RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780936|ref|YP_003065349.1| hypothetical protein
CLIBASIA_04175 [Candidatus Liberibacter asiaticus str. psy62]
         (182 letters)



>gnl|CDD|31621 COG1432, COG1432, Uncharacterized conserved protein [Function
           unknown].
          Length = 181

 Score =  125 bits (314), Expect = 1e-29
 Identities = 72/185 (38%), Positives = 95/185 (51%), Gaps = 12/185 (6%)

Query: 1   MFDPREKIALFIDGANLYASS-KALGFDIDYRKLLKAFRSRAIVIRAYYYTTVVGDPEQQ 59
                ++IALFIDG NLYAS  K LG  IDYRKLL+    R  +  A  YT   GD E Q
Sbjct: 1   TPIMVDRIALFIDGKNLYASQRKNLGILIDYRKLLRKELKRIYLYEAAPYTAEYGDIEIQ 60

Query: 60  FSPLHPLLDWLHYNGFQVVAKVAKEFTENCGRKRVKSSMDVELAVDAFEQS--EGLEHLV 117
              +      L  +GF VV      FT+    +  K  +DVELAVDA E +  + ++ +V
Sbjct: 61  --EVFLNEYELRSDGFTVVTSNLDGFTD---LRITKGDVDVELAVDAMELADKKNVDTIV 115

Query: 118 IFSGDGCFTTLVAALQRKVKKVTIVSTVLSDPSMASDQLRRQADYFMDLAYLKNEIARDP 177
           +FSGDG F  LV A + K K+V +         M S  LR  ADY++DL  L+  I    
Sbjct: 116 LFSGDGDFIPLVEAARDKGKRVEVAGIE----PMTSSDLRNAADYYIDLKSLEEAILLPE 171

Query: 178 DEDKK 182
            E ++
Sbjct: 172 IEREE 176


>gnl|CDD|145225 pfam01936, DUF88, Protein of unknown function DUF88.  This highly
           conserved bacterial protein has no known function. The
           alignment contains many conserved aspartates, suggesting
           an enzymatic function such as an endonuclease or
           glycosyl hydrolase (Bateman A pers. obs).
          Length = 140

 Score =  105 bits (264), Expect = 7e-24
 Identities = 51/162 (31%), Positives = 73/162 (45%), Gaps = 25/162 (15%)

Query: 7   KIALFIDGANLYASSKALGFDIDYRKLLKAFRSRAIVIRAYYYTTVVGDPEQQFSPLHPL 66
           ++A+FIDG N    +      IDYRK+L+  +S   V+RA  Y       +     L   
Sbjct: 1   RVAVFIDGENCPVPAG-----IDYRKVLEEIKSGGEVVRARAYG------DWSDPKLRKF 49

Query: 67  LDWLHYNGFQVVAKVAKEFTENCGRKRVKSSMDVELAVDAFEQSE--GLEHLVIFSGDGC 124
            D L   G  V  K           K  K+++DV LAVDA E +     +  V+ SGDG 
Sbjct: 50  PDALSSTGIPVQHKPLT--------KSGKNAVDVGLAVDALELAYDNNPDTFVLVSGDGD 101

Query: 125 FTTLVAALQRKVKKVTIVSTVLSDPSMASDQLRRQADYFMDL 166
           F  L+  L+ + K+V ++          SD L   AD F+DL
Sbjct: 102 FAPLLERLRERGKRVEVLGA----EPSTSDALINAADRFIDL 139


>gnl|CDD|100118 cd06167, LabA_like, LabA_like proteins. A well conserved group of
           bacterial proteins with no defined function. LabA, a
           member from Synechococcus elongatus PCC 7942, has been
           shown to play a role in cyanobacterial circadian timing.
           It is required for negative feedback regulation of the
           autokinase/autophosphatase KaiC, a central component of
           the circadian clock system. In particular, LabA seems
           necessary for KaiC-dependent repression of gene
           expression..
          Length = 149

 Score = 99.3 bits (248), Expect = 5e-22
 Identities = 54/164 (32%), Positives = 80/164 (48%), Gaps = 18/164 (10%)

Query: 6   EKIALFIDGANLYASSKALG-FDIDYRKLLKAFRSRAIVIRAYYYTTVVGDPEQQFSPLH 64
           +++A+FIDG NLY S + LG    DYRKLL+  R    ++ A  Y        Q+     
Sbjct: 1   KRVAVFIDGENLYYSLRDLGGKRFDYRKLLEFLRDGGEIVLARAYGNWTSPERQR----- 55

Query: 65  PLLDWLHYNGFQVVAKVAKEFTENCGRKRVKSSMDVELAVDAFEQS--EGLEHLVIFSGD 122
             LD L   GF+ + K  +           K  +DV LA+DA E +    ++ +V+ SGD
Sbjct: 56  GFLDALRRLGFEPIQKPLRTR------GSGKKGVDVALAIDALELAYKRRIDTIVLVSGD 109

Query: 123 GCFTTLVAALQRKVKKVTIVSTVLSDPSMASDQLRRQADYFMDL 166
             F  LV  L+   K+V +V       +  S +LR+ AD F+DL
Sbjct: 110 SDFVPLVERLRELGKRVIVVGF----EAKTSRELRKAADRFIDL 149


>gnl|CDD|31400 COG1207, GlmU, N-acetylglucosamine-1-phosphate uridyltransferase
           (contains nucleotidyltransferase and I-patch
           acetyltransferase domains) [Cell envelope biogenesis,
           outer membrane].
          Length = 460

 Score = 26.7 bits (59), Expect = 3.5
 Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 24/85 (28%)

Query: 90  GRKRVKSSMDVELAVDAFEQSEGL------------------EHLVIFSGDGCFTT---- 127
           G ++V+ ++     V+   Q E L                    +++  GD    T    
Sbjct: 55  GAEQVREALAERDDVEFVLQEEQLGTGHAVLQALPALADDYDGDVLVLYGDVPLITAETL 114

Query: 128 --LVAALQRKVKKVTIVSTVLSDPS 150
             L+AA        T+++  L DP+
Sbjct: 115 EELLAAHPAHGAAATVLTAELDDPT 139


>gnl|CDD|112056 pfam03225, Viral_Hsp90, Viral heat shock protein Hsp90 homologue. 
          Length = 511

 Score = 26.9 bits (60), Expect = 3.6
 Identities = 6/28 (21%), Positives = 10/28 (35%)

Query: 142 VSTVLSDPSMASDQLRRQADYFMDLAYL 169
           V  +L +P +  + LR     F      
Sbjct: 313 VVEILDEPVLVGEYLRYVESVFEVSNSN 340


>gnl|CDD|145242 pfam01960, ArgJ, ArgJ family.  Members of the ArgJ family catalyse
           the first EC:2.3.1.1 and fifth steps EC:2.3.1.35 in
           arginine biosynthesis.
          Length = 387

 Score = 25.9 bits (58), Expect = 7.0
 Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 3/44 (6%)

Query: 2   FDPREKIALFIDGANLYASSKALGFDIDYRKLLKAFRSRAIVIR 45
           FDP +K+ +   G  +  + + + FD +        +   I IR
Sbjct: 317 FDP-DKVDISFGGVLVVENGEPVDFDEE--AASAILKEDEITIR 357


>gnl|CDD|132921 cd07038, TPP_PYR_PDC_IPDC_like, Pyrimidine (PYR) binding domain of
           pyruvate decarboxylase (PDC), indolepyruvate
           decarboxylase (IPDC) and related proteins.  Thiamine
           pyrophosphate (TPP family), pyrimidine (PYR) binding
           domain of  pyruvate decarboxylase (PDC) and
           indolepyruvate decarboxylase (IPDC) subfamily. The PYR
           domain is found in many key metabolic enzymes which use
           TPP (also known as thiamine diphosphate) as a cofactor.
           TPP binds in the cleft formed by a PYR domain and a PP
           domain. The PYR domain, binds the aminopyrimidine ring
           of TPP, the PP domain binds the diphosphate residue. The
           PYR and PP domains have a common fold, but do not share
           strong sequence conservation. The PP domain is not
           included in this sub-family. Most TPP-dependent enzymes
           have the PYR and PP domains on the same subunit although
           these domains can be alternatively arranged in the
           primary structure. TPP-dependent enzymes are
           multisubunit proteins, the smallest catalytic unit being
           a dimer-of-active sites, for many the active sites lie
           between PP and PYR domains on different subunits. PDC
           catalyzes the conversion of pyruvate to acetaldehyde and
           CO2 in alcoholic fermentation. IPDC plays a role in the
           indole-3-pyruvic acid (IPA) pathway in plants and
           various plant-associated bacteria, it catalyzes the
           decarboxylation of IPA to IAA. Also belonging to this
           group is Mycobacterium tuberculosis alpha-keto acid
           decarboxylase (MtKDC) which participates in amino acid
           degradation via the Ehrlich pathway, and Lactococcus
           lactis branched-chain keto acid decarboxylase (KdcA) an
           enzyme identified as being involved in cheese ripening,
           which exhibits a very broad substrate range in the
           decarboxylation and carboligation reactions.
          Length = 162

 Score = 25.9 bits (58), Expect = 7.4
 Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 11/54 (20%)

Query: 108 EQSEG--LEHLVIFSGDGCFTTLVAALQRKV-KKVTIVSTVLSDPSMASDQLRR 158
            Q+ G  L H +   GDG F         K+ +++T  +  L+DP  A++++ R
Sbjct: 99  AQASGLLLHHTL---GDGDFDV-----FLKMFEEITCAAARLTDPENAAEEIDR 144


>gnl|CDD|36582 KOG1368, KOG1368, KOG1368, Threonine aldolase [Amino acid transport
           and metabolism].
          Length = 384

 Score = 25.3 bits (55), Expect = 8.7
 Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 2/38 (5%)

Query: 5   REKIALFIDGANLYASSKALGFDIDYRKLLKAFRSRAI 42
           R  + L +DGA ++ ++ A G  +  +K+  AF S +I
Sbjct: 186 RHGLKLHMDGARIFNAAVASGVPV--KKICSAFDSVSI 221


>gnl|CDD|29437 cd00363, PFK, Phosphofructokinase, a key regulatory enzyme in
           glycolysis, catalyzes the phosphorylation of
           fructose-6-phosphate to fructose-1,6-biphosphate. The
           members belong to PFK family that includes ATP- and
           pyrophosphate (PPi)- dependent phosphofructokinases.
           Some members evolved by gene duplication and thus have a
           large C-terminal/N-terminal extension comprising a
           second PFK domain. Generally, ATP-PFKs are allosteric
           homotetramers, and  PPi-PFKs are dimeric and
           nonallosteric except for plant PPi-PFKs which are
           allosteric heterotetramers..
          Length = 338

 Score = 25.6 bits (56), Expect = 8.7
 Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 10/59 (16%)

Query: 68  DWLHYNGFQVVAKVAKEFTENCGRKRVKSSMDVELAVDAFEQSEGLEHLVIFSGDGCFT 126
           D ++  G  + +   KEF    GR +   ++          +  G++ LV+  GDG +T
Sbjct: 58  DIINRGGTIIGSARCKEFRTEEGRAKAAENL----------KKHGIDALVVIGGDGSYT 106


  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    0.137    0.393 

Gapped
Lambda     K      H
   0.267   0.0784    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,234,173
Number of extensions: 110721
Number of successful extensions: 311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 296
Number of HSP's successfully gapped: 20
Length of query: 182
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 94
Effective length of database: 4,362,145
Effective search space: 410041630
Effective search space used: 410041630
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: 54 (24.5 bits)