RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780618|ref|YP_003065031.1| F0F1 ATP synthase subunit
delta [Candidatus Liberibacter asiaticus str. psy62]
         (186 letters)



>gnl|CDD|143970 pfam00213, OSCP, ATP synthase delta (OSCP) subunit.  The ATP D
           subunit from E. coli is the same as the OSCP subunit
           which is this family. The ATP D subunit from metazoa are
           found in family pfam00401.
          Length = 171

 Score =  134 bits (341), Expect = 1e-32
 Identities = 63/166 (37%), Positives = 98/166 (59%), Gaps = 1/166 (0%)

Query: 13  GRYSHSLFGVSNEEGVLDIVSDDISRLEALLMESADLRFFIHNPLFSMKDRRSVIDDLVK 72
            RY+ +LF ++ E+G LD V +D+  L+A+L E+ DLR F+ NPL S +++++++  +  
Sbjct: 3   RRYAKALFELAKEKGSLDEVEEDLEALKAVLAENPDLREFLSNPLISAEEKKALLKAVFG 62

Query: 73  DAHFCAITANFLRILVANGRLSVLPAIIKSFRAVCMYYRNEVMAFVRAFSGLSLLQQNKL 132
                 +T NFL++L  NGRLS+LP I + F  +   +R  V A V +   LS  Q   L
Sbjct: 63  G-KLSELTKNFLKLLAENGRLSLLPEIAEEFEELYNEHRGIVEATVTSAVPLSEEQLKAL 121

Query: 133 GECLEKIVGKTVILDVMEDSALMGGFIVEIGAHQIDASLRTQLLKL 178
              LEK  GK V L+   D +L+GG +V +G   ID S+R +L +L
Sbjct: 122 KAALEKKTGKKVKLETKVDPSLIGGVVVRVGDKVIDGSVRGKLERL 167


>gnl|CDD|31056 COG0712, AtpH, F0F1-type ATP synthase, delta subunit (mitochondrial
           oligomycin sensitivity protein) [Energy production and
           conversion].
          Length = 178

 Score =  112 bits (281), Expect = 7e-26
 Identities = 58/173 (33%), Positives = 96/173 (55%), Gaps = 1/173 (0%)

Query: 6   ALFSDVPGRYSHSLFGVSNEEGVLDIVSDDISRLEALLMESADLRFFIHNPLFSMKDRRS 65
           +  S V  RY+ +LF ++ E+G L+ V ++++ L  +L  S  L+  + +P  S +D++ 
Sbjct: 2   SELSTVARRYAKALFELAEEKGQLEEVEEELTFLAEILKNSPKLKQLLSSPAVSAEDKKE 61

Query: 66  VIDDLVKDAHFCAITANFLRILVANGRLSVLPAIIKSFRAVCMYYRNEVMAFVRAFSGLS 125
           ++  + K      +  NFLR+L  N RL++LP I++ F  +    R  V A V +   LS
Sbjct: 62  LLISIFKK-IGDPLLQNFLRLLAENKRLNLLPEILEEFLKLAAESRGIVEAEVTSAFELS 120

Query: 126 LLQQNKLGECLEKIVGKTVILDVMEDSALMGGFIVEIGAHQIDASLRTQLLKL 178
             Q  KL   LEK  GK V L+   D +L+GG I+++G   ID S+R +L +L
Sbjct: 121 DEQLTKLEAKLEKKFGKKVKLNNKIDPSLIGGLIIKVGDEVIDGSVRGKLKRL 173


>gnl|CDD|36875 KOG1662, KOG1662, KOG1662, Mitochondrial F1F0-ATP synthase, subunit
           OSCP/ATP5 [Energy production and conversion].
          Length = 210

 Score =  110 bits (276), Expect = 2e-25
 Identities = 59/176 (33%), Positives = 101/176 (57%), Gaps = 2/176 (1%)

Query: 11  VPGRYSHSLFGVSNEEGVLDIVSDDISRLEALLMESADLRFFIHNPLFSMKDRRSVIDDL 70
           + GRY+ +L+  + +   LD V  D+++LE +L        F+ NP  + + +++ IDD+
Sbjct: 33  LEGRYATALYSAAVKNSKLDQVETDLNKLEQVLKTDPKFAQFVLNPTLTREKKKTAIDDI 92

Query: 71  VKDAHFCAITANFLRILVANGRLSVLPAIIKSFRAVCMYYRNEVMAFVRAFSGLSLLQQN 130
           V+      +T NFL +L  NGRL+ L  I+K+F  +   +R EV   V +   L   Q  
Sbjct: 93  VEKLKLAPLTKNFLNLLAENGRLNNLTEIVKAFETLMNAHRGEVKVEVTSAEPLDAKQLK 152

Query: 131 KLGECLEKIV--GKTVILDVMEDSALMGGFIVEIGAHQIDASLRTQLLKLGCILKE 184
           +L + L+KI+  GK + ++   D +++GG IVEIG   +D S++T+L KL  +L+E
Sbjct: 153 QLEKALQKILGGGKKLKVENKVDPSIIGGLIVEIGDKYVDMSIKTRLQKLNKLLEE 208


>gnl|CDD|177042 CHL00119, atpD, ATP synthase CF1 delta subunit; Validated.
          Length = 184

 Score = 85.8 bits (213), Expect = 7e-18
 Identities = 50/166 (30%), Positives = 89/166 (53%), Gaps = 2/166 (1%)

Query: 15  YSHSLFGVSNEEGVLDIVSDDISRLEALLMESADLRFFIHNPLFSMKDRRSVIDDLVKDA 74
           Y+ +L   + E+ +++ ++ DI  +   L ES +L+ F+ NPL S   ++ VI       
Sbjct: 12  YAEALLEFAKEKNIMEQITADIQLILTFLNESPELKKFLANPLISKNAKKEVIKKTFGS- 70

Query: 75  HFCAITANFLRILVANGRLSVLPAIIKSFRAVCMYYRNEVMAFVRAFSGLSLLQQNKLGE 134
                T  FL +LV  GR+++L AII+ +  +     +  +A V     LS  Q+  L E
Sbjct: 71  QINENTLKFLMVLVDRGRIALLDAIIEKYLELVYKLASIKIAEVSTAVPLSSAQEEALIE 130

Query: 135 CLEKIVG-KTVILDVMEDSALMGGFIVEIGAHQIDASLRTQLLKLG 179
            L+++   K + L +  D +L+GGF+++IG+  ID S++ QL +L 
Sbjct: 131 KLKEMTNAKEIKLVITVDPSLIGGFLIKIGSKVIDTSIKGQLKQLA 176


>gnl|CDD|107204 cd01561, CBS_like, CBS_like: This subgroup includes Cystathionine
          beta-synthase (CBS) and Cysteine synthase. CBS is a
          unique heme-containing enzyme that catalyzes a
          pyridoxal 5'-phosphate (PLP)-dependent condensation of
          serine and homocysteine to give cystathionine.
          Deficiency of CBS leads to homocystinuria, an inherited
          disease of sulfur metabolism characterized by increased
          levels of the toxic metabolite homocysteine. Cysteine
          synthase on the other hand catalyzes the last step of
          cysteine biosynthesis.  This subgroup also includes an
          O-Phosphoserine sulfhydrylase found in
          hyperthermophilic archaea which produces L-cysteine
          from sulfide and the more thermostable
          O-phospho-L-serine..
          Length = 291

 Score = 26.3 bits (59), Expect = 4.7
 Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 4/29 (13%)

Query: 47 ADLRFFIHNPLFSMKDR--RSVIDDLVKD 73
          A L FF  NP  S+KDR    +I+D  K 
Sbjct: 21 AKLEFF--NPGGSVKDRIALYMIEDAEKR 47


>gnl|CDD|31508 COG1317, FliH, Flagellar biosynthesis/type III secretory pathway
           protein [Cell motility and secretion / Intracellular
           trafficking and secretion].
          Length = 234

 Score = 26.5 bits (58), Expect = 4.9
 Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)

Query: 136 LEKIVGKTVILDVMEDSALMGGFIVEIGAHQIDASLRTQLLKL 178
              ++G  + L V + +   GG I+E     IDASL TQL  L
Sbjct: 179 ELSLLGWRLEL-VADPALSPGGCIIETEFGIIDASLDTQLAAL 220


>gnl|CDD|111867 pfam03023, MVIN, MviN-like protein.  Deletion of the mviN virulence
           gene in Salmonella enterica serovar. Typhimurium greatly
           reduces virulence in a mouse model of typhoid-like
           disease. Open reading frames encoding homologues of MviN
           have since been identified in a variety of bacteria,
           including pathogens and non-pathogens and
           plant-symbionts. In the nitrogen-fixing symbiont
           Rhizobium tropici, mviN is required for motility. The
           MviM protein is predicted to be membrane-associated.
          Length = 452

 Score = 26.5 bits (59), Expect = 5.1
 Identities = 18/58 (31%), Positives = 23/58 (39%), Gaps = 3/58 (5%)

Query: 68  DDLVKDAHFCAI-TANFLRILVANGRLSVLPAIIKSFRAVCMYYRNEVMAFVRAFSGL 124
              + DA   A    N LR L A G  S   A +  F  +    ++E   FVR  S L
Sbjct: 7   AGPLADAFNVAFRIPNLLRRLFAEGAFSS--AFVPVFAELKQADKDEAAEFVRRVSTL 62


  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
   0.327    0.141    0.401 

Gapped
Lambda     K      H
   0.267   0.0742    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,158,652
Number of extensions: 109596
Number of successful extensions: 335
Number of sequences better than 10.0: 1
Number of HSP's gapped: 329
Number of HSP's successfully gapped: 16
Length of query: 186
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 98
Effective length of database: 4,362,145
Effective search space: 427490210
Effective search space used: 427490210
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: 54 (24.6 bits)