RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780472|ref|YP_003064885.1| cytochrome o ubiquinol oxidase
subunit III [Candidatus Liberibacter asiaticus str. psy62]
         (210 letters)



>gnl|CDD|131889 TIGR02842, CyoC, cytochrome o ubiquinol oxidase, subunit III.
           Cytochrome o terminal oxidase complex is the component
           of the aerobic respiratory chain which reacts with
           oxygen, reducing it to water with the concomitant
           transport of 4 protons across the membrane. Also known
           as the cytochrome bo complex, cytochrome o ubiquinol
           oxidase contains four subunits, two heme b cofactors and
           a copper atom which is believed to be the oxygen active
           site. This complex is structurally related to the
           cytochrome caa3 oxidases which utilize cytochrome c as
           the reductant and contain heme a cofactors, as well as
           the intermediate form aa3 oxidases which also react
           directly with quinones as the reductant.
          Length = 180

 Score =  234 bits (598), Expect = 2e-62
 Identities = 103/181 (56%), Positives = 130/181 (71%), Gaps = 1/181 (0%)

Query: 30  TYLGFWIYLMSDCLMFAVFFVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSLSCS 89
           T  GFW+YLMSDC++FA  F TYAVL  N A GP+  ++FD+  + V T +LLLSS++  
Sbjct: 1   TIFGFWLYLMSDCILFATLFATYAVLSNNTAGGPSGKEIFDLPFVLVETFLLLLSSITFG 60

Query: 90  FAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSFFALV 149
           FAMLA   K      + WL +T   G+ FI MEIYEF HLI+    P RSAFLS+FF LV
Sbjct: 61  FAMLAMNKKNKK-MVILWLAITFLLGLGFIGMEIYEFYHLIAEGNGPDRSAFLSAFFTLV 119

Query: 150 GLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICVFSFVYLMGV 209
           G HGLHV  GLIW+ V++IQ+ K GL   N+RRL CLS+FWHFLD++WICVF+FVYL+GV
Sbjct: 120 GTHGLHVTSGLIWIIVMIIQVYKYGLTKINRRRLACLSLFWHFLDIVWICVFTFVYLLGV 179

Query: 210 V 210
           +
Sbjct: 180 L 180


>gnl|CDD|182628 PRK10663, PRK10663, cytochrome o ubiquinol oxidase subunit III;
           Provisional.
          Length = 204

 Score =  208 bits (530), Expect = 1e-54
 Identities = 96/178 (53%), Positives = 126/178 (70%), Gaps = 1/178 (0%)

Query: 33  GFWIYLMSDCLMFAVFFVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSLSCSFAM 92
           GFWIYLMSDC++F++ F TYAVL    A GP   D+F++  + V T +LL SS++   A 
Sbjct: 28  GFWIYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSITYGMAA 87

Query: 93  LASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSFFALVGLH 152
           +A   K    + +SWL +T  FG  FI MEIYEF HLI     P RS FLS+FFALVG H
Sbjct: 88  IA-MYKNNKSQVISWLALTFLFGAGFIGMEIYEFHHLIVEGMGPDRSGFLSAFFALVGTH 146

Query: 153 GLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICVFSFVYLMGVV 210
           GLHV  GLIW+ VL++Q+ ++GL S N+ R++CLS+FWHFLD++WICVF+ VYLMG +
Sbjct: 147 GLHVTSGLIWMAVLMVQVARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYLMGAM 204


>gnl|CDD|131943 TIGR02897, QoxC, cytochrome aa3 quinol oxidase, subunit III.  This
           family (QoxC) encodes subunit III of the aa3-type
           quinone oxidase, one of several bacterial terminal
           oxidases. This complex couples oxidation of reduced
           quinones with the reduction of molecular oxygen to water
           and the pumping of protons to form a proton gradient
           utilized for ATP production. aa3-type oxidases contain
           two heme a cofactors as well as copper atoms in the
           active site.
          Length = 190

 Score =  137 bits (346), Expect = 2e-33
 Identities = 70/180 (38%), Positives = 108/180 (60%), Gaps = 2/180 (1%)

Query: 32  LGFWIYLMSDCLMFAVFFVTYAVL-GKNYAAGPAPIDVFDISGIFVSTIVLLLSSLSCSF 90
           LGFWI+L ++  +FA  F TY VL      AG  P ++F++  + + T +LL SS +C  
Sbjct: 12  LGFWIFLGAEIALFATLFATYLVLQHGGDYAGKMPAELFELPLVLIMTFLLLFSSFTCGI 71

Query: 91  AMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSFFALVG 150
           A +    K      + W+++T   G  F+  EIYEFAH  S    PQ  ++ SSFF L+G
Sbjct: 72  A-IYEMRKENQKLMMFWMIITLLLGAGFVGFEIYEFAHYASEGVTPQIGSYWSSFFVLLG 130

Query: 151 LHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICVFSFVYLMGVV 210
            HG HV  G++W   L+IQI ++GL      ++  +S++WHFLD++W+ +F+ VYL+G+V
Sbjct: 131 THGCHVTLGIVWAICLLIQIQRRGLTPYTAPKVFIVSLYWHFLDVVWVFIFTAVYLIGMV 190


>gnl|CDD|177845 PLN02194, PLN02194, cytochrome-c oxidase.
          Length = 265

 Score = 50.4 bits (120), Expect = 3e-07
 Identities = 52/190 (27%), Positives = 90/190 (47%), Gaps = 17/190 (8%)

Query: 29  GTYLGFWIYLMSDCLMFAVFF--VTYAVLGKNYAAG----PAPIDVFDISGI-FVSTIVL 81
           G   G  ++++S+ + F  FF   +++ L      G    P  I+V D   I F++T +L
Sbjct: 81  GPRYGSILFIVSEVMFFFAFFWASSHSSLAPAVEIGGIWPPKGIEVLDPWEIPFLNTPIL 140

Query: 82  LLSSLSCSFA---MLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQR 138
             S  + ++A   +LA   KR ++  V+ +L+   F   F  ME Y+    IS       
Sbjct: 141 PSSGAAVTWAHHAILAGKEKRAVYALVATVLLALVFTG-FQGMEYYQAPFTIS------D 193

Query: 139 SAFLSSFFALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWI 198
           S + S+FF   G HG HV  G ++L +  I+     L   +       + +WHF+D++W+
Sbjct: 194 SIYGSTFFLATGFHGFHVIIGTLFLIICGIRQYLGHLTKEHHVGFEAAAWYWHFVDVVWL 253

Query: 199 CVFSFVYLMG 208
            +F  +Y  G
Sbjct: 254 FLFVSIYWWG 263


>gnl|CDD|180549 PRK06381, PRK06381, threonine synthase; Validated.
          Length = 319

 Score = 28.1 bits (63), Expect = 1.5
 Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 4/48 (8%)

Query: 122 EIYEFAHLI-SMEAVPQRSAFLSSFFALVGLHGLHVFFGLIWLFVLVI 168
           E+ ++A L+  ME +   +A  +S  AL  L       G+    V VI
Sbjct: 270 EMVKYAELLRRMEGL---NALPASASALAALVKYLKKNGVNDNVVAVI 314


>gnl|CDD|180094 PRK05454, PRK05454, glucosyltransferase MdoH; Provisional.
          Length = 696

 Score = 28.0 bits (63), Expect = 2.0
 Identities = 21/108 (19%), Positives = 39/108 (36%), Gaps = 15/108 (13%)

Query: 73  GIFVSTIVLLLSS--LSCSFAMLASATKR-----LIHKTVSWLLVTAFFGMIFIIMEIYE 125
            +F +T+VLL     L     +L    +R      +   +S LL T F  ++  I  ++ 
Sbjct: 455 ALFAATMVLLFLPKLLGL-LLVLLDPKRRRAFGGALRLLLSVLLETLFSALLAPIRMLFH 513

Query: 126 FAHLISMEA-------VPQRSAFLSSFFALVGLHGLHVFFGLIWLFVL 166
              ++S+           +R    + +      HG H   GL+     
Sbjct: 514 TRFVVSILLGRDVGWNSQRRDDGSTPWGEAFRRHGWHTLLGLVLAAGA 561


>gnl|CDD|181596 PRK08961, PRK08961, bifunctional aspartate kinase/diaminopimelate
           decarboxylase protein; Provisional.
          Length = 861

 Score = 27.7 bits (62), Expect = 2.0
 Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 2/30 (6%)

Query: 129 LISMEAVP--QRSAFLSSFFALVGLHGLHV 156
           L+SME +   Q+  FL+  F L   HGL V
Sbjct: 324 LVSMETIGMWQQVGFLADVFTLFKKHGLSV 353


>gnl|CDD|130176 TIGR01106, ATPase-IIC_X-K, sodium or proton efflux -- potassium
           uptake antiporter, P-type ATPase, alpha subunit.
           Sequences from Blastocladiella emersonii (GP|6636502,
           GP|6636502 and PIR|T43025), C. elegans (GP|2315419,
           GP|6671808 and PIR|T31763) and Drosophila melanogaster
           (GP|7291424) score below trusted cutoff, apparently due
           to long branch length (excessive divergence from the
           last common ancestor) as evidenced by a phylogenetic
           tree. Experimental evidence is needed to determine
           whether these sequences represent ATPases with conserved
           function. Aside from fragments, other sequences between
           trusted and noise appear to be bacterial ATPases of
           unclear lineage, but most likely calcium pumps.
          Length = 997

 Score = 27.8 bits (62), Expect = 2.2
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 9/71 (12%)

Query: 119 IIMEIYEFAHLISMEAVPQRSAFLS-SFFALVGLHGLHVFFGLIWLFVLVIQILKKGLIS 177
           I +EI  F H+I+  AV     FL  SFF L  + G      +I+L  +++  + +GL++
Sbjct: 258 IAIEIEHFIHIITGVAV-----FLGVSFFILSLILGYTWLEAVIFLIGIIVANVPEGLLA 312

Query: 178 GNQRRLICLSM 188
                 +CL++
Sbjct: 313 ---TVTVCLTL 320


>gnl|CDD|178648 PLN03100, PLN03100, Permease subunit of ER-derived-lipid
           transporter; Provisional.
          Length = 292

 Score = 25.5 bits (56), Expect = 9.8
 Identities = 10/22 (45%), Positives = 14/22 (63%)

Query: 108 LLVTAFFGMIFIIMEIYEFAHL 129
           LL ++F GM+F I  + EF  L
Sbjct: 93  LLTSSFVGMVFTIQFVREFTKL 114


  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
   0.335    0.146    0.465 

Gapped
Lambda     K      H
   0.267   0.0744    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,431,024
Number of extensions: 214926
Number of successful extensions: 921
Number of sequences better than 10.0: 1
Number of HSP's gapped: 905
Number of HSP's successfully gapped: 95
Length of query: 210
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 121
Effective length of database: 4,071,361
Effective search space: 492634681
Effective search space used: 492634681
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 55 (24.9 bits)