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)