = 5e-65
 Identities = 98/250 (39%), Positives = 140/250 (56%), Gaps = 19/250 (7%)

Query: 78  LKTGEYEIEKGSSMSQIAEKIMYGKVLMHSISFPEGFTVKQMARRLKDNP---------L 128
           LK GEYE+  G S+++I E++  GK     ++ PEG+T+KQ+A+ L              
Sbjct: 1   LKAGEYELSPGMSLAEILERLTSGKSAQVKVTIPEGYTLKQIAKALSKAGGLSDAEFLAA 60

Query: 129 LVGELPLEL-----PLEGTLCPSTYNFPLGTHRSEILNQAMLKQKQVVDEVWEIRDVDHP 183
           L     + L     PLEG L P TY FP G    ++L + + +  +V++E W  R    P
Sbjct: 61  LKDPAFILLGDPKYPLEGYLFPDTYEFPKGATPEDLLKRMVKRFDKVLEEAWAAR-AGLP 119

Query: 184 IKSKEDLVILASIVEKETSRADERAHVASVFINRFSKSIRLQSDSTVIYGILEGDYDLTN 243
             +  +++ LASIVEKE    +ER  +A VF NR  K +RLQSD TVIYG+     +   
Sbjct: 120 GLTPYEVLTLASIVEKEAGLPEERPLIAGVFYNRLKKGMRLQSDPTVIYGL----GEHKK 175

Query: 244 RKISRSDFSIKTPYNSYLMNGLPPTAISNPGRLSLEAVAKPLHTEDLYFVGDGKGGHFFS 303
             I++ D  I +PYN+Y + GLPP  I+NPG  +LEA   P  T+ LYFV DG G H+FS
Sbjct: 176 GTITKKDLEIDSPYNTYKIKGLPPGPIANPGLAALEAALNPAKTDYLYFVADGTGTHYFS 235

Query: 304 TNFKDHTINV 313
             +++H  NV
Sbjct: 236 KTYEEHNKNV 245


>gnl|CDD|146135 pfam03343, SART-1, SART-1 family.  SART-1 is a protein involved in
           cell cycle arrest and pre-mRNA splicing. It has been
           shown to be a component of U4/U6 x U5 tri-snRNP complex
           in human, Schizosaccharomyces pombe and Saccharomyces
           cerevisiae. SART-1 is a known tumour antigen in a range
           of cancers recognized by T cells.
          Length = 577

 Score = 29.7 bits (67), Expect = 1.2
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 3/49 (6%)

Query: 163 AMLKQKQVVDEVWEIRDVDHPIKSKEDLVILASI---VEKETSRADERA 208
           A+LK + ++ +    R+    +K KE L +LA I   +E+E  R D + 
Sbjct: 454 ALLKSRGLLKKNQLERERREFLKEKERLKLLAEIRERIERERDRNDGKY 502


>gnl|CDD|33687 COG3899, COG3899, Predicted ATPase [General function prediction
           only].
          Length = 849

 Score = 28.0 bits (62), Expect = 3.5
 Identities = 9/50 (18%), Positives = 16/50 (32%)

Query: 173 EVWEIRDVDHPIKSKEDLVILASIVEKETSRADERAHVASVFINRFSKSI 222
               I  +     +   +  LA+ ++K      E    A+   NRF    
Sbjct: 279 WQCSIASLGILATTDAVVEFLAARLQKLPGTTREVLKAAACIGNRFDLDT 328


>gnl|CDD|30888 COG0542, ClpA, ATPases with chaperone activity, ATP-binding subunit
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 786

 Score = 28.0 bits (62), Expect = 3.9
 Identities = 10/18 (55%), Positives = 16/18 (88%)

Query: 115 TVKQMARRLKDNPLLVGE 132
           T++ ++RR K+NP+LVGE
Sbjct: 182 TIQILSRRTKNNPVLVGE 199


>gnl|CDD|163680 cd07942, DRE_TIM_LeuA, Mycobacterium tuberculosis LeuA3 and related
           proteins, N-terminal catalytic TIM barrel domain.
           Alpha-isopropylmalate synthase (LeuA), a key enzyme in
           leucine biosynthesis, catalyzes the first committed step
           in the pathway, converting acetyl-CoA and
           alpha-ketoisovalerate to alpha-isopropyl malate and CoA.
            Although the reaction catalyzed by LeuA is similar to
           that of the Arabidopsis thaliana IPMS1 protein, the two
           fall into phylogenetically distinct families within the
           same superfamily.  LeuA has and N-terminal TIM barrel
           catalytic domain, a helical linker domain, and a
           C-terminal regulatory domain.  LeuA forms a homodimer in
           which the linker domain of one monomer sits over the
           catalytic domain of the other, inserting residues into
           the active site that may be important for catalysis.
           Homologs of LeuA are found in bacteria as well as fungi.
            This family includes alpha-isopropylmalate synthases I
           (LEU4) and II (LEU9) from Saccharomyces cerevisiae.
           This family 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 = 284

 Score = 27.5 bits (62), Expect = 4.6
 Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 4/33 (12%)

Query: 17  GVHIHVIRVYNATGPLQNDTIFLVRNNMSLKEI 49
           G    ++ +YNAT PLQ   +F      S +EI
Sbjct: 90  GAKKAIVHLYNATSPLQRRVVF----GKSKEEI 118


  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
   0.320    0.138    0.398 

Gapped
Lambda     K      H
   0.267   0.0785    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,912,449
Number of extensions: 204601
Number of successful extensions: 453
Number of sequences better than 10.0: 1
Number of HSP's gapped: 443
Number of HSP's successfully gapped: 16
Length of query: 325
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 231
Effective length of database: 4,232,491
Effective search space: 977705421
Effective search space used: 977705421
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: 57 (25.6 bits)