RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780161|ref|YP_003064574.1| phytoene synthase protein
[Candidatus Liberibacter asiaticus str. psy62]
         (299 letters)



>gnl|CDD|178239 PLN02632, PLN02632, phytoene synthase.
          Length = 334

 Score = 37.0 bits (86), Expect = 0.006
 Identities = 34/130 (26%), Positives = 53/130 (40%), Gaps = 9/130 (6%)

Query: 98  PFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEH-YAFRISSR--LIHLA 154
                L   V ++ L  Q F DMIE    D    S ++     + Y + ++    L+ + 
Sbjct: 123 MLDAALADTVSKFPLDIQPFRDMIEGMRMD-LVKSRYENFDELYLYCYYVAGTVGLMSVP 181

Query: 155 TMILDSERYSASLRVIKYAGIAQFIG-QLICQLPI---HYHRGQLYFPLDILGAVGLDRE 210
            M +  E   AS   +  A +A  I  QL   L        RG++Y P D L   GL  E
Sbjct: 182 VMGIAPE-SKASTESVYNAALALGIANQLTNILRDVGEDARRGRVYLPQDELAQFGLTDE 240

Query: 211 SFLSGQNSDR 220
              +G+ +D+
Sbjct: 241 DIFAGKVTDK 250


>gnl|CDD|163278 TIGR03465, HpnD, squalene synthase HpnD.  The genes of this family
           are often found in the same genetic locus with
           squalene-hopene cyclase genes, and are never associated
           with genes for the metabolism of phytoene. In the
           organisms Zymomonas mobilis and Bradyrhizobium japonicum
           these genes have been characterized as squalene
           synthases (farnesyl-pyrophosphate ligases). Often, these
           genes appear in tandem with the HpnC gene which appears
           to have resulted from an ancient gene duplication event.
           Presumably these proteins form a heteromeric complex,
           but this has not yet been experimentally demonstrated.
          Length = 266

 Score = 36.1 bits (84), Expect = 0.012
 Identities = 43/191 (22%), Positives = 77/191 (40%), Gaps = 14/191 (7%)

Query: 36  YLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRDMRLQWWKDIFESSTKGLIAES 95
           Y    L PP  R +++ LY F  E+  + D   +P     +L WW+   +    G     
Sbjct: 9   YYGMRLLPPERRRAMTALYAFCREVDDIVDEDSDPEVAQAKLAWWRAEIDRLYAG---AP 65

Query: 96  ISPFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLAT 155
             P +  L    R++DLP + FL++I+    D       D  + + Y  R++  +  L+ 
Sbjct: 66  SHPVARALADPARRFDLPQEDFLEVIDGMEMDLEQTRYPDFAELDLYCDRVAGAVGRLSA 125

Query: 156 MIL-----DSERYSASLRVIKYAGIAQFIGQLICQLPIHYHRGQLYFPLDILGAVGLDRE 210
            I       +  Y+  L      G A  +  ++  +     RG++Y P + L   G+   
Sbjct: 126 RIFGATDARTLEYAHHL------GRALQLTNILRDVGEDARRGRIYLPAEELQRFGVPAA 179

Query: 211 SFLSGQNSDRI 221
             L G+ S  +
Sbjct: 180 DILEGRYSPAL 190


>gnl|CDD|163277 TIGR03464, HpnC, squalene synthase HpnC.  This family of genes are
           members of a superfamily (pfam00494) of phytoene and
           squalene synthases which catalyze the head-t0-head
           condensation of polyisoprene pyrophosphates. The genes
           of this family are often found in the same genetic locus
           with squalene-hopene cyclase genes, and are never
           associated with genes for the metabolism of phytoene. In
           the organisms Zymomonas mobilis and Bradyrhizobium
           japonicum these genes have been characterized as
           squalene synthases (farnesyl-pyrophosphate ligases).
           Often, these genes appear in tandem with the HpnD gene
           which appears to have resulted from an ancient gene
           duplication event. Presumably these proteins form a
           heteromeric complex, but this has not yet been
           experimentally demonstrated.
          Length = 266

 Score = 35.0 bits (81), Expect = 0.022
 Identities = 34/138 (24%), Positives = 53/138 (38%), Gaps = 39/138 (28%)

Query: 98  PFSVELLSIVRQYDLPNQYFLDMIEAHFFDSYNDSIFDCKQFEHYAFRISSRLIHLATM- 156
           P  V L   V+++ LP + FLD+++A                    FR    +   AT  
Sbjct: 69  PVFVALARTVQRHGLPIEPFLDLLDA--------------------FRQDVVVTRYATWA 108

Query: 157 -ILDSERYSAS------LRVIKYAGIAQF-IGQLIC---QLPIH-------YHRGQLYFP 198
            +LD  RYSA+      L +   +      +   IC   QL          Y +G++Y P
Sbjct: 109 ELLDYCRYSANPVGRLVLDLYGASDPENVALSDAICTALQLINFWQDVGVDYRKGRVYLP 168

Query: 199 LDILGAVGLDRESFLSGQ 216
            D L   G+  E   +G+
Sbjct: 169 RDDLARFGVSEEDLAAGR 186


>gnl|CDD|180546 PRK06370, PRK06370, mercuric reductase; Validated.
          Length = 463

 Score = 30.2 bits (69), Expect = 0.68
 Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 15/53 (28%)

Query: 130 NDSIF---DCKQ---FEHYA---FRISSRLIHLATMILDSERYSASLRVIKYA 173
           N  I+   DC     F H A    RI      +A  +LD  R   S R++ YA
Sbjct: 301 NPGIYAAGDCNGRGAFTHTAYNDARI------VAANLLDGGRRKVSDRIVPYA 347


>gnl|CDD|163472 TIGR03760, ICE_TraI_Pfluor, integrating conjugative element
           relaxase, PFL_4751 family.  Members of this protein
           family are the TraI putative relaxases required for
           transfer by a subclass of integrating conjugative
           elements (ICE) as found in Pseudomonas fluorescens Pf-5,
           and understood from study of two related ICE, SXT and
           R391. This model represents the N-terminal domain. Note
           that no homology is detected to the similarly named TraI
           relaxase of the F plasmid.
          Length = 218

 Score = 28.4 bits (64), Expect = 2.3
 Identities = 7/31 (22%), Positives = 14/31 (45%)

Query: 169 VIKYAGIAQFIGQLICQLPIHYHRGQLYFPL 199
            + YA +   +G+L   + +    GQ + P 
Sbjct: 107 AVFYAALLHDLGKLAVDIEVELQDGQRWHPW 137


>gnl|CDD|185492 PTZ00166, PTZ00166, DNA polymerase delta catalytic subunit;
           Provisional.
          Length = 1054

 Score = 28.1 bits (63), Expect = 3.0
 Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 3/39 (7%)

Query: 12  KEEKIFSR--DSLFVLRNLRDIDYDRYLACLLSPPLYRI 48
           K    + R  D L+VL N   ID   YL   +  PL RI
Sbjct: 886 KGAPQYERAEDPLYVLENNIPIDTQYYLDQ-IKNPLLRI 923


>gnl|CDD|178063 PLN02444, PLN02444, HMP-P synthase.
          Length = 642

 Score = 27.6 bits (61), Expect = 3.6
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 252 PAFIPVSITESVLKHAQNHGF 272
           P F  + ITE V K+A+ HG+
Sbjct: 573 PKFCSMKITEDVRKYAEEHGY 593


>gnl|CDD|185191 PRK15291, PRK15291, fimbrial protein StgD; Provisional.
          Length = 355

 Score = 27.4 bits (60), Expect = 4.3
 Identities = 14/40 (35%), Positives = 21/40 (52%)

Query: 35 RYLACLLSPPLYRISLSFLYYFHTELMRVRDTARNPITRD 74
          R L  L S   Y++  S L +F +    V  TAR+P++ D
Sbjct: 57 RDLETLTSSESYKVGCSCLTHFSSTFREVYYTARSPLSID 96


>gnl|CDD|149890 pfam08963, DUF1878, Protein of unknown function (DUF1878).  This
           domain is found in a set of hypothetical bacterial
           proteins.
          Length = 113

 Score = 26.2 bits (58), Expect = 9.3
 Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 5/30 (16%)

Query: 175 IAQFIGQLICQLPIH-----YHRGQLYFPL 199
           +A F GQL  +L +H      H   L+ PL
Sbjct: 72  LALFAGQLNEKLEVHETIFALHAQGLFKPL 101


  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
   0.328    0.141    0.423 

Gapped
Lambda     K      H
   0.267   0.0729    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,936,526
Number of extensions: 320137
Number of successful extensions: 776
Number of sequences better than 10.0: 1
Number of HSP's gapped: 773
Number of HSP's successfully gapped: 19
Length of query: 299
Length of database: 5,994,473
Length adjustment: 93
Effective length of query: 206
Effective length of database: 3,984,929
Effective search space: 820895374
Effective search space used: 820895374
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 57 (25.7 bits)