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)