RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780281|ref|YP_003064694.1| cytochrome-c oxidase assembly factor protein [Candidatus Liberibacter asiaticus str. psy62] (201 letters) >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 = 132 bits (334), Expect = 5e-32 Identities = 57/143 (39%), Positives = 81/143 (56%), Gaps = 5/143 (3%) Query: 38 DVHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTL-LNAY 96 D L QDG +LS L KP +V+FG+T+C VCPTTL+ L + LKQ+ G + Sbjct: 4 DFTLTDQDGRPVTLSDLKGKPVLVYFGYTHCPDVCPTTLANLAQALKQLGADGGDDVQVV 63 Query: 97 FITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKY 156 FI+VDP+RDTPEV+K + + F IG++G P ++ +AK F +Y V + Y Sbjct: 64 FISVDPERDTPEVLKAYAKAFGPGWIGLTGTPEEIEALAKAFGVYYEKV----PEDDGDY 119 Query: 157 FVDHTTALLLFDTAGSIVGVIPY 179 VDH+ A+ L D G +V Sbjct: 120 LVDHSAAIYLVDPDGKLVRYYGG 142 >gnl|CDD|32182 COG1999, COG1999, Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]. Length = 207 Score = 126 bits (318), Expect = 3e-30 Identities = 70/199 (35%), Positives = 101/199 (50%), Gaps = 10/199 (5%) Query: 3 ALGIILGTILLAVLGSIAYVSFSSKFVDGNRRFNS-----DVHLVAQDGTDFSLSSLYIK 57 AL ++L LL +L S K N + D L QDG F+L L K Sbjct: 9 ALSLLLLLALLFLLLVGLAAEASDKGDRFNLDAAAVYIGGDFELTDQDGKPFTLKDLKGK 68 Query: 58 PSIVFFGFTNCSAVCPTTLSRLDRLLKQVD-PTGTLLNAYFITVDPKRDTPEVMKKFV-Q 115 PS+VFFG+T+C VCPTTL+ L LLK++ G + FITVDP+RDTPEV+KK+ Sbjct: 69 PSLVFFGYTHCPDVCPTTLAELKALLKKLGEGEGDDVQVVFITVDPERDTPEVLKKYAEL 128 Query: 116 RFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKYFVDHTTALLLFDTAGSIVG 175 F R IG++G P + VAK + ++ + V + Y +DH+ L D G +G Sbjct: 129 NFDPRWIGLTGTPEQIEEVAKAYGVFYSKV---PLDDSQNYTIDHSAGFYLIDADGRFLG 185 Query: 176 VIPYKDDSDSAIEKINRLI 194 Y + + + +L+ Sbjct: 186 TYDYGEPPEEIAADLKKLL 204 >gnl|CDD|38003 KOG2792, KOG2792, KOG2792, Putative cytochrome C oxidase assembly protein [Energy production and conversion]. Length = 280 Score = 106 bits (267), Expect = 3e-24 Identities = 50/198 (25%), Positives = 92/198 (46%), Gaps = 15/198 (7%) Query: 5 GIILGTILLAVLGSIAYVSFSSKFVDGNRR-----------FNSDVHLVAQDGTDFSLSS 53 + + L + G++AY+ + R LV DG + Sbjct: 77 LLATFALGLGLGGALAYLKKEKARLLEKERESANRTAGKPAIGGPFSLVDHDGKRVTEKD 136 Query: 54 LYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDP-TGTLLNAYFITVDPKRDTPEVMKK 112 K S+++FGFT+C +CP L ++ ++ +++ G FI+VDP+RD+ EV+ + Sbjct: 137 FLGKWSLIYFGFTHCPDICPDELEKMSAVVDEIEAKPGLPPVPLFISVDPERDSVEVVAE 196 Query: 113 FVQRFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKYFVDHTTALLLFDTAGS 172 +V F +++G++G V +VAK +R+Y + + ++ Y VDH+ + L D G Sbjct: 197 YVSEFHPKLLGLTGTTEQVKQVAKKYRVYFSTGPKD---EDQDYLVDHSIFMYLIDPEGE 253 Query: 173 IVGVIPYKDDSDSAIEKI 190 V D+D + I Sbjct: 254 FVDYYGRNYDADELADSI 271 >gnl|CDD|145666 pfam02630, SCO1-SenC, SCO1/SenC. This family is involved in biogenesis of respiratory and photosynthetic systems. SCO1 is required for a post-translational step in the accumulation of subunits COXI and COXII of cytochrome c oxidase. SenC is required for optimal cytochrome c oxidase activity and maximal induction of genes encoding the light-harvesting and reaction centre complexes of R. capsulatus. Length = 159 Score = 105 bits (265), Expect = 7e-24 Identities = 48/136 (35%), Positives = 84/136 (61%), Gaps = 2/136 (1%) Query: 39 VHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYFI 98 L+ Q+G +F+ +L K S+++FGFTNC +CP L RL ++K++ + FI Sbjct: 20 FTLIDQNGKNFTSENLKGKLSLIYFGFTNCPDICPPALDRLTDIIKKLKAENIDVQPVFI 79 Query: 99 TVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKYFV 158 +VDP+RDTP+V+K++++ F IG++G ++ VAK F+++ + V+ +K + Y V Sbjct: 80 SVDPERDTPKVLKEYLKNFHPSFIGLTGTTDEIKSVAKKFKVFYSKVIVDKPEQD--YLV 137 Query: 159 DHTTALLLFDTAGSIV 174 DH++ L D G I+ Sbjct: 138 DHSSFFYLIDPDGKIL 153 >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 = 39.5 bits (92), Expect = 7e-04 Identities = 30/140 (21%), Positives = 45/140 (32%), Gaps = 26/140 (18%) Query: 38 DVHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYF 97 D L DG SLS L K +V F + C C + L+ L K+ G Sbjct: 1 DFSLPDLDGKPVSLSDLKGKVVLVNFWASWC-PPCRAEMPELEALAKEYKDDGVE----V 55 Query: 98 ITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKYF 157 + V+ D P +K F+++ + I +L + + Y Sbjct: 56 VGVNVDDDDPAAVKAFLKK---------------------YGITFPVLLDPDGELAKAYG 94 Query: 158 VDHTTALLLFDTAGSIVGVI 177 V L D G I Sbjct: 95 VRGLPTTFLIDRDGRIRARH 114 >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 = 33.0 bits (76), Expect = 0.059 Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 6/78 (7%) Query: 41 LVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYFITV 100 L DG + SLS K ++FF + + VC T L L L ++ L + V Sbjct: 10 LPDLDGKEVSLSDYKGKWVVLFFYPKDFTPVCTTELPALADLYEEFKK----LGVEVLGV 65 Query: 101 DPKRDTPEVMKKFVQRFS 118 D+PE KKF ++ Sbjct: 66 SV--DSPESHKKFAEKLG 81 >gnl|CDD|30799 COG0450, AhpC, Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]. Length = 194 Score = 32.1 bits (73), Expect = 0.095 Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 2/56 (3%) Query: 47 TDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYFITVDP 102 + +LS Y K ++FF + + VCPT + + ++ G ++ D Sbjct: 24 EEITLSDYYGKWVVLFFYPADFTFVCPTEIIAFAKRYEEFQKRGV--EVIGVSTDS 77 >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 = 31.0 bits (70), Expect = 0.23 Identities = 23/82 (28%), Positives = 33/82 (40%), Gaps = 12/82 (14%) Query: 38 DVHLVAQDGTDFSLSSLYIKPSIVFF---GFTNCSAVCPTTLSRLDRLLKQVDPTGTLLN 94 D L A DG + SLS K ++FF FT VC T L L ++ Sbjct: 4 DFTLPATDGGEVSLSDFKGKWVVLFFYPKDFT---PVCTTELCAFRDLAEEFA----KGG 56 Query: 95 AYFITVDPKRDTPEVMKKFVQR 116 A + V D+P K + ++ Sbjct: 57 AEVLGVSV--DSPFSHKAWAEK 76 >gnl|CDD|38979 KOG3775, KOG3775, KOG3775, Mitogen-activated protein kinase scaffold protein JIP [Signal transduction mechanisms]. Length = 482 Score = 30.4 bits (68), Expect = 0.37 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 1/78 (1%) Query: 97 FITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKY 156 + + + T + +FV R D + GD + V A +F N+ + G+ + Sbjct: 255 LVNGEEQEQTHRAVFRFVPRHPDELELEIGDAVLVEAEADDFWFEGFNLRTGERGIFPAF 314 Query: 157 FVDHTTALLLFDTAGSIV 174 + H D GS+ Sbjct: 315 YA-HEVDGPEEDLLGSLR 331 >gnl|CDD|31418 COG1225, Bcp, Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]. Length = 157 Score = 29.0 bits (65), Expect = 0.81 Identities = 38/159 (23%), Positives = 66/159 (41%), Gaps = 18/159 (11%) Query: 38 DVHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYF 97 D L QDG SLS L KP +++F + + C T LL++ + L A Sbjct: 12 DFELPDQDGETVSLSDLRGKPVVLYFYPKDFTPGCTTEACDFRDLLEEFEK----LGAVV 67 Query: 98 ITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVMRVAKNFRIYVNNVLAEKSGVEEKYF 157 + + P D+P+ KKF ++ +S + VA+ + V EK ++Y Sbjct: 68 LGISP--DSPKSHKKFAEKHGLTFPLLSDED---GEVAEAY-----GVWGEKKMYGKEYM 117 Query: 158 VDHTTALLLFDTAGSIVGV---IPYKDDSDSAIEKINRL 193 + ++ D G I V + K +D + + +L Sbjct: 118 GIERSTFVI-DPDGKIRYVWRKVKVKGHADEVLAALKKL 155 >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 = 28.7 bits (64), Expect = 1.1 Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 10/72 (13%) Query: 45 DGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQVDPTGTLLNAYFITVDPKR 104 DG F L SL KP +V+F T C VC T +++L ++V + Sbjct: 9 DGEQFDLESLSGKPVLVYFWATWC-PVCRFTSPTVNQLAADYP---------VVSVALRS 58 Query: 105 DTPEVMKKFVQR 116 + +F+Q+ Sbjct: 59 GDDGAVARFMQK 70 >gnl|CDD|34137 COG4458, SrfC, Uncharacterized protein conserved in bacteria, putative virulence factor [Function unknown]. Length = 821 Score = 27.3 bits (60), Expect = 3.0 Identities = 10/34 (29%), Positives = 16/34 (47%) Query: 81 RLLKQVDPTGTLLNAYFITVDPKRDTPEVMKKFV 114 RLL + D L NA+F+ +R T + + Sbjct: 133 RLLSETDIAKILGNAFFLDGPAERRTYLAPESVI 166 >gnl|CDD|34575 COG4968, PilE, Tfp pilus assembly protein PilE [Cell motility and secretion / Intracellular trafficking and secretion]. Length = 139 Score = 27.3 bits (60), Expect = 3.3 Identities = 20/93 (21%), Positives = 32/93 (34%), Gaps = 4/93 (4%) Query: 11 ILLAVLGSIAYVSFSSKFVDGNRRFNSDVHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSA 70 ++ +L IAY S+ + + R S + F ++ T Sbjct: 18 AIVGILALIAYPSYQNYVLRSRR---SAAKAALLENAQFMERYYALQNGYAGTTSTLAPK 74 Query: 71 VCPTTLSRLDRLLKQVDPTGT-LLNAYFITVDP 102 V P+ D L V P G L A+ +T P Sbjct: 75 VPPSANEDFDYRLSAVTPAGKATLTAFTLTATP 107 >gnl|CDD|33308 COG3505, VirD4, Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]. Length = 596 Score = 26.9 bits (59), Expect = 3.9 Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 10/68 (14%) Query: 17 GSIAYVSFSSKFVDGNRRFNSDVHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTL 76 S + SS + + A G+DF + L K + V+FG P + Sbjct: 327 TSGVLSTASSAL----TLLMNPLVAAATSGSDFDIRDLRKKKTTVYFGLD------PDRI 376 Query: 77 SRLDRLLK 84 SR+ LL+ Sbjct: 377 SRVKPLLR 384 >gnl|CDD|35096 COG5537, IRR1, Cohesin [Cell division and chromosome partitioning]. Length = 740 Score = 26.5 bits (58), Expect = 4.6 Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 3/41 (7%) Query: 96 YFITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDVMRVAK 136 + + P D +++FV+RF DRI+ D +R+ Sbjct: 340 FLCSRIPHTDA---IRRFVERFKDRILEFLRTDSDCVRICS 377 >gnl|CDD|143420 cd07102, ALDH_EDX86601, Uncharacterized aldehyde dehydrogenase of Synechococcus sp. PCC 7335 (EDX86601). Uncharacterized aldehyde dehydrogenase of Synechococcus sp. PCC 7335 (locus EDX86601) and other similar sequences, are present in this CD. Length = 452 Score = 26.4 bits (59), Expect = 5.1 Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 1/34 (2%) Query: 158 VDHTTALLLFDTAGSIVGVIPYKDDSDSAIEKIN 191 VDH+ ++ +T G +VG++ K D AI +N Sbjct: 348 VDHSMRVMREETFGPVVGIMKVKSD-AEAIALMN 380 >gnl|CDD|143417 cd07099, ALDH_DDALDH, Methylomonas sp. 4,4'-diapolycopene-dialdehyde dehydrogenase-like. The 4,4'-diapolycopene-dialdehyde dehydrogenase (DDALDH) involved in C30 carotenoid synthesis in Methylomonas sp. strain 16a and other similar sequences are present in this CD. DDALDH converts 4,4'-diapolycopene-dialdehyde into 4,4'-diapolycopene-diacid. Length = 453 Score = 26.4 bits (59), Expect = 5.9 Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 1/34 (2%) Query: 158 VDHTTALLLFDTAGSIVGVIPYKDDSDSAIEKIN 191 V H ++ +T G ++ V+P D+ D AI N Sbjct: 347 VPHDMDVMREETFGPVLPVMPVADE-DEAIALAN 379 >gnl|CDD|143461 cd07143, ALDH_AldA_AN0554, Aspergillus nidulans aldehyde dehydrogenase, AldA (AN0554)-like. NAD(P)+-dependent aldehyde dehydrogenase (AldA) of Aspergillus nidulans (locus AN0554), and other similar sequences, are present in this CD. Length = 481 Score = 26.3 bits (58), Expect = 6.4 Identities = 32/119 (26%), Positives = 51/119 (42%), Gaps = 36/119 (30%) Query: 109 VMKKFVQRFSDRIIGIS-GDPID--------VMRVAKNFRI--YVNNVLAEKSGVE---- 153 + KFV+RF ++ + GDP V ++ RI Y+ + AE + VE Sbjct: 300 IYDKFVKRFKEKAKKLKVGDPFAEDTFQGPQVSQIQYE-RIMSYIESGKAEGATVETGGK 358 Query: 154 ----EKYFVDHTTALLLFDTA-----------GSIVGVIPYKDDSDSAIEKINRLITYG 197 E YF++ T + D G +V VI +K + + AI++ N TYG Sbjct: 359 RHGNEGYFIEPT---IFTDVTEDMKIVKEEIFGPVVAVIKFKTEEE-AIKRAND-STYG 412 >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 = 26.3 bits (58), Expect = 6.5 Identities = 12/26 (46%), Positives = 15/26 (57%) Query: 38 DVHLVAQDGTDFSLSSLYIKPSIVFF 63 D L QDG SLS L KP +++F Sbjct: 5 DFTLPDQDGETVSLSDLRGKPVVLYF 30 >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 = 26.2 bits (58), Expect = 6.5 Identities = 11/51 (21%), Positives = 22/51 (43%) Query: 35 FNSDVHLVAQDGTDFSLSSLYIKPSIVFFGFTNCSAVCPTTLSRLDRLLKQ 85 F + + + + SLS K ++FF + + VCPT + ++ Sbjct: 8 FKATAVVPNGEFKEISLSDYKGKWVVLFFYPLDFTFVCPTEIIAFSDRYEE 58 >gnl|CDD|107350 cd06355, PBP1_FmdD_like, Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems. Length = 348 Score = 26.1 bits (58), Expect = 6.6 Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 7/36 (19%) Query: 96 YFITVDPKRDTPEVMKKFVQRFSDRI--IGISGDPI 129 YF +VD TPE KKFV F R ++ DP+ Sbjct: 247 YFQSVD----TPE-NKKFVAAFKARYGQDRVTNDPM 277 >gnl|CDD|143431 cd07113, ALDH_PADH_NahF, Escherichia coli NAD+-dependent phenylacetaldehyde dehydrogenase PadA-like. NAD+-dependent, homodimeric, phenylacetaldehyde dehydrogenase (PADH, EC=1.2.1.39) PadA of Escherichia coli involved in the catabolism of 2-phenylethylamine, and other related sequences, are present in this CD. Also included is the Pseudomonas fluorescens ST StyD PADH involved in styrene catabolism, the Sphingomonas sp. LB126 FldD protein involved in fluorene degradation, and the Novosphingobium aromaticivorans NahF salicylaldehyde dehydrogenase involved in the NAD+-dependent conversion of salicylaldehyde to salicylate. Length = 477 Score = 26.3 bits (58), Expect = 6.7 Identities = 25/111 (22%), Positives = 40/111 (36%), Gaps = 33/111 (29%) Query: 108 EVMKKFVQRFSDRIIGISGDP-------------------IDVMRVAKNFRIYVNNVLAE 148 E++ K Q S +G D +D R + + LA Sbjct: 299 ELVTKLKQALSSFQVGSPMDESVMFGPLANQPHFDKVCSYLDDARAEGDEIVRGGEALAG 358 Query: 149 KSGVEEKYFVDHT--------TALLLFDTAGSIVGVIPYKDDSDSAIEKIN 191 E YFV T + L+ +T G +V +PY+D+ + I+ IN Sbjct: 359 -----EGYFVQPTLVLARSADSRLMREETFGPVVSFVPYEDE-EELIQLIN 403 >gnl|CDD|34830 COG5233, GRH1, Peripheral Golgi membrane protein [Intracellular trafficking and secretion]. Length = 417 Score = 25.9 bits (56), Expect = 7.9 Identities = 7/29 (24%), Positives = 14/29 (48%) Query: 110 MKKFVQRFSDRIIGISGDPIDVMRVAKNF 138 +K D I+GI+ DP+ + + + Sbjct: 76 AEKAGMVVGDYILGINEDPLRFLEMNRRR 104 >gnl|CDD|31437 COG1244, COG1244, Predicted Fe-S oxidoreductase [General function prediction only]. Length = 358 Score = 25.7 bits (56), Expect = 8.2 Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 2/49 (4%) Query: 108 EVMKKFVQRFSDRIIGI--SGDPIDVMRVAKNFRIYVNNVLAEKSGVEE 154 E K+ +F + ++ I SG +D V + R Y+ ++E V+E Sbjct: 90 EAYSKYEGKFDEFVVKIFTSGSFLDPEEVPREARRYILERISENDNVKE 138 >gnl|CDD|112592 pfam03786, UxuA, D-mannonate dehydratase (UxuA). UxuA (this family) and UxuB are required for hexuronate degradation. Length = 350 Score = 25.8 bits (57), Expect = 8.4 Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 4/46 (8%) Query: 74 TTLSRLDRLLKQVD-PTG--TLLNAYFITVDPKRDTPEVMKKFVQR 116 T + RLL+ VD P TL + P D PE++++F R Sbjct: 221 TNIEDYQRLLELVDSPYNGITLCTGSY-GARPDNDLPEMIREFADR 265 >gnl|CDD|37461 KOG2250, KOG2250, KOG2250, Glutamate/leucine/phenylalanine/valine dehydrogenases [Amino acid transport and metabolism]. Length = 514 Score = 25.7 bits (56), Expect = 9.2 Identities = 12/34 (35%), Positives = 20/34 (58%) Query: 98 ITVDPKRDTPEVMKKFVQRFSDRIIGISGDPIDV 131 I +DPK + +++ +RF+D +I I G DV Sbjct: 148 ILIDPKGKSDNEIERITRRFTDELIDIIGPDTDV 181 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 0.140 0.398 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: 2,412,582 Number of extensions: 127214 Number of successful extensions: 448 Number of sequences better than 10.0: 1 Number of HSP's gapped: 440 Number of HSP's successfully gapped: 37 Length of query: 201 Length of database: 6,263,737 Length adjustment: 89 Effective length of query: 112 Effective length of database: 4,340,536 Effective search space: 486140032 Effective search space used: 486140032 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 (21.9 bits) S2: 55 (25.0 bits)