RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780368|ref|YP_003064781.1| electron transfer flavoprotein beta subunit [Candidatus Liberibacter asiaticus str. psy62] (249 letters) >gnl|CDD|38390 KOG3180, KOG3180, KOG3180, Electron transfer flavoprotein, beta subunit [Energy production and conversion]. Length = 254 Score = 254 bits (649), Expect = 2e-68 Identities = 118/248 (47%), Positives = 172/248 (69%), Gaps = 3/248 (1%) Query: 1 MKILVPIKGVINYNTKVRIKNDYSGIETENTKISMNPFDEIALEESLQLREKGIATEVIV 60 ++ILV +K V++Y K+R+K D +G+ T K SMNPF EIA+EE+++L+EK +A EVI Sbjct: 4 LRILVGVKRVVDYAVKIRVKPDKTGVVTSGVKHSMNPFCEIAVEEAVRLKEKKLAEEVIA 63 Query: 61 VSIGSCKVEEVLKNSLAMGADRGILIESN--ETLEPLSIAKILREIVKKENPIIVIAGKQ 118 VSIG + +E+L+ +LA GADRG+ +E E LEPL +AKIL+++V+KE +V+ GKQ Sbjct: 64 VSIGPAQSQEILRTALAKGADRGVHVEVVGAEELEPLHVAKILKKLVEKEKSDLVLLGKQ 123 Query: 119 TTDNESNQTGQMLAALMRWPQATFVSNIKIIDN-HAIVTREVGHGTMTMETPLPAVITVD 177 D++ NQTGQMLAAL+ WPQATF S +++ + VTRE+ G T++ LPAVIT D Sbjct: 124 AIDDDCNQTGQMLAALLGWPQATFASKVELEGDKRVKVTREIDGGLETLKVKLPAVITTD 183 Query: 178 LNLNEPRYISLPNIIKARKKRIEKKKATDFAIDLTPRLKVLRFEENRAERKGLRLYSTTK 237 L LN PRY +LPNI+KA+KK ++K D +D+TP+L+ + EE + G+ + S + Sbjct: 184 LRLNTPRYATLPNIMKAKKKPLKKMTIKDLGVDITPQLETVSVEEPPQRQAGVMVKSVDE 243 Query: 238 LIEILKSK 245 L+ LK Sbjct: 244 LVAKLKEL 251 >gnl|CDD|32269 COG2086, FixA, Electron transfer flavoprotein, beta subunit [Energy production and conversion]. Length = 260 Score = 224 bits (573), Expect = 2e-59 Identities = 106/256 (41%), Positives = 157/256 (61%), Gaps = 11/256 (4%) Query: 1 MKILVPIKGVINYNTKVRIKNDYSGIETENTKISMNPFDEIALEESLQLREKGIATEVIV 60 MKILV IK V++ +K+R+ D ++ +S+NPFD A+EE+L+L+EKG EV V Sbjct: 1 MKILVLIKKVVDDESKIRVDPDTGTLDRSGVPLSINPFDLNAVEEALRLKEKGYGGEVTV 60 Query: 61 VSIGSCKVEEVLKNSLAMGADRGILIE--SNETLEPLSIAKILREIVKKENPIIVIAGKQ 118 +++G + EE L+ +LAMGADR ILI + +PL+ AK L VKK P +V+ GKQ Sbjct: 61 LTMGPPQAEEALREALAMGADRAILITDRAFAGADPLATAKALAAAVKKIGPDLVLTGKQ 120 Query: 119 TTDNESNQTGQMLAALMRWPQATFVSNIKIIDN-HAIVTREVGHGTMTMETPLPAVITVD 177 D ++ Q G +LA L+ WPQ T+VS I+I+D V RE+ G T+E PLPAV+TVD Sbjct: 121 AIDGDTGQVGPLLAELLGWPQVTYVSKIEIVDGGKVTVERELEGGLETVEAPLPAVVTVD 180 Query: 178 LNLNEPRYISLPNIIKARKKRIEKKKATDFAIDL---TPRLKVLRFEENRAERKGLRLYS 234 L +NEPRY SLP I+ A+KK ++K D +++ LKV++ + G+++ Sbjct: 181 LRINEPRYPSLPGIMAAKKKPVKKWSLADLGLNVGLAGSPLKVVKVTPPPERKAGVKVKD 240 Query: 235 T-----TKLIEILKSK 245 +L+E LK + Sbjct: 241 GPEEIAAELVEKLKEE 256 >gnl|CDD|30169 cd01714, ETF_beta, The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an alpha and a beta subunit which binds one molecule of FAD per dimer . A similar system also exists in some bacteria. The homologous pair of proteins (FixA/FixB) are essential for nitrogen fixation. The beta subunit protein is distantly related to and forms a heterodimer with the alpha subunit.. Length = 202 Score = 215 bits (550), Expect = 8e-57 Identities = 90/204 (44%), Positives = 124/204 (60%), Gaps = 4/204 (1%) Query: 2 KILVPIKGVINYNTKVRIKNDYSGIETENTKISMNPFDEIALEESLQLREKGIATEVIVV 61 ILV +K V + K + I+ E + +NP+DE A+EE+L+L+EK EV VV Sbjct: 1 NILVCVKQVPDTEEKRVDPDT-GTIDREGVPLIINPYDEYAVEEALRLKEK-YGGEVTVV 58 Query: 62 SIGSCKVEEVLKNSLAMGADRGILIESNET--LEPLSIAKILREIVKKENPIIVIAGKQT 119 S+G + EE L+ +LAMGADR IL+ + L+ AK L +KK +++ GKQ+ Sbjct: 59 SMGPPQAEEALREALAMGADRAILVSDRAFAGADTLATAKALAAAIKKIGVDLILTGKQS 118 Query: 120 TDNESNQTGQMLAALMRWPQATFVSNIKIIDNHAIVTREVGHGTMTMETPLPAVITVDLN 179 D ++ Q G +LA L+ WPQ T+VS I+I V RE+ G T+E LPAVITVDL Sbjct: 119 IDGDTGQVGPLLAELLGWPQITYVSKIEIEGGKVTVERELEGGVETVEVKLPAVITVDLG 178 Query: 180 LNEPRYISLPNIIKARKKRIEKKK 203 +NEPRY SLP I+KA+KK IE Sbjct: 179 INEPRYPSLPGIMKAKKKPIEVVS 202 >gnl|CDD|30172 cd01985, ETF, The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an alpha and a beta subunit which binds one molecule of FAD per dimer . A similar system also exists in some bacteria. The homologous pair of proteins (FixA/FixB) are essential for nitrogen fixation. The alpha subunit of ETF is structurally related to the bacterial nitrogen fixation protein fixB which could play a role in a redox process and feed electrons to ferredoxin. The beta subunit protein is distantly related to and forms a heterodimer with the alpha subunit.. Length = 181 Score = 131 bits (330), Expect = 2e-31 Identities = 72/206 (34%), Positives = 106/206 (51%), Gaps = 31/206 (15%) Query: 2 KILVPIKGVINYNTKVRIKNDYSGIETENTKISMNPFDEIALEESLQLREKGIATEVIVV 61 KILV ++ V + V +NP D A+E +L+L+E G EV + Sbjct: 1 KILVLVEHVPDTAELV-----------------LNPLDLEAVEAALRLKEYG--GEVTAL 41 Query: 62 SIGSCKVEEVLKNSLAMGADRGILIESN--ETLEPLSIAKILREIVKKENPIIVIAGKQT 119 IG E L+ +LAMGAD+ +L+E +P + AK L ++KKE P +++AG + Sbjct: 42 VIGPPAAEVALREALAMGADKVLLVEDPALAGYDPEATAKALAALIKKEKPDLILAGATS 101 Query: 120 TDNESNQTGQMLAALMRWPQATFVSNIKIIDNHAIVTREV--GHGTMTMETP-LPAVITV 176 Q +AAL+ PQ + V+ ++I VTR + G+G T+E+P LPAVITV Sbjct: 102 I---GKQLAPRVAALLGVPQISDVTKLEIDGGDLTVTRPIYAGNGLETVESPDLPAVITV 158 Query: 177 DLNLNEPRYISLPNIIKARKKRIEKK 202 EPRY S P +KK +EK Sbjct: 159 RPGAFEPRYPSGPG----KKKPVEKV 180 >gnl|CDD|144557 pfam01012, ETF, Electron transfer flavoprotein domain. This family includes the homologous domain shared between the alpha and beta subunits of the electron transfer flavoprotein. Length = 161 Score = 116 bits (292), Expect = 8e-27 Identities = 52/164 (31%), Positives = 74/164 (45%), Gaps = 14/164 (8%) Query: 26 IETENTKISMNPFDEIALEESLQLREKGIATEVIVVSIGSCK-VEEVLKNSLAMGADRGI 84 E N K+ NP D ALE + QL E EV V +G E L AMGAD+ + Sbjct: 6 AEHGNGKL--NPVDLEALEAARQLAEAL-GGEVTAVVVGPVPAAAEALL--AAMGADKVL 60 Query: 85 LIES--NETLEPLSIAKILREIVKKENPIIVIAGKQTTDNESNQTGQMLAALMRWPQATF 142 ++E + + A L ++KKE P +V+AG + + LAAL+ P T Sbjct: 61 VVEDPALAGYDAEAYAAALAALIKKEGPDLVLAGATSIGKD---LAPRLAALLGAPLITD 117 Query: 143 VSNIKIIDNHAIVTREVGHGTMTMETPLP---AVITVDLNLNEP 183 V+ +++ VTR + G LP AV+TV EP Sbjct: 118 VTALEVEGGKLTVTRPIYGGNAIATVKLPDPPAVLTVRPGAFEP 161 >gnl|CDD|143484 cd06808, PLPDE_III, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes. The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity. Length = 211 Score = 35.4 bits (82), Expect = 0.015 Identities = 29/126 (23%), Positives = 55/126 (43%), Gaps = 13/126 (10%) Query: 38 FDEIALEESLQLREKGIATEVIVVSIGSCKVEEVLKNSLAMGADRGILIESNETLEPLSI 97 FD +L E+L LR GI E I+ +V E L A++G+++ + ++LE Sbjct: 41 FDVASLGEALLLRAAGIPPEPILFLGPCKQVSE-----LEDAAEQGVIVVTVDSLE---E 92 Query: 98 AKILREIVKKENPIIVIAGKQTTDNESNQTG---QMLAALMRWPQATFVSNIKIIDNHAI 154 + L E K P + + T +E+ + G + L AL+ + +++++ H Sbjct: 93 LEKLEEAALKAGPPARVLLRIDTGDENGKFGVRPEELKALLERAKEL--PHLRLVGLHTH 150 Query: 155 VTREVG 160 Sbjct: 151 FGSADE 156 >gnl|CDD|111722 pfam02866, Ldh_1_C, lactate/malate dehydrogenase, alpha/beta C-terminal domain. L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. Length = 173 Score = 28.1 bits (63), Expect = 2.4 Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 6/57 (10%) Query: 5 VPIKGVINYNTKVRIKNDYSGIETENTKISMNPFDEIALEES----LQLREKGIATE 57 I ++ V + D G+E + +N F+ LE+S + EKG A Sbjct: 119 YGSPDDIYFSVPVVLGKD--GVEKVVEILPLNDFEREKLEKSAAELKKEIEKGFAFV 173 >gnl|CDD|144533 pfam00975, Thioesterase, Thioesterase domain. Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates. There are also modules within the peptide synthetases that also share this similarity. With respect to antibiotic production, thioesterases are required for the addition of the last amino acid to the peptide antibiotic, thereby forming a cyclic antibiotic. Thioesterases (non-integrated) have molecular masses of 25-29 kDa. Length = 224 Score = 28.1 bits (63), Expect = 2.6 Identities = 11/57 (19%), Positives = 19/57 (33%), Gaps = 2/57 (3%) Query: 41 IALEESLQLREKGIATEVIVVSIGSCKVEEVLKNS--LAMGADRGILIESNETLEPL 95 +A E + +L +G +++S + S L L T E L Sbjct: 78 LAFEVARRLERRGEEPAGLILSDAYAPHFGRREASHLLGDDELLAELRRIGGTPEAL 134 >gnl|CDD|35424 KOG0203, KOG0203, KOG0203, Na+/K+ ATPase, alpha subunit [Inorganic ion transport and metabolism]. Length = 1019 Score = 26.7 bits (59), Expect = 6.4 Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 6/59 (10%) Query: 77 AMGADRGILIESNETLEPLSIAKILREIVKKENP----IIVIAGKQTTDNESNQTGQML 131 A+ GI+ E +ET+E IAK L V++ N VI G + D S Q ++L Sbjct: 622 AIAKSVGIISEGSETVE--DIAKRLNIPVEQVNSRDAKAAVIHGSELPDMSSEQLDELL 678 >gnl|CDD|73307 cd02149, NfsB_like_nitroreductase, NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family includes FRase I in Vibrio fischeri, wihich reduces FMN into FMNH2 as part of the bioluminescent reaction. The family also includes oxygen-insensitive nitroreductases that use NADH or NADPH as an electron donor in the ping pong bi bi mechanism. This type of nitroreductase can be used in cancer chemotherapy to activate a range of prodrugs.. Length = 157 Score = 26.7 bits (59), Expect = 7.0 Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 1/41 (2%) Query: 35 MNPFDEIALEESLQLREKGIATEVIVVSIGSCKVEEVLKNS 75 + FD L+E L L EKG + ++V++G E L S Sbjct: 111 IEGFDPAKLDEILGLDEKGYGS-SVMVALGYRSEEAKLPKS 150 >gnl|CDD|80351 cd02129, PA_hSPPL_like, PA_hSPPL_like: Protease-associated domain containing human signal peptide peptidase-like (hSPPL)-like. This group contains various PA domain-containing proteins similar to hSPPL2a and 2b. These SPPLs are GxGD aspartic proteases. SPPL2a is sorted to the late endosomes, SPPL2b to the plasma membrane. In activated dendritic cells, hSPPL2a and 2b catalyze the intramembrane proteolysis of tumor necrosis factor alpha triggering IL-12 production. hSPPL2a and 2b may have a broad substrate spectrum. The significance of the PA domain to these SPPLs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.. Length = 120 Score = 26.4 bits (58), Expect = 7.4 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%) Query: 48 QLREKGIATEVIVVSIGSCKVEEVLKNSLAMGADRGILIESNETLEPLS 96 + G+ + +VV G+C E + + ++GA G+LI S E L P S Sbjct: 37 DVPPGGLKGKAVVVMRGNCTFYEKARLAQSLGA-EGLLIVSRERLVPPS 84 >gnl|CDD|143606 cd07582, nitrilase_4, Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. Length = 294 Score = 26.2 bits (58), Expect = 9.8 Identities = 27/107 (25%), Positives = 41/107 (38%), Gaps = 22/107 (20%) Query: 76 LAM-GAD---RGILIESNETLEPLSIAKILREIVKKENPIIVIAGKQTTDNESNQTGQML 131 LAM GA+ R + L+P IA R + EN V++ +N G Sbjct: 185 LAMNGAEVLLRSSSEVPSVELDPWEIANRARAL---ENLAYVVS--------ANSGGIYG 233 Query: 132 AALMRWPQATFVSNIKIIDNHAIVTREVGHGTMTMETPLPAVITVDL 178 + P +F I+D V E G+G +M A +D+ Sbjct: 234 SPY---PADSFGGGSMIVDYKGRVLAEAGYGPGSMV----AGAEIDI 273 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 0.316 0.133 0.359 Gapped Lambda K H 0.267 0.0706 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,754,527 Number of extensions: 139946 Number of successful extensions: 429 Number of sequences better than 10.0: 1 Number of HSP's gapped: 414 Number of HSP's successfully gapped: 24 Length of query: 249 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 158 Effective length of database: 4,297,318 Effective search space: 678976244 Effective search space used: 678976244 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 56 (25.4 bits)