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)