RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781041|ref|YP_003065454.1| succinate dehydrogenase
protein, cytochrome b subunit [Candidatus Liberibacter asiaticus str.
psy62]
         (129 letters)



>gnl|CDD|48060 cd03499, SQR_TypeC_SdhC, Succinate:quinone oxidoreductase (SQR)
           Type C subfamily, Succinate dehydrogenase C (SdhC)
           subunit; composed of bacterial SdhC and eukaryotic large
           cytochrome b binding (CybL) proteins. SQR catalyzes the
           oxidation of succinate to fumarate coupled to the
           reduction of quinone to quinol. Members of this family
           reduce high potential quinones such as ubiquinone. SQR
           is also called succinate dehydrogenase or Complex II,
           and is part of the citric acid cycle and the aerobic
           respiratory chain.  SQR is composed of a flavoprotein
           catalytic subunit, an iron-sulfur protein and one or two
           hydrophobic transmembrane subunits. Proteins in this
           subfamily are classified as Type C SQRs because they
           contain two transmembrane subunits and one heme group.
           The heme and quinone binding sites reside in the
           transmembrane subunits. The SdhC or CybL protein is one
           of the  two transmembrane subunits of bacterial and
           eukaryotic SQRs. The two-electron oxidation of succinate
           in the flavoprotein active site is coupled to the
           two-electron reduction of quinone in the membrane anchor
           subunits via electron transport through FAD and three
           iron-sulfur centers. The reversible reduction of quinone
           is an essential feature of respiration, allowing
           transfer of electrons between respiratory complexes..
          Length = 117

 Score = 96.7 bits (241), Expect = 2e-21
 Identities = 41/117 (35%), Positives = 70/117 (59%)

Query: 8   RPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGS 67
           RPLSPHL IYR   T  +SI+HRITG  ++LG P++++W     +   +  S+   +   
Sbjct: 1   RPLSPHLTIYRPPLTAILSILHRITGVALFLGLPLLLWWLLASLSSPESFESVSALLGSW 60

Query: 68  VFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILTVLIVWI 124
           + ++ LF  TWA+ +H+L GIR+LIWD+   L+ K   +     ++ S++  +++ I
Sbjct: 61  LGKLVLFGLTWALFYHLLNGIRHLIWDLGKGLELKTVYKSGYAVLVLSVVLTVLLGI 117


>gnl|CDD|144645 pfam01127, Sdh_cyt, Succinate dehydrogenase/Fumarate reductase
           transmembrane subunit.  This family includes a
           transmembrane protein from both the Succinate
           dehydrogenase and Fumarate reductase complexes.
          Length = 122

 Score = 69.3 bits (170), Expect = 3e-13
 Identities = 36/120 (30%), Positives = 60/120 (50%), Gaps = 3/120 (2%)

Query: 6   NNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSS---LRC 62
            NRPLSPHL +YR      +SI+HRITG  + +    ++ W   +A      S    +  
Sbjct: 3   KNRPLSPHLGLYRAHLGTILSILHRITGVALAVLLIHLLLWLLLLALLLGPDSYARVVVA 62

Query: 63  YMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILTVLIV 122
           ++      + L L   A+ +H   G+R+LIWDV   L+ K A +   + +  S++  L++
Sbjct: 63  WLSSPFKLILLLLLLLALFYHAANGLRHLIWDVGKGLELKTARKTGLLVLALSLVLTLLL 122


>gnl|CDD|32192 COG2009, SdhC, Succinate dehydrogenase/fumarate reductase,
           cytochrome b subunit [Energy production and conversion].
          Length = 132

 Score = 60.7 bits (147), Expect = 1e-10
 Identities = 34/122 (27%), Positives = 60/122 (49%), Gaps = 4/122 (3%)

Query: 8   RPLSPHLQIYRLIPTMFVSIVHRITGSV----VYLGTPVVVFWFFCIANGEHTLSSLRCY 63
           RP+SPHLQIYR   TM+ SI+HRI+G +    +++   +   W    A+           
Sbjct: 3   RPVSPHLQIYRPPITMYASILHRISGVILAFFLFVHILLASSWLAGSASFNAAFEFYHAL 62

Query: 64  MDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILTVLIVW 123
           +   + ++ L     A+++H L GIR+L+WD    L+ K         +  S +T+ ++ 
Sbjct: 63  LGSFIVKLVLLGLVLALLYHGLNGIRHLLWDFGYGLELKGVGYTGAALVFFSAVTLTLLL 122

Query: 124 II 125
            +
Sbjct: 123 WV 124


>gnl|CDD|35670 KOG0449, KOG0449, KOG0449, Succinate dehydrogenase, cytochrome b
           subunit [Carbohydrate transport and metabolism].
          Length = 168

 Score = 58.0 bits (140), Expect = 8e-10
 Identities = 32/94 (34%), Positives = 49/94 (52%), Gaps = 2/94 (2%)

Query: 3   SIKNNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFC-IANGEHTLSSLR 61
           + ++NRPLSPHL IY+   T  +SI HRI+G V+  G  +V       + +   T+S + 
Sbjct: 44  NQRSNRPLSPHLTIYQPQLTWMLSIFHRISGVVLAGGVWLVGVSGLLGMGDITATVSKVY 103

Query: 62  -CYMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWD 94
              +  +V     F   +   +H   GIR+LIWD
Sbjct: 104 QLKLPTAVQWPAKFSIAYPFAYHTGNGIRHLIWD 137


>gnl|CDD|48054 cd03493, SQR_QFR_TM, Succinate:quinone oxidoreductase (SQR) and
           Quinol:fumarate reductase (QFR) family, transmembrane
           subunits; SQR catalyzes the oxidation of succinate to
           fumarate coupled to the reduction of quinone to quinol,
           while QFR catalyzes the reverse reaction. SQR, also
           called succinate dehydrogenase or Complex II, is part of
           the citric acid cycle and the aerobic respiratory chain,
           while QFR is involved in anaerobic respiration with
           fumarate as the terminal electron acceptor. SQRs may
           reduce either high or low potential quinones while QFRs
           oxidize only low potential quinols. SQR and QFR share a
           common subunit arrangement, composed of a flavoprotein
           catalytic subunit, an iron-sulfur protein and one or two
           hydrophobic transmembrane subunits. The structural
           arrangement allows efficient electron transfer between
           the catalytic subunit, through iron-sulfur centers, and
           the transmembrane subunit(s) containing the electron
           donor/acceptor (quinol or quinone). The reversible
           reduction of quinone is an essential feature of
           respiration, allowing the transfer of electrons between
           respiratory complexes. SQRs and QFRs can be classified
           into five types (A-E) according to the number of their
           hydrophobic subunits and heme groups. This
           classification is consistent with the characteristics
           and phylogeny of the catalytic and iron-sulfur subunits.
           Type E proteins, e.g. non-classical archael SQRs,
           contain atypical transmembrane subunits and are not
           included in this hierarchy. The heme and quinone binding
           sites reside in the transmembrane subunits. Although
           succinate oxidation and fumarate reduction are carried
           out by separate enzymes in most organisms, some
           bifunctional enzymes that exhibit both SQR and QFR
           activities exist..
          Length = 98

 Score = 41.9 bits (98), Expect = 6e-05
 Identities = 24/98 (24%), Positives = 49/98 (50%)

Query: 27  IVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLG 86
           I+HRITG  + L  P+ +     +  G +  + +  ++   + ++   L   A+++H L 
Sbjct: 1   ILHRITGVALLLFLPLHLLGLLALLGGPYAFAEVVAFLSSPLGKLLYLLLLLALLYHALN 60

Query: 87  GIRYLIWDVSLCLDKKIATQMAKINIIASILTVLIVWI 124
           GIR+LIWD    L+ K+   +    +  S+L  +++  
Sbjct: 61  GIRHLIWDYGKGLELKLRKALGYAVLALSVLLTVLLLF 98


>gnl|CDD|39649 KOG4448, KOG4448, KOG4448, Uncharacterized conserved protein,
           contains phosphotyrosine interaction (PI) domain
           [Function unknown].
          Length = 374

 Score = 27.4 bits (60), Expect = 1.2
 Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 1/35 (2%)

Query: 29  HRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCY 63
           HRIT      G P V  W +    G+   S LRC+
Sbjct: 127 HRITYCRAPSGYPKVFCWIYR-HEGKQLKSELRCH 160


>gnl|CDD|48062 cd03501, SQR_TypeA_SdhC_like, Succinate:quinone oxidoreductase
           (SQR) Type A subfamily, Succinate dehydrogenase C
           (SdhC)-like subunit; SQR catalyzes the oxidation of
           succinate to fumarate coupled to the reduction of
           quinone to quinol. Members of this subfamily reduce low
           potential quinones such as menaquinone and
           thermoplasmaquinone.  SQR is also called succinate
           dehydrogenase or Complex II, and is part of the citric
           acid cycle and the aerobic respiratory chain. SQR is
           composed of a flavoprotein catalytic subunit, an
           iron-sulfur protein and one or two hydrophobic
           transmembrane subunits. Members of this subfamily are
           similar to the Thermoplasma acidophilum SQR and are
           classified as Type A because they contain two
           transmembrane subunits as well as two heme groups.
           Although there are no structures available for this
           subfamily, the presence of two hemes has been proven
           spectroscopically for T. acidophilum.  The two membrane
           anchor subunits are similar to the SdhD and SdhC
           subunits of bacterial SQRs, which contain heme and
           quinone binding sites. The two-electron oxidation of
           succinate in the flavoprotein active site is coupled to
           the two-electron reduction of quinone in the membrane
           anchor subunits via electron transport through FAD and
           three iron-sulfur centers. The reversible reduction of
           quinone is an essential feature of respiration, allowing
           transfer of electrons between respiratory complexes..
          Length = 101

 Score = 25.5 bits (56), Expect = 4.7
 Identities = 22/101 (21%), Positives = 43/101 (42%)

Query: 23  MFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIH 82
           M+  ++HRITG V+     + V     +  G  T +++       +F++  F    AV+ 
Sbjct: 1   MWAWVLHRITGVVILFYLFLHVLDLSSLRRGPETYNAVIATYKSPIFKLGEFGLVAAVVF 60

Query: 83  HMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILTVLIVW 123
           H L GIR ++ D      +        + ++  +L V   +
Sbjct: 61  HALNGIRLILVDFGSGGPRYQRQLFYIVLVLTVVLIVAAGY 101


>gnl|CDD|145714 pfam02705, K_trans, K+ potassium transporter.  This is a family of
           K+ potassium transporters that are conserved across
           phyla, having both bacterial (KUP), yeast (HAK), and
           plant (AtKT) sequences as members.
          Length = 731

 Score = 25.4 bits (56), Expect = 5.1
 Identities = 12/32 (37%), Positives = 16/32 (50%)

Query: 20  IPTMFVSIVHRITGSVVYLGTPVVVFWFFCIA 51
           I  +  SI H  T  V +L  P+V+ W   IA
Sbjct: 177 ILVLLFSIQHFGTDKVGFLFAPIVLLWLLSIA 208


>gnl|CDD|32325 COG2142, SdhD, Succinate dehydrogenase, hydrophobic anchor subunit
           [Energy production and conversion].
          Length = 117

 Score = 25.1 bits (55), Expect = 5.7
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 2/82 (2%)

Query: 27  IVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMDGSVFEVCLFLYTWAVIHHMLG 86
           ++ R+T   V L   V+   +F +     T ++   ++    ++V L L   A + H   
Sbjct: 18  LLQRVTA--VILVLLVIWHLYFLLTWLNATYAAWVAFLANPFWKVFLLLLLVAALIHAWN 75

Query: 87  GIRYLIWDVSLCLDKKIATQMA 108
           G+R +I D       ++A Q+ 
Sbjct: 76  GLRVIIEDYIKPEKLRLALQIL 97


>gnl|CDD|146268 pfam03537, DUF297, TM1410 hypothetical-related protein. 
          Length = 203

 Score = 25.0 bits (55), Expect = 6.3
 Identities = 8/26 (30%), Positives = 10/26 (38%)

Query: 52  NGEHTLSSLRCYMDGSVFEVCLFLYT 77
           NG   L +L   +DG V E       
Sbjct: 150 NGFELLPALAPLVDGVVNESLFQGVD 175


>gnl|CDD|146315 pfam03612, EIIBC-GUT_N, Sorbitol phosphotransferase enzyme II
           N-terminus. 
          Length = 182

 Score = 24.5 bits (54), Expect = 8.6
 Identities = 7/17 (41%), Positives = 9/17 (52%)

Query: 100 DKKIATQMAKINIIASI 116
            KKI  Q  K  ++A I
Sbjct: 146 SKKITEQSDKGGLLAKI 162


>gnl|CDD|38948 KOG3744, KOG3744, KOG3744, Uncharacterized conserved protein
           [Function unknown].
          Length = 311

 Score = 24.5 bits (53), Expect = 8.6
 Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 8/75 (10%)

Query: 24  FVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMD--------GSVFEVCLFL 75
           +V+ VH    +V  L T V +++ FC+         L   +           ++    F 
Sbjct: 140 YVTTVHCTHEAVYPLYTIVFIYYAFCLVLMMLLRPLLVKKIACGGKSDRFKPIYAALYFF 199

Query: 76  YTWAVIHHMLGGIRY 90
               VIH + GG+ Y
Sbjct: 200 PILTVIHAVGGGLLY 214


>gnl|CDD|38820 KOG3614, KOG3614, KOG3614, Ca2+/Mg2+-permeable cation channels
           (LTRPC family) [Inorganic ion transport and metabolism,
           Signal transduction mechanisms].
          Length = 1381

 Score = 24.5 bits (53), Expect = 9.0
 Identities = 4/15 (26%), Positives = 8/15 (53%)

Query: 37  YLGTPVVVFWFFCIA 51
           +   P+V FW   ++
Sbjct: 787 FYSAPIVKFWLNVLS 801


  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
   0.333    0.144    0.468 

Gapped
Lambda     K      H
   0.267   0.0737    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,654,153
Number of extensions: 82873
Number of successful extensions: 298
Number of sequences better than 10.0: 1
Number of HSP's gapped: 293
Number of HSP's successfully gapped: 35
Length of query: 129
Length of database: 6,263,737
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,470,190
Effective search space: 205628740
Effective search space used: 205628740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 52 (23.8 bits)