RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781042|ref|YP_003065455.1| succinate dehydrogenase hydrophobic membrane anchor [Candidatus Liberibacter asiaticus str. psy62] (130 letters) >gnl|CDD|32325 COG2142, SdhD, Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion]. Length = 117 Score = 85.6 bits (212), Expect = 3e-18 Identities = 33/117 (28%), Positives = 61/117 (52%) Query: 9 LGRVRGMGSAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVAS 68 L RG GSA+ G+ ++ QR TA+ + +I+ + F + + +A Y V+ L+N Sbjct: 1 LMVARGSGSARYGSHDWLLQRVTAVILVLLVIWHLYFLLTWLNATYAAWVAFLANPFWKV 60 Query: 69 IMGLGTISISVHMQLGMQVIIEDYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLLKIA 125 + L ++ +H G++VIIEDYI L++ + ++L ++ F L +A Sbjct: 61 FLLLLLVAALIHAWNGLRVIIEDYIKPEKLRLALQILLVLALVLTGVYGTFVLWGVA 117 >gnl|CDD|48056 cd03495, SQR_TypeC_SdhD_like, Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory Complex II SdhD subunit of the only eukaryotic member, Reclinomonas americana. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. It 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. E. coli SQR is classified as Type C SQRs because it contains two transmembrane subunits and one heme group. The SdhD and SdhC subunits are membrane anchor subunits containing 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 = 100 Score = 77.9 bits (192), Expect = 8e-16 Identities = 30/100 (30%), Positives = 55/100 (55%) Query: 23 GHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQ 82 H+ QR TA+A +P +++F+ A Y ++V+ L++ A ++ L +S H + Sbjct: 1 HHWWAQRVTAVALVPLVLWFVFSVALLLGASYAEVVAWLAHPFNAILLILTLVSAFYHAR 60 Query: 83 LGMQVIIEDYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLL 122 LGMQV+IEDY+H L++ + F + +F++L Sbjct: 61 LGMQVVIEDYVHSEGLRLALIIAVKLFAIATAAAGIFAIL 100 >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 = 41.2 bits (97), Expect = 7e-05 Identities = 24/119 (20%), Positives = 45/119 (37%), Gaps = 5/119 (4%) Query: 3 FDMRSSLGRVRGMGSAKDGTGHFIKQRFTAIAN----IPFIIFFIAFFIKYGDAPYEQI- 57 L G+ A GT I R T +A I +++ + + G Y ++ Sbjct: 1 MRKNRPLSPHLGLYRAHLGTILSILHRITGVALAVLLIHLLLWLLLLALLLGPDSYARVV 60 Query: 58 VSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHYRLLKIMFLFMNSCFVLLLIIF 116 V+ LS+ ++ L +++ H G++ +I D LK L L++ Sbjct: 61 VAWLSSPFKLILLLLLLLALFYHAANGLRHLIWDVGKGLELKTARKTGLLVLALSLVLT 119 >gnl|CDD|48055 cd03494, SQR_TypeC_SdhD, Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the high potential quinine, 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. Members of this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. SdhD and SdhC are the two transmembrane proteins of bacterial SQRs. They 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 = 99 Score = 37.4 bits (87), Expect = 0.001 Identities = 20/100 (20%), Positives = 48/100 (48%), Gaps = 4/100 (4%) Query: 25 FIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLG 84 ++ QR TA+ + IF + F + YE + S++ + L +++ +H +G Sbjct: 2 WLVQRVTAVIMALYTIFLVGFLLASPPLTYEAWSGLFSSLWMKIFTLLALLALLLHAWIG 61 Query: 85 MQVIIEDYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLLKI 124 + I+ DY+ L+++ + ++L++ L ++I Sbjct: 62 LWDILTDYVKPAGLRLLLQVL----IILVLFGYLIWGIQI 97 >gnl|CDD|36299 KOG1083, KOG1083, KOG1083, Putative transcription factor ASH1/LIN-59 [Transcription]. Length = 1306 Score = 32.4 bits (73), Expect = 0.034 Identities = 14/45 (31%), Positives = 18/45 (40%) Query: 17 SAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVL 61 S+K+ H K R T P+ F F Y PY Q +L Sbjct: 667 SSKNDHKHRQKHRHTFYHEGPYPSIFRINFNHYYTVPYIQYDPLL 711 >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 = 29.9 bits (67), Expect = 0.22 Identities = 18/94 (19%), Positives = 40/94 (42%), Gaps = 2/94 (2%) Query: 28 QRFTAIANIPFIIFFIAFFI--KYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGM 85 R T +A + F+ + + G + ++V+ LS+ + L +++ H G+ Sbjct: 3 HRITGVALLLFLPLHLLGLLALLGGPYAFAEVVAFLSSPLGKLLYLLLLLALLYHALNGI 62 Query: 86 QVIIEDYIHYRLLKIMFLFMNSCFVLLLIIFCLF 119 + +I DY LK+ + L +++ L Sbjct: 63 RHLIWDYGKGLELKLRKALGYAVLALSVLLTVLL 96 >gnl|CDD|146346 pfam03661, UPF0121, Uncharacterized protein family (UPF0121). Uncharacterized integral membrane protein family. Length = 248 Score = 27.0 bits (60), Expect = 1.6 Identities = 17/37 (45%), Positives = 23/37 (62%), Gaps = 1/37 (2%) Query: 86 QVIIEDYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLL 122 Q+I+ED HY L ++FL + LL +F LFSLL Sbjct: 87 QLILEDSCHYLLYSLIFLNSYPVTMSLLPVF-LFSLL 122 >gnl|CDD|143966 pfam00209, SNF, Sodium:neurotransmitter symporter family. Length = 506 Score = 26.5 bits (59), Expect = 2.5 Identities = 16/77 (20%), Positives = 28/77 (36%), Gaps = 7/77 (9%) Query: 40 IFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTISISVHMQLGMQVIIEDYIHYRLLK 99 I+ F Y + V +A+A + GL + LG + K Sbjct: 392 IYVFTLFDYYAASFGLLFVVFFECIAIAWVYGLDRFYDDIKEMLGFRP-------GLFWK 444 Query: 100 IMFLFMNSCFVLLLIIF 116 + + F++ +L L IF Sbjct: 445 LCWKFVSPLILLFLFIF 461 >gnl|CDD|36764 KOG1551, KOG1551, KOG1551, Uncharacterized conserved protein [Function unknown]. Length = 371 Score = 25.8 bits (56), Expect = 3.4 Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 1/34 (2%) Query: 49 YGD-APYEQIVSVLSNVAVASIMGLGTISISVHM 81 YG P EQI+ +L V MG TI V + Sbjct: 152 YGQRVPEEQIIHMLEYVTDLFKMGRATIQEFVKL 185 >gnl|CDD|147489 pfam05328, CybS, CybS. This family consists of several eukaryotic succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial precursor (CybS) proteins. SDHD encodes the small subunit (cybS) of cytochrome b in succinate-ubiquinone oxidoreductase (mitochondrial complex II). Mitochondrial complex II is involved in the Krebs cycle and in the aerobic electron transport chain. It contains four proteins. The catalytic core consists of a flavoprotein and an iron-sulfur protein; these proteins are anchored to the mitochondrial inner membrane by the large subunit of cytochrome b (cybL) and cybS, which together comprise the heme-protein cytochrome b. Mutations in the SDHD gene can lead to hereditary paraganglioma, characterized by the development of benign, vascularized tumours in the head and neck. Length = 107 Score = 25.6 bits (57), Expect = 3.5 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 17/84 (20%) Query: 17 SAKDGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSNVAVASIMGLGTIS 76 + G+ H+ +R A+ +P F +P + ++L+ + Sbjct: 2 NKSHGSYHWTFERILAVGLLPLTP--APFL---AGSPSPVMDAILA------------AA 44 Query: 77 ISVHMQLGMQVIIEDYIHYRLLKI 100 + +H G Q I DYI R+ Sbjct: 45 LLLHCHWGFQSCIIDYIPKRVYGK 68 >gnl|CDD|38872 KOG3668, KOG3668, KOG3668, Phosphatidylinositol transfer protein [Lipid transport and metabolism, Signal transduction mechanisms]. Length = 269 Score = 25.6 bits (56), Expect = 3.8 Identities = 7/29 (24%), Positives = 12/29 (41%) Query: 84 GMQVIIEDYIHYRLLKIMFLFMNSCFVLL 112 GMQ +E++IH ++ F Sbjct: 203 GMQTKVENFIHKVERRVFTRAHRQAFCWQ 231 >gnl|CDD|177187 MTH00129, COX2, cytochrome c oxidase subunit II; Provisional. Length = 230 Score = 24.7 bits (54), Expect = 7.0 Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 4/38 (10%) Query: 82 QLGMQ----VIIEDYIHYRLLKIMFLFMNSCFVLLLII 115 QLG Q ++E+ +H+ +M +F+ S VL +I+ Sbjct: 6 QLGFQDAASPVMEELLHFHDHALMIVFLISTLVLYIIV 43 >gnl|CDD|143424 cd07106, ALDH_AldA-AAD23400, Streptomyces aureofaciens putative aldehyde dehydrogenase AldA (AAD23400)-like. Putative aldehyde dehydrogenase, AldA, from Streptomyces aureofaciens (locus AAD23400) and other similar sequences are present in this CD. Length = 446 Score = 24.8 bits (55), Expect = 7.5 Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 2/34 (5%) Query: 4 DMRSSLGRVRGMGSAKDGTGHFIKQRFTAIANIP 37 D ++ +V G DG G+FI T + + P Sbjct: 312 DAKAKGAKVLAGGEPLDGPGYFI--PPTIVDDPP 343 >gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes, Class 1. Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoterpenes, diterpenes, and sesquiterpenes, are formed from their respective linear isoprenoid diphosphates by class I terpene cyclases. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Cyclization of these 30- and 40-carbon linear forms are catalyzed by class II cyclases. Both the isoprenoid chain elongation reactions and the class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Generally, the enzymes in this family exhibit an all-trans reaction pathway, an exception, is the cis-trans terpene cyclase, trichodiene synthase. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD. Length = 243 Score = 24.8 bits (54), Expect = 7.7 Identities = 8/38 (21%), Positives = 14/38 (36%) Query: 89 IEDYIHYRLLKIMFLFMNSCFVLLLIIFCLFSLLKIAI 126 +E+Y+ Y K L C + + LL+ Sbjct: 109 LEEYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALR 146 >gnl|CDD|30131 cd01515, Arch_FBPase_1, Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family (FBPase class IV). These are Mg++ dependent phosphatases. Members in this family may have both fructose-1,6-bisphosphatase and inositol-monophosphatase activity. In hyperthermophilic archaea, inositol monophosphatase is thought to play a role in the biosynthesis of di-myo-inositol-1,1'-phosphate, an osmolyte unique to hyperthermophiles.. Length = 257 Score = 24.4 bits (53), Expect = 9.6 Identities = 14/44 (31%), Positives = 17/44 (38%), Gaps = 7/44 (15%) Query: 20 DGTGHFIKQRFTAIANIPFIIFFIAFFIKYGDAPYEQIVSVLSN 63 DGT + AI IPF +A F PY V L+ Sbjct: 85 DGT-------YNAINGIPFYSVSVAVFKIDKSDPYYGYVYNLAT 121 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 0.337 0.149 0.436 Gapped Lambda K H 0.267 0.0723 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,588,489 Number of extensions: 82958 Number of successful extensions: 789 Number of sequences better than 10.0: 1 Number of HSP's gapped: 767 Number of HSP's successfully gapped: 120 Length of query: 130 Length of database: 6,263,737 Length adjustment: 83 Effective length of query: 47 Effective length of database: 4,470,190 Effective search space: 210098930 Effective search space used: 210098930 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 (21.7 bits) S2: 52 (23.8 bits)