RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780212|ref|YP_003064625.1| bacterioferritin comigratory
protein [Candidatus Liberibacter asiaticus str. psy62]
         (157 letters)



>gnl|CDD|31418 COG1225, Bcp, Peroxiredoxin [Posttranslational modification,
           protein turnover, chaperones].
          Length = 157

 Score =  190 bits (483), Expect = 2e-49
 Identities = 80/156 (51%), Positives = 104/156 (66%)

Query: 1   MTSLSVGDKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADF 60
           M  L VGDKAP F LP  D + +SL  L G  +VLYFYPKD T GCT EA +F  L  +F
Sbjct: 1   MMMLKVGDKAPDFELPDQDGETVSLSDLRGKPVVLYFYPKDFTPGCTTEACDFRDLLEEF 60

Query: 61  DEESTILIGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVV 120
           ++   +++GISPDS  SHKKF +KH L+  LL+DE  EV ++Y VW EK M+GK+YMG+ 
Sbjct: 61  EKLGAVVLGISPDSPKSHKKFAEKHGLTFPLLSDEDGEVAEAYGVWGEKKMYGKEYMGIE 120

Query: 121 RTTFLIDEKGIIAQIWKPVTLKNHAQSVLKMVKSLK 156
           R+TF+ID  G I  +W+ V +K HA  VL  +K L 
Sbjct: 121 RSTFVIDPDGKIRYVWRKVKVKGHADEVLAALKKLA 156


>gnl|CDD|48566 cd03017, PRX_BCP, Peroxiredoxin (PRX) family, Bacterioferritin
           comigratory protein (BCP) subfamily; composed of
           thioredoxin-dependent thiol peroxidases, widely
           expressed in pathogenic bacteria, that protect cells
           against toxicity from reactive oxygen species by
           reducing and detoxifying hydroperoxides. The protein was
           named BCP based on its electrophoretic mobility before
           its function was known. BCP shows substrate selectivity
           toward fatty acid hydroperoxides rather than hydrogen
           peroxide or alkyl hydroperoxides. BCP contains the
           peroxidatic cysteine but appears not to possess a
           resolving cysteine (some sequences, not all, contain a
           second cysteine but its role is still unknown). Unlike
           other PRXs, BCP exists as a monomer. The plant homolog
           of BCP is PRX Q, which is expressed only in leaves and
           is cellularly localized in the chloroplasts and the
           guard cells of stomata. Also included in this subfamily
           is the fungal nuclear protein,  Dot5p (for disrupter of
           telomere silencing protein 5), which functions as an
           alkyl-hydroperoxide reductase during post-diauxic
           growth..
          Length = 140

 Score =  178 bits (453), Expect = 6e-46
 Identities = 71/143 (49%), Positives = 93/143 (65%), Gaps = 3/143 (2%)

Query: 8   DKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEESTIL 67
           DKAP F LP  D + +SL  L G  +VLYFYPKDDT GCT EA +F  L  +F     ++
Sbjct: 1   DKAPDFTLPDQDGETVSLSDLRGKPVVLYFYPKDDTPGCTKEACDFRDLYEEFKALGAVV 60

Query: 68  IGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVVRTTFLID 127
           IG+SPDS+ SH KF +K+ L   LL+D   ++ K+Y VW EK    KKYMG+ R+TFLID
Sbjct: 61  IGVSPDSVESHAKFAEKYGLPFPLLSDPDGKLAKAYGVWGEKK---KKYMGIERSTFLID 117

Query: 128 EKGIIAQIWKPVTLKNHAQSVLK 150
             G I ++W+ V  K HA+ VL+
Sbjct: 118 PDGKIVKVWRKVKPKGHAEEVLE 140


>gnl|CDD|144244 pfam00578, AhpC-TSA, AhpC/TSA family.  This family contains
           proteins related to alkyl hydroperoxide reductase (AhpC)
           and thiol specific antioxidant (TSA).
          Length = 124

 Score =  143 bits (362), Expect = 3e-35
 Identities = 56/130 (43%), Positives = 73/130 (56%), Gaps = 6/130 (4%)

Query: 6   VGDKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEEST 65
           VGDKAP F LP  D +E+SL    G  +VL+FYPKD T  CT E    + L  +F +   
Sbjct: 1   VGDKAPDFELPDLDGKEVSLSDYKGKWVVLFFYPKDFTPVCTTELPALADLYEEFKKLGV 60

Query: 66  ILIGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVVRTTFL 125
            ++G+S DS  SHKKF +K  L   LL+D   EV ++Y V  E      +  G +RTTF+
Sbjct: 61  EVLGVSVDSPESHKKFAEKLGLPFPLLSDPDGEVARAYGVLNE------EAGGALRTTFV 114

Query: 126 IDEKGIIAQI 135
           ID  G I  I
Sbjct: 115 IDPDGKIRYI 124


>gnl|CDD|48520 cd02971, PRX_family, Peroxiredoxin (PRX) family; composed of the
           different classes of PRXs including many proteins
           originally known as bacterioferritin comigratory
           proteins (BCP), based on their electrophoretic mobility
           before their function was identified. PRXs are
           thiol-specific antioxidant (TSA) proteins also known as
           TRX peroxidases and alkyl hydroperoxide reductase C22
           (AhpC) proteins. They confer a protective antioxidant
           role in cells through their peroxidase activity in which
           hydrogen peroxide, peroxynitrate, and organic
           hydroperoxides are reduced and detoxified using reducing
           equivalents derived from either TRX, glutathione,
           trypanothione and AhpF. They are distinct from other
           peroxidases in that they have no cofactors such as
           metals or prosthetic groups. The first step of
           catalysis, common to all PRXs, is the nucleophilic
           attack by the catalytic cysteine (also known as the
           peroxidatic cysteine) on the peroxide leading to
           cleavage of the oxygen-oxygen bond and the formation of
           a cysteine sulfenic acid intermediate. The second step
           of the reaction, the resolution of the intermediate,
           distinguishes the different types of PRXs. The presence
           or absence of a second cysteine (the resolving cysteine)
           classifies PRXs as either belonging to the 2-cys or
           1-cys type. The resolving cysteine of 2-cys PRXs is
           either on the same chain (atypical) or on the second
           chain (typical) of a functional homodimer. Structural
           and motif analysis of this growing family supports the
           need for a new classification system. The peroxidase
           activity of PRXs is regulated in vivo by irreversible
           cysteine over-oxidation into a sulfinic acid,
           phosphorylation and limited proteolysis..
          Length = 140

 Score =  140 bits (354), Expect = 2e-34
 Identities = 52/143 (36%), Positives = 68/143 (47%), Gaps = 4/143 (2%)

Query: 9   KAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEESTILI 68
           KAP F LP+ D  E+SL    G  +VL+FYPKD T  CT E   F  L  +F +    ++
Sbjct: 1   KAPDFTLPATDGGEVSLSDFKGKWVVLFFYPKDFTPVCTTELCAFRDLAEEFAKGGAEVL 60

Query: 69  GISPDSIASHKKFHQKH-NLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVVRTTFLID 127
           G+S DS  SHK + +K   L+  LL+D   E  K+Y V  EKS          R TF+ID
Sbjct: 61  GVSVDSPFSHKAWAEKEGGLNFPLLSDPDGEFAKAYGVLIEKSA---GGGLAARATFIID 117

Query: 128 EKGIIAQIWKPVTLKNHAQSVLK 150
             G I  +             L 
Sbjct: 118 PDGKIRYVEVEPLPTGRNAEELL 140


>gnl|CDD|48567 cd03018, PRX_AhpE_like, Peroxiredoxin (PRX) family, AhpE-like
           subfamily; composed of proteins similar to Mycobacterium
           tuberculosis AhpE. AhpE is described as a 1-cys PRX
           because of the absence of a resolving cysteine. The
           structure and sequence of AhpE, however, show greater
           similarity to 2-cys PRXs than 1-cys PRXs. PRXs are
           thiol-specific antioxidant (TSA) proteins that confer a
           protective role in cells through their peroxidase
           activity in which hydrogen peroxide, peroxynitrate, and
           organic hydroperoxides are reduced and detoxified using
           reducing equivalents derived from either thioredoxin,
           glutathione, trypanothione and AhpF. The first step of
           catalysis is the nucleophilic attack by the peroxidatic
           cysteine on the peroxide leading to the formation of a
           cysteine sulfenic acid intermediate. The absence of a
           resolving cysteine suggests that functional AhpE is
           regenerated by an external reductant. The solution
           behavior and crystal structure of AhpE show that it
           forms dimers and octamers..
          Length = 149

 Score =  104 bits (261), Expect = 1e-23
 Identities = 47/136 (34%), Positives = 65/136 (47%), Gaps = 9/136 (6%)

Query: 4   LSVGDKAPHFVLPSNDEQEISLL-ALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDE 62
           L VGDKAP F LP  + QE+ L    G   +VL F+P   T  CT E          F+ 
Sbjct: 1   LEVGDKAPDFELPDQNGQEVRLSEFRGRKPVVLVFFPLAFTPVCTKELCALRDSLELFEA 60

Query: 63  ESTILIGISPDSIASHKKFHQKHNLSITLLAD--ESKEVLKSYDVWKEKSMFGKKYMGVV 120
               ++GIS DS  S + + +++ L+  LL+D     EV K+Y V+ E     +      
Sbjct: 61  AGAEVLGISVDSPFSLRAWAEENGLTFPLLSDFWPHGEVAKAYGVFDEDLGVAE------ 114

Query: 121 RTTFLIDEKGIIAQIW 136
           R  F+ID  GII   W
Sbjct: 115 RAVFVIDRDGIIRYAW 130


>gnl|CDD|48564 cd03015, PRX_Typ2cys, Peroxiredoxin (PRX) family, Typical 2-Cys PRX
           subfamily; PRXs are thiol-specific antioxidant (TSA)
           proteins, which confer a protective role in cells
           through its peroxidase activity by reducing hydrogen
           peroxide, peroxynitrite, and organic hydroperoxides. The
           functional unit of typical 2-cys PRX is a homodimer. A
           unique intermolecular redox-active disulfide center is
           utilized for its activity. Upon reaction with peroxides,
           its peroxidatic cysteine is oxidized into a sulfenic
           acid intermediate which is resolved by bonding with the
           resolving cysteine from the other subunit of the
           homodimer. This intermolecular disulfide bond is then
           reduced by thioredoxin, tryparedoxin or AhpF. Typical
           2-cys PRXs, like 1-cys PRXs, form decamers which are
           stabilized by reduction of the active site cysteine.
           Typical 2-cys PRX interacts through beta strands at one
           edge of the monomer (B-type interface) to form the
           functional homodimer, and uses an A-type interface
           (similar to the dimeric interface in atypical 2-cys PRX
           and PRX5) at the opposite end of the monomer to form the
           stable decameric (pentamer of dimers) structure..
          Length = 173

 Score = 90.9 bits (226), Expect = 1e-19
 Identities = 51/142 (35%), Positives = 73/142 (51%), Gaps = 19/142 (13%)

Query: 6   VGDKAPHF----VLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFD 61
           VG KAP F    V+P+ + +EISL    G  +VL+FYP D T  C  E I FS    +F 
Sbjct: 1   VGKKAPDFKATAVVPNGEFKEISLSDYKGKWVVLFFYPLDFTFVCPTEIIAFSDRYEEFK 60

Query: 62  EESTILIGISPDSIASHKKFHQKH-------NLSITLLADESKEVLKSYDVWKEKSMFGK 114
           + +  ++G+S DS  SH  +            ++  LLAD  K++ + Y V  E+     
Sbjct: 61  KLNAEVLGVSTDSHFSHLAWRNTPRKEGGLGKINFPLLADPKKKISRDYGVLDEEE---- 116

Query: 115 KYMGV-VRTTFLIDEKGIIAQI 135
              GV +R TF+ID +GII  I
Sbjct: 117 ---GVALRGTFIIDPEGIIRHI 135


>gnl|CDD|30799 COG0450, AhpC, Peroxiredoxin [Posttranslational modification,
           protein turnover, chaperones].
          Length = 194

 Score = 88.0 bits (218), Expect = 1e-18
 Identities = 46/167 (27%), Positives = 80/167 (47%), Gaps = 20/167 (11%)

Query: 3   SLSVGDKAPHFVLPS----NDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKA 58
              +G KAP F   +       +EI+L    G  +VL+FYP D T  C  E I F+    
Sbjct: 2   MSLIGKKAPDFTANAVLGGEIFEEITLSDYYGKWVVLFFYPADFTFVCPTEIIAFAKRYE 61

Query: 59  DFDEESTILIGISPDSIASHKKFHQK-------HNLSITLLADESKEVLKSYDVWKEKSM 111
           +F +    +IG+S DS+ SHK +            +   ++AD   E+ ++Y V   +  
Sbjct: 62  EFQKRGVEVIGVSTDSVFSHKAWKATIREAGGIGKIKFPMIADPKGEIARAYGVLHPEE- 120

Query: 112 FGKKYMGV-VRTTFLIDEKGII-AQIWKPVTLKNHAQSVLKMVKSLK 156
                 G+ +R TF+ID  G+I   +  P+T+  +   +L+++ +L+
Sbjct: 121 ------GLALRGTFIIDPDGVIRHILVNPLTIGRNVDEILRVIDALQ 161


>gnl|CDD|36073 KOG0855, KOG0855, KOG0855, Alkyl hydroperoxide reductase, thiol
           specific antioxidant and related enzymes
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 211

 Score = 82.9 bits (204), Expect = 4e-17
 Identities = 47/136 (34%), Positives = 65/136 (47%), Gaps = 6/136 (4%)

Query: 3   SLSVGDKAPHFVLPSNDEQEISLLALGGSK-IVLYFYPKDDTSGCTAEAINFSSLKADFD 61
            ++ GD  P F L   D + ISL  + G+K +VL+FYP   T GCT +A  F      F 
Sbjct: 62  KVNKGDAIPDFTLKDEDGKSISLKKITGNKPVVLFFYPAASTPGCTKQACGFRDNYEKFK 121

Query: 62  EESTILIGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVVR 121
           +    +IG+S D  AS K F  K NL   LL+D   EV+K       K  FG       R
Sbjct: 122 KAGAEVIGLSGDDSASQKAFASKQNLPYHLLSDPKNEVIKDLGA--PKDPFGGL---PGR 176

Query: 122 TTFLIDEKGIIAQIWK 137
           + ++ D+ G+   I  
Sbjct: 177 SHYIFDKGGVKQLIKN 192


>gnl|CDD|48565 cd03016, PRX_1cys, Peroxiredoxin (PRX) family, 1-cys PRX subfamily;
           composed of PRXs containing only one conserved cysteine,
           which serves as the peroxidatic cysteine. They are
           homodimeric thiol-specific antioxidant (TSA) proteins
           that confer a protective role in cells by reducing and
           detoxifying hydrogen peroxide, peroxynitrite, and
           organic hydroperoxides. As with all other PRXs, a
           cysteine sulfenic acid intermediate is formed upon
           reaction of 1-cys PRX with its substrates. Having no
           resolving cysteine, the oxidized enzyme is resolved by
           an external small-molecule or protein reductant such as
           thioredoxin or glutaredoxin. Similar to typical 2-cys
           PRX, 1-cys PRX forms a functional dimeric unit with a
           B-type interface, as well as a decameric structure which
           is stabilized in the reduced form of the enzyme. Other
           oligomeric forms, tetramers and hexamers, have also been
           reported. Mammalian 1-cys PRX is localized cellularly in
           the cytosol and is expressed at high levels in brain,
           eye, testes and lung. The seed-specific plant 1-cys PRXs
           protect tissues from reactive oxygen species during
           desiccation and are also called rehydrins..
          Length = 203

 Score = 76.3 bits (188), Expect = 3e-15
 Identities = 44/159 (27%), Positives = 72/159 (45%), Gaps = 13/159 (8%)

Query: 6   VGDKAPHFVLPSNDEQEISLLA-LGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEES 64
           +GD AP+F   +     I     LG S  +L+ +P D T  CT E   F+ L  +F + +
Sbjct: 1   LGDTAPNFEADT-THGPIKFHDYLGDSWGILFSHPADFTPVCTTELGAFAKLAPEFKKRN 59

Query: 65  TILIGISPDSIASHKKF------HQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMG 118
             LIG+S DS+ SH K+      +    +   ++AD  +EV K   +             
Sbjct: 60  VKLIGLSVDSVESHIKWIEDIEEYTGVEIPFPIIADPDREVAKLLGMIDP----DAGSTL 115

Query: 119 VVRTTFLIDEKGII-AQIWKPVTLKNHAQSVLKMVKSLK 156
            VR  F+ID    I   ++ P T   +   +L++V +L+
Sbjct: 116 TVRAVFIIDPDKKIRLILYYPATTGRNFDEILRVVDALQ 154


>gnl|CDD|36070 KOG0852, KOG0852, KOG0852, Alkyl hydroperoxide reductase, thiol
           specific antioxidant and related enzymes
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 196

 Score = 68.8 bits (168), Expect = 6e-13
 Identities = 45/122 (36%), Positives = 62/122 (50%), Gaps = 13/122 (10%)

Query: 21  QEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEESTILIGISPDSIASH-- 78
           +EI L    G  +VL+FYP D T  C  E I FS    +F + +T ++GIS DS+ SH  
Sbjct: 24  KEIKLSDYKGKYVVLFFYPLDFTFVCPTEIIAFSDRAPEFRKLNTEVLGISTDSVFSHLA 83

Query: 79  -----KKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVVRTTFLIDEKGIIA 133
                +K      L+I LL+D + E+ + Y V KE    G       R  F+ID  GI+ 
Sbjct: 84  WINTPRKQGGLGPLNIPLLSDLNHEISRDYGVLKEDE--GIAL----RGLFIIDPDGILR 137

Query: 134 QI 135
           QI
Sbjct: 138 QI 139


>gnl|CDD|48563 cd03014, PRX_Atyp2cys, Peroxiredoxin (PRX) family, Atypical 2-cys
           PRX subfamily; composed of PRXs containing peroxidatic
           and resolving cysteines, similar to the homodimeric
           thiol specific antioxidant (TSA) protein also known as
           TRX-dependent thiol peroxidase (Tpx). Tpx is a bacterial
           periplasmic peroxidase which differs from other PRXs in
           that it shows substrate specificity toward alkyl
           hydroperoxides over hydrogen peroxide. As with all other
           PRXs, the peroxidatic cysteine (N-terminal) of Tpx is
           oxidized into a sulfenic acid intermediate upon reaction
           with peroxides. Tpx is able to resolve this intermediate
           by forming an intramolecular disulfide bond with a
           conserved C-terminal cysteine (the resolving cysteine),
           which can then be reduced by thioredoxin. This differs
           from the typical 2-cys PRX which resolves the oxidized
           cysteine by forming an intermolecular disulfide bond
           with the resolving cysteine from the other subunit of
           the homodimer. Atypical 2-cys PRX homodimers have a
           loop-based interface (A-type for alternate), in contrast
           with the B-type interface of typical 2-cys and 1-cys
           PRXs..
          Length = 143

 Score = 60.6 bits (147), Expect = 2e-10
 Identities = 41/138 (29%), Positives = 61/138 (44%), Gaps = 24/138 (17%)

Query: 5   SVGDKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEES 64
            VGDKAP F L ++D  E+SL    G   V+  +P  DT  C  +   F+   A  D   
Sbjct: 1   KVGDKAPDFTLVTSDLSEVSLADFAGKVKVISVFPSIDTPVCATQTKRFNKEAAKLDN-- 58

Query: 65  TILIGISPDSIASHKKFHQKHNL-SITLLADESKEVLKSYDVWKEKSMFGKKYMGVV--- 120
           T+++ IS D   + K++     + ++T L+D                 FGK Y GV+   
Sbjct: 59  TVVLTISADLPFAQKRWCGAEGVDNVTTLSDF------------RDHSFGKAY-GVLIKD 105

Query: 121 -----RTTFLIDEKGIIA 133
                R  F+IDE G + 
Sbjct: 106 LGLLARAVFVIDENGKVI 123


>gnl|CDD|36072 KOG0854, KOG0854, KOG0854, Alkyl hydroperoxide reductase, thiol
           specific antioxidant and related enzymes
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 224

 Score = 56.6 bits (136), Expect = 3e-09
 Identities = 43/166 (25%), Positives = 75/166 (45%), Gaps = 10/166 (6%)

Query: 1   MTSLSVGDKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADF 60
              L +GD  P+F   +   +      LG S  VL+ +P D T  CT E   F+ L  +F
Sbjct: 3   GPRLRLGDTVPNFEADTTVGKIKFHDYLGDSWGVLFSHPADFTPVCTTELGRFAKLAPEF 62

Query: 61  DEESTILIGISPDSIASHKKFHQ---------KHNLSITLLADESKEVLKSYDVWKEKSM 111
           D+ +  LI +S D + SHK + +          H++   ++AD ++E+    ++   +  
Sbjct: 63  DKRNVKLIALSVDDVESHKDWIKDIKSYAKVKNHSVPYPIIADPNRELAFLLNMLDPEEK 122

Query: 112 FGKKYMGVVRTTFLID-EKGIIAQIWKPVTLKNHAQSVLKMVKSLK 156
                   VR  F+ID +K I      P T   +   +L+++ SL+
Sbjct: 123 KNIGDGKTVRAVFVIDPDKKIRLSFLYPSTTGRNFDEILRVIDSLQ 168


>gnl|CDD|32260 COG2077, Tpx, Peroxiredoxin [Posttranslational modification,
           protein turnover, chaperones].
          Length = 158

 Score = 54.9 bits (132), Expect = 9e-09
 Identities = 37/135 (27%), Positives = 60/135 (44%), Gaps = 9/135 (6%)

Query: 2   TSLSVGDKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFD 61
               VGDKAP F L   D  ++SL    G K V+  +P  DT  C  +   F+   A   
Sbjct: 16  NEPQVGDKAPDFTLVGKDLNDVSLADFAGKKKVISVFPSIDTPVCATQVRKFNEEAAKLG 75

Query: 62  EESTILIGISPDSIASHKKFHQKHNLS-ITLLAD-ESKEVLKSYDVW-KEKSMFGKKYMG 118
             +T+++ IS D   + K+F     +  +  L+D   +   ++Y V   E  + G     
Sbjct: 76  --NTVVLCISMDLPFAQKRFCGAEGIENVITLSDFRDRAFGENYGVLINEGPLAGL---- 129

Query: 119 VVRTTFLIDEKGIIA 133
           + R  F++DE G + 
Sbjct: 130 LARAVFVLDENGKVT 144


>gnl|CDD|48515 cd02966, TlpA_like_family, TlpA-like family; composed of  TlpA,
           ResA, DsbE and similar proteins. TlpA, ResA and DsbE are
           bacterial protein disulfide reductases with important
           roles in cytochrome maturation. They are
           membrane-anchored proteins with a soluble TRX domain
           containing a CXXC motif located in the periplasm. The
           TRX domains of this family contain an insert,
           approximately 25 residues in length, which correspond to
           an extra alpha helix and a beta strand when compared
           with TRX. TlpA catalyzes an essential reaction in the
           biogenesis of cytochrome aa3, while ResA and DsbE are
           essential proteins in cytochrome c maturation. Also
           included in this family are proteins containing a
           TlpA-like TRX domain with domain architectures similar
           to E. coli DipZ protein, and the N-terminal TRX domain
           of PilB protein from Neisseria which acts as a disulfide
           reductase that can recylce methionine sulfoxide
           reductases..
          Length = 116

 Score = 50.7 bits (121), Expect = 2e-07
 Identities = 34/128 (26%), Positives = 58/128 (45%), Gaps = 21/128 (16%)

Query: 13  FVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCT---AEAINFSSLKADFDEESTILIG 69
           F LP  D + +SL  L G  +++ F+     S C    AE     +L  ++ ++   ++G
Sbjct: 2   FSLPDLDGKPVSLSDLKGKVVLVNFW----ASWCPPCRAEMPELEALAKEYKDDGVEVVG 57

Query: 70  IS--PDSIASHKKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMGVVRTTFLID 127
           ++   D  A+ K F +K+ ++  +L D   E+ K+Y V              + TTFLID
Sbjct: 58  VNVDDDDPAAVKAFLKKYGITFPVLLDPDGELAKAYGV------------RGLPTTFLID 105

Query: 128 EKGIIAQI 135
             G I   
Sbjct: 106 RDGRIRAR 113


>gnl|CDD|48519 cd02970, PRX_like2, Peroxiredoxin (PRX)-like 2 family; hypothetical
           proteins that show sequence similarity to PRXs. Members
           of this group contain a CXXC motif, similar to TRX. The
           second cysteine in the motif corresponds to the
           peroxidatic cysteine of PRX, however, these proteins do
           not contain the other two residues of the catalytic
           triad of PRX. PRXs confer a protective antioxidant role
           in cells through their peroxidase activity in which
           hydrogen peroxide, peroxynitrate, and organic
           hydroperoxides are reduced and detoxified using reducing
           equivalents derived from either thioredoxin,
           glutathione, trypanothione and AhpF. TRXs alter the
           redox state of target proteins by catalyzing the
           reduction of their disulfide bonds via the CXXC motif
           using reducing equivalents derived from either NADPH or
           ferredoxins..
          Length = 149

 Score = 50.0 bits (119), Expect = 3e-07
 Identities = 28/135 (20%), Positives = 52/135 (38%), Gaps = 13/135 (9%)

Query: 9   KAPHFVLPSNDEQEISLLAL-GGSKIVLYFY-----PKDDTSGCTAEAINFSSLKADFDE 62
            AP F LP    + ++L AL G   +V+ FY     P      C       S L  + D 
Sbjct: 1   TAPDFELPDAGGETVTLSALLGEGPVVVVFYRGFGCPF-----CREYLRALSKLLPELDA 55

Query: 63  ESTILIGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDVWKE--KSMFGKKYMGVV 120
               L+ + P+S    + F +   L   + AD  +++ ++  + +    S   +      
Sbjct: 56  LGVELVAVGPESPEKLEAFDKGKFLPFPVYADPDRKLYRALGLVRSLPWSNTPRALWKNA 115

Query: 121 RTTFLIDEKGIIAQI 135
              F  +++G   Q+
Sbjct: 116 AIGFRGNDEGDGLQL 130


>gnl|CDD|48518 cd02969, PRX_like1, Peroxiredoxin (PRX)-like 1 family; hypothetical
           proteins that show sequence similarity to PRXs. Members
           of this group contain a conserved cysteine that aligns
           to the first cysteine in the CXXC motif of TRX. This
           does not correspond to the peroxidatic cysteine found in
           PRXs, which aligns to the second cysteine in the CXXC
           motif of TRX. In addition, these proteins do not contain
           the other two conserved residues of the catalytic triad
           of PRX. PRXs confer a protective antioxidant role in
           cells through their peroxidase activity in which
           hydrogen peroxide, peroxynitrate, and organic
           hydroperoxides are reduced and detoxified using reducing
           equivalents derived from either thioredoxin,
           glutathione, trypanothione and AhpF..
          Length = 171

 Score = 42.9 bits (101), Expect = 4e-05
 Identities = 29/137 (21%), Positives = 50/137 (36%), Gaps = 24/137 (17%)

Query: 7   GDKAPHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEESTI 66
           G  AP F LP  D +  SL      K ++  +  +      A     + L  ++  +   
Sbjct: 1   GSPAPDFSLPDTDGKTYSLADFADGKALVVMFICNHCPYVKAIEDRLNRLAKEYGAKGVA 60

Query: 67  LIGISPDSIASH--------KKFHQKHNLSITLLADESKEVLKSYDVWKEKSMFGKKYMG 118
           ++ I+ + I ++        K   ++H      L DE++EV K+Y              G
Sbjct: 61  VVAINSNDIEAYPEDSPENMKAKAKEHGYPFPYLLDETQEVAKAY--------------G 106

Query: 119 VVRT--TFLIDEKGIIA 133
              T   FL D  G + 
Sbjct: 107 AACTPDFFLFDPDGKLV 123


>gnl|CDD|48560 cd03011, TlpA_like_ScsD_MtbDsbE, TlpA-like family, suppressor for
           copper sensitivity D protein (ScsD) and actinobacterial
           DsbE homolog subfamily; composed of ScsD, the DsbE
           homolog of Mycobacterium tuberculosis (MtbDsbE) and
           similar proteins, all containing a redox-active CXXC
           motif. The Salmonella typhimurium ScsD is a
           thioredoxin-like protein which confers copper tolerance
           to copper-sensitive mutants of E. coli. MtbDsbE has been
           characterized as an oxidase in vitro, catalyzing the
           disulfide bond formation of substrates like hirudin. The
           reduced form of MtbDsbE is more stable than its oxidized
           form, consistent with an oxidase function. This is in
           contrast to the function of DsbE from gram-negative
           bacteria which is a specific reductase of apocytochrome
           c..
          Length = 123

 Score = 34.8 bits (80), Expect = 0.010
 Identities = 18/99 (18%), Positives = 38/99 (38%), Gaps = 12/99 (12%)

Query: 11  PHFVLPSNDEQEISLLALGGSKIVLYFY----PKDDTSGCTAEAINFSSLKADFDEESTI 66
           P F   + D ++  L +L G  +++YF+    P      C   +   + L AD+     +
Sbjct: 1   PLFTATTLDGEQFDLESLSGKPVLVYFWATWCPV-----CRFTSPTVNQLAADY---PVV 52

Query: 67  LIGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDV 105
            + +      +  +F QK      ++ D    +   + V
Sbjct: 53  SVALRSGDDGAVARFMQKKGYGFPVINDPDGVISARWGV 91


>gnl|CDD|48517 cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c
           Oxidase) family; composed of proteins similar to Sco1, a
           membrane-anchored protein possessing a soluble domain
           with a TRX fold. Members of this family are required for
           the proper assembly of cytochrome c oxidase (COX). They
           contain a metal binding motif, typically CXXXC, which is
           located in a flexible loop. COX, the terminal enzyme in
           the respiratory chain, is imbedded in the inner
           mitochondrial membrane of all eukaryotes and in the
           plasma membrane of some prokaryotes. It is composed of
           two subunits, COX I and COX II. It has been proposed
           that Sco1 specifically delivers copper to the CuA site,
           a dinuclear copper center, of the COX II subunit.
           Mutations in human Sco1 and Sco2 cause fatal infantile
           hepatoencephalomyopathy and cardioencephalomyopathy,
           respectively. Both disorders are associated with severe
           COX deficiency in affected tissues. More recently, it
           has been argued that the redox sensitivity of the copper
           binding properties of Sco1 implies that it participates
           in signaling events rather than functioning as a
           chaperone that transfers copper to COX II..
          Length = 142

 Score = 33.7 bits (77), Expect = 0.023
 Identities = 25/141 (17%), Positives = 50/141 (35%), Gaps = 12/141 (8%)

Query: 10  APHFVLPSNDEQEISLLALGGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEEST---- 65
            P F L   D + ++L  L G  +++YF        C     N +        +      
Sbjct: 2   GPDFTLTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADGGDDVQ 61

Query: 66  -ILIGISP--DSIASHKKFHQKHNLSITLL---ADESKEVLKSYDVWKEKSMFGKKYMGV 119
            + I + P  D+    K + +        L    +E + + K++ V+ EK         V
Sbjct: 62  VVFISVDPERDTPEVLKAYAKAFGPGWIGLTGTPEEIEALAKAFGVYYEKVPEDDGDYLV 121

Query: 120 VRTT--FLIDEKGIIAQIWKP 138
             +   +L+D  G + + +  
Sbjct: 122 DHSAAIYLVDPDGKLVRYYGG 142


>gnl|CDD|80347 cd02125, PA_VSR, PA_VSR: Protease-associated (PA) domain-containing
           plant vacuolar sorting receptor (VSR). This group
           includes various PA domain-containing VSRs such as
           garden pea BP-80, pumpkin PV72, and various Arabidopsis
           VSRs including AtVSR1. In contrast to most eukaryotes,
           which only have one or two VSRs, plants have several.
           This may in part be a reflection of having a more
           complex vacuolar system with both lytic vacuoles and
           storage vacuoles. The lytic vacuole is thought to be
           equivalent to the mammalian lysosome and the yeast
           vacuole. Pea BP-80 is a type 1 transmembrane protein,
           involved in the targeting of proteins to the lytic
           vacuole; it has been suggested that this protein also
           mediates targeting to the storage vacuole. PV72 and
           AtVSR1 may mediate transport of seed storage proteins to
           protein storage vacuoles. The significance of the PA
           domain to VSRs 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 = 127

 Score = 28.4 bits (63), Expect = 0.82
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 29  GGSKIVLYFYPKDDTSGCTAEAINFSSLKADFDEESTILIGISPDSIASHKKFH-QKHNL 87
           GG+   +  YPK++ +GC    + F   K++      IL+        + K ++ Q+   
Sbjct: 8   GGTLTGVVVYPKENRTGCKEFDVFFKPKKSEPGRRPVILLLDRGGCFFTLKAWNAQQAGA 67

Query: 88  SITLLADESKEVLKSYD 104
           +  L+AD   E L + D
Sbjct: 68  AAVLVADNVDEPLLTMD 84


>gnl|CDD|144913 pfam01496, V_ATPase_I, V-type ATPase 116kDa subunit family.  This
           family consists of the 116kDa V-type ATPase (vacuolar
           (H+)-ATPases) subunits, as well as V-type ATP synthase
           subunit i. The V-type ATPases family are proton pumps
           that acidify intracellular compartments in eukaryotic
           cells for example yeast central vacuoles,
           clathrin-coated and synaptic vesicles. They have
           important roles in membrane trafficking processes. The
           116kDa subunit (subunit a) in the V-type ATPase is part
           of the V0 functional domain responsible for proton
           transport. The a subunit is a transmembrane glycoprotein
           with multiple putative transmembrane helices it has a
           hydrophilic amino terminal and a hydrophobic carboxy
           terminal. It has roles in proton transport and assembly
           of the V-type ATPase complex. This subunit is encoded by
           two homologous gene in yeast VPH1 and STV1.
          Length = 707

 Score = 27.7 bits (62), Expect = 1.3
 Identities = 23/114 (20%), Positives = 43/114 (37%), Gaps = 21/114 (18%)

Query: 37  FYPKDDTSGCTAEAINFSSLKADFDEESTILIGISPDSIASHKKFHQKHNLSITLLADES 96
            Y   +T G  +E I+   +    +E   +L     +   SH +          +L   +
Sbjct: 210 LYDVPETEGERSELISK--VNKRIEELQRVL-----EQTESHLE---------KVLVKIA 253

Query: 97  KEVLKSYDVWKEKSMFGKKYMGVVRTTFLIDEKGIIAQIWKPVTLKNHAQSVLK 150
            E+L     W E+ +  +K +      F  D K +IA+ W P       ++ L+
Sbjct: 254 DELL----AWDEQ-VSKEKAVYETLNLFNYDTKTLIAEGWVPAKDLEKLKAALE 302


>gnl|CDD|173788 cd04056, Peptidases_S53, Peptidase domain in the S53 family.
           Members of the peptidases S53 (sedolisin) family include
           endopeptidases and exopeptidases sedolisin, kumamolysin,
           and (PSCP) Pepstatin-insensitive Carboxyl Proteinase.
           The S53 family contains a catalytic triad Glu/Asp/Ser
           with an additional acidic residue Asp in the oxyanion
           hole, similar to that of Asn in subtilisin. The
           stability of these enzymes may be enhanced by calcium,
           some members have been shown to bind up to 4 ions via
           binding sites with different affinity. Some members of
           this clan contain disulfide bonds. These enzymes can be
           intra- and extracellular, some function at extreme
           temperatures and pH values. Characterized sedolisins
           include Kumamolisin, an extracellular calcium-dependent
           thermostable endopeptidase from Bacillus. The enzyme is
           synthesized with a 188 amino acid N-terminal preprotein
           region which is cleaved after the extraction into the
           extracellular space with low pH. One kumamolysin
           paralog, kumamolisin-As, is believed to be a
           collagenase. TPP1 is a serine protease that functions as
           a tripeptidyl exopeptidase as well as an endopeptidase.
           Less is known about PSCP from Pseudomonas which is
           thought to be an aspartic proteinase.
          Length = 361

 Score = 26.1 bits (58), Expect = 4.5
 Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 6/50 (12%)

Query: 2   TSLSVGDKAPHFVLPSNDEQEISL-----LALG-GSKIVLYFYPKDDTSG 45
             + V          S    E SL      A+  G+ I LYF P   T+G
Sbjct: 55  FIVVVIGGGNAPGTSSGWGGEASLDVEYAGAIAPGANITLYFAPGTVTNG 104


>gnl|CDD|133422 cd01337, MDH_glyoxysomal_mitochondrial, Glyoxysomal and
           mitochondrial malate dehydrogenases.  MDH is one of the
           key enzymes in the citric acid cycle, facilitating both
           the conversion of malate to oxaloacetate and
           replenishing levels of oxalacetate by reductive
           carboxylation of pyruvate. Members of this subfamily are
           localized to the glycosome and mitochondria. MDHs are
           part of the NAD(P)-binding Rossmann fold superfamily,
           which includes a wide variety of protein families
           including the NAD(P)-binding domains of alcohol
           dehydrogenases, tyrosine-dependent oxidoreductases,
           glyceraldehyde-3-phosphate dehydrogenases,
           formate/glycerate dehydrogenases, siroheme synthases,
           6-phosphogluconate dehydrogenases, aminoacid
           dehydrogenases, repressor rex, and NAD-binding potassium
           channel domains, among others.
          Length = 310

 Score = 25.5 bits (57), Expect = 6.3
 Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 1/35 (2%)

Query: 98  EVLKSYDVWKEKSMFGKKYMGVVRT-TFLIDEKGI 131
           EVLK   V+  K +FG   + VVR  TF+ +  G+
Sbjct: 129 EVLKKAGVYDPKRLFGVTTLDVVRANTFVAELLGL 163


>gnl|CDD|36707 KOG1494, KOG1494, KOG1494, NAD-dependent malate dehydrogenase
           [Energy production and conversion].
          Length = 345

 Score = 25.6 bits (56), Expect = 6.3
 Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 1/36 (2%)

Query: 97  KEVLKSYDVWKEKSMFGKKYMGVVRT-TFLIDEKGI 131
            EVLK   V+  K +FG   + VVR  TF+ +   +
Sbjct: 156 AEVLKKAGVYDPKKLFGVTTLDVVRANTFVAEVLNL 191


>gnl|CDD|35558 KOG0337, KOG0337, KOG0337, ATP-dependent RNA helicase [RNA
           processing and modification].
          Length = 529

 Score = 25.4 bits (55), Expect = 6.7
 Identities = 22/111 (19%), Positives = 46/111 (41%), Gaps = 10/111 (9%)

Query: 51  INFSSLKADFDEESTILIGISPDSIASHK-KFHQK---HNLSITLLADESKEVLKSYDVW 106
           + F+    ++D + T +IG SP S+ S + + HQ     N  + +LA  + +    Y   
Sbjct: 384 LIFAISHFEYDCDDTTVIGRSPQSLVSLESEGHQSILESNRELQVLARTADKAEMLY--- 440

Query: 107 KEKSMFGKKYMGVVRTTFLIDEKGIIAQIWKPVTLKNHAQSVLKMVKSLKQ 157
             ++        + R   +I  KG+  +       +N  +  L ++  +K 
Sbjct: 441 -TRTRPSPSPESLKRAKEMISSKGLHPR--FKSFGENEEKEKLDILYKIKN 488


>gnl|CDD|38634 KOG3424, KOG3424, KOG3424, 40S ribosomal protein S24 [Translation,
           ribosomal structure and biogenesis].
          Length = 132

 Score = 25.3 bits (55), Expect = 8.0
 Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 3/83 (3%)

Query: 47  TAEAINFSSLKADFDEESTILIGISPDSIASHKKFHQKHNLSITLLADESKEVLKSYDVW 106
           T +A+     +  F    +    +  DS+   KKF  K+ L    LA++ K   K     
Sbjct: 51  TPDAVFVFGFRTHFGGGKSTGFALIYDSVEYAKKFEPKYRLVRLGLAEKIKTSRK---QR 107

Query: 107 KEKSMFGKKYMGVVRTTFLIDEK 129
           KE+    KK  G  +      +K
Sbjct: 108 KERKNRMKKIFGTGKRKAKKAKK 130


>gnl|CDD|146370 pfam03699, UPF0182, Uncharacterized protein family (UPF0182).  This
           family contains uncharacterized integral membrane
           proteins.
          Length = 771

 Score = 25.2 bits (56), Expect = 9.0
 Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 12/48 (25%)

Query: 7   GDKAPHFVL-----PSNDEQEISLLALGGS------KIVLYFYPKDDT 43
           G+K P F+L     PS  +  I+ LA   S      K+VLY +PKD  
Sbjct: 701 GEKKPEFILLLPFTPSGRDNLIAWLA-ARSDGENYGKLVLYEFPKDRL 747


  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
   0.315    0.131    0.370 

Gapped
Lambda     K      H
   0.267   0.0638    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,773,118
Number of extensions: 83295
Number of successful extensions: 218
Number of sequences better than 10.0: 1
Number of HSP's gapped: 201
Number of HSP's successfully gapped: 35
Length of query: 157
Length of database: 6,263,737
Length adjustment: 86
Effective length of query: 71
Effective length of database: 4,405,363
Effective search space: 312780773
Effective search space used: 312780773
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: 53 (24.4 bits)