RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780477|ref|YP_003064890.1| DSBA oxidoreductase
[Candidatus Liberibacter asiaticus str. psy62]
         (232 letters)



>gnl|CDD|31837 COG1651, DsbG, Protein-disulfide isomerase [Posttranslational
           modification, protein turnover, chaperones].
          Length = 244

 Score = 96.0 bits (238), Expect = 7e-21
 Identities = 54/180 (30%), Positives = 72/180 (40%), Gaps = 10/180 (5%)

Query: 52  PSTMKDVSIGQKDAPVTMVEYASMTCFHCAEFHNKTFKYLEDKYIKTGKLRYILREFPLD 111
               KDV +G   APVT+VE+   TC +C E   +    L+ KYI  GK+R +LREFP  
Sbjct: 71  TPDGKDVVLGNPYAPVTVVEFFDYTCPYCKEAFPE----LKKKYIDDGKVRLVLREFPFL 126

Query: 112 S----VSTVAVMLARCAEKRMDGGYWGFVSLLFNKQDDWINSKNYRDALLNMAKFAGFSK 167
                    A   ARCA  +    YW F   LF  Q +   +       L  A  A    
Sbjct: 127 DPACPYCRRAAQAARCAADQGIVRYWAFHDALFGSQAEAWAASILCAKDLAKADLAAL-D 185

Query: 168 NDFDTCLNDQNILDDIKAGKKRASEDFAIDSTPVFFIGGNLYLGDMSEGVFSKIIDSMIQ 227
                 LN +     I    K A +   ++ TP F + G L  G         IID  ++
Sbjct: 186 EGKKAKLNQKACDALIAKNYKLA-QQLGVNGTPTFIVNGKLVPGLPDLDELKAIIDEALK 244


>gnl|CDD|48572 cd03023, DsbA_Com1_like, DsbA family, Com1-like subfamily; composed
           of proteins similar to Com1, a 27-kDa outer
           membrane-associated immunoreactive protein originally
           found in both acute and chronic disease strains of the
           pathogenic bacteria Coxiella burnetti. It contains a
           CXXC motif, assumed to be imbedded in a DsbA-like
           structure. Its homology to DsbA suggests that the
           protein is a protein disulfide oxidoreductase. The role
           of such a protein in pathogenesis is unknown..
          Length = 154

 Score = 56.3 bits (136), Expect = 6e-09
 Identities = 42/164 (25%), Positives = 65/164 (39%), Gaps = 11/164 (6%)

Query: 61  GQKDAPVTMVEYASMTCFHCAEFHNKTFKYLEDKYIKTGKLRYILREFP-LDSVSTVAVM 119
           G  +  VT+VE+    C +C     K    LE    +   +R + +EFP L   S +A  
Sbjct: 1   GNPNGDVTIVEFFDYNCGYCK----KLAPELEKLLKEDPDVRVVFKEFPILGESSVLAAR 56

Query: 120 LARCAEKRMDGGYWGFVSLLFNKQDDWINSKNYRDALLNMAKFAGFSKNDFDTCLNDQNI 179
           +A    K   G Y  F + L          +   ++LL +AK AG  +      ++D  I
Sbjct: 57  VALAVWKNGPGKYLEFHNALMAT-----RGRLNEESLLRIAKKAGLDEAKLKKDMDDPEI 111

Query: 180 LDDIKAGKKRASEDFAIDSTPVFFIGGNLYLGDMSEGVFSKIID 223
              I   ++ A     I  TP F IG  +  G +      + ID
Sbjct: 112 EATIDKNRQLA-RALGITGTPAFIIGDTVIPGAVPADTLKEAID 154


>gnl|CDD|73335 cd02972, DsbA_family, DsbA family; consists of DsbA and DsbA-like
           proteins, including DsbC, DsbG, glutathione (GSH)
           S-transferase kappa (GSTK),
           2-hydroxychromene-2-carboxylate (HCCA) isomerase, an
           oxidoreductase (FrnE) presumed to be involved in
           frenolicin biosynthesis, a 27-kDa outer membrane
           protein, and similar proteins. Members of this family
           contain a redox active CXXC motif (except GSTK and HCCA
           isomerase) imbedded in a TRX fold, and an alpha helical
           insert of about 75 residues (shorter in DsbC and DsbG)
           relative to TRX. DsbA is involved in the oxidative
           protein folding pathway in prokaryotes, catalyzing
           disulfide bond formation of proteins secreted into the
           bacterial periplasm. DsbC and DsbG function as protein
           disulfide isomerases and chaperones to correct
           non-native disulfide bonds formed by DsbA and prevent
           aggregation of incorrectly folded proteins..
          Length = 98

 Score = 39.7 bits (92), Expect = 6e-04
 Identities = 20/80 (25%), Positives = 29/80 (36%), Gaps = 9/80 (11%)

Query: 69  MVEYASMTCFHCAEFHNKTFKYLEDKYIKTGKLRYILREFPLDSV----STVAVMLARCA 124
           +VE+    C +C  F  +  K L   Y   G +R + R FPL       S  A   A  A
Sbjct: 1   IVEFFDPLCPYCYLFEPELEKLL---YADDGGVRVVYRPFPLLGGMPPNSLAAARAALAA 57

Query: 125 EKRMDGGYWGFVSLLFNKQD 144
             +  G +      L +   
Sbjct: 58  AAQ--GKFEALHEALADTAL 75


>gnl|CDD|48568 cd03019, DsbA_DsbA, DsbA family, DsbA subfamily; DsbA is a
           monomeric thiol disulfide oxidoreductase protein
           containing a redox active CXXC motif imbedded in a TRX
           fold. It is involved in the oxidative protein folding
           pathway in prokaryotes, and is the strongest thiol
           oxidant known, due to the unusual stability of the
           thiolate anion form of the first cysteine in the CXXC
           motif. The highly unstable oxidized form of DsbA
           directly donates disulfide bonds to reduced proteins
           secreted into the bacterial periplasm. This rapid and
           unidirectional process helps to catalyze the folding of
           newly-synthesized polypeptides. To regain catalytic
           activity, reduced DsbA is then reoxidized by the
           membrane protein DsbB, which generates its disulfides
           from oxidized quinones, which in turn are reoxidized by
           the electron transport chain..
          Length = 178

 Score = 36.4 bits (84), Expect = 0.006
 Identities = 29/179 (16%), Positives = 60/179 (33%), Gaps = 23/179 (12%)

Query: 58  VSIGQKDAPVTMVEYASMTCFHCAEFHNKTFKYLEDKYIKTGKLRYILREFPLDSVSTVA 117
           +S         ++E+ S  C HC  F                 +++   + P+       
Sbjct: 8   LSPPIPSGKPEVIEFFSYGCPHCYNFEP---ILEAWVKKLPKDVKF--EKVPVVFGGGEG 62

Query: 118 VMLARC--------AEKRMDGGYWGFVSLLFNKQDDWINSKNYRDALLNMAKFAGFSKND 169
             LAR          E ++    +  +     K+   ++  + R   L+     G  K  
Sbjct: 63  EPLARAFYAAEALGLEDKLHAALFEAI---HEKRKRLLDPDDIRKIFLS----QGVDKKK 115

Query: 170 FDTCLNDQNILDDIKAGKKRASEDFAIDSTPVFFIGGNLYLGDMSEGVFS--KIIDSMI 226
           FD   N  ++   +   +K A + + I   P F + G   +   + G     +++D +I
Sbjct: 116 FDAAYNSFSVKALVAKAEKLA-KKYKITGVPAFVVNGKYVVNPSAIGGDDTLQVLDELI 173


>gnl|CDD|39778 KOG4578, KOG4578, KOG4578, Uncharacterized conserved protein,
           contains KAZAL and TY domains [General function
           prediction only].
          Length = 421

 Score = 30.0 bits (67), Expect = 0.59
 Identities = 28/119 (23%), Positives = 38/119 (31%), Gaps = 14/119 (11%)

Query: 66  PVTMVEYASMTCFHCAEFHNKTFKYLEDKYIKTGKLRYILREFPLDSVSTVAVMLARCA- 124
           P T   Y    C   A       K          K    L    LD++ T  VM    A 
Sbjct: 264 PGTSTRYGKPKCEETARTAVDPKKVRRLNGCPEKKKTEFLTSL-LDALKTDMVMSGINAS 322

Query: 125 --------EKRMDGGYWGFVSLLFNKQDDWINS--KNYRDALLNMAKFAGFSKNDFDTC 173
                   E+R+   +W F  L  N  +D      K ++  LL  +K    S+  F  C
Sbjct: 323 NGRKSEPDEERV--VHWYFNQLDKNSNNDIERREWKPFKRVLLKKSKPRKCSRKFFKYC 379


>gnl|CDD|37090 KOG1879, KOG1879, KOG1879, UDP-glucose:glycoprotein
           glucosyltransferase [Carbohydrate transport and
           metabolism].
          Length = 1470

 Score = 28.0 bits (62), Expect = 2.2
 Identities = 12/53 (22%), Positives = 16/53 (30%), Gaps = 5/53 (9%)

Query: 57  DVSIGQKDAPVTMVEYASMTCFHCAEFHNKTFKYLEDKYIKTGKLRYILREFP 109
            V  G        + Y  +       FH    K       K GK+ Y+ R F 
Sbjct: 162 HVVPGSNTESPVAILYGELGTIDFRNFHKLLEKL-----AKNGKINYVFRHFL 209


>gnl|CDD|38644 KOG3434, KOG3434, KOG3434, 60S ribosomal protein L22 [Translation,
           ribosomal structure and biogenesis].
          Length = 125

 Score = 27.2 bits (60), Expect = 3.6
 Identities = 21/73 (28%), Positives = 29/73 (39%), Gaps = 2/73 (2%)

Query: 36  PIPDGVVDFRALLAASPSTMKDVS-IGQKDAPVTMVEYASMTCFHC-AEFHNKTFKYLED 93
           P+ DG++D   L       +K    +G     VT+    S         F  +  KYL  
Sbjct: 27  PVEDGILDIADLEKFLQERIKVNGKVGNLGNVVTIERSKSKITVVSTVHFSKRYLKYLTK 86

Query: 94  KYIKTGKLRYILR 106
           KY+K   LR  LR
Sbjct: 87  KYLKKNNLRDWLR 99


>gnl|CDD|33703 COG3917, NahD, 2-hydroxychromene-2-carboxylate isomerase [Secondary
           metabolites biosynthesis, transport, and catabolism].
          Length = 203

 Score = 27.2 bits (60), Expect = 3.8
 Identities = 14/58 (24%), Positives = 21/58 (36%), Gaps = 1/58 (1%)

Query: 154 DALLNMAKFAGFSKNDFDTCLNDQNILDDIKAGKKRASEDFAIDSTPVFFIGGNLYLG 211
           + +  +A  AG         L D  I   +KA    A     +   P F +G  L+ G
Sbjct: 133 EVVYAVANAAGLDGAALLALLGDDEIKARLKANTAEAVSR-GVFGAPTFIVGDQLFWG 189


>gnl|CDD|29489 cd02865, Heme_Cu_Oxidase_III_2, Heme-copper oxidase subunit III
          subfamily.  Heme-copper oxidases are transmembrane
          protein complexes in the respiratory chains of
          prokaryotes and mitochondria which couple the reduction
          of molecular oxygen to water to, proton pumping across
          the membrane. The heme-copper oxidase superfamily is
          diverse in terms of electron donors, subunit
          composition, and heme types.  This superfamily includes
          cytochrome c and ubiquinol oxidases.  Bacterial
          oxidases typically contain 3 or 4 subunits in contrast
          to the 13 subunit bovine cytochrome c oxidase (CcO).
          Subunits I, II, and III of mammalian CcO are encoded
          within the mitochondrial genome and the remaining 10
          subunits are encoded within the nuclear genome.
          Subunits I, II and III of ubiquinol oxidase are
          homologous to the corresponding subunits in CcO.
          Although not required for catalytic activity, subunit
          III is believed to play a role in assembly of the
          multimer complex. Rhodobacter CcO subunit III
          stabilizes the integrity of the binuclear center in
          subunit I.  It has been proposed that Archaea acquired
          heme-copper oxidases through gene transfer from
          Gram-positive bacteria..
          Length = 184

 Score = 27.2 bits (60), Expect = 4.4
 Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 8  IGVLGGIVLLFIASYFFYTRKGSALNELPIPDGVVDF--RALLAASPSTM 55
          + V G +  L I++YF     G      P+P   +     A+LAAS   M
Sbjct: 17 MAVEGTLFALLISAYFMRMTSGDWQPGAPLPLPNLLSLNTAVLAASSVAM 66


>gnl|CDD|31616 COG1427, COG1427, Predicted periplasmic solute-binding protein
          [General function prediction only].
          Length = 252

 Score = 26.8 bits (59), Expect = 5.5
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 2/54 (3%)

Query: 32 LNELPIPDGVVDFRALLAASPSTM-KDVSIGQKD-APVTMVEYASMTCFHCAEF 83
          +N LP+  G+     ++ A PS + + +  G+ D A V+ V YA          
Sbjct: 12 INSLPLFLGLEQRERVVKAVPSELNELLLSGRIDAALVSSVAYAEDDLKLLPGL 65


>gnl|CDD|48072 cd01968, Nitrogenase_NifE_I, Nitrogenase_NifE_I: a subgroup of the
           NifE subunit of the NifEN complex: NifE forms an
           alpha2beta2 tetramer with NifN.  NifE and NifN are
           structurally homologous to nitrogenase MoFe protein
           alpha and beta subunits respectively.  NifEN
           participates in the synthesis of the iron-molybdenum
           cofactor (FeMoco) of the MoFe protein.  NifB-co (an iron
           and sulfur containing precursor of the FeMoco) from NifB
           is transferred to the NifEN complex where it is further
           processed to FeMoco. The NifEN bound precursor of FeMoco
           has been identified as a molybdenum-free, iron- and
           sulfur- containing analog of FeMoco. It has been
           suggested that this NifEN bound precursor also acts as a
           cofactor precursor in nitrogenase systems which require
           a cofactor other than FeMoco: i.e. iron-vanadium
           cofactor (FeVco) or iron only cofactor (FeFeco)..
          Length = 410

 Score = 26.7 bits (59), Expect = 5.7
 Identities = 15/31 (48%), Positives = 16/31 (51%), Gaps = 3/31 (9%)

Query: 179 ILDDIKAGKKRASEDFAIDSTPV---FFIGG 206
           I DDI A  K ASE F I   PV    F+G 
Sbjct: 101 IGDDIDAVCKTASEKFGIPVIPVHSPGFVGN 131


>gnl|CDD|32194 COG2011, AbcD, ABC-type metal ion transport system, permease
           component [Inorganic ion transport and metabolism].
          Length = 222

 Score = 26.2 bits (58), Expect = 7.7
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 1   MVMSTTRIGVLGGIVLLFIASYFFYTRK-GSALNELPIPDGVVDFRALLAASPST 54
           +++ T+ IG    IV L I +  F  R   SAL E  +  GV++    + ASP  
Sbjct: 86  LIVGTS-IGTTAAIVPLTIGAAPFVARLVESALRE--VDKGVIEAAQAMGASPWQ 137


  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
   0.323    0.138    0.410 

Gapped
Lambda     K      H
   0.267   0.0681    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,777,452
Number of extensions: 142069
Number of successful extensions: 394
Number of sequences better than 10.0: 1
Number of HSP's gapped: 388
Number of HSP's successfully gapped: 16
Length of query: 232
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 141
Effective length of database: 4,297,318
Effective search space: 605921838
Effective search space used: 605921838
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.4 bits)