Query 033772
Match_columns 112
No_of_seqs 163 out of 549
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 06:07:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033772.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033772hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4600 Mitochondrial ribosoma 100.0 8.3E-36 1.8E-40 224.6 6.0 84 14-112 2-89 (144)
2 COG0211 RpmA Ribosomal protein 100.0 2.6E-34 5.5E-39 202.0 4.7 58 55-112 1-62 (87)
3 PRK05435 rpmA 50S ribosomal pr 100.0 9.4E-34 2E-38 197.3 5.6 58 55-112 1-62 (82)
4 CHL00121 rpl27 ribosomal prote 100.0 8.6E-34 1.9E-38 198.9 5.0 58 55-112 1-62 (86)
5 TIGR00062 L27 ribosomal protei 100.0 1.3E-33 2.7E-38 196.9 5.0 58 55-112 1-62 (83)
6 PF01016 Ribosomal_L27: Riboso 100.0 5E-33 1.1E-37 192.8 4.9 57 56-112 1-61 (81)
7 PF14382 ECR1_N: Exosome compl 80.8 2.3 4.9E-05 25.7 2.9 28 84-112 1-30 (39)
8 PF13533 Biotin_lipoyl_2: Biot 78.8 1.9 4.1E-05 26.4 2.1 19 76-94 15-33 (50)
9 COG4015 Predicted dinucleotide 45.1 6 0.00013 32.1 -0.4 25 77-101 48-73 (217)
10 PF02749 QRPTase_N: Quinolinat 39.0 20 0.00044 23.9 1.5 21 77-97 49-69 (88)
11 PF00529 HlyD: HlyD family sec 36.7 23 0.0005 26.8 1.6 17 77-93 15-31 (305)
12 TIGR02971 heterocyst_DevB ABC 28.8 42 0.00091 26.4 2.0 23 72-94 25-47 (327)
13 cd06850 biotinyl_domain The bi 26.2 67 0.0015 18.7 2.1 17 77-93 13-29 (67)
14 PF00364 Biotin_lipoyl: Biotin 22.7 56 0.0012 20.9 1.4 17 77-93 20-36 (74)
15 COG0157 NadC Nicotinate-nucleo 22.6 64 0.0014 27.2 2.0 21 77-97 68-88 (280)
16 PF07831 PYNP_C: Pyrimidine nu 21.7 63 0.0014 21.5 1.5 28 67-94 24-53 (75)
17 TIGR01000 bacteriocin_acc bact 21.7 64 0.0014 27.3 1.9 20 75-94 71-90 (457)
18 COG1566 EmrA Multidrug resista 20.3 75 0.0016 27.1 2.1 17 77-93 67-83 (352)
19 PRK08225 acetyl-CoA carboxylas 20.1 99 0.0021 19.2 2.1 17 77-93 52-68 (70)
No 1
>KOG4600 consensus Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.3e-36 Score=224.57 Aligned_cols=84 Identities=51% Similarity=0.699 Sum_probs=74.8
Q ss_pred eeeeeeccCcccceecCCcccccCcceecCCCCCCcceeEEeeeccCCcccCCCCCCCCcccceEeeCCeEeecCcEEEe
Q 033772 14 FKGLSLSSSSSSSFLKGDFTVCPKSVTVSLPPTSPLPLTIESAHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVR 93 (112)
Q Consensus 14 f~glsl~s~~sssf~~g~~~~~~~~~~~~~p~~~~~~~~ir~A~KK~gGStkNgrdS~~KrLGvK~~~Gq~V~~G~IIvR 93 (112)
|+.|.|++ +|+++.|+.+.+ ..++||+|+||++|||||+|||+|||||||+|+||+|+|||||+|
T Consensus 2 ~~~l~l~t--as~~~~~~ss~~-------------~~l~vR~AtKk~aGStKN~~dS~grrlGvKk~egq~V~~G~IIvr 66 (144)
T KOG4600|consen 2 VNALRLST--ASSSLDGSSSGL-------------SFLAVRWATKKGAGSTKNGRDSAGRRLGVKKYEGQSVIPGNIIVR 66 (144)
T ss_pred ccceecch--hhhhhcCCCCcc-------------eeeeeeeecccccCccccCCCCCcccccceecCCeeeecccEEEE
Confidence 57788877 555666665322 467899999999999999999999999999999999999999999
Q ss_pred ecCCC---CCceeecccc-eeeC
Q 033772 94 QRGTK---GKMWGLARTI-QYSL 112 (112)
Q Consensus 94 QRGtk---G~nVg~GrD~-lfAl 112 (112)
||||| |+|||||||| ||||
T Consensus 67 QRgtkfHPG~nVGiGKDhtifaL 89 (144)
T KOG4600|consen 67 QRGTKFHPGDNVGIGKDHTIFAL 89 (144)
T ss_pred ecccccCCCcccccCCcceEEEe
Confidence 99999 9999999999 9997
No 2
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.6e-34 Score=201.99 Aligned_cols=58 Identities=60% Similarity=0.898 Sum_probs=57.3
Q ss_pred eeeccCCcccCCCCCCCCcccceEeeCCeEeecCcEEEeecCCC---CCceeecccc-eeeC
Q 033772 55 SAHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTK---GKMWGLARTI-QYSL 112 (112)
Q Consensus 55 ~A~KK~gGStkNgrdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtk---G~nVg~GrD~-lfAl 112 (112)
|||||++|||+|||||++||||+|++|||+|.+|+||||||||+ |+|||+|+|| ||||
T Consensus 1 mA~KKg~GSt~NgRDS~~krLGvK~~~Gq~v~aG~IivRQRGTk~hpG~NVG~GkDhTlFAl 62 (87)
T COG0211 1 MAHKKGGGSTRNGRDSESKRLGVKKFGGQFVKAGSIIVRQRGTKFHPGVNVGRGKDHTLFAL 62 (87)
T ss_pred CcccccccccccCccccccccceeeeCCeEEecccEEEEeccccccCCcccccCCCceEEEe
Confidence 79999999999999999999999999999999999999999999 9999999999 9996
No 3
>PRK05435 rpmA 50S ribosomal protein L27; Validated
Probab=100.00 E-value=9.4e-34 Score=197.25 Aligned_cols=58 Identities=60% Similarity=0.888 Sum_probs=57.2
Q ss_pred eeeccCCcccCCCCCCCCcccceEeeCCeEeecCcEEEeecCCC---CCceeecccc-eeeC
Q 033772 55 SAHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTK---GKMWGLARTI-QYSL 112 (112)
Q Consensus 55 ~A~KK~gGStkNgrdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtk---G~nVg~GrD~-lfAl 112 (112)
|||||++|||+|||||+|||||||+++||+|.||+||||||||+ |+||+||||| |||+
T Consensus 1 mA~KK~~GStkNgrdS~~krLGvK~~~g~~V~~G~IivRQRGtk~~PG~nVg~GrD~TlfA~ 62 (82)
T PRK05435 1 MAHKKGGGSTRNGRDSESKRLGVKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGKDHTLFAL 62 (82)
T ss_pred CCcccccCcCCCCCCCCcccceeEecCCEEEcCCcEEEEeCCCeECCCCCEeecCCceEEEe
Confidence 79999999999999999999999999999999999999999999 9999999999 9996
No 4
>CHL00121 rpl27 ribosomal protein L27; Reviewed
Probab=100.00 E-value=8.6e-34 Score=198.91 Aligned_cols=58 Identities=59% Similarity=0.895 Sum_probs=57.3
Q ss_pred eeeccCCcccCCCCCCCCcccceEeeCCeEeecCcEEEeecCCC---CCceeecccc-eeeC
Q 033772 55 SAHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTK---GKMWGLARTI-QYSL 112 (112)
Q Consensus 55 ~A~KK~gGStkNgrdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtk---G~nVg~GrD~-lfAl 112 (112)
|||||++|||+|||||+|||||||+++||+|.||+||||||||+ |+|||||||| |||+
T Consensus 1 mA~KK~~GStkNgrdS~~KrLGvK~~~gq~V~~G~IivRQRGtk~hPG~NVg~GrD~TlfAl 62 (86)
T CHL00121 1 MAHKKGAGSTKNGRDSNAKRLGVKRFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDFTLYAL 62 (86)
T ss_pred CCcccccCcCCCCCCCCcccceeEEcCCEEEcCCcEEEEcCCCeECCCCcccccCCceEEEc
Confidence 79999999999999999999999999999999999999999999 9999999999 9996
No 5
>TIGR00062 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain.
Probab=100.00 E-value=1.3e-33 Score=196.93 Aligned_cols=58 Identities=57% Similarity=0.848 Sum_probs=57.2
Q ss_pred eeeccCCcccCCCCCCCCcccceEeeCCeEeecCcEEEeecCCC---CCceeecccc-eeeC
Q 033772 55 SAHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTK---GKMWGLARTI-QYSL 112 (112)
Q Consensus 55 ~A~KK~gGStkNgrdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtk---G~nVg~GrD~-lfAl 112 (112)
|||||++|||+|||||+|||||||+++||+|.||+||||||||+ |+||+||||| |||+
T Consensus 1 ~A~Kk~~GSt~NgrdS~~krLGvK~~~gq~V~~G~IivRQRGtk~hPG~nVg~GrD~TlfAl 62 (83)
T TIGR00062 1 MATKKGVGSTKNGRDSEAKRLGVKRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGKDHTLFAL 62 (83)
T ss_pred CCcccccCcCCCCCCCCCccceeEecCCEEEcCCcEEEEcCCceECCCCcccccCCCeEEEe
Confidence 79999999999999999999999999999999999999999999 9999999999 9996
No 6
>PF01016 Ribosomal_L27: Ribosomal L27 protein; InterPro: IPR001684 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L27 is a protein from the large (50S) subunit; it is essential for ribosome function, but its exact role is unclear. It belongs to a family of ribosomal proteins, examples of which are found in bacteria, chloroplasts of plants and red algae and the mitochondria of fungi (e.g. MRP7 from yeast mitochondria). The schematic relationship between these groups of proteins is shown below. Bacterial L27 Nxxxxxxxxx Algal L27 Nxxxxxxxxx Plant L27 tttttNxxxxxxxxxxxxx Yeast MRP7 tttNxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 't': transit peptide. 'N': N-terminal of mature protein. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2ZJQ_T 2ZJP_T 3PIP_T 3DLL_T 3PIO_T 1Y69_U 3CF5_T 2ZJR_T 1VSA_U 3PYT_W ....
Probab=99.97 E-value=5e-33 Score=192.85 Aligned_cols=57 Identities=65% Similarity=0.962 Sum_probs=51.6
Q ss_pred eeccCCcccCCCCCCCCcccceEeeCCeEeecCcEEEeecCCC---CCceeecccc-eeeC
Q 033772 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTK---GKMWGLARTI-QYSL 112 (112)
Q Consensus 56 A~KK~gGStkNgrdS~~KrLGvK~~~Gq~V~~G~IIvRQRGtk---G~nVg~GrD~-lfAl 112 (112)
||||++|||+|||||+|||||||+++||+|.||+||||||||+ |+||+||||| |||+
T Consensus 1 A~KK~~GSt~NgrdS~~krlGvK~~~G~~V~~G~IivRQRgtk~hPG~NVg~GrD~TLfAl 61 (81)
T PF01016_consen 1 AHKKGGGSTKNGRDSNPKRLGVKKFGGQFVKAGNIIVRQRGTKFHPGENVGMGRDHTLFAL 61 (81)
T ss_dssp --SSSSSSSS--S-STTTTSEESSSTTCEESSTSEEEEBSSSSSEEBTTEEEETTSEEEES
T ss_pred CCccccccccCCCCCCCcccEEEEeCCEEEcCCCEEEEeCCCcCcCCCCEEECCCCcEEEe
Confidence 8999999999999999999999999999999999999999999 9999999999 9996
No 7
>PF14382 ECR1_N: Exosome complex exonuclease RRP4 N-terminal region; PDB: 2NN6_I 3M7N_C 2BA1_A 3M85_C.
Probab=80.84 E-value=2.3 Score=25.73 Aligned_cols=28 Identities=18% Similarity=0.144 Sum_probs=20.6
Q ss_pred EeecCcEEEeecCCC-CCceeecccc-eeeC
Q 033772 84 VAKPGAIIVRQRGTK-GKMWGLARTI-QYSL 112 (112)
Q Consensus 84 ~V~~G~IIvRQRGtk-G~nVg~GrD~-lfAl 112 (112)
.|.||+.|....... |+++.. +|. |||.
T Consensus 1 iV~PG~~l~~~~e~~~G~GTY~-~~g~I~as 30 (39)
T PF14382_consen 1 IVVPGDRLGSSEEYMPGHGTYV-RDGNIYAS 30 (39)
T ss_dssp EE-TT-EEEETTTSEESTTEEE-ETTEEEES
T ss_pred CCCCCCEeecCCCEecCCCEEE-eCCEEEEE
Confidence 488999999987666 999988 666 9873
No 8
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=78.84 E-value=1.9 Score=26.36 Aligned_cols=19 Identities=21% Similarity=0.267 Sum_probs=15.9
Q ss_pred ceEeeCCeEeecCcEEEee
Q 033772 76 GVKIFGDQVAKPGAIIVRQ 94 (112)
Q Consensus 76 GvK~~~Gq~V~~G~IIvRQ 94 (112)
=+...+|++|++|++|++=
T Consensus 15 ~v~V~~G~~VkkGd~L~~l 33 (50)
T PF13533_consen 15 SVYVKEGQQVKKGDVLLVL 33 (50)
T ss_pred EEEecCCCEEcCCCEEEEE
Confidence 3566799999999999973
No 9
>COG4015 Predicted dinucleotide-utilizing enzyme of the ThiF/HesA family [General function prediction only]
Probab=45.12 E-value=6 Score=32.15 Aligned_cols=25 Identities=32% Similarity=0.542 Sum_probs=22.5
Q ss_pred eEeeCCeEeecCcEEEeecCCC-CCc
Q 033772 77 VKIFGDQVAKPGAIIVRQRGTK-GKM 101 (112)
Q Consensus 77 vK~~~Gq~V~~G~IIvRQRGtk-G~n 101 (112)
+-.+|||.|.+.+||.|..|.+ |+|
T Consensus 48 i~v~Dgqrve~dDiihrr~Ga~~GEy 73 (217)
T COG4015 48 IYVFDGQRVEEDDIIHRRLGAKVGEY 73 (217)
T ss_pred EEEecCcccCchhhHHHHhCCCcchh
Confidence 5679999999999999999999 775
No 10
>PF02749 QRPTase_N: Quinolinate phosphoribosyl transferase, N-terminal domain; InterPro: IPR022412 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2.4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0016763 transferase activity, transferring pentosyl groups; PDB: 3L0G_B 1QAP_A 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 2I14_C 1X1O_B 2B7Q_B ....
Probab=38.98 E-value=20 Score=23.91 Aligned_cols=21 Identities=19% Similarity=0.381 Sum_probs=15.5
Q ss_pred eEeeCCeEeecCcEEEeecCC
Q 033772 77 VKIFGDQVAKPGAIIVRQRGT 97 (112)
Q Consensus 77 vK~~~Gq~V~~G~IIvRQRGt 97 (112)
+.+.||+.|.||++|++=+|.
T Consensus 49 ~~~~dG~~v~~g~~i~~i~G~ 69 (88)
T PF02749_consen 49 WLVKDGDRVEPGDVILEIEGP 69 (88)
T ss_dssp ESS-TT-EEETTCEEEEEEEE
T ss_pred EEeCCCCCccCCcEEEEEEeC
Confidence 345799999999999987763
No 11
>PF00529 HlyD: HlyD family secretion protein the corresponding Prosite entry.; InterPro: IPR006143 This entry represents a large family of polypeptides, the MFP (for membrane fusion protein) family. MFPs are a component of the of the RND family of transporters (RND refers to resistance, nodulation, and cell division). MFPs are proposed to span the periplasm in some way linking the inner and outer membranes []. However, some members of this family are found in Gram-positive bacteria, where there is no outer membrane. MFPs are involved in the export of a variety of compounds, from drug molecules to large polypeptides, and are united by their similar overall structural organisation, combined with some conserved regions []. This family includes: Haemolysin secretion protein D (HlyD) from Escherichia coli. Lactococcin A secretion protein LcnD from Lactococcus lactis []. RTX-I toxin determinant D from Actinobacillus pleuropneumoniae. Calmodulin-sensitive adenylate cyclase-haemolysin (cyclolysin) CyaD from Bordetella pertussis. Colicin V secretion protein CvaA from E. coli []. Proteases secretion protein PrtE from Erwinia chrysanthemi []. Alkaline protease secretion protein AprE from Pseudomonas aeruginosa []. Several multidrug resistance proteins []. ; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 1T5E_E 1VF7_K 2V4D_I 4DK1_C 2F1M_B.
Probab=36.70 E-value=23 Score=26.76 Aligned_cols=17 Identities=24% Similarity=0.405 Sum_probs=12.5
Q ss_pred eEeeCCeEeecCcEEEe
Q 033772 77 VKIFGDQVAKPGAIIVR 93 (112)
Q Consensus 77 vK~~~Gq~V~~G~IIvR 93 (112)
+-+-+||+|++|++|++
T Consensus 15 i~V~eG~~VkkGq~L~~ 31 (305)
T PF00529_consen 15 ILVKEGQRVKKGQVLAR 31 (305)
T ss_dssp E-S-TTEEE-TTSECEE
T ss_pred EEccCcCEEeCCCEEEE
Confidence 45678999999999997
No 12
>TIGR02971 heterocyst_DevB ABC exporter membrane fusion protein, DevB family. Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. DevB from Anabaena sp. strain PCC 7120 is partially characterized as a membrane fusion protein of the DevBCA ABC exporter, probably a glycolipid exporter, required for heterocyst formation. Most Cyanobacteria have one member only, but Nostoc sp. PCC 7120 has seven members.
Probab=28.82 E-value=42 Score=26.38 Aligned_cols=23 Identities=4% Similarity=0.115 Sum_probs=19.0
Q ss_pred CcccceEeeCCeEeecCcEEEee
Q 033772 72 GQRLGVKIFGDQVAKPGAIIVRQ 94 (112)
Q Consensus 72 ~KrLGvK~~~Gq~V~~G~IIvRQ 94 (112)
|+=.-+.+.+|+.|++|++|++=
T Consensus 25 G~V~~i~V~eG~~V~~G~~L~~l 47 (327)
T TIGR02971 25 DRIKKLLVAEGDRVQAGQVLAEL 47 (327)
T ss_pred cEEEEEEccCCCEecCCcEEEEe
Confidence 45556778899999999999983
No 13
>cd06850 biotinyl_domain The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine.
Probab=26.19 E-value=67 Score=18.73 Aligned_cols=17 Identities=12% Similarity=0.118 Sum_probs=13.7
Q ss_pred eEeeCCeEeecCcEEEe
Q 033772 77 VKIFGDQVAKPGAIIVR 93 (112)
Q Consensus 77 vK~~~Gq~V~~G~IIvR 93 (112)
+..-.|++|.+|+.|++
T Consensus 13 ~~v~~G~~v~~g~~l~~ 29 (67)
T cd06850 13 VLVKEGDKVEAGQPLAV 29 (67)
T ss_pred EEeCCCCEECCCCEEEE
Confidence 56677888888888886
No 14
>PF00364 Biotin_lipoyl: Biotin-requiring enzyme; InterPro: IPR000089 The biotin / lipoyl attachment domain has a conserved lysine residue that binds biotin or lipoic acid. Biotin plays a catalytic role in some carboxyl transfer reactions and is covalently attached, via an amide bond, to a lysine residue in enzymes requiring this coenzyme []. E2 acyltransferases have an essential cofactor, lipoic acid, which is covalently bound via an amide linkage to a lysine group []. The lipoic acid cofactor is found in a variety of proteins that include, H-protein of the glycine cleavage system (GCS), mammalian and yeast pyruvate dehydrogenases and fast migrating protein (FMP) (gene acoC) from Ralstonia eutropha (Alcaligenes eutrophus).; PDB: 2EJG_D 2D5D_A 2EJF_C 2EVB_A 1IYV_A 1IYU_A 1LAC_A 1LAB_A 1DCZ_A 1DD2_A ....
Probab=22.68 E-value=56 Score=20.94 Aligned_cols=17 Identities=12% Similarity=0.055 Sum_probs=14.4
Q ss_pred eEeeCCeEeecCcEEEe
Q 033772 77 VKIFGDQVAKPGAIIVR 93 (112)
Q Consensus 77 vK~~~Gq~V~~G~IIvR 93 (112)
|.+..|+.|.+|+.|+.
T Consensus 20 ~~v~~G~~V~~G~~l~~ 36 (74)
T PF00364_consen 20 WLVEEGDKVKKGDPLAE 36 (74)
T ss_dssp ESSSTTEEESTTSEEEE
T ss_pred EEECCCCEEEcCceEEE
Confidence 77888999999998865
No 15
>COG0157 NadC Nicotinate-nucleotide pyrophosphorylase [Coenzyme metabolism]
Probab=22.64 E-value=64 Score=27.21 Aligned_cols=21 Identities=19% Similarity=0.366 Sum_probs=18.3
Q ss_pred eEeeCCeEeecCcEEEeecCC
Q 033772 77 VKIFGDQVAKPGAIIVRQRGT 97 (112)
Q Consensus 77 vK~~~Gq~V~~G~IIvRQRGt 97 (112)
+.+-||++|+||++|.+=+|.
T Consensus 68 ~~~~DG~~v~~g~~i~~~~G~ 88 (280)
T COG0157 68 WLVKDGDRVKPGDVLAEIEGP 88 (280)
T ss_pred EEcCCCCEeCCCCEEEEEecc
Confidence 467899999999999998775
No 16
>PF07831 PYNP_C: Pyrimidine nucleoside phosphorylase C-terminal domain; InterPro: IPR013102 This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [, ]. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP, P77826 from SWISSPROT) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as Escherichia coli thymidine phosphorylase (TP, P07650 from SWISSPROT) []. The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer []. ; GO: 0016763 transferase activity, transferring pentosyl groups, 0006213 pyrimidine nucleoside metabolic process; PDB: 1AZY_A 1OTP_A 2TPT_A 3H5Q_A 1BRW_A 2WK5_C 2J0F_C 2WK6_B 1UOU_A 2DSJ_B ....
Probab=21.73 E-value=63 Score=21.49 Aligned_cols=28 Identities=11% Similarity=0.115 Sum_probs=16.7
Q ss_pred CCCCCCcccceE--eeCCeEeecCcEEEee
Q 033772 67 GRDSRGQRLGVK--IFGDQVAKPGAIIVRQ 94 (112)
Q Consensus 67 grdS~~KrLGvK--~~~Gq~V~~G~IIvRQ 94 (112)
..|..-..-|+. +--|++|.+|+.|++=
T Consensus 24 k~d~ID~~vGi~l~~k~Gd~V~~Gd~l~~i 53 (75)
T PF07831_consen 24 KEDPIDPAVGIELHKKVGDRVEKGDPLATI 53 (75)
T ss_dssp TTS---TT-EEEESS-TTSEEBTTSEEEEE
T ss_pred CCCccCcCcCeEecCcCcCEECCCCeEEEE
Confidence 335555556654 3459999999999873
No 17
>TIGR01000 bacteriocin_acc bacteriocin secretion accessory protein. This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193.
Probab=21.73 E-value=64 Score=27.25 Aligned_cols=20 Identities=15% Similarity=0.162 Sum_probs=17.0
Q ss_pred cceEeeCCeEeecCcEEEee
Q 033772 75 LGVKIFGDQVAKPGAIIVRQ 94 (112)
Q Consensus 75 LGvK~~~Gq~V~~G~IIvRQ 94 (112)
.-+.+-+||.|++|++|++=
T Consensus 71 ~~i~V~eG~~V~~G~~L~~l 90 (457)
T TIGR01000 71 KENYLKENKFVKKGDLLVVY 90 (457)
T ss_pred EEEEcCCCCEecCCCEEEEE
Confidence 34778899999999999973
No 18
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=20.34 E-value=75 Score=27.11 Aligned_cols=17 Identities=29% Similarity=0.599 Sum_probs=15.5
Q ss_pred eEeeCCeEeecCcEEEe
Q 033772 77 VKIFGDQVAKPGAIIVR 93 (112)
Q Consensus 77 vK~~~Gq~V~~G~IIvR 93 (112)
|-.-++|+|++|++|+|
T Consensus 67 V~V~dnq~Vk~Gd~L~~ 83 (352)
T COG1566 67 VNVKDNQLVKKGDVLFR 83 (352)
T ss_pred EEecCCCEecCCCeEEE
Confidence 66789999999999998
No 19
>PRK08225 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated
Probab=20.13 E-value=99 Score=19.24 Aligned_cols=17 Identities=6% Similarity=0.384 Sum_probs=13.8
Q ss_pred eEeeCCeEeecCcEEEe
Q 033772 77 VKIFGDQVAKPGAIIVR 93 (112)
Q Consensus 77 vK~~~Gq~V~~G~IIvR 93 (112)
+....||.|.+|+.|++
T Consensus 52 ~~~~~G~~V~~g~~l~~ 68 (70)
T PRK08225 52 INVQEGDFVNEGDVLLE 68 (70)
T ss_pred EEecCCCEECCCCEEEE
Confidence 45677899999999875
Done!